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mmeineke |
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#include <cstring> |
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#include <iostream> |
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#include <fstream> |
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#ifdef IS_MPI |
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#include <mpi.h> |
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gezelter |
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#include <mpi++.h> |
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mmeineke |
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#include "mpiSimulation.hpp" |
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chuckv |
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#define TAKE_THIS_TAG_CHAR 1 |
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#define TAKE_THIS_TAG_INT 2 |
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mmeineke |
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#endif //is_mpi |
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#include "ReadWrite.hpp" |
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#include "simError.h" |
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DumpWriter::DumpWriter( SimInfo* the_entry_plug ){ |
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entry_plug = the_entry_plug; |
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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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strcpy( outName, entry_plug->sampleName ); |
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outFile.open(outName, ios::out | ios::trunc ); |
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if( !outFile ){ |
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sprintf( painCave.errMsg, |
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"Could not open \"%s\" for dump output.\n", |
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outName); |
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painCave.isFatal = 1; |
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simError(); |
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} |
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//outFile.setf( ios::scientific ); |
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#ifdef IS_MPI |
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} |
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sprintf( checkPointMsg, |
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"Sucessfully opened output file for dumping.\n"); |
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MPIcheckPoint(); |
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#endif // is_mpi |
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} |
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DumpWriter::~DumpWriter( ){ |
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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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outFile.close(); |
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#ifdef IS_MPI |
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} |
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#endif // is_mpi |
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} |
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void DumpWriter::writeDump( double currentTime ){ |
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const int BUFFERSIZE = 2000; |
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char tempBuffer[BUFFERSIZE]; |
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char writeLine[BUFFERSIZE]; |
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gezelter |
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int i, j, which_node, done, game_over, which_atom, local_index; |
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mmeineke |
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double q[4]; |
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DirectionalAtom* dAtom; |
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int nAtoms = entry_plug->n_atoms; |
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Atom** atoms = entry_plug->atoms; |
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#ifndef IS_MPI |
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outFile << nAtoms << "\n"; |
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outFile << currentTime << "\t" |
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<< entry_plug->box_x << "\t" |
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<< entry_plug->box_y << "\t" |
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<< entry_plug->box_z << "\n"; |
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for( i=0; i<nAtoms; i++ ){ |
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sprintf( tempBuffer, |
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"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", |
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atoms[i]->getType(), |
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atoms[i]->getX(), |
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atoms[i]->getY(), |
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atoms[i]->getZ(), |
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atoms[i]->get_vx(), |
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atoms[i]->get_vy(), |
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atoms[i]->get_vz()); |
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strcpy( writeLine, tempBuffer ); |
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if( atoms[i]->isDirectional() ){ |
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dAtom = (DirectionalAtom *)atoms[i]; |
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dAtom->getQ( q ); |
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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[0], |
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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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strcat( writeLine, tempBuffer ); |
