updating

.github/actions/ubuntu-setup/action.yml

@@ -23,7 +23,7 @@ runs:
       run: |
         echo "::group::config.mk"
         cd .testing
-        echo "FCFLAGS_DEBUG = -g -O0 -Wextra -Wno-compare-reals -fbacktrace -ffpe-trap=invalid,zero,overflow -fcheck=bounds" >> config.mk
+        echo "FCFLAGS_DEBUG = -g -O0 -std=f2018 -Wextra -Wno-compare-reals -fbacktrace -ffpe-trap=invalid,zero,overflow -fcheck=bounds" >> config.mk
         echo "FCFLAGS_REPRO = -g -O2 -fbacktrace" >> config.mk
         echo "FCFLAGS_INIT = -finit-real=snan -finit-integer=2147483647 -finit-derived" >> config.mk
         echo "FCFLAGS_FMS = -g -fbacktrace -O0" >> config.mk

.testing/Makefile

@@ -83,19 +83,21 @@ export FMS_URL
 # TODO: This needs more automated configuration
 MPIRUN ?= mpirun
 
-# Generic compiler variables are pass through to the builds
+# Generic compiler variables are passed through to the builds
 export CC
 export MPICC
 export FC
 export MPIFC
 
 # Builds are distinguished by FCFLAGS
-FCFLAGS_DEBUG ?= -g -O0
+FCFLAGS ?= -g -O0
+
+FCFLAGS_DEBUG ?= $(FCFLAGS)
 FCFLAGS_REPRO ?= -g -O2
 FCFLAGS_OPT ?= -g -O3 -mavx -fno-omit-frame-pointer
 FCFLAGS_INIT ?=
 FCFLAGS_COVERAGE ?= -g -O0 -fbacktrace --coverage
-FCFLAGS_FMS ?= $(FCFLAGS_DEBUG)
+FCFLAGS_FMS ?= $(FCFLAGS)
 # Additional notes:
 # - These default values are simple, minimalist flags, supported by nearly all
 #   compilers, and are somewhat analogous to GFDL's DEBUG and REPRO builds.

.testing/tc1/MOM_input

@@ -278,6 +278,12 @@ BOUND_CORIOLIS = True           !   [Boolean] default = False
                                 ! have no effect on the SADOURNY Coriolis scheme if it
                                 ! were possible to use centered difference thickness fluxes.
 
+! === module MOM_PressureForce_FV ===
+MASS_WEIGHT_IN_PRESSURE_GRADIENT = True !   [Boolean] default = False
+                                ! If true, use mass weighting when interpolating T/S for integrals
+                                ! near the bathymetry in FV pressure gradient calculations.
+
+
 ! === module MOM_hor_visc ===
 AH_VEL_SCALE = 0.05             !   [m s-1] default = 0.0
                                 ! The velocity scale which is multiplied by the cube of

.testing/tc2/MOM_input

@@ -302,11 +302,16 @@ PGF_STANLEY_T2_DET_COEFF = -1.0 !   [nondim] default = -1.0
                                 ! gradient in the deterministic part of the Stanley form of the Brankart
                                 ! correction. Negative values disable the scheme.
 
+! === module MOM_PressureForce_FV ===
+MASS_WEIGHT_IN_PRESSURE_GRADIENT = True !   [Boolean] default = False
+                                ! If true, use mass weighting when interpolating T/S for integrals
+                                ! near the bathymetry in FV pressure gradient calculations.
+
 ! === module MOM_hor_visc ===
 LAPLACIAN = True
 KH_VEL_SCALE = 0.05
 SMAGORINSKY_KH = True           !   [Boolean] default = False
-SMAG_LAP_CONST = 0.06            !   [nondim] default = 0.0
+SMAG_LAP_CONST = 0.06           !   [nondim] default = 0.0
 AH_VEL_SCALE = 0.05             !   [m s-1] default = 0.0
                                 ! The velocity scale which is multiplied by the cube of
                                 ! the grid spacing to calculate the Laplacian viscosity.

