| 1 |
#!@PERLINTERP@ -w |
| 2 |
|
| 3 |
# program that builds water boxes |
| 4 |
|
| 5 |
# author = "Chris Fennell |
| 6 |
# version = "$Revision: 1.4 $" |
| 7 |
# date = "$Date: 2006-10-02 23:54:30 $" |
| 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 |
|
| 28 |
# get our options |
| 29 |
getopts('hmrvd:l:n:o:w:'); |
| 30 |
|
| 31 |
# if we don't have a filename, drop to -h |
| 32 |
$opt_h = 'true' if $#ARGV != -1; |
| 33 |
|
| 34 |
# our option output |
| 35 |
if ($opt_h){ |
| 36 |
print "waterBoxer: builds water boxes\n\n"; |
| 37 |
print "usage: waterBoxer [-hmrv] [-d density] [-l lattice] [-n # waters]\n"; |
| 38 |
print "\t[-o file name] [-w water name] \n\n"; |
| 39 |
print " -h : show this message\n"; |
| 40 |
print " -m : print out a water.md file (file with all water models)\n"; |
| 41 |
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 " -o char : output file name\n"; |
| 50 |
print " (default: freshWater.md)\n"; |
| 51 |
print " -w char : name of the water stunt double\n"; |
| 52 |
print " (default: SPCE)\n"; |
| 53 |
print "Example:\n"; |
| 54 |
die " waterBoxer -d 0.997 -n 864 -w SSD_RF -o ssdrfWater.md\n"; |
| 55 |
} |
| 56 |
|
| 57 |
# set some variables to be used in the code |
| 58 |
if (defined($opt_o)){ |
| 59 |
$fileName = $opt_o; |
| 60 |
} else { |
| 61 |
$fileName = 'freshWater.md'; |
| 62 |
} |
| 63 |
if ($opt_m){ |
| 64 |
die "$fileName cannot be \"water.md\"\n\tPlease choose a different name\n" if $fileName eq 'water.md'; |
| 65 |
$waterFileHandle = 'WATERMD'; |
| 66 |
} else { |
| 67 |
$waterFileHandle = 'OUTFILE'; |
| 68 |
} |
| 69 |
if ($opt_r){ |
| 70 |
$doRandomize = $opt_r; |
| 71 |
} |
| 72 |
|
| 73 |
if (defined($opt_w)){ |
| 74 |
$waterName = $opt_w; |
| 75 |
} else { |
| 76 |
$waterName = 'SPCE'; |
| 77 |
} |
| 78 |
validateWater(); |
| 79 |
if ($invalidWater == 1){ |
| 80 |
print "Warning: \'$waterName\' is not a recognized water model name.\n"; |
| 81 |
print " Use the \'-m\' option to generate a \'water.md\' with the\n"; |
| 82 |
print " recognized water model geometries.\n"; |
| 83 |
} |
| 84 |
if (defined($opt_d)){ |
| 85 |
if ($opt_d =~ /^[0-9]/) { |
| 86 |
$density = $opt_d; |
| 87 |
} else { |
| 88 |
die "\t-d value ($opt_d) is not a valid number\n\tPlease choose a positive real # value\n"; |
| 89 |
} |
| 90 |
} |
| 91 |
if (defined($opt_l)){ |
| 92 |
if ($opt_l =~ /^[0-9]/) { |
| 93 |
$lattice = $opt_l; |
| 94 |
if ($lattice != 0 && $lattice != 1){ |
| 95 |
