| 71 |
|
nGlobalIntegrableObjects_(0), nGlobalRigidBodies_(0), |
| 72 |
|
nAtoms_(0), nBonds_(0), nBends_(0), nTorsions_(0), nInversions_(0), |
| 73 |
|
nRigidBodies_(0), nIntegrableObjects_(0), nCutoffGroups_(0), |
| 74 |
< |
nConstraints_(0), sman_(NULL), fortranInitialized_(false), |
| 74 |
> |
nConstraints_(0), sman_(NULL), topologyDone_(false), |
| 75 |
|
calcBoxDipole_(false), useAtomicVirial_(true) { |
| 76 |
|
|
| 77 |
|
MoleculeStamp* molStamp; |
| 125 |
|
//equal to the total number of atoms minus number of atoms belong to |
| 126 |
|
//cutoff group defined in meta-data file plus the number of cutoff |
| 127 |
|
//groups defined in meta-data file |
| 128 |
– |
std::cerr << "nGA = " << nGlobalAtoms_ << "\n"; |
| 129 |
– |
std::cerr << "nCA = " << nCutoffAtoms << "\n"; |
| 130 |
– |
std::cerr << "nG = " << nGroups << "\n"; |
| 128 |
|
|
| 129 |
|
nGlobalCutoffGroups_ = nGlobalAtoms_ - nCutoffAtoms + nGroups; |
| 133 |
– |
|
| 134 |
– |
std::cerr << "nGCG = " << nGlobalCutoffGroups_ << "\n"; |
| 130 |
|
|
| 131 |
|
//every free atom (atom does not belong to rigid bodies) is an |
| 132 |
|
//integrable object therefore the total number of integrable objects |
| 268 |
|
fdf_ = fdf_local; |
| 269 |
|
#endif |
| 270 |
|
return fdf_; |
| 271 |
+ |
} |
| 272 |
+ |
|
| 273 |
+ |
unsigned int SimInfo::getNLocalCutoffGroups(){ |
| 274 |
+ |
int nLocalCutoffAtoms = 0; |
| 275 |
+ |
Molecule* mol; |
| 276 |
+ |
MoleculeIterator mi; |
| 277 |
+ |
CutoffGroup* cg; |
| 278 |
+ |
Molecule::CutoffGroupIterator ci; |
| 279 |
+ |
|
| 280 |
+ |
for (mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) { |
| 281 |
+ |
|
| 282 |
+ |
for (cg = mol->beginCutoffGroup(ci); cg != NULL; |
| 283 |
+ |
cg = mol->nextCutoffGroup(ci)) { |
| 284 |
+ |
nLocalCutoffAtoms += cg->getNumAtom(); |
| 285 |
+ |
|
| 286 |
+ |
} |
| 287 |
+ |
} |
| 288 |
+ |
|
| 289 |
+ |
return nAtoms_ - nLocalCutoffAtoms + nCutoffGroups_; |
| 290 |
|
} |
| 291 |
|
|
| 292 |
|
void SimInfo::calcNdfRaw() { |
| 826 |
|
} |
| 827 |
|
|
| 828 |
|
|
| 829 |
< |
void SimInfo::setupFortran() { |
| 816 |
< |
int isError; |
| 829 |
> |
void SimInfo::prepareTopology() { |
| 830 |
|
int nExclude, nOneTwo, nOneThree, nOneFour; |
| 818 |
– |
vector<int> fortranGlobalGroupMembership; |
| 819 |
– |
|
| 820 |
– |
isError = 0; |
| 831 |
|
|
| 822 |
– |
//globalGroupMembership_ is filled by SimCreator |
| 823 |
– |
for (int i = 0; i < nGlobalAtoms_; i++) { |
| 824 |
– |
fortranGlobalGroupMembership.push_back(globalGroupMembership_[i] + 1); |
| 825 |
– |
} |
| 826 |
– |
|
| 832 |
|
//calculate mass ratio of cutoff group |
| 828 |
– |
vector<RealType> mfact; |
| 833 |
|
SimInfo::MoleculeIterator mi; |
| 834 |
|
Molecule* mol; |
| 835 |
|
Molecule::CutoffGroupIterator ci; |
| 838 |
|
Atom* atom; |
| 839 |
|
RealType totalMass; |
| 840 |
|
|
| 841 |
< |
//to avoid memory reallocation, reserve enough space for mfact |
| 842 |
< |
mfact.reserve(getNCutoffGroups()); |
| 841 |
> |
//to avoid memory reallocation, reserve enough space for massFactors_ |
| 842 |
> |
massFactors_.clear(); |
| 843 |
> |
massFactors_.reserve(getNCutoffGroups()); |
| 844 |
|
|
| 845 |
|
for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) { |
| 846 |
< |
for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) { |
| 846 |
> |
for (cg = mol->beginCutoffGroup(ci); cg != NULL; |
| 847 |
> |
cg = mol->nextCutoffGroup(ci)) { |
| 848 |
|
|
| 849 |
|
totalMass = cg->getMass(); |
| 850 |
|
for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) { |
| 851 |
|
// Check for massless groups - set mfact to 1 if true |
| 852 |
|
if (totalMass != 0) |
| 853 |
