Merge pull request #620 from ekluzek/noanthrocompset

Add in NoAnthro compsets and tests
ESCOMP · Feb 14, 2019 · 24515c5 · 24515c5
2 parents b623c0c + 7b67ac4
commit 24515c5
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diff --git a/Externals.cfg b/Externals.cfg
@@ -30,7 +30,7 @@ required = True
 local_path = cime
 protocol = git
 repo_url = https://github.com/ESMCI/cime
-tag = cime_cesm2_1_rel_06
+tag = cime5.6.11
 required = True
 
 [externals_description]

diff --git a/bld/CLMBuildNamelist.pm b/bld/CLMBuildNamelist.pm
@@ -2428,7 +2428,12 @@ sub setup_logic_initial_conditions {
           add_default($opts,  $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, "init_interp_how_close" );
           my $close = $nl->get_value("init_interp_how_close");
           foreach my $sim_yr ( split( /,/, $nl->get_value("init_interp_sim_years") )) {
-             my $how_close = abs($st_year - $sim_yr);
+             my $how_close = undef;
+             if ( $nl_flags->{'sim_year'} eq "PtVg" ) {
+                $how_close = abs(1850 - $sim_yr);
+             } else {
+                $how_close = abs($st_year - $sim_yr);
+             }
              if ( ($how_close < $nl->get_value("init_interp_how_close")) && ($how_close < $close) ) {
                 $close = $how_close;
                 $settings{'sim_year'} = $sim_yr;

diff --git a/bld/namelist_files/createMkSrfEntry.py b/bld/namelist_files/createMkSrfEntry.py
@@ -5,12 +5,12 @@
 class mksrfDataEntry_prog:
 
    # Class data
-   year_start = 2016
-   year_end   = 2100
-   ssp_rcp    = "SSP4-6.0"
-   subdir     = "pftcftdynharv.0.25x0.25.SSP4-6.0.simyr2016-2100.c181217"
-   cdate      = 181217
-   desc       = "SSP4RCP60_clm5"
+   year_start = 850
+   year_end   = 1849
+   ssp_rcp    = "hist"
+   subdir     = "pftcftdynharv.0.25x0.25.LUH2.histsimyr0850-1849.c171012"
+   cdate      = 171012
+   desc       = "histclm50_LUH2"
 
    def parse_cmdline_args( self ):
       "Parse the command line arguments for create data entry list"

diff --git a/bld/namelist_files/namelist_defaults_clm4_5.xml b/bld/namelist_files/namelist_defaults_clm4_5.xml
@@ -27,6 +27,7 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
 <co2_ppmv sim_year="2000"      >379.0</co2_ppmv>
 <co2_ppmv sim_year="2010"      >388.8</co2_ppmv>
 <co2_ppmv sim_year="1850"      >284.7</co2_ppmv>
+<co2_ppmv sim_year="PtVg"      >284.7</co2_ppmv>
 
 <!-- CO2 type -->
 <co2_type>constant</co2_type>
@@ -828,6 +829,10 @@ lnd/clm2/surfdata_map/surfdata_ne120np4_78pfts_CMIP6_simyr1850_c170824.nc</fsurd
 <fsurdat hgrid="conus_30_x8"    sim_year="1850" use_crop=".true." >
 lnd/clm2/surfdata_map/surfdata_conus_30_x8_78pfts_CMIP6_simyr1850_c181003.nc</fsurdat>
 
+<!-- Potential vegetation land use dataset, crop is off, and zeroed, all areas are natural vegetation without human disturbance -->
+<fsurdat hgrid="0.9x1.25"     sim_year="PtVg" use_crop=".false." irrigate=".false."
+>lnd/clm2/surfdata_map/surfdata_0.9x1.25_hist_16pfts_nourb_CMIP6_simyrPtVg_c181114.nc</fsurdat>
+
 <!-- Dynamic PFT surface datasets (relative to {csmdata}) -->
 
