Start cleaning namelists.

COMPILATION/Makefile.depend

@@ -59,6 +59,7 @@ stella_mod = \
 	 $(OBJ_DIR)/mp.o \
 	 $(OBJ_DIR)/mp_lu_decomposition.o \
 	 $(OBJ_DIR)/multibox.o \
+	 $(OBJ_DIR)/namelist_adiabatic_electrons.o \
 	 $(OBJ_DIR)/namelist_dissipation.o \
 	 $(OBJ_DIR)/neasyf.o \
 	 $(OBJ_DIR)/neoclassical_terms.o \
@@ -131,6 +132,7 @@ update_input_file_program_mod = \
 	 $(OBJ_DIR)/mp.o \
 	 $(OBJ_DIR)/mp_lu_decomposition.o \
 	 $(OBJ_DIR)/multibox.o \
+	 $(OBJ_DIR)/namelist_adiabatic_electrons.o \
 	 $(OBJ_DIR)/namelist_dissipation.o \
 	 $(OBJ_DIR)/neoclassical_terms.o \
 	 $(OBJ_DIR)/netcdf_utils.o \
@@ -806,6 +808,10 @@ $(OBJ_DIR)/multibox.o: \
 	 $(OBJ_DIR)/stella_time.o \
 	 $(OBJ_DIR)/text_options.o \
 	 $(OBJ_DIR)/zgrid.o 
+$(OBJ_DIR)/namelist_adiabatic_electrons.o: \
+	 $(OBJ_DIR)/file_utils.o \
+	 $(OBJ_DIR)/mp.o \
+	 $(OBJ_DIR)/text_options.o 
 $(OBJ_DIR)/namelist_dissipation.o: \
 	 $(OBJ_DIR)/file_utils.o \
 	 $(OBJ_DIR)/mp.o 
@@ -874,6 +880,7 @@ $(OBJ_DIR)/parameters_numerical.o: \
 $(OBJ_DIR)/parameters_physics.o: \
 	 $(OBJ_DIR)/file_utils.o \
 	 $(OBJ_DIR)/mp.o \
+	 $(OBJ_DIR)/namelist_adiabatic_electrons.o \
 	 $(OBJ_DIR)/text_options.o 
 $(OBJ_DIR)/ran.o: 
 $(OBJ_DIR)/redistribute.o: \
@@ -1078,6 +1085,7 @@ $(OBJ_DIR)/update_input_file.o: \
 	 $(OBJ_DIR)/hyper.o \
 	 $(OBJ_DIR)/init_g.o \
 	 $(OBJ_DIR)/multibox.o \
+	 $(OBJ_DIR)/namelist_adiabatic_electrons.o \
 	 $(OBJ_DIR)/namelist_dissipation.o \
 	 $(OBJ_DIR)/neoclassical_terms.o \
 	 $(OBJ_DIR)/parameters_diagnostics.o \

COMPILATION/Makefile.stella

@@ -54,14 +54,14 @@ export GEOMETRY=$(STELLA_DIR)/geometry
 export GRIDS=$(STELLA_DIR)/grids
 export GYROKINETIC_TERMS=$(STELLA_DIR)/gyrokinetic_terms
 export NEOCLASSICAL=$(STELLA_DIR)/neoclassical
-export PARAMETERS=$(STELLA_DIR)/parameters
+export NAMELISTS=$(STELLA_DIR)/namelists
 export RADIAL_VARIATION=$(STELLA_DIR)/radial_variation
-export INPUTFILETOOL=$(STELLA_DIR)/parameters/input_file_tool
+export INPUTFILETOOL=$(STELLA_DIR)/namelists/input_file_tool
 SUBFOLDERS := $(CALCULATIONS) $(DIAGNOSTICS) $(COLLISIONS) $(FIELDS) $(GEOMETRY) $(GRIDS) 
-SUBFOLDERS := $(SUBFOLDERS) $(GYROKINETIC_TERMS) $(NEOCLASSICAL) $(PARAMETERS) $(RADIAL_VARIATION)
+SUBFOLDERS := $(SUBFOLDERS) $(GYROKINETIC_TERMS) $(NEOCLASSICAL) $(NAMELISTS) $(RADIAL_VARIATION)
 SUBFOLDERS := $(SUBFOLDERS) $(INPUTFILETOOL)
 VPATH_SUBFOLDERS := :$(CALCULATIONS):$(DIAGNOSTICS):$(COLLISIONS):$(FIELDS):$(GEOMETRY):$(GRIDS):
-VPATH_SUBFOLDERS := :$(VPATH_SUBFOLDERS):$(GYROKINETIC_TERMS):$(NEOCLASSICAL):$(PARAMETERS):$(RADIAL_VARIATION):
+VPATH_SUBFOLDERS := :$(VPATH_SUBFOLDERS):$(GYROKINETIC_TERMS):$(NEOCLASSICAL):$(NAMELISTS):$(RADIAL_VARIATION):
 VPATH_SUBFOLDERS := :$(VPATH_SUBFOLDERS):$(INPUTFILETOOL):
 
