# | Line 42 | Line 42 | SimInfo::SimInfo(){ | |
---|---|---|
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; | |
# | Line 63 | Line 62 | SimInfo::SimInfo(){ | |
62 | useReactionField = 0; | |
63 | useGB = 0; | |
64 | useEAM = 0; | |
65 | < | useMolecularCutoffs = 0; |
65 | > | useSolidThermInt = 0; |
66 | > | useLiquidThermInt = 0; |
67 | > | |
68 | > | haveCutoffGroups = false; |
69 | ||
70 | excludes = Exclude::Instance(); | |
71 | ||
# | Line 444 | Line 446 | void SimInfo::refreshSim(){ | |
446 | excl = excludes->getFortranArray(); | |
447 | ||
448 | #ifdef IS_MPI | |
449 | < | n_global = mpiSim->getTotAtoms(); |
449 | > | n_global = mpiSim->getNAtomsGlobal(); |
450 | #else | |
451 | n_global = n_atoms; | |
452 | #endif | |
# | Line 452 | Line 454 | void SimInfo::refreshSim(){ | |
454 | isError = 0; | |
455 | ||
456 | getFortranGroupArray(this, mfact, ngroup, groupList, groupStart); | |
457 | < | |
457 | > | //it may not be a good idea to pass the address of first element in vector |
458 | > | //since c++ standard does not require vector to be stored continuously in meomory |
459 | > | //Most of the compilers will organize the memory of vector continuously |
460 | setFsimulation( &fInfo, &n_global, &n_atoms, identArray, &n_exclude, excl, | |
461 | &nGlobalExcludes, globalExcludes, molMembershipArray, | |
462 | &mfact[0], &ngroup, &groupList[0], &groupStart[0], &isError); | |
# | Line 480 | Line 484 | void SimInfo::setDefaultRcut( double theRcut ){ | |
484 | ||
485 | haveRcut = 1; | |
486 | rCut = theRcut; | |
487 | + | rList = rCut + 1.0; |
488 | ||
489 | < | ( rCut > ecr )? rList = rCut + 1.0: rList = ecr + 1.0; |
485 | < | |
486 | < | notifyFortranCutOffs( &rCut, &rList, &ecr, &est ); |
489 | > | notifyFortranCutOffs( &rCut, &rSw, &rList ); |
490 | } | |
491 | ||
492 | < | void SimInfo::setDefaultEcr( double theEcr ){ |
492 | > | void SimInfo::setDefaultRcut( double theRcut, double theRsw ){ |
493 | ||
494 | < | haveEcr = 1; |
495 | < | ecr = theEcr; |
493 | < | |
494 | < | ( rCut > ecr )? rList = rCut + 1.0: rList = ecr + 1.0; |
495 | < | |
496 | < | notifyFortranCutOffs( &rCut, &rList, &ecr, &est ); |
494 | > | rSw = theRsw; |
495 | > | setDefaultRcut( theRcut ); |
496 | } | |
497 | ||
499 | – | void SimInfo::setDefaultEcr( double theEcr, double theEst ){ |
498 | ||
501 | – | est = theEst; |
502 | – | setDefaultEcr( theEcr ); |
503 | – | } |
504 | – | |
505 | – | |
499 | void SimInfo::checkCutOffs( void ){ | |
500 | ||
501 | if( boxIsInit ){ | |
# | Line 511 | Line 504 | void SimInfo::checkCutOffs( void ){ | |
504 | ||
505 | if( rCut > maxCutoff ){ | |
506 | sprintf( painCave.errMsg, | |
507 | < | "LJrcut is too large for the current periodic box.\n" |
508 | < | "\tCurrent Value of LJrcut = %G at time %G\n " |
507 | > | "cutoffRadius is too large for the current periodic box.\n" |
508 | > | "\tCurrent Value of cutoffRadius = %G at time %G\n " |
509 | "\tThis is larger than half of at least one of the\n" | |
510 | "\tperiodic box vectors. Right now, the Box matrix is:\n" | |
511 | "\n" | |
# | Line 525 | Line 518 | void SimInfo::checkCutOffs( void ){ | |
518 | Hmat[2][0], Hmat[2][1], Hmat[2][2]); | |
519 | painCave.isFatal = 1; | |
520 | simError(); | |
521 | < | } |
529 | < | |
530 | < | if( haveEcr ){ |
531 | < | if( ecr > maxCutoff ){ |
532 | < | sprintf( painCave.errMsg, |
533 | < | "electrostaticCutoffRadius is too large for the current\n" |
534 | < | "\tperiodic box.\n\n" |
535 | < | "\tCurrent Value of ECR = %G at time %G\n " |
536 | < | "\tThis is larger than half of at least one of the\n" |
537 | < | "\tperiodic box vectors. Right now, the Box matrix is:\n" |
538 | < | "\n" |
539 | < | "\t[ %G %G %G ]\n" |
540 | < | "\t[ %G %G %G ]\n" |
541 | < | "\t[ %G %G %G ]\n", |
542 | < | ecr, currentTime, |
543 | < | Hmat[0][0], Hmat[0][1], Hmat[0][2], |
544 | < | Hmat[1][0], Hmat[1][1], Hmat[1][2], |