< |
mfact.push_back(atom->getMass()/totalMass); |
| 853 |
> |
massFactors_.push_back(atom->getMass()/totalMass); |
| 854 |
|
else |
| 855 |
< |
mfact.push_back( 1.0 ); |
| 855 |
> |
massFactors_.push_back( 1.0 ); |
| 856 |
|
} |
| 857 |
|
} |
| 858 |
|
} |
| 866 |
|
identArray_.push_back(atom->getIdent()); |
| 867 |
|
} |
| 868 |
|
} |
| 863 |
– |
|
| 864 |
– |
//fill molMembershipArray |
| 865 |
– |
//molMembershipArray is filled by SimCreator |
| 866 |
– |
vector<int> molMembershipArray(nGlobalAtoms_); |
| 867 |
– |
for (int i = 0; i < nGlobalAtoms_; i++) { |
| 868 |
– |
molMembershipArray[i] = globalMolMembership_[i] + 1; |
| 869 |
– |
} |
| 869 |
|
|
| 870 |
< |
//setup fortran simulation |
| 870 |
> |
//scan topology |
| 871 |
|
|
| 872 |
|
nExclude = excludedInteractions_.getSize(); |
| 873 |
|
nOneTwo = oneTwoInteractions_.getSize(); |
| 887 |
|
// &molMembershipArray[0], &mfact[0], &nCutoffGroups_, |
| 888 |
|
// &fortranGlobalGroupMembership[0], &isError); |
| 889 |
|
|
| 890 |
< |
// if( isError ){ |
| 892 |
< |
// |
| 893 |
< |
// sprintf( painCave.errMsg, |
| 894 |
< |
// "There was an error setting the simulation information in fortran.\n" ); |
| 895 |
< |
// painCave.isFatal = 1; |
| 896 |
< |
// painCave.severity = OPENMD_ERROR; |
| 897 |
< |
// simError(); |
| 898 |
< |
//} |
| 899 |
< |
|
| 900 |
< |
|
| 901 |
< |
// sprintf( checkPointMsg, |
| 902 |
< |
// "succesfully sent the simulation information to fortran.\n"); |
| 903 |
< |
|
| 904 |
< |
// errorCheckPoint(); |
| 905 |
< |
|
| 906 |
< |
// Setup number of neighbors in neighbor list if present |
| 907 |
< |
//if (simParams_->haveNeighborListNeighbors()) { |
| 908 |
< |
// int nlistNeighbors = simParams_->getNeighborListNeighbors(); |
| 909 |
< |
// setNeighbors(&nlistNeighbors); |
| 910 |
< |
//} |
| 911 |
< |
|
| 912 |
< |
#ifdef IS_MPI |
| 913 |
< |
// mpiSimData parallelData; |
| 914 |
< |
|
| 915 |
< |
//fill up mpiSimData struct |
| 916 |
< |
// parallelData.nMolGlobal = getNGlobalMolecules(); |
| 917 |
< |
// parallelData.nMolLocal = getNMolecules(); |
| 918 |
< |
// parallelData.nAtomsGlobal = getNGlobalAtoms(); |
| 919 |
< |
// parallelData.nAtomsLocal = getNAtoms(); |
| 920 |
< |
// parallelData.nGroupsGlobal = getNGlobalCutoffGroups(); |
| 921 |
< |
// parallelData.nGroupsLocal = getNCutoffGroups(); |
| 922 |
< |
// parallelData.myNode = worldRank; |
| 923 |
< |
// MPI_Comm_size(MPI_COMM_WORLD, &(parallelData.nProcessors)); |
| 924 |
< |
|
| 925 |
< |
//pass mpiSimData struct and index arrays to fortran |
| 926 |
< |
//setFsimParallel(¶llelData, &(parallelData.nAtomsLocal), |
| 927 |
< |
// &localToGlobalAtomIndex[0], &(parallelData.nGroupsLocal), |
| 928 |
< |
// &localToGlobalCutoffGroupIndex[0], &isError); |
| 929 |
< |
|
| 930 |
< |
// if (isError) { |
| 931 |
< |
// sprintf(painCave.errMsg, |
| 932 |
< |
// "mpiRefresh errror: fortran didn't like something we gave it.\n"); |
| 933 |
< |
// painCave.isFatal = 1; |
| 934 |
< |
// simError(); |
| 935 |
< |
// } |
| 936 |
< |
|
| 937 |
< |
// sprintf(checkPointMsg, " mpiRefresh successful.\n"); |
| 938 |
< |
// errorCheckPoint(); |
| 939 |
< |
#endif |
| 940 |
< |
|
| 941 |
< |
// initFortranFF(&isError); |
| 942 |
< |
// if (isError) { |
| 943 |
< |
// sprintf(painCave.errMsg, |
| 944 |
< |
// "initFortranFF errror: fortran didn't like something we gave it.\n"); |
| 945 |
< |
// painCave.isFatal = 1; |
| 946 |
< |
// simError(); |
| 947 |
< |
// } |
| 948 |
< |
// fortranInitialized_ = true; |
| 890 |
> |
topologyDone_ = true; |
| 891 |
|
} |
| 892 |
|
|
| 893 |
|
void SimInfo::addProperty(GenericData* genData) { |
