Merge pull request ESCOMP#992 from cacraigucar/cam_zm_clean_up

cam6_3_158: ZM clean up round 2 for CAM
bstephens82 · Apr 22, 2024 · 776400d · 776400d
2 parents 82ed900 + 963876d
commit 776400d
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diff --git a/.gitignore b/.gitignore
@@ -14,7 +14,7 @@ src/physics/pumas
 src/physics/pumas-frozen
 src/physics/rrtmgp/data
 src/physics/rrtmgp/ext
-src/dynamics/fv3/atmos_cubed_sphere
+src/dynamics/fv3
 libraries/FMS
 libraries/mct
 libraries/parallelio

diff --git a/Externals.cfg b/Externals.cfg
@@ -64,7 +64,7 @@ local_path = libraries/parallelio
 required = True
 
 [cime]
-tag = cime6.0.217_httpsbranch02
+tag = cime6.0.236_httpsbranch01
 protocol = git
 repo_url = https://github.com/ESMCI/cime
 local_path = cime

diff --git a/Externals_CAM.cfg b/Externals_CAM.cfg
@@ -50,7 +50,7 @@ tag = ALI_ARMS_v1.0.1
 required = True
 
 [atmos_phys]
-tag = atmos_phys0_02_000
+tag = atmos_phys0_02_006
 protocol = git
 repo_url = https://github.com/ESCOMP/atmospheric_physics
 required = True

diff --git a/bld/configure b/bld/configure
@@ -2189,9 +2189,9 @@ sub write_filepath
     if ($chem_src_dir) {
         print $fh "$chem_src_dir\n";
     }
- 
+
     # GEOS-Chem must be prior to Mozart
-    if ($chem_pkg =~ 'geoschem') {	
+    if ($chem_pkg =~ 'geoschem') {
 	print $fh "$chem_src_dir/geoschem_src/GeosCore\n";
 	print $fh "$chem_src_dir/geoschem_src/GeosUtil\n";
 	print $fh "$chem_src_dir/geoschem_src/Headers\n";
@@ -2303,7 +2303,7 @@ sub write_filepath
     print $fh "$camsrcdir/src/physics/cam\n";
 
     #Add the CCPP'ized subdirectories
-    print $fh "$camsrcdir/src/atmos_phys/zm\n";
+    print $fh "$camsrcdir/src/atmos_phys/zhang_mcfarlane\n";
 
