[ViewVC] Annotation of: group/trunk/OOPSE-4/src/applications/utilities/waterBoxer

#!/usr/bin/env perl

# program that builds water boxes

# author    = "Chris Fennell
# version   = "$Revision: 1.2 $"
# date      = "$Date: 2007-01-09 03:42:14 $"
# copyright = "Copyright (c) 2006 by the University of Notre Dame"
# license   = "OOPSE"

use Getopt::Std;

$tolerance = 1.0E-8;
$mass = 2.99151E-23; # mass of H2O in grams
$cm3ToAng3 = 1E24;   # convert cm^3 to angstroms^3
$densityConvert = $mass*$cm3ToAng3;
$lattice = 0;
$nMol = 500;
$density = 1.0;
$doRandomize = 0;
$cutoff = 12;
$alpha = 0.2125;
$alphaInt = 0.5125;
$alphaSlope = 0.025;
$invalidWater = 0;
$waterCase = -1;
$nothingSelected = 1;

# get our options
getopts('hmrvd:l:n:o:w:x:y:z:');

# just to test opt_h
$opt_h = "true" if $#ARGV >= 0;

# our option output 
if ($opt_h){
    print "waterBoxer: builds water boxes\n\n";
    print "usage: waterBoxer [-hmrv] [-d density] [-l lattice] [-n # waters]\n";
    print "\t[-o file name] [-w water name] \n\n";
    print "  -h : show this message\n";
    print "  -m : print out a water.md file (file with all water models)\n";
    print "  -r : randomize orientations\n";
    print "  -v : verbose output\n\n";
    print "  -d real    : density in g/cm^3\n";
    print "                 (default: 1)\n";
    print "  -l integer : 0 - face centered cubic, 1 - simple cubic\n";
    print "                 (default: 0)\n";
    print "  -n integer : # of water molecules\n";
    print "                 (default: 500)\n";
    print "  -o char    : output file name\n";
    print "                 (default: freshWater.md)\n";
    print "  -w char    : name of the water stunt double\n";
    print "                 (default: SPCE)\n";
    print "  -x real    : dimension of the box along the x direction\n";
    print "  -y real    : dimension of the box along the y direction\n";
    print "  -z real    : dimension of the box along the z direction\n\n";
    print "Note: you can only use values of x, y, or z that are smaller\n";
    print "      than the derived box length for a given density and\n";
    print "      number of molecules.\n\n";
    print "Example:\n";
    die   "   waterBoxer -d 0.997 -n 864 -w SSD_RF -o ssdrfWater.md\n";
}

# set some variables to be used in the code
if (defined($opt_o)){
  $fileName = $opt_o;
  $nothingSelected = 0;
} else {
    $fileName = 'freshWater.md';
}
if ($opt_m){
  die "Error: $fileName cannot be \"water.md\"\n       Please choose a different name\n" if $fileName eq 'water.md';
  $waterFileHandle = 'WATERMD';
  $nothingSelected = 0;
} else {
  $waterFileHandle = 'OUTFILE';
}
if ($opt_r){
  $doRandomize = $opt_r;
  $nothingSelected = 0;
}

if (defined($opt_d)){
  $nothingSelected = 0;
  if ($opt_d =~ /^[0-9]/) {
    $density = $opt_d;
  } else {
    die "Error: the value for '-d' ($opt_d) is not a valid number\n       Please choose a positive real # value\n";
  }
}
if (defined($opt_w)){
  $waterName = $opt_w;
  $nothingSelected = 0;
} else {
  $waterName = 'SPCE';
}
validateWater();
if ($invalidWater == 1){
  print "Warning: \'$waterName\' is not a recognized water model name.\n";
  print "         Use the \'-m\' option to generate a \'water.md\' with the\n";
  print "         recognized water model geometries.\n\n"; 
}
if ($waterName eq 'DPD') {
  # DPD waters are stand-ins for 4 water molecules
  $density = $density * 0.25;
}

if (defined($opt_l)){
  $nothingSelected = 0;
  if ($opt_l =~ /^[0-9]/) {
    $lattice = $opt_l;
    if ($lattice != 0 && $lattice != 1){
      die "Error: the '-l' value ($opt_l) is not a valid number\n       Please choose 0 or 1\n";
    }
  } else {
    die "Error: the '-l' value ($opt_l) is not a valid number\n       Please choose 0 or 1\n";
  }
}
if (defined($opt_n)){
  $nothingSelected = 0;
  if ($opt_n =~ /^[0-9]/) {
    $nMol = $opt_n;
  } else { 
    die "Error: the '-n' value ($opt_n) is not a valid number\n       Please choose a non-negative integer\n";
  }
}
if (defined($opt_x)){
  $nothingSelected = 0;
  if ($opt_x =~ /^[0-9]/) {
    $boxx = $opt_x;
  } else {
    die "Error: the value for '-x' ($opt_x) is not a valid number\n       Please choose a positive real # value\n";
  }
}
if (defined($opt_y)){
  $nothingSelected = 0;
  if ($opt_y =~ /^[0-9]/) {
    $boxy = $opt_y;
  } else {
    die "Error: the value for '-y' ($opt_y) is not a valid number\n       Please choose a positive real # value\n";
  }
}
if (defined($opt_z)){
  $nothingSelected = 0;
  if ($opt_z =~ /^[0-9]/) {
    $boxz = $opt_z;
  } else {
    die "Error: the value for '-z' ($opt_z) is not a valid number\n       Please choose a positive real # value\n";
  }
}


# open the file writer
open(OUTFILE, ">./$fileName") || die "Error: can't open file $fileName\n";

# check to set magic lattice numbers
if ($lattice == 0){
  $crystalNumReal = ($nMol/4.0)**(1.0/3.0);
  $crystalNum = int($crystalNumReal + $tolerance);
  $remainder = $crystalNumReal - $crystalNum;
  
  # if crystalNumReal wasn't an integer, we bump the crystal to the next
  # magic number
  if ($remainder > $tolerance){
    $crystalNum = $crystalNum + 1;
    $newMol = 4 * $crystalNum**3;
    print "Warning: The number chosen ($nMol) failed to build a clean fcc lattice.\n";
    print "         The number of molecules has been increased to the next magic number ($newMol).\n\n";
    $nMol = $newMol;
  }
} elsif ($lattice == 1){
  $crystalNumReal = ($nMol/1.0)**(1.0/3.0);
  $crystalNum = int($crystalNumReal);
  $remainder = $crystalNumReal - $crystalNum;
  