 # Check directories
@@ -266,7 +266,7 @@ $(OBJ)/%.o: $(GYROKINETIC_TERMS)/%.f90 $(external_modules) | $(OBJ) $(MOD)
 $(OBJ)/%.o: $(NEOCLASSICAL)/%.f90 $(external_modules) | $(OBJ) $(MOD)
 	@echo "   (stella) *.f90 to *.o: $(notdir $<)" 
 	@$(FC) $(F90FLAGS) $(INC_FLAGS) $(MOD_FLAGS_STELLA) -o $@ -c $< 
-$(OBJ)/%.o: $(PARAMETERS)/%.f90 $(external_modules) | $(OBJ) $(MOD)
+$(OBJ)/%.o: $(NAMELISTS)/%.f90 $(external_modules) | $(OBJ) $(MOD)
 	@echo "   (stella) *.f90 to *.o: $(notdir $<)" 
 	@$(FC) $(F90FLAGS) $(INC_FLAGS) $(MOD_FLAGS_STELLA) -o $@ -c $< 
 $(OBJ)/%.o: $(RADIAL_VARIATION)/%.f90 $(external_modules) | $(OBJ) $(MOD)
@@ -432,7 +432,7 @@ remove-temp-files:
 	@echo "   - remove temp files" 
 	@-rm -f $(UTILS)/*~ $(CALCULATIONS)/*~ $(DIAGNOSTICS)/*~ $(COLLISIONS)/*~ 
 	@-rm -f $(FIELDS)/*~ $(GEOMETRY)/*~ $(GRIDS)/*~ $(GYROKINETIC_TERMS)/*~ 
-	@-rm -f $(NEOCLASSICAL)/*~ $(PARAMETERS)/*~ $(RADIAL_VARIATION)/*~ 
+	@-rm -f $(NEOCLASSICAL)/*~ $(NAMELISTS)/*~ $(RADIAL_VARIATION)/*~ 
 
