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crin2
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crin2
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#!/usr/bin/perl -w
# todo
# fix scf done line in xyz (from molden)
# delete hlc and sym file (G3engmol?)
# symmetry read
# change scf=gdiis
# Gives csv file in G3engmol?
# isolate Br, and 3rd row for com, so, normally, one don't need basis library.
# iodine?
#
# ccsd for close shell ; uccsd for open shell (by default)
################################################################
# CRIN 1.0
# Create Inputs
# David Brittain
# 11/10/06
#
# Modified Leaf 04Jan08
#
# Program to take file containing geometries, extract
# the geometries, and create Gaussian/Q-Chem/Molpro/Gamess Input
#
# Syntax: crin [format] $mol.[log com xyz zmat ar inp uhfna.punch sad.punch opt.punch]
#
# Which is which?
# .log : Gaussian output
# .com : Gaussian input
# .xyz : can be Spartan xyz, which has only lines of xyz coordinate. (?)
# : or Normal xyz, which has Natom, blank line and xyz coordinate.
# : or Molden xyz, which has Natom, comment line and xyz coordinate.
# : or Modified xyz, which has Natom, charge and multiplicity and xyz coordinate.
# .zmat : zmatrix from molden, with or without charge and multiplicity on the top.
# .ar : Gaussian Archive
# .inp : Gamess input
# .uhfna.punch : Gamess uhf punch file
# .sad.punch : Gamess sad punch file
# .opt.punch : Gamess opt punch file
#
# Q-Chem is not working (?)
#
#
# Features:
# Can be used to turn all files in a directory into input
# files with the same directives, eg. turn a directory
# full of molden z-matrices into B3LYP/6-31g* optimizations,
# or turn a dir full of optimized geometry .log files into
# molpro ccsd(t)/6-31g* inputs
#
# Works with both zmat and cartesian coordinates in all input
# formats. Even supports old g98 archive zmat format.
#
# Gaussian:
# Supports multiple --Link1-- jobs. So long as the header and
# footer are matched in that the %chk lines are the same, the
# output will run correctly. The charge/multiplicity line is
# corrected from whatever it is in the footer file to whatever
# it is in the input geometry file.
#
# All comment lines are changed to the current (stripped)
# filename, even if there are multiple --Link1-- jobs.
#
# Molpro:
# Fixes wf card so that nelec and spin are correct and the
# irreducible representation number is as specified on the
# command line.
#
# Puts (stripped) filename in the title card.
#
#
#Changelog:
#
#To do:
#
# -put standard inputs in a library dir in $HOME, then put
# variables pointing to these files in .cshrc
#
# -qchem - strip a possible zero (8th field) from zmat
# input. This arises when using old (g98) archives that
# were opt=zmatrix.
#
#
################################################################
#declarations:
#my($output_type,$symm,$headerfile,$footerfile,$inputfile,$geometry,$stripped_geometry);
#my($i,$inputfile_stripped,$cm,$header,$footer,$finaldeck, $iszmat, $nelec,$c,$m,$spin);
#my($job,@xyz);
#my($data,$mult,$norb,$det,$fin,@vec,$punchline,$T);
#my($HOME,$multi,$charge);
$DIR = $ENV{REMOTE_DIR};
$USR = $ENV{REMOTE_USER};
$HOME="home/$DIR/$USR";
if(@ARGV <2){
die "More arguments needed.\nSyntax: crin [options] \$mol.log \n";
}
$job = $ARGV[0];
if($job =~ /gau/ ) {$output_type="gaussian";} # gaussian job - theory, basis set, opt, freq can all be chosen
elsif($job =~ /xyz/i ) {$output_type="gaussian";} # create xyz file
elsif($job =~ /ar/i ) {$output_type="gaussian";} # strip archive file from end of gaussian .log
elsif($job =~ /sphf/i ) {$output_type="gaussian";} # free choice of theory + 6-31(+)G* single point
elsif($job =~ /oi/i ) {$output_type="gaussian";} # free choice of theory + basis set - Formcheck + POP=full single point
elsif($job =~ /dens/i ) {$output_type="gaussian";} # free choice of theory + basis set - Formcheck + Density=current
elsif($job =~ /b3sp/i ) {$output_type="gaussian";} # B3LYP/6-31(+)G* single point
elsif($job =~ /optb/i ) {$output_type="gaussian";} # B3LYP/6-31(+)G* +lacvp for heavy atoms opt freq
elsif($job =~ /optf/i ) {$output_type="gaussian";} # B3LYP/6-31(+)G* +lacvp for heavy atoms opt freq(noraman)
elsif($job =~ /opts/i ) {$output_type="gaussian";} # B3LYP/6-31(+)G* +lacvp for heavy atoms opt freq for ts
elsif($job =~ /optz/i ) {$output_type="gaussian";} # B3LYP/6-31(+)G* +lacvp for heavy atoms opt(z-matrix) freq
elsif($job =~ /freq/i ) {$output_type="gaussian";} # B3LYP/6-31(+)G* +lacvp for heavy atoms freq
elsif($job =~ /mdbs/i ) {$output_type="gaussian";} # M062X/aug-cc-pVTZ choice of opt + freq
elsif($job =~ /optm/i ) {$output_type="gaussian";} # M062X/6-31(+)G* opt
elsif($job =~ /freqm/i ) {$output_type="gaussian";} # M062X/6-31(+)G* sp choice of freq or not
elsif($job =~ /bmk/i ) {$output_type="gaussian";} # BMK/6-31+G(2df,p) choice of opt + freq
elsif($job =~ /mpw/i ) {$output_type="gaussian";} # MPWB95 choice of basis - opt
elsif($job =~ /mp2opt/i ) {$output_type="gaussian";} # MP2(full)/aug-cc-pVDZ opt
elsif($job =~ /gcc2/i ) {$output_type="gaussian";} # UCCSD(T)/aug-cc-pVTZ - gaussian
elsif($job =~ /gcc/i ) {$output_type="gaussian";} # UCCSD(T)/aug-cc-pVTZ - gaussian
elsif($job =~ /dcc/i ) {$output_type="molpro";} # CCSD(T)/aug-cc-pVTZ - molpro
elsif($job =~ /ccsdt/i) {$output_type="molpro";} # CCSDT/6-31(+)G* single point
elsif($job =~ /cisdt/i) {$output_type="molpro";} # UCISD/6-31G* single point
elsif($job =~ /fullg3/i ) {$output_type="gaussian";} # standard G3 with option of TS
elsif($job =~ /fullg4/i ) {$output_type="gaussian";} # standard G4 with option of TS
elsif($job =~ /g4mp26x/i ) {$output_type="gaussian";} # G4MP2-6X using BMK/6-31+G(2df,p) geom + freq
elsif($job =~ /g3mp2rad/i ) {$output_type="gaussian";} # G3MP2-RAD MP2 calcs using lacvp ecp for very heavy atoms
elsif($job =~ /g3/i ) {$output_type="gaussian";} # G4MP2-6X using BMK/6-31+G(2df,p) geom + freq
elsif($job =~ /w1m/i ) {$output_type="molpro";} #W1m
elsif($job =~ /w1/i ) {$output_type="gaussian";} #W1
elsif($job =~ /cbsrad/i ) {$output_type="gaussian";} #CBS-RAD
elsif($job =~ /qb3/i ) {$output_type="gaussian";} # CBS-QB3
elsif($job =~ /cbs4m/i ) {$output_type="gaussian";} # CBS-4m
elsif($job =~ /uahf/i ) {$output_type="gaussian";} # UHF/6-31(+)G* CPCM UAHF with prompt for solvent - dovac single point
elsif($job =~ /spcrs/i ) {$output_type="gaussian";} # [method choice]/6-31(+)G* CPCM UAHF with prompt for solvent - dovac single point
elsif($job =~ /vol/i ) {$output_type="gaussian";} # UHF/6-31(+)G* CPCM UAHF single point with Volume keyword
