Merge tag 'ctsm5.1.dev074' into cn-matrix_v3

 Introducing new option to solve below ground decomposition: MIMICSWieder2015.
 The old option (CENTURYKoven2013) remains available. User will select one or
 the other via the namelist variable soil_decomp_method.

 Elin's MIMICS+ github issue relates: ESCOMP#1260.
 MIMICS spinup issues relate and are listed in caveats for users.

 Conflicts:
	src/biogeochem/CNDriverMod.F90
	src/biogeochem/CNGapMortalityMod.F90
	src/biogeochem/CNVegCarbonFluxType.F90
	src/biogeochem/CNVegNitrogenStateType.F90
	src/main/clm_varpar.F90
	src/soilbiogeochem/SoilBiogeochemCarbonFluxType.F90
	src/soilbiogeochem/SoilBiogeochemCarbonStateType.F90
	src/soilbiogeochem/SoilBiogeochemDecompCascadeBGCMod.F90
	src/soilbiogeochem/SoilBiogeochemDecompMod.F90
	src/soilbiogeochem/SoilBiogeochemNitrogenStateType.F90

bld/CLMBuildNamelist.pm

@@ -90,7 +90,7 @@ OPTIONS
                                 sp    = Satellite Phenology (SP)
                                     This toggles off the namelist variable: use_cn
                                 bgc   = Carbon Nitrogen with methane, nitrification, vertical soil C,
-                                        CENTURY decomposition
+                                        CENTURY or MIMICS decomposition
                                     This toggles on the namelist variables:
                                           use_cn, use_lch4, use_nitrif_denitrif
                                 fates = FATES/Ecosystem Demography with below ground BGC
@@ -856,7 +856,6 @@ sub setup_cmdl_bgc {
      $log->fatal_error("The namelist variable use_fates is inconsistent with the -bgc option");
   }
 
-
   # Now set use_cn and use_fates
   foreach $var ( "use_cn", "use_fates" ) {
      $val = $nl_flags->{$var};
@@ -880,7 +879,7 @@ sub setup_cmdl_bgc {
         $log->fatal_error("$var must NOT be None if use_cn or use_fates are on");
      }
   } elsif ( $soil_decomp_method ne "None" ) {
-     $log->fatal_error("$var must be None if use_cn or use_fates are not");
+     $log->fatal_error("$var must be None if use_cn and use_fates are off");
   }
   #
   # Soil decomposition control variables, methane and Nitrification-Denitrification
@@ -2881,7 +2880,6 @@ sub setup_logic_bgc_shared {
   if ( $nl_flags->{'bgc_mode'} ne "sp" ) {
      add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'constrain_stress_deciduous_onset', 'phys'=>$physv->as_string() );
   }
-  add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'decomp_depth_efolding', 'phys'=>$physv->as_string() );
 }
 
 #-------------------------------------------------------------------------------

bld/namelist_files/namelist_defaults_ctsm.xml

@@ -495,9 +495,9 @@ 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.c210923.nc</paramfile>
-<paramfile phys="clm5_0" >lnd/clm2/paramdata/clm50_params.c210803.nc</paramfile>
-<paramfile phys="clm4_5" >lnd/clm2/paramdata/clm45_params.c210803.nc</paramfile>
+<paramfile phys="clm5_1" >lnd/clm2/paramdata/ctsm51_params.c211112.nc</paramfile>
+<paramfile phys="clm5_0" >lnd/clm2/paramdata/clm50_params.c211112.nc</paramfile>
+<paramfile phys="clm4_5" >lnd/clm2/paramdata/clm45_params.c211112.nc</paramfile>
 
 <!-- ================================================================== -->
 <!-- FATES default parameter file                                       -->
@@ -580,11 +580,6 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
 <onset_thresh_depends_on_veg                                    >.false.</onset_thresh_depends_on_veg>
 <min_critical_dayl_method                                       >Constant</min_critical_dayl_method>
 
-<!-- turnover time modifications    -->
-<decomp_depth_efolding phys="clm4_5" >0.5</decomp_depth_efolding>
-<decomp_depth_efolding phys="clm5_0" >10.0</decomp_depth_efolding>
-<decomp_depth_efolding phys="clm5_1" >10.0</decomp_depth_efolding>
-
 <!-- use additional stress deciduous onset trigger    -->
 <constrain_stress_deciduous_onset phys="clm4_5" >.false.</constrain_stress_deciduous_onset>
 <constrain_stress_deciduous_onset phys="clm5_0" >.true.</constrain_stress_deciduous_onset>
@@ -2579,7 +2574,7 @@ lnd/clm2/surfdata_map/release-clm5.0.30/surfdata_ne0np4.CONUS.ne30x8_hist_78pfts
 >lnd/clm2/paramdata/finundated_inversiondata_0.9x1_ESMFmesh_cdf5_130621.nc</stream_meshfile_ch4finundated>
 
