| 3d9b82b | Hyun Kang | 01 December 2023, 18:39:56 UTC | Fix bugs on variable names | 01 December 2023, 18:39:56 UTC |
| af8ee25 | Hyun Kang | 01 December 2023, 17:26:25 UTC | First commit on hkang/ocean/div-on-vertex - Compute divergence, vertVelocity, vertTransportVelocity on vertex - AMOC streamfunction computation changes to integrate from top to bottom | 01 December 2023, 17:26:25 UTC |
| 88488dc | Jon Wolfe | 30 November 2023, 16:07:52 UTC | Merge branch 'proteanplanet/seaice/fix-nc-metadata' (PR #6084) MPAS-SeaIce netcdf output finalization for E3SM V3 This PR corrects and improves netcdf metadata in MPAS-SeaIce output for E3SM V3. The following changes have been made: Correction of existing long names and units to match the CF convention and addition of missing units and long names consistent with CF conventions. [BFB] | 30 November 2023, 16:07:52 UTC |
| 839d1cf | Jon Wolfe | 28 November 2023, 18:00:09 UTC | Merge branch 'jonbob/mpaso/change-default-redi-min-layers' (PR #6077) Change default config_Redi_min_layers_diag_terms to 0 Changes a single default setting for config_Redi_min_layers_diag_terms from 6 to 0. This has otherwise been set in user_nl_mpaso by run scripts during coupled model testing. [NML] [non-BFB] | 28 November 2023, 18:00:09 UTC |
| 8ee229d | Andrew Roberts | 27 November 2023, 19:22:57 UTC | Adds, updates and improves netcdf metadata long names and units, including to match CF conventions | 27 November 2023, 19:22:57 UTC |
| a58c5b6 | Benjamin Hillman | 21 November 2023, 20:52:00 UTC | Merge branch 'beharrop/mmf/add_macv2-sp_rebase' (#5905) Adds in the MACv2-SP aerosol scheme for a simplified form of anthropogenic aerosols that combines with the prescribed natural aerosol. The current implementation is only for the E3SM-MMF. These changes are controlled via atm namelist options, the default setting is off for the MACv2 scheme. [stealth] | 21 November 2023, 20:52:00 UTC |
| f9acba6 | Jon Wolfe | 21 November 2023, 18:57:58 UTC | Merge branch 'mark-petersen/ocn/btr-weights' (PR #6035) Update weights for ocean barotropic subcycling in split-explicit solver This PR updates the weights config_btr_gam1_velWt1, config_btr_gam2_SSHWt1 in the MPAS-Ocean barotropic solver based on recent analysis of this scheme. This update applies to "split explicit" time stepping schemes, i.e. config_time_integrator = 'split_explicit' and the new config_time_integrator = 'split_explicit_ab2' in #5989. The new weights allow for a barotropic time step config_btr_dt to be 25% longer in the tests of EC30to60, thus speeding up the barotropic subcycling. We expect that values of config_btr_dt can be increased by 25% for all meshes. [NML] [non-BFB] | 21 November 2023, 18:57:58 UTC |
| 317cf68 | Jon Wolfe | 21 November 2023, 18:54:35 UTC | Merge branch 'hkang/ocean/AB2-timestep' (PR #5989) Add split-explicit AB2 time stepping capability to the ocean component The second-order Adams Bashforth (AB2) time stepping method is applied to the baroclinic system of MPAS-Ocean to enable faster computation of the baroclinic system. The AB2 time stepping method, one of multistep methods, computes time stepping procedure (Stage 1~3) once per time step, while the predictor-corrector which is a default scheme computes it twice per time step. In practice, the AB2 method can provide a speedup of 1.5x to 1.8x. Due to its high sensitivity to time step size, the predictor-corrector scheme is only applied to the layer thickness equation. All subroutines and the barotropic system advance (Stage 2) in the AB2 code are the same as used in the split-explicit code (mpas_ocn_time_integration_split.F). [NML] [non-BFB] | 21 November 2023, 18:54:35 UTC |
| 343e922 | Jon Wolfe | 20 November 2023, 21:45:37 UTC | Change default config_Redi_min_layers_diag_terms to 0 | 20 November 2023, 21:45:37 UTC |
| 93ab10c | Peter Schwartz | 20 November 2023, 15:31:09 UTC | Merge remote-tracking branch 'glemfork/lnd/fates-crossgrid-seeddispersal' (PR #5555) This PR enables FATES to disperse seeds across neighboring grid cells using MPI. The API update includes calls to new fates dispersal procedures and as such should be coordinated with NGEET/fates#1005. [B4B] except for FATES | 20 November 2023, 15:31:09 UTC |
