| 1 |
#!/usr/bin/env perl |
| 2 |
|
| 3 |
# program that builds water boxes |
| 4 |
|
| 5 |
# author = "Chris Fennell |
| 6 |
# version = "$Revision: 1.5 $" |
| 7 |
# date = "$Date: 2008-01-23 21:22:18 $" |
| 8 |
# copyright = "Copyright (c) 2006 by the University of Notre Dame" |
| 9 |
# license = "OOPSE" |
| 10 |
|
| 11 |
use Getopt::Std; |
| 12 |
|
| 13 |
$tolerance = 1.0E-8; |
| 14 |
$mass = 2.99151E-23; # mass of H2O in grams |
| 15 |
$cm3ToAng3 = 1E24; # convert cm^3 to angstroms^3 |
| 16 |
$densityConvert = $mass*$cm3ToAng3; |
| 17 |
$lattice = 0; |
| 18 |
$nMol = 500; |
| 19 |
$density = 1.0; |
| 20 |
$doRandomize = 0; |
| 21 |
$cutoff = 12; |
| 22 |
$alpha = 0.2125; |
| 23 |
$alphaInt = 0.5125; |
| 24 |
$alphaSlope = 0.025; |
| 25 |
$invalidWater = 0; |
| 26 |
$waterCase = -1; |
| 27 |
$nothingSelected = 1; |
| 28 |
|
| 29 |
# get our options |
| 30 |
getopts('hmrvd:l:n:o:w:x:y:z:'); |
| 31 |
|
| 32 |
# just to test opt_h |
| 33 |
$opt_h = "true" if $#ARGV >= 0; |
| 34 |
|
| 35 |
# our option output |
| 36 |
if ($opt_h){ |
| 37 |
print "waterBoxer: builds water boxes\n\n"; |
| 38 |
print "usage: waterBoxer [-hmrv] [-d density] [-l lattice] [-n # waters]\n"; |
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print "\t[-o file name] [-w water name] \n\n"; |
| 40 |
print " -h : show this message\n"; |
| 41 |
print " -m : print out a water.md file (file with all water models)\n"; |
| 42 |
print " -r : randomize orientations\n"; |
| 43 |
print " -v : verbose output\n\n"; |
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print " -d real : density in g/cm^3\n"; |
| 45 |
print " (default: 1)\n"; |
| 46 |
print " -l integer : 0 - face centered cubic, 1 - simple cubic\n"; |
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print " (default: 0)\n"; |
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print " -n integer : # of water molecules\n"; |
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print " (default: 500)\n"; |
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print " -o char : output file name\n"; |
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print " (default: freshWater.md)\n"; |
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print " -w char : name of the water stunt double\n"; |
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print " (default: SPCE)\n"; |
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print " -x real : dimension of the box along the x direction\n"; |
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print " -y real : dimension of the box along the y direction\n"; |
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print " -z real : dimension of the box along the z direction\n\n"; |
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print "Note: you can only use values of x, y, or z that are smaller\n"; |
| 58 |
print " than the derived box length for a given density and\n"; |
| 59 |
print " number of molecules.\n\n"; |
| 60 |
print "Example:\n"; |
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die " waterBoxer -d 0.997 -n 864 -w SSD_RF -o ssdrfWater.md\n"; |
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} |
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|
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# set some variables to be used in the code |
| 65 |
if (defined($opt_o)){ |
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$fileName = $opt_o; |
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$nothingSelected = 0; |
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} else { |
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$fileName = 'freshWater.md'; |
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} |
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if ($opt_m){ |
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die "Error: $fileName cannot be \"water.md\"\n Please choose a different name\n" if $fileName eq 'water.md'; |
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$waterFileHandle = 'WATERMD'; |
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$nothingSelected = 0; |
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} else { |
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$waterFileHandle = 'OUTFILE'; |
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} |
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if ($opt_r){ |
