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#include <cstring> |
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#include <iostream> |
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#include <fstream> |
4 |
|
5 |
#ifdef IS_MPI |
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#include <mpi.h> |
7 |
#include "mpiSimulation.hpp" |
8 |
#endif //is_mpi |
9 |
|
10 |
#include "ReadWrite.hpp" |
11 |
#include "simError.h" |
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|
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|
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|
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|
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|
17 |
DumpWriter::DumpWriter( SimInfo* the_entry_plug ){ |
18 |
|
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#ifdef IS_MPI |
20 |
if(worldRank == 0 ){ |
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#endif // is_mpi |
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|
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entry_plug = the_entry_plug; |
24 |
|
25 |
strcpy( outName, entry_plug->sampleName ); |
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|
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std::cerr << "Opening " << outName << " for dumping.\n"; |
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|
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outFile.open(outName, ios::out | ios::trunc ); |
30 |
|
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if( !outFile ){ |
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|
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sprintf( painCave.errMsg, |
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"Could not open \"%s\" for dump output.\n", |
35 |
outName); |
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painCave.isFatal = 1; |
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simError(); |
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} |
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|
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//outFile.setf( ios::scientific ); |
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|
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#ifdef IS_MPI |
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} |
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#endif // is_mpi |
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} |
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|
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DumpWriter::~DumpWriter( ){ |
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|
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#ifdef IS_MPI |
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if(worldRank == 0 ){ |
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#endif // is_mpi |
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|
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outFile.close(); |
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|
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#ifdef IS_MPI |
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} |
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#endif // is_mpi |
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} |
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|
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void DumpWriter::writeDump( double currentTime ){ |
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|
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const int BUFFERSIZE = 2000; |
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char tempBuffer[500]; |
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char writeLine[BUFFERSIZE]; |
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|
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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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|
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|
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#ifndef IS_MPI |
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|
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outFile << nAtoms << "\n"; |
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|
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outFile << currentTime << "\t" |
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<< entry_plug->box_x << "\t" |
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<< entry_plug->box_y << "\t" |
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<< entry_plug->box_z << "\n"; |
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|
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for( i=0; i<nAtoms; i++ ){ |
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|
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sprintf( tempBuffer, |
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"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", |
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atoms[i]->getType(), |
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atoms[i]->getX(), |
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atoms[i]->getY(), |
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atoms[i]->getZ(), |
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atoms[i]->get_vx(), |
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atoms[i]->get_vy(), |
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atoms[i]->get_vz()); |
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strcpy( writeLine, tempBuffer ); |
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|
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if( atoms[i]->isDirectional() ){ |
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|
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dAtom = (DirectionalAtom *)atoms[i]; |
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dAtom->getQ( q ); |
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|
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sprintf( tempBuffer, |
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"%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n", |
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q[0], |
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q[1], |
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q[2], |
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q[3], |
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dAtom->getJx(), |
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dAtom->getJy(), |
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dAtom->getJz()); |
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strcat( writeLine, tempBuffer ); |
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} |
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else |
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strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" ); |
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|
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outFile << writeLine; |
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} |
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outFile.flush(); |
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|
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#else // is_mpi |
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|
