ConfSearch-carts

#! /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.
#                       
############################################################################    

# Modified by Naomi Haworth 17/3/2015


############################################################################
$ProjectCode[0] = ("$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};
}
$ruser = $ENV{REMOTE_USER};
#$rdir = $ENV{PROJECT};
#$rdir = "f81";
$email = "$ENV{email}";             
$debug=0;
$machine="raijin";
$sub="rjsub";
############################################################################

$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//;
$atom1=$ARGV[1];
$atom2=$ARGV[2];
system(clear);
if ($ARGV[1]){
    if (!$ARGV[3] ){
        $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{
        $gooddist=$ARGV[3];
        print "Bond length specified at $gooddist A.\n";
        if (!$ARGV[4]){
            print "No appropriate bond length tolerance specified, 0.00 A has been used.\n";
            $toldist=0.00;
        }
        else{
            $toldist=$ARGV[4];
            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}) {
    $p1 = 1;
    print "Not enough SU available on project $p use $ProjectCode[1].\n";
}
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 according to total energy...\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];
#       $p = "f81"; 
        @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 Normal $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 !~ /Normal/) && (-e "$file.log.bak")) {
            print color 'red';
            print "$file has failed twice - not resubmitting.\n\n";
            print color 'reset';
            return 0; 
        }
        elsif ($test2 !~ /Normal/) {
            print color 'red';
            print "$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];
            @crap = split(/\s+/,`grep Done $i.log | tail -n 1 `);
            $eng[$count]=$crap[5];
#            open output, "$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{
                $iii=0;
            }
        }
        if ($iii ==0){
            print todo "$mol.$todo[$kk]\n";
        }
    }
    close moldone;
    close todo;
    close torc;
}

############################################################################
#                          Window                                          #
#     < CF-$mol.done.window CF-$mol.round1.uh.sq.$i > CF-$mol.window                #
############################################################################    

sub window {
    my ($donewd,$uhi)=@_;

    open wd,">CF-$mol.window" or die $!;

    open uhi, "$uhi" or die $!;
    while ($dihh= readline(uhi)){
        @crap=split(/\s/,$dihh);    
        $dih = $crap[0];
        print wd "$dih ";
    }
    print wd "\n";
    close uhi;

    open donewd, $donewd or die $!;
    $count=0;
    while ($dihh= readline(donewd)){
        @crap=split(/\s/,$dihh);
        $dih = $crap[3];
        $dih =~ s/(\d)/$1\./g;
        print wd "$dih ";
    }
    close wd;
    close donewd;
}


############################################################################
#                          Window                                          #
#     < CF-$mol.done.window CF-$mol.round1.uh.sq.$i > CF-$mol.window       #
############################################################################    
sub reorder{
    @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");

    my $order = shift(@_);
    open molorder,">CF-$mol.order" or die $!;

    open order, $order or die $!;
    while ($dihhh= readline(order)){
        @crap=split(/\./,$dihhh);
        print molorder "CF-$mol.";
        for ($count=@crap; $count >0 ; $count--){
            $dih[$count] = $crap[$count];
            @ttt = split(/\d+/,$dih[$count]);
            $a[$count]= $ttt[0];
            $n[$count]= $ttt[1];
            for ($j=0; $j<26; $j++){
                if ("$a[$count]" eq "$list[$j]") {
                    $ooo[$j] = $dih[$count]; 
                }
            }
        }
        for ($j=0; $j<26; $j++){       
            print molorder "$ooo[$j]";
        }
        @ooo = ();
        print molorder "\n";
    }

    close order;
    close molorder;
}

#----------------------------(  promptUser  )-----------------------------#
#                                                                         #
#  FUNCTION:    promptUser                                                #
#                                                                         #
#  PURPOSE: Prompt the user for some type of input, and return the        #
#       input back to the calling program.                                #
#                                                                         #
#  ARGS:    $promptString - what you want to prompt the user with         #
#       $defaultValue - (optional) a default value for the prompt         #
#                                                                         #
#-------------------------------------------------------------------------#

sub promptUser {

    #-------------------------------------------------------------------#
    #  two possible input arguments - $promptString, and $defaultValue  #
    #  make the input arguments local variables.                        #
    #-------------------------------------------------------------------#

    local($promptString,$defaultValue) = @_;

