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ChangeLog
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===============================================================================
Tag Creator: mlevy
Developers: klindsay, mlevy
Tag Date: 10 Apr 2019
Tag Name: pop2/trunk_tags/cesm_pop_2_1_20190410
Tag Summary: Allow pop to run with nblocks_clinic = 0 on a task
Also improves support of general case where
nblocks_clinic < max_blocks_clinic
Testing: aux_pop on cheyenne - C tests were bit-for-bit with
20190325, G compsets didn't have a baseline to compare
against (previous testing didn't use CICE tag compatible
with CIME 5.8). Also, the following four new tests ran
successfully but failed BASELINE and NLCOMP due to being
new tests:
SMS_Ld2_P72_D.T62_g37.C1850ECO.cheyenne_intel.pop-ecosys_81blocks_100x116_spacecurve
SMS_Ld2_P80_D.T62_g37.C1850ECO.cheyenne_intel.pop-ecosys_81blocks_100x116_spacecurve
SMS_Ld1_P136_D.T62_g17.C.cheyenne_intel.pop-144blocks_320x384_spacecurve
SMS_Ld1_P144_D.T62_g17.C.cheyenne_intel.pop-144blocks_320x384_spacecurve
M cime_config/testdefs/testlist_pop.xml
A + cime_config/testdefs/testmods_dirs/pop/144blocks_320x384_spacecurve
A + cime_config/testdefs/testmods_dirs/pop/81blocks_100x116_spacecurve
A + cime_config/testdefs/testmods_dirs/pop/ecosys_144blocks_320x384_spacecurve
A + cime_config/testdefs/testmods_dirs/pop/ecosys_81blocks_100x116_spacecurve
M drivers/cpl/ocn_comp_mct.F90
M source/POP_SpaceCurveMod.F90
M source/distribution.F90
M source/ecosys_driver.F90
M source/ecosys_forcing_mod.F90
M source/geoheatflux.F90
M source/overflows.F90
M source/step_mod.F90
M source/tavg.F90
M source/tidal_mixing.F90
===============================================================================
Tag Creator: mlevy
Developers: jedwards
Tag Date: 25 Mar 2019
Tag Name: pop2/trunk_tags/cesm_pop_2_1_20190325
Tag Summary: Make buildlib compatible with cime5.8
Testing: aux_pop on cheyenne (no baselines to compare against since change
in cime is not backwards compatible); all C compsets built and ran
but G compsets did not (cice is not yet cime5.8 compatible).
M cime_config/buildlib
===============================================================================
Tag Creator: mlevy
Developers: jedwards
Tag Date: 23 Mar 2019
Tag Name: pop2/trunk_tags/cesm_pop_2_1_20190323
Tag Summary: Remove duplicate code in io_pio.F90
Testing: aux_pop on cheyenne_intel and a single hobart_nag test
M source/io_pio.F90
===============================================================================
Tag Creator: mlevy
Developers: mlevy, jluo
Tag Date: 22 Mar 2019
Tag Name: pop2/trunk_tags/cesm_pop_2_1_20190322
Tag Summary: Update MARBL to include Jessica's SPECTRA model (and add an
aux_pop_MARBL test for it). Requires a temporary additional valid
value for OCN_BGC_CONFIG in order to get the default initial conditions
right, and also increases max tavg variable count
Testing: aux_pop on cheyenne_intel (ran aux_pop_MARBL on marbl_dev_n104 tag).
NLCOMP failures for all [CG]1850ECO compsets because new parameters
were introduced. Also, same tests are not bit-for-bit on cheyenne_intel
and hobart_nag because of compiler optimization of x**1.5 in MARBL. Other
compilers (and non-ecosystem compsets) are bit-for-bit.
