| 1 |
#include <cstdlib> |
| 2 |
#include <cstdio> |
| 3 |
#include <cstring> |
| 4 |
|
| 5 |
#include <iostream> |
| 6 |
using namespace std; |
| 7 |
|
| 8 |
#include "ForceFields.hpp" |
| 9 |
#include "SRI.hpp" |
| 10 |
#include "simError.h" |
| 11 |
|
| 12 |
#include <fortranWrappers.hpp> |
| 13 |
|
| 14 |
#ifdef IS_MPI |
| 15 |
#include "mpiForceField.h" |
| 16 |
#endif // is_mpi |
| 17 |
|
| 18 |
namespace TPE { // restrict the access of the folowing to this file only. |
| 19 |
|
| 20 |
|
| 21 |
// Declare the structures that will be passed by MPI |
| 22 |
|
| 23 |
typedef struct{ |
| 24 |
char name[15]; |
| 25 |
double mass; |
| 26 |
double epslon; |
| 27 |
double sigma; |
| 28 |
double dipole; |
| 29 |
double w0; |
| 30 |
double v0; |
| 31 |
int isSSD; |
| 32 |
int isDipole; |
| 33 |
int ident; |
| 34 |
int last; // 0 -> default |
| 35 |
// 1 -> tells nodes to stop listening |
| 36 |
} atomStruct; |
| 37 |
|
| 38 |
|
| 39 |
typedef struct{ |
| 40 |
char nameA[15]; |
| 41 |
char nameB[15]; |
| 42 |
char type[30]; |
| 43 |
double d0; |
| 44 |
int last; // 0 -> default |
| 45 |
// 1 -> tells nodes to stop listening |
| 46 |
} bondStruct; |
| 47 |
|
| 48 |
|
| 49 |
typedef struct{ |
| 50 |
char nameA[15]; |
| 51 |
char nameB[15]; |
| 52 |
char nameC[15]; |
| 53 |
char type[30]; |
| 54 |
double k1, k2, k3, t0; |
| 55 |
int last; // 0 -> default |
| 56 |
// 1 -> tells nodes to stop listening |
| 57 |
} bendStruct; |
| 58 |
|
| 59 |
|
| 60 |
typedef struct{ |
| 61 |
char nameA[15]; |
| 62 |
char nameB[15]; |
| 63 |
char nameC[15]; |
| 64 |
char nameD[15]; |
| 65 |
char type[30]; |
| 66 |
double k1, k2, k3, k4; |
| 67 |
int last; // 0 -> default |
| 68 |
// 1 -> tells nodes to stop listening |
| 69 |
} torsionStruct; |
| 70 |
|
| 71 |
|
| 72 |
int parseAtom( char *lineBuffer, int lineNum, atomStruct &info ); |
| 73 |
int parseBond( char *lineBuffer, int lineNum, bondStruct &info ); |
| 74 |
int parseBend( char *lineBuffer, int lineNum, bendStruct &info ); |
| 75 |
int parseTorsion( char *lineBuffer, int lineNum, torsionStruct &info ); |
| 76 |
|
| 77 |
|
| 78 |
#ifdef IS_MPI |
| 79 |
|
| 80 |
MPI_Datatype mpiAtomStructType; |
| 81 |
MPI_Datatype mpiBondStructType; |
| 82 |
MPI_Datatype mpiBendStructType; |
| 83 |
MPI_Datatype mpiTorsionStructType; |
| 84 |
|
| 85 |
#endif |
| 86 |
|
| 87 |
} // namespace |
| 88 |
|
| 89 |
using namespace TPE; |
| 90 |
|
| 91 |
|
| 92 |
//**************************************************************** |
| 93 |
// begins the actual forcefield stuff. |
| 94 |
//**************************************************************** |
| 95 |
|
| 96 |
|
| 97 |
TraPPE_ExFF::TraPPE_ExFF(){ |
| 98 |
|
| 99 |
char fileName[200]; |
| 100 |
char* ffPath_env = "FORCE_PARAM_PATH"; |
| 101 |
char* ffPath; |
| 102 |
char temp[200]; |
| 103 |
char errMsg[1000]; |
| 104 |
|
| 105 |
// do the funtion wrapping |
| 106 |
wrapMeFF( this ); |
| 107 |
|
| 108 |
|
| 109 |
#ifdef IS_MPI |
| 110 |
int i; |
| 111 |
|
| 112 |
// ********************************************************************** |
| 113 |
// Init the atomStruct mpi type |
| 114 |
|
| 115 |
atomStruct atomProto; // mpiPrototype |
| 116 |
int atomBC[3] = {15,6,4}; // block counts |
| 117 |
MPI_Aint atomDspls[3]; // displacements |
| 118 |
MPI_Datatype atomMbrTypes[3]; // member mpi types |
| 119 |
|
| 120 |
MPI_Address(&atomProto.name, &atomDspls[0]); |
| 121 |
MPI_Address(&atomProto.mass, &atomDspls[1]); |
| 122 |
MPI_Address(&atomProto.isSSD, &atomDspls[2]); |
| 123 |
|
| 124 |
atomMbrTypes[0] = MPI_CHAR; |
| 125 |
atomMbrTypes[1] = MPI_DOUBLE; |
| 126 |
atomMbrTypes[2] = MPI_INT; |
| 127 |
|
| 128 |
for (i=2; i >= 0; i--) atomDspls[i] -= atomDspls[0]; |
| 129 |
|
| 130 |
MPI_Type_struct(3, atomBC, atomDspls, atomMbrTypes, &mpiAtomStructType); |
| 131 |
MPI_Type_commit(&mpiAtomStructType); |
| 132 |
|
| 133 |
|
| 134 |
// ********************************************************************** |
| 135 |
// Init the bondStruct mpi type |
| 136 |
|
| 137 |
bondStruct bondProto; // mpiPrototype |
| 138 |
int bondBC[3] = {60,1,1}; // block counts |
| 139 |
MPI_Aint bondDspls[3]; // displacements |
| 140 |
MPI_Datatype bondMbrTypes[3]; // member mpi types |
| 141 |
|
| 142 |
MPI_Address(&bondProto.nameA, &bondDspls[0]); |
| 143 |
MPI_Address(&bondProto.d0, &bondDspls[1]); |
| 144 |
MPI_Address(&bondProto.last, &bondDspls[2]); |
| 145 |
|
| 146 |
bondMbrTypes[0] = MPI_CHAR; |
| 147 |
bondMbrTypes[1] = MPI_DOUBLE; |
| 148 |
bondMbrTypes[2] = MPI_INT; |
| 149 |
|
| 150 |
for (i=2; i >= 0; i--) bondDspls[i] -= bondDspls[0]; |
| 151 |
|
| 152 |
MPI_Type_struct(3, bondBC, bondDspls, bondMbrTypes, &mpiBondStructType); |
| 153 |
MPI_Type_commit(&mpiBondStructType); |
| 154 |
|
| 155 |
|
| 156 |
// ********************************************************************** |
| 157 |
// Init the bendStruct mpi type |
| 158 |
|
| 159 |
bendStruct bendProto; // mpiPrototype |
| 160 |
int bendBC[3] = {75,4,1}; // block counts |
| 161 |
MPI_Aint bendDspls[3]; // displacements |
| 162 |
MPI_Datatype bendMbrTypes[3]; // member mpi types |
| 163 |
|
| 164 |
MPI_Address(&bendProto.nameA, &bendDspls[0]); |
| 165 |
MPI_Address(&bendProto.k1, &bendDspls[1]); |
| 166 |
MPI_Address(&bendProto.last, &bendDspls[2]); |
| 167 |
|
| 168 |
bendMbrTypes[0] = MPI_CHAR; |
| 169 |
bendMbrTypes[1] = MPI_DOUBLE; |
| 170 |
bendMbrTypes[2] = MPI_INT; |
| 171 |
|
| 172 |
for (i=2; i >= 0; i--) bendDspls[i] -= bendDspls[0]; |
| 173 |
|
| 174 |
MPI_Type_struct(3, bendBC, bendDspls, bendMbrTypes, &mpiBendStructType); |
| 175 |
MPI_Type_commit(&mpiBendStructType); |
| 176 |
|
| 177 |
|
| 178 |
// ********************************************************************** |
| 179 |
// Init the torsionStruct mpi type |
| 180 |
|
| 181 |
torsionStruct torsionProto; // mpiPrototype |
| 182 |
int torsionBC[3] = {90,4,1}; // block counts |
| 183 |
MPI_Aint torsionDspls[3]; // displacements |
| 184 |
MPI_Datatype torsionMbrTypes[3]; // member mpi types |
| 185 |
|
| 186 |
MPI_Address(&torsionProto.nameA, &torsionDspls[0]); |
| 187 |
MPI_Address(&torsionProto.k1, &torsionDspls[1]); |
| 188 |
MPI_Address(&torsionProto.last, &torsionDspls[2]); |
| 189 |
|
| 190 |
torsionMbrTypes[0] = MPI_CHAR; |
| 191 |
torsionMbrTypes[1] = MPI_DOUBLE; |
| 192 |
torsionMbrTypes[2] = MPI_INT; |
| 193 |
|
| 194 |
for (i=2; i >= 0; i--) torsionDspls[i] -= torsionDspls[0]; |
| 195 |
|
| 196 |
MPI_Type_struct(3, torsionBC, torsionDspls, torsionMbrTypes, |
| 197 |
&mpiTorsionStructType); |
| 198 |
MPI_Type_commit(&mpiTorsionStructType); |
| 199 |
|
| 200 |
// *********************************************************************** |