 <!-- =========================================  -->
-<!-- Defaults for different BGC modes           -->
+<!-- Defaults for different BGC/decomp modes    -->
 <!-- =========================================  -->
 
 <soil_decomp_method use_cn=".true."    >CENTURYKoven2013</soil_decomp_method>

bld/namelist_files/namelist_definition_ctsm.xml

@@ -2171,12 +2171,6 @@ Base advective flux (downwards) for SOM.
 Maximum depth to mix soils to by croturbation, in permafrost soils.
 </entry>
 
-<!-- turnover time modifications    -->
-<entry id="decomp_depth_efolding" type="real" category="clm_vertcn"
-       group="bgc_shared" valid_values="" >
-E-folding depth over which decomposition is slowed with depth in all soils.
-</entry>
-
 <entry id="anoxia" type="logical" category="clm_vertcn"
        group="clm_inparm" valid_values="" >
 If TRUE, reduce heterotrophic respiration according to available oxygen predicted by CH4 submodel.
@@ -2213,10 +2207,11 @@ Number of days over which to use exponential relaxation of NPP in N fixation cal
 
 <!-- Soil decomposition options  -->
 <entry id="soil_decomp_method" type="char*20" category="clm_physics"
-       group="soilbgc_decomp" valid_values="None,CENTURYKoven2013" >
+       group="soilbgc_decomp" valid_values="None,CENTURYKoven2013,MIMICSWieder2015" >
 Soil decomposition method
   None --  No soil decomposition is done
   CENTURYKoven2013 -- CENTURY model in CTSM from Koven et. al. 2013
+  MIMICSWieder2015 -- MIMICS model in CTSM from Wieder et. al. 2015
 
 An active soil decomposition method requires the BGC or FATES model to work 
 And both BGC and FATES models require an active soil decomposition model

cime_config/testdefs/testlist_clm.xml

@@ -588,6 +588,33 @@
       <option name="wallclock">00:20:00</option>
     </options>
   </test>
+  <test name="ERP_D_P36x2_Ld3" grid="f10_f10_mg37" compset="I1850Clm51BgcCrop" testmods="clm/mimics">
+    <machines>
+      <machine name="cheyenne" compiler="gnu" category="aux_clm"/>
+    </machines>
+    <options>
+      <option name="wallclock">00:20:00</option>
+      <option name="comment"  >Test soil_decomp_method = 'MIMICSWieder2015'</option>
+    </options>
+  </test>
+  <test name="SMS_Ld5_Mmpi-serial" grid="1x1_brazil" compset="IHistClm50BgcQianRs" testmods="clm/mimics">
+    <machines>
+      <machine name="izumi" compiler="gnu" category="aux_clm"/>
+    </machines>
+    <options>
+      <option name="wallclock">00:20:00</option>
+      <option name="comment"  >Test soil_decomp_method = 'MIMICSWieder2015'</option>
+    </options>
+  </test>
+  <test name="SMS_Ly5_Mmpi-serial" grid="1x1_brazil" compset="IHistClm50BgcQianRs" testmods="clm/newton_krylov_spinup">
+    <machines>
+      <machine name="cheyenne" compiler="intel" category="aux_clm"/>
+    </machines>
+    <options>
+      <option name="wallclock">00:20:00</option>
+      <option name="comment"  >Test soil_decomp_method = 'MIMICSWieder2015'</option>
+    </options>
+  </test>
   <test name="ERP_D_P36x2_Ld3" grid="f10_f10_mg37" compset="I2000Clm50BgcCru" testmods="clm/flexCN_FUN">
     <machines>
       <machine name="cheyenne" compiler="intel" category="aux_clm"/>

cime_config/testdefs/testmods_dirs/clm/ciso_cwd_hr/README

@@ -1,5 +1,5 @@
 This points to an alternate params file with
-rf_cwdl2_bgc = 0.5
+rf_cwdl2     = 0.5
 rf_cwdl3_bgc = 0.5
 while by default these parameters equal zero.
 

