| 42 |
|
namespace oopse { |
| 43 |
|
|
| 44 |
|
SimInfo::SimInfo(std::vector<std::pair<MoleculeStamp*, int> >& molStampPairs, |
| 45 |
< |
ForceField* ff, Globals* globals) : |
| 46 |
< |
forceField_(ff), globals_(globals), nAtoms_(0), nBonds_(0), |
| 47 |
< |
nBends_(0), nTorsions_(0), nRigidBodies_(0), nIntegrableObjects_(0), |
| 48 |
< |
nCutoffGroups_(0), nConstraints_(0), nZconstraint_(0), sman_(NULL), |
| 49 |
< |
fortranInitialized_(false) { |
| 45 |
> |
ForceField* ff, Globals* simParams) : |
| 46 |
> |
forceField_(ff), simParams_(simParams), |
| 47 |
> |
ndf_(0), ndfRaw_(0), ndfTrans_(0), nZconstraint_(0), |
| 48 |
> |
nGlobalMols_(0), nGlobalAtoms_(0), nGlobalCutoffGroups_(0), |
| 49 |
> |
nGlobalIntegrableObjects_(0), nGlobalRigidBodies_(0), |
| 50 |
> |
nAtoms_(0), nBonds_(0), nBends_(0), nTorsions_(0), nRigidBodies_(0), |
| 51 |
> |
nIntegrableObjects_(0), nCutoffGroups_(0), nConstraints_(0), |
| 52 |
> |
sman_(NULL), fortranInitialized_(false) { |
| 53 |
|
|
| 54 |
+ |
|
| 55 |
|
std::vector<std::pair<MoleculeStamp*, int> >::iterator i; |
| 56 |
|
MoleculeStamp* molStamp; |
| 57 |
|
int nMolWithSameStamp; |
| 58 |
< |
int nCutoffAtoms; // number of atoms belong to cutoff groups |
| 59 |
< |
int nGroups; //total cutoff groups defined in meta-data file |
| 60 |
< |
CutoffGroupStamp* cgStamp; |
| 57 |
< |
int nAtomsInGroups; |
| 58 |
< |
int nCutoffGroupsInStamp; |
| 59 |
< |
|
| 58 |
> |
int nCutoffAtoms = 0; // number of atoms belong to cutoff groups |
| 59 |
> |
int nGroups = 0; //total cutoff groups defined in meta-data file |
| 60 |
> |
CutoffGroupStamp* cgStamp; |
| 61 |
|
RigidBodyStamp* rbStamp; |
| 62 |
< |
int nAtomsInRigidBodies; |
| 62 |
< |
int nRigidBodiesInStamp; |
| 63 |
< |
int nRigidAtoms; |
| 64 |
< |
int nRigidBodies; |
| 65 |
< |
|
| 66 |
< |
nGlobalAtoms_ = 0; |
| 62 |
> |
int nRigidAtoms = 0; |
| 63 |
|
|
| 68 |
– |
nGroups = 0; |
| 69 |
– |
nCutoffAtoms = 0; |
| 70 |
– |
nRigidBodies = 0; |
| 71 |
– |
|
| 64 |
|
for (i = molStampPairs.begin(); i !=molStampPairs.end(); ++i) { |
| 65 |
|
molStamp = i->first; |
| 66 |
|
nMolWithSameStamp = i->second; |
| 72 |
|
|
| 73 |
|
|
| 74 |
|
//calculate atoms in cutoff groups |
| 75 |
< |
nAtomsInGroups = 0; |
| 76 |
< |
nCutoffGroupsInStamp = molStamp->getNCutoffGroups(); |
| 75 |
> |
int nAtomsInGroups = 0; |
| 76 |
> |
int nCutoffGroupsInStamp = molStamp->getNCutoffGroups(); |
| 77 |
|
|
| 78 |
|
for (int j=0; j < nCutoffGroupsInStamp; j++) { |
| 79 |
|
cgStamp = molStamp->getCutoffGroup(j); |
| 84 |
|
nCutoffAtoms += nAtomsInGroups * nMolWithSameStamp; |
| 85 |
|
|
| 86 |
|
//calculate atoms in rigid bodies |
| 87 |
< |
nAtomsInRigidBodies = 0; |
| 88 |
< |
nRigidBodiesInStamp = molStamp->getNCutoffGroups(); |
| 87 |
> |
int nAtomsInRigidBodies = 0; |