die "\t-l value ($opt_l) is not a valid number\n\tPlease choose 0 or 1\n"; |
| 96 |
} |
| 97 |
} else { |
| 98 |
die "\t-l value ($opt_l) is not a valid number\n\tPlease choose 0 or 1\n"; |
| 99 |
} |
| 100 |
} |
| 101 |
if (defined($opt_n)){ |
| 102 |
if ($opt_n =~ /^[0-9]/) { |
| 103 |
$nMol = $opt_n; |
| 104 |
} else { |
| 105 |
die "\t-n value ($opt_n) is not a valid number\n\tPlease choose a non-negative integer\n"; |
| 106 |
} |
| 107 |
} |
| 108 |
|
| 109 |
# open the file writer |
| 110 |
open(OUTFILE, ">./$fileName") || die "\tError: can't open file $fileName\n"; |
| 111 |
|
| 112 |
# check to set magic lattice numbers |
| 113 |
if ($lattice == 0){ |
| 114 |
$crystalNumReal = ($nMol/4.0)**(1.0/3.0); |
| 115 |
$crystalNum = int($crystalNumReal + $tolerance); |
| 116 |
$remainder = $crystalNumReal - $crystalNum; |
| 117 |
|
| 118 |
# if crystalNumReal wasn't an integer, we bump the crystal to the next |
| 119 |
# magic number |
| 120 |
if ($remainder > $tolerance){ |
| 121 |
$crystalNum = $crystalNum + 1; |
| 122 |
$newMol = 4 * $crystalNum**3; |
| 123 |
print "WARNING: The number chosen ($nMol) failed to build a clean\n"; |
| 124 |
print "fcc lattice. The number of molecules has been increased to\n"; |
| 125 |
print "the next magic number ($newMol).\n"; |
| 126 |
$nMol = $newMol; |
| 127 |
} |
| 128 |
} elsif ($lattice == 1){ |
| 129 |
$crystalNumReal = ($nMol/1.0)**(1.0/3.0); |
| 130 |
$crystalNum = int($crystalNumReal); |
| 131 |
$remainder = $crystalNumReal - $crystalNum; |
| 132 |
|
| 133 |
# again, if crystalNumReal wasn't an integer, we bump the crystal to the next |
| 134 |
# magic number |
| 135 |
if ($remainder > $tolerance){ |
| 136 |
$crystalNum = $crystalNum + 1; |
| 137 |
$newMol = $crystalNum**3; |
| 138 |
print "WARNING: The number chosen ($nMol) failed to build a clean\n"; |
| 139 |
print "simple cubic lattice. The number of molecules has been\n"; |
| 140 |
print "increased to the next magic number ($newMol).\n"; |
| 141 |
$nMol = $newMol; |
| 142 |
} |
| 143 |
} |
| 144 |
|
| 145 |
# now we can start building the crystals |
| 146 |
$boxLength = ($nMol*$densityConvert/$density)**(1.0/3.0); |
| 147 |
$cellLength = $boxLength / $crystalNum; |
| 148 |
$cell2 = $cellLength*0.5; |
| 149 |
|
| 150 |
if ($lattice == 0) { |
| 151 |
# build the unit cell |
| 152 |
# molecule 0 |
| 153 |
$xCorr[0] = 0.0; |
| 154 |
$yCorr[0] = 0.0; |
| 155 |
$zCorr[0] = 0.0; |
| 156 |
# molecule 1 |
| 157 |
$xCorr[1] = 0.0; |