  # again, if crystalNumReal wasn't an integer, we bump the crystal to the next
  # magic number
  if ($remainder > $tolerance){
    $crystalNum = $crystalNum + 1;
    $newMol = $crystalNum**3;
    print "Warning: The number chosen ($nMol) failed to build a clean simple cubic lattice.\n";
    print "         The number of molecules has been increased to the next magic number ($newMol).\n\n";
    $nMol = $newMol;
  }
}

# now we can start building the crystals
$boxLength = ($nMol*$densityConvert/$density)**(1.0/3.0);
$cellLength = $boxLength / $crystalNum;

if ($boxx != 0) {
  if ($boxLength < $boxx) {
    print "Computed box length is smaller than requested x axis.  Use more\n";
    die "molecules.";    
  }
} else {
  $boxx = $boxLength;
}
if ($boxy != 0) {
  if ($boxLength < $boxy) {
    print "Computed box length is smaller than requested y axis.  Use more\n";
    die "molecules.";    
  }
} else {
  $boxy = $boxLength;
}
if ($boxz != 0) {
  if ($boxLength < $boxz) {
    print "Computed box length is smaller than requested z axis.  Use more\n";
    die "molecules.";    
  }
} else {
  $boxz = $boxLength;
}

$nx = int($boxx / $cellLength);
$ny = int($boxy / $cellLength);
$nz = int($boxz / $cellLength);

if ($lattice == 0) {
  $nMol = 4 * $nx * $ny * $nz;
} else {
  $nMol = $nx * $ny * $nz;
}

$newDensity = $nMol * $densityConvert / ($boxx*$boxy*$boxz);

if (abs($newDensity-$density) > $tolerance) {
  print "Resetting density to $newDensity to make chosen box sides work out\n";
}
$cellLengthX = $boxx/$nx;
$cellLengthY = $boxy/$ny;
$cellLengthZ = $boxz/$nz;

$cell2X = $cellLengthX*0.5;
$cell2Y = $cellLengthY*0.5;
$cell2Z = $cellLengthZ*0.5;

if ($lattice == 0) {
# build the unit cell
# molecule 0
  $xCorr[0] = 0.0;
  $yCorr[0] = 0.0;
  $zCorr[0] = 0.0;
# molecule 1
  $xCorr[1] = 0.0;
  $yCorr[1] = $cell2Y;
  $zCorr[1] = $cell2Z;
# molecule 2
  $xCorr[2] = $cell2X;
  $yCorr[2] = $cell2Y;
  $zCorr[2] = 0.0;
# molecule 3
  $xCorr[3] = $cell2X;
  $yCorr[3] = 0.0;
  $zCorr[3] = $cell2Z;
# assemble the lattice
  $counter = 0;
  for ($z = 0; $z < $nx; $z++) {
    for ($y = 0; $y < $ny; $y++) {
      for ($x = 0; $x < $nz; $x++) {
        for ($uc = 0; $uc < 4; $uc++) {
          $xCorr[$uc+$counter] = $xCorr[$uc] + $cellLengthX*$x;
          $yCorr[$uc+$counter] = $yCorr[$uc] + $cellLengthY*$y;
          $zCorr[$uc+$counter] = $zCorr[$uc] + $cellLengthZ*$z;
        }
        $counter = $counter + 4;
      }
    }
  }
  
} elsif ($lattice == 1) {
  # build the unit cell
  # molecule 0
  $xCorr[0] = $cell2X;
  $yCorr[0] = $cell2Y;
  $zCorr[0] = $cell2Z;
#assemble the lattice
  $counter = 0;
  for ($z = 0; $z < $nx; $z++) {
    for ($y = 0; $y < $ny; $y++) {
      for ($x = 0; $x < $nz; $x++) {
        $xCorr[$counter] = $xCorr[0] + $cellLengthX*$x;
        $yCorr[$counter] = $yCorr[0] + $cellLengthY*$y;
        $zCorr[$counter] = $zCorr[0] + $cellLengthZ*$z;
        
        $counter++;
      }
    }
  }
}

writeOutFile();
print "The water box \"$fileName\" was generated.\n";

if ($opt_m){
  printWaterMD();
  print "The file \"water.md\" was generated for inclusion in \"$fileName\"\n";
}

if ($nothingSelected == 1) {
    print "(For help, use the \'-h\' option.)\n";
}


# this marks the end of the main program, below is subroutines

sub acos {
  my ($rad) = @_;
  my $ret = atan2(sqrt(1 - $rad*$rad), $rad);
  return $ret;
}

sub writeOutFile {
  # write out the header
  print OUTFILE "<OOPSE version=4>\n";
  findCutoff();
  findAlpha();
  printMetaData();
  printFrameData();
  print OUTFILE "    <StuntDoubles>\n";
  
  # shift the box center to the origin and write out the coordinates
  for ($i = 0; $i < $nMol; $i++) {
    $xCorr[$i] -= 0.5*$boxx;
    $yCorr[$i] -= 0.5*$boxy;
    $zCorr[$i] -= 0.5*$boxz;
    
    $q0 = 1.0;
    $q1 = 0.0;
    $q2 = 0.0;
    $q3 = 0.0;
    
    if ($doRandomize == 1){
      $cosTheta = 2.0*rand() - 1.0;
      $theta = acos($cosTheta);
      $phi = 2.0*3.14159265359*rand();
      $psi = 2.0*3.14159265359*rand();
      
      $q0 = cos(0.5*$theta)*cos(0.5*($phi + $psi));
      $q1 = sin(0.5*$theta)*cos(0.5*($phi - $psi));
      $q2 = sin(0.5*$theta)*sin(0.5*($phi - $psi));
      $q3 = cos(0.5*$theta)*sin(0.5*($phi + $psi));
    }
    
    print OUTFILE "$i\tpq\t$xCorr[$i] $yCorr[$i] $zCorr[$i] ";
    print OUTFILE "$q0 $q1 $q2 $q3\n";
  }

  print OUTFILE "    </StuntDoubles>\n  </Snapshot>\n</OOPSE>\n";
}

sub printMetaData {
  print OUTFILE "  <MetaData>\n";

# print the water model or includes
  if ($opt_m){
    print OUTFILE "#include \"water.md\"";
  } else {
    printWaterModel();
  }
  printFakeWater() if $invalidWater == 1;