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} |
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else |
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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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outFile << writeLine; |
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} |
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outFile.flush(); |
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#else // is_mpi |
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gezelter |
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MPI::Status istatus; |
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int *AtomToProcMap = mpiSim->getAtomToProcMap(); |
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gezelter |
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|
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mmeineke |
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// write out header and node 0's coordinates |
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gezelter |
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|
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mmeineke |
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if( worldRank == 0 ){ |
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outFile << mpiSim->getTotAtoms() << "\n"; |
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gezelter |
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mmeineke |
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outFile << currentTime << "\t" |
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<< entry_plug->box_x << "\t" |
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<< entry_plug->box_y << "\t" |
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<< entry_plug->box_z << "\n"; |
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chuckv |
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outFile.flush(); |
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gezelter |
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for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) { |
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gezelter |
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// Get the Node number which has this atom; |
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mmeineke |
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|
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gezelter |
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which_node = AtomToProcMap[i]; |
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chuckv |
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if (which_node == 0 ) { |
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mmeineke |
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chuckv |
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which_atom = i; |
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local_index=-1; |
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for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) { |
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if (atoms[j]->getGlobalIndex() == which_atom) local_index = j; |
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} |
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if (local_index != -1) { |
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//format the line |
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sprintf( tempBuffer, |
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"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", |
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atoms[local_index]->getType(), |
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atoms[local_index]->getX(), |
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atoms[local_index]->getY(), |
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atoms[local_index]->getZ(), |
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atoms[local_index]->get_vx(), |
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atoms[local_index]->get_vy(), |
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atoms[local_index]->get_vz()); // check here. |
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strcpy( writeLine, tempBuffer ); |
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mmeineke |
377 |
|
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chuckv |
436 |
if( atoms[local_index]->isDirectional() ){ |
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dAtom = (DirectionalAtom *)atoms[local_index]; |
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dAtom->getQ( q ); |
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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[0], |
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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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strcat( writeLine, tempBuffer ); |
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} |
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else |
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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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strcpy( writeLine, "ATOM NOT FOUND ON THIS PROCESSOR"); |
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} |
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} |
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else { |
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gezelter |
415 |
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chuckv |
436 |
//std::cerr << "node 0: sending node " << which_node << " request for atom " << i << "\n"; |
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MPI::COMM_WORLD.Send(&i, 1, MPI_INT, which_node, TAKE_THIS_TAG_INT); |
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//std::cerr << "node 0: sent!\n"; |
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gezelter |
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MPI::COMM_WORLD.Recv(writeLine, BUFFERSIZE, MPI_CHAR, which_node, |
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chuckv |
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TAKE_THIS_TAG_CHAR, istatus); |
