Merge branch 'docs_test2' into docs_test

.DoxygenLayout.xml

@@ -20,6 +20,10 @@
       <tab type="globals" visible="yes" title="Globals" intro=""/>
     </tab>
     <tab type="examples" visible="yes" title="Examples" intro=""/> 
+    <tab type="usergroup" title="Wikis and Related Pages">
+      <tab type="user" title="Getting Started" url="https://github.com/NOAA-GFDL/MOM6-examples/wiki"/>
+      <tab type="user" title="Developer's wiki" url="https://github.com/NOAA-GFDL/MOM6/wiki"/>
+    </tab>
   </navindex>
 
   <!-- Layout definition for a class page -->

.doxygen

@@ -1,4 +1,4 @@
-# Doxyfile 1.8.12
+# Doxyfile 1.8.14
 
 # This file describes the settings to be used by the documentation system
 # doxygen (www.doxygen.org) for a project.
@@ -777,10 +777,12 @@ WARN_LOGFILE           = doxygen.log
 # The INPUT tag is used to specify the files and/or directories that contain
 # documented source files. You may enter file names like myfile.cpp or
 # directories like /usr/src/myproject. Separate the files or directories with
-# spaces.
+# spaces. See also FILE_PATTERNS and EXTENSION_MAPPING
 # Note: If this tag is empty the current directory is searched.
 
-INPUT                  = config_src src README.md
+INPUT                  = config_src \
+                         src \
+                         README.md
 
 # This tag can be used to specify the character encoding of the source files
 # that doxygen parses. Internally doxygen uses the UTF-8 encoding. Doxygen uses
@@ -802,8 +804,8 @@ INPUT_ENCODING         = UTF-8
 # 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.
+# *.m, *.markdown, *.md, *.mm, *.dox, *.py, *.pyw, *.f90, *.f95, *.f03, *.f08,
+# *.f, *.for, *.tcl, *.vhd, *.vhdl, *.ucf and *.qsf.
 
 FILE_PATTERNS          = *.c \
                          *.cc \
@@ -872,7 +874,8 @@ EXCLUDE_SYMBOLS        =
 # that contain example code fragments that are included (see the \include
 # command).
 
-EXAMPLE_PATH           = config_src src
+EXAMPLE_PATH           = config_src \
+                         src
 
 # If the value of the EXAMPLE_PATH tag contains directories, you can use the
 # EXAMPLE_PATTERNS tag to specify one or more wildcard pattern (like *.cpp and
@@ -892,7 +895,9 @@ EXAMPLE_RECURSIVE      = NO
 # that contain images that are to be included in the documentation (see the
 # \image command).
 
-IMAGE_PATH             = .images config_src src
+IMAGE_PATH             = .images \
+                         config_src \
+                         src
 
 # The INPUT_FILTER tag can be used to specify a program that doxygen should
 # invoke to filter for each input file. Doxygen will invoke the filter program
@@ -994,7 +999,7 @@ REFERENCES_RELATION    = YES
 # link to the documentation.
 # The default value is: YES.
 
-REFERENCES_LINK_SOURCE = YES
+REFERENCES_LINK_SOURCE = NO
 
 # If SOURCE_TOOLTIPS is enabled (the default) then hovering a hyperlink in the
 # source code will show a tooltip with additional information such as prototype,
@@ -1184,12 +1189,23 @@ 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.
+# documentation is up to date.
+# The default value is: NO.
 # This tag requires that the tag GENERATE_HTML is set to YES.
 
 HTML_TIMESTAMP         = NO
 
+# If the HTML_DYNAMIC_MENUS tag is set to YES then the generated HTML
+# documentation will contain a main index with vertical navigation menus that
+# are dynamically created via Javascript. If disabled, the navigation index will
+# consists of multiple levels of tabs that are statically embedded in every HTML
+# page. Disable this option to support browsers that do not have Javascript,
+# like the Qt help browser.
+# The default value is: YES.
+# This tag requires that the tag GENERATE_HTML is set to YES.
+
+HTML_DYNAMIC_MENUS     = YES
+
 # If the HTML_DYNAMIC_SECTIONS tag is set to YES then the generated HTML
 # documentation will contain sections that can be hidden and shown after the
 # page has loaded.
@@ -2368,6 +2384,11 @@ DIAFILE_DIRS           =
 
 PLANTUML_JAR_PATH      =
 
+# When using plantuml, the PLANTUML_CFG_FILE tag can be used to specify a
+# configuration file for plantuml.
+
+PLANTUML_CFG_FILE      =
+
 # When using plantuml, the specified paths are searched for files specified by
 # the !include statement in a plantuml block.
 

config_src/solo_driver/MOM_driver.F90

@@ -191,7 +191,12 @@ program MOM_main
 #include "version_variable.h"
   character(len=40)  :: mod = "MOM_main (MOM_driver)" ! This module's name.
 