.testing/tc4/MOM_input

@@ -269,6 +269,9 @@ BOUND_CORIOLIS = True           !   [Boolean] default = False
 ! === module MOM_PressureForce ===
 
 ! === module MOM_PressureForce_FV ===
+MASS_WEIGHT_IN_PRESSURE_GRADIENT = True !   [Boolean] default = False
+                                ! If true, use mass weighting when interpolating T/S for integrals
+                                ! near the bathymetry in FV pressure gradient calculations.
 RECONSTRUCT_FOR_PRESSURE = False !   [Boolean] default = True
                                 ! If True, use vertical reconstruction of T & S within the integrals of the FV
                                 ! pressure gradient calculation. If False, use the constant-by-layer algorithm.

ac/makedep

@@ -214,68 +214,91 @@ def create_deps(src_dirs, skip_dirs, makefile, debug, exec_target, fc_rule,
     # Create new makefile
     with open(makefile, 'w') as file:
         print("# %s created by makedep" % (makefile), file=file)
-        print("", file=file)
+        print(file=file)
         print("# Invoked as", file=file)
         print('#   '+' '.join(sys.argv), file=file)
-        print("", file=file)
+        print(file=file)
         print("all:", " ".join(targets), file=file)
-        print("", file=file)
 
+        # print(file=file)
         # print("# SRC_DIRS is usually set in the parent Makefile but in case is it not we", file=file)
         # print("# record it here from when makedep was previously invoked.", file=file)
         # print("SRC_DIRS ?= ${SRC_DIRS}", file=file)
-        # print("", file=file)
 
+        # print(file=file)
         # print("# all_files:", ' '.join(all_files), file=file)
-        # print("", file=file)
 
         # Write rule for each object from Fortran
-        for o in sorted(o2F90.keys()):
-            found_mods = [m for m in o2uses[o] if m in all_modules]
-            found_objs = [mod2o[m] for m in o2uses[o] if m in all_modules]
+        for obj in sorted(o2F90.keys()):
+            found_mods = [m for m in o2uses[obj] if m in all_modules]
+            found_objs = [mod2o[m] for m in o2uses[obj] if m in all_modules]
             found_deps = [
                 dep for pair in zip(found_mods, found_objs) for dep in pair
             ]
-            missing_mods = [m for m in o2uses[o] if m not in all_modules]
+            missing_mods = [m for m in o2uses[obj] if m not in all_modules]
 
-            incs, inc_used = nested_inc(o2h[o] + o2inc[o], f2F, defines)
-            inc_mods = [u for u in inc_used if u not in found_mods and u in all_modules]
+            incs, inc_used = nested_inc(o2h[obj] + o2inc[obj], f2F, defines)
+            inc_mods = [
+                u for u in inc_used if u not in found_mods and u in all_modules
+            ]
 
             incdeps = sorted(set([f2F[f] for f in incs if f in f2F]))
-            incargs = sorted(set(['-I'+os.path.dirname(f) for f in incdeps]))
+            incargs = sorted(set(['-I' + os.path.dirname(f) for f in incdeps]))
+
+            # Header
+            print(file=file)
             if debug:
-                print("# Source file {} produces:".format(o2F90[o]), file=file)
-                print("#   object:", o, file=file)
-                print("#   modules:", ' '.join(o2mods[o]), file=file)
-                print("#   uses:", ' '.join(o2uses[o]), file=file)
+                print("# Source file {} produces:".format(o2F90[obj]), file=file)
+                print("#   object:", obj, file=file)
+                print("#   modules:", ' '.join(o2mods[obj]), file=file)
+                print("#   uses:", ' '.join(o2uses[obj]), file=file)
                 print("#   found mods:", ' '.join(found_mods), file=file)
                 print("#   found objs:", ' '.join(found_objs), file=file)
                 print("#   missing:", ' '.join(missing_mods), file=file)
                 print("#   includes_all:", ' '.join(incs), file=file)
                 print("#   includes_pth:", ' '.join(incdeps), file=file)
                 print("#   incargs:", ' '.join(incargs), file=file)
-                print("#   program:", ' '.join(o2prg[o]), file=file)
-            if o2mods[o]:
-                print(' '.join(o2mods[o])+':', o, file=file)
-            print(o + ':', o2F90[o], ' '.join(inc_mods + incdeps + found_deps), file=file)
-            print('\t'+fc_rule, ' '.join(incargs), file=file)
+                print("#   program:", ' '.join(o2prg[obj]), file=file)
+
+            # Fortran Module dependencies
+            if o2mods[obj]:
+                print(' '.join(o2mods[obj]) + ':', obj, file=file)
+
+            # Fortran object dependencies
+            obj_incs = ' '.join(inc_mods + incdeps + found_deps)
+            print(obj + ':', o2F90[obj], obj_incs, file=file)
+
+            # Fortran object build rule
+            obj_rule = ' '.join([fc_rule] + incargs + ['-c', '$<'])
+            print('\t' + obj_rule, file=file)
 