| 158 |
$yCorr[1] = $cell2; |
| 159 |
$zCorr[1] = $cell2; |
| 160 |
# molecule 2 |
| 161 |
$xCorr[2] = $cell2; |
| 162 |
$yCorr[2] = $cell2; |
| 163 |
$zCorr[2] = 0.0; |
| 164 |
# molecule 3 |
| 165 |
$xCorr[3] = $cell2; |
| 166 |
$yCorr[3] = 0.0; |
| 167 |
$zCorr[3] = $cell2; |
| 168 |
# assemble the lattice |
| 169 |
$counter = 0; |
| 170 |
for ($z = 0; $z < $crystalNum; $z++) { |
| 171 |
for ($y = 0; $y < $crystalNum; $y++) { |
| 172 |
for ($x = 0; $x < $crystalNum; $x++) { |
| 173 |
for ($uc = 0; $uc < 4; $uc++) { |
| 174 |
$xCorr[$uc+$counter] = $xCorr[$uc] + $cellLength*$x; |
| 175 |
$yCorr[$uc+$counter] = $yCorr[$uc] + $cellLength*$y; |
| 176 |
$zCorr[$uc+$counter] = $zCorr[$uc] + $cellLength*$z; |
| 177 |
} |
| 178 |
$counter = $counter + 4; |
| 179 |
} |
| 180 |
} |
| 181 |
} |
| 182 |
|
| 183 |
} elsif ($lattice == 1) { |
| 184 |
# build the unit cell |
| 185 |
# molecule 0 |
| 186 |
$xCorr[0] = $cell2; |
| 187 |
$yCorr[0] = $cell2; |
| 188 |
$zCorr[0] = $cell2; |
| 189 |
#assemble the lattice |
| 190 |
$counter = 0; |
| 191 |
for ($z = 0; $z < $crystalNum; $z++) { |
| 192 |
for ($y = 0; $y < $crystalNum; $y++) { |
| 193 |
for ($x = 0; $x < $crystalNum; $x++) { |
| 194 |
$xCorr[$counter] = $xCorr[0] + $cellLength*$x; |
| 195 |
$yCorr[$counter] = $yCorr[0] + $cellLength*$y; |
| 196 |
$zCorr[$counter] = $zCorr[0] + $cellLength*$z; |
| 197 |
|
| 198 |
$counter++; |
| 199 |
} |
| 200 |
} |
| 201 |
} |
| 202 |
} |
| 203 |
|
| 204 |
writeOutFile(); |
| 205 |
print "Water box \"$fileName\" generated.\n"; |
| 206 |
|
| 207 |
if ($opt_m){ |
| 208 |
printWaterMD(); |
| 209 |
print "File \"water.md\" generated for inclusion in \"$fileName\"\n"; |
| 210 |
} |
| 211 |
|
| 212 |
# this marks the end of the main program, below is subroutines |
| 213 |
|
| 214 |
sub acos { |
| 215 |
my ($rad) = @_; |
| 216 |
my $ret = atan2(sqrt(1 - $rad*$rad), $rad); |
| 217 |
return $ret; |
| 218 |
} |
| 219 |
|
| 220 |
sub writeOutFile { |
| 221 |
# write out the header |
| 222 |
print OUTFILE "<OOPSE version=4>\n"; |
| 223 |
findCutoff(); |
| 224 |
findAlpha(); |
| 225 |
printMetaData(); |
| 226 |
printFrameData(); |
| 227 |
print OUTFILE " <StuntDoubles>\n"; |
| 228 |
|
| 229 |
# shift the box center to the origin and write out the coordinates |
| 230 |
for ($i = 0; $i < $nMol; $i++) { |
| 231 |
$xCorr[$i] -= 0.5*$boxLength; |
| 232 |
$yCorr[$i] -= 0.5*$boxLength; |
| 233 |
$zCorr[$i] -= 0.5*$boxLength; |
| 234 |
|
| 235 |
$q0 = 1.0; |