-  namelist /ocean_solo_nml/ date_init, calendar, months, days, hours, minutes, seconds
+  integer :: ocean_nthreads = 1
+  integer :: ncores_per_node = 36
+  logical :: use_hyper_thread = .false.
+  integer :: omp_get_num_threads,omp_get_thread_num,get_cpu_affinity,adder,base_cpu
+  namelist /ocean_solo_nml/ date_init, calendar, months, days, hours, minutes, seconds,&
+                            ocean_nthreads, ncores_per_node, use_hyper_thread
 
   !#######################################################################
 
@@ -232,6 +237,23 @@ program MOM_main
     endif
   endif
 
+!$  call omp_set_num_threads(ocean_nthreads)
+!$OMP PARALLEL private(adder)
+!$  base_cpu = get_cpu_affinity()
+!$  if (use_hyper_thread) then
+!$     if (imod(omp_get_thread_num(),2) == 0) then
+!$        adder = omp_get_thread_num()/2
+!$     else
+!$        adder = ncores_per_node + omp_get_thread_num()/2
+!$     endif
+!$  else
+!$     adder = omp_get_thread_num()
+!$  endif
+!$  call set_cpu_affinity (base_cpu + adder)
+!$  write(6,*) " ocean  ", omp_get_num_threads(), get_cpu_affinity(), adder, omp_get_thread_num()
+!$  call flush(6)
+!$OMP END PARALLEL
+
   ! Read ocean_solo restart, which can override settings from the namelist.
   if (file_exists(trim(dirs%restart_input_dir)//'ocean_solo.res')) then
     call open_file(unit,trim(dirs%restart_input_dir)//'ocean_solo.res', &

src/ALE/MOM_ALE.F90

@@ -654,8 +654,8 @@ subroutine remap_all_state_vars(CS_remapping, CS_ALE, G, GV, h_old, h_new, dxInt
 
   ! Remap tracer
 !$OMP parallel default(none) shared(G,GV,h_old,h_new,dxInterface,CS_remapping,nz,Reg,u,v,ntr,show_call_tree, &
-!$OMP                               dt,h2,CS_ALE,work_conc,work_cont,work_2d,Idt,ppt2mks) &
-!$OMP                       private(h1,dx,u_column)
+!$OMP                               dt,CS_ALE,work_conc,work_cont,work_2d,Idt,ppt2mks) &
+!$OMP                       private(h1,h2,dx,u_column)
   if (ntr>0) then
     if (show_call_tree) call callTree_waypoint("remapping tracers (remap_all_state_vars)")
 !$OMP do
@@ -832,8 +832,8 @@ subroutine ALE_remap_scalar(CS, G, GV, nk_src, h_src, s_src, h_dst, s_dst, all_c
   n_points = nk_src
 
 !$OMP parallel default(none) shared(CS,G,GV,h_src,s_src,h_dst,s_dst &
-!$OMP                               ,ignore_vanished_layers, use_remapping_core_w, nk_src,dx ) &
-!$OMP                        firstprivate(n_points)
+!$OMP                               ,ignore_vanished_layers, use_remapping_core_w, nk_src ) &
+!$OMP                        firstprivate(n_points,dx)
 !$OMP do
   do j = G%jsc,G%jec
     do i = G%isc,G%iec

src/ALE/MOM_regridding.F90

@@ -347,9 +347,13 @@ subroutine initialize_regridding(CS, GV, max_depth, param_file, mod, coord_mode,
           'Unable to interpret "'//trim(string)//'".')
     endif
     allocate(dz(ke))
-    dz(:) = uniformResolution(ke, coord_mode, tmpReal, &
+    if (ke==1) then
+      dz(:) = uniformResolution(ke, coord_mode, tmpReal, GV%Rlay(1), GV%Rlay(1))
+    else
+      dz(:) = uniformResolution(ke, coord_mode, tmpReal, &
                    GV%Rlay(1)+0.5*(GV%Rlay(1)-GV%Rlay(2)), &
                    GV%Rlay(ke)+0.5*(GV%Rlay(ke)-GV%Rlay(ke-1)) )
+    endif
     if (main_parameters) call log_param(param_file, mod, "!"//coord_res_param, dz, &
                    trim(message), units=trim(coord_units))
   elseif (trim(string)=='PARAM') then
@@ -1125,9 +1129,10 @@ subroutine build_zstar_grid( CS, G, GV, h, dzInterface, frac_shelf_h)
     if (associated(frac_shelf_h)) ice_shelf = .true.
   endif
 
