| 0b00cbe | Walter Hannah | 05 October 2023, 20:07:52 UTC | add Kokkos_ENABLE_OPENMP=Off for gnugpu on Frontier | 05 October 2023, 20:07:52 UTC |
| 11385cc | Walter Hannah | 05 October 2023, 17:52:59 UTC | add Kokkos_ENABLE_OPENMP=Off for Summit | 05 October 2023, 17:52:59 UTC |
| a88c772 | Walter Hannah | 05 October 2023, 15:21:53 UTC | remove configure support for MMF m2005 microphysics | 05 October 2023, 15:21:53 UTC |
| dcf047d | Walter Hannah | 05 October 2023, 15:13:23 UTC | configure clean up and remove samomp support | 05 October 2023, 15:13:23 UTC |
| 388011d | Walter Hannah | 05 October 2023, 15:05:20 UTC | add new lines | 05 October 2023, 15:05:20 UTC |
| 33f6261 | Walter Hannah | 04 October 2023, 23:03:11 UTC | re-enable CRM variance and momentum transport for MMF1 | 04 October 2023, 23:03:11 UTC |
| 96d93d5 | Walter Hannah | 04 October 2023, 22:57:58 UTC | add new line at end of pam_debug | 04 October 2023, 22:57:58 UTC |
| 4ef07e2 | Walter Hannah | 04 October 2023, 22:52:48 UTC | update default PAM time step | 04 October 2023, 22:52:48 UTC |
| 3cc85e2 | Walter Hannah | 04 October 2023, 20:24:00 UTC | update PAM submodule | 04 October 2023, 20:24:00 UTC |
| cb05869 | Walter Hannah | 04 October 2023, 19:15:57 UTC | disable kokkos finalize in PAM driver | 04 October 2023, 19:15:57 UTC |
| f1a646a | Walter Hannah | 03 October 2023, 22:24:49 UTC | add hyperdiffusion to PAM and refactor PAM driver | 03 October 2023, 22:24:49 UTC |
| 66a7723 | Walter Hannah | 03 October 2023, 20:50:22 UTC | update pam_statistics | 03 October 2023, 20:50:22 UTC |
| 4e92e09 | Walter Hannah | 03 October 2023, 20:49:52 UTC | refactor pam_output | 03 October 2023, 20:49:52 UTC |
| a88ffb4 | Walter Hannah | 03 October 2023, 15:37:39 UTC | clean-up pam_state | 03 October 2023, 15:37:39 UTC |
| a0c4e56 | Walter Hannah | 20 September 2023, 22:18:49 UTC | update PAM submodule | 20 September 2023, 22:18:49 UTC |
| 01fc63f | Walter Hannah | 20 September 2023, 18:55:24 UTC | update PAM submodule | 20 September 2023, 18:55:24 UTC |
| 4df5ecc | Walter Hannah | 20 September 2023, 18:43:22 UTC | bug fix for pam_state | 20 September 2023, 18:43:22 UTC |
| 93ce233 | Walter Hannah | 20 September 2023, 18:39:53 UTC | update PAM submodule | 20 September 2023, 18:39:53 UTC |
| 8d83e77 | Walter Hannah | 20 September 2023, 18:25:41 UTC | add output for CRM mean dry and vapor densities | 20 September 2023, 18:25:41 UTC |
| bfbfde8 | Walter Hannah | 20 September 2023, 18:20:14 UTC | remove dycor defaults for PAM | 20 September 2023, 18:20:14 UTC |
| 2cb15c8 | Walter Hannah | 20 September 2023, 18:07:36 UTC | fix to diffuse number concentration w/ P3 | 20 September 2023, 18:07:36 UTC |
| 2455eba | Walter Hannah | 08 September 2023, 15:57:09 UTC | remove commented lines and add note | 08 September 2023, 15:57:09 UTC |
| 1b8c362 | Walter Hannah | 31 August 2023, 20:59:57 UTC | Merge remote-tracking branch 'origin/master' into whannah/mmf/pam-impl | 31 August 2023, 20:59:57 UTC |
| b346202 | Walter Hannah | 31 August 2023, 20:55:22 UTC | more clean up | 31 August 2023, 20:55:22 UTC |
| 7556a9c | Walter Hannah | 31 August 2023, 20:54:18 UTC | clean up for PAM integration PR | 31 August 2023, 20:54:18 UTC |
| 41f857d | Walter Hannah | 31 August 2023, 20:47:21 UTC | Merge branch 'whannah/mmf/pam-impl' of github.com:E3SM-Project/E3SM into whannah/mmf/pam-impl | 31 August 2023, 20:47:21 UTC |
| 9e36fa5 | Walter Hannah | 31 August 2023, 19:20:25 UTC | add MMF2 test for MMF integration suite | 31 August 2023, 19:20:25 UTC |
| e34e5a7 | Walter Hannah | 31 August 2023, 19:05:39 UTC | update PAM submodule | 31 August 2023, 19:05:39 UTC |
