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Copy pathmdavg
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executable file
·268 lines (257 loc) · 6.38 KB
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#!/usr/bin/perl
# MDAVG is a Perl script to compute averages and block average
# standard deviations from a Tinker dynamics trajectory log file
#
# Original version written by Pengyu Ren, Ponder Lab, July 2000
# Modified to give std dev of block averages, Jay Ponder, Oct 2011
if ($#ARGV > 2 or $#ARGV < 0) {die "$0: logfile start(in frame) end\n";}
if ($#ARGV == 0) {$ARGV[1]=1;$ARGV[2]=1000000000;}
if ($#ARGV == 1) {$ARGV[2]=1000000000;}
#In perl, $ARG[0] is the first argument, $0 is the name of prog
$start=88+$ARGV[1]*14;
@tot=();
@totrms=();
@totrms2=();
@pot=();
@potrms=();
@potrms2=();
@kin=();
@kinrms=();
@kinrms2=();
@inter=();
@interms=();
@interms2=();
@ele=();
@elerms=();
@elerms2=();
@vdw=();
@vdwrms=();
@vdwrms2=();
@pol=();
@polrms=();
@polrms2=();
@temp=();
@temprms=();
@temprms2=();
@press=();
@pressrms=();
@pressrms2=();
@den=();
@denrms=();
@denrms2=();
$i=0;
$count=0;
open(LOG,"$ARGV[0]")||die "can't open log file\n";
while(<LOG>){
if (substr($_,1,12) eq "Total Energy") {
$i++;
$etot=substr($_,23,13);
$etotrms=substr($_,53,7);
if ($i>=$ARGV[1] && $i<=$ARGV[2]) {
$count++;
push(@tot, $etot);
push(@totrms, $etot);
push(@totrms2, $etotrms);
}
}
if (substr($_,1,9) eq "Potential") {
$epot=substr($_,23,13);
$epotrms=substr($_,53,7);
if ($i>=$ARGV[1] && $i<=$ARGV[2]) {
push(@pot, $epot);
push(@potrms, $epot);
push(@potrms2, $epotrms);
}
}
if (substr($_,1,7) eq "Kinetic") {
$ekin=substr($_,23,13);
$ekinrms=substr($_,53,7);
if ($i>=$ARGV[1] && $i<=$ARGV[2]) {
push(@kin, $ekin);
push(@kinrms, $ekin);
push(@kinrms2, $ekinrms);
}
}
if (substr($_,1,14) eq "Intermolecular") {
$ei=substr($_,23,13);
$eirms=substr($_,53,7);
if ($i>=$ARGV[1] && $i<=$ARGV[2]) {
push(@inter, $ei);
push(@interms, $ei);
push(@interms2, $eirms);
}
}
if (substr($_,1,13) eq "Electrostatic") {
$ee=substr($_,23,13);
$eerms=substr($_,53,7);
if ($i>=$ARGV[1] && $i<=$ARGV[2]) {
push(@ele, $ee);
push(@elerms, $ee);
push(@elerms2, $eerms);
}
}
if (substr($_,1,13) eq "van der Waals") {
$ev=substr($_,23,13);
$evrms=substr($_,53,7);
if ($i>=$ARGV[1] && $i<=$ARGV[2]) {
push(@vdw, $ev);
push(@vdwrms, $ev);
push(@vdwrms2, $evrms);
}
}
if (substr($_,1,12) eq "Polarization") {
$ep=substr($_,23,13);
$eprms=substr($_,53,7);
if ($i>=$ARGV[1] && $i<=$ARGV[2]) {
push(@pol, $ep);
push(@polrms, $ep);
push(@polrms2, $eprms);
}
}
if (substr($_,1,11) eq "Temperature") {
$tm=substr($_,23,13);
$tmrms=substr($_,53,7);
if ($i>=$ARGV[1] && $i<=$ARGV[2]) {
push(@temp, $tm);
push(@temprms, $tm);
push(@temprms2, $tmrms);
}
}
if (substr($_,1,8) eq "Pressure") {