     # Dynamics package and test utilities
     print $fh "$camsrcdir/src/dynamics/$dyn\n";

diff --git a/doc/ChangeLog b/doc/ChangeLog
@@ -1,3 +1,80 @@
+
+===============================================================
+
+Tag name: cam6_3_158
+Originator(s): cacraig
+Date: April 22, 2024
+One-line Summary: ZM clean up round 2 for CAM and cime update for GEOS-Chem
+Github PR URL: https://github.com/ESCOMP/CAM/pull/992
+
+Purpose of changes (include the issue number and title text for each relevant GitHub issue):
+ - change zm directory to be zhang_mcfarlane:  https://github.com/ESCOMP/CAM/issues/965
+ - Reimplement writing within ZM and remove pflx variable: https://github.com/ESCOMP/CAM/issues/978
+ - ZM cleanup: https://github.com/ESCOMP/CAM/issues/984
+ - Tag cam6_3_157 missing updated .gitignore: https://github.com/ESCOMP/CAM/issues/1012
+ - GEOS-Chem compsets will fail due to bugs in CAM and CIME: https://github.com/ESCOMP/CAM/issues/1004
+
+Describe any changes made to build system: N/A
+
+Describe any changes made to the namelist: N/A
+
+List any changes to the defaults for the boundary datasets: N/A
+
+Describe any substantial timing or memory changes: N/A
+
+Code reviewed by: nusbaume
+
+List all files eliminated: N/A
+
+List all files added and what they do: N/A
+
+List all existing files that have been modified, and describe the changes:
+M       .gitignore
+          - Update FV3 listing
+
+M       externals.cfg
+          - Update cime to bring in bug fix for GEOS-Chem
+
+M       Externals_CAM.cfg
+          - Update atmospheric_physics external to bring in changes for ZM
+
+M       bld/configure
+          - Change directory from zm to zhang-mcfarlane
+
+M       src/physics/cam/cam_snapshot.F90
+M       src/physics/cam/convect_deep.F90
+M       src/physics/cam/physpkg.F90
+M       src/physics/cam_dev/cam_snapshot.F90
+M       src/physics/cam_dev/physpkg.F90
+          - Remove pflx variable which is not used
+
+M       src/physics/cam/zm_conv_intr.F90
+          - Split winds into separate variable
+	  - remove pflx
+	  - reintroduce writing within ZM
+
+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.
+
+derecho/intel/aux_cam: all BFB, except:
+  ERP_Ln9.f09_f09_mg17.FCSD_HCO.derecho_intel.cam-outfrq9s (Overall: FAIL) details:
+    - pre-existing failure
+
+  SMS_Lh12.f09_f09_mg17.FCSD_HCO.derecho_intel.cam-outfrq3h (Overall: DIFF) details:
+    - Answer change for HEMCO - approved by Francis and Lizzie due to HEMCO giving different answers when layout changes are made
+
+  SMS_Ld1.f09_f09_mg17.FCHIST_GC.derecho_intel.cam-outfrq1d (Overall: DIFF) details:
+     - no previous baseline
+
+izumi/nag/aux_cam:
+  DAE.f45_f45_mg37.FHS94.izumi_nag.cam-dae (Overall: FAIL) details:
+     - pre-existing failure
+
+izumi/gnu/aux_cam: all BFB
+
+===============================================================
 ===============================================================
 
 Tag name: cam6_3_157

diff --git a/src/physics/cam/cam_snapshot.F90 b/src/physics/cam/cam_snapshot.F90
@@ -58,7 +58,7 @@ subroutine cam_snapshot_init(cam_in_arr, cam_out_arr, pbuf, index)
 
    call phys_getopts(cam_snapshot_before_num_out = cam_snapshot_before_num, &
                      cam_snapshot_after_num_out  = cam_snapshot_after_num)
-                     
+
 
    ! Return if not turned on
    if (cam_snapshot_before_num <= 0 .and. cam_snapshot_after_num <= 0) return ! No snapshot files are being requested
@@ -76,7 +76,7 @@ subroutine cam_snapshot_init(cam_in_arr, cam_out_arr, pbuf, index)
 end subroutine cam_snapshot_init
 
 subroutine cam_snapshot_all_outfld_tphysbc(file_num, state, tend, cam_in, cam_out, pbuf, flx_heat, cmfmc, cmfcme, &
-        pflx, zdu, rliq, rice, dlf, dlf2, rliq2, det_s, det_ice, net_flx)
+        zdu, rliq, rice, dlf, dlf2, rliq2, det_s, det_ice, net_flx)
 
 use time_manager,   only: is_first_step, is_first_restart_step
 
@@ -95,7 +95,6 @@ subroutine cam_snapshot_all_outfld_tphysbc(file_num, state, tend, cam_in, cam_ou
    real(r8),            intent(in) :: flx_heat(:)   ! Heat flux for check_energy_chng.
    real(r8),            intent(in) :: cmfmc(:,:)    ! convective mass flux
    real(r8),            intent(in) :: cmfcme(:,:)   ! cmf condensation - evaporation
-   real(r8),            intent(in) :: pflx(:,:)     ! convective rain flux throughout bottom of level
    real(r8),            intent(in) :: zdu(:,:)      ! detraining mass flux from deep convection
    real(r8),            intent(in) :: rliq(:)       ! vertical integral of liquid not yet in q(ixcldliq)
    real(r8),            intent(in) :: rice(:)       ! vertical integral of ice not yet in q(ixcldice)
@@ -111,15 +110,14 @@ subroutine cam_snapshot_all_outfld_tphysbc(file_num, state, tend, cam_in, cam_ou
    ! Return if the first timestep as not all fields may be filled in and this will cause a core dump
    if (is_first_step().or. is_first_restart_step()) return
 
