| 1 |
#include <stdlib.h> |
| 2 |
#include <stdio.h> |
| 3 |
#include <string.h> |
| 4 |
|
| 5 |
#include <iostream> |
| 6 |
using namespace std; |
| 7 |
|
| 8 |
#ifdef IS_MPI |
| 9 |
#include <mpi.h> |
| 10 |
#endif //is_mpi |
| 11 |
|
| 12 |
#include "UseTheForce/ForceFields.hpp" |
| 13 |
#include "primitives/SRI.hpp" |
| 14 |
#include "utils/simError.h" |
| 15 |
|
| 16 |
|
| 17 |
#include "UseTheForce/DarkSide/atype_interface.h" |
| 18 |
#include "UseTheForce/DarkSide/sticky_interface.h" |
| 19 |
|
| 20 |
#ifdef IS_MPI |
| 21 |
#include "UseTheForce/mpiForceField.h" |
| 22 |
#endif // is_mpi |
| 23 |
|
| 24 |
|
| 25 |
|
| 26 |
namespace WATER_NS{ |
| 27 |
|
| 28 |
// Declare the structures that will be passed by the parser and MPI |
| 29 |
|
| 30 |
typedef struct{ |
| 31 |
char name[15]; |
| 32 |
double mass; |
| 33 |
double epslon; |
| 34 |
double sigma; |
| 35 |
double charge; |
| 36 |
int isDirectional; |
| 37 |
int isLJ; |
| 38 |
int isCharge; |
| 39 |
int ident; |
| 40 |
int last; // 0 -> default |
| 41 |
// 1 -> in MPI: tells nodes to stop listening |
| 42 |
} atomStruct; |
| 43 |
|
| 44 |
typedef struct{ |
| 45 |
char name[15]; |
| 46 |
double Ixx; |
| 47 |
double Iyy; |
| 48 |
double Izz; |
| 49 |
double dipole; |
| 50 |
double w0; |
| 51 |
double v0; |
| 52 |
double v0p; |
| 53 |
double rl; |
| 54 |
double ru; |
| 55 |
double rlp; |
| 56 |
double rup; |
| 57 |
int isDipole; |
| 58 |
int isSticky; |
| 59 |
int last; // 0 -> default |
| 60 |
// 1 -> in MPI: tells nodes to stop listening |
| 61 |
} directionalStruct; |
| 62 |
|
| 63 |
int parseAtom( char *lineBuffer, int lineNum, atomStruct &info ); |
| 64 |
int parseDirectional( char *lineBuffer, int lineNum, directionalStruct &info ); |
| 65 |
|
| 66 |
|
| 67 |
#ifdef IS_MPI |
| 68 |
|
| 69 |
MPI_Datatype mpiAtomStructType; |
| 70 |
MPI_Datatype mpiDirectionalStructType; |
| 71 |
|
| 72 |
#endif |
| 73 |
|
| 74 |
class LinkedAtomType { |
| 75 |
public: |
| 76 |
LinkedAtomType(){ |
| 77 |
next = NULL; |
| 78 |
name[0] = '\0'; |
| 79 |
} |
| 80 |
~LinkedAtomType(){ if( next != NULL ) delete next; } |
| 81 |
|
| 82 |
LinkedAtomType* find(char* key){ |
| 83 |
if( !strcmp(name, key) ) return this; |
| 84 |
if( next != NULL ) return next->find(key); |
| 85 |
return NULL; |
| 86 |
} |
| 87 |
|
| 88 |
|
| 89 |
void add( atomStruct &info ){ |
| 90 |
|
| 91 |
// check for duplicates |
| 92 |
|
| 93 |
if( !strcmp( info.name, name ) ){ |
| 94 |
sprintf( painCave.errMsg, |
| 95 |
"Duplicate WATER atom type \"%s\" found in " |
| 96 |
"the WATER param file./n", |
| 97 |
name ); |
| 98 |
painCave.isFatal = 1; |
| 99 |
simError(); |
| 100 |
} |
| 101 |
|
| 102 |
if( next != NULL ) next->add(info); |
| 103 |
else{ |
| 104 |
next = new LinkedAtomType(); |
| 105 |
strcpy(next->name, info.name); |
| 106 |
next->isDirectional = info.isDirectional; |
| 107 |
next->isLJ = info.isLJ; |
| 108 |
next->isCharge = info.isCharge; |
| 109 |
next->mass = info.mass; |
| 110 |
next->epslon = info.epslon; |
| 111 |
next->sigma = info.sigma; |
| 112 |
next->charge = info.charge; |
| 113 |
next->ident = info.ident; |
| 114 |
} |
| 115 |
} |
| 116 |
|
| 117 |
#ifdef IS_MPI |
| 118 |
|
| 119 |
void duplicate( atomStruct &info ){ |
| 120 |
strcpy(info.name, name); |
| 121 |
info.isDirectional = isDirectional; |
| 122 |
info.isLJ = isLJ; |
| 123 |
info.isCharge = isCharge; |
| 124 |
info.mass = mass; |
| 125 |
info.epslon = epslon; |
| 126 |
info.sigma = sigma; |
| 127 |
info.charge = charge; |
| 128 |
info.ident = ident; |
| 129 |
info.last = 0; |
| 130 |
} |
| 131 |
|
| 132 |
#endif |
| 133 |
|
| 134 |
char name[15]; |
| 135 |
int isDirectional; |
| 136 |
int isLJ; |
| 137 |
int isCharge; |
| 138 |
double mass; |
| 139 |
double epslon; |
| 140 |
double sigma; |
| 141 |
double charge; |
| 142 |
int ident; |
| 143 |
LinkedAtomType* next; |
| 144 |
}; |
| 145 |
|
| 146 |
class LinkedDirectionalType { |
| 147 |
public: |
| 148 |
LinkedDirectionalType(){ |
| 149 |
next = NULL; |
| 150 |
name[0] = '\0'; |
| 151 |
} |
| 152 |
~LinkedDirectionalType(){ if( next != NULL ) delete next; } |
| 153 |
|
| 154 |
LinkedDirectionalType* find(char* key){ |
| 155 |
if( !strcmp(name, key) ) return this; |
| 156 |