M Externals_POP.cfg
M MARBL_scripts/MARBL_wrappers/MARBL_settings.py
M bld/namelist_files/namelist_defaults_pop.xml
M cime_config/config_component.xml
M cime_config/testdefs/testlist_pop.xml
A + cime_config/testdefs/testmods_dirs/pop/ecosys_spectra_pfts
M source/tavg.F90
===============================================================================
Tag Creator: klindsay
Developers: klindsay
Tag Date: 06 Mar 2019
Tag Name: pop2/trunk_tags/cesm_pop_2_1_20190306
Tag Summary: correct ssp compset longname string matching
Testing: none
M cime_config/config_component.xml
===============================================================================
Tag Creator: klindsay
Developers: klindsay, altuntas
Tag Date: 22 Feb 2019
Tag Name: pop2/trunk_tags/cesm_pop_2_1_20190222
Tag Summary: Add support for OCN_TRANSIENT=ssp126,ssp585
Testing: aux_pop on cheyenne/intel (with ssp585 changes)
all tests pass, all tests passed b4b
M bld/build-namelist
M bld/namelist_files/namelist_defaults_pop.xml
M cime_config/config_component.xml
===============================================================================
Tag Creator: altuntas
Developers: altuntas
Tag Date: 18 Jan 2019
Tag Name: pop2/trunk_tags/cesm_pop_2_1_20190118
Tag Summary: Set sfwf_weak_restore to 4 years for CORE2 and 1 year for JRA
Remove several unnecessary _HIRES ifdefs
(Additional CORE2 and JRA forcing changes in CIME PR #2984)
Testing: aux_pop and aux_pop_tripole on cheyenne/intel, answer changes in
all forced cases (due to changes in sfwf_weak_restore and
coldair_outbreak_mod)
M bld/build-namelist
M bld/namelist_files/namelist_defaults_pop.xml
M source/step_mod.F90
M source/tavg.F90
===============================================================================
Tag Creator: jedwards
Developers: jedwards
Tag Date: 15 Jan 2019
Tag Name: pop2/trunk_tags/cesm_pop_2_1_20190115
Tag Summary: Allow buildcpp to rewrite case env_build.xml
M cime_config/buildlib
M cime_config/buildnml
===============================================================================
Tag Creator: altuntas
Developers: altuntas
Tag Date: 19 Dec 2018
Tag Name: pop2/trunk_tags/cesm_pop_2_1_20181219
Tag Summary: Add the 48yr/day PE layout decomposition
Testing: aux_pop on cheyenne/intel, b4b
Files Modified:
M bld/generate_pop_decomp.xml
===============================================================================
Tag Creator: mlevy
Developers: mlevy
Tag Date: 22 Oct 2018
Tag Name: pop2/trunk_tags/cesm_pop_2_1_20181022
Tag Summary: Bring in MARBL code clean-up
Testing: aux_pop on cheyenne/intel, aux_pop_MARBL on cheyenne/{intel,gnu} and
hobart/{nag,pgi}. All tests pass except NLCOMP when ecosys tracer
module is turned on. (Note: BASELINE tests pass, even with ecosys)
Files Modified:
M Externals_POP.cfg
M MARBL_scripts/MARBL_wrappers/MARBL_settings.py
===============================================================================
Tag Creator: altuntas
Developers: altuntas
Tag Date: 19 Oct 2018
Tag Name: pop2/trunk_tags/cesm_pop_2_1_20181019
Tag Summary: Enable MOC computation with land-block elimination
- ignore missing values during lbe aux grid check
- set gather_global_dbl missing value to undefined_nf_r8 instead of undefined_nf
- add gx1v7 spacecurve decompositions
- add gx1v7 spacecurve test
Testing: aux_pop on cheyenne/intel. bfb except the new test.
Files Modified:
M mpi/gather_scatter.F90
M source/diags_on_lat_aux_grid.F90
M bld/generate_pop_decomp.xml
M cime_config/testdefs/testlist_pop.xml
A cime_config/testdefs/testmods_dirs/pop/default_spacecurve
A cime_config/testdefs/testmods_dirs/pop/default_spacecurve/shell_commands
A cime_config/testdefs/testmods_dirs/pop/default_spacecurve/user_nl_pop
===============================================================================
Tag Creator: mlevy
Developers: mlevy
Tag Date: 15 Oct 2018
Tag Name: pop2/trunk_tags/cesm_pop_2_1_20181015
Tag Summary: Update CVMix to latest version (bfb, better performance)
Also, change cvmix test (which uses lcvmix = .true.) to
no_cvmix test (which uses lcvmix = .false.) -- default value
of lcvmix is already true, so we need a test using the old KPP
module.
Testing: aux_pop on cheyenne/intel. bfb except the renamed test.
M Externals_POP.cfg
M cime_config/testdefs/testlist_pop.xml
D cime_config/testdefs/testmods_dirs/pop/cvmix
D cime_config/testdefs/testmods_dirs/pop/cvmix/include_user_mods
D cime_config/testdefs/testmods_dirs/pop/cvmix/user_nl_pop
A cime_config/testdefs/testmods_dirs/pop/no_cvmix
A cime_config/testdefs/testmods_dirs/pop/no_cvmix/include_user_mods
A cime_config/testdefs/testmods_dirs/pop/no_cvmix/user_nl_pop
===============================================================================
Tag Creator: altuntas
Developers: jedwards
Tag Date: 04 Oct 2018
Tag Name: pop2/trunk_tags/cesm_pop_2_1_20181004
Tag Summary: A fix for cime issue #2822 and run the cime interface scripts through py3 pylint
Also, added a multi-instance C1850ECO test in aux_pop
Testing: aux_pop on cheyenne/intel. bfb except the new test.