| 201 |
|
| 202 |
if( worldRank == 0 ){ |
| 203 |
#endif |
| 204 |
|
| 205 |
// generate the force file name |
| 206 |
|
| 207 |
strcpy( fileName, "TraPPE_Ex.frc" ); |
| 208 |
// fprintf( stderr,"Trying to open %s\n", fileName ); |
| 209 |
|
| 210 |
// attempt to open the file in the current directory first. |
| 211 |
|
| 212 |
frcFile = fopen( fileName, "r" ); |
| 213 |
|
| 214 |
if( frcFile == NULL ){ |
| 215 |
|
| 216 |
// next see if the force path enviorment variable is set |
| 217 |
|
| 218 |
ffPath = getenv( ffPath_env ); |
| 219 |
if( ffPath == NULL ) { |
| 220 |
STR_DEFINE(ffPath, FRC_PATH ); |
| 221 |
} |
| 222 |
|
| 223 |
|
| 224 |
strcpy( temp, ffPath ); |
| 225 |
strcat( temp, "/" ); |
| 226 |
strcat( temp, fileName ); |
| 227 |
strcpy( fileName, temp ); |
| 228 |
|
| 229 |
frcFile = fopen( fileName, "r" ); |
| 230 |
|
| 231 |
if( frcFile == NULL ){ |
| 232 |
|
| 233 |
sprintf( painCave.errMsg, |
| 234 |
"Error opening the force field parameter file: %s\n" |
| 235 |
"Have you tried setting the FORCE_PARAM_PATH environment " |
| 236 |
"vairable?\n", |
| 237 |
fileName ); |
| 238 |
painCave.isFatal = 1; |
| 239 |
simError(); |
| 240 |
} |
| 241 |
} |
| 242 |
|
| 243 |
#ifdef IS_MPI |
| 244 |
} |
| 245 |
|
| 246 |
sprintf( checkPointMsg, "TraPPE_ExFF file opened sucessfully." ); |
| 247 |
MPIcheckPoint(); |
| 248 |
|
| 249 |
#endif // is_mpi |
| 250 |
} |
| 251 |
|
| 252 |
|
| 253 |
TraPPE_ExFF::~TraPPE_ExFF(){ |
| 254 |
|
| 255 |
#ifdef IS_MPI |
| 256 |
if( worldRank == 0 ){ |
| 257 |
#endif // is_mpi |
| 258 |
|
| 259 |
fclose( frcFile ); |
| 260 |
|
| 261 |
#ifdef IS_MPI |
| 262 |
} |
| 263 |
#endif // is_mpi |
| 264 |
} |
| 265 |
|
| 266 |
void TraPPE_ExFF::doForces( int calcPot ){ |
| 267 |
|
| 268 |
int i, isError; |
| 269 |
double* frc; |
| 270 |
double* pos; |
| 271 |
double* tau; |
| 272 |
short int passedCalcPot = (short int)calcPot; |
| 273 |
|
| 274 |
// forces are zeroed here, before any are acumulated. |
| 275 |
// NOTE: do not rezero the forces in Fortran. |
| 276 |
|
| 277 |
for(i=0; i<entry_plug->n_atoms; i++){ |
| 278 |
entry_plug->atoms[i]->zeroForces(); |
| 279 |
} |
| 280 |
|
| 281 |
frc = Atom::getFrcArray(); |
| 282 |
pos = Atom::getPosArray(); |
| 283 |
tau = entry_plug->tau; |
| 284 |
|
| 285 |
isError = 0; |
| 286 |
fortranForceLoop( pos, frc, &(entry_plug->lrPot), tau, |
| 287 |
&passedCalcPot, &isError ); |
| 288 |
|
| 289 |
|
| 290 |
if( isError ){ |
| 291 |
sprintf( painCave.errMsg, |
| 292 |
"Error returned from the fortran force calculation.\n" ); |
| 293 |
painCave.isFatal = 1; |
| 294 |
simError(); |
| 295 |
} |
| 296 |
|
| 297 |
#ifdef IS_MPI |
| 298 |
sprintf( checkPointMsg, |
| 299 |
"successfully returned from the force calculation.\n" ); |
| 300 |
MPIcheckPoint(); |
| 301 |
#endif // is_mpi |
| 302 |
|
| 303 |
} |
| 304 |
|
| 305 |
|
| 306 |
void TraPPE_ExFF::initializeAtoms( void ){ |
| 307 |
|
| 308 |
class LinkedType { |
| 309 |
public: |
| 310 |
LinkedType(){ |
| 311 |
next = NULL; |
| 312 |
name[0] = '\0'; |
| 313 |
} |
| 314 |
~LinkedType(){ if( next != NULL ) delete next; } |
| 315 |
|
| 316 |
LinkedType* find(char* key){ |
| 317 |
if( !strcmp(name, key) ) return this; |
| 318 |
if( next != NULL ) return next->find(key); |
| 319 |
return NULL; |
| 320 |
} |
| 321 |
|
| 322 |
void add( atomStruct &info ){ |
| 323 |
|
| 324 |
// check for duplicates |
| 325 |
|
| 326 |
if( !strcmp( info.name, name ) ){ |
| 327 |
sprintf( painCave.errMsg, |
| 328 |
"Duplicate TraPPE_Ex atom type \"%s\" found in " |
| 329 |
"the TraPPE_ExFF param file./n", |
| 330 |
name ); |
| 331 |
painCave.isFatal = 1; |
| 332 |
simError(); |
| 333 |
} |
| 334 |
|
| 335 |
if( next != NULL ) next->add(info); |
| 336 |
else{ |
| 337 |
next = new LinkedType(); |
| 338 |
strcpy(next->name, info.name); |
| 339 |
next->isDipole = info.isDipole; |
| 340 |
next->isSSD = info.isSSD; |
| 341 |
next->mass = info.mass; |
| 342 |
next->epslon = info.epslon; |
| 343 |
next->sigma = info.sigma; |
| 344 |
next->dipole = info.dipole; |
| 345 |
next->w0 = info.w0; |
| 346 |
next->v0 = info.v0; |
| 347 |
next->ident = info.ident; |
| 348 |
} |
| 349 |
} |
| 350 |
|
| 351 |
#ifdef IS_MPI |
| 352 |
|
| 353 |
void duplicate( atomStruct &info ){ |
| 354 |
strcpy(info.name, name); |
| 355 |
info.isDipole = isDipole; |
| 356 |
info.isSSD = isSSD; |
| 357 |
info.mass = mass; |
| 358 |
info.epslon = epslon; |
| 359 |
info.sigma = sigma; |
| 360 |
info.dipole = dipole; |
| 361 |
info.w0 = w0; |
| 362 |
info.v0 = v0; |
| 363 |
info.last = 0; |
| 364 |
} |
| 365 |
|
| 366 |
|
| 367 |
#endif |
| 368 |
|
| 369 |
char name[15]; |
| 370 |
int isDipole; |
| 371 |
int isSSD; |
| 372 |
double mass; |
| 373 |
double epslon; |
| 374 |
double sigma; |
| 375 |
double dipole; |
| 376 |
double w0; |
| 377 |
double v0; |
| 378 |
int ident; |
| 379 |
LinkedType* next; |
| 380 |
}; |
| 381 |
|
| 382 |
LinkedType* headAtomType; |
| 383 |
LinkedType* currentAtomType; |
| 384 |
atomStruct info; |
| 385 |
info.last = 1; // initialize last to have the last set. |
| 386 |
// if things go well, last will be set to 0 |
| 387 |
|
| 388 |
|
| 389 |
|
| 390 |
int i; |
| 391 |
int identNum; |
| 392 |
|
| 393 |
Atom** the_atoms; |
| 394 |
int nAtoms; |
| 395 |
the_atoms = entry_plug->atoms; |
| 396 |
nAtoms = entry_plug->n_atoms; |
| 397 |
|
| 398 |
|
| 399 |
////////////////////////////////////////////////// |
| 400 |
// a quick water fix |
| 401 |
|
| 402 |
double waterI[3][3]; |
| 403 |
waterI[0][0] = 1.76958347772500; |
| 404 |
waterI[0][1] = 0.0; |
| 405 |
waterI[0][2] = 0.0; |
| 406 |
|
| 407 |
waterI[1][0] = 0.0; |
| 408 |
waterI[1][1] = 0.614537057924513; |
| 409 |
waterI[1][2] = 0.0; |
| 410 |
|
| 411 |
waterI[2][0] = 0.0; |
| 412 |
waterI[2][1] = 0.0; |
| 413 |
waterI[2][2] = 1.15504641980049; |
| 414 |
|
| 415 |
|
| 416 |
double headI[3][3]; |
| 417 |
headI[0][0] = 1125; |
| 418 |
headI[0][1] = 0.0; |
| 419 |
headI[0][2] = 0.0; |
| 420 |
|
| 421 |
headI[1][0] = 0.0; |
| 422 |
headI[1][1] = 1125; |
| 423 |
headI[1][2] = 0.0; |
| 424 |
|
| 425 |
headI[2][0] = 0.0; |
| 426 |
headI[2][1] = 0.0; |
| 427 |
headI[2][2] = 250; |
| 428 |
|
| 429 |
|
| 430 |
|
| 431 |
////////////////////////////////////////////////// |
| 432 |
|
| 433 |
|
| 434 |
#ifdef IS_MPI |
| 435 |
if( worldRank == 0 ){ |
| 436 |
#endif |
| 437 |
|
| 438 |
// read in the atom types. |
| 439 |
|
| 440 |
headAtomType = new LinkedType; |
| 441 |
|
| 442 |
fastForward( "AtomTypes", "initializeAtoms" ); |
| 443 |
|
| 444 |
// we are now at the AtomTypes section. |
| 445 |
|
| 446 |
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
| 447 |
lineNum++; |
| 448 |
|
| 449 |
|
