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CMIP6 compset modifiers; usermods for output; other output enhancements (1) Support %BGC-CROP-CMIP6DECK and %BGC-CROP-CMIP6WACCMDECK compset modifiers, so that we can turn on the necessary options (output-related and others) via new CMIP6-specific compsets. (2) Turn on carbon isotopes in CMIP6 runs (from Erik Kluzek) (3) Remove setting of CCSM_BGC=CO2A in the cmip6 usermods (4) Add usermods directories for getting typical extra output that's wanted in many cases: output_crop, output_crop_highfreq, output_bgc, output_bgc_highfreq, output_sp, and output_sp_highfreq. These can be enabled by adding something like '--user-mods-dir output_crop' on the create_newcase line (that short-hand works for an I compset; for F or B compsets, you need to provide the full path to the usermod directory). (4) Allow holes in the number of history tapes. Holes are cases where, for example, we have h0, h1 and h3 tapes, but no h2 tape (because there are no fields on the h2 tape). (This is needed for (3).) (5) Fix reading and writing of 1-d logical global arrays. This fixes #24 for real (rather than just preventing an attempt to read/write 1-d logical arrays, as was done in the previous 'fix'). (6) Add C13_NBP and C14_NBP diagnostic fields (from Keith Oleson) (7) Make a bunch of carbon isotope diagnostic fields inactive by default (8) Don't allow interpolation (use_init_interp) from a case without carbon isotopes to a case with carbon isotopes: Due to #67, interpolation from a case without carbon isotopes to a case with carbon isotopes yields incorrect initialization values for the carbon isotopes. Now that we're turning carbon isotopes on via some semi-out-of-the-box usermods (for cmip6), it is becoming more important to check to make sure someone doesn't shoot themselves in the foot this way. (9) Add tests of the new output usermods as well as of the CMIP6 compset modifiers Issues fixed: - Fixes #24 for real (ncd_io_1d_log_glob is broken) - Fixes #529 (Organize usermods_dirs to facilitate running cases with the right output)
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This testmods directory is for tests where we want to use the | ||
out-of-the-box output options, but still want the minimal changes that | ||
we apply for nearly all tests. | ||
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("default" would probably be a good name for this, but we already use | ||
"default" to mean "the standard output changes that are applied for most | ||
tests" (adding some streams and fields, double precision, etc.). We may | ||
want to consider renaming that one and using "default" for this one.) |
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use_c13 = .true. | ||
use_c14 = .true. | ||
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! BUG(wjs, 2018-10-25, ESCOMP/ctsm#67) There is a bug that causes incorrect values for C | ||
! isotopes if running init_interp from a case without C isotopes to a case with C | ||
! isotopes (https://github.com/ESCOMP/ctsm/issues/67). Normally, an error-check prevents | ||
! you from doing this interpolation (until we have fixed that bug). However, we | ||
! sometimes want to bypass this error-check in system tests. This namelist flag bypasses | ||
! this error-check. | ||
for_testing_allow_interp_non_ciso_to_ciso = .true. |
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cime_config/testdefs/testmods_dirs/clm/cmip6_deck/include_user_mods
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../../../../usermods_dirs/cmip6_deck |
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cime_config/testdefs/testmods_dirs/clm/cmip6_deck/shell_commands
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#!/bin/bash | ||
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./xmlchange BFBFLAG="TRUE" |
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cime_config/testdefs/testmods_dirs/clm/output_bgc_highfreq/README
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Tests the output_bgc_highfreq usermods |
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cime_config/testdefs/testmods_dirs/clm/output_bgc_highfreq/include_user_mods
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../../../../usermods_dirs/output_bgc_highfreq | ||
../basic |
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cime_config/testdefs/testmods_dirs/clm/output_crop_highfreq/README
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Tests the output_crop_highfreq usermods |
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cime_config/testdefs/testmods_dirs/clm/output_crop_highfreq/include_user_mods
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../../../../usermods_dirs/output_crop_highfreq | ||
../basic |
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cime_config/testdefs/testmods_dirs/clm/output_sp_highfreq/README
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Tests the output_sp_highfreq usermods |