| faac9f0 | Wuyin Lin | 17 November 2023, 17:04:20 UTC | Merge branch 'quantheory:quantheory/fix-negative-snow_depth' (PR #6034) Move h2osno limiter to ensure positive snow depth In LakeHydrologyMod, when applying the effects of sublimation and dew to snow, the snow_depth variable is set using the h2osno variable before that variable is limited to positive values. This commit changes the order of those statements to ensure that snow_depth is not accidentally set to a negative value. It is important to note that in the existing code, only extremely small-magnitude negative values are typically produced, because of another limiter applied earlier in the code. Specifically, h2osno variable is set using h2osno(c) = h2osno(c) - qflx_sub_snow(p)*dtime and qflx_sub_snow is set using qflx_sub_snow(p) = min(qflx_evap_soi(p), h2osno(c)/dtime) Thus, h2osno can only be temporarily negative due to limited floating point precision, i.e. the fact that we can get a slightly negative output from h2osno(c) - (h2osno(c)/dtime)*dtime For this reason, this commit only produces roundoff-level changes in answers under typical conditions. It is also known that invalid values of snow_depth and snowdp are implicated in some rare model crashes (see #5798). The causes are unknown, but in at least one case involved exponentially growing negative snow depth. It is possible that this change will prevent such crashes; investigation is ongoing at the time of this commit. [non-BFB] Possible, only if negative h2osno occur during the course of a test. | 17 November 2023, 17:04:20 UTC |
| 3e1a1bd | Wuyin Lin | 17 November 2023, 17:02:15 UTC | Merge branch 'quantheory:quantheory/gustiness-fixes-for-v3' (PR #5850) Fixes for multiple issues in gustiness calculations This is designed to fix the following issues: . Confusion between scalar and vector stress calculations #5834 . Incorrect calculation of gustiness #5835 . EAM's 'U10' output includes a gustiness enhancement #5836 . Possible double-counting of boundary-layer gustiness contributions over land #5837 The first of these was fixed by forcing ATM_SUPPLIES_GUSTINESS=TRUE for all EAM cases, and the second was fixed purely by rewriting the Fortran formulas. These two changes are climate changing, and will generally tend to reduce the impact of gustiness on the mean winds, i.e. mean wind speed will increase. The third fix is to the U10 diagnostic only, and will decrease the output U10. A value that has not been "fixed" in this way can be obtained by outputting the new history variable 'U10WITHGUSTS' from EAM. The final fix is to remove some double-counting between gustiness parameterizations in EAM and ELM. The fix can be "undone" by setting force_land_gustiness = .true. in the ELM namelist. Note that these fixes are only applied over land and ocean. At the request of sea ice developers, this tag also disables gustiness over sea ice completely. Fixes #5834 Fixes #5835 Fixes #5836 Fixes #5837 [CC] [NML] | 17 November 2023, 17:02:15 UTC |
| d2ffe91 | Wuyin Lin | 16 November 2023, 20:26:59 UTC | Merge branch 'wlin/atm/fix_tests_with_L80' (PR #6054) Fix tests incompatitle with L80 and restore tentative config options for SSP The PR fixes two sets of tests. . SSP tests with tentative fix from # 5965 stops working. The EAM%CMIP6 generic pattern match needs to be removed to have it work. This is due to the -vbs option that would be set if having the generic pattern match. The additive style of EAM configure option would then have no mechansim to disable vbs once set. . Update the vertical dimension for 3D variables that condidiag tests track. [BFB] Only the above mentioned tests will diff; and the the differences for these tests following this fix are due to #5996, and other went in on the same day. | 16 November 2023, 20:26:59 UTC |
| 7680d57 | Gautam Bisht | 16 November 2023, 19:29:27 UTC | Merge branch 'hongyili/mosart/mosart-heat-fix' (PR #5940) Adding the initialization of a variable used in MOSART-heat; otherwise, the main-channel temperature will be overestimated. The change made only affects stream temperature, nothing else. Fixes #5941 [BFB] | 16 November 2023, 19:29:27 UTC |
| a3a53ba | Peter Schwartz | 16 November 2023, 19:05:26 UTC | Merge remote-tracking branch 'donghuixfork/donghuix/lnd/wetland-inundation-scheme' (PR #5974) In default, the infiltration rate is the same for the non-water surface and surface water storage within the grid cell. This assumption results in a significant underestimation of surface water because the infiltration in the surface water storage is not constrained. In this PR, we introduced a modified infiltration scheme to constrain the infiltration in the surface water storage. The infiltration rate in the surface water storage is smaller than the infiltration rate in the non-water surface. More details about this new scheme and corresponding evaluations can be found in the preprint: https://doi.org/10.21203/rs.3.rs-2733749/v1 The manuscript is still under review. The new infiltration scheme can be turned by adding use_modified_infil = .true. in user_nl_elm. We passed all the tests in e3sm_land_developer test suite. We also created a test for the simulation of surface water dynamics with the new infiltration scheme and calibrated parameter for NLDAS domain: surface_water_dynamics. This test was added into e3sm_land_developer test suite. [BFB] | 16 November 2023, 19:05:26 UTC |
