Fix compile/whitespace, add files to modules

JCSDA · Jun 17, 2021 · c963ff4 · c963ff4
1 parent c47cad2
commit c963ff4
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Showing 21 changed files with 66 additions and 75 deletions.
diff --git a/docs/Doxyfile.in b/docs/Doxyfile.in
@@ -294,7 +294,7 @@ OPTIMIZE_OUTPUT_VHDL   = NO
 # Note that for custom extensions you also need to set FILE_PATTERNS otherwise
 # the files are not read by doxygen.
 
-EXTENSION_MAPPING      = F90=FortranFree inc=FortranFree h=FortranFree
+EXTENSION_MAPPING      = F90=FortranFree inc=FortranFree
 
 # If the MARKDOWN_SUPPORT tag is enabled then doxygen pre-processes all comments
 # according to the Markdown format, which allows for more readable

diff --git a/horiz_interp/horiz_interp_spherical.F90 b/horiz_interp/horiz_interp_spherical.F90
@@ -113,7 +113,6 @@ subroutine horiz_interp_spherical_new(Interp, lon_in,lat_in,lon_out,lat_out, &
     real, intent(in),  dimension(:,:)      :: lat_in !< Longitude (radians) for source data grid
     real, intent(in),  dimension(:,:)      :: lon_out !< Longitude (radians) for output data grid
     real, intent(in),  dimension(:,:)      :: lat_out !< Latitude (radians) for output data grid
-    integer, intent(in),          optional :: verbose !< flag for amount of print output
     logical, intent(in),          optional :: src_modulo !< indicates if the boundary condition
                                           !! along zonal boundary is cyclic or not. Cyclic when true
     integer, intent(in),        optional   :: num_nbrs !< Number of nearest neighbors for regridding
@@ -275,8 +274,7 @@ end subroutine horiz_interp_spherical_new
   !> Subroutine for performing the horizontal interpolation between two grids.
   !! horiz_interp_spherical_new must be called before calling this routine.
   subroutine horiz_interp_spherical( Interp, data_in, data_out, verbose, mask_in, mask_out, missing_value)
-    type (horiz_interp_type), intent(in)        :: Interp
-    type(horiz_interp_type), intent(inout) :: Interp !< A derived type variable containing indices
+    type(horiz_interp_type), intent(in) :: Interp !< A derived type variable containing indices
                                           !! and weights for subsequent interpolations. Returned
                                           !! by a previous call to horiz_interp_spherical_new
     real, intent(in),  dimension(:,:)           :: data_in !< Input data on source grid

diff --git a/mpp/include/mpp_comm.inc b/mpp/include/mpp_comm.inc
@@ -19,8 +19,8 @@
 !* License along with FMS.  If not, see <http://www.gnu.org/licenses/>.
 !***********************************************************************
 !> @file
-!> @ingroup mpp
-!> @brief Imports various routines used for communications and calculations
+!> @ingroup mpp_mod
+!> @brief Imports checksum, gather, and scatter routines used for communications and calculations
 !! between PE's in @ref mpp
 
 #if defined(use_libMPI)

diff --git a/mpp/include/mpp_data_mpi.inc b/mpp/include/mpp_data_mpi.inc
@@ -20,7 +20,7 @@
 !***********************************************************************
 
 !> @file
-!> @ingroup mpp
+!> @ingroup mpp_data_mod
 !> @brief Holds dummy constants and stack data for @ref mpp_mod and @ref mpp_domains_mod.
 !! Accessible through @ref mpp_data_mod
 

diff --git a/mpp/include/mpp_data_nocomm.inc b/mpp/include/mpp_data_nocomm.inc
@@ -19,7 +19,7 @@
 !* License along with FMS.  If not, see <http://www.gnu.org/licenses/>.
 !***********************************************************************
 !> @file
-!> @ingroup mpp
+!> @ingroup mpp_data_mod
 !> @brief Holds dummy constants and stack data for @ref mpp_mod and @ref mpp_domains_mod.
 !! Accessible through @ref mpp_data_mod
 

diff --git a/mpp/include/mpp_define_nest_domains.inc b/mpp/include/mpp_define_nest_domains.inc
@@ -21,7 +21,7 @@
 !***********************************************************************
 
