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#include <cstring> |
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#define _LARGEFILE_SOURCE64 |
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#define _FILE_OFFSET_BITS 64 |
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|
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#include <string.h> |
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#include <iostream> |
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#include <fstream> |
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#include <algorithm> |
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#include <utility> |
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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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|
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namespace dWrite{ |
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void DieDieDie( void ); |
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} |
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|
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using namespace dWrite; |
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#endif //is_mpi |
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|
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#include "ReadWrite.hpp" |
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#include "simError.h" |
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|
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|
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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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|
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|
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|
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strcpy( outName, entry_plug->sampleName ); |
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|
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outFile.open(outName, ios::out | ios::trunc ); |
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|
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if( !outFile ){ |
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|
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|
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dumpFile.open(entry_plug->sampleName, ios::out | ios::trunc ); |
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|
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if( !dumpFile ){ |
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|
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sprintf( painCave.errMsg, |
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"Could not open \"%s\" for dump output.\n", |
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outName); |
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entry_plug->sampleName); |
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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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#ifdef IS_MPI |
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} |
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|
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//sort the local atoms by global index |
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sortByGlobalIndex(); |
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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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if(worldRank == 0 ){ |
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#endif // is_mpi |
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|
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outFile.close(); |
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dumpFile.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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#ifdef IS_MPI |
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|
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/** |
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* A hook function to load balancing |
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*/ |