# now back to the metaData output
  print OUTFILE "\n\ncomponent{
  type = \"$waterName\";
  nMol = $nMol;
}

ensemble = NVE;
forceField = \"DUFF\";
electrostaticSummationMethod = \"shifted_force\";
electrostaticScreeningMethod = \"damped\";
cutoffRadius = $cutoff;

targetTemp = 300;
targetPressure = 1.0;

tauThermostat = 1e3;
tauBarostat = 1e4;

dt = 2.0;
runTime = 1e3;

tempSet = \"true\";
thermalTime = 10;
sampleTime = 100;
statusTime = 2;
  </MetaData>\n";
}

sub findCutoff {
  if ($boxy < $boxx) {
    $bm = $boxy;
  } else {
    $bm = $boxx;
  } 
  if ($boxz < $bm) {
    $bm = $boxz;
  }
  $boxLength2 = 0.5*$bm;
  if ($boxLength2 > $cutoff){
    # the default is good
  } else {
    $cutoff = int($boxLength2);
  }
}

sub findAlpha {
  $alpha = $alphaInt - $cutoff*$alphaSlope;
}

sub printFrameData {
print OUTFILE 
"  <Snapshot>
    <FrameData>
        Time: 0
        Hmat: {{ $boxx, 0, 0 }, { 0, $boxy, 0 }, { 0, 0, $boxz }}
    </FrameData>\n";
}

sub printWaterMD {
  open(WATERMD, ">./water.md") || die "Error: can't open file water.md\n";
  $waterFileHandle = 'WATERMD';

  print WATERMD "#ifndef _WATER_MD_\n#define _WATER_MD_\n";
  printCl();
  printNa();
  printSSD_E();
  printSSD_RF();
  printSSD();
  printSSD1();
  printTRED();
  printTIP3P();
  printTIP4P();
  printTIP4PEw();
  printTIP5P();
  printTIP5PE();
  printSPCE();
  printSPC();
  printDPD();
  print WATERMD "\n\n#endif";
}

sub printCl {
  print $waterFileHandle "\n\nmolecule{
  name = \"Cl-\";
  
  atom[0]{
    type = \"Cl-\";
    position(0.0, 0.0, 0.0);
  }
}"
}

sub printNa {
  print $waterFileHandle "\n\nmolecule{
  name = \"Na+\";
  
  atom[0]{
    type = \"Na+\";
    position(0.0, 0.0, 0.0);
  }
}"
}

sub printSSD_E {
  print $waterFileHandle "\n\nmolecule{
  name = \"SSD_E\";
  
  atom[0]{
    type = \"SSD_E\";
    position( 0.0, 0.0, 0.0 );
    orientation( 0.0, 0.0, 0.0 );
  }
}"
}

sub printSSD_RF {
  print $waterFileHandle "\n\nmolecule{
  name = \"SSD_RF\";
  
  atom[0]{
    type = \"SSD_RF\";
    position( 0.0, 0.0, 0.0 );
    orientation( 0.0, 0.0, 0.0 );
  }
}"
}

sub printSSD {
  print $waterFileHandle "\n\nmolecule{
  name = \"SSD\";
  
  atom[0]{
    type = \"SSD\";
    position( 0.0, 0.0, 0.0 );
    orientation( 0.0, 0.0, 0.0 );
  }
}"
}

sub printSSD1 {
  print $waterFileHandle "\n\nmolecule{
  name = \"SSD1\";
  
  atom[0]{
    type = \"SSD1\";
    position( 0.0, 0.0, 0.0 );
    orientation( 0.0, 0.0, 0.0 );
  }
}"
}

sub printTRED {
  print $waterFileHandle "\n\nmolecule{
  name = \"TRED\";
  
  atom[0]{
    type = \"TRED\";
    position( 0.0, 0.0, 0.0 );
    orientation( 0.0, 0.0, 0.0 );
  }
  atom[1]{
    type = \"EP_TRED\";
    position( 0.0, 0.0, 0.5 );
  }

  rigidBody[0]{
    members(0, 1);
  }

  cutoffGroup{
    members(0, 1);
  }
}"
}

sub printTIP3P {
  print $waterFileHandle "\n\nmolecule{
  name = \"TIP3P\";
  
  atom[0]{
    type = \"O_TIP3P\";
    position( 0.0, 0.0, -0.06556 );
  }
  atom[1]{
    type = \"H_TIP3P\";
    position( 0.0, 0.75695, 0.52032 );
  }
  atom[2]{
    type = \"H_TIP3P\";
    position( 0.0, -0.75695, 0.52032 );
  }

  rigidBody[0]{
    members(0, 1, 2);
  }

  cutoffGroup{
    members(0, 1, 2);
  }
}"
}

sub printTIP4P {
  print $waterFileHandle "\n\nmolecule{
  name = \"TIP4P\";
  
  atom[0]{
    type = \"O_TIP4P\";
    position( 0.0, 0.0, -0.06556 );
  }
  atom[1]{
    type = \"H_TIP4P\";
    position( 0.0, 0.75695, 0.52032 );
  }
  atom[2]{
    type = \"H_TIP4P\";
    position( 0.0, -0.75695, 0.52032 );
  }
  atom[3]{
    type = \"EP_TIP4P\";
    position( 0.0, 0.0, 0.08444 );
  }

  rigidBody[0]{
    members(0, 1, 2, 3);
  }

  cutoffGroup{
    members(0, 1, 2, 3);
  }
}"
}

sub printTIP4PEw {
  print $waterFileHandle "\n\nmolecule{
  name = \"TIP4P-Ew\";
  
  atom[0]{
    type = \"O_TIP4P-Ew\";
    position( 0.0, 0.0, -0.06556 );
  }
  atom[1]{
    type = \"H_TIP4P-Ew\";
    position( 0.0, 0.75695, 0.52032 );
  }
  atom[2]{
    type = \"H_TIP4P-Ew\";
    position( 0.0, -0.75695, 0.52032 );
  }
  atom[3]{
    type = \"EP_TIP4P-Ew\";
    position( 0.0, 0.0, 0.05944 );
  }
  
  rigidBody[0]{
    members(0, 1, 2, 3);
  }

  cutoffGroup{
    members(0, 1, 2, 3);
  }
}"
}

sub printTIP5P {
  print $waterFileHandle "\n\nmolecule{
  name = \"TIP5P\";
  
