Merge pull request #677 from fvitt/physgrid_tem_diags

cam6_3_089:  TEM diagnostics calculated on the physics grid

bld/namelist_files/namelist_defaults_cam.xml

@@ -244,6 +244,7 @@
 
 <ncdata dyn="se" hgrid="ne5np4"   nlev="66"           ic_ymd="101">atm/waccm/ic/wa3_ne5np4_1950_spinup.cam2.i.1960-01-01-00000_c150810.nc</ncdata>
 <ncdata dyn="se" hgrid="ne30np4"  nlev="70"           ic_ymd="101">atm/waccm/ic/FW2000_ne30_L70_01-01-0001_c200602.nc</ncdata>
+<ncdata dyn="se" hgrid="ne30np4"  nlev="70"  npg="3" chem="waccm_sc_mam4">atm/waccm/ic/FWsc2000climo_ne30pg3_L70_0002-01-01_c221103.nc</ncdata>
 <ncdata dyn="se" hgrid="ne30np4"  nlev="70"  npg="3"  ic_ymd="101">atm/waccm/ic/FW2000_ne30pg3_L70_01-01-0001_c200602.nc</ncdata>
 <ncdata dyn="se" hgrid="ne30np4"  nlev="110"          ic_ymd="101">atm/waccm/ic/FWsc2000_ne30pg3_L110_01-01-0001_c200521.nc</ncdata>
 

bld/namelist_files/namelist_definition.xml

@@ -422,6 +422,24 @@ Default: .false.,  unless it is overridden (WACCM with interactive chemistry and
           configurations do this)
 </entry>
 
+<entry id="phys_grid_ctem_zm_nbas" type="integer"  category="diagnostics"
+       group="phys_grid_ctem_opts" valid_values="" >
+Number of zonal mean basis functions (number of m=0 spherical harmonics) used in
+Transformed Eulerian Mean (TEM) diagnostics
+</entry>
+
+<entry id="phys_grid_ctem_za_nlat" type="integer"  category="diagnostics"
+       group="phys_grid_ctem_opts" valid_values="" >
+Number of latitude grid points for zonal average TEM diagnostics history fields
+</entry>
+
+<entry id="phys_grid_ctem_nfreq" type="integer"  category="diagnostics"
+       group="phys_grid_ctem_opts" valid_values="" >
+  Frequency of TEM diagnostics calucation.
+  If &gt; 0, frequency is specified as number of timesteps.
+  If &lt; 0, frequency is specified as number of hours.
+</entry>
+
 <entry id="print_energy_errors" type="logical"  category="diagnostics"
        group="check_energy_nl" valid_values="" >
 Turn on verbose output identifying columns that fail energy/water

bld/namelist_files/use_cases/waccm_sc_2000_cam6.xml

@@ -11,7 +11,7 @@
 <solar_parms_data_file>atm/cam/solar/SolarForcing1995-2005avg_c160929.nc</solar_parms_data_file>
 
 <!--Species IC -->
-<ncdata dyn="fv"  hgrid="0.9x1.25">cesm2_init/f.e21.FWsc2000climo.f09_f09_mg17.cesm2.1-exp011.001/0003-01-01/f.e21.FWsc2000climo.f09_f09_mg17.cesm2.1-exp011.001.cam.i.0003-01-01-00000.nc</ncdata>
+<ncdata dyn="fv"  hgrid="0.9x1.25">cesm2_init/f.e21.FWsc2000climo.f09_f09_mg17.cesm2.1-exp011.001_v2/0003-01-01/f.e21.FWsc2000climo.f09_f09_mg17.cesm2.1-exp011.001_v2.cam.i.0003-01-01-00000.nc</ncdata>
 <ncdata dyn="fv"  hgrid="1.9x2.5" >atm/waccm/ic/f2000.waccm-mam3_1.9x2.5_L70.cam2.i.0017-01-01.c120410.nc</ncdata>
 
 <!-- LBC, UBC Files -->
@@ -91,7 +91,7 @@
 </srf_emis_specifier>
 
 <!-- History Files -->
-<do_circulation_diags>.true.</do_circulation_diags>
+<do_circulation_diags dyn="fv">.true.</do_circulation_diags>
 <history_chemistry>.true.</history_chemistry>
 
 <mfilt>             1,  30, 120, 240, 240, 480, 365,  73,  30  </mfilt>
@@ -109,7 +109,7 @@
 </fincl7>
 