         # Write rule for each object from C
-        for o in sorted(o2c.keys()):
-            incdeps = sorted(set([f2F[h] for h in o2h[o] if h in f2F]))
-            incargs = sorted(set(['-I'+os.path.dirname(f) for f in incdeps]))
+        for obj in sorted(o2c.keys()):
+            incdeps = sorted(set([f2F[h] for h in o2h[obj] if h in f2F]))
+            incargs = sorted(set(['-I' + os.path.dirname(f) for f in incdeps]))
+
+            # Header
+            print(file=file)
             if debug:
-                print("# Source file %s produces:" % (o2c[o]), file=file)
-                print("#   object:", o, file=file)
-                print("#   includes_all:", ' '.join(o2h[o]), file=file)
+                print("# Source file %s produces:" % (o2c[obj]), file=file)
+                print("#   object:", obj, file=file)
+                print("#   includes_all:", ' '.join(o2h[obj]), file=file)
                 print("#   includes_pth:", ' '.join(incdeps), file=file)
                 print("#   incargs:", ' '.join(incargs), file=file)
-            print(o+':', o2c[o], ' '.join(incdeps), file=file)
-            print('\t$(CC) $(DEFS) $(CPPFLAGS) $(CFLAGS) -c $<', ' '.join(incargs), file=file)
+
+            # C object dependencies
+            print(obj + ':', o2c[obj], ' '.join(incdeps), file=file)
+
+            # C object build rule
+            c_rule = ' '.join(
+              ['$(CC) $(DEFS) $(CPPFLAGS) $(CFLAGS)'] + incargs + ['-c', '$<']
+            )
+            #print('\t' + c_rule, ' '.join(incargs), '-c', '$<', file=file)
+            print('\t' + c_rule, file=file)
 
         # Externals (so called)
         if link_externals:
-            print("", file=file)
+            print(file=file)
             print("# Note: The following object files are not associated with "
                   "modules so we assume we should link with them:", file=file)
             print("# ", ' '.join(externals), file=file)
@@ -286,23 +309,23 @@ def create_deps(src_dirs, skip_dirs, makefile, debug, exec_target, fc_rule,
         # Write rules for linking executables
         for p in sorted(prg2o.keys()):
             o = prg2o[p]
-            print("", file=file)
+            print(file=file)
             print(p+':', ' '.join(link_obj(o, o2uses, mod2o, all_modules) + externals), file=file)
             print('\t$(LD) $(LDFLAGS) -o $@ $^ $(LIBS)', file=file)
 
         # Write rules for building libraries
         for lb in sorted(targ_libs):
-            print("", file=file)
+            print(file=file)
             print(lb+':', ' '.join(list(o2F90.keys()) + list(o2c.keys())), file=file)
             print('\t$(AR) $(ARFLAGS) $@ $^', file=file)
 
         # Write cleanup rules
-        print("", file=file)
+        print(file=file)
         print("clean:", file=file)
         print('\trm -f *.mod *.o', ' '.join(list(prg2o.keys()) + targ_libs), file=file)
 
         # Write re-generation rules
-        print("", file=file)
+        print(file=file)
         print("remakedep:", file=file)
         print('\t'+' '.join(sys.argv), file=file)
 
@@ -366,24 +389,23 @@ def scan_fortran_file(src_file, defines=None):
 
     cpp_defines = defines if defines is not None else []
 
