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#define _FILE_OFFSET_BITS 64 |
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#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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#define TAKE_THIS_TAG_CHAR 1 |
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#define TAKE_THIS_TAG_INT 2 |
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|
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namespace dWrite{ |
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void nodeZeroError( void ); |
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void anonymousNodeDie( 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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DumpWriter::DumpWriter( SimInfo* the_entry_plug ){ |
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entry_plug = the_entry_plug; |
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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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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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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, 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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double pos[3], vel[3]; |
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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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outFile << currentTime << ";\t" |
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<< entry_plug->Hmat[0][0] << "\t" |
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<< entry_plug->Hmat[1][0] << "\t" |
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<< entry_plug->Hmat[2][0] << ";\t" |
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|
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<< entry_plug->Hmat[0][1] << "\t" |
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<< entry_plug->Hmat[1][1] << "\t" |
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<< entry_plug->Hmat[2][1] << ";\t" |
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|
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<< entry_plug->Hmat[0][2] << "\t" |
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<< entry_plug->Hmat[1][2] << "\t" |
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<< entry_plug->Hmat[2][2] << ";\n"; |
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|
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for( i=0; i<nAtoms; i++ ){ |
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atoms[i]->getPos(pos); |
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atoms[i]->getVel(vel); |
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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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pos[0], |
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pos[1], |
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pos[2], |
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vel[0], |
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vel[1], |
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vel[2]); |
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strcpy( writeLine, tempBuffer ); |
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|
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if( atoms[i]->isDirectional() ){ |
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#else // is_mpi |
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|
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int masterIndex; |
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int nodeAtomsStart; |
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int nodeAtomsEnd; |
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int mpiErr; |
