add option to set parameters from the command-line

.gitignore

@@ -2,3 +2,4 @@
 build
 configure.mk
 result
+src/gray_cli_params.f90

Makefile

@@ -12,18 +12,20 @@
 #  └── build - build artifacts
 #      ├── bin - binaries
 #      ├── lib - libraries
-#      └── obj - objects
+#      ├── obj - objects
+#      └── inc - files to #include
 SRCDIR   = src
 BUILDDIR = build
 SHAREDIR = build/share
 BINDIR   = build/bin
 LIBDIR   = build/lib
 OBJDIR   = build/obj
+INCDIR   = build/inc
 
 PREFIX ?= /usr/bin
 
 # Directories that need to be created
-DIRS = $(BINDIR) $(OBJDIR) $(LIBDIR) $(SHAREDIR)
+DIRS = $(BINDIR) $(OBJDIR) $(INCDIR) $(LIBDIR) $(SHAREDIR)
 
 ##
 ## Files
@@ -32,7 +34,7 @@ DIRS = $(BINDIR) $(OBJDIR) $(LIBDIR) $(SHAREDIR)
 # All Fortran source files
 SOURCES = $(wildcard $(SRCDIR)/*.f90)
 
-# All Generated makefiles describing object dependencies
+# All Fortran object
 OBJECTS = $(patsubst $(SRCDIR)/%.f90,$(OBJDIR)/%.o,$(SOURCES))
 
 # Generated makefiles describing object dependencies
@@ -64,7 +66,7 @@ GIT_DIRTY ?= $(shell test -n "$$(git status --porcelain)" && echo "-dirty")
 # Note: can't use ?= for FC because GNU Make defaults to f77
 FC        = gfortran
 LD        = gfortran
-FFLAGS   += -O3 -J$(OBJDIR) -ffree-line-length-none
+FFLAGS   += -O3 -J$(OBJDIR) -I$(INCDIR) -ffree-line-length-none
 CPPFLAGS += -DREVISION=\"$(GIT_REV)$(GIT_DIRTY)\" -DPREFIX=\"$(PREFIX)\"
 
 # Static build options
@@ -150,14 +152,19 @@ $(OBJDIR)/%.d: $(SRCDIR)/%.f90 | $(OBJDIR)
 	sed -nE 's@^[[:blank:]]*use[[:blank:]]+'\
 	'([^,[:blank:]&]+).*@$(OBJDIR)/\1.o \\@p' | \
 	 sort -u >> '$@'
+	@sed -nE 's@^#include "(.+)"@$(INCDIR)/\1 \\\n@p' '$<' >> '$@'
 
 # Load the generated rules
 include $(DEPS)
 
 # Compile a generic Fortran source
-$(OBJDIR)/%.o: $(SRCDIR)/%.f90 | $(OBJDIR)
+$(OBJDIR)/%.o: $(SRCDIR)/%.f90 | $(OBJDIR) $(INCDIR)
 	$(FC) -cpp $(CPPFLAGS) $(FFLAGS) -c '$<' -o '$@'
 
+# Generate Fortran code from shell script
+$(INCDIR)/%.inc: $(SRCDIR)/%.sh | $(INCDIR)
+	sh '$<' > '$@'
+
 # Create directories
 $(DIRS):
 	mkdir -p '$@'

depend

@@ -15,6 +15,8 @@ walk_dag(){
   while read -r line; do
     # skip the first line (file own name)
     contains "$line" ': ' && continue
+    # only look up object files
+    contains "$line" '.o ' || continue
     line="${line% \\}"
     contains "$visited" "$line" && continue
     visited="$line:$visited"

src/gray_cli.f90

@@ -8,6 +8,7 @@ module gray_cli
   ! Note: if you change these, remember to update:
   !  1. the print_help() subroutine
   !  2. the print_cli_options() subroutine
+  !  3. the man page
   type cli_options
     ! Switches
     logical :: quiet
@@ -21,7 +22,8 @@ module gray_cli
   end type
 
   private
-  public :: cli_options, print_cli_options, parse_cli_options
+  public :: cli_options, print_cli_options, parse_cli_options, &
+            deinit_cli_options, parse_param_overrides
 
