From 484b5195477a6241243f7443da0a368b1c9acd3e Mon Sep 17 00:00:00 2001
From: Sofia Kostoglou <skostogl@lxplus092.cern.ch>
Date: Tue, 27 Feb 2018 09:19:31 +0100
Subject: [PATCH 1/4] fort13 added

---
 utilities/bash/dot_profile        |  19 +++
 utilities/bash/mad6t.sh           |   9 +-
 utilities/bash/run_six.sh         | 214 +++++++++++++++++++++---------
 utilities/bash/set_env.sh         |  91 +++++++++----
 utilities/templates/lsf/mad6t1.sh |  20 ++-
 5 files changed, 261 insertions(+), 92 deletions(-)

diff --git a/utilities/bash/dot_profile b/utilities/bash/dot_profile
index 068fe00..4f64dc6 100755
--- a/utilities/bash/dot_profile
+++ b/utilities/bash/dot_profile
@@ -685,6 +685,25 @@ sixdeskAllTunes(){
     tunesYY=( ${tunesYY} )
     inttunesYY=( ${inttunesYY} )
 }
+sixdeskAllAmplitudes_fort13(){
+    pairs_per_job=$((sixdeskpairs*15))
+    if [ -d "${sixdeskjobs_logs}/fort.13_jobs" ]; then
+      rm -rf ${sixdeskjobs_logs}/fort.13_jobs/*
+    else
+      mkdir ${sixdeskjobs_logs}/fort.13_jobs
+    fi
+    split -d -l $pairs_per_job fort.13 ${sixdeskjobs_logs}/fort.13_jobs/fort.13.
+    fort13_jobs=( $(find ${sixdeskjobs_logs}/fort.13_jobs/ -type f -name 'fort.13.*') )
+    nb_fort13_jobs=${#fort13_jobs[@]}
+    echo Fort.13 will be split in $nb_fort13_jobs jobs
+    allAmplitudeSteps=( $(seq 1 1 $nb_fort13_jobs) )
+    fAmpStarts=("${allAmplitudeSteps[@]}")
+    fAmpEnds=("${allAmplitudeSteps[@]}")
+    ampstart=${fAmpStarts[0]}
+    let __iLast=${#fAmpEnds[@]}-1
+    ampfinish=${fAmpEnds[${__iLast}]}
+}
+
 sixdeskAllAmplitudes(){
     # A.Mereghetti, 2017-04-08
     # new function, to generate all amplitude steps
diff --git a/utilities/bash/mad6t.sh b/utilities/bash/mad6t.sh
index 3b0173b..315627f 100755
--- a/utilities/bash/mad6t.sh
+++ b/utilities/bash/mad6t.sh
@@ -150,9 +150,13 @@ function submit(){
 	# Loop over seeds
 	mad6tjob=$lsfFilesPath/mad6t1.sh
 	for (( iMad=$istamad ; iMad<=$iendmad ; iMad++ )) ; do
-	    
+            if [ ${lflag_fort13} = true ]  ; then
+              files="2 8 13 16 34"
+            else
+              files="2 8 16 34"
+   	    fi    
 	    # clean away any existing results for this seed
-	    for f in 2 8 16 34 ; do
+	    for f in files ; do
 		rm -f $sixtrack_input/fort.$f"_"$iMad.gz
 	    done
 	    
@@ -168,6 +172,7 @@ function submit(){
 		-e 's?%FORT_34%?'$fort_34'?g' \
 		-e 's?%MADX_PATH%?'$MADX_PATH'?g' \
 		-e 's?%MADX%?'$MADX'?g' \
+		-e 's?%lflag_fort13%?'$lflag_fort13'?g' \
 		-e 's?%SIXTRACK_INPUT%?'$sixtrack_input'?g' $mad6tjob > mad6t_"$iMad".sh
 	    chmod 755 mad6t_"$iMad".sh
 	    
diff --git a/utilities/bash/run_six.sh b/utilities/bash/run_six.sh
index 9ed7549..655c25c 100755
--- a/utilities/bash/run_six.sh
+++ b/utilities/bash/run_six.sh
@@ -264,23 +264,43 @@ function preProcessFort3(){
 	local __dp1=.0
 	local __dp2=.0
     fi
-    sed -e 's/%turnss/%turnsl/g' \
-	-e 's/%nss/'$sixdeskpairs'/g' \
-	-e 's/%imc/'$__imc'/g' \
-	-e 's/%iclo6/'$__iclo6'/g' \
-	-e 's/%ax0s/%ax0l/g' \
-	-e 's/%ax1s/%ax1l/g' \
-	-e 's/%writebins/%writebinl/g' \
-	-e 's/%ratios/%ratiol/g' \
-	-e 's/%dp1/'$__dp1'/g' \
-	-e 's/%dp2/'$__dp2'/g' \
-	-e 's/%e0/'$e0'/g' \
-	-e 's/%ition/'$__ition'/g' \
-	-e 's/%idfor/'$idfor'/g' \
-	-e 's/%ibtype/'$ibtype'/g' \
-	-e 's/%bunch_charge/'$bunch_charge'/g' \
-	-e 's?%Runnam?%Runnam '"$sixdeskTitle"'?g' \
-        $sixdeskjobs_logs/fort.3.mother1 > $sixdeskjobs_logs/fortl.3.mask
+  
+    if [ $lflag_fort13 ]; then
+      sed -e 's/%turnss/%turnsl/g' \
+          -e 's/%imc/'$__imc'/g' \
+          -e 's/%iclo6/'$__iclo6'/g' \
+          -e 's/%ax0s/%ax0l/g' \
+          -e 's/%ax1s/%ax1l/g' \
+          -e 's/%writebins/%writebinl/g' \
+          -e 's/%ratios/%ratiol/g' \
+          -e 's/%dp1/'$__dp1'/g' \
+          -e 's/%dp2/'$__dp2'/g' \
+          -e 's/%e0/'$e0'/g' \
+          -e 's/%ition/'$__ition'/g' \
+          -e 's/%idfor/'$idfor'/g' \
+          -e 's/%ibtype/'$ibtype'/g' \
+          -e 's/%bunch_charge/'$bunch_charge'/g' \
+          -e 's?%Runnam?%Runnam '"$sixdeskTitle"'?g' \
+          $sixdeskjobs_logs/fort.3.mother1 > $sixdeskjobs_logs/fortl.3.mask
+    else
+      sed -e 's/%turnss/%turnsl/g' \
+          -e 's/%nss/'$sixdeskpairs'/g' \
+          -e 's/%imc/'$__imc'/g' \
+          -e 's/%iclo6/'$__iclo6'/g' \
+          -e 's/%ax0s/%ax0l/g' \
+          -e 's/%ax1s/%ax1l/g' \
+          -e 's/%writebins/%writebinl/g' \
+          -e 's/%ratios/%ratiol/g' \
+          -e 's/%dp1/'$__dp1'/g' \
+          -e 's/%dp2/'$__dp2'/g' \
+          -e 's/%e0/'$e0'/g' \
+          -e 's/%ition/'$__ition'/g' \
+          -e 's/%idfor/'$idfor'/g' \
+          -e 's/%ibtype/'$ibtype'/g' \
+          -e 's/%bunch_charge/'$bunch_charge'/g' \
+          -e 's?%Runnam?%Runnam '"$sixdeskTitle"'?g' \
+          $sixdeskjobs_logs/fort.3.mother1 > $sixdeskjobs_logs/fortl.3.mask
+    fi
     let __lerr+=$?
     # - multipole blocks
     cat $sixdeskjobs_logs/fort.3.mad >> $sixdeskjobs_logs/fortl.3.mask 
@@ -508,7 +528,11 @@ function preProcessBoinc(){
 function submitChromaJobs(){
 
