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#include <cstring> |
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#include <iostream> |
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#include <fstream> |
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|
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#ifdef IS_MPI |
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#include <mpi.h> |
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#include <mpi++.h> |
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#include "mpiSimulation.hpp" |
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#define TAKE_THIS_TAG 0 |
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#endif //is_mpi |
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|
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#include "ReadWrite.hpp" |
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#include "simError.h" |
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|
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DumpWriter::DumpWriter( SimInfo* the_entry_plug ){ |
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|
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entry_plug = the_entry_plug; |
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|
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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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|
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|
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|
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strcpy( outName, entry_plug->sampleName ); |
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|
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outFile.open(outName, ios::out | ios::trunc ); |
28 |
|
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if( !outFile ){ |
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|
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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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|
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//outFile.setf( ios::scientific ); |
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|
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#ifdef IS_MPI |
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} |
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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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|
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DumpWriter::~DumpWriter( ){ |
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|
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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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|
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outFile.close(); |
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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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} |
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|
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void DumpWriter::writeDump( double currentTime ){ |
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|
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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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|
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int i, j, which_node, done, game_over, which_atom, local_index; |
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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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|
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|
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#ifndef IS_MPI |
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|
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outFile << nAtoms << "\n"; |
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|
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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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|
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for( i=0; i<nAtoms; i++ ){ |
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|
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|
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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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|
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if( atoms[i]->isDirectional() ){ |
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|
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dAtom = (DirectionalAtom *)atoms[i]; |
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dAtom->getQ( q ); |
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|
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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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outFile << writeLine; |
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} |
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outFile.flush(); |
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|
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#else // is_mpi |
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|
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MPI::Status istatus; |
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int *AtomToProcMap = mpiSim->getAtomToProcMap(); |
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|
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// write out header and node 0's coordinates |
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|
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if( worldRank == 0 ){ |
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outFile << mpiSim->getTotAtoms() << "\n"; |
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|
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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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|
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for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) { |
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// Get the Node number which has this atom; |
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|
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which_node = AtomToProcMap[i]; |
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|
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if (which_node == mpiSim->getMyNode()) { |
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|
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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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|
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if( atoms[i]->isDirectional() ){ |
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|
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dAtom = (DirectionalAtom *)atoms[i]; |
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dAtom->getQ( q ); |
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|
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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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|
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MPI::COMM_WORLD.Send(&i, 1, MPI_INT, which_node, TAKE_THIS_TAG); |
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MPI::COMM_WORLD.Recv(writeLine, BUFFERSIZE, MPI_CHAR, which_node, |
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TAKE_THIS_TAG, istatus); |
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} |
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|
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outFile << writeLine; |
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} |
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|
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// kill everyone off: |
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game_over = -1; |
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for (j = 0; j < mpiSim->getNumberProcessors(); j++) { |
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MPI::COMM_WORLD.Send(&game_over, 1, MPI_INT, j, TAKE_THIS_TAG); |
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} |
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|
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} else { |
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|
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done = 0; |
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while (!done) { |
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MPI::COMM_WORLD.Recv(&which_atom, 1, MPI_INT, 0, |
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TAKE_THIS_TAG, istatus); |
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|
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if (which_atom == -1) { |
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done=1; |
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continue; |
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} else { |