-   ! Return if not turned on 
+   ! Return if not turned on
    if (cam_snapshot_before_num <= 0 .and. cam_snapshot_after_num <= 0) return ! No snapshot files are being requested
 
    lchnk = state%lchnk
 
    call outfld('tphysbc_flx_heat', flx_heat, pcols, lchnk)
    call outfld('tphysbc_cmfmc', cmfmc, pcols, lchnk)
    call outfld('tphysbc_cmfcme', cmfcme, pcols, lchnk)
-   call outfld('tphysbc_pflx', pflx, pcols, lchnk)
    call outfld('tphysbc_zdu', zdu, pcols, lchnk)
    call outfld('tphysbc_rliq', rliq, pcols, lchnk)
    call outfld('tphysbc_rice', rice, pcols, lchnk)
@@ -160,7 +158,7 @@ subroutine cam_snapshot_all_outfld_tphysac(file_num, state, tend, cam_in, cam_ou
    ! Return if the first timestep as not all fields may be filled in and this will cause a core dump
    if (is_first_step()) return
 
-   ! Return if not turned on 
+   ! Return if not turned on
    if (cam_snapshot_before_num <= 0 .and. cam_snapshot_after_num <= 0) return ! No snapshot files are being requested
 
    lchnk = state%lchnk
@@ -182,7 +180,7 @@ subroutine cam_tphysbc_snapshot_init(cam_snapshot_before_num, cam_snapshot_after
 !--------------------------------------------------------
 
    integer,intent(in) :: cam_snapshot_before_num, cam_snapshot_after_num
-    
+
    ntphysbc_var = 0
 
    !--------------------------------------------------------
@@ -199,9 +197,6 @@ subroutine cam_tphysbc_snapshot_init(cam_snapshot_before_num, cam_snapshot_after
    call snapshot_addfld( ntphysbc_var, tphysbc_snapshot,  cam_snapshot_before_num, cam_snapshot_after_num, &
      'cmfcme',        'tphysbc_cmfcme',         'unset',              'lev')
 
-   call snapshot_addfld( ntphysbc_var, tphysbc_snapshot,  cam_snapshot_before_num, cam_snapshot_after_num, &
-     'pflx',        'tphysbc_pflx',         'unset',              'lev')
-
    call snapshot_addfld( ntphysbc_var, tphysbc_snapshot,  cam_snapshot_before_num, cam_snapshot_after_num, &
      'zdu',        'tphysbc_zdu',         'unset',              'lev')
 
@@ -240,7 +235,7 @@ subroutine cam_tphysac_snapshot_init(cam_snapshot_before_num, cam_snapshot_after
 !--------------------------------------------------------
 
    integer,intent(in) :: cam_snapshot_before_num, cam_snapshot_after_num
-    
+
    ntphysac_var = 0
 
