| 1 |
#!@PERLINTERP@ -w |
| 2 |
|
| 3 |
# program that builds water boxes |
| 4 |
|
| 5 |
# author = "Chris Fennell |
| 6 |
# version = "$Revision: 1.1 $" |
| 7 |
# date = "$Date: 2006-09-01 21:08:03 $" |
| 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 |
|
| 26 |
# get our options |
| 27 |
getopts('hrvd:l:n:w:'); |
| 28 |
|
| 29 |
# if we don't have a filename, drop to -h |
| 30 |
$opt_h = 'true' if $#ARGV != 0; |
| 31 |
|
| 32 |
# our option output |
| 33 |
if ($opt_h){ |
| 34 |
print "waterBoxer: builds water boxes\n\n"; |
| 35 |
print "usage: waterBoxer [-hv] [-d density] [-l lattice] [-n # waters]\n"; |
| 36 |
print "\t[-w water name] [file name]\n\n"; |
| 37 |
print " -h : show this message\n"; |
| 38 |
print " -r : randomize orientations\n"; |
| 39 |
print " -v : verbose output\n\n"; |
| 40 |
print " -d real : density in g/cm^3\n"; |
| 41 |
print " (default: 1)\n"; |
| 42 |
print " -l integer : 0 - face centered cubic, 1 - simple cubic\n"; |
| 43 |
print " (default: 0)\n"; |
| 44 |
print " -n integer : # of water molecules\n"; |
| 45 |
print " (default: 500)\n"; |
| 46 |
print " -w char : name of the water stunt double\n"; |
| 47 |
print " (default: SPCE)\n"; |
| 48 |
print "Example:\n"; |
| 49 |
die " waterBoxer -d 0.997 -n 864 -w SSD_RF ssdrfWater.md\n"; |
| 50 |
} |
| 51 |
|
| 52 |
# set some variables to be used in the code |
| 53 |
$fileName = $ARGV[0]; |
| 54 |
if (defined($fileName)){ |
| 55 |
} else { |
| 56 |
$fileName = 'waterBox'; |
| 57 |
} |
| 58 |
if ($opt_r){ |
| 59 |
$doRandomize = $opt_r; |
| 60 |
} |
| 61 |
if (defined($opt_w)){ |
| 62 |
$waterName = $opt_w; |
| 63 |
} else { |
| 64 |
$waterName = 'SPCE'; |
| 65 |
} |
| 66 |
|
| 67 |
if (defined($opt_d)){ |
| 68 |
if ($opt_d =~ /^[0-9]/) { |
| 69 |
$density = $opt_d; |
| 70 |
} else { |
| 71 |
die "\t-d value ($opt_d) is not a valid number\n\tPlease choose a positive real # value\n"; |
| 72 |
} |
| 73 |
} |
| 74 |
if (defined($opt_l)){ |
| 75 |
if ($opt_l =~ /^[0-9]/) { |
| 76 |
$lattice = $opt_l; |
| 77 |
if ($lattice != 0 && $lattice != 1){ |
| 78 |
die "\t-l value ($opt_l) is not a valid number\n\tPlease choose 0 or 1\n"; |
| 79 |
} |
| 80 |
} else { |
| 81 |
die "\t-l value ($opt_l) is not a valid number\n\tPlease choose 0 or 1\n"; |
| 82 |
} |
| 83 |
} |
| 84 |
if (defined($opt_n)){ |
| 85 |
if ($opt_n =~ /^[0-9]/) { |
| 86 |
$nMol = $opt_n; |
| 87 |
} else { |
| 88 |
die "\t-n value ($opt_n) is not a valid number\n\tPlease choose a non-negative integer\n"; |
| 89 |
} |
| 90 |
} |
| 91 |
|
| 92 |
# open the file writer |
| 93 |
open(OUTFILE, ">./$fileName") || die "\tError: can't open file $fileName\n"; |
| 94 |
|
| 95 |
# check to set magic lattice numbers |
| 96 |
if ($lattice == 0){ |
| 97 |
$crystalNumReal = ($nMol/4.0)**(1.0/3.0); |
| 98 |
$crystalNum = int($crystalNumReal + $tolerance); |
| 99 |
$remainder = $crystalNumReal - $crystalNum; |
| 100 |
|
| 101 |
# if crystalNumReal wasn't an integer, we bump the crystal to the next |
| 102 |