| 450 |
// read a line, and start parseing out the atom types |
| 451 |
|
| 452 |
if( eof_test == NULL ){ |
| 453 |
sprintf( painCave.errMsg, |
| 454 |
"Error in reading Atoms from force file at line %d.\n", |
| 455 |
lineNum ); |
| 456 |
painCave.isFatal = 1; |
| 457 |
simError(); |
| 458 |
} |
| 459 |
|
| 460 |
identNum = 1; |
| 461 |
// stop reading at end of file, or at next section |
| 462 |
while( readLine[0] != '#' && eof_test != NULL ){ |
| 463 |
|
| 464 |
// toss comment lines |
| 465 |
if( readLine[0] != '!' ){ |
| 466 |
|
| 467 |
// the parser returns 0 if the line was blank |
| 468 |
if( parseAtom( readLine, lineNum, info ) ){ |
| 469 |
info.ident = identNum; |
| 470 |
headAtomType->add( info );; |
| 471 |
identNum++; |
| 472 |
} |
| 473 |
} |
| 474 |
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
| 475 |
lineNum++; |
| 476 |
} |
| 477 |
|
| 478 |
#ifdef IS_MPI |
| 479 |
|
| 480 |
// send out the linked list to all the other processes |
| 481 |
|
| 482 |
sprintf( checkPointMsg, |
| 483 |
"TraPPE_ExFF atom structures read successfully." ); |
| 484 |
MPIcheckPoint(); |
| 485 |
|
| 486 |
currentAtomType = headAtomType->next; //skip the first element who is a place holder. |
| 487 |
while( currentAtomType != NULL ){ |
| 488 |
currentAtomType->duplicate( info ); |
| 489 |
|
| 490 |
|
| 491 |
|
| 492 |
sendFrcStruct( &info, mpiAtomStructType ); |
| 493 |
|
| 494 |
sprintf( checkPointMsg, |
| 495 |
"successfully sent TraPPE_Ex force type: \"%s\"\n", |
| 496 |
info.name ); |
| 497 |
MPIcheckPoint(); |
| 498 |
|
| 499 |
currentAtomType = currentAtomType->next; |
| 500 |
} |
| 501 |
info.last = 1; |
| 502 |
sendFrcStruct( &info, mpiAtomStructType ); |
| 503 |
|
| 504 |
} |
| 505 |
|
| 506 |
else{ |
| 507 |
|
| 508 |
// listen for node 0 to send out the force params |
| 509 |
|
| 510 |
MPIcheckPoint(); |
| 511 |
|
| 512 |
headAtomType = new LinkedType; |
| 513 |
recieveFrcStruct( &info, mpiAtomStructType ); |
| 514 |
|
| 515 |
while( !info.last ){ |
| 516 |
|
| 517 |
|
| 518 |
|
| 519 |
headAtomType->add( info ); |
| 520 |
|
| 521 |
MPIcheckPoint(); |
| 522 |
|
| 523 |
recieveFrcStruct( &info, mpiAtomStructType ); |
| 524 |
} |
| 525 |
} |
| 526 |
#endif // is_mpi |
| 527 |
|
| 528 |
// call new A_types in fortran |
| 529 |
|
| 530 |
int isError; |
| 531 |
|
| 532 |
// dummy variables |
| 533 |
|
| 534 |
int isGB = 0; |
| 535 |
int isLJ = 1; |
| 536 |
|
| 537 |
|
| 538 |
currentAtomType = headAtomType; |
| 539 |
while( currentAtomType != NULL ){ |
| 540 |
|
| 541 |
if( currentAtomType->name[0] != '\0' ){ |
| 542 |
isError = 0; |
| 543 |
newTPEtype( &(currentAtomType->ident), |
| 544 |
&(currentAtomType->mass), |
| 545 |
&(currentAtomType->epslon), |
| 546 |
&(currentAtomType->sigma), |
| 547 |
&isLJ, |
| 548 |
&(currentAtomType->isSSD), |
| 549 |
&(currentAtomType->isDipole), |
| 550 |
&isGB, |
| 551 |
&(currentAtomType->w0), |
| 552 |
&(currentAtomType->v0), |
| 553 |
&(currentAtomType->dipole), |
| 554 |
&isError ); |
| 555 |
if( isError ){ |
| 556 |
sprintf( painCave.errMsg, |
| 557 |
"Error initializing the \"%s\" atom type in fortran\n", |
| 558 |
currentAtomType->name ); |
| 559 |
painCave.isFatal = 1; |
| 560 |
simError(); |
| 561 |
} |
| 562 |
} |
| 563 |
currentAtomType = currentAtomType->next; |
| 564 |
} |
| 565 |
|
| 566 |
#ifdef IS_MPI |
| 567 |
sprintf( checkPointMsg, |
| 568 |
"TraPPE_ExFF atom structures successfully sent to fortran\n" ); |
| 569 |
MPIcheckPoint(); |
| 570 |
#endif // is_mpi |
| 571 |
|
| 572 |
|
| 573 |
// initialize the atoms |
| 574 |
|
| 575 |
double bigSigma = 0.0; |
| 576 |
DirectionalAtom* dAtom; |
| 577 |
|
| 578 |
for( i=0; i<nAtoms; i++ ){ |
| 579 |
|
| 580 |
currentAtomType = headAtomType->find( the_atoms[i]->getType() ); |
| 581 |
if( currentAtomType == NULL ){ |
| 582 |
sprintf( painCave.errMsg, |
| 583 |
"AtomType error, %s not found in force file.\n", |
| 584 |
the_atoms[i]->getType() ); |
| 585 |
painCave.isFatal = 1; |
| 586 |
simError(); |
| 587 |
} |
| 588 |
|
| 589 |
the_atoms[i]->setMass( currentAtomType->mass ); |
| 590 |
the_atoms[i]->setEpslon( currentAtomType->epslon ); |
| 591 |
the_atoms[i]->setSigma( currentAtomType->sigma ); |
| 592 |
the_atoms[i]->setLJ(); |
| 593 |
|
| 594 |
if( bigSigma < currentAtomType->sigma ) bigSigma = currentAtomType->sigma; |
| 595 |
|
| 596 |
if( currentAtomType->isDipole ){ |
| 597 |
if( the_atoms[i]->isDirectional() ){ |
| 598 |
|
| 599 |
dAtom = (DirectionalAtom *) the_atoms[i]; |
| 600 |
dAtom->setMu( currentAtomType->dipole ); |
| 601 |
dAtom->setHasDipole( 1 ); |
| 602 |
dAtom->setJx( 0.0 ); |
| 603 |
dAtom->setJy( 0.0 ); |
| 604 |
dAtom->setJz( 0.0 ); |
| 605 |
|
| 606 |
if(!strcmp("SSD",the_atoms[i]->getType())){ |
| 607 |
dAtom->setI( waterI ); |
| 608 |
dAtom->setSSD( 1 ); |
| 609 |
} |
| 610 |
else if(!strcmp("HEAD",the_atoms[i]->getType())){ |
| 611 |
dAtom->setI( headI ); |
| 612 |
dAtom->setSSD( 0 ); |
| 613 |
} |
| 614 |
else{ |
| 615 |
sprintf(painCave.errMsg, |
| 616 |
"AtmType error, %s does not have a moment of inertia set.\n", |
| 617 |
the_atoms[i]->getType() ); |
| 618 |
painCave.isFatal = 1; |
| 619 |
simError(); |
| 620 |
} |
| 621 |
entry_plug->n_dipoles++; |
| 622 |
} |
| 623 |
else{ |
| 624 |
|
| 625 |
sprintf( painCave.errMsg, |
| 626 |
"TraPPE_ExFF error: Atom \"%s\" is a dipole, yet no standard" |
| 627 |
" orientation was specifed in the BASS file.\n", |
| 628 |
currentAtomType->name ); |
| 629 |
painCave.isFatal = 1; |
| 630 |
simError(); |
| 631 |
} |
| 632 |
} |
| 633 |
else{ |
| 634 |
if( the_atoms[i]->isDirectional() ){ |
| 635 |
sprintf( painCave.errMsg, |
| 636 |
"TraPPE_ExFF error: Atom \"%s\" was given a standard" |
| 637 |
"orientation in the BASS file, yet it is not a dipole.\n", |
| 638 |
currentAtomType->name); |
| 639 |
painCave.isFatal = 1; |
| 640 |
simError(); |
| 641 |
} |
| 642 |
} |
| 643 |
} |
| 644 |
|
| 645 |
#ifdef IS_MPI |
| 646 |
double tempBig = bigSigma; |
| 647 |
MPI::COMM_WORLD.Allreduce( &tempBig, &bigSigma, 1, MPI_DOUBLE, MPI_MAX ); |
| 648 |
#endif //is_mpi |
| 649 |
|
| 650 |
//calc rCut and rList |
| 651 |
|
| 652 |
entry_plug->rCut = 2.5 * bigSigma; |
| 653 |
|
| 654 |
if(entry_plug->rCut > (entry_plug->box_x / 2.0)) |
| 655 |
entry_plug->rCut = entry_plug->box_x / 2.0; |
| 656 |
|
| 657 |
if(entry_plug->rCut > (entry_plug->box_y / 2.0)) |
| 658 |
entry_plug->rCut = entry_plug->box_y / 2.0; |
| 659 |
|
| 660 |
if(entry_plug->rCut > (entry_plug->box_z / 2.0)) |
| 661 |
entry_plug->rCut = entry_plug->box_z / 2.0; |
| 662 |
|
| 663 |
entry_plug->rList = entry_plug->rCut + 1.0; |
| 664 |
|
| 665 |
|
| 666 |
// clean up the memory |
| 667 |
|
| 668 |
