esm-tools · mandresm · Apr 30, 2024 · Apr 30, 2024 · Apr 30, 2024 · Apr 30, 2024
diff --git a/configs/components/pism/pism.recipes.yaml b/configs/components/pism/pism.recipes.yaml
@@ -15,6 +15,7 @@ prepcompute_recipe:
 
         - "assemble"
         - "log_used_files"
+        - "wait_for_iterative_coupling"
         - "_write_finalized_config"
           #- "assemble_filelists"
         #- "copy_tools_to_thisrun"

diff --git a/couplings/fesom/coupling_fesom2ice.functions b/couplings/fesom/coupling_fesom2ice.functions
@@ -563,6 +563,8 @@ function fesom_ice_concatenate_files {
         echo ""; echo " *   concatenating files"
 	# New cdo versions sometimes do not allow to overwrite files for
 	# "collective" commands. Hence delete existing old output file
+    [[ -f temp.tmp.nc ]] && rm temp.tmp.nc
+    [[ -f salt.tmp.nc ]] && rm salt.tmp.nc
 	[[ -f ocean_file_for_ice.nc ]] && rm ocean_file_for_ice.nc
 	${cdo} -s ensmean ${processed_fesom1x_file3D_T_list_for_ice} temp.tmp.nc
 	${cdo} -s ensmean ${processed_fesom1x_file3D_S_list_for_ice} salt.tmp.nc
@@ -573,7 +575,6 @@ function fesom_ice_concatenate_files {
 	#    ${processed_fesom1x_file2D_list_for_ice} \
 	#    ${processed_fesom1x_file2Dstatic_list_for_ice} \
 	#    ocean_file_for_ice.nc
-
 	_flag_extract_depth=1
 	# Extract depth axis and Clean up temporary files
 	for file in \

diff --git a/couplings/fesom/coupling_ice2fesom.functions b/couplings/fesom/coupling_ice2fesom.functions
@@ -8,10 +8,10 @@ function ice2fesom {
     . ${FUNCTION_PATH}/../pism/coupling_ocean2pism.functions
 
     echo "ICE_TO_FESOM=${ICE_TO_FESOM:-0}"
-    if [[ "x$ICE_TO_FESOM" == "x0" ]]; then
+    if [[ "x$ICE_TO_FESOM"=="x0" ]]; then
         echo " NOT generating ice forcing for ocean model"
-	echo "   since ICE_TO_FESOM=${ICE_TO_FESOM}"
-	return
+	    echo " since ICE_TO_FESOM=${ICE_TO_FESOM}"
+	    return
     else
         echo " Only generating iceberg forcing so far ..."
         iterative_coupling_pism_ocean_prepare_ocean_icebergmodel_forcing
@@ -230,41 +230,9 @@ function iterative_coupling_pism_ocean_prepare_ocean_icebergmodel_forcing {
     cdo -s -timmean -selname,tendency_of_ice_amount_due_to_discharge \
             -setgrid,${COUPLE_DIR}/ice.griddes ${pism_discharge_file} ${COUPLE_DIR}/latest_discharge.nc
 
-    #module unload python
-    #if [ "$MACHINE" == "ollie" ]; then
-    #    module load python3/3.7.7_intel2020u2
-    #elif [ "$MACHINE" == "mistral" ]; then
-    #    module load anaconda3/bleeding_edge
-    #fi
-    #if [ -f ${COUPLE_DIR}/num_non_melted_icb_file ]; then
-    #    rm ${COUPLE_DIR}/num_non_melted_icb_file
-    #fi
-
-    #if [[ "xMESH_ROTATED_fesom"=="x1" ]]; then
-    #    if [[ ! -f ${COUPLE_DIR}/nod2d.out.rot ]]; then
-    #        python ${FUNCTION_PATH}/../utils/rotate_mesh.py ${MESH_DIR_fesom} ${COUPLE_DIR}
-    #        cp ${MESH_DIR_fesom}/elem2d.out ${COUPLE_DIR}/elem2d.out
-    #    fi
-    #    python ${FUNCTION_PATH}/../utils/icb_apply_distribution.py ${COUPLE_DIR}/latest_discharge.nc ${COUPLE_DIR} ${COUPLE_DIR} ${BASIN_FILE}
-    #else
-    #    python ${FUNCTION_PATH}/../utils/icb_apply_distribution.py ${COUPLE_DIR}/latest_discharge.nc ${MESH_DIR_fesom} ${COUPLE_DIR} ${BASIN_FILE}
-    #fi
-
-    #echo; echo "    * Finished iceberg generation"
-    #if [ -f ${COUPLE_DIR}/../restart/fesom/iceberg.restart.ISM ]; then
-    #    wc -l ${COUPLE_DIR}/../restart/fesom/iceberg.restart.ISM | awk '{ print $1 }' > ${COUPLE_DIR}/num_non_melted_icb_file
-    #fi
     use_icesheet_coupling=1
 }
 
