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gdsub_updated
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gdsub_updated
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#! /usr/bin/perl
if (@ARGV < 1) { die "Syntax: rjsub filename [optional flags]
Optional Flags (order doesn't matter):
-rproj [f81/x69] choose project to run on
-time [xh] max runtime in hours
-mem [xmb] max virtual memory in mb or gb
-jobfs [xgb] max disk space in mb or gb
-nproc [x] number of processors
-e submit to express queue
-ver program version eg. use 09c01 to use Gaussian 09, Revision C.01 (often resolves Internal Consistency Failure problem for MP2/GTMP2Large and can also help avoid geometry optimisations getting stuck in unproductive cycles)
-ichk copy initial gaussian checkpoint file to raijin - filename must match .com file - not recommended as files become corrupted more often than not.
-ochk copy gaussian checkpoint file back from raijin after calculation - not recommended as files become corrupted more often than not. \n\n" }
$|++;
$machine = "gadi";
$GD = "GDN";
chomp($ARGV[0]);
$scanjob=0;
$proj[0]=$ENV{PROJECT};
$proj[1]=$ENV{PROJECT2};
$home=$ENV{HOME};
if (!($ENV{PROJ1GRANT})) {
die "Please edit your .bashrc to include the following lines and source: \nexport PROJECT=f81\nexport PROJECT2=x69\nexport PROJ1GRANT=400\nexport PROJ2GRANT=750\n";
}
else {
$grant{$proj[0]} = $ENV{PROJ1GRANT};
$grant{$proj[1]} = $ENV{PROJ2GRANT};
}
$ruser = $ENV{REMOTE_USER};
$rproj = $proj[0];
$definerproj = "n";
$utime = "";
$umem = "";
$upmem = "";
$pmem = "";
$ujobfs = "";
$unproc = "";
$ichk = "";
$ochk = "";
$cs = "";
$maxQ{x69} = 10000; # Max is 400 but can be slow to update
$maxQ{f81} = 10000; # Max is 400 but can be slow to update
$maxU{x69} = 10000; # Limited to 350 to allow space for other group members
$maxU{f81} = 10000; # Please do not increase unless you're sure you won't inconvenience others
$sleep_queue = 10000;
$sqtest = "no";
for ($i = 0; $i <= 30; $i++) {
if ($ARGV[$i]){
if ($ARGV[$i] =~ /^-rproj/){
$rproj = $ARGV[$i+1];
$definerproj = "y";
}
if ($ARGV[$i] =~ /^-ver/){
$ver = "-ver $ARGV[$i+1]";
}
if ($ARGV[$i] =~ /^-uq/){
$m = $ARGV[$i+1];
$sqtest = "yes";
}
if ($ARGV[$i] =~ /^-tq/){
$n = $ARGV[$i+1];
$sqtest = "yes";
}
if (($ARGV[$i] =~ /^-lt/) || ($ARGV[$i] =~ /^-time/)) {
$utime = $ARGV[$i+1];
}
if (($ARGV[$i] =~ /^-lw/) || ($ARGV[$i] =~ /^-mem/)) {
$umem = $ARGV[$i+1];
}
if (($ARGV[$i] =~ /^-pm/)) {
$upmem = $ARGV[$i+1];
}
if (($ARGV[$i] =~ /^-lf/) || ($ARGV[$i] =~ /^-jobfs/)) {
$ujobfs = $ARGV[$i+1];
}
if ($ARGV[$i] =~ /^-nproc/) {
$unproc = $ARGV[$i+1];
}
if ($ARGV[$i] =~/^-e/){
$GD = "GDE";
}
if ($ARGV[$i] =~/^-ichk/){
$ichk = "-ichk";
}
if ($ARGV[$i] =~/^-ochk/){
$ochk = "-ochk";
}
if ($ARGV[$i] =~/^-cs/){
$cs = "yes";
}
}
}
if (($sqtest =~ "no") && ($cs !~ "yes") && ($definerproj =~ "n")) {
@alloctime = split(/\s+/,`ssh $machine -l \$REMOTE_USER nci_account -P $proj[0] | grep 'Overall' `);
if ($alloctime[6]/1000 > $grant{$proj[0]}) {
$rproj = $proj[1];
print "No SU available on project $proj[0] - submit to $rproj.\n";
}
}
if($ARGV[0] =~/inp/){
# GAMESS INPUT
if ($ARGV[0] =~ /uhf/){
$vmem = "1gb";
$jobfs = "1gb";
$time = "3h";
$nproc = "24";
}
elsif ($ARGV[0] =~/sad/ or $ARGV[0] =~/opt/){
$vmem = "5gb";
$jobfs = "6gb";
$time = "3h";
$nproc = "24";
}
elsif ($ARGV[0] =~/sp/){
$vmem = "3gb";