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//std::cerr << "node 0: got this line: " << writeLine; |
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mmeineke |
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} |
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gezelter |
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|
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mmeineke |
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outFile << writeLine; |
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chuckv |
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outFile.flush(); |
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mmeineke |
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} |
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gezelter |
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// kill everyone off: |
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gezelter |
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game_over = -1; |
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for (j = 0; j < mpiSim->getNumberProcessors(); j++) { |
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chuckv |
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MPI::COMM_WORLD.Send(&game_over, 1, MPI_INT, j, TAKE_THIS_TAG_INT); |
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mmeineke |
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} |
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gezelter |
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} else { |
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done = 0; |
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while (!done) { |
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chuckv |
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//std::cerr << "node: " << mpiSim->getMyNode() << " Waiting for receive \n"; |
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gezelter |
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MPI::COMM_WORLD.Recv(&which_atom, 1, MPI_INT, 0, |
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chuckv |
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TAKE_THIS_TAG_INT, istatus); |
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//std::cerr << "node: " << mpiSim->getMyNode() << " got request for atom " << which_atom << "\n"; |
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gezelter |
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if (which_atom == -1) { |
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gezelter |
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done=1; |
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continue; |
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} else { |
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gezelter |
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local_index=-1; |
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chuckv |
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for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) { |
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gezelter |
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if (atoms[j]->getGlobalIndex() == which_atom) local_index = j; |
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} |
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if (local_index != -1) { |
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//format the line |
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sprintf( tempBuffer, |
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"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", |
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atoms[local_index]->getType(), |
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atoms[local_index]->getX(), |
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atoms[local_index]->getY(), |
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atoms[local_index]->getZ(), |
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atoms[local_index]->get_vx(), |
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atoms[local_index]->get_vy(), |
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atoms[local_index]->get_vz()); // check here. |
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strcpy( writeLine, tempBuffer ); |
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mmeineke |
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|
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gezelter |
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if( atoms[local_index]->isDirectional() ){ |
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dAtom = (DirectionalAtom *)atoms[local_index]; |
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dAtom->getQ( q ); |
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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[0], |
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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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strcat( writeLine, tempBuffer ); |
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} |
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else |
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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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chuckv |
436 |
// std::cerr << "node: " << mpiSim->getMyNode() << " sending this line" << writeLine; |
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gezelter |
419 |
MPI::COMM_WORLD.Send(writeLine, BUFFERSIZE, MPI_CHAR, 0, |
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chuckv |
436 |
TAKE_THIS_TAG_CHAR); |
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gezelter |
419 |
} else { |
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strcpy( writeLine, "ATOM NOT FOUND ON THIS PROCESSOR"); |
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MPI::COMM_WORLD.Send(writeLine, BUFFERSIZE, MPI_CHAR, 0, |
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chuckv |
436 |
TAKE_THIS_TAG_CHAR); |
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gezelter |
419 |
} |
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mmeineke |