# magic number |
| 103 |
if ($remainder > $tolerance){ |
| 104 |
$crystalNum = $crystalNum + 1; |
| 105 |
$newMol = 4 * $crystalNum**3; |
| 106 |
print "WARNING: The number chosen ($nMol) failed to build a clean\n"; |
| 107 |
print "fcc lattice. The number of molecules has been increased to\n"; |
| 108 |
print "the next magic number ($newMol).\n"; |
| 109 |
$nMol = $newMol; |
| 110 |
} |
| 111 |
} elsif ($lattice == 1){ |
| 112 |
$crystalNumReal = ($nMol/1.0)**(1.0/3.0); |
| 113 |
$crystalNum = int($crystalNumReal); |
| 114 |
$remainder = $crystalNumReal - $crystalNum; |
| 115 |
|
| 116 |
# again, if crystalNumReal wasn't an integer, we bump the crystal to the next |
| 117 |
# magic number |
| 118 |
if ($remainder > $tolerance){ |
| 119 |
$crystalNum = $crystalNum + 1; |
| 120 |
$newMol = $crystalNum**3; |
| 121 |
print "WARNING: The number chosen ($nMol) failed to build a clean\n"; |
| 122 |
print "simple cubic lattice. The number of molecules has been\n"; |
| 123 |
print "increased to the next magic number ($newMol).\n"; |
| 124 |
$nMol = $newMol; |
| 125 |
} |
| 126 |
} |
| 127 |
|
| 128 |
# now we can start building the crystals |
| 129 |
$boxLength = ($nMol*$densityConvert/$density)**(1.0/3.0); |
| 130 |
$cellLength = $boxLength / $crystalNum; |
| 131 |
$cell2 = $cellLength*0.5; |
| 132 |
|
| 133 |
if ($lattice == 0) { |
| 134 |
# build the unit cell |
| 135 |
# molecule 0 |
| 136 |
$xCorr[0] = 0.0; |
| 137 |
$yCorr[0] = 0.0; |
| 138 |
$zCorr[0] = 0.0; |
| 139 |
# molecule 1 |
| 140 |
$xCorr[1] = 0.0; |
| 141 |
$yCorr[1] = $cell2; |
| 142 |
$zCorr[1] = $cell2; |
| 143 |
# molecule 2 |
| 144 |
$xCorr[2] = $cell2; |
| 145 |
$yCorr[2] = $cell2; |
| 146 |
$zCorr[2] = 0.0; |
| 147 |
# molecule 3 |
| 148 |
$xCorr[3] = $cell2; |
| 149 |
$yCorr[3] = 0.0; |
| 150 |
$zCorr[3] = $cell2; |
| 151 |
# assemble the lattice |
| 152 |
$counter = 0; |
| 153 |
for ($z = 0; $z < $crystalNum; $z++) { |
| 154 |
for ($y = 0; $y < $crystalNum; $y++) { |
| 155 |
for ($x = 0; $x < $crystalNum; $x++) { |
| 156 |
for ($uc = 0; $uc < 4; $uc++) { |
| 157 |
$xCorr[$uc+$counter] = $xCorr[$uc] + $cellLength*$x; |
| 158 |
$yCorr[$uc+$counter] = $yCorr[$uc] + $cellLength*$y; |
| 159 |
$zCorr[$uc+$counter] = $zCorr[$uc] + $cellLength*$z; |
| 160 |
} |
| 161 |
$counter = $counter + 4; |
| 162 |
} |
| 163 |
} |
| 164 |
} |
| 165 |
|
| 166 |
} elsif ($lattice == 1) { |
| 167 |
# build the unit cell |
| 168 |
# molecule 0 |
| 169 |
$xCorr[0] = $cell2; |
| 170 |
$yCorr[0] = $cell2; |
| 171 |
$zCorr[0] = $cell2; |
| 172 |
#assemble the lattice |
| 173 |
$counter = 0; |
| 174 |
for ($z = 0; $z < $crystalNum; $z++) { |
| 175 |
for ($y = 0; $y < $crystalNum; $y++) { |
| 176 |
for ($x = 0; $x < $crystalNum; $x++) { |
| 177 |
$xCorr[$counter] = $xCorr[0] + $cellLength*$x; |
| 178 |
$yCorr[$counter] = $yCorr[0] + $cellLength*$y; |
| 179 |
$zCorr[$counter] = $zCorr[0] + $cellLength*$z; |
| 180 |
|
| 181 |
$counter++; |
| 182 |
} |
| 183 |
} |
| 184 |