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cime_config/testdefs/testmods_dirs/clm/output_sp_highfreq/include_user_mods
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../../../../usermods_dirs/output_sp_highfreq | ||
../basic |
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This directory contains usermods directories that are meant to be | ||
included in other usermods directories, not used directly |
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cime_config/usermods_dirs/_includes/cmip6_carbon_isotopes/user_nl_clm
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!---------------------------------------------------------------------------------- | ||
! Settings from cmip6_carbon_isotopes | ||
!---------------------------------------------------------------------------------- | ||
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use_c13 = .true. | ||
use_c14 = .true. | ||
use_c13_timeseries = .true. | ||
use_c14_bombspike = .true. | ||
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! h3 stream (yearly average, gridcell-level) | ||
hist_fincl4 += 'C14_SOIL1C_vr', 'C14_SOIL2C_vr', 'C14_SOIL3C_vr' | ||
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.../usermods_dirs/cmip6_glaciers/user_nl_clm → ...6_glaciers_virtual_antarctica/user_nl_clm
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!---------------------------------------------------------------------------------- | ||
! Settings from cmip6_glaciers_virtual_antarctica | ||
!---------------------------------------------------------------------------------- | ||
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! This differs from the default in that it turns on virtual columns over Antarctica | ||
! This is desired so that we have the output needed to drive a later offline CISM Antarctica simulation | ||
! However, this increases the cost of CLM by about 10% | ||
glacier_region_behavior = 'single_at_atm_topo', 'virtual', 'virtual', 'virtual' | ||
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This usermods directory provides a common base on which other usermods | ||
can build for changing the out-of-the-box output to something more | ||
generally useful. | ||
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This should not be used directly. Instead, use one of the other usermods | ||
directories that builds on this. |
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cime_config/usermods_dirs/_includes/output_base/user_nl_clm
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!---------------------------------------------------------------------------------- | ||
! Users should add all user specific namelist changes below in the form of | ||
! namelist_var = new_namelist_value | ||
! | ||
! EXCEPTIONS: | ||
! Set use_cndv by the compset you use and the CLM_BLDNML_OPTS -dynamic_vegetation setting | ||
! Set use_vichydro by the compset you use and the CLM_BLDNML_OPTS -vichydro setting | ||
! Set use_cn by the compset you use and CLM_BLDNML_OPTS -bgc setting | ||
! Set use_crop by the compset you use and CLM_BLDNML_OPTS -crop setting | ||
! Set spinup_state by the CLM_BLDNML_OPTS -bgc_spinup setting | ||
! Set irrigate by the CLM_BLDNML_OPTS -irrig setting | ||
! Set co2_ppmv with CCSM_CO2_PPMV option | ||
! Set dtime with L_NCPL option | ||
! Set fatmlndfrc with LND_DOMAIN_PATH/LND_DOMAIN_FILE options | ||
! Set finidat with RUN_REFCASE/RUN_REFDATE/RUN_REFTOD options for hybrid or branch cases | ||
! (includes $inst_string for multi-ensemble cases) | ||
! Set maxpatch_glcmec with GLC_NEC option | ||
! Set glc_do_dynglacier with GLC_TWO_WAY_COUPLING env variable | ||
!---------------------------------------------------------------------------------- | ||
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!---------------------------------------------------------------------------------- | ||
! Settings from output_base | ||
!---------------------------------------------------------------------------------- | ||
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! h0 stream (monthly average, gridcell-level) | ||
! h0 stream ICE variables and other variables inactive by default (monthly average, gridcell-level) | ||
! Emon, Lmon, LIMon | ||
hist_mfilt(1) = 1 | ||
hist_dov2xy(1) = .true. | ||
hist_nhtfrq(1) = 0 | ||
hist_type1d_pertape(1) = ' ' | ||
hist_fexcl1 += 'PCT_GLC_MEC','PCT_NAT_PFT' | ||
hist_fincl1 += 'EFLX_LH_TOT_ICE', 'FIRE_ICE', 'FLDS_ICE', 'FSH_ICE', 'FSNO_ICE', 'FSR_ICE', 'QFLX_SUB_SNOW_ICE', 'QRUNOFF_ICE', 'QSNOFRZ_ICE', 'QSNOMELT_ICE', 'RAIN_ICE', 'SNOW_ICE', 'SNOWICE_ICE', 'SNOWLIQ_ICE', 'SNOTXMASS_ICE', 'TG_ICE', 'TOPO_COL_ICE', 'TSA_ICE', 'TSOI_ICE' | ||
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! h1 stream (monthly average, finest sub-grid) | ||
! Emon, Lmon | ||
hist_mfilt(2) = 1 | ||
hist_dov2xy(2) = .false. | ||
hist_nhtfrq(2) = 0 | ||
hist_type1d_pertape(2) = ' ' | ||