 contains
 
@@ -48,7 +50,12 @@ contains
     print '(a)', '  -p, --params-file FILE    set the parameters file'
     print '(a)', '                            (default: gray_params.data)'
     print '(a)', '  -s, --sum FILE            sum the output profiles from a list of files'
-    print '(a)', '  -u, --units ID[,ID...]    select which units to output (default: 4, 7)'
+    print '(a)', '  -u, --units ID[,ID...]    select which units to output (default: 4, 7);'
+    print '(a)', '                            see the manual for all unit IDs.'
+    print '(a)', '  -g, --gray-param ID=VAL   set a GRAY parameter, overriding the value'
+    print '(a)', '                            specified via --params-file;'
+    print '(a)', '                            the ID is GROUP.NAME, ex. antenna.fghz;'
+    print '(a)', '                            see the manual for available parameters.'
     print '(a)', ''
     print '(a)', '*Exit status*'
     print '(a)', ' 0  if OK,'
@@ -126,10 +133,12 @@ contains
       select case (argument)
         case ('-h', '--help')
           call print_help()
+          deallocate(argument)
           call exit(0)
 
         case ('-V', '--version')
           call print_version()
+          deallocate(argument)
           call exit(0)
 
         case ('-v', '--verbose')
@@ -159,27 +168,106 @@ contains
           allocate(opts%units(commas + 1))
 
           ! read the list of table IDs
-          read(temp, *, iostat=error) opts%units
+          read (temp, *, iostat=error) opts%units
-          if (error .gt. 0) then
+          if (error > 0) then
             print '(a,a)', 'invalid table IDs: ', temp
+            deallocate(argument)
+            deallocate(temp)
             call exit(1)
           end if
           deallocate(temp)
           skip_next = .true.
 
+        case ('-g', '--gray-param')
+          ! these overrides are parsed later since they need to
+          ! be applied to the final gray_parameters structure
+          skip_next = .true.
+
         case default
           print '(a,a,/)', 'Unknown option: ', argument
           call print_help()
+          deallocate(argument)
           call exit(1)
 
       end select
     end do
 
     ! free temporary string
-    if (nargs .gt. 0) deallocate(argument)
+    if (nargs > 0) deallocate(argument)
   end subroutine
 
 
+  subroutine parse_param_overrides(params)
+    ! Reads GRAY parameters from CLI and overrides `params` accordingly
+
+    use gray_params, only : gray_parameters, update_parameter
+
+    implicit none
+
+    ! subroutine arguments
+    type(gray_parameters), intent(inout) :: params
+
+    ! local variables
+    character(len=:), allocatable :: argument, temp, id, val
+    logical :: skip_next = .false.
+    integer :: i, nargs
+    integer :: error, sep
+
+    nargs = command_argument_count()
+    do i = 1, nargs
+      call get_command_string(i, argument)
+
+      ! skip one cycle if the last argument was a value
+      if (skip_next) then
+        skip_next = .false.
+        cycle
+      end if
+
+      ! parse gray parameters
+      select case (argument)
+        case ('-g', '--gray-param')
+          call get_command_string(i + 1, temp)
+
+          ! split at "=" (id=value)
+          sep = findloc([(temp(i:i) == '=', i = 1, len(temp))], .true., 1)
+          id  = temp(1:sep - 1)
+          val = temp(sep + 1:)
+
+          if (sep == 0) then
+            print '(a,a)', 'invalid GRAY parameter declaration: ', temp
+            print '(a)', 'correct syntax is ID=VALUE, ex. antenna.alpha=45'
+            deallocate(temp)
+            call exit(1)
+          end if
+
+          ! match the name string to a parameter
+          select case (update_parameter(params, id, val))
+            case (1)
+              print '(4a)', 'invalid value for ', id, ': ', val
+              deallocate(temp)
+              call exit(1)
+
+            case (2)
+              print '(a,a)', 'unknown GRAY parameter: ', id
+              deallocate(temp)
+              call exit(1)
+          end select
+
+          deallocate(temp)
+          skip_next = .true.
+
+        ! skip everything else
+        case default
+          cycle
+
+      end select
+    end do
+
+    ! free temporary string
+    if (nargs > 0) deallocate(argument)
+  end subroutine parse_param_overrides
+
+
   subroutine get_command_string(i, arg)
     ! Reads a CLI argument into a deferred-length string
 
@@ -198,4 +286,19 @@ contains
     call get_command_argument(i, arg)        ! copy
   end subroutine
 