if( next != NULL ) return next->find(key); |
| 157 |
return NULL; |
| 158 |
} |
| 159 |
|
| 160 |
|
| 161 |
void add( directionalStruct &info ){ |
| 162 |
|
| 163 |
// check for duplicates |
| 164 |
|
| 165 |
if( !strcmp( info.name, name ) ){ |
| 166 |
sprintf( painCave.errMsg, |
| 167 |
"Duplicate WATER directional type \"%s\" found in " |
| 168 |
"the WATER param file./n", |
| 169 |
name ); |
| 170 |
painCave.isFatal = 1; |
| 171 |
simError(); |
| 172 |
} |
| 173 |
|
| 174 |
if( next != NULL ) next->add(info); |
| 175 |
else{ |
| 176 |
next = new LinkedDirectionalType(); |
| 177 |
strcpy(next->name, info.name); |
| 178 |
next->isDipole = info.isDipole; |
| 179 |
next->isSticky = info.isSticky; |
| 180 |
next->Ixx = info.Ixx; |
| 181 |
next->Iyy = info.Iyy; |
| 182 |
next->Izz = info.Izz; |
| 183 |
next->dipole = info.dipole; |
| 184 |
next->w0 = info.w0; |
| 185 |
next->v0 = info.v0; |
| 186 |
next->v0p = info.v0p; |
| 187 |
next->rl = info.rl; |
| 188 |
next->ru = info.ru; |
| 189 |
next->rlp = info.rlp; |
| 190 |
next->rup = info.rup; |
| 191 |
} |
| 192 |
} |
| 193 |
|
| 194 |
#ifdef IS_MPI |
| 195 |
|
| 196 |
void duplicate( directionalStruct &info ){ |
| 197 |
strcpy(info.name, name); |
| 198 |
info.isDipole = isDipole; |
| 199 |
info.isSticky = isSticky; |
| 200 |
info.Ixx = Ixx; |
| 201 |
info.Iyy = Iyy; |
| 202 |
info.Izz = Izz; |
| 203 |
info.dipole = dipole; |
| 204 |
info.w0 = w0; |
| 205 |
info.v0 = v0; |
| 206 |
info.v0p = v0p; |
| 207 |
info.rl = rl; |
| 208 |
info.ru = ru; |
| 209 |
info.rlp = rlp; |
| 210 |
info.rup = rup; |
| 211 |
info.last = 0; |
| 212 |
} |
| 213 |
|
| 214 |
#endif |
| 215 |
|
| 216 |
char name[15]; |
| 217 |
int isDipole; |
| 218 |
int isSticky; |
| 219 |
double Ixx; |
| 220 |
double Iyy; |
| 221 |
double Izz; |
| 222 |
double dipole; |
| 223 |
double w0; |
| 224 |
double v0; |
| 225 |
double v0p; |
| 226 |
double rl; |
| 227 |
double ru; |
| 228 |
double rlp; |
| 229 |
double rup; |
| 230 |
LinkedDirectionalType* next; |
| 231 |
}; |
| 232 |
|
| 233 |
LinkedAtomType* headAtomType; |
| 234 |
LinkedAtomType* currentAtomType; |
| 235 |
LinkedDirectionalType* headDirectionalType; |
| 236 |
LinkedDirectionalType* currentDirectionalType; |
| 237 |
} // namespace |
| 238 |
|
| 239 |
using namespace WATER_NS; |
| 240 |
|
| 241 |
//**************************************************************** |
| 242 |
// begins the actual forcefield stuff. |
| 243 |
//**************************************************************** |
| 244 |
|
| 245 |
|
| 246 |
WATER::WATER(){ |
| 247 |
|
| 248 |
char fileName[200]; |
| 249 |
char* ffPath_env = "FORCE_PARAM_PATH"; |
| 250 |
char* ffPath; |
| 251 |
char temp[200]; |
| 252 |
|
| 253 |
headAtomType = NULL; |
| 254 |
currentAtomType = NULL; |
| 255 |
headDirectionalType = NULL; |
| 256 |
currentDirectionalType = NULL; |
| 257 |
|
| 258 |
#ifdef IS_MPI |
| 259 |
int i; |
| 260 |
|
| 261 |
// ********************************************************************** |
| 262 |
// Init the atomStruct mpi type |
| 263 |
|
| 264 |
atomStruct atomProto; // mpiPrototype |
| 265 |
int atomBC[3] = {15,4,5}; // block counts |
| 266 |
MPI_Aint atomDspls[3]; // displacements |
| 267 |
MPI_Datatype atomMbrTypes[3]; // member mpi types |
| 268 |
|
| 269 |
MPI_Address(&atomProto.name, &atomDspls[0]); |
| 270 |
MPI_Address(&atomProto.mass, &atomDspls[1]); |
| 271 |
MPI_Address(&atomProto.isDirectional, &atomDspls[2]); |
| 272 |
|
| 273 |
atomMbrTypes[0] = MPI_CHAR; |
| 274 |
atomMbrTypes[1] = MPI_DOUBLE; |
| 275 |
atomMbrTypes[2] = MPI_INT; |
| 276 |
|
| 277 |
for (i=2; i >= 0; i--) atomDspls[i] -= atomDspls[0]; |
| 278 |
|
| 279 |
MPI_Type_struct(3, atomBC, atomDspls, atomMbrTypes, &mpiAtomStructType); |
| 280 |
MPI_Type_commit(&mpiAtomStructType); |
| 281 |
|
| 282 |
// *********************************************************************** |
| 283 |
|
| 284 |
// ********************************************************************** |
| 285 |
// Init the directionalStruct mpi type |
| 286 |
|
| 287 |
directionalStruct directionalProto; // mpiPrototype |
| 288 |
int directionalBC[3] = {15,11,3}; // block counts |
| 289 |
MPI_Aint directionalDspls[3]; // displacements |
| 290 |
MPI_Datatype directionalMbrTypes[3]; // member mpi types |
