diff --git a/.gitmodules b/.gitmodules index c6b16d384f..dcf9de5638 100644 --- a/.gitmodules +++ b/.gitmodules @@ -27,8 +27,8 @@ # [submodule "fates"] path = src/fates -url = https://github.com/NGEET/fates -fxtag = sci.1.78.3_api.36.1.0 +url = https://github.com/NorESMhub/fates +fxtag = sci.1.78.3_api.36.1.0_noresm_v1 fxrequired = AlwaysRequired # Standard Fork to compare to with "git fleximod test" to ensure personal forks aren't committed fxDONOTUSEurl = https://github.com/NCAR/fates-release diff --git a/bld/CLMBuildNamelist.pm b/bld/CLMBuildNamelist.pm index cfdb4e9278..6362b5c643 100755 --- a/bld/CLMBuildNamelist.pm +++ b/bld/CLMBuildNamelist.pm @@ -978,7 +978,7 @@ sub setup_cmdl_bgc { # Set soil matrix (which is needed later for spinup) $var = "use_soil_matrixcn"; add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, $var, - , 'use_fates'=>$nl_flags->{'use_fates'}, + , 'use_fates'=>$nl_flags->{'use_fates'}, , 'soil_decomp_method'=>$nl_flags->{'soil_decomp_method'}, , 'phys'=>$nl_flags->{'phys'}, clm_accelerated_spinup=>$nl_flags->{'clm_accelerated_spinup'} ); if ( &value_is_true($nl->get_value($var)) ) { @@ -1214,7 +1214,7 @@ sub setup_cmdl_spinup { if ( &value_is_true($nl_flags->{'use_cn'}) ) { add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, "spinup_state", clm_accelerated_spinup=>$nl_flags->{'clm_accelerated_spinup'}, - use_cn=>$nl_flags->{'use_cn'}, use_fates=>$nl_flags->{'use_fates'}, + use_cn=>$nl_flags->{'use_cn'}, use_fates=>$nl_flags->{'use_fates'}, use_soil_matrixcn=>$nl_flags->{"use_soil_matrixcn"} ); if ( $nl->get_value("spinup_state") ne 0 ) { $nl_flags->{'bgc_spinup'} = "on"; @@ -4148,12 +4148,8 @@ sub setup_logic_megan { add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'megan_factors_file'); } if ( defined($nl->get_value('megan_specifier')) || - defined($nl->get_value('megan_factors_file')) ) { + defined($nl->get_value('megan_factors_file')) ) { check_megan_spec( $opts, $nl, $definition ); - if ( &value_is_true( $nl_flags->{'use_fates'} ) ) { - $log->warning("MEGAN can NOT be on when FATES is also on.\n" . - " Use the '-no-megan' option when '-bgc fates' is activated"); - } } } @@ -4966,7 +4962,7 @@ sub setup_logic_exice { # excess ice streams, must be set before initial conditions # my ($opts, $nl_flags, $definition, $defaults, $nl, $physv) = @_; - add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'use_excess_ice', 'phys'=>$physv->as_string()); + add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'use_excess_ice', 'phys'=>$physv->as_string()); my $use_exice = $nl->get_value( 'use_excess_ice' ); # Put use_exice into nl_flags so can be referenced later if ( value_is_true($use_exice) ) { diff --git a/bld/namelist_files/namelist_defaults_ctsm.xml b/bld/namelist_files/namelist_defaults_ctsm.xml index 54d3afd5c1..fe0817fd6a 100644 --- a/bld/namelist_files/namelist_defaults_ctsm.xml +++ b/bld/namelist_files/namelist_defaults_ctsm.xml @@ -553,8 +553,8 @@ attributes from the config_cache.xml file (with keys converted to upper-case). -lnd/clm2/paramdata/fates_params_api.36.1.0_14pft_c241003.nc - + +lnd/clm2/paramdata/fates_params_api.36.1.0_14pft_c241003_megan.nc @@ -1908,10 +1908,10 @@ lnd/clm2/surfdata_esmf/NEON/ctsm5.3.0/surfdata_1x1_NEON_TOOL_hist_2000_78pfts_c2 lnd/clm2/surfdata_esmf/ctsm5.3.0/landuse.timeseries_4x5_SSP2-4.5_1850-2100_78pfts_c240908.nc -lnd/clm2/surfdata_esmf/ctsm5.3.0/landuse.timeseries_10x15_SSP2-4.5_1850-2100_78pfts_c240908.nc -lnd/clm2/surfdata_esmf/ctsm5.3.0/landuse.timeseries_360x720cru_SSP2-4.5_1850-2100_78pfts_c240908.nc -Specifies CTSM physics +Specifies CTSM physics """ @@ -105,11 +105,6 @@ def buildnml(case, caseroot, compname): "clm5_0_QIAN": "clm5_0_GSWP3v1", "clm5_0_NLDAS2": "clm5_0_GSWP3v1", "clm5_0_ERA5": "clm5_0_GSWP3v1", - "clm5_1_1PT": "clm5_1_GSWP3v1", - "clm5_1_QIAN": "clm5_1_GSWP3v1", - "clm5_1_NLDAS2": "clm5_1_GSWP3v1", - "clm5_1_ERA5": "clm5_1_GSWP3v1", - "clm5_1_CRUv7": "clm5_1_GSWP3v1", "clm6_0_1PT": "clm6_0_GSWP3v1", "clm6_0_QIAN": "clm6_0_GSWP3v1", "clm6_0_NLDAS2": "clm6_0_GSWP3v1", @@ -136,13 +131,9 @@ def buildnml(case, caseroot, compname): # to the CAM version) tuning_based_on = { "clm6_0_GSWP3v1": "clm5_0_GSWP3v1", - "clm5_1_GSWP3v1": "clm5_0_GSWP3v1", "clm6_0_cam6.0": "clm5_0_cam6.0", "clm6_0_cam5.0": "clm5_0_cam6.0", "clm6_0_cam4.0": "clm5_0_cam6.0", - "clm5_1_cam6.0": "clm5_0_cam6.0", - "clm5_1_cam5.0": "clm5_0_cam6.0", - "clm5_1_cam4.0": "clm5_0_cam6.0", "clm5_0_cam5.0": "clm5_0_cam6.0", "clm5_0_cam4.0": "clm5_0_cam6.0", "clm4_5_cam6.0": "clm5_0_cam6.0", diff --git a/cime_config/config_component.xml b/cime_config/config_component.xml index 2a568eb7dc..2506b8954a 100644 --- a/cime_config/config_component.xml +++ b/cime_config/config_component.xml @@ -15,7 +15,6 @@ clm4.5: clm5.0: - clm5.1: clm6.0: Satellite phenology: @@ -79,7 +78,7 @@ UNSET - clm5_0_cam6.0,clm5_0_cam7.0,clm5_0_cam5.0,clm5_0_cam4.0,clm5_0_GSWP3v1,clm5_0_CRUv7,clm5_0_QIAN,clm5_0_1PT,clm5_0_NLDAS2,clm5_0_ERA5,clm4_5_CRUv7,clm4_5_GSWP3v1,clm4_5_QIAN,clm4_5_cam6.0,clm4_5_cam7.0,clm4_5_cam5.0,clm4_5_cam4.0,clm4_5_1PT,clm4_5_NLDAS2,clm4_5_ERA5,clm5_1_CRUv7,clm5_1_GSWP3v1,clm5_1_cam6.0,clm5_1_QIAN,clm5_1_1PT,clm5_1_NLDAS2,clm5_1_ERA5,clm6_0_CRUv7,clm6_0_GSWP3v1,clm6_0_cam6.0,clm6_0_cam7.0,clm6_0_cam5.0,clm6_0_cam4.0,clm6_0_QIAN,clm6_0_1PT,clm6_0_NLDAS2,clm6_0_ERA5 + clm5_0_cam6.0,clm5_0_cam7.0,clm5_0_cam5.0,clm5_0_cam4.0,clm5_0_GSWP3v1,clm5_0_CRUv7,clm5_0_QIAN,clm5_0_1PT,clm5_0_NLDAS2,clm5_0_ERA5,clm4_5_CRUv7,clm4_5_GSWP3v1,clm4_5_QIAN,clm4_5_cam6.0,clm4_5_cam7.0,clm4_5_cam5.0,clm4_5_cam4.0,clm4_5_1PT,clm4_5_NLDAS2,clm4_5_ERA5,clm6_0_CRUv7,clm6_0_GSWP3v1,clm6_0_cam6.0,clm6_0_cam7.0,clm6_0_cam5.0,clm6_0_cam4.0,clm6_0_QIAN,clm6_0_1PT,clm6_0_NLDAS2,clm6_0_ERA5 @@ -114,14 +113,6 @@ clm5_0_1PT clm5_0_NLDAS2 clm5_0_ERA5 - - clm5_1_GSWP3v1 - INVALID_USE_CLM60_NOT_CLM51 - clm5_1_cam4.0 - clm5_1_cam5.0 - clm5_1_cam6.0 - INVALID_USE_CLM60_NOT_CLM51_FOR_CAM70 - INVALID_USE_CLM60_NOT_CLM51_FOR_CPLHIST clm6_0_CRUv7 clm6_0_CRUv7 @@ -148,7 +139,7 @@ char - clm4_5,clm5_0,clm5_1,clm6_0 + clm4_5,clm5_0,clm6_0 run_component_cpl env_run.xml If CTSM will set the dust settings in drv_flds_in (TRUE), or if ATM (i.e. CAM) will - DO NOT EDIT (set by compset name) @@ -256,9 +244,9 @@ -bgc sp -bgc bgc -bgc bgc -crop - -bgc fates -no-megan - -bgc fates -no-megan - -bgc fates -no-megan + -bgc fates -nomeg + -bgc fates + -bgc fates -bgc bgc -dynamic_vegetation @@ -367,12 +355,10 @@ - $COMP_ROOT_DIR_LND/cime_config/usermods_dirs/fates_sp - $COMP_ROOT_DIR_LND/cime_config/usermods_dirs/fates_sp - $COMP_ROOT_DIR_LND/cime_config/usermods_dirs/cmip6_deck - $COMP_ROOT_DIR_LND/cime_config/usermods_dirs/fates_sp - $COMP_ROOT_DIR_LND/cime_config/usermods_dirs/fates_nocomp - $COMP_ROOT_DIR_LND/cime_config/usermods_dirs/cmip6_nociso_deck + $COMP_ROOT_DIR_LND/cime_config/usermods_dirs/fates_sp + $COMP_ROOT_DIR_LND/cime_config/usermods_dirs/fates_nocomp + $COMP_ROOT_DIR_LND/cime_config/usermods_dirs/cmip6_deck + $COMP_ROOT_DIR_LND/cime_config/usermods_dirs/cmip6_nociso_deck $COMP_ROOT_DIR_LND/cime_config/usermods_dirs/cmip6_waccm_deck $COMP_ROOT_DIR_LND/cime_config/usermods_dirs/cmip6_waccm_nociso_deck $COMP_ROOT_DIR_LND/cime_config/usermods_dirs/cmip6_deck diff --git a/cime_config/config_compsets.xml b/cime_config/config_compsets.xml index e5d716384a..8ab6254029 100644 --- a/cime_config/config_compsets.xml +++ b/cime_config/config_compsets.xml @@ -14,7 +14,7 @@ Where for the CAM specific compsets below the following is supported TIME = Time period (e.g. 2000, HIST, SSP585...) ATM = [CAM40, CAM50, CAM60] - LND = [CLM45, CLM50, CLM51, CLM60, SLND] + LND = [CLM45, CLM50, CLM60, SLND] ICE = [CICE, DICE, SICE] OCN = [DOCN, ,AQUAP, SOCN] ROF = [RTM, SROF] @@ -344,12 +344,6 @@ - - - IHistClm51Sp - HIST_DATM%GSWP3v1_CLM51%SP_SICE_SOCN_MOSART_SGLC_SWAV - - IHistClm60SpRs HIST_DATM%GSWP3v1_CLM60%SP_SICE_SOCN_SROF_SGLC_SWAV @@ -407,7 +401,7 @@ HIST_DATM%QIA_CLM60%BGC_SICE_SOCN_SROF_SGLC_SWAV - @@ -610,7 +604,7 @@ 2000_DATM%CRUv7_CLM45%SP-VIC_SICE_SOCN_RTM_SGLC_SWAV - @@ -660,12 +654,6 @@ - - - I1850Clm51BgcCropG - 1850_DATM%GSWP3v1_CLM51%BGC-CROP_SICE_SOCN_MOSART_CISM2%GRIS-EVOLVE_SWAV - - diff --git a/cime_config/config_pes.xml b/cime_config/config_pes.xml index 01b25ab7c0..17e2947d7f 100644 --- a/cime_config/config_pes.xml +++ b/cime_config/config_pes.xml @@ -7,34 +7,34 @@ none - -1 - -1 - -1 - -1 - -1 - -1 - -1 - -1 + -1 + -1 + -1 + -1 + -1 + -1 + -1 + -1 - 1 - 1 - 1 - 1 - 1 - 1 - 1 - 1 + 1 + 1 + 1 + 1 + 1 + 1 + 1 + 1 - 0 - 0 - 0 - 0 - 0 - 0 - 0 - 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 @@ -44,34 +44,34 @@ none - -1 - -9 - -9 - -9 - -9 - -9 - -9 - -9 + -1 + -9 + -9 + -9 + -9 + -9 + -9 + -9 - 1 - 1 - 1 - 1 - 1 - 1 - 1 - 1 + 1 + 1 + 1 + 1 + 1 + 1 + 1 + 1 - 0 - -1 - -1 - -1 - -1 - -1 - -1 - -1 + 0 + -1 + -1 + -1 + -1 + -1 + -1 + -1 @@ -91,24 +91,24 @@ -4 - 1 - 1 - 1 - 1 - 1 - 1 - 1 - 1 + 1 + 1 + 1 + 1 + 1 + 1 + 1 + 1 - 0 - -1 - -1 - -1 - -1 - -1 - -1 - -1 + 0 + -1 + -1 + -1 + -1 + -1 + -1 + -1 @@ -155,34 +155,34 @@ none - -2 - -2 - -2 - -2 - -2 - -2 - -2 - -2 + -2 + -2 + -2 + -2 + -2 + -2 + -2 + -2 - 1 - 1 - 1 - 1 - 1 - 1 - 1 - 1 + 1 + 1 + 1 + 1 + 1 + 1 + 1 + 1 - 0 - 0 - 0 - 0 - 0 - 0 - 0 - 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 @@ -192,34 +192,34 @@ none - 180 - 180 - 180 - 180 - 180 - 180 - 180 - 180 + 180 + 180 + 180 + 180 + 180 + 180 + 180 + 180 - 1 - 1 - 1 - 1 - 1 - 1 - 1 - 1 + 1 + 1 + 1 + 1 + 1 + 1 + 1 + 1 - 0 - 0 - 0 - 0 - 0 - 0 - 0 - 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 @@ -229,7 +229,7 @@ none - -1 + -1 -40 -40 -40 @@ -239,24 +239,24 @@ -40 - 1 - 1 - 1 - 1 - 1 - 1 - 1 - 1 + 1 + 1 + 1 + 1 + 1 + 1 + 1 + 1 - 0 - -1 - -1 - -1 - -1 - -1 - -1 - -1 + 0 + -1 + -1 + -1 + -1 + -1 + -1 + -1 @@ -451,7 +451,7 @@ none - -1 + -1 -50 -50 -50 @@ -461,24 +461,24 @@ -50 - 1 - 1 - 1 - 1 - 1 - 1 - 1 - 1 + 1 + 1 + 1 + 1 + 1 + 1 + 1 + 1 - 0 - -1 - -1 - -1 - -1 - -1 - -1 - -1 + 0 + -1 + -1 + -1 + -1 + -1 + -1 + -1 @@ -673,71 +673,71 @@ none - -8 - -8 - -8 - -8 - -8 - -8 - -8 - -8 + -8 + -8 + -8 + -8 + -8 + -8 + -8 + -8 - 1 - 1 - 1 - 1 - 1 - 1 - 1 - 1 + 1 + 1 + 1 + 1 + 1 + 1 + 1 + 1 - 0 - 0 - 0 - 0 - 0 - 0 - 0 - 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 - + none - -16 - -16 - -16 - -16 - -16 - -16 - -16 - -16 + -16 + -16 + -16 + -16 + -16 + -16 + -16 + -16 - 1 - 1 - 1 - 1 - 1 - 1 - 1 - 1 + 1 + 