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#include <cstring> |
2 |
#include <iostream> |
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#include <fstream> |
4 |
|
5 |
#ifdef IS_MPI |
6 |
#include <mpi.h> |
7 |
#include <mpi++.h> |
8 |
#include "mpiSimulation.hpp" |
9 |
#define TAKE_THIS_TAG_CHAR 1 |
10 |
#define TAKE_THIS_TAG_INT 2 |
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#endif //is_mpi |
12 |
|
13 |
#include "ReadWrite.hpp" |
14 |
#include "simError.h" |
15 |
|
16 |
DumpWriter::DumpWriter( SimInfo* the_entry_plug ){ |
17 |
|
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entry_plug = the_entry_plug; |
19 |
|
20 |
#ifdef IS_MPI |
21 |
if(worldRank == 0 ){ |
22 |
#endif // is_mpi |
23 |
|
24 |
|
25 |
|
26 |
strcpy( outName, entry_plug->sampleName ); |
27 |
|
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outFile.open(outName, ios::out | ios::trunc ); |
29 |
|
30 |
if( !outFile ){ |
31 |
|
32 |
sprintf( painCave.errMsg, |
33 |
"Could not open \"%s\" for dump output.\n", |
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outName); |
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painCave.isFatal = 1; |
36 |
simError(); |
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} |
38 |
|
39 |
//outFile.setf( ios::scientific ); |
40 |
|
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#ifdef IS_MPI |
42 |
} |
43 |
|
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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 |
48 |
} |
49 |
|
50 |
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 ){ |
64 |
|
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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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int i, j, which_node, done, game_over, which_atom, local_index; |
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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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|
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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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MPI::Status istatus; |
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int *AtomToProcMap = mpiSim->getAtomToProcMap(); |
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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 << 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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outFile.flush(); |
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for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) { |
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// Get the Node number which has this atom; |
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|
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which_node = AtomToProcMap[i]; |
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|
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if (which_node == 0 ) { |
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|
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which_atom = i; |
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local_index=-1; |
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for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) { |
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if (atoms[j]->getGlobalIndex() == which_atom) local_index = j; |
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} |
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if (local_index != -1) { |
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//format the line |
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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[local_index]->getType(), |
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atoms[local_index]->getX(), |
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atoms[local_index]->getY(), |
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atoms[local_index]->getZ(), |
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atoms[local_index]->get_vx(), |
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atoms[local_index]->get_vy(), |
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atoms[local_index]->get_vz()); // check here. |
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strcpy( writeLine, tempBuffer ); |
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|
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if( atoms[local_index]->isDirectional() ){ |
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|
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dAtom = (DirectionalAtom *)atoms[local_index]; |
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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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} |
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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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else { |
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strcpy( writeLine, "ATOM NOT FOUND ON THIS PROCESSOR"); |
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} |
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} |
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else { |
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|
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//std::cerr << "node 0: sending node " << which_node << " request for atom " << i << "\n"; |
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MPI::COMM_WORLD.Send(&i, 1, MPI_INT, which_node, TAKE_THIS_TAG_INT); |
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//std::cerr << "node 0: sent!\n"; |
