| 1 |
#include <cstdlib> |
| 2 |
#include <iostream> |
| 3 |
#include <cmath> |
| 4 |
|
| 5 |
#include "SimSetup.hpp" |
| 6 |
#include "parse_me.h" |
| 7 |
#include "LRI.hpp" |
| 8 |
#include "Integrator.hpp" |
| 9 |
#include "simError.h" |
| 10 |
|
| 11 |
#ifdef IS_MPI |
| 12 |
#include "mpiBASS.h" |
| 13 |
#include "bassDiag.hpp" |
| 14 |
#endif |
| 15 |
|
| 16 |
SimSetup::SimSetup(){ |
| 17 |
stamps = new MakeStamps(); |
| 18 |
globals = new Globals(); |
| 19 |
|
| 20 |
#ifdef IS_MPI |
| 21 |
strcpy( checkPointMsg, "SimSetup creation successful" ); |
| 22 |
MPIcheckPoint(); |
| 23 |
#endif // IS_MPI |
| 24 |
} |
| 25 |
|
| 26 |
SimSetup::~SimSetup(){ |
| 27 |
delete stamps; |
| 28 |
delete globals; |
| 29 |
} |
| 30 |
|
| 31 |
void SimSetup::parseFile( char* fileName ){ |
| 32 |
|
| 33 |
#ifdef IS_MPI |
| 34 |
if( worldRank == 0 ){ |
| 35 |
#endif // is_mpi |
| 36 |
|
| 37 |
inFileName = fileName; |
| 38 |
set_interface_stamps( stamps, globals ); |
| 39 |
|
| 40 |
#ifdef IS_MPI |
| 41 |
mpiEventInit(); |
| 42 |
#endif |
| 43 |
|
| 44 |
yacc_BASS( fileName ); |
| 45 |
|
| 46 |
#ifdef IS_MPI |
| 47 |
throwMPIEvent(NULL); |
| 48 |
} |
| 49 |
else receiveParse(); |
| 50 |
#endif |
| 51 |
|
| 52 |
} |
| 53 |
|
| 54 |
#ifdef IS_MPI |
| 55 |
void SimSetup::receiveParse(void){ |
| 56 |
|
| 57 |
set_interface_stamps( stamps, globals ); |
| 58 |
mpiEventInit(); |
| 59 |
MPIcheckPoint(); |
| 60 |
mpiEventLoop(); |
| 61 |
|
| 62 |
} |
| 63 |
|
| 64 |
|
| 65 |
void SimSetup::testMe(void){ |
| 66 |
bassDiag* dumpMe = new bassDiag(globals,stamps); |
| 67 |
dumpMe->dumpStamps(); |
| 68 |
delete dumpMe; |
| 69 |
} |
| 70 |
#endif |
| 71 |
|
| 72 |
void SimSetup::createSim( void ){ |
| 73 |
|
| 74 |
MakeStamps *the_stamps; |
| 75 |
Globals* the_globals; |
| 76 |
int i, j; |
| 77 |
|
| 78 |
// get the stamps and globals; |
| 79 |
the_stamps = stamps; |
| 80 |
the_globals = globals; |
| 81 |
|
| 82 |
// set the easy ones first |
| 83 |
simnfo->target_temp = the_globals->getTargetTemp(); |
| 84 |
simnfo->dt = the_globals->getDt(); |
| 85 |
simnfo->run_time = the_globals->getRunTime(); |
| 86 |
|
| 87 |
// get the ones we know are there, yet still may need some work. |
| 88 |
n_components = the_globals->getNComponents(); |
| 89 |
strcpy( force_field, the_globals->getForceField() ); |
| 90 |
strcpy( ensemble, the_globals->getEnsemble() ); |
| 91 |
|
| 92 |
if( !strcmp( force_field, "TraPPE" ) ) the_ff = new TraPPEFF(); |
| 93 |
else if( !strcmp( force_field, "DipoleTest" ) ) the_ff = new DipoleTestFF(); |
| 94 |
else if( !strcmp( force_field, "TraPPE_Ex" ) ) the_ff = new TraPPE_ExFF(); |
| 95 |
else{ |
| 96 |
sprintf( painCave.errMsg, |
| 97 |
"SimSetup Error. Unrecognized force field -> %s\n", |
| 98 |
force_field ); |
| 99 |
painCave.isFatal = 1; |
| 100 |
simError(); |
| 101 |
} |
| 102 |
|
| 103 |
#ifdef IS_MPI |
| 104 |
strcpy( checkPointMsg, "ForceField creation successful" ); |
| 105 |
MPIcheckPoint(); |
| 106 |
#endif // is_mpi |
| 107 |
|
| 108 |
// get the components and calculate the tot_nMol and indvidual n_mol |
| 109 |
the_components = the_globals->getComponents(); |
| 110 |
components_nmol = new int[n_components]; |
| 111 |
comp_stamps = new MoleculeStamp*[n_components]; |
| 112 |
|
| 113 |
if( !the_globals->haveNMol() ){ |
| 114 |
// we don't have the total number of molecules, so we assume it is |
| 115 |
// given in each component |
| 116 |
|