 !> @file
-!> @ingroup mpp
+!> @ingroup mpp_domains_mod
 !> @brief Routines for use in @ref mpp_domains_mod for routines utilizing
 !! domains with nested grids
 
@@ -55,34 +55,34 @@
 !! test_fms/mpp/test_mpp_domains.F90.\n
 !!\n
 !! @code{.F90}
-!! 		if( concurrent ) then
-!!   			call mpp_broadcast_domain(domain_fine)
-!!   			call mpp_broadcast_domain(domain_coarse)
-!! 		endif
+!! if( concurrent ) then
+!!   call mpp_broadcast_domain(domain_fine)
+!!   call mpp_broadcast_domain(domain_coarse)
+!! endif
 !!
-!! 		call mpp_define_nest_domains(nest_domain,domain,num_nest,nest_level(1:num_nest), &
-!!                              tile_fine(1:num_nest), tile_coarse(1:num_nest), &
+!! call mpp_define_nest_domains(nest_domain,domain,num_nest,nest_level(1:num_nest), &
+!!                             tile_fine(1:num_nest), tile_coarse(1:num_nest), &
 !!                              istart_coarse(1:num_nest), icount_coarse(1:num_nest), &
 !!                              jstart_coarse(1:num_nest), jcount_coarse(1:num_nest), &
 !!                              npes_nest_tile, x_refine(1:num_nest), y_refine(1:num_nest), &
 !!                              extra_halo=extra_halo, name="nest_domain")
 !!
-!! 		call mpp_get_C2F_index(nest_domain, isw_f, iew_f, jsw_f, jew_f, isw_c, iew_c, jsw_c, jew_c, WEST, level)
-!! 		call mpp_get_C2F_index(nest_domain, ise_f, iee_f, jse_f, jee_f, ise_c, iee_c, jse_c, jee_c, EAST, level)
-!! 		call mpp_get_C2F_index(nest_domain, iss_f, ies_f, jss_f, jes_f, iss_c, ies_c, jss_c, jes_c, SOUTH, level)
-!! 		call mpp_get_C2F_index(nest_domain, isn_f, ien_f, jsn_f, jen_f, isn_c, ien_c, jsn_c, jen_c, NORTH, level)
+!! call mpp_get_C2F_index(nest_domain, isw_f, iew_f, jsw_f, jew_f, isw_c, iew_c, jsw_c, jew_c, WEST, level)
+!! call mpp_get_C2F_index(nest_domain, ise_f, iee_f, jse_f, jee_f, ise_c, iee_c, jse_c, jee_c, EAST, level)
+!! call mpp_get_C2F_index(nest_domain, iss_f, ies_f, jss_f, jes_f, iss_c, ies_c, jss_c, jes_c, SOUTH, level)
+!! call mpp_get_C2F_index(nest_domain, isn_f, ien_f, jsn_f, jen_f, isn_c, ien_c, jsn_c, jen_c, NORTH, level)
 !!
-!!    		allocate(wbuffer(isw_c:iew_c, jsw_c:jew_c,nz))
-!!    		allocate(ebuffer(ise_c:iee_c, jse_c:jee_c,nz))
-!!    		allocate(sbuffer(iss_c:ies_c, jss_c:jes_c,nz))
-!!    		allocate(nbuffer(isn_c:ien_c, jsn_c:jen_c,nz))
-!!    		call mpp_update_nest_fine(x, nest_domain, wbuffer, sbuffer, ebuffer, nbuffer)
+!! allocate(wbuffer(isw_c:iew_c, jsw_c:jew_c,nz))
+!! allocate(ebuffer(ise_c:iee_c, jse_c:jee_c,nz))
+!! allocate(sbuffer(iss_c:ies_c, jss_c:jes_c,nz))
+!! allocate(nbuffer(isn_c:ien_c, jsn_c:jen_c,nz))
+!! call mpp_update_nest_fine(x, nest_domain, wbuffer, sbuffer, ebuffer, nbuffer)
 !!
-!!    		call mpp_get_F2C_index(nest_domain, is_c, ie_c, js_c, je_c, is_f, ie_f, js_f, je_f, nest_level=level)
-!!    		allocate(buffer (is_f:ie_f, js_f:je_f,nz))
-!!    		call mpp_update_nest_coarse(x, nest_domain, buffer)
+!! call mpp_get_F2C_index(nest_domain, is_c, ie_c, js_c, je_c, is_f, ie_f, js_f, je_f, nest_level=level)
+!! allocate(buffer (is_f:ie_f, js_f:je_f,nz))
+!! call mpp_update_nest_coarse(x, nest_domain, buffer)
 !
-!! 		call mpp_define_nest_domains (nest_domain, domain, num_nest, nest_level, tile_fine, tile_coarse, &
+!! call mpp_define_nest_domains (nest_domain, domain, num_nest, nest_level, tile_fine, tile_coarse, &
 !!                               istart_coarse, icount_coarse, jstart_coarse, jcount_coarse, &
 !!                                    npes_nest_tile, x_refine, y_refine, extra_halo, name)
 !! @endcode
@@ -1526,10 +1526,11 @@ function search_C2F_nest_overlap(nest_domain, nest_level, extra_halo, position)
   !> Get the index of the data passed from coarse grid to fine grid.
   !!
   !! <br>Example usage:
-  !!
-  !! 		call mpp_get_C2F_index(nest_domain, is_fine, ie_fine, js_fine, je_fine,
+  !! @code{.F90}
+  !! call mpp_get_C2F_index(nest_domain, is_fine, ie_fine, js_fine, je_fine,
   !!                            is_coarse, ie_coarse, js_coarse, je_coarse, dir,
   !!                            nest_level, position)
+  !! @endcode
   subroutine mpp_get_C2F_index(nest_domain, is_fine, ie_fine, js_fine, je_fine, &
                 is_coarse, ie_coarse, js_coarse, je_coarse, dir, nest_level, position)
 