| 4d97de8 | Walter Hannah | 31 August 2023, 19:05:04 UTC | Merge branch 'whannah/mmf/pam-impl' of github.com:E3SM-Project/E3SM into whannah/mmf/pam-impl | 31 August 2023, 19:05:04 UTC |
| 431905b | Walter Hannah | 31 August 2023, 19:04:32 UTC | remove real-size flag for intel compiler | 31 August 2023, 19:04:32 UTC |
| 908f55d | Jon Wolfe | 31 August 2023, 18:24:24 UTC | Merge branch 'cbegeman/ocn/new-se-upwind-feature' (PR #5829) New upwinded advection feature for split-explicit time integrator This PR adds the option to use upwinded advection with the split-explicit time integrator. Formerly, upwinded advection was only available with the RK4 time integrator. For the barotropic subcycle's SSH predictor and corrector steps, the barotropic velocity is first computed on edges, then used to determine the water column thickness on edges (either centered or upwinded), then both barotropic velocity and water column thickness on edges is used to compute the SSH tendency on cells. We also compute the normal velocity correction factor using layerThickEdgeFlux, which is updated if upwinded advection is used. Upwinding of the water column thickness is done with a new diagnostic subroutine, ocn_diagnostic_solve_wctEdge, which is modeled after ocn_diagnostic_solve_layerThicknessEdge. [BFB] stealth | 31 August 2023, 18:24:24 UTC |
| ff9157c | Jon Wolfe | 29 August 2023, 22:59:46 UTC | Add new stealth test and corresponding testdef | 29 August 2023, 22:59:46 UTC |
| d115180 | noel | 29 August 2023, 17:38:28 UTC | Merge branch E3SM-Project/ndk/machinefiles/remove-NERSC-server (PR #5900) Remove NERSC inputdata server | 29 August 2023, 17:38:28 UTC |
| 1f6314c | noel | 28 August 2023, 21:06:58 UTC | remove NERSC inputdata server | 28 August 2023, 21:06:58 UTC |
| 640bb28 | James Foucar | 28 August 2023, 18:16:09 UTC | Merge branch 'jgfouca/change_ocean_petsc_libs' into master (PR #5824) mpas-ocean: Do not link petsc unless USE_PETSC is on [BFB] | 28 August 2023, 18:16:09 UTC |
| 8364b40 | Walter Hannah | 28 August 2023, 17:05:38 UTC | update PAM submodule | 28 August 2023, 17:05:38 UTC |
| ac7c892 | Jon Wolfe | 28 August 2023, 16:21:39 UTC | Merge branch 'philipwjones/mpas-ocean/sal-acc-fix' (PR #5874) Fix openacc data directive on non-existent ssh_sal array An openacc data transfer on the self-attraction ssh change was outside any conditional for SAL so was operating on a non-existent array if SAL is turned off. This mod changes the location of the data directive so it is within the compute SAL routine and only executed of SAL is turned on Fixes #5866 [BFB] | 28 August 2023, 16:21:39 UTC |
| 394fdb7 | Jon Wolfe | 25 August 2023, 16:03:07 UTC | Merge branch 'cbegeman/ocn/fix-tendency-metadata' (PR #5883) Correct the units of active tracer tendencies The units of active tracer tendencies in the Registry should have an additional factor of m. The activeTracerTend's are divided by a factor of layerThickness when they are used in the code to update active tracers. This operation is also needed to evaluate tracer conservation from activeTracerTend output. [BFB] | 25 August 2023, 16:03:07 UTC |
| 4b00636 | Gautam Bisht | 24 August 2023, 20:00:45 UTC | Merge branch 'lnd/fates-refactor' (PR #5849) This pull request changes the names of a number of FATES use statements and type names to be consistent with the associated FATES refactor. The FATES submodule pointer is updated as a results as well. [B4B] for non-fates tests | 24 August 2023, 20:00:45 UTC |
| e33c20d | Jon Wolfe | 24 August 2023, 17:49:03 UTC | Merge branch 'jonbob/scripts/update-ne30pg2-orrs18to6v3' (PR #5865) Update mapping and domain files for ne30pg2-oRRS18to6v3 Adds new domain and mapping files for the ne30pg2-oRRS18to6v3 resolution, as well as smoothed runoff between r05 and oRRS18to6v3 [BFB] for all tested configurations | 24 August 2023, 17:49:03 UTC |
