Merge pull request #2 from DirkOlivie/release-clm5.0.14-Nor

taken over some functionalities from NorESM2 (related to SSP scenarios)

bld/namelist_files/namelist_definition_clm4_5.xml

@@ -507,6 +507,23 @@ Allowed values are:
 Only applies when melt_non_icesheet_ice_runoff is .true.
 </entry>
 
+<entry id="glacier_region_rain_to_snow_behavior" type="char*32(10)" category="clm_physics"
+       group="clm_glacier_behavior"
+       valid_values="converted_to_snow,runs_off" >
+When rain-snow repartitioning / downscaling results in rain being converted to
+snow, the behavior of the resulting additional snow.
+First item corresponds to GLACIER_REGION with ID 0 in the surface dataset,
+second to GLACIER_REGION with ID 1, etc.
+Allowed values are:
+'converted_to_snow': rain is converted to snow, with a corresponding sensible
+   heat flux correction
+'runs_off': rather than being converted to snow, the excess rain runs off
+   immediately
+IMPORTANT NOTE: Unlike other glacier_region*behavior namelist options, this
+option applies to all landunit types in the given regions.
+Only applies when repartition_rain_snow is .true.
+</entry>
+
 <entry id="glc_snow_persistence_max_days" type="integer" category="clm_physics"
        group="clm_inparm" valid_values="" >
 Number of days before one considers the perennially snow-covered point 'land ice'
@@ -596,6 +613,11 @@ Toggle to turn on the FATES model
 (use_fates= '.true.' is EXPERIMENTAL NOT SUPPORTED!)
 </entry>
 
+<entry id="fates_parteh_mode" type="integer" category="physics"
+        group="clm_inparm" valid_values="1">
+Switch deciding which nutrient model to use in FATES.
+</entry>
+
 <entry id="use_fates_spitfire" type="logical" category="physics"
         group="clm_inparm" valid_values="" value=".false.">
 Toggle to turn on spitfire module for modeling fire (only relevant if FATES is being used).
@@ -1707,7 +1729,7 @@ Mapping file to go from one resolution/land-mask to another resolution/land-mask
 
 <entry id="lmask" type="char*10" category="mksurfdata"
        group="default_settings"  
-       valid_values="nomask,navy,AVHRR,MODIS,USGS,IGBPmergeICESatGIS,IGBP-GSDP,ISRIC-WISE,LandScan2004,GLOBE-Gardner,GLOBE-Gardner-mergeGIS,GRDC,HYDRO1K-merge-nomask,ORNL-Soil">
+       valid_values="nomask,navy,AVHRR,MODIS,MODISv2,USGS,IGBPmergeICESatGIS,IGBP-GSDP,ISRIC-WISE,LandScan2004,GLOBE-Gardner,GLOBE-Gardner-mergeGIS,GRDC,HYDRO1K-merge-nomask,ORNL-Soil">
 Land mask description for mksurfdata input files
 </entry> 
 
@@ -1759,9 +1781,9 @@ CLM run type.
 <entry id="res" type="char*30" category="default_settings"
        group="default_settings"  
        valid_values=
-"512x1024,360x720cru,128x256,64x128,48x96,32x64,8x16,94x192,0.23x0.31,0.47x0.63,0.9x1.25,1.9x2.5,2.5x3.33,4x5,10x15,5x5_amazon,1x1_camdenNJ,1x1_vancouverCAN,1x1_mexicocityMEX,1x1_asphaltjungleNJ,1x1_brazil,1x1_urbanc_alpha,1x1_numaIA,1x1_smallvilleIA,0.1x0.1,0.25x0.25,0.5x0.5,3x3min,5x5min,10x10min,0.33x0.33,0.125x0.125,ne4np4,ne16np4,ne30np4,ne60np4,ne120np4,ne240np4,1km-merge-10min">
+"conus_30_x8,512x1024,360x720cru,128x256,64x128,48x96,94x192,0.23x0.31,0.47x0.63,0.9x1.25,1.9x2.5,2.5x3.33,4x5,10x15,5x5_amazon,1x1_camdenNJ,1x1_vancouverCAN,1x1_mexicocityMEX,1x1_asphaltjungleNJ,1x1_brazil,1x1_urbanc_alpha,1x1_numaIA,1x1_smallvilleIA,0.1x0.1,0.25x0.25,0.5x0.5,3x3min,5x5min,10x10min,0.33x0.33,0.125x0.125,ne4np4,ne16np4,ne30np4,ne60np4,ne120np4,ne240np4,1km-merge-10min">
 Horizontal resolutions
-Note: 0.1x0.1, 0.25x0.25, 0.5x0.5, 5x5min, 10x10min, 3x3min and 0.33x0.33 are only used for CLM tools
+Note: 0.1x0.1, 0.25x0.25, 0.5x0.5, 5x5min, 10x10min, 3x3min, 1km-merge-10min and 0.33x0.33 are only used for CLM tools
 </entry> 
 