-!$OMP parallel do default(none) shared(G,GV,dzInterface,CS,nz,h,frac_shelf_h)                 &
-!$OMP                          private(nominalDepth,totalThickness,minThickness, &
-!$OMP                                  zNew,dh,zOld,ice_shelf)
+!$OMP parallel do default(none) shared(G,GV,dzInterface,CS,nz,h,frac_shelf_h, &
+!$OMP                                  ice_shelf,minThickness) &
+!$OMP                          private(nominalDepth,totalThickness, &
+!$OMP                                  zNew,dh,zOld)
   do j = G%jsc-1,G%jec+1
     do i = G%isc-1,G%iec+1
 

src/core/MOM.F90

@@ -23,7 +23,7 @@ module MOM
 use MOM_variables, only: thermo_var_ptrs
 
 ! Infrastructure modules
-use MOM_checksums,            only : MOM_checksums_init, hchksum, uchksum, vchksum
+use MOM_debugging,            only : MOM_debugging_init, hchksum, uchksum, vchksum
 use MOM_checksum_packages,    only : MOM_thermo_chksum, MOM_state_chksum, MOM_accel_chksum
 use MOM_cpu_clock,            only : cpu_clock_id, cpu_clock_begin, cpu_clock_end
 use MOM_cpu_clock,            only : CLOCK_COMPONENT, CLOCK_SUBCOMPONENT
@@ -90,7 +90,7 @@ module MOM
 use MOM_EOS,                   only : EOS_init
 use MOM_EOS,                   only : gsw_sp_from_sr, gsw_pt_from_ct
 use MOM_EOS,                   only : calculate_density
-use MOM_error_checking,        only : check_redundant
+use MOM_debugging,             only : check_redundant
 use MOM_grid,                  only : ocean_grid_type, set_first_direction
 use MOM_grid,                  only : MOM_grid_init, MOM_grid_end
 use MOM_hor_index,             only : hor_index_type, hor_index_init
@@ -2065,7 +2065,7 @@ subroutine initialize_MOM(Time, param_file, dirs, CS, Time_in, offline_tracer_mo
 #endif
   call callTree_waypoint("domains initialized (initialize_MOM)")
 
-  call MOM_checksums_init(param_file)
+  call MOM_debugging_init(param_file)
   call diag_mediator_infrastructure_init()
   call MOM_io_init(param_file)
 

src/core/MOM_CoriolisAdv.F90

@@ -149,6 +149,7 @@ subroutine CorAdCalc(u, v, h, uh, vh, CAu, CAv, OBC, AD, G, GV, CS)
     ep_u, ep_v  ! Additional pseudo-Coriolis terms in the Arakawa and Lamb
                 ! discretization, in m-1 s-1 or m2 kg-1 s-1.
   real, dimension(SZIB_(G),SZJB_(G)) :: &
+    dvdx,dudy, &! Contributions to the circulation around q-points (m2 s-1)
     abs_vort, & ! Absolute vorticity at q-points, in s-1.
     q2, &       ! Relative vorticity over thickness.
     max_fvq, &  ! The maximum or minimum of the
@@ -195,7 +196,7 @@ subroutine CorAdCalc(u, v, h, uh, vh, CAu, CAv, OBC, AD, G, GV, CS)
   real :: h_tiny        ! A very small thickness, in m or kg m-2.
   real :: UHeff, VHeff  ! More temporary variables, in m3 s-1 or kg s-1.
   real :: QUHeff,QVHeff ! More temporary variables, in m3 s-2 or kg s-2.
-  integer :: i, j, k, is, ie, js, je, Isq, Ieq, Jsq, Jeq, nz
+  integer :: i, j, k, n, is, ie, js, je, Isq, Ieq, Jsq, Jeq, nz
 