     local __destination=$1
-    local __GLOBIGNORE='fort.[2,8]:fort.16:fort*.3.*:fort.10*:sixdesklock:chromaJob0?:lin*:betaJob'
+    if [ ${lflag_fort13} = true ]; then
+      local __GLOBIGNORE='fort.[2,8]:fort.16:fort*.3.*:fort.10*:fort.13*:sixdesklock:chromaJob0?:lin*:betaJob'
+    else
+      local __GLOBIGNORE='fort.[2,8]:fort.16:fort*.3.*:fort.10*:sixdesklock:chromaJob0?:lin*:betaJob'
+    fi
     
     # --------------------------------------------------------------------------
     # generate appropriate fort.3 files as: fort.3.tx + fort.3.mad + fort.3.m2
@@ -579,6 +603,9 @@ function submitChromaJobs(){
     sixdeskmess  1 "Running the first one turn job for chromaticity"
     cat fort.3.t1 fort.3.mad fort.3.m2 > fort.3
     rm -f fort.10
+    if [ ${lflag_fort13} = true ]; then
+      cp $sixdeskhome/fort.13 .
+    fi
     $SIXTRACKEXE > first_oneturn
     if test $? -ne 0 -o ! -s fort.10 ; then
         sixdeskmess -1 "The first turn Sixtrack for chromaticity FAILED!!!"
@@ -588,8 +615,12 @@ function submitChromaJobs(){
     fi
     # save all interesting files from first job
     rm -rf chromaJob01
-    mkdir chromaJob01
-    cp fort.2 fort.3 fort.8 fort.16 fort.10 first_oneturn chromaJob01
+    mkdir chromaJob01 
+    if [ ${lflag_fort13} = true ]; then
+      cp fort.2 fort.3 fort.8 fort.16 fort.10 fort.13 first_oneturn chromaJob01
+    else 
+      cp fort.2 fort.3 fort.8 fort.16 fort.10 first_oneturn chromaJob01
+    fi
     gzip -f chromaJob01/*
     mv fort.10 fort.10_first_oneturn
     # clean dir
@@ -601,6 +632,9 @@ function submitChromaJobs(){
     sixdeskmess  1 "Running the second one turn job for chromaticity"
     cat fort.3.t2 fort.3.mad fort.3.m2 > fort.3
     rm -f fort.10
+    if [ ${lflag_fort13} = true ]; then
+      cp $sixdeskhome/fort.13 .
+    fi
     $SIXTRACKEXE > second_oneturn
     if test $? -ne 0 -o ! -s fort.10 ; then
         sixdeskmess -1 "The second turn Sixtrack for chromaticity FAILED!!!"
@@ -611,7 +645,11 @@ function submitChromaJobs(){
     # save all interesting files from second job
     rm -rf chromaJob02
     mkdir chromaJob02
-    cp fort.2 fort.3 fort.8 fort.16 fort.10 second_oneturn chromaJob02
+    if [ ${lflag_fort13} = true ]; then
+      cp fort.2 fort.3 fort.8 fort.16 fort.10 fort.13 second_oneturn chromaJob02
+    else
+      cp fort.2 fort.3 fort.8 fort.16 fort.10 second_oneturn chromaJob02
+    fi
     gzip -f chromaJob02/*
     mv fort.10 fort.10_second_oneturn
     # clean dir
@@ -633,8 +671,11 @@ function submitChromaJobs(){
 function submitBetaJob(){
     