diff --git a/mpp/include/mpp_domains_comm.inc b/mpp/include/mpp_domains_comm.inc
@@ -21,7 +21,7 @@
 !***********************************************************************
 
 !> @file
-!> @ingroup mpp
+!> @ingroup mpp_domains_mod
 !> @brief Routines for domain communications via @ref domaincommunicator2d
 
     function mpp_redistribute_init_comm(domain_in,l_addrs_in, domain_out,l_addrs_out, &

diff --git a/mpp/include/mpp_domains_define.inc b/mpp/include/mpp_domains_define.inc
@@ -21,7 +21,7 @@
 !***********************************************************************
 
 !> @file
-!> @ingroup mpp
+!> @ingroup mpp_domains_mod
 !> @brief Various routines handling domains in @ref mpp_domains_mod
 
   ! <SUBROUTINE NAME="mpp_define_layout2D" INTERFACE="mpp_define_layout">

diff --git a/mpp/include/mpp_domains_misc.inc b/mpp/include/mpp_domains_misc.inc
@@ -19,7 +19,7 @@
 !***********************************************************************
 
 !> @file
-!> @ingroup mpp
+!> @ingroup mpp_domains_mod
 !> @brief Initialization and finalization routines for @ref mpp_domains_mod as well
 !! as other utility routines.
 

diff --git a/mpp/include/mpp_domains_reduce.inc b/mpp/include/mpp_domains_reduce.inc
@@ -20,7 +20,7 @@
 !***********************************************************************
 
 !> @file
-!> @ingroup mpp
+!> @ingroup mpp_domains_mod
 !> @brief Routines for calculating data from distributed arrays
 
 !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!

diff --git a/mpp/include/mpp_domains_util.inc b/mpp/include/mpp_domains_util.inc
@@ -20,7 +20,7 @@
 !***********************************************************************
 
 !> @file
-!> @ingroup mpp
+!> @ingroup mpp_domains_mod
 !> @brief Utility routines for getting and setting values in @ref mpp_domains_mod
 