1 + 1 + 1 + 1 + 1 + 1 + 1 - 0 - 0 - 0 - 0 - 0 - 0 - 0 - 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 @@ -747,34 +747,34 @@ none - -4 - -4 - -4 - -4 - -4 - -4 - -4 - -4 + -4 + -4 + -4 + -4 + -4 + -4 + -4 + -4 - 1 - 1 - 1 - 1 - 1 - 1 - 1 - 1 + 1 + 1 + 1 + 1 + 1 + 1 + 1 + 1 - 0 - 0 - 0 - 0 - 0 - 0 - 0 - 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 @@ -1117,34 +1117,34 @@ none - -16 - -16 - -16 - -16 - -16 - -16 - -16 - -16 + -16 + -16 + -16 + -16 + -16 + -16 + -16 + -16 - 1 - 1 - 1 - 1 - 1 - 1 - 1 - 1 + 1 + 1 + 1 + 1 + 1 + 1 + 1 + 1 - 0 - 0 - 0 - 0 - 0 - 0 - 0 - 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 @@ -1154,34 +1154,34 @@ none - -32 - -32 - -32 - -32 - -32 - -32 - -32 - -32 + -32 + -32 + -32 + -32 + -32 + -32 + -32 + -32 - 1 - 1 - 1 - 1 - 1 - 1 - 1 - 1 + 1 + 1 + 1 + 1 + 1 + 1 + 1 + 1 - 0 - 0 - 0 - 0 - 0 - 0 - 0 - 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 @@ -1413,34 +1413,34 @@ none - 1 - 1 - 1 - 1 - 1 - 1 - 1 - 1 + 1 + 1 + 1 + 1 + 1 + 1 + 1 + 1 - 1 - 1 - 1 - 1 - 1 - 1 - 1 - 1 + 1 + 1 + 1 + 1 + 1 + 1 + 1 + 1 - 0 - 0 - 0 - 0 - 0 - 0 - 0 - 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 @@ -1450,34 +1450,34 @@ none - 5 - 5 - 5 - 5 - 5 - 5 - 5 - 5 + 5 + 5 + 5 + 5 + 5 + 5 + 5 + 5 - 1 - 1 - 1 - 1 - 1 - 1 - 1 - 1 + 1 + 1 + 1 + 1 + 1 + 1 + 1 + 1 - 0 - 0 - 0 - 0 - 0 - 0 - 0 - 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 @@ -1487,35 +1487,35 @@ none - -4 - -4 - -4 - -4 - -4 - -4 - -4 - -4 - -4 + -4 + -4 + -4 + -4 + -4 + -4 + -4 + -4 + -4 1> - 1 - 1 - 1 - 1 - 1 - 1 - 1 + 1 + 1 + 1 + 1 + 1 + 1 + 1 - 0 - 0 - 0 - 0 - 0 - 0 - 0 - 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 @@ -1525,35 +1525,35 @@ none - -2 - -2 - -2 - -2 - -2 - -2 - -2 - -2 - -2 + -2 + -2 + -2 + -2 + -2 + -2 + -2 + -2 + -2 1> - 1 - 1 - 1 - 1 - 1 - 1 - 1 + 1 + 1 + 1 + 1 + 1 + 1 + 1 - 0 - 0 - 0 - 0 - 0 - 0 - 0 - 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 @@ -1601,35 +1601,35 @@ none - -1 - -1 - -1 - -1 - -1 - -1 - -1 - -1 - -1 + -1 + -1 + -1 + -1 + -1 + -1 + -1 + -1 + -1 1> - 1 - 1 - 1 - 1 - 1 - 1 - 1 + 1 + 1 + 1 + 1 + 1 + 1 + 1 - 0 - 0 - 0 - 0 - 0 - 0 - 0 - 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 @@ -1976,34 +1976,34 @@ Need at least 4 nodes to default to normal queue - -1 - -3 - -3 - -3 - -3 - -3 - -3 - -3 + -1 + -3 + -3 + -3 + -3 + -3 + -3 + -3 - 1 - 1 - 1 - 1 - 1 - 1 - 1 - 1 + 1 + 1 + 1 + 1 + 1 + 1 + 1 + 1 - 0 - -1 - -1 - -1 - -1 - -1 - -1 - -1 + 0 + -1 + -1 + -1 + -1 + -1 + -1 + -1 @@ -2013,34 +2013,34 @@ none - -1 - -7 - -7 - -7 - -7 - -7 - -7 - -7 + -1 + -7 + -7 + -7 + -7 + -7 + -7 + -7 - 1 - 1 - 1 - 1 - 1 - 1 - 1 - 1 + 1 + 1 + 1 + 1 + 1 + 1 + 1 + 1 - 0 - -1 - -1 - -1 - -1 - -1 - -1 - -1 + 0 + -1 + -1 + -1 + -1 + -1 + -1 + -1 @@ -2050,34 +2050,34 @@ Need at least 2 nodes to devel queue - -2 - -2 - -2 - -2 - -2 - -2 - -2 - -2 + -4 + -4 + -4 + -4 + -4 + -4 + -4 + -4 - 1 - 1 - 1 - 1 - 1 - 1 - 1 - 1 + 1 + 1 + 1 + 1 + 1 + 1 + 1 + 1 - 0 - 0 - 0 - 0 - 0 - 0 - 0 - 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 @@ -2088,34 +2088,34 @@ none - -2 - -7 - -7 - -7 - -7 - -7 - -7 - -7 + -2 + -7 + -7 + -7 + -7 + -7 + -7 + -7 - 1 - 1 - 1 - 1 - 1 - 1 - 1 - 1 + 1 + 1 + 1 + 1 + 1 + 1 + 1 + 1 - 0 - -2 - -2 - -2 - -2 - -2 - -2 - -2 + 0 + -2 + -2 + -2 + -2 + -2 + -2 + -2 @@ -2126,35 +2126,35 @@ none - -1 - -1 - -1 - -1 - -1 - -1 - -1 - -1 - -1 + -1 + -1 + -1 + -1 + -1 + -1 + -1 + -1 + -1 1 - 1 - 1 - 1 - 1 - 1 - 1 - 1 + 1 + 1 + 1 + 1 + 1 + 1 + 1 - 0 - 0 - 0 - 0 - 0 - 0 - 0 - 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 diff --git a/cime_config/testdefs/testlist_clm.xml b/cime_config/testdefs/testlist_clm.xml index f9d45ab17b..db00b605b6 100644 --- a/cime_config/testdefs/testlist_clm.xml +++ b/cime_config/testdefs/testlist_clm.xml @@ -14,6 +14,7 @@ matrixcn: Tests exercising the matrix-CN capability --> + @@ -123,14 +124,12 @@ - - + - @@ -198,7 +197,7 @@ - + @@ -751,7 +750,7 @@ - + @@ -865,7 +864,7 @@ - + @@ -904,7 +903,7 @@ - + @@ -914,7 +913,7 @@ - + @@ -970,15 +969,13 @@ - - + - - + @@ -1447,7 +1444,7 @@ - + @@ -1457,7 +1454,7 @@ - + @@ -1465,10 +1462,10 @@ - + - + @@ -1476,7 +1473,7 @@ - + @@ -1487,7 +1484,7 @@ - + @@ -1528,13 +1525,13 @@ - + - + @@ -1564,7 +1561,7 @@ - + @@ -1574,7 +1571,7 @@ - + @@ -1612,7 +1609,7 @@ - + @@ -1710,7 +1707,7 @@ - + @@ -1738,7 +1735,7 @@ - + @@ -1747,7 +1744,7 @@ - + @@ -1939,7 +1936,7 @@ - + @@ -1949,7 +1946,7 @@ - + @@ -1957,7 +1954,7 @@ - + @@ -2031,7 +2028,6 @@ - @@ -2069,23 +2065,65 @@ - + + + + + + + + + + + + + + + + + + + + + + - + + + + + + + + + + + + + + + + + + + + + + @@ -2098,18 +2136,29 @@ - + + + + + + + + + + + + - + @@ -2118,32 +2167,35 @@ - + + - + + - + + @@ -2361,7 +2413,7 @@ - + @@ -2427,7 +2479,7 @@ - + @@ -2436,7 +2488,7 @@ - + @@ -2580,7 +2632,7 @@ - + @@ -2589,7 +2641,7 @@ - + @@ -2680,7 +2732,7 @@ - + @@ -2689,7 +2741,7 @@ - + @@ -2700,7 +2752,6 @@ - @@ -2730,7 +2781,6 @@ - @@ -2757,21 +2807,22 @@ - + + - + - + @@ -3740,5 +3791,253 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/cime_config/testdefs/testmods_dirs/clm/Fates/shell_commands b/cime_config/testdefs/testmods_dirs/clm/Fates/shell_commands index 41a2342a51..5c06a9b93d 100644 --- a/cime_config/testdefs/testmods_dirs/clm/Fates/shell_commands +++ b/cime_config/testdefs/testmods_dirs/clm/Fates/shell_commands @@ -1,2 +1 @@ -./xmlchange CLM_BLDNML_OPTS="-no-megan" --append ./xmlchange BFBFLAG="TRUE" diff --git a/cime_config/testdefs/testmods_dirs/clm/FatesColdAllVars/shell_commands b/cime_config/testdefs/testmods_dirs/clm/FatesColdAllVars/shell_commands index 20db712f77..2b9889d32e 100644 --- a/cime_config/testdefs/testmods_dirs/clm/FatesColdAllVars/shell_commands +++ b/cime_config/testdefs/testmods_dirs/clm/FatesColdAllVars/shell_commands @@ -1,3 +1,2 @@ -./xmlchange CLM_BLDNML_OPTS="-no-megan" --append ./xmlchange BFBFLAG="TRUE" ./xmlchange CLM_FORCE_COLDSTART="on" \ No newline at end of file diff --git a/src/biogeochem/MEGANFactorsMod.F90 b/src/biogeochem/MEGANFactorsMod.F90 index 661bfbdde2..1f5caedbe6 100644 --- a/src/biogeochem/MEGANFactorsMod.F90 +++ b/src/biogeochem/MEGANFactorsMod.F90 @@ -58,9 +58,9 @@ subroutine megan_factors_get( comp_name, factors, class_n, molecwght ) ! ! !ARGUMENTS: character(len=*),intent(in) :: comp_name ! MEGAN compound name - real(r8), intent(out) :: factors(npfts) ! vegitation type factors for the compound of intrest - integer, intent(out) :: class_n ! MEGAN class number for the compound of intrest - real(r8), intent(out) :: molecwght ! molecular weight of the compound of intrest + real(r8), intent(out) :: factors(npfts) ! vegetation type factors for the compound of interest + integer, intent(out) :: class_n ! MEGAN class number for the compound of interest + real(r8), intent(out) :: molecwght ! molecular weight of the compound of interest ! ! LOCAL VARS: integer :: hashkey, ndx diff --git a/src/biogeochem/VOCEmissionMod.F90 b/src/biogeochem/VOCEmissionMod.F90 index 400b6d5561..74afda8980 100644 --- a/src/biogeochem/VOCEmissionMod.F90 +++ b/src/biogeochem/VOCEmissionMod.F90 @@ -416,6 +416,7 @@ subroutine VOCEmission (bounds, num_soilp, filter_soilp, & ! ! !USES: use subgridAveMod , only : p2g + use clm_varctl , only : use_fates ! ! !ARGUMENTS: type(bounds_type) , intent(in) :: bounds @@ -451,6 +452,7 @@ subroutine VOCEmission (bounds, num_soilp, filter_soilp, & real(r8) :: par240_sha ! temporary integer :: class_num, n_meg_comps, imech, imeg, ii + integer :: patchpft ! to transfer FATES PFT space into CLM PFT space. character(len=16) :: mech_name type(shr_megan_megcomp_t), pointer :: meg_cmp real(r8) :: cp, alpha, Eopt, topt ! for history output @@ -497,7 +499,7 @@ subroutine VOCEmission (bounds, num_soilp, filter_soilp, & fsun240 => canopystate_inst%fsun240_patch , & ! Input: [real(r8) (:) ] sunlit fraction of canopy last 240 hrs elai => canopystate_inst%elai_patch , & ! Input: [real(r8) (:) ] one-sided leaf area index with burying by snow elai240 => canopystate_inst%elai240_patch , & ! Input: [real(r8) (:) ] one-sided leaf area index with burying by snow last 240 hrs - + ci_fates => canopystate_inst%ci_patch , & !Input: [real(r8) (:) ] FATES-calculated internalleaf ci cisun_z => photosyns_inst%cisun_z_patch , & ! Input: [real(r8) (:,:) ] sunlit intracellular CO2 (Pa) cisha_z => photosyns_inst%cisha_z_patch , & ! Input: [real(r8) (:,:) ] shaded intracellular CO2 (Pa) @@ -581,33 +583,45 @@ subroutine VOCEmission (bounds, num_soilp, filter_soilp, & ! set emis factor ! if specified, set EF for isoprene with mapped values + if(use_fates)then + patchpft = canopystate_inst%voc_pftindex_patch(p) + else + patchpft = patch%itype(p) + endif + if ( trim(meg_cmp%name) == 'isoprene' .and. shr_megan_mapped_emisfctrs) then - epsilon = get_map_EF(patch%itype(p),g, vocemis_inst) + epsilon = get_map_EF(patchpft,g, vocemis_inst) else - epsilon = meg_cmp%emis_factors(patch%itype(p)) + epsilon = meg_cmp%emis_factors(patchpft) end if + class_num = meg_cmp%class_number ! Activity factor for PPFD gamma_p = get_gamma_P(par_sun, par24_sun, par240_sun, par_sha, par24_sha, par240_sha, & fsun(p), fsun240(p), forc_solad240(p),forc_solai240(p), LDF(class_num), cp, alpha) - + ! Activity factor for T gamma_t = get_gamma_T(t_veg240(p), t_veg24(p),t_veg(p), ct1(class_num), ct2(class_num),& - betaT(class_num),LDF(class_num), Ceo(class_num), Eopt, topt, patch%itype(p)) + betaT(class_num),LDF(class_num), Ceo(class_num), Eopt, topt, patchpft) ! Activity factor for Leaf Age - gamma_a = get_gamma_A(patch%itype(p), elai240(p),elai(p),class_num) + gamma_a = get_gamma_A(patchpft, elai240(p),elai(p),class_num) ! Activity factor for CO2 (only for isoprene) if (trim(meg_cmp%name) == 'isoprene') then co2_ppmv = 1.e6_r8*forc_pco2(g)/forc_pbot(c) - gamma_c = get_gamma_C(cisun_z(p,1),cisha_z(p,1),forc_pbot(c),fsun(p), co2_ppmv) + if(use_fates)then + gamma_c = get_gamma_C(ci_fates(p),ci_fates(p),forc_pbot(c),fsun(p), co2_ppmv) + else + gamma_c = get_gamma_C(cisun_z(p,1),cisha_z(p,1),forc_pbot(c),fsun(p), co2_ppmv) + endif + else gamma_c = 1._r8 end if - + ! Calculate total scaling factor gamma = gamma_l * gamma_sm * gamma_a * gamma_p * gamma_T * gamma_c @@ -618,7 +632,6 @@ subroutine VOCEmission (bounds, num_soilp, filter_soilp, & ! assign to arrays for history file output (not weighted by landfrac) meg_out(imeg)%flux_out(p) = meg_out(imeg)%flux_out(p) & + epsilon * gamma * megemis_units_factor*1.e-3_r8 ! Kg/m2/sec - if (imeg==1) then ! gamma_out(p)=gamma @@ -692,7 +705,6 @@ function get_map_EF(ivt_in, g_in, vocemis_inst) ! vocemis_inst%efisop_patch ! Output: [real(r8) (:,:)] emission factors for isoprene for each patch [ug m-2 h-1] get_map_EF = 0._r8 - if ( ivt_in == ndllf_evr_tmp_tree & .or. ivt_in == ndllf_evr_brl_tree) then !fineleaf evergreen get_map_EF = vocemis_inst%efisop_grc(2,g_in) @@ -710,7 +722,7 @@ function get_map_EF(ivt_in, g_in, vocemis_inst) else if (ivt_in >= nc3crop) then !crops get_map_EF = vocemis_inst%efisop_grc(6,g_in) end if - + end function get_map_EF !