42 |
|
thermalTime = 0.0; |
43 |
|
currentTime = 0.0; |
44 |
|
rCut = 0.0; |
45 |
< |
ecr = 0.0; |
46 |
< |
est = 0.0; |
45 |
> |
rSw = 0.0; |
46 |
|
|
47 |
|
haveRcut = 0; |
48 |
< |
haveEcr = 0; |
48 |
> |
haveRsw = 0; |
49 |
|
boxIsInit = 0; |
50 |
|
|
51 |
|
resetTime = 1e99; |
62 |
|
useReactionField = 0; |
63 |
|
useGB = 0; |
64 |
|
useEAM = 0; |
65 |
+ |
|
66 |
+ |
haveCutoffGroups = false; |
67 |
|
|
68 |
|
excludes = Exclude::Instance(); |
69 |
|
|
72 |
|
has_minimizer = false; |
73 |
|
the_minimizer =NULL; |
74 |
|
|
75 |
+ |
ngroup = 0; |
76 |
+ |
|
77 |
|
wrapMeSimInfo( this ); |
78 |
|
} |
79 |
|
|
86 |
|
|
87 |
|
for(i = properties.begin(); i != properties.end(); i++) |
88 |
|
delete (*i).second; |
89 |
< |
|
89 |
> |
|
90 |
|
} |
91 |
|
|
92 |
|
void SimInfo::setBox(double newBox[3]) { |
442 |
|
|
443 |
|
n_exclude = excludes->getSize(); |
444 |
|
excl = excludes->getFortranArray(); |
445 |
< |
|
445 |
> |
|
446 |
|
#ifdef IS_MPI |
447 |
|
n_global = mpiSim->getTotAtoms(); |
448 |
|
#else |
449 |
|
n_global = n_atoms; |
450 |
|
#endif |
451 |
< |
|
451 |
> |
|
452 |
|
isError = 0; |
453 |
< |
|
454 |
< |
setFsimulation( &fInfo, &n_global, &n_atoms, identArray, &n_exclude, excl, |
455 |
< |
&nGlobalExcludes, globalExcludes, molMembershipArray, |
456 |
< |
&isError ); |
457 |
< |
|
458 |
< |
if( isError ){ |
459 |
< |
|
453 |
> |
|
454 |
> |
getFortranGroupArray(this, mfact, ngroup, groupList, groupStart); |
455 |
> |
//it may not be a good idea to pass the address of first element in vector |
456 |
> |
//since c++ standard does not require vector to be stored continously in meomory |
457 |
> |
//Most of the compilers will organize the memory of vector continously |
458 |
> |
setFsimulation( &fInfo, &n_global, &n_atoms, identArray, &n_exclude, excl, |
459 |
> |
&nGlobalExcludes, globalExcludes, molMembershipArray, |
460 |
> |
&mfact[0], &ngroup, &groupList[0], &groupStart[0], &isError); |
461 |
> |
|
462 |
> |
if( isError ){ |
463 |
> |
|
464 |
|
sprintf( painCave.errMsg, |
465 |
< |
"There was an error setting the simulation information in fortran.\n" ); |
465 |
> |
"There was an error setting the simulation information in fortran.\n" ); |
466 |
|
painCave.isFatal = 1; |
467 |
|
simError(); |
468 |
|
} |
469 |
< |
|
469 |
> |
|
470 |
|
#ifdef IS_MPI |
471 |
|
sprintf( checkPointMsg, |
472 |
|
"succesfully sent the simulation information to fortran.\n"); |
473 |
|
MPIcheckPoint(); |
474 |
|
#endif // is_mpi |
475 |
< |
|
475 |
> |
|
476 |
|
this->ndf = this->getNDF(); |
477 |
|
this->ndfRaw = this->getNDFraw(); |
