mirror of https://github.com/QMCPACK/qmcpack.git
Multiple perl scripts including setup-qmc.pl for automating common tasks when using pwscf as a starting point. Also performance improvements for energy.pl
git-svn-id: https://subversion.assembla.com/svn/qmcdev/trunk@5374 e5b18d87-469d-4833-9cc0-8cdfa06e9491
This commit is contained in:
Luke Shulenburger
parent
b48c6c2819
commit
89188b7850
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@ -1,15 +1,16 @@
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#!/usr/bin/perl -w
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#!/usr/bin/env perl
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use POSIX qw/floor/;
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use strict;
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use FileHandle;
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use Getopt::Long;
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# This tool uses energy.pl to plot the energy of a series of VMC optimizations.
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# Simply give it the filename of one of the .scalar.dat files and it will plot
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# the energy as a function of sequence. The locations of gnuplot and energy.pl
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# may need to be configured on the next lines
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my %config = do "/remote/lshulen/sharedmaintenance/qmcpack/utils/setup-qmc-conf.pl";
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my $gnuplot = "/usr/bin/gnuplot";
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my $energytool = "/bin/energy.pl";
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my $gnuplot = $config{gnuplot};
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my $energytool = $config{energytool};
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my $epsfile;
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GetOptions('eps=s' => \$epsfile);
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my $template = shift || die "Must give a template file name as the first argument here\n";
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my $start = shift;
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@ -20,6 +21,7 @@ if (!(defined $plotstart)) {
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}
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$template =~ /(.*\.s)(\d\d\d)(\.scalar\.dat)/;
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my $prefix = $1;
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my $tnum = $2;
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@ -49,22 +51,28 @@ foreach my $file (sort bySequence @rawfiles) {
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my $str = `$energytool $file $start | head -1`;
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my @data = split(/\s+/,$str);
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my $energy = "$data[2] $data[4]";
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print "$sequence $energy\n";
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push @energies, $energy;
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$str = `$energytool $file $start | tail -1`;
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@data = split(/\s+/,$str);
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my $correnergy = "$data[3] $data[5]";
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push @correnergies, $correnergy;
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# $str = `$energytool $file $start | tail -1`;
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# @data = split(/\s+/,$str);
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# my $correnergy = "$data[3] $data[5]";
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# push @correnergies, $correnergy;
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}
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my $plotstring = "set title \"Sequence vs Energy for VMC optimization\" \n";
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if ($epsfile) {
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$plotstring .= "set term post color enhanced 20\n set output \"$epsfile\"\n";
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}
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$plotstring .= "set xlabel \"sequence\"; set ylabel \"energy (Ha)\"\n";
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my $st = $plotstart-1.2;
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my $ed = $#sequences+0.2;
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my $xtics = "set xtics (";
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$plotstring .= "plot [$st:$ed] \"-\" u 1:2:3 notitle w e \n";
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for (my $i = 0; $i <= $#sequences; $i++) {
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$plotstring .= "$i $correnergies[$i]\n";
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# $plotstring .= "$i $correnergies[$i]\n";
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$plotstring .= "$i $energies[$i]\n";
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$xtics .= "\"$sequences[$i]\" $i";
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if ($i < $#sequences) {
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$xtics .= ", " ;
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@ -72,13 +80,17 @@ for (my $i = 0; $i <= $#sequences; $i++) {
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}
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$xtics .= ")\n";
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$plotstring .= "end \n";
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$plotstring .= "pause -1\n";
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unless ($epsfile) {
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$plotstring .= "pause -1\n";
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}
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$plotstring = "$xtics $plotstring";
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open(GPL, "|$gnuplot");
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GPL->autoflush(1);
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print GPL $plotstring;
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my $redundantString = <>; # Hack to leave graph up until user hits a key
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unless($epsfile) {
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my $redundantString = <>; # Hack to leave graph up until user hits a key
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}
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close(GPL);
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@ -113,9 +125,8 @@ sub getColumn {
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}
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#***************************************************************************
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#**************************************************************************
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# $RCSfile$ $Author: lshulenburger $
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# $Revision: 5115 $ $Date: 2011-2-7 8:15:23 -0700 (Mon, 7 Feb 2011) $
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# $Id: OptProgress.pl 5115 2011-2-7 8:15:23 lshulenburger $
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# $Revision: 5115 $ $Date: 2011-9-15 10:19:08 -0700 (Thu, 15 Sep 2011) $
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# $Id: OptProgress.pl 5115 2011-9-15 10:19:08 lshulenburger $
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#*************************************************************************/
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@ -1,15 +1,14 @@
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#!/usr/bin/perl -w
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#!/usr/bin/env perl
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use POSIX qw/floor/;
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use strict;
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use FileHandle;
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use Getopt::Long;
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# this is a drop in replacement for PlotDMC.py which can be useful when python
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# libraries are not available on a system. Simply give the script the name
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# of a .dmc.dat file to analyze and the step at which to start analysis and
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# it will plot the local energy, population and histograms of the same.