     local __destination=$1
-    local __GLOBIGNORE='fort.[2,8]:fort.16:fort*.3.*:fort.10*:sixdesklock:chromaJob0?:lin*:betaJob'
-    
+    if [ ${lflag_fort13} = true ];then
+      local __GLOBIGNORE='fort.[2,8]:fort.16:fort*.3.*:fort.10*:fort.13*:sixdesklock:chromaJob0?:lin*:betaJob'
+    else
+      local __GLOBIGNORE='fort.[2,8]:fort.16:fort*.3.*:fort.10*:sixdesklock:chromaJob0?:lin*:betaJob'
+    fi 
     # --------------------------------------------------------------------------
     # generate appropriate fort.3 files as: fort.3.m1 + fort.3.mad + fort.3.m2
     sed -e 's/%turnss/'1'/g' \
@@ -681,6 +722,9 @@ function submitBetaJob(){
     # --------------------------------------------------------------------------
     # actually run
     rm -f fort.10
+    if [ ${lflag_fort13} = true ];then
+      cp $sixdeskhome/fort.13 .
+    fi
     $SIXTRACKEXE > lin
     if test $? -ne 0 -o ! -s fort.10 ; then
         sixdeskmess -1 "The one turn Sixtrack for betavalues FAILED!!!"
@@ -691,7 +735,11 @@ function submitBetaJob(){
     # save all interesting files from beta job
     rm -rf betaJob
     mkdir betaJob
-    cp fort.2 fort.3 fort.8 fort.16 fort.10 lin betaJob
+    if [ ${lflag_fort13} = true ];then 
+      cp fort.2 fort.3 fort.8 fort.16 fort.10 fort.13 lin betaJob
+    else
+      cp fort.2 fort.3 fort.8 fort.16 fort.10 fort.13 lin betaJob
+    fi
     gzip -f betaJob/*
     mv lin lin_old
     cp fort.10 fort.10_old
@@ -760,18 +808,28 @@ function submitCreateFinalFort3Short(){
 
 function submitCreateFinalFort3Long(){
 
-    local __lerr=0
 
-    # returns ratio
-    sixdeskRatio $kang $lbackcomp
-    [ -n "${ratio}" ] || let __lerr+=1
-    # returns ax0 and ax1
-    sixdeskax0 $factor $beta_x $beta_x2 $beta_y $beta_y2 $ratio $kang $square $fampstart $fampend $lbackcomp
-    [ -n "${ax0}" ] || let __lerr+=1
-    [ -n "${ax1}" ] || let __lerr+=1
+    if [ $lflag_fort13 ]; then
+      ax0=0.0
+      ax1=0.0
+      cp ${fort13_jobs[${nConsidered} -1]} $sixdeskjobs_logs/fort.13
+      fort13_current=$sixdeskjobs_logs/fort.13
+      n_lines_fort13_current=$(cat $fort13_current | wc -l )
+      sixdeskpairs_current=$(echo $n_lines_fort13_current 15 | awk '{printf ("%.f", ($1/$2))}') 
+    else
+      local __lerr=0
+      # returns ratio
+      sixdeskRatio $kang $lbackcomp
+      [ -n "${ratio}" ] || let __lerr+=1
+      # returns ax0 and ax1
+      sixdeskax0 $factor $beta_x $beta_x2 $beta_y $beta_y2 $ratio $kang $square $fampstart $fampend $lbackcomp
+      [ -n "${ax0}" ] || let __lerr+=1
+      [ -n "${ax1}" ] || let __lerr+=1
+    fi
     #
     sed -e 's/%turnsl/'$turnsl'/g' \
 	-e 's/%ax0l/'$ax0'/g' \
+        -e 's/%nss/'$sixdeskpairs_current'/g' \
 	-e 's/%ax1l/'$ax1'/g' \
 	-e 's/%ratiol/'$ratio'/g' \
 	-e 's/%tunex/'$tunexx'/g' \
@@ -800,8 +858,12 @@ function submitCreateFinalInputs(){
     sixdeskmess  1 "Taking care of SIXTRACK fort.2/fort.3/fort.8/fort.16 in $RundirFullPath"
 
     # fort.3
-    gzip -c $sixdeskjobs_logs/fort.3 > $RundirFullPath/fort.3.gz
-	
+    if [ $lflag_fort13 ];then
+      gzip -c $fort13_current > $RundirFullPath/fort.13.gz
+      gzip -c $sixdeskjobs_logs/fort.3 > $RundirFullPath/fort.3.gz
+    else
+      gzip -c $sixdeskjobs_logs/fort.3 > $RundirFullPath/fort.3.gz
+    fi  	
     # input from MADX: fort.2/.8/.16
     for iFort in 2 8 16 ; do
 	[ ! -e $RundirFullPath/fort.${iFort}.gz ] || rm -f $RundirFullPath/fort.${iFort}.gz
@@ -1435,9 +1497,14 @@ function treatLong(){
 