M bld/build-namelist
M cime_config/buildcpp
M cime_config/buildlib
M cime_config/buildnml
M cime_config/testdefs/testlist_pop.xml
===============================================================================
Tag Creator: klindsay
Developers: klindsay
Tag Date: 26 Sep 2018
Tag Name: pop2/trunk_tags/cesm_pop_2_1_20180926
Tag Summary: update ndep for OCN_TRANSIENT=1850-2000
updated ndep forcing files are from CESM 2.1 BWHIST runs, and span 1849-2015
introduce new test into cheyenne/intel, aux_pop and aux_pop_MARBL:
ERS.T62_g17.C1850ECO.cheyenne_intel.pop-ecosys_ocn_transient_1850_2000
Testing: aux_pop on cheyenne/intel
tests pass, including baseline comparison to cesm_pop_2_1_20180921
(new test fails NLCOMP and BASELINE)
Files Modified:
M ChangeLog
M bld/namelist_files/namelist_defaults_pop.xml
M cime_config/testdefs/testlist_pop.xml
A cime_config/testdefs/testmods_dirs/pop/ecosys_ocn_transient_1850_2000
A cime_config/testdefs/testmods_dirs/pop/ecosys_ocn_transient_1850_2000/include_user_mods
A cime_config/testdefs/testmods_dirs/pop/ecosys_ocn_transient_1850_2000/shell_commands
===============================================================================
Tag Creator: altuntas
Developers: altuntas
Tag Date: 21 Sep 2018
Tag Name: pop2/trunk_tags/cesm_pop_2_1_20180921
Tag Summary: add coordinates to tavg_TEMP2 (for CMIP6 diags)
Testing: aux_pop on cheyenne/intel
Files Modified:
M source/baroclinic.F90
===============================================================================
Tag Creator: klindsay
Developers: klindsay
Tag Date: 12 Sep 2018
Tag Name: pop2/trunk_tags/cesm_pop_2_1_20180912
Tag Summary: add support for abio_dic_dic14 in CMIP6 historical runs
merged from abio_cmip6_historical_n01_cesm_pop_2_1_20180830
Testing: aux_pop on cheyenne/intel
except for tests mentioned below, all tests pass
NLCOMP fails for tests with abio_dic_dic14, because of new namelist var
some MEMCOMP failures
if OCN_TRANSIENT='1850-2000' then set abio_atm_co2_opt='drv_diag', abio_atm_d14c_opt='file'
add ABIO-DIC modifier to POP2 in compset longnames, enable abio_dic_dic14 if it is present
extend pattern matching to allow POP2 compset modifiers to be in arbitrary order
(remove ECO-PHYS-CYCLE modifier, replace usage with %ECO%PHYS-CYCLE)
add abio_dic_dic14_restfile_fallback namelist var
if abio_dic_dic14 is reading from a restart file, and module tracers are not present,
then read them from the file specified by abio_dic_dic14_restfile_fallback
set abio_dic_dic14_restfile_fallback to most recent results from CMIP6 B1850 control run (for g17 only)
Files Modified:
M .
M ChangeLog
M bld/build-namelist
M bld/namelist_files/namelist_defaults_pop.xml
M bld/namelist_files/namelist_definition_pop.xml
M cime_config/config_component.xml
M cime_config/config_compsets.xml
M input_templates/ocn.abio_dic_dic14.tavg.csh
M source/abio_dic_dic14_mod.F90
===============================================================================
Tag Creator: mlevy
Developers: mlevy
Tag Date: 30 August 2018
Tag Name: pop2/trunk_tags/cesm_pop_2_1_20180830
Tag Summary: Merge latest marbl_dev branch tag (n98) onto trunk
-- bit-for-bit code-cleanup / refactor in MARBL requires some
changes to the pop driver as well
Testing: aux_pop on cheyenne_intel and aux_pop_MARBL on cheyenne_{intel,gnu}
as well as hobart_{nag,pgi}. Testing was done on marbl_dev_n98 which
is identical to this tag
M Externals_POP.cfg
M source/ecosys_driver.F90
M source/ecosys_forcing_mod.F90
M source/ecosys_running_mean_saved_state_mod.F90
M source/ecosys_tavg.F90
M source/ecosys_tracers_and_saved_state_mod.F90
M source/passive_tracers.F90
===============================================================================
Tag Creator: mlevy
Developers: mlevy
Tag Date: 29 August 2018
Tag Name: pop2/trunk_tags/cesm_pop_2_1_20180829
Tag Summary: Update manage_externals to manic-v1.1.5
(Also updated the .git remote)
-- Requested by Bill Sacks due to bug in older versions
Testing: None (ensured that CVMix and MARBL were checked out properly)
CVMIX tag: v0.90-beta
MARBL tag: marbl0.31.0
M externals/manage_externals
[Lots of files modified in the above directory]
===============================================================================
Tag Creator: klindsay
Developers: klindsay
Tag Date: 4 August 2018
Tag Name: pop2/trunk_tags/cesm_pop_2_1_20180804
Tag Summary: Merge latest final_CMIP6_BGC_tags branch tag (n13) onto trunk
correct IAGE reset when lrobert_filter=.true., add CMIP tracer budget diagnostics
move submeso and diag_gm_bolus-dependent tavg vars into separate tavg_contents files
update 1850 Ndep forcing from recent coupled B1850 WACCM run
correct EBM tavg vars, enable some 2D EBM tavg vars by default
Testing: aux_pop intel/cheyenne
MARBL tag marbl0.31.0 from marbl-ecosys/MARBL
tests pass, including BASELINE to cesm_pop_2_1_20180720
BASELINE fails for lrobert_filter=.true., because IAGE changed
NLCOMP and BASELINE failed for all ECO compsets, because of namelist/forcing changes