cime_config/testdefs/testmods_dirs/clm/ciso_cwd_hr/user_nl_clm

@@ -1,2 +1,2 @@
-paramfile = '/glade/p/cesm/cseg/inputdata/lnd/clm2/paramdata/ctsm51_params.c210827.nc'
+paramfile = '/glade/p/cesm/cseg/inputdata/lnd/clm2/paramdata/ctsm51_ciso_cwd_hr_params.c211112.nc'
 hist_fincl1 = 'CWDC_HR','C13_CWDC_HR','C14_CWDC_HR','CWD_HR_L2','CWD_HR_L2_vr','CWD_HR_L3','CWD_HR_L3_vr'

cime_config/testdefs/testmods_dirs/clm/mimics/README

@@ -0,0 +1,6 @@
+This test mod turns on the MIMICS instead of the CENTURY below-ground
+biogeochemistry.
+
+As of 2021/11/15 this test inherits mods from the ../coldStart directory;
+however the plan is to change that to ../default when we have an acceptable
+spun up finidat file to initialize MIMICS with.

cime_config/testdefs/testmods_dirs/clm/mimics/include_user_mods

@@ -0,0 +1 @@
+../coldStart

cime_config/testdefs/testmods_dirs/clm/mimics/user_nl_clm

@@ -0,0 +1 @@
+soil_decomp_method = 'MIMICSWieder2015'

cime_config/testdefs/testmods_dirs/clm/newton_krylov_spinup/README

@@ -0,0 +1,8 @@
+slevis 2022/2/1:
+This testmod tests the newton_krylov_spinup usermod found in
+cime_config/usermods_dirs/newton_krylov_spinup
+combined with the mimics testmod.
+
+By default this usermod runs for 20 yrs and writes a history file at that
+time. To save time running the test-suite, we're changing
+hist_nhtfrq = 0,-43800 (from 0,-175200)

cime_config/testdefs/testmods_dirs/clm/newton_krylov_spinup/include_user_mods

@@ -0,0 +1,2 @@
+../mimics
+../../../../usermods_dirs/newton_krylov_spinup

cime_config/testdefs/testmods_dirs/clm/newton_krylov_spinup/user_nl_clm

@@ -0,0 +1 @@
+hist_nhtfrq = 0,-43800

cime_config/usermods_dirs/newton_krylov_spinup/README

@@ -0,0 +1,4 @@
+user_nl_clm contains this line:
+hist_nhtfrq = 0,-175200
+0 means monthly history frequency and
+-175200 means 20 years history frequency (indicated in hours)

cime_config/usermods_dirs/newton_krylov_spinup/shell_commands

@@ -0,0 +1,3 @@
+#!/bin/bash
+./xmlchange CLM_FORCE_COLDSTART="on"
+

cime_config/usermods_dirs/newton_krylov_spinup/user_nl_clm

@@ -0,0 +1,15 @@
+hist_dov2xy = .true.,.false.
+hist_nhtfrq = 0,-175200
+hist_mfilt = 1,1
+hist_fincl2 = 'FPI_vr', 'K_PAS_SOM', 'K_SLO_SOM', 'K_ACT_SOM',
+              'K_CWD', 'K_CEL_LIT', 'K_LIG_LIT', 'K_MET_LIT',
+              'CWD_PATHFRAC_L2_vr', 'CWD_RESP_FRAC_L2_vr',
+              'CWD_PATHFRAC_L3_vr', 'CWD_RESP_FRAC_L3_vr',
+              'L1_PATHFRAC_S1_vr', 'L1_RESP_FRAC_S1_vr',
+              'L2_PATHFRAC_S1_vr', 'L2_RESP_FRAC_S1_vr',
+              'L3_PATHFRAC_S2_vr', 'L3_RESP_FRAC_S2_vr',
+              'S1_PATHFRAC_S2_vr', 'S1_RESP_FRAC_S2_vr'
+              'S1_PATHFRAC_S3_vr', 'S1_RESP_FRAC_S3_vr'
+              'S2_PATHFRAC_S1_vr', 'S2_RESP_FRAC_S1_vr'
+              'S2_PATHFRAC_S3_vr', 'S2_RESP_FRAC_S3_vr'
+              'S3_PATHFRAC_S1_vr', 'S3_RESP_FRAC_S1_vr'

