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#include <algorithm> |
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#include "brains/SimInfo.hpp" |
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#include "primitives/Molecule.hpp" |
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#include "UseTheForce/doForces_interface.h" |
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#include "UseTheForce/notifyCutoffs_interface.h" |
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#include "utils/MemoryUtils.hpp" |
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#include "utils/simError.h" |
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namespace oopse { |
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< |
SimInfo::SimInfo(const std::vector<std::pair<MoleculeStamp*, int> >& molStampPairs, |
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SimInfo::SimInfo(std::vector<std::pair<MoleculeStamp*, int> >& molStampPairs, |
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ForceField* ff, Globals* globals) : |
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forceField_(ff), globals_(globals), nAtoms_(0), nBonds_(0), |
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nBends_(0), nTorsions_(0), nRigidBodies_(0), nIntegrableObjects_(0), |
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nCutoffGroups_(0), nConstraints_(0), nZConstraint_(0), sman_(NULL), |
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nCutoffGroups_(0), nConstraints_(0), nZconstraint_(0), sman_(NULL), |
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fortranInitialized_(false) { |
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std::vector<std::pair<MoleculeStamp*, int> >::iterator i; |
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int nCutoffAtoms; // number of atoms belong to cutoff groups |
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int ngroups; //total cutoff groups defined in meta-data file |
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MoleculeStamp* molStamp; |
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int nMolWithSameStamp; |
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int nCutoffAtoms; // number of atoms belong to cutoff groups |
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int nGroups; //total cutoff groups defined in meta-data file |
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CutoffGroupStamp* cgStamp; |
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int nAtomsIngroups; |
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int nCutoffGroupsInStamp; |
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|
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int nAtomsInGroups; |
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int nCutoffGroupsInStamp; |
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|
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RigidBodyStamp* rbStamp; |
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int nAtomsInRigidBodies; |
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int nRigidBodiesInStamp; |
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int nRigidAtoms; |
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int nRigidBodies; |
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> |
|
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nGlobalAtoms_ = 0; |
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ngroups = 0; |
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|
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nGroups = 0; |
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nCutoffAtoms = 0; |
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nRigidBodies = 0; |
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|
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for (i = molStampPairs.begin(); i !=molStampPairs.end(); ++i) { |
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molStamp = i->first; |
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nMolWithSameStamp = i->second; |
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addMoleculeStamp(molStamp, nMolWithSameStamp); |
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|
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> |
//calculate atoms in molecules |
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nGlobalAtoms_ += molStamp->getNAtoms() *nMolWithSameStamp; |
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|
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nAtomsIngroups = 0; |
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|
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|
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//calculate atoms in cutoff groups |
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nAtomsInGroups = 0; |
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nCutoffGroupsInStamp = molStamp->getNCutoffGroups(); |
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|
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for (int j=0; j < nCutoffGroupsInStamp; j++) { |
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cgStamp = molStamp->getCutoffGroup(j); |
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nAtomsIngroups += cgStamp->getNMembers(); |
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nAtomsInGroups += cgStamp->getNMembers(); |
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} |
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ngroups += *nMolWithSameStamp; |
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nCutoffAtoms += nAtomsIngroups * nMolWithSameStamp; |
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nGroups += nCutoffGroupsInStamp * nMolWithSameStamp; |
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nCutoffAtoms += nAtomsInGroups * nMolWithSameStamp; |
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|
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//calculate atoms in rigid bodies |
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nAtomsInRigidBodies = 0; |
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nRigidBodiesInStamp = molStamp->getNCutoffGroups(); |
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|
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for (int j=0; j < nRigidBodiesInStamp; j++) { |
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rbStamp = molStamp->getRigidBody(j); |
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nRigidBodiesInStamp += rbStamp->getNMembers(); |
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} |
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|
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nRigidBodies += nRigidBodiesInStamp * nMolWithSameStamp; |
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nRigidAtoms += nAtomsInRigidBodies * nMolWithSameStamp; |
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|
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} |
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//every free atom (atom does not belong to cutoff groups) is a cutoff group |
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//therefore the total number of cutoff groups in the system is equal to |
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//the total number of atoms minus number of atoms belong to cutoff group defined in meta-data |
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//file plus the number of cutoff groups defined in meta-data file |
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nGlobalCutoffGroups_ = nGlobalAtoms_ - nCutoffAtoms + ngroups; |
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nGlobalCutoffGroups_ = nGlobalAtoms_ - nCutoffAtoms + nGroups; |
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|
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//every free atom (atom does not belong to rigid bodies) is a rigid body |
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//therefore the total number of cutoff groups in the system is equal to |
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//the total number of atoms minus number of atoms belong to rigid body defined in meta-data |
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//file plus the number of rigid bodies defined in meta-data file |
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nGlobalIntegrableObjects_ = nGlobalAtoms_ - nRigidAtoms + nRigidBodies; |
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|