some MEMCOMP failures
M ChangeLog
M bld/build-namelist
M bld/namelist_files/namelist_defaults_pop.xml
M bld/namelist_files/namelist_definition_pop.xml
A + input_templates/gm_bolus_terms_tavg_contents
A + input_templates/gm_bolus_terms_tavg_contents_high_freq
M input_templates/gx1v6_tavg_contents
M input_templates/gx1v6_tavg_contents_high_freq
M input_templates/gx1v7_tavg_contents
M input_templates/gx1v7_tavg_contents_high_freq
M input_templates/gx3v5_tavg_contents
M input_templates/gx3v7_tavg_contents
M input_templates/ocn.cfc.tavg.csh
M input_templates/ocn.iage.tavg.csh
M input_templates/ocn.sf6.tavg.csh
A + input_templates/submeso_terms_tavg_contents
A + input_templates/submeso_terms_tavg_contents_high_freq
M source/IRF_mod.F90
M source/estuary_vsf_mod.F90
M source/hmix_gm.F90
M source/hmix_gm_aniso.F90
A + source/hmix_gm_share.F90
M source/horizontal_mix.F90
M source/mix_submeso.F90
M source/passive_tracers.F90
M source/step_mod.F90
M source/tavg.F90
===============================================================================
Tag Creator: mlevy
Developers: mlevy
Tag Date: 20 July 2018
Tag Name: pop2/trunk_tags/cesm_pop_2_1_20180720
Tag Summary: Merge latest marbl_dev branch tag (n95) onto trunk
1) POP changes
- New OCN_BGC_CONFIG variable in env_run.xml determines which
tunings to use
- Some namelist variables have different defaults depending on
OCN_BGC_CONFIG
- New test run in aux_pop and aux_pop_MARBL ensures no
unexpected changes to old tunings
2) MARBL changes
- Multiple default settings files to allow running with old
defaults (e.g. CESM 2.0 configuration); POP selects file
based on OCN_BGC_CONFIG value
Testing: aux_pop on cheyenne (intel) (identical code on marbl_dev and
marbl_dev_levy tested with aux_pop_MARBL on cheyenne and hobart)
-- all tests pass except new ecosys_cesm2_0_settings fail NLCOMP
and BASELINE due to lack of existing baselines
M Externals_POP.cfg
M MARBL_scripts/MARBL_wrappers/MARBL_diagnostics.py
M MARBL_scripts/MARBL_wrappers/MARBL_settings.py
M bld/namelist_files/namelist_defaults_pop.xml
M cime_config/buildcpp
M cime_config/buildnml
M cime_config/config_component.xml
M cime_config/testdefs/testlist_pop.xml
A + cime_config/testdefs/testmods_dirs/pop/ecosys_cesm2_0_settings
===============================================================================
Tag Creator: mlevy
Developers: klindsay
Tag Date: 19 July 2018
Tag Name: pop2/trunk_tags/cesm_pop_2_1_20180716
Tag Summary: Tune ocean BGC for CMIP 6 -- this requires an updated MARBL tag
and some new POP namelist options to control new features in MARBL.
Also, three bugfixes:
1. Missing scale_factor for N_SALT diagnostic
2. Correct illegal argument aliasing in time_management.F90
3. Tracer states and some other diagnostics were computed incorrectly
when the Robert filter was enabled (i.e. in gx1v7 runs)
Testing: aux_pop on cheyenne/intel - all POP2%ECO tests fail BASELINE and
NLCOMP; all non-ECO gx1v7 tests fail BASELINE (but pass NLCOMP),
all non-ECO gx3v7 tests pass both BASELINE and NLCOMP.
M Externals_POP.cfg
M MARBL_scripts/MARBL_wrappers/MARBL_settings.py
M MARBL_scripts/MARBL_wrappers/POP_ecosys_diagnostics.py
M bld/build-namelist
M bld/namelist_files/namelist_defaults_pop.xml
M bld/namelist_files/namelist_definition_pop.xml
M cime_config/config_component.xml
M input_templates/gx1v6_tavg_contents
M input_templates/gx1v7_tavg_contents
M input_templates/gx3v7_tavg_contents
M input_templates/ocn.abio_dic_dic14.tavg.csh
M input_templates/ocn.cfc.tavg.csh
M input_templates/ocn.iage.tavg.csh
M input_templates/ocn.sf6.tavg.csh
M source/baroclinic.F90
M source/diagnostics.F90
M source/ecosys_forcing_mod.F90
M source/passive_tracers.F90
M source/step_mod.F90
M source/tavg.F90
M source/time_management.F90
===============================================================================
Tag Creator: altuntas
Developers: jedwards, altuntas
Tag Date: 5 July 2018
Tag Name: pop2/trunk_tags/cesm_pop_2_1_20180705
Tag Summary: Add optional NDEP modifier for POP compsets. The modifier
determines whether OCN_NDEP_DRIVER is to be set to True. Also
added latent_heat_fusion_mks field for CMIP6 vars.
Testing: aux_pop on cheyenne/intel. b4b.
M bld/build-namelist
M cime_config/config_component.xml
M source/tavg.F90
===============================================================================
Tag Creator: mlevy
Developers: mlevy
Tag Date: 14 June 2018
Tag Name: pop2/trunk_tags/cesm_pop_2_1_20180614
Tag Summary: Update MARBL to latest version and make python scripts compatible
with python3
Testing: built a single case on my laptop (no Fortran changes, so should
be bit-for-bit with previous tag)
M Externals_POP.cfg
M MARBL_scripts/MARBL_wrappers/__init__.py
===============================================================================
Tag Creator: altuntas
Developers: altuntas
Tag Date: 31 May 2018
Tag Name: pop2/trunk_tags/cesm_pop_2_1_20180531
Tag Summary: Remove/fix bad compsets. Get MARBL external from github repo, not from svn.