 # In case cmake was used, clean it up as well
 CMAKE := $(COMPILATION_DIR)/build_cmake

STELLA_CODE/namelists/namelist_adiabatic_electrons.f90

@@ -0,0 +1,125 @@
+!###############################################################################
+!###################### READ ADIABATIC ELECTRONS NAMELIST ######################
+!###############################################################################
+! Read the <adiabatic_electrons> namelist in the input file:
+! 
+! &adiabatic_electroms
+!  adiabatic_option = 'field-line-average-term'
+!  tite = 1.0
+!  nine = 1.0
+!/
+!###############################################################################
+module namelist_adiabatic_electrons
+
+   implicit none
+
+   public :: read_namelist
+
+   private
+
+contains
+
+   subroutine read_namelist(adiabatic_option_switch, nine, tite, &
+      adiabatic_option_fieldlineavg, adiabatic_option_periodic)
+
+      use mp, only: proc0
+
+      implicit none
+
+      real, intent(out) :: tite, nine 
+      integer, intent(out) :: adiabatic_option_switch
+      integer, intent(out) :: adiabatic_option_periodic
+      integer, intent(out) :: adiabatic_option_fieldlineavg
+
+      ! Local variable to set <adiabatic_option_switch>
+      character(30) :: adiabatic_option
+
+      if (.not. proc0) return
+      call set_default_parameters
+      call read_input_file
+      call check_inputs
+
+   contains
+
+      !**********************************************************************
+      !                         DEFAULT PARAMETERS                          !
+      !**********************************************************************
+      ! Set the default input parameters.
+      !**********************************************************************
+      subroutine set_default_parameters()
+
+         implicit none
+
+         adiabatic_option = 'field-line-average-term'
+         tite = 1.0
+         nine = 1.0
+
+      end subroutine set_default_parameters
+
+
+      !**********************************************************************
+      !                          READ INPUT FILE                            !
+      !**********************************************************************
+      ! Overwrite any default options with those specified in the input file. 
+      ! Then change the other parameters consistently.
+      !**********************************************************************
+      subroutine read_input_file
+
+         use file_utils, only: input_unit_exist, error_unit
+         use text_options, only: text_option, get_option_value
+
+         implicit none
+
+         ! Variables needed to read the input file
+         integer :: ierr, in_file
+         logical :: dexist
+
+         ! Create parameters for the text option
+         integer, parameter :: periodic = 1 
+         integer, parameter :: fieldlineavg = 2
+
+         ! Link text options for <adiabatic_option> to an integer value
+         type(text_option), dimension(6), parameter :: adiabaticopts = &
+            (/text_option('default', fieldlineavg), &
+            text_option('no-field-line-average-term', periodic), &
+            text_option('field-line-average-term', fieldlineavg), &
+            text_option('iphi00=0', periodic), &
+            text_option('iphi00=1', periodic), &
+            text_option('iphi00=2', fieldlineavg)/)
+
+         ! Define variables in the <adiabatic_electrons> namelist
+         namelist /adiabatic_electrons/ adiabatic_option, tite, nine
+
+         !----------------------------------------------------------------------
+
+         ! Save the values of the adiabatic option
+         adiabatic_option_periodic = periodic
+         adiabatic_option_fieldlineavg = fieldlineavg
+
+         ! Overwrite the default input parameters by those specified in the input file
+         in_file = input_unit_exist("adiabatic_electrons", dexist)
+         if (dexist) read (unit=in_file, nml=adiabatic_electrons)
+
+         ! Read the text option in <adiabatic_option> and store it in <adiabatic_option_switch>
+         ierr = error_unit()
+         call get_option_value(adiabatic_option, adiabaticopts, adiabatic_option_switch, &
+            ierr, "adiabatic_option in parameters_physics")
+
+      end subroutine read_input_file
+
+
+      !**********************************************************************
+      !                           CHECK INPUTS                             !
+      !**********************************************************************
+      ! Make sure that the input variables are set correctly.
+      !**********************************************************************
+      subroutine check_inputs
+
+         implicit none
+
+      end subroutine check_inputs
+
+   end subroutine read_namelist
+
+end module namelist_adiabatic_electrons
+

STELLA_CODE/namelists/namelist_dissipation.f90

@@ -0,0 +1,92 @@
+!###############################################################################
+!########################## READ DISSIPATION NAMELIST ##########################
+!###############################################################################
+! Read the <dissipation> namelist in the input file
+!###############################################################################
+module namelist_dissipation
+
+   implicit none
+
+   public :: read_namelist
+
+   private
+
+contains
+
+   subroutine read_namelist(include_collisions, collisions_implicit, collision_model, hyper_dissipation)
+
+      use mp, only: proc0
+
+      implicit none
+
+      logical, intent(out) :: include_collisions, collisions_implicit, hyper_dissipation
+      character(30), intent(out) :: collision_model
+
+      if (.not. proc0) return
+      call set_default_parameters
+      call read_input_file
+      call check_inputs
+
+   contains
+
+      !**********************************************************************
+      !                          READ INPUT FILE                            !
+      !**********************************************************************
+      ! Overwrite any default options with those specified in the input file. 
+      ! Then change the other parameters consistently.
+      !**********************************************************************
+      subroutine read_input_file
+
+         use file_utils, only: input_unit_exist
+
+         implicit none
+
+         integer :: in_file
+         logical :: dexist
+
+         ! Variables in the <dissipation> namelist
+         namelist /dissipation/ include_collisions, collisions_implicit, collision_model, hyper_dissipation
+
+         ! Overwrite the default input parameters by those specified in the input file
+         in_file = input_unit_exist("dissipation", dexist)
+         if (dexist) read (unit=in_file, nml=dissipation)
+
+      end subroutine read_input_file
+
+
+      !**********************************************************************
+      !                           CHECK INPUTS                             !
+      !**********************************************************************
+      ! Make sure that the input variables are set correctly.
+      !**********************************************************************
+      subroutine check_inputs
+
+         implicit none
+
+         if (.not. include_collisions) collisions_implicit = .false.
+
+      end subroutine check_inputs
+
+
+      !**********************************************************************
+      !                         DEFAULT PARAMETERS                          !
+      !**********************************************************************
+      ! Set the default input parameters.
+      !**********************************************************************
+      subroutine set_default_parameters()
+
+         implicit none
+
+         include_collisions = .false.
+         collisions_implicit = .true.
+         hyper_dissipation = .false.
+
+         ! dougherty or fokker-planck
+         collision_model = "dougherty" 
+
+      end subroutine set_default_parameters
+
+   end subroutine read_namelist
+
+end module namelist_dissipation
+