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//initialize globalGroupMembership_, every element of this array will be 0 |
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globalGroupMembership_.insert(globalGroupMembership_.end(), nGlobalAtoms_, 0); |
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// nZconstraints_ is global, as are the 3 COM translations for the |
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// entire system: |
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ndf_ = ndf_ - 3 - nZconstraints_; |
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ndf_ = ndf_ - 3 - nZconstraint_; |
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} |
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ndfTrans_ = ndfTrans_local; |
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#endif |
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ndfTrans_ = ndfTrans_ - 3 - nZconstraints_; |
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ndfTrans_ = ndfTrans_ - 3 - nZconstraint_; |
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} |
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exclude_.addPair(b, c); |
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} |
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for (torsion= mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextBond(torsionIter)) { |
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for (torsion= mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) { |
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a = torsion->getAtomA()->getGlobalIndex(); |
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b = torsion->getAtomB()->getGlobalIndex(); |
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c = torsion->getAtomC()->getGlobalIndex(); |
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exclude_.removePair(b, c); |
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} |
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for (torsion= mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextBond(torsionIter)) { |
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for (torsion= mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) { |
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a = torsion->getAtomA()->getGlobalIndex(); |
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b = torsion->getAtomB()->getGlobalIndex(); |
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c = torsion->getAtomC()->getGlobalIndex(); |
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curStampId = molStampIds_.size(); |
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moleculeStamps_.push_back(molStamp); |
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molStampIds_.insert(molStampIds_.end(), nmol, curStampId) |
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molStampIds_.insert(molStampIds_.end(), nmol, curStampId); |
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} |
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void SimInfo::update() { |
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setupFortranSim(); |
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//setup fortran force field |
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/** @deprecate */ |
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int isError = 0; |
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initFortranFF( &fInfo_.SIM_uses_RF , &isError ); |
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if(isError){ |
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sprintf( painCave.errMsg, |
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"ForceField error: There was an error initializing the forceField in fortran.\n" ); |
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painCave.isFatal = 1; |
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simError(); |
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} |
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|
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|
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setupCutoff(); |
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//notify fortran whether reaction field is used or not. It is deprecated now |
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//int isError = 0; |
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//initFortranFF( &useReactionField, &isError ); |
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|
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//if(isError){ |
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// sprintf( painCave.errMsg, |
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// "SimCreator::initFortran() error: There was an error initializing the forceField in fortran.\n" ); |
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// painCave.isFatal = 1; |
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// simError(); |
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//} |
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|
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calcNdf(); |
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calcNdfRaw(); |
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calcNdfTrans(); |
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} |
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std::set<AtomType*> SimInfo::getUniqueAtomTypes() { |
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typename SimInfo::MoleculeIterator mi; |
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SimInfo::MoleculeIterator mi; |
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Molecule* mol; |
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typename Molecule::AtomIterator ai; |
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Molecule::AtomIterator ai; |
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Atom* atom; |
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std::set<AtomType*> atomTypes; |
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//loop over all of the atom types |
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for (i = atomTypes.begin(); i != atomTypes.end(); ++i) { |
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useLennardJones |= i->isLennardJones(); |
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useElectrostatic |= i->isElectrostatic(); |
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useEAM |= i->isEAM(); |
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useCharge |= i->isCharge(); |
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useDirectional |= i->isDirectional(); |
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useDipole |= i->isDipole(); |
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useGayBerne |= i->isGayBerne(); |
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useSticky |= i->isSticky(); |
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useShape |= i->isShape(); |
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useLennardJones |= (*i)->isLennardJones(); |
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useElectrostatic |= (*i)->isElectrostatic(); |
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useEAM |= (*i)->isEAM(); |
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useCharge |= (*i)->isCharge(); |
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useDirectional |= (*i)->isDirectional(); |
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useDipole |= (*i)->isDipole(); |
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useGayBerne |= (*i)->isGayBerne(); |
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useSticky |= (*i)->isSticky(); |
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useShape |= (*i)->isShape(); |
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} |
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if (useSticky || useDipole || useGayBerne || useShape) { |
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fInfo_.SIM_uses_RF = useRF; |
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if( fInfo_.SIM_uses_Dipoles && fInfo_.SIM_uses_RF) { |
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< |
fInfo_.dielect = dielectric; |
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|
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if (globals_->haveDielectric()) { |
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fInfo_.dielect = globals_->getDielectric(); |
