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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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#include "selection/SelectionManager.hpp" |
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#ifdef IS_MPI |
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#include "UseTheForce/mpiComponentPlan.h" |
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namespace oopse { |
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|
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< |
SimInfo::SimInfo(std::vector<std::pair<MoleculeStamp*, int> >& molStampPairs, |
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> |
SimInfo::SimInfo(MakeStamps* stamps, std::vector<std::pair<MoleculeStamp*, int> >& molStampPairs, |
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ForceField* ff, Globals* simParams) : |
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forceField_(ff), simParams_(simParams), |
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> |
stamps_(stamps), 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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//calculate atoms in rigid bodies |
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int nAtomsInRigidBodies = 0; |
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< |
int nRigidBodiesInStamp = molStamp->getNCutoffGroups(); |
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> |
int nRigidBodiesInStamp = molStamp->getNRigidBodies(); |
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for (int j=0; j < nRigidBodiesInStamp; j++) { |
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rbStamp = molStamp->getRigidBody(j); |
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#ifdef IS_MPI |
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molToProcMap_.resize(nGlobalMols_); |
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#endif |
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< |
|
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> |
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} |
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SimInfo::~SimInfo() { |
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< |
//MemoryUtils::deleteVectorOfPointer(molecules_); |
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< |
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< |
MemoryUtils::deleteVectorOfPointer(moleculeStamps_); |
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< |
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> |
std::map<int, Molecule*>::iterator i; |
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> |
for (i = molecules_.begin(); i != molecules_.end(); ++i) { |
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> |
delete i->second; |
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> |
} |
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> |
molecules_.clear(); |
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> |
|
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> |
delete stamps_; |
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delete sman_; |
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delete simParams_; |
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delete forceField_; |
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} |
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int SimInfo::getNGlobalConstraints() { |
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exclude_.addPair(c, d); |
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} |
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< |
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> |
Molecule::RigidBodyIterator rbIter; |
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> |
RigidBody* rb; |
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> |
for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) { |
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> |
std::vector<Atom*> atoms = rb->getAtoms(); |
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> |
for (int i = 0; i < atoms.size() -1 ; ++i) { |
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> |
for (int j = i + 1; j < atoms.size(); ++j) { |
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> |
a = atoms[i]->getGlobalIndex(); |
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> |
b = atoms[j]->getGlobalIndex(); |
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> |
exclude_.addPair(a, b); |
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> |
} |
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> |
} |
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> |
} |
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> |
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} |
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void SimInfo::removeExcludePairs(Molecule* mol) { |
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exclude_.removePair(b, d); |
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exclude_.removePair(c, d); |
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} |
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+ |
|
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Molecule::RigidBodyIterator rbIter; |
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RigidBody* rb; |
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+ |
for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) { |
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std::vector<Atom*> atoms = rb->getAtoms(); |
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for (int i = 0; i < atoms.size() -1 ; ++i) { |
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for (int j = i + 1; j < atoms.size(); ++j) { |
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a = atoms[i]->getGlobalIndex(); |
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b = atoms[j]->getGlobalIndex(); |
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exclude_.removePair(a, b); |
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} |
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} |
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} |
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} |
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} |
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//setup fortran simulation |
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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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int nGlobalExcludes = 0; |
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int* globalExcludes = NULL; |
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int* excludeList = exclude_.getExcludeList(); |
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return maxCutoffRadius; |
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} |
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< |
void SimInfo::setupCutoff() { |
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< |
double rcut_; //cutoff radius |
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< |
double rsw_; //switching radius |
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> |
void SimInfo::getCutoff(double& rcut, double& rsw) { |
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if (fInfo_.SIM_uses_Charges | fInfo_.SIM_uses_Dipoles | fInfo_.SIM_uses_RF) { |
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|
| 787 |
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"\tfor the cutoffRadius.\n"); |
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painCave.isFatal = 0; |
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simError(); |
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< |
rcut_ = 15.0; |
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> |
rcut = 15.0; |
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} else{ |
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< |
rcut_ = simParams_->getRcut(); |
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> |
rcut = simParams_->getRcut(); |
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} |
| 794 |
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| 795 |
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if (!simParams_->haveRsw()){ |
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"\t0.95 * cutoffRadius for the switchingRadius\n"); |
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painCave.isFatal = 0; |
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simError(); |
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< |
rsw_ = 0.95 * rcut_; |
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> |
rsw = 0.95 * rcut; |
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} else{ |
| 804 |
< |
rsw_ = simParams_->getRsw(); |
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> |
rsw = simParams_->getRsw(); |
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} |
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} else { |
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//meta-data file, the maximum cutoff radius calculated from forcefiled will be used |
| 810 |
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if (simParams_->haveRcut()) { |
| 812 |
< |
rcut_ = simParams_->getRcut(); |
| 812 |
> |
rcut = simParams_->getRcut(); |
| 813 |
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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 |
| 815 |
< |
rcut_ = calcMaxCutoffRadius(); |
| 815 |
> |
rcut = calcMaxCutoffRadius(); |
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} |
| 817 |
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| 818 |
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if (simParams_->haveRsw()) { |
| 819 |
< |
rsw_ = simParams_->getRsw(); |
| 819 |
> |
rsw = simParams_->getRsw(); |
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} else { |
| 821 |
< |
rsw_ = rcut_; |
| 821 |
> |
rsw = rcut; |
| 822 |
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} |
| 823 |
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|
| 824 |
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} |
| 825 |
< |
|
| 825 |
> |
} |
| 826 |
> |
|
| 827 |
> |
void SimInfo::setupCutoff() { |
| 828 |
> |
getCutoff(rcut_, rsw_); |
| 829 |
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double rnblist = rcut_ + 1; // skin of neighbor list |
| 830 |
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|
| 831 |
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//Pass these cutoff radius etc. to fortran. This function should be called once and only once |
| 857 |
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} |
| 858 |
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|
| 859 |
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void SimInfo::setSnapshotManager(SnapshotManager* sman) { |
| 860 |
+ |
if (sman_ == sman) { |
| 861 |
+ |
return; |
| 862 |
+ |
} |
| 863 |
+ |
delete sman_; |
| 864 |
|
sman_ = sman; |
| 865 |
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|
| 866 |
|
Molecule* mol; |
