Fix OTF backend compilation errors

kmos/fortran_src/base_otf.f90

@@ -293,7 +293,7 @@ subroutine add_proc(proc, site, rate)
   ! ARGUMENTS
   !
   !    * ``proc`` positive integer number that represents the process to be added.
-  !    * ``site`` positive integer number that represents the site to be manipulated
+  !    * ``site`` positive integer that represents the site to be manipulated
   !******
   integer(kind=iint), intent(in) :: proc, site
   real(kind=rdouble), intent(in) :: rate

kmos/fortran_src/proclist_constants_otf.mpy

@@ -9,22 +9,12 @@ gpl = self._gpl_message()
 #@
 #@ module {module_name}
 #@ use kind_values
-#@ use lattice, only: &
-site_params = []
-for layer in data.layer_list:
-    #@     {layer.name}, &
-    for site in layer.sites:
-        site_params.append((site.name, layer.name))
-
-for i, (site, layer) in enumerate(site_params):
-    #@     {layer}_{site}, &
-#@     get_species
-#@ 
-#@ 
+#@
+#@
 #@ implicit none
-#@ 
-#@ 
-#@ 
+#@
+#@
+#@
 
 # initialize various parameter kind of data
 #@  ! Species constants

kmos/io.py

@@ -2752,7 +2752,19 @@ def write_proclist_pars_otf(self, data, out, separate_files=False):
         out.write("use kind_values\n")
         out.write("use base, only: &\n")
         out.write("%srates\n" % (" " * indent))
-        out.write("use proclist_constants\n")
+        # Import species and process constants from proclist_constants
+        # Avoid importing species that conflict with user parameter names
+        parameter_names = [p.name for p in data.parameter_list]
+        out.write("use proclist_constants, only: &\n")
+        for i, species in enumerate(data.species_list):
+            # Only import species that don't conflict with user parameters
+            if species.name not in parameter_names:
+                out.write("%s%s, &\n" % (" " * indent, species.name))
+        for i, process in enumerate(data.process_list):
+            if i < len(data.process_list) - 1:
+                out.write("%s%s, &\n" % (" " * indent, process.name))
+            else:
+                out.write("%s%s\n" % (" " * indent, process.name))
         out.write("use lattice, only: &\n")
         site_params = []
         for layer in data.layer_list:
@@ -2762,7 +2774,14 @@ def write_proclist_pars_otf(self, data, out, separate_files=False):
         for site, layer in site_params:
             out.write("%s%s_%s, &\n" % (" " * indent, layer, site))
         out.write("%sget_species\n" % (" " * indent))
-        out.write("\nimplicit none\n\n")
+        out.write("\nimplicit none\n")
+        # Make rate_* functions private so f2py doesn't try to wrap them
+        out.write("private :: ")
+        for i, process in enumerate(data.process_list):
+            if i < len(data.process_list) - 1:
+                out.write("rate_{0}, ".format(process.name))
+            else:
+                out.write("rate_{0}\n\n".format(process.name))
 
         units_list, masses_list, chempot_list = self._otf_get_auxilirary_params(data)
 
@@ -3235,8 +3254,23 @@ def write_proclist_otf(self, data, out, separate_files=True, debug=False):
         )
 
         out.write("    get_species\n")
-        out.write("use proclist_constants\n")
-        out.write("use proclist_pars\n")
+        # Import species and processes from proclist_constants to avoid conflicts
+        out.write("use proclist_constants, only: &\n")
+        out.write("    default_species, &\n")
+        for i, species in enumerate(data.species_list):
+            out.write("    %s, &\n" % species.name)
+        for i, process in enumerate(data.process_list):
+            if i < len(data.process_list) - 1:
+                out.write("    %s, &\n" % process.name)
+            else:
+                out.write("    %s\n" % process.name)
+        # Import only gr_* functions from proclist_pars to avoid conflicts with user parameters
+        out.write("use proclist_pars, only: &\n")
+        for i, process in enumerate(data.process_list):
+            if i < len(data.process_list) - 1:
+                out.write("    gr_%s, &\n" % process.name)
+            else:
+                out.write("    gr_%s\n" % process.name)
         if separate_files and self.separate_proclist_pars:
             for i in range(len(data.process_list)):
                 out.write("use run_proc_{0:04d}; use gr_{0:04d}\n".format(i + 1))
@@ -3394,8 +3428,36 @@ def write_proclist_run_proc_name_otf(
                 out2 = open("{0}/run_proc_{1:04d}.f90".format(self.dir, iproc + 1), "w")
                 out2.write("module run_proc_{0:04d}\n\n".format(iproc + 1))
                 out2.write("use kind_values\n")
-                out2.write("use lattice\n")
-                out2.write("use proclist_pars\n")
+                # Import lattice manipulation functions from lattice module
+                # (lattice provides wrappers that accept arrays and convert internally)
+                out2.write("use lattice, only: &\n")
+                site_params = []
+                for layer in data.layer_list:
+                    for site in layer.sites:
+                        site_params.append((site.name, layer.name))
+                for i, (site, layer) in enumerate(site_params):
+                    out2.write("%s%s_%s, &\n" % (" " * indent, layer, site))
+                out2.write("%scan_do, &\n" % (" " * indent))
+                out2.write("%sdel_proc, &\n" % (" " * indent))
+                out2.write("%sadd_proc, &\n" % (" " * indent))
+                out2.write("%sreplace_species, &\n" % (" " * indent))
+                out2.write("%sget_species\n" % (" " * indent))
+                # Import species and processes from proclist_constants to avoid conflict with parameter indices
+                out2.write("use proclist_constants, only: &\n")
+                for i, species in enumerate(data.species_list):
+                    out2.write("%s%s, &\n" % (" " * indent, species.name))
+                for i, process in enumerate(data.process_list):
+                    if i < len(data.process_list) - 1:
+                        out2.write("%s%s, &\n" % (" " * indent, process.name))
+                    else:
+                        out2.write("%s%s\n" % (" " * indent, process.name))
+                # Import only gr_* functions from proclist_pars to avoid conflicts with user parameters
+                out2.write("use proclist_pars, only: &\n")
+                for i, process in enumerate(data.process_list):
+                    if i < len(data.process_list) - 1:
+                        out2.write("%sgr_%s, &\n" % (" " * indent, process.name))
+                    else:
+                        out2.write("%sgr_%s\n" % (" " * indent, process.name))
                 if self.separate_proclist_pars:
                     for i in range(nprocs):
                         out2.write("use gr_{0:04d}\n".format(i + 1))

