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#include "io/ForceFieldOptions.hpp" |
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#include "UseTheForce/ForceField.hpp" |
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#include "nonbonded/SwitchingFunction.hpp" |
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#ifdef IS_MPI |
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#include <mpi.h> |
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#endif |
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using namespace std; |
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namespace OpenMD { |
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Atom* atom; |
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set<AtomType*> atomTypes; |
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|
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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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for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) { |
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for(atom = mol->beginAtom(ai); atom != NULL; |
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atom = mol->nextAtom(ai)) { |
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atomTypes.insert(atom->getAtomType()); |
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} |
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} |
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|
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#ifdef IS_MPI |
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|
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// loop over the found atom types on this processor, and add their |
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// numerical idents to a vector: |
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|
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vector<int> foundTypes; |
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set<AtomType*>::iterator i; |
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for (i = atomTypes.begin(); i != atomTypes.end(); ++i) |
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|
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// count_local holds the number of found types on this processor |
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int count_local = foundTypes.size(); |
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|
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// count holds the total number of found types on all processors |
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// (some will be redundant with the ones found locally): |
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int count; |
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MPI::COMM_WORLD.Allreduce(&count_local, &count, 1, MPI::INT, MPI::SUM); |
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|
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// create a vector to hold the globally found types, and resize it: |
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vector<int> ftGlobal; |
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ftGlobal.resize(count); |
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vector<int> counts; |
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|
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int nproc = MPI::COMM_WORLD.Get_size(); |
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counts.resize(nproc); |
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vector<int> disps; |
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disps.resize(nproc); |
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|
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// now spray out the foundTypes to all the other processors: |
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// we need arrays to hold the counts and displacement vectors for |
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// all processors |
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vector<int> counts(nproc, 0); |
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vector<int> disps(nproc, 0); |
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|
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// fill the counts array |
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MPI::COMM_WORLD.Allgather(&count_local, 1, MPI::INT, &counts[0], |
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1, MPI::INT); |
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|
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// use the processor counts to compute the displacement array |
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disps[0] = 0; |
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int totalCount = counts[0]; |
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for (int iproc = 1; iproc < nproc; iproc++) { |
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disps[iproc] = disps[iproc-1] + counts[iproc-1]; |
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totalCount += counts[iproc]; |
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} |
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|
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// we need a (possibly redundant) set of all found types: |
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vector<int> ftGlobal(totalCount); |
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|
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// now spray out the foundTypes to all the other processors: |
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MPI::COMM_WORLD.Allgatherv(&foundTypes[0], count_local, MPI::INT, |
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&ftGlobal[0], &counts[0], &disps[0], MPI::INT); |
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&ftGlobal[0], &counts[0], &disps[0], |
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MPI::INT); |
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|
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vector<int>::iterator j; |
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|
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// foundIdents is a stl set, so inserting an already found ident |
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// will have no effect. |
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set<int> foundIdents; |
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vector<int>::iterator j; |
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|
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for (j = ftGlobal.begin(); j != ftGlobal.end(); ++j) |
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foundIdents.insert((*j)); |
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|
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// now iterate over the foundIdents and get the actual atom types |
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// that correspond to these: |
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set<int>::iterator it; |
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for (it = foundIdents.begin(); it != foundIdents.end(); ++it) |
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for (it = foundIdents.begin(); it != foundIdents.end(); ++it) |
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atomTypes.insert( forceField_->getAtomType((*it)) ); |
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#endif |
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return atomTypes; |
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} |
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if ( simParams_->getAccumulateBoxDipole() ) { |
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calcBoxDipole_ = true; |
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} |
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|
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set<AtomType*>::iterator i; |
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set<AtomType*> atomTypes; |
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atomTypes = getSimulatedAtomTypes(); |
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usesMetallic |= (*i)->isMetal(); |
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usesDirectional |= (*i)->isDirectional(); |
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} |
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|
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#ifdef IS_MPI |
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int temp; |
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temp = usesDirectional; |
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MPI_Allreduce(&temp, &usesDirectionalAtoms_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD); |
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> |
|
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temp = usesMetallic; |
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MPI_Allreduce(&temp, &usesMetallicAtoms_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD); |
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> |
|
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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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#else |
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|
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usesDirectionalAtoms_ = usesDirectional; |
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usesMetallicAtoms_ = usesMetallic; |
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usesElectrostaticAtoms_ = usesElectrostatic; |
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|
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#endif |
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|
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requiresPrepair_ = usesMetallicAtoms_ ? true : false; |
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requiresSkipCorrection_ = usesElectrostaticAtoms_ ? true : false; |
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requiresSelfCorrection_ = usesElectrostaticAtoms_ ? true : false; |
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} |
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|
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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 massFactors_ |
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> |
/** |
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> |
* The mass factor is the relative mass of an atom to the total |
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> |
* mass of the cutoff group it belongs to. By default, all atoms |
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> |
* are their own cutoff groups, and therefore have mass factors of |
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> |
* 1. We need some special handling for massless atoms, which |
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* will be treated as carrying the entire mass of the cutoff |
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* group. |
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*/ |
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massFactors_.clear(); |
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massFactors_.reserve(getNCutoffGroups()); |
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> |
massFactors_.resize(getNAtoms(), 1.0); |
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|
| 875 |
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for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) { |
| 876 |
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for (cg = mol->beginCutoffGroup(ci); cg != NULL; |
| 879 |
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totalMass = cg->getMass(); |
| 880 |
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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 |
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< |
if (totalMass != 0) |
| 883 |
< |
massFactors_.push_back(atom->getMass()/totalMass); |
| 882 |
> |
if (totalMass != 0) |
| 883 |
> |
massFactors_[atom->getLocalIndex()] = atom->getMass()/totalMass; |
| 884 |
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else |
| 885 |
< |
massFactors_.push_back( 1.0 ); |
| 885 |
> |
massFactors_[atom->getLocalIndex()] = 1.0; |
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} |
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} |
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} |
| 909 |
|
int* oneThreeList = oneThreeInteractions_.getPairList(); |
| 910 |
|
int* oneFourList = oneFourInteractions_.getPairList(); |
| 911 |
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|
| 882 |
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//setFortranSim( &fInfo_, &nGlobalAtoms_, &nAtoms_, &identArray_[0], |
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// &nExclude, excludeList, |
| 884 |
– |
// &nOneTwo, oneTwoList, |
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// &nOneThree, oneThreeList, |
| 886 |
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// &nOneFour, oneFourList, |
| 887 |
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// &molMembershipArray[0], &mfact[0], &nCutoffGroups_, |
| 888 |
– |
// &fortranGlobalGroupMembership[0], &isError); |
| 889 |
– |
|
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topologyDone_ = true; |
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} |
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