| 64 |
|
void (*newLJtype)( int* ident, double* mass, double* epslon, double* sigma, |
| 65 |
|
int* status ); |
| 66 |
|
|
| 67 |
< |
void (*initLJfortran) ( int *nLocal, int *identArray, int *isError ) |
| 67 |
> |
void (*initLJfortran) ( int *nLocal, int *identArray, int *isError ); |
| 68 |
|
|
| 69 |
|
LJ_FF* currentLJwrap; |
| 70 |
|
|
| 207 |
|
|
| 208 |
|
void LJfunctionWrapper( void (*p1)( int* ident, double* mass, double* epslon, |
| 209 |
|
double* sigma, int* status ), |
| 210 |
< |
void (*p2)( void ), |
| 210 |
> |
void (*p2)( int*, int*, int* ), |
| 211 |
|
void (*p3)( double* positionArray,double* forceArray, |
| 212 |
|
double* potentialEnergy, |
| 213 |
|
short int* doPotentialCalc ) ){ |
| 214 |
|
|
| 215 |
|
|
| 216 |
< |
p1 = newLJtype; |
| 217 |
< |
p2 = initLJfortran; |
| 218 |
< |
this->setLJfortran( p3 ); |
| 216 |
> |
newLJtype = p1; |
| 217 |
> |
initLJfortran = p2; |
| 218 |
> |
currentLJwrap->setLJfortran( p3 ); |
| 219 |
|
} |
| 220 |
|
|
| 221 |
|
|
| 242 |
|
// check for duplicates |
| 243 |
|
|
| 244 |
|
if( !strcmp( info.name, name ) ){ |
| 245 |
< |
sprintf( simError.painCave, |
| 245 |
> |
sprintf( painCave.errMsg, |
| 246 |
|
"Duplicate LJ atom type \"%s\" found in " |
| 247 |
|
"the LJ_FF param file./n", |
| 248 |
|
name ); |
| 307 |
|
|
| 308 |
|
headAtomType = new LinkedType; |
| 309 |
|
|
| 310 |
< |
fastFoward( "AtomTypes", "initializeAtoms" ); |
| 310 |
> |
fastForward( "AtomTypes", "initializeAtoms" ); |
| 311 |
|
|
| 312 |
|
// we are now at the AtomTypes section. |
| 313 |
|
|
| 386 |
|
|
| 387 |
|
if( currentAtomType->name[0] != '\0' ){ |
| 388 |
|
isError = 0; |
| 389 |
< |
newLJtype( &(currentAtomType->ident), |
| 389 |
> |
newLJtype( &(currentAtomType->ident), |
| 390 |
|
&(currentAtomType->mass), |
| 391 |
|
&(currentAtomType->epslon), |
| 392 |
|
&(currentAtomType->sigma), |
| 412 |
|
|
| 413 |
|
// initialize the atoms |
| 414 |
|
|
| 415 |
+ |
double bigSigma = 0.0; |
| 416 |
|
Atom* thisAtom; |
| 417 |
|
|
| 418 |
|
for( i=0; i<nAtoms; i++ ){ |
| 431 |
|
the_atoms[i]->setSigma( currentAtomType->sigma ); |
| 432 |
|
the_atoms[i]->setIdent( currentAtomType->ident ); |
| 433 |
|
the_atoms[i]->setLJ(); |
| 434 |
+ |
|
| 435 |
+ |
if( bigSigma < currentAtomType->sigma ) bigSigma = currentAtomType->sigma; |
| 436 |
|
} |
| 437 |
|
|
| 438 |
+ |
|
| 439 |
+ |
#ifdef IS_MPI |
| 440 |
+ |
double tempBig = bigSigma; |
| 441 |
+ |
MPI::COMM_WORLD::Allreduce( &tempBig, &bigSigma, 1, MPI_DOUBLE, MPI_MAX ); |
| 442 |
+ |
#endif //is_mpi |
| 443 |
|
|
| 444 |
+ |
//calc rCut and rList |
| 445 |
+ |
|
| 446 |
+ |
entry_plug->rCut = 2.5 * bigSigma; |
| 447 |
+ |
if(entry_plug->rCut > (entry_plug->box_x / 2.0)) entry_plug->rCut = entry_plug->box_x / 2.0; |
| 448 |
+ |
if(entry_plug->rCut > (entry_plug->box_y / 2.0)) entry_plug->rCut = entry_plug->box_y / 2.0; |
| 449 |
+ |
if(entry_plug->rCut > (entry_plug->box_z / 2.0)) entry_plug->rCut = entry_plug->box_z / 2.0; |
| 450 |
+ |
|
| 451 |
+ |
entry_plug->rList = entry_plug->rCut + 1.0; |
| 452 |
+ |
|
| 453 |
|
// clean up the memory |
| 454 |
|
|
| 455 |
|
delete headAtomType; |
| 460 |
|
#endif // is_mpi |
| 461 |
|
|
| 462 |
|
initFortran(); |
| 463 |
+ |
entry_plug->refreshSim(); |
| 464 |
|
|
| 465 |
|
} |
| 466 |
|
|
| 610 |
|
int i; |
| 611 |
|
double* frc; |
| 612 |
|
double* pos; |
| 613 |
< |
double potE; |
| 596 |
< |
short int calcPot = 0; |
| 613 |
> |
short int calcPot = 1; |
| 614 |
|
|
| 615 |
|
// forces are zeroed here, before any are acumulated. |
| 616 |
|
// NOTE: do not rezero the forces in Fortran. |
| 622 |
|
frc = Atom::getFrcArray(); |
| 623 |
|
pos = Atom::getPosArray(); |
| 624 |
|
|
| 625 |
< |
doLJfortran( pos, frc, potE, calcPot ); |
| 625 |
> |
doLJfortran( pos, frc, &(entry_plug->lrPot), &calcPot ); |
| 626 |
|
} |
| 627 |
|
|
| 628 |
|
void LJ_FF::initFortran( void ){ |
| 635 |
|
ident = new int[nLocal]; |
| 636 |
|
|
| 637 |
|
for(i=0; i<nLocal; i++){ |
| 638 |
< |
ident[i] = entryplug->atoms[i]->getIdent(); |
| 638 |
> |
ident[i] = entry_plug->atoms[i]->getIdent(); |
| 639 |
|
} |
| 640 |
|
|
| 641 |
|
isError = 0; |