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int sendError; |
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int procIndex; |
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|
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MPI_Status istatus[MPI_STATUS_SIZE]; |
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// first thing first, suspend fatalities. |
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painCave.isEventLoop = 1; |
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|
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|
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// write out header and node 0's coordinates |
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int myStatus; // 1 = wakeup & success; 0 = error; -1 = AllDone |
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int haveError; |
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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->Hmat[0][0] << "\t" |
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<< entry_plug->Hmat[1][0] << "\t" |
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<< entry_plug->Hmat[2][0] << ";\t" |
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|
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outFile << currentTime << "\t" |
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<< entry_plug->box_x << "\t" |
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<< entry_plug->box_y << "\t" |
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<< entry_plug->box_z << "\n"; |
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|
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masterIndex = 0; |
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for( i=0; i<nAtoms; i++ ){ |
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<< entry_plug->Hmat[0][1] << "\t" |
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<< entry_plug->Hmat[1][1] << "\t" |
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<< entry_plug->Hmat[2][1] << ";\t" |
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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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<< entry_plug->Hmat[0][2] << "\t" |
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<< entry_plug->Hmat[1][2] << "\t" |
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<< entry_plug->Hmat[2][2] << ";\n"; |
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|
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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]; |
174 |
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|
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if (which_node == 0 ) { |
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|
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if( atoms[i]->isDirectional() ){ |
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haveError = 0; |
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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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} |
183 |
> |
if (local_index != -1) { |
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//format the line |
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|
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dAtom = (DirectionalAtom *)atoms[i]; |
187 |
< |
dAtom->getQ( q ); |
186 |
> |
atoms[local_index]->getPos(pos); |
187 |
> |
atoms[local_index]->getVel(vel); |
188 |
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|
189 |
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sprintf( tempBuffer, |
190 |
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"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", |
191 |
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atoms[local_index]->getType(), |
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pos[0], |
