NOAA-GFDL · adcroft · Mar 2, 2016 · Feb 12, 2016 · Feb 18, 2016 · Feb 18, 2016
diff --git a/ice_ocean_SIS2/OM4_025/ocn_annual.frepp b/ice_ocean_SIS2/OM4_025/ocn_annual.frepp
@@ -110,6 +110,9 @@ set mosaicDir=/archive/gold/datasets/OM4_025/mosaic.v20140610.unpacked
 
 echo The following command is going to be invoked
 
+mkdir -p $out_dir/ocean_${yr1}-${yr2}/heat_transport
+$script_dir/poleward_heat_transport.py -g $mosaicDir -o $out_dir/ocean_${yr1}-${yr2}/heat_transport -l ${yr1}-${yr2} $in_data_dir/ocean_annual.$yr1-$yr2.ann.nc
+
 mkdir -p $out_dir/ocean_${yr1}-${yr2}/heat_salt_0_300m
 $script_dir/TS_depth_integrals.py -r $woa05 -s 0 -e 300 -g $mosaicDir -o $out_dir/ocean_${yr1}-${yr2}/heat_salt_0_300m -l ${yr1}-${yr2} $in_data_dir/ocean_annual.$yr1-$yr2.ann.nc
 \rm -f $out_dir/ocean_${yr1}-${yr2}/heat_salt_0_300m/*_heat_salt_0_300.nc # Clean up large nc files
diff --git a/ice_ocean_SIS2/OM4_05/ocn_annual.frepp b/ice_ocean_SIS2/OM4_05/ocn_annual.frepp
@@ -0,0 +1,118 @@
+#!/bin/csh -fx
+#------------------------------------
+#PBS -N ocean_ts_annual
+#PBS -l size=1
+#PBS -l walltime=04:00:00
+#PBS -r y
+#PBS -j oe
+#PBS -o
+#PBS -q batch 
+#----------------------------------
+
+echo $0 $*
+
+# ============== VARIABLES SET BY FREPP =============
+# original arguments passed to this script when it was created by frepp
+set argu
+# experiment name (as appears in output directory names)
+set descriptor  
+# path to NetCDF files postprocessed by frepp, as specified in XML
+set in_data_dir 
+# input data file[s], without any path prefix;
+# currently only used by timeAverage diagnostics
+set in_data_file
+# final output directory for diagnostics generated by this script
+set out_dir
+# working directory -- do whatever you want in here
+# we may have to create this (use "mkdir -p" to be sure)
+# and then clean up at end
+set WORKDIR    
+# a string to indicate the mode: "batch" or "interactive"
+set mode       
+# actual start/end years of diagnostics (start_year & end_year in XML)
+set yr1
+set yr2 
+# alternate way to specify a single year (instead of yr1==yr2)
+set specify_year
+# Data years, only used in scripts using time series as input, to
+# generate a Ferret descriptor file from consecutive NetCDF chunks.
+# start year of first chunk
+set databegyr   
+# end year of last chunk
+set dataendyr   
+# chunk length (an integer number), as specified in XML
+set datachunk   
+# atmospheric land mask file
+set staticfile
+set script_path
+set fremodule
+# a string: "monthly" or "annual" for timeseries data
+set freq
+# first year of integration (4-digits, e.g. the year of initial condition)
+set MODEL_start_yr
+# Specify MOM version; "om2" or "om3" because some files depend on mom's grid
+set mom_version
+# full path to the grid specification file, which contains the land/sea mask
+set gridspecfile
+# history directory where the original "*.nc.cpio" files are found
+set hist_dir
+set nlon
+set nlat
+set frexml
+set freanalysismodule
+set stdoutdir
+set analysis_options
+set platform
+set target
+# ============== END OF VARIABLES SET BY FREPP =============
+# Invoke script with arguments tcsh ocn_annual.frepp in_data_dir yr1 yr2 out_dir 
+if ($#argv == "4") then
+  if ($in_data_dir == "") set in_data_dir = $1
+  if ($yr1 == "") set yr1 = $2
+  if ($yr2 == "") set yr2 = $3
+  if ($out_dir == "") set out_dir = $4
+endif
+
+#set freanalysismodule = fre-analysis/test
+
+# make sure valid platform and required modules are loaded
+if (`gfdl_platform` == "hpcs-csc") then
+   source $MODULESHOME/init/csh
+   module use -a /home/fms/local/modulefiles #/usr/local/paida/Modules
+   module purge
+#   module load $fremodule
+#   module load $freanalysismodule
+#   module load gcc
+   module load netcdf/4.2
+   module load python/2.7.3
+   module load intel_compilers
+   module load git
+else
+   echo "ERROR: invalid platform"
+   #exit 1
+endif
+
+# check again?
