Merge branch 'dev/gfdl' into read_salin_in_ppt

ac/Makefile.in

@@ -19,7 +19,6 @@ SRC_DIRS = @SRC_DIRS@
 
 -include Makefile.dep
 
-
 # Generate Makefile from template
 Makefile: @srcdir@/ac/Makefile.in config.status
 	./config.status
@@ -33,7 +32,7 @@ rwildcard=$(foreach d,$(wildcard $(1:=/*)),$(call rwildcard,$d,$2) $(filter $(su
 .PHONY: depend
 depend: Makefile.dep
 Makefile.dep: $(MAKEDEP) $(call rwildcard,$(SRC_DIRS),*.h *.c *.inc *.F90)
-	$(PYTHON) $(MAKEDEP) -o Makefile.dep -e $(SRC_DIRS)
+	$(PYTHON) $(MAKEDEP) $(DEFS) -o Makefile.dep -e $(SRC_DIRS)
 
 
 # Delete any files associated with configuration (including the Makefile).

ac/makedep

@@ -13,9 +13,16 @@ import sys
 # Pre-compile re searches
 re_module = re.compile(r"^ *module +([a-z_0-9]+)")
 re_use = re.compile(r"^ *use +([a-z_0-9]+)")
+re_cpp_define = re.compile(r"^ *# *define +[_a-zA-Z][_a-zA-Z0-9]")
+re_cpp_undef = re.compile(r"^ *# *undef +[_a-zA-Z][_a-zA-Z0-9]")
+re_cpp_ifdef = re.compile(r"^ *# *ifdef +[_a-zA-Z][_a-zA-Z0-9]")
+re_cpp_ifndef = re.compile(r"^ *# *ifndef +[_a-zA-Z][_a-zA-Z0-9]")
+re_cpp_if = re.compile(r"^ *# *if +")
+re_cpp_else = re.compile(r"^ *# *else")
+re_cpp_endif = re.compile(r"^ *# *endif")
 re_cpp_include = re.compile(r"^ *# *include *[<\"']([a-zA-Z_0-9\.]+)[>\"']")
 re_f90_include = re.compile(r"^ *include +[\"']([a-zA-Z_0-9\.]+)[\"']")
-re_program = re.compile(r"^ *[pP][rR][oO][gG][rR][aA][mM] +([a-zA-Z_0-9]+)")
+re_program = re.compile(r"^ *program +([a-z_0-9]+)", re.IGNORECASE)
 re_end = re.compile(r"^ *end *(module|procedure) ", re.IGNORECASE)
 # NOTE: This excludes comments and tokens with substrings containing `function`
 # or `subroutine`, but will fail if the keywords appear in other contexts.
@@ -26,7 +33,7 @@ re_procedure = re.compile(
 
 
 def create_deps(src_dirs, skip_dirs, makefile, debug, exec_target, fc_rule,
-                link_externals, script_path):
+                link_externals, defines):
     """Create "makefile" after scanning "src_dis"."""
 
     # Scan everything Fortran related
@@ -66,7 +73,7 @@ def create_deps(src_dirs, skip_dirs, makefile, debug, exec_target, fc_rule,
     o2mods, o2uses, o2h, o2inc, o2prg, prg2o, mod2o = {}, {}, {}, {}, {}, {}, {}
     externals, all_modules = [], []
     for f in F90_files:
-        mods, used, cpp, inc, prg, has_externals = scan_fortran_file(f)
+        mods, used, cpp, inc, prg, has_externals = scan_fortran_file(f, defines)
         # maps object file to modules produced
         o2mods[object_file(f)] = mods
         # maps module produced to object file
@@ -272,10 +279,16 @@ def nested_inc(inc_files, f2F):
     return inc_files + sorted(set(hlst)), used_mods
 
 
-def scan_fortran_file(src_file):
+def scan_fortran_file(src_file, defines=None):
     """Scan the Fortran file "src_file" and return lists of module defined,
     module used, and files included."""
     module_decl, used_modules, cpp_includes, f90_includes, programs = [], [], [], [], []
+
+    cpp_defines = defines if defines is not None else []
+
+    cpp_macros = [define.split('=')[0] for define in cpp_defines]
+    cpp_group_stack = []
+
     with io.open(src_file, 'r', errors='replace') as file:
         lines = file.readlines()
 
@@ -285,7 +298,72 @@ def scan_fortran_file(src_file):
         file_has_externals = False
             # True if the file contains any external objects
 
