Merge pull request #1340 from slevisconsulting/premimics_refactor

MIMICS-related refactor before introducing MIMICS
ESCOMP · Jun 3, 2021 · 1e3cc27 · 1e3cc27
2 parents 448fa92 + a1186e3
commit 1e3cc27
Show file tree

Hide file tree

Showing 30 changed files with 1,044 additions and 1,327 deletions.
diff --git a/bld/CLMBuildNamelist.pm b/bld/CLMBuildNamelist.pm
@@ -1645,11 +1645,6 @@ sub process_namelist_inline_logic {
   #############################################
   setup_logic_friction_vel($opts,  $nl_flags, $definition, $defaults, $nl);
 
-  ################################################
-  # namelist group: century_soilbgcdecompcascade #
-  ################################################
-  setup_logic_century_soilbgcdecompcascade($opts,  $nl_flags, $definition, $defaults, $nl);
-
   #############################
   # namelist group: cngeneral #
   #############################
@@ -3621,23 +3616,6 @@ sub setup_logic_soilwater_movement {
 }
 #-------------------------------------------------------------------------------
 
-sub setup_logic_century_soilbgcdecompcascade {
-  #
-  my ($opts, $nl_flags, $definition, $defaults, $nl) = @_;
-
-  if ( (&value_is_true($nl->get_value('use_cn')) || &value_is_true($nl->get_value('use_fates'))) &&
-       &value_is_true($nl->get_value('use_century_decomp')) ) {
-    add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'initial_Cstocks',
-                'use_cn' => $nl->get_value('use_cn'), 'use_fates' => $nl->get_value('use_fates'),
-                'use_century_decomp' => $nl->get_value('use_century_decomp') );
-    add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'initial_Cstocks_depth', 
-                'use_cn' => $nl->get_value('use_cn'), 'use_fates' => $nl->get_value('use_fates'),
-                'use_century_decomp' => $nl->get_value('use_century_decomp') ); 
-  }
-}
-
-#-------------------------------------------------------------------------------
-
 sub setup_logic_cnvegcarbonstate {
   #  MUST be AFTER: setup_logic_dynamic_plant_nitrogen_alloc as depends on mm_nuptake_opt which is set there
   my ($opts, $nl_flags, $definition, $defaults, $nl) = @_;

diff --git a/bld/namelist_files/namelist_defaults_ctsm.xml b/bld/namelist_files/namelist_defaults_ctsm.xml
@@ -483,9 +483,9 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
 <!-- The default filenames are given relative to the root directory
      for the CLM2 data in the CESM distribution -->
 <!-- Plant function types (relative to {csmdata}) -->
-<paramfile phys="clm5_1" >lnd/clm2/paramdata/ctsm51_params.c210305.nc</paramfile>
-<paramfile phys="clm5_0" >lnd/clm2/paramdata/clm50_params.c210217.nc</paramfile>
-<paramfile phys="clm4_5" >lnd/clm2/paramdata/clm45_params.c210217.nc</paramfile>
+<paramfile phys="clm5_1" >lnd/clm2/paramdata/ctsm51_params.c210528.nc</paramfile>
+<paramfile phys="clm5_0" >lnd/clm2/paramdata/clm50_params.c210528.nc</paramfile>
+<paramfile phys="clm4_5" >lnd/clm2/paramdata/clm45_params.c210528.nc</paramfile>
 
 <!-- ================================================================== -->
 <!-- FATES default parameter file                                       -->
@@ -1422,20 +1422,6 @@ lnd/clm2/surfdata_map/release-clm5.0.30/surfdata_ne0np4.CONUS.ne30x8_hist_78pfts
 <leaf_mr_vcm phys="clm5_0" >0.015d00</leaf_mr_vcm>
 <leaf_mr_vcm phys="clm4_5" >0.015d00</leaf_mr_vcm>
 
-<!-- Initial Carbon stocks for BGC -->
-<initial_Cstocks phys="clm4_5"  use_cn=".true."  use_fates=".false." use_century_decomp=".true." >20.0d00, 20.0d00, 20.0d00</initial_Cstocks>
-<initial_Cstocks phys="clm5_0"  use_cn=".true."  use_fates=".false." use_century_decomp=".true." >200.0d00, 200.0d00, 200.0d00</initial_Cstocks>
-<initial_Cstocks phys="clm5_1"  use_cn=".true."  use_fates=".false." use_century_decomp=".true." >200.0d00, 200.0d00, 200.0d00</initial_Cstocks>
-<initial_Cstocks phys="clm4_5"  use_cn=".false." use_fates=".true."  use_century_decomp=".true." >20.0d00, 20.0d00, 20.0d00</initial_Cstocks>
-<initial_Cstocks phys="clm5_0"  use_cn=".false." use_fates=".true."  use_century_decomp=".true." >200.0d00, 200.0d00, 200.0d00</initial_Cstocks>
-<initial_Cstocks phys="clm5_1"  use_cn=".false." use_fates=".true."  use_century_decomp=".true." >200.0d00, 200.0d00, 200.0d00</initial_Cstocks>
-
-<initial_Cstocks_depth phys="clm5_1"  use_cn=".true."   use_fates=".false." use_century_decomp=".true." >1.50d00</initial_Cstocks_depth>
-<initial_Cstocks_depth phys="clm5_0"  use_cn=".true."   use_fates=".false." use_century_decomp=".true." >1.50d00</initial_Cstocks_depth>
-<initial_Cstocks_depth phys="clm4_5"  use_cn=".true."   use_fates=".false." use_century_decomp=".true." >0.3</initial_Cstocks_depth>
-<initial_Cstocks_depth phys="clm5_1"  use_cn=".false."  use_fates=".true."  use_century_decomp=".true." >1.50d00</initial_Cstocks_depth>
-<initial_Cstocks_depth phys="clm5_0"  use_cn=".false."  use_fates=".true."  use_century_decomp=".true." >1.50d00</initial_Cstocks_depth>
-<initial_Cstocks_depth phys="clm4_5"  use_cn=".false."  use_fates=".true."  use_century_decomp=".true." >0.3</initial_Cstocks_depth>
 
