416 lines
11 KiB
Plaintext
416 lines
11 KiB
Plaintext
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#!/usr/bin/perl -w
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use strict;
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#use List::MoreUtils qw / pairwise/;
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use File::Temp qw/ tempfile tempdir /;
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use File::Copy;
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use Getopt::Long;
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my $conf = {"cleanup" => 0, "oute"=> "energy", "name" => "XYZ"};
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my $RUN_PREFIX = ""; #"mpirun --host node10,node11 -np 8";
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my $siesta = "siesta";
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my $PSEUDODIR = "/home/gkolesov/run/Pseudo/GGA";
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$PSEUDODIR = $ENV{PSEUDODIR} if $ENV{PSEUDODIR};
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$PSEUDODIR = $ENV{SIESTA_PSEUDO} if $ENV{SIESTA_PSEUDO};
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my @argv_orig = @ARGV;
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GetOptions(
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"c|cleanup!" => \$conf->{cleanup},
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"v|verbose!" => \$conf->{verbose},
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"n|dry!" => \$conf->{dry},
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"o|oute=s" => \$conf->{oute},
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"x|name=s" => \$conf->{name},
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"e|cmd=s" => \$siesta,
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"p|ppdir=s" => \$PSEUDODIR,
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"r|runprefix=s" => \$RUN_PREFIX,
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"h|help!" => \&print_usage_and_die,
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);
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if(@ARGV>0){
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my $remotecmd = pop @argv_orig;
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print STDERR "ARGV: @ARGV\n";
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$remotecmd = "@ARGV" if @ARGV>1;
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#$remotecmd = "node" unless defined $remotecmd;
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exit( mysystem("$remotecmd runstruct_siesta @argv_orig") );
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}
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my $anumber = atom_number_table();
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my ($lvec,$atoms) = parse_strout("str.out");
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my $ddd =1;
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# make_fdf("/tmp/y", $lvec, $atoms);
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my $E=run_siesta($lvec,$atoms);
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if($E==99999.){
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open(my $fw, '>', 'error') || die "Can not open file for writing: $!";
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close $fw;
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}
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print "E = $E\n" if $conf->{verbose};
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unless($conf->{dry}){
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open(my $fw, '>', $conf->{oute}) || die "Can not open file: $!";
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print $fw $E;
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close $fw;
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}
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sub make_fdf{
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my ($fname,$lvec,$atoms) = @_;
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my %h=();
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my $k = 1;
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foreach my $a (@$atoms){
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$h{$a->{type}} = $k++ unless defined $h{$a->{type}};
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}
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my $acnt = scalar keys %h;
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open(my $fw, '>', $fname) || die "Can not open file for writing: $!";
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print $fw siesta_head();
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print $fw "SystemLabel $conf->{name}\n";
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print $fw "LatticeConstant 1.0 Ang\n";
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print $fw "Number_of_species $acnt\n";
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print $fw "NumberOfAtoms ",scalar @$atoms,"\n\n";
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print $fw "%block Chemical_Species_label\n";
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foreach my $t (sort {$h{$a} <=> $h{$b}} keys %h){
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printf $fw " %-2d %-3d %s\n", $h{$t}, $anumber->{$t}, $t;
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}
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print $fw "%endblock Chemical_Species_label\n\n";
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print $fw "%block LatticeVectors\n";
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foreach my $v (@$lvec){
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printf $fw " % -3.8f % -3.8f % -3.8f\n", @$v;
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}
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print $fw "%endblock LatticeVectors\n\n";
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print $fw "%block AtomicCoordinatesAndAtomicSpecies\n";
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foreach my $a (@$atoms){
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printf $fw " % -3.8f % -3.8f % -3.8f %d\n", @{$a->{coord}},
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$h{$a->{type}};
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}
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print $fw "%endblock AtomicCoordinatesAndAtomicSpecies\n";
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close $fw;
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}
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sub get_energy{
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my ($siestaout) = @_;
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open(my $fh, $siestaout) || die "Can not open file: $!";
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my $readtot = 0;
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my $energy = 99999.;
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while(<$fh>){
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if($readtot){
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if(/^siesta.*?Total\s*=\s*(\S+)/i){
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$energy = $1;
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last;
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}
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next;
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}
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$readtot=1 if /^siesta:\s*Final\s+energy/;
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}
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close $fh;
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return $energy;
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}
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sub run_siesta{
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my ($lvec,$atoms) = @_;
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my $tdir = "siesta.$conf->{name}"; #tempdir(DIR => "./", CLEANUP => $conf->{cleanup});
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mkdir $tdir || die "Can not mkdir $tdir : $!";
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chdir $tdir || die "Can not chdir into dir : $!";
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my $fname = "$conf->{name}.fdf";
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my $siestaout = "siesta.out";
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make_fdf($fname, $lvec, $atoms);