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$doRandomize = $opt_r; |
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$nothingSelected = 0; |
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} |
| 82 |
|
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if (defined($opt_d)){ |
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$nothingSelected = 0; |
| 85 |
if ($opt_d =~ /^[0-9]/) { |
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$density = $opt_d; |
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} else { |
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die "Error: the value for '-d' ($opt_d) is not a valid number\n Please choose a positive real # value\n"; |
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} |
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} |
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if (defined($opt_w)){ |
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$waterName = $opt_w; |
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$nothingSelected = 0; |
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} else { |
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$waterName = 'SPCE'; |
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} |
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validateWater(); |
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if ($invalidWater == 1){ |
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print "Warning: \'$waterName\' is not a recognized water model name.\n"; |
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print " Use the \'-m\' option to generate a \'water.md\' with the\n"; |
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print " recognized water model geometries.\n\n"; |
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} |
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if ($waterName eq 'DPD') { |
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# DPD waters are stand-ins for 4 water molecules |
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$density = $density * 0.25; |
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} |
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if ($waterName eq 'CG2') { |
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# CG2 waters are stand-ins for 2 water molecules |
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$density = $density * 0.5; |
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} |
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|
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if (defined($opt_l)){ |
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$nothingSelected = 0; |
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if ($opt_l =~ /^[0-9]/) { |
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$lattice = $opt_l; |
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if ($lattice != 0 && $lattice != 1){ |
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die "Error: the '-l' value ($opt_l) is not a valid number\n Please choose 0 or 1\n"; |
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} |
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} else { |
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die "Error: the '-l' value ($opt_l) is not a valid number\n Please choose 0 or 1\n"; |
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} |
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} |
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if (defined($opt_n)){ |
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$nothingSelected = 0; |
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if ($opt_n =~ /^[0-9]/) { |
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$nMol = $opt_n; |
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} else { |
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die "Error: the '-n' value ($opt_n) is not a valid number\n Please choose a non-negative integer\n"; |
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} |
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} |
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if (defined($opt_x)){ |
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$nothingSelected = 0; |
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if ($opt_x =~ /^[0-9]/) { |
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$boxx = $opt_x; |