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|
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void DumpWriter::update(){ |
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sortByGlobalIndex(); |
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} |
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|
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const int BUFFERSIZE = 2000; |
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char tempBuffer[BUFFERSIZE]; |
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char writeLine[BUFFERSIZE]; |
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/** |
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* Auxiliary sorting function |
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*/ |
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|
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bool indexSortingCriterion(const pair<int, int>& p1, const pair<int, int>& p2){ |
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return p1.second < p2.second; |
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} |
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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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/** |
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* Sorting the local index by global index |
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*/ |
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|
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void DumpWriter::sortByGlobalIndex(){ |
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Atom** atoms = entry_plug->atoms; |
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|
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|
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indexArray.clear(); |
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|
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for(int i = 0; i < mpiSim->getMyNlocal();i++) |
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indexArray.push_back(make_pair(i, atoms[i]->getGlobalIndex())); |
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|
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sort(indexArray.begin(), indexArray.end(), indexSortingCriterion); |
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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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#endif |
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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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void DumpWriter::writeDump(double currentTime){ |
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|
105 |
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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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ofstream finalOut; |
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vector<ofstream*> fileStreams; |
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|
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#ifdef IS_MPI |
109 |
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if(worldRank == 0 ){ |
110 |
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#endif |
111 |
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finalOut.open( entry_plug->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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entry_plug->finalName ); |
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painCave.isFatal = 1; |
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simError(); |
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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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#ifdef IS_MPI |
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} |
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outFile.flush(); |
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#endif // is_mpi |
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|
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#else // is_mpi |
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fileStreams.push_back(&finalOut); |
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fileStreams.push_back(&dumpFile); |