+        cpp_exclude = False
+            # True if the parser excludes the subsequent lines
+
+        cpp_group_stack = []
+            # Stack of condition group exclusion states
+
         for line in lines:
+            # Start of #ifdef condition group
+            match = re_cpp_ifdef.match(line)
+            if match:
+                cpp_group_stack.append(cpp_exclude)
+
+                # If outer group is excluding or macro is missing, then exclude
+                macro = line.lstrip()[1:].split()[1]
+                cpp_exclude = cpp_exclude or macro not in cpp_macros
+
+            # Start of #ifndef condition group
+            match = re_cpp_ifndef.match(line)
+            if match:
+                cpp_group_stack.append(cpp_exclude)
+
+                # If outer group is excluding or macro is present, then exclude
+                macro = line.lstrip()[1:].split()[1]
+                cpp_exclude = cpp_exclude or macro in cpp_macros
+
+            # Start of #if condition group
+            match = re_cpp_if.match(line)
+            if match:
+                cpp_group_stack.append(cpp_exclude)
+
+                # XXX: Don't attempt to parse #if statements, but store the state.
+                # if/endif stack.  For now, assume that these always fail.
+                cpp_exclude = False
+
+            # Complement #else condition group
+            match = re_cpp_else.match(line)
+            if match:
+                # Reverse the exclude state, if there is no outer exclude state
+                outer_grp_exclude = cpp_group_stack and cpp_group_stack[-1]
+                cpp_exclude = not cpp_exclude or outer_grp_exclude
+
+            # Restore exclude state when exiting conditional block
+            match = re_cpp_endif.match(line)
+            if match:
+                cpp_exclude = cpp_group_stack.pop()
+
+            # Skip lines inside of false condition blocks
+            if cpp_exclude:
+                continue
+
+            # Activate a new macro (ignoring the value)
+            match = re_cpp_define.match(line)
+            if match:
+                new_macro = line.lstrip()[1:].split()[1]
+                cpp_macros.append(new_macro)
+
+            # Deactivate a macro
+            match = re_cpp_undef.match(line)
+            if match:
+                new_macro = line.lstrip()[1:].split()[1]
+                try:
+                    cpp_macros.remove(new_macro)
+                except:
+                    # Ignore missing macros (for now?)
+                    continue
+
             match = re_module.match(line.lower())
             if match:
                 if match.group(1) not in 'procedure':   # avoid "module procedure" statements
@@ -404,8 +482,13 @@ parser.add_argument(
     action='append',
     help="Skip directory in source code search."
 )
+parser.add_argument(
+    '-D', '--define',
+    action='append',
+    help="Apply preprocessor define macros (of the form -DMACRO[=value])",
+)
 args = parser.parse_args()
 
 # Do the thing
 create_deps(args.path, args.skip, args.makefile, args.debug, args.exec_target,
-            args.fc_rule, args.link_externals, sys.argv[0])
+            args.fc_rule, args.link_externals, args.define)

src/core/MOM_continuity.F90

@@ -3,159 +3,28 @@ module MOM_continuity
 
 ! This file is part of MOM6. See LICENSE.md for the license.
 
-use MOM_continuity_PPM, only : continuity_PPM, continuity_PPM_init
-use MOM_continuity_PPM, only : continuity_PPM_stencil
-use MOM_continuity_PPM, only : continuity_PPM_CS
-use MOM_diag_mediator, only : time_type, diag_ctrl
-use MOM_error_handler, only : MOM_error, MOM_mesg, FATAL, WARNING, is_root_pe
-use MOM_file_parser, only : get_param, log_version, param_file_type
-use MOM_string_functions, only : uppercase
-use MOM_grid, only : ocean_grid_type
-use MOM_open_boundary, only : ocean_OBC_type
-use MOM_unit_scaling, only : unit_scale_type
-use MOM_variables, only : BT_cont_type, porous_barrier_type
-use MOM_verticalGrid, only : verticalGrid_type
+use MOM_continuity_PPM, only : continuity=>continuity_PPM
+use MOM_continuity_PPM, only : continuity_stencil=>continuity_PPM_stencil
+use MOM_continuity_PPM, only : continuity_init=>continuity_PPM_init
+use MOM_continuity_PPM, only : continuity_CS=>continuity_PPM_CS
+use MOM_continuity_PPM, only : continuity_fluxes, continuity_adjust_vel
+use MOM_continuity_PPM, only : zonal_mass_flux, meridional_mass_flux
+use MOM_continuity_PPM, only : zonal_edge_thickness, meridional_edge_thickness
+use MOM_continuity_PPM, only : continuity_zonal_convergence, continuity_merdional_convergence
+use MOM_continuity_PPM, only : zonal_flux_thickness, meridional_flux_thickness
+use MOM_continuity_PPM, only : zonal_BT_mass_flux, meridional_BT_mass_flux
+use MOM_continuity_PPM, only : set_continuity_loop_bounds, cont_loop_bounds_type
 
