1 |
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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gezelter |
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#define GAME_OVER -1 |
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mmeineke |
377 |
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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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gezelter |
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|
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mmeineke |
377 |
MPI_Status istatus[MPI_STATUS_SIZE]; |
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gezelter |
415 |
|
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mmeineke |
377 |
// write out header and node 0's coordinates |
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gezelter |
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|
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mmeineke |
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if( worldRank == 0 ){ |
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outFile << mpiSim->getTotAtoms() << "\n"; |
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gezelter |
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mmeineke |
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outFile << currentTime << "\t" |
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<< entry_plug->box_x << "\t" |
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<< entry_plug->box_y << "\t" |
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<< entry_plug->box_z << "\n"; |
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gezelter |
415 |
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for (i = 0 ; i < mpiPlug->nAtomsGlobal; i++ ) { |
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// Get the Node number which has this molecule: |
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mmeineke |
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|
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gezelter |
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which_node = AtomToProcMap[i]; |
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if (which_node == mpiPlug->myNode) { |
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sprintf( tempBuffer, |
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"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", |
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atoms[i]->getType(), |
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atoms[i]->getX(), |
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atoms[i]->getY(), |
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atoms[i]->getZ(), |
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atoms[i]->get_vx(), |
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atoms[i]->get_vy(), |
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atoms[i]->get_vz()); |
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strcpy( writeLine, tempBuffer ); |
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mmeineke |
377 |
|
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gezelter |
415 |
if( atoms[i]->isDirectional() ){ |
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mmeineke |
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|
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gezelter |
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dAtom = (DirectionalAtom *)atoms[i]; |
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dAtom->getQ( q ); |
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mmeineke |
377 |
|
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gezelter |
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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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} else { |
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MPI::COMM_WORLD.Send(&i, 1, MPI_INT, which_node, TAKE_THIS_TAG); |
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MPI::COMM_WORLD.Receive(writeLine, BUFFERSIZE, MPI_CHAR, which_node, |
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TAKE_THIS_TAG, istatus); |
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mmeineke |
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} |
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gezelter |
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mmeineke |
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outFile << writeLine; |
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} |
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gezelter |
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// kill everyone off: |
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for (j = 0; j < mpiPlug->numberProcessors; j++) { |
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MPI::COMM_WORLD.Send(GAME_OVER, 1, MPI_INT, j, TAKE_THIS_TAG); |
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mmeineke |
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} |
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gezelter |
415 |
} else { |
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done = 0; |
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while (!done) { |
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MPI::COMM_WORLD.Receive(&which_atom, 1, MPI_INT, 0, |
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TAKE_THIS_TAG, istatus); |
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mmeineke |
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gezelter |
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if (which_atom == GAME_OVER) { |
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done=1; |
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continue; |
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} else { |
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mmeineke |
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|
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gezelter |
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//format the line |
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mmeineke |
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sprintf( tempBuffer, |
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"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", |
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gezelter |
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atoms[which_atom]->getType(), |
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atoms[which_atom]->getX(), |
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atoms[which_atom]->getY(), |
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atoms[which_atom]->getZ(), |
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atoms[which_atom]->get_vx(), |
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atoms[which_atom]->get_vy(), |
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atoms[which_atom]->get_vz()); // check here. |
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mmeineke |
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strcpy( writeLine, tempBuffer ); |
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gezelter |
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if( atoms[which_atom]->isDirectional() ){ |
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mmeineke |
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gezelter |
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dAtom = (DirectionalAtom *)atoms[which_atom]; |
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mmeineke |
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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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gezelter |
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MPI::COMM_WORLD.Send(writeLine, BUFFERSIZE, MPI_CHAR, 0, |
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TAKE_THIS_TAG); |
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mmeineke |
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} |
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} |
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gezelter |
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} |
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outFile.flush(); |
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sprintf( checkPointMsg, |
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"Sucessfully took a dump.\n"); |
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MPIcheckPoint(); |
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mmeineke |
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#endif // is_mpi |
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} |
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void DumpWriter::writeFinal(){ |
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char finalName[500]; |