545 | < | Hmat[2][0], Hmat[2][1], Hmat[2][2]); |
546 | < | painCave.isFatal = 1; |
547 | < | simError(); |
548 | < | } |
549 | < | } |
521 | > | } |
522 | } else { | |
523 | // initialize this stuff before using it, OK? | |
524 | sprintf( painCave.errMsg, | |
# | Line 597 | Line 569 | void getFortranGroupArray(SimInfo* info, vector<double | |
569 | ||
570 | void getFortranGroupArray(SimInfo* info, vector<double>& mfact, int& ngroup, | |
571 | vector<int>& groupList, vector<int>& groupStart){ | |
572 | < | Molecule* mol; |
572 | > | Molecule* myMols; |
573 | Atom** myAtoms; | |
574 | int numAtom; | |
575 | int curIndex; | |
576 | double mtot; | |
577 | < | |
577 | > | int numMol; |
578 | > | int numCutoffGroups; |
579 | > | CutoffGroup* myCutoffGroup; |
580 | > | vector<CutoffGroup*>::iterator iterCutoff; |
581 | > | Atom* cutoffAtom; |
582 | > | vector<Atom*>::iterator iterAtom; |
583 | > | int atomIndex; |
584 | > | double totalMass; |
585 | > | |
586 | mfact.clear(); | |
587 | groupList.clear(); | |
588 | groupStart.clear(); | |
589 | ||
590 | //Be careful, fortran array begin at 1 | |
591 | curIndex = 1; | |
612 | – | |
613 | – | if(info->useMolecularCutoffs){ |
614 | – | |
615 | – | #ifdef IS_MPI |
616 | – | ngroup = mpiSim->getMyNMol(); |
617 | – | #else |
618 | – | ngroup = info->n_mol; |
619 | – | #endif |
620 | – | |
621 | – | for(int i = 0; i < ngroup; i ++){ |
622 | – | mol = &(info->molecules[i]); |
623 | – | numAtom = mol->getNAtoms(); |
624 | – | myAtoms = mol->getMyAtoms(); |
625 | – | mtot = 0.0; |
592 | ||
593 | < | for(int j=0; j < numAtom; j++) |
594 | < | mtot += myAtoms[j]->getMass(); |
595 | < | |
596 | < | for(int j=0; j < numAtom; j++){ |
597 | < | |
598 | < | // We want the local Index: |
633 | < | groupList.push_back(myAtoms[j]->getIndex() + 1); |
634 | < | mfact.push_back(myAtoms[j]->getMass() / mtot); |
593 | > | myMols = info->molecules; |
594 | > | numMol = info->n_mol; |
595 | > | for(int i = 0; i < numMol; i++){ |
596 | > | numCutoffGroups = myMols[i].getNCutoffGroups(); |
597 | > | for(myCutoffGroup =myMols[i].beginCutoffGroup(iterCutoff); myCutoffGroup != NULL; |
598 | > | myCutoffGroup =myMols[i].nextCutoffGroup(iterCutoff)){ |
599 | ||
600 | < | } |
600 | > | totalMass = myCutoffGroup->getMass(); |
601 | ||
602 | < | groupStart.push_back(curIndex); |
603 | < | curIndex += numAtom; |
604 | < | |
605 | < | } //end for(int i =0 ; i < ngroup; i++) |
606 | < | } |
643 | < | else{ |
644 | < | //using atomic cutoff, every single atom is just a group |
645 | < | |
646 | < | #ifdef IS_MPI |
647 | < | ngroup = mpiSim->getMyNlocal(); |
602 | > | for(cutoffAtom = myCutoffGroup->beginAtom(iterAtom); cutoffAtom != NULL; |
603 | > | cutoffAtom = myCutoffGroup->nextAtom(iterAtom)){ |
604 | > | mfact.push_back(cutoffAtom->getMass()/totalMass); |
605 | > | #ifdef IS_MPI |
606 | > | groupList.push_back(cutoffAtom->getGlobalIndex() + 1); |
607 | #else | |
608 | < | ngroup = info->n_atoms; |
608 | > | groupList.push_back(cutoffAtom->getIndex() + 1); |
609 | #endif | |
610 | < | |
611 | < | for(int i =0 ; i < ngroup; i++){ |
612 | < | groupStart.push_back(curIndex++); |
613 | < | groupList.push_back((info->atoms[i])->getIndex() + 1); |
614 | < | mfact.push_back(1.0); |
615 | < | |
616 | < | }//end for(int i =0 ; i < ngroup; i++) |
617 | < | |
618 | < | }//end if (info->useMolecularCutoffs) |
619 | < | |
610 | > | } |
611 | > | |
612 | > | groupStart.push_back(curIndex); |
613 | > | curIndex += myCutoffGroup->getNumAtom(); |
614 | > | |
615 | > | }//end for(myCutoffGroup =myMols[i].beginCutoffGroup(iterCutoff)) |
616 | > | |
617 | > | }//end for(int i = 0; i < numMol; i++) |
618 | > | |
619 | > | |
620 | > | //The last cutoff group need more element to indicate the end of the cutoff |
621 | > | ngroup = groupStart.size(); |
622 | } |
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