| 55 |
|
#include "primitives/Molecule.hpp" |
| 56 |
|
#include "primitives/StuntDouble.hpp" |
| 57 |
|
#include "UseTheForce/DarkSide/neighborLists_interface.h" |
| 58 |
+ |
#include "UseTheForce/doForces_interface.h" |
| 59 |
|
#include "utils/MemoryUtils.hpp" |
| 60 |
|
#include "utils/simError.h" |
| 61 |
|
#include "selection/SelectionManager.hpp" |
| 132 |
|
//equal to the total number of atoms minus number of atoms belong to |
| 133 |
|
//cutoff group defined in meta-data file plus the number of cutoff |
| 134 |
|
//groups defined in meta-data file |
| 135 |
+ |
std::cerr << "nGA = " << nGlobalAtoms_ << "\n"; |
| 136 |
+ |
std::cerr << "nCA = " << nCutoffAtoms << "\n"; |
| 137 |
+ |
std::cerr << "nG = " << nGroups << "\n"; |
| 138 |
+ |
|
| 139 |
|
nGlobalCutoffGroups_ = nGlobalAtoms_ - nCutoffAtoms + nGroups; |
| 140 |
+ |
|
| 141 |
+ |
std::cerr << "nGCG = " << nGlobalCutoffGroups_ << "\n"; |
| 142 |
|
|
| 143 |
|
//every free atom (atom does not belong to rigid bodies) is an |
| 144 |
|
//integrable object therefore the total number of integrable objects |
| 824 |
|
} |
| 825 |
|
} |
| 826 |
|
|
| 827 |
< |
//fill ident array of local atoms (it is actually ident of |
| 821 |
< |
//AtomType, it is so confusing !!!) |
| 822 |
< |
vector<int> identArray; |
| 827 |
> |
// Build the identArray_ |
| 828 |
|
|
| 829 |
< |
//to avoid memory reallocation, reserve enough space identArray |
| 830 |
< |
identArray.reserve(getNAtoms()); |
| 826 |
< |
|
| 829 |
> |
identArray_.clear(); |
| 830 |
> |
identArray_.reserve(getNAtoms()); |
| 831 |
|
for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) { |
| 832 |
|
for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) { |
| 833 |
< |
identArray.push_back(atom->getIdent()); |
| 833 |
> |
identArray_.push_back(atom->getIdent()); |
| 834 |
|
} |
| 835 |
|
} |
| 836 |
|
|
| 853 |
|
int* oneThreeList = oneThreeInteractions_.getPairList(); |
| 854 |
|
int* oneFourList = oneFourInteractions_.getPairList(); |
| 855 |
|
|
| 856 |
< |
setFortranSim( &fInfo_, &nGlobalAtoms_, &nAtoms_, &identArray[0], |
| 856 |
> |
setFortranSim( &fInfo_, &nGlobalAtoms_, &nAtoms_, &identArray_[0], |
| 857 |
|
&nExclude, excludeList, |
| 858 |
|
&nOneTwo, oneTwoList, |
| 859 |
|
&nOneThree, oneThreeList, |
| 928 |
|
sprintf(checkPointMsg, " mpiRefresh successful.\n"); |
| 929 |
|
errorCheckPoint(); |
| 930 |
|
#endif |
| 931 |
+ |
|
| 932 |
+ |
initFortranFF(&isError); |
| 933 |
+ |
if (isError) { |
| 934 |
+ |
sprintf(painCave.errMsg, |
| 935 |
+ |
"initFortranFF errror: fortran didn't like something we gave it.\n"); |
| 936 |
+ |
painCave.isFatal = 1; |
| 937 |
+ |
simError(); |
| 938 |
+ |
} |
| 939 |
|
fortranInitialized_ = true; |
| 940 |
|
} |
| 941 |
|
|
| 973 |
|
Molecule* mol; |
| 974 |
|
RigidBody* rb; |
| 975 |
|
Atom* atom; |
| 976 |
+ |
CutoffGroup* cg; |
| 977 |
|
SimInfo::MoleculeIterator mi; |
| 978 |
|
Molecule::RigidBodyIterator rbIter; |
| 979 |
< |
Molecule::AtomIterator atomIter;; |
| 979 |
> |
Molecule::AtomIterator atomIter; |
| 980 |
> |
Molecule::CutoffGroupIterator cgIter; |
| 981 |
|
|
| 982 |
|
for (mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) { |
| 983 |
|
|
| 987 |
|
|
| 988 |
|
for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) { |
| 989 |
|
rb->setSnapshotManager(sman_); |
| 990 |
+ |
} |
| 991 |
+ |
|
| 992 |
+ |
for (cg = mol->beginCutoffGroup(cgIter); cg != NULL; cg = mol->nextCutoffGroup(cgIter)) { |
| 993 |
+ |
cg->setSnapshotManager(sman_); |
| 994 |
|
} |
| 995 |
|
} |
| 996 |
|
|