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pos[1], |
194 |
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pos[2], |
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vel[0], |
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vel[1], |
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vel[2]); // check here. |
198 |
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strcpy( writeLine, tempBuffer ); |
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|
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< |
sprintf( tempBuffer, |
201 |
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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], |
206 |
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dAtom->getJx(), |
207 |
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dAtom->getJy(), |
208 |
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dAtom->getJz()); |
209 |
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strcat( writeLine, tempBuffer ); |
200 |
> |
if( atoms[local_index]->isDirectional() ){ |
201 |
> |
|
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> |
dAtom = (DirectionalAtom *)atoms[local_index]; |
203 |
> |
dAtom->getQ( q ); |
204 |
> |
|
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sprintf( tempBuffer, |
206 |
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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 ); |
215 |
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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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sprintf(painCave.errMsg, |
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"Atom %d not found on processor %d\n", |
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i, worldRank ); |
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haveError= 1; |
225 |
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simError(); |
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} |
227 |
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|
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if(haveError) nodeZeroError(); |
229 |
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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" ); |
231 |
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else { |
232 |
> |
myStatus = 1; |
233 |
> |
MPI_Send(&myStatus, 1, MPI_INT, which_node, |
234 |
> |
TAKE_THIS_TAG_INT, MPI_COMM_WORLD); |
235 |
> |
MPI_Send(&i, 1, MPI_INT, which_node, TAKE_THIS_TAG_INT, |
236 |
> |
MPI_COMM_WORLD); |
237 |
> |
MPI_Recv(writeLine, BUFFERSIZE, MPI_CHAR, which_node, |
238 |
> |
TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD, &istatus); |
239 |
> |
MPI_Recv(&myStatus, 1, MPI_INT, which_node, |
240 |
> |
TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus); |
241 |
|
|
242 |
+ |
if(!myStatus) nodeZeroError(); |
243 |
+ |
|
244 |
+ |
} |
245 |
+ |
|
246 |
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outFile << writeLine; |
247 |
< |
masterIndex++; |
247 |
> |
outFile.flush(); |
248 |
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} |
249 |
< |
outFile.flush(); |
250 |
< |
} |
249 |
> |
|
250 |
> |
// kill everyone off: |
251 |
> |
myStatus = -1; |
252 |
> |
for (j = 0; j < mpiSim->getNumberProcessors(); j++) { |
253 |
> |
MPI_Send(&myStatus, 1, MPI_INT, j, |
254 |
> |
TAKE_THIS_TAG_INT, MPI_COMM_WORLD); |
255 |
> |
} |
256 |
|
|
257 |
< |
sprintf( checkPointMsg, |
186 |
< |
"Sucessfully wrote node 0's dump configuration.\n"); |
187 |
< |
MPIcheckPoint(); |
257 |
> |
} else { |
258 |
|
|
259 |
< |
for (procIndex = 1; procIndex < mpiSim->getNumberProcessors(); |
260 |
< |
procIndex++){ |
259 |
> |
done = 0; |
260 |
> |
while (!done) { |
261 |
> |
|
262 |
> |
MPI_Recv(&myStatus, 1, MPI_INT, 0, |
263 |
> |
TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus); |
264 |
|
|
265 |
< |
if( worldRank == 0 ){ |