| 236 |
$q1 = 0.0; |
| 237 |
$q2 = 0.0; |
| 238 |
$q3 = 0.0; |
| 239 |
|
| 240 |
if ($doRandomize == 1){ |
| 241 |
$cosTheta = 2.0*rand() - 1.0; |
| 242 |
$theta = acos($cosTheta); |
| 243 |
$phi = 2.0*3.14159265359*rand(); |
| 244 |
$psi = 2.0*3.14159265359*rand(); |
| 245 |
|
| 246 |
$q0 = cos(0.5*$theta)*cos(0.5*($phi + $psi)); |
| 247 |
$q1 = sin(0.5*$theta)*cos(0.5*($phi - $psi)); |
| 248 |
$q2 = sin(0.5*$theta)*sin(0.5*($phi - $psi)); |
| 249 |
$q3 = cos(0.5*$theta)*sin(0.5*($phi + $psi)); |
| 250 |
} |
| 251 |
|
| 252 |
print OUTFILE "$i\tpq\t$xCorr[$i] $yCorr[$i] $zCorr[$i] "; |
| 253 |
print OUTFILE "$q0 $q1 $q2 $q3\n"; |
| 254 |
} |
| 255 |
|
| 256 |
print OUTFILE " </StuntDoubles>\n </Snapshot>\n</OOPSE>\n"; |
| 257 |
} |
| 258 |
|
| 259 |
sub printMetaData { |
| 260 |
print OUTFILE " <MetaData>\n"; |
| 261 |
|
| 262 |
# print the water model or includes |
| 263 |
if ($opt_m){ |
| 264 |
print OUTFILE "#include \"water.md\""; |
| 265 |
} else { |
| 266 |
printWaterModel(); |
| 267 |
} |
| 268 |
printFakeWater() if $invalidWater == 1; |
| 269 |
|
| 270 |
# now back to the metaData output |
| 271 |
print OUTFILE "\n\ncomponent{ |
| 272 |
type = \"$waterName\"; |
| 273 |
nMol = $nMol; |
| 274 |
} |
| 275 |
|
| 276 |
ensemble = NVE; |
| 277 |
forceField = \"DUFF\"; |
| 278 |
electrostaticSummationMethod = \"shifted_force\"; |
| 279 |
electrostaticScreeningMethod = \"damped\"; |
| 280 |
cutoffRadius = $cutoff; |
| 281 |
|
| 282 |
targetTemp = 300; |
| 283 |
targetPressure = 1.0; |
| 284 |
|
| 285 |
tauThermostat = 1e3; |
| 286 |
tauBarostat = 1e4; |
| 287 |
|
| 288 |
dt = 2.0; |
| 289 |
runTime = 1e3; |
| 290 |
|
| 291 |
tempSet = \"true\"; |
| 292 |
thermalTime = 10; |
| 293 |
sampleTime = 100; |
| 294 |
statusTime = 2; |
| 295 |
</MetaData>\n"; |
| 296 |
} |
| 297 |
|
| 298 |
sub findCutoff { |
| 299 |
$boxLength2 = 0.5*$boxLength; |
| 300 |
if ($boxLength2 > $cutoff){ |
| 301 |
# the default is good |
| 302 |
} else { |
| 303 |
$cutoff = int($boxLength2); |
| 304 |
} |
| 305 |
} |
| 306 |
|
| 307 |
sub findAlpha { |
| 308 |
$alpha = $alphaInt - $cutoff*$alphaSlope; |
| 309 |
} |
| 310 |
|
| 311 |
sub printFrameData { |
| 312 |
print OUTFILE |
| 313 |
" <Snapshot> |
| 314 |
<FrameData> |
| 315 |
Time: 0 |
| 316 |
Hmat: {{ $boxLength, 0, 0 }, { 0, $boxLength, 0 }, { 0, 0, $boxLength }} |
| 317 |
</FrameData>\n"; |
| 318 |
} |
| 319 |
|
| 320 |
sub printWaterMD { |
| 321 |
