applications/utilities/waterBoxer.in

#!@PERLINTERP@ -w

# program that builds water boxes

# author    = "Chris Fennell
# version   = "$Revision: 1.3 $"
# date      = "$Date: 2006-10-02 23:27:40 $"
# 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;

# get our options
getopts('hmrvd:l:n:w:');

# if we don't have a filename, drop to -h
$opt_h = 'true' if $#ARGV != 0;

# our option output 
if ($opt_h){
    print "waterBoxer: builds water boxes\n\n";
    print "usage: waterBoxer [-hv] [-d density] [-l lattice] [-n # waters]\n";
    print "\t[-w water name] [file 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 "  -w char    : name of the water stunt double\n";
    print "                 (default: SPCE)\n";
    print "Example:\n";
    die   "   waterBoxer -d 0.997 -n 864 -w SSD_RF ssdrfWater.md\n";
}

# set some variables to be used in the code
$fileName = $ARGV[0];
if (defined($fileName)){
} else {
    $fileName = 'waterBox';
}
if ($opt_m){
  die "$fileName cannot be \"water.md\"\n\tPlease choose a different name\n" if $fileName eq 'water.md';
  $waterFileHandle = 'WATERMD';
} else {
  $waterFileHandle = 'OUTFILE';
}
if ($opt_r){
  $doRandomize = $opt_r;
}

if (defined($opt_w)){
  $waterName = $opt_w;
} else {
  $waterName = 'SPCE';
}
validateWater();
if (defined($opt_d)){
  if ($opt_d =~ /^[0-9]/) {
    $density = $opt_d;
  } else {
    die "\t-d value ($opt_d) is not a valid number\n\tPlease choose a positive real # value\n";
  }
}
if (defined($opt_l)){
  if ($opt_l =~ /^[0-9]/) {
    $lattice = $opt_l;
    if ($lattice != 0 && $lattice != 1){
      die "\t-l value ($opt_l) is not a valid number\n\tPlease choose 0 or 1\n";
    }
  } else {
    die "\t-l value ($opt_l) is not a valid number\n\tPlease choose 0 or 1\n";
  }
}
if (defined($opt_n)){
  if ($opt_n =~ /^[0-9]/) {
    $nMol = $opt_n;
  } else { 
    die "\t-n value ($opt_n) is not a valid number\n\tPlease choose a non-negative integer\n";
  }
}

# open the file writer
open(OUTFILE, ">./$fileName") || die "\tError: 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\n";
    print "fcc lattice. The number of molecules has been increased to\n";
    print "the next magic number ($newMol).\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\n";
    print "simple cubic lattice. The number of molecules has been\n";
    print "increased to the next magic number ($newMol).\n";
    $nMol = $newMol;
  }
}

# now we can start building the crystals
$boxLength = ($nMol*$densityConvert/$density)**(1.0/3.0);
$cellLength = $boxLength / $crystalNum;
$cell2 = $cellLength*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] = $cell2;
  $zCorr[1] = $cell2;
# molecule 2
  $xCorr[2] = $cell2;
  $yCorr[2] = $cell2;
  $zCorr[2] = 0.0;
# molecule 3
  $xCorr[3] = $cell2;
  $yCorr[3] = 0.0;
  $zCorr[3] = $cell2;
# assemble the lattice
  $counter = 0;
  for ($z = 0; $z < $crystalNum; $z++) {
    for ($y = 0; $y < $crystalNum; $y++) {
      for ($x = 0; $x < $crystalNum; $x++) {
        for ($uc = 0; $uc < 4; $uc++) {
          $xCorr[$uc+$counter] = $xCorr[$uc] + $cellLength*$x;
          $yCorr[$uc+$counter] = $yCorr[$uc] + $cellLength*$y;
          $zCorr[$uc+$counter] = $zCorr[$uc] + $cellLength*$z;
        }
        $counter = $counter + 4;
      }
    }
  }
  