| 117 |
tot_nmol = 0; |
| 118 |
for( i=0; i<n_components; i++ ){ |
| 119 |
|
| 120 |
if( !the_components[i]->haveNMol() ){ |
| 121 |
// we have a problem |
| 122 |
sprintf( painCave.errMsg, |
| 123 |
"SimSetup Error. No global NMol or component NMol" |
| 124 |
" given. Cannot calculate the number of atoms.\n" ); |
| 125 |
painCave.isFatal = 1; |
| 126 |
simError(); |
| 127 |
} |
| 128 |
|
| 129 |
tot_nmol += the_components[i]->getNMol(); |
| 130 |
components_nmol[i] = the_components[i]->getNMol(); |
| 131 |
} |
| 132 |
} |
| 133 |
else{ |
| 134 |
sprintf( painCave.errMsg, |
| 135 |
"SimSetup error.\n" |
| 136 |
"\tSorry, the ability to specify total" |
| 137 |
" nMols and then give molfractions in the components\n" |
| 138 |
"\tis not currently supported." |
| 139 |
" Please give nMol in the components.\n" ); |
| 140 |
painCave.isFatal = 1; |
| 141 |
simError(); |
| 142 |
|
| 143 |
|
| 144 |
// tot_nmol = the_globals->getNMol(); |
| 145 |
|
| 146 |
// //we have the total number of molecules, now we check for molfractions |
| 147 |
// for( i=0; i<n_components; i++ ){ |
| 148 |
|
| 149 |
// if( !the_components[i]->haveMolFraction() ){ |
| 150 |
|
| 151 |
// if( !the_components[i]->haveNMol() ){ |
| 152 |
// //we have a problem |
| 153 |
// std::cerr << "SimSetup error. Neither molFraction nor " |
| 154 |
// << " nMol was given in component |
| 155 |
|
| 156 |
} |
| 157 |
|
| 158 |
#ifdef IS_MPI |
| 159 |
strcpy( checkPointMsg, "Have the number of components" ); |
| 160 |
MPIcheckPoint(); |
| 161 |
#endif // is_mpi |
| 162 |
|
| 163 |
// make an array of molecule stamps that match the components used. |
| 164 |
// also extract the used stamps out into a separate linked list |
| 165 |
|
| 166 |
simnfo->nComponents = n_components; |
| 167 |
simnfo->componentsNmol = components_nmol; |
| 168 |
simnfo->compStamps = comp_stamps; |
| 169 |
simnfo->headStamp = new LinkedMolStamp(); |
| 170 |
|
| 171 |
char* id; |
| 172 |
LinkedMolStamp* headStamp = simnfo->headStamp; |
| 173 |
LinkedMolStamp* currentStamp = NULL; |
| 174 |
for( i=0; i<n_components; i++ ){ |
| 175 |
|
| 176 |
id = the_components[i]->getType(); |
| 177 |
comp_stamps[i] = NULL; |
| 178 |
|
| 179 |
// check to make sure the component isn't already in the list |
| 180 |
|
| 181 |
comp_stamps[i] = headStamp->match( id ); |
| 182 |
if( comp_stamps[i] == NULL ){ |
| 183 |
|
| 184 |
// extract the component from the list; |
| 185 |
|
| 186 |
currentStamp = the_stamps->extractMolStamp( id ); |
| 187 |
if( currentStamp == NULL ){ |
| 188 |
sprintf( painCave.errMsg, |
| 189 |
"SimSetup error: Component \"%s\" was not found in the " |
| 190 |
"list of declared molecules\n" |
| 191 |
id ); |
| 192 |
painCave.isFatal = 1; |
| 193 |
simError(); |
| 194 |
} |
| 195 |
|
| 196 |
headStamp->add( currentStamp ); |
| 197 |
comp_stamps[i] = headStamp->match( id ); |
| 198 |
} |
| 199 |
} |
| 200 |
|
| 201 |
#ifdef IS_MPI |
| 202 |
strcpy( checkPointMsg, "Component stamps successfully extracted\n" ); |
| 203 |
MPIcheckPoint(); |
| 204 |
#endif // is_mpi |
| 205 |
|
| 206 |
|
| 207 |
|
| 208 |
|
| 209 |
// caclulate the number of atoms, bonds, bends and torsions |
| 210 |
|
| 211 |
tot_atoms = 0; |
| 212 |
tot_bonds = 0; |
| 213 |
tot_bends = 0; |
| 214 |
tot_torsions = 0; |
| 215 |
for( i=0; i<n_components; i++ ){ |
| 216 |
|
| 217 |
tot_atoms += components_nmol[i] * comp_stamps[i]->getNAtoms(); |
| 218 |