 ! To work, the following fields must be set outside of the usual
 ! is to ie range before this subroutine is called:
@@ -237,16 +238,43 @@ subroutine CorAdCalc(u, v, h, uh, vh, CAu, CAv, OBC, AD, G, GV, CS)
     ! are calculated.  hq is  second order accurate in space.  Relative
     ! vorticity is second order accurate everywhere with free slip b.c.s,
     ! but only first order accurate at boundaries with no slip b.c.s.
+    ! First calculate the contributions to the circulation around the q-point.
+    do J=Jsq-1,Jeq+1 ; do I=Isq-1,Ieq+1
+      dvdx(I,J) = v(i+1,J,k)*G%dyCv(i+1,J) - v(i,J,k)*G%dyCv(i,J)
+      dudy(I,J) = u(I,j+1,k)*G%dxCu(I,j+1) - u(I,j,k)*G%dxCu(I,j)
+    enddo ; enddo
+    ! Adjust circulation components to relative vorticity on open boundaries.
+    if (associated(OBC)) then ; if (OBC%zero_vorticity .or. OBC%freeslip_vorticity) then
+      do n=1,OBC%number_of_segments
+        if (OBC%segment(n)%is_N_or_S) then
+          J = OBC%segment(n)%HI%JsdB
+          do I=OBC%segment(n)%HI%IsdB,OBC%segment(n)%HI%IedB
+            if (OBC%zero_vorticity) then
+              dvdx(I,J) = 0.
+              dudy(I,J) = 0.
+            elseif (OBC%freeslip_vorticity) then
+              dudy(I,J) = 0.
+            endif
+          enddo
+        elseif (OBC%segment(n)%is_E_or_W) then
+          I = OBC%segment(n)%HI%IsdB
+          do J=OBC%segment(n)%HI%JsdB,OBC%segment(n)%HI%JedB
+            if (OBC%zero_vorticity) then
+              dvdx(I,J) = 0.
+              dudy(I,J) = 0.
+            elseif (OBC%freeslip_vorticity) then
+              dvdx(I,J) = 0.
+            endif
+          enddo
+        endif
+      enddo
+    endif ; endif
     do J=Jsq-1,Jeq+1 ; do I=Isq-1,Ieq+1
       if (CS%no_slip ) then
-        relative_vorticity = (2.0-G%mask2dBu(I,J)) * &
-           ((v(i+1,J,k)*G%dyCv(i+1,J) - v(i,J,k)*G%dyCv(i,J)) - &
-            (u(I,j+1,k)*G%dxCu(I,j+1) - u(I,j,k)*G%dxCu(I,j))) * &
+        relative_vorticity = (2.0-G%mask2dBu(I,J)) * (dvdx(I,J) - dudy(I,J)) * &
             (G%IdxBu(I,J) * G%IdyBu(I,J)) ! ### Using G%IareaBu(I,J) changes answers.
       else
-        relative_vorticity = G%mask2dBu(I,J) * &
-           ((v(i+1,J,k)*G%dyCv(i+1,J) - v(i,J,k)*G%dyCv(i,J)) - &
-            (u(I,j+1,k)*G%dxCu(I,j+1) - u(I,j,k)*G%dxCu(I,j))) * &
+        relative_vorticity = G%mask2dBu(I,J) * (dvdx(I,J) - dudy(I,J)) * &
             (G%IdxBu(I,J) * G%IdyBu(I,J)) ! ### Using G%IareaBu(I,J) changes answers.
       endif
       absolute_vorticity = G%CoriolisBu(I,J) + relative_vorticity
@@ -696,7 +724,7 @@ subroutine gradKE(u, v, h, uh, vh, KE, KEx, KEy, k, OBC, G, CS)
   real :: um, up, vm, vp         ! Temporary variables with units of m s-1.
   real :: um2, up2, vm2, vp2     ! Temporary variables with units of m2 s-2.
   real :: um2a, up2a, vm2a, vp2a ! Temporary variables with units of m4 s-2.
-  integer :: i, j, is, ie, js, je, Isq, Ieq, Jsq, Jeq, nz
+  integer :: i, j, is, ie, js, je, Isq, Ieq, Jsq, Jeq, nz, n
 
   is = G%isc ; ie = G%iec ; js = G%jsc ; je = G%jec ; nz = G%ke
   Isq = G%IscB ; Ieq = G%IecB ; Jsq = G%JscB ; Jeq = G%JecB
@@ -747,12 +775,17 @@ subroutine gradKE(u, v, h, uh, vh, KE, KEx, KEy, k, OBC, G, CS)
   enddo ; enddo
 
   if (associated(OBC)) then
-    do j=js,je ; do I=Isq,Ieq
-      if (OBC%OBC_segment_u(I,j)>0) KEx(I,j) = 0.
-    enddo ; enddo
-    do J=Jsq,Jeq ; do i=is,ie
-      if (OBC%OBC_segment_v(i,J)>0) KEy(i,J) = 0.
-    enddo ; enddo
+    do n=1,OBC%number_of_segments
+      if (OBC%segment(n)%is_N_or_S) then
+        do i=OBC%segment(n)%HI%isd,OBC%segment(n)%HI%ied
+          KEy(i,OBC%segment(n)%HI%JsdB) = 0.
+        enddo
+      elseif (OBC%segment(n)%is_E_or_W) then
+        do j=OBC%segment(n)%HI%jsd,OBC%segment(n)%HI%jed
+          KEx(OBC%segment(n)%HI%IsdB,j) = 0.
+        enddo
+      endif
+    enddo
   endif
 
 end subroutine gradKE