} elsif ($lattice == 1) {
# build the unit cell
# molecule 0
  $xCorr[0] = $cell2;
  $yCorr[0] = $cell2;
  $zCorr[0] = $cell2;
#assemble the lattice
  $counter = 0;
  for ($z = 0; $z < $crystalNum; $z++) {
    for ($y = 0; $y < $crystalNum; $y++) {
      for ($x = 0; $x < $crystalNum; $x++) {
        $xCorr[$counter] = $xCorr[0] + $cellLength*$x;
        $yCorr[$counter] = $yCorr[0] + $cellLength*$y;
        $zCorr[$counter] = $zCorr[0] + $cellLength*$z;
        
        $counter++;
      }
    }
  }
}

writeOutFile();

if ($opt_m || $invalidWater){
  printWaterMD();
}

# 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*$boxLength;
    $yCorr[$i] -= 0.5*$boxLength;
    $zCorr[$i] -= 0.5*$boxLength;
    
    $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 {
  $boxLength2 = 0.5*$boxLength;
  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: {{ $boxLength, 0, 0 }, { 0, $boxLength, 0 }, { 0, 0, $boxLength }}
    </FrameData>\n";
}

sub printWaterMD {
  open(WATERMD, ">./water.md") || die "\tError: 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:	3030
Committed:	Mon Oct 2 23:27:40 2006 UTC (17 years, 11 months ago) by chrisfen
File size:	14884 byte(s)
Log Message:	fixed a bug in waterBoxer for invalid water names
#	User	Rev	Content
1	chrisfen	2996	#!@PERLINTERP@ -w
2
3			# program that builds water boxes
4
5			# author = "Chris Fennell
6	chrisfen	3030	# version = "$Revision: 1.3 $"
7			# date = "$Date: 2006-10-02 23:27:40 $"
8	chrisfen	2996	# 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	chrisfen	2997	$invalidWater = 0;
26	chrisfen	3030	$waterCase = -1;
27	chrisfen	2996
28			# get our options
29	chrisfen	2997	getopts('hmrvd:l:n:w:');
30	chrisfen	2996
31			# if we don't have a filename, drop to -h
32			$opt_h = 'true' if $#ARGV != 0;
33
34			# our option output
35			if ($opt_h){
36			print "waterBoxer: builds water boxes\n\n";
37			print "usage: waterBoxer [-hv] [-d density] [-l lattice] [-n # waters]\n";
38			print "\t[-w water name] [file name]\n\n";
39			print " -h : show this message\n";
40	chrisfen	2997	print " -m : print out a water.md file (file with all water models)\n";
41	chrisfen	2996	print " -r : randomize orientations\n";
42			print " -v : verbose output\n\n";
43			print " -d real : density in g/cm^3\n";
44			print " (default: 1)\n";
45			print " -l integer : 0 - face centered cubic, 1 - simple cubic\n";
46			print " (default: 0)\n";
47			print " -n integer : # of water molecules\n";
48			print " (default: 500)\n";
49			print " -w char : name of the water stunt double\n";
50			print " (default: SPCE)\n";
51			print "Example:\n";
52			die " waterBoxer -d 0.997 -n 864 -w SSD_RF ssdrfWater.md\n";
53			}
54
55			# set some variables to be used in the code
56			$fileName = $ARGV[0];
57			if (defined($fileName)){
58			} else {
59			$fileName = 'waterBox';
60			}
61	chrisfen	2997	if ($opt_m){
62			die "$fileName cannot be \"water.md\"\n\tPlease choose a different name\n" if $fileName eq 'water.md';
63			$waterFileHandle = 'WATERMD';
64			} else {
65			$waterFileHandle = 'OUTFILE';
66			}
67	chrisfen	2996	if ($opt_r){
68			$doRandomize = $opt_r;