377 |
} |
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} |
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gezelter |
415 |
} |
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outFile.flush(); |
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sprintf( checkPointMsg, |
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"Sucessfully took a dump.\n"); |
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MPIcheckPoint(); |
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mmeineke |
377 |
#endif // is_mpi |
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} |
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void DumpWriter::writeFinal(){ |
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gezelter |
416 |
|
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mmeineke |
377 |
char finalName[500]; |
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ofstream finalOut; |
275 |
gezelter |
416 |
|
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const int BUFFERSIZE = 2000; |
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char tempBuffer[BUFFERSIZE]; |
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char writeLine[BUFFERSIZE]; |
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280 |
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double q[4]; |
281 |
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DirectionalAtom* dAtom; |
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int nAtoms = entry_plug->n_atoms; |
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Atom** atoms = entry_plug->atoms; |
284 |
gezelter |
419 |
int i, j, which_node, done, game_over, which_atom, local_index; |
285 |
mmeineke |
377 |
|
286 |
gezelter |
416 |
|
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mmeineke |
377 |
#ifdef IS_MPI |
288 |
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if(worldRank == 0 ){ |
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#endif // is_mpi |
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strcpy( finalName, entry_plug->finalName ); |
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finalOut.open( finalName, ios::out | ios::trunc ); |
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if( !finalOut ){ |
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sprintf( painCave.errMsg, |
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"Could not open \"%s\" for final dump output.\n", |
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finalName ); |
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painCave.isFatal = 1; |
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simError(); |
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} |
301 |
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// finalOut.setf( ios::scientific ); |
303 |
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304 |
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#ifdef IS_MPI |
305 |
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} |
306 |
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sprintf(checkPointMsg,"Opened file for final configuration\n"); |
308 |
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MPIcheckPoint(); |
309 |
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310 |
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#endif //is_mpi |
311 |
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312 |
gezelter |
415 |
|
313 |
mmeineke |
377 |
#ifndef IS_MPI |
314 |
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315 |
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finalOut << nAtoms << "\n"; |
316 |
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finalOut << entry_plug->box_x << "\t" |
318 |
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<< entry_plug->box_y << "\t" |
319 |
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<< entry_plug->box_z << "\n"; |
320 |
gezelter |
416 |
|
321 |
mmeineke |
377 |
for( i=0; i<nAtoms; i++ ){ |
322 |
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323 |
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sprintf( tempBuffer, |
324 |
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"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", |
325 |
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atoms[i]->getType(), |
326 |
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atoms[i]->getX(), |
327 |
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atoms[i]->getY(), |
328 |
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atoms[i]->getZ(), |
329 |
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atoms[i]->get_vx(), |
330 |
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atoms[i]->get_vy(), |
331 |
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atoms[i]->get_vz()); |
332 |
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strcpy( writeLine, tempBuffer ); |
333 |
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334 |
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if( atoms[i]->isDirectional() ){ |
335 |
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336 |
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dAtom = (DirectionalAtom *)atoms[i]; |
337 |
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dAtom->getQ( q ); |
338 |
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339 |
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sprintf( tempBuffer, |
340 |
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"%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n", |
341 |
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q[0], |
342 |
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q[1], |
343 |
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q[2], |
344 |
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q[3], |
345 |
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dAtom->getJx(), |
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dAtom->getJy(), |
347 |
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dAtom->getJz()); |
348 |
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strcat( writeLine, tempBuffer ); |
349 |
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} |
350 |
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else |
