Merge branch 'bioenergy_ctsm1.0.dev080'

Add two bioenergy crops (switchgrass and miscanthus) Main change is from Yanyan Cheng: adding parameters and code for two bioenergy crops, switchgrass and miscanthus. Along with this, there is a new potential flux from crop leaves and stems to the crop product pool at harvest, representing biofuel products; a new pft-specific parameter controls this flux (biofuel_harvfrac). Currently, the out-of-the-box surface datasets do not specify any area for these crops, but the new parameter file will allow them to be present if specified on the surface dataset or landuse_timeseries file. Note that this is only an option for CLM5.0, NOT for CLM4.5. (See #884 for details.) Also, some minor fixes from Bill Sacks: - Resolves #203 - Fixes creation of harvest-related variables on surface datasets created with the all_veg option - smallville, PTCLM, etc. (documented in #1019) - Resolves #930 - Makes gindex_ocn intent(inout) rather than intent(out) - Resolves #1021 - Changes SSP test to only do symlink if needed
ESCOMP · May 25, 2020 · 6ec6e0a · 6ec6e0a
2 parents e39e9f3 + 0e3aa2b
commit 6ec6e0a
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diff --git a/bld/namelist_files/namelist_defaults_ctsm.xml b/bld/namelist_files/namelist_defaults_ctsm.xml
@@ -393,8 +393,8 @@ 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_0">lnd/clm2/paramdata/clm5_params.c200402.nc</paramfile>
-<paramfile phys="clm4_5">lnd/clm2/paramdata/clm_params.c200402.nc</paramfile>
+<paramfile phys="clm5_0">lnd/clm2/paramdata/clm5_params.c200519.nc</paramfile>
+<paramfile phys="clm4_5">lnd/clm2/paramdata/clm_params.c200519.nc</paramfile>
 
 <!-- ================================================================== -->
 <!-- FATES default parameter file                                       -->
@@ -781,7 +781,7 @@ lnd/clm2/surfdata_map/release-clm5.0.18/surfdata_4x5_hist_78pfts_CMIP6_simyr2000
 <fsurdat hgrid="1x1_numaIA"       sim_year="2000" use_crop=".true." >
 lnd/clm2/surfdata_map/release-clm5.0.18/surfdata_1x1_numaIA_hist_78pfts_CMIP6_simyr2000_c190214.nc</fsurdat>
 <fsurdat hgrid="1x1_smallvilleIA" sim_year="2000" use_crop=".true." >
-lnd/clm2/surfdata_map/release-clm5.0.18/surfdata_1x1_smallvilleIA_hist_78pfts_CMIP6_simyr2000_c190214.nc</fsurdat>
+lnd/clm2/surfdata_map/ctsm1.0.dev094-2-g633be0eb/surfdata_1x1_smallvilleIA_hist_78pfts_CMIP6_simyr2000_c200521.nc</fsurdat>
 
 <fsurdat hgrid="ne30np4"     sim_year="2000" use_crop=".true.">
 lnd/clm2/surfdata_map/release-clm5.0.18/surfdata_ne30np4_hist_78pfts_CMIP6_simyr2000_c190303.nc</fsurdat>

diff --git a/cime_config/SystemTests/ssp.py b/cime_config/SystemTests/ssp.py
@@ -83,7 +83,14 @@ def run_phase(self):
         rest_path = os.path.join(dout_sr, "rest", "{}-{}".format(refdate, refsec))
 
         for item in glob.glob("{}/*{}*".format(rest_path, refdate)):
-            os.symlink(item, os.path.join(rundir, os.path.basename(item)))
+            link_name = os.path.join(rundir, os.path.basename(item))
+            if os.path.islink(link_name) and os.readlink(link_name) == item:
+                # Link is already set up correctly: do nothing
+                # (os.symlink raises an exception if you try to replace an
+                # existing file)
+                pass
+            else:
+                os.symlink(item, link_name)
 
         for item in glob.glob("{}/*rpointer*".format(rest_path)):
             shutil.copy(item, rundir)

diff --git a/cime_config/testdefs/ExpectedTestFails.xml b/cime_config/testdefs/ExpectedTestFails.xml
@@ -33,7 +33,7 @@
   <test name="ERS_Lm20_Mmpi-serial.1x1_smallvilleIA.I2000Clm50BgcCropQianGs.cheyenne_gnu.clm-monthly">
     <phase name="RUN">
       <status>FAIL</status>
-      <issue>#158</issue>
+      <issue>#203</issue>
     </phase>
   </test>
 

