| 54 |
|
#include "math/Vector3.hpp" |
| 55 |
|
#include "primitives/Molecule.hpp" |
| 56 |
|
#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 "UseTheForce/ForceField.hpp" |
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#include "nonbonded/SwitchingFunction.hpp" |
| 63 |
|
|
| 66 |
– |
#ifdef IS_MPI |
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– |
#include "UseTheForce/mpiComponentPlan.h" |
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– |
#include "UseTheForce/DarkSide/simParallel_interface.h" |
| 69 |
– |
#endif |
| 70 |
– |
|
| 64 |
|
using namespace std; |
| 65 |
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namespace OpenMD { |
| 66 |
|
|
| 71 |
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nGlobalIntegrableObjects_(0), nGlobalRigidBodies_(0), |
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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 |
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calcBoxDipole_(false), useAtomicVirial_(true) { |
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|
| 77 |
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MoleculeStamp* molStamp; |
| 770 |
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temp = usesElectrostatic; |
| 771 |
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MPI_Allreduce(&temp, &usesElectrostaticAtoms_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD); |
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#endif |
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– |
fInfo_.SIM_uses_PBC = usesPeriodicBoundaries_; |
| 781 |
– |
fInfo_.SIM_uses_DirectionalAtoms = usesDirectionalAtoms_; |
| 782 |
– |
fInfo_.SIM_uses_MetallicAtoms = usesMetallicAtoms_; |
| 783 |
– |
fInfo_.SIM_requires_SkipCorrection = usesElectrostaticAtoms_; |
| 784 |
– |
fInfo_.SIM_requires_SelfCorrection = usesElectrostaticAtoms_; |
| 785 |
– |
fInfo_.SIM_uses_AtomicVirial = usesAtomicVirial_; |
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} |
| 774 |
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|
| 788 |
– |
void SimInfo::setupFortran() { |
| 789 |
– |
int isError; |
| 790 |
– |
int nExclude, nOneTwo, nOneThree, nOneFour; |
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– |
vector<int> fortranGlobalGroupMembership; |
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– |
|
| 793 |
– |
isError = 0; |
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|
|
| 776 |
< |
//globalGroupMembership_ is filled by SimCreator |
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< |
for (int i = 0; i < nGlobalAtoms_; i++) { |
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< |
fortranGlobalGroupMembership.push_back(globalGroupMembership_[i] + 1); |
| 776 |
> |
vector<int> SimInfo::getGlobalAtomIndices() { |
| 777 |
> |
SimInfo::MoleculeIterator mi; |
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> |
Molecule* mol; |
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> |
Molecule::AtomIterator ai; |
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> |
Atom* atom; |
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> |
|
| 782 |
> |
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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> |
|
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> |
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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> |
} |
| 792 |
> |
|
| 793 |
> |
|
| 794 |
> |
vector<int> SimInfo::getGlobalGroupIndices() { |
| 795 |
> |
SimInfo::MoleculeIterator mi; |
| 796 |
> |
Molecule* mol; |
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> |
Molecule::CutoffGroupIterator ci; |
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> |
CutoffGroup* cg; |
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> |
|
| 800 |
> |
vector<int> GlobalGroupIndices; |
