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ConfSearch-carts-dGT
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#! /usr/bin/perl
$|++;
use Term::ANSIColor;
############################################################################
# ConfSearch #
# #
# This code is for performing a conformer search, implementing the EDTS #
# method. #
# #
# To execute the code, first make the script executable by running #
# >> "chmod +x ConfSearch" #
# from the containing directory. #
# #
# USAGE #
# ----- #
# ConfSearch $mol [$atom1 $atom2] [$gooddist] --> for transition state #
# optimisation, if r12 is fixed, this can be used to help determine the #
# optimised geometry is valid. #
# #
# REQUIRES #
# -------- #
# 1. Input file format "$mol.$dih.com" -> ensure the use of the #
# period (.) as opposed to underscores (_) or hyphens (-) #
# 2. $mol.list in the input directory. #
# 3. ~/bin/crinxyz
# #
# Several default values are listed below #
# $window ($EC1 and $EC2) #
# $Nmax #
# #
# While optimising Error (Address Error) -> Email to ask continue #
# While Runtime Terminate (killed) -> Email to ask continue #
# Not yet deal with Large system where the round2/3 maybe 1000 #
# All the job.list is printout in CF-* #
# CF-$mol.round1 (if 2nd lowest < 4kJ) -> CF-$mol.round2 -> CF-$mol.round3-$i.tosub
# (if 2nd lowest > 4kJ) -> CF-$mol.round3-$i.tosub
# A few other useful files:
# 1. CF-$mol.round$x.uh/lh (upper/lower half with the energy difference)
# 2. CF-$mol.*.window (those energies within 4kJ and the first Nmax with their energy difference)
# 3. CF-$mol.done (At every stage, the done file will tell you what has been done)
# 4. At the end of the program, you can look into CF-$mol.done.*, which tell you the all Energy difference.
# To adjust the sleep time:
# Current setting: Check full Queue = every $sleep_queue seconds;
# Check Job finished = every day.
#
############################################################################
# Developed from ConfSearch-carts by Naomi Haworth 17/3/2015
############################################################################
$ruser = $ENV{REMOTE_USER};
#$rdir = $ENV{PROJECT};
#$rdir = "f81";
$email = "$ENV{email}";
$debug=0;
$machine="raijin";
$sub="rjsub";
$ProjectCode[0] = ("$ENV{PROJECT}");
$ProjectCode[1] = ("$ENV{PROJECT2}");
if (!($ENV{PROJ1GRANT})) {
die "Please edit your .bashrc to include the following lines and source: \nexport PROJECT=f81\nexport PROJECT2=x69\nexport PROJ1GRANT=500\nexport PROJ2GRANT=800\n";
}
else {
$grant{$ProjectCode[0]} = $ENV{PROJ1GRANT};
$grant{$ProjectCode[1]} = $ENV{PROJ2GRANT};
}
############################################################################
$maxQ{x69} = 690; # Max is 400 but can be slow to update
$maxQ{f81} = 690; # Max is 400 but can be slow to update
$maxQ{user} = 650; # Limited to 350 to allow space for other group members
$maxCPU{x69} = 50000; # Default for vu normal queue
$maxCPU{f81} = 50000; # Default for vu normal queue
$maxCPU{user} = 50000; # Default for vu normal queue
$Nmax = 5; # Default
$EC1 = 3; # Default 3kJ/mol
$EC2 = 4; # Default 4kJ/mol
$sleep_job = 600;
$sleep_queue = 360;
$ncpus = 4;
$mol=$ARGV[0];
$mol=~s/.xyz//;
$T = 298.15;
$cutoff = 30;
for ($i = 1; $i <= 12; $i++) {
if ($ARGV[$i]) {
if ($ARGV[$i] =~ /^-T/) {
$T = $ARGV[$i+1];
}
if ($ARGV[$i] =~ /^-c/) {
$cutoff = $ARGV[$i+1];
}
if ($ARGV[$i] =~ /^-a1/) {
$atom1 = $ARGV[$i+1];
$tols = "yes";
}
if ($ARGV[$i] =~ /^-a2/) {
$atom2 = $ARGV[$i+1];
}
if ($ARGV[$i] =~ /^-gd/) {
$gooddist = $ARGV[$i+1];
}
if ($ARGV[$i] =~ /^-td/) {
$toldist = $ARGV[$i+1];
}
}
}
system(clear);
if ($atom1){
if (!$gooddist ){
$gooddist=2.5;
$toldist=0.1;
print "No appropriate bond length specified, $gooddist A will be used.\n";
print "No appropriate bond length tolerance specified, $toldist A will be used.\n";
}
else{
print "Bond length specified at $gooddist A.\n";
if (!$toldist){
print "No appropriate bond length tolerance specified, 0.00 A has been used.\n";
$toldist=0.00;
}
else{
print "Bond length tolerance specified at $toldist A.\n";
}
}
}
chomp($mol);
#$time1 = `quotasu -P x69 | grep 'Service Units remaining' |sed 's/.*\\*//' | sed 's/ //g'` ;
#$time2 = `quotasu -P f81 | grep 'Service Units remaining' |sed 's/.*\\*//' | sed 's/ //g'` ;
#chomp ($time1);
#chomp ($time2);
#$time = $time1 + $time2;
#Print Out Warnings!