open(WATERMD, ">./water.md") || die "\tError: can't open file water.md\n"; |
| 322 |
$waterFileHandle = 'WATERMD'; |
| 323 |
|
| 324 |
print WATERMD "#ifndef _WATER_MD_\n#define _WATER_MD_\n"; |
| 325 |
printCl(); |
| 326 |
printNa(); |
| 327 |
printSSD_E(); |
| 328 |
printSSD_RF(); |
| 329 |
printSSD(); |
| 330 |
printSSD1(); |
| 331 |
printTRED(); |
| 332 |
printTIP3P(); |
| 333 |
printTIP4P(); |
| 334 |
printTIP4PEw(); |
| 335 |
printTIP5P(); |
| 336 |
printTIP5PE(); |
| 337 |
printSPCE(); |
| 338 |
printSPC(); |
| 339 |
printDPD(); |
| 340 |
print WATERMD "\n\n#endif"; |
| 341 |
} |
| 342 |
|
| 343 |
sub printCl { |
| 344 |
print $waterFileHandle "\n\nmolecule{ |
| 345 |
name = \"Cl-\"; |
| 346 |
|
| 347 |
atom[0]{ |
| 348 |
type = \"Cl-\"; |
| 349 |
position(0.0, 0.0, 0.0); |
| 350 |
} |
| 351 |
}" |
| 352 |
} |
| 353 |
|
| 354 |
sub printNa { |
| 355 |
print $waterFileHandle "\n\nmolecule{ |
| 356 |
name = \"Na+\"; |
| 357 |
|
| 358 |
atom[0]{ |
| 359 |
type = \"Na+\"; |
| 360 |
position(0.0, 0.0, 0.0); |
| 361 |
} |
| 362 |
}" |
| 363 |
} |
| 364 |
|
| 365 |
sub printSSD_E { |
| 366 |
print $waterFileHandle "\n\nmolecule{ |
| 367 |
name = \"SSD_E\"; |
| 368 |
|
| 369 |
atom[0]{ |
| 370 |
type = \"SSD_E\"; |
| 371 |
position( 0.0, 0.0, 0.0 ); |
| 372 |
orientation( 0.0, 0.0, 0.0 ); |
| 373 |
} |
| 374 |
}" |
| 375 |
} |
| 376 |
|
| 377 |
sub printSSD_RF { |
| 378 |
print $waterFileHandle "\n\nmolecule{ |
| 379 |
name = \"SSD_RF\"; |
| 380 |
|
| 381 |
atom[0]{ |
| 382 |
type = \"SSD_RF\"; |
| 383 |
position( 0.0, 0.0, 0.0 ); |
| 384 |
orientation( 0.0, 0.0, 0.0 ); |
| 385 |
} |
| 386 |
}" |
| 387 |
} |
| 388 |
|
| 389 |
sub printSSD { |
| 390 |
print $waterFileHandle "\n\nmolecule{ |
| 391 |
name = \"SSD\"; |
| 392 |
|
| 393 |
atom[0]{ |
| 394 |
type = \"SSD\"; |
| 395 |
position( 0.0, 0.0, 0.0 ); |
| 396 |
orientation( 0.0, 0.0, 0.0 ); |
| 397 |
} |
| 398 |
}" |
| 399 |
} |
| 400 |
|
| 401 |
sub printSSD1 { |
| 402 |
print $waterFileHandle "\n\nmolecule{ |
| 403 |
name = \"SSD1\"; |
| 404 |
|
| 405 |
atom[0]{ |
| 406 |
type = \"SSD1\"; |
| 407 |
position( 0.0, 0.0, 0.0 ); |
| 408 |
orientation( 0.0, 0.0, 0.0 ); |
| 409 |
} |
| 410 |
}" |
| 411 |
} |
| 412 |
|
| 413 |
sub printTRED { |
| 414 |
print $waterFileHandle "\n\nmolecule{ |
| 415 |
name = \"TRED\"; |
| 416 |
|
| 417 |
atom[0]{ |
| 418 |
type = \"TRED\"; |
| 419 |
position( 0.0, 0.0, 0.0 ); |
| 420 |
orientation( 0.0, 0.0, 0.0 ); |
| 421 |
} |
| 422 |
atom[1]{ |
| 423 |
type = \"EP_TRED\"; |
