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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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//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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< |
|
141 |
> |
|
142 |
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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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< |
|
147 |
< |
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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|
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} |
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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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|
370 |
< |
|
370 |
> |
Molecule::RigidBodyIterator rbIter; |
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> |
RigidBody* rb; |
372 |
> |
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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> |
} |
382 |
> |
|
383 |
> |
Molecule::CutoffGroupIterator cgIter; |
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> |
CutoffGroup* cg; |
385 |
> |
for (cg = mol->beginCutoffGroup(cgIter); cg != NULL; cg = mol->nextCutoffGroup(cgIter)) { |
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> |
std::vector<Atom*> atoms = cg->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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> |
} |
395 |
> |
|
396 |
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} |
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|
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void SimInfo::removeExcludePairs(Molecule* mol) { |
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exclude_.removePair(c, d); |
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} |
439 |
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|
440 |
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Molecule::RigidBodyIterator rbIter; |
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RigidBody* rb; |
442 |
+ |
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(); |
447 |
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b = atoms[j]->getGlobalIndex(); |
448 |
+ |
exclude_.removePair(a, b); |
449 |
+ |
} |
450 |
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} |
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} |
452 |
+ |
|
453 |
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Molecule::CutoffGroupIterator cgIter; |
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CutoffGroup* cg; |
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+ |
for (cg = mol->beginCutoffGroup(cgIter); cg != NULL; cg = mol->nextCutoffGroup(cgIter)) { |
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std::vector<Atom*> atoms = cg->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(); |
460 |
+ |
b = atoms[j]->getGlobalIndex(); |
461 |
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exclude_.removePair(a, b); |
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} |
463 |
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} |
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} |
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|
466 |
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} |
467 |
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|
468 |
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|
697 |
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} |
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|
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//setup fortran simulation |
645 |
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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? |
647 |
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//OOPSE = Object-Obfuscated Parallel Simulation Engine |
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int nGlobalExcludes = 0; |
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int* globalExcludes = NULL; |
702 |
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int* excludeList = exclude_.getExcludeList(); |
803 |
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return maxCutoffRadius; |
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} |
805 |
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|
806 |
< |
void SimInfo::setupCutoff() { |
755 |
< |
double rcut_; //cutoff radius |
756 |
< |
double rsw_; //switching radius |
806 |
> |
void SimInfo::getCutoff(double& rcut, double& rsw) { |
807 |
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|
808 |
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if (fInfo_.SIM_uses_Charges | fInfo_.SIM_uses_Dipoles | fInfo_.SIM_uses_RF) { |
809 |
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|
814 |
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"\tfor the cutoffRadius.\n"); |
815 |
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painCave.isFatal = 0; |
816 |
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simError(); |
817 |
< |
rcut_ = 15.0; |
817 |
> |
rcut = 15.0; |
818 |
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} else{ |
819 |
< |
rcut_ = simParams_->getRcut(); |
819 |
> |
rcut = simParams_->getRcut(); |
820 |
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} |
821 |
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|
822 |
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if (!simParams_->haveRsw()){ |
826 |
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"\t0.95 * cutoffRadius for the switchingRadius\n"); |
827 |
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painCave.isFatal = 0; |
828 |
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simError(); |
829 |
< |
rsw_ = 0.95 * rcut_; |
829 |
> |
rsw = 0.95 * rcut; |
830 |
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} else{ |
831 |
< |
rsw_ = simParams_->getRsw(); |
831 |
> |
rsw = simParams_->getRsw(); |
832 |
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} |
833 |
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|
834 |
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} else { |
836 |
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//meta-data file, the maximum cutoff radius calculated from forcefiled will be used |
837 |
|
|
838 |
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if (simParams_->haveRcut()) { |
839 |
< |
rcut_ = simParams_->getRcut(); |
839 |
> |
rcut = simParams_->getRcut(); |
840 |
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} else { |
841 |
|
//set cutoff radius to the maximum cutoff radius based on atom types in the whole system |
842 |
< |
rcut_ = calcMaxCutoffRadius(); |
842 |
> |
rcut = calcMaxCutoffRadius(); |
843 |
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} |
844 |
|
|
845 |
|
if (simParams_->haveRsw()) { |
846 |
< |
rsw_ = simParams_->getRsw(); |
846 |
> |
rsw = simParams_->getRsw(); |
847 |
|
} else { |
848 |
< |
rsw_ = rcut_; |
848 |
> |
rsw = rcut; |
849 |
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} |
850 |
|
|
851 |
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} |
852 |
< |
|
852 |
> |
} |
853 |
> |
|
854 |
> |
void SimInfo::setupCutoff() { |
855 |
> |
getCutoff(rcut_, rsw_); |
856 |
|
double rnblist = rcut_ + 1; // skin of neighbor list |
857 |
|
|
858 |
|
//Pass these cutoff radius etc. to fortran. This function should be called once and only once |
884 |
|
} |
885 |
|
|
886 |
|
void SimInfo::setSnapshotManager(SnapshotManager* sman) { |
887 |
+ |
if (sman_ == sman) { |
888 |
+ |
return; |
889 |
+ |
} |
890 |
+ |
delete sman_; |
891 |
|
sman_ = sman; |
892 |
|
|
893 |
|
Molecule* mol; |