Standardize time metadata (we will mark this as the release tag for ctsm5.3)

.git-blame-ignore-revs

@@ -27,6 +27,7 @@ d866510188d26d51bcd6d37239283db690af7e82
 e096358c832ab292ddfd22dd5878826c7c788968
 475831f0fb0e31e97f630eac4e078c886558b61c
 fd5f177131d63d39e79a13918390bdfb642d781e
+a51816e0de380300b69db9fc3e2c7fa83b267b64
 # Ran SystemTests and python/ctsm through black python formatter
 5364ad66eaceb55dde2d3d598fe4ce37ac83a93c
 8056ae649c1b37f5e10aaaac79005d6e3a8b2380

.gitmodules

@@ -44,15 +44,15 @@ fxDONOTUSEurl = https://github.com/ESCOMP/CISM-wrapper
 [submodule "rtm"]
 path = components/rtm
 url = https://github.com/ESCOMP/RTM
-fxtag = rtm1_0_80
+fxtag = rtm1_0_83
 fxrequired = ToplevelRequired
 # Standard Fork to compare to with "git fleximod test" to ensure personal forks aren't committed
 fxDONOTUSEurl = https://github.com/ESCOMP/RTM
 
 [submodule "mosart"]
 path = components/mosart
 url = https://github.com/ESCOMP/MOSART
-fxtag = mosart1.1.02
+fxtag = mosart1.1.05
 fxrequired = ToplevelRequired
 # Standard Fork to compare to with "git fleximod test" to ensure personal forks aren't committed
 fxDONOTUSEurl = https://github.com/ESCOMP/MOSART

cime_config/SystemTests/rxcropmaturity.py

@@ -106,7 +106,7 @@ def __init__(self, case):
         # Which conda environment should we use?
         self._get_conda_env()
 
-    def _run_phase(self, skip_gen=False):
+    def _run_phase(self, skip_gen=False, h1_inst=False):
         # Modeling this after the SSP test, we create a clone to be the case whose outputs we don't
         # want to be saved as baseline.
 
@@ -129,7 +129,7 @@ def _run_phase(self, skip_gen=False):
         self._set_active_case(case_gddgen)
 
         # Set up stuff that applies to both tests
-        self._setup_all()
+        self._setup_all(h1_inst)
 
         # Add stuff specific to GDD-Generating run
         logger.info("RXCROPMATURITY log:  modify user_nl files: generate GDDs")
@@ -196,7 +196,7 @@ def _run_phase(self, skip_gen=False):
         self._set_active_case(case_rxboth)
 
         # Set up stuff that applies to both tests
-        self._setup_all()
+        self._setup_all(h1_inst)
 
         # Add stuff specific to Prescribed Calendars run
         logger.info("RXCROPMATURITY log:  modify user_nl files: Prescribed Calendars")
@@ -264,7 +264,7 @@ def _get_rx_dates(self):
             logger.error(error_message)
             raise RuntimeError(error_message)
 
-    def _setup_all(self):
+    def _setup_all(self, h1_inst):
         logger.info("RXCROPMATURITY log:  _setup_all start")
 
         # Get some info
@@ -274,7 +274,7 @@ def _setup_all(self):
 
         # Set sowing dates file (and other crop calendar settings) for all runs
         logger.info("RXCROPMATURITY log:  modify user_nl files: all tests")
-        self._modify_user_nl_allruns()
+        self._modify_user_nl_allruns(h1_inst)
         logger.info("RXCROPMATURITY log:  _setup_all done")
 
     # Make a surface dataset that has every crop in every gridcell
@@ -399,7 +399,7 @@ def _run_check_rxboth_run(self, skip_gen):
             tool_path,
         )
 
-    def _modify_user_nl_allruns(self):
+    def _modify_user_nl_allruns(self, h1_inst):
         nl_additions = [
             "cropcals_rx = .true.",
             "cropcals_rx_adapt = .false.",
@@ -417,6 +417,8 @@ def _modify_user_nl_allruns(self):
             "hist_type1d_pertape(2) = 'PFTS'",
             "hist_dov2xy(2) = .false.",
         ]
+        if h1_inst:
+            nl_additions.append("hist_avgflag_pertape(2) = 'I'")
         self._append_to_user_nl_clm(nl_additions)
 
     def _run_generate_gdds(self, case_gddgen):

