cam6_3_020: MPAS bug fixes, performance enhancements, allow initial files writes, refactor/cleanup

bld/build-namelist

@@ -3701,21 +3701,6 @@ if ($dyn =~ /mpas/) {
         add_default($nl, 'mpas_block_decomp_file_prefix');
     }
 
-    # invoke MPAS utility to generate streams files
-    my $mpas_libdir = $cfg->get('mpas_libdir');
-
-    # Check that the executable file streams_gen is present.  streams_gen is built
-    # at the same time as the MPAS library.  This allows build-namelist
-    # to be called before the MPAS library is built (via CESM scripts).
-    if ( -x "$mpas_libdir/streams_gen") {
-
-        my $cmnd = "$mpas_libdir/streams_gen $mpas_libdir/Registry_processed.xml ".
-               "streams.atmosphere stream_list.atmosphere. listed ";
-
-        system($cmnd) == 0 or die
-            "$ProgName - ERROR: generating MPAS streams files via command:\n".
-            "$cmnd";
-    }
 }
 
 # Defaults for history output

bld/namelist_files/namelist_defaults_cam.xml

@@ -43,8 +43,8 @@
 <ncdata nlev="32" analytic_ic="1" >atm/cam/inic/cam_vcoords_L32_c180105.nc</ncdata>
 
 <!-- Vertical coordinates and grid only -->
-<ncdata hgrid="mpasa480" nlev="32" analytic_ic="1" >atm/cam/inic/mpas/mpasa480_L32_v6.1.grid_c190924.nc</ncdata>
-<ncdata hgrid="mpasa120" nlev="32" analytic_ic="1" >atm/cam/inic/mpas/mpasa120_L32_topo_grid_c201022.nc</ncdata>
+<ncdata hgrid="mpasa480" nlev="32" analytic_ic="1" >atm/cam/inic/mpas/mpasa480_L32_notopo_grid_c201125.nc</ncdata>
+<ncdata hgrid="mpasa120" nlev="32" analytic_ic="1" >atm/cam/inic/mpas/mpasa120_L32_notopo_grid_c201216.nc</ncdata>
 
 <!-- Files with initial conditions -->
 <ncdata dyn="fv"  hgrid="0.23x0.31" nlev="26" ic_ymd="101"      >atm/cam/inic/fv/cami_0000-01-01_0.23x0.31_L26_c100513.nc</ncdata>
@@ -2684,7 +2684,7 @@
 <mpas_time_integration        > SRK3 </mpas_time_integration>
 <mpas_time_integration_order  > 2 </mpas_time_integration_order>
 <mpas_dt                      > 1800.0D0 </mpas_dt>
-<mpas_dt hgrid="mpasa120"     >  600.0D0 </mpas_dt>
+<mpas_dt hgrid="mpasa120"     >  900.0D0 </mpas_dt>
 
 <mpas_split_dynamics_transport>.true.</mpas_split_dynamics_transport>
 <mpas_number_of_sub_steps     > 2 </mpas_number_of_sub_steps>
@@ -2712,7 +2712,7 @@
 <mpas_scalar_advection        > .true. </mpas_scalar_advection>
 <mpas_positive_definite       > .false. </mpas_positive_definite>
 <mpas_monotonic               > .true. </mpas_monotonic>
-<mpas_coef_3rd_order          > 0.25D0 </mpas_coef_3rd_order>
+<mpas_coef_3rd_order          > 1.0D0 </mpas_coef_3rd_order>
 <mpas_smagorinsky_coef        > 0.125D0 </mpas_smagorinsky_coef>
 <mpas_mix_full                > .true. </mpas_mix_full>
 <mpas_epssm                   > 0.1D0 </mpas_epssm>

doc/ChangeLog

@@ -1,5 +1,129 @@
 ===============================================================
 
