From ae907fb953a0bfe352e8e9654119814c03a3d231 Mon Sep 17 00:00:00 2001 From: ErolBa Date: Thu, 1 Dec 2022 17:31:21 +0100 Subject: [PATCH 01/36] Updates to writing Ipdt to .end file; and constratining total pflux to a constant for slab geom. and Lconstraint 3 --- src/dforce.f90 | 371 +++++++++++++++++++++++++++---------------------- src/dfp100.f90 | 25 +++- src/global.f90 | 4 +- src/preset.f90 | 14 +- 4 files changed, 239 insertions(+), 175 deletions(-) diff --git a/src/dforce.f90 b/src/dforce.f90 index 05f59b2c..0e7e326e 100644 --- a/src/dforce.f90 +++ b/src/dforce.f90 @@ -134,7 +134,8 @@ subroutine dforce( NGdof, position, force, LComputeDerivatives, LComputeAxis) LocalConstraint, xoffset, & solution, IPdtdPf, & IsMyVolume, IsMyVolumeValue, WhichCpuID, & - ext ! For outputing Lcheck = 6 test + ext, & ! For outputing Lcheck = 6 test + total_pflux !-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-! @@ -190,9 +191,9 @@ subroutine dforce( NGdof, position, force, LComputeDerivatives, LComputeAxis) !-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-! if( LcomputeDerivatives ) then -#ifdef DEBUG - FATAL( dforce, .not.allocated(dBBdmp), do not pass go ) -#endif + #ifdef DEBUG + FATAL( dforce, .not.allocated(dBBdmp), do not pass go ) + #endif dBBdmp(1:LGdof,1:Mvol,0:1,1:2) = zero endif @@ -239,8 +240,13 @@ subroutine dforce( NGdof, position, force, LComputeDerivatives, LComputeAxis) ! Mvol-1 surface current plus 1 poloidal linking current constraints Ndofgl = Mvol else - ! Mvol-1 surface current constraints - Ndofgl = Mvol-1 + ! add an additional constraint to make the total pflux = 0 -- Edit Erol + if(Igeometry.eq.1) then + Ndofgl = Mvol + else + ! Mvol-1 surface current constraints + Ndofgl = Mvol-1 + endif endif SALLOCATE( Fvec, (1:Ndofgl), zero ) @@ -253,10 +259,15 @@ subroutine dforce( NGdof, position, force, LComputeDerivatives, LComputeAxis) if ( myid .eq. 0 ) then dpfluxout = Fvec - call DGESV( Ndofgl, 1, IPdtdPf, Ndofgl, ipiv, dpfluxout, Ndofgl, idgesv ) + call DGESV( Ndofgl, 1, IPdtdPf(1:Ndofgl,1:Ndofgl), Ndofgl, ipiv, dpfluxout(1:Ndofgl), Ndofgl, idgesv ) ! one step Newton's method dpflux(2:Mvol) = dpflux(2:Mvol) - dpfluxout(1:Mvol-1) + + if(Igeometry.eq.1) then + dpflux(1) = dpflux(1) - dpfluxout(Mvol) + endif + if( Lfreebound.eq.1 ) then dtflux(Mvol) = dtflux(Mvol ) - dpfluxout(Mvol ) endif @@ -268,7 +279,7 @@ subroutine dforce( NGdof, position, force, LComputeDerivatives, LComputeAxis) if( Lfreebound.eq.1 ) then RlBCAST(dtflux(Mvol), 1, 0) endif - + do vvol = 2, Mvol WCALL(dforce, IsMyVolume, (vvol)) @@ -305,6 +316,38 @@ subroutine dforce( NGdof, position, force, LComputeDerivatives, LComputeAxis) enddo ! end of do vvol = 1, Mvol + !add an additional constraint to make the total pflux = 0 -- Edit Erol + if(Igeometry.eq.1) then + + vvol = 1 + + WCALL(dforce, IsMyVolume, (vvol)) + + if( IsMyVolumeValue .EQ. 0 ) then + + else if( IsMyVolumeValue .EQ. -1) then + FATAL(dforce, .true., Unassociated volume) + else + NN = NAdof(vvol) + + SALLOCATE( solution, (1:NN, 0:2), zero) + + ! Pack field and its derivatives + packorunpack = 'P' + WCALL( dforce, packab, ( packorunpack, vvol, NN, solution(1:NN,0), 0 ) ) ! packing; + WCALL( dforce, packab, ( packorunpack, vvol, NN, solution(1:NN,2), 2 ) ) ! packing; + + ! compute the field with renewed dpflux via single Newton method step + solution(1:NN, 0) = solution(1:NN, 0) - dpfluxout(Mvol) * solution(1:NN, 2) + + ! Unpack field in vector potential Fourier harmonics + packorunpack = 'U' + WCALL( dforce, packab, ( packorunpack, vvol, NN, solution(1:NN,0), 0 ) ) ! unpacking; + + DALLOCATE( solution ) + endif + endif + DALLOCATE(Fvec) DALLOCATE(dpfluxout) @@ -362,16 +405,16 @@ subroutine dforce( NGdof, position, force, LComputeDerivatives, LComputeAxis) !-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-! -#ifdef DEBUG - if( Lcheck.eq.2 ) then - write(ounit,'("dforce : ", 10x ," : myid=",i3," ; finished computing derivatives of rotational-transform wrt mu and dpflux ;")') myid - stop "dforce : : myid= ; finished computing derivatives of rotational-transform wrt mu and dpflux ;" ! this will allow other cpus to finish; - endif + #ifdef DEBUG + if( Lcheck.eq.2 ) then + write(ounit,'("dforce : ", 10x ," : myid=",i3," ; finished computing derivatives of rotational-transform wrt mu and dpflux ;")') myid + stop "dforce : : myid= ; finished computing derivatives of rotational-transform wrt mu and dpflux ;" ! this will allow other cpus to finish; + endif - FATAL( dforce, Lcheck.eq.2, finished computing derivatives of rotational-transform wrt mu and dpflux ) + FATAL( dforce, Lcheck.eq.2, finished computing derivatives of rotational-transform wrt mu and dpflux ) - if( Wdforce ) write(ounit,'("dforce : " 10x " : myid="i3" ; LComputeDerivatives="L2" ; ImagneticOK="999L2)') myid, LComputeDerivatives, ImagneticOK(1:Mvol) -#endif + if( Wdforce ) write(ounit,'("dforce : " 10x " : myid="i3" ; LComputeDerivatives="L2" ; ImagneticOK="999L2)') myid, LComputeDerivatives, ImagneticOK(1:Mvol) + #endif !-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-! @@ -430,9 +473,9 @@ subroutine dforce( NGdof, position, force, LComputeDerivatives, LComputeAxis) + ( + Somn(2:mn ,vvol+0,1) ) * sweight(vvol+0) & ! poloidal length constraint; - ( Somn(2:mn ,vvol+1,0) ) * sweight(vvol+1) - ! if( Ntor.gt.0 ) then ! poloidal angle origin is not otherwise constrained ; - ! force(tdoc+idoc+1:tdoc+idoc+Ntor ) = ( Pomn(2:Ntor+1,vvol+1,0) - Pomn(2:Ntor+1,vvol+0,1) ) * apsilon ! choice of spectral constraint can be enforced; - ! endif + ! if( Ntor.gt.0 ) then ! poloidal angle origin is not otherwise constrained ; + ! force(tdoc+idoc+1:tdoc+idoc+Ntor ) = ( Pomn(2:Ntor+1,vvol+1,0) - Pomn(2:Ntor+1,vvol+0,1) ) * apsilon ! choice of spectral constraint can be enforced; + ! endif IIo(vvol) = max( sum( abs( force(tdoc+idoc+1:tdoc+idoc+mn-1) ) ) / (mn-1), logtolerance ) ! screen diagnostics; @@ -454,9 +497,9 @@ subroutine dforce( NGdof, position, force, LComputeDerivatives, LComputeAxis) + ( + Semn(1:mn ,vvol+0,1) ) * sweight(vvol+0) & ! poloidal length constraint; - ( Semn(1:mn ,vvol+1,0) ) * sweight(vvol+1) - ! if( Ntor.ge.0 ) then - ! force(tdoc+idoc+1:tdoc+idoc+Ntor+1) = ( Pemn(1:Ntor+1,vvol+1,0) - Pemn(1:Ntor+1,vvol+0,1) ) * apsilon ! choice of spectral constraint can be enforced; - ! endif + ! if( Ntor.ge.0 ) then + ! force(tdoc+idoc+1:tdoc+idoc+Ntor+1) = ( Pemn(1:Ntor+1,vvol+1,0) - Pemn(1:Ntor+1,vvol+0,1) ) * apsilon ! choice of spectral constraint can be enforced; + ! endif IIe(vvol) = max( sum( abs( force(tdoc+idoc+1:tdoc+idoc+mn ) ) ) / (mn ), logtolerance ) ! screen diagnostics; @@ -466,9 +509,9 @@ subroutine dforce( NGdof, position, force, LComputeDerivatives, LComputeAxis) endif ! end of if( NOTstellsym ) ; -#ifdef DEBUG - FATAL( dforce, idoc.ne.LGdof, counting error ) ! this has caught bugs; -#endif + #ifdef DEBUG + FATAL( dforce, idoc.ne.LGdof, counting error ) ! this has caught bugs; + #endif else ! matches if( ImagneticOK(vvol) .and. ImagneticOK(vvol+1) ); @@ -728,18 +771,14 @@ subroutine dforce( NGdof, position, force, LComputeDerivatives, LComputeAxis) endif ! end of if( LcomputeDerivatives ) ; - - - - ! CONSTRUCT FORCE GRADIENT ! ------------------------ if( LcomputeDerivatives .and. Lhessianallocated) then ! construct Hessian; -#ifdef DEBUG - FATAL( dforce, .not.Lhessianallocated, need to allocate hessian ) -#endif + #ifdef DEBUG + FATAL( dforce, .not.Lhessianallocated, need to allocate hessian ) + #endif hessian(1:NGdof,1:NGdof) = zero @@ -749,29 +788,29 @@ subroutine dforce( NGdof, position, force, LComputeDerivatives, LComputeAxis) idof = 0 ! labels degree-of-freedom = Fourier harmonic of surface geometry; -#ifdef DEBUG - if( idof.gt.LGdof ) write(ounit,1000) myid, vvol, -1, -1, -1, idof, LGdof ! can be deleted; -#endif + #ifdef DEBUG + if( idof.gt.LGdof ) write(ounit,1000) myid, vvol, -1, -1, -1, idof, LGdof ! can be deleted; + #endif do ii = 1, mn ! loop over degrees-of-freedom; -#ifdef DEBUG - if( idof.gt.LGdof ) write(ounit,1000) myid, vvol, ii, -1, -1, idof, LGdof ! can be deleted; -#endif + #ifdef DEBUG + if( idof.gt.LGdof ) write(ounit,1000) myid, vvol, ii, -1, -1, idof, LGdof ! can be deleted; + #endif do irz = 0, 1 ! Fourier harmonic of R, Fourier harmonic of Z; -#ifdef DEBUG - if( idof.gt.LGdof ) write(ounit,1000) myid, vvol, ii, irz, -1, idof, LGdof ! can be deleted; -#endif + #ifdef DEBUG + if( idof.gt.LGdof ) write(ounit,1000) myid, vvol, ii, irz, -1, idof, LGdof ! can be deleted; + #endif if( irz.eq.1 .and. Igeometry.lt.3 ) cycle ! no dependence on Z; do issym = 0, 1 ! stellarator symmetry; -#ifdef DEBUG - if( idof.gt.LGdof ) write(ounit,1000) myid, vvol, ii, irz, issym, idof, LGdof ! can be deleted; -#endif + #ifdef DEBUG + if( idof.gt.LGdof ) write(ounit,1000) myid, vvol, ii, irz, issym, idof, LGdof ! can be deleted; + #endif if( issym.eq.1 .and. YESstellsym ) cycle ! no dependence on the non-stellarator symmetric harmonics; @@ -780,11 +819,11 @@ subroutine dforce( NGdof, position, force, LComputeDerivatives, LComputeAxis) idof = idof + 1 ! labels degree-of-freedom; -#ifdef DEBUG - if( idof.gt.LGdof ) write(ounit,1000) myid, vvol, ii, irz, issym, idof, LGdof ! can be deleted; -1000 format("hforce : " 10x " : myid=",i3," ; vvol=",i3," ; ii= ",i3," ; irz="i3" ; issym="i3" ; idof="i3" ; LGdof="i3" ;") - FATAL( hforce, idof.gt.LGdof, illegal degree-of-freedom index constructing hessian ) ! can be deleted; -#endif + #ifdef DEBUG + if( idof.gt.LGdof ) write(ounit,1000) myid, vvol, ii, irz, issym, idof, LGdof ! can be deleted; + 1000 format("hforce : " 10x " : myid=",i3," ; vvol=",i3," ; ii= ",i3," ; irz="i3" ; issym="i3" ; idof="i3" ; LGdof="i3" ;") + FATAL( hforce, idof.gt.LGdof, illegal degree-of-freedom index constructing hessian ) ! can be deleted; + #endif if( LocalConstraint ) then ! Derivative with respect to previous interface @@ -890,11 +929,11 @@ subroutine dforce( NGdof, position, force, LComputeDerivatives, LComputeAxis) enddo ! end of do vvol; ! Evaluate force gradient -#ifdef DEBUG - if( Lcheck.eq.6 ) then - WCALL(dforce, fndiff_dforce, ( NGdof ) ) - endif -#endif + #ifdef DEBUG + if( Lcheck.eq.6 ) then + WCALL(dforce, fndiff_dforce, ( NGdof ) ) + endif + #endif endif ! end of if( LcomputeDerivatives ) ; @@ -911,162 +950,162 @@ end subroutine dforce subroutine fndiff_dforce( NGdof ) -use constants, only: zero, one, half, two + use constants, only: zero, one, half, two -use fileunits, only: ounit + use fileunits, only: ounit -use inputlist, only: Wmacros, Wdforce, & - Igeometry, & - dRZ, Lcheck + use inputlist, only: Wmacros, Wdforce, & + Igeometry, & + dRZ, Lcheck -use cputiming, only: Tdforce + use cputiming, only: Tdforce -use allglobal, only: ncpu, myid, cpus, MPI_COMM_SPEC, & - Mvol, mn, im, in, & - iRbc, iZbs, iRbs, iZbc, & - LGdof, psifactor, dBdX, & - YESstellsym, NOTstellsym, & - hessian, ext + use allglobal, only: ncpu, myid, cpus, MPI_COMM_SPEC, & + Mvol, mn, im, in, & + iRbc, iZbs, iRbs, iZbc, & + LGdof, psifactor, dBdX, & + YESstellsym, NOTstellsym, & + hessian, ext -LOCALS + LOCALS -INTEGER, intent(in) :: NGdof + INTEGER, intent(in) :: NGdof -INTEGER :: vvol, idof, ii, irz, issym, isymdiff ! loop indices -INTEGER :: tdof ! hessian index + INTEGER :: vvol, idof, ii, irz, issym, isymdiff ! loop indices + INTEGER :: tdof ! hessian index -REAL :: lfactor -CHARACTER :: packorunpack -LOGICAL :: LComputeAxis + REAL :: lfactor + CHARACTER :: packorunpack + LOGICAL :: LComputeAxis -REAL, allocatable :: oRbc(:,:), oZbs(:,:), oRbs(:,:), oZbc(:,:) ! used to store original geometry; -REAL, allocatable :: iposition(:,:), iforce(:,:) ! perturbed interfaces position and force -REAL, allocatable :: finitediff_estimate(:,:) ! store finite differences + REAL, allocatable :: oRbc(:,:), oZbs(:,:), oRbs(:,:), oZbc(:,:) ! used to store original geometry; + REAL, allocatable :: iposition(:,:), iforce(:,:) ! perturbed interfaces position and force + REAL, allocatable :: finitediff_estimate(:,:) ! store finite differences -BEGIN(dforce) + BEGIN(dforce) - write(ounit, '("fndiff : Starting finite difference evaluation of hessian ...")') + write(ounit, '("fndiff : Starting finite difference evaluation of hessian ...")') - if( ncpu.eq.1) then + if( ncpu.eq.1) then - SALLOCATE( finitediff_estimate, (1:NGdof, 1:NGdof), zero ) + SALLOCATE( finitediff_estimate, (1:NGdof, 1:NGdof), zero ) - dBdX%L = .false. - SALLOCATE( oRbc, (1:mn,0:Mvol), iRbc(1:mn,0:Mvol) ) !save unperturbed geometry - SALLOCATE( oZbs, (1:mn,0:Mvol), iZbs(1:mn,0:Mvol) ) - SALLOCATE( oRbs, (1:mn,0:Mvol), iRbs(1:mn,0:Mvol) ) - SALLOCATE( oZbc, (1:mn,0:Mvol), iZbc(1:mn,0:Mvol) ) - SALLOCATE( iforce, (-2:2, 0:NGdof), zero) - SALLOCATE( iposition, (-2:2, 0:NGdof), zero) + dBdX%L = .false. + SALLOCATE( oRbc, (1:mn,0:Mvol), iRbc(1:mn,0:Mvol) ) !save unperturbed geometry + SALLOCATE( oZbs, (1:mn,0:Mvol), iZbs(1:mn,0:Mvol) ) + SALLOCATE( oRbs, (1:mn,0:Mvol), iRbs(1:mn,0:Mvol) ) + SALLOCATE( oZbc, (1:mn,0:Mvol), iZbc(1:mn,0:Mvol) ) + SALLOCATE( iforce, (-2:2, 0:NGdof), zero) + SALLOCATE( iposition, (-2:2, 0:NGdof), zero) - do vvol = 1, Mvol-1 ! loop over interior surfaces; - idof = 0 + do vvol = 1, Mvol-1 ! loop over interior surfaces; + idof = 0 - do ii = 1, mn ! Loop over Fourier modes + do ii = 1, mn ! Loop over Fourier modes - lfactor = psifactor(ii,vvol) ! this "pre-conditions" the geometrical degrees-of-freedom; + lfactor = psifactor(ii,vvol) ! this "pre-conditions" the geometrical degrees-of-freedom; - do irz = 0, 1 ! loop over R or Z coordinate + do irz = 0, 1 ! loop over R or Z coordinate - if( irz.eq.1 .and. Igeometry.lt.3 ) cycle + if( irz.eq.1 .and. Igeometry.lt.3 ) cycle - do issym = 0, 1 ! stellarator symmetry; + do issym = 0, 1 ! stellarator symmetry; - if( issym.eq.1 .and. YESstellsym ) cycle ! no dependence on the non-stellarator symmetric harmonics; + if( issym.eq.1 .and. YESstellsym ) cycle ! no dependence on the non-stellarator symmetric harmonics; - if( ii.eq.1 .and. irz.eq.1 .and. issym.eq.0 ) cycle ! no dependence on Zbs_{m=0,n=0}; - if( ii.eq.1 .and. irz.eq.0 .and. issym.eq.1 ) cycle ! no dependence on Rbs_{m=0,n=0}; + if( ii.eq.1 .and. irz.eq.1 .and. issym.eq.0 ) cycle ! no dependence on Zbs_{m=0,n=0}; + if( ii.eq.1 .and. irz.eq.0 .and. issym.eq.1 ) cycle ! no dependence on Rbs_{m=0,n=0}; - idof = idof + 1 ! labels degree-of-freedom; + idof = idof + 1 ! labels degree-of-freedom; - do isymdiff = -2, 2 ! symmetric fourth-order, finite-difference used to approximate derivatives; + do isymdiff = -2, 2 ! symmetric fourth-order, finite-difference used to approximate derivatives; - if( isymdiff.eq.0 ) cycle + if( isymdiff.eq.0 ) cycle - ! Reset initial geometry - iRbc(1:mn,0:Mvol) = oRbc(1:mn,0:Mvol) - iZbs(1:mn,0:Mvol) = oZbs(1:mn,0:Mvol) - iRbs(1:mn,0:Mvol) = oRbs(1:mn,0:Mvol) - iZbc(1:mn,0:Mvol) = oZbc(1:mn,0:Mvol) + ! Reset initial geometry + iRbc(1:mn,0:Mvol) = oRbc(1:mn,0:Mvol) + iZbs(1:mn,0:Mvol) = oZbs(1:mn,0:Mvol) + iRbs(1:mn,0:Mvol) = oRbs(1:mn,0:Mvol) + iZbc(1:mn,0:Mvol) = oZbc(1:mn,0:Mvol) - ! Perturb geometry - if( issym.eq.0 .and. irz.eq.0 ) then - iRbc(ii,vvol) = iRbc(ii,vvol) + dRZ * isymdiff ! perturb geometry; - else if( issym.eq.0 .and. irz.eq.1 ) then - iZbs(ii,vvol) = iZbs(ii,vvol) + dRZ * isymdiff ! perturb geometry; - else if( issym.eq.1 .and. irz.eq.0 ) then - iRbs(ii,vvol) = iRbs(ii,vvol) + dRZ * isymdiff ! perturb geometry; - else if( issym.eq.1 .and. irz.eq.1 ) then - iZbc(ii,vvol) = iZbc(ii,vvol) + dRZ * isymdiff ! perturb geometry; - endif + ! Perturb geometry + if( issym.eq.0 .and. irz.eq.0 ) then + iRbc(ii,vvol) = iRbc(ii,vvol) + dRZ * isymdiff ! perturb geometry; + else if( issym.eq.0 .and. irz.eq.1 ) then + iZbs(ii,vvol) = iZbs(ii,vvol) + dRZ * isymdiff ! perturb geometry; + else if( issym.eq.1 .and. irz.eq.0 ) then + iRbs(ii,vvol) = iRbs(ii,vvol) + dRZ * isymdiff ! perturb geometry; + else if( issym.eq.1 .and. irz.eq.1 ) then + iZbc(ii,vvol) = iZbc(ii,vvol) + dRZ * isymdiff ! perturb geometry; + endif - packorunpack = 'P' ! pack geometrical degrees-of-freedom; - !LComputeAxis = .false. ! keep axis fixed - LComputeAxis = .true. + packorunpack = 'P' ! pack geometrical degrees-of-freedom; + !LComputeAxis = .false. ! keep axis fixed + LComputeAxis = .true. - WCALL(dforce, packxi,( NGdof, iposition(isymdiff,0:NGdof), Mvol, mn,iRbc(1:mn,0:Mvol),iZbs(1:mn,0:Mvol),iRbs(1:mn,0:Mvol),& - iZbc(1:mn,0:Mvol),packorunpack, .false., LComputeAxis ) ) - WCALL(dforce, dforce,( NGdof, iposition(isymdiff,0:NGdof), iforce(isymdiff,0:NGdof), .false., LComputeAxis) ) - enddo + WCALL(dforce, packxi,( NGdof, iposition(isymdiff,0:NGdof), Mvol, mn,iRbc(1:mn,0:Mvol),iZbs(1:mn,0:Mvol),iRbs(1:mn,0:Mvol),& + iZbc(1:mn,0:Mvol),packorunpack, .false., LComputeAxis ) ) + WCALL(dforce, dforce,( NGdof, iposition(isymdiff,0:NGdof), iforce(isymdiff,0:NGdof), .false., LComputeAxis) ) + enddo - ! Fourth order centered finite difference scheme - iforce(0, 0:NGdof) = ( - 1 * iforce( 2,0:NGdof) & - + 8 * iforce( 1,0:NGdof) & - - 8 * iforce(-1,0:NGdof) & - + 1 * iforce(-2,0:NGdof)) / ( 12 * dRZ ) + ! Fourth order centered finite difference scheme + iforce(0, 0:NGdof) = ( - 1 * iforce( 2,0:NGdof) & + + 8 * iforce( 1,0:NGdof) & + - 8 * iforce(-1,0:NGdof) & + + 1 * iforce(-2,0:NGdof)) / ( 12 * dRZ ) - tdof = (vvol-1) * LGdof + idof - finitediff_estimate(1:NGdof, tdof) = iforce(0, 1:NGdof)* lfactor + tdof = (vvol-1) * LGdof + idof + finitediff_estimate(1:NGdof, tdof) = iforce(0, 1:NGdof)* lfactor - enddo !issym - enddo !irz - enddo !ii - enddo !vvol + enddo !issym + enddo !irz + enddo !ii + enddo !vvol - DALLOCATE(iforce) - DALLOCATE(iposition) - DALLOCATE(oZbc) - DALLOCATE(oRbs) - DALLOCATE(oZbs) - DALLOCATE(oRbc) + DALLOCATE(iforce) + DALLOCATE(iposition) + DALLOCATE(oZbc) + DALLOCATE(oRbs) + DALLOCATE(oZbs) + DALLOCATE(oRbc) - ! Print in file for diagnostics - if(myid.eq.0) then - ! Print hessian - open(10, file=trim(ext)//'.Lcheck6_output.txt', status='unknown') - write(ounit,'(A)') NEW_LINE('A') + ! Print in file for diagnostics + if(myid.eq.0) then + ! Print hessian + open(10, file=trim(ext)//'.Lcheck6_output.txt', status='unknown') + write(ounit,'(A)') NEW_LINE('A') - do ii=1, SIZE(im) - write(ounit,1345) myid, im(ii), in(ii), hessian(ii,:) - write(10 ,1347) hessian(ii,:) - enddo - close(10) + do ii=1, SIZE(im) + write(ounit,1345) myid, im(ii), in(ii), hessian(ii,:) + write(10 ,1347) hessian(ii,:) + enddo + close(10) - write(ounit,'(A)') NEW_LINE('A') + write(ounit,'(A)') NEW_LINE('A') - ! Print finite differences - open(10, file=trim(ext)//'.Lcheck6_output.FiniteDiff.txt', status='unknown') - do ii=1, SIZE(im) - write(ounit,1346) myid, im(ii), in(ii), finitediff_estimate(ii,:) - write(10 ,1347) finitediff_estimate(ii,:) - enddo - write(ounit,'(A)') NEW_LINE('A') - close(10) + ! Print finite differences + open(10, file=trim(ext)//'.Lcheck6_output.FiniteDiff.txt', status='unknown') + do ii=1, SIZE(im) + write(ounit,1346) myid, im(ii), in(ii), finitediff_estimate(ii,:) + write(10 ,1347) finitediff_estimate(ii,:) + enddo + write(ounit,'(A)') NEW_LINE('A') + close(10) - 1345 format("dforce: myid=",i3," ; (",i4,",",i4," ; Hessian = ",512f16.10 " ;") - 1346 format("dforce: myid=",i3," ; (",i4,",",i4," ; Finite differences = ",512f16.10 " ;") - 1347 format(512F22.16, " ") + 1345 format("dforce: myid=",i3," ; (",i4,",",i4," ; Hessian = ",512f16.10 " ;") + 1346 format("dforce: myid=",i3," ; (",i4,",",i4," ; Finite differences = ",512f16.10 " ;") + 1347 format(512F22.16, " ") - endif + endif - DALLOCATE(finitediff_estimate) - endif + DALLOCATE(finitediff_estimate) + endif -FATAL(fndiff, .true., Finite differences have been evaluated. ) + FATAL(fndiff, .true., Finite differences have been evaluated. ) -RETURN(dforce) + RETURN(dforce) end subroutine fndiff_dforce diff --git a/src/dfp100.f90 b/src/dfp100.f90 index acb75e37..f3e6550a 100644 --- a/src/dfp100.f90 +++ b/src/dfp100.f90 @@ -63,7 +63,7 @@ subroutine dfp100(Ndofgl, x, Fvec, LComputeDerivatives) DDtzcc, DDtzcs, DDtzsc, DDtzss, & DDzzcc, DDzzcs, DDzzsc, DDzzss, & dMA, dMB, dMD, dMG, MBpsi, solution, & - Nt, Nz, LILUprecond, Lsavedguvij, NOTMatrixFree, guvijsave, izbs + Nt, Nz, LILUprecond, Lsavedguvij, NOTMatrixFree, guvijsave, izbs, total_pflux LOCALS !------ @@ -116,7 +116,7 @@ subroutine dfp100(Ndofgl, x, Fvec, LComputeDerivatives) WCALL( dfp100, compute_guvijsave, (Iquad(vvol), vvol, ideriv, Lcurvature) ) Lsavedguvij = .true. - ! we need to construct the preconditioner if needed + ! we need to construct the preconditioner if needed if (LILUprecond) then WCALL( dfp100, spsint, ( Iquad(vvol), mn, vvol, ll ) ) WCALL( dfp100, spsmat, ( vvol, mn, ll) ) @@ -135,7 +135,7 @@ subroutine dfp100(Ndofgl, x, Fvec, LComputeDerivatives) Lsavedguvij = .false. -!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-! + !-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-! call intghs_workspace_destroy() call deallocate_Beltrami_matrices(LcomputeDerivatives) @@ -155,9 +155,9 @@ subroutine dfp100(Ndofgl, x, Fvec, LComputeDerivatives) if( Lvacuumregion ) then -#ifdef DEBUG - FATAL( dfp100, vvol.ne.Mvol, Incorrect vvol in last volume) -#endif + #ifdef DEBUG + FATAL( dfp100, vvol.ne.Mvol, Incorrect vvol in last volume) + #endif ideriv=1 ! derivatives of Btheta w.r.t tflux iocons=0 ! Only need inner side of volume derivatives @@ -205,6 +205,19 @@ subroutine dfp100(Ndofgl, x, Fvec, LComputeDerivatives) Fvec(1:Mvol-1) = IPDt(1:Mvol-1) - Isurf(1:Mvol-1) endif + ! Edit by Erol to set total pflux to 0 + if(Igeometry.eq.1) then + + IPDtDpf(1,Mvol) = -pi2 * Bt00(1,1,2) + IPdtdPf(2:Mvol,Mvol) = 0.0 + IPDtDpf(Mvol,1:Mvol) = 1.0 + + ! Constraint the total pflux (pflux(Mvol)) + ! zero for symmetric initial profiles + ! non-zero for asymmetric profiles + Fvec(Mvol) = sum(dpflux(1:Mvol)) - total_pflux + endif + ! Compute poloidal linking current constraint as well in case of free boundary computation if ( Lfreebound.eq.1 ) then diff --git a/src/global.f90 b/src/global.f90 index c69c6eb5..009d2bb8 100644 --- a/src/global.f90 +++ b/src/global.f90 @@ -255,6 +255,8 @@ module allglobal INTEGER :: Mvol + REAL :: total_pflux ! total pflux, used in Lconstraint=3, Igeometry=1 -- Edit by Erol + LOGICAL :: YESstellsym !< internal shorthand copies of Istellsym, which is an integer input; LOGICAL :: NOTstellsym !< internal shorthand copies of Istellsym, which is an integer input; @@ -1654,7 +1656,7 @@ subroutine wrtend write(iunit,'(" adiabatic = ",257es23.15)') adiabatic(1:Mvol) write(iunit,'(" mu = ",257es23.15)') mu(1:Mvol) write(iunit,'(" Ivolume = ",257es23.15)') Ivolume(1:Mvol) - write(iunit,'(" Isurf = ",257es23.15)') Isurf(1:Mvol-1) + write(iunit,'(" Isurf = ",257es23.15)') IPDt(1:Mvol) ! EDIT by EROL !!!! write(iunit,'(" Lconstraint = ",i9 )') Lconstraint write(iunit,'(" pl = ",257i23 )') pl(0:Mvol) write(iunit,'(" ql = ",257i23 )') ql(0:Mvol) diff --git a/src/preset.f90 b/src/preset.f90 index db447429..6d0d50eb 100644 --- a/src/preset.f90 +++ b/src/preset.f90 @@ -508,8 +508,12 @@ subroutine preset SALLOCATE( dtflux, (1:Mvol), zero ) SALLOCATE( dpflux, (1:Mvol), zero ) + if(Lconstraint.eq.3 .and. Igeometry.eq.1) then + total_pflux = pflux(Mvol) * phiedge / pi2 + endif + select case( Igeometry ) - case( 1 ) ; dtflux(1) = tflux(1) ; dpflux(1) = pflux(1) ! Cartesian ; this is the "inverse" operation defined in xspech; 09 Mar 17; + case( 1 ) ; dtflux(1) = tflux(1) ; dpflux(1) = pflux(1); pflux(Mvol) = 0 ! Edit by Erol, to keep total pflux 0 case( 2:3 ) ; dtflux(1) = tflux(1) ; dpflux(1) = zero ! cylindrical or toroidal; end select @@ -519,6 +523,7 @@ subroutine preset dtflux(1:Mvol) = dtflux(1:Mvol) * phiedge / pi2 dpflux(1:Mvol) = dpflux(1:Mvol) * phiedge / pi2 + !-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-! !latex \subsubsection{\type{mu(1:Mvol)} evaluation of \inputvar{mu} from \inputvar{Ivolume};} @@ -807,7 +812,12 @@ subroutine preset if( Lfreebound.eq.1 ) then SALLOCATE( IPDtDpf, (1:Mvol , 1:Mvol ), zero) else - SALLOCATE( IPDtDpf, (1:Mvol-1, 1:Mvol-1), zero) + if(Igeometry.eq.1) then + ! add an additional constraint to make the total pflux = 0 -- Edit Erol + SALLOCATE( IPDtDpf, (1:Mvol, 1:Mvol), zero) + else + SALLOCATE( IPDtDpf, (1:Mvol-1, 1:Mvol-1), zero) + endif endif SALLOCATE( cheby, (0:Mrad,0:2), zero ) From 9cc0112d23690ceb4bc43ce605c72aa261c5f2dd Mon Sep 17 00:00:00 2001 From: ErolBa Date: Wed, 7 Dec 2022 17:36:30 +0100 Subject: [PATCH 02/36] small fix --- src/preset.f90 | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/src/preset.f90 b/src/preset.f90 index 6d0d50eb..afbd8c8b 100644 --- a/src/preset.f90 +++ b/src/preset.f90 @@ -510,10 +510,11 @@ subroutine preset if(Lconstraint.eq.3 .and. Igeometry.eq.1) then total_pflux = pflux(Mvol) * phiedge / pi2 + pflux(Mvol) = 0 endif select case( Igeometry ) - case( 1 ) ; dtflux(1) = tflux(1) ; dpflux(1) = pflux(1); pflux(Mvol) = 0 ! Edit by Erol, to keep total pflux 0 + case( 1 ) ; dtflux(1) = tflux(1) ; dpflux(1) = pflux(1) ! Edit by Erol, to keep total pflux 0 case( 2:3 ) ; dtflux(1) = tflux(1) ; dpflux(1) = zero ! cylindrical or toroidal; end select @@ -1109,8 +1110,7 @@ subroutine preset SALLOCATE( Azo(vvol,ideriv,ii)%i, (0:Lrad(vvol)), 0 ) enddo ! end of do ii; - - + select case( Linitgues ) ! for iterative solver of the Beltrami fields, an initial guess is required; 11 Mar 16; case( 0 ) ; case( 1 ) ; Ate(vvol,0,1)%s(0:1) = dtflux(vvol) * half ! this is an integrable approximation; NEEDS CHECKING; 26 Feb 13; From c341344ab4c077f137f775b50413332137b4ea26 Mon Sep 17 00:00:00 2001 From: ErolBa Date: Wed, 12 Apr 2023 11:10:10 +0200 Subject: [PATCH 03/36] minor changes --- src/dforce.f90 | 46 ++++++--- src/dfp200.f90 | 120 +++++++++++------------ src/hesian.f90 | 196 +++++++++++++++++++------------------ src/lbpol.f90 | 15 +++ src/mp00ac.f90 | 8 +- src/newton.f90 | 36 +++---- src/packab.f90 | 1 - src/spsint.f90 | 30 +++--- src/spsmat.f90 | 2 +- src/xspech.f90 | 260 ++++++++++++++++++++++++------------------------- 10 files changed, 380 insertions(+), 334 deletions(-) diff --git a/src/dforce.f90 b/src/dforce.f90 index 0e7e326e..c5cd7b53 100644 --- a/src/dforce.f90 +++ b/src/dforce.f90 @@ -107,6 +107,8 @@ subroutine dforce( NGdof, position, force, LComputeDerivatives, LComputeAxis) mupftol, & Lfreebound, LHmatrix + use fileunits, only : ounit, hunit, munit ! added by Erol + use cputiming, only : Tdforce use allglobal, only : ncpu, myid, cpus, MPI_COMM_SPEC, & @@ -351,16 +353,16 @@ subroutine dforce( NGdof, position, force, LComputeDerivatives, LComputeAxis) DALLOCATE(Fvec) DALLOCATE(dpfluxout) -! #ifdef DEBUG -! select case( ihybrd1 ) -! case( 1 ) ; write(ounit,'("dforce : ",f10.2," : finished ; success ; dpflux = ", es12.5, ", its="i7";")') cput-cpus, dpflux, nfev -! case( 0 ) ; write(ounit,'("dforce : ",f10.2," : finished ; input error ; dpflux = ", es12.5, ", its="i7";")') cput-cpus, dpflux, nfev -! case( 2 ) ; write(ounit,'("dforce : ",f10.2," : finished ; max. iter ; dpflux = ", es12.5, ", its="i7";")') cput-cpus, dpflux, nfev -! case( 3 ) ; write(ounit,'("dforce : ",f10.2," : finished ; xtol too small ; dpflux = ", es12.5, ", its="i7";")') cput-cpus, dpflux, nfev -! case( 4:5 ) ; write(ounit,'("dforce : ",f10.2," : finished ; bad progress ; dpflux = ", es12.5, ", its="i7";")') cput-cpus, dpflux, nfev -! case default ; write(ounit,'("dforce : ",f10.2," : finished ; illegal ifail ; dpflux = ", es12.5, ", its="i7";")') cput-cpus, dpflux, nfev -! end select -! #endif + ! #ifdef DEBUG + ! select case( ihybrd1 ) + ! case( 1 ) ; write(ounit,'("dforce : ",f10.2," : finished ; success ; dpflux = ", es12.5, ", its="i7";")') cput-cpus, dpflux, nfev + ! case( 0 ) ; write(ounit,'("dforce : ",f10.2," : finished ; input error ; dpflux = ", es12.5, ", its="i7";")') cput-cpus, dpflux, nfev + ! case( 2 ) ; write(ounit,'("dforce : ",f10.2," : finished ; max. iter ; dpflux = ", es12.5, ", its="i7";")') cput-cpus, dpflux, nfev + ! case( 3 ) ; write(ounit,'("dforce : ",f10.2," : finished ; xtol too small ; dpflux = ", es12.5, ", its="i7";")') cput-cpus, dpflux, nfev + ! case( 4:5 ) ; write(ounit,'("dforce : ",f10.2," : finished ; bad progress ; dpflux = ", es12.5, ", its="i7";")') cput-cpus, dpflux, nfev + ! case default ; write(ounit,'("dforce : ",f10.2," : finished ; illegal ifail ; dpflux = ", es12.5, ", its="i7";")') cput-cpus, dpflux, nfev + ! end select + ! #endif endif !matches if( LocalConstraint ) @@ -444,7 +446,7 @@ subroutine dforce( NGdof, position, force, LComputeDerivatives, LComputeAxis) ! CONSTRUCT FORCE ! --------------- - ; force(0:NGdof) = zero + force(0:NGdof) = zero do vvol = 1, Mvol-1 @@ -941,8 +943,28 @@ subroutine dforce( NGdof, position, force, LComputeDerivatives, LComputeAxis) !-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-! - RETURN(dforce) + !add by Erol + !if(LcomputeDerivatives .and. Lhessianallocated .and. Igeometry .eq. 1) then + !if(Lhessianallocated .and. Igeometry .eq. 1) then + if(Lhessianallocated) then + if( myid.eq.0 ) then ; cput = GETTIME ; write(ounit,'("hesian : ",f10.2," : LHmatrix="L2" ;")')cput-cpus, LHmatrix ; + write(*,*) "Writing .hessian file..." + open(munit, file="."//trim(ext)//".hessian", status="unknown", form="unformatted") + write(munit) NGdof + write(munit) hessian(1:NGdof,1:NGdof) + close(munit) + + write(*,*) 'Writing hessian from dforce' + + ! do ii=1,NGdof + ! write(*,*)ii, hessian(ii,1:NGdof) + ! enddo + + endif + endif + RETURN(dforce) + !-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-! end subroutine dforce diff --git a/src/dfp200.f90 b/src/dfp200.f90 index 2015b3b6..6c7ef634 100644 --- a/src/dfp200.f90 +++ b/src/dfp200.f90 @@ -147,7 +147,7 @@ subroutine dfp200( LcomputeDerivatives, vvol) if( LocalConstraint ) then - do vvol = 1, Mvol + do vvol = 1, Mvol WCALL(dfp200, IsMyVolume, (vvol)) @@ -164,14 +164,14 @@ subroutine dfp200( LcomputeDerivatives, vvol) ll = Lrad(vvol) ! Shorthand NN = NAdof(vvol) ! shorthand; -!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-! + !-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-! vflag = 1 WCALL( dfp200, volume, ( vvol, vflag ) ) ! compute volume; !!----Hessian2D cleared----- -!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-! + !-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-! do iocons = 0, 1 ! construct field magnitude on inner and outer interfaces; inside do vvol; if( vvol.eq.1 .and. iocons.eq.0 ) cycle ! fixed inner boundary (or coordinate axis); @@ -198,34 +198,34 @@ subroutine dfp200( LcomputeDerivatives, vvol) packorunpack = 'P' WCALL( dfp200, packab, ( packorunpack, vvol, NN, solution(1:NN,0), 0 ) ) ! packing, put the solutions back to the solution matrix; -!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-! + !-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-! - ! Invert beltrami matrix. Required for matrix perturbation theory - call get_LU_Beltrami_matrices(vvol, oBI(vvol), NN) + ! Invert beltrami matrix. Required for matrix perturbation theory + call get_LU_Beltrami_matrices(vvol, oBI(vvol), NN) - dBdX%L = .true. ! will need derivatives; - idof = 0 ! labels degree of freedom; local to interface; + dBdX%L = .true. ! will need derivatives; + idof = 0 ! labels degree of freedom; local to interface; - do ii = 1, mn ! loop over deformations in Fourier harmonics; inside do vvol; + do ii = 1, mn ! loop over deformations in Fourier harmonics; inside do vvol; - dBdX%ii = ii ! controls construction of derivatives in subroutines called below; - do irz = 0, 1 ! loop over deformations in R and Z; inside do vvol; inside do ii; + dBdX%ii = ii ! controls construction of derivatives in subroutines called below; + do irz = 0, 1 ! loop over deformations in R and Z; inside do vvol; inside do ii; - if( irz.eq.1 .and. Igeometry.lt.3 ) cycle ! no dependence on Z; - dBdX%irz = irz ! controls construction of derivatives; + if( irz.eq.1 .and. Igeometry.lt.3 ) cycle ! no dependence on Z; + dBdX%irz = irz ! controls construction of derivatives; - do issym = 0, 1 ! loop over stellarator and non-stellarator symmetric terms; + do issym = 0, 1 ! loop over stellarator and non-stellarator symmetric terms; - if( issym.eq.1 .and. YESstellsym ) cycle ! no dependence on non-stellarator symmetric harmonics; - if( ii.eq.1 .and. irz.eq.1 .and. issym.eq.0 ) cycle ! no dependence on Zbs_{m=0,n=0}; - if( ii.eq.1 .and. irz.eq.0 .and. issym.eq.1 ) cycle ! no dependence on Rbs_{m=0,n=0}; + if( issym.eq.1 .and. YESstellsym ) cycle ! no dependence on non-stellarator symmetric harmonics; + if( ii.eq.1 .and. irz.eq.1 .and. issym.eq.0 ) cycle ! no dependence on Zbs_{m=0,n=0}; + if( ii.eq.1 .and. irz.eq.0 .and. issym.eq.1 ) cycle ! no dependence on Rbs_{m=0,n=0}; - dBdX%issym = issym ! controls construction of derivatives; - idof = idof + 1 ! this labels the degree-of-freedom that the derivative is taken with respect to; this is outside do innout; + dBdX%issym = issym ! controls construction of derivatives; + idof = idof + 1 ! this labels the degree-of-freedom that the derivative is taken with respect to; this is outside do innout; -#ifdef DEBUG - FATAL( dfp200, idof.gt.LGdof, illegal degree-of-freedom index constructing derivatives ) ! this can be deleted; -#endif + #ifdef DEBUG + FATAL( dfp200, idof.gt.LGdof, illegal degree-of-freedom index constructing derivatives ) ! this can be deleted; + #endif do innout = 0, 1 ! loop over deformations to inner and outer interface; inside do vvol; inside do ii; inside do irz; @@ -296,7 +296,7 @@ subroutine dfp200( LcomputeDerivatives, vvol) ll = Lrad(vvol) ! Shorthand NN = NAdof(vvol) ! shorthand; -!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-! + !-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-! vflag = 1 WCALL( dfp200, volume, ( vvol, vflag ) ) ! compute volume; @@ -439,9 +439,9 @@ subroutine dfp200( LcomputeDerivatives, vvol) dBdX%issym = issym ! controls construction of derivatives; idof = idof + 1 ! this labels the degree-of-freedom that the derivative is taken with respect to; this is outside do innout; -#ifdef DEBUG - FATAL( dfp200, idof.gt.LGdof, illegal degree-of-freedom index constructing derivatives ) ! this can be deleted; -#endif + #ifdef DEBUG + FATAL( dfp200, idof.gt.LGdof, illegal degree-of-freedom index constructing derivatives ) ! this can be deleted; + #endif do lvol = vvol, vvol+1 @@ -609,7 +609,7 @@ subroutine dfp200( LcomputeDerivatives, vvol) - endif ! End of if( LocalConstraint ) +endif ! End of if( LocalConstraint ) if( LcomputeDerivatives ) then DALLOCATE(constraint) @@ -630,7 +630,7 @@ subroutine dfp200( LcomputeDerivatives, vvol) DALLOCATE(length) -2000 continue + 2000 continue RETURN(dfp200) @@ -971,11 +971,11 @@ subroutine evaluate_dmupfdx(innout, idof, ii, issym, irz) if( ( Lcoordinatesingularity .and. iocons.eq.0 ) .or. ( Lvacuumregion .and. iocons.eq.1 ) ) cycle WCALL(dfp200, lbpol, (pvol, Bt00(1:Mvol, 0:1, -1:2), 2, iocons)) ! Stores derivative in global variable Btemn enddo -#ifdef DEBUG - if( .false. ) then - write(ounit, 8375) myid, dBdX%vol, dBdX%innout, 2, pvol, Bt00(pvol, 0:1, 2) - endif -#endif + #ifdef DEBUG + if( .false. ) then + write(ounit, 8375) myid, dBdX%vol, dBdX%innout, 2, pvol, Bt00(pvol, 0:1, 2) + endif + #endif enddo dBdmpf(1:order,1:order) = zero ! Initialize. TODO: useless? @@ -986,18 +986,18 @@ subroutine evaluate_dmupfdx(innout, idof, ii, issym, irz) dBdmpf(Mvol-1,Mvol-1) = Bt00(Mvol, 0, 2) -! do pvol=1,Mvol -! LREGION(pvol) + ! do pvol=1,Mvol + ! LREGION(pvol) -! do iocons = 0, 1 -! WCALL(dfp200, lbpol, (pvol, Bt00(1:Mvol, 0:1, -1:2), 0, iocons)) -! enddo -! #ifdef DEBUG -! if( .false. ) then -! write(ounit, 8375) myid, dBdX%vol, dBdX%innout, 0, pvol, Bt00(pvol, 0:1, 0) -! endif -! #endif -! enddo + ! do iocons = 0, 1 + ! WCALL(dfp200, lbpol, (pvol, Bt00(1:Mvol, 0:1, -1:2), 0, iocons)) + ! enddo + ! #ifdef DEBUG + ! if( .false. ) then + ! write(ounit, 8375) myid, dBdX%vol, dBdX%innout, 0, pvol, Bt00(pvol, 0:1, 0) + ! endif + ! #endif + ! enddo ! RHS coefficients evaluation do pvol = vvol, vvol+1 @@ -1013,12 +1013,12 @@ subroutine evaluate_dmupfdx(innout, idof, ii, issym, irz) WCALL(dfp200, lbpol, (pvol, Bt00(1:Mvol, 0:1, -1:2), -1, iocons)) ! derivate w.r.t geometry enddo -#ifdef DEBUG - if( .false. ) then - write(ounit, 8375) myid, dBdX%vol, dBdX%innout, -1, pvol, Bt00(pvol, 0:1, -1) -8375 format("dfp200 : myid=",i3, ", vvol=",i3,", innout=", i3 ,", ideriv=", i3, ", lvol=",i3,"; Bt00=",2f10.6) - endif -#endif + #ifdef DEBUG + if( .false. ) then + write(ounit, 8375) myid, dBdX%vol, dBdX%innout, -1, pvol, Bt00(pvol, 0:1, -1) + 8375 format("dfp200 : myid=",i3, ", vvol=",i3,", innout=", i3 ,", ideriv=", i3, ", lvol=",i3,"; Bt00=",2f10.6) + endif + #endif enddo dBdx2(1:Mvol-1) = zero @@ -1030,7 +1030,7 @@ subroutine evaluate_dmupfdx(innout, idof, ii, issym, irz) ; dBdx2(vvol+1) = Bt00(vvol+1, 1, -1) endif -!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-! + !-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-! if( Lfreebound.eq.1 ) then ! Need to modify last two equations ! Set all last column to zero - maybe not necessary ? @@ -1056,12 +1056,12 @@ subroutine evaluate_dmupfdx(innout, idof, ii, issym, irz) else ! Inner interface is perturbed dBdx2( Mvol ) = zero endif -#ifdef DEBUG - if( .false. ) then - write(ounit, 8827) vvol, dBdmpf(Mvol-1, Mvol-1), Btemn(1, 0, Mvol), dItGpdxtp( 1, 2, Mvol), dItGpdxtp( 1, 1, Mvol), dBdx2(Mvol-1), dBdx2(Mvol) -8827 format("dfp200: vvol = ", i3, ", dBdpsip = ", f10.8, ", dBdpsit = ", f10.8, ", dIpdpsip = ", f10.8, ", dIpdpsit = ", f16.10, ", dBdx2(N-1) = ", f10.8, ", dIpdxj = ", f10.8) - endif -#endif + #ifdef DEBUG + if( .false. ) then + write(ounit, 8827) vvol, dBdmpf(Mvol-1, Mvol-1), Btemn(1, 0, Mvol), dItGpdxtp( 1, 2, Mvol), dItGpdxtp( 1, 1, Mvol), dBdx2(Mvol-1), dBdx2(Mvol) + 8827 format("dfp200: vvol = ", i3, ", dBdpsip = ", f10.8, ", dBdpsit = ", f10.8, ", dIpdpsip = ", f10.8, ", dIpdpsit = ", f16.10, ", dBdx2(N-1) = ", f10.8, ", dIpdxj = ", f10.8) + endif + #endif endif @@ -1270,7 +1270,7 @@ subroutine evaluate_dmupfdx(innout, idof, ii, issym, irz) WCALL(dfp200, allocate_geometry_matrices, (vvol,LcomputeDerivatives)) endif -8294 continue + 8294 continue ! Evaluate derivatives using finite differences if( LocalConstraint ) then imupf_local(1:2,0) = ( - 1 * imupf_local(1:2, 2) + 8 * imupf_local(1:2, 1)& @@ -1303,8 +1303,8 @@ subroutine evaluate_dmupfdx(innout, idof, ii, issym, irz) write(ounit,3004) cput-cpus, myid, vvol, im(ii), in(ii), irz, issym, 1, "dpflux analytic ", dmupfdx(1:Mvol,vvol,2,idof,1) / lfactor endif -3003 format("dfp200 : ",f10.2," : ",:,"myid=",i3," ; vvol=",i2," ; (",i2,",",i3," ) ; irz=",i1," ; issym=",i1," ; innout=",i1," ; ",a18," : dmupf=",8f11.05" ;") -3004 format("dfp200 : ",f10.2," : ",:,"myid=",i3," ; vvol=",i2," ; (",i2,",",i3," ) ; irz=",i1," ; issym=",i1," ; innout=",i1," ; ",a18," : dmupf=",8f11.05" ;") + 3003 format("dfp200 : ",f10.2," : ",:,"myid=",i3," ; vvol=",i2," ; (",i2,",",i3," ) ; irz=",i1," ; issym=",i1," ; innout=",i1," ; ",a18," : dmupf=",8f11.05" ;") + 3004 format("dfp200 : ",f10.2," : ",:,"myid=",i3," ; vvol=",i2," ; (",i2,",",i3," ) ; irz=",i1," ; issym=",i1," ; innout=",i1," ; ",a18," : dmupf=",8f11.05" ;") ! Re-evaluate unperturbed solution diff --git a/src/hesian.f90 b/src/hesian.f90 index d4fb9e33..31566fb6 100644 --- a/src/hesian.f90 +++ b/src/hesian.f90 @@ -237,9 +237,8 @@ subroutine hesian( NGdof, position, Mvol, mn, LGdof ) LComputeAxis = .false. WCALL( hesian, dforce, ( NGdof, position(0:NGdof), force(0:NGdof), LComputeDerivatives, LComputeAxis) ) ! calculate force-imbalance & hessian; - - ohessian(1:NGdof,1:NGdof) = hessian2D(1:NGdof,1:NGdof) ! internal copy; 22 Apr 15; - + ! ohessian(1:NGdof,1:NGdof) = hessian2D(1:NGdof,1:NGdof) ! internal copy; 22 Apr 15; + ! ohessian(1:NGdof,1:NGdof) = 0 !-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-! @@ -257,137 +256,137 @@ subroutine hesian( NGdof, position, Mvol, mn, LGdof ) if( Lcheck.eq.5 ) then ! check construction of Hessian; 01 Jul 14; - xx(0,-2:2)= zero ; dRZ = 1.0E-04 + xx(0,-2:2)= zero ; dRZ = 1.0E-04 - write(svol,'(i3.3)')myid -! open(lunit+myid,file="."//trim(ext)//".hessian."//svol,status="unknown") + write(svol,'(i3.3)')myid + ! open(lunit+myid,file="."//trim(ext)//".hessian."//svol,status="unknown") -! lmu(1:Nvol) = mu(1:Nvol) ; lpflux(1:Nvol) = pflux(1:Nvol) ; lhelicity(1:Nvol) = helicity(1:Nvol) ! save original profile information; 20 Jun 14; + ! lmu(1:Nvol) = mu(1:Nvol) ; lpflux(1:Nvol) = pflux(1:Nvol) ; lhelicity(1:Nvol) = helicity(1:Nvol) ! save original profile information; 20 Jun 14; - tdof = 0 ! geometrical degree-of-freedom counter; labels derivative; + tdof = 0 ! geometrical degree-of-freedom counter; labels derivative; - do vvol = 1, Mvol-1 ! loop over internal interfaces; + do vvol = 1, Mvol-1 ! loop over internal interfaces; - cput = GETTIME -! write(lunit+myid,'("hesian : ", 10x ," : ")') -! write(lunit+myid,'("hesian : ",f10.2," : myid=",i3," ; vvol=",i3," ; dRZ=",es9.1," ;")') cput-cpus, myid, vvol, dRZ -! write(lunit+myid,'("hesian : ", 10x ," : ")') + cput = GETTIME + ! write(lunit+myid,'("hesian : ", 10x ," : ")') + ! write(lunit+myid,'("hesian : ",f10.2," : myid=",i3," ; vvol=",i3," ; dRZ=",es9.1," ;")') cput-cpus, myid, vvol, dRZ + ! write(lunit+myid,'("hesian : ", 10x ," : ")') - do ii = 1, mn ! loop over Fourier harmonics degrees of freedom; + do ii = 1, mn ! loop over Fourier harmonics degrees of freedom; - do irz = 0, 1 ! loop over R,Z degrees of freedom; + do irz = 0, 1 ! loop over R,Z degrees of freedom; - if( irz.eq.1 .and. Igeometry.lt.3 ) cycle ! no dependence on Z; 26 Feb 13; + if( irz.eq.1 .and. Igeometry.lt.3 ) cycle ! no dependence on Z; 26 Feb 13; - do issym = 0, 1 + do issym = 0, 1 - if( issym.eq.1 .and. YESstellsym ) cycle ! no dependence on non-stellarator symmetric harmonics; 26 Feb 13; + if( issym.eq.1 .and. YESstellsym ) cycle ! no dependence on non-stellarator symmetric harmonics; 26 Feb 13; - if( ii.eq.1 .and. irz.eq.1 .and. issym.eq.0 ) cycle ! this is not a degree of freedom; no dependence on Zbs_{m,n} for m=0, n=0; - if( ii.eq.1 .and. irz.eq.0 .and. issym.eq.1 ) cycle ! this is not a degree of freedom; no dependence on Rbs_{m,n} for m=0, n=0; + if( ii.eq.1 .and. irz.eq.1 .and. issym.eq.0 ) cycle ! this is not a degree of freedom; no dependence on Zbs_{m,n} for m=0, n=0; + if( ii.eq.1 .and. irz.eq.0 .and. issym.eq.1 ) cycle ! this is not a degree of freedom; no dependence on Rbs_{m,n} for m=0, n=0; - tdof = tdof + 1 + tdof = tdof + 1 - do isymdiff = -2, 2 + do isymdiff = -2, 2 - if( isymdiff.eq.0 ) cycle + if( isymdiff.eq.0 ) cycle - xx(1:NGdof,isymdiff) = position(1:NGdof) ! reset geometry to original; + xx(1:NGdof,isymdiff) = position(1:NGdof) ! reset geometry to original; - xx(tdof,isymdiff) = position(tdof) + isymdiff * dRZ ! perturb appropriate geometric harmonic; + xx(tdof,isymdiff) = position(tdof) + isymdiff * dRZ ! perturb appropriate geometric harmonic; - LComputeDerivatives = .false. - LComputeAxis = .true. - WCALL( hesian, dforce, ( NGdof, xx(0:NGdof,isymdiff), ff(0:NGdof,isymdiff), LComputeDerivatives, LComputeAxis) ) ! force-imbalance; + LComputeDerivatives = .false. + LComputeAxis = .true. + WCALL( hesian, dforce, ( NGdof, xx(0:NGdof,isymdiff), ff(0:NGdof,isymdiff), LComputeDerivatives, LComputeAxis) ) ! force-imbalance; - enddo ! end of do isymdiff; 20 Jun 14; + enddo ! end of do isymdiff; 20 Jun 14; - df(1:NGdof) = ( - ff(1:NGdof,+2) + 8 * ff(1:NGdof,+1) - 8 * ff(1:NGdof,-1) + ff(1:NGdof,-2) ) / ( 12 * dRZ ) + df(1:NGdof) = ( - ff(1:NGdof,+2) + 8 * ff(1:NGdof,+1) - 8 * ff(1:NGdof,-1) + ff(1:NGdof,-2) ) / ( 12 * dRZ ) - tdoc = 0 + tdoc = 0 - do jvol = 1, Mvol-1 + do jvol = 1, Mvol-1 - do jj = 1, mn + do jj = 1, mn - do jrz = 0, 1 ! loop over R,Z degrees of freedom; + do jrz = 0, 1 ! loop over R,Z degrees of freedom; - if( jrz.eq.1 .and. Igeometry.lt.3 ) cycle ! no dependence on Z; 26 Feb 13; + if( jrz.eq.1 .and. Igeometry.lt.3 ) cycle ! no dependence on Z; 26 Feb 13; - do jssym = 0, 1 + do jssym = 0, 1 - if( jssym.eq.1 .and. YESstellsym ) cycle ! no dependence on non-stellarator symmetric harmonics; 26 Feb 13; + if( jssym.eq.1 .and. YESstellsym ) cycle ! no dependence on non-stellarator symmetric harmonics; 26 Feb 13; - if( jj.eq.1 .and. jrz.eq.1 .and. jssym.eq.0 ) cycle ! this is not a constraint; I_{m,n} for m=0, n=0 is irrelevant; - if( jj.eq.1 .and. jrz.eq.0 .and. jssym.eq.1 ) cycle ! this is not a constraint; I_{m,n} for m=0, n=0 is irrelevant; + if( jj.eq.1 .and. jrz.eq.1 .and. jssym.eq.0 ) cycle ! this is not a constraint; I_{m,n} for m=0, n=0 is irrelevant; + if( jj.eq.1 .and. jrz.eq.0 .and. jssym.eq.1 ) cycle ! this is not a constraint; I_{m,n} for m=0, n=0 is irrelevant; - tdoc = tdoc + 1 + tdoc = tdoc + 1 - FATAL( hesian, tdoc.lt. 1, needs attention ) - FATAL( hesian, tdoc.gt.NGdof, needs attention ) + FATAL( hesian, tdoc.lt. 1, needs attention ) + FATAL( hesian, tdoc.gt.NGdof, needs attention ) - cput = GETTIME + cput = GETTIME - error = abs( df(tdoc)-hessian(tdoc,tdof) ) + error = abs( df(tdoc)-hessian(tdoc,tdof) ) - if( abs(hessian(tdoc,tdof)).gt.1.0e-05 .or. abs(df(tdoc)).gt.1.0e-05 .or. error.gt.dRZ ) then ! write to screen; 20 Jan 15; - write(ounit ,1001) cput-cpus, myid, & - vvol, im(ii), in(ii), irz, issym, tdof, & - jvol, im(jj), in(jj), jrz, jssym, tdoc, & - df(tdoc), tdoc, tdof, hessian(tdoc,tdof), error - endif + if( abs(hessian(tdoc,tdof)).gt.1.0e-05 .or. abs(df(tdoc)).gt.1.0e-05 .or. error.gt.dRZ ) then ! write to screen; 20 Jan 15; + write(ounit ,1001) cput-cpus, myid, & + vvol, im(ii), in(ii), irz, issym, tdof, & + jvol, im(jj), in(jj), jrz, jssym, tdoc, & + df(tdoc), tdoc, tdof, hessian(tdoc,tdof), error + endif -! if( abs(hessian(tdoc,tdof)).gt.1.0e-05 .or. abs(df(tdoc)).gt.1.0e-05 .or. error.gt.dRZ ) then ! write to file; 20 Jan 15; -! write(lunit+myid,1001) cput-cpus, myid, & -! vvol, im(ii), in(ii), irz, issym, tdof, & -! jvol, im(jj), in(jj), jrz, jssym, tdoc, & -! df(tdoc), tdoc, tdof, hessian(tdoc,tdof), error -! endif + ! if( abs(hessian(tdoc,tdof)).gt.1.0e-05 .or. abs(df(tdoc)).gt.1.0e-05 .or. error.gt.dRZ ) then ! write to file; 20 Jan 15; + ! write(lunit+myid,1001) cput-cpus, myid, & + ! vvol, im(ii), in(ii), irz, issym, tdof, & + ! jvol, im(jj), in(jj), jrz, jssym, tdoc, & + ! df(tdoc), tdoc, tdof, hessian(tdoc,tdof), error + ! endif - enddo ! end of do jssym; 19 Sep 13; + enddo ! end of do jssym; 19 Sep 13; - enddo ! end of do irz; + enddo ! end of do irz; -#ifdef DEBUG -! pause -#endif + #ifdef DEBUG + ! pause + #endif - enddo ! end of do jj; + enddo ! end of do jj; -#ifdef DEBUG -! pause -#endif + #ifdef DEBUG + ! pause + #endif - enddo ! end of do jvol; + enddo ! end of do jvol; -#ifdef DEBUG -! pause -#endif + #ifdef DEBUG + ! pause + #endif -1001 format("hesian : ",f10.2," : myid=",i3, & - " ; vvol=",i3," ; ("i4" ,"i4" ); irz="i2" ; issym="i2" ; tdof="i6 & - " ; jvol="i4" ; ("i4" ,"i4" ); jrz="i2" ; jssym="i2" ; tdoc="i6 & - " ; fd-estimate="es13.5" & hessian("i6","i6" )="es13.5" ;":" err="es13.5" ;":,f12.4" ;") + 1001 format("hesian : ",f10.2," : myid=",i3, & + " ; vvol=",i3," ; ("i4" ,"i4" ); irz="i2" ; issym="i2" ; tdof="i6 & + " ; jvol="i4" ; ("i4" ,"i4" ); jrz="i2" ; jssym="i2" ; tdoc="i6 & + " ; fd-estimate="es13.5" & hessian("i6","i6" )="es13.5" ;":" err="es13.5" ;":,f12.4" ;") - enddo ! end of do issym; + enddo ! end of do issym; - enddo ! end of do irz; + enddo ! end of do irz; - enddo ! end of do ii; + enddo ! end of do ii; - enddo ! end of do vvol; + enddo ! end of do vvol; - pack = 'U' !; position(0) = zero ! this is not used; 11 Aug 14; - WCALL( hesian, packxi, ( NGdof, position(0:NGdof), Mvol, mn, iRbc(1:mn,0:Mvol), iZbs(1:mn,0:Mvol), iRbs(1:mn,0:Mvol), iZbc(1:mn,0:Mvol), pack, .false., LComputeAxis ) ) + pack = 'U' !; position(0) = zero ! this is not used; 11 Aug 14; + WCALL( hesian, packxi, ( NGdof, position(0:NGdof), Mvol, mn, iRbc(1:mn,0:Mvol), iZbs(1:mn,0:Mvol), iRbs(1:mn,0:Mvol), iZbc(1:mn,0:Mvol), pack, .false., LComputeAxis ) ) - mu(1:Nvol) = lmu(1:Nvol) ; pflux(1:Nvol) = lpflux(1:Nvol) ; helicity(1:Nvol) = lhelicity(1:Nvol) + mu(1:Nvol) = lmu(1:Nvol) ; pflux(1:Nvol) = lpflux(1:Nvol) ; helicity(1:Nvol) = lhelicity(1:Nvol) -! xx(1:NGdof,0) = position(1:NGdof) ! reset geometry to original; -! -! LComputeDerivatives = .false. -! WCALL(hesian,dforce,( NGdof, xx(1:NGdof,0), ff(0:NGdof,0), LComputeDerivatives )) ! calculate the force-imbalance; + ! xx(1:NGdof,0) = position(1:NGdof) ! reset geometry to original; + ! + ! LComputeDerivatives = .false. + ! WCALL(hesian,dforce,( NGdof, xx(1:NGdof,0), ff(0:NGdof,0), LComputeDerivatives )) ! calculate the force-imbalance; - !close(lunit+myid) + !close(lunit+myid) endif ! end of if( Lcheck.eq.5 ) ; 01 Jul 14; @@ -423,7 +422,13 @@ subroutine hesian( NGdof, position, Mvol, mn, LGdof ) write(munit) NGdof write(munit) ohessian(1:NGdof,1:NGdof) close(munit) - endif + + ! add by Erol + ! do ii=1,NGdof + ! write(*,*)ii, ohessian(ii,1:NGdof) + ! enddo + + endif endif @@ -447,12 +452,12 @@ subroutine hesian( NGdof, position, Mvol, mn, LGdof ) hessian2D(1:NGdof,1:NGdof) = ohessian(1:NGdof,1:NGdof) -!#ifdef NAG18 -! call F02EBF( JOB, NGdof, hessian(1:LDA,1:NGdof), LDA, evalr(1:NGdof), evali(1:NGdof), & -! evecr(1:Ldvr,1:NGdof), Ldvr, eveci(1:Ldvi,1:NGdof), Ldvi, work(1:Lwork), Lwork, if02ebf ) -!#else -! FATAL( global, .true., eigenvalue solver needs updating to F08NAF ) -!#endif + !#ifdef NAG18 + ! call F02EBF( JOB, NGdof, hessian(1:LDA,1:NGdof), LDA, evalr(1:NGdof), evali(1:NGdof), & + ! evecr(1:Ldvr,1:NGdof), Ldvr, eveci(1:Ldvi,1:NGdof), Ldvi, work(1:Lwork), Lwork, if02ebf ) + !#else + ! FATAL( global, .true., eigenvalue solver needs updating to F08NAF ) + !#endif call dgeev('N', JOB, NGdof, hessian2D(1:LDA,1:NGdof), LDA, evalr(1:NGdof), evali(1:NGdof), & evecl(1:Ldvr,1:NGdof), Ldvr, revecr(1:Ldvr,1:2*NGdof), Ldvr, work(1:Lwork), Lwork, if02ebf ) evecr(1:Ldvr,1:NGdof) = revecr(1:Ldvr,1:NGdof) @@ -583,6 +588,11 @@ subroutine hesian( NGdof, position, Mvol, mn, LGdof ) close(hunit) endif ! end of if( myid.eq.0 ) ; 04 Dec 14; + ! ! add by Erol + ! do ii=1,NGdof + ! write(*,*)ii, evalr(ii), evali(ii) + ! enddo + endif ! end of if( ( LHevalues .or. LHevectors ) ) !-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-! @@ -695,7 +705,7 @@ subroutine hesian( NGdof, position, Mvol, mn, LGdof ) DALLOCATE(hessian2D) - write(ounit,*) 5656 + ! write(ounit,*) 5656 DALLOCATE(dessian2D) diff --git a/src/lbpol.f90 b/src/lbpol.f90 index c4958705..ac09f917 100644 --- a/src/lbpol.f90 +++ b/src/lbpol.f90 @@ -126,6 +126,21 @@ subroutine lbpol(lvol, Bt00, ideriv, iocons) ! Now Btemn(1, 0, vvol) and Btemn(1, 1, vvol) contain Bte00(s=-1) and Bte00(s=1) for each volume vvol. + ! if((lvol.eq.10.and.iocons.eq.1).or.(lvol.eq.11.and.iocons.eq.0)) then + ! write(*,*) "lvol", lvol, "iocons", iocons, "ideriv", ideriv + ! write(*,*) "Bt", Bt(1:Ntz) + ! ! write(*,*) "Bz",Bz(1:Ntz) ! also different, but fractionally less + ! ! write(*,*) guvij(1:Ntz,1,1,0),guvij(1:Ntz,2,2,0),guvij(1:Ntz,3,3,0) ! SAME + ! ! write(*,*) guvij(1:Ntz,2,3,0) + ! ! write(*,*) "dAz", dAz(1:Ntz ) ! differetn + ! ! write(*,*) "__mn", efmn(1:mn) + ! write(*,*) "Ate%s" + ! do ii = 1, mn + ! do ll=0,Lrad(lvol) + ! write(*,*) ii,ll, Ate(lvol,ideriv,ii)%s(ll) + ! enddo + ! enddo + ! endif RETURN(lbpol) diff --git a/src/mp00ac.f90 b/src/mp00ac.f90 index 2ecaf1ab..2c3c56be 100644 --- a/src/mp00ac.f90 +++ b/src/mp00ac.f90 @@ -726,10 +726,10 @@ subroutine mp00ac( Ndof, Xdof, Fdof, Ddof, Ldfjac, iflag ) ! argument list is fi end select endif -3000 format("mp00ac : ",f10.2," : myid=",i3," ; lvol=",i3," ; (mu,dp)=("es23.15" ,"es23.15" ) ; iflag="i2" ;":" F="2es13.05" ;") -3010 format("mp00ac : ",f10.2," : myid=",i3," ; lvol=",i3," ; (mu,dp)=("es23.15" ,"es23.15" ) ; iflag="i2" ;":" D="4es13.05" ;") -3001 format("mp00ac : ",f10.2," : myid=",i3," ; lvol=",i3," ; (dt,dp)=("es23.15" ,"es23.15" ) ; iflag="i2" ;":" F="2es13.05" ;") -3011 format("mp00ac : ",f10.2," : myid=",i3," ; lvol=",i3," ; (dt,dp)=("es23.15" ,"es23.15" ) ; iflag="i2" ;":" D="4es13.05" ;") + 3000 format("mp00ac : ",f10.2," : myid=",i3," ; lvol=",i3," ; (mu,dp)=("es23.15" ,"es23.15" ) ; iflag="i2" ;":" F="2es13.05" ;") + 3010 format("mp00ac : ",f10.2," : myid=",i3," ; lvol=",i3," ; (mu,dp)=("es23.15" ,"es23.15" ) ; iflag="i2" ;":" D="4es13.05" ;") + 3001 format("mp00ac : ",f10.2," : myid=",i3," ; lvol=",i3," ; (dt,dp)=("es23.15" ,"es23.15" ) ; iflag="i2" ;":" F="2es13.05" ;") + 3011 format("mp00ac : ",f10.2," : myid=",i3," ; lvol=",i3," ; (dt,dp)=("es23.15" ,"es23.15" ) ; iflag="i2" ;":" D="4es13.05" ;") endif ! end of if( Wmp00ac .or. Wma02aa ) ; diff --git a/src/newton.f90 b/src/newton.f90 index 7bd26216..0c74b6b0 100644 --- a/src/newton.f90 +++ b/src/newton.f90 @@ -659,9 +659,9 @@ subroutine fcn2( NGdof, xx, fvec, fjac, Ldfjac, irevcm ) case( 2 ) ! before re-entry to C05PDF, fjac must contain the derivatives; -#ifdef DEBUG - FATAL( newton, .not.Lhessianallocated, need to allocate hessian ) -#endif + #ifdef DEBUG + FATAL( newton, .not.Lhessianallocated, need to allocate hessian ) + #endif nDcalls = nDcalls + 1 @@ -687,9 +687,9 @@ subroutine fcn2( NGdof, xx, fvec, fjac, Ldfjac, irevcm ) LComputeAxis = .true. WCALL( newton, dforce, ( NGdof, position(0:NGdof), force(0:NGdof), LComputeDerivatives, LComputeAxis ) ) ! calculate the force-imbalance; -#ifdef DEBUG - FATAL( newton, Lcheck.eq.4, derivatives of Beltrami field have been computed ) -#endif + #ifdef DEBUG + FATAL( newton, Lcheck.eq.4, derivatives of Beltrami field have been computed ) + #endif endif @@ -697,23 +697,23 @@ subroutine fcn2( NGdof, xx, fvec, fjac, Ldfjac, irevcm ) if( myid.eq.0 ) call writereadgf( 'W', NGdof, ireadhessian ) ! will always save derivative matrix; -#ifdef DEBUG + #ifdef DEBUG - if( Lcheck.eq.3 ) then - write(ounit,'("newton : ", 10x ," : myid=",i3," ; volume derivatives have been compared ;")') myid - stop "newton : : myid= ; volume derivatives have been compared ;" - endif + if( Lcheck.eq.3 ) then + write(ounit,'("newton : ", 10x ," : myid=",i3," ; volume derivatives have been compared ;")') myid + stop "newton : : myid= ; volume derivatives have been compared ;" + endif - FATAL( newton, Lcheck.eq.3, volume derivatives have been compared ) ! the first process will terminate all processes; + FATAL( newton, Lcheck.eq.3, volume derivatives have been compared ) ! the first process will terminate all processes; - if( (Lcheck.eq.4) .and. (nDcalls.ne.1) ) then - write(ounit,'("newton : ", 10x ," : myid=",i3," ; field derivatives have been compared ;")') myid - stop "newton : : myid= ; field derivatives have been compared ;" - endif + if( (Lcheck.eq.4) .and. (nDcalls.ne.1) ) then + write(ounit,'("newton : ", 10x ," : myid=",i3," ; field derivatives have been compared ;")') myid + stop "newton : : myid= ; field derivatives have been compared ;" + endif - FATAL( newton, (Lcheck.eq.4) .and. (nDcalls.ne.1), field derivatives have been compared ) ! the first process will terminate all processes; + FATAL( newton, (Lcheck.eq.4) .and. (nDcalls.ne.1), field derivatives have been compared ) ! the first process will terminate all processes; -#endif + #endif !-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-! diff --git a/src/packab.f90 b/src/packab.f90 index b2b5ccc2..296d7df3 100644 --- a/src/packab.f90 +++ b/src/packab.f90 @@ -109,7 +109,6 @@ subroutine packab( packorunpack, lvol, NN, solution, ideriv ) #endif if( YESstellsym ) then - do ii = 1, mn do ll = 0, llrad ; id = Ate(lvol,0,ii)%i(ll) ; if (id/=0) then; Ate(lvol,ideriv,ii)%s(ll) = solution(id) diff --git a/src/spsint.f90 b/src/spsint.f90 index 1c423eda..2eaf6489 100644 --- a/src/spsint.f90 +++ b/src/spsint.f90 @@ -193,21 +193,21 @@ subroutine spsint( lquad, mn, lvol, lrad ) DDzzcc( ll1, pp1, mi+1, 1 ) = DDzzcc( ll1, pp1, mi+1, 1 ) + DlDp * fzzcc if (NOTstellsym) then -!$OMP ATOMIC UPDATE - DTooss( ll1, pp1, mi+1, 1 ) = DTooss( ll1, pp1, mi+1, 1 ) + DlTp * fooss -!$OMP ATOMIC UPDATE - TTsscc( ll1, pp1, mi+1, 1 ) = TTsscc( ll1, pp1, mi+1, 1 ) + TlTp * fsscc -!$OMP ATOMIC UPDATE - TDstcc( ll1, pp1, mi+1, 1 ) = TDstcc( ll1, pp1, mi+1, 1 ) + TlDp * fstcc -!$OMP ATOMIC UPDATE - TDszcc( ll1, pp1, mi+1, 1 ) = TDszcc( ll1, pp1, mi+1, 1 ) + TlDp * fszcc -!$OMP ATOMIC UPDATE - TDszss( ll1, pp1, mi+1, 1 ) = TDszss( ll1, pp1, mi+1, 1 ) + TlDp * fszss -!$OMP ATOMIC UPDATE - DDttss( ll1, pp1, mi+1, 1 ) = DDttss( ll1, pp1, mi+1, 1 ) + DlDp * fttss -!$OMP ATOMIC UPDATE - DDtzss( ll1, pp1, mi+1, 1 ) = DDtzss( ll1, pp1, mi+1, 1 ) + DlDp * ftzss -!$OMP ATOMIC UPDATE + !$OMP ATOMIC UPDATE + DTooss( ll1, pp1, mi+1, 1 ) = DTooss( ll1, pp1, mi+1, 1 ) + DlTp * fooss + !$OMP ATOMIC UPDATE + TTsscc( ll1, pp1, mi+1, 1 ) = TTsscc( ll1, pp1, mi+1, 1 ) + TlTp * fsscc + !$OMP ATOMIC UPDATE + TDstcc( ll1, pp1, mi+1, 1 ) = TDstcc( ll1, pp1, mi+1, 1 ) + TlDp * fstcc + !$OMP ATOMIC UPDATE + TDszcc( ll1, pp1, mi+1, 1 ) = TDszcc( ll1, pp1, mi+1, 1 ) + TlDp * fszcc + !$OMP ATOMIC UPDATE + TDszss( ll1, pp1, mi+1, 1 ) = TDszss( ll1, pp1, mi+1, 1 ) + TlDp * fszss + !$OMP ATOMIC UPDATE + DDttss( ll1, pp1, mi+1, 1 ) = DDttss( ll1, pp1, mi+1, 1 ) + DlDp * fttss + !$OMP ATOMIC UPDATE + DDtzss( ll1, pp1, mi+1, 1 ) = DDtzss( ll1, pp1, mi+1, 1 ) + DlDp * ftzss + !$OMP ATOMIC UPDATE DDzzss( ll1, pp1, mi+1, 1 ) = DDzzss( ll1, pp1, mi+1, 1 ) + DlDp * fzzss end if !NOTstellsym diff --git a/src/spsmat.f90 b/src/spsmat.f90 index ff7fbd4e..3480fac6 100644 --- a/src/spsmat.f90 +++ b/src/spsmat.f90 @@ -129,7 +129,7 @@ subroutine spsmat( lvol, mn, lrad ) TTMdata(0:lrad,ii) = TT(0:lrad,0,0) enddo endif - + !-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-! if( YESstellsym ) then diff --git a/src/xspech.f90 b/src/xspech.f90 index 05fbcc0a..b487e328 100644 --- a/src/xspech.f90 +++ b/src/xspech.f90 @@ -319,7 +319,7 @@ subroutine spec version, & MPI_COMM_SPEC -!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-! + !-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-! LOCALS @@ -341,12 +341,12 @@ subroutine spec SALLOCATE( position, (0:NGdof), zero ) ! position ; NGdof = #geometrical degrees-of-freedom was computed in preset; -!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-! + !-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-! nfreeboundaryiterations = -1 -! This is the free-boundary iteration loop (implemented using GOTO); 08 Jun 16; -9000 nfreeboundaryiterations = nfreeboundaryiterations + 1 + ! This is the free-boundary iteration loop (implemented using GOTO); 08 Jun 16; + 9000 nfreeboundaryiterations = nfreeboundaryiterations + 1 ! run fix_boundary for the first free_boundary iteration if LautoinitBn was set to 1 if (Lfreebound.eq.1 .and. LautoinitBn.eq.1) then @@ -369,14 +369,14 @@ subroutine spec endif endif -!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-! + !-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-! -!> **packing geometrical degrees-of-freedom into vector** -!> -!>
    -!>
  • If \c NGdof.gt.0 , where \c NGdof counts the geometrical degrees-of-freedom, i.e. the \f$R_{bc}\f$, \f$Z_{bs}\f$, etc., -!> then packxi() is called to "pack" the geometrical degrees-of-freedom into \c position(0:NGdof) .
    • -!>
+ !> **packing geometrical degrees-of-freedom into vector** + !> + !>
    + !>
  • If \c NGdof.gt.0 , where \c NGdof counts the geometrical degrees-of-freedom, i.e. the \f$R_{bc}\f$, \f$Z_{bs}\f$, etc., + !> then packxi() is called to "pack" the geometrical degrees-of-freedom into \c position(0:NGdof) .
    • + !>
if( NGdof.gt.0 ) then ! pack geometry into vector; 14 Jan 13; @@ -387,17 +387,17 @@ subroutine spec endif -!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-! + !-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-! -!> **initialize adiabatic constants** -!> -!>
    -!>
  • If \c Ladiabatic.eq.0 , then the "adiabatic constants" in each region, \f$P_v\f$, are calculated as -!> \f{eqnarray}{ P_v \equiv p_v V_v^\gamma, \label{eq:adiabatic_xspech} -!> \f} -!> where \f$p_v\equiv\,\f$\c pressure(vvol) , the volume \f$V_v\f$ of each region is computed by volume() , -!> and the adiabatic index \f$\gamma\equiv\,\f$\c gamma .
    • -!>
+ !> **initialize adiabatic constants** + !> + !>
    + !>
  • If \c Ladiabatic.eq.0 , then the "adiabatic constants" in each region, \f$P_v\f$, are calculated as + !> \f{eqnarray}{ P_v \equiv p_v V_v^\gamma, \label{eq:adiabatic_xspech} + !> \f} + !> where \f$p_v\equiv\,\f$\c pressure(vvol) , the volume \f$V_v\f$ of each region is computed by volume() , + !> and the adiabatic index \f$\gamma\equiv\,\f$\c gamma .
    • + !>
do vvol = 1, Mvol @@ -417,28 +417,28 @@ subroutine spec write(ounit,'("xspech : ",f10.2," : myid=",i3," ; adiabatic constants = "999es13.5)') cput-cpus, myid, adiabatic(1:Mvol) endif -!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-! - -!> **solving force-balance** -!> -!>
    -!>
  • If there are geometrical degress of freedom, i.e. if \c NGdof.gt.0 , then -!>
      -!>
    • \todo If \c Lminimize.eq.1 , call pc00aa() to find minimum of energy functional -!> using quasi-Newton, preconditioned conjugate gradient method, \c E04DGF -!> -!>
      • -!>
    • If \c Lfindzero.gt.0 , call newton() to find extremum of constrained energy functional using a Newton method, \c C05PDF .
      • -!>
    • -!>
+ !-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-! -! if( Lminimize.eq.1 ) then -! -! ifail = 1 ! this is probably not required; 26 Feb 13; -! -! WCALL(xspech,pc00aa,( NGdof, position(1:NGdof), Mvol, mn, ifail )) -! -! endif + !> **solving force-balance** + !> + !>
    + !>
  • If there are geometrical degress of freedom, i.e. if \c NGdof.gt.0 , then + !>
      + !>
    • \todo If \c Lminimize.eq.1 , call pc00aa() to find minimum of energy functional + !> using quasi-Newton, preconditioned conjugate gradient method, \c E04DGF + !> + !>
      • + !>
    • If \c Lfindzero.gt.0 , call newton() to find extremum of constrained energy functional using a Newton method, \c C05PDF .
      • + !>
    • + !>
+ + ! if( Lminimize.eq.1 ) then + ! + ! ifail = 1 ! this is probably not required; 26 Feb 13; + ! + ! WCALL(xspech,pc00aa,( NGdof, position(1:NGdof), Mvol, mn, ifail )) + ! + ! endif if( NGdof.gt.0 ) then @@ -457,31 +457,31 @@ subroutine spec endif -!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-! + !-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-! -!> **post diagnostics** -!> -!>
    -!>
  • The pressure is computed from the adiabatic constants from Eqn.\f$(\ref{eq:adiabatic_xspech})\f$, i.e. \f$p=P/V^\gamma\f$.
    • -!>
  • The Beltrami/vacuum fields in each region are re-calculated using dforce() .
    • -!>
  • If \c Lcheck.eq.5 \c .or. \c LHevalues \c .or. \c LHevectors \c .or. \c Lperturbed.eq.1 , then the force-gradient matrix is examined using hesian() .
    • -!>
+ !> **post diagnostics** + !> + !>
    + !>
  • The pressure is computed from the adiabatic constants from Eqn.\f$(\ref{eq:adiabatic_xspech})\f$, i.e. \f$p=P/V^\gamma\f$.
    • + !>
  • The Beltrami/vacuum fields in each region are re-calculated using dforce() .
    • + !>
  • If \c Lcheck.eq.5 \c .or. \c LHevalues \c .or. \c LHevectors \c .or. \c Lperturbed.eq.1 , then the force-gradient matrix is examined using hesian() .
    • + !>
-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-! + !-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-! -! set/reset input variables; + ! set/reset input variables; -! if( Lconstraint.lt.2 ) helicity(1:Nvol) = lABintegral(1:Nvol) ! updated ``input'' quantity; + ! if( Lconstraint.lt.2 ) helicity(1:Nvol) = lABintegral(1:Nvol) ! updated ``input'' quantity; -#ifdef DEBUG - do vvol = 1, Mvol - FATAL( xspech, vvolume(vvol).lt.vsmall, error dividing adiabatic by volume ) - enddo -#endif + #ifdef DEBUG + do vvol = 1, Mvol + FATAL( xspech, vvolume(vvol).lt.vsmall, error dividing adiabatic by volume ) + enddo + #endif pressure(1:Mvol) = adiabatic(1:Mvol) / vvolume(1:Mvol)**gamma ! this matches construction of adiabatic above; -!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-! + !-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-! SALLOCATE( gradient, (0:NGdof), zero ) @@ -489,27 +489,27 @@ subroutine spec LComputeDerivatives = .false. LComputeAxis = .true. -! vvol = Mvol ; ideriv = 0 ; ii = 1 -! write(ounit,'("xspech : ", 10x ," : sum(Ate(",i3,",",i2,",",i2,")%s) =",99es23.15)') vvol, ideriv, ii, sum(Ate(vvol,ideriv,ii)%s(0:Lrad(vvol))) + ! vvol = Mvol ; ideriv = 0 ; ii = 1 + ! write(ounit,'("xspech : ", 10x ," : sum(Ate(",i3,",",i2,",",i2,")%s) =",99es23.15)') vvol, ideriv, ii, sum(Ate(vvol,ideriv,ii)%s(0:Lrad(vvol))) WCALL( xspech, dforce, ( NGdof, position(0:NGdof), gradient(0:NGdof), LComputeDerivatives, LComputeAxis) ) ! (re-)calculate Beltrami fields; DALLOCATE(gradient) -#ifdef DEBUG - do vvol = 1, Mvol-1 - ; FATAL( xspech, BBe(vvol).lt.logtolerance, underflow ) - if( Igeometry.eq.3 ) then ! include spectral constraints; 04 Dec 14; - ;FATAL( xspech, IIo(vvol).lt.logtolerance, underflow ) - endif - if( NOTstellsym ) then - ;FATAL( xspech, BBo(vvol).lt.logtolerance, underflow ) + #ifdef DEBUG + do vvol = 1, Mvol-1 + ; FATAL( xspech, BBe(vvol).lt.logtolerance, underflow ) if( Igeometry.eq.3 ) then ! include spectral constraints; 04 Dec 14; - FATAL( xspech, IIe(vvol).lt.logtolerance, underflow ) + ;FATAL( xspech, IIo(vvol).lt.logtolerance, underflow ) endif - endif - enddo -#endif + if( NOTstellsym ) then + ;FATAL( xspech, BBo(vvol).lt.logtolerance, underflow ) + if( Igeometry.eq.3 ) then ! include spectral constraints; 04 Dec 14; + FATAL( xspech, IIe(vvol).lt.logtolerance, underflow ) + endif + endif + enddo + #endif if( myid.eq.0 ) then cput = GETTIME @@ -525,10 +525,10 @@ subroutine spec endif endif -1000 format("xspech : ",f10.2," : #freeits=",i3," ; ":"|f|="es12.5" ; ":"time=",f10.2,"s ;":" log"a5,:"="28f6.2" ...") -1001 format("xspech : ", 10x ," : ",3x," ; ":" " 12x " ":" ", 10x ," ;":" log"a5,:"="28f6.2" ...") + 1000 format("xspech : ",f10.2," : #freeits=",i3," ; ":"|f|="es12.5" ; ":"time=",f10.2,"s ;":" log"a5,:"="28f6.2" ...") + 1001 format("xspech : ", 10x ," : ",3x," ; ":" " 12x " ":" ", 10x ," ;":" log"a5,:"="28f6.2" ...") -!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-! + !-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-! if( Lcheck.eq.5 .or. LHevalues .or. LHevectors .or. LHmatrix .or. Lperturbed.eq.1 ) then ! check construction of Hessian; 01 Jul 14; @@ -542,7 +542,7 @@ subroutine spec endif ! end of if( Lcheck.eq.5 ) ; 01 Jul 14; -!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-! + !-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-! select case( Igeometry ) ! 08 Feb 16; case( 1 ) ; tflux(1) = dtflux(1) ; pflux(1) = dpflux(1) ! 08 Feb 16; @@ -556,51 +556,51 @@ subroutine spec tflux(1:Mvol) = tflux(1:Mvol) * pi2 / phiedge ! this is the "inverse" operation defined in preset; 19 Jul 16; pflux(1:Mvol) = pflux(1:Mvol) * pi2 / phiedge -!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-! + !-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-! -!> **free-boundary: re-computing normal field** -!> -!>
    -!>
  • If \c Lfreebound.eq.1 and \c Lfindzero.gt.0 and \c mfreeits.ne.0 , -!> then the magnetic field at the computational boundary produced by the plasma currents is computed using bnorml() .
    • -!>
  • The "new" magnetic field at the computational boundary produced by the plasma currents is updated using a Picard scheme: -!> \f{eqnarray}{ \texttt{Bns}_i^{j} = \lambda \, \texttt{Bns}_i^{j-1} + (1-\lambda) \texttt{Bns}_i, \label{eq:blending_xspech} -!> \f} -!> where \f$j\f$ labels free-boundary iterations, the "blending parameter" is \f$\lambda\equiv\,\f$\c gBnbld , -!> and \c Bns \f$_i\f$ is computed by virtual casing. -!> The subscript "$i$" labels Fourier harmonics.
    • -!>
  • If the new (unblended) normal field is _not_ sufficiently close to the old normal field, as quantified by \c gBntol , -!> then the free-boundary iterations continue. -!> This is quantified by -!> \f{eqnarray}{ \sum_i | \texttt{Bns}_i^{j-1} - \texttt{Bns}_i | / N, \label{eq:gBntol_xspech} -!> \f} -!> where \f$N\f$ is the total number of Fourier harmonics.
    • -!>
  • There are several choices that are available: -!>
      -!>
    • if \c mfreeits=-2 : the vacuum magnetic field -!> (really, the normal component of the field produced by the external currents at the computational boundary) -!> required to hold the given equlibrium is written to file. -!> This information is required as input by FOCUS \cite y2017_zhu -!> for example. (This option probably needs to revised.)
      • -!>
    • if \c mfreeits=-1 : after the plasma field is computed by virtual casing, -!> the vacuum magnetic field is set to exactly balance the plasma field -!> (again, we are really talking about the normal component at the computational boundary.) -!> This will ensure that the computational boundary itself if a flux surface of the total magnetic field.
      • -!>
    • if \c mfreeits=0 : the plasma field at the computational boundary is not updated; no "free-boundary" iterations take place.
      • -!>
    • if \c mfreeits>0 : the plasma field at the computational boundary is updated according to the above blending Eqn.\f$(\ref{eq:blending_xspech})\f$, -!> and the free-boundary iterations will continue until either the tolerance condition is met (see \c gBntol and Eqn.\f$(\ref{eq:gBntol_xspech})\f$) -!> or the maximum number of free-boundary iterations, namely \c mfreeits , is reached. -!> For this case, \c Lzerovac is relevant: -!> if \c Lzerovac=1 , then the vacuum field is set equal to the normal field at every iteration, -!> which results in the computational boundary being a flux surface. -!> (I am not sure if this is identical to setting \c mfreeits=-1 ; the logic etc. needs to be revised.)
      • -!>
    • -!>
+ !> **free-boundary: re-computing normal field** + !> + !>
    + !>
  • If \c Lfreebound.eq.1 and \c Lfindzero.gt.0 and \c mfreeits.ne.0 , + !> then the magnetic field at the computational boundary produced by the plasma currents is computed using bnorml() .
    • + !>
  • The "new" magnetic field at the computational boundary produced by the plasma currents is updated using a Picard scheme: + !> \f{eqnarray}{ \texttt{Bns}_i^{j} = \lambda \, \texttt{Bns}_i^{j-1} + (1-\lambda) \texttt{Bns}_i, \label{eq:blending_xspech} + !> \f} + !> where \f$j\f$ labels free-boundary iterations, the "blending parameter" is \f$\lambda\equiv\,\f$\c gBnbld , + !> and \c Bns \f$_i\f$ is computed by virtual casing. + !> The subscript "$i$" labels Fourier harmonics.
    • + !>
  • If the new (unblended) normal field is _not_ sufficiently close to the old normal field, as quantified by \c gBntol , + !> then the free-boundary iterations continue. + !> This is quantified by + !> \f{eqnarray}{ \sum_i | \texttt{Bns}_i^{j-1} - \texttt{Bns}_i | / N, \label{eq:gBntol_xspech} + !> \f} + !> where \f$N\f$ is the total number of Fourier harmonics.
    • + !>
  • There are several choices that are available: + !>
      + !>
    • if \c mfreeits=-2 : the vacuum magnetic field + !> (really, the normal component of the field produced by the external currents at the computational boundary) + !> required to hold the given equlibrium is written to file. + !> This information is required as input by FOCUS \cite y2017_zhu + !> for example. (This option probably needs to revised.)
      • + !>
    • if \c mfreeits=-1 : after the plasma field is computed by virtual casing, + !> the vacuum magnetic field is set to exactly balance the plasma field + !> (again, we are really talking about the normal component at the computational boundary.) + !> This will ensure that the computational boundary itself if a flux surface of the total magnetic field.
      • + !>
    • if \c mfreeits=0 : the plasma field at the computational boundary is not updated; no "free-boundary" iterations take place.
      • + !>
    • if \c mfreeits>0 : the plasma field at the computational boundary is updated according to the above blending Eqn.\f$(\ref{eq:blending_xspech})\f$, + !> and the free-boundary iterations will continue until either the tolerance condition is met (see \c gBntol and Eqn.\f$(\ref{eq:gBntol_xspech})\f$) + !> or the maximum number of free-boundary iterations, namely \c mfreeits , is reached. + !> For this case, \c Lzerovac is relevant: + !> if \c Lzerovac=1 , then the vacuum field is set equal to the normal field at every iteration, + !> which results in the computational boundary being a flux surface. + !> (I am not sure if this is identical to setting \c mfreeits=-1 ; the logic etc. needs to be revised.)
      • + !>
    • + !>
LContinueFreeboundaryIterations = .false. ; LupdateBn = .false. ! default; -! if( Lfreebound.eq.1 .and. Lfindzero.gt.0 ) then + ! if( Lfreebound.eq.1 .and. Lfindzero.gt.0 ) then if( Lfreebound.eq.1) then ! removed Lfindzero check; Loizu Dec 18; if( mfreeits.gt.0 .and. nfreeboundaryiterations.lt.mfreeits ) LupdateBn = .true. if( mfreeits.lt.0 ) LupdateBn = .true. @@ -727,18 +727,18 @@ subroutine spec ; ; write(ounit,1003) endif ! end of if( myid.eq.0 ) ; 24 Nov 16; -1003 format("xspech : " 10x " : ") -1004 format("xspech : "f10.2" : nfreeboundaryiterations = "i6" / "i6.5" ; gBntol ="es8.1" ; bnserr =",es12.5," ; bnorml time ="f10.2"s ;") + 1003 format("xspech : " 10x " : ") + 1004 format("xspech : "f10.2" : nfreeboundaryiterations = "i6" / "i6.5" ; gBntol ="es8.1" ; bnserr =",es12.5," ; bnorml time ="f10.2"s ;") endif ! end of if( LupdateBn ) ; -!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-! + !-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-! -!> **output files: vector potential** -!> -!>
    -!>
  • The vector potential is written to file using ra00aa() .
    • -!>
+ !> **output files: vector potential** + !> + !>
    + !>
  • The vector potential is written to file using ra00aa() .
