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#ifdef IS_MPI |
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#include <mpi.h> |
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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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#define TAKE_THIS_TAG 1 |
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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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#define GAME_OVER -1 |
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|
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DumpWriter::DumpWriter( SimInfo* the_entry_plug ){ |
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|
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entry_plug = the_entry_plug; |
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char tempBuffer[BUFFERSIZE]; |
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char writeLine[BUFFERSIZE]; |
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|
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int i; |
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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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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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MPI_Status istatus[MPI_STATUS_SIZE]; |
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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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<< 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 < mpiPlug->nAtomsGlobal; i++ ) { |
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// Get the Node number which has this molecule: |
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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 == mpiPlug->myNode) { |
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|
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sprintf( tempBuffer, |
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if (which_node == mpiSim->getMyNode()) { |
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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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|
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} else { |
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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); |
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MPI::COMM_WORLD.Receive(writeLine, BUFFERSIZE, MPI_CHAR, which_node, |
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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, istatus); |
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std::cerr << "node 0: got this line: " << writeLine; |
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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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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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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); |
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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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MPI::COMM_WORLD.Receive(&which_atom, 1, MPI_INT, 0, |
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TAKE_THIS_TAG, istatus); |
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|
199 |
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if (which_atom == GAME_OVER) { |
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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, 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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|
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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[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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strcpy( writeLine, tempBuffer ); |
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local_index=-1; |
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for (j=0; j < mpiSim->getMyNlocal(); j++) { |
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if (atoms[j]->getGlobalIndex() == which_atom) local_index = j; |
207 |
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} |
208 |
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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(), |
216 |
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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[which_atom]->isDirectional() ){ |
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|
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dAtom = (DirectionalAtom *)atoms[which_atom]; |
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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], |
230 |
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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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|
240 |
< |
MPI::COMM_WORLD.Send(writeLine, BUFFERSIZE, MPI_CHAR, 0, |
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TAKE_THIS_TAG); |
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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, |
227 |
> |
"%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n", |
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> |
q[0], |
229 |
> |
q[1], |
230 |
> |
q[2], |
231 |
> |
q[3], |
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> |
dAtom->getJx(), |
233 |
> |
dAtom->getJy(), |
234 |
> |
dAtom->getJz()); |
235 |
> |
strcat( writeLine, tempBuffer ); |
236 |
> |
} |
237 |
> |
else |
238 |
> |
strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" ); |
239 |
> |
std::cerr << "node: " << mpiSim->getMyNode() << " sending this line" << writeLine; |
240 |
> |
MPI::COMM_WORLD.Send(writeLine, BUFFERSIZE, MPI_CHAR, 0, |
241 |
> |
TAKE_THIS_TAG); |
242 |
> |
} else { |
243 |
> |
strcpy( writeLine, "ATOM NOT FOUND ON THIS PROCESSOR"); |
244 |
> |
MPI::COMM_WORLD.Send(writeLine, BUFFERSIZE, MPI_CHAR, 0, |
245 |
> |
TAKE_THIS_TAG); |
246 |
> |
} |
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} |
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} |
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} |
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} |
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|
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void DumpWriter::writeFinal(){ |
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< |
|
258 |
> |
|
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char finalName[500]; |