    !--------------------------------------------------------

diff --git a/src/physics/cam/convect_deep.F90 b/src/physics/cam/convect_deep.F90
@@ -5,7 +5,7 @@ module convect_deep
 !
 ! CAM interface to several deep convection interfaces. Currently includes:
 !    Zhang-McFarlane (default)
-!    Kerry Emanuel 
+!    Kerry Emanuel
 !
 !
 ! Author: D.B. Coleman, Sep 2004
@@ -28,34 +28,34 @@ module convect_deep
       convect_deep_tend,               &! return tendencies
       convect_deep_tend_2,             &! return tendencies
       deep_scheme_does_scav_trans             ! = .t. if scheme does scavenging and conv. transport
-   
+
 ! Private module data
    character(len=16) :: deep_scheme    ! default set in phys_control.F90, use namelist to change
-! Physics buffer indices 
-   integer     ::  icwmrdp_idx      = 0 
-   integer     ::  rprddp_idx       = 0 
-   integer     ::  nevapr_dpcu_idx  = 0 
-   integer     ::  cldtop_idx       = 0 
-   integer     ::  cldbot_idx       = 0 
-   integer     ::  cld_idx          = 0 
-   integer     ::  fracis_idx       = 0 
-
-   integer     ::  pblh_idx        = 0 
-   integer     ::  tpert_idx       = 0 
+! Physics buffer indices
+   integer     ::  icwmrdp_idx      = 0
+   integer     ::  rprddp_idx       = 0
+   integer     ::  nevapr_dpcu_idx  = 0
+   integer     ::  cldtop_idx       = 0
+   integer     ::  cldbot_idx       = 0
+   integer     ::  cld_idx          = 0
+   integer     ::  fracis_idx       = 0
+
+   integer     ::  pblh_idx        = 0
+   integer     ::  tpert_idx       = 0
    integer     ::  prec_dp_idx     = 0
    integer     ::  snow_dp_idx     = 0
 
    integer     ::  ttend_dp_idx        = 0
 
 !=========================================================================================
-  contains 
+  contains
 
 !=========================================================================================
 function deep_scheme_does_scav_trans()
 !
 ! Function called by tphysbc to determine if it needs to do scavenging and convective transport
 ! or if those have been done by the deep convection scheme. Each scheme could have its own
-! identical query function for a less-knowledgable interface but for now, we know that KE 
+! identical query function for a less-knowledgable interface but for now, we know that KE
 ! does scavenging & transport, and ZM doesn't
 !
 
@@ -76,7 +76,7 @@ subroutine convect_deep_register
 ! Purpose: register fields with the physics buffer
 !----------------------------------------
 
-  
+
   use physics_buffer, only : pbuf_add_field, dtype_r8
   use zm_conv_intr, only: zm_conv_register
   use phys_control, only: phys_getopts, use_gw_convect_dp
@@ -118,12 +118,12 @@ subroutine convect_deep_init(pref_edge)
 ! Purpose:  declare output fields, initialize variables needed by convection
 !----------------------------------------
 
-  use cam_history,    only: addfld                          
+  use cam_history,    only: addfld
   use pmgrid,         only: plevp
   use spmd_utils,     only: masterproc
   use zm_conv_intr,   only: zm_conv_init
   use cam_abortutils, only: endrun
-  
+
   use physics_buffer, only: physics_buffer_desc, pbuf_get_index
 
   implicit none
@@ -169,14 +169,14 @@ end subroutine convect_deep_init
 
 subroutine convect_deep_tend( &
      mcon    ,cme     ,          &
-     pflx    ,zdu      , &
+     zdu      , &
      rliq    ,rice     , &
      ztodt   , &
      state   ,ptend   ,landfrac ,pbuf)
 
 
    use physics_types, only: physics_state, physics_ptend, physics_tend, physics_ptend_init
-   
+
    use cam_history,    only: outfld
    use constituents,   only: pcnst
    use zm_conv_intr,   only: zm_conv_tend
@@ -187,27 +187,26 @@ subroutine convect_deep_tend( &
 ! Arguments
    type(physics_state), intent(in ) :: state   ! Physics state variables
    type(physics_ptend), intent(out) :: ptend   ! individual parameterization tendencies
-   
+
 
    type(physics_buffer_desc), pointer :: pbuf(:)
    real(r8), intent(in) :: ztodt               ! 2 delta t (model time increment)
    real(r8), intent(in) :: landfrac(pcols)     ! Land fraction
-      
+
 