Testing: aux_pop on cheyenne (intel)
M Externals_POP.cfg
M cime_config/config_compsets.xml
===============================================================================
Tag Creator: mlevy
Developers: mlevy, klindsay
Tag Date: 14 May 2018
Tag Name: pop2/trunk_tags/cesm_pop_2_1_20180514
Tag Summary: Merge latest marbl_dev branch tag (n92) onto trunk
1) POP changes
- Running mean saved state comes from same restart file as
ecosys base tracers, not ciso
- build-namelist checks value of CPL_I2O_PER_CAT and only
calls xmlchange if needed
- Better pe layouts on hobart, remove references to yellowstone
in config_pes.xml
- Add gx1v7 test to hobart_nag aux_pop_MARBL, and add a gx3v7
with the ecosystem on to prealpha (also hobart_nag)
- performance_eval test works with ecosystem on
- New river nutrient input file for gx3v7 to be consistent with
mapping files created April 30
2) MARBL changes
- New calcToFloor diagnostic
Testing: aux_pop on cheyenne (intel), aux_pop_MARBL on hobart (nag, intel,
and pgi)
- all gx3v7 tests with ecosystem on fail NLCOMP and BASELINE due
to new river nutrient input file
- all gx3v7 tests on hobart fail NLCOMP and BASELINE due to new
pe layout (so reverting river nutrient input will not be b4b
on that machine)
- gx1v7 hobart_intel test does not successfully run. PGI does
run and nag has ~50% success rate (resubmitting failed nag
test usually results in success)
- all other tests pass
M Externals_POP.cfg
M bld/build-namelist
M bld/namelist_files/namelist_defaults_pop.xml
M cime_config/config_pes.xml
M cime_config/testdefs/testlist_pop.xml
M cime_config/testdefs/testmods_dirs/pop/performance_eval/user_nl_marbl
M source/ecosys_driver.F90
A + source/ecosys_running_mean_saved_state_mod.F90
M source/ecosys_tracers_and_saved_state_mod.F90
===============================================================================
Tag Creator: altuntas
Developers: youngsun, dennis
Tag Date: 12 May 2018
Tag Name: pop2/trunk_tags/cesm_pop_2_1_20180512
Tag Summary: Update to POP's halo update that improves model performance.
M mpi/POP_HaloMod.F90
Testing: aux_pop and aux_pop_tripole on cheyenne (intel). b4b
===============================================================================
Tag Creator: altuntas
Developers: altuntas
Tag Date: 01 May 2018
Tag Name: pop2/trunk_tags/cesm_pop_2_1_20180501
Tag Summary: - debug tidal_mixing module for cases where ltidal_mixing is false by default.
- print error msg if pop decomp not set for the ocn grid.
- add tx0.1v3 size to generate_pop_decomp.xml.
- add/change tx0.1v3 namelist defaults.
- update default nox_flux_monthly_input and nhy_flux_monthly_input
- add new test suite: aux_pop_tripole
- add new compsets for high-res testing: C_HR, C_JRA, C_JRA_HR, GIAF_HR
- unset verbose ocn.vmix.tavg.csh to prevent build-namelist printing the entire script
Testing: aux_pop on cheyenne (intel). bit-for-bit except ECO
aux_pop_tripole
===============================================================================
Tag Creator: altuntas
Developers: altuntas
Tag Date: 30 Apr 2018
Tag Name: pop2/trunk_tags/cesm_pop_2_1_20180430
Tag Summary: add model_doi_url. unsuppress error msg from build-namelist
Testing: aux_pop on cheyenne (intel). bit-for-bit
M cime_config/buildcpp
M cime_config/buildnml
M drivers/cpl/ocn_comp_mct.F90
M source/constants.F90
M source/tavg.F90
===============================================================================
Tag Creator: mlevy
Developers: mlevy, klindsay
Tag Date: 27 Apr 2018
Tag Name: pop2/trunk_tags/cesm_pop_2_1_20180427
Tag Summary: Merge latest marbl_dev branch tag (n87) onto trunk
1) POP changes
- Fix units of U10_SQR in diagnostics
- Change ciso_init_tracer_ext to account for changes from
zoo1[34]C -> zootot1[34]C in MARBL tracer name
- clean up use of ecosys_cfg hash in build-namelist, and
suppress ciso namelist variables from non-ciso runs
- only write about successful marbl_in read from master_task
2) MARBL changes
- only compute nhx_surface_emis if lcompute_nhx_surface_emis
is .true. otherwise return zero (if requested)
- replace several 3D diagnostic fields with surface values and
weighted average over 100m (full 3D fields available still
but not included in default diagnostics)
- Rename zoo1[34]C to zootot1[34]C (in general, use zootot for
all occurences of zoo in marbl_ciso_mod.F90)
- make caco3_bury_thres_omega_calc a tunable parameter
- increase Jint_Ctot_thres_molpm2pyr by order of magnitude
- Introduce new DOP_loss_P_bal to avoid Jint_Ptot inbalance
when very small P:C ratio leads to POP%prod < 0
Testing: aux_pop on cheyenne (intel)
* NLCOMP failures for all ecosys tests (ciso variables changed
and non-ciso tests no longer include ciso variables)
* BASELINE failures for some ecosys tests
- ERI.T62_g17.C1850ECO.cheyenne_intel.pop-ecosys has O(1e-8)
changes due to negative values of POP%prod far from zero
being changed to zero
- Other tests have round-off level changes due to negative
values of POP%prod close to zero being changed to zero
aux_pop_MARBL on hobart (nag, intel, pgi)
* no comparison to baselines but verified that model builds
and runs with these compilers.
