| 336 |
|
// call new A_types in fortran |
| 337 |
|
|
| 338 |
|
int isError; |
| 339 |
+ |
|
| 340 |
+ |
// dummy variables |
| 341 |
+ |
int isLJ = 1; |
| 342 |
+ |
int isDipole = 0; |
| 343 |
+ |
int isSSD = 0; |
| 344 |
+ |
int isGB = 0; |
| 345 |
+ |
double w0 = 0.0; |
| 346 |
+ |
double v0 = 0.0; |
| 347 |
+ |
double dipole = 0.0; |
| 348 |
+ |
|
| 349 |
+ |
|
| 350 |
|
currentAtomType = headAtomType; |
| 351 |
|
while( currentAtomType != NULL ){ |
| 352 |
|
|
| 353 |
|
if( currentAtomType->name[0] != '\0' ){ |
| 354 |
|
isError = 0; |
| 355 |
< |
newLJtype( &(currentAtomType->ident), |
| 356 |
< |
&(currentAtomType->mass), |
| 357 |
< |
&(currentAtomType->epslon), |
| 358 |
< |
&(currentAtomType->sigma), |
| 359 |
< |
&isError ); |
| 355 |
> |
newAtype( &(currentAtomType->ident), |
| 356 |
> |
&(currentAtomType->mass), |
| 357 |
> |
&(currentAtomType->epslon), |
| 358 |
> |
&(currentAtomType->sigma), |
| 359 |
> |
&isLJ, &isSSD, &isDipole, &isGB, &w0, &v0, &dipole, |
| 360 |
> |
&isError ); |
| 361 |
|
if( isError ){ |
| 362 |
|
sprintf( painCave.errMsg, |
| 363 |
|
"Error initializing the \"%s\" atom type in fortran\n", |
| 426 |
|
MPIcheckPoint(); |
| 427 |
|
#endif // is_mpi |
| 428 |
|
|
| 429 |
< |
initFortran(); |
| 429 |
> |
this->initFortran(); |
| 430 |
|
entry_plug->refreshSim(); |
| 431 |
< |
|
| 431 |
> |
|
| 432 |
|
} |
| 433 |
|
|
| 434 |
|
void LJ_FF::initializeBonds( bond_pair* the_bonds ){ |
| 467 |
|
painCave.isFatal = 1; |
| 468 |
|
simError(); |
| 469 |
|
} |
| 458 |
– |
#ifdef IS_MPI |
| 459 |
– |
MPIcheckPoint(); |
| 460 |
– |
#endif // is_mpi |
| 461 |
– |
|
| 462 |
– |
} |
| 463 |
– |
|
| 464 |
– |
void LJ_FF::doForces( int calcPot ){ |
| 465 |
– |
|
| 466 |
– |
int i, isError; |
| 467 |
– |
double* frc; |
| 468 |
– |
double* pos; |
| 469 |
– |
double* tau; |
| 470 |
– |
short int passedCalcPot = (short int)calcPot; |
| 471 |
– |
|
| 472 |
– |
// forces are zeroed here, before any are acumulated. |
| 473 |
– |
// NOTE: do not rezero the forces in Fortran. |
| 474 |
– |
|
| 475 |
– |
for(i=0; i<entry_plug->n_atoms; i++){ |
| 476 |
– |
entry_plug->atoms[i]->zeroForces(); |
| 477 |
– |
} |
| 478 |
– |
|
| 479 |
– |
frc = Atom::getFrcArray(); |
| 480 |
– |
pos = Atom::getPosArray(); |
| 481 |
– |
tau = entry_plug->tau; |
| 482 |
– |
|
| 483 |
– |
isError = 0; |
| 484 |
– |
doLJfortran( pos, frc, &(entry_plug->lrPot), tau, &passedCalcPot, &isError ); |
| 485 |
– |
|
| 486 |
– |
|
| 487 |
– |
if( isError ){ |
| 488 |
– |
sprintf( painCave.errMsg, |
| 489 |
– |
"Error returned from the fortran force calculation.\n" ); |
| 490 |
– |
painCave.isFatal = 1; |
| 491 |
– |
simError(); |
| 492 |
– |
} |
| 493 |
– |
|
| 470 |
|
#ifdef IS_MPI |
| 495 |
– |
sprintf( checkPointMsg, |
| 496 |
– |
"returned from the force calculation.\n" ); |
| 471 |
|
MPIcheckPoint(); |
| 472 |
|
#endif // is_mpi |
| 473 |
|
|
| 474 |
|
} |
| 501 |
– |
|
| 502 |
– |
void LJ_FF::initFortran( void ){ |
| 503 |
– |
|
| 504 |
– |
int nLocal = entry_plug->n_atoms; |
| 505 |
– |
int *ident; |
| 506 |
– |
int isError; |
| 507 |
– |
int i; |
| 475 |
|
|
| 509 |
– |
ident = new int[nLocal]; |
| 510 |
– |
|
| 511 |
– |
for(i=0; i<nLocal; i++){ |
| 512 |
– |
ident[i] = entry_plug->atoms[i]->getIdent(); |
| 513 |
– |
} |
| 514 |
– |
|
| 515 |
– |
isError = 0; |
| 516 |
– |
initLJfortran( &nLocal, ident, &isError ); |
| 517 |
– |
|
| 518 |
– |
if(isError){ |
| 519 |
– |
sprintf( painCave.errMsg, |
| 520 |
– |
"LJ_FF error: There was an error initializing the component list in fortran.\n" ); |
| 521 |
– |
painCave.isFatal = 1; |
| 522 |
– |
simError(); |
| 523 |
– |
} |
| 524 |
– |
|
| 525 |
– |
|
| 526 |
– |
#ifdef IS_MPI |
| 527 |
– |
sprintf( checkPointMsg, "LJ_FF successfully initialized the fortran component list.\n" ); |
| 528 |
– |
MPIcheckPoint(); |
| 529 |
– |
#endif // is_mpi |
| 530 |
– |
|
| 531 |
– |
delete[] ident; |
| 532 |
– |
|
| 533 |
– |
} |
| 534 |
– |
|
| 535 |
– |
|
| 476 |
|
void LJ_FF::fastForward( char* stopText, char* searchOwner ){ |
| 477 |
|
|
| 478 |
|
int foundText = 0; |