| a3ea386 | jayeshkrishna | 16 November 2023, 18:56:13 UTC | Merge branch 'dqwu/machinefiles/upgrade-anlgce-ub18' (PR #6026) Recently, two ANL GCE nodes (compute-01 and compute-02) have been upgraded from Ubuntu 18.04 to 22.04. Create a new machine named anlgce-ub22 to replace deprecated anlgce-ub18. Also remove deprecated CMake macro ZLIB_PATH for anlgce/anlgce-ub22. [BFB] * dqwu/machinefiles/upgrade-anlgce-ub18: Removing deprecated CMake macro ZLIB_PATH for anlgce/anlgce-ub22 Adding support for two ANL GCE nodes that use Ubuntu 22.04 | 16 November 2023, 18:56:13 UTC |
| b2067b7 | Hyun Kang | 15 November 2023, 20:41:31 UTC | Change the header of the AB2 code | 15 November 2023, 20:41:31 UTC |
| 0908426 | James Foucar | 15 November 2023, 18:53:30 UTC | Merge branch 'jgfouca/cmake_names_in_macros' into master (PR #6014) Use CMake variables/names in our cmake macros This should be the last major PR in CMAKE V2 effort. Changes Summary: * Macro structure changes * Add post-process step to set final values for a few items * Make cmake conversion more robust by storing pre-macro values and comparing instead of just looking at new variables * Change all macros to set variables that cmake knows about! This is a huge change with wide impacts * We no longer have to set flag properties on all files. This simplifies things but makes it hard to support e3sm_remove_flags so that feature has been removed. You should always be able to append flags to achieve the same effect as removing a flag. * Try to remove as much of the linker flag micromanagement as possible * We now default to cxx linker. Intel and PGI still have to use fortran unfortunately since our main function is in fortran * Remove as many non-cmake settings as possible from the macros * Add script for converting macros from the old style to new style * Upgrade the compare-flags tool to support parsing the e3sm.bldlog file. This is a tougher way to compare flags since you have to build the cases with -j 1, but it's more robust than looking at cmake internal files. * Remove lots of unneeded stuff from main cmake files (build_model and common_setup) * Remove unused old makefiles for COSP and MPAS * Move gptl build to cmake Testing: * mappy_gnu: e3sm_developer, with full flag compare on a couple big cases * anlgce: e3sm_developer builds * pm-cpu_intel: e3sm_developer, with full flag compare on one big case * chrysalis_intel: e3sm_developer, with full flag compare on one big case * summit: build one big case with pgigpu, ibmgpu, pgi [BFB] | 15 November 2023, 18:53:30 UTC |
| 10f1bac | James Foucar | 14 November 2023, 18:49:40 UTC | Update upstream macros | 14 November 2023, 18:55:59 UTC |
| 42c41fc | James Foucar | 14 November 2023, 18:42:44 UTC | Merge remote-tracking branch 'origin/master' into jgfouca/cmake_names_in_macros * origin/master: Homme/SL: Address a warning. Homme: Fix latitude in dcmip2016_test1_forcing. Minor updates to ELM tech doc. Homme: Add gllfvremap_planar_ut unit test. Homme(xx): Set up C++-vs-F90 standalone planar pg2 test. Homme: Add planar capability to gllfvremap_mod. Homme: Modify dcmip2016_test1_pg_forcing to handle planar case. Change minimum concentration and mass of sea ice velocity solution Add single missing variable to OMP private Use small pe layout for TSC test Add size 'S' pes for chrysalis ne4 tests | 14 November 2023, 18:42:44 UTC |
| f4fef0b | Andrew M. Bradley | 14 November 2023, 17:24:11 UTC | Merge branch 'ambrad/homme/dp-pg' (PR #6057) Homme(xx)/pgN: Add pgN feature to doubly periodic planar mode. * Add pgN feature to planar doubly periodic mode. * Add some standalone-hommexx infrastructure to support using the same unit-test exe in multiple tests. * Add an init-planar capability to Hommexx unit tests. * Add a unit test: gllfvremap_planar_ut, planar version of old gllfvremap_ut unit test. * Add a BFB test for F90/C++ dycore consistency in planar mode with pg2 physics grid. e3sm_developer passes on Chrysalis. Additional tests for GPU/EAMxx pass on various machines. [BFB] except for new tests in homme_integration | 14 November 2023, 17:24:11 UTC |
| c336779 | Jon Wolfe | 14 November 2023, 17:08:44 UTC | Merge branch 'jonbob/mpaso/fix-small-omp' (PR #6037) Add single missing variable to OMP private Adds one new variable to an OMP private directive in a recently modified routine. It doesn't appear to cause PET failures but still should be added. [non-BFB] potentially for threaded runs with active ocean | 14 November 2023, 17:08:44 UTC |