 <!-- Reduce output size by removing some variables. -->
-<fexcl1>
+<fexcl1 dyn="fv">
  'BTAUN', 'BTAUS', 'BTAUE', 'BTAUW', 'BTAUNET', 'BUTEND1', 'BUTEND2', 'BUTEND3', 'BUTEND4', 'BUTEND5', 'BVTGWSPEC',
  'MAXQ0', 'HDEPTH', 'NETDT', 'TAUN', 'TAUS', 'TAUE', 'TAUW', 'TAUGWX', 'TAUGWY', 'UTEND1', 'UTEND2', 'UTEND3',
  'UTEND4', 'UTEND5', 'FRONTGF', 'FRONTGFA', 'EKGW', 'QNO', 'QRLNLTE', 'QRL_TOT', 'DUV', 'DVV', 'TTPXMLC'

cime_config/testdefs/testlist_cam.xml

@@ -738,6 +738,41 @@
       <option name="wallclock">00:30:00</option>
     </options>
   </test>
+<!-- TEM diagnostics and zonal-average output -->
+  <test compset="QPWmaC4" grid="ne5_ne5_mg37" name="SMS_D_Ln6_Vnuopc" testmods="cam/outfrq3s_physgrid_tem">
+    <machines>
+      <machine name="izumi" compiler="nag" category="aux_cam"/>
+      <machine name="izumi" compiler="nag" category="waccm"/>
+      <machine name="cheyenne" compiler="intel" category="waccm"/>
+      <machine name="izumi" compiler="nag" category="tem_diags"/>
+      <machine name="cheyenne" compiler="intel" category="tem_diags"/>
+    </machines>
+    <options>
+      <option name="comment" >TEM diagnostics and zonal-average output</option>
+      <option name="wallclock">00:10:00</option>
+    </options>
+  </test>
+  <test compset="FWsc2000climo" grid="mpasa120_mpasa120" name="ERS_Ld3_Vnuopc_P360x1" testmods="cam/outfrq1d_physgrid_tem_mpasa120_wcmsc">
+    <machines>
+      <machine name="cheyenne" compiler="intel" category="prealpha"/>
+      <machine name="cheyenne" compiler="intel" category="waccm"/>
+      <machine name="cheyenne" compiler="intel" category="tem_diags"/>
+   </machines>
+    <options>
+      <option name="comment" >TEM diagnostics and zonal-average output</option>
+      <option name="wallclock">00:20:00</option>
+    </options>
+  </test>
+  <test compset="FWsc2000climo" grid="f09_f09_mg17" name="ERP_Ln9_Vnuopc" testmods="cam/outfrq9s_physgrid_tem_1deg">
+    <machines>
+      <machine name="cheyenne" compiler="intel" category="waccm"/>
+      <machine name="cheyenne" compiler="intel" category="tem_diags"/>
+    </machines>
+    <options>
+      <option name="comment" >TEM diagnostics and zonal-average output</option>
+      <option name="wallclock">00:20:00</option>
+    </options>
+  </test>
 <!--              carma sulfate           -->
   <test compset="FW4ma2000" grid="f10_f10_mg37" name="SMS_D_Ln9_Vnuopc" testmods="cam/carma_sulfate">
     <machines>

cime_config/testdefs/testmods_dirs/cam/outfrq1d_physgrid_tem_mpasa120_wcmsc/shell_commands

@@ -0,0 +1,2 @@
+./xmlchange ROF_NCPL=\$ATM_NCPL
+./xmlchange LND_DOMAIN_FILE="domain.lnd.mpasa120_gx1v7.201215.nc"

cime_config/testdefs/testmods_dirs/cam/outfrq1d_physgrid_tem_mpasa120_wcmsc/user_nl_cam