478 |
|
this->ndfTrans = this->getNDFtranslational(); |
479 |
|
} |
480 |
|
|
481 |
|
void SimInfo::setDefaultRcut( double theRcut ){ |
482 |
< |
|
482 |
> |
|
483 |
|
haveRcut = 1; |
484 |
|
rCut = theRcut; |
485 |
< |
|
479 |
< |
( rCut > ecr )? rList = rCut + 1.0: rList = ecr + 1.0; |
480 |
< |
|
481 |
< |
notifyFortranCutOffs( &rCut, &rList, &ecr, &est ); |
482 |
< |
} |
483 |
< |
|
484 |
< |
void SimInfo::setDefaultEcr( double theEcr ){ |
485 |
< |
|
486 |
< |
haveEcr = 1; |
487 |
< |
ecr = theEcr; |
485 |
> |
rList = rCut + 1.0; |
486 |
|
|
487 |
< |
( rCut > ecr )? rList = rCut + 1.0: rList = ecr + 1.0; |
490 |
< |
|
491 |
< |
notifyFortranCutOffs( &rCut, &rList, &ecr, &est ); |
487 |
> |
notifyFortranCutOffs( &rCut, &rSw, &rList ); |
488 |
|
} |
489 |
|
|
490 |
< |
void SimInfo::setDefaultEcr( double theEcr, double theEst ){ |
490 |
> |
void SimInfo::setDefaultRcut( double theRcut, double theRsw ){ |
491 |
|
|
492 |
< |
est = theEst; |
493 |
< |
setDefaultEcr( theEcr ); |
492 |
> |
rSw = theRsw; |
493 |
> |
setDefaultRcut( theRcut ); |
494 |
|
} |
495 |
|
|
496 |
|
|
502 |
|
|
503 |
|
if( rCut > maxCutoff ){ |
504 |
|
sprintf( painCave.errMsg, |
505 |
< |
"LJrcut is too large for the current periodic box.\n" |
506 |
< |
"\tCurrent Value of LJrcut = %G at time %G\n " |
505 |
> |
"cutoffRadius is too large for the current periodic box.\n" |
506 |
> |
"\tCurrent Value of cutoffRadius = %G at time %G\n " |
507 |
|
"\tThis is larger than half of at least one of the\n" |
508 |
|
"\tperiodic box vectors. Right now, the Box matrix is:\n" |
509 |
|
"\n" |
516 |
|
Hmat[2][0], Hmat[2][1], Hmat[2][2]); |
517 |
|
painCave.isFatal = 1; |
518 |
|
simError(); |
519 |
< |
} |
524 |
< |
|
525 |
< |
if( haveEcr ){ |
526 |
< |
if( ecr > maxCutoff ){ |
527 |
< |
sprintf( painCave.errMsg, |
528 |
< |
"electrostaticCutoffRadius is too large for the current\n" |
529 |
< |
"\tperiodic box.\n\n" |
530 |
< |
"\tCurrent Value of ECR = %G at time %G\n " |
531 |
< |
"\tThis is larger than half of at least one of the\n" |
532 |
< |
"\tperiodic box vectors. Right now, the Box matrix is:\n" |
533 |
< |
"\n" |
534 |
< |
"\t[ %G %G %G ]\n" |
535 |
< |
"\t[ %G %G %G ]\n" |
536 |
< |
"\t[ %G %G %G ]\n", |
537 |
< |
ecr, currentTime, |
538 |
< |
Hmat[0][0], Hmat[0][1], Hmat[0][2], |
539 |
< |
Hmat[1][0], Hmat[1][1], Hmat[1][2], |
540 |
< |
Hmat[2][0], Hmat[2][1], Hmat[2][2]); |
541 |
< |
painCave.isFatal = 1; |
542 |
< |
simError(); |
543 |
< |
} |
544 |
< |
} |
519 |
> |
} |
520 |
|
} else { |
521 |
|
// initialize this stuff before using it, OK? |