 	# separate output for current case from previous one
 	echo ""
-
-        sixdeskmess -1 "Considering amplitude step: $Ampl"
-
+        
+        if [ $lflag_fort13=true ];then 
+          sixdeskmess -1 "Considering job #$Ampl from fort.13"
+        else
+          sixdeskmess -1 "Considering amplitude step: $Ampl"
+        fi
+        #echo $lflag_fort13 hereeeeee2
+        #exit
         if ${lReduceAngsWithAmplitude}; then 
           jAmple=${iAmple}
         else
@@ -2173,7 +2240,13 @@ if ${lgenerate} || ${lfix} ; then
     echo "$emit  $gamma" > $sixdesktrackStudy/general_input
     let __lerr+=$?
     # - set up of fort.3
-    for tmpFile in fort.3.mad fort.3.mother1 fort.3.mother2 ; do
+    if [ $lflag_fort13 = false ]; then 
+      tmpFiles=(fort.3.mad fort.3.mother1 fort.3.mother2)
+    else
+      tmpFiles=(fort.3.mad fort.3.mother1 fort.3.mother2 fort.13)
+    fi
+    #for tmpFile in fort.3.mad fort.3.mother1 fort.3.mother2 ; do
+    for tmpFile in ${tmpFiles[@]}; do
 	cp ${sixtrack_input}/${tmpFile} $sixdeskjobs_logs
 	if [ $? -ne 0 ] ; then
 	    sixdeskmess -1 "unable to copy ${sixtrack_input}/${tmpFile} to $sixdeskjobs_logs"
@@ -2378,30 +2451,41 @@ else
 	    sixdeskmess -1 "  --> along a line in (Qx,Qy) - total: ${iTotalTunes} pairs;"
 	fi
     fi
-    if [ $long -eq 1 ] ; then
-	# generate array of amplitudes (it returns allAmplitudeSteps, fAmpStarts, fAmpEnds, ampstart, ampfinish)
-	sixdeskAllAmplitudes
-	iTotalAmplitudeSteps=${#allAmplitudeSteps[@]}
-	sixdeskmess -1 "- Amplitudes: from $ns1l to $ns2l by $nsincl - total: ${iTotalAmplitudeSteps} amplitude steps;"
-        # generate array of angles (it returns KKs, Angles and kAngs, and KKs_ampl)
-	sixdeskAllAngles $kinil $kendl $kmaxl $kstep $ampstart $ampfinish $lbackcomp ${lReduceAngsWithAmplitude} ${totAngle} ${ampFactor}
-	iTotalAngles=${#KKs[@]}
-	sixdeskmess -1 "- Angles: $kinil, $kendl, $kmaxl by $kstep - total: ${iTotalAngles} angles"
-	if ${lReduceAngsWithAmplitude} ; then
-	    sixdeskmess -1 "  --> reduced angles with amplitude functionality active"
-	    let iTotal=${iTotalMad}*${iTotalTunes}*${iTotalAngles}
-	else
-	    let iTotal=${iTotalMad}*${iTotalTunes}*${iTotalAmplitudeSteps}*${iTotalAngles}
-	fi
-    elif [ $short -eq 1 ] || [ $da -eq 1 ] ; then
-	iTotalAmplitudeSteps=1
-	sixdeskmess -1 "- Amplitudes: from $ns1s to $ns2s by $nss - total: ${iTotalAmplitudeSteps} amplitude steps;"
-	# generate array of angles (it returns KKs, Angles and kAngs, and KKs_ampl)
-	sixdeskAllAngles $kini $kend $kmax $kstep $ampstart $ampfinish $lbackcomp ${lReduceAngsWithAmplitude} ${totAngle} ${ampFactor}
-	iTotalAngles=${#KKs[@]}
-	sixdeskmess -1 "- Angles: $kini, $kend, $kmax by $kstep - total: ${iTotalAngles} angles"
-	let iTotal=${iTotalMad}*${iTotalTunes}*${iTotalAmplitudeSteps}*${iTotalAngles}
-    fi
+    if [ $lflag_fort13 = false ]; then
+      if [ $long -eq 1 ] ; then
+          # generate array of amplitudes (it returns allAmplitudeSteps, fAmpStarts, fAmpEnds, ampstart, ampfinish)
+          sixdeskAllAmplitudes
+          iTotalAmplitudeSteps=${#allAmplitudeSteps[@]}
+          sixdeskmess -1 "- Amplitudes: from $ns1l to $ns2l by $nsincl - total: ${iTotalAmplitudeSteps} amplitude steps;"
+          # generate array of angles (it returns KKs, Angles and kAngs, and KKs_ampl)
+          sixdeskAllAngles $kinil $kendl $kmaxl $kstep $ampstart $ampfinish $lbackcomp ${lReduceAngsWithAmplitude} ${totAngle} ${ampFactor}
+          iTotalAngles=${#KKs[@]}
+          sixdeskmess -1 "- Angles: $kinil, $kendl, $kmaxl by $kstep - total: ${iTotalAngles} angles"
+          if ${lReduceAngsWithAmplitude} ; then
+              sixdeskmess -1 "  --> reduced angles with amplitude functionality active"
+              let iTotal=${iTotalMad}*${iTotalTunes}*${iTotalAngles}
+          else
+              let iTotal=${iTotalMad}*${iTotalTunes}*${iTotalAmplitudeSteps}*${iTotalAngles}
+          fi
+      elif [ $short -eq 1 ] || [ $da -eq 1 ] ; then
+          iTotalAmplitudeSteps=1
+          sixdeskmess -1 "- Amplitudes: from $ns1s to $ns2s by $nss - total: ${iTotalAmplitudeSteps} amplitude steps;"
+          # generate array of angles (it returns KKs, Angles and kAngs, and KKs_ampl)
+          sixdeskAllAngles $kini $kend $kmax $kstep $ampstart $ampfinish $lbackcomp ${lReduceAngsWithAmplitude} ${totAngle} ${ampFactor}
+          iTotalAngles=${#KKs[@]}
+          sixdeskmess -1 "- Angles: $kini, $kend, $kmax by $kstep - total: ${iTotalAngles} angles"
+          let iTotal=${iTotalMad}*${iTotalTunes}*${iTotalAmplitudeSteps}*${iTotalAngles}
+          sixdeskmess -1 "for a total of ${iTotal} points."
+      fi
+    else
+      echo "-> Flag for fort.13 input is active"
+      ## To be changed!!
+      sixdeskAllAmplitudes_fort13
+      sixdeskAllAngles $kinil $kendl $kmaxl $kstep $ampstart $ampfinish $lbackcomp ${lReduceAngsWithAmplitude} ${totAngle} ${ampFactor}
+      iTotalAmplitudeSteps=${#allAmplitudeSteps[@]}
+      iTotalAngles=${#KKs[@]}
+    fi
+    let iTotal=${iTotalMad}*${iTotalTunes}*${iTotalAmplitudeSteps}*${iTotalAngles}
     sixdeskmess -1 "for a total of ${iTotal} points."
 fi
 
