From c54b5b76587561f1a6a458f0efe7007b02d54453 Mon Sep 17 00:00:00 2001
From: tbritton <tbritton@jlab.org>
Date: Fri, 21 Apr 2017 10:53:30 -0400
Subject: [PATCH] better output structure

---
 MCwrapper/MakeMC.csh | 13 +++++++++++--
 MCwrapper/MakeMC.sh  | 10 +++++++++-
 2 files changed, 20 insertions(+), 3 deletions(-)

diff --git a/MCwrapper/MakeMC.csh b/MCwrapper/MakeMC.csh
index 6fc69073..074e26d4 100755
--- a/MCwrapper/MakeMC.csh
+++ b/MCwrapper/MakeMC.csh
@@ -150,6 +150,12 @@ endif
 if ( ! -d "$OUTDIR/configurations/" ) then
     mkdir $OUTDIR/configurations/
 endif
+if ( ! -d "$OUTDIR/configurations/generation/" ) then
+    mkdir $OUTDIR/configurations/generation/
+endif
+if ( ! -d "$OUTDIR/configurations/geant/" ) then
+    mkdir $OUTDIR/configurations/geant/
+endif
 if ( ! -d "$OUTDIR/hddm/" ) then
     mkdir $OUTDIR/hddm/
 endif
@@ -351,6 +357,8 @@ if ( "$GENR" != "0" ) then
 	    sed -i 's/TEMPMINE/0.0012/' control'_'$formatted_runNumber'_'$formatted_fileNumber.in
 	endif
 
+	cp $PWD/control'_'$formatted_runNumber'_'$formatted_fileNumber.in $OUTDIR/configurations/geant/
+
 	mv $PWD/control'_'$formatted_runNumber'_'$formatted_fileNumber.in $PWD/control.in
 	
 	if ( "$GEANTVER" == "3" ) then
@@ -401,6 +409,7 @@ if ( "$GENR" != "0" ) then
 		if ( "$recon_pre" == "file" ) then
 		    echo "using config file: "$jana_config_file
 		    hd_root ./$STANDARD_NAME'_geant'$GEANTVER'_smeared.hddm' --config=jana_config.cfg -PNTHREADS=$NUMTHREADS
+			rm jana_config.cfg
 		else
 		    set pluginlist=("danarest" "monitoring_hists")
 	     
@@ -450,7 +459,7 @@ if ( "$GENR" != "0" ) then
 	    	set filename_root=`echo $rootfile | sed -r 's/.{5}$//'`
 			set filetomv="$rootfile"
 			set filecheck=`echo $current_files | grep -c $filetomv`
-			
+
 			if ( "$filecheck" == "0" ) then
 		    	mv $filetomv $filename_root\_$STANDARD_NAME.root
 		    	mv $PWD/$filename_root\_$STANDARD_NAME.root $OUTDIR/root/
@@ -464,7 +473,7 @@ if ( "$GENR" != "0" ) then
 endif
 
 if ( "$gen_pre" != "file" ) then
-    mv $PWD/*.conf $OUTDIR/configurations/
+    mv $PWD/*.conf $OUTDIR/configurations/generation/
 endif
 
 set hddmfiles=`ls | grep .hddm`
diff --git a/MCwrapper/MakeMC.sh b/MCwrapper/MakeMC.sh
index 348a4425..2cae0dfb 100755
--- a/MCwrapper/MakeMC.sh
+++ b/MCwrapper/MakeMC.sh
@@ -150,6 +150,12 @@ fi
 if [[ ! -d "$OUTDIR/configurations/" ]]; then
     mkdir $OUTDIR/configurations/
 fi
+if [[ ! -d "$OUTDIR/configurations/generation/" ]]; then
+    mkdir $OUTDIR/configurations/generation/
+fi
+if [[ ! -d "$OUTDIR/configurations/geant/" ]]; then
+    mkdir $OUTDIR/configurations/geant/
+fi
 if [[ ! -d "$OUTDIR/hddm/" ]]; then
     mkdir $OUTDIR/hddm/
 fi
@@ -354,6 +360,7 @@ if [[ "$GENR" != "0" ]]; then
 	    sed -i 's/TEMPMINE/0.0012/' control'_'$formatted_runNumber'_'$formatted_fileNumber.in
 	fi
 	
+	cp $PWD/control'_'$formatted_runNumber'_'$formatted_fileNumber.in $OUTDIR/configurations/geant/
 	mv $PWD/control'_'$formatted_runNumber'_'$formatted_fileNumber.in $PWD/control.in
 	
 	if [[ "$GEANTVER" == "3" ]]; then
@@ -405,6 +412,7 @@ if [[ "$GENR" != "0" ]]; then
 		if [[ "$recon_pre" == "file" ]]; then
 			echo "using config file: "$jana_config_file
 			hd_root ./$STANDARD_NAME'_geant'$GEANTVER'_smeared.hddm' --config=jana_config.cfg -PNTHREADS=$NUMTHREADS
+			rm jana_config.cfg
 		else
 		
 			declare -a pluginlist=("danarest" "monitoring_hists")
@@ -469,7 +477,7 @@ if [[ "$GENR" != "0" ]]; then
     fi
 fi
 if [[ "$gen_pre" != "file" ]]; then
-	mv $PWD/*.conf $OUTDIR/configurations/
+	mv $PWD/*.conf $OUTDIR/configurations/generation/
 fi
 hddmfiles=$(ls | grep .hddm)
 if [[ "$hddmfiles" != "" ]]; then