 <entry id="rcp" type="real" category="default_settings"
@@ -1771,9 +1793,9 @@ Representative concentration pathway for future scenarios [radiative forcing at
 -999.9 means do NOT use a future scenario, just use historical data.
 </entry> 
 
-<entry id="ssp-rcp" type="character*8" category="default_settings"
+<entry id="ssp_rcp" type="char*8" category="default_settings"
        group="default_settings"  
-       valid_values="hist,SSP1-2.6,SSP3-7.0,SSP4-3.4,SSP4-6.0,SSP5-8.5">
+       valid_values=",hist,SSP1-2.6,SSP3-7.0,SSP5-3.4,SSP2-4.5,SSP1-1.9,SSP4-3.4,SSP4-6.0,SSP5-8.5">
 Shared Socioeconomic Pathway (SSP) and Representative Concentration Pathway (RCP) combination for future scenarios 
 The form is SSPn-m.m Where n is the SSP number and m.m is RCP radiative forcing at peak or 2100 in W/m^2
 n is just the whole number of the specific SSP scenario. The lower numbers have higher mitigation
@@ -1783,7 +1805,7 @@ hist means do NOT use a future scenario, just use historical data.
 
 <entry id="mask" type="char*10" category="default_settings"
        group="default_settings"  
-       valid_values="USGS,gx3v7,gx1v6,gx1v7,navy,test,tx0.1v2,tx1v1,T62,cruncep">
+       valid_values="USGS,gx3v7,gx1v6,gx1v7,navy,test,tx0.1v2,tx1v1,T62,cruncep,tnx1v1,tnx0.25v1,tnx0.25v3,tnx0.25v4,tnx1v4,tnx1v3">
 Land mask description
 </entry> 
 
@@ -1801,19 +1823,20 @@ to run with a different type of atmospheric forcing.
 If 1, turn on the MEGAN model for BVOC's (Biogenic Volitile Organic Compounds)
 </entry> 
 
-<entry id="sim_year" type="integer" category="default_settings"
+<entry id="sim_year" type="char*4" category="default_settings"
        group="default_settings" valid_values=
-"1000,850,1100,1350,1600,1850,1855,1865,1875,1885,1895,1905,1915,1925,1935,1945,1955,1965,1975,1980,1985,1995,2000,2005,2010,2015,2025,2035,2045,2055,2065,2075,2085,2095,2105">
+"PtVg,1000,850,1100,1350,1600,1850,1855,1865,1875,1885,1895,1905,1915,1925,1935,1945,1955,1965,1975,1980,1985,1995,2000,2005,2010,2015,2025,2035,2045,2055,2065,2075,2085,2095,2105">
 Year to simulate and to provide datasets for (such as surface datasets, initial conditions, aerosol-deposition, Nitrogen deposition rates etc.)
 A sim_year of 1000 corresponds to data used for testing only, NOT corresponding to any real datasets.
-A sim_year greater than 2005 corresponds to rcp scenario data
+A sim_year greater than 2015 corresponds to ssp_rcp scenario data
+A sim_year of PtVg refers to the Potential Vegetation dataset, that doesn't include human influences
 Most years are only used for clm_tools and there aren't CLM datasets that correspond to them.
 CLM datasets exist for years: 1000 (for testing), 1850, and 2000
 </entry> 
 