kmos/utils/__init__.py

@@ -304,19 +304,29 @@ def import_selected_kind():
                     "f2py_selected_kind",
                 ]
                 print("%s\n" % os.path.abspath(os.curdir))
+
+                # Find gfortran compiler
+                import shutil
+
+                gfortran_path = shutil.which("gfortran")
+
+                # Set up environment with correct compiler paths
+                env_vars = {
+                    "LIBRARY_PATH": os.environ.get("LIBRARY_PATH", "")
+                    + ":/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/lib"
+                }
+                if gfortran_path:
+                    env_vars["FC"] = gfortran_path
+
                 result = subprocess.run(
                     f2py_command,
                     capture_output=True,
                     text=True,
-                    env=dict(
-                        os.environ,
-                        **{
-                            "LIBRARY_PATH": os.environ.get("LIBRARY_PATH", "")
-                            + ":/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/lib"
-                        },
-                    ),
+                    env=dict(os.environ, **env_vars),
                 )
                 print(result.stdout)
+                if result.stderr:
+                    print(result.stderr)
             try:
                 import f2py_selected_kind
             except Exception as e:
@@ -489,6 +499,16 @@ def build(options):
     # Set FC for meson backend (Python >= 3.12) to compiler name only
     # Meson has issues with FC containing full paths
     if sys.version_info >= (3, 12):
+        # Ensure gfortran is in PATH for meson to find
+        import shutil
+
+        gfortran_path = shutil.which("gfortran")
+        if gfortran_path:
+            gfortran_dir = os.path.dirname(gfortran_path)
+            current_path = os.environ.get("PATH", "")
+            if gfortran_dir not in current_path:
+                os.environ["PATH"] = f"{gfortran_dir}:{current_path}"
+
         fc_map = {
             "gfortran": "gfortran",
             "gnu95": "gfortran",

tests/export_test/reference_export_intZGB_otf/base.f90

@@ -293,7 +293,7 @@ subroutine add_proc(proc, site, rate)
   ! ARGUMENTS
   !
   !    * ``proc`` positive integer number that represents the process to be added.
-  !    * ``site`` positive integer number that represents the site to be manipulated
+  !    * ``site`` positive integer that represents the site to be manipulated
   !******
   integer(kind=iint), intent(in) :: proc, site
   real(kind=rdouble), intent(in) :: rate

tests/export_test/reference_export_intZGB_otf/proclist.f90

@@ -26,8 +26,32 @@ module proclist
     update_rates_matrix, &
     spuck, &
     get_species
-use proclist_constants
-use proclist_pars
+use proclist_constants, only: &
+    default_species, &
+    CO, &
+    O, &
+    empty, &
+    CO_ads, &
+    CO_des, &
+    CO_oxidation_00, &
+    CO_oxidation_01, &
+    CO_oxidation_02, &
+    CO_oxidation_03, &
+    O2_des_right, &
+    O2_des_up, &
+    O_ads_00, &
+    O_ads_01
+use proclist_pars, only: &
+    gr_CO_ads, &
+    gr_CO_des, &
+    gr_CO_oxidation_00, &
+    gr_CO_oxidation_01, &
+    gr_CO_oxidation_02, &
+    gr_CO_oxidation_03, &
+    gr_O2_des_right, &
+    gr_O2_des_up, &
+    gr_O_ads_00, &
+    gr_O_ads_01
 use run_proc_0001
 use run_proc_0002
 use run_proc_0003