print color 'green';
print "#########################################################################\n";
print "# Starting ConfSearch... #\n";
print "# Ensure you don't have a period (.) in the name of the molecule. #\n";
print "#########################################################################\n\n";
print color 'reset';
print "Checking queues... ";
$p = $ProjectCode[0];
@alloctime = split(/\s+/,`ssh $machine -l \$REMOTE_USER nci_account -P $p | grep 'Overall' `);
if ($alloctime[6]/1000 + 20 > $grant{$p}) {
print "Not enough SU available on project $ProjectCode[0] use $ProjectCode[1].\n";
$ProjectCode[0] = ("$ENV{PROJECT2}");
$ProjectCode[1] = ("$ENV{PROJECT}");
$p1 = 0;
}
else {
$freetime = $grant{$p} - $alloctime[6]/1000;
printf "%4.0f kSU available on project %3s.\n", $freetime, $p;
$p1 = 0;
}
print "\nConformer search for $mol \naccording to Gibbs free energy at $T K with $cutoff cm-1 QHO cutoff...\n\n-------------------------------------------------------------------------\n\n";
#print " Remaining Project Hours $time hr?\n" ;
###################################################################################
$InputDir = ".";
###################################################################################
# Round1 #
###################################################################################
print color 'blue';
print "#########################################################################\n";
print "# Beginning round 1... #\n";
print "#########################################################################\n\n";
print color 'reset';
if (!-e "CF-$mol.round1"){
#system("rm CF-$mol.round1");
open fr,">CF-$mol.round1" or die $!;
open comlist, "$mol.list" or die $!;
while (<comlist>){
#@crap=split(/\./,$_);
$dih = $_;
if (length($dih) <4 || (length($dih)<6 && $dih=~/a1/) ){
print fr "$mol.$dih";
}
}
close comlist;
close fr;
}
open round1, "CF-$mol.round1" or die $!;
while ($r1 = <round1>){
foreach $item ($r1){
chomp($item);
if (! -e "$item.log" and ! -e "$item.job") {
while (!($queue = freeQ())){
print color 'red';
print "Queue on machine $machine is full.\n\n";
print color 'reset';
sleep $sleep_queue;
}
testThenSubmit($queue,$item);
}
}
}
close round1;
sub testThenSubmit {
my ($q,$j) = @_;
if (!isBadComFile($j)) {
system("echo $sub $j.com -rproj $q -cs");
if($debug==0){
system("$sub $j.com -rproj $q -cs");
system("touch $j.job");
}
}
else {
print color 'red';
print "$j is too crowded.\n";
print color 'reset';
}
}
###################################################################################
# Round2 #
###################################################################################
system("cat CF-$mol.round1 | sort | uniq > CF-$mol.done");
open done, "CF-$mol.done" or die $!;
while ($done = <done>){
chomp($done);
foreach $y ($done){
$ok = 0;
if (-e "$y.log" ) {
$ok = check("$y");
}
while (! -e "$y.log" ){
$fin = `ssh -l $ruser $machine "if \[ -e JOB/$y.batch \] ;then echo 1 ;fi "`;
if ($fin == 1){
@rdir = split(/\s+/, `ssh -l $ruser $machine grep Project JOB/$y.batch`);
if ($rdir[1] =~ /Project/) {
`scp $ruser\@$machine:/short/$rdir[2]/$ruser/RUN/$y/$y.log .`;
}
else {
@rdir = split(/\s+/, `ssh -l $ruser $machine grep saved JOB/$y.batch`);
$rdir2 = substr($rdir[1], 0, -1);
`scp $ruser\@$machine:$rdir2/$y.log .`;
}
if (-e "$y.log" ){
`ssh -l $ruser $machine mv JOB/$y.batch BATCH/$y.batch`;
$ok = check("$y");
}
else {