 <entry id="sim_year_range" type="char*9" category="default_settings"
        group="default_settings" valid_values=
-"constant,1000-1002,1000-1004,850-1100,1100-1350,1350-1600,1600-1850,1850-1855,1850-2000,1850-2005,1850-2100,1980-2015,2000-2100">
+"constant,1000-1002,1000-1004,850-1100,1100-1350,1350-1600,1600-1850,1850-1855,1850-2000,1850-2005,1850-2100,1980-2015,2000-2100,2100-2300">
 Range of years to simulate transitory datasets for (such as dynamic: land-use datasets, aerosol-deposition, Nitrogen deposition rates etc.)
 Constant means simulation will be held at a constant year given in sim_year.
 A sim_year_range of 1000-1002 or 1000-1004 corresponds to data used for testing only, NOT corresponding to any real datasets.
@@ -1840,8 +1863,8 @@ Attributes to use when looking for an initial condition file (finidat) if interp
 How close in years to use when looking for an initial condition file (finidat) if interpolation is turned on (use_init_interp is .true.)
 </entry>
 
-<entry id="init_interp_sim_years" type="integer(2)"  category="default_settings"
-       group="default_settings" valid_values="1850,2000" >
+<entry id="init_interp_sim_years" type="integer(4)"  category="default_settings"
+       group="default_settings" valid_values="1850,2000,2010,2015" >
 Simulation years you can look for in initial condition files (finidat) if interpolation is turned on (use_init_interp is .true.)
 </entry>
 
@@ -1952,6 +1975,11 @@ Number of days over which to use exponential relaxation of NPP in N fixation cal
 Flag to reseed any dead plants on startup from reading the initial conditions file
 </entry>
 
+<entry id="dribble_crophrv_xsmrpool_2atm" type="logical" category="clm_physics"
+       group="cn_general" valid_values="" >
+Harvest the XSMR pool at crop harvest time to the atmosphere slowly at an exponential rate
+</entry>
+
 <!-- C isotope flags    -->
 <entry id="use_c13" type="logical" category="clm_isotope"
        group="clm_inparm" valid_values="" >

bld/namelist_files/use_cases/1850-2100_SSP1-1.9_transient.xml

@@ -0,0 +1,19 @@
+<?xml version="1.0"?>
+
+<namelist_defaults>
+
+<use_case_desc            >Simulate transient land-use, and aerosol deposition changes from 1850 to current day with historical data, and then to 2100 with the CMIP6 SSP1-1.9 scenario</use_case_desc>
+<use_case_desc use_cn=".true." >Simulate transient land-use, aerosol deposition, and Nitrogen deposition changes from 1850 to current day with historical data, and then to 2100 with the CMIP6 SSP1-1.9 scenario</use_case_desc>
+
+<!-- Have a minimal list of things set here, sim_year, sim_year_range, and ssp_rcp, other things should be dependent on these and
+     set in a namelist_defaults xml file -->
+
+<sim_year>1850</sim_year>
+
+<sim_year_range>1850-2100</sim_year_range>
+
+<ssp_rcp>SSP1-1.9</ssp_rcp>
+
+<clm_demand >flanduse_timeseries</clm_demand>
+
+</namelist_defaults>

bld/namelist_files/use_cases/1850-2100_SSP1-2.6_transient.xml

@@ -0,0 +1,19 @@
+<?xml version="1.0"?>
+
+<namelist_defaults>
+
+<use_case_desc            >Simulate transient land-use, and aerosol deposition changes from 1850 to current day with historical data, and then to 2100 with the CMIP6 SSP1-2.6 scenario</use_case_desc>
+<use_case_desc use_cn=".true." >Simulate transient land-use, aerosol deposition, and Nitrogen deposition changes from 1850 to current day with historical data, and then to 2100 with the CMIP6 SSP1-2.6 scenario</use_case_desc>
+
+<!-- Have a minimal list of things set here, sim_year, sim_year_range, and ssp_rcp, other things should be dependent on these and
+     set in a namelist_defaults xml file -->
+
+<sim_year>1850</sim_year>
+
+<sim_year_range>1850-2100</sim_year_range>
+
+<ssp_rcp>SSP1-2.6</ssp_rcp>
+
+<clm_demand >flanduse_timeseries</clm_demand>
+
+</namelist_defaults>

