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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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#include "mpiSimulation.hpp" |
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#define TAKE_THIS_TAG 0 |
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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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int i; |
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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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int masterIndex; |
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int nodeAtomsStart; |
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int nodeAtomsEnd; |
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int mpiErr; |
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int sendError; |
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int procIndex; |
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MPI_Status istatus[MPI_STATUS_SIZE]; |
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// write out header and node 0's coordinates |
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if( worldRank == 0 ){ |
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outFile << mpiSim->getTotAtoms() << "\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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masterIndex = 0; |
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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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masterIndex++; |
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} |
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outFile.flush(); |
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} |
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sprintf( checkPointMsg, |
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"Sucessfully wrote node 0's dump configuration.\n"); |
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MPIcheckPoint(); |
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for (procIndex = 1; procIndex < mpiSim->getNumberProcessors(); |
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procIndex++){ |
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if( worldRank == 0 ){ |
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mpiErr = MPI_Recv(&nodeAtomsStart,1,MPI_INT,procIndex, |
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TAKE_THIS_TAG,MPI_COMM_WORLD,istatus); |
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mpiErr = MPI_Recv(&nodeAtomsEnd,1,MPI_INT,procIndex, |
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TAKE_THIS_TAG,MPI_COMM_WORLD, istatus); |
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// Make sure where node 0 is writing to, matches where the |
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// receiving node expects it to be. |
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if (masterIndex != nodeAtomsStart){ |
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sendError = 1; |
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mpiErr = MPI_Send(&sendError,1,MPI_INT,procIndex,TAKE_THIS_TAG, |
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MPI_COMM_WORLD); |
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sprintf(painCave.errMsg, |
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"DumpWriter error: atoms start index (%d) for " |
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"node %d not equal to master index (%d)", |
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nodeAtomsStart,procIndex,masterIndex ); |
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painCave.isFatal = 1; |
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simError(); |
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} |
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sendError = 0; |
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mpiErr = MPI_Send(&sendError,1,MPI_INT,procIndex,TAKE_THIS_TAG, |
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MPI_COMM_WORLD); |
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// recieve the nodes writeLines |
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for ( i = nodeAtomsStart; i <= nodeAtomsEnd; i++){ |
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mpiErr = MPI_Recv(writeLine,BUFFERSIZE,MPI_CHAR,procIndex, |
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TAKE_THIS_TAG,MPI_COMM_WORLD,istatus ); |