diff --git a/cime_config/testdefs/testlist_clm.xml b/cime_config/testdefs/testlist_clm.xml
@@ -348,7 +348,7 @@
       <option name="wallclock">00:20:00</option>
     </options>
   </test>
-  <test name="ERP_D_P36x2_Ld3" grid="f10_f10_musgs" compset="I2000Clm50BgcCrop" testmods="clm/cropColdStart">
+  <test name="ERP_D_P36x2_Ld3" grid="f10_f10_musgs" compset="I2000Clm50BgcCrop" testmods="clm/coldStart">
     <machines>
       <machine name="cheyenne" compiler="intel" category="aux_clm"/>
     </machines>
@@ -905,13 +905,22 @@
       <option name="wallclock">00:20:00</option>
     </options>
   </test>
-  <test name="ERS_Lm20_Mmpi-serial" grid="1x1_smallvilleIA" compset="I2000Clm50BgcCropQianGs" testmods="clm/monthly">
+  <test name="ERS_Lm20_Mmpi-serial" grid="1x1_smallvilleIA" compset="I2000Clm50BgcCropQianGs" testmods="clm/monthly_noinitial">
     <machines>
       <machine name="cheyenne" compiler="gnu" category="aux_clm"/>
     </machines>
     <options>
       <option name="wallclock">01:20:00</option>
-      <option name="comment"  >tests mid-year restart, with the restart file being written in the middle of the first year; 12-15-2017: now that we generally use init_interp, this test needs to be changed to point to a blank finidat file to truly test mid-year restart in the first year; 4-19-2019: should change this to use Qian forcing to speed it up (but I'm waiting to make this change until this test starts passing again)</option>
+      <option name="comment"  >tests mid-year restart, with the restart file being written in the middle of the first year after cold start initialization</option>
+    </options>
+  </test>
+  <test name="ERS_Ly5_Mmpi-serial" grid="1x1_smallvilleIA" compset="I2000Clm50BgcCropQianGs" testmods="clm/ciso_monthly">
+    <machines>
+      <machine name="cheyenne" compiler="gnu" category="aux_clm"/>
+    </machines>
+    <options>
+      <option name="wallclock">02:00:00</option>
+      <option name="comment"  >multi-year test with crops and isotopes that includes all crop types; added (2020-05-21) in order to test the new switchgrass and miscanthus crops (which otherwise aren't currently tested)</option>
     </options>
   </test>
   <test name="ERS_Lm40_Mmpi-serial" grid="1x1_numaIA" compset="I2000Clm50BgcCropQianGs" testmods="clm/monthly">