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MPI::COMM_WORLD.Recv(writeLine, BUFFERSIZE, MPI_CHAR, which_node, |
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TAKE_THIS_TAG_CHAR, istatus); |
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//std::cerr << "node 0: got this line: " << writeLine; |
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} |
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|
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outFile << writeLine; |
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outFile.flush(); |
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} |
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|
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// kill everyone off: |
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game_over = -1; |
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for (j = 0; j < mpiSim->getNumberProcessors(); j++) { |
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MPI::COMM_WORLD.Send(&game_over, 1, MPI_INT, j, TAKE_THIS_TAG_INT); |
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} |
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|
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} else { |
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|
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done = 0; |
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while (!done) { |
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//std::cerr << "node: " << mpiSim->getMyNode() << " Waiting for receive \n"; |
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MPI::COMM_WORLD.Recv(&which_atom, 1, MPI_INT, 0, |
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TAKE_THIS_TAG_INT, istatus); |
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//std::cerr << "node: " << mpiSim->getMyNode() << " got request for atom " << which_atom << "\n"; |
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if (which_atom == -1) { |
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done=1; |
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continue; |
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} else { |
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local_index=-1; |
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for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) { |
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if (atoms[j]->getGlobalIndex() == which_atom) local_index = j; |
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} |
222 |
if (local_index != -1) { |
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//format the line |
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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[local_index]->getType(), |
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atoms[local_index]->getX(), |
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atoms[local_index]->getY(), |
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atoms[local_index]->getZ(), |
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atoms[local_index]->get_vx(), |
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atoms[local_index]->get_vy(), |
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atoms[local_index]->get_vz()); // check here. |
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strcpy( writeLine, tempBuffer ); |
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|
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if( atoms[local_index]->isDirectional() ){ |
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|
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dAtom = (DirectionalAtom *)atoms[local_index]; |
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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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// std::cerr << "node: " << mpiSim->getMyNode() << " sending this line" << writeLine; |
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MPI::COMM_WORLD.Send(writeLine, BUFFERSIZE, MPI_CHAR, 0, |
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TAKE_THIS_TAG_CHAR); |
256 |
} else { |
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strcpy( writeLine, "ATOM NOT FOUND ON THIS PROCESSOR"); |
258 |
MPI::COMM_WORLD.Send(writeLine, BUFFERSIZE, MPI_CHAR, 0, |
259 |
TAKE_THIS_TAG_CHAR); |
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} |
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} |
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} |
263 |
} |
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outFile.flush(); |
265 |
sprintf( checkPointMsg, |
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"Sucessfully took a dump.\n"); |
267 |
MPIcheckPoint(); |
268 |
#endif // is_mpi |
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} |
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|
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void DumpWriter::writeFinal(){ |
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|
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char finalName[500]; |
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ofstream finalOut; |
275 |
|
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const int BUFFERSIZE = 2000; |
277 |
char tempBuffer[BUFFERSIZE]; |
278 |
char writeLine[BUFFERSIZE]; |
279 |
|
280 |
double q[4]; |
281 |
DirectionalAtom* dAtom; |
282 |
int nAtoms = entry_plug->n_atoms; |
283 |
Atom** atoms = entry_plug->atoms; |
284 |
int i, j, which_node, done, game_over, which_atom, local_index; |
285 |
|
286 |
|
287 |
#ifdef IS_MPI |
288 |
if(worldRank == 0 ){ |
289 |
#endif // is_mpi |
290 |
|
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strcpy( finalName, entry_plug->finalName ); |