    #-------------------------------------------------------------------#
    #  if there is a default value, use the first print statement; if   #
    #  no default is provided, print the second string.                 #
    #-------------------------------------------------------------------#

    if ($defaultValue) {
        print $promptString, "[", $defaultValue, "]: ";
    } else {
        print $promptString, ": ";
    }

    $| = 1;               # force a flush after our print
    $_ = <STDIN>;         # get the input from STDIN (presumably the keyboard)


    #------------------------------------------------------------------#
    # remove the newline character from the end of the input the user  #
    # gave us.                                                         #
    #------------------------------------------------------------------#

    chomp;

    #-----------------------------------------------------------------#
    #  if we had a $default value, and the user gave us input, then   #
    #  return the input; if we had a default, and they gave us no     #
    #  no input, return the $defaultValue.                            #
    #                                                                 # 
    #  if we did not have a default value, then just return whatever  #
    #  the user gave us.  if they just hit the <enter> key,           #
    #  the calling routine will have to deal with that.               #
    #-----------------------------------------------------------------#

    if ("$defaultValue") {
        return $_ ? $_ : $defaultValue;    # return $_ if it has a value
    } else {
        return $_;
    }
}


#if (isBadComFile($ARGV[0])) {
#    print "Com file too crowded\n";
#}

##############################################################

# Usage isBadComFile(nameOfMolecule)
sub isBadComFile {
    my $maxBadness = 2;
    my $tol = 0.3;

    #atomic radii(empirical) (picometres)
    #http://en.wikipedia.org/wiki/Atomic_radii_of_the_elements_%28data_page%29
    my @symbol=("H","He",
               "Li","Be",                                                   "B", "C", "N", "O", "F","Ne",
               "Na","Mg",                                                  "Al","Si", "P", "S","Cl","Ar",
               "K","Ca","Sc","Ti", "V","Cr","Mn","Fe","Co","Ni","Cu","Zn","Ga","Ge","As","Se","Br","Kr",
               "Rb","Sr", "Y","Zr","Nb","Mo","Tc","Ru","Rh","Pd","Ag","Cd","In","Sn","Sb","Te", "I","Xe",
               "Cs","Ba",
               "La","Ce","Pr","Nd","Pm","Sm","Eu","Gd","Tb","Dy","Ho","Er","Tm","Yb","Lu",
               "Hf","Ta", "W","Re","Os","Ir","Pt","Au","Hg","Tl","Pb","Bi","Po","At","Rn",
               "Fr","Ra",
               "Ac","Th","Pa", "U","Np","Pu","Am","Cm","Bk","Cf","Es","Fm","Md","No","Lr");

    my @radii= ( 25,  0,145,105, 85, 70, 65, 60, 50,  0,
                180,150,125,110,100,100,100, 71,220,180,
                160,140,135,140,140,140,135,135,135,135,
                130,125,115,115,115,  0,235,200,180,155,
                145,145,135,130,135,140,160,155,155,145,
                145,140,140,  0,260,215,195,185,185,185,
                185,185,185,180,175,175,175,175,175,175,
                175,155,145,135,135,130,135,135,135,150,
                190,180,160,190,  0,  0,  0,215,195,180,
                180,175,175,175,175,  0,  0,  0,  0,  0,
                0,  0,  0); 

