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mmeineke |
377 |
#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(){ |
297 |
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298 |
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299 |
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const int BUFFERSIZE = 2000; |
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char tempBuffer[500]; |
301 |
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char writeLine[BUFFERSIZE]; |
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char finalName[500]; |
304 |
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305 |
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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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313 |
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#ifdef IS_MPI |
314 |
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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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330 |
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#ifdef IS_MPI |
331 |
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} |
332 |
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333 |
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sprintf(checkPointMsg,"Opened file for final configuration\n"); |
334 |
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MPIcheckPoint(); |
335 |
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#endif //is_mpi |
337 |
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338 |
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339 |
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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], |
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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" ); |
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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 |
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|
395 |
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396 |
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// write out header and node 0's coordinates |
397 |
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398 |
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if( worldRank == 0 ){ |
399 |
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finalOut << mpiSim->getTotAtoms() << "\n"; |
400 |
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401 |
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finalOut << entry_plug->box_x << "\t" |
402 |
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<< entry_plug->box_y << "\t" |
403 |
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<< entry_plug->box_z << "\n"; |
404 |
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405 |
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masterIndex = 0; |
406 |
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407 |
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for( i=0; i<nAtoms; i++ ){ |
408 |
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409 |
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sprintf( tempBuffer, |
410 |
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"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", |
411 |
|
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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 |
|
|
} |