print "something has gone wrong with the transfer of $y.log.\n";
$fin = 0;
}
}
else{
print color 'yellow';
print "$y.log in round 1 does not exist. Waiting for log file from \n $machine ...\n\n";
print color 'reset';
sleep $sleep_job;
}
}
}
}
close done;
opteng("CF-$mol.round1",$EC1);
system("wc CF-$mol.round1.lh > CF-$mol.round1.ll" );
open alength, "CF-$mol.round1.ll" or die $!;
while ($asd = readline(alength)){
@crapl=split(/\s+/,$asd);
$l = $crapl[1];
}
close alength;
squeeze("CF-$mol.round1.uh");
if ($l ne "1"){
print color 'blue';
print "########################################################################\n";
print "# Beginning round 2... #\n";
print "########################################################################\n\n";
print color 'reset';
squeeze("CF-$mol.round1.lh");
group("CF-$mol.round1.lh.sq");
combine("CF-$mol.round1.lh.sq.gp");
system("sort CF-$mol.i | uniq | sed 's/\\.//g' | sed 's/\^/$mol./'> CF-$mol.round1.todo");
system("rm CF-$mol.i");
recomb("CF-$mol.round1.todo");
system("mv CF-$mol.round1.todo.uniq CF-$mol.round2");
open round2, "CF-$mol.round2" or die $!;
while ($r2 = <round2>){
foreach $j ($r2){
chomp($j);
if (! -e "$j.log" and ! -e "$j.job") {
while (!($queue = freeQ())){
print color 'red';
print "Queue on machine $machine is full.\n\n";
print color 'reset';
sleep $sleep_queue;
}
testThenSubmit($queue,$j);
}
}
}
close round2;
open round2, "CF-$mol.round2" or die $!;
while ($round2 = <round2>){
chomp($round2);
foreach $y ($round2){
$ok = 0;
if (-e "$y.log" ) {
$ok = check("$y");
}
while (! -e "$y.log" ){
$fin = `ssh -l $ruser $machine "if \[ -e JOB/$y.batch \] ;then echo 1 ;fi "`;
if ($fin == 1){
@rdir = split(/\s+/, `ssh -l $ruser $machine grep Project JOB/$y.batch`);
if ($rdir[1] =~ /Project/) {
`scp $ruser\@$machine:/short/$rdir[2]/$ruser/RUN/$y/$y.log .`;
}
else {
@rdir = split(/\s+/, `ssh -l $ruser $machine grep saved JOB/$y.batch`);
$rdir2 = substr($rdir[1], 0, -1);
`scp $ruser\@$machine:$rdir2/$y.log .`;
}
if (-e "$y.log" ){
`ssh -l $ruser $machine mv JOB/$y.batch BATCH/$y.batch`;
$ok = check("$y");
}
else {
print "something has gone wrong with the transfer of $y.log.\n";
$fin = 0;
}
}
else{
print color 'yellow';
print "$y.log in round 2 does not exist. Waiting for log file from \n $machine ...\n\n";
print color 'reset';
sleep $sleep_job;
}
}
}
}
close round2;
}
else {
print color 'blue';
print "########################################################################\n";
print "# Beginning round 3... #\n";
print "########################################################################\n\n";
print color 'reset';
}
###################################################################################
# Round3 #
###################################################################################
if (-e "CF-$mol.round3"){
system("/bin/rm CF-$mol.round3");
}
system("touch CF-$mol.round2 CF-$mol.round3");
open r1uh, "CF-$mol.round1.uh.sq" or die $!;
$uhi = 0;
while (<r1uh>){
foreach $x ($_){
open r1uhlist, ">CF-$mol.round1.uh.sq.$uhi" or die $!;
print r1uhlist $x;
close r1uhlist;
}
system("cat CF-$mol.round1 CF-$mol.round2 CF-$mol.round3 | sort | uniq > CF-$mol.done");
opteng("CF-$mol.done",$EC2);
window("CF-$mol.done.window","CF-$mol.round1.uh.sq.$uhi");
combine("CF-$mol.window");
system("cat CF-$mol.i | sed 's/\^/CF-$mol./' > CF-$mol.needreorder");
system("rm CF-$mol.i");
reorder("CF-$mol.needreorder");
#Before submit round3-1, check if there is anything in DONE!