elsif($job =~ /ts1/i ) {$output_type="gaussian";} # UHF/6-31(+)G* CPCM UAHF TS opt - dovac
elsif($job =~ /smd/i ) {$output_type="gaussian";} # [method choice]/6-31(+)G* SMD choice of solvent and opt - dovac
elsif($job =~ /optcrs/i ) {$output_type="gaussian";} # [method choice]/6-31G(+)G* CPCM UAKS opt choice of solvent - dovac
elsif($job =~ /optetac/i ) {$output_type="gaussian";} # B3LYP/6-31G* CPCM UAKS opt solvent=etac
elsif($job =~ /rmp2/i ) {$output_type="gaussian";} # ROMP2/6-311+G(3df,2p) single point
elsif($job =~ /ump2/i ) {$output_type="gaussian";} # UMP2/6-311+G(3df,2p) single point
elsif($job =~ /usmp2/i ) {$output_type="gaussian";} # UHF/6-31G* followed by UMP2/aug-cc-pVDZ single points
elsif($job =~ /ulmp2/i ) {$output_type="gaussian";} # UHF/6-31G* followed by UMP2/aug-cc-pVTZ single points
elsif($job =~ /mr/ ) {$output_type="gamess";} #MCSCF using 6-31G* - can have mruhf mrpt2 mropt mrsad mrhess
elsif($job =~ /rim/i ) {$output_type="qchem";} # RIMP2
elsif($job =~ /qhf/i ) {$output_type="qchem";}
elsif($job =~ /qec/i ) {$output_type="qchem";}
elsif($job =~ /adf/i ) {$output_type="adf";} # BP/TZVP COSMO-RS
else {die "unsupported output type $job.\n";}
# ARGV[2] is the diffuse fun switch
if (!$ARGV[2] or $ARGV[2] =~ /0/){
print "no diffuse function\n";
$basis = "6-31G(d)";
$genbasis = "6-31Gd";
}
elsif ($ARGV[2] =~ /[p+]/) {
print "add diffuse function\n";
$basis = "6-31+G(d)";
$genbasis = "6-31pGd";
}
$optno = "first";
if (($ARGV[3]) && ($ARGV[3] =~ /last/)) { $optno = "last" }
if (!$ARGV[3]){
$T=298;
}
else{
$T = $ARGV[3];
}
#check to see all of the files exist
#strip the geometries from whatever the input file is.
$inputfile = $ARGV[1];
if ($inputfile =~ /\.ar/) {
$inputfile_stripped = stripname($inputfile,"\.ar"); # strip .ar from $inputfilename
$geometry = striparc($inputfile,0); # get geometry string
$stripped_geometry = stripcom($geometry); # cull leading and trailing rubbish
heavyatom($stripped_geometry);
}
elsif($inputfile =~ /\.log/ ){
if($inputfile =~ /\.297\.mecn\.log/ and $job =~ /mecn/i){
$inputfile_stripped = stripname($inputfile,"\.298\.mecn\.log");
print $inputfile_stripped ;
}
else{
$inputfile_stripped = stripname($inputfile,"\.log"); # strip .log from $inputfilename
}
$geometry = striparc($inputfile,0); # get geometry string
(*field) = stripfield($inputfile);
if (($field[0] != 0) || ($field[1] != 0) || ($field[2] != 0)) { $appfield = "y"} else { $appfield = "n" }
if ($geometry eq ""){
print "Caution! $inputfile This is not optimised geometry!\n";
$stripped_geometry = striplastxyz($inputfile);
}
else{
$stripped_geometry = stripcom($geometry); # cull leading and trailing rubbish
}
heavyatom($stripped_geometry);
}
elsif($inputfile =~ /\.com/ ){
$inputfile_stripped = stripname($inputfile,"\.com"); # strip .com from $inputfilename
$geometry = strip($inputfile);
$stripped_geometry = stripcom($geometry);
$stripped_geometry =~ s/\s*\n$//;
if ($job =~ /opt/i){
rename($inputfile,$inputfile_stripped.".oldcom")||die "Can't mv $inputfile to $inputfile_stripped".".old\n";
}
heavyatom($stripped_geometry);
$stripped_geometry = ${stripped_geometry}."\n";
}
elsif($inputfile =~ /\.zmat/ ){
$inputfile_stripped = stripname($inputfile,"\.zmat"); # strip .zmat from $inputfilename
$geometry = strip($inputfile);
$geometry =~ s/\s*\n$//;
if ($geometry =~ /^\s*-*\d+/){
$stripped_geometry = $geometry;
}
else{
print "$inputfile\n";
$charge = &promptUser(" What is the charge of this molecule?",0);
$multi = &promptUser(" What is the multiplicity of this molecule?",1);
$stripped_geometry = ${charge}." ".${multi}."\n".${geometry};
}
$stripped_geometry = ${stripped_geometry}."\n";
}
elsif($inputfile =~ /\.inp/ ){
$inputfile_stripped = stripname($inputfile,"\.inp"); # strip .inp from $inputfilename
$geometry = strip($inputfile);
$stripped_geometry = stripcom($geometry);
}
elsif($inputfile =~ /\.gin/ ){
$inputfile_stripped = stripname($inputfile,"\.gin"); # strip .xyz from $inputfilename
$stripped_geometry = strip($inputfile);
$stripped_geometry =~ s/\s+\n/\n/;
}
elsif($inputfile =~ /\.xyz/ ){
$inputfile_stripped = stripname($inputfile,"\.xyz"); # strip .xyz from $inputfilename
$stripped_geometry = strip($inputfile);
$stripped_geometry =~ s/scf done:\s*-*\d+.\d+//;
$stripped_geometry =~ s/^\s*\d+\s*\n//;
$stripped_geometry =~ s/^\s*\n//;
$stripped_geometry =~ s/\s*\n$//;
if ($stripped_geometry =~ /^\s*-*\d+/){
$stripped_geometry = $stripped_geometry;
}
else{
print "$inputfile\n";
$charge = &promptUser(" What is the charge of this molecule?",0);
$multi = &promptUser(" What is the multiplicity of this molecule?",1);
$stripped_geometry = ${charge}." ".${multi}."\n".${stripped_geometry};
}
heavyatom($stripped_geometry);
$stripped_geometry = ${stripped_geometry}."\n";
}
elsif($inputfile =~ /\.uhfna\.punch/ ){
$inputfile_stripped = stripname($inputfile,"\.punch"); # strip .inp from $inputfilename
$stripped_geometry = stripnatural($inputfile);
($data,$mult,$norb,$det) = stripgam("$inputfile_stripped.inp");
}
elsif($inputfile =~ /\.sad\.punch/ ){
$inputfile_stripped = stripname($inputfile,"\.punch"); # strip .inp from $inputfilename
$stripped_geometry = strippunch($inputfile);
($data,$mult,$norb,$det) = stripgam("$inputfile_stripped.inp");
}
elsif($inputfile =~ /\.opt\.punch/ ){
$inputfile_stripped = stripname($inputfile,"\.punch"); # strip .inp from $inputfilename
$stripped_geometry = strippunch($inputfile);
($data,$mult,$norb,$det) = stripgam("$inputfile_stripped.inp");
}
elsif($inputfile =~ /\.out$/){
$inputfile_stripped = stripname($inputfile,"\.out\$");
$stripped_geometry = stripout($inputfile);
$stripped_geometry =~ s/^\s*\d+\s*\n//;
$stripped_geometry =~ s/^\s*\n//;
if ($stripped_geometry =~ /^\s*-*\d+/){
$stripped_geometry = $stripped_geometry;
}
else{
#$charge = &promptUser(" What is the charge of this molecule?",0);
#$multi = &promptUser(" What is the multiplicity of this molecule?",1);
$charge = "";
$multi = "";
$stripped_geometry = ${charge}." ".${multi}."\n".${stripped_geometry};
}
}
else {
print "Unknown file extension. Supported filetypes:\n";
print "Gaussian .log and .com (zmat and cartesian)\n";
print "Molden .zmat (gaussian format)\n";
print "Qchem .inp\n";
print "Molpro .out\n";
print "Any file containing a charge/multiplicity line,\n";
print "immediately followed by cartesian or zmat (gaussian)\n";
print "coordinates, where the file has a .com, .inp or .zmat\n";
print "extension. Leading and/or trailing garbage is allowed.\n";
die;
}
#Now, create the output.