| 463a53e | Robert Jacob | 14 November 2023, 15:14:01 UTC | Merge branch 'mkstratos/cime/nbfb-pes-change' (PR #6030) Adds a small (S) layout: 1 node per instance for the ne4 grid on chrysalis, to reduce the number of nodes requested for multi-instance tests Switches the TSC nightly test in e3sm_atm_nbfb to use this layout Nightly test node requests are reduced as follows MVK: 90 -> 30; TSC: 36 -> 12 Wall-clock times are increased by ~1.6x for TSC and ~2.6x for MVK [BFB] | 14 November 2023, 15:14:01 UTC |
| ee14d67 | Wuyin Lin | 14 November 2023, 02:42:12 UTC | Implement an adaptable index as pver in condidiag nml | 14 November 2023, 02:42:12 UTC |
| 8324c66 | Andrew M. Bradley | 13 November 2023, 22:09:45 UTC | Homme/SL: Address a warning. | 13 November 2023, 22:09:45 UTC |
| 40efc90 | Gautam Bisht | 13 November 2023, 19:31:10 UTC | Merge branch 'bishtgautam/lnd/fix-docs' (PR #6059) Updates the description of ELM technical documentation. [BFB] | 13 November 2023, 19:31:10 UTC |
| 375b69b | Jon Wolfe | 10 November 2023, 15:55:35 UTC | Merge branch 'proteanplanet/seaice/vsolvelim' (PR #6050) Align minimum concentration and mass limits in MPAS-SeaIce This changes the minimum sea ice concentration and mass per unit area used to solve the sea ice momentum equation to 10^-11 and 10^-10, respectively, aligning the concentration cutoff with the value used in sea ice column physics. The values have been reduced from 10^-3 and 10^-2, respectively. The impact of this change is the removal of numerical diffusion in coupling to the ocean, thus sharpening the sea ice edge, and removing "shadow" fields in low-concentration sea ice mass, heat and salt fluxes with the ocean. This PR does not impact flux conservation between models, nor within MPAS-SeaIce [CC] | 10 November 2023, 15:55:35 UTC |
| 49e6d68 | Wuyin Lin | 10 November 2023, 00:54:41 UTC | Change to use ne4pg2_oQU480 for WCYCL1850NS tests | 10 November 2023, 00:54:41 UTC |
| 6def04a | James Foucar | 09 November 2023, 23:18:59 UTC | Merge remote-tracking branch 'origin/master' into jgfouca/cmake_names_in_macros * origin/master: Add muller machine Address few reviewer comments Second attempt at fixing bmatrix equation Fixes one more equation Fixes eqnarray for Github Changes how equations are defined Updates references Adds labels to equations and cross-references Adds mathjax.js for equation numbering add mkdocs-bibtex to pip install Initial commit of TOP parameterization documentation adds syntax highlighting Minor updates Adds notes on running e3sm land developer testsuite | 09 November 2023, 23:18:59 UTC |
| 63709e0 | noel | 09 November 2023, 17:46:46 UTC | Merge branch E3SM-Project/ndk/machinefiles/add-machine-muller (PR #6061) Add muller -- small internal machine at NERSC with GPU nodes similar to pm-gpu | 09 November 2023, 17:46:46 UTC |
| 4951e07 | Wuyin Lin | 09 November 2023, 16:54:18 UTC | Replace ne11_oQU240 WCYCL1850NS tests with ne4 | 09 November 2023, 16:54:18 UTC |
| 7735241 | noel | 08 November 2023, 19:40:07 UTC | Add muller machine | 08 November 2023, 19:40:07 UTC |
| 0b7cdf4 | donghuix | 08 November 2023, 05:10:25 UTC | remove frac_h2osfc_act from output | 08 November 2023, 05:10:25 UTC |
| 50d641d | Andrew M. Bradley | 06 November 2023, 18:49:15 UTC | Homme: Fix latitude in dcmip2016_test1_forcing. This is an old bug in the original forcing function. The physgrid variant, dcmip2016_test1_forcing, is fine. | 07 November 2023, 20:09:52 UTC |
| 1c3e9c3 | Gautam Bisht | 07 November 2023, 16:10:15 UTC | Minor updates to ELM tech doc. Updates the description of ELM technical documentation. | 07 November 2023, 16:10:15 UTC |
| 9a1dca9 | Gautam Bisht | 07 November 2023, 16:01:50 UTC | Merge branch 'bishtgautam/docs/lnd-baseline-notes' (PR #5978) Adds notes on explaining creating baselines and comparing against those baselines for the `e3sm_land_developer` test suite. [BFB] | 07 November 2023, 16:01:50 UTC |
| ae74855 | Wuyin Lin | 07 November 2023, 03:39:34 UTC | Add default IC (ncdata) for ne120np4 with L80 | 07 November 2023, 03:39:34 UTC |
| e7921a0 | Gregory Lemieux | 06 November 2023, 17:44:04 UTC | update fates interface and submodule for hetresp issue fix | 06 November 2023, 22:12:19 UTC |
| a15a967 | YanlanLiu | 03 June 2022, 22:04:09 UTC | Add fates cross-grid seed dispersal mechanism | 06 November 2023, 22:10:52 UTC |
| 0dd0883 | Peter Schwartz | 06 November 2023, 20:00:22 UTC | Merge branch 'bishtgautam/doc/top-parameterization'(PR #5980) Adds the technical documentation for parameterization of the topographic solar radiation. [BFB] | 06 November 2023, 20:00:22 UTC |
| e1a1356 | Andrew M. Bradley | 02 November 2023, 02:55:00 UTC | Homme: Add gllfvremap_planar_ut unit test. | 06 November 2023, 18:41:40 UTC |
| 804b3b9 | Andrew M. Bradley | 02 November 2023, 01:30:07 UTC | Homme(xx): Set up C++-vs-F90 standalone planar pg2 test. | 06 November 2023, 18:40:45 UTC |