| 291 |
|
| 292 |
MPI_Address(&directionalProto.name, &directionalDspls[0]); |
| 293 |
MPI_Address(&directionalProto.Ixx, &directionalDspls[1]); |
| 294 |
MPI_Address(&directionalProto.isDipole, &directionalDspls[2]); |
| 295 |
|
| 296 |
directionalMbrTypes[0] = MPI_CHAR; |
| 297 |
directionalMbrTypes[1] = MPI_DOUBLE; |
| 298 |
directionalMbrTypes[2] = MPI_INT; |
| 299 |
|
| 300 |
for (i=2; i >= 0; i--) directionalDspls[i] -= directionalDspls[0]; |
| 301 |
|
| 302 |
MPI_Type_struct(3, directionalBC, directionalDspls, directionalMbrTypes, |
| 303 |
&mpiDirectionalStructType); |
| 304 |
MPI_Type_commit(&mpiDirectionalStructType); |
| 305 |
|
| 306 |
// *********************************************************************** |
| 307 |
|
| 308 |
if( worldRank == 0 ){ |
| 309 |
#endif |
| 310 |
|
| 311 |
// generate the force file name |
| 312 |
|
| 313 |
strcpy( fileName, "WATER.frc" ); |
| 314 |
// fprintf( stderr,"Trying to open %s\n", fileName ); |
| 315 |
|
| 316 |
// attempt to open the file in the current directory first. |
| 317 |
|
| 318 |
frcFile = fopen( fileName, "r" ); |
| 319 |
|
| 320 |
if( frcFile == NULL ){ |
| 321 |
|
| 322 |
// next see if the force path enviorment variable is set |
| 323 |
|
| 324 |
ffPath = getenv( ffPath_env ); |
| 325 |
if( ffPath == NULL ) { |
| 326 |
STR_DEFINE(ffPath, FRC_PATH ); |
| 327 |
} |
| 328 |
|
| 329 |
|
| 330 |
strcpy( temp, ffPath ); |
| 331 |
strcat( temp, "/" ); |
| 332 |
strcat( temp, fileName ); |
| 333 |
strcpy( fileName, temp ); |
| 334 |
|
| 335 |
frcFile = fopen( fileName, "r" ); |
| 336 |
|
| 337 |
if( frcFile == NULL ){ |
| 338 |
|
| 339 |
sprintf( painCave.errMsg, |
| 340 |
"Error opening the force field parameter file:\n" |
| 341 |
"\t%s\n" |
| 342 |
"\tHave you tried setting the FORCE_PARAM_PATH environment " |
| 343 |
"variable?\n", |
| 344 |
fileName ); |
| 345 |
painCave.severity = OOPSE_ERROR; |
| 346 |
painCave.isFatal = 1; |
| 347 |
simError(); |
| 348 |
} |
| 349 |
} |
| 350 |
|
| 351 |
#ifdef IS_MPI |
| 352 |
} |
| 353 |
|
| 354 |
sprintf( checkPointMsg, "WATER file opened sucessfully." ); |
| 355 |
MPIcheckPoint(); |
| 356 |
|
| 357 |
#endif // is_mpi |
| 358 |
} |
| 359 |
|
| 360 |
|
| 361 |
WATER::~WATER(){ |
| 362 |
|
| 363 |
if( headAtomType != NULL ) delete headAtomType; |
| 364 |
if( headDirectionalType != NULL ) delete headDirectionalType; |
| 365 |
|
| 366 |
#ifdef IS_MPI |
| 367 |
if( worldRank == 0 ){ |
| 368 |
#endif // is_mpi |
| 369 |
|
| 370 |
fclose( frcFile ); |
| 371 |
|
| 372 |
#ifdef IS_MPI |
| 373 |
} |
| 374 |
#endif // is_mpi |
| 375 |
} |
| 376 |
|
| 377 |
void WATER::cleanMe( void ){ |
| 378 |
|
| 379 |
#ifdef IS_MPI |
| 380 |
|
| 381 |
// keep the linked list in the mpi version |
| 382 |
|
| 383 |
#else // is_mpi |
| 384 |
|
| 385 |
// delete the linked list in the single processor version |
| 386 |
|
| 387 |
if( headAtomType != NULL ) delete headAtomType; |
| 388 |
if( headDirectionalType != NULL ) delete headDirectionalType; |
| 389 |
|
| 390 |
#endif // is_mpi |
| 391 |
} |
| 392 |
|
| 393 |
|
| 394 |
void WATER::initForceField(){ |
| 395 |
|
| 396 |
initFortran(entry_plug->useReactionField ); |
| 397 |
} |
| 398 |
|
| 399 |
|
| 400 |
void WATER::readParams( void ){ |
| 401 |
|
| 402 |
int identNum; |
| 403 |
int tempDirect0, tempDirect1; |
| 404 |
|
| 405 |
atomStruct atomInfo; |
| 406 |
directionalStruct directionalInfo; |
| 407 |
fpos_t *atomPos; |
| 408 |
|
| 409 |
atomInfo.last = 1; // initialize last to have the last set. |
| 410 |
directionalInfo.last = 1; // if things go well, last will be set to 0 |
| 411 |
|
| 412 |
atomPos = new fpos_t; |
| 413 |
bigSigma = 0.0; |
| 414 |
|
| 415 |
#ifdef IS_MPI |
| 416 |
if( worldRank == 0 ){ |
| 417 |
#endif |
| 418 |
|
| 419 |
// read in the atom types. |
| 420 |
|
| 421 |
headAtomType = new LinkedAtomType; |
| 422 |
headDirectionalType = new LinkedDirectionalType; |
| 423 |
|
| 424 |
fastForward( "AtomTypes", "initializeAtoms" ); |
| 425 |
|
| 426 |
// we are now at the AtomTypes section. |
| 427 |
|
| 428 |
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
| 429 |
lineNum++; |
| 430 |
|
| 431 |
|
| 432 |
// read a line, and start parsing out the atom types |
