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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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chuckv |
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#ifdef IS_MPI |
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mmeineke |
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#include <mpi.h> |
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chuckv |
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#include "mpiSimulation.hpp" |
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#endif //is_mpi |
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mmeineke |
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#include "ReadWrite.hpp" |
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mmeineke |
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#include "simError.h" |
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mmeineke |
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chuckv |
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mmeineke |
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DumpWriter::DumpWriter( SimInfo* the_entry_plug ){ |
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mmeineke |
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#ifdef IS_MPI |
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mmeineke |
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if(worldRank == 0 ){ |
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mmeineke |
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#endif // is_mpi |
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entry_plug = the_entry_plug; |
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strcpy( outName, entry_plug->sampleName ); |
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std::cerr << "Opening " << outName << " for dumping.\n"; |
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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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mmeineke |
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mmeineke |
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//outFile.setf( ios::scientific ); |
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#ifdef IS_MPI |
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mmeineke |
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} |
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mmeineke |
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#endif // is_mpi |
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mmeineke |
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} |
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DumpWriter::~DumpWriter( ){ |
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mmeineke |
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#ifdef IS_MPI |
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mmeineke |
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if(worldRank == 0 ){ |
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mmeineke |
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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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mmeineke |
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} |
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void DumpWriter::writeDump( double currentTime ){ |
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mmeineke |
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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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mmeineke |
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mmeineke |
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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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mmeineke |
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mmeineke |
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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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mmeineke |
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mmeineke |
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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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mmeineke |
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mmeineke |
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MPI_Status istatus[MPI_STATUS_SIZE]; |
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mmeineke |
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mmeineke |
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// write out header and node 0's coordinates |
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if( worldRank == 0 ){ |
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chuckv |
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outFile << mpiSim->getTotAtoms() << "\n"; |
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mmeineke |
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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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mmeineke |
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masterIndex = 0; |
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mmeineke |
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for( i=0; i<nAtoms; i++ ){ |
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mmeineke |