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outFile << writeLine; |
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masterIndex++; |
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} |
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} |
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else if( worldRank == procIndex ){ |
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nodeAtomsStart = mpiSim->getMyAtomStart(); |
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nodeAtomsEnd = mpiSim->getMyAtomEnd(); |
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mpiErr = MPI_Send(&nodeAtomsStart,1,MPI_INT,0,TAKE_THIS_TAG, |
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MPI_COMM_WORLD); |
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mpiErr = MPI_Send(&nodeAtomsEnd,1,MPI_INT,0,TAKE_THIS_TAG, |
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MPI_COMM_WORLD); |
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sendError = -1; |
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mpiErr = MPI_Recv(&sendError,1,MPI_INT,0,TAKE_THIS_TAG, |
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MPI_COMM_WORLD, istatus); |
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if (sendError) MPIcheckPoint(); |
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// send current node's configuration line by line. |
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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()); // check here. |
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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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mpiErr = MPI_Send(writeLine,BUFFERSIZE,MPI_CHAR,0,TAKE_THIS_TAG, |
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MPI_COMM_WORLD); |
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} |
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} |
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sprintf(checkPointMsg,"Node %d sent dump configuration.", |
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procIndex); |
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MPIcheckPoint(); |
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} |
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#endif // is_mpi |
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} |
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void DumpWriter::writeFinal(){ |
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const int BUFFERSIZE = 2000; |
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char tempBuffer[500]; |
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char writeLine[BUFFERSIZE]; |
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char finalName[500]; |
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int i; |
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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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ofstream finalOut; |
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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( 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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} |
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// finalOut.setf( ios::scientific ); |
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#ifdef IS_MPI |
| 331 |
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} |
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sprintf(checkPointMsg,"Opened file for final configuration\n"); |
| 334 |
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MPIcheckPoint(); |
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#endif //is_mpi |
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| 340 |
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#ifndef IS_MPI |
| 341 |
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finalOut << nAtoms << "\n"; |
| 343 |
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| 344 |
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finalOut << entry_plug->box_x << "\t" |
| 345 |
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<< entry_plug->box_y << "\t" |
| 346 |
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<< entry_plug->box_z << "\n"; |
| 347 |
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| 348 |
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for( i=0; i<nAtoms; i++ ){ |
| 349 |
