ctsm5.3.021: Standardize time metadata (we will mark this as the release tag for ctsm5.3)

.git-blame-ignore-revs

@@ -1,4 +1,5 @@
 # Ran python directory through black python formatter
+d89c86e7776bbf7451860b60038b4725fe7a0560
 b429b63824e09f82e95d2982f14311cbbd8e4a37
 d229b5c6689efc4c2a6cef077515c4ccd5c18ff6
 4cd83cb3ee6d85eb909403487abf5eeaf4d98911

.gitmodules

@@ -52,7 +52,7 @@ fxDONOTUSEurl = https://github.com/ESCOMP/RTM
 [submodule "mosart"]
 path = components/mosart
 url = https://github.com/ESCOMP/MOSART
-fxtag = mosart1.1.07
+fxtag = mosart1.1.08
 fxrequired = ToplevelRequired
 # Standard Fork to compare to with "git fleximod test" to ensure personal forks aren't committed
 fxDONOTUSEurl = https://github.com/ESCOMP/MOSART
@@ -68,7 +68,7 @@ fxDONOTUSEurl = https://github.com/ESCOMP/mizuRoute
 [submodule "ccs_config"]
 path = ccs_config
 url = https://github.com/ESMCI/ccs_config_cesm.git
-fxtag = ccs_config_cesm1.0.16
+fxtag = ccs_config_cesm1.0.20
 fxrequired = ToplevelRequired
 # Standard Fork to compare to with "git fleximod test" to ensure personal forks aren't committed
 fxDONOTUSEurl = https://github.com/ESMCI/ccs_config_cesm.git

WhatsNewInCTSM5.3.md

@@ -1,48 +1,108 @@
-# What's new in CTSM 5.3 (tag `ctsm5.3.0`)
+# What's new in CTSM 5.3 (tag `ctsm5.3.021`)
 
 ## Purpose and description of changes since CTSM 5.2 (tag `ctsm5.2.005`)
-- Adds CN Matrix method to speed up spinup for the BGC model.
-- Updates surface datasets.
-- Brings in new Leung 2023 dust emissions.
-- Adds explicit air conditioning for the urban model.
-- Updates crop calendars.
-- Updates fire model with various improvements, including default parameterization against climate reanalysis from CRU-JRA instead of GSWP.
-- FATES compsets can now be run with transient land use.
-
-These changes were needed ahead of the CESM3 capability/functionality "chill". For `clm6_0` physics these options are now turned on by default, in addition to Sturm snow and excess ice.
-
-## Changes to CTSM infrastructure
- - `manage_externals` removed and replaced by `git-fleximod`
- - Ability to handle CAM7 in `LND_TUNING_MODE`
-
-## Changes to CTSM answers
-
- Changes to defaults for `clm6_0` physics:
-  - Urban explicit A/C turned on
-  - Snow thermal conductivity method is now `Sturm_1997`
-  - New initial conditions file for f09 ("1-degree") 1850, with more in progress
-  - New crop calendars
-  - Dust emissions method is now `Leung_2023`
-  - Excess ice is turned on
-  - Updates to MEGAN for BVOCs
-  - Updates to BGC fire method
-
- Changes for all physics versions:
-  - Parameter files updated
-  - FATES parameter file updated
-  - Glacier region 1 is now undefined
-  - Update in FATES transient land use
-  - Pass active glacier (CISM) runoff directly to river model (MOSART)
-  - Add the option for using Matrix CN method for Carbon/Nitrogen BGC spinup
-
-## New surface datasets
-
-- With new surface datasets the following GLC fields have region "1" set to UNSET: glacier_region_behavior, glacier_region_melt_behavior, glacier_region_ice_runoff_behavior
-- Updates to allow creating transient landuse timeseries files going back to 1700.
-- Fix an important bug on soil fields that was there since `ctsm5.2.0`. This has the side effect of `mksurfdata_esmf` now giving identical answers with a change in number of processors, as it should.
-- Surface datasets now provided for the `ne0np4.POLARCAP.ne30x4` grid.
-- Surface datasets now have their version number embedded to prevent mismatch of surface dataset and CTSM version.
-- Remove the `--hires_pft` option from `mksurfdata_esmf` as we don't have the datasets for it.
-- Remove `VIC` fields from surface datasets.
-- Updates to input datasets in PFT/LAI/soil-color raw datasets (now from the TRENDY2024 timeseries that ends in 2023), as well as two fire datasets (crop fire peak month, peatland fraction), and the glacier behavior dataset.
 