265 |
> |
if(!myStatus) anonymousNodeDie(); |
266 |
|
|
267 |
< |
mpiErr = MPI_Recv(&nodeAtomsStart,1,MPI_INT,procIndex, |
268 |
< |
TAKE_THIS_TAG,MPI_COMM_WORLD,istatus); |
267 |
> |
if(myStatus < 0) break; |
268 |
> |
|
269 |
> |
MPI_Recv(&which_atom, 1, MPI_INT, 0, |
270 |
> |
TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus); |
271 |
|
|
272 |
< |
mpiErr = MPI_Recv(&nodeAtomsEnd,1,MPI_INT,procIndex, |
273 |
< |
TAKE_THIS_TAG,MPI_COMM_WORLD, istatus); |
274 |
< |
|
275 |
< |
// 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(); |
272 |
> |
myStatus = 1; |
273 |
> |
local_index=-1; |
274 |
> |
for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) { |
275 |
> |
if (atoms[j]->getGlobalIndex() == which_atom) local_index = j; |
276 |
|
} |
277 |
< |
|
278 |
< |
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 |
< |
} |
277 |
> |
if (local_index != -1) { |
278 |
> |
//format the line |
279 |
|
|
280 |
< |
else if( worldRank == procIndex ){ |
280 |
> |
atoms[local_index]->getPos(pos); |
281 |
> |
atoms[local_index]->getVel(vel); |
282 |
|
|
233 |
– |
nodeAtomsStart = mpiSim->getMyAtomStart(); |
234 |
– |
nodeAtomsEnd = mpiSim->getMyAtomEnd(); |
235 |
– |
|
236 |
– |
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 |
– |
|
283 |
|
sprintf( tempBuffer, |
284 |
|
"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", |
285 |
< |
atoms[i]->getType(), |
286 |
< |
atoms[i]->getX(), |
287 |
< |
atoms[i]->getY(), |
288 |
< |
atoms[i]->getZ(), |
289 |
< |
atoms[i]->get_vx(), |
290 |
< |
atoms[i]->get_vy(), |
291 |
< |
atoms[i]->get_vz()); // check here. |
285 |
> |
atoms[local_index]->getType(), |
286 |
> |
pos[0], |
287 |
> |
pos[1], |
288 |
> |
pos[2], |
289 |
> |
vel[0], |
290 |
> |
vel[1], |
291 |
> |
vel[2]); // check here. |
292 |
|
strcpy( writeLine, tempBuffer ); |
293 |
+ |
|
294 |
+ |
if( atoms[local_index]->isDirectional() ){ |
295 |
|
|
296 |
< |
if( atoms[i]->isDirectional() ){ |
263 |
< |
|
264 |
< |
dAtom = (DirectionalAtom *)atoms[i]; |
296 |
> |
dAtom = (DirectionalAtom *)atoms[local_index]; |
297 |
|
dAtom->getQ( q ); |
298 |
< |
|
298 |
> |
|
299 |
|
sprintf( tempBuffer, |
300 |
|
"%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n", |
301 |
|
q[0], |
307 |
|
dAtom->getJz()); |
308 |
|
strcat( writeLine, tempBuffer ); |
309 |
|
} |
310 |
< |
else |
310 |
> |
else{ |
311 |
|
strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" ); |
312 |
< |
|
313 |
< |
mpiErr = MPI_Send(writeLine,BUFFERSIZE,MPI_CHAR,0,TAKE_THIS_TAG, |
314 |
< |
MPI_COMM_WORLD); |
312 |
> |
} |
313 |
> |
} |
314 |
> |
else { |
315 |
> |
sprintf(painCave.errMsg, |
316 |
> |
"Atom %d not found on processor %d\n", |
317 |
> |
which_atom, worldRank ); |
318 |
> |
myStatus = 0; |
319 |
> |
simError(); |
320 |
> |
|
321 |
> |
strcpy( writeLine, "Hello, I'm an error.\n"); |
322 |
|
} |
323 |
+ |
|
324 |
+ |
MPI_Send(writeLine, BUFFERSIZE, MPI_CHAR, 0, |
325 |
+ |
TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD); |
326 |
+ |
MPI_Send( &myStatus, 1, MPI_INT, 0, |
327 |
+ |
TAKE_THIS_TAG_INT, MPI_COMM_WORLD); |
328 |
|
} |
329 |
< |
|
330 |
< |
sprintf(checkPointMsg,"Node %d sent dump configuration.", |
331 |
< |
procIndex); |
332 |
< |
MPIcheckPoint(); |
333 |
< |
} |
334 |
< |
|
329 |
> |
} |
330 |
> |
outFile.flush(); |
331 |
> |
sprintf( checkPointMsg, |
332 |
> |
"Sucessfully took a dump.\n"); |
333 |
> |
MPIcheckPoint(); |
334 |
> |
|
335 |
> |
// last thing last, enable fatalities. |
336 |
> |
painCave.isEventLoop = 0; |
337 |
> |
|
338 |
|
#endif // is_mpi |
339 |
|
} |
340 |
|
|
341 |
+ |
void DumpWriter::writeFinal(double finalTime){ |
342 |
|
|
343 |
+ |
char finalName[500]; |
344 |
+ |
ofstream finalOut; |
345 |
|
|
296 |
– |
void DumpWriter::writeFinal(){ |
297 |
– |
|
298 |
– |
|
346 |
|
const int BUFFERSIZE = 2000; |
347 |
< |
char tempBuffer[500]; |
348 |
< |
char writeLine[BUFFERSIZE]; |