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local_index=-1; |
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for (j=0; j < mpiSim->getMyNlocal(); 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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|
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if( atoms[local_index]->isDirectional() ){ |
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|
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dAtom = (DirectionalAtom *)atoms[local_index]; |
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dAtom->getQ( q ); |
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|
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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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MPI::COMM_WORLD.Send(writeLine, BUFFERSIZE, MPI_CHAR, 0, |
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TAKE_THIS_TAG); |
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} 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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TAKE_THIS_TAG); |
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} |
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} |
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} |
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} |
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outFile.flush(); |
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sprintf( checkPointMsg, |
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"Sucessfully took a dump.\n"); |
249 |
MPIcheckPoint(); |
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#endif // is_mpi |
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} |
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|
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void DumpWriter::writeFinal(){ |
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|
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char finalName[500]; |
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ofstream finalOut; |
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|
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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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|
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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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int i, j, which_node, done, game_over, which_atom, local_index; |
267 |
|
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|
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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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|
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strcpy( finalName, entry_plug->finalName ); |
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|
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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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} |
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|
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// finalOut.setf( ios::scientific ); |
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|
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#ifdef IS_MPI |
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} |
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|
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sprintf(checkPointMsg,"Opened file for final configuration\n"); |
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MPIcheckPoint(); |
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|
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#endif //is_mpi |
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|
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|
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#ifndef IS_MPI |
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|
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finalOut << nAtoms << "\n"; |
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|
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finalOut << 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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|
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for( i=0; i<nAtoms; i++ ){ |
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|
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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(), |
309 |
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()); |
314 |
strcpy( writeLine, tempBuffer ); |
315 |
|
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if( atoms[i]->isDirectional() ){ |
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|
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dAtom = (DirectionalAtom *)atoms[i]; |
319 |
dAtom->getQ( q ); |
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|
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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()); |
330 |
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" ); |
334 |
|
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finalOut << writeLine; |
336 |
} |
337 |
finalOut.flush(); |
338 |
finalOut.close(); |
339 |
|
340 |
#else // is_mpi |
341 |
|
342 |
MPI::Status istatus; |
343 |
int *AtomToProcMap = mpiSim->getAtomToProcMap(); |
344 |
|
345 |
// write out header and node 0's coordinates |
346 |
|
347 |
if( worldRank == 0 ){ |
348 |
finalOut << mpiSim->getTotAtoms() << "\n"; |
349 |
|
350 |
finalOut << entry_plug->box_x << "\t" |
351 |
<< entry_plug->box_y << "\t" |
352 |
<< entry_plug->box_z << "\n"; |
353 |
|
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for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) { |
355 |
// Get the Node number which has this molecule: |
356 |
|
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which_node = AtomToProcMap[i]; |
358 |
|
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if (which_node == mpiSim->getMyNode()) { |
360 |
|
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sprintf( tempBuffer, |
362 |
"%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(), |
365 |
atoms[i]->getY(), |
366 |
atoms[i]->getZ(), |
367 |
atoms[i]->get_vx(), |
368 |
atoms[i]->get_vy(), |
369 |
atoms[i]->get_vz()); |
370 |
strcpy( writeLine, tempBuffer ); |
371 |
|
372 |
if( atoms[i]->isDirectional() ){ |
373 |
|
374 |
dAtom = (DirectionalAtom *)atoms[i]; |
375 |
dAtom->getQ( q ); |
376 |
|
377 |
sprintf( tempBuffer, |
378 |
"%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n", |
379 |
q[0], |
380 |
q[1], |
381 |
q[2], |
382 |
q[3], |
383 |
dAtom->getJx(), |
384 |
dAtom->getJy(), |
385 |
dAtom->getJz()); |
386 |
strcat( writeLine, tempBuffer ); |
387 |
} |
388 |
else |
389 |
strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" ); |
390 |
|
391 |
} else { |
392 |
|
393 |
MPI::COMM_WORLD.Send(&i, 1, MPI_INT, which_node, TAKE_THIS_TAG); |
394 |
MPI::COMM_WORLD.Recv(writeLine, BUFFERSIZE, MPI_CHAR, which_node, |
395 |
TAKE_THIS_TAG, istatus); |
396 |
} |
397 |
|
398 |
finalOut << writeLine; |
399 |
} |
400 |
|
401 |
// kill everyone off: |
402 |
game_over = -1; |
403 |
for (j = 0; j < mpiSim->getNumberProcessors(); j++) { |
404 |
MPI::COMM_WORLD.Send(&game_over, 1, MPI_INT, j, TAKE_THIS_TAG); |
405 |
} |
406 |
|
407 |
} else { |
408 |
|
409 |
done = 0; |
410 |
while (!done) { |
411 |
MPI::COMM_WORLD.Recv(&which_atom, 1, MPI_INT, 0, |
412 |
TAKE_THIS_TAG, istatus); |
413 |
|
414 |
if (which_atom == -1) { |
415 |
done=1; |
416 |
continue; |
417 |
} else { |
418 |
|
419 |
local_index=-1; |
420 |
for (j=0; j < mpiSim->getMyNlocal(); j++) { |
421 |
if (atoms[j]->getGlobalIndex() == which_atom) local_index = j; |
422 |
} |
423 |
if (local_index != -1) { |
424 |
|
425 |
//format the line |
426 |
sprintf( tempBuffer, |
427 |
"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", |
428 |
atoms[local_index]->getType(), |
429 |
atoms[local_index]->getX(), |
430 |
atoms[local_index]->getY(), |
431 |
atoms[local_index]->getZ(), |
432 |
atoms[local_index]->get_vx(), |
433 |
atoms[local_index]->get_vy(), |
434 |
atoms[local_index]->get_vz()); // check here. |
435 |
strcpy( writeLine, tempBuffer ); |
436 |
|
437 |
if( atoms[local_index]->isDirectional() ){ |
438 |
|
439 |
dAtom = (DirectionalAtom *)atoms[local_index]; |
440 |
dAtom->getQ( q ); |
441 |
|
442 |
sprintf( tempBuffer, |
443 |
"%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n", |
444 |
q[0], |
445 |
q[1], |
446 |
q[2], |
447 |
q[3], |
448 |
dAtom->getJx(), |
449 |
dAtom->getJy(), |
450 |
dAtom->getJz()); |
451 |
strcat( writeLine, tempBuffer ); |
452 |
} |
453 |
else |
454 |
strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" ); |
455 |
|
456 |
MPI::COMM_WORLD.Send(writeLine, BUFFERSIZE, MPI_CHAR, 0, |
457 |
TAKE_THIS_TAG); |
458 |
} else { |
459 |
strcpy( writeLine, "ATOM NOT FOUND ON THIS PROCESSOR"); |
460 |
MPI::COMM_WORLD.Send(writeLine, BUFFERSIZE, MPI_CHAR, 0, |
461 |
TAKE_THIS_TAG); |
462 |
} |
463 |
} |
464 |
} |
465 |
} |
466 |
finalOut.flush(); |
467 |
sprintf( checkPointMsg, |
468 |
"Sucessfully took a dump.\n"); |
469 |
MPIcheckPoint(); |
470 |
|
471 |
if( worldRank == 0 ) finalOut.close(); |
472 |
#endif // is_mpi |
473 |
} |