recomb("CF-$mol.order");
system("sort CF-$mol.order.uniq | uniq > CF-$mol.round3-$uhi.tosub");
system("cat CF-$mol.round3-$uhi.tosub >> CF-$mol.round3");
open R3tosub, "CF-$mol.round3-$uhi.tosub" or die $!;
print color 'blue';
print "########################################################################\n";
print "# Beginning round 3-$uhi... #\n";
print "########################################################################\n\n";
print color 'reset';
while ($R3 = <R3tosub>){
chomp($R3);
foreach $y ($R3){
if (! -e "$y.log" and ! -e "$y.job") {
while (!($queue = freeQ())){
print color 'red';
print "Queue on machine $machine is full.\n\n";
print color 'reset';
sleep $sleep_queue;
}
testThenSubmit($queue,$y);
}
}
}
close R3tosub;
$fileexist= 1;
open R3tosub, "CF-$mol.round3-$uhi.tosub" or die $!;
while ($R3tosub = <R3tosub>){
chomp($R3tosub);
foreach $y ($R3tosub){
$ok = 0;
if (-e "$y.log" ) {
$ok = check("$y");
}
while (! -e "$y.log" ){
$fin = `ssh -l $ruser $machine "if \[ -e JOB/$y.batch \] ;then echo 1 ;fi "`;
if ($fin == 1){
@rdir = split(/\s+/, `ssh -l $ruser $machine grep Project JOB/$y.batch`);
if ($rdir[1] =~ /Project/) {
`scp $ruser\@$machine:/short/$rdir[2]/$ruser/RUN/$y/$y.log .`;
}
else {
@rdir = split(/\s+/, `ssh -l $ruser $machine grep saved JOB/$y.batch`);
$rdir2 = substr($rdir[1], 0, -1);
`scp $ruser\@$machine:$rdir2/$y.log .`;
}
if (-e "$y.log" ){
`ssh -l $ruser $machine mv JOB/$y.batch BATCH/$y.batch`;
$ok = check("$y");
}
else {
print "something has gone wrong with the transfer of $y.log.\n";
$fin = 0;
}
}
else{
print color 'yellow';
print "$y.log in round 3 does not exist. Waiting for log file from \n $machine ...\n\n";
print color 'reset';
sleep $sleep_job;
}
}
}
}
close R3tosub;
$uhi++;
}
close r1uh;
system("cat CF-$mol.round1 CF-$mol.round2 CF-$mol.round3 | sort | uniq > CF-$mol.done");
opteng("CF-$mol.done",$EC2);
system("rm CF-$mol.*order* CF-$mol.*sq* CF-$mol.*.ll");
print color 'green';
print "########################################################################\n";
print "# Conformer search complete. #\n";
print "########################################################################\n\n";
print color 'reset';
system("touch CF-$mol.complete");
############################################################################
# freeQ #
############################################################################
sub freeQ{
for ($i = $p1; $i <= $#ProjectCode; $i++) {
$p = $ProjectCode[$i];
@totalQ = split(/\s+/,`ssh $machine -l \$REMOTE_USER /opt/pbs/default/bin/nqstat -P $p | grep ' $ruser ' | grep ' $p ' | wc `);
@Queuejob = `ssh $machine -l \$REMOTE_USER /opt/pbs/default/bin/nqstat -P $p | grep ' $p ' | sed 's/.*MB//' | sed 's/.*GB//'`;
print "\n";
print "Total queued jobs for project $p is $#Queuejob. ";
if($#Queuejob >= $maxQ{$p}){
print "This is greater than the limit of $maxQ{$p} per project.\n";
}
else{
print "This is less than the limit of $maxQ{$p} per project.\n";
print "Total queued jobs for $ruser on project $p = ", $totalQ[1],". ";
if ($totalQ[1] >= $maxQ{user}){
print "This is greater than the limit of $maxQ{user} per user.\n";
}
else{
print "This is less than the limit of $maxQ{user} per user.\n";
return $p;
}
}
}
return 0;
}
#sub freeQ{
