Replace runScriptSamples directory with symlink to source in GCHP rundir

The runScriptSamples directory is stored in the source code and no
modifications are made when copying to the run directory. It is therefore
more efficient to point to the directory in the source code rather than
copy all the example files.

This update also removes a residual symbolic link created for gFTL in
GCHP run directories that is no longer needed.

Signed-off-by: Lizzie Lundgren <elundgren@seas.harvard.edu>

run/GCHPctm/createRunDir.sh

@@ -223,7 +223,7 @@ while [ "$valid_path" -eq 0 ]; do
 done
 
 #-----------------------------------------------------------------
-# Ask user to define run directoy name if not passed as argument
+# Ask user to define run directory name if not passed as argument
 #-----------------------------------------------------------------
 if [ -z "$1" ]; then
     printf "${thinline}Enter run directory name, or press return to use default:${thinline}"
@@ -285,16 +285,13 @@ if [[ ${sim_name} = "fullchem" ]]; then
     cp -r ${gcdir}/run/shared/metrics.py  ${rundir}
     chmod 744 ${rundir}/metrics.py
 fi
-cp -r ./runScriptSamples              ${rundir}
 mkdir ${rundir}/OutputDir
 
 # Set permissions
 chmod 744 ${rundir}/setEnvironment.sh
 chmod 744 ${rundir}/cleanRunDir.sh
 chmod 744 ${rundir}/runConfig.sh
 chmod 744 ${rundir}/archiveRun.sh
-chmod 744 ${rundir}/runScriptSamples/*
-chmod 644 ${rundir}/runScriptSamples/README
 
 # Copy species database; append APM or TOMAS species if needed
 cp -r ${gcdir}/run/shared/species_database.yml   ${rundir}
@@ -306,15 +303,15 @@ fi
 
 # If benchmark simulation, put run script in directory
 if [[ ${sim_extra_option} = "benchmark" ]]; then
-    cp ./runScriptSamples/gchp.benchmark.run ${rundir}
+    cp ${gcdir}/run/GCHPctm/runScriptSamples/gchp.benchmark.run ${rundir}
     chmod 744 ${rundir}/gchp.benchmark.run
 fi
 
-# Create symbolic links to data directories, restart files, and code
+# Create symbolic links to data directories, restart files, code, run scripts
 ln -s ${gchpdir}                                ${rundir}/CodeDir
+ln -s ${gcdir}/run/GCHPctm/runScriptSamples     ${rundir}/runScriptSamples
 ln -s ${GC_DATA_ROOT}/CHEM_INPUTS               ${rundir}/ChemDir
 ln -s ${GC_DATA_ROOT}/HEMCO                     ${rundir}/HcoDir
-ln -s ${GFTL}                                   ${rundir}/gFTL
 if [ "${met_name}" == "GEOSFP" ]; then
    ln -s ${GC_DATA_ROOT}/GEOS_0.25x0.3125/GEOS_FP  ${rundir}/MetDir
 else
@@ -480,10 +477,10 @@ while [ "$valid_response" -eq 0 ]; do
 	printf "\n"
 	git init
 	git add *.rc *.sh *.yml *.run input.geos input.nml
-        if [[ ${sim_name} = "fullchem" ]]; then
+	if [[ ${sim_name} = "fullchem" ]]; then
             git add *.py
-        fi
-	git add runScriptSamples/* README .gitignore
+	fi
+	git add README .gitignore
 	printf " " >> ${version_log}
 	git commit -m "Initial run directory" >> ${version_log}
 	cd ${srcrundir}