  atom[0]{
    type = \"O_TIP5P\";
    position( 0.0, 0.0, -0.06556 );
  }
  atom[1]{
    type = \"H_TIP5P\";
    position( 0.0, 0.75695, 0.52032 );
  }
  atom[2]{
    type = \"H_TIP5P\";
    position( 0.0, -0.75695, 0.52032 );
  }
  atom[3]{
    type = \"EP_TIP5P\";
    position( 0.57154, 0.0, -0.46971 );
  }
  atom[4]{
    type = \"EP_TIP5P\";
    position( -0.57154, 0.0, -0.46971 );
  }
  
  rigidBody[0]{
    members(0, 1, 2, 3, 4);
  }

  cutoffGroup{
    members(0, 1, 2, 3, 4);
  }
}"
}

sub printTIP5PE {
  print $waterFileHandle "\n\nmolecule{
  name = \"TIP5P-E\";
  
  atom[0]{
    type = \"O_TIP5P-E\";
    position( 0.0, 0.0, -0.06556 );
  }
  atom[1]{
    type = \"H_TIP5P\";
    position( 0.0, 0.75695, 0.52032 );
  }
  atom[2]{
    type = \"H_TIP5P\";
    position( 0.0, -0.75695, 0.52032 );
  }
  atom[3]{
    type = \"EP_TIP5P\";
    position( 0.57154, 0.0, -0.46971 );
  }
  atom[4]{
    type = \"EP_TIP5P\";
    position( -0.57154, 0.0, -0.46971 );
  }
  
  rigidBody[0]{
    members(0, 1, 2, 3, 4);
  }

  cutoffGroup{
    members(0, 1, 2, 3, 4);
  }
}"
}

sub printSPCE {
print $waterFileHandle "\n\nmolecule{
  name = \"SPCE\";
  
  atom[0]{
    type = \"O_SPCE\";
    position( 0.0, 0.0, -0.06461 );
  }
  atom[1]{
    type = \"H_SPCE\";
    position( 0.0, 0.81649, 0.51275 );
  }
  atom[2]{
    type = \"H_SPCE\";
    position( 0.0, -0.81649, 0.51275 );
  }
  
  rigidBody[0]{
    members(0, 1, 2);
  }

  cutoffGroup{
    members(0, 1, 2);
  }
}"
}

sub printSPC {
print $waterFileHandle "\n\nmolecule{
  name = \"SPC\";
  
  atom[0]{
    type = \"O_SPC\";
    position( 0.0, 0.0, -0.06461 );
  }
  atom[1]{
    type = \"H_SPC\";
    position( 0.0, 0.81649, 0.51275 );
  }
  atom[2]{
    type = \"H_SPC\";
    position( 0.0, -0.81649, 0.51275 );
  }
  
  rigidBody[0]{
    members(0, 1, 2);
  }

  cutoffGroup{
    members(0, 1, 2);
  }
}"
}

sub printDPD {
  print $waterFileHandle "\n\nmolecule{
  name = \"DPD\";
  
  atom[0]{
    type = \"DPD\";
    position(0.0, 0.0, 0.0);
  }
}"
}


sub printFakeWater {
  print $waterFileHandle "\n\nmolecule{
  name = \"$waterName\";
  
  atom[0]{
    type = \"$waterName\";
    position(0.0, 0.0, 0.0);
  }
}"
}


sub validateWater {
  if    ($waterName eq 'Cl-')      { $waterCase = 0;    }
  elsif ($waterName eq 'Na+')      { $waterCase = 1;    }
  elsif ($waterName eq 'SSD_E')    { $waterCase = 2;    }
  elsif ($waterName eq 'SSD_RF')   { $waterCase = 3;    }
  elsif ($waterName eq 'SSD')      { $waterCase = 4;    }
  elsif ($waterName eq 'SSD1')     { $waterCase = 5;    }
  elsif ($waterName eq 'TIP3P')    { $waterCase = 6;    }
  elsif ($waterName eq 'TIP4P')    { $waterCase = 7;    }
  elsif ($waterName eq 'TIP4P-Ew') { $waterCase = 8;    }
  elsif ($waterName eq 'TIP5P')    { $waterCase = 9;    }
  elsif ($waterName eq 'TIP5P-E')  { $waterCase = 10;   }
  elsif ($waterName eq 'SPCE')     { $waterCase = 11;   }
  elsif ($waterName eq 'SPC')      { $waterCase = 12;   }
  elsif ($waterName eq 'DPD')      { $waterCase = 13;   }
  else                             { $invalidWater = 1; }
}