bld/namelist_files/use_cases/1850-2100_SSP2-4.5_transient.xml

@@ -0,0 +1,19 @@
+<?xml version="1.0"?>
+
+<namelist_defaults>
+
+<use_case_desc            >Simulate transient land-use, and aerosol deposition changes from 1850 to current day with historical data, and then to 2100 with the CMIP6 SSP2-4.5 scenario</use_case_desc>
+<use_case_desc use_cn=".true." >Simulate transient land-use, aerosol deposition, and Nitrogen deposition changes from 1850 to current day with historical data, and then to 2100 with the CMIP6 SSP2-4.5 scenario</use_case_desc>
+
+<!-- Have a minimal list of things set here, sim_year, sim_year_range, and ssp_rcp, other things should be dependent on these and
+     set in a namelist_defaults xml file -->
+
+<sim_year>1850</sim_year>
+
+<sim_year_range>1850-2100</sim_year_range>
+
+<ssp_rcp>SSP2-4.5</ssp_rcp>
+
+<clm_demand >flanduse_timeseries</clm_demand>
+
+</namelist_defaults>

bld/namelist_files/use_cases/1850-2100_SSP3-7.0_transient.xml

@@ -0,0 +1,19 @@
+<?xml version="1.0"?>
+
+<namelist_defaults>
+
+<use_case_desc            >Simulate transient land-use, and aerosol deposition changes from 1850 to current day with historical data, and then to 2100 with the CMIP6 SSP3-7.0 scenario</use_case_desc>
+<use_case_desc use_cn=".true." >Simulate transient land-use, aerosol deposition, and Nitrogen deposition changes from 1850 to current day with historical data, and then to 2100 with the CMIP6 SSP3-7.0 scenario</use_case_desc>
+
+<!-- Have a minimal list of things set here, sim_year, sim_year_range, and ssp_rcp, other things should be dependent on these and
+     set in a namelist_defaults xml file -->
+
+<sim_year>1850</sim_year>
+
+<sim_year_range>1850-2100</sim_year_range>
+
+<ssp_rcp>SSP3-7.0</ssp_rcp>
+
+<clm_demand >flanduse_timeseries</clm_demand>
+
+</namelist_defaults>

bld/namelist_files/use_cases/1850-2100_SSP4-3.4_transient.xml

@@ -0,0 +1,19 @@
+<?xml version="1.0"?>
+
+<namelist_defaults>
+
+<use_case_desc            >Simulate transient land-use, and aerosol deposition changes from 1850 to current day with historical data, and then to 2100 with the CMIP6 SSP4-3.4 scenario</use_case_desc>
+<use_case_desc use_cn=".true." >Simulate transient land-use, aerosol deposition, and Nitrogen deposition changes from 1850 to current day with historical data, and then to 2100 with the CMIP6 SSP4-3.4 scenario</use_case_desc>
+
+<!-- Have a minimal list of things set here, sim_year, sim_year_range, and ssp_rcp, other things should be dependent on these and
+     set in a namelist_defaults xml file -->
+
+<sim_year>1850</sim_year>
+
+<sim_year_range>1850-2100</sim_year_range>
+
+<ssp_rcp>SSP4-3.4</ssp_rcp>
+
+<clm_demand >flanduse_timeseries</clm_demand>
+
+</namelist_defaults>

bld/namelist_files/use_cases/1850-2100_SSP4-6.0_transient.xml

@@ -0,0 +1,19 @@
+<?xml version="1.0"?>
+
+<namelist_defaults>
+
+<use_case_desc            >Simulate transient land-use, and aerosol deposition changes from 1850 to current day with historical data, and then to 2100 with the CMIP6 SSP4-6.0 scenario</use_case_desc>
+<use_case_desc use_cn=".true." >Simulate transient land-use, aerosol deposition, and Nitrogen deposition changes from 1850 to current day with historical data, and then to 2100 with the CMIP6 SSP4-6.0 scenario</use_case_desc>
+
+<!-- Have a minimal list of things set here, sim_year, sim_year_range, and ssp_rcp, other things should be dependent on these and
+     set in a namelist_defaults xml file -->
+
+<sim_year>1850</sim_year>
+
+<sim_year_range>1850-2100</sim_year_range>
+
+<ssp_rcp>SSP4-6.0</ssp_rcp>
+
+<clm_demand >flanduse_timeseries</clm_demand>
+
+</namelist_defaults>