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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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writeFrame(fileStreams, currentTime); |
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|
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|
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// write out header and node 0's coordinates |
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#ifdef IS_MPI |
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finalOut.close(); |
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#endif |
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|
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} |
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|
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if( worldRank == 0 ){ |
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outFile << mpiSim->getTotAtoms() << "\n"; |
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|
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outFile << currentTime << "\t" |
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<< entry_plug->box_x << "\t" |
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<< entry_plug->box_y << "\t" |
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<< entry_plug->box_z << "\n"; |
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void DumpWriter::writeFinal(double currentTime){ |
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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(), |
155 |
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atoms[i]->get_vx(), |
156 |
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atoms[i]->get_vy(), |
157 |
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atoms[i]->get_vz()); |
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strcpy( writeLine, tempBuffer ); |
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|
160 |
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if( atoms[i]->isDirectional() ){ |
161 |
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|
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dAtom = (DirectionalAtom *)atoms[i]; |
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dAtom->getQ( q ); |
164 |
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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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ofstream finalOut; |
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vector<ofstream*> fileStreams; |
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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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|
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for (procIndex = 1; procIndex < mpiSim->getNumberProcessors(); |
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procIndex++){ |
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#ifdef IS_MPI |
140 |
> |
if(worldRank == 0 ){ |
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#endif // is_mpi |
142 |
|
|
143 |
< |
if( worldRank == 0 ){ |
193 |
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|
194 |
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mpiErr = MPI_Recv(&nodeAtomsStart,1,MPI_INT,procIndex, |
195 |
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TAKE_THIS_TAG,MPI_COMM_WORLD,istatus); |
196 |
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|
197 |
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mpiErr = MPI_Recv(&nodeAtomsEnd,1,MPI_INT,procIndex, |
198 |
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TAKE_THIS_TAG,MPI_COMM_WORLD, istatus); |
199 |
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|
200 |
< |
// Make sure where node 0 is writing to, matches where the |
201 |
< |
// receiving node expects it to be. |
202 |
< |
|
203 |
< |
if (masterIndex != nodeAtomsStart){ |
204 |
< |
sendError = 1; |
205 |
< |
mpiErr = MPI_Send(&sendError,1,MPI_INT,procIndex,TAKE_THIS_TAG, |
206 |
< |
MPI_COMM_WORLD); |
207 |
< |
sprintf(painCave.errMsg, |
208 |
< |
"DumpWriter error: atoms start index (%d) for " |
209 |
< |
"node %d not equal to master index (%d)", |
210 |
< |
nodeAtomsStart,procIndex,masterIndex ); |