69			}
70	chrisfen	2997
71	chrisfen	2996	if (defined($opt_w)){
72			$waterName = $opt_w;
73			} else {
74			$waterName = 'SPCE';
75			}
76	chrisfen	2997	validateWater();
77	chrisfen	2996	if (defined($opt_d)){
78			if ($opt_d =~ /^[0-9]/) {
79			$density = $opt_d;
80			} else {
81			die "\t-d value ($opt_d) is not a valid number\n\tPlease choose a positive real # value\n";
82			}
83			}
84			if (defined($opt_l)){
85			if ($opt_l =~ /^[0-9]/) {
86			$lattice = $opt_l;
87			if ($lattice != 0 && $lattice != 1){
88			die "\t-l value ($opt_l) is not a valid number\n\tPlease choose 0 or 1\n";
89			}
90			} else {
91			die "\t-l value ($opt_l) is not a valid number\n\tPlease choose 0 or 1\n";
92			}
93			}
94			if (defined($opt_n)){
95			if ($opt_n =~ /^[0-9]/) {
96			$nMol = $opt_n;
97			} else {
98			die "\t-n value ($opt_n) is not a valid number\n\tPlease choose a non-negative integer\n";
99			}
100			}
101
102			# open the file writer
103			open(OUTFILE, ">./$fileName") \|\| die "\tError: can't open file $fileName\n";
104
105			# check to set magic lattice numbers
106			if ($lattice == 0){
107			$crystalNumReal = ($nMol/4.0)**(1.0/3.0);
108			$crystalNum = int($crystalNumReal + $tolerance);
109			$remainder = $crystalNumReal - $crystalNum;
110
111			# if crystalNumReal wasn't an integer, we bump the crystal to the next
112			# magic number
113			if ($remainder > $tolerance){
114			$crystalNum = $crystalNum + 1;
115			$newMol = 4 * $crystalNum**3;
116			print "WARNING: The number chosen ($nMol) failed to build a clean\n";
117			print "fcc lattice. The number of molecules has been increased to\n";
118			print "the next magic number ($newMol).\n";
119			$nMol = $newMol;
120			}
121			} elsif ($lattice == 1){
122			$crystalNumReal = ($nMol/1.0)**(1.0/3.0);
123			$crystalNum = int($crystalNumReal);
124			$remainder = $crystalNumReal - $crystalNum;
125
126			# again, if crystalNumReal wasn't an integer, we bump the crystal to the next
127			# magic number
128			if ($remainder > $tolerance){
129			$crystalNum = $crystalNum + 1;
130			$newMol = $crystalNum**3;
131			print "WARNING: The number chosen ($nMol) failed to build a clean\n";
132			print "simple cubic lattice. The number of molecules has been\n";
133			print "increased to the next magic number ($newMol).\n";
134			$nMol = $newMol;
135			}
136			}
137
138			# now we can start building the crystals
139			$boxLength = ($nMol$densityConvert/$density)*(1.0/3.0);
140			$cellLength = $boxLength / $crystalNum;
141			$cell2 = $cellLength*0.5;
142
143			if ($lattice == 0) {
144			# build the unit cell
145			# molecule 0
146			$xCorr[0] = 0.0;
147			$yCorr[0] = 0.0;
148			$zCorr[0] = 0.0;
149			# molecule 1
150			$xCorr[1] = 0.0;
151			$yCorr[1] = $cell2;
152			$zCorr[1] = $cell2;
153			# molecule 2
154			$xCorr[2] = $cell2;
155			$yCorr[2] = $cell2;
156			$zCorr[2] = 0.0;
157			# molecule 3
158			$xCorr[3] = $cell2;
159			$yCorr[3] = 0.0;
160			$zCorr[3] = $cell2;
161			# assemble the lattice
162			$counter = 0;
163			for ($z = 0; $z < $crystalNum; $z++) {
164			for ($y = 0; $y < $crystalNum; $y++) {
165			for ($x = 0; $x < $crystalNum; $x++) {