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| 350 |
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sprintf( tempBuffer, |
| 351 |
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"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", |
| 352 |
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atoms[i]->getType(), |
| 353 |
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atoms[i]->getX(), |
| 354 |
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atoms[i]->getY(), |
| 355 |
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atoms[i]->getZ(), |
| 356 |
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atoms[i]->get_vx(), |
| 357 |
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atoms[i]->get_vy(), |
| 358 |
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atoms[i]->get_vz()); |
| 359 |
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strcpy( writeLine, tempBuffer ); |
| 360 |
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| 361 |
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if( atoms[i]->isDirectional() ){ |
| 362 |
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| 363 |
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dAtom = (DirectionalAtom *)atoms[i]; |
| 364 |
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dAtom->getQ( q ); |
| 365 |
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| 366 |
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sprintf( tempBuffer, |
| 367 |
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"%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n", |
| 368 |
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q[0], |
| 369 |
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q[1], |
| 370 |
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q[2], |
| 371 |
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q[3], |
| 372 |
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dAtom->getJx(), |
| 373 |
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dAtom->getJy(), |
| 374 |
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dAtom->getJz()); |
| 375 |
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strcat( writeLine, tempBuffer ); |
| 376 |
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} |
| 377 |
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else |
| 378 |
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strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" ); |
| 379 |
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| 380 |
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finalOut << writeLine; |
| 381 |
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} |
| 382 |
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finalOut.flush(); |
| 383 |
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| 384 |
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#else // is_mpi |
| 385 |
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| 386 |
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int masterIndex; |
| 387 |
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int nodeAtomsStart; |
| 388 |
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int nodeAtomsEnd; |
| 389 |
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int mpiErr; |
| 390 |
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int sendError; |
| 391 |
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int procIndex; |
| 392 |
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| 393 |
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MPI_Status istatus[MPI_STATUS_SIZE]; |
| 394 |
|
|
|
| 395 |
|
|
|
| 396 |
|
|
// write out header and node 0's coordinates |
| 397 |
|
|
|
| 398 |
|
|
if( worldRank == 0 ){ |
| 399 |
|
|
finalOut << mpiSim->getTotAtoms() << "\n"; |
| 400 |
|
|
|
| 401 |
|
|
finalOut << entry_plug->box_x << "\t" |
| 402 |
|
|
<< entry_plug->box_y << "\t" |
| 403 |
|
|
<< entry_plug->box_z << "\n"; |
| 404 |
|
|
|
| 405 |
|
|
masterIndex = 0; |
| 406 |
|
|
|
| 407 |
|
|
for( i=0; i<nAtoms; i++ ){ |
| 408 |
|
|
|
| 409 |
|
|
sprintf( tempBuffer, |
| 410 |
|
|
"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", |
| 411 |
|
|
atoms[i]->getType(), |
| 412 |
|
|
atoms[i]->getX(), |
| 413 |
|
|
atoms[i]->getY(), |
| 414 |
|
|
atoms[i]->getZ(), |
| 415 |
|
|
atoms[i]->get_vx(), |
| 416 |
|
|
atoms[i]->get_vy(), |
| 417 |
|
|
atoms[i]->get_vz()); |
| 418 |
|
|
strcpy( writeLine, tempBuffer ); |
| 419 |
|
|
|
| 420 |
|
|
if( atoms[i]->isDirectional() ){ |
| 421 |
|
|
|
| 422 |
|
|