    • + !>
WCALL( xspech, ra00aa, ('W') ) ! this writes vector potential to file; @@ -746,16 +746,16 @@ subroutine spec WCALL( xspech, wrtend ) ! write restart file; save initial input; endif -!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-! + !-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-! if( LContinueFreeboundaryIterations .and. nfreeboundaryiterations.lt.mfreeits ) goto 9000 ! removed Lfindzero check; Loizu Dec 18; if( Lfreebound.eq.1 .and. First_free_bound ) goto 9000 ! going back to normal free_boundary calculation; Zhu 20190701; -!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-! + !-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-! -! FREE-BOUNDARY ITERATIONS HAVE FINISHED; + ! FREE-BOUNDARY ITERATIONS HAVE FINISHED; -!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-! + !-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-! end subroutine spec @@ -870,7 +870,7 @@ subroutine final_diagnostics ! Computes the surface current at each interface for output SALLOCATE( Bt00, (1:Mvol, 0:1, -1:2) , zero) - + do vvol = 1, Mvol LREGION(vvol) From 044cc7f7dbea117b9ecfb50740972d3c9f07d9f1 Mon Sep 17 00:00:00 2001 From: ErolBa Date: Wed, 12 Apr 2023 12:51:49 +0200 Subject: [PATCH 04/36] change to requirements --- Utilities/pythontools/requirements.txt | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/Utilities/pythontools/requirements.txt b/Utilities/pythontools/requirements.txt index 932ff2c4..be8bb1d3 100644 --- a/Utilities/pythontools/requirements.txt +++ b/Utilities/pythontools/requirements.txt @@ -2,4 +2,5 @@ h5py matplotlib f90nml numpy -coilpy \ No newline at end of file +scipy +coilpy From 0d7ce7cfad58470969fc1530d6ec4d14b82b99b9 Mon Sep 17 00:00:00 2001 From: ErolBa Date: Wed, 12 Apr 2023 15:36:49 +0200 Subject: [PATCH 05/36] Formatting changes. So the wrapper compiles for this branch --- src/bfield.f90 | 4 +- src/dforce.f90 | 362 ++++++++++++++++++++++++------------------------- src/dfp100.f90 | 16 +-- src/dfp200.f90 | 120 ++++++++-------- src/global.f90 | 4 +- src/hesian.f90 | 196 +++++++++++++------------- src/lbpol.f90 | 15 -- src/mp00ac.f90 | 8 +- src/newton.f90 | 36 ++--- src/packab.f90 | 1 + src/preset.f90 | 6 +- src/sphdf5.f90 | 1 + src/spsint.f90 | 30 ++-- src/spsmat.f90 | 2 +- src/xspech.f90 | 267 ++++++++++++++++++------------------ 15 files changed, 524 insertions(+), 544 deletions(-) diff --git a/src/bfield.f90 b/src/bfield.f90 index f0d000a5..5c2daa8c 100644 --- a/src/bfield.f90 +++ b/src/bfield.f90 @@ -167,7 +167,9 @@ subroutine bfield( zeta, st, Bst ) cput-cpus, lvol, zeta, st(1:2), dBu(3) FATAL( bfield, abs(dBu(3)).lt.vsmall, field is not toroidal ) - + !if( abs( dBu(3)).lt.vsmall ) then + ! write(ounit,'("WARNING: bfield: field is not toroidal")') + !endif endif !-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-! diff --git a/src/dforce.f90 b/src/dforce.f90 index c5cd7b53..0983fa07 100644 --- a/src/dforce.f90 +++ b/src/dforce.f90 @@ -136,8 +136,7 @@ subroutine dforce( NGdof, position, force, LComputeDerivatives, LComputeAxis) LocalConstraint, xoffset, & solution, IPdtdPf, & IsMyVolume, IsMyVolumeValue, WhichCpuID, & - ext, & ! For outputing Lcheck = 6 test - total_pflux + ext ! For outputing Lcheck = 6 test !-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-! @@ -193,9 +192,9 @@ subroutine dforce( NGdof, position, force, LComputeDerivatives, LComputeAxis) !-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-! if( LcomputeDerivatives ) then - #ifdef DEBUG - FATAL( dforce, .not.allocated(dBBdmp), do not pass go ) - #endif +#ifdef DEBUG + FATAL( dforce, .not.allocated(dBBdmp), do not pass go ) +#endif dBBdmp(1:LGdof,1:Mvol,0:1,1:2) = zero endif @@ -261,15 +260,10 @@ subroutine dforce( NGdof, position, force, LComputeDerivatives, LComputeAxis) if ( myid .eq. 0 ) then dpfluxout = Fvec - call DGESV( Ndofgl, 1, IPdtdPf(1:Ndofgl,1:Ndofgl), Ndofgl, ipiv, dpfluxout(1:Ndofgl), Ndofgl, idgesv ) + call DGESV( Ndofgl, 1, IPdtdPf, Ndofgl, ipiv, dpfluxout, Ndofgl, idgesv ) ! one step Newton's method dpflux(2:Mvol) = dpflux(2:Mvol) - dpfluxout(1:Mvol-1) - - if(Igeometry.eq.1) then - dpflux(1) = dpflux(1) - dpfluxout(Mvol) - endif - if( Lfreebound.eq.1 ) then dtflux(Mvol) = dtflux(Mvol ) - dpfluxout(Mvol ) endif @@ -281,7 +275,7 @@ subroutine dforce( NGdof, position, force, LComputeDerivatives, LComputeAxis) if( Lfreebound.eq.1 ) then RlBCAST(dtflux(Mvol), 1, 0) endif - + do vvol = 2, Mvol WCALL(dforce, IsMyVolume, (vvol)) @@ -320,7 +314,7 @@ subroutine dforce( NGdof, position, force, LComputeDerivatives, LComputeAxis) !add an additional constraint to make the total pflux = 0 -- Edit Erol if(Igeometry.eq.1) then - + vvol = 1 WCALL(dforce, IsMyVolume, (vvol)) @@ -353,16 +347,16 @@ subroutine dforce( NGdof, position, force, LComputeDerivatives, LComputeAxis) DALLOCATE(Fvec) DALLOCATE(dpfluxout) - ! #ifdef DEBUG - ! select case( ihybrd1 ) - ! case( 1 ) ; write(ounit,'("dforce : ",f10.2," : finished ; success ; dpflux = ", es12.5, ", its="i7";")') cput-cpus, dpflux, nfev - ! case( 0 ) ; write(ounit,'("dforce : ",f10.2," : finished ; input error ; dpflux = ", es12.5, ", its="i7";")') cput-cpus, dpflux, nfev - ! case( 2 ) ; write(ounit,'("dforce : ",f10.2," : finished ; max. iter ; dpflux = ", es12.5, ", its="i7";")') cput-cpus, dpflux, nfev - ! case( 3 ) ; write(ounit,'("dforce : ",f10.2," : finished ; xtol too small ; dpflux = ", es12.5, ", its="i7";")') cput-cpus, dpflux, nfev - ! case( 4:5 ) ; write(ounit,'("dforce : ",f10.2," : finished ; bad progress ; dpflux = ", es12.5, ", its="i7";")') cput-cpus, dpflux, nfev - ! case default ; write(ounit,'("dforce : ",f10.2," : finished ; illegal ifail ; dpflux = ", es12.5, ", its="i7";")') cput-cpus, dpflux, nfev - ! end select - ! #endif +! #ifdef DEBUG +! select case( ihybrd1 ) +! case( 1 ) ; write(ounit,'("dforce : ",f10.2," : finished ; success ; dpflux = ", es12.5, ", its="i7";")') cput-cpus, dpflux, nfev +! case( 0 ) ; write(ounit,'("dforce : ",f10.2," : finished ; input error ; dpflux = ", es12.5, ", its="i7";")') cput-cpus, dpflux, nfev +! case( 2 ) ; write(ounit,'("dforce : ",f10.2," : finished ; max. iter ; dpflux = ", es12.5, ", its="i7";")') cput-cpus, dpflux, nfev +! case( 3 ) ; write(ounit,'("dforce : ",f10.2," : finished ; xtol too small ; dpflux = ", es12.5, ", its="i7";")') cput-cpus, dpflux, nfev +! case( 4:5 ) ; write(ounit,'("dforce : ",f10.2," : finished ; bad progress ; dpflux = ", es12.5, ", its="i7";")') cput-cpus, dpflux, nfev +! case default ; write(ounit,'("dforce : ",f10.2," : finished ; illegal ifail ; dpflux = ", es12.5, ", its="i7";")') cput-cpus, dpflux, nfev +! end select +! #endif endif !matches if( LocalConstraint ) @@ -407,16 +401,16 @@ subroutine dforce( NGdof, position, force, LComputeDerivatives, LComputeAxis) !-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-! - #ifdef DEBUG - if( Lcheck.eq.2 ) then - write(ounit,'("dforce : ", 10x ," : myid=",i3," ; finished computing derivatives of rotational-transform wrt mu and dpflux ;")') myid - stop "dforce : : myid= ; finished computing derivatives of rotational-transform wrt mu and dpflux ;" ! this will allow other cpus to finish; - endif +#ifdef DEBUG + if( Lcheck.eq.2 ) then + write(ounit,'("dforce : ", 10x ," : myid=",i3," ; finished computing derivatives of rotational-transform wrt mu and dpflux ;")') myid + stop "dforce : : myid= ; finished computing derivatives of rotational-transform wrt mu and dpflux ;" ! this will allow other cpus to finish; + endif - FATAL( dforce, Lcheck.eq.2, finished computing derivatives of rotational-transform wrt mu and dpflux ) + FATAL( dforce, Lcheck.eq.2, finished computing derivatives of rotational-transform wrt mu and dpflux ) - if( Wdforce ) write(ounit,'("dforce : " 10x " : myid="i3" ; LComputeDerivatives="L2" ; ImagneticOK="999L2)') myid, LComputeDerivatives, ImagneticOK(1:Mvol) - #endif + if( Wdforce ) write(ounit,'("dforce : " 10x " : myid="i3" ; LComputeDerivatives="L2" ; ImagneticOK="999L2)') myid, LComputeDerivatives, ImagneticOK(1:Mvol) +#endif !-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-! @@ -446,7 +440,7 @@ subroutine dforce( NGdof, position, force, LComputeDerivatives, LComputeAxis) ! CONSTRUCT FORCE ! --------------- - force(0:NGdof) = zero + ; force(0:NGdof) = zero do vvol = 1, Mvol-1 @@ -475,9 +469,9 @@ subroutine dforce( NGdof, position, force, LComputeDerivatives, LComputeAxis) + ( + Somn(2:mn ,vvol+0,1) ) * sweight(vvol+0) & ! poloidal length constraint; - ( Somn(2:mn ,vvol+1,0) ) * sweight(vvol+1) - ! if( Ntor.gt.0 ) then ! poloidal angle origin is not otherwise constrained ; - ! force(tdoc+idoc+1:tdoc+idoc+Ntor ) = ( Pomn(2:Ntor+1,vvol+1,0) - Pomn(2:Ntor+1,vvol+0,1) ) * apsilon ! choice of spectral constraint can be enforced; - ! endif + ! if( Ntor.gt.0 ) then ! poloidal angle origin is not otherwise constrained ; + ! force(tdoc+idoc+1:tdoc+idoc+Ntor ) = ( Pomn(2:Ntor+1,vvol+1,0) - Pomn(2:Ntor+1,vvol+0,1) ) * apsilon ! choice of spectral constraint can be enforced; + ! endif IIo(vvol) = max( sum( abs( force(tdoc+idoc+1:tdoc+idoc+mn-1) ) ) / (mn-1), logtolerance ) ! screen diagnostics; @@ -499,9 +493,9 @@ subroutine dforce( NGdof, position, force, LComputeDerivatives, LComputeAxis) + ( + Semn(1:mn ,vvol+0,1) ) * sweight(vvol+0) & ! poloidal length constraint; - ( Semn(1:mn ,vvol+1,0) ) * sweight(vvol+1) - ! if( Ntor.ge.0 ) then - ! force(tdoc+idoc+1:tdoc+idoc+Ntor+1) = ( Pemn(1:Ntor+1,vvol+1,0) - Pemn(1:Ntor+1,vvol+0,1) ) * apsilon ! choice of spectral constraint can be enforced; - ! endif + ! if( Ntor.ge.0 ) then + ! force(tdoc+idoc+1:tdoc+idoc+Ntor+1) = ( Pemn(1:Ntor+1,vvol+1,0) - Pemn(1:Ntor+1,vvol+0,1) ) * apsilon ! choice of spectral constraint can be enforced; + ! endif IIe(vvol) = max( sum( abs( force(tdoc+idoc+1:tdoc+idoc+mn ) ) ) / (mn ), logtolerance ) ! screen diagnostics; @@ -511,9 +505,9 @@ subroutine dforce( NGdof, position, force, LComputeDerivatives, LComputeAxis) endif ! end of if( NOTstellsym ) ; - #ifdef DEBUG - FATAL( dforce, idoc.ne.LGdof, counting error ) ! this has caught bugs; - #endif +#ifdef DEBUG + FATAL( dforce, idoc.ne.LGdof, counting error ) ! this has caught bugs; +#endif else ! matches if( ImagneticOK(vvol) .and. ImagneticOK(vvol+1) ); @@ -773,14 +767,18 @@ subroutine dforce( NGdof, position, force, LComputeDerivatives, LComputeAxis) endif ! end of if( LcomputeDerivatives ) ; + + + + ! CONSTRUCT FORCE GRADIENT ! ------------------------ if( LcomputeDerivatives .and. Lhessianallocated) then ! construct Hessian; - #ifdef DEBUG - FATAL( dforce, .not.Lhessianallocated, need to allocate hessian ) - #endif +#ifdef DEBUG + FATAL( dforce, .not.Lhessianallocated, need to allocate hessian ) +#endif hessian(1:NGdof,1:NGdof) = zero @@ -790,29 +788,29 @@ subroutine dforce( NGdof, position, force, LComputeDerivatives, LComputeAxis) idof = 0 ! labels degree-of-freedom = Fourier harmonic of surface geometry; - #ifdef DEBUG - if( idof.gt.LGdof ) write(ounit,1000) myid, vvol, -1, -1, -1, idof, LGdof ! can be deleted; - #endif +#ifdef DEBUG + if( idof.gt.LGdof ) write(ounit,1000) myid, vvol, -1, -1, -1, idof, LGdof ! can be deleted; +#endif do ii = 1, mn ! loop over degrees-of-freedom; - #ifdef DEBUG - if( idof.gt.LGdof ) write(ounit,1000) myid, vvol, ii, -1, -1, idof, LGdof ! can be deleted; - #endif +#ifdef DEBUG + if( idof.gt.LGdof ) write(ounit,1000) myid, vvol, ii, -1, -1, idof, LGdof ! can be deleted; +#endif do irz = 0, 1 ! Fourier harmonic of R, Fourier harmonic of Z; - #ifdef DEBUG - if( idof.gt.LGdof ) write(ounit,1000) myid, vvol, ii, irz, -1, idof, LGdof ! can be deleted; - #endif +#ifdef DEBUG + if( idof.gt.LGdof ) write(ounit,1000) myid, vvol, ii, irz, -1, idof, LGdof ! can be deleted; +#endif if( irz.eq.1 .and. Igeometry.lt.3 ) cycle ! no dependence on Z; do issym = 0, 1 ! stellarator symmetry; - #ifdef DEBUG - if( idof.gt.LGdof ) write(ounit,1000) myid, vvol, ii, irz, issym, idof, LGdof ! can be deleted; - #endif +#ifdef DEBUG + if( idof.gt.LGdof ) write(ounit,1000) myid, vvol, ii, irz, issym, idof, LGdof ! can be deleted; +#endif if( issym.eq.1 .and. YESstellsym ) cycle ! no dependence on the non-stellarator symmetric harmonics; @@ -821,11 +819,11 @@ subroutine dforce( NGdof, position, force, LComputeDerivatives, LComputeAxis) idof = idof + 1 ! labels degree-of-freedom; - #ifdef DEBUG - if( idof.gt.LGdof ) write(ounit,1000) myid, vvol, ii, irz, issym, idof, LGdof ! can be deleted; - 1000 format("hforce : " 10x " : myid=",i3," ; vvol=",i3," ; ii= ",i3," ; irz="i3" ; issym="i3" ; idof="i3" ; LGdof="i3" ;") - FATAL( hforce, idof.gt.LGdof, illegal degree-of-freedom index constructing hessian ) ! can be deleted; - #endif +#ifdef DEBUG + if( idof.gt.LGdof ) write(ounit,1000) myid, vvol, ii, irz, issym, idof, LGdof ! can be deleted; +1000 format("hforce : " 10x " : myid=",i3," ; vvol=",i3," ; ii= ",i3," ; irz="i3" ; issym="i3" ; idof="i3" ; LGdof="i3" ;") + FATAL( hforce, idof.gt.LGdof, illegal degree-of-freedom index constructing hessian ) ! can be deleted; +#endif if( LocalConstraint ) then ! Derivative with respect to previous interface @@ -931,11 +929,11 @@ subroutine dforce( NGdof, position, force, LComputeDerivatives, LComputeAxis) enddo ! end of do vvol; ! Evaluate force gradient - #ifdef DEBUG - if( Lcheck.eq.6 ) then - WCALL(dforce, fndiff_dforce, ( NGdof ) ) - endif - #endif +#ifdef DEBUG + if( Lcheck.eq.6 ) then + WCALL(dforce, fndiff_dforce, ( NGdof ) ) + endif +#endif endif ! end of if( LcomputeDerivatives ) ; @@ -953,18 +951,18 @@ subroutine dforce( NGdof, position, force, LComputeDerivatives, LComputeAxis) write(munit) NGdof write(munit) hessian(1:NGdof,1:NGdof) close(munit) - + write(*,*) 'Writing hessian from dforce' - + ! do ii=1,NGdof ! write(*,*)ii, hessian(ii,1:NGdof) ! enddo - + endif endif RETURN(dforce) - + !-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-! end subroutine dforce @@ -972,162 +970,162 @@ end subroutine dforce subroutine fndiff_dforce( NGdof ) - use constants, only: zero, one, half, two +use constants, only: zero, one, half, two - use fileunits, only: ounit +use fileunits, only: ounit - use inputlist, only: Wmacros, Wdforce, & - Igeometry, & - dRZ, Lcheck +use inputlist, only: Wmacros, Wdforce, & + Igeometry, & + dRZ, Lcheck - use cputiming, only: Tdforce +use cputiming, only: Tdforce - use allglobal, only: ncpu, myid, cpus, MPI_COMM_SPEC, & - Mvol, mn, im, in, & - iRbc, iZbs, iRbs, iZbc, & - LGdof, psifactor, dBdX, & - YESstellsym, NOTstellsym, & - hessian, ext +use allglobal, only: ncpu, myid, cpus, MPI_COMM_SPEC, & + Mvol, mn, im, in, & + iRbc, iZbs, iRbs, iZbc, & + LGdof, psifactor, dBdX, & + YESstellsym, NOTstellsym, & + hessian, ext - LOCALS +LOCALS - INTEGER, intent(in) :: NGdof +INTEGER, intent(in) :: NGdof - INTEGER :: vvol, idof, ii, irz, issym, isymdiff ! loop indices - INTEGER :: tdof ! hessian index +INTEGER :: vvol, idof, ii, irz, issym, isymdiff ! loop indices +INTEGER :: tdof ! hessian index - REAL :: lfactor - CHARACTER :: packorunpack - LOGICAL :: LComputeAxis +REAL :: lfactor +CHARACTER :: packorunpack +LOGICAL :: LComputeAxis - REAL, allocatable :: oRbc(:,:), oZbs(:,:), oRbs(:,:), oZbc(:,:) ! used to store original geometry; - REAL, allocatable :: iposition(:,:), iforce(:,:) ! perturbed interfaces position and force - REAL, allocatable :: finitediff_estimate(:,:) ! store finite differences +REAL, allocatable :: oRbc(:,:), oZbs(:,:), oRbs(:,:), oZbc(:,:) ! used to store original geometry; +REAL, allocatable :: iposition(:,:), iforce(:,:) ! perturbed interfaces position and force +REAL, allocatable :: finitediff_estimate(:,:) ! store finite differences - BEGIN(dforce) +BEGIN(dforce) - write(ounit, '("fndiff : Starting finite difference evaluation of hessian ...")') + write(ounit, '("fndiff : Starting finite difference evaluation of hessian ...")') - if( ncpu.eq.1) then + if( ncpu.eq.1) then - SALLOCATE( finitediff_estimate, (1:NGdof, 1:NGdof), zero ) + SALLOCATE( finitediff_estimate, (1:NGdof, 1:NGdof), zero ) - dBdX%L = .false. - SALLOCATE( oRbc, (1:mn,0:Mvol), iRbc(1:mn,0:Mvol) ) !save unperturbed geometry - SALLOCATE( oZbs, (1:mn,0:Mvol), iZbs(1:mn,0:Mvol) ) - SALLOCATE( oRbs, (1:mn,0:Mvol), iRbs(1:mn,0:Mvol) ) - SALLOCATE( oZbc, (1:mn,0:Mvol), iZbc(1:mn,0:Mvol) ) - SALLOCATE( iforce, (-2:2, 0:NGdof), zero) - SALLOCATE( iposition, (-2:2, 0:NGdof), zero) + dBdX%L = .false. + SALLOCATE( oRbc, (1:mn,0:Mvol), iRbc(1:mn,0:Mvol) ) !save unperturbed geometry + SALLOCATE( oZbs, (1:mn,0:Mvol), iZbs(1:mn,0:Mvol) ) + SALLOCATE( oRbs, (1:mn,0:Mvol), iRbs(1:mn,0:Mvol) ) + SALLOCATE( oZbc, (1:mn,0:Mvol), iZbc(1:mn,0:Mvol) ) + SALLOCATE( iforce, (-2:2, 0:NGdof), zero) + SALLOCATE( iposition, (-2:2, 0:NGdof), zero) - do vvol = 1, Mvol-1 ! loop over interior surfaces; - idof = 0 + do vvol = 1, Mvol-1 ! loop over interior surfaces; + idof = 0 - do ii = 1, mn ! Loop over Fourier modes + do ii = 1, mn ! Loop over Fourier modes - lfactor = psifactor(ii,vvol) ! this "pre-conditions" the geometrical degrees-of-freedom; + lfactor = psifactor(ii,vvol) ! this "pre-conditions" the geometrical degrees-of-freedom; - do irz = 0, 1 ! loop over R or Z coordinate + do irz = 0, 1 ! loop over R or Z coordinate - if( irz.eq.1 .and. Igeometry.lt.3 ) cycle + if( irz.eq.1 .and. Igeometry.lt.3 ) cycle - do issym = 0, 1 ! stellarator symmetry; + do issym = 0, 1 ! stellarator symmetry; - if( issym.eq.1 .and. YESstellsym ) cycle ! no dependence on the non-stellarator symmetric harmonics; + if( issym.eq.1 .and. YESstellsym ) cycle ! no dependence on the non-stellarator symmetric harmonics; - if( ii.eq.1 .and. irz.eq.1 .and. issym.eq.0 ) cycle ! no dependence on Zbs_{m=0,n=0}; - if( ii.eq.1 .and. irz.eq.0 .and. issym.eq.1 ) cycle ! no dependence on Rbs_{m=0,n=0}; + if( ii.eq.1 .and. irz.eq.1 .and. issym.eq.0 ) cycle ! no dependence on Zbs_{m=0,n=0}; + if( ii.eq.1 .and. irz.eq.0 .and. issym.eq.1 ) cycle ! no dependence on Rbs_{m=0,n=0}; - idof = idof + 1 ! labels degree-of-freedom; + idof = idof + 1 ! labels degree-of-freedom; - do isymdiff = -2, 2 ! symmetric fourth-order, finite-difference used to approximate derivatives; + do isymdiff = -2, 2 ! symmetric fourth-order, finite-difference used to approximate derivatives; - if( isymdiff.eq.0 ) cycle + if( isymdiff.eq.0 ) cycle - ! Reset initial geometry - iRbc(1:mn,0:Mvol) = oRbc(1:mn,0:Mvol) - iZbs(1:mn,0:Mvol) = oZbs(1:mn,0:Mvol) - iRbs(1:mn,0:Mvol) = oRbs(1:mn,0:Mvol) - iZbc(1:mn,0:Mvol) = oZbc(1:mn,0:Mvol) + ! Reset initial geometry + iRbc(1:mn,0:Mvol) = oRbc(1:mn,0:Mvol) + iZbs(1:mn,0:Mvol) = oZbs(1:mn,0:Mvol) + iRbs(1:mn,0:Mvol) = oRbs(1:mn,0:Mvol) + iZbc(1:mn,0:Mvol) = oZbc(1:mn,0:Mvol) - ! Perturb geometry - if( issym.eq.0 .and. irz.eq.0 ) then - iRbc(ii,vvol) = iRbc(ii,vvol) + dRZ * isymdiff ! perturb geometry; - else if( issym.eq.0 .and. irz.eq.1 ) then - iZbs(ii,vvol) = iZbs(ii,vvol) + dRZ * isymdiff ! perturb geometry; - else if( issym.eq.1 .and. irz.eq.0 ) then - iRbs(ii,vvol) = iRbs(ii,vvol) + dRZ * isymdiff ! perturb geometry; - else if( issym.eq.1 .and. irz.eq.1 ) then - iZbc(ii,vvol) = iZbc(ii,vvol) + dRZ * isymdiff ! perturb geometry; - endif + ! Perturb geometry + if( issym.eq.0 .and. irz.eq.0 ) then + iRbc(ii,vvol) = iRbc(ii,vvol) + dRZ * isymdiff ! perturb geometry; + else if( issym.eq.0 .and. irz.eq.1 ) then + iZbs(ii,vvol) = iZbs(ii,vvol) + dRZ * isymdiff ! perturb geometry; + else if( issym.eq.1 .and. irz.eq.0 ) then + iRbs(ii,vvol) = iRbs(ii,vvol) + dRZ * isymdiff ! perturb geometry; + else if( issym.eq.1 .and. irz.eq.1 ) then + iZbc(ii,vvol) = iZbc(ii,vvol) + dRZ * isymdiff ! perturb geometry; + endif - packorunpack = 'P' ! pack geometrical degrees-of-freedom; - !LComputeAxis = .false. ! keep axis fixed - LComputeAxis = .true. + packorunpack = 'P' ! pack geometrical degrees-of-freedom; + !LComputeAxis = .false. ! keep axis fixed + LComputeAxis = .true. - WCALL(dforce, packxi,( NGdof, iposition(isymdiff,0:NGdof), Mvol, mn,iRbc(1:mn,0:Mvol),iZbs(1:mn,0:Mvol),iRbs(1:mn,0:Mvol),& - iZbc(1:mn,0:Mvol),packorunpack, .false., LComputeAxis ) ) - WCALL(dforce, dforce,( NGdof, iposition(isymdiff,0:NGdof), iforce(isymdiff,0:NGdof), .false., LComputeAxis) ) - enddo + WCALL(dforce, packxi,( NGdof, iposition(isymdiff,0:NGdof), Mvol, mn,iRbc(1:mn,0:Mvol),iZbs(1:mn,0:Mvol),iRbs(1:mn,0:Mvol),& + iZbc(1:mn,0:Mvol),packorunpack, .false., LComputeAxis ) ) + WCALL(dforce, dforce,( NGdof, iposition(isymdiff,0:NGdof), iforce(isymdiff,0:NGdof), .false., LComputeAxis) ) + enddo - ! Fourth order centered finite difference scheme - iforce(0, 0:NGdof) = ( - 1 * iforce( 2,0:NGdof) & - + 8 * iforce( 1,0:NGdof) & - - 8 * iforce(-1,0:NGdof) & - + 1 * iforce(-2,0:NGdof)) / ( 12 * dRZ ) + ! Fourth order centered finite difference scheme + iforce(0, 0:NGdof) = ( - 1 * iforce( 2,0:NGdof) & + + 8 * iforce( 1,0:NGdof) & + - 8 * iforce(-1,0:NGdof) & + + 1 * iforce(-2,0:NGdof)) / ( 12 * dRZ ) - tdof = (vvol-1) * LGdof + idof - finitediff_estimate(1:NGdof, tdof) = iforce(0, 1:NGdof)* lfactor + tdof = (vvol-1) * LGdof + idof + finitediff_estimate(1:NGdof, tdof) = iforce(0, 1:NGdof)* lfactor - enddo !issym - enddo !irz - enddo !ii - enddo !vvol + enddo !issym + enddo !irz + enddo !ii + enddo !vvol - DALLOCATE(iforce) - DALLOCATE(iposition) - DALLOCATE(oZbc) - DALLOCATE(oRbs) - DALLOCATE(oZbs) - DALLOCATE(oRbc) + DALLOCATE(iforce) + DALLOCATE(iposition) + DALLOCATE(oZbc) + DALLOCATE(oRbs) + DALLOCATE(oZbs) + DALLOCATE(oRbc) - ! Print in file for diagnostics - if(myid.eq.0) then - ! Print hessian - open(10, file=trim(ext)//'.Lcheck6_output.txt', status='unknown') - write(ounit,'(A)') NEW_LINE('A') + ! Print in file for diagnostics + if(myid.eq.0) then + ! Print hessian + open(10, file=trim(ext)//'.Lcheck6_output.txt', status='unknown') + write(ounit,'(A)') NEW_LINE('A') - do ii=1, SIZE(im) - write(ounit,1345) myid, im(ii), in(ii), hessian(ii,:) - write(10 ,1347) hessian(ii,:) - enddo - close(10) + do ii=1, SIZE(im) + write(ounit,1345) myid, im(ii), in(ii), hessian(ii,:) + write(10 ,1347) hessian(ii,:) + enddo + close(10) - write(ounit,'(A)') NEW_LINE('A') + write(ounit,'(A)') NEW_LINE('A') - ! Print finite differences - open(10, file=trim(ext)//'.Lcheck6_output.FiniteDiff.txt', status='unknown') - do ii=1, SIZE(im) - write(ounit,1346) myid, im(ii), in(ii), finitediff_estimate(ii,:) - write(10 ,1347) finitediff_estimate(ii,:) - enddo - write(ounit,'(A)') NEW_LINE('A') - close(10) + ! Print finite differences + open(10, file=trim(ext)//'.Lcheck6_output.FiniteDiff.txt', status='unknown') + do ii=1, SIZE(im) + write(ounit,1346) myid, im(ii), in(ii), finitediff_estimate(ii,:) + write(10 ,1347) finitediff_estimate(ii,:) + enddo + write(ounit,'(A)') NEW_LINE('A') + close(10) - 1345 format("dforce: myid=",i3," ; (",i4,",",i4," ; Hessian = ",512f16.10 " ;") - 1346 format("dforce: myid=",i3," ; (",i4,",",i4," ; Finite differences = ",512f16.10 " ;") - 1347 format(512F22.16, " ") + 1345 format("dforce: myid=",i3," ; (",i4,",",i4," ; Hessian = ",512f16.10 " ;") + 1346 format("dforce: myid=",i3," ; (",i4,",",i4," ; Finite differences = ",512f16.10 " ;") + 1347 format(512F22.16, " ") - endif + endif - DALLOCATE(finitediff_estimate) - endif + DALLOCATE(finitediff_estimate) + endif - FATAL(fndiff, .true., Finite differences have been evaluated. ) +FATAL(fndiff, .true., Finite differences have been evaluated. ) - RETURN(dforce) +RETURN(dforce) end subroutine fndiff_dforce diff --git a/src/dfp100.f90 b/src/dfp100.f90 index f3e6550a..7ff1310e 100644 --- a/src/dfp100.f90 +++ b/src/dfp100.f90 @@ -116,7 +116,7 @@ subroutine dfp100(Ndofgl, x, Fvec, LComputeDerivatives) WCALL( dfp100, compute_guvijsave, (Iquad(vvol), vvol, ideriv, Lcurvature) ) Lsavedguvij = .true. - ! we need to construct the preconditioner if needed + ! we need to construct the preconditioner if needed if (LILUprecond) then WCALL( dfp100, spsint, ( Iquad(vvol), mn, vvol, ll ) ) WCALL( dfp100, spsmat, ( vvol, mn, ll) ) @@ -135,7 +135,7 @@ subroutine dfp100(Ndofgl, x, Fvec, LComputeDerivatives) Lsavedguvij = .false. - !-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-! +!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-! call intghs_workspace_destroy() call deallocate_Beltrami_matrices(LcomputeDerivatives) @@ -155,9 +155,9 @@ subroutine dfp100(Ndofgl, x, Fvec, LComputeDerivatives) if( Lvacuumregion ) then - #ifdef DEBUG - FATAL( dfp100, vvol.ne.Mvol, Incorrect vvol in last volume) - #endif +#ifdef DEBUG + FATAL( dfp100, vvol.ne.Mvol, Incorrect vvol in last volume) +#endif ideriv=1 ! derivatives of Btheta w.r.t tflux iocons=0 ! Only need inner side of volume derivatives @@ -205,13 +205,13 @@ subroutine dfp100(Ndofgl, x, Fvec, LComputeDerivatives) Fvec(1:Mvol-1) = IPDt(1:Mvol-1) - Isurf(1:Mvol-1) endif - ! Edit by Erol to set total pflux to 0 + ! Edit by Erol to set total pflux to 0 if(Igeometry.eq.1) then - + IPDtDpf(1,Mvol) = -pi2 * Bt00(1,1,2) IPdtdPf(2:Mvol,Mvol) = 0.0 IPDtDpf(Mvol,1:Mvol) = 1.0 - + ! Constraint the total pflux (pflux(Mvol)) ! zero for symmetric initial profiles ! non-zero for asymmetric profiles diff --git a/src/dfp200.f90 b/src/dfp200.f90 index 6c7ef634..2015b3b6 100644 --- a/src/dfp200.f90 +++ b/src/dfp200.f90 @@ -147,7 +147,7 @@ subroutine dfp200( LcomputeDerivatives, vvol) if( LocalConstraint ) then - do vvol = 1, Mvol + do vvol = 1, Mvol WCALL(dfp200, IsMyVolume, (vvol)) @@ -164,14 +164,14 @@ subroutine dfp200( LcomputeDerivatives, vvol) ll = Lrad(vvol) ! Shorthand NN = NAdof(vvol) ! shorthand; - !-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-! +!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-! vflag = 1 WCALL( dfp200, volume, ( vvol, vflag ) ) ! compute volume; !!----Hessian2D cleared----- - !-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-! +!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-! do iocons = 0, 1 ! construct field magnitude on inner and outer interfaces; inside do vvol; if( vvol.eq.1 .and. iocons.eq.0 ) cycle ! fixed inner boundary (or coordinate axis); @@ -198,34 +198,34 @@ subroutine dfp200( LcomputeDerivatives, vvol) packorunpack = 'P' WCALL( dfp200, packab, ( packorunpack, vvol, NN, solution(1:NN,0), 0 ) ) ! packing, put the solutions back to the solution matrix; - !-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-! +!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-! - ! Invert beltrami matrix. Required for matrix perturbation theory - call get_LU_Beltrami_matrices(vvol, oBI(vvol), NN) + ! Invert beltrami matrix. Required for matrix perturbation theory + call get_LU_Beltrami_matrices(vvol, oBI(vvol), NN) - dBdX%L = .true. ! will need derivatives; - idof = 0 ! labels degree of freedom; local to interface; + dBdX%L = .true. ! will need derivatives; + idof = 0 ! labels degree of freedom; local to interface; - do ii = 1, mn ! loop over deformations in Fourier harmonics; inside do vvol; + do ii = 1, mn ! loop over deformations in Fourier harmonics; inside do vvol; - dBdX%ii = ii ! controls construction of derivatives in subroutines called below; - do irz = 0, 1 ! loop over deformations in R and Z; inside do vvol; inside do ii; + dBdX%ii = ii ! controls construction of derivatives in subroutines called below; + do irz = 0, 1 ! loop over deformations in R and Z; inside do vvol; inside do ii; - if( irz.eq.1 .and. Igeometry.lt.3 ) cycle ! no dependence on Z; - dBdX%irz = irz ! controls construction of derivatives; + if( irz.eq.1 .and. Igeometry.lt.3 ) cycle ! no dependence on Z; + dBdX%irz = irz ! controls construction of derivatives; - do issym = 0, 1 ! loop over stellarator and non-stellarator symmetric terms; + do issym = 0, 1 ! loop over stellarator and non-stellarator symmetric terms; - if( issym.eq.1 .and. YESstellsym ) cycle ! no dependence on non-stellarator symmetric harmonics; - if( ii.eq.1 .and. irz.eq.1 .and. issym.eq.0 ) cycle ! no dependence on Zbs_{m=0,n=0}; - if( ii.eq.1 .and. irz.eq.0 .and. issym.eq.1 ) cycle ! no dependence on Rbs_{m=0,n=0}; + if( issym.eq.1 .and. YESstellsym ) cycle ! no dependence on non-stellarator symmetric harmonics; + if( ii.eq.1 .and. irz.eq.1 .and. issym.eq.0 ) cycle ! no dependence on Zbs_{m=0,n=0}; + if( ii.eq.1 .and. irz.eq.0 .and. issym.eq.1 ) cycle ! no dependence on Rbs_{m=0,n=0}; - dBdX%issym = issym ! controls construction of derivatives; - idof = idof + 1 ! this labels the degree-of-freedom that the derivative is taken with respect to; this is outside do innout; + dBdX%issym = issym ! controls construction of derivatives; + idof = idof + 1 ! this labels the degree-of-freedom that the derivative is taken with respect to; this is outside do innout; - #ifdef DEBUG - FATAL( dfp200, idof.gt.LGdof, illegal degree-of-freedom index constructing derivatives ) ! this can be deleted; - #endif +#ifdef DEBUG + FATAL( dfp200, idof.gt.LGdof, illegal degree-of-freedom index constructing derivatives ) ! this can be deleted; +#endif do innout = 0, 1 ! loop over deformations to inner and outer interface; inside do vvol; inside do ii; inside do irz; @@ -296,7 +296,7 @@ subroutine dfp200( LcomputeDerivatives, vvol) ll = Lrad(vvol) ! Shorthand NN = NAdof(vvol) ! shorthand; - !-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-! +!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-! vflag = 1 WCALL( dfp200, volume, ( vvol, vflag ) ) ! compute volume; @@ -439,9 +439,9 @@ subroutine dfp200( LcomputeDerivatives, vvol) dBdX%issym = issym ! controls construction of derivatives; idof = idof + 1 ! this labels the degree-of-freedom that the derivative is taken with respect to; this is outside do innout; - #ifdef DEBUG - FATAL( dfp200, idof.gt.LGdof, illegal degree-of-freedom index constructing derivatives ) ! this can be deleted; - #endif +#ifdef DEBUG + FATAL( dfp200, idof.gt.LGdof, illegal degree-of-freedom index constructing derivatives ) ! this can be deleted; +#endif do lvol = vvol, vvol+1 @@ -609,7 +609,7 @@ subroutine dfp200( LcomputeDerivatives, vvol) -endif ! End of if( LocalConstraint ) + endif ! End of if( LocalConstraint ) if( LcomputeDerivatives ) then DALLOCATE(constraint) @@ -630,7 +630,7 @@ subroutine dfp200( LcomputeDerivatives, vvol) DALLOCATE(length) - 2000 continue +2000 continue RETURN(dfp200) @@ -971,11 +971,11 @@ subroutine evaluate_dmupfdx(innout, idof, ii, issym, irz) if( ( Lcoordinatesingularity .and. iocons.eq.0 ) .or. ( Lvacuumregion .and. iocons.eq.1 ) ) cycle WCALL(dfp200, lbpol, (pvol, Bt00(1:Mvol, 0:1, -1:2), 2, iocons)) ! Stores derivative in global variable Btemn enddo - #ifdef DEBUG - if( .false. ) then - write(ounit, 8375) myid, dBdX%vol, dBdX%innout, 2, pvol, Bt00(pvol, 0:1, 2) - endif - #endif +#ifdef DEBUG + if( .false. ) then + write(ounit, 8375) myid, dBdX%vol, dBdX%innout, 2, pvol, Bt00(pvol, 0:1, 2) + endif +#endif enddo dBdmpf(1:order,1:order) = zero ! Initialize. TODO: useless? @@ -986,18 +986,18 @@ subroutine evaluate_dmupfdx(innout, idof, ii, issym, irz) dBdmpf(Mvol-1,Mvol-1) = Bt00(Mvol, 0, 2) - ! do pvol=1,Mvol - ! LREGION(pvol) +! do pvol=1,Mvol +! LREGION(pvol) - ! do iocons = 0, 1 - ! WCALL(dfp200, lbpol, (pvol, Bt00(1:Mvol, 0:1, -1:2), 0, iocons)) - ! enddo - ! #ifdef DEBUG - ! if( .false. ) then - ! write(ounit, 8375) myid, dBdX%vol, dBdX%innout, 0, pvol, Bt00(pvol, 0:1, 0) - ! endif - ! #endif - ! enddo +! do iocons = 0, 1 +! WCALL(dfp200, lbpol, (pvol, Bt00(1:Mvol, 0:1, -1:2), 0, iocons)) +! enddo +! #ifdef DEBUG +! if( .false. ) then +! write(ounit, 8375) myid, dBdX%vol, dBdX%innout, 0, pvol, Bt00(pvol, 0:1, 0) +! endif +! #endif +! enddo ! RHS coefficients evaluation do pvol = vvol, vvol+1 @@ -1013,12 +1013,12 @@ subroutine evaluate_dmupfdx(innout, idof, ii, issym, irz) WCALL(dfp200, lbpol, (pvol, Bt00(1:Mvol, 0:1, -1:2), -1, iocons)) ! derivate w.r.t geometry enddo - #ifdef DEBUG - if( .false. ) then - write(ounit, 8375) myid, dBdX%vol, dBdX%innout, -1, pvol, Bt00(pvol, 0:1, -1) - 8375 format("dfp200 : myid=",i3, ", vvol=",i3,", innout=", i3 ,", ideriv=", i3, ", lvol=",i3,"; Bt00=",2f10.6) - endif - #endif +#ifdef DEBUG + if( .false. ) then + write(ounit, 8375) myid, dBdX%vol, dBdX%innout, -1, pvol, Bt00(pvol, 0:1, -1) +8375 format("dfp200 : myid=",i3, ", vvol=",i3,", innout=", i3 ,", ideriv=", i3, ", lvol=",i3,"; Bt00=",2f10.6) + endif +#endif enddo dBdx2(1:Mvol-1) = zero @@ -1030,7 +1030,7 @@ subroutine evaluate_dmupfdx(innout, idof, ii, issym, irz) ; dBdx2(vvol+1) = Bt00(vvol+1, 1, -1) endif - !-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-! +!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-! if( Lfreebound.eq.1 ) then ! Need to modify last two equations ! Set all last column to zero - maybe not necessary ? @@ -1056,12 +1056,12 @@ subroutine evaluate_dmupfdx(innout, idof, ii, issym, irz) else ! Inner interface is perturbed dBdx2( Mvol ) = zero endif - #ifdef DEBUG - if( .false. ) then - write(ounit, 8827) vvol, dBdmpf(Mvol-1, Mvol-1), Btemn(1, 0, Mvol), dItGpdxtp( 1, 2, Mvol), dItGpdxtp( 1, 1, Mvol), dBdx2(Mvol-1), dBdx2(Mvol) - 8827 format("dfp200: vvol = ", i3, ", dBdpsip = ", f10.8, ", dBdpsit = ", f10.8, ", dIpdpsip = ", f10.8, ", dIpdpsit = ", f16.10, ", dBdx2(N-1) = ", f10.8, ", dIpdxj = ", f10.8) - endif - #endif +#ifdef DEBUG + if( .false. ) then + write(ounit, 8827) vvol, dBdmpf(Mvol-1, Mvol-1), Btemn(1, 0, Mvol), dItGpdxtp( 1, 2, Mvol), dItGpdxtp( 1, 1, Mvol), dBdx2(Mvol-1), dBdx2(Mvol) +8827 format("dfp200: vvol = ", i3, ", dBdpsip = ", f10.8, ", dBdpsit = ", f10.8, ", dIpdpsip = ", f10.8, ", dIpdpsit = ", f16.10, ", dBdx2(N-1) = ", f10.8, ", dIpdxj = ", f10.8) + endif +#endif endif @@ -1270,7 +1270,7 @@ subroutine evaluate_dmupfdx(innout, idof, ii, issym, irz) WCALL(dfp200, allocate_geometry_matrices, (vvol,LcomputeDerivatives)) endif - 8294 continue +8294 continue ! Evaluate derivatives using finite differences if( LocalConstraint ) then imupf_local(1:2,0) = ( - 1 * imupf_local(1:2, 2) + 8 * imupf_local(1:2, 1)& @@ -1303,8 +1303,8 @@ subroutine evaluate_dmupfdx(innout, idof, ii, issym, irz) write(ounit,3004) cput-cpus, myid, vvol, im(ii), in(ii), irz, issym, 1, "dpflux analytic ", dmupfdx(1:Mvol,vvol,2,idof,1) / lfactor endif - 3003 format("dfp200 : ",f10.2," : ",:,"myid=",i3," ; vvol=",i2," ; (",i2,",",i3," ) ; irz=",i1," ; issym=",i1," ; innout=",i1," ; ",a18," : dmupf=",8f11.05" ;") - 3004 format("dfp200 : ",f10.2," : ",:,"myid=",i3," ; vvol=",i2," ; (",i2,",",i3," ) ; irz=",i1," ; issym=",i1," ; innout=",i1," ; ",a18," : dmupf=",8f11.05" ;") +3003 format("dfp200 : ",f10.2," : ",:,"myid=",i3," ; vvol=",i2," ; (",i2,",",i3," ) ; irz=",i1," ; issym=",i1," ; innout=",i1," ; ",a18," : dmupf=",8f11.05" ;") +3004 format("dfp200 : ",f10.2," : ",:,"myid=",i3," ; vvol=",i2," ; (",i2,",",i3," ) ; irz=",i1," ; issym=",i1," ; innout=",i1," ; ",a18," : dmupf=",8f11.05" ;") ! Re-evaluate unperturbed solution diff --git a/src/global.f90 b/src/global.f90 index 009d2bb8..6d05d3f1 100644 --- a/src/global.f90 +++ b/src/global.f90 @@ -66,7 +66,7 @@ module constants REAL, parameter :: mu0 = 2.0E-07 * pi2 !< \f$4\pi\cdot10^{-7}\f$ REAL, parameter :: goldenmean = 1.618033988749895 !< golden mean = \f$( 1 + \sqrt 5 ) / 2\f$ ; - REAL, parameter :: version = 3.20 !< version of SPEC + REAL, parameter :: version = 3.21 !< version of SPEC end module constants @@ -1656,7 +1656,7 @@ subroutine wrtend write(iunit,'(" adiabatic = ",257es23.15)') adiabatic(1:Mvol) write(iunit,'(" mu = ",257es23.15)') mu(1:Mvol) write(iunit,'(" Ivolume = ",257es23.15)') Ivolume(1:Mvol) - write(iunit,'(" Isurf = ",257es23.15)') IPDt(1:Mvol) ! EDIT by EROL !!!! + write(iunit,'(" Isurf = ",257es23.15)') IPDt(1:Mvol) ! EDIT by EROL !!!! write(iunit,'(" Lconstraint = ",i9 )') Lconstraint write(iunit,'(" pl = ",257i23 )') pl(0:Mvol) write(iunit,'(" ql = ",257i23 )') ql(0:Mvol) diff --git a/src/hesian.f90 b/src/hesian.f90 index 31566fb6..d4fb9e33 100644 --- a/src/hesian.f90 +++ b/src/hesian.f90 @@ -237,8 +237,9 @@ subroutine hesian( NGdof, position, Mvol, mn, LGdof ) LComputeAxis = .false. WCALL( hesian, dforce, ( NGdof, position(0:NGdof), force(0:NGdof), LComputeDerivatives, LComputeAxis) ) ! calculate force-imbalance & hessian; - ! ohessian(1:NGdof,1:NGdof) = hessian2D(1:NGdof,1:NGdof) ! internal copy; 22 Apr 15; - ! ohessian(1:NGdof,1:NGdof) = 0 + + ohessian(1:NGdof,1:NGdof) = hessian2D(1:NGdof,1:NGdof) ! internal copy; 22 Apr 15; + !-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-! @@ -256,137 +257,137 @@ subroutine hesian( NGdof, position, Mvol, mn, LGdof ) if( Lcheck.eq.5 ) then ! check construction of Hessian; 01 Jul 14; - xx(0,-2:2)= zero ; dRZ = 1.0E-04 + xx(0,-2:2)= zero ; dRZ = 1.0E-04 - write(svol,'(i3.3)')myid - ! open(lunit+myid,file="."//trim(ext)//".hessian."//svol,status="unknown") + write(svol,'(i3.3)')myid +! open(lunit+myid,file="."//trim(ext)//".hessian."//svol,status="unknown") - ! lmu(1:Nvol) = mu(1:Nvol) ; lpflux(1:Nvol) = pflux(1:Nvol) ; lhelicity(1:Nvol) = helicity(1:Nvol) ! save original profile information; 20 Jun 14; +! lmu(1:Nvol) = mu(1:Nvol) ; lpflux(1:Nvol) = pflux(1:Nvol) ; lhelicity(1:Nvol) = helicity(1:Nvol) ! save original profile information; 20 Jun 14; - tdof = 0 ! geometrical degree-of-freedom counter; labels derivative; + tdof = 0 ! geometrical degree-of-freedom counter; labels derivative; - do vvol = 1, Mvol-1 ! loop over internal interfaces; + do vvol = 1, Mvol-1 ! loop over internal interfaces; - cput = GETTIME - ! write(lunit+myid,'("hesian : ", 10x ," : ")') - ! write(lunit+myid,'("hesian : ",f10.2," : myid=",i3," ; vvol=",i3," ; dRZ=",es9.1," ;")') cput-cpus, myid, vvol, dRZ - ! write(lunit+myid,'("hesian : ", 10x ," : ")') + cput = GETTIME +! write(lunit+myid,'("hesian : ", 10x ," : ")') +! write(lunit+myid,'("hesian : ",f10.2," : myid=",i3," ; vvol=",i3," ; dRZ=",es9.1," ;")') cput-cpus, myid, vvol, dRZ +! write(lunit+myid,'("hesian : ", 10x ," : ")') - do ii = 1, mn ! loop over Fourier harmonics degrees of freedom; + do ii = 1, mn ! loop over Fourier harmonics degrees of freedom; - do irz = 0, 1 ! loop over R,Z degrees of freedom; + do irz = 0, 1 ! loop over R,Z degrees of freedom; - if( irz.eq.1 .and. Igeometry.lt.3 ) cycle ! no dependence on Z; 26 Feb 13; + if( irz.eq.1 .and. Igeometry.lt.3 ) cycle ! no dependence on Z; 26 Feb 13; - do issym = 0, 1 + do issym = 0, 1 - if( issym.eq.1 .and. YESstellsym ) cycle ! no dependence on non-stellarator symmetric harmonics; 26 Feb 13; + if( issym.eq.1 .and. YESstellsym ) cycle ! no dependence on non-stellarator symmetric harmonics; 26 Feb 13; - if( ii.eq.1 .and. irz.eq.1 .and. issym.eq.0 ) cycle ! this is not a degree of freedom; no dependence on Zbs_{m,n} for m=0, n=0; - if( ii.eq.1 .and. irz.eq.0 .and. issym.eq.1 ) cycle ! this is not a degree of freedom; no dependence on Rbs_{m,n} for m=0, n=0; + if( ii.eq.1 .and. irz.eq.1 .and. issym.eq.0 ) cycle ! this is not a degree of freedom; no dependence on Zbs_{m,n} for m=0, n=0; + if( ii.eq.1 .and. irz.eq.0 .and. issym.eq.1 ) cycle ! this is not a degree of freedom; no dependence on Rbs_{m,n} for m=0, n=0; - tdof = tdof + 1 + tdof = tdof + 1 - do isymdiff = -2, 2 + do isymdiff = -2, 2 - if( isymdiff.eq.0 ) cycle + if( isymdiff.eq.0 ) cycle - xx(1:NGdof,isymdiff) = position(1:NGdof) ! reset geometry to original; + xx(1:NGdof,isymdiff) = position(1:NGdof) ! reset geometry to original; - xx(tdof,isymdiff) = position(tdof) + isymdiff * dRZ ! perturb appropriate geometric harmonic; + xx(tdof,isymdiff) = position(tdof) + isymdiff * dRZ ! perturb appropriate geometric harmonic; - LComputeDerivatives = .false. - LComputeAxis = .true. - WCALL( hesian, dforce, ( NGdof, xx(0:NGdof,isymdiff), ff(0:NGdof,isymdiff), LComputeDerivatives, LComputeAxis) ) ! force-imbalance; + LComputeDerivatives = .false. + LComputeAxis = .true. + WCALL( hesian, dforce, ( NGdof, xx(0:NGdof,isymdiff), ff(0:NGdof,isymdiff), LComputeDerivatives, LComputeAxis) ) ! force-imbalance; - enddo ! end of do isymdiff; 20 Jun 14; + enddo ! end of do isymdiff; 20 Jun 14; - df(1:NGdof) = ( - ff(1:NGdof,+2) + 8 * ff(1:NGdof,+1) - 8 * ff(1:NGdof,-1) + ff(1:NGdof,-2) ) / ( 12 * dRZ ) + df(1:NGdof) = ( - ff(1:NGdof,+2) + 8 * ff(1:NGdof,+1) - 8 * ff(1:NGdof,-1) + ff(1:NGdof,-2) ) / ( 12 * dRZ ) - tdoc = 0 + tdoc = 0 - do jvol = 1, Mvol-1 + do jvol = 1, Mvol-1 - do jj = 1, mn + do jj = 1, mn - do jrz = 0, 1 ! loop over R,Z degrees of freedom; + do jrz = 0, 1 ! loop over R,Z degrees of freedom; - if( jrz.eq.1 .and. Igeometry.lt.3 ) cycle ! no dependence on Z; 26 Feb 13; + if( jrz.eq.1 .and. Igeometry.lt.3 ) cycle ! no dependence on Z; 26 Feb 13; - do jssym = 0, 1 + do jssym = 0, 1 - if( jssym.eq.1 .and. YESstellsym ) cycle ! no dependence on non-stellarator symmetric harmonics; 26 Feb 13; + if( jssym.eq.1 .and. YESstellsym ) cycle ! no dependence on non-stellarator symmetric harmonics; 26 Feb 13; - if( jj.eq.1 .and. jrz.eq.1 .and. jssym.eq.0 ) cycle ! this is not a constraint; I_{m,n} for m=0, n=0 is irrelevant; - if( jj.eq.1 .and. jrz.eq.0 .and. jssym.eq.1 ) cycle ! this is not a constraint; I_{m,n} for m=0, n=0 is irrelevant; + if( jj.eq.1 .and. jrz.eq.1 .and. jssym.eq.0 ) cycle ! this is not a constraint; I_{m,n} for m=0, n=0 is irrelevant; + if( jj.eq.1 .and. jrz.eq.0 .and. jssym.eq.1 ) cycle ! this is not a constraint; I_{m,n} for m=0, n=0 is irrelevant; - tdoc = tdoc + 1 + tdoc = tdoc + 1 - FATAL( hesian, tdoc.lt. 1, needs attention ) - FATAL( hesian, tdoc.gt.NGdof, needs attention ) + FATAL( hesian, tdoc.lt. 1, needs attention ) + FATAL( hesian, tdoc.gt.NGdof, needs attention ) - cput = GETTIME + cput = GETTIME - error = abs( df(tdoc)-hessian(tdoc,tdof) ) + error = abs( df(tdoc)-hessian(tdoc,tdof) ) - if( abs(hessian(tdoc,tdof)).gt.1.0e-05 .or. abs(df(tdoc)).gt.1.0e-05 .or. error.gt.dRZ ) then ! write to screen; 20 Jan 15; - write(ounit ,1001) cput-cpus, myid, & - vvol, im(ii), in(ii), irz, issym, tdof, & - jvol, im(jj), in(jj), jrz, jssym, tdoc, & - df(tdoc), tdoc, tdof, hessian(tdoc,tdof), error - endif + if( abs(hessian(tdoc,tdof)).gt.1.0e-05 .or. abs(df(tdoc)).gt.1.0e-05 .or. error.gt.dRZ ) then ! write to screen; 20 Jan 15; + write(ounit ,1001) cput-cpus, myid, & + vvol, im(ii), in(ii), irz, issym, tdof, & + jvol, im(jj), in(jj), jrz, jssym, tdoc, & + df(tdoc), tdoc, tdof, hessian(tdoc,tdof), error + endif - ! if( abs(hessian(tdoc,tdof)).gt.1.0e-05 .or. abs(df(tdoc)).gt.1.0e-05 .or. error.gt.dRZ ) then ! write to file; 20 Jan 15; - ! write(lunit+myid,1001) cput-cpus, myid, & - ! vvol, im(ii), in(ii), irz, issym, tdof, & - ! jvol, im(jj), in(jj), jrz, jssym, tdoc, & - ! df(tdoc), tdoc, tdof, hessian(tdoc,tdof), error - ! endif +! if( abs(hessian(tdoc,tdof)).gt.1.0e-05 .or. abs(df(tdoc)).gt.1.0e-05 .or. error.gt.dRZ ) then ! write to file; 20 Jan 15; +! write(lunit+myid,1001) cput-cpus, myid, & +! vvol, im(ii), in(ii), irz, issym, tdof, & +! jvol, im(jj), in(jj), jrz, jssym, tdoc, & +! df(tdoc), tdoc, tdof, hessian(tdoc,tdof), error +! endif - enddo ! end of do jssym; 19 Sep 13; + enddo ! end of do jssym; 19 Sep 13; - enddo ! end of do irz; + enddo ! end of do irz; - #ifdef DEBUG - ! pause - #endif +#ifdef DEBUG +! pause +#endif - enddo ! end of do jj; + enddo ! end of do jj; - #ifdef DEBUG - ! pause - #endif +#ifdef DEBUG +! pause +#endif - enddo ! end of do jvol; + enddo ! end of do jvol; - #ifdef DEBUG - ! pause - #endif +#ifdef DEBUG +! pause +#endif - 1001 format("hesian : ",f10.2," : myid=",i3, & - " ; vvol=",i3," ; ("i4" ,"i4" ); irz="i2" ; issym="i2" ; tdof="i6 & - " ; jvol="i4" ; ("i4" ,"i4" ); jrz="i2" ; jssym="i2" ; tdoc="i6 & - " ; fd-estimate="es13.5" & hessian("i6","i6" )="es13.5" ;":" err="es13.5" ;":,f12.4" ;") +1001 format("hesian : ",f10.2," : myid=",i3, & + " ; vvol=",i3," ; ("i4" ,"i4" ); irz="i2" ; issym="i2" ; tdof="i6 & + " ; jvol="i4" ; ("i4" ,"i4" ); jrz="i2" ; jssym="i2" ; tdoc="i6 & + " ; fd-estimate="es13.5" & hessian("i6","i6" )="es13.5" ;":" err="es13.5" ;":,f12.4" ;") - enddo ! end of do issym; + enddo ! end of do issym; - enddo ! end of do irz; + enddo ! end of do irz; - enddo ! end of do ii; + enddo ! end of do ii; - enddo ! end of do vvol; + enddo ! end of do vvol; - pack = 'U' !; position(0) = zero ! this is not used; 11 Aug 14; - WCALL( hesian, packxi, ( NGdof, position(0:NGdof), Mvol, mn, iRbc(1:mn,0:Mvol), iZbs(1:mn,0:Mvol), iRbs(1:mn,0:Mvol), iZbc(1:mn,0:Mvol), pack, .false., LComputeAxis ) ) + pack = 'U' !; position(0) = zero ! this is not used; 11 Aug 14; + WCALL( hesian, packxi, ( NGdof, position(0:NGdof), Mvol, mn, iRbc(1:mn,0:Mvol), iZbs(1:mn,0:Mvol), iRbs(1:mn,0:Mvol), iZbc(1:mn,0:Mvol), pack, .false., LComputeAxis ) ) - mu(1:Nvol) = lmu(1:Nvol) ; pflux(1:Nvol) = lpflux(1:Nvol) ; helicity(1:Nvol) = lhelicity(1:Nvol) + mu(1:Nvol) = lmu(1:Nvol) ; pflux(1:Nvol) = lpflux(1:Nvol) ; helicity(1:Nvol) = lhelicity(1:Nvol) - ! xx(1:NGdof,0) = position(1:NGdof) ! reset geometry to original; - ! - ! LComputeDerivatives = .false. - ! WCALL(hesian,dforce,( NGdof, xx(1:NGdof,0), ff(0:NGdof,0), LComputeDerivatives )) ! calculate the force-imbalance; +! xx(1:NGdof,0) = position(1:NGdof) ! reset geometry to original; +! +! LComputeDerivatives = .false. +! WCALL(hesian,dforce,( NGdof, xx(1:NGdof,0), ff(0:NGdof,0), LComputeDerivatives )) ! calculate the force-imbalance; - !close(lunit+myid) + !close(lunit+myid) endif ! end of if( Lcheck.eq.5 ) ; 01 Jul 14; @@ -422,13 +423,7 @@ subroutine hesian( NGdof, position, Mvol, mn, LGdof ) write(munit) NGdof write(munit) ohessian(1:NGdof,1:NGdof) close(munit) - - ! add by Erol - ! do ii=1,NGdof - ! write(*,*)ii, ohessian(ii,1:NGdof) - ! enddo - - endif + endif endif @@ -452,12 +447,12 @@ subroutine hesian( NGdof, position, Mvol, mn, LGdof ) hessian2D(1:NGdof,1:NGdof) = ohessian(1:NGdof,1:NGdof) - !#ifdef NAG18 - ! call F02EBF( JOB, NGdof, hessian(1:LDA,1:NGdof), LDA, evalr(1:NGdof), evali(1:NGdof), & - ! evecr(1:Ldvr,1:NGdof), Ldvr, eveci(1:Ldvi,1:NGdof), Ldvi, work(1:Lwork), Lwork, if02ebf ) - !#else - ! FATAL( global, .true., eigenvalue solver needs updating to F08NAF ) - !#endif +!#ifdef NAG18 +! call F02EBF( JOB, NGdof, hessian(1:LDA,1:NGdof), LDA, evalr(1:NGdof), evali(1:NGdof), & +! evecr(1:Ldvr,1:NGdof), Ldvr, eveci(1:Ldvi,1:NGdof), Ldvi, work(1:Lwork), Lwork, if02ebf ) +!#else +! FATAL( global, .true., eigenvalue solver needs updating to F08NAF ) +!#endif call dgeev('N', JOB, NGdof, hessian2D(1:LDA,1:NGdof), LDA, evalr(1:NGdof), evali(1:NGdof), & evecl(1:Ldvr,1:NGdof), Ldvr, revecr(1:Ldvr,1:2*NGdof), Ldvr, work(1:Lwork), Lwork, if02ebf ) evecr(1:Ldvr,1:NGdof) = revecr(1:Ldvr,1:NGdof) @@ -588,11 +583,6 @@ subroutine hesian( NGdof, position, Mvol, mn, LGdof ) close(hunit) endif ! end of if( myid.eq.0 ) ; 04 Dec 14; - ! ! add by Erol - ! do ii=1,NGdof - ! write(*,*)ii, evalr(ii), evali(ii) - ! enddo - endif ! end of if( ( LHevalues .or. LHevectors ) ) !-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-! @@ -705,7 +695,7 @@ subroutine hesian( NGdof, position, Mvol, mn, LGdof ) DALLOCATE(hessian2D) - ! write(ounit,*) 5656 + write(ounit,*) 5656 DALLOCATE(dessian2D) diff --git a/src/lbpol.f90 b/src/lbpol.f90 index ac09f917..c4958705 100644 --- a/src/lbpol.f90 +++ b/src/lbpol.f90 @@ -126,21 +126,6 @@ subroutine lbpol(lvol, Bt00, ideriv, iocons) ! Now Btemn(1, 0, vvol) and Btemn(1, 1, vvol) contain Bte00(s=-1) and Bte00(s=1) for each volume vvol. - ! if((lvol.eq.10.and.iocons.eq.1).or.(lvol.eq.11.and.iocons.eq.0)) then - ! write(*,*) "lvol", lvol, "iocons", iocons, "ideriv", ideriv - ! write(*,*) "Bt", Bt(1:Ntz) - ! ! write(*,*) "Bz",Bz(1:Ntz) ! also different, but fractionally less - ! ! write(*,*) guvij(1:Ntz,1,1,0),guvij(1:Ntz,2,2,0),guvij(1:Ntz,3,3,0) ! SAME - ! ! write(*,*) guvij(1:Ntz,2,3,0) - ! ! write(*,*) "dAz", dAz(1:Ntz ) ! differetn - ! ! write(*,*) "__mn", efmn(1:mn) - ! write(*,*) "Ate%s" - ! do ii = 1, mn - ! do ll=0,Lrad(lvol) - ! write(*,*) ii,ll, Ate(lvol,ideriv,ii)%s(ll) - ! enddo - ! enddo - ! endif RETURN(lbpol) diff --git a/src/mp00ac.f90 b/src/mp00ac.f90 index 2c3c56be..2ecaf1ab 100644 --- a/src/mp00ac.f90 +++ b/src/mp00ac.f90 @@ -726,10 +726,10 @@ subroutine mp00ac( Ndof, Xdof, Fdof, Ddof, Ldfjac, iflag ) ! argument list is fi end select endif - 3000 format("mp00ac : ",f10.2," : myid=",i3," ; lvol=",i3," ; (mu,dp)=("es23.15" ,"es23.15" ) ; iflag="i2" ;":" F="2es13.05" ;") - 3010 format("mp00ac : ",f10.2," : myid=",i3," ; lvol=",i3," ; (mu,dp)=("es23.15" ,"es23.15" ) ; iflag="i2" ;":" D="4es13.05" ;") - 3001 format("mp00ac : ",f10.2," : myid=",i3," ; lvol=",i3," ; (dt,dp)=("es23.15" ,"es23.15" ) ; iflag="i2" ;":" F="2es13.05" ;") - 3011 format("mp00ac : ",f10.2," : myid=",i3," ; lvol=",i3," ; (dt,dp)=("es23.15" ,"es23.15" ) ; iflag="i2" ;":" D="4es13.05" ;") +3000 format("mp00ac : ",f10.2," : myid=",i3," ; lvol=",i3," ; (mu,dp)=("es23.15" ,"es23.15" ) ; iflag="i2" ;":" F="2es13.05" ;") +3010 format("mp00ac : ",f10.2," : myid=",i3," ; lvol=",i3," ; (mu,dp)=("es23.15" ,"es23.15" ) ; iflag="i2" ;":" D="4es13.05" ;") +3001 format("mp00ac : ",f10.2," : myid=",i3," ; lvol=",i3," ; (dt,dp)=("es23.15" ,"es23.15" ) ; iflag="i2" ;":" F="2es13.05" ;") +3011 format("mp00ac : ",f10.2," : myid=",i3," ; lvol=",i3," ; (dt,dp)=("es23.15" ,"es23.15" ) ; iflag="i2" ;":" D="4es13.05" ;") endif ! end of if( Wmp00ac .or. Wma02aa ) ; diff --git a/src/newton.f90 b/src/newton.f90 index 0c74b6b0..7bd26216 100644 --- a/src/newton.f90 +++ b/src/newton.f90 @@ -659,9 +659,9 @@ subroutine fcn2( NGdof, xx, fvec, fjac, Ldfjac, irevcm ) case( 2 ) ! before re-entry to C05PDF, fjac must contain the derivatives; - #ifdef DEBUG - FATAL( newton, .not.Lhessianallocated, need to allocate hessian ) - #endif +#ifdef DEBUG + FATAL( newton, .not.Lhessianallocated, need to allocate hessian ) +#endif nDcalls = nDcalls + 1 @@ -687,9 +687,9 @@ subroutine fcn2( NGdof, xx, fvec, fjac, Ldfjac, irevcm ) LComputeAxis = .true. WCALL( newton, dforce, ( NGdof, position(0:NGdof), force(0:NGdof), LComputeDerivatives, LComputeAxis ) ) ! calculate the force-imbalance; - #ifdef DEBUG - FATAL( newton, Lcheck.eq.4, derivatives of Beltrami field have been computed ) - #endif +#ifdef DEBUG + FATAL( newton, Lcheck.eq.4, derivatives of Beltrami field have been computed ) +#endif endif @@ -697,23 +697,23 @@ subroutine fcn2( NGdof, xx, fvec, fjac, Ldfjac, irevcm ) if( myid.eq.0 ) call writereadgf( 'W', NGdof, ireadhessian ) ! will always save derivative matrix; - #ifdef DEBUG +#ifdef DEBUG - if( Lcheck.eq.3 ) then - write(ounit,'("newton : ", 10x ," : myid=",i3," ; volume derivatives have been compared ;")') myid - stop "newton : : myid= ; volume derivatives have been compared ;" - endif + if( Lcheck.eq.3 ) then + write(ounit,'("newton : ", 10x ," : myid=",i3," ; volume derivatives have been compared ;")') myid + stop "newton : : myid= ; volume derivatives have been compared ;" + endif - FATAL( newton, Lcheck.eq.3, volume derivatives have been compared ) ! the first process will terminate all processes; + FATAL( newton, Lcheck.eq.3, volume derivatives have been compared ) ! the first process will terminate all processes; - if( (Lcheck.eq.4) .and. (nDcalls.ne.1) ) then - write(ounit,'("newton : ", 10x ," : myid=",i3," ; field derivatives have been compared ;")') myid - stop "newton : : myid= ; field derivatives have been compared ;" - endif + if( (Lcheck.eq.4) .and. (nDcalls.ne.1) ) then + write(ounit,'("newton : ", 10x ," : myid=",i3," ; field derivatives have been compared ;")') myid + stop "newton : : myid= ; field derivatives have been compared ;" + endif - FATAL( newton, (Lcheck.eq.4) .and. (nDcalls.ne.1), field derivatives have been compared ) ! the first process will terminate all processes; + FATAL( newton, (Lcheck.eq.4) .and. (nDcalls.ne.1), field derivatives have been compared ) ! the first process will terminate all processes; - #endif +#endif !-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-! diff --git a/src/packab.f90 b/src/packab.f90 index 296d7df3..b2b5ccc2 100644 --- a/src/packab.f90 +++ b/src/packab.f90 @@ -109,6 +109,7 @@ subroutine packab( packorunpack, lvol, NN, solution, ideriv ) #endif if( YESstellsym ) then + do ii = 1, mn do ll = 0, llrad ; id = Ate(lvol,0,ii)%i(ll) ; if (id/=0) then; Ate(lvol,ideriv,ii)%s(ll) = solution(id) diff --git a/src/preset.f90 b/src/preset.f90 index afbd8c8b..37ab4b75 100644 --- a/src/preset.f90 +++ b/src/preset.f90 @@ -514,7 +514,7 @@ subroutine preset endif select case( Igeometry ) - case( 1 ) ; dtflux(1) = tflux(1) ; dpflux(1) = pflux(1) ! Edit by Erol, to keep total pflux 0 + case( 1 ) ; dtflux(1) = tflux(1) ; dpflux(1) = pflux(1) ! Edit by Erol -- Cartesian ; this is the "inverse" operation defined in xspech; 09 Mar 17; case( 2:3 ) ; dtflux(1) = tflux(1) ; dpflux(1) = zero ! cylindrical or toroidal; end select @@ -524,7 +524,6 @@ subroutine preset dtflux(1:Mvol) = dtflux(1:Mvol) * phiedge / pi2 dpflux(1:Mvol) = dpflux(1:Mvol) * phiedge / pi2 - !-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-! !latex \subsubsection{\type{mu(1:Mvol)} evaluation of \inputvar{mu} from \inputvar{Ivolume};} @@ -1110,7 +1109,8 @@ subroutine preset SALLOCATE( Azo(vvol,ideriv,ii)%i, (0:Lrad(vvol)), 0 ) enddo ! end of do ii; - + + select case( Linitgues ) ! for iterative solver of the Beltrami fields, an initial guess is required; 11 Mar 16; case( 0 ) ; case( 1 ) ; Ate(vvol,0,1)%s(0:1) = dtflux(vvol) * half ! this is an integrable approximation; NEEDS CHECKING; 26 Feb 13; diff --git a/src/sphdf5.f90 b/src/sphdf5.f90 index 43aca629..5f4d144f 100644 --- a/src/sphdf5.f90 +++ b/src/sphdf5.f90 @@ -365,6 +365,7 @@ subroutine mirror_input_to_outfile HWRITELV( grpInputDiagnostics, 1, LHevalues , (/ LHevalues /)) HWRITELV( grpInputDiagnostics, 1, LHevectors , (/ LHevectors /)) HWRITELV( grpInputDiagnostics, 1, LHmatrix , (/ LHmatrix /)) + HWRITELV( grpInputDiagnostics, 1, Ltransform , (/ Ltransform /)) HWRITEIV( grpInputDiagnostics, 1, Lperturbed , (/ Lperturbed /)) HWRITEIV( grpInputDiagnostics, 1, dpp , (/ dpp /)) HWRITEIV( grpInputDiagnostics, 1, dqq , (/ dqq /)) diff --git a/src/spsint.f90 b/src/spsint.f90 index 2eaf6489..1c423eda 100644 --- a/src/spsint.f90 +++ b/src/spsint.f90 @@ -193,21 +193,21 @@ subroutine spsint( lquad, mn, lvol, lrad ) DDzzcc( ll1, pp1, mi+1, 1 ) = DDzzcc( ll1, pp1, mi+1, 1 ) + DlDp * fzzcc if (NOTstellsym) then - !$OMP ATOMIC UPDATE - DTooss( ll1, pp1, mi+1, 1 ) = DTooss( ll1, pp1, mi+1, 1 ) + DlTp * fooss - !$OMP ATOMIC UPDATE - TTsscc( ll1, pp1, mi+1, 1 ) = TTsscc( ll1, pp1, mi+1, 1 ) + TlTp * fsscc - !$OMP ATOMIC UPDATE - TDstcc( ll1, pp1, mi+1, 1 ) = TDstcc( ll1, pp1, mi+1, 1 ) + TlDp * fstcc - !$OMP ATOMIC UPDATE - TDszcc( ll1, pp1, mi+1, 1 ) = TDszcc( ll1, pp1, mi+1, 1 ) + TlDp * fszcc - !$OMP ATOMIC UPDATE - TDszss( ll1, pp1, mi+1, 1 ) = TDszss( ll1, pp1, mi+1, 1 ) + TlDp * fszss - !$OMP ATOMIC UPDATE - DDttss( ll1, pp1, mi+1, 1 ) = DDttss( ll1, pp1, mi+1, 1 ) + DlDp * fttss - !$OMP ATOMIC UPDATE - DDtzss( ll1, pp1, mi+1, 1 ) = DDtzss( ll1, pp1, mi+1, 1 ) + DlDp * ftzss - !$OMP ATOMIC UPDATE +!$OMP ATOMIC UPDATE + DTooss( ll1, pp1, mi+1, 1 ) = DTooss( ll1, pp1, mi+1, 1 ) + DlTp * fooss +!$OMP ATOMIC UPDATE + TTsscc( ll1, pp1, mi+1, 1 ) = TTsscc( ll1, pp1, mi+1, 1 ) + TlTp * fsscc +!$OMP ATOMIC UPDATE + TDstcc( ll1, pp1, mi+1, 1 ) = TDstcc( ll1, pp1, mi+1, 1 ) + TlDp * fstcc +!$OMP ATOMIC UPDATE + TDszcc( ll1, pp1, mi+1, 1 ) = TDszcc( ll1, pp1, mi+1, 1 ) + TlDp * fszcc +!$OMP ATOMIC UPDATE + TDszss( ll1, pp1, mi+1, 1 ) = TDszss( ll1, pp1, mi+1, 1 ) + TlDp * fszss +!$OMP ATOMIC UPDATE + DDttss( ll1, pp1, mi+1, 1 ) = DDttss( ll1, pp1, mi+1, 1 ) + DlDp * fttss +!$OMP ATOMIC UPDATE + DDtzss( ll1, pp1, mi+1, 1 ) = DDtzss( ll1, pp1, mi+1, 1 ) + DlDp * ftzss +!$OMP ATOMIC UPDATE DDzzss( ll1, pp1, mi+1, 1 ) = DDzzss( ll1, pp1, mi+1, 1 ) + DlDp * fzzss end if !NOTstellsym diff --git a/src/spsmat.f90 b/src/spsmat.f90 index 3480fac6..ff7fbd4e 100644 --- a/src/spsmat.f90 +++ b/src/spsmat.f90 @@ -129,7 +129,7 @@ subroutine spsmat( lvol, mn, lrad ) TTMdata(0:lrad,ii) = TT(0:lrad,0,0) enddo endif - + !-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-! if( YESstellsym ) then diff --git a/src/xspech.f90 b/src/xspech.f90 index b487e328..1bb7b694 100644 --- a/src/xspech.f90 +++ b/src/xspech.f90 @@ -319,7 +319,7 @@ subroutine spec version, & MPI_COMM_SPEC - !-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-! +!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-! LOCALS @@ -341,12 +341,12 @@ subroutine spec SALLOCATE( position, (0:NGdof), zero ) ! position ; NGdof = #geometrical degrees-of-freedom was computed in preset; - !-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-! +!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-! nfreeboundaryiterations = -1 - ! This is the free-boundary iteration loop (implemented using GOTO); 08 Jun 16; - 9000 nfreeboundaryiterations = nfreeboundaryiterations + 1 +! This is the free-boundary iteration loop (implemented using GOTO); 08 Jun 16; +9000 nfreeboundaryiterations = nfreeboundaryiterations + 1 ! run fix_boundary for the first free_boundary iteration if LautoinitBn was set to 1 if (Lfreebound.eq.1 .and. LautoinitBn.eq.1) then @@ -369,14 +369,14 @@ subroutine spec endif endif - !-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-! +!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-! - !> **packing geometrical degrees-of-freedom into vector** - !> - !>
    - !>
  • If \c NGdof.gt.0 , where \c NGdof counts the geometrical degrees-of-freedom, i.e. the \f$R_{bc}\f$, \f$Z_{bs}\f$, etc., - !> then packxi() is called to "pack" the geometrical degrees-of-freedom into \c position(0:NGdof) .
    • - !>
+!> **packing geometrical degrees-of-freedom into vector** +!> +!>
    +!>
  • If \c NGdof.gt.0 , where \c NGdof counts the geometrical degrees-of-freedom, i.e. the \f$R_{bc}\f$, \f$Z_{bs}\f$, etc., +!> then packxi() is called to "pack" the geometrical degrees-of-freedom into \c position(0:NGdof) .
    • +!>
if( NGdof.gt.0 ) then ! pack geometry into vector; 14 Jan 13; @@ -387,17 +387,17 @@ subroutine spec endif - !-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-! +!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-! - !> **initialize adiabatic constants** - !> - !>
    - !>
  • If \c Ladiabatic.eq.0 , then the "adiabatic constants" in each region, \f$P_v\f$, are calculated as - !> \f{eqnarray}{ P_v \equiv p_v V_v^\gamma, \label{eq:adiabatic_xspech} - !> \f} - !> where \f$p_v\equiv\,\f$\c pressure(vvol) , the volume \f$V_v\f$ of each region is computed by volume() , - !> and the adiabatic index \f$\gamma\equiv\,\f$\c gamma .
    • - !>
+!> **initialize adiabatic constants** +!> +!>
    +!>
  • If \c Ladiabatic.eq.0 , then the "adiabatic constants" in each region, \f$P_v\f$, are calculated as +!> \f{eqnarray}{ P_v \equiv p_v V_v^\gamma, \label{eq:adiabatic_xspech} +!> \f} +!> where \f$p_v\equiv\,\f$\c pressure(vvol) , the volume \f$V_v\f$ of each region is computed by volume() , +!> and the adiabatic index \f$\gamma\equiv\,\f$\c gamma .
    • +!>
do vvol = 1, Mvol @@ -417,28 +417,28 @@ subroutine spec write(ounit,'("xspech : ",f10.2," : myid=",i3," ; adiabatic constants = "999es13.5)') cput-cpus, myid, adiabatic(1:Mvol) endif - !-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-! +!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-! + +!> **solving force-balance** +!> +!>
    +!>
  • If there are geometrical degress of freedom, i.e. if \c NGdof.gt.0 , then +!>
      +!>
    • \todo If \c Lminimize.eq.1 , call pc00aa() to find minimum of energy functional +!> using quasi-Newton, preconditioned conjugate gradient method, \c E04DGF +!> +!>
      • +!>
    • If \c Lfindzero.gt.0 , call newton() to find extremum of constrained energy functional using a Newton method, \c C05PDF .
      • +!>
    • +!>
- !> **solving force-balance** - !> - !>
    - !>
  • If there are geometrical degress of freedom, i.e. if \c NGdof.gt.0 , then - !>
      - !>
    • \todo If \c Lminimize.eq.1 , call pc00aa() to find minimum of energy functional - !> using quasi-Newton, preconditioned conjugate gradient method, \c E04DGF - !> - !>
      • - !>
    • If \c Lfindzero.gt.0 , call newton() to find extremum of constrained energy functional using a Newton method, \c C05PDF .
      • - !>
    • - !>
- - ! if( Lminimize.eq.1 ) then - ! - ! ifail = 1 ! this is probably not required; 26 Feb 13; - ! - ! WCALL(xspech,pc00aa,( NGdof, position(1:NGdof), Mvol, mn, ifail )) - ! - ! endif +! if( Lminimize.eq.1 ) then +! +! ifail = 1 ! this is probably not required; 26 Feb 13; +! +! WCALL(xspech,pc00aa,( NGdof, position(1:NGdof), Mvol, mn, ifail )) +! +! endif if( NGdof.gt.0 ) then @@ -457,31 +457,31 @@ subroutine spec endif - !-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-! +!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-! - !> **post diagnostics** - !> - !>
    - !>
  • The pressure is computed from the adiabatic constants from Eqn.\f$(\ref{eq:adiabatic_xspech})\f$, i.e. \f$p=P/V^\gamma\f$.
    • - !>
  • The Beltrami/vacuum fields in each region are re-calculated using dforce() .
    • - !>
  • If \c Lcheck.eq.5 \c .or. \c LHevalues \c .or. \c LHevectors \c .or. \c Lperturbed.eq.1 , then the force-gradient matrix is examined using hesian() .
    • - !>
+!> **post diagnostics** +!> +!>
    +!>
  • The pressure is computed from the adiabatic constants from Eqn.\f$(\ref{eq:adiabatic_xspech})\f$, i.e. \f$p=P/V^\gamma\f$.
    • +!>
  • The Beltrami/vacuum fields in each region are re-calculated using dforce() .
    • +!>
  • If \c Lcheck.eq.5 \c .or. \c LHevalues \c .or. \c LHevectors \c .or. \c Lperturbed.eq.1 , then the force-gradient matrix is examined using hesian() .
    • +!>
- !-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-! +!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-! - ! set/reset input variables; +! set/reset input variables; - ! if( Lconstraint.lt.2 ) helicity(1:Nvol) = lABintegral(1:Nvol) ! updated ``input'' quantity; +! if( Lconstraint.lt.2 ) helicity(1:Nvol) = lABintegral(1:Nvol) ! updated ``input'' quantity; - #ifdef DEBUG - do vvol = 1, Mvol - FATAL( xspech, vvolume(vvol).lt.vsmall, error dividing adiabatic by volume ) - enddo - #endif +#ifdef DEBUG + do vvol = 1, Mvol + FATAL( xspech, vvolume(vvol).lt.vsmall, error dividing adiabatic by volume ) + enddo +#endif pressure(1:Mvol) = adiabatic(1:Mvol) / vvolume(1:Mvol)**gamma ! this matches construction of adiabatic above; - !-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-! +!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-! SALLOCATE( gradient, (0:NGdof), zero ) @@ -489,27 +489,27 @@ subroutine spec LComputeDerivatives = .false. LComputeAxis = .true. - ! vvol = Mvol ; ideriv = 0 ; ii = 1 - ! write(ounit,'("xspech : ", 10x ," : sum(Ate(",i3,",",i2,",",i2,")%s) =",99es23.15)') vvol, ideriv, ii, sum(Ate(vvol,ideriv,ii)%s(0:Lrad(vvol))) +! vvol = Mvol ; ideriv = 0 ; ii = 1 +! write(ounit,'("xspech : ", 10x ," : sum(Ate(",i3,",",i2,",",i2,")%s) =",99es23.15)') vvol, ideriv, ii, sum(Ate(vvol,ideriv,ii)%s(0:Lrad(vvol))) WCALL( xspech, dforce, ( NGdof, position(0:NGdof), gradient(0:NGdof), LComputeDerivatives, LComputeAxis) ) ! (re-)calculate Beltrami fields; DALLOCATE(gradient) - #ifdef DEBUG - do vvol = 1, Mvol-1 - ; FATAL( xspech, BBe(vvol).lt.logtolerance, underflow ) +#ifdef DEBUG + do vvol = 1, Mvol-1 + ; FATAL( xspech, BBe(vvol).lt.logtolerance, underflow ) + if( Igeometry.eq.3 ) then ! include spectral constraints; 04 Dec 14; + ;FATAL( xspech, IIo(vvol).lt.logtolerance, underflow ) + endif + if( NOTstellsym ) then + ;FATAL( xspech, BBo(vvol).lt.logtolerance, underflow ) if( Igeometry.eq.3 ) then ! include spectral constraints; 04 Dec 14; - ;FATAL( xspech, IIo(vvol).lt.logtolerance, underflow ) + FATAL( xspech, IIe(vvol).lt.logtolerance, underflow ) endif - if( NOTstellsym ) then - ;FATAL( xspech, BBo(vvol).lt.logtolerance, underflow ) - if( Igeometry.eq.3 ) then ! include spectral constraints; 04 Dec 14; - FATAL( xspech, IIe(vvol).lt.logtolerance, underflow ) - endif - endif - enddo - #endif + endif + enddo +#endif if( myid.eq.0 ) then cput = GETTIME @@ -525,10 +525,10 @@ subroutine spec endif endif - 1000 format("xspech : ",f10.2," : #freeits=",i3," ; ":"|f|="es12.5" ; ":"time=",f10.2,"s ;":" log"a5,:"="28f6.2" ...") - 1001 format("xspech : ", 10x ," : ",3x," ; ":" " 12x " ":" ", 10x ," ;":" log"a5,:"="28f6.2" ...") +1000 format("xspech : ",f10.2," : #freeits=",i3," ; ":"|f|="es12.5" ; ":"time=",f10.2,"s ;":" log"a5,:"="28f6.2" ...") +1001 format("xspech : ", 10x ," : ",3x," ; ":" " 12x " ":" ", 10x ," ;":" log"a5,:"="28f6.2" ...") - !-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-! +!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-! if( Lcheck.eq.5 .or. LHevalues .or. LHevectors .or. LHmatrix .or. Lperturbed.eq.1 ) then ! check construction of Hessian; 01 Jul 14; @@ -542,7 +542,7 @@ subroutine spec endif ! end of if( Lcheck.eq.5 ) ; 01 Jul 14; - !-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-! +!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-! select case( Igeometry ) ! 08 Feb 16; case( 1 ) ; tflux(1) = dtflux(1) ; pflux(1) = dpflux(1) ! 08 Feb 16; @@ -556,51 +556,51 @@ subroutine spec tflux(1:Mvol) = tflux(1:Mvol) * pi2 / phiedge ! this is the "inverse" operation defined in preset; 19 Jul 16; pflux(1:Mvol) = pflux(1:Mvol) * pi2 / phiedge - !-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-! +!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-! - !> **free-boundary: re-computing normal field** - !> - !>
    - !>
  • If \c Lfreebound.eq.1 and \c Lfindzero.gt.0 and \c mfreeits.ne.0 , - !> then the magnetic field at the computational boundary produced by the plasma currents is computed using bnorml() .
    • - !>
  • The "new" magnetic field at the computational boundary produced by the plasma currents is updated using a Picard scheme: - !> \f{eqnarray}{ \texttt{Bns}_i^{j} = \lambda \, \texttt{Bns}_i^{j-1} + (1-\lambda) \texttt{Bns}_i, \label{eq:blending_xspech} - !> \f} - !> where \f$j\f$ labels free-boundary iterations, the "blending parameter" is \f$\lambda\equiv\,\f$\c gBnbld , - !> and \c Bns \f$_i\f$ is computed by virtual casing. - !> The subscript "$i$" labels Fourier harmonics.
    • - !>
  • If the new (unblended) normal field is _not_ sufficiently close to the old normal field, as quantified by \c gBntol , - !> then the free-boundary iterations continue. - !> This is quantified by - !> \f{eqnarray}{ \sum_i | \texttt{Bns}_i^{j-1} - \texttt{Bns}_i | / N, \label{eq:gBntol_xspech} - !> \f} - !> where \f$N\f$ is the total number of Fourier harmonics.
    • - !>
  • There are several choices that are available: - !>
      - !>
    • if \c mfreeits=-2 : the vacuum magnetic field - !> (really, the normal component of the field produced by the external currents at the computational boundary) - !> required to hold the given equlibrium is written to file. - !> This information is required as input by FOCUS \cite y2017_zhu - !> for example. (This option probably needs to revised.)
      • - !>
    • if \c mfreeits=-1 : after the plasma field is computed by virtual casing, - !> the vacuum magnetic field is set to exactly balance the plasma field - !> (again, we are really talking about the normal component at the computational boundary.) - !> This will ensure that the computational boundary itself if a flux surface of the total magnetic field.
      • - !>
    • if \c mfreeits=0 : the plasma field at the computational boundary is not updated; no "free-boundary" iterations take place.
      • - !>
    • if \c mfreeits>0 : the plasma field at the computational boundary is updated according to the above blending Eqn.\f$(\ref{eq:blending_xspech})\f$, - !> and the free-boundary iterations will continue until either the tolerance condition is met (see \c gBntol and Eqn.\f$(\ref{eq:gBntol_xspech})\f$) - !> or the maximum number of free-boundary iterations, namely \c mfreeits , is reached. - !> For this case, \c Lzerovac is relevant: - !> if \c Lzerovac=1 , then the vacuum field is set equal to the normal field at every iteration, - !> which results in the computational boundary being a flux surface. - !> (I am not sure if this is identical to setting \c mfreeits=-1 ; the logic etc. needs to be revised.)
      • - !>
    • - !>
+!> **free-boundary: re-computing normal field** +!> +!>
    +!>
  • If \c Lfreebound.eq.1 and \c Lfindzero.gt.0 and \c mfreeits.ne.0 , +!> then the magnetic field at the computational boundary produced by the plasma currents is computed using bnorml() .
    • +!>
  • The "new" magnetic field at the computational boundary produced by the plasma currents is updated using a Picard scheme: +!> \f{eqnarray}{ \texttt{Bns}_i^{j} = \lambda \, \texttt{Bns}_i^{j-1} + (1-\lambda) \texttt{Bns}_i, \label{eq:blending_xspech} +!> \f} +!> where \f$j\f$ labels free-boundary iterations, the "blending parameter" is \f$\lambda\equiv\,\f$\c gBnbld , +!> and \c Bns \f$_i\f$ is computed by virtual casing. +!> The subscript "$i$" labels Fourier harmonics.
    • +!>
  • If the new (unblended) normal field is _not_ sufficiently close to the old normal field, as quantified by \c gBntol , +!> then the free-boundary iterations continue. +!> This is quantified by +!> \f{eqnarray}{ \sum_i | \texttt{Bns}_i^{j-1} - \texttt{Bns}_i | / N, \label{eq:gBntol_xspech} +!> \f} +!> where \f$N\f$ is the total number of Fourier harmonics.
    • +!>
  • There are several choices that are available: +!>
      +!>
    • if \c mfreeits=-2 : the vacuum magnetic field +!> (really, the normal component of the field produced by the external currents at the computational boundary) +!> required to hold the given equlibrium is written to file. +!> This information is required as input by FOCUS \cite y2017_zhu +!> for example. (This option probably needs to revised.)
      • +!>
    • if \c mfreeits=-1 : after the plasma field is computed by virtual casing, +!> the vacuum magnetic field is set to exactly balance the plasma field +!> (again, we are really talking about the normal component at the computational boundary.) +!> This will ensure that the computational boundary itself if a flux surface of the total magnetic field.
      • +!>
    • if \c mfreeits=0 : the plasma field at the computational boundary is not updated; no "free-boundary" iterations take place.
      • +!>
    • if \c mfreeits>0 : the plasma field at the computational boundary is updated according to the above blending Eqn.\f$(\ref{eq:blending_xspech})\f$, +!> and the free-boundary iterations will continue until either the tolerance condition is met (see \c gBntol and Eqn.\f$(\ref{eq:gBntol_xspech})\f$) +!> or the maximum number of free-boundary iterations, namely \c mfreeits , is reached. +!> For this case, \c Lzerovac is relevant: +!> if \c Lzerovac=1 , then the vacuum field is set equal to the normal field at every iteration, +!> which results in the computational boundary being a flux surface. +!> (I am not sure if this is identical to setting \c mfreeits=-1 ; the logic etc. needs to be revised.)
      • +!>
    • +!>
LContinueFreeboundaryIterations = .false. ; LupdateBn = .false. ! default; - ! if( Lfreebound.eq.1 .and. Lfindzero.gt.0 ) then +! if( Lfreebound.eq.1 .and. Lfindzero.gt.0 ) then if( Lfreebound.eq.1) then ! removed Lfindzero check; Loizu Dec 18; if( mfreeits.gt.0 .and. nfreeboundaryiterations.lt.mfreeits ) LupdateBn = .true. if( mfreeits.lt.0 ) LupdateBn = .true. @@ -727,18 +727,18 @@ subroutine spec ; ; write(ounit,1003) endif ! end of if( myid.eq.0 ) ; 24 Nov 16; - 1003 format("xspech : " 10x " : ") - 1004 format("xspech : "f10.2" : nfreeboundaryiterations = "i6" / "i6.5" ; gBntol ="es8.1" ; bnserr =",es12.5," ; bnorml time ="f10.2"s ;") +1003 format("xspech : " 10x " : ") +1004 format("xspech : "f10.2" : nfreeboundaryiterations = "i6" / "i6.5" ; gBntol ="es8.1" ; bnserr =",es12.5," ; bnorml time ="f10.2"s ;") endif ! end of if( LupdateBn ) ; - !-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-! +!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-! - !> **output files: vector potential** - !> - !>
    - !>
  • The vector potential is written to file using ra00aa() .
    • - !>
+!> **output files: vector potential** +!> +!>
    +!>
  • The vector potential is written to file using ra00aa() .
