Merge pull request ESCOMP#891 from nusbaume/atmos_phys_update

cam6_3_134: Update atmospheric_physics external

Externals_CAM.cfg

@@ -55,9 +55,9 @@ tag = ALI_ARMS_v1.0.1
 required = True
 
 [atmos_phys]
-tag = atmos_phys0_00_011
+tag = atmos_phys0_01_000
 protocol = git
-repo_url = https://github.com/NCAR/atmospheric_physics
+repo_url = https://github.com/ESCOMP/atmospheric_physics
 required = True
 local_path = src/atmos_phys
 

bld/configure

@@ -2269,6 +2269,7 @@ sub write_filepath
     print $fh "$camsrcdir/src/cpl/$cpl\n";
     print $fh "$camsrcdir/src/control\n";
     print $fh "$camsrcdir/src/utils\n";
+    print $fh "$camsrcdir/src/utils/cam_ccpp\n";
     print $fh "$camsrcdir/src/atmos_phys/utilities\n";
 
 

doc/ChangeLog

@@ -1,5 +1,133 @@
 ===============================================================
 
+Tag name: cam6_3_134
+Originator(s): nusbaume, jimmielin
+Date: 31 Oct 2023
+One-line Summary: Update atmospheric_physics external
+Github PR URL: https://github.com/ESCOMP/CAM/pull/891
+
+Purpose of changes (include the issue number and title text for each relevant GitHub issue):
+
+This PR updates the atmospheric_physics external in CAM,
+which requires some source modifications on the CAM-side.
+There has also been some replacement of CAM code with CCPP
+physics routines in order to reduce duplication.
+
+This PR also fixes a bug found in Kessler where it was using
+the wrong pressure when converting to/from potential temperature
+via the exner function.
+
+Finally, this change also brings in a rename of the SE
+dycore's 'time_mod' module to 'se_dyn_time_mod' in order
+to avoid name collision with GEOS-Chem code.
+
+Fixes #752  -> Update atmospheric_physics external
+Fixes #802  -> Kessler physics using inconsistent reference pressures
+
+Closes #904 -> Rename SE dycore time_mod to dyn_time_mod (PR)
+
+Describe any changes made to build system:
+
+Added the "src/utils/cam_ccpp" and "src/atmos_phys/utilities" directory
+to the list of directories used during compilation.
+
+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: cacraigucar, PeterHjortLauritzen, jtruesdal, peverwhee
+
+List all files eliminated:
+
+R       src/dynamics/se/dycore/time_mod.F90
+ - Renamed to 'se_dyn_time_mod'
+R       src/utils/ccpp_kinds.F90
+ - Moved to 'src/utils/cam_ccpp/ccpp_kinds.F90'
+
+List all files added and what they do:
+
+A       src/utils/cam_ccpp/ccpp_constituent_prop_mod.F90
+ - Creates a "CCPP Constituent Properties" object for CAM.
+
+List all existing files that have been modified, and describe the changes:
+
+M       Externals_CAM.cfg
+ - Update 'atmospheric_physics' external
+
+M       bld/configure
+ - Add 'src/utils/cam_ccpp' and 'src/atmos_phys/utilities' to build file paths
+
+M       src/dynamics/se/dp_coupling.F90
+ - Use CCPP-ized 'update_dry_static_energy_run' subroutine
+
+M       src/physics/cam/geopotential.F90
+ - Use CCPP-ized 'geopotential_temp_run' subroutine
+
+M       src/physics/cam/ref_pres.F90
+ - Update comment in order to avoid future confusion
+
+M       src/physics/cam/physpkg.F90
+M       src/physics/cam_dev/physpkg.F90
+M       src/physics/simple/held_suarez_cam.F90
+M       src/physics/simple/physpkg.F90
+ - Update physics calls and add new const. prop. DDT to work with new
+   atmospheric_physics external
+
+M       src/physics/simple/kessler_cam.F90
+- Update physics calls and add new const. prop. DDT to work with new
+  atmospheric_physics external.  Also replace use of "standard pressure"
+  with "reference pressure" in order to avoid unphysical mismatches.
+
+M       src/dynamics/se/dycore/fvm_consistent_se_cslam.F90
+M       src/dynamics/se/dycore/prim_advance_mod.F90
+M       src/dynamics/se/dycore/prim_advection_mod.F90
+M       src/dynamics/se/dycore/prim_driver_mod.F90
+M       src/dynamics/se/dycore/prim_init.F90
+M       src/dynamics/se/dycore/prim_state_mod.F90
+M       src/dynamics/se/stepon.F90
+ - Replace 'time_mod' with 'se_dyn_time_mod'
+
+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 tests have NLCOMP failures due to changes in input data paths on Cheyenne.
+
+ ERP_Ln9_Vnuopc.C96_C96_mg17.F2000climo.cheyenne_intel.cam-outfrq9s_mg3 (Overall: FAIL) details:
+    FAIL ERP_Ln9_Vnuopc.C96_C96_mg17.F2000climo.cheyenne_intel.cam-outfrq9s_mg3 NLCOMP
+    FAIL ERP_Ln9_Vnuopc.C96_C96_mg17.F2000climo.cheyenne_intel.cam-outfrq9s_mg3 MODEL_BUILD time=3
+ ERP_Ln9_Vnuopc.f09_f09_mg17.FCSD_HCO.cheyenne_intel.cam-outfrq9s (Overall: FAIL) details:
+    FAIL ERP_Ln9_Vnuopc.f09_f09_mg17.FCSD_HCO.cheyenne_intel.cam-outfrq9s NLCOMP
+    FAIL ERP_Ln9_Vnuopc.f09_f09_mg17.FCSD_HCO.cheyenne_intel.cam-outfrq9s COMPARE_base_rest
+ SMS_Lh12_Vnuopc.f09_f09_mg17.FCSD_HCO.cheyenne_intel.cam-outfrq3h (Overall: DIFF) details:
+    FAIL SMS_Lh12_Vnuopc.f09_f09_mg17.FCSD_HCO.cheyenne_intel.cam-outfrq3h NLCOMP
+    FAIL SMS_Lh12_Vnuopc.f09_f09_mg17.FCSD_HCO.cheyenne_intel.cam-outfrq3h BASELINE /glade/p/cesm/amwg/cesm_baselines/cam6_3_133: DIFF
+ - pre-existing failure
+
+izumi/nag/aux_cam:
+
+ DAE_Vnuopc.f45_f45_mg37.FHS94.izumi_nag.cam-dae (Overall: FAIL) details:
+    FAIL DAE_Vnuopc.f45_f45_mg37.FHS94.izumi_nag.cam-dae RUN time=9
+ - pre-existing failure
+
+ ERS_Ln27_Vnuopc.ne5pg3_ne5pg3_mg37.FKESSLER.izumi_nag.cam-outfrq9s (Overall: DIFF) details:
+    FAIL ERS_Ln27_Vnuopc.ne5pg3_ne5pg3_mg37.FKESSLER.izumi_nag.cam-outfrq9s BASELINE /fs/cgd/csm/models/atm/cam/pretag_bl/cam6_3_133_nag: DIFF
+ - expected failure
+
+izumi/gnu/aux_cam: All PASS
+
+Summarize any changes to answers:
+  All compsets which use Kessler idealized physics
+  will have larger-than-roundoff answer changes due
+  to reference pressure bug fix.
+
+===============================================================
+
 Tag name: cam6_3_133
 Originator(s): fvitt
 Date: 19 Oct 2023