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} else { |
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die "Error: the value for '-x' ($opt_x) is not a valid number\n Please choose a positive real # value\n"; |
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} |
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} |
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if (defined($opt_y)){ |
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$nothingSelected = 0; |
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if ($opt_y =~ /^[0-9]/) { |
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$boxy = $opt_y; |
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} else { |
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die "Error: the value for '-y' ($opt_y) is not a valid number\n Please choose a positive real # value\n"; |
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} |
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} |
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if (defined($opt_z)){ |
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$nothingSelected = 0; |
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if ($opt_z =~ /^[0-9]/) { |
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$boxz = $opt_z; |
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} else { |
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die "Error: the value for '-z' ($opt_z) is not a valid number\n Please choose a positive real # value\n"; |
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} |
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} |
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|
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|
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# open the file writer |
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open(OUTFILE, ">./$fileName") || die "Error: can't open file $fileName\n"; |
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|
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# check to set magic lattice numbers |
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if ($lattice == 0){ |
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$crystalNumReal = ($nMol/4.0)**(1.0/3.0); |
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$crystalNum = int($crystalNumReal + $tolerance); |
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$remainder = $crystalNumReal - $crystalNum; |
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|
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# if crystalNumReal wasn't an integer, we bump the crystal to the next |
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# magic number |
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if ($remainder > $tolerance){ |
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$crystalNum = $crystalNum + 1; |
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$newMol = 4 * $crystalNum**3; |
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print "Warning: The number chosen ($nMol) failed to build a clean fcc lattice.\n"; |
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print " The number of molecules has been increased to the next magic number ($newMol).\n\n"; |
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$nMol = $newMol; |
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} |
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} elsif ($lattice == 1){ |
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$crystalNumReal = ($nMol/1.0)**(1.0/3.0); |
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$crystalNum = int($crystalNumReal + $tolerance); |
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$remainder = $crystalNumReal - $crystalNum; |
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|
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# again, if crystalNumReal wasn't an integer, we bump the crystal to the next |
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# magic number |
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if ($remainder > $tolerance){ |
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$crystalNum = $crystalNum + 1; |
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$newMol = $crystalNum**3; |
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print "Warning: The number chosen ($nMol) failed to build a clean simple cubic lattice.\n"; |