| 4b54afa | Andrew M. Bradley | 01 November 2023, 20:44:19 UTC | Homme: Add planar capability to gllfvremap_mod. | 06 November 2023, 18:40:02 UTC |
| 206a093 | Andrew M. Bradley | 31 October 2023, 23:42:31 UTC | Homme: Modify dcmip2016_test1_pg_forcing to handle planar case. | 06 November 2023, 18:39:26 UTC |
| 336123b | Wuyin Lin | 03 November 2023, 23:05:43 UTC | Fix tests incompatitle with L80 and restore tentative config options for SSP | 03 November 2023, 23:05:43 UTC |
| bc35c3b | James Foucar | 03 November 2023, 20:59:01 UTC | Fixes for fortran linking | 03 November 2023, 20:59:01 UTC |
| fe1b459 | James Foucar | 03 November 2023, 20:43:46 UTC | Fixes for pgi | 03 November 2023, 20:43:46 UTC |
| f9c0795 | Andrew Roberts | 03 November 2023, 18:30:50 UTC | Change minimum concentration and mass of sea ice velocity solution | 03 November 2023, 18:30:50 UTC |
| 435ce72 | James Foucar | 03 November 2023, 18:04:25 UTC | Merge remote-tracking branch 'origin/master' into jgfouca/cmake_names_in_macros * origin/master: (156 commits) Avoid calling add_default when no generic values present for gw_convect_hcf and hdepth_scaling_factor Reset hdepth_scaling_factor for MMF config Add settings to re-tune QBO, kPOM, and additional hyperviscosity modifier to allow use of rough topography Make "column_package" the default column_physics_type for BGC Add build-namelist default for chemdyg vertical indicies Add namelist definitions of UCIgaschmbudget_2D_L* remove unnecessary chemdyg settings in user_nl_eam for tests remove default chemdyg vertical indices in F90 code Add default chemdyg vertical indices in xml Update default chemdyg vertical indices in xml Update bld files to match Registry changes, using automated scripts Move some description changes from bld files to Registry Homme: Fix config.h comment style. Homme: Distinguish between F90 and C++ in HOMMEXX_ENABLE_GPU symbol use. Homme: Comment out two builds that aren't used in ctests. Hommexx: Fix issues related to qsize=0. Hommexx: Remove redundant HOMMEXX_ENABLE_GPU definition. Homme: Fix potential bad access to an array. Homme: Add USE_MPI_RUN_SCRIPT to standalone system. Homme(xx)/SL: Add SL-transport feature to doubly periodic mode. ... | 03 November 2023, 18:04:25 UTC |
| 19bd6d5 | James Foucar | 03 November 2023, 17:47:35 UTC | Allow fortran linking if we have to | 03 November 2023, 17:47:35 UTC |
| 1df0c3b | Wuyin Lin | 03 November 2023, 17:28:51 UTC | Merge branch 'wlin/atm/new_settings_qbo_kpom_hvref' (PR #6043) Add settings to re-tune QBO, kPOM, and additional hyperviscosity modifier The following settings are changed or added . hdepth_scaling_factor is halved to improve QBO . New mam_pom file with modified hygroscopicity to reflect the tuning of kPOM = 0.04, for v3 configurations . Additional optional hv_ref_profiles value for use with rough topography (which is not used by default) [NBFB] All tests involving EAM except for FIDEAL, FDPSCREAM, and MMF [NML] a modified parameter value and an updated input file | 03 November 2023, 17:28:51 UTC |
| 6a8c964 | Wuyin Lin | 03 November 2023, 17:26:51 UTC | Merge branch 'tangq/atm/chemdyg-L80' (PR #6032) Implement default chemdyg vertical indices automatically adjust to L80 or L72 The L80 configuration #5996 will require a different default set of chemdyg vertical indices of namelist variables. This PR will automatically pick the correct chemdyg indices for L80 or L72, so the chemdyg budget diagnostics will be correct regardless of the vertical level setting. [BFB] [NML] new nml variables for control output for chemdyg | 03 November 2023, 17:26:51 UTC |
| b658327 | Wuyin Lin | 03 November 2023, 17:24:53 UTC | Merge branch 'zyuying/atm/fix-CLD_CAL_TMP' (PR #6011) Bug fix for output of COSP lidar simulator CLD_CAL_TMPICE and CLD_CAL_TMPLIQ are given the wrong values for liquid and ice in the interface code. The dimension for the variables with “_TMP” should be temperature instead of height (cosp_ht). Add a coordinate “cosp_temp” and change the long_name for “_TMP” variables. Fixes #6002 Fixes #6010 [BFB] for all tests except for cosp meta data and a new cosp_temp coordinate variable. | 03 November 2023, 17:24:53 UTC |
| 6bf384e | Wuyin Lin | 03 November 2023, 17:20:46 UTC | Merge branch 'whannah/atm/add-L80-support' (PR #5996) Add L80 support for v3 Modify default configurations to use a new 80 layer vertical grid, mainly for enhancing the QBO in E3SMv3. Since this PR touches many compsets and tests I took the opportunity to clean up how the configurations are specified and delete some unused compsets. New atmosphere initial condition files (i.e. ncdata) have been added for ne4, n30, and ne120 grids, but only for cases with realistic topography. The process of creating new initial conditions for idealized compsets like aquaplanet and RCE was complicated by the new aerosol/chemistry options, so these configurations will continue to use the v2 settings, including L72, and will be updated later. [non-BFB] [NML] | 03 November 2023, 17:20:46 UTC |
