| 92 |
|
nGlobalIntegrableObjects_(0), nGlobalRigidBodies_(0), |
| 93 |
|
nAtoms_(0), nBonds_(0), nBends_(0), nTorsions_(0), nRigidBodies_(0), |
| 94 |
|
nIntegrableObjects_(0), nCutoffGroups_(0), nConstraints_(0), |
| 95 |
< |
sman_(NULL), fortranInitialized_(false), calcBoxDipole_(false) { |
| 95 |
> |
sman_(NULL), fortranInitialized_(false), calcBoxDipole_(false), |
| 96 |
> |
useAtomicVirial_(true) { |
| 97 |
|
|
| 98 |
|
MoleculeStamp* molStamp; |
| 99 |
|
int nMolWithSameStamp; |
| 667 |
|
int useSF; |
| 668 |
|
int useSP; |
| 669 |
|
int useBoxDipole; |
| 670 |
+ |
|
| 671 |
|
std::string myMethod; |
| 672 |
|
|
| 673 |
|
// set the useRF logical |
| 692 |
|
if (simParams_->getAccumulateBoxDipole()) |
| 693 |
|
useBoxDipole = 1; |
| 694 |
|
|
| 695 |
+ |
useAtomicVirial_ = simParams_->getUseAtomicVirial(); |
| 696 |
+ |
|
| 697 |
|
//loop over all of the atom types |
| 698 |
|
for (i = atomTypes.begin(); i != atomTypes.end(); ++i) { |
| 699 |
|
useLennardJones |= (*i)->isLennardJones(); |
| 771 |
|
temp = useBoxDipole; |
| 772 |
|
MPI_Allreduce(&temp, &useBoxDipole, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD); |
| 773 |
|
|
| 774 |
+ |
temp = useAtomicVirial_; |
| 775 |
+ |
MPI_Allreduce(&temp, &useAtomicVirial_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD); |
| 776 |
+ |
|
| 777 |
|
#endif |
| 778 |
|
|
| 779 |
|
fInfo_.SIM_uses_PBC = usePBC; |
| 793 |
|
fInfo_.SIM_uses_SF = useSF; |
| 794 |
|
fInfo_.SIM_uses_SP = useSP; |
| 795 |
|
fInfo_.SIM_uses_BoxDipole = useBoxDipole; |
| 796 |
+ |
fInfo_.SIM_uses_AtomicVirial = useAtomicVirial_; |
| 797 |
|
} |
| 798 |
|
|
| 799 |
|
void SimInfo::setupFortranSim() { |
| 881 |
|
|
| 882 |
|
// Setup number of neighbors in neighbor list if present |
| 883 |
|
if (simParams_->haveNeighborListNeighbors()) { |
| 884 |
< |
setNeighbors(simParams_->getNeighborListNeighbors()); |
| 884 |
> |
int nlistNeighbors = simParams_->getNeighborListNeighbors(); |
| 885 |
> |
setNeighbors(&nlistNeighbors); |
| 886 |
|
} |
| 887 |
|
|
| 888 |
|
|
| 955 |
|
// Check the cutoff policy |
| 956 |
|
int cp = TRADITIONAL_CUTOFF_POLICY; // Set to traditional by default |
| 957 |
|
|
| 958 |
+ |
// Set LJ shifting bools to false |
| 959 |
+ |
ljsp_ = false; |
| 960 |
+ |
ljsf_ = false; |
| 961 |
+ |
|
| 962 |
|
std::string myPolicy; |
| 963 |
|
if (forceFieldOptions_.haveCutoffPolicy()){ |
| 964 |
|
myPolicy = forceFieldOptions_.getCutoffPolicy(); |
| 1022 |
|
simError(); |
| 1023 |
|
} |
| 1024 |
|
} |
| 1025 |
< |
|
| 1026 |
< |
notifyFortranCutoffs(&rcut_, &rsw_); |
| 1025 |
> |
|
| 1026 |
> |
if (simParams_->haveElectrostaticSummationMethod()) { |
| 1027 |
> |
std::string myMethod = simParams_->getElectrostaticSummationMethod(); |
| 1028 |
> |
toUpper(myMethod); |
| 1029 |
> |
|
| 1030 |
> |
if (myMethod == "SHIFTED_POTENTIAL") { |
| 1031 |
> |
ljsp_ = true; |
| 1032 |
> |
} else if (myMethod == "SHIFTED_FORCE") { |
| 1033 |
> |
ljsf_ = true; |
| 1034 |
> |
} |
| 1035 |
> |
} |
| 1036 |
> |
notifyFortranCutoffs(&rcut_, &rsw_, &ljsp_, &ljsf_); |
| 1037 |
|
|
| 1038 |
|
} else { |
| 1039 |
|
|
| 1050 |
|
if (simParams_->haveElectrostaticSummationMethod()) { |
| 1051 |
|
std::string myMethod = simParams_->getElectrostaticSummationMethod(); |
| 1052 |
|
toUpper(myMethod); |
| 1053 |
< |
if (myMethod == "SHIFTED_POTENTIAL" || myMethod == "SHIFTED_FORCE") { |
| 1053 |
> |
|
| 1054 |
> |
// For the time being, we're tethering the LJ shifted behavior to the |
| 1055 |
> |
// electrostaticSummationMethod keyword options |
| 1056 |
> |
if (myMethod == "SHIFTED_POTENTIAL") { |
| 1057 |
> |
ljsp_ = true; |
| 1058 |
> |
} else if (myMethod == "SHIFTED_FORCE") { |
| 1059 |
> |
ljsf_ = true; |
| 1060 |
> |
} |
| 1061 |
> |
if (myMethod == "SHIFTED_POTENTIAL" || myMethod == "SHIFTED_FORCE") { |
| 1062 |
|
if (simParams_->haveSwitchingRadius()){ |
| 1063 |
|
sprintf(painCave.errMsg, |
| 1064 |
|
"SimInfo Warning: A value was set for the switchingRadius\n" |
| 1081 |
|
simError(); |
| 1082 |
|
rsw_ = 0.85 * rcut_; |
| 1083 |
|
} |
| 1084 |
< |
notifyFortranCutoffs(&rcut_, &rsw_); |
| 1084 |
> |
|
| 1085 |
> |
notifyFortranCutoffs(&rcut_, &rsw_, &ljsp_, &ljsf_); |
| 1086 |
> |
|
| 1087 |
|
} else { |
| 1088 |
|
// We didn't set rcut explicitly, and we don't have electrostatic atoms, so |
| 1089 |
|
// We'll punt and let fortran figure out the cutoffs later. |