    • +!>
WCALL( xspech, ra00aa, ('W') ) ! this writes vector potential to file; @@ -746,16 +746,16 @@ subroutine spec WCALL( xspech, wrtend ) ! write restart file; save initial input; endif - !-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-! +!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-! if( LContinueFreeboundaryIterations .and. nfreeboundaryiterations.lt.mfreeits ) goto 9000 ! removed Lfindzero check; Loizu Dec 18; if( Lfreebound.eq.1 .and. First_free_bound ) goto 9000 ! going back to normal free_boundary calculation; Zhu 20190701; - !-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-! +!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-! - ! FREE-BOUNDARY ITERATIONS HAVE FINISHED; +! FREE-BOUNDARY ITERATIONS HAVE FINISHED; - !-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-! +!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-! end subroutine spec @@ -770,7 +770,7 @@ end subroutine spec subroutine final_diagnostics use inputlist, only: nPtrj, nPpts, Igeometry, Lcheck, Nvol, odetol, & - Isurf, Ivolume, mu, Wmacros, Ltransform + Isurf, Ivolume, mu, Wmacros, Ltransform, Lsvdiota use fileunits, only: ounit use constants, only: zero use allglobal, only: pi2, myid, ncpu, MPI_COMM_SPEC, cpus, Mvol, Ntz, mn, & @@ -838,6 +838,8 @@ subroutine final_diagnostics ! Evaluate rotational transform and straight field line coordinate transformation if( Ltransform ) then + FATAL(xspech, Lsvdiota.ne.1, Lsvdiota needs to be one for s.f.l transformation) + do vvol=1,Mvol call brcast(vvol) enddo @@ -870,13 +872,14 @@ subroutine final_diagnostics ! Computes the surface current at each interface for output SALLOCATE( Bt00, (1:Mvol, 0:1, -1:2) , zero) - + do vvol = 1, Mvol LREGION(vvol) do iocons = 0, 1 - if( ( Lcoordinatesingularity .and. iocons.eq.0 ) .or. ( Lvacuumregion .and. iocons.eq.1 ) ) cycle + if( Lcoordinatesingularity .and. iocons.eq.0 ) cycle + if( vvol.eq.Nvol+1 .and. iocons.eq.1 ) cycle ! Compute covariant magnetic field at interface call lbpol(vvol, Bt00(1:Mvol, 0:1, -1:2), 0, iocons) From 9d56d7b81fdd1f8fc6fe38ca5ce79754ef27574d Mon Sep 17 00:00:00 2001 From: ErolBa Date: Thu, 13 Apr 2023 11:31:22 +0200 Subject: [PATCH 06/36] hessian file should be visible --- src/dforce.f90 | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/dforce.f90 b/src/dforce.f90 index 0983fa07..a722cd48 100644 --- a/src/dforce.f90 +++ b/src/dforce.f90 @@ -947,7 +947,7 @@ subroutine dforce( NGdof, position, force, LComputeDerivatives, LComputeAxis) if(Lhessianallocated) then if( myid.eq.0 ) then ; cput = GETTIME ; write(ounit,'("hesian : ",f10.2," : LHmatrix="L2" ;")')cput-cpus, LHmatrix ; write(*,*) "Writing .hessian file..." - open(munit, file="."//trim(ext)//".hessian", status="unknown", form="unformatted") + open(munit, file=trim(ext)//".sp.hessian", status="unknown", form="unformatted") write(munit) NGdof write(munit) hessian(1:NGdof,1:NGdof) close(munit) From e0cb4f48396d48a030f7188aaa28727f62d058ef Mon Sep 17 00:00:00 2001 From: ErolBa Date: Mon, 17 Apr 2023 16:22:29 +0200 Subject: [PATCH 07/36] Fixed bug in dforce --- .gitignore | 6 ++++++ src/dforce.f90 | 5 +++++ src/dfp100.f90 | 2 +- 3 files changed, 12 insertions(+), 1 deletion(-) diff --git a/.gitignore b/.gitignore index c0c569eb..ead53c9a 100644 --- a/.gitignore +++ b/.gitignore @@ -57,3 +57,9 @@ _skbuild/ # Temp fortran files src/mxspech.f90 src/msphdf5.f90 + +# vscode files +.vscode/ + +# conda files +etc/conda/ diff --git a/src/dforce.f90 b/src/dforce.f90 index a722cd48..29300651 100644 --- a/src/dforce.f90 +++ b/src/dforce.f90 @@ -264,6 +264,11 @@ subroutine dforce( NGdof, position, force, LComputeDerivatives, LComputeAxis) ! one step Newton's method dpflux(2:Mvol) = dpflux(2:Mvol) - dpfluxout(1:Mvol-1) + + if(Igeometry.eq.1) then + dpflux(1) = dpflux(1) - dpfluxout(Mvol) + endif + if( Lfreebound.eq.1 ) then dtflux(Mvol) = dtflux(Mvol ) - dpfluxout(Mvol ) endif diff --git a/src/dfp100.f90 b/src/dfp100.f90 index 7ff1310e..b0a0132a 100644 --- a/src/dfp100.f90 +++ b/src/dfp100.f90 @@ -217,7 +217,7 @@ subroutine dfp100(Ndofgl, x, Fvec, LComputeDerivatives) ! non-zero for asymmetric profiles Fvec(Mvol) = sum(dpflux(1:Mvol)) - total_pflux endif - + ! Compute poloidal linking current constraint as well in case of free boundary computation if ( Lfreebound.eq.1 ) then From fcc6bdb8183fd0243df566dbac2fbfb559e078d8 Mon Sep 17 00:00:00 2001 From: ErolBa Date: Mon, 17 Apr 2023 17:36:12 +0200 Subject: [PATCH 08/36] Do not need the .DF file --- src/dfp100.f90 | 2 +- src/newton.f90 | 20 ++++++++++---------- 2 files changed, 11 insertions(+), 11 deletions(-) diff --git a/src/dfp100.f90 b/src/dfp100.f90 index b0a0132a..388e21d6 100644 --- a/src/dfp100.f90 +++ b/src/dfp100.f90 @@ -217,7 +217,7 @@ subroutine dfp100(Ndofgl, x, Fvec, LComputeDerivatives) ! non-zero for asymmetric profiles Fvec(Mvol) = sum(dpflux(1:Mvol)) - total_pflux endif - + ! Compute poloidal linking current constraint as well in case of free boundary computation if ( Lfreebound.eq.1 ) then diff --git a/src/newton.f90 b/src/newton.f90 index 7bd26216..7c5a62f6 100644 --- a/src/newton.f90 +++ b/src/newton.f90 @@ -333,20 +333,20 @@ subroutine writereadgf( readorwrite, NGdof , ireadhessian ) case( 'W' ) ! will write derivative matrix to file; - ! reset I/O state - ios = 0 + !! reset I/O state + !ios = 0 - open( dunit, file="."//trim(ext)//".sp.DF", status="replace", form="unformatted", iostat=ios ) ! save derivative matrix to file; - FATAL( newton, ios.ne.0, error opening derivative matrix file ) + !open( dunit, file="."//trim(ext)//".sp.DF", status="replace", form="unformatted", iostat=ios ) ! save derivative matrix to file; + !FATAL( newton, ios.ne.0, error opening derivative matrix file ) - write( dunit, iostat=ios ) Igeometry, Istellsym, Lfreebound, Nvol, Mpol, Ntor, NGdof ! enable resolution consistency check; - FATAL( newton, ios.ne.0, error writing Nvol, Mpol, Ntor, NGdof ) + !write( dunit, iostat=ios ) Igeometry, Istellsym, Lfreebound, Nvol, Mpol, Ntor, NGdof ! enable resolution consistency check; + !FATAL( newton, ios.ne.0, error writing Nvol, Mpol, Ntor, NGdof ) - write( dunit, iostat=ios ) hessian(1:NGdof,1:NGdof) - FATAL( newton, ios.ne.0, error writing hessian to file ) + !write( dunit, iostat=ios ) hessian(1:NGdof,1:NGdof) + !FATAL( newton, ios.ne.0, error writing hessian to file ) - close( dunit, iostat=ios ) - FATAL( newton, ios.ne.0, error closing derivative matrix file ) + !close( dunit, iostat=ios ) + !FATAL( newton, ios.ne.0, error closing derivative matrix file ) case( 'R' ) From 93827fce9e992ea9f910e490ba3b17c553a85f5d Mon Sep 17 00:00:00 2001 From: ErolBa Date: Tue, 21 Nov 2023 17:18:15 +0100 Subject: [PATCH 09/36] updates to beta --- src/dforce.f90 | 47 ++++++++++++++++++++++++++++++++++++++++++++--- src/global.f90 | 1 + src/newton.f90 | 3 ++- src/pp00ab.f90 | 8 +++++--- src/sphdf5.f90 | 22 ++++++++++++++++++---- src/volume.f90 | 7 ++++++- src/xspech.f90 | 6 +++--- 7 files changed, 79 insertions(+), 15 deletions(-) diff --git a/src/dforce.f90 b/src/dforce.f90 index 29300651..39e9a94c 100644 --- a/src/dforce.f90 +++ b/src/dforce.f90 @@ -105,7 +105,7 @@ subroutine dforce( NGdof, position, force, LComputeDerivatives, LComputeAxis) Lconstraint, Lcheck, dRZ, & Lextrap, & mupftol, & - Lfreebound, LHmatrix + Lfreebound, LHmatrix, gamma, pscale, adiabatic, rpol, rtor use fileunits, only : ounit, hunit, munit ! added by Erol @@ -136,7 +136,8 @@ subroutine dforce( NGdof, position, force, LComputeDerivatives, LComputeAxis) LocalConstraint, xoffset, & solution, IPdtdPf, & IsMyVolume, IsMyVolumeValue, WhichCpuID, & - ext ! For outputing Lcheck = 6 test + ext, vvolume, & ! For outputing Lcheck = 6 test + BetaTotal !-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-! @@ -166,6 +167,9 @@ subroutine dforce( NGdof, position, force, LComputeDerivatives, LComputeAxis) LOGICAL :: LComputeAxis, dfp100_logical + REAL :: press, voltotal + REAL :: betavol(1:Mvol) + #ifdef DEBUG INTEGER :: isymdiff REAL :: dvol(-1:+1), evolume, imupf(1:2,-2:2), lfactor @@ -437,8 +441,45 @@ subroutine dforce( NGdof, position, force, LComputeDerivatives, LComputeAxis) lBBintegral(1:Nvol) = lBBintegral(1:Nvol) * half + ! write(*,*) "lBBintegral" + ! write(*,*) lBBintegral(1:Nvol) + + ! vflag = 1 ! this flag instructs volume to continue even if the volume is invalid; + ! WCALL( dforce, volume, ( vvol, vflag ) ) ! compute volume; this corrupts calculation of dvolume; + + voltotal = 0.0 + + do vvol = 1, Mvol + WCALL(dforce, IsMyVolume, (vvol)) + if( IsMyVolumeValue .EQ. 0 ) then + cycle + else if( IsMyVolumeValue .EQ. -1) then + FATAL(dforce, .true., Unassociated volume) + endif + + vvolume(vvol) = vvolume(vvol) + + press = adiabatic(vvol) * pscale / vvolume(vvol)**gamma + + betavol(vvol) = press * vvolume(vvol) / lBBintegral(vvol) + betavol(vvol) = betavol(vvol) * vvolume(vvol) + ! write(*,*) "vvol", vvol, "lBBintegral", lBBintegral(vvol), "volume", vvolume(vvol), "press", press + ! write(*,*) "vvol", vvol, "beta", betavol(vvol) / vvolume(vvol) + + voltotal = voltotal+vvolume(vvol) + + enddo + + + ! Calculate total beta which is obtained from individual betas + ! write(*,*) "all betas", betavol(1:Nvol) + BetaTotal = sum(betavol(1:Nvol))/voltotal + ! write(*,*) "Total BETA ", BetaTotal + ! write(*,*)"total vol", voltotal + Energy = sum( lBBintegral(1:Nvol) ) ! should also compute beta; + ! write(*,*)"total Energy", Energy !-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-! ! --------------- @@ -990,7 +1031,7 @@ subroutine fndiff_dforce( NGdof ) iRbc, iZbs, iRbs, iZbc, & LGdof, psifactor, dBdX, & YESstellsym, NOTstellsym, & - hessian, ext + hessian, ext, vvolume LOCALS diff --git a/src/global.f90 b/src/global.f90 index 6d05d3f1..68704f02 100644 --- a/src/global.f90 +++ b/src/global.f90 @@ -250,6 +250,7 @@ module allglobal REAL :: ForceErr !< total force-imbalance REAL :: Energy !< MHD energy + REAL :: BetaTotal=0.0 !< Beta, averaged over entire domain REAL , allocatable :: IPDt(:), IPDtDpf(:,:) !< Toroidal pressure-driven current diff --git a/src/newton.f90 b/src/newton.f90 index 7c5a62f6..f50dbb0e 100644 --- a/src/newton.f90 +++ b/src/newton.f90 @@ -97,7 +97,8 @@ subroutine newton( NGdof, position, ihybrd ) INTEGER :: ML, MU ! required for only Lc05ndf; - LOGICAL :: Lexit = .true. ! perhaps this could be made user input; + ! LOGICAL :: Lexit = .true. ! perhaps this could be made user input; + LOGICAL :: Lexit = .false. ! Erol modification, so hessian is printed even w/ initial force balance LOGICAL :: LComputeAxis INTEGER :: nprint = 1, nfev, njev diff --git a/src/pp00ab.f90 b/src/pp00ab.f90 index a4963797..c4547952 100644 --- a/src/pp00ab.f90 +++ b/src/pp00ab.f90 @@ -33,7 +33,7 @@ subroutine pp00ab( lvol, sti, Nz, nPpts, poincaredata, fittedtransform, utflag ) !-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-! - use constants, only : zero, one, two, pi2 + use constants, only : zero, one, two, pi2, pi use numerical, only : small @@ -115,12 +115,14 @@ subroutine pp00ab( lvol, sti, Nz, nPpts, poincaredata, fittedtransform, utflag ) !-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-! + + do kk = 0, Nz-1 ! loop over toroidal Poincare cross sections; !-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-! - stz(1:3) = (/ ppt(2), mod(ppt(1),pi2), zst /) ! toroidal coordinates; - + + if( abs(stz(1)).gt.one ) then ; ; utflag = 0 ; exit ! exit do kk loop; 22 Apr 13; ! 28 Feb 17; endif diff --git a/src/sphdf5.f90 b/src/sphdf5.f90 index 5f4d144f..051e25f4 100644 --- a/src/sphdf5.f90 +++ b/src/sphdf5.f90 @@ -45,6 +45,7 @@ module sphdf5 integer(hid_t) :: dt_nDcalls_id !< Memory datatype identifier (for "nDcalls" dataset in "/iterations") integer(hid_t) :: dt_Energy_id !< Memory datatype identifier (for "Energy" dataset in "/iterations") integer(hid_t) :: dt_ForceErr_id !< Memory datatype identifier (for "ForceErr" dataset in "/iterations") + integer(hid_t) :: dt_BetaTotal_id !< Memory datatype identifier (for "ForceErr" dataset in "/iterations") integer(hid_t) :: dt_iRbc_id !< Memory datatype identifier (for "iRbc" dataset in "/iterations") integer(hid_t) :: dt_iZbs_id !< Memory datatype identifier (for "iZbs" dataset in "/iterations") integer(hid_t) :: dt_iRbs_id !< Memory datatype identifier (for "iRbs" dataset in "/iterations") @@ -458,7 +459,13 @@ subroutine init_convergence_output H5CALL( sphdf5, h5tinsert_f, (iteration_dtype_id, "Energy", offset, H5T_NATIVE_DOUBLE, hdfier) ) ! insert "Energy" field in datatype offset = offset + type_size_d ! increment offset by size of field H5CALL( sphdf5, h5tinsert_f, (iteration_dtype_id, "ForceErr", offset, H5T_NATIVE_DOUBLE, hdfier) ) ! insert "ForceErr" field in datatype - offset = offset + type_size_d ! increment offset by size of field + offset = offset + type_size_d + write(*,*) "GOT HERE YEA" + ! Erol addition + ! H5CALL( sphdf5, h5tinsert_f, (iteration_dtype_id, "BetaTotal", offset, H5T_NATIVE_DOUBLE, hdfier) ) ! insert "ForceErr" field in datatype + ! offset = offset + type_size_d + write(*,*) "GOT HERE YEA22" + ! increment offset by size of field H5CALL( sphdf5, h5tinsert_f, (iteration_dtype_id, "iRbc", offset, iRZbscArray_id, hdfier) ) ! insert "iRbc" field in datatype offset = offset + irbc_size ! increment offset by size of field H5CALL( sphdf5, h5tinsert_f, (iteration_dtype_id, "iZbs", offset, iRZbscArray_id, hdfier) ) ! insert "iZbs" field in datatype @@ -480,6 +487,7 @@ subroutine init_convergence_output H5CALL( sphdf5, h5tcreate_f, (H5T_COMPOUND_F, type_size_i, dt_nDcalls_id, hdfier) ) H5CALL( sphdf5, h5tcreate_f, (H5T_COMPOUND_F, type_size_d, dt_Energy_id, hdfier) ) H5CALL( sphdf5, h5tcreate_f, (H5T_COMPOUND_F, type_size_d, dt_ForceErr_id, hdfier) ) + H5CALL( sphdf5, h5tcreate_f, (H5T_COMPOUND_F, type_size_d, dt_BetaTotal_id, hdfier) ) H5CALL( sphdf5, h5tcreate_f, (H5T_COMPOUND_F, irbc_size, dt_iRbc_id, hdfier) ) H5CALL( sphdf5, h5tcreate_f, (H5T_COMPOUND_F, irbc_size, dt_iZbs_id, hdfier) ) H5CALL( sphdf5, h5tcreate_f, (H5T_COMPOUND_F, irbc_size, dt_iRbs_id, hdfier) ) @@ -488,6 +496,7 @@ subroutine init_convergence_output H5CALL( sphdf5, h5tinsert_f, (dt_nDcalls_id, "nDcalls", offset, H5T_NATIVE_INTEGER, hdfier) ) H5CALL( sphdf5, h5tinsert_f, (dt_Energy_id, "Energy", offset, H5T_NATIVE_DOUBLE, hdfier) ) H5CALL( sphdf5, h5tinsert_f, (dt_ForceErr_id, "ForceErr", offset, H5T_NATIVE_DOUBLE, hdfier) ) + H5CALL( sphdf5, h5tinsert_f, (dt_BetaTotal_id, "BetaTotal", offset, H5T_NATIVE_DOUBLE, hdfier) ) H5CALL( sphdf5, h5tinsert_f, (dt_iRbc_id, "iRbc", offset, iRZbscArray_id, hdfier) ) H5CALL( sphdf5, h5tinsert_f, (dt_iZbs_id, "iZbs", offset, iRZbscArray_id, hdfier) ) H5CALL( sphdf5, h5tinsert_f, (dt_iRbs_id, "iRbs", offset, iRZbscArray_id, hdfier) ) @@ -511,7 +520,7 @@ end subroutine init_convergence_output !> subroutine write_convergence_output( nDcalls, ForceErr ) - use allglobal, only : myid, mn, Mvol, Energy, iRbc, iZbs, iRbs, iZbc + use allglobal, only : myid, mn, Mvol, Energy, iRbc, iZbs, iRbs, iZbc, BetaTotal LOCALS INTEGER, intent(in) :: nDcalls @@ -545,6 +554,8 @@ subroutine write_convergence_output( nDcalls, ForceErr ) & mem_space_id=memspace, file_space_id=dataspace, xfer_prp=plist_id), __FILE__, __LINE__) H5CALL( sphdf5, h5dwrite_f, (iteration_dset_id, dt_ForceErr_id, ForceErr, INT((/1/), HSIZE_T), hdfier, & & mem_space_id=memspace, file_space_id=dataspace, xfer_prp=plist_id), __FILE__, __LINE__) + H5CALL( sphdf5, h5dwrite_f, (iteration_dset_id, dt_BetaTotal_id, BetaTotal, INT((/1/), HSIZE_T), hdfier, & + & mem_space_id=memspace, file_space_id=dataspace, xfer_prp=plist_id), __FILE__, __LINE__) H5CALL( sphdf5, h5dwrite_f, (iteration_dset_id, dt_iRbc_id, iRbc, INT((/mn,Mvol+1/), HSIZE_T), hdfier, & & mem_space_id=memspace, file_space_id=dataspace, xfer_prp=plist_id), __FILE__, __LINE__) H5CALL( sphdf5, h5dwrite_f, (iteration_dset_id, dt_iZbs_id, iZbs, INT((/mn,Mvol+1/), HSIZE_T), hdfier, & @@ -982,7 +993,7 @@ subroutine hdfint use fileunits, only : ounit use inputlist use allglobal, only : ncpu, cpus, & - Mvol, ForceErr, & + Mvol, ForceErr, BetaTotal, & mn, im, in, iRbc, iZbs, iRbs, iZbc, & mns, ims, ins, & dRbc, dZbs, dRbs, dZbc, & @@ -1046,12 +1057,14 @@ subroutine hdfint ! HWRITERV( grpOutput, 1, forcetol, (/ forcetol /)) ! already in /input/global !latex \type{ForceErr} & real & \pb{force-balance error across interfaces} \\ HWRITERV( grpOutput, 1, ForceErr, (/ ForceErr /)) +!latex \type{ForceErr} & real & \pb{force-balance error across interfaces} \\ + HWRITERV( grpOutput, 1, BetaTotal, (/ BetaTotal /)) !latex \type{Ivolume} & real & \pb{Volume current at output (parallel, externally induced)} HWRITERV( grpOutput, Mvol, Ivolume, Ivolume(1:Mvol)) !latex \type{IPDt} & real & \pb{Surface current at output} HWRITERV( grpOutput, Mvol, IPDt, IPDt(1:Mvol)) - ! the following quantites can be different from input value + ! the following quantites can be diffeerent from input value HWRITERV( grpOutput, Mvol, adiabatic , adiabatic(1:Nvol) ) HWRITERV( grpOutput, Nvol, helicity , helicity(1:Nvol) ) HWRITERV( grpOutput, Mvol, mu , mu(1:Mvol) ) @@ -1150,6 +1163,7 @@ subroutine finish_outfile H5CALL( sphdf5, h5tclose_f, (dt_nDcalls_id, hdfier) , __FILE__, __LINE__) H5CALL( sphdf5, h5tclose_f, (dt_Energy_id, hdfier) , __FILE__, __LINE__) H5CALL( sphdf5, h5tclose_f, (dt_ForceErr_id, hdfier) , __FILE__, __LINE__) + H5CALL( sphdf5, h5tclose_f, (dt_BetaTotal_id, hdfier) , __FILE__, __LINE__) H5CALL( sphdf5, h5tclose_f, (dt_iRbc_id, hdfier) , __FILE__, __LINE__) H5CALL( sphdf5, h5tclose_f, (dt_iZbs_id, hdfier) , __FILE__, __LINE__) H5CALL( sphdf5, h5tclose_f, (dt_iRbs_id, hdfier) , __FILE__, __LINE__) diff --git a/src/volume.f90 b/src/volume.f90 index 76581dd1..bced63df 100644 --- a/src/volume.f90 +++ b/src/volume.f90 @@ -41,7 +41,7 @@ subroutine volume( lvol, vflag ) use fileunits, only : ounit - use inputlist, only : Wvolume, Igeometry, Nvol, pscale + use inputlist, only : Wvolume, Igeometry, Nvol, pscale, rpol, rtor use cputiming @@ -120,6 +120,9 @@ subroutine volume( lvol, vflag ) if( dBdX%issym.eq.0 ) dvolume = one ! note that the sign factor for the lower interface is included below; 20 Jun 14; endif + ! Erol -- potential fix + vol(innout) = vol(innout) * rpol * rtor + !-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-! case( 2 ) !>
  • \c Igeometry.eq.2 : cylindrical : \f$\sqrt g = R R_s = \frac{1}{2}\partial_s (R^2)\f$ @@ -331,6 +334,8 @@ subroutine volume( lvol, vflag ) write(ounit,'("volume : ",f10.2," : myid=",i3," ; Igeometry=",i2," ; vvolume(",i3," ) =",es23.15" ;")') cput-cpus, myid, Igeometry, lvol, vvolume(lvol) endif + ! write(*,*)"lvol ", lvol, "volume", vvolume(lvol) + !-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-! FATAL( volume, vflag.eq.0 .and. vvolume(lvol).lt.small, volume cannot be zero or negative ) ! 15 Jan 13; diff --git a/src/xspech.f90 b/src/xspech.f90 index 1bb7b694..ca426f35 100644 --- a/src/xspech.f90 +++ b/src/xspech.f90 @@ -100,13 +100,13 @@ subroutine xspech ! initialize internal arrays based on data from input file call preset() - + ! initialize HDF5 library and open output file ext.h5 for writing during execution call init_outfile() - + ! mirror input file contents to output file call mirror_input_to_outfile() - + !-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-! if ( myid .eq. 0 ) then ! save restart file; From db4e7b03448d3f58820da0bf9f7543bc47014d02 Mon Sep 17 00:00:00 2001 From: ErolBa Date: Mon, 27 Nov 2023 17:09:53 +0100 Subject: [PATCH 10/36] allow more volumes --- src/global.f90 | 42 +++++++++++++++++++++--------------------- src/inputlist.f90 | 2 +- 2 files changed, 22 insertions(+), 22 deletions(-) diff --git a/src/global.f90 b/src/global.f90 index 68704f02..d8aab129 100644 --- a/src/global.f90 +++ b/src/global.f90 @@ -1647,28 +1647,28 @@ subroutine wrtend write(iunit,'(" Nvol = ",i9 )') Nvol write(iunit,'(" Mpol = ",i9 )') Mpol write(iunit,'(" Ntor = ",i9 )') Ntor - write(iunit,'(" Lrad = ",257i23 )') Lrad(1:Mvol) - write(iunit,'(" tflux = ",257es23.15)') tflux(1:Mvol) - write(iunit,'(" pflux = ",257es23.15)') pflux(1:Mvol) - write(iunit,'(" helicity = ",256es23.15)') helicity(1:Mvol) + write(iunit,'(" Lrad = ",1025i23 )') Lrad(1:Mvol) + write(iunit,'(" tflux = ",1025es23.15)') tflux(1:Mvol) + write(iunit,'(" pflux = ",1025es23.15)') pflux(1:Mvol) + write(iunit,'(" helicity = ",1025es23.15)') helicity(1:Mvol) write(iunit,'(" pscale = ",es23.15 )') pscale write(iunit,'(" Ladiabatic = ",i9 )') Ladiabatic - write(iunit,'(" pressure = ",257es23.15)') pressure(1:Mvol) - write(iunit,'(" adiabatic = ",257es23.15)') adiabatic(1:Mvol) - write(iunit,'(" mu = ",257es23.15)') mu(1:Mvol) - write(iunit,'(" Ivolume = ",257es23.15)') Ivolume(1:Mvol) - write(iunit,'(" Isurf = ",257es23.15)') IPDt(1:Mvol) ! EDIT by EROL !!!! + write(iunit,'(" pressure = ",1025es23.15)') pressure(1:Mvol) + write(iunit,'(" adiabatic = ",1025es23.15)') adiabatic(1:Mvol) + write(iunit,'(" mu = ",1025es23.15)') mu(1:Mvol) + write(iunit,'(" Ivolume = ",1025es23.15)') Ivolume(1:Mvol) + write(iunit,'(" Isurf = ",1025es23.15)') IPDt(1:Mvol) ! EDIT by EROL !!!! write(iunit,'(" Lconstraint = ",i9 )') Lconstraint - write(iunit,'(" pl = ",257i23 )') pl(0:Mvol) - write(iunit,'(" ql = ",257i23 )') ql(0:Mvol) - write(iunit,'(" pr = ",257i23 )') pr(0:Mvol) - write(iunit,'(" qr = ",257i23 )') qr(0:Mvol) - write(iunit,'(" iota = ",257es23.15)') iota(0:Mvol) - write(iunit,'(" lp = ",257i23 )') lp(0:Mvol) - write(iunit,'(" lq = ",257i23 )') lq(0:Mvol) - write(iunit,'(" rp = ",257i23 )') rp(0:Mvol) - write(iunit,'(" rq = ",257i23 )') rq(0:Mvol) - write(iunit,'(" oita = ",257es23.15)') oita(0:Mvol) + write(iunit,'(" pl = ",1025i23 )') pl(0:Mvol) + write(iunit,'(" ql = ",1025i23 )') ql(0:Mvol) + write(iunit,'(" pr = ",1025i23 )') pr(0:Mvol) + write(iunit,'(" qr = ",1025i23 )') qr(0:Mvol) + write(iunit,'(" iota = ",1025es23.15)') iota(0:Mvol) + write(iunit,'(" lp = ",1025i23 )') lp(0:Mvol) + write(iunit,'(" lq = ",1025i23 )') lq(0:Mvol) + write(iunit,'(" rp = ",1025i23 )') rp(0:Mvol) + write(iunit,'(" rq = ",1025i23 )') rq(0:Mvol) + write(iunit,'(" oita = ",1025es23.15)') oita(0:Mvol) write(iunit,'(" mupftol = ",es23.15 )') mupftol write(iunit,'(" mupfits = ",i9 )') mupfits write(iunit,'(" Lreflect = ",i9 )') Lreflect @@ -1854,7 +1854,7 @@ subroutine wrtend !write(iunit,'(" epsr = ",es23.15 )') epsr write(iunit,'(" nPpts = ",i9 )') nPpts write(iunit,'(" Ppts = ",es23.15 )') Ppts - write(iunit,'(" nPtrj = ",256i6 )') nPtrj(1:Mvol) + write(iunit,'(" nPtrj = ",656i6 )') nPtrj(1:Mvol) write(iunit,'(" LHevalues = ",L9 )') LHevalues write(iunit,'(" LHevectors = ",L9 )') LHevectors write(iunit,'(" LHmatrix = ",L9 )') LHmatrix @@ -1884,7 +1884,7 @@ subroutine wrtend #endif ! write initial guess of interface geometry - do imn = 1, mn ; write(iunit,'(2i6,1024es23.15)') im(imn), in(imn)/Nfp, ( iRbc(imn,vvol), iZbs(imn,vvol), iRbs(imn,vvol), iZbc(imn,vvol), vvol = 1, Nvol ) + do imn = 1, mn ; write(iunit,'(2i6,20000es23.15)') im(imn), in(imn)/Nfp, ( iRbc(imn,vvol), iZbs(imn,vvol), iRbs(imn,vvol), iZbc(imn,vvol), vvol = 1, Nvol ) enddo close(iunit) diff --git a/src/inputlist.f90 b/src/inputlist.f90 index 30c0b04b..505f3490 100644 --- a/src/inputlist.f90 +++ b/src/inputlist.f90 @@ -9,7 +9,7 @@ module inputlist implicit none ! The following parameters set the maximum allowed resolution: - INTEGER, parameter :: MNvol = 256 !< The maximum value of \c Nvol is \c MNvol=256. + INTEGER, parameter :: MNvol = 1024 !< The maximum value of \c Nvol is \c MNvol=256. INTEGER, parameter :: MMpol = 128 !< The maximum value of \c Mpol is \c MNpol=64. INTEGER, parameter :: MNtor = 128 !< The maximum value of \c Ntor is \c MNtor=64. From 91dc66a4191bcc4a5c6b9fccbaa4f526f6265cf3 Mon Sep 17 00:00:00 2001 From: ErolBa Date: Mon, 19 Feb 2024 18:17:56 +0100 Subject: [PATCH 11/36] change --- src/sphdf5.f90 | 2 -- 1 file changed, 2 deletions(-) diff --git a/src/sphdf5.f90 b/src/sphdf5.f90 index 051e25f4..643b07a1 100644 --- a/src/sphdf5.f90 +++ b/src/sphdf5.f90 @@ -460,11 +460,9 @@ subroutine init_convergence_output offset = offset + type_size_d ! increment offset by size of field H5CALL( sphdf5, h5tinsert_f, (iteration_dtype_id, "ForceErr", offset, H5T_NATIVE_DOUBLE, hdfier) ) ! insert "ForceErr" field in datatype offset = offset + type_size_d - write(*,*) "GOT HERE YEA" ! Erol addition ! H5CALL( sphdf5, h5tinsert_f, (iteration_dtype_id, "BetaTotal", offset, H5T_NATIVE_DOUBLE, hdfier) ) ! insert "ForceErr" field in datatype ! offset = offset + type_size_d - write(*,*) "GOT HERE YEA22" ! increment offset by size of field H5CALL( sphdf5, h5tinsert_f, (iteration_dtype_id, "iRbc", offset, iRZbscArray_id, hdfier) ) ! insert "iRbc" field in datatype offset = offset + irbc_size ! increment offset by size of field From 3c08d8fd06113ef7b99267f327581c28065bc1ac Mon Sep 17 00:00:00 2001 From: ErolBa Date: Fri, 8 Mar 2024 11:46:07 +0100 Subject: [PATCH 12/36] out stability metrics to h5 file --- src/hesian.f90 | 23 ++++++++++++++++------- src/sphdf5.f90 | 26 ++++++++++++++++++++++++++ 2 files changed, 42 insertions(+), 7 deletions(-) diff --git a/src/hesian.f90 b/src/hesian.f90 index d4fb9e33..be587da6 100644 --- a/src/hesian.f90 +++ b/src/hesian.f90 @@ -37,7 +37,9 @@ subroutine hesian( NGdof, position, Mvol, mn, LGdof ) Lhessian3Dallocated,denergydrr, denergydrz,denergydzr,denergydzz, & LocalConstraint -!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-! + use sphdf5, only : write_stability + + !-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-! LOCALS @@ -418,12 +420,12 @@ subroutine hesian( NGdof, position, Mvol, mn, LGdof ) if( LHmatrix ) then - if( myid.eq.0 ) then ; cput = GETTIME ; write(ounit,'("hesian : ",f10.2," : LHmatrix="L2" ;")')cput-cpus, LHmatrix ; - open(munit, file="."//trim(ext)//".GF.ma", status="unknown", form="unformatted") - write(munit) NGdof - write(munit) ohessian(1:NGdof,1:NGdof) - close(munit) - endif + if( myid.eq.0 ) then ; cput = GETTIME ; write(ounit,'("hesian : ",f10.2," : LHmatrix="L2" ;")')cput-cpus, LHmatrix ; + open(munit, file="."//trim(ext)//".GF.ma", status="unknown", form="unformatted") + write(munit) NGdof + write(munit) ohessian(1:NGdof,1:NGdof) + close(munit) + endif endif @@ -517,6 +519,10 @@ subroutine hesian( NGdof, position, Mvol, mn, LGdof ) enddo enddo + ! do ii = 1, mn ; write(ounit,*) 'psifact', ii, psifactor(ii,Mvol-1) + ! enddo + + !-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-! if( myid.eq.0 ) then ! screen output; 04 Dec 14; @@ -585,6 +591,9 @@ subroutine hesian( NGdof, position, Mvol, mn, LGdof ) endif ! end of if( ( LHevalues .or. LHevectors ) ) + ! output hessian, eigenvalues, and eigenvectors to the .h5 file + WCALL( hesian, write_stability, (ohessian, evalr, evali, evecr, NGdof) ) + !-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-! if( myid.eq.0 .and. Lperturbed.eq.1 ) then diff --git a/src/sphdf5.f90 b/src/sphdf5.f90 index 643b07a1..c54ee78a 100644 --- a/src/sphdf5.f90 +++ b/src/sphdf5.f90 @@ -986,6 +986,32 @@ end subroutine write_vector_potential !> \brief Write the final state of the equilibrium to the output file. !> \ingroup grp_output !> + +subroutine write_stability(ohessian, evalr, evali, evecr, NGdof) + + LOCALS + integer, intent(in) :: NGdof + REAL, intent(in) :: ohessian(:,:), evalr(:), evali(:), evecr(:,:) + integer(hid_t) :: grpStability + + BEGIN( sphdf5 ) + + if (myid.eq.0 .and. .not.skip_write) then + + HDEFGRP( file_id, stability, grpStability) + + HWRITERA( grpStability, NGdof, NGdof, ohessian, ohessian(1:NGdof,1:NGdof) ) + HWRITERA( grpStability, NGdof, NGdof, evecr, evecr(1:NGdof,1:NGdof) ) + HWRITERV( grpStability, NGdof, evalr, evalr(1:NGdof) ) + HWRITERV( grpStability, NGdof, evali, evali(1:NGdof) ) + + HCLOSEGRP( grpStability ) + + endif ! myid.eq.0 + +end subroutine write_stability + + subroutine hdfint use fileunits, only : ounit From 7bc2c202bc25fd58dba3b85a1bea3b6e5a8e523b Mon Sep 17 00:00:00 2001 From: ErolBa Date: Fri, 8 Mar 2024 12:00:02 +0100 Subject: [PATCH 13/36] change --- src/bfield.f90 | 3 --- 1 file changed, 3 deletions(-) diff --git a/src/bfield.f90 b/src/bfield.f90 index 5c2daa8c..b83b580b 100644 --- a/src/bfield.f90 +++ b/src/bfield.f90 @@ -167,9 +167,6 @@ subroutine bfield( zeta, st, Bst ) cput-cpus, lvol, zeta, st(1:2), dBu(3) FATAL( bfield, abs(dBu(3)).lt.vsmall, field is not toroidal ) - !if( abs( dBu(3)).lt.vsmall ) then - ! write(ounit,'("WARNING: bfield: field is not toroidal")') - !endif endif !-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-! From 42a4748b20e4c9e24138d7f43cdca7d82dd0538b Mon Sep 17 00:00:00 2001 From: ErolBa Date: Fri, 8 Mar 2024 12:00:47 +0100 Subject: [PATCH 14/36] change2 --- src/bfield.f90 | 1 + 1 file changed, 1 insertion(+) diff --git a/src/bfield.f90 b/src/bfield.f90 index b83b580b..9b811b90 100644 --- a/src/bfield.f90 +++ b/src/bfield.f90 @@ -167,6 +167,7 @@ subroutine bfield( zeta, st, Bst ) cput-cpus, lvol, zeta, st(1:2), dBu(3) FATAL( bfield, abs(dBu(3)).lt.vsmall, field is not toroidal ) + endif !-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-! From 5c2e6694af8aca9552ddf3d7efdaf6da9f1af432 Mon Sep 17 00:00:00 2001 From: ErolBa Date: Fri, 8 Mar 2024 12:01:19 +0100 Subject: [PATCH 15/36] change2 --- src/bfield.f90 | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/bfield.f90 b/src/bfield.f90 index 9b811b90..101ab3ce 100644 --- a/src/bfield.f90 +++ b/src/bfield.f90 @@ -167,7 +167,7 @@ subroutine bfield( zeta, st, Bst ) cput-cpus, lvol, zeta, st(1:2), dBu(3) FATAL( bfield, abs(dBu(3)).lt.vsmall, field is not toroidal ) - + endif !-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-! From f45ca557faca87525c78967aeb1c69b3eb1efde0 Mon Sep 17 00:00:00 2001 From: ErolBa Date: Fri, 8 Mar 2024 12:01:50 +0100 Subject: [PATCH 16/36] change3 --- src/bfield.f90 | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/bfield.f90 b/src/bfield.f90 index 101ab3ce..f0d000a5 100644 --- a/src/bfield.f90 +++ b/src/bfield.f90 @@ -167,7 +167,7 @@ subroutine bfield( zeta, st, Bst ) cput-cpus, lvol, zeta, st(1:2), dBu(3) FATAL( bfield, abs(dBu(3)).lt.vsmall, field is not toroidal ) - + endif !-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-! From f3b9b821abd5cc63c9537fafb7b7fe5b79c3e2af Mon Sep 17 00:00:00 2001 From: ErolBa Date: Fri, 8 Mar 2024 12:19:15 +0100 Subject: [PATCH 17/36] Mostly formatting --- .gitignore | 3 --- Utilities/pythontools/requirements.txt | 1 - src/dforce.f90 | 10 ++++------ src/global.f90 | 6 +++--- src/pp00ab.f90 | 6 ++---- src/preset.f90 | 5 +++-- src/volume.f90 | 4 +--- src/xspech.f90 | 6 +++--- 8 files changed, 16 insertions(+), 25 deletions(-) diff --git a/.gitignore b/.gitignore index ead53c9a..b20cfee5 100644 --- a/.gitignore +++ b/.gitignore @@ -60,6 +60,3 @@ src/msphdf5.f90 # vscode files .vscode/ - -# conda files -etc/conda/ diff --git a/Utilities/pythontools/requirements.txt b/Utilities/pythontools/requirements.txt index be8bb1d3..c8362d66 100644 --- a/Utilities/pythontools/requirements.txt +++ b/Utilities/pythontools/requirements.txt @@ -2,5 +2,4 @@ h5py matplotlib f90nml numpy -scipy coilpy diff --git a/src/dforce.f90 b/src/dforce.f90 index 39e9a94c..bac4aca1 100644 --- a/src/dforce.f90 +++ b/src/dforce.f90 @@ -98,16 +98,14 @@ subroutine dforce( NGdof, position, force, LComputeDerivatives, LComputeAxis) use numerical, only : logtolerance - use fileunits, only : ounit + use fileunits, only : ounit, munit use inputlist, only : Wmacros, Wdforce, Nvol, Ntor, Lrad, Igeometry, & epsilon, & Lconstraint, Lcheck, dRZ, & Lextrap, & mupftol, & - Lfreebound, LHmatrix, gamma, pscale, adiabatic, rpol, rtor - - use fileunits, only : ounit, hunit, munit ! added by Erol + Lfreebound, LHmatrix, gamma, pscale, adiabatic use cputiming, only : Tdforce @@ -136,8 +134,8 @@ subroutine dforce( NGdof, position, force, LComputeDerivatives, LComputeAxis) LocalConstraint, xoffset, & solution, IPdtdPf, & IsMyVolume, IsMyVolumeValue, WhichCpuID, & - ext, vvolume, & ! For outputing Lcheck = 6 test - BetaTotal + ext, & ! For outputing Lcheck = 6 test + BetaTotal, vvolume !-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-! diff --git a/src/global.f90 b/src/global.f90 index d8aab129..2ba83c8a 100644 --- a/src/global.f90 +++ b/src/global.f90 @@ -66,7 +66,7 @@ module constants REAL, parameter :: mu0 = 2.0E-07 * pi2 !< \f$4\pi\cdot10^{-7}\f$ REAL, parameter :: goldenmean = 1.618033988749895 !< golden mean = \f$( 1 + \sqrt 5 ) / 2\f$ ; - REAL, parameter :: version = 3.21 !< version of SPEC + REAL, parameter :: version = 3.20 !< version of SPEC end module constants @@ -250,13 +250,13 @@ module allglobal REAL :: ForceErr !< total force-imbalance REAL :: Energy !< MHD energy - REAL :: BetaTotal=0.0 !< Beta, averaged over entire domain + REAL :: BetaTotal = 0.0 !< Beta, averaged over entire domain REAL , allocatable :: IPDt(:), IPDtDpf(:,:) !< Toroidal pressure-driven current INTEGER :: Mvol - REAL :: total_pflux ! total pflux, used in Lconstraint=3, Igeometry=1 -- Edit by Erol + REAL :: total_pflux ! used when Lconstraint=3, Igeometry=1 LOGICAL :: YESstellsym !< internal shorthand copies of Istellsym, which is an integer input; LOGICAL :: NOTstellsym !< internal shorthand copies of Istellsym, which is an integer input; diff --git a/src/pp00ab.f90 b/src/pp00ab.f90 index c4547952..805b07c7 100644 --- a/src/pp00ab.f90 +++ b/src/pp00ab.f90 @@ -33,7 +33,7 @@ subroutine pp00ab( lvol, sti, Nz, nPpts, poincaredata, fittedtransform, utflag ) !-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-! - use constants, only : zero, one, two, pi2, pi + use constants, only : zero, one, two, pi2 use numerical, only : small @@ -115,13 +115,11 @@ subroutine pp00ab( lvol, sti, Nz, nPpts, poincaredata, fittedtransform, utflag ) !-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-! - - do kk = 0, Nz-1 ! loop over toroidal Poincare cross sections; !-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-! - stz(1:3) = (/ ppt(2), mod(ppt(1),pi2), zst /) ! toroidal coordinates; + stz(1:3) = (/ ppt(2), mod(ppt(1),pi2), zst /) ! toroidal coordinates; if( abs(stz(1)).gt.one ) then ; ; utflag = 0 ; exit ! exit do kk loop; 22 Apr 13; ! 28 Feb 17; diff --git a/src/preset.f90 b/src/preset.f90 index 37ab4b75..02e4c86e 100644 --- a/src/preset.f90 +++ b/src/preset.f90 @@ -508,13 +508,14 @@ subroutine preset SALLOCATE( dtflux, (1:Mvol), zero ) SALLOCATE( dpflux, (1:Mvol), zero ) + ! with Igeom=1, Lcons=3, need to provide total pflux if(Lconstraint.eq.3 .and. Igeometry.eq.1) then total_pflux = pflux(Mvol) * phiedge / pi2 pflux(Mvol) = 0 endif select case( Igeometry ) - case( 1 ) ; dtflux(1) = tflux(1) ; dpflux(1) = pflux(1) ! Edit by Erol -- Cartesian ; this is the "inverse" operation defined in xspech; 09 Mar 17; + case( 1 ) ; dtflux(1) = tflux(1) ; dpflux(1) = pflux(1) ! Cartesian ; this is the "inverse" operation defined in xspech; 09 Mar 17; case( 2:3 ) ; dtflux(1) = tflux(1) ; dpflux(1) = zero ! cylindrical or toroidal; end select @@ -813,7 +814,7 @@ subroutine preset SALLOCATE( IPDtDpf, (1:Mvol , 1:Mvol ), zero) else if(Igeometry.eq.1) then - ! add an additional constraint to make the total pflux = 0 -- Edit Erol + ! add an additional constraint to make the total pflux = 0 SALLOCATE( IPDtDpf, (1:Mvol, 1:Mvol), zero) else SALLOCATE( IPDtDpf, (1:Mvol-1, 1:Mvol-1), zero) diff --git a/src/volume.f90 b/src/volume.f90 index bced63df..5ee2e635 100644 --- a/src/volume.f90 +++ b/src/volume.f90 @@ -120,7 +120,7 @@ subroutine volume( lvol, vflag ) if( dBdX%issym.eq.0 ) dvolume = one ! note that the sign factor for the lower interface is included below; 20 Jun 14; endif - ! Erol -- potential fix + ! respecting rpol, rtor sizes of slab vol(innout) = vol(innout) * rpol * rtor !-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-! @@ -334,8 +334,6 @@ subroutine volume( lvol, vflag ) write(ounit,'("volume : ",f10.2," : myid=",i3," ; Igeometry=",i2," ; vvolume(",i3," ) =",es23.15" ;")') cput-cpus, myid, Igeometry, lvol, vvolume(lvol) endif - ! write(*,*)"lvol ", lvol, "volume", vvolume(lvol) - !-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-! FATAL( volume, vflag.eq.0 .and. vvolume(lvol).lt.small, volume cannot be zero or negative ) ! 15 Jan 13; diff --git a/src/xspech.f90 b/src/xspech.f90 index ca426f35..1bb7b694 100644 --- a/src/xspech.f90 +++ b/src/xspech.f90 @@ -100,13 +100,13 @@ subroutine xspech ! initialize internal arrays based on data from input file call preset() - + ! initialize HDF5 library and open output file ext.h5 for writing during execution call init_outfile() - + ! mirror input file contents to output file call mirror_input_to_outfile() - + !-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-! if ( myid .eq. 0 ) then ! save restart file; From e1e15aecb2e1f7f8f08c2c53fc90f0e675efe0f2 Mon Sep 17 00:00:00 2001 From: ErolBa Date: Fri, 8 Mar 2024 12:25:33 +0100 Subject: [PATCH 18/36] Formatting ... --- src/dforce.f90 | 5 ++--- src/dfp100.f90 | 2 +- src/pp00ab.f90 | 6 +++--- 3 files changed, 6 insertions(+), 7 deletions(-) diff --git a/src/dforce.f90 b/src/dforce.f90 index bac4aca1..287c96fe 100644 --- a/src/dforce.f90 +++ b/src/dforce.f90 @@ -243,7 +243,7 @@ subroutine dforce( NGdof, position, force, LComputeDerivatives, LComputeAxis) ! Mvol-1 surface current plus 1 poloidal linking current constraints Ndofgl = Mvol else - ! add an additional constraint to make the total pflux = 0 -- Edit Erol + ! add an additional constraint to make the total pflux = 0 if(Igeometry.eq.1) then Ndofgl = Mvol else @@ -319,7 +319,7 @@ subroutine dforce( NGdof, position, force, LComputeDerivatives, LComputeAxis) enddo ! end of do vvol = 1, Mvol - !add an additional constraint to make the total pflux = 0 -- Edit Erol + !add an additional constraint to make the total pflux 0 if(Igeometry.eq.1) then vvol = 1 @@ -985,7 +985,6 @@ subroutine dforce( NGdof, position, force, LComputeDerivatives, LComputeAxis) !-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-! - !add by Erol !if(LcomputeDerivatives .and. Lhessianallocated .and. Igeometry .eq. 1) then !if(Lhessianallocated .and. Igeometry .eq. 1) then if(Lhessianallocated) then diff --git a/src/dfp100.f90 b/src/dfp100.f90 index 388e21d6..2abd1b8a 100644 --- a/src/dfp100.f90 +++ b/src/dfp100.f90 @@ -205,7 +205,7 @@ subroutine dfp100(Ndofgl, x, Fvec, LComputeDerivatives) Fvec(1:Mvol-1) = IPDt(1:Mvol-1) - Isurf(1:Mvol-1) endif - ! Edit by Erol to set total pflux to 0 + ! Set the total pflux to 0 if(Igeometry.eq.1) then IPDtDpf(1,Mvol) = -pi2 * Bt00(1,1,2) diff --git a/src/pp00ab.f90 b/src/pp00ab.f90 index 805b07c7..a4963797 100644 --- a/src/pp00ab.f90 +++ b/src/pp00ab.f90 @@ -118,9 +118,9 @@ subroutine pp00ab( lvol, sti, Nz, nPpts, poincaredata, fittedtransform, utflag ) do kk = 0, Nz-1 ! loop over toroidal Poincare cross sections; !-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-! - - stz(1:3) = (/ ppt(2), mod(ppt(1),pi2), zst /) ! toroidal coordinates; - + + stz(1:3) = (/ ppt(2), mod(ppt(1),pi2), zst /) ! toroidal coordinates; + if( abs(stz(1)).gt.one ) then ; ; utflag = 0 ; exit ! exit do kk loop; 22 Apr 13; ! 28 Feb 17; endif From 8d5ab5d7e17e29666f2ae09b9dd30000c43c0b7f Mon Sep 17 00:00:00 2001 From: Erol Balkovic Date: Mon, 11 Mar 2024 10:23:42 +0100 Subject: [PATCH 19/36] better printing of stability items --- src/dforce.f90 | 27 +++++++++------------ src/hesian.f90 | 64 ++++++++++++++++++++++++-------------------------- src/sphdf5.f90 | 28 +++++++++++++++------- 3 files changed, 62 insertions(+), 57 deletions(-) diff --git a/src/dforce.f90 b/src/dforce.f90 index 287c96fe..b1ef069b 100644 --- a/src/dforce.f90 +++ b/src/dforce.f90 @@ -987,22 +987,17 @@ subroutine dforce( NGdof, position, force, LComputeDerivatives, LComputeAxis) !if(LcomputeDerivatives .and. Lhessianallocated .and. Igeometry .eq. 1) then !if(Lhessianallocated .and. Igeometry .eq. 1) then - if(Lhessianallocated) then - if( myid.eq.0 ) then ; cput = GETTIME ; write(ounit,'("hesian : ",f10.2," : LHmatrix="L2" ;")')cput-cpus, LHmatrix ; - write(*,*) "Writing .hessian file..." - open(munit, file=trim(ext)//".sp.hessian", status="unknown", form="unformatted") - write(munit) NGdof - write(munit) hessian(1:NGdof,1:NGdof) - close(munit) - - write(*,*) 'Writing hessian from dforce' - - ! do ii=1,NGdof - ! write(*,*)ii, hessian(ii,1:NGdof) - ! enddo - - endif - endif + + ! if(Lhessianallocated) then + ! if( myid.eq.0 ) then ; cput = GETTIME ; write(ounit,'("hesian : ",f10.2," : LHmatrix="L2" ;")')cput-cpus, LHmatrix ; + ! write(*,*) "Writing .hessian file..." + ! open(munit, file=trim(ext)//".sp.hessian", status="unknown", form="unformatted") + ! write(munit) NGdof + ! write(munit) hessian(1:NGdof,1:NGdof) + ! close(munit) + + ! endif + ! endif RETURN(dforce) diff --git a/src/hesian.f90 b/src/hesian.f90 index be587da6..68f7f5fa 100644 --- a/src/hesian.f90 +++ b/src/hesian.f90 @@ -54,7 +54,7 @@ subroutine hesian( NGdof, position, Mvol, mn, LGdof ) INTEGER :: vvol, idof, ii, mi, ni, irz, issym, isymdiff, lvol, ieval(1:1), igdof, ifd REAL :: oldEnergy(-2:2), error, cpul - + REAL :: oldBB(1:Mvol,-2:2), oBBdRZ(1:Mvol,0:1,1:LGdof), ohessian(1:NGdof,1:NGdof) REAL :: oRbc(1:mn,0:Mvol), oZbs(1:mn,0:Mvol), oRbs(1:mn,0:Mvol), oZbc(1:mn,0:Mvol), determinant @@ -102,7 +102,6 @@ subroutine hesian( NGdof, position, Mvol, mn, LGdof ) !-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-! - #ifdef MINIMIZE oldBB(1:Mvol,0) = lBBintegral(1:Mvol) @@ -228,18 +227,17 @@ subroutine hesian( NGdof, position, Mvol, mn, LGdof ) SALLOCATE( hessian2D, (1:NGdof,1:NGdof), zero ) SALLOCATE( dessian2D, (1:NGdof,1:LGdof), zero ) ! part of hessian that depends on boundary variations; 18 Dec 14; - !if (LHmatrix) then + ! if (LHmatrix) then Lhessian3Dallocated = .true. - !else - ! Lhessianallocated = .true. - !endif + ! else + ! Lhessianallocated = .true. + ! endif !This step cleared. LComputeDerivatives = .true. !; position(0) = zero ! this is not used; 11 Aug 14; LComputeAxis = .false. WCALL( hesian, dforce, ( NGdof, position(0:NGdof), force(0:NGdof), LComputeDerivatives, LComputeAxis) ) ! calculate force-imbalance & hessian; - ohessian(1:NGdof,1:NGdof) = hessian2D(1:NGdof,1:NGdof) ! internal copy; 22 Apr 15; @@ -418,16 +416,15 @@ subroutine hesian( NGdof, position, Mvol, mn, LGdof ) !-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-! - if( LHmatrix ) then - - if( myid.eq.0 ) then ; cput = GETTIME ; write(ounit,'("hesian : ",f10.2," : LHmatrix="L2" ;")')cput-cpus, LHmatrix ; - open(munit, file="."//trim(ext)//".GF.ma", status="unknown", form="unformatted") - write(munit) NGdof - write(munit) ohessian(1:NGdof,1:NGdof) - close(munit) - endif - - endif + ! write the .ma file + ! if( LHmatrix ) then + ! if( myid.eq.0 ) then ; cput = GETTIME ; write(ounit,'("hesian : ",f10.2," : LHmatrix="L2" ;")')cput-cpus, LHmatrix ; + ! open(munit, file="."//trim(ext)//".GF.ma", status="unknown", form="unformatted") + ! write(munit) NGdof + ! write(munit) ohessian(1:NGdof,1:NGdof) + ! close(munit) + ! endif + ! endif ! if( myid.eq.0 .and. ( LHevalues .or. LHevectors ) ) then ! the call to dforce below requires all cpus; 04 Dec 14; @@ -455,10 +452,11 @@ subroutine hesian( NGdof, position, Mvol, mn, LGdof ) !#else ! FATAL( global, .true., eigenvalue solver needs updating to F08NAF ) !#endif + call dgeev('N', JOB, NGdof, hessian2D(1:LDA,1:NGdof), LDA, evalr(1:NGdof), evali(1:NGdof), & - evecl(1:Ldvr,1:NGdof), Ldvr, revecr(1:Ldvr,1:2*NGdof), Ldvr, work(1:Lwork), Lwork, if02ebf ) - evecr(1:Ldvr,1:NGdof) = revecr(1:Ldvr,1:NGdof) - eveci(1:Ldvr,1:NGdof) = revecr(1:Ldvr,NGdof+1:2*NGdof) + evecl(1:Ldvr,1:NGdof), Ldvr, revecr(1:Ldvr,1:2*NGdof), Ldvr, work(1:Lwork), Lwork, if02ebf ) + evecr(1:Ldvr,1:NGdof) = revecr(1:Ldvr,1:NGdof) + eveci(1:Ldvr,1:NGdof) = revecr(1:Ldvr,NGdof+1:2*NGdof) if( myid.eq.0 ) then cput = GETTIME @@ -578,22 +576,23 @@ subroutine hesian( NGdof, position, Mvol, mn, LGdof ) !-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-! - - if( myid.eq.0 ) then ! write to file; 04 Dec 14; - open(hunit, file="."//trim(ext)//".GF.ev", status="unknown", form="unformatted") - write(hunit) NGdof, Ldvr, Ldvi - write(hunit) evalr - write(hunit) evali - write(hunit) evecr - write(hunit) eveci - close(hunit) - endif ! end of if( myid.eq.0 ) ; 04 Dec 14; + ! write eigvals and eigvecs to .ev file + ! if( myid.eq.0 ) then ! write to file; 04 Dec 14; + ! open(hunit, file="."//trim(ext)//".GF.ev", status="unknown", form="unformatted") + ! write(hunit) NGdof, Ldvr, Ldvi + ! write(hunit) evalr + ! write(hunit) evali + ! write(hunit) evecr + ! write(hunit) eveci + ! close(hunit) + ! endif ! end of if( myid.eq.0 ) ; 04 Dec 14; endif ! end of if( ( LHevalues .or. LHevectors ) ) ! output hessian, eigenvalues, and eigenvectors to the .h5 file - WCALL( hesian, write_stability, (ohessian, evalr, evali, evecr, NGdof) ) - + if( LHmatrix ) then + WCALL( hesian, write_stability, (ohessian, evalr, evali, evecr, NGdof) ) + endif !-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-! if( myid.eq.0 .and. Lperturbed.eq.1 ) then @@ -704,7 +703,6 @@ subroutine hesian( NGdof, position, Mvol, mn, LGdof ) DALLOCATE(hessian2D) - write(ounit,*) 5656 DALLOCATE(dessian2D) diff --git a/src/sphdf5.f90 b/src/sphdf5.f90 index c54ee78a..8b4a8ba9 100644 --- a/src/sphdf5.f90 +++ b/src/sphdf5.f90 @@ -989,6 +989,8 @@ end subroutine write_vector_potential subroutine write_stability(ohessian, evalr, evali, evecr, NGdof) + use inputlist, only : LHevalues, LHevectors, LHmatrix + LOCALS integer, intent(in) :: NGdof REAL, intent(in) :: ohessian(:,:), evalr(:), evali(:), evecr(:,:) @@ -996,18 +998,28 @@ subroutine write_stability(ohessian, evalr, evali, evecr, NGdof) BEGIN( sphdf5 ) - if (myid.eq.0 .and. .not.skip_write) then + if (.not.LHevalues .and. .not.LHevectors .and. .not.LHmatrix) return - HDEFGRP( file_id, stability, grpStability) + if (myid.eq.0 .and. .not.skip_write) then - HWRITERA( grpStability, NGdof, NGdof, ohessian, ohessian(1:NGdof,1:NGdof) ) - HWRITERA( grpStability, NGdof, NGdof, evecr, evecr(1:NGdof,1:NGdof) ) - HWRITERV( grpStability, NGdof, evalr, evalr(1:NGdof) ) - HWRITERV( grpStability, NGdof, evali, evali(1:NGdof) ) + HDEFGRP( file_id, stability, grpStability) - HCLOSEGRP( grpStability ) + if (LHmatrix) then + HWRITERA( grpStability, NGdof, NGdof, ohessian, ohessian(1:NGdof,1:NGdof) ) + endif + + if (LHevectors) then + HWRITERA( grpStability, NGdof, NGdof, evecr, evecr(1:NGdof,1:NGdof) ) + endif - endif ! myid.eq.0 + if (LHevalues) then + HWRITERV( grpStability, NGdof, evalr, evalr(1:NGdof) ) + HWRITERV( grpStability, NGdof, evali, evali(1:NGdof) ) + endif + + HCLOSEGRP( grpStability ) + + endif ! myid.eq.0 end subroutine write_stability From 9f76ee11d997cccd4809ecf2c141fc076d2cd3a4 Mon Sep 17 00:00:00 2001 From: ErolBa Date: Mon, 11 Mar 2024 12:27:15 +0100 Subject: [PATCH 20/36] Catching up to main --- Utilities/BoozerXForms/README.md | 6 + Utilities/BoozerXForms/Tutorial1.txt | 33 + Utilities/BoozerXForms/init_from_spec.py | 269 +++ Utilities/BoozerXForms/run_boz.py | 121 ++ Utilities/BoozerXForms/testBmn.py | 100 + .../matlabtools/SPEC_Namelist/SPEC_Namelist.m | 1760 +++++++++++++++++ .../SPEC_Namelist/nm_tutorial_001.md | 146 ++ .../SPEC_Namelist/rw_namelist/license.txt | 24 + .../SPEC_Namelist/rw_namelist/read_namelist.m | 340 ++++ .../rw_namelist/write_namelist.m | 100 + Utilities/matlabtools/Tutorial.01.txt | 4 +- Utilities/matlabtools/Tutorial.02.txt | 2 +- Utilities/matlabtools/compare_spec_outputs.m | 26 +- Utilities/matlabtools/contra2cov.m | 108 +- Utilities/matlabtools/extract_shear.m | 39 + Utilities/matlabtools/get_SFL_fourier_modB.m | 82 + .../matlabtools/get_boozer_coordinates.m | 43 + Utilities/matlabtools/get_boozer_modB.m | 45 + Utilities/matlabtools/get_metric_QA.m | 27 + Utilities/matlabtools/get_metric_QH.m | 36 + Utilities/matlabtools/get_spec_Bxyz.m | 104 + .../matlabtools/get_spec_R_derivatives.m | 130 +- Utilities/matlabtools/get_spec_area.m | 11 +- Utilities/matlabtools/get_spec_beta.m | 6 +- Utilities/matlabtools/get_spec_energy_slab.m | 75 +- Utilities/matlabtools/get_spec_fractaldim.m | 401 ++++ .../matlabtools/get_spec_helicity_slab.m | 97 +- Utilities/matlabtools/get_spec_jacobian.m | 31 +- Utilities/matlabtools/get_spec_magfield.m | 4 - Utilities/matlabtools/get_spec_metric.m | 98 +- .../matlabtools/get_spec_metric_contrav.m | 85 +- Utilities/matlabtools/get_spec_modB.m | 18 +- Utilities/matlabtools/get_spec_polflux.m | 32 +- .../matlabtools/get_spec_polynomial_basis.m | 186 +- .../get_spec_regularisation_factor.m | 90 + .../get_spec_straight_fieldlines.m | 37 + .../matlabtools/get_spec_torcurr_kam_net.m | 13 +- Utilities/matlabtools/get_spec_torflux.m | 55 +- Utilities/matlabtools/get_spec_vecpot.m | 117 +- Utilities/matlabtools/get_spec_volume.m | 32 +- .../matlabtools/get_spec_volume_current.m | 52 +- Utilities/matlabtools/plot_SFL_modB.m | 53 + .../matlabtools/plot_SFL_modB_boundary.m | 104 + .../matlabtools/plot_boozer_fieldlines.m | 72 + Utilities/matlabtools/plot_boozer_modB.m | 53 + .../matlabtools/plot_boozer_modB_boundary.m | 123 ++ Utilities/matlabtools/plot_spec_Bgrid.m | 216 +- Utilities/matlabtools/plot_spec_Ivolume.m | 43 +- Utilities/matlabtools/plot_spec_boundary.m | 97 + .../matlabtools/plot_spec_current_profile.m | 133 ++ Utilities/matlabtools/plot_spec_fieldlines.m | 86 + Utilities/matlabtools/plot_spec_fluxfun.m | 70 + Utilities/matlabtools/plot_spec_grid.m | 11 +- Utilities/matlabtools/plot_spec_iota.m | 334 ++-- Utilities/matlabtools/plot_spec_iotakam.m | 119 +- Utilities/matlabtools/plot_spec_iterations.m | 138 ++ Utilities/matlabtools/plot_spec_jacobian.m | 121 +- Utilities/matlabtools/plot_spec_kam.m | 200 +- Utilities/matlabtools/plot_spec_modB.m | 159 +- .../matlabtools/plot_spec_modB_boundary.m | 132 +- Utilities/matlabtools/plot_spec_poincare.m | 149 +- Utilities/matlabtools/plot_spec_poincare_3d.m | 174 ++ Utilities/matlabtools/plot_spec_polflux.m | 69 +- Utilities/matlabtools/plot_spec_pressure.m | 59 +- .../matlabtools/plot_spec_surface_current.m | 56 + Utilities/matlabtools/plot_spec_torflux.m | 68 +- Utilities/matlabtools/plot_spec_wall.m | 91 +- Utilities/matlabtools/produce_spec_movie.m | 1 + Utilities/matlabtools/read_boozer.m | 36 + Utilities/matlabtools/read_spec.m | 2 +- Utilities/matlabtools/scan_shear_auto_optim.m | 253 +++ Utilities/matlabtools/write_spec_rzgrid.m | 3 +- Utilities/pythontools/py_spec/__init__.py | 4 +- .../py_spec/input/spec_namelist.py | 168 +- .../pythontools/py_spec/math/spec_fft.py | 192 ++ .../pythontools/py_spec/math/spec_invfft.py | 89 + .../pythontools/py_spec/output/_plot_iota.py | 2 +- .../py_spec/output/_plot_poincare.py | 2 +- .../pythontools/py_spec/output/_processing.py | 414 +++- Utilities/pythontools/py_spec/output/spec.py | 15 +- Utilities/pythontools/py_spec/tests/README.md | 4 + .../py_spec/tests/test_math/test_spec_fft.py | 99 + Utilities/pythontools/requirements.txt | 4 + Utilities/pythontools/setup.py | 2 +- src/dforce.f90 | 13 +- src/hesian.f90 | 4 +- src/newton.f90 | 5 +- src/xspech.f90 | 4 +- 88 files changed, 7902 insertions(+), 1329 deletions(-) create mode 100644 Utilities/BoozerXForms/README.md create mode 100644 Utilities/BoozerXForms/Tutorial1.txt create mode 100644 Utilities/BoozerXForms/init_from_spec.py create mode 100644 Utilities/BoozerXForms/run_boz.py create mode 100644 Utilities/BoozerXForms/testBmn.py create mode 100644 Utilities/matlabtools/SPEC_Namelist/SPEC_Namelist.m create mode 100644 Utilities/matlabtools/SPEC_Namelist/nm_tutorial_001.md create mode 100644 Utilities/matlabtools/SPEC_Namelist/rw_namelist/license.txt create mode 100755 Utilities/matlabtools/SPEC_Namelist/rw_namelist/read_namelist.m create mode 100755 Utilities/matlabtools/SPEC_Namelist/rw_namelist/write_namelist.m create mode 100644 Utilities/matlabtools/extract_shear.m create mode 100644 Utilities/matlabtools/get_SFL_fourier_modB.m create mode 100644 Utilities/matlabtools/get_boozer_coordinates.m create mode 100644 Utilities/matlabtools/get_boozer_modB.m create mode 100644 Utilities/matlabtools/get_metric_QA.m create mode 100644 Utilities/matlabtools/get_metric_QH.m create mode 100644 Utilities/matlabtools/get_spec_Bxyz.m create mode 100644 Utilities/matlabtools/get_spec_fractaldim.m create mode 100644 Utilities/matlabtools/get_spec_regularisation_factor.m create mode 100644 Utilities/matlabtools/get_spec_straight_fieldlines.m create mode 100644 Utilities/matlabtools/plot_SFL_modB.m create mode 100644 Utilities/matlabtools/plot_SFL_modB_boundary.m create mode 100644 Utilities/matlabtools/plot_boozer_fieldlines.m create mode 100644 Utilities/matlabtools/plot_boozer_modB.m create mode 100644 Utilities/matlabtools/plot_boozer_modB_boundary.m create mode 100644 Utilities/matlabtools/plot_spec_boundary.m create mode 100644 Utilities/matlabtools/plot_spec_current_profile.m create mode 100644 Utilities/matlabtools/plot_spec_fieldlines.m create mode 100644 Utilities/matlabtools/plot_spec_fluxfun.m create mode 100644 Utilities/matlabtools/plot_spec_iterations.m create mode 100644 Utilities/matlabtools/plot_spec_poincare_3d.m create mode 100644 Utilities/matlabtools/plot_spec_surface_current.m create mode 100644 Utilities/matlabtools/read_boozer.m create mode 100644 Utilities/matlabtools/scan_shear_auto_optim.m create mode 100644 Utilities/pythontools/py_spec/math/spec_fft.py create mode 100644 Utilities/pythontools/py_spec/math/spec_invfft.py create mode 100644 Utilities/pythontools/py_spec/tests/README.md create mode 100644 Utilities/pythontools/py_spec/tests/test_math/test_spec_fft.py diff --git a/Utilities/BoozerXForms/README.md b/Utilities/BoozerXForms/README.md new file mode 100644 index 00000000..234c0592 --- /dev/null +++ b/Utilities/BoozerXForms/README.md @@ -0,0 +1,6 @@ +# BoozerXForms +Python routines to achieve Boozer coordinates transformation from SPEC output +Useful e.g to plot modB + +For any questions or mistake spotted, contact me at +salomon.guinchard@epfl.ch diff --git a/Utilities/BoozerXForms/Tutorial1.txt b/Utilities/BoozerXForms/Tutorial1.txt new file mode 100644 index 00000000..926325cc --- /dev/null +++ b/Utilities/BoozerXForms/Tutorial1.txt @@ -0,0 +1,33 @@ +This is a basic tutorial on how to use the Booz-xform package (M.Landreman) from SPECout file, using routines init_from_spec.py and run_boz.py + +0. Make sure you have the booz-xforms package installed. If not, can be installed with + $ pip install booz-xform (or see doc at https://hiddensymmetries.github.io/booz_xform/) + +0b. Requires additional packages: py_spec, numpy and h5py + +1. Load function to initialise a booz-xforms instance out of a SPEC output (.h5) with + > from init_from_spec import init_from_spec + +2. Call init_from_spec function with test file QA_002.sp.h5 + > b = init_from_spec('QA_002.sp.h5') + +3. Call internal run method as follows + > b.run() + +4. The output data sets can be written in .h5 file running all the commands from run_boz.py + > f = h5.File('./OutputBOZ/'+ bozout, 'w') + > print(f.filename) + > grp = f.create_group('Booz_xForms') + > ... + > ... + > outputs.create_dataset('boozer_i_all', data = b.Boozer_I_all) + > f.close() + +5. Plot the magnetic field intensity in Boozer coordinates + > plt.figure + > bx.surfplot(b, js=0, fill=False, cmap=plt.cm.jet, ntheta=50, nphi=90, ncontours=25) + > plt.savefig('QA002.eps') + > plt.show() + +6. If major issue can't be solved / code mistake + contact: S.Guinchard - salomon.guinchard@epfl.ch diff --git a/Utilities/BoozerXForms/init_from_spec.py b/Utilities/BoozerXForms/init_from_spec.py new file mode 100644 index 00000000..3a4ef542 --- /dev/null +++ b/Utilities/BoozerXForms/init_from_spec.py @@ -0,0 +1,269 @@ +#!/usr/bin/env python3 +# -*- coding: utf-8 -*- +""" +Created on Mon May 9 17:51:56 2022 +This file initialises a booz x form instance +without changing the SPEC output file +@authors: A.Baillod, S.Guinchard +""" + +import py_spec as sp +import booz_xform as bx +import numpy as np + +###################################################### +############### EXTRACT ALL SPECOUT DATA ############# +###################################################### + + +def init_from_spec( filename ): + d = sp.SPECout( filename ) + + compute_surfs = np.array([0]) + verbose = 1 + asym = False #False if stellarator symmetric + nfp = d.input.physics.Nfp + mpol = d.input.physics.Mpol+1 + ntor = d.input.physics.Ntor + nvol = d.input.physics.Nvol + mpol_nyq = mpol + ntor_nyq = ntor + mnmax = ntor +1 + (mpol-1) *(2*ntor +1) + mnmax_nyq = ntor_nyq+1 + (mpol_nyq-1)*(2*ntor_nyq+1) + xm = d.output.im + xn = d.output.in_ + xm_nyq = xm + xn_nyq = xn + ns_in = int(2*nvol-1) + s_in = np.ndarray(ns_in, dtype = np.float64) + s_in[0] = d.output.tflux; + iota = np.array([d.output.lambdamn[1][0][0]]) + rmnc = np.array([list(d.output.Rbc[1,:])]).transpose() + rmns = np.array([]) + zmnc = np.array([]) + zmns = np.array([list(d.output.Zbs[1,:])]).transpose() + + # build lmns + lambdamn = d.output.lambdamn[1][:].transpose() + xms = d.output.ims + xns = d.output.ins + mns = d.output.mns + lmns = np.zeros([mnmax,ns_in]) + lmnc = np.array([]) + + for ii in range (0,mns): + mm = xms[ii] + nn = xns[ii] + + if mm==0 and nn==0: #mode (0,0) is zero + continue + if mm>mpol-1 or mm<0: + continue + if nn<-ntor*nfp or nn>ntor*nfp: + continue + + for jj in range(0,mnmax): + if mm==xm[jj] and nn==xn[jj]: + lmns[jj] = lambdamn[ii] + continue + + + bsubumnc = np.array([list(d.output.Btemn[1,:])]).transpose() + bsubvmnc = np.array([list(d.output.Bzemn[1,:])]).transpose() + bsubumns = np.array([]) + bsubvmns = np.array([]) + mboz = np.max(xm) + nboz = int(1/nfp * np.max(xn)) + aspect = np.nan + toroidal_flux = d.input.physics.phiedge + + # modB computation + Nt = d.grid.Nt + Nz = d.grid.Nz + sarr = np.linspace(0,1,2) + tarr = np.linspace(0,2*np.pi,Nt) + zarr = np.linspace(0,2*np.pi/nfp,Nz) + + Bcontrav = d.get_B(lvol = 0, sarr = sarr, tarr = tarr, zarr = zarr) + [R, Z, jac, g] = d.get_grid_and_jacobian_and_metric(lvol = 0, sarr = sarr, tarr= tarr, zarr = zarr) + + modB = d.get_modB(Bcontrav, g) + modBsurf = modB[1][:][:] + modBcos = np.zeros(np.shape(modBsurf)) + K = 2*np.pi**2/nfp + Bmn_ = np.zeros((mpol,2*ntor+1)) + + for m in range (0,mpol): + for n in range (-ntor,ntor+1): + if m == 0 and n<0: + continue + for line in range (0,Nt): + for column in range (0,Nz): + modBcos[line,column] = modBsurf[line][column]* np.cos(np.double(m)*tarr[line] - np.double(n)*np.double(nfp)*zarr[column]) + + tmp = np.trapz(modBcos, x = tarr, axis = 0) + Bmn_[m,n+ntor] = 1/K*np.trapz(tmp, x=zarr) + + + Bmn_[0,ntor] = 1/2*Bmn_[0,ntor] + + + Bmnc = np.zeros((mnmax,ns_in)) + jj = 0 #index of surface + for ii in range(0,mnmax): + m = xm[ii] + n = int(xn[ii] / nfp) + Bmnc[ii,jj] = Bmn_[m,n+ntor] + + Bmns = np.array([]) + + + ########################################################## + # Initialisation of a Booz_xform instance b # + ########################################################## + + b = bx.Booz_xform() + + if ns_in<1: + raise ValueError('ns has to be larger than zero') + + if nfp<1: + raise ValueError('Nfp has to be larger than zero') + + if iota.size!=ns_in: + raise ValueError('Iota has not the size ns_in') + + if xm.size!=mnmax: + raise ValueError('xm has not the size mnmax') + if xn.size!=mnmax: + raise ValueError('xn has not the size mnmax') + if xm_nyq.size!=mnmax_nyq: + raise ValueError('xm_nyq has not the size mnmax') + if xn_nyq.size!=mnmax_nyq: + raise ValueError('xn_nyq has not the size mnmax') + + if xm[0]!=0: + raise ValueError('xm first element is not right') + if xn[0]!=0: + raise ValueError('xn first element is not right') + if xm_nyq[0]!=0: + raise ValueError('xm_nyq first element is not right') + if xn_nyq[0]!=0: + raise ValueError('xn_nyq first element is not right') + + if xm[-1]!=mpol-1: + raise ValueError('xm last element is not right') + if xn[-1]!=nfp*ntor: + raise ValueError('xn last element is not right') + if xm_nyq[-1]!=mpol_nyq-1: + raise ValueError('xm_nyq last element is not right') + if xn_nyq[-1]!=nfp*ntor_nyq: + raise ValueError('xn_nyq last element is not right') + + if rmnc.shape[0]!=mnmax: + raise ValueError('Rmnc should have mnmax rows') + if zmns.shape[0]!=mnmax: + raise ValueError('Zmns should have mnmax rows') + if asym: + if rmns.shape[0]!=mnmax: + raise ValueError('Rmns should have mnmax rows') + if zmnc.shape[0]!=mnmax: + raise ValueError('Zmnc should have mnmax rows') + + if rmnc.shape[1]!=ns_in: + raise ValueError('Rmnc should have ns_in columns') + if zmns.shape[1]!=ns_in: + raise ValueError('Zmns should have ns_in columns') + if asym: + if rmns.shape[1]!=ns_in: + raise ValueError('Rmns should have ns_in columns') + if zmnc.shape[1]!=ns_in: + raise ValueError('Zmnc should have ns_in columns') + + if bsubumnc.shape[0]!=mnmax: + raise ValueError('Rmnc should have mnmax rows') + if bsubvmnc.shape[0]!=mnmax: + raise ValueError('Rmns should have mnmax rows') + if asym: + if bsubumns.shape[0]!=mnmax: + raise ValueError('Zmnc should have mnmax rows') + if bsubvmns.shape[0]!=mnmax: + raise ValueError('Zmns should have mnmax rows') + + if bsubumnc.shape[1]!=ns_in: + raise ValueError('Rmnc should have ns_in columns') + if bsubvmnc.shape[1]!=ns_in: + raise ValueError('Rmns should have ns_in columns') + if asym: + if bsubumns.shape[1]!=ns_in: + raise ValueError('Zmnc should have ns_in columns') + if bsubvmns.shape[1]!=ns_in: + raise ValueError('Zmns should have ns_in columns') + + if Bmnc.shape[0]!=mnmax: + raise ValueError('Invalid number of modes for Bmnc') + if Bmnc.shape[1]!=ns_in: + raise ValueError('Invalid number of surfaces for Bmnc') + if asym: + if Bmns.shape[0]!=mnmax: + raise ValueError('Invalid number of modes for Bmns') + if Bmns.shape[1]!=ns_in: + raise ValueError('Invalid number of surfaces for Bmns') + + if lmns.shape[0]!=mnmax: + raise ValueError('Invalid number of modes for lmns') + if lmns.shape[1]!=ns_in: + raise ValueError('Invalid number of surfaces for lmns') + if asym: + if lmnc.shape[0]!=mnmax: + raise ValueError('Invalid number of modes for lmnc') + if lmnc.shape[1]!=ns_in: + raise ValueError('Invalid number of surfaces for lmnc') + + if any(compute_surfs<0): + raise ValueError('Compute_surfs should be zero or positive') + if any(compute_surfs>=ns_in): + raise ValueError('Compute_surfs should be smaller than ns_in') + + + + + + + b.verbose = verbose + b.asym = 0.0; + b.nfp = nfp + b.mpol = mpol + b.ntor = ntor + b.mnmax = mnmax + b.mpol_nyq = mpol_nyq + b.ntor_nyq = ntor_nyq + b.mnmax_nyq = mnmax_nyq + b.xn = xn + b.xm=xm + b.xm_nyq = xm_nyq + b.xn_nyq = xn_nyq + b.ns_in = ns_in + b.s_in = s_in + b.iota = iota + b.rmnc = rmnc + b.rmns = rmns + b.zmnc = zmnc + b.zmns = zmns + b.lmns = lmns + b.lmnc = lmnc + b.bmnc = Bmnc + b.bmns = Bmns + b.bsubumnc = bsubumnc + b.bsubvmnc = bsubvmnc + b.bsubumns = bsubumns + b.bsubvmns = bsubvmns + b.mboz = mboz + b.nboz = nboz + b.compute_surfs = compute_surfs + b.aspect = aspect + b.toroidal_flux = toroidal_flux + + + + return b diff --git a/Utilities/BoozerXForms/run_boz.py b/Utilities/BoozerXForms/run_boz.py new file mode 100644 index 00000000..20671fcc --- /dev/null +++ b/Utilities/BoozerXForms/run_boz.py @@ -0,0 +1,121 @@ +#!/usr/bin/env python3 +# -*- coding: utf-8 -*- +""" +Created on Mon May 9 17:50:56 2022 + +This file initialises a booz_xForms instance +and runs it before writing all outputs to +an hdf5 file. + +@author: S.Guinchard +""" + +############ +# PACKAGES # +############ + +from init_from_spec import init_from_spec +import matplotlib.pyplot as plt +import booz_xform as bx +import numpy as np +import h5py as h5 + +############## +# INIT + RUN # +############## + +file = 'Name' +filename = file + '.sp.h5' +bozout = file +'.boz.h5' +b = init_from_spec('path_to_file'+filename) +b.verbose = 2 +print("Selected surfaces:", b.compute_surfs) +b.run() + +########################## +# CREATE OUTPUT DATASETS # +########################## + +f = h5.File('path_to_Boozer_out_file'+ bozout, 'w') +print(f.filename) +grp = f.create_group('Booz_xForms') +grp.create_group('Inputs') +inputs = grp['Inputs'] +inputs['verbose'] = b.verbose +inputs['asym'] = b.asym +inputs['nfp'] = b.nfp +inputs['ntor'] = b.ntor +inputs['mpol'] = b.mpol +inputs['mnmax'] = b.mnmax +inputs['mnmax_nyq'] = b.mnmax_nyq +inputs['mpol_nyq'] = b.mpol_nyq +inputs['ntor_nyq'] = b.ntor_nyq +inputs['xn'] = b.xn +inputs['xm'] = b.xm +inputs['xn_nyq'] = b.xn_nyq +inputs['xm_nyq'] = b.xm_nyq +inputs['ns_in'] = b.ns_in +inputs['iota'] = b.iota +inputs['rmnc'] = b.rmnc +inputs['rmns'] = b.rmns +inputs['zmnc'] = b.zmnc +inputs['zmns'] = b.zmns +inputs['bmn'] = b.bmnc +inputs['bsubumnc'] = b.bsubumnc +inputs['bsubvmnc'] = b.bsubvmnc +inputs['compute_surfs'] = b.compute_surfs +inputs['aspect'] = b.aspect +inputs['toroidal_flux'] = b.toroidal_flux +inputs['mboz'] = b.mboz +inputs['nboz'] = b.nboz +inputs['lmns'] = b.lmns +inputs['lmnc'] = b.lmnc + +grp.create_group('Outputs') +outputs = grp['Outputs'] +outputs.create_dataset('ns_b', data = b.ns_b) +outputs.create_dataset('s_b', data = b.s_b) +outputs.create_dataset('mnboz', data = b.mnboz) +outputs.create_dataset('xm_b', data = b.xm_b) +outputs.create_dataset('xn_b', data = b.xn_b) +outputs.create_dataset('bmnc_b', data = b.bmnc_b) +outputs.create_dataset('bmns_b', data = b.bmns_b) +outputs.create_dataset('gmnc_b', data = b.gmnc_b) +outputs.create_dataset('gmns_b', data = b.gmns_b) +outputs.create_dataset('rmnc_b', data = b.rmnc_b) +outputs.create_dataset('zmnc_b', data = b.zmnc_b) +outputs.create_dataset('rmns_b', data = b.rmns_b) +outputs.create_dataset('zmns_b', data = b.zmns_b) +outputs.create_dataset('numnc_b', data = b.numnc_b) +outputs.create_dataset('numns_b', data = b.numns_b) +outputs.create_dataset('boozer_g', data = b.Boozer_G) +outputs.create_dataset('boozer_g_all', data = b.Boozer_G_all) +outputs.create_dataset('boozer_i', data = b.Boozer_I) +outputs.create_dataset('boozer_i_all', data = b.Boozer_I_all) + + +f.close() + + + +########### +# FIGURES # +########### + +plt.figure +bx.surfplot(b, js=0, fill=False, cmap=plt.cm.jet, ntheta=50, nphi=90, ncontours=25) +plt.savefig('Contour.eps') +plt.show() + + +plt.figure +bx.surfplot(b, js=0, cmap=plt.cm.jet, shading = 'gouraud') +plt.savefig('Filled.eps') +plt.show() + +# ANOTHER EXAMPLE +# plt.figure +# bx.surfplot(b, js=0, fill=False, cmap=plt.cm.jet, levels=np.arange(0.8, 1.3, 0.05)) +# plt.show() + + diff --git a/Utilities/BoozerXForms/testBmn.py b/Utilities/BoozerXForms/testBmn.py new file mode 100644 index 00000000..9272ce94 --- /dev/null +++ b/Utilities/BoozerXForms/testBmn.py @@ -0,0 +1,100 @@ +#!/usr/bin/env python3 +# -*- coding: utf-8 -*- +""" +Created on Mon May 9 13:32:45 2022 + +This file enables to test if the modB +Fourier modes were correctly implemented +in Python, in order to pass them as a +Booz_X_Form input + +@author: S.Guinchard +""" +import py_spec as sp +import booz_xform as bx +import numpy as np +import matplotlib.pyplot as plt +import h5py as h5 + + +d = sp.SPECout('Filename.sp.h5') + +verbose = 1 +asym = False +nfp = d.input.physics.Nfp +mpol = d.input.physics.Mpol +ntor = d.input.physics.Ntor +nvol = d.input.physics.Nvol +mnmax = d.output.mn +mpol_nyq = mpol +ntor_nyq = ntor +mnmax_nyq = mnmax +xm = d.output.im +xn = d.output.in_ +xm_nyq = xm +xn_nyq = xn +ns_in = int(2*nvol-1) +s_in = np.ndarray(ns_in, dtype = np.float64) +s_in[0] = d.output.tflux; +iota = d.transform.fiota[1][:] +rmnc = d.output.Rbc +rmns = d.output.Rbs +zmnc = d.output.Zbc +zmns = d.output.Zbs +lmns = d.output.lambdamn[1][:] + +bsubumnc = d.output.Btemn +bsubvmnc = d.output.Bzemn +mboz = np.max(xm) +nboz = int(1/nfp * np.max(xn)) +aspect = np.nan +toroidal_flux = d.input.physics.phiedge + +######## MOD B ######## + +Nt = d.grid.Nt +Nz = d.grid.Nz +sarr = np.linspace(0,1,2) +tarr = np.linspace(0,2*np.pi,Nt) +zarr = np.linspace(0,2*np.pi/nfp,Nz) + +Bcontrav = d.get_B(lvol = 0, sarr = sarr, tarr = tarr, zarr = zarr) +[R, Z, jac, g] = d.get_grid_and_jacobian_and_metric(lvol = 0, sarr = sarr, tarr= tarr, zarr = zarr) +modB = d.get_modB(Bcontrav, g) +modBsurf = modB[1][:][:] +modBcos = np.zeros(np.shape(modBsurf)) +K = 2*np.pi**2/nfp +Bmn_ = np.zeros((mpol+1,2*ntor+1)) +X,Y = np.meshgrid(tarr, zarr) + + + +for m in range (0,mpol): + for n in range (-ntor,ntor): + if m == 0 and n<0: + continue + + modBcos = modBsurf * np.cos(np.double(m)*X - np.double(n)*np.double(nfp)*Y) + tmp = np.trapz(modBcos, x=tarr, axis = 0) + Bmn_[m,n+ntor] = 1/K*np.trapz(tmp, x=zarr) + +Bmn_[0,ntor] = 1/2*Bmn_[0,ntor] + + +Bmn = np.zeros((mnmax_nyq,)) +Bmn_trunc = np.zeros((mpol,2*ntor+1)) + +for jj in range(0,mpol): + Bmn_trunc[jj][:] = Bmn_[jj+1][:] +Bmn_trunc = np.reshape(Bmn_trunc, np.size(Bmn_trunc)) + +for ii in range(-ntor,0): + Bmn[ii+ntor] = Bmn_[0][ii+2*ntor] + + +for ll in range(0,np.size(Bmn_trunc)): + Bmn[ll+ntor+1] = Bmn_trunc[ll] + + +print('Bmn_ = ', Bmn_) + diff --git a/Utilities/matlabtools/SPEC_Namelist/SPEC_Namelist.m b/Utilities/matlabtools/SPEC_Namelist/SPEC_Namelist.m new file mode 100644 index 00000000..49c1609f --- /dev/null +++ b/Utilities/matlabtools/SPEC_Namelist/SPEC_Namelist.m @@ -0,0 +1,1760 @@ +classdef SPEC_Namelist + properties (Access=public) + lists + physicslist + numericlist + locallist + globallist + diagnosticslist + screenlist + initial_guess + end + + properties (Access=private) + mpol = 0; + ntor = 0; + array_size = [0, 0]; + Mvol = 0; + nvol = 0; + verbose = true; + lboundary = 0; + + end + + methods (Access=public) + % Class constructor + function obj = SPEC_Namelist( filename, varargin ) + % + % SPEC_NAMELIST( FILENAME ) + % ========================= + % + % Class constructor of the class SPEC_Namelist. This class + % reads the SPEC input file, checks that the data is correctly + % formatted, allow some plottings and easy changes in the input + % file, and provides a routine to write SPEC input file. + % + % INPUTS + % ------ + % -FILENAME: SPEC input file (.sp) + % -VArArGIN: Any couple of input: + % - 'Liniguess': set to true to read initial guess, false + % to skip it. default: true + % + % + % OUTPUTS + % ------- + % -OBJ: An instance of the class SPEC_Namelist + % + % + + % read optional input + l = length(varargin); + if mod(l,2)~=0 + error('InputError: invalid number of inputs') + end + + opt.Liniguess = true; % Decide whether or not we read initial guess + opt.verbose = true; % Print additional warnings + for ii=1:l/2 + opt.(varargin{2*ii-1}) = varargin{2*ii}; + end + + obj.verbose = opt.verbose; + + % read input file + work = read_namelist( filename ); + obj.lists = fields(work); + for ii=1:length(obj.lists) + obj.(obj.lists{ii}) = work.(obj.lists{ii}); + end + + % Check that the size of arrays makes sense, fills with zeros + % otherwise + obj = obj.initialize_structure(); + + % Find the largest Fourier resolution used in the input file; + % reformat all spectral quantities to have the same resolution + obj = obj.set_fourier_resolution(); + + % read initial guess + if opt.Liniguess + obj = obj.read_initial_guess( filename ); + else + obj.initial_guess = struct([]); + end + + end + + function obj = read_initial_guess( obj, filename ) + % + % READ_INITIAL_GUESS( FILENAME ) + % ============================== + % + % read the initial guess from the input file filename. + % + % If the Fourier resolution of the initial guess is larger than + % the Fourier resolution of the other physical qunatities, these + % are extended with zeros. + % + % If the initial guess requires less Fourier harmonics, then it + % is extended with zeros to match the Fourier resolution of the + % other physical quantities + % + % If no initial guess are provided in filename, return an empty + % structure. + + + % First, open file and read relevant portion. We look for the + % end of the category "screenlist" and then read each line. + % Each line is then saved as a string in a structure. + fid = fopen( filename, 'r' ); + save_line = false; % This is switched to true once + % we are at the end of the screelist + category = ''; % Save the name of the category + + initial_guess_str = {}; + + while( ~feof(fid) ) % while it is not the end of the file + + tline = fgetl(fid); + tline = strtrim(tline); + + if isempty( tline ) + continue + end + + if( save_line ) % write line + initial_guess_str{end+1} = tline; + + else % otherwise look for beginning of initial guess + if( strcmp(tline, '/') ) + if( strcmp(category,'screenlist') ) + save_line = true; + end + + else + % read category + if strcmp(tline(end-3:end),'list') + category = tline(2:end); + end + + end + end + end % end of while + + fclose(fid); % Close file + + % Check if structure is empty - i.e. no initial guess is + % provided + if isempty( initial_guess_str ) + obj.initial_guess = struct([]); % generate empty structure + return + end + + % Check size. The number of elements should be 2 + 4 * Nvol. + % The first two elements are the mode numbers m and n, then we + % have Rbc, Zbs, Rbs, Zbc for each volume interface + l = length(str2num( initial_guess_str{1} )); + l = l-2; % remove m, n + if mod(l,4)~=0 + error('Invalid number of modes in initial guess') + end + + if l/4obj.nvol + error('Too many volumes in initial guess') + end + + % read format of initial guess + tmp = SPEC_Namelist( filename, 'Liniguess', false ); + + if tmp.physicslist.lboundary~=obj.physicslist.lboundary + error(['The initial guess from file %s does not use the',... + 'same boundary representation.'], filename) + end + + % Check if there is an initial guess + nlines = length(initial_guess_str); + if nlines<1 + obj.initial_guess = struct([]); % generate empty structure + return + end + + % read mpol, ntor + mpol_in = 0; ntor_in = 0; + for iline=1:nlines + % Scan line + line_data = str2num( initial_guess_str{iline} ); + + % Find corresponding index + mm = line_data(1); nn = line_data(2); + mpol_in = max([mm, mpol_in]); + ntor_in = max([abs(nn), ntor_in]); + end + + % Check if resolution is smaller or larger than inner + % resolution. This changes obj.mpol and obj.ntor if + % necessary + if (mpol_in>obj.mpol) || (ntor_in>obj.ntor) + obj = obj.change_fourier_resolution( mpol_in, ntor_in ); + end + + % Now format initial guess in a structure + switch obj.physicslist.lboundary + case 0 % rmn, zmn representation + + % Allocate memory + ric = zeros(2*obj.ntor+1, obj.mpol+1, obj.Mvol); + ris = zeros(2*obj.ntor+1, obj.mpol+1, obj.Mvol); + zic = zeros(2*obj.ntor+1, obj.mpol+1, obj.Mvol); + zis = zeros(2*obj.ntor+1, obj.mpol+1, obj.Mvol); + + % Fill initial guess arrays + for iline=1:nlines + + % Scan line + line_data = str2num( initial_guess_str{iline} ); + + % Find corresponding index + m = line_data(1); n = line_data(2); + im = m+1; + in = n+obj.ntor+1; + + for ivol=1:obj.nvol + ric(in,im,ivol) = line_data(ivol*4-1); + zis(in,im,ivol) = line_data(ivol*4 ); + ris(in,im,ivol) = line_data(ivol*4+1); + zic(in,im,ivol) = line_data(ivol*4+2); + end + end + + % Fill structure + obj.initial_guess.ric = ric; + obj.initial_guess.zis = zis; + obj.initial_guess.ris = ris; + obj.initial_guess.zic = zic; + + case 1 % Henneberg representation + + rhoi = zeros(2*obj.ntor+1, obj.mpol+1, obj.nvol); + bin = zeros(obj.ntor+1, obj.nvol); + r0ic = zeros(obj.ntor+1, obj.nvol); + z0is = zeros(obj.ntor+1, obj.nvol); + + for iline=1:nlines + + line_data = str2num( initial_guess_str{iline} ); + + m = line_data(1); n = line_data(2); + im = m+1; + in = n+obj.ntor+1; + + for ivol=1:obj.nvol + + if n>=0 && m==0 + bin( n+1, ivol) = line_data(ivol*4-1); + r0ic(n+1, ivol) = line_data(ivol*4 ); + z0is(n+1, ivol) = line_data(ivol*4+1); + end + + if m>0 + rhoi(in, im, ivol ) = line_data( ivol*4+2 ); + end + end + + end + + + obj.initial_guess.rhoi = rhoi; + obj.initial_guess.bin = bin; + obj.initial_guess.r0ic = r0ic; + obj.initial_guess.z0is = z0is; + + otherwise + error('Invalid lboundary!') + end + + end + + + function obj = set_boundary_from_namelist( obj, filename, boundary ) + % + % SET_BOUNDARY_FROM_NAMELIST( FILENAME ) + % ====================================== + % + % Read the plasma or computational boundary from another SPEC + % namelist and use it for the current instance + % + % INPUT + % ----- + % -filename: Filename of the other SPEC input namelist + % -boundary: PB for Plasma Boundary or CB for computational + % boundary + % + % OUTPUT + % ------ + % -obj: Updated output of SPEC Namelist + + + % Read input SPEC Namelist + nm = SPEC_Namelist( filename ); + + % Get relevant boundary + switch boundary + case 'PB' + Remn = nm.physicslist.rbc; + Romn = nm.physicslist.rbs; + Zemn = nm.physicslist.zbc; + Zomn = nm.physicslist.zbs; + case 'CB' + Remn = nm.physicslist.rwc; + Romn = nm.physicslist.rws; + Zemn = nm.physicslist.zwc; + Zomn = nm.physicslist.zws; + otherwise + error('InputError: Invalid boundary') + end + + % Check size + if any(size(Remn)~=size(Romn)) + error('Size mismatch') + end + if any(size(Remn)~=size(Zemn)) + error('Size mismatch') + end + if any(size(Remn)~=size(Zomn)) + error('Size mismatch') + end + + % Get Fourier resolution + s = size(Remn); + ntor_in = (s(1)-1) / 2.0; + mpol_in = s(2)-1; + + % Change FOurier resolution to the largest one between obj and + % nm + if mpol_in>obj.mpol + obj = obj.change_fourier_resolution( mpol_in, obj.ntor ); + elseif mpol_inobj.ntor + obj = obj.change_fourier_resolution( obj.mpol, ntor_in ); + elseif ntor_inobj.mpol + warning('M is larger than the Fourier resolution') + out = 0; + return + end + + if abs(n)>obj.ntor + warning('M is larger than the Fourier resolution') + out = 0; + return + end + + % Need to make the difference between initial guess harmonics + % or harmonics from the physics list. rhoi, bin, R0ic and Z0is + % are related to the Henneberg representation + if strcmp(field, 'ric') || strcmp(field, 'ris') ... + || strcmp(field, 'zic') || strcmp(field, 'zis') ... + || strcmp(field, 'rhoi') || strcmp(field, 'bin') ... + || strcmp(field, 'r0ic') || strcmp(field, 'z0is') + + if isempty(obj.initial_guess) + error('No initial guess available') + end + + ivol = varargin{1}; + + if ivol<1 || ivol>obj.nvol + error('Invalid ivol') + end + + cat = 'initial_guess'; + + else + cat = 'physicslist'; + ivol = 1; + + end + + % Read relevant harmonic + out = obj.(cat).(field)(n+obj.ntor+1, m+1, ivol); + + end + + % ================================================================= + % Setter + function obj = set_harmonics_to_zero( obj, field ) + % + % SET_HARMONICS_TO_ZERO( FIELD ) + % ============================== + % + % Set all Fourier harmonics of the field to zero + % + % INPUT + % ----- + % -FIELD: Field to set harmonics to zero + % + % OUTPUT + % ------ + % -OBJ: Updated instance of SPEC_Namelist\ + % + + + if strcmp(field, 'ric') || strcmp(field, 'ris') ... + || strcmp(field, 'zic') || strcmp(field, 'zis') ... + || strcmp(field, 'rhoi') || strcmp(field, 'bin') ... + || strcmp(field, 'r0ic') || strcmp(field, 'z0is') + + cat = 'initial_guess'; + else + cat = 'physicslist'; + end + + obj.(cat).(field) = zeros( obj.array_size ); + + end + + + + function obj = set_fourier_harmonics( obj, field, im, in, value, varargin ) + % + % SET_FOURiER_HARMONICS( FIELD, M, N, (IVOL) ) + % ============================================ + % + % Sets the fourier harmonics associated to the field, + % poloidal mode number m and toroidal mode number n + % + % INPUTS + % ------ + % -field: 'rbc', 'zws', 'ric', ... + % -im : Poloidal mode number, size 1xmn + % -in : Toroidal mode number, size 1xmn + % -value: Value for the mode, size 1xmn + % -(ivol): Optional argument, required for fourier harmonics + % of the initial guess + + + % First check the input size + mn = length(im); + if length(in)~=mn + error('The array in has not the same length as im') + end + if length(value)~=mn + error('The array value has not the same length as im') + end + + % If some modes are greater than the actual resolution, + % increase the resolution accordingly + mpol_in = max(im); + if mpol_in>obj.mpol + warning('Poloidal resolution has to be increased ...') + obj = obj.change_fourier_resolution( mpol_in, obj.ntor ); + end + + ntor_in = max(abs(in)); + if ntor_in>obj.ntor + warning('Toroidal resolution has to be increased ...') + obj = obj.change_fourier_resolution( obj.mpol, ntor_in ); + end + + % Loop over the input harmonics + for imn=1:mn + m = im(imn); + n = in(imn); + + + % Check if the quantity is located in the initial guess + % structure or in the physicslist structure. + if strcmp(field, 'ric') || strcmp(field, 'ris') ... + || strcmp(field, 'zic') || strcmp(field, 'zis') ... + || strcmp(field, 'rhoi') || strcmp(field, 'bin') ... + || strcmp(field, 'r0ic') || strcmp(field, 'z0is') + + if isempty(obj.initial_guess) + warning('No initial guess available... filling with zeros') + + % If the initial guess is empty (i.e. no initial guess + % are available), then we create one filled with zeros + if obj.lboundary == 0 + obj.initial_guess.ric = zeros( obj.array_size(1), obj.array_size(2), obj.nvol ); + obj.initial_guess.ris = zeros( obj.array_size(1), obj.array_size(2), obj.nvol ); + obj.initial_guess.zic = zeros( obj.array_size(1), obj.array_size(2), obj.nvol ); + obj.initial_guess.zis = zeros( obj.array_size(1), obj.array_size(2), obj.nvol ); + else + obj.initial_guess.rhoi = zeros( obj.array_size(1), obj.array_size(2), obj.nvol ); + obj.initial_guess.bin = zeros( obj.ntor+1, obj.nvol ); + obj.initial_guess.r0ic = zeros( obj.ntor+1, obj.nvol ); + obj.initial_guess.z0is = zeros( obj.ntor+1, obj.nvol ); + end + end + + ivol = varargin{1}; + + if ivol<1 || ivol>obj.nvol + error('Invalid ivol') + end + + obj.initial_guess.(field)(n+obj.ntor+1, m+1, ivol) = value(imn); + + else + + obj.physicslist.