166			for ($uc = 0; $uc < 4; $uc++) {
167			$xCorr[$uc+$counter] = $xCorr[$uc] + $cellLength*$x;
168			$yCorr[$uc+$counter] = $yCorr[$uc] + $cellLength*$y;
169			$zCorr[$uc+$counter] = $zCorr[$uc] + $cellLength*$z;
170			}
171			$counter = $counter + 4;
172			}
173			}
174			}
175
176			} elsif ($lattice == 1) {
177			# build the unit cell
178			# molecule 0
179			$xCorr[0] = $cell2;
180			$yCorr[0] = $cell2;
181			$zCorr[0] = $cell2;
182			#assemble the lattice
183			$counter = 0;
184			for ($z = 0; $z < $crystalNum; $z++) {
185			for ($y = 0; $y < $crystalNum; $y++) {
186			for ($x = 0; $x < $crystalNum; $x++) {
187			$xCorr[$counter] = $xCorr[0] + $cellLength*$x;
188			$yCorr[$counter] = $yCorr[0] + $cellLength*$y;
189			$zCorr[$counter] = $zCorr[0] + $cellLength*$z;
190
191			$counter++;
192			}
193			}
194			}
195			}
196
197			writeOutFile();
198
199	chrisfen	2997	if ($opt_m \|\| $invalidWater){
200			printWaterMD();
201			}
202
203	chrisfen	2996	# this marks the end of the main program, below is subroutines
204
205			sub acos {
206			my ($rad) = @_;
207			my $ret = atan2(sqrt(1 - $rad*$rad), $rad);
208			return $ret;
209			}
210
211	chrisfen	3030	sub writeOutFile {
212	chrisfen	2996	# write out the header
213			print OUTFILE "<OOPSE version=4>\n";
214			findCutoff();
215			findAlpha();
216			printMetaData();
217			printFrameData();
218			print OUTFILE " <StuntDoubles>\n";
219
220			# shift the box center to the origin and write out the coordinates
221			for ($i = 0; $i < $nMol; $i++) {
222			$xCorr[$i] -= 0.5*$boxLength;
223			$yCorr[$i] -= 0.5*$boxLength;
224			$zCorr[$i] -= 0.5*$boxLength;
225
226			$q0 = 1.0;
227			$q1 = 0.0;
228			$q2 = 0.0;
229			$q3 = 0.0;
230
231			if ($doRandomize == 1){
232			$cosTheta = 2.0*rand() - 1.0;
233			$theta = acos($cosTheta);
234			$phi = 2.03.14159265359rand();
235			$psi = 2.03.14159265359rand();
236
237			$q0 = cos(0.5$theta)cos(0.5*($phi + $psi));
238			$q1 = sin(0.5$theta)cos(0.5*($phi - $psi));
239			$q2 = sin(0.5$theta)sin(0.5*($phi - $psi));
240			$q3 = cos(0.5$theta)sin(0.5*($phi + $psi));
241			}
242
243			print OUTFILE "$i\tpq\t$xCorr[$i] $yCorr[$i] $zCorr[$i] ";
244			print OUTFILE "$q0 $q1 $q2 $q3\n";
245			}
246
247			print OUTFILE " </StuntDoubles>\n </Snapshot>\n</OOPSE>\n";
248			}
249
250			sub printMetaData {
251	chrisfen	2997	print OUTFILE " <MetaData>\n";
252	chrisfen	2996
253	chrisfen	2997	# print the water model or includes
254			if ($opt_m){
255			print OUTFILE "#include \"water.md\"";
256			} else {
257			printWaterModel();
258			}
259			printFakeWater() if $invalidWater == 1;
260
261			# now back to the metaData output
262			print OUTFILE "\n\ncomponent{
263	chrisfen	2996	type = \"$waterName\";
264			nMol = $nMol;
265			}
266
267			ensemble = NVE;
268			forceField = \"DUFF\";
269			electrostaticSummationMethod = \"shifted_force\";
270			electrostaticScreeningMethod = \"damped\";
271			cutoffRadius = $cutoff;
272
273			targetTemp = 300;
274			targetPressure = 1.0;
275
276			tauThermostat = 1e3;
277			tauBarostat = 1e4;
278
279			dt = 2.0;
280			runTime = 1e3;
281
282			tempSet = \"true\";
283			thermalTime = 10;
