| 9 |
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#include "SRI.hpp" |
| 10 |
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#include "simError.h" |
| 11 |
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|
| 12 |
– |
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| 12 |
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// Declare the structures that will be passed by the parser and MPI |
| 13 |
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| 14 |
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typedef struct{ |
| 24 |
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int parseAtomLJ( char *lineBuffer, int lineNum, atomStruct &info ); |
| 25 |
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| 26 |
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#ifdef IS_MPI |
| 28 |
– |
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| 27 |
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#include "mpiForceField.h" |
| 28 |
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| 29 |
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MPI_Datatype mpiAtomStructType; |
| 71 |
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// begins the actual forcefield stuff. |
| 72 |
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//**************************************************************** |
| 73 |
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|
| 74 |
+ |
|
| 75 |
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LJ_FF::LJ_FF(){ |
| 76 |
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| 77 |
|
char fileName[200]; |
| 212 |
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short int* doPotentialCalc ) ){ |
| 213 |
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| 214 |
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|
| 215 |
< |
p1 = newLJtype; |
| 216 |
< |
p2 = initLJfortran; |
| 215 |
> |
newLJtype = p1; |
| 216 |
> |
initLJfortran = p2; |
| 217 |
|
currentLJwrap->setLJfortran( p3 ); |
| 218 |
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} |
| 219 |
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|
| 350 |
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"LJ_FF atom structures read successfully." ); |
| 351 |
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MPIcheckPoint(); |
| 352 |
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|
| 353 |
< |
currentAtomType = headAtomType; |
| 353 |
> |
currentAtomType = headAtomType->next; //skip the first element who is a place holder. |
| 354 |
|
while( currentAtomType != NULL ){ |
| 355 |
|
currentAtomType->duplicate( info ); |
| 356 |
+ |
|
| 357 |
+ |
|
| 358 |
+ |
|
| 359 |
|
sendFrcStruct( &info, mpiAtomStructType ); |
| 360 |
+ |
|
| 361 |
+ |
sprintf( checkPointMsg, |
| 362 |
+ |
"successfully sent lJ force type: \"%s\"\n", |
| 363 |
+ |
info.name ); |
| 364 |
+ |
MPIcheckPoint(); |
| 365 |
+ |
|
| 366 |
|
currentAtomType = currentAtomType->next; |
| 367 |
|
} |
| 368 |
|
info.last = 1; |
| 378 |
|
|
| 379 |
|
headAtomType = new LinkedType; |
| 380 |
|
recieveFrcStruct( &info, mpiAtomStructType ); |
| 381 |
+ |
|
| 382 |
|
while( !info.last ){ |
| 383 |
+ |
|
| 384 |
+ |
|
| 385 |
|
|
| 386 |
|
headAtomType->add( info ); |
| 387 |
+ |
|
| 388 |
+ |
MPIcheckPoint(); |
| 389 |
+ |
|
| 390 |
|
recieveFrcStruct( &info, mpiAtomStructType ); |
| 391 |
|
} |
| 392 |
|
} |
| 400 |
|
|
| 401 |
|
if( currentAtomType->name[0] != '\0' ){ |
| 402 |
|
isError = 0; |
| 403 |
< |
newLJtype( &(currentAtomType->ident), |
| 403 |
> |
newLJtype( &(currentAtomType->ident), |
| 404 |
|
&(currentAtomType->mass), |
| 405 |
|
&(currentAtomType->epslon), |
| 406 |
|
&(currentAtomType->sigma), |
| 452 |
|
|
| 453 |
|
#ifdef IS_MPI |
| 454 |
|
double tempBig = bigSigma; |
| 455 |
< |
MPI::COMM_WORLD::Allreduce( &tempBig, &bigSigma, 1, MPI_DOUBLE, MPI_MAX ); |
| 455 |
> |
MPI::COMM_WORLD.Allreduce( &tempBig, &bigSigma, 1, MPI_DOUBLE, MPI_MAX ); |
| 456 |
|
#endif //is_mpi |
| 457 |
|
|
| 458 |
|
//calc rCut and rList |
| 619 |
|
} |
| 620 |
|
|
| 621 |
|
|
| 622 |
< |
void LJ_FF::doForces( void ){ |
| 622 |
> |
void LJ_FF::doForces( int calcPot ){ |
| 623 |
|
|
| 624 |
|
int i; |
| 625 |
|
double* frc; |
| 626 |
|
double* pos; |
| 627 |
< |
short int calcPot = 1; |
| 627 |
> |
short int passedCalcPot = (short int)calcPot; |
| 628 |
|
|
| 629 |
|
// forces are zeroed here, before any are acumulated. |
| 630 |
|
// NOTE: do not rezero the forces in Fortran. |
| 636 |
|
frc = Atom::getFrcArray(); |
| 637 |
|
pos = Atom::getPosArray(); |
| 638 |
|
|
| 639 |
< |
doLJfortran( pos, frc, &(entry_plug->lrPot), &calcPot ); |
| 639 |
> |
// entry_plug->lrPot = -1; |
| 640 |
> |
doLJfortran( pos, frc, &(entry_plug->lrPot), &passedCalcPot ); |
| 641 |
> |
|
| 642 |
> |
|
| 643 |
> |
// fprintf( stderr, |
| 644 |
> |
// "lrPot = %lf\n", entry_plug->lrPot ); |
| 645 |
> |
|
| 646 |
|
} |
| 647 |
|
|
| 648 |
|
void LJ_FF::initFortran( void ){ |