(field)(n+obj.ntor+1, m+1) = value(imn); + + + end + end + + end + + function obj = truncate_fourier_series( obj, mpol, ntor ) + % + % TRUNCATE_FOURiER_SERiES( mpol, ntor ) + % ===================================== + % + % Truncates all spectral quantities to the requested poloidal + % and toroidal resolution This can also be used to increase + % the Fourier resolution. + % + % INPUTS + % ------ + % -mpol: Poloidal resolution + % -ntor: Toroidal resolution + % + % OUTPUT + % ------ + % -OBJ: Truncated instance of SPEC_Namelist + % + + obj = obj.change_fourier_resolution( mpol, ntor ); + + end + + function obj = change_boundary_representation( obj, new_lboundary ) + % + % CHANGE_BOUNDArY_rEPrESENTATION( NEW_lbOUNDArY ) + % =============================================== + % + % Changes from the hudson representation to the henneberg's one + % and vice versa. + % + % INPUT + % ----- + % -new_lboundary: New value for lboundary + + + if obj.lboundary==0 && new_lboundary==1 + + obj.physicslist.rhomn = zeros(2*obj.ntor+1, obj.mpol); + obj.physicslist.shift.rhomn = [obj.ntor+1, 1]; + obj.physicslist.bn = zeros(obj.ntor+1, 1); + obj.physicslist.r0c = zeros(obj.ntor+1, 1); + obj.physicslist.z0s = zeros(obj.ntor+1, 1); + + obj.physicslist = rmfield( obj.physicslist, 'rbc' ); + obj.physicslist = rmfield( obj.physicslist, 'rbs' ); + obj.physicslist = rmfield( obj.physicslist, 'zbc' ); + obj.physicslist = rmfield( obj.physicslist, 'zbs' ); + + elseif obj.lboundary==1 && new_lboundary==0 + obj.physicslist.rbc = zeros(2*obj.ntor+1, obj.mpol); + obj.physicslist.rbs = zeros(2*obj.ntor+1, obj.mpol); + obj.physicslist.zbc = zeros(2*obj.ntor+1, obj.mpol); + obj.physicslist.zbs = zeros(2*obj.ntor+1, obj.mpol); + + obj.physicslist = rmfield( obj.physicslist, 'rhomn' ); + obj.physicslist = rmfield( obj.physicslist, 'bn' ); + obj.physicslist = rmfield( obj.physicslist, 'r0c' ); + obj.physicslist = rmfield( obj.physicslist, 'z0s' ); + + obj.physicslist.shift.rbc = [obj.ntor+1, 1]; + obj.physicslist.shift.rbs = [obj.ntor+1, 1]; + obj.physicslist.shift.zbc = [obj.ntor+1, 1]; + obj.physicslist.shift.zbs = [obj.ntor+1, 1]; + + end + + obj.physicslist.lboundary = new_lboundary; + obj.lboundary = new_lboundary; + + + + + end + + % ================================================================= + % Plotters + function plot_plasma_boundary( obj, nt, phi, newfig, varargin ) + % + % PLOT_PLASMA_BOUNDArY + % ==================== + % + % Plot the boundary given by rbc, zbs, rbs, zbc + % + % INPUTS + % ------ + % -NT: Number of poloidal points + % -PHI: Toroidal angle + % -NEWFIG: =0: plot on gca + % =1: plot on a new figure + % =2: erase and plot on gca + % -varargin: Any input you could give to plot() + % + % + + if obj.lboundary==0 + rbc = obj.physicslist.rbc; + rbs = obj.physicslist.rbs; + zbc = obj.physicslist.zbc; + zbs = obj.physicslist.zbs; + + obj.plot_surface_lb0( rbc, zbs, rbs, zbc, nt, phi, newfig, varargin{:} ) + else + rhomn = obj.physicslist.rhomn; + bn = obj.physicslist.bn; + r0c = obj.physicslist.r0c; + z0s = obj.physicslist.z0s; + + obj.plot_surface_lb1( rhomn, bn, r0c, z0s, nt, phi, newfig, varargin{:} ) + end + end + + function plot_computational_boundary( obj, nt, phi, VorB, newfig, varargin ) + % + % PLOT_PLASMA_BOUNDArY + % ==================== + % + % Plot the boundary given by rbc, zbs, rbs, zbc + % + % INPUTS + % ------ + % -NT: Number of poloidal points + % -PHI: Toroidal angle + % -VorB: ='V' + % ='B' + % ='F' + % ='N' + % -NEWFIG: =0: plot on gca + % =1: plot on a new figure + % =2: erase and plot on gca + % -varargin: Any input you could give to plot() + % + % + + if obj.lboundary == 0 + rwc = obj.physicslist.rwc; + rws = obj.physicslist.rws; + zwc = obj.physicslist.zwc; + zws = obj.physicslist.zws; + + obj.plot_surface_lb0( rwc, zws, rws, zwc, nt, phi, newfig, varargin{:} ) + else + error('Not implemented') + end + + if VorB~='N' + newfig = 0; + obj.plot_normal_field( floor(nt/10), phi, VorB, newfig ) + end + end + + function plot_initial_guess( obj, nt, phi, newfig, varargin ) + % + % PLOT_PLASMA_BOUNDArY( NT, PHI, NEWFIG, VArArGIN ) + % ================================================= + % + % Plot the boundary given by rbc, zbs, rbs, zbc + % + % INPUTS + % ------ + % -NT: Number of poloidal points + % -PHI: Toroidal angle + % -NEWFIG: =0: plot on gca + % =1: plot on a new figure + % =2: erase and plot on gca + % -varargin: Any input you could give to plot() + % + % + + if isempty(obj.initial_guess) + error('No initial guess is provided') + end + + if obj.lboundary == 0 + for ivol=1:obj.nvol + ric = obj.initial_guess.ric(:,:,ivol); + ris = obj.initial_guess.ris(:,:,ivol); + zic = obj.initial_guess.zic(:,:,ivol); + zis = obj.initial_guess.zis(:,:,ivol); + + if ivol>=2 + newfig=0; + end + + obj.plot_surface_lb0( ric, zis, ris, zic, nt, phi, newfig, varargin{:} ) + end + else + for ivol=1:obj.nvol + rhoi = obj.initial_guess.rhoi(:,:,ivol); + bin = obj.initial_guess.bin(:, ivol); + r0ic = obj.initial_guess.r0ic(:, ivol); + z0is = obj.initial_guess.z0is(:, ivol); + + if ivol>=2 + newfig=0; + end + + obj.plot_surface_lb1( rhoi, bin, r0ic, z0is, nt, phi, newfig, varargin{:} ) + end + end + end + + % ================================================================= + % Write method + function write_input_file(obj, filename ) + % + % WriTE_INPUT_FILE( filename ) + % ============================ + % + % Write namelist in an input file. Be careful: if the file filename + % provided as input exist, it will be overwritten! + % + % INPUT + % ----- + % - filename: path where to save the input file. + % + + % Set minimal toroidal resolution to one, otherwise writting + % routine does not detect arrays. This is not ideal and should + % be fixed + if obj.ntor==0 + obj = obj.change_fourier_resolution( obj.mpol, 1 ); + end + + % Create a structure with the different lists + nlists = length(obj.lists); + S = struct; + for ii=1:nlists + S.(obj.lists{ii}) = obj.(obj.lists{ii}); + end + + % Create a shift quantity - this tells the writing routine how + % much each index has to be shifted. In MATLAB, indices start + % at 1, while in the FORTRAN Namelist, we want to write + S.shift.rbc = [obj.ntor+1, 1]; + S.shift.rbs = [obj.ntor+1, 1]; + S.shift.zbc = [obj.ntor+1, 1]; + S.shift.zbs = [obj.ntor+1, 1]; + S.shift.rwc = [obj.ntor+1, 1]; + S.shift.rws = [obj.ntor+1, 1]; + S.shift.zws = [obj.ntor+1, 1]; + S.shift.zwc = [obj.ntor+1, 1]; + S.shift.vnc = [obj.ntor+1, 1]; + S.shift.vns = [obj.ntor+1, 1]; + S.shift.bnc = [obj.ntor+1, 1]; + S.shift.bns = [obj.ntor+1, 1]; + S.shift.rhomn = [obj.ntor+1, 1]; + + % remove unnecessary fields + if obj.lboundary == 0 + if isfield( S.physicslist, 'rhomn' ) + S.physicslist = rmfield(S.physicslist, 'rhomn'); + end + if isfield( S.physicslist, 'bn' ) + S.physicslist = rmfield(S.physicslist, 'bn'); + end + if isfield( S.physicslist, 'r0c' ) + S.physicslist = rmfield(S.physicslist, 'r0c'); + end + if isfield( S.physicslist, 'z0s' ) + S.physicslist = rmfield(S.physicslist, 'z0s'); + end + + else % lboundary==1 + if isfield( S.physicslist, 'rbc' ) + S.physicslist = rmfield(S.physicslist, 'rbc'); + end + if isfield( S.physicslist, 'rbs' ) + S.physicslist = rmfield(S.physicslist, 'rbs'); + end + if isfield( S.physicslist, 'zbc' ) + S.physicslist = rmfield(S.physicslist, 'zbc'); + end + if isfield( S.physicslist, 'zbs' ) + S.physicslist = rmfield(S.physicslist, 'zbs'); + end + + end + + if obj.physicslist.lfreebound==0 % Then no need to freeboundary info + if isfield( S.physicslist, 'rwc' ) + S.physicslist = rmfield(S.physicslist, 'rwc'); + end + if isfield( S.physicslist, 'rws' ) + S.physicslist = rmfield(S.physicslist, 'rws'); + end + if isfield( S.physicslist, 'zwc' ) + S.physicslist = rmfield(S.physicslist, 'zwc'); + end + if isfield( S.physicslist, 'zws' ) + S.physicslist = rmfield(S.physicslist, 'zws'); + end + if isfield( S.physicslist, 'vnc' ) + S.physicslist = rmfield(S.physicslist, 'vnc'); + end + if isfield( S.physicslist, 'vns' ) + S.physicslist = rmfield(S.physicslist, 'vns'); + end + if isfield( S.physicslist, 'bnc' ) + S.physicslist = rmfield(S.physicslist, 'bnc'); + end + if isfield( S.physicslist, 'bns' ) + S.physicslist = rmfield(S.physicslist, 'bns'); + end + + end + + + % Build initial guess strings + if obj.physicslist.lboundary==0 + if ~isempty(obj.initial_guess) + s = size(obj.initial_guess.ric); + initialguess = cell(1, s(1)*s(2)); + iline=0; + for ii=1:s(1) + for jj=1:s(2) + iline = iline+1; + mm = jj-1; + nn = ii-obj.ntor-1; + + initialguess{iline} = sprintf( '%i %i ', mm, nn ); + for ivol=1:s(3) + initialguess{iline} = sprintf( '%s %0.12E %0.12E %0.12E %0.12E', initialguess{iline}, ... + obj.initial_guess.ric(ii,jj,ivol), ... + obj.initial_guess.zis(ii,jj,ivol), ... + obj.initial_guess.ris(ii,jj,ivol), ... + obj.initial_guess.zic(ii,jj,ivol) ); + end + end + end + else + initialguess = cell(0); + end + + else + + % Now prepare initial guess... + if isfield(obj.initial_guess, 'bin') + sb = size(obj.initial_guess.bin); + srho = size(obj.initial_guess.rhoi); + ntor = (srho(2)-1)/2.0; + initialguess = cell(1, sb(1) + srho(1)*srho(2)); + + % Modes m=0, n + for ii=1:sb(1) + nn = ii-1; + initialguess{ii} = sprintf('0 %i ', nn); + for ivol=1:sb(2) + initialguess{ii} = sprintf('%s %0.12E %0.12E %0.12E %0.12E', initialguess{ii}, ... + obj.initial_guess.bin( ii, ivol ), ... + obj.initial_guess.r0ic(ii, ivol ), ... + obj.initial_guess.z0is(ii, ivol ), 0.0 ); + end + end + + it = sb(1); + for ii=1:srho(2) + + nn = ii-ntor-1; + + for jj=1:srho(1) + + it = it+1; + + mm = jj; + + initialguess{it} = sprintf('%i %i ', mm, nn); + + for ivol=1:srho(3) + + initialguess{it} = sprintf('%s %0.12E %0.12E %0.12E %0.12E', initialguess{ii},... + 0.0, 0.0, 0.0, obj.initial_guess.rhoi(ii, jj, ivol)); + + end + end + end + else + initialguess = cell(0); + + end + + + + end + + % Call namelist writer + write_namelist( S, filename, initialguess ); + + + end + end + + methods (Access=private) + + function obj = initialize_structure( obj ) + % + % INITIALIzE_STrUCTUrE( OBJ ) + % =========================== + % + % Use to check that all required inputs are correctly set; + % check that the sizes of arrays are correct. raise errors in + % case crucial informations is missing. + % + % + + % Fill some important inputs + if ~isfield(obj.physicslist, 'nvol') + error('Missing nvol') + end + if ~isfield(obj.physicslist, 'lfreebound') + error('Missing lfreebound') + end + + obj.Mvol = obj.physicslist.nvol + obj.physicslist.lfreebound; + obj.nvol = obj.physicslist.nvol; + + if isfield(obj.physicslist, 'lboundary') + obj.lboundary = obj.physicslist.lboundary; + else + warning('lboundary not provided. Setting with 0...') + obj.lboundary = 0; + end + + % PHYSICSLIST + % ----------- + % lrad + if ~isfield(obj.physicslist, 'lrad') && obj.verbose + warning('Missing lrad. Filling with 4...') + obj.physicslist.lrad = ones(1,obj.Mvol) * 4; + else + % Fill potential missing elements with 4s + obj.physicslist.lrad(end+1:obj.Mvol) = 4; + end + + % tflux + if ~isfield(obj.physicslist, 'tflux') && obj.verbose + warning('Missing tflux. Filling equal radial distances') + obj.physicslist.tflux = (1:obj.Mvol).^2; + else + if length(obj.physicslist.tflux)~=obj.Mvol + error('Invalid number of tflux elements') + end + end + + % pflux + if ~isfield(obj.physicslist, 'pflux') + warning('Missing pflux. Filling with 0...') + obj.physicslist.pflux = zeros(1,obj.Mvol); + else + % Fill potential missing elements with zeros + obj.physicslist.pflux(end+1:obj.Mvol) = 0; + end + + % helicity + if ~isfield(obj.physicslist, 'helicity') + warning('Missing lrad. Filling with 0...') + obj.physicslist.helicity = zeros(1,obj.Mvol); + else + % Fill potential missing elements with zeros + obj.physicslist.helicity(end+1:obj.Mvol) = 0; + end + + % pscale + if ~isfield(obj.physicslist, 'pscale') + warning('Missing pscale. Setting to zero...') + obj.physicslist.pscale = 0.0; + end + + % ladiabatic + if ~isfield(obj.physicslist, 'ladiabatic') + warning('Missing ladiabatic. Setting to zero...') + obj.physicslist.ladiabatic = 0.0; + end + + % Pressure + if ~isfield(obj.physicslist, 'pressure') + warning('Missing pressure. Filling with 0...') + obj.physicslist.pressure = zeros(1,obj.Mvol); + else + % Fill potential missing elements with zeros + obj.physicslist.pressure(end+1:obj.Mvol) = 0; + end + + % Adiabatic + if obj.physicslist.ladiabatic==1 + if ~isfield(obj.physicslist, 'adiabatic') + warning('Missing adiabatic. Filling with 0...') + obj.physicslist.adiabatic = zeros(1,obj.Mvol); + else + % Fill potential missing elements with zeros + obj.physicslist.adiabatic(end+1:obj.Mvol) = 0; + end + end + + % mu + if ~isfield(obj.physicslist, 'mu') + warning('Missing mu. Filling with 0...') + obj.physicslist.mu = zeros(1,obj.Mvol); + else + % Fill potential missing elements with zeros + obj.physicslist.mu(end+1:obj.Mvol) = 0; + end + + % lconstraint + if ~isfield(obj.physicslist, 'lconstraint') + warning('Missing lconstraint. Setting to 0...') + obj.physicslist.lconstraint = 0; + end + + if ~any(obj.physicslist.lconstraint==[0,1,2,3]) + error('Invalid lconstraint') + end + + + % Ivolume, Isurf + if obj.physicslist.lconstraint==3 + if ~isfield(obj.physicslist, 'Ivolume') + warning('Missing Ivolume. Filling with 0...') + obj.physicslist.Ivolume = zeros(1,obj.Mvol); + else + % Fill potential missing elements with zeros + obj.physicslist.Ivolume(end+1:obj.Mvol) = 0; + end + if ~isfield(obj.physicslist, 'Isurf') + warning('Missing Isurf. Filling with 0...') + obj.physicslist.Isurf = zeros(1,obj.Mvol); + else + % Fill potential missing elements with zeros + obj.physicslist.Isurf(end+1:obj.Mvol) = 0; + end + end + + if obj.physicslist.lconstraint==1 + if ~isfield(obj.physicslist, 'iota') + warning('Missing iota. Filling with sqrt(2)...') + obj.physicslist.iota = sqrt(2)*ones(1,obj.Mvol); + else + % Fill potential missing elements with zeros + obj.physicslist.iota(end+1:obj.Mvol) = sqrt(2); + end + if ~isfield(obj.physicslist, 'oita') + warning('Missing oita. Filling with sqrt(2)...') + obj.physicslist.oita = sqrt(2)*ones(1,obj.Mvol); + else + % Fill potential missing elements with zeros + obj.physicslist.oita(end+1:obj.Mvol) = sqrt(2); + end + end + + % mupftol + if ~isfield(obj.physicslist, 'mupftol') + warning('Missing mupftol. Setting to 1E-12...') + obj.physicslist.mupftol = 1E-12; + end + + % mupfits + if ~isfield(obj.physicslist, 'mupfits') + warning('Missing mupfits. Setting to 128...') + obj.physicslist.mupfits = 128; + end + + % Check geometry + if ~isfield(obj.physicslist, 'mpol') + error('Missing mpol information') + end + if ~isfield(obj.physicslist, 'ntor') + error('Missing ntor information') + end + if ~isfield(obj.physicslist, 'lboundary') + warning('Missing lboundary. Setting to zero') + obj.physicslist.lboundary = 0; + end + + mpol_in = obj.physicslist.mpol; + ntor_in = obj.physicslist.ntor; + + if obj.lboundary==0 + if ~isfield(obj.physicslist, 'rbc') + obj.physicslist.shift.rbc = [ntor_in+1, 1]; + obj.physicslist.rbc = zeros(2*ntor_in+1, mpol_in); + end + if ~isfield(obj.physicslist, 'rbs') + obj.physicslist.shift.rbs = [ntor_in+1, 1]; + obj.physicslist.rbs = zeros(2*ntor_in+1, mpol_in); + end + if ~isfield(obj.physicslist, 'zbc') + obj.physicslist.shift.zbc = [ntor_in+1, 1]; + obj.physicslist.zbc = zeros(2*ntor_in+1, mpol_in); + end + if ~isfield(obj.physicslist, 'zbs') + obj.physicslist.shift.zbs = [ntor_in+1, 1]; + obj.physicslist.zbs = zeros(2*ntor_in+1, mpol_in); + end + + % Check that sizes are consistent with each others + if any(size(obj.physicslist.rbc)~=size(obj.physicslist.rbs)) + error('Size mismatch between rbc and rbs') + end + if any(size(obj.physicslist.rbc)~=size(obj.physicslist.zbc)) + error('Size mismatch between rbc and zbc') + end + if any(size(obj.physicslist.rbc)~=size(obj.physicslist.zbs)) + error('Size mismatch between rbc and zbs') + end + + + else %lboundary==1 + if ~isfield( obj.physicslist, 'bn' ) + obj.physicslist.bn = zeros( ntor_in+1, 1 ); + end + + % Now fill missing elements with zeros + obj.physicslist.bn(end+1:ntor_in+1) = 0.0; + + if ~isfield( obj.physicslist, 'r0c' ) + obj.physicslist.r0c = zeros( ntor_in+1, 1 ); + end + + % Now fill missing elements with zeros + obj.physicslist.r0c(end+1:ntor_in+1) = 0.0; + + if ~isfield( obj.physicslist, 'z0s' ) + obj.physicslist.z0s = zeros( ntor_in+1, 1 ); + end + + % Now fill missing elements with zeros + obj.physicslist.z0s(end+1:ntor_in+1) = 0.0; + + if ~isfield( obj.physicslist, 'rhomn' ) + obj.physicslist.shift.rhomn = [ntor_in+1, 1]; + obj.physicslist.rhomn = zeros( 2*ntor_in+1, mpol_in+1 ); + end + + % Check sizes + if any(length(obj.physicslist.bn)~=ntor_in+1) + obj.physicslist.bn(end+1:ntor_in+1) = 0; + obj.physicslist.bn = obj.physicslist.bn(ntor_in+1); + end + if any(length(obj.physicslist.r0c)~=ntor_in+1) + obj.physicslist.r0c(end+1:ntor_in+1) = 0; + obj.physicslist.r0c = obj.physicslist.r0c(ntor_in+1); + end + if any(length(obj.physicslist.z0s)~=ntor_in+1) + obj.physicslist.z0s(end+1:ntor_in+1) = 0; + obj.physicslist.z0s = obj.physicslist.z0s(ntor_in+1); + end + + + end + + + + if ~isfield(obj.physicslist, 'rwc') + obj.physicslist.shift.rwc = [ntor_in+1, 1]; + obj.physicslist.rwc = zeros(2*ntor_in+1, mpol_in); + end + if ~isfield(obj.physicslist, 'rws') + obj.physicslist.shift.rws = [ntor_in+1, 1]; + obj.physicslist.rws = zeros(2*ntor_in+1, mpol_in); + end + if ~isfield(obj.physicslist, 'zwc') + obj.physicslist.shift.zwc = [ntor_in+1, 1]; + obj.physicslist.zwc = zeros(2*ntor_in+1, mpol_in); + end + if ~isfield(obj.physicslist, 'zws') + obj.physicslist.shift.zws = [ntor_in+1, 1]; + obj.physicslist.zws = zeros(2*ntor_in+1, mpol_in); + end + + % Check that sizes are consistent with each others + if any(size(obj.physicslist.rwc)~=size(obj.physicslist.rws)) + error('Size mismatch between rwc and rws') + end + if any(size(obj.physicslist.rwc)~=size(obj.physicslist.zwc)) + error('Size mismatch between rwc and zwc') + end + if any(size(obj.physicslist.rwc)~=size(obj.physicslist.zws)) + error('Size mismatch between rwc and zws') + end + + + + if ~isfield(obj.physicslist, 'vnc') + obj.physicslist.shift.vnc = [ntor_in+1, 1]; + obj.physicslist.vnc = zeros(2*ntor_in+1, mpol_in); + end + if ~isfield(obj.physicslist, 'vns') + obj.physicslist.shift.vns = [ntor_in+1, 1]; + obj.physicslist.vns = zeros(2*ntor_in+1, mpol_in); + end + if ~isfield(obj.physicslist, 'bnc') + obj.physicslist.shift.bnc = [ntor_in+1, 1]; + obj.physicslist.bnc = zeros(2*ntor_in+1, mpol_in); + end + if ~isfield(obj.physicslist, 'bns') + obj.physicslist.shift.bns = [ntor_in+1, 1]; + obj.physicslist.bns = zeros(2*ntor_in+1, mpol_in); + end + + % Check that sizes are consistent with each others + if any(size(obj.physicslist.vnc)~=size(obj.physicslist.vns)) + error('Size mismatch between vnc and vns') + end + if any(size(obj.physicslist.bnc)~=size(obj.physicslist.bnc)) + error('Size mismatch between bnc and bns') + end + + % DIAGNOSTICSLIST + % --------------- + if ~isfield(obj.diagnosticslist, 'nppts') + warning('Missing nppts. Setting to zero') + obj.diagnosticslist.nppts = 0; + end + + if ~isfield(obj.diagnosticslist, 'nptrj') + warning('Missing nptrj. Setting to zero') + obj.diagnosticslist.nptrj = 0; + end + end + + + function obj = change_fourier_resolution( obj, mpol_new, ntor_new ) + % + % CHANGE_FOUriEr_rESOLUTION( mpol_NEW, ntor_NEW ) + % =============================================== + % + % Change inner Fourier resolution of an instance of + % SPEC_Namelist. + % + % INPUTS + % ------ + % -mpol_new: New poloidal resolution + % -ntor_new: New toroidal resolution + % + % OUTPUT + % ------ + % -obj: Updated instance of SPEC_Namelist + % + + if mpol_new<1 + error('InputError, mpol_new should be larger than 0') + end + if ntor_new<0 + error('InputError, ntor_new should be larger or equal to zero') + end + + obj.mpol = mpol_new; + obj.ntor = ntor_new; + obj.array_size = [2*obj.ntor+1, obj.mpol+1]; + + % Check that all arrays have the same size; otherwise, fill + % with zeros the missing elements + if obj.lboundary == 0 + if any(size(obj.physicslist.rbc)~=obj.array_size) + obj = obj.reshape_array( 'rbc' ); + obj = obj.reshape_array( 'rbs' ); + obj = obj.reshape_array( 'zbc' ); + obj = obj.reshape_array( 'zbs' ); + end + + if any(size(obj.physicslist.rwc)~=obj.array_size) + obj = obj.reshape_array( 'rwc' ); + obj = obj.reshape_array( 'rws' ); + obj = obj.reshape_array( 'zwc' ); + obj = obj.reshape_array( 'zws' ); + end + else + if any(size(obj.physicslist.rhomn)~=obj.array_size) + obj = obj.reshape_array( 'rhomn' ); + end + + if any(size(obj.physicslist.bn)~=[obj.ntor+1, 1]) + obj.physicslist.bn(end+1:obj.ntor+1) = 0; + obj.physicslist.bn = obj.physicslist.bn(1:obj.ntor+1); + end + if any(size(obj.physicslist.r0c)~=[obj.ntor+1, 1]) + obj.physicslist.r0c(end+1:obj.ntor+1) = 0; + obj.physicslist.r0c = obj.physicslist.r0c(1:obj.ntor+1); + end + if any(size(obj.physicslist.z0s)~=[obj.ntor+1, 1]) + obj.physicslist.z0s(end+1:obj.ntor+1) = 0; + obj.physicslist.z0s = obj.physicslist.z0s(1:obj.ntor+1); + end + + end + + + if any(size(obj.physicslist.vnc)~=obj.array_size) + obj = obj.reshape_array( 'vnc' ); + obj = obj.reshape_array( 'vns' ); + end + + if any(size(obj.physicslist.bnc)~=obj.array_size) + obj = obj.reshape_array( 'bnc' ); + obj = obj.reshape_array( 'bns' ); + end + end + + + function obj = set_fourier_resolution( obj ) + % + % SET_FOUriEr_rESOLUTION( OBJ ) + % ============================= + % + % Set the obj internal Fourier resolution to the maximal value + % required to store the given data; then, reshapees all arrays + % to have the size obj.array_size. + % + % Check beforehand that the resolution of rbc is the same as + % rbs, zbc and zbs. Do something similar for vnc, vns, bnc, bns + % and rwc, rws, zws, zwc. + % + + + % Find largest Fourier resolution in the input file + mpol_in = obj.physicslist.mpol; + ntor_in = obj.physicslist.ntor; + + if obj.lboundary == 0 + s_bc = size(obj.physicslist.rbc); + shift = obj.physicslist.shift.rbc(1); + mpol_bc = s_bc(2)-1 ; + ntor_bc = max([abs(1-shift), s_bc(1)-shift]); + else + s_bc = size(obj.physicslist.rhomn); + shift = obj.physicslist.shift.rhomn(1); + mpol_bc = s_bc(2)-1; + + lbn = length( obj.physicslist.bn ); + lrc = length( obj.physicslist.r0c ); + lzs = length( obj.physicslist.z0s ); + ntor_bc = max([abs(1-shift), s_bc(1)-shift, lbn, lrc, lzs]); + end + + s_wc = size(obj.physicslist.rwc); + shift = obj.physicslist.shift.rwc(1); + mpol_wc = s_wc(2)-1 ; + ntor_wc = max([abs(1-shift), s_wc(1)-shift]); + + s_vb = size(obj.physicslist.vnc); + shift = obj.physicslist.shift.vnc(1); + mpol_vb = s_vb(2)-1 ; + ntor_vb = max([abs(1-shift), s_vb(1)-shift]); + + mpol_new = max([mpol_in, mpol_bc, mpol_wc, mpol_vb]); + ntor_new = max([ntor_in, ntor_bc, ntor_wc, ntor_vb]); + obj = obj.change_fourier_resolution( mpol_new, ntor_new ); + end + + + function obj = reshape_array( obj, field ) + % + % rESHAPE_ArrAY( OBJ, FIELD ) + % ======================================= + % + % reshape the input array in a an array of size obj.array_size + % and fills missing elements with zeros + % + % INPUTS + % ------ + % -field: Field, in obj.physicslist, to be modified + % + % OUTPUT + % ------ + % -obj: Updated instance of SPEC_Namelist + % + + array = obj.physicslist.(field); + shift = obj.physicslist.shift.(field); + + s = size(array); + + new_array = zeros(obj.array_size); + for ii=1:s(1) + for jj=1:s(2) + nn = ii-shift(1); + mm = jj-shift(2); + + if abs(nn)>obj.ntor || mm>obj.mpol + continue + end + + new_array(nn+obj.ntor+1, mm+1) = array(ii, jj); + end + end + + obj.physicslist.(field) = new_array; + end + + + function plot_surface_lb0( obj, rmnc, zmns, rmns, zmnc, nt, phi, ... + newfig, varargin ) + % + % PLOT_SUrFACE( rMNC, zMNS, rMNS, zMNC, NT, NEWFIG, VArArGIN ) + % =========================================================== + % + % Plot a surface parametrized by the standard representation + % + % INPUTS + % ------ + % -rmnc: Even Fourier modes of r, format (2*ntor+1, mpol+1) + % -zmns: Odd Fourier modes of z, format (2*ntor+1, mpol+1) + % -rmns: Odd Fourier modes of r, format (2*ntor+1, mpol+1) + % -zmnc: Even Fourier modes of z, format (2*ntor+1, mpol+1) + % -NT : Number of poloidal points + % -PHI : Toroidal angle + % -newfig: =0: plot on gca + % =1: plot on a new figure + % =2: erase and plot on gca + % - varargin: Any input you could give to plot() + + switch newfig + case 0 + hold on + case 1 + figure('Color','w','Position',[200 200 900 700]) + hold on + case 2 + hold off + otherwise + error('InputError: invalid newfig') + end + + s = size(rmnc); + + if any(s~=size(rmns)) + error('InputError: rmnc has not the same size as rmns') + end + if any(s~=size(zmns)) + error('InputError: rmnc has not the same size as zmns') + end + if any(s~=size(zmnc)) + error('InputError: rmnc has not the same size as zmnc') + end + if nt<1 + error('InputError: nt should be larger than 1') + end + + N = (s(1)-1) / 2.0; + + tarr = linspace( 0, 2*pi, nt ); + r = zeros( 1, nt ); + z = zeros( 1, nt ); + nfp = double(obj.physicslist.nfp); + + + for in=1:s(1) + nn = in-1-N; + for im=1:s(2) + mm = im-1; + + arg = mm*tarr - nn*nfp*phi; + + r = r + rmnc(in,im) * cos(arg) + rmns(in,im) * sin(arg); + z = z + zmnc(in,im) * cos(arg) + zmns(in,im) * sin(arg); + end + end + + plot( r, z, varargin{:} ) + + axis equal + end + + + function plot_surface_lb1( obj, rhomn, bn, r0c, z0s, nt, phi, newfig, varargin ) + % + % PLOT_SUrFACE_lb1( rHOMN, bn, r0C, z0S, NT, PHI, NEWFIG, VArArGIN ) + % ================================================================== + % + % Plots a surface using the Henneberg representation + % + % INPUTS + % ------ + % -rhomn: rho_mn harmonics, format (2*ntor+1, mpol+1) + % -bn: b_n harmonics, format (ntor+1, 1) + % -r0c: r_0c harmonics, format (ntor+1, 1) + % -z0s: z_0s harmonics, format (ntor+1, 1) + % -nt: Number of poloidal points + % -phi: Toroidal angle + % -newfig: =0: plot on gca + % =1: plot on a new figure + % =2: erase and plot on gca + % -varargin: Optionnal input arguments, used as inputs to + % plot() + % + % + + + + switch newfig + case 0 + hold on + case 1 + figure('Color','w','Position',[200 200 900 700]) + hold on + case 2 + hold off + otherwise + error('InputError: invalid newfig') + end + + s = size(rhomn); + N = (s(1)-1) / 2.0; + + if any(length(bn)~=N+1) + error('InputError: bn has not the size ntor+1') + end + if any(length(r0c)~=N+1) + error('InputError: r0c has not the size ntor+1') + end + if any(length(z0s)~=N+1) + error('InputError: z0s has not the size ntor+1') + end + if nt<1 + error('InputError: nt should be larger than 1') + end + + tarr = linspace(0, 2*pi, nt); + rho = zeros(1, nt); + alpha = obj.physicslist.twoalpha / 2.0; + nfp = double(obj.physicslist.nfp); + + for im=1:s(2) + mm = im-1; + for in=1:s(1) + nn = in-N-1; + rho = rho + rhomn(in,im) * cos(mm*tarr + nn*nfp*phi - alpha*nfp*phi); + end + end + + r0 = 0; + z0 = 0; + b = 0; + for nn=0:N + r0 = r0 + r0c(nn+1) * cos(nn*nfp*phi); + b = b + bn(nn+1 ) * cos(nn*nfp*phi); + z0 = z0 + z0s(nn+1) * sin(nn*nfp*phi); + end + + zeta = b.*sin( tarr - alpha*nfp*phi ); + + r = r0 + rho * cos(alpha*nfp*phi) - zeta * sin(alpha*nfp*phi); + z = z0 + rho * sin(alpha*nfp*phi) + zeta * cos(alpha*nfp*phi); + + plot(r, z, varargin{:}) + axis equal + end + + function plot_normal_field( obj, nt, phi, VorB, newfig ) + % + % PLOT_NORMAL_FIELD( NT, PHI, VORB, NEWFIG ) + % ==================================== + % + % Plots the normal field on the computational boundary as a + % vector field + % + % INPUTS + % ------ + % -NT: Number of poloidal points + % -PHI: Toroidal angle + % -VORB: ='V': Only vacuum field + % ='B': Only plasma field + % ='F': Add vacuum to plasma field + % -NEWFIG: =0: plot on gca + % =1: plot on a new figure + % =2: erase and plot on gca + + % First, build coordinate + tarr = linspace( 0, 2*pi, nt ); + r = zeros( 1, nt ); + z = zeros( 1, nt ); + + rmnc = obj.physicslist.rwc; + rmns = obj.physicslist.rws; + zmnc = obj.physicslist.zwc; + zmns = obj.physicslist.zws; + + Nfp = double(obj.physicslist.nfp); + + s = size(rmnc); + + if any(s~=size(rmns)) + error('InputError: rmnc has not the same size as rmns') + end + if any(s~=size(zmns)) + error('InputError: rmnc has not the same size as zmns') + end + if any(s~=size(zmnc)) + error('InputError: rmnc has not the same size as zmnc') + end + if nt<1 + error('InputError: nt should be larger than 1') + end + + N = (s(1)-1) / 2.0; + nfp = double(obj.physicslist.nfp); + + + for in=1:s(1) + nn = in-1-N; + for im=1:s(2) + mm = im-1; + + arg = mm*tarr - nn*nfp*phi; + + r = r + rmnc(in,im) * cos(arg) + rmns(in,im) * sin(arg); + z = z + zmnc(in,im) * cos(arg) + zmns(in,im) * sin(arg); + end + end + + % Then evaluate norm of normal field + switch VorB + case 'V' + fmnc = obj.physicslist.vnc; + fmns = obj.physicslist.vns; + case 'B' + fmnc = obj.physicslist.bnc; + fmns = obj.physicslist.bns; + case 'F' + fmnc = obj.physicslist.bnc + obj.physicslist.vnc; + fmns = obj.physicslist.bns + obj.physicslist.vns; + otherwise + error('InputError: Invalid VorB') + end + + bnorm = zeros(1, nt); + for mm=0:obj.mpol + for nn=-obj.ntor:obj.ntor + if mm==0 && nn<0 + continue + end + im = mm+1; + in = nn+obj.ntor+1; + arg = mm*tarr - nn*Nfp*phi; + + bnorm = bnorm + fmnc(in,im) * cos( arg ) ... + + fmns(in,im) * sin( arg ); + end + end + + bnorm = bnorm / max(bnorm); + + % Evaluate normal direction + bnormal = zeros(2, nt); + dt = 1e-5; + for it = 1:nt + + rj = 0; zj = 0; tj = tarr(it)-dt; + rk = 0; zk = 0; tk = tarr(it)+dt; + for in=1:s(1) + nn = in-1-N; + for im=1:s(2) + mm = im-1; + + argj = mm*tj - nn*nfp*phi; + rj = rj + rmnc(in,im) * cos(argj) + rmns(in,im) * sin(argj); + zj = zj + zmnc(in,im) * cos(argj) + zmns(in,im) * sin(argj); + + argk = mm*tk - nn*nfp*phi; + rk = rk + rmnc(in,im) * cos(argk) + rmns(in,im) * sin(argk); + zk = zk + zmnc(in,im) * cos(argk) + zmns(in,im) * sin(argk); + end + end + + bnormal(1,it) = zk-zj ; + bnormal(2,it) = -(rk-rj); + + bnormal(:,it) = bnorm(it) * bnormal(:,it) / sqrt(bnormal(1,it)^2+bnormal(2,it)^2); + end + + + + % Plot + quiver( r, z, bnormal(1,:), bnormal(2,:) ) + + + + end + end + +end + + + + + + + + + + + + + + + + + + diff --git a/Utilities/matlabtools/SPEC_Namelist/nm_tutorial_001.md b/Utilities/matlabtools/SPEC_Namelist/nm_tutorial_001.md new file mode 100644 index 00000000..9bd20c13 --- /dev/null +++ b/Utilities/matlabtools/SPEC_Namelist/nm_tutorial_001.md @@ -0,0 +1,146 @@ +# Introduction + +The class SPEC\_Namelist is a matlab tool to read, edit and write SPEC input files. Be careful though, always double check what kind of input file you generate - some errors are spotted by some tests in SPEC\_Namelist, but not everything is covered! + +In this tutorial, we will show how to read a namelist, edit its Fourier resolution and change some specific Fourier harmonics, plot the initial guess and finally write the namelist. + +# Reading a Namelist + +## Adding SPEC\_Namelist path to MATLAB +First of all, make sure that the path to SPEC\_Namelist is provided to MATLAB. To do so, you can write +```Matlab +addpath(genpath('my/path/to/SPEC/Utilities/matlabtools')) +``` + +to check that MATLAB is using the right SPEC\_Namelist class, you can check which file it is using with the command +```Matlab +which SPEC_Namelist +``` + +## Read a SPEC input file +To create a SPEC\_Namelist instance from a SPEC input file, you need to give its absolute or relative path to the constructor of the class. For example, try +```Matlab +nm = SPEC_Namelist('path/to/SPEC/InputFiles/TestCases/G3V08L3Fr.001.sp') +``` + +This will read the SPEC\_Namelist, create a MATLAB structure with all the input in a specific format, and check that some crucial inputs are provided. In case of missing inputs, it will print a few warnings: + +```Matlab +nm = SPEC_Namelist('~/SPEC/InputFiles/TestCases/G3V08L3Fr.001.sp') +Warning: lboundary not provided. Setting with 0... +> In SPEC_Namelist/initialize_structure (line 972) + In SPEC_Namelist (line 73) +Warning: Missing Ivolume. Filling with 0... +> In SPEC_Namelist/initialize_structure (line 1070) + In SPEC_Namelist (line 73) +Warning: Missing Isurf. Filling with 0... +> In SPEC_Namelist/initialize_structure (line 1077) + In SPEC_Namelist (line 73) +Warning: Missing lboundary. Setting to zero +> In SPEC_Namelist/initialize_structure (line 1122) + In SPEC_Namelist (line 73) +Warning: lboundary not provided. Setting with 0... +> In SPEC_Namelist/initialize_structure (line 972) + In SPEC_Namelist (line 73) + In SPEC_Namelist/read_initial_guess (line 172) + In SPEC_Namelist (line 81) +Warning: Missing Ivolume. Filling with 0... +> In SPEC_Namelist/initialize_structure (line 1070) + In SPEC_Namelist (line 73) + In SPEC_Namelist/read_initial_guess (line 172) + In SPEC_Namelist (line 81) +Warning: Missing Isurf. Filling with 0... +> In SPEC_Namelist/initialize_structure (line 1077) + In SPEC_Namelist (line 73) + In SPEC_Namelist/read_initial_guess (line 172) + In SPEC_Namelist (line 81) +Warning: Missing lboundary. Setting to zero +> In SPEC_Namelist/initialize_structure (line 1122) + In SPEC_Namelist (line 73) + In SPEC_Namelist/read_initial_guess (line 172) + In SPEC_Namelist (line 81) + +nm = + + SPEC_Namelist with properties: + + lists: {6x1 cell} + physicslist: [1x1 struct] + numericlist: [1x1 struct] + locallist: [1x1 struct] + globallist: [1x1 struct] + diagnosticslist: [1x1 struct] + screenlist: [1x1 struct] + initial_guess: [1x1 struct] +``` + +## Data structure format +SPEC\_Namelist stores SPEC input data in nested structures. All structure and data names uses lower case - be careful whenever you access the data! + +In addition, the class has an internal Fourier resolution, which is set by default to the largest poloidal and toroidal mode number in the input file. This resolution is a private attribute of the class and is not accessible to the user; to change it and increase or truncate all physical quantities in Fourier space to the resolution `mpol`, `ntor`, you can use + +```Matlab +nm = nm.truncate_fourier_series( mpol, ntor ) +``` + +All Fourier modes are stored in matrices of size `2*ntor+1 x mpol+1`. To get a specific mode, for example `Rbc(n,m)`, use +```Matlab +nm.get_fourier_harmonics( 'rbc', m, n ) +``` + +# Modifying a SPEC\_Namelist +To modify any input, you can simply access it as you would with any MATLAB structure. For example, to change the toroidal flux in the third volume to one, write +```Matlab +nm.physicslist.tflux(3) = 1; +``` + +For the Fourier modes, setters routines are provided. For example, to change the mode Rbc(n,m) to a value `value`, write +```Matlab +nm = nm.set_fourier_harmonics( 'rbc', 1, 0, value ); +``` + +If you want to set multiple modes, you can set them by providing arrays of values for `m`, `n` and `value`. Finally, if you want to use a computational boundary, a plasma boundary or the initial guess for the internal interfaces geometry from another SPEC input, you can use respectively `nm.set_boundary_from_namelist( filename, 'CB' )`, `nm.set_boundary_from_namelist( filename, 'PB' )` or `nm.read_initial_guess(filename)`. More information can be obtained by reading the documentation. + +**DO NOT CHANGE HARMONICS WITHOUT THESE ROUTINES!** This might break the class and some of your input will be ignored. + +# Visualizing the geometry of an input +Sometimes, SPEC crashes and it is difficult to know why. Some information can be obtained by plotting the geometry of computational boundary, the plasma boundary and the initial guess from the input file. + +## Plotting the plasma boundary +To plot the plasma boundary, write +```Matlab +nt = 1024; %Number of poloidal points +phi = 0; %Toroidal angle +nm.plot_plasma_boundary( nt, phi, 1 ); +``` + +The initial guess, if any, can be plotted with +```Matlab +nm.plot_initial_guess( nt, phi, 0 ); +``` + +## Plotting the computational boundary +Similarly, the computational boundary can be plotted with +```Matlab +nm.plot_computational_boundary( nt, phi, 'N', 1 ); +``` + +If you want to see the normal field on the computational boundary, switch `'N'` to (i) `'V'` to see the coils contribution, (ii) `'B'` to see the initial guess for the plasma contribution and (iii) `'F'` for the sum of both. + + +# Writing the namelist into a file +To write the Namelist, use the built in subroutine `write_input_file(filename)`. For example, do +```Matlab +nm.write_input_file( 'test.sp' ) +``` + +will write an input file called test.sp with all the relevant quantities. Some input won\'t be written if not required - for example, if `nm.physicslist.Lfreebound` is set to zero, the fields `rwc`, `rws`, `zwc` and `zws` will not be written. + + + + + + + + + diff --git a/Utilities/matlabtools/SPEC_Namelist/rw_namelist/license.txt b/Utilities/matlabtools/SPEC_Namelist/rw_namelist/license.txt new file mode 100644 index 00000000..793f7d6b --- /dev/null +++ b/Utilities/matlabtools/SPEC_Namelist/rw_namelist/license.txt @@ -0,0 +1,24 @@ +Copyright (c) 2012, Darien Pardinas Diaz +All rights reserved. + +Redistribution and use in source and binary forms, with or without +modification, are permitted provided that the following conditions are +met: + + * Redistributions of source code must retain the above copyright + notice, this list of conditions and the following disclaimer. + * Redistributions in binary form must reproduce the above copyright + notice, this list of conditions and the following disclaimer in + the documentation and/or other materials provided with the distribution + +THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" +AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE +IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE +ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE +LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR +CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF +SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS +INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN +CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) +ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE +POSSIBILITY OF SUCH DAMAGE. diff --git a/Utilities/matlabtools/SPEC_Namelist/rw_namelist/read_namelist.m b/Utilities/matlabtools/SPEC_Namelist/rw_namelist/read_namelist.m new file mode 100755 index 00000000..7bce09c3 --- /dev/null +++ b/Utilities/matlabtools/SPEC_Namelist/rw_namelist/read_namelist.m @@ -0,0 +1,340 @@ +function S = read_namelist(filename) +% S = READ_NAMELIST(FILENAME) returns the struct S containg namelists and +% variables in the file FILENAME organised in hierachical way: +% +% |--VAR1 +% |--VAR2 +% |-- NMLST_A--|... +% | |--VARNa +% | +% | |--VAR1 +% |-- NMLST_B--|--VAR2 +% | |... +% S --| ... |--VARNb +% | +% | |--VAR1 +% |-- NMLST_M--|--VAR2 +% |... +% |--VARNm +% +% Note: The function can read multidimensioal variables as well. The +% function assumes that there is no more than one namelist section per +% line. At this time there is no syntax checking functionality so the +% function will crash in case of errors. +% +% Example: +% NMLST = read_namelist('OPTIONS.nam'); +% NMLST.NAM_FRAC.XUNIF_NATURE = 0.1; +% write_namelist(NMlST, 'MOD_OPTIONS.nam'); +% +% Written by: Darien Pardinas Diaz (darien.pardinas-diaz@monash.edu) +% Version: 1.0 +% Date: 16 Dec 2011 + +S = struct(); +% Open and read the text file containing the namelists +fid = fopen(filename,'r'); +c = 0; +lines = cell(1); + +% Read all the text lines in namelist file +while ~feof(fid) + line = fgetl(fid); + % Remove comments if any on the line + idx = find(line == '!'); + if ~isempty(idx), + line = line(1:idx(1)-1); + end + if ~isempty(line), + c = c + 1; + lines{c} = line; + end +end +fclose(fid); + +i = 0; +while i < c; + % Find a record + i = i + 1; + line = lower(lines{i}); + idx = find(line == '&'); + if ~isempty(idx), % i.e. a namelist start + line = line(idx(1) + 1:end); + % find next space + idx = find(line == ' '); + if ~isempty(idx), + namelst = lower(line(1:idx(1) - 1)); + line = line(idx(1) + 1:end); + else + namelst = lower(line); + line = []; + end + nmlst_bdy = []; + idx = strfind(line,'/'); + % Get the variable specification section + while isempty(idx) && i < c, + nmlst_bdy = [nmlst_bdy ' ' line]; + i = i + 1; + line = lines{i}; + idx = strfind(line,'/'); + end + if ~isempty(idx) && idx(1) > 1, + nmlst_bdy = [nmlst_bdy ' ' line]; + end + if nmlst_bdy==' ' + S.(namelst) = struct; + continue + end + % Parse current namelist (set of variables) + [S.(namelst), shift] = parse_namelist(nmlst_bdy); + S.(namelst).shift = shift; + end +end +function [S, shift] = parse_namelist(strng) +% Internal function to parse the body text of a namelist section. +% Limitations: the following patterns are prohibited inside the literal +% strings: '.t.' '.f.' '.true.' '.false.' '(:)' + +% Get all .true., .t. and .false., .f. to T and F +strng = regexprep(strng,'\.true\.' ,'T','ignorecase'); +strng = regexprep(strng,'\.false\.','F','ignorecase'); +strng = regexprep(strng,'\.t\.','T','ignorecase'); +strng = regexprep(strng,'\.f\.','F','ignorecase'); + +% Make evaluable the (:) expression in MATLAB if any +strng = regexprep(strng, '\(:\)', '(1,:)'); +[strng, islit] = parse_literal_strings([strng ' ']); + +% Find the position of all the '=' +eq_idx = find(strng == '='); +nvars = length(eq_idx); + +arg_start = eq_idx + 1; +arg_end = zeros(size(eq_idx)); +vars = cell(nvars,1); +S = struct; + +% Loop through every variable +for k = 1:nvars + i = eq_idx(k) - 1; + % Move to the left and discard blank spaces + while strng(i) == ' ', i = i - 1; end + % Now we are over the variable name or closing parentesis + j = i; + if strng(i) == ')' + while strng(i) ~= '(', i = i - 1; end + i = i - 1; + % Move to the left and discard any possible blank spaces + while strng(i) == ' ', i = i - 1; end + end + + % Now we are over the last character of the variable name + while strng(i) ~= ' ', i = i - 1; end + + if k > 1, arg_end(k - 1) = i; end + vars{k} = ['S.' lower(strng(i + 1: j))]; +end + +arg_end(end) = length(strng); + + +% Find all array, shift indices +shift = struct; +k_array = zeros(1,nvars); +for k=1:nvars + v = lower(vars{k}); + + % Check if it is an array + ind_open = find(v=='('); + if isempty(ind_open) + continue + end + + ind_close = find(v==')'); + if isempty(ind_close) + continue + end + + % Store info + k_array(k) = 1; + + % get how many dimensions + v_name = lower(v(3:ind_open-1)); + v_ind = v(ind_open+1:ind_close-1); + + indices = str2num(v_ind); + dim = length(indices); + + + % Loop on dimensions + if( isfield(shift, v_name) ) + for idim = 1:dim + ind = indices(idim); + + % Check if shift larger + new_shift = 1 - ind; + old_shift = shift.(v_name)(idim); + shift.(v_name)(idim) = max( new_shift, old_shift ); + end + else % First encounter with this variable + for idim = 1:dim + ind = indices(idim); + if ind>0 + shift.(v_name)(idim) = 0.0; + else + shift.(v_name)(idim) = 1-ind; + end + end + end + + + +end + + + +% This variables are used in the eval function to evaluate True/False, +% so don't remove it! +T = '.true.'; +F = '.false.'; +% Loop through every variable guess variable type +for k = 1:nvars + arg = strng(arg_start(k):arg_end(k)); + arglit = islit(arg_start(k):arg_end(k))'; + + % Remove commas in non literal string... + commas = ~arglit & arg == ','; + if any(commas) + arg(commas) = ' '; + end + + if any(arglit) + % We are parsing a variable that is literal string + arg = ['{' arg '};']; + elseif ~isempty(find( arg == 'T' | arg == 'F', 1)) + % We are parsing a boolean variable + arg = ['{' arg '};']; + else + % We are parsing a numerical array + arg = ['[' arg '];']; + end + + + % Eval the modified syntax in Matlab + if k_array(k)==0 + eval([vars{k} ' = ' arg]); + else % apply shift + v = lower(vars{k}); + ind_open = find(v=='('); + ind_close = find(v==')'); + v_name = lower(v(3:ind_open-1)); + v_ind = v(ind_open+1:ind_close-1); + + tmp = find(v_ind==','); + dim = length(tmp)+1; + + + %indices = str2num(v_ind); + + newstr = ['S.', lower(v_name), '(']; + for idim = 1:dim + if idim==1 + ind_start=1; + else + ind_start=tmp(idim-1)+1; + end + + if idim==dim + ind_end=length(v_ind); + else + ind_end=tmp(idim)-1; + end + + strdim = v_ind(ind_start:ind_end); + + indsmcl = find(strdim==':'); + + if isempty(indsmcl) + new_ind = str2num(strdim) + shift.(v_name)(idim); + new_ind = sprintf('%i', new_ind); + else + a = str2num(strdim(1:indsmcl-1)) + shift.(v_name)(idim); + b = str2num(strdim(indsmcl+1:end)) + shift.(v_name)(idim); + new_ind = sprintf('%i:%i', a, b); + end + + if idim==1 + newstr = sprintf( '%s%s', newstr, new_ind ); + else + newstr = sprintf( '%s,%s', newstr, new_ind ); + end + + end + newstr = sprintf( '%s) = %s', newstr, arg ); + + eval(newstr); + end +end +function [strng, is_lit] = parse_literal_strings(strng) +% Parse the literal declarations of strings and change to Matlab syntax + +len = length(strng); +add_squote = []; % Positions to add a scape single quote on syntax +rem_dquote = []; % Positions to remove a double quote scape on syntax +i = 1; +while i < len + if strng(i) == '''', % Opening string with single quote... + i = i + 1; + while i < len && strng(i) ~= '''' || strcmp(strng(i:i+1),'''''') , + i = i + 1; + if strcmp(strng(i-1:i),''''''), + i = i + 1; + end + end + end + if strng(i) == '"', % Opening string with double quote... + strng(i) = ''''; % Change to single quote + i = i + 1; + while strng(i) ~= '"' || strcmp(strng(i:i+1),'""') && i < len, + % Check for a possible sigle quote here + if strng(i) == '''', + add_squote = [add_squote i]; + end + i = i + 1; + if strcmp(strng(i-1:i),'""'), + rem_dquote = [rem_dquote i-1]; + i = i + 1; + end + end + strng(i) = ''''; % Change to single quote + end + i = i + 1; +end +for i = 1:length(add_squote); + strng = [strng(1:add_squote(i)) strng(add_squote(i):end)]; +end +for i = 1:length(rem_dquote); + strng = [strng(1:rem_dquote(i)-1) strng(rem_squote(i)+1:end)]; +end + +% Now everything should be in Matlab string syntax +% Classify syntax as literal or regular expression +i = 1; +len = length(strng); +is_lit = zeros(len,1); +while i < len, + if strng(i) == '''', % Opening string with single quote... + is_lit(i) = 1; + i = i + 1; + while i < len && strng(i) ~= '''' || strcmp(strng(i:i+1),''''''), + is_lit(i) = 1; + i = i + 1; + if strcmp(strng(i-1:i),''''''), + is_lit(i) = 1; + i = i + 1; + end + end + is_lit(i) = 1; + end + i = i + 1; +end \ No newline at end of file diff --git a/Utilities/matlabtools/SPEC_Namelist/rw_namelist/write_namelist.m b/Utilities/matlabtools/SPEC_Namelist/rw_namelist/write_namelist.m new file mode 100755 index 00000000..9f0dedb1 --- /dev/null +++ b/Utilities/matlabtools/SPEC_Namelist/rw_namelist/write_namelist.m @@ -0,0 +1,100 @@ +function write_namelist(S, filename, endlines) +% WRITE_NAMELIST(S, FILENAME) writes a namelist data structure S to a +% file FILENAME. S should follow the following structure: +% +% |--VAR1 +% |--VAR2 +% |-- NMLST_A--|... +% | |--VARNa +% | +% | |--VAR1 +% |-- NMLST_B--|--VAR2 +% | |... +% S --| ... |--VARNb +% | +% | |--VAR1 +% |-- NMLST_M--|--VAR2 +% |... +% |--VARNm +% +% Notes: Only supports variables of type: +% Scalars, vectors and 2D numeric arrays (integers and floating points) +% Scalars and 1D boolean arrays specified as '.true.' and '.false.' strings +% Single and 1D arrays of strings +% +% Example: +% NMLST = read_namelist('OPTIONS.nam'); +% NMLST.NAM_FRAC.XUNIF_NATURE = 0.1; +% write_namelist(NMlST, 'MOD_OPTIONS.nam'); +% +% Written by: Darien Pardinas Diaz (darien.pardinas-diaz@monash.edu) +% Version: 1.0 +% Date: 16 Dec 2011 + +fid = fopen(filename, 'w'); +name_lists = fieldnames(S); +n_name_lists = length(name_lists); + +for i = 1:n_name_lists + % Write individual namelist records + if strcmp(name_lists{i}, 'shift') + continue + end + + fprintf(fid, '&%s\n', name_lists{i}); + rcrds = S.(name_lists{i}); + + + rcrds_name = fieldnames(rcrds); + n_rcrds = length(rcrds_name); + + for j = 1:n_rcrds + if strcmp(rcrds_name{j},'shift') + continue + end + + var = rcrds.(rcrds_name{j}); + % Find variable type... + if iscell(var) + fprintf(fid, ' %s =', rcrds_name{j}); + if strcmp(var{1},'.true.') || strcmp(var{1},'.false.') + for k = 1:length(var) + fprintf(fid, ' %s,', var{k}); + end + else + for k = 1:length(var) + fprintf(fid, ' %s,', ['''' var{k} '''']); + end + end + fprintf(fid, '%s\n', ''); + else + [n,m] = size(var); + if m == 1 || n == 1 + % Variable is a scalar or vector + fprintf(fid, ' %s =', rcrds_name{j}); + fprintf(fid, ' %g,', var); + fprintf(fid, '%s\n', ''); + else + % Varible is a two dimensional array + for k = 1:n + fprintf(fid, ' %s(%i,%i:%i) =', rcrds_name{j}, k-S.shift.(rcrds_name{j})(1), ... + 1-S.shift.(rcrds_name{j})(2), ... + m-S.shift.(rcrds_name{j})(2) ); + fprintf(fid, ' %g,', var(k,:)); + fprintf(fid, '%s\n', ''); + end + end + end + end + fprintf(fid, '%s\n', '/'); +end + +s = length(endlines); +for ii=1:s + + fprintf(fid, '%s\n', endlines{ii}); + +end + + + diff --git a/Utilities/matlabtools/Tutorial.01.txt b/Utilities/matlabtools/Tutorial.01.txt index 9594c413..92391167 100644 --- a/Utilities/matlabtools/Tutorial.01.txt +++ b/Utilities/matlabtools/Tutorial.01.txt @@ -22,11 +22,11 @@ 3. Call ploting routine for Poincare section: - plot_spec_poincare(data,1,5,0,1); + plot_spec_poincare(data,1,1,1); 4. Call ploting routine for ideal-interfaces on Poincare section: - plot_spec_kam(data,0,0); + plot_spec_kam(data,1,0); %%% More details %%% diff --git a/Utilities/matlabtools/Tutorial.02.txt b/Utilities/matlabtools/Tutorial.02.txt index b7420250..8aaaff1a 100644 --- a/Utilities/matlabtools/Tutorial.02.txt +++ b/Utilities/matlabtools/Tutorial.02.txt @@ -21,7 +21,7 @@ 3. Call ploting routine for |B| on the boundary surface: - plot_spec_modB_boundary(data,2,32,64); + plot_spec_modB_boundary(data, 2, 0, 64, 64, 3); 3. Call ploting routine for |B| on a cross-section for volumes lvol=2 and lvol=1: diff --git a/Utilities/matlabtools/compare_spec_outputs.m b/Utilities/matlabtools/compare_spec_outputs.m index d4588b30..30da8e99 100644 --- a/Utilities/matlabtools/compare_spec_outputs.m +++ b/Utilities/matlabtools/compare_spec_outputs.m @@ -1,19 +1,27 @@ -function [Dabs, Drel, df] = compare_spec_outputs(fname1,fname2) +function [Dabs, Drel, df] = compare_spec_outputs(data1,data2) +% +% COMPARE_SPEC_OUTPUTS( DATA1, DATA2 ) +% ==================================== +% % Compares the interface geometry of two spec outputs % Two outputs are considered "the same" if df ~ 1e-15 (or less) % % INPUT -% - fname1 : path to the hdf5 output file #1 -% - fname2 : path to the hdf5 output file #2 +% ----- +% - data1: data obtained via read_spec( fname1 ) +% - data2: data obtained via read_spec( fname2 ) % % OUTPUT +% ------ % - Dabs : absolute maximum distance % - Drel : relative maximum distance % - df : expected change in force-balance if one output is used as input for the other run % % written by J.Loizu (08.2017) % modified by J.Loizu (10.2017) +% +% TODO: UPDATE - IS THIS STILL CORRECT ? % % Rmn1 = h5read(fname1,'/Rbc'); @@ -23,13 +31,13 @@ % Rmn2 = h5read(fname2,'/Rbc'); % Zmn2 = h5read(fname2,'/Zbs'); -data = read_spec(fname1); -Rmn1 = data.output.Rbc; -Zmn1 = data.output.Zbs; +%data = read_spec(fname1); +Rmn1 = data1.output.Rbc; +Zmn1 = data1.output.Zbs; -data = read_spec(fname2); -Rmn2 = data.output.Rbc; -Zmn2 = data.output.Zbs; +%data = read_spec(fname2); +Rmn2 = data2.output.Rbc; +Zmn2 = data2.output.Zbs; maxR = max(max(abs(Rmn1-Rmn2))); diff --git a/Utilities/matlabtools/contra2cov.m b/Utilities/matlabtools/contra2cov.m index ae42ec42..be901b7c 100644 --- a/Utilities/matlabtools/contra2cov.m +++ b/Utilities/matlabtools/contra2cov.m @@ -8,11 +8,10 @@ % % INPUT % ----- -% data: via read_spec(filename) +% data: via read_spec(filename) % vol: volume +% vcontrav: structure containing contravariant components as a function of r, size = 3xlength(r) % s: radial coordinate -% vcontrav: contravariant vector as a function of r, size = 3xlength(r) -% ns: number of point in each volume for interpolation % theta: theta angle % phi: phi angle % norm: use the unitary (canonical) basis (=1) or the general @@ -21,74 +20,61 @@ % OUTPUT % ------ % vcov: covariant vector as a function v +% +% -% Read geometry -G = data.input.physics.Igeometry; - - -% Get R derivatives -[s, R] = get_spec_R_derivatives(data, vol, s, theta, phi, 'R'); -[s, Z] = get_spec_R_derivatives(data, vol, s, theta, phi, 'Z'); - - -nt = length(theta); -np = length(phi); -ns = length(s); - -% transform in covariant basis -g = get_spec_metric(data, vol, s, theta, phi); - -switch G - case 1 - norm1 = sqrt(1 + R{3}.^2 + R{4}.^2) ./ R{2}; - norm2 = ones(size(R{1})); - norm3 = ones(size(R{1})); - - case 2 - norm1 = sqrt(R{3}.^2 + R{1}.^2 + (R{1}.*R{4}).^2) ./ (R{2}.*R{1}); - norm2 = 1 ./ R{1}; - norm3 = ones(size(R{1})); - - case 3 - norm1 = sqrt((R{3}.*Z{4}).^2 + (R{4}.*Z{3}).^2 + (R{1}.*Z{3}).^2 ... - -2*R{3}.*R{4}.*Z{3}.*Z{4} + (R{1}.*R{3}).^2); - norm2 = sqrt((R{4}.*Z{2}).^2 + (R{1}.*Z{2}).^2 + (R{2}.*Z{4}).^2 + (R{1}.*R{2}).^2 ... - -2*R{2}.*R{4}.*Z{2}.*Z{4}); - norm3 = sqrt((R{2}.*Z{3}).^2 + (R{3}.*Z{2}).^2 -2*R{2}.*R{3}.*Z{2}.*Z{3}); - -end +% TODO: test - is this useful ? -% Compute covariant components -temp = cell(1,3); -vcov = cell(1,3); -for ii=1:3 - temp{ii} = zeros(ns, nt, np); - vcov{ii} = zeros(ns, nt, np); -end + % Read geometry + G = data.input.physics.Igeometry; + % Get R derivatives + R = get_spec_R_derivatives(data, vol, s, theta, phi, 'R'); + Z = get_spec_R_derivatives(data, vol, s, theta, phi, 'Z'); -for is = 1:ns - for it = 1:nt - for ip = 1:np - temp{1} = vcontrav{1}.*g{1}{1} + vcontrav{2}.*g{1}{2} + vcontrav{3}.*g{1}{3}; - temp{2} = vcontrav{1}.*g{2}{1} + vcontrav{2}.*g{2}{2} + vcontrav{3}.*g{2}{3}; - temp{3} = vcontrav{1}.*g{3}{1} + vcontrav{2}.*g{3}{2} + vcontrav{3}.*g{3}{3}; - end + % transform in covariant basis + g = get_spec_metric(data, vol, s, theta, phi); + + % Compute covariant components + vcov = cell(1,3); + + for ii=1:3 + vcov{ii} = zeros(size(vcontrav)); end -end -% Normalize to canonical basis if necessary -if norm - vcov{1} = temp{1} .* norm1; - vcov{2} = temp{2} .* norm2; - vcov{3} = temp{3} .* norm3; -else - vcov = temp; -end + vcov{1} = vcontrav{1}.*g{1,1} + vcontrav{2}.*g{1,2} + vcontrav{3}.*g{1,3}; + vcov{2} = vcontrav{1}.*g{2,1} + vcontrav{2}.*g{2,2} + vcontrav{3}.*g{2,3}; + vcov{3} = vcontrav{1}.*g{3,1} + vcontrav{2}.*g{3,2} + vcontrav{3}.*g{3,3}; + + % Normalize to canonical basis (unit vector) if necessary + if norm + + switch G + case 1 + norm1 = sqrt(1 + R{3}.^2 + R{4}.^2) ./ R{2}; + norm2 = ones(size(R{1})); + norm3 = ones(size(R{1})); + + case 2 + norm1 = sqrt(R{3}.^2 + R{1}.^2 + (R{1}.*R{4}).^2) ./ (R{2}.*R{1}); + norm2 = 1 ./ R{1}; + norm3 = ones(size(R{1})); + case 3 + norm1 = sqrt((R{3}.*Z{4}).^2 + (R{4}.*Z{3}).^2 + (R{1}.*Z{3}).^2 ... + -2*R{3}.*R{4}.*Z{3}.*Z{4} + (R{1}.*R{3}).^2); + norm2 = sqrt((R{4}.*Z{2}).^2 + (R{1}.*Z{2}).^2 + (R{2}.*Z{4}).^2 + (R{1}.*R{2}).^2 ... + -2*R{2}.*R{4}.*Z{2}.*Z{4}); + norm3 = sqrt((R{2}.*Z{3}).^2 + (R{3}.*Z{2}).^2 -2*R{2}.*R{3}.*Z{2}.*Z{3}); + end + + vcov{1} = vcov{1} .* norm1; + vcov{2} = vcov{2} .* norm2; + vcov{3} = vcov{3} .* norm3; + end end diff --git a/Utilities/matlabtools/extract_shear.m b/Utilities/matlabtools/extract_shear.m new file mode 100644 index 00000000..8632529f --- /dev/null +++ b/Utilities/matlabtools/extract_shear.m @@ -0,0 +1,39 @@ +%% extract_shear(DATA, n, shift, n_surf) +% ======================================= +% +% Compute the shear (from iota) out of +% a SPEC out data +% +% INPUT +% ----- +% -data : must be produced using read_spec +% -n : length(iota) - (n_surf+shift-1); +% -shift : shift of the indices we take into account when computing +% shear (1st indices might not be relevant (too close to axis)) +% -n_surf : index of the first surface that encircles the magnetic axis +% +% ------------------------------------% +% Written by S.Guinchard (05/12/22) % +% ------------------------------------% +function out = extract_shear(d, n, shift, n_surf) + + id = n_surf+shift; + radial_coord = (d.transform.fiota(:,1)); % extract radial coordinate + out.mat_iota = d.transform.fiota(id:end,2); % extract iota + out.mat_r_coord = radial_coord(id:end); % truncates the radial coordinates (remove 5 first terms) + out.mat_s_coord = ((out.mat_r_coord + 1)./2); % change of variable r <--> s + out.scan_11 = d.output.Rbc(11,2); % Value of R11 + out.scan_10 = d.output.Rbc(2,2); % Value of R10 + + % CENTERED FINITE DIFFERENCES + out.derivatives(1) = (out.mat_iota(2) - out.mat_iota(1)) / (out.mat_s_coord(2) - out.mat_s_coord(1)); + out.derivatives(n) = (out.mat_iota(n) - out.mat_iota(n-1)) / (out.mat_s_coord(n) - out.mat_s_coord(n-1)); + + for j=2:n-1 + out.derivatives(j) = (out.mat_iota(j+1) - out.mat_iota(j-1)) / (out.mat_s_coord(j+1) - out.mat_s_coord(j-1)); + end + + out.coeff = out.mat_s_coord ./ (out.mat_iota) ; + out.shear = (out.coeff)' .* out.derivatives; + out.avg_shear = mean(out.shear); % Avg shear +end \ No newline at end of file diff --git a/Utilities/matlabtools/get_SFL_fourier_modB.m b/Utilities/matlabtools/get_SFL_fourier_modB.m new file mode 100644 index 00000000..462dd245 --- /dev/null +++ b/Utilities/matlabtools/get_SFL_fourier_modB.m @@ -0,0 +1,82 @@ +%% get_SFL_fourier_modB( DATA, NTHETA, NPHI, ) +% ============================================= +% +% Generates an output data struct for the fourier +% coefficients Bmn of mod(B)in SFL coordinates +% +% INPUT +% ----- +% -data : must be produced by calling read_spec(filename) +% -Ntheta : number of meshpoints for theta array +% -Nphi : number of meshpoints for phi array +% +% ------------------------------------% +% Written by S.Guinchard (05/23/22) % +% ------------------------------------% +function data_Bmn = get_SFL_fourier_modB(d, Ntheta, Nphi) + + + Nfp = d.input.physics.Nfp; + Ntor = d.input.physics.Ntor; + Mpol = d.input.physics.Mpol; + K = 2*pi^2/double(Nfp); + + lambdamn = squeeze(d.output.lambdamn); + lambdamn = lambdamn(1:end,2); + mprime = d.output.ims; + nprime = d.output.ins/double(Nfp); + + data_Bmn.Theta = linspace(0, 2*pi, Ntheta); + %data_Bmn.Phi = linspace(0, 2*pi/double(Nfp), Nphi); %change accordingly + data_Bmn.Phi = linspace(0, 2*pi, Nphi); + + + data_Bmn.modB = zeros(Ntheta, Nphi); + modB_SPEC = squeeze(get_spec_modB(d,1,1,data_Bmn.Theta,data_Bmn.Phi)); + + sumlmn = 0.0; + + for ind =2:length(lambdamn) + for line = 1:Ntheta + for column = 1:Nphi + sumlmn = sumlmn + mprime(ind)*lambdamn(ind)*cos(double(mprime(ind))*data_Bmn.Theta(line)-double(nprime(ind))*data_Bmn.Phi(column)); + end + end + end + + data_Bmn.jacobian = abs(double(1+sumlmn)); + + for m=0:Mpol + for n=-Ntor:Ntor + if m == 0 && n<0 + continue + end + for line = 1:Ntheta + for column = 1:Nphi + % evaluate modB_SPEC*cos(m theta - n phi) on the grid (theta, phi) + data_Bmn.modBcos(line,column) = modB_SPEC(line,column)* data_Bmn.jacobian ... + * cos(double(m)*data_Bmn.Theta(line) - double(Nfp)*double(n)*data_Bmn.Phi(column)); + end + end + + data_Bmn.Bmn(m+1,n+Ntor+1) = 1/K*trapz(data_Bmn.Phi,trapz(data_Bmn.Theta,data_Bmn.modBcos,1)); + end + end +% introduce missing 1/2 coefficient for mode (0,0) + data_Bmn.Bmn(1,Ntor+1) = 1/2*data_Bmn.Bmn(1,Ntor+1); + + for i=1:Ntheta + for m=0:Mpol + for n=-Ntor:Ntor + if m == 0 && n<0 + continue + end + data_Bmn.modB(i,:) = data_Bmn.modB(i,:) + data_Bmn.Bmn(m+1,n+Ntor+1)* ... + cos(double(m)*data_Bmn.Theta(i) - double(Nfp)*double(n)*data_Bmn.Phi); + end + end + end + data_Bmn.modB = data_Bmn.modB/2; + +%end of function +end \ No newline at end of file diff --git a/Utilities/matlabtools/get_boozer_coordinates.m b/Utilities/matlabtools/get_boozer_coordinates.m new file mode 100644 index 00000000..7ae57333 --- /dev/null +++ b/Utilities/matlabtools/get_boozer_coordinates.m @@ -0,0 +1,43 @@ +%% get_boozer_coordinates( BDATA, DATA, NPOINTS, NPERIODS ) +% ============================================= +% +% Computes the Boozer coordinates from a .boz.h5 file +% .boz.h5 file must be generated using run_boz.py (see corresponding repo) +% +% INPUT +% ----- +% -bdata : must be produced by calling read_boozer(filename, root) +% -data : must be produced using read_spec(filename) +% -Npoints : number of points to be used for the grid +% -Nperiods : Number of toroidal periods +% +% OUTPUT +% ------ +% -coordb : matlab struct with 2 fields - phi_boz, theta_boz +% ------------------------------------% +% Written by S.Guinchard (03/29/22) % +% ------------------------------------% + +function coordb = get_boozer_coordinates(b,d, Npoints, Nperiods) + +m = b.Booz_xForms.Outputs.xm_b; +n = b.Booz_xForms.Outputs.xn_b; + +coord = get_spec_straight_fieldlines(d,Npoints,Nperiods); +iota = b.Booz_xForms.Inputs.iota; +phi = coord.phi; +theta = coord.theta_sfl; +numns = b.Booz_xForms.Outputs.numns_b; +theta_b = theta; + +for i = 1:Npoints + for j =1:length(n) + phi(i) = phi(i) + numns(j) * sin(double(m(j))*theta(i) - double(n(j))*phi(i)); + theta_b(i) = theta_b(i) + iota * numns(j) * sin(double(m(j))*theta(i) - double(n(j))*phi(i)); + end +end + +coordb.phib = wrapTo2Pi(phi); +coordb.thetab = wrapTo2Pi(theta_b); + +end \ No newline at end of file diff --git a/Utilities/matlabtools/get_boozer_modB.m b/Utilities/matlabtools/get_boozer_modB.m new file mode 100644 index 00000000..2622e76e --- /dev/null +++ b/Utilities/matlabtools/get_boozer_modB.m @@ -0,0 +1,45 @@ +%% get_boozer_modB( BDATA, NTHETA, NPHI ) +% ============================================= +% +% Generates an output data struct for the fourier +% coefficients Bmn of mod(B) in Boozer coordinates +% +% INPUT +% ----- +% -bdata : must be produced by calling read_boozer(filename,root) +% -Ntheta : number of meshpoints for theta array +% -Nphi : number of meshpoints for phi array +% +% ------------------------------------% +% Written by S.Guinchard (05/18/22) % +% ------------------------------------% + +function modB = get_boozer_modB(b, Ntheta, Nphi) + + xm = double(b.Booz_xForms.Outputs.xm_b); + xn = double(b.Booz_xForms.Outputs.xn_b); + BmnB = b.Booz_xForms.Outputs.bmnc_b; + Nfp = double(b.Booz_xForms.Inputs.nfp); + + theta = linspace(0, 2*pi, Ntheta); + %phi = linspace(0, 2*pi/double(Nfp), Nphi); % (for 2D plot of modB boozer) + phi = linspace(0, 2*pi, Nphi); % (for 3D plot of modB boozer) + + [modB.Phi, modB.Theta] = meshgrid(phi, theta); + + + modB.modB = zeros(size(modB.Theta)); + for i =1:length(xm) + m = xm(i); + n = xn(i); + angle = (m* modB.Theta - n*modB.Phi); + modB.modB = modB.modB + BmnB(i)*cos(angle); + % case of stellarator symmetry (see init.from.spec.py) + if b.Booz_xForms.Inputs.asym == 1.0 + modB.modB = modB.modB + BmnB(i)*sin(angle); + end + end + + +end + \ No newline at end of file diff --git a/Utilities/matlabtools/get_metric_QA.m b/Utilities/matlabtools/get_metric_QA.m new file mode 100644 index 00000000..7997b880 --- /dev/null +++ b/Utilities/matlabtools/get_metric_QA.m @@ -0,0 +1,27 @@ +%% get_metric_QA(BDATA) +% ====================== +% +% Extract the QA metric from a Booz_xForms output +% +% INPUT +% ----- +% -bdata: must be produced calling read_boozer +% +% OUTPUT +% ------ +% -metric: the value of the QA_metric +% computed summing all bmnc_b^2 modes +% s.t n=!0 and normalising by mn_b*bmnc_b(0)^2 +% +% ------------------------------------% +% Written by S.Guinchard (05/12/22) % +% ------------------------------------% +function metric = get_metric_QA(b) + + bmnc_b = b.Booz_xForms.Outputs.bmnc_b; + xn_b = b.Booz_xForms.Outputs.xn_b; + ind = find(xn_b ~= 0); + metric = sum(bmnc_b(ind).^2)/(bmnc_b(1)^2); % Not divide enables convergence of metric w.r.t mpol + %metric = sum(bmnc_b(ind).^2)/(length(ind)*bmnc_b(1)^2); + +end \ No newline at end of file diff --git a/Utilities/matlabtools/get_metric_QH.m b/Utilities/matlabtools/get_metric_QH.m new file mode 100644 index 00000000..1349b5fc --- /dev/null +++ b/Utilities/matlabtools/get_metric_QH.m @@ -0,0 +1,36 @@ +%% get_metric_QH(BDATA, C) +% ====================== +% +% Extract the QH metric from a Booz_xForms output +% +% INPUT +% ----- +% -bdata: must be produced calling read_boozer +% -c : constant s.t c*m = n (Fourier modes) +% +% OUTPUT +% ------ +% -metric: the value of the QH_metric +% +% ------------------------------------% +% Written by S.Guinchard (05/12/22) % +% ------------------------------------% +function metric = get_metric_QH(b, c) + +bmnc_b = b.Booz_xForms.Outputs.bmnc_b; +xn_b = b.Booz_xForms.Outputs.xn_b; +xm_b = b.Booz_xForms.Outputs.xm_b; +nfp = double(b.Booz_xForms.Inputs.nfp); + +Mpol = b.Booz_xForms.Inputs.mpol; +Ntor = b.Booz_xForms.Inputs.ntor; +eq = find(xn_b ~= c*xm_b); % indices s.t c*m ~= n +m = find(abs(xm_b) <= Mpol ); % indices s.t abs(m) < Mpol +n = find(abs(xn_b) <= Ntor*nfp); % indices s.t abs(n) < Ntor +[val, indm, indn] = intersect(m,n); % val = indices s.t abs(m) < Mpol & abs(n) < Ntor +ind_to_sum = intersect(val,eq); % ind_to_sum = indices s.t c*m=!n and previous conditions + +metric = sum(bmnc_b(ind_to_sum).^2)/bmnc_b(1)^2; + + +end \ No newline at end of file diff --git a/Utilities/matlabtools/get_spec_Bxyz.m b/Utilities/matlabtools/get_spec_Bxyz.m new file mode 100644 index 00000000..726afb79 --- /dev/null +++ b/Utilities/matlabtools/get_spec_Bxyz.m @@ -0,0 +1,104 @@ +function xyz = get_spec_Bxyz( data, lvol, sarr, tarr, zarr ) +% +% GET_SPEC_BXYZ( DATA, LVOL, SARR, TARR, ZARR ) +% ============================================= +% +% Write the cartesian components of the magnetic field on a +% (x,y,z) grid on the outer side of the plasma-vacuum interface +% given a SPEC equilibrium. +% +% INPUTS +% ------ +% * DATA: data read from spec output via read_spec( fname ) +% * LVOL: volume +% * SARR: Array of s-coordinate +% * TARR: Array of poloidal angles +% * ZARR: Array of toroidal angles +% +% Written by A. Baillod (2021) +% + +% Check input +Igeometry = data.input.physics.Igeometry; +if Igeometry~=3 + error('Invalide geometry') +end + +% Read some input from data +Mvol = data.output.Mvol; + +if( lvol<1 || lvol>Mvol ) + error('invalid volume') +end + +% Reshape input +ns = length(sarr); +sarr = reshape( sarr, 1, ns); + +nt = length(tarr); +theta = reshape( tarr, 1, nt ); + +nz = length(zarr); +phi = reshape( zarr, 1, nz ); + +Rarr = get_spec_R_derivatives( data, Mvol, sarr, theta, phi, 'R' ); +Zarr = get_spec_R_derivatives( data, Mvol, sarr, theta, phi, 'Z' ); + + +% Transform to cartesian coordinates (x,y,z) +x = zeros(ns,nt,nz); +y = zeros(ns,nt,nz); +for is = 1:ns + for it = 1:nt + Rtmp = reshape(Rarr{1}(is,it,:), 1, nz); + + x(is,it,:) = Rtmp.*cos(phi); + y(is,it,:) = Rtmp.*sin(phi); + end +end +z = Zarr{1}; +z = reshape(z, ns, nt, nz); + +% Now evaluate field on each grid point +Bcontrav = get_spec_magfield( data, Mvol, sarr, theta, phi ); + +Bx = zeros(ns,nt,nz); +By = zeros(ns,nt,nz); +Bz = zeros(ns,nt,nz); + +for is = 1:ns + for it=1:nt + Bs = reshape( Bcontrav{1}(is,it,:), 1, nz); + Bt = reshape( Bcontrav{2}(is,it,:), 1, nz); + Bphi = reshape( Bcontrav{3}(is,it,:), 1, nz); + + R = reshape( Rarr{1}(is,it,:), 1, nz ); + Rs = reshape( Rarr{2}(is,it,:), 1, nz ); + Rt = reshape( Rarr{3}(is,it,:), 1, nz ); + Rz = reshape( Rarr{4}(is,it,:), 1, nz ); + + Zs = reshape( Zarr{2}(is,it,:), 1, nz ); + Zt = reshape( Zarr{3}(is,it,:), 1, nz ); + Zz = reshape( Zarr{4}(is,it,:), 1, nz ); + + Bx(is,it,:) = Bs.*(Rs.*cos(phi) ) ... + + Bt.*(Rt.*cos(phi) ) ... + + Bphi.*(Rz.*cos(phi) - R.*sin(phi)); + By(is,it,:) = Bs.*(Rs.*sin(phi) ) ... + + Bt.*(Rt.*sin(phi) ) ... + + Bphi.*(Rz.*sin(phi) + R.*cos(phi)); + Bz(is,it,:) = Bs.*Zs ... + + Bt.*Zt ... + + Bphi.*Zz; + end + +xyz.theta = theta; +xyz.phi = phi; +xyz.x = x; +xyz.y = y; +xyz.z = z; +xyz.Bx = Bx; +xyz.By = By; +xyz.Bz = Bz; + +end diff --git a/Utilities/matlabtools/get_spec_R_derivatives.m b/Utilities/matlabtools/get_spec_R_derivatives.m index 0fc30dfc..089279c1 100644 --- a/Utilities/matlabtools/get_spec_R_derivatives.m +++ b/Utilities/matlabtools/get_spec_R_derivatives.m @@ -1,4 +1,4 @@ -function [sarr, out] = get_spec_R_derivatives(data, vol, sarr, tarr, zarr, RorZ) +function out = get_spec_R_derivatives(data, vol, sarr, tarr, zarr, RorZ) % % GET_SPEC_R_DERIVATIVES( DATA, VOL, SARR, TARR, ZARR, RORZ ) @@ -25,70 +25,82 @@ % Written by A.Baillod (2019) % + % Test input + Istellsym = data.input.physics.Istellsym; + if Istellsym~=1 + error('Only implemented for stellarator symmetric equilibria') + end -% Load geometry -mn = data.output.mn; -im = double(data.output.im); -in = double(data.output.in); -Rmn = data.output.Rbc(:,vol ); -Rmn_p = data.output.Rbc(:,vol+1); -Zmn = data.output.Zbs(:,vol ); -Zmn_p = data.output.Zbs(:,vol+1); - -% Allocate data for R and its derivative in s, theta and phi (4), for each -% and for ns points -if(size(sarr,1)==1) -sarr = transpose(sarr); -end -ns = length(sarr); -nt = length(tarr); -nz = length(zarr); -Rarr = cell(2); -Zarr = cell(2); - -for ii=1:4 - Rarr{ii} = zeros(ns, nt, nz); - Zarr{ii} = zeros(ns, nt, nz); -end -% Compute the regularisation factor -factor = get_spec_regularization_factor(data, vol, sarr, 'G'); - -% And R derivatives -if RorZ=='R' - for imn=1:mn - for it=1:nt - for iz=1:nz - cosa = cos(double(im(imn)*tarr(it) - in(imn)*zarr(iz))); - sina = sin(double(im(imn)*tarr(it) - in(imn)*zarr(iz))); - - Rarr{1}(:,it,iz) = Rarr{1}(:,it,iz) + ( Rmn(imn) + (Rmn_p(imn) - Rmn(imn)) .* factor{imn}{1}) * cosa; - Rarr{2}(:,it,iz) = Rarr{2}(:,it,iz) + ( (Rmn_p(imn) - Rmn(imn)) .* factor{imn}{2}) * cosa; - Rarr{3}(:,it,iz) = Rarr{3}(:,it,iz) - ( Rmn(imn) + (Rmn_p(imn) - Rmn(imn)) .* factor{imn}{1}) * double(im(imn)) * sina; - Rarr{4}(:,it,iz) = Rarr{4}(:,it,iz) + ( Rmn(imn) + (Rmn_p(imn) - Rmn(imn)) .* factor{imn}{1}) * double(in(imn)) * sina; - end + % Load geometry + mn = data.output.mn; + im = double(data.output.im); + in = double(data.output.in); + Rmn = data.output.Rbc(:,vol ); + Rmn_p = data.output.Rbc(:,vol+1); + Zmn = data.output.Zbs(:,vol ); + Zmn_p = data.output.Zbs(:,vol+1); + + % Allocate data for R and its derivative in s, theta and phi (4), for each + % and for ns points + ns = length(sarr); + nt = length(tarr); + nz = length(zarr); + + sarr = reshape(sarr, ns, 1); + tarr = reshape(tarr, nt, 1); + zarr = reshape(zarr, nz, 1); + + Rarr = cell(1,4); + Zarr = cell(1,4); + + for ii=1:4 + Rarr{ii} = zeros(ns, nt, nz); + Zarr{ii} = zeros(ns, nt, nz); end - end - out = Rarr; - -elseif RorZ=='Z' - for imn=1:mn - for it=1:nt - for iz=1:nz - cosa = cos(double(im(imn)*tarr(it) - in(imn)*zarr(iz))); - sina = sin(double(im(imn)*tarr(it) - in(imn)*zarr(iz))); - - Zarr{1}(:,it,iz) = Zarr{1}(:,it,iz) + ( Zmn(imn) + (Zmn_p(imn) - Zmn(imn)) .* factor{imn}{1}) * sina; - Zarr{2}(:,it,iz) = Zarr{2}(:,it,iz) + ( (Zmn_p(imn) - Zmn(imn)) .* factor{imn}{2}) * sina; - Zarr{3}(:,it,iz) = Zarr{3}(:,it,iz) + ( Zmn(imn) + (Zmn_p(imn) - Zmn(imn)) .* factor{imn}{1}) * double(im(imn))* cosa; - Zarr{4}(:,it,iz) = Zarr{4}(:,it,iz) - ( Zmn(imn) + (Zmn_p(imn) - Zmn(imn)) .* factor{imn}{1}) * double(in(imn))* cosa; + + % Compute the regularisation factor + factor = get_spec_regularisation_factor(data, vol, sarr, 'G'); + + + + % And R derivatives + if RorZ=='R' + for imn=1:mn + for it=1:nt + for iz=1:nz + cosa = cos(double(im(imn)*tarr(it) - in(imn)*zarr(iz))); + sina = sin(double(im(imn)*tarr(it) - in(imn)*zarr(iz))); + + Rarr{1}(:,it,iz) = Rarr{1}(:,it,iz) + ( Rmn(imn) + (Rmn_p(imn) - Rmn(imn)) .* factor{imn}{1}) * cosa; + Rarr{2}(:,it,iz) = Rarr{2}(:,it,iz) + ( (Rmn_p(imn) - Rmn(imn)) .* factor{imn}{2}) * cosa; + Rarr{3}(:,it,iz) = Rarr{3}(:,it,iz) - ( Rmn(imn) + (Rmn_p(imn) - Rmn(imn)) .* factor{imn}{1}) * double(im(imn)) * sina; + Rarr{4}(:,it,iz) = Rarr{4}(:,it,iz) + ( Rmn(imn) + (Rmn_p(imn) - Rmn(imn)) .* factor{imn}{1}) * double(in(imn)) * sina; + end + end end + out = Rarr; + + elseif RorZ=='Z' + for imn=1:mn + for it=1:nt + for iz=1:nz + cosa = cos(double(im(imn)*tarr(it) - in(imn)*zarr(iz))); + sina = sin(double(im(imn)*tarr(it) - in(imn)*zarr(iz))); + + Zarr{1}(:,it,iz) = Zarr{1}(:,it,iz) + ( Zmn(imn) + (Zmn_p(imn) - Zmn(imn)) .* factor{imn}{1}) * sina; + Zarr{2}(:,it,iz) = Zarr{2}(:,it,iz) + ( (Zmn_p(imn) - Zmn(imn)) .* factor{imn}{2}) * sina; + Zarr{3}(:,it,iz) = Zarr{3}(:,it,iz) + ( Zmn(imn) + (Zmn_p(imn) - Zmn(imn)) .* factor{imn}{1}) * double(im(imn))* cosa; + Zarr{4}(:,it,iz) = Zarr{4}(:,it,iz) - ( Zmn(imn) + (Zmn_p(imn) - Zmn(imn)) .* factor{imn}{1}) * double(in(imn))* cosa; + end + end + end + out = Zarr; + + else + error(['Not defined for RorZ=',RorZ]); end - end - out = Zarr; -else - error(['Not defined for RorZ=',RorZ]); end diff --git a/Utilities/matlabtools/get_spec_area.m b/Utilities/matlabtools/get_spec_area.m index 7a0e4772..a2389a41 100644 --- a/Utilities/matlabtools/get_spec_area.m +++ b/Utilities/matlabtools/get_spec_area.m @@ -1,4 +1,4 @@ -function Avol = get_spec_area(data,lvol,ns,nt,phi0) +function Avol = get_spec_area(data,lvol,smax,ns,nt,phi0) % % GET_SPEC_AREA( DATA, LVOL, NS, NT, PHI0 ) @@ -10,6 +10,7 @@ % ----- % -data : must be produced by calling read_spec(filename) % -lvol : volume number +% -smax : max s % -ns : is the resolution in the s-coordinate (e.g. 64) % -nt : is the resolution in the theta-coordinate (e.g. 64) % -phi0 : toroidal angle defining a toroidal plane @@ -25,14 +26,16 @@ smin = -0.999; %avoids singular inversion of the metric matrix -sarr = linspace(smin,1,ns); +% Define arrays +sarr = linspace(smin,smax,ns); tarr = linspace(0,2*pi,nt); +% Evaluate Jacobian and metric jacobian = get_spec_jacobian(data,lvol,sarr,tarr,phi0); gcontrav = get_spec_metric_contrav(data,lvol,sarr,tarr,phi0); - sqrtgradphi = sqrt(gcontrav{3}{3}); -Avol = sum(sum(jacobian(2:end,:).*sqrtgradphi(2:end,:)))*(2*2*pi)/(ns*nt); +% Evaluate area +Avol = trapz(tarr, trapz(sarr, jacobian.*sqrtgradphi, 1) ); end diff --git a/Utilities/matlabtools/get_spec_beta.m b/Utilities/matlabtools/get_spec_beta.m index 016247b3..3a9ef50b 100644 --- a/Utilities/matlabtools/get_spec_beta.m +++ b/Utilities/matlabtools/get_spec_beta.m @@ -14,7 +14,8 @@ % % OUTPUT % ------ -% -beta : value of beta on axis +% -beta_ax : value of beta on axis +% -beta_av : value of beta on average % % written by J.Loizu (2016) % modified by J.Loizu (05.2017) @@ -60,13 +61,12 @@ beta_av = sum(av_beta) / volume; ind = find(vols==1); -if length(ind)==0 volume_number = vols(lvol); +if length(ind)==0 volume_number = 1; volume = get_spec_volume(data,volume_number,64,64,64); modB = get_spec_modB(data,volume_number,sarr,tarr,zarr); jacobian = get_spec_jacobian(data, volume_number, sarr, tarr, zarr); arg = jacobian ./ (modB.^2); - av_beta(lvol) = press(volume_number)*trapz(zarr, trapz(tarr, trapz(sarr, arg, 1), 2), 3) / volume; beta_ax = av_beta(1); else beta_ax = av_beta(ind); diff --git a/Utilities/matlabtools/get_spec_energy_slab.m b/Utilities/matlabtools/get_spec_energy_slab.m index 222efe14..fab2d59d 100644 --- a/Utilities/matlabtools/get_spec_energy_slab.m +++ b/Utilities/matlabtools/get_spec_energy_slab.m @@ -22,44 +22,41 @@ % % written by J.Loizu (2018) -Nvol = data.input.physics.Nvol; - -W = 0; - -sarr = linspace(-1,1,ns); -tarr = linspace(0,2*pi,nt); -zarr = linspace(0,2*pi,nz); - -if(lv==0) - - for lvol=1:Nvol - - modB = get_spec_modB(data,lvol,sarr,tarr,zarr); - - jac = get_spec_jacobian_slab(data,lvol,sarr,tarr,zarr); - - F = jac.*modB.^2; - - dW = trapz(sarr,trapz(tarr,trapz(zarr,F,3),2)); - - W = W + 0.5*dW; - - end - -else - - lvol = lv; - - modB = get_spec_modB(data,lvol,sarr,tarr,zarr); - - jac = get_spec_jacobian_slab(data,lvol,sarr,tarr,zarr); - - F = jac.*modB.^2; - - dW = trapz(sarr,trapz(tarr,trapz(zarr,F,3),2)); - - W = W + 0.5*dW; - -end + % Test input + Igeometry = data.input.physics.Igeometry; + if Igeometry~=1 + error('This routine is only for slab geometries') + end + + % Read data + Nvol = data.input.physics.Nvol; + + W = 0; + + sarr = linspace(-1,1,ns); + tarr = linspace(0,2*pi,nt); + zarr = linspace(0,2*pi,nz); + + if(lv==0) + lvol_start=1; + lvol_end =Nvol; + else + lvol_start=lv; + lvol_end =lv; + end + + + for lvol=lvol_start:lvol_end + + % Evaluate mod B and jacobian + modB = get_spec_modB(data,lvol,sarr,tarr,zarr); + jac = get_spec_jacobian(data,lvol,sarr,tarr,zarr); + + % Integrate + F = jac.*modB.^2; + + dW = trapz(sarr,trapz(tarr,trapz(zarr,F,3),2)); + W = W + 0.5*dW; + end diff --git a/Utilities/matlabtools/get_spec_fractaldim.m b/Utilities/matlabtools/get_spec_fractaldim.m new file mode 100644 index 00000000..1bb4ad48 --- /dev/null +++ b/Utilities/matlabtools/get_spec_fractaldim.m @@ -0,0 +1,401 @@ +function [x, y, Dfrac, N, Lmin, Lmax] = get_spec_fractaldim(data, numline, mth, polyfit_degree, varargin) + +% +% GET_FRACTALDIM( N, L, CASE_TITLE, POLYFIT_DEGREE, N_PTS, PLOTFIG ) +% ================================================================== +% +% Plot the N, L parameters resulting from get_NL_boxcount and deduce the fractal dimension +% Ex : +% [D_polyfit, D_num, D_slope, Lmin_polyfit, Lmax_polyfit, Lmin_num, Lmax_num] = get_fractaldim(N_cantor, L_cantor, 1, 'Cantor', 6); +% +% INPUT +% ----- +% -data : SPEC output data, read from read_spec(filename) +% -numline : Line number +% -mth : 0: uses the mean value to get the fractal dim +% 1: evaluates numerically the curvature and +% extract the linear part +% 2: polyfits the curve and evaluate the curvature +% analytically to extract the linear part. +% -polyfit_degree : degree of the polyfit used to approximate the fractal +% dim. Only used if mth=2 +% +% OUTPUT +% ------ +% -x : log10( Lmax/L ) +% -y : log10( N ) +% -Dfrac : fractal dimension +% -N : Number of points as function of L +% -Lmin : Maximal L taken into account for evaluation of Dfrac +% -Lmax : Minimal L taken into account for evaluation of Dfrac +% + + % Optional input + % --------------- + torplane = 1; + base_exponent = 2; + kmin = 2; + kmax = 8; + newfig = 0; + + % Optional outputs + % ---------------- + Lmin = 0; + Lmax = 0; + + l = length(varargin); + if mod(l,2)~=0 + error('Invalid number of input arguments') + end + + for ii=1:l/2 + field = varargin{2*ii-1}; + value = varargin{2*ii }; + + switch field + case 'torplane' + torplane = value; + case 'base_exponent' + base_exponent = value; + case 'kmin' + kmin = value; + case 'kmax' + kmax = value; + case 'newfig' + newfig = value; + otherwise + warning(['Inknown input field: ', field, '. Ignored...']) + end + end + + + % Read some important input + % -------------------------- + R = data.poincare.R(numline,torplane,:); + Z = data.poincare.Z(numline,torplane,:); + + s = size( R ); + n_pts = s(3); + + % Perform box counting + % --------------------- + [N, L] = get_NL_boxcount(base_exponent, kmin, kmax, R, Z); + + % Set up... + idx = 1:length(N); + + % Get slopes between each datapoints + xp = diff(-log(L)); + yp = diff(log(N)); + + if newfig + figure('Color','w') + loglog( L, N, 'o', 'MarkerFaceColor', 'b') + ylabel('Number of box with a point N') + xlabel('Box size') + + end + + switch mth + case 0 % mean slope + + % take the centered finite differences and having forward and backward + % finite diff for the last points + xp_ = (xp(1:end-1) + xp(2:end))/2; + yp_ = (yp(1:end-1) + yp(2:end))/2; + slopes = [yp(1)/xp(1), yp_./xp_, yp(end)/xp(end)]; + + % For output... + Lmax = max(L); + Lmin = min(L); + + % polyf_1d = polyfit(-log(L),log(N), 1); + % D_slope = polyf_1d(1); + Dfrac = mean(slopes); + + + case 1 % numerical curvature + % idea is to remove the saturation plateau + % the -1 comes from the correspondance between the curvature and the slopes + min_plateau_idx_num = min(idx(N>0.95*n_pts))-1; + + % take the centered finite differences and having forward and backward + % finite diff for the last points + xp_ = (xp(1:end-1) + xp(2:end))/2; + yp_ = (yp(1:end-1) + yp(2:end))/2; + slopes = [yp(1)/xp(1), yp_./xp_, yp(end)/xp(end)]; + + % curvature + curv_num = curvature(-log(L),log(N)); + + % threshold (kind of arbitrary for the moment) + % we take the max w.r.t. a very low curvature in the case where the + % points are already all well aligned + threshold_num = max(max(curv_num)/2, 0.2); + + % find min, max indices + % there are always at least two points in between + [idx_min_num, idx_max_num] = find_idx_min_max(curv_num, threshold_num, min_plateau_idx_num); + + % we take the best points to compute the dimension + % the +1 are due to the correspondance between the curvature and the slopes + % taking a polyfit yields a similar accuracy than the mean slope + Dfrac = mean(slopes(idx_min_num+1:idx_max_num+1)); + + % determine the corresponding Lmin_num and Lmax_num + Lmin = L(idx_max_num+1); + Lmax = L(idx_min_num+1); + + case 2 % polyfit curvature + + % 100 logarithmically spaced values exp(x) with x between [beg, end] + Lfit = exp(linspace(log(L(1)), log(L(end)), 100)); + one_over_L = 1./Lfit; + + % the -1 comes from the correspondance between the curvature and the slopes + min_plateau_idx_polyfit = uint64((min(idx(N>0.95*n_pts))-1)*100/length(N)); + + % fit the whole data + p = polyfit(-log(L),log(N), polyfit_degree); + pp = polyder(p); + ppp = polyder(pp); + + curv_polyfit = abs(polyval(ppp,log(one_over_L)))./(1+polyval(pp,log(one_over_L)).^2).^(3/2); + + % threshold (kind of arbitrary for the moment) + threshold_polyfit = max(max(curv_polyfit)/10, 0.2); + + % find all zones (min, max indices) with curvature below threshold + [idx_min_polyfit, idx_max_polyfit] = find_idx_min_max(curv_polyfit, threshold_polyfit, min_plateau_idx_polyfit); + + % determine the corresponding Lmin_polyfit and Lmax_polyfit associated + % with kmax_edge and kmin_edge respectively if idx_min_polyfit or + % idx_max_polyfit is empty, it is a consequence of a too low threshold ! + Lmin = 1/one_over_L(idx_max_polyfit); + Lmax = 1/one_over_L(idx_min_polyfit); + + % taking a polyfit yields a similar accuracy than the mean slope + Dfrac = mean(polyval(pp,log(one_over_L(idx_min_polyfit:idx_max_polyfit-1)))); + + if newfig + hold on; + xx = log(Lfit); + yy = polyval(p, -xx); + loglog( exp(xx), exp(yy), 'LineWidth', 2 ) + ax = gca; + yy = ax.YLim; + loglog( Lmin_polyfit*[1,1], yy, 'k--' ) + loglog( Lmax_polyfit*[1,1], yy, 'k--' ) + end + + otherwise + + error('Invalid input') + + end + + x = log10(Lmax./L); + y = log10( N ); + +end + +% ========================================================================= +% ========================================================================= +function curv = curvature(x, y) + + % + % CURV = CURVATURE( X, Y ) + % ======================== + % + % Compute the curvature of the curve defined by x,y (the starting point and the endpoints have not defined curvature here, it is not checked whether the starting point and the endpoint coincide) + % + % INPUT + % ----- + % -x,y : coordinates of the curve + % + % OUTPUT + % ------ + % -curv : curvature of the curve + % + + xp = diff(x); xpp = diff(xp); + yp = diff(y); ypp = diff(yp); + + curv = zeros(1, length(x)-2); + % take the centered finite differences + xp_ = (xp(1:end-1) + xp(2:end))/2; + yp_ = (yp(1:end-1) + yp(2:end))/2; + + curv = abs(xp_.*ypp - yp_.*xpp)./(xp_.^2 + yp_.^2).