bld/namelist_files/use_cases/1850-2100_SSP5-3.4_transient.xml

@@ -0,0 +1,19 @@
+<?xml version="1.0"?>
+
+<namelist_defaults>
+
+<use_case_desc            >Simulate transient land-use, and aerosol deposition changes from 1850 to current day with historical data, and then to 2100 with the CMIP6 SSP5-3.4 scenario</use_case_desc>
+<use_case_desc use_cn=".true." >Simulate transient land-use, aerosol deposition, and Nitrogen deposition changes from 1850 to current day with historical data, and then to 2100 with the CMIP6 SSP5-3.4 scenario</use_case_desc>
+
+<!-- Have a minimal list of things set here, sim_year, sim_year_range, and ssp_rcp, other things should be dependent on these and
+     set in a namelist_defaults xml file -->
+
+<sim_year>1850</sim_year>
+
+<sim_year_range>1850-2100</sim_year_range>
+
+<ssp_rcp>SSP5-3.4</ssp_rcp>
+
+<clm_demand >flanduse_timeseries</clm_demand>
+
+</namelist_defaults>

bld/namelist_files/use_cases/1850-2100_SSP5-8.5_transient.xml

@@ -0,0 +1,19 @@
+<?xml version="1.0"?>
+
+<namelist_defaults>
+
+<use_case_desc            >Simulate transient land-use, and aerosol deposition changes from 1850 to current day with historical data, and then to 2100 with the CMIP6 SSP5-8.5 scenario</use_case_desc>
+<use_case_desc use_cn=".true." >Simulate transient land-use, aerosol deposition, and Nitrogen deposition changes from 1850 to current day with historical data, and then to 2100 with the CMIP6 SSP5-8.5 scenario</use_case_desc>
+
+<!-- Have a minimal list of things set here, sim_year, sim_year_range, and ssp_rcp, other things should be dependent on these and
+     set in a namelist_defaults xml file -->
+
+<sim_year>1850</sim_year>
+
+<sim_year_range>1850-2100</sim_year_range>
+
+<ssp_rcp>SSP5-8.5</ssp_rcp>
+
+<clm_demand >flanduse_timeseries</clm_demand>
+
+</namelist_defaults>

bld/namelist_files/use_cases/2014_control.xml

@@ -0,0 +1,36 @@
+<?xml version="1.0"?>
+
+<namelist_defaults>
+
+<use_case_desc>Conditions to simulate 2014 land-use</use_case_desc>
+
+<sim_year>2000</sim_year>
+
+<sim_year_range>constant</sim_year_range>
+
+<irrigate use_crop=".true." phys="clm5_0" use_cndv=".false.">.true.</irrigate>
+<irrigate use_crop=".true." phys="clm5_0" use_cndv=".true." >.false.</irrigate>
+<irrigate use_crop=".true." phys="clm4_5"                   >.false.</irrigate>
+
+<stream_year_first_ndep phys="clm4_0" bgc="cn"   >2014</stream_year_first_ndep>
+<stream_year_last_ndep  phys="clm4_0" bgc="cn"   >2014</stream_year_last_ndep>
+
+<stream_year_first_ndep phys="clm4_0" bgc="cndv" >2014</stream_year_first_ndep>
+<stream_year_last_ndep  phys="clm4_0" bgc="cndv" >2014</stream_year_last_ndep>
+
+<stream_year_first_ndep phys="clm4_5" use_cn=".true." >2014</stream_year_first_ndep>
+<stream_year_last_ndep  phys="clm4_5" use_cn=".true." >2014</stream_year_last_ndep>
+
+<stream_year_first_ndep phys="clm5_0" use_cn=".true." >2014</stream_year_first_ndep>
+<stream_year_last_ndep  phys="clm5_0" use_cn=".true." >2014</stream_year_last_ndep>
+
+<stream_year_first_popdens phys="clm4_5" cnfireson=".true." >2014</stream_year_first_popdens>
+<stream_year_last_popdens  phys="clm4_5" cnfireson=".true." >2014</stream_year_last_popdens>
+
+<stream_year_first_popdens phys="clm5_0" cnfireson=".true." >2014</stream_year_first_popdens>
+<stream_year_last_popdens  phys="clm5_0" cnfireson=".true." >2014</stream_year_last_popdens>
+
+<stream_year_first_urbantv phys="clm5_0" >2014</stream_year_first_urbantv>
+<stream_year_last_urbantv  phys="clm5_0" >2014</stream_year_last_urbantv>
+
+</namelist_defaults>