tot_bonds += components_nmol[i] * comp_stamps[i]->getNBonds(); |
| 219 |
tot_bends += components_nmol[i] * comp_stamps[i]->getNBends(); |
| 220 |
tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions(); |
| 221 |
} |
| 222 |
|
| 223 |
tot_SRI = tot_bonds + tot_bends + tot_torsions; |
| 224 |
|
| 225 |
simnfo->n_atoms = tot_atoms; |
| 226 |
simnfo->n_bonds = tot_bonds; |
| 227 |
simnfo->n_bends = tot_bends; |
| 228 |
simnfo->n_torsions = tot_torsions; |
| 229 |
simnfo->n_SRI = tot_SRI; |
| 230 |
simnfo->n_mol = tot_nmol; |
| 231 |
|
| 232 |
|
| 233 |
#ifdef IS_MPI |
| 234 |
|
| 235 |
// divide the molecules among processors here. |
| 236 |
|
| 237 |
mpiSimulation* mpiSim = new mpiSimulation( simnfo ); |
| 238 |
|
| 239 |
mpiSim->divideLabor(); |
| 240 |
|
| 241 |
// set up the local variables |
| 242 |
|
| 243 |
int localMol; |
| 244 |
int local_atoms, local_bonds, local_bends, local_torsions, local_SRI; |
| 245 |
|
| 246 |
localMol = 0; |
| 247 |
local_atoms = 0; |
| 248 |
local_bonds = 0; |
| 249 |
local_bends = 0; |
| 250 |
local_torsions = 0; |
| 251 |
for( i=0; i<n_components; i++ ){ |
| 252 |
|
| 253 |
for( j=0; j<components_nmol[i]; j++ ){ |
| 254 |
|
| 255 |
if( mpiSim->getMyMolStart() <= j && |
| 256 |
j <= mpiSim->getMyMolEnd() ){ |
| 257 |
|
| 258 |
local_atoms += comp_stamps[i]->getNAtoms(); |
| 259 |
local_bonds += comp_stamps[i]->getNBonds(); |
| 260 |
local_bends += comp_stamps[i]->getNBends(); |
| 261 |
local_torsions += comp_stamps[i]->getNTorsions(); |
| 262 |
localMol++; |
| 263 |
} |
| 264 |
} |
| 265 |
} |
| 266 |
|
| 267 |
|
| 268 |
|
| 269 |
simnfo->n_atoms = mpiSim->getMyNlocal(); |
| 270 |
|
| 271 |
|
| 272 |
#endif // is_mpi |
| 273 |
|
| 274 |
|
| 275 |
// create the atom and short range interaction arrays |
| 276 |
|
| 277 |
Atom::createArrays(simnfo->n_atoms); |
| 278 |
the_atoms = new Atom*[simnfo->n_atoms]; |
| 279 |
the_molecules = new Molecule[simnfo->n_mol]; |
| 280 |
|
| 281 |
|
| 282 |
if( simnfo->n_SRI ){ |
| 283 |
the_sris = new SRI*[simnfo->n_SRI]; |
| 284 |
the_excludes = new ex_pair[simnfo->n_SRI]; |
| 285 |
} |
| 286 |
|
| 287 |
// set the arrays into the SimInfo object |
| 288 |
|
| 289 |
simnfo->atoms = the_atoms; |
| 290 |
simnfo->sr_interactions = the_sris; |
| 291 |
simnfo->n_exclude = tot_SRI; |
| 292 |
simnfo->excludes = the_excludes; |
| 293 |
|
| 294 |
|
| 295 |
// initialize the arrays |
| 296 |
|
| 297 |
the_ff->setSimInfo( simnfo ); |
| 298 |
|
| 299 |
makeAtoms(); |
| 300 |
|
| 301 |
if( tot_bonds ){ |
| 302 |
makeBonds(); |
| 303 |
} |
| 304 |
|
| 305 |
if( tot_bends ){ |
| 306 |
makeBends(); |
| 307 |
} |
| 308 |
|
| 309 |
if( tot_torsions ){ |
| 310 |
makeTorsions(); |
| 311 |
} |
| 312 |
|
| 313 |
|
| 314 |
// get some of the tricky things that may still be in the globals |
| 315 |
|
| 316 |
if( simnfo->n_dipoles ){ |
| 317 |
|
| 318 |
if( !the_globals->haveRRF() ){ |
| 319 |
sprintf( painCave.errMsg, |
| 320 |
"SimSetup Error, system has dipoles, but no rRF was set.\n"); |
| 321 |
painCave.isFatal = 1; |
| 322 |
simError(); |
| 323 |
} |
| 324 |
if( !the_globals->haveDielectric() ){ |
| 325 |
sprintf( painCave.errMsg, |
| 326 |
"SimSetup Error, system has dipoles, but no" |
| 327 |
" dielectric was set.\n" ); |
| 328 |
painCave.isFatal = 1; |
| 329 |
simError(); |
| 330 |
} |
| 331 |
|
| 332 |
simnfo->rRF = the_globals->getRRF(); |
| 333 |
simnfo->dielectric = the_globals->getDielectric(); |