+Tag name:
+Originator(s):
+Date:
+One-line Summary:
+Github PR URL:
+
+Purpose of changes (include the issue number and title text for each relevant GitHub issue):
+
+. Remove unused code in build-namelist for generating MPAS streams files.
+
+. Fix to allow MPAS to run with 1 task.
+
+. Fix to allow MPAS to run with NAG/debug.
+
+. Replace bad grid file for running 480-km res with no topo.
+
+. Fix for bug when MPAS dycore is substepping during physics timestep.
+
+. Update calculation of hydrostatic pressure from MPAS state.
+
+. Add ability to write initial file when using MPAS dycore.
+
+Describe any changes made to build system:
+
+Describe any changes made to the namelist:
+
+List any changes to the defaults for the boundary datasets:
+
+Describe any substantial timing or memory changes:
+
+Code reviewed by:
+
+List all files eliminated:
+
+List all files added and what they do:
+
+List all existing files that have been modified, and describe the changes:
+
+bld/build-namelist
+. remove code that executes the mpas streams_gen utility.  It's not being
+  used.
+
+bld/namelist_files/namelist_defaults_cam.xml
+. replace mpas grid file mpasa480_L32_v6.1.grid_c190924.nc by
+  mpasa480_L32_notopo_grid_c201125.nc
+. new defaults: longer time step, change 3rd-order scalar transport upwind coefficient
+	mpas_dt 600s => 900s
+	mpas_coef_3rd_order 0.25 => 1.0
+
+src/dynamics/mpas/dyn_comp.F90
+. Add target attribute to the module data arrays for height which are
+  pointed to by the hist_coords objects in the cam_history_support module.
+  NAG/debug requires this.
+. remove the variable swap_time_level_ptrs
+. cam_mpas_namelist_read
+  - allow the &decomposition namelist group to be missing by removing the
+    endrun call.  When running with 1 task the partition file specified in
+    this group is not read.
+. dyn_init
+  - change the dyn_out components with 2 time levels to point to the same
+    memory locations as the dyn_in components
+  - remove the code that copied dyn_in to dyn_out.  The dyn_out pointers now point
+    to the same memory locations as the dyn_in pointers.
+  - remove setting swap_time_level_ptrs  
+. dyn_run
+  - after call to cam_mpas_run update the dyn_in/dyn_out pointers to point
+    to the MPAS current state in pool arrays with timeLevel=1
+. read_inidat
+  - update computation of hydrostatic pressure profiles.
+. set_base_state
+  - update computation of hydrostatic pressure used by base state.
+
+src/dynamics/mpas/stepon.F90
+. stepon_run1
+  - remove code to swap pointers after d_p_coupling
+. shift_time_levels
+  - remove this routine.  no longer needed.
+. write_initial_file
+  - new subroutine to generate the initial filename, open a pio filehandle
+    to that file, and call the same mpas routines that are used to write to
+    the restart file. 
+. write_dynvar
+  - add conditional using write_inithist to call write_initial_file and
+    have MPAS write the initial file.
+
+
+If there were any failures reported from running test_driver.sh on any test
+platform, and checkin with these failures has been OK'd by the gatekeeper,
+then copy the lines from the td.*.status files for the failed tests to the
+appropriate machine below.  All failed tests must be justified.
+
+cheyenne/intel/aux_cam:
+
+izumi/nag/aux_cam:
+
+izumi/pgi/aux_cam:
+
+CAM tag used for the baseline comparison tests if different than previous
+tag:
+
+Summarize any changes to answers, i.e.,
+- what code configurations:
+- what platforms/compilers:
+- nature of change (roundoff; larger than roundoff but same climate; new
+  climate):
+
+If bitwise differences were observed, how did you show they were no worse
+than roundoff?
+
+If this tag changes climate describe the run(s) done to evaluate the new
+climate in enough detail that it(they) could be reproduced, i.e.,
+- source tag (all code used must be in the repository):
+- platform/compilers:
+- configure commandline:
+- build-namelist command (or complete namelist):
+- MSS location of output:
+
+MSS location of control simulations used to validate new climate:
+
+URL for AMWG diagnostics output used to validate new climate:
+
+===============================================================
+===============================================================
+
 Tag name: cam6_3_006
 Originator(s): herrington, cacraig
 Date: Dec 3, 2020