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njeffery committed Apr 4, 2024
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Showing 11 changed files with 27 additions and 27 deletions.
2 changes: 1 addition & 1 deletion cime
Submodule cime updated 66 files
+0 −187 .github/scripts/ghcr-prune.py
+60 −0 .github/workflows/container.yml
+0 −24 .github/workflows/ghcr-prune.yml
+39 −80 .github/workflows/testing.yml
+0 −1 .gitignore
+2 −2 CIME/BuildTools/configure.py
+4 −0 CIME/SystemTests/erp.py
+1 −0 CIME/SystemTests/nck.py
+1 −1 CIME/SystemTests/nodefail.py
+1 −0 CIME/SystemTests/pea.py
+1 −0 CIME/SystemTests/pem.py
+5 −0 CIME/SystemTests/pet.py
+5 −6 CIME/SystemTests/pgn.py
+1 −0 CIME/SystemTests/seq.py
+6 −9 CIME/SystemTests/system_tests_common.py
+0 −4 CIME/SystemTests/system_tests_compare_two.py
+4 −6 CIME/SystemTests/tsc.py
+12 −29 CIME/Tools/Makefile
+1 −10 CIME/Tools/jenkins_generic_job
+0 −9 CIME/Tools/wait_for_tests
+23 −32 CIME/XML/env_batch.py
+3 −9 CIME/XML/env_mach_specific.py
+1 −7 CIME/XML/env_workflow.py
+0 −2 CIME/XML/files.py
+10 −21 CIME/XML/generic_xml.py
+16 −131 CIME/XML/machines.py
+1 −1 CIME/baselines/performance.py
+21 −27 CIME/bless_test_results.py
+1 −1 CIME/build.py
+0 −5 CIME/build_scripts/buildlib.mpi-serial
+3 −8 CIME/case/case.py
+3 −1 CIME/case/case_clone.py
+14 −9 CIME/case/case_run.py
+7 −8 CIME/case/case_setup.py
+14 −16 CIME/case/case_submit.py
+1 −1 CIME/case/check_input_data.py
+1 −2 CIME/data/config/cesm/config_files.xml
+6 −1 CIME/data/config/xml_schemas/config_machines_template.xml
+0 −330 CIME/data/config/xml_schemas/config_machines_version3.xsd
+2 −2 CIME/data/config/xml_schemas/env_mach_specific.xsd
+0 −2 CIME/jenkins_generic_job.py
+1 −1 CIME/non_py/cprnc
+1 −5 CIME/non_py/src/timing/Makefile
+0 −11 CIME/scripts/create_test.py
+0 −2 CIME/test_scheduler.py
+0 −11 CIME/test_status.py
+0 −4 CIME/tests/scripts_regression_tests.py
+2 −2 CIME/tests/test_sys_cime_case.py
+4 −6 CIME/tests/test_sys_create_newcase.py
+5 −5 CIME/tests/test_sys_test_scheduler.py
+17 −22 CIME/tests/test_sys_unittest.py
+10 −18 CIME/tests/test_unit_bless_test_results.py
+13 −6 CIME/tests/test_unit_case.py
+0 −50 CIME/tests/test_unit_case_run.py
+4 −4 CIME/tests/test_unit_xml_machines.py
+1 −22 CIME/utils.py
+0 −6 CIME/wait_for_tests.py
+73 −0 CMakeLists.txt
+6 −6 Externals.cfg
+0 −7 docker/.cime/config_machines.v3.xml
+0 −39 docker/.cime/docker/config_machines.xml
+28 −49 docker/Dockerfile
+1 −1 docker/config_machines.xml
+0 −0 docker/docker.cmake
+188 −55 docker/entrypoint.sh
+42 −42 scripts/climate_reproducibility/README.md
2 changes: 1 addition & 1 deletion components/eam/src/physics/crm/pam/external
Submodule external updated 57 files
+0 −3 .github/workflows/mmf-simplified-ubuntu.yml
+0 −3 .github/workflows/pamc-idealized-ubuntu.yml
+0 −3 .github/workflows/pamc-unit-ubuntu.yml
+4 −4 dynamics/awfl/TransformMatrices_variable.h
+3 −3 dynamics/spam/CMakeLists.txt
+11 −15 dynamics/spam/Dycore.h
+4 −5 dynamics/spam/src/common.h
+0 −4 dynamics/spam/src/core/params.h
+11 −23 dynamics/spam/src/extrudedmodel-common.h
+0 −79 dynamics/spam/src/grids/geometry.h
+12 −13 dynamics/spam/src/hamiltonians/kinetic_energy.h
+8 −21 dynamics/spam/src/hamiltonians/refstate.h
+42 −188 dynamics/spam/src/hamiltonians/variableset.h
+667 −2,195 dynamics/spam/src/models/extrudedmodel.h
+1 −8 dynamics/spam/src/models/layermodel.h
+28 −36 dynamics/spam/src/models/model.h
+3 −3 dynamics/spam/src/operators/TransformMatrices_variable.h
+6 −6 dynamics/spam/src/operators/cfv_recon.h
+85 −94 dynamics/spam/src/operators/ext_deriv.h
+12 −12 dynamics/spam/src/operators/fct.h