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print " The number of molecules has been increased to the next magic number ($newMol).\n\n"; |
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$nMol = $newMol; |
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} |
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} |
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|
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# now we can start building the crystals |
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$boxLength = ($nMol*$densityConvert/$density)**(1.0/3.0); |
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$cellLength = $boxLength / $crystalNum; |
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|
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if ($boxx != 0) { |
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if ($boxLength < $boxx) { |
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print "Computed box length is smaller than requested x axis. Use more\n"; |
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die "molecules."; |
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} |
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} else { |
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$boxx = $boxLength; |
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} |
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if ($boxy != 0) { |
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if ($boxLength < $boxy) { |
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print "Computed box length is smaller than requested y axis. Use more\n"; |
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die "molecules."; |
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} |
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} else { |
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$boxy = $boxLength; |
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} |
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if ($boxz != 0) { |
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if ($boxLength < $boxz) { |
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print "Computed box length is smaller than requested z axis. Use more\n"; |
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die "molecules."; |
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} |
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} else { |
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$boxz = $boxLength; |
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} |
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|
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$nx = int($boxx / $cellLength); |
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$ny = int($boxy / $cellLength); |
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$nz = int($boxz / $cellLength); |
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|
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if ($lattice == 0) { |
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$nMol = 4 * $nx * $ny * $nz; |
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} else { |
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$nMol = $nx * $ny * $nz; |
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} |
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|
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$newDensity = $nMol * $densityConvert / ($boxx*$boxy*$boxz); |
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|
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if (abs($newDensity-$density) > $tolerance) { |
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print "Resetting density to $newDensity to make chosen box sides work out\n"; |
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} |
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$cellLengthX = $boxx/$nx; |
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$cellLengthY = $boxy/$ny; |
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$cellLengthZ = $boxz/$nz; |
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|
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$cell2X = $cellLengthX*0.5; |
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$cell2Y = $cellLengthY*0.5; |
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$cell2Z = $cellLengthZ*0.5; |