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> |
|
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> |
for (mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) { |
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> |
|
| 804 |
> |
//local index of cutoff group is trivial, it only depends on the |
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> |
//order of travesing |
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> |
for (cg = mol->beginCutoffGroup(ci); cg != NULL; |
| 807 |
> |
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::prepareTopology() { |
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+ |
int nExclude, nOneTwo, nOneThree, nOneFour; |
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+ |
|
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|
//calculate mass ratio of cutoff group |
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– |
vector<RealType> mfact; |
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SimInfo::MoleculeIterator mi; |
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|
Molecule* mol; |
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Molecule::CutoffGroupIterator ci; |
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Atom* atom; |
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|
RealType totalMass; |
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|
| 827 |
< |
//to avoid memory reallocation, reserve enough space for mfact |
| 828 |
< |
mfact.reserve(getNCutoffGroups()); |
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> |
//to avoid memory reallocation, reserve enough space for massFactors_ |
| 828 |
> |
massFactors_.clear(); |
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> |
massFactors_.reserve(getNCutoffGroups()); |
| 830 |
|
|
| 831 |
|
for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) { |
| 832 |
< |
for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) { |
| 832 |
> |
for (cg = mol->beginCutoffGroup(ci); cg != NULL; |
| 833 |
> |
cg = mol->nextCutoffGroup(ci)) { |
| 834 |
|
|
| 835 |
|
totalMass = cg->getMass(); |
| 836 |
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for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) { |
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|
// Check for massless groups - set mfact to 1 if true |
| 838 |
|
if (totalMass != 0) |
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< |
mfact.push_back(atom->getMass()/totalMass); |
| 839 |
> |
massFactors_.push_back(atom->getMass()/totalMass); |
| 840 |
|
else |
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< |
mfact.push_back( 1.0 ); |
| 841 |
> |
massFactors_.push_back( 1.0 ); |
| 842 |
|
} |
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|
} |
| 844 |
|
} |
| 845 |
|
|
| 846 |
< |
//fill ident array of local atoms (it is actually ident of |
| 828 |
< |
//AtomType, it is so confusing !!!) |
| 829 |
< |
vector<int> identArray; |
| 846 |
> |
// Build the identArray_ |
| 847 |
|
|
| 848 |
< |
//to avoid memory reallocation, reserve enough space identArray |
| 849 |
< |
identArray.reserve(getNAtoms()); |
| 833 |
< |
|
| 848 |
> |
identArray_.clear(); |
| 849 |
> |
identArray_.reserve(getNAtoms()); |
| 850 |
|
for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) { |
| 851 |
|
for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) { |
| 852 |
< |
identArray.push_back(atom->getIdent()); |
| 852 |
> |
identArray_.push_back(atom->getIdent()); |
| 853 |
|
} |
| 854 |
|
} |
| 839 |
– |
|
| 840 |
– |
//fill molMembershipArray |
| 841 |
– |
//molMembershipArray is filled by SimCreator |
| 842 |
– |
vector<int> molMembershipArray(nGlobalAtoms_); |
| 843 |
– |
for (int i = 0; i < nGlobalAtoms_; i++) { |
| 844 |
– |
molMembershipArray[i] = globalMolMembership_[i] + 1; |
| 845 |
– |
} |
| 855 |
|
|
| 856 |
< |
//setup fortran simulation |