delete headAtomType; |
| 669 |
|
| 670 |
#ifdef IS_MPI |
| 671 |
sprintf( checkPointMsg, "TraPPE_Ex atoms initialized succesfully" ); |
| 672 |
MPIcheckPoint(); |
| 673 |
#endif // is_mpi |
| 674 |
|
| 675 |
initFortran(); |
| 676 |
entry_plug->refreshSim(); |
| 677 |
|
| 678 |
} |
| 679 |
|
| 680 |
void TraPPE_ExFF::initializeBonds( bond_pair* the_bonds ){ |
| 681 |
|
| 682 |
class LinkedType { |
| 683 |
public: |
| 684 |
LinkedType(){ |
| 685 |
next = NULL; |
| 686 |
nameA[0] = '\0'; |
| 687 |
nameB[0] = '\0'; |
| 688 |
type[0] = '\0'; |
| 689 |
} |
| 690 |
~LinkedType(){ if( next != NULL ) delete next; } |
| 691 |
|
| 692 |
LinkedType* find(char* key1, char* key2){ |
| 693 |
if( !strcmp(nameA, key1 ) && !strcmp( nameB, key2 ) ) return this; |
| 694 |
if( !strcmp(nameA, key2 ) && !strcmp( nameB, key1 ) ) return this; |
| 695 |
if( next != NULL ) return next->find(key1, key2); |
| 696 |
return NULL; |
| 697 |
} |
| 698 |
|
| 699 |
|
| 700 |
void add( bondStruct &info ){ |
| 701 |
|
| 702 |
// check for duplicates |
| 703 |
int dup = 0; |
| 704 |
|
| 705 |
if( !strcmp(nameA, info.nameA ) && !strcmp( nameB, info.nameB ) ) dup = 1; |
| 706 |
if( !strcmp(nameA, info.nameB ) && !strcmp( nameB, info.nameA ) ) dup = 1; |
| 707 |
|
| 708 |
if(dup){ |
| 709 |
sprintf( painCave.errMsg, |
| 710 |
"Duplicate TraPPE_Ex bond type \"%s - %s\" found in " |
| 711 |
"the TraPPE_ExFF param file./n", |
| 712 |
nameA, nameB ); |
| 713 |
painCave.isFatal = 1; |
| 714 |
simError(); |
| 715 |
} |
| 716 |
|
| 717 |
|
| 718 |
if( next != NULL ) next->add(info); |
| 719 |
else{ |
| 720 |
next = new LinkedType(); |
| 721 |
strcpy(next->nameA, info.nameA); |
| 722 |
strcpy(next->nameB, info.nameB); |
| 723 |
strcpy(next->type, info.type); |
| 724 |
next->d0 = info.d0; |
| 725 |
} |
| 726 |
} |
| 727 |
|
| 728 |
#ifdef IS_MPI |
| 729 |
void duplicate( bondStruct &info ){ |
| 730 |
strcpy(info.nameA, nameA); |
| 731 |
strcpy(info.nameB, nameB); |
| 732 |
strcpy(info.type, type); |
| 733 |
info.d0 = d0; |
| 734 |
info.last = 0; |
| 735 |
} |
| 736 |
|
| 737 |
|
| 738 |
#endif |
| 739 |
|
| 740 |
char nameA[15]; |
| 741 |
char nameB[15]; |
| 742 |
char type[30]; |
| 743 |
double d0; |
| 744 |
|
| 745 |
LinkedType* next; |
| 746 |
}; |
| 747 |
|
| 748 |
|
| 749 |
|
| 750 |
LinkedType* headBondType; |
| 751 |
LinkedType* currentBondType; |
| 752 |
bondStruct info; |
| 753 |
info.last = 1; // initialize last to have the last set. |
| 754 |
// if things go well, last will be set to 0 |
| 755 |
|
| 756 |
SRI **the_sris; |
| 757 |
Atom** the_atoms; |
| 758 |
int nBonds; |
| 759 |
the_sris = entry_plug->sr_interactions; |
| 760 |
the_atoms = entry_plug->atoms; |
| 761 |
nBonds = entry_plug->n_bonds; |
| 762 |
|
| 763 |
int i, a, b; |
| 764 |
char* atomA; |
| 765 |
char* atomB; |
| 766 |
|
| 767 |
#ifdef IS_MPI |
| 768 |
if( worldRank == 0 ){ |
| 769 |
#endif |
| 770 |
|
| 771 |
// read in the bond types. |
| 772 |
|
| 773 |
headBondType = new LinkedType; |
| 774 |
|
| 775 |
fastForward( "BondTypes", "initializeBonds" ); |
| 776 |
|
| 777 |
// we are now at the bondTypes section |
| 778 |
|
| 779 |
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
| 780 |
lineNum++; |
| 781 |
|
| 782 |
|
| 783 |
// read a line, and start parseing out the atom types |
| 784 |
|
| 785 |
if( eof_test == NULL ){ |
| 786 |
sprintf( painCave.errMsg, |
| 787 |
"Error in reading bonds from force file at line %d.\n", |
| 788 |
lineNum ); |
| 789 |
painCave.isFatal = 1; |
| 790 |
simError(); |
| 791 |
} |
| 792 |
|
| 793 |
// stop reading at end of file, or at next section |
| 794 |
while( readLine[0] != '#' && eof_test != NULL ){ |
| 795 |
|
| 796 |
// toss comment lines |
| 797 |
if( readLine[0] != '!' ){ |
| 798 |
|
| 799 |
// the parser returns 0 if the line was blank |
| 800 |
if( parseBond( readLine, lineNum, info ) ){ |
| 801 |
headBondType->add( info ); |
| 802 |
} |
| 803 |
} |
| 804 |
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
| 805 |
lineNum++; |
| 806 |
} |
| 807 |
|
| 808 |
#ifdef IS_MPI |
| 809 |
|
| 810 |
// send out the linked list to all the other processes |
| 811 |
|
| 812 |
sprintf( checkPointMsg, |
| 813 |
"TraPPE_Ex bond structures read successfully." ); |
| 814 |
MPIcheckPoint(); |
| 815 |
|
| 816 |
currentBondType = headBondType; |
| 817 |
while( currentBondType != NULL ){ |
| 818 |
currentBondType->duplicate( info ); |
| 819 |
sendFrcStruct( &info, mpiBondStructType ); |
| 820 |
currentBondType = currentBondType->next; |
| 821 |
} |
| 822 |
info.last = 1; |
| 823 |
sendFrcStruct( &info, mpiBondStructType ); |
| 824 |
|
| 825 |
} |
| 826 |
|
| 827 |
else{ |
| 828 |
|
| 829 |
// listen for node 0 to send out the force params |
| 830 |
|
| 831 |
MPIcheckPoint(); |
| 832 |
|
| 833 |
headBondType = new LinkedType; |
| 834 |
recieveFrcStruct( &info, mpiBondStructType ); |
| 835 |
while( !info.last ){ |
| 836 |
|
| 837 |
headBondType->add( info ); |
| 838 |
recieveFrcStruct( &info, mpiBondStructType ); |
| 839 |
} |
| 840 |
} |
| 841 |
#endif // is_mpi |
| 842 |
|
| 843 |
|
| 844 |
// initialize the Bonds |
| 845 |
|
| 846 |
|
| 847 |
for( i=0; i<nBonds; i++ ){ |
| 848 |
|
| 849 |
a = the_bonds[i].a; |
| 850 |
b = the_bonds[i].b; |
| 851 |
|
| 852 |
atomA = the_atoms[a]->getType(); |
| 853 |
atomB = the_atoms[b]->getType(); |
| 854 |
currentBondType = headBondType->find( atomA, atomB ); |
| 855 |
if( currentBondType == NULL ){ |
| 856 |
sprintf( painCave.errMsg, |
| 857 |
"BondType error, %s - %s not found in force file.\n", |
| 858 |
atomA, atomB ); |
| 859 |
painCave.isFatal = 1; |
| 860 |
simError(); |
| 861 |
} |
| 862 |
|
| 863 |
if( !strcmp( currentBondType->type, "fixed" ) ){ |
| 864 |
|
| 865 |
the_sris[i] = new ConstrainedBond( *the_atoms[a], |
| 866 |
*the_atoms[b], |
| 867 |
currentBondType->d0 ); |
| 868 |
entry_plug->n_constraints++; |
| 869 |
} |
| 870 |
} |
| 871 |
|
| 872 |
|
| 873 |
// clean up the memory |
| 874 |
|
| 875 |
delete headBondType; |
| 876 |
|
| 877 |
#ifdef IS_MPI |
| 878 |
sprintf( checkPointMsg, "TraPPE_Ex bonds initialized succesfully" ); |
| 879 |
MPIcheckPoint(); |
| 880 |
#endif // is_mpi |
| 881 |
|
| 882 |
} |
| 883 |
|
| 884 |
void TraPPE_ExFF::initializeBends( bend_set* the_bends ){ |
| 885 |
|
| 886 |
class LinkedType { |
| 887 |
public: |
| 888 |
LinkedType(){ |
| 889 |
next = NULL; |
| 890 |
nameA[0] = '\0'; |
| 891 |
nameB[0] = '\0'; |
| 892 |
nameC[0] = '\0'; |
| 893 |
type[0] = '\0'; |
| 894 |
} |
| 895 |
~LinkedType(){ if( next != NULL ) delete next; } |
| 896 |
|
| 897 |
LinkedType* find( char* key1, char* key2, char* key3 ){ |
| 898 |
if( !strcmp( nameA, key1 ) && !strcmp( nameB, key2 ) |
| 899 |