    my @coord= (1,  1,  1,  2,  3,  4,  3,  2,  1,  1,
                1,  2,  3,  4,  5,  6,  1,  1,  1,  2,
                8,  8,  8,  8,  8,  8,  8,  8,  8,  8,
                8,  8,  8,  8,  8,  8,  8,  8,  8,  8,
                8,  8,  8,  8,  8,  8,  8,  8,  8,  8,
                8,  8,  8,  8,  8,  8,  8,  8,  8,  8,
                8,  8,  8,  8,  8,  8,  8,  8,  8,  8,
                8,  8,  8,  8,  8,  8,  8,  8,  8,  8,
                8,  8,  8,  8,  8,  8,  8,  8,  8,  8,
                8,  8,  8,  8,  8,  8,  8,  8,  8,  8,
                8,  8,  8,  8,  8,  8,  8,  8,  8,  8,
                8,  8,  8,  8,  8,  8,  8,  8,  8,  8,
                8,  8,  8,  8,  8,  8,  8,  8,  8,  8,
                8,  8,  8); 

    my $molecule = shift;

    my @atom;
    my @X, @Y, @Z;

    my $badnessCount = 0;
    
    #zmtCom2xyz($molecule, \@atom, \@X, \@Y, \@Z);

    $cominput=file2string("$molecule.com");
    stripcom($cominput);

    if ($iszmat){
        zmtCom2xyz($molecule, \@atom, \@X, \@Y, \@Z);
    }
    else{
        #print $cominput;
        @lines= split(/\n/,$cominput);
        for ($i =0 ; $i <= $#cominput ; $i++){
            ($Z[$i],$Y[$i],$X[$i],$atom[$i]) = reverse(split(/\s+/,$lines[$i]));
        }
    }


    for ($i=0;$i <= $#atom; $i++){
        for ($j=0;$j < $i; $j++){
            $bonding[$i]=0;
            $bonding[$j]=0;
        }
    }

    for ($i=0;$i <= $#atom; $i++){
        for ($k=0; $k <= $#symbol; $k++){
            if (lc($atom[$i]) eq lc($symbol[$k])){
                $allow[$i] = $radii[$k]*0.01;
                $coordN[$i] = $coord[$k];
            }
        }
        for ($j=0;$j < $i; $j++){
            $dist[$i][$j] = sqrt(($X[$i] - $X[$j])**2 + ($Y[$i] - $Y[$j])**2 +($Z[$i] - $Z[$j])**2) ;
            $sbond[$i][$j] = $allow[$i] + $allow[$j] -$tol;
            $lbond[$i][$j] = $allow[$i] + $allow[$j] +$tol;



            # test if one atom is too close to another
            if ($sbond[$i][$j] > $dist[$i][$j]){
                print color 'red';
                printf "Atoms %s and %s have a bond length of %f, which is less than\n", $i+1, $j+1, $dist[$i][$j];
                printf "the allowed value %f.\n\n", $sbond[$i][$j] ;
                print color 'reset';
                $badnessCount++;
            }

            # test if an atom has too many neighbours
            if ($lbond[$i][$j] > $dist[$i][$j]){
                $bonding[$i]++;      
                $bonding[$j]++;      
                #            printf "bonding site: %s, %s\n",$i+1,$j+1;
            }
        }
    }
    for ($i=0;$i <= $#atom; $i++){
        #print "$i+1, $bonding[$i]\n";
        if ($bonding[$i] > $coordN[$i])
        {
            print color 'red';
            printf "Atom %s has %s bonds, greater than the allowed number, %s.\n",$i+1,$bonding[$i], $coordN[$i];
            print color 'reset';
            $badnessCount++;
        }
    }

    print color 'blue';
    print "$molecule.com file badness rating = $badnessCount\n";
    print color 'reset';

    if ($badnessCount > $maxBadness) {
        fakeGaussian($molecule);
        return 1;
    }
    return 0;
}