+#if (! $?FRE_ANALYSIS_HOME) then
+#   echo "ERROR: environment variable FRE_ANALYSIS_HOME not set."
+#   exit 1
+#endif
+
+# Build MIDAS libs and set PYTHONPATH
+(cd ${out_dir}/mom6/tools/python ; make frepp_local )
+setenv PYTHONPATH ${out_dir}/mom6/tools/python/local/lib/python
+
+# Run script
+set src_dir = ${out_dir}/mom6/tools/analysis
+set script_dir = ${out_dir}/mom6/tools/analysis
+set woa05=/archive/gold/datasets/OM4_05/obs/WOA05_ptemp_salt_annual.v2015.12.03.nc
+set mosaicDir=/archive/gold/datasets/OM4_05/mosaic.v20151203.unpacked
+
+echo The following command is going to be invoked
+
+mkdir -p $out_dir/ocean_${yr1}-${yr2}/heat_transport
+$script_dir/poleward_heat_transport.py -g $mosaicDir -o $out_dir/ocean_${yr1}-${yr2}/heat_transport -l ${yr1}-${yr2} $in_data_dir/ocean_annual.$yr1-$yr2.ann.nc
+
+mkdir -p $out_dir/ocean_${yr1}-${yr2}/heat_salt_0_300m
+$script_dir/TS_depth_integrals.py -r $woa05 -s 0 -e 300 -g $mosaicDir -o $out_dir/ocean_${yr1}-${yr2}/heat_salt_0_300m -l ${yr1}-${yr2} $in_data_dir/ocean_annual.$yr1-$yr2.ann.nc
+\rm -f $out_dir/ocean_${yr1}-${yr2}/heat_salt_0_300m/*_heat_salt_0_300.nc # Clean up large nc files
diff --git a/ice_ocean_SIS2/OM4_05/ocn_annual_z.frepp b/ice_ocean_SIS2/OM4_05/ocn_annual_z.frepp
@@ -0,0 +1,125 @@
+#!/bin/csh -fx
+#------------------------------------
+#PBS -N ocean_ts_annual
+#PBS -l size=1
+#PBS -l walltime=04:00:00
+#PBS -r y
+#PBS -j oe
+#PBS -o
+#PBS -q batch 
+#----------------------------------
+
+echo $0 $*
+
+# ============== VARIABLES SET BY FREPP =============
+# original arguments passed to this script when it was created by frepp
+set argu
+# experiment name (as appears in output directory names)
+set descriptor  
+# path to NetCDF files postprocessed by frepp, as specified in XML
+set in_data_dir 
+# input data file[s], without any path prefix;
+# currently only used by timeAverage diagnostics
+set in_data_file
+# final output directory for diagnostics generated by this script
+set out_dir
+# working directory -- do whatever you want in here
+# we may have to create this (use "mkdir -p" to be sure)
+# and then clean up at end
+set WORKDIR    
+# a string to indicate the mode: "batch" or "interactive"
+set mode       
+# actual start/end years of diagnostics (start_year & end_year in XML)
+set yr1
+set yr2 
+# alternate way to specify a single year (instead of yr1==yr2)
+set specify_year
+# Data years, only used in scripts using time series as input, to
+# generate a Ferret descriptor file from consecutive NetCDF chunks.
+# start year of first chunk
+set databegyr   
+# end year of last chunk
+set dataendyr   
+# chunk length (an integer number), as specified in XML
+set datachunk   
+# atmospheric land mask file
+set staticfile
+set script_path
+set fremodule
+# a string: "monthly" or "annual" for timeseries data
+set freq
+# first year of integration (4-digits, e.g. the year of initial condition)
+set MODEL_start_yr
+# Specify MOM version; "om2" or "om3" because some files depend on mom's grid
+set mom_version
+# full path to the grid specification file, which contains the land/sea mask
+set gridspecfile
+# history directory where the original "*.nc.cpio" files are found
+set hist_dir
+set nlon
+set nlat
+set frexml
+set freanalysismodule
+set stdoutdir
+set analysis_options
+set platform
+set target
+# ============== END OF VARIABLES SET BY FREPP =============
+# Invoke script with arguments tcsh ocn_annual_z.frepp in_data_dir yr1 yr2 out_dir 
+if ($#argv == "4") then
+  if ($in_data_dir == "") set in_data_dir = $1
+  if ($yr1 == "") set yr1 = $2
+  if ($yr2 == "") set yr2 = $3
+  if ($out_dir == "") set out_dir = $4
+endif
+
+#set freanalysismodule = fre-analysis/test
+
+# make sure valid platform and required modules are loaded
+if (`gfdl_platform` == "hpcs-csc") then
+   source $MODULESHOME/init/csh
+   module use -a /home/fms/local/modulefiles
+   module purge
+   module load $fremodule
+   module load $freanalysismodule
+   module load gcc
+   module load netcdf/4.2
+   module load python/2.7.3
+else
+   echo "ERROR: invalid platform"
+   #exit 1
+endif
+
+# check again?