&& !strcmp( nameC, key3 ) ) return this; |
| 900 |
if( !strcmp( nameA, key3 ) && !strcmp( nameB, key2 ) |
| 901 |
&& !strcmp( nameC, key1 ) ) return this; |
| 902 |
if( next != NULL ) return next->find(key1, key2, key3); |
| 903 |
return NULL; |
| 904 |
} |
| 905 |
|
| 906 |
void add( bendStruct &info ){ |
| 907 |
|
| 908 |
// check for duplicates |
| 909 |
int dup = 0; |
| 910 |
|
| 911 |
if( !strcmp( nameA, info.nameA ) && !strcmp( nameB, info.nameB ) |
| 912 |
&& !strcmp( nameC, info.nameC ) ) dup = 1; |
| 913 |
if( !strcmp( nameA, info.nameC ) && !strcmp( nameB, info.nameB ) |
| 914 |
&& !strcmp( nameC, info.nameA ) ) dup = 1; |
| 915 |
|
| 916 |
if(dup){ |
| 917 |
sprintf( painCave.errMsg, |
| 918 |
"Duplicate TraPPE_Ex bend type \"%s - %s - %s\" found in " |
| 919 |
"the TraPPE_ExFF param file./n", |
| 920 |
nameA, nameB, nameC ); |
| 921 |
painCave.isFatal = 1; |
| 922 |
simError(); |
| 923 |
} |
| 924 |
|
| 925 |
if( next != NULL ) next->add(info); |
| 926 |
else{ |
| 927 |
next = new LinkedType(); |
| 928 |
strcpy(next->nameA, info.nameA); |
| 929 |
strcpy(next->nameB, info.nameB); |
| 930 |
strcpy(next->nameC, info.nameC); |
| 931 |
strcpy(next->type, info.type); |
| 932 |
next->k1 = info.k1; |
| 933 |
next->k2 = info.k2; |
| 934 |
next->k3 = info.k3; |
| 935 |
next->t0 = info.t0; |
| 936 |
} |
| 937 |
} |
| 938 |
|
| 939 |
#ifdef IS_MPI |
| 940 |
|
| 941 |
void duplicate( bendStruct &info ){ |
| 942 |
strcpy(info.nameA, nameA); |
| 943 |
strcpy(info.nameB, nameB); |
| 944 |
strcpy(info.nameC, nameC); |
| 945 |
strcpy(info.type, type); |
| 946 |
info.k1 = k1; |
| 947 |
info.k2 = k2; |
| 948 |
info.k3 = k3; |
| 949 |
info.t0 = t0; |
| 950 |
info.last = 0; |
| 951 |
} |
| 952 |
|
| 953 |
#endif // is_mpi |
| 954 |
|
| 955 |
char nameA[15]; |
| 956 |
char nameB[15]; |
| 957 |
char nameC[15]; |
| 958 |
char type[30]; |
| 959 |
double k1, k2, k3, t0; |
| 960 |
|
| 961 |
LinkedType* next; |
| 962 |
}; |
| 963 |
|
| 964 |
LinkedType* headBendType; |
| 965 |
LinkedType* currentBendType; |
| 966 |
bendStruct info; |
| 967 |
info.last = 1; // initialize last to have the last set. |
| 968 |
// if things go well, last will be set to 0 |
| 969 |
|
| 970 |
QuadraticBend* qBend; |
| 971 |
GhostBend* gBend; |
| 972 |
SRI **the_sris; |
| 973 |
Atom** the_atoms; |
| 974 |
int nBends; |
| 975 |
the_sris = entry_plug->sr_interactions; |
| 976 |
the_atoms = entry_plug->atoms; |
| 977 |
nBends = entry_plug->n_bends; |
| 978 |
|
| 979 |
int i, a, b, c; |
| 980 |
char* atomA; |
| 981 |
char* atomB; |
| 982 |
char* atomC; |
| 983 |
|
| 984 |
|
| 985 |
#ifdef IS_MPI |
| 986 |
if( worldRank == 0 ){ |
| 987 |
#endif |
| 988 |
|
| 989 |
// read in the bend types. |
| 990 |
|
| 991 |
headBendType = new LinkedType; |
| 992 |
|
| 993 |
fastForward( "BendTypes", "initializeBends" ); |
| 994 |
|
| 995 |
// we are now at the bendTypes section |
| 996 |
|
| 997 |
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
| 998 |
lineNum++; |
| 999 |
|
| 1000 |
// read a line, and start parseing out the bend types |
| 1001 |
|
| 1002 |
if( eof_test == NULL ){ |
| 1003 |
sprintf( painCave.errMsg, |
| 1004 |
"Error in reading bends from force file at line %d.\n", |
| 1005 |
lineNum ); |
| 1006 |
painCave.isFatal = 1; |
| 1007 |
simError(); |
| 1008 |
} |
| 1009 |
|
| 1010 |
// stop reading at end of file, or at next section |
| 1011 |
while( readLine[0] != '#' && eof_test != NULL ){ |
| 1012 |
|
| 1013 |
// toss comment lines |
| 1014 |
if( readLine[0] != '!' ){ |
| 1015 |
|
| 1016 |
// the parser returns 0 if the line was blank |
| 1017 |
if( parseBend( readLine, lineNum, info ) ){ |
| 1018 |
headBendType->add( info ); |
| 1019 |
} |
| 1020 |
} |
| 1021 |
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
| 1022 |
lineNum++; |
| 1023 |
} |
| 1024 |
|
| 1025 |
#ifdef IS_MPI |
| 1026 |
|
| 1027 |
// send out the linked list to all the other processes |
| 1028 |
|
| 1029 |
sprintf( checkPointMsg, |
| 1030 |
"TraPPE_Ex bend structures read successfully." ); |
| 1031 |
MPIcheckPoint(); |
| 1032 |
|
| 1033 |
currentBendType = headBendType; |
| 1034 |
while( currentBendType != NULL ){ |
| 1035 |
currentBendType->duplicate( info ); |
| 1036 |
sendFrcStruct( &info, mpiBendStructType ); |
| 1037 |
currentBendType = currentBendType->next; |
| 1038 |
} |
| 1039 |
info.last = 1; |
| 1040 |
sendFrcStruct( &info, mpiBendStructType ); |
| 1041 |
|
| 1042 |
} |
| 1043 |
|
| 1044 |
else{ |
| 1045 |
|
| 1046 |
// listen for node 0 to send out the force params |
| 1047 |
|
| 1048 |
MPIcheckPoint(); |
| 1049 |
|
| 1050 |
headBendType = new LinkedType; |
| 1051 |
recieveFrcStruct( &info, mpiBendStructType ); |
| 1052 |
while( !info.last ){ |
| 1053 |
|
| 1054 |
headBendType->add( info ); |
| 1055 |
recieveFrcStruct( &info, mpiBendStructType ); |
| 1056 |
} |
| 1057 |
} |
| 1058 |
#endif // is_mpi |
| 1059 |
|
| 1060 |
// initialize the Bends |
| 1061 |
|
| 1062 |
int index; |
| 1063 |
|
| 1064 |
for( i=0; i<nBends; i++ ){ |
| 1065 |
|
| 1066 |
a = the_bends[i].a; |
| 1067 |
b = the_bends[i].b; |
| 1068 |
c = the_bends[i].c; |
| 1069 |
|
| 1070 |
atomA = the_atoms[a]->getType(); |
| 1071 |
atomB = the_atoms[b]->getType(); |
| 1072 |
|
| 1073 |
if( the_bends[i].isGhost ) atomC = "GHOST"; |
| 1074 |
else atomC = the_atoms[c]->getType(); |
| 1075 |
|
| 1076 |
currentBendType = headBendType->find( atomA, atomB, atomC ); |
| 1077 |
if( currentBendType == NULL ){ |
| 1078 |
sprintf( painCave.errMsg, "BendType error, %s - %s - %s not found" |
| 1079 |
" in force file.\n", |
| 1080 |
atomA, atomB, atomC ); |
| 1081 |
painCave.isFatal = 1; |
| 1082 |
simError(); |
| 1083 |
} |
| 1084 |
|
| 1085 |
if( !strcmp( currentBendType->type, "quadratic" ) ){ |
| 1086 |
|
| 1087 |
index = i + entry_plug->n_bonds; |
| 1088 |
|
| 1089 |
if( the_bends[i].isGhost){ |
| 1090 |
|
| 1091 |
if( the_bends[i].ghost == b ){ |
| 1092 |
// do nothing |
| 1093 |
} |
| 1094 |
else if( the_bends[i].ghost == a ){ |
| 1095 |
c = a; |
| 1096 |
a = b; |
| 1097 |
b = a; |
| 1098 |
} |
| 1099 |
else{ |
| 1100 |
sprintf( painCave.errMsg, |
| 1101 |
"BendType error, %s - %s - %s,\n" |
| 1102 |
" --> central atom is not " |
| 1103 |
"correctly identified with the " |
| 1104 |
"\"ghostVectorSource = \" tag.\n", |
| 1105 |
atomA, atomB, atomC ); |
| 1106 |
painCave.isFatal = 1; |
| 1107 |
simError(); |
| 1108 |
} |
| 1109 |
|
| 1110 |
gBend = new GhostBend( *the_atoms[a], |
| 1111 |
*the_atoms[b] ); |
| 1112 |
gBend->setConstants( currentBendType->k1, |
| 1113 |
currentBendType->k2, |
| 1114 |
currentBendType->k3, |
| 1115 |
currentBendType->t0 ); |
| 1116 |
the_sris[index] = gBend; |
| 1117 |
} |
| 1118 |