$jobfs = "5gb";
$time = "1h";
$nproc = "24";
}
else {
$vmem = "3gb";
$jobfs = "5gb";
$time = "20h";
$nproc = "24";
}
if ($GD =~/GDE/){
$time = "1h";
$vmem = "3gb";
$jobfs = "5gb";
$nproc = "24";
}
}
elsif ($ARGV[0] =~/ccsdt.ini/ or $ARGV[0] =~/cisdt.ini/){
# MOLPRO INPUT
open INI, "$ARGV[0]", or die $!;
while (<INI>){
if (/geometry/){
$natom = readline(INI);
}
}
close INI;
if ($natom <=10){
$vmem = "5gb";
$nproc = "24";
$jobfs = "10gb";
$time = "10";
}
elsif($natom <=20){
$vmem = "8500mb";
$nproc = "24";
$jobfs = "20gb";
$time = "20";
}
elsif($natom <= 40 ){
$vmem = "40gb";
$nproc = "24";
$jobfs = "100gb";
$time = "48";
}
else{
$vmem = "60gb";
$nproc = "48";
$jobfs = "200gb";
$time = "48";
}
if ($GD =~/GDE/){
# $time = "1";
# $vmem = "4gb";
# $jobfs = "2gb";
# $nproc = "4";
if($time >= 48){
$time = 48;
}
}
$time = ${time}."h";
}
elsif ($ARGV[0] =~/\.in/){
# Q-Chem INPUT
if ($GD =~/GDE/){
$time = "1h";
$vmem = "2gb";
$jobfs = "2gb";
$nproc = "1";
}
else{
$vmem = "2200mb";
$nproc = "1";
$jobfs = "10gb";
$time = "30h";
}
}
elsif ($ARGV[0] =~/mtfull/){
$vmem = "16000mb";
$nproc = "1";
$jobfs = "200gb";
$time = "400h";
}
elsif ($ARGV[0] =~/tz.ini/ or $ARGV[0] =~/\.mt/){
$vmem = "4gb";
$nproc = "4";
$jobfs = "20gb";
$time = "1h";
$ini_mem = "80";
}
elsif ($ARGV[0] =~/qz/){
$vmem = "16000mb";
$nproc = "4";
$jobfs = "400gb";
$time = "400h";
$ini_mem = "2000";
}
else {
if ($ichk !~ "chk") {
$cominput=file2string($ARGV[0]);
stripcom($cominput);
$hydrogens=0;
$heavyatoms=0;
if ($iszmat){
my $molecule = $ARGV[0];
zmtCom2xyz($molecule, \@atom, \@X, \@Y, \@Z);
for ($i = 0; $i < $natoms; $i++){
if($atom[$i] =~ /^H$/i){
$hydrogens++;
}
else{
$heavyatoms++;
}
}
}
else{
@atom1= split(/\n/,$cominput);
for ($i = 0; $i <= $#cominput; $i++){
@atom1[$i] =~ s/^\s+//;
@atom[$i] = split(/\s+/,@atom1[$i]);
if($atom[$i] =~ /^H$/i){
$hydrogens++;
}
else{
$heavyatoms++;
}
}
}
print "$ARGV[0]\t has $heavyatoms heavy atoms\n";
}
else {
print "Input data will be taken from checkpoint file\n";
}
#print "natoms=",$hydrogens+$heavyatoms,"\n";
#print $cominput;
if ($ARGV[0] =~/run/){
# ADF INPUT
$vmem = "1gb";
$jobfs = "1gb";
$time = "1h";
$nproc = "4";
}
request();
if (!$ARGV[1]){
}
else{
if ($ARGV[1] eq "dog3m"){
print "usagd_updated $GD $ARGV[0] -lf $jobfs -lw $vmem -lt $time -nproc $nproc -rproj $rproj -g3 mp2\n";
system("usagd_updated $GD $ARGV[0] -lf $jobfs -lw $vmem -lt $time -nproc $nproc -rproj $rproj -g3 mp2");
}
elsif ($ARGV[1] eq "dog3mdiff"){
print "usagd_updated $GD $ARGV[0] -lf $jobfs -lw $vmem -lt $time -nproc $nproc -rproj $rproj -g3 mp2-diff\n";
system("usagd_updated $GD $ARGV[0] -lf $jobfs -lw $vmem -lt $time -nproc $nproc -rproj $rproj -g3 mp2-diff");
}
elsif ($ARGV[1] eq "dog3"){
print "usagd_updated $GD $ARGV[0] -lf $jobfs -lw $vmem -lt $time -nproc $nproc -rproj $rproj -g3 mp2rad\n";
system("usagd_updated $GD $ARGV[0] -lf $jobfs -lw $vmem -lt $time -nproc $nproc -rproj $rproj -g3 mp2rad");
}
elsif ($ARGV[1] eq "dog3diff"){
print "usagd_updated $GD $ARGV[0] -lf $jobfs -lw $vmem -lt $time -nproc $nproc -rproj $rproj -g3 mp2rad-diff\n";
system("usagd_updated $GD $ARGV[0] -lf $jobfs -lw $vmem -lt $time -nproc $nproc -rproj $rproj -g3 mp2rad-diff");
}
elsif ($ARGV[1] eq "dog3full"){
print "usagd_updated $GD $ARGV[0] -lf $jobfs -lw $vmem -lt $time -nproc $nproc -rproj $rproj -g3 full\n";