| ba85852 | Peter Schwartz | 23 August 2023, 20:33:33 UTC | Merge branch 'bishtgautam/lnd/rename-clm-modules' (PR #5689) Renames clm_time_manager module as elm_time_manager. [BFB] | 23 August 2023, 20:33:33 UTC |
| 07054d3 | Walter Hannah | 22 August 2023, 22:42:44 UTC | Merge remote-tracking branch 'origin/master' into whannah/mmf/pam-impl | 22 August 2023, 22:42:44 UTC |
| b115338 | Walter Hannah | 22 August 2023, 19:11:45 UTC | cmake update to build kokkos on pm-gpu | 22 August 2023, 19:11:45 UTC |
| 6aa22b1 | James Foucar | 21 August 2023, 16:27:57 UTC | Merge branch 'jasonb5/cime/adds_testing_excludes' into master (PR #5812) CIME's archive configuration is used for determining which history files are compared during the COMPARE_PHASE of tests. There was a fix in CIME that corrected the generated regex that was used to search for these files. Since the fix additional active component history files are being matched and generating test failures as they are required for archiving but not for the COMPARE_PHASE of a test. This PR excludes these components from the COMPARE_PHASE of tests. This PR includes a CIME update: Changes: 1) jenkins_generic_job: Add flag for ignoring memleaks 2) Always use the BATCH_COMMAND_FLAGS argument. This allows users to alter with xmlchange and append with --append 3) Default to single-build in PEM tests 4) Adds the force-rebuild argument to create_test and cs.status. This argument will set the SHAREDLIB_BUILD_PHASE to PEND for all tests. 5) Do not re-invoke make on repeat case.build calls 6) env_batch: replace PROJECT arg with nothing if PROJECT not required - Adds --driver to query_config Deprecates --comp_interface for query_config Fixes driver_choices in create_test 7) Add support for MPASO_USE_PETSC 8) Better error for missing config_machines.xml file 9) Adds skip-submit argument to case.build 10) change method of detecting fv3 dycore in cam and path to libfv3.a 11) add which to find ncdump and an error message if not found 12) do not allow EXEROOT or OBJDIR or LIBROOT to be CASEROOT 13) Add flexible controls of GPU configuration 14) Removes DAE.ww3a.ADWAV from cime_developers 15) Fixes hist_files excluding components during actual compare Fixes: 1) Fix create_test --single-exe option 2) Fixes issue causing case context to exit early. This would result in ERROR: Cannot modify case, read_only... errors. 3) Fixes regex pattern used to match history files. Only considers .nc files when copying history files for a tests COMPARE_PHASE. Adds a new optional attribute exclude_testing for comp_archive_spec which allows a components history files to be archived but excluded from the COMPARE_PHASE of tests when active. 4) Fixes creating directory for input data 5) batch: improve the account remove and add support for slurm 6) Docker CI fixes [BFB] | 21 August 2023, 16:27:57 UTC |
| a33b38a | Carolyn Begeman | 17 August 2023, 17:36:07 UTC | Fixup diag routine for upwinded wctEdge | 20 August 2023, 17:39:05 UTC |
| 2c3e8c1 | Carolyn Begeman | 15 August 2023, 14:48:43 UTC | Exclude boundaries from centered wctEdge | 20 August 2023, 17:39:05 UTC |
| e3607d4 | Carolyn Begeman | 11 May 2023, 23:56:51 UTC | Add upwinded ssh to SE and routine to diagnostics | 20 August 2023, 17:38:55 UTC |
| ff27c9d | Carolyn Begeman | 13 August 2023, 17:08:15 UTC | Use diag routine for wctEdge | 20 August 2023, 17:38:28 UTC |