sub printWaterModel {
  if    ($waterCase == 0)  { printCl();      }
  elsif ($waterCase == 1)  { printNa();      }
  elsif ($waterCase == 2)  { printSSD_E();   }
  elsif ($waterCase == 3)  { printSSD_RF();  }
  elsif ($waterCase == 4)  { printSSD();     }
  elsif ($waterCase == 5)  { printSSD1();    }
  elsif ($waterCase == 6)  { printTIP3P();   }
  elsif ($waterCase == 7)  { printTIP4P();   }
  elsif ($waterCase == 8)  { printTIP4PEw(); }
  elsif ($waterCase == 9)  { printTIP5P();   }
  elsif ($waterCase == 10) { printTIP5PE();  }
  elsif ($waterCase == 11) { printSPCE();    }
  elsif ($waterCase == 12) { printSPC();     }
  elsif ($waterCase == 13) { printDPD();     }
}
Revision:	3113
Committed:	Tue Jan 9 03:42:14 2007 UTC (17 years, 6 months ago) by gezelter
File size:	18025 byte(s)
Log Message:	Added the ability of waterBoxer to deal with non-cubical boxes.
#	User	Rev	Content
1	chrisfen	3037	#!/usr/bin/env perl
2
3			# program that builds water boxes
4
5			# author = "Chris Fennell
6	gezelter	3113	# version = "$Revision: 1.2 $"
7			# date = "$Date: 2007-01-09 03:42:14 $"
8	chrisfen	3037	# 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	gezelter	3113	getopts('hmrvd:l:n:o:w:x:y:z:');
31	chrisfen	3037
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";
39			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";
44			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";
47			print " (default: 0)\n";
48			print " -n integer : # of water molecules\n";
49			print " (default: 500)\n";
50			print " -o char : output file name\n";
51			print " (default: freshWater.md)\n";
52			print " -w char : name of the water stunt double\n";
53	gezelter	3113	print " (default: SPCE)\n";
54			print " -x real : dimension of the box along the x direction\n";
55			print " -y real : dimension of the box along the y direction\n";
56			print " -z real : dimension of the box along the z direction\n\n";
57			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	chrisfen	3037	print "Example:\n";
61			die " waterBoxer -d 0.997 -n 864 -w SSD_RF -o ssdrfWater.md\n";
62			}
63
64			# set some variables to be used in the code
65			if (defined($opt_o)){
66			$fileName = $opt_o;
67			$nothingSelected = 0;
68			} else {
69			$fileName = 'freshWater.md';
70			}
71			if ($opt_m){
72			die "Error: $fileName cannot be \"water.md\"\n Please choose a different name\n" if $fileName eq 'water.md';
73			$waterFileHandle = 'WATERMD';
74			$nothingSelected = 0;
75			} else {
76			$waterFileHandle = 'OUTFILE';
77			}
78			if ($opt_r){
79			$doRandomize = $opt_r;
80			$nothingSelected = 0;
81			}
82
83	gezelter	3113	if (defined($opt_d)){
84			$nothingSelected = 0;
85			if ($opt_d =~ /^[0-9]/) {
86			$density = $opt_d;
87			} else {
88			die "Error: the value for '-d' ($opt_d) is not a valid number\n Please choose a positive real # value\n";
89			}
90			}
91	chrisfen	3037	if (defined($opt_w)){
92			$waterName = $opt_w;
93			$nothingSelected = 0;
94			} else {
95			$waterName = 'SPCE';
96			}
97			validateWater();
98			if ($invalidWater == 1){
99			print "Warning: \'$waterName\' is not a recognized water model name.\n";
100			print " Use the \'-m\' option to generate a \'water.md\' with the\n";
101			print " recognized water model geometries.\n\n";
102			}
103	gezelter	3113	if ($waterName eq 'DPD') {
104			# DPD waters are stand-ins for 4 water molecules
105			$density = $density * 0.25;
106	chrisfen	3037	}
107	gezelter	3113
108	chrisfen	3037	if (defined($opt_l)){
109			$nothingSelected = 0;
110			if ($opt_l =~ /^[0-9]/) {
111			$lattice = $opt_l;
112			if ($lattice != 0 && $lattice != 1){
113			die "Error: the '-l' value ($opt_l) is not a valid number\n Please choose 0 or 1\n";
114			}
115			} else {
116			die "Error: the '-l' value ($opt_l) is not a valid number\n Please choose 0 or 1\n";
117			}
118			}
119			if (defined($opt_n)){
120			$nothingSelected = 0;
121			if ($opt_n =~ /^[0-9]/) {
122			$nMol = $opt_n;
123			} else {
124			die "Error: the '-n' value ($opt_n) is not a valid number\n Please choose a non-negative integer\n";
125			}
126			}
127	gezelter	3113	if (defined($opt_x)){
128			$nothingSelected = 0;
129			if ($opt_x =~ /^[0-9]/) {
130			$boxx = $opt_x;
131			} else {
132			die "Error: the value for '-x' ($opt_x) is not a valid number\n Please choose a positive real # value\n";
133			}
134			}
135			if (defined($opt_y)){
136			$nothingSelected = 0;
137			if ($opt_y =~ /^[0-9]/) {
138			$boxy = $opt_y;
139			} else {
140			die "Error: the value for '-y' ($opt_y) is not a valid number\n Please choose a positive real # value\n";
141			}
142			}
143			if (defined($opt_z)){
144			$nothingSelected = 0;
145			if ($opt_z =~ /^[0-9]/) {
146			$boxz = $opt_z;
147			} else {
148			die "Error: the value for '-z' ($opt_z) is not a valid number\n Please choose a positive real # value\n";
149			}
150			}
151	chrisfen	3037
152	gezelter	3113
153	chrisfen	3037	# open the file writer
154			open(OUTFILE, ">./$fileName") \|\| die "Error: can't open file $fileName\n";
155
156			# check to set magic lattice numbers
157			if ($lattice == 0){
158			$crystalNumReal = ($nMol/4.0)**(1.0/3.0);
159			$crystalNum = int($crystalNumReal + $tolerance);