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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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|
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MPI_Status istatus[MPI_STATUS_SIZE]; |
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|
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|
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// write out header and node 0's coordinates |
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|
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if( worldRank == 0 ){ |
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outFile << entry_plug->mpiSim->getTotAtoms() << "\n"; |
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|
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outFile << currentTime << "\t" |
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<< entry_plug->box_x << "\t" |
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<< entry_plug->box_y << "\t" |
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<< entry_plug->box_z << "\n"; |
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|
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masterIndex = 0; |
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for( i=0; i<nAtoms; i++ ){ |
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|
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sprintf( tempBuffer, |
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"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", |
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atoms[i]->getType(), |
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atoms[i]->getX(), |
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atoms[i]->getY(), |
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atoms[i]->getZ(), |
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atoms[i]->get_vx(), |
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atoms[i]->get_vy(), |
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atoms[i]->get_vz()); |
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strcpy( writeLine, tempBuffer ); |
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|
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if( atoms[i]->isDirectional() ){ |
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|
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dAtom = (DirectionalAtom *)atoms[i]; |
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dAtom->getQ( q ); |
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|
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sprintf( tempBuffer, |
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"%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n", |
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q[0], |
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q[1], |
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q[2], |
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q[3], |
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dAtom->getJx(), |
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dAtom->getJy(), |
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dAtom->getJz()); |
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strcat( writeLine, tempBuffer ); |
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} |
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else |
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strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" ); |
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|
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outfile << writeLine; |
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masterIndex++; |
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} |
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outFile.flush(); |
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} |
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|
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for (procIndex = 1; procIndex < entry_plug->mpiSim->getNumberProcessors(); |
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procIndex++){ |
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|
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if( worldRank == 0 ){ |
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|
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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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|
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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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|
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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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|
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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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} |
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|
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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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|
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// recieve the nodes writeLines |
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|
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for ( i = nodeAtomStart; i <= nodeAtomEnd, i++){ |
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|
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mpiErr = MPI_Recv(&read_buffer,BUFFERSIZE,MPI_CHAR,procIndex, |
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MPI_ANY_TAG,MPI_COMM_WORLD,istatus ); |
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|
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outFile << writeLine; |
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masterIndex++; |
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} |
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} |
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|
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else if( worldRank == procIndex ){ |
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|
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nodeAtomStart = entry_plug->mpiSim->getMyAtomStart(); |
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nodeAtomEnd = entry_plug->mpiSim->getMyAtomEnd(); |
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|
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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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|
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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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if (sendError) mpiCheckpoint(); |
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|
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// send current node's configuration line by line. |
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|
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for( i=0; i<nAtoms; i++ ){ |
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|
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sprintf( tempBuffer, |
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"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", |
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atoms[i]->getType(), |
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atoms[i]->getX(), |