    real(r8), intent(out) :: mcon(pcols,pverp)  ! Convective mass flux--m sub c
-   real(r8), intent(out) :: pflx(pcols,pverp)  ! scattered precip flux at each level
    real(r8), intent(out) :: cme(pcols,pver)    ! cmf condensation - evaporation
    real(r8), intent(out) :: zdu(pcols,pver)    ! detraining mass flux
 
    real(r8), intent(out) :: rliq(pcols) ! reserved liquid (not yet in cldliq) for energy integrals
    real(r8), intent(out) :: rice(pcols) ! reserved ice (not yet in cldice) for energy integrals
 
    real(r8), pointer :: prec(:)   ! total precipitation
-   real(r8), pointer :: snow(:)   ! snow from ZM convection 
+   real(r8), pointer :: snow(:)   ! snow from ZM convection
 
    real(r8), pointer, dimension(:) :: jctop
    real(r8), pointer, dimension(:) :: jcbot
-   real(r8), pointer, dimension(:,:,:) :: cld        
+   real(r8), pointer, dimension(:,:,:) :: cld
    real(r8), pointer, dimension(:,:) :: ql        ! wg grid slice of cloud liquid water.
    real(r8), pointer, dimension(:,:) :: rprd      ! rain production rate
    real(r8), pointer, dimension(:,:,:) :: fracis  ! fraction of transported species that are insoluble
@@ -230,9 +229,8 @@ subroutine convect_deep_tend( &
 
   select case ( deep_scheme )
   case('off', 'UNICON', 'CLUBB_SGS') ! in UNICON case the run method is called from convect_shallow_tend
-    zero = 0     
+    zero = 0
     mcon = 0
-    pflx = 0
     cme = 0
     zdu = 0
     rliq = 0
@@ -244,7 +242,7 @@ subroutine convect_deep_tend( &
 ! Associate pointers with physics buffer fields
 !
 
-    call pbuf_get_field(pbuf, cld_idx,         cld,    start=(/1,1/),   kount=(/pcols,pver/) ) 
+    call pbuf_get_field(pbuf, cld_idx,         cld,    start=(/1,1/),   kount=(/pcols,pver/) )
     call pbuf_get_field(pbuf, rprddp_idx,      rprd )
     call pbuf_get_field(pbuf, fracis_idx,      fracis, start=(/1,1,1/), kount=(/pcols, pver, pcnst/) )
     call pbuf_get_field(pbuf, nevapr_dpcu_idx, evapcdp )
@@ -267,7 +265,7 @@ subroutine convect_deep_tend( &
      call pbuf_get_field(pbuf, tpert_idx, tpert)
 
      call zm_conv_tend( pblh    ,mcon    ,cme     , &
-          tpert   ,pflx    ,zdu      , &
+          tpert   ,zdu      , &
           rliq    ,rice    , &
           ztodt   , &
           jctop, jcbot , &
@@ -291,22 +289,22 @@ end subroutine convect_deep_tend
 subroutine convect_deep_tend_2( state,  ptend,  ztodt, pbuf)
 
    use physics_types, only: physics_state, physics_ptend, physics_ptend_init
-   
+
    use physics_buffer,  only: physics_buffer_desc
    use constituents, only: pcnst
    use zm_conv_intr, only: zm_conv_tend_2
 
 ! Arguments
    type(physics_state), intent(in ) :: state          ! Physics state variables
    type(physics_ptend), intent(out) :: ptend          ! indivdual parameterization tendencies
-   
+
    type(physics_buffer_desc), pointer :: pbuf(:)
 
    real(r8), intent(in) :: ztodt                          ! 2 delta t (model time increment)
 
 
    if ( deep_scheme .eq. 'ZM' ) then  ! Zhang-McFarlane
-      call zm_conv_tend_2( state,   ptend,  ztodt,  pbuf) 
+      call zm_conv_tend_2( state,   ptend,  ztodt,  pbuf)
    else
       call physics_ptend_init(ptend, state%psetcols, 'convect_deep')
    end if