| 45 |
|
fortranInitialized_(false) { |
| 46 |
|
|
| 47 |
|
std::vector<std::pair<MoleculeStamp*, int> >::iterator i; |
| 48 |
– |
int nCutoffAtoms; // number of atoms belong to cutoff groups |
| 49 |
– |
int ngroups; //total cutoff groups defined in meta-data file |
| 48 |
|
MoleculeStamp* molStamp; |
| 49 |
|
int nMolWithSameStamp; |
| 50 |
+ |
int nCutoffAtoms; // number of atoms belong to cutoff groups |
| 51 |
+ |
int nGroups; //total cutoff groups defined in meta-data file |
| 52 |
|
CutoffGroupStamp* cgStamp; |
| 53 |
< |
int nAtomsIngroups; |
| 54 |
< |
int nCutoffGroupsInStamp; |
| 55 |
< |
|
| 53 |
> |
int nAtomsInGroups; |
| 54 |
> |
int nCutoffGroupsInStamp; |
| 55 |
> |
|
| 56 |
> |
RigidBodyStamp* rbStamp; |
| 57 |
> |
int nAtomsInRigidBodies; |
| 58 |
> |
int nRigidBodiesInStamp; |
| 59 |
> |
int nRigidAtoms; |
| 60 |
> |
int nRigidBodies; |
| 61 |
> |
|
| 62 |
|
nGlobalAtoms_ = 0; |
| 57 |
– |
ngroups = 0; |
| 63 |
|
|
| 64 |
+ |
nGroups = 0; |
| 65 |
+ |
nCutoffAtoms = 0; |
| 66 |
+ |
|
| 67 |
+ |
nRigidBodies |
| 68 |
+ |
nRigidBodies = 0; |
| 69 |
+ |
|
| 70 |
|
for (i = molStampPairs.begin(); i !=molStampPairs.end(); ++i) { |
| 71 |
|
molStamp = i->first; |
| 72 |
|
nMolWithSameStamp = i->second; |
| 73 |
|
|
| 74 |
|
addMoleculeStamp(molStamp, nMolWithSameStamp); |
| 75 |
< |
|
| 75 |
> |
|
| 76 |
> |
//calculate atoms in molecules |
| 77 |
|
nGlobalAtoms_ += molStamp->getNAtoms() *nMolWithSameStamp; |
| 78 |
< |
|
| 79 |
< |
nAtomsIngroups = 0; |
| 78 |
> |
|
| 79 |
> |
|
| 80 |
> |
//calculate atoms in cutoff groups |
| 81 |
> |
nAtomsInGroups = 0; |
| 82 |
|
nCutoffGroupsInStamp = molStamp->getNCutoffGroups(); |
| 83 |
|
|
| 84 |
|
for (int j=0; j < nCutoffGroupsInStamp; j++) { |
| 85 |
|
cgStamp = molStamp->getCutoffGroup(j); |
| 86 |
< |
nAtomsIngroups += cgStamp->getNMembers(); |
| 86 |
> |
nAtomsInGroups += cgStamp->getNMembers(); |
| 87 |
|
} |
| 88 |
|
|
| 89 |
< |
ngroups += *nMolWithSameStamp; |
| 90 |
< |
nCutoffAtoms += nAtomsIngroups * nMolWithSameStamp; |
| 89 |
> |
nGroups += nCutoffGroupsInStamp * nMolWithSameStamp; |
| 90 |
> |
nCutoffAtoms += nAtomsInGroups * nMolWithSameStamp; |
| 91 |
> |
|
| 92 |
> |
//calculate atoms in rigid bodies |
| 93 |
> |
nAtomsInRigidBodies = 0; |
| 94 |
> |
nRigidBodiesInStamp = molStamp->getNCutoffGroups(); |
| 95 |
> |
|
| 96 |
> |
for (int j=0; j < nRigidBodiesInStamp; j++) { |
| 97 |
> |
rbStamp = molStamp->getRigidBody(j); |
| 98 |
> |
nRigidBodiesInStamp += rbStamp->getNMembers(); |
| 99 |
> |
} |
| 100 |
> |
|
| 101 |
> |
nRigidBodies += nRigidBodiesInStamp * nMolWithSameStamp; |
| 102 |
> |
nRigidAtoms += nAtomsInRigidBodies * nMolWithSameStamp; |
| 103 |
> |
|
| 104 |
|
} |
| 105 |
|
|
| 106 |
|
//every free atom (atom does not belong to cutoff groups) is a cutoff group |
| 107 |
|
//therefore the total number of cutoff groups in the system is equal to |
| 108 |
|
//the total number of atoms minus number of atoms belong to cutoff group defined in meta-data |
| 109 |
|
//file plus the number of cutoff groups defined in meta-data file |
| 110 |
< |
nGlobalCutoffGroups_ = nGlobalAtoms_ - nCutoffAtoms + ngroups; |
| 110 |
> |
nGlobalCutoffGroups_ = nGlobalAtoms_ - nCutoffAtoms + nGroups; |
| 111 |
> |
|
| 112 |
> |
//every free atom (atom does not belong to rigid bodies) is a rigid body |
| 113 |
> |
//therefore the total number of cutoff groups in the system is equal to |
| 114 |
> |
//the total number of atoms minus number of atoms belong to rigid body defined in meta-data |
| 115 |
> |
//file plus the number of rigid bodies defined in meta-data file |
| 116 |
> |
nGlobalIntegrableObjects_ = nGlobalAtoms_ - nRigidAtoms + nRigidBodies; |
| 117 |
|
|
| 118 |
|
//initialize globalGroupMembership_, every element of this array will be 0 |
| 119 |
|
globalGroupMembership_.insert(globalGroupMembership_.end(), nGlobalAtoms_, 0); |