@@ -2430,7 +2514,11 @@ else
         echo ""
         sixdeskmess -1 "MADX seed $iMad"
         if ${lgenerate} || ${lfix} ; then
-    	    iForts="2 8 16"
+            if [ ${lflag_fort13} = true ]  ; then
+    	      iForts="2 8 13 16"
+            else
+    	      iForts="2 8 16"
+            fi
     	    if [ "$fort_34" != "" ] ; then
     		iForts="${iForts} 34"
     	    fi
diff --git a/utilities/bash/set_env.sh b/utilities/bash/set_env.sh
index 751a511..8667ea8 100755
--- a/utilities/bash/set_env.sh
+++ b/utilities/bash/set_env.sh
@@ -139,35 +139,74 @@ function setFurtherEnvs(){
     # set exes
     sixdeskSetExes
     # scan angles:
-    lReduceAngsWithAmplitude=false
- 
-    if [ -n "${reduce_angs_with_aplitude}" ] ; then
-        sixdeskmess -1 "wrong spelling of reduce_angs_with_amplitude. Please correct it for future use"
-        reduce_angs_with_amplitude=${reduce_angs_with_aplitude}
-    fi   
-    
-    if [ -z "${reduce_angs_with_amplitude}" ]; then
-        reduce_angs_with_amplitude=0         
-    elif (( $(echo "${reduce_angs_with_amplitude}" | awk '{print ($1 >=0)}') )); then 
-        if [ ${long} -ne 1 ]; then
-            sixdeskmess -1 "reduced angles with amplitudes available only for long simulations!"
+    lflag_fort13=false
+    ## if flag exists in sixdeskenv
+    if [ -n "${flag_fort13}" ]; then
+      ### if flag is > 0
+      if (( $(echo "${flag_fort13}" | awk '{print ($1 > 0)}'))); then
+        ## if fort.13 exists in sixjobs and it is not empty
+        if [ -s $sixdeskhome/fort.13 ]; then
+          n_lines_fort13=$(cat ${sixdeskhome}/fort.13 | wc -l )
+          ## if the number of lines is divided by 15
+          if (( $n_lines_fort13 % 15 == 0 ));then
+            ## if it is a long run
+            if [ ${long} -eq 1 ] ; then
+              lflag_fort13=true
+              idfor=2
+              ## lock at 1 angle
+              kinil=1
+              kendl=1
+              kmaxl=1
+              sixdeskmess="Flag for fort.13 is ON. The initial distribution will be created from the fort.13 file. idfor is set to 2"
+              sixdeskmess
+            else
+              sixdeskmess -1 "Fort.13 input is implemented only for long runs"
+	      sixdeskexit 9
+            fi
+          else
+            sixdeskmess -1 "The format of the fort.13 is not correct"
 	    sixdeskexit 9
+          fi
         else
-            if [ ${kinil} -ne 1 ] || [ ${kendl} -ne ${kmaxl} ] || [ ${kstep} -ne 1 ]; then
-                sixdeskmess -1 "reduced angles with amplitudes available only for kmin=1, kend=kmax and kstep=1"
-		sixdeskexit 10
-            elif (( $(echo "${reduce_angs_with_amplitude} ${ns2l}" | awk '{print ($1 >= $2)}') )); then
-                sixdeskmess -1 "reduced angles with amplitudes flag greater than maximum amplitude. Please de-activate the flag"
-		sixdeskexit 11
-            else 
-                lReduceAngsWithAmplitude=true
-            fi 
+          sixdeskmess -1 "Flag for fort.13 is activated but fort.13 file was not found in ${sixdeskhome} or is empty. Either de-activate the flag or include a fort.13 "
+	  sixdeskexit 9
         fi
-    else
-        sixdeskmess -1 "reduced angles with amplitudes set to negative value. Flag de-activated"
+      fi
+    fi
+
+    lReduceAngsWithAmplitude=false
+    if [ $lflag_fort13 = false ]; then
+      if [ -n "${reduce_angs_with_aplitude}" ] ; then
+          sixdeskmess -1 "wrong spelling of reduce_angs_with_amplitude. Please correct it for future use"
+          reduce_angs_with_amplitude=${reduce_angs_with_aplitude}
+      fi   
+      
+      if [ -z "${reduce_angs_with_amplitude}" ]; then
+          reduce_angs_with_amplitude=0         
+      elif (( $(echo "${reduce_angs_with_amplitude}" | awk '{print ($1 >=0)}') )); then 
+          if [ ${long} -ne 1 ]; then
+              sixdeskmess -1 "reduced angles with amplitudes available only for long simulations!"
+              sixdeskexit 9
+          else
+              if [ ${kinil} -ne 1 ] || [ ${kendl} -ne ${kmaxl} ] || [ ${kstep} -ne 1 ]; then
+                  sixdeskmess -1 "reduced angles with amplitudes available only for kmin=1, kend=kmax and kstep=1"
+          	sixdeskexit 10
+              elif (( $(echo "${reduce_angs_with_amplitude} ${ns2l}" | awk '{print ($1 >= $2)}') )); then
+                  sixdeskmess -1 "reduced angles with amplitudes flag greater than maximum amplitude. Please de-activate the flag"
+          	sixdeskexit 11
+              else 
+                  lReduceAngsWithAmplitude=true
+              fi 
+          fi
+      else
+          sixdeskmess -1 "reduced angles with amplitudes set to negative value. Flag de-activated"
+      fi
+
     fi
+    
     export totAngle=90
     export lReduceAngsWithAmplitude
+    export lflag_fort13
 }
 