284			sampleTime = 100;
285			statusTime = 2;
286			</MetaData>\n";
287			}
288
289	chrisfen	3030	sub findCutoff {
290	chrisfen	2996	$boxLength2 = 0.5*$boxLength;
291			if ($boxLength2 > $cutoff){
292			# the default is good
293			} else {
294			$cutoff = int($boxLength2);
295			}
296			}
297
298	chrisfen	3030	sub findAlpha {
299	chrisfen	2996	$alpha = $alphaInt - $cutoff*$alphaSlope;
300			}
301
302	chrisfen	3030	sub printFrameData {
303	chrisfen	2996	print OUTFILE
304			" <Snapshot>
305			<FrameData>
306			Time: 0
307			Hmat: {{ $boxLength, 0, 0 }, { 0, $boxLength, 0 }, { 0, 0, $boxLength }}
308			</FrameData>\n";
309			}
310	chrisfen	2997
311	chrisfen	3030	sub printWaterMD {
312	chrisfen	2997	open(WATERMD, ">./water.md") \|\| die "\tError: can't open file water.md\n";
313	chrisfen	3030	$waterFileHandle = 'WATERMD';
314	chrisfen	2997
315			print WATERMD "#ifndef _WATER_MD_\n#define _WATER_MD_\n";
316			printCl();
317			printNa();
318			printSSD_E();
319			printSSD_RF();
320			printSSD();
321			printSSD1();
322			printTRED();
323			printTIP3P();
324			printTIP4P();
325			printTIP4PEw();
326			printTIP5P();
327			printTIP5PE();
328			printSPCE();
329			printSPC();
330			printDPD();
331			print WATERMD "\n\n#endif";
332			}
333
334	chrisfen	3030	sub printCl {
335	chrisfen	2997	print $waterFileHandle "\n\nmolecule{
336			name = \"Cl-\";
337
338			atom[0]{
339			type = \"Cl-\";
340			position(0.0, 0.0, 0.0);
341			}
342			}"
343			}
344
345	chrisfen	3030	sub printNa {
346	chrisfen	2997	print $waterFileHandle "\n\nmolecule{
347			name = \"Na+\";
348
349			atom[0]{
350			type = \"Na+\";
351			position(0.0, 0.0, 0.0);
352			}
353			}"
354			}
355
356	chrisfen	3030	sub printSSD_E {
357	chrisfen	2997	print $waterFileHandle "\n\nmolecule{
358			name = \"SSD_E\";
359
360			atom[0]{
361			type = \"SSD_E\";
362			position( 0.0, 0.0, 0.0 );
363			orientation( 0.0, 0.0, 0.0 );
364			}
365			}"
366			}
367
368	chrisfen	3030	sub printSSD_RF {
369	chrisfen	2997	print $waterFileHandle "\n\nmolecule{
370			name = \"SSD_RF\";
371
372			atom[0]{
373			type = \"SSD_RF\";
374			position( 0.0, 0.0, 0.0 );
375			orientation( 0.0, 0.0, 0.0 );
376			}
377			}"
378			}
379
380	chrisfen	3030	sub printSSD {
381	chrisfen	2997	print $waterFileHandle "\n\nmolecule{
382			name = \"SSD\";
383
384			atom[0]{
385			type = \"SSD\";
386			position( 0.0, 0.0, 0.0 );
387			orientation( 0.0, 0.0, 0.0 );
388			}
389			}"
390			}
391
392	chrisfen	3030	sub printSSD1 {
393	chrisfen	2997	print $waterFileHandle "\n\nmolecule{
394			name = \"SSD1\";
395
396			atom[0]{
397			type = \"SSD1\";
398			position( 0.0, 0.0, 0.0 );
399			orientation( 0.0, 0.0, 0.0 );
400			}
401			}"
402			}
403
404	chrisfen	3030	sub printTRED {
405	chrisfen	2997	print $waterFileHandle "\n\nmolecule{
406			name = \"TRED\";
407
408			atom[0]{
409			type = \"TRED\";
410			position( 0.0, 0.0, 0.0 );
411			orientation( 0.0, 0.0, 0.0 );
412			}
413			atom[1]{
414			type = \"EP_TRED\";
415			position( 0.0, 0.0, 0.5 );
416			}
417
418			rigidBody[0]{
419			members(0, 1);
420			}
421
422			cutoffGroup{
423			members(0, 1);
424			}
425			}"
426			}
427
