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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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> |
int nRigidAtoms = 0; |
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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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//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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//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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|
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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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//initialize globalGroupMembership_, every element of this array will be 0 |
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globalGroupMembership_.insert(globalGroupMembership_.end(), nGlobalAtoms_, 0); |
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MemoryUtils::deleteVectorOfPointer(moleculeStamps_); |
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| 128 |
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delete sman_; |
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< |
delete globals_; |
| 129 |
> |
delete simParams_; |
| 130 |
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delete forceField_; |
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| 132 |
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} |
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MoleculeIterator i; |
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| 138 |
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i = molecules_.find(mol->getGlobalIndex()); |
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< |
if (i != molecules_.end() ) { |
| 139 |
> |
if (i == molecules_.end() ) { |
| 140 |
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| 141 |
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molecules_.insert(std::make_pair(mol->getGlobalIndex(), mol)); |
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int useFLARB = 0; //it is not in AtomType yet |
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int useDirectionalAtom = 0; |
| 456 |
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int useElectrostatics = 0; |
| 457 |
< |
//usePBC and useRF are from globals |
| 458 |
< |
bool usePBC = globals_->getPBC(); |
| 459 |
< |
bool useRF = globals_->getUseRF(); |
| 457 |
> |
//usePBC and useRF are from simParams |
| 458 |
> |
bool usePBC = simParams_->getPBC(); |
| 459 |
> |
bool useRF = simParams_->getUseRF(); |
| 460 |
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//loop over all of the atom types |
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for (i = atomTypes.begin(); i != atomTypes.end(); ++i) { |
| 535 |
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| 536 |
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if( fInfo_.SIM_uses_Dipoles && fInfo_.SIM_uses_RF) { |
| 537 |
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| 538 |
< |
if (globals_->haveDielectric()) { |
| 539 |
< |
fInfo_.dielect = globals_->getDielectric(); |
| 538 |
> |
if (simParams_->haveDielectric()) { |
| 539 |
> |
fInfo_.dielect = simParams_->getDielectric(); |
| 540 |
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} else { |
| 541 |
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sprintf(painCave.errMsg, |
| 542 |
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"SimSetup Error: No Dielectric constant was set.\n" |
| 724 |
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| 725 |
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if (fInfo_.SIM_uses_Charges | fInfo_.SIM_uses_Dipoles | fInfo_.SIM_uses_RF) { |
| 726 |
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|
| 727 |
< |
if (!globals_->haveRcut()){ |
| 727 |
> |
if (!simParams_->haveRcut()){ |
| 728 |
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sprintf(painCave.errMsg, |
| 729 |
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"SimCreator Warning: No value was set for the cutoffRadius.\n" |
| 730 |
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"\tOOPSE will use a default value of 15.0 angstroms" |
| 733 |
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simError(); |
| 734 |
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rcut_ = 15.0; |
| 735 |
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} else{ |
| 736 |
< |
rcut_ = globals_->getRcut(); |
| 736 |
> |
rcut_ = simParams_->getRcut(); |
| 737 |
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} |
| 738 |
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|
| 739 |
< |
if (!globals_->haveRsw()){ |
| 739 |
> |
if (!simParams_->haveRsw()){ |
| 740 |
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sprintf(painCave.errMsg, |
| 741 |
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"SimCreator Warning: No value was set for switchingRadius.\n" |
| 742 |
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"\tOOPSE will use a default value of\n" |
| 745 |
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simError(); |
| 746 |
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rsw_ = 0.95 * rcut_; |
| 747 |
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} else{ |
| 748 |
< |
rsw_ = globals_->getRsw(); |
| 748 |
> |
rsw_ = simParams_->getRsw(); |
| 749 |
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} |
| 750 |
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|
| 751 |
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} else { |
| 752 |
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// if charge, dipole or reaction field is not used and the cutofff radius is not specified in |
| 753 |
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//meta-data file, the maximum cutoff radius calculated from forcefiled will be used |
| 754 |
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|
| 755 |
< |
if (globals_->haveRcut()) { |
| 756 |
< |
rcut_ = globals_->getRcut(); |
| 755 |
> |
if (simParams_->haveRcut()) { |
| 756 |
> |
rcut_ = simParams_->getRcut(); |
| 757 |
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} else { |
| 758 |
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//set cutoff radius to the maximum cutoff radius based on atom types in the whole system |
| 759 |
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rcut_ = calcMaxCutoffRadius(); |
| 760 |
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} |
| 761 |
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| 762 |
< |
if (globals_->haveRsw()) { |
| 763 |
< |
rsw_ = globals_->getRsw(); |
| 762 |
> |
if (simParams_->haveRsw()) { |
| 763 |
> |
rsw_ = simParams_->getRsw(); |
| 764 |
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} else { |
| 765 |
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rsw_ = rcut_; |
| 766 |
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} |