----------------------------------------------------------------------- diff --git a/src/biogeophys/CanopyStateType.F90 b/src/biogeophys/CanopyStateType.F90 index 4bfc08fc80..f4cf3f17d2 100644 --- a/src/biogeophys/CanopyStateType.F90 +++ b/src/biogeophys/CanopyStateType.F90 @@ -46,12 +46,14 @@ module CanopyStateType real(r8) , pointer :: hbot_patch (:) ! patch canopy bottom (m) real(r8) , pointer :: z0m_patch (:) ! patch momentum roughness length (m) real(r8) , pointer :: displa_patch (:) ! patch displacement height (m) + real(r8) , pointer :: ci_patch (:) ! Internal leaf CO2 concentration for MEGAN real(r8) , pointer :: fsun_patch (:) ! patch sunlit fraction of canopy real(r8) , pointer :: fsun24_patch (:) ! patch 24hr average of sunlit fraction of canopy real(r8) , pointer :: fsun240_patch (:) ! patch 240hr average of sunlit fraction of canopy real(r8) , pointer :: dleaf_patch (:) ! patch characteristic leaf width (diameter) [m] - ! for non-ED/FATES this is the same as pftcon%dleaf() + ! for non-ED/FATES this is the same as pftcon%dleaf() + integer , pointer :: voc_pftindex_patch (:) ! FATES specific MEGAN pft index. real(r8) , pointer :: rscanopy_patch (:) ! patch canopy stomatal resistance (s/m) (ED specific) real(r8) , pointer :: vegwp_patch (:,:) ! patch vegetation water matric potential (mm) @@ -139,11 +141,13 @@ subroutine InitAllocate(this, bounds) allocate(this%hbot_patch (begp:endp)) ; this%hbot_patch (:) = nan allocate(this%z0m_patch (begp:endp)) ; this%z0m_patch (:) = nan allocate(this%displa_patch (begp:endp)) ; this%displa_patch (:) = nan + allocate(this%ci_patch (begp:endp)) ; this%ci_patch (:) = nan allocate(this%fsun_patch (begp:endp)) ; this%fsun_patch (:) = nan allocate(this%fsun24_patch (begp:endp)) ; this%fsun24_patch (:) = nan allocate(this%fsun240_patch (begp:endp)) ; this%fsun240_patch (:) = nan allocate(this%dleaf_patch (begp:endp)) ; this%dleaf_patch (:) = nan + allocate(this%voc_pftindex_patch (begp:endp)) ; this%voc_pftindex_patch (:) = 0 allocate(this%rscanopy_patch (begp:endp)) ; this%rscanopy_patch (:) = nan ! allocate(this%gccanopy_patch (begp:endp)) ; this%gccanopy_patch (:) = 0.0_r8 allocate(this%vegwp_patch (begp:endp,1:nvegwcs)) ; this%vegwp_patch (:,:) = nan diff --git a/src/fates b/src/fates index 825579d0b4..f2ea09eaee 160000 --- a/src/fates +++ b/src/fates @@ -1 +1 @@ -Subproject commit 825579d0b406fe99344591b5ed8356e5c7aeebec +Subproject commit f2ea09eaee1a028d9d72007a37774892ad1b397d diff --git a/src/soilbiogeochem/CNSoilMatrixMod.F90 b/src/soilbiogeochem/CNSoilMatrixMod.F90 index 56c1f11b5c..d4115ef659 100644 --- a/src/soilbiogeochem/CNSoilMatrixMod.F90 +++ b/src/soilbiogeochem/CNSoilMatrixMod.F90 @@ -5,18 +5,19 @@ module CNSoilMatrixMod ! The matrix model of CLM5.0 was developed by Yiqi Luo EcoLab members, ! Drs. Xingjie Lu, Yuanyuan Huang and Zhengguang Du, at Northern Arizona University !---------------------------------------------------------------------------------- - ! + ! ! DESCRIPTION: ! Module for CLM5.0BGC matrices - ! The matrix equation + ! The matrix equation ! Xn+1 = Xn + I*dt + (A*K(ksi) - Kfire - tri/dz)*Xn*dt ! Or ! Xn+1 = Xn + I*dt + (A*K(ksi) - Kfire - V)*Xn*dt - + ! !USES: use shr_kind_mod , only : r8 => shr_kind_r8 use shr_log_mod , only : errMsg => shr_log_errMsg - use decompMod , only : bounds_type + use spmdMod , only : masterproc + use decompMod , only : bounds_type use abortutils , only : endrun use clm_time_manager , only : get_step_size, is_end_curr_month,get_curr_date,update_DA_nstep use clm_time_manager , only : is_first_restart_step,is_beg_curr_year,is_end_curr_year,is_first_step_of_this_run_segment @@ -31,11 +32,11 @@ module CNSoilMatrixMod use SoilBiogeochemCarbonStateType , only : soilbiogeochem_carbonstate_type use SoilBiogeochemCarbonFluxType , only : soilbiogeochem_carbonflux_type use SoilBiogeochemNitrogenStateType , only : soilbiogeochem_nitrogenstate_type - use SoilBiogeochemNitrogenFluxType , only : soilbiogeochem_nitrogenflux_type + use SoilBiogeochemNitrogenFluxType , only : soilbiogeochem_nitrogenflux_type use CNSharedParamsMod , only : CNParamsShareInst - use SoilStateType , only : soilstate_type + use SoilStateType , only : soilstate_type use clm_varctl , only : spinup_matrixcn, hist_wrt_matrixcn_diag, nyr_forcing, nyr_SASU, iloop_avg - use ColumnType , only : col + use ColumnType , only : col use GridcellType , only : grc use clm_varctl , only : use_c13, use_c14, iulog use perf_mod , only : t_startf, t_stopf @@ -64,23 +65,25 @@ subroutine CNSoilMatrixInit( ) ! !LOCAL VARIABLES: !