@@ -0,0 +1,25 @@
+ncdata = '$DIN_LOC_ROOT/atm/waccm/ic/mpasa120km.waccm_fulltopo_c220818.nc'
+
+mpas_cam_coef = 0.2D0
+mpas_rayleigh_damp_u_timescale_days = 5.D0
+mpas_zd = 80000.0D0
+mpas_apvm_upwinding = 0.0D0
+mpas_dt = 600.D0
+mpas_dynamics_split_steps = 4
+mpas_epssm = 0.5D0
+
+use_gw_front = .false.
+
+phys_grid_ctem_nfreq = -12
+phys_grid_ctem_zm_nbas = 120
+phys_grid_ctem_za_nlat = 90
+
+fincl1 = ' '
+fexcl1 = ' '
+
+fincl2 = 'VTHzaphys','WTHzaphys','UVzaphys','UWzaphys'
+
+mfilt=1,1,1,1,1,1,1,1,1,1
+ndens=1,1,1,1,1,1,1,1,1,1
+nhtfrq=-24,-24,-24,-24,-24,-24,-24,-24,-24,-24
+inithist='ENDOFRUN'

cime_config/testdefs/testmods_dirs/cam/outfrq1d_physgrid_tem_mpasa120_wcmsc/user_nl_clm

@@ -0,0 +1,4 @@
+hist_nhtfrq = -24
+hist_mfilt  = 1
+hist_ndens  = 1
+fsurdat = '${DIN_LOC_ROOT}/lnd/clm2/surfdata_map/release-clm5.0.34/surfdata_mpasa120_hist_78pfts_CMIP6_simyr2000_c201215.nc'

cime_config/testdefs/testmods_dirs/cam/outfrq3s_physgrid_tem/shell_commands

@@ -0,0 +1,2 @@
+./xmlchange ROF_NCPL=\$ATM_NCPL
+./xmlchange GLC_NCPL=\$ATM_NCPL

cime_config/testdefs/testmods_dirs/cam/outfrq3s_physgrid_tem/user_nl_cam

@@ -0,0 +1,8 @@
+mfilt=1,1,1,1,1,1,1,1,1
+ndens=1,1,1,1,1,1,1,1,1
+nhtfrq=3,3,3,3,3,3,3,3,3
+inithist='ENDOFRUN'
+phys_grid_ctem_nfreq=3
+phys_grid_ctem_zm_nbas=16
+phys_grid_ctem_za_nlat=15
+fincl3 = 'VTHzaphys','WTHzaphys','UVzaphys','UWzaphys'

cime_config/testdefs/testmods_dirs/cam/outfrq3s_physgrid_tem/user_nl_clm

@@ -0,0 +1,26 @@
+!----------------------------------------------------------------------------------
+! Users should add all user specific namelist changes below in the form of
+! namelist_var = new_namelist_value
+!
+! Include namelist variables for drv_flds_in ONLY if -megan and/or -drydep options
+! are set in the CLM_NAMELIST_OPTS env variable.
+!
+! EXCEPTIONS:
+! Set use_cndv           by the compset you use and the CLM_BLDNML_OPTS -dynamic_vegetation setting
+! Set use_vichydro       by the compset you use and the CLM_BLDNML_OPTS -vichydro           setting
+! Set use_cn             by the compset you use and CLM_BLDNML_OPTS -bgc  setting
+! Set use_crop           by the compset you use and CLM_BLDNML_OPTS -crop setting
+! Set spinup_state       by the CLM_BLDNML_OPTS -bgc_spinup      setting
+! Set irrigate           by the CLM_BLDNML_OPTS -irrig           setting
+! Set dtime              with L_NCPL                             option
+! Set fatmlndfrc         with LND_DOMAIN_PATH/LND_DOMAIN_FILE    options
+! Set finidat            with RUN_REFCASE/RUN_REFDATE/RUN_REFTOD options for hybrid or branch cases
+!                        (includes $inst_string for multi-ensemble cases)
+! Set glc_grid           with CISM_GRID                          option
+! Set glc_smb            with GLC_SMB                            option
+! Set maxpatch_glcmec    with GLC_NEC                            option
+! Set glc_do_dynglacier  with GLC_TWO_WAY_COUPLING               env variable
+!----------------------------------------------------------------------------------
+hist_nhtfrq = 3
+hist_mfilt  = 1
+hist_ndens  = 1

cime_config/testdefs/testmods_dirs/cam/outfrq9s_physgrid_tem_1deg/shell_commands

@@ -0,0 +1,2 @@
+./xmlchange ROF_NCPL=\$ATM_NCPL
+./xmlchange GLC_NCPL=\$ATM_NCPL