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} else { |
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sprintf(painCave.errMsg, |
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"SimSetup Error: No Dielectric constant was set.\n" |
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"\tYou are trying to use Reaction Field without" |
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"\tsetting a dielectric constant!\n"); |
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painCave.isFatal = 1; |
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simError(); |
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} |
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> |
|
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} else { |
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fInfo_.dielect = 0.0; |
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} |
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//calculate mass ratio of cutoff group |
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std::vector<double> mfact; |
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< |
typename SimInfo::MoleculeIterator mi; |
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> |
SimInfo::MoleculeIterator mi; |
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Molecule* mol; |
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< |
typename Molecule::CutoffGroupIterator ci; |
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> |
Molecule::CutoffGroupIterator ci; |
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CutoffGroup* cg; |
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typename Molecule::AtomIterator ai; |
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Molecule::AtomIterator ai; |
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Atom* atom; |
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double totalMass; |
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//gloalExcludes and molMembershipArray should go away (They are never used) |
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//why the hell fortran need to know molecule? |
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//OOPSE = Object-Obfuscated Parallel Simulation Engine |
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< |
|
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< |
setFortranSim( &fInfo_, &nGlobalAtoms_, &nAtoms_, &identArray[0], &nExclude, exclude_->getExcludeList(), |
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< |
&nGlobalExcludes, globalExcludes, molMembershipArray, |
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> |
int nGlobalExcludes = 0; |
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> |
int* globalExcludes = NULL; |
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> |
int* excludeList = exclude_.getExcludeList(); |
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> |
setFortranSim( &fInfo_, &nGlobalAtoms_, &nAtoms_, &identArray[0], &nExclude, excludeList , |
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&nGlobalExcludes, globalExcludes, &molMembershipArray[0], |
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&mfact[0], &nCutoffGroups_, &fortranGlobalGroupMembership[0], &isError); |
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if( isError ){ |
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//SimInfo is responsible for creating localToGlobalAtomIndex and localToGlobalGroupIndex |
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std::vector<int> localToGlobalAtomIndex(getNAtoms(), 0); |
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std::vector<int> localToGlobalCutoffGroupIndex; |
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< |
typename SimInfo::MoleculeIterator mi; |
654 |
< |
typename Molecule::AtomIterator ai; |
655 |
< |
typename Molecule::CutoffGroupIterator ci; |
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> |
SimInfo::MoleculeIterator mi; |
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> |
Molecule::AtomIterator ai; |
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> |
Molecule::CutoffGroupIterator ci; |
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Molecule* mol; |
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Atom* atom; |
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CutoffGroup* cg; |
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double SimInfo::calcMaxCutoffRadius() { |
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|
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|
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< |
std::vector<AtomType*> atomTypes; |
710 |
< |
std::vector<AtomType*>::iterator i; |
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> |
std::set<AtomType*> atomTypes; |
710 |
> |
std::set<AtomType*>::iterator i; |
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std::vector<double> cutoffRadius; |
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|
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//get the unique atom types |
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cutoffRadius.push_back(forceField_->getRcutFromAtomType(*i)); |
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} |
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|
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< |
double maxCutoffRadius = std::max_element(cutoffRadius.begin(), cutoffRadius.end()); |
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> |
double maxCutoffRadius = *(std::max_element(cutoffRadius.begin(), cutoffRadius.end())); |
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#ifdef IS_MPI |
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//pick the max cutoff radius among the processors |
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#endif |
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} |
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|
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if (globals_->haveRsw()) { |
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< |
rsw_ = globals_->getRsw() |
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> |
rsw_ = globals_->getRsw(); |
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} else { |
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rsw_ = rcut_; |
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} |
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return properties_.getPropertyByName(propName); |
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} |
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|
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+ |
void SimInfo::setSnapshotManager(SnapshotManager* sman) { |
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sman_ = sman; |
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|
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+ |
Molecule* mol; |
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+ |
RigidBody* rb; |
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Atom* atom; |
814 |
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SimInfo::MoleculeIterator mi; |
815 |
+ |
Molecule::RigidBodyIterator rbIter; |
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Molecule::AtomIterator atomIter;; |
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+ |
|
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+ |
for (mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) { |
819 |
+ |
|
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for (atom = mol->beginAtom(atomIter); atom != NULL; atom = mol->nextAtom(atomIter)) { |
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atom->setSnapshotManager(sman_); |
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} |
823 |
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|
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for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) { |
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+ |
rb->setSnapshotManager(sman_); |
826 |
+ |
} |
827 |
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} |
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+ |
|
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} |
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|
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std::ostream& operator <<(ostream& o, SimInfo& info) { |
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|
833 |
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return o; |