cime_config/SystemTests/rxcropmaturityinst.py

@@ -0,0 +1,6 @@
+from rxcropmaturity import RXCROPMATURITYSHARED
+
+
+class RXCROPMATURITYINST(RXCROPMATURITYSHARED):
+    def run_phase(self):
+        self._run_phase(h1_inst=True)

cime_config/SystemTests/rxcropmaturityskipgeninst.py

@@ -0,0 +1,6 @@
+from rxcropmaturity import RXCROPMATURITYSHARED
+
+
+class RXCROPMATURITYSKIPGENINST(RXCROPMATURITYSHARED):
+    def run_phase(self):
+        self._run_phase(skip_gen=True, h1_inst=True)

cime_config/config_tests.xml

@@ -145,6 +145,16 @@ This defines various CTSM-specific system tests
     <HIST_N>$STOP_N</HIST_N>
   </test>
 
+  <test NAME="RXCROPMATURITYINST">
+    <DESC>As RXCROPMATURITY but ensure instantaneous h1. Can be removed once instantaneous and other variables are on separate files.</DESC>
+    <INFO_DBUG>1</INFO_DBUG>
+    <DOUT_S>FALSE</DOUT_S>
+    <CONTINUE_RUN>FALSE</CONTINUE_RUN>
+    <REST_OPTION>never</REST_OPTION>
+    <HIST_OPTION>$STOP_OPTION</HIST_OPTION>
+    <HIST_N>$STOP_N</HIST_N>
+  </test>
+
   <test NAME="RXCROPMATURITYSKIPGEN">
     <DESC>As RXCROPMATURITY but don't actually generate GDDs. Allows short testing with existing GDD inputs.</DESC>
     <INFO_DBUG>1</INFO_DBUG>
@@ -155,6 +165,16 @@ This defines various CTSM-specific system tests
     <HIST_N>$STOP_N</HIST_N>
   </test>
 
+  <test NAME="RXCROPMATURITYSKIPGENINST">
+    <DESC>As RXCROPMATURITYSKIPGEN but ensure instantaneous h1. Can be removed once instantaneous and other variables are on separate files.</DESC>
+    <INFO_DBUG>1</INFO_DBUG>
+    <DOUT_S>FALSE</DOUT_S>
+    <CONTINUE_RUN>FALSE</CONTINUE_RUN>
+    <REST_OPTION>never</REST_OPTION>
+    <HIST_OPTION>$STOP_OPTION</HIST_OPTION>
+    <HIST_N>$STOP_N</HIST_N>
+  </test>
+
 <!--
 SSP    smoke CLM spinup test (only valid for CLM compsets with CLM45)
        do an initial spin test (setting CLM_ACCELERATED_SPINUP to on)

cime_config/testdefs/testlist_clm.xml

@@ -3540,6 +3540,17 @@
     </options>
   </test>
 
+  <test name="RXCROPMATURITYINST_Lm61" grid="f10_f10_mg37" compset="IHistClm60BgcCrop"  testmods="clm/cropMonthOutput">
+    <machines>
+      <machine name="derecho" compiler="intel" category="rxcropmaturity"/>
+      <machine name="derecho" compiler="intel" category="crop_calendars"/>
+    </machines>
+    <options>
+      <option name="wallclock">6:00:00</option>
+      <option name="comment">As RXCROPMATURITY, but ensure that h1 file is instantaneous. Can be removed once instantaneous and other variables are separated onto separate files.</option>
+    </options>
+  </test>
+
   <test name="RXCROPMATURITYSKIPGEN_Ld1097" grid="f10_f10_mg37" compset="IHistClm60BgcCrop"  testmods="clm/cropMonthOutput">
     <machines>
       <machine name="derecho" compiler="intel" category="aux_clm"/>
@@ -3552,6 +3563,17 @@
     </options>
   </test>
 