| 433 |
|
| 434 |
if( eof_test == NULL ){ |
| 435 |
sprintf( painCave.errMsg, |
| 436 |
"Error in reading Atoms from force file at line %d.\n", |
| 437 |
lineNum ); |
| 438 |
painCave.isFatal = 1; |
| 439 |
simError(); |
| 440 |
} |
| 441 |
|
| 442 |
identNum = 1; |
| 443 |
// stop reading at end of file, or at next section |
| 444 |
while( readLine[0] != '#' && eof_test != NULL ){ |
| 445 |
|
| 446 |
// toss comment lines |
| 447 |
if( readLine[0] != '!' ){ |
| 448 |
|
| 449 |
// the parser returns 0 if the line was blank |
| 450 |
if( parseAtom( readLine, lineNum, atomInfo ) ){ |
| 451 |
atomInfo.ident = identNum; |
| 452 |
headAtomType->add( atomInfo ); |
| 453 |
if ( atomInfo.isDirectional ) { |
| 454 |
|
| 455 |
// if the atom is directional, skip to the directional section |
| 456 |
// and parse directional info. |
| 457 |
fgetpos( frcFile, atomPos ); |
| 458 |
sectionSearch( "DirectionalTypes", atomInfo.name, |
| 459 |
"initializeDirectional" ); |
| 460 |
parseDirectional( readLine, lineNum, directionalInfo ); |
| 461 |
headDirectionalType->add( directionalInfo ); |
| 462 |
|
| 463 |
// return to the AtomTypes section |
| 464 |
fsetpos( frcFile, atomPos ); |
| 465 |
} |
| 466 |
identNum++; |
| 467 |
} |
| 468 |
} |
| 469 |
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
| 470 |
lineNum++; |
| 471 |
} |
| 472 |
|
| 473 |
#ifdef IS_MPI |
| 474 |
|
| 475 |
// send out the linked list to all the other processes |
| 476 |
|
| 477 |
sprintf( checkPointMsg, |
| 478 |
"WATER atom and directional structures read successfully." ); |
| 479 |
MPIcheckPoint(); |
| 480 |
currentAtomType = headAtomType->next; //skip the first element place holder |
| 481 |
currentDirectionalType = headDirectionalType->next; // same w/ directional |
| 482 |
|
| 483 |
while( currentAtomType != NULL ){ |
| 484 |
currentAtomType->duplicate( atomInfo ); |
| 485 |
|
| 486 |
sendFrcStruct( &atomInfo, mpiAtomStructType ); |
| 487 |
|
| 488 |
sprintf( checkPointMsg, |
| 489 |
"successfully sent WATER force type: \"%s\"\n", |
| 490 |
atomInfo.name ); |
| 491 |
|
| 492 |
if ( atomInfo.isDirectional ){ |
| 493 |
// send out the directional linked list to all the other processes |
| 494 |
|
| 495 |
currentDirectionalType->duplicate( directionalInfo ); |
| 496 |
sendFrcStruct( &directionalInfo, mpiDirectionalStructType ); |
| 497 |
|
| 498 |
sprintf( checkPointMsg, |
| 499 |
"successfully sent WATER directional type: \"%s\"\n", |
| 500 |
directionalInfo.name ); |
| 501 |
} |
| 502 |
|
| 503 |
MPIcheckPoint(); |
| 504 |
tempDirect0 = atomInfo.isDirectional; |
| 505 |
currentAtomType = currentAtomType->next; |
| 506 |
if( tempDirect0 ) |
| 507 |
currentDirectionalType = currentDirectionalType->next; |
| 508 |
} |
| 509 |
|
| 510 |
atomInfo.last = 1; |
| 511 |
sendFrcStruct( &atomInfo, mpiAtomStructType ); |
| 512 |
directionalInfo.last = 1; |
| 513 |
if ( atomInfo.isDirectional ) |
| 514 |
sendFrcStruct( &directionalInfo, mpiDirectionalStructType ); |
| 515 |
} |
| 516 |
|
| 517 |
else{ |
| 518 |
// listen for node 0 to send out the force params |
| 519 |
|
| 520 |
MPIcheckPoint(); |
| 521 |
|
| 522 |
headAtomType = new LinkedAtomType; |
| 523 |
headDirectionalType = new LinkedDirectionalType; |
| 524 |
receiveFrcStruct( &atomInfo, mpiAtomStructType ); |
| 525 |
|
| 526 |
if ( atomInfo.isDirectional ) |
| 527 |
receiveFrcStruct( &directionalInfo, mpiDirectionalStructType ); |
| 528 |
|
| 529 |
while( !atomInfo.last ){ |
| 530 |
|
| 531 |
headAtomType->add( atomInfo ); |
| 532 |
|
| 533 |
MPIcheckPoint(); |
| 534 |
|
| 535 |
receiveFrcStruct( &atomInfo, mpiAtomStructType ); |
| 536 |
|
| 537 |
if( atomInfo.isDirectional ){ |
| 538 |
headDirectionalType->add( directionalInfo ); |
| 539 |
|
| 540 |
receiveFrcStruct( &directionalInfo, mpiDirectionalStructType ); |
| 541 |
} |
| 542 |
} |
| 543 |
} |
| 544 |
|
| 545 |
#endif // is_mpi |
| 546 |
|
| 547 |
// call new A_types in fortran |
| 548 |
|
| 549 |
int isError; |
| 550 |
|
| 551 |
// dummy variables |
| 552 |
int isGB = 0; |
| 553 |
int isEAM = 0; |
| 554 |
int notDipole = 0; |
| 555 |
int notSSD = 0; |
| 556 |
double noDipMoment = 0.0; |
| 557 |
|
| 558 |
|
| 559 |
currentAtomType = headAtomType->next; |
| 560 |