302 |
< |
|
303 |
< |
char finalName[500]; |
347 |
> |
char tempBuffer[BUFFERSIZE]; |
348 |
> |
char writeLine[BUFFERSIZE]; |
349 |
|
|
305 |
– |
int i; |
350 |
|
double q[4]; |
351 |
|
DirectionalAtom* dAtom; |
352 |
|
int nAtoms = entry_plug->n_atoms; |
353 |
|
Atom** atoms = entry_plug->atoms; |
354 |
+ |
int i, j, which_node, done, game_over, which_atom, local_index; |
355 |
|
|
356 |
< |
ofstream finalOut; |
356 |
> |
double pos[3], vel[3]; |
357 |
|
|
358 |
|
#ifdef IS_MPI |
359 |
|
if(worldRank == 0 ){ |
380 |
|
|
381 |
|
#endif //is_mpi |
382 |
|
|
383 |
< |
|
339 |
< |
|
383 |
> |
|
384 |
|
#ifndef IS_MPI |
385 |
|
|
386 |
|
finalOut << nAtoms << "\n"; |
387 |
|
|
388 |
< |
finalOut << entry_plug->box_x << "\t" |
389 |
< |
<< entry_plug->box_y << "\t" |
390 |
< |
<< entry_plug->box_z << "\n"; |
388 |
> |
finalOut << finalTime << ";\t" |
389 |
> |
<< entry_plug->Hmat[0][0] << "\t" |
390 |
> |
<< entry_plug->Hmat[1][0] << "\t" |
391 |
> |
<< entry_plug->Hmat[2][0] << ";\t" |
392 |
|
|
393 |
+ |
<< entry_plug->Hmat[0][1] << "\t" |
394 |
+ |
<< entry_plug->Hmat[1][1] << "\t" |
395 |
+ |
<< entry_plug->Hmat[2][1] << ";\t" |
396 |
+ |
|
397 |
+ |
<< entry_plug->Hmat[0][2] << "\t" |
398 |
+ |
<< entry_plug->Hmat[1][2] << "\t" |
399 |
+ |
<< entry_plug->Hmat[2][2] << ";\n"; |
400 |
+ |
|
401 |
|
for( i=0; i<nAtoms; i++ ){ |
402 |
|
|
403 |
+ |
atoms[i]->getPos(pos); |
404 |
+ |
atoms[i]->getVel(vel); |
405 |
+ |
|
406 |
|
sprintf( tempBuffer, |
407 |
|
"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", |
408 |
|
atoms[i]->getType(), |
409 |
< |
atoms[i]->getX(), |
410 |
< |
atoms[i]->getY(), |
411 |
< |
atoms[i]->getZ(), |
412 |
< |
atoms[i]->get_vx(), |
413 |
< |
atoms[i]->get_vy(), |
414 |
< |
atoms[i]->get_vz()); |
409 |
> |
pos[0], |
410 |
> |
pos[1], |
411 |
> |
pos[2], |
412 |
> |
vel[0], |
413 |
> |
vel[1], |
414 |
> |
vel[2]); |
415 |
|
strcpy( writeLine, tempBuffer ); |
416 |
|
|
417 |
|
if( atoms[i]->isDirectional() ){ |
436 |
|
finalOut << writeLine; |
437 |
|
} |
438 |
|
finalOut.flush(); |
439 |
+ |
finalOut.close(); |
440 |
|
|
441 |
|
#else // is_mpi |
442 |
+ |
|
443 |
+ |
// first thing first, suspend fatalities. |
444 |
+ |
painCave.isEventLoop = 1; |
445 |
|
|
446 |
< |
int masterIndex; |
447 |
< |
int nodeAtomsStart; |
388 |
< |
int nodeAtomsEnd; |
389 |
< |
int mpiErr; |
390 |
< |
int sendError; |
391 |
< |
int procIndex; |
392 |
< |
|
393 |
< |
MPI_Status istatus[MPI_STATUS_SIZE]; |
446 |
> |
int myStatus; // 1 = wakeup & success; 0 = error; -1 = AllDone |
447 |
> |
int haveError; |
448 |
|
|
449 |
< |
|
450 |
< |
// write out header and node 0's coordinates |
449 |
> |
MPI_Status istatus; |
450 |
> |
int *AtomToProcMap = mpiSim->getAtomToProcMap(); |
451 |
|
|
452 |
+ |
// write out header and node 0's coordinates |
453 |
+ |
|
454 |
+ |
haveError = 0; |
455 |
|
if( worldRank == 0 ){ |
456 |
|
finalOut << mpiSim->getTotAtoms() << "\n"; |
457 |
+ |
|
458 |
+ |
finalOut << finalTime << ";\t" |
459 |
+ |
<< entry_plug->Hmat[0][0] << "\t" |
460 |
+ |
<< entry_plug->Hmat[1][0] << "\t" |
461 |
+ |
<< entry_plug->Hmat[2][0] << ";\t" |
462 |
|
|
463 |
< |
finalOut << entry_plug->box_x << "\t" |
464 |
< |
<< entry_plug->box_y << "\t" |
465 |
< |
<< entry_plug->box_z << "\n"; |
463 |
> |
<< entry_plug->Hmat[0][1] << "\t" |
464 |
> |
<< entry_plug->Hmat[1][1] << "\t" |
465 |
> |
<< entry_plug->Hmat[2][1] << ";\t" |
466 |
> |
|
467 |
> |
<< entry_plug->Hmat[0][2] << "\t" |
468 |
> |
<< entry_plug->Hmat[1][2] << "\t" |
469 |
> |
<< entry_plug->Hmat[2][2] << ";\n"; |
470 |
|
|
471 |
< |
masterIndex = 0; |
472 |
< |
|
407 |
< |
for( i=0; i<nAtoms; i++ ){ |
471 |
> |
for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) { |
472 |
> |
// Get the Node number which has this molecule: |
473 |
|
|
474 |
< |
sprintf( tempBuffer, |
475 |
< |
"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", |
476 |
