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#include <algorithm> |
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#include <set> |
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#include "brains/SimInfo.hpp" |
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#include "math/Vector3.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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#ifdef IS_MPI |
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#include "UseTheForce/mpiComponentPlan.h" |
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#include "UseTheForce/DarkSide/simParallel_interface.h" |
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#endif |
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|
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namespace oopse { |
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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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fortranInitialized_(false) { |
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ForceField* ff, Globals* simParams) : |
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forceField_(ff), simParams_(simParams), |
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ndf_(0), ndfRaw_(0), ndfTrans_(0), nZconstraint_(0), |
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nGlobalMols_(0), nGlobalAtoms_(0), nGlobalCutoffGroups_(0), |
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nGlobalIntegrableObjects_(0), nGlobalRigidBodies_(0), |
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nAtoms_(0), nBonds_(0), nBends_(0), nTorsions_(0), nRigidBodies_(0), |
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nIntegrableObjects_(0), nCutoffGroups_(0), nConstraints_(0), |
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sman_(NULL), fortranInitialized_(false) { |
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|
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std::vector<std::pair<MoleculeStamp*, int> >::iterator i; |
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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 nCutoffAtoms = 0; // number of atoms belong to cutoff groups |
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int nGroups = 0; //total cutoff groups defined in meta-data file |
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CutoffGroupStamp* cgStamp; |
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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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|
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nGroups = 0; |
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nCutoffAtoms = 0; |
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nRigidBodies = 0; |
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int nRigidAtoms = 0; |
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for (i = molStampPairs.begin(); i !=molStampPairs.end(); ++i) { |
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molStamp = i->first; |
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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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int nAtomsInGroups = 0; |
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int nCutoffGroupsInStamp = molStamp->getNCutoffGroups(); |
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for (int j=0; j < nCutoffGroupsInStamp; j++) { |
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cgStamp = molStamp->getCutoffGroup(j); |
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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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int nAtomsInRigidBodies = 0; |
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int nRigidBodiesInStamp = molStamp->getNCutoffGroups(); |
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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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nAtomsInRigidBodies += rbStamp->getNMembers(); |
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} |
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nRigidBodies += nRigidBodiesInStamp * nMolWithSameStamp; |
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nGlobalRigidBodies_ += nRigidBodiesInStamp * nMolWithSameStamp; |
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nRigidAtoms += nAtomsInRigidBodies * nMolWithSameStamp; |
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} |
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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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//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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//every free atom (atom does not belong to rigid bodies) is an integrable object |
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//therefore the total number of integrable objects 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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nGlobalIntegrableObjects_ = nGlobalAtoms_ - nRigidAtoms + nGlobalRigidBodies_; |
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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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nGlobalMols_ = molStampIds_.size(); |
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#ifdef IS_MPI |
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MemoryUtils::deleteVectorOfPointer(moleculeStamps_); |
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delete sman_; |
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delete globals_; |
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delete simParams_; |
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delete forceField_; |
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} |
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MoleculeIterator i; |
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i = molecules_.find(mol->getGlobalIndex()); |
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if (i != molecules_.end() ) { |
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if (i == molecules_.end() ) { |
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molecules_.insert(make_pair(mol->getGlobalIndex(), mol)); |
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molecules_.insert(std::make_pair(mol->getGlobalIndex(), mol)); |
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nAtoms_ += mol->getNAtoms(); |
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nBonds_ += mol->getNBonds(); |
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nCutoffGroups_ += mol->getNCutoffGroups(); |
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nConstraints_ += mol->getNConstraints(); |
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addExcludePairs(mol); |
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return true; |
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} else { |
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return false; |
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nCutoffGroups_ -= mol->getNCutoffGroups(); |
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nConstraints_ -= mol->getNConstraints(); |
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removeExcludePairs(mol); |
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molecules_.erase(mol->getGlobalIndex()); |
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delete mol; |
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int useFLARB = 0; //it is not in AtomType yet |
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int useDirectionalAtom = 0; |
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int useElectrostatics = 0; |
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//usePBC and useRF are from globals |
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bool usePBC = globals_->getPBC(); |
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bool useRF = globals_->getUseRF(); |
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//usePBC and useRF are from simParams |
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int usePBC = simParams_->getPBC(); |
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int useRF = simParams_->getUseRF(); |
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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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if( fInfo_.SIM_uses_Dipoles && fInfo_.SIM_uses_RF) { |
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if (globals_->haveDielectric()) { |
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fInfo_.dielect = globals_->getDielectric(); |
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if (simParams_->haveDielectric()) { |
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fInfo_.dielect = simParams_->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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//molMembershipArray is filled by SimCreator |
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std::vector<int> molMembershipArray(nGlobalAtoms_); |
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for (int i = 0; i < nGlobalAtoms_; i++) { |