bld/namelist_files/use_cases/2101-2300_SSP5-8.5_transient.xml

@@ -0,0 +1,19 @@
+<?xml version="1.0"?>
+
+<namelist_defaults>
+
+<use_case_desc            >Simulate transient land-use, and aerosol deposition changes from 1850 to current day with historical data, and then to 2100 with the CMIP6 SSP5-8.5 scenario</use_case_desc>
+<use_case_desc use_cn=".true." >Simulate transient land-use, aerosol deposition, and Nitrogen deposition changes from 1850 to current day with historical data, and then to 2100 with the CMIP6 SSP5-8.5 scenario</use_case_desc>
+
+<!-- Have a minimal list of things set here, sim_year, sim_year_range, and ssp_rcp, other things should be dependent on these and
+     set in a namelist_defaults xml file -->
+
+<sim_year>1850</sim_year>
+
+<sim_year_range>2100-2300</sim_year_range>
+
+<ssp_rcp>SSP5-8.5</ssp_rcp>
+
+<clm_demand >flanduse_timeseries</clm_demand>
+
+</namelist_defaults>

cime_config/buildnml

@@ -60,6 +60,7 @@ def buildnml(case, caseroot, compname):
     run_reftod = case.get_value("RUN_REFTOD")
     glc_nec = case.get_value("GLC_NEC")
     mask = case.get_value("MASK_GRID")
+    ocn_grid = case.get_value("OCN_GRID")
 
     # -----------------------------------------------------
     # Set clmconf
@@ -230,8 +231,17 @@ def buildnml(case, caseroot, compname):
         create_namelist_infile(case, user_nl_file, namelist_infile, "\n".join(infile_lines))
 
         cmd = os.path.join(lnd_root,"bld","build-namelist")
-
-        command = ("%s -cimeroot %s -infile %s -csmdata %s -inputdata %s %s -namelist \"&clm_inparm  start_ymd=%s %s/ \" "
+        if ocn_grid == "tnx1v1" or ocn_grid == "tnx0.25v1" or ocn_grid == "tnx1v3" or ocn_grid == "tnx1v4" or ocn_grid == "tnx0.25v3" or ocn_grid == "tnx0.25v4":
+            command = ("%s -cimeroot %s -infile %s -csmdata %s -inputdata %s %s -namelist \"&clm_inparm  start_ymd=%s %s/ \" "
+                   "%s %s -res %s %s -clm_start_type %s -envxml_dir %s -l_ncpl %s "
+                   "-lnd_frac %s -glc_nec %s -co2_ppmv %s -co2_type %s -config %s "
+                   "%s %s %s %s -mask %s"
+                   %(cmd, _CIMEROOT, infile, din_loc_root, inputdata_file, ignore, start_ymd, clm_namelist_opts,
+                     nomeg, usecase, lnd_grid, clmusr, start_type, caseroot, lnd_ncpl,
+                     lndfrac_file, glc_nec, ccsm_co2_ppmv, clm_co2_type, config_cache_file,
+                     clm_bldnml_opts, spinup, tuning, gridmask, ocn_grid))
+        else:
+            command = ("%s -cimeroot %s -infile %s -csmdata %s -inputdata %s %s -namelist \"&clm_inparm  start_ymd=%s %s/ \" "
                    "%s %s -res %s %s -clm_start_type %s -envxml_dir %s -l_ncpl %s "
                    "-lnd_frac %s -glc_nec %s -co2_ppmv %s -co2_type %s -config %s "
                    "%s %s %s %s"