dAtom = (DirectionalAtom *)atoms[i]; |
| 423 |
|
|
dAtom->getQ( q ); |
| 424 |
|
|
|
| 425 |
|
|
sprintf( tempBuffer, |
| 426 |
|
|
"%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n", |
| 427 |
|
|
q[0], |
| 428 |
|
|
q[1], |
| 429 |
|
|
q[2], |
| 430 |
|
|
q[3], |
| 431 |
|
|
dAtom->getJx(), |
| 432 |
|
|
dAtom->getJy(), |
| 433 |
|
|
dAtom->getJz()); |
| 434 |
|
|
strcat( writeLine, tempBuffer ); |
| 435 |
|
|
} |
| 436 |
|
|
else |
| 437 |
|
|
strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" ); |
| 438 |
|
|
|
| 439 |
|
|
finalOut << writeLine; |
| 440 |
|
|
masterIndex++; |
| 441 |
|
|
} |
| 442 |
|
|
finalOut.flush(); |
| 443 |
|
|
} |
| 444 |
|
|
|
| 445 |
|
|
for (procIndex = 1; procIndex < mpiSim->getNumberProcessors(); |
| 446 |
|
|
procIndex++){ |
| 447 |
|
|
|
| 448 |
|
|
if( worldRank == 0 ){ |
| 449 |
|
|
|
| 450 |
|
|
mpiErr = MPI_Recv(&nodeAtomsStart,1,MPI_INT,procIndex, |
| 451 |
|
|
TAKE_THIS_TAG,MPI_COMM_WORLD,istatus); |
| 452 |
|
|
|
| 453 |
|
|
mpiErr = MPI_Recv(&nodeAtomsEnd,1,MPI_INT,procIndex, |
| 454 |
|
|
TAKE_THIS_TAG,MPI_COMM_WORLD, istatus); |
| 455 |
|
|
|
| 456 |
|
|
// Make sure where node 0 is writing to, matches where the |
| 457 |
|
|
// receiving node expects it to be. |
| 458 |
|
|
|
| 459 |
|
|
if (masterIndex != nodeAtomsStart){ |
| 460 |
|
|
sendError = 1; |
| 461 |
|
|
mpiErr = MPI_Send(&sendError,1,MPI_INT,procIndex,TAKE_THIS_TAG, |
| 462 |
|
|
MPI_COMM_WORLD); |
| 463 |
|
|
sprintf(painCave.errMsg, |
| 464 |
|
|
"DumpWriter error: atoms start index (%d) for " |
| 465 |
|
|
"node %d not equal to master index (%d)", |
| 466 |
|
|
nodeAtomsStart,procIndex,masterIndex ); |
| 467 |
|
|
painCave.isFatal = 1; |
| 468 |
|
|
simError(); |
| 469 |
|
|
} |
| 470 |
|
|
|
| 471 |
|
|
sendError = 0; |
| 472 |
|
|
mpiErr = MPI_Send(&sendError,1,MPI_INT,procIndex,TAKE_THIS_TAG, |
| 473 |
|
|
MPI_COMM_WORLD); |
| 474 |
|
|
|
| 475 |
|
|
// recieve the nodes writeLines |
| 476 |
|
|
|
| 477 |
|
|
for ( i = nodeAtomsStart; i <= nodeAtomsEnd; i++){ |
| 478 |
|
|
|
| 479 |
|
|
mpiErr = MPI_Recv(writeLine,BUFFERSIZE,MPI_CHAR,procIndex, |
| 480 |
|
|
TAKE_THIS_TAG,MPI_COMM_WORLD,istatus ); |
| 481 |
|
|
|
| 482 |
|
|
finalOut << writeLine; |
| 483 |
|
|
masterIndex++; |
| 484 |
|
|
} |
| 485 |
|
|
|
| 486 |
|
|
finalOut.flush(); |
| 487 |
|
|
} |
| 488 |
|
|
|
| 489 |
|
|
else if( worldRank == procIndex ){ |
| 490 |
|
|
|
| 491 |
|
|
nodeAtomsStart = mpiSim->getMyAtomStart(); |
| 492 |
|
|
nodeAtomsEnd = mpiSim->getMyAtomEnd(); |
| 493 |
|
|
|
| 494 |
|
|
mpiErr = MPI_Send(&nodeAtomsStart,1,MPI_INT,0,TAKE_THIS_TAG, |
| 495 |
|
|
MPI_COMM_WORLD); |
| 496 |
|
|
mpiErr = MPI_Send(&nodeAtomsEnd,1,MPI_INT,0,TAKE_THIS_TAG, |
| 497 |
|
|
MPI_COMM_WORLD); |
| 498 |
|
|
|
| 499 |
|
|
mpiErr = MPI_Recv(&sendError,1,MPI_INT,0,TAKE_THIS_TAG, |
| 500 |
|
|
MPI_COMM_WORLD, istatus); |
| 501 |
|
|
if (sendError) MPIcheckPoint(); |
| 502 |
|
|
|
| 503 |
|
|
// send current node's configuration line by line. |
| 504 |
|
|
|
| 505 |
|
|
for( i=0; i<nAtoms; i++ ){ |
| 506 |
|
|
|
| 507 |
|
|
sprintf( tempBuffer, |
| 508 |
|
|
"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", |
| 509 |
|
|
atoms[i]->getType(), |
| 510 |
|
|
atoms[i]->getX(), |
| 511 |
|
|
atoms[i]->getY(), |
| 512 |
|
|
atoms[i]->getZ(), |
| 513 |
|
|
atoms[i]->get_vx(), |
| 514 |
|
|
atoms[i]->get_vy(), |
| 515 |
|
|
atoms[i]->get_vz()); |
| 516 |
|
|
strcpy( writeLine, tempBuffer ); |
| 517 |
|
|
|
| 518 |
|
|
if( atoms[i]->isDirectional() ){ |
| 519 |
|
|
|
| 520 |
|
|
dAtom = (DirectionalAtom *)atoms[i]; |
| 521 |
|
|
dAtom->getQ( q ); |
| 522 |
|
|
|
| 523 |
|
|
sprintf( tempBuffer, |
| 524 |
|
|
"%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n", |
| 525 |
|
|
q[0], |
| 526 |
|
|
q[1], |
| 527 |
|
|
q[2], |
| 528 |
|
|
q[3], |
| 529 |
|
|
dAtom->getJx(), |
| 530 |
|
|
dAtom->getJy(), |
| 531 |
|
|
dAtom->getJz()); |
| 532 |
|
|
strcat( writeLine, tempBuffer ); |
| 533 |
|
|
} |
| 534 |
|
|
else |
| 535 |
|
|
strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" ); |
| 536 |
|
|
|
| 537 |
|
|
mpiErr = MPI_Send(writeLine,BUFFERSIZE,MPI_CHAR,0,TAKE_THIS_TAG, |
| 538 |
|
|
MPI_COMM_WORLD); |
| 539 |
|
|
} |
| 540 |
|
|
} |
| 541 |
|
|
|
| 542 |
|
|
sprintf(checkPointMsg,"Node %d sent dump configuration.", |
| 543 |
|
|
procIndex); |
| 544 |
|
|
MPIcheckPoint(); |
| 545 |
|
|
} |
| 546 |
|
|
|
| 547 |
|
|
if( worldRank == 0 ) finalOut.close(); |
| 548 |
|
|
|
| 549 |
|
|
|
| 550 |
|
|
#endif // is_mpi |
| 551 |
|
|
} |
