| 156 |
|
+ nGlobalRigidBodies_; |
| 157 |
|
|
| 158 |
|
nGlobalMols_ = molStampIds_.size(); |
| 159 |
– |
|
| 160 |
– |
#ifdef IS_MPI |
| 159 |
|
molToProcMap_.resize(nGlobalMols_); |
| 162 |
– |
#endif |
| 163 |
– |
|
| 160 |
|
} |
| 161 |
|
|
| 162 |
|
SimInfo::~SimInfo() { |
| 856 |
|
int nGlobalExcludes = 0; |
| 857 |
|
int* globalExcludes = NULL; |
| 858 |
|
int* excludeList = exclude_.getExcludeList(); |
| 859 |
< |
setFortranSim( &fInfo_, &nGlobalAtoms_, &nAtoms_, &identArray[0], &nExclude, excludeList , |
| 860 |
< |
&nGlobalExcludes, globalExcludes, &molMembershipArray[0], |
| 861 |
< |
&mfact[0], &nCutoffGroups_, &fortranGlobalGroupMembership[0], &isError); |
| 862 |
< |
|
| 859 |
> |
setFortranSim( &fInfo_, &nGlobalAtoms_, &nAtoms_, &identArray[0], |
| 860 |
> |
&nExclude, excludeList , &nGlobalExcludes, globalExcludes, |
| 861 |
> |
&molMembershipArray[0], &mfact[0], &nCutoffGroups_, |
| 862 |
> |
&fortranGlobalGroupMembership[0], &isError); |
| 863 |
> |
|
| 864 |
|
if( isError ){ |
| 865 |
< |
|
| 865 |
> |
|
| 866 |
|
sprintf( painCave.errMsg, |
| 867 |
|
"There was an error setting the simulation information in fortran.\n" ); |
| 868 |
|
painCave.isFatal = 1; |
| 869 |
|
painCave.severity = OOPSE_ERROR; |
| 870 |
|
simError(); |
| 871 |
|
} |
| 872 |
< |
|
| 873 |
< |
#ifdef IS_MPI |
| 872 |
> |
|
| 873 |
> |
|
| 874 |
|
sprintf( checkPointMsg, |
| 875 |
|
"succesfully sent the simulation information to fortran.\n"); |
| 876 |
< |
MPIcheckPoint(); |
| 877 |
< |
#endif // is_mpi |
| 878 |
< |
|
| 876 |
> |
|
| 877 |
> |
errorCheckPoint(); |
| 878 |
> |
|
| 879 |
|
// Setup number of neighbors in neighbor list if present |
| 880 |
|
if (simParams_->haveNeighborListNeighbors()) { |
| 881 |
|
int nlistNeighbors = simParams_->getNeighborListNeighbors(); |
| 886 |
|
} |
| 887 |
|
|
| 888 |
|
|
| 892 |
– |
#ifdef IS_MPI |
| 889 |
|
void SimInfo::setupFortranParallel() { |
| 890 |
< |
|
| 890 |
> |
#ifdef IS_MPI |
| 891 |
|
//SimInfo is responsible for creating localToGlobalAtomIndex and localToGlobalGroupIndex |
| 892 |
|
std::vector<int> localToGlobalAtomIndex(getNAtoms(), 0); |
| 893 |
|
std::vector<int> localToGlobalCutoffGroupIndex; |
| 937 |
|
} |
| 938 |
|
|
| 939 |
|
sprintf(checkPointMsg, " mpiRefresh successful.\n"); |
| 940 |
< |
MPIcheckPoint(); |
| 945 |
< |
|
| 946 |
< |
|
| 947 |
< |
} |
| 940 |
> |
errorCheckPoint(); |
| 941 |
|
|
| 942 |
|
#endif |
| 943 |
+ |
} |
| 944 |
|
|
| 945 |
|
void SimInfo::setupCutoff() { |
| 946 |
|
|
| 949 |
|
// Check the cutoff policy |
| 950 |
|
int cp = TRADITIONAL_CUTOFF_POLICY; // Set to traditional by default |
| 951 |
|
|
| 952 |
+ |
// Set LJ shifting bools to false |
| 953 |
+ |
ljsp_ = false; |
| 954 |
+ |
ljsf_ = false; |
| 955 |
+ |
|
| 956 |
|
std::string myPolicy; |
| 957 |
|
if (forceFieldOptions_.haveCutoffPolicy()){ |
| 958 |
|
myPolicy = forceFieldOptions_.getCutoffPolicy(); |
| 1016 |
|
simError(); |
| 1017 |
|
} |
| 1018 |
|
} |
| 1019 |
< |
|
| 1020 |
< |
notifyFortranCutoffs(&rcut_, &rsw_); |
| 1019 |
> |
|
| 1020 |
> |
if (simParams_->haveElectrostaticSummationMethod()) { |
| 1021 |
> |
std::string myMethod = simParams_->getElectrostaticSummationMethod(); |
| 1022 |
> |
toUpper(myMethod); |
| 1023 |
> |
|
| 1024 |
> |
if (myMethod == "SHIFTED_POTENTIAL") { |
| 1025 |
> |
ljsp_ = true; |
| 1026 |
> |
} else if (myMethod == "SHIFTED_FORCE") { |
| 1027 |
> |
ljsf_ = true; |
| 1028 |
> |
} |
| 1029 |
> |
} |
| 1030 |
> |
notifyFortranCutoffs(&rcut_, &rsw_, &ljsp_, &ljsf_); |
| 1031 |
|
|
| 1032 |
|
} else { |
| 1033 |
|
|
| 1044 |
|
if (simParams_->haveElectrostaticSummationMethod()) { |
| 1045 |
|
std::string myMethod = simParams_->getElectrostaticSummationMethod(); |
| 1046 |
|
toUpper(myMethod); |
| 1047 |
< |
if (myMethod == "SHIFTED_POTENTIAL" || myMethod == "SHIFTED_FORCE") { |
| 1047 |
> |
|
| 1048 |
> |
// For the time being, we're tethering the LJ shifted behavior to the |
| 1049 |
> |
// electrostaticSummationMethod keyword options |
| 1050 |
> |
if (myMethod == "SHIFTED_POTENTIAL") { |
| 1051 |
> |
ljsp_ = true; |
| 1052 |
> |
} else if (myMethod == "SHIFTED_FORCE") { |
| 1053 |
> |
ljsf_ = true; |
| 1054 |
> |
} |
| 1055 |
> |
if (myMethod == "SHIFTED_POTENTIAL" || myMethod == "SHIFTED_FORCE") { |
| 1056 |
|
if (simParams_->haveSwitchingRadius()){ |
| 1057 |
|
sprintf(painCave.errMsg, |
| 1058 |
|
"SimInfo Warning: A value was set for the switchingRadius\n" |
| 1075 |
|
simError(); |
| 1076 |
|
rsw_ = 0.85 * rcut_; |
| 1077 |
|
} |
| 1078 |
< |
notifyFortranCutoffs(&rcut_, &rsw_); |
| 1078 |
> |
|
| 1079 |
> |
notifyFortranCutoffs(&rcut_, &rsw_, &ljsp_, &ljsf_); |
| 1080 |
> |
|
| 1081 |
|
} else { |
| 1082 |
|
// We didn't set rcut explicitly, and we don't have electrostatic atoms, so |
| 1083 |
|
// We'll punt and let fortran figure out the cutoffs later. |