| 4f4f6fa | Wuyin Lin | 03 November 2023, 17:18:30 UTC | Merge branch 'mingxuanwupnnl/atm/fix_VBS_SOAG_DryDep' (PR #5962) Fix gas dry deposition for VBS SOAG gas species This PR fixes the issue on dry deposition of VBS SOAG gases. Dry deposition for VBS SOAG gas species, namely SOAG0, SOAG15, SOAG24, SOAG35, SOAG34, SOAG33, SOAG32, SOAG31, is now included in shared seq_drydep_mod.F90 and namelist drydep_list. Fixes #5963 [CC] [NML] | 03 November 2023, 17:18:30 UTC |
| 1fa7ef7 | Gautam Bisht | 02 November 2023, 18:22:07 UTC | Address few reviewer comments | 02 November 2023, 18:22:07 UTC |
| d27af88 | Mark Petersen | 02 November 2023, 17:31:06 UTC | Change halo computation to nEdgesAll | 02 November 2023, 17:31:06 UTC |
| 77a847e | Hyun Kang | 02 November 2023, 13:51:13 UTC | Fix a bug for the decomposition error after rebase - Fix a bug for the decomposition error after rebase - Added a line in mpas_ocn_time_integration_split_ab2.F: call mpas_dmpar_field_halo_exch(domain, 'tangentialVelocity') | 02 November 2023, 13:51:13 UTC |
| 4d44ecd | James Foucar | 01 November 2023, 21:21:47 UTC | gptl build fixes | 01 November 2023, 21:21:47 UTC |
| 8771928 | James Foucar | 01 November 2023, 20:29:38 UTC | Turn on verbose makefiles for gptl | 01 November 2023, 20:29:38 UTC |
| 94d6a36 | James Foucar | 01 November 2023, 19:07:07 UTC | Remove last uses of e3sm_remove_flag in Depends files | 01 November 2023, 19:07:07 UTC |
| 3872f4c | Jon Wolfe | 01 November 2023, 18:42:27 UTC | Merge branch 'jonbob/seaice/fix-bgc-column-physics-type' (PR #6036) Make "column_package" the default column_physics_type for BGC With icepack now the default seaice column physics package, we need to make "column_package" the default when seaice BGC is on until it's completely supported in icepack. [non-BFB] only for BGC configurations with active seaice (which are currently broken) | 01 November 2023, 18:42:27 UTC |
| 8af0c4f | Wuyin Lin | 01 November 2023, 17:22:12 UTC | Avoid calling add_default when no generic values present for gw_convect_hcf and hdepth_scaling_factor | 01 November 2023, 17:22:12 UTC |
| 253dd26 | James Foucar | 01 November 2023, 16:11:40 UTC | We haven't used Makefiles to build cosp in years | 01 November 2023, 16:11:40 UTC |
| 73b395a | James Foucar | 01 November 2023, 15:52:40 UTC | More fixes to sharedlibs | 01 November 2023, 15:52:40 UTC |
| a4c868a | James Foucar | 01 November 2023, 15:27:12 UTC | More fixes to buildlib.kokkos and post_process.cmake needs to not blow away things set up by the project command | 01 November 2023, 15:27:12 UTC |
| ae2d6d4 | Wuyin Lin | 01 November 2023, 03:02:38 UTC | Reset hdepth_scaling_factor for MMF config | 01 November 2023, 03:02:38 UTC |
| 1ab9633 | Wuyin Lin | 01 November 2023, 02:39:03 UTC | Add settings to re-tune QBO, kPOM, and additional hyperviscosity modifier to allow use of rough topography | 01 November 2023, 02:39:03 UTC |
| 3af01f9 | James Foucar | 31 October 2023, 22:08:04 UTC | Revert "Not sure we keep this" This reverts commit c0a92a2214b0a2019c0cc24630aff1c441ba4590. | 31 October 2023, 22:08:04 UTC |
| 81d80e0 | James Foucar | 31 October 2023, 22:03:37 UTC | Cleanup kokkos sharedlib build wrapper | 31 October 2023, 22:03:37 UTC |
| 9e6f04e | James Foucar | 31 October 2023, 21:50:12 UTC | Remove FFLAGS_NOOPT concept | 31 October 2023, 21:50:12 UTC |
| db42f2a | Benjamin Hillman | 31 October 2023, 21:43:50 UTC | Merge branch 'whannah/mmf/fix-gw-heating' (#5982) Previously the MMF heating tendency used for the convective gravity wave parameterization included the effect of radiation. This moves the calculation so that radiative heating can be removed at all levels. [non-BFB] for all MMF tests | 31 October 2023, 21:43:50 UTC |
| f4d112b | Hyun Kang | 31 October 2023, 21:39:16 UTC | Change the default config_time_integrator to split_explicit_ab2 - Change the default baroclinic time stepping method (config_time_integrator) to 'split_explicit_ab2' - Add a note to the 'config_n_ts_iter' description in Registry.xml on how the iteration works when 'config_time_integrator = 'split_explicit_ab2' | 31 October 2023, 21:39:16 UTC |
| bb4ec51 | Jon Wolfe | 31 October 2023, 19:15:12 UTC | Add single missing variable to OMP private | 31 October 2023, 19:15:12 UTC |
| aca5dc0 | Mark Petersen | 31 October 2023, 18:50:01 UTC | change config_btr_dt of 75s to 1:15 format | 31 October 2023, 18:50:01 UTC |