# @totalQ = split(/\s+/,`ssh $machine -l \$REMOTE_USER /opt/pbs/default/bin/nqstat -P $rdir | grep ' $ruser ' | grep ' $rdir ' | wc `);
# @totalCpus = `ssh $machine -l \$REMOTE_USER /opt/pbs/default/bin/nqstat | grep ' \$REMOTE_USER ' | grep ' $rdir ' | sed 's/.*MB//' | sed 's/.*GB//' `;
# $Cpus = add(@totalCpus);
# print "\n";
# if ($totalQ[1] >= $maxQ{user}){
# print "Total queued jobs = ", $totalQ[1]," is greater than $maxQ{user} per user.\n";
# print "test\n";
# }
# elsif ($Cpus + $ncpus >= $maxCPU{user}){
# $Cpus1 = $Cpus + $ncpus;
# print "Total CPUs in use = ", $Cpus1 , " is greater than $maxCPU{user} per user.\n";
# }
# else{
# print "Total CPUSs in use = ", $Cpus , " is less than $maxCPU{user} per user.\n";
# print "Total queued jobs = ", $totalQ[1]," is less than $maxQ{user} per user.\n";
# foreach $p (@ProjectCode){
# for ($i = 0; $i <= 1; $i++) {
# if ($i == 0) {$p = "f81"} else {$p = "x69"}
# @Queuejob = `ssh $machine -l \$REMOTE_USER /opt/pbs/default/bin/nqstat -P $p | grep ' $p ' | sed 's/.*MB//' | sed 's/.*GB//'`;
# $currentCpus =add(@Queuejob);
# print "Total CPUs in use for project $p is $currentCpus.\n";
# print "Total queued jobs for project $p is $#Queuejob.\n\n";
# if ($currentCpus + $ncpus >= $maxCPU{$p}){ # this is for max 1000 per project.
# print "Total queued cpus = ", $currentCpus + $ncpus," is greater than $maxCPU{$p} per project.\n";
# }
# if($#Queuejob+1 >= $maxQ{$p}){
# print "Total queued jobs = ", $#Queuejob+1," is greater than $maxQ{$p} per project.\n";
# }
# else{
# return $p;
# }
# }
# }
# return 0;
#}
############################################################################
# add #
############################################################################
sub add{
$sum = 0;
while (@_) {
$Q = shift @_;
next unless($Q =~ m/[0-9]/);
$sum+=$Q;
}
return $sum;
}
############################################################################
# Check Output file is Valid + (Good Distance) for TS Optimisation #
############################################################################
sub check {
my $file = shift(@_);
$jobdone =-2 ;
if (! $tols){
$test1 = `grep Done $file.log | tail -n 1`;
$test2 = `grep Frequ $file.log | tail -n 1`;
$test3 = `grep "fake Gaussian" $file.log | tail -n 1`;
if ($test3 =~ /fake/) {
print color 'red';
print "$file is too crowded - not considerd.\n\n";
print color 'reset';
return 0;
}
elsif ($test1 !~ /Done/) {
print color 'red';
print "$file did not run correctly - submitting again.\n";
print color 'reset';
system("$sub $file.com -cs");
`mv $file.log $file.log.bak`;
`touch $file.job`;
return 1;
}
elsif (($test2 !~ /Frequ/) && (-e "$file.log.bak")) {
print color 'red';
print "$file has failed twice - not resubmitting.\n\n";
print color 'reset';
return 0;
}
elsif ($test2 !~ /Frequ/) {
print color 'red';
print "$file failed - rerunning.\n";
print color 'reset';
system("rerun $file.log");
`mv $file.log $file.log.bak`;
`touch $file.job`;
return 1;
}
else{
print color 'green';
printf "%s terminated normally.\n\n",$file;
print color 'reset';
return 0;
}
}
elsif ($tols){
open ifh, "$file.log" or die $!;
system("crinxyz $file.log ");
open xyzfile, "$file.xyz" or die $!;
readline(xyzfile);
readline(xyzfile);
$natom=1;
while ($atomline = readline(xyzfile)){
@atom = split(/\s+/,$atomline);
$atomx[$natom]= $atom[1];
$atomy[$natom]= $atom[2];
$atomz[$natom]= $atom[3];
$natom ++;
}
close xyzfile;
if ($atom[1] =~/Xx/){
$bondlength =0.0
}
else{
$bondlength =
sqrt(($atomx[$atom1] - $atomx[$atom2])**2 + ($atomy[$atom1] - $atomy[$atom2])**2 + ($atomz[$atom1] - $atomz[$atom2])**2);