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|
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if ($lattice == 0) { |
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# build the unit cell |
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# molecule 0 |
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$xCorr[0] = 0.0; |
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$yCorr[0] = 0.0; |
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$zCorr[0] = 0.0; |
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# molecule 1 |
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$xCorr[1] = 0.0; |
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$yCorr[1] = $cell2Y; |
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$zCorr[1] = $cell2Z; |
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# molecule 2 |
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$xCorr[2] = $cell2X; |
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$yCorr[2] = $cell2Y; |
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$zCorr[2] = 0.0; |
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# molecule 3 |
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$xCorr[3] = $cell2X; |
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$yCorr[3] = 0.0; |
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$zCorr[3] = $cell2Z; |
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# assemble the lattice |
| 262 |
$counter = 0; |
| 263 |
for ($z = 0; $z < $nz; $z++) { |
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for ($y = 0; $y < $ny; $y++) { |
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for ($x = 0; $x < $nx; $x++) { |
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for ($uc = 0; $uc < 4; $uc++) { |
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$xCorr[$uc+$counter] = $xCorr[$uc] + $cellLengthX*$x; |
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$yCorr[$uc+$counter] = $yCorr[$uc] + $cellLengthY*$y; |
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$zCorr[$uc+$counter] = $zCorr[$uc] + $cellLengthZ*$z; |
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} |
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$counter = $counter + 4; |
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} |
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} |
| 274 |
} |
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|
| 276 |
} elsif ($lattice == 1) { |
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# build the unit cell |
| 278 |
# molecule 0 |
| 279 |
$xCorr[0] = $cell2X; |
| 280 |
$yCorr[0] = $cell2Y; |
| 281 |
$zCorr[0] = $cell2Z; |
| 282 |
#assemble the lattice |
| 283 |
$counter = 0; |
| 284 |
for ($z = 0; $z < $nz; $z++) { |
| 285 |
for ($y = 0; $y < $ny; $y++) { |
| 286 |
for ($x = 0; $x < $nx; $x++) { |
| 287 |
$xCorr[$counter] = $xCorr[0] + $cellLengthX*$x; |
| 288 |
$yCorr[$counter] = $yCorr[0] + $cellLengthY*$y; |
| 289 |
$zCorr[$counter] = $zCorr[0] + $cellLengthZ*$z; |
| 290 |
|
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$counter++; |
| 292 |
} |
| 293 |
} |
| 294 |
} |
| 295 |
} |
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|
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writeOutFile(); |
| 298 |
print "The water box \"$fileName\" was generated.\n"; |
| 299 |
|
| 300 |
if ($opt_m){ |
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printWaterMD(); |
| 302 |
print "The file \"water.md\" was generated for inclusion in \"$fileName\"\n"; |
| 303 |
} |
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|
| 305 |
if ($nothingSelected == 1) { |
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print "(For help, use the \'-h\' option.)\n"; |
| 307 |
} |
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|
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|
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# this marks the end of the main program, below is subroutines |
| 311 |
|
| 312 |
sub acos { |
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my ($rad) = @_; |
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my $ret = atan2(sqrt(1 - $rad*$rad), $rad); |
| 315 |
return $ret; |
| 316 |
} |
| 317 |
|
| 318 |
sub writeOutFile { |
| 319 |
# write out the header |
| 320 |
print OUTFILE "<OOPSE version=4>\n"; |
| 321 |
findCutoff(); |
| 322 |
findAlpha(); |
| 323 |
printMetaData(); |