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mmeineke |
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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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mmeineke |
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if( atoms[i]->isDirectional() ){ |
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mmeineke |
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mmeineke |
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dAtom = (DirectionalAtom *)atoms[i]; |
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dAtom->getQ( q ); |
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mmeineke |
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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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mmeineke |
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chuckv |
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outFile << writeLine; |
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mmeineke |
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masterIndex++; |
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} |
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outFile.flush(); |
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} |
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chuckv |
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for (procIndex = 1; procIndex < mpiSim->getNumberProcessors(); |
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mmeineke |
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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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MPI_ANY_TAG,MPI_COMM_WORLD,istatus); |
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mpiErr = MPI_Recv(&nodeAtomsEnd,1,MPI_INT,procIndex, |
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MPI_ANY_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,MPI_ANY_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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mmeineke |
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} |
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mmeineke |
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sendError = 0; |
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mpiErr = MPI_Send(&sendError,1,MPI_INT,procIndex,MPI_ANY_TAG, |
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MPI_COMM_WORLD); |
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// recieve the nodes writeLines |
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chuckv |
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for ( i = nodeAtomsStart; i <= nodeAtomsEnd; i++){ |
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mmeineke |
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chuckv |
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mpiErr = MPI_Recv(writeLine,BUFFERSIZE,MPI_CHAR,procIndex, |
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mmeineke |
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MPI_ANY_TAG,MPI_COMM_WORLD,istatus ); |
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outFile << writeLine; |
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masterIndex++; |
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mmeineke |
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} |
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mmeineke |
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} |
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mmeineke |
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mmeineke |
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else if( worldRank == procIndex ){ |
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chuckv |
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nodeAtomsStart = mpiSim->getMyAtomStart(); |
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nodeAtomsEnd = mpiSim->getMyAtomEnd(); |
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mmeineke |
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mpiErr = MPI_Send(&nodeAtomsStart,1,MPI_INT,0,MPI_ANY_TAG, |
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MPI_COMM_WORLD); |
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mpiErr = MPI_Send(&nodeAtomsEnd,1,MPI_INT,0,MPI_ANY_TAG, |
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MPI_COMM_WORLD); |
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mpiErr = MPI_Recv(&sendError,1,MPI_INT,0,MPI_ANY_TAG, |
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MPI_COMM_WORLD, istatus); |
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chuckv |
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if (sendError) MPIcheckPoint(); |
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mmeineke |
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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()); |
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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,MPI_ANY_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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chuckv |
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MPIcheckPoint(); |
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mmeineke |
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} |
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mmeineke |
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mmeineke |