cime_config/testdefs/testmods_dirs/cam/outfrq9s_physgrid_tem_1deg/user_nl_cam

@@ -0,0 +1,8 @@
+mfilt=1,1,1,1,1,1,1,1,1
+ndens=1,1,1,1,1,1,1,1,1
+nhtfrq=9,9,9,9,9,9,9,9,9
+inithist='ENDOFRUN'
+phys_grid_ctem_nfreq=-2
+phys_grid_ctem_zm_nbas=120
+phys_grid_ctem_za_nlat=90
+fincl3 = 'VTHzaphys','WTHzaphys','UVzaphys','UWzaphys'

cime_config/testdefs/testmods_dirs/cam/outfrq9s_physgrid_tem_1deg/user_nl_clm

@@ -0,0 +1,27 @@
+!----------------------------------------------------------------------------------
+! Users should add all user specific namelist changes below in the form of 
+! namelist_var = new_namelist_value 
+!
+! Include namelist variables for drv_flds_in ONLY if -megan and/or -drydep options
+! are set in the CLM_NAMELIST_OPTS env variable.
+!
+! EXCEPTIONS: 
+! Set use_cndv           by the compset you use and the CLM_BLDNML_OPTS -dynamic_vegetation setting
+! Set use_vichydro       by the compset you use and the CLM_BLDNML_OPTS -vichydro           setting
+! Set use_cn             by the compset you use and CLM_BLDNML_OPTS -bgc  setting
+! Set use_crop           by the compset you use and CLM_BLDNML_OPTS -crop setting
+! Set spinup_state       by the CLM_BLDNML_OPTS -bgc_spinup      setting
+! Set irrigate           by the CLM_BLDNML_OPTS -irrig           setting
+! Set dtime              with L_NCPL                             option
+! Set fatmlndfrc         with LND_DOMAIN_PATH/LND_DOMAIN_FILE    options
+! Set finidat            with RUN_REFCASE/RUN_REFDATE/RUN_REFTOD options for hybrid or branch cases
+!                        (includes $inst_string for multi-ensemble cases)
+! Set glc_grid           with CISM_GRID                          option
+! Set glc_smb            with GLC_SMB                            option
+! Set maxpatch_glcmec    with GLC_NEC                            option
+! Set glc_do_dynglacier  with GLC_TWO_WAY_COUPLING               env variable
+!----------------------------------------------------------------------------------
+hist_nhtfrq = 9
+hist_mfilt  = 1
+hist_ndens  = 1
+

doc/ChangeLog

@@ -1,5 +1,114 @@
 ===============================================================
 