| 334 |
} |
| 335 |
|
| 336 |
#ifdef IS_MPI |
| 337 |
strcpy( checkPointMsg, "rRf and dielectric check out" ); |
| 338 |
MPIcheckPoint(); |
| 339 |
#endif // is_mpi |
| 340 |
|
| 341 |
if( the_globals->haveBox() ){ |
| 342 |
simnfo->box_x = the_globals->getBox(); |
| 343 |
simnfo->box_y = the_globals->getBox(); |
| 344 |
simnfo->box_z = the_globals->getBox(); |
| 345 |
} |
| 346 |
else if( the_globals->haveDensity() ){ |
| 347 |
|
| 348 |
double vol; |
| 349 |
vol = (double)tot_nmol / the_globals->getDensity(); |
| 350 |
simnfo->box_x = pow( vol, ( 1.0 / 3.0 ) ); |
| 351 |
simnfo->box_y = simnfo->box_x; |
| 352 |
simnfo->box_z = simnfo->box_x; |
| 353 |
} |
| 354 |
else{ |
| 355 |
if( !the_globals->haveBoxX() ){ |
| 356 |
sprintf( painCave.errMsg, |
| 357 |
"SimSetup error, no periodic BoxX size given.\n" ); |
| 358 |
painCave.isFatal = 1; |
| 359 |
simError(); |
| 360 |
} |
| 361 |
simnfo->box_x = the_globals->getBoxX(); |
| 362 |
|
| 363 |
if( !the_globals->haveBoxY() ){ |
| 364 |
sprintf( painCave.errMsg, |
| 365 |
"SimSetup error, no periodic BoxY size given.\n" ); |
| 366 |
painCave.isFatal = 1; |
| 367 |
simError(); |
| 368 |
} |
| 369 |
simnfo->box_y = the_globals->getBoxY(); |
| 370 |
|
| 371 |
if( !the_globals->haveBoxZ() ){ |
| 372 |
sprintf( painCave.errMsg, |
| 373 |
"SimSetup error, no periodic BoxZ size given.\n" ); |
| 374 |
painCave.isFatal = 1; |
| 375 |
simError(); |
| 376 |
} |
| 377 |
simnfo->box_z = the_globals->getBoxZ(); |
| 378 |
} |
| 379 |
|
| 380 |
#ifdef IS_MPI |
| 381 |
strcpy( checkPointMsg, "Box size set up" ); |
| 382 |
MPIcheckPoint(); |
| 383 |
#endif // is_mpi |
| 384 |
|
| 385 |
|
| 386 |
|
| 387 |
// if( the_globals->haveInitialConfig() ){ |
| 388 |
// InitializeFromFile* fileInit; |
| 389 |
// fileInit = new InitializeFromFile( the_globals->getInitialConfig() ); |
| 390 |
|
| 391 |
// fileInit->read_xyz( simnfo ); // default velocities on |
| 392 |
|
| 393 |
// delete fileInit; |
| 394 |
// } |
| 395 |
// else{ |
| 396 |
|
| 397 |
#ifdef IS_MPI |
| 398 |
|
| 399 |
// no init from bass |
| 400 |
|
| 401 |
sprintf( painCave.errMsg, |
| 402 |
"Cannot intialize a parallel simulation without an initial configuration file.\n" ); |
| 403 |
painCave.isFatal; |
| 404 |
simError(); |
| 405 |
|
| 406 |
#else |
| 407 |
|
| 408 |
initFromBass(); |
| 409 |
|
| 410 |
#endif // is_mpi |
| 411 |
|
| 412 |
#ifdef IS_MPI |
| 413 |
strcpy( checkPointMsg, "Successfully read in the initial configuration" ); |
| 414 |
MPIcheckPoint(); |
| 415 |
#endif // is_mpi |
| 416 |
|
| 417 |
|
| 418 |
|
| 419 |
|
| 420 |
|
| 421 |
// } |
| 422 |
|
| 423 |
#ifdef IS_MPI |
| 424 |
if( worldRank == 0 ){ |
| 425 |
#endif // is_mpi |
| 426 |
|
| 427 |
if( the_globals->haveFinalConfig() ){ |
| 428 |
strcpy( simnfo->finalName, the_globals->getFinalConfig() ); |
| 429 |
} |
| 430 |
else{ |
| 431 |
strcpy( simnfo->finalName, inFileName ); |
| 432 |
char* endTest; |
| 433 |
int nameLength = strlen( simnfo->finalName ); |
| 434 |
endTest = &(simnfo->finalName[nameLength - 5]); |
| 435 |
if( !strcmp( endTest, ".bass" ) ){ |
| 436 |
strcpy( endTest, ".eor" ); |
| 437 |
} |
| 438 |
else if( !strcmp( endTest, ".BASS" ) ){ |
| 439 |
strcpy( endTest, ".eor" ); |
| 440 |
} |
| 441 |
else{ |
| 442 |
endTest = &(simnfo->finalName[nameLength - 4]); |
| 443 |
if( !strcmp( endTest, ".bss" ) ){ |
| 444 |
strcpy( endTest, ".eor" ); |
| 445 |
} |
| 446 |