 <!-- Note that, to reduce the number of necessary datasets, we use an RCP

diff --git a/bld/namelist_files/namelist_defaults_clm4_5_tools.xml b/bld/namelist_files/namelist_defaults_clm4_5_tools.xml
diff --git a/bld/namelist_files/use_cases/1850_noanthro_control.xml b/bld/namelist_files/use_cases/1850_noanthro_control.xml
@@ -0,0 +1,56 @@
+<?xml version="1.0"?>
+
+<namelist_defaults>
+
+<use_case_desc>Simulate current conditions without ANY anthropogenic influnces</use_case_desc>
+
+<sim_year>PtVg</sim_year>
+
+<sim_year_range>constant</sim_year_range>
+
+<irrigate>.false.</irrigate>
+
+<stream_year_first_ndep phys="clm4_0" bgc="cn"   >1850</stream_year_first_ndep>
+<stream_year_last_ndep  phys="clm4_0" bgc="cn"   >1850</stream_year_last_ndep>
+
+<stream_year_first_ndep phys="clm4_0" bgc="cndv" >1850</stream_year_first_ndep>
+<stream_year_last_ndep  phys="clm4_0" bgc="cndv" >1850</stream_year_last_ndep>
+
+<stream_year_first_ndep phys="clm4_5" use_cn=".true." >1850</stream_year_first_ndep>
+<stream_year_last_ndep  phys="clm4_5" use_cn=".true." >1850</stream_year_last_ndep>
+
+<stream_year_first_ndep phys="clm5_0" use_cn=".true." >1850</stream_year_first_ndep>
+<stream_year_last_ndep  phys="clm5_0" use_cn=".true." >1850</stream_year_last_ndep>
+
+<ndep_taxmode            phys="clm5_0" use_cn=".true." >cycle</ndep_taxmode>
+<ndep_varlist            phys="clm5_0" use_cn=".true." >NDEP_month</ndep_varlist>
+
+<stream_year_first_popdens phys="clm4_0" cnfireson=".true." >1925</stream_year_first_popdens>
+<stream_year_last_popdens  phys="clm4_0" cnfireson=".true." >1925</stream_year_last_popdens>
+
+<stream_year_first_popdens phys="clm4_5" cnfireson=".true." >1925</stream_year_first_popdens>
+<stream_year_last_popdens  phys="clm4_5" cnfireson=".true." >1925</stream_year_last_popdens>
+
+<stream_year_first_popdens phys="clm5_0" cnfireson=".true." >1925</stream_year_first_popdens>
+<stream_year_last_popdens  phys="clm5_0" cnfireson=".true." >1925</stream_year_last_popdens>
+
+<!-- zero population density file -->
+<stream_fldfilename_popdens hgrid="0.5x0.5"   use_cn=".true."
+>lnd/clm2/firedata/clmforc.no_anthro_zero_hdm_1x1_simyr1925_181113.nc</stream_fldfilename_popdens>
+<popdensmapalgo use_cn=".true.">nn</popdensmapalgo>
+
+<stream_year_first_urbantv phys="clm5_0"  >1850</stream_year_first_urbantv>
+<stream_year_last_urbantv  phys="clm5_0"  >1850</stream_year_last_urbantv>
+
+<!-- Turn calculation of human stress indices all the way off to save some CPU -->
+<calc_human_stress_indices     >NONE</calc_human_stress_indices>
+
+<!-- Turn off URBAN heating and A/C, and turn off harvesting of forests -->
+<urban_hac                     >OFF</urban_hac>
+<do_harvest                    >.false.</do_harvest>
+
+<!-- Set contants having to do with fire due to human influences to zero (human ignition counts, and crop fires -->
+<pot_hmn_ign_counts_alpha      >0.0</pot_hmn_ign_counts_alpha>
+<cropfire_a1                   >0.0</cropfire_a1>
+
+</namelist_defaults>
diff --git a/bld/unit_testers/build-namelist_test.pl b/bld/unit_testers/build-namelist_test.pl
@@ -123,9 +123,9 @@ sub make_env_run {
 #
 # Figure out number of tests that will run
 #
-my $ntests = 950;
+my $ntests = 956;
 if ( defined($opts{'compare'}) ) {
-   $ntests += 600;
+   $ntests += 603;
 }
 plan( tests=>$ntests );
 
@@ -317,6 +317,7 @@ sub make_env_run {
                       "-bgc fates  -use_case 2000_control -no-megan",
                       "-bgc cn  -use_case 1850-2100_rcp8.5_transient -namelist '&a start_ymd=19201023/'",
                       "-bgc bgc -use_case 2000_control -namelist \"&a fire_method='nofire'/\" -crop",
+                      "-res 0.9x1.25 -bgc bgc -use_case 1850_noanthro_control -drydep -fire_emis -light_res 360x720",
                      ) {
    my $file = $startfile;
    &make_env_run();
@@ -863,6 +864,16 @@ sub make_env_run {
                                      GLC_TWO_WAY_COUPLING=>"FALSE",
                                      conopts=>"-phys clm5_0",
                                    },
+     "noanthro_w_crop"            =>{ options=>"-envxml_dir . -res 0.9x1.25 -bgc bgc -crop -use_case 1850_noanthro_control",
+                                     namelst=>"",
+                                     GLC_TWO_WAY_COUPLING=>"FALSE",
+                                     conopts=>"-phys clm5_0",
+                                   },
+     "noanthro_w_irrig"           =>{ options=>"-envxml_dir . -res 0.9x1.25 -bgc bgc -use_case 1850_noanthro_control",
+                                     namelst=>"irrigate=T",
+                                     GLC_TWO_WAY_COUPLING=>"FALSE",
+                                     conopts=>"-phys clm5_0",
+                                   },
      "spdotransconflict"          =>{ options=>"-envxml_dir . -bgc sp -use_case 20thC_transient",
                                      namelst=>"do_transient_pfts=T,do_transient_crops=.false.",
                                      GLC_TWO_WAY_COUPLING=>"FALSE",

