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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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> |
|
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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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> |
|
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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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// 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], |
| 745 |
> |
MPI::INT); |
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|
| 747 |
+ |
vector<int>::iterator j; |
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+ |
|
| 749 |
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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; |
| 752 |
> |
|
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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; |
| 759 |
< |
for (it = foundIdents.begin(); it != foundIdents.end(); ++it) |
| 759 |
> |
for (it = foundIdents.begin(); it != foundIdents.end(); ++it) |
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atomTypes.insert( forceField_->getAtomType((*it)) ); |
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|
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#endif |
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< |
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| 763 |
> |
|
| 764 |
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return atomTypes; |
| 765 |
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} |
| 766 |
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|
| 872 |
|
massFactors_.clear(); |
| 873 |
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massFactors_.resize(getNAtoms(), 1.0); |
| 874 |
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|
| 862 |
– |
cerr << "mfs in si = " << massFactors_.size() << "\n"; |
| 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; |
| 877 |
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cg = mol->nextCutoffGroup(ci)) { |