| 856 |
> |
//scan topology |
| 857 |
|
|
| 858 |
|
nExclude = excludedInteractions_.getSize(); |
| 859 |
|
nOneTwo = oneTwoInteractions_.getSize(); |
| 865 |
|
int* oneThreeList = oneThreeInteractions_.getPairList(); |
| 866 |
|
int* oneFourList = oneFourInteractions_.getPairList(); |
| 867 |
|
|
| 868 |
< |
setFortranSim( &fInfo_, &nGlobalAtoms_, &nAtoms_, &identArray[0], |
| 869 |
< |
&nExclude, excludeList, |
| 870 |
< |
&nOneTwo, oneTwoList, |
| 871 |
< |
&nOneThree, oneThreeList, |
| 872 |
< |
&nOneFour, oneFourList, |
| 873 |
< |
&molMembershipArray[0], &mfact[0], &nCutoffGroups_, |
| 874 |
< |
&fortranGlobalGroupMembership[0], &isError); |
| 868 |
> |
//setFortranSim( &fInfo_, &nGlobalAtoms_, &nAtoms_, &identArray_[0], |
| 869 |
> |
// &nExclude, excludeList, |
| 870 |
> |
// &nOneTwo, oneTwoList, |
| 871 |
> |
// &nOneThree, oneThreeList, |
| 872 |
> |
// &nOneFour, oneFourList, |
| 873 |
> |
// &molMembershipArray[0], &mfact[0], &nCutoffGroups_, |
| 874 |
> |
// &fortranGlobalGroupMembership[0], &isError); |
| 875 |
|
|
| 876 |
< |
if( isError ){ |
| 868 |
< |
|
| 869 |
< |
sprintf( painCave.errMsg, |
| 870 |
< |
"There was an error setting the simulation information in fortran.\n" ); |
| 871 |
< |
painCave.isFatal = 1; |
| 872 |
< |
painCave.severity = OPENMD_ERROR; |
| 873 |
< |
simError(); |
| 874 |
< |
} |
| 875 |
< |
|
| 876 |
< |
|
| 877 |
< |
sprintf( checkPointMsg, |
| 878 |
< |
"succesfully sent the simulation information to fortran.\n"); |
| 879 |
< |
|
| 880 |
< |
errorCheckPoint(); |
| 881 |
< |
|
| 882 |
< |
// Setup number of neighbors in neighbor list if present |
| 883 |
< |
if (simParams_->haveNeighborListNeighbors()) { |
| 884 |
< |
int nlistNeighbors = simParams_->getNeighborListNeighbors(); |
| 885 |
< |
setNeighbors(&nlistNeighbors); |
| 886 |
< |
} |
| 887 |
< |
|
| 888 |
< |
#ifdef IS_MPI |
| 889 |
< |
//SimInfo is responsible for creating localToGlobalAtomIndex and |
| 890 |
< |
//localToGlobalGroupIndex |
| 891 |
< |
vector<int> localToGlobalAtomIndex(getNAtoms(), 0); |
| 892 |
< |
vector<int> localToGlobalCutoffGroupIndex; |
| 893 |
< |
mpiSimData parallelData; |
| 894 |
< |
|
| 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 |
< |
|
| 909 |
< |
//fill up mpiSimData struct |
| 910 |
< |
parallelData.nMolGlobal = getNGlobalMolecules(); |
| 911 |
< |
parallelData.nMolLocal = getNMolecules(); |
| 912 |
< |
parallelData.nAtomsGlobal = getNGlobalAtoms(); |
| 913 |
< |
parallelData.nAtomsLocal = getNAtoms(); |
| 914 |
< |
parallelData.nGroupsGlobal = getNGlobalCutoffGroups(); |
| 915 |
< |
parallelData.nGroupsLocal = getNCutoffGroups(); |
| 916 |
< |
parallelData.myNode = worldRank; |
| 917 |
< |
MPI_Comm_size(MPI_COMM_WORLD, &(parallelData.nProcessors)); |
| 918 |
< |
|
| 919 |
< |
//pass mpiSimData struct and index arrays to fortran |
| 920 |
< |
setFsimParallel(¶llelData, &(parallelData.nAtomsLocal), |
| 921 |
< |
&localToGlobalAtomIndex[0], &(parallelData.nGroupsLocal), |
| 922 |
< |
&localToGlobalCutoffGroupIndex[0], &isError); |
| 923 |
< |
|
| 924 |
< |
if (isError) { |
| 925 |
< |
sprintf(painCave.errMsg, |
| 926 |
< |
"mpiRefresh errror: fortran didn't like something we gave it.\n"); |
| 927 |
< |
painCave.isFatal = 1; |
| 928 |
< |
simError(); |
| 929 |
< |
} |
| 930 |
< |
|
| 931 |
< |
sprintf(checkPointMsg, " mpiRefresh successful.\n"); |
| 932 |
< |
errorCheckPoint(); |
| 933 |
< |
#endif |
| 934 |
< |
|
| 935 |
< |
initFortranFF(&isError); |
| 936 |
< |
if (isError) { |
| 937 |
< |
sprintf(painCave.errMsg, |
| 938 |
< |
"initFortranFF errror: fortran didn't like something we gave it.\n"); |
| 939 |
< |
painCave.isFatal = 1; |
| 940 |
< |
simError(); |
| 941 |
< |
} |
| 942 |
< |
fortranInitialized_ = true; |
| 876 |
> |
topologyDone_ = true; |
| 877 |
|
} |
| 878 |
|
|
| 879 |
|
void SimInfo::addProperty(GenericData* genData) { |