diff --git a/cime_config/config_component.xml b/cime_config/config_component.xml
@@ -16,16 +16,18 @@
   <description modifier_mode="1">
     <desc lnd="CLM40[%SP][%CN][%CNDV][%CN-CROP][%CNDV-CROP]"                                                                         >clm4.0:</desc>
     <desc lnd="CLM45[%SP][%SP-VIC][%CN][%CNDV][%CN-CROP][%CNDV-CROP][%BGC][%BGC-CROP][%FATES][%BGCDV][%BGCDV-CROP]"                  >clm4.5:</desc>
-    <desc lnd="CLM50[%SP][%SP-VIC][%CN][%BGC][%BGC-CROP][%FATES][%BGCDV][%BGCDV-CROP][%BGC-CROP-CMIP6DECK][%BGC-CROP-CMIP6WACCMDECK]">clm5.0:</desc>
+    <desc lnd="CLM50[%SP][%SP-VIC][%SP-NOANTHRO][%BGC-NOANTHRO][%CN][%BGC][%BGC-CROP][%FATES][%BGCDV][%BGCDV-CROP][%BGC-CROP-CMIP6DECK][%BGC-CROP-CMIP6WACCMDECK]">clm5.0:</desc>
     <desc option="SP"              >Satellite phenology:</desc>
     <desc option="CN"              >CN: Carbon Nitrogen model</desc>
     <desc option="CNDV"            >CNDV: CN with Dynamic Vegetation</desc>
     <desc option="CN-CROP"         >CN with prognostic crop:</desc>
     <desc option="CNDV-CROP"       >CNDV with prognostic crop:</desc>
 
     <desc option="SP-VIC"          >Satellite phenology with VIC hydrology:</desc>
+    <desc option="SP-NOANTHRO"     >Satellite phenology without anthropomorphic influences</desc>
     <desc option="BGC"             >BGC (vert. resol. CN and methane):</desc>
     <desc option="BGC-CROP"        >BGC (vert. resol. CN and methane) with prognostic crop:</desc>
+    <desc option="BGC-NOANTHRO"    >BGC (vert. resol. CN and methane) without anthropomorphic influences:</desc>
     <desc option="FATES"           >FATES (Functionally Assembled Terrestrial Ecosystem Simulator) Ecosystem Demography model: (experimental)</desc>
     <desc option="BGCDV"           >BGC (vert. resol. CN and methane) with dynamic vegetation:</desc>
     <desc option="BGCDV-CROP"      >BGC (vert. resol. CN and methane) with dynamic vegetation and prognostic crop:</desc>
@@ -102,16 +104,17 @@
     <default_value>UNSET</default_value>
     <values>
       <!-- Use rcp4.5 for PI to PDAY so will have data up to the current year available (for WACCM compsets that use PDAY) -->
-      <value compset="^2010_"		>2010_control</value>
-      <value compset="^2000_"		>2000_control</value>
-      <value compset="^1850_"		>1850_control</value>
-      <value compset="^HIST_"		>20thC_transient</value>
-      <value compset="^RCP6_"		>1850-2100_rcp6_transient</value>
-      <value compset="^RCP4_"		>1850-2100_rcp4.5_transient</value>
-      <value compset="^RCP2_"		>1850-2100_rcp2.6_transient</value>
-      <value compset="^RCP8_"		>1850-2100_rcp8.5_transient</value>
-      <value compset="^AMIP_"		>20thC_transient</value>
-      <value compset="^PIPD_"           >1850-2100_rcp4.5_transient</value>
+      <value compset="^2010_"		            >2010_control</value>
+      <value compset="^2000_"		            >2000_control</value>
+      <value compset="^1850_"		            >1850_control</value>
+      <value compset="^1850_.*_CLM50%[^_]*NOANTHRO" >1850_noanthro_control</value>
+      <value compset="^HIST_"		            >20thC_transient</value>
+      <value compset="^RCP6_"	            	    >1850-2100_rcp6_transient</value>
+      <value compset="^RCP4_"	            	    >1850-2100_rcp4.5_transient</value>
+      <value compset="^RCP2_"		            >1850-2100_rcp2.6_transient</value>
+      <value compset="^RCP8_"	   	            >1850-2100_rcp8.5_transient</value>
+      <value compset="^AMIP_"		            >20thC_transient</value>
+      <value compset="^PIPD_"                       >1850-2100_rcp4.5_transient</value>
     </values>
     <group>run_component_clm</group>
     <file>env_run.xml</file>