211 |
< |
painCave.isFatal = 1; |
212 |
< |
simError(); |
213 |
< |
} |
214 |
< |
|
215 |
< |
sendError = 0; |
216 |
< |
mpiErr = MPI_Send(&sendError,1,MPI_INT,procIndex,TAKE_THIS_TAG, |
217 |
< |
MPI_COMM_WORLD); |
218 |
< |
|
219 |
< |
// recieve the nodes writeLines |
220 |
< |
|
221 |
< |
for ( i = nodeAtomsStart; i <= nodeAtomsEnd; i++){ |
222 |
< |
|
223 |
< |
mpiErr = MPI_Recv(writeLine,BUFFERSIZE,MPI_CHAR,procIndex, |
224 |
< |
TAKE_THIS_TAG,MPI_COMM_WORLD,istatus ); |
225 |
< |
|
226 |
< |
outFile << writeLine; |
227 |
< |
masterIndex++; |
228 |
< |
} |
229 |
< |
} |
143 |
> |
finalOut.open( entry_plug->finalName, ios::out | ios::trunc ); |
144 |
|
|
145 |
< |
else if( worldRank == procIndex ){ |
146 |
< |
|
147 |
< |
nodeAtomsStart = mpiSim->getMyAtomStart(); |
148 |
< |
nodeAtomsEnd = mpiSim->getMyAtomEnd(); |
149 |
< |
|
150 |
< |
mpiErr = MPI_Send(&nodeAtomsStart,1,MPI_INT,0,TAKE_THIS_TAG, |
237 |
< |
MPI_COMM_WORLD); |
238 |
< |
mpiErr = MPI_Send(&nodeAtomsEnd,1,MPI_INT,0,TAKE_THIS_TAG, |
239 |
< |
MPI_COMM_WORLD); |
240 |
< |
|
241 |
< |
sendError = -1; |
242 |
< |
mpiErr = MPI_Recv(&sendError,1,MPI_INT,0,TAKE_THIS_TAG, |
243 |
< |
MPI_COMM_WORLD, istatus); |
244 |
< |
|
245 |
< |
if (sendError) MPIcheckPoint(); |
246 |
< |
|
247 |
< |
// send current node's configuration line by line. |
248 |
< |
|
249 |
< |
for( i=0; i<nAtoms; i++ ){ |
250 |
< |
|
251 |
< |
sprintf( tempBuffer, |
252 |
< |
"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", |
253 |
< |
atoms[i]->getType(), |
254 |
< |
atoms[i]->getX(), |
255 |
< |
atoms[i]->getY(), |
256 |
< |
atoms[i]->getZ(), |
257 |
< |
atoms[i]->get_vx(), |
258 |
< |
atoms[i]->get_vy(), |
259 |
< |
atoms[i]->get_vz()); // check here. |
260 |
< |
strcpy( writeLine, tempBuffer ); |
261 |
< |
|
262 |
< |
if( atoms[i]->isDirectional() ){ |
263 |
< |
|
264 |
< |
dAtom = (DirectionalAtom *)atoms[i]; |
265 |
< |
dAtom->getQ( q ); |
266 |
< |
|
267 |
< |
sprintf( tempBuffer, |
268 |
< |
"%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n", |
269 |
< |
q[0], |
270 |
< |
q[1], |
271 |
< |
q[2], |
272 |
< |
q[3], |
273 |
< |
dAtom->getJx(), |
274 |
< |
dAtom->getJy(), |
275 |
< |
dAtom->getJz()); |
276 |
< |
strcat( writeLine, tempBuffer ); |
277 |
< |
} |
278 |
< |
else |
279 |
< |
strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" ); |
280 |
< |
|
281 |
< |
mpiErr = MPI_Send(writeLine,BUFFERSIZE,MPI_CHAR,0,TAKE_THIS_TAG, |
282 |
< |
MPI_COMM_WORLD); |
283 |
< |
} |
145 |
> |
if( !finalOut ){ |
146 |
> |
sprintf( painCave.errMsg, |
147 |
> |
"Could not open \"%s\" for final dump output.\n", |
148 |
> |
entry_plug->finalName ); |
149 |
> |
painCave.isFatal = 1; |
150 |
> |
simError(); |
151 |
|
} |
152 |
< |
|
153 |
< |
sprintf(checkPointMsg,"Node %d sent dump configuration.", |
287 |
< |
procIndex); |
288 |
< |
MPIcheckPoint(); |
152 |
> |
|
153 |
> |
#ifdef IS_MPI |
154 |
|
} |
290 |
– |
|
155 |
|
#endif // is_mpi |
156 |
+ |
|
157 |
+ |
fileStreams.push_back(&finalOut); |
158 |
+ |
writeFrame(fileStreams, currentTime); |
159 |
+ |
|
160 |
+ |
#ifdef IS_MPI |
161 |
+ |
finalOut.close(); |
162 |
+ |
#endif |
163 |
+ |
|
164 |
|
} |
165 |
|
|
166 |
+ |
void DumpWriter::writeFrame( vector<ofstream*>& outFile, double currentTime ){ |
167 |
|
|
168 |
+ |
const int BUFFERSIZE = 2000; |
169 |
+ |
const int MINIBUFFERSIZE = 100; |
170 |
|
|
171 |
< |
void DumpWriter::writeFinal(){ |
171 |
> |
char tempBuffer[BUFFERSIZE]; |
172 |
> |
char writeLine[BUFFERSIZE]; |
173 |
|
|
174 |
+ |
int i, k; |
175 |
|
|
176 |
< |
const int BUFFERSIZE = 2000; |
300 |
< |
char tempBuffer[500]; |
301 |
< |
char writeLine[BUFFERSIZE]; |
176 |
> |
#ifdef IS_MPI |
177 |
|
|
178 |
< |
char finalName[500]; |
178 |
> |
/********************************************************************* |
179 |
> |
* Documentation? You want DOCUMENTATION? |
180 |
> |
* |
181 |
> |
* Why all the potatoes below? |
182 |
> |
* |
183 |
> |
* To make a long story short, the original version of DumpWriter |
184 |
> |
* worked in the most inefficient way possible. Node 0 would |
185 |
> |
* poke each of the node for an individual atom's formatted data |
186 |
> |
* as node 0 worked its way down the global index. This was particularly |
187 |
> |