| 88 |
> |
int nRigidBodiesInStamp = molStamp->getNCutoffGroups(); |
| 89 |
|
|
| 90 |
|
for (int j=0; j < nRigidBodiesInStamp; j++) { |
| 91 |
|
rbStamp = molStamp->getRigidBody(j); |
| 92 |
< |
nRigidBodiesInStamp += rbStamp->getNMembers(); |
| 92 |
> |
nAtomsInRigidBodies += rbStamp->getNMembers(); |
| 93 |
|
} |
| 94 |
|
|
| 95 |
< |
nRigidBodies += nRigidBodiesInStamp * nMolWithSameStamp; |
| 95 |
> |
nGlobalRigidBodies_ += nRigidBodiesInStamp * nMolWithSameStamp; |
| 96 |
|
nRigidAtoms += nAtomsInRigidBodies * nMolWithSameStamp; |
| 97 |
|
|
| 98 |
|
} |
| 103 |
|
//file plus the number of cutoff groups defined in meta-data file |
| 104 |
|
nGlobalCutoffGroups_ = nGlobalAtoms_ - nCutoffAtoms + nGroups; |
| 105 |
|
|
| 106 |
< |
//every free atom (atom does not belong to rigid bodies) is a rigid body |
| 107 |
< |
//therefore the total number of cutoff groups in the system is equal to |
| 106 |
> |
//every free atom (atom does not belong to rigid bodies) is an integrable object |
| 107 |
> |
//therefore the total number of integrable objects in the system is equal to |
| 108 |
|
//the total number of atoms minus number of atoms belong to rigid body defined in meta-data |
| 109 |
|
//file plus the number of rigid bodies defined in meta-data file |
| 110 |
< |
nGlobalIntegrableObjects_ = nGlobalAtoms_ - nRigidAtoms + nRigidBodies; |
| 110 |
> |
nGlobalIntegrableObjects_ = nGlobalAtoms_ - nRigidAtoms + nGlobalRigidBodies_; |
| 111 |
|
|
| 120 |
– |
//initialize globalGroupMembership_, every element of this array will be 0 |
| 121 |
– |
globalGroupMembership_.insert(globalGroupMembership_.end(), nGlobalAtoms_, 0); |
| 122 |
– |
|
| 112 |
|
nGlobalMols_ = molStampIds_.size(); |
| 113 |
|
|
| 114 |
|
#ifdef IS_MPI |
| 123 |
|
MemoryUtils::deleteVectorOfPointer(moleculeStamps_); |
| 124 |
|
|
| 125 |
|
delete sman_; |
| 126 |
< |
delete globals_; |
| 126 |
> |
delete simParams_; |
| 127 |
|
delete forceField_; |
| 128 |
|
|
| 129 |
|
} |
| 133 |
|
MoleculeIterator i; |
| 134 |
|
|
| 135 |
|
i = molecules_.find(mol->getGlobalIndex()); |
| 136 |
< |
if (i != molecules_.end() ) { |
| 136 |
> |
if (i == molecules_.end() ) { |
| 137 |
|
|
| 138 |
< |
molecules_.insert(make_pair(mol->getGlobalIndex(), mol)); |
| 138 |
> |
molecules_.insert(std::make_pair(mol->getGlobalIndex(), mol)); |
| 139 |
|
|
| 140 |
|
nAtoms_ += mol->getNAtoms(); |
| 141 |
|
nBonds_ += mol->getNBonds(); |
| 451 |
|
int useFLARB = 0; //it is not in AtomType yet |
| 452 |
|
int useDirectionalAtom = 0; |
| 453 |
|
int useElectrostatics = 0; |
| 454 |
< |
//usePBC and useRF are from globals |
| 455 |
< |
bool usePBC = globals_->getPBC(); |
| 456 |
< |
bool useRF = globals_->getUseRF(); |
| 454 |
> |
//usePBC and useRF are from simParams |
