Merge GEOS-Chem 14.5.2 into dev/14.6.0

.zenodo.json

@@ -0,0 +1,22 @@
+{
+    "access_right": "open",
+    "creators": [
+	{
+	    "name": "The International GEOS-Chem User Community"
+	}
+    ],
+    "description": "GEOS-Chem (science codebase)",
+    "keywords": [
+	"atmospheric-chemistry",
+	"atmospheric-composition",
+	"atmospheric-modeling",
+	"aws",
+	"climate-modeling",
+	"cloud-computing",
+	"geos-chem",
+	"atmospheric-computing",
+	"scientific-computing"
+    ],
+    "license": "mit-license",
+    "upload_type": "software"
+}

CHANGELOG.md

@@ -4,14 +4,34 @@ This file documents all notable changes to the GEOS-Chem repository starting in
 
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/), and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
+## [14.5.2] - 2025-02-12
+### Added
+- Implemented the Global Rice Patty Inventory (GRPI) for CH4 and carbon simulations to replace EDGAR rice emissions
+- Added run directory creation for processed cubed-sphere GEOS-IT meteorology
+- Added GC-Classic and GCHP environment files, build scripts, and run scripts for MSU Orion cluster
+
+### Changed
+- Updated GC-Classic and GCHP environment files, build scripts, and run scripts for NASA discover cluster
+- Updated rundir scripts to ask for confirmation before building the KPP-Standalone executable
+- Updated rundir scripts to print a reminder to compile with `-DKPPSA=y` to build the KPP-Standalone executable
+- Updated `integrationTestCreate.sh` and `parallelTestCreate.sh` scripts to decline building the KPP-Standalone.
+
+### Fixed
+- Fixed GCHP refresh time for `CO2_WEEKLY` scale factors so updated daily
+- Fixed bug in GCHP GEOS-IT run directory using raw lat-lon fields on NASA discover cluster
+
 ## [14.5.1] - 2025-01-10
 ### Added
 - Added Australian Hg emissions for 2000-2019 from MacFarlane et. al. [2022], plus corresponding mask file
 - Added comments in GEOS-Chem Classic `HISTORY.rc` template files advising users not to change the `BoundaryConditions.frequency` setting
+- Added `.zenodo.json` for auto-DOI generation upon version releases
 
 ### Fixed
 - Reverted CH4 livestock emissions to EDGAR v7 to avoid hotspots and to apply seasonality
 
+### Removed
+- Removed unused RUNDIR settings for GCHP pressure units and scaling
+
 ## [14.5.1] - 2025-01-10
 ### Added
 - Added allocate guards for arrays in `pressure_mod`

run/GCClassic/HEMCO_Config.rc.templates/HEMCO_Config.rc.CH4

@@ -63,6 +63,7 @@ VerboseOnCores:              root       # Accepted values: root all
     --> Scarpelli_Mexico       :       true     # 2015
 # ----- GLOBAL INVENTORIES ----------------------------------------------------
     --> GFEIv2                 :       true     # 2019
+    --> GRPI                   :       true     # 2022
     --> EDGARv8                :       true     # 2010-2022
     --> QFED2                  :       false    # 2009-2015
     --> JPL_WETCHARTS          :       true     # 2009-2017
@@ -367,6 +368,15 @@ VerboseOnCores:              root       # Accepted values: root all
 0 GFEI_CH4_COAL $ROOT/CH4/v2022-01/GFEIv2/Global_Fuel_Exploitation_Inventory_v2_2019_Coal.nc     emis_ch4 2019/1/1/0 C xy molec/cm2/s CH4 -  3 5
 )))GFEIv2
 