currentDirectionalType = headDirectionalType->next; |
| 561 |
|
| 562 |
while( currentAtomType != NULL ){ |
| 563 |
|
| 564 |
if( currentAtomType->isLJ ) entry_plug->useLJ = 1; |
| 565 |
if( currentAtomType->isCharge ) entry_plug->useCharges = 1; |
| 566 |
if( currentAtomType->isDirectional ){ |
| 567 |
// only directional atoms can have dipoles or be sticky |
| 568 |
if ( currentDirectionalType->isDipole ) entry_plug->useDipoles = 1; |
| 569 |
if ( currentDirectionalType->isSticky ) { |
| 570 |
entry_plug->useSticky = 1; |
| 571 |
makeStickyType( &(currentDirectionalType->w0), |
| 572 |
&(currentDirectionalType->v0), |
| 573 |
&(currentDirectionalType->v0p), |
| 574 |
&(currentDirectionalType->rl), |
| 575 |
&(currentDirectionalType->ru), |
| 576 |
&(currentDirectionalType->rlp), |
| 577 |
&(currentDirectionalType->rup)); |
| 578 |
} |
| 579 |
if( currentAtomType->name[0] != '\0' ){ |
| 580 |
isError = 0; |
| 581 |
makeAtype( &(currentAtomType->ident), |
| 582 |
&(currentAtomType->isLJ), |
| 583 |
&(currentDirectionalType->isSticky), |
| 584 |
&(currentDirectionalType->isDipole), |
| 585 |
&isGB, |
| 586 |
&isEAM, |
| 587 |
&(currentAtomType->isCharge), |
| 588 |
&(currentAtomType->epslon), |
| 589 |
&(currentAtomType->sigma), |
| 590 |
&(currentAtomType->charge), |
| 591 |
&(currentDirectionalType->dipole), |
| 592 |
&isError ); |
| 593 |
if( isError ){ |
| 594 |
sprintf( painCave.errMsg, |
| 595 |
"Error initializing the \"%s\" atom type in fortran\n", |
| 596 |
currentAtomType->name ); |
| 597 |
painCave.isFatal = 1; |
| 598 |
simError(); |
| 599 |
} |
| 600 |
} |
| 601 |
currentDirectionalType->next; |
| 602 |
} |
| 603 |
|
| 604 |
else { |
| 605 |
// use all dummy variables if this is not a directional atom |
| 606 |
if( currentAtomType->name[0] != '\0' ){ |
| 607 |
isError = 0; |
| 608 |
makeAtype( &(currentAtomType->ident), |
| 609 |
&(currentAtomType->isLJ), |
| 610 |
¬SSD, |
| 611 |
¬Dipole, |
| 612 |
&isGB, |
| 613 |
&isEAM, |
| 614 |
&(currentAtomType->isCharge), |
| 615 |
&(currentAtomType->epslon), |
| 616 |
&(currentAtomType->sigma), |
| 617 |
&(currentAtomType->charge), |
| 618 |
&noDipMoment, |
| 619 |
&isError ); |
| 620 |
if( isError ){ |
| 621 |
sprintf( painCave.errMsg, |
| 622 |
"Error initializing the \"%s\" atom type in fortran\n", |
| 623 |
currentAtomType->name ); |
| 624 |
painCave.isFatal = 1; |
| 625 |
simError(); |
| 626 |
} |
| 627 |
} |
| 628 |
} |
| 629 |
currentAtomType = currentAtomType->next; |
| 630 |
} |
| 631 |
|
| 632 |
#ifdef IS_MPI |
| 633 |
sprintf( checkPointMsg, |
| 634 |
"WATER atom and directional structures successfully" |
| 635 |
"sent to fortran\n" ); |
| 636 |
MPIcheckPoint(); |
| 637 |
#endif // is_mpi |
| 638 |
|
| 639 |
} |
| 640 |
|
| 641 |
|
| 642 |
void WATER::initializeAtoms( int nAtoms, Atom** the_atoms ){ |
| 643 |
|
| 644 |
int i,j,k; |
| 645 |
|
| 646 |
// initialize the atoms |
| 647 |
DirectionalAtom* dAtom; |
| 648 |
double ji[3]; |
| 649 |
double inertialMat[3][3]; |
| 650 |
|
| 651 |
for( i=0; i<nAtoms; i++ ){ |
| 652 |
currentAtomType = headAtomType->find( the_atoms[i]->getType() ); |
| 653 |
if( currentAtomType == NULL ){ |
| 654 |
sprintf( painCave.errMsg, |
| 655 |
"AtomType error, %s not found in force file.\n", |
| 656 |
the_atoms[i]->getType() ); |
| 657 |
painCave.isFatal = 1; |
| 658 |
simError(); |
| 659 |
} |
| 660 |
the_atoms[i]->setMass( currentAtomType->mass ); |
| 661 |
the_atoms[i]->setIdent( currentAtomType->ident ); |
| 662 |
|
| 663 |
if( bigSigma < currentAtomType->sigma ) bigSigma = currentAtomType->sigma; |
| 664 |
|
| 665 |
the_atoms[i]->setHasCharge(currentAtomType->isCharge); |
| 666 |
|
| 667 |
if( currentAtomType->isDirectional ){ |
| 668 |
currentDirectionalType = |
| 669 |
headDirectionalType->find( the_atoms[i]->getType() ); |
| 670 |
if( currentDirectionalType == NULL ){ |
| 671 |
sprintf( painCave.errMsg, |
| 672 |
"DirectionalType error, %s not found in force file.\n", |
| 673 |
the_atoms[i]->getType() ); |
| 674 |
painCave.isFatal = 1; |
| 675 |
simError(); |
| 676 |
} |
| 677 |
|
| 678 |
// zero out the moments of inertia matrix |
| 679 |
for( j=0; j<3; j++ ) |
| 680 |
for( k=0; k<3; k++ ) |
| 681 |
inertialMat[j][k] = 0.0; |
| 682 |
|
| 683 |