}
while ($line = readline(ifh)) {
if ($line=~ /Normal/){
$jobdone=1;
}
elsif ($line=~ /Address/){
$jobdone=-1;
}
elsif ($line=~ /kill/){
$jobdone=-2;
}
}
close ifh;
if (($jobdone <=-2) ) {
if ( $bondlength<= $gooddist+$toldist and $bondlength >= $gooddist-$toldist){
printf "%s killed, no resubmit\t %5.2f\t(within %5.2f-%5.2f )\n",$file,$bondlength,$gooddist-$toldist,$gooddist+$toldist;
$resub = "N"; # maybe yes
system("mailx -s 'Resubmit $file (killed), bond length is $bondlength within $gooddist-$toldist and $gooddist+$toldist' $email < $file.xyz ") ;
}
else{
printf "%s killed, no resubmit\t %5.2f\t(shorter than %5.2f or longer than %5.2f)\n",$file,$bondlength,$gooddist-$toldist,$gooddist+$toldist;
$resub = "N";
system("mailx -s 'NO Resubmit $file (killed), bond length is $bondlength shorter than $gooddist-$toldist or longer than $gooddist+$toldist' $email < $file.xyz ") ;
}
}
if ($resub eq "Y"){
system("cat $file.log >> $file.log.2; /bin/rm $file.log");
return 0;
}
elsif (($jobdone ==-1) ) {
if ( $bondlength<= $gooddist+$toldist and $bondlength >= $gooddist-$toldist){
printf "%s Address Error, resubmit\t %5.2f\t(within %5.2f- %5.2f)\n",$file,$bondlength,$gooddist-$toldist,$gooddist+$toldist;
$resub = "N"; # maybe yes
system("mailx -s 'Resubmit $file (Address Error), bond length is $bondlength (within $gooddist-$toldist and $gooddist +$toldist), but we adivice you to check what causes this Address Error Termination' $email < $file.xyz ") ;
}
else{
printf "%s Address Error, no resubmit\t %5.2f\t(shorter than %5.2f or longer than %5.2f)\n",$file,$bondlength,$gooddist-$toldist,$gooddist+$toldist;
$resub = "N";
system("mailx -s 'NO Resubmit $file (Address Error), bond length is $bondlength (shorter than $gooddist -$toldist or longer than $gooddist+$toldist), ' $email < $file.xyz ") ;
}
}
if ($resub eq "Y"){
system("cat $file.log >> $file.log.2; /bin/rm $file.log");
return 0;
}
elsif ($jobdone ==1){
if ( $bondlength<= $gooddist+$toldist and $bondlength >= $gooddist-$toldist){
print color 'green';
printf "%s terminated normally\t %5.2f\t(within %5.2f- %5.2f)\n",$file,$bondlength,$gooddist-$toldist,$gooddist+$toldist;
print color 'reset';
}
else{
print color 'green';
printf "%s terminated normally.\t %5.2f\t(shorter than %5.2f or longer than %5.2f)\n",$file,$bondlength,$gooddist-$toldist,$gooddist+$toldist;
print color 'reset';
}
}
return 0;
}
}
############################################################################
# OptEng #
############################################################################
sub opteng{
$count = 0;
my ($roundlist,$window) = @_;
open roundlist, $roundlist or die $!;
while ($round = <roundlist>) {
foreach $i ($round){
chomp($i);
@roundlist=split(/\./,$i);
$dih[$count] = $roundlist[1];
@line = split(/\s+/,`grep Done $i.log | tail -n 1 `);
$E[$count]=$line[5];
open datfile, ">>$i.$T.dat" or die $!;
open logfile, "$i.log" or die $!;
local $/;
open(LOG, "$i.log") || die "Can't open $i.log for reading.\n";
undef $/;
@log = split(/ifsldjfalj/,<LOG>,-1);
close(LOG)|| die "Can't close $i.log.\n";
if ($log[0] =~ /Frequ/) {
$zpve = 0;
$tc = 0;
$entropy = 0;
$TS = 0;
if (! -e $i.$T.dat) {
`tchem-qho $i.log $T $cutoff`;
}
@line = split(/\s+/,`grep Stotal $i.$T.dat`);
$entropy = $line[5];
$TS = $entropy*$T/627.51/4.184/1000;
@line = split(/\s+/,`grep "TC Harm" $i.$T.dat`);
$tc = $line[5];
$tc = $tc/627.51/4.184;