if ($output_type eq "adf"){
$inputfile_stripped =~ s/.opt.etac//;
$inputfile_stripped = "$inputfile_stripped.adf";
$cm = getcm("$stripped_geometry");
($c,$m)=split(/[ \t]+/,$cm);
$spin = $m-1;
$header ="#! /bin/sh\n\n# ==============================\n# The Molecule\n# ==============================\n\n\"\$ADFBIN/adf\" <<eor\nTITLE fragment\n\nATOMS\n";
$footer = "END\n\nCHARGE $c.0 $spin \n\n";
if($spin!=0){
$footer = ${footer}."UNRESTRICTED\n\n";
}
$footer = ${footer}."\n\nBASIS\ntype TZP\ncore Large\nEND\n\nXC\nGGA Becke Perdew\nEND\n\nSAVE TAPE21 TAPE13\n\neor\n";
$stripped_geometry =~ s/^\s*-*\d+.*\n//g;
$finaldeck = ${header}.${stripped_geometry}."\n".${footer};
writedeck($finaldeck,$inputfile_stripped.".fragment.run");
$header ="#! /bin/sh\n\n# dependency: $inputfile_stripped $inputfile_stripped.fragment.t21\n# ==============================\n# The Molecule\n# ==============================\n\n\"\$ADFBIN/adf\" <<eor\nTITLE \n\nATOMS\n";
$footer = "END\n\nCHARGE $c.0 $spin \n\n";
if($spin!=0){
$footer = ${footer}."UNRESTRICTED\n\n";
}
$footer = ${footer}."SYMMETRY NOSYM\n\nSOLVATION\n\tSurf Delley\n\tDiv ndiv=4\n\tSolvent name=CRS cav0=0.0 cav1=0.0\n\tCharged method=CONJ corr\n\tC-Mat EXACT\n\tSCF VAR ALL\nEND\nBASIS\ntype TZP\ncore Large\nEND\n\nXC\nGGA Becke Perdew\nEND\n\nRESTART\t$inputfile_stripped.fragment.t21\n\nSAVE TAPE21 TAPE13\n\neor\n";
@atom = split(/\n/,$stripped_geometry);
@radiiline = split(/\n/,$stripped_geometry);
for $i (0..$#atom){
$atom[$i] =~ s/-*\d+.*//g;
$atom[$i] =~ s/\s+//g;
$radii = adfradii($atom[$i]);
$radiiline[$i] =~ s/$/\tR=$radii/g;
}
$stripped_geometry = join("\n",@radiiline);
$finaldeck = ${header}.${stripped_geometry}."\n".${footer};
writedeck($finaldeck,$inputfile_stripped.".run");
}
if ($output_type eq "gaussian"){
$grid="INT(grid=ultrafine)";
$cm = getcm("$stripped_geometry");
$iszmat = check_geometry_type($stripped_geometry);
#if it is, only print the first 7 fields of the zmat
#if the no. of fields is 8.
##$finaldeck = ${stripped_geometry}."\n";
#$finaldeck = addcomment($inputfile_stripped, $finaldeck);
if($job =~ /gau/i ){
@if = split(/\./,$inputfile_stripped);
$inputfile_stripped = $if[0];
$level = &promptUser(" What level of theory do you want to use?","M062X");
if (($level =~ /CCSD/) || ($level =~ /ccsd/) || ($level =~ /QCI/) || ($level =~ /qci/) || ($level =~ /mp2/) || ($level =~ /mp2/) || ($level =~ /HF/) || ($level =~ /hf/)) {
$grid = "";
}
$id = $level;
$basis = &promptUser(" Which basis do you want to use?","6-31G*");
if (($basis =~ /6-31G\*/) || ($basis =~ /6-31\+G\*/) || ($basis =~ /6-31G\(d\)/) || ($basis =~ /6-31\+G\(d\)/)) {
$qnew = &promptUser(" Do you want to use the Rassolov version?","Y");
if ($qnew =~ /[yY]/) {
if (($basis =~ /6-31G\*/) || ($basis =~ /6-31G\(d\)/)) {
$genbasis = "6-31Gd";
}
else {
$genbasis = "6-31pGd";
}
$basis = "Gen 6D";
$basfooter ="@/$HOME/Basis/$genbasis.gbs/N\n\n";
}
else {
$basfooter = "";
}
}
else {
$basfooter = "";
}
$jobtype = &promptUser(" Do you want to optimise the geometry?",N);
$zm = "";
if($jobtype =~ /[yY]/ ){
$zmq = &promptUser(" Do you want to use Opt=z-matrix?",N);
$opttype = &promptUser(" Is it a TS?",N);
if($opttype =~ /[yY]/ ){
if ($zmq =~ /[yY]/) { $zm = ",z-matrix" }
$opt = "OPT=(TS,calcfc$zm,noeigentest,maxcyc=200) IOP(2/17=4)";
}
else {
if ($zmq =~ /[yY]/) { $zm = "(z-matrix)" }
$opt ="OPT$zm IOP(2/17=4)";
}
$freqtype = "Y";
$freq = "Freq=Noraman";
}
else {
$opt = "";
$freqtype = &promptUser(" Do you want to calculate the frequencies?",N);
if($freqtype =~ /[yY]/ ){
$freq = "Freq=Noraman";
}
else {
$freq = "";
}
}
$solvq = &promptUser(" Do you want to use a solvent model?","N");
if ($solvq =~ /[Yy]/){
$solv = &promptUser(" What solvent model do you want to use (uaks, smd)?","smd");
$solvent = &promptUser(" What is the solvent you want to use (toluene,etac,h2o)?","h2o");
$gsolv = &promptUser(" Do you want to calculated dGsolv?","N");
$id = "$solv.$solvent";
if ($gsolv =~ /[Yy]/) {
$dovac = ",dovac,self";
}
else {
$dovac = "";
}
if ($solv eq "uaks") {
if ($solvent eq "toluene"){
$scrf = "SCRF=(CPCM,Solvent=$solvent,Read)";
$scrf2 = "SCRF=(CPCM,Solvent=$solvent,Read$dovac)";
$radiiline = "RADII=UAKS\nAlpha=1.3\n";
$nonelec = "Cav\nDis\nRep\n";
$solvnline = "";
}
elsif ($solvent eq "etac"){
$scrf = "SCRF=(CPCM,Solvent=DiethylEther,Read)";
$scrf2 = "SCRF=(CPCM,Solvent=DiethylEther,Read$dovac)";
$radiiline = "RADII=UAKS\nAlpha=1.2\n";
$nonelec = "Cav\nDis\nRep\n";
$solvnline = "DENSITY=0.00613\nRSOLV=2.648\nEPS=5.9867\nVMOL=89.4\n";
}
elsif ($solvent eq "h2o"){
$scrf = "SCRF=(PCM,Solvent=water,Read)";
$scrf2 = "SCRF=(PCM,Solvent=water,Read$dovac)";
$radiiline = "RADII=UAKS\nAlpha=1.2\n";
$nonelec = "Cav\nDis\nRep\n";
$solvnline = "";