# 1. writes out a .log and .fin file as if gaussian had run
#    - .log file contains a big energy
#    - .fin file is blank
# 2. emails user so they can double check
sub fakeGaussian {
    my $mol = shift;
    open flog, "> $mol.log" or die $!;
    print flog "Normal termination (fake Gaussian)\n SCF Done:  E(UB+HF-LYP) =  10000.00000000\n";
    close flog;
    #system("mailx -s 'Conformer $mol deemed to be too crowded for submission.' $email < $mol.com ") ;
}



sub stripcom{
    #stripcom("geometry_string"), returns stripped geometry string.
    my($geometry, @file, $cm_flag, $bk, $cm_index, $i);
    my($temp2, @temp);

    $geometry = $_[0];
    @file = split(/\n/,$geometry);
    $cm_flag = 0;   # whether we've hit the (first) charge/multiplicity section or not.
    $bk = 0;        #blank line counter for zmat section
    @cominput = ();
    $cm_index = 9999999;

    for($i = 0; $i <= $#file; $i++){
        #match the charge/multiplicity section.
        if ($file[$i] =~/#/){
            $theory =${theory}.${file[$i]};
        }

        if ($file[$i] =~/^[ \t]*-*\+*[ \t]*[0-9]{1,2}[ \t]*\+*[ \t]*[0-9]{1,2}[ \t]*$/){
            $cm_flag +=1;         #means you only get the top geometry.
            if ($cm_flag == 1){
                #   push(@cominput, $file[$i]);       #put cm into array
                $cm_index = $i;                #mark where cm is
                $temp2 = $file[$i+1];              #get next line
                $temp2 =~s/^[ \t]*//;             #strip leading whitespace
                $temp2 =~s/[ \t]*$//;              #strip trailing whitespace
                @temp = split(/[ \t]+/,$temp2);        #split
                if ($temp[0] =~ /\b[a-z]{1,2}\b/i){        #see if zmat
                    if (@temp == 1){
                        $iszmat = 1;
                    }else{
                        if (@temp == 4){
                            $iszmat = 0;
                        }else{
                            die "$temp2 : Not xyz or xmat!\n";
                        }
                    }
                }else{
                    die "$temp[0] : not an atom!!\n";
                }
            }
        }
        if ($i > $cm_index && $cm_flag == 1){    #discard useless header and footer
            if($iszmat == 0 && $file[$i] =~/^[ \t]*[a-zA-Z]{1,2}[ \t]{1,}-?\+? *\.?[0-9]{1,}\.?[0-9]*[ \t]{1,}-?\+? *\.?[0-9]{1,}\.?[0-9]*[ \t]{1,}-?\+? *\.?[0-9]{1,}\.?[0-9]*[ \t]*$/){     #if zmat and a coordinate
                push(@cominput, $file[$i]);
            }
            if($iszmat == 1){
                if($file[$i] =~ /^[ \t]*$/){
                    $bk+=1;             #count blank lines in zmat
                }
                if ($bk < 2){      # if zmat and before the end of it, then
                    push(@cominput, $file[$i]);
                }
            }
        }
    }
    $cominput = join("\n",@cominput);
    return $cominput;
}

sub file2string {
    # file2string("filename") : gets a txt file, turns it into a string.
    my ($i,$file,$temp);
    local $/;

    open(INPUTFILE, $_[0]) ||die "Can't open $_[0] for reading.\n";
    undef $/;
    $file = <INPUTFILE>;
    close(INPUTFILE)|| die "Can't close $_[0].\n";
    return $file;
}

# usage: zmtCom2xyz($molecule, \@atom, \@X, \@Y, \@Z);
sub zmtCom2xyz {
    my $mol = shift;
    $atom = shift;
    my ($x,$y,$z) = @_;
    
    open COMFILE, "< $mol.com" or die "Couldn't open file $mol.com.\n\n$!";
    