@line = split(/\s+/,`grep "ZPVE in" $i.$T.dat`);
$zpve = $line[5];
$zpve = $zpve/627.51/4.184;
$H[$count] = $E[$count] + $zpve + $tc;
$G[$count] = $H[$count] - $TS;
print datfile "\n DFT Energy ZPVE TC Entropy TS H G \n";
printf datfile "%12.6f %12.6f %12.6f %12.6f %12.6f %12.6f %12.6f\n", $E[$count], $zpve, $tc, $entropy, $TS, $H[$count], $G[$count];
}
else {
$G[$count] = 1000.0;
}
printf datfile "\nGfinal %12.6f\n", $G[$count];
close (datfile);
$eng[$count] = $G[$count];
# open output, "$i.log" or die $!; # this might be taking too much time, to get energy for each of them. need reoptimize!! Leaf
# while (<output>) {
# if (/SCF D/) {
# @crap=split(/\s+/,$_);
# $eng[$count]=$crap[5];
# }
# }
# close output;
if ($tols){
system("crinxyz $i.log ");
open xyzfile, "$i.xyz" or die $!;
readline(xyzfile);
readline(xyzfile);
$natom=1;
while ($atomline = readline(xyzfile)){
@atom = split(/\s+/,$atomline);
$atomx[$natom]= $atom[1];
$atomy[$natom]= $atom[2];
$atomz[$natom]= $atom[3];
$natom ++;
}
close xyzfile;
$bonddist[$count] =
sqrt(($atomx[$atom1] - $atomx[$atom2])**2 + ($atomy[$atom1] - $atomy[$atom2])**2 + ($atomz[$atom1] - $atomz[$atom2])**2);
if ( $bonddist[$count] >= $gooddist+$toldist or $bonddist[$count] <= $gooddist-$toldist){
$eng[$count] = 0.0;
}
#print "$dih[$count] , $bonddist[$count]\n";
}
#print "$dih[$count] , $eng[$count]\n";
$count ++;
}
}
close roundlist;
sub numerically { $a <=> $b; }
@sorteng = sort numerically @eng;
$sortk=0;
while ($sortk <$count){
for ($k = 0; $k < $count ; $k++){
if ($sorteng[$sortk] == $eng[$k] ){
$sortdih[$sortk] = $dih[$k];
$sortk++;
}
}
}
open fla, ">$roundlist.all" or die $!;
open flh, ">$roundlist.lh" or die $!;
open flw, ">$roundlist.window" or die $!;
open fuh, ">$roundlist.uh" or die $!;
$Lowest = ($sorteng[1]-$sorteng[0]) *2625.5;
if ($Lowest < $window){
for ($sortk = 0; $sortk < $count ; $sortk++){
$Deng[$sortk]= ($sorteng[$sortk]-$sorteng[0]) *2625.5;
if (($Deng[$sortk] < $window && $Deng[$sortk]> -$window)&& $sortk < $Nmax ){
printf flw "Less than %.2fkJ/mol= %s \t%f\n", $window, $sortdih[$sortk], $Deng[$sortk];
}
if ($sortk < $count/2) {
printf flh "Lower Half = %s \t%f\n", $sortdih[$sortk], $Deng[$sortk];
printf fla "Lower Half = %s \t%f kJ/mol or %f Hartree\n", $sortdih[$sortk], $Deng[$sortk], $sorteng[$sortk];
}
else{
printf fuh "Upper Half = %s \t%f\n", $sortdih[$sortk], $Deng[$sortk];
printf fla "Upper Half = %s \t%f kJ/mol or %f Hartree\n", $sortdih[$sortk], $Deng[$sortk], $sorteng[$sortk];
}
}
print "\n-----------------------------------------------------------\n";
printf "Lowest energy conformer is %s \t%f Hartree\n", $sortdih[0], $sorteng[0];
printf "The next lowest is %s \t+%f kJ/mol\n", $sortdih[1] ,$Lowest ;
print "-----------------------------------------------------------\n";
}
else {
print "\n-----------------------------------------------------------\n";
printf "Lowest 1 = %s \t%f Hartree\n", $sortdih[0], $sorteng[0];
printf "No other conformer has energy less than %.2fkJ/mol\n", $window;
print "-----------------------------------------------------------\n";
printf flh "Lowest 1 = %s \t%f\n", $sortdih[0], $Deng[0];
printf fla "Lowest 1 = %s \t%f kJ/mol or %f Hartree\n", $sortdih[0], $Deng[0], $sorteng[0];
printf flw "Less than %.2fkJ/mol= %s \t%f\n", $window, $sortdih[0], $Deng[0];
for ($sortk = 1; $sortk < $count ; $sortk++){
$Deng[$sortk]= ($sorteng[$sortk]-$sorteng[0]) *2625.5;
