# | Line 62 | Line 62 | SimInfo::SimInfo(){ | |
---|---|---|
62 | useReactionField = 0; | |
63 | useGB = 0; | |
64 | useEAM = 0; | |
65 | + | useSolidThermInt = 0; |
66 | + | useLiquidThermInt = 0; |
67 | ||
68 | + | haveCutoffGroups = false; |
69 | + | |
70 | excludes = Exclude::Instance(); | |
71 | ||
72 | myConfiguration = new SimState(); | |
# | Line 442 | 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 | |
453 | ||
454 | isError = 0; | |
455 | ||
456 | < | getFortranGroupArray(this, mfact, ngroup, groupList, groupStart); |
457 | < | |
456 | > | getFortranGroupArrays(this, FglobalGroupMembership, mfact); |
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); |
462 | > | &mfact[0], &ngroup, &FglobalGroupMembership[0], &isError); |
463 | ||
464 | if( isError ){ | |
465 | ||
# | Line 561 | Line 567 | GenericData* SimInfo::getProperty(const string& propNa | |
567 | } | |
568 | ||
569 | ||
570 | < | void getFortranGroupArray(SimInfo* info, vector<double>& mfact, int& ngroup, |
571 | < | vector<int>& groupList, vector<int>& groupStart){ |
572 | < | Molecule* mol; |
570 | > | void SimInfo::getFortranGroupArrays(SimInfo* info, |
571 | > | vector<int>& FglobalGroupMembership, |
572 | > | vector<double>& mfact){ |
573 | > | |
574 | > | Molecule* myMols; |
575 | Atom** myAtoms; | |
576 | int numAtom; | |
569 | – | int curIndex; |
577 | double mtot; | |
578 | < | |
579 | < | mfact.clear(); |
580 | < | groupList.clear(); |
581 | < | groupStart.clear(); |
578 | > | int numMol; |
579 | > | int numCutoffGroups; |
580 | > | CutoffGroup* myCutoffGroup; |
581 | > | vector<CutoffGroup*>::iterator iterCutoff; |
582 | > | Atom* cutoffAtom; |
583 | > | vector<Atom*>::iterator iterAtom; |
584 | > | int atomIndex; |
585 | > | double totalMass; |
586 | ||
587 | < | //Be careful, fortran array begin at 1 |
588 | < | curIndex = 1; |
587 | > | mfact.clear(); |
588 | > | FglobalGroupMembership.clear(); |
589 | ||
590 | < | if(info->useMolecularCutoffs){ |
591 | < | |
590 | > | |
591 | > | // Fix the silly fortran indexing problem |
592 | #ifdef IS_MPI | |
593 | < | ngroup = mpiSim->getMyNMol(); |
593 | > | numAtom = mpiSim->getNAtomsGlobal(); |
594 | #else | |
595 | < | ngroup = info->n_mol; |
595 | > | numAtom = n_atoms; |
596 | #endif | |
597 | < | |
598 | < | for(int i = 0; i < ngroup; i ++){ |
588 | < | mol = &(info->molecules[i]); |
589 | < | numAtom = mol->getNAtoms(); |
590 | < | myAtoms = mol->getMyAtoms(); |
591 | < | mtot = 0.0; |
597 | > | for (int i = 0; i < numAtom; i++) |
598 | > | FglobalGroupMembership.push_back(globalGroupMembership[i] + 1); |
599 | ||
600 | < | for(int j=0; j < numAtom; j++) |
601 | < | mtot += myAtoms[j]->getMass(); |
602 | < | |
603 | < | for(int j=0; j < numAtom; j++){ |
604 | < | |
605 | < | // We want the local Index: |
606 | < | groupList.push_back(myAtoms[j]->getIndex() + 1); |
600 | < | mfact.push_back(myAtoms[j]->getMass() / mtot); |
600 | > | myMols = info->molecules; |
601 | > | numMol = info->n_mol; |
602 | > | for(int i = 0; i < numMol; i++){ |
603 | > | numCutoffGroups = myMols[i].getNCutoffGroups(); |
604 | > | for(myCutoffGroup =myMols[i].beginCutoffGroup(iterCutoff); |
605 | > | myCutoffGroup != NULL; |
606 | > | myCutoffGroup =myMols[i].nextCutoffGroup(iterCutoff)){ |
607 | ||
608 | < | } |
608 | > | totalMass = myCutoffGroup->getMass(); |
609 | ||
610 | < | groupStart.push_back(curIndex); |
611 | < | curIndex += numAtom; |
612 | < | |
613 | < | } //end for(int i =0 ; i < ngroup; i++) |
610 | > | for(cutoffAtom = myCutoffGroup->beginAtom(iterAtom); |
611 | > | cutoffAtom != NULL; |
612 | > | cutoffAtom = myCutoffGroup->nextAtom(iterAtom)){ |
613 | > | mfact.push_back(cutoffAtom->getMass()/totalMass); |
614 | > | } |
615 | > | } |
616 | } | |
617 | < | else{ |
610 | < | //using atomic cutoff, every single atom is just a group |
611 | < | |
612 | < | #ifdef IS_MPI |
613 | < | ngroup = mpiSim->getMyNlocal(); |
614 | < | #else |
615 | < | ngroup = info->n_atoms; |
616 | < | #endif |
617 | < | |
618 | < | for(int i =0 ; i < ngroup; i++){ |
619 | < | groupStart.push_back(curIndex++); |
620 | < | groupList.push_back((info->atoms[i])->getIndex() + 1); |
621 | < | mfact.push_back(1.0); |
622 | < | |
623 | < | }//end for(int i =0 ; i < ngroup; i++) |
624 | < | |
625 | < | }//end if (info->useMolecularCutoffs) |
626 | < | |
617 | > | |
618 | } |
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