+  <test name="RXCROPMATURITYSKIPGENINST_Ld1097" grid="f10_f10_mg37" compset="IHistClm60BgcCrop"  testmods="clm/cropMonthOutput">
+    <machines>
+      <machine name="derecho" compiler="intel" category="rxcropmaturity"/>
+      <machine name="derecho" compiler="intel" category="crop_calendars"/>
+    </machines>
+    <options>
+      <option name="wallclock">00:45:00</option>
+      <option name="comment">As RXCROPMATURITYSKIPGEN, but ensure that h1 file is instantaneous. Can be removed once instantaneous and other variables are separated onto separate files.</option>
+    </options>
+  </test>
+
   <test name="ERP_D_P64x2_Ld10" grid="f10_f10_mg37" compset="I2000Clm60Bgc" testmods="clm/Hillslope">
     <machines>
       <machine name="derecho" compiler="intel" category="aux_clm"/>

doc/ChangeLog

@@ -1,4 +1,108 @@
 ===============================================================
+Tag name: ctsm5.3.014
+Originator(s): slevis (Samuel Levis,UCAR/TSS,303-665-1310)
+Date: Fri 15 Nov 2024 01:24:45 PM MST
+One-line Summary: Change history time to be the middle of the time bounds
+
+Purpose and description of changes
+----------------------------------
+
+ Making the change in order to be consistent with CAM and to make history output more intuitive.
+
+
+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.]
+
+[ ] clm6_0
+
+[ ] clm5_1
+
+[ ] clm5_0
+
+[ ] ctsm5_0-nwp
+
+[ ] clm4_5
+
+
+Bugs fixed
+----------
+List of CTSM issues fixed (include CTSM Issue # and description) [one per line]:
+ Partly addresses issue #1059
+
+Notes of particular relevance for users
+---------------------------------------
+Caveats for users (e.g., need to interpolate initial conditions):
+ The history time variable now equals the middle of the time bounds.
+ Instantaneous history tapes now do not include time bounds.
+ Mixed history tapes do not change the treatment of instantaneous fields or move them to separate tapes, yet.
+
+
+Notes of particular relevance for developers:
+---------------------------------------------
+Caveats for developers (e.g., code that is duplicated that requires double maintenance):
+
+Changes to tests or testing:
+ This tag introduces changes to the mosart/rtm testlists.
+
+Testing summary:
+----------------
+
+ [PASS means all tests PASS; OK means tests PASS other than expected fails.]
+
+  python testing (if python code has changed; see instructions in python/README.md; document testing done):
+
+    derecho -
+
+  regular tests (aux_clm: https://github.com/ESCOMP/CTSM/wiki/System-Testing-Guide#pre-merge-system-testing):
+
+    derecho ----- OK
+    izumi ------- OK
+
+  mosart
+    derecho ----- OK
+    izumi ------- OK
+
+  rtm
+    derecho ----- OK
+
+  any other testing (give details below):
+
+  ctsm_sci
+     derecho ----
+
+If the tag used for baseline comparisons was NOT the previous tag, note that here:
+
+
+Answer changes
+--------------
+
+Changes answers relative to baseline: Only time variable
+
+  Summarize any changes to answers, i.e.,
+    - what code configurations: all
+    - what platforms/compilers: all
+    - nature of change: only the time variable
+
+
+Other details
+-------------
+List any git submodules updated (cime, rtm, mosart, cism, fates, etc.):
+ rtm, mosart
+
+Pull Requests that document the changes (include PR ids):
+ https://github.com/ESCOMP/ctsm/pull/2838
+ https://github.com/ESCOMP/MOSART/pull/70
+ https://github.com/ESCOMP/RTM/issues/54
+ https://github.com/ESCOMP/MOSART/pull/106
+ https://github.com/ESCOMP/RTM/pull/39
+
+===============================================================
+===============================================================
 Tag name: ctsm5.3.012
 Originator(s): afoster (Adrianna Foster,UCAR/TSS,303-497-1728)
 Date: Wed 13 Nov 2024 09:53:51 AM MST

doc/ChangeSum

@@ -1,5 +1,6 @@
 Tag                   Who      Date  Summary
 ============================================================================================================================
+       ctsm5.3.014   slevis 11/18/2024 Change history time to be the middle of the time bounds
        ctsm5.3.012  afoster 11/13/2024 update fates tag
        ctsm5.3.011 samrabin 11/11/2024 Improve handling of cold-start finidat
        ctsm5.3.010  afoster 11/09/2024 Merge b4b-dev

python/ctsm/crop_calendars/convert_axis_time2gs.py

@@ -5,6 +5,7 @@
 import sys
 import numpy as np
 import xarray as xr
+from ctsm.crop_calendars.cropcal_utils import get_integer_years
 
 try:
     import pandas as pd
@@ -85,7 +86,7 @@ def set_up_ds_with_gs_axis(ds_in):
         if not any(x in ["mxsowings", "mxharvests"] for x in ds_in[var].dims):
             data_vars[var] = ds_in[var]
     # Set up the new dataset
-    gs_years = [t.year - 1 for t in ds_in.time.values[:-1]]
+    gs_years = get_integer_years(ds_in)[:-1]
     coords = ds_in.coords
     coords["gs"] = gs_years
     ds_out = xr.Dataset(data_vars=data_vars, coords=coords, attrs=ds_in.attrs)

python/ctsm/crop_calendars/cropcal_figs_module.py

@@ -12,6 +12,7 @@
 from matplotlib import cm
 import matplotlib.collections as mplcol
 