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# The location of gnuplot on the next line need to be updated
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my $gnuplot = "/usr/bin/gnuplot";
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my %config = do "/remote/lshulen/sharedmaintenance/qmcpack/utils/setup-qmc-conf.pl";
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my $gnuplot = $config{gnuplot};
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my $epsfile;
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GetOptions('eps=s' => \$epsfile);
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my $file = shift;
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my $start = shift;
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@ -38,14 +37,25 @@ my $popmax;
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($popmin, $popmax) = getMinMax(\@filedata, 5, $start, $end);
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my $popTicString = getTicString($popmin,$popmax);
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my $plotstring = "set title \"$file\"\n set multiplot\n";
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$plotstring .= "set ylabel \"Energy (Hartrees)\"\n ";
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my $plotstring = "set title \"$file\"\n";
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if ($epsfile) {
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$plotstring .= "set term post color enhanced 20\n set output \"$epsfile\"\n";
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}
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$plotstring .= "set multiplot\n set ylabel \"Energy (Hartrees)\"\n ";
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$plotstring .= "set origin 0,0.5\n set size 0.82,0.5\n";
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$plotstring .= "set format x \"\"\n set ytics $enTicString \n unset y2tics\n set lmargin 12\n";
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$plotstring .= "plot [$start:][$min:$max] \"$file\" u 1:2 w l notitle, \"\" u 1:6 lt 3 notitle w l \n";
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if ($end < 0) {
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$plotstring .= "plot [$start:][$min:$max] \"$file\" u 1:2 w l notitle, \"\" u 1:5 lt 3 notitle w l \n";
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} else {
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$plotstring .= "plot [$start:$end][$min:$max] \"$file\" u 1:2 w l notitle, \"\" u 1:5 lt 3 notitle w l \n";
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}
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$plotstring .= "set format x \n unset title\n set xlabel \"DMC step\"\n set ylabel \"Population (Walkers)\"\n";
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$plotstring .= "set xtics\n set ytics $popTicString\n set bmargin 4\n";
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$plotstring .= "set origin 0,0\n plot [$start:][$popmin:$popmax] \"\" u 1:5 w l notitle\n";
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if ($end < 0) {
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$plotstring .= "set origin 0,0\n plot [$start:][$popmin:$popmax] \"\" u 1:5 w l notitle\n";
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} else {
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$plotstring .= "set origin 0,0\n plot [$start:$end][$popmin:$popmax] \"\" u 1:5 w l notitle\n";
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}
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$plotstring .= "set format x \"\"\n";
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$plotstring .= "set origin 0.8,0.5\n set size 0.2, 0.5\n set title \"histogram\"\n";
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$plotstring .= "set lmargin 0\n unset xlabel\n unset ylabel \n set bmargin 1\n";
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@ -54,13 +64,17 @@ $plotstring .= getGPLHistString(\@filedata, 2, $start, $end);
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$plotstring .= "set origin 0.8,0.0\n set size 0.2, 0.5\n unset title \n set y2tics $popTicString \n";
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$plotstring .= "set format y2 \"\"\n set xlabel \"counts\"\n set bmargin 4\n";
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$plotstring .= getGPLHistString(\@filedata, 5, $start, $end);
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$plotstring .= "unset multiplot\n pause -1\n";
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$plotstring .= "unset multiplot\n";
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unless($epsfile) {
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$plotstring .= "pause -1\n";
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}
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open(GPL, "|$gnuplot");
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GPL->autoflush(1);
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print GPL $plotstring;
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my $blah = <>; # Hack to leave graph up until user hits a key
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unless($epsfile) {
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my $blah = <>; # Hack to leave graph up until user hits a key
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}
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close(GPL);
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@ -188,7 +202,8 @@ sub getColumn {
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return @outmat;
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}
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#**************************************************************************
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#***************************************************************************
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# $RCSfile$ $Author: lshulenburger $
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# $Revision: 5115 $ $Date: 2011-2-7 8:15:23 -0700 (Mon, 7 Feb 2011) $
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# $Id: PlotDMC.pl 5115 2011-2-7 8:15:23 lshulenburger $
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@ -1,4 +1,4 @@
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#!/usr/bin/perl -w
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#!/usr/bin/env perl
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use POSIX qw/floor/;
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use strict;
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use FileHandle;
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@ -8,7 +8,8 @@ use FileHandle;
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# to the script and it will plot all matching files it can find. Before using the
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# script, the location of gnuplot may need to be set on the previous line
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my $gnuplot = "/usr/bin/gnuplot";
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my %config = do "/remote/lshulen/sharedmaintenance/qmcpack/utils/setup-qmc-conf.pl";