else if( !strcmp( endTest, ".mdl" ) ){ |
| 447 |
strcpy( endTest, ".eor" ); |
| 448 |
} |
| 449 |
else{ |
| 450 |
strcat( simnfo->finalName, ".eor" ); |
| 451 |
} |
| 452 |
} |
| 453 |
} |
| 454 |
|
| 455 |
// make the sample and status out names |
| 456 |
|
| 457 |
strcpy( simnfo->sampleName, inFileName ); |
| 458 |
char* endTest; |
| 459 |
int nameLength = strlen( simnfo->sampleName ); |
| 460 |
endTest = &(simnfo->sampleName[nameLength - 5]); |
| 461 |
if( !strcmp( endTest, ".bass" ) ){ |
| 462 |
strcpy( endTest, ".dump" ); |
| 463 |
} |
| 464 |
else if( !strcmp( endTest, ".BASS" ) ){ |
| 465 |
strcpy( endTest, ".dump" ); |
| 466 |
} |
| 467 |
else{ |
| 468 |
endTest = &(simnfo->sampleName[nameLength - 4]); |
| 469 |
if( !strcmp( endTest, ".bss" ) ){ |
| 470 |
strcpy( endTest, ".dump" ); |
| 471 |
} |
| 472 |
else if( !strcmp( endTest, ".mdl" ) ){ |
| 473 |
strcpy( endTest, ".dump" ); |
| 474 |
} |
| 475 |
else{ |
| 476 |
strcat( simnfo->sampleName, ".dump" ); |
| 477 |
} |
| 478 |
} |
| 479 |
|
| 480 |
strcpy( simnfo->statusName, inFileName ); |
| 481 |
nameLength = strlen( simnfo->statusName ); |
| 482 |
endTest = &(simnfo->statusName[nameLength - 5]); |
| 483 |
if( !strcmp( endTest, ".bass" ) ){ |
| 484 |
strcpy( endTest, ".stat" ); |
| 485 |
} |
| 486 |
else if( !strcmp( endTest, ".BASS" ) ){ |
| 487 |
strcpy( endTest, ".stat" ); |
| 488 |
} |
| 489 |
else{ |
| 490 |
endTest = &(simnfo->statusName[nameLength - 4]); |
| 491 |
if( !strcmp( endTest, ".bss" ) ){ |
| 492 |
strcpy( endTest, ".stat" ); |
| 493 |
} |
| 494 |
else if( !strcmp( endTest, ".mdl" ) ){ |
| 495 |
strcpy( endTest, ".stat" ); |
| 496 |
} |
| 497 |
else{ |
| 498 |
strcat( simnfo->statusName, ".stat" ); |
| 499 |
} |
| 500 |
} |
| 501 |
|
| 502 |
#ifdef IS_MPI |
| 503 |
} |
| 504 |
#endif // is_mpi |
| 505 |
|
| 506 |
// set the status, sample, and themal kick times |
| 507 |
|
| 508 |
if( the_globals->haveSampleTime() ){ |
| 509 |
simnfo->sampleTime = the_globals->getSampleTime(); |
| 510 |
simnfo->statusTime = simnfo->sampleTime; |
| 511 |
simnfo->thermalTime = simnfo->sampleTime; |
| 512 |
} |
| 513 |
else{ |
| 514 |
simnfo->sampleTime = the_globals->getRunTime(); |
| 515 |
simnfo->statusTime = simnfo->sampleTime; |
| 516 |
simnfo->thermalTime = simnfo->sampleTime; |
| 517 |
} |
| 518 |
|
| 519 |
if( the_globals->haveStatusTime() ){ |
| 520 |
simnfo->statusTime = the_globals->getStatusTime(); |
| 521 |
} |
| 522 |
|
| 523 |
if( the_globals->haveThermalTime() ){ |
| 524 |
simnfo->thermalTime = the_globals->getThermalTime(); |
| 525 |
} |
| 526 |
|
| 527 |
// check for the temperature set flag |
| 528 |
|
| 529 |
if( the_globals->haveTempSet() ) simnfo->setTemp = the_globals->getTempSet(); |
| 530 |
|
| 531 |
|
| 532 |
// make the longe range forces and the integrator |
| 533 |
|
| 534 |
new AllLong( simnfo ); |
| 535 |
|
| 536 |
if( !strcmp( force_field, "TraPPE" ) ) new Verlet( *simnfo ); |
| 537 |
if( !strcmp( force_field, "DipoleTest" ) ) new Symplectic( simnfo ); |
| 538 |
if( !strcmp( force_field, "TraPPE_Ex" ) ) new Symplectic( simnfo ); |
| 539 |
} |
| 540 |
|
| 541 |
void SimSetup::makeAtoms( void ){ |
| 542 |
|
| 543 |
int i, j, k, index; |
| 544 |
double ux, uy, uz, uSqr, u; |
| 545 |
AtomStamp* current_atom; |
| 546 |
DirectionalAtom* dAtom; |
| 547 |
int molIndex, molStart, molEnd, nMemb; |
| 548 |
|
| 549 |
|
| 550 |
molIndex = 0; |
| 551 |
index = 0; |
| 552 |
