83 |
|
MoleculeStamp* molStamp; |
84 |
|
int nMolWithSameStamp; |
85 |
|
int nCutoffAtoms = 0; // number of atoms belong to cutoff groups |
86 |
< |
int nGroups = 0; //total cutoff groups defined in meta-data file |
86 |
> |
int nGroups = 0; //total cutoff groups defined in meta-data file |
87 |
|
CutoffGroupStamp* cgStamp; |
88 |
|
RigidBodyStamp* rbStamp; |
89 |
|
int nRigidAtoms = 0; |
108 |
|
} |
109 |
|
|
110 |
|
nGroups += nCutoffGroupsInStamp * nMolWithSameStamp; |
111 |
+ |
|
112 |
|
nCutoffAtoms += nAtomsInGroups * nMolWithSameStamp; |
113 |
|
|
114 |
|
//calculate atoms in rigid bodies |
125 |
|
|
126 |
|
} |
127 |
|
|
128 |
< |
//every free atom (atom does not belong to cutoff groups) is a cutoff group |
129 |
< |
//therefore the total number of cutoff groups in the system is equal to |
130 |
< |
//the total number of atoms minus number of atoms belong to cutoff group defined in meta-data |
131 |
< |
//file plus the number of cutoff groups defined in meta-data file |
128 |
> |
//every free atom (atom does not belong to cutoff groups) is a cutoff |
129 |
> |
//group therefore the total number of cutoff groups in the system is |
130 |
> |
//equal to the total number of atoms minus number of atoms belong to |
131 |
> |
//cutoff group defined in meta-data file plus the number of cutoff |
132 |
> |
//groups defined in meta-data file |
133 |
|
nGlobalCutoffGroups_ = nGlobalAtoms_ - nCutoffAtoms + nGroups; |
134 |
|
|
135 |
< |
//every free atom (atom does not belong to rigid bodies) is an integrable object |
136 |
< |
//therefore the total number of integrable objects in the system is equal to |
137 |
< |
//the total number of atoms minus number of atoms belong to rigid body defined in meta-data |
138 |
< |
//file plus the number of rigid bodies defined in meta-data file |
139 |
< |
nGlobalIntegrableObjects_ = nGlobalAtoms_ - nRigidAtoms + nGlobalRigidBodies_; |
140 |
< |
|
135 |
> |
//every free atom (atom does not belong to rigid bodies) is an |
136 |
> |
//integrable object therefore the total number of integrable objects |
137 |
> |
//in the system is equal to the total number of atoms minus number of |
138 |
> |
//atoms belong to rigid body defined in meta-data file plus the number |
139 |
> |
//of rigid bodies defined in meta-data file |
140 |
> |
nGlobalIntegrableObjects_ = nGlobalAtoms_ - nRigidAtoms |
141 |
> |
+ nGlobalRigidBodies_; |
142 |
> |
|
143 |
|
nGlobalMols_ = molStampIds_.size(); |
144 |
|
|
145 |
|
#ifdef IS_MPI |
527 |
|
int useElectrostatics = 0; |
528 |
|
//usePBC and useRF are from simParams |
529 |
|
int usePBC = simParams_->getPBC(); |
530 |
+ |
int useRF; |
531 |
|
|
532 |
+ |
// set the useRF logical |
533 |
+ |
std::string myMethod = simParams_->getElectrostaticSummationMethod(); |
534 |
+ |
if (myMethod == "REACTION_FIELD") |
535 |
+ |
useRF = 1; |
536 |
+ |
else |
537 |
+ |
useRF = 0; |
538 |
+ |
|
539 |
|
//loop over all of the atom types |
540 |
|
for (i = atomTypes.begin(); i != atomTypes.end(); ++i) { |
541 |
|
useLennardJones |= (*i)->isLennardJones(); |
597 |
|
temp = useFLARB; |
598 |
|
MPI_Allreduce(&temp, &useFLARB, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD); |
599 |
|
|
600 |
+ |
temp = useRF; |
601 |
+ |
MPI_Allreduce(&temp, &useRF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD); |
602 |
+ |
|
603 |
|
#endif |
604 |
|
|
605 |
|
fInfo_.SIM_uses_PBC = usePBC; |
614 |
|
fInfo_.SIM_uses_EAM = useEAM; |
615 |
|
fInfo_.SIM_uses_Shapes = useShape; |
616 |
|
fInfo_.SIM_uses_FLARB = useFLARB; |
617 |
+ |
fInfo_.SIM_uses_RF = useRF; |
618 |
|
|
619 |
< |
if( fInfo_.SIM_uses_Dipoles && fInfo_.SIM_uses_RF) { |
619 |
> |
if( fInfo_.SIM_uses_Dipoles && myMethod == "REACTION_FIELD") { |
620 |
|
|
621 |
|
if (simParams_->haveDielectric()) { |
622 |
|
fInfo_.dielect = simParams_->getDielectric(); |
666 |
|
|
667 |
|
totalMass = cg->getMass(); |
668 |
|
for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) { |
669 |
< |
mfact.push_back(atom->getMass()/totalMass); |
669 |
> |
// Check for massless groups - set mfact to 1 if true |
670 |
> |
if (totalMass != 0) |
671 |
> |
mfact.push_back(atom->getMass()/totalMass); |
672 |
> |
else |
673 |
> |
mfact.push_back( 1.0 ); |
674 |
|
} |
675 |
|
|
676 |
|
} |
876 |
|
} |
877 |
|
} |
878 |
|
} |
879 |
+ |
} |
880 |
+ |
|
881 |
+ |
|
882 |
+ |
if (simParams_->haveSkinThickness()) { |
883 |
+ |
double skinThickness = simParams_->getSkinThickness(); |
884 |
|
} |
885 |
+ |
|
886 |
|
notifyFortranCutoffs(&rcut_, &rsw_, &rnblist, &cp); |
887 |
|
// also send cutoff notification to electrostatics |
888 |
|
setElectrostaticCutoffRadius(&rcut_); |