printf fuh "Upper Rest = %s \t%f\n", $sortdih[$sortk], $Deng[$sortk];
printf fla "Upper Rest = %s \t%f kJ/mol or %f Hartree\n", $sortdih[$sortk], $Deng[$sortk], $sorteng[$sortk];
}
}
close fla;
close flh;
close flw;
close fuh;
}
############################################################################
# Squeeze #
############################################################################
sub squeeze{
my $tosq=shift(@_);
open filesq,">$tosq.sq" or die $!;
open tosq, $tosq or die $!;
$count=0;
while ($dihhh= readline(tosq)){
@crap=split(/\s/,$dihhh);
$dih = $crap[3];
if (length($dih) <4 ){
print filesq "$dih\n";
}
else {
@IndDih= split(/a1/,$dih);
print filesq "$IndDih[1]\n";
}
}
close tosq;
close filesq;
}
############################################################################
# Group #
############################################################################
sub group{
my $togp=shift(@_);
$count = 0;
$maxk = 0;
@list = ("a","b","c","d","e","f","g","h","i","j","k","l","m","n","o","p","q","r","s","t","u","v","w","x","y","z");
open togp, "$togp" or die $!;
while ($dih[$count] = readline(togp)){
chomp($dih[$count]);
@diha = split(/\d+/,$dih[$count]);
$aaa[$count] = $diha[0];
chomp($aaa[$count]);
for ($k=0;$k<=length[$list];$k++){
#$group[$k][0]="";
if ("$aaa[$count]" eq "$list[$k]"){
$group[$k][$gp[$k][$dep]]= $dih[$count] ;
$gp[$k][$dep]++;
if ($k > $maxk){ $maxk = $k;}
}
}
$count++;
}
close togp;
open filegp, ">$togp.gp" or die $!;
for ($i=0;$i<=$maxk; $i++) {
if ( length($group[$i]) > 0 ){
for ($j=0;$j<=$gp[$i][$dep];$j++) {
print filegp "$group[$i][$j] " ;
}
print filegp "\n";
}
}
close filegp;
}
############################################################################
# Combine without. #
############################################################################
sub combine{
@data = ();
#use Data::Dumper;
my $tocomb = shift(@_);
open tocomb,"$tocomb" or die $!;
while ($nnn=readline(tocomb)){
push(@data,[split(/\s+/,$nnn)]);;
}
close tocomb;
open moli, ">CF-$mol.i" or die $!;
# start at 1 to skip the empty selection
for ($i = 3; $i < 2**@data; $i++) {
@bin = dec2bin($i);
my @tmp = ();
for ($j = 0; $j < @bin ;$j++) {
push(@tmp,$data[$j]) if ($bin[$j]);
}
perm("",@tmp);
}
sub dec2bin {
my $str = unpack("B32", pack("N", shift));
$str =~ s/^0+(?=\d)//;
return split(//,reverse($str));
}
sub perm {
my ($s,@a) = @_;
my $i;
if (@a) {
my @b = @{$a[0]};
shift (@a);
for (@b) {
#change this line later
perm($s."$_.",@a);
}
}else {
#print length($s),"\n";
#print "$s\n";
if (length($s)>3){
if ($s =~ /a/) {
print moli "$s\n";
}
else{
print moli "a1.$s\n";
}
}
}
return;
}
close moli;
}
############################################################################
# ReCombine #
############################################################################
sub recomb{
my $torc = shift(@_);
chomp($torc);
open torc, "$torc" or die $!;
open moldone,"CF-$mol.done" or die $!;
$count1=0;
$count2=0;
while ($crap1[$count1] = readline(torc)){
chomp($crap1[$count1]);
@crap2 = split(/\./,$crap1[$count1]);
$todo[$count1] = $crap2[1];
$count1++;
}
while ($crap2[$count2] = readline(moldone)){
chomp($crap2[$count2]);
@crap3 = split(/\./,$crap2[$count2]);
$done[$count2] = $crap3[1];
$count2++;
}
open todo, ">$torc.uniq" or die $!;
for ($kk=0;$kk< $count1 ; $kk++){
for ($jj=0;$jj<$count2;$jj++){
if ("$done[$jj]" eq "$todo[$kk]"){
$iii=1;
}
else{
$iii=0;
}