src/dynamics/se/dp_coupling.F90

@@ -54,7 +54,7 @@ subroutine d_p_coupling(phys_state, phys_tend,  pbuf2d, dyn_out)
    use phys_control,           only: use_gw_front, use_gw_front_igw
    use hycoef,                 only: hyai, ps0
    use fvm_mapping,            only: dyn2phys_vector, dyn2phys_all_vars
-   use time_mod,               only: timelevel_qdp
+   use se_dyn_time_mod,        only: timelevel_qdp
    use control_mod,            only: qsplit
    use test_fvm_mapping,       only: test_mapping_overwrite_dyn_state, test_mapping_output_phys_state
    use prim_advance_mod,       only: tot_energy_dyn
@@ -546,15 +546,17 @@ subroutine derived_phys_dry(phys_state, phys_tend, pbuf2d)
    use shr_const_mod,   only: shr_const_rwv
    use phys_control,    only: waccmx_is
    use geopotential,    only: geopotential_t
+   use static_energy,   only: update_dry_static_energy_run
    use check_energy,    only: check_energy_timestep_init
    use hycoef,          only: hyai, ps0
    use shr_vmath_mod,   only: shr_vmath_log
    use qneg_module,     only: qneg3
    use dyn_tests_utils, only: vc_dry_pressure
+   use shr_kind_mod,    only: shr_kind_cx
    ! arguments
    type(physics_state), intent(inout), dimension(begchunk:endchunk) :: phys_state
    type(physics_tend ), intent(inout), dimension(begchunk:endchunk) :: phys_tend
-   type(physics_buffer_desc),      pointer     :: pbuf2d(:,:)
+   type(physics_buffer_desc), pointer :: pbuf2d(:,:)
 
