View of /trunk/scripts/nx.sh

#!/bin/bash

source utils.sh
#On exit remove tmp files
tmp_files=(tmp* )
trap 'err_report $LINENO' ERR
trap cleanup EXIT INT
exe=$(basename $0)

#Enter HL or LL 
tag=$1

if [ -f tsscds.dat ];then
   inputfile=tsscds.dat
else
   echo "tsscds input file is missing. You sure you are in the right folder?"
   exit
fi
molecule=`awk '{if($1=="molecule") print $2}' $inputfile`
tsdir=tsdir${tag}_${molecule}
final=FINAL_${tag}_${molecule}
rxnet=${final}/RXNet.cg
rate=` awk '/Rate/{if ($2=="canonical") print "0";if($2=="microcanonical") print "1" }' $inputfile `
temperature=` awk 'BEGIN{t=0};/TKMC/{t=$2};END{print t}'  $inputfile `
energy=` awk 'BEGIN{e=0};/EKMC/{e=$2};END{print e}'  $inputfile `
if [ $rate -eq 0 ]; then
     kmcfile=${tsdir}/KMC/kmcT${temperature}.out
fi
if [ $rate -eq 1 ]; then
     kmcfile=${tsdir}/KMC/kmcE${energy}.out
fi

#Safety checks before proceeding
if [ ! -f $rxnet ];then
   echo $rxnet has not been created
   exit 0
fi
if [ ! -f $kmcfile ];then
   echo $kmcfile has not been created
   exit 0
fi


awk '/counts per process/{p=1};{if(p==1 && NF==2) print $2}' $kmcfile > tmp_cppinp
paste $tsdir/KMC/processinformation tmp_cppinp  | awk '{if($NF>0) print $0}' > tmp_cppi

awk '{nts[NR]=$4;m1[NR]=$5;m2[NR]=$6;nn[NR]=$7};END{nts[NR+1]=0;nts[0]=0;for(i=1;i<=NR;i++) { {if(nts[i]!=nts[i+1] && nts[i]!=nts[i-1] ) print nts[i],nn[i]};{if(nts[i]==nts[i+1]) print nts[i],nn[i]+nn[i+1]}} }' tmp_cppi > tmp_cppii

awk 'NR>1{if($NF!="DISCONN") print $0}' $rxnet |  awk '{if($3=="MIN" && $6=="MIN" ) print $1,$4,$7}
{if($6=="PROD") {++pn;p[pn]=$7;m[pn]=$4;ts[pn]=$1} }
{if($1=="PROD") {++pn2;p2[pn2]=$2;pc[pn2]=$3$4$5$6$7$8$9} }
END{for(i=1;i<=pn;i++){
  for(j=1;j<=pn2;j++) {if(p[i]==p2[j]) print ts[i],m[i],pc[j]}
  }
}'  > tmp_cppiii

cat tmp_cppii tmp_cppiii | awk '{ 
if(NF==2)
   { 
   ++rel
   nts[rel]=$1
   nn[rel]=$2 
   sum+=$2}
else
   for(i=1;i<=rel;i++) {if($1==nts[i]) print $2,$3,nn[i]/sum}
}'   > tmp_cppiv

#from multigraph to graph

awk '{s1[NR]=$2;s2[NR]=$3;w[NR]=1}
END{k=0
for(i=1;i<=NR;i++) {
  if(w[i]>0) {k=k+1;wf[k]=w[i];s1f[k]=s1[i];s2f[k]=s2[i]}
  for(j=i+1;j<=NR;j++){
    if( s1[i]==s1[j] && s2[i]==s2[j]) {
          wf[k]+=w[j]
          w[j]=0
          ni=0}
    if( s1[i]==s2[j] && s2[i]==s1[j]) {
          wf[k]+=+w[j]
          w[j]=0
          ni=0}
         }
    }
for(i=1;i<=k;i++) print s1f[i],s2f[i],wf[i]} ' tmp_cppiii >${final}/rxn_all.txt

awk '{s1[NR]=$1;s2[NR]=$2;w[NR]=$3}
END{k=0
for(i=1;i<=NR;i++) {
  if(w[i]>0) {k=k+1;wf[k]=w[i];s1f[k]=s1[i];s2f[k]=s2[i]}
  for(j=i+1;j<=NR;j++){
    if( s1[i]==s1[j] && s2[i]==s2[j]) {
          wf[k]+=w[j]
          w[j]=0
          ni=0}
    if( s1[i]==s2[j] && s2[i]==s1[j]) {
          wf[k]+=+w[j]
          w[j]=0
          ni=0}
         }
    }
for(i=1;i<=k;i++) print s1f[i],s2f[i],wf[i]} ' tmp_cppiv >${final}/rxn_kin.txt