    # this takes Gaussian input file with geometry given as
    # Zmat, and converts it to the XYZ format (cartesians)
    # This is an educational script, hence many comments.
    # The script is a filter, i.e., should be used as
    #   cat name.inp | g9xinp2xyz.pl > name.xyz
    # where name.inp is the Gaussian input file and
    # name.xyz is a file with cartesian coordinates a la XMol
    # It is assumed that G9x input file has a format:
    #   % part (e.g., checkpoint specs)
    #   # keywords/links part
    #     empty line
    #   title lines
    #     empty line
    #   charge multiplicity line
    #   zmatrix lines
    #     empty line or "Variables"
    #   symbolic variables for Z-matrix (if ZMAT has symbolic parameters)
    #     empty line or "Constants"
    #   symbolic constants for Z-matriz (if all references were not resolved yet)
    #     empty line or line starting with "-"
    #
    #  Written by Jan Labanowski in July 1997 <jkl@ccl.net>

    #

    $keywords = "";
    while($line = <COMFILE>) { # read next lines of keywords (route section)
      last if ($line =~ /\s*\d\s+\d\s*/);
    }


    $natoms = 0;    #number of atoms found initialized
    while ($line = <COMFILE>) {  # read molecule description lines
      chop($line);
      $line =~ tr/a-z/A-Z/;
      $line =~ s/^\s+//;   # get rid of front and back spaces
      $line =~ s/\s+$//;   # get rid of front and back spaces
      if(($line !~ /\S/) ||
         ($line =~ /variab/i) ||
         ($line =~ /consta/i)) {  # if blank line or end of Zmat
        last;              # exit the loop
        }
      if($natoms == 0) {   # first atom is only an atomic symbol
        $symbol[$natoms] = $line;
        # no parameters necessary for atom 1
        ($bf[$natoms], $af[$natoms], $tf[$natoms]) =  (1, 1, 1);
        }
      else {
        # split the line into individual fields:
        (@fields) =  split(/\s+/, $line);   # split line into fields

        # assumed most standard z-matrix form, so check number of entries
        if((($#fields != 2) && ($natoms == 1)) &&
           (($#fields != 4) && ($natoms == 2)) &&
           (($#fields != 6) && ($natoms >= 3))) {
          printf STDERR "Error in Z-Matrix for atom %d .\n\n", $natoms+1;
          exit(2);   # abort 
          }

        for($i = $#fields+1; $i <8; $i++) {  # fill up with empty strings
          $fields[$i] = "";
          }

        # parse fields  symbol_i  j  d_ij   k   theta_ijk  l  phi_ijkl 
        ($symbol[$natoms],  # atom symbol
         $bondat[$natoms],  # bonded atom
         $blen[$natoms],    # bond length
         $angat[$natoms],   # atom in an angle
         $angle[$natoms],   # angle
         $torat[$natoms],   # last atom in torsion angle
         $tors[$natoms])    # torsion angle
                              = (@fields);
        # initialize flags for required parameters to "NotFound" status (i.e., 0)
        if($natoms == 1) {
          ($bf[$natoms], $af[$natoms], $tf[$natoms]) =  (0, 1, 1);
          }
        elsif($natoms == 2) {
          ($bf[$natoms], $af[$natoms], $tf[$natoms]) =  (0, 0, 1);
          }
        else {
          ($bf[$natoms], $af[$natoms], $tf[$natoms]) =  (0, 0, 0);
          }
        
        # check if parameters are given as numbers (i.e., sign, possibly followed
        # by digits, possibly followed by period, possibly followed by digits
        # and containing at least one digit total. Set flag if number.
        if(($blen[$natoms] =~ /^[-+]?[0-9]*\.?[0-9]*$/) &&
           ($blen[$natoms] =~ /[0-9]+/)) {
          $bf[$natoms] = 1;
          }
        if(($angle[$natoms] =~ /^[-+]?[0-9]*\.?[0-9]*$/) &&
           ($angle[$natoms] =~ /[0-9]+/)) {
          $af[$natoms] = 1;
          }
        if(($tors[$natoms] =~ /^[-+]?[0-9]*\.?[0-9]*$/) &&
           ($tors[$natoms] =~ /[0-9]+/)) {
          $tf[$natoms] = 1;
          }