+
+  subroutine deinit_cli_options(opts)
+    ! Frees all memory allocated by the parse_cli_options subroutine
+
+    implicit none
+
+    ! subroutine arguments
+    type(cli_options), intent(inout) :: opts
+
+    if (allocated(opts%output_dir))   deallocate(opts%output_dir)
+    if (allocated(opts%params_file))  deallocate(opts%params_file)
+    if (allocated(opts%sum_filelist)) deallocate(opts%sum_filelist)
+    if (allocated(opts%units))        deallocate(opts%units)
+  end subroutine deinit_cli_options
+
 end module gray_cli

src/gray_params.f90

@@ -228,6 +228,30 @@ contains
   end subroutine print_parameters
 
 
+  function update_parameter(params, name, value) result(error)
+    ! Updates the value of a parameter, addressed by a string
+    ! The return error is:
+    !   0 on success;
+    !   1 on invalid parameter value;
+    !   2 on unknown parameter name.
+    !
+    ! Ex. update_parameter(params, 'raytracing.nrayr', '10')
+    implicit none
+
+    ! function arguments
+    type(gray_parameters),         intent(inout) :: params
+    character(len=:), allocatable, intent(in)    :: name, value
+    integer :: error
+
+    select case (name)
+#include "gray_params.inc"
+      case default
+        error = 2
+    end select
+
+  end function update_parameter
+
+
   subroutine read_parameters(filename, params, unit)
     use utils,  only : get_free_unit
     use logger, only : log_error

src/gray_params.sh

@@ -0,0 +1,30 @@
+#!/bin/sh
+
+# This script generates the very repetitive code for parsing the
+# GRAY parameters from a string. The output is embedded
+# into gray_params.f90 using a CPP include directive.
+
+sets='antenna equilibrium profiles raytracing ecrh_cd output misc'
+
+# shellcheck disable=SC2034
+{
+antenna='alpha beta power psi chi iox ibeam filenm fghz pos w ri phi'
+equilibrium='ssplps ssplf factb sgnb sgni ixp iequil icocos ipsinorm idesc ifreefmt filenm'
+profiles='psnbnd sspld factne factte iscal irho iprof filenm'
+raytracing='rwmax dst nrayr nrayth nstep igrad idst ipass ipol'
+ecrh_cd='iwarm ilarm imx ieccd'
+output='ipec nrho istpr istpl'
+misc='rwall'
+}
+
+deref() { eval "echo \$$1"; }
+
+for set in $sets; do
+  for param in $(deref "$set"); do
+    cat <<EOF
+      case ('$set.$param')
+        read (value, *, iostat=error) params%$set%$param
+        if (error > 0) error = 1
+EOF
+  done
+done

src/main.f90

@@ -2,7 +2,8 @@ program main
   use const_and_precisions, only : wp_, one, zero
   use logger,               only : INFO, ERROR, set_log_level, log_message
   use units,                only : set_active_units, close_units
-  use gray_cli,             only : cli_options, parse_cli_options
+  use gray_cli,             only : cli_options, parse_cli_options, &
+                                   deinit_cli_options, parse_param_overrides
   use gray_core,            only : gray_main
   use gray_params,          only : gray_parameters, gray_data, gray_results, &
                                    read_parameters, params_set_globals => set_globals
@@ -27,9 +28,11 @@ program main
   ! Activate the given output units
   call set_active_units(opts%units)
 
-  ! Load the parameters and also copy them into
+  ! Load the parameters from file, apply CLI
-  ! global variables exported by the gray_params
+  ! overrides, and copy them into global
+  ! variables exported by the gray_params
   call read_parameters(opts%params_file, params)
+  call parse_param_overrides(params)
   call params_set_globals(params)
 
   ! Read the input data and set the global variables
@@ -125,6 +128,7 @@ program main
         close(100 + i)
       end do
      deallocate(dpdv, jcd, jphi, currins, pins, rtin, rpin)
+     deallocate(opts%params_file)
    end block sum
   else
     call gray_main(params, data, results, err)
@@ -142,6 +146,7 @@ program main
   call deinit_equilibrium(data%equilibrium)
   call deinit_profiles(data%profiles)
   call deinit_misc
+  call deinit_cli_options(opts)
   deallocate(results%dpdv, results%jcd)
   call close_units