* inefficient since the method blocked all processors at every atom |
188 |
> |
* (and did it twice!). |
189 |
> |
* |
190 |
> |
* An intermediate version of DumpWriter could be described from Node |
191 |
> |
* zero's perspective as follows: |
192 |
> |
* |
193 |
> |
* 1) Have 100 of your friends stand in a circle. |
194 |
> |
* 2) When you say go, have all of them start tossing potatoes at |
195 |
> |
* you (one at a time). |
196 |
> |
* 3) Catch the potatoes. |
197 |
> |
* |
198 |
> |
* It was an improvement, but MPI has buffers and caches that could |
199 |
> |
* best be described in this analogy as "potato nets", so there's no |
200 |
> |
* need to block the processors atom-by-atom. |
201 |
> |
* |
202 |
> |
* This new and improved DumpWriter works in an even more efficient |
203 |
> |
* way: |
204 |
> |
* |
205 |
> |
* 1) Have 100 of your friend stand in a circle. |
206 |
> |
* 2) When you say go, have them start tossing 5-pound bags of |
207 |
> |
* potatoes at you. |
208 |
> |
* 3) Once you've caught a friend's bag of potatoes, |
209 |
> |
* toss them a spud to let them know they can toss another bag. |
210 |
> |
* |
211 |
> |
* How's THAT for documentation? |
212 |
> |
* |
213 |
> |
*********************************************************************/ |
214 |
|
|
215 |
< |
int i; |
215 |
> |
int *potatoes; |
216 |
> |
int myPotato; |
217 |
> |
|
218 |
> |
int nProc; |
219 |
> |
int j, which_node, done, which_atom, local_index, currentIndex; |
220 |
> |
double atomData6[6]; |
221 |
> |
double atomData13[13]; |
222 |
> |
int isDirectional; |
223 |
> |
char* atomTypeString; |
224 |
> |
char MPIatomTypeString[MINIBUFFERSIZE]; |
225 |
> |
|
226 |
> |
#else //is_mpi |
227 |
> |
int nAtoms = entry_plug->n_atoms; |
228 |
> |
#endif //is_mpi |
229 |
> |
|
230 |
|
double q[4]; |
231 |
|
DirectionalAtom* dAtom; |
308 |
– |
int nAtoms = entry_plug->n_atoms; |
232 |
|
Atom** atoms = entry_plug->atoms; |
233 |
+ |
double pos[3], vel[3]; |
234 |
+ |
|
235 |
+ |
#ifndef IS_MPI |
236 |
|
|
237 |
< |
ofstream finalOut; |
238 |
< |
|
239 |
< |
#ifdef IS_MPI |
240 |
< |
if(worldRank == 0 ){ |
241 |
< |
#endif // is_mpi |
242 |
< |
|
243 |
< |
strcpy( finalName, entry_plug->finalName ); |
244 |
< |
|
245 |
< |
finalOut.open( finalName, ios::out | ios::trunc ); |
246 |
< |
if( !finalOut ){ |
247 |
< |
sprintf( painCave.errMsg, |
248 |
< |
"Could not open \"%s\" for final dump output.\n", |
249 |
< |
finalName ); |
250 |
< |
painCave.isFatal = 1; |
251 |
< |
simError(); |
252 |
< |
} |
253 |
< |
|
254 |
< |
// finalOut.setf( ios::scientific ); |
329 |
< |
|
330 |
< |
#ifdef IS_MPI |
237 |
> |
for(k = 0; k < outFile.size(); k++){ |
238 |
> |
*outFile[k] << nAtoms << "\n"; |
239 |
> |
|
240 |
> |
*outFile[k] << currentTime << ";\t" |
241 |
> |
<< entry_plug->Hmat[0][0] << "\t" |
242 |
> |
<< entry_plug->Hmat[1][0] << "\t" |
243 |
> |
<< entry_plug->Hmat[2][0] << ";\t" |
244 |
> |
|
245 |
> |
<< entry_plug->Hmat[0][1] << "\t" |
246 |
> |
<< entry_plug->Hmat[1][1] << "\t" |
247 |
> |
<< entry_plug->Hmat[2][1] << ";\t" |
248 |
> |
|
249 |
> |
<< entry_plug->Hmat[0][2] << "\t" |
250 |
> |
<< entry_plug->Hmat[1][2] << "\t" |
251 |
> |
<< entry_plug->Hmat[2][2] << ";"; |
252 |
> |
|
253 |
> |
//write out additional parameters, such as chi and eta |
254 |
> |
*outFile[k] << entry_plug->the_integrator->getAdditionalParameters() << endl; |
255 |
|
} |
256 |
|
|
257 |
< |
sprintf(checkPointMsg,"Opened file for final configuration\n"); |
334 |
< |
MPIcheckPoint(); |
335 |
< |
|
336 |
< |
#endif //is_mpi |
257 |
> |
for( i=0; i<nAtoms; i++ ){ |
258 |
|
|
259 |
< |
|
259 |
> |
atoms[i]->getPos(pos); |
260 |
> |
atoms[i]->getVel(vel); |
261 |
|
|
340 |
– |
#ifndef IS_MPI |
341 |
– |
|
342 |
– |
finalOut << nAtoms << "\n"; |
343 |
– |
|
344 |
– |
finalOut << entry_plug->box_x << "\t" |
345 |
– |
<< entry_plug->box_y << "\t" |
346 |
– |
<< entry_plug->box_z << "\n"; |
347 |
– |
|
348 |
– |
for( i=0; i<nAtoms; i++ ){ |
349 |
– |
|
262 |
|
sprintf( tempBuffer, |
263 |
|
"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", |
264 |
|
atoms[i]->getType(), |
265 |
< |
atoms[i]->getX(), |
266 |
< |
atoms[i]->getY(), |
267 |
< |
atoms[i]->getZ(), |
268 |
< |
atoms[i]->get_vx(), |
269 |
< |
atoms[i]->get_vy(), |
270 |
< |
atoms[i]->get_vz()); |
265 |