-#function get_ib_num_after_ice_sheet_coupling {
-#    _a="$( wc -l icb/LON.dat | awk '{ print $1 }' )"
-#    _b="$( cat ../icb/num_non_melted_icb_file )"
-#
-#    ib_num=$(( $_a + $_b ))
-#    general_replace_namelist_value namelist.config icebergs ib_num $ib_num
-#    general_replace_namelist_value namelist.config icebergs use_icesheet_coupling ".true."
-#}
 ############################################################################
 ############################################################################
 

diff --git a/couplings/fesom/env_fesom.py b/couplings/fesom/env_fesom.py
@@ -15,7 +15,7 @@ def prepare_environment(config):
             "EXP_ID": config["general"]["command_line_config"]["expid"],
             "iter_coup_regrid_method_ice2oce": "INTERPOLATE",
             "fesom_use_icebergs": config["fesom"].get("use_icebergs", ""), 
-            "BASIN_FILE": config["fesom"].get("basin_file"),
+            #"BASIN_FILE": config["fesom"].get("basin_file"),
             "MACHINE": config["computer"]["name"],
             "ICEBERG_DIR": config["fesom"].get("iceberg_dir", ""),
 

diff --git a/couplings/pism/coupling_atmosphere2pism.functions b/couplings/pism/coupling_atmosphere2pism.functions
@@ -1556,7 +1556,7 @@ ic_atm2debm_ablation_debm_run_modify_nml() {
         TMP=$( grep cobld $( ls -t ${COUPLE_DIR}/../run_*/work/namelist.echam | head -1 ) | sed 's/^[ \t]*//' )
         prefix="cobld = "
         MY_OBLIQUITY=${TMP#"$prefix"}
-        obliquity_value=${MY_OBLIQUITY:-"23.17"}
+        obliquity_value=${MY_OBLIQUITY:-"23.441"}
 
         echo -e "\t\t- Generating namelist for dEBM Mass Balance Model" 
         echo -e "\t\t- Obliquity = ${obliquity_value}"

diff --git a/couplings/pism/coupling_pism2atmosphere.functions b/couplings/pism/coupling_pism2atmosphere.functions
@@ -60,10 +60,10 @@ function pism_atmosphere_get_newest_output {
 
         # Define list of variables selected from PISM output depending on whether icebergs are used or not
         if [ "x${fesom_use_iceberg}" == "x1" ]; then
-            echo "LA DEBUG: 1"
+            echo " * use iceberg coupling and exclude iceberg discharge from mass balance"
             CDO_SELECT_VAR_LIST="thk,climatic_mass_balance,topg,${OROG_VARNAME_pism},${GLACIAL_MASK_VARNAME_pism},tendency_of_ice_amount,tendency_of_ice_amount_due_to_conservation_error,tendency_of_ice_amount_due_to_surface_mass_flux,tendency_of_ice_amount_due_to_basal_mass_flux,tendency_of_ice_amount_due_to_discharge,tendency_of_ice_amount_due_to_flow"
         else 
-            echo "LA DEBUG: 2"
+            echo " * no iceberg coupling"
             CDO_SELECT_VAR_LIST="thk,climatic_mass_balance,topg,${OROG_VARNAME_pism},${GLACIAL_MASK_VARNAME_pism},tendency_of_ice_amount"
         fi 
 

diff --git a/couplings/utils/fesom_scalar_array_to_LonLat.py b/couplings/utils/fesom_scalar_array_to_LonLat.py
@@ -85,7 +85,7 @@ def parse_arguments():
 #
 #print('* Read the data file args.FESOM_FILE=' + " ".join(args.FESOM_FILE))
 #FID = MFDataset(args.FESOM_PATH + "".join("/temp.fesom.*.01.nc"))
-FID = xr.open_dataset(str(args.FESOM_PATH[0]) + str(args.FESOM_VARIABLE[0]) + ".fesom." + str(args.FESOM_YEARS[0]) + ".nc")
+FID = xr.open_dataset(str(args.FESOM_PATH[0]) + str(args.FESOM_VARIABLE[0]) + ".fesom." + str(args.FESOM_YEARS[0]) + ".nc", decode_times=False)
 
 # ----------------------------------------------------------------
 #
@@ -164,7 +164,7 @@ def parse_arguments():
         #
         # Prepare data for final netcdf output
         #
-        #ilevel = ilevel + 1
+        ilevel = ilevel + 1
 
         flag_verbose=False
 
@@ -173,7 +173,7 @@ def parse_arguments():
             pf.get_data(args.FESOM_PATH[0], args.FESOM_VARIABLE[0], int(args.FESOM_YEARS[0]), mesh, depth=idepth, how="mean") #, flag_verbose)
         else:
             level_data = \
-            pf.get_data(args.FESOM_PATH[0], args.FESOM_VARIABLE[0], [int(args.FESOM_YEARS[0]), int(args.FESOM_YEARS[1])], mesh, depth=idepth, how="mean") #, flag_verbose)
+            pf.get_data(args.FESOM_PATH[0], args.FESOM_VARIABLE[0], [int(args.FESOM_YEARS[0]), int(args.FESOM_YEARS[1])], mesh, depth=idepth, how="mean", use_cftime=True) #, flag_verbose)
         level_data[np.where(np.isnan(level_data))] = NAN_REPLACE
         TempFields_out[itime, ilevel, :] = level_data
 

diff --git a/setup.cfg b/setup.cfg
@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 6.29.4
+current_version = 6.29.5
 commit = True
 tag = True
 

diff --git a/setup.py b/setup.py
@@ -105,6 +105,6 @@
     test_suite="tests",
     tests_require=test_requirements,
     url="https://github.com/esm-tools/esm_tools",
-    version="6.29.4",
+    version="6.29.5",
     zip_safe=False,
 )
diff --git a/src/esm_archiving/__init__.py b/src/esm_archiving/__init__.py
@@ -4,7 +4,7 @@
 