160			$remainder = $crystalNumReal - $crystalNum;
161
162			# if crystalNumReal wasn't an integer, we bump the crystal to the next
163			# magic number
164			if ($remainder > $tolerance){
165			$crystalNum = $crystalNum + 1;
166			$newMol = 4 * $crystalNum**3;
167			print "Warning: The number chosen ($nMol) failed to build a clean fcc lattice.\n";
168			print " The number of molecules has been increased to the next magic number ($newMol).\n\n";
169			$nMol = $newMol;
170			}
171			} elsif ($lattice == 1){
172			$crystalNumReal = ($nMol/1.0)**(1.0/3.0);
173			$crystalNum = int($crystalNumReal);
174			$remainder = $crystalNumReal - $crystalNum;
175
176			# again, if crystalNumReal wasn't an integer, we bump the crystal to the next
177			# magic number
178			if ($remainder > $tolerance){
179			$crystalNum = $crystalNum + 1;
180			$newMol = $crystalNum**3;
181			print "Warning: The number chosen ($nMol) failed to build a clean simple cubic lattice.\n";
182			print " The number of molecules has been increased to the next magic number ($newMol).\n\n";
183			$nMol = $newMol;
184			}
185			}
186
187			# now we can start building the crystals
188			$boxLength = ($nMol$densityConvert/$density)*(1.0/3.0);
189			$cellLength = $boxLength / $crystalNum;
190
191	gezelter	3113	if ($boxx != 0) {
192			if ($boxLength < $boxx) {
193			print "Computed box length is smaller than requested x axis. Use more\n";
194			die "molecules.";
195			}
196			} else {
197			$boxx = $boxLength;
198			}
199			if ($boxy != 0) {
200			if ($boxLength < $boxy) {
201			print "Computed box length is smaller than requested y axis. Use more\n";
202			die "molecules.";
203			}
204			} else {
205			$boxy = $boxLength;
206			}
207			if ($boxz != 0) {
208			if ($boxLength < $boxz) {
209			print "Computed box length is smaller than requested z axis. Use more\n";
210			die "molecules.";
211			}
212			} else {
213			$boxz = $boxLength;
214			}
215
216			$nx = int($boxx / $cellLength);
217			$ny = int($boxy / $cellLength);
218			$nz = int($boxz / $cellLength);
219
220	chrisfen	3037	if ($lattice == 0) {
221	gezelter	3113	$nMol = 4 * $nx * $ny * $nz;
222			} else {
223			$nMol = $nx * $ny * $nz;
224			}
225
226			$newDensity = $nMol * $densityConvert / ($boxx$boxy$boxz);
227
228			if (abs($newDensity-$density) > $tolerance) {
229			print "Resetting density to $newDensity to make chosen box sides work out\n";
230			}
231			$cellLengthX = $boxx/$nx;
232			$cellLengthY = $boxy/$ny;
233			$cellLengthZ = $boxz/$nz;
234
235			$cell2X = $cellLengthX*0.5;
236			$cell2Y = $cellLengthY*0.5;
237			$cell2Z = $cellLengthZ*0.5;
238
239			if ($lattice == 0) {
240	chrisfen	3037	# build the unit cell
241			# molecule 0
242			$xCorr[0] = 0.0;
243			$yCorr[0] = 0.0;
244			$zCorr[0] = 0.0;
245			# molecule 1
246			$xCorr[1] = 0.0;
247	gezelter	3113	$yCorr[1] = $cell2Y;
248			$zCorr[1] = $cell2Z;
249	chrisfen	3037	# molecule 2
250	gezelter	3113	$xCorr[2] = $cell2X;
251			$yCorr[2] = $cell2Y;
252	chrisfen	3037	$zCorr[2] = 0.0;
253			# molecule 3
254	gezelter	3113	$xCorr[3] = $cell2X;
255	chrisfen	3037	$yCorr[3] = 0.0;
256	gezelter	3113	$zCorr[3] = $cell2Z;
257	chrisfen	3037	# assemble the lattice
258			$counter = 0;
259	gezelter	3113	for ($z = 0; $z < $nx; $z++) {
260			for ($y = 0; $y < $ny; $y++) {
261			for ($x = 0; $x < $nz; $x++) {
262	chrisfen	3037	for ($uc = 0; $uc < 4; $uc++) {
263	gezelter	3113	$xCorr[$uc+$counter] = $xCorr[$uc] + $cellLengthX*$x;
264			$yCorr[$uc+$counter] = $yCorr[$uc] + $cellLengthY*$y;
265			$zCorr[$uc+$counter] = $zCorr[$uc] + $cellLengthZ*$z;
266	chrisfen	3037	}
267			$counter = $counter + 4;
268			}
269			}
270			}
271
272			} elsif ($lattice == 1) {
273	gezelter	3113	# build the unit cell
274			# molecule 0
275			$xCorr[0] = $cell2X;
276			$yCorr[0] = $cell2Y;
277			$zCorr[0] = $cell2Z;
278	chrisfen	3037	#assemble the lattice
279			$counter = 0;
280	gezelter	3113	for ($z = 0; $z < $nx; $z++) {
281			for ($y = 0; $y < $ny; $y++) {
282			for ($x = 0; $x < $nz; $x++) {
283			$xCorr[$counter] = $xCorr[0] + $cellLengthX*$x;
284			$yCorr[$counter] = $yCorr[0] + $cellLengthY*$y;
285			$zCorr[$counter] = $zCorr[0] + $cellLengthZ*$z;
286	chrisfen	3037
287			$counter++;
288			}
289			}
290			}
291			}
292
293			writeOutFile();
294			print "The water box \"$fileName\" was generated.\n";
295
296			if ($opt_m){
297			printWaterMD();
298			print "The file \"water.md\" was generated for inclusion in \"$fileName\"\n";
299			}
300
301			if ($nothingSelected == 1) {
302			print "(For help, use the \'-h\' option.)\n";
303			}
304
305
306			# this marks the end of the main program, below is subroutines
307
308			sub acos {
309			my ($rad) = @_;
310			my $ret = atan2(sqrt(1 - $rad*$rad), $rad);
311			return $ret;
312			}
313
314			sub writeOutFile {
315			# write out the header
316			print OUTFILE "<OOPSE version=4>\n";
317			findCutoff();
318			findAlpha();
319			printMetaData();
320			printFrameData();
321			print OUTFILE " <StuntDoubles>\n";
322
323			# shift the box center to the origin and write out the coordinates
324			for ($i = 0; $i < $nMol; $i++) {
325	gezelter	3113	$xCorr[$i] -= 0.5*$boxx;
326			$yCorr[$i] -= 0.5*$boxy;
327			$zCorr[$i] -= 0.5*$boxz;
328	chrisfen	3037
329			$q0 = 1.0;