+### New features
+
+* `manage_externals` replaced by [`git-fleximod`](https://github.com/ESMCI/git-fleximod/blob/main/README.md). ([PR \#2559](https://github.com/ESCOMP/CTSM/pull/2559))
+* No longer runs the 0th time step in first segment of startup and hybrid runs; branch and continue runs never had this 0th time step. ([PR \#2084](https://github.com/ESCOMP/CTSM/pull/2084))
+* New CN Matrix method speeds up spinup for the BGC model. ([PR \#640](https://github.com/ESCOMP/CTSM/pull/640); [Liao et al. 2023](https://agupubs.onlinelibrary.wiley.com/doi/10.1029/2023MS003625)).
+* New `Leung_2023` dust emissions. ([PR \#1897](https://github.com/ESCOMP/CTSM/pull/1897); [Leung et al 2023](https://doi.org/10.5194/acp-23-6487-2023), [Leung et al. 2024](https://doi.org/10.5194/acp-24-2287-2024))
+* Explicit air conditioning for the urban model. ([PR \#2275](https://github.com/ESCOMP/CTSM/pull/2275); [Li et al. 2024](https://agupubs.onlinelibrary.wiley.com/share/NY4AYPREB8Y8BUDP7DXD?target=10.1029/2023MS004107))
+* FATES compsets can now be run with transient land use; off by default. ([PR \#2507](https://github.com/ESCOMP/CTSM/pull/2507))
+* Ability to handle CAM7 in `LND_TUNING_MODE`. ([PR \#2632](https://github.com/ESCOMP/CTSM/pull/2632))
+
+### Answer changes
+
+Changes to defaults for `clm6_0` physics:
+
+* Urban explicit A/C turned on (links above).
+* Snow thermal conductivity method is now `Sturm1997`. ([PR \#2348](https://github.com/ESCOMP/CTSM/pull/2348); see also [discussion \#1960](https://github.com/ESCOMP/CTSM/discussions/1960))
+* New initial conditions files for f09 ("1-degree" 1850, 2000), f19 (“2-degree” 1850), and ne30 (1850, 1979, 2000) resolutions.
+* New crop calendars. ([PR \#2664](https://github.com/ESCOMP/CTSM/pull/2664); informed by [Rabin et al., 2023](https://gmd.copernicus.org/articles/16/7253/2023/gmd-16-7253-2023.html))
+* Dust emissions method is now `Leung_2023` (links above).
+* Excess ice is turned on. ([PR \#1787](https://github.com/ESCOMP/CTSM/pull/1787))
+* Updates to MEGAN for BVOCs. ([PR \#2588](https://github.com/ESCOMP/CTSM/pull/2588))
+* New BGC fire method `li2024crujra`: Avoid crop fires during growing season; allow lightning ignitions in tropical closed forests; add effect of landscape fragmentation on ignitions and duration; recalibrate against GFED5 burned area and with CRU-JRA climate. ([PR \#2684](https://github.com/ESCOMP/CTSM/pull/2684), [PR \#2711](https://github.com/ESCOMP/CTSM/pull/2711), [PR \#2715](https://github.com/ESCOMP/CTSM/issues/2715))
+
+Changes for all physics versions:
+
+* Parameters updated for CRU-JRA forcing: PPE-based modifications were made to the parameters `leafcn`, `slatop`, `froot_leaf`, `medlynslope`, and `kmax`. Lowers LAI and biomass in boreal and tropical forests, without reducing latent heat in the tropics. Affected PFTs: NET temperate, NET boreal, BET tropical, BDS boreal, C3 arctic grass. ([PR \#2500](https://github.com/ESCOMP/CTSM/pull/2500))
+* FATES parameter file updated (see section below).
+* Pass active glacier (CISM) runoff directly to river model (MOSART) ([MOSART PR \#94](https://github.com/ESCOMP/MOSART/pull/94))
+* New surface datasets and landuse timeseries files (see section below).
+* CNMatrix is new default spinup method (links above).
+
+### Heads up
+
+* Small glacier changes mean that you can’t use a 5.3 surface dataset with pre-5.3 code and vice versa anymore. (Merged with [PR \#2500](https://github.com/ESCOMP/CTSM/pull/2500))