> |
pos[0], |
266 |
> |
pos[1], |
267 |
> |
pos[2], |
268 |
> |
vel[0], |
269 |
> |
vel[1], |
270 |
> |
vel[2]); |
271 |
|
strcpy( writeLine, tempBuffer ); |
272 |
|
|
273 |
|
if( atoms[i]->isDirectional() ){ |
274 |
< |
|
274 |
> |
|
275 |
|
dAtom = (DirectionalAtom *)atoms[i]; |
276 |
|
dAtom->getQ( q ); |
277 |
< |
|
277 |
> |
|
278 |
|
sprintf( tempBuffer, |
279 |
|
"%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n", |
280 |
|
q[0], |
288 |
|
} |
289 |
|
else |
290 |
|
strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" ); |
291 |
< |
|
292 |
< |
finalOut << writeLine; |
291 |
> |
|
292 |
> |
for(k = 0; k < outFile.size(); k++) |
293 |
> |
*outFile[k] << writeLine; |
294 |
|
} |
382 |
– |
finalOut.flush(); |
295 |
|
|
296 |
|
#else // is_mpi |
297 |
|
|
298 |
< |
int masterIndex; |
299 |
< |
int nodeAtomsStart; |
300 |
< |
int nodeAtomsEnd; |
301 |
< |
int mpiErr; |
302 |
< |
int sendError; |
303 |
< |
int procIndex; |
304 |
< |
|
305 |
< |
MPI_Status istatus[MPI_STATUS_SIZE]; |
298 |
> |
/* code to find maximum tag value */ |
299 |
> |
|
300 |
> |
int *tagub, flag, MAXTAG; |
301 |
> |
MPI_Attr_get(MPI_COMM_WORLD, MPI_TAG_UB, &tagub, &flag); |
302 |
> |
if (flag) { |
303 |
> |
MAXTAG = *tagub; |
304 |
> |
} else { |
305 |
> |
MAXTAG = 32767; |
306 |
> |
} |
307 |
|
|
308 |
< |
|
308 |
> |
int haveError; |
309 |
> |
|
310 |
> |
MPI_Status istatus; |
311 |
> |
int *AtomToProcMap = mpiSim->getAtomToProcMap(); |
312 |
> |
|
313 |
|
// write out header and node 0's coordinates |
314 |
|
|
315 |
|
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++){ |
316 |
|
|
317 |
< |
if( worldRank == 0 ){ |
449 |
< |
|
450 |
< |
mpiErr = MPI_Recv(&nodeAtomsStart,1,MPI_INT,procIndex, |
451 |
< |
TAKE_THIS_TAG,MPI_COMM_WORLD,istatus); |
317 |
> |
// Node 0 needs a list of the magic potatoes for each processor; |
318 |
|
|
319 |
< |
mpiErr = MPI_Recv(&nodeAtomsEnd,1,MPI_INT,procIndex, |
320 |
< |
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); |
319 |
> |
nProc = mpiSim->getNumberProcessors(); |
320 |
> |
potatoes = new int[nProc]; |
321 |
|
|
322 |
< |
// recieve the nodes writeLines |
322 |
> |
//write out the comment lines |
323 |
> |
for (i = 0; i < nProc; i++) |
324 |
> |
potatoes[i] = 0; |
325 |
> |
|
326 |
> |
for(k = 0; k < outFile.size(); k++){ |
327 |
> |
*outFile[k] << mpiSim->getTotAtoms() << "\n"; |
328 |
|
|
329 |
< |
for ( i = nodeAtomsStart; i <= nodeAtomsEnd; i++){ |
330 |
< |
|
331 |
< |
mpiErr = MPI_Recv(writeLine,BUFFERSIZE,MPI_CHAR,procIndex, |
332 |
< |
TAKE_THIS_TAG,MPI_COMM_WORLD,istatus ); |
329 |
> |
*outFile[k] << currentTime << ";\t" |
330 |
> |
<< entry_plug->Hmat[0][0] << "\t" |
331 |
> |
<< entry_plug->Hmat[1][0] << "\t" |
332 |
> |
<< entry_plug->Hmat[2][0] << ";\t" |
333 |
|
|
334 |
< |
finalOut << writeLine; |
335 |
< |
masterIndex++; |
336 |
< |
} |
334 |
> |
<< entry_plug->Hmat[0][1] << "\t" |
335 |
> |
<< entry_plug->Hmat[1][1] << "\t" |
336 |
> |
<< entry_plug->Hmat[2][1] << ";\t" |
337 |
|
|
338 |
< |
finalOut.flush(); |
338 |
> |
<< entry_plug->Hmat[0][2] << "\t" |
339 |
> |
<< entry_plug->Hmat[1][2] << "\t" |
340 |
> |
<< entry_plug->Hmat[2][2] << ";"; |
341 |
> |
|
342 |
> |
*outFile[k] << entry_plug->the_integrator->getAdditionalParameters() << endl; |
343 |
|
} |
344 |
|
|
345 |
< |
else if( worldRank == procIndex ){ |
345 |
> |
currentIndex = 0; |
346 |
|
|
347 |
< |
nodeAtomsStart = mpiSim->getMyAtomStart(); |
348 |
< |
nodeAtomsEnd = mpiSim->getMyAtomEnd(); |
347 |
> |
for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) { |
348 |
> |
|
349 |
> |
// Get the Node number which has this atom; |
350 |
> |
|
351 |
> |
which_node = AtomToProcMap[i]; |
352 |
> |
|
353 |
> |
if (which_node != 0) { |
354 |
> |
|
355 |
> |
if (potatoes[which_node] + 3 >= MAXTAG) { |
356 |
> |
// The potato was going to exceed the maximum value, |
357 |
> |
// so wrap this processor potato back to 0: |
358 |
> |
|
359 |
> |
potatoes[which_node] = 0; |
360 |
> |
MPI_Send(0, 1, MPI_INT, which_node, 0, MPI_COMM_WORLD); |
361 |
> |
|
362 |
> |
} |
363 |
> |
|
364 |
> |
myPotato = potatoes[which_node]; |
365 |
> |
|
366 |
> |
MPI_Recv(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, which_node, |
367 |
> |
myPotato, MPI_COMM_WORLD, &istatus); |
368 |