else{ |
| 1119 |
qBend = new QuadraticBend( *the_atoms[a], |
| 1120 |
*the_atoms[b], |
| 1121 |
*the_atoms[c] ); |
| 1122 |
qBend->setConstants( currentBendType->k1, |
| 1123 |
currentBendType->k2, |
| 1124 |
currentBendType->k3, |
| 1125 |
currentBendType->t0 ); |
| 1126 |
the_sris[index] = qBend; |
| 1127 |
} |
| 1128 |
} |
| 1129 |
} |
| 1130 |
|
| 1131 |
|
| 1132 |
// clean up the memory |
| 1133 |
|
| 1134 |
delete headBendType; |
| 1135 |
|
| 1136 |
#ifdef IS_MPI |
| 1137 |
sprintf( checkPointMsg, "TraPPE_Ex bends initialized succesfully" ); |
| 1138 |
MPIcheckPoint(); |
| 1139 |
#endif // is_mpi |
| 1140 |
|
| 1141 |
} |
| 1142 |
|
| 1143 |
void TraPPE_ExFF::initializeTorsions( torsion_set* the_torsions ){ |
| 1144 |
|
| 1145 |
class LinkedType { |
| 1146 |
public: |
| 1147 |
LinkedType(){ |
| 1148 |
next = NULL; |
| 1149 |
nameA[0] = '\0'; |
| 1150 |
nameB[0] = '\0'; |
| 1151 |
nameC[0] = '\0'; |
| 1152 |
type[0] = '\0'; |
| 1153 |
} |
| 1154 |
~LinkedType(){ if( next != NULL ) delete next; } |
| 1155 |
|
| 1156 |
LinkedType* find( char* key1, char* key2, char* key3, char* key4 ){ |
| 1157 |
if( !strcmp( nameA, key1 ) && !strcmp( nameB, key2 ) && |
| 1158 |
!strcmp( nameC, key3 ) && !strcmp( nameD, key4 ) ) return this; |
| 1159 |
|
| 1160 |
if( !strcmp( nameA, key4 ) && !strcmp( nameB, key3 ) && |
| 1161 |
!strcmp( nameC, key2 ) && !strcmp( nameD, key1 ) ) return this; |
| 1162 |
|
| 1163 |
if( next != NULL ) return next->find(key1, key2, key3, key4); |
| 1164 |
return NULL; |
| 1165 |
} |
| 1166 |
|
| 1167 |
void add( torsionStruct &info ){ |
| 1168 |
|
| 1169 |
// check for duplicates |
| 1170 |
int dup = 0; |
| 1171 |
|
| 1172 |
if( !strcmp( nameA, info.nameA ) && !strcmp( nameB, info.nameB ) && |
| 1173 |
!strcmp( nameC, info.nameC ) && !strcmp( nameD, info.nameD ) ) dup = 1; |
| 1174 |
|
| 1175 |
if( !strcmp( nameA, info.nameD ) && !strcmp( nameB, info.nameC ) && |
| 1176 |
!strcmp( nameC, info.nameB ) && !strcmp( nameD, info.nameA ) ) dup = 1; |
| 1177 |
|
| 1178 |
if(dup){ |
| 1179 |
sprintf( painCave.errMsg, |
| 1180 |
"Duplicate TraPPE_Ex torsion type \"%s - %s - %s - %s\" found in " |
| 1181 |
"the TraPPE_ExFF param file./n", nameA, nameB, nameC, nameD ); |
| 1182 |
painCave.isFatal = 1; |
| 1183 |
simError(); |
| 1184 |
} |
| 1185 |
|
| 1186 |
if( next != NULL ) next->add(info); |
| 1187 |
else{ |
| 1188 |
next = new LinkedType(); |
| 1189 |
strcpy(next->nameA, info.nameA); |
| 1190 |
strcpy(next->nameB, info.nameB); |
| 1191 |
strcpy(next->nameC, info.nameC); |
| 1192 |
strcpy(next->type, info.type); |
| 1193 |
next->k1 = info.k1; |
| 1194 |
next->k2 = info.k2; |
| 1195 |
next->k3 = info.k3; |
| 1196 |
next->k4 = info.k4; |
| 1197 |
} |
| 1198 |
} |
| 1199 |
|
| 1200 |
#ifdef IS_MPI |
| 1201 |
|
| 1202 |
void duplicate( torsionStruct &info ){ |
| 1203 |
strcpy(info.nameA, nameA); |
| 1204 |
strcpy(info.nameB, nameB); |
| 1205 |
strcpy(info.nameC, nameC); |
| 1206 |
strcpy(info.nameD, nameD); |
| 1207 |
strcpy(info.type, type); |
| 1208 |
info.k1 = k1; |
| 1209 |
info.k2 = k2; |
| 1210 |
info.k3 = k3; |
| 1211 |
info.k4 = k4; |
| 1212 |
info.last = 0; |
| 1213 |
} |
| 1214 |
|
| 1215 |
#endif |
| 1216 |
|
| 1217 |
char nameA[15]; |
| 1218 |
char nameB[15]; |
| 1219 |
char nameC[15]; |
| 1220 |
char nameD[15]; |
| 1221 |
char type[30]; |
| 1222 |
double k1, k2, k3, k4; |
| 1223 |
|
| 1224 |
LinkedType* next; |
| 1225 |
}; |
| 1226 |
|
| 1227 |
LinkedType* headTorsionType; |
| 1228 |
LinkedType* currentTorsionType; |
| 1229 |
torsionStruct info; |
| 1230 |
info.last = 1; // initialize last to have the last set. |
| 1231 |
// if things go well, last will be set to 0 |
| 1232 |
|
| 1233 |
int i, a, b, c, d, index; |
| 1234 |
char* atomA; |
| 1235 |
char* atomB; |
| 1236 |
char* atomC; |
| 1237 |
char* atomD; |
| 1238 |
CubicTorsion* cTors; |
| 1239 |
|
| 1240 |
SRI **the_sris; |
| 1241 |
Atom** the_atoms; |
| 1242 |
int nTorsions; |
| 1243 |
the_sris = entry_plug->sr_interactions; |
| 1244 |
the_atoms = entry_plug->atoms; |
| 1245 |
nTorsions = entry_plug->n_torsions; |
| 1246 |
|
| 1247 |
#ifdef IS_MPI |
| 1248 |
if( worldRank == 0 ){ |
| 1249 |
#endif |
| 1250 |
|
| 1251 |
// read in the torsion types. |
| 1252 |
|
| 1253 |
headTorsionType = new LinkedType; |
| 1254 |
|
| 1255 |
fastForward( "TorsionTypes", "initializeTorsions" ); |
| 1256 |
|
| 1257 |
// we are now at the torsionTypes section |
| 1258 |
|
| 1259 |
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
| 1260 |
lineNum++; |
| 1261 |
|
| 1262 |
|
| 1263 |
// read a line, and start parseing out the atom types |
| 1264 |
|
| 1265 |
if( eof_test == NULL ){ |
| 1266 |
sprintf( painCave.errMsg, |
| 1267 |
"Error in reading torsions from force file at line %d.\n", |
| 1268 |
lineNum ); |
| 1269 |
painCave.isFatal = 1; |
| 1270 |
simError(); |
| 1271 |
} |
| 1272 |
|
| 1273 |
// stop reading at end of file, or at next section |
| 1274 |
while( readLine[0] != '#' && eof_test != NULL ){ |
| 1275 |
|
| 1276 |
// toss comment lines |
| 1277 |
if( readLine[0] != '!' ){ |
| 1278 |
|
| 1279 |
// the parser returns 0 if the line was blank |
| 1280 |
if( parseTorsion( readLine, lineNum, info ) ){ |
| 1281 |
headTorsionType->add( info ); |
| 1282 |
} |
| 1283 |
} |
| 1284 |
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
| 1285 |
lineNum++; |
| 1286 |
} |
| 1287 |
|
| 1288 |
#ifdef IS_MPI |
| 1289 |
|
| 1290 |
// send out the linked list to all the other processes |
| 1291 |
|
| 1292 |
sprintf( checkPointMsg, |
| 1293 |
"TraPPE_Ex torsion structures read successfully." ); |
| 1294 |
MPIcheckPoint(); |
| 1295 |
|
| 1296 |
currentTorsionType = headTorsionType; |
| 1297 |
while( currentTorsionType != NULL ){ |
| 1298 |
currentTorsionType->duplicate( info ); |
| 1299 |
sendFrcStruct( &info, mpiTorsionStructType ); |
| 1300 |
currentTorsionType = currentTorsionType->next; |
| 1301 |
} |
| 1302 |
info.last = 1; |
| 1303 |
sendFrcStruct( &info, mpiTorsionStructType ); |
| 1304 |
|
| 1305 |
} |
| 1306 |
|
| 1307 |
else{ |
| 1308 |
|
| 1309 |
// listen for node 0 to send out the force params |
| 1310 |
|
| 1311 |
MPIcheckPoint(); |
| 1312 |
|
| 1313 |
headTorsionType = new LinkedType; |
| 1314 |
recieveFrcStruct( &info, mpiTorsionStructType ); |
| 1315 |
while( !info.last ){ |
| 1316 |
|
| 1317 |
headTorsionType->add( info ); |
| 1318 |
recieveFrcStruct( &info, mpiTorsionStructType ); |
| 1319 |
} |
| 1320 |
} |
| 1321 |
#endif // is_mpi |
| 1322 |
|
| 1323 |
// initialize the Torsions |
| 1324 |
|
| 1325 |
for( i=0; i<nTorsions; i++ ){ |
| 1326 |
|
| 1327 |
a = the_torsions[i].a; |
| 1328 |
b = the_torsions[i].b; |
| 1329 |
c = the_torsions[i].c; |