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my %atype = map {$_->{type} => 1} @$atoms;
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foreach my $a (keys %atype){
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if(-e "$PSEUDODIR/$a.psf"){
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copy("$PSEUDODIR/$a.psf", "$a.psf");
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}
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else{
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die "No pseudopotential for element $a is found.\n";
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}
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}
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my $cmd = "$RUN_PREFIX $siesta < $fname > $siestaout";
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mysystem($cmd);
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my $E = get_energy($siestaout);
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chdir "../" || die "Can not chdir ../ : $!";
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if($conf->{cleanup}){
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system("/bin/rm -rf $tdir");
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}
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return $E;
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}
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sub mysystem{
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if($conf->{dry} || $conf->{verbose}){
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print STDOUT "@_\n";
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return system("/bin/true",3) if $conf->{dry} && $conf->{verbose};
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return 0 if $conf->{dry};
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}
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return system(@_);
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}
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sub parse_strout{
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my ($file) = @_;
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open(my $fh, $file) || die "Can not open file: $!";
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my @cvec = map {$_=<$fh>; [split] } (0..2);
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my @lvec = map {$_=<$fh>; [split] } (0..2);
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my @clvec = map {cvec2cart($_,\@cvec)} @lvec;
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my @atoms = ();
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while(<$fh>){
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my @t = split /[\s,]+/;
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my $a = pop @t;
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my $v = cvec2cart(\@t,\@cvec);
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push @atoms, {type => $a, coord => $v};
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}
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close $fh;
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return (\@clvec,\@atoms);
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}
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sub cvec2cart{
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my ($v,$cvec) = @_;
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local $^W = 0;
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#my @t=pairwise { [map {$a *$_} @$b] } @$v,@$cvec;
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my @t = ();
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for(my $i=0; $i<@$v; $i++){
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my $a = $v->[$i];
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my $b = $cvec->[$i];
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push @t, [map {$a * $_} @$b];
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}
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my @l = ();
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for(my $i=0; $i<3; $i++){
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do { $l[$i]+=$_->[$i] } foreach @t;
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}
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return \@l;
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}
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sub atom_number_table{
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my %t = (
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"H" => 1 ,
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"He" => 2 ,
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"Li" => 3 ,
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"Be" => 4 ,
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"B" => 5 ,
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"C" => 6 ,
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"N" => 7 ,
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"O" => 8 ,
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"F" => 9 ,
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"Ne" => 10 ,
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"Na" => 11 ,
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"Mg" => 12 ,
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"Al" => 13 ,
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"Si" => 14 ,
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"P" => 15 ,
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"S" => 16 ,
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"Cl" => 17 ,
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"Ar" => 18 ,
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"K" => 19 ,
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"Ca" => 20 ,
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"Sc" => 21 ,
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"Ti" => 22 ,
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"V" => 23 ,
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"Cr" => 24 ,
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"Mn" => 25 ,
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"Fe" => 26 ,
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"Co" => 27 ,
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"Ni" => 28 ,
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"Cu" => 29 ,
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"Zn" => 30 ,
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"Ga" => 31 ,
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"Ge" => 32 ,
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"As" => 33 ,
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"Se" => 34 ,
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"Br" => 35 ,
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"Kr" => 36 ,
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"Rb" => 37 ,
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"Sr" => 38 ,
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"Y" => 39 ,
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"Zr" => 40 ,
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"Nb" => 41 ,
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"Mo" => 42 ,
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"Tc" => 43 ,
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"Ru" => 44 ,
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"Rh" => 45 ,
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"Pd" => 46 ,
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"Ag" => 47 ,
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"Cd" => 48 ,
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"In" => 49 ,
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"Sn" => 50 ,
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"Sb" => 51 ,
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"Te" => 52 ,
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"I" => 53 ,
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"Xe" => 54 ,
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"Cs" => 55 ,
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"Ba" => 56 ,
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"La" => 57 ,
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"Ce" => 58 ,
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"Pr" => 59 ,
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"Nd" => 60 ,
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"Pm" => 61 ,
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"Sm" => 62 ,
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"Eu" => 63 ,