M Externals_POP.cfg
M MARBL_scripts/MARBL_wrappers/POP_ecosys_diagnostics.py
M bld/build-namelist
M bld/namelist_files/namelist_defaults_pop.xml
M source/ecosys_driver.F90
M source/forcing.F90
===============================================================================
Tag Creator: altuntas
Developers: altuntas
Tag Date: 19 Apr 2018
Tag Name: pop2/trunk_tags/cesm_pop_2_1_20180419
Tag Summary: add testlist version to testlist_pop
Testing: aux_pop on cheyenne/intel. bfb
M cime_config/testdefs/testlist_pop.xml
===============================================================================
Tag Creator: altuntas
Developers: altuntas, klindsay
Tag Date: 12 Apr 2018
Tag Name: pop2/trunk_tags/cesm_pop_2_1_20180412
Tag Summary: update to testlist v.2 and CVMix v0.90.
- update from testlist v.1 (phased out as of cime5.4.0-alpha.25) to v.2
- correct exp_hab_zetar allocation both in CVMix and POP.
- bugfix for enable START_DATE on last day of month or year. (klindsay)
Testing: aux_pop on cheyenne (intel). bit-for-bit
M Externals_POP.cfg
M cime_config/testdefs/testlist_pop.xml
M drivers/cpl/ocn_comp_mct.F90
M source/vmix_kpp.F90
===============================================================================
Tag Creator: mlevy
Developers: mlevy, klindsay
Tag Date: 6 Apr 2018
Tag Name: pop2/trunk_tags/cesm_pop_2_1_20180406
Tag Summary: Merge latest marbl_dev branch tag (n82) onto trunk
1) POP changes
- atm D14C default values use CMIP6 lat_band values
- improve how marbl_in is read / passed to MARBL
- PHYS-CYCLE compset works now, added ECO-PHYS-CYCLE option
as well
- updated some gx1v7 initial conditions which were out of
sync with gx1v6
- Added box_atm_trace_gas to use box model for atm_co2
- implemented fe_bioavail fix
- update to MARBL 0.28.5
2) MARBL changes
- fix bug so ALK restoring is applied
- Use in situ temperature rather than potential
- Add some divide-by-0 checks
- Fix denominator of POP_bury_coeff
- Change kinetic fraction during gas transfer to match CMIP6
- MARBL now tells POP what diagnostics to include in tavg_contents
- Introduce more carbon diagnostics (some fluxes replaced with
vertical integrals in default settings)
- DO{13,14}C -> DO{13,14}Ctot to because they represent
semi-labile + refractory
- MARBL aborts if mass balance conservation is violated
(users no longer need to inspect vertical integrals in
diagnostic output)
- new tunings to go with fe_bioavail fix
Also fixed bugs introduced in
Testing: aux_pop on cheyenne (intel)
* NLCOMP failures for all ecosys tests and all abio tests
* BASELINE failures for the same, except the non-ecosys abio_transient
test is bit-for-bit
aux_pop_MARBL on hobart (nag, intel, pgi)
* no comparison to baselines since we expect all tests to fail,
just verified that model builds and runs with these
compilers.