| b42f4d8 | Balwinder Singh | 18 August 2023, 22:15:28 UTC | Merge remote-tracking branch 'mkstratos/mkstratos/fix-pgn-test'(PR #5872) Add micro_p3 to list of possible ptend names in physpkg Fixes missing field error when running PGN test ERROR: GET_MASTERLIST_INDX: attemping to output field s_micro_p3 not on master list Fixed by adding micro_p3 to the list of possible ptend field names. [BFB] * mkstratos/mkstratos/fix-pgn-test: Add micro_p3 to list of possible ptend names | 18 August 2023, 22:15:28 UTC |
| 032bd09 | Andrew M. Bradley | 18 August 2023, 19:30:27 UTC | Merge branch 'ambrad/eam/rm-bld-DNC4' (PR #5854) EAM/HOMME: Remove -DNC=4 in bld/configure; NC is an unused symbol. It is believed that NC was used in HOMME long ago. In any case, it is not used any longer. Remove it from bld/configure. e3sm_developer passes on Chrysalis. [BFB] | 18 August 2023, 19:30:27 UTC |
| dc14534 | James Foucar | 17 August 2023, 19:36:56 UTC | Update CIME again | 17 August 2023, 19:36:56 UTC |
| 83dea76 | James Foucar | 17 August 2023, 19:34:38 UTC | Merge remote-tracking branch 'origin/master' into jasonb5/cime/adds_testing_excludes * origin/master: Fix array shapes in where assignment statements in micro_p3_interface.F90 revert to explicit initialization due to complaint by nvidia compiler Change to use implicit loop to populate P3_input_dim and P3_output_dim arrays Update WCYCL PE-layouts on Chrysalis Bugfix: rework P3_input_dim and P3_output_dim for hist_coord bug fix in crm_physics.F90 | 17 August 2023, 19:34:38 UTC |
| 466583d | Walter Hannah | 17 August 2023, 17:16:59 UTC | update PAM submodule | 17 August 2023, 17:16:59 UTC |
| 0fd9c2c | Walter Hannah | 17 August 2023, 15:34:01 UTC | set EKAT_ENABLE_YAML_PARSER to disable ekat yaml build | 17 August 2023, 15:34:01 UTC |
| 62897cf | Walter Hannah | 17 August 2023, 15:33:35 UTC | update PAM submodule | 17 August 2023, 15:33:35 UTC |
| 8d81d0b | Wuyin Lin | 17 August 2023, 14:41:50 UTC | Merge branch 'wlin/atm/fix_where_assignment_shapes' (PR #5886) Fix array shapes in where assignment statements in micro_p3_interface.F90 Mismatch of array shapes in where assignment statements and where mask expression causing three diagostic variables, AQRAIN, ANRAIN, FREQR, to differ from one run to another when using gnu compiler. The declared shapes of the three arrays are the same as the array rain. While the scope could be narrowed with rain(:ncol,top_lev:) in the mask expression, the assignment statments for the three affected variables still use the full scope. Although test with other compilers, e.g., intel, does not report diff, the diagnostic output for these three variables are assumed to have also be affected. Fixes #5864 [NBFB] for tests that compare eam.h0 with diff in AQRAIN, ANRAIN and FREQR. The test results are otherwise not affected. | 17 August 2023, 14:41:50 UTC |
| 1161cf7 | Wuyin Lin | 16 August 2023, 19:14:30 UTC | Merge branch 'wlin/atm/fix_p3_input_output_dims' (PR #5876) Bugfix: rework P3_input_dim and P3_output_dim for hist_coord The constant integer scalar and array in calling add_hist_coord to define P3_input_dim and P3_output_dim can cause type mismatch for some compilers, leading to invalid values of these two coordinate arrays in eam history output, along with randomness from one run to another. This behavior causes tests to be labelled diff although they are otherwise BFB. Fixes #5863 [BFB] for all actual test results. Some baselines (that compare eam.h#) may contain invalid values for P3_input_dim and/or P3_output_dim, and the tests would report diff. * origin/wlin/atm/fix_p3_input_output_dims: revert to explicit initialization due to complaint by nvidia compiler Change to use implicit loop to populate P3_input_dim and P3_output_dim arrays Bugfix: rework P3_input_dim and P3_output_dim for hist_coord | 16 August 2023, 19:14:30 UTC |