}
$solfooter = "$radiiline$nonelec$solvnline";
if ($qnew =~ /[yY]/) {
$nl = "\n";
}
}
elsif ($solv eq "smd") {
$scrf = "SCRF=(SMD,Solvent=$solvent)";
$scrf2 = "SCRF=(SMD,Solvent=$solvent$dovac)";
# $scrf = "SCRF=(Read,SMD,Solvent=$solvent)";
$solvnline ="";
# $solvnline ="surface=sas\nrsolv=0";
$radiiline = "";
$nonelec = "";
$solfooter = "$radiiline$nonelec$solvnline";
$nl = "";
}
}
else {
$scrf = "";
$scrf2 = "";
$solfooter = "";
$nl = "";
$gsolv = "N";
}
$fieldq = &promptUser(" Do you want to use an external electric field?","N");
if ($fieldq =~ /[Yy]/){
if ($appfield =~ /n/) {
$appfield = "Y";
$field[0] = &promptUser(" What is the X component of the field?", "0.0");
$field[1] = &promptUser(" What is the Y component of the field?", "0.0");
$field[2] = &promptUser(" What is the Z component of the field?", "0.0");
}
$fld = "Field=Read Nosymm";
$fieldfooter = "$field[0]\n$field[1]\n$field[2]\n";
}
else {
$fld = "";
$fieldfooter = "";
}
if (($jobtype =~ /[Yy]/) && ($gsolv =~ /[Yy]/)) {
$header ="\%chk=$inputfile_stripped.$id.chk\n\# $level/$basis SCF=Tight $grid $opt $scrf $fld\n\n$inputfile_stripped.$id\n\n";
$footer ="$basfooter$solfooter$fieldfooter\n--Link1--\n\%chk=$inputfile_stripped.$id.chk\n\# $level/$basis SCF=Tight $grid $freq $scrf $fld geom=check guess=read IOP(2/17=4)\n\n$inputfile_stripped.$id\n\n$cm\n\n$basfooter$solfooter$fieldfooter\n--Link1--\n\%chk=$inputfile_stripped.$id.chk\n\# $level/$basis SCF=Tight $grid $scrf2 $fld geom=check guess=read IOP(2/17=4)\n\n$inputfile_stripped.$id\n\n$cm\n\n$solfooter$nl$basfooter$fieldfooter";
}
elsif ($jobtype =~ /[Yy]/) {
$header ="\%chk=$inputfile_stripped.$id.chk\n\# $level/$basis SCF=Tight $grid $opt $scrf $fld\n\n$inputfile_stripped.$id\n\n";
$footer ="$basfooter$solfooter$fieldfooter\n--Link1--\n\%chk=$inputfile_stripped.$id.chk\n\# $level/$basis SCF=Tight $grid $freq $scrf $fld geom=check guess=read IOP(2/17=4)\n\n$inputfile_stripped.$id\n\n$cm\n\n$basfooter$solfooter$fieldfooter";
}
else {
$header ="\%chk=$inputfile_stripped.$id.chk\n\# $level/$basis SCF=Tight $grid $opt $freq $scrf2 $fld \n\n$inputfile_stripped.$id\n\n";
$footer ="$basfooter$solfooter$fieldfooter";
}
}
elsif($job =~ /w1ts/i) {
@mult=split(/\s+/,$cm);
if ($mult[1] != 1){
$header ="\%chk=$inputfile_stripped.w1ts.chk\n\#UB3LYP/cc-pVTZ+d OPT=(TS,calcfc,noeigentest) IOP(2/17=4) Freq=noraman\n\n$inputfile_stripped.w1ts\n\n";
}
else{
$header ="\%chk=$inputfile_stripped.w1ts.chk\n\#RB3LYP/cc-pVTZ+d OPT=(TS,calcfc,noeigentest) IOP(2/17=4) Freq=noraman\n\n$inputfile_stripped.w1ts\n\n";
}
$footer ="\n";
}
elsif($job =~ /w1opt/i ){
@mult=split(/\s+/,$cm);
if ($mult[1] != 1){
$header ="\%chk=$inputfile_stripped.w1opt.chk\n\#UB3LYP/cc-pVTZ+d OPT IOP(2/17=4)\n\n$inputfile_stripped.w1opt\n\n";
$footer =${footer}."\n--Link1--\n\%chk=$inputfile_stripped.w1opt.chk\n\#UB3LYP/cc-pVTZ+d SCF=Tight pseudo=read guess=read geom=check Freq=noraman\n\n$inputfile_stripped.w1opt\n\n$cm\n\n";
}
else{
$header ="\%chk=$inputfile_stripped.w1opt.chk\n\#RB3LYP/cc-pVTZ+d OPT IOP(2/17=4)\n\n$inputfile_stripped.w1opt\n\n";
$footer =${footer}."\n--Link1--\n\%chk=$inputfile_stripped.w1opt.chk\n\#RB3LYP/cc-pVTZ+d SCF=Tight pseudo=read guess=read geom=check Freq=noraman\n\n$inputfile_stripped.w1opt\n\n$cm\n\n";
}
$footer ="\n";
}
elsif($job =~ /optetac/i ){
$level = "B3LYP";
$solvent = "etac";
$scrf = "CPCM,Solvent=DiethylEther,Read";
$radiiline = "RADII=UAKS\nAlpha=1.2\n";
$nonelec = "Cav\nDis\nRep\n";
$solvnline = "DENSITY=0.00613\nRSOLV=2.734\nEPS=5.9867\nVMOL=98.5\n";
$nm = "etac";
$header ="\%chk=$inputfile_stripped.opt.$nm.chk\n\#$level/$basis 6D IOP(2/17=4) OPT SCF=Tight SCRF=($scrf) INT(grid=ultrafine)\n\n$inputfile_stripped.opt.$nm\n\n";
$footer ="";
$footer =${footer}."$radiiline$nonelec$solvnline\n\n";
}
elsif($job =~ /optcrs/i ){
print "$inputfile_stripped\n";
$level = &promptUser(" What method do you want to use?","UB3LYP");
$solvent = &promptUser(" What is the solvent you want to use (toluene,etac,h2o,ch3cn,dmso,acetone,dcle,benzene)?","dcle");
if ($solvent eq "toluene"){
$scrf = "CPCM,Solvent=$solvent,Read";
$radiiline = "RADII=UAKS\nAlpha=1.3\n";
$nonelec = "Cav\nDis\nRep\n";
$solvnline = "";
$nm = "tol";
}
elsif ($solvent eq "benzene"){
$scrf = "CPCM,Solvent=$solvent,Read";
$radiiline = "RADII=UAKS\nAlpha=1.3\n";
$nonelec = "Cav\nDis\nRep\n";
$solvnline = "";
$nm = "bzn";
}
elsif ($solvent eq "dcle"){
$scrf = "CPCM,Solvent=DiChloroEthane,Read";
$radiiline = "RADII=UAKS\nAlpha=1.3\n";
$nonelec = "Cav\nDis\nRep\n";
$solvnline = "";
$nm = "dcle";
}
elsif ($solvent eq "acetone"){
$scrf = "CPCM,Solvent=$solvent,Read";
$radiiline = "RADII=UAKS\nAlpha=1.3\n";
$nonelec = "Cav\nDis\nRep\n";
$solvnline = "";
$nm = "actn";
}
elsif ($solvent eq "dmso"){
