| 305 |
|
MPI_Type_commit(&mpiDirectionalStructType); |
| 306 |
|
|
| 307 |
|
// *********************************************************************** |
| 308 |
< |
|
| 308 |
> |
|
| 309 |
|
if( worldRank == 0 ){ |
| 310 |
|
#endif |
| 311 |
|
|
| 399 |
|
void WATER::readParams( void ){ |
| 400 |
|
|
| 401 |
|
int identNum; |
| 402 |
+ |
int tempDirect0, tempDirect1; |
| 403 |
|
|
| 404 |
|
atomStruct atomInfo; |
| 405 |
|
directionalStruct directionalInfo; |
| 410 |
|
|
| 411 |
|
atomPos = new fpos_t; |
| 412 |
|
bigSigma = 0.0; |
| 413 |
< |
|
| 413 |
> |
|
| 414 |
|
#ifdef IS_MPI |
| 415 |
|
if( worldRank == 0 ){ |
| 416 |
|
#endif |
| 421 |
|
headDirectionalType = new LinkedDirectionalType; |
| 422 |
|
|
| 423 |
|
fastForward( "AtomTypes", "initializeAtoms" ); |
| 424 |
< |
|
| 424 |
> |
|
| 425 |
|
// we are now at the AtomTypes section. |
| 426 |
|
|
| 427 |
|
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
| 429 |
|
|
| 430 |
|
|
| 431 |
|
// read a line, and start parsing out the atom types |
| 432 |
< |
|
| 432 |
> |
|
| 433 |
|
if( eof_test == NULL ){ |
| 434 |
|
sprintf( painCave.errMsg, |
| 435 |
|
"Error in reading Atoms from force file at line %d.\n", |
| 470 |
|
} |
| 471 |
|
|
| 472 |
|
#ifdef IS_MPI |
| 473 |
< |
|
| 473 |
> |
|
| 474 |
|
// send out the linked list to all the other processes |
| 475 |
|
|
| 476 |
|
sprintf( checkPointMsg, |
| 477 |
< |
"WATER atom structures read successfully." ); |
| 477 |
> |
"WATER atom and directional structures read successfully." ); |
| 478 |
|
MPIcheckPoint(); |
| 479 |
< |
currentAtomType = headAtomType->next; //skip the first element who is a place holder. |
| 479 |
> |
currentAtomType = headAtomType->next; //skip the first element place holder |
| 480 |
> |
currentDirectionalType = headDirectionalType->next; // same w/ directional |
| 481 |
> |
|
| 482 |
|
while( currentAtomType != NULL ){ |
| 483 |
|
currentAtomType->duplicate( atomInfo ); |
| 484 |
< |
|
| 484 |
> |
|
| 485 |
|
sendFrcStruct( &atomInfo, mpiAtomStructType ); |
| 486 |
|
|
| 487 |
|
sprintf( checkPointMsg, |
| 488 |
|
"successfully sent WATER force type: \"%s\"\n", |
| 489 |
|
atomInfo.name ); |
| 487 |
– |
MPIcheckPoint(); |
| 490 |
|
|
| 491 |
+ |
if ( atomInfo.isDirectional ){ |
| 492 |
+ |
// send out the directional linked list to all the other processes |
| 493 |
+ |
|
| 494 |
+ |
currentDirectionalType->duplicate( directionalInfo ); |
| 495 |
+ |
sendFrcStruct( &directionalInfo, mpiDirectionalStructType ); |
| 496 |
+ |
|
| 497 |
+ |
sprintf( checkPointMsg, |
| 498 |
+ |
"successfully sent WATER directional type: \"%s\"\n", |
| 499 |
+ |
directionalInfo.name ); |
| 500 |
+ |
} |
| 501 |
+ |
|
| 502 |
+ |
MPIcheckPoint(); |
| 503 |
+ |
tempDirect0 = atomInfo.isDirectional; |
| 504 |
|
currentAtomType = currentAtomType->next; |
| 505 |
+ |
if( tempDirect0 ) |
| 506 |
+ |
currentDirectionalType = currentDirectionalType->next; |
| 507 |
|
} |
| 508 |
< |
|
| 508 |
> |
|
| 509 |
|
atomInfo.last = 1; |
| 510 |
|