+#==============================================================================
+# --- Global Rice Patty Inventory (GRPI, Zichong Chen et al., 2025) ---
+#
+# This inventory will replace EDGAR (rice)
+#==============================================================================
+(((GRPI
+0 GRPI_CH4_RICE $ROOT/CH4/v2025-01/GRPI/GRPI_01x01.nc emi_ch4 2022/1-12/1/0 C xy kg/m2/s CH4 -  7 5
+)))GRPI
+
 #==============================================================================
 # --- EDGAR v8.0 emissions ---
 #

run/GCClassic/HEMCO_Config.rc.templates/HEMCO_Config.rc.carbon

@@ -70,6 +70,7 @@ Mask fractions:              false
     --> Scarpelli_Mexico       :       true     # 2015
 # ..... Global Inventories ...........
     --> GFEIv2                 :       true     # 2019
+    --> GRPI                   :       true     # 2022
     --> EDGARv8                :       true     # 2010-2022
     --> QFED2                  :       false    # 2009-2015
     --> JPL_WETCHARTS          :       true     # 2009-2017
@@ -409,6 +410,15 @@ Mask fractions:              false
 0 GFEI_CH4_COAL $ROOT/CH4/v2022-01/GFEIv2/Global_Fuel_Exploitation_Inventory_v2_2019_Coal.nc     emis_ch4 2019/1/1/0 C xy molec/cm2/s CH4 -  3 5
 )))GFEIv2
 
+#==============================================================================
+# --- Global Rice Patty Inventory (GRPI, Zichong Chen et al., 2025) ---
+#
+# This inventory will replace EDGAR (rice)
+#==============================================================================
+(((GRPI
+0 GRPI_CH4_RICE $ROOT/CH4/v2025-01/GRPI/GRPI_01x01.nc emi_ch4 2022/1-12/1/0 C xy kg/m2/s CH4 -  7 5
+)))GRPI
+
 #==============================================================================
 # --- CH4: EDGAR v8.0 emissions ---
 #

run/GCClassic/createRunDir.sh

@@ -898,12 +898,6 @@ if [[ "x${sim_name}" == "xfullchem" || "x${sim_name}" == "xCH4" ]]; then
     chmod 744 ${rundir}/metrics.py
 fi
 
-# Copy the KPP standalone interface config file to ther rundir (fullchem only)
-if [[ "x${sim_name}" == "xfullchem"  ]]; then
-    cp -r ${gcdir}/run/shared/kpp_standalone_interface.yml ${rundir}
-    chmod 644 ${rundir}/kpp_standalone_interface.yml
-fi
-
 # Set permissions
 chmod 744 ${rundir}/cleanRunDir.sh
 chmod 744 ${rundir}/archiveRun.sh
@@ -1202,21 +1196,42 @@ while [ "$valid_response" -eq 0 ]; do
     fi
 done
 