    ! local variables
    integer :: lchnk
@@ -564,6 +566,10 @@ subroutine derived_phys_dry(phys_state, phys_tend, pbuf2d)
 
    integer :: m, i, k, ncol, m_cnst
    type(physics_buffer_desc), pointer :: pbuf_chnk(:)
+
+   !Needed for "update_dry_static_energy" CCPP scheme
+   integer :: errflg
+   character(len=shr_kind_cx) :: errmsg
    !----------------------------------------------------------------------------
 
    ! Evaluate derived quantities
@@ -686,18 +692,17 @@ subroutine derived_phys_dry(phys_state, phys_tend, pbuf2d)
       end do
 
       ! Compute initial geopotential heights - based on full pressure
-      call geopotential_t (phys_state(lchnk)%lnpint, phys_state(lchnk)%lnpmid  , phys_state(lchnk)%pint  , &
-         phys_state(lchnk)%pmid  , phys_state(lchnk)%pdel    , phys_state(lchnk)%rpdel , &
-         phys_state(lchnk)%t     , phys_state(lchnk)%q(:,:,:), rairv(:,:,lchnk),  gravit,  zvirv       , &
-         phys_state(lchnk)%zi    , phys_state(lchnk)%zm      , ncol                )
+      call geopotential_t(phys_state(lchnk)%lnpint, phys_state(lchnk)%lnpmid  , phys_state(lchnk)%pint, &
+         phys_state(lchnk)%pmid  , phys_state(lchnk)%pdel    , phys_state(lchnk)%rpdel                , &
+         phys_state(lchnk)%t     , phys_state(lchnk)%q(:,:,:), rairv(:,:,lchnk), gravit, zvirv        , &
+         phys_state(lchnk)%zi    , phys_state(lchnk)%zm      , ncol)
 
       ! Compute initial dry static energy, include surface geopotential
-      do k = 1, pver
-         do i = 1, ncol
-            phys_state(lchnk)%s(i,k) = cpairv(i,k,lchnk)*phys_state(lchnk)%t(i,k) &
-                                     + gravit*phys_state(lchnk)%zm(i,k) + phys_state(lchnk)%phis(i)
-         end do
-      end do
+      call update_dry_static_energy_run(pver, gravit, phys_state(lchnk)%t(1:ncol,:),  &
+                                        phys_state(lchnk)%zm(1:ncol,:),               &
+                                        phys_state(lchnk)%phis(1:ncol),               &
+                                        phys_state(lchnk)%s(1:ncol,:),                &
+                                        cpairv(1:ncol,:,lchnk), errflg, errmsg)
 
       ! Ensure tracers are all positive
       call qneg3('D_P_COUPLING',lchnk  ,ncol    ,pcols   ,pver    , &

src/dynamics/se/dycore/fvm_consistent_se_cslam.F90

@@ -6,7 +6,7 @@ module fvm_consistent_se_cslam
   use cam_abortutils,         only: endrun
   use cam_logfile,            only: iulog
 
-  use time_mod,               only: timelevel_t
+  use se_dyn_time_mod,        only: timelevel_t
   use element_mod,            only: element_t
   use fvm_control_volume_mod, only: fvm_struct
   use hybrid_mod,             only: hybrid_t, config_thread_region, get_loop_ranges, threadOwnsVertLevel

src/dynamics/se/dycore/prim_advance_mod.F90

@@ -53,7 +53,7 @@ subroutine prim_advance_exp(elem, fvm, deriv, hvcoord, hybrid,dt, tl,  nets, net
     use element_mod,       only: element_t
     use hybvcoord_mod,     only: hvcoord_t
     use hybrid_mod,        only: hybrid_t
-    use time_mod,          only: TimeLevel_t,  timelevel_qdp, tevolve
+    use se_dyn_time_mod,   only: TimeLevel_t,  timelevel_qdp, tevolve
     use fvm_control_volume_mod, only: fvm_struct
     use cam_thermo,        only: get_kappa_dry
     use air_composition,   only: thermodynamic_active_species_num