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my $gnuplot = $config{gnuplot};
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my $template = shift || die "Must give a template file name as the first argument here\n";
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my $start = shift;
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@ -96,7 +97,8 @@ sub getColumn {
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#**************************************************************************
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# $RCSfile$ $Author: lshulenburger $
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# $Revision: 5115 $ $Date: 2011-2-7 8:15:23 -0700 (Mon, 7 Feb 2011) $
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# $Id: PlotTwists.pl 5115 2011-2-7 8:15:23 lshulenburger $
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# $Revision: 5115 $ $Date: 2011-9-15 10:19:08 -0700 (Thu, 15 Sep 2011) $
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# $Id: PlotTwists.pl 5115 2011-9-15 10:19:08 lshulenburger $
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#*************************************************************************/
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@ -1,4 +1,4 @@
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#!/usr/bin/perl -w
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#!/usr/bin/env perl
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use POSIX qw/floor/;
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use strict;
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@ -25,10 +25,10 @@ if (!(defined $end)) {
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#print "template = $template\n";
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#print "numfiles = $numfiles\n";
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$template =~ /(.*-tw)(\d+)\..*(\.s...\.scalar\.dat)/;
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$template =~ /(.*-tw)(\d+)(\..*)?(\.s...\.scalar\.dat)/;
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my $prefix = $1;
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my $tnum = $2;
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my $suffix = $3;
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my $suffix = $4;
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#print "prefix = $prefix, tnum = $tnum, suffix = $suffix\n";
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@ -40,19 +40,27 @@ closedir DIR;
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my @twistens;
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my @twisterrs;
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my @rawfiles;
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for (my $i = $tnum; $i < $tnum+$numfiles; $i++) {
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my @match = grep /$prefix$i\..+$suffix/, @files;
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if ($numfiles > 1) {
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my $curfile;
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if ($match[0]) {
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$curfile = shift @match;
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push @rawfiles, $curfile;
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push @twistens, 0.0;
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push @twisterrs, 0.0;
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} else {
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die "Cannot find enough raw data files to satsify this request\n";
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}
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for (my $i = $tnum; $i < $tnum+$numfiles; $i++) {
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my @match = grep /$prefix$i(\..*)?$suffix/, @files;
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my $curfile;
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if ($match[0]) {
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$curfile = shift @match;
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push @rawfiles, $curfile;
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push @twistens, 0.0;
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push @twisterrs, 0.0;
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} else {
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die "Cannot find enough raw data files to satsify this request\n";
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}
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# print "Looking for a file like $prefix" . $i . ".????$suffix: found $curfile\n";
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}
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} else {
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$tnum = 0;
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push @rawfiles, $template;
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push @twistens, 0.0;
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push @twisterrs, 0.0;
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}
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open (FILE, "$template") || die "Cannot open file $template\n";
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@ -292,7 +300,7 @@ sub formatString {
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#**************************************************************************
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# $RCSfile$ $Author: lshulenburger $
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# $Revision: 5115 $ $Date: 2011-2-7 8:15:23 -0700 (Mon, 7 Feb 2011) $
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# $Id: TwistAvg.pl 5115 2011-2-7 8:15:23 lshulenburger $
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# $Revision: 5115 $ $Date: 2011-9-15 10:19:08 -0700 (Thu, 15 Sep 2011) $
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# $Id: TwistAvg.pl 5115 2011-9-15 10:19:08 lshulenburger $
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#*************************************************************************/
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@ -1,4 +1,4 @@
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#!/usr/bin/perl -w
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#!/usr/bin/env perl
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use POSIX qw/floor/;
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use strict;
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@ -43,22 +43,20 @@ my $blockweight=0;
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for (my $i = 2; $i <= $#{$filedata[0]}; $i++) {
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my $colname = $filedata[0][$i];
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my @arr = getColumn(\@filedata,$i,$start,$end);
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for (my $j = 0; $j <= $#arr; $j++) {
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if ($colname eq 'AcceptRatio' || $colname eq 'BlockCPU' || $colname eq 'BlockWeight') {