^(3/2); + + % can also be implemented such as the following (exact same formula actually) + % for i = 1:length(xp)-1 + % % twice the area of the triangle between these 3 pts + % D = norm(xp(i)*yp(i+1)-yp(i)*xp(i+1)); + % a = (x(i)-x(i+1))^2 + (y(i)-y(i+1))^2; + % b = (x(i+1)-x(i+2))^2 + (y(i+1)-y(i+2))^2; + % c = (x(i)-x(i+2))^2 + (y(i)-y(i+2))^2; + % curv(i) = 2*D/(a*b*c); + % end +end + +% ============================================== +% ============================================== +function [idx_min, idx_max] = find_idx_min_max(curv, threshold, min_plateau_idx) + + % + % FIND_IDX_MIN_MAX( CURV, threshold, min_plateau_idx ) + % ================================================= + % + % Find the zones (min and max indices) associated with the minimal curvature under the threshold (one of them is the best linear zone) + % + % INPUT + % ----- + % -curv : curvature of the curve + % -threshold : threshold for the minimal curvature + % -plateau_idx : indices of the pts near the saturation plateau at log(n_pts) + % + % OUTPUT + % ------ + % -idx_min,idx_max : min and max indices for the linear zone + % + + n_curv = length(curv); + + % find all the indices such that both neighbours are below the threshold + start_pt_2_idx_below_threshold = []; + end_pt_2_idx_below_threshold = []; + for i = 1:n_curv + % finds the pts such that \_ + if i>1 && curv(i) < threshold && curv(i-1) > threshold || i==1 && curv(1) < threshold + start_pt_2_idx_below_threshold(end+1) = i; + end + % finds the pts such that _/ + if i threshold && curv(i) < threshold || i==n_curv && curv(n_curv) < threshold + end_pt_2_idx_below_threshold(end+1) = i; + end + end + + if length(end_pt_2_idx_below_threshold) > 1 + if ~isempty(min_plateau_idx) + % remove the plateau from the possibilities + while start_pt_2_idx_below_threshold(end) >= min_plateau_idx && length(end_pt_2_idx_below_threshold) > 1 + start_pt_2_idx_below_threshold(end) = []; + end_pt_2_idx_below_threshold(end) = []; + end + end + + % find the largest zone delta L + [~, idx_largest_delta_L] = max(end_pt_2_idx_below_threshold-start_pt_2_idx_below_threshold); + % as indices of curv + idx_min = start_pt_2_idx_below_threshold(idx_largest_delta_L); + idx_max = end_pt_2_idx_below_threshold(idx_largest_delta_L); + else + % as indices of curv + idx_min = start_pt_2_idx_below_threshold; + idx_max = end_pt_2_idx_below_threshold; + end +end + +function [N, L] = get_NL_boxcount(base_exponent, kmin, kmax, x, y) + + % + % GET_NL_BOXCOUNT( BASE_EXPONENT, KMIN, KMAX, X, Y ) + % ================================================== + % + % Get the N, L parameters necessary for fractal dimension computation using box-counting + % + % INPUT + % ----- + % -base_exponent : base of the exponential factor by which the box sizes are reduced (1 < base <= 2 is good) + % -kmin : min exponent linked to the size of the boxes (integer >= 0) + % -kmax : max exponent linked to the size of the boxes + % -x,y : coordinates of the points in the set to analyse (y optional) + % + % OUTPUT + % ------ + % -N : number of box counted + % -L : size of the box counted (normalized by the max size of the boxes Lmax) + % + + switch nargin + case 4 + dim = 1; + case 5 + dim = 2; + otherwise + error('Too many or not enough input arguments. Type "help get_NL_fractaldim" for more informations') + end + + n_pts = length(x); + N = zeros(1,kmax-kmin+1); + L = zeros(1,kmax-kmin+1); + x_min = min(x); + x_max = max(x); + p = 1; + + switch dim + case 1 % fractal is represented in 1D + Lmax = x_max-x_min; + + for k = kmin:kmax + s = base_exponent^k; + L(p) = Lmax/s; + + counter = zeros(1,ceil(s)); + + for i = 1:n_pts + % x-y indices of the i-th pt + is = 1+floor((x(i)-x_min)/L(p) ); + + try + counter(1,is) = 1; + catch + error(';problem') + end + end + + N(p) = sum(counter); + % increment p (boxsize parameter) + p = p+1; + end + + case 2 % fractal is represented in 2D + y_min = min(y); + y_max = max(y); + + % At least 1 box in each coordinate - total of 100 boxes + % Better precision than if one takes : + % Lmax = max([x_max-x_min, y_max-y_min]); + % However one must be careful with the memory allocation! + Lmax_x = x_max - x_min; + Lmax_y = y_max - y_min; + Lmax = min([Lmax_x, Lmax_y]); + if abs(Lmax) < 1e-7 + % due to points being possible + Lmax = 1; + end + for k = kmin:kmax + s = base_exponent^k; + L(p) = Lmax/s; + + counter = zeros(ceil(s * Lmax_x / Lmax), ceil(s * Lmax_y / Lmax)); + + for i = 1:n_pts + % x-y indices of the i-th pt + is = 1+floor((x(i)-x_min)/L(p) ); + js = 1+floor((y(i)-y_min)/L(p) ); + + try + counter(is,js) = 1; + catch + error(';problem') + end + end + + N(p) = sum(sum(counter)); + % increment p (boxsize parameter) + p = p+1; + end + end +end diff --git a/Utilities/matlabtools/get_spec_helicity_slab.m b/Utilities/matlabtools/get_spec_helicity_slab.m index 737aa935..2249257e 100644 --- a/Utilities/matlabtools/get_spec_helicity_slab.m +++ b/Utilities/matlabtools/get_spec_helicity_slab.m @@ -23,65 +23,70 @@ % % written by J.Loizu (2018) -Ate = data.vector_potential.Ate{lvol}; -Aze = data.vector_potential.Aze{lvol}; + % Test input + Igeometry = data.input.physics.Igeometry; + if( Igeometry~=1 ) + error('Invalid geometry. Only available for slab') + end -sarr = linspace(-1,1,ns); -tarr = linspace(0,2*pi,nt); -zarr = linspace(0,2*pi,nz); -sarr = transpose(sarr); -sbar = (sarr+1)/2; + % Read data + Ate = data.vector_potential.Ate{lvol}; + Aze = data.vector_potential.Aze{lvol}; -Lrad = data.input.physics.Lrad(lvol); -mn = data.output.mn; -im = double(data.output.im); -in = double(data.output.in); + sarr = linspace(-1,1,ns); + tarr = linspace(0,2*pi,nt); + zarr = linspace(0,2*pi,nz); + sarr = transpose(sarr); -h1 = zeros(ns,nt,nz); % allocate data for magnetic helicity integrand 1 -h2 = zeros(ns,nt,nz); % allocate data for magnetic helicity integrand 2 -h3 = zeros(ns,nt,nz); % allocate data for magnetic helicity integrand 3 -h4 = zeros(ns,nt,nz); % allocate data for magnetic helicity integrand 4 + Lrad = data.input.physics.Lrad(lvol); + mn = data.output.mn; + im = double(data.output.im); + in = double(data.output.in); -% Construct Chebyshev polynomials and their derivatives + h1 = zeros(ns,nt,nz); % allocate data for magnetic helicity integrand 1 + h2 = zeros(ns,nt,nz); % allocate data for magnetic helicity integrand 2 + h3 = zeros(ns,nt,nz); % allocate data for magnetic helicity integrand 3 + h4 = zeros(ns,nt,nz); % allocate data for magnetic helicity integrand 4 -T = get_spec_polynomial_basis(data, lvol, sarr); + % Construct Chebyshev polynomials and their derivatives -% Construct regularization factors and their derivatives + T = get_spec_polynomial_basis(data, lvol, sarr); -fac = get_spec_regularization_factor(data,lvol,sarr,'F'); + % Construct regularization factors and their derivatives -% Construct magnetic helicity integrand + fac = get_spec_regularisation_factor(data,lvol,sarr,'F'); -Lsingularity = false; -if (lvol==1) && (data.input.physics.Igeometry~=1) - Lsingularity = true; -end + % Construct magnetic helicity integrand -for l=1:Lrad+1 - for j=1:mn - if Lsingularity - basis = T{l}{1}(im(j)+1); - dbasis = T{l}{2}(im(j)+1); - else - basis = T{l}{1}; - dbasis = T{l}{2}; + Lsingularity = false; + if (lvol==1) && (data.input.physics.Igeometry~=1) + Lsingularity = true; end - for it=1:nt - for iz=1:nz - cosa = cos(im(j)*tarr(it)-in(j)*zarr(iz)); - sina = sin(im(j)*tarr(it)-in(j)*zarr(iz)); - h1(:,it,iz) = h1(:,it,iz) + fac{j}{1}.* basis.*Ate(l,j)*cosa; %A_t - h2(:,it,iz) = h2(:,it,iz) - (fac{j}{1}.*dbasis+fac{j}{2}.* basis).*Aze(l,j)*cosa; % -dA_z/ds - h3(:,it,iz) = h3(:,it,iz) + fac{j}{1}.* basis.*Aze(l,j)*cosa; %A_z - h4(:,it,iz) = h4(:,it,iz) + (fac{j}{1}.*dbasis+fac{j}{2}.* basis).*Ate(l,j)*cosa; % +dA_t/ds + for l=1:Lrad+1 + for j=1:mn + if Lsingularity + basis = T{l}{1}(im(j)+1); + dbasis = T{l}{2}(im(j)+1); + else + basis = T{l}{1}; + dbasis = T{l}{2}; + end + + for it=1:nt + for iz=1:nz + cosa = cos(im(j)*tarr(it)-in(j)*zarr(iz)); + h1(:,it,iz) = h1(:,it,iz) + fac{j}{1}.* basis .*Ate(l,j)*cosa; %A_t + h2(:,it,iz) = h2(:,it,iz) - (fac{j}{1}.*dbasis+fac{j}{2}.* basis).*Aze(l,j)*cosa; % -dA_z/ds + h3(:,it,iz) = h3(:,it,iz) + fac{j}{1}.* basis .*Aze(l,j)*cosa; %A_z + h4(:,it,iz) = h4(:,it,iz) + (fac{j}{1}.*dbasis+fac{j}{2}.* basis).*Ate(l,j)*cosa; % +dA_t/ds + end + end end end - end -end - -h = h1.*h2 + h3.*h4; - -H = trapz(sarr,trapz(tarr,trapz(zarr,h,3),2)); + % Evaluate helicity + h = h1.*h2 + h3.*h4; + H = trapz(sarr,trapz(tarr,trapz(zarr,h,3),2)); +end diff --git a/Utilities/matlabtools/get_spec_jacobian.m b/Utilities/matlabtools/get_spec_jacobian.m index ea11664d..5ce74412 100644 --- a/Utilities/matlabtools/get_spec_jacobian.m +++ b/Utilities/matlabtools/get_spec_jacobian.m @@ -23,17 +23,24 @@ % written by J.Loizu (2016) % modified by A. Baillod (2019) -[sarr, Rarr] = get_spec_R_derivatives(data, lvol, sarr, tarr, zarr, 'R'); + % Check input + Istellsym = data.input.physics.Istellsym; + if Istellsym==0 + error('Non stellarator symmetric not implemented') + end -switch data.input.physics.Igeometry - case 1 - jacobian = Rarr{2}; - case 2 - jacobian = Rarr{1}.*Rarr{2}; - case 3 - [sarr, Zarr] = get_spec_R_derivatives(data, lvol, sarr, tarr, zarr, 'Z'); - jacobian = Rarr{1}.*(Rarr{3}.*Zarr{2} - Rarr{2}.*Zarr{3}); - otherwise - error('Unsupported geometry in get_spec_jacobian') -end + Rarr = get_spec_R_derivatives(data, lvol, sarr, tarr, zarr, 'R'); + switch data.input.physics.Igeometry + case 1 + jacobian = Rarr{2}; + case 2 + jacobian = Rarr{1}.*Rarr{2}; + case 3 + Zarr = get_spec_R_derivatives(data, lvol, sarr, tarr, zarr, 'Z'); + jacobian = Rarr{1}.*(Rarr{3}.*Zarr{2} - Rarr{2}.*Zarr{3}); + otherwise + error('Unsupported geometry in get_spec_jacobian') + end + +end \ No newline at end of file diff --git a/Utilities/matlabtools/get_spec_magfield.m b/Utilities/matlabtools/get_spec_magfield.m index 91e4cce2..ef7f6e59 100644 --- a/Utilities/matlabtools/get_spec_magfield.m +++ b/Utilities/matlabtools/get_spec_magfield.m @@ -48,11 +48,7 @@ T = get_spec_polynomial_basis(data, lvol, sarr'); -% Construct regularization factors and their derivatives -%fac = get_spec_regularisation_factor(data, lvol, sarr, 'F'); - % Construct magnetic field contravariant components - Lsingularity = false; if (lvol==1) && (data.input.physics.Igeometry~=1) Lsingularity = true; diff --git a/Utilities/matlabtools/get_spec_metric.m b/Utilities/matlabtools/get_spec_metric.m index 09022d54..31dd8263 100644 --- a/Utilities/matlabtools/get_spec_metric.m +++ b/Utilities/matlabtools/get_spec_metric.m @@ -21,57 +21,65 @@ % Note: Stellarator symmetry is assumed % % written by J.Loizu (2016) -% modified by A. Baillod (2019) +% modified by A. Baillod (2019)] -% Allocate data for the metric matrix -ns = length(sarr); -nt = length(tarr); -nz = length(zarr); + % Check input + Istellsym = data.input.physics.Istellsym; + if Istellsym==0 + error('Non stellarator symmetric not implemented') + end + + % Allocate data for the metric matrix + ns = length(sarr); + nt = length(tarr); + nz = length(zarr); -gmat = cell(3,3); + gmat = cell(3,3); -for k=1:3 - for p=1:3 - gmat{k}{p} = zeros(ns,nt,nz); - end -end - -% Get R and Z and their derivatives + for k=1:3 + for p=1:3 + gmat{k,p} = zeros(ns,nt,nz); + end + end -[out, Rarr] = get_spec_R_derivatives(data,lvol,sarr,tarr,zarr,'R'); -[out, Zarr] = get_spec_R_derivatives(data,lvol,sarr,tarr,zarr,'Z'); + % Get R and its derivatives + Rarr = get_spec_R_derivatives(data,lvol,sarr,tarr,zarr,'R'); + % Construct metric elements -% Construct metric elements - -switch data.input.physics.Igeometry - case 1 - gmat{1}{1} = Rarr{2}.^2; - gmat{2}{2} = 1 + Rarr{3}.^2; - gmat{3}{3} = 1 + Rarr{4}.^2; - gmat{1}{2} = Rarr{2}.*Rarr{3}; - gmat{1}{3} = Rarr{2}.*Rarr{4}; - gmat{2}{3} = Rarr{3}.*Rarr{4}; - case 2 - gmat{1}{1} = Rarr{2}.^2; %gss - gmat{2}{2} = Rarr{3}.^2 + Rarr{1}.^2; %gtt - gmat{3}{3} = Rarr{4}.^2 + 1; %gzz - gmat{1}{2} = Rarr{2}.*Rarr{3}; %gst - gmat{1}{3} = Rarr{2}.*Rarr{4}; %gsz - gmat{2}{3} = Rarr{3}.*Rarr{4}; %gtz - case 3 - gmat{1}{1} = Rarr{2}.^2 + Zarr{2}.^2; %gss - gmat{2}{2} = Rarr{3}.^2 + Zarr{3}.^2; %gtt - gmat{3}{3} = Rarr{1}.^2 + Rarr{4}.^2 + Zarr{4}.^2; %gzz - gmat{1}{2} = Rarr{2}.*Rarr{3} + Zarr{2}.*Zarr{3}; %gst - gmat{1}{3} = Rarr{2}.*Rarr{4} + Zarr{2}.*Zarr{4}; %gsz - gmat{2}{3} = Rarr{3}.*Rarr{4} + Zarr{3}.*Zarr{4}; %gtz - otherwise - error('Unsupported geometry in get_spec_metric.m') -end + switch data.input.physics.Igeometry + case 1 % Slab geometry + gmat{1,1} = Rarr{2}.^2; + gmat{2,2} = 1 + Rarr{3}.^2; + gmat{3,3} = 1 + Rarr{4}.^2; + gmat{1,2} = Rarr{2}.*Rarr{3}; + gmat{1,3} = Rarr{2}.*Rarr{4}; + gmat{2,3} = Rarr{3}.*Rarr{4}; + + case 2 % Cylindrical geometry + gmat{1,1} = Rarr{2}.^2; %gss + gmat{2,2} = Rarr{3}.^2 + Rarr{1}.^2; %gtt + gmat{3,3} = Rarr{4}.^2 + 1; %gzz + gmat{1,2} = Rarr{2}.*Rarr{3}; %gst + gmat{1,3} = Rarr{2}.*Rarr{4}; %gsz + gmat{2,3} = Rarr{3}.*Rarr{4}; %gtz + + case 3 %Toroidal geometry + % Get Z and its derivatives + Zarr = get_spec_R_derivatives(data,lvol,sarr,tarr,zarr,'Z'); + + gmat{1,1} = Rarr{2}.^2 + Zarr{2}.^2; %gss + gmat{2,2} = Rarr{3}.^2 + Zarr{3}.^2; %gtt + gmat{3,3} = Rarr{1}.^2 + Rarr{4}.^2 + Zarr{4}.^2; %gzz + gmat{1,2} = Rarr{2}.*Rarr{3} + Zarr{2}.*Zarr{3}; %gst + gmat{1,3} = Rarr{2}.*Rarr{4} + Zarr{2}.*Zarr{4}; %gsz + gmat{2,3} = Rarr{3}.*Rarr{4} + Zarr{3}.*Zarr{4}; %gtz + otherwise + error('Unsupported geometry in get_spec_metric.m') + end -gmat{2}{1} = gmat{1}{2}; % by symmetry of g -gmat{3}{1} = gmat{1}{3}; -gmat{3}{2} = gmat{2}{3}; + gmat{2,1} = gmat{1,2}; % by symmetry of g + gmat{3,1} = gmat{1,3}; + gmat{3,2} = gmat{2,3}; end diff --git a/Utilities/matlabtools/get_spec_metric_contrav.m b/Utilities/matlabtools/get_spec_metric_contrav.m index 8ca27c04..e3589062 100644 --- a/Utilities/matlabtools/get_spec_metric_contrav.m +++ b/Utilities/matlabtools/get_spec_metric_contrav.m @@ -15,12 +15,16 @@ % % OUTPUT % ------ -% gmatcon{i}{j}(s,theta,zeta) +% gmatcon{i,j}(s,theta,zeta) % % Note: Stellarator symmetry is assumed % % written by J.Loizu (2017) +Istellsym = data.input.physics.Istellsym; +if Istellsym~=1 + error('Only valid for stellarator symmetric equilibria') +end % Auxiliary variables @@ -30,19 +34,11 @@ nz = length(zarr); % First get the covariant metric matrix - gmatcov = get_spec_metric(data,lvol,sarr,tarr,zarr); % Allocate space for contravariant metric matrix - gmatcon = cell(3,3); -for k=1:3 - for p=1:3 - gmatcon{k}{p} = zeros(ns,nt,nz); - end -end - % Initiate calculation loop (over each position on the surface) for is=1:ns @@ -53,66 +49,51 @@ % Define arrays of gcov, gcon, and rhs rhs = transpose([1 1 1 0 0 0]); - gcon = zeros(6,1); - gcov = zeros(6,1); - - gcov(1) = gmatcov{1}{1}(is,it,iz); - gcov(2) = gmatcov{2}{2}(is,it,iz); - gcov(3) = gmatcov{3}{3}(is,it,iz); - gcov(4) = gmatcov{1}{2}(is,it,iz); - gcov(5) = gmatcov{1}{3}(is,it,iz); - gcov(6) = gmatcov{2}{3}(is,it,iz); % Define transformation matrix G - G = zeros(6,6); - G(1,1) = gmatcov{1}{1}(is,it,iz); - G(2,2) = gmatcov{2}{2}(is,it,iz); - G(3,3) = gmatcov{3}{3}(is,it,iz); - G(4,4) = gmatcov{1}{1}(is,it,iz); - G(5,5) = gmatcov{1}{1}(is,it,iz); - G(6,6) = gmatcov{2}{2}(is,it,iz); + G(1,1) = gmatcov{1,1}(is,it,iz); + G(2,2) = gmatcov{2,2}(is,it,iz); + G(3,3) = gmatcov{3,3}(is,it,iz); + G(4,4) = gmatcov{1,1}(is,it,iz); + G(5,5) = gmatcov{1,1}(is,it,iz); + G(6,6) = gmatcov{2,2}(is,it,iz); - G(1,4) = gmatcov{1}{2}(is,it,iz); - G(1,5) = gmatcov{1}{3}(is,it,iz); + G(1,4) = gmatcov{1,2}(is,it,iz); + G(1,5) = gmatcov{1,3}(is,it,iz); - G(2,4) = gmatcov{1}{2}(is,it,iz); - G(2,6) = gmatcov{2}{3}(is,it,iz); + G(2,4) = gmatcov{1,2}(is,it,iz); + G(2,6) = gmatcov{2,3}(is,it,iz); - G(3,5) = gmatcov{1}{3}(is,it,iz); - G(3,6) = gmatcov{2}{3}(is,it,iz); - - G(4,2) = gmatcov{1}{2}(is,it,iz); - G(4,6) = gmatcov{1}{3}(is,it,iz); + G(3,5) = gmatcov{1,3}(is,it,iz); + G(3,6) = gmatcov{2,3}(is,it,iz); - G(5,3) = gmatcov{1}{3}(is,it,iz); - G(5,6) = gmatcov{1}{2}(is,it,iz); + G(4,2) = gmatcov{1,2}(is,it,iz); + G(4,6) = gmatcov{1,3}(is,it,iz); - G(6,3) = gmatcov{2}{3}(is,it,iz); - G(6,5) = gmatcov{1}{2}(is,it,iz); + G(5,3) = gmatcov{1,3}(is,it,iz); + G(5,6) = gmatcov{1,2}(is,it,iz); - % Invert transformation matrix - - Ginv = inv(G); + G(6,3) = gmatcov{2,3}(is,it,iz); + G(6,5) = gmatcov{1,2}(is,it,iz); % Calculate gcon elements - - gcon = Ginv*rhs; + gcon = G\rhs; % Construct contravariant metric matrix - gmatcon{1}{1}(is,it,iz) = gcon(1); %g^ss - gmatcon{2}{2}(is,it,iz) = gcon(2); %g^tt - gmatcon{3}{3}(is,it,iz) = gcon(3); %g^zz - gmatcon{1}{2}(is,it,iz) = gcon(4); %g^st - gmatcon{1}{3}(is,it,iz) = gcon(5); %g^sz - gmatcon{2}{3}(is,it,iz) = gcon(6); %g^tz + gmatcon{1,1}(is,it,iz) = gcon(1); %g^ss + gmatcon{2,2}(is,it,iz) = gcon(2); %g^tt + gmatcon{3,3}(is,it,iz) = gcon(3); %g^zz + gmatcon{1,2}(is,it,iz) = gcon(4); %g^st + gmatcon{1,3}(is,it,iz) = gcon(5); %g^sz + gmatcon{2,3}(is,it,iz) = gcon(6); %g^tz - gmatcon{2}{1}(is,it,iz) = gmatcon{1}{2}(is,it,iz); % by symmetry of g - gmatcon{3}{1}(is,it,iz) = gmatcon{1}{3}(is,it,iz); - gmatcon{3}{2}(is,it,iz) = gmatcon{2}{3}(is,it,iz); + gmatcon{2,1}(is,it,iz) = gmatcon{1,2}(is,it,iz); % by symmetry of g + gmatcon{3,1}(is,it,iz) = gmatcon{1,3}(is,it,iz); + gmatcon{3,2}(is,it,iz) = gmatcon{2,3}(is,it,iz); end end diff --git a/Utilities/matlabtools/get_spec_modB.m b/Utilities/matlabtools/get_spec_modB.m index c773366a..38525908 100644 --- a/Utilities/matlabtools/get_spec_modB.m +++ b/Utilities/matlabtools/get_spec_modB.m @@ -40,15 +40,15 @@ for is=1:ns for it=1:nt for iz=1:nz - a0 = gmat{1}{1}(is,it,iz); - b0 = gmat{1}{2}(is,it,iz); - c0 = gmat{1}{3}(is,it,iz); - d0 = gmat{2}{1}(is,it,iz); - e0 = gmat{2}{2}(is,it,iz); - f0 = gmat{2}{3}(is,it,iz); - g0 = gmat{3}{1}(is,it,iz); - h0 = gmat{3}{2}(is,it,iz); - i0 = gmat{3}{3}(is,it,iz); + a0 = gmat{1,1}(is,it,iz); + b0 = gmat{1,2}(is,it,iz); + c0 = gmat{1,3}(is,it,iz); + d0 = gmat{2,1}(is,it,iz); + e0 = gmat{2,2}(is,it,iz); + f0 = gmat{2,3}(is,it,iz); + g0 = gmat{3,1}(is,it,iz); + h0 = gmat{3,2}(is,it,iz); + i0 = gmat{3,3}(is,it,iz); bs = bvec{1}(is,it,iz); bt = bvec{2}(is,it,iz); diff --git a/Utilities/matlabtools/get_spec_polflux.m b/Utilities/matlabtools/get_spec_polflux.m index 690051a3..f8579c31 100644 --- a/Utilities/matlabtools/get_spec_polflux.m +++ b/Utilities/matlabtools/get_spec_polflux.m @@ -1,11 +1,12 @@ -function psipol = get_spec_polflux(data,lvol,theta,start,send,ns,nz) +function psipol = get_spec_polflux(data,lvol,theta,sarr,nz) % -% GET_SPEC_POLFLUX( DATA, LVOL, THETA, START, SEND, NS, NZ ) -% ========================================================== +% GET_SPEC_POLFLUX( DATA, LVOL, THETA, SARR, NZ ) +% =============================================== % % Computes total enclosed poloidal flux in the surface defined by theta -% inside the volume number lvol and across the radial extension defined by start and send +% inside the volume number lvol and across the radial extension defined by +% start and send % % INPUT % ----- @@ -22,24 +23,21 @@ % -psipol : total enclosed poloidal flux % % written by J.Loizu (2016) -% modified by A. Baillod (2019) - Added switch for geometry -sarr = linspace(start,send,ns); +% Check input +Igeometry = data.input.physics.Igeometry; +if (sarr(1)==-1) && (lvol==1) && (Igeometry~=1) + error('Singularity in first volume for s=-1. Set sarr to start from >-1') +end +% Build zeta array zarr = linspace(0,2*pi,nz); -ds = sarr(2)-sarr(1); - -dz = zarr(2)-zarr(1); - - +% Get B theta contravariant and the jacobian Bcontrav = get_spec_magfield(data,lvol,sarr,theta,zarr); +Btheta = squeeze(Bcontrav{2}); jac = squeeze(get_spec_jacobian(data,lvol,sarr,theta,zarr)); - - -Btheta = Bcontrav{2}; - + % Compute surface integral - -psipol = sum(sum( jac(2:end,:).*Btheta(2:end,:) ))*ds*dz; +psipol = trapz(zarr, trapz(sarr, jac.*Btheta, 1 ) ); diff --git a/Utilities/matlabtools/get_spec_polynomial_basis.m b/Utilities/matlabtools/get_spec_polynomial_basis.m index 4524d04f..edf20287 100644 --- a/Utilities/matlabtools/get_spec_polynomial_basis.m +++ b/Utilities/matlabtools/get_spec_polynomial_basis.m @@ -15,101 +15,111 @@ % OUTPUT % ------ % T{i}{j}: Polynom of order i (j=1) and its derivative (j=2) +% T{i}{j}: Polynom of order i (j=1) +% and its derivative with respect to s (j=2) % % % Written by A. Baillod (2020) % -Lrad = double(data.input.physics.Lrad(lvol)); -ns = length(sarr); -Mpol = data.input.physics.Mpol; - -Lzernike = false; -if ((lvol==1) && (data.input.physics.Igeometry~=1)) - Lzernike = true; -end - - -T = cell(Lrad+1,2); % allocate data for Chebyshev polynomials and their derivatives - -T{1}{1} = ones(ns,1); -T{1}{2} = zeros(ns,1); - -T{2}{1} = sarr; -T{2}{2} = ones(ns,1); - - -if( Lzernike ) % Build zernike polynomials -% Copy pasted from Frotran source, translated to Matlab language -% Tested on the 16.09.2020 (A. Baillod) against SPEC source. perfect match - zernike = zeros(Lrad+1,Mpol+1,2,length(sarr)); - rm = ones(size(sarr)); - rm1 = zeros(size(sarr)); - - sbar = (1 + sarr ) / 2.0; - ns = length(sbar); - - for m = 0:Mpol - if (Lrad >= m) - zernike(m+1,m+1,1,:) = rm; - zernike(m+1,m+1,2,:) = double(m)*rm1; + % Read input data + Lrad = double(data.input.physics.Lrad(lvol)); + ns = length(sarr); + Mpol = data.input.physics.Mpol; + + % Check if zernike or Chebychev polynomials are required + Lzernike = false; + if ((lvol==1) && (data.input.physics.Igeometry~=1)) + if data.version<3.0 + Lzernike = false; + else + Lzernike = true; + end end - if (Lrad >= m+2) - zernike(m+3,m+1,1,:) = double(m+2) *rm.*sbar.^2 - double(m+1) *rm; - zernike(m+3,m+1,2,:) = double((m+2)^2) *rm.*sbar - double((m+1)*m)*rm1; - end - for n = m+4:2:Lrad - factor1 = double(n) / double(n^2 - m^2); - factor2 = double(4 * (n-1)); - factor3 = double((n-2+m)^2)/double(n-2) + double((n-m)^2)/double(n); - factor4 = double((n-2)^2-m^2) / double(n-2); - - zernike(n+1, m+1, 1, :) = factor1 * ((factor2*sbar.^2 - factor3) .* reshape(zernike(n-1, m+1, 1, :), [ns,1]) - factor4 * reshape(zernike(n-3, m+1, 1, :), [ns, 1])); - zernike(n+1, m+1, 2, :) = factor1 * (2.0*factor2*sbar .* reshape(zernike(n-1, m+1, 1, :), [ns,1]) + (factor2*sbar.^2 - factor3) .* reshape(zernike(n-1, m+1, 2, :), [ns,1]) - factor4 * reshape(zernike(n-3, m+1, 2, :), [ns,1])); - end - - rm1 = rm; - rm = rm .* sbar; - end - - for n = 2:2:Lrad - zernike(n+1,1,1,:) = zernike(n+1,1,1, :) - (-1)^(n/2); - end - - if (Mpol >= 1) - for n = 3:2:Lrad - zernike(n+1,2,1,:) = reshape(zernike(n+1,2,1,:), [ns,1]) - (-1)^((n-1)/2) * double((n+1)/2) * sbar; - zernike(n+1,2,2,:) = reshape(zernike(n+1,2,2,:), [ns,1]) - (-1)^((n-1)/2) * double((n+1)/2); + % Allocate memory + T = cell(Lrad+1,2); + + T{1}{1} = ones(ns,1); + T{1}{2} = zeros(ns,1); + + T{2}{1} = sarr; + T{2}{2} = ones(ns,1); + + + if( Lzernike ) % Build zernike polynomials + % Copy pasted from Frotran source, translated to Matlab language + % Tested on the 16.09.2020 (A. Baillod) against SPEC source. perfect match + zernike = zeros(Lrad+1,Mpol+1,2,length(sarr)); + rm = ones(size(sarr)); + rm1 = zeros(size(sarr)); + + sbar = (1 + sarr ) / 2.0; + ns = length(sbar); + + for m = 0:Mpol + if (Lrad >= m) + zernike(m+1,m+1,1,:) = rm; + zernike(m+1,m+1,2,:) = double(m)*rm1; + end + + if (Lrad >= m+2) + zernike(m+3,m+1,1,:) = double(m+2) *rm.*sbar.^2 - double(m+1) *rm; + zernike(m+3,m+1,2,:) = double((m+2)^2) *rm.*sbar - double((m+1)*m)*rm1; + end + + for n = m+4:2:Lrad + factor1 = double(n) / double(n^2 - m^2); + factor2 = double(4 * (n-1)); + factor3 = double((n-2+m)^2)/double(n-2) + double((n-m)^2)/double(n); + factor4 = double((n-2)^2-m^2) / double(n-2); + + zernike(n+1, m+1, 1, :) = factor1 * ((factor2*sbar.^2 - factor3) .* reshape(zernike(n-1, m+1, 1, :), [ns,1]) - factor4 * reshape(zernike(n-3, m+1, 1, :), [ns, 1])); + zernike(n+1, m+1, 2, :) = factor1 * (2.0*factor2*sbar .* reshape(zernike(n-1, m+1, 1, :), [ns,1]) + (factor2*sbar.^2 - factor3) .* reshape(zernike(n-1, m+1, 2, :), [ns,1]) - factor4 * reshape(zernike(n-3, m+1, 2, :), [ns,1])); + end + + rm1 = rm; + rm = rm .* sbar; + end + + for n = 2:2:Lrad + zernike(n+1,1,1,:) = zernike(n+1,1,1, :) - (-1)^(n/2); + end + + if (Mpol >= 1) + for n = 3:2:Lrad + zernike(n+1,2,1,:) = reshape(zernike(n+1,2,1,:), [ns,1]) - (-1)^((n-1)/2) * double((n+1)/2) * sbar; + zernike(n+1,2,2,:) = reshape(zernike(n+1,2,2,:), [ns,1]) - (-1)^((n-1)/2) * double((n+1)/2); + end + end + + for m = 0:Mpol + for n = m:2:Lrad + zernike(n+1,m+1,:,:) = zernike(n+1,m+1,:,:) / double(n+1); + end + end + + % Store in T{}{} structure + for ll = 1:Lrad+1 + T{ll}{1} = reshape(zernike(ll,:,1,:) , Mpol+1, length(sarr)); + T{ll}{2} = reshape(zernike(ll,:,2,:) / 2.0, Mpol+1, length(sarr)); + end + + else % Otherwise construct Chebychev basis + + for l=3:Lrad+1 + T{l}{1} = 2*sarr.*T{l-1}{1} - T{l-2}{1}; + T{l}{2} = 2*T{l-1}{1} + 2*sarr.*T{l-1}{2} - T{l-2}{2}; + end + + for l = 1:Lrad + T{l+1}{1} = T{l+1}{1} - (-1)^l; + end + + for l = 0:Lrad + T{l+1}{1} = T{l+1}{1} / double(l+1); % scale for better conditioning + T{l+1}{2} = T{l+1}{2} / double(l+1); % scale for better conditioning + end end - end - - for m = 0:Mpol - for n = m:2:Lrad - zernike(n+1,m+1,:,:) = zernike(n+1,m+1,:,:) / double(n+1); - end - end - - % Store in T{}{} structure - for ll = 1:Lrad+1 - T{ll}{1} = reshape(zernike(ll,:,1,:) , Mpol+1, length(sarr)); - T{ll}{2} = reshape(zernike(ll,:,2,:) / 2.0, Mpol+1, length(sarr)); - end - -else % Otherwise construct Chebychev basis - - for l=3:Lrad+1 - T{l}{1} = 2*sarr.*T{l-1}{1} - T{l-2}{1}; - T{l}{2} = 2*T{l-1}{1} + 2*sarr.*T{l-1}{2} - T{l-2}{2}; - end - - for l = 1:Lrad - T{l+1}{1} = T{l+1}{1} - (-1)^l; - end - - for l = 0:Lrad - T{l+1}{1} = T{l+1}{1} / double(l+1); % scale for better conditioning - T{l+1}{2} = T{l+1}{2} / double(l+1); % scale for better conditioning - end end diff --git a/Utilities/matlabtools/get_spec_regularisation_factor.m b/Utilities/matlabtools/get_spec_regularisation_factor.m new file mode 100644 index 00000000..57516880 --- /dev/null +++ b/Utilities/matlabtools/get_spec_regularisation_factor.m @@ -0,0 +1,90 @@ +function fac = get_spec_regularisation_factor(data, lvol, sarr, ForG) + +% +% GET_SPEC_REGULARISATION_FACTOR( DATA, LVOL, SARR, FORG ) +% ======================================================== +% +% Computes the regularisation factor in the correct geometry +% +% INPUT +% ----- +% data: Produced by read_spec(filename); +% lvol: Volume number +% sarr: s-coordinate array, shape (ns, 1) +% ForG: 'F' for field reg. factor, 'G' for geometry reg. factor +% +% OUPUT +% ----- +% fac: mnx2 cell array composed of fj and its derivatives +% +% +% Written by A.Baillod (2019) +% + + ns = length( sarr ); + sarr = reshape( sarr, ns, 1 ); + + Igeometry = data.input.physics.Igeometry; + mn = data.output.mn; + im = double(data.output.im); + ns = length(sarr); + fac = cell(mn,2); + sbar = (1+sarr)/2.0; + + if ForG=='G' + switch Igeometry + case 1 % Slab geometry + + for j=1:mn + fac{j}{1} = sbar; + fac{j}{2} = 0.5*ones(ns,1); + end + + case 2 % Cylindrical geometry + for j=1:mn + if(lvol==1) + if im(j)==0 + fac{j}{1} = sbar; + fac{j}{2} = 0.5*ones(ns,1); + else + fac{j}{1} = sbar.^(im(j)+1); + fac{j}{2} = reshape(0.5 * (im(j)+1) * fac{j}{1} ./ sbar, ns, 1); + end + else + fac{j}{1} = sbar; + fac{j}{2} = 0.5 * ones(ns,1); + end + end + + case 3 % Toroidal geometry + + for j=1:mn + if lvol==1 %coordinate singularity + if im(j)==0 + fac{j}{1} = sbar.^2; + fac{j}{2} = sbar; + else + fac{j}{1} = sbar.^im(j); + fac{j}{2} = reshape(0.5 * im(j) * fac{j}{1} ./ sbar, ns, 1); + end + else + fac{j}{1} = sbar; + fac{j}{2} = 0.5 * ones(ns,1); + end + end + otherwise + error('Unsupported geometry in get_spec_regularisation_factor') + end + + + + elseif ForG=='F' + for j=1:mn + fac{j}{1} = ones(ns,1); + fac{j}{2} = zeros(ns,1); + end + + else + error('Unsupported ForG value in get_spec_regularisation_factor.') + end +end diff --git a/Utilities/matlabtools/get_spec_straight_fieldlines.m b/Utilities/matlabtools/get_spec_straight_fieldlines.m new file mode 100644 index 00000000..3f396096 --- /dev/null +++ b/Utilities/matlabtools/get_spec_straight_fieldlines.m @@ -0,0 +1,37 @@ +%% GET_SPEC_STRAIGHT_FIELDLINES( d, NPOINTS, Nperiods ) +% ======================================================= +% +% Gives as output the straightfieldlines coordinates from SPEC out file +% +% INPUT +% ----- +% -data : must be produced by calling read_boozer(filename, root) +% -Npoints : number of points for toroidal resolution +% -Nperiods : number of toroidal periods +% +% ------------------------------------% +% Written by S.Guinchard (05/17/22) % +% ------------------------------------% +function SFL_coord = get_spec_straight_fieldlines(d,Npoints,Nperiods) + + m = double(d.output.ims); + n = double(d.output.ins); + lambda_mn = d.output.lambdamn(1:end,1,2); + + coord = plot_spec_fieldlines(d,Npoints,Nperiods,0); + theta = coord.theta; + phi = coord.phi; + + theta_sfl = theta; + + for i = 1:length(phi) + for j = 1:length(lambda_mn) + + theta_sfl(i) = theta_sfl(i) + lambda_mn(j,1,1)*sin(m(j)*theta(i) - n(j)*phi(i)); + + end + end + + SFL_coord.theta_sfl = wrapTo2Pi(theta_sfl); + SFL_coord.phi = wrapTo2Pi(phi); +end \ No newline at end of file diff --git a/Utilities/matlabtools/get_spec_torcurr_kam_net.m b/Utilities/matlabtools/get_spec_torcurr_kam_net.m index 36e68f7c..08303b6d 100644 --- a/Utilities/matlabtools/get_spec_torcurr_kam_net.m +++ b/Utilities/matlabtools/get_spec_torcurr_kam_net.m @@ -20,17 +20,16 @@ % written by J.Loizu (2017) -Nvol = data.input.physics.Nvol; -Itor = zeros(1,Nvol-1); +Mvol = data.output.Mvol; +Itor = zeros(1,Mvol-1); zarr = 0; tarr = linspace(0,2*pi,ntheta); -dtheta = tarr(2)-tarr(1); sarr = [1 -1]; intB = [0 0]; -for ikam=1:Nvol-1 +for ikam=1:Mvol-1 lvol = [ikam ikam+1]; @@ -43,9 +42,9 @@ Bt = Bcontrav{2}; Bz = Bcontrav{3}; - gst = gmat{1}{2}; - gtt = gmat{2}{2}; - gzt = gmat{3}{2}; + gst = gmat{1,2}; + gtt = gmat{2,2}; + gzt = gmat{3,2}; intB(i) = trapz(tarr, Bs.*gst + Bt.*gtt + Bz.*gzt); diff --git a/Utilities/matlabtools/get_spec_torflux.m b/Utilities/matlabtools/get_spec_torflux.m index 141ef64d..d90e7ebc 100644 --- a/Utilities/matlabtools/get_spec_torflux.m +++ b/Utilities/matlabtools/get_spec_torflux.m @@ -26,28 +26,55 @@ % modified by J.Loizu (06.2017) % modified by A.Baillod (06.2019) - added switch for geometry + %Check inputs + Igeometry = data.input.physics.Igeometry; + if lvol==1 && Igeometry~=1 && start==1 + error('InputError: start should be >1 in first volume') + end -sarr = linspace(start,send,ns); + Mvol = data.output.Mvol; + if lvol<1 || lvol>Mvol + error('InputError: Invalid lvol') + end -tarr = linspace(0,2*pi,nt); + if start<-1 || start>send + error('InputError: invalid start') + end -ds = sarr(2)-sarr(1); + if send1 + error('InputError: invalid send') + end -dth = tarr(2)-tarr(1); + if ns<1 + error('InputError: invalid ns') + end -if(ds==0 || dth==0) + if nt<1 + error('InputError: invalid nt') + end - psitor = 0; - -else + % Prepare coordinate arrays + sarr = linspace(start,send,ns); + tarr = linspace(0,2*pi,nt); -Bcontrav = get_spec_magfield(data,lvol,sarr,tarr,zeta); -jac = get_spec_jacobian(data,lvol,sarr,tarr,zeta); - + ds = sarr(2)-sarr(1); - % Compute surface integral + dth = tarr(2)-tarr(1); - Bzeta = Bcontrav{3}; - psitor = sum(sum( jac(2:end,:).*Bzeta(2:end,:) ))*ds*dth; + if(ds==0 || dth==0) + + psitor = 0; + + else + + Bcontrav = get_spec_magfield(data,lvol,sarr,tarr,zeta); + jac = get_spec_jacobian(data,lvol,sarr,tarr,zeta); + + + % Compute surface integral + + Bzeta = Bcontrav{3}; + psitor = trapz( sarr, trapz( tarr, jac.*Bzeta, 2 ) ); + end end diff --git a/Utilities/matlabtools/get_spec_vecpot.m b/Utilities/matlabtools/get_spec_vecpot.m index d594a2d4..66ef9035 100644 --- a/Utilities/matlabtools/get_spec_vecpot.m +++ b/Utilities/matlabtools/get_spec_vecpot.m @@ -20,67 +20,74 @@ % % written by J.Loizu (2018) + % Test input + Mvol = data.output.Mvol; + if lvol<1 || lvol>Mvol + error('InputError: invalid lvol') + end -Ate = data.vector_potential.Ate{lvol}; -Aze = data.vector_potential.Aze{lvol}; -Ato = data.vector_potential.Ato{lvol}; -Azo = data.vector_potential.Azo{lvol}; - -Lrad = data.input.physics.Lrad(lvol); - -if(size(sarr,1)==1) -sarr = transpose(sarr); -end -ns = length(sarr); -nt = length(tarr); -nz = length(zarr); -sbar = (sarr+1)/2; - -mn = data.output.mn; -im = double(data.output.im); -in = double(data.output.in); - -At = zeros(ns,nt,nz); % allocate data for vector potential along theta -Az = zeros(ns,nt,nz); % allocate data for vector potential along zeta - - -% Construct Chebyshev polynomials - -T = get_spec_polynomial_basis(data, lvol, sarr); - -% Construct regularization factors - -fac = get_spec_regularization_factor(data, lvol, sarr, 'F'); + if isempty(sarr) + error('InputError: empty sarr') + end + if isempty(tarr) + error('InputError: empty tarr') + end + if isempty(zarr) + error('InputError: empty zarr') + end -% Construct vector potential covariant components + if sarr(1)<-1 || sarr(end)>1 + error('InputError: invalid sarr') + end -Lsingularity = false; -if (lvol==1) && (data.input.physics.Igeometry~=1) - Lsingularity = true; -end + % Read data + Ate = data.vector_potential.Ate{lvol}; + Aze = data.vector_potential.Aze{lvol}; + Ato = data.vector_potential.Ato{lvol}; + Azo = data.vector_potential.Azo{lvol}; + Lrad = data.input.physics.Lrad(lvol); -for l=1:Lrad+1 - for j=1:mn - if( Lsingularity ) - basis = T{l}{1}(im(j)+1); - dbasis = T{l}{2}(im(j)+1); - else - basis = T{l}{1}; - dbasis = T{l}{2}; + if(size(sarr,1)==1) + sarr = transpose(sarr); end - - for it=1:nt - for iz=1:nz - cosa = cos(im(j)*tarr(it)-in(j)*zarr(iz)); - sina = sin(im(j)*tarr(it)-in(j)*zarr(iz)); - At(:,it,iz) = At(:,it,iz) + fac{j}{1}.* basis.*( Ate(l,j)*cosa + Ato(l,j)*sina ); - Az(:,it,iz) = Az(:,it,iz) + fac{j}{1}.* basis.*( Aze(l,j)*cosa + Azo(l,j)*sina ); - end + ns = length(sarr); + nt = length(tarr); + nz = length(zarr); + + mn = data.output.mn; + im = double(data.output.im); + in = double(data.output.in); + + At = zeros(ns,nt,nz); % allocate data for vector potential along theta + Az = zeros(ns,nt,nz); % allocate data for vector potential along zeta + + % Construct vector potential covariant components + T = get_spec_polynomial_basis(data, lvol, sarr); + + % Construct vector potential covariant components + Lsingularity = (lvol==1) && (data.input.physics.Igeometry~=1); + + for l=1:Lrad+1 + for j=1:length(im) + if( Lsingularity ) + basis = T{l}{1}(im(j)+1); + else + basis = T{l}{1}; + end + + for it=1:nt + for iz=1:nz + cosa = cos(im(j)*tarr(it)-in(j)*zarr(iz)); + sina = sin(im(j)*tarr(it)-in(j)*zarr(iz)); + At(:,it,iz) = At(:,it,iz) + basis.*( Ate(l,j)*cosa + Ato(l,j)*sina ); + Az(:,it,iz) = Az(:,it,iz) + basis.*( Aze(l,j)*cosa + Azo(l,j)*sina ); + end + end + end end - end -end -Acov{1} = At; -Acov{2} = Az; + Acov{1} = At; + Acov{2} = Az; +end diff --git a/Utilities/matlabtools/get_spec_volume.m b/Utilities/matlabtools/get_spec_volume.m index 72c281da..0697cfb4 100644 --- a/Utilities/matlabtools/get_spec_volume.m +++ b/Utilities/matlabtools/get_spec_volume.m @@ -22,11 +22,33 @@ % % written by J.Loizu (2016) + % Test input + Mvol = data.output.Mvol; + if lvol<1 || lvol>Mvol + error('InputError: invalid lvol') + end + if ns<1 + error('Invalid ns') + end + if nt<1 + error('Invalid nt') + end + if nz<1 + error('Invalid nz') + end -sarr = linspace(-1,1,ns); -tarr = linspace(0,2*pi,nt); -zarr = linspace(0,2*pi,nz); + Igeometry=data.input.physics.Igeometry; + if lvol==1 && Igeometry~=1 + start=-0.999; + else + start=-1; + end + + sarr = linspace(start,1,ns); + tarr = linspace(0,2*pi,nt); + zarr = linspace(0,2*pi,nz); -jacobian = get_spec_jacobian(data,lvol,sarr,tarr,zarr); + jacobian = get_spec_jacobian(data,lvol,sarr,tarr,zarr); -volume = sum(sum(sum(jacobian(2:end,:,:))))*(2*2*pi*2*pi)/(ns*nt*nz); + volume = trapz(sarr, trapz(tarr, trapz(zarr, jacobian, 3), 2) ); +end diff --git a/Utilities/matlabtools/get_spec_volume_current.m b/Utilities/matlabtools/get_spec_volume_current.m index 136d196f..8c3868e9 100644 --- a/Utilities/matlabtools/get_spec_volume_current.m +++ b/Utilities/matlabtools/get_spec_volume_current.m @@ -9,47 +9,47 @@ % INPUT % ----- % data: data obtained via read_spec(filename) +% cumul: Choose if quantity is cumulative or not % % OUTPUT % ------ % psi_coord: The toroidal flux enclosed by each interface % I_vol: The toroidal volume current flowing in each volume -% (cumulative) % % Written by A.Baillod (2019) -% Data loading -Nvol = data.input.physics.Nvol; % Total number of volumes + % Data loading + Mvol = data.output.Mvol; % Total number of volumes -% Data processing + % Data processing -% First, get the current in each volume -psi_coord = zeros(1, Nvol); % Allocate memory -I_vol = zeros(1, Nvol); + % First, get the current in each volume + psi_coord = zeros(1, Mvol); % Allocate memory + I_vol = zeros(1, Mvol); -mu = data.output.mu; -tflux = data.output.tflux; -sumI = 0; -phiedge = data.input.physics.phiedge; - -for ivol=1:Nvol + mu = data.output.mu; + tflux = data.output.tflux; + sumI = 0; + phiedge = data.input.physics.phiedge; - if ivol==1 - I_vol(ivol) = mu(ivol) * tflux(ivol) * phiedge; - else - % Add previous current volumes (sumI) since we use a cumulative - % representation - if cumul - I_vol(ivol) = mu(ivol) * (tflux(ivol) - tflux(ivol-1)) * phiedge + sumI; + for ivol=1:Mvol + + if ivol==1 + I_vol(ivol) = mu(ivol) * tflux(ivol) * phiedge; else - I_vol(ivol) = mu(ivol) * (tflux(ivol) - tflux(ivol-1)) * phiedge; + % Add previous current volumes (sumI) since we use a cumulative + % representation + if cumul + I_vol(ivol) = mu(ivol) * (tflux(ivol) - tflux(ivol-1)) * phiedge + sumI; + else + I_vol(ivol) = mu(ivol) * (tflux(ivol) - tflux(ivol-1)) * phiedge; + end end + + psi_coord(ivol) = tflux(ivol); + + sumI = I_vol(ivol); end - - psi_coord(ivol) = tflux(ivol); - - sumI = I_vol(ivol); -end end diff --git a/Utilities/matlabtools/plot_SFL_modB.m b/Utilities/matlabtools/plot_SFL_modB.m new file mode 100644 index 00000000..207414d5 --- /dev/null +++ b/Utilities/matlabtools/plot_SFL_modB.m @@ -0,0 +1,53 @@ +%% plot_SFL_modB( DATA, NTHETA, NPHI, FILLED, NEWFIG ) +% ============================================= +% +% Plot of modB in SFL coordinates +% +% INPUT +% ----- +% -data : must be produced by calling read_spec(filename) +% -Ntheta : number of meshpoints for theta array +% -Nphi : number of meshpoints for phi array +% -filled : (=1) pcolor, (=2) contourplot +% -newfig : opens (=1) or not (=0) a newfig or overwrites (=2) +% previous figure +% +% ------------------------------------% +% Written by S.Guinchard (05/23/22) % +% ------------------------------------% +function plot_SFL_modB(b, Ntheta, Nphi, filled, Newfig) + + modB = get_SFL_fourier_modB(b,Ntheta,Nphi); + Theta = modB.Theta; + Phi = modB.Phi; + modB = modB.modB; + + switch Newfig + + case 0 + hold on + + case 1 + figure + + case 2 + hold off + + end + + switch filled + + case 1 + pcolor(Phi, Theta, modB); + shading interp + colorbar + hold on + contour(Phi, Theta, modB, 6, 'k', 'linewidth', 1) + + case 2 + %contourf(Theta, Phi, modB,linspace(min(min(modB)), max(max(modB)),20)); + contour(Phi, Theta, modB,linspace(min(min(modB)), max(max(modB)),20), 'linewidth', 1.5) + colorbar + colormap(jet) + end +end \ No newline at end of file diff --git a/Utilities/matlabtools/plot_SFL_modB_boundary.m b/Utilities/matlabtools/plot_SFL_modB_boundary.m new file mode 100644 index 00000000..b6b812b6 --- /dev/null +++ b/Utilities/matlabtools/plot_SFL_modB_boundary.m @@ -0,0 +1,104 @@ +function plot_SFL_modB_boundary(data,interface,innout,nt,nz,dimension) + +% +% PLOT_SPEC_MODB_BOUNDARY( BDATA, DATA, VOL, NT, NZ ) +% ============================================ +% +% Produces plot of |B|_b on the full boundary surface in toroidal geometry. +% +% INPUT +% ----- +% -bdata : data obtained via read_boozer(filename, root) +% -data : data obtained via read_spec(filename) +% -interface : Volume on which modB should be plotted +% -innout: (0) - inner side of interface +% (1) - outer side of interface +% -nt : poloidal resolution for the plotting (e.g. nt=64) +% -nz : toroidal resolution for the plotting (e.g. nz=64) +% -dimension: (2) - plot a colorplot on a theta-phi grid +% (3) - plot a colorplot on a 3d surface +% +% ------------------------------------% +% Written by S.Guinchard (05/30/22) % +% ------------------------------------% +% +% TODO: adapt for more than 1 volume +% when booz_xform has been adapted +innout =0; +interface = 1; +Mvol = data.output.Mvol; + +if interface<1 || interface>Mvol + error('Invalid interface') +end + +switch innout + case 0 + vol = interface; + sarr = 1; + case 1 + if interface==Mvol + error('Cannot plot on the outer side of last interface!') + end + vol = interface+1; + sarr = -1; + otherwise + error('Interface should be 0 or 1') +end + +tarr = linspace(0,2*pi,nt); +zarr = linspace(0,2*pi,nz); + +if(vol>Mvol || vol<1) + error('vol not valid') +end + + +switch dimension + case 2 + + plot_SFL_modB(data,nt,nz,1,1) + xlabel('$\phi_b$', 'Interpreter', 'latex') + ylabel('$\theta_b$', 'Interpreter', 'latex') + set(gca,'FontSize',20) + set(gcf,'Position',[200 200 900 700]) + + + case 3 + + % Compute |B| + modB = get_SFL_fourier_modB(data,nt,nz); + + % Compute function (R,Z)(s,theta,zeta) + sarr = 1; + rzdata = get_spec_rzarr(data,vol,sarr,tarr,zarr); + + R = squeeze(rzdata{1}); + Z = squeeze(rzdata{2}); + + + % Construct cartesian corrdinates + + X = zeros(nt,nz); + Y = zeros(nt,nz); + + for it=1:nt + for iz=1:nz + X(it,iz) = R(it,iz)*cos(zarr(iz)); + Y(it,iz) = R(it,iz)*sin(zarr(iz)); + end + end + + + % Plot + + figure + h=surf(X,Y,Z,squeeze(modB.modB)); + axis equal + shading interp + colorbar + title('$| B_b |$', 'interpreter', 'latex') + + otherwise + error('Invalid dimension') +end diff --git a/Utilities/matlabtools/plot_boozer_fieldlines.m b/Utilities/matlabtools/plot_boozer_fieldlines.m new file mode 100644 index 00000000..53a89108 --- /dev/null +++ b/Utilities/matlabtools/plot_boozer_fieldlines.m @@ -0,0 +1,72 @@ +%% plot_boozer_fieldlines( COORDB, NEWFIG ) +% ============================================= +% +% Plots a magnetic fieldline in Boozer coordinates +% starting from the point (thetab, phib) = (0,0) +% +% INPUT +% ----- +% +% -coordb : must be produced using get_boozer_coordinates +% -Newfig : opens (=1) or not (=0) a new figure, or overwrites (=2) +% last plot +% +% ------------------------------------% +% Written by S.Guinchard (05/15/22) % +% ------------------------------------% + +function plot_boozer_fieldlines(coordb, Newfig) + + phiB = coordb.phib; + thetaB = coordb.thetab; + Fs = 18; + switch Newfig + + case 0 + hold on + scatter(phiB, thetaB, 'k.') + ax = gca; + ax.TickLabelInterpreter = 'latex'; + xticks([0 pi/3 2*pi/3 pi 4*pi/3 5*pi/3 2*pi]) + xticklabels({'$0$','$\frac{\pi}{3}$','$\frac{2\pi}{3}$','$\pi$', '$\frac{4\pi}{3}$','$\frac{5\pi}{3}$','$2\pi$'}); + yticks([0 pi/3 2*pi/3 pi 4*pi/3 5*pi/3 2*pi]) + yticklabels({'$0$','$\frac{\pi}{3}$','$\frac{2\pi}{3}$','$\pi$', '$\frac{4\pi}{3}$','$\frac{5\pi}{3}$','$2\pi$'}); + xlim([0 2*pi]) + ylim([0 2*pi]) + set (gca, 'fontsize', Fs) + xlabel('$\phi_B$', 'FontSize', Fs+10 , 'Interpreter', 'latex') + ylabel('$\theta_B$', 'FontSize', Fs+10 , 'Interpreter', 'latex') + + case 1 + figure + scatter(phiB, thetaB, 'k.') + ax = gca; + ax.TickLabelInterpreter = 'latex'; + xticks([0 pi/3 2*pi/3 pi 4*pi/3 5*pi/3 2*pi]) + xticklabels({'$0$','$\frac{\pi}{3}$','$\frac{2\pi}{3}$','$\pi$', '$\frac{4\pi}{3}$','$\frac{5\pi}{3}$','$2\pi$'}); + yticks([0 pi/3 2*pi/3 pi 4*pi/3 5*pi/3 2*pi]) + yticklabels({'$0$','$\frac{\pi}{3}$','$\frac{2\pi}{3}$','$\pi$', '$\frac{4\pi}{3}$','$\frac{5\pi}{3}$','$2\pi$'}); + xlim([0 2*pi]) + ylim([0 2*pi]) + set (gca, 'fontsize', Fs) + xlabel('$\phi_B$', 'FontSize', Fs+10 , 'Interpreter', 'latex') + ylabel('$\theta_B$', 'FontSize', Fs+10 , 'Interpreter', 'latex') + + case 2 + hold off + scatter(phiB, thetaB, 'k.') + ax = gca; + ax.TickLabelInterpreter = 'latex'; + xticks([0 pi/3 2*pi/3 pi 4*pi/3 5*pi/3 2*pi]) + xticklabels({'$0$','$\frac{\pi}{3}$','$\frac{2\pi}{3}$','$\pi$', '$\frac{4\pi}{3}$','$\frac{5\pi}{3}$','$2\pi$'}); + yticks([0 pi/3 2*pi/3 pi 4*pi/3 5*pi/3 2*pi]) + yticklabels({'$0$','$\frac{\pi}{3}$','$\frac{2\pi}{3}$','$\pi$', '$\frac{4\pi}{3}$','$\frac{5\pi}{3}$','$2\pi$'}); + xlim([0 2*pi]) + ylim([0 2*pi]) + set (gca, 'fontsize', Fs) + xlabel('$\phi_B$', 'FontSize', Fs+10 , 'Interpreter', 'latex') + ylabel('$\theta_B$', 'FontSize', Fs+10 , 'Interpreter', 'latex') + + end + +end \ No newline at end of file diff --git a/Utilities/matlabtools/plot_boozer_modB.m b/Utilities/matlabtools/plot_boozer_modB.m new file mode 100644 index 00000000..6ffeb0cc --- /dev/null +++ b/Utilities/matlabtools/plot_boozer_modB.m @@ -0,0 +1,53 @@ +%% plot_boozer_modB( BDATA, NTHETA, NPHI, FILLED, NEWFIG ) +% ============================================= +% +% Plot of modB in Boozer coordinates +% +% INPUT +% ----- +% -bdata : must be produced by calling read_boozer(filename,root) +% -Ntheta : number of meshpoints for theta array +% -Nphi : number of meshpoints for phi array +% -filled : (=1) pcolor, (=2) contourplot +% -newfig : opens (=1) or not (=0) a newfig or overwrites (=2) +% previous figure +% +% ------------------------------------% +% Written by S.Guinchard (05/18/22) % +% ------------------------------------% +function plot_boozer_modB(b, Ntheta, Nphi, filled, Newfig) + + modB = get_boozer_modB(b,Ntheta,Nphi); + Theta = modB.Theta; + Phi = modB.Phi; + modB = modB.modB; + + switch Newfig + + case 0 + hold on + + case 1 + figure + + case 2 + hold off + + end + + switch filled + + case 1 + pcolor(Phi, Theta, modB); + shading interp + colorbar + hold on + contour(Phi, Theta, modB, 6, 'k', 'linewidth', 1) + + case 2 + + contour(Phi, Theta, modB,linspace(min(min(modB)), max(max(modB)),20), 'linewidth', 1.5) + colorbar + colormap(jet) + end +end \ No newline at end of file diff --git a/Utilities/matlabtools/plot_boozer_modB_boundary.m b/Utilities/matlabtools/plot_boozer_modB_boundary.m new file mode 100644 index 00000000..8701c155 --- /dev/null +++ b/Utilities/matlabtools/plot_boozer_modB_boundary.m @@ -0,0 +1,123 @@ +function plot_boozer_modB_boundary(b,data,interface,innout,nt,nz,dimension, newfig) + +% PLOT_BOOZER_MODB_BOUNDARY( BDATA, DATA, INTERFACE, INNOUT, NT, NZ, DIM, NEWFIG ) +% ============================================ +% +% Produces plot of |B|_b on the full boundary surface in toroidal geometry. +% +% INPUT +% ----- +% -bdata : data obtained via read_boozer(filename, root) +% -data : data obtained via read_spec(filename) +% -interface : Volume on which modB should be plotted +% -innout: (0) - inner side of interface +% (1) - outer side of interface +% -nt : poloidal resolution for the plotting (e.g. nt=64) +% -nz : toroidal resolution for the plotting (e.g. nz=64) +% -dimension: (2) - plot a colorplot on a theta-phi grid +% (3) - plot a colorplot on a 3d surface +% -newfig: opens (=1) or not (=0) a new figure or ovewrites (=2) previous +% plot +% +% ------------------------------------% +% Written by S.Guinchard (05/30/22) % +% ------------------------------------% +% +% TODO: adapt for more than 1 volume +% when booz_xform has been adapted + +innout = 0; % will be changed when adapted +interface = 1; +Mvol = (b.Booz_xForms.Inputs.ns_in+1)/2; + +if interface<1 || interface>Mvol + error('Invalid interface') +end + +switch innout + case 0 + vol = interface; + sarr = 1; + case 1 + if interface==Mvol + error('Cannot plot on the outer side of last interface!') + end + vol = interface+1; + sarr = -1; + otherwise + error('Interface should be 0 or 1') +end + +tarr = linspace(0,2*pi,nt); +zarr = linspace(0,2*pi,nz); + +if(vol>Mvol || vol<1) + error('vol not valid') +end + + +switch dimension + case 2 + + switch newfig + case 0 + hold on + case 1 + figure + case 2 + hold off + end + plot_boozer_modB(b,nt,nz,1,0) + xlabel('$\phi_b$', 'Interpreter', 'latex') + ylabel('$\theta_b$', 'Interpreter', 'latex') + set(gca,'FontSize',20) + set(gcf,'Position',[200 200 900 700]) + + + case 3 + + switch newfig + case 0 + hold on + case 1 + figure + case 2 + hold off + end + % Compute |B| + + modB = get_boozer_modB(b,nt,nz); + % Compute function (R,Z)(s,theta,zeta) + sarr = 1; + rzdata = get_spec_rzarr(data,vol,sarr,tarr,zarr); + + R = squeeze(rzdata{1}); + Z = squeeze(rzdata{2}); + + + % Construct cartesian coordinates + + X = zeros(nt,nz); + + Y = zeros(nt,nz); + + for it=1:nt + for iz=1:nz + X(it,iz) = R(it,iz)*cos(zarr(iz)); + Y(it,iz) = R(it,iz)*sin(zarr(iz)); + end + end + + + % Plot + + h=surf(X,Y,Z,squeeze(modB.modB)); + + axis equal + shading interp + colorbar + title('$| B_b |$', 'interpreter', 'latex') + + otherwise + error('Invalid dimension') +end diff --git a/Utilities/matlabtools/plot_spec_Bgrid.m b/Utilities/matlabtools/plot_spec_Bgrid.m index 4f0a5f73..c8cd178c 100644 --- a/Utilities/matlabtools/plot_spec_Bgrid.m +++ b/Utilities/matlabtools/plot_spec_Bgrid.m @@ -19,109 +19,151 @@ function plot_spec_Bgrid(data,nz0,plotstyle,newfig) % % OUTDATED - NEED DEBUG -if(newfig==1) -figure +% Check inputs +if ~strcmp(string(plotstyle),string('pcolor')) && ~strcmp(string(plotstyle),string('scatter')) + error('InputError: Invalid plotstyle') +end +if nz0<1 + error('nzo should be greater than zero') +end +switch newfig + case 0 + hold on + case 1 + figure('Color','w','Position',[200 200 1500, 600]) + hold on + case 2 + hold off + otherwise + error('Invalide newfig') end -nvol = data.output.Mvol; +Mvol = data.output.Mvol; Lrad = data.input.physics.Lrad; Nt = data.grid.Nt; -Nz = data.grid.Nz; Nfp = data.input.physics.Nfp; -Rij = data.grid.Rij; -Zij = data.grid.Zij; -BR = data.grid.BR; -Bp = data.grid.Bp; -BZ = data.grid.BZ; iz = nz0-1; phi0 = double((2*pi/Nfp)*(iz/Nt)); -rzdata = get_spec_rzarr(data,nvol,1,linspace(0,2*pi,32),phi0); -rmax = max(rzdata{1}); -rmin = min(rzdata{1}); -zmax = max(rzdata{2}); -zmin = min(rzdata{2}); +R = get_spec_R_derivatives(data, Mvol, 1, linspace(0,2*pi,64), phi0, 'R'); +Z = get_spec_R_derivatives(data, Mvol, 1, linspace(0,2*pi,64), phi0, 'Z'); + +rmax = max(R{1}); +rmin = min(R{1}); +zmax = max(Z{1}); +zmin = min(Z{1}); if(strcmp(plotstyle,'pcolor')==1) -for i=1:nvol - ngrid = Lrad(i)+1; - - if(i==1) - nstart = 2; - else - nstart = 1; - end - - np1 = Nt; - np2 = 1+ngrid-nstart; - - Rc = reshape(Rij(i,1+Nt*iz:(iz+1)*Nt,nstart:ngrid),np1,np2); - Zc = reshape(Zij(i,1+Nt*iz:(iz+1)*Nt,nstart:ngrid),np1,np2); - br = reshape(BR(i,1+Nt*iz:(iz+1)*Nt,nstart:ngrid),np1,np2); - bp = reshape(Bp(i,1+Nt*iz:(iz+1)*Nt,nstart:ngrid).*Rij(i,1+Nt*iz:(iz+1)*Nt,nstart:ngrid),np1,np2); - bz = reshape(BZ(i,1+Nt*iz:(iz+1)*Nt,nstart:ngrid),np1,np2); - - subplot(3,1,1) - pcolor(Rc,Zc,br) - axis equal; colorbar; hold on - xlim([0.95*rmin 1.05*rmax]) - ylim([1.05*zmin 1.05*zmax]) - title('B_R') - subplot(3,1,2) - pcolor(Rc,Zc,bp) - axis equal; colorbar; hold on - xlim([0.95*rmin 1.05*rmax]) - ylim([1.05*zmin 1.05*zmax]) - title('B_{\phi}') - subplot(3,1,3) - pcolor(Rc,Zc,bz) - axis equal; colorbar; hold on - xlim([0.95*rmin 1.05*rmax]) - ylim([1.05*zmin 1.05*zmax]) - title('B_Z') -end + for i=1:Mvol + ngrid = Lrad(i)+1; + + % Read data corresponding to correct volume + Rij = data.grid.Rij{i}; + Zij = data.grid.Zij{i}; + BR = data.grid.BR{i}; + Bp = data.grid.Bp{i}; + BZ = data.grid.BZ{i}; + + % Reshape as an array + if(i==1) + nstart = 2; + else + nstart = 1; + end + + np1 = Nt; + np2 = 1+ngrid-nstart; + + Rc = reshape(Rij(1+Nt*iz:(iz+1)*Nt,nstart:ngrid),np1,np2); + Zc = reshape(Zij(1+Nt*iz:(iz+1)*Nt,nstart:ngrid),np1,np2); + br = reshape(BR( 1+Nt*iz:(iz+1)*Nt,nstart:ngrid),np1,np2); + bp = reshape(Bp( 1+Nt*iz:(iz+1)*Nt,nstart:ngrid) ... + .*Rij(1+Nt*iz:(iz+1)*Nt,nstart:ngrid),np1,np2); + bz = reshape(BZ( 1+Nt*iz:(iz+1)*Nt,nstart:ngrid),np1,np2); + + % Double first entry to fill entire plane + Rc(end+1,:) = Rc(1,:); + Zc(end+1,:) = Zc(1,:); + br(end+1,:) = br(1,:); + bp(end+1,:) = bp(1,:); + bz(end+1,:) = bz(1,:); + + % Plots + subplot(1,3,1) + pcolor(Rc,Zc,br) + shading interp + axis equal; colorbar; hold on + xlim([0.95*rmin 1.05*rmax]) + ylim([1.05*zmin 1.05*zmax]) + title('B_R') + + subplot(1,3,2) + pcolor(Rc,Zc,bp) + shading interp + axis equal; colorbar; hold on + xlim([0.95*rmin 1.05*rmax]) + ylim([1.05*zmin 1.05*zmax]) + title('B_{\phi}') + + subplot(1,3,3) + pcolor(Rc,Zc,bz) + shading interp + axis equal; colorbar; hold on + xlim([0.95*rmin 1.05*rmax]) + ylim([1.05*zmin 1.05*zmax]) + title('B_Z') + end elseif(strcmp(plotstyle,'scatter')==1) -cthick = 12 ; - -for i=1:nvol - ngrid = Lrad(i)+1; - if(i==1) - nstart = 2; - else - nstart = 1; - end - for l=nstart:ngrid - Rc = Rij(i,1+Nt*iz:(iz+1)*Nt,l); - Zc = Zij(i,1+Nt*iz:(iz+1)*Nt,l); - colR = BR(i,1+Nt*iz:(iz+1)*Nt,l); - colp = Bp(i,1+Nt*iz:(iz+1)*Nt,l).*Rc; - colZ = BZ(i,1+Nt*iz:(iz+1)*Nt,l); - - subplot(3,1,1) - scatter(Rc,Zc,cthick,colR) - axis equal; colorbar; hold on - xlim([0.95*rmin 1.05*rmax]) - ylim([1.05*zmin 1.05*zmax]) - title('B_R') - subplot(3,1,2) - scatter(Rc,Zc,cthick,colp) - axis equal; colorbar; hold on - xlim([0.95*rmin 1.05*rmax]) - ylim([1.05*zmin 1.05*zmax]) - title('B_{\phi}') - subplot(3,1,3) - scatter(Rc,Zc,cthick,colZ) - axis equal; colorbar; hold on - xlim([0.95*rmin 1.05*rmax]) - ylim([1.05*zmin 1.05*zmax]) - title('B_Z') - end -end + cthick = 12 ; + + for i=1:Mvol + % Read data corresponding to correct volume + Rij = data.grid.Rij{i}; + Zij = data.grid.Zij{i}; + BR = data.grid.BR{i}; + Bp = data.grid.Bp{i}; + BZ = data.grid.BZ{i}; + + ngrid = Lrad(i)+1; + if(i==1) + nstart = 2; + else + nstart = 1; + end + for l=nstart:ngrid + Rc = Rij(1+Nt*iz:(iz+1)*Nt,l); + Zc = Zij(1+Nt*iz:(iz+1)*Nt,l); + colR = BR(1+Nt*iz:(iz+1)*Nt,l); + colp = Bp(1+Nt*iz:(iz+1)*Nt,l).*Rc; + colZ = BZ(1+Nt*iz:(iz+1)*Nt,l); + + subplot(1,3,1) + scatter(Rc,Zc,cthick,colR) + axis equal; colorbar; hold on + xlim([0.95*rmin 1.05*rmax]) + ylim([1.05*zmin 1.05*zmax]) + title('B_R') + + subplot(1,3,2) + scatter(Rc,Zc,cthick,colp) + axis equal; colorbar; hold on + xlim([0.95*rmin 1.05*rmax]) + ylim([1.05*zmin 1.05*zmax]) + title('B_{\phi}') + + subplot(1,3,3) + scatter(Rc,Zc,cthick,colZ) + axis equal; colorbar; hold on + xlim([0.95*rmin 1.05*rmax]) + ylim([1.05*zmin 1.05*zmax]) + title('B_Z') + end + end end diff --git a/Utilities/matlabtools/plot_spec_Ivolume.m b/Utilities/matlabtools/plot_spec_Ivolume.m index f0a07f9a..e051d39b 100644 --- a/Utilities/matlabtools/plot_spec_Ivolume.m +++ b/Utilities/matlabtools/plot_spec_Ivolume.m @@ -16,30 +16,29 @@ function plot_spec_Ivolume(data, cumul, newfig) % Written by A. Baillod (2019) % + if ~any(cumul==[0,1]) + error('InputError: invalid cumul') + end -[psi_coord, I_vol] = get_spec_volume_current(data, cumul); + switch newfig + case 0 + hold on + case 1 + figure + hold on + case 2 + hold off + end -% some plots + [~, I_vol] = get_spec_volume_current(data, cumul); -switch newfig - case 0 - hold on - case 1 - figure - hold on - case 2 - hold off -end -%plot(psi_coord, I_vol, '*', 'DisplayName', '$I^{vol}_\phi$') -bar(I_vol); -%leg = legend('Location','northwest'); -ylab = ylabel('$I_\mathcal{V}$[A]'); -%xlab = xlabel('$\psi_t / \psi_{edge}$'); -xlab = xlabel('Volume label'); -set(gca, 'FontSize', 14) -%set(leg,'Interpreter','latex'); -set(xlab,'Interpreter','latex'); -set(ylab,'Interpreter','latex'); -grid on; + bar(I_vol); + xlab = xlabel('Volume label'); + ylab = ylabel('$\mu_0I_\mathcal{V}$[A]'); + set(gca, 'FontSize', 14) + set(xlab,'Interpreter','latex'); + set(ylab,'Interpreter','latex'); + grid on; +end diff --git a/Utilities/matlabtools/plot_spec_boundary.m b/Utilities/matlabtools/plot_spec_boundary.m new file mode 100644 index 00000000..b3cd6937 --- /dev/null +++ b/Utilities/matlabtools/plot_spec_boundary.m @@ -0,0 +1,97 @@ +%% plot_spec_boundary( DATA, NPOINTS, NEWFIG ) +% ======================================================= +% +% Traces the plasma boundary in the (R,Z) plane +% with the specified number of points +% +% INPUT +% ----- +% -data : must be produced by calling read_spec(filename) +% -Npoints : number of points for theta +% -phi0 : toroidal angle at which the boundary is plotted +% -Newfig : opens (=1) or not (=0) a new figure, or overwrites (=2) +% last plot +% +% ------------------------------------% +% Written by S.Guinchard (05/17/22) % +% ------------------------------------% + +function plot_spec_boundary(d, Npoints, phi0, Newfig) + + Rbc = d.output.Rbc(:,2); + Zbs = d.output.Zbs(:,2); + + N = 10000; + theta = linspace(0,2*pi, N); + phi = linspace(0,2*pi, N); + + m = double(d.output.im); + n = double(d.output.in/d.input.physics.Nfp); + R = zeros(size(theta)); + Z = zeros(size(phi)); + + R_ = zeros(1,Npoints); + Z_ = R_; + + for i=1:length(m) + for j =1:length(theta) + R(j) = R(j) + Rbc(i)*cos(m(i)*theta(j) - n(i)*phi0); + Z(j) = Z(j) + Zbs(i)*sin(m(i)*theta(j) - n(i)*phi0); + end + end + + + for ii = 1:Npoints + R_(ii) = R((ii-1)*floor(N/Npoints)+1); + Z_(ii) = Z((ii-1)*floor(N/Npoints)+1); + end + + p = polyshape(R,Z); + + switch Newfig + case 0 + hold on + pg=plot(p); + pg.FaceColor = ([1 1 1]); + pg.EdgeColor = ([1 0 0]); + pg.LineWidth = 3; + hold on + scatter(R_,Z_, 'filled', 'ko') + xlabel('R') + ylabel('Z') + legend(strcat('$\phi_0$ = ', num2str(phi0)), 'Location','best','Interpreter','latex'); + set(legend,'FontSize',18); + set (gca, 'fontsize', 20) + + case 1 + figure + pg=plot(p); + pg.FaceColor = ([1 1 1]); + pg.EdgeColor = ([1 0 0]); + pg.LineWidth = 3; + hold on + scatter(R_,Z_, 'filled', 'ko') + xlabel('R', 'Interpreter', 'Latex') + ylabel('Z', 'Interpreter', 'Latex') + legend(strcat('$\phi_0$ = ', num2str(phi0)), 'Location','best','Interpreter','latex'); + set(legend,'FontSize',18); + set (gca, 'fontsize', 20) + + case 2 + hold off + pg=plot(p); + pg.FaceColor = ([1 1 1]); + pg.EdgeColor = ([1 0 0]); + pg.LineWidth = 3; + hold on + scatter(R_,Z_, 'filled', 'ko') + xlabel('R') + ylabel('Z') + legend(strcat('$\phi_0$ = ', num2str(phi0)), 'Location','best','Interpreter','latex'); + set(legend,'FontSize',18); + set (gca, 'fontsize', 20) + + end + + +end diff --git a/Utilities/matlabtools/plot_spec_current_profile.m b/Utilities/matlabtools/plot_spec_current_profile.m new file mode 100644 index 00000000..088f6478 --- /dev/null +++ b/Utilities/matlabtools/plot_spec_current_profile.m @@ -0,0 +1,133 @@ +function plot_spec_current_profile( data, iflag, newfig, varargin ) +% +% PLOT_SPEC_CURRENT_PROFILE( DATA, NEWFIG ) +% ========================================= +% +% Plot the total enclosed toroidal current as a function of the minor +% radius for a given SPEC equilibrium. +% +% INPUTS +% ------ +% * data: SPEC output data obtained with read_spec(filename) +% * iflag: (0) plots Ivolume +% (1) plots Isurf +% (2) plots both +% * newfig: (0) plot on current figure +% (1) open a new figure +% (2) Erase current figure and use it +% * Optional input: any combination of +% -'LineWidth', value (default 2) +% -'Color', value (default 'r') +% -'Marker', value (default 'none') +% -'MarkerSize', value (default 8) +% -'LineStyle', value (default '-') +% +% Written by A. Baillod (2020) +% + + % Check inputs + if ~any(iflag==[0,1,2]) + error('InputError: Invalid iflag') + end + + switch newfig + case 0 + hold on + case 1 + figure('Position', [200 200 900 700],'Color','w') + hold on + case 2 + hold off + otherwise + error('InputError: invalid newfig') + end + + + l = length(varargin); + if mod(l,2)~=0 + error('Invalid number of argument') + end + + opt.LineWidth = 2; + opt.Color = 'r'; + opt.Marker = 'none'; + opt.MarkerSize = 8; + opt.LineStyle = '-'; + for ii=1:l/2 + field = varargin{2*ii-1}; + value = varargin{2*ii }; + + opt.(field) = value; + end + + + nsucctrj = length(data.poincare.R(:,1,1)); % number of successfully followed trajectories + sval = data.transform.fiota(1:nsucctrj,1); + nvol = data.input.physics.Nvol; + mvol = data.output.Mvol; + nptrj = zeros(1,mvol); + count = 1; + + ind = find(sval==-2); %Remove wrongly written data + sval(ind) = []; + + for is=1:length(sval)-1 + if(sval(is)>0 && sval(is+1)<0) %Reached the end of a volume + if(count==1) + nptrj(count) = is; + else + nptrj(count) = is-sum(nptrj); + end + count = count+1; + end + end + nptrj(mvol) = length(sval)-sum(nptrj); + + + ns = 32; + nt = 32; + cumflux = 0; + cumcur = 0; + kstart = 1; + psitor = zeros(1,length(sval)); + + Iphi = zeros(1, length(sval) ); + mu = data.output.mu; + + for lvol=1:mvol + start = -1; + if lvol==1 + start=-0.999; + end + + for k=kstart:kstart-1+nptrj(lvol) + tflux = get_spec_torflux(data,lvol,0,start,sval(k),ns,nt); + psitor(k) = cumflux + tflux; + + if iflag==0 || iflag==2 + Iphi(k) = cumcur + mu(lvol) * tflux; + else + Iphi(k) = cumcur; + end + end + cumflux = psitor(k); + kstart = kstart+nptrj(lvol); + %cumcur = Iphi(k); + + if iflag==1 || iflag==2 + cumcur = Iphi(k) + data.output.IPDt(lvol); % add surface current + else + cumcur = Iphi(k); + end + end + + phiedge=psitor(end); + + + plot( sqrt(psitor / phiedge), Iphi, 'LineWidth', opt.LineWidth, 'Color', opt.Color, 'Marker', opt.Marker, 'LineStyle', opt.LineStyle ) + xlabel('$(\Psi_t / \Psi_{edge})^{1/2}$', 'Interpreter', 'latex') + ylabel('$\mu_0I_\phi$[Tm]', 'Interpreter', 'latex') + set(gca, 'FontSize', 18) + hold on; + +end \ No newline at end of file diff --git a/Utilities/matlabtools/plot_spec_fieldlines.m b/Utilities/matlabtools/plot_spec_fieldlines.m new file mode 100644 index 00000000..3816d1c9 --- /dev/null +++ b/Utilities/matlabtools/plot_spec_fieldlines.m @@ -0,0 +1,86 @@ +%% plot_spec_fieldlines( DATA, NPOINTS, NPERIODS, NEWFIG ) +% ======================================================= +% +% Traces magnetic field lines in the (phi, theta) plane +% and gives an output containing the coordinates +% (used e.g with the code get_spec_straightfieldlines) +% +% INPUT +% ----- +% -data : must be produced by calling read_spec(filename) +% -Npoints : number of points along the field line +% -Nperiods : number of toroidal periods over which the field line is +% traced +% -Newfig : opens (=1) or not (=0) a new figure, or overwrites (=2) +% last plot +% +% ------------------------------------% +% Written by S.Guinchard (03/01/22) % +% Last modified (05/15/22) % +% ------------------------------------% + +function coord = plot_spec_fieldlines(d,Npoints,Nperiods,newfig) + + phi = linspace(0,2*Nperiods*pi,Npoints); + dphi = phi(2)-phi(1); + s = 1; + Fs = 18; + theta_temp(1) = 0; + + for i = 1:length(phi)-1 + Bfield_temp = get_spec_magfield(d,1,s,theta_temp(i),phi(i)); + theta_temp(i+1) = theta_temp(i)+dphi*(cell2mat(Bfield_temp(2))/cell2mat(Bfield_temp(3))); + end + + coord.theta = wrapTo2Pi(theta_temp); + coord.phi = wrapTo2Pi(phi); + switch newfig + + case 0 + hold on + scatter(coord.phi, coord.theta, 'b.') + ax = gca; + ax.TickLabelInterpreter = 'latex'; + xticks([0 pi/3 2*pi/3 pi 4*pi/3 5*pi/3 2*pi]) + xticklabels({'$0$','$\frac{\pi}{3}$','$\frac{2\pi}{3}$','$\pi$', '$\frac{4\pi}{3}$','$\frac{5\pi}{3}$','$2\pi$'}); + yticks([0 pi/3 2*pi/3 pi 4*pi/3 5*pi/3 2*pi]) + yticklabels({'$0$','$\frac{\pi}{3}$','$\frac{2\pi}{3}$','$\pi$', '$\frac{4\pi}{3}$','$\frac{5\pi}{3}$','$2\pi$'}); + xlim([0 2*pi]) + ylim([0 2*pi]) + set (gca, 'fontsize', Fs) + xlabel('$\phi$', 'FontSize', Fs+10 , 'Interpreter', 'latex') + ylabel('$\theta$', 'FontSize', Fs+10 , 'Interpreter', 'latex') + + case 1 + figure + scatter(coord.phi, coord.theta, 'b.') + ax = gca; + ax.TickLabelInterpreter = 'latex'; + xticks([0 pi/3 2*pi/3 pi 4*pi/3 5*pi/3 2*pi]) + xticklabels({'$0$','$\frac{\pi}{3}$','$\frac{2\pi}{3}$','$\pi$', '$\frac{4\pi}{3}$','$\frac{5\pi}{3}$','$2\pi$'}); + yticks([0 pi/3 2*pi/3 pi 4*pi/3 5*pi/3 2*pi]) + yticklabels({'$0$','$\frac{\pi}{3}$','$\frac{2\pi}{3}$','$\pi$', '$\frac{4\pi}{3}$','$\frac{5\pi}{3}$','$2\pi$'}); + xlim([0 2*pi]) + ylim([0 2*pi]) + set (gca, 'fontsize', Fs) + xlabel('$\phi$', 'FontSize', Fs+10 , 'Interpreter', 'latex') + ylabel('$\theta$', 'FontSize', Fs+10 , 'Interpreter', 'latex') + + case 2 + hold off + scatter(coord.phi, coord.theta, 'b.') + ax = gca; + ax.TickLabelInterpreter = 'latex'; + xticks([0 pi/3 2*pi/3 pi 4*pi/3 5*pi/3 2*pi]) + xticklabels({'$0$','$\frac{\pi}{3}$','$\frac{2\pi}{3}$','$\pi$', '$\frac{4\pi}{3}$','$\frac{5\pi}{3}$','$2\pi$'}); + yticks([0 pi/3 2*pi/3 pi 4*pi/3 5*pi/3 2*pi]) + yticklabels({'$0$','$\frac{\pi}{3}$','$\frac{2\pi}{3}$','$\pi$', '$\frac{4\pi}{3}$','$\frac{5\pi}{3}$','$2\pi$'}); + xlim([0 2*pi]) + ylim([0 2*pi]) + set (gca, 'fontsize', Fs) + xlabel('$\phi$', 'FontSize', Fs+10 , 'Interpreter', 'latex') + ylabel('$\theta$', 'FontSize', Fs+10 , 'Interpreter', 'latex') + + end + +end \ No newline at end of file diff --git a/Utilities/matlabtools/plot_spec_fluxfun.m b/Utilities/matlabtools/plot_spec_fluxfun.m new file mode 100644 index 00000000..221588a0 --- /dev/null +++ b/Utilities/matlabtools/plot_spec_fluxfun.m @@ -0,0 +1,70 @@ +function plot_spec_fluxfun(data,lvol,ns,nt,z0,ncont,newfig) + +% +% PLOT_SPEC_OUTFLUXFUN( DATA, NS, NT, Z0, NCONT, NEWFIG ) +% ======================================================= +% +% Plots iso-contours of Az on a given cross-section +% +% INPUT +% ----- +% -data : must be produced by calling read_spec(filename) +% -lvol : volume number +% -ns : radial resolution for construction of Az +% -nt : poloidal resolution for construction of Az +% -z0 : toroidal angle at which Az is evaluated +% -ncont : number of iso-contour lines +% -newfig : flag for whether a new figure should be open (=1) or not(=0) +% +% Note: should only work for free-boundary equilibria +% Note: poloidal flux function is psi=-A_phi if A_phi is the covariant component and psi=-R*A_phi if A_phi is the canonical component +% +% written by J.Loizu (2018) + + + % Check input + if lvol>data.output.Mvol || lvol<1 + error('Invalid lvol') + end + + if ns<1 + error('Invalid ns') + end + + if nt<1 + error('Invalid nt') + end + + if ncont<1 + error('Invalid ncont') + end + + switch newfig + case 0 + hold on + case 1 + figure + hold on + case 2 + hold off + otherwise + error('Invalid newfig') + end + + % Generate coordinate arrays + sarr = linspace(-1,1,ns); + tarr = linspace(0,2*pi,nt); + + acov = get_spec_vecpot(data,lvol,sarr,tarr,z0); + R = get_spec_R_derivatives(data,lvol,sarr,tarr,z0,'R'); + Z = get_spec_R_derivatives(data,lvol,sarr,tarr,z0,'Z'); + + ffun = -acov{2}; + + if(newfig==1) + figure; hold on; + end + + contour(R{1},Z{1},ffun,ncont,'k') + +end diff --git a/Utilities/matlabtools/plot_spec_grid.m b/Utilities/matlabtools/plot_spec_grid.m index 88ecac72..a38611f1 100644 --- a/Utilities/matlabtools/plot_spec_grid.m +++ b/Utilities/matlabtools/plot_spec_grid.m @@ -11,7 +11,7 @@ function plot_spec_grid(data,nz0,newfig) % -data : must be produced by calling read_spec(filename) % -nz0 : toroidal plane number at which coordinates are shown (nz0=1 at toroidal angle phi=0) % -newfig : opens(=1) or not(=0) a new figure, or overwrite selected -% figure (=2) +% figure (=2) % % written by J.Loizu (2015) % @@ -24,23 +24,24 @@ function plot_spec_grid(data,nz0,newfig) hold on case 2 hold off + otherwise + error('InputError: invalid newfig') end -nvol = data.input.physics.Nvol+data.input.physics.Lfreebound; +Mvol = data.output.Mvol; Lrad = data.input.physics.Lrad; Nt = data.grid.Nt; -Nz = data.grid.Nz; Rij = data.grid.Rij; Zij = data.grid.Zij; ccol = 'm'; -cthick = 12; +cthick = 6; iz = nz0-1; -for i=1:nvol +for i=1:Mvol for l=1:Lrad(i)+1 R_tmp = Rij{i}; diff --git a/Utilities/matlabtools/plot_spec_iota.m b/Utilities/matlabtools/plot_spec_iota.m index 2a65626b..b8db004e 100644 --- a/Utilities/matlabtools/plot_spec_iota.m +++ b/Utilities/matlabtools/plot_spec_iota.m @@ -1,4 +1,4 @@ -function out = plot_spec_iota(data,iorq,xaxis,newfig) +function out = plot_spec_iota(data,iorq,xaxis,newfig,varargin) % % PLOT_SPEC_IOTA( DATA, IORQ, XAXIS, NEWFIG ) @@ -8,13 +8,20 @@ % % INPUT % ----- -% -data : produced by calling read_spec(fname) -% -iorq : plot iota('i') or safety factor ('q') -% -xaxis='s' : plots s-coordinnate as the x-axis -% -xaxis='R' : plots R-coordinnate as the x-axis -% -xaxis='f' : plots toroidal flux as the x-axis -% -xaxis='r' : plots sqrt(toroidal flux) as the x-axis -% -newfig : opens(=1) or not(=0) a new figure, or overwrites(=2) current plot +% -data : produced by calling read_spec(fname) +% -iorq : plot iota('i') or safety factor ('q') +% -xaxis : 's' plots s-coordinnate as the x-axis +% 'R' plots R-coordinnate as the x-axis +% 'f' plots toroidal flux as the x-axis +% 'r' plots sqrt(toroidal flux) as the x-axis +% -newfig: opens (=1) or not (=0) a new figure, or overwrites (=2) +% current plot +% -varargin: Optional arguments. Can be any of the following pairs, +% 'LineWidth', linewidth +% 'Color', color +% 'Marker', marker +% 'MarkerSize', makersize +% 'LineStyle', linestyle % % OUTPUT % ------ @@ -26,139 +33,196 @@ % modified by A.Baillod (01.2019) % modified by J.Loizu (01.2020) -if(newfig==1) - figure - hold on; -elseif newfig==0 - hold on; -elseif newfig==2 % A.Baillod (06.2019) - hold off; -end + % Check inputs + if ~any(iorq==['iq']) + error('InputError: invalid iorq') + end + + if ~any(xaxis==['sRfr']) + error('InputError: invalid xaxis') + end -if(iorq=='i') -F = data.transform.fiota(1:end,2); -Flabel='\iota'; -elseif(iorq=='q') -F = 1./data.transform.fiota(1:end,2); -Flabel='q'; -end + l = length(varargin); + if mod(l,2)~=0 + error('InputError: invalid number of argument') + end + + switch newfig + case 1 + figure('Position', [200 200 900 700], 'Color', 'w') + hold on; + case 0 + hold on; + case 2 + hold off; + otherwise + error('InputError: invalid newfig') + end + + % Read optional inputs + opt.LineWidth = 2; + opt.Color = 'r'; + opt.Marker = '*'; + opt.MarkerSize = 8; + opt.LineStyle = 'none'; + for ii=1:l/2 + field = varargin{2*ii-1}; + value = varargin{2*ii }; -nsucctrj = length(data.poincare.R(:,1,1)); % number of successfully followed trajectories - -switch xaxis - case 's' - plot(data.transform.fiota(1:nsucctrj,1),F(1:nsucctrj),'*','MarkerSize',8,'LineWidth',2) - ylabel(Flabel) - out = cell(2); - out{1} = data.transform.fiota(:,1); - out{2} = F; - - case 'R' - plot(transpose(data.poincare.R(:,1,1)),F(1:nsucctrj),'*','MarkerSize',8,'LineWidth',2) - ylabel(Flabel) - out = cell(2); - out{1} = data.poincare.R(:,1,1); - out{2} = F(1:nsucctrj); - - case 'f' - sval = data.transform.fiota(1:nsucctrj,1); - nvol = data.output.Mvol; - nptrj = zeros(1,nvol); - count = 1; - - ind = find(sval==-2); %Remove wrongly written data - sval(ind) = []; - F(ind) = []; - nsucctrj = nsucctrj - length(ind); - - for is=1:length(sval)-1 - if(sval(is)>0 && sval(is+1)<0) %Reached the end of a volume - if(count==1) - nptrj(count) = is; - else - nptrj(count) = is-sum(nptrj); + opt.(field) = value; end - count = count+1; - end - end - nptrj(nvol) = length(sval)-sum(nptrj); - - ns = 32; - nt = 32; - cumflux = 0; - kstart = 1; - psitor = zeros(1,length(sval)); - - - for lvol=1:nvol - - if lvol==nvol % Required if last value had a -2 (often in free bound) - phiedge = cumflux + get_spec_torflux(data, nvol, 0, -1, 1, ns, nt); + + + + if(iorq=='i') + F = data.transform.fiota(1:end,2); + Flabel='\iota'; + elseif(iorq=='q') + F = 1./data.transform.fiota(1:end,2); + Flabel='q'; + end + + nsucctrj = length(data.poincare.R(:,1,1)); % number of successfully followed trajectories + + switch xaxis + case 's' + plot(data.transform.fiota(1:nsucctrj,1),F(1:nsucctrj),'Marker',opt.Marker,... + 'MarkerSize',opt.MarkerSize,'LineWidth',opt.LineWidth,'MarkerEdgeColor',... + opt.Color,'LineStyle',opt.LineStyle,'Color',opt.Color) + ylabel(Flabel) + out = cell(2); + out{1} = data.transform.fiota(:,1); + out{2} = F; + + case 'R' + plot(transpose(data.poincare.R(:,1,1)),F(1:nsucctrj),'Marker',opt.Marker,... + 'MarkerSize',opt.MarkerSize,'LineWidth',opt.LineWidth,'MarkerEdgeColor',... + opt.Color,'LineStyle',opt.LineStyle,'Color',opt.Color) + ylabel(Flabel) + out = cell(2); + out{1} = data.poincare.R(:,1,1); + out{2} = F(1:nsucctrj); + + case 'f' + sval = data.transform.fiota(1:nsucctrj,1); + nvol = data.input.physics.Nvol; + mvol = data.output.Mvol; + nptrj = zeros(1,mvol); + count = 1; + + ind = find(sval==-2); %Remove wrongly written data + sval(ind) = []; + F(ind) = []; + nsucctrj = nsucctrj - length(ind); + + for is=1:length(sval)-1 + if(sval(is)>0 && sval(is+1)<0) %Reached the end of a volume + if(count==1) + nptrj(count) = is; + else + nptrj(count) = is-sum(nptrj); + end + count = count+1; + end end - - for k=kstart:kstart-1+nptrj(lvol) - psitor(k) = cumflux + get_spec_torflux(data,lvol,0,-1,sval(k),ns,nt); + nptrj(mvol) = length(sval)-sum(nptrj); + + ns = 32; + nt = 32; + cumflux = 0; + kstart = 1; + psitor = zeros(1,length(sval)); + + for lvol=1:mvol + + start = -1; + if lvol==1 + start = -0.999; + end + + if lvol==nvol % Required if last value had a -2 (often in free bound) + phiedge = cumflux + get_spec_torflux(data, nvol, 0, start, 1 , ns, nt); + end + + for k=kstart:kstart-1+nptrj(lvol) + psitor(k) = cumflux + get_spec_torflux(data,lvol,0, start, sval(k),ns,nt); + end + cumflux = psitor(k); + kstart = kstart+nptrj(lvol); end - cumflux = psitor(k); - kstart = kstart+nptrj(lvol); - end - - plot(psitor/phiedge,F(1:nsucctrj),'*','MarkerSize',8,'LineWidth',2) - ylabel(Flabel) - xlabel('\Psi / \Psi_{edge}') - - out = cell(2); - out{1} = psitor/psitor(end); - out{2} = F(1:nsucctrj); - -case 'r' - sval = data.transform.fiota(1:nsucctrj,1); - nvol = data.output.Mvol; - nptrj = zeros(1,nvol); - count = 1; - - ind = find(sval==-2); %Remove wrongly written data - sval(ind) = []; - F(ind) = []; - nsucctrj = nsucctrj - length(ind); - - for is=1:length(sval)-1 - if(sval(is)>0 && sval(is+1)<0) - if(count==1) - nptrj(count) = is; - else - nptrj(count) = is-sum(nptrj); - end - count = count+1; - end - end - nptrj(nvol) = length(sval)-sum(nptrj); - - ns = 32; - nt = 32; - cumflux = 0; - kstart = 1; - psitor = zeros(1,length(sval)); - - for lvol=1:nvol - - if lvol==nvol % Required if last value had a -2 (often in free bound) - phiedge = cumflux + get_spec_torflux(data, nvol, 0, -1, 1, ns, nt); + + plot(psitor/phiedge,F(1:nsucctrj),'Marker',opt.Marker,'MarkerSize',opt.MarkerSize,... + 'LineWidth',opt.LineWidth,'MarkerEdgeColor',opt.Color,... + 'LineStyle',opt.LineStyle,'Color',opt.Color) + ylabel(Flabel) + xlabel('\Psi / \Psi_{edge}') + + out = cell(2); + out{1} = psitor/psitor(end); + out{2} = F(1:nsucctrj); + + case 'r' + sval = data.transform.fiota(1:nsucctrj,1); + nvol = data.input.physics.Nvol; + mvol = data.output.Mvol; + nptrj = zeros(1,nvol); + count = 1; + + ind = find(sval==-2); %Remove wrongly written data + sval(ind) = []; + F(ind) = []; + nsucctrj = nsucctrj - length(ind); + + for is=1:length(sval)-1 + if(sval(is)>0 && sval(is+1)<0) + if(count==1) + nptrj(count) = is; + else + nptrj(count) = is-sum(nptrj); + end + count = count+1; + end end - - for k=kstart:kstart-1+nptrj(lvol) - psitor(k) = cumflux + get_spec_torflux(data,lvol,0,-1,sval(k),ns,nt); + nptrj(mvol) = length(sval)-sum(nptrj); + + ns = 32; + nt = 32; + cumflux = 0; + kstart = 1; + psitor = zeros(1,length(sval)); + + for lvol=1:mvol + + start = -1; + if lvol==1 + start = -0.999; + end + + if lvol==nvol % Required if last value had a -2 (often in free bound) + phiedge = cumflux + get_spec_torflux(data, nvol, 0, start, 1 , ns, nt); + end + + for k=kstart:kstart-1+nptrj(lvol) + psitor(k) = cumflux + get_spec_torflux(data,lvol,0, start, sval(k),ns,nt); + end + cumflux = psitor(k); + kstart = kstart+nptrj(lvol); end - cumflux = psitor(k); - kstart = kstart+nptrj(lvol); - end + + % phiedge = data.input.physics.phiedge; + + plot(sqrt(psitor/phiedge),F(1:nsucctrj),'Marker',opt.Marker,'MarkerSize',... + opt.MarkerSize,'LineWidth',opt.LineWidth,'MarkerEdgeColor',... + opt.Color,'LineStyle',opt.LineStyle,'Color',opt.Color) + ylabel(Flabel) + xlabel('(\Psi / \Psi_{edge})^{1/2}') + + out = cell(2); + out{1} = sqrt(psitor/psitor(end)); + out{2} = F(1:nsucctrj); + + end + + set(gca,'FontSize',18) - plot(sqrt(psitor/phiedge),F(1:nsucctrj),'*','MarkerSize',8,'LineWidth',2) - ylabel(Flabel) - xlabel('(\Psi / \Psi_{edge})^{1/2}') - - out = cell(2); - out{1} = psitor/psitor(end); - out{2} = F(1:nsucctrj); - end diff --git a/Utilities/matlabtools/plot_spec_iotakam.m b/Utilities/matlabtools/plot_spec_iotakam.m index 52b78707..f4f7d168 100644 --- a/Utilities/matlabtools/plot_spec_iotakam.m +++ b/Utilities/matlabtools/plot_spec_iotakam.m @@ -8,70 +8,79 @@ function plot_spec_iotakam(data,iorq,xaxis,newfig) % % INPUT % ----- -% -data : produced by calling read_spec(fname) -% -iorq : plot iota('i') or safety factor ('q') -% -xaxis='R' : plots R-position of interfaces (at phi=0) as the x-axis -% -xaxis='f' : plots toroidal flux as the x-axis -% -xaxis='r' : plots sqrt(toroidal flux) as the x-axis -% -newfig : opens(=1) or not(=0) a new figure +% -data : produced by calling read_spec(fname) +% -iorq : plot iota('i') or safety factor ('q') +% -xaxis : 'R' plots R-position of interfaces (at phi=0) as the x-axis +% 'f' plots toroidal flux as the x-axis +% 'r' plots sqrt(toroidal flux) as the x-axis +% -newfig: opens(=1) or not(=0) a new figure % % written by J.Loizu (2017) + % Check input + if ~any(iorq==['i','q']) + error('InputError: invalid iorq') + end + if ~any(xaxis==['R','f','r']) + error('InputError: invalid xaxis') + end -Nvol = data.input.physics.Nvol; -tflux = data.input.physics.tflux; -iota = data.input.physics.iota; -oita = data.input.physics.oita; -Rmn = data.output.Rbc; -im = data.output.im; -in = data.output.in; -mn = data.output.mn; -freeb = data.input.physics.Lfreebound; + switch newfig + case 0 + hold on + case 1 + figure('Color','w') + hold on + case 2 + hold off + otherwise + error('InputError: invalid newfig') + end -R0 = zeros(1,Nvol); + Nvol = data.input.physics.Nvol; + tflux = data.input.physics.tflux; + iota = data.input.physics.iota; + oita = data.input.physics.oita; + Rmn = data.output.Rbc; + freeb = data.input.physics.Lfreebound; -for l=1:Nvol - R0(l) = sum(Rmn(:,l+1)); -end + R0 = zeros(1,Nvol); -switch newfig -case 0 - hold on -case 1 - figure -case 2 - hold off -end + for l=1:Nvol + R0(l) = sum(Rmn(:,l+1)); + end -if(iorq=='i') -F = iota(2:end); -G = oita(2:end); -Flabel='\iota'; -elseif(iorq=='q') -F = 1./iota(2:end); -G = 1./oita(2:end); -Flabel='q'; -end + if(iorq=='i') + F = iota(2:end); + G = oita(2:end); + Flabel='\iota'; + elseif(iorq=='q') + F = 1./iota(2:end); + G = 1./oita(2:end); + Flabel='q'; + end -switch xaxis - case 'R' - plot(R0,F,'r+','MarkerSize',6,'LineWidth',2) - hold on; - plot(R0,G,'m+','MarkerSize',6,'LineWidth',2) - xlabel('R') - ylabel(Flabel) - case 'f' - plot(tflux(1:end-freeb),F,'r+','MarkerSize',6,'LineWidth',2) - hold on; - plot(tflux(1:end-freeb),G,'m+','MarkerSize',6,'LineWidth',2) - xlabel('\Psi / \Psi_{edge}') - ylabel(Flabel) - case 'r' - plot(sqrt(tflux(1:end-freeb)),F,'r+','MarkerSize',6,'LineWidth',2) - hold on; - plot(sqrt(tflux(1:end-freeb)),G,'m+','MarkerSize',6,'LineWidth',2) - xlabel('(\Psi / \Psi_{edge})^{1/2}') - ylabel(Flabel) + switch xaxis + case 'R' + plot(R0,F,'r+','MarkerSize',6,'LineWidth',2) + hold on; + plot(R0,G,'m+','MarkerSize',6,'LineWidth',2) + xlabel('R') + ylabel(Flabel) + case 'f' + plot(tflux(1:end-freeb),F,'r+','MarkerSize',6,'LineWidth',2) + hold on; + plot(tflux(1:end-freeb),G,'m+','MarkerSize',6,'LineWidth',2) + xlabel('\Psi / \Psi_{edge}') + ylabel(Flabel) + case 'r' + plot(sqrt(tflux(1:end-freeb)),F,'r+','MarkerSize',6,'LineWidth',2) + hold on; + plot(sqrt(tflux(1:end-freeb)),G,'m+','MarkerSize',6,'LineWidth',2) + xlabel('(\Psi / \Psi_{edge})^{1/2}') + ylabel(Flabel) + end + end diff --git a/Utilities/matlabtools/plot_spec_iterations.m b/Utilities/matlabtools/plot_spec_iterations.m new file mode 100644 index 00000000..01cf2a12 --- /dev/null +++ b/Utilities/matlabtools/plot_spec_iterations.m @@ -0,0 +1,138 @@ +function plot_spec_iterations( data, xl, yl ) + +% PLOT_SPEC_ITERATIONS( DATA, XL, YL ) +% ==================================== +% +% Plot the volumes interfaces at any iteration of SPEC. Change the +% iteration using a slider +% +% INPUT +% ----- +% -DATA: Obtained from read_spec( filename ) +% -xl : xlimit +% -yl : ylimit +% +% OUTPUT +% ------ +% A magnificient plot! +% + + % Open figure + figure( 'Position', [200 200 900 700], 'Color', 'w' ) + fig = gcf; + ax = gca; + ax.Position = [0.1300 0.2386 0.7750 0.6864]; + + % Read size + Nfp = double(data.input.physics.Nfp); + [~, ~, Niter] = size(data.iterations.iRbc); + + if Niter==0 + error('No iterations available') + end + + % Create some sliders for controling the iteration and the toroidal + % angle + sld_phi = uicontrol(fig, 'style', 'slider', 'Position', [200 25 500 20],'units','pixel', ... + 'Value',0,'Max',2*pi / Nfp,'Min',0); + sld_it = uicontrol(fig, 'style', 'slider', 'Position', [200 63 500 20],'units','pixel', ... + 'Value',1,'Max', Niter,'Min',1, 'SliderStep', [1/(Niter-1), 1/(Niter-1)]); + + addlistener( sld_phi, 'ContinuousValueChange', @(sld_phi, event) updatePlot(sld_phi, sld_it, data, xl, yl) ); + addlistener( sld_it , 'ContinuousValueChange', @(sld_it , event) updatePlot(sld_phi, sld_it, data, xl, yl) ); + + % Plot + plot_iteration( data, 1, 0, xl, yl ) + mytitle = sprintf('%s=%2.3f, iteration %05i', '\phi', 0, 1); + title(mytitle,'FontSize',18) +end + + + + +function updatePlot(sld_phi, sld_it, data, xl, yl) +% +% UPDATEPLOT( SLD_PHI, SLD_IT, DATA, XL, YL ) +% =========================================== +% +% Update plot when a slider value has changed +% +% INPUTS +% ------ +% -sld_phi: handle to toroidal angle slider +% -sld_it : handle to iteration slider +% -data : obtained from read_spec(filename) +% -xl : xlimit +% -yl : ylimit +% + + phi = sld_phi.Value; + iter = round(sld_it.Value); + + plot_iteration( data, iter, phi, xl, yl ) + + mytitle = sprintf('%s=%2.3f, iteration %05i', '\phi', phi, iter); + title(mytitle,'FontSize',18) +end + + +function plot_iteration( data, iter, phi, xl, yl ) +% +% PLOT_ITERATION( DATA, ITER, PHI, XL, YL ) +% ========================================= +% +% Generate plot from SPEC data +% +% INPUTS +% ------ +% -data: obtained from read_spec( filename ) +% -iter: iteration number +% -phi : toroidal angle +% -xl : xlimit +% -yl : ylimit +% + + Nfp = double(data.input.physics.Nfp); + im = double(data.output.im); + in = double(data.output.in) / Nfp; + Mvol = double(data.output.Mvol); + Ntor = double(data.input.physics.Ntor); + + % Erase previous plot + hold off + + % Axis + Ra = 0; + Za = 0; + for nn=0:Ntor + Ra = Ra + data.iterations.iRbc(nn+1,1,iter) * cos( nn*Nfp*phi ); + Za = Za - data.iterations.iZbs(nn+1,1,iter) * sin( nn*Nfp*phi ); + end + + scatter( Ra, Za, 50, 'MarkerFaceColor', 'r', 'MarkerEdgeColor', 'r' ) + + hold on + % volume boundaries + for ivol=2:Mvol+1 + Rmn = data.iterations.iRbc(:,ivol,iter); + Zmn = data.iterations.iZbs(:,ivol,iter); + + tarr = linspace( 0, 2*pi, 1024 ); + R = zeros(1,1024); + Z = zeros(1,1024); + for ii=1:length(Rmn) + arg = im(ii) * tarr - in(ii) * Nfp * phi; + R = R + Rmn(ii) * cos( arg ); + Z = Z + Zmn(ii) * sin( arg ); + end + + scatter( R, Z ) + hold on + axis equal + end + + + xlim(xl) + ylim(yl) +end + diff --git a/Utilities/matlabtools/plot_spec_jacobian.m b/Utilities/matlabtools/plot_spec_jacobian.m index 82c84fe4..7910d29c 100644 --- a/Utilities/matlabtools/plot_spec_jacobian.m +++ b/Utilities/matlabtools/plot_spec_jacobian.m @@ -9,7 +9,7 @@ % INPUT % ----- % -data : data obtained via read_spec(filename) -% -lvol : volume number +% -lvol : volume number. Set to 0 for plotting all volumes % -sarr : is the array of values for the s-coordinate ('d' for default) % -tarr : is the array of values for the theta-coordinate ('d' for default) % -zarr : is the array of values for the zeta-coordinate ('d' for default) @@ -23,70 +23,113 @@ % written by J.Loizu (2016) if(sarr=='d') -sarr=linspace(-1,1,64); + sarr=linspace(-1,1,64); end if(tarr=='d') -tarr=linspace(0,2*pi,64); + tarr=linspace(0,2*pi,64); end if(zarr=='d') -zarr=0; + zarr=0; end -rzbdata = cell(3); - -% Compute sqrt(g) - -jac = get_spec_jacobian(data,lvol,sarr,tarr,zarr); - -% Compute function (R,Z)(s,theta,zeta) +% Check inputs +if lvol<1 || lvol>data.output.Mvol + error('InputError: invalid lvol') +end -rzdata = get_spec_rzarr(data,lvol,sarr,tarr,zarr); +if isempty(sarr) + error('InputError: sarr is empty') +end +if isempty(tarr) + error('InputError: tarr is empty') +end +if isempty(zarr) + error('InputError: zarr is empty') +end -R = rzdata{1}; -Z = rzdata{2}; +if sarr(1)<-1 || sarr(end)>1 + error('InputError: invalid sarr') +end -% Plot +if any(diff(sarr)<0) + error('InputError: sarr is not monotonic') +end switch newfig case 0 hold on case 1 - figure + figure('Color','w','Position',[200 200 900 700]) hold on case 2 hold off + otherwise + error('InputError: invalid newfig') end -Rtemp = R; -Ztemp = Z; -switch data.input.physics.Igeometry - case 1 - R = tarr; - Z = Rtemp; - case 2 - for it=1:length(tarr) - R(:,it,:) = Rtemp(:,it,:) .