351 |
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strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" ); |
352 |
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finalOut << writeLine; |
354 |
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} |
355 |
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finalOut.flush(); |
356 |
gezelter |
415 |
finalOut.close(); |
357 |
mmeineke |
377 |
|
358 |
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#else // is_mpi |
359 |
gezelter |
415 |
|
360 |
gezelter |
416 |
MPI::Status istatus; |
361 |
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int *AtomToProcMap = mpiSim->getAtomToProcMap(); |
362 |
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|
363 |
mmeineke |
377 |
// write out header and node 0's coordinates |
364 |
gezelter |
415 |
|
365 |
mmeineke |
377 |
if( worldRank == 0 ){ |
366 |
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finalOut << mpiSim->getTotAtoms() << "\n"; |
367 |
gezelter |
415 |
|
368 |
mmeineke |
377 |
finalOut << entry_plug->box_x << "\t" |
369 |
gezelter |
415 |
<< entry_plug->box_y << "\t" |
370 |
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<< entry_plug->box_z << "\n"; |
371 |
mmeineke |
377 |
|
372 |
gezelter |
416 |
for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) { |
373 |
gezelter |
415 |
// Get the Node number which has this molecule: |
374 |
mmeineke |
377 |
|
375 |
gezelter |
415 |
which_node = AtomToProcMap[i]; |
376 |
|
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|
377 |
gezelter |
416 |
if (which_node == mpiSim->getMyNode()) { |
378 |
chuckv |
437 |
|
379 |
|
|
which_atom = i; |
380 |
|
|
local_index=-1; |
381 |
|
|
for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) { |
382 |
|
|
if (atoms[j]->getGlobalIndex() == which_atom) local_index = j; |
383 |
|
|
} |
384 |
|
|
if (local_index != -1) { |
385 |
|
|
sprintf( tempBuffer, |
386 |
|
|
"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", |
387 |
|
|
atoms[local_index]->getType(), |
388 |
|
|
atoms[local_index]->getX(), |
389 |
|
|
atoms[local_index]->getY(), |
390 |
|
|
atoms[local_index]->getZ(), |
391 |
|
|
atoms[local_index]->get_vx(), |
392 |
|
|
atoms[local_index]->get_vy(), |
393 |
|
|
atoms[local_index]->get_vz()); |
394 |
|
|
strcpy( writeLine, tempBuffer ); |
395 |
mmeineke |
377 |
|
396 |
chuckv |
437 |
if( atoms[local_index]->isDirectional() ){ |
397 |
|
|
|
398 |
|
|
dAtom = (DirectionalAtom *)atoms[local_index]; |
399 |
|
|
dAtom->getQ( q ); |
400 |
|
|
|
401 |
|
|
sprintf( tempBuffer, |
402 |
|
|
"%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n", |
403 |
|
|
q[0], |
404 |
|
|
q[1], |
405 |
|
|
q[2], |
406 |
|
|
q[3], |
407 |
|
|
dAtom->getJx(), |
408 |
|
|
dAtom->getJy(), |
409 |
|
|
dAtom->getJz()); |
410 |
|
|
strcat( writeLine, tempBuffer ); |
411 |
|
|
} |
412 |
|
|
else |
413 |
|
|
strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" ); |
414 |
|
|
} |
415 |
|
|
else { |
416 |
|
|
strcpy( writeLine, "ATOM NOT FOUND ON THIS PROCESSOR"); |
417 |
|
|
} |
418 |
|
|
|
419 |
gezelter |
415 |
} else { |
420 |
|
|
|
421 |
chuckv |
436 |
MPI::COMM_WORLD.Send(&i, 1, MPI_INT, which_node, TAKE_THIS_TAG_INT); |
422 |
gezelter |
416 |
MPI::COMM_WORLD.Recv(writeLine, BUFFERSIZE, MPI_CHAR, which_node, |
423 |
chuckv |
436 |
TAKE_THIS_TAG_CHAR, istatus); |
424 |
mmeineke |
377 |
} |
425 |
gezelter |
415 |
|
426 |
mmeineke |
377 |
finalOut << writeLine; |
427 |
|
|
} |
428 |
|
|
|
429 |
gezelter |
415 |
// kill everyone off: |
430 |
gezelter |
416 |
game_over = -1; |
431 |
|
|
for (j = 0; j < mpiSim->getNumberProcessors(); j++) { |
432 |
chuckv |
436 |
MPI::COMM_WORLD.Send(&game_over, 1, MPI_INT, j, TAKE_THIS_TAG_INT); |
433 |
mmeineke |
377 |
} |
434 |
|
|
|
435 |
gezelter |
415 |
} else { |
436 |
|
|
|
437 |
|
|
done = 0; |
438 |
|
|
while (!done) { |
439 |
gezelter |
416 |
MPI::COMM_WORLD.Recv(&which_atom, 1, MPI_INT, 0, |
440 |
chuckv |
436 |
TAKE_THIS_TAG_INT, istatus); |
441 |
mmeineke |
377 |
|
442 |
gezelter |
416 |
if (which_atom == -1) { |
443 |
gezelter |
415 |
done=1; |
444 |
|
|
continue; |
445 |
|
|
} else { |
446 |
mmeineke |
377 |
|
447 |
gezelter |
419 |
local_index=-1; |
448 |
|
|
for (j=0; j < mpiSim->getMyNlocal(); j++) { |
449 |
|
|
if (atoms[j]->getGlobalIndex() == which_atom) local_index = j; |
450 |
|
|
} |
451 |
|
|
if (local_index != -1) { |
452 |
|
|
|
453 |
|
|
//format the line |
454 |
|
|
sprintf( tempBuffer, |
455 |
|
|
"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", |
456 |
|
|
atoms[local_index]->getType(), |
457 |
|
|
atoms[local_index]->getX(), |
458 |
|
|
atoms[local_index]->getY(), |
459 |
|
|
atoms[local_index]->getZ(), |
460 |
|
|
atoms[local_index]->get_vx(), |
461 |
|
|
atoms[local_index]->get_vy(), |
462 |
|
|
atoms[local_index]->get_vz()); // check here. |
463 |
|
|
strcpy( writeLine, tempBuffer ); |
464 |
mmeineke |
377 |
|
465 |
gezelter |
419 |
if( atoms[local_index]->isDirectional() ){ |
466 |
|
|
|
467 |
|
|
dAtom = (DirectionalAtom *)atoms[local_index]; |
468 |
|
|
dAtom->getQ( q ); |
469 |
mmeineke |
377 |
|
470 |
gezelter |
419 |
sprintf( tempBuffer, |
471 |
|
|
"%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n", |
472 |
|
|
q[0], |
473 |
|
|
q[1], |
474 |
|
|
q[2], |
475 |
|
|
q[3], |
476 |
|
|
dAtom->getJx(), |
477 |
|
|
dAtom->getJy(), |
478 |
|
|
dAtom->getJz()); |
479 |
|
|
strcat( writeLine, tempBuffer ); |
480 |
|
|
} |
481 |
|
|
else |
482 |
|
|
strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" ); |
483 |
|
|
|
484 |
|
|
MPI::COMM_WORLD.Send(writeLine, BUFFERSIZE, MPI_CHAR, 0, |
485 |
chuckv |
436 |
TAKE_THIS_TAG_CHAR); |
486 |
gezelter |
419 |
} else { |
487 |
|
|
strcpy( writeLine, "ATOM NOT FOUND ON THIS PROCESSOR"); |
488 |
|
|
MPI::COMM_WORLD.Send(writeLine, BUFFERSIZE, MPI_CHAR, 0, |
489 |
chuckv |
436 |
TAKE_THIS_TAG_CHAR); |
490 |
gezelter |
419 |
} |
491 |
mmeineke |
377 |
} |
492 |
|
|
} |
493 |
gezelter |
419 |
} |
494 |
gezelter |
415 |
finalOut.flush(); |
495 |
|
|
sprintf( checkPointMsg, |
496 |
|
|
"Sucessfully took a dump.\n"); |
497 |
|
|
MPIcheckPoint(); |
498 |
mmeineke |
377 |
|
499 |
gezelter |
415 |
if( worldRank == 0 ) finalOut.close(); |
500 |
mmeineke |
377 |
#endif // is_mpi |
501 |
|
|
} |