Merge branch 'dev/master' of github.com:NOAA-GFDL/MOM6 into dev/master

.doxygen

@@ -1,4 +1,4 @@
-# Doxyfile 1.8.9.1
+# Doxyfile 1.8.12
 
 # This file describes the settings to be used by the documentation system
 # doxygen (www.doxygen.org) for a project.
@@ -293,6 +293,15 @@ EXTENSION_MAPPING      =
 
 MARKDOWN_SUPPORT       = YES
 
+# When the TOC_INCLUDE_HEADINGS tag is set to a non-zero value, all headings up
+# to that level are automatically included in the table of contents, even if
+# they do not have an id attribute.
+# Note: This feature currently applies only to Markdown headings.
+# Minimum value: 0, maximum value: 99, default value: 0.
+# This tag requires that the tag MARKDOWN_SUPPORT is set to YES.
+
+TOC_INCLUDE_HEADINGS   = 0
+
 # When enabled doxygen tries to link words that correspond to documented
 # classes, or namespaces to their corresponding documentation. Such a link can
 # be prevented in individual cases by putting a % sign in front of the word or
@@ -341,7 +350,14 @@ IDL_PROPERTY_SUPPORT   = YES
 # all members of a group must be documented explicitly.
 # The default value is: NO.
 
-DISTRIBUTE_GROUP_DOC   = NO
+DISTRIBUTE_GROUP_DOC   = YES
+
+# If one adds a struct or class to a group and this option is enabled, then also
+# any nested class or struct is added to the same group. By default this option
+# is disabled and one has to add nested compounds explicitly via \ingroup.
+# The default value is: NO.
+
+GROUP_NESTED_COMPOUNDS = NO
 
 # Set the SUBGROUPING tag to YES to allow class member groups of the same type
 # (for instance a group of public functions) to be put as a subgroup of that
@@ -732,6 +748,12 @@ WARN_IF_DOC_ERROR      = YES
 
 WARN_NO_PARAMDOC       = NO
 
+# If the WARN_AS_ERROR tag is set to YES then doxygen will immediately stop when
+# a warning is encountered.
+# The default value is: NO.
+
+WARN_AS_ERROR          = NO
+
 # The WARN_FORMAT tag determines the format of the warning messages that doxygen
 # can produce. The string should contain the $file, $line, and $text tags, which
 # will be replaced by the file and line number from which the warning originated
@@ -771,14 +793,38 @@ INPUT_ENCODING         = UTF-8
 
 # If the value of the INPUT tag contains directories, you can use the
 # FILE_PATTERNS tag to specify one or more wildcard patterns (like *.cpp and
-# *.h) to filter out the source-files in the directories. If left blank the
-# following patterns are tested:*.c, *.cc, *.cxx, *.cpp, *.c++, *.java, *.ii,
-# *.ixx, *.ipp, *.i++, *.inl, *.idl, *.ddl, *.odl, *.h, *.hh, *.hxx, *.hpp,
-# *.h++, *.cs, *.d, *.php, *.php4, *.php5, *.phtml, *.inc, *.m, *.markdown,
-# *.md, *.mm, *.dox, *.py, *.f90, *.f, *.for, *.tcl, *.vhd, *.vhdl, *.ucf,
-# *.qsf, *.as and *.js.
-
-FILE_PATTERNS          =
+# *.h) to filter out the source-files in the directories.
+#
+# Note that for custom extensions or not directly supported extensions you also
+# need to set EXTENSION_MAPPING for the extension otherwise the files are not
+# read by doxygen.
+#
+# If left blank the following patterns are tested:*.c, *.cc, *.cxx, *.cpp,
+# *.c++, *.java, *.ii, *.ixx, *.ipp, *.i++, *.inl, *.idl, *.ddl, *.odl, *.h,
+# *.hh, *.hxx, *.hpp, *.h++, *.cs, *.d, *.php, *.php4, *.php5, *.phtml, *.inc,
+# *.m, *.markdown, *.md, *.mm, *.dox, *.py, *.pyw, *.f90, *.f, *.for, *.tcl,
+# *.vhd, *.vhdl, *.ucf and *.qsf.
+
+FILE_PATTERNS          = *.c \
+                         *.cc \
+                         *.cxx \
+                         *.cpp \
+                         *.c++ \
+                         *.h \
+                         *.hh \
+                         *.hxx \
+                         *.hpp \
+                         *.h++ \
+                         *.inc \
+                         *.m \
+                         *.markdown \
+                         *.md \
+                         *.mm \
+                         *.dox \
+                         *.f90 \
+                         *.f \
+                         *.for \
+                         *.F90
 
 # The RECURSIVE tag can be used to specify whether or not subdirectories should
 # be searched for input files as well.
@@ -833,7 +879,7 @@ EXAMPLE_PATH           =
 # *.h) to filter out the source-files in the directories. If left blank all
 # files are included.
 