+Tag name: cam6_3_089
+Originator(s): fvitt, patc
+Date: 10 Jan 2013
+One-line Summary: Introduce zonal mean and Transformed Eulerian Mean diagnostics capabilities on arbitrary grids
+Github PR URL: https://github.com/ESCOMP/CAM/pull/677
+
+Purpose of changes (include the issue number and title text for each relevant GitHub issue):
+
+ Add capability to calculate zonal mean of physics fields on arbatrary grids (structured or unstructured).
+ The synthesis of zonal mean values is based on m=0 spherical harmonics. (patc)
+
+ Implement TEM circulation diagnostics in physics #653
+ Need to add zonal mean grid to history for fields on arbitrary grids #652
+
+Describe any changes made to build system: N/A
+
+Describe any changes made to the namelist:
+
+ Namelist options added:
+
+   phys_grid_ctem_zm_nbas:
+     Number of zonal mean basis functions (number of m=0 spherical harmonics) used in
+     Transformed Eulerian Mean (TEM) diagnostics
+
+   phys_grid_ctem_za_nlat:
+     Number of latitude grid points for zonal average TEM diagnostics history fields
+
+   phys_grid_ctem_nfreq:
+     Frequency of TEM diagnostics calucation.
+     If > 0, frequency is specified as number of timesteps.
+     If < 0, frequency is specified as number of hours.
+
+List any changes to the defaults for the boundary datasets: N/A
+
+Describe any substantial timing or memory changes:
+
+  The physics grid TEM diagnostics is expected have a small impact (on the order of a few percent)
+  when activated.
+
+Code reviewed by: peverwhee, cacraigucar, nusbaume
+
+List all files eliminated: N/A
+
+List all files added and what they do:
+
+A	src/physics/cam/phys_grid_ctem.F90
+ - computes terms of the TEM diags on the physics grid
+
+A	src/utils/zonal_mean_mod.F90
+ - computes zonal means on arbitrary physics grids based on m=0 order spherical harmonics
+
+A	cime_config/testdefs/testmods_dirs/cam/outfrq1d_physgrid_tem_mpasa120_wcmsc/shell_commands
+A	cime_config/testdefs/testmods_dirs/cam/outfrq1d_physgrid_tem_mpasa120_wcmsc/user_nl_cam
+A	cime_config/testdefs/testmods_dirs/cam/outfrq1d_physgrid_tem_mpasa120_wcmsc/user_nl_clm
+A	cime_config/testdefs/testmods_dirs/cam/outfrq3s_physgrid_tem/shell_commands
+A	cime_config/testdefs/testmods_dirs/cam/outfrq3s_physgrid_tem/user_nl_cam
+A	cime_config/testdefs/testmods_dirs/cam/outfrq3s_physgrid_tem/user_nl_clm
+A	cime_config/testdefs/testmods_dirs/cam/outfrq9s_physgrid_tem_1deg/shell_commands
+A	cime_config/testdefs/testmods_dirs/cam/outfrq9s_physgrid_tem_1deg/user_nl_cam
+A	cime_config/testdefs/testmods_dirs/cam/outfrq9s_physgrid_tem_1deg/user_nl_clm
+ - for testing TEM diags on physics grids
+
+List all existing files that have been modified, and describe the changes:
+
+M	bld/namelist_files/namelist_definition.xml
+ - new phys_grid_ctem options (see above)
+
+M       bld/namelist_files/namelist_defaults_cam.xml
+ - update IC file for WACCM-SC on ne30pg3 grid (spun up stable IC file)
+
+M	bld/namelist_files/use_cases/waccm_sc_2000_cam6.xml
+ - correct IC file path for 0.9x1.25 grid
+
+M	cime_config/testdefs/testlist_cam.xml
+ - add tests for TEM diags on physics grids
+
+M	src/control/cam_comp.F90
+ - invoke phys_grid_ctem_reg
+
+M	src/control/runtime_opts.F90
+ - invoke phys_grid_ctem_readnl
+
+M	src/physics/cam/physpkg.F90
+ - invoke :
+    phys_grid_ctem_init
+    phys_grid_ctem_final
+    phys_grid_ctem_diags
+
+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: All PASS
+
+izumi/nag/aux_cam:
+  DAE_Vnuopc.f45_f45_mg37.FHS94.izumi_nag.cam-dae (Overall: FAIL) details:
+ - pre-existing failure
+
+  SMS_D_Ln6_Vnuopc.ne5_ne5_mg37.QPWmaC4.izumi_nag.cam-outfrq3s_physgrid_tem (Overall: DIFF) details:
+ - new test
+
+izumi/gnu/aux_cam: All PASS
+
+Summarize any changes to answers: bit-for-bit unchanged
+
+===============================================================
+===============================================================
+
 Tag name: cam6_3_088
 Originator(s): cacraig
 Date: Dec 21, 2022

src/control/cam_comp.F90

@@ -92,6 +92,7 @@ subroutine cam_init(                                             &
 #if (defined BFB_CAM_SCAM_IOP)
    use history_defaults, only: initialize_iop_history
 #endif
+   use phys_grid_ctem,   only: phys_grid_ctem_reg
 
    ! Arguments
    character(len=cl), intent(in) :: caseid                ! case ID
@@ -168,6 +169,9 @@ subroutine cam_init(                                             &
    ! Initialize physics grid decomposition
    call phys_grid_init()
 
+   ! Register zonal average grid for phys TEM diagnostics
+   call phys_grid_ctem_reg()
+
    ! Register advected tracers and physics buffer fields
    call phys_register ()
 

src/control/runtime_opts.F90

@@ -97,6 +97,7 @@ subroutine read_namelist(nlfilename, single_column, scmlat, scmlon)
    use qneg_module,         only: qneg_readnl
    use lunar_tides,         only: lunar_tides_readnl
    use upper_bc,            only: ubc_readnl
+   use phys_grid_ctem,      only: phys_grid_ctem_readnl
 
    !---------------------------Arguments-----------------------------------
 
@@ -195,6 +196,7 @@ subroutine read_namelist(nlfilename, single_column, scmlat, scmlon)
    call dyn_readnl(nlfilename)
    call ionosphere_readnl(nlfilename)
    call qneg_readnl(nlfilename)
+   call phys_grid_ctem_readnl(nlfilename)
 
 end subroutine read_namelist