   ! <SUBROUTINE NAME="mpp_domains_set_stack_size">
@@ -301,10 +301,10 @@
   !> @brief Modifies the indices of the input domain to create the supergrid domain
   !!
   !> This is an example of how to use mpp_create_super_grid_domain
-  !!
-  !! 		call mpp_copy_domain(domain_in, domain_out)
-  !! 		call super_grid_domain(domain_out)
-  !!
+  !! @code{.F90}
+  !! call mpp_copy_domain(domain_in, domain_out)
+  !! call super_grid_domain(domain_out)
+  !! @endcode
   !! domain_in is the original domain, domain_out is the domain with the supergrid indices.
   subroutine mpp_create_super_grid_domain(domain)
     type(domain2D), intent(inout) :: domain !< Input domain

diff --git a/mpp/include/mpp_io_connect.inc b/mpp/include/mpp_io_connect.inc
@@ -19,7 +19,7 @@
 !* License along with FMS.  If not, see <http://www.gnu.org/licenses/>.
 !***********************************************************************
 !> @file
-!> @ingroup mpp
+!> @ingroup mpp_io_mod
 !> @brief Handles opening and closing files in @ref mpp_io_mod
 
 ! <SUBROUTINE NAME="mpp_open">

diff --git a/mpp/include/mpp_io_misc.inc b/mpp/include/mpp_io_misc.inc
@@ -19,7 +19,7 @@
 !* License along with FMS.  If not, see <http://www.gnu.org/licenses/>.
 !***********************************************************************
 !> @file
-!> @ingroup mpp
+!> @ingroup mpp_io_mod
 !> @brief Misc. routines including initialization and finalization of @ref mpp_io_mod
 
 !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!

diff --git a/mpp/include/mpp_io_read.inc b/mpp/include/mpp_io_read.inc
@@ -19,7 +19,7 @@
 !* License along with FMS.  If not, see <http://www.gnu.org/licenses/>.
 !***********************************************************************
 !> @file
-!> @ingroup mpp
+!> @ingroup mpp_io_mod
 !> @brief Parallel file read routines for structured grids for use in @ref mpp_io_mod
 
 !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!

diff --git a/mpp/include/mpp_io_unstructured_read.inc b/mpp/include/mpp_io_unstructured_read.inc
@@ -18,7 +18,7 @@
 !***********************************************************************
 
 !> @file
-!> @ingroup mpp
+!> @ingroup mpp_io_mod
 !> @brief Parallel file reads for unstructured grids, used in @ref mpp_io_mod
 !----------
 !ug support

diff --git a/mpp/include/mpp_io_unstructured_write.inc b/mpp/include/mpp_io_unstructured_write.inc
@@ -18,7 +18,7 @@
 !***********************************************************************
 
 !> @file
-!> @ingroup mpp
+!> @ingroup mpp_io_mod
 !> @brief Parallel file writes for unstructured grids, used in @ref mpp_io_mod
 !----------
 !ug support

diff --git a/mpp/include/mpp_io_util.inc b/mpp/include/mpp_io_util.inc
@@ -21,7 +21,7 @@
 !***********************************************************************
 
 !> @file
-!> @ingroup mpp
+!> @ingroup mpp_io_mod
 !> @brief Routines to retrieve data used in @ref mpp_io_mod
 
   !#####################################################################
@@ -45,7 +45,9 @@
     !> @brief Get some general information about a file.
     !!
     !> <br>Example usage:
-    !! 			call mpp_get_info( unit, ndim, nvar, natt, ntime )
+    !! @code{.F90}
+    !! call mpp_get_info( unit, ndim, nvar, natt, ntime )
+    !! @endcode
     subroutine mpp_get_info( unit, ndim, nvar, natt, ntime )
 
