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Copy paths-transrot
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Copy paths-transrot
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executable file
·62 lines (46 loc) · 1.61 KB
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#!/usr/bin/perl
$file=$ARGV[0];
$key=$ARGV[1];
if ($#ARGV<1){die "command line syntax: xyz_file key_file\n";}
$k=1.3806503*10**-23;
$T=298;
$sig=1;
$h=(6.6260693*10**-34);#/(2*3.14159)???????;
$rho= 4.72973855516282e+26;
open file, "$file";
@file=<file>;
$M=0;
foreach(1..$#file){
$name=(split '', (split ' ',$file[$_])[1])[0];
if($name eq 'C'){$m=12.0107;}
elsif($name eq 'O'){$m=15.9994;}
elsif($name eq 'H'){$m=1.00794;}
elsif($name eq 'N'){$m=14.0067;}
elsif($name eq 'S'){$m=32.065;}
elsif($name eq 'M'){$m=24.3050;}
elsif($name eq 'Z'){$m=65.409;}
elsif($name eq 'P'){$m=30.973;}
else{die "error\n";}
$M+=$m;
}
$M=$M*.001/(6.0221415*10**23); #convert g/mol -> kg
$At=1.5*$k*$T-(2.5+1.5*log(2*3.14159*$M*$k*$T*$h**-2)-log($rho))*$k*$T;
$At=0.001*($At)*6.0221415*10**23; #corrected for J-->kJ/mol
print "A(trans) = $At kJ/mol\n";
$At=0.239005736*($At);
print "A(trans) = $At kcal/mol\n\n";
`analyze.x $file -k $key em >tmp`;
@I=`grep -A 4 'Moments (' tmp`;
$Ia=(split ' ', $I[2])[0];
$Ib=(split ' ', $I[3])[0];
$Ic=(split ' ', $I[4])[0];
$Ia=$Ia*.001/(6.0221415*10**23)*10**-20; #convert amu*ang^2 -> kg*m^2
$Ib=$Ib*.001/(6.0221415*10**23)*10**-20;
$Ic=$Ic*.001/(6.0221415*10**23)*10**-20;
#$III=4.731*10**16*(.001/(6.0221415*10**23)*10**-20)**3;
#$Ar=1.5*$k*$T-(1.5+0.5*log(3.14159*$III)+1.5*log(8*3.14159**2*$k*$T/$h**2) -log($sig))*$k*$T;
$Ar=1.5*$k*$T-(1.5+0.5*log(3.14159*$Ia*$Ib*$Ic)+1.5*log(8*3.14159**2*$k*$T/$h**2) -log($sig))*$k*$T;
$Ar=0.001*($Ar)*6.0221415*10**23; #corrected for J-->kJ/mol
print "A(rot) = $Ar kJ/mol\n";
$Ar=0.239005736*($Ar);
print "A(rot) = $Ar kcal/mol\n\n";