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ofstream finalOut; |
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#ifdef IS_MPI |
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if(worldRank == 0 ){ |
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#endif // is_mpi |
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strcpy( finalName, entry_plug->finalName ); |
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finalOut.open( finalName, ios::out | ios::trunc ); |
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if( !finalOut ){ |
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sprintf( painCave.errMsg, |
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"Could not open \"%s\" for final dump output.\n", |
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finalName ); |
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painCave.isFatal = 1; |
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simError(); |
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} |
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// finalOut.setf( ios::scientific ); |
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#ifdef IS_MPI |
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} |
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sprintf(checkPointMsg,"Opened file for final configuration\n"); |
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MPIcheckPoint(); |
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#endif //is_mpi |
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gezelter |
415 |
|
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mmeineke |
377 |
#ifndef IS_MPI |
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finalOut << nAtoms << "\n"; |
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finalOut << 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 ); |
299 |
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300 |
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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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finalOut << writeLine; |
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} |
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finalOut.flush(); |
317 |
gezelter |
415 |
finalOut.close(); |
318 |
mmeineke |
377 |
|
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#else // is_mpi |
320 |
gezelter |
415 |
|
321 |
mmeineke |
377 |
MPI_Status istatus[MPI_STATUS_SIZE]; |
322 |
gezelter |
415 |
|
323 |
mmeineke |
377 |
// write out header and node 0's coordinates |
324 |
gezelter |
415 |
|
325 |
mmeineke |
377 |
if( worldRank == 0 ){ |
326 |
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finalOut << mpiSim->getTotAtoms() << "\n"; |
327 |
gezelter |
415 |
|
328 |
mmeineke |
377 |
finalOut << entry_plug->box_x << "\t" |
329 |
gezelter |
415 |
<< entry_plug->box_y << "\t" |
330 |
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<< entry_plug->box_z << "\n"; |
331 |
mmeineke |
377 |
|
332 |
gezelter |
415 |
for (i = 0 ; i < mpiPlug->nAtomsGlobal; i++ ) { |
333 |
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// Get the Node number which has this molecule: |
334 |
mmeineke |
377 |
|
335 |
gezelter |
415 |
which_node = AtomToProcMap[i]; |
336 |
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337 |
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if (which_node == mpiPlug->myNode) { |
338 |
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339 |
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sprintf( tempBuffer, |
340 |
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"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", |
341 |
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atoms[i]->getType(), |
342 |
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atoms[i]->getX(), |
343 |
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atoms[i]->getY(), |
344 |
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atoms[i]->getZ(), |
345 |
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atoms[i]->get_vx(), |
346 |
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atoms[i]->get_vy(), |
347 |
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atoms[i]->get_vz()); |
348 |
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strcpy( writeLine, tempBuffer ); |
349 |
mmeineke |
377 |
|
350 |
gezelter |
415 |
if( atoms[i]->isDirectional() ){ |
351 |
mmeineke |
377 |
|
352 |
gezelter |
415 |
dAtom = (DirectionalAtom *)atoms[i]; |
353 |
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dAtom->getQ( q ); |
354 |
mmeineke |
377 |
|
355 |
gezelter |
415 |
sprintf( tempBuffer, |
356 |
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"%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n", |
357 |
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q[0], |
358 |
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q[1], |
359 |
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q[2], |
360 |
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q[3], |
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dAtom->getJx(), |
362 |
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dAtom->getJy(), |
363 |
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dAtom->getJz()); |
364 |
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strcat( writeLine, tempBuffer ); |
365 |
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} |
366 |
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else |
367 |
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strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" ); |
368 |
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369 |
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} else { |
370 |
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371 |
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MPI::COMM_WORLD.Send(&i, 1, MPI_INT, which_node, TAKE_THIS_TAG); |
372 |
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MPI::COMM_WORLD.Receive(writeLine, BUFFERSIZE, MPI_CHAR, which_node, |
373 |
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TAKE_THIS_TAG, istatus); |
374 |
mmeineke |
377 |
} |
375 |
gezelter |
415 |
|
376 |
mmeineke |
377 |
finalOut << writeLine; |
377 |
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} |
378 |
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|
379 |
gezelter |
415 |
// kill everyone off: |
380 |
|
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for (j = 0; j < mpiPlug->numberProcessors; j++) { |
381 |
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MPI::COMM_WORLD.Send(GAME_OVER, 1, MPI_INT, j, TAKE_THIS_TAG); |
382 |
mmeineke |
377 |
} |
383 |
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|
384 |
gezelter |
415 |
} else { |
385 |
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|
386 |
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done = 0; |
387 |
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while (!done) { |
388 |
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MPI::COMM_WORLD.Receive(&which_atom, 1, MPI_INT, 0, |
389 |
|
|
TAKE_THIS_TAG, istatus); |
390 |
mmeineke |
377 |
|
391 |
gezelter |
415 |
if (which_atom == GAME_OVER) { |
392 |
|
|
done=1; |
393 |
|
|
continue; |
394 |
|
|
} else { |
395 |
mmeineke |
377 |
|
396 |
gezelter |
415 |
//format the line |
397 |
mmeineke |
377 |
sprintf( tempBuffer, |
398 |
|
|
"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", |
399 |
gezelter |
415 |
atoms[which_atom]->getType(), |
400 |
|
|
atoms[which_atom]->getX(), |
401 |
|
|
atoms[which_atom]->getY(), |
402 |
|
|
atoms[which_atom]->getZ(), |
403 |
|
|
atoms[which_atom]->get_vx(), |
404 |
|
|
atoms[which_atom]->get_vy(), |
405 |
|
|
atoms[which_atom]->get_vz()); // check here. |
406 |
mmeineke |
377 |
strcpy( writeLine, tempBuffer ); |
407 |
|
|
|
408 |
gezelter |
415 |
if( atoms[which_atom]->isDirectional() ){ |
409 |
mmeineke |
377 |
|
410 |
gezelter |
415 |
dAtom = (DirectionalAtom *)atoms[which_atom]; |
411 |
mmeineke |
377 |
dAtom->getQ( q ); |
412 |
|
|
|
413 |
|
|
sprintf( tempBuffer, |
414 |
|
|
"%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n", |
415 |
|
|
q[0], |
416 |
|
|
q[1], |
417 |
|
|
q[2], |
418 |
|
|
q[3], |
419 |
|
|
dAtom->getJx(), |
420 |
|
|
dAtom->getJy(), |
421 |
|
|
dAtom->getJz()); |
422 |
|
|
strcat( writeLine, tempBuffer ); |
423 |
|
|
} |
424 |
|
|
else |
425 |
|
|
strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" ); |
426 |
gezelter |
415 |
|
427 |
|
|
MPI::COMM_WORLD.Send(writeLine, BUFFERSIZE, MPI_CHAR, 0, |
428 |
|
|
TAKE_THIS_TAG); |
429 |
mmeineke |
377 |
} |
430 |
|
|
} |
431 |
gezelter |
415 |
} |
432 |
|
|
finalOut.flush(); |
433 |
|
|
sprintf( checkPointMsg, |
434 |
|
|
"Sucessfully took a dump.\n"); |
435 |
|
|
MPIcheckPoint(); |
436 |
mmeineke |
377 |
|
437 |
gezelter |
415 |
if( worldRank == 0 ) finalOut.close(); |
438 |
mmeineke |
377 |
#endif // is_mpi |
439 |
|
|
} |