292 |
|
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finalOut.open( finalName, ios::out | ios::trunc ); |
294 |
if( !finalOut ){ |
295 |
sprintf( painCave.errMsg, |
296 |
"Could not open \"%s\" for final dump output.\n", |
297 |
finalName ); |
298 |
painCave.isFatal = 1; |
299 |
simError(); |
300 |
} |
301 |
|
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// finalOut.setf( ios::scientific ); |
303 |
|
304 |
#ifdef IS_MPI |
305 |
} |
306 |
|
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sprintf(checkPointMsg,"Opened file for final configuration\n"); |
308 |
MPIcheckPoint(); |
309 |
|
310 |
#endif //is_mpi |
311 |
|
312 |
|
313 |
#ifndef IS_MPI |
314 |
|
315 |
finalOut << nAtoms << "\n"; |
316 |
|
317 |
finalOut << entry_plug->box_x << "\t" |
318 |
<< entry_plug->box_y << "\t" |
319 |
<< entry_plug->box_z << "\n"; |
320 |
|
321 |
for( i=0; i<nAtoms; i++ ){ |
322 |
|
323 |
sprintf( tempBuffer, |
324 |
"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", |
325 |
atoms[i]->getType(), |
326 |
atoms[i]->getX(), |
327 |
atoms[i]->getY(), |
328 |
atoms[i]->getZ(), |
329 |
atoms[i]->get_vx(), |
330 |
atoms[i]->get_vy(), |
331 |
atoms[i]->get_vz()); |
332 |
strcpy( writeLine, tempBuffer ); |
333 |
|
334 |
if( atoms[i]->isDirectional() ){ |
335 |
|
336 |
dAtom = (DirectionalAtom *)atoms[i]; |
337 |
dAtom->getQ( q ); |
338 |
|
339 |
sprintf( tempBuffer, |
340 |
"%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n", |
341 |
q[0], |
342 |
q[1], |
343 |
q[2], |
344 |
q[3], |
345 |
dAtom->getJx(), |
346 |
dAtom->getJy(), |
347 |
dAtom->getJz()); |
348 |
strcat( writeLine, tempBuffer ); |
349 |
} |
350 |
else |
351 |
strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" ); |
352 |
|
353 |
finalOut << writeLine; |
354 |
} |
355 |
finalOut.flush(); |
356 |
finalOut.close(); |
357 |
|
358 |
#else // is_mpi |
359 |
|
360 |
MPI::Status istatus; |
361 |
int *AtomToProcMap = mpiSim->getAtomToProcMap(); |
362 |
|
363 |
// write out header and node 0's coordinates |
364 |
|
365 |
if( worldRank == 0 ){ |
366 |
finalOut << mpiSim->getTotAtoms() << "\n"; |
367 |
|
368 |
finalOut << entry_plug->box_x << "\t" |
369 |
<< entry_plug->box_y << "\t" |
370 |
<< entry_plug->box_z << "\n"; |
371 |
|
372 |
for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) { |
373 |
// Get the Node number which has this molecule: |
374 |
|
375 |
which_node = AtomToProcMap[i]; |
376 |
|
377 |
if (which_node == mpiSim->getMyNode()) { |
378 |
|
379 |
sprintf( tempBuffer, |
380 |
"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", |
381 |
atoms[i]->getType(), |
382 |
atoms[i]->getX(), |
383 |
atoms[i]->getY(), |
384 |
atoms[i]->getZ(), |
385 |
atoms[i]->get_vx(), |
386 |
atoms[i]->get_vy(), |
387 |
atoms[i]->get_vz()); |
388 |
strcpy( writeLine, tempBuffer ); |
389 |
|
390 |
if( atoms[i]->isDirectional() ){ |
391 |
|
392 |
dAtom = (DirectionalAtom *)atoms[i]; |
393 |
dAtom->getQ( q ); |
394 |
|
395 |
sprintf( tempBuffer, |
396 |
"%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n", |
397 |
q[0], |
398 |
q[1], |
399 |
q[2], |
400 |
q[3], |
401 |
dAtom->getJx(), |
402 |
dAtom->getJy(), |
403 |
dAtom->getJz()); |
404 |
strcat( writeLine, tempBuffer ); |
405 |
} |
406 |
else |
407 |
strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" ); |
408 |
|
409 |
} else { |
410 |
|
411 |
MPI::COMM_WORLD.Send(&i, 1, MPI_INT, which_node, TAKE_THIS_TAG_INT); |
412 |
MPI::COMM_WORLD.Recv(writeLine, BUFFERSIZE, MPI_CHAR, which_node, |
413 |
TAKE_THIS_TAG_CHAR, istatus); |
414 |
} |
415 |
|
416 |
finalOut << writeLine; |
417 |
} |
418 |
|
419 |
// kill everyone off: |
420 |
game_over = -1; |
421 |
for (j = 0; j < mpiSim->getNumberProcessors(); j++) { |
422 |
MPI::COMM_WORLD.Send(&game_over, 1, MPI_INT, j, TAKE_THIS_TAG_INT); |
423 |
} |
424 |
|
425 |
} else { |
426 |
|
427 |
done = 0; |
428 |
while (!done) { |
429 |
MPI::COMM_WORLD.Recv(&which_atom, 1, MPI_INT, 0, |
430 |
TAKE_THIS_TAG_INT, istatus); |
431 |
|
432 |
if (which_atom == -1) { |
433 |
done=1; |
434 |
continue; |
435 |
} else { |
436 |
|
437 |
local_index=-1; |
438 |
for (j=0; j < mpiSim->getMyNlocal(); j++) { |
439 |
if (atoms[j]->getGlobalIndex() == which_atom) local_index = j; |
440 |
} |
441 |
if (local_index != -1) { |
442 |
|
443 |
//format the line |
444 |
sprintf( tempBuffer, |
445 |
"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", |
446 |
atoms[local_index]->getType(), |
447 |
atoms[local_index]->getX(), |
448 |
atoms[local_index]->getY(), |
449 |
atoms[local_index]->getZ(), |
450 |
atoms[local_index]->get_vx(), |
451 |
atoms[local_index]->get_vy(), |
452 |
atoms[local_index]->get_vz()); // check here. |
453 |
strcpy( writeLine, tempBuffer ); |
454 |
|
455 |
if( atoms[local_index]->isDirectional() ){ |
456 |
|
457 |
dAtom = (DirectionalAtom *)atoms[local_index]; |
458 |
dAtom->getQ( q ); |
459 |
|
460 |
sprintf( tempBuffer, |
461 |
"%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n", |
462 |
q[0], |
463 |
q[1], |
464 |
q[2], |
465 |
q[3], |
466 |
dAtom->getJx(), |
467 |
dAtom->getJy(), |
468 |
dAtom->getJz()); |
469 |
strcat( writeLine, tempBuffer ); |
470 |
} |
471 |
else |
472 |
strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" ); |
473 |
|
474 |
MPI::COMM_WORLD.Send(writeLine, BUFFERSIZE, MPI_CHAR, 0, |
475 |
TAKE_THIS_TAG_CHAR); |
476 |
} else { |
477 |
strcpy( writeLine, "ATOM NOT FOUND ON THIS PROCESSOR"); |
478 |
MPI::COMM_WORLD.Send(writeLine, BUFFERSIZE, MPI_CHAR, 0, |
479 |
TAKE_THIS_TAG_CHAR); |
480 |
} |
481 |
} |
482 |
} |
483 |
} |
484 |
finalOut.flush(); |
485 |
sprintf( checkPointMsg, |
486 |
"Sucessfully took a dump.\n"); |
487 |
MPIcheckPoint(); |
488 |
|
489 |
if( worldRank == 0 ) finalOut.close(); |
490 |
#endif // is_mpi |
491 |
} |