} |
| 185 |
} |
| 186 |
|
| 187 |
writeOutFile(); |
| 188 |
|
| 189 |
# this marks the end of the main program, below is subroutines |
| 190 |
|
| 191 |
sub acos { |
| 192 |
my ($rad) = @_; |
| 193 |
my $ret = atan2(sqrt(1 - $rad*$rad), $rad); |
| 194 |
return $ret; |
| 195 |
} |
| 196 |
|
| 197 |
sub writeOutFile{ |
| 198 |
# write out the header |
| 199 |
print OUTFILE "<OOPSE version=4>\n"; |
| 200 |
findCutoff(); |
| 201 |
findAlpha(); |
| 202 |
printMetaData(); |
| 203 |
printFrameData(); |
| 204 |
print OUTFILE " <StuntDoubles>\n"; |
| 205 |
|
| 206 |
# shift the box center to the origin and write out the coordinates |
| 207 |
for ($i = 0; $i < $nMol; $i++) { |
| 208 |
$xCorr[$i] -= 0.5*$boxLength; |
| 209 |
$yCorr[$i] -= 0.5*$boxLength; |
| 210 |
$zCorr[$i] -= 0.5*$boxLength; |
| 211 |
|
| 212 |
$q0 = 1.0; |
| 213 |
$q1 = 0.0; |
| 214 |
$q2 = 0.0; |
| 215 |
$q3 = 0.0; |
| 216 |
|
| 217 |
if ($doRandomize == 1){ |
| 218 |
$cosTheta = 2.0*rand() - 1.0; |
| 219 |
$theta = acos($cosTheta); |
| 220 |
$phi = 2.0*3.14159265359*rand(); |
| 221 |
$psi = 2.0*3.14159265359*rand(); |
| 222 |
|
| 223 |
$q0 = cos(0.5*$theta)*cos(0.5*($phi + $psi)); |
| 224 |
$q1 = sin(0.5*$theta)*cos(0.5*($phi - $psi)); |
| 225 |
$q2 = sin(0.5*$theta)*sin(0.5*($phi - $psi)); |
| 226 |
$q3 = cos(0.5*$theta)*sin(0.5*($phi + $psi)); |
| 227 |
} |
| 228 |
|
| 229 |
print OUTFILE "$i\tpq\t$xCorr[$i] $yCorr[$i] $zCorr[$i] "; |
| 230 |
print OUTFILE "$q0 $q1 $q2 $q3\n"; |
| 231 |
} |
| 232 |
|
| 233 |
print OUTFILE " </StuntDoubles>\n </Snapshot>\n</OOPSE>\n"; |
| 234 |
} |
| 235 |
|
| 236 |
sub printMetaData { |
| 237 |
print OUTFILE" <MetaData> |
| 238 |
#include \"water.md\" |
| 239 |
|
| 240 |
component{ |
| 241 |
type = \"$waterName\"; |
| 242 |
nMol = $nMol; |
| 243 |
} |
| 244 |
|
| 245 |
|
| 246 |
ensemble = NVE; |
| 247 |
forceField = \"DUFF\"; |
| 248 |
electrostaticSummationMethod = \"shifted_force\"; |
| 249 |
electrostaticScreeningMethod = \"damped\"; |
| 250 |
dampingAlpha = $alpha; |
| 251 |
cutoffRadius = $cutoff; |
| 252 |
|
| 253 |
targetTemp = 300; |
| 254 |
targetPressure = 1.0; |
| 255 |
|
| 256 |
tauThermostat = 1e3; |
| 257 |
tauBarostat = 1e4; |
| 258 |
|
| 259 |
dt = 2.0; |
| 260 |
runTime = 1e3; |
| 261 |
|
| 262 |
tempSet = \"true\"; |
| 263 |
thermalTime = 10; |
| 264 |
sampleTime = 100; |
| 265 |
statusTime = 2; |
| 266 |
</MetaData>\n"; |
| 267 |
} |
| 268 |
|
| 269 |
sub findCutoff{ |
| 270 |
$boxLength2 = 0.5*$boxLength; |
| 271 |
if ($boxLength2 > $cutoff){ |
| 272 |
# the default is good |
| 273 |
} else { |
| 274 |
$cutoff = int($boxLength2); |
| 275 |
} |
| 276 |
} |
| 277 |
|
| 278 |
sub findAlpha{ |
| 279 |
$alpha = $alphaInt - $cutoff*$alphaSlope; |
| 280 |
} |
| 281 |
|
| 282 |
sub printFrameData{ |
| 283 |
print OUTFILE |
| 284 |
" <Snapshot> |
| 285 |
<FrameData> |
| 286 |
Time: 0 |
| 287 |
Hmat: {{ $boxLength, 0, 0 }, { 0, $boxLength, 0 }, { 0, 0, $boxLength }} |
| 288 |
</FrameData>\n"; |
| 289 |
} |