----------------------------------------------------------------------- - if ( use_soil_matrixcn ) then - write(iulog,*) 'CN Soil matrix solution is on' - write(iulog,*) '*****************************' - if ( spinup_matrixcn ) then - write(iulog,*) ' Matrix spinup is on' - write(iulog,*) ' *******************' - write(iulog,*) ' nyr_forcing = ', nyr_forcing - write(iulog,*) ' nyr_SASU = ', nyr_SASU - write(iulog,*) ' iloop_avg = ', iloop_avg - end if - if ( hist_wrt_matrixcn_diag )then - write(iulog,*) ' Extra matrix solution tracability output is turned on' + if ( masterproc) then + if ( use_soil_matrixcn ) then + write(iulog,*) 'CN Soil matrix solution is on' + write(iulog,*) '*****************************' + if ( spinup_matrixcn ) then + write(iulog,*) ' Matrix spinup is on' + write(iulog,*) ' *******************' + write(iulog,*) ' nyr_forcing = ', nyr_forcing + write(iulog,*) ' nyr_SASU = ', nyr_SASU + write(iulog,*) ' iloop_avg = ', iloop_avg + end if + if ( hist_wrt_matrixcn_diag )then + write(iulog,*) ' Extra matrix solution tracability output is turned on' + else + write(iulog,*) ' no extra matrix solution tracability output' + end if else - write(iulog,*) ' no extra matrix solution tracability output' + write(iulog,*) 'CN Soil matrix solution is off' end if - else - write(iulog,*) 'CN Soil matrix solution is off' end if end subroutine CNSoilMatrixInit @@ -113,11 +116,11 @@ subroutine CNSoilMatrix(bounds,num_soilc, filter_soilc, num_actfirec, filter_act ! !LOCAL VARIABLES: integer :: fc,j,i, l,k ! indices - integer :: c ! + integer :: c ! real(r8):: dt ! time step (seconds) real(r8):: epsi,fire_delta ! small number - integer :: begc,endc ! bounds + integer :: begc,endc ! bounds real(r8),dimension(bounds%begc:bounds%endc,nlevdecomp*(ndecomp_cascade_transitions-ndecomp_cascade_outtransitions)) :: a_ma_vr,na_ma_vr real(r8),dimension(bounds%begc:bounds%endc,1:ndecomp_pools_vr,1) :: soilmatrixc_cap,soilmatrixc13_cap,soilmatrixc14_cap,soilmatrixn_cap @@ -144,23 +147,23 @@ subroutine CNSoilMatrix(bounds,num_soilc, filter_soilc, num_actfirec, filter_act !----------------------------------------------------------------------- begc = bounds%begc; endc = bounds%endc - + ! SHR_ASSERT_ALL((ubound(cn_decomp_pools) == (/endc,nlevdecomp,ndecomp_pools/)) , errMsg(sourcefile, __LINE__)) associate( & cs_soil => soilbiogeochem_carbonstate_inst , & ! In/Output ns_soil => soilbiogeochem_nitrogenstate_inst , & ! In/Output - cs13_soil => c13_soilbiogeochem_carbonstate_inst, & ! In/Output - cs14_soil => c14_soilbiogeochem_carbonstate_inst, & ! In/Output - cf13_soil => c13_soilbiogeochem_carbonflux_inst, & ! In/Output - cf14_soil => c14_soilbiogeochem_carbonflux_inst, & ! In/Output + cs13_soil => c13_soilbiogeochem_carbonstate_inst, & ! In/Output + cs14_soil => c14_soilbiogeochem_carbonstate_inst, & ! In/Output + cf13_soil => c13_soilbiogeochem_carbonflux_inst, & ! In/Output + cf14_soil => c14_soilbiogeochem_carbonflux_inst, & ! In/Output fpi_vr => soilbiogeochem_state_inst%fpi_vr_col ,&!Input:[real(r8)(:,:)]fraction of potential immobilization (no units) cascade_donor_pool => decomp_cascade_con%cascade_donor_pool ,&!Input:[integer(:)]which pool is C taken from for a given decomposition step - cascade_receiver_pool => decomp_cascade_con%cascade_receiver_pool ,&!Input:[integer(:)]which pool is C added to for a given decomposition step + cascade_receiver_pool => decomp_cascade_con%cascade_receiver_pool ,&!Input:[integer(:)]which pool is C added to for a given decomposition step floating_cn_ratio_decomp_pools=> decomp_cascade_con%floating_cn_ratio_decomp_pools ,&!Input:[logical(:)]TRUE => pool has fixed C:N ratio initial_cn_ratio => decomp_cascade_con%initial_cn_ratio ,&!Input:[real(r8)(:)]c:n ratio for initialization of pools rf_decomp_cascade => soilbiogeochem_carbonflux_inst%rf_decomp_cascade_col ,&!Input:[real(r8)(:,:,:)]respired fraction in decomposition step (frac) - pathfrac_decomp_cascade => soilbiogeochem_carbonflux_inst%pathfrac_decomp_cascade_col,&!Input:[real(r8)(:,:,:)]what fraction of C leaving a given pool passes + pathfrac_decomp_cascade => soilbiogeochem_carbonflux_inst%pathfrac_decomp_cascade_col,&!Input:[real(r8)(:,:,:)]what fraction of C leaving a given pool passes ! through a given transition (frac) is_cwd => decomp_cascade_con%is_cwd ,&!Input:[logical(:)]TRUE => pool is a cwd pool is_litter => decomp_cascade_con%is_litter ,&!Input:[logical(:)]TRUE => pool is a litter pool @@ -222,7 +225,7 @@ subroutine CNSoilMatrix(bounds,num_soilc, filter_soilc, num_actfirec, filter_act list_fire_AKVfire=> decomp_cascade_con%list_fire_AKVfire,&!In/Output:[Integer(:)] Saves mapping indices from Kfire to (A*K+V-Kfire) in the addition subroutine SPMP_ABC list_AK_AKVfire => decomp_cascade_con%list_AK_AKVfire ,&!In/Output:[Integer(:)] Saves mapping indices from A*K to (A*K+V-Kfire) in the addition subroutine SPMP_ABC list_AK_AKV => decomp_cascade_con%list_AK_AKV ,&!In/Output:[Integer(:)] Saves mapping indices from A*K to (A*K+V) in the addition subroutine SPMP_AB - list_V_AKV => decomp_cascade_con%list_V_AKV &!In/Output:[Integer(:)] Saves mapping indices from V to (A*K+V) in the addition subroutine SPMP_AB + list_V_AKV => decomp_cascade_con%list_V_AKV &!In/Output:[Integer(:)] Saves mapping indices from V to (A*K+V) in the addition subroutine SPMP_AB ) ! set time steps @@ -230,7 +233,7 @@ subroutine CNSoilMatrix(bounds,num_soilc, filter_soilc, num_actfirec, filter_act dt = real( get_step_size(), r8 ) Ntrans = (ndecomp_cascade_transitions-ndecomp_cascade_outtransitions)*nlevdecomp - epsi = 1.e-8_r8 + epsi = 1.e-8_r8 isbegofyear = is_beg_curr_year() @@ -254,13 +257,13 @@ subroutine CNSoilMatrix(bounds,num_soilc, filter_soilc, num_actfirec, filter_act cn_decomp_pools(c,j,l) = initial_cn_ratio(l) end do end do - end if + end if end do call t_stopf('CN Soil matrix-init. matrix') call t_startf('CN Soil matrix-assign matrix-a-na') - ! Calculate non-diagonal entries (a_ma_vr and na_ma_vr) in transfer coefficient matrix A + ! Calculate non-diagonal entries (a_ma_vr and na_ma_vr) in transfer coefficient matrix A do k = 1, ndecomp_cascade_transitions if(cascade_receiver_pool(k) .ne. 0)then !transition to atmosphere do j = 1, nlevdecomp @@ -289,10 +292,10 @@ subroutine CNSoilMatrix(bounds,num_soilc, filter_soilc, num_actfirec, filter_act do j = 1, nlevdecomp do fc = 1,num_soilc c = filter_soilc(fc) - matrix_Cinter%V(c,j+(i-1)*nlevdecomp) = cs_soil%decomp_cpools_vr_col(c,j,i) - Cinter_old(c,j+(i-1)*nlevdecomp) = cs_soil%decomp_cpools_vr_col(c,j,i) + matrix_Cinter%V(c,j+(i-1)*nlevdecomp) = cs_soil%decomp_cpools_vr_col(c,j,i) + Cinter_old(c,j+(i-1)*nlevdecomp) = cs_soil%decomp_cpools_vr_col(c,j,i) !Cinter_old is saved for accumulation of C transfer calculation and C flux (hr and fire) adjustment - matrix_Ninter%V(c,j+(i-1)*nlevdecomp) = ns_soil%decomp_npools_vr_col(c,j,i) + matrix_Ninter%V(c,j+(i-1)*nlevdecomp) = ns_soil%decomp_npools_vr_col(c,j,i) Ninter_old(c,j+(i-1)*nlevdecomp) = ns_soil%decomp_npools_vr_col(c,j,i) !Ninter_old is saved for accumulation of N transfer calculation end do @@ -338,7 +341,7 @@ subroutine CNSoilMatrix(bounds,num_soilc, filter_soilc, num_actfirec, filter_act end do ! Save the C and N pool size at begin of each year, which are used to calculate C and N capacity at end of each year. call t_startf('CN Soil matrix-assign matrix-decomp0') - if (is_beg_curr_year())then + if (is_beg_curr_year())then iyr = iyr + 1 if(mod(iyr-1,nyr_forcing) .eq. 0)then iloop = iloop + 1 @@ -368,7 +371,7 @@ subroutine CNSoilMatrix(bounds,num_soilc, filter_soilc, num_actfirec, filter_act end where end if if(use_c14)then - where(cs14_soil%decomp0_cpools_vr_col .lt. epsi*c14ratio) + where(cs14_soil%decomp0_cpools_vr_col .lt. epsi*c14ratio) cs14_soil%decomp0_cpools_vr_col = epsi*c14ratio end where end if @@ -378,7 +381,7 @@ subroutine CNSoilMatrix(bounds,num_soilc, filter_soilc, num_actfirec, filter_act end if end if call t_stopf('CN Soil matrix-assign matrix-decomp0') - + ! Set C transfer matrix Ac from a_ma_vr call t_startf('CN Soil matrix-matrix mult1-lev3-SetValueAK1') call AKsoilc%SetValueA(begc,endc,num_soilc,filter_soilc,a_ma_vr,A_i,A_j,Ntrans,init_readyAsoilc,list_Asoilc,RI_a,CI_a) @@ -465,7 +468,7 @@ subroutine CNSoilMatrix(bounds,num_soilc, filter_soilc, num_actfirec, filter_act trcr_ntendency(c,ilev,idecomp) = trcr_ntendency(c,ilev,idecomp) + AVsoil%M(c,i)*matrix_Ninter%V(c,AVsoil%CI(i)) / dt end do end do - + call matrix_Cinter%SPMM_AX(num_soilc,filter_soilc,AKallsoilc) call matrix_Ninter%SPMM_AX(num_soilc,filter_soilc,AKallsoiln) @@ -497,8 +500,8 @@ subroutine CNSoilMatrix(bounds,num_soilc, filter_soilc, num_actfirec, filter_act matrix_Cinter13%V(c,j) = matrix_Cinput13%V(c,j) + matrix_Cinter13%V(c,j) end do end do - end if - + end if + ! Update soil C14 pool size: X(matrix_Cinter14) = X(matrix_Cinter14) + (A*K + AVsoil + AKfiresoil) * X(matrix_Cinter14) + I(matrix_Cinput14) if ( use_c14)then do j = 1, ndecomp_pools_vr @@ -525,7 +528,7 @@ subroutine CNSoilMatrix(bounds,num_soilc, filter_soilc, num_actfirec, filter_act end do end do end do - + if( use_c13 ) then do i=1,ndecomp_pools do j = 1,nlevdecomp @@ -551,7 +554,7 @@ subroutine CNSoilMatrix(bounds,num_soilc, filter_soilc, num_actfirec, filter_act call t_stopf('CN Soil matrix-assign back') if(use_soil_matrixcn .and. (hist_wrt_matrixcn_diag .or. spinup_matrixcn))then - + ! Accumulate C transfers during a whole calendar year to calculate the C and N capacity do j=1,ndecomp_pools*nlevdecomp do fc = 1,num_soilc @@ -584,21 +587,21 @@ subroutine CNSoilMatrix(bounds,num_soilc, filter_soilc, num_actfirec, filter_act ! if(use_c14)then ! call cf14_soil%AKallsoilc%SetValueCopySM (num_soilc,filter_soilc,AKallsoilc) ! end if - ! Calculate all the soil C transfers in current time step. + ! Calculate all the soil C transfers in current time step. ! After this step, AKallsoilc represents all the C transfers (gC/m3/step) call Xdiagsoil%SetValueDM(begc,endc,num_soilc,filter_soilc,Cinter_old(begc:endc,1:ndecomp_pools_vr)) call AKallsoilc%SPMM_AK(num_soilc,filter_soilc,Xdiagsoil) - + if(use_c13)then call Xdiagsoil%SetValueDM(begc,endc,num_soilc,filter_soilc,C13inter_old(begc:endc,1:ndecomp_pools_vr)) call cf13_soil%AKallsoilc%SPMM_AK(num_soilc,filter_soilc,Xdiagsoil) end if - + if(use_c14)then call