| f92ce02 | Jon Wolfe | 31 October 2023, 18:40:38 UTC | Make "column_package" the default column_physics_type for BGC | 31 October 2023, 18:40:38 UTC |
| cdfebee | James Foucar | 31 October 2023, 18:34:58 UTC | Clean up deoptimization a bit | 31 October 2023, 18:34:58 UTC |
| 17df36d | Hyun Kang | 30 October 2023, 19:14:00 UTC | Update weights for BTR subcycling in split-explicit solver * Update weight for the barotropic subcycling in split_explicit and split_explicit_ab2 solver by @dengwirda - config_btr_gam1_velWt1: 0.5 -> 0.5333 - config_btr_gam2_SSHWt1: 1.0 -> 0.5333 - config_btr_dt for EC30to60 meshes: 60 s -> 75 s * PR in E3SM-Ocean-Discussion https://github.com/E3SM-Ocean-Discussion/E3SM/pull/48 | 31 October 2023, 18:22:06 UTC |
| 198c7b8 | James Foucar | 31 October 2023, 17:13:35 UTC | Fixes for free/fixed and macro exp | 31 October 2023, 17:13:35 UTC |
| abe445e | Andrew M. Bradley | 31 October 2023, 16:44:42 UTC | Merge branch 'ambrad/homme/dp-sl' (PR #6013) * Add semi-Lagrangian transport feature to planar doubly periodic mode. * Add a BFB test for F90/C++ dycore consistency. * Fix some C++ dycore issues related to qsize=0. * Add a bit of infrastructure to make running standalone tests on Summit much easier. Passes e3sm_developer and homme_integration on Chrysalis. Passes new BFB test on Ascent. [BFB] except for new tests in homme_integration | 31 October 2023, 16:44:42 UTC |
| a27115e | Jon Wolfe | 31 October 2023, 16:35:06 UTC | Merge branch 'proteanplanet/ocean/pslv' (PR #5999) Fixes PMSL coupling between ocean and atmosphere This fixes a major bug in E3SM by replacing an incorrect coupling of PBOT (pressure in the mid-bottom atmospheric layer), with PSLV (atmosphere model sea level pressure) in the ocean-atmosphere coupled fields. The consequences of this PR are widespread: It was diagnosed from intermittent crashes that have been experienced in the Mediterranean Sea, it changes widespread pressure fields experienced on all ocean surfaces, and fixes sea ice biases. This pull request only affects B-cases. In G-cases, PBOT and PSLV are currently identically set to pressure at mean sea level, thus a reason why this bug has previously gone undetected. Reference to PBOT has been completely removed in the sea ice coupling code as part of this PR to avoid future confusion, because it is was not being used. [CC] for B-cases | 31 October 2023, 16:35:06 UTC |
| d18c6e9 | Jon Wolfe | 31 October 2023, 16:30:04 UTC | Merge branch 'eclare108213/seaice/icepack-integration' (PR #5958) Initial icepack integration Installs Icepack in E3SM. This PR includes MPAS-seaice changes necessary to run Icepack in equivalent physics configurations as the original column package code. The entire Icepack repository is installed as a submodule linked from the main branch of E3SM’s Icepack fork. Some minor changes were made to the original column package code for consistency with Icepack during testing. Icepack replaces colpkg as the default column physics package in this PR. Fully coupled E3SM v3alpha trigrid with Icepack physics is statistically compatible with the 100-year control at the 99% confidence interval. Icepack is thoroughly and promptly documented in its git repository (the source code is in icepack/doc/). [NML] [CC] | 31 October 2023, 16:30:04 UTC |
| 5330bd8 | James Foucar | 31 October 2023, 16:25:40 UTC | Better way to handle free/fixed fortran | 31 October 2023, 16:25:40 UTC |
| 522cd9f | Jon Wolfe | 31 October 2023, 15:59:39 UTC | Merge branch 'erinethomas/mpas-si/reduce_flux_iterations' (PR #5921) Reduce number of sea ice flux iterations from 10 to 5 The current number of iterations to calculate sea ice fluxes is excessive. Convergence of atm-sea ice fluxes is reached within a few iterations, therefore, the default value for the number of iterations should be reduced from 10 to 5. [NML] [non-BFB] | 31 October 2023, 15:59:39 UTC |
| 18b455d | James Foucar | 31 October 2023, 15:37:05 UTC | Fixes for using cmake vars | 31 October 2023, 15:37:05 UTC |
| c05d008 | Sean Patrick Santos | 30 October 2023, 22:05:06 UTC | Move `h2osno` limiter to ensure positive snow depth. In `LakeHydrologyMod`, when applying the effects of sublimation and dew to snow, the `snow_depth` variable is set using the `h2osno` variable before that variable is limited to positive values. This commit changes the order of those statements to ensure that `snow_depth` is not accidentally set to a negative value. It is important to note that in the existing code, only extremely small-magnitude negative values are typically produced, because of another limiter applied earlier in the code. Specifically, `h2osno` variable is set using ``` h2osno(c) = h2osno(c) - qflx_sub_snow(p)*dtime ``` and `qflx_sub_snow` is set using ``` qflx_sub_snow(p) = min(qflx_evap_soi(p), h2osno(c)/dtime) ``` Thus, `h2osno` can only be temporarily negative due to limited floating point precision, i.e. the fact that we can get a slightly negative output from ``` h2osno(c) - (h2osno(c)/dtime)*dtime ``` For this reason, this commit only produces roundoff-level changes in answers under typical conditions. It is also known that invalid values of `snow_depth` and `snowdp` are implicated in some rare model crashes (see #5798). The causes are unknown, but in at least one case involved exponentially growing negative snow depth. It is possible that this change will prevent such crashes; investigation is ongoing at the time of this commit. [non-BFB] | 30 October 2023, 22:05:06 UTC |