| 424 |
position( 0.0, 0.0, 0.5 ); |
| 425 |
} |
| 426 |
|
| 427 |
rigidBody[0]{ |
| 428 |
members(0, 1); |
| 429 |
} |
| 430 |
|
| 431 |
cutoffGroup{ |
| 432 |
members(0, 1); |
| 433 |
} |
| 434 |
}" |
| 435 |
} |
| 436 |
|
| 437 |
sub printTIP3P { |
| 438 |
print $waterFileHandle "\n\nmolecule{ |
| 439 |
name = \"TIP3P\"; |
| 440 |
|
| 441 |
atom[0]{ |
| 442 |
type = \"O_TIP3P\"; |
| 443 |
position( 0.0, 0.0, -0.06556 ); |
| 444 |
} |
| 445 |
atom[1]{ |
| 446 |
type = \"H_TIP3P\"; |
| 447 |
position( 0.0, 0.75695, 0.52032 ); |
| 448 |
} |
| 449 |
atom[2]{ |
| 450 |
type = \"H_TIP3P\"; |
| 451 |
position( 0.0, -0.75695, 0.52032 ); |
| 452 |
} |
| 453 |
|
| 454 |
rigidBody[0]{ |
| 455 |
members(0, 1, 2); |
| 456 |
} |
| 457 |
|
| 458 |
cutoffGroup{ |
| 459 |
members(0, 1, 2); |
| 460 |
} |
| 461 |
}" |
| 462 |
} |
| 463 |
|
| 464 |
sub printTIP4P { |
| 465 |
print $waterFileHandle "\n\nmolecule{ |
| 466 |
name = \"TIP4P\"; |
| 467 |
|
| 468 |
atom[0]{ |
| 469 |
type = \"O_TIP4P\"; |
| 470 |
position( 0.0, 0.0, -0.06556 ); |
| 471 |
} |
| 472 |
atom[1]{ |
| 473 |
type = \"H_TIP4P\"; |
| 474 |
position( 0.0, 0.75695, 0.52032 ); |
| 475 |
} |
| 476 |
atom[2]{ |
| 477 |
type = \"H_TIP4P\"; |
| 478 |
position( 0.0, -0.75695, 0.52032 ); |
| 479 |
} |
| 480 |
atom[3]{ |
| 481 |
type = \"EP_TIP4P\"; |
| 482 |
position( 0.0, 0.0, 0.08444 ); |
| 483 |
} |
| 484 |
|
| 485 |
rigidBody[0]{ |
| 486 |
members(0, 1, 2, 3); |
| 487 |
} |
| 488 |
|
| 489 |
cutoffGroup{ |
| 490 |
members(0, 1, 2, 3); |
| 491 |
} |
| 492 |
}" |
| 493 |
} |
| 494 |
|
| 495 |
sub printTIP4PEw { |
| 496 |
print $waterFileHandle "\n\nmolecule{ |
| 497 |
name = \"TIP4P-Ew\"; |
| 498 |
|
| 499 |
atom[0]{ |
| 500 |
type = \"O_TIP4P-Ew\"; |
| 501 |
position( 0.0, 0.0, -0.06556 ); |
| 502 |
} |
| 503 |
atom[1]{ |
| 504 |
type = \"H_TIP4P-Ew\"; |
| 505 |
position( 0.0, 0.75695, 0.52032 ); |
| 506 |
} |
| 507 |
atom[2]{ |
| 508 |
type = \"H_TIP4P-Ew\"; |
| 509 |
position( 0.0, -0.75695, 0.52032 ); |
| 510 |
} |
| 511 |
atom[3]{ |
| 512 |
type = \"EP_TIP4P-Ew\"; |
| 513 |
position( 0.0, 0.0, 0.05944 ); |
| 514 |
} |
| 515 |
|
| 516 |
rigidBody[0]{ |
| 517 |
members(0, 1, 2, 3); |
| 518 |
} |
| 519 |
|
| 520 |
cutoffGroup{ |
| 521 |
members(0, 1, 2, 3); |
| 522 |
} |
| 523 |
}" |
| 524 |
} |
| 525 |
|
| 526 |
sub printTIP5P { |
| 527 |
print $waterFileHandle "\n\nmolecule{ |
| 528 |
name = \"TIP5P\"; |
| 529 |
|
| 530 |
atom[0]{ |
| 531 |
type = \"O_TIP5P\"; |
| 532 |