330			$q1 = 0.0;
331			$q2 = 0.0;
332			$q3 = 0.0;
333
334			if ($doRandomize == 1){
335			$cosTheta = 2.0*rand() - 1.0;
336			$theta = acos($cosTheta);
337			$phi = 2.03.14159265359rand();
338			$psi = 2.03.14159265359rand();
339
340			$q0 = cos(0.5$theta)cos(0.5*($phi + $psi));
341			$q1 = sin(0.5$theta)cos(0.5*($phi - $psi));
342			$q2 = sin(0.5$theta)sin(0.5*($phi - $psi));
343			$q3 = cos(0.5$theta)sin(0.5*($phi + $psi));
344			}
345
346			print OUTFILE "$i\tpq\t$xCorr[$i] $yCorr[$i] $zCorr[$i] ";
347			print OUTFILE "$q0 $q1 $q2 $q3\n";
348			}
349
350			print OUTFILE " </StuntDoubles>\n </Snapshot>\n</OOPSE>\n";
351			}
352
353			sub printMetaData {
354			print OUTFILE " <MetaData>\n";
355
356			# print the water model or includes
357			if ($opt_m){
358			print OUTFILE "#include \"water.md\"";
359			} else {
360			printWaterModel();
361			}
362			printFakeWater() if $invalidWater == 1;
363
364			# now back to the metaData output
365			print OUTFILE "\n\ncomponent{
366			type = \"$waterName\";
367			nMol = $nMol;
368			}
369
370			ensemble = NVE;
371			forceField = \"DUFF\";
372			electrostaticSummationMethod = \"shifted_force\";
373			electrostaticScreeningMethod = \"damped\";
374			cutoffRadius = $cutoff;
375
376			targetTemp = 300;
377			targetPressure = 1.0;
378
379			tauThermostat = 1e3;
380			tauBarostat = 1e4;
381
382			dt = 2.0;
383			runTime = 1e3;
384
385			tempSet = \"true\";
386			thermalTime = 10;
387			sampleTime = 100;
388			statusTime = 2;
389			</MetaData>\n";
390			}
391
392			sub findCutoff {
393	gezelter	3113	if ($boxy < $boxx) {
394			$bm = $boxy;
395			} else {
396			$bm = $boxx;
397			}
398			if ($boxz < $bm) {
399			$bm = $boxz;
400			}
401			$boxLength2 = 0.5*$bm;
402	chrisfen	3037	if ($boxLength2 > $cutoff){
403			# the default is good
404			} else {
405			$cutoff = int($boxLength2);
406			}
407			}
408
409			sub findAlpha {
410			$alpha = $alphaInt - $cutoff*$alphaSlope;
411			}
412
413			sub printFrameData {
414			print OUTFILE
415			" <Snapshot>
416			<FrameData>
417			Time: 0
418	gezelter	3113	Hmat: {{ $boxx, 0, 0 }, { 0, $boxy, 0 }, { 0, 0, $boxz }}
419	chrisfen	3037	</FrameData>\n";
420			}
421
422			sub printWaterMD {
423			open(WATERMD, ">./water.md") \|\| die "Error: can't open file water.md\n";
424			$waterFileHandle = 'WATERMD';
425
426			print WATERMD "#ifndef _WATER_MD_\n#define _WATER_MD_\n";
427			printCl();
428			printNa();
429			printSSD_E();
430			printSSD_RF();
431			printSSD();
432			printSSD1();
433			printTRED();
434			printTIP3P();
435			printTIP4P();
436			printTIP4PEw();
437			printTIP5P();
438			printTIP5PE();
439			printSPCE();
440			printSPC();
441			printDPD();
442			print WATERMD "\n\n#endif";
443			}
444
445			sub printCl {
446			print $waterFileHandle "\n\nmolecule{
447			name = \"Cl-\";
448
449			atom[0]{
450			type = \"Cl-\";
451			position(0.0, 0.0, 0.0);
452			}
453			}"
454			}
455
456			sub printNa {
457			print $waterFileHandle "\n\nmolecule{
458			name = \"Na+\";
459
460			atom[0]{
461			type = \"Na+\";
462			position(0.0, 0.0, 0.0);
463			}
464			}"
465			}
466
467			sub printSSD_E {
468			print $waterFileHandle "\n\nmolecule{
469			name = \"SSD_E\";
470
471			atom[0]{
472			type = \"SSD_E\";
473			position( 0.0, 0.0, 0.0 );
474			orientation( 0.0, 0.0, 0.0 );
475			}
476			}"
477			}
478
479			sub printSSD_RF {
480			print $waterFileHandle "\n\nmolecule{
481			name = \"SSD_RF\";
482
483			atom[0]{
484			type = \"SSD_RF\";
485			position( 0.0, 0.0, 0.0 );
486			orientation( 0.0, 0.0, 0.0 );
487			}
488			}"
489			}
490
491			sub printSSD {
492			print $waterFileHandle "\n\nmolecule{
493			name = \"SSD\";
494
495			atom[0]{
496			type = \"SSD\";
497			position( 0.0, 0.0, 0.0 );
498			orientation( 0.0, 0.0, 0.0 );
499			}
500			}"
501			}
502
503			sub printSSD1 {
504			print $waterFileHandle "\n\nmolecule{
505			name = \"SSD1\";
506
507			atom[0]{
508			type = \"SSD1\";
509			position( 0.0, 0.0, 0.0 );
510			orientation( 0.0, 0.0, 0.0 );
511			}
512			}"
513			}
514
515			sub printTRED {
516			print $waterFileHandle "\n\nmolecule{
517			name = \"TRED\";
518
519			atom[0]{
520			type = \"TRED\";
521			position( 0.0, 0.0, 0.0 );
522			orientation( 0.0, 0.0, 0.0 );
523			}
524			atom[1]{
525			type = \"EP_TRED\";
526			position( 0.0, 0.0, 0.5 );
527			}
528
529			rigidBody[0]{
530			members(0, 1);
531			}
532
533			cutoffGroup{
534			members(0, 1);
535			}
536			}"
537			}
538
539			sub printTIP3P {
540			print $waterFileHandle "\n\nmolecule{
541			name = \"TIP3P\";
542
543			atom[0]{
544			type = \"O_TIP3P\";
545			position( 0.0, 0.0, -0.06556 );
546			}
547			atom[1]{
548			type = \"H_TIP3P\";
549			position( 0.0, 0.75695, 0.52032 );
550			}
551			atom[2]{
552			type = \"H_TIP3P\";
553			position( 0.0, -0.75695, 0.52032 );
554			}
555
556			rigidBody[0]{
557			members(0, 1, 2);
558			}
559
560			cutoffGroup{
561			members(0, 1, 2);
562			}
563			}"
564			}
565
566			sub printTIP4P {
567			print $waterFileHandle "\n\nmolecule{
568			name = \"TIP4P\";
569
570			atom[0]{
571			type = \"O_TIP4P\";
572			position( 0.0, 0.0, -0.06556 );
573			}
574			atom[1]{
575			type = \"H_TIP4P\";
576			position( 0.0, 0.75695, 0.52032 );
577			}
578			atom[2]{