+#-----------------------------------------------------------------
+# Ask user whether to build the KPP-standalone box model
+#-----------------------------------------------------------------
+enable_kppsa=""
+if [[ "x${sim_name}" == "xfullchem" ]]; then
+    printf "${thinline}Do you want to build the KPP-Standalone Box Model? (y/n)${thinline}"
+    valid_response=0
+    while [ "$valid_response" -eq 0 ]; do
+	read -p "${USER_PROMPT}" enable_kppsa
+	if [[ "x${enable_kppsa}" == "xy" ]]; then
+	    cp -r ${gcdir}/run/shared/kpp_standalone_interface.yml  ${rundir}
+	    chmod 644 ${rundir}/kpp_standalone_interface.yml
+	    valid_response=1
+	elif [[ "x${enable_kppsa}" = "xn" ]]; then
+	    valid_response=1
+	else
+	    printf "Input not recognized. Try again.\n"
+	fi
+    done
+fi
+
 #---------------------------------------------------------------------------
 # Add reminders to compile with CMake options for simulations that need them
 #---------------------------------------------------------------------------
 hdr="\n>>>> REMINDER: You must compile with options:"
 ftr="<<<<\n"
-
 EXTRA_CMAKE_OPTIONS=""
-[[ "x${sim_name}" == "xcarbon" ]] && EXTRA_CMAKE_OPTIONS="-DMECH=carbon"
-[[ "x${sim_name}" == "xHg"     ]] && EXTRA_CMAKE_OPTIONS="-DMECH=Hg -DFASTJX=y"
+[[ "x${sim_name}" == "xcarbon" ]] && EXTRA_CMAKE_OPTIONS="-DMECH=carbon "
+[[ "x${sim_name}" == "xHg"     ]] && EXTRA_CMAKE_OPTIONS="-DMECH=Hg -DFASTJX=y "
 if [[ "x${sim_name}" == "xfullchem" ]]; then
-    [[ "x${sim_extra_option}" == "xAPM"     ]] && EXTRA_CMAKE_OPTIONS="-DAPM=y"
-    [[ "x${sim_extra_option}" == "xRRTMG"   ]] && EXTRA_CMAKE_OPTIONS="-DRRTMG=y"
-    [[ "x${sim_extra_option}" == "xTOMAS15" ]] && EXTRA_CMAKE_OPTIONS="-DTOMAS=y -DTOMAS_BINS=15"
-    [[ "x${sim_extra_option}" == "xTOMAS40" ]] && EXTRA_CMAKE_OPTIONS="-DTOMAS=y -DTOMAS_BINS=40"
+    [[ "x${sim_extra_option}" == "xAPM"     ]] && EXTRA_CMAKE_OPTIONS="-DAPM=y "
+    [[ "x${sim_extra_option}" == "xRRTMG"   ]] && EXTRA_CMAKE_OPTIONS="-DRRTMG=y "
+    [[ "x${sim_extra_option}" == "xTOMAS15" ]] && EXTRA_CMAKE_OPTIONS="-DTOMAS=y -DTOMAS_BINS=15 "
+    [[ "x${sim_extra_option}" == "xTOMAS40" ]] && EXTRA_CMAKE_OPTIONS="-DTOMAS=y -DTOMAS_BINS=40 "
 fi
+[[ "x${enable_kppsa}" == "xy" ]] && EXTRA_CMAKE_OPTIONS+="-DKPPSA=y"
 
 # Add to RUNDIR_VARS
 RUNDIR_VARS+="EXTRA_CMAKE_OPTIONS=${EXTRA_CMAKE_OPTIONS}"

run/GCClassic/runScriptSamples/operational_examples/msu_orion/README

@@ -0,0 +1,4 @@
+Contact:
+Lizzie Lundgren
+GEOS-Chem Support Team at Harvard University
+geos-chem-support@g.harvard.edu

run/GCClassic/runScriptSamples/operational_examples/msu_orion/gcclassic.carbon.build

@@ -0,0 +1,15 @@
+#!/bin/bash
+
+# For MSU Orion cluster
+#SBATCH --time 00:05:00
+#SBATCH --nodes=1 --ntasks-per-node=12
+#SBATCH --mem 3G
+#SBATCH --job-name=gcclassic.build
+
+# Assumes file or symbolic link gcclassic.env is in run directory
+source gcclassic.env
+cd build
+cmake ../CodeDir -DRUNDIR=.. -DMECH=carbon
+make -j
+make install
+cd ..

run/GCClassic/runScriptSamples/operational_examples/msu_orion/gcclassic.intel-2022.2.1.env