diff --git a/cime_config/testdefs/testmods_dirs/clm/cropColdStart/include_user_mods b/cime_config/testdefs/testmods_dirs/clm/cropColdStart/include_user_mods
diff --git a/cime_config/testdefs/testmods_dirs/clm/cropColdStart/shell_commands b/cime_config/testdefs/testmods_dirs/clm/cropColdStart/shell_commands
diff --git a/doc/ChangeLog b/doc/ChangeLog
@@ -1,4 +1,193 @@
 ===============================================================
+Tag name:  ctsm1.0.dev097
+Originator(s): ycheng (Yanyan Cheng)
+Date:  Mon May 25 15:14:56 MDT 2020
+One-line Summary: Add two bioenergy crops (switchgrass and miscanthus)
+
+Purpose of changes
+------------------
+
+Main change is from Yanyan Cheng: adding parameters and code for two
+bioenergy crops, switchgrass and miscanthus. Along with this, there is a
+new potential flux from crop leaves and stems to the crop product pool
+at harvest, representing biofuel products; a new pft-specific parameter
+controls this flux (biofuel_harvfrac). Currently, the out-of-the-box
+surface datasets do not specify any area for these crops, but the new
+parameter file will allow them to be present if specified on the surface
+dataset or landuse_timeseries file. Note that this is only an option for
+CLM5.0, NOT for CLM4.5. (See https://github.com/ESCOMP/CTSM/pull/884 for
+details.)
+
+Also, some minor fixes from Bill Sacks: See notes under "bugs fixed"
+below.
+
+Bugs fixed or introduced
+------------------------
+
+Issues fixed (include CTSM Issue #):
+- Resolves ESCOMP/CTSM#203 - Fixes creation of harvest-related variables
+  on surface datasets created with the all_veg option - smallville,
+  PTCLM, etc. (documented in https://github.com/ESCOMP/CTSM/pull/1019)
+- Resolves ESCOMP/CTSM#930 - Makes gindex_ocn intent(inout) rather than
+  intent(out)
+- Resolves ESCOMP/CTSM#1021 - Changes SSP test to only do symlink if
+  needed
+
+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_0
+
+[ ] ctsm5_0-nwp
+
+[ ] clm4_5
+
+Notes of particular relevance for users
+---------------------------------------
+
+Caveats for users (e.g., need to interpolate initial conditions):
+- For transient crop cases, now more crops in memory. This creates a
+  need for interpolation of initial conditions for initial conditions
+  generated from a transient case.
+
+Changes to CTSM's user interface (e.g., new/renamed XML or namelist variables): none
+
+Changes made to namelist defaults (e.g., changed parameter values):
+- Changed parameter values for switchgrass and miscanthus (only for clm5.0)
+- New pft-specific parameter, biofuel_harvfrac (for both clm4.5 and clm5.0)
+
+Changes to the datasets (e.g., parameter, surface or initial files):
+- New parameter files with the above changes
+
+Substantial timing or memory changes: none
+
+Notes of particular relevance for developers: (including Code reviews and testing)
+---------------------------------------------
+NOTE: Be sure to review the steps in README.CHECKLIST.master_tags as well as the coding style in the Developers Guide
+
+Caveats for developers (e.g., code that is duplicated that requires double maintenance): none
+
+Changes to tests or testing:
+- Changed smallville ERS_Lm20 test to be cold start (see comment in
+  commit 8368f222 for details)
+- Added a multi-year smallville test that includes these new crops
+
+Code reviewed by: Bill Sacks, Danica Lombardozzi
+
+
+CTSM testing:
+
+ [PASS means all tests PASS and OK means tests PASS other than expected fails.]
+
+  build-namelist tests:
+
+    cheyenne - not run
+
+  tools-tests (test/tools):
+
+    cheyenne - ok
+
+    Pass except for expected baseline failures
+
+    Ran on 633be0eb, with comparison against ctsm1.0.dev095; tests pass
+    except these expected baseline failures:
+
+        030 blf84 TBLscript_tools.sh PTCLM PTCLMmkdata PTCLM_USUMB_clm4_5^buildtools ....................\c
+         rc=7 FAIL
+
+        032 blfc4 TBLscript_tools.sh PTCLM PTCLMmkdata PTCLM_USUMB_Cycle_clm4_5^buildtools ..............\c
+         rc=7 FAIL
+
+        Diffs for these are just in the harvest-related fields on the surface dataset, as expected.
+
+  PTCLM testing (tools/shared/PTCLM/test):
+
+    cheyenne - not run
+
+  python testing (see instructions in python/README.md; document testing done):
+
+    (any machine) - not run
+
+  regular tests (aux_clm):
+
+    cheyenne ---- ok
+    izumi ------- pass
+
+    For cheyenne testing: a few tests had baseline failures. The
+    differences just arise in the h1 (vector) files, due to differences
+    in dimension sizes. These differences are expected. See below for
+    details.
+
+    Ran most testing on 8309c213. Reran two SSP tests on 4665c9ce
+
+If the tag used for baseline comparisons was NOT the previous tag, note that here:
+
+
+Answer changes
+--------------
+
+Changes answers relative to baseline: YES, but diagnostic only due to
+change in dimension sizes - does not change answers in any meaningful
+way
+
+  If a tag changes answers relative to baseline comparison the
+  following should be filled in (otherwise remove this section):
+
+  Summarize any changes to answers, i.e.,
+    - what code configurations: Transient CLM50 cases with crops; just
+      changes dimensions on vector (h1) history files
+    - what platforms/compilers: All
+    - nature of change (roundoff; larger than roundoff/same climate; new climate): 
+      diagnostic change only
+
+      Differences were observed in the following tests:
+
+          ERS_Ly3_Mmpi-serial.1x1_smallvilleIA.IHistClm50BgcCropQianGs.cheyenne_gnu.clm-cropMonthOutput
+          SMS_Ld5.f10_f10_musgs.ISSP245Clm50BgcCrop.cheyenne_gnu.clm-ciso_dec2050Start
+          SMS_Ld5.f10_f10_musgs.ISSP370Clm50BgcCrop.cheyenne_gnu.clm-ciso_dec2050Start
+          ERP_D_Ld10_P36x2.f10_f10_musgs.IHistClm50BgcCrop.cheyenne_intel.clm-ciso_decStart
+          ERP_D_Ld5.f10_f10_musgs.IHistClm50BgcCrop.cheyenne_intel.clm-allActive
+          ERP_Ly3_P72x2.f10_f10_musgs.IHistClm50BgcCrop.cheyenne_intel.clm-cropMonthOutput
+          ERS_D_Ld7_Mmpi-serial.1x1_smallvilleIA.IHistClm50BgcCropGs.cheyenne_intel.clm-decStart1851_noinitial
+          ERS_Ly3_P72x2.f10_f10_musgs.IHistClm50BgcCropG.cheyenne_intel.clm-cropMonthOutput
+          ERS_Ly5_P144x1.f10_f10_musgs.IHistClm50BgcCrop.cheyenne_intel.clm-cropMonthOutput
+          ERS_Ly6_Mmpi-serial.1x1_smallvilleIA.IHistClm50BgcCropQianGs.cheyenne_intel.clm-cropMonthOutput
+          LCISO_Lm13.f10_f10_musgs.IHistClm50BgcCrop.cheyenne_intel.clm-ciso_monthly
+          SMS_Ld5.f10_f10_musgs.ISSP585Clm50BgcCrop.cheyenne_intel.clm-ciso_dec2050Start
+
+      The differences just arise in the h1 files, due to differences in
+      dimension sizes. I reran these tests with a paramfile where I
+      reverted the mergeToPft variable; then they were all bfb with
+      master.
+
+      Other than this, there were FIELDLIST differences, as expected.
+
+   If bitwise differences were observed, how did you show they were no worse
+   than roundoff? N/A
+
+   If this tag changes climate describe the run(s) done to evaluate the new
+   climate (put details of the simulations in the experiment database)
+       - casename: N/A
+
+   URL for LMWG diagnostics output used to validate new climate: N/A
+
+
+Detailed list of changes
+------------------------
+
+List any externals directories updated (cime, rtm, mosart, cism, fates, etc.): none
+
+Pull Requests that document the changes (include PR ids):
+- https://github.com/ESCOMP/CTSM/pull/884
+- https://github.com/ESCOMP/CTSM/pull/1019
+
+===============================================================
+===============================================================
 Tag name:  ctsm1.0.dev096
 Originator(s):  slevis (Samuel Levis,SLevis Consulting LLC,303-665-1310)
 Date:  Thu May 21 19:18:24 MDT 2020