428	chrisfen	3030	sub printTIP3P {
429	chrisfen	2997	print $waterFileHandle "\n\nmolecule{
430			name = \"TIP3P\";
431
432			atom[0]{
433			type = \"O_TIP3P\";
434			position( 0.0, 0.0, -0.06556 );
435			}
436			atom[1]{
437			type = \"H_TIP3P\";
438			position( 0.0, 0.75695, 0.52032 );
439			}
440			atom[2]{
441			type = \"H_TIP3P\";
442			position( 0.0, -0.75695, 0.52032 );
443			}
444
445			rigidBody[0]{
446			members(0, 1, 2);
447			}
448
449			cutoffGroup{
450			members(0, 1, 2);
451			}
452			}"
453			}
454
455	chrisfen	3030	sub printTIP4P {
456	chrisfen	2997	print $waterFileHandle "\n\nmolecule{
457			name = \"TIP4P\";
458
459			atom[0]{
460			type = \"O_TIP4P\";
461			position( 0.0, 0.0, -0.06556 );
462			}
463			atom[1]{
464			type = \"H_TIP4P\";
465			position( 0.0, 0.75695, 0.52032 );
466			}
467			atom[2]{
468			type = \"H_TIP4P\";
469			position( 0.0, -0.75695, 0.52032 );
470			}
471			atom[3]{
472			type = \"EP_TIP4P\";
473			position( 0.0, 0.0, 0.08444 );
474			}
475
476			rigidBody[0]{
477			members(0, 1, 2, 3);
478			}
479
480			cutoffGroup{
481			members(0, 1, 2, 3);
482			}
483			}"
484			}
485
486	chrisfen	3030	sub printTIP4PEw {
487	chrisfen	2997	print $waterFileHandle "\n\nmolecule{
488			name = \"TIP4P-Ew\";
489
490			atom[0]{
491			type = \"O_TIP4P-Ew\";
492			position( 0.0, 0.0, -0.06556 );
493			}
494			atom[1]{
495			type = \"H_TIP4P-Ew\";
496			position( 0.0, 0.75695, 0.52032 );
497			}
498			atom[2]{
499			type = \"H_TIP4P-Ew\";
500			position( 0.0, -0.75695, 0.52032 );
501			}
502			atom[3]{
503			type = \"EP_TIP4P-Ew\";
504			position( 0.0, 0.0, 0.05944 );
505			}
506
507			rigidBody[0]{
508			members(0, 1, 2, 3);
509			}
510
511			cutoffGroup{
512			members(0, 1, 2, 3);
513			}
514			}"
515			}
516
517	chrisfen	3030	sub printTIP5P {
518	chrisfen	2997	print $waterFileHandle "\n\nmolecule{
519			name = \"TIP5P\";
520
521			atom[0]{
522			type = \"O_TIP5P\";
523			position( 0.0, 0.0, -0.06556 );
524			}
525			atom[1]{
526			type = \"H_TIP5P\";
527			position( 0.0, 0.75695, 0.52032 );
528			}
529			atom[2]{
530			type = \"H_TIP5P\";
531			position( 0.0, -0.75695, 0.52032 );
532			}
533			atom[3]{
534			type = \"EP_TIP5P\";
535			position( 0.57154, 0.0, -0.46971 );
536			}
537			atom[4]{
538			type = \"EP_TIP5P\";
539			position( -0.57154, 0.0, -0.46971 );
540			}
541
542			rigidBody[0]{
543			members(0, 1, 2, 3, 4);
544			}
545
546			cutoffGroup{
547			members(0, 1, 2, 3, 4);
548			}
549			}"
550			}
551
552	chrisfen	3030	sub printTIP5PE {
553	chrisfen	2997	print $waterFileHandle "\n\nmolecule{
554			name = \"TIP5P-E\";
555
556			atom[0]{
557			type = \"O_TIP5P-E\";
558			position( 0.0, 0.0, -0.06556 );
559			}
560			atom[1]{
561			type = \"H_TIP5P\";
562			position( 0.0, 0.75695, 0.52032 );
563			}
564			atom[2]{
565			type = \"H_TIP5P\";
566			position( 0.0, -0.75695, 0.52032 );
567			}
568			atom[3]{
569			type = \"EP_TIP5P\";
570			position( 0.57154, 0.0, -0.46971 );
571			}
572			atom[4]{
573			type = \"EP_TIP5P\";
574			position( -0.57154, 0.0, -0.46971 );
575			}
576
577			rigidBody[0]{
578			members(0, 1, 2, 3, 4);
579			}
580
581			cutoffGroup{