$scrf = "CPCM,Solvent=DiMethylSulfoxide,Read";
$radiiline = "RADII=UAKS\nAlpha=1.35\n";
$nonelec = "Cav\nDis\nRep\n";
$solvnline = "";
$nm = "dmso";
}
elsif ($solvent eq "etac"){
$scrf = "CPCM,Solvent=DiethylEther,Read";
$radiiline = "RADII=UAKS\nAlpha=1.2\n";
$nonelec = "Cav\nDis\nRep\n";
$solvnline = "DENSITY=0.00613\nRSOLV=2.734\nEPS=5.9867\nVMOL=98.5\n";
$nm = "etac"
}
elsif ($solvent eq "h2o"){
$scrf = "PCM,Solvent=water,Read";
$radiiline = "RADII=UAKS\nAlpha=1.2\n";
$nonelec = "Cav\nDis\nRep\n";
$solvnline = "";
$nm = "h2o"
}
elsif ($solvent eq "ch3cn"){
$scrf = "CPCM,Solvent=CH3CN,Read";
$radiiline = "RADII=UAKS\nAlpha=1.45\n";
$nonelec = "Cav\nDis\nRep\n";
$solvnline = "";
$nm = "acn"
}
$opttype = &promptUser(" Is it a TS?",N);
if($opttype =~ /[yY]/ ){
$header ="\%chk=$inputfile_stripped.optcrs.$nm.chk\n\#$level/$basis 6D IOP(2/17=4) OPT=(TS,calcfc,noeigentest,maxcyc=200) SCF=Tight SCRF=($scrf) INT(grid=ultrafine)\n\n$inputfile_stripped.optcrs.$nm\n\n";
$footer ="$radiiline$nonelec$solvnline\n\n";
$footer =${footer}."\n--Link1--\n\%chk=$inputfile_stripped.optcrs.$nm.chk\n\#$level/$basis 6D SCF=Tight Freq=Noraman IOP(2/17=4) SCRF=($scrf) INT(grid=ultrafine) guess=read geom=check\n\n$inputfile_stripped.optcrs.$nm\n\n$cm\n\n";
}
else{
$header ="\%chk=$inputfile_stripped.optcrs.$nm.chk\n\#$level/$basis 6D IOP(2/17=4) OPT SCF=Tight SCRF=($scrf) INT(grid=ultrafine)\n\n$inputfile_stripped.optcrs.$nm\n\n";
$footer ="";
}
$footer =${footer}."$radiiline$nonelec$solvnline\n\n";
$footer =${footer}."\n--Link1--\n\%chk=$inputfile_stripped.optcrs.$nm.chk\n\#$level/$basis 6D SCF=Tight IOP(2/17=4) SCRF=($scrf,dovac,self) INT(grid=ultrafine) guess=read geom=check\n\n$inputfile_stripped.optcrs.$nm\n\n$cm\n\n$radiiline$nonelec$solvnline\n\n";
}
elsif($job =~ /uahf/i ){
print "$inputfile_stripped\n";
$level = "UHF";
$solvent = &promptUser(" What is the solvent you want to use (toluene,etac,h2o,ch3cn,dmso,acetone,dcle)?","toluene");
if ($solvent eq "toluene"){
$scrf = "CPCM,Solvent=$solvent,Read";
$radiiline = "RADII=UAHF\nAlpha=1.3\n";
$nonelec = "Cav\nDis\nRep\n";
$solvnline = "";
$nm = "tol";
}
elsif ($solvent eq "dcle"){
$scrf = "CPCM,Solvent=DiChloroEthane,Read";
$radiiline = "RADII=UAHF\nAlpha=1.3\n";
$nonelec = "Cav\nDis\nRep\n";
$solvnline = "";
$nm = "dcle";
}
elsif ($solvent eq "acetone"){
$scrf = "CPCM,Solvent=$solvent,Read";
$radiiline = "RADII=UAHF\nAlpha=1.3\n";
$nonelec = "Cav\nDis\nRep\n";
$solvnline = "";
$nm = "actn";
}
elsif ($solvent eq "dmso"){
$scrf = "CPCM,Solvent=DiMethylSulfoxide,Read";
$radiiline = "RADII=UAHF\nAlpha=1.35\n";
$nonelec = "Cav\nDis\nRep\n";
$solvnline = "";
$nm = "dmso";
}
elsif ($solvent eq "etac"){
$scrf = "CPCM,Solvent=DiethylEther,Read";
$radiiline = "RADII=UAHF\nAlpha=1.2\n";
$nonelec = "Cav\nDis\nRep\n";
$solvnline = "DENSITY=0.00613\nRSOLV=2.734\nEPS=5.9867\nVMOL=98.5\n";
$nm = "etac"
}
elsif ($solvent eq "h2o"){
$scrf = "PCM,Solvent=water,Read";
$radiiline = "RADII=UAHF\nAlpha=1.2\n";
$nonelec = "Cav\nDis\nRep\n";
$solvnline = "";
$nm = "h2o"
}
elsif ($solvent eq "ch3cn"){
$scrf = "CPCM,Solvent=CH3CN,Read";
$radiiline = "RADII=UAHF\nAlpha=1.45\n";
$nonelec = "Cav\nDis\nRep\n";
$solvnline = "";
$nm = "acn"
}
$header ="\%chk=$inputfile_stripped.uahf.$nm.chk\n\#$level/$basis 6D IOP(2/17=4) SCF=Tight SCRF=($scrf,dovac,self) \n\n$inputfile_stripped.uahf.$nm\n\n";
$footer ="$radiiline$nonelec$solvnline\n\n";
}
elsif($job =~ /spcrs/i ){
$level = &promptUser(" What method do you want to use?","UB3LYP");
$solvent = &promptUser(" What is the solvent you want to use (toluene,etac,h2o,ch3cn)?","h2o");
if ($solvent eq "toluene"){
$scrf = "CPCM,Solvent=$solvent,Read";
$radiiline = "RADII=UAKS\nAlpha=1.3\n";
$nonelec = "Cav\nDis\nRep\n";
$solvnline = "";
$nm = "tol";
}
elsif ($solvent eq "etac"){
$scrf = "CPCM,Solvent=DiethylEther,Read";
$radiiline = "RADII=UAKS\nAlpha=1.2\n";
$nonelec = "Cav\nDis\nRep\n";
$solvnline = "DENSITY=0.00613\nRSOLV=2.734\nEPS=5.9867\nVMOL=98.5\n";
$nm = "etac"
}
elsif ($solvent eq "h2o"){
$scrf = "PCM,Solvent=water,Read";
$radiiline = "RADII=UAKS\nAlpha=1.2\n";
$nonelec = "Cav\nDis\nRep\n";
$solvnline = "";
$nm = "h2o"
}
elsif ($solvent eq "ch3cn"){
$scrf = "CPCM,Solvent=CH3CN,Read";
$radiiline = "RADII=UAKS\nAlpha=1.45\n";
$nonelec = "Cav\nDis\nRep\n";
$solvnline = "";
$nm = "acn"
}
$header ="\%chk=$inputfile_stripped.spcrs.$nm.chk\n\#$level/$basis 6D IOP(2/17=4) SCF=Tight SCRF=($scrf,dovac,self) INT(grid=ultrafine)\n\n$inputfile_stripped.spcrs.$nm\n\n";
$footer ="$radiiline$nonelec$solvnline\n\n";
}
elsif($job =~ /smdbenz/i ){
$solvn = "Benzene";
$nm = "benz";
$level = "M052X";
$basis = "Gen";
$basfooter ="@/$HOME/Basis/$genbasis.gbs/N\n";