system("usagd_updated $GD $ARGV[0] -lf $jobfs -lw $vmem -lt $time -nproc $nproc -rproj $rproj -g3 full");
}
elsif ($ARGV[1] eq "dog3core"){
print "usagd_updated $GD $ARGV[0] -lf $jobfs -lw $vmem -lt $time -nproc $nproc -rproj $rproj -g3 core\n";
system("usagd_updated $GD $ARGV[0] -lf $jobfs -lw $vmem -lt $time -nproc $nproc -rproj $rproj -g3 core");
}
elsif ($ARGV[1] eq "dow1"){
print "usagd_updated $GD $ARGV[0] -lf $jobfs -lw $vmem -lt $time -nproc $nproc -rproj $rproj -g3 w1\n";
system("usagd_updated $GD $ARGV[0] -lf $jobfs -lw $vmem -lt $time -nproc $nproc -rproj $rproj -g3 w1");
}
else{
}
}
}
if ($utime =~ /\d/) { $time = $utime }
if ($umem =~ /\d/) { $vmem = $umem }
if ($upmem =~ /\d/) { $pmem = "-pm $upmem" }
if ($ujobfs =~ /\d/) { $jobfs = $ujobfs }
if ($unproc =~ /\d/) { $nproc = $unproc }
#if (($GD =~ /GDE/) && (($time =~ /\d\d/) || ($time =~ /9/))) { $time = "8h" }
#if (($GD =~ /GDE/) && (time =~ /\d\d/)) { $time = "10h" }
# print "Attempting to submit on project $rproj\n";
if (($sqtest =~ "yes") && (($m >= $maxU{$rproj}) || ($n+1 >= $maxQ{$rproj}))){
while (!($queue = freeQ($rproj,$m,$n))){
print color 'red';
print "Queue on $machine is full. Waiting...\n\n";
print color 'reset';
sleep $sleep_queue;
}
}
print "usagd_updated $GD $ARGV[0] -lf $jobfs -lw $vmem $pmem -lt $time -nproc $nproc -rproj $rproj $ichk $ochk $ver\n";
$jobid = `usagd_updated $GD $ARGV[0] -lf $jobfs -lw $vmem $pmem -lt $time -nproc $nproc -rproj $rproj $ichk $ochk $ver`;
chomp ($jobid);
$jobid =~ s/\.r-man2//;
$jobid =~ s/\n//;
printf "Jobid: %-10s\n",$jobid;
$recfile = "$home/JOB/recordfile";
open RECORD, ">>$recfile" or die "Couldn't open file $recfile for appending\n";
printf RECORD "%-10s %-100s\n",$jobid, $ARGV[0];
close (RECORD);
######################################################################################################
sub request{
if ($theory =~/pm6/i ){
$vmem = "1500mb";
$nproc = "24";
$jobfs = "1";
$time = "0.2";
}
elsif (($theory =~/lyp/i or $theory =~/bmk/i or $theory =~/M05/i or $theory =~/M06/i) and ($scanjob==1 or $ARGV[0] =~/scan/i) ){
$vmem = "4000mb";
$nproc = "24";
$jobfs = int($heavyatoms/4)*4;
$time = 5*int($heavyatoms/10);
}
elsif (($theory =~/lyp/i or $theory =~/bmk/i or $theory =~/M05/i or $theory =~/M06/i) and $scanjob==0 ){
$vmem = "10000mb";
$nproc = "24";
$jobfs = int($heavyatoms/4)*4;
$time = int($heavyatoms);
}
elsif ($theory =~/ccsd/i ){
$vmem = "40gb";
$nproc = "24";
$jobfs = "40";
$time = int($heavyatoms/10*5);
}
elsif ($theory =~/MP2\/gen/i ){
$vmem = "20000mb";
$nproc = "24";
$jobfs = $heavyatoms*2;
$time = $heavyatoms*1;
}
elsif ($theory =~/6-311/i ){
$vmem = "20000mb";
$nproc = "24";
$jobfs = "50";
$time = int($heavyatoms*1);
}
elsif ($theory =~/GTMP2LARGE/i ){
$vmem = "15000mb";
$nproc = "24";
$jobfs = $heavyatoms*2;
$time = $heavyatoms*1;
}
elsif ($theory =~/hf/i ){
$vmem = "2500mb";
$nproc = "24";
$jobfs = "5";
$time = int($heavyatoms/10*1);
}
elsif ($theory =~/g3mp2b3/i ){
$vmem = "15000mb";
$nproc = "24";
$jobfs = "50";
$time = $heavyatoms*1;
}
else{
$vmem = "15000mb";
$nproc = "24";
$jobfs = "50";
$time = int($heavyatoms/10*5);
}
if ($heavyatoms > 20) {
$nproc = "24";
}
if ($jobfs<5){
$jobfs=5;
}
elsif ($jobfs > 26){
$jobfs=26;
}
$jobfs = ${jobfs}."gb";
if ($time eq "0"){
$time = "10";
}
if ($time > "48"){
$time = "48";
}
if (($GD =~ /GDE/) && ($time > "48")) {
$time = "48";
}
$time = ${time}."h";
