| 54 |
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#include "math/Vector3.hpp" |
| 55 |
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#include "primitives/Molecule.hpp" |
| 56 |
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#include "primitives/StuntDouble.hpp" |
| 57 |
– |
#include "UseTheForce/DarkSide/neighborLists_interface.h" |
| 58 |
– |
#include "UseTheForce/doForces_interface.h" |
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#include "utils/MemoryUtils.hpp" |
| 58 |
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#include "utils/simError.h" |
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#include "selection/SelectionManager.hpp" |
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#include "io/ForceFieldOptions.hpp" |
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#include "UseTheForce/ForceField.hpp" |
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#include "nonbonded/SwitchingFunction.hpp" |
| 65 |
– |
|
| 66 |
– |
#ifdef IS_MPI |
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– |
#include "UseTheForce/mpiComponentPlan.h" |
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– |
#include "UseTheForce/DarkSide/simParallel_interface.h" |
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#endif |
| 63 |
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|
| 64 |
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using namespace std; |
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namespace OpenMD { |
| 777 |
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fInfo_.SIM_requires_SelfCorrection = usesElectrostaticAtoms_; |
| 778 |
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fInfo_.SIM_uses_AtomicVirial = usesAtomicVirial_; |
| 779 |
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} |
| 780 |
+ |
|
| 781 |
|
|
| 782 |
+ |
vector<int> SimInfo::getGlobalAtomIndices() { |
| 783 |
+ |
SimInfo::MoleculeIterator mi; |
| 784 |
+ |
Molecule* mol; |
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+ |
Molecule::AtomIterator ai; |
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+ |
Atom* atom; |
| 787 |
+ |
|
| 788 |
+ |
vector<int> GlobalAtomIndices(getNAtoms(), 0); |
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+ |
|
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+ |
for (mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) { |
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+ |
|
| 792 |
+ |
for (atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) { |
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+ |
GlobalAtomIndices[atom->getLocalIndex()] = atom->getGlobalIndex(); |
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+ |
} |
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+ |
} |
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+ |
return GlobalAtomIndices; |
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+ |
} |
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+ |
|
| 799 |
+ |
|
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+ |
vector<int> SimInfo::getGlobalGroupIndices() { |
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+ |
SimInfo::MoleculeIterator mi; |
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+ |
Molecule* mol; |
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+ |
Molecule::CutoffGroupIterator ci; |
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+ |
CutoffGroup* cg; |
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+ |
|
| 806 |
+ |
vector<int> GlobalGroupIndices; |
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+ |
|
| 808 |
+ |
for (mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) { |
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+ |
|
| 810 |
+ |
//local index of cutoff group is trivial, it only depends on the |
| 811 |
+ |
//order of travesing |
| 812 |
+ |
for (cg = mol->beginCutoffGroup(ci); cg != NULL; |
| 813 |
+ |
cg = mol->nextCutoffGroup(ci)) { |
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+ |
GlobalGroupIndices.push_back(cg->getGlobalIndex()); |
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+ |
} |
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+ |
} |
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+ |
return GlobalGroupIndices; |
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+ |
} |
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+ |
|
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+ |
|
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|
void SimInfo::setupFortran() { |