* cos(tarr(it)); - Z(:,it,:) = Rtemp(:,it,:) .* sin(tarr(it)); - end - case 3 - R = Rtemp; - Z = Ztemp; + + +% Check input +if (length(sarr)>1) && length(tarr)>1 && length(zarr)>1 + error('This is a 2d plotting routine; one input array has to be a scalar') end - -for iz=1:length(zarr) - - pcolor(R(:,:,iz),Z(:,:,iz),jac(:,:,iz)); shading interp; colorbar - hold on - axis equal - title('|B|'); - xlabel('R'); - ylabel('Z'); +% Allocate memory +rzbdata = cell(3); + +if lvol==0 + lstart=1; + lend =data.output.Mvol; +else + lstart=lvol; + lend =lvol; +end + +for ivol=lstart:lend + % Compute sqrt(g) + jac = squeeze(get_spec_jacobian(data,ivol,sarr,tarr,zarr)); + + % Compute function (R,Z)(s,theta,zeta) + R = get_spec_R_derivatives(data,ivol,sarr,tarr,zarr,'R'); + Z = get_spec_R_derivatives(data,ivol,sarr,tarr,zarr,'Z'); + + R = R{1}; + Z = Z{1}; + + % Plot + Rtemp = R; + Ztemp = Z; + switch data.input.physics.Igeometry + case 1 + R = tarr; + Z = Rtemp; + case 2 + for it=1:length(tarr) + R(:,it,:) = Rtemp(:,it,:) .* cos(tarr(it)); + Z(:,it,:) = Rtemp(:,it,:) .* sin(tarr(it)); + end + case 3 + R = squeeze(Rtemp); + Z = squeeze(Ztemp); + end + + + pcolor(R,Z,jac); + shading interp; + colorbar + hold on end +axis equal +title('|B|'); +xlabel('R'); +ylabel('Z'); +set(gca, 'FontSize', 18) + + % Output data rzbdata{1} = R; diff --git a/Utilities/matlabtools/plot_spec_kam.m b/Utilities/matlabtools/plot_spec_kam.m index 28226ae5..d5d3f4bb 100644 --- a/Utilities/matlabtools/plot_spec_kam.m +++ b/Utilities/matlabtools/plot_spec_kam.m @@ -1,107 +1,121 @@ -function plot_spec_kam(data,zetaov2pi,newfig) +function plot_spec_kam(data, zeta, newfig, varargin) % -% PLOT_SPEC_KAM( DATA, ZETAOV2PI, NEWFIG ) -% ======================================== +% PLOT_SPEC_KAM( DATA, NZ0, NEWFIG ) +% ================================== % % Produces a "Poincare plot" of the KAM surfaces. % % INPUT % ----- % -data : obtained from read_spec(fname) -% -zetaov2pi : shows the toroidal plane at zeta=2*pi*(zetaov2pi) +% -zeta : toroidal angle % -newfig : opens(=1) or not(=0) a new figure, or overplots(=2) on existing figure % % written by J.Loizu (2016) -% upgraded by J.Loizu (07.2017) -% modified by A. Baillod (06.2019) -% modified by J.Loizu (01.2020) - - -Nvol = double(data.input.physics.Nvol); -mn = data.output.mn; -im = data.output.im; -in = data.output.in; -Rbcmn = data.output.Rbc; -Rbsmn = data.output.Rbs; -Zbcmn = data.output.Zbc; -Zbsmn = data.output.Zbs; -Igeometry = data.input.physics.Igeometry; -try - rpol = data.input.physics.rpol; -catch - rpol = 1; -end - -% Compute (x,y) coordinates of each KAM surface - -zeta = zetaov2pi*(2*pi); - -nth = 2048; -dth = 2*pi/nth; -theta = dth:dth:2*pi; - -X = zeros(Nvol,nth); -Y = zeros(Nvol,nth); - - -switch Igeometry - case 1 - X = zeros(Nvol+1,nth); - Y = zeros(Nvol+1,nth); - for i=1:Nvol+1 - X(i,:) = rpol*theta; - for k=1:mn - alpha = double(im(k))*theta-double(in(k))*zeta; - Y(i,:) = Y(i,:) + Rbcmn(k,i)*cos(alpha) + Rbsmn(k,i)*sin(alpha); + + % Check inputs + switch newfig + case 0 + hold on + case 1 + figure + hold on + case 2 + hold off + otherwise + error('InputError: invalid newfig') + end + + + l = length(varargin); + if mod(l,2)~=0 + error('InputError: Invalid number of argument') + end + + opt.InterfaceColor = 'r'; + for ii=1:l/2 + field = varargin{2*ii-1}; + value = varargin{2*ii }; + + opt.(field)=value; + end + + Ndiscrete = double(data.input.numerics.Ndiscrete); + Ntor = double(max(abs(data.output.in))); + Nplan = max(Ndiscrete*4*Ntor, 1); + + Nvol = double(data.input.physics.Nvol); + mn = data.output.mn; + im = data.output.im; + in = data.output.in; + Rbcmn = data.output.Rbc; + Rbsmn = data.output.Rbs; + Zbcmn = data.output.Zbc; + Zbsmn = data.output.Zbs; + Igeometry = data.input.physics.Igeometry; + try + rpol = data.input.physics.rpol; + catch + rpol = 1; + end + + % Compute (x,y) coordinates of each KAM surface + nth = 2048; + dth = 2*pi/nth; + theta = dth:dth:2*pi; + + X = zeros(Nvol,nth); + Y = zeros(Nvol,nth); + + + switch Igeometry + case 1 + X = zeros(Nvol+1,nth); + Y = zeros(Nvol+1,nth); + for i=1:Nvol+1 + X(i,:) = rpol*theta; + for k=1:mn + alpha = double(im(k))*theta-double(in(k))*zeta; + Y(i,:) = Y(i,:) + Rbcmn(k,i)*cos(alpha) + Rbsmn(k,i)*sin(alpha); + end end - end - case 2 - for i=1:Nvol - for k=1:mn - alpha = double(im(k))*theta-double(in(k))*zeta; - X(i,:) = X(i,:) + (Rbcmn(k,i+1)*cos(alpha) + Rbsmn(k,i+1)*sin(alpha)).*cos(theta); - Y(i,:) = Y(i,:) + (Rbcmn(k,i+1)*cos(alpha) + Rbsmn(k,i+1)*sin(alpha)).*sin(theta); + case 2 + for i=1:Nvol + for k=1:mn + alpha = double(im(k))*theta-double(in(k))*zeta; + X(i,:) = X(i,:) + (Rbcmn(k,i+1)*cos(alpha) + Rbsmn(k,i+1)*sin(alpha)).*cos(theta); + Y(i,:) = Y(i,:) + (Rbcmn(k,i+1)*cos(alpha) + Rbsmn(k,i+1)*sin(alpha)).*sin(theta); + end end - end - case 3 - for i=1:Nvol - for k=1:mn - alpha = double(im(k))*theta-double(in(k))*zeta; - X(i,:) = X(i,:) + Rbcmn(k,i+1)*cos(alpha) + Rbsmn(k,i+1)*sin(alpha); - Y(i,:) = Y(i,:) + Zbsmn(k,i+1)*sin(alpha) + Zbcmn(k,i+1)*cos(alpha); + case 3 + for i=1:Nvol + for k=1:mn + alpha = double(im(k))*theta-double(in(k))*zeta; + X(i,:) = X(i,:) + Rbcmn(k,i+1)*cos(alpha) + Rbsmn(k,i+1)*sin(alpha); + Y(i,:) = Y(i,:) + Zbsmn(k,i+1)*sin(alpha) + Zbcmn(k,i+1)*cos(alpha); + end end - end - otherwise - error('Unsupported geometry') -end - - -% Plot Poincare section - -switch newfig - case 0 - hold on - case 1 - figure - hold on - case 2 - hold off -end - -for i=1:size(X,1) - scatter(X(i,:),Y(i,:),3,'filled','r') - hold on -end - -hold on -set(gca,'FontSize',12) - -if Igeometry~=1 - axis equal - xlabel('R','FontSize',12) - ylabel('Z','FontSize',12) -else - xlabel('\theta r_{pol}','FontSize',12) - ylabel('R','FontSize',12) -end + otherwise + error('Unsupported geometry') + end + + + % Plot Poincare section + for i=1:size(X,1) + scatter(X(i,:),Y(i,:),3,'filled','MarkerFaceColor',opt.InterfaceColor,'MarkerEdgeColor',opt.InterfaceColor) + hold on + end + + hold on + set(gca,'FontSize',12) + + if Igeometry~=1 + axis equal + xlabel('R','FontSize',12) + ylabel('Z','FontSize',12) + else + xlabel('\theta r_{pol}','FontSize',12) + ylabel('R','FontSize',12) + end +end \ No newline at end of file diff --git a/Utilities/matlabtools/plot_spec_modB.m b/Utilities/matlabtools/plot_spec_modB.m index 4034f956..fcfda5f0 100644 --- a/Utilities/matlabtools/plot_spec_modB.m +++ b/Utilities/matlabtools/plot_spec_modB.m @@ -4,7 +4,7 @@ % PLOT_SPEC_MODB( DATA, LVOL, SARR, TARR, ZARR, NEWFIG ) % ====================================================== % -% Produces plot of |B| in (R,Z,zarr) cross-section(s) +% Produces plot of |B| in (R,Z) cross-section(s), for any toroidal angle % % INPUT % ----- @@ -14,7 +14,7 @@ % -tarr : is the array of values for the theta-coordinate ('d' for default) % -zarr : is the array of values for the zeta-coordinate ('d' for default) % -newfig : opens(=1) or not(=0) a new figure, or overwrite existing one -% (=2) +% (=2) % % OUTPUT % ------ @@ -22,75 +22,100 @@ % % written by J.Loizu (2016) -if(sarr=='d') -sarr=linspace(-1,1,64); -end - -if(tarr=='d') -tarr=linspace(0,2*pi,64); -end - -if(zarr=='d') -zarr=0; -end - -rzbdata = cell(3); - - -% Compute |B| - -modB = get_spec_modB(data,lvol,sarr,tarr,zarr); - -% Compute function (R,Z)(s,theta,zeta) - -rzdata = get_spec_rzarr(data,lvol,sarr,tarr,zarr); - -R = rzdata{1}; -Z = rzdata{2}; - -% Plot + % Default inputs + if(sarr=='d') + sarr=linspace(-1,1,64); + end + + if(tarr=='d') + tarr=linspace(0,2*pi,64); + end + + if(zarr=='d') + zarr=0; + end + + % Check inputs + Mvol = data.output.Mvol; + if lvol<1 || lvol>Mvol + error('InputError: invalid lvol') + end + + if isempty(sarr) + error('InputError: sarr is empty') + end + if isempty(tarr) + error('InputError: tarr is empty') + end + if isempty(zarr) + error('InputError: zarr is empty') + end + + if sarr(1)<-1 || sarr(end)>1 + error('InputError: invalid sarr') + end + if any(diff(sarr)<0) + error('InputError: sarr is not monotonic') + end + + rzbdata = cell(3); + + + % Compute |B| + + modB = get_spec_modB(data,lvol,sarr,tarr,zarr); + + % Compute function (R,Z)(s,theta,zeta) + R = get_spec_R_derivatives(data,lvol,sarr,tarr,zarr,'R'); + Z = get_spec_R_derivatives(data,lvol,sarr,tarr,zarr,'Z'); + + R = R{1}; + Z = Z{1}; + + % Plot + Rtemp = R; + Ztemp = Z; + switch data.input.physics.Igeometry + case 1 + R = tarr; + Z = Rtemp; + case 2 + for it=1:length(tarr) + R(:,it,:) = Rtemp(:,it,:) .* cos(tarr(it)); + Z(:,it,:) = Rtemp(:,it,:) .* sin(tarr(it)); + end + case 3 + R = Rtemp; + Z = Ztemp; + end + + + for iz=1:length(zarr) + switch newfig + case 0 + hold on + case 1 + figure + hold on + case 2 + hold off + otherwise + error('InputError: Invalid newfig') + end -switch newfig - case 0 - hold on - case 1 - figure + pcolor(R(:,:,iz),Z(:,:,iz),modB(:,:,iz)); shading interp; colorbar hold on - case 2 - hold off -end -Rtemp = R; -Ztemp = Z; -switch data.input.physics.Igeometry - case 1 - R = tarr; - Z = Rtemp; - case 2 - for it=1:length(tarr) - R(:,it,:) = Rtemp(:,it,:) .* cos(tarr(it)); - Z(:,it,:) = Rtemp(:,it,:) .* sin(tarr(it)); - end - case 3 - R = Rtemp; - Z = Ztemp; -end - + axis equal + title('|B|'); + xlabel('R'); + ylabel('Z'); + end -for iz=1:length(zarr) - - pcolor(R(:,:,iz),Z(:,:,iz),modB(:,:,iz)); shading interp; colorbar - hold on + % Output data - axis equal - title('|B|'); - xlabel('R'); - ylabel('Z'); + rzbdata{1} = R; + rzbdata{2} = Z; + rzbdata{3} = modB; end -% Output data - -rzbdata{1} = R; -rzbdata{2} = Z; -rzbdata{3} = modB; - diff --git a/Utilities/matlabtools/plot_spec_modB_boundary.m b/Utilities/matlabtools/plot_spec_modB_boundary.m index a92feb89..43addcda 100644 --- a/Utilities/matlabtools/plot_spec_modB_boundary.m +++ b/Utilities/matlabtools/plot_spec_modB_boundary.m @@ -1,68 +1,128 @@ -function plot_spec_modB_boundary(data,vol,nt,nz) +function plot_spec_modB_boundary(data,interface,innout,nt,nz,dimension) % -% PLOT_SPEC_MODB_BOUNDARY( DATA, VOL, NT, NZ ) -% ============================================ +% PLOT_SPEC_MODB_BOUNDARY( DATA, INTERFACE, INNOUT, NT, NZ, DIMENSION ) +% ===================================================================== % % Produces plot of |B| on the full boundary surface in toroidal geometry. % % INPUT % ----- % -data : data obtained via read_spec(filename) -% -vol : Volume on which modB should be plotted +% -interface : Interface on which modB should be plotted +% -innout: (0) - inner side of interface +% (1) - outer side of interface % -nt : poloidal resolution for the plotting (e.g. nt=64) % -nz : toroidal resolution for the plotting (e.g. nz=64) +% -dimension: (2) - plot a colorplot on a theta-phi grid +% (3) - plot a colorplot on a 3d surface % % written by J.Loizu (2016) % modified by J.Loizu (01.2017) -sarr = 1; + Mvol = data.output.Mvol; + if interface<1 || interface>Mvol + error('InputError: invalid interface') + end + + switch innout + case 0 + vol = interface; + sarr = 1; + case 1 + if interface==Mvol + error('InputError: Cannot plot on the outer side of last interface!') + end + vol = interface+1; + sarr = -1; + otherwise + error('InputError: interface should be 0 or 1') + end + + if nt<1 + error('InputError: invalid nt') + end + if nz<1 + error('InputError: invalid nz') + end + if ~any(dimension==[2,3]) + error('InputError: invalid dimension') + end + + tarr = linspace(0,2*pi,nt); + zarr = linspace(0,2*pi,nz); + + if(vol>Mvol || vol<1) + error('vol not valid') + end -tarr = linspace(0,2*pi,nt); +if(vol>Mvol) + % Compute |B| +end -zarr = linspace(0,2*pi,nz); + modB = get_spec_modB(data,vol,sarr,tarr,zarr); + switch dimension + case 2 + figure -Mvol = data.output.Mvol; -if(vol>Mvol) - error('vol not valid') -end + [t,z] = meshgrid(tarr, zarr); + modB = reshape(modB, nt, nz); -% Compute |B| + pcolor( z, t, modB' ) + shading interp -modB = get_spec_modB(data,vol,sarr,tarr,zarr); + colorbar + xlabel('$\phi$', 'Interpreter', 'latex') + ylabel('$\theta$', 'Interpreter', 'latex') + ax = gca; + ax.YTick = [pi/4,pi/2,3*pi/4,pi,5*pi/4,3*pi/2,7*pi/4]; + ax.YTickLabel = {'$\frac{\pi}{4}$','$\frac{\pi}{2}$','$\frac{3\pi}{4}$','$\pi$','$\frac{5\pi}{4}$', '$\frac{3\pi}{2}$','$\frac{7\pi}{4}$'}; + ax.XTick = [pi/4,pi/2,3*pi/4,pi,5*pi/4,3*pi/2,7*pi/4]; + ax.XTickLabel = {'$\frac{\pi}{4}$','$\frac{\pi}{2}$','$\frac{3\pi}{4}$','$\pi$','$\frac{5\pi}{4}$', '$\frac{3\pi}{2}$','$\frac{7\pi}{4}$'}; + ax.TickLabelInterpreter = 'latex'; -% Compute function (R,Z)(s,theta,zeta) + set(gca,'FontSize',18) + set(gcf,'Position',[200 200 900 700]) -rzdata = get_spec_rzarr(data,vol,sarr,tarr,zarr); -R = squeeze(rzdata{1}); -Z = squeeze(rzdata{2}); + case 3 + % Compute function (R,Z)(s,theta,zeta) + R = get_spec_R_derivatives(data,vol,sarr,tarr,zarr,'R'); + Z = get_spec_R_derivatives(data,vol,sarr,tarr,zarr,'Z'); + R = squeeze(R{1}); + Z = squeeze(Z{1}); -% Construct cartesian corrdinates -X = zeros(nt,nz); + % Construct cartesian corrdinates -Y = zeros(nt,nz); - -for it=1:nt - for iz=1:nz - X(it,iz) = R(it,iz)*cos(zarr(iz)); - Y(it,iz) = R(it,iz)*sin(zarr(iz)); - end -end - - -% Plot + X = zeros(nt,nz); + + Y = zeros(nt,nz); -figure + for it=1:nt + for iz=1:nz + X(it,iz) = R(it,iz)*cos(zarr(iz)); + Y(it,iz) = R(it,iz)*sin(zarr(iz)); + end + end -h=surf(X,Y,Z,squeeze(modB(1,:,:))); -axis equal -shading interp -colorbar -title('| B |') + % Plot + + figure + + h=surf(X,Y,Z,squeeze(modB(1,:,:))); + + axis equal + shading interp + colorbar + title('| B |') + + otherwise + error('Invalid dimension') + end +end diff --git a/Utilities/matlabtools/plot_spec_poincare.m b/Utilities/matlabtools/plot_spec_poincare.m index 2bbda005..7cb9842c 100644 --- a/Utilities/matlabtools/plot_spec_poincare.m +++ b/Utilities/matlabtools/plot_spec_poincare.m @@ -1,35 +1,72 @@ -function plot_spec_poincare(data,nz0,nfp,arr,newfig) +function phi = plot_spec_poincare(data,nz0,arr,kam,newfig,varargin) % -% PLOT_SPEC_POINCARE( DATA, NZ0, NFP, ARR, NEWFIG ) -% ================================================= +% PLOT_SPEC_POINCARE( DATA, NZ0, NFP, ARR, NEWFIG, VARARGIN ) +% =========================================================== % -% Produces Poincare plots of the field lines on different sections (within one field period) +% Produces Poincare plots of the field lines on different sections (within +% one field period) % % INPUT % ----- % -data : must be produced by calling read_spec(fname) % -nz0 : shows the nz0 toroidal plane or equidistant planes (nz0=-1) % -nfp : number of field periods -% -arr : step to skip field-line trajectories when ploting (arr=1 means all trajectories are ploted) -% : can be an array of which field line should be plotted, if size(arra)>1 -% -newfig : opens(=1) or not(=0) a new figure, or overwrites (=2) last plot +% -arr : step to skip field-line trajectories when ploting (arr=1 +% means all trajectories are ploted) +% : can be an array of which field line should be plotted, if +% size(arra)>1 +% -kam : Plots (=1) or not (=0) the KAM surfaces. +% -newfig : opens(=1) or not(=0) a new figure, or overwrites (=2) last +% plot +% -varargin : Optional arguments. Any of the following pairs are +% supported: +% - 'BoundaryColor', value: color of the plasma boundary or +% wall. default: red +% - 'step', n: plot one every n toroidal transit. This allows +% lighter plts when exporting to eps. By +% default, all toroidal transit are plotted +% (n=1) % % written by J.Loizu (2015) % modified by A.Baillod (2019) % modified by J.Loizu (2020) -try - rpol = data.input.physics.rpol; % get size of slab -catch - rpol = 1; +ll = length(varargin); +if mod(ll,2)~=0 + error('InputError: invalid number of optional arguments') end -nptraj = size(data.poincare.R,1); % # of poincare trajectories (field lines) +opt.BoundaryColor = 'r'; +opt.step = 1; +for ii=1:ll/2 + opt.(varargin{2*ii-1}) = varargin{2*ii}; +end +stp = opt.step; + +% Check that Poincare data is available +if data.input.diagnostics.nPpts==0 || all(data.input.diagnostics.nPtrj==0) + error('No Poincare data available') +end +% Read some data... +nfp = data.input.physics.Nfp; + +if data.input.physics.Igeometry==1 + try + rpol = data.input.physics.rpol; % get size of slab + catch + rpol = 1; + end +end + +% Read size +nptraj = size(data.poincare.R,1); % # of poincare trajectories (field lines) nz = size(data.poincare.R,2); % # of toroidal planes +if nz0<1 || nz0>nz + error('InputError: invalid toroidal plane. Should be 0nptraj); if ~isempty(ind) @@ -40,62 +77,26 @@ function plot_spec_poincare(data,nz0,nfp,arr,newfig) arr = 1:arr:nptraj; end - - -disp(' '); -disp('Number of toroidal planes available: (one field period)'); -nz -disp(' '); - - -rmax = max(max(max(data.poincare.R))); -rmin = min(min(min(data.poincare.R))); -zmax = max(max(max(data.poincare.Z))); -zmin = min(min(min(data.poincare.Z))); - -switch data.input.physics.Igeometry - case 1 - xmin = 0; - xmax = 2*pi*rpol; - ymin = -0.1; - ymax = data.output.Rbc(1,end)+0.1; - case 2 - xmin = -1.1*rmax; - xmax = 1.1*rmax; - ymin = -1.1*rmax; - ymax = 1.1*rmax; - case 3 - xmin = 0.9*rmin; - xmax = 1.1*rmax; - ymin = 1.1*zmin; - ymax = 1.1*zmax; -end - - -nth = 5096; %ploting options for the boundary -bcol = 'r'; +%ploting options for the boundary +nth = 5096; +bcol = opt.BoundaryColor; bthick = 3; +lthick = 1; if(data.input.physics.Lfreebound==1) -bcol = 'k'; -bthick = 1; -end - - - -if(flag2col=='T') - pcol = ['k' 'b']; -else - pcol = ['k' 'k']; + bcol = opt.BoundaryColor; + bthick = 1; end switch newfig case 0 hold on case 1 - figure + figure('Color','w','Position',[200 200 900 700]) hold on case 2 hold off + otherwise + error('InputError: invalid newfig') end switch nz0 @@ -116,21 +117,21 @@ function plot_spec_poincare(data,nz0,nfp,arr,newfig) R = squeeze(data.poincare.R(:,j,:)); T = rpol*mod(squeeze(data.poincare.t(:,j,:)),2*pi); for i=arr %for each field line trajectory - scatter(T(i,:),R(i,:),10,'.k') + scatter(T(i,:),R(i,:),lthick,'.k') hold on end case 2 R = squeeze(data.poincare.R(:,j,:)); T = squeeze(data.poincare.t(:,j,:)); for i=arr %for each field line trajectory - scatter(R(i,:).*cos(T(i,:)),R(i,:).*sin(T(i,:)),10,'.k') + scatter(R(i,:).*cos(T(i,:)),R(i,:).*sin(T(i,:)),lthick,'.k') hold on; end case 3 R = squeeze(data.poincare.R(:,j,:)); Z = squeeze(data.poincare.Z(:,j,:)); for i=arr %for each field line trajectory - scatter(R(i,:),Z(i,:),10,'.k') + scatter(R(i,:),Z(i,:),lthick,'.k') hold on; end otherwise @@ -140,6 +141,7 @@ function plot_spec_poincare(data,nz0,nfp,arr,newfig) dth = 2*pi/nth; theta = dth:dth:2*pi; zeta = (j-1)*(2*pi/nz)/nfp; + phi = NaN; switch data.input.physics.Igeometry case 1 @@ -187,31 +189,28 @@ function plot_spec_poincare(data,nz0,nfp,arr,newfig) ylabel('R','FontSize',12) end - xlim([xmin xmax]) - ylim([ymin ymax]) - end otherwise %if nz0>0 switch data.input.physics.Igeometry case 1 - R = squeeze(data.poincare.R(:,nz0,:)); - T = rpol*mod(squeeze(data.poincare.t(:,nz0,:)),2*pi); + R = squeeze(data.poincare.R(:,nz0,1:stp:end)); + T = rpol*mod(squeeze(data.poincare.t(:,nz0,1:stp:end)),2*pi); for i=arr %for each field line trajectory scatter(T(i,:),R(i,:),10,'.k') hold on end case 2 - R = squeeze(data.poincare.R(:,nz0,:)); - T = squeeze(data.poincare.t(:,nz0,:)); + R = squeeze(data.poincare.R(:,nz0,1:stp:end)); + T = squeeze(data.poincare.t(:,nz0,1:stp:end)); for i=arr %for each field line trajectory scatter(R(i,:).*cos(T(i,:)),R(i,:).*sin(T(i,:)),10,'.k') hold on; end case 3 - R = squeeze(data.poincare.R(:,nz0,:)); - Z = squeeze(data.poincare.Z(:,nz0,:)); + R = squeeze(data.poincare.R(:,nz0,1:stp:end)); + Z = squeeze(data.poincare.Z(:,nz0,1:stp:end)); for i=arr %for each field line trajectory scatter(R(i,:),Z(i,:),10,'.k') hold on; @@ -224,6 +223,7 @@ function plot_spec_poincare(data,nz0,nfp,arr,newfig) dth = 2*pi/nth; theta = dth:dth:2*pi; zeta = (nz0-1.0)*(2.0*pi/nz)/double(nfp); + phi = zeta; switch data.input.physics.Igeometry @@ -257,7 +257,7 @@ function plot_spec_poincare(data,nz0,nfp,arr,newfig) end if data.input.physics.Igeometry ~= 1 - scatter(Rb,Zb,bthick,'*',bcol) + scatter(Rb,Zb,bthick,'*','MarkerFaceColor',bcol,'MarkerEdgeColor',bcol) hold on set(gca,'FontSize',12) axis equal @@ -272,11 +272,14 @@ function plot_spec_poincare(data,nz0,nfp,arr,newfig) ylabel('R','FontSize',12) end - xlim([xmin xmax]) - ylim([ymin ymax]) + set(gca,'FontSize',18) end +if kam + phi = 2*pi*(nz0-1) / (double(nfp)*nz); + plot_spec_kam(data, phi, 0 ) +end disp(' '); disp('--- end of program ---'); diff --git a/Utilities/matlabtools/plot_spec_poincare_3d.m b/Utilities/matlabtools/plot_spec_poincare_3d.m new file mode 100644 index 00000000..90f58483 --- /dev/null +++ b/Utilities/matlabtools/plot_spec_poincare_3d.m @@ -0,0 +1,174 @@ +function plot_spec_poincare_3d( data, varargin ) +% +% PLOT_SPEC_POINCARE_3D( DATA ) +% ----------------------------- +% +% Plot parts of the 3d stellarator geometry, the Poincare plot and traces a +% field line +% +% INPUTS +% ------ +% * data: Obtained with read_spec(filename) +% * varargin: optional inputs. Can be any pairs of +% 'nt': Number of poloidal points. Default is 64 +% 'nz': Number of toroidal points. Default is 64 +% 'phiend': Plots 3d shape from phi=0 to phiend. Default is 2pi/Nfp +% 'tstart': Start field line tracing at this value of theta. Can be +% an array. Default is 0. + + + % Load the colors and some data + col = EPFL_colors; + Nvol = double(data.input.physics.Nvol); + Nfp = double(data.input.physics.Nfp); + + % Set up options + opt.nt = 64; + opt.nz = 64; + opt.phiend = 2*pi / max(Nfp,2); + opt.tstart = 0; + + l = length(varargin); + if mod(l,2)~=0 + error('Invalid number of arguments') + end + + for ii=1:l/2 + opt.(varargin{2*ii-1}) = varargin{2*ii}; + end + + opt.tstart = reshape(opt.tstart, length(opt.tstart), 1); + + % Define coordinate arrays in real space + sarr = 1; % We plot on the outermost surface, i.e. the plasma boundary + tarr = linspace(0,2*pi ,opt.nt); + zarr = linspace(0,opt.phiend ,opt.nz); + + R = get_spec_R_derivatives(data,Nvol,sarr,tarr,zarr,'R'); + Z = get_spec_R_derivatives(data,Nvol,sarr,tarr,zarr,'Z'); + + R = squeeze(R{1}); + Z = squeeze(Z{1}); + + + % Construct cartesian corrdinates + + X = zeros(opt.nt,opt.nz); + Y = zeros(opt.nt,opt.nz); + + for it=1:opt.nt + for iz=1:opt.nz + X(it,iz) = R(it,iz)*cos(zarr(iz)); + Y(it,iz) = R(it,iz)*sin(zarr(iz)); + end + end + + + % Plot + + figure('Position', [200 200 900 700], 'Color', 'w') + + s = size(X); + c = zeros(s(1), s(2), 3); + c(:,:,1) = 1; + mesh(X,Y,Z,c); + hold on + + axis equal + shading interp + + xlabel('X') + ylabel('Y') + zlabel('Z') + set(gca, 'FontSize', 18 ) + + % Add white surface on plane y=0 + M = makehgtform('xrotate',pi/2); + t = hgtransform('Matrix', M); + + pshape = polyshape(X(:,1), Z(:,1)); + plot(pshape, 'Parent', t, 'FaceColor', 'w', 'FaceAlpha', 0.9 ) + + + + + % Add Poincare plot + X = squeeze(data.poincare.R(:,1,:)); + + s = size(X); + + Y = zeros(size(X)); + Z = squeeze(data.poincare.Z(:,1,:)); + for i=1:s(1) %for each field line trajectory + scatter3(X(i,:),Y(i,:),Z(i,:),10,'.k') + hold on; + end + + % Add KAM surfaces + mn = data.output.mn; + im = data.output.im; + Rbcmn = data.output.Rbc; + Rbsmn = data.output.Rbs; + Zbcmn = data.output.Zbc; + Zbsmn = data.output.Zbs; + + nt = 1024; + tarr = linspace(0, 2*pi, nt); + + X = zeros(Nvol,nt); + Y = zeros(Nvol,nt); + for i=1:Nvol + for k=1:mn + alpha = double(im(k))*tarr; %phi = 0 + X(i,:) = X(i,:) + Rbcmn(k,i+1)*cos(alpha) + Rbsmn(k,i+1)*sin(alpha); + Y(i,:) = Y(i,:) + Zbsmn(k,i+1)*sin(alpha) + Zbcmn(k,i+1)*cos(alpha); + end + end + + for i=1:size(X,1) + scatter3(X(i,:),zeros(nt,1),Y(i,:),3,'filled','MarkerFaceColor','r','MarkerEdgeColor','r') + hold on + end + + % Add a field line + tarr = opt.tstart; + + + if ~isempty(tarr) + phi = 0; + + nstep = 1024; + dstep = opt.phiend/1024; + + for istep=1:nstep + phi(istep+1) = phi(istep) + dstep; + + B = get_spec_magfield( data, Nvol, 1, tarr(:,istep), phi(istep) ); + + Bt = reshape(B{2}, length(B{2}), 1); + Bz = reshape(B{3}, length(B{2}), 1); + + tarr(:,istep+1) = tarr(:,istep) + Bt./Bz * dstep; + + end + + nline = length(opt.tstart); + for jj=1:nline + X = []; + Y = []; + Z = []; + for ii = 1:nstep + Rd = get_spec_R_derivatives(data,Nvol,sarr,tarr(jj,ii),phi(ii),'R'); + Zd = get_spec_R_derivatives(data,Nvol,sarr,tarr(jj,ii),phi(ii),'Z'); + + X(ii) = squeeze(Rd{1}) * cos(phi(ii)); + Y(ii) = squeeze(Rd{1}) * sin(phi(ii)); + Z(ii) = squeeze(Zd{1}); + end + + scatter3( X, Y, Z, 10, 'MarkerFaceColor', col.Leman, 'MarkerEdgeColor', col.Leman) + end + end + + +end \ No newline at end of file diff --git a/Utilities/matlabtools/plot_spec_polflux.m b/Utilities/matlabtools/plot_spec_polflux.m index 9b4f3824..26280b48 100644 --- a/Utilities/matlabtools/plot_spec_polflux.m +++ b/Utilities/matlabtools/plot_spec_polflux.m @@ -1,4 +1,4 @@ -function plot_spec_polflux(data, zeta, cumulative, newfig) +function plot_spec_polflux(data, theta, cumulative, newfig) % % % PLOT_SPEC_POLFLUX( FILENAME, ZETA, CUMULATIVE, NEWFIG ) @@ -10,7 +10,7 @@ function plot_spec_polflux(data, zeta, cumulative, newfig) % INPUTS % ------ % data: data obtained from read_spec(filename); -% zeta: Toroidal angle +% theta: Poloidal angle % cumulative: True to get cumulative plot (\psi_a = \int_0^a B_\phi dS) % or False to get a non-cumulative plot (\psi_a = % \int_{a-1}^a B_\phi dS) @@ -24,44 +24,45 @@ function plot_spec_polflux(data, zeta, cumulative, newfig) % % -Nvol = data.input.physics.Nvol; + Nvol = data.input.physics.Nvol; -polflux = zeros(1,Nvol); + polflux = zeros(1,Nvol); -% Start at one only if slab geometry (otherwise it is zero by definition) -if data.input.physics.Igeometry==1 - polflux(1) = get_spec_polflux(data,1,zeta,-1,1,64,64); -end + % Start at one only if slab geometry (otherwise it is zero by definition) + sarr = linspace(-1, 1, 64); + if data.input.physics.Igeometry==1 + polflux(1) = get_spec_polflux(data,1,theta,sarr,64); + end + + for lvol=2:Nvol + tmp = get_spec_polflux(data,lvol,theta,sarr,64); + + if cumulative + polflux(lvol) = polflux(lvol-1) + tmp; + else + polflux(lvol)=tmp; + end -for lvol=2:Nvol - tmp = get_spec_polflux(data,lvol,zeta,-1,1,64,64); - - if cumulative - polflux(lvol) = polflux(lvol-1) + tmp; - else - polflux(lvol)=tmp; end - -end -switch newfig - case 0 - hold on; - case 1 - figure - hold on; - case 2 - hold off; - otherwise - error('Unsupported newfig value') -end + switch newfig + case 0 + hold on; + case 1 + figure + hold on; + case 2 + hold off; + otherwise + error('InputError: invalid newfig') + end -bar(polflux) -xlabel('Volume label') -ylabel('Poloidal flux') -set(gca, 'FontSize', 14) -xticks(1:1:Nvol) -grid on; + bar(polflux) + xlabel('Volume label') + ylabel('Poloidal flux') + set(gca, 'FontSize', 14) + xticks(1:1:Nvol) + grid on; end diff --git a/Utilities/matlabtools/plot_spec_pressure.m b/Utilities/matlabtools/plot_spec_pressure.m index ce4f235f..0e3f9959 100644 --- a/Utilities/matlabtools/plot_spec_pressure.m +++ b/Utilities/matlabtools/plot_spec_pressure.m @@ -1,21 +1,47 @@ -function plot_spec_pressure(data, newfig) +function plot_spec_pressure(data, norm, newfig, varargin) % -% PLOT_SPEC_PRESSURE( DATA, NEWFIG ) -% ================================== +% PLOT_SPEC_PRESSURE( DATA, NORM, NEWFIG, VARARGIN ) +% ================================================== % % Plots stepped-pressure profile versus normalized toroidal flux used in SPEC % % INPUT % ----- % -data : data obtained from read_spec(fname) +% -norm : (0) plot p, (1) plot p / p0 % -newfig : open a new figue (=1), plots on an existing one (=0) or overwrite last plot (=2) % % written by J.Loizu (2018) % modified by A. Baillod (2019) +if ~any(norm==[0,1]) + error('InputError: invalid norm') +end + +l = length(varargin); +if mod(l,2)~=0 + error('InputError: invalid number of argument') +end + +opt.Color='b'; +opt.LineWidth=2.0; +for ii=1:l/2 + value = varargin{2*ii}; + field = varargin{2*ii-1}; + + opt.(field)=value; +end + + pvol = data.input.physics.pressure * data.input.physics.pscale; + +if norm + pvol = pvol / pvol(1); +end + + pmax = max(pvol); pmin = min(pvol); @@ -35,28 +61,30 @@ function plot_spec_pressure(data, newfig) hold off end +% First volume p0(1:end) = pvol(1); tmin = 0; tmax = tfl(1); tarr = linspace(tmin,tmax,10); -plot(tarr,p0,'b') +plot(tarr,p0,'Color',opt.Color,'LineWidth',opt.LineWidth) hold on x = [tfl(1),tfl(1)]; if Nvol>1 y = [pvol(2) pvol(1)]; - plot(x,y,'b') + plot(x,y,'Color',opt.Color,'LineWidth',opt.LineWidth) end +% Next volumes for i=2:Nvol-1 p0(1:end) = pvol(i); tmin = tfl(i-1); tmax = tfl(i); tarr = linspace(tmin,tmax,10); - plot(tarr,p0,'b') + plot(tarr,p0,'Color',opt.Color,'LineWidth',opt.LineWidth) x = [tfl(i),tfl(i)]; y = [pvol(i+1) pvol(i)]; - plot(x,y,'b') + plot(x,y,'Color',opt.Color,'LineWidth',opt.LineWidth) end @@ -65,18 +93,25 @@ function plot_spec_pressure(data, newfig) tmin = tfl(Nvol-1); tmax = tfl(Nvol); tarr = linspace(tmin,tmax,10); - plot(tarr,p0,'b') + plot(tarr,p0,'Color',opt.Color,'LineWidth',opt.LineWidth) x = [tfl(Nvol),tfl(Nvol)]; y = [0 pvol(Nvol)]; - plot(x,y,'b') + plot(x,y,'Color',opt.Color,'LineWidth',opt.LineWidth) end -ylabel('p') -xlabel('\Psi / \Psi_{edge}') +if( norm ) + ylabel('$p / p_0$', 'Interpreter', 'latex') +else + ylabel('$p$', 'Interpreter', 'latex') +end +xlabel('$\Psi / \Psi_{edge}$', 'Interpreter', 'latex') if (pmin~=0 || pmax~=0) - ylim([0.9*pmin, 1.1*pmax]); + ylim([0, 1.1*pmax]); end +set(gcf, 'Color', 'w') +set(gcf,'Position',[200 200 900 700]) +set(gca,'FontSize',18) diff --git a/Utilities/matlabtools/plot_spec_surface_current.m b/Utilities/matlabtools/plot_spec_surface_current.m new file mode 100644 index 00000000..f364eb68 --- /dev/null +++ b/Utilities/matlabtools/plot_spec_surface_current.m @@ -0,0 +1,56 @@ +function plot_spec_surface_current(data, nt, newfig) + +% +% PLOT_SPEC_SURFACE_CURRENT( DATA, NS, NT, NEWFIG ) +% =================================================== +% +% Plot pressure-driven currents located at each volume interface +% +% INPUT +% ----- +% -data : data obtained via read_spec(filename) +% -nt : number of poloidal interpolation points +% -newfig : plots on an existing figure (=0), a new figure (=1) or +% overwrites last figure (=2) +% +% written by A.Baillod (2019) +% + + % Test input + if nt<1 + error('InputError: Invalid nt') + end + + + switch newfig + case 0 + hold on + case 1 + figure + hold on + case 2 + hold off + otherwise + error('InputError: Invalid newfig') + end + + % Evaluate toroidal current + Itor = get_spec_torcurr_kam_net(data, nt); + Mvol = data.output.Mvol; + + + %plot(tflux(1:end-1), IPDt, '*') + bar(Itor, 'BarWidth', 0.3); + grid on + %xl = xlabel('$\psi_t / \psi_{edge}$'); + xl = xlabel('Surface label'); + yl = ylabel('$\mu_0 I_\mathcal{S}$[A]'); + xlim([0, Mvol]) + + set(xl, 'Interpreter', 'latex'); + set(yl, 'Interpreter', 'latex'); + + set(gca, 'FontSize', 14) + + +end diff --git a/Utilities/matlabtools/plot_spec_torflux.m b/Utilities/matlabtools/plot_spec_torflux.m index bf15f342..c757f2a3 100644 --- a/Utilities/matlabtools/plot_spec_torflux.m +++ b/Utilities/matlabtools/plot_spec_torflux.m @@ -11,8 +11,8 @@ function plot_spec_torflux(data, zeta, cumulative, newfig) % ------ % data: data obtained from read_spec(filename) % zeta: Toroidal angle -% cumulative: True to get cumulative plot (\psi_a = \int_0^a B_\phi dS) -% or False to get a non-cumulative plot (\psi_a = +% cumulative: true to get cumulative plot (\psi_a = \int_0^a B_\phi dS) +% or false to get a non-cumulative plot (\psi_a = % \int_{a-1}^a B_\phi dS) % newfig: 0: plots on an existing figure without erasing previous % plot @@ -22,44 +22,46 @@ function plot_spec_torflux(data, zeta, cumulative, newfig) % % Written by A. Baillod (2019) % + Mvol = data.output.Mvol; + torflux = zeros(1,Mvol); + for lvol=1:Mvol + start=-1; + if(lvol==1) + start=-0.999; + end + tmp = get_spec_torflux(data,lvol,zeta,start,1,64,64); Nvol = data.input.physics.Nvol; - -torflux = zeros(1,Nvol); - -for lvol=1:Nvol - tmp = get_spec_torflux(data,lvol,zeta,-1,1,64,64); - - if cumulative - if lvol==1 - torflux(lvol)=tmp; + if cumulative + if lvol==1 + torflux(lvol)=tmp; + else + torflux(lvol) = torflux(lvol-1) + tmp; + end else - torflux(lvol) = torflux(lvol-1) + tmp; + torflux(lvol)=tmp; end - else - torflux(lvol)=tmp; + end - -end -switch newfig - case 0 - hold on; - case 1 - figure - hold on; - case 2 - hold off; - otherwise - error('Unsupported newfig value') -end + switch newfig + case 0 + hold on; + case 1 + figure + hold on; + case 2 + hold off; + otherwise + error('InputError: Invalid newfig') + end -bar(torflux) -xlabel('Volume label') -ylabel('Toroidal flux') -set(gca, 'FontSize', 14) -xticks(1:1:Nvol) -grid on; + bar(torflux) + xlabel('Volume label') + ylabel('Toroidal flux') + set(gca, 'FontSize', 14) + xticks(1:1:Nvol) + grid on; end diff --git a/Utilities/matlabtools/plot_spec_wall.m b/Utilities/matlabtools/plot_spec_wall.m index 6786af3b..7660cb16 100644 --- a/Utilities/matlabtools/plot_spec_wall.m +++ b/Utilities/matlabtools/plot_spec_wall.m @@ -4,7 +4,7 @@ function plot_spec_wall(data,zetaov2pi,newfig) % PLOT_SPEC_WALL( DATA, ZETAOV2PI, NEWFIG ) % ========================================= % -% Produces a "Poincare plot" of the computational boundary surface in toroidal geometry. +% Plots the computational boundary surface in toroidal geometry. % % INPUT % ----- @@ -14,53 +14,70 @@ function plot_spec_wall(data,zetaov2pi,newfig) % % written by J.Loizu (2018) % modified by J.Loizu (2020) +% + if data.input.physics.Igeometry~=3 + error('InputError: only works in toroidal geometry') + end -mn = data.output.mn; -im = data.output.im; -in = data.output.in; -Rbcmn = data.output.Rbc; -Rbsmn = data.output.Rbs; -Zbcmn = data.output.Zbc; -Zbsmn = data.output.Zbs; + if data.input.physics.Lfreebound==0 + warning(['This will plot the plasma boundary, since no walls are' ... + 'defined in fixed-boundary equilibria']) + end -Rwcmn = Rbcmn(:,end); -Rwsmn = Rbsmn(:,end); -Zwcmn = Zbcmn(:,end); -Zwsmn = Zbsmn(:,end); -% Compute (x,y) coordinates of the boundary surface + mn = data.output.mn; + im = data.output.im; + in = data.output.in; + Rbcmn = data.output.Rbc; + Rbsmn = data.output.Rbs; + Zbcmn = data.output.Zbc; + Zbsmn = data.output.Zbs; -zeta = zetaov2pi*(2*pi); + Rwcmn = Rbcmn(:,end); + Rwsmn = Rbsmn(:,end); + Zwcmn = Zbcmn(:,end); + Zwsmn = Zbsmn(:,end); -nth = 2048; -dth = 2*pi/nth; -theta = dth:dth:2*pi; + % Compute (x,y) coordinates of the boundary surface -X = zeros(1,nth); -Y = zeros(1,nth); + zeta = zetaov2pi*(2*pi); -for k=1:mn - alpha = double(im(k))*theta-double(in(k))*zeta; - X = X + Rwcmn(k)*cos(alpha) + Rwsmn(k)*sin(alpha); - Y = Y + Zwsmn(k)*sin(alpha) + Zwcmn(k)*cos(alpha); -end + nth = 2048; + dth = 2*pi/nth; + theta = dth:dth:2*pi; + X = zeros(1,nth); + Y = zeros(1,nth); + for k=1:mn + alpha = double(im(k))*theta-double(in(k))*zeta; + X = X + Rwcmn(k)*cos(alpha) + Rwsmn(k)*sin(alpha); + Y = Y + Zwsmn(k)*sin(alpha) + Zwcmn(k)*cos(alpha); + end -% Plot Poincare section -if(newfig==1) -figure -end -hold on -scatter(X,Y,3,'filled', 'b') + % Plot Poincare section -axis equal -hold on -set(gca,'FontSize',12) -xlabel('R','FontSize',12) -ylabel('Z','FontSize',12) -%xlim([-1.1*rmax 1.1*rmax]) -%ylim([-1.1*zmax 1.1*zmax]) + switch newfig + case 0 + hold on + case 1 + figure('Color','w','Position',[200 200 900 700]) + case 2 + hold off + otherwise + error('InputError: invalid newfig') + end + + scatter(X,Y,3,'filled', 'b') + + axis equal + hold on + set(gca,'FontSize',12) + xlabel('R','FontSize',12) + ylabel('Z','FontSize',12) + %xlim([-1.1*rmax 1.1*rmax]) + %ylim([-1.1*zmax 1.1*zmax]) +end diff --git a/Utilities/matlabtools/produce_spec_movie.m b/Utilities/matlabtools/produce_spec_movie.m index 428edfd5..4433b424 100644 --- a/Utilities/matlabtools/produce_spec_movie.m +++ b/Utilities/matlabtools/produce_spec_movie.m @@ -25,6 +25,7 @@ function produce_spec_movie(inputroot,seqstart,seqstep,seqend,framerate,nfp,nz0, % written by J.Loizu (2017) % modified by J.Loizu (2019) +error('DEPRECATED: this needs to be reviewed') % writerObj = VideoWriter('spec_movie.avi'); diff --git a/Utilities/matlabtools/read_boozer.m b/Utilities/matlabtools/read_boozer.m new file mode 100644 index 00000000..7432cff3 --- /dev/null +++ b/Utilities/matlabtools/read_boozer.m @@ -0,0 +1,36 @@ +%% read_boozer( FILENAME, ROOT) +% ============================= +% +% Reads hdf5 output from Boozer_xForms +% and produces data struct +% +% INPUT +% ----- +% -filename : name of Boz output +% -root : root directory +% +% ------------------------------------% +% Written by S.Guinchard (05/22) % +% from read_spec routine % +% ------------------------------------% + +function g_data = read_boozer(filename, root ) + g_data_info = h5info(filename, root); + ngroups = length(g_data_info.Groups); + nvars = length(g_data_info.Datasets); + % Get datasets in root node + for i = 1: nvars + g_data.([g_data_info.Datasets(i).Name]) = h5read(filename,[root '/' g_data_info.Datasets(i).Name]); + natts = length(g_data_info.Datasets(i).Attributes); + for j=1:natts + g_data.([g_data_info.Datasets(i).Attributes(j).Name]) = g_data_info.Datasets(i).Attributes(j).Value{1}; + end + end + % get groups in root node + if ngroups > 0 + for i = 1 : ngroups + g_path = strsplit(g_data_info.Groups(i).Name, '/'); + g_data.([g_path{end}]) = read_boozer(filename, g_data_info.Groups(i).Name); + end + end +end diff --git a/Utilities/matlabtools/read_spec.m b/Utilities/matlabtools/read_spec.m index e155d329..84192599 100644 --- a/Utilities/matlabtools/read_spec.m +++ b/Utilities/matlabtools/read_spec.m @@ -25,7 +25,6 @@ disp(['ERROR: Opening HDF5 File: ' filename]); disp([' -identifier: ' h5info_error.identifier]); disp([' -message: ' h5info_error.message]); - disp(' For information type: help read_hdf5'); return end @@ -150,5 +149,6 @@ data.grid.Bp = cBp; data.grid.BZ = cBZ; + end diff --git a/Utilities/matlabtools/scan_shear_auto_optim.m b/Utilities/matlabtools/scan_shear_auto_optim.m new file mode 100644 index 00000000..65e03d9b --- /dev/null +++ b/Utilities/matlabtools/scan_shear_auto_optim.m @@ -0,0 +1,253 @@ +%% SCRIPT SCANNING R10 and R11 FROM SPEC AND EXTRACTING MAGNETIC SHEAR %% +%-----------------------------------------% +% Created by Salomon Guinchard (04/26/22) % +% Last modified (10/10/22) % +%-----------------------------------------% + +%% Paths to get_spec_mat_iota_torsion and other SPEC analysis routines (change path according to output folder) +addpath(genpath('/path_to_OutputSPEC')) +addpath(genpath('/path_to_/OutputBOZ')) +fs=18; lw=1.5; % Fontsize, linewidth + + +%% PARAMETERS %% +nscan = 20; +f = strings(nscan,nscan); +nn = length(f(:,1)); +parfor i=1:nn + for j=1:nn + f(i,j) = ['File', num2str(i), '_', num2str(j) '.sp.h5']; + end +end +filenames = reshape(f,1,nn^2); +ll = length(filenames); +d0 = read_spec(char(filenames(1))); + +l = d0.transform.fiota(:,2); +avg_shear = zeros(1,ll) ; +shift = 5; + +disp 'Done initialising...' +%% DISCRETISATION OF SPACE %% +scan__11 = linspace(-0.7,0.7,nscan); % values between which the mode 11 will be scanned +scan__10 = linspace(-3,3,nscan); % same for 10 mode (01 - see SPEC input format) + +%% RUN %% +tic % set timer on +parfor ii=1:ll + try + d = read_spec(char(filenames(ii))); + phi = 0; + + Nfp = double(d.input.physics.Nfp); % Number of field periods + Ntor = double(d.input.physics.Ntor); % Number of toroidal planes + Nppts = d.input.diagnostics.nPpts; % # points Poincare plots + + R0n = double(d.output.Rbc(1:Ntor+1,1)); + Z0n = double(d.output.Zbs(1:Ntor+1,1)); + + % Define coordinate axis position + Raxis = double(0); + Zaxis = double(0); + for i=0:Ntor + Raxis = Raxis + R0n(i+1) * cos(i * phi); + Zaxis = Zaxis + Z0n(i+1) * sin(i * phi); + end + + Pos_Axis = [Raxis Zaxis]; + + tt = length(d.poincare.R(:,1,1)); + jj=1; + X = reshape(d.poincare.R(jj,1,:),[1 ,Nppts]); + Y = reshape(d.poincare.Z(jj,1,:),[1 ,Nppts]); + Xbar = mean(X); + Ybar = mean(Y); + theta = atan2(Y-Ybar , X-Xbar); + theta = mod(theta, 2*pi); + + [theta, ind] = sort(theta); + + X = X(ind); + Y = Y(ind); + p = polyshape(X,Y); + %clc + is = isinterior(p,Pos_Axis); + + while is == 0 + jj = jj+1; + + X = reshape(d.poincare.R(jj,1,:),[1 ,Nppts]); + Y = reshape(d.poincare.Z(jj,1,:),[1 ,Nppts]); + + Xbar = mean(X); + Ybar = mean(Y); + theta = atan2(Y-Ybar , X-Xbar); + theta = mod(theta, 2*pi); + + [theta, ind] = sort(theta); + + X = X(ind); + Y = Y(ind); + p = polyshape(X,Y); + %clc + is = isinterior(p,Pos_Axis); + + end + n_surf = jj; + n = length(l) - (n_surf+shift-1); + + mat_iota = zeros(1,n); + mat_r_coord = zeros(1,n); + mat_s_coord = zeros(1,n); + derivatives = zeros(1,n); + shear = zeros(1,n); + coeff = zeros(1,n); + + out = extract_shear(d,n,shift, n_surf); + mat_iota = out.mat_iota; + mat_r_coord = out.mat_r_coord; + mat_s_coord = out.mat_s_coord; + scan_11(ii) = out.scan_11; + scan_10(ii) = out.scan_10; + derivatives = out.derivatives; + avg_shear(ii) = out.avg_shear; + catch + warning('Problem extracting shear. Assigning a value of -1 to d and all parameters to NaN'); + d = -1; + n = 1; + mat_iota = NaN(1,n); + mat_r_coord = NaN(1,n); + mat_s_coord = NaN(1,n); + scan_11(ii) = NaN; + scan_10(ii) = NaN; + derivatives = NaN(1,n); + avg_shear(ii) = NaN; + end + +end + +disp 'Done running...' +toc % set timer off +%% Plot last polyshape and coordinate axis %% + figure('color','w') + pg=plot(p); + pg.FaceColor = ([1 1 1]); + pg.EdgeColor = ([1 0 0]); + pg.LineWidth = 3; + hold on + plot(Pos_Axis(1), Pos_Axis(2), 'k+', 'linewidth' , 3, 'MarkerSize',8) + set (gca, 'fontsize', 16) + xlabel('R', 'interpreter', 'latex', 'FontSize', 24) + ylabel('Z', 'interpreter', 'latex','FontSize', 24) + +%% Shear %% + +shear_mat = reshape(avg_shear,[nn,nn])'; +r10_tilde = reshape(scan_10, [nn,nn]); +r11_tilde = reshape(scan_11, [nn,nn]); +parfor i=1:nn + r11(i) = r11_tilde(1,i); + r10(i) = r10_tilde(i,1); + + for j=1:nn + S(i,j) = shear_mat(i,j); + end +end +[R10,R11] = meshgrid(r10,r11); + + +%% PCOLOR SHEAR %% +figure +pcolor(R11,R10,S) +shading interp +hold on +contour(R11,R10,S,[0,0], 'r', 'LineWidth', 3) +set (gca, 'fontsize', fs) +colorbar +xlabel('$R_{11}$', 'interpreter', 'latex') +ylabel('$R_{10}$', 'interpreter', 'latex') + + +%% PLOT PROFIL IOTA ACROSS ZERO SHEAR LEVEL CURVE %% + +filename_1 = ['File1', num2str(index_R10_1), '_' num2str(index_R11) '.sp.h5']; +filename_2 = ['File2', num2str(index_R10_2), '_' num2str(index_R11) '.sp.h5']; + +shift = 8; % shift in extract shear function. Has to be determined from iota profile + +d_bel = read_spec(filename_1); +d_abov = read_spec(filename_2); + +coord_1 = d_bel.transform.fiota(shift:end,1); +coord_2 = d_abov.transform.fiota(shift:end,1); + +iota_1 = d_bel.transform.fiota(shift:end,2); +iota_2 = d_abov.transform.fiota(shift:end,2); + +figure +plot(coord_1,iota_1,'b+', 'linewidth', 2, 'MarkerSize', 7) +grid on +hold on +plot(coord_2,iota_2,'r+', 'linewidth', 2, 'MarkerSize', 7) +set(gca, 'fontsize', 17) +xlabel('$r$', 'Interpreter','latex', 'FontSize',30) +ylabel('$\iota$', 'Interpreter','latex', 'FontSize',30) +legend('$\iota_{a}$', '$\iota_{b}$', 'Interpreter', 'latex', 'FontSize', 27) + + +%% PCOLOR & SURF MULTIPLOT %% + +figure +subplot(1,2,1) +%---------------------------------------------------------- +pcolor(R11,R10, S) +title('Shear($R_{11},R_{10}$)', 'interpreter', 'latex') +shading interp +hold on +contour(R11,R10,S,[0,0], 'r', 'LineWidth', 3) +hold on +plot(scan11_trunc, scan10_trunc, 'w--', 'linewidth', 1); +hold on +plot(scan11_trunc2, scan10_trunc2, 'w--', 'linewidth', 1); +set (gca, 'fontsize', fs) +colorbar +xlabel('$R_{11}$', 'interpreter', 'latex') +ylabel('$R_{10}$', 'interpreter', 'latex') + +subplot(1,2,2) +%--------------------------------------------------------- +surf(R11,R10,S) +shading interp +hold on +contour(R11,R10,S,[0,0], 'r', 'LineWidth', 3) +set (gca, 'fontsize', fs) +colorbar +xlabel('$R_{11}$', 'interpreter', 'latex') +ylabel('$R_{10}$', 'interpreter', 'latex') + +clc + + +%% Extract %% +function out = extract_shear(d, n, shift, n_surf) % can be found in extract_shear.m file too + + id = n_surf+shift; + radial_coord = (d.transform.fiota(:,1)); % extract radial coordinate + out.mat_iota = d.transform.fiota(id:end,2); % extract iota + out.mat_r_coord = radial_coord(id:end); % truncates the radial coordinates (remove 5 first terms) + out.mat_s_coord = ((out.mat_r_coord + 1)./2); % change of variable r <--> s + out.scan_11 = d.output.Rbc(11,2); % Value of R11 + out.scan_10 = d.output.Rbc(2,2); % Value of R10 + + % CENTERED FINITE DIFFERENCES + out.derivatives(1) = (out.mat_iota(2) - out.mat_iota(1)) / (out.mat_s_coord(2) - out.mat_s_coord(1)); + out.derivatives(n) = (out.mat_iota(n) - out.mat_iota(n-1)) / (out.mat_s_coord(n) - out.mat_s_coord(n-1)); + + for j=2:n-1 + out.derivatives(j) = (out.mat_iota(j+1) - out.mat_iota(j-1)) / (out.mat_s_coord(j+1) - out.mat_s_coord(j-1)); + end + + out.coeff = out.mat_s_coord ./ (out.mat_iota) ; + out.shear = (out.coeff)' .* out.derivatives; + out.avg_shear = mean(out.shear); % Avg shear +end \ No newline at end of file diff --git a/Utilities/matlabtools/write_spec_rzgrid.m b/Utilities/matlabtools/write_spec_rzgrid.m index 61f9cf5f..c4f95849 100644 --- a/Utilities/matlabtools/write_spec_rzgrid.m +++ b/Utilities/matlabtools/write_spec_rzgrid.m @@ -5,7 +5,8 @@ function write_spec_rzgrid(data, nz0,lvol,outfname) % WRITE_SPEC_RZGRID( DATA, NZ0, LVOL, OUTFNAME ) % ============================================== % -% Writes text file with grid coordinate data points R,Z on a given volume, on a toroidal plane, as two columns +% Writes text file with grid coordinate data points R,Z on a given volume, +% on a toroidal plane, as two columns % % INPUT % ----- diff --git a/Utilities/pythontools/py_spec/__init__.py b/Utilities/pythontools/py_spec/__init__.py index 260f4170..5203a4a5 100644 --- a/Utilities/pythontools/py_spec/__init__.py +++ b/Utilities/pythontools/py_spec/__init__.py @@ -1,6 +1,8 @@ # import of all SPEC-related python scripts. -__version__ = "3.1.0" +__version__ = "3.3.3" from .ci import test from .input.spec_namelist import SPECNamelist from .output.spec import SPECout +from .math.spec_fft import spec_fft +from .math.spec_invfft import spec_invfft diff --git a/Utilities/pythontools/py_spec/input/spec_namelist.py b/Utilities/pythontools/py_spec/input/spec_namelist.py index 9b843796..d40605e0 100644 --- a/Utilities/pythontools/py_spec/input/spec_namelist.py +++ b/Utilities/pythontools/py_spec/input/spec_namelist.py @@ -10,7 +10,7 @@ from f90nml import Namelist import numpy as np - +import matplotlib.pyplot as plt class SPECNamelist(Namelist): """The SPEC namelist class @@ -428,14 +428,32 @@ def get_interface_guess(self, m, n, ivol, key="Rbc"): return self.interface_guess[(m, n)][key][ivol] - def set_interface_guess(self, value, m, n, ivol, key="Rbc"): + def set_vacuum_field( self, value, m, n, mykey='Bns'): + """Set the guess of the coils field harmonics + parameters: + value -- the value that one wants to set + m,n -- the m and n number of the guess, must be within the allowed Mpol and Ntor range + the n number is the one without multiplying by Nfp + mykey -- which guess, can be 'Bnc' or 'Bns' + """ + if m > self._Mpol or m < 0: + raise ValueError("0 <= m <= Mpol") + if n > self._Ntor or n < -self._Ntor: + raise ValueError("-Ntor <= n <= Ntor") + if mykey not in ['Bns', 'Bnc']: + raise ValueError("mykey must be in ['Bns', 'Bnc']") + + self['physicslist'][mykey][m][n+self._Ntor] = value + + + def set_interface_guess(self, value, m, n, ivol, mykey="Rbc"): """Set the guess of the interface Fourier harmonic parameters: value -- the value that one wants to set m,n -- the m and n number of the guess, must be within the allowed Mpol and Ntor range the n number is the one without multiplying by Nfp ivol -- which volume, Python convention, starting from 0 - key -- which guess, can be 'Rbc', 'Zbs', 'Rbs', 'Zbc' + mykey -- which guess, can be 'Rbc', 'Zbs', 'Rbs', 'Zbc' """ if ivol >= self._Nvol or ivol < 0: raise ValueError("ivol must be between 0 and Nvol-1") @@ -443,8 +461,8 @@ def set_interface_guess(self, value, m, n, ivol, key="Rbc"): raise ValueError("0 <= m <= Mpol") if n > self._Ntor or n < -self._Ntor: raise ValueError("-Ntor <= n <= Ntor") - if key not in ["Rbc", "Rbs", "Zbc", "Zbs"]: - raise ValueError("key must be in ['Rbc', 'Rbs', 'Zbc', 'Zbs']") + if mykey not in ["Rbc", "Rbs", "Zbc", "Zbs"]: + raise ValueError("mykey must be in ['Rbc', 'Rbs', 'Zbc', 'Zbs']") if (m, n) not in self.interface_guess.keys(): # add a new item @@ -452,7 +470,88 @@ def set_interface_guess(self, value, m, n, ivol, key="Rbc"): for key in ["Rbc", "Rbs", "Zbc", "Zbs"]: self.interface_guess[(m, n)][key] = np.zeros([self._Nvol]) - self.interface_guess[(m, n)][key][ivol] = value + self.interface_guess[(m, n)][mykey][ivol] = value + + def set_plasma_boundary(self, value, m, n, key='Rbc'): + """Set the value of the plasma boundary + + parameters: + value -- the new value + m,n -- poloidal and toroidal mode number. Has to be within the allowed Mpol and Ntor Fourier resolution + n is has to be a multiple of Nfp + key -- any of 'Rbc', 'Rbs', 'Zbc', 'Zbs'. + """ + + if m > self._Mpol or m < 0: + raise ValueError("0 <= m <= Mpol") + if n > self._Ntor or n < -self._Ntor: + raise ValueError("-Ntor <= n <= Ntor") + if key not in ["Rbc", "Rbs", "Zbc", "Zbs"]: + raise ValueError("key must be in ['Rbc', 'Rbs', 'Zbc', 'Zbs']") + + if type(m)!=int: m=int(m) + if type(n)!=int: n=int(n) + if type(value)!=float: value = float(value) + + self['physicslist'][key][m][n+self._Ntor] = value + + + def get_plasma_boundary(self, m, n, key="Rbc"): + """Get the guess of the interface Fourier harmonic + parameters: + m,n -- the m and n number of the guess, must be within the allowed Mpol and Ntor range + the n number is the one without multiplying by Nfp + ivol -- which volume, Python convention, starting from 0 + key -- which item, can be 'Rbc', 'Zbs', 'Rbs', 'Zbc' + Returns: + guess -- the initial guess of the interface harmonic used in SPEC + """ + if key not in ["Rbc", "Rbs", "Zbc", "Zbs"]: + raise ValueError("key must be in ['Rbc', 'Rbs', 'Zbc', 'Zbs']") + + ll = self['physicslist'][key] + + if m>=len(ll): + return 0 + else: + nl = len(ll[m]) + ntor = int((nl-1)/2) + if abs(n)>ntor: + return 0 + else: + return ll[m][n+ntor] + + def set_plasma_boundary(self, value, m, n, key="Rbc"): + """Set the guess of the interface Fourier harmonic + parameters: + value -- the value that one wants to set + m,n -- the m and n number of the guess, must be within the allowed Mpol and Ntor range + the n number is the one without multiplying by Nfp + ivol -- which volume, Python convention, starting from 0 + key -- which guess, can be 'Rbc', 'Zbs', 'Rbs', 'Zbc' + """ + if key not in ["Rbc", "Rbs", "Zbc", "Zbs"]: + raise ValueError("key must be in ['Rbc', 'Rbs', 'Zbc', 'Zbs']") + + ll = self['physicslist'][key] + + if m>=len(ll): + for m in range(len(ll), m+1): + self['physicslist'][key].append([0]*(2*self._Ntor+1)) + else: + nl = len(ll[m]) + ntor = int((nl-1)/2) + if abs(n)>ntor: + for n in range(ntor+1, abs(n)+1): + self['physicslist'][key][m].append(0) + self['physicslist'][key][m].insert(0, 0) + + # Change indexing + self['physicslist'].start_index[key][0] = -abs(n) + + nl = len(self['physicslist'][key][m]) + ntor = int((nl-1)/2) + self['physicslist'][key][m][n+ntor] = value def remove_interface_guess(self, m, n): """Remove the guess of the interface Fourier harmonic with some m,n @@ -465,6 +564,57 @@ def remove_interface_guess(self, m, n): raise ValueError("unknown m or n") else: del self.interface_guess[(m, n)] + def plot_initial_guess(self, phi=0, nt=1024, **kwargs): + """ + Plot the guess for the inner interfaces on a toroidal plane + + parameters: + phi -- toroidal angle + nt -- number of points per interface, 1024 by default + """ + + fig, ax = plt.subplots() + + tarr = np.linspace(0, 2*np.pi, nt) + nvol = self['physicslist']['Nvol'] + nfp = self['physicslist']['Nfp'] + + nmodes = len(self.interface_guess) + for ivol in range(0,nvol-1): + r = np.zeros(nt) + z = np.zeros(nt) + + for key in self.interface_guess.keys(): + mm = key[0] + nn = key[1] * nfp + + if mm>self['physicslist']['Mpol'] or abs(nn)>self['physicslist']['Ntor']: continue + + cosa = np.cos(mm*tarr - nn*phi) + sina = np.sin(mm*tarr - nn*phi) + r += self.interface_guess[key]['Rbc'][ivol] * cosa + \ + self.interface_guess[key]['Rbs'][ivol] * sina + z += self.interface_guess[key]['Zbc'][ivol] * cosa + \ + self.interface_guess[key]['Zbs'][ivol] * sina + + ax.scatter( r, z, **kwargs ) + + # Plot plasma boundary + r = np.zeros(nt) + z = np.zeros(nt) + for mm in range(0, self._Mpol+1): + for nn in range(-self._Ntor, self._Ntor+1): + cosa = np.cos(mm*tarr - nn*phi) + sina = np.sin(mm*tarr - nn*phi) + r += self['physicslist']['Rbc'][mm][nn+self._Ntor] * cosa \ + +self['physicslist']['Rbs'][mm][nn+self._Ntor] * sina + z += self['physicslist']['Zbc'][mm][nn+self._Ntor] * cosa \ + +self['physicslist']['Zbs'][mm][nn+self._Ntor] * sina + + ax.scatter( r, z, **kwargs ) + + plt.draw() + def _rectify_namelist(self): """correct the size/type of the namelist objects and so on""" @@ -487,7 +637,7 @@ def _rectify_namelist(self): for key in self.boundary_keys: if key.lower() not in self["physicslist"].keys(): self["physicslist"][key] = np.zeros( - [self._Mpol, self._Ntor * 2 + 1], dtype=np.float + [self._Mpol, self._Ntor * 2 + 1], dtype=np.float64 ).tolist() self["physicslist"].start_index[key.lower()] = [-self._Ntor, 0] else: @@ -501,7 +651,7 @@ def _rectify_namelist(self): for key in self.axis_keys: if key.lower() not in self["physicslist"].keys(): self["physicslist"][key] = np.zeros( - [self._Ntor + 1], dtype=np.float + [self._Ntor + 1], dtype=np.float64 ).tolist() self["physicslist"].start_index[key.lower()] = [0] else: @@ -596,7 +746,7 @@ def _read_interface_guess(self, file_object): # ignore empty lines if len(line_split) == 0: - break + continue # check if this line meet our expectation valid_line = True diff --git a/Utilities/pythontools/py_spec/math/spec_fft.py b/Utilities/pythontools/py_spec/math/spec_fft.py new file mode 100644 index 00000000..a1c0c187 --- /dev/null +++ b/Utilities/pythontools/py_spec/math/spec_fft.py @@ -0,0 +1,192 @@ +import numpy as np +import copy +import warnings + +def spec_fft(tarr: np.array, + zarr: np.array, + freal: np.array, + Mpol: int=None, + Ntor: int=None, + output: str='1D'): + """ + Fourier transform as in SPEC fortran source + + Args: + - tarr: 1D numpy array of size nt. Poloidal angle coordinate, each point + should be equidistant + - zarr: 1D numpy array of size nz. Toroidal angle coordinate, each point + should be equidistant + - freal: 2D numpy array of size (nz,nt). Function, in real space, for which + Fourier harmonics should be evaluated + - Mpol: integer. Poloidal resolution. Default is nt/2. + - Ntor: integer. Toroidal resolution. Default is nz/2. + - output: either '1D' or '2D'. Determine the form of the output. + + Output: + If output=='1D', the output is a 4-tuple 1D numpy array, with modes + organized as in SPEC (first increasing n, then increasing m). First + tuple element are the even modes, second are the odd modes, third + are the poloidal mode number, and fourth the toroidal mode number. + If output=='2D', the output is tuple of 2D numpy array, with modes (m,n) + in element (Ntor+n,m). First tuple elements are the even modes, + seconds are the odd modes + """ + + # Check input + # ----------- + # tarr + if not isinstance(tarr, np.ndarray): + raise ValueError('tarr should be a numpy array') + if tarr.ndim>1: + raise ValueError('tarr should be one-dimensional') + + nt = tarr.size + if nt<3: + raise ValueError('Not enough points in tarr') + + # zarr + if not isinstance(zarr, np.ndarray): + raise ValueError('zarr should be a numpy array') + if zarr.ndim>1: + raise ValueError('zarr should be one-dimensional') + + nz = zarr.size + if nz<3: + raise ValueError('Not enough points in zarr') + + # freal + if not isinstance(freal, np.ndarray): + raise ValueError('freal should be a numpy array') + if freal.ndim!=2: + raise ValueError('freal should be two-dimensional') + if freal.shape!=(nz,nt): + raise ValueError('freal should be of size (nz,nt)') + + if tarr[0]+2*np.pi==tarr[-1]: + warnings.warn('tarr[-1] should not be equal to tarr[0]. Removing last element...') + tarr = tarr[:-1] + nt -= 1 + freal = freal[:,:-1] + + if zarr[0]+2*np.pi==zarr[-1]: + warnings.warn('zarr[-1] should not be equal to zarr[0]. Removing last element...') + zarr = zarr[:-1] + nz -= 1 + freal = freal[:-1,:] + + if not np.all(np.abs(np.diff(np.diff(tarr)))<1e-14): + raise ValueError('Points should be equidistant in tarr') + if not np.all(np.abs(np.diff(np.diff(zarr)))<1e-14): + raise ValueError('Points should be equidistant in zarr') + + # Mpol + M = int(np.floor(nt/2)) + if Mpol is None: + Mpol = M + if not isinstance(Mpol, int): + raise ValueError('Mpol should be an integer') + if Mpol<1 or Mpol>nt/2: + raise ValueError('Mpol should be at least 1 and smaller than nt/2') + + # Ntor + N = int(np.floor(nz/2)) + if Ntor is None: + Ntor = N + if not isinstance(Ntor, int): + raise ValueError('Ntor should be an integer') + if Ntor<1 or Ntor>nz/2: + raise ValueError('Ntor should be at least 1 and smaller than nt=z/2') + + # output + if not isinstance(output, str): + raise ValueError('output should be a string') + if not (output=='1D' or output=='2D'): + raise ValueError('output should be 1D or 2D') + + # Do the fft + # ---------- + # Actual fft + fmn = np.fft.fft2( freal ) / (nt*nz) + + # Now construct 2D array. Negative m-modes have to be added to positive + # m-modes, i.e. (m,n)+(-m,-n) for even modes, and (m,n)-(-m,-n) for odd + # modes. + # Difference if the number of elements (either nt or nz) is odd - this is + # due to the internal implementation of numpy.fft.fft. + efmn = copy.deepcopy(fmn) + efmn[1:,1:] = fmn[1:,1:] + np.flip(fmn[1:,1:]) + + ofmn = copy.deepcopy(fmn) + ofmn[1:,1:] = fmn[1:,1:] - np.flip(fmn[1:,1:]) + if np.mod(nt,2)==0: + efmn[0,1:M+1] += np.flip(fmn[0,M:]) #n=0 + ofmn[0,1:M+1] -= np.flip(fmn[0,M:]) + else: + efmn[0,1:M+1] += np.flip(fmn[0,M+1:]) #n=0 + ofmn[0,1:M+1] -= np.flip(fmn[0,M+1:]) + + if np.mod(nz,2)==0: + efmn[1:N+1,0] += np.flip(fmn[N:,0]) # m=0 + ofmn[1:N+1,0] -= np.flip(fmn[N:,0]) + else: + efmn[1:N+1,0] += np.flip(fmn[N+1:,0]) # m=0 + ofmn[1:N+1,0] -= np.flip(fmn[N+1:,0]) + + efmn = (np.absolute(efmn) * np.cos(np.angle(efmn)))[:,0:M+1] + ofmn = (np.absolute(ofmn) * np.sin(np.angle(ofmn)))[:,0:M+1] + + # Change sign of m>0 odd modes + ofmn[:,1:] = -ofmn[:,1:] + + # Shift result to be centered around n=0 mode + efmn = np.fft.fftshift(efmn, axes=0) + ofmn = np.fft.fftshift(ofmn, axes=0) + + # Invert n -> -n + if np.mod(nz,2)==0: + efmn[1:,1:] = np.flip(efmn[1:,1:],axis=0) + ofmn[1:,1:] = np.flip(ofmn[1:,1:],axis=0) + else: + efmn[:,1:] = np.flip(efmn[:,1:],axis=0) + ofmn[:,1:] = np.flip(ofmn[:,1:],axis=0) + + + # Prepare output + # -------------- + if output=='2D': + # 2D - truncate efmn, ofmn to the required resolution + even_out = efmn[N-Ntor:N+Ntor+1,0:Mpol+1] + odd_out = ofmn[N-Ntor:N+Ntor+1,0:Mpol+1] + return (even_out, odd_out) + + elif output=='1D': + # 1D - construct array mode by mode + nmn = Ntor+1 + Mpol*(2*Ntor+1) + even_out = np.zeros((nmn,)) + odd_out = np.zeros((nmn,)) + _im = np.zeros((nmn,), dtype=int) + _in = np.zeros((nmn,), dtype=int) + + ind = -1 + for mm in range(0,Mpol+1): + for nn in range(-Ntor,Ntor+1): + if mm==0 and nn<0: + continue + + ind += 1 + + _im[ind]=mm + _in[ind]=nn + even_out[ind] = efmn[N+nn,mm] + odd_out[ind] = ofmn[N+nn,mm] + + return (even_out, odd_out, _im, _in) + + else: + raise ValueError('Invalid output') + + + + + + diff --git a/Utilities/pythontools/py_spec/math/spec_invfft.py b/Utilities/pythontools/py_spec/math/spec_invfft.py new file mode 100644 index 00000000..14022777 --- /dev/null +++ b/Utilities/pythontools/py_spec/math/spec_invfft.py @@ -0,0 +1,89 @@ +import numpy as np + +def spec_invfft(tarr:np.ndarray, zarr:np.ndarray, + efmn:np.ndarray, ofmn:np.ndarray, + _im:np.ndarray, _in:np.ndarray): + """ + Inverse Fourier transform as in SPEC Fortran source. + + Args: + - tarr: 1D numpy array of size nt. Poloidal angle coordinate. + - zarr: 1D numpy array of size nz. Toroidal angle coordinate. + - efmn: 1D numpy array of size nmn. Even mode numbers. + - ofmn: 1D numpy array of size nmn. Odd mode numbers. + - _im: 1D numpy array of size nmn. Poloidal mode numbers + - _in: 1D numpy array of size nmn. Toroidal mode numbers (multiples of Nfp) + + Output: + - freal: 2D numpy array of size nz x nt. Function evaluation in real space. + """ + + # Check input + # ----------- + # tarr + if not isinstance(tarr, np.ndarray): + raise ValueError('tarr should be a numpy array') + if tarr.ndim>1: + raise ValueError('tarr should be one-dimensional') + + nt = tarr.size + + # zarr + if not isinstance(zarr, np.ndarray): + raise ValueError('zarr should be a numpy array') + if zarr.ndim>1: + raise ValueError('zarr should be one-dimensional') + + nz = zarr.size + + # efmn + if not isinstance(efmn, np.ndarray): + raise ValueError('efmn should be a numpy array') + if efmn.ndim>1: + raise ValueError('efmn should be one-dimensional') + + nmn = efmn.size + + # ofmn + if not isinstance(ofmn, np.ndarray): + raise ValueError('ofmn should be a numpy array') + if ofmn.ndim>1: + raise ValueError('ofmn should be one-dimensional') + if ofmn.size!=nmn: + raise ValueError('ofmn should have the same size as efmn') + + # _im + if not isinstance(_im, np.ndarray): + raise ValueError('_im should be a numpy array') + if _im.ndim>1: + raise ValueError('_im should be one-dimensional') + if _im.size!=nmn: + raise ValueError('_im should have the same size as efmn') + if not np.all(_im>=0): + raise ValueError('_im should not have any negative values') + + # _in + if not isinstance(_in, np.ndarray): + raise ValueError('_in should be a numpy array') + if _in.ndim>1: + raise ValueError('_in should be one-dimensional') + if _in.size!=nmn: + raise ValueError('_in should have the same size as efmn') + + # Inverse Fourier transform + # ------------------------- + + # Generate grid: + tgrid, zgrid = np.meshgrid(tarr, zarr) + + # Evaluate function: + freal = np.zeros((nz,nt)) + for mm, nn, emode, omode in zip(_im, _in, efmn, ofmn): + freal += emode * np.cos(mm*tgrid - nn*zgrid) \ + + omode * np.sin(mm*tgrid - nn*zgrid) + + # Output + return freal + + + diff --git a/Utilities/pythontools/py_spec/output/_plot_iota.py b/Utilities/pythontools/py_spec/output/_plot_iota.py index 8de0c2e3..362075e5 100644 --- a/Utilities/pythontools/py_spec/output/_plot_iota.py +++ b/Utilities/pythontools/py_spec/output/_plot_iota.py @@ -29,7 +29,7 @@ def plot_iota(self, xaxis="R", yaxis="i", ax=None, **kwargs): xlabel = r"s" elif xaxis == "R": xdata = self.poincare.R[:, 0, 0] - ydata = self.transform.fiota[1, :] + ydata = self.transform.fiota[1, self.poincare.success == 1] xlabel = r"R" else: raise ValueError("xaxis should be one of ['R', 's'].") diff --git a/Utilities/pythontools/py_spec/output/_plot_poincare.py b/Utilities/pythontools/py_spec/output/_plot_poincare.py index d1002931..6de93211 100644 --- a/Utilities/pythontools/py_spec/output/_plot_poincare.py +++ b/Utilities/pythontools/py_spec/output/_plot_poincare.py @@ -73,4 +73,4 @@ def plot_poincare(self, toroidalIdx=0, prange="full", ax=None, **kwargs): plt.xticks(fontsize=16) plt.yticks(fontsize=16) - return \ No newline at end of file + return ax diff --git a/Utilities/pythontools/py_spec/output/_processing.py b/Utilities/pythontools/py_spec/output/_processing.py index 6479a6fe..a5f6c2d6 100644 --- a/Utilities/pythontools/py_spec/output/_processing.py +++ b/Utilities/pythontools/py_spec/output/_processing.py @@ -1,5 +1,131 @@ import numpy as np +from scipy import integrate +def get_RZ_derivatives( + self, + lvol=0, + sarr=np.linspace(1, 1, 1), + tarr=np.linspace(0, 0, 1), + zarr=np.linspace(0, 0, 1), + input1D=False +): + + Igeometry = self.input.physics.Igeometry + + if lvol==0 and (sarr==-1).any() and Igeometry!=0: + raise ValueError('Cannot evaluate coordinate derivative on magnetic axis !') + + sym = self.input.physics.Istellsym == 1 + + Rac, Rbc = self.output.Rbc[lvol : lvol + 2] + Ras, Rbs = self.output.Rbs[lvol : lvol + 2] + Zas, Zbs = self.output.Zbs[lvol : lvol + 2] + Zac, Zbc = self.output.Zbc[lvol : lvol + 2] + + mn = Rac.size # s.output.mn + im = self.output.im + in_ = self.output.in_ + + #sbar = (sarr + 1) / 2 + sbar = np.divide(np.add(sarr, 1.0), 2.0) + fac = [] + + rpol = self.input.physics.rpol + rtor = self.input.physics.rtor + + if Igeometry == 1: + for j in range(mn): + fac.append([sbar, 0.5 * np.ones(sarr.size), np.zeros(sarr.size)]) + elif Igeometry == 2: + for j in range(mn): + if lvol > 0 or im[j] == 0: + fac.append([sbar, 0.5 * np.ones(sarr.size), np.zeros(sarr.size)]) + else: + fac.append( + [ + sbar ** (im[j] + 1.0), + (im[j] + 1.0) / 2.0 * sbar ** (im[j]), + (im[j] + 1.0) * (im[j]) / 4.0 * sbar ** (im[j] - 1), + ] + ) + elif Igeometry == 3: + for j in range(mn): + if lvol == 0 and im[j] == 0: + fac.append([sbar ** 2, sbar, 0.5 * np.ones(sarr.size)]) + elif lvol == 0 and im[j] > 0: + fac.append( + [ + sbar ** im[j], + (im[j] / 2.0) * sbar ** (im[j] - 1.0), + (im[j] * (im[j] - 1) / 4.0) * sbar ** (im[j] - 2.0), + ] + ) + else: + fac.append([sbar, 0.5 * np.ones(sarr.size), np.zeros(sarr.size)]) + + # now fac has the dimension (number of modes, number of derivatives, number of s points) + fac = np.array(fac) + # transpose to (number of derivatives, number of modes, number of s points) + fac = np.moveaxis(fac, 0, 1) + + nax = np.newaxis + if not input1D: + im = im[:, nax, nax, nax] + in_ = in_[:, nax, nax, nax] + ang_arg = +im * tarr[nax, nax, :, nax] - in_ * zarr[nax, nax, nax, :] + else: + im = im[:, nax] + in_ = in_[:, nax] + ang_arg = im * tarr[nax, :] - in_ * zarr[nax, :] + + cos = np.cos(ang_arg) + sin = np.sin(ang_arg) + + if not input1D: + fac = fac[:, :, :, nax, nax] + Rac = Rac[:, nax, nax, nax] + Rbc = Rbc[:, nax, nax, nax] + Zas = Zas[:, nax, nax, nax] + Zbs = Zbs[:, nax, nax, nax] + if not sym: + Ras = Ras[:, nax, nax, nax] + Rbs = Rbs[:, nax, nax, nax] + Zac = Zac[:, nax, nax, nax] + Zbc = Zbc[:, nax, nax, nax] + else: + Rac = Rac[:, nax] + Rbc = Rbc[:, nax] + Zas = Zas[:, nax] + Zbs = Zbs[:, nax] + if not sym: + Ras = Ras[:, nax] + Rbs = Rbs[:, nax] + Zac = Zac[:, nax] + Zbc = Zbc[:, nax] + + dR1 = Rac + fac[0] * (Rbc - Rac) + Rarr0 = np.sum(dR1 * cos, axis=0) + + Rarr1 = np.sum(fac[1] * (Rbc - Rac) * cos, axis=0) + Rarr2 = np.sum(-im * dR1 * sin, axis=0) + Rarr3 = np.sum(in_ * dR1 * sin, axis=0) + + Rarr = np.array([Rarr1, Rarr2, Rarr3]) + + # We only need Z for Igeometry=3 + if Igeometry == 3: + dZ1 = Zas + fac[0] * (Zbs - Zas) + Zarr0 = np.sum(dZ1 * sin, axis=0) + + Zarr1 = np.sum(fac[1] * (Zbs - Zas) * sin, axis=0) + Zarr2 = np.sum(im * dZ1 * cos, axis=0) + Zarr3 = np.sum(-in_ * dZ1 * cos, axis=0) + + Zarr = np.array([Zarr1, Zarr2, Zarr3]) + else: + Zarr0 = None + + return Rarr0, Rarr1, Rarr2, Rarr3, Zarr0, Zarr1, Zarr2, Zarr3 def get_grid_and_jacobian_and_metric( self, @@ -231,7 +357,6 @@ def get_grid_and_jacobian_and_metric( else: return Rarr0, Zarr0, jacobian, g - def grid( self, lvol=0, @@ -246,7 +371,6 @@ def grid( ) return Rarr0, Zarr0 - def jacobian( self, lvol=0, @@ -261,7 +385,6 @@ def jacobian( ) return jacobian - def metric( self, lvol=0, @@ -276,7 +399,6 @@ def metric( ) return g - def get_B( self, lvol=0, @@ -353,12 +475,114 @@ def get_modB(self, Bcontrav, g, derivative=False, dBcontrav=None, dg=None): ) + np.einsum("...i,...kji,...j->...k", Bcontrav, dg, Bcontrav) return modB, dmodB2 - def get_B_covariant(self, Bcontrav, g, derivative=False): """Get covariant component of B""" Bco = np.einsum("...i,...ji->...j", Bcontrav, g) return Bco +def get_volume(self, ivol, ns=64, nt=64, nz=64): + """Returns volume occupied by volume ivol""" + + # Create coordinate grid + nfp = self.input.physics.Nfp + tarr = np.linspace(0, 2*np.pi, nt, endpoint=True) + zarr = np.linspace(0, 2*np.pi / nfp, nz, endpoint=True) + + if ivol==0: sarr=np.linspace(-0.999,1,ns) + else: sarr=np.linspace(-1, 1, ns) + + # Get jacobian + j = self.jacobian(lvol=ivol, sarr=sarr, tarr=tarr, zarr=zarr) + + # Integrate + dt = tarr[1]-tarr[0] + dz = zarr[1]-zarr[0] + ds = sarr[1]-sarr[0] + return nfp * integrate.simpson( y=integrate.simpson( y=integrate.simpson( y=j, x=zarr ), x=tarr ), x=sarr ) + +def get_average_beta(self, ns=64, nt=64, nz=64): + """Get beta averaged in plasma volume""" + + # Read pressure + press = self.input.physics.pressure * self.input.physics.pscale + + # Create coordinate grid + nfp = self.input.physics.Nfp + tarr = np.linspace(0, 2*np.pi, nt) + zarr = np.linspace(0, 2*np.pi / nfp, nz) + + # Get beta in each volume + nvol = self.input.physics.Nvol + + vols = np.zeros((nvol,)) + betavol = np.zeros((nvol,)) + + if (press==0).all(): return 0 + + if nvol==1: + sarr=np.linspace(-0.999,1, ns) + vols = self.get_volume( 0 ) + _, _, sg, g = self.get_grid_and_jacobian_and_metric( + lvol=0, sarr=sarr, tarr=tarr, zarr=zarr + ) + Bcontrav = self.get_B( + lvol=0, jacobian=sg, sarr=sarr, tarr=tarr, zarr=zarr + ) + modB = self.get_modB( Bcontrav, g ) + + betavol = 2 * nfp * press * integrate.simpson( + y=integrate.simpson( + y=integrate.simpson( + y=sg / modB**2, x=zarr ), x=tarr ), x=sarr ) + + return betavol / vols + else: + for ivol in range(0,nvol): + if ivol==0: sarr=np.linspace(-0.999,1, ns) + if ivol!=0: sarr=np.linspace(-1, 1, ns) + + vols[ivol] = self.get_volume( ivol ) + + _, _, sg, g = self.get_grid_and_jacobian_and_metric( + lvol=ivol, sarr=sarr, tarr=tarr, zarr=zarr + ) + Bcontrav = self.get_B( + lvol=ivol, jacobian=sg, sarr=sarr, tarr=tarr, zarr=zarr + ) + modB = self.get_modB( Bcontrav, g ) + + betavol[ivol] = 2 * nfp * press[ivol] * integrate.simpson( + y=integrate.simpson( + y=integrate.simpson( + y=sg / modB**2, x=zarr ), x=tarr ), x=sarr ) + + return betavol.sum() / vols.sum() + +def get_peak_beta(self, ns=64, nt=64, nz=64): + if self.input.physics.pressure.size>1: + press = self.input.physics.pressure[0] * self.input.physics.pscale + else: + press = self.input.physics.pressure * self.input.physics.pscale + + nfp = self.input.physics.Nfp + tarr = np.linspace(0, 2*np.pi, nt) + zarr = np.linspace(0, 2*np.pi / nfp, nz) + sarr=np.linspace(-0.999,1, ns) + + vol = self.get_volume( 0 ) + _, _, sg, g = self.get_grid_and_jacobian_and_metric( + lvol=0, sarr=sarr, tarr=tarr, zarr=zarr + ) + Bcontrav = self.get_B( + lvol=0, jacobian=sg, sarr=sarr, tarr=tarr, zarr=zarr + ) + modB = self.get_modB( Bcontrav, g ) + + return 2 * nfp * press * integrate.simpson( + y=integrate.simpson( + y=integrate.simpson( + y=sg / modB**2, x=zarr ), x=tarr ), x=sarr ) / vol + def test_derivatives(self, lvol=0, s=0.3, t=0.4, z=0.5, delta=1e-6, tol=1e-6): ds = delta R, Z, j, g = self.get_grid_and_jacobian_and_metric(lvol, np.array([s-ds, s+ds]), np.array([t-ds, t+ds]), np.array([z-ds, z+ds])) @@ -381,3 +605,183 @@ def test_derivatives(self, lvol=0, s=0.3, t=0.4, z=0.5, delta=1e-6, tol=1e-6): print((g[1,0,0,:,:] - g[0,0,0,:,:])/ds/2-dg[0,0,0,0,:,:]) print((g[0,1,0,:,:] - g[0,0,0,:,:])/ds/2-dg[0,0,0,1,:,:]) print((g[0,0,1,:,:] - g[0,0,0,:,:])/ds/2-dg[0,0,0,2,:,:]) + +def get_surface_current_density(self, lsurf:int=None, nt:int=64, nz:int=64): + """Compute j_surf.B on each side of the provided interfaces + + Args: + - lsurf: Interface number, between 1 and Mvol-1. + - nt: Number of poloidal points + - nz: Number of toroidal points + + Returns: + - j_dot_B: mu0*j_surf.B evaluated on the grid. Shape (nsurf, nt, nz), + with nsurf the size of lsurf + - tarr: theta array, size (nt,) + - zarr: zeta array, size (nz,) + + Raises: + - ValueError: if input is wrong (invalid lsurf, nt<=0, nz<=0) + """ + + mvol = self.output.Mvol + nfp = self.input.physics.Nfp + + if mvol==1: raise ValueError('Mvol=1; no interface current!') + if not isinstance(lsurf, np.ndarray): raise ValueError('lsurf should be a np.ndarray') + if lsurf is None: raise ValueError('Need to provide lsurf') + if (lsurf<1).any() or (lsurf>mvol-1).any(): raise ValueError('lsurf should be in [1,mvol-1]') + if nt<1: raise ValueError('nt should greater than zero') + if nz<1: raise ValueError('nz should greater than zero') + + # Construct grid + tarr = np.linspace(0, 2*np.pi, nt, endpoint=True) + zarr = np.linspace(0, 2*np.pi/nfp, nz, endpoint=True) + + # Evaluate geometry elements + nsurf = lsurf.size*2 + j_dot_B = np.zeros((mvol-1, 2, nt, nz)) + for s in lsurf: + # Construct geometry elements - these are independent of the + # interface side + R0, R1, R2, R3, Z0, Z1, Z2, Z3 = self.get_RZ_derivatives( + lvol=int(s-1), + sarr=np.asarray([1]), + tarr=tarr, + zarr=zarr + ) + et_x_ez = np.sqrt((R2*Z3)**2 + (R3*Z2)**2 + (R0*Z2)**2 + (R0*R2)**2 - 2*R2*R3*Z2*Z3) + + gtt = R2**2+Z2**2 + gzz = R0**2 + R3**2 + Z3**2 + gtz = R2*R3 + Z2*Z3 + g = gtt*gzz - gtz**2 + + # project on each side of interface + Bcontrav = np.zeros((2,nt,nz,3)) + for innout in [0,1]: + # if innout=0, inner side of interface, thus vvol=s-1 and sarr=1 + # if innout=1, outer side of interface, thus vvol=s and sarr=-1 + lvol = s - np.mod(innout+1,2) + sarr = np.asarray([-innout*2+1]) + + # Get magnetic field + Bcontrav[innout,:,:,:] = self.get_B( + lvol=lvol, + sarr=sarr, + tarr=tarr, + zarr=zarr + )[0] + + Bcontrav_jump = Bcontrav[1]-Bcontrav[0] + + for innout in [0,1]: + j_dot_B[s-1, innout] = g / et_x_ez * ( + Bcontrav[innout, :, :, 1]*Bcontrav_jump[:, :, 2] + - Bcontrav[innout, :, :, 2]*Bcontrav_jump[:, :, 1] + ) + + return j_dot_B, tarr, zarr + +def get_surface(self, lsurf:int=None, nt:int=64, nz:int=64): + """Compute the surface area of a volume interface + + Args: + - lsurf: Interface number, between 1 and Mvol-1. + - nt: Number of poloidal points for integration, default is 64 + - nz: Number of toroidal points for integration, default is 64 + + Returns: + - S: the surface area + + Raises: + - ValueError: if input is wrong (invalid lsurf, nt<=0, nz<=0) + """ + + mvol = self.output.Mvol + nfp = self.input.physics.Nfp + if lsurf is None: + lsurf = np.arange(1,mvol) + + if mvol==1: + raise ValueError('Mvol=1; no interface current!') + if not isinstance(lsurf, np.ndarray): + raise ValueError('lsurf should be a np.ndarray') + if (lsurf<1).any() or (lsurf>mvol-1).any(): + raise ValueError('lsurf should be in [1,mvol-1]') + if nt<1: + raise ValueError('nt should greater than zero') + if nz<1: + raise ValueError('nz should greater than zero') + + # Construct grid + tarr = np.linspace(0, 2*np.pi, nt, endpoint=True) + zarr = np.linspace(0, 2*np.pi/nfp, nz, endpoint=True) + + # Create variable for storing the surface area + S = np.zeros((mvol-1,)) + + # Loop on interfaces + for s in lsurf: + # Construct geometry elements + R0, R1, R2, R3, Z0, Z1, Z2, Z3 = self.get_RZ_derivatives( + lvol=int(s-1), + sarr=np.asarray([1]), + tarr=tarr, + zarr=zarr + ) + #e theta x e phi + et_x_ez = np.sqrt((R2*Z3)**2 + (R3*Z2)**2 + (R0*Z2)**2 + (R0*R2)**2 - 2*R2*R3*Z2*Z3) + + S = nfp*integrate.simps(integrate.simps(et_x_ez,zarr,axis=2),tarr,axis=1) + + return S + +def get_flux_surface_average( self, lsurf, f, tarr, zarr ): + """Returns the flux surface average of a function f. + + For each surface lsurf, the average is made by computing the jacobian on the + inner side of the interface (i.e. lvol=lsurf-1, sarr=1) + + Args: + - lsurf (1D numpy array): Interface number, between 1 and Mvol-1 + - f (2D numpy array): function evaluated on a grid + - tgrid (2D numpy array): theta grid + - zgrid (2D numpy array): phi grid + + Returns> + - fsavg (1D numpy array): The flux surface average of f on each surface + given in lsurf + """ + + # Get jacobian + output = np.zeros(lsurf.shape) + for ii, ll in enumerate(lsurf): + sqrtg = self.jacobian( + lvol=ll-1, + sarr=np.array([1]), + tarr=tarr, + zarr=zarr + ) + + qrtg = np.squeeze(sqrtg) + + numerator = integrate.simps( + integrate.simps(np.multiply(f, qrtg), tarr, axis=0), zarr + ) + denumerator = integrate.simps( + integrate.simps(qrtg, tarr, axis=0), zarr + ) + + output[ii] = numerator / denumerator + + return output + + + + + + + + + diff --git a/Utilities/pythontools/py_spec/output/spec.py b/Utilities/pythontools/py_spec/output/spec.py index 733c48e0..99d06ca3 100644 --- a/Utilities/pythontools/py_spec/output/spec.py +++ b/Utilities/pythontools/py_spec/output/spec.py @@ -37,7 +37,14 @@ class SPECout: get_B, get_modB, get_B_covariant, - test_derivatives + test_derivatives, + get_surface_current_density, + get_surface, + get_RZ_derivatives, + get_volume, + get_average_beta, + get_peak_beta, + get_flux_surface_average ) from ._plot_modB import plot_modB from ._plot_iota import plot_iota @@ -100,9 +107,9 @@ def __init__(self, *args, **kwargs): # these define the target dimensions in the radial direction Nvol = self.input.physics.Nvol + Mvol = Nvol if self.input.physics.Lfreebound: - Nvol += 1 - self.input.physics.Nvol += 1 + Mvol += 1 Lrad = self.input.physics.Lrad @@ -122,7 +129,7 @@ def __init__(self, *args, **kwargs): # split up radial matrix dimension into list of matrices for each of the nested volumes start = 0 - for i in range(Nvol): + for i in range(Mvol): # vector potential cAte.append( np.atleast_2d(self.vector_potential.Ate)[ diff --git a/Utilities/pythontools/py_spec/tests/README.md b/Utilities/pythontools/py_spec/tests/README.md new file mode 100644 index 00000000..2211cf31 --- /dev/null +++ b/Utilities/pythontools/py_spec/tests/README.md @@ -0,0 +1,4 @@ +To run tests, do +``` +python -m unittest -v test_math.test_spec_fft +``` diff --git a/Utilities/pythontools/py_spec/tests/test_math/test_spec_fft.py b/Utilities/pythontools/py_spec/tests/test_math/test_spec_fft.py new file mode 100644 index 00000000..03cc77c6 --- /dev/null +++ b/Utilities/pythontools/py_spec/tests/test_math/test_spec_fft.py @@ -0,0 +1,99 @@ +import unittest +import numpy as np +from py_spec.math.spec_fft import spec_fft as fft +from py_spec.math.spec_invfft import spec_invfft as invfft + + +class fftTests(unittest.TestCase): + def test_fft_1d(self): + """ + Test spec_fft on an analytical function, 1D output + """ + + nt = 33 # Number of theta points + nz = 17 # Number of zeta points + tarr = np.linspace(0, 2*np.pi, nt, endpoint=False) + zarr = np.linspace(0, 2*np.pi, nz, endpoint=False) + + tgrid, zgrid = np.meshgrid( tarr, zarr ) # grid + + f = 0.3 \ + + 2*np.cos(tgrid) \ + - 3*np.cos(2*tgrid-zgrid) \ + + 1*np.cos(2*tgrid+zgrid) \ + - 3.8*np.sin(tgrid+2*zgrid) \ + - 2.4*np.sin(3*zgrid) + + efmn, ofmn, _, _ = fft( tarr, zarr, f, Mpol=2, Ntor=3 ) + + places=8 + self.assertAlmostEqual(efmn[ 0], 0.3, places=places) + self.assertAlmostEqual(efmn[ 7], 2, places=places) + self.assertAlmostEqual(efmn[13], 1, places=places) + self.assertAlmostEqual(efmn[15], -3, places=places) + self.assertAlmostEqual(ofmn[ 3], 2.4, places=places) + self.assertAlmostEqual(ofmn[ 5],-3.8, places=places) + + + def test_fft_2d(self): + """ + Test spec_fft on an analytical function, 2D output + """ + + nt = 32 # Number of theta points + nz = 21 # Number of zeta points + tarr = np.linspace(0, 2*np.pi, nt, endpoint=False) + zarr = np.linspace(0, 2*np.pi, nz, endpoint=True) + + tgrid, zgrid = np.meshgrid( tarr, zarr ) # grid + + f = 0.3 \ + + 2*np.cos(tgrid) \ + - 3*np.cos(2*tgrid-zgrid) \ + + 1*np.cos(2*tgrid+zgrid) \ + - 3.8*np.sin(tgrid+2*zgrid) \ + - 2.4*np.sin(3*zgrid) + + Mpol=4 + Ntor=8 + efmn, ofmn = fft( tarr, zarr, f, Mpol=Mpol, Ntor=Ntor, output='2D' ) + + places=8 + self.assertAlmostEqual(efmn[Ntor,0], 0.3, places=places) + self.assertAlmostEqual(efmn[Ntor,1], 2, places=places) + self.assertAlmostEqual(efmn[Ntor-1,2], 1, places=places) + self.assertAlmostEqual(efmn[Ntor+1,2], -3, places=places) + self.assertAlmostEqual(ofmn[Ntor-2,1],-3.8, places=places) + self.assertAlmostEqual(ofmn[Ntor+3,0], 2.4, places=places) + + + def test_invfft(self): + """ + Test spec_invfft using analytical function. + """ + + nt = 64 # Number of theta points + nz = 48 # Number of zeta points + tarr = np.linspace(0, 2*np.pi, nt, endpoint=False) + zarr = np.linspace(0, 2*np.pi, nz, endpoint=True) + + tgrid, zgrid = np.meshgrid( tarr, zarr ) # grid + + f = 0.3 \ + + 2*np.cos(tgrid) \ + - 3*np.cos(2*tgrid-zgrid) \ + + 1*np.cos(2*tgrid+zgrid) \ + - 3.8*np.sin(tgrid+2*zgrid) \ + - 2.4*np.sin(3*zgrid) + + Mpol=8 + Ntor=8 + efmn, ofmn, _im, _in = fft( tarr, zarr, f, Mpol=Mpol, Ntor=Ntor, output='1D' ) + + freal = invfft(tarr, zarr, efmn, ofmn, _im, _in) + + self.assertTrue( np.max(np.max(np.abs((freal-f)/f)))<1e-8 ) + + + + \ No newline at end of file diff --git a/Utilities/pythontools/requirements.txt b/Utilities/pythontools/requirements.txt index c8362d66..79349753 100644 --- a/Utilities/pythontools/requirements.txt +++ b/Utilities/pythontools/requirements.txt @@ -2,4 +2,8 @@ h5py matplotlib f90nml numpy + +# Version 1.7.0 or higher is required - otherwise scipy.integrate.simpson does not exist +scipy>=1.7.0 + coilpy diff --git a/Utilities/pythontools/setup.py b/Utilities/pythontools/setup.py index 8ffdf9b1..67d45afd 100644 --- a/Utilities/pythontools/setup.py +++ b/Utilities/pythontools/setup.py @@ -19,5 +19,5 @@ url="https://princetonuniversity.github.io/SPEC/", author="SPEC developers", license="GNU 3.0", - packages=setuptools.find_packages(), + packages=['py_spec', 'py_spec.input', 'py_spec.output', 'py_spec.ci'] ) diff --git a/src/dforce.f90 b/src/dforce.f90 index b1ef069b..78bc58db 100644 --- a/src/dforce.f90 +++ b/src/dforce.f90 @@ -439,12 +439,6 @@ subroutine dforce( NGdof, position, force, LComputeDerivatives, LComputeAxis) lBBintegral(1:Nvol) = lBBintegral(1:Nvol) * half - ! write(*,*) "lBBintegral" - ! write(*,*) lBBintegral(1:Nvol) - - ! vflag = 1 ! this flag instructs volume to continue even if the volume is invalid; - ! WCALL( dforce, volume, ( vvol, vflag ) ) ! compute volume; this corrupts calculation of dvolume; - voltotal = 0.0 do vvol = 1, Mvol @@ -461,14 +455,9 @@ subroutine dforce( NGdof, position, force, LComputeDerivatives, LComputeAxis) betavol(vvol) = press * vvolume(vvol) / lBBintegral(vvol) betavol(vvol) = betavol(vvol) * vvolume(vvol) - ! write(*,*) "vvol", vvol, "lBBintegral", lBBintegral(vvol), "volume", vvolume(vvol), "press", press - ! write(*,*) "vvol", vvol, "beta", betavol(vvol) / vvolume(vvol) - voltotal = voltotal+vvolume(vvol) - enddo - ! Calculate total beta which is obtained from individual betas ! write(*,*) "all betas", betavol(1:Nvol) BetaTotal = sum(betavol(1:Nvol))/voltotal @@ -476,8 +465,8 @@ subroutine dforce( NGdof, position, force, LComputeDerivatives, LComputeAxis) ! write(*,*)"total vol", voltotal Energy = sum( lBBintegral(1:Nvol) ) ! should also compute beta; - ! write(*,*)"total Energy", Energy + !