522 |
|
sprintf( painCave.errMsg, |
564 |
|
return NULL; |
565 |
|
} |
566 |
|
|
567 |
+ |
|
568 |
+ |
void getFortranGroupArray(SimInfo* info, vector<double>& mfact, int& ngroup, |
569 |
+ |
vector<int>& groupList, vector<int>& groupStart){ |
570 |
+ |
Molecule* myMols; |
571 |
+ |
Atom** myAtoms; |
572 |
+ |
int numAtom; |
573 |
+ |
int curIndex; |
574 |
+ |
double mtot; |
575 |
+ |
int numMol; |
576 |
+ |
int numCutoffGroups; |
577 |
+ |
CutoffGroup* myCutoffGroup; |
578 |
+ |
vector<CutoffGroup*>::iterator iterCutoff; |
579 |
+ |
Atom* cutoffAtom; |
580 |
+ |
vector<Atom*>::iterator iterAtom; |
581 |
+ |
int atomIndex; |
582 |
+ |
double totalMass; |
583 |
+ |
|
584 |
+ |
mfact.clear(); |
585 |
+ |
groupList.clear(); |
586 |
+ |
groupStart.clear(); |
587 |
+ |
|
588 |
+ |
//Be careful, fortran array begin at 1 |
589 |
+ |
curIndex = 1; |
590 |
+ |
|
591 |
+ |
myMols = info->molecules; |
592 |
+ |
numMol = info->n_mol; |
593 |
+ |
for(int i = 0; i < numMol; i++){ |
594 |
+ |
numAtom = myMols[i].getNAtoms(); |
595 |
+ |
myAtoms = myMols[i].getMyAtoms(); |
596 |
+ |
|
597 |
+ |
|
598 |
+ |
for(int j = 0; j < numAtom; j++){ |
599 |
+ |
|
600 |
+ |
|
601 |
+ |
#ifdef IS_MPI |
602 |
+ |
atomIndex = myAtoms[j]->getGlobalIndex(); |
603 |
+ |
#else |
604 |
+ |
atomIndex = myAtoms[j]->getIndex(); |
605 |
+ |
#endif |
606 |
+ |
|
607 |
+ |
if(myMols[i].belongToCutoffGroup(atomIndex)) |
608 |
+ |
continue; |
609 |
+ |
else{ |
610 |
+ |
mfact.push_back(myAtoms[j]->getMass()); |
611 |
+ |
groupList.push_back(myAtoms[j]->getIndex() + 1); |
612 |
+ |
groupStart.push_back(curIndex++); |
613 |
+ |
} |
614 |
+ |
} |
615 |
+ |
|
616 |
+ |
numCutoffGroups = myMols[i].getNCutoffGroups(); |
617 |
+ |
for(myCutoffGroup =myMols[i].beginCutoffGroup(iterCutoff); myCutoffGroup != NULL; |
618 |
+ |
myCutoffGroup =myMols[i].nextCutoffGroup(iterCutoff)){ |
619 |
+ |
|
620 |
+ |
totalMass = myCutoffGroup->getMass(); |
621 |
+ |
|
622 |
+ |
for(cutoffAtom = myCutoffGroup->beginAtom(iterAtom); cutoffAtom != NULL; |
623 |
+ |
cutoffAtom = myCutoffGroup->nextAtom(iterAtom)){ |
624 |
+ |
mfact.push_back(cutoffAtom->getMass()/totalMass); |
625 |
+ |
groupList.push_back(cutoffAtom->getIndex() + 1); |
626 |
+ |
} |
627 |
+ |
|
628 |
+ |
groupStart.push_back(curIndex); |
629 |
+ |
curIndex += myCutoffGroup->getNumAtom(); |
630 |
+ |
|
631 |
+ |
}//end for(myCutoffGroup =myMols[i].beginCutoffGroup(iterCutoff)) |
632 |
+ |
|
633 |
+ |
}//end for(int i = 0; i < numMol; i++) |
634 |
+ |
|
635 |
+ |
ngroup = groupStart.size(); |
636 |
+ |
} |