| 2fcda09 | Walter Hannah | 16 August 2023, 15:10:48 UTC | bug fix for MSA cease flag | 16 August 2023, 15:10:48 UTC |
| b8b7519 | Wuyin Lin | 16 August 2023, 02:28:38 UTC | Fix array shapes in where assignment statements in micro_p3_interface.F90 Mismatch of array shapes in where assignment statements and where mask expression causing three diagostic variables, AQRAIN, ANRAIN, FREQR, to differ from one run to another when using gnu compiler. The declared shapes of the three arrays are the same as the array rain. While the scope could be narrowed with rain(:ncol,top_lev:) in the mask expression, the assignment statments for the three affected variables still use the full scope. Although test with other compilers, e.g., intel, does not report diff, the diagnostic output for these three variables are assumed to have also be affected. Fixes #5864 [NBFB] for tests that compare eam.h0 with diff in AQRAIN, ANRAIN and FREQR. The test results are otherwise not affected. | 16 August 2023, 02:28:38 UTC |
| 8ada657 | Wuyin Lin | 15 August 2023, 15:50:26 UTC | revert to explicit initialization due to complaint by nvidia compiler | 15 August 2023, 15:50:26 UTC |
| b9cdd88 | Carolyn Begeman | 29 June 2023, 16:34:50 UTC | Correct the units of active tracer tendencies | 15 August 2023, 14:13:14 UTC |
| 2e3be1d | Azamat Mametjanov | 15 August 2023, 01:41:07 UTC | Merge branch 'azamat/chrysalis/update-v3-wcycl-pes' (PR #5879) Update WCYCL PE-layouts on Chrysalis. [BFB] | 15 August 2023, 01:41:07 UTC |
| 2a4ef31 | Wuyin Lin | 14 August 2023, 20:15:19 UTC | Change to use implicit loop to populate P3_input_dim and P3_output_dim arrays | 14 August 2023, 20:15:19 UTC |
| 31f1e12 | Azamat Mametjanov | 14 August 2023, 19:09:48 UTC | Update WCYCL PE-layouts on Chrysalis [BFB] | 14 August 2023, 19:09:48 UTC |
| 6d5a875 | Benjamin Hillman | 14 August 2023, 18:06:03 UTC | Merge branch 'whannah/mmf/surface-flux-bug-fix' (#5838) Fix a bug in which surface sensible and latent surface fluxes have been unintentionally swapped in the CRM interface. The impact of this fix will generally be small because these fluxes are currently only used to influence the internal CRM friction calculation. The application of suface fluxes in the PBL scheme outside of the CRM (in tphysac) are still correct, so there is no fundamental impact to the water mass or energy budgets. [non-BFB] for MMF cases. | 14 August 2023, 18:06:03 UTC |
| 714d2cf | Walter Hannah | 14 August 2023, 15:59:39 UTC | misc fixes for pam_accelerate | 14 August 2023, 15:59:39 UTC |
| 8d88f9a | Walter Hannah | 14 August 2023, 15:32:52 UTC | add AWFL compsets for testing alternate PAM dycor | 14 August 2023, 15:32:52 UTC |
| f3fb461 | Walter Hannah | 14 August 2023, 15:14:24 UTC | lower PAM time step to 4 sec | 14 August 2023, 15:14:24 UTC |
| bcaa21d | Carolyn Begeman | 11 August 2023, 21:12:10 UTC | Compute sshGrad once per edge | 13 August 2023, 21:33:41 UTC |
| b58039e | Wuyin Lin | 11 August 2023, 16:52:45 UTC | Bugfix: rework P3_input_dim and P3_output_dim for hist_coord | 11 August 2023, 16:52:45 UTC |
| b77febc | Phil Jones | 11 August 2023, 15:13:42 UTC | fix openacc data directive on non-existent ssh_sal array an openacc data transfer on the self-attraction ssh change was outside any conditional for SAL so was operating on a non-existent array if SAL is turned off. This mod changes the location of the data directive so it is within the compute SAL routine and only executed of SAL is turned on | 11 August 2023, 15:13:42 UTC |
| 3ca0a18 | Mike Kelleher | 11 August 2023, 13:30:46 UTC | Add micro_p3 to list of possible ptend names | 11 August 2023, 13:30:46 UTC |