for( i=0; i<n_components; i++ ){ |
| 553 |
|
| 554 |
for( j=0; j<components_nmol[i]; j++ ){ |
| 555 |
|
| 556 |
molStart = index; |
| 557 |
nMemb = comp_stamps[i]->getNAtoms(); |
| 558 |
for( k=0; k<comp_stamps[i]->getNAtoms(); k++ ){ |
| 559 |
|
| 560 |
current_atom = comp_stamps[i]->getAtom( k ); |
| 561 |
if( current_atom->haveOrientation() ){ |
| 562 |
|
| 563 |
dAtom = new DirectionalAtom(index); |
| 564 |
simnfo->n_oriented++; |
| 565 |
the_atoms[index] = dAtom; |
| 566 |
|
| 567 |
ux = current_atom->getOrntX(); |
| 568 |
uy = current_atom->getOrntY(); |
| 569 |
uz = current_atom->getOrntZ(); |
| 570 |
|
| 571 |
uSqr = (ux * ux) + (uy * uy) + (uz * uz); |
| 572 |
|
| 573 |
u = sqrt( uSqr ); |
| 574 |
ux = ux / u; |
| 575 |
uy = uy / u; |
| 576 |
uz = uz / u; |
| 577 |
|
| 578 |
dAtom->setSUx( ux ); |
| 579 |
dAtom->setSUy( uy ); |
| 580 |
dAtom->setSUz( uz ); |
| 581 |
} |
| 582 |
else{ |
| 583 |
the_atoms[index] = new GeneralAtom(index); |
| 584 |
} |
| 585 |
the_atoms[index]->setType( current_atom->getType() ); |
| 586 |
the_atoms[index]->setIndex( index ); |
| 587 |
|
| 588 |
// increment the index and repeat; |
| 589 |
index++; |
| 590 |
} |
| 591 |
|
| 592 |
molEnd = index -1; |
| 593 |
the_molecules[molIndex].setNMembers( nMemb ); |
| 594 |
the_molecules[molIndex].setStartAtom( molStart ); |
| 595 |
the_molecules[molIndex].setEndAtom( molEnd ); |
| 596 |
the_molecules[molIndex].setStampID( i ); |
| 597 |
molIndex++; |
| 598 |
|
| 599 |
} |
| 600 |
} |
| 601 |
|
| 602 |
the_ff->initializeAtoms(); |
| 603 |
} |
| 604 |
|
| 605 |
void SimSetup::makeBonds( void ){ |
| 606 |
|
| 607 |
int i, j, k, index, offset; |
| 608 |
bond_pair* the_bonds; |
| 609 |
BondStamp* current_bond; |
| 610 |
|
| 611 |
the_bonds = new bond_pair[tot_bonds]; |
| 612 |
index = 0; |
| 613 |
offset = 0; |
| 614 |
for( i=0; i<n_components; i++ ){ |
| 615 |
|
| 616 |
for( j=0; j<components_nmol[i]; j++ ){ |
| 617 |
|
| 618 |
for( k=0; k<comp_stamps[i]->getNBonds(); k++ ){ |
| 619 |
|
| 620 |
current_bond = comp_stamps[i]->getBond( k ); |
| 621 |
the_bonds[index].a = current_bond->getA() + offset; |
| 622 |
the_bonds[index].b = current_bond->getB() + offset; |
| 623 |
|
| 624 |
the_excludes[index].i = the_bonds[index].a; |
| 625 |
the_excludes[index].j = the_bonds[index].b; |
| 626 |
|
| 627 |
// increment the index and repeat; |
| 628 |
index++; |
| 629 |
} |
| 630 |
offset += comp_stamps[i]->getNAtoms(); |
| 631 |
} |
| 632 |
} |
| 633 |
|
| 634 |
the_ff->initializeBonds( the_bonds ); |
| 635 |
} |
| 636 |
|
| 637 |
void SimSetup::makeBends( void ){ |
| 638 |
|
| 639 |
int i, j, k, index, offset; |
| 640 |
bend_set* the_bends; |
| 641 |
BendStamp* current_bend; |
| 642 |
|
| 643 |
the_bends = new bend_set[tot_bends]; |
| 644 |
index = 0; |
| 645 |
offset = 0; |
| 646 |
for( i=0; i<n_components; i++ ){ |
| 647 |
|
| 648 |
for( j=0; j<components_nmol[i]; j++ ){ |
| 649 |
|
| 650 |
for( k=0; k<comp_stamps[i]->getNBends(); k++ ){ |
| 651 |
|
| 652 |
current_bend = comp_stamps[i]->getBend( k ); |
| 653 |
the_bends[index].a = current_bend->getA() + offset; |
| 654 |
the_bends[index].b = current_bend->getB() + offset; |
| 655 |
the_bends[index].c = current_bend->getC() + offset; |
| 656 |
|
| 657 |
the_excludes[index + tot_bonds].i = the_bends[index].a; |
| 658 |
the_excludes[index + tot_bonds].j = the_bends[index].c; |
| 659 |
|
| 660 |
// increment the index and repeat; |