-    #cpp_macros = [define.split('=')[0] for define in cpp_defines]
     cpp_macros = dict([t.split('=') for t in cpp_defines])
     cpp_group_stack = []
 
     with io.open(src_file, 'r', errors='replace') as file:
         lines = file.readlines()
 
         external_namespace = True
-            # True if we are in the external (i.e. global) namespace
+        # True if we are in the external (i.e. global) namespace
 
         file_has_externals = False
-            # True if the file contains any external objects
+        # True if the file contains any external objects
 
         cpp_exclude = False
-            # True if the parser excludes the subsequent lines
+        # True if the parser excludes the subsequent lines
 
         cpp_group_stack = []
-            # Stack of condition group exclusion states
+        # Stack of condition group exclusion states
 
         for line in lines:
             # Start of #ifdef condition group
@@ -446,14 +468,16 @@ def scan_fortran_file(src_file, defines=None):
             if match:
                 new_macro = line.lstrip()[1:].split()[1]
                 try:
-                    cpp_macros.remove(new_macro)
-                except:
-                    # Ignore missing macros (for now?)
+                    cpp_macros.pop(new_macro)
+                except KeyError:
+                    # C99: "[A macro] is ignored if the specified identifier is
+                    # not currently defined as a macro name."
                     continue
 
             match = re_module.match(line.lower())
             if match:
-                if match.group(1) not in 'procedure':   # avoid "module procedure" statements
+                # Avoid "module procedure" statements
+                if match.group(1) not in 'procedure':
                     module_decl.append(match.group(1))
                     external_namespace = False
 
@@ -632,9 +656,9 @@ parser.add_argument(
 )
 parser.add_argument(
     '-f', '--fc_rule',
-    default="$(FC) $(DEFS) $(FCFLAGS) $(CPPFLAGS) -c $<",
+    default="$(FC) $(DEFS) $(CPPFLAGS) $(FCFLAGS)",
     help="String to use in the compilation rule. Default is: "
-         "'$(FC) $(DEFS) $(FCFLAGS) $(CPPFLAGS) -c $<'"
+         "'$(FC) $(DEFS) $(CPPFLAGS) $(FCFLAGS)'"
 )
 parser.add_argument(
     '-x', '--exec_target',