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ofstream finalOut; |
261 |
+ |
|
262 |
+ |
const int BUFFERSIZE = 2000; |
263 |
+ |
char tempBuffer[BUFFERSIZE]; |
264 |
+ |
char writeLine[BUFFERSIZE]; |
265 |
+ |
|
266 |
+ |
double q[4]; |
267 |
+ |
DirectionalAtom* dAtom; |
268 |
+ |
int nAtoms = entry_plug->n_atoms; |
269 |
+ |
Atom** atoms = entry_plug->atoms; |
270 |
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int i, j, which_node, done, game_over, which_atom, local_index; |
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|
|
272 |
+ |
|
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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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finalOut << entry_plug->box_x << "\t" |
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<< entry_plug->box_y << "\t" |
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<< entry_plug->box_z << "\n"; |
306 |
< |
|
306 |
> |
|
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for( i=0; i<nAtoms; i++ ){ |
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|
309 |
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sprintf( tempBuffer, |
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|
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#else // is_mpi |
345 |
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|
346 |
< |
MPI_Status istatus[MPI_STATUS_SIZE]; |
347 |
< |
|
346 |
> |
MPI::Status istatus; |
347 |
> |
int *AtomToProcMap = mpiSim->getAtomToProcMap(); |
348 |
> |
|
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// write out header and node 0's coordinates |
350 |
|
|
351 |
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if( worldRank == 0 ){ |
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<< entry_plug->box_y << "\t" |
356 |
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<< entry_plug->box_z << "\n"; |
357 |
|
|
358 |
< |
for (i = 0 ; i < mpiPlug->nAtomsGlobal; i++ ) { |
358 |
> |
for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) { |
359 |
|
// Get the Node number which has this molecule: |
360 |
|
|
361 |
|
which_node = AtomToProcMap[i]; |
362 |
|
|
363 |
< |
if (which_node == mpiPlug->myNode) { |
363 |
> |
if (which_node == mpiSim->getMyNode()) { |
364 |
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|
365 |
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sprintf( tempBuffer, |
366 |
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"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", |
395 |
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} else { |
396 |
|
|
397 |
|
MPI::COMM_WORLD.Send(&i, 1, MPI_INT, which_node, TAKE_THIS_TAG); |
398 |
< |
MPI::COMM_WORLD.Receive(writeLine, BUFFERSIZE, MPI_CHAR, which_node, |
398 |
> |
MPI::COMM_WORLD.Recv(writeLine, BUFFERSIZE, MPI_CHAR, which_node, |
399 |
|
TAKE_THIS_TAG, istatus); |
400 |
|
} |
401 |
|
|
403 |
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} |
404 |
|
|
405 |
|
// kill everyone off: |
406 |
< |
for (j = 0; j < mpiPlug->numberProcessors; j++) { |
407 |
< |
MPI::COMM_WORLD.Send(GAME_OVER, 1, MPI_INT, j, TAKE_THIS_TAG); |
406 |
> |
game_over = -1; |
407 |
> |
for (j = 0; j < mpiSim->getNumberProcessors(); j++) { |
408 |
> |
MPI::COMM_WORLD.Send(&game_over, 1, MPI_INT, j, TAKE_THIS_TAG); |
409 |
|
} |
410 |
|
|
411 |
|
} else { |
412 |
|
|
413 |
|
done = 0; |
414 |
|
while (!done) { |
415 |
< |
MPI::COMM_WORLD.Receive(&which_atom, 1, MPI_INT, 0, |
416 |
< |
TAKE_THIS_TAG, istatus); |
415 |
> |
MPI::COMM_WORLD.Recv(&which_atom, 1, MPI_INT, 0, |
416 |
> |
TAKE_THIS_TAG, istatus); |
417 |
|
|
418 |
< |
if (which_atom == GAME_OVER) { |
418 |
> |
if (which_atom == -1) { |
419 |
|
done=1; |
420 |
|
continue; |
421 |
|
} else { |
422 |
|
|
423 |
< |
//format the line |
424 |
< |
sprintf( tempBuffer, |
425 |
< |
"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", |
426 |
< |
atoms[which_atom]->getType(), |
427 |
< |
atoms[which_atom]->getX(), |
428 |
< |
atoms[which_atom]->getY(), |
429 |
< |
atoms[which_atom]->getZ(), |
430 |
< |
atoms[which_atom]->get_vx(), |
431 |
< |
atoms[which_atom]->get_vy(), |
432 |
< |
atoms[which_atom]->get_vz()); // check here. |
433 |
< |
strcpy( writeLine, tempBuffer ); |
423 |
> |
local_index=-1; |
424 |
> |
for (j=0; j < mpiSim->getMyNlocal(); j++) { |
425 |
> |
if (atoms[j]->getGlobalIndex() == which_atom) local_index = j; |
426 |
> |
} |
427 |
> |
if (local_index != -1) { |
428 |
> |
|
429 |
> |
//format the line |
430 |
> |
sprintf( tempBuffer, |
431 |
> |
"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", |
432 |
> |
atoms[local_index]->getType(), |
433 |
> |
atoms[local_index]->getX(), |
434 |
> |
atoms[local_index]->getY(), |
435 |
> |
atoms[local_index]->getZ(), |
436 |
> |
atoms[local_index]->get_vx(), |
437 |
> |
atoms[local_index]->get_vy(), |
438 |
> |
atoms[local_index]->get_vz()); // check here. |
439 |
> |
strcpy( writeLine, tempBuffer ); |
440 |
|
|
441 |
< |
if( atoms[which_atom]->isDirectional() ){ |
441 |
> |
if( atoms[local_index]->isDirectional() ){ |
442 |
> |
|
443 |
> |
dAtom = (DirectionalAtom *)atoms[local_index]; |
444 |
> |
dAtom->getQ( q ); |
445 |
|
|
446 |
< |
dAtom = (DirectionalAtom *)atoms[which_atom]; |
447 |
< |
dAtom->getQ( q ); |
448 |
< |
|
449 |
< |
sprintf( tempBuffer, |
450 |
< |
"%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n", |
451 |
< |
q[0], |
452 |
< |
q[1], |
453 |
< |
q[2], |
454 |
< |
q[3], |
455 |
< |
dAtom->getJx(), |
456 |
< |
dAtom->getJy(), |
457 |
< |
dAtom->getJz()); |
458 |
< |
strcat( writeLine, tempBuffer ); |
459 |
< |
} |
460 |
< |
else |
461 |
< |
strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" ); |
462 |
< |
|
463 |
< |
MPI::COMM_WORLD.Send(writeLine, BUFFERSIZE, MPI_CHAR, 0, |
464 |
< |
TAKE_THIS_TAG); |
446 |
> |
sprintf( tempBuffer, |
447 |
> |
"%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n", |
448 |
> |
q[0], |
449 |
> |
q[1], |
450 |
> |
q[2], |
451 |
> |
q[3], |
452 |
> |
dAtom->getJx(), |
453 |
> |
dAtom->getJy(), |
454 |
> |
dAtom->getJz()); |
455 |
> |
strcat( writeLine, tempBuffer ); |
456 |
> |
} |
457 |
> |
else |
458 |
> |
strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" ); |
459 |
> |
|
460 |
> |
MPI::COMM_WORLD.Send(writeLine, BUFFERSIZE, MPI_CHAR, 0, |
461 |
> |
TAKE_THIS_TAG); |
462 |
> |
} else { |
463 |
> |
strcpy( writeLine, "ATOM NOT FOUND ON THIS PROCESSOR"); |
464 |
> |
MPI::COMM_WORLD.Send(writeLine, BUFFERSIZE, MPI_CHAR, 0, |
465 |
> |
TAKE_THIS_TAG); |
466 |
> |
} |
467 |
|
} |
468 |
|
} |
469 |
< |
} |
469 |
> |
} |
470 |
|
finalOut.flush(); |
471 |
|
sprintf( checkPointMsg, |
472 |
|
"Sucessfully took a dump.\n"); |