sendFrcStruct( &atomInfo, mpiAtomStructType ); |
| 511 |
< |
|
| 512 |
< |
if ( atomInfo.isDirectional ){ |
| 496 |
< |
// send out the linked list to all the other processes |
| 497 |
< |
|
| 498 |
< |
sprintf( checkPointMsg, |
| 499 |
< |
"WATER directional structures read successfully." ); |
| 500 |
< |
MPIcheckPoint(); |
| 501 |
< |
|
| 502 |
< |
currentDirectionalType = headDirectionalType->next; |
| 503 |
< |
while( currentDirectionalType != NULL ){ |
| 504 |
< |
currentDirectionalType->duplicate( directionalInfo ); |
| 505 |
< |
sendFrcStruct( &directionalInfo, mpiDirectionalStructType ); |
| 506 |
< |
currentDirectionalType = currentDirectionalType->next; |
| 507 |
< |
} |
| 508 |
< |
directionalInfo.last = 1; |
| 511 |
> |
directionalInfo.last = 1; |
| 512 |
> |
if ( atomInfo.isDirectional ) |
| 513 |
|
sendFrcStruct( &directionalInfo, mpiDirectionalStructType ); |
| 510 |
– |
} |
| 514 |
|
} |
| 515 |
< |
|
| 515 |
> |
|
| 516 |
|
else{ |
| 514 |
– |
|
| 517 |
|
// listen for node 0 to send out the force params |
| 518 |
|
|
| 519 |
|
MPIcheckPoint(); |
| 520 |
|
|
| 521 |
|
headAtomType = new LinkedAtomType; |
| 522 |
< |
receiveFrcStruct( &atomInfo, mpiAtomStructType ); |
| 523 |
< |
|
| 522 |
> |
headDirectionalType = new LinkedDirectionalType; |
| 523 |
> |
receiveFrcStruct( &atomInfo, mpiAtomStructType ); |
| 524 |
> |
|
| 525 |
> |
if ( atomInfo.isDirectional ) |
| 526 |
> |
receiveFrcStruct( &directionalInfo, mpiDirectionalStructType ); |
| 527 |
> |
|
| 528 |
|
while( !atomInfo.last ){ |
| 529 |
< |
|
| 529 |
> |
|
| 530 |
|
headAtomType->add( atomInfo ); |
| 531 |
|
|
| 532 |
|
MPIcheckPoint(); |
| 533 |
< |
|
| 533 |
> |
|
| 534 |
|
receiveFrcStruct( &atomInfo, mpiAtomStructType ); |
| 529 |
– |
} |
| 535 |
|
|
| 536 |
< |
if ( atomInfo.isDirectional ) { |
| 532 |
< |
// listen for node 0 to send out the force params |
| 533 |
< |
|
| 534 |
< |
MPIcheckPoint(); |
| 535 |
< |
|
| 536 |
< |
headDirectionalType = new LinkedDirectionalType; |
| 537 |
< |
receiveFrcStruct( &directionalInfo, mpiDirectionalStructType ); |
| 538 |
< |
while( !directionalInfo.last ){ |
| 539 |
< |
|
| 536 |
> |
if( atomInfo.isDirectional ){ |
| 537 |
|
headDirectionalType->add( directionalInfo ); |
| 538 |
+ |
|
| 539 |
|
receiveFrcStruct( &directionalInfo, mpiDirectionalStructType ); |
| 540 |
|
} |
| 543 |
– |
|
| 544 |
– |
sprintf( checkPointMsg, |
| 545 |
– |
"WATER directional structures broadcast successfully." ); |
| 546 |
– |
MPIcheckPoint(); |
| 541 |
|
} |
| 542 |
|
} |
| 543 |
|
|
| 630 |
|
|
| 631 |
|
#ifdef IS_MPI |
| 632 |
|
sprintf( checkPointMsg, |
| 633 |
< |
"WATER atom structures successfully sent to fortran\n" ); |
| 633 |
> |
"WATER atom and directional structures successfully" |
| 634 |
> |
"sent to fortran\n" ); |
| 635 |
|
MPIcheckPoint(); |
| 636 |
|
#endif // is_mpi |
| 637 |
|
|
| 640 |
|
|
| 641 |
|
void WATER::initializeAtoms( int nAtoms, Atom** the_atoms ){ |
| 642 |
|
|
| 643 |
< |
int i,j; |
| 643 |
> |
int i,j,k; |
| 644 |
|
|
| 645 |
|
// initialize the atoms |