diff --git a/doc/ChangeSum b/doc/ChangeSum
@@ -1,5 +1,6 @@
 Tag                   Who      Date  Summary
 ============================================================================================================================
+  ctsm1.0.dev097   ycheng 05/25/2020 Add two bioenergy crops (switchgrass and miscanthus)
   ctsm1.0.dev096   slevis 05/21/2020 Gridcell-level balance checks for carbon and nitrogen
   ctsm1.0.dev095    sacks 05/21/2020 Update cime and cmeps externals; rework initialization of CNFire object
   ctsm1.0.dev094    sacks 05/15/2020 Minor bug fixes needed for latest cime

diff --git a/doc/source/tech_note/CN_Allocation/CLM50_Tech_Note_CN_Allocation.rst b/doc/source/tech_note/CN_Allocation/CLM50_Tech_Note_CN_Allocation.rst
@@ -186,7 +186,15 @@ favorable growth environments (Allen et al., 2005; Vanninen and Makela,
  +----------------------------------+-----------------------+-----------------------+-----------------------+-----------------------+---------------------------+-------------------------+-------------------------+-------------------------+
  | Soybean I                        | 2                     | 0                     | 0                     | 1                     | 25                        | 42                      | 50                      | 500                     |
  +----------------------------------+-----------------------+-----------------------+-----------------------+-----------------------+---------------------------+-------------------------+-------------------------+-------------------------+
-
+ | Miscanthus R                     | 2                     | 0                     | 0                     | 1                     | 25                        | 42                      | 50                      | 500                     |
+ +----------------------------------+-----------------------+-----------------------+-----------------------+-----------------------+---------------------------+-------------------------+-------------------------+-------------------------+
+ | Miscanthus I                     | 2                     | 0                     | 0                     | 1                     | 25                        | 42                      | 50                      | 500                     |
+ +----------------------------------+-----------------------+-----------------------+-----------------------+-----------------------+---------------------------+-------------------------+-------------------------+-------------------------+
+ | Switchgrass R                    | 2                     | 0                     | 0                     | 1                     | 25                        | 42                      | 50                      | 500                     |
+ +----------------------------------+-----------------------+-----------------------+-----------------------+-----------------------+---------------------------+-------------------------+-------------------------+-------------------------+
+ | Switchgrass I                    | 2                     | 0                     | 0                     | 1                     | 25                        | 42                      | 50                      | 500                     |
+ +----------------------------------+-----------------------+-----------------------+-----------------------+-----------------------+---------------------------+-------------------------+-------------------------+-------------------------+
+
 Carbon to nitrogen ratios are defined for different tissue types as
 follows:
 

diff --git a/doc/source/tech_note/CN_Pools/CLM50_Tech_Note_CN_Pools.rst b/doc/source/tech_note/CN_Pools/CLM50_Tech_Note_CN_Pools.rst
@@ -116,5 +116,8 @@ stoichiometry are described in Chapter :numref:`rst_CN Allocation`.
  +----------------------------------+-------------------+
  | Tropical Soybean                 |        20.00      |
  +----------------------------------+-------------------+
-
+ | Miscanthus                       |        25.00      |
+ +----------------------------------+-------------------+
+ | Switchgrass                      |        25.00      |
+ +----------------------------------+-------------------+