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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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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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> |
sman_(NULL), fortranInitialized_(false), selectMan_(NULL) { |
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std::vector<std::pair<MoleculeStamp*, int> >::iterator i; |
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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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|
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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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> |
selectMan_ = new SelectionManager(this); |
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> |
selectMan_->selectAll(); |
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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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> |
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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+ |
MemoryUtils::deletePointers(moleculeStamps_); |
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+ |
|
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delete sman_; |
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delete simParams_; |
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delete forceField_; |
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> |
delete selectMan_; |
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} |
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int SimInfo::getNGlobalConstraints() { |
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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 |
| 761 |
> |
void SimInfo::getCutoff(double& rcut, double& rsw) { |
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|
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if (fInfo_.SIM_uses_Charges | fInfo_.SIM_uses_Dipoles | fInfo_.SIM_uses_RF) { |
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|
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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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} |
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|
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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{ |
| 786 |
< |
rsw_ = simParams_->getRsw(); |
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> |
rsw = simParams_->getRsw(); |
| 787 |
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} |
| 788 |
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} else { |
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//meta-data file, the maximum cutoff radius calculated from forcefiled will be used |
| 792 |
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|
| 793 |
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if (simParams_->haveRcut()) { |
| 794 |
< |
rcut_ = simParams_->getRcut(); |
| 794 |
> |
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 |
| 797 |
< |
rcut_ = calcMaxCutoffRadius(); |
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> |
rcut = calcMaxCutoffRadius(); |
| 798 |
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} |
| 799 |
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|
| 800 |
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if (simParams_->haveRsw()) { |
| 801 |
< |
rsw_ = simParams_->getRsw(); |
| 801 |
> |
rsw = simParams_->getRsw(); |
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} else { |
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< |
rsw_ = rcut_; |
| 803 |
> |
rsw = rcut; |
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} |
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} |
| 807 |
< |
|
| 807 |
> |
} |
| 808 |
> |
|
| 809 |
> |
void SimInfo::setupCutoff() { |
| 810 |
> |
getCutoff(rcut_, rsw_); |
| 811 |
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double rnblist = rcut_ + 1; // skin of neighbor list |
| 812 |
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|
| 813 |
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//Pass these cutoff radius etc. to fortran. This function should be called once and only once |
| 839 |
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} |
| 840 |
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|
| 841 |
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void SimInfo::setSnapshotManager(SnapshotManager* sman) { |
| 842 |
+ |
//if (sman_ == sman_) { |
| 843 |
+ |
// return; |
| 844 |
+ |
//} |
| 845 |
+ |
|
| 846 |
+ |
//delete sman_; |
| 847 |
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sman_ = sman; |
| 848 |
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|
| 849 |
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Molecule* mol; |
