Convert a CP.x from QuantumEspresso into QUIP-GAP and DeepMD

Author: tavanfran

cp2quip_deepmd.f90

@@ -0,0 +1,172 @@
+program hisread
+!---------------------------------------------------------------------
+!   read lammps trajectory file and wirte the trajectory in PDB format
+!   written by Francesco Tavanti, March 2020
+!   CNR-NANO S3, Modena, Italy
+!
+!   USAGE:
+!   build the fortran executable ==> gfortran lammpstraj2pdb.f90
+!   then ./a.out
+!   insert the name of input lammps file
+!   insert the name of output file in pdb format
+!---------------------------------------------------------------------
+implicit none
+integer natmax,ncouplemax
+
+parameter(natmax=50000)
+
+
+integer it,hkey,pdbkey,t,nat,itemp,j,k,i,num(natmax)
+integer nn,index(natmax),n,numero(natmax)
+integer fluct,h,step,step_end,dump,eneyn,foryn
+character*8 ctemp
+character*2 atyp,chain(natmax),catena
+character*2 atype(natmax)
+character*3 resi(natmax)
+character*70 ctemp2
+character*80 title,tfilename
+
+real*8 pos(3,natmax),vel(3,natmax),for(3,natmax)
+real*8 temptot,raggio(natmax),speed,force
+real*8 xa,xb,xc,ya,yb,yc,za,zb,zc,energy
+real*8 fx(natmax),fy(natmax),fz(natmax),nothing
+character*8 chskip
+character*4 res(natmax),residuo
+integer skip,nca,mass,charge,replica,index1,timestep,yn
+
+character*1 option
+character*4 atname
+character*80 lammpsfile,pdbfile
+
+!------------------------------------------------------------------
+!     read the lammps file
+!------------------------------------------------------------------
+write(*,*)''
+write(*,*)'*********************'
+write(*,*)'  This script reads a lammps trajectory file and writes the trajectory in PDB format'
+write(*,*)'  The trajectory could come both from serial and from parallel simulations'
+write(*,*)'  written by Francesco Tavanti, March 2020'
+write(*,*)'  CNR-NANO S3, Modena, Italy'
+write(*,*)'*********************'
+write(*,*)''
+
+write(*,*)'Write name of lammps trajcetory file'
+!read(*,*)lammpsfile
+
+open(10,file='Ge50Se50_P.pos',status='old')
+open(11,file='Ge50Se50_P.evp')
+
+open(13,file='GeSe.label')
+open(14,file='Ge50Se50_P.for')
+open(15,file='conf_deepmd.xyz')
+
+!write(*,*)'Do you want energy? 0 = NO , 1 = YES'
+!read(*,*)eneyn
+
+eneyn=1
+!write(*,*)'Do you want forces? 0 = NO , 1 = YES'
+!read(*,*)foryn
+foryn=1
+write(*,*)'Dump frames'
+read(*,*)dump
+write(*,*)'Do you want forces? 0=no 1=yes'
+read(*,*)yn
+
+do j=1,50
+    read(13,'(a2)')atype(j)
+enddo
+
+!dump=10
+
+step=1
+step_end=100000
+read(11,*)
+
+xb= 21.4735
+yb= 21.4735
+zb= 21.4735
+do it=1,step_end
+    read(10,900)title
+    read(11,*)nothing,nothing,nothing,nothing,nothing,energy
+if((it.ge.step).and.(it.le.step_end).and.((modulo(it,dump)).eq.0))then
+
+    write(15,'(i2)')50
+    if(yn.eq.1)then
+    write(15,'(a27,9f10.5,a1,a52,f11.4,a12)')'config_type=1000 Lattice=" ',xb/1.8897,0.0,0.0,0.0,yb/1.8897,0.0,0.0,0.0,zb/1.8897, &
+    '"',' Properties=species:S:1:pos:R:3:forces:R:3 energy=',energy*27.2114,' pbc="T T T"'
+    else
+    write(15,'(a27,9f10.5,a1,a42,f11.4,a12)')'config_type=1000 Lattice=" ',xb/1.8897,0.0,0.0,0.0,yb/1.8897,0.0,0.0,0.0,zb/1.8897, &
+        '"',' Properties=species:S:1:pos:R:3 energy=',energy*27.2114,' pbc="T T T"'
+    endif
+endif
+
+
+read(14,*)title
+do j=1,50
+read(14,*)fx(j),fy(j),fz(j)
+fx(j)=fx(j)*51.422086
+fy(j)=fy(j)*51.422086
+fz(j)=fz(j)*51.422086
+if(foryn.eq.0)then
+fx(j)=0
+fy(j)=0
+fz(j)=0
+endif
+read(10,*)(pos(k,j),k=1,3)
+if((pos(1,j).gt.xb))then
+    pos(1,j)=MOD(pos(1,j),xb)
+elseif((pos(1,j).lt.0))then
+    pos(1,j)=MOD(pos(1,j),xb)+xb
+endif
+if((pos(2,j).gt.yb))then
+    pos(2,j)=MOD(pos(2,j),yb)
+elseif((pos(2,j).lt.0))then
+    pos(2,j)=MOD(pos(2,j),yb)+yb
+endif
+if((pos(3,j).gt.zb))then
+    pos(3,j)=MOD(pos(3,j),zb)
+elseif((pos(3,j).lt.0))then
+    pos(3,j)=MOD(pos(3,j),zb)+zb
+endif
+
+
+
+
+!if(pos(1,j).gt.xb)then
+!    pos(1,j)=pos(1,j)-xb
+!elseif(pos(1,j).lt.0)then
+!    pos(1,j)=pos(1,j)+xb
+!elseif(pos(2,j).gt.yb)then
+!    pos(2,j)=pos(2,j)-yb
+!elseif(pos(2,j).lt.0)then
+!    pos(2,j)=pos(2,j)+yb
+!elseif(pos(3,j).gt.yb)then
+!    pos(3,j)=pos(3,j)-zb
+!elseif(pos(3,j).lt.0)then
+!    pos(3,j)=pos(3,j)+zb
+!else
+!endif
+
+
+
+if((it.ge.step).and.(it.le.step_end).and.((modulo(it,dump)).eq.0))then
+    if(yn.eq.1)then
+    write(15,'(a2,6f17.9)')atype(j),pos(1,j)/1.8897,pos(2,j)/1.8897,pos(3,j)/1.8897,fx(j),fy(j),fz(j)
+    else
+    write(15,'(a2,3f17.9)')atype(j),pos(1,j)/1.8897,pos(2,j)/1.8897,pos(3,j)/1.8897
+    endif
+endif
+enddo
+
+
+enddo
+
+170  format(a6)
+
+900  format(a80)
+
+1070 format(a4,2x,i5,1x,a2,3x,a3,i6,4x,f8.3,f8.3,f8.3,f6.2,f6.2)
+
+end
+!------------------------------------------------------------------------
+