config_src/drivers/FMS_cap/MOM_surface_forcing_gfdl.F90

@@ -1099,10 +1099,10 @@ subroutine extract_IOB_stresses(IOB, index_bounds, Time, G, US, CS, taux, tauy,
         tau_mag = 0.0 ; gustiness = CS%gust_const
         if (((G%mask2dBu(I,J) + G%mask2dBu(I-1,J-1)) + &
              (G%mask2dBu(I,J-1) + G%mask2dBu(I-1,J))) > 0.0) then
-          tau_mag = sqrt(((G%mask2dBu(I,J)*(taux_in_B(I,J)**2 + tauy_in_B(I,J)**2) + &
-              G%mask2dBu(I-1,J-1)*(taux_in_B(I-1,J-1)**2 + tauy_in_B(I-1,J-1)**2)) + &
-             (G%mask2dBu(I,J-1)*(taux_in_B(I,J-1)**2 + tauy_in_B(I,J-1)**2) + &
-              G%mask2dBu(I-1,J)*(taux_in_B(I-1,J)**2 + tauy_in_B(I-1,J)**2)) ) / &
+          tau_mag = sqrt(((G%mask2dBu(I,J)*((taux_in_B(I,J)**2) + (tauy_in_B(I,J)**2)) + &
+              G%mask2dBu(I-1,J-1)*((taux_in_B(I-1,J-1)**2) + (tauy_in_B(I-1,J-1)**2))) + &
+             (G%mask2dBu(I,J-1)*((taux_in_B(I,J-1)**2) + (tauy_in_B(I,J-1)**2)) + &
+              G%mask2dBu(I-1,J)*((taux_in_B(I-1,J)**2) + (tauy_in_B(I-1,J)**2))) ) / &
             ((G%mask2dBu(I,J) + G%mask2dBu(I-1,J-1)) + (G%mask2dBu(I,J-1) + G%mask2dBu(I-1,J))) )
           if (CS%read_gust_2d) gustiness = CS%gust(i,j)
         endif
@@ -1117,7 +1117,7 @@ subroutine extract_IOB_stresses(IOB, index_bounds, Time, G, US, CS, taux, tauy,
       enddo ; enddo
     elseif (wind_stagger == AGRID) then
       do j=js,je ; do i=is,ie
-        tau_mag = G%mask2dT(i,j) * sqrt(taux_in_A(i,j)**2 + tauy_in_A(i,j)**2)
+        tau_mag = G%mask2dT(i,j) * sqrt((taux_in_A(i,j)**2) + (tauy_in_A(i,j)**2))
         gustiness = CS%gust_const
         if (CS%read_gust_2d .and. (G%mask2dT(i,j) > 0.0)) gustiness = CS%gust(i,j)
         if (do_ustar) ustar(i,j) = sqrt(gustiness*IRho0 + IRho0 * tau_mag)
@@ -1133,10 +1133,10 @@ subroutine extract_IOB_stresses(IOB, index_bounds, Time, G, US, CS, taux, tauy,
       do j=js,je ; do i=is,ie
         taux2 = 0.0 ; tauy2 = 0.0
         if ((G%mask2dCu(I-1,j) + G%mask2dCu(I,j)) > 0.0) &
-          taux2 = (G%mask2dCu(I-1,j)*taux_in_C(I-1,j)**2 + G%mask2dCu(I,j)*taux_in_C(I,j)**2) / &
+          taux2 = (G%mask2dCu(I-1,j)*(taux_in_C(I-1,j)**2) + G%mask2dCu(I,j)*(taux_in_C(I,j)**2)) / &
                   (G%mask2dCu(I-1,j) + G%mask2dCu(I,j))
         if ((G%mask2dCv(i,J-1) + G%mask2dCv(i,J)) > 0.0) &
-          tauy2 = (G%mask2dCv(i,J-1)*tauy_in_C(i,J-1)**2 + G%mask2dCv(i,J)*tauy_in_C(i,J)**2) / &
+          tauy2 = (G%mask2dCv(i,J-1)*(tauy_in_C(i,J-1)**2) + G%mask2dCv(i,J)*(tauy_in_C(i,J)**2)) / &
                   (G%mask2dCv(i,J-1) + G%mask2dCv(i,J))
         tau_mag = sqrt(taux2 + tauy2)
 

config_src/drivers/FMS_cap/ocean_model_MOM.F90

@@ -1065,10 +1065,10 @@ subroutine ocean_model_data2D_get(OS, Ocean, name, array2D, isc, jsc)
   type(ocean_public_type),    intent(in) :: Ocean !< A structure containing various publicly
                                                   !! visible ocean surface fields.
   character(len=*)          , intent(in) :: name  !< The name of the field to extract
-  real, dimension(isc:,jsc:), intent(out):: array2D !< The values of the named field, it must
-                                                  !! cover only the computational domain [various]
   integer                   , intent(in) :: isc   !< The starting i-index of array2D
   integer                   , intent(in) :: jsc   !< The starting j-index of array2D
+  real, dimension(isc:,jsc:), intent(out):: array2D !< The values of the named field, it must
+                                                  !! cover only the computational domain [various]
 
   integer :: g_isc, g_iec, g_jsc, g_jec, g_isd, g_ied, g_jsd, g_jed, i, j
 
@@ -1188,10 +1188,10 @@ subroutine ocean_model_get_UV_surf(OS, Ocean, name, array2D, isc, jsc)
   type(ocean_public_type),    intent(in) :: Ocean !< A structure containing various publicly
                                                   !! visible ocean surface fields.
   character(len=*)          , intent(in) :: name  !< The name of the current (ua or va) to extract
-  real, dimension(isc:,jsc:), intent(out):: array2D !< The values of the named field, it must
-                                                  !! cover only the computational domain [L T-1 ~> m s-1]
   integer                   , intent(in) :: isc   !< The starting i-index of array2D
   integer                   , intent(in) :: jsc   !< The starting j-index of array2D
+  real, dimension(isc:,jsc:), intent(out):: array2D !< The values of the named field, it must
+                                                  !! cover only the computational domain [L T-1 ~> m s-1]
 
   type(ocean_grid_type) , pointer :: G            !< The ocean's grid structure
   type(surface),          pointer :: sfc_state    !< A structure containing fields that