$header ="\%chk=$inputfile_stripped.smd.$nm.chk\n\#$level/$basis 6D SCF=Tight IOP(2/17=4) SCRF=(Read,dovac,self,SMD,Solvent=$solvn) INT(grid=ultrafine)\n\n$inputfile_stripped.smd\n\n";
$footer ="surface=sas\nrsolv=0\n\n$basfooter\n\n";
}
elsif($job =~ /smdch3cn/i ){
$solvn = "Acetonitrile";
$nm = "ch3cn";
$level = "M052X";
$basis = "Gen";
$basfooter ="@/$HOME/Basis/$genbasis.gbs/N\n";
$header ="\%chk=$inputfile_stripped.smd.$nm.chk\n\#$level/$basis 6D SCF=Tight IOP(2/17=4) SCRF=(Read,dovac,self,SMD,Solvent=$solvn) INT(grid=ultrafine)\n\n$inputfile_stripped.smd\n\n";
$footer ="surface=sas\nrsolv=0\n\n$basfooter\n\n";
}
elsif($job =~ /smd/i ){
$solvn = &promptUser(" Which solvent do you want to use?","toluene");
if($solvn =~ /water/ ){
$nm ="h2o";
}
elsif($solvn =~ /toluene/ ){
$nm ="tol";
}
else {
$nm = &promptUser(" Which filename ext do you want ot use for this solvent?","$solvn");
}
$level = &promptUser(" Which level of theory do you want to use?","M062X");
$basis = "Gen";
$basfooter ="@/$HOME/Basis/$genbasis.gbs/N\n";
$opttype1 = &promptUser(" Do you want to optimise the geometries?",N);
if($opttype1 =~ /N/ ){
$header ="\%chk=$inputfile_stripped.smd.$nm.chk\n\#$level/$basis 6D SCF=Tight IOP(2/17=4) SCRF=(Read,dovac,self,SMD,Solvent=$solvn) INT(grid=ultrafine)\n\n$inputfile_stripped.smd\n\n";
$footer ="surface=sas\nrsolv=0\n\n$basfooter\n\n";
}
else{
$opttype = &promptUser(" Is it a TS?",N);
if($opttype =~ /[yY]/ ){
$header ="\%chk=$inputfile_stripped.smd.chk\n\#$level/$basis 6D IOP(2/17=4) OPT=(TS,calcfc,noeigentest,maxcyc=200) SCF=Tight SCRF=(SMD,Solvent=$solvn,Read) INT(grid=ultrafine)\n\n$inputfile_stripped.smd\n\n";
}
else{
$header ="\%chk=$inputfile_stripped.smd.chk\n\#$level/$basis 6D IOP(2/17=4) OPT SCF=Tight SCRF=(SMD,Solvent=$solvn,Read) INT(grid=ultrafine)\n\n$inputfile_stripped.smd\n\n";
}
$footer ="$basfooter\nsurface=sas\nrsolv=0\n\n";
$footer =${footer}."\n--Link1--\n\%chk=$inputfile_stripped.smd.chk\n\#$level/$basis 6D SCF=Tight IOP(2/17=4) SCRF=(Read,dovac,self,SMD,Solvent=$solvn) INT(grid=ultrafine) guess=read geom=check\n\n$inputfile_stripped.smd\n\n$cm\n\n$basfooter\nsurface=sas\nrsolv=0\n\n\n";
}
}
elsif($job =~ /b3sp/i ){
$header ="\%chk=$inputfile_stripped.b3sp.chk\n\#B3LYP/$basis 6D IOP(2/17=4) INT(grid=ultrafine) SCF=Tight\n\n$inputfile_stripped.b3lyp.singlepoint\n\n";
$footer ="";
}
# elsif($job =~ /uahf/i ){
# $header ="\%chk=$inputfile_stripped.uahf.chk\n\#UHF/$basis 6D SCRF=(CPCM,Solvent=water,Read) OPT int(Grid=Ultrafine) IOP(2/17=4)\n\n$inputfile_stripped.uahf\n\n";
# $footer ="Radii=UAHF\nAlpha=1.2\nRep\nDis\nCav\n\n";
# $footer =${footer}."\n--Link1--\n\%chk=$inputfile_stripped.uahf.chk\n\#UHF/$basis 6D SCRF=(CPCM,Solvent=water,Read,dovac,self) IOP(2/17=4) int(Grid=Ultrafine) guess=read geom=check\n\n$inputfile_stripped.uahf\n\n$cm\n\nRadii=UAHF\nAlpha=1.2\nRep\nDis\nCav\n\n";
# }
elsif($job =~ /sphf/i ){
$level = &promptUser(" What level of theory do you want to use?","ROHF");
$header ="\%chk=$inputfile_stripped.sphf.chk\n\#$level/gen 6D SCF=Tight\n\n$inputfile_stripped.sphf\n\n";
$footer ="@/$HOME/Basis/$genbasis.gbs/N\n\n";
}
elsif($job =~ /vol/i ){
$header ="\%chk=$inputfile_stripped.vol.chk\n\#UHF/gen 6D SCRF=(CPCM,Solvent=water,Read) Volume int(Grid=Ultrafine) \n\n$inputfile_stripped.uahf\n\n";
$footer ="@/$HOME/Basis/$genbasis.gbs/N\n\nRadii=UAHF\nAlpha=1.4\nRep\nDis\nCav\n\n";
}
elsif($job =~ /oi/i ){
$level = &promptUser(" What level of theory do you want to use?","UHF");
if($level =~ /UHF/ ){
$ln ="uhf";
}
elsif($level =~ /M06/ ){
$ln ="m06";
}
else{
$ln = &promptUser(" Enter subtitle for the theory");
}
$basis = &promptUser(" Which basis do you want to use?","STO-3G");
if($basis =~ /STO/ ){
$bn ="sto";
}
elsif($basis =~ /6-31/ ){
$bn ="gbs";
}
else{
$bn = &promptUser(" Enter subtitle for the basis");
}
$header ="\%chk=$inputfile_stripped.oi.$ln.$bn.chk\n\#P $level/$basis SCF=Tight FormCheck Pop=Full Nosymm IOP(3/33=1) \n\n$inputfile_stripped.oi.$ln.$bn\n\n";
$footer ="\n\n";
}
elsif($job =~ /dens/i ){
$level = &promptUser(" What level of theory do you want to use?","MP2");
if($level =~ /MP2/ ){
$ln ="mp2";
}
else{
$ln = &promptUser(" Enter subtitle for the theory");
}
$basis = &promptUser(" Which basis do you want to use?","aug-cc-pVTZ");
$header ="\%chk=$inputfile_stripped.dens.$ln.chk\n\#P $level/$basis SCF=Tight FormCheck Density=current \n\n$inputfile_stripped.dens.$ln\n\n";
$footer ="\n\n";
}
elsif($job =~ /ts1/i ){
$header ="\%chk=$inputfile_stripped.ts1.chk\n\#UHF/$basis 6D SCRF=(CPCM,Solvent=water,Read) IOP(2/17=4) OPT=(Cartesian,TS,calcfc,noeigentest,maxcyc=200) int(Grid=Ultrafine)\n\n$inputfile_stripped.ts1\n\n";
$footer ="Radii=UAHF\nAlpha=1.4\nRep\nDis\nCav\n\n";