| 324 |
printFrameData(); |
| 325 |
print OUTFILE " <StuntDoubles>\n"; |
| 326 |
|
| 327 |
# shift the box center to the origin and write out the coordinates |
| 328 |
for ($i = 0; $i < $nMol; $i++) { |
| 329 |
$xCorr[$i] -= 0.5*$boxx; |
| 330 |
$yCorr[$i] -= 0.5*$boxy; |
| 331 |
$zCorr[$i] -= 0.5*$boxz; |
| 332 |
|
| 333 |
$q0 = 1.0; |
| 334 |
$q1 = 0.0; |
| 335 |
$q2 = 0.0; |
| 336 |
$q3 = 0.0; |
| 337 |
|
| 338 |
if ($doRandomize == 1){ |
| 339 |
$cosTheta = 2.0*rand() - 1.0; |
| 340 |
$theta = acos($cosTheta); |
| 341 |
$phi = 2.0*3.14159265359*rand(); |
| 342 |
$psi = 2.0*3.14159265359*rand(); |
| 343 |
|
| 344 |
$q0 = cos(0.5*$theta)*cos(0.5*($phi + $psi)); |
| 345 |
$q1 = sin(0.5*$theta)*cos(0.5*($phi - $psi)); |
| 346 |
$q2 = sin(0.5*$theta)*sin(0.5*($phi - $psi)); |
| 347 |
$q3 = cos(0.5*$theta)*sin(0.5*($phi + $psi)); |
| 348 |
} |
| 349 |
|
| 350 |
print OUTFILE "$i\tpq\t$xCorr[$i] $yCorr[$i] $zCorr[$i] "; |
| 351 |
print OUTFILE "$q0 $q1 $q2 $q3\n"; |
| 352 |
} |
| 353 |
|
| 354 |
print OUTFILE " </StuntDoubles>\n </Snapshot>\n</OOPSE>\n"; |
| 355 |
} |
| 356 |
|
| 357 |
sub printMetaData { |
| 358 |
print OUTFILE " <MetaData>\n"; |
| 359 |
|
| 360 |
# print the water model or includes |
| 361 |
if ($opt_m){ |
| 362 |
print OUTFILE "#include \"water.md\""; |
| 363 |
} else { |
| 364 |
printWaterModel(); |
| 365 |
} |
| 366 |
printFakeWater() if $invalidWater == 1; |
| 367 |
|
| 368 |
# now back to the metaData output |
| 369 |
print OUTFILE "\n\ncomponent{ |
| 370 |
type = \"$waterName\"; |
| 371 |
nMol = $nMol; |
| 372 |
} |
| 373 |
|
| 374 |
ensemble = NVE; |
| 375 |
forceField = \"DUFF\"; |
| 376 |
electrostaticSummationMethod = \"shifted_force\"; |
| 377 |
electrostaticScreeningMethod = \"damped\"; |
| 378 |
cutoffRadius = $cutoff; |
| 379 |
|
| 380 |
targetTemp = 300; |
| 381 |
targetPressure = 1.0; |
| 382 |
|
| 383 |
tauThermostat = 1e3; |
| 384 |
tauBarostat = 1e4; |
| 385 |
|
| 386 |
dt = 2.0; |
| 387 |
runTime = 1e3; |
| 388 |
|
| 389 |
tempSet = \"true\"; |
| 390 |
thermalTime = 10; |
| 391 |
sampleTime = 100; |
| 392 |
statusTime = 2; |
| 393 |
</MetaData>\n"; |
| 394 |
} |
| 395 |
|
| 396 |
sub findCutoff { |
| 397 |
if ($boxy < $boxx) { |
| 398 |
$bm = $boxy; |
| 399 |
} else { |
| 400 |
$bm = $boxx; |
| 401 |
} |
| 402 |
if ($boxz < $bm) { |
| 403 |
$bm = $boxz; |
| 404 |
} |
| 405 |
$boxLength2 = 0.5*$bm; |
| 406 |
if ($boxLength2 > $cutoff){ |
| 407 |
# the default is good |
| 408 |
} else { |
| 409 |
$cutoff = int($boxLength2); |
| 410 |
} |
| 411 |
} |
| 412 |
|
| 413 |
sub findAlpha { |
| 414 |
$alpha = $alphaInt - $cutoff*$alphaSlope; |
| 415 |
} |
| 416 |
|
| 417 |
sub printFrameData { |
| 418 |
print OUTFILE |
| 419 |
" <Snapshot> |
| 420 |
<FrameData> |
| 421 |
Time: 0 |
| 422 |
Hmat: {{ $boxx, 0, 0 }, { 0, $boxy, 0 }, { 0, 0, $boxz }} |
| 423 |
</FrameData>\n"; |
| 424 |
} |
| 425 |
|
| 426 |
sub printWaterMD { |
| 427 |
open(WATERMD, ">./water.md") || die "Error: can't open file water.md\n"; |
| 428 |
$waterFileHandle = 'WATERMD'; |
| 429 |
|
| 430 |
print WATERMD "#ifndef _WATER_MD_\n#define _WATER_MD_\n"; |
| 431 |
printCl(); |
| 432 |
printNa(); |
| 433 |
printSSD_E(); |
| 434 |
printSSD_RF(); |
| 435 |
printSSD(); |
| 436 |
printSSD1(); |
| 437 |
printTRED(); |
| 438 |
printTIP3P(); |
| 439 |
printTIP4P(); |
| 440 |
printTIP4PEw(); |
| 441 |
printTIP5P(); |
| 442 |
printTIP5PE(); |
| 443 |
printSPCE(); |
| 444 |
printSPC(); |
| 445 |
printDPD(); |
| 446 |
printCG2(); |
| 447 |
print WATERMD "\n\n#endif"; |
| 448 |
} |
| 449 |
|
| 450 |
sub printCl { |
| 451 |
print $waterFileHandle "\n\nmolecule{ |
| 452 |
name = \"Cl-\"; |
| 453 |
|
| 454 |
atom[0]{ |
| 455 |
type = \"Cl-\"; |
| 456 |
position(0.0, 0.0, 0.0); |
| 457 |
} |
| 458 |
}" |
| 459 |
} |
| 460 |
|
| 461 |
sub printNa { |
| 462 |
print $waterFileHandle "\n\nmolecule{ |
| 463 |
name = \"Na+\"; |
| 464 |
|
| 465 |
atom[0]{ |
| 466 |
type = \"Na+\"; |
| 467 |
position(0.0, 0.0, 0.0); |
| 468 |
} |
| 469 |
}" |
| 470 |
} |
| 471 |
|
| 472 |
sub printSSD_E { |
| 473 |
print $waterFileHandle "\n\nmolecule{ |
| 474 |
name = \"SSD_E\"; |
| 475 |
|
| 476 |
atom[0]{ |
| 477 |
type = \"SSD_E\"; |
| 478 |
position( 0.0, 0.0, 0.0 ); |
| 479 |
orientation( 0.0, 0.0, 0.0 ); |
| 480 |
} |
| 481 |
}" |
| 482 |
} |
| 483 |
|
| 484 |
sub printSSD_RF { |
| 485 |
print $waterFileHandle "\n\nmolecule{ |
| 486 |