> |
|
369 |
> |
atomTypeString = MPIatomTypeString; |
370 |
|
|
371 |
< |
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(); |
371 |
> |
myPotato++; |
372 |
|
|
373 |
< |
// send current node's configuration line by line. |
373 |
> |
MPI_Recv(&isDirectional, 1, MPI_INT, which_node, |
374 |
> |
myPotato, MPI_COMM_WORLD, &istatus); |
375 |
> |
|
376 |
> |
myPotato++; |
377 |
|
|
378 |
< |
for( i=0; i<nAtoms; i++ ){ |
379 |
< |
|
380 |
< |
sprintf( tempBuffer, |
381 |
< |
"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", |
382 |
< |
atoms[i]->getType(), |
383 |
< |
atoms[i]->getX(), |
384 |
< |
atoms[i]->getY(), |
385 |
< |
atoms[i]->getZ(), |
386 |
< |
atoms[i]->get_vx(), |
387 |
< |
atoms[i]->get_vy(), |
388 |
< |
atoms[i]->get_vz()); |
389 |
< |
strcpy( writeLine, tempBuffer ); |
390 |
< |
|
391 |
< |
if( atoms[i]->isDirectional() ){ |
378 |
> |
if (isDirectional) { |
379 |
> |
MPI_Recv(atomData13, 13, MPI_DOUBLE, which_node, |
380 |
> |
myPotato, MPI_COMM_WORLD, &istatus); |
381 |
> |
} else { |
382 |
> |
MPI_Recv(atomData6, 6, MPI_DOUBLE, which_node, |
383 |
> |
myPotato, MPI_COMM_WORLD, &istatus); |
384 |
> |
} |
385 |
> |
|
386 |
> |
myPotato++; |
387 |
> |
potatoes[which_node] = myPotato; |
388 |
> |
|
389 |
> |
} else { |
390 |
> |
|
391 |
> |
haveError = 0; |
392 |
> |
which_atom = i; |
393 |
> |
|
394 |
> |
local_index = indexArray[currentIndex].first; |
395 |
> |
|
396 |
> |
if (which_atom == indexArray[currentIndex].second) { |
397 |
|
|
398 |
< |
dAtom = (DirectionalAtom *)atoms[i]; |
521 |
< |
dAtom->getQ( q ); |
398 |
> |
atomTypeString = atoms[local_index]->getType(); |
399 |
|
|
400 |
< |
sprintf( tempBuffer, |
401 |
< |
"%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" ); |
400 |
> |
atoms[local_index]->getPos(pos); |
401 |
> |
atoms[local_index]->getVel(vel); |
402 |
|
|
403 |
< |
mpiErr = MPI_Send(writeLine,BUFFERSIZE,MPI_CHAR,0,TAKE_THIS_TAG, |
404 |
< |
MPI_COMM_WORLD); |
403 |
> |
atomData6[0] = pos[0]; |
404 |
> |
atomData6[1] = pos[1]; |
405 |
> |
atomData6[2] = pos[2]; |
406 |
> |
|
407 |
> |
atomData6[3] = vel[0]; |
408 |
> |
atomData6[4] = vel[1]; |
409 |
> |
atomData6[5] = vel[2]; |
410 |
> |
|
411 |
> |
isDirectional = 0; |
412 |
> |
|
413 |
> |
if( atoms[local_index]->isDirectional() ){ |
414 |
> |
|
415 |
> |
isDirectional = 1; |
416 |
> |
|
417 |
> |
dAtom = (DirectionalAtom *)atoms[local_index]; |
418 |
> |
dAtom->getQ( q ); |
419 |
> |
|
420 |
> |
for (int j = 0; j < 6 ; j++) |
421 |
> |
atomData13[j] = atomData6[j]; |
422 |
> |
|
423 |
> |
atomData13[6] = q[0]; |
424 |
> |
atomData13[7] = q[1]; |
425 |
> |
atomData13[8] = q[2]; |
426 |
> |
atomData13[9] = q[3]; |
427 |
> |
|
428 |
> |
atomData13[10] = dAtom->getJx(); |
429 |
> |
atomData13[11] = dAtom->getJy(); |
430 |
> |
atomData13[12] = dAtom->getJz(); |
431 |
> |
} |
432 |
> |
|
433 |
> |
} else { |
434 |
> |
sprintf(painCave.errMsg, |
435 |
> |
"Atom %d not found on processor %d, currentIndex = %d, local_index = %d\n", |
436 |
> |
which_atom, worldRank, currentIndex, local_index ); |
437 |
> |
haveError= 1; |
438 |
> |
simError(); |
439 |
> |
} |
440 |
> |
|
441 |
> |
if(haveError) DieDieDie(); |
442 |
> |
|
443 |
> |
currentIndex++; |
444 |
|
} |
445 |
+ |
// If we've survived to here, format the line: |
446 |
+ |
|
447 |
+ |
if (!isDirectional) { |
448 |
+ |
|
449 |
+ |
sprintf( writeLine, |
450 |
+ |
"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", |
451 |
+ |
atomTypeString, |
452 |
+ |
atomData6[0], |
453 |
+ |
atomData6[1], |
454 |
+ |
atomData6[2], |
455 |
+ |
atomData6[3], |
456 |
+ |
atomData6[4], |
457 |
+ |
atomData6[5]); |
458 |
+ |
|
459 |
+ |
strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" ); |
460 |
+ |
|
461 |
+ |
} else { |
462 |
+ |
|
463 |
+ |
sprintf( writeLine, |
464 |
+ |
"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n", |
465 |
+ |
atomTypeString, |
466 |
+ |
atomData13[0], |
467 |
+ |
atomData13[1], |
468 |
+ |
atomData13[2], |
469 |
+ |
atomData13[3], |
470 |
+ |
atomData13[4], |
471 |
+ |
atomData13[5], |
472 |
+ |
atomData13[6], |
473 |
+ |
atomData13[7], |
474 |
+ |
atomData13[8], |
475 |
+ |
atomData13[9], |
476 |
+ |
atomData13[10], |
477 |
+ |
atomData13[11], |
478 |
+ |
atomData13[12]); |
479 |
+ |
|
480 |
+ |
} |
481 |
