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#define _LARGEFILE_SOURCE64 |
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#define _FILE_OFFSET_BITS 64 |
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#include <string.h> |
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if(worldRank == 0 ){ |
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#endif // is_mpi |
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dumpFile.open(entry_plug->sampleName, ios::out | ios::trunc ); |
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if( !dumpFile ){ |
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indexArray.clear(); |
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for(int i = 0; i < mpiSim->getMyNlocal();i++) |
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for(int i = 0; i < mpiSim->getMyNlocal();i++) |
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indexArray.push_back(make_pair(i, atoms[i]->getGlobalIndex())); |
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sort(indexArray.begin(), indexArray.end(), indexSortingCriterion); |
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} |
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#endif |
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void DumpWriter::writeDump(double currentTime){ |
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#ifdef IS_MPI |
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if(worldRank == 0 ){ |
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#endif |
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finalOut.open( entry_plug->finalName, ios::out | ios::trunc ); |
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if( !finalOut ){ |
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sprintf( painCave.errMsg, |
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painCave.isFatal = 1; |
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simError(); |
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} |
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#ifdef IS_MPI |
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} |
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#endif // is_mpi |
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#ifdef IS_MPI |
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if(worldRank == 0 ){ |
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#endif // is_mpi |
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finalOut.open( entry_plug->finalName, ios::out | ios::trunc ); |
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simError(); |
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} |
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#ifdef IS_MPI |
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} |
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#endif // is_mpi |
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int nAtoms = entry_plug->n_atoms; |
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#endif //is_mpi |
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double q[4]; |
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double q[4], ji[3]; |
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DirectionalAtom* dAtom; |
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Atom** atoms = entry_plug->atoms; |
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double pos[3], vel[3]; |
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dAtom = (DirectionalAtom *)atoms[i]; |
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dAtom->getQ( q ); |
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dAtom->getJ( ji ); |
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sprintf( tempBuffer, |
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"%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n", |
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q[1], |
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q[2], |
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q[3], |
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dAtom->getJx(), |
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dAtom->getJy(), |
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dAtom->getJz()); |
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ji[0], |
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ji[1], |
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ji[2]); |
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strcat( writeLine, tempBuffer ); |
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} |
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else |
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} else { |
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haveError = 0; |
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which_atom = i; |
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which_atom = i; |
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local_index = indexArray[currentIndex].first; |
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if (which_atom == indexArray[currentIndex].second) { |
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local_index = indexArray[currentIndex].first; |
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atomTypeString = atoms[local_index]->getType(); |
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atoms[local_index]->getPos(pos); |
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atoms[local_index]->getVel(vel); |
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if (which_atom == indexArray[currentIndex].second) { |
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atomTypeString = atoms[local_index]->getType(); |
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atoms[local_index]->getPos(pos); |
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atoms[local_index]->getVel(vel); |
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atomData6[0] = pos[0]; |
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atomData6[1] = pos[1]; |
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atomData6[2] = pos[2]; |
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dAtom = (DirectionalAtom *)atoms[local_index]; |
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dAtom->getQ( q ); |
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dAtom->getJ( ji ); |
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for (int j = 0; j < 6 ; j++) |
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atomData13[j] = atomData6[j]; |
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atomData13[8] = q[2]; |
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atomData13[9] = q[3]; |
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atomData13[10] = dAtom->getJx(); |
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atomData13[11] = dAtom->getJy(); |
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atomData13[12] = dAtom->getJz(); |
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atomData13[10] = ji[0]; |
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atomData13[11] = ji[1]; |
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atomData13[12] = ji[2]; |
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} |
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} else { |
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sprintf(painCave.errMsg, |
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"Atom %d not found on processor %d\n", |
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i, worldRank ); |
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haveError= 1; |
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simError(); |
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} |
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sprintf(painCave.errMsg, |
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"Atom %d not found on processor %d, currentIndex = %d, local_index = %d\n", |
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which_atom, worldRank, currentIndex, local_index ); |
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haveError= 1; |
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simError(); |
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} |
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if(haveError) DieDieDie(); |
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currentIndex ++; |
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currentIndex++; |