diff --git a/cime_config/config_compsets.xml b/cime_config/config_compsets.xml
@@ -163,6 +163,16 @@
      <lname>1850_DATM%GSWP3v1_CLM50%BGC_SICE_SOCN_MOSART_CISM2%NOEVOLVE_SWAV</lname>
    </compset>
 
+  <compset>
+     <alias>I1850Clm50BgcNoAnthro</alias>
+     <lname>1850_DATM%GSWP3v1_CLM50%BGC-NOANTHRO_SICE_SOCN_MOSART_CISM2%NOEVOLVE_SWAV</lname>
+   </compset>
+
+  <compset>
+     <alias>I1850Clm50SpNoAnthro</alias>
+     <lname>1850_DATM%GSWP3v1_CLM50%SP-NOANTHRO_SICE_SOCN_MOSART_CISM2%NOEVOLVE_SWAV</lname>
+   </compset>
+
   <compset>
     <alias>IHistClm50BgcCrop</alias>
     <lname>HIST_DATM%GSWP3v1_CLM50%BGC-CROP_SICE_SOCN_MOSART_CISM2%NOEVOLVE_SWAV</lname>

diff --git a/cime_config/testdefs/testlist_clm.xml b/cime_config/testdefs/testlist_clm.xml
@@ -8,6 +8,14 @@
       <option name="wallclock">00:20:00</option>
     </options>
   </test>
+  <test name="SMS_D_Ld9" grid="f09_g17_gl4" compset="I1850Clm50BgcNoAnthro" testmods="clm/decStart1851_noinitial">
+    <machines>
+      <machine name="cheyenne" compiler="intel" category="aux_clm"/>
+    </machines>
+    <options>
+      <option name="wallclock">00:20:00</option>
+    </options>
+  </test>
   <test name="ERI_D_Ld9" grid="1x1_camdenNJ" compset="I2000Clm50BgcCruGs" testmods="clm/default">
     <machines>
       <machine name="cheyenne" compiler="intel" category="prebeta"/>

diff --git a/doc/ChangeSum b/doc/ChangeSum
@@ -1,5 +1,6 @@
 Tag                   Who      Date  Summary
 ============================================================================================================================
+release-clm5.0.18     erik 02/13/2019 Add NoAnthro compset, reduce fields on fsurdat in mksurfdata_map, initial add of tools/contrib directory
 release-clm5.0.17    sacks 01/23/2019 History fields for vertically-resolved sums of soil C and N, and minor fixes
   ctsm1.0.dev025     sacks 01/23/2019 History fields for vertically-resolved sums of soil C and N, and minor fixes
 release-clm5.0.16     erik 01/15/2019 PtVg and ssp_rcp future scenario options and Antarctica wetlands fix to mksurfdata, and option to dribble crop harvest XSMRPOOL flux to atmosphere

