add systemtest for potential vegetation spin up

cime_config/SystemTests/pvt.py

@@ -0,0 +1,120 @@
+"""
+FATES land use potential vegetation spin up + transient test
+
+This is a FATES specific test:
+
+1) conduct a spinup with use_fates_potentialveg on
+    - write restart file
+    - use CLM_ACCELERATED_SPINUP?
+2) run a transient landuse case with use_fates_lupft
+    - start from the restart file generated in (1)
+
+"""
+from CIME.XML.standard_module_setup import *
+from CIME.SystemTests.system_tests_common import SystemTestsCommon
+from systemtest_utils import read_user_nl_clm
+import shutil, glob, os
+
+logger = logging.getLogger(__name__)
+
+class PVT(SystemTestsCommon):
+    def __init_(self,case):
+        SystemTestsCommon.__init__(self,case)
+
+        # Do not allow PVT to be run with certain testmods
+        # Should this be targeted to a specific testmod for simplicity for now?
+        # Technically this could be run with the luh fates_harvest_modes
+        casebaseid = self._case.get_value("CASEBASEID")
+        casebasid = casebaseid.split("-")[-1]
+        if casebaseid[0:10] != "FatesLUPFT":
+            error_message = (
+                "Only call PVT with test FatesLUPFT"
+            )
+            logger.error(error_message)
+            raise RuntimeError(error_message)
+
+        # Only allow to run if resolution is 4x5 for now
+        # Eventually we could set this up to generate the necessary land use x pft mapping
+        # on the fly, although this would also require generating the land use timeseries
+        # regridding on the fly which is a more time consuming endevour currently
+        lnd_grid = self._case.get_value("LND_GRID")
+        if lnd_grid != "4x5":
+            error_message = (
+                "PVT can currently only be run with 4x5 resolution"
+            )
+            logger.error(error_message)
+            raise RuntimeError(error_message)
+
+    def run_phase(self):
+        # -------------------------------------------------------------------
+        # (1) Run FATES spin-up case in potential vegetation mode
+        # -------------------------------------------------------------------
+        orig_case = self._case
+        orig_casevar = self._case.get_value("CASE")
+        caseroot = self._case.get_value("CASEROOT")
+
+        # clone the main case to create spinup case
+        logger.info("PVT log:  cloning setup")
+        clone_path = "{}.potveg".format(caseroot)
+        if os.path.exists(clone_path):
+            shutil.rmtree(clone_path)
+        logger.info("PVT log:  cloning")
+        clone = self._case.create_clone(clone_path, keepexe=True)
+        logger.info("PVT log: cloning complete")
+
+        # setup the clone case
+        os.chdir(clone_path)
+        self._set_active_case(clone)
+        self._setup_all()
+
+        # Modify the spin up case to use the potential vegetation mode.
+        # Checks for incompatible cases and necessary mapping files are
+        # handled in the build case.
+        # use_fates_lupft should be set to true in the testmod
+        # save off the harvest mode for reinstating later
+        found, hmode = self.read_user_nl_clm('fates_harvest_mode')
+        logger.info("PVT log:  modify user_nl_clm file for spin up run")
+        # TODO: remove fates_harvest_mode if found
+        self._append_to_user_nl_clm(
+            [
+                "use_fates_potentialveg = .true.",
+            ]
+        )
+
+        stop_n_pveg = 1
+        with clone:
+            # clone.set_value("CLM_ACCELERATED_SPINUP", "on")
+            clone.set_value("STOP_N", stop_n_pveg)
+
+        # Run the spin up case
+        # As per SSP test:
+        # "No history files expected, set suffix=None to avoid compare error"
+        logger.info("PVT log:  starting spin-up run")
+        dout_sr = clone.get_value("DOUT_S_ROOT")
+        self._skip_pnl = False
+        self.run_indv(suffix=None, st_archive=True)
+
+        # -------------------------------------------------------------------
+        # (2) Run FATES transient case using restart file from spin-up
+        # -------------------------------------------------------------------
+        os.chdir(caseroot)
+        self._set_active_case(orig_case)
+
+        # logger.info("PVT log:  modify user_nl_clm file for transient run")
+        # self._append_to_user_nl_clm(
+        #     [
+        #         "use_fates_potentialveg = .true.",
+        #     ]
+        # )
+
+
+        self._case.set_value("CLM_ACCELERATED_SPINUP", "off")
+        self._case.set_value("RUN_TYPE", "hybrid")
+        self._case.set_value("GET_REFCASE", False)
+        self._case.set_value("RUN_REFCASE", "{}.potveg".format(orig_casevar))
+        self._case.set_value("RUN_REFDATE", "1700-01-01")
+        self._case.set_value("DOUT_S", False)
+        self._case.flush()
+
+        # do the restart run (short term archiving is off)
+        self.run_indv()

cime_config/SystemTests/systemtest_utils.py

@@ -2,7 +2,7 @@
 Reduce code duplication by putting reused functions here.
 """
 
-import os, subprocess
+import os, subprocess, re
 
 
 def cmds_to_setup_conda(caseroot):
@@ -84,3 +84,21 @@ def run_python_script(caseroot, this_conda_env, command_in, tool_path):
     except:
         print(f"ERROR trying to run {tool_name}.")
         raise
+
+def read_user_nl_clm(self,namelist_option):
+    user_nl_clm_path = os.path.join(self._get_caseroot(), "user_nl_clm")
+    with open(user_nl_clm_path) as f:
+        user_nl_clm_text = f.read()
+        reg = fr'{namelist_option}\s*=\s*([^\n]+)'
+        find_out = re.findall(reg, user_nl_clm_text)
+        # This could be more robust
+        if len(find_out) == 0:
+            return 0, False
+        elif len(find_out) > 1:
+            error_message = (
+                "ERROR: read_user_nl_clm: namelist option is set more than once"
+            )
+            # logger.error(error_message)
+            raise RuntimeError(error_message)
+        else:
+            return find_out[0], True