name = \"SSD_RF\"; |
| 487 |
|
| 488 |
atom[0]{ |
| 489 |
type = \"SSD_RF\"; |
| 490 |
position( 0.0, 0.0, 0.0 ); |
| 491 |
orientation( 0.0, 0.0, 0.0 ); |
| 492 |
} |
| 493 |
}" |
| 494 |
} |
| 495 |
|
| 496 |
sub printSSD { |
| 497 |
print $waterFileHandle "\n\nmolecule{ |
| 498 |
name = \"SSD\"; |
| 499 |
|
| 500 |
atom[0]{ |
| 501 |
type = \"SSD\"; |
| 502 |
position( 0.0, 0.0, 0.0 ); |
| 503 |
orientation( 0.0, 0.0, 0.0 ); |
| 504 |
} |
| 505 |
}" |
| 506 |
} |
| 507 |
|
| 508 |
sub printSSD1 { |
| 509 |
print $waterFileHandle "\n\nmolecule{ |
| 510 |
name = \"SSD1\"; |
| 511 |
|
| 512 |
atom[0]{ |
| 513 |
type = \"SSD1\"; |
| 514 |
position( 0.0, 0.0, 0.0 ); |
| 515 |
orientation( 0.0, 0.0, 0.0 ); |
| 516 |
} |
| 517 |
}" |
| 518 |
} |
| 519 |
|
| 520 |
sub printTRED { |
| 521 |
print $waterFileHandle "\n\nmolecule{ |
| 522 |
name = \"TRED\"; |
| 523 |
|
| 524 |
atom[0]{ |
| 525 |
type = \"TRED\"; |
| 526 |
position( 0.0, 0.0, 0.0 ); |
| 527 |
orientation( 0.0, 0.0, 0.0 ); |
| 528 |
} |
| 529 |
atom[1]{ |
| 530 |
type = \"EP_TRED\"; |
| 531 |
position( 0.0, 0.0, 0.5 ); |
| 532 |
} |
| 533 |
|
| 534 |
rigidBody[0]{ |
| 535 |
members(0, 1); |
| 536 |
} |
| 537 |
|
| 538 |
cutoffGroup{ |
| 539 |
members(0, 1); |
| 540 |
} |
| 541 |
}" |
| 542 |
} |
| 543 |
|
| 544 |
sub printTIP3P { |
| 545 |
print $waterFileHandle "\n\nmolecule{ |
| 546 |
name = \"TIP3P\"; |
| 547 |
|
| 548 |
atom[0]{ |
| 549 |
type = \"O_TIP3P\"; |
| 550 |
position( 0.0, 0.0, -0.06556 ); |
| 551 |
} |
| 552 |
atom[1]{ |
| 553 |
type = \"H_TIP3P\"; |
| 554 |
position( 0.0, 0.75695, 0.52032 ); |
| 555 |
} |
| 556 |
atom[2]{ |
| 557 |
type = \"H_TIP3P\"; |
| 558 |
position( 0.0, -0.75695, 0.52032 ); |
| 559 |
} |
| 560 |
|
| 561 |
rigidBody[0]{ |
| 562 |
members(0, 1, 2); |
| 563 |
} |
| 564 |
|
| 565 |
cutoffGroup{ |
| 566 |
members(0, 1, 2); |
| 567 |
} |
| 568 |
}" |
| 569 |
} |
| 570 |
|
| 571 |
sub printTIP4P { |
| 572 |
print $waterFileHandle "\n\nmolecule{ |
| 573 |
name = \"TIP4P\"; |
| 574 |
|
| 575 |
atom[0]{ |
| 576 |
type = \"O_TIP4P\"; |
| 577 |
position( 0.0, 0.0, -0.06556 ); |
| 578 |
} |
| 579 |
atom[1]{ |
| 580 |
type = \"H_TIP4P\"; |
| 581 |
position( 0.0, 0.75695, 0.52032 ); |
| 582 |
} |
| 583 |
atom[2]{ |
| 584 |
type = \"H_TIP4P\"; |
| 585 |
position( 0.0, -0.75695, 0.52032 ); |
| 586 |
} |
| 587 |
atom[3]{ |
| 588 |
type = \"EP_TIP4P\"; |
| 589 |
position( 0.0, 0.0, 0.08444 ); |
| 590 |
} |
| 591 |
|
| 592 |
rigidBody[0]{ |
| 593 |
members(0, 1, 2, 3); |
| 594 |
} |
| 595 |
|
| 596 |
cutoffGroup{ |
| 597 |
members(0, 1, 2, 3); |
| 598 |
} |
| 599 |
}" |
| 600 |
} |
| 601 |
|
| 602 |
sub printTIP4PEw { |
| 603 |
print $waterFileHandle "\n\nmolecule{ |
| 604 |
name = \"TIP4P-Ew\"; |
| 605 |
|
| 606 |
atom[0]{ |
| 607 |
type = \"O_TIP4P-Ew\"; |
| 608 |
position( 0.0, 0.0, -0.06556 ); |
| 609 |
} |
| 610 |
atom[1]{ |
| 611 |
type = \"H_TIP4P-Ew\"; |
| 612 |
position( 0.0, 0.75695, 0.52032 ); |
| 613 |
} |
| 614 |
atom[2]{ |
| 615 |
type = \"H_TIP4P-Ew\"; |
| 616 |
position( 0.0, -0.75695, 0.52032 ); |
| 617 |
} |
| 618 |
atom[3]{ |
| 619 |
type = \"EP_TIP4P-Ew\"; |
| 620 |
position( 0.0, 0.0, 0.05944 ); |
| 621 |
} |
| 622 |
|
| 623 |
rigidBody[0]{ |
| 624 |
members(0, 1, 2, 3); |
| 625 |
} |
| 626 |
|
| 627 |
cutoffGroup{ |
| 628 |
members(0, 1, 2, 3); |
| 629 |
} |
| 630 |
}" |
| 631 |
} |
| 632 |
|
| 633 |
sub printTIP5P { |
| 634 |
print $waterFileHandle "\n\nmolecule{ |
| 635 |
name = \"TIP5P\"; |
| 636 |
|
| 637 |
atom[0]{ |
| 638 |
type = \"O_TIP5P\"; |
| 639 |
position( 0.0, 0.0, -0.06556 ); |
| 640 |
} |
| 641 |
atom[1]{ |
| 642 |
type = \"H_TIP5P\"; |
| 643 |
position( 0.0, 0.75695, 0.52032 ); |
| 644 |
} |
| 645 |
atom[2]{ |
| 646 |
type = \"H_TIP5P\"; |
| 647 |
position( 0.0, -0.75695, 0.52032 ); |
| 648 |
} |
| 649 |
atom[3]{ |
| 650 |
type = \"EP_TIP5P\"; |
| 651 |
position( 0.57154, 0.0, -0.46971 ); |
| 652 |
} |
| 653 |
atom[4]{ |
| 654 |
type = \"EP_TIP5P\"; |
| 655 |
position( -0.57154, 0.0, -0.46971 ); |
| 656 |
} |
| 657 |
|
| 658 |
rigidBody[0]{ |
| 659 |
members(0, 1, 2, 3, 4); |
| 660 |
} |
| 661 |
|
| 662 |
cutoffGroup{ |
| 663 |
members(0, 1, 2, 3, 4); |
| 664 |
} |
| 665 |
}" |
| 666 |
} |
| 667 |
|
| 668 |
sub printTIP5PE { |
| 669 |
print $waterFileHandle "\n\nmolecule{ |
| 670 |
name = \"TIP5P-E\"; |
| 671 |
|
| 672 |
atom[0]{ |
| 673 |
type = \"O_TIP5P-E\"; |
| 674 |
position( 0.0, 0.0, -0.06556 ); |