| 7ba8fbd | Carolyn Begeman | 10 August 2023, 21:03:42 UTC | Split barotropic subcycle loops | 10 August 2023, 21:03:42 UTC |
| 40a5d80 | Jon Wolfe | 08 August 2023, 23:17:11 UTC | Update mapping and domain files for ne30pg2-oRRS18to6v3 | 08 August 2023, 23:17:11 UTC |
| ab0eddb | Walter Hannah | 08 August 2023, 20:52:25 UTC | add MMF2 RCE compset | 08 August 2023, 20:52:25 UTC |
| 2b05547 | Walter Hannah | 08 August 2023, 20:47:06 UTC | fix restart when using PAM | 08 August 2023, 20:47:06 UTC |
| 4dc55f8 | Walter Hannah | 08 August 2023, 20:46:27 UTC | update PAM submodule | 08 August 2023, 20:46:27 UTC |
| b8be65d | Gregory Lemieux | 31 July 2023, 17:33:20 UTC | update fates type names for fates refactor | 08 August 2023, 18:35:50 UTC |
| f7bb269 | James Foucar | 08 August 2023, 17:08:27 UTC | Merge remote-tracking branch 'origin/master' into jasonb5/cime/adds_testing_excludes * origin/master: (114 commits) Make chemistry preprocessor processed files permanent for chemistry package superfast_mam5_resus_mom_soag, ridding use of -usr_mech_infile. Fixed cime submodule Update shell_commands for eam-chem_pp test with v3 chem_mech Update use_cases for BGCEXP_LNDATM_CNPRDCTC Rename ncdata file for SCM use cases Fix FIDEAL test - added back ideal_phys_option removed in MAM5 PR Fix issue when ZM is off and reset FAQP to use v2 config Update arm97 and generic SCM to use v3atm Remove prescribed volcanic aerosol and tracer specifier CH4 from v3atm use_case files Run exact-restart wcycl-debug test with 2 threads On pm-cpu only, make default compiler by Intel (from GNU) [bfb] fixes indexing bug in mpas cvmix interface Ensure seasaltaod gets fillvalue at nighttime add alternative impl for tro/str AODSO4 Reset non-default PSTRID to 1 Add back spa as chem package option Update pm-cpu intel compiler version Enable compset specific option for dust_emis_scheme Revert "Merge branch 'tangq/atm/lightning-NOx' into v3atm/eam/master_MAM5_wetaero_chemdyg (PR #5806)" Add reference for dust emission scheme 2 ... | 08 August 2023, 17:08:27 UTC |
| 78a5ea1 | noel | 07 August 2023, 16:05:20 UTC | Merge branch #5845 from E3SM-Project/ndk/machinefiles/pm-cpu-use-intel-by-default (PR #5845) On pm-cpu, change default compiler to Intel | 07 August 2023, 16:05:20 UTC |
| 915e929 | Wuyin Lin | 07 August 2023, 14:47:35 UTC | Merge branch 'v3atm/eam/master_MAM5_wetaero_chemdyg' (PR #5781) Three climate changing features, consolidated compsets, and some code cleanup for EAMv3 Add remaining climate changing features for v3 atm. - Improve the aerosol wet removal parameterization (CC for both v2 and v3 compsets). Significantly reduce the aerosol loading overestimation and help decrease the overly strong aerosol radiative forcing. . Use vertical velocity from ZMmp to calculate the (previously prescribed) in-cloud supersaturation, Lagrangian timestep, and pdraft fraction. . Consider the cloud-borne aerosol detrainment. This makes cloud-borne aerosol evolution consistent with the convective cloud condensate. . Reorder the deep convection wet removal and stratiform wet removal as described in: Shan, Y., X., Liu, L., Lin, Z., Ke, Z., Lu (2021): An improved representation of in-cloud wet removal processes in a global climate model and impacts on simulated aerosol vertical profiles, J. Geophys. Res.