        # Atom numbers must be all digits
        if(($bondat[$natoms] !~ /^[0-9]+$/) ||
           (($angat[$natoms] !~ /^[0-9]+$/) && ($natoms > 1)) ||
           (($torat[$natoms] !~ /^[0-9]+$/) && ($natoms > 2))) {
          printf STDERR "Error in atom definition for %d .\n\n", $i+1;
          exit(2); 
          }
        }
      $natoms++;
      }

    # check any symbolic parameters are given in the Z-mat
    $parms_given = 0;
    for($i = 0; $i < $natoms; $i++) {
      if(($bf[$i] == 0) || 
         ($af[$i] == 0) || 
         ($tf[$i] == 0)) {
        $parms_given = 1;     # symbolic parameters present
        last;
        }
      }

    if($parms_given == 1) { # read in symbolic parameters (variables) when present
      while($line = <COMFILE>) {
        $line =~ s/^\s//;        # trailing blanks out!
        $line =~ s/\s$//;
        $line =~ tr/a-z/A-Z/;    # convert to uppercase
        if(($line !~ /\S/) ||
           ($line =~ /const/i)) {  # if blank line or end of Variables
          last;              # exit the loop
          }

        ($name, $value) = @fields = split(/[ =,]+/, $line);  # retrieve fields
        if($#fields != 1) {
          die "Wrong format on variables assignment line.\n\n";
          }
        if(($value !~ /^[-+]?[0-9]*\.?[0-9]*$/) ||
           ($value !~ /[0-9]+/)) {
          die "Wrong number format of variables assignment line.\n";
          }


        # substitute parameter in Z-Matrix. The symbolic parameter name is
        # allowed to be preceded with a sign, so take this into account
        $parameter_found = 0;
        for($i = 0; $i < $natoms; $i++) {
          if($bf[$i] == 0) {
            if($blen[$i] =~ /^([-+]?)$name$/) {
              $sign = $1 . "1.0";
              $blen[$i] = $sign * $value;
              $parameter_found = 1;
              $bf[$i] = 1;
              }
            }

          if($af[$i] == 0) {
            if($angle[$i] =~ /^([-+]?)$name$/) {
              $sign = $1 . "1.0";
              $angle[$i] = $sign * $value;
              $parameter_found = 1;
              $af[$i] = 1;
              }
            }

          if($tf[$i] == 0) {
            if($tors[$i] =~ /^([-+]?)$name$/) {
              $sign = $1 . "1.0";
              $tors[$i] = $sign * $value;
              $parameter_found = 1;
              $tf[$i] = 1;
              }
            }
          }
        # parameter, if given, must appear at least once in Z-Matrix
        if($parameter_found == 0) {
          die "Parameter $name = $value does not appear in Z-Matrix.\n\n";
          }

        }
      }

    # check if all symbolic paramemters were resolved
    $parms_given = 0;
    for($i = 0; $i < $natoms; $i++) {
      if(($bf[$i] == 0) || 
         ($af[$i] == 0) || 
         ($tf[$i] == 0)) {
        $parms_given = 1;    # symbolic parameters present
        last;
        }
      }
    # if all parameters are not resloved, read in the Constants section
    if($parms_given == 1) { # read in symbolic parameters (variables) when present
      while($line = <COMFILE>) {
        $line =~ s/^\s//;        # trailing blanks out!
        $line =~ s/\s$//;
        $line =~ tr/a-z/A-Z/;    # convert to uppercase
        if($line =~ /const/i) {
          next;
          }
        if(($line !~ /\S/) ||
           ($line =~ /^\s*\-/)) {  # if blank line or - at the front
          last;              # exit the loop
          }
        ($name, $value) = @fields = split(/[ =,]+/, $line);  # retrieve fields
        if($#fields != 1) {
          die "Wrong format of constants assignment line.\n\n";
          }
        if(($value !~ /^[-+]?[0-9]*\.?[0-9]*$/) ||
           ($value !~ /[0-9]+/)) {
          die "Wrong number format on constants assignment line.\n\n";
          }