 # ==============================================================================
@@ -481,6 +520,9 @@ else
 	    if ${llocalfort3} ; then
 		cp ${envFilesPath}/fort.3.local studies/${LHCDescrip}
 	    fi
+	    if ${lflag_fort13} ; then
+		cp ${envFilesPath}/fort.13 studies/${LHCDescrip}
+	    fi
 	    if ${__lnew} ; then
   	        # new study
 		sixdeskmess -1 "Created a NEW study $LHCDescrip"
@@ -494,6 +536,9 @@ else
 	    if ${llocalfort3} ; then
 		cp ${envFilesPath}/fort.3.local .
 	    fi
+	    if ${lflag_fort13} ; then
+		cp ${envFilesPath}/fort.13 .
+	    fi
 	    sixdeskmess -1 "Switched to study $LHCDescrip"
 	fi
     fi
diff --git a/utilities/templates/lsf/mad6t1.sh b/utilities/templates/lsf/mad6t1.sh
index fb55cb0..cffa3f9 100644
--- a/utilities/templates/lsf/mad6t1.sh
+++ b/utilities/templates/lsf/mad6t1.sh
@@ -7,6 +7,7 @@ export CORR_TEST=%CORR_TEST%
 export fort_34=%FORT_34%
 export MADX_PATH=%MADX_PATH%
 export MADX=%MADX%
+export lflag_fort13=%lflag_fort13%
 echo "Calling madx version $MADX in $MADX_PATH"
 $MADX_PATH/$MADX < $junktmp/$filejob."$i" > $filejob.out."$i"
 cp -f $filejob.out."$i" $junktmp
@@ -115,7 +116,12 @@ touch fc.34
 mv fc.2 fort.2
 mv fc.16 fort.16
 mv fc.8 fort.8
-for fil in fort.2 fort.8 fort.16
+if [ $lflag_fort13 = true ]; then
+  fils=(fort.2 fort.8 fort.13 fort.16)
+else
+  fils=(fort.2 fort.8 fort.16)
+fi
+for fil in ${fils[@]}
 do
   if test -s $sixtrack_input/"$fil"_"$i".gz
   then
@@ -131,9 +137,15 @@ do
       cat diffs >> $sixtrack_input/WARNINGS
     fi
   fi
-  mv "$fil" "$fil"_"$i"
-  gzip "$fil"_"$i"
-  cp "$fil"_"$i".gz $sixtrack_input
+  if [ $fil = "fort.13" ];then 
+    cp $sixdeskhome/fort.13 $sixtrack_input
+    cp $sixtrack_input/fort.13 $sixtrack_input/fort.13_$i
+    gzip $sixtrack_input/fort.13_$i
+  else
+    mv "$fil" "$fil"_"$i"
+    gzip "$fil"_"$i"
+    cp "$fil"_"$i".gz $sixtrack_input
+  fi
 done
 if test "$CORR_TEST" -ne 0
 then

From 5a4b8e4df07f56bd8da4ae2999c73e103a7207c4 Mon Sep 17 00:00:00 2001
From: Sofia Kostoglou <skostogl@lxplus092.cern.ch>
Date: Tue, 27 Feb 2018 10:30:53 +0100
Subject: [PATCH 2/4] fort.13

---
 utilities/bash/dot_profile        |  3 +-
 utilities/bash/mad6t.sh           |  4 +--
 utilities/bash/run_six.sh         | 47 +++++++++++++------------------
 utilities/bash/set_env.sh         |  2 +-
 utilities/templates/lsf/mad6t1.sh |  2 +-
 5 files changed, 26 insertions(+), 32 deletions(-)

diff --git a/utilities/bash/dot_profile b/utilities/bash/dot_profile
index 4f64dc6..faa0e58 100755
--- a/utilities/bash/dot_profile
+++ b/utilities/bash/dot_profile
@@ -686,7 +686,8 @@ sixdeskAllTunes(){
     inttunesYY=( ${inttunesYY} )
 }
 sixdeskAllAmplitudes_fort13(){
-    pairs_per_job=$((sixdeskpairs*15))
+    ## This function splits the fort.13 file according to the number of pairs set in sixdeskenv. A new directory fort13_jobs in the work directory is created which contains all the fort.13 jobs. The amplitude steps are named after the number of the job.  
+    pairs_per_job=$((sixdeskpairs*15))  ## each pair correspons to 15 lines
     if [ -d "${sixdeskjobs_logs}/fort.13_jobs" ]; then
       rm -rf ${sixdeskjobs_logs}/fort.13_jobs/*
     else
diff --git a/utilities/bash/mad6t.sh b/utilities/bash/mad6t.sh
index 315627f..a61d7bb 100755
--- a/utilities/bash/mad6t.sh
+++ b/utilities/bash/mad6t.sh
@@ -150,8 +150,8 @@ function submit(){
 	# Loop over seeds
 	mad6tjob=$lsfFilesPath/mad6t1.sh
 	for (( iMad=$istamad ; iMad<=$iendmad ; iMad++ )) ; do
-            if [ ${lflag_fort13} = true ]  ; then
-              files="2 8 13 16 34"
+            if [ "${lflag_fort13}" = true ]  ; then
+              files="2 8 13 16 34" ## fort.13 is also included in sixtrack_input
             else
               files="2 8 16 34"
    	    fi    
diff --git a/utilities/bash/run_six.sh b/utilities/bash/run_six.sh
index 655c25c..16610c6 100755
--- a/utilities/bash/run_six.sh
+++ b/utilities/bash/run_six.sh
@@ -264,8 +264,8 @@ function preProcessFort3(){
 	local __dp1=.0
 	local __dp2=.0
     fi
-  
-    if [ $lflag_fort13 ]; then
+    ## if fort.13 flag is on keep %nss. There could be an unequal number of pairs in each fort.13 jobs 
+    if $lflag_fort13; then
       sed -e 's/%turnss/%turnsl/g' \
           -e 's/%imc/'$__imc'/g' \
           -e 's/%iclo6/'$__iclo6'/g' \
@@ -528,7 +528,7 @@ function preProcessBoinc(){
 function submitChromaJobs(){
 