 implicit none ; private
 
-#include <MOM_memory.h>
-
-public continuity, continuity_init, continuity_stencil
-
-!> Control structure for mom_continuity
-type, public :: continuity_CS ; private
-  integer :: continuity_scheme !< Selects the discretization for the continuity solver.
-                               !! Valid values are:
-                               !! - PPM - A directionally split piecewise parabolic reconstruction solver.
-                               !! The default, PPM, seems most appropriate for use with our current
-                               !! time-splitting strategies.
-  type(continuity_PPM_CS) :: PPM  !< Control structure for mom_continuity_ppm
-end type continuity_CS
-
-integer, parameter :: PPM_SCHEME = 1 !< Enumerated constant to select PPM
-character(len=20), parameter :: PPM_STRING = "PPM" !< String to select PPM
-
-contains
-
-!> Time steps the layer thicknesses, using a monotonically limited, directionally split PPM scheme,
-!! based on Lin (1994).
-subroutine continuity(u, v, hin, h, uh, vh, dt, G, GV, US, CS, OBC, pbv, uhbt, vhbt, &
-                      visc_rem_u, visc_rem_v, u_cor, v_cor, BT_cont)
-  type(ocean_grid_type),   intent(inout) :: G   !< Ocean grid structure.
-  type(verticalGrid_type), intent(in)    :: GV  !< Vertical grid structure.
-  real, dimension(SZIB_(G),SZJ_(G),SZK_(GV)), &
-                           intent(in)    :: u   !< Zonal velocity [L T-1 ~> m s-1].
-  real, dimension(SZI_(G),SZJB_(G),SZK_(GV)), &
-                           intent(in)    :: v   !< Meridional velocity [L T-1 ~> m s-1].
-  real, dimension(SZI_(G),SZJ_(G),SZK_(GV)),  &
-                           intent(in)    :: hin !< Initial layer thickness [H ~> m or kg m-2].
-  real, dimension(SZI_(G),SZJ_(G),SZK_(GV)),  &
-                           intent(inout) :: h   !< Final layer thickness [H ~> m or kg m-2].
-  real, dimension(SZIB_(G),SZJ_(G),SZK_(GV)), &
-                           intent(out)   :: uh  !< Volume flux through zonal faces =
-                                                !! u*h*dy [H L2 T-1 ~> m3 s-1 or kg s-1].
-  real, dimension(SZI_(G),SZJB_(G),SZK_(GV)), &
-                           intent(out)   :: vh  !< Volume flux through meridional faces =
-                                                !! v*h*dx [H L2 T-1 ~> m3 s-1 or kg s-1].
-  real,                    intent(in)    :: dt  !< Time increment [T ~> s].
-  type(unit_scale_type),   intent(in)    :: US  !< A dimensional unit scaling type
-  type(continuity_CS),     intent(in)    :: CS  !< Control structure for mom_continuity.
-  type(ocean_OBC_type),    pointer       :: OBC !< Open boundaries control structure.
-  type(porous_barrier_type), intent(in)  :: pbv !< porous barrier fractional cell metrics
-  real, dimension(SZIB_(G),SZJ_(G)), &
-                 optional, intent(in)    :: uhbt !< The vertically summed volume
-                                                !! flux through zonal faces [H L2 T-1 ~> m3 s-1 or kg s-1].
-  real, dimension(SZI_(G),SZJB_(G)), &
-                 optional, intent(in)    :: vhbt !< The vertically summed volume
-                                                !! flux through meridional faces [H L2 T-1 ~> m3 s-1 or kg s-1].
-  real, dimension(SZIB_(G),SZJ_(G),SZK_(GV)), &
-                 optional, intent(in)    :: visc_rem_u !< Both the fraction of
-          !! zonal momentum that remains after a time-step of viscosity, and the fraction of a time-step's
-          !! worth of a barotropic acceleration that a layer experiences after viscosity is applied [nondim].
-          !! Non-dimensional between 0 (at the bottom) and 1 (far above the bottom).
-  real, dimension(SZI_(G),SZJB_(G),SZK_(GV)), &
-                 optional, intent(in)    :: visc_rem_v !< Both the fraction of
-          !! meridional momentum that remains after a time-step of viscosity, and the fraction of a time-step's
-          !! worth of a barotropic acceleration that a layer experiences after viscosity is applied [nondim].
-          !! Non-dimensional between 0 (at the bottom) and 1 (far above the bottom).
-  real, dimension(SZIB_(G),SZJ_(G),SZK_(GV)), &
-                 optional, intent(out)   :: u_cor !< The zonal velocities that
-          !! give uhbt as the depth-integrated transport [L T-1 ~> m s-1].