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int isError; |
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int nExclude, nOneTwo, nOneThree, nOneFour; |
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} |
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} |
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|
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< |
//fill ident array of local atoms (it is actually ident of |
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//AtomType, it is so confusing !!!) |
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vector<int> identArray; |
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> |
// Build the identArray_ |
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|
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//to avoid memory reallocation, reserve enough space identArray |
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< |
identArray.reserve(getNAtoms()); |
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< |
|
| 862 |
> |
identArray_.clear(); |
| 863 |
> |
identArray_.reserve(getNAtoms()); |
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for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) { |
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for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) { |
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< |
identArray.push_back(atom->getIdent()); |
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> |
identArray_.push_back(atom->getIdent()); |
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} |
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} |
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|
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int* oneThreeList = oneThreeInteractions_.getPairList(); |
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int* oneFourList = oneFourInteractions_.getPairList(); |
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|
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setFortranSim( &fInfo_, &nGlobalAtoms_, &nAtoms_, &identArray[0], |
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&nExclude, excludeList, |
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< |
&nOneTwo, oneTwoList, |
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< |
&nOneThree, oneThreeList, |
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< |
&nOneFour, oneFourList, |
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< |
&molMembershipArray[0], &mfact[0], &nCutoffGroups_, |
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< |
&fortranGlobalGroupMembership[0], &isError); |
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> |
//setFortranSim( &fInfo_, &nGlobalAtoms_, &nAtoms_, &identArray_[0], |
| 890 |
> |
// &nExclude, excludeList, |
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> |
// &nOneTwo, oneTwoList, |
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> |
// &nOneThree, oneThreeList, |
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> |
// &nOneFour, oneFourList, |
| 894 |
> |
// &molMembershipArray[0], &mfact[0], &nCutoffGroups_, |
| 895 |
> |
// &fortranGlobalGroupMembership[0], &isError); |
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|
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< |
if( isError ){ |
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< |
|
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< |
sprintf( painCave.errMsg, |
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< |
"There was an error setting the simulation information in fortran.\n" ); |
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< |
painCave.isFatal = 1; |
| 902 |
< |
painCave.severity = OPENMD_ERROR; |
| 903 |
< |
simError(); |
| 904 |
< |
} |
| 897 |
> |
// if( isError ){ |
| 898 |
> |
// |
| 899 |
> |
// sprintf( painCave.errMsg, |
| 900 |
> |
// "There was an error setting the simulation information in fortran.\n" ); |
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> |
// painCave.isFatal = 1; |
| 902 |
> |
// painCave.severity = OPENMD_ERROR; |
| 903 |
> |
// simError(); |
| 904 |
> |
//} |
| 905 |
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|
| 906 |
|
|
| 907 |
< |
sprintf( checkPointMsg, |
| 908 |
< |
"succesfully sent the simulation information to fortran.\n"); |
| 907 |
> |
// sprintf( checkPointMsg, |
| 908 |
> |
// "succesfully sent the simulation information to fortran.\n"); |
| 909 |
|
|
| 910 |
< |
errorCheckPoint(); |
| 910 |
> |
// errorCheckPoint(); |