+* Updates the definition of history variable “time” from *end* of `time_bounds` to *middle* of `time_bounds`. ([PR \#2838](https://github.com/ESCOMP/CTSM/pull/2838); see section below)
+* Standardizes history variable attributes and a history dimension name. ([PR \#2052](https://github.com/ESCOMP/CTSM/pull/2052); see section below)
+
+##
+
+## Additional detail
+
+### Changes related to time and history files
+
+(Note that the same information in this section applies to MOSART and RTM.)
+
+Startup and hybrid runs no longer run the 0th time step, consistent with the same change in CAM. (Branch and continue runs never had this 0th time step.) This means you will not get an extraneous initial history file anymore. In some circumstances this may also affect the names of history files.
+
+In most cases, the history `time` variable is now defined as the middle of a history file’s `time_bounds` instead of the end, for consistency with the same change in CAM. The exception is if you specify `hist_avgflag_pertape = 'I'` for that file, in which case it will be treated as an “instantaneous” file. Instantaneous history files (a) have their `time` coordinate set to the end of the last timestep (as did all history files before this tag) and (b) do not include `time_bounds`.
+
+The history dimension name `hist_interval` (of output variable `time_bounds`) is standardized to be `nbnd`. History variables `time_bounds`, `mcdate`, `mcsec`, `mdcur`, and `mscur` are standardized to include the calendar attribute.
+
+### New surface datasets and landuse timeseries files ([PR \#2500](https://github.com/ESCOMP/CTSM/pull/2500))
+
+* Transient landuse timeseries files going back to 1700 now possible (and made for f09).
+* Fix an important bug on soil fields that was there since `ctsm5.2.0`. This has the side effect of `mksurfdata_esmf` now giving identical answers with a change in number of processors, as it should. ([Issue \#2744](https://github.com/ESCOMP/CTSM/issues/2744))
+* Surface datasets now provided for the `ne0np4.POLARCAP.ne30x4` grid. ([PR \#2716](https://github.com/ESCOMP/CTSM/pull/2716), [issue \#2720](https://github.com/ESCOMP/CTSM/issues/2720))
+* Surface datasets now have their version number embedded to prevent mismatch of surface dataset and CTSM version. ([Issue \#2723](https://github.com/ESCOMP/CTSM/issues/2723))
+* Remove outdated hydrology `VIC` (Variable Infiltration Capacity Hydrology model) fields from surface datasets.
+* Updates to input datasets:
+  * PFT/LAI/soil-color raw datasets; now from the TRENDY2024 timeseries that ends in 2023. (Issues [\#2570](https://github.com/ESCOMP/CTSM/issues/2570) and [\#2452](https://github.com/ESCOMP/CTSM/issues/2452))
+  * Two fire datasets: crop fire peak month and peatland fraction. (Issue [\#2618](https://github.com/ESCOMP/CTSM/issues/2618))
+  * Glacier behavior dataset (related to how non-Greenland glaciers are handled). (Issue [\#423](https://github.com/ESCOMP/CTSM/issues/423))
+
+### Changes to FATES parameter file
+
+* [PR \#2507](https://github.com/ESCOMP/CTSM/pull/2507) ([ctsm5.2.013](https://github.com/ESCOMP/CTSM/releases/tag/ctsm5.2.013)) / [FATES PR \#1116](https://github.com/NGEET/fates/pull/1116) ([sci.1.77.1\_api.36.0.0](https://github.com/NGEET/fates/releases/tag/sci.1.77.0_api.36.0.0))
+  * Adds new parameters for new land use harvest mode and land use by PFT capabilities
+* [PR \#2700](https://github.com/ESCOMP/CTSM/pull/2700) ([ctsm5.3.003](https://github.com/ESCOMP/CTSM/releases/tag/ctsm5.3.003)) / [FATES PR \#1255](https://github.com/NGEET/fates/pull/1255) ([sci.1.78.3\_api.36.1.0](https://github.com/NGEET/fates/releases/tag/sci.1.78.3_api.36.1.0))