-  real, dimension(SZI_(G),SZJB_(G),SZK_(GV)), &
-                 optional, intent(out)   :: v_cor !< The meridional velocities that
-          !! give vhbt as the depth-integrated transport [L T-1 ~> m s-1].
-  type(BT_cont_type), &
-                 optional, pointer       :: BT_cont !< A structure with elements
-          !! that describe the effective open face areas as a function of barotropic flow.
-
-  if (present(visc_rem_u) .neqv. present(visc_rem_v)) call MOM_error(FATAL, &
-      "MOM_continuity: Either both visc_rem_u and visc_rem_v or neither"// &
-       " one must be present in call to continuity.")
-  if (present(u_cor) .neqv. present(v_cor)) call MOM_error(FATAL, &
-      "MOM_continuity: Either both u_cor and v_cor or neither"// &
-       " one must be present in call to continuity.")
-
-  if (CS%continuity_scheme == PPM_SCHEME) then
-    call continuity_PPM(u, v, hin, h, uh, vh, dt, G, GV, US, CS%PPM, OBC, pbv, uhbt, vhbt, &
-                        visc_rem_u, visc_rem_v, u_cor, v_cor, BT_cont=BT_cont)
-  else
-    call MOM_error(FATAL, "continuity: Unrecognized value of continuity_scheme")
-  endif
-
-end subroutine continuity
-
-!> Initializes continuity_cs
-subroutine continuity_init(Time, G, GV, US, param_file, diag, CS)
-  type(time_type), target, intent(in)    :: Time       !< Current model time.
-  type(ocean_grid_type),   intent(in)    :: G          !< Ocean grid structure.
-  type(verticalGrid_type), intent(in)    :: GV         !< Vertical grid structure.
-  type(unit_scale_type),   intent(in)    :: US  !< A dimensional unit scaling type
-  type(param_file_type),   intent(in)    :: param_file !< Parameter file handles.
-  type(diag_ctrl), target, intent(inout) :: diag       !< Diagnostics control structure.
-  type(continuity_CS),     intent(inout) :: CS         !< Control structure for mom_continuity.
-
-  ! This include declares and sets the variable "version".
-# include "version_variable.h"
-  character(len=40)  :: mdl = "MOM_continuity" ! This module's name.
-  character(len=20)  :: tmpstr
-
-  ! Read all relevant parameters and write them to the model log.
-  call log_version(param_file, mdl, version, "")
-  call get_param(param_file, mdl, "CONTINUITY_SCHEME", tmpstr, &
-                 "CONTINUITY_SCHEME selects the discretization for the "//&
-                 "continuity solver. The only valid value currently is: \n"//&
-                 "\t PPM - use a positive-definite (or monotonic) \n"//&
-                 "\t       piecewise parabolic reconstruction solver.", &
-                 default=PPM_STRING)
-
-  tmpstr = uppercase(tmpstr) ; CS%continuity_scheme = 0
-  select case (trim(tmpstr))
-    case (PPM_STRING) ; CS%continuity_scheme = PPM_SCHEME
-    case default
-      call MOM_mesg('continuity_init: CONTINUITY_SCHEME ="'//trim(tmpstr)//'"', 0)
-      call MOM_mesg("continuity_init: The only valid value is currently "// &
-                     trim(PPM_STRING), 0)
-      call MOM_error(FATAL, "continuity_init: Unrecognized setting "// &
-            "#define CONTINUITY_SCHEME "//trim(tmpstr)//" found in input file.")
-  end select
-
-  if (CS%continuity_scheme == PPM_SCHEME) then
-    call continuity_PPM_init(Time, G, GV, US, param_file, diag, CS%PPM)
-  endif
-
-end subroutine continuity_init
-
-
-!> continuity_stencil returns the continuity solver stencil size
-function continuity_stencil(CS) result(stencil)
-  type(continuity_CS), intent(in) :: CS !< Module's control structure.
-  integer ::  stencil !< The continuity solver stencil size with the current settings.
-
-  stencil = 1
-
-  if (CS%continuity_scheme == PPM_SCHEME) then
-    stencil = continuity_PPM_stencil(CS%PPM)
-  endif
-end function continuity_stencil
+! These are direct pass-throughs of routines in continuity_PPM
+public continuity, continuity_init, continuity_stencil, continuity_CS
+public continuity_fluxes, continuity_adjust_vel
+public zonal_mass_flux, meridional_mass_flux
+public zonal_edge_thickness, meridional_edge_thickness
+public continuity_zonal_convergence, continuity_merdional_convergence
+public zonal_flux_thickness, meridional_flux_thickness
+public zonal_BT_mass_flux, meridional_BT_mass_flux
+public set_continuity_loop_bounds, cont_loop_bounds_type
 
 end module MOM_continuity