-EXAMPLE_PATTERNS       =
+EXAMPLE_PATTERNS       = *
 
 # If the EXAMPLE_RECURSIVE tag is set to YES then subdirectories will be
 # searched for input files to be used with the \include or \dontinclude commands
@@ -862,6 +908,10 @@ IMAGE_PATH             =
 # Note that the filter must not add or remove lines; it is applied before the
 # code is scanned, but not when the output code is generated. If lines are added
 # or removed, the anchors will not be placed correctly.
+#
+# Note that for custom extensions or not directly supported extensions you also
+# need to set EXTENSION_MAPPING for the extension otherwise the files are not
+# properly processed by doxygen.
 
 INPUT_FILTER           =
 
@@ -871,6 +921,10 @@ INPUT_FILTER           =
 # (like *.cpp=my_cpp_filter). See INPUT_FILTER for further information on how
 # filters are used. If the FILTER_PATTERNS tag is empty or if none of the
 # patterns match the file name, INPUT_FILTER is applied.
+#
+# Note that for custom extensions or not directly supported extensions you also
+# need to set EXTENSION_MAPPING for the extension otherwise the files are not
+# properly processed by doxygen.
 
 FILTER_PATTERNS        =
 
@@ -1129,6 +1183,7 @@ HTML_COLORSTYLE_GAMMA  = 80
 
 # If the HTML_TIMESTAMP tag is set to YES then the footer of each generated HTML
 # page will contain the date and time when the page was generated. Setting this
+# to YES can help to show when doxygen was last run and thus if the
 # to NO can help when comparing the output of multiple runs.
 # The default value is: YES.
 # This tag requires that the tag GENERATE_HTML is set to YES.
@@ -1604,9 +1659,12 @@ COMPACT_LATEX          = NO
 PAPER_TYPE             = a4
 
 # The EXTRA_PACKAGES tag can be used to specify one or more LaTeX package names
-# that should be included in the LaTeX output. To get the times font for
-# instance you can specify
-# EXTRA_PACKAGES=times
+# that should be included in the LaTeX output. The package can be specified just
+# by its name or with the correct syntax as to be used with the LaTeX
+# \usepackage command. To get the times font for instance you can specify :
+# EXTRA_PACKAGES=times or EXTRA_PACKAGES={times}
+# To use the option intlimits with the amsmath package you can specify:
+# EXTRA_PACKAGES=[intlimits]{amsmath}
 # If left blank no extra packages will be included.
 # This tag requires that the tag GENERATE_LATEX is set to YES.
 
@@ -1709,6 +1767,14 @@ LATEX_SOURCE_CODE      = NO
 
 LATEX_BIB_STYLE        = plain
 
+# If the LATEX_TIMESTAMP tag is set to YES then the footer of each generated
+# page will contain the date and time when the page was generated. Setting this
+# to NO can help when comparing the output of multiple runs.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_LATEX is set to YES.
+
+LATEX_TIMESTAMP        = NO
+
 #---------------------------------------------------------------------------
 # Configuration options related to the RTF output
 #---------------------------------------------------------------------------
@@ -1940,15 +2006,15 @@ ENABLE_PREPROCESSING   = YES
 # The default value is: NO.
 # This tag requires that the tag ENABLE_PREPROCESSING is set to YES.
 
-MACRO_EXPANSION        = NO
+MACRO_EXPANSION        = YES
 
 # If the EXPAND_ONLY_PREDEF and MACRO_EXPANSION tags are both set to YES then
 # the macro expansion is limited to the macros specified with the PREDEFINED and
 # EXPAND_AS_DEFINED tags.
 # The default value is: NO.
 # This tag requires that the tag ENABLE_PREPROCESSING is set to YES.
 
-EXPAND_ONLY_PREDEF     = NO
+EXPAND_ONLY_PREDEF     = YES
 
 # If the SEARCH_INCLUDES tag is set to YES, the include files in the
 # INCLUDE_PATH will be searched if a #include is found.
@@ -1980,7 +2046,7 @@ INCLUDE_FILE_PATTERNS  =
 # recursively expanded use the := operator instead of the = operator.
 # This tag requires that the tag ENABLE_PREPROCESSING is set to YES.
 