 __author__ = """Paul Gierz"""
 __email__ = "[email protected]"
-__version__ = "6.29.4"
+__version__ = "6.29.5"
 
 from .esm_archiving import (archive_mistral, check_tar_lists,
                             delete_original_data, determine_datestamp_location,

diff --git a/src/esm_calendar/__init__.py b/src/esm_calendar/__init__.py
@@ -2,6 +2,6 @@
 
 __author__ = """Dirk Barbi"""
 __email__ = "[email protected]"
-__version__ = "6.29.4"
+__version__ = "6.29.5"
 
 from .esm_calendar import *
diff --git a/src/esm_cleanup/__init__.py b/src/esm_cleanup/__init__.py
@@ -2,4 +2,4 @@
 
 __author__ = """Dirk Barbi"""
 __email__ = "[email protected]"
-__version__ = "6.29.4"
+__version__ = "6.29.5"
diff --git a/src/esm_database/__init__.py b/src/esm_database/__init__.py
@@ -2,4 +2,4 @@
 
 __author__ = """Dirk Barbi"""
 __email__ = "[email protected]"
-__version__ = "6.29.4"
+__version__ = "6.29.5"
diff --git a/src/esm_environment/__init__.py b/src/esm_environment/__init__.py
@@ -2,6 +2,6 @@
 
 __author__ = """Dirk Barbi"""
 __email__ = "[email protected]"
-__version__ = "6.29.4"
+__version__ = "6.29.5"
 
 from .esm_environment import *
diff --git a/src/esm_master/__init__.py b/src/esm_master/__init__.py
@@ -2,7 +2,7 @@
 
 __author__ = """Dirk Barbi"""
 __email__ = "[email protected]"
-__version__ = "6.29.4"
+__version__ = "6.29.5"
 
 
 from . import database
diff --git a/src/esm_motd/__init__.py b/src/esm_motd/__init__.py
@@ -2,6 +2,6 @@
 
 __author__ = """Dirk Barbi"""
 __email__ = "[email protected]"
-__version__ = "6.29.4"
+__version__ = "6.29.5"
 
 from .esm_motd import *
diff --git a/src/esm_parser/__init__.py b/src/esm_parser/__init__.py
@@ -2,7 +2,7 @@
 
 __author__ = """Dirk Barbi"""
 __email__ = "[email protected]"
-__version__ = "6.29.4"
+__version__ = "6.29.5"
 
 
 from .esm_parser import *

diff --git a/src/esm_plugin_manager/__init__.py b/src/esm_plugin_manager/__init__.py
@@ -2,6 +2,6 @@
 
 __author__ = """Dirk Barbi, Paul Gierz, Sebastian Wahl"""
 __email__ = "[email protected]"
-__version__ = "6.29.4"
+__version__ = "6.29.5"
 
 from .esm_plugin_manager import *
diff --git a/src/esm_profile/__init__.py b/src/esm_profile/__init__.py
@@ -2,6 +2,6 @@
 
 __author__ = """Dirk Barbi"""
 __email__ = "[email protected]"
-__version__ = "6.29.4"
+__version__ = "6.29.5"
 
 from .esm_profile import *
diff --git a/src/esm_runscripts/__init__.py b/src/esm_runscripts/__init__.py
@@ -2,7 +2,7 @@
 
 __author__ = """Dirk Barbi"""
 __email__ = "[email protected]"
-__version__ = "6.29.4"
+__version__ = "6.29.5"
 
 from .batch_system import *
 from .chunky_parts import *

diff --git a/src/esm_tests/__init__.py b/src/esm_tests/__init__.py
@@ -2,7 +2,7 @@
 
 __author__ = """Miguel Andres-Martinez"""
 __email__ = "[email protected]"
-__version__ = "6.29.4"
+__version__ = "6.29.5"
 
 from .initialization import *
 from .read_shipped_data import *

diff --git a/src/esm_tools/__init__.py b/src/esm_tools/__init__.py
@@ -23,7 +23,7 @@
 
 __author__ = """Dirk Barbi, Paul Gierz"""
 __email__ = "[email protected]"
-__version__ = "6.29.4"
+__version__ = "6.29.5"
 
 import functools
 import inspect

diff --git a/src/esm_utilities/__init__.py b/src/esm_utilities/__init__.py
@@ -2,6 +2,6 @@
 
 __author__ = """Paul Gierz"""
 __email__ = "[email protected]"
-__version__ = "6.29.4"
+__version__ = "6.29.5"
 
 from .utils import *