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} |
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// If we've survived to here, format the line: |
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if (!isDirectional) { |
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sprintf( writeLine, |
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"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", |
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atomTypeString, |
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atomData6[0], |
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atomData6[1], |
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atomData6[2], |
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atomData6[3], |
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atomData6[4], |
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atomData6[5]); |
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strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" ); |
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"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", |
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atomTypeString, |
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atomData6[0], |
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atomData6[1], |
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atomData6[2], |
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atomData6[3], |
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atomData6[4], |
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atomData6[5]); |
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strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" ); |
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|
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} else { |
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sprintf( writeLine, |
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"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n", |
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atomTypeString, |
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atomData13[0], |
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atomData13[1], |
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atomData13[2], |
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atomData13[3], |
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atomData13[4], |
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atomData13[5], |
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atomData13[6], |
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atomData13[7], |
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atomData13[8], |
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atomData13[9], |
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atomData13[10], |
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atomData13[11], |
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atomData13[12]); |
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sprintf( writeLine, |
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"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n", |
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> |
atomTypeString, |
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atomData13[0], |
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atomData13[1], |
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atomData13[2], |
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atomData13[3], |
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atomData13[4], |
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atomData13[5], |
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atomData13[6], |
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atomData13[7], |
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atomData13[8], |
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atomData13[9], |
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atomData13[10], |
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atomData13[11], |
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atomData13[12]); |
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} |
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sprintf( checkPointMsg, |
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"Sucessfully took a dump.\n"); |
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MPIcheckPoint(); |
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delete[] potatoes; |
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} else { |
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// worldRank != 0, so I'm a remote node. |
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if (AtomToProcMap[i] == worldRank) { |
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if (myPotato + 3 >= MAXTAG) { |
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// The potato was going to exceed the maximum value, |
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// so wrap this processor potato back to 0 (and block until |
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// node 0 says we can go: |
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> |
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MPI_Recv(&myPotato, 1, MPI_INT, 0, 0, MPI_COMM_WORLD, &istatus); |
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} |
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which_atom = i; |
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local_index = indexArray[currentIndex].first; |
523 |
> |
|
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> |
local_index = indexArray[currentIndex].first; |
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526 |
< |
if (which_atom == indexArray[currentIndex].second) { |
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> |
if (which_atom == indexArray[currentIndex].second) { |
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atomTypeString = atoms[local_index]->getType(); |
529 |
< |
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530 |
< |
atoms[local_index]->getPos(pos); |
531 |
< |
atoms[local_index]->getVel(vel); |
532 |
< |
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529 |
> |
|
530 |
> |
atoms[local_index]->getPos(pos); |
531 |
> |
atoms[local_index]->getVel(vel); |
532 |
> |
|
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atomData6[0] = pos[0]; |
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atomData6[1] = pos[1]; |
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atomData6[2] = pos[2]; |
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dAtom = (DirectionalAtom *)atoms[local_index]; |
548 |
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dAtom->getQ( q ); |
549 |
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dAtom->getJ( ji ); |
550 |
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for (int j = 0; j < 6 ; j++) |
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atomData13[j] = atomData6[j]; |
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atomData13[8] = q[2]; |
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atomData13[9] = q[3]; |
558 |
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559 |
< |
atomData13[10] = dAtom->getJx(); |
560 |
< |
atomData13[11] = dAtom->getJy(); |
561 |
< |
atomData13[12] = dAtom->getJz(); |
559 |
> |
atomData13[10] = ji[0]; |
560 |
> |
atomData13[11] = ji[1]; |
561 |
> |
atomData13[12] = ji[2]; |
562 |
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} |
563 |
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564 |
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} else { |
565 |
< |
sprintf(painCave.errMsg, |
566 |
< |
"Atom %d not found on processor %d\n", |
567 |
< |
i, worldRank ); |
568 |
< |
haveError= 1; |
569 |
< |
simError(); |
570 |
< |
} |
571 |
< |
|
565 |
> |
sprintf(painCave.errMsg, |
566 |
> |
"Atom %d not found on processor %d, currentIndex = %d, local_index = %d\n", |
567 |
> |
which_atom, worldRank, currentIndex, local_index ); |
568 |
> |
haveError= 1; |
569 |
> |
simError(); |
570 |
> |
} |
571 |
> |
|
572 |
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strncpy(MPIatomTypeString, atomTypeString, MINIBUFFERSIZE); |
573 |
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574 |
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// null terminate the string before sending (just in case): |