+29 −38 dynamics/spam/src/operators/hodge_star.h
+124 −192 dynamics/spam/src/operators/hodge_star_extruded.h
+38 −42 dynamics/spam/src/operators/hodge_star_layer.h
+24 −24 dynamics/spam/src/operators/recon.h
+34 −34 dynamics/spam/src/operators/wedge.h
+9 −10 dynamics/spam/src/operators/weno_func_recon.h
+5 −5 dynamics/spam/src/operators/weno_func_recon_variable.h
+6 −6 dynamics/spam/src/operators/weno_recon.h
+3 −2 dynamics/spam/src/timesteppers/KGRK.h
+3 −2 dynamics/spam/src/timesteppers/LSRK.h
+3 −2 dynamics/spam/src/timesteppers/SI_Fixed.h
+7 −4 dynamics/spam/src/timesteppers/SI_Newton.h
+3 −2 dynamics/spam/src/timesteppers/SSPRK.h
+8 −9 dynamics/spam/src/timesteppers/time_integrator.h
+1 −1 externals/YAKL
+0 −10 physics/micro/kessler/Microphysics.h
+2 −8 physics/micro/none/Microphysics.h
+0 −12 physics/micro/p3/Microphysics.h
+1 −10 physics/scream_cxx_interfaces/scream_cxx_interface_p3.cpp
+0 −1 physics/scream_cxx_interfaces/scream_cxx_interface_p3.h
+2 −18 physics/scream_cxx_interfaces/scream_cxx_interface_shoc.cpp
+1 −1 standalone/machines/ci/macos-clang.env
+1 −1 standalone/machines/ci/ubuntu-clang.env
+4 −4 standalone/machines/ci/ubuntu-gcc.env
+1 −1 standalone/mmf_simplified/CMakeLists.txt
+0 −2 standalone/mmf_simplified/build/cmakescript_pamc.sh
+0 −4 standalone/mmf_simplified/driver.cpp
+2 −6 standalone/mmf_simplified/inputs/pamc_idealized/pamc_input_extruded_densitycurrent.yaml
+2 −3 standalone/mmf_simplified/inputs/pamc_idealized/pamc_input_extruded_moistrisingbubble.yaml
+0 −53 standalone/mmf_simplified/inputs/pamc_idealized/pamc_input_extruded_supercell.yaml
+7 −0 standalone/mmf_simplified/pam-c/debug_run_extruded_script.sh
+7 −0 standalone/mmf_simplified/pam-c/debug_run_layer_script.sh
+4 −0 standalone/mmf_simplified/pam-c/make_debug_script.sh
+4 −0 standalone/mmf_simplified/pam-c/make_script.sh
+4 −29 standalone/mmf_simplified/pam-c/run_extruded_script.sh
+3 −21 standalone/mmf_simplified/pam-c/run_layer_script.sh
+9 −0 standalone/mmf_simplified/pam-c/set_pamc_cmakevars.sh
30 changes: 15 additions & 15 deletions components/mpas-seaice/src/Registry.xml
Original file line number Diff line number Diff line change
Expand Up @@ -5531,91 +5531,91 @@
type="real"
dimensions="maxAlgaeType nCells Time"
units="mmol m-2 s-1"
description="Algal nitrogen flux to ocean weighted by ice area fraction"
description="Algal nitrogen flux to ocean weighted by ice area fraction"
/>
<var name="oceanDOCFluxArea"
type="real"
dimensions="maxDOCType nCells Time"
units="mmol m-2 s-1"
description="Dissolved organic carbon flux to ocean weighted by ice area fraction"
description="Dissolved organic carbon flux to ocean weighted by ice area fraction"
/>
<var name="oceanDICFluxArea"
type="real"
dimensions="maxDICType nCells Time"
units="mmol m-2 s-1"
description="Dissolved inorganic carbon flux to ocean weighted by ice area fraction"
description="Dissolved inorganic carbon flux to ocean weighted by ice area fraction"
/>
<var name="oceanDONFluxArea"
type="real"
dimensions="maxDONType nCells Time"
units="mmol m-2 s-1"
description="Dissolved organic nitrogen flux to ocean weighted by ice area fraction"
description="Dissolved organic nitrogen flux to ocean weighted by ice area fraction"
/>
<var name="oceanNitrateFluxArea"
type="real"
dimensions="nCells Time"
units="mmol m-2 s-1"
description="Nitrate flux to ocean weighted by ice area fraction"
description="Nitrate flux to ocean weighted by ice area fraction"
/>
<var name="oceanSilicateFluxArea"
type="real"
dimensions="nCells Time"
units="mmol m-2 s-1"
description="Silicate flux to ocean weighted by ice area fraction"