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#endif // is_mpi |
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mmeineke |
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} |
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mmeineke |
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mmeineke |
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void DumpWriter::writeFinal(){ |
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mmeineke |
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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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mmeineke |
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#ifdef IS_MPI |
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mmeineke |
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if(worldRank == 0 ){ |
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mmeineke |
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#endif // is_mpi |
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mmeineke |
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|
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mmeineke |
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strcpy( finalName, entry_plug->finalName ); |
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mmeineke |
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finalOut.open( finalName, ios::out | ios::trunc ); |
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mmeineke |
184 |
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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mmeineke |
10 |
|
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mmeineke |
184 |
// finalOut.setf( ios::scientific ); |
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mmeineke |
214 |
#ifdef IS_MPI |
319 |
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} |
320 |
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chuckv |
254 |
sprintf(checkPointMsg,"Opened file for final configuration\n"); |
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MPIcheckPoint(); |
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mmeineke |
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#endif //is_mpi |
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mmeineke |
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mmeineke |
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#ifndef IS_MPI |
329 |
mmeineke |
184 |
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mmeineke |
214 |
finalOut << nAtoms << "\n"; |
331 |
mmeineke |
184 |
|
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chuckv |
249 |
finalOut << entry_plug->box_x << "\t" |
333 |
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<< entry_plug->box_y << "\t" |
334 |
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<< entry_plug->box_z << "\n"; |
335 |
mmeineke |
184 |
|
336 |
mmeineke |
214 |
for( i=0; i<nAtoms; i++ ){ |
337 |
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338 |
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sprintf( tempBuffer, |
339 |
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"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", |
340 |
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atoms[i]->getType(), |
341 |
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atoms[i]->getX(), |
342 |
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atoms[i]->getY(), |
343 |
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atoms[i]->getZ(), |
344 |
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atoms[i]->get_vx(), |
345 |
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atoms[i]->get_vy(), |
346 |
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atoms[i]->get_vz()); |
347 |
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strcpy( writeLine, tempBuffer ); |
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349 |
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if( atoms[i]->isDirectional() ){ |
350 |
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351 |
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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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} |
365 |
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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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finalOut << writeLine; |
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} |
370 |
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finalOut.flush(); |
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#else // is_mpi |
373 |
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374 |
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int masterIndex; |
375 |
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int nodeAtomsStart; |
376 |
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int nodeAtomsEnd; |
377 |
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int mpiErr; |
378 |
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int sendError; |
379 |
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int procIndex; |
380 |
mmeineke |
184 |
|
381 |
mmeineke |
214 |
MPI_Status istatus[MPI_STATUS_SIZE]; |
382 |
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|
383 |
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|
384 |
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// write out header and node 0's coordinates |
385 |
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|