position( 0.0, 0.0, -0.06556 ); |
| 533 |
} |
| 534 |
atom[1]{ |
| 535 |
type = \"H_TIP5P\"; |
| 536 |
position( 0.0, 0.75695, 0.52032 ); |
| 537 |
} |
| 538 |
atom[2]{ |
| 539 |
type = \"H_TIP5P\"; |
| 540 |
position( 0.0, -0.75695, 0.52032 ); |
| 541 |
} |
| 542 |
atom[3]{ |
| 543 |
type = \"EP_TIP5P\"; |
| 544 |
position( 0.57154, 0.0, -0.46971 ); |
| 545 |
} |
| 546 |
atom[4]{ |
| 547 |
type = \"EP_TIP5P\"; |
| 548 |
position( -0.57154, 0.0, -0.46971 ); |
| 549 |
} |
| 550 |
|
| 551 |
rigidBody[0]{ |
| 552 |
members(0, 1, 2, 3, 4); |
| 553 |
} |
| 554 |
|
| 555 |
cutoffGroup{ |
| 556 |
members(0, 1, 2, 3, 4); |
| 557 |
} |
| 558 |
}" |
| 559 |
} |
| 560 |
|
| 561 |
sub printTIP5PE { |
| 562 |
print $waterFileHandle "\n\nmolecule{ |
| 563 |
name = \"TIP5P-E\"; |
| 564 |
|
| 565 |
atom[0]{ |
| 566 |
type = \"O_TIP5P-E\"; |
| 567 |
position( 0.0, 0.0, -0.06556 ); |
| 568 |
} |
| 569 |
atom[1]{ |
| 570 |
type = \"H_TIP5P\"; |
| 571 |
position( 0.0, 0.75695, 0.52032 ); |
| 572 |
} |
| 573 |
atom[2]{ |
| 574 |
type = \"H_TIP5P\"; |
| 575 |
position( 0.0, -0.75695, 0.52032 ); |
| 576 |
} |
| 577 |
atom[3]{ |
| 578 |
type = \"EP_TIP5P\"; |
| 579 |
position( 0.57154, 0.0, -0.46971 ); |
| 580 |
} |
| 581 |
atom[4]{ |
| 582 |
type = \"EP_TIP5P\"; |
| 583 |
position( -0.57154, 0.0, -0.46971 ); |
| 584 |
} |
| 585 |
|
| 586 |
rigidBody[0]{ |
| 587 |
members(0, 1, 2, 3, 4); |
| 588 |
} |
| 589 |
|
| 590 |
cutoffGroup{ |
| 591 |
members(0, 1, 2, 3, 4); |
| 592 |
} |
| 593 |
}" |
| 594 |
} |
| 595 |
|
| 596 |
sub printSPCE { |
| 597 |
print $waterFileHandle "\n\nmolecule{ |
| 598 |
name = \"SPCE\"; |
| 599 |
|
| 600 |
atom[0]{ |
| 601 |
type = \"O_SPCE\"; |
| 602 |
position( 0.0, 0.0, -0.06461 ); |
| 603 |
} |
| 604 |
atom[1]{ |
| 605 |
type = \"H_SPCE\"; |
| 606 |
position( 0.0, 0.81649, 0.51275 ); |
| 607 |
} |
| 608 |
atom[2]{ |
| 609 |
type = \"H_SPCE\"; |
| 610 |
position( 0.0, -0.81649, 0.51275 ); |
| 611 |
} |
| 612 |
|
| 613 |
rigidBody[0]{ |
| 614 |
members(0, 1, 2); |
| 615 |
} |
| 616 |
|
| 617 |
cutoffGroup{ |
| 618 |
members(0, 1, 2); |
| 619 |
} |
| 620 |
}" |
| 621 |
} |
| 622 |
|
| 623 |
sub printSPC { |
| 624 |
print $waterFileHandle "\n\nmolecule{ |
| 625 |
name = \"SPC\"; |
| 626 |
|
| 627 |
atom[0]{ |
| 628 |
type = \"O_SPC\"; |
| 629 |
position( 0.0, 0.0, -0.06461 ); |
| 630 |
} |
| 631 |
atom[1]{ |
| 632 |
type = \"H_SPC\"; |
| 633 |
position( 0.0, 0.81649, 0.51275 ); |
| 634 |
} |
| 635 |
atom[2]{ |
| 636 |