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$arr[$j] *= 1;
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} else {
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$arr[$j] /= $factor;
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}
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}
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my $avg;
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my $error;
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($avg, $error) = stats(\@arr);
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if ($colname eq 'AcceptRatio' || $colname eq 'BlockCPU' || $colname eq 'BlockWeight' || $colname eq 'Efficiency') {
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($avg, $error) = simplestats(\@arr);
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} else {
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($avg, $error) = stats(\@arr, $factor);
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}
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if ($colname eq 'LocalEnergy_sq') {
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$colname = 'Variance';
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my @arr2 = getColumn(\@filedata, $i-1, $start, $end);
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my $avg2;
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my $err2;
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($avg2, $err2) = stats(\@arr2);
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($avg2, $err2) = stats(\@arr2, $factor);
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$avg = $avg - $avg2*$avg2/$factor;
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}
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if ($colname eq 'LocalEnergy') {
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@ -101,10 +99,24 @@ if (abs($correction) > 1.0e-12) {
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printf("%-21s = $formatStr +/- $formatStr\n", "Corrected Energy", $Locen+$correction, $enerr);
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}
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sub simplestats {
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my $arr = shift;
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my $avg;
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my $sqavg;
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($avg, $sqavg) = getAvgAndSqAv($arr);
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my $var = $sqavg-$avg*$avg;
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return ($avg, sqrt($var/$#{$arr}));
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}
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sub stats {
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my $arr = shift;
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my $avg = getAvg($arr);
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my $sqav = getSqAvg($arr);
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my $locfac = shift;
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my $avg;
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my $sqav;
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($avg, $sqav) = getAvgAndSqAv($arr);
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$avg /= $locfac;
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$sqav /= $locfac*$locfac;
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my $var = $sqav-$avg*$avg;
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my $c=0;
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my $N = $#{$arr}+1;
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@ -113,7 +125,7 @@ sub stats {
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while($tempC > 0 and $c < ($N-1)) {
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$kappa+=2*$tempC;
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$c += 1;
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$tempC=corr($c, $arr, $avg, $var);
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$tempC=corr($c, $arr, $avg*$locfac, $var*$locfac*$locfac);
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}
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if ($kappa == 0.0) {
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$kappa = 1.0;
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@ -168,21 +180,19 @@ sub getSum {
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return $outval;
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}
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sub getAvg {
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sub getAvgAndSqAv {
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my $arr = shift;
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my $size = $#{$arr};
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return getSum($arr)/($size+1);
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my $sum;
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my $sumsq;
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for (my $i = 0; $i <= $#{$arr}; $i++) {
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$sum += ${$arr}[$i];
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$sumsq += ${$arr}[$i]*${$arr}[$i];
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}
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return ($sum/($#{$arr}+1), $sumsq/($#{$arr}+1));
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}
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sub getSqAvg {
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my $arr = shift;
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my @newarr;
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for (my $i = 0; $i <= $#{$arr}; $i++) {
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my $val = ${$arr}[$i];
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push @newarr, $val*$val;
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}
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return getAvg(\@newarr);
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}
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sub corr {
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my $i = shift;
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@ -219,7 +229,6 @@ sub formatString {
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#**************************************************************************
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# $RCSfile$ $Author: lshulenburger $
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# $Revision: 5115 $ $Date: 2011-2-7 8:15:23 -0700 (Mon, 7 Feb 2011) $
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# $Id: energy.pl 5115 2011-2-7 8:15:23 lshulenburger $
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# $Revision: 5115 $ $Date: 2011-9-15 10:19:08 -0700 (Thu, 15 Sep 2011) $
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# $Id: energy.pl 5115 2011-9-15 10:19:08 lshulenburger $
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#*************************************************************************/
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