579			type = \"H_TIP4P\";
580			position( 0.0, -0.75695, 0.52032 );
581			}
582			atom[3]{
583			type = \"EP_TIP4P\";
584			position( 0.0, 0.0, 0.08444 );
585			}
586
587			rigidBody[0]{
588			members(0, 1, 2, 3);
589			}
590
591			cutoffGroup{
592			members(0, 1, 2, 3);
593			}
594			}"
595			}
596
597			sub printTIP4PEw {
598			print $waterFileHandle "\n\nmolecule{
599			name = \"TIP4P-Ew\";
600
601			atom[0]{
602			type = \"O_TIP4P-Ew\";
603			position( 0.0, 0.0, -0.06556 );
604			}
605			atom[1]{
606			type = \"H_TIP4P-Ew\";
607			position( 0.0, 0.75695, 0.52032 );
608			}
609			atom[2]{
610			type = \"H_TIP4P-Ew\";
611			position( 0.0, -0.75695, 0.52032 );
612			}
613			atom[3]{
614			type = \"EP_TIP4P-Ew\";
615			position( 0.0, 0.0, 0.05944 );
616			}
617
618			rigidBody[0]{
619			members(0, 1, 2, 3);
620			}
621
622			cutoffGroup{
623			members(0, 1, 2, 3);
624			}
625			}"
626			}
627
628			sub printTIP5P {
629			print $waterFileHandle "\n\nmolecule{
630			name = \"TIP5P\";
631
632			atom[0]{
633			type = \"O_TIP5P\";
634			position( 0.0, 0.0, -0.06556 );
635			}
636			atom[1]{
637			type = \"H_TIP5P\";
638			position( 0.0, 0.75695, 0.52032 );
639			}
640			atom[2]{
641			type = \"H_TIP5P\";
642			position( 0.0, -0.75695, 0.52032 );
643			}
644			atom[3]{
645			type = \"EP_TIP5P\";
646			position( 0.57154, 0.0, -0.46971 );
647			}
648			atom[4]{
649			type = \"EP_TIP5P\";
650			position( -0.57154, 0.0, -0.46971 );
651			}
652
653			rigidBody[0]{
654			members(0, 1, 2, 3, 4);
655			}
656
657			cutoffGroup{
658			members(0, 1, 2, 3, 4);
659			}
660			}"
661			}
662
663			sub printTIP5PE {
664			print $waterFileHandle "\n\nmolecule{
665			name = \"TIP5P-E\";
666
667			atom[0]{
668			type = \"O_TIP5P-E\";
669			position( 0.0, 0.0, -0.06556 );
670			}
671			atom[1]{
672			type = \"H_TIP5P\";
673			position( 0.0, 0.75695, 0.52032 );
674			}
675			atom[2]{
676			type = \"H_TIP5P\";
677			position( 0.0, -0.75695, 0.52032 );
678			}
679			atom[3]{
680			type = \"EP_TIP5P\";
681			position( 0.57154, 0.0, -0.46971 );
682			}
683			atom[4]{
684			type = \"EP_TIP5P\";
685			position( -0.57154, 0.0, -0.46971 );
686			}
687
688			rigidBody[0]{
689			members(0, 1, 2, 3, 4);
690			}
691
692			cutoffGroup{
693			members(0, 1, 2, 3, 4);
694			}
695			}"
696			}
697
698			sub printSPCE {
699			print $waterFileHandle "\n\nmolecule{
700			name = \"SPCE\";
701
702			atom[0]{
703			type = \"O_SPCE\";
704			position( 0.0, 0.0, -0.06461 );
705			}
706			atom[1]{
707			type = \"H_SPCE\";
708			position( 0.0, 0.81649, 0.51275 );
709			}
710			atom[2]{
711			type = \"H_SPCE\";
712			position( 0.0, -0.81649, 0.51275 );
713			}
714
715			rigidBody[0]{
716			members(0, 1, 2);
717			}
718
719			cutoffGroup{
720			members(0, 1, 2);
721			}
722			}"
723			}
724
725			sub printSPC {
726			print $waterFileHandle "\n\nmolecule{
727			name = \"SPC\";
728
729			atom[0]{
730			type = \"O_SPC\";
731			position( 0.0, 0.0, -0.06461 );
732			}
733			atom[1]{
734			type = \"H_SPC\";
735			position( 0.0, 0.81649, 0.51275 );
736			}
737			atom[2]{
738			type = \"H_SPC\";
739			position( 0.0, -0.81649, 0.51275 );
740			}
741
742			rigidBody[0]{
743			members(0, 1, 2);
744			}
745
746			cutoffGroup{
747			members(0, 1, 2);
748			}
749			}"
750			}
751
752			sub printDPD {
753			print $waterFileHandle "\n\nmolecule{
754			name = \"DPD\";
755
756			atom[0]{
757			type = \"DPD\";
758			position(0.0, 0.0, 0.0);
759			}
760			}"
761			}
762
763
764			sub printFakeWater {
765			print $waterFileHandle "\n\nmolecule{
766			name = \"$waterName\";
767
768			atom[0]{
769			type = \"$waterName\";
770			position(0.0, 0.0, 0.0);
771			}
772			}"
773			}
774
775
776			sub validateWater {
777			if ($waterName eq 'Cl-') { $waterCase = 0; }
778			elsif ($waterName eq 'Na+') { $waterCase = 1; }
779			elsif ($waterName eq 'SSD_E') { $waterCase = 2; }
780			elsif ($waterName eq 'SSD_RF') { $waterCase = 3; }
781			elsif ($waterName eq 'SSD') { $waterCase = 4; }
782			elsif ($waterName eq 'SSD1') { $waterCase = 5; }
783			elsif ($waterName eq 'TIP3P') { $waterCase = 6; }
784			elsif ($waterName eq 'TIP4P') { $waterCase = 7; }
785			elsif ($waterName eq 'TIP4P-Ew') { $waterCase = 8; }
786			elsif ($waterName eq 'TIP5P') { $waterCase = 9; }
787			elsif ($waterName eq 'TIP5P-E') { $waterCase = 10; }
788			elsif ($waterName eq 'SPCE') { $waterCase = 11; }
789			elsif ($waterName eq 'SPC') { $waterCase = 12; }
790			elsif ($waterName eq 'DPD') { $waterCase = 13; }
791			else { $invalidWater = 1; }
792			}
793
794			sub printWaterModel {
795			if ($waterCase == 0) { printCl(); }
796			elsif ($waterCase == 1) { printNa(); }
797			elsif ($waterCase == 2) { printSSD_E(); }
798			elsif ($waterCase == 3) { printSSD_RF(); }
799			elsif ($waterCase == 4) { printSSD(); }
800			elsif ($waterCase == 5) { printSSD1(); }
801			elsif ($waterCase == 6) { printTIP3P(); }
802			elsif ($waterCase == 7) { printTIP4P(); }
803			elsif ($waterCase == 8) { printTIP4PEw(); }
804			elsif ($waterCase == 9) { printTIP5P(); }
805			elsif ($waterCase == 10) { printTIP5PE(); }
806			elsif ($waterCase == 11) { printSPCE(); }
807			elsif ($waterCase == 12) { printSPC(); }
808			elsif ($waterCase == 13) { printDPD(); }
809			}