     local __destination=$1
-    if [ ${lflag_fort13} = true ]; then
+    if ${lflag_fort13}; then
       local __GLOBIGNORE='fort.[2,8]:fort.16:fort*.3.*:fort.10*:fort.13*:sixdesklock:chromaJob0?:lin*:betaJob'
     else
       local __GLOBIGNORE='fort.[2,8]:fort.16:fort*.3.*:fort.10*:sixdesklock:chromaJob0?:lin*:betaJob'
@@ -603,7 +603,7 @@ function submitChromaJobs(){
     sixdeskmess  1 "Running the first one turn job for chromaticity"
     cat fort.3.t1 fort.3.mad fort.3.m2 > fort.3
     rm -f fort.10
-    if [ ${lflag_fort13} = true ]; then
+    if ${lflag_fort13}; then
       cp $sixdeskhome/fort.13 .
     fi
     $SIXTRACKEXE > first_oneturn
@@ -615,8 +615,8 @@ function submitChromaJobs(){
     fi
     # save all interesting files from first job
     rm -rf chromaJob01
-    mkdir chromaJob01 
-    if [ ${lflag_fort13} = true ]; then
+    mkdir chromaJob01
+    if ${lflag_fort13}; then
       cp fort.2 fort.3 fort.8 fort.16 fort.10 fort.13 first_oneturn chromaJob01
     else 
       cp fort.2 fort.3 fort.8 fort.16 fort.10 first_oneturn chromaJob01
@@ -627,12 +627,11 @@ function submitChromaJobs(){
     export GLOBIGNORE=${__GLOBIGNORE}
     rm -f *
     export GLOBIGNORE=
-
     # - second job
     sixdeskmess  1 "Running the second one turn job for chromaticity"
     cat fort.3.t2 fort.3.mad fort.3.m2 > fort.3
     rm -f fort.10
-    if [ ${lflag_fort13} = true ]; then
+    if ${lflag_fort13}; then
       cp $sixdeskhome/fort.13 .
     fi
     $SIXTRACKEXE > second_oneturn
@@ -645,7 +644,7 @@ function submitChromaJobs(){
     # save all interesting files from second job
     rm -rf chromaJob02
     mkdir chromaJob02
-    if [ ${lflag_fort13} = true ]; then
+    if ${lflag_fort13}; then
       cp fort.2 fort.3 fort.8 fort.16 fort.10 fort.13 second_oneturn chromaJob02
     else
       cp fort.2 fort.3 fort.8 fort.16 fort.10 second_oneturn chromaJob02
@@ -671,7 +670,7 @@ function submitChromaJobs(){
 function submitBetaJob(){
     
     local __destination=$1
-    if [ ${lflag_fort13} = true ];then
+    if ${lflag_fort13};then
       local __GLOBIGNORE='fort.[2,8]:fort.16:fort*.3.*:fort.10*:fort.13*:sixdesklock:chromaJob0?:lin*:betaJob'
     else
       local __GLOBIGNORE='fort.[2,8]:fort.16:fort*.3.*:fort.10*:sixdesklock:chromaJob0?:lin*:betaJob'
@@ -722,7 +721,7 @@ function submitBetaJob(){
     # --------------------------------------------------------------------------
     # actually run
     rm -f fort.10
-    if [ ${lflag_fort13} = true ];then
+    if ${lflag_fort13};then
       cp $sixdeskhome/fort.13 .
     fi
     $SIXTRACKEXE > lin
@@ -735,7 +734,7 @@ function submitBetaJob(){
     # save all interesting files from beta job
     rm -rf betaJob
     mkdir betaJob
-    if [ ${lflag_fort13} = true ];then 
+    if ${lflag_fort13};then 
       cp fort.2 fort.3 fort.8 fort.16 fort.10 fort.13 lin betaJob
     else
       cp fort.2 fort.3 fort.8 fort.16 fort.10 fort.13 lin betaJob
@@ -807,9 +806,7 @@ function submitCreateFinalFort3Short(){
 }
 
 function submitCreateFinalFort3Long(){
-
-
-    if [ $lflag_fort13 ]; then
+    if $lflag_fort13; then
       ax0=0.0
       ax1=0.0
       cp ${fort13_jobs[${nConsidered} -1]} $sixdeskjobs_logs/fort.13
@@ -826,7 +823,7 @@ function submitCreateFinalFort3Long(){
       [ -n "${ax0}" ] || let __lerr+=1
       [ -n "${ax1}" ] || let __lerr+=1
     fi
-    #
+    ## if fort.13 flag is on %nss will now be substituted with the number of pairs in the current fort.13 job otherwise %nss does not exist anymore 
     sed -e 's/%turnsl/'$turnsl'/g' \
 	-e 's/%ax0l/'$ax0'/g' \
         -e 's/%nss/'$sixdeskpairs_current'/g' \
@@ -858,7 +855,7 @@ function submitCreateFinalInputs(){
     sixdeskmess  1 "Taking care of SIXTRACK fort.2/fort.3/fort.8/fort.16 in $RundirFullPath"
 
     # fort.3
-    if [ $lflag_fort13 ];then
+    if $lflag_fort13;then
       gzip -c $fort13_current > $RundirFullPath/fort.13.gz
       gzip -c $sixdeskjobs_logs/fort.3 > $RundirFullPath/fort.3.gz
     else
@@ -1498,13 +1495,11 @@ function treatLong(){
 	# separate output for current case from previous one
 	echo ""
         
-        if [ $lflag_fort13=true ];then 
+        if $lflag_fort13;then 
           sixdeskmess -1 "Considering job #$Ampl from fort.13"
         else
           sixdeskmess -1 "Considering amplitude step: $Ampl"
         fi
-        #echo $lflag_fort13 hereeeeee2
-        #exit
         if ${lReduceAngsWithAmplitude}; then 
           jAmple=${iAmple}
         else
@@ -1613,7 +1608,6 @@ function treatLong(){
 	        	    sixdeskmess  1 "Carrying on with next WU"
 	        	    continue
 	        	fi
-	        	
 	        	# final preparation of all SIXTRACK files
 	        	# NB: for boinc, it returns workunitName
 	        	submitCreateFinalInputs
@@ -2240,12 +2234,11 @@ if ${lgenerate} || ${lfix} ; then
     echo "$emit  $gamma" > $sixdesktrackStudy/general_input
     let __lerr+=$?
     # - set up of fort.3
-    if [ $lflag_fort13 = false ]; then 
-      tmpFiles=(fort.3.mad fort.3.mother1 fort.3.mother2)
-    else
+    if $lflag_fort13; then 
       tmpFiles=(fort.3.mad fort.3.mother1 fort.3.mother2 fort.13)
+    else
+      tmpFiles=(fort.3.mad fort.3.mother1 fort.3.mother2)
     fi
-    #for tmpFile in fort.3.mad fort.3.mother1 fort.3.mother2 ; do
     for tmpFile in ${tmpFiles[@]}; do
 	cp ${sixtrack_input}/${tmpFile} $sixdeskjobs_logs
 	if [ $? -ne 0 ] ; then
@@ -2451,7 +2444,7 @@ else
 	    sixdeskmess -1 "  --> along a line in (Qx,Qy) - total: ${iTotalTunes} pairs;"
 	fi
     fi
-    if [ $lflag_fort13 = false ]; then
+    if [ "$lflag_fort13" = false ]; then
       if [ $long -eq 1 ] ; then
           # generate array of amplitudes (it returns allAmplitudeSteps, fAmpStarts, fAmpEnds, ampstart, ampfinish)
           sixdeskAllAmplitudes
@@ -2514,7 +2507,7 @@ else
         echo ""
         sixdeskmess -1 "MADX seed $iMad"
         if ${lgenerate} || ${lfix} ; then
-            if [ ${lflag_fort13} = true ]  ; then
+            if ${lflag_fort13}; then
     	      iForts="2 8 13 16"
             else
     	      iForts="2 8 16"
diff --git a/utilities/bash/set_env.sh b/utilities/bash/set_env.sh
index 8667ea8..3e1c7d3 100755
--- a/utilities/bash/set_env.sh
+++ b/utilities/bash/set_env.sh
@@ -175,7 +175,7 @@ function setFurtherEnvs(){
     fi
 