| 911 |
|
|
| 912 |
|
// Setup number of neighbors in neighbor list if present |
| 913 |
< |
if (simParams_->haveNeighborListNeighbors()) { |
| 914 |
< |
int nlistNeighbors = simParams_->getNeighborListNeighbors(); |
| 915 |
< |
setNeighbors(&nlistNeighbors); |
| 916 |
< |
} |
| 913 |
> |
//if (simParams_->haveNeighborListNeighbors()) { |
| 914 |
> |
// int nlistNeighbors = simParams_->getNeighborListNeighbors(); |
| 915 |
> |
// setNeighbors(&nlistNeighbors); |
| 916 |
> |
//} |
| 917 |
|
|
| 918 |
|
#ifdef IS_MPI |
| 919 |
< |
//SimInfo is responsible for creating localToGlobalAtomIndex and |
| 890 |
< |
//localToGlobalGroupIndex |
| 891 |
< |
vector<int> localToGlobalAtomIndex(getNAtoms(), 0); |
| 892 |
< |
vector<int> localToGlobalCutoffGroupIndex; |
| 893 |
< |
mpiSimData parallelData; |
| 919 |
> |
// mpiSimData parallelData; |
| 920 |
|
|
| 895 |
– |
for (mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) { |
| 896 |
– |
|
| 897 |
– |
//local index(index in DataStorge) of atom is important |
| 898 |
– |
for (atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) { |
| 899 |
– |
localToGlobalAtomIndex[atom->getLocalIndex()] = atom->getGlobalIndex() + 1; |
| 900 |
– |
} |
| 901 |
– |
|
| 902 |
– |
//local index of cutoff group is trivial, it only depends on the order of travesing |
| 903 |
– |
for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) { |
| 904 |
– |
localToGlobalCutoffGroupIndex.push_back(cg->getGlobalIndex() + 1); |
| 905 |
– |
} |
| 906 |
– |
|
| 907 |
– |
} |
| 908 |
– |
|
| 921 |
|
//fill up mpiSimData struct |
| 922 |
< |
parallelData.nMolGlobal = getNGlobalMolecules(); |
| 923 |
< |
parallelData.nMolLocal = getNMolecules(); |
| 924 |
< |
parallelData.nAtomsGlobal = getNGlobalAtoms(); |
| 925 |
< |
parallelData.nAtomsLocal = getNAtoms(); |
| 926 |
< |
parallelData.nGroupsGlobal = getNGlobalCutoffGroups(); |
| 927 |
< |
parallelData.nGroupsLocal = getNCutoffGroups(); |
| 928 |
< |
parallelData.myNode = worldRank; |
| 929 |
< |
MPI_Comm_size(MPI_COMM_WORLD, &(parallelData.nProcessors)); |
| 922 |
> |
// parallelData.nMolGlobal = getNGlobalMolecules(); |
| 923 |
> |
// parallelData.nMolLocal = getNMolecules(); |
| 924 |
> |
// parallelData.nAtomsGlobal = getNGlobalAtoms(); |
| 925 |
> |
// parallelData.nAtomsLocal = getNAtoms(); |
| 926 |
> |
// parallelData.nGroupsGlobal = getNGlobalCutoffGroups(); |
| 927 |
> |
// parallelData.nGroupsLocal = getNCutoffGroups(); |
| 928 |
> |
// parallelData.myNode = worldRank; |
| 929 |
> |
// MPI_Comm_size(MPI_COMM_WORLD, &(parallelData.nProcessors)); |
| 930 |
|
|
| 931 |
|
//pass mpiSimData struct and index arrays to fortran |
| 932 |
< |
setFsimParallel(¶llelData, &(parallelData.nAtomsLocal), |
| 933 |
< |
&localToGlobalAtomIndex[0], &(parallelData.nGroupsLocal), |
| 934 |
< |
&localToGlobalCutoffGroupIndex[0], &isError); |
| 932 |
> |
//setFsimParallel(¶llelData, &(parallelData.nAtomsLocal), |
| 933 |
> |
// &localToGlobalAtomIndex[0], &(parallelData.nGroupsLocal), |
| 934 |
> |
// &localToGlobalCutoffGroupIndex[0], &isError); |
| 935 |
|
|
| 936 |
< |
if (isError) { |
| 937 |
< |
sprintf(painCave.errMsg, |
| 938 |
< |
"mpiRefresh errror: fortran didn't like something we gave it.\n"); |
| 939 |
< |
painCave.isFatal = 1; |
| 940 |
< |
simError(); |
| 941 |
< |
} |
| 936 |
> |
// if (isError) { |
| 937 |
> |
// sprintf(painCave.errMsg, |
| 938 |
> |
// "mpiRefresh errror: fortran didn't like something we gave it.\n"); |
| 939 |
> |
// painCave.isFatal = 1; |
| 940 |
> |
// simError(); |
| 941 |
> |
// } |
| 942 |
|
|
| 943 |
< |
sprintf(checkPointMsg, " mpiRefresh successful.\n"); |
| 944 |
< |
errorCheckPoint(); |
| 943 |
> |
// sprintf(checkPointMsg, " mpiRefresh successful.\n"); |
| 944 |
> |
// errorCheckPoint(); |
| 945 |
|
#endif |
| 946 |
|
|
| 947 |
< |
initFortranFF(&isError); |
| 948 |
< |
if (isError) { |
| 949 |
< |
sprintf(painCave.errMsg, |
| 950 |
< |
"initFortranFF errror: fortran didn't like something we gave it.\n"); |
| 951 |
< |
painCave.isFatal = 1; |
| 952 |
< |
simError(); |
| 953 |
< |
} |
| 954 |
< |
fortranInitialized_ = true; |
| 947 |
> |
// initFortranFF(&isError); |
| 948 |
> |
// if (isError) { |
| 949 |
> |
// sprintf(painCave.errMsg, |
| 950 |
> |
// "initFortranFF errror: fortran didn't like something we gave it.\n"); |
| 951 |
> |
// painCave.isFatal = 1; |
| 952 |
> |
// simError(); |
| 953 |
> |
// } |
| 954 |
> |
// fortranInitialized_ = true; |
| 955 |
|
} |
| 956 |
|
|
| 957 |
|
void SimInfo::addProperty(GenericData* genData) { |