| 646 |
|
DirectionalAtom* dAtom; |
| 647 |
|
double inertialMat[3][3]; |
| 648 |
|
|
| 649 |
|
for( i=0; i<nAtoms; i++ ){ |
| 655 |
– |
fprintf(stderr, "flag 1\n"); |
| 650 |
|
currentAtomType = headAtomType->find( the_atoms[i]->getType() ); |
| 657 |
– |
fprintf(stderr, "%s is the type\n", the_atoms[i]->getType()); |
| 651 |
|
if( currentAtomType == NULL ){ |
| 652 |
|
sprintf( painCave.errMsg, |
| 653 |
|
"AtomType error, %s not found in force file.\n", |
| 655 |
|
painCave.isFatal = 1; |
| 656 |
|
simError(); |
| 657 |
|
} |
| 665 |
– |
fprintf(stderr, "flag 2\n"); |
| 658 |
|
if( currentAtomType->isLJ ) the_atoms[i]->setLJ(); |
| 659 |
|
if( currentAtomType->isCharge ) the_atoms[i]->setCharged(); |
| 660 |
|
the_atoms[i]->setMass( currentAtomType->mass ); |
| 661 |
|
the_atoms[i]->setIdent( currentAtomType->ident ); |
| 662 |
< |
fprintf(stderr, "flag 3\n"); |
| 662 |
> |
|
| 663 |
|
if( bigSigma < currentAtomType->sigma ) bigSigma = currentAtomType->sigma; |
| 664 |
|
|
| 665 |
|
if( currentAtomType->isDirectional ){ |
| 674 |
– |
fprintf(stderr, "flag 4\n"); |
| 666 |
|
currentDirectionalType = |
| 667 |
|
headDirectionalType->find( the_atoms[i]->getType() ); |
| 677 |
– |
fprintf(stderr, "%s is the type\n", the_atoms[i]->getType()); |
| 668 |
|
if( currentDirectionalType == NULL ){ |
| 669 |
|
sprintf( painCave.errMsg, |
| 670 |
|
"DirectionalType error, %s not found in force file.\n", |
| 674 |
|
} |
| 675 |
|
|
| 676 |
|
// zero out the moments of inertia matrix |
| 677 |
< |
for( i=0; i<3; i++ ) |
| 678 |
< |
for( j=0; j<3; j++ ) |
| 679 |
< |
inertialMat[i][j] = 0.0; |
| 677 |
> |
for( j=0; j<3; j++ ) |
| 678 |
> |
for( k=0; k<3; k++ ) |
| 679 |
> |
inertialMat[j][k] = 0.0; |
| 680 |
|
|
| 681 |
|
// load the force file moments of inertia |
| 682 |
|
inertialMat[0][0] = currentDirectionalType->Ixx; |
| 683 |
|
inertialMat[1][1] = currentDirectionalType->Iyy; |
| 684 |
|
inertialMat[2][2] = currentDirectionalType->Izz; |
| 685 |
< |
fprintf(stderr, "Let's try pointing to isDirectional\n"); |
| 696 |
< |
fprintf(stderr, "%i what is this\n",the_atoms[i]->isDirectional()); |
| 685 |
> |
|
| 686 |
|
dAtom = (DirectionalAtom *) the_atoms[i]; |
| 698 |
– |
fprintf(stderr, "%i is isDipole\n", currentDirectionalType->isDipole); |
| 687 |
|
dAtom->setHasDipole( currentDirectionalType->isDipole ); |
| 688 |
|
dAtom->setMu( currentDirectionalType->dipole ); |
| 701 |
– |
fprintf(stderr, "flag 5\n"); |
| 689 |
|
dAtom->setMu( currentDirectionalType->dipole ); |
| 690 |
< |
fprintf(stderr,"flag 6\n"); |
| 690 |
> |
|
| 691 |
|
// if it's sticky then it's an SSD type |
| 692 |
|
dAtom->setSSD( currentDirectionalType->isSticky ); |
| 693 |
|
dAtom->setJx( 0.0 ); |
| 694 |
|
dAtom->setJy( 0.0 ); |
| 695 |
|
dAtom->setJz( 0.0 ); |
| 696 |
|
dAtom->setI( inertialMat ); |
| 697 |
< |
fprintf(stderr, "flag 7\n"); |
| 697 |
> |
|
| 698 |
|
entry_plug->n_dipoles++; |
| 712 |
– |
fprintf(stderr, "flag 8\n"); |
| 699 |
|
} |
| 700 |
|
else{ |
| 701 |
|
sprintf( painCave.errMsg, |