        # substitute parameter in Z-Matrix. The symbolic parameter name is
        # allowed to be preceded with a sign, so take this into account
        $parameter_found = 0;
        for($i = 0; $i < $natoms; $i++) {
          if($bf[$i] == 0) {
            if($blen[$i] =~ /^([-+]?)$name$/) {
              $sign = $1 . "1.0";
              $blen[$i] = $sign * $value;
              $parameter_found = 1;
              $bf[$i] = 1;
              }
            }

          if($af[$i] == 0) {
            if($angle[$i] =~ /^([-+]?)$name$/) {
              $sign = $1 . "1.0";
              $angle[$i] = $sign * $value;
              $parameter_found = 1;
              $af[$i] = 1;
              }
            }

          if($tf[$i] == 0) {
            if($tors[$i] =~ /^([-+]?)$name$/) {
              $sign = $1 . "1.0";
              $tors[$i] = $sign * $value;
              $parameter_found = 1;
              $tf[$i] = 1;
              }
            }
          }

        # parameter, if given, must appear at least once in Z-Matrix
        if($parameter_found == 0) {
          die "Parameter $name = $value does not appear in Z-Matrix.\n\n";
          }
        }
      }

    # check if all symbolic paramemters were reslolved
    $parms_given = 0;
    for($i = 0; $i < $natoms; $i++) {
      if(($bf[$i] == 0) || 
         ($af[$i] == 0) || 
         ($tf[$i] == 0)) {
        $parms_given = 1;    # symbolic parameters present
        last;
        }
      }
    if($parms_given == 1) {
      print STDERR
      "The follwing symbolic parameters are not resolved in Z-matrix:\n";
      for($i = 0; $i < $natoms; $i++) {
        if($bf[$i] == 0) {
          printf STDERR "   %s for bond length for atom %d.\n", $blen[$i], $i;
          }
        if($af[$i] == 0) {
          printf STDERR "   %s for angle value for atom %d.\n", $angle[$i], $i;
          }
        if($tf[$i] == 0) {
          printf STDERR "   %s for torsion for atom %d.\n", $tors[$i], $i;
          }
        }
      exit(2);
      }


    # output cartesian coordinates in XYZ XMol format
    for ($i = 0; $i < $natoms; $i++) {
        oneatom($i+1, $bondat[$i], $blen[$i], $angat[$i], $angle[$i],
              $torat[$i], $tors[$i]);

        $$atom[$i] = $symbol[$i];
        $$z[$i] = $Zcoor[$i+1];
        $$x[$i] = $Xcoor[$i+1];
        $$y[$i] = $Ycoor[$i+1];

        #printf STDOUT "%-3s  %12.6f  %12.6f  %12.6f\n",$$atom[$i],$$z[$i],$$x[$i],$$y[$i];

    }

    close COMFILE;

}

# -- Takes Z-mat line, i.e., 
#        atomnumber, ibond, bondlen, iangle, bondangle, itors, torsangle
#    and updates NONLOCAL arrays Xcoor, Ycoor, Zcoor which hold cartesian
#    coordinates. It is assumed that atom numbering starts from 1
#    (not from 0 as usually in C and perl)
#    USES nonlocal array Xcoor, Ycoor, Zcoor where it stores coordinates
#    It is assumed that angles are given in DEGREEs and bondlen in the same
#    units in which cartesian coordinates will be given.
#                  
#             ibond -- iangle
#              /             \ 
#          atnum             itors
#
#  CAUTIONS -- contrary to the UNIX/PERL/C tradition, the
#  arrays XYZ start from subscript 1 (not 0), and XYZ[0] are left unused,
#  in other words, array element numbers correspond to atom numbers.