+if (! $?FRE_ANALYSIS_HOME) then
+   echo "ERROR: environment variable FRE_ANALYSIS_HOME not set."
+   #exit 1
+endif
+
+# Run script
+set src_dir = ${out_dir}/mom6/tools/analysis
+set script_dir = ${out_dir}/mom6/tools/analysis
+set woa05=/archive/gold/datasets/OM4_05/obs/WOA05_ptemp_salt_annual.v2015.12.03.nc
+set mosaicDir=/archive/gold/datasets/OM4_05/mosaic.v20151203.unpacked
+
+echo The following command is going to be invoked
+
+mkdir -p $out_dir/ocean_${yr1}-${yr2}/ptemp
+$script_dir/SST_bias_WOA05.py -w $woa05 -g $mosaicDir -o $out_dir/ocean_${yr1}-${yr2}/ptemp -l ${yr1}-${yr2} $in_data_dir/ocean_annual_z.$yr1-$yr2.ann.nc
+$script_dir/zonal_T_bias_WOA05.py -w $woa05 -g $mosaicDir -o $out_dir/ocean_${yr1}-${yr2}/ptemp -l ${yr1}-${yr2} $in_data_dir/ocean_annual_z.$yr1-$yr2.ann.nc
+$script_dir/depth_average_T_bias.py -w $woa05 -g $mosaicDir -zb 100 -o $out_dir/ocean_${yr1}-${yr2}/ptemp -l ${yr1}-${yr2} $in_data_dir/ocean_annual_z.$yr1-$yr2.ann.nc
+$script_dir/depth_average_T_bias.py -w $woa05 -g $mosaicDir -zb 300 -o $out_dir/ocean_${yr1}-${yr2}/ptemp -l ${yr1}-${yr2} $in_data_dir/ocean_annual_z.$yr1-$yr2.ann.nc
+$script_dir/depth_average_T_bias.py -w $woa05 -g $mosaicDir -zb 700 -o $out_dir/ocean_${yr1}-${yr2}/ptemp -l ${yr1}-${yr2} $in_data_dir/ocean_annual_z.$yr1-$yr2.ann.nc
+$script_dir/depth_average_T_bias.py -w $woa05 -g $mosaicDir -zb 2000 -o $out_dir/ocean_${yr1}-${yr2}/ptemp -l ${yr1}-${yr2} $in_data_dir/ocean_annual_z.$yr1-$yr2.ann.nc
+$script_dir/depth_average_T_bias.py -w $woa05 -g $mosaicDir -zt 2000 -zb 4000 -o $out_dir/ocean_${yr1}-${yr2}/ptemp -l ${yr1}-${yr2} $in_data_dir/ocean_annual_z.$yr1-$yr2.ann.nc
+$script_dir/depth_average_T_bias.py -w $woa05 -g $mosaicDir -zb 6500 -o $out_dir/ocean_${yr1}-${yr2}/ptemp -l ${yr1}-${yr2} $in_data_dir/ocean_annual_z.$yr1-$yr2.ann.nc
+
+mkdir -p $out_dir/ocean_${yr1}-${yr2}/salinity
+$script_dir/SSS_bias_WOA05.py -w $woa05 -g $mosaicDir -o $out_dir/ocean_${yr1}-${yr2}/salinity -l ${yr1}-${yr2} $in_data_dir/ocean_annual_z.$yr1-$yr2.ann.nc
+$script_dir/zonal_S_bias_WOA05.py -w $woa05 -g $mosaicDir -o $out_dir/ocean_${yr1}-${yr2}/salinity -l ${yr1}-${yr2} $in_data_dir/ocean_annual_z.$yr1-$yr2.ann.nc
+
+mkdir -p $out_dir/ocean_${yr1}-${yr2}/sections
+$script_dir/vertical_sections_annual_bias_WOA05.py -g $mosaicDir -o $out_dir/ocean_${yr1}-${yr2}/sections -w $woa05 -l ${yr1}-${yr2} $in_data_dir/ocean_annual_z.$yr1-$yr2.ann.nc
+
+mkdir -p $out_dir/ocean_${yr1}-${yr2}/MOC
+$script_dir/meridional_overturning.py -g $mosaicDir -o $out_dir/ocean_${yr1}-${yr2}/MOC -l ${yr1}-${yr2} $in_data_dir/ocean_annual_z.$yr1-$yr2.ann.nc
diff --git a/ice_ocean_SIS2/OM4_05/ocn_monthly.frepp b/ice_ocean_SIS2/OM4_05/ocn_monthly.frepp
@@ -0,0 +1,106 @@
+#!/bin/csh -fx
+#------------------------------------
+#PBS -N ocean_ts_annual
+#PBS -l size=1
+#PBS -l walltime=04:00:00
+#PBS -r y
+#PBS -j oe
+#PBS -o
+#PBS -q batch 
+#----------------------------------
+
+echo $0 $*
+
+# ============== VARIABLES SET BY FREPP =============
+# original arguments passed to this script when it was created by frepp