       integer, intent(in) :: unit
@@ -323,26 +325,13 @@
 
   end function mpp_get_default_calendar
 
-  !#####################################################################
-! <SUBROUTINE NAME="mpp_get_times">
-!   <OVERVIEW>
-!     Get file time data.
-!   </OVERVIEW>
-!   <DESCRIPTION>
-!     Get file time data.
-!   </DESCRIPTION>
-!   <TEMPLATE>
-!     call mpp_get_times( unit, time_values )
-!   </TEMPLATE>
-!   <IN NAME="unit" TYPE="integer"> </IN>
-!   <INOUT NAME="time_values" TYPE="real(r8_kind)" DIM="(:)"> </INOUT>
-! </SUBROUTINE>
-
    !> @brief Get file time data.
    !!
    !> Copy time information from file and convert to time_type
    !! <br>Example usage:
-   !! 		call mpp_get_times( unit, time_values)
+   !! @code{.F90}
+   !! call mpp_get_times( unit, time_values)
+   !! @endcode
    subroutine mpp_get_times( unit, time_values )
       integer, intent(in) :: unit
       real, intent(inout) :: time_values(:)

diff --git a/mpp/include/mpp_io_write.inc b/mpp/include/mpp_io_write.inc
@@ -24,7 +24,7 @@
 !                             MPP_WRITE_META                                 !
 !                                                                            !
 !> @file
-!> @ingroup mpp
+!> @ingroup mpp_io_mod
 !> @brief This series of routines is used to describe the contents of the file
 !! being written on <unit>.
 !!
@@ -94,16 +94,16 @@
 !! I/O). If the <datLINK> element is allocated, it is considered to be a
 !! space axis, otherwise it is a time axis with an unlimited dimension.
 !! Only one time axis is allowed per file.
-!!
-!!  	subroutine mpp_write_meta_field( unit, field, axes, name, units, longname
-!!       				standard_name, min, max, missing, fill, scale, add, pack)
-!!     		integer, intent(in) :: unit
-!!     		type(fieldtype), intent(out) :: field
-!!     		type(axistype), intent(in) :: axes(:)
-!!     		character(len=*), intent(in) :: name, units, longname, standard_name
-!!     		real, intent(in), optional :: min, max, missing, fill, scale, add
-!!     		integer, intent(in), optional :: pack
-!!
+!! @code{.F90}
+!!  subroutine mpp_write_meta_field( unit, field, axes, name, units, longname 
+!!                                   standard_name, min, max, missing, fill, scale, add, pack)
+!!     integer, intent(in) :: unit
+!!     type(fieldtype), intent(out) :: field
+!!     type(axistype), intent(in) :: axes(:)
+!!     character(len=*), intent(in) :: name, units, longname, standard_name
+!!     real, intent(in), optional :: min, max, missing, fill, scale, add
+!!     integer, intent(in), optional :: pack
+!! @endcode
 !! This form defines a field. Metadata corresponding to the type
 !! above are written to the file on <unit>. A unique ID for subsequent
 !! references to this field is returned in field%id. At least one axis

diff --git a/mpp/include/mpp_unstruct_domain.inc b/mpp/include/mpp_unstruct_domain.inc
@@ -18,7 +18,7 @@
 !***********************************************************************
 
 !> @file
-!> @ingroup mpp
+!> @ingroup mpp_domains_mod
 !> @brief Routines for defining and managing unstructured grids
 
   !#####################################################################

diff --git a/mpp/include/mpp_util.inc b/mpp/include/mpp_util.inc
@@ -20,7 +20,7 @@
 !* License along with FMS.  If not, see <http://www.gnu.org/licenses/>.
 !***********************************************************************
 !> @file
-!> @ingroup mpp
+!> @ingroup mpp_mod
 !> @brief General utility functions for use in @ref mpp_utilities_mod
 
 #if defined(use_libMPI)

diff --git a/mpp/include/system_clock.h b/mpp/include/system_clock.h
@@ -16,6 +16,9 @@
 !* You should have received a copy of the GNU Lesser General Public
 !* License along with FMS.  If not, see <http://www.gnu.org/licenses/>.
 !***********************************************************************
+!> @file
+!> @ingroup mpp_mod
+
 #if defined(use_libMPI)
 #define SYSTEM_CLOCK system_clock_mpi