80 |
|
return result; |
81 |
|
} |
82 |
|
|
83 |
< |
SimInfo::SimInfo(MakeStamps* stamps, std::vector<std::pair<MoleculeStamp*, int> >& molStampPairs, |
84 |
< |
ForceField* ff, Globals* simParams) : |
85 |
< |
stamps_(stamps), forceField_(ff), simParams_(simParams), |
83 |
> |
SimInfo::SimInfo(ForceField* ff, Globals* simParams) : |
84 |
> |
forceField_(ff), simParams_(simParams), |
85 |
|
ndf_(0), ndfRaw_(0), ndfTrans_(0), nZconstraint_(0), |
86 |
|
nGlobalMols_(0), nGlobalAtoms_(0), nGlobalCutoffGroups_(0), |
87 |
|
nGlobalIntegrableObjects_(0), nGlobalRigidBodies_(0), |
89 |
|
nIntegrableObjects_(0), nCutoffGroups_(0), nConstraints_(0), |
90 |
|
sman_(NULL), fortranInitialized_(false) { |
91 |
|
|
93 |
– |
|
94 |
– |
std::vector<std::pair<MoleculeStamp*, int> >::iterator i; |
92 |
|
MoleculeStamp* molStamp; |
93 |
|
int nMolWithSameStamp; |
94 |
|
int nCutoffAtoms = 0; // number of atoms belong to cutoff groups |
96 |
|
CutoffGroupStamp* cgStamp; |
97 |
|
RigidBodyStamp* rbStamp; |
98 |
|
int nRigidAtoms = 0; |
99 |
< |
|
100 |
< |
for (i = molStampPairs.begin(); i !=molStampPairs.end(); ++i) { |
101 |
< |
molStamp = i->first; |
102 |
< |
nMolWithSameStamp = i->second; |
99 |
> |
std::vector<Component*> components = simParams->getComponents(); |
100 |
> |
|
101 |
> |
for (std::vector<Component*>::iterator i = components.begin(); i !=components.end(); ++i) { |
102 |
> |
molStamp = (*i)->getMoleculeStamp(); |
103 |
> |
nMolWithSameStamp = (*i)->getNMol(); |
104 |
|
|
105 |
|
addMoleculeStamp(molStamp, nMolWithSameStamp); |
106 |
|
|
107 |
|
//calculate atoms in molecules |
108 |
|
nGlobalAtoms_ += molStamp->getNAtoms() *nMolWithSameStamp; |
109 |
|
|
112 |
– |
|
110 |
|
//calculate atoms in cutoff groups |
111 |
|
int nAtomsInGroups = 0; |
112 |
|
int nCutoffGroupsInStamp = molStamp->getNCutoffGroups(); |
113 |
|
|
114 |
|
for (int j=0; j < nCutoffGroupsInStamp; j++) { |
115 |
< |
cgStamp = molStamp->getCutoffGroup(j); |
115 |
> |
cgStamp = molStamp->getCutoffGroupStamp(j); |
116 |
|
nAtomsInGroups += cgStamp->getNMembers(); |
117 |
|
} |
118 |
|
|
125 |
|
int nRigidBodiesInStamp = molStamp->getNRigidBodies(); |
126 |
|
|
127 |
|
for (int j=0; j < nRigidBodiesInStamp; j++) { |
128 |
< |
rbStamp = molStamp->getRigidBody(j); |
128 |
> |
rbStamp = molStamp->getRigidBodyStamp(j); |
129 |
|
nAtomsInRigidBodies += rbStamp->getNMembers(); |
130 |
|
} |
131 |
|
|
164 |
|
} |
165 |
|
molecules_.clear(); |
166 |
|
|
170 |
– |
delete stamps_; |
167 |
|
delete sman_; |
168 |
|
delete simParams_; |
169 |
|
delete forceField_; |
270 |
|
} |
271 |
|
} |
272 |
|
|
273 |
< |
}//end for (integrableObject) |
274 |
< |
}// end for (mol) |
273 |
> |
} |
274 |
> |
} |
275 |
|
|
276 |
|
// n_constraints is local, so subtract them on each processor |
277 |
|
ndf_local -= nConstraints_; |