| 661 |
index++; |
| 662 |
} |
| 663 |
offset += comp_stamps[i]->getNAtoms(); |
| 664 |
} |
| 665 |
} |
| 666 |
|
| 667 |
the_ff->initializeBends( the_bends ); |
| 668 |
} |
| 669 |
|
| 670 |
void SimSetup::makeTorsions( void ){ |
| 671 |
|
| 672 |
int i, j, k, index, offset; |
| 673 |
torsion_set* the_torsions; |
| 674 |
TorsionStamp* current_torsion; |
| 675 |
|
| 676 |
the_torsions = new torsion_set[tot_torsions]; |
| 677 |
index = 0; |
| 678 |
offset = 0; |
| 679 |
for( i=0; i<n_components; i++ ){ |
| 680 |
|
| 681 |
for( j=0; j<components_nmol[i]; j++ ){ |
| 682 |
|
| 683 |
for( k=0; k<comp_stamps[i]->getNTorsions(); k++ ){ |
| 684 |
|
| 685 |
current_torsion = comp_stamps[i]->getTorsion( k ); |
| 686 |
the_torsions[index].a = current_torsion->getA() + offset; |
| 687 |
the_torsions[index].b = current_torsion->getB() + offset; |
| 688 |
the_torsions[index].c = current_torsion->getC() + offset; |
| 689 |
the_torsions[index].d = current_torsion->getD() + offset; |
| 690 |
|
| 691 |
the_excludes[index + tot_bonds + tot_bends].i = the_torsions[index].a; |
| 692 |
the_excludes[index + tot_bonds + tot_bends].j = the_torsions[index].d; |
| 693 |
|
| 694 |
// increment the index and repeat; |
| 695 |
index++; |
| 696 |
} |
| 697 |
offset += comp_stamps[i]->getNAtoms(); |
| 698 |
} |
| 699 |
} |
| 700 |
|
| 701 |
the_ff->initializeTorsions( the_torsions ); |
| 702 |
} |
| 703 |
|
| 704 |
void SimSetup::initFromBass( void ){ |
| 705 |
|
| 706 |
int i, j, k; |
| 707 |
int n_cells; |
| 708 |
double cellx, celly, cellz; |
| 709 |
double temp1, temp2, temp3; |
| 710 |
int n_per_extra; |
| 711 |
int n_extra; |
| 712 |
int have_extra, done; |
| 713 |
|
| 714 |
temp1 = (double)tot_nmol / 4.0; |
| 715 |
temp2 = pow( temp1, ( 1.0 / 3.0 ) ); |
| 716 |
temp3 = ceil( temp2 ); |
| 717 |
|
| 718 |
have_extra =0; |
| 719 |
if( temp2 < temp3 ){ // we have a non-complete lattice |
| 720 |
have_extra =1; |
| 721 |
|
| 722 |
n_cells = (int)temp3 - 1; |
| 723 |
cellx = simnfo->box_x / temp3; |
| 724 |
celly = simnfo->box_y / temp3; |
| 725 |
cellz = simnfo->box_z / temp3; |
| 726 |
n_extra = tot_nmol - ( 4 * n_cells * n_cells * n_cells ); |
| 727 |
temp1 = ((double)n_extra) / ( pow( temp3, 3.0 ) - pow( n_cells, 3.0 ) ); |
| 728 |
n_per_extra = (int)ceil( temp1 ); |
| 729 |
|
| 730 |
if( n_per_extra > 4){ |
| 731 |
sprintf( painCave.errMsg, |
| 732 |
"SimSetup error. There has been an error in constructing" |
| 733 |
" the non-complete lattice.\n" ); |
| 734 |
painCave.isFatal = 1; |
| 735 |
simError(); |
| 736 |
} |
| 737 |
} |
| 738 |
else{ |
| 739 |
n_cells = (int)temp3; |
| 740 |
cellx = simnfo->box_x / temp3; |
| 741 |
celly = simnfo->box_y / temp3; |
| 742 |
cellz = simnfo->box_z / temp3; |
| 743 |
} |
| 744 |
|
| 745 |
current_mol = 0; |
| 746 |
current_comp_mol = 0; |
| 747 |
current_comp = 0; |
| 748 |
current_atom_ndx = 0; |
| 749 |
|
| 750 |
for( i=0; i < n_cells ; i++ ){ |
| 751 |
for( j=0; j < n_cells; j++ ){ |
| 752 |
for( k=0; k < n_cells; k++ ){ |
| 753 |
|
| 754 |
makeElement( i * cellx, |
| 755 |
j * celly, |
| 756 |
k * cellz ); |
| 757 |
|
| 758 |
makeElement( i * cellx + 0.5 * cellx, |
| 759 |
j * celly + 0.5 * celly, |
| 760 |
k * cellz ); |
| 761 |
|
| 762 |
makeElement( i * cellx, |
| 763 |
j * celly + 0.5 * celly, |
| 764 |
k * cellz + 0.5 * cellz ); |
| 765 |
|
| 766 |
makeElement( i * cellx + 0.5 * cellx, |
| 767 |
j * celly, |
| 768 |