$footer =${footer}."\n--Link1--\n\%chk=$inputfile_stripped.ts1.chk\n\#UHF/$basis 6D SCRF=(CPCM,Solvent=water,Read,dovac,self) IOP(2/17=4) int(Grid=Ultrafine) guess=read geom=check\n\n$inputfile_stripped.ts1\n\n$cm\n\nRadii=UAHF\nAlpha=1.4\nRep\nDis\nCav\n\n";
}
elsif($job =~ /cbsrad/i ){
$opttype = &promptUser(" Is it a TS?",N);
if($opttype =~ /[yY]/ ){
$header ="\%chk=$inputfile_stripped.cbsrad.chk\n\#B3LYP/6-31G(d) Freq=Noraman \n\n$inputfile_stripped.geometry\n\n";
$footer ="\n--Link1--\n\%chk=$inputfile_stripped.cbsrad.chk\n\#QCISD(fc)/6-31G(d) OPT=(TS,readfc,noeigentest,maxcyc=200) guess=tcheck geom=allcheck \n\n$inputfile_stripped.geometry\n\n$cm\n\n\n--Link1--\n";
}
else {
$header ="\%chk=$inputfile_stripped.cbsrad.chk\n\#QCISD(fc)/6-31G(d) OPT \n\n$inputfile_stripped.geometry\n\n";
$footer ="\n--Link1--\n";
}
$footer =${footer}."\%chk=$inputfile_stripped.cbsrad.chk\n\#QCISD(fc)/6-31G(d) guess=tcheck geom=allcheck Freq=noraman\n\n$inputfile_stripped.frequency\n\n$cm\n\n";
$footer =${footer}."\n--Link1--\n\%chk=$inputfile_stripped.cbsrad.chk\n\#CCSD(T,T1Diag,fc)/6-31+G(d') guess=tcheck geom=allcheck\n\n$inputfile_stripped.cbs-rad\n\n$cm\n\n";
$footer =${footer}."\n--Link1--\n\%chk=$inputfile_stripped.cbsrad.chk\n\#MP4(SDQ,fc)/CBSB4 guess=tcheck geom=allcheck\n\n$inputfile_stripped.cbs-rad\n\n$cm\n\n";
$footer =${footer}."\n--Link1--\n\%chk=$inputfile_stripped.cbsrad.chk\n\#MP2(fc)/CBSB3 CBSExtrapolate=(NMin=10,MinPop) guess=tcheck geom=allcheck\n\n$inputfile_stripped.cbs-rad\n\n$cm\n\n";
}
elsif($job =~ /qb3/i ){
$opttype = &promptUser(" Is it a TS?",N);
if($opttype =~ /[yY]/ ){
$header ="\%chk=$inputfile_stripped.qb3.chk\n\# CBS-QB3 OPT=(TS,calcfc,noeigentest,maxcyc=200) \n\n$inputfile_stripped CBS-QB3\n\n";
$footer ="\n\n";
}
else {
$header ="\%chk=$inputfile_stripped.qb3.chk\n\# CBS-QB3 \n\n$inputfile_stripped CBS-QB3\n\n";
$footer ="\n\n";
}
}
elsif($job =~ /cbs4m/i ){
$opttype = &promptUser(" Is it a TS?",N);
if($opttype =~ /[yY]/ ){
$header ="\%chk=$inputfile_stripped.cbs4m.chk\n\# CBS-4M OPT=(TS,calcfc,noeigentest,maxcyc=200) \n\n$inputfile_stripped CBS-4M\n\n";
$footer ="\n\n";
}
else {
$header ="\%chk=$inputfile_stripped.cbs4m.chk\n\# CBS-4M \n\n$inputfile_stripped CBS-4M\n\n";
$footer ="\n\n";
}
}
elsif($job =~ /gcc2/i ){
$header ="\%chk=$inputfile_stripped.gcc.chk\n\#ROCCSD(T,FrzG3,T1Diag)/gen 6D SCF=Tight\n\n$inputfile_stripped.geometry\n\n";
$footer ="@/$HOME/Basis/$genbasis.gbs/N\n\n";
}
elsif($job =~ /gcc/i ){
$header ="\%chk=$inputfile_stripped.gcc.chk\n\#UCCSD(T,T1Diag)/aug-cc-pVTZ SCF=Tight\n\n$inputfile_stripped.geometry\n\n";
$footer ="\n\n";
}
# elsif($job =~ /dcc/i ){
# $header ="\%chk=$inputfile_stripped.dcc.chk\n\#CCSD(T,T1Diag)/aug-cc-pVTZ INT(grid=ultrafine) SCF=Tight\n\n$inputfile_stripped ccsd(t) with dunning's basis set \n\n";
# $footer ="\n";
# }
elsif($job =~ /fullg3/i ){
$opttype = &promptUser(" Is it a TS?",N);
if($opttype =~ /[yY]/ ){
$header ="\%chk=$inputfile_stripped.fullg3.chk\n\#G3 OPT=(TS,calcfc,noeigentest,maxcyc=200)\n\n$inputfile_stripped G3\n\n";
$footer ="\n\n";
}
else {
$header ="\%chk=$inputfile_stripped.fullg3.chk\n\#G3 \n\n$inputfile_stripped G3\n\n";
$footer ="\n\n";
}
}
elsif($job =~ /fullg4/i ){
$opttype = &promptUser(" Is it a TS?",N);
if($opttype =~ /[yY]/ ){
$header ="\%chk=$inputfile_stripped.fullg4.chk\n\#G4 OPT=(TS,calcfc,noeigentest,maxcyc=200)\n\n$inputfile_stripped G4\n\n";
$footer ="\n\n";
}
else {
$header ="\%chk=$inputfile_stripped.fullg4.chk\n\#G4 \n\n$inputfile_stripped G4\n\n";
$footer ="\n\n";
}
}
elsif($job =~ /g4mp26x/i ){
$opttype = &promptUser(" Is it a TS?",N);
if($opttype =~ /[yY]/ ){
$header ="\%chk=$inputfile_stripped.g4mp26x.chk\n\# BMK/6-31+G(2df,p) Opt=(TS,calcfc,noeigentest,maxcyc=250) \n\n$inputfile_stripped G4MP2-6x by Chan & Radom\n\n";
$footer ="\n";
}
else {
$header ="\%chk=$inputfile_stripped.g4mp26x.chk\n\# BMK/6-31+G(2df,p) Opt \n\n$inputfile_stripped G4MP2-6x by Chan & Radom\n\n";
$footer ="\n";
}
$footer ="\n--Link1--\n\%chk=$inputfile_stripped.g4mp26x.chk\n\# Geom=AllCheck Guess=Read BMK/6-31+G(2df,p) Freq\n\n";
$footer =${footer}."\n--Link1--\n\%chk=$inputfile_stripped.g4mp26x.chk\n\# Geom=AllCheck Guess=Read CCSD(T,T1Diag,FrzG4)/GTBas1\n\n";
$footer =${footer}."\n--Link1--\n\%chk=$inputfile_stripped.g4mp26x.chk\n\# Geom=AllCheck Guess=Read MP2(FrzG4)/GTMP2LargeXP\n\n";
$footer =${footer}."\n--Link1--\n\%chk=$inputfile_stripped.g4mp26x.chk\n\# Geom=AllCheck Guess=Read HF/GFHFB3\n\n";
$footer =${footer}."\n--Link1--\n\%chk=$inputfile_stripped.g4mp26x.chk\n\# Geom=AllCheck Guess=Read HF/GFHFB4\n\n";
}
elsif($job =~ /g3cc/i ){
if ($heavy){
$header ="\%chk=$inputfile_stripped.cc.chk\n\#UCCSD(T,T1Diag)/gen pseudo=read 6D SCF=tight\n\n$inputfile_stripped.ccsd\n\n";
$footer ="@/$HOME/Basis/$genbasis.gbs/N\n\n";
