Merge pull request arfc#100 from yardasol/fix-j312

Fix bugs in `process_j312.sh`

scripts/README.md

@@ -4,7 +4,8 @@ of your SaltProc simulations.
 
 ### `xsdata`
 The script in this directory downloads and processes the JEFF 
-3.1.2 cross section library for running the integration tests 
+3.1.2 cross section library -- as well as spontaneous and delayed fission neutron and
+decay data -- for running the integration tests 
 on a UNIX-like machine. Set the `DATADIR` variable inside 
 the script to the directory where you want to store the cross 
 section libraries.
@@ -18,5 +19,5 @@ which will download and process the libraries at all available temperatures.
 
 To run the script, execute
 ```
-source process_j312.sh
+source process_j312.bash
 ```

scripts/xsdata/process_j312.sh → scripts/xsdata/process_j312.bash

@@ -1,8 +1,10 @@
 ################
 ### DOWNLOAD ###
 ################
-#DATADIR is the directory where the xs library is extracted to
-DATADIR=$(pwd)
+# DATADIR is the directory where the xs library is extracted to
+# @yardasol reccomends naming the parent directory where the files
+# will be extractd to as "jeff312"
+DATADIR=$PWD/jeff312
 LN="https://www.oecd-nea.org/dbforms/data/eva/evatapes/jeff_31/JEFF312/ACE/"
 SLUG="ACEs_"
 EXT="K.zip"
@@ -17,29 +19,47 @@ TEMPS=(900)
 
 for T in ${TEMPS[@]}
 do
-    wget -P $DATADIR $LN$SLUG$T$EXT
+    if [[ ! -f $DATADIR/$SLUG$T$EXT ]]
+    then
+        wget -P $DATADIR $LN$SLUG$T$EXT
+    fi
 done
 
 # Get thermal XS
-wget -O $DATADIR/ACEs_THERMK.zip $LN$SLUG1
+if [[ ! -f $DATADIR/ACEs_THERMK.zip ]]
+then
+    wget -O $DATADIR/ACEs_THERMK.zip $LN$SLUG1
+fi
+
+
+# Get neutron induced and spontaneous fission yield data from JEFF 3.3
+if [[ ! -f $DATADIR/sss_jeff33.nfy ]]
+then
+    wget -O $DATADIR/sss_jeff33.nfy https://www.oecd-nea.org/dbdata/jeff/jeff33/downloads/JEFF33-nfy.asc
+fi
 
-# Get neutron induces and spontaneous fission yield data from JEFF 3.3
-wget -O $DATADIR/sss_jeff33.nfy https://www.oecd-nea.org/dbdata/jeff/jeff33/downloads/JEFF33-nfy.asc
-wget -O $DATADIR/sss_jeff33.sfy https://www.oecd-nea.org/dbdata/jeff/jeff33/downloads/JEFF33-sfy.asc
+if [[ ! -f $DATADIR/sss_jeff33.sfy ]]
+then
+    wget -O $DATADIR/sss_jeff33.sfy https://www.oecd-nea.org/dbdata/jeff/jeff33/downloads/JEFF33-sfy.asc
+fi
+
+# Also get decay chains
+if [[ ! -f $DATADIR/sss_jeff33.dec ]]
+then
+    wget -O $DATADIR/sss_jeff33.dec https://www.oecd-nea.org/dbdata/jeff/jeff33/downloads/JEFF33-rdd_all.asc
+fi
 
 ###############
 ### PROCESS ###
 ###############
 DIRFILE=$DATADIR/sss_jeff312.xsdir
-echo "datapath=$DATADIR/jeff312/acedata" | cat - > $DIRFILE 
+echo "datapath=$DATADIR/acedata" | cat - > $DIRFILE
 echo "atomic weight ratios" | cat - >> $DIRFILE
 mkdir -p $DATADIR/acedata
 
-TEMPS=(900 "THERM")
-#Uncomment if you have dowloaded the entire JEFF 3.1.2 libary
-#TEMPS=(500 600 800 900 1000 1200 1500 "THERM")
+TEMPS+=("THERM")
 
-# Regular expressions for changing the ZAI of 
+# Regular expressions for changing the ZAI of
 # metastable isotopes
 REGEXMETA=[A-Z][a-z]{0,1}[0-9]{1,3}M
 REGEXZAI=[0-9]{1,3}[0-9]{3}\.[0-9]{2}c
@@ -53,7 +73,7 @@ do
     #Create directories for each temp and extract
     mkdir -p $DATADIR/$T
     unzip -j $DATADIR/ACEs_$T$EXT -d $DATADIR/$T
-    
+
     # Change filenames to include temperature so we can put them all in the same
     # directory
     if [[ $T == "THERM" ]]
@@ -87,10 +107,10 @@ do
 
         # Convert DOS to UNIX
         awk '{sub("\r$", ""); print }' $file > temp.ACE
-        mv temp.ACE > $file
+        mv temp.ACE $file
 
         # Get atomic weights
-        if [[ $T == 900 ]]
+        if [[ $T == ${TEMPS[0]} ]]
         then
             LN="$(head -n 1 $PRE.dir)"
             [[ $LN =~ $REGEXZAI ]]
@@ -101,16 +121,23 @@ do
             ZAI="${ZAI:0:$len-4}"
             echo " $ZAI $AWT" | cat - >> $DIRFILE
         fi
-    
+
         mv "$file" ${arr[0]}$SUF
     done
-        
+
     mv $DATADIR/$T/*.ACE $DATADIR/acedata/.
 
-    echo "directory" | cat - >> $DIRFILE
+    # Add the "directory" line only once
+    if [[ $T == ${TEMPS[0]} ]]
+    then
+        echo "directory" | cat - >> $DIRFILE
+    fi
+
     # Add dir files to global dir file
-    cat $DATADIR/$T/*.dir >> $DIRFILE 
-    
+    cat $DATADIR/$T/*.dir >> $DIRFILE
+
     # Cleanup
     rm $DATADIR/$T/*.dir
+    rm -r $DATADIR/$T
+
 done