-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-! ! --------------- diff --git a/src/hesian.f90 b/src/hesian.f90 index 68f7f5fa..fdc6481b 100644 --- a/src/hesian.f90 +++ b/src/hesian.f90 @@ -185,8 +185,8 @@ subroutine hesian( NGdof, position, Mvol, mn, LGdof ) write(ounit,1001) cput-cpus, myid, vvol, irz, mi, ni, ( oBBdRZ(vvol,1,idof) + oBBdRZ(vvol+1,0,idof) ) / psifactor(ii,vvol) ! ENERGY GRADIENT; FATAL( hesian, Igeometry.eq.1, Cartesian geometry does not need regularization factor ) -1000 format("hesian : ",f10.2," : ":"myid=",i3," ; ":"vvol=",i3," ; ":"irz="i2" ; (",i3," ,",i3," ) ; "a17" ["es15.7","es15.7" ]") -1001 format("hesian : ",f10.2," : ":"myid=",i3," ; ":"vvol=",i3," ; ":"irz="i2" ; (",i3," ,",i3," ) ; "es15.7" ; ") + 1000 format("hesian : ",f10.2," : ":"myid=",i3," ; ":"vvol=",i3," ; ":"irz="i2" ; (",i3," ,",i3," ) ; "a17" ["es15.7","es15.7" ]") + 1001 format("hesian : ",f10.2," : ":"myid=",i3," ; ":"vvol=",i3," ; ":"irz="i2" ; (",i3," ,",i3," ) ; "es15.7" ; ") enddo ! end of do issym; 26 Feb 13; diff --git a/src/newton.f90 b/src/newton.f90 index f50dbb0e..4e9f275d 100644 --- a/src/newton.f90 +++ b/src/newton.f90 @@ -97,8 +97,7 @@ subroutine newton( NGdof, position, ihybrd ) INTEGER :: ML, MU ! required for only Lc05ndf; - ! LOGICAL :: Lexit = .true. ! perhaps this could be made user input; - LOGICAL :: Lexit = .false. ! Erol modification, so hessian is printed even w/ initial force balance + LOGICAL :: Lexit = .false. ! if false, hessian is printed even with initial force balance LOGICAL :: LComputeAxis INTEGER :: nprint = 1, nfev, njev @@ -334,7 +333,7 @@ subroutine writereadgf( readorwrite, NGdof , ireadhessian ) case( 'W' ) ! will write derivative matrix to file; - !! reset I/O state + ! reset I/O state !ios = 0 !open( dunit, file="."//trim(ext)//".sp.DF", status="replace", form="unformatted", iostat=ios ) ! save derivative matrix to file; diff --git a/src/xspech.f90 b/src/xspech.f90 index 1bb7b694..0ceb417c 100644 --- a/src/xspech.f90 +++ b/src/xspech.f90 @@ -308,7 +308,7 @@ subroutine spec Lcoordinatesingularity, Lplasmaregion, Lvacuumregion, & dtflux, dpflux, & ImagneticOK, & - ForceErr, & + ForceErr, BnsErr,& efmn, ofmn, cfmn, sfmn, & iBns, iBnc, iVns, iVnc, & Ate, Aze, Ato, Azo, & ! only required for debugging; 09 Mar 17; @@ -326,7 +326,7 @@ subroutine spec LOGICAL :: LComputeDerivatives, LContinueFreeboundaryIterations, exist, LupdateBn, LComputeAxis INTEGER :: imn, lmn, lNfp, lim, lin, ii, ideriv, stat INTEGER :: vvol, ifail, wflag, iflag, vflag - REAL :: rflag, lastcpu, bnserr, lRwc, lRws, lZwc, lZws, lItor, lGpol, lgBc, lgBs + REAL :: rflag, lastcpu, lRwc, lRws, lZwc, lZws, lItor, lGpol, lgBc, lgBs REAL, allocatable :: position(:), gradient(:) CHARACTER :: pack INTEGER :: Lfindzero_old, mfreeits_old From b8420c7e80b2380f296347d0e1b1e8f19afedb97 Mon Sep 17 00:00:00 2001 From: ErolBa Date: Mon, 11 Mar 2024 12:40:13 +0100 Subject: [PATCH 21/36] utilities --- Utilities/matlabtools/get_full_field.m | 104 ------------- Utilities/matlabtools/get_spec_Bgrid.m | 46 ------ Utilities/matlabtools/get_spec_radius.m | 56 ------- .../get_spec_regularization_factor.m | 137 ------------------ Utilities/matlabtools/get_spec_rtarr.m | 66 --------- Utilities/matlabtools/get_spec_rzarr.m | 63 -------- .../matlabtools/get_spec_surface_current.m | 66 --------- Utilities/matlabtools/plot_spec_Bfield.m | 66 --------- Utilities/matlabtools/plot_spec_hessian.m | 21 --- Utilities/matlabtools/plot_spec_outfluxfun.m | 41 ------ Utilities/matlabtools/plot_spec_surfcurent.m | 49 ------- Utilities/matlabtools/read_hdf5.m | 81 ----------- Utilities/matlabtools/read_spec_hessian.m | 82 ----------- .../matlabtools/run_spec_iter_fixtorcurr.m | 137 ------------------ Utilities/matlabtools/write_spec_input_L0.m | 113 --------------- Utilities/matlabtools/write_spec_input_L1.m | 125 ---------------- Utilities/matlabtools/write_spec_input_L3.m | 131 ----------------- 17 files changed, 1384 deletions(-) delete mode 100644 Utilities/matlabtools/get_full_field.m delete mode 100644 Utilities/matlabtools/get_spec_Bgrid.m delete mode 100644 Utilities/matlabtools/get_spec_radius.m delete mode 100644 Utilities/matlabtools/get_spec_regularization_factor.m delete mode 100644 Utilities/matlabtools/get_spec_rtarr.m delete mode 100644 Utilities/matlabtools/get_spec_rzarr.m delete mode 100644 Utilities/matlabtools/get_spec_surface_current.m delete mode 100644 Utilities/matlabtools/plot_spec_Bfield.m delete mode 100644 Utilities/matlabtools/plot_spec_hessian.m delete mode 100644 Utilities/matlabtools/plot_spec_outfluxfun.m delete mode 100644 Utilities/matlabtools/plot_spec_surfcurent.m delete mode 100644 Utilities/matlabtools/read_hdf5.m delete mode 100644 Utilities/matlabtools/read_spec_hessian.m delete mode 100644 Utilities/matlabtools/run_spec_iter_fixtorcurr.m delete mode 100644 Utilities/matlabtools/write_spec_input_L0.m delete mode 100644 Utilities/matlabtools/write_spec_input_L1.m delete mode 100644 Utilities/matlabtools/write_spec_input_L3.m diff --git a/Utilities/matlabtools/get_full_field.m b/Utilities/matlabtools/get_full_field.m deleted file mode 100644 index 0fbb0138..00000000 --- a/Utilities/matlabtools/get_full_field.m +++ /dev/null @@ -1,104 +0,0 @@ -function B = get_full_field(data, r, theta, zeta, nr) - -% -% GET_FULL_FIELD( DATA, R, THETA, ZETA, NR ) -% ========================================== -% -% Return SPEC magnetic field solution componants as a function of r, theta, -% zeta. The coordinate r is constructed from the radial position of the -% volume interface for a given pair (theta, zeta) and from the coordinate -% s. -% -% INPUT -% ----- -% data: data obtained from read_spec(filename) -% r: Radial coordinate (array of doubles) -% theta: Theta coordinate (double) -% zeta: Zeta coordinate (double) -% nr: Number of points in each volume for radial interpolation -% -% OUTPUT -% ------ -% B: 3xlength(r)xlength(theta)xlength array containing the B field solution -% interpolated at r -% -% Written by A.Baillod(2019) - - -% Load data -G = data.input.physics.Igeometry; -Nvol = data.output.Mvol; - -epsilon = 1E-16; - -nt = length(theta); -nz = length(zeta); - -B_temp = zeros(3, nr*Nvol, nt, nz); % Allocate memory -r_temp = zeros(1, nr*Nvol, nt, nz); % Allocate memory - -iimin = 1; -iimax = 0; - -r0 = get_spec_radius(data, theta, zeta, 0); -B = zeros(3,length(r),nt,nz); -for i=1:Nvol - - % if first volume, don't take rmin=0 - if i==1 - rmin = epsilon; - else - [ri, zi] = get_spec_radius(data, theta, zeta, i-1); - rmin = sqrt((ri-r0)^2+zi^2); - end - - [ri, zi] = get_spec_radius(data, theta, zeta, i); - rmax = sqrt((ri-r0)^2+zi^2); - - r_vol = linspace(rmin, rmax, nr+1); % Minor radius - r_vol = r_vol(2:end); - - if i==1 - if G == 1 - sarr = 2.0 * (r_vol - rmin) ./ (rmax - rmin) - 1; - else - sarr = 2.0 * ((r_vol - rmin) ./ (rmax - rmin)).^2 - 1; - end - else - sarr = 2.0 * (r_vol - rmin) ./ (rmax - rmin) - 1; - end - Bcontrav = get_spec_magfield(data, i, sarr, theta, zeta); - - % Generate radial coordinate array - iimax = iimax + length(r_vol); - r_temp(iimin:iimax) = r_vol; - - % And convert it to covariant basis (normalized here) - B_cov = contra2cov(data, i, Bcontrav, sarr, theta, zeta, 1); - - B_temp(1, iimin:iimax, :, :) = B_cov{1}; - B_temp(2, iimin:iimax, :, :) = B_cov{2}; - B_temp(3, iimin:iimax, :, :) = B_cov{3}; - - iimin = iimin + length(r_vol); - - - for comp = 1:3 - ind = find(r<=rmax); - r_int = r(ind); - ind = find(r_int>=rmin); - r_int = r_int(ind); - - for j = 1:nt - for k = 1:nz - B(comp, ind, j, k) = interp1(r_vol, B_cov{comp}(:,j,k), r_int, 'spline'); - end - end - end -end - - - - - - diff --git a/Utilities/matlabtools/get_spec_Bgrid.m b/Utilities/matlabtools/get_spec_Bgrid.m deleted file mode 100644 index 3a23c259..00000000 --- a/Utilities/matlabtools/get_spec_Bgrid.m +++ /dev/null @@ -1,46 +0,0 @@ -function bdata = get_spec_Bgrid(data,nz0,lvol) - -% -% GET_SPEC_BGRID( DATA, NZ0, LVOL ) -% ================================= -% -% Obtains the canonical cylindrical components of B, namely (B^R, R*B^phi, B^Z), on the coordinate grid points -% -% INPUT -% ----- -% -data : must be produced by calling read_spec(filename) -% -nz0 : toroidal plane number at which B is obtained (nz0=1 at toroidal angle phi=0) -% -lvol : volume number in which B is obtained -% -% OUTPUT -% ------ -% -bdata : cell of size 5 containing the values of R, Z, B^R, R*B^phi, B^Z on the grid points -% -% written by J.Loizu (2018) - -Lrad = data.input.physics.Lrad; -Nt = data.grid.Nt; -Nz = data.grid.Nz; - -Rij = data.grid.Rij; -Zij = data.grid.Zij; -BR = data.grid.BR; -Bp = data.grid.Bp; -BZ = data.grid.BZ; - -iz = nz0-1; -ngrid = Lrad(lvol)+1; - -if(lvol==1) - nstart = 2; -else - nstart = 1; -end - -bdata{1} = squeeze(Rij(lvol,1+Nt*iz:(iz+1)*Nt,nstart:ngrid)); -bdata{2} = squeeze(Zij(lvol,1+Nt*iz:(iz+1)*Nt,nstart:ngrid)); -bdata{3} = squeeze(BR(lvol,1+Nt*iz:(iz+1)*Nt,nstart:ngrid)); -bdata{4} = squeeze(Bp(lvol,1+Nt*iz:(iz+1)*Nt,nstart:ngrid)).*bdata{1}; -bdata{5} = squeeze(BZ(lvol,1+Nt*iz:(iz+1)*Nt,nstart:ngrid)); - - diff --git a/Utilities/matlabtools/get_spec_radius.m b/Utilities/matlabtools/get_spec_radius.m deleted file mode 100644 index 09db55be..00000000 --- a/Utilities/matlabtools/get_spec_radius.m +++ /dev/null @@ -1,56 +0,0 @@ -function [r_out, z_out] = get_spec_radius(data, theta, zeta, vol) - -% -% GET_SPEC_RADIUS( DATA, THETA, ZETA, VOL ) -% ========================================= -% -% Return the radial position of a KAM surface for a given theta, zeta and -% Nvol -% -% INPUT -% ----- -% data Obtained via read_spec(filename) -% theta: Poloidal angle -% zeta: Toroidal angle -% vol: Volume number -% -% OUPUT -% ----- -% r_out: Radial position of the KAM surface - - -% Load a bunch of stuff - -mn = data.output.mn; -im = data.output.im; -in = data.output.in; -Rmn = data.output.Rbc; -Zmn = data.output.Zbs; -G = data.input.physics.Igeometry; - - -switch G - case 1 - r_out = 0; - - for k=1:mn - r_out = r_out + Rmn(k, vol+1) * cos(double(im(k)) * theta - double(in(k)) * zeta); - end - z_out = 0; - case 2 - r_out = 0; - - for k=1:mn - r_out = r_out + Rmn(k, vol+1) * cos(double(im(k)) * theta - double(in(k)) * zeta); - end - z_out = 0; - case 3 - r_out = 0; - z_out = 0; - - for k=1:mn - r_out = r_out + Rmn(k, vol+1) * cos(double(im(k)) * theta - double(in(k)) * zeta); - z_out = z_out + Zmn(k, vol+1) * sin(double(im(k)) * theta - double(in(k)) * zeta); - end - -end diff --git a/Utilities/matlabtools/get_spec_regularization_factor.m b/Utilities/matlabtools/get_spec_regularization_factor.m deleted file mode 100644 index e64f4f04..00000000 --- a/Utilities/matlabtools/get_spec_regularization_factor.m +++ /dev/null @@ -1,137 +0,0 @@ -function fac = get_spec_regularization_factor(data, lvol, sarr, ForG) -% -% -% Computes the regularisation factor in the correct geometry -% -% INPUT -% ----- -% data: Produced by fdata_from_data(data); -% lvol: Volume number -% sarr: s-coordinate array, shape (ns, 1) -% ForG: 'F' for field reg. factor, 'G' for geometry reg. factor -% -% OUPUT -% ----- -% fac: mnx2 cell array composed of fj and its derivatives -% -% -% Written by A.Baillod (2019) -% -% - -%sarr = transpose(sarr); - -Igeometry= data.input.physics.Igeometry; -mn = data.output.mn; -im = double(data.output.im); -ns = length(sarr); -fac = cell(mn,2); -sbar = (1+sarr)/2.0; -Mregular= double(data.input.numerics.Mregular); - - -regumm = im / 2.0; -if Mregular>1 - ind = find(regumm>Mregular); - regumm(ind) = Mregular / 2.0; -end - -halfmm = im / 2.0; - - - -if ForG=='G' - switch Igeometry - case 1 % Slab geometry - - for j=1:mn - fac{j}{1} = sbar; - fac{j}{2} = 0.5*ones(ns,1); - end - - case 2 % Cylindrical geometry - %TODO: add glab if Lextrap is not set to 1! - for j=1:mn - if(lvol==1) - if im(j)==0 - fac{j}{1} = sqrt(sbar); - fac{j}{2} = 0.25 * fac{j}{1} ./ sbar; - else - fac{j}{1} = sbar.^halfmm(j); - fac{j}{2} = 0.5 * halfmm(j) * fac{j}{1} ./ sbar; - end - else - fac{j}{1} = sbar; - fac{j}{2} = 0.5 * ones(ns,1); - end - end - - case 3 % Toroidal geometry - - for j=1:mn - if lvol==1 %coordinate singularity - if im(j)==0 - fac{j}{1} = sbar; - fac{j}{2} = 0.5; - else - fac{j}{1} = sbar.^halfmm(j); - fac{j}{2} = 0.5 * halfmm(j) * fac{j}{1} ./ sbar; - end - else - fac{j}{1} = sbar; - fac{j}{2} = 0.5 * ones(ns,1); - end - end - otherwise - error('Unsupported geometry in get_spec_regularisation_factor') - end - - - -elseif ForG=='F' - switch Igeometry - case 1 - for j=1:mn - fac{j}{1} = ones(ns,1); - fac{j}{2} = zeros(ns,1); - end - - case 2 - for j=1:mn - if lvol==1 % coordinate singularity - if im(j)==0 - fac{j}{1} = 1; - fac{j}{2} = 0; - else - fac{j}{1} = sbar.^regumm(j); - fac{j}{2} = 0.5 * regumm(j) * fac{j}{1} ./ sbar; - end - else - fac{j}{1} = 1; - fac{j}{2} = 0; - end - end - - case 3 - for j=1:mn - if lvol==1 % coordinate singularity - if im(j)==0 - fac{j}{1} = 1; - fac{j}{2} = 0; - else - fac{j}{1} = sbar.^regumm(j); - fac{j}{2} = 0.5 * regumm(j) * fac{j}{1} ./ sbar; - end - else - fac{j}{1} = 1; - fac{j}{2} = 0; - end - end - - otherwise - error('Unsupported geometry in get_spec_regularisation_factor') - end - -else - error('Unsupported ForG value in get_spec_regularisation_factor.') -end diff --git a/Utilities/matlabtools/get_spec_rtarr.m b/Utilities/matlabtools/get_spec_rtarr.m deleted file mode 100644 index f9e557f3..00000000 --- a/Utilities/matlabtools/get_spec_rtarr.m +++ /dev/null @@ -1,66 +0,0 @@ -function rtdata = get_spec_rtarr(data,lvol,sarr,tarr,zarr0) - -% -% GET_SPEC_RTARR( DATA, LVOL, SARR, TARR, ZARR0 ) -% =============================================== -% -% Transforms (s,theta) array into (R,theta) array in volume number lvol in slab or cylindrical geometry -% -% INPUT -% ----- -% -data : must be produced by calling e.g. read_spec(filename) -% -lvol : volume number -% -sarr : is the array of values for the s-coordinate -% -tarr : is the array of values for the theta-coordinate -% -zarr : is the array of values for the zeta-coordinate -% -% OUTPUT -% ------ -% -rtdata : array with (R,theta,dRds) data array with size 3*ns*nt where ns=length(sarr),nt=length(tarr) -% -% Note: Stellarator symmetry is assumed -% -% written by J.Loizu (2018) -% updated by J.Loizu (2020) - - -Rac = data.output.Rbc(:,lvol); % inner volume boundary harmonics -Rbc = data.output.Rbc(:,lvol+1); % outer volume boundary harmonics - -if(size(sarr,1)==1) -sarr = transpose(sarr); -end - -ns = length(sarr); -nt = length(tarr); -sbar = (sarr+1)/2; - -mn = data.output.mn; -im = double(data.output.im); -in = double(data.output.in); - -Rarr = zeros(ns,nt); % allocate data for R-array -Tarr = zeros(ns,nt); % allocate data for theta-array -dRarr = zeros(ns,nt); % allocate data for R-array derivative (in s) - - - -% Construct regularization factors - -fac = get_spec_regularization_factor(data, lvol, sarr, 'G'); - -% Construct (R,theta) coordinates array - -for j=1:mn - for it=1:nt - cosa = cos(im(j)*tarr(it)-in(j)*zarr0); - sina = sin(im(j)*tarr(it)-in(j)*zarr0); - Rarr(:,it) = Rarr(:,it) + (Rac(j) + fac{j}{1}.*(Rbc(j)-Rac(j)) )*cosa; - dRarr(:,it) = dRarr(:,it) + fac{j}{2}*(Rbc(j)-Rac(j))*cosa; - Tarr(:,it) = tarr(it); - end -end - -rtdata{1} = Rarr; -rtdata{2} = Tarr; -rtdata{3} = dRarr; diff --git a/Utilities/matlabtools/get_spec_rzarr.m b/Utilities/matlabtools/get_spec_rzarr.m deleted file mode 100644 index 65dc9b8e..00000000 --- a/Utilities/matlabtools/get_spec_rzarr.m +++ /dev/null @@ -1,63 +0,0 @@ -function rzdata = get_spec_rzarr(data,lvol,sarr,tarr,zarr) - -% -% GET_SPEC_RZARR( DATA, LVOL, SARR, TARR, ZARR ) -% ============================================== -% -% Transforms (s,theta,zeta) array into (R,Z) array in volume number lvol -% -% INPUT -% ----- -% -data : must be produced by calling e.g. read_spec(filename) -% -lvol : volume number -% -sarr : is the array of values for the s-coordinate -% -tarr : is the array of values for the theta-coordinate -% -zarr : is the array of values for the zeta-coordinate -% -% OUTPUT -% ------ -% -rzdata : array with (R,Z) data array with size 2*ns*nt*nz where ns=length(sarr),nt=length(zarr),nt=length(zarr) -% -% Note: Stellarator symmetry is assumed -% -% written by J.Loizu (2016) - - -Rac = data.output.Rbc(:,lvol); % inner volume boundary harmonics -Zas = data.output.Zbs(:,lvol); -Rbc = data.output.Rbc(:,lvol+1); % outer volume boundary harmonics -Zbs = data.output.Zbs(:,lvol+1); - -sarr = transpose(sarr); -ns = length(sarr); -nt = length(tarr); -nz = length(zarr); -sbar = (sarr+1)/2; - -mn = data.output.mn; -im = double(data.output.im); -in = double(data.output.in); - -Rarr = zeros(ns,nt,nz); % allocate data for R-array -Zarr = zeros(ns,nt,nz); % allocate data for Z-array - - -% Construct REG FACTOR - -fac = get_spec_regularisation_factor(data, lvol, sarr', 'G'); - -% Construct (R,Z) coordinates array - -for j=1:mn - for it=1:nt - for iz=1:nz - cosa = cos(im(j)*tarr(it)-in(j)*zarr(iz)); - sina = sin(im(j)*tarr(it)-in(j)*zarr(iz)); - Rarr(:,it,iz) = Rarr(:,it,iz) + (Rac(j) + fac{j}{1}.*(Rbc(j)-Rac(j)) )*cosa; - Zarr(:,it,iz) = Zarr(:,it,iz) + (Zas(j) + fac{j}{1}.*(Zbs(j)-Zas(j)) )*sina; - end - end -end - -rzdata{1} = Rarr; -rzdata{2} = Zarr; diff --git a/Utilities/matlabtools/get_spec_surface_current.m b/Utilities/matlabtools/get_spec_surface_current.m deleted file mode 100644 index f7ebf12e..00000000 --- a/Utilities/matlabtools/get_spec_surface_current.m +++ /dev/null @@ -1,66 +0,0 @@ -function [tflux, IPDt] = get_spec_surface_current(data, ns, nt, zeta) - -% -% GET_SPEC_SURFACE_CURRENT( DATA, NS, NT, ZETA ) -% ============================================== -% -% OUTDATED - should directly do 2*pi*[[B_\theta]] -% -% Returns the sheet current flowing through each interface, normalized by -% mu_0. This routine computes the actual integral of the poloidal field to -% compute the current via Ampere's law. This requires to specify zeta; -% however, since the surface current is a flux function, zeta should not -% have any influence on the result. -% -% INPUT -% ----- -% data: data obtained via read_spec(filename) -% ns: Radial resolution -% nt: Poloidal resolution -% zeta: Toroidal angle - see introduction remark -% -% OUTPUT -% ------ -% tflux: The toroidal flux enclosed by each interface (1xNvol) -% IPDt: The toroidal surface current in each interface (1xNvol-1), -% normalized by mu_0 -% -% Written by A.Baillod (2019) - - -% Constant definition -mu0 = 4*pi*1E-7; -epsilon = 1E-5; - -% Data loading -Nvol = data.output.Mvol; % Total number of volumes -sarr = linspace(-1, 1, ns); - -% Allocate memory -Bcov = cell(1, Nvol); - -theta = linspace(0, 2*pi, nt); - -IPDt = zeros(1, Nvol-1); - -% Get magnetic field -for ivol=1:Nvol - if ivol==1 - sarr(1)=-1+epsilon; - else - sarr(1)=-1; - end - - temp = get_spec_magfield(data, ivol, sarr, theta, zeta); - - Bcov{ivol} = contra2cov(data, ivol, temp, sarr, theta, zeta, 0); -end - -for ivol=1:Nvol-1 - dBtheta = -Bcov{ivol}{2}(end,:,1) + Bcov{ivol+1}{2}(1,:,1); - IPDt(ivol) = trapz(theta, dBtheta); -end - -tflux = data.output.tflux; - -end diff --git a/Utilities/matlabtools/plot_spec_Bfield.m b/Utilities/matlabtools/plot_spec_Bfield.m deleted file mode 100644 index 4d97c366..00000000 --- a/Utilities/matlabtools/plot_spec_Bfield.m +++ /dev/null @@ -1,66 +0,0 @@ -function plot_spec_Bfield(data, component, theta, phi, nr, newfig) - -% -% PLOT_SPEC_BFIELD( DATA, COMPONENT, THETA, PHI, NR, NEWFIG ) -% =========================================================== -% -% Plot SPEC magnetic field solution -% -% INPUT -% ----- -% data: data obtained from read_spec(filename) -% component: ='psi' to plot r-component, 'theta' to plot theta component -% and 'phi' to plot phi component, ='all' for all components -% theta: Angle theta at which the field is plotted -% phi: Angle phi at which the field is plotted -% nr: Number of radial points -% newfig: open (=1) a new figure or use the current figure and hold -% on (=0) or old off (=2) -% -% -% Written by A.Baillod (2019) - - switch newfig - case 0 - hold on; - case 1 - figure - hold on; - case 2 - hold off; - end - - [r_end, z_end] = get_spec_radius(data, theta, phi, data.output.Mvol); - [r_start, z_start] = get_spec_radius(data, theta, phi, 0); - a = sqrt((r_end-r_start)^2 + (z_end-z_start)^2); - - r = linspace(0, a, nr); - B = get_full_field(data, r, theta, phi, nr); - - switch component - case 'psi' - plot(r, B(1,:)) - ylab = ylabel('$B_\psi$ [T]'); - case 'theta' - plot(r, B(2,:)) - ylab = ylabel('$B_\theta$ [T]'); - case 'phi' - plot(r, B(3,:)) - ylab = ylabel('$B_\zeta$ [T]'); - case 'all' - plot(r, B(1,:)) - hold on; - plot(r, B(2,:)) - plot(r, B(3,:)) - ylab = ylabel('B [T]'); - leg = legend('$B_\psi$', '$B_\theta$','$B_\zeta$' ); - set(leg,'Interpreter','latex'); - end - - xlab = xlabel('Distance to magnetic axis [m]'); - - set(gca, 'FontSize', 14) - set(xlab,'Interpreter','latex'); - set(ylab,'Interpreter','latex'); - -end diff --git a/Utilities/matlabtools/plot_spec_hessian.m b/Utilities/matlabtools/plot_spec_hessian.m deleted file mode 100644 index 49b58995..00000000 --- a/Utilities/matlabtools/plot_spec_hessian.m +++ /dev/null @@ -1,21 +0,0 @@ -function plot_spec_hessian(data) - -% -% PLOT_SPEC_HESSIAN( DATA ) -% ========================= -% -% Plots the hessian matrix elements -% -% INPUT -% ----- -% -data : must be produced by calling read_spec_hessian(filename) -% -% written by J.Loizu (2017) - -figure - -imagesc(data) - -colorbar - -%set(gca, 'CLim', [-0.1 0.1]); diff --git a/Utilities/matlabtools/plot_spec_outfluxfun.m b/Utilities/matlabtools/plot_spec_outfluxfun.m deleted file mode 100644 index c3e28d75..00000000 --- a/Utilities/matlabtools/plot_spec_outfluxfun.m +++ /dev/null @@ -1,41 +0,0 @@ -function plot_spec_outfluxfun(data,ns,nt,z0,ncont,newfig) - -% -% PLOT_SPEC_OUTFLUXFUN( DATA, NS, NT, Z0, NCONT, NEWFIG ) -% ======================================================= -% -% Plots iso-contours of Az on a given cross-section -% -% INPUT -% ----- -% -data : must be produced by calling read_spec(filename) -% -ns : radial resolution for construction of Az -% -nt : poloidal resolution for construction of Az -% -z0 : toroidal angle at which Az is evaluated -% -ncont : number of iso-contour lines -% -newfig : flag for whether a new figure should be open (=1) or not(=0) -% -% Note: should only work for free-boundary equilibria -% Note: poloidal flux function is psi=-A_phi if A_phi is the covariant component and psi=-R*A_phi if A_phi is the canonical component -% -% written by J.Loizu (2018) - - -Nvol = data.input.physics.Nvol; - -lvol = Nvol+1; - -sarr = linspace(-1,1,ns); - -tarr = linspace(0,2*pi,nt); - -acov = get_spec_vecpot(data,lvol,sarr,tarr,z0); -rz = get_spec_rzarr( data,lvol,sarr,tarr,z0); - -ffun = -acov{2}; - -if(newfig==1) - figure; hold on; -end - -contour(rz{1},rz{2},ffun,ncont,'k') diff --git a/Utilities/matlabtools/plot_spec_surfcurent.m b/Utilities/matlabtools/plot_spec_surfcurent.m deleted file mode 100644 index feb04142..00000000 --- a/Utilities/matlabtools/plot_spec_surfcurent.m +++ /dev/null @@ -1,49 +0,0 @@ -function plot_spec_surfcurent(data, ns, nt, zeta, newfig) - -% -% PLOT_SPEC_SURFCURRENT( DATA, NS, NT, ZETA, NEWFIG ) -% =================================================== -% -% Plot pressure-driven currents located at each volume interface -% -% INPUT -% ----- -% -data : data obtained via read_spec(filename) -% -ns : number of radial interpolation points -% -nt : number of poloidal interpolation points -% -zeta : toroidal angle -% -newfig : plots on an existing figure (=0), a new figure (=1) or -% overwrites last figure (=2) -% -% written by A.Baillod (2019) -% - -[tflux, IPDt] = get_spec_surface_current(data, ns, nt, zeta); - -Nvol = data.input.physics.Nvol + data.input.physics.Lfreebound; - -switch newfig - case 0 - hold on - case 1 - figure - hold on - case 2 - hold off -end - -%plot(tflux(1:end-1), IPDt, '*') -bar(IPDt, 'BarWidth', 0.3); -grid on -%xl = xlabel('$\psi_t / \psi_{edge}$'); -xl = xlabel('Surface label'); -yl = ylabel('$\mu_0 I_\mathcal{S}$[A]'); -xlim([0, Nvol]) - -set(xl, 'Interpreter', 'latex'); -set(yl, 'Interpreter', 'latex'); - -set(gca, 'FontSize', 14) - - -end diff --git a/Utilities/matlabtools/read_hdf5.m b/Utilities/matlabtools/read_hdf5.m deleted file mode 100644 index 7390b05f..00000000 --- a/Utilities/matlabtools/read_hdf5.m +++ /dev/null @@ -1,81 +0,0 @@ -function data = read_hdf5(filename) - -% -% OUTDATED ? -% -% READ_HDF5( FILENAME ) -% ===================== -% -% The READ_HDF5 function reads an HDF5 file and returns the contents of -% that file as the fields of a structure. Groups are treated as elements -% of their parent structure. If the file file cannot be opened a -1 is -% returned. -% -% Example -% data=read_hdf5('input.h5'); -% -% Version 1.0 -% Maintained by: Samuel Lazerson (lazerson@pppl.gov) -% Date 05/02/2012 - - -% Try to read the file first -try - data_info = h5info(filename,'/'); -catch h5info_error - data=-1; - disp(['ERROR: Opening HDF5 File: ' filename]); - disp([' -identifier: ' h5info_error.identifier]); - disp([' -message: ' h5info_error.message]); - disp(' For information type: help read_hdf5'); - return -end - -ngroups = length(data_info.Groups); -nvars = length(data_info.Datasets); -% Get root datasets -for i = 1: nvars - data.([data_info.Datasets(i).Name]) = h5read(filename,['/' data_info.Datasets(i).Name]); - natts = length(data_info.Datasets(i).Attributes); - for j=1:natts - data.([data_info.Datasets(i).Attributes(j).Name]) = data_info.Datasets(i).Attributes(j).Value{1}; - end - % Fix by Weatherby,Gerard 10/17/13 - %for j=2:natts - % data.([data_info.Datasets(i).Attributes(j).Name]) = data_info.Datasets(i).Attributes(j).Value{1}; - %end - %if natts == 1 - % data.([data_info.Datasets(i).Attributes(1).Name]) = data_info.Datasets(i).Attributes(1); - %end -end - -% Get each subgroup -if ngroups > 0 - for i = 1 : ngroups - data.([data_info.Groups(i).Name]) = getGroup(['/' data_info.Groups(i).Name]); - end -end -return -end - -function data = getGroup(root) -data_info = h5info(filename,root); -ngroups = length(data_info.Groups); -nvars = length(data_info.Datasets); -% Get root datasets -for i = 1: nvars - data.([data_info.Datasets(i).Name]) = h5read(filename,[root data_info.Datasets(i).Name]); - natts = length(data_info.Datasets(i).Attributes); - for j=1:natts - data.([data_info.Datasets(i).Attributes(j).Name]) = data_info.Datasets(i).Attributes(j).Value{1}; - end -end - -% Get each subgroup -if ngroups > 0 - for i = 1 : ngroups - data.([data_info.Groups(i).Name]) = getGroup(['/' data_info.Groups(i).Name]); - end -end -return -end diff --git a/Utilities/matlabtools/read_spec_hessian.m b/Utilities/matlabtools/read_spec_hessian.m deleted file mode 100644 index 7a7d805b..00000000 --- a/Utilities/matlabtools/read_spec_hessian.m +++ /dev/null @@ -1,82 +0,0 @@ -function Hmatrix = read_spec_hessian(filename) - -% -% READ_SPEC_HESSIAN( FILENAME ) -% ============================= -% -% Reads Hessian matrix using output from SPEC -% -% INPUT -% ----- -% - filename : path to the hdf5 output file (e.g. 'testcase.sp.h5') -% -% OUTPUT -% ------ -% - Hmatrix : Hessian matrix, which can be fed into several routines for analyzing and ploting -% -% written by J.Loizu (2017) -% updated by J.Loizu (2020) - - -global machform; - -machform = 's'; - - -% Read the hessian file - -machine_format = machform; % needs to be 's' (intel) or 'a' (gnu); format is swapped if an error occurs -triedallform = 0; % whether all formats have been tried (1) or not (0) -success = 0; -int_format = 'int32'; -float_format = 'float64'; -spacer_format = 'int32'; - - -while(success==0) -try - - if(machine_format ~= machform) - machine_format = machform; % update value - end - hessian_file = ['.' filename(1:length(filename)-6) '.GF.ma']; - fid = fopen(hessian_file,'r',machine_format); - if (fid > 0) - % Read through NGdof - fread(fid,1,spacer_format); - ngdof = fread(fid,1,int_format); % NGdof - fread(fid,1,spacer_format); - else - disp(' - File does not exist'); break; - end - - fread(fid,1,spacer_format); - Hmatrix = fread(fid,[ngdof ngdof],float_format); - fread(fid,1,spacer_format); - - success=1; - -catch - - if(triedallform==1) - disp(' - Could not read hessian file'); break; - end - if(machform~='s') - machform ='s'; - triedallform = 1; - else - machform ='a'; - triedallform = 1; - end - if (fid ~= -1) - fclose(fid); - fid = -1; - end -end - -end - -if (fid ~= -1) - fclose(fid); -end - diff --git a/Utilities/matlabtools/run_spec_iter_fixtorcurr.m b/Utilities/matlabtools/run_spec_iter_fixtorcurr.m deleted file mode 100644 index 94d61684..00000000 --- a/Utilities/matlabtools/run_spec_iter_fixtorcurr.m +++ /dev/null @@ -1,137 +0,0 @@ -function currents = run_spec_iter_fixtorcurr(execom,inputroot,Nvol,Lrad,nptr,startit,nit,Iref) - - -% Runs SPEC iteratively to find nearby equilibria with mu=0 in each volume and net toroidal surface-current Iref (units mu0*I). -% Target current is achieved by iterating on the enclosed poloidal flux. -% -% INPUT -% - execom : command for the execution of SPEC executable (e.g. './xspec' or 'mpirun -n 2 ./xspec') -% - inputroot : spec input file name of the form 'somename_iter', and 'somename_iter0.sp.end/.h5' must already exist. -% - Nvol : number of volumes -% - Lrad : radial resolution in each volume (one value) -% - nptr : number of poincare trajectories traced in each volume -% - startit : starting iteration number -% - nit : number of iterations -% - Iref : targeted net-toroidal-current (array of size Nvol-1) -% -% OUTPUT -% - currents : array of net-toroidal-currents obtained on each interface at each interation step -% -% written by J.Loizu (2017) -% upgraded by J.Loizu (2018) - - -specexec = strcat(execom,{' '}); - -specexec = specexec{1}; - -currents = zeros(nit+1,Nvol-1); - -pfac = 1e-9; % factor for the amplitude of the perturbation in pflux for Jacobian evaluation (reference: 1e-6) - -ntheta = 128; % poloidal resolution for the loop integral evaluating the current - -mu = zeros(1,Nvol); % as of now zero volume-currents are imposed - - -for i=1+startit:startit+nit - - display(' '); - display(['START OF CURRENT ITERATION ' num2str(i)]); - display(' '); - - %-------- Initial input and hdf5 files -------- - - spec_input = strcat(inputroot,num2str(i-1),'.sp.end'); - spec_hdf5 = strcat(inputroot,num2str(i-1),'.sp.h5'); - - tflux = h5read(spec_hdf5,'/tflux'); - pflux = h5read(spec_hdf5,'/pflux'); - pre = h5read(spec_hdf5,'/pressure'); - IKAMtor = get_spec_torcurr_kam_net(spec_hdf5,ntheta); - - currents(i-startit,1:Nvol-1) = IKAMtor; - - %-------- Evaluation of J=dI/dX --------- - - tfl = zeros(1,Nvol); - - pfl = zeros(1,Nvol); - - dX = zeros(1,Nvol); - - dIdX = zeros(Nvol-1,Nvol-1); - - dX = pflux*pfac; - - lrad = Lrad*ones(1,Nvol); - - template = spec_input; - - - % jacobian evaluation runs - - for lvol=2:Nvol - - display(' '); - display(['JACOBIAN EVALUATION...' num2str(lvol-1)]); - display(' '); - - tfl = tflux; - - pfl = pflux; - - pfl(lvol) = pfl(lvol) + dX(lvol); - - newinput = strcat(inputroot,'jacobian',num2str(lvol),'.sp'); - - write_spec_input_L0(template,newinput,Nvol,tfl,pfl,mu,pre,lrad,nptr); - - system(strcat([specexec newinput(1:end-3)])); - - spec_hdf5 = strcat(newinput(1:end-3),'.sp.h5'); - - newIKAMtor = get_spec_torcurr_kam_net(spec_hdf5,ntheta); - - dIdX(:,lvol-1) = (newIKAMtor-IKAMtor)/dX(lvol); - - end - - - %-------- Evaluation of dX steps from Newton method --------- - - Jinv = inv(dIdX); - curr(1:Nvol-1) = IKAMtor; - zfun(1:Nvol-1) = IKAMtor-Iref; - - dX(2:Nvol) = -Jinv*transpose(zfun); - - display(' '); - display(['CALCULATED STEP: ' num2str(transpose(dX)) ]); - display(' '); - - %-------- Final run with appropriate X+dXstep --------- - - tfl = tflux; - pfl = pflux; - pfl(2:Nvol) = pfl(2:Nvol) + dX(2:Nvol); - - newinput = strcat(inputroot,num2str(i),'.sp'); - - write_spec_input_L0(template,newinput,Nvol,tfl,pfl,mu,pre,lrad,nptr); - - system(strcat([specexec newinput(1:end-3)])); - - - %-------- Update .DF file from last output -------- - - system(strcat(['cp ' '.' inputroot num2str(i) '.sp.DF' ' .sp.DF'])); - - -end - -spec_hdf5 = strcat(inputroot,num2str(startit+nit),'.sp.h5'); -IKAMtor = get_spec_torcurr_kam_net(spec_hdf5,ntheta); -currents(nit+1,1:Nvol-1) = IKAMtor; - - diff --git a/Utilities/matlabtools/write_spec_input_L0.m b/Utilities/matlabtools/write_spec_input_L0.m deleted file mode 100644 index bacc7797..00000000 --- a/Utilities/matlabtools/write_spec_input_L0.m +++ /dev/null @@ -1,113 +0,0 @@ -function write_spec_input_L0(template,inputname,Nvol,phiedge,tfl,pfl,mu,pre,lrad,nptr) - -% -% WRITE_SPEC_INPUT_L0( TEMPLATE, INPUTNAME, NVOL, PHIEDGE, TFL, PFL, MU, PRE, LRAD, NPTR ) -% ======================================================================================== -% -% Writes spec input file from template with constraints corresponding to Lconstraint=0 (tfl,pfl,mu) -% -% INPUT -% ----- -% -template : template input file name with .sp format -% -inputname : new input file name with .sp format -% -Nvol : number of volumes -% -tfl : toroidal flux enclosed by each interface -% -pfl : poloidal flux enclosed by each interface -% -mu : beltrami parameter in each volume -% -pre : pressure in each volume -% -lrad : radial resolution in each volume -% -nptr : number of Poincare trajectories in each volume -% -% written by J.Loizu (2016) - -nlmod = 8; - -sref{1} = ' pressure ='; -sref{2} = ' tflux ='; -sref{3} = ' pflux ='; -sref{4} = ' mu ='; -sref{5} = ' Lrad ='; -sref{6} = ' nPtrj ='; -sref{7} = ' phiedge ='; -sref{8} = ' Nvol ='; - -snew1 = sref{1}; -snew2 = sref{2}; -snew3 = sref{3}; -snew4 = sref{4}; -snew5 = sref{5}; -snew6 = sref{6}; -snew7 = strcat(sref{7},{' '}, num2str(phiedge)); -snew8 = strcat(sref{8}, {' '}, num2str(Nvol)); - -for i=1:Nvol - snew1 = strcat(snew1,{' '},num2str(pre(i),16), {' '}); - snew2 = strcat(snew2,{' '},num2str(tfl(i),16), {' '}); - snew3 = strcat(snew3,{' '},num2str(pfl(i),16), {' '}); - snew4 = strcat(snew4,{' '},num2str(mu(i),16), {' '}); - snew5 = strcat(snew5,{' '},num2str(lrad(i),16),{' '}); - snew6 = strcat(snew6,{' '},num2str(nptr(i),16),{' '}); -end - -snew{1} = snew1{1}; -snew{2} = snew2{1}; -snew{3} = snew3{1}; -snew{4} = snew4{1}; -snew{5} = snew5{1}; -snew{6} = snew6{1}; -snew{7} = snew7{1}; -snew{8} = snew8{1}; - -% Open template file for reading - -fid = fopen(template,'rt'); - -tline = fgetl(fid); - -count = 1; - -lnum = zeros(1,nlmod); - -A{1} = tline; - - -% Read template file, copy lines in A, and identify reference lines - -while ischar(tline) - for i=1:nlmod - if(size(tline)>=size(sref{i})) - if(strcmp(tline(1:length(sref{i})),sref{i})==1) - lnum(i) = count; - end - end - end - tline = fgetl(fid); - count = count + 1; - A{count} = tline; -end - -fclose(fid); - - -% Modify cell A at reference lines - -for i=1:nlmod - A{lnum(i)} = sprintf('%s',snew{i}); -end - -% Write cell A into new input file - -fid = fopen(inputname, 'w'); - -for i = 1:numel(A) - if(A{i+1} == -1) - fprintf(fid,'%s', A{i}); - break - else - fprintf(fid,'%s\n', A{i}); - end -end - -fclose(fid); - - diff --git a/Utilities/matlabtools/write_spec_input_L1.m b/Utilities/matlabtools/write_spec_input_L1.m deleted file mode 100644 index c4d6fa71..00000000 --- a/Utilities/matlabtools/write_spec_input_L1.m +++ /dev/null @@ -1,125 +0,0 @@ -function write_spec_input_L1(template, inputname, Nvol, tfl, pfl, iota, oita, phit_edge, pre, mu, lrad, nptr) - -% -% WRITE_SPEC_INPUT_L1( TEMPLATE, INPUTNAME, NVOL, TFL, PFL, IOTA, OITA, PHIT_EDGE, PRE, MU, LRAD, NPTR ) -% ====================================================================================================== -% -% Writes spec input file from template with constraints corresponding to -% Lconstraint=1 (tfl,iota,oita) -% -% INPUT -% ----- -% -template : template input file name with .sp format -% -inputname : new input file name with .sp format -% -Nvol : number of volumes -% -tfl : toroidal flux enclosed by each interface -% -pfl : poloidal flux enclosed by each interface -% -iota : rotational transform on the inner side of the interface -% -oita : rotational transform on the outer side of the interface -% -phit_edge : total toroidal flux -% -pre : pressure in each volume -% -mu : Lagrange multiplier in each volume -% -lrad : radial resolution in each volume -% -nptr : number of Poincare trajectories in each volume -% -% written by A.Baillod (2019) - -nlmod = 10; - -sref{1} = ' pressure ='; -sref{2} = ' tflux ='; -sref{3} = ' iota ='; -sref{4} = ' oita ='; -sref{5} = ' Lrad ='; -sref{6} = ' nPtrj ='; -sref{7} = ' Nvol ='; -sref{8} = ' pflux ='; -sref{9} = ' mu ='; -sref{10} = ' phiedge ='; - -snew1 = sref{1}; -snew2 = sref{2}; -snew3 = strcat(sref{3}, {' '}, num2str(iota(1), 16), {' '}); -snew4 = strcat(sref{4}, {' '}, num2str(oita(1), 16), {' '}); -snew5 = sref{5}; -snew6 = sref{6}; -snew7 = strcat(sref{7},{' '},num2str(Nvol), {' '}); -snew8 = sref{8}; -snew9 = sref{9}; -snew10 = strcat(sref{10}, {' '}, num2str(phit_edge), {' '}); - -for i=1:Nvol - snew1 = strcat(snew1, {' '},num2str(pre(i) ,16), {' '}); - snew2 = strcat(snew2, {' '},num2str(tfl(i) ,16), {' '}); - snew3 = strcat(snew3, {' '},num2str(iota(i),16), {' '}); - snew4 = strcat(snew4, {' '},num2str(oita(i),16), {' '}); - snew5 = strcat(snew5, {' '},num2str(lrad(i),16), {' '}); - snew6 = strcat(snew6, {' '},num2str(nptr(i),16), {' '}); - snew8 = strcat(snew8, {' '},num2str(pfl(i) ,16), {' '}); - snew9 = strcat(snew9, {' '},num2str(mu(i) ,16), {' '}); -end - -snew{1} = snew1{1}; -snew{2} = snew2{1}; -snew{3} = snew3{1}; -snew{4} = snew4{1}; -snew{5} = snew5{1}; -snew{6} = snew6{1}; -snew{7} = snew7{1}; -snew{8} = snew8{1}; -snew{9} = snew9{1}; -snew{10} = snew10{1}; - - - -% Open template file for reading - -fid = fopen(template,'rt'); - -tline = fgetl(fid); - -count = 1; - -lnum = zeros(1,nlmod); - -A{1} = tline; - - -% Read template file, copy lines in A, and identify reference lines - -while ischar(tline) - for i=1:nlmod - if(size(tline)>=size(sref{i})) - if(strcmp(tline(1:length(sref{i})),sref{i})==1) - lnum(i) = count; - end - end - end - tline = fgetl(fid); - count = count + 1; - A{count} = tline; -end - -fclose(fid); - - -% Modify cell A at reference lines - -for i=1:nlmod - A{lnum(i)} = sprintf('%s',snew{i}); -end - -% Write cell A into new input file - -fid = fopen(inputname, 'w'); - -for i = 1:numel(A) - if(A{i+1} == -1) - fprintf(fid,'%s', A{i}); - break - else - fprintf(fid,'%s\n', A{i}); - end -end - -fclose(fid); diff --git a/Utilities/matlabtools/write_spec_input_L3.m b/Utilities/matlabtools/write_spec_input_L3.m deleted file mode 100644 index 7a214914..00000000 --- a/Utilities/matlabtools/write_spec_input_L3.m +++ /dev/null @@ -1,131 +0,0 @@ -function write_spec_input_L3(template, inputname, Nvol, Lfreebound, tfl, phit_edge, ... - pflux, Ivol, Isurf, curtor, pressure, lrad, nptr, Linitialize) - -% -% WRITE_SPEC_INPUT_L3( TEMPLATE, INPUTNAME, NVOL, LFREEBOUND, TFL, PHIT_EDGE, ... ) -% ================================================================================= -% -% Writes spec input file from template with constraints corresponding to -% Lconstraint=1 (tfl,iota,oita) -% -% INPUT -% ----- -% -template : template input file name with .sp format -% -inputname : new input file name with .sp format -% -Nvol : number of volume -% -Lfreebound : Flag for free boundary -% -tfl : toroidal flux enclosed by each interface -% -phit_edge : total toroidal flux -% -pflux : Poloidal flux (used as guess) -% -Ivol : volume current in each volume -% -Isurf : surface current at each interface -% -curtor : Total plasma current. only relevant if Lfreebound=1 -% -pressure : pressure in each volume -% -lrad : radial resolution in each volume -% -nptr : number of Poincare trajectories in each volume -% -Linitialize: How to initialize interfaces -% -% written by A.Baillod (2019) - -Mvol = Nvol+Lfreebound; - -nlmod = 11; - -sref{1} = ' pressure ='; -sref{2} = ' tflux ='; -sref{3} = ' Lrad ='; -sref{4} = ' nPtrj ='; -sref{5} = ' Nvol ='; -sref{6} = ' phiedge ='; -sref{7} = ' Ivolume ='; -sref{8} = ' Isurf ='; -sref{9} = ' curtor ='; -sref{10} = ' pflux ='; -sref{11} = ' Linitialize ='; - -snew1 = sref{1}; -snew2 = sref{2}; -snew3 = sref{3}; -snew4 = sref{4}; -snew5 = strcat(sref{5}, {' '}, num2str(Nvol) , {' '}); -snew6 = strcat(sref{6}, {' '}, num2str(phit_edge), {' '}); -snew7 = sref{7}; -snew8 = sref{8}; -snew9 = strcat(sref{9}, {' '}, num2str(curtor), {' '}); -snew10 = sref{10}; -snew11 = strcat(sref{11}, {' '}, num2str(Linitialize), {' '}); - -for i=1:Mvol - snew1 = strcat(snew1, {' '},num2str(pressure(i) ,16), {' '}); - snew2 = strcat(snew2, {' '},num2str(tfl(i) ,16), {' '}); - snew3 = strcat(snew3, {' '},num2str(lrad(i) ,16), {' '}); - snew4 = strcat(snew4, {' '},num2str(nptr(i) ,16), {' '}); - snew7 = strcat(snew7, {' '},num2str(Ivol(i) ,16), {' '}); - snew8 = strcat(snew8, {' '},num2str(Isurf(i) ,16), {' '}); - snew10 = strcat(snew10, {' '},num2str(pflux(i) ,16), {' '}); -end - -snew{1} = snew1{1}; -snew{2} = snew2{1}; -snew{3} = snew3{1}; -snew{4} = snew4{1}; -snew{5} = snew5{1}; -snew{6} = snew6{1}; -snew{7} = snew7{1}; -snew{8} = snew8{1}; -snew{9} = snew9{1}; -snew{10} = snew10{1}; -snew{11} = snew11{1}; - - -% Open template file for reading - -fid = fopen(template,'rt'); - -tline = fgetl(fid); - -count = 1; - -lnum = zeros(1,nlmod); - -A{1} = tline; - - -% Read template file, copy lines in A, and identify reference lines - -while ischar(tline) - for i=1:nlmod - if(size(tline)>=size(sref{i})) - if(strcmp(tline(1:length(sref{i})),sref{i})==1) - lnum(i) = count; - end - end - end - tline = fgetl(fid); - count = count + 1; - A{count} = tline; -end - -fclose(fid); - - -% Modify cell A at reference lines - -for i=1:nlmod - A{lnum(i)} = sprintf('%s',snew{i}); -end - -% Write cell A into new input file - -fid = fopen(inputname, 'w'); - -for i = 1:numel(A) - if(A{i+1} == -1) - fprintf(fid,'%s', A{i}); - break - else - fprintf(fid,'%s\n', A{i}); - end -end - -fclose(fid); From d4d9e95d44d456b4abb296bfbe9085b9d8f81009 Mon Sep 17 00:00:00 2001 From: ErolBa Date: Mon, 11 Mar 2024 15:58:31 +0100 Subject: [PATCH 22/36] merge with master... --- .github/workflows/build.yml | 100 ++-- .github/workflows/build_cmake.yml | 118 ++--- .github/workflows/py_spec.yml | 3 +- .github/workflows/python_wrapper.yml | 2 +- LICENSE | 674 +++++++++++++++++++++++++++ setup.py | 2 +- 6 files changed, 792 insertions(+), 107 deletions(-) create mode 100644 LICENSE diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml index b6e47299..25cb635a 100644 --- a/.github/workflows/build.yml +++ b/.github/workflows/build.yml @@ -4,58 +4,66 @@ on: [push, pull_request] jobs: build: runs-on: ubuntu-latest - container: csmiet/testspec + strategy: + fail-fast: false env: - MACHINE: docker SPEC_PATH: ${{ github.workspace }} PYTHONPATH: ${{ github.workspace }}/Utilities/pythontools OMPI_ALLOW_RUN_AS_ROOT: 1 OMPI_ALLOW_RUN_AS_ROOT_CONFIRM: 1 steps: - - name: checkout sources - uses: actions/checkout@master - - name: compile_xspec - run: | - cd ${SPEC_PATH} - make -j BUILD_ENV=gfortran xspec - - name: compile_dspec - run: | - cd ${SPEC_PATH} - make BUILD_ENV=gfortran dspec - - name: run_fast_cartesian - run: | - cd ${SPEC_PATH}/ci/G1V03L2Fi - echo ${PYTHONPATH} - export OMP_NUM_THREADS=1 - mpiexec -n 2 --allow-run-as-root ${SPEC_PATH}/xspec G1V03L2Fi.001.sp - python3 -m py_spec.ci.test compare.h5 G1V03L2Fi.001.sp.h5 - - name: run_fast_cylinder - run: | - cd ${SPEC_PATH}/ci/G2V32L1Fi - echo ${PYTHONPATH} - export OMP_NUM_THREADS=1 - mpiexec -n 2 --allow-run-as-root ${SPEC_PATH}/xspec G2V32L1Fi.001.sp - python3 -m py_spec.ci.test compare.h5 G2V32L1Fi.001.sp.h5 - - name: toroidal_freeboundary_vacuum - run: | - cd ${SPEC_PATH}/ci/toroidal_freeboundary_vacuum - export OMP_NUM_THREADS=1 - mpiexec -n 2 --allow-run-as-root ${SPEC_PATH}/xspec G3V02L0Fr_LU.sp - mpiexec -n 2 --allow-run-as-root ${SPEC_PATH}/xspec G3V02L0Fr.sp - python3 -m py_spec.ci.test compare.h5 G3V02L0Fr_LU.sp.h5 --tol 1e-11 - python3 -m py_spec.ci.test compare.h5 G3V02L0Fr.sp.h5 --tol 1e-11 - - name: current_constraint_fixed_boundary - run: | - cd ${SPEC_PATH}/ci/G3V08L3Fi - export OMP_NUM_THREADS=1 - mpiexec -n 2 --allow-run-as-root ${SPEC_PATH}/xspec G3V08L3Fi.001.sp - python3 -m py_spec.ci.test compare.h5 G3V08L3Fi.001.sp.h5 --tol 1e-10 - - name: current_constraint_free_boundary - run: | - cd ${SPEC_PATH}/ci/G3V08L3Fr - export OMP_NUM_THREADS=1 - mpiexec -n 2 --allow-run-as-root ${SPEC_PATH}/xspec G3V08L3Fr.001.sp - python3 -m py_spec.ci.test compare.h5 G3V08L3Fr.001.sp.h5 --tol 1e-10 + - uses: actions/checkout@v3 + - name: Python version info + run: | + python3 --version + pip3 --version + - name: Install dependencies + run: | + sudo apt-get update + sudo apt-get install gfortran mpi-default-bin mpi-default-dev libhdf5-103 libhdf5-dev libfftw3-bin libfftw3-dev libopenblas0-openmp libopenblas-dev + pip3 install --user numpy f90nml scikit-build scipy h5py matplotlib + - name: compile_xspec + run: | + cd ${SPEC_PATH} + make -j BUILD_ENV=gfortran_ubuntu xspec + - name: compile_dspec + run: | + cd ${SPEC_PATH} + make BUILD_ENV=gfortran_ubuntu dspec + - name: run_fast_cartesian + run: | + cd ${SPEC_PATH}/ci/G1V03L2Fi + echo ${PYTHONPATH} + export OMP_NUM_THREADS=1 + mpiexec -n 2 --allow-run-as-root ${SPEC_PATH}/xspec G1V03L2Fi.001.sp + python3 -m py_spec.ci.test compare.h5 G1V03L2Fi.001.sp.h5 + - name: run_fast_cylinder + run: | + cd ${SPEC_PATH}/ci/G2V32L1Fi + echo ${PYTHONPATH} + export OMP_NUM_THREADS=1 + mpiexec -n 2 --allow-run-as-root ${SPEC_PATH}/xspec G2V32L1Fi.001.sp + python3 -m py_spec.ci.test compare.h5 G2V32L1Fi.001.sp.h5 + - name: toroidal_freeboundary_vacuum + run: | + cd ${SPEC_PATH}/ci/toroidal_freeboundary_vacuum + export OMP_NUM_THREADS=1 + mpiexec -n 2 --allow-run-as-root ${SPEC_PATH}/xspec G3V02L0Fr_LU.sp + mpiexec -n 2 --allow-run-as-root ${SPEC_PATH}/xspec G3V02L0Fr.sp + python3 -m py_spec.ci.test compare.h5 G3V02L0Fr_LU.sp.h5 --tol 1e-11 + python3 -m py_spec.ci.test compare.h5 G3V02L0Fr.sp.h5 --tol 1e-11 + - name: current_constraint_fixed_boundary + run: | + cd ${SPEC_PATH}/ci/G3V08L3Fi + export OMP_NUM_THREADS=1 + mpiexec -n 2 --allow-run-as-root ${SPEC_PATH}/xspec G3V08L3Fi.001.sp + python3 -m py_spec.ci.test compare.h5 G3V08L3Fi.001.sp.h5 --tol 1e-10 + - name: current_constraint_free_boundary + run: | + cd ${SPEC_PATH}/ci/G3V08L3Fr + export OMP_NUM_THREADS=1 + mpiexec -n 2 --allow-run-as-root ${SPEC_PATH}/xspec G3V08L3Fr.001.sp + python3 -m py_spec.ci.test compare.h5 G3V08L3Fr.001.sp.h5 --tol 1e-10 diff --git a/.github/workflows/build_cmake.yml b/.github/workflows/build_cmake.yml index 138c42ca..866a50a9 100644 --- a/.github/workflows/build_cmake.yml +++ b/.github/workflows/build_cmake.yml @@ -4,68 +4,70 @@ on: [push, pull_request] jobs: build: runs-on: ubuntu-latest - container: csmiet/testspec + strategy: + fail-fast: false env: - MACHINE: docker SPEC_PATH: ${{ github.workspace }} PYTHONPATH: ${{ github.workspace }}/Utilities/pythontools OMPI_ALLOW_RUN_AS_ROOT: 1 OMPI_ALLOW_RUN_AS_ROOT_CONFIRM: 1 steps: - - name: checkout sources - uses: actions/checkout@master - - name: Install prereqs - run: | - pip3 install ninja cmake - yum install -y hdf5-static - - name: Build & Test - uses: ashutoshvarma/action-cmake-build@master - with: - build-dir: ${{ runner.workspace }}/build - build-type: Release - # Extra options pass to cmake while configuring project - configure-options: -DCMAKE_C_COMPILER=mpicc -DCMAKE_CXX_COMPILER=mpicxx -DCMAKE_Fortran_COMPILER=mpifort -DBLA_VENDOR=OpenBLAS -DHDF5_NO_FIND_PACKAGE_CONFIG_FILE=TRUE -DHDF5_PREFER_PARALLEL=TRUE -GNinja # -DCMAKE_INSTALL_PREFIX=${SPEC_PATH}/install - # install the build using cmake --install - install-build: true - #- name: compile_xspec - # run: | - # pip3 install ninja cmake - # cd ${SPEC_PATH}/build - # cmake -DCMAKE_C_COMPILER=mpicc -DCMAKE_CXX_COMPILER=mpicxx -DCMAKE_Fortran_COMPILER=mpifort -DBLA_VENDOR=OpenBLAS -DHDF5_NO_FIND_PACKAGE_CONFIG_FILE=TRUE -DHDF5_PREFER_PARALLEL=TRUE .. -GNinja -DCMAKE_INSTALL_PREFIX=${SPEC_PATH}/install - # cmake --build . - # cmake --install . - - name: run_fast_cartesian - run: | - cd ${SPEC_PATH}/ci/G1V03L2Fi - echo ${PYTHONPATH} - export OMP_NUM_THREADS=1 - mpiexec -n 3 --allow-run-as-root xspec G1V03L2Fi.001.sp - python3 -m py_spec.ci.test compare.h5 G1V03L2Fi.001.sp.h5 - - name: run_fast_cylinder - run: | - cd ${SPEC_PATH}/ci/G2V32L1Fi - echo ${PYTHONPATH} - export OMP_NUM_THREADS=1 - mpiexec -n 2 --allow-run-as-root xspec G2V32L1Fi.001.sp - python3 -m py_spec.ci.test compare.h5 G2V32L1Fi.001.sp.h5 - - name: toroidal_freeboundary_vacuum - run: | - cd ${SPEC_PATH}/ci/toroidal_freeboundary_vacuum - export OMP_NUM_THREADS=1 - mpiexec -n 3 --allow-run-as-root xspec G3V02L0Fr_LU.sp - mpiexec -n 3 --allow-run-as-root xspec G3V02L0Fr.sp - python3 -m py_spec.ci.test compare.h5 G3V02L0Fr_LU.sp.h5 --tol 1e-11 - python3 -m py_spec.ci.test compare.h5 G3V02L0Fr.sp.h5 --tol 1e-11 - - name: current_constraint_fixed_boundary - run: | - cd ${SPEC_PATH}/ci/G3V08L3Fi - export OMP_NUM_THREADS=1 - mpiexec -n 3 --allow-run-as-root xspec G3V08L3Fi.001.sp - python3 -m py_spec.ci.test compare.h5 G3V08L3Fi.001.sp.h5 --tol 1e-10 - - name: current_constraint_free_boundary - run: | - cd ${SPEC_PATH}/ci/G3V08L3Fr - export OMP_NUM_THREADS=1 - mpiexec -n 3 --allow-run-as-root xspec G3V08L3Fr.001.sp - python3 -m py_spec.ci.test compare.h5 G3V08L3Fr.001.sp.h5 --tol 1e-10 + - uses: actions/checkout@v3 + - name: Install prereqs + run: | + sudo apt-get update + sudo apt-get install gfortran mpi-default-bin mpi-default-dev libhdf5-103 libhdf5-dev libfftw3-bin libfftw3-dev libopenblas0-openmp libopenblas-dev + pip3 install --upgrade pip + pip3 install --user ninja cmake scipy + pip3 install --user numpy f90nml scikit-build scipy h5py matplotlib + - name: Build & Test + uses: ashutoshvarma/action-cmake-build@master + with: + build-dir: ${{ runner.workspace }}/build + build-type: Release + # Extra options pass to cmake while configuring project + configure-options: -DCMAKE_C_COMPILER=mpicc -DCMAKE_CXX_COMPILER=mpicxx -DCMAKE_Fortran_COMPILER=mpifort -DBLA_VENDOR=OpenBLAS -DHDF5_NO_FIND_PACKAGE_CONFIG_FILE=TRUE -DHDF5_PREFER_PARALLEL=TRUE -DCMAKE_INSTALL_PREFIX=${SPEC_PATH}/install -GNinja # -DCMAKE_INSTALL_PREFIX=${SPEC_PATH}/install + # install the build using cmake --install + install-build: true + #- name: compile_xspec + # run: | + # pip3 install ninja cmake + # cd ${SPEC_PATH}/build + # cmake -DCMAKE_C_COMPILER=mpicc -DCMAKE_CXX_COMPILER=mpicxx -DCMAKE_Fortran_COMPILER=mpifort -DBLA_VENDOR=OpenBLAS -DHDF5_NO_FIND_PACKAGE_CONFIG_FILE=TRUE -DHDF5_PREFER_PARALLEL=TRUE .. -GNinja -DCMAKE_INSTALL_PREFIX=${SPEC_PATH}/install + # cmake --build . + # cmake --install . + - name: run_fast_cartesian + run: | + cd ${SPEC_PATH}/ci/G1V03L2Fi + echo ${PYTHONPATH} + export OMP_NUM_THREADS=1 + mpiexec -n 2 --allow-run-as-root $SPEC_PATH/install/bin/xspec G1V03L2Fi.001.sp + python3 -m py_spec.ci.test compare.h5 G1V03L2Fi.001.sp.h5 + - name: run_fast_cylinder + run: | + cd ${SPEC_PATH}/ci/G2V32L1Fi + echo ${PYTHONPATH} + export OMP_NUM_THREADS=1 + mpiexec -n 2 --allow-run-as-root $SPEC_PATH/install/bin/xspec G2V32L1Fi.001.sp + python3 -m py_spec.ci.test compare.h5 G2V32L1Fi.001.sp.h5 + - name: toroidal_freeboundary_vacuum + run: | + cd ${SPEC_PATH}/ci/toroidal_freeboundary_vacuum + export OMP_NUM_THREADS=1 + mpiexec -n 2 --allow-run-as-root $SPEC_PATH/install/bin/xspec G3V02L0Fr_LU.sp + mpiexec -n 2 --allow-run-as-root $SPEC_PATH/install/bin/xspec G3V02L0Fr.sp + python3 -m py_spec.ci.test compare.h5 G3V02L0Fr_LU.sp.h5 --tol 1e-11 + python3 -m py_spec.ci.test compare.h5 G3V02L0Fr.sp.h5 --tol 1e-11 + - name: current_constraint_fixed_boundary + run: | + cd ${SPEC_PATH}/ci/G3V08L3Fi + export OMP_NUM_THREADS=1 + mpiexec -n 2 --allow-run-as-root $SPEC_PATH/install/bin/xspec G3V08L3Fi.001.sp + python3 -m py_spec.ci.test compare.h5 G3V08L3Fi.001.sp.h5 --tol 1e-10 + - name: current_constraint_free_boundary + run: | + cd ${SPEC_PATH}/ci/G3V08L3Fr + export OMP_NUM_THREADS=1 + mpiexec -n 2 --allow-run-as-root $SPEC_PATH/install/bin/xspec G3V08L3Fr.001.sp + python3 -m py_spec.ci.test compare.h5 G3V08L3Fr.001.sp.h5 --tol 1e-10 diff --git a/.github/workflows/py_spec.yml b/.github/workflows/py_spec.yml index 495d1880..f621c376 100644 --- a/.github/workflows/py_spec.yml +++ b/.github/workflows/py_spec.yml @@ -18,8 +18,9 @@ jobs: - name: Install dependencies working-directory: ${{ env.PY_SPEC_DIR }} run: | + pip install --upgrade pip pip3 install -r requirements.txt - pip3 install setuptools wheel twine + pip3 install setuptools wheel twine - name: Build py_spec working-directory: ${{ env.PY_SPEC_DIR }} diff --git a/.github/workflows/python_wrapper.yml b/.github/workflows/python_wrapper.yml index 158451d5..55952dfe 100644 --- a/.github/workflows/python_wrapper.yml +++ b/.github/workflows/python_wrapper.yml @@ -18,7 +18,7 @@ jobs: run: | sudo apt-get update sudo apt-get install gfortran mpi-default-bin mpi-default-dev libhdf5-103 libhdf5-dev libfftw3-bin libfftw3-dev libopenblas0-openmp libopenblas-dev cmake ninja-build - pip3 install --user numpy f90nml scikit-build + pip3 install --user numpy f90nml scikit-build scipy pip3 install --user git+https://github.com/zhucaoxiang/f90wrap - name: Build python_wrapper diff --git a/LICENSE b/LICENSE new file mode 100644 index 00000000..f288702d --- /dev/null +++ b/LICENSE @@ -0,0 +1,674 @@ + GNU GENERAL PUBLIC LICENSE + Version 3, 29 June 2007 + + Copyright (C) 2007 Free Software Foundation, Inc. + Everyone is permitted to copy and distribute verbatim copies + of this license document, but changing it is not allowed. + + Preamble + + The GNU General Public License is a free, copyleft license for +software and other kinds of works. + + The licenses for most software and other practical works are designed +to take away your freedom to share and change the works. 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If not, see . + +Also add information on how to contact you by electronic and paper mail. + + If the program does terminal interaction, make it output a short +notice like this when it starts in an interactive mode: + + Copyright (C) + This program comes with ABSOLUTELY NO WARRANTY; for details type `show w'. + This is free software, and you are welcome to redistribute it + under certain conditions; type `show c' for details. + +The hypothetical commands `show w' and `show c' should show the appropriate +parts of the General Public License. Of course, your program's commands +might be different; for a GUI interface, you would use an "about box". + + You should also get your employer (if you work as a programmer) or school, +if any, to sign a "copyright disclaimer" for the program, if necessary. +For more information on this, and how to apply and follow the GNU GPL, see +. + + The GNU General Public License does not permit incorporating your program +into proprietary programs. If your program is a subroutine library, you +may consider it more useful to permit linking proprietary applications with +the library. If this is what you want to do, use the GNU Lesser General +Public License instead of this License. But first, please read +. diff --git a/setup.py b/setup.py index 8af1e4f2..b42480ee 100644 --- a/setup.py +++ b/setup.py @@ -38,7 +38,7 @@ setup( name="spec", - version="0.0.1", + version="0.0.2", #license="MIT", packages=['spec'], package_dir={'': 'Utilities/python_wrapper'}, From 6fd54fd8c9a50779df859a1cba104dc4176fadb5 Mon Sep 17 00:00:00 2001 From: ErolBa Date: Mon, 11 Mar 2024 17:42:11 +0100 Subject: [PATCH 23/36] catchin up 2... --- .gitignore | 3 +++ CMakeLists.txt | 21 ++++++++++++++++----- cmake_machines/intel_SUSE.json | 8 ++++++++ src/bfield.f90 | 4 +++- src/global.f90 | 1 + src/newton.f90 | 18 +++++++++--------- src/sphdf5.f90 | 10 +++------- src/tr00ab.f90 | 1 + 8 files changed, 44 insertions(+), 22 deletions(-) create mode 100644 cmake_machines/intel_SUSE.json diff --git a/.gitignore b/.gitignore index b20cfee5..290d9bd9 100644 --- a/.gitignore +++ b/.gitignore @@ -58,5 +58,8 @@ _skbuild/ src/mxspech.f90 src/msphdf5.f90 +# Apple Mac related +.DS_Store + # vscode files .vscode/ diff --git a/CMakeLists.txt b/CMakeLists.txt index ef806494..98dc87d9 100644 --- a/CMakeLists.txt +++ b/CMakeLists.txt @@ -49,6 +49,17 @@ else () endif () endif () + +if(CMAKE_Fortran_COMPILER_ID STREQUAL "Intel") + set(CMAKE_Fortran_FLAGS "${CMAKE_Fortran_FLAGS} -DIFORT") +endif() + +if(CMAKE_Fortran_COMPILER_ID STREQUAL "GNU") + if(CMAKE_Fortran_COMPILER_VERSION VERSION_GREATER "10.0") + set(CMAKE_Fortran_FLAGS "${CMAKE_Fortran_FLAGS} -fallow-argument-mismatch") + endif() +endif() + find_program(AWK awk mawk gawk) # Find LAPACK @@ -60,11 +71,11 @@ find_program(AWK awk mawk gawk) # If Intel MKL is not desired, change BLA_VENDOR variabale during configuration #set(BLA_VENDOR Intel10_64lp CACHE STRING # "Define BLAS vendor. Some of the popular options are Intel10_64lp OpenBLAS Apple Generic") -find_package (BLAS REQUIRED) -message(STATUS "BLAS vendor is ${BLA_VENDOR}") -if (NOT ${BLA_VENDOR} MATCHES "^Intel" AND NOT ${BLA_VENDOR} MATCHES "^OpenBLAS") - find_package (LAPACK REQUIRED) -endif() +# find_package (BLAS REQUIRED) +# message(STATUS "BLAS vendor is ${BLA_VENDOR}") +# if (NOT ${BLA_VENDOR} MATCHES "^Intel" AND NOT ${BLA_VENDOR} MATCHES "^OpenBLAS") +find_package (LAPACK REQUIRED) +#endif() # Find FFTW3. # Intel oneAPI has FFT3 available as part of MKL. Just linking against MKL gives FFTW functionality. diff --git a/cmake_machines/intel_SUSE.json b/cmake_machines/intel_SUSE.json new file mode 100644 index 00000000..398c9534 --- /dev/null +++ b/cmake_machines/intel_SUSE.json @@ -0,0 +1,8 @@ +{ + "cmake_args": [ + "-DCMAKE_C_COMPILER=mpicc", + "-DCMAKE_CXX_COMPILER=mpicc", + "-DCMAKE_Fortran_COMPILER=mpif90", + "-DBLA_VENDOR=Intel10_64lp" + ] +} diff --git a/src/bfield.f90 b/src/bfield.f90 index f0d000a5..5c2daa8c 100644 --- a/src/bfield.f90 +++ b/src/bfield.f90 @@ -167,7 +167,9 @@ subroutine bfield( zeta, st, Bst ) cput-cpus, lvol, zeta, st(1:2), dBu(3) FATAL( bfield, abs(dBu(3)).lt.vsmall, field is not toroidal ) - + !if( abs( dBu(3)).lt.vsmall ) then + ! write(ounit,'("WARNING: bfield: field is not toroidal")') + !endif endif !-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-! diff --git a/src/global.f90 b/src/global.f90 index 2ba83c8a..7ec25f58 100644 --- a/src/global.f90 +++ b/src/global.f90 @@ -250,6 +250,7 @@ module allglobal REAL :: ForceErr !< total force-imbalance REAL :: Energy !< MHD energy + REAL :: BnsErr !< (in freeboundary) error in self-consistency of field on plasma boundary (Picard iteration) REAL :: BetaTotal = 0.0 !< Beta, averaged over entire domain REAL , allocatable :: IPDt(:), IPDtDpf(:,:) !< Toroidal pressure-driven current diff --git a/src/newton.f90 b/src/newton.f90 index 4e9f275d..23f4007d 100644 --- a/src/newton.f90 +++ b/src/newton.f90 @@ -334,19 +334,19 @@ subroutine writereadgf( readorwrite, NGdof , ireadhessian ) case( 'W' ) ! will write derivative matrix to file; ! reset I/O state - !ios = 0 + ios = 0 - !open( dunit, file="."//trim(ext)//".sp.DF", status="replace", form="unformatted", iostat=ios ) ! save derivative matrix to file; - !FATAL( newton, ios.ne.0, error opening derivative matrix file ) + open( dunit, file="."//trim(ext)//".sp.DF", status="replace", form="unformatted", iostat=ios ) ! save derivative matrix to file; + FATAL( newton, ios.ne.0, error opening derivative matrix file ) - !write( dunit, iostat=ios ) Igeometry, Istellsym, Lfreebound, Nvol, Mpol, Ntor, NGdof ! enable resolution consistency check; - !FATAL( newton, ios.ne.0, error writing Nvol, Mpol, Ntor, NGdof ) + write( dunit, iostat=ios ) Igeometry, Istellsym, Lfreebound, Nvol, Mpol, Ntor, NGdof ! enable resolution consistency check; + FATAL( newton, ios.ne.0, error writing Nvol, Mpol, Ntor, NGdof ) - !write( dunit, iostat=ios ) hessian(1:NGdof,1:NGdof) - !FATAL( newton, ios.ne.0, error writing hessian to file ) + write( dunit, iostat=ios ) hessian(1:NGdof,1:NGdof) + FATAL( newton, ios.ne.0, error writing hessian to file ) - !close( dunit, iostat=ios ) - !FATAL( newton, ios.ne.0, error closing derivative matrix file ) + close( dunit, iostat=ios ) + FATAL( newton, ios.ne.0, error closing derivative matrix file ) case( 'R' ) diff --git a/src/sphdf5.f90 b/src/sphdf5.f90 index 8b4a8ba9..59d92eb0 100644 --- a/src/sphdf5.f90 +++ b/src/sphdf5.f90 @@ -459,11 +459,7 @@ subroutine init_convergence_output H5CALL( sphdf5, h5tinsert_f, (iteration_dtype_id, "Energy", offset, H5T_NATIVE_DOUBLE, hdfier) ) ! insert "Energy" field in datatype offset = offset + type_size_d ! increment offset by size of field H5CALL( sphdf5, h5tinsert_f, (iteration_dtype_id, "ForceErr", offset, H5T_NATIVE_DOUBLE, hdfier) ) ! insert "ForceErr" field in datatype - offset = offset + type_size_d - ! Erol addition - ! H5CALL( sphdf5, h5tinsert_f, (iteration_dtype_id, "BetaTotal", offset, H5T_NATIVE_DOUBLE, hdfier) ) ! insert "ForceErr" field in datatype - ! offset = offset + type_size_d - ! increment offset by size of field + offset = offset + type_size_d ! increment offset by size of field H5CALL( sphdf5, h5tinsert_f, (iteration_dtype_id, "iRbc", offset, iRZbscArray_id, hdfier) ) ! insert "iRbc" field in datatype offset = offset + irbc_size ! increment offset by size of field H5CALL( sphdf5, h5tinsert_f, (iteration_dtype_id, "iZbs", offset, iRZbscArray_id, hdfier) ) ! insert "iZbs" field in datatype @@ -1029,7 +1025,7 @@ subroutine hdfint use fileunits, only : ounit use inputlist use allglobal, only : ncpu, cpus, & - Mvol, ForceErr, BetaTotal, & + Mvol, ForceErr, BnsErr, BetaTotal, & mn, im, in, iRbc, iZbs, iRbs, iZbc, & mns, ims, ins, & dRbc, dZbs, dRbs, dZbc, & @@ -1100,7 +1096,7 @@ subroutine hdfint !latex \type{IPDt} & real & \pb{Surface current at output} HWRITERV( grpOutput, Mvol, IPDt, IPDt(1:Mvol)) - ! the following quantites can be diffeerent from input value + ! the following quantites can be different from input value HWRITERV( grpOutput, Mvol, adiabatic , adiabatic(1:Nvol) ) HWRITERV( grpOutput, Nvol, helicity , helicity(1:Nvol) ) HWRITERV( grpOutput, Mvol, mu , mu(1:Mvol) ) diff --git a/src/tr00ab.f90 b/src/tr00ab.f90 index 8a6b973b..260f19ce 100644 --- a/src/tr00ab.f90 +++ b/src/tr00ab.f90 @@ -767,6 +767,7 @@ subroutine tr00ab( lvol, mn, NN, Nt, Nz, iflag, ldiota ) ! construct straight-fi work(1:Lwork), Lwork, iwork(1:Liwork), idgelsd ) ldiota(innout,0) = dlambda(1,0) + dlambdaout(1:NN, lvol, innout) = dlambda(1:NN,0) case( 1 ) ! Lsvdiota = 1; jderiv = 1; 02 Sep 14; From 0611dd0bff027eb383d6423773d9233366b47125 Mon Sep 17 00:00:00 2001 From: ErolBa Date: Thu, 11 Apr 2024 16:30:48 +0200 Subject: [PATCH 24/36] print .hessian --- src/dforce.f90 | 23 ++++++++++++----------- 1 file changed, 12 insertions(+), 11 deletions(-) diff --git a/src/dforce.f90 b/src/dforce.f90 index 78bc58db..42a7e85f 100644 --- a/src/dforce.f90 +++ b/src/dforce.f90 @@ -456,8 +456,8 @@ subroutine dforce( NGdof, position, force, LComputeDerivatives, LComputeAxis) betavol(vvol) = press * vvolume(vvol) / lBBintegral(vvol) betavol(vvol) = betavol(vvol) * vvolume(vvol) voltotal = voltotal+vvolume(vvol) + !write(*,*) "Calc beta: ", betavol(vvol), vvolume(vvol) enddo - ! Calculate total beta which is obtained from individual betas ! write(*,*) "all betas", betavol(1:Nvol) BetaTotal = sum(betavol(1:Nvol))/voltotal @@ -466,6 +466,7 @@ subroutine dforce( NGdof, position, force, LComputeDerivatives, LComputeAxis) Energy = sum( lBBintegral(1:Nvol) ) ! should also compute beta; ! write(*,*)"total Energy", Energy + write(*,*) "Betatotal", BetaTotal, voltotal !-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-! @@ -977,16 +978,16 @@ subroutine dforce( NGdof, position, force, LComputeDerivatives, LComputeAxis) !if(LcomputeDerivatives .and. Lhessianallocated .and. Igeometry .eq. 1) then !if(Lhessianallocated .and. Igeometry .eq. 1) then - ! if(Lhessianallocated) then - ! if( myid.eq.0 ) then ; cput = GETTIME ; write(ounit,'("hesian : ",f10.2," : LHmatrix="L2" ;")')cput-cpus, LHmatrix ; - ! write(*,*) "Writing .hessian file..." - ! open(munit, file=trim(ext)//".sp.hessian", status="unknown", form="unformatted") - ! write(munit) NGdof - ! write(munit) hessian(1:NGdof,1:NGdof) - ! close(munit) - - ! endif - ! endif + if(Lhessianallocated .and. Igeometry.eq.1) then + if( myid.eq.0 ) then ; cput = GETTIME ; write(ounit,'("hesian : ",f10.2," : LHmatrix="L2" ;")')cput-cpus, LHmatrix ; + write(*,*) "Writing .hessian file..." + open(munit, file=trim(ext)//".sp.hessian", status="unknown", form="unformatted") + write(munit) NGdof + write(munit) hessian(1:NGdof,1:NGdof) + close(munit) + + endif + endif RETURN(dforce) From 2f30b523e4d071bdd4ac73f271c762ef2338e6a9 Mon Sep 17 00:00:00 2001 From: ErolBa Date: Wed, 4 Dec 2024 10:03:46 +0100 Subject: [PATCH 25/36] pulling changes from master --- .github/workflows/build.yml | 5 +- .github/workflows/build_cmake.yml | 5 +- .github/workflows/py_spec.yml | 1 - .github/workflows/python_wrapper.yml | 17 +++---- Utilities/pythontools/py_spec/__init__.py | 9 +++- .../py_spec/output/_plot_pressure.py | 4 +- .../pythontools/py_spec/output/_processing.py | 49 +++++++++++++------ Utilities/pythontools/py_spec/output/spec.py | 12 ++--- Utilities/pythontools/pyproject.toml | 31 ++++++++++++ Utilities/pythontools/requirements.txt | 1 - Utilities/pythontools/setup.py | 19 +------ 11 files changed, 90 insertions(+), 63 deletions(-) create mode 100644 Utilities/pythontools/pyproject.toml diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml index 25cb635a..d6b8fb7a 100644 --- a/.github/workflows/build.yml +++ b/.github/workflows/build.yml @@ -8,7 +8,6 @@ jobs: fail-fast: false env: SPEC_PATH: ${{ github.workspace }} - PYTHONPATH: ${{ github.workspace }}/Utilities/pythontools OMPI_ALLOW_RUN_AS_ROOT: 1 OMPI_ALLOW_RUN_AS_ROOT_CONFIRM: 1 steps: @@ -22,6 +21,8 @@ jobs: sudo apt-get update sudo apt-get install gfortran mpi-default-bin mpi-default-dev libhdf5-103 libhdf5-dev libfftw3-bin libfftw3-dev libopenblas0-openmp libopenblas-dev pip3 install --user numpy f90nml scikit-build scipy h5py matplotlib + cd ${{ github.workspace }}/Utilities/pythontools + pip3 install -v . - name: compile_xspec run: | cd ${SPEC_PATH} @@ -33,14 +34,12 @@ jobs: - name: run_fast_cartesian run: | cd ${SPEC_PATH}/ci/G1V03L2Fi - echo ${PYTHONPATH} export OMP_NUM_THREADS=1 mpiexec -n 2 --allow-run-as-root ${SPEC_PATH}/xspec G1V03L2Fi.001.sp python3 -m py_spec.ci.test compare.h5 G1V03L2Fi.001.sp.h5 - name: run_fast_cylinder run: | cd ${SPEC_PATH}/ci/G2V32L1Fi - echo ${PYTHONPATH} export OMP_NUM_THREADS=1 mpiexec -n 2 --allow-run-as-root ${SPEC_PATH}/xspec G2V32L1Fi.001.sp python3 -m py_spec.ci.test compare.h5 G2V32L1Fi.001.sp.h5 diff --git a/.github/workflows/build_cmake.yml b/.github/workflows/build_cmake.yml index 866a50a9..3ea86651 100644 --- a/.github/workflows/build_cmake.yml +++ b/.github/workflows/build_cmake.yml @@ -8,7 +8,6 @@ jobs: fail-fast: false env: SPEC_PATH: ${{ github.workspace }} - PYTHONPATH: ${{ github.workspace }}/Utilities/pythontools OMPI_ALLOW_RUN_AS_ROOT: 1 OMPI_ALLOW_RUN_AS_ROOT_CONFIRM: 1 steps: @@ -20,6 +19,8 @@ jobs: pip3 install --upgrade pip pip3 install --user ninja cmake scipy pip3 install --user numpy f90nml scikit-build scipy h5py matplotlib + cd ${{ github.workspace }}/Utilities/pythontools + pip3 install -v . - name: Build & Test uses: ashutoshvarma/action-cmake-build@master with: @@ -39,14 +40,12 @@ jobs: - name: run_fast_cartesian run: | cd ${SPEC_PATH}/ci/G1V03L2Fi - echo ${PYTHONPATH} export OMP_NUM_THREADS=1 mpiexec -n 2 --allow-run-as-root $SPEC_PATH/install/bin/xspec G1V03L2Fi.001.sp python3 -m py_spec.ci.test compare.h5 G1V03L2Fi.001.sp.h5 - name: run_fast_cylinder run: | cd ${SPEC_PATH}/ci/G2V32L1Fi - echo ${PYTHONPATH} export OMP_NUM_THREADS=1 mpiexec -n 2 --allow-run-as-root $SPEC_PATH/install/bin/xspec G2V32L1Fi.001.sp python3 -m py_spec.ci.test compare.h5 G2V32L1Fi.001.sp.h5 diff --git a/.github/workflows/py_spec.yml b/.github/workflows/py_spec.yml index f621c376..66ce4093 100644 --- a/.github/workflows/py_spec.yml +++ b/.github/workflows/py_spec.yml @@ -19,7 +19,6 @@ jobs: working-directory: ${{ env.PY_SPEC_DIR }} run: | pip install --upgrade pip - pip3 install -r requirements.txt pip3 install setuptools wheel twine - name: Build py_spec diff --git a/.github/workflows/python_wrapper.yml b/.github/workflows/python_wrapper.yml index 55952dfe..8977807c 100644 --- a/.github/workflows/python_wrapper.yml +++ b/.github/workflows/python_wrapper.yml @@ -6,26 +6,25 @@ jobs: name: python_wrapper build steps: - - uses: actions/checkout@v2 + - uses: actions/checkout@v4 # Python3 should be pre-installed on 'ubuntu-latest' - name: Python version info run: | - python3 --version - pip3 --version + python --version + pip --version - name: Install dependencies run: | sudo apt-get update - sudo apt-get install gfortran mpi-default-bin mpi-default-dev libhdf5-103 libhdf5-dev libfftw3-bin libfftw3-dev libopenblas0-openmp libopenblas-dev cmake ninja-build - pip3 install --user numpy f90nml scikit-build scipy - pip3 install --user git+https://github.com/zhucaoxiang/f90wrap + sudo apt-get install gfortran mpi-default-bin mpi-default-dev libhdf5-dev libfftw3-bin libfftw3-dev libopenblas-dev cmake ninja-build + pip install numpy f90nml scikit-build scipy meson meson-python + pip install f90wrap - name: Build python_wrapper run: | - python3 setup.py bdist_wheel - pip3 install --user dist/*.whl + pip install . - name: Test if installation is ok run: | - python3 -c "import spec; print('success')" + python -c "import spec; print('success')" diff --git a/Utilities/pythontools/py_spec/__init__.py b/Utilities/pythontools/py_spec/__init__.py index 5203a4a5..412e22fa 100644 --- a/Utilities/pythontools/py_spec/__init__.py +++ b/Utilities/pythontools/py_spec/__init__.py @@ -1,5 +1,10 @@ -# import of all SPEC-related python scripts. -__version__ = "3.3.3" +try: + from importlib import metadata +except ImportError: + # Running on pre-3.8 Python; use importlib-metadata package + import importlib_metadata as metadata + +__version__ = metadata.version(__package__ or __name__) from .ci import test from .input.spec_namelist import SPECNamelist diff --git a/Utilities/pythontools/py_spec/output/_plot_pressure.py b/Utilities/pythontools/py_spec/output/_plot_pressure.py index cb459a05..97d51d0b 100644 --- a/Utilities/pythontools/py_spec/output/_plot_pressure.py +++ b/Utilities/pythontools/py_spec/output/_plot_pressure.py @@ -9,8 +9,8 @@ def plot_pressure(self, normalize=True, ax=None, **kwargs): import numpy as np import matplotlib.pyplot as plt - pressure = self.input.physics.pressure * self.input.physics.pscale - tflux = self.output.tflux[: len(pressure)] + pressure = np.atleast_1d(self.input.physics.pressure) * self.input.physics.pscale + tflux = np.atleast_1d(self.output.tflux)[: len(pressure)] if not normalize: # remove mu_0 pressure /= 4 * np.pi * 1.0e-7 diff --git a/Utilities/pythontools/py_spec/output/_processing.py b/Utilities/pythontools/py_spec/output/_processing.py index a5f6c2d6..3e481f78 100644 --- a/Utilities/pythontools/py_spec/output/_processing.py +++ b/Utilities/pythontools/py_spec/output/_processing.py @@ -1,5 +1,6 @@ import numpy as np from scipy import integrate +import typing def get_RZ_derivatives( self, @@ -504,7 +505,7 @@ def get_average_beta(self, ns=64, nt=64, nz=64): """Get beta averaged in plasma volume""" # Read pressure - press = self.input.physics.pressure * self.input.physics.pscale + press = np.atleast_1d(self.input.physics.pressure) * self.input.physics.pscale # Create coordinate grid nfp = self.input.physics.Nfp @@ -606,11 +607,32 @@ def test_derivatives(self, lvol=0, s=0.3, t=0.4, z=0.5, delta=1e-6, tol=1e-6): print((g[0,1,0,:,:] - g[0,0,0,:,:])/ds/2-dg[0,0,0,1,:,:]) print((g[0,0,1,:,:] - g[0,0,0,:,:])/ds/2-dg[0,0,0,2,:,:]) -def get_surface_current_density(self, lsurf:int=None, nt:int=64, nz:int=64): +def _validate_lsurf(lsurf:np.ndarray, mvol:int)->np.ndarray: + """Check + + Args: + - lsurf: Interface number(s), between 1 and Mvol-1. default is np.arange(1, mvol) + - mvol: Number of volumes + Returns: + - lsurf: 1d array of interface numbers + + Raises: + - ValueError: if input is outside of range or wrong type (lsurf) + """ + + if lsurf is None: + lsurf = np.arange(1,mvol) + else: + lsurf = np.atleast_1d(lsurf) + if (lsurf<1).any() or (lsurf>mvol-1).any(): raise ValueError('lsurf should be in [1,mvol-1]') + + return lsurf + +def get_surface_current_density(self, lsurf:np.ndarray, nt:int=64, nz:int=64)->typing.Tuple[np.ndarray, np.ndarray, np.ndarray]: """Compute j_surf.B on each side of the provided interfaces Args: - - lsurf: Interface number, between 1 and Mvol-1. + - lsurf: Interface number(s), between 1 and Mvol-1. default is np.arange(1, mvol) - nt: Number of poloidal points - nz: Number of toroidal points @@ -628,9 +650,7 @@ def get_surface_current_density(self, lsurf:int=None, nt:int=64, nz:int=64): nfp = self.input.physics.Nfp if mvol==1: raise ValueError('Mvol=1; no interface current!') - if not isinstance(lsurf, np.ndarray): raise ValueError('lsurf should be a np.ndarray') - if lsurf is None: raise ValueError('Need to provide lsurf') - if (lsurf<1).any() or (lsurf>mvol-1).any(): raise ValueError('lsurf should be in [1,mvol-1]') + lsurf = _validate_lsurf(lsurf, mvol) if nt<1: raise ValueError('nt should greater than zero') if nz<1: raise ValueError('nz should greater than zero') @@ -683,11 +703,11 @@ def get_surface_current_density(self, lsurf:int=None, nt:int=64, nz:int=64): return j_dot_B, tarr, zarr -def get_surface(self, lsurf:int=None, nt:int=64, nz:int=64): +def get_surface(self, lsurf:np.ndarray=None, nt:int=64, nz:int=64): """Compute the surface area of a volume interface Args: - - lsurf: Interface number, between 1 and Mvol-1. + - lsurf: Interface number(s), between 1 and Mvol-1. default is np.arange(1, mvol) - nt: Number of poloidal points for integration, default is 64 - nz: Number of toroidal points for integration, default is 64 @@ -700,15 +720,10 @@ def get_surface(self, lsurf:int=None, nt:int=64, nz:int=64): mvol = self.output.Mvol nfp = self.input.physics.Nfp - if lsurf is None: - lsurf = np.arange(1,mvol) if mvol==1: raise ValueError('Mvol=1; no interface current!') - if not isinstance(lsurf, np.ndarray): - raise ValueError('lsurf should be a np.ndarray') - if (lsurf<1).any() or (lsurf>mvol-1).any(): - raise ValueError('lsurf should be in [1,mvol-1]') + lsurf = _validate_lsurf(lsurf, mvol) if nt<1: raise ValueError('nt should greater than zero') if nz<1: @@ -744,7 +759,7 @@ def get_flux_surface_average( self, lsurf, f, tarr, zarr ): inner side of the interface (i.e. lvol=lsurf-1, sarr=1) Args: - - lsurf (1D numpy array): Interface number, between 1 and Mvol-1 + - lsurf: Interface number(s), between 1 and Mvol-1. default is np.arange(1, mvol) - f (2D numpy array): function evaluated on a grid - tgrid (2D numpy array): theta grid - zgrid (2D numpy array): phi grid @@ -752,7 +767,11 @@ def get_flux_surface_average( self, lsurf, f, tarr, zarr ): Returns> - fsavg (1D numpy array): The flux surface average of f on each surface given in lsurf + Raises: + - ValueError: if input is wrong (invalid lsurf) """ + + lsurf = _validate_lsurf(lsurf, self.output.Mvol) # Get jacobian output = np.zeros(lsurf.shape) diff --git a/Utilities/pythontools/py_spec/output/spec.py b/Utilities/pythontools/py_spec/output/spec.py index 99d06ca3..428b59a3 100644 --- a/Utilities/pythontools/py_spec/output/spec.py +++ b/Utilities/pythontools/py_spec/output/spec.py @@ -95,15 +95,9 @@ def __init__(self, *args, **kwargs): if isinstance(_content, h5py.File): _content.close() - # make sure that Lrad is always an array - if np.isscalar(self.input.physics.Lrad): - self.input.physics.Lrad = np.array([self.input.physics.Lrad]) - # make sure that im always an array - if np.isscalar(self.output.im): - self.output.im = np.array([self.output.im]) - # make sure that in_ is always an array - if np.isscalar(self.output.in_): - self.output.in_ = np.array([self.output.in_]) + self.input.physics.Lrad = np.atleast_1d(self.input.physics.Lrad) + self.output.im = np.atleast_1d(self.output.im) + self.output.in_ = np.atleast_1d(self.output.in_) # these define the target dimensions in the radial direction Nvol = self.input.physics.Nvol diff --git a/Utilities/pythontools/pyproject.toml b/Utilities/pythontools/pyproject.toml new file mode 100644 index 00000000..60e6e551 --- /dev/null +++ b/Utilities/pythontools/pyproject.toml @@ -0,0 +1,31 @@ +[build-system] +requires = ["setuptools"] +build-backend = "setuptools.build_meta" + + +[project] +name="py_spec" +version="3.3.5" +dependencies = ["numpy>=1.21.1", + "f90nml", + "h5py", + "matplotlib", + "coilpy; python_version<'3.12'", + "scipy>=1.7.0"] +description="SPEC(Stepped-Pressure Equilibrium Code) python utilities" +readme="README.md" +authors = [ + { name = "Christopher Berg Smiet", email = "christopher.smiet@epfl.ch" }, + { name = "Caoxiang Zhu", email = "caoxiangzhu@gmail.com" }, + { name = "SPEC developers"} +] +maintainers = [ + { name = "Christopher Berg Smiet", email = "christopher.smiet@epfl.ch" }, +] +classifiers=[ + "Development Status :: 3 - Alpha", + "License :: OSI Approved :: GNU Lesser General Public License v3 or later (LGPLv3+)", + "Programming Language :: Python :: 3", + "Topic :: Scientific/Engineering", +] +license = {text = "GNU 3.0"} diff --git a/Utilities/pythontools/requirements.txt b/Utilities/pythontools/requirements.txt index 79349753..987fc86c 100644 --- a/Utilities/pythontools/requirements.txt +++ b/Utilities/pythontools/requirements.txt @@ -1,7 +1,6 @@ h5py matplotlib f90nml -numpy # Version 1.7.0 or higher is required - otherwise scipy.integrate.simpson does not exist scipy>=1.7.0 diff --git a/Utilities/pythontools/setup.py b/Utilities/pythontools/setup.py index 67d45afd..7aa39660 100644 --- a/Utilities/pythontools/setup.py +++ b/Utilities/pythontools/setup.py @@ -1,23 +1,6 @@ import setuptools -from py_spec import __version__ - -with open("README.md", "r") as fh: - long_description = fh.read() setuptools.setup( name="py_spec", - version=__version__, - description="SPEC(Stepped-Pressure Equilibrium Code) python utilities", - long_description=long_description, - long_description_content_type="text/markdown", - classifiers=[ - "Development Status :: 3 - Alpha", - "License :: OSI Approved :: GNU Lesser General Public License v3 or later (LGPLv3+)", - "Programming Language :: Python :: 3", - "Topic :: Scientific/Engineering", - ], - url="https://princetonuniversity.github.io/SPEC/", - author="SPEC developers", - license="GNU 3.0", - packages=['py_spec', 'py_spec.input', 'py_spec.output', 'py_spec.ci'] + packages=['py_spec', 'py_spec.input', 'py_spec.output', 'py_spec.ci', 'py_spec.math'] ) From 7dddaa9a2e888d92ac5e77311b6eb15da80418de Mon Sep 17 00:00:00 2001 From: ErolBa Date: Wed, 4 Dec 2024 13:30:48 +0100 Subject: [PATCH 26/36] keep up w master 2 --- outdated_compilation_instuctions.md | 520 ++++++++++++++++++++++++++++ setup.py | 2 +- setup_conda.sh | 26 -- spec_conda_env.yml | 19 - src/xspech.f90 | 2 +- 5 files changed, 522 insertions(+), 47 deletions(-) create mode 100644 outdated_compilation_instuctions.md delete mode 100755 setup_conda.sh delete mode 100644 spec_conda_env.yml diff --git a/outdated_compilation_instuctions.md b/outdated_compilation_instuctions.md new file mode 100644 index 00000000..be440f16 --- /dev/null +++ b/outdated_compilation_instuctions.md @@ -0,0 +1,520 @@ +# Compilation hints for SPEC + +This document tries to summarize the steps necessary to setup SPEC on your machine. +Two approaches are discussed. +The first one is the CMake setup. +The second one is the more classical `Makefile` setup. + +## CMake and Anaconda + +The Anaconda system provides an ecosystem of compilers, precompiled libraries and python packages ready to be used. +The main goal is to decouple the conda environment from the host system, +so that you can use modern software and tools also on machines with outdated local software. + +This guide was written while testing the commands on a Debian 9 x86_64 Linux system. +This should be deemed old enough to demonstrate the weirdest errors if something is not under control, +hence facilitating the correctness of these instructions. + +### Install Anaconda +The Anaconda installer is available from [the Anaconda website](https://www.anaconda.com/products/individual). +At the time of writing, the URL to the actual file is: https://repo.anaconda.com/archive/Anaconda3-2021.11-Linux-x86_64.sh + +Go into folder where the anaconda installer will be downloaded to +and download the Anaconda installer: + +```bash +cd ~/Downloads +wget https://repo.anaconda.com/archive/Anaconda3-2021.11-Linux-x86_64.sh +``` + +Launch the Anaconda installer: + +```bash +bash Anaconda3-2021.11-Linux-x86_64.sh +``` + + * press ENTER to contine + * Accept License Agreement: `yes` + * Confirm the default installation location (here: `/home/IPP-HGW/jons/anaconda3` == `~/anaconda3`) + * Allow the installer to run `conda init`: `yes` + +At this point, the Anaconda installer will modify your `~/.bashrc`. +In order to make these changes take effect, you can logout and log back in, +close and re-open your Terminal window or do: + +```bash +source ~/.bashrc +``` + +Disable the activation of the Anaconda base environment on login: + +```bash +conda config --set auto_activate_base False +``` + +Anaconda works in so-called virtual environments, where environment variables get managed by Anaconda +to setup paths to compilers, libraries and include directories semi-automagically. + +For SPEC, it is suggested to create a new conda environment. +A setup script to perform these actions is provided in the SPEC repository. +Thus, we need to clone the SPEC repository now. + +### Clone the SPEC repository + +In this guide, we assume that your copy of SPEC will be located at `~/SPEC`. + +If you want to upload your changes to the SPEC repository, +you should setup your SSH key in your GitHub Settings and use the following +URL for the repository instead: `git@github.com:PrincetonUniversity/SPEC.git` + +Clone the repository from GitHub into a folder `SPEC` in your home directory:: + +```bash +cd ~ +git clone https://github.com/PrincetonUniversity/SPEC.git +``` + +### Setup a Conda Environment for SPEC + +The conda environment setup needed to compile and run SPEC is in `setup_conda.sh`. +This scripts takes a specification of the conda packages to install from `spec_conda_env.yml` +and created a conda environment called `spec_env`. +Also, two scripts are created in `etc/conda/activate.d` and `etc/conda/deactivate.d` +of the `spec_env` environment to mask the system's `LD_LIBRARY_PATH` +when entering the conda environment and to restore it to its previous value +when leaving the `spec_env` environment. +Also, the environment variable `FFTW_ROOT` is set to the conda environment +to tell SPEC to use the conda-provided version of FFTW. + +Change into the freshly-cloned SPEC repository and run this script: + +```bash +cd ~/SPEC +./setup_conda.sh +``` + +This might take a while, but at the end you should end up with a message similar to this: + +``` +... lots of stuff above here ... +done +# +# To activate this environment, use +# +# $ conda activate spec_env +# +# To deactivate an active environment, use +# +# $ conda deactivate + +~/anaconda3/envs/spec_env ~/SPEC +~/SPEC +``` + +Activate the conda environment for SPEC: + +```bash +conda activate spec_env +``` + +A forked version of `f90wrap` is required to build the SPEC Python wrapper (for now). +Install that next (inside the `spec_env` conda environment !!!): + +```bash +pip install -U git+https://github.com/zhucaoxiang/f90wrap +``` + +The CMake setup is controlled via the `setup.py` Python script from the SPEC repository. +It parses the `CMAKE_ARGS` environment variable provided by conda. + +Additional machine-dependent CMake options are loaded from `cmake_config.json`. +This is a soft-link to a file in `cmake_machines`. +Anaconda provides all libraries required to build SPEC, +but we still need to make sure that the `cmake_config.json` link points to +`cmake_machines/conda_debian.json`. +Note that `conda.json` in `cmake_machines` is outdated, as it includes machine-dependent options (`-DHDF5_ROOT=~/opt/miniconda3/envs/simsopt/`). + +Now force the `cmake_config.json` link to point to the correct file: + +```bash +ln -sf cmake_machines/conda_debian.json cmake_config.json +``` + +This concludes the preliminary setup steps and we can progress by starting the build process: + +```bash +python setup.py bdist_wheel +``` + +This step also takes quite a while. +At the end, the SPEC python package (`spec-0.0.1-cp310-cp310-linux_x86_64.whl` or similar) should be available in `dist`. + +Install it now: + +```bash +pip install dist/*.whl +``` + +Note that the Python package you just installed also contains the regular stand-alone SPEC executable `xspec`, +which gets installed into `bin/xspec` of your conda environment. +Verify this by calling `which xspec`. +You should get a message similar to: + +``` +/home/IPP-HGW/jons/anaconda3/envs/spec_env/bin/xspec +``` + +### Testing your SPEC installation + +First, verify that the stand-alone executable is usable. +A few test cases are provided in `InputFiles/TestCases`. + +Create a new directory for SPEC runs and change into it + +```bash +mkdir ~/SPEC_runs +cd ~/SPEC_runs +``` + +Copy a demo input file into the current working directory: + +```bash +cp ~/SPEC/InputFiles/TestCases/G3V01L0Fi.001.sp . +``` + +Call SPEC with an input file (`*.sp`) as argument on the command line: + +```bash +xspec G3V01L0Fi.001.sp +``` + +You should see the screen output of the SPEC run. +Among the last lines should be something similar to this: + +``` +ending : 0.88 : myid= 0 ; completion ; time= 0.88s = 0.01m = 0.00h = 0.00d ; date= 2022/02/17 ; time= 17:35:33 ; ext = G1V02L0Fi.001 +ending : : +xspech : : +xspech : 0.88 : myid= 0 : time= 0.01m = 0.00h = 0.00d ; +``` + +This indicates that the stand-alone executable is usable. + +Next, the python wrapper is tested. + +1. Check that the SPEC version can be found: + + ```bash + python -c "from spec import spec_f90wrapped as spec; print('SPEC version: {:}'.format(spec.constants.version))" + ``` + + This should print a message like "SPEC version: 3.1" on the screen. + +2. Check that the Python wrapper can be used as a stand-alone code: + + ```bash + OMP_NUM_THREADS=1 python ~/SPEC/Utilities/python_wrapper/spec/core.py G3V01L0Fi.001.sp + ``` + + This should conclude with the message `SPEC called from python finished!