// load the force file moments of inertia |
| 684 |
inertialMat[0][0] = currentDirectionalType->Ixx; |
| 685 |
inertialMat[1][1] = currentDirectionalType->Iyy; |
| 686 |
inertialMat[2][2] = currentDirectionalType->Izz; |
| 687 |
|
| 688 |
dAtom = (DirectionalAtom *) the_atoms[i]; |
| 689 |
dAtom->setHasDipole( currentDirectionalType->isDipole ); |
| 690 |
|
| 691 |
ji[0] = 0.0; |
| 692 |
ji[1] = 0.0; |
| 693 |
ji[2] = 0.0; |
| 694 |
dAtom->setJ( ji ); |
| 695 |
dAtom->setI( inertialMat ); |
| 696 |
|
| 697 |
entry_plug->n_dipoles++; |
| 698 |
} |
| 699 |
} |
| 700 |
} |
| 701 |
|
| 702 |
void WATER::initializeBonds( int nBonds, Bond** BondArray, |
| 703 |
bond_pair* the_bonds ){ |
| 704 |
|
| 705 |
if( nBonds ){ |
| 706 |
sprintf( painCave.errMsg, |
| 707 |
"WATER does not support bonds.\n" ); |
| 708 |
painCave.isFatal = 1; |
| 709 |
simError(); |
| 710 |
} |
| 711 |
} |
| 712 |
|
| 713 |
void WATER::initializeBends( int nBends, Bend** bendArray, |
| 714 |
bend_set* the_bends ){ |
| 715 |
|
| 716 |
if( nBends ){ |
| 717 |
sprintf( painCave.errMsg, |
| 718 |
"WATER does not support bends.\n" ); |
| 719 |
painCave.isFatal = 1; |
| 720 |
simError(); |
| 721 |
} |
| 722 |
} |
| 723 |
|
| 724 |
void WATER::initializeTorsions( int nTorsions, Torsion** torsionArray, |
| 725 |
torsion_set* the_torsions ){ |
| 726 |
|
| 727 |
if( nTorsions ){ |
| 728 |
sprintf( painCave.errMsg, |
| 729 |
"WATER does not support torsions.\n" ); |
| 730 |
painCave.isFatal = 1; |
| 731 |
simError(); |
| 732 |
} |
| 733 |
} |
| 734 |
|
| 735 |
void WATER::fastForward( char* stopText, char* searchOwner ){ |
| 736 |
|
| 737 |
int foundText = 0; |
| 738 |
char* the_token; |
| 739 |
|
| 740 |
rewind( frcFile ); |
| 741 |
lineNum = 0; |
| 742 |
|
| 743 |
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
| 744 |
lineNum++; |
| 745 |
if( eof_test == NULL ){ |
| 746 |
sprintf( painCave.errMsg, "Error fast forwarding force file for %s: " |
| 747 |
" file is empty.\n", |
| 748 |
searchOwner ); |
| 749 |
painCave.isFatal = 1; |
| 750 |
simError(); |
| 751 |
} |
| 752 |
|
| 753 |
|
| 754 |
while( !foundText ){ |
| 755 |
while( eof_test != NULL && readLine[0] != '#' ){ |
| 756 |
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
| 757 |
lineNum++; |
| 758 |
} |
| 759 |
if( eof_test == NULL ){ |
| 760 |
sprintf( painCave.errMsg, |
| 761 |
"Error fast forwarding force file for %s at " |
| 762 |
"line %d: file ended unexpectedly.\n", |
| 763 |
searchOwner, |
| 764 |
lineNum ); |
| 765 |
painCave.isFatal = 1; |
| 766 |
simError(); |
| 767 |
} |
| 768 |
|
| 769 |
the_token = strtok( readLine, " ,;\t#\n" ); |
| 770 |
foundText = !strcmp( stopText, the_token ); |
| 771 |
|
| 772 |
if( !foundText ){ |
| 773 |
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
| 774 |
lineNum++; |
| 775 |
|
| 776 |
if( eof_test == NULL ){ |
| 777 |
sprintf( painCave.errMsg, |
| 778 |
"Error fast forwarding force file for %s at " |
| 779 |
"line %d: file ended unexpectedly.\n", |
| 780 |
searchOwner, |
| 781 |
lineNum ); |
| 782 |
painCave.isFatal = 1; |
| 783 |
simError(); |
| 784 |
} |
| 785 |
} |
| 786 |
} |
| 787 |
} |
| 788 |
|
| 789 |
void WATER::sectionSearch( char* secHead, char* stopText, char* searchOwner ){ |
| 790 |
|
| 791 |
int foundSection = 0; |
| 792 |
int foundText = 0; |
| 793 |
char* the_token; |
| 794 |
fpos_t *tempPos; |
| 795 |
|
| 796 |
rewind( frcFile ); |
| 797 |
lineNum = 0; |
| 798 |
tempPos = new fpos_t; |
| 799 |
|
| 800 |
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
| 801 |
lineNum++; |
| 802 |
if( eof_test == NULL ){ |
| 803 |
sprintf( painCave.errMsg, "Error fast forwarding force file for %s: " |
| 804 |
" file is empty.\n", |
| 805 |
searchOwner ); |
| 806 |
painCave.isFatal = 1; |
| 807 |
simError(); |
| 808 |
} |
| 809 |
|
| 810 |
while( !foundSection ){ |
| 811 |
while( eof_test != NULL && readLine[0] != '#' ){ |
| 812 |
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
| 813 |
lineNum++; |
| 814 |
} |
| 815 |
if( eof_test == NULL ){ |
| 816 |
sprintf( painCave.errMsg, |
| 817 |
"Error fast forwarding force file for %s at " |
| 818 |
"line %d: file ended unexpectedly.\n", |
| 819 |
searchOwner, |
| 820 |
lineNum ); |
| 821 |
painCave.isFatal = 1; |