@@ -0,0 +1,50 @@
+
+# Environment file to load before building and running GEOS-Chem Classic
+# on the MSU Orion cluster
+# - Lizzie Lundgren, GEOS-Chem Support Team, 27Jan2025
+
+module purge
+
+# Modules need to build and run GEOS-Chem Classic
+module load intel-oneapi-compilers/2022.2.1
+module load intel-oneapi-mpi/2021.7.1
+module load hdf5/1.12.2
+module load netcdf-c/4.9.0
+module load netcdf-fortran/4.6.0
+
+## Other potentially useful modules for analyses and code development
+#module load intel-oneapi-mkl/2022.2.1
+#module load hdf4/4.2.16
+#module load r/4.2.2
+#module load nco/5.0.1
+#module load udunits/2.2.28
+#module load zlib/1.2.13
+#module load nco/5.0.1
+#module load libszip/2.1.1
+#module load ffmpeg/4.4.1
+#module load ncl/6.6.2
+#module load gdal/3.5.3
+#module load gmt/6.2.0
+#module load ghostscript/9.56.1
+#module load imagemagick/7.0.8-7
+#module load contrib noaatools
+#module load python/3.10.8
+#module load ncview
+
+# Environment variables and settings needed for GEOS-Chem Classic
+export CC=icx
+export CXX=icx
+export FC=ifort
+export F77=${FC}
+if [[ "x${NETCDF_HOME}" == "x" ]]; then
+   export NETCDF_HOME="${NETCDF_C_HOME}"
+fi
+export NETCDF_C_ROOT="${NETCDF_HOME}"
+export NETCDF_FORTRAN_ROOT="${NETCDF_FORTRAN_HOME}"
+
+# Require memory settings
+ulimit -c unlimited   # coredumpsize
+ulimit -u 50000       # maxproc
+ulimit -v unlimited   # vmemoryuse
+ulimit -s unlimited   # stacksize
+export OMP_STACKSIZE=500m

run/GCClassic/runScriptSamples/operational_examples/msu_orion/gcclassic.run

@@ -0,0 +1,32 @@
+#!/bin/bash
+
+#SBATCH -c 24
+#SBATCH -N 1
+#SBATCH -t 0-00:30
+#SBATCH --mem=15G
+#SBATCH --qos=batch
+
+###############################################################################
+### Sample GEOS-Chem Classic run script for Harvard Cannon (using SLURM).
+###
+### If you are running a nested-grid simulation at fine resolution, you
+### will likely need to request additional memory, cores, and time.
+###
+### -c           : Requests this many cores
+### -N           : Requests a single node
+### --mem        : Requests this amount of memory in GB
+### -p           : Requests these partitions where the job can run
+### -t           : Requests time for the job (days-hours:minutes)
+###  --exclusive : Reserves entire nodes (i.e. to prevent backfilling jobs)
+###############################################################################
+
+# Set the proper # of threads for OpenMP
+# SLURM_CPUS_PER_TASK ensures this matches the number you set with -c above
+export OMP_NUM_THREADS=$SLURM_CPUS_PER_TASK
+
+# Run GEOS_Chem
+./gcclassic >> GC.log
+
+# Exit normally
+exit 0
+

run/GCClassic/runScriptSamples/operational_examples/nasa_discover/README

@@ -1,3 +1,4 @@
 Contact:
+Lizzie Lundgren
 GEOS-Chem Support Team at Harvard University
 geos-chem-support@g.harvard.edu

run/GCClassic/runScriptSamples/operational_examples/nasa_discover/gcclassic.build

@@ -0,0 +1,17 @@
+#!/bin/bash
+
+# For discover
+#SBATCH --time 00:05:00
+#SBATCH --nodes=1 --ntasks-per-node=12
+#SBATCH --mem 3G
+#SBATCH --job-name=gcclassic.build
+#SBATCH --constraint=mil
+#SBATCH --account=s____
+
+# Assumes file or symbolic link gcclassic.env is in run directory
+source gcclassic.env
+cd build
+cmake ../CodeDir -DRUNDIR=..
+make -j
+make install
+cd ..

run/GCClassic/runScriptSamples/operational_examples/nasa_discover/gcclassic.run

@@ -0,0 +1,17 @@
+#!/bin/bash
+
+# For use on NASA discover cluster. Edit prior to run.
+#SBATCH --time 00:10:00
+#SBATCH --nodes=1 --ntasks-per-node=24
+#SBATCH --mem 10G
+#SBATCH --job-name=gcclassic.run
+#SBATCH --constraint=mil
+#SBATCH --account=s____
+##SBATCH --exclusive
+##SBATCH --qos=debug
+##SBATCH --qos=long
+
+
+# Assume file or symbolic link gcclassic.env exists in run directory
+source gcclassic.env
+./gcclassic > GC.log