description="Silicate flux to ocean weighted by ice area fraction"
/>
<var name="oceanAmmoniumFluxArea"
type="real"
dimensions="nCells Time"
units="mmol m-2 s-1"
description="Ammonium flux to ocean weighted by ice area fraction"
description="Ammonium flux to ocean weighted by ice area fraction"
/>
<var name="oceanDMSFluxArea"
type="real"
dimensions="nCells Time"
units="mmol m-2 s-1"
description="Dimethylsulfide flux to ocean weighted by ice area fraction"
description="Dimethylsulfide flux to ocean weighted by ice area fraction"
/>
<var name="oceanDMSPpFluxArea"
type="real"
dimensions="nCells Time"
units="mmol m-2 s-1"
description="Particulate DMSP flux to ocean weighted by ice area fraction"
description="Particulate DMSP flux to ocean weighted by ice area fraction"
/>
<var name="oceanDMSPdFluxArea"
type="real"
dimensions="nCells Time"
units="mmol m-2 s-1"
description="Dissolved DMSP flux to ocean weighted by ice area fraction"
description="Dissolved DMSP flux to ocean weighted by ice area fraction"
/>
<var name="oceanHumicsFluxArea"
type="real"
dimensions="nCells Time"
units="mmol m-2 s-1"
description="Refractory DOC flux to ocean weighted by ice area fraction"
description="Refractory DOC flux to ocean weighted by ice area fraction"
/>
<var name="oceanParticulateIronFluxArea"
type="real"
dimensions="maxIronType nCells Time"
units="umol m-2 s-1"
description="Particulate iron flux to ocean weighted by ice area fraction"
description="Particulate iron flux to ocean weighted by ice area fraction"
/>
<var name="oceanDissolvedIronFluxArea"
type="real"
dimensions="maxIronType nCells Time"
units="umol m-2 s-1"
description="Dissolved iron flux to ocean weighted by ice area fraction"
description="Dissolved iron flux to ocean weighted by ice area fraction"
/>
<var name="oceanDustIronFluxArea"
type="real"
dimensions="nCells Time"
units="mg m-2 s-1"
description="Total iron dust flux to ocean weighted by ice area fraction"
description="Total iron dust flux to ocean weighted by ice area fraction"
/>
<var name="oceanBlackCarbonFluxArea"
type="real"
dimensions="nCells Time"
units="mg m-2 s-1"
description="Total black carbon flux to ocean weighted by ice area fraction"
description="Total black carbon flux to ocean weighted by ice area fraction"
/>
<var name="bioTracerShortwave"
type="real"
Expand Down
2 changes: 1 addition & 1 deletion components/mpas-seaice/src/column/ice_algae.F90
Original file line number Diff line number Diff line change
Expand Up @@ -2885,7 +2885,7 @@ subroutine check_conservation_FCT &
endif

if (abs(diff_dt) > accuracy ) then
l_stop = .true.
!l_stop = .true.
write(warning,*) 'Conservation of zbgc low order solution failed: diff_dt:',&
diff_dt
call add_warning(warning)
Expand Down
6 changes: 3 additions & 3 deletions components/mpas-seaice/src/column/ice_zbgc.F90
Original file line number Diff line number Diff line change
Expand Up @@ -182,9 +182,9 @@ subroutine add_new_ice_bgc (dt, nblyr, &
vsurp = hsurp * aicen_init(n)
vbrin(n) = vbrin(n) + vsurp
vice_new = vicen_init(n) + vsurp
if (tr_brine .and. vice_new > c0) then ! NJvicen(n) > c0) then
brine_frac_init(n) = trcrn(nt_fbri,n) !NJ
trcrn(nt_fbri,n) = vbrin(n)/vice_new !NJ vicen(n)
if (tr_brine .and. vice_new > c0) then
brine_frac_init(n) = trcrn(nt_fbri,n)
trcrn(nt_fbri,n) = vbrin(n)/vice_new
elseif (tr_brine .and. vicen(n) <= c0) then
trcrn(nt_fbri,n) = c1
endif
Expand Down
2 changes: 1 addition & 1 deletion externals/YAKL
Submodule YAKL updated 180 files
2 changes: 1 addition & 1 deletion externals/mam4xx
Submodule mam4xx updated 211 files

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