| 822 |
simError(); |
| 823 |
} |
| 824 |
the_token = strtok( readLine, " ,;\t#\n" ); |
| 825 |
foundSection = !strcmp( secHead, the_token ); |
| 826 |
|
| 827 |
if( !foundSection ){ |
| 828 |
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
| 829 |
lineNum++; |
| 830 |
|
| 831 |
if( eof_test == NULL ){ |
| 832 |
sprintf( painCave.errMsg, |
| 833 |
"Error section searching force file for %s at " |
| 834 |
"line %d: file ended unexpectedly.\n", |
| 835 |
searchOwner, |
| 836 |
lineNum ); |
| 837 |
painCave.isFatal = 1; |
| 838 |
simError(); |
| 839 |
} |
| 840 |
} |
| 841 |
} |
| 842 |
|
| 843 |
while( !foundText ){ |
| 844 |
|
| 845 |
fgetpos( frcFile, tempPos ); |
| 846 |
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
| 847 |
lineNum++; |
| 848 |
|
| 849 |
if( eof_test == NULL ){ |
| 850 |
sprintf( painCave.errMsg, |
| 851 |
"Error fast forwarding force file for %s at " |
| 852 |
"line %d: file ended unexpectedly.\n", |
| 853 |
searchOwner, |
| 854 |
lineNum ); |
| 855 |
painCave.isFatal = 1; |
| 856 |
simError(); |
| 857 |
} |
| 858 |
|
| 859 |
the_token = strtok( readLine, " ,;\t#\n" ); |
| 860 |
if( the_token != NULL ){ |
| 861 |
foundText = !strcmp( stopText, the_token ); |
| 862 |
} |
| 863 |
} |
| 864 |
fsetpos( frcFile, tempPos ); |
| 865 |
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
| 866 |
lineNum++; |
| 867 |
} |
| 868 |
|
| 869 |
|
| 870 |
int WATER_NS::parseAtom( char *lineBuffer, int lineNum, atomStruct &info ){ |
| 871 |
|
| 872 |
char* the_token; |
| 873 |
|
| 874 |
the_token = strtok( lineBuffer, " \n\t,;" ); |
| 875 |
if( the_token != NULL ){ |
| 876 |
|
| 877 |
strcpy( info.name, the_token ); |
| 878 |
|
| 879 |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
| 880 |
sprintf( painCave.errMsg, |
| 881 |
"Error parseing AtomTypes: line %d\n", lineNum ); |
| 882 |
painCave.isFatal = 1; |
| 883 |
simError(); |
| 884 |
} |
| 885 |
|
| 886 |
info.isDirectional = atoi( the_token ); |
| 887 |
|
| 888 |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
| 889 |
sprintf( painCave.errMsg, |
| 890 |
"Error parseing AtomTypes: line %d\n", lineNum ); |
| 891 |
painCave.isFatal = 1; |
| 892 |
simError(); |
| 893 |
} |
| 894 |
|
| 895 |
info.isLJ = atoi( the_token ); |
| 896 |
|
| 897 |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
| 898 |
sprintf( painCave.errMsg, |
| 899 |
"Error parseing AtomTypes: line %d\n", lineNum ); |
| 900 |
painCave.isFatal = 1; |
| 901 |
simError(); |
| 902 |
} |
| 903 |
|
| 904 |
info.isCharge = atoi( the_token ); |
| 905 |
|
| 906 |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
| 907 |
sprintf( painCave.errMsg, |
| 908 |
"Error parseing AtomTypes: line %d\n", lineNum ); |
| 909 |
painCave.isFatal = 1; |
| 910 |
simError(); |
| 911 |
} |
| 912 |
|
| 913 |
info.mass = atof( the_token ); |
| 914 |
|
| 915 |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
| 916 |
sprintf( painCave.errMsg, |
| 917 |
"Error parseing AtomTypes: line %d\n", lineNum ); |
| 918 |
painCave.isFatal = 1; |
| 919 |
simError(); |
| 920 |
} |
| 921 |
|
| 922 |
info.epslon = atof( the_token ); |
| 923 |
|
| 924 |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
| 925 |
sprintf( painCave.errMsg, |
| 926 |
"Error parseing AtomTypes: line %d\n", lineNum ); |
| 927 |
painCave.isFatal = 1; |
| 928 |
simError(); |
| 929 |
} |
| 930 |
|
| 931 |
info.sigma = atof( the_token ); |
| 932 |
|
| 933 |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
| 934 |
sprintf( painCave.errMsg, |
| 935 |
"Error parseing AtomTypes: line %d\n", lineNum ); |
| 936 |
painCave.isFatal = 1; |
| 937 |
simError(); |
| 938 |
} |
| 939 |
|
| 940 |
info.charge = atof( the_token ); |
| 941 |
|
| 942 |
return 1; |
| 943 |
} |
| 944 |
else return 0; |
| 945 |
} |
| 946 |
|
| 947 |
int WATER_NS::parseDirectional( char *lineBuffer, int lineNum, directionalStruct &info ){ |
| 948 |
|
| 949 |
char* the_token; |
| 950 |
|
| 951 |
the_token = strtok( lineBuffer, " \n\t,;" ); |
| 952 |
if( the_token != NULL ){ |
| 953 |
|
| 954 |
strcpy( info.name, the_token ); |
| 955 |
|
| 956 |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
| 957 |
sprintf( painCave.errMsg, |
| 958 |
"Error parseing DirectionalTypes: line %d\n", lineNum ); |