+  * Adds two arctic shrub PFTs, increasing the number of default PFTs to 14 and update arctic grass parameters ([FATES PR\#1236](https://github.com/NGEET/fates/pull/1236))
+  * Splits `fates_turnover_leaf` parameter into canopy and understory specific turnover rates and provides new values for both ([FATES PR\#1136](https://github.com/NGEET/fates/pull/1136))
+  * Updates grass allometry parameters ([FATES PR\#1206](https://github.com/NGEET/fates/pull/1206))
+  * Changes the prescribe nutrient uptake defaults from 1 to 0 for all PFTs (only relevant to ELM-FATES)
+
+### Changes to rpointer files
+
+The rpointer files are simple text files that CESM uses to keep track of how far simulations have progressed, pointing to the filename of the latest restart file for that component. There is one such file for each component, so for CTSM `I` cases that's `lnd`, `cpl`, and `atm` (and `rof` if it's active). Normally, when the user is just extending the length  of simulations, there’s no need to worry about these files.
+
+However, if there was a problem when a simulation shut down, it's possible that different components will have mismatched restarts and rpointer files. In the past, this meant figuring out what restart file should be pointed to in each component rpointer file and correcting it by hand in an editor. There was only the final set of rpointer files that was kept for a case.
+
+Now, with this update, the `lnd`, `cpl`, and `atm` rpointer files have the simulation date in the filenames, so it's easy to spot if the restarts are mismatched for one of the components. Also, since there are matching rpointer files for each time restarts are created, it's now easier to (a) make sure restarts and rpointer files are all correctly matched and (b) for a user to take a set of restarts and matching rpointer files to start up from for any part of an existing simulation. This means you don't have to hand-edit the rpointer files, making sure you don't make a mistake when you do.
+
+Old rpointer filenames:
+
+* `rpointer.atm`
+* `rpointer.cpl`
+* `rpointer.lnd`
+
+New names:
+
+* `rpointer.atm.YYYY-MM-DD-SSSSS`
+* `rpointer.cpl.YYYY-MM-DD-SSSSS`
+* `rpointer.lnd.YYYY-MM-DD-SSSSS`
+
+Where `YYYY-MM-DD-SSSSS` is the year, month, day, and seconds into the day for the simulation timestamp. For example, `rpointer.lnd.2000-01-01-00000` for a rpointer file for starting at midnight (beginning of the day) on January 1st, 2000\.
+
+Note that this is backwards-compatible, so for all the components you can use either the new or old format for the rpointer filenames. Thus, if you are restarting from an existing case before `ctsm5.3.016`, you CAN use the rpointer filenames that don't have the timestamps in the name.
+
+## Simulations supporting this release
+
+- f19 `Clm60Bgc` 16pft: [https://github.com/NCAR/LMWG\_dev/issues/70](https://github.com/NCAR/LMWG_dev/issues/70)
+- f09 with `Clm60BgcCrop`: [https://github.com/NCAR/LMWG\_dev/issues/69](https://github.com/NCAR/LMWG_dev/issues/69)
+- ne30 with `Clm60BgcCrop`: [https://github.com/NCAR/LMWG\_dev/issues/68](https://github.com/NCAR/LMWG_dev/issues/68)
+
+Note: Dust emissions in CTSM 5.3 will be different from the above simulations because of a tuning update that came in after those.

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

@@ -3649,6 +3649,17 @@
     </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"/>
@@ -3661,6 +3672,17 @@
     </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"/>