| 455 |
> |
bool usePBC = simParams_->getPBC(); |
| 456 |
> |
bool useRF = simParams_->getUseRF(); |
| 457 |
|
|
| 458 |
|
//loop over all of the atom types |
| 459 |
|
for (i = atomTypes.begin(); i != atomTypes.end(); ++i) { |
| 532 |
|
|
| 533 |
|
if( fInfo_.SIM_uses_Dipoles && fInfo_.SIM_uses_RF) { |
| 534 |
|
|
| 535 |
< |
if (globals_->haveDielectric()) { |
| 536 |
< |
fInfo_.dielect = globals_->getDielectric(); |
| 535 |
> |
if (simParams_->haveDielectric()) { |
| 536 |
> |
fInfo_.dielect = simParams_->getDielectric(); |
| 537 |
|
} else { |
| 538 |
|
sprintf(painCave.errMsg, |
| 539 |
|
"SimSetup Error: No Dielectric constant was set.\n" |
| 721 |
|
|
| 722 |
|
if (fInfo_.SIM_uses_Charges | fInfo_.SIM_uses_Dipoles | fInfo_.SIM_uses_RF) { |
| 723 |
|
|
| 724 |
< |
if (!globals_->haveRcut()){ |
| 724 |
> |
if (!simParams_->haveRcut()){ |
| 725 |
|
sprintf(painCave.errMsg, |
| 726 |
|
"SimCreator Warning: No value was set for the cutoffRadius.\n" |
| 727 |
|
"\tOOPSE will use a default value of 15.0 angstroms" |
| 730 |
|
simError(); |
| 731 |
|
rcut_ = 15.0; |
| 732 |
|
} else{ |
| 733 |
< |
rcut_ = globals_->getRcut(); |
| 733 |
> |
rcut_ = simParams_->getRcut(); |
| 734 |
|
} |
| 735 |
|
|
| 736 |
< |
if (!globals_->haveRsw()){ |
| 736 |
> |
if (!simParams_->haveRsw()){ |
| 737 |
|
sprintf(painCave.errMsg, |
| 738 |
|
"SimCreator Warning: No value was set for switchingRadius.\n" |
| 739 |
|
"\tOOPSE will use a default value of\n" |
| 742 |
|
simError(); |
| 743 |
|
rsw_ = 0.95 * rcut_; |
| 744 |
|
} else{ |
| 745 |
< |
rsw_ = globals_->getRsw(); |
| 745 |
> |
rsw_ = simParams_->getRsw(); |
| 746 |
|
} |
| 747 |
|
|
| 748 |
|
} else { |
| 749 |
|
// if charge, dipole or reaction field is not used and the cutofff radius is not specified in |
| 750 |
|
//meta-data file, the maximum cutoff radius calculated from forcefiled will be used |
| 751 |
|
|
| 752 |
< |
if (globals_->haveRcut()) { |
| 753 |
< |
rcut_ = globals_->getRcut(); |
| 752 |
> |
if (simParams_->haveRcut()) { |
| 753 |
> |
rcut_ = simParams_->getRcut(); |
| 754 |
|
} else { |
| 755 |
|
//set cutoff radius to the maximum cutoff radius based on atom types in the whole system |
| 756 |
|
rcut_ = calcMaxCutoffRadius(); |
| 757 |
|
} |
| 758 |
|
|
| 759 |
< |
if (globals_->haveRsw()) { |
| 760 |
< |
rsw_ = globals_->getRsw(); |
| 759 |
> |
if (simParams_->haveRsw()) { |
| 760 |
> |
rsw_ = simParams_->getRsw(); |
| 761 |
|
} else { |
| 762 |
|
rsw_ = rcut_; |
| 763 |
|
} |
| 817 |
|
|
| 818 |
|
} |
| 819 |
|
|
| 820 |
< |
std::ostream& operator <<(ostream& o, SimInfo& info) { |
| 820 |
> |
std::ostream& operator <<(std::ostream& o, SimInfo& info) { |
| 821 |
|
|
| 822 |
|
return o; |
| 823 |
|
} |
| 824 |
|
|
| 825 |
|
}//end namespace oopse |
| 826 |
+ |
|