| 959 |
painCave.isFatal = 1; |
| 960 |
simError(); |
| 961 |
} |
| 962 |
|
| 963 |
info.isDipole = atoi( the_token ); |
| 964 |
|
| 965 |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
| 966 |
sprintf( painCave.errMsg, |
| 967 |
"Error parseing DirectionalTypes: line %d\n", lineNum ); |
| 968 |
painCave.isFatal = 1; |
| 969 |
simError(); |
| 970 |
} |
| 971 |
|
| 972 |
info.isSticky = atoi( the_token ); |
| 973 |
|
| 974 |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
| 975 |
sprintf( painCave.errMsg, |
| 976 |
"Error parseing DirectionalTypes: line %d\n", lineNum ); |
| 977 |
painCave.isFatal = 1; |
| 978 |
simError(); |
| 979 |
} |
| 980 |
|
| 981 |
info.Ixx = atof( the_token ); |
| 982 |
|
| 983 |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
| 984 |
sprintf( painCave.errMsg, |
| 985 |
"Error parseing DirectionalTypes: line %d\n", lineNum ); |
| 986 |
painCave.isFatal = 1; |
| 987 |
simError(); |
| 988 |
} |
| 989 |
|
| 990 |
info.Iyy = atof( the_token ); |
| 991 |
|
| 992 |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
| 993 |
sprintf( painCave.errMsg, |
| 994 |
"Error parseing DirectionalTypes: line %d\n", lineNum ); |
| 995 |
painCave.isFatal = 1; |
| 996 |
simError(); |
| 997 |
} |
| 998 |
|
| 999 |
info.Izz = atof( the_token ); |
| 1000 |
|
| 1001 |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
| 1002 |
sprintf( painCave.errMsg, |
| 1003 |
"Error parseing DirectionalTypes: line %d\n", lineNum ); |
| 1004 |
painCave.isFatal = 1; |
| 1005 |
simError(); |
| 1006 |
} |
| 1007 |
|
| 1008 |
|
| 1009 |
info.dipole = atof( the_token ); |
| 1010 |
|
| 1011 |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
| 1012 |
sprintf( painCave.errMsg, |
| 1013 |
"Error parseing DirectionalTypes: line %d\n", lineNum ); |
| 1014 |
painCave.isFatal = 1; |
| 1015 |
simError(); |
| 1016 |
} |
| 1017 |
|
| 1018 |
info.w0 = atof( the_token ); |
| 1019 |
|
| 1020 |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
| 1021 |
sprintf( painCave.errMsg, |
| 1022 |
"Error parseing DirectionalTypes: line %d\n", lineNum ); |
| 1023 |
painCave.isFatal = 1; |
| 1024 |
simError(); |
| 1025 |
} |
| 1026 |
|
| 1027 |
info.v0 = atof( the_token ); |
| 1028 |
|
| 1029 |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
| 1030 |
sprintf( painCave.errMsg, |
| 1031 |
"Error parseing DirectionalTypes: line %d\n", lineNum ); |
| 1032 |
painCave.isFatal = 1; |
| 1033 |
simError(); |
| 1034 |
} |
| 1035 |
|
| 1036 |
info.v0p = atof( the_token ); |
| 1037 |
|
| 1038 |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
| 1039 |
sprintf( painCave.errMsg, |
| 1040 |
"Error parseing DirectionalTypes: line %d\n", lineNum ); |
| 1041 |
painCave.isFatal = 1; |
| 1042 |
simError(); |
| 1043 |
} |
| 1044 |
|
| 1045 |
info.rl = atof( the_token ); |
| 1046 |
|
| 1047 |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
| 1048 |
sprintf( painCave.errMsg, |
| 1049 |
"Error parseing DirectionalTypes: line %d\n", lineNum ); |
| 1050 |
painCave.isFatal = 1; |
| 1051 |
simError(); |
| 1052 |
} |
| 1053 |
|
| 1054 |
info.ru = atof( the_token ); |
| 1055 |
|
| 1056 |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
| 1057 |
sprintf( painCave.errMsg, |
| 1058 |
"Error parseing DirectionalTypes: line %d\n", lineNum ); |
| 1059 |
painCave.isFatal = 1; |
| 1060 |
simError(); |
| 1061 |
} |
| 1062 |
|
| 1063 |
info.rlp = atof( the_token ); |
| 1064 |
|
| 1065 |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
| 1066 |
sprintf( painCave.errMsg, |
| 1067 |
"Error parseing DirectionalTypes: line %d\n", lineNum ); |
| 1068 |
painCave.isFatal = 1; |
| 1069 |
simError(); |
| 1070 |
} |
| 1071 |
|
| 1072 |
info.rup = atof( the_token ); |
| 1073 |
|
| 1074 |
return 1; |
| 1075 |
} |
| 1076 |
else return 0; |
| 1077 |
} |
| 1078 |
double WATER::getAtomTypeMass (char* atomType) { |
| 1079 |
|
| 1080 |
currentAtomType = headAtomType->find( atomType ); |
| 1081 |
if( currentAtomType == NULL ){ |
| 1082 |
sprintf( painCave.errMsg, |
| 1083 |
"AtomType error, %s not found in force file.\n", |
| 1084 |
atomType ); |
| 1085 |
painCave.isFatal = 1; |
| 1086 |
simError(); |
| 1087 |
} |
| 1088 |
|
| 1089 |
return currentAtomType->mass; |
| 1090 |
} |