-PREDEFINED             =
+PREDEFINED             = ALLOCABLE_=allocatable
 
 # If the MACRO_EXPANSION and EXPAND_ONLY_PREDEF tags are set to YES then this
 # tag can be used to specify a list of macro names that should be expanded. The
@@ -2207,7 +2273,8 @@ INCLUDED_BY_GRAPH      = YES
 #
 # Note that enabling this option will significantly increase the time of a run.
 # So in most cases it will be better to enable call graphs for selected
-# functions only using the \callgraph command.
+# functions only using the \callgraph command. Disabling a call graph can be
+# accomplished by means of the command \hidecallgraph.
 # The default value is: NO.
 # This tag requires that the tag HAVE_DOT is set to YES.
 
@@ -2218,7 +2285,8 @@ CALL_GRAPH             = YES
 #
 # Note that enabling this option will significantly increase the time of a run.
 # So in most cases it will be better to enable caller graphs for selected
-# functions only using the \callergraph command.
+# functions only using the \callergraph command. Disabling a caller graph can be
+# accomplished by means of the command \hidecallergraph.
 # The default value is: NO.
 # This tag requires that the tag HAVE_DOT is set to YES.
 
@@ -2241,11 +2309,15 @@ GRAPHICAL_HIERARCHY    = YES
 DIRECTORY_GRAPH        = YES
 
 # The DOT_IMAGE_FORMAT tag can be used to set the image format of the images
-# generated by dot.
+# generated by dot. For an explanation of the image formats see the section
+# output formats in the documentation of the dot tool (Graphviz (see:
+# http://www.graphviz.org/)).
 # Note: If you choose svg you need to set HTML_FILE_EXTENSION to xhtml in order
 # to make the SVG files visible in IE 9+ (other browsers do not have this
 # requirement).
-# Possible values are: png, jpg, gif and svg.
+# Possible values are: png, jpg, gif, svg, png:gd, png:gd:gd, png:cairo,
+# png:cairo:gd, png:cairo:cairo, png:cairo:gdiplus, png:gdiplus and
+# png:gdiplus:gdiplus.
 # The default value is: png.
 # This tag requires that the tag HAVE_DOT is set to YES.
 

src/ALE/MOM_regridding.F90

@@ -2770,7 +2770,7 @@ subroutine regridding_memory_deallocation( CS )
 
 end subroutine regridding_memory_deallocation
 
-!> \namespace MOM_regridding
+!> \namespace mom_regridding
 !!
 !! A vertical grid is defined solely by the cell thicknesses, \f$h\f$.
 !! Most calculations in this module start with the coordinate at the bottom

src/core/MOM_forcing_type.F90

@@ -121,14 +121,15 @@ module MOM_forcing_type
 
   ! land ice-shelf related inputs
   real, pointer, dimension(:,:) :: &
-  ustar_shelf   => NULL(), & !< friction velocity under ice-shelves (m/s)
-                             !! as computed by the ocean at the previous time step.
-  frac_shelf_h  => NULL(), & !< Fractional ice shelf coverage of h-, u-, and v-
-  frac_shelf_u  => NULL(), & !< cells, nondimensional from 0 to 1. These are only
-  frac_shelf_v  => NULL(), & !< associated if ice shelves are enabled, and are
-                             !! exactly 0 away from shelves or on land.
-  rigidity_ice_u => NULL(),& !< Depth-integrated lateral viscosity of ice
-  rigidity_ice_v => NULL()   !< shelves or sea ice at u- or v-points (m3/s)
+  ustar_shelf   => NULL(), &   !< friction velocity under ice-shelves (m/s)
+                               !! as computed by the ocean at the previous time step.
+  frac_shelf_h  => NULL(), &   !< Fractional ice shelf coverage of h-, u-, and v-
+  frac_shelf_u  => NULL(), &   !< cells, nondimensional from 0 to 1. These are only
+  frac_shelf_v  => NULL(), &   !< associated if ice shelves are enabled, and are
+                               !! exactly 0 away from shelves or on land.
+  iceshelf_melt   => NULL(), & !< ice shelf melt rate (positive) or freezing (negative) ( m/year )
+  rigidity_ice_u => NULL(),&   !< Depth-integrated lateral viscosity of ice
+  rigidity_ice_v => NULL()     !< shelves or sea ice at u- or v-points (m3/s)
 