+set argu
+# experiment name (as appears in output directory names)
+set descriptor  
+# path to NetCDF files postprocessed by frepp, as specified in XML
+set in_data_dir 
+# input data file[s], without any path prefix;
+# currently only used by timeAverage diagnostics
+set in_data_file
+# final output directory for diagnostics generated by this script
+set out_dir
+# working directory -- do whatever you want in here
+# we may have to create this (use "mkdir -p" to be sure)
+# and then clean up at end
+set WORKDIR    
+# a string to indicate the mode: "batch" or "interactive"
+set mode       
+# actual start/end years of diagnostics (start_year & end_year in XML)
+set yr1
+set yr2 
+# alternate way to specify a single year (instead of yr1==yr2)
+set specify_year
+# Data years, only used in scripts using time series as input, to
+# generate a Ferret descriptor file from consecutive NetCDF chunks.
+# start year of first chunk
+set databegyr   
+# end year of last chunk
+set dataendyr   
+# chunk length (an integer number), as specified in XML
+set datachunk   
+# atmospheric land mask file
+set staticfile
+set script_path
+set fremodule
+# a string: "monthly" or "annual" for timeseries data
+set freq
+# first year of integration (4-digits, e.g. the year of initial condition)
+set MODEL_start_yr
+# Specify MOM version; "om2" or "om3" because some files depend on mom's grid
+set mom_version
+# full path to the grid specification file, which contains the land/sea mask
+set gridspecfile
+# history directory where the original "*.nc.cpio" files are found
+set hist_dir
+set nlon
+set nlat
+set frexml
+set freanalysismodule
+set stdoutdir
+set analysis_options
+set platform
+set target
+# ============== END OF VARIABLES SET BY FREPP =============
+# Invoke script with arguments tcsh ocn_monthly.frepp in_data_dir yr1 yr2 out_dir
+if ($#argv == "4") then
+  if ($in_data_dir == "") set in_data_dir = $1
+  if ($yr1 == "") set yr1 = $2
+  if ($yr2 == "") set yr2 = $3
+  if ($out_dir == "") set out_dir = $4
+endif
+
+#set freanalysismodule = fre-analysis/test
+
+# make sure valid platform and required modules are loaded
+if (`gfdl_platform` == "hpcs-csc") then
+   source $MODULESHOME/init/csh
+   module use -a /home/fms/local/modulefiles
+   module purge
+   module load $fremodule
+   module load $freanalysismodule
+   module load gcc
+   module load netcdf/4.2
+   module load python/2.7.3
+else
+   echo "ERROR: invalid platform"
+   #exit 1
+endif
+
+# check again?
+if (! $?FRE_ANALYSIS_HOME) then
+   echo "ERROR: environment variable FRE_ANALYSIS_HOME not set."
+   #exit 1
+endif
+
+# Run script
+set script_dir = ${out_dir}/mom6/tools/analysis
+set mosaicDir=/archive/gold/datasets/OM4_05/mosaic.v20151203.unpacked
+
+echo The following command is going to be invoked
+
+mkdir -p $out_dir/ocean_${yr1}-${yr2}/Hosoda_MLD
+$script_dir/MLD_003.py -g $mosaicDir -o $out_dir/ocean_${yr1}-${yr2}/Hosoda_MLD -l ${yr1}-${yr2} $in_data_dir/ocean_monthly.${yr1}01-${yr2}12.MLD_003.nc
diff --git a/src/MOM6 b/src/MOM6
diff --git a/src/SIS2 b/src/SIS2