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atoms[i]->getY(), |
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atoms[i]->getZ(), |
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atoms[i]->get_vx(), |
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atoms[i]->get_vy(), |
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atoms[i]->get_vz()); |
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strcpy( writeLine, tempBuffer ); |
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|
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if( atoms[i]->isDirectional() ){ |
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|
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dAtom = (DirectionalAtom *)atoms[i]; |
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dAtom->getQ( q ); |
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|
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sprintf( tempBuffer, |
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"%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n", |
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q[0], |
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q[1], |
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q[2], |
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q[3], |
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dAtom->getJx(), |
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dAtom->getJy(), |
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dAtom->getJz()); |
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strcat( writeLine, tempBuffer ); |
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} |
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else |
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strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" ); |
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|
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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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|
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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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|
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#endif // is_mpi |
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} |
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|
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|
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|
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void DumpWriter::writeFinal(){ |
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|
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|
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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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|
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char finalName[500]; |
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|
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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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|
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ofstream finalOut; |
300 |
|
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#ifdef IS_MPI |
302 |
if(worldRank == 0 ){ |
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#endif // is_mpi |
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|
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strcpy( finalName, entry_plug->finalName ); |
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|
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finalOut.open( finalName, ios::out | ios::trunc ); |
308 |
if( !finalOut ){ |
309 |
sprintf( painCave.errMsg, |
310 |
"Could not open \"%s\" for final dump output.\n", |
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finalName ); |
312 |
painCave.isFatal = 1; |
313 |
simError(); |
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} |
315 |
|
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// finalOut.setf( ios::scientific ); |
317 |
|
318 |
#ifdef IS_MPI |
319 |
} |
320 |
|
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sprintf(checkPointMsg,"Opened file for final configuration\n",procIndex); |
322 |
mpiCheckPoint(); |
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|
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#endif //is_mpi |
325 |
|
326 |
|
327 |
|
328 |
#ifndef IS_MPI |
329 |
|
330 |
finalOut << nAtoms << "\n"; |
331 |
|
332 |
finalOut << entry_plug->box_x << "\t" |
333 |
<< entry_plug->box_y << "\t" |
334 |
<< entry_plug->box_z << "\n"; |
335 |
|
336 |
for( i=0; i<nAtoms; i++ ){ |
337 |
|
338 |
sprintf( tempBuffer, |
339 |
"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", |
340 |
atoms[i]->getType(), |
341 |
atoms[i]->getX(), |
342 |
atoms[i]->getY(), |
343 |
atoms[i]->getZ(), |
344 |
atoms[i]->get_vx(), |
345 |
atoms[i]->get_vy(), |
346 |
atoms[i]->get_vz()); |
347 |
strcpy( writeLine, tempBuffer ); |
348 |
|
349 |
if( atoms[i]->isDirectional() ){ |
350 |
|
351 |
dAtom = (DirectionalAtom *)atoms[i]; |
352 |
dAtom->getQ( q ); |
353 |
|
354 |
sprintf( tempBuffer, |
355 |
"%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n", |
356 |
q[0], |
357 |
q[1], |
358 |
q[2], |
359 |
q[3], |
360 |
dAtom->getJx(), |
361 |
dAtom->getJy(), |
362 |
dAtom->getJz()); |
363 |
strcat( writeLine, tempBuffer ); |
364 |
} |
365 |
else |
366 |
strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" ); |
367 |
|
368 |
finalOut << writeLine; |
369 |
} |
370 |
finalOut.flush(); |
371 |
|
372 |
#else // is_mpi |
373 |
|
374 |
int masterIndex; |
375 |
int nodeAtomsStart; |
376 |
int nodeAtomsEnd; |
377 |
int mpiErr; |
378 |
int sendError; |
379 |
int procIndex; |
380 |
|
381 |
MPI_Status istatus[MPI_STATUS_SIZE]; |
382 |
|
383 |
|
384 |
// write out header and node 0's coordinates |
385 |
|
386 |
if( worldRank == 0 ){ |
387 |
finalOut << entry_plug->mpiSim->getTotAtoms() << "\n"; |
388 |
|
389 |
finalOut << entry_plug->box_x << "\t" |
390 |
<< entry_plug->box_y << "\t" |
391 |
<< entry_plug->box_z << "\n"; |
392 |
|
393 |
masterIndex = 0; |
394 |
for( i=0; i<nAtoms; i++ ){ |
395 |
|
396 |
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 |
if( atoms[i]->isDirectional() ){ |
408 |
|
409 |
dAtom = (DirectionalAtom *)atoms[i]; |
410 |
dAtom->getQ( q ); |
411 |
|
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 |
|
426 |
outfile << writeLine; |
427 |
masterIndex++; |
428 |
} |
429 |
finalOut.flush(); |
430 |
} |
431 |
|
432 |
for (procIndex = 1; procIndex < entry_plug->mpiSim->getNumberProcessors(); |
433 |
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 |
} |
457 |
|
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 |
for ( i = nodeAtomStart; i <= nodeAtomEnd, i++){ |
465 |
|
466 |
mpiErr = MPI_Recv(&read_buffer,BUFFERSIZE,MPI_CHAR,procIndex, |
467 |
MPI_ANY_TAG,MPI_COMM_WORLD,istatus ); |
468 |
|
469 |
finalOut << writeLine; |
470 |
masterIndex++; |
471 |
} |
472 |
|
473 |
finalOut.flush(); |
474 |
} |
475 |
|
476 |
else if( worldRank == procIndex ){ |
477 |
|
478 |
nodeAtomStart = entry_plug->mpiSim->getMyAtomStart(); |
479 |
nodeAtomEnd = entry_plug->mpiSim->getMyAtomEnd(); |
480 |
|
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 |
if (sendError) mpiCheckpoint(); |
489 |
|
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 |
mpiCheckPoint(); |
532 |
} |
533 |
|
534 |
if( worldRank == 0 ) finalOut.close(); |
535 |
|
536 |
|
537 |
#endif // is_mpi |
538 |
} |