sub oneatom {
  # variables are declared local, so they do not interfere with
  # variables outside this subroutine
  local ($atnum,
         $ibond, $bondlen,
         $iangle, $bondangle,
         $itors, $torsangle);
  local ($deg2r);
  local ($rinv, $aux);
  local ($xa, $ya, $za);
  local ($xb, $yb, $zb);
  local ($xc, $yc, $zc);
  local ($xx, $yy, $zz);

  $atnum = $_[0];

  if($atnum == 2) {
    ($atnum, $ibond, $bondlen) = @_;
    }
  elsif ($atnum == 3) {
    ($atnum, $ibond, $bondlen, $iangle, $bondangle) = @_;
    }
  elsif ($atnum > 3) {
    ($atnum, $ibond, $bondlen, $iangle, $bondangle, $itors, $torsangle) = @_;
    }

  $deg2r = atan2(1.0, 1.0)*4.0/180.0;

  # first atom in the origin of coordinate system      
  if($atnum == 1) {
    $Xcoor[1] = 0.0;
    $Ycoor[1] = 0.0;
    $Zcoor[1] = 0.0;
    return;
    }

  # second atom on Z-axis, bondlen from the first atom
  if($atnum == 2) {
    $Xcoor[2] = 0.0;
    $Ycoor[2] = 0.0;
    $Zcoor[2] = $bondlen;
    return;
    }

  # bonded atom coordinates
  $x0 = $Xcoor[$ibond];
  $y0 = $Ycoor[$ibond];
  $z0 = $Zcoor[$ibond];

  if($atnum == 3) {    # third atom placed on the Oxz plane
    $Xcoor[3] = $x0+$bondlen*sin($bondangle*$deg2r);
    $Ycoor[3] = 0.0;
    $aux = $bondlen*cos($bondangle*$deg2r);
    if($ibond == 1) {
      $Zcoor[3] = $z0+$aux;
      }
    elsif ($ibond == 2) {
      $Zcoor[3] = $z0-$aux;
      }
    return;
    }


  # vector from j-->k
  $xx = $Xcoor[$iangle] - $Xcoor[$ibond];
  $yy = $Ycoor[$iangle] - $Ycoor[$ibond];
  $zz = $Zcoor[$iangle] - $Zcoor[$ibond];

  # inverted vector length
  $rinv = 1.0/sqrt($xx*$xx + $yy*$yy + $zz*$zz);

  # unit vector ibond--->iangle
  $xa = $xx*$rinv;
  $ya = $yy*$rinv;
  $za = $zz*$rinv;

  # vector from ibond--->itors  
  $xb = $Xcoor[$itors] - $Xcoor[$ibond];
  $yb = $Ycoor[$itors] - $Ycoor[$ibond];
  $zb = $Zcoor[$itors] - $Zcoor[$ibond];

# unit vector ibond--->itors
  $xc = $ya*$zb - $za*$yb;
  $yc = $za*$xb - $xa*$zb;
  $zc = $xa*$yb - $ya*$xb;

  $rinv = 1.0/sqrt($xc*$xc + $yc*$yc + $zc*$zc);

  $xc = $xc*$rinv;
  $yc = $yc*$rinv;
  $zc = $zc*$rinv;

  $xb = $yc*$za - $zc*$ya;
  $yb = $zc*$xa - $xc*$za;
  $zb = $xc*$ya - $yc*$xa;

  $zz = $bondlen*cos($bondangle*$deg2r);
  $xx = $bondlen*sin($bondangle*$deg2r)*cos($torsangle*$deg2r);
  $yy = $bondlen*sin($bondangle*$deg2r)*sin($torsangle*$deg2r);

  $Xcoor[$atnum] = $x0 + $xa*$zz + $xb*$xx + $xc*$yy;
  $Ycoor[$atnum] = $y0 + $ya*$zz + $yb*$xx + $yc*$yy;
  $Zcoor[$atnum] = $z0 + $za*$zz + $zb*$xx + $zc*$yy;

  return;
  }

__END__