M Externals.cfg
M Externals_POP.cfg
A + MARBL_scripts
M bld/build-namelist
M bld/namelist_files/namelist_defaults_pop.xml
M bld/namelist_files/namelist_definition_pop.xml
D cime_config/MARBL_settings_wrapper
D cime_config/MARBL_settings_wrapper/MARBL_settings.py
D cime_config/MARBL_settings_wrapper/__init__.py
M cime_config/buildcpp
M cime_config/buildnml
M cime_config/config_component.xml
M cime_config/config_compsets.xml
M cime_config/testdefs/testlist_pop.xml
A + cime_config/testdefs/testmods_dirs/pop/ecosys_box_atm_co2
M drivers/cpl/ocn_import_export.F90
M externals/manage_externals/.git/index
D input_templates/ocn.ciso.tavg.csh
M input_templates/ocn.ecosys.tavg.csh
M input_templates/ocn.vmix.tavg.csh
M source/abio_dic_dic14_mod.F90
A + source/box_atm_trace_gas_mod.F90
M source/c14_atm_forcing_mod.F90
A + source/ecosys_diagnostics_operators_mod.F90
M source/ecosys_driver.F90
M source/ecosys_forcing_mod.F90
A + source/ecosys_forcing_saved_state_mod.F90
M source/ecosys_tavg.F90
M source/ecosys_tracers_and_saved_state_mod.F90
M source/forcing.F90
M source/forcing_coupled.F90
M source/forcing_fields.F90
M source/passive_tracers.F90
M source/restart.F90
M source/running_mean_mod.F90
M source/tavg.F90
M source/tidal_mixing.F90
A + source/utils_mod.F90
M source/vmix_kpp.F90
===============================================================================
Tag Creator: altuntas
Developers: altuntas
Tag Date: 05 Apr 2018
Tag Name: pop2/trunk_tags/cesm_pop_2_1_20180405
Tag Summary: Tidal PBC, JRA forcing updates, update testlist, correct unit
- Enable default tidal mixing parameterization (Jayne et al.) with partial bottom cells
(Sourcemods from gokhan, adapted to new tidal mixing module)
- JRA forcing updates:
* new init_ts_file, sfwf_filename for gx1v7 for both JRA and CORE2
* sfwf restoring set to 1 yr for gx1v7 by default for both JRA and CORE2
* new ebm_param_filename for gx1v7 JRA (CORE2 unchanged)
- Testlist updates:
* all bluewaters and eos tests removed. (prealpha and prebeta)
* added JRA tests to aux_pop and prebeta
- Correct tavg_SST2 unit
Testing: - aux_pop on cheyenne/intel. all except gx1v7 bit for bit. gx1v7 differs due to new
ic and sfwf files
- G.TL319_t13.startup two-month smoke test for tidal PBC
M bld/build-namelist
M bld/namelist_files/namelist_defaults_pop.xml
M cime_config/testdefs/testlist_pop.xml
? manage_externals.log
M source/baroclinic.F90
M source/tidal_mixing.F90
M source/vmix_kpp.F90
===============================================================================
Tag Creator: altuntas
Developers: njn01
Tag Date: 22 Mar 2018
Tag Name: pop2/trunk_tags/cesm_pop_2_1_20180322
Tag Summary: add new tidal mixing methods, options, variables, energy datasets
- tidal mixing methods: jayne, polzin, schmittner
- Changed initialization calling sequences and split init_tidal_mixing into two routines.
- CVMix changes. (added Schmittner)
- New Geothermal options, variables, options.
Testing: aux_pop on cheyenne (intel)
M Externals_POP.cfg
M bld/build-namelist
M bld/namelist_files/namelist_defaults_pop.xml
M bld/namelist_files/namelist_definition_pop.xml
A input_templates/ocn.base.tavg.csh.nstep
A input_templates/ocn.vmix.tavg.csh
M source/baroclinic.F90
M source/budget_diagnostics.F90
A source/geoheatflux.F90
M source/initial.F90
M source/niw_mixing.F90
M source/restart.F90
M source/step_mod.F90
M source/tavg.F90
M source/tidal_mixing.F90
M source/time_management.F90
M source/vertical_mix.F90
M source/vmix_kpp.F90
===============================================================================
Tag Creator: altuntas
Developers: altuntas
Tag Date: 16 Feb 2018
Tag Name: pop2/trunk_tags/cesm_pop_2_1_20180216
Tag Summary: add tests in a new aux_cime_baselines category
Testing: ran the new test category (with 4 new SMS tests). all pass.
M cime_config/testdefs/testlist_pop.xml
===============================================================================
Tag Creator: mlevy
Developers: mlevy
Tag Date: 5 Feb 2018
Tag Name: pop2/trunk_tags/cesm_pop_2_1_20180205
Tag Summary: Use manage_externals to get CVMix and MARBL rather than
svn:externals (see README_EXTERNALS for details)
Testing: Ensure code still builds and runs with new externals
M .
A Externals.cfg
A Externals_POP.cfg
A README_EXTERNALS
D SVN_EXTERNAL_DIRECTORIES
A externals
A externals/manage_externals
A externals/manage_externals/.dir_locals.el
A externals/manage_externals/.git
A externals/manage_externals/.git/HEAD
A externals/manage_externals/.git/branches
A externals/manage_externals/.git/config
A externals/manage_externals/.git/description
A externals/manage_externals/.git/hooks
A externals/manage_externals/.git/hooks/applypatch-msg.sample
A externals/manage_externals/.git/hooks/commit-msg.sample
A externals/manage_externals/.git/hooks/post-update.sample
A externals/manage_externals/.git/hooks/pre-applypatch.sample
A externals/manage_externals/.git/hooks/pre-commit.sample
A externals/manage_externals/.git/hooks/pre-push.sample
A externals/manage_externals/.git/hooks/pre-rebase.sample
A externals/manage_externals/.git/hooks/pre-receive.sample
A externals/manage_externals/.git/hooks/prepare-commit-msg.sample
A externals/manage_externals/.git/hooks/update.sample
A externals/manage_externals/.git/index
A externals/manage_externals/.git/info
A externals/manage_externals/.git/info/exclude
A externals/manage_externals/.git/logs
A externals/manage_externals/.git/logs/HEAD
A externals/manage_externals/.git/logs/refs