+ |
|
482 |
+ |
for(k = 0; k < outFile.size(); k++) |
483 |
+ |
*outFile[k] << writeLine; |
484 |
|
} |
485 |
+ |
|
486 |
+ |
for(k = 0; k < outFile.size(); k++) |
487 |
+ |
outFile[k]->flush(); |
488 |
+ |
|
489 |
+ |
sprintf( checkPointMsg, |
490 |
+ |
"Sucessfully took a dump.\n"); |
491 |
+ |
|
492 |
+ |
MPIcheckPoint(); |
493 |
+ |
|
494 |
+ |
delete[] potatoes; |
495 |
+ |
|
496 |
+ |
} else { |
497 |
+ |
|
498 |
+ |
// worldRank != 0, so I'm a remote node. |
499 |
+ |
|
500 |
+ |
// Set my magic potato to 0: |
501 |
+ |
|
502 |
+ |
myPotato = 0; |
503 |
+ |
currentIndex = 0; |
504 |
+ |
|
505 |
+ |
for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) { |
506 |
|
|
507 |
< |
sprintf(checkPointMsg,"Node %d sent dump configuration.", |
508 |
< |
procIndex); |
509 |
< |
MPIcheckPoint(); |
545 |
< |
} |
507 |
> |
// Am I the node which has this atom? |
508 |
> |
|
509 |
> |
if (AtomToProcMap[i] == worldRank) { |
510 |
|
|
511 |
< |
if( worldRank == 0 ) finalOut.close(); |
511 |
> |
if (myPotato + 3 >= MAXTAG) { |
512 |
> |
|
513 |
> |
// The potato was going to exceed the maximum value, |
514 |
> |
// so wrap this processor potato back to 0 (and block until |
515 |
> |
// node 0 says we can go: |
516 |
> |
|
517 |
> |
MPI_Recv(&myPotato, 1, MPI_INT, 0, 0, MPI_COMM_WORLD, &istatus); |
518 |
> |
|
519 |
> |
} |
520 |
> |
which_atom = i; |
521 |
|
|
522 |
+ |
local_index = indexArray[currentIndex].first; |
523 |
+ |
|
524 |
+ |
if (which_atom == indexArray[currentIndex].second) { |
525 |
+ |
|
526 |
+ |
atomTypeString = atoms[local_index]->getType(); |
527 |
+ |
|
528 |
+ |
atoms[local_index]->getPos(pos); |
529 |
+ |
atoms[local_index]->getVel(vel); |
530 |
+ |
|
531 |
+ |
atomData6[0] = pos[0]; |
532 |
+ |
atomData6[1] = pos[1]; |
533 |
+ |
atomData6[2] = pos[2]; |
534 |
+ |
|
535 |
+ |
atomData6[3] = vel[0]; |
536 |
+ |
atomData6[4] = vel[1]; |
537 |
+ |
atomData6[5] = vel[2]; |
538 |
+ |
|
539 |
+ |
isDirectional = 0; |
540 |
+ |
|
541 |
+ |
if( atoms[local_index]->isDirectional() ){ |
542 |
+ |
|
543 |
+ |
isDirectional = 1; |
544 |
+ |
|
545 |
+ |
dAtom = (DirectionalAtom *)atoms[local_index]; |
546 |
+ |
dAtom->getQ( q ); |
547 |
+ |
|
548 |
+ |
for (int j = 0; j < 6 ; j++) |
549 |
+ |
atomData13[j] = atomData6[j]; |
550 |
+ |
|
551 |
+ |
atomData13[6] = q[0]; |
552 |
+ |
atomData13[7] = q[1]; |
553 |
+ |
atomData13[8] = q[2]; |
554 |
+ |
atomData13[9] = q[3]; |
555 |
+ |
|
556 |
+ |
atomData13[10] = dAtom->getJx(); |
557 |
+ |
atomData13[11] = dAtom->getJy(); |
558 |
+ |
atomData13[12] = dAtom->getJz(); |
559 |
+ |
} |
560 |
+ |
|
561 |
+ |
} else { |
562 |
+ |
sprintf(painCave.errMsg, |
563 |
+ |
"Atom %d not found on processor %d, currentIndex = %d, local_index = %d\n", |
564 |
+ |
which_atom, worldRank, currentIndex, local_index ); |
565 |
+ |
haveError= 1; |
566 |
+ |
simError(); |
567 |
+ |
} |
568 |
+ |
|
569 |
+ |
strncpy(MPIatomTypeString, atomTypeString, MINIBUFFERSIZE); |
570 |
+ |
|
571 |
+ |
// null terminate the string before sending (just in case): |
572 |
+ |
MPIatomTypeString[MINIBUFFERSIZE-1] = '\0'; |
573 |
+ |
|
574 |
+ |
MPI_Send(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, 0, |
575 |
+ |
myPotato, MPI_COMM_WORLD); |
576 |
+ |
|
577 |
+ |
myPotato++; |
578 |
+ |
|
579 |
+ |
MPI_Send(&isDirectional, 1, MPI_INT, 0, |
580 |
+ |
myPotato, MPI_COMM_WORLD); |
581 |
+ |
|
582 |
+ |
myPotato++; |
583 |
+ |
|
584 |
+ |
if (isDirectional) { |
585 |
+ |
|
586 |
+ |
MPI_Send(atomData13, 13, MPI_DOUBLE, 0, |
587 |
+ |
myPotato, MPI_COMM_WORLD); |
588 |
+ |
|
589 |
+ |
} else { |
590 |
+ |
|
591 |
+ |
MPI_Send(atomData6, 6, MPI_DOUBLE, 0, |
592 |
+ |
myPotato, MPI_COMM_WORLD); |
593 |
+ |
} |
594 |
+ |
|
595 |
+ |
myPotato++; |
596 |
+ |
currentIndex++; |
597 |
+ |
} |
598 |
+ |
} |
599 |
+ |
|
600 |
+ |
sprintf( checkPointMsg, |
601 |
+ |
"Sucessfully took a dump.\n"); |
602 |
+ |
MPIcheckPoint(); |
603 |
|
|
604 |
+ |
} |
605 |
+ |
|
606 |
|
#endif // is_mpi |
607 |
|
} |
608 |
+ |
|
609 |
+ |
#ifdef IS_MPI |
610 |
+ |
|
611 |
+ |
// a couple of functions to let us escape the write loop |
612 |
+ |
|
613 |
+ |
void dWrite::DieDieDie( void ){ |
614 |
+ |
|
615 |
+ |
MPI_Finalize(); |
616 |
+ |
exit (0); |
617 |
+ |
} |
618 |
+ |
|
619 |
+ |
#endif //is_mpi |