| 675 |
} |
| 676 |
atom[1]{ |
| 677 |
type = \"H_TIP5P\"; |
| 678 |
position( 0.0, 0.75695, 0.52032 ); |
| 679 |
} |
| 680 |
atom[2]{ |
| 681 |
type = \"H_TIP5P\"; |
| 682 |
position( 0.0, -0.75695, 0.52032 ); |
| 683 |
} |
| 684 |
atom[3]{ |
| 685 |
type = \"EP_TIP5P\"; |
| 686 |
position( 0.57154, 0.0, -0.46971 ); |
| 687 |
} |
| 688 |
atom[4]{ |
| 689 |
type = \"EP_TIP5P\"; |
| 690 |
position( -0.57154, 0.0, -0.46971 ); |
| 691 |
} |
| 692 |
|
| 693 |
rigidBody[0]{ |
| 694 |
members(0, 1, 2, 3, 4); |
| 695 |
} |
| 696 |
|
| 697 |
cutoffGroup{ |
| 698 |
members(0, 1, 2, 3, 4); |
| 699 |
} |
| 700 |
}" |
| 701 |
} |
| 702 |
|
| 703 |
sub printSPCE { |
| 704 |
print $waterFileHandle "\n\nmolecule{ |
| 705 |
name = \"SPCE\"; |
| 706 |
|
| 707 |
atom[0]{ |
| 708 |
type = \"O_SPCE\"; |
| 709 |
position( 0.0, 0.0, -0.06461 ); |
| 710 |
} |
| 711 |
atom[1]{ |
| 712 |
type = \"H_SPCE\"; |
| 713 |
position( 0.0, 0.81649, 0.51275 ); |
| 714 |
} |
| 715 |
atom[2]{ |
| 716 |
type = \"H_SPCE\"; |
| 717 |
position( 0.0, -0.81649, 0.51275 ); |
| 718 |
} |
| 719 |
|
| 720 |
rigidBody[0]{ |
| 721 |
members(0, 1, 2); |
| 722 |
} |
| 723 |
|
| 724 |
cutoffGroup{ |
| 725 |
members(0, 1, 2); |
| 726 |
} |
| 727 |
}" |
| 728 |
} |
| 729 |
|
| 730 |
sub printSPC { |
| 731 |
print $waterFileHandle "\n\nmolecule{ |
| 732 |
name = \"SPC\"; |
| 733 |
|
| 734 |
atom[0]{ |
| 735 |
type = \"O_SPC\"; |
| 736 |
position( 0.0, 0.0, -0.06461 ); |
| 737 |
} |
| 738 |
atom[1]{ |
| 739 |
type = \"H_SPC\"; |
| 740 |
position( 0.0, 0.81649, 0.51275 ); |
| 741 |
} |
| 742 |
atom[2]{ |
| 743 |
type = \"H_SPC\"; |
| 744 |
position( 0.0, -0.81649, 0.51275 ); |
| 745 |
} |
| 746 |
|
| 747 |
rigidBody[0]{ |
| 748 |
members(0, 1, 2); |
| 749 |
} |
| 750 |
|
| 751 |
cutoffGroup{ |
| 752 |
members(0, 1, 2); |
| 753 |
} |
| 754 |
}" |
| 755 |
} |
| 756 |
|
| 757 |
sub printDPD { |
| 758 |
print $waterFileHandle "\n\nmolecule{ |
| 759 |
name = \"DPD\"; |
| 760 |
|
| 761 |
atom[0]{ |
| 762 |
type = \"DPD\"; |
| 763 |
position(0.0, 0.0, 0.0); |
| 764 |
} |
| 765 |
}" |
| 766 |
} |
| 767 |
|
| 768 |
sub printCG2 { |
| 769 |
print $waterFileHandle "\n\nmolecule{ |
| 770 |
name = \"CG2\"; |
| 771 |
|
| 772 |
atom[0]{ |
| 773 |
type = \"CG2\"; |
| 774 |
position(0.0, 0.0, 0.0); |
| 775 |
} |
| 776 |
}" |
| 777 |
} |
| 778 |
|
| 779 |
sub printFakeWater { |
| 780 |
print $waterFileHandle "\n\nmolecule{ |
| 781 |
name = \"$waterName\"; |
| 782 |
|
| 783 |
atom[0]{ |
| 784 |
type = \"$waterName\"; |
| 785 |
position(0.0, 0.0, 0.0); |
| 786 |
} |
| 787 |
}" |
| 788 |
} |
| 789 |
|
| 790 |
|
| 791 |
sub validateWater { |
| 792 |
if ($waterName eq 'Cl-') { $waterCase = 0; } |
| 793 |
elsif ($waterName eq 'Na+') { $waterCase = 1; } |
| 794 |
elsif ($waterName eq 'SSD_E') { $waterCase = 2; } |
| 795 |
elsif ($waterName eq 'SSD_RF') { $waterCase = 3; } |
| 796 |
elsif ($waterName eq 'SSD') { $waterCase = 4; } |
| 797 |
elsif ($waterName eq 'SSD1') { $waterCase = 5; } |
| 798 |
elsif ($waterName eq 'TIP3P') { $waterCase = 6; } |
| 799 |
elsif ($waterName eq 'TIP4P') { $waterCase = 7; } |
| 800 |
elsif ($waterName eq 'TIP4P-Ew') { $waterCase = 8; } |
| 801 |
elsif ($waterName eq 'TIP5P') { $waterCase = 9; } |
| 802 |
elsif ($waterName eq 'TIP5P-E') { $waterCase = 10; } |
| 803 |
elsif ($waterName eq 'SPCE') { $waterCase = 11; } |
| 804 |
elsif ($waterName eq 'SPC') { $waterCase = 12; } |
| 805 |
elsif ($waterName eq 'DPD') { $waterCase = 13; } |
| 806 |
elsif ($waterName eq 'CG2') { $waterCase = 14; } |
| 807 |
else { $invalidWater = 1; } |
| 808 |
} |
| 809 |
|
| 810 |
sub printWaterModel { |
| 811 |
if ($waterCase == 0) { printCl(); } |
| 812 |
elsif ($waterCase == 1) { printNa(); } |
| 813 |
elsif ($waterCase == 2) { printSSD_E(); } |
| 814 |
elsif ($waterCase == 3) { printSSD_RF(); } |
| 815 |
elsif ($waterCase == 4) { printSSD(); } |
| 816 |
elsif ($waterCase == 5) { printSSD1(); } |
| 817 |
elsif ($waterCase == 6) { printTIP3P(); } |
| 818 |
elsif ($waterCase == 7) { printTIP4P(); } |
| 819 |
elsif ($waterCase == 8) { printTIP4PEw(); } |
| 820 |
elsif ($waterCase == 9) { printTIP5P(); } |
| 821 |
elsif ($waterCase == 10) { printTIP5PE(); } |
| 822 |
elsif ($waterCase == 11) { printSPCE(); } |
| 823 |
elsif ($waterCase == 12) { printSPC(); } |
| 824 |
elsif ($waterCase == 13) { printDPD(); } |
| 825 |
elsif ($waterCase == 14) { printCG2(); } |
| 826 |
} |