 <initial_vegC phys="clm5_1"  use_cn=".true."  mm_nuptake_opt=".true." >100.d00</initial_vegC>
 <initial_vegC phys="clm5_0"  use_cn=".true."  mm_nuptake_opt=".true." >100.d00</initial_vegC>

diff --git a/bld/namelist_files/namelist_definition_ctsm.xml b/bld/namelist_files/namelist_definition_ctsm.xml
@@ -306,16 +306,6 @@ Critical threshold of negative Nitrogen to die (abort when Nitrogen states are b
 Critical threshold of negative Carbon to die (abort when Carbon states are below this value)
 </entry>
 
-<entry id="initial_Cstocks" type="real(3)" category="clm_physics"
-       group="century_soilbgcdecompcascade" >
-Initial stocks of Carbon to use in soil organic matter pools for CENTURY decomposition
-</entry>
-
-<entry id="initial_Cstocks_depth" type="real(3)" category="clm_physics"
-       group="century_soilbgcdecompcascade" >
-Soil depth to place initial stocks of Carbon in soil organic matter pools for CENTURY decomposition
-</entry>
-
 <entry id="freelivfix_slope_wET" type="real" category="clm_physics"
        group="mineral_nitrogen_dynamics" >
 Slope of free living Nitrogen fixation with annual ET

diff --git a/cime_config/testdefs/ExpectedTestFails.xml b/cime_config/testdefs/ExpectedTestFails.xml
@@ -79,6 +79,48 @@
     </phase>
   </test>
 
+  <test name="ERP_D_Ld9.f19_g17.I2000Clm50Cn.cheyenne_intel.clm-drydepnomegan"
+    <phase name="RUN">
+      <status>FAIL</status>
+      <issue>#1356</issue>
+    </phase>
+  </test>
+
+  <test name="ERP_P36x2_D_Ld5.f10_f10_mg37.I1850Clm45Cn.cheyenne_intel.clm-default">
+    <phase name="RUN">
+      <status>FAIL</status>
+      <issue>#1356</issue>
+    </phase>
+  </test>
+
+  <test name="ERP_P36x2_D_Ld5.f10_f10_mg37.I2000Clm50Cn.cheyenne_gnu.clm-default">
+    <phase name="RUN">
+      <status>FAIL</status>
+      <issue>#1356</issue>
+    </phase>
+  </test>
+
+  <test name="ERP_P36x2_D_Ld5.f10_f10_mg37.I2000Clm50Cn.cheyenne_intel.clm-default"
+    <phase name="RUN">
+      <status>FAIL</status>
+      <issue>#1356</issue>
+    </phase>
+  </test>
+
+  <test name="SMS.f19_g17.I2000Clm50Cn.cheyenne_intel.clm-default">
+    <phase name="RUN">
+      <status>FAIL</status>
+      <issue>#1356</issue>
+    </phase>
+  </test>
+
+  <test name="SMS_D_Ld1.f19_g17.I1850Clm45Cn.izumi_gnu.clm-default">
+    <phase name="RUN">
+      <status>FAIL</status>
+      <issue>#1356</issue>
+    </phase>
+  </test>
+
   <!-- fates test suite failures -->
 