-Atmos, 126, e2020JD034173. https://doi.org/10.1029/2020JD034173. - Implement MAM5, which adds an additional stratospheric sulfate mode on top of the existing MAM4 aerosol scheme (CC) MAM5 is able to better represent the stratospheric sulfate aerosol and can work with both Simple chemistry (SC) and Full chemistry (FC). MAM5-SC is linked to chemUCI. - Fix the the aqueous chemistry bug where total condensate (liquid +ice) mass mixing ratio was used for the SO2 aqueous chemistry process. The problem is that only liquid water mass mixing ratio should be used here. The bug was found because P3 produces more ice mass which leads to a much larger sulfate production from aqueous chemistry compared to MG2. By working together with Dick Easter, we identified this problem and we also got confirmation from NCAR. - Add compsets with full v3atm configuration, and finalization of it. - Add consolidated v3 compsets and configurations based on v3alpha02. . The compset names, both the aliases and the longnames, retain the format used in V2. For example, F1850, F2010, F20TR have corresponding longnames of 1850_EAM%CMIP6.+, 2010_EAM%CMIP6.+ and 20TR_EAM%CMIP6.+. . The new physics and chemistry from v3atm, including chemUCI, Linozv3, MAM5, VBS-SOA, and ZM enhancements, do not appear in the compset names but are active after this PR. . The new physics and chemistry are indicated in the description of the compsets, and reflected in the new use_case files. . This PR will retire V2 compsets under the same names upon merging. . Additional changes are added to enable or fix nightly tests that will use the new code base along with the consolidated compsets. These include FIDEAL, FAQP, SCM, BGC, clubb-only, chem_pp. . Lightning NOx bugfix that was on this branch was reverted. A revert of revert should be done when v3alpha02 based runs are completed. . Make preprocessed files permanent for v3 chemistry package superfast_mam5_resus_mom_soag. . Some code clean-up. [CC] [NML] Fixes #5713 | 07 August 2023, 14:47:35 UTC |
| bc20044 | Andrew M. Bradley | 03 August 2023, 18:45:20 UTC | EAM/HOMME: Remove -DNC=4 in bld/configure; NC is an unused symbol. | 04 August 2023, 22:39:17 UTC |
| d8d7f26 | Walter Hannah | 04 August 2023, 22:26:46 UTC | configure change to build MMF dummy modules | 04 August 2023, 22:26:46 UTC |
| 6eb0322 | Walter Hannah | 04 August 2023, 22:21:58 UTC | bug fix | 04 August 2023, 22:21:58 UTC |
| 69976aa | Walter Hannah | 04 August 2023, 22:21:37 UTC | add dummy modules to fix build issues | 04 August 2023, 22:21:37 UTC |
| d103a16 | Walter Hannah | 04 August 2023, 22:19:46 UTC | minor cleanup | 04 August 2023, 22:19:46 UTC |
| 496e6d4 | Andrew M. Bradley | 03 August 2023, 18:45:20 UTC | EAM/HOMME: Remove -DNC=4 in bld/configure; NC is an unused symbol. | 03 August 2023, 18:45:20 UTC |
| b3454bb | Wuyin Lin | 03 August 2023, 18:27:57 UTC | Make chemistry preprocessor processed files permanent for chemistry package superfast_mam5_resus_mom_soag, ridding use of -usr_mech_infile. | 03 August 2023, 18:27:57 UTC |
| 855bd01 | Azamat Mametjanov | 03 August 2023, 17:21:59 UTC | Merge branch 'azamat/tests/superbfb-atm-wcycl' (PR #5717) Add initial superBFB tests for EAM and WCYCL The purpose of this suite is to make sure new code maintains bit-for-bit properties we demand of the model. These properties include: - exact restart: the model should be able to restart during a run with bit-for-bit identical results compared to a model which ran for the same total time without restarting. - MPI-task count invariance: The model should give the same answers between two runs that only differed by the number of MPI tasks used. - OpenMP thread count invariance: The model should give the same answers between two runs that only differ by number of OpenMP threads used. There is a suite for each major component model (`atm`, `ocn`, `ice`, `lnd`, `rof`, and fully-coupled `wcycl`). They cover the standard-resolution grids in both release/optimized and debug configurations. [BFB] | 03 August 2023, 17:21:59 UTC |