hist_fincl2 += 'TLAI', 'TSA','TREFMNAV','TREFMXAV', 'BTRANMN', 'Vcmx25Z', 'FSH', 'VEGWP', 'FCTR', 'FCEV', 'FGEV', 'FIRE', 'FSR', 'FIRA', 'FSA', 'GSSUNLN', 'GSSHALN', 'TSKIN' | ||
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! h2 stream (monthly average, landunit-level) | ||
! Emon | ||
hist_mfilt(3) = 1 | ||
hist_dov2xy(3) = .false. | ||
hist_nhtfrq(3) = 0 | ||
hist_type1d_pertape(3) = 'LAND' | ||
hist_fincl3 += 'FSR', 'H2OSNO', 'Q2M', 'SNOWDP', 'TSA', 'TREFMNAV', 'TREFMXAV', 'TG', 'QRUNOFF', 'FSH', 'FIRE', 'FIRA', 'FGR', 'EFLX_LH_TOT', 'RH2M', 'TLAI', 'SOILWATER_10CM', 'TOTSOILLIQ', 'TOTSOILICE', 'U10', 'TSOI_10CM', 'QIRRIG', 'URBAN_HEAT', 'WASTEHEAT', 'TSKIN' | ||
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! h3 stream (yearly average, gridcell-level) | ||
! Eyr | ||
hist_mfilt(4) = 1 | ||
hist_dov2xy(4) = .true. | ||
hist_nhtfrq(4) = -8760 | ||
hist_type1d_pertape(4) = ' ' | ||
hist_fincl4 += 'PCT_GLC_MEC', 'QICE_FORC', 'TSRF_FORC', 'TOPO_FORC', 'PCT_NAT_PFT','PCT_LANDUNIT','FSNO_ICE' | ||
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! h4 stream (yearly average, landunit-level) | ||
! Eyr landuse tiles | ||
! (No fields in base, but other usermods add to this stream) | ||
hist_mfilt(5) = 1 | ||
hist_dov2xy(5) = .false. | ||
hist_nhtfrq(5) = -8760 | ||
hist_type1d_pertape(5) = 'LAND' | ||
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cime_config/usermods_dirs/_includes/output_base_highfreq/README
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This usermods directory provides a common base on which other usermods | ||
can build for changing the out-of-the-box output to something useful | ||
when you want to include high-frequency output (daily and more | ||
frequent). | ||
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This should not be used directly. Instead, use one of the other usermods | ||
directories that builds on this. |
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cime_config/usermods_dirs/_includes/output_base_highfreq/include_user_mods
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../output_base |
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cime_config/usermods_dirs/_includes/output_base_highfreq/user_nl_clm
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!---------------------------------------------------------------------------------- | ||
! Settings from output_base_highfreq | ||
!---------------------------------------------------------------------------------- | ||
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! h5 stream (daily average, gridcell-level) | ||
! day, Eday | ||
hist_mfilt(6) = 365 | ||
hist_dov2xy(6) = .true. | ||
hist_nhtfrq(6) = -24 | ||
hist_type1d_pertape(6) = ' ' | ||
hist_fincl6 += 'SOILWATER_10CM', 'TOTSOILLIQ', 'TOTSOILICE', 'EFLX_LH_TOT', 'FSH', 'FGR12', 'FSM', 'QSNOEVAP', 'TLAI', 'QDRAI', 'QDRAI_PERCH', 'QOVER', 'QFLX_SUB_SNOW', 'FSA', 'FIRA', 'H2OSNO', 'SNOCAN', 'QSNOFRZ', 'QFLX_SNOW_DRAIN', 'SNOWDP', 'H2OSFC', 'TV', 'TG', 'TAUX', 'TAUY', 'QVEGT', 'TWS', 'H2OCAN', 'QVEGE', 'QSOIL', 'TSKIN', 'FSDS','FSNO','SNOFSRVD','SNOFSRVI','SNOFSRND','SNOFSRNI','FSDSVD','FSDSVI','FSDSND','FSDSNI','SNOWLIQ','SOILICE','SOILLIQ','QINTR','SNOBCMSL','TSOI','SNOTXMASS','SNOWICE','SNOWLIQ','QRUNOFF','RAIN','SNOW' | ||
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! h6 stream (daily average, landunit-level) | ||
! Eday | ||
hist_mfilt(7) = 365 | ||
hist_dov2xy(7) = .false. | ||
hist_nhtfrq(7) = -24 | ||
hist_type1d_pertape(7) = 'LAND' | ||
hist_fincl7 += 'TREFMXAV','TREFMNAV' | ||
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! h7 stream (3-hourly average, gridcell-level) | ||
! 3hr, E3hr, CF3hr | ||
! 3hr requires QRUNOFF for time mean, and SOILWATER_10CM, TSKIN for time point (I) | ||
! CF3hr requires QFLX_SUB_SNOW for time point (I) | ||
hist_mfilt(8) = 2920 | ||
hist_dov2xy(8) = .true. | ||
hist_nhtfrq(8) = -3 | ||
hist_type1d_pertape(8) = ' ' | ||
hist_fincl8 += 'TSA','RH2M','SOILWATER_10CM:I','FSH','EFLX_LH_TOT','FSDS','QRUNOFF','QFLX_SUB_SNOW:I','TSKIN:I' | ||
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../_includes/cmip6_glaciers_cplhist | ||
../_includes/cmip6_glaciers_virtual_antarctica | ||
../_includes/cmip6_carbon_isotopes | ||
../output_crop |
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cime_config/usermods_dirs/cmip6_evolving_icesheet/include_user_mods
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../cmip6 | ||
../cmip6_deck |
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cime_config/usermods_dirs/cmip6_evolving_icesheet/user_nl_clm
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!---------------------------------------------------------------------------------- | ||
! Settings from cmip6_evolving_icesheet | ||
!---------------------------------------------------------------------------------- | ||
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! h3 stream (yearly average, gridcell-level) | ||
hist_fincl4 += 'ICE_MODEL_FRACTION' | ||
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