diff --git a/doc/release-clm5.0.ChangeLog b/doc/release-clm5.0.ChangeLog
@@ -1,4 +1,125 @@
 ===============================================================
+Tag name:  release-clm5.0.18
+Originator(s):  erik (Erik Kluzek,UCAR/TSS,303-497-1326)
+Date: Wed Feb 13 19:01:26 MST 2019
+One-line Summary: Add NoAnthro compset, reduce fields on fsurdat in mksurfdata_map, initial add of tools/contrib directory
+
+Purpose of this version:
+------------------------
+
+New NoAnthro compsets: I1850Clm50BgcNoAnthro, I1850Clm50SpNoAnthro and tests for it.
+More updates to surface dataset generation, to reduce the fields that are output, removing ones
+that aren't used.
+
+New tools/contrib directory with initial add of some useful scripts for users. Currently unsupported
+and only expected to run on cheyenne. The following scripts are added:
+
+   run_clm_historical ---- does all the setup and submission required to do a 1850-2010 CLM historical
+   subset_surfdata ------- create regional domain, surface data, and rtm directional files by 
+          extracting data from global datasets 
+   singlept -------------- create single point domain, surface data, and datm forcing files by 
+           extracting data from global datasets
+   SpinupStability.ncl --- This script assesses the equilibrium state of a spinup run
+   run_clmtowers --------- This script will run any number of flux tower sites.
+
+Add new default f09 Potential Vegetation (PtVg) surface dataset. For mksurfdata new high resolution
+PFT datasets (at 3x3min) for 2005. New rawdata PFT files from 0850-1849.
+
+CTSM Master Tag This Corresponds To: ctsm1.0.dev025 (with many changes missing)
+
+Summary of changes:
+-------------------
+
+Issues fixed (include CTSM Issue #): Fixes #629 #557 #262
+   #629 -- Unused fields from fsurdat files
+   #557 -- No anthro compset
+   #262 -- hirespft option doesn't work for mksurfdata.pl
+
+Science changes since: release-clm5.0.17
+   None
+
+Software changes since: release-clm5.0.17
+   PtVg and pre-millenial raw PFT datasets
+   reduce fields created on fsurdat files
+
+Changes to User Interface since: release-clm5.0.17
+   New NoAnthro compsets: I1850Clm50BgcNoAnthro, I1850Clm50SpNoAnthro
+   Add new option "-vic" to mksurfdata.pl to output fields needed for VIC (only have a few resolutions with VIC on by default)
+   Add 2005 high resolution datasets that can be used for the -hirespft option to mksrfdata.pl
+
+Testing:
+--------
+
+ [PASS means all tests PASS and OK means tests PASS other than expected fails.]
+
+  build-namelist tests:
+
+    cheyenne - PASS
+
+  unit-tests (components/clm/src):
+
+    cheyenne - PASS
+    hobart --- PASS
+
+  tools-tests (components/clm/test/tools):
+
+    cheyenne - OK
+    hobart --- OK
+
+  PTCLM testing (components/clm/tools/shared/PTCLM/test):
+
+     cheyenne - OK
+
+  regular tests (aux_clm):
+
+    cheyenne_intel ---- OK
+    cheyenne_gnu ------ OK
+    hobart_nag -------- OK
+    hobart_pgi -------- OK
+    hobart_intel ------ OK
+
+  regular tests (prealpha):
+
+    cheyenne_intel - OK
+    cheyenne_gnu --- OK
+    hobart_nag ----- OK
+
+  regular tests (prebeta):
+
+    cheyenne_intel - OK
+    cheyenne_gnu --- OK
+
+Summary of Answer changes:
+-------------------------
+
+Baseline version for comparison: release-clm5.0.17
+
+Changes answers relative to baseline: No (bit-for-bit)
+
+Detailed list of changes:
+------------------------
+
+Externals being used: Change cime to cime5.6.11 (just a name change)
+
+   cism:   release-cesm2.0.04
+   rtm:    release-cesm2.0.02
+   mosart: release-cesm2.0.03
+   cime:   cime5.6.11
+   FATES:  fates_s1.8.1_a3.0.0
+   PTCLM:  PTCLM2_180611
+
+CTSM Tag versions pulled over from master development branch: None
+
+Pull Requests that document the changes (include PR ids): #619 #620 #634
+(https://github.com/ESCOMP/ctsm/pull)
+
+  #619 -- Begin adding "contrib" tools directory
+  #620 -- Add NoAnthro compset and tests
+  #634 -- Remove some of the fields added to fsurdat files in mksurfdata_map
+
+
+===============================================================
+===============================================================
 Tag name:  release-clm5.0.17
 Originator(s): Keith Oleson, Bill Sacks
 Date: Wed Jan 23 11:03:22 MST 2019

diff --git a/tools/mksurfdata_map/mksurfdata.pl b/tools/mksurfdata_map/mksurfdata.pl
@@ -518,7 +518,7 @@ sub write_namelist_file {
    my @years   = split( ",", $opts{'years'} );
    # Check that resolutions are valid
    foreach my $sim_year ( @years ) {
-     if ("-" eq substr($sim_year, 4, 1)) {
+     if ( ("-" eq substr($sim_year, 4, 1)) || ("-" eq substr($sim_year, 3, 1)) ) {
        # range of years for transient run
        if ( ! $definition->is_valid_value( "sim_year_range", "'$sim_year'" ) ) {
          print "** Invalid simulation simulation year range: $sim_year\n";