tests/export_test/reference_export_intZGB_otf/proclist_constants.f90

@@ -27,10 +27,6 @@
 
 module proclist_constants
 use kind_values
-use lattice, only: &
-    square, &
-    square_default, &
-    get_species
 
 
 implicit none

tests/export_test/reference_export_intZGB_otf/proclist_pars.f90

@@ -22,13 +22,27 @@ module proclist_pars
 use kind_values
 use base, only: &
     rates
-use proclist_constants
+use proclist_constants, only: &
+    CO, &
+    O, &
+    empty, &
+    CO_ads, &
+    CO_des, &
+    CO_oxidation_00, &
+    CO_oxidation_01, &
+    CO_oxidation_02, &
+    CO_oxidation_03, &
+    O2_des_right, &
+    O2_des_up, &
+    O_ads_00, &
+    O_ads_01
 use lattice, only: &
     square, &
     square_default, &
     get_species
 
 implicit none
+private :: rate_CO_ads, rate_CO_des, rate_CO_oxidation_00, rate_CO_oxidation_01, rate_CO_oxidation_02, rate_CO_oxidation_03, rate_O2_des_right, rate_O2_des_up, rate_O_ads_00, rate_O_ads_01
 
 ! User parameters
 integer(kind=iint), public :: J_CO_CO = 1

tests/export_test/reference_export_intZGB_otf/run_proc_0001.f90

@@ -1,8 +1,38 @@
 module run_proc_0001
 
 use kind_values
-use lattice
-use proclist_pars
+use lattice, only: &
+    square_default, &
+    can_do, &
+    del_proc, &
+    add_proc, &
+    replace_species, &
+    get_species
+use proclist_constants, only: &
+    CO, &
+    O, &
+    empty, &
+    CO_ads, &
+    CO_des, &
+    CO_oxidation_00, &
+    CO_oxidation_01, &
+    CO_oxidation_02, &
+    CO_oxidation_03, &
+    O2_des_right, &
+    O2_des_up, &
+    O_ads_00, &
+    O_ads_01
+use proclist_pars, only: &
+    gr_CO_ads, &
+    gr_CO_des, &
+    gr_CO_oxidation_00, &
+    gr_CO_oxidation_01, &
+    gr_CO_oxidation_02, &
+    gr_CO_oxidation_03, &
+    gr_O2_des_right, &
+    gr_O2_des_up, &
+    gr_O_ads_00, &
+    gr_O_ads_01
 
 implicit none
 contains

tests/export_test/reference_export_intZGB_otf/run_proc_0002.f90

@@ -1,8 +1,38 @@
 module run_proc_0002
 
 use kind_values
-use lattice
-use proclist_pars
+use lattice, only: &
+    square_default, &
+    can_do, &
+    del_proc, &
+    add_proc, &
+    replace_species, &
+    get_species
+use proclist_constants, only: &
+    CO, &
+    O, &
+    empty, &
+    CO_ads, &
+    CO_des, &
+    CO_oxidation_00, &
+    CO_oxidation_01, &
+    CO_oxidation_02, &
+    CO_oxidation_03, &
+    O2_des_right, &
+    O2_des_up, &
+    O_ads_00, &
+    O_ads_01
+use proclist_pars, only: &
+    gr_CO_ads, &
+    gr_CO_des, &
+    gr_CO_oxidation_00, &
+    gr_CO_oxidation_01, &
+    gr_CO_oxidation_02, &
+    gr_CO_oxidation_03, &
+    gr_O2_des_right, &
+    gr_O2_des_up, &
+    gr_O_ads_00, &
+    gr_O_ads_01
 
 implicit none
 contains

tests/export_test/reference_export_intZGB_otf/run_proc_0003.f90

@@ -1,8 +1,38 @@
 module run_proc_0003
 
 use kind_values
-use lattice
-use proclist_pars
+use lattice, only: &
+    square_default, &
+    can_do, &
+    del_proc, &
+    add_proc, &
+    replace_species, &
+    get_species
+use proclist_constants, only: &
+    CO, &
+    O, &
+    empty, &
+    CO_ads, &
+    CO_des, &
+    CO_oxidation_00, &
+    CO_oxidation_01, &
+    CO_oxidation_02, &
+    CO_oxidation_03, &
+    O2_des_right, &
+    O2_des_up, &
+    O_ads_00, &
+    O_ads_01
+use proclist_pars, only: &
+    gr_CO_ads, &
+    gr_CO_des, &
+    gr_CO_oxidation_00, &
+    gr_CO_oxidation_01, &
+    gr_CO_oxidation_02, &
+    gr_CO_oxidation_03, &
+    gr_O2_des_right, &
+    gr_O2_des_up, &
+    gr_O_ads_00, &
+    gr_O_ads_01
 
 implicit none
 contains