}
################################################################################
sub file2string {
# file2string("filename") : gets a txt file, turns it into a string.
my ($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 $file;
}
sub getcm {
#getcm("geometry") : gets charge/multiplicity line from "geometry" string.
my ($geometry, @geometry, $cm);
$geometry = $_[0];
@geometry = split(/\n/, $geometry);
$cm = $geometry[0];
return $cm;
}
sub stripcom{
#stripcom("geometry_string"), returns stripped geometry string.
my($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;
}
elsif (@temp == 5) {
$iszmat = 1;
}
else{
die "$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 $cominput;
}
sub check_geometry_type{
# check_geometry_type("cominput") : checks to see if the cominput is xyz or zmat.
my($cominput,@cominput, $i, $temp2, $temp, @temp, $iszmat);
$cominput = $_[0];
@cominput = split(/\n/,$cominput);
for($i = 0; $i <= $#cominput; $i++){
if ($cominput[$i] =~/^[ \t]*-*\+*[ \t]*[0-9]{1,2}[ \t]*\+*[ \t]*[0-9]{1,2}[ \t]*$/){
$temp2 = $cominput[$i+1]; #get next line
$temp2 =~s/^[ \t]*//; #get rid of leading whitespace
$temp2 =~s/[ \t]*$//; #get rid of 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 zmat!\n";
}
}
}else{
die "$temp[0] : not an atom!!\n";
}
}
}
return $iszmat;
}
# usage: zmtCom2xyz($molecule, \@atom, \@X, \@Y, \@Z);
sub zmtCom2xyz {
my $mol = shift;
$atom = shift;
my ($x,$y,$z) = @_;
open COMFILE, "< $mol" or die "Couldn't open file $mol\n$!";
# 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 <[email protected]>
#
$keywords = "";
while($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
$line =~ s/\s+$//;
if(($line !~ /\S/) ||
($line =~ /variab/i) ||
($line =~ /consta/i)) { # if blank line or end of Zmat
last; # exit the loop
}
(@fields) = split(/\s+|,/, $line); # split line into fields
if (($natoms == 0) && ($fields[1] !~ /0/)) { # first atom is only an atomic symbol
$symbol[$natoms] = $line;
($bf[$natoms], $af[$natoms], $tf[$natoms]) = (1, 1, 1);
}
elsif ($natoms == 0) { # first atom is only an atomic symbol
$symbol[$natoms] = $fields[0];
$blen[$natoms] = $fields[2];
$angle[$natoms] = $fields[3];
$tors[$natoms] = $fields[4];
($bf[$natoms], $af[$natoms], $tf[$natoms]) = (0, 0, 0);
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;
}
}
else {
# split the line into individual 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", $natoms+1;
# exit(2); # abort
# }
for($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", $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) {
if($fields[2]=~ /s/i ){
$scanjob=1;
}
}
if(($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";
}
}
}
# 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)) {
$parms_given = 1; # symbolic parameters present
last;
}
}
# if all parameters are not resloved, read in the Constants section
if($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
# print "#fields is $#fields\n";
# if($#fields != 1) {
# print "fields0 is $fields[0]\n";
# print "fields1 is $fields[1]\n";
# die "Wrong format of Constants assignment line\n";
# }
if(($value !~ /^[-+]?[0-9]*\.?[0-9]*$/) ||
($value !~ /[0-9]+/)) {
die "Wrong number format on Constants 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";
}
}
}
# 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;