A externals/manage_externals/.git/logs/refs/heads
A externals/manage_externals/.git/logs/refs/heads/master
A externals/manage_externals/.git/logs/refs/remotes
A externals/manage_externals/.git/logs/refs/remotes/origin
A externals/manage_externals/.git/logs/refs/remotes/origin/HEAD
A externals/manage_externals/.git/objects
A externals/manage_externals/.git/objects/info
A externals/manage_externals/.git/objects/pack
A externals/manage_externals/.git/objects/pack/pack-a8d23c04cd24205be25174239305ea4f240d683a.idx
A externals/manage_externals/.git/objects/pack/pack-a8d23c04cd24205be25174239305ea4f240d683a.pack
A externals/manage_externals/.git/packed-refs
A externals/manage_externals/.git/refs
A externals/manage_externals/.git/refs/heads
A externals/manage_externals/.git/refs/heads/master
A externals/manage_externals/.git/refs/remotes
A externals/manage_externals/.git/refs/remotes/origin
A externals/manage_externals/.git/refs/remotes/origin/HEAD
A externals/manage_externals/.git/refs/tags
A externals/manage_externals/.github
A externals/manage_externals/.github/ISSUE_TEMPLATE.md
A externals/manage_externals/.github/PULL_REQUEST_TEMPLATE.md
A externals/manage_externals/.gitignore
A externals/manage_externals/.travis.yml
A externals/manage_externals/LICENSE.txt
A externals/manage_externals/README.md
A externals/manage_externals/README_FIRST
A externals/manage_externals/checkout_externals
A externals/manage_externals/manic
A externals/manage_externals/manic/__init__.py
A externals/manage_externals/manic/checkout.py
A externals/manage_externals/manic/externals_description.py
A externals/manage_externals/manic/externals_status.py
A externals/manage_externals/manic/global_constants.py
A externals/manage_externals/manic/repository.py
A externals/manage_externals/manic/repository_factory.py
A externals/manage_externals/manic/repository_git.py
A externals/manage_externals/manic/repository_svn.py
A externals/manage_externals/manic/sourcetree.py
A externals/manage_externals/manic/utils.py
A externals/manage_externals/test
A externals/manage_externals/test/.coveragerc
A externals/manage_externals/test/.gitignore
A externals/manage_externals/test/.pylint.rc
A externals/manage_externals/test/Makefile
A externals/manage_externals/test/README.md
A externals/manage_externals/test/doc
A externals/manage_externals/test/doc/.gitignore
A externals/manage_externals/test/doc/Makefile
A externals/manage_externals/test/doc/conf.py
A externals/manage_externals/test/doc/develop.rst
A externals/manage_externals/test/doc/index.rst
A externals/manage_externals/test/doc/testing.rst
A externals/manage_externals/test/repos
A externals/manage_externals/test/repos/container.git
A externals/manage_externals/test/repos/container.git/HEAD
A externals/manage_externals/test/repos/container.git/config
A externals/manage_externals/test/repos/container.git/description
A externals/manage_externals/test/repos/container.git/info
A externals/manage_externals/test/repos/container.git/info/exclude
A externals/manage_externals/test/repos/container.git/objects
A externals/manage_externals/test/repos/container.git/objects/41
A externals/manage_externals/test/repos/container.git/objects/41/1de5d96ee418c1c55f3e96e6e6e7c06bb95801
A externals/manage_externals/test/repos/container.git/objects/71
A externals/manage_externals/test/repos/container.git/objects/71/5b8f3e4afe1802a178e1d603af404ba45d59de
A externals/manage_externals/test/repos/container.git/objects/b0
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A externals/manage_externals/test/repos/container.git/objects/f9
A externals/manage_externals/test/repos/container.git/objects/f9/e08370a737e941de6f6492e3f427c2ef4c1a03
A externals/manage_externals/test/repos/container.git/refs
A externals/manage_externals/test/repos/container.git/refs/heads
A externals/manage_externals/test/repos/container.git/refs/heads/master
A externals/manage_externals/test/repos/error
A externals/manage_externals/test/repos/error/readme.txt
A externals/manage_externals/test/repos/mixed-cont-ext.git
A externals/manage_externals/test/repos/mixed-cont-ext.git/HEAD
A externals/manage_externals/test/repos/mixed-cont-ext.git/config
A externals/manage_externals/test/repos/mixed-cont-ext.git/description
A externals/manage_externals/test/repos/mixed-cont-ext.git/info
A externals/manage_externals/test/repos/mixed-cont-ext.git/info/exclude
A externals/manage_externals/test/repos/mixed-cont-ext.git/objects
A externals/manage_externals/test/repos/mixed-cont-ext.git/objects/06
A externals/manage_externals/test/repos/mixed-cont-ext.git/objects/06/ea30b03ffa2f8574705f8b9583f7ca7e2dccf7
A externals/manage_externals/test/repos/mixed-cont-ext.git/objects/37
A externals/manage_externals/test/repos/mixed-cont-ext.git/objects/37/f0e70b609adc90f4c09ee21d82ed1d79c81d69
A externals/manage_externals/test/repos/mixed-cont-ext.git/objects/41
A externals/manage_externals/test/repos/mixed-cont-ext.git/objects/41/1de5d96ee418c1c55f3e96e6e6e7c06bb95801
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A externals/manage_externals/test/repos/mixed-cont-ext.git/objects/fd/15a5ad5204356229c60a831d2a8120a43ac901
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A externals/manage_externals/test/repos/simple-ext-fork.git/description
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A externals/manage_externals/test/repos/simple-ext-fork.git/packed-refs
A externals/manage_externals/test/repos/simple-ext-fork.git/refs