582			members(0, 1, 2, 3, 4);
583			}
584			}"
585			}
586
587	chrisfen	3030	sub printSPCE {
588	chrisfen	2997	print $waterFileHandle "\n\nmolecule{
589			name = \"SPCE\";
590
591			atom[0]{
592			type = \"O_SPCE\";
593			position( 0.0, 0.0, -0.06461 );
594			}
595			atom[1]{
596			type = \"H_SPCE\";
597			position( 0.0, 0.81649, 0.51275 );
598			}
599			atom[2]{
600			type = \"H_SPCE\";
601			position( 0.0, -0.81649, 0.51275 );
602			}
603
604			rigidBody[0]{
605			members(0, 1, 2);
606			}
607
608			cutoffGroup{
609			members(0, 1, 2);
610			}
611			}"
612			}
613
614	chrisfen	3030	sub printSPC {
615	chrisfen	2997	print $waterFileHandle "\n\nmolecule{
616			name = \"SPC\";
617
618			atom[0]{
619			type = \"O_SPC\";
620			position( 0.0, 0.0, -0.06461 );
621			}
622			atom[1]{
623			type = \"H_SPC\";
624			position( 0.0, 0.81649, 0.51275 );
625			}
626			atom[2]{
627			type = \"H_SPC\";
628			position( 0.0, -0.81649, 0.51275 );
629			}
630
631			rigidBody[0]{
632			members(0, 1, 2);
633			}
634
635			cutoffGroup{
636			members(0, 1, 2);
637			}
638			}"
639			}
640
641	chrisfen	3030	sub printDPD {
642	chrisfen	2997	print $waterFileHandle "\n\nmolecule{
643			name = \"DPD\";
644
645			atom[0]{
646			type = \"DPD\";
647			position(0.0, 0.0, 0.0);
648			}
649			}"
650			}
651
652
653	chrisfen	3030	sub printFakeWater {
654	chrisfen	2997	print $waterFileHandle "\n\nmolecule{
655			name = \"$waterName\";
656
657			atom[0]{
658			type = \"$waterName\";
659			position(0.0, 0.0, 0.0);
660			}
661			}"
662			}
663
664
665	chrisfen	3030	sub validateWater {
666	chrisfen	2997	if ($waterName eq 'Cl-') { $waterCase = 0; }
667			elsif ($waterName eq 'Na+') { $waterCase = 1; }
668			elsif ($waterName eq 'SSD_E') { $waterCase = 2; }
669			elsif ($waterName eq 'SSD_RF') { $waterCase = 3; }
670			elsif ($waterName eq 'SSD') { $waterCase = 4; }
671			elsif ($waterName eq 'SSD1') { $waterCase = 5; }
672			elsif ($waterName eq 'TIP3P') { $waterCase = 6; }
673			elsif ($waterName eq 'TIP4P') { $waterCase = 7; }
674			elsif ($waterName eq 'TIP4P-Ew') { $waterCase = 8; }
675			elsif ($waterName eq 'TIP5P') { $waterCase = 9; }
676			elsif ($waterName eq 'TIP5P-E') { $waterCase = 10; }
677			elsif ($waterName eq 'SPCE') { $waterCase = 11; }
678			elsif ($waterName eq 'SPC') { $waterCase = 12; }
679			elsif ($waterName eq 'DPD') { $waterCase = 13; }
680			else { $invalidWater = 1; }
681			}
682
683	chrisfen	3030	sub printWaterModel {
684	chrisfen	2997	if ($waterCase == 0) { printCl(); }
685			elsif ($waterCase == 1) { printNa(); }
686			elsif ($waterCase == 2) { printSSD_E(); }
687			elsif ($waterCase == 3) { printSSD_RF(); }
688			elsif ($waterCase == 4) { printSSD(); }
689			elsif ($waterCase == 5) { printSSD1(); }
690			elsif ($waterCase == 6) { printTIP3P(); }
691			elsif ($waterCase == 7) { printTIP4P(); }
692			elsif ($waterCase == 8) { printTIP4PEw(); }
693			elsif ($waterCase == 9) { printTIP5P(); }
694			elsif ($waterCase == 10) { printTIP5PE(); }
695			elsif ($waterCase == 11) { printSPCE(); }
696			elsif ($waterCase == 12) { printSPC(); }
697			elsif ($waterCase == 13) { printDPD(); }
698			}