| 1330 |
d = the_torsions[i].d; |
| 1331 |
|
| 1332 |
atomA = the_atoms[a]->getType(); |
| 1333 |
atomB = the_atoms[b]->getType(); |
| 1334 |
atomC = the_atoms[c]->getType(); |
| 1335 |
atomD = the_atoms[d]->getType(); |
| 1336 |
currentTorsionType = headTorsionType->find( atomA, atomB, atomC, atomD ); |
| 1337 |
if( currentTorsionType == NULL ){ |
| 1338 |
sprintf( painCave.errMsg, |
| 1339 |
"TorsionType error, %s - %s - %s - %s not found" |
| 1340 |
" in force file.\n", |
| 1341 |
atomA, atomB, atomC, atomD ); |
| 1342 |
painCave.isFatal = 1; |
| 1343 |
simError(); |
| 1344 |
} |
| 1345 |
|
| 1346 |
if( !strcmp( currentTorsionType->type, "cubic" ) ){ |
| 1347 |
index = i + entry_plug->n_bonds + entry_plug->n_bends; |
| 1348 |
|
| 1349 |
cTors = new CubicTorsion( *the_atoms[a], *the_atoms[b], |
| 1350 |
*the_atoms[c], *the_atoms[d] ); |
| 1351 |
cTors->setConstants( currentTorsionType->k1, currentTorsionType->k2, |
| 1352 |
currentTorsionType->k3, currentTorsionType->k4 ); |
| 1353 |
the_sris[index] = cTors; |
| 1354 |
} |
| 1355 |
} |
| 1356 |
|
| 1357 |
|
| 1358 |
// clean up the memory |
| 1359 |
|
| 1360 |
delete headTorsionType; |
| 1361 |
|
| 1362 |
#ifdef IS_MPI |
| 1363 |
sprintf( checkPointMsg, "TraPPE_Ex torsions initialized succesfully" ); |
| 1364 |
MPIcheckPoint(); |
| 1365 |
#endif // is_mpi |
| 1366 |
|
| 1367 |
} |
| 1368 |
|
| 1369 |
void TraPPE_ExFF::fastForward( char* stopText, char* searchOwner ){ |
| 1370 |
|
| 1371 |
int foundText = 0; |
| 1372 |
char* the_token; |
| 1373 |
|
| 1374 |
rewind( frcFile ); |
| 1375 |
lineNum = 0; |
| 1376 |
|
| 1377 |
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
| 1378 |
lineNum++; |
| 1379 |
if( eof_test == NULL ){ |
| 1380 |
sprintf( painCave.errMsg, "Error fast forwarding force file for %s: " |
| 1381 |
" file is empty.\n", |
| 1382 |
searchOwner ); |
| 1383 |
painCave.isFatal = 1; |
| 1384 |
simError(); |
| 1385 |
} |
| 1386 |
|
| 1387 |
|
| 1388 |
while( !foundText ){ |
| 1389 |
while( eof_test != NULL && readLine[0] != '#' ){ |
| 1390 |
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
| 1391 |
lineNum++; |
| 1392 |
} |
| 1393 |
if( eof_test == NULL ){ |
| 1394 |
sprintf( painCave.errMsg, |
| 1395 |
"Error fast forwarding force file for %s at " |
| 1396 |
"line %d: file ended unexpectedly.\n", |
| 1397 |
searchOwner, |
| 1398 |
lineNum ); |
| 1399 |
painCave.isFatal = 1; |
| 1400 |
simError(); |
| 1401 |
} |
| 1402 |
|
| 1403 |
the_token = strtok( readLine, " ,;\t#\n" ); |
| 1404 |
foundText = !strcmp( stopText, the_token ); |
| 1405 |
|
| 1406 |
if( !foundText ){ |
| 1407 |
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
| 1408 |
lineNum++; |
| 1409 |
|
| 1410 |
if( eof_test == NULL ){ |
| 1411 |
sprintf( painCave.errMsg, |
| 1412 |
"Error fast forwarding force file for %s at " |
| 1413 |
"line %d: file ended unexpectedly.\n", |
| 1414 |
searchOwner, |
| 1415 |
lineNum ); |
| 1416 |
painCave.isFatal = 1; |
| 1417 |
simError(); |
| 1418 |
} |
| 1419 |
} |
| 1420 |
} |
| 1421 |
} |
| 1422 |
|
| 1423 |
|
| 1424 |
int parseAtom( char *lineBuffer, int lineNum, atomStruct &info ){ |
| 1425 |
|
| 1426 |
char* the_token; |
| 1427 |
|
| 1428 |
the_token = strtok( lineBuffer, " \n\t,;" ); |
| 1429 |
if( the_token != NULL ){ |
| 1430 |
|
| 1431 |
strcpy( info.name, the_token ); |
| 1432 |
|
| 1433 |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
| 1434 |
sprintf( painCave.errMsg, |
| 1435 |
"Error parseing AtomTypes: line %d\n", lineNum ); |
| 1436 |
painCave.isFatal = 1; |
| 1437 |
simError(); |
| 1438 |
} |
| 1439 |
|
| 1440 |
info.isDipole = atoi( the_token ); |
| 1441 |
|
| 1442 |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
| 1443 |
sprintf( painCave.errMsg, |
| 1444 |
"Error parseing AtomTypes: line %d\n", lineNum ); |
| 1445 |
painCave.isFatal = 1; |
| 1446 |
simError(); |
| 1447 |
} |
| 1448 |
|
| 1449 |
info.isSSD = atoi( the_token ); |
| 1450 |
|
| 1451 |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
| 1452 |
sprintf( painCave.errMsg, |
| 1453 |
"Error parseing AtomTypes: line %d\n", lineNum ); |
| 1454 |
painCave.isFatal = 1; |
| 1455 |
simError(); |
| 1456 |
} |
| 1457 |
|
| 1458 |
info.mass = atof( the_token ); |
| 1459 |
|
| 1460 |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
| 1461 |
sprintf( painCave.errMsg, |
| 1462 |
"Error parseing AtomTypes: line %d\n", lineNum ); |
| 1463 |
painCave.isFatal = 1; |
| 1464 |
simError(); |
| 1465 |
} |
| 1466 |
|
| 1467 |
info.epslon = atof( the_token ); |
| 1468 |
|
| 1469 |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
| 1470 |
sprintf( painCave.errMsg, |
| 1471 |
"Error parseing AtomTypes: line %d\n", lineNum ); |
| 1472 |
painCave.isFatal = 1; |
| 1473 |
simError(); |
| 1474 |
} |
| 1475 |
|
| 1476 |
info.sigma = atof( the_token ); |
| 1477 |
|
| 1478 |
if( info.isDipole ){ |
| 1479 |
|
| 1480 |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
| 1481 |
sprintf( painCave.errMsg, |
| 1482 |
"Error parseing AtomTypes: line %d\n", lineNum ); |
| 1483 |
painCave.isFatal = 1; |
| 1484 |
simError(); |
| 1485 |
} |
| 1486 |
|
| 1487 |
info.dipole = atof( the_token ); |
| 1488 |
} |
| 1489 |
else info.dipole = 0.0; |
| 1490 |
|
| 1491 |
if( info.isSSD ){ |
| 1492 |
|
| 1493 |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
| 1494 |
sprintf( painCave.errMsg, |
| 1495 |
"Error parseing AtomTypes: line %d\n", lineNum ); |
| 1496 |
painCave.isFatal = 1; |
| 1497 |
simError(); |
| 1498 |
} |
| 1499 |
|
| 1500 |
info.w0 = atof( the_token ); |
| 1501 |
|
| 1502 |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
| 1503 |
sprintf( painCave.errMsg, |
| 1504 |
"Error parseing AtomTypes: line %d\n", lineNum ); |
| 1505 |
painCave.isFatal = 1; |
| 1506 |
simError(); |
| 1507 |
} |
| 1508 |
|
| 1509 |
info.v0 = atof( the_token ); |
| 1510 |
} |
| 1511 |
else info.v0 = info.w0 = 0.0; |
| 1512 |
|
| 1513 |
return 1; |
| 1514 |
} |
| 1515 |
else return 0; |
| 1516 |
} |
| 1517 |
|
| 1518 |
int parseBond( char *lineBuffer, int lineNum, bondStruct &info ){ |
| 1519 |
|
| 1520 |
char* the_token; |
| 1521 |
|
| 1522 |
the_token = strtok( lineBuffer, " \n\t,;" ); |
| 1523 |
if( the_token != NULL ){ |
| 1524 |
|
| 1525 |
strcpy( info.nameA, the_token ); |
| 1526 |
|
| 1527 |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
| 1528 |
sprintf( painCave.errMsg, |
| 1529 |
"Error parseing BondTypes: line %d\n", lineNum ); |
| 1530 |
painCave.isFatal = 1; |
| 1531 |
simError(); |
| 1532 |
} |
| 1533 |
|
| 1534 |
strcpy( info.nameB, the_token ); |
| 1535 |
|
| 1536 |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
| 1537 |
sprintf( painCave.errMsg, |
| 1538 |