+# pylint: disable=abstract-class-instantiated
 
 # Colormaps (maps)
 cropcal_colors = {

python/ctsm/crop_calendars/cropcal_module.py

@@ -20,24 +20,16 @@ def check_and_trim_years(year_1, year_n, ds_in):
     """
     After importing a file, restrict it to years of interest.
     """
-    ### In annual outputs, file with name Y is actually results from year Y-1.
-    ### Note that time values refer to when it was SAVED. So 1981-01-01 is for year 1980.
-
-    def get_year_from_cftime(cftime_date):
-        # Subtract 1 because the date for annual files is when it was SAVED
-        return cftime_date.year - 1
 
     # Check that all desired years are included
-    if get_year_from_cftime(ds_in.time.values[0]) > year_1:
-        raise RuntimeError(
-            f"Requested year_1 is {year_1} but first year in outputs is "
-            + f"{get_year_from_cftime(ds_in.time.values[0])}"
-        )
-    if get_year_from_cftime(ds_in.time.values[-1]) < year_1:
+    year = utils.get_timestep_year(ds_in, ds_in.time.values[0])
+    if year > year_1:
         raise RuntimeError(
-            f"Requested year_n is {year_n} but last year in outputs is "
-            + f"{get_year_from_cftime(ds_in.time.values[-1])}"
+            f"Requested year_1 is {year_1} but first year in outputs is {year}"
         )
+    year = utils.get_timestep_year(ds_in, ds_in.time.values[-1])
+    if year < year_1:
+        raise RuntimeError(f"Requested year_n is {year_n} but last year in outputs is {year}")
 
     # Remove years outside range of interest
     ### Include an extra year at the end to finish out final seasons.
@@ -443,10 +435,7 @@ def import_output(
         )
 
     # Convert time axis to integer year, saving original as 'cftime'
-    this_ds_gs = this_ds_gs.assign_coords(
-        {"cftime": this_ds["time_bounds"].isel({"hist_interval": 0})}
-    )
-    this_ds_gs = this_ds_gs.assign_coords({"time": [t.year for t in this_ds_gs["cftime"].values]})
+    this_ds_gs = convert_time_to_int_year(filename, this_ds, this_ds_gs)
 
     # Get number of harvests
     this_ds_gs["NHARVESTS"] = (this_ds_gs["GDDHARV_PERHARV"] > 0).sum(dim="mxharvests")
@@ -458,6 +447,35 @@ def import_output(
     return this_ds_gs, any_bad
 
 
+def convert_time_to_int_year(filename, this_ds, this_ds_gs):
+    """
+    Convert time axis to integer year, saving original as 'cftime'
+    """
+    if "time_bounds" in this_ds:
+        # Always true before PR #2838, when even files with all instantaneous variables got
+        # time_bounds saved. After that PR (and before the segregation of instantaneous and other
+        # variables onto separate files), files with an instantaneous variable first in their list
+        # do not get time_bounds saved.
+        this_ds_gs = this_ds_gs.assign_coords(
+            {"cftime": this_ds["time_bounds"].isel({"hist_interval": 0})}
+        )
+        this_ds_gs = this_ds_gs.assign_coords(
+            {"time": [t.year for t in this_ds_gs["cftime"].values]}
+        )
+    elif this_ds["time"].attrs["long_name"] == "time at end of time step":
+        # This is an "instantaneous file."
+        this_ds_gs = this_ds_gs.assign_coords({"cftime": this_ds["time"]})
+        this_ds_gs = this_ds_gs.assign_coords(
+            {"time": [t.year - 1 for t in this_ds_gs["cftime"].values]}
+        )
+    else:
+        raise RuntimeError(
+            f"{filename} is neither an instantaneous nor a combined/non-instantaneous file."
+        )
+
+    return this_ds_gs
+
+
 def handle_zombie_crops(this_ds):
     """
     When doing transient runs, it's somehow possible for crops in newly-active patches to be