   <test name="ERS_Ld60.f45_f45_mg37.I2000Clm45Fates.hobart_nag.clm-Fates">

diff --git a/doc/ChangeLog b/doc/ChangeLog
@@ -1,4 +1,111 @@
 ===============================================================
+Tag name:  ctsm5.1.dev043
+Originator(s):  slevis/ekluzek (Samuel Levis,SLevis Consulting,303-665-1310)
+Date: Thu Jun  3 17:14:30 MDT 2021
+One-line Summary: Refactor in preparation for MIMICS
+
+Purpose and description of changes
+----------------------------------
+
+ Refactor aspects of the CTSM in preparation for our introduction of
+ MIMICS, which has started in #1318 .
+
+
+Significant changes to scientifically-supported configurations
+--------------------------------------------------------------
+
+Does this tag change answers significantly for any of the following physics configurations? NO
+(Details of any changes will be given in the "Answer changes" section below.)
+
+    [Put an [X] in the box for any configuration with significant answer changes.]
+
+[ ] clm5_1
+
+[ ] clm5_0
+
+[ ] ctsm5_0-nwp
+
+[ ] clm4_5
+
+
+Bugs fixed or introduced
+------------------------
+Known bugs introduced in this tag (include issue #): #1356, #1392
+   #1356 -- CN is no longer just deprecated it breaks when you try to use it
+   #1392 -- Some soil decomposition history fields have the pool number rather than a descr.
+
+Notes of particular relevance for users
+---------------------------------------
+Changes to CTSM's user interface (e.g., new/renamed XML or namelist variables):
+ Moved initial_Cstocks_depth_bgc and initial_Cstocks_bgc from the
+ namelist to the params file. Also renamed tau_cwd to tau_cwd_bgc and
+ k_frag to k_frag_cn in the params file according to the models that use
+ these parameters.
+
+Changes made to namelist defaults (e.g., changed parameter values):
+ initial_Cstocks_depth_bgc and initial_Cstocks_bgc are not namelist
+ variables anymore.
+
+Changes to the datasets (e.g., parameter, surface or initial files):
+ There are new params files for clm45, clm50, and ctsm51.
+
+Substantial timing or memory changes:
+ FAIL PFS_Ld20.f09_g17.I2000Clm50BgcCrop.cheyenne_intel MEMCOMP Error: Memory usage increase > 10% from baseline
+  Throughput doesn't seem to change. There might be an increase in memory as it's indicated for 20 tests.
+  And some arrays were changed to add an extra dimension.
+
+Testing summary:
+----------------
+
+ [PASS means all tests PASS; OK means tests PASS other than expected fails.]
+
+  build-namelist tests (if CLMBuildNamelist.pm has changed):
+
+    cheyenne - PASS (785 tests are different because of new params files and removed namelist items)
+
+  python testing (if python code has changed; see instructions in python/README.md; document testing done):
+
+    cheyenne - PASS
+
+  regular tests (aux_clm: https://github.com/ESCOMP/CTSM/wiki/System-Testing-Guide#pre-merge-system-testing):
+
+    cheyenne ---- OK (read above in "bugs introduced" about CN failures)
+    izumi ------- OK (read below in "other testing" about pgi failures)
+
+  any other testing (give details below):
+ Two unexpected tests fail on izumi, so I performed additional testing.
+ The tests that fail:
+ 1) SMS_D.f10_f10_mg37.I2000Clm51BgcCrop.izumi_pgi.clm-crop
+ BASELINE ctsm5.1.dev042: DIFF roundoff
+ 2) SMS.f10_f10_mg37.I2000Clm50BgcCrop.izumi_pgi.clm-crop
+ BASELINE ctsm5.1.dev042: DIFF greater than roundoff for CH4-related vars
+ I confirmed same result with my earlier commit against BASELINE dev033.
+
+ Same tests but with gnu/intel instead of pgi pass on izumi for both
+ comparisons to dev042 and to dev033. These tests are part of the izumi
+ test-suite already.
+
+ Additional testing:
+ Repeated these gnu/intel tests (had to run for baseline first) on cheyenne
+ and they passed.
+
+If the tag used for baseline comparisons was NOT the previous tag, note that here:
+
+
+Answer changes
+--------------
+
+Changes answers relative to baseline: NO
+
+
+Other details
+-------------
+
+Pull Requests that document the changes (include PR ids):
+ https://github.com/ESCOMP/CTSM/pull/1340
+
+===============================================================
+===============================================================
 Tag name:  ctsm5.1.dev042
 Originator(s):  erik (Erik Kluzek,UCAR/TSS,303-497-1326)
 Date: Fri May 28 14:07:45 MDT 2021

diff --git a/doc/ChangeSum b/doc/ChangeSum
@@ -1,5 +1,6 @@
 Tag                   Who      Date  Summary
 ============================================================================================================================
+    ctsm5.1.dev043   slevis 06/03/2021 Refactor of CascadeBGC code in preparation for MIMICS
     ctsm5.1.dev042     erik 05/28/2021 Small answer changes for double precision constants and soil limits
     ctsm5.1.dev041   rgknox 05/27/2021 bring FATES API up to sci.1.46.0_api.16.0.0 (methane and cn hooks)
     ctsm5.1.dev040   slevis 05/20/2021 mksurfdata_map: replace SRC files of various masks with SRC files w no mask

diff --git a/src/biogeochem/CNC14DecayMod.F90 b/src/biogeochem/CNC14DecayMod.F90
@@ -6,7 +6,7 @@ module CNC14DecayMod
   ! !USES:
   use shr_kind_mod                       , only : r8 => shr_kind_r8
   use clm_time_manager                   , only : get_step_size_real, get_days_per_year
-  use clm_varpar                         , only : ndecomp_cascade_transitions, nlevdecomp, ndecomp_pools
+  use clm_varpar                         , only : nlevdecomp, ndecomp_pools
   use clm_varcon                         , only : secspday
   use clm_varctl                         , only : spinup_state
   use decompMod                          , only : bounds_type