$footer =${footer}."@/$HOME/Basis/lacvp.ecp/N\n\n";
}
else{
$header ="\%chk=$inputfile_stripped.cc.chk\n\#UCCSD(T,T1Diag)/gen 6D SCF=tight\n\n$inputfile_stripped.ccsd\n\n";
$footer ="@/$HOME/Basis/$genbasis.gbs/N\n\n";
}
}
elsif($job =~ /g3mp2rad/i ){
if ($heavy){
$header ="\%chk=$inputfile_stripped.mp2.chk\n\#ROMP2/gen 6D pseudo=read SCF=tight\n\n$inputfile_stripped.mp2s\n\n";
$footer ="@/$HOME/Basis/$genbasis.gbs/N\n\n";
$footer =${footer}."@/$HOME/Basis/lacvp.ecp/N\n\n";
$footer =${footer}."--link1--\n\%chk=$inputfile_stripped.mp2.chk\n\#ROMP2/gen 5D pseudo=read SCF=tight guess=read geom=check\n\n$inputfile_stripped.mp2l\n\n$cm\n";
$footer =${footer}."\n@/$HOME/Basis/GTMP2LARGE.gbs/N\n\n";
$footer =${footer}."@/$HOME/Basis/aug-cc-pVTZ-PP.ecp/N\n\n";
}
else{
if ($appfield =~ /y/) {
$fld = "Field=Read Nosymm";
$fieldfooter = "\n$field[0]\n$field[1]\n$field[2]\n";
}
else {
$fld = "";
$fieldfooter = "";
}
$header ="\%chk=$inputfile_stripped.mp2.chk\n\#ROMP2/gen 6D SCF=tight $fld\n\n$inputfile_stripped.mp2s\n\n";
$footer ="@/$HOME/Basis/$genbasis.gbs/N\n$fieldfooter\n";
$footer =${footer}."--link1--\n\%chk=$inputfile_stripped.mp2.chk\n\#ROMP2/gen 5D SCF=tight $fld guess=read geom=check\n\n$inputfile_stripped.mp2l\n\n$cm\n";
$footer =${footer}."\n@/$HOME/Basis/GTMP2LARGE.gbs/N\n$fieldfooter";
}
}
elsif($job =~ /g3full/i ){
$header ="\%chk=$inputfile_stripped.mp2.chk\n\#ROMP2/gen 6D SCF=tight\n\n$inputfile_stripped.mp2s\n\n";
$footer ="@/$HOME/Basis/$genbasis.gbs/N\n\n";
$footer =${footer}."--link1--\n\%chk=$inputfile_stripped.mp2.chk\n\#ROMP2/6-311+G(3df,2p) SCF=tight guess=read geom=check\n\n$inputfile_stripped.mp2m\n\n$cm\n\n";
}
elsif($job =~ /g3s/i ){
$header ="\%chk=$inputfile_stripped.mp2.chk\n\#ROMP2/6-31G(d) SCF=tight\n\n$inputfile_stripped.mp2s\n\n";
$footer ="";
}
elsif($job =~ /optf/i ){
if ($heavy){
$header ="\%chk=$inputfile_stripped.chk\n\#B3LYP/gen 6D pseudo=read $grid OPT IOP(2/17=4) Freq=noraman\n\n$inputfile_stripped.freq\n\n";
$footer ="@/$HOME/Basis/$genbasis.gbs/N\n\n";
$footer =${footer}."@/$HOME/Basis/lacvp.ecp/N\n\n";
}
else{
$header ="\%chk=$inputfile_stripped.chk\n\#B3LYP/gen 6D $grid OPT IOP(2/17=4) Freq=noraman\n\n$inputfile_stripped.freq\n\n";
$footer ="@/$HOME/Basis/$genbasis.gbs/N\n";
}
}
elsif($job =~ /opts/i ){
if ($heavy){
$header ="\%chk=$inputfile_stripped.chk\n\#B3LYP/gen 6D pseudo=read $grid OPT=(TS,calcfc,noeigentest,maxcyc=200) IOP(2/17=4) Freq=noraman \n\n$inputfile_stripped.freq\n\n";
$footer ="@/$HOME/Basis/$genbasis.gbs/N\n\n";
$footer =${footer}."@/$HOME/Basis/lacvp.ecp/N\n\n";
}
else{
$header ="\%chk=$inputfile_stripped.chk\n\#B3LYP/gen 6D $grid OPT=(TS,calcfc,noeigentest,maxcyc=200) IOP(2/17=4) Freq=noraman \n\n$inputfile_stripped.freq\n\n";
$footer ="@/$HOME/Basis/$genbasis.gbs/N\n";
}
}
elsif($job =~ /optz/i ){
if ($heavy){
$header ="\%chk=$inputfile_stripped.chk\n\#B3LYP/gen 6D pseudo=read $grid OPT=(z-matrix) IOP(2/17=4) \n\n$inputfile_stripped.freq\n\n";
$footer ="@/$HOME/Basis/$genbasis.gbs/N\n\n";
$footer =${footer}."@/$HOME/Basis/lacvp.ecp/N\n\n";
}
else{
$header ="\%chk=$inputfile_stripped.chk\n\#B3LYP/gen 6D $grid OPT=(z-matrix) IOP(2/17=4) \n\n$inputfile_stripped.freq\n\n";
$footer ="@/$HOME/Basis/$genbasis.gbs/N\n";
}
}
elsif($job =~ /optb/i ){
if ($heavy){
$header ="\%chk=$inputfile_stripped.chk\n\#B3LYP/gen 6D pseudo=read $grid OPT Freq IOP(2/17=4) \n\n$inputfile_stripped.freq\n\n";
$footer ="@/$HOME/Basis/$genbasis.gbs/N\n\n";
$footer =${footer}."@/$HOME/Basis/lacvp.ecp/N\n\n";
}
else{
$header ="\%chk=$inputfile_stripped.chk\n\#B3LYP/gen 6D $grid OPT IOP(2/17=4) \n\n$inputfile_stripped.freq\n\n";
$footer ="@/$HOME/Basis/$genbasis.gbs/N\n";
}
}
elsif($job =~ /freq/i ){
if ($heavy){
$header ="\%chk=$inputfile_stripped.chk\n\#B3LYP/gen 6D pseudo=read $grid SCF=tight Freq=(noraman)\n\n$inputfile_stripped.freq\n\n";
$footer ="@/$HOME/Basis/$genbasis.gbs/N\n\n";
$footer =${footer}."@/$HOME/Basis/lacvp.ecp/N\n\n";
}
else{
$header ="\%chk=$inputfile_stripped.chk\n\#B3LYP/gen 6D $grid SCF=tight Freq=(noraman)\n\n$inputfile_stripped.freq\n\n";
$footer ="@/$HOME/Basis/$genbasis.gbs/N\n\n";
}
}
elsif($job =~ /mdbs/i ){
$jobtype = &promptUser(" Do you want to optimise the geometry?",N);
$nm ="mdbs";
if($jobtype =~ /[yY]/ ){
$opttype = &promptUser(" Is it a TS?",N);
if($opttype =~ /[yY]/ ){
$header ="\%chk=$inputfile_stripped.$nm.chk\n\# M062X/aug-cc-pVTZ SCF=Tight Int(Grid=Ultrafine) OPT=(TS,calcfc,noeigentest,maxcyc=200) IOP(2/17=4)\n\n$inputfile_stripped.$nm\n\n";
$footer ="\n--Link1--\n\%chk=$inputfile_stripped.$nm.chk\n\# M062X/aug-cc-pVTZ SCF=Tight Int(Grid=Ultrafine) Freq=Noraman geom=check guess=read IOP(2/17=4)\n\n$inputfile_stripped.$nm\n\n$cm\n\n";
}
else {