     lReduceAngsWithAmplitude=false
-    if [ $lflag_fort13 = false ]; then
+    if [ "$lflag_fort13" = false ]; then
       if [ -n "${reduce_angs_with_aplitude}" ] ; then
           sixdeskmess -1 "wrong spelling of reduce_angs_with_amplitude. Please correct it for future use"
           reduce_angs_with_amplitude=${reduce_angs_with_aplitude}
diff --git a/utilities/templates/lsf/mad6t1.sh b/utilities/templates/lsf/mad6t1.sh
index cffa3f9..d4f506a 100644
--- a/utilities/templates/lsf/mad6t1.sh
+++ b/utilities/templates/lsf/mad6t1.sh
@@ -116,7 +116,7 @@ touch fc.34
 mv fc.2 fort.2
 mv fc.16 fort.16
 mv fc.8 fort.8
-if [ $lflag_fort13 = true ]; then
+if $lflag_fort13; then
   fils=(fort.2 fort.8 fort.13 fort.16)
 else
   fils=(fort.2 fort.8 fort.16)

From e4d3b9c4feab2dac43bd6058b6117a7a6c68ebcc Mon Sep 17 00:00:00 2001
From: skostogl <skostogl@lxplus057.cern.ch>
Date: Sat, 3 Mar 2018 23:35:44 +0100
Subject: [PATCH 3/4] fort.13 for submission

---
 utilities/bash/mad6t.sh           | 1 +
 utilities/templates/lsf/mad6t1.sh | 3 ++-
 2 files changed, 3 insertions(+), 1 deletion(-)

diff --git a/utilities/bash/mad6t.sh b/utilities/bash/mad6t.sh
index a61d7bb..ddd59dc 100755
--- a/utilities/bash/mad6t.sh
+++ b/utilities/bash/mad6t.sh
@@ -173,6 +173,7 @@ function submit(){
 		-e 's?%MADX_PATH%?'$MADX_PATH'?g' \
 		-e 's?%MADX%?'$MADX'?g' \
 		-e 's?%lflag_fort13%?'$lflag_fort13'?g' \
+                -e 's?%sixdeskstudy%?'$sixdeskstudy'?g' \
 		-e 's?%SIXTRACK_INPUT%?'$sixtrack_input'?g' $mad6tjob > mad6t_"$iMad".sh
 	    chmod 755 mad6t_"$iMad".sh
 	    
diff --git a/utilities/templates/lsf/mad6t1.sh b/utilities/templates/lsf/mad6t1.sh
index d4f506a..3312783 100644
--- a/utilities/templates/lsf/mad6t1.sh
+++ b/utilities/templates/lsf/mad6t1.sh
@@ -8,6 +8,7 @@ export fort_34=%FORT_34%
 export MADX_PATH=%MADX_PATH%
 export MADX=%MADX%
 export lflag_fort13=%lflag_fort13%
+export sixdeskstudy=%sixdeskstudy%
 echo "Calling madx version $MADX in $MADX_PATH"
 $MADX_PATH/$MADX < $junktmp/$filejob."$i" > $filejob.out."$i"
 cp -f $filejob.out."$i" $junktmp
@@ -138,7 +139,7 @@ do
     fi
   fi
   if [ $fil = "fort.13" ];then 
-    cp $sixdeskhome/fort.13 $sixtrack_input
+    cp $sixdeskstudy/fort.13 $sixtrack_input
     cp $sixtrack_input/fort.13 $sixtrack_input/fort.13_$i
     gzip $sixtrack_input/fort.13_$i
   else

From e0fe1bbb4d4330ae3722ccab84508668bbe0bcee Mon Sep 17 00:00:00 2001
From: skostogl <skostogl@lxplus092.cern.ch>
Date: Wed, 25 Apr 2018 11:10:16 +0200
Subject: [PATCH 4/4] split modified

---
 utilities/bash/dot_profile | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/utilities/bash/dot_profile b/utilities/bash/dot_profile
index faa0e58..1c57675 100755
--- a/utilities/bash/dot_profile
+++ b/utilities/bash/dot_profile
@@ -693,7 +693,7 @@ sixdeskAllAmplitudes_fort13(){
     else
       mkdir ${sixdeskjobs_logs}/fort.13_jobs
     fi
-    split -d -l $pairs_per_job fort.13 ${sixdeskjobs_logs}/fort.13_jobs/fort.13.
+    split -a 6 -d -l $pairs_per_job fort.13 ${sixdeskjobs_logs}/fort.13_jobs/fort.13.
     fort13_jobs=( $(find ${sixdeskjobs_logs}/fort.13_jobs/ -type f -name 'fort.13.*') )
     nb_fort13_jobs=${#fort13_jobs[@]}
     echo Fort.13 will be split in $nb_fort13_jobs jobs