src/dynamics/se/dycore/prim_advection_mod.F90

@@ -23,7 +23,7 @@ module prim_advection_mod
   use element_mod,            only: element_t
   use fvm_control_volume_mod, only: fvm_struct
   use hybvcoord_mod,          only: hvcoord_t
-  use time_mod,               only: TimeLevel_t, TimeLevel_Qdp
+  use se_dyn_time_mod,        only: TimeLevel_t, TimeLevel_Qdp
   use control_mod,            only: nu_q, nu_p, limiter_option, hypervis_subcycle_q, rsplit
   use edge_mod,               only: edgevpack, edgevunpack, initedgebuffer, initedgesbuffer
 

src/dynamics/se/dycore/prim_driver_mod.F90

@@ -28,8 +28,8 @@ subroutine prim_init2(elem, fvm, hybrid, nets, nete, tl, hvcoord)
     use dimensions_mod,         only: irecons_tracer, fvm_supercycling
     use dimensions_mod,         only: fv_nphys, nc
     use parallel_mod,           only: syncmp
-    use time_mod,               only: timelevel_t, tstep, phys_tscale, nsplit, TimeLevel_Qdp
-    use time_mod,               only: nsplit_baseline,rsplit_baseline
+    use se_dyn_time_mod,        only: timelevel_t, tstep, phys_tscale, nsplit, TimeLevel_Qdp
+    use se_dyn_time_mod,        only: nsplit_baseline,rsplit_baseline
     use prim_state_mod,         only: prim_printstate
     use control_mod,            only: runtype, topology, rsplit, qsplit, rk_stage_user,         &
                                       nu, nu_q, nu_div, hypervis_subcycle, hypervis_subcycle_q, &
@@ -218,7 +218,7 @@ subroutine prim_run_subcycle(elem, fvm, hybrid,nets,nete, dt, tl, hvcoord,nsubst
 !
 !
     use hybvcoord_mod, only : hvcoord_t
-    use time_mod,               only: TimeLevel_t, timelevel_update, timelevel_qdp, nsplit
+    use se_dyn_time_mod,        only: TimeLevel_t, timelevel_update, timelevel_qdp, nsplit
     use control_mod,            only: statefreq,qsplit, rsplit, variable_nsplit
     use prim_advance_mod,       only: applycamforcing
     use prim_advance_mod,       only: tot_energy_dyn,compute_omega
@@ -407,7 +407,7 @@ subroutine prim_step(elem, fvm, hybrid,nets,nete, dt, tl, hvcoord, rstep)
     !       tl%n0    time t + dt_q
     !
     use hybvcoord_mod,          only: hvcoord_t
-    use time_mod,               only: TimeLevel_t, timelevel_update
+    use se_dyn_time_mod,        only: TimeLevel_t, timelevel_update
     use control_mod,            only: statefreq, qsplit, nu_p
     use thread_mod,             only: omp_get_thread_num
     use prim_advance_mod,       only: prim_advance_exp

src/dynamics/se/dycore/prim_init.F90

@@ -28,7 +28,7 @@ subroutine prim_init1(elem, fvm, par, Tl)
     use element_mod,            only: element_t, allocate_element_desc
     use fvm_mod,                only: fvm_init1
     use mesh_mod,               only: MeshUseMeshFile
-    use time_mod,               only: timelevel_init, timelevel_t
+    use se_dyn_time_mod,        only: timelevel_init, timelevel_t
     use mass_matrix_mod,        only: mass_matrix
     use derivative_mod,         only: allocate_subcell_integration_matrix_cslam
     use derivative_mod,         only: allocate_subcell_integration_matrix_physgrid

src/dynamics/se/dycore/prim_state_mod.F90

@@ -4,7 +4,7 @@ module prim_state_mod
   use dimensions_mod,   only: nlev, np, nc, qsize_d, ntrac_d
   use parallel_mod,     only: ordered
   use hybrid_mod,       only: hybrid_t
-  use time_mod,         only: timelevel_t, TimeLevel_Qdp, time_at
+  use se_dyn_time_mod,  only: timelevel_t, TimeLevel_Qdp, time_at
   use control_mod,      only: qsplit, statediag_numtrac
   use global_norms_mod, only: global_integrals_general
   use element_mod,      only: element_t
@@ -24,7 +24,7 @@ subroutine prim_printstate(elem, tl,hybrid,nets,nete, fvm, omega_cn)
     use air_composition,        only: thermodynamic_active_species_idx_dycore, dry_air_species_num
     use air_composition,        only: thermodynamic_active_species_num,thermodynamic_active_species_idx
     use cam_control_mod,        only: initial_run
-    use time_mod,               only: tstep
+    use se_dyn_time_mod,        only: tstep
     use control_mod,            only: rsplit, qsplit
     use perf_mod,       only: t_startf, t_stopf
     type (element_t),             intent(inout) :: elem(:)
@@ -345,10 +345,10 @@ end subroutine prim_printstate_cslam_gamma
   subroutine adjust_nsplit(elem, tl,hybrid,nets,nete, fvm, omega_cn)
     use dimensions_mod,         only: ksponge_end
     use dimensions_mod,         only: fvm_supercycling, fvm_supercycling_jet
-    use time_mod,               only: tstep
+    use se_dyn_time_mod,        only: tstep
     use control_mod,            only: rsplit, qsplit
     use perf_mod,               only: t_startf, t_stopf
-    use time_mod,               only: nsplit, nsplit_baseline,rsplit_baseline
+    use se_dyn_time_mod,        only: nsplit, nsplit_baseline,rsplit_baseline
     use control_mod,            only: qsplit, rsplit
     use time_manager,           only: get_step_size
     use cam_abortutils,         only: endrun