   ! Scalars set by surface forcing modules
   real :: vPrecGlobalAdj     !< adjustment to restoring vprec to zero out global net ( kg/(m^2 s) )
@@ -1615,6 +1616,13 @@ subroutine forcing_accumulate(flux_tmp, fluxes, dt, G, wt2)
       fluxes%ustar_shelf(i,j)  = flux_tmp%ustar_shelf(i,j)
     enddo ; enddo
   endif
+
+  if (associated(fluxes%iceshelf_melt) .and. associated(flux_tmp%iceshelf_melt)) then
+    do i=isd,ied ; do j=jsd,jed
+      fluxes%iceshelf_melt(i,j)  = flux_tmp%iceshelf_melt(i,j)
+    enddo ; enddo
+  endif
+
   if (associated(fluxes%frac_shelf_h) .and. associated(flux_tmp%frac_shelf_h)) then
     do i=isd,ied ; do j=jsd,jed
       fluxes%frac_shelf_h(i,j)  = flux_tmp%frac_shelf_h(i,j)
@@ -2198,6 +2206,7 @@ subroutine allocate_forcing_type(G, fluxes, stress, ustar, water, heat, shelf, p
   call myAlloc(fluxes%frac_shelf_u,IsdB,IedB,jsd,jed, shelf)
   call myAlloc(fluxes%frac_shelf_v,isd,ied,JsdB,JedB, shelf)
   call myAlloc(fluxes%ustar_shelf,isd,ied,jsd,jed, shelf)
+  call myAlloc(fluxes%iceshelf_melt,isd,ied,jsd,jed, shelf)
   call myAlloc(fluxes%rigidity_ice_u,IsdB,IedB,jsd,jed, shelf)
   call myAlloc(fluxes%rigidity_ice_v,isd,ied,JsdB,JedB, shelf)
 
@@ -2263,6 +2272,7 @@ subroutine deallocate_forcing_type(fluxes)
   if (associated(fluxes%TKE_tidal))            deallocate(fluxes%TKE_tidal)
   if (associated(fluxes%ustar_tidal))          deallocate(fluxes%ustar_tidal)
   if (associated(fluxes%ustar_shelf))          deallocate(fluxes%ustar_shelf)
+  if (associated(fluxes%iceshelf_melt))        deallocate(fluxes%iceshelf_melt)
   if (associated(fluxes%frac_shelf_h))         deallocate(fluxes%frac_shelf_h)
   if (associated(fluxes%frac_shelf_u))         deallocate(fluxes%frac_shelf_u)
   if (associated(fluxes%frac_shelf_v))         deallocate(fluxes%frac_shelf_v)

src/ice_shelf/MOM_ice_shelf.F90

@@ -678,10 +678,12 @@ subroutine shelf_calc_flux(state, fluxes, Time, time_step, CS)
       else !not shelf
         CS%t_flux(i,j) = 0.0
       endif
-
     enddo ! i-loop
   enddo ! j-loop
 
+  ! melt in m/year
+  fluxes%iceshelf_melt = CS%lprec  * (86400.0*365.0/CS%density_ice)
+
   if (CS%DEBUG) then
    call hchksum (CS%h_shelf, "melt rate", G, haloshift=0)
   endif
@@ -1382,6 +1384,7 @@ subroutine initialize_ice_shelf(param_file, ocn_grid, Time, CS, diag, fluxes, Ti
     allocate( fluxes%frac_shelf_u(Isdq:Iedq,jsd:jed) ) ; fluxes%frac_shelf_u(:,:) = 0.0
     allocate( fluxes%frac_shelf_v(isd:ied,Jsdq:Jedq) ) ; fluxes%frac_shelf_v(:,:) = 0.0
     allocate( fluxes%ustar_shelf(isd:ied,jsd:jed) ) ; fluxes%ustar_shelf(:,:) = 0.0
+    allocate( fluxes%iceshelf_melt(isd:ied,jsd:jed) ) ; fluxes%iceshelf_melt(:,:) = 0.0
     if (.not.associated(fluxes%p_surf)) then
     allocate( fluxes%p_surf(isd:ied,jsd:jed) ) ; fluxes%p_surf(:,:) = 0.0
     endif
@@ -1445,6 +1448,8 @@ subroutine initialize_ice_shelf(param_file, ocn_grid, Time, CS, diag, fluxes, Ti
   if (.not. solo_ice_sheet) then
     vd = var_desc("ustar_shelf","m s-1","Friction velocity under ice shelves",z_grid='1')
     call register_restart_field(fluxes%ustar_shelf, vd, .true., CS%restart_CSp)
+    vd = var_desc("iceshelf_melt","m year-1","Ice Shelf Melt Rate",z_grid='1')
+    call register_restart_field(fluxes%iceshelf_melt, vd, .true., CS%restart_CSp)
   endif
 
   CS%restart_output_dir = dirs%restart_output_dir