Xdiagsoil%SetValueDM(begc,endc,num_soilc,filter_soilc,C14inter_old(begc:endc,1:ndecomp_pools_vr)) call cf14_soil%AKallsoilc%SPMM_AK(num_soilc,filter_soilc,Xdiagsoil) end if - + ! Calculate all the soil N transfers in current time step ! After this step, AKallsoiln represents all the N transfers (gN/m3/step) call Xdiagsoil%SetValueDM(begc,endc,num_soilc,filter_soilc,Ninter_old(begc:endc,1:ndecomp_pools_vr)) @@ -700,17 +703,17 @@ subroutine CNSoilMatrix(bounds,num_soilc, filter_soilc, num_actfirec, filter_act c = filter_soilc(fc) if (abs(cs_soil%tran_acc(c,i,i)) .le. epsi)then !avoid inversion nan cs_soil%tran_acc(c,i,i) = 1.e+36_r8 - end if + end if end do end do - + if(use_c13)then do i=1,ndecomp_pools_vr do fc = 1,num_soilc c = filter_soilc(fc) if (abs(cs13_soil%tran_acc(c,i,i)) .le. epsi)then !avoid inversion nan cs13_soil%tran_acc(c,i,i) = 1.e+36_r8 - end if + end if end do end do end if @@ -721,7 +724,7 @@ subroutine CNSoilMatrix(bounds,num_soilc, filter_soilc, num_actfirec, filter_act c = filter_soilc(fc) if (abs(cs14_soil%tran_acc(c,i,i)) .le. epsi)then !avoid inversion nan cs14_soil%tran_acc(c,i,i) = 1.e+36_r8 - end if + end if end do end do end if @@ -731,11 +734,11 @@ subroutine CNSoilMatrix(bounds,num_soilc, filter_soilc, num_actfirec, filter_act c = filter_soilc(fc) if (abs(ns_soil%tran_nacc(c,i,i)) .le. epsi)then ns_soil%tran_nacc(c,i,i) = 1.e+36_r8 - end if + end if end do end do - ! Calculate capacity + ! Calculate capacity do fc = 1,num_soilc c = filter_soilc(fc) call inverse(cs_soil%tran_acc(c,1:ndecomp_pools_vr,1:ndecomp_pools_vr),AKinv(1:ndecomp_pools_vr,1:ndecomp_pools_vr),ndecomp_pools_vr) @@ -771,7 +774,7 @@ subroutine CNSoilMatrix(bounds,num_soilc, filter_soilc, num_actfirec, filter_act end do end do end do - + do i = 1,ndecomp_pools do j = 1,nlevdecomp @@ -812,7 +815,7 @@ subroutine CNSoilMatrix(bounds,num_soilc, filter_soilc, num_actfirec, filter_act ! If spin up is on, the capacity replaces the pool size with capacity. ! Copy the capacity into a 3D variable, and be ready to write to history files. - do i=1,ndecomp_pools + do i=1,ndecomp_pools do j = 1,nlevdecomp do fc = 1,num_soilc c = filter_soilc(fc) @@ -870,7 +873,7 @@ subroutine CNSoilMatrix(bounds,num_soilc, filter_soilc, num_actfirec, filter_act end do end do end do - + if(spinup_matrixcn)call update_DA_nstep() if(iloop .eq. iloop_avg .and. iyr .eq. nyr_forcing)iloop = 0 if(iyr .eq. nyr_forcing)iyr = 0 @@ -905,7 +908,7 @@ subroutine CNSoilMatrix(bounds,num_soilc, filter_soilc, num_actfirec, filter_act call t_stopf('CN Soil matrix-calc. C capacity') end if !is out_matrix - end associate + end associate end subroutine CNSoilMatrix !----------------------------------------------------------------------- @@ -935,6 +938,5 @@ subroutine CNSoilMatrixRest( ncid, flag ) !------------------------------------------------------------------------ end subroutine CNSoilMatrixRest - -end module CNSoilMatrixMod +end module CNSoilMatrixMod diff --git a/src/utils/clmfates_interfaceMod.F90 b/src/utils/clmfates_interfaceMod.F90 index cff7679e9d..1f83d29603 100644 --- a/src/utils/clmfates_interfaceMod.F90 +++ b/src/utils/clmfates_interfaceMod.F90 @@ -1485,6 +1485,7 @@ subroutine wrap_update_hlmfates_dyn(this, nc, bounds_clump, & z0m => canopystate_inst%z0m_patch , & ! Output: [real(r8) (:) ] momentum roughness length (m) displa => canopystate_inst%displa_patch, & dleaf_patch => canopystate_inst%dleaf_patch, & + voc_pftindex => canopystate_inst%voc_pftindex_patch, & snow_depth => waterdiagnosticbulk_inst%snow_depth_col, & frac_sno_eff => waterdiagnosticbulk_inst%frac_sno_eff_col, & frac_veg_nosno_alb => canopystate_inst%frac_veg_nosno_alb_patch) @@ -1608,7 +1609,7 @@ subroutine wrap_update_hlmfates_dyn(this, nc, bounds_clump, & z0m(col%patchi(c)+1:col%patchf(c)) = 0.0_r8 displa(col%patchi(c)+1:col%patchf(c)) = 0.0_r8 dleaf_patch(col%patchi(c)+1:col%patchf(c)) = 0.0_r8 - + voc_pftindex(col%patchi(c)+1:col%patchf(c)) = 0 frac_veg_nosno_alb(col%patchi(c):col%patchf(c)) = 0.0_r8 ! Set the bareground patch indicator @@ -1670,6 +1671,7 @@ subroutine wrap_update_hlmfates_dyn(this, nc, bounds_clump, & z0m(p) = this%fates(nc)%bc_out(s)%z0m_pa(ifp) displa(p) = this%fates(nc)%bc_out(s)%displa_pa(ifp) dleaf_patch(p) = this%fates(nc)%bc_out(s)%dleaf_pa(ifp) + voc_pftindex(p) = this%fates(nc)%bc_out(s)%nocomp_MEGAN_pft_label_pa(ifp) end do ! veg pach if(abs(areacheck - 1.0_r8).gt.1.e-9_r8)then @@ -2575,8 +2577,8 @@ subroutine wrap_photosynthesis(this, nc, bounds, fn, filterp, & rssun => photosyns_inst%rssun_patch , & rssha => photosyns_inst%rssha_patch, & psnsun => photosyns_inst%psnsun_patch, & - psnsha => photosyns_inst%psnsha_patch) - + psnsha => photosyns_inst%psnsha_patch, & + ci => canopystate_inst%ci_patch) do s = 1, this%fates(nc)%nsites c = this%f2hmap(nc)%fcolumn(s) @@ -2643,7 +2645,7 @@ subroutine wrap_photosynthesis(this, nc, bounds, fn, filterp, & this%fates(nc)%bc_in(s)%filter_photo_pa(ifp) = 3 rssun(p) = this%fates(nc)%bc_out(s)%rssun_pa(ifp) rssha(p) = this%fates(nc)%bc_out(s)%rssha_pa(ifp) - + ci(p) = this%fates(nc)%bc_out(s)%ci_pa(ifp) ! These fields are marked with a bad-value flag photosyns_inst%psnsun_patch(p) = spval photosyns_inst%psnsha_patch(p) = spval