doc/ChangeLog

@@ -1,4 +1,118 @@
 ===============================================================
+Tag name: ctsm5.1.dev074
+Originator(s): slevis (Samuel Levis,SLevis Consulting,303-665-1310)
+Date: Wed Feb  2 00:44:27 MST 2022
+One-line Summary: Introduce vert. resolved MIMICS as new method to solve below ground decomp.
+
+Purpose and description of changes
+----------------------------------
+
+ Introducing new option to solve below ground decomposition: MIMICSWieder2015.
+ The old option (CENTURYKoven2013) remains available. User will select one or
+ the other via the namelist variable soil_decomp_method.
+
+ Elin's MIMICS+ github issue relates: #1260.
+ MIMICS spinup issues relate and are listed in caveats for users.
+
+
+Significant changes to scientifically-supported configurations
+--------------------------------------------------------------
+
+Does this tag change answers significantly for any of the following physics configurations?
+(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
+------------------------
+Issues fixed (include CTSM Issue #):
+ #1473 : decomp_depth_efolding appears (with the same value) in the namelist
+         and the params files; the model ends up using the one from the namelist
+
+
+Notes of particular relevance for users
+---------------------------------------
+Caveats for users (e.g., need to interpolate initial conditions):
+ MIMICS spinup method is in development
+ Issues related to spinup
+ #1451 -- MIMICS spinup
+ #1455 -- Additional history output for Newton-Krylov spinup
+ #1457 -- Adding history variables for Newton-Krylov spinup
+
+Changes to CTSM's user interface (e.g., new/renamed XML or namelist variables):
+ New option MIMICSWieder2015 for use with namelist variable soil_decomp_method
+ decomp_depth_efolding removed as values on param files was already being used
+
+Changes to the datasets (e.g., parameter, surface or initial files):
+ CLM parameter files now include new MIMICS-related parameters prefixed with
+ mimics_. Existing CENTURYKoven-specific parameters were renamed to include the
+ prefix bgc_. Parameters used by both CENTURYKoven2013 and MIMICSWieder2015 have
+ neither prefix.
+
+Substantial timing or memory changes:
+ Timing comparison between CENTURYKoven (BGC for short) and MIMICSWieder:
+ In a 1x1_brazil test writing annual output and restarts every 10 yrs,
+ BGC took ~2.8 hrs/100 yrs, MIMICS took ~3.6 hrs/100 yrs.
+
+ More timing comparisons shown here:
+ https://github.com/ESCOMP/CTSM/pull/1318#issuecomment-1008211485
+
+Notes of particular relevance for developers:
+---------------------------------------------
+Changes to tests or testing:
+ New test-suite tests:
+ ERP_D_P36x2_Ld3.f10_f10_mg37.I1850Clm51BgcCrop.cheyenne_gnu.clm-mimics
+ SMS_Ld5_Mmpi-serial.1x1_brazil.IHistClm50BgcQianRs.izumi_gnu.clm-mimics
+ SMS_Ly5_Mmpi-serial.1x1_brazil.IHistClm50BgcQianRs.cheyenne_intel.clm-newton_krylov_spinup
+
+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 (831 tests are different from baseline because of new param files)
+
+   python testing (if python code has changed; see instructions in python/README.md; document testing done):
+
+    cheyenne ---- OK (black test fails)
+
+  regular tests (aux_clm: https://github.com/ESCOMP/CTSM/wiki/System-Testing-Guide#pre-merge-system-testing):
+
+    cheyenne ---- PASS
+    izumi ------- OK (see one answer change below)
+
+
+Answer changes
+--------------
+
+Changes answers relative to baseline: NO (almost)
+
+ One test in the izumi test-suite fails
+ SMS_Vmct.f10_f10_mg37.I2000Clm50BgcCrop.izumi_pgi.clm-crop
+ and this is due to diffs from baseline (dev073).
+ cprnc.out shows diffs only in one variable:
+ RMS TOTECOSYSC 1.9853E-12 NORMALIZED 6.5087E-17
+
+
+Other details
+-------------
+
+Pull Requests that document the changes (include PR ids):
+ https://github.com/ESCOMP/ctsm/pull/1318 -- MIMICS into vertically resolved CTSM
+
+===============================================================
+===============================================================
 Tag name: ctsm5.1.dev073
 Originator(s): sacks (Bill Sacks)
 Date: Tue Jan 25 16:33:06 MST 2022

doc/ChangeSum

@@ -1,5 +1,6 @@
 Tag                   Who      Date  Summary
 ============================================================================================================================
+    ctsm5.1.dev074   slevis 02/02/2022 Introduce vert. resolved MIMICS as new method to solve below ground decomp.
     ctsm5.1.dev073    sacks 01/25/2022 Some fixes for Gregorian calendar
     ctsm5.1.dev072   negins 01/17/2022 mksurfdat toolchain part 1: gen_mksurf_namelist
     ctsm5.1.dev071 glemieux 01/16/2022 Small changes to enable new fates dimension and update fates tag