| 54 |
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#include "math/Vector3.hpp" |
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#include "primitives/Molecule.hpp" |
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#include "primitives/StuntDouble.hpp" |
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– |
#include "UseTheForce/DarkSide/neighborLists_interface.h" |
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– |
#include "UseTheForce/doForces_interface.h" |
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#include "utils/MemoryUtils.hpp" |
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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" |
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|
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– |
#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 |
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|
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using namespace std; |
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namespace OpenMD { |
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|
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nGlobalIntegrableObjects_(0), nGlobalRigidBodies_(0), |
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nAtoms_(0), nBonds_(0), nBends_(0), nTorsions_(0), nInversions_(0), |
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nRigidBodies_(0), nIntegrableObjects_(0), nCutoffGroups_(0), |
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< |
nConstraints_(0), sman_(NULL), fortranInitialized_(false), |
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> |
nConstraints_(0), sman_(NULL), topologyDone_(false), |
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calcBoxDipole_(false), useAtomicVirial_(true) { |
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|
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MoleculeStamp* molStamp; |
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temp = usesElectrostatic; |
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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_; |
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fInfo_.SIM_uses_DirectionalAtoms = usesDirectionalAtoms_; |
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fInfo_.SIM_uses_MetallicAtoms = usesMetallicAtoms_; |
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fInfo_.SIM_requires_SkipCorrection = usesElectrostaticAtoms_; |
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fInfo_.SIM_requires_SelfCorrection = usesElectrostaticAtoms_; |
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fInfo_.SIM_uses_AtomicVirial = usesAtomicVirial_; |
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} |
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|
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|
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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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> |
void SimInfo::prepareTopology() { |
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int nExclude, nOneTwo, nOneThree, nOneFour; |
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vector<int> fortranGlobalGroupMembership; |
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|
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isError = 0; |
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|
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//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); |
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} |
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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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|
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< |
//to avoid memory reallocation, reserve enough space for mfact |
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< |
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 |
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|
| 831 |
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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)) { |
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|
| 835 |
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totalMass = cg->getMass(); |
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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 |
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if (totalMass != 0) |
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< |
mfact.push_back(atom->getMass()/totalMass); |
| 839 |
> |
massFactors_.push_back(atom->getMass()/totalMass); |
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else |
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< |
mfact.push_back( 1.0 ); |
| 841 |
> |
massFactors_.push_back( 1.0 ); |
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} |
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} |
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} |
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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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//fill molMembershipArray |
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//molMembershipArray is filled by SimCreator |
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vector<int> molMembershipArray(nGlobalAtoms_); |
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for (int i = 0; i < nGlobalAtoms_; i++) { |
| 881 |
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molMembershipArray[i] = globalMolMembership_[i] + 1; |
| 882 |
– |
} |
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|
| 856 |
< |
//setup fortran simulation |
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> |
//scan topology |
| 857 |
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|
| 858 |
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nExclude = excludedInteractions_.getSize(); |
| 859 |
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nOneTwo = oneTwoInteractions_.getSize(); |
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int* oneThreeList = oneThreeInteractions_.getPairList(); |
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int* oneFourList = oneFourInteractions_.getPairList(); |
| 867 |
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|
| 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 |
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|
| 876 |
< |
if( isError ){ |
| 905 |
< |
|
| 906 |
< |
sprintf( painCave.errMsg, |
| 907 |
< |
"There was an error setting the simulation information in fortran.\n" ); |
| 908 |
< |
painCave.isFatal = 1; |
| 909 |
< |
painCave.severity = OPENMD_ERROR; |
| 910 |
< |
simError(); |
| 911 |
< |
} |
| 912 |
< |
|
| 913 |
< |
|
| 914 |
< |
sprintf( checkPointMsg, |
| 915 |
< |
"succesfully sent the simulation information to fortran.\n"); |
| 916 |
< |
|
| 917 |
< |
errorCheckPoint(); |
| 918 |
< |
|
| 919 |
< |
// Setup number of neighbors in neighbor list if present |
| 920 |
< |
if (simParams_->haveNeighborListNeighbors()) { |
| 921 |
< |
int nlistNeighbors = simParams_->getNeighborListNeighbors(); |
| 922 |
< |
setNeighbors(&nlistNeighbors); |
| 923 |
< |
} |
| 924 |
< |
|
| 925 |
< |
#ifdef IS_MPI |
| 926 |
< |
mpiSimData parallelData; |
| 927 |
< |
|
| 928 |
< |
//fill up mpiSimData struct |
| 929 |
< |
parallelData.nMolGlobal = getNGlobalMolecules(); |
| 930 |
< |
parallelData.nMolLocal = getNMolecules(); |
| 931 |
< |
parallelData.nAtomsGlobal = getNGlobalAtoms(); |
| 932 |
< |
parallelData.nAtomsLocal = getNAtoms(); |
| 933 |
< |
parallelData.nGroupsGlobal = getNGlobalCutoffGroups(); |
| 934 |
< |
parallelData.nGroupsLocal = getNCutoffGroups(); |
| 935 |
< |
parallelData.myNode = worldRank; |
| 936 |
< |
MPI_Comm_size(MPI_COMM_WORLD, &(parallelData.nProcessors)); |
| 937 |
< |
|
| 938 |
< |
//pass mpiSimData struct and index arrays to fortran |
| 939 |
< |
//setFsimParallel(¶llelData, &(parallelData.nAtomsLocal), |
| 940 |
< |
// &localToGlobalAtomIndex[0], &(parallelData.nGroupsLocal), |
| 941 |
< |
// &localToGlobalCutoffGroupIndex[0], &isError); |
| 942 |
< |
|
| 943 |
< |
if (isError) { |
| 944 |
< |
sprintf(painCave.errMsg, |
| 945 |
< |
"mpiRefresh errror: fortran didn't like something we gave it.\n"); |
| 946 |
< |
painCave.isFatal = 1; |
| 947 |
< |
simError(); |
| 948 |
< |
} |
| 949 |
< |
|
| 950 |
< |
sprintf(checkPointMsg, " mpiRefresh successful.\n"); |
| 951 |
< |
errorCheckPoint(); |
| 952 |
< |
#endif |
| 953 |
< |
|
| 954 |
< |
initFortranFF(&isError); |
| 955 |
< |
if (isError) { |
| 956 |
< |
sprintf(painCave.errMsg, |
| 957 |
< |
"initFortranFF errror: fortran didn't like something we gave it.\n"); |
| 958 |
< |
painCave.isFatal = 1; |
| 959 |
< |
simError(); |
| 960 |
< |
} |
| 961 |
< |
fortranInitialized_ = true; |
| 876 |
> |
topologyDone_ = true; |
| 877 |
|
} |
| 878 |
|
|
| 879 |
|
void SimInfo::addProperty(GenericData* genData) { |