| 4ee9da3 | Walter Hannah | 03 August 2023, 17:09:43 UTC | update PAM submodule | 03 August 2023, 17:09:43 UTC |
| ea8b3b9 | Jon Wolfe | 03 August 2023, 15:56:23 UTC | Merge branch 'vanroekel/ocean/fix-cvmix-indexing-bug' (PR #5842) Fixes indexing bug in mpas cvmix interface There is a small indexing error in the MPAS ocean interface to CVMix. It has only emerged in GPU configurations, but may emerge in cases where minLevelCell is not equal to 1 Fixes #5840 [BFB] | 03 August 2023, 15:56:23 UTC |
| f56cc6c | Walter Hannah | 03 August 2023, 15:39:18 UTC | MMF fixes in configure | 03 August 2023, 15:39:18 UTC |
| fa5d687 | Walter Hannah | 03 August 2023, 15:38:19 UTC | update global variables in pam_accelerate | 03 August 2023, 15:38:19 UTC |
| 011b898 | Walter Hannah | 03 August 2023, 15:36:51 UTC | update PAM submodule | 03 August 2023, 15:36:51 UTC |
| 06d37b7 | Wuyin Lin | 03 August 2023, 12:17:24 UTC | Merge branch 'mahf708:add_so4_aods' into v3atm/eam/master_MAM5_wetaero_chemdyg (PR #5833) EAM: split AODSO4 into tropospheric and stratospheric components This small PR splits AODSO4 into its stratospheric and tropospheric components following previous (v2) practice. Note that there is already "stratospheric sulfate AOD" (from v3) that's not modified by this PR. This implementation has two distinct advantages over the current one from v3: 1) it follows the logic of previous implementation of speciated AODs; 2) it follows the naming scheme of the previous implementation and aligns it with the naming of burdens (SAODVIS vs AODSO4_STR, cf ABURDENSO4_STR). [BFB] | 03 August 2023, 12:17:24 UTC |
| 0cf98a8 | Wuyin Lin | 03 August 2023, 12:04:09 UTC | Merge branch 'wlin/atm/v3compsets_alpha02' into v3atm/eam/master_MAM5_wetaero_chemdyg (PR #5823) Consolidate v3 compsets with v3alpha02 configuration v3atm based simulations have been relying on a combination of physics/chemistry specific compsets and customized run scripts. The run scripts typically contain additional configuration options replacing physics, chem package, chemistry mechanism file, forcing files, and tuning options. In this PR, all the above are consolidated into compsets and the corresponding complete configuration options for the component (EAM). The v3alpha02 configuration is made default for the consolidated compsets. The compset names, both the aliases and the longnames, retain the format used in V2. For example, F1850, F2010, F20TR have corresponding longnames of 1850_EAM%CMIP6.+, 2010_EAM%CMIP6.+ and 20TR_EAM%CMIP6.+. The new physics and chemistry from v3atm, including chemUCI, Linozv3, MAM5, VBS-SOA, and ZM enhancements, do not appear in the compset names. The new physics and chemistry are indicated in the description of the compsets, and reflected in the new use_case files. This PR will retire V2 compsets under the same names upon merging. Additional changes are added to enable or fix nightly tests that will use the new code base along with the consolidated compsets. These include FIDEAL, FAQP, SCM, BGC, clubb-only, chem_pp. [BFB] for all equivalent v3 configurations that previously were controlled via run script. | 03 August 2023, 12:04:09 UTC |
| 8fd79e8 | Walter Hannah | 02 August 2023, 22:25:36 UTC | add dummy module for microp_driver | 02 August 2023, 22:25:36 UTC |
| e044259 | Walter Hannah | 02 August 2023, 22:25:08 UTC | delete white space | 02 August 2023, 22:25:08 UTC |
| c48f968 | Walter Hannah | 02 August 2023, 22:24:40 UTC | minor cmake update | 02 August 2023, 22:24:40 UTC |
| 5422091 | Walter Hannah | 02 August 2023, 22:23:34 UTC | update comments | 02 August 2023, 22:23:34 UTC |