type = \"H_SPC\"; |
| 637 |
position( 0.0, -0.81649, 0.51275 ); |
| 638 |
} |
| 639 |
|
| 640 |
rigidBody[0]{ |
| 641 |
members(0, 1, 2); |
| 642 |
} |
| 643 |
|
| 644 |
cutoffGroup{ |
| 645 |
members(0, 1, 2); |
| 646 |
} |
| 647 |
}" |
| 648 |
} |
| 649 |
|
| 650 |
sub printDPD { |
| 651 |
print $waterFileHandle "\n\nmolecule{ |
| 652 |
name = \"DPD\"; |
| 653 |
|
| 654 |
atom[0]{ |
| 655 |
type = \"DPD\"; |
| 656 |
position(0.0, 0.0, 0.0); |
| 657 |
} |
| 658 |
}" |
| 659 |
} |
| 660 |
|
| 661 |
|
| 662 |
sub printFakeWater { |
| 663 |
print $waterFileHandle "\n\nmolecule{ |
| 664 |
name = \"$waterName\"; |
| 665 |
|
| 666 |
atom[0]{ |
| 667 |
type = \"$waterName\"; |
| 668 |
position(0.0, 0.0, 0.0); |
| 669 |
} |
| 670 |
}" |
| 671 |
} |
| 672 |
|
| 673 |
|
| 674 |
sub validateWater { |
| 675 |
if ($waterName eq 'Cl-') { $waterCase = 0; } |
| 676 |
elsif ($waterName eq 'Na+') { $waterCase = 1; } |
| 677 |
elsif ($waterName eq 'SSD_E') { $waterCase = 2; } |
| 678 |
elsif ($waterName eq 'SSD_RF') { $waterCase = 3; } |
| 679 |
elsif ($waterName eq 'SSD') { $waterCase = 4; } |
| 680 |
elsif ($waterName eq 'SSD1') { $waterCase = 5; } |
| 681 |
elsif ($waterName eq 'TIP3P') { $waterCase = 6; } |
| 682 |
elsif ($waterName eq 'TIP4P') { $waterCase = 7; } |
| 683 |
elsif ($waterName eq 'TIP4P-Ew') { $waterCase = 8; } |
| 684 |
elsif ($waterName eq 'TIP5P') { $waterCase = 9; } |
| 685 |
elsif ($waterName eq 'TIP5P-E') { $waterCase = 10; } |
| 686 |
elsif ($waterName eq 'SPCE') { $waterCase = 11; } |
| 687 |
elsif ($waterName eq 'SPC') { $waterCase = 12; } |
| 688 |
elsif ($waterName eq 'DPD') { $waterCase = 13; } |
| 689 |
else { $invalidWater = 1; } |
| 690 |
} |
| 691 |
|
| 692 |
sub printWaterModel { |
| 693 |
if ($waterCase == 0) { printCl(); } |
| 694 |
elsif ($waterCase == 1) { printNa(); } |
| 695 |
elsif ($waterCase == 2) { printSSD_E(); } |
| 696 |
elsif ($waterCase == 3) { printSSD_RF(); } |
| 697 |
elsif ($waterCase == 4) { printSSD(); } |
| 698 |
elsif ($waterCase == 5) { printSSD1(); } |
| 699 |
elsif ($waterCase == 6) { printTIP3P(); } |
| 700 |
elsif ($waterCase == 7) { printTIP4P(); } |
| 701 |
elsif ($waterCase == 8) { printTIP4PEw(); } |
| 702 |
elsif ($waterCase == 9) { printTIP5P(); } |
| 703 |
elsif ($waterCase == 10) { printTIP5PE(); } |
| 704 |
elsif ($waterCase == 11) { printSPCE(); } |
| 705 |
elsif ($waterCase == 12) { printSPC(); } |
| 706 |
elsif ($waterCase == 13) { printDPD(); } |
| 707 |
} |