$pre=substr($_,23,13);
$prerms=substr($_,53,7);
if ($i>=$ARGV[1] && $i<=$ARGV[2]) {
push(@press, $pre);
push(@pressrms, $pre);
push(@pressrms2, $prerms);
}
}
if (substr($_,1,7) eq "Density") {
$d=substr($_,23,13);
$drms=substr($_,53,7);
if ($i>=$ARGV[1] && $i<=$ARGV[2]) {
push(@den, $d);
push(@denrms, $d);
push(@denrms2, $drms);
}
}
}
if ($#tot != -1) {
$avgtot=&AVG(@tot);
$stdtot=&STD(@totrms);
$stdtot2=&STD2(@totrms2);
}
if ($#pot != -1) {
$avgpot=&AVG(@pot);
$stdpot=&STD(@potrms);
$stdpot2=&STD2(@potrms2);
}
if ($#kin != -1) {
$avgkin=&AVG(@kin);
$stdkin=&STD(@kinrms);
$stdkin2=&STD2(@kinrms2);
}
if ($#inter != -1) {
$avgi=&AVG(@inter);
$stdi=&STD(@interms);
$stdi2=&STD2(@interms2);
}
if ($#ele != -1) {
$avge=&AVG(@ele);
$stde=&STD(@elerms);
$stde2=&STD2(@elerms2);
}
if ($#vdw != -1) {
$avgv=&AVG(@vdw);
$stdv=&STD(@vdwrms);
$stdv2=&STD2(@vdwrms2);
}
if ($#pol != -1) {
$avgp=&AVG(@pol);
$stdp=&STD(@polrms);
$stdp2=&STD2(@polrms2);
}
if ($#temp != -1) {
$avgt=&AVG(@temp);
$stdt=&STD(@temprms);
$stdt2=&STD2(@temprms2);
}
if ($#press != -1) {
$avgpr=&AVG(@press);
$stdpr=&STD(@pressrms);
$stdpr2=&STD2(@pressrms2);
}
if ($#den != -1) {
$avgd=&AVG(@den);
$stdd=&STD(@denrms);
$stdd2=&STD2(@denrms2);
}
sub AVG{
$sum=0.0;
$cnt=0;
foreach $ii (@_) {
$sum=$ii+$sum;
$cnt=$cnt+1;
}
$avg=$sum/$cnt;
}
sub STD{
$sum2=0.0;
$sum1=0.0;
$cnt=0;
foreach $ii (@_) {
$sum1=$ii+$sum1;
$cnt=$cnt+1;
}
$avg=$sum/$cnt;
foreach $ii (@_) {
$sum2=($avg-$ii)*($avg-$ii)+$sum2;
}
$std=sqrt($sum2/($cnt-1));
}
sub STD2{
$sum2=0.0;
$sum1=0.0;
$cnt=0;
for($i=0;$i<$#_;$i=$i+2){
$cnt=$cnt+100;
$sum1=$_[$i]*100.0+$sum1;
$sum2=$sum2+($_[$i+1]**2+$_[$i]**2)*100.0;
$std2=$sum2/$cnt-($sum1/$cnt)**2;
}
if ($std2 > -0.0001 && $std2 < 0) { $std2=0.0; }
$std2=sqrt($std2);
}
if ($count > -1) {
printf " Total MD Blocks %15d Blocks\n", "$count";
}
if ($#tot > -1) {
printf " Total Energy %15.4f Kcal/mole (+/-%9.4f)\n", "$avgtot","$stdtot";
}
if ($#pot > -1) {
printf " Potential Energy %15.4f Kcal/mole (+/-%9.4f)\n", "$avgpot","$stdpot";
}
if ($#kin > -1) {
printf " Kinetic Energy %15.4f Kcal/mole (+/-%9.4f)\n", "$avgkin","$stdkin";
}
if ($#inter > -1) {
printf " Intermolecular %15.4f Kcal/mole (+/-%9.4f)\n", "$avgi","$stdi";
}
if ($#ele > -1) {
printf " Electrostatic %15.4f Kcal/mole (+/-%9.4f)\n", "$avge","$stde";
}
if ($#vdw > -1) {
printf " van der Waals %15.4f Kcal/mole (+/-%9.4f)\n", "$avgv","$stdv";
}
if ($#pol > -1) {
printf " Polarization %15.4f Kcal/mole (+/-%9.4f)\n", "$avgp","$stdp";
}
if ($#temp > -1) {
printf " Temperature %15.2f Kelvin (+/-%9.2f)\n", "$avgt","$stdt";
}
if ($#press > -1) {
printf " Pressure %15.2f Atomsphere (+/-%9.2f)\n", "$avgpr","$stdpr";
}
if ($#den > -1) {
printf " Density %15.4f Grams/cc (+/-%9.4f)\n", "$avgd","$stdd";
}