STELLA_CODE/parameters/update_input_file.f90 → STELLA_CODE/namelists/update_input_file.f90

@@ -194,12 +194,13 @@ subroutine write_parameters_physics(unit_number, write_input_file)
       use file_utils, only: input_unit_exist
       use parameters_physics, only: set_default_parameters_physics => set_default_parameters
       use parameters_physics, only: include_parallel_streaming, include_mirror, nonlinear
-      use parameters_physics, only: xdriftknob, ydriftknob, wstarknob, adiabatic_option, prp_shear_enabled
+      use parameters_physics, only: xdriftknob, ydriftknob, wstarknob, prp_shear_enabled
       use parameters_physics, only: hammett_flow_shear, include_pressure_variation, include_geometric_variation
       use parameters_physics, only: include_parallel_nonlinearity, suppress_zonal_interaction, full_flux_surface
       use parameters_physics, only: include_apar, include_bpar, radial_variation
-      use parameters_physics, only: beta, zeff, tite, nine, rhostar, vnew_ref
+      use parameters_physics, only: beta, zeff, rhostar, vnew_ref
       use parameters_physics, only: g_exb, g_exbfac, omprimfac, irhostar
+      use namelist_adiabatic_electrons, only: read_adiabatic_electrons_namelist => read_namelist
 
       implicit none
 
@@ -212,13 +213,19 @@ subroutine write_parameters_physics(unit_number, write_input_file)
       integer :: unit_number_temp
       logical :: new_nml_exist
 
+      ! Define the variables in the namelist <adiabatic_electrons>
+      integer :: adiabatic_option_switch, adiabatic_option_periodic, adiabatic_option_fieldlineavg
+      character(30) :: adiabatic_option
+      real :: tite, nine
+
       ! Current namelist
       namelist /parameters_physics/ include_parallel_streaming, include_mirror, nonlinear, &
         adiabatic_option, prp_shear_enabled, include_apar, include_bpar, radial_variation, &
         hammett_flow_shear, include_pressure_variation, include_geometric_variation, &
         include_parallel_nonlinearity, suppress_zonal_interaction, full_flux_surface, & 
         xdriftknob, ydriftknob, wstarknob, g_exb, g_exbfac, omprimfac, irhostar, &
-        beta, zeff, tite, nine, rhostar, vnew_ref 
+        beta, zeff, tite, nine, rhostar, vnew_ref
+      namelist /adiabatic_electrons/ adiabatic_option, tite, nine
 
       !------------------------------------------------------------------------- 
 
@@ -236,9 +243,16 @@ subroutine write_parameters_physics(unit_number, write_input_file)
          call backwards_compatibility_physics_flags()
          call backwards_compatibility_time_advance_knobs()
       end if  
+
+      ! TODO - Finish this
+      call read_adiabatic_electrons_namelist(adiabatic_option_switch, nine, tite, &
+         adiabatic_option_fieldlineavg, adiabatic_option_periodic)
+      if (adiabatic_option_switch==adiabatic_option_periodic) adiabatic_option = 'no-field-line-average-term'
+      if (adiabatic_option_switch==adiabatic_option_fieldlineavg) adiabatic_option = 'field-line-average-term'
 
       ! Write the namelist to <run_name>_with_defaults.in or default_stella_input.in
       write(unit=unit_number, nml=parameters_physics)
+      write(unit=unit_number, nml=adiabatic_electrons)
 
    contains