386 |
|
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if( worldRank == 0 ){ |
387 |
chuckv |
254 |
finalOut << mpiSim->getTotAtoms() << "\n"; |
388 |
mmeineke |
214 |
|
389 |
chuckv |
249 |
finalOut << entry_plug->box_x << "\t" |
390 |
|
|
<< entry_plug->box_y << "\t" |
391 |
|
|
<< entry_plug->box_z << "\n"; |
392 |
|
|
|
393 |
mmeineke |
214 |
masterIndex = 0; |
394 |
mmeineke |
184 |
for( i=0; i<nAtoms; i++ ){ |
395 |
mmeineke |
10 |
|
396 |
mmeineke |
214 |
sprintf( tempBuffer, |
397 |
|
|
"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", |
398 |
|
|
atoms[i]->getType(), |
399 |
|
|
atoms[i]->getX(), |
400 |
|
|
atoms[i]->getY(), |
401 |
|
|
atoms[i]->getZ(), |
402 |
|
|
atoms[i]->get_vx(), |
403 |
|
|
atoms[i]->get_vy(), |
404 |
|
|
atoms[i]->get_vz()); |
405 |
|
|
strcpy( writeLine, tempBuffer ); |
406 |
|
|
|
407 |
mmeineke |
184 |
if( atoms[i]->isDirectional() ){ |
408 |
mmeineke |
214 |
|
409 |
mmeineke |
184 |
dAtom = (DirectionalAtom *)atoms[i]; |
410 |
|
|
dAtom->getQ( q ); |
411 |
mmeineke |
214 |
|
412 |
|
|
sprintf( tempBuffer, |
413 |
|
|
"%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n", |
414 |
|
|
q[0], |
415 |
|
|
q[1], |
416 |
|
|
q[2], |
417 |
|
|
q[3], |
418 |
|
|
dAtom->getJx(), |
419 |
|
|
dAtom->getJy(), |
420 |
|
|
dAtom->getJz()); |
421 |
|
|
strcat( writeLine, tempBuffer ); |
422 |
|
|
} |
423 |
|
|
else |
424 |
|
|
strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" ); |
425 |
mmeineke |
184 |
|
426 |
chuckv |
254 |
outFile << writeLine; |
427 |
mmeineke |
214 |
masterIndex++; |
428 |
|
|
} |
429 |
|
|
finalOut.flush(); |
430 |
|
|
} |
431 |
|
|
|
432 |
chuckv |
254 |
for (procIndex = 1; procIndex < mpiSim->getNumberProcessors(); |
433 |
mmeineke |
214 |
procIndex++){ |
434 |
|
|
|
435 |
|
|
if( worldRank == 0 ){ |
436 |
|
|
|
437 |
|
|
mpiErr = MPI_Recv(&nodeAtomsStart,1,MPI_INT,procIndex, |
438 |
|
|
MPI_ANY_TAG,MPI_COMM_WORLD,istatus); |
439 |
|
|
|
440 |
|
|
mpiErr = MPI_Recv(&nodeAtomsEnd,1,MPI_INT,procIndex, |
441 |
|
|
MPI_ANY_TAG,MPI_COMM_WORLD, istatus); |
442 |
|
|
|
443 |
|
|
// Make sure where node 0 is writing to, matches where the |
444 |
|
|
// receiving node expects it to be. |
445 |
|
|
|
446 |
|
|
if (masterIndex != nodeAtomsStart){ |
447 |
|
|
sendError = 1; |
448 |
|
|
mpiErr = MPI_Send(&sendError,1,MPI_INT,procIndex,MPI_ANY_TAG, |
449 |
|
|
MPI_COMM_WORLD); |
450 |
|
|
sprintf(painCave.errMsg, |
451 |
|
|
"DumpWriter error: atoms start index (%d) for " |
452 |
|
|
"node %d not equal to master index (%d)", |
453 |
|
|
nodeAtomsStart,procIndex,masterIndex ); |
454 |
|
|
painCave.isFatal = 1; |
455 |
|
|
simError(); |
456 |
mmeineke |
184 |
} |
457 |
mmeineke |
214 |
|
458 |
|
|
sendError = 0; |
459 |
|
|
mpiErr = MPI_Send(&sendError,1,MPI_INT,procIndex,MPI_ANY_TAG, |
460 |
|
|
MPI_COMM_WORLD); |
461 |
|
|
|
462 |
|
|
// recieve the nodes writeLines |
463 |
|
|
|
464 |
chuckv |
254 |
for ( i = nodeAtomsStart; i <= nodeAtomsEnd; i++){ |
465 |
mmeineke |
214 |
|
466 |
chuckv |
254 |
mpiErr = MPI_Recv(writeLine,BUFFERSIZE,MPI_CHAR,procIndex, |
467 |
mmeineke |
214 |
MPI_ANY_TAG,MPI_COMM_WORLD,istatus ); |
468 |
|
|
|
469 |
|
|
finalOut << writeLine; |
470 |
|
|
masterIndex++; |
471 |
mmeineke |
184 |
} |
472 |
mmeineke |
214 |
|
473 |
|
|
finalOut.flush(); |
474 |
mmeineke |
10 |
} |
475 |
mmeineke |
214 |
|
476 |
|
|
else if( worldRank == procIndex ){ |
477 |
|
|
|
478 |
chuckv |
254 |
nodeAtomsStart = mpiSim->getMyAtomStart(); |
479 |
|
|
nodeAtomsEnd = mpiSim->getMyAtomEnd(); |
480 |
mmeineke |
214 |
|
481 |
|
|
mpiErr = MPI_Send(&nodeAtomsStart,1,MPI_INT,0,MPI_ANY_TAG, |
482 |
|
|
MPI_COMM_WORLD); |
483 |
|
|
mpiErr = MPI_Send(&nodeAtomsEnd,1,MPI_INT,0,MPI_ANY_TAG, |
484 |
|
|
MPI_COMM_WORLD); |
485 |
|
|
|
486 |
|
|
mpiErr = MPI_Recv(&sendError,1,MPI_INT,0,MPI_ANY_TAG, |
487 |
|
|
MPI_COMM_WORLD, istatus); |
488 |
chuckv |
254 |
if (sendError) MPIcheckPoint(); |
489 |
mmeineke |
214 |
|
490 |
|
|
// send current node's configuration line by line. |
491 |
|
|
|
492 |
|
|
for( i=0; i<nAtoms; i++ ){ |
493 |
|
|
|
494 |
|
|
sprintf( tempBuffer, |
495 |
|
|
"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", |
496 |
|
|
atoms[i]->getType(), |
497 |
|
|
atoms[i]->getX(), |
498 |
|
|
atoms[i]->getY(), |
499 |
|
|
atoms[i]->getZ(), |
500 |
|
|
atoms[i]->get_vx(), |
501 |
|
|
atoms[i]->get_vy(), |
502 |
|
|
atoms[i]->get_vz()); |
503 |
|
|
strcpy( writeLine, tempBuffer ); |
504 |
|
|
|
505 |
|
|
if( atoms[i]->isDirectional() ){ |
506 |
|
|
|
507 |
|
|
dAtom = (DirectionalAtom *)atoms[i]; |
508 |
|
|
dAtom->getQ( q ); |
509 |
|
|
|
510 |
|
|
sprintf( tempBuffer, |
511 |
|
|
"%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n", |
512 |
|
|
q[0], |
513 |
|
|
q[1], |
514 |
|
|
q[2], |
515 |
|
|
q[3], |
516 |
|
|
dAtom->getJx(), |
517 |
|
|
dAtom->getJy(), |
518 |
|
|
dAtom->getJz()); |
519 |
|
|
strcat( writeLine, tempBuffer ); |
520 |
|
|
} |
521 |
|
|
else |
522 |
|
|
strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" ); |
523 |
|
|
|
524 |
|
|
mpiErr = MPI_Send(writeLine,BUFFERSIZE,MPI_CHAR,0,MPI_ANY_TAG, |
525 |
|
|
MPI_COMM_WORLD); |
526 |
|
|
} |
527 |
|
|
} |
528 |
|
|
|
529 |
|
|
sprintf(checkPointMsg,"Node %d sent dump configuration.", |
530 |
|
|
procIndex); |
531 |
chuckv |
254 |
MPIcheckPoint(); |
532 |
mmeineke |
214 |
} |
533 |
|
|
|
534 |
|
|
if( worldRank == 0 ) finalOut.close(); |
535 |
|
|
|
536 |
mmeineke |
184 |
|
537 |
|
|
#endif // is_mpi |
538 |
mmeineke |
10 |
} |