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"Gd" => 64 ,
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"Tb" => 65 ,
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"Dy" => 66 ,
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"Ho" => 67 ,
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"Er" => 68 ,
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"Tm" => 69 ,
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"Yb" => 70 ,
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"Lu" => 71 ,
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"Hf" => 72 ,
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"Ta" => 73 ,
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"W" => 74 ,
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"Re" => 75 ,
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"Os" => 76 ,
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"Ir" => 77 ,
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"Pt" => 78 ,
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"Au" => 79 ,
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"Hg" => 80 ,
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"Tl" => 81 ,
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"Pb" => 82 ,
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"Bi" => 83 ,
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"Po" => 84 ,
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"At" => 85 ,
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"Rn" => 86 ,
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"Fr" => 87 ,
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"Ra" => 88 ,
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"Ac" => 89 ,
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"Th" => 90 ,
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"Pa" => 91 ,
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"U" => 92 ,
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"Np" => 93 ,
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"Pu" => 94 ,
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"Am" => 95 ,
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"Cm" => 96 ,
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"Bk" => 97 ,
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"Cf" => 98 ,
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"Es" => 99 ,
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"Fm" => 100,
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"Md" => 101,
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"No" => 102,
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"Lr" => 103,
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"Rf" => 104,
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"Db" => 105,
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"Sg" => 106,
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"Bh" => 107,
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"Hs" => 108,
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"Mt" => 109,
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"Ds" => 110,
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"Rg" => 111,
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"Cn" => 112,
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"Uut" => 113,
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"Fl" => 114,
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"Uup" => 115,
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"Lv" => 116,
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"Uus" => 117,
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"Uuo" => 118
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);
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return \%t;
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}
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sub siesta_head{
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foreach my $head ("siesta.wrap", "../siesta.wrap","../../siesta.wrap"){
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if(-f $head){
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open(my $fh, $head) || die "Can not open $head: $!";
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local $/ = undef;
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my $t = <$fh>;
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close $fh;
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return $t;
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}
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}
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return <<SHEAD;
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DM.MixingWeight 0.01
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DM.Tolerance 0.001
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DM.NumberPulay 5
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# DM.Require.Energy.Convergence .true.
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# DM.Energy.Tolerance 0.01
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PAO.BasisSize dz
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SolutionMethod diagon
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AtomicCoordinatesFormat Ang
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MaxSCFIterations 1000
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SpinPolarized False
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MeshCutoff 4081.709348 eV
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LatticeConstant 1.0 Ang
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%block kgrid_Monkhorst_Pack
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5 0 0 0.5
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0 5 0 0.5
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0 0 5 0.5
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%endblock kgrid_Monkhorst_Pack
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MD.TypeOfRun CG # Type of dynamics:
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MD.VariableCell .false.
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#MD.NumCGsteps 50
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#MD.NumCGsteps 1
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WriteKbands .false.
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WriteBands .false.
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UseSaveData True
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DM.UseSaveDM True
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SHEAD
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}
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sub print_usage_and_die{
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print STDERR <<USAGE;
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$0 [OPTION] [remotecmd host]
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-v, --verbose
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-n, --dry Dry mode. Doesn't actually do anything, just
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|
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says what it would do
|
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|
|
-c, --cleanup Remove siesta working directory (default=false)
|
||
|
|
-o, --oute File to write energy value into (default=energy)
|
||
|
|
-x, --name Siesta system name label and file prefix (default=XYZ)
|
||
|
|
-e, --cmd Siesta executable name (default=siesta)
|
||
|
|
-p, --ppdir Pseudopotential directory; can be set also with
|
||
|
|
environment variables PSEUDODIR or SIESTA_PSEUDO
|
||
|
|
-r, --runprefix siesta run prefix, e.g. "mpirun -np 4"
|
||
|
|
-h, --help print this message
|
||
|
|
|
||
|
|
AUTHOR:
|
||
|
|
Grigori Kolesov gkolesov@uwyo.edu
|
||
|
|
|
||
|
|
EXAMPLE:
|
||
|
|
pollmach runstruct_siesta -e siesta.static -p ~/run/Pseudo/GGA
|
||
|
|
|
||
|
|
If siesta.wrap file exists in the current directory or in ../ , or in
|
||
|
|
../../ the script will use it as a siesta input fdf file (and will add the
|
||
|
|
geometry and atomic specie setup), otherwise the default at the bottom of
|
||
|
|
this script will be used.
|
||
|
|
|
||
|
|
Note that the siesta.wrap file should not contain LatticeConstant and
|
||
|
|
SystemLabel fields which are also setup by the script.
|
||
|
|
|
||
|
|
If the ~/.machines.rc file is set up and contains something like
|
||
|
|
ssh node1 sar -u 1 1 | getvalue "Average: all" + node -s node1
|
||
|
|
the script should be able to run siesta via "node" script / ssh.
|
||
|
|
|
||
|
|
USAGE
|
||
|
|
exit(0);
|
||
|
|
}
|