k * cellz + 0.5 * cellz ); |
| 769 |
} |
| 770 |
} |
| 771 |
} |
| 772 |
|
| 773 |
if( have_extra ){ |
| 774 |
done = 0; |
| 775 |
|
| 776 |
int start_ndx; |
| 777 |
for( i=0; i < (n_cells+1) && !done; i++ ){ |
| 778 |
for( j=0; j < (n_cells+1) && !done; j++ ){ |
| 779 |
|
| 780 |
if( i < n_cells ){ |
| 781 |
|
| 782 |
if( j < n_cells ){ |
| 783 |
start_ndx = n_cells; |
| 784 |
} |
| 785 |
else start_ndx = 0; |
| 786 |
} |
| 787 |
else start_ndx = 0; |
| 788 |
|
| 789 |
for( k=start_ndx; k < (n_cells+1) && !done; k++ ){ |
| 790 |
|
| 791 |
makeElement( i * cellx, |
| 792 |
j * celly, |
| 793 |
k * cellz ); |
| 794 |
done = ( current_mol >= tot_nmol ); |
| 795 |
|
| 796 |
if( !done && n_per_extra > 1 ){ |
| 797 |
makeElement( i * cellx + 0.5 * cellx, |
| 798 |
j * celly + 0.5 * celly, |
| 799 |
k * cellz ); |
| 800 |
done = ( current_mol >= tot_nmol ); |
| 801 |
} |
| 802 |
|
| 803 |
if( !done && n_per_extra > 2){ |
| 804 |
makeElement( i * cellx, |
| 805 |
j * celly + 0.5 * celly, |
| 806 |
k * cellz + 0.5 * cellz ); |
| 807 |
done = ( current_mol >= tot_nmol ); |
| 808 |
} |
| 809 |
|
| 810 |
if( !done && n_per_extra > 3){ |
| 811 |
makeElement( i * cellx + 0.5 * cellx, |
| 812 |
j * celly, |
| 813 |
k * cellz + 0.5 * cellz ); |
| 814 |
done = ( current_mol >= tot_nmol ); |
| 815 |
} |
| 816 |
} |
| 817 |
} |
| 818 |
} |
| 819 |
} |
| 820 |
|
| 821 |
|
| 822 |
for( i=0; i<simnfo->n_atoms; i++ ){ |
| 823 |
simnfo->atoms[i]->set_vx( 0.0 ); |
| 824 |
simnfo->atoms[i]->set_vy( 0.0 ); |
| 825 |
simnfo->atoms[i]->set_vz( 0.0 ); |
| 826 |
} |
| 827 |
} |
| 828 |
|
| 829 |
void SimSetup::makeElement( double x, double y, double z ){ |
| 830 |
|
| 831 |
int k; |
| 832 |
AtomStamp* current_atom; |
| 833 |
DirectionalAtom* dAtom; |
| 834 |
double rotMat[3][3]; |
| 835 |
|
| 836 |
for( k=0; k<comp_stamps[current_comp]->getNAtoms(); k++ ){ |
| 837 |
|
| 838 |
current_atom = comp_stamps[current_comp]->getAtom( k ); |
| 839 |
if( !current_atom->havePosition() ){ |
| 840 |
sprintf( painCave.errMsg, |
| 841 |
"SimSetup:initFromBass error.\n" |
| 842 |
"\tComponent %s, atom %s does not have a position specified.\n" |
| 843 |
"\tThe initialization routine is unable to give a start" |
| 844 |
" position.\n", |
| 845 |
comp_stamps[current_comp]->getID(), |
| 846 |
current_atom->getType() ); |
| 847 |
painCave.isFatal = 1; |
| 848 |
simError(); |
| 849 |
} |
| 850 |
|
| 851 |
the_atoms[current_atom_ndx]->setX( x + current_atom->getPosX() ); |
| 852 |
the_atoms[current_atom_ndx]->setY( y + current_atom->getPosY() ); |
| 853 |
the_atoms[current_atom_ndx]->setZ( z + current_atom->getPosZ() ); |
| 854 |
|
| 855 |
if( the_atoms[current_atom_ndx]->isDirectional() ){ |
| 856 |
|
| 857 |
dAtom = (DirectionalAtom *)the_atoms[current_atom_ndx]; |
| 858 |
|
| 859 |
rotMat[0][0] = 1.0; |
| 860 |
rotMat[0][1] = 0.0; |
| 861 |
rotMat[0][2] = 0.0; |
| 862 |
|
| 863 |
rotMat[1][0] = 0.0; |
| 864 |
rotMat[1][1] = 1.0; |
| 865 |
rotMat[1][2] = 0.0; |
| 866 |
|
| 867 |
rotMat[2][0] = 0.0; |
| 868 |
rotMat[2][1] = 0.0; |
| 869 |
rotMat[2][2] = 1.0; |
| 870 |
|
| 871 |
dAtom->setA( rotMat ); |
| 872 |
} |
| 873 |
|
| 874 |
current_atom_ndx++; |
| 875 |
} |
| 876 |
|
| 877 |
current_mol++; |
| 878 |
current_comp_mol++; |
| 879 |
|
| 880 |
if( current_comp_mol >= components_nmol[current_comp] ){ |
| 881 |
|
| 882 |
current_comp_mol = 0; |
| 883 |
current_comp++; |
| 884 |
} |
| 885 |
} |