"Error parseing BondTypes: line %d\n", lineNum ); |
| 1539 |
painCave.isFatal = 1; |
| 1540 |
simError(); |
| 1541 |
} |
| 1542 |
|
| 1543 |
strcpy( info.type, the_token ); |
| 1544 |
|
| 1545 |
if( !strcmp( info.type, "fixed" ) ){ |
| 1546 |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
| 1547 |
sprintf( painCave.errMsg, |
| 1548 |
"Error parseing BondTypes: line %d\n", lineNum ); |
| 1549 |
painCave.isFatal = 1; |
| 1550 |
simError(); |
| 1551 |
} |
| 1552 |
|
| 1553 |
info.d0 = atof( the_token ); |
| 1554 |
} |
| 1555 |
else{ |
| 1556 |
sprintf( painCave.errMsg, |
| 1557 |
"Unknown TraPPE_Ex bond type \"%s\" at line %d\n", |
| 1558 |
info.type, |
| 1559 |
lineNum ); |
| 1560 |
painCave.isFatal = 1; |
| 1561 |
simError(); |
| 1562 |
} |
| 1563 |
|
| 1564 |
return 1; |
| 1565 |
} |
| 1566 |
else return 0; |
| 1567 |
} |
| 1568 |
|
| 1569 |
|
| 1570 |
int parseBend( char *lineBuffer, int lineNum, bendStruct &info ){ |
| 1571 |
|
| 1572 |
char* the_token; |
| 1573 |
|
| 1574 |
the_token = strtok( lineBuffer, " \n\t,;" ); |
| 1575 |
if( the_token != NULL ){ |
| 1576 |
|
| 1577 |
strcpy( info.nameA, the_token ); |
| 1578 |
|
| 1579 |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
| 1580 |
sprintf( painCave.errMsg, |
| 1581 |
"Error parseing BondTypes: line %d\n", lineNum ); |
| 1582 |
painCave.isFatal = 1; |
| 1583 |
simError(); |
| 1584 |
} |
| 1585 |
|
| 1586 |
strcpy( info.nameB, the_token ); |
| 1587 |
|
| 1588 |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
| 1589 |
sprintf( painCave.errMsg, |
| 1590 |
"Error parseing BondTypes: line %d\n", lineNum ); |
| 1591 |
painCave.isFatal = 1; |
| 1592 |
simError(); |
| 1593 |
} |
| 1594 |
|
| 1595 |
strcpy( info.nameC, the_token ); |
| 1596 |
|
| 1597 |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
| 1598 |
sprintf( painCave.errMsg, |
| 1599 |
"Error parseing BondTypes: line %d\n", lineNum ); |
| 1600 |
painCave.isFatal = 1; |
| 1601 |
simError(); |
| 1602 |
} |
| 1603 |
|
| 1604 |
strcpy( info.type, the_token ); |
| 1605 |
|
| 1606 |
if( !strcmp( info.type, "quadratic" ) ){ |
| 1607 |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
| 1608 |
sprintf( painCave.errMsg, |
| 1609 |
"Error parseing BendTypes: line %d\n", lineNum ); |
| 1610 |
painCave.isFatal = 1; |
| 1611 |
simError(); |
| 1612 |
} |
| 1613 |
|
| 1614 |
info.k1 = atof( the_token ); |
| 1615 |
|
| 1616 |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
| 1617 |
sprintf( painCave.errMsg, |
| 1618 |
"Error parseing BendTypes: line %d\n", lineNum ); |
| 1619 |
painCave.isFatal = 1; |
| 1620 |
simError(); |
| 1621 |
} |
| 1622 |
|
| 1623 |
info.k2 = atof( the_token ); |
| 1624 |
|
| 1625 |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
| 1626 |
sprintf( painCave.errMsg, |
| 1627 |
"Error parseing BendTypes: line %d\n", lineNum ); |
| 1628 |
painCave.isFatal = 1; |
| 1629 |
simError(); |
| 1630 |
} |
| 1631 |
|
| 1632 |
info.k3 = atof( the_token ); |
| 1633 |
|
| 1634 |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
| 1635 |
sprintf( painCave.errMsg, |
| 1636 |
"Error parseing BendTypes: line %d\n", lineNum ); |
| 1637 |
painCave.isFatal = 1; |
| 1638 |
simError(); |
| 1639 |
} |
| 1640 |
|
| 1641 |
info.t0 = atof( the_token ); |
| 1642 |
} |
| 1643 |
|
| 1644 |
else{ |
| 1645 |
sprintf( painCave.errMsg, |
| 1646 |
"Unknown TraPPE_Ex bend type \"%s\" at line %d\n", |
| 1647 |
info.type, |
| 1648 |
lineNum ); |
| 1649 |
painCave.isFatal = 1; |
| 1650 |
simError(); |
| 1651 |
} |
| 1652 |
|
| 1653 |
return 1; |
| 1654 |
} |
| 1655 |
else return 0; |
| 1656 |
} |
| 1657 |
|
| 1658 |
int parseTorsion( char *lineBuffer, int lineNum, torsionStruct &info ){ |
| 1659 |
|
| 1660 |
char* the_token; |
| 1661 |
|
| 1662 |
the_token = strtok( lineBuffer, " \n\t,;" ); |
| 1663 |
if( the_token != NULL ){ |
| 1664 |
|
| 1665 |
strcpy( info.nameA, the_token ); |
| 1666 |
|
| 1667 |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
| 1668 |
sprintf( painCave.errMsg, |
| 1669 |
"Error parseing TorsionTypes: line %d\n", lineNum ); |
| 1670 |
painCave.isFatal = 1; |
| 1671 |
simError(); |
| 1672 |
} |
| 1673 |
|
| 1674 |
strcpy( info.nameB, the_token ); |
| 1675 |
|
| 1676 |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
| 1677 |
sprintf( painCave.errMsg, |
| 1678 |
"Error parseing TorsionTypes: line %d\n", lineNum ); |
| 1679 |
painCave.isFatal = 1; |
| 1680 |
simError(); |
| 1681 |
} |
| 1682 |
|
| 1683 |
strcpy( info.nameC, the_token ); |
| 1684 |
|
| 1685 |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
| 1686 |
sprintf( painCave.errMsg, |
| 1687 |
"Error parseing TorsionTypes: line %d\n", lineNum ); |
| 1688 |
painCave.isFatal = 1; |
| 1689 |
simError(); |
| 1690 |
} |
| 1691 |
|
| 1692 |
strcpy( info.nameD, the_token ); |
| 1693 |
|
| 1694 |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
| 1695 |
sprintf( painCave.errMsg, |
| 1696 |
"Error parseing TorsionTypes: line %d\n", lineNum ); |
| 1697 |
painCave.isFatal = 1; |
| 1698 |
simError(); |
| 1699 |
} |
| 1700 |
|
| 1701 |
strcpy( info.type, the_token ); |
| 1702 |
|
| 1703 |
if( !strcmp( info.type, "cubic" ) ){ |
| 1704 |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
| 1705 |
sprintf( painCave.errMsg, |
| 1706 |
"Error parseing TorsionTypes: line %d\n", lineNum ); |
| 1707 |
painCave.isFatal = 1; |
| 1708 |
simError(); |
| 1709 |
} |
| 1710 |
|
| 1711 |
info.k1 = atof( the_token ); |
| 1712 |
|
| 1713 |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
| 1714 |
sprintf( painCave.errMsg, |
| 1715 |
"Error parseing TorsionTypes: line %d\n", lineNum ); |
| 1716 |
painCave.isFatal = 1; |
| 1717 |
simError(); |
| 1718 |
} |
| 1719 |
|
| 1720 |
info.k2 = atof( the_token ); |
| 1721 |
|
| 1722 |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
| 1723 |
sprintf( painCave.errMsg, |
| 1724 |
"Error parseing TorsionTypes: line %d\n", lineNum ); |
| 1725 |
painCave.isFatal = 1; |
| 1726 |
simError(); |
| 1727 |
} |
| 1728 |
|
| 1729 |
info.k3 = atof( the_token ); |
| 1730 |
|
| 1731 |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
| 1732 |
sprintf( painCave.errMsg, |
| 1733 |
"Error parseing TorsionTypes: line %d\n", lineNum ); |
| 1734 |
painCave.isFatal = 1; |
| 1735 |
simError(); |
| 1736 |
} |
| 1737 |
|
| 1738 |
info.k4 = atof( the_token ); |
| 1739 |
|
| 1740 |
} |
| 1741 |
|
| 1742 |
else{ |
| 1743 |
sprintf( painCave.errMsg, |
| 1744 |
"Unknown TraPPE_Ex torsion type \"%s\" at line %d\n", |
| 1745 |
info.type, |
| 1746 |
lineNum ); |
| 1747 |
painCave.isFatal = 1; |
| 1748 |
simError(); |
| 1749 |
} |
| 1750 |
|
| 1751 |
return 1; |
| 1752 |
} |
| 1753 |
|
| 1754 |
else return 0; |
| 1755 |
} |