`. + +3. Run the optimization example code: + + ```bash + OMP_NUM_THREADS=1 python ~/SPEC/Utilities/python_wrapper/examples/example.py + ``` + + This should run a basic optimization problem, + where the SPEC inputs are controlled via `scipy.optimize`. + +4. Run the interactive re-convergence example code: + + ```bash + OMP_NUM_THREADS=1 python ~/SPEC/Utilities/python_wrapper/examples/example_2.py + ``` + + This should compute a SPEC equilibrium, then change the central pressure, + re-converge SPEC, etc. for a set of five values of the central pressure + in a two-volume classical Stellarator case. + After the pressure scan with re-convergence, + a plot of the MHD energy vs. the central pressure is shown. + +### Acknowledgements +Here are a few links that proved useful in setting this up: +* https://docs.anaconda.com/anaconda/install/linux/ +* https://www.anaconda.com/products/individual +* https://www.rosehosting.com/blog/how-to-install-anaconda-python-on-debian-9/ +* https://github.com/RcppCore/Rcpp/issues/770#issuecomment-346716808 +* https://computing.docs.ligo.org/conda/compiling/ +* https://stackoverflow.com/a/64253999 +* https://stackoverflow.com/a/46833531 +* https://stackoverflow.com/a/49238956 +* https://conda.io/projects/conda-build/en/latest/resources/use-shared-libraries.html + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +# BELOW INSTRUCTIONS ARE OUTDATED + +# BELOW INSTRUCTIONS ARE OUTDATED + +# BELOW INSTRUCTIONS ARE OUTDATED + + + +In order to run SPEC, you need a copy of the HDF5 libraries installed, which has the Fortran interface enabled. + +## Installation with CMake + +Using CMake, SPEC can be built as a stand-alone executable and as a python extension, +where SPEC can be run directly from python, with all variables passed directly in memory. + + +Download the package from git. And change to the root directory of SPEC source code by running +```bash +cd +``` + +## Stand-alone Executable Compiling + +Compiling SPEC requires MPI, HDF5, and numerical libraries such as BLAS, LAPACK, FFTW. For numerical libraries, you could use system supplied libraries or you could use intel math kernel library (MKL). + +Machine-specific settings when building the python wrapper are put into separate `json` files in the `cmake_machines` directory. +For building the regular SPEC executable, the default settings should work. + +In order to select a machine-specific settings file, create a soft link to the indented file in `cmake_machines`: + +```bash +ln -sf cmake_machines/gfortran_ubuntu.json cmake_config.json +``` + +### CentOS +Here instructions are given for CentOS 7 + +#### Dependencies +Install OpenBLAS, FFTW3, and hdf5 using the command +```bash +yum install -y gcc-gfortran openmpi openmpi-devel hdf5 hdf5-devel fftw3 fftw3-devel openblas openblas-devel python3 python3-devel cmake ninja-build +``` +If you don't have the latest version of cmake avaialable on your system, you can create a python virtual environment ([instructions are here](https://packaging.python.org/guides/installing-using-pip-and-virtual-environments/)), activate it, and then install cmake in that virtual environment using pip +```bash +pip install cmake ninja +``` + +#### Configure +When using cmake to build SPEC, the first step is to configure compilers and the locations of libraries. Cmake can detect compilers and libraries at standard locations easily but needs hand-holding when the required libraries are non-standard locations. + +The following command was used to configure cmake build setup for SPEC on Centos +```bash +cmake -S. -Bbuild -GNinja -DCMAKE_Fortran_COMPILER=mpifort -DBLA_VENDOR=OpenBLAS -DHDF5_NO_FIND_PACKAGE_CONFIG_FILE=TRUE -DHDF5_PREFER_PARALLEL=TRUE -DCMAKE_INSTALL_PREFIX=${SPEC_ROOT}/install --trace-source=CMakeLists.txt 2>&1 | tee log +``` +There are few points to note on the above command + - All the build related files will be in build folder. + - Ninja build system is used. If your system doesn't have ninja installed, remove the -G option. The default is the standard `make` tool. + - We ae using OpenBLAS for BLAS and LAPACK and MPI fortran compiler + - Since most of the libraries are in standard location, we don't have to specify them. We are giving couple of options related to HDF5 libraries. + - The installation path is install subfolder location within SPEC folder. + - We are interested in a verbose output and also want to store the output in `log` file. + +#### Build +After successful completion of cmake configuration step, building is trivial +```bash +cmake --build build +```` +#### Install +The last step is to install the executable by running +```bash +cmake --install build +``` + +That's it! If all the above steps completed without errors, you have the SPEC executable `xspec` installed at `install/bin` folder + +## Python Extension Compiling +Building the SPEC python extension will also build the SPEC executable. +In the SPEC root folder, edit the `cmake_config.json` as necessary for your system. Few example `.json` files are provided in the `cmake_machines` folder. + +### Dependencies +It is strongly suggested to use a python virtual environment either conda or python venv. After virtual environment is installed and activated, install the python related dependencies. Please note that these are in addition to the dependencies listed earlier in stand-alone installation steps. If you are using conda virtual environment try installing the dependencies using `conda install` command +```bash +conda install -n numpy f90nml scikit-build cmake ninja +``` + +If you are using venv virtual environment, run +```bash +pip install numpy f90nml scikit-build cmake ninja +``` +Now install f90wrap. Please keep in mind that numpy has to be installed before installing f90wrap. +```bash +pip install -U git+https://github.com/zhucaoxiang/f90wrap +``` + +Now install the SPEC extension by running the setup.py script present in the SPEC root folder. +```bash +python setup.py bdist_wheel; cd dist/; pip install *.whl +``` +in succession. At this point, you should be able to import the `spec` module in python. To test this, you can try the following command from the shell: +```bash +python -c "import spec; print('success')" +``` + +If you want editable install, run +``` +python setup.py develop +``` + + +## Stellar cluster at PPPL + +### Python wrapper +Below are the steps to build python wrappers for SPEC on stellar. + +1. Needed modules are + > i. hdf5/gcc/1.10.6 + > ii. intel-mkl/2021.1.1 + > iii. openmpi/gcc/4.1.0 + > iv. anaconda3/2021.5. + --- + **Note** + + FFTW is supplied as part of Intel MKL and we just need to link against MKL. + + --- + Load the modules by running + ``` + module load hdf5/gcc/1.10.6 intel-mkl/2021.1.1 openmpi/gcc/4.1.0 anaconda3/2021.5 + ``` +2. Create conda virtual environment. + ``` + conda create -n spec_ve python=3.8 + ``` + You have to press enter twice. Here a conda virtual environment named `spec_ve` is created with python version 3.8 and lot of packages are installed. Activate by running + ``` + conda activate spec_ve + ``` +3. Install `cmake`, `ninja`, `scikit-build`, `numpy` using either conda or pip. + ``` + conda install cmake ninja scikit-build numpy + ``` + or + ``` + pip install cmake ninja scikit-build numpy + ``` +4. Install `f90wrap` by running + ``` + pip install git+https://github.com/zhucaoxiang/f90wrap.git + ``` +5. Clone the spec repo from github + ``` + git clone https://github.com/PrincetonUniversity/SPEC.git + ``` + Change the working directory by running `cd SPEC`. +6. Edit the cmake_config.json to populate correct cmake_flags. For stellar, cmake_config.json should look like + ``` + { + "cmake_args": [ + "-DCMAKE_C_COMPILER=mpicc", + "-DCMAKE_CXX_COMPILER=mpicxx", + "-DCMAKE_Fortran_COMPILER=mpifort", + "-DBLA_VENDOR=Intel10_64lp", + "-DHDF5_ROOT=/usr/local/hdf5/gcc/1.10.6", + "-DHDF5_PREFER_PARALLEL=False"] + } + ``` +7. Then build the python wheel for SPEC wrapper using + ``` + python setup.py bdist_wheel + ``` + The resulting wheel is located in `dist` folder. Install SPEC python wrapper by running + ``` + pip install dist/spec*.whl + ``` + +8. Install mpi4py using pip/conda. If using pip, don't forget to use `--no-cache-dir` flag + ``` + pip install --no-cache-dir mpi4py + ``` + or + ``` + conda install mpi4py + ``` + +### SPEC executable. +The python wrapper builds spec executable but it gets installed at an obscure location. If you mainly want SPEC executable `xspec`, the steps are similar. +1. Load the required modules. Refer to the first step in the python wrapper instructions. +2. Clone the SPEC repo and make SPEC as working directory. Refer to the 5th step above. +3. Run the cmake configuration by running + ``` + cmake -Bbuild -S . -DCMAKE_C_COMPILER=mpicc -DCMAKE_CXX_COMPILER=mpicxx -DCMAKE_Fortran_COMPILER=mpifort -DBLA_VENDOR=Intel10_64lp \ + -DHDF5_ROOT=/usr/local/hdf5/gcc/1.10.6 -DHDF5_PREFER_PARALLEL=False -DCMAKE_INSTALL_PREFIX= + ``` + Please note SPEC gets installed at `/bin`, where `` is the folder of your choice. Building of SPEC library will be done in the folder `build`, where all the intermediary compilation files will be located. +4. Compile the code by running + ``` + cmake --build build + ``` + This command will invoke `make` build generator. Alternatively, you can switch to build folder and run make utility manually. + ``` + cd build + make + ``` +5. Install the SPEC executable by running + ``` + cmake --install build + ``` + SPEC library gets installed `/lib` and SPEC executable get installed at `/bin` + +## Mac + +Here is how to build the HDF5 library : +1. download `hdf5-1.10.5.tar.gz` from https://www.hdfgroup.org/downloads/hdf5/source-code/ +2. extract: `tar xzf hdf5-1.10.5.tar.gz` +3. cd into source folder: `cd hdf5-1.10.5` +4. make a build folder: `mkdir build` +5. cd into build folder: `cd build` +6. run cmake with options for the Fortran interface: `cmake -DHDF5_BUILD_FORTRAN:BOOL=ON ..` +7. actually build the HDF5 library: `make` + +This should leave you with a file "hdf5-1.10.5.dmg" or similar, which you can install just as any other Mac application. +See e.g. this document for more detailed instructions: +https://support.hdfgroup.org/ftp/HDF5/current/src/unpacked/release_docs/INSTALL_CMake.txt + +The compilation of SPEC itself then proceeds as usual. +You then only need to specify the HDF5 folder in the Makefile, which will likely be +`/Applications/HDF_Group/HDF5/1.10.5`. diff --git a/setup.py b/setup.py index b42480ee..e0ac7fad 100644 --- a/setup.py +++ b/setup.py @@ -38,7 +38,7 @@ setup( name="spec", - version="0.0.2", + version="0.0.3", #license="MIT", packages=['spec'], package_dir={'': 'Utilities/python_wrapper'}, diff --git a/setup_conda.sh b/setup_conda.sh deleted file mode 100755 index 12d93104..00000000 --- a/setup_conda.sh +++ /dev/null @@ -1,26 +0,0 @@ - - -# create conda environment for SPEC -conda env create -f spec_conda_env.yml - -# make sure environment variables get managed correctly -pushd ~/anaconda3/envs/spec_env -mkdir -p ./etc/conda/activate.d -mkdir -p ./etc/conda/deactivate.d - -echo " -export OLD_LD_LIBRARY_PATH=\${LD_LIBRARY_PATH} -export LD_LIBRARY_PATH=\${HOME}/anaconda3/envs/spec_env/lib:\${LD_LIBRARY_PATH} - -export FFTW_ROOT=\${HOME}/anaconda3/envs/spec_env -" > ./etc/conda/activate.d/env_vars.sh - -echo " -export LD_LIBRARY_PATH=\${OLD_LD_LIBRARY_PATH} -unset OLD_LD_LIBRARY_PATH - -unset FFTW_ROOT -" > ./etc/conda/deactivate.d/env_vars.sh - -popd - diff --git a/spec_conda_env.yml b/spec_conda_env.yml deleted file mode 100644 index a34a03dd..00000000 --- a/spec_conda_env.yml +++ /dev/null @@ -1,19 +0,0 @@ -name: spec_env -channels: - - conda-forge - - defaults -dependencies: - - c-compiler - - fortran-compiler - - mpi4py - - ninja - - cmake - - scikit-build - - fftw - - hdf5 - - numpy - - openmp - - openblas - - matplotlib - - scipy - diff --git a/src/xspech.f90 b/src/xspech.f90 index 0ceb417c..1389b232 100644 --- a/src/xspech.f90 +++ b/src/xspech.f90 @@ -204,7 +204,7 @@ subroutine read_command_args use fileunits, only: ounit use inputlist, only: Wreadin - use allglobal, only: cpus, myid, ext, MPI_COMM_SPEC, write_spec_namelist + use allglobal, only: cpus, myid, ext, get_hidden, MPI_COMM_SPEC, write_spec_namelist LOCALS From d7c944c6549e0c10f8b67784be70970bc74c19a0 Mon Sep 17 00:00:00 2001 From: ErolBa Date: Wed, 4 Dec 2024 13:33:21 +0100 Subject: [PATCH 27/36] keep up w master 3 --- .gitignore | 2 - Compile.md | 520 ------------------------------------ compilation_instructions.md | 181 +++++++++++++ src/dforce.f90 | 2 +- src/dfp100.f90 | 12 +- src/hesian.f90 | 9 +- src/memory.f90 | 2 + src/sphdf5.f90 | 27 ++ 8 files changed, 228 insertions(+), 527 deletions(-) delete mode 100644 Compile.md create mode 100644 compilation_instructions.md diff --git a/.gitignore b/.gitignore index 290d9bd9..564e14d3 100644 --- a/.gitignore +++ b/.gitignore @@ -61,5 +61,3 @@ src/msphdf5.f90 # Apple Mac related .DS_Store -# vscode files -.vscode/ diff --git a/Compile.md b/Compile.md deleted file mode 100644 index be440f16..00000000 --- a/Compile.md +++ /dev/null @@ -1,520 +0,0 @@ -# Compilation hints for SPEC - -This document tries to summarize the steps necessary to setup SPEC on your machine. -Two approaches are discussed. -The first one is the CMake setup. -The second one is the more classical `Makefile` setup. - -## CMake and Anaconda - -The Anaconda system provides an ecosystem of compilers, precompiled libraries and python packages ready to be used. -The main goal is to decouple the conda environment from the host system, -so that you can use modern software and tools also on machines with outdated local software. - -This guide was written while testing the commands on a Debian 9 x86_64 Linux system. -This should be deemed old enough to demonstrate the weirdest errors if something is not under control, -hence facilitating the correctness of these instructions. - -### Install Anaconda -The Anaconda installer is available from [the Anaconda website](https://www.anaconda.com/products/individual). -At the time of writing, the URL to the actual file is: https://repo.anaconda.com/archive/Anaconda3-2021.11-Linux-x86_64.sh - -Go into folder where the anaconda installer will be downloaded to -and download the Anaconda installer: - -```bash -cd ~/Downloads -wget https://repo.anaconda.com/archive/Anaconda3-2021.11-Linux-x86_64.sh -``` - -Launch the Anaconda installer: - -```bash -bash Anaconda3-2021.11-Linux-x86_64.sh -``` - - * press ENTER to contine - * Accept License Agreement: `yes` - * Confirm the default installation location (here: `/home/IPP-HGW/jons/anaconda3` == `~/anaconda3`) - * Allow the installer to run `conda init`: `yes` - -At this point, the Anaconda installer will modify your `~/.bashrc`. -In order to make these changes take effect, you can logout and log back in, -close and re-open your Terminal window or do: - -```bash -source ~/.bashrc -``` - -Disable the activation of the Anaconda base environment on login: - -```bash -conda config --set auto_activate_base False -``` - -Anaconda works in so-called virtual environments, where environment variables get managed by Anaconda -to setup paths to compilers, libraries and include directories semi-automagically. - -For SPEC, it is suggested to create a new conda environment. -A setup script to perform these actions is provided in the SPEC repository. -Thus, we need to clone the SPEC repository now. - -### Clone the SPEC repository - -In this guide, we assume that your copy of SPEC will be located at `~/SPEC`. - -If you want to upload your changes to the SPEC repository, -you should setup your SSH key in your GitHub Settings and use the following -URL for the repository instead: `git@github.com:PrincetonUniversity/SPEC.git` - -Clone the repository from GitHub into a folder `SPEC` in your home directory:: - -```bash -cd ~ -git clone https://github.com/PrincetonUniversity/SPEC.git -``` - -### Setup a Conda Environment for SPEC - -The conda environment setup needed to compile and run SPEC is in `setup_conda.sh`. -This scripts takes a specification of the conda packages to install from `spec_conda_env.yml` -and created a conda environment called `spec_env`. -Also, two scripts are created in `etc/conda/activate.d` and `etc/conda/deactivate.d` -of the `spec_env` environment to mask the system's `LD_LIBRARY_PATH` -when entering the conda environment and to restore it to its previous value -when leaving the `spec_env` environment. -Also, the environment variable `FFTW_ROOT` is set to the conda environment -to tell SPEC to use the conda-provided version of FFTW. - -Change into the freshly-cloned SPEC repository and run this script: - -```bash -cd ~/SPEC -./setup_conda.sh -``` - -This might take a while, but at the end you should end up with a message similar to this: - -``` -... lots of stuff above here ... -done -# -# To activate this environment, use -# -# $ conda activate spec_env -# -# To deactivate an active environment, use -# -# $ conda deactivate - -~/anaconda3/envs/spec_env ~/SPEC -~/SPEC -``` - -Activate the conda environment for SPEC: - -```bash -conda activate spec_env -``` - -A forked version of `f90wrap` is required to build the SPEC Python wrapper (for now). -Install that next (inside the `spec_env` conda environment !!!): - -```bash -pip install -U git+https://github.com/zhucaoxiang/f90wrap -``` - -The CMake setup is controlled via the `setup.py` Python script from the SPEC repository. -It parses the `CMAKE_ARGS` environment variable provided by conda. - -Additional machine-dependent CMake options are loaded from `cmake_config.json`. -This is a soft-link to a file in `cmake_machines`. -Anaconda provides all libraries required to build SPEC, -but we still need to make sure that the `cmake_config.json` link points to -`cmake_machines/conda_debian.json`. -Note that `conda.json` in `cmake_machines` is outdated, as it includes machine-dependent options (`-DHDF5_ROOT=~/opt/miniconda3/envs/simsopt/`). - -Now force the `cmake_config.json` link to point to the correct file: - -```bash -ln -sf cmake_machines/conda_debian.json cmake_config.json -``` - -This concludes the preliminary setup steps and we can progress by starting the build process: - -```bash -python setup.py bdist_wheel -``` - -This step also takes quite a while. -At the end, the SPEC python package (`spec-0.0.1-cp310-cp310-linux_x86_64.whl` or similar) should be available in `dist`. - -Install it now: - -```bash -pip install dist/*.whl -``` - -Note that the Python package you just installed also contains the regular stand-alone SPEC executable `xspec`, -which gets installed into `bin/xspec` of your conda environment. -Verify this by calling `which xspec`. -You should get a message similar to: - -``` -/home/IPP-HGW/jons/anaconda3/envs/spec_env/bin/xspec -``` - -### Testing your SPEC installation - -First, verify that the stand-alone executable is usable. -A few test cases are provided in `InputFiles/TestCases`. - -Create a new directory for SPEC runs and change into it - -```bash -mkdir ~/SPEC_runs -cd ~/SPEC_runs -``` - -Copy a demo input file into the current working directory: - -```bash -cp ~/SPEC/InputFiles/TestCases/G3V01L0Fi.001.sp . -``` - -Call SPEC with an input file (`*.sp`) as argument on the command line: - -```bash -xspec G3V01L0Fi.001.sp -``` - -You should see the screen output of the SPEC run. -Among the last lines should be something similar to this: - -``` -ending : 0.88 : myid= 0 ; completion ; time= 0.88s = 0.01m = 0.00h = 0.00d ; date= 2022/02/17 ; time= 17:35:33 ; ext = G1V02L0Fi.001 -ending : : -xspech : : -xspech : 0.88 : myid= 0 : time= 0.01m = 0.00h = 0.00d ; -``` - -This indicates that the stand-alone executable is usable. - -Next, the python wrapper is tested. - -1. Check that the SPEC version can be found: - - ```bash - python -c "from spec import spec_f90wrapped as spec; print('SPEC version: {:}'.format(spec.constants.version))" - ``` - - This should print a message like "SPEC version: 3.1" on the screen. - -2. Check that the Python wrapper can be used as a stand-alone code: - - ```bash - OMP_NUM_THREADS=1 python ~/SPEC/Utilities/python_wrapper/spec/core.py G3V01L0Fi.001.sp - ``` - - This should conclude with the message `SPEC called from python finished!`. - -3. Run the optimization example code: - - ```bash - OMP_NUM_THREADS=1 python ~/SPEC/Utilities/python_wrapper/examples/example.py - ``` - - This should run a basic optimization problem, - where the SPEC inputs are controlled via `scipy.optimize`. - -4. Run the interactive re-convergence example code: - - ```bash - OMP_NUM_THREADS=1 python ~/SPEC/Utilities/python_wrapper/examples/example_2.py - ``` - - This should compute a SPEC equilibrium, then change the central pressure, - re-converge SPEC, etc. for a set of five values of the central pressure - in a two-volume classical Stellarator case. - After the pressure scan with re-convergence, - a plot of the MHD energy vs. the central pressure is shown. - -### Acknowledgements -Here are a few links that proved useful in setting this up: -* https://docs.anaconda.com/anaconda/install/linux/ -* https://www.anaconda.com/products/individual -* https://www.rosehosting.com/blog/how-to-install-anaconda-python-on-debian-9/ -* https://github.com/RcppCore/Rcpp/issues/770#issuecomment-346716808 -* https://computing.docs.ligo.org/conda/compiling/ -* https://stackoverflow.com/a/64253999 -* https://stackoverflow.com/a/46833531 -* https://stackoverflow.com/a/49238956 -* https://conda.io/projects/conda-build/en/latest/resources/use-shared-libraries.html - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -# BELOW INSTRUCTIONS ARE OUTDATED - -# BELOW INSTRUCTIONS ARE OUTDATED - -# BELOW INSTRUCTIONS ARE OUTDATED - - - -In order to run SPEC, you need a copy of the HDF5 libraries installed, which has the Fortran interface enabled. - -## Installation with CMake - -Using CMake, SPEC can be built as a stand-alone executable and as a python extension, -where SPEC can be run directly from python, with all variables passed directly in memory. - - -Download the package from git. And change to the root directory of SPEC source code by running -```bash -cd -``` - -## Stand-alone Executable Compiling - -Compiling SPEC requires MPI, HDF5, and numerical libraries such as BLAS, LAPACK, FFTW. For numerical libraries, you could use system supplied libraries or you could use intel math kernel library (MKL). - -Machine-specific settings when building the python wrapper are put into separate `json` files in the `cmake_machines` directory. -For building the regular SPEC executable, the default settings should work. - -In order to select a machine-specific settings file, create a soft link to the indented file in `cmake_machines`: - -```bash -ln -sf cmake_machines/gfortran_ubuntu.json cmake_config.json -``` - -### CentOS -Here instructions are given for CentOS 7 - -#### Dependencies -Install OpenBLAS, FFTW3, and hdf5 using the command -```bash -yum install -y gcc-gfortran openmpi openmpi-devel hdf5 hdf5-devel fftw3 fftw3-devel openblas openblas-devel python3 python3-devel cmake ninja-build -``` -If you don't have the latest version of cmake avaialable on your system, you can create a python virtual environment ([instructions are here](https://packaging.python.org/guides/installing-using-pip-and-virtual-environments/)), activate it, and then install cmake in that virtual environment using pip -```bash -pip install cmake ninja -``` - -#### Configure -When using cmake to build SPEC, the first step is to configure compilers and the locations of libraries. Cmake can detect compilers and libraries at standard locations easily but needs hand-holding when the required libraries are non-standard locations. - -The following command was used to configure cmake build setup for SPEC on Centos -```bash -cmake -S. -Bbuild -GNinja -DCMAKE_Fortran_COMPILER=mpifort -DBLA_VENDOR=OpenBLAS -DHDF5_NO_FIND_PACKAGE_CONFIG_FILE=TRUE -DHDF5_PREFER_PARALLEL=TRUE -DCMAKE_INSTALL_PREFIX=${SPEC_ROOT}/install --trace-source=CMakeLists.txt 2>&1 | tee log -``` -There are few points to note on the above command - - All the build related files will be in build folder. - - Ninja build system is used. If your system doesn't have ninja installed, remove the -G option. The default is the standard `make` tool. - - We ae using OpenBLAS for BLAS and LAPACK and MPI fortran compiler - - Since most of the libraries are in standard location, we don't have to specify them. We are giving couple of options related to HDF5 libraries. - - The installation path is install subfolder location within SPEC folder. - - We are interested in a verbose output and also want to store the output in `log` file. - -#### Build -After successful completion of cmake configuration step, building is trivial -```bash -cmake --build build -```` -#### Install -The last step is to install the executable by running -```bash -cmake --install build -``` - -That's it! If all the above steps completed without errors, you have the SPEC executable `xspec` installed at `install/bin` folder - -## Python Extension Compiling -Building the SPEC python extension will also build the SPEC executable. -In the SPEC root folder, edit the `cmake_config.json` as necessary for your system. Few example `.json` files are provided in the `cmake_machines` folder. - -### Dependencies -It is strongly suggested to use a python virtual environment either conda or python venv. After virtual environment is installed and activated, install the python related dependencies. Please note that these are in addition to the dependencies listed earlier in stand-alone installation steps. If you are using conda virtual environment try installing the dependencies using `conda install` command -```bash -conda install -n numpy f90nml scikit-build cmake ninja -``` - -If you are using venv virtual environment, run -```bash -pip install numpy f90nml scikit-build cmake ninja -``` -Now install f90wrap. Please keep in mind that numpy has to be installed before installing f90wrap. -```bash -pip install -U git+https://github.com/zhucaoxiang/f90wrap -``` - -Now install the SPEC extension by running the setup.py script present in the SPEC root folder. -```bash -python setup.py bdist_wheel; cd dist/; pip install *.whl -``` -in succession. At this point, you should be able to import the `spec` module in python. To test this, you can try the following command from the shell: -```bash -python -c "import spec; print('success')" -``` - -If you want editable install, run -``` -python setup.py develop -``` - - -## Stellar cluster at PPPL - -### Python wrapper -Below are the steps to build python wrappers for SPEC on stellar. - -1. Needed modules are - > i. hdf5/gcc/1.10.6 - > ii. intel-mkl/2021.1.1 - > iii. openmpi/gcc/4.1.0 - > iv. anaconda3/2021.5. - --- - **Note** - - FFTW is supplied as part of Intel MKL and we just need to link against MKL. - - --- - Load the modules by running - ``` - module load hdf5/gcc/1.10.6 intel-mkl/2021.1.1 openmpi/gcc/4.1.0 anaconda3/2021.5 - ``` -2. Create conda virtual environment. - ``` - conda create -n spec_ve python=3.8 - ``` - You have to press enter twice. Here a conda virtual environment named `spec_ve` is created with python version 3.8 and lot of packages are installed. Activate by running - ``` - conda activate spec_ve - ``` -3. Install `cmake`, `ninja`, `scikit-build`, `numpy` using either conda or pip. - ``` - conda install cmake ninja scikit-build numpy - ``` - or - ``` - pip install cmake ninja scikit-build numpy - ``` -4. Install `f90wrap` by running - ``` - pip install git+https://github.com/zhucaoxiang/f90wrap.git - ``` -5. Clone the spec repo from github - ``` - git clone https://github.com/PrincetonUniversity/SPEC.git - ``` - Change the working directory by running `cd SPEC`. -6. Edit the cmake_config.json to populate correct cmake_flags. For stellar, cmake_config.json should look like - ``` - { - "cmake_args": [ - "-DCMAKE_C_COMPILER=mpicc", - "-DCMAKE_CXX_COMPILER=mpicxx", - "-DCMAKE_Fortran_COMPILER=mpifort", - "-DBLA_VENDOR=Intel10_64lp", - "-DHDF5_ROOT=/usr/local/hdf5/gcc/1.10.6", - "-DHDF5_PREFER_PARALLEL=False"] - } - ``` -7. Then build the python wheel for SPEC wrapper using - ``` - python setup.py bdist_wheel - ``` - The resulting wheel is located in `dist` folder. Install SPEC python wrapper by running - ``` - pip install dist/spec*.whl - ``` - -8. Install mpi4py using pip/conda. If using pip, don't forget to use `--no-cache-dir` flag - ``` - pip install --no-cache-dir mpi4py - ``` - or - ``` - conda install mpi4py - ``` - -### SPEC executable. -The python wrapper builds spec executable but it gets installed at an obscure location. If you mainly want SPEC executable `xspec`, the steps are similar. -1. Load the required modules. Refer to the first step in the python wrapper instructions. -2. Clone the SPEC repo and make SPEC as working directory. Refer to the 5th step above. -3. Run the cmake configuration by running - ``` - cmake -Bbuild -S . -DCMAKE_C_COMPILER=mpicc -DCMAKE_CXX_COMPILER=mpicxx -DCMAKE_Fortran_COMPILER=mpifort -DBLA_VENDOR=Intel10_64lp \ - -DHDF5_ROOT=/usr/local/hdf5/gcc/1.10.6 -DHDF5_PREFER_PARALLEL=False -DCMAKE_INSTALL_PREFIX= - ``` - Please note SPEC gets installed at `/bin`, where `` is the folder of your choice. Building of SPEC library will be done in the folder `build`, where all the intermediary compilation files will be located. -4. Compile the code by running - ``` - cmake --build build - ``` - This command will invoke `make` build generator. Alternatively, you can switch to build folder and run make utility manually. - ``` - cd build - make - ``` -5. Install the SPEC executable by running - ``` - cmake --install build - ``` - SPEC library gets installed `/lib` and SPEC executable get installed at `/bin` - -## Mac - -Here is how to build the HDF5 library : -1. download `hdf5-1.10.5.tar.gz` from https://www.hdfgroup.org/downloads/hdf5/source-code/ -2. extract: `tar xzf hdf5-1.10.5.tar.gz` -3. cd into source folder: `cd hdf5-1.10.5` -4. make a build folder: `mkdir build` -5. cd into build folder: `cd build` -6. run cmake with options for the Fortran interface: `cmake -DHDF5_BUILD_FORTRAN:BOOL=ON ..` -7. actually build the HDF5 library: `make` - -This should leave you with a file "hdf5-1.10.5.dmg" or similar, which you can install just as any other Mac application. -See e.g. this document for more detailed instructions: -https://support.hdfgroup.org/ftp/HDF5/current/src/unpacked/release_docs/INSTALL_CMake.txt - -The compilation of SPEC itself then proceeds as usual. -You then only need to specify the HDF5 folder in the Makefile, which will likely be -`/Applications/HDF_Group/HDF5/1.10.5`. diff --git a/compilation_instructions.md b/compilation_instructions.md new file mode 100644 index 00000000..181af979 --- /dev/null +++ b/compilation_instructions.md @@ -0,0 +1,181 @@ +# SPEC compilation instructions + +The default installation method for SPEC uses CMake and installs +the python wrappers and an xspec executable. + +## Installation using Anaconda + +We recommend you use Anaconda to create a coherent build environment and prevent +dependency conflicts. + +Control over the installation can be had by editing `cmake_config.json`, to guide +CMake to the right compilers etc. +Configurations for different machines are stored in `${SPEC_ROOT}/cmake_machines`, +to use these, link them to cmake_config.json: `ln -s cmake_config cmake_machines/` + +>[!TIP] +>install as much as possible in your environment using the `conda` command, +>only use 'pip' at the very end for the last packages. +>if you have not added the `conda-forge` channel do so by +>`conda config --add channels conda-forge` + +Get the repository and install the necessary compilers and libraries +```bash +git clone git@github.com:PrincetonUniversity/SPEC.git +conda create -n "spec_wrapper" python=3.11 # create your environment for SPEC +conda activate spec_wrapper +conda install gcc_linux-64 gxx_linux-64 gfortran_linux-64 # or macOS versions, see note below +conda install hdf5 openblas libopenblas fftw scalapack openmpi cmake ninja +conda install h5py matplotlib f90nml scipy scikit-build mpi4py ipython +pip install f90wrap +``` + +>[!NOTE] +> for macOS users use the respective compiler packages; +> `conda install clang_osx-64 clangxx_osx-64 gfortran_osx-64` + + +Finally, install SPEC and the wrapper (logs will be in `compile.log`) +``` +pip install -v . 2>&1 | tee compile.log +``` + +Install the `py_spec` python library +``` +cd Utilities/pythontools/ +pip install -e . +``` + +### Troubleshooting Anaconda install +If using a newer version of python, `f2py3` is no longer shipped. If your system contains an old python install (for example from your OS), CMake can find its `f2py3` and give try to use it to compile the wrappers instead of your environments `f2py`. +Test this by looking if you have an `f2py3` in your path: `$which f2py3`. +The easiest workaround is to create a link called f2py3 that links to f2py so it is found first. +``` +ln -s ~/anaconda3/envs/spec_wrapper/bin/f2py ~/anaconda3/envs/spec_wrapper/bin/f2py3 +``` + +You might have HDF5 or FFTW environment variables set (for example for a VMEC install). This can throw off CMake, which we want to use only anaconda. +``` +unset HDF5, HDF5_ROOT, HDF5_HOME, FFTW, FFTW_DIR +``` + + + +### Testing your SPEC installation + +First, verify that the stand-alone executable is usable. +A few test cases are provided in `InputFiles/TestCases`. + +Create a new directory for SPEC runs and change into it + +```bash +mkdir ~/SPEC_runs +cd ~/SPEC_runs +``` + +Copy a demo input file into the current working directory: + +```bash +cp ~/SPEC/InputFiles/TestCases/G3V01L0Fi.001.sp . +``` + +Call SPEC with an input file (`*.sp`) as argument on the command line: + +```bash +xspec G3V01L0Fi.001.sp +``` + +You should see the screen output of the SPEC run. +Among the last lines should be something similar to this: + +``` +ending : 0.88 : myid= 0 ; completion ; time= 0.88s = 0.01m = 0.00h = 0.00d ; date= 2022/02/17 ; time= 17:35:33 ; ext = G1V02L0Fi.001 +ending : : +xspech : : +xspech : 0.88 : myid= 0 : time= 0.01m = 0.00h = 0.00d ; +``` + +This indicates that the stand-alone executable is usable. + +Next, the python wrapper is tested. + +1. Check that the SPEC version can be found: + + ```bash + python -c "from spec import spec_f90wrapped as spec; print('SPEC version: {:}'.format(spec.constants.version))" + ``` + + This should print a message like "SPEC version: 3.1" on the screen. + +2. Check that the Python wrapper can be used as a stand-alone code: + + ```bash + OMP_NUM_THREADS=1 python ~/SPEC/Utilities/python_wrapper/spec/core.py G3V01L0Fi.001.sp + ``` + + This should conclude with the message `SPEC called from python finished!`. + +3. Run the optimization example code: + + ```bash + OMP_NUM_THREADS=1 python ~/SPEC/Utilities/python_wrapper/examples/example.py + ``` + + This should run a basic optimization problem, + where the SPEC inputs are controlled via `scipy.optimize`. + +4. Run the interactive re-convergence example code: + + ```bash + OMP_NUM_THREADS=1 python ~/SPEC/Utilities/python_wrapper/examples/example_2.py + ``` + + This should compute a SPEC equilibrium, then change the central pressure, + re-converge SPEC, etc. for a set of five values of the central pressure + in a two-volume classical Stellarator case. + After the pressure scan with re-convergence, + a plot of the MHD energy vs. the central pressure is shown. + + +## Other legacy installations +It is still possible to compile SPEC using `make` or `cmake` directly, and bypass the wrapper installation. + +### CMake installation +Spec can be installed using CMake to find the relevant libraries to link against. +You can control +in the root directory of SPEC do the following: +```bash +mkdir build +cd build +cmake .. +make +``` +This will compile SPEC (not the wrappers). The `xspec` executable is found in ${SPEC_ROOT}/build/build/bin/xspec + +### Make installation +SPEC can also be installed using the `make` command in the root directory. + +The `make` install is controlled by the `BUILD_ENV` environment variable. +Available options are found in the `SPECfile` +where different link and compile flags for many machines are found. + +If you cannot find your machine in the list, copy a similar machine and adapt as needed. +Then compile by running the command + +```bash +BUILD_ENV= make +``` + +The `make` process creates files in the SPEC_ROOT directory, and creates the `xspec` executable there. + + +## Build process +the source files are found in the `${SPEC_ROOT}/src/ directory`. +The `.f90` files contain macros that are expanded during the make process using the `m4` command. + +Depending on the build type, the macro-expanded code is either found in `build/src/`, in the root directory, or in the `_skbuild` folder. + +>[!TIP] +>The line numbers in error messages correspond to the macro-expanded code + +The macros are defined in `src/macros` diff --git a/src/dforce.f90 b/src/dforce.f90 index 42a7e85f..e013c916 100644 --- a/src/dforce.f90 +++ b/src/dforce.f90 @@ -466,7 +466,7 @@ subroutine dforce( NGdof, position, force, LComputeDerivatives, LComputeAxis) Energy = sum( lBBintegral(1:Nvol) ) ! should also compute beta; ! write(*,*)"total Energy", Energy - write(*,*) "Betatotal", BetaTotal, voltotal + !write(*,*) "Betatotal", BetaTotal, voltotal !-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-! diff --git a/src/dfp100.f90 b/src/dfp100.f90 index 2abd1b8a..669fc91a 100644 --- a/src/dfp100.f90 +++ b/src/dfp100.f90 @@ -65,6 +65,8 @@ subroutine dfp100(Ndofgl, x, Fvec, LComputeDerivatives) dMA, dMB, dMD, dMG, MBpsi, solution, & Nt, Nz, LILUprecond, Lsavedguvij, NOTMatrixFree, guvijsave, izbs, total_pflux + use sphdf5, only : write_matrices + LOCALS !------ ! vvol: loop index on volumes @@ -81,8 +83,6 @@ subroutine dfp100(Ndofgl, x, Fvec, LComputeDerivatives) LOGICAL :: LComputeDerivatives INTEGER :: deriv, Lcurvature - - BEGIN(dfp100) dpflux(2:Mvol) = x - xoffset @@ -130,6 +130,14 @@ subroutine dfp100(Ndofgl, x, Fvec, LComputeDerivatives) WCALL( dfp100, matrixBG, ( vvol, mn, ll ) ) endif + ! if(.true.) then + ! write(ounit,"('Writing dMA to .h5 for vvol=3')") + ! ! write(*,*) vvol, ALLOCATED(dMA) + ! ! write(*,*) dMA(1:5, 1:4) + ! WCALL( dfp100, write_matrices, (dMA) ) + ! endif + + ! Call Beltrami solver to get the magnetic field in the current volume. WCALL( dfp100, ma02aa, ( vvol, NN ) ) diff --git a/src/hesian.f90 b/src/hesian.f90 index fdc6481b..4897720c 100644 --- a/src/hesian.f90 +++ b/src/hesian.f90 @@ -22,7 +22,7 @@ subroutine hesian( NGdof, position, Mvol, mn, LGdof ) use inputlist, only : Wmacros, Whesian, Igeometry, Nvol, pflux, helicity, mu, Lfreebound, & LHevalues, LHevectors, LHmatrix, & Lperturbed, dpp, dqq, & - Lcheck, Lfindzero + Lcheck, Lfindzero, Lconstraint use cputiming, only : Thesian @@ -92,6 +92,11 @@ subroutine hesian( NGdof, position, Mvol, mn, LGdof ) BEGIN(hesian) + ! Only makes sense to compute the Hessian if helicity is constrained + if(Lconstraint.ne.2) then + return + endif + !-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-! lmu(1:Nvol) = mu(1:Nvol) ; lpflux(1:Nvol) = pflux(1:Nvol) ; lhelicity(1:Nvol) = helicity(1:Nvol) ! save original profile information; 20 Jun 14; @@ -590,7 +595,7 @@ subroutine hesian( NGdof, position, Mvol, mn, LGdof ) endif ! end of if( ( LHevalues .or. LHevectors ) ) ! output hessian, eigenvalues, and eigenvectors to the .h5 file - if( LHmatrix ) then + if( LHmatrix .and. Lconstraint.eq.2) then WCALL( hesian, write_stability, (ohessian, evalr, evali, evecr, NGdof) ) endif !-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-! diff --git a/src/memory.f90 b/src/memory.f90 index 744cd16d..8073fe3f 100644 --- a/src/memory.f90 +++ b/src/memory.f90 @@ -27,6 +27,7 @@ subroutine allocate_Beltrami_matrices(vvol, LcomputeDerivatives) if (NOTMatrixFree .or. LcomputeDerivatives) then SALLOCATE( dMA, (0:NN,0:NN), zero ) ! required for both plasma region and vacuum region; + ! write(ounit,"('dMA allocate')") SALLOCATE( dMD, (0:NN,0:NN), zero ) else SALLOCATE( Adotx, (0:NN), zero) @@ -75,6 +76,7 @@ subroutine deallocate_Beltrami_matrices(LcomputeDerivatives) if (NOTMatrixFree .or. LcomputeDerivatives) then DALLOCATE(dMA) + ! write(ounit,"('dMA DEallocate')") DALLOCATE(dMD) else DALLOCATE(Adotx) diff --git a/src/sphdf5.f90 b/src/sphdf5.f90 index 59d92eb0..732b5207 100644 --- a/src/sphdf5.f90 +++ b/src/sphdf5.f90 @@ -1020,6 +1020,33 @@ subroutine write_stability(ohessian, evalr, evali, evecr, NGdof) end subroutine write_stability +subroutine write_matrices(M_dMA) + + use inputlist, only : M_dMA + + LOCALS + REAL, intent(in) :: M_dMA(:,:) + integer(hid_t) :: grpMatrices + integer :: sizeM + + BEGIN( sphdf5 ) + + if (myid.eq.0) then + + HDEFGRP( file_id, matrices, grpMatrices) + + sizeM = SIZE(M_dMA, DIM = 1) + ! write(*,*) M_dMA(1:12, 1:3) + write(*,*) 'sizeM = ', sizeM + HWRITERA( grpMatrices, sizeM, sizeM, M_dMA, M_dMA(1:sizeM,1:sizeM)) + + HCLOSEGRP( grpMatrices ) + + endif ! myid.eq.0 + +end subroutine write_matrices + + subroutine hdfint use fileunits, only : ounit From 1ad8de2f30215a36a2d0023eefaac04203518f95 Mon Sep 17 00:00:00 2001 From: ErolBa Date: Wed, 4 Dec 2024 14:15:41 +0100 Subject: [PATCH 28/36] keep up w master 4 --- ...md => outdated_compilation_instructions.md | 0 src/dfp100.f90 | 10 --- src/dfp200.f90 | 4 +- src/global.f90 | 4 +- src/hesian.f90 | 74 +++++++++---------- src/inputlist.f90 | 2 +- src/memory.f90 | 2 - src/newton.f90 | 12 +-- src/pp00aa.f90 | 6 +- src/ra00aa.f90 | 8 +- src/sphdf5.f90 | 27 ------- 11 files changed, 52 insertions(+), 97 deletions(-) rename outdated_compilation_instuctions.md => outdated_compilation_instructions.md (100%) diff --git a/outdated_compilation_instuctions.md b/outdated_compilation_instructions.md similarity index 100% rename from outdated_compilation_instuctions.md rename to outdated_compilation_instructions.md diff --git a/src/dfp100.f90 b/src/dfp100.f90 index 669fc91a..2666beed 100644 --- a/src/dfp100.f90 +++ b/src/dfp100.f90 @@ -65,8 +65,6 @@ subroutine dfp100(Ndofgl, x, Fvec, LComputeDerivatives) dMA, dMB, dMD, dMG, MBpsi, solution, & Nt, Nz, LILUprecond, Lsavedguvij, NOTMatrixFree, guvijsave, izbs, total_pflux - use sphdf5, only : write_matrices - LOCALS !------ ! vvol: loop index on volumes @@ -130,14 +128,6 @@ subroutine dfp100(Ndofgl, x, Fvec, LComputeDerivatives) WCALL( dfp100, matrixBG, ( vvol, mn, ll ) ) endif - ! if(.true.) then - ! write(ounit,"('Writing dMA to .h5 for vvol=3')") - ! ! write(*,*) vvol, ALLOCATED(dMA) - ! ! write(*,*) dMA(1:5, 1:4) - ! WCALL( dfp100, write_matrices, (dMA) ) - ! endif - - ! Call Beltrami solver to get the magnetic field in the current volume. WCALL( dfp100, ma02aa, ( vvol, NN ) ) diff --git a/src/dfp200.f90 b/src/dfp200.f90 index 2015b3b6..311a7dfa 100644 --- a/src/dfp200.f90 +++ b/src/dfp200.f90 @@ -2110,12 +2110,12 @@ subroutine hessian3D_dFFdRZ(lvol, idof, innout, issym, irz, ii, dBB, XX, YY, len !write(ounit,1000) 'values are:' Mvol, efcol1mn(1:mn) !write(90,1000) efcol1mn(1:mn) !1000 format(" "10x" "es23.15" ") - !open(nm1unit, file="."//trim(ext)//".GF.hcol1", status="unknown", form="unformatted") + !open(nm1unit, file=trim(get_hidden(ext))//".GF.hcol1", status="unknown", form="unformatted") !write(nm1unit) NGdof, Mvol !write(nm1unit) efcol1mn(1:Ntz) !close(nm1unit) - !open(nm2unit, file="."//trim(ext)//".GF.hcol2", status="unknown", form="unformatted") + !open(nm2unit, file=trim(get_hidden(ext))//".GF.hcol2", status="unknown", form="unformatted") !!write(nm2unit) NGdof, Mvol !write(nm2unit) efcol2mn(1:Ntz) !close(nm2unit) diff --git a/src/global.f90 b/src/global.f90 index 7ec25f58..334afa48 100644 --- a/src/global.f90 +++ b/src/global.f90 @@ -66,7 +66,7 @@ module constants REAL, parameter :: mu0 = 2.0E-07 * pi2 !< \f$4\pi\cdot10^{-7}\f$ REAL, parameter :: goldenmean = 1.618033988749895 !< golden mean = \f$( 1 + \sqrt 5 ) / 2\f$ ; - REAL, parameter :: version = 3.20 !< version of SPEC + REAL, parameter :: version = 3.23 !< version of SPEC end module constants @@ -246,7 +246,7 @@ module allglobal !-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-! - CHARACTER(LEN=1000) :: ext ! extension of input filename, i.e., "G3V01L1Fi.001" for an input file G3V01L1Fi.001.sp + CHARACTER(LEN=1000) :: ext ! extension of input filename, i.e., "path/G3V01L1Fi.001" for an input file path/G3V01L1Fi.001.sp REAL :: ForceErr !< total force-imbalance REAL :: Energy !< MHD energy diff --git a/src/hesian.f90 b/src/hesian.f90 index 4897720c..6a40b4b9 100644 --- a/src/hesian.f90 +++ b/src/hesian.f90 @@ -1,7 +1,7 @@ !> \file -!> \brief Computes eigenvalues and eigenvectors of derivative matrix, \f$\nabla_{\bf \xi}{\bf F}\f$. +!> \brief Computes eigenvalues and eigenvectors of derivative matrix, \f$\nabla_{\bf xi}{\bf F}\f$. -!> \brief Computes eigenvalues and eigenvectors of derivative matrix, \f$\nabla_{\bf \xi}{\bf F}\f$. +!> \brief Computes eigenvalues and eigenvectors of derivative matrix, \f$\nabla_{\bf xi}{\bf F}\f$. !> \ingroup grp_diagnostics !> !> @param[in] NGdof number of global degrees of freedom @@ -26,7 +26,7 @@ subroutine hesian( NGdof, position, Mvol, mn, LGdof ) use cputiming, only : Thesian - use allglobal, only : ncpu, myid, cpus, MPI_COMM_SPEC, ext, & + use allglobal, only : ncpu, myid, cpus, MPI_COMM_SPEC, ext, get_hidden, & im, in, & iRbc, iZbs, iRbs, iZbc, & dRbc, dZbs, dRbs, dZbc, & @@ -53,8 +53,7 @@ subroutine hesian( NGdof, position, Mvol, mn, LGdof ) REAL :: xx(0:NGdof,-2:2), ff(0:NGdof,-2:2), df(1:NGdof)!, deriv INTEGER :: vvol, idof, ii, mi, ni, irz, issym, isymdiff, lvol, ieval(1:1), igdof, ifd - REAL :: oldEnergy(-2:2), error, cpul - + REAL :: oldEnergy(-2:2), error, cpul REAL :: oldBB(1:Mvol,-2:2), oBBdRZ(1:Mvol,0:1,1:LGdof), ohessian(1:NGdof,1:NGdof) REAL :: oRbc(1:mn,0:Mvol), oZbs(1:mn,0:Mvol), oRbs(1:mn,0:Mvol), oZbc(1:mn,0:Mvol), determinant @@ -105,7 +104,6 @@ subroutine hesian( NGdof, position, Mvol, mn, LGdof ) xx(0,-2:2)= zero - !-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-! #ifdef MINIMIZE @@ -190,8 +188,8 @@ subroutine hesian( NGdof, position, Mvol, mn, LGdof ) write(ounit,1001) cput-cpus, myid, vvol, irz, mi, ni, ( oBBdRZ(vvol,1,idof) + oBBdRZ(vvol+1,0,idof) ) / psifactor(ii,vvol) ! ENERGY GRADIENT; FATAL( hesian, Igeometry.eq.1, Cartesian geometry does not need regularization factor ) - 1000 format("hesian : ",f10.2," : ":"myid=",i3," ; ":"vvol=",i3," ; ":"irz="i2" ; (",i3," ,",i3," ) ; "a17" ["es15.7","es15.7" ]") - 1001 format("hesian : ",f10.2," : ":"myid=",i3," ; ":"vvol=",i3," ; ":"irz="i2" ; (",i3," ,",i3," ) ; "es15.7" ; ") +1000 format("hesian : ",f10.2," : ":"myid=",i3," ; ":"vvol=",i3," ; ":"irz="i2" ; (",i3," ,",i3," ) ; "a17" ["es15.7","es15.7" ]") +1001 format("hesian : ",f10.2," : ":"myid=",i3," ; ":"vvol=",i3," ; ":"irz="i2" ; (",i3," ,",i3," ) ; "es15.7" ; ") enddo ! end of do issym; 26 Feb 13; @@ -232,11 +230,11 @@ subroutine hesian( NGdof, position, Mvol, mn, LGdof ) SALLOCATE( hessian2D, (1:NGdof,1:NGdof), zero ) SALLOCATE( dessian2D, (1:NGdof,1:LGdof), zero ) ! part of hessian that depends on boundary variations; 18 Dec 14; - ! if (LHmatrix) then + !if (LHmatrix) then Lhessian3Dallocated = .true. - ! else - ! Lhessianallocated = .true. - ! endif + !else + Lhessianallocated = .true. + !endif !This step cleared. LComputeDerivatives = .true. !; position(0) = zero ! this is not used; 11 Aug 14; @@ -407,7 +405,7 @@ subroutine hesian( NGdof, position, Mvol, mn, LGdof ) !>
  • The eigenvalues and eigenvectors (if required) are written to the file \c .ext.GF.ev as follows: !> !> ``` -!> open(hunit,file="."//trim(ext)//".GF.ev",status="unknown",form="unformatted") +!> open(hunit,file=trim(get_hidden(ext))//".GF.ev",status="unknown",form="unformatted") !> write(hunit)NGdof,Ldvr,Ldvi ! integers; if only the eigenvalues were computed then Ldvr=Ldvi=1; !> write(hunit)evalr(1:NGdof) ! reals ; real part of eigenvalues; !> write(hunit)evali(1:NGdof) ! reals ; imaginary part of eigenvalues; @@ -421,15 +419,16 @@ subroutine hesian( NGdof, position, Mvol, mn, LGdof ) !-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-! - ! write the .ma file - ! if( LHmatrix ) then - ! if( myid.eq.0 ) then ; cput = GETTIME ; write(ounit,'("hesian : ",f10.2," : LHmatrix="L2" ;")')cput-cpus, LHmatrix ; - ! open(munit, file="."//trim(ext)//".GF.ma", status="unknown", form="unformatted") - ! write(munit) NGdof - ! write(munit) ohessian(1:NGdof,1:NGdof) - ! close(munit) - ! endif - ! endif + if( LHmatrix ) then + + if( myid.eq.0 ) then ; cput = GETTIME ; write(ounit,'("hesian : ",f10.2," : LHmatrix="L2" ;")')cput-cpus, LHmatrix ; + open(munit, file=trim(get_hidden(ext))//".GF.ma", status="unknown", form="unformatted") + write(munit) NGdof + write(munit) ohessian(1:NGdof,1:NGdof) + close(munit) + endif + + endif ! if( myid.eq.0 .and. ( LHevalues .or. LHevectors ) ) then ! the call to dforce below requires all cpus; 04 Dec 14; @@ -457,11 +456,10 @@ subroutine hesian( NGdof, position, Mvol, mn, LGdof ) !#else ! FATAL( global, .true., eigenvalue solver needs updating to F08NAF ) !#endif - call dgeev('N', JOB, NGdof, hessian2D(1:LDA,1:NGdof), LDA, evalr(1:NGdof), evali(1:NGdof), & - evecl(1:Ldvr,1:NGdof), Ldvr, revecr(1:Ldvr,1:2*NGdof), Ldvr, work(1:Lwork), Lwork, if02ebf ) - evecr(1:Ldvr,1:NGdof) = revecr(1:Ldvr,1:NGdof) - eveci(1:Ldvr,1:NGdof) = revecr(1:Ldvr,NGdof+1:2*NGdof) + evecl(1:Ldvr,1:NGdof), Ldvr, revecr(1:Ldvr,1:2*NGdof), Ldvr, work(1:Lwork), Lwork, if02ebf ) + evecr(1:Ldvr,1:NGdof) = revecr(1:Ldvr,1:NGdof) + eveci(1:Ldvr,1:NGdof) = revecr(1:Ldvr,NGdof+1:2*NGdof) if( myid.eq.0 ) then cput = GETTIME @@ -522,10 +520,6 @@ subroutine hesian( NGdof, position, Mvol, mn, LGdof ) enddo enddo - ! do ii = 1, mn ; write(ounit,*) 'psifact', ii, psifactor(ii,Mvol-1) - ! enddo - - !-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-! if( myid.eq.0 ) then ! screen output; 04 Dec 14; @@ -581,16 +575,15 @@ subroutine hesian( NGdof, position, Mvol, mn, LGdof ) !-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-! - ! write eigvals and eigvecs to .ev file - ! if( myid.eq.0 ) then ! write to file; 04 Dec 14; - ! open(hunit, file="."//trim(ext)//".GF.ev", status="unknown", form="unformatted") - ! write(hunit) NGdof, Ldvr, Ldvi - ! write(hunit) evalr - ! write(hunit) evali - ! write(hunit) evecr - ! write(hunit) eveci - ! close(hunit) - ! endif ! end of if( myid.eq.0 ) ; 04 Dec 14; + if( myid.eq.0 ) then ! write to file; 04 Dec 14; + open(hunit, file=trim(get_hidden(ext))//".GF.ev", status="unknown", form="unformatted") + write(hunit) NGdof, Ldvr, Ldvi + write(hunit) evalr + write(hunit) evali + write(hunit) evecr + write(hunit) eveci + close(hunit) + endif ! end of if( myid.eq.0 ) ; 04 Dec 14; endif ! end of if( ( LHevalues .or. LHevectors ) ) @@ -708,6 +701,7 @@ subroutine hesian( NGdof, position, Mvol, mn, LGdof ) DALLOCATE(hessian2D) + write(ounit,*) 5656 DALLOCATE(dessian2D) diff --git a/src/inputlist.f90 b/src/inputlist.f90 index 505f3490..30c0b04b 100644 --- a/src/inputlist.f90 +++ b/src/inputlist.f90 @@ -9,7 +9,7 @@ module inputlist implicit none ! The following parameters set the maximum allowed resolution: - INTEGER, parameter :: MNvol = 1024 !< The maximum value of \c Nvol is \c MNvol=256. + INTEGER, parameter :: MNvol = 256 !< The maximum value of \c Nvol is \c MNvol=256. INTEGER, parameter :: MMpol = 128 !< The maximum value of \c Mpol is \c MNpol=64. INTEGER, parameter :: MNtor = 128 !< The maximum value of \c Ntor is \c MNtor=64. diff --git a/src/memory.f90 b/src/memory.f90 index 8073fe3f..744cd16d 100644 --- a/src/memory.f90 +++ b/src/memory.f90 @@ -27,7 +27,6 @@ subroutine allocate_Beltrami_matrices(vvol, LcomputeDerivatives) if (NOTMatrixFree .or. LcomputeDerivatives) then SALLOCATE( dMA, (0:NN,0:NN), zero ) ! required for both plasma region and vacuum region; - ! write(ounit,"('dMA allocate')") SALLOCATE( dMD, (0:NN,0:NN), zero ) else SALLOCATE( Adotx, (0:NN), zero) @@ -76,7 +75,6 @@ subroutine deallocate_Beltrami_matrices(LcomputeDerivatives) if (NOTMatrixFree .or. LcomputeDerivatives) then DALLOCATE(dMA) - ! write(ounit,"('dMA DEallocate')") DALLOCATE(dMD) else DALLOCATE(Adotx) diff --git a/src/newton.f90 b/src/newton.f90 index 23f4007d..25655733 100644 --- a/src/newton.f90 +++ b/src/newton.f90 @@ -64,7 +64,7 @@ subroutine newton( NGdof, position, ihybrd ) use cputiming, only : Tnewton - use allglobal, only : myid, ncpu, cpus, MPI_COMM_SPEC, ext, & + use allglobal, only : myid, ncpu, cpus, MPI_COMM_SPEC, ext, get_hidden, & NOTstellsym, & ForceErr, Energy, & mn, im, in, iRbc, iZbs, iRbs, iZbc, Mvol, & @@ -313,7 +313,7 @@ subroutine writereadgf( readorwrite, NGdof , ireadhessian ) use cputiming, only : Tnewton - use allglobal, only : myid, cpus, MPI_COMM_SPEC, ext, & + use allglobal, only : myid, cpus, MPI_COMM_SPEC, ext, get_hidden, & mn, im, in, hessian, Lhessianallocated LOCALS @@ -336,7 +336,7 @@ subroutine writereadgf( readorwrite, NGdof , ireadhessian ) ! reset I/O state ios = 0 - open( dunit, file="."//trim(ext)//".sp.DF", status="replace", form="unformatted", iostat=ios ) ! save derivative matrix to file; + open( dunit, file=trim(get_hidden(ext))//".sp.DF", status="replace", form="unformatted", iostat=ios ) ! save derivative matrix to file; FATAL( newton, ios.ne.0, error opening derivative matrix file ) write( dunit, iostat=ios ) Igeometry, Istellsym, Lfreebound, Nvol, Mpol, Ntor, NGdof ! enable resolution consistency check; @@ -352,11 +352,11 @@ subroutine writereadgf( readorwrite, NGdof , ireadhessian ) cput = GETTIME - inquire( file="."//trim(ext)//".sp.DF", exist=exist ) ! the derivative matrix; + inquire( file=trim(get_hidden(ext))//".sp.DF", exist=exist ) ! the derivative matrix; if( exist ) then ! 01234567890123456789012345678901 write(ounit,2000) cput-cpus, myid, "reading .ext.sp.DF ; " - open( dunit, file="."//trim(ext)//".sp.DF", status="old", form="unformatted", iostat=ios ) + open( dunit, file=trim(get_hidden(ext))//".sp.DF", status="old", form="unformatted", iostat=ios ) else ! 01234567890123456789012345678901 write(ounit,2000) cput-cpus, myid, ".ext.sp.DF does not exist ; " inquire( file=".sp.DF", exist=exist ) ! the derivative matrix; @@ -442,7 +442,7 @@ subroutine fcn1( NGdof, xx, fvec, irevcm ) use cputiming, only : Tnewton - use allglobal, only : wrtend, myid, ncpu, cpus, MPI_COMM_SPEC, ext, & + use allglobal, only : wrtend, myid, ncpu, cpus, MPI_COMM_SPEC, ext, get_hidden, & NOTstellsym, & ForceErr, Energy, & mn, im, in, iRbc, iZbs, iRbs, iZbc, Mvol, & diff --git a/src/pp00aa.f90 b/src/pp00aa.f90 index dc91ff31..7d59bbb7 100644 --- a/src/pp00aa.f90 +++ b/src/pp00aa.f90 @@ -25,7 +25,7 @@ !> !>~~~~~~~~~~~~ !> write(svol,'(i4.4)')lvol ! lvol labels volume; -!> open(lunit+myid,file="."//trim(ext)//".poincare."//svol,status="unknown",form="unformatted") +!> open(lunit+myid,file=trim(get_hidden(ext))//".poincare."//svol,status="unknown",form="unformatted") !> do until end of file !> write(lunit+myid) Nz, nPpts ! integers !> write(lunit+myid) data(1:4,0:Nz-1,1:nPpts) ! doubles @@ -55,7 +55,7 @@ !>
  • The rotational-transform data is written to \c .ext.transform:xxxx , where \c xxxx is an integer indicating the volume. !> The format of this file is as follows: !> ``` -!> open(lunit+myid,file="."//trim(ext)//".sp.t."//svol,status="unknown",form="unformatted") +!> open(lunit+myid,file=trim(get_hidden(ext))//".sp.t."//svol,status="unknown",form="unformatted") !> write(lunit+myid) lnPtrj-ioff+1 ! integer !> write(lunit+myid) diotadxup(0:1,0,lvol) ! doubles !> write(lunit+myid) ( fiota(itrj,1:2), itrj = ioff, lnPtrj ) ! doubles @@ -145,7 +145,7 @@ subroutine pp00aa SALLOCATE( utflag, (ioff:lnPtrj ), 0 ) ! error flag that indicates if fieldlines successfully followed; 22 Apr 13; SALLOCATE( fiota, (ioff:lnPtrj, 1:2 ), zero ) ! will always need fiota(0,1:2); -!$OMP PARALLEL DO SHARED(lnPtrj,ioff,Wpp00aa,Nz,data,fiota,utflag,iota,oita,myid,vvol,cpus,Lconstraint,nPpts,ppts) PRIVATE(itrj,sti) +!$OMP PARALLEL DO SHARED(lnPtrj,ioff,Wpp00aa,Nz,data,fiota,utflag,iota,oita,myid,vvol,cpus,Lconstraint,nPpts,ppts) PRIVATE(itrj,sti) SCHEDULE(dynamic) do itrj = ioff, lnPtrj ! initialize Poincare plot with trajectories regularly spaced between interfaces along \t=0; ; sti(1:2) = (/ - one + itrj * two / lnPtrj , Ppts*pi /) diff --git a/src/ra00aa.f90 b/src/ra00aa.f90 index 81553e76..0cc88505 100644 --- a/src/ra00aa.f90 +++ b/src/ra00aa.f90 @@ -24,7 +24,7 @@ !>
      !>
    • The format of the files containing the vector potential is as follows: !> ``` -!> open(aunit, file="."//trim(ext)//".sp.A", status="replace", form="unformatted" ) +!> open(aunit, file=trim(get_hidden(ext))//".sp.A", status="replace", form="unformatted" ) !> write(aunit) Mvol, Mpol, Ntor, mn, Nfp ! integers; !> write(aunit) im(1:mn) ! integers; poloidal modes; !> write(aunit) in(1:mn) ! integers; toroidal modes; @@ -57,7 +57,7 @@ subroutine ra00aa( writeorread ) use cputiming, only : Tra00aa - use allglobal, only : myid, ncpu, cpus, MPI_COMM_SPEC, ext, Mvol, mn, im, in, Ate, Aze, Ato, Azo + use allglobal, only : myid, ncpu, cpus, MPI_COMM_SPEC, ext, get_hidden, Mvol, mn, im, in, Ate, Aze, Ato, Azo use sphdf5, only : write_vector_potential @@ -148,12 +148,12 @@ subroutine ra00aa( writeorread ) if( myid.eq.0 ) then - inquire(file="."//trim(ext)//".sp.A",exist=exist) + inquire(file=trim(get_hidden(ext))//".sp.A",exist=exist) if( .not.exist ) then ; write(ounit,'("ra00aa : ",f10.2," : myid=",i3," ; error ; .ext.sp.A does not exist ;")') cput-cpus, myid ; goto 9998 endif - open(aunit,file="."//trim(ext)//".sp.A",status="old",form="unformatted",iostat=ios) ! this will contain initial guess for vector potential; + open(aunit,file=trim(get_hidden(ext))//".sp.A",status="old",form="unformatted",iostat=ios) ! this will contain initial guess for vector potential; if( ios.ne.0 ) then ; write(ounit,'("ra00aa : ",f10.2," : myid=",i3," ; error ; opening .ext.sp.A ;")') cput-cpus, myid ; goto 9997 endif diff --git a/src/sphdf5.f90 b/src/sphdf5.f90 index 732b5207..59d92eb0 100644 --- a/src/sphdf5.f90 +++ b/src/sphdf5.f90 @@ -1020,33 +1020,6 @@ subroutine write_stability(ohessian, evalr, evali, evecr, NGdof) end subroutine write_stability -subroutine write_matrices(M_dMA) - - use inputlist, only : M_dMA - - LOCALS - REAL, intent(in) :: M_dMA(:,:) - integer(hid_t) :: grpMatrices - integer :: sizeM - - BEGIN( sphdf5 ) - - if (myid.eq.0) then - - HDEFGRP( file_id, matrices, grpMatrices) - - sizeM = SIZE(M_dMA, DIM = 1) - ! write(*,*) M_dMA(1:12, 1:3) - write(*,*) 'sizeM = ', sizeM - HWRITERA( grpMatrices, sizeM, sizeM, M_dMA, M_dMA(1:sizeM,1:sizeM)) - - HCLOSEGRP( grpMatrices ) - - endif ! myid.eq.0 - -end subroutine write_matrices - - subroutine hdfint use fileunits, only : ounit From 58e4e0d85f50db8167277da52c7a422a33e61030 Mon Sep 17 00:00:00 2001 From: ErolBa Date: Wed, 4 Dec 2024 14:18:40 +0100 Subject: [PATCH 29/36] keep up w master 5 --- src/sphdf5.f90 | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/src/sphdf5.f90 b/src/sphdf5.f90 index 59d92eb0..851d53b9 100644 --- a/src/sphdf5.f90 +++ b/src/sphdf5.f90 @@ -1085,8 +1085,8 @@ subroutine hdfint HWRITERA( grpOutput, mn, (Mvol+1), Rbs, iRbs(1:mn,0:Mvol) ) !latex \type{iZbc(1:mn,0:Mvol)} & real & \pb{Fourier harmonics, $Z_{m,n}$, of interfaces} \\ HWRITERA( grpOutput, mn, (Mvol+1), Zbc, iZbc(1:mn,0:Mvol) ) -!l tex \type{forcetol} & real & \pb{force-balance error across interfaces} \\ -! HWRITERV( grpOutput, 1, forcetol, (/ forcetol /)) ! already in /input/global +!latex \type{BnsErr} & real & \pb{error in self-consistency of field on plasma boundary (in freeboundary)} \\ + HWRITERV( grpOutput, 1, BnsErr, (/ BnsErr /)) ! already in /input/global !latex \type{ForceErr} & real & \pb{force-balance error across interfaces} \\ HWRITERV( grpOutput, 1, ForceErr, (/ ForceErr /)) !latex \type{ForceErr} & real & \pb{force-balance error across interfaces} \\ From 5919a62eaee06a80463d8a0de62c70004869ec7e Mon Sep 17 00:00:00 2001 From: ErolBa Date: Wed, 4 Dec 2024 14:20:33 +0100 Subject: [PATCH 30/36] keep up w master 5b --- src/sphdf5.f90 | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/sphdf5.f90 b/src/sphdf5.f90 index 851d53b9..07407173 100644 --- a/src/sphdf5.f90 +++ b/src/sphdf5.f90 @@ -1085,7 +1085,7 @@ subroutine hdfint HWRITERA( grpOutput, mn, (Mvol+1), Rbs, iRbs(1:mn,0:Mvol) ) !latex \type{iZbc(1:mn,0:Mvol)} & real & \pb{Fourier harmonics, $Z_{m,n}$, of interfaces} \\ HWRITERA( grpOutput, mn, (Mvol+1), Zbc, iZbc(1:mn,0:Mvol) ) -!latex \type{BnsErr} & real & \pb{error in self-consistency of field on plasma boundary (in freeboundary)} \\ +!latex \type{BnsErr} & real & \pb{error in self-consistency of field on plasma boundary (in freeboundary)} \\ HWRITERV( grpOutput, 1, BnsErr, (/ BnsErr /)) ! already in /input/global !latex \type{ForceErr} & real & \pb{force-balance error across interfaces} \\ HWRITERV( grpOutput, 1, ForceErr, (/ ForceErr /)) From 2a42194a290a3998b7cd5d15e3a7e8c81a00ecd6 Mon Sep 17 00:00:00 2001 From: ErolBa Date: Wed, 4 Dec 2024 14:28:00 +0100 Subject: [PATCH 31/36] keep up w master 6 --- src/hesian.f90 | 15 ++++++++++----- src/sphdf5.f90 | 2 +- 2 files changed, 11 insertions(+), 6 deletions(-) diff --git a/src/hesian.f90 b/src/hesian.f90 index 6a40b4b9..e7c37f20 100644 --- a/src/hesian.f90 +++ b/src/hesian.f90 @@ -54,6 +54,7 @@ subroutine hesian( NGdof, position, Mvol, mn, LGdof ) INTEGER :: vvol, idof, ii, mi, ni, irz, issym, isymdiff, lvol, ieval(1:1), igdof, ifd REAL :: oldEnergy(-2:2), error, cpul + REAL :: oldBB(1:Mvol,-2:2), oBBdRZ(1:Mvol,0:1,1:LGdof), ohessian(1:NGdof,1:NGdof) REAL :: oRbc(1:mn,0:Mvol), oZbs(1:mn,0:Mvol), oRbs(1:mn,0:Mvol), oZbc(1:mn,0:Mvol), determinant @@ -104,8 +105,10 @@ subroutine hesian( NGdof, position, Mvol, mn, LGdof ) xx(0,-2:2)= zero + !-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-! -#ifdef MINIMIZE + + #ifdef MINIMIZE oldBB(1:Mvol,0) = lBBintegral(1:Mvol) @@ -241,6 +244,7 @@ subroutine hesian( NGdof, position, Mvol, mn, LGdof ) LComputeAxis = .false. WCALL( hesian, dforce, ( NGdof, position(0:NGdof), force(0:NGdof), LComputeDerivatives, LComputeAxis) ) ! calculate force-imbalance & hessian; + ohessian(1:NGdof,1:NGdof) = hessian2D(1:NGdof,1:NGdof) ! internal copy; 22 Apr 15; @@ -263,7 +267,7 @@ subroutine hesian( NGdof, position, Mvol, mn, LGdof ) xx(0,-2:2)= zero ; dRZ = 1.0E-04 write(svol,'(i3.3)')myid -! open(lunit+myid,file="."//trim(ext)//".hessian."//svol,status="unknown") +! open(lunit+myid,file=trim(get_hidden(ext))//".hessian."//svol,status="unknown") ! lmu(1:Nvol) = mu(1:Nvol) ; lpflux(1:Nvol) = pflux(1:Nvol) ; lhelicity(1:Nvol) = helicity(1:Nvol) ! save original profile information; 20 Jun 14; @@ -457,9 +461,9 @@ subroutine hesian( NGdof, position, Mvol, mn, LGdof ) ! FATAL( global, .true., eigenvalue solver needs updating to F08NAF ) !#endif call dgeev('N', JOB, NGdof, hessian2D(1:LDA,1:NGdof), LDA, evalr(1:NGdof), evali(1:NGdof), & - evecl(1:Ldvr,1:NGdof), Ldvr, revecr(1:Ldvr,1:2*NGdof), Ldvr, work(1:Lwork), Lwork, if02ebf ) - evecr(1:Ldvr,1:NGdof) = revecr(1:Ldvr,1:NGdof) - eveci(1:Ldvr,1:NGdof) = revecr(1:Ldvr,NGdof+1:2*NGdof) + evecl(1:Ldvr,1:NGdof), Ldvr, revecr(1:Ldvr,1:2*NGdof), Ldvr, work(1:Lwork), Lwork, if02ebf ) + evecr(1:Ldvr,1:NGdof) = revecr(1:Ldvr,1:NGdof) + eveci(1:Ldvr,1:NGdof) = revecr(1:Ldvr,NGdof+1:2*NGdof) if( myid.eq.0 ) then cput = GETTIME @@ -575,6 +579,7 @@ subroutine hesian( NGdof, position, Mvol, mn, LGdof ) !-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-! + if( myid.eq.0 ) then ! write to file; 04 Dec 14; open(hunit, file=trim(get_hidden(ext))//".GF.ev", status="unknown", form="unformatted") write(hunit) NGdof, Ldvr, Ldvi diff --git a/src/sphdf5.f90 b/src/sphdf5.f90 index 07407173..741c9448 100644 --- a/src/sphdf5.f90 +++ b/src/sphdf5.f90 @@ -1085,7 +1085,7 @@ subroutine hdfint HWRITERA( grpOutput, mn, (Mvol+1), Rbs, iRbs(1:mn,0:Mvol) ) !latex \type{iZbc(1:mn,0:Mvol)} & real & \pb{Fourier harmonics, $Z_{m,n}$, of interfaces} \\ HWRITERA( grpOutput, mn, (Mvol+1), Zbc, iZbc(1:mn,0:Mvol) ) -!latex \type{BnsErr} & real & \pb{error in self-consistency of field on plasma boundary (in freeboundary)} \\ +!latex \type{BnsErr} & real & \pb{error in self-consistency of field on plasma boundary (in freeboundary)} \\ HWRITERV( grpOutput, 1, BnsErr, (/ BnsErr /)) ! already in /input/global !latex \type{ForceErr} & real & \pb{force-balance error across interfaces} \\ HWRITERV( grpOutput, 1, ForceErr, (/ ForceErr /)) From 65e1e01cd6b6beed6fa8db3e0f8073a437927073 Mon Sep 17 00:00:00 2001 From: ErolBa Date: Wed, 4 Dec 2024 14:38:21 +0100 Subject: [PATCH 32/36] keep up w master 7 --- src/dforce.f90 | 16 ++++--------- src/dfp100.f90 | 2 ++ src/global.f90 | 64 +++++++++++++++++++++++++++++++++----------------- src/sphdf5.f90 | 2 +- 4 files changed, 49 insertions(+), 35 deletions(-) diff --git a/src/dforce.f90 b/src/dforce.f90 index e013c916..ccc7da32 100644 --- a/src/dforce.f90 +++ b/src/dforce.f90 @@ -458,15 +458,10 @@ subroutine dforce( NGdof, position, force, LComputeDerivatives, LComputeAxis) voltotal = voltotal+vvolume(vvol) !write(*,*) "Calc beta: ", betavol(vvol), vvolume(vvol) enddo - ! Calculate total beta which is obtained from individual betas - ! write(*,*) "all betas", betavol(1:Nvol) - BetaTotal = sum(betavol(1:Nvol))/voltotal - ! write(*,*) "Total BETA ", BetaTotal - ! write(*,*)"total vol", voltotal + + BetaTotal = sum(betavol(1:Nvol))/voltotal ! Calculate total beta which is obtained from individual betas Energy = sum( lBBintegral(1:Nvol) ) ! should also compute beta; - ! write(*,*)"total Energy", Energy - !write(*,*) "Betatotal", BetaTotal, voltotal !-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-! @@ -974,10 +969,7 @@ subroutine dforce( NGdof, position, force, LComputeDerivatives, LComputeAxis) !call MPI_BARRIER( MPI_COMM_WORLD, ierr ) !-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-! - - !if(LcomputeDerivatives .and. Lhessianallocated .and. Igeometry .eq. 1) then - !if(Lhessianallocated .and. Igeometry .eq. 1) then - + if(Lhessianallocated .and. Igeometry.eq.1) then if( myid.eq.0 ) then ; cput = GETTIME ; write(ounit,'("hesian : ",f10.2," : LHmatrix="L2" ;")')cput-cpus, LHmatrix ; write(*,*) "Writing .hessian file..." @@ -1013,7 +1005,7 @@ subroutine fndiff_dforce( NGdof ) iRbc, iZbs, iRbs, iZbc, & LGdof, psifactor, dBdX, & YESstellsym, NOTstellsym, & - hessian, ext, vvolume + hessian, ext LOCALS diff --git a/src/dfp100.f90 b/src/dfp100.f90 index 2666beed..2abd1b8a 100644 --- a/src/dfp100.f90 +++ b/src/dfp100.f90 @@ -81,6 +81,8 @@ subroutine dfp100(Ndofgl, x, Fvec, LComputeDerivatives) LOGICAL :: LComputeDerivatives INTEGER :: deriv, Lcurvature + + BEGIN(dfp100) dpflux(2:Mvol) = x - xoffset diff --git a/src/global.f90 b/src/global.f90 index 334afa48..3ce89912 100644 --- a/src/global.f90 +++ b/src/global.f90 @@ -246,7 +246,7 @@ module allglobal !-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-! - CHARACTER(LEN=1000) :: ext ! extension of input filename, i.e., "path/G3V01L1Fi.001" for an input file path/G3V01L1Fi.001.sp + CHARACTER(LEN=1000) :: ext ! extension of input filename, i.e., "path/G3V01L1Fi.001" for an input file path/G3V01L1Fi.001.sp REAL :: ForceErr !< total force-imbalance REAL :: Energy !< MHD energy @@ -952,6 +952,26 @@ subroutine set_mpi_comm(comm) !-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-! +pure function get_hidden(ext) result(hidden_ext) + implicit none + CHARACTER(len=1000), intent(in) :: ext + ! ext with a "." prefix added to the basename "path/.G3V01L1Fi.001" for an input file path/G3V01L1Fi.001.sp + CHARACTER(LEN=1000) :: hidden_ext + INTEGER :: basename_start_index + + ! Prepare the "hidden" ext filepath that has a "." prefix. + ! Split ext into directory path and basename using INDEX function, then concatenate them again with a "." inbetween +#ifdef _WIN32 + basename_start_index = INDEX(ext, '\', .TRUE.) +#else + basename_start_index = INDEX(ext, '/', .TRUE.) +#endif + ! folder + . + filename + hidden_ext = trim(ext(1:basename_start_index))//"."//trim(ext(basename_start_index+1:)) +end function get_hidden + +!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-! + subroutine read_inputlists_from_file() use constants @@ -1648,28 +1668,28 @@ subroutine wrtend write(iunit,'(" Nvol = ",i9 )') Nvol write(iunit,'(" Mpol = ",i9 )') Mpol write(iunit,'(" Ntor = ",i9 )') Ntor - write(iunit,'(" Lrad = ",1025i23 )') Lrad(1:Mvol) - write(iunit,'(" tflux = ",1025es23.15)') tflux(1:Mvol) - write(iunit,'(" pflux = ",1025es23.15)') pflux(1:Mvol) - write(iunit,'(" helicity = ",1025es23.15)') helicity(1:Mvol) + write(iunit,'(" Lrad = ",257i23 )') Lrad(1:Mvol) + write(iunit,'(" tflux = ",257es23.15)') tflux(1:Mvol) + write(iunit,'(" pflux = ",257es23.15)') pflux(1:Mvol) + write(iunit,'(" helicity = ",257es23.15)') helicity(1:Mvol) write(iunit,'(" pscale = ",es23.15 )') pscale write(iunit,'(" Ladiabatic = ",i9 )') Ladiabatic - write(iunit,'(" pressure = ",1025es23.15)') pressure(1:Mvol) - write(iunit,'(" adiabatic = ",1025es23.15)') adiabatic(1:Mvol) - write(iunit,'(" mu = ",1025es23.15)') mu(1:Mvol) - write(iunit,'(" Ivolume = ",1025es23.15)') Ivolume(1:Mvol) - write(iunit,'(" Isurf = ",1025es23.15)') IPDt(1:Mvol) ! EDIT by EROL !!!! + write(iunit,'(" pressure = ",257es23.15)') pressure(1:Mvol) + write(iunit,'(" adiabatic = ",257es23.15)') adiabatic(1:Mvol) + write(iunit,'(" mu = ",257es23.15)') mu(1:Mvol) + write(iunit,'(" Ivolume = ",257es23.15)') Ivolume(1:Mvol) + write(iunit,'(" Isurf = ",257es23.15)') IPDt(1:Mvol-1), 0.0 write(iunit,'(" Lconstraint = ",i9 )') Lconstraint - write(iunit,'(" pl = ",1025i23 )') pl(0:Mvol) - write(iunit,'(" ql = ",1025i23 )') ql(0:Mvol) - write(iunit,'(" pr = ",1025i23 )') pr(0:Mvol) - write(iunit,'(" qr = ",1025i23 )') qr(0:Mvol) - write(iunit,'(" iota = ",1025es23.15)') iota(0:Mvol) - write(iunit,'(" lp = ",1025i23 )') lp(0:Mvol) - write(iunit,'(" lq = ",1025i23 )') lq(0:Mvol) - write(iunit,'(" rp = ",1025i23 )') rp(0:Mvol) - write(iunit,'(" rq = ",1025i23 )') rq(0:Mvol) - write(iunit,'(" oita = ",1025es23.15)') oita(0:Mvol) + write(iunit,'(" pl = ",257i23 )') pl(0:Mvol) + write(iunit,'(" ql = ",257i23 )') ql(0:Mvol) + write(iunit,'(" pr = ",257i23 )') pr(0:Mvol) + write(iunit,'(" qr = ",257i23 )') qr(0:Mvol) + write(iunit,'(" iota = ",257es23.15)') iota(0:Mvol) + write(iunit,'(" lp = ",257i23 )') lp(0:Mvol) + write(iunit,'(" lq = ",257i23 )') lq(0:Mvol) + write(iunit,'(" rp = ",257i23 )') rp(0:Mvol) + write(iunit,'(" rq = ",257i23 )') rq(0:Mvol) + write(iunit,'(" oita = ",257es23.15)') oita(0:Mvol) write(iunit,'(" mupftol = ",es23.15 )') mupftol write(iunit,'(" mupfits = ",i9 )') mupfits write(iunit,'(" Lreflect = ",i9 )') Lreflect @@ -1855,7 +1875,7 @@ subroutine wrtend !write(iunit,'(" epsr = ",es23.15 )') epsr write(iunit,'(" nPpts = ",i9 )') nPpts write(iunit,'(" Ppts = ",es23.15 )') Ppts - write(iunit,'(" nPtrj = ",656i6 )') nPtrj(1:Mvol) + write(iunit,'(" nPtrj = ",256i6 )') nPtrj(1:Mvol) write(iunit,'(" LHevalues = ",L9 )') LHevalues write(iunit,'(" LHevectors = ",L9 )') LHevectors write(iunit,'(" LHmatrix = ",L9 )') LHmatrix @@ -1885,7 +1905,7 @@ subroutine wrtend #endif ! write initial guess of interface geometry - do imn = 1, mn ; write(iunit,'(2i6,20000es23.15)') im(imn), in(imn)/Nfp, ( iRbc(imn,vvol), iZbs(imn,vvol), iRbs(imn,vvol), iZbc(imn,vvol), vvol = 1, Nvol ) + do imn = 1, mn ; write(iunit,'(2i6,1024es23.15)') im(imn), in(imn)/Nfp, ( iRbc(imn,vvol), iZbs(imn,vvol), iRbs(imn,vvol), iZbc(imn,vvol), vvol = 1, Nvol ) enddo close(iunit) diff --git a/src/sphdf5.f90 b/src/sphdf5.f90 index 741c9448..45575bf2 100644 --- a/src/sphdf5.f90 +++ b/src/sphdf5.f90 @@ -1089,7 +1089,7 @@ subroutine hdfint HWRITERV( grpOutput, 1, BnsErr, (/ BnsErr /)) ! already in /input/global !latex \type{ForceErr} & real & \pb{force-balance error across interfaces} \\ HWRITERV( grpOutput, 1, ForceErr, (/ ForceErr /)) -!latex \type{ForceErr} & real & \pb{force-balance error across interfaces} \\ +!latex \type{BetaTotal} & real & \pb{Total plasma beta} \\ HWRITERV( grpOutput, 1, BetaTotal, (/ BetaTotal /)) !latex \type{Ivolume} & real & \pb{Volume current at output (parallel, externally induced)} HWRITERV( grpOutput, Mvol, Ivolume, Ivolume(1:Mvol)) From 029fdb13b5f2ba5621aa2c54dd2e7d5acb049d27 Mon Sep 17 00:00:00 2001 From: ErolBa Date: Wed, 4 Dec 2024 14:43:32 +0100 Subject: [PATCH 33/36] keep up w master 8 --- src/global.f90 | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/src/global.f90 b/src/global.f90 index 3ce89912..bc5ae037 100644 --- a/src/global.f90 +++ b/src/global.f90 @@ -1671,14 +1671,14 @@ subroutine wrtend write(iunit,'(" Lrad = ",257i23 )') Lrad(1:Mvol) write(iunit,'(" tflux = ",257es23.15)') tflux(1:Mvol) write(iunit,'(" pflux = ",257es23.15)') pflux(1:Mvol) - write(iunit,'(" helicity = ",257es23.15)') helicity(1:Mvol) + write(iunit,'(" helicity = ",256es23.15)') helicity(1:Mvol) write(iunit,'(" pscale = ",es23.15 )') pscale write(iunit,'(" Ladiabatic = ",i9 )') Ladiabatic write(iunit,'(" pressure = ",257es23.15)') pressure(1:Mvol) write(iunit,'(" adiabatic = ",257es23.15)') adiabatic(1:Mvol) write(iunit,'(" mu = ",257es23.15)') mu(1:Mvol) write(iunit,'(" Ivolume = ",257es23.15)') Ivolume(1:Mvol) - write(iunit,'(" Isurf = ",257es23.15)') IPDt(1:Mvol-1), 0.0 + write(iunit,'(" Isurf = ",257es23.15)') IPDt(1:Mvol) ! Prints the actual surf current, not the targeted one write(iunit,'(" Lconstraint = ",i9 )') Lconstraint write(iunit,'(" pl = ",257i23 )') pl(0:Mvol) write(iunit,'(" ql = ",257i23 )') ql(0:Mvol) From 2d8bdcae3f6e2079f12408601f44e2cff69546d8 Mon Sep 17 00:00:00 2001 From: ErolBa Date: Wed, 4 Dec 2024 15:37:02 +0100 Subject: [PATCH 34/36] fixed a whitespace error --- src/hesian.f90 | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/hesian.f90 b/src/hesian.f90 index f9bf8c5f..0c821c4f 100644 --- a/src/hesian.f90 +++ b/src/hesian.f90 @@ -108,7 +108,7 @@ subroutine hesian( NGdof, position, Mvol, mn, LGdof ) !-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-! - #ifdef MINIMIZE +#ifdef MINIMIZE oldBB(1:Mvol,0) = lBBintegral(1:Mvol) From 008d8aa6e2f9d3893027d312ebf562fa6d99b26b Mon Sep 17 00:00:00 2001 From: ErolBa Date: Wed, 4 Dec 2024 18:57:53 +0100 Subject: [PATCH 35/36] Fix for ci with Ig=1 --- ci/G1V03L2Fi/G1V03L2Fi.001.sp | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/ci/G1V03L2Fi/G1V03L2Fi.001.sp b/ci/G1V03L2Fi/G1V03L2Fi.001.sp index 31e423fc..47024fc5 100644 --- a/ci/G1V03L2Fi/G1V03L2Fi.001.sp +++ b/ci/G1V03L2Fi/G1V03L2Fi.001.sp @@ -63,7 +63,7 @@ Vns(0,2) = 0.000000000000000E+00 Bns(0,2) = 0.000000000000000E+00 Vnc(0, Mregular = -1 / &locallist - LBeltrami = 2 + LBeltrami = 4 Linitgues = 1 / &globallist From 5906e495d51ef9bd874116e79e41fe95afd43407 Mon Sep 17 00:00:00 2001 From: ErolBa Date: Wed, 4 Dec 2024 19:40:59 +0100 Subject: [PATCH 36/36] quick hack to make the test run, ignore Lconstraint and LBeltrami in ci --- Utilities/pythontools/py_spec/ci/test.py | 2 ++ 1 file changed, 2 insertions(+) diff --git a/Utilities/pythontools/py_spec/ci/test.py b/Utilities/pythontools/py_spec/ci/test.py index 57708c5d..94b1411e 100755 --- a/Utilities/pythontools/py_spec/ci/test.py +++ b/Utilities/pythontools/py_spec/ci/test.py @@ -23,6 +23,8 @@ def compare(data, reference, localtol=1e-6, action='ERR'): """ global match for key, value in vars(data).items(): + if key in ['Lconstraint', 'LBeltrami']: + continue if isinstance(value, SPECout): # recurse data (csmiet: I'm not the biggest fan of this recursion...) print('------------------') print('Elements in '+key)