src/dynamics/se/dycore/time_mod.F90 → src/dynamics/se/dycore/se_dyn_time_mod.F90

@@ -1,4 +1,4 @@
-module time_mod
+module se_dyn_time_mod
   !------------------
   use shr_kind_mod,   only: r8=>shr_kind_r8
   !------------------
@@ -132,4 +132,4 @@ subroutine TimeLevel_update(tl,uptype)
 !$OMP BARRIER    
   end subroutine TimeLevel_update
 
-end module time_mod
+end module se_dyn_time_mod

src/dynamics/se/dyn_comp.F90

@@ -42,7 +42,7 @@ module dyn_comp
 use dimensions_mod,         only: qsize, use_cslam
 use element_mod,            only: element_t, elem_state_t
 use fvm_control_volume_mod, only: fvm_struct
-use time_mod,               only: nsplit
+use se_dyn_time_mod,        only: nsplit
 use edge_mod,               only: initEdgeBuffer, edgeVpack, edgeVunpack, FreeEdgeBuffer
 use edgetype_mod,           only: EdgeBuffer_t
 use bndry_mod,              only: bndry_exchange
@@ -963,11 +963,11 @@ subroutine dyn_run(dyn_state)
    use air_composition,  only: thermodynamic_active_species_idx_dycore
    use prim_driver_mod,  only: prim_run_subcycle
    use dimensions_mod,   only: cnst_name_gll
-   use time_mod,         only: tstep, nsplit, timelevel_qdp
+   use se_dyn_time_mod,  only: tstep, nsplit, timelevel_qdp
    use hybrid_mod,       only: config_thread_region, get_loop_ranges
    use control_mod,      only: qsplit, rsplit, ftype_conserve
    use thread_mod,       only: horz_num_threads
-   use time_mod,         only: tevolve
+   use se_dyn_time_mod,  only: tevolve
 
    type(dyn_export_t), intent(inout) :: dyn_state
 

src/dynamics/se/dyn_grid.F90

@@ -48,7 +48,7 @@ module dyn_grid
 use prim_init,              only: prim_init1
 use edge_mod,               only: initEdgeBuffer
 use edgetype_mod,           only: EdgeBuffer_t
-use time_mod,               only: TimeLevel_t
+use se_dyn_time_mod,        only: TimeLevel_t
 use dof_mod,                only: UniqueCoords, UniquePoints
 
 implicit none
@@ -133,7 +133,7 @@ subroutine dyn_grid_init()
    use hybrid_mod,          only: hybrid_t, init_loop_ranges, &
                                   get_loop_ranges, config_thread_region
    use control_mod,         only: qsplit, rsplit
-   use time_mod,            only: tstep, nsplit
+   use se_dyn_time_mod,     only: tstep, nsplit
    use fvm_mod,             only: fvm_init2, fvm_init3, fvm_pg_init
    use dimensions_mod,      only: irecons_tracer
    use comp_gll_ctr_vol,    only: gll_grid_write

src/dynamics/se/restart_dynamics.F90

@@ -46,7 +46,7 @@ module restart_dynamics
 use dimensions_mod,   only: np, npsq, ne, nlev, qsize, nelemd, nc, ntrac, use_cslam
 use dof_mod,          only: UniquePoints
 use element_mod,      only: element_t
-use time_mod,         only: tstep, TimeLevel_Qdp
+use se_dyn_time_mod,  only: tstep, TimeLevel_Qdp
 
 use edge_mod,         only: initEdgeBuffer, edgeVpack, edgeVunpack, FreeEdgeBuffer
 use edgetype_mod,     only: EdgeBuffer_t