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#include "SRI.hpp" |
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#include "simError.h" |
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// Declare the structures that will be passed by the parser and MPI |
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typedef struct{ |
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int parseAtomLJ( char *lineBuffer, int lineNum, atomStruct &info ); |
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#ifdef IS_MPI |
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#include "mpiForceField.h" |
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MPI_Datatype mpiAtomStructType; |
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void (*newLJtype)( int* ident, double* mass, double* epslon, double* sigma, |
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int* status ); |
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| 65 |
< |
void (*initLJfortran) ( int *nLocal, int *identArray, int *isError ) |
| 65 |
> |
void (*initLJfortran) ( int *nLocal, int *identArray, int *isError ); |
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LJ_FF* currentLJwrap; |
| 68 |
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// begins the actual forcefield stuff. |
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//**************************************************************** |
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| 74 |
+ |
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| 75 |
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LJ_FF::LJ_FF(){ |
| 76 |
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| 77 |
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char fileName[200]; |
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| 207 |
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void LJfunctionWrapper( void (*p1)( int* ident, double* mass, double* epslon, |
| 208 |
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double* sigma, int* status ), |
| 209 |
< |
void (*p2)( void ), |
| 209 |
> |
void (*p2)( int*, int*, int* ), |
| 210 |
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void (*p3)( double* positionArray,double* forceArray, |
| 211 |
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double* potentialEnergy, |
| 212 |
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short int* doPotentialCalc ) ){ |
| 213 |
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| 214 |
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| 215 |
< |
p1 = newLJtype; |
| 216 |
< |
p2 = initLJfortran; |
| 217 |
< |
this->setLJfortran( p3 ); |
| 215 |
> |
newLJtype = p1; |
| 216 |
> |
initLJfortran = p2; |
| 217 |
> |
currentLJwrap->setLJfortran( p3 ); |
| 218 |
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} |
| 219 |
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| 220 |
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| 241 |
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// check for duplicates |
| 242 |
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| 243 |
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if( !strcmp( info.name, name ) ){ |
| 244 |
< |
sprintf( simError.painCave, |
| 244 |
> |
sprintf( painCave.errMsg, |
| 245 |
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"Duplicate LJ atom type \"%s\" found in " |
| 246 |
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"the LJ_FF param file./n", |
| 247 |
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name ); |
| 306 |
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| 307 |
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headAtomType = new LinkedType; |
| 308 |
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| 309 |
< |
fastFoward( "AtomTypes", "initializeAtoms" ); |
| 309 |
> |
fastForward( "AtomTypes", "initializeAtoms" ); |
| 310 |
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| 311 |
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// we are now at the AtomTypes section. |
| 312 |
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| 385 |
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| 386 |
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if( currentAtomType->name[0] != '\0' ){ |
| 387 |
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isError = 0; |
| 388 |
< |
newLJtype( &(currentAtomType->ident), |
| 388 |
> |
newLJtype( &(currentAtomType->ident), |
| 389 |
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&(currentAtomType->mass), |
| 390 |
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&(currentAtomType->epslon), |
| 391 |
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&(currentAtomType->sigma), |
| 411 |
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| 412 |
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// initialize the atoms |
| 413 |
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| 414 |
+ |
double bigSigma = 0.0; |
| 415 |
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Atom* thisAtom; |
| 416 |
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| 417 |
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for( i=0; i<nAtoms; i++ ){ |
| 430 |
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the_atoms[i]->setSigma( currentAtomType->sigma ); |
| 431 |
|
the_atoms[i]->setIdent( currentAtomType->ident ); |
| 432 |
|
the_atoms[i]->setLJ(); |
| 433 |
+ |
|
| 434 |
+ |
if( bigSigma < currentAtomType->sigma ) bigSigma = currentAtomType->sigma; |
| 435 |
|
} |
| 436 |
+ |
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| 437 |
+ |
|
| 438 |
+ |
#ifdef IS_MPI |
| 439 |
+ |
double tempBig = bigSigma; |
| 440 |
+ |
MPI::COMM_WORLD.Allreduce( &tempBig, &bigSigma, 1, MPI_DOUBLE, MPI_MAX ); |
| 441 |
+ |
#endif //is_mpi |
| 442 |
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| 443 |
+ |
//calc rCut and rList |
| 444 |
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|
| 445 |
+ |
entry_plug->rCut = 2.5 * bigSigma; |
| 446 |
+ |
if(entry_plug->rCut > (entry_plug->box_x / 2.0)) entry_plug->rCut = entry_plug->box_x / 2.0; |
| 447 |
+ |
if(entry_plug->rCut > (entry_plug->box_y / 2.0)) entry_plug->rCut = entry_plug->box_y / 2.0; |
| 448 |
+ |
if(entry_plug->rCut > (entry_plug->box_z / 2.0)) entry_plug->rCut = entry_plug->box_z / 2.0; |
| 449 |
+ |
|
| 450 |
+ |
entry_plug->rList = entry_plug->rCut + 1.0; |
| 451 |
+ |
|
| 452 |
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// clean up the memory |
| 453 |
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| 454 |
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delete headAtomType; |
| 459 |
|
#endif // is_mpi |
| 460 |
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| 461 |
|
initFortran(); |
| 462 |
+ |
entry_plug->refreshSim(); |
| 463 |
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| 464 |
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} |
| 465 |
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| 604 |
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} |
| 605 |
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| 606 |
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|
| 607 |
< |
void LJ_FF::doForces( void ){ |
| 607 |
> |
void LJ_FF::doForces( int calcPot ){ |
| 608 |
|
|
| 609 |
|
int i; |
| 610 |
|
double* frc; |
| 611 |
|
double* pos; |
| 612 |
< |
double potE; |
| 596 |
< |
short int calcPot = 0; |
| 612 |
> |
short int passedCalcPot = (short int)calcPot; |
| 613 |
|
|
| 614 |
|
// forces are zeroed here, before any are acumulated. |
| 615 |
|
// NOTE: do not rezero the forces in Fortran. |
| 621 |
|
frc = Atom::getFrcArray(); |
| 622 |
|
pos = Atom::getPosArray(); |
| 623 |
|
|
| 624 |
< |
doLJfortran( pos, frc, potE, calcPot ); |
| 624 |
> |
// entry_plug->lrPot = -1; |
| 625 |
> |
doLJfortran( pos, frc, &(entry_plug->lrPot), &passedCalcPot ); |
| 626 |
> |
|
| 627 |
> |
|
| 628 |
> |
// fprintf( stderr, |
| 629 |
> |
// "lrPot = %lf\n", entry_plug->lrPot ); |
| 630 |
> |
|
| 631 |
|
} |
| 632 |
|
|
| 633 |
|
void LJ_FF::initFortran( void ){ |
| 640 |
|
ident = new int[nLocal]; |
| 641 |
|
|
| 642 |
|
for(i=0; i<nLocal; i++){ |
| 643 |
< |
ident[i] = entryplug->atoms[i]->getIdent(); |
| 643 |
> |
ident[i] = entry_plug->atoms[i]->getIdent(); |
| 644 |
|
} |
| 645 |
|
|
| 646 |
|
isError = 0; |