| f2e04d4 | James Foucar | 30 October 2023, 19:26:17 UTC | Updating compare-flags to look at logs | 30 October 2023, 19:26:17 UTC |
| 7f5b078 | James Foucar | 30 October 2023, 16:10:57 UTC | Clean up some logic in build_model | 30 October 2023, 16:10:57 UTC |
| 70b4126 | Wuyin Lin | 30 October 2023, 13:08:02 UTC | Merge branch 'wlin/lnd/extra_surfdata_with_top' (PR #6008) Update surfdata with TOP for ne4np4/ne4pg2 simyr1850 and ne30np4_simyr2010 The surfdata with TOP is needed for ne30_oECv3.F2010 and ne4_oQU240.WCYCL1850NS tests. The surfdata for ne4pg2_simyr1850 is also updated. Fixes #6007. [BFB] No other tests are affected. [NML] fsurdat changed for above mentioned test grids/compsets combinations | 30 October 2023, 13:08:02 UTC |
| 8189158 | Wuyin Lin | 30 October 2023, 13:05:25 UTC | Merge branch 'whannah/atm/add-hdepth_scaling_factor' (PR #5985) Merge branch 'whannah/atm/add-hdepth_scaling_factor' into next (PR #5985) Add hdepth scaling factor for convective gravity waves Adds a namelist variable "hdepth_scaling_factor" for the convective gravity wave scheme that will be needed for tuning the QBO in v3. The default value of 1 will retain the current behavior. [BFB] [NML] new nml variable hdepth_scaling_factor for all tests involving eam | 30 October 2023, 13:05:25 UTC |
| f94e7e3 | dqwu | 26 October 2023, 20:40:17 UTC | Removing deprecated CMake macro ZLIB_PATH for anlgce/anlgce-ub22 Recently, the dependency on CIME/Tools/Makefile has been removed for SCORPIO and we no longer need CMake macro ZLIB_PATH for anlgce or anlgce-ub22. | 28 October 2023, 02:24:23 UTC |
| 7d29f0b | dqwu | 26 October 2023, 18:39:00 UTC | Adding support for two ANL GCE nodes that use Ubuntu 22.04 Create a new machine named anlgce-ub22 for two ANL GCE nodes that have recently been upgraded from Ubuntu 18.04 to 22.04. This change also replaces the deprecated machine anlgce-ub18. | 28 October 2023, 02:24:21 UTC |
| 50924a3 | Qi Tang | 27 October 2023, 22:20:23 UTC | Add build-namelist default for chemdyg vertical indicies | 27 October 2023, 22:20:23 UTC |
| 696c8a6 | Qi Tang | 27 October 2023, 22:13:21 UTC | Add namelist definitions of UCIgaschmbudget_2D_L* | 27 October 2023, 22:13:21 UTC |
| 7f9228a | James Foucar | 27 October 2023, 21:39:24 UTC | Merge remote-tracking branch 'origin/master' into jgfouca/cmake_names_in_macros * origin/master: (41 commits) Ascent needs to use static hdf5 libs Don't change submodule Reorg csm_share Depends Clean up csm_share depends files a bit Add missing variable to omp directive Add missing variable to omp directive Update CIME submodule Fix a few things I missed Update new mapping files to use updated algotihms and naming convention For NERSC machines only, update to latest AMD compiler Add some modules to remove before loading what we want. Set default as config_Redi_quasi_monotone_safety_factor=0.9 Set E3SM default to config_Redi_use_quasi_monotone_limiter=true Remove RediKappaScaling creation and initialization Update bld files to match Registry changes Make bld files consistent with Registry changes Fixed OpenMP changes redi namelist options fixes build errors Changes redi tapering and slopes add domain to RK4 subroutine ... | 27 October 2023, 21:39:24 UTC |
| f76c5f8 | James Foucar | 27 October 2023, 21:37:41 UTC | Progress | 27 October 2023, 21:37:41 UTC |
| 0ec006d | James Foucar | 27 October 2023, 21:21:53 UTC | Merge branch 'jgfouca/ascent_fix' into master (PR #6028) Ascent needs to use static hdf5 libs The ibm linker chokes on the .so's due to the non-standard suffix. FindHDF5 for some reason does not use the symlinks which have a normal suffix. [BFB] | 27 October 2023, 21:21:53 UTC |
| a8b7065 | Michael Kelleher | 27 October 2023, 21:12:05 UTC | Use small pe layout for TSC test | 27 October 2023, 21:12:05 UTC |
| f501def | Michael Kelleher | 27 October 2023, 21:10:59 UTC | Add size 'S' pes for chrysalis ne4 tests | 27 October 2023, 21:10:59 UTC |
| 1107d6b | James Foucar | 27 October 2023, 20:50:59 UTC | Progress | 27 October 2023, 20:50:59 UTC |