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molMembershipArray.push_back(globalMolMembership_[i] + 1); |
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molMembershipArray[i] = globalMolMembership_[i] + 1; |
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} |
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//setup fortran simulation |
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parallelData.nGroupsGlobal = getNGlobalCutoffGroups(); |
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parallelData.nGroupsLocal = getNCutoffGroups(); |
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parallelData.myNode = worldRank; |
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MPI_Comm_size(MPI_COMM_WORLD, &(parallelData->nProcessors)); |
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MPI_Comm_size(MPI_COMM_WORLD, &(parallelData.nProcessors)); |
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//pass mpiSimData struct and index arrays to fortran |
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setFsimParallel(parallelData, &(parallelData->nAtomsLocal), |
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&localToGlobalAtomIndex[0], &(parallelData->nGroupsLocal), |
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setFsimParallel(¶llelData, &(parallelData.nAtomsLocal), |
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&localToGlobalAtomIndex[0], &(parallelData.nGroupsLocal), |
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&localToGlobalCutoffGroupIndex[0], &isError); |
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if (isError) { |
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if (fInfo_.SIM_uses_Charges | fInfo_.SIM_uses_Dipoles | fInfo_.SIM_uses_RF) { |
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if (!globals_->haveRcut()){ |
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if (!simParams_->haveRcut()){ |
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sprintf(painCave.errMsg, |
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"SimCreator Warning: No value was set for the cutoffRadius.\n" |
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"\tOOPSE will use a default value of 15.0 angstroms" |
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simError(); |
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rcut_ = 15.0; |
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} else{ |
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rcut_ = globals_->getRcut(); |
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rcut_ = simParams_->getRcut(); |
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} |
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if (!globals_->haveRsw()){ |
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if (!simParams_->haveRsw()){ |
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sprintf(painCave.errMsg, |
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"SimCreator Warning: No value was set for switchingRadius.\n" |
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"\tOOPSE will use a default value of\n" |
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simError(); |
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rsw_ = 0.95 * rcut_; |
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} else{ |
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rsw_ = globals_->getRsw(); |
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rsw_ = simParams_->getRsw(); |
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} |
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} else { |
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// if charge, dipole or reaction field is not used and the cutofff radius is not specified in |
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//meta-data file, the maximum cutoff radius calculated from forcefiled will be used |
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if (globals_->haveRcut()) { |
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rcut_ = globals_->getRcut(); |
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if (simParams_->haveRcut()) { |
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rcut_ = simParams_->getRcut(); |
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} else { |
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//set cutoff radius to the maximum cutoff radius based on atom types in the whole system |
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rcut_ = calcMaxCutoffRadius(); |
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} |
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if (globals_->haveRsw()) { |
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rsw_ = globals_->getRsw(); |
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if (simParams_->haveRsw()) { |
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rsw_ = simParams_->getRsw(); |
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} else { |
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rsw_ = rcut_; |
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} |
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} |
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std::ostream& operator <<(ostream& o, SimInfo& info) { |
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Vector3d SimInfo::getComVel(){ |
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SimInfo::MoleculeIterator i; |
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Molecule* mol; |
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Vector3d comVel(0.0); |
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double totalMass = 0.0; |
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|
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for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) { |
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double mass = mol->getMass(); |
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totalMass += mass; |
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comVel += mass * mol->getComVel(); |
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} |
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|
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#ifdef IS_MPI |
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double tmpMass = totalMass; |
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Vector3d tmpComVel(comVel); |
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MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
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MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
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#endif |
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|
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comVel /= totalMass; |
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return comVel; |
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} |
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|
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Vector3d SimInfo::getCom(){ |
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SimInfo::MoleculeIterator i; |
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Molecule* mol; |
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|
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Vector3d com(0.0); |
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double totalMass = 0.0; |
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|
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for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) { |
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double mass = mol->getMass(); |
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totalMass += mass; |
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com += mass * mol->getCom(); |
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} |
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|
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#ifdef IS_MPI |
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double tmpMass = totalMass; |
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Vector3d tmpCom(com); |
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MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
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MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
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#endif |
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|
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com /= totalMass; |
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return com; |
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|
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} |
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|
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std::ostream& operator <<(std::ostream& o, SimInfo& info) { |
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|
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return o; |
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} |
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}//end namespace oopse |
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