< |
atoms[i]->getType(), |
477 |
< |
atoms[i]->getX(), |
478 |
< |
atoms[i]->getY(), |
479 |
< |
atoms[i]->getZ(), |
480 |
< |
atoms[i]->get_vx(), |
481 |
< |
atoms[i]->get_vy(), |
482 |
< |
atoms[i]->get_vz()); |
483 |
< |
strcpy( writeLine, tempBuffer ); |
484 |
< |
|
485 |
< |
if( atoms[i]->isDirectional() ){ |
474 |
> |
which_node = AtomToProcMap[i]; |
475 |
> |
|
476 |
> |
if (which_node == mpiSim->getMyNode()) { |
477 |
> |
|
478 |
> |
which_atom = i; |
479 |
> |
local_index=-1; |
480 |
> |
for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) { |
481 |
> |
if (atoms[j]->getGlobalIndex() == which_atom) local_index = j; |
482 |
> |
} |
483 |
> |
if (local_index != -1) { |
484 |
> |
|
485 |
> |
atoms[local_index]->getPos(pos); |
486 |
> |
atoms[local_index]->getVel(vel); |
487 |
|
|
488 |
< |
dAtom = (DirectionalAtom *)atoms[i]; |
489 |
< |
dAtom->getQ( q ); |
488 |
> |
sprintf( tempBuffer, |
489 |
> |
"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", |
490 |
> |
atoms[local_index]->getType(), |
491 |
> |
pos[0], |
492 |
> |
pos[1], |
493 |
> |
pos[2], |
494 |
> |
vel[0], |
495 |
> |
vel[1], |
496 |
> |
vel[2]); |
497 |
> |
strcpy( writeLine, tempBuffer ); |
498 |
|
|
499 |
< |
sprintf( tempBuffer, |
500 |
< |
"%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n", |
501 |
< |
q[0], |
502 |
< |
q[1], |
503 |
< |
q[2], |
504 |
< |
q[3], |
505 |
< |
dAtom->getJx(), |
506 |
< |
dAtom->getJy(), |
507 |
< |
dAtom->getJz()); |
508 |
< |
strcat( writeLine, tempBuffer ); |
509 |
< |
} |
510 |
< |
else |
511 |
< |
strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" ); |
499 |
> |
if( atoms[local_index]->isDirectional() ){ |
500 |
> |
|
501 |
> |
dAtom = (DirectionalAtom *)atoms[local_index]; |
502 |
> |
dAtom->getQ( q ); |
503 |
> |
|
504 |
> |
sprintf( tempBuffer, |
505 |
> |
"%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n", |
506 |
> |
q[0], |
507 |
> |
q[1], |
508 |
> |
q[2], |
509 |
> |
q[3], |
510 |
> |
dAtom->getJx(), |
511 |
> |
dAtom->getJy(), |
512 |
> |
dAtom->getJz()); |
513 |
> |
strcat( writeLine, tempBuffer ); |
514 |
> |
} |
515 |
> |
else |
516 |
> |
strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" ); |
517 |
> |
} |
518 |
> |
else { |
519 |
> |
sprintf(painCave.errMsg, |
520 |
> |
"Atom %d not found on processor %d\n", |
521 |
> |
i, worldRank ); |
522 |
> |
haveError= 1; |
523 |
> |
simError(); |
524 |
> |
} |
525 |
> |
|
526 |
> |
if(haveError) nodeZeroError(); |
527 |
> |
|
528 |
> |
} |
529 |
> |
else { |
530 |
> |
|
531 |
> |
myStatus = 1; |
532 |
> |
MPI_Send(&myStatus, 1, MPI_INT, which_node, |
533 |
> |
TAKE_THIS_TAG_INT, MPI_COMM_WORLD); |
534 |
> |
MPI_Send(&i, 1, MPI_INT, which_node, TAKE_THIS_TAG_INT, |
535 |
> |
MPI_COMM_WORLD); |
536 |
> |
MPI_Recv(writeLine, BUFFERSIZE, MPI_CHAR, which_node, |
537 |
> |
TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD, &istatus); |
538 |
> |
MPI_Recv(&myStatus, 1, MPI_INT, which_node, |
539 |
> |
TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus); |
540 |
|
|
541 |
+ |
if(!myStatus) nodeZeroError(); |
542 |
+ |
} |
543 |
+ |
|
544 |
|
finalOut << writeLine; |
440 |
– |
masterIndex++; |
545 |
|
} |
442 |
– |
finalOut.flush(); |
443 |
– |
} |
546 |
|
|
547 |
< |
for (procIndex = 1; procIndex < mpiSim->getNumberProcessors(); |
548 |
< |
procIndex++){ |
547 |
> |
// kill everyone off: |
548 |
> |
myStatus = -1; |
549 |
> |
for (j = 0; j < mpiSim->getNumberProcessors(); j++) { |
550 |
> |
MPI_Send(&myStatus, 1, MPI_INT, j, |
551 |
> |
TAKE_THIS_TAG_INT, MPI_COMM_WORLD); |
552 |
> |
} |
553 |
|
|
554 |
< |
if( worldRank == 0 ){ |
555 |
< |
|
556 |
< |
mpiErr = MPI_Recv(&nodeAtomsStart,1,MPI_INT,procIndex, |
557 |
< |
TAKE_THIS_TAG,MPI_COMM_WORLD,istatus); |
554 |
> |
} else { |
555 |
> |
|
556 |
> |
done = 0; |
557 |
> |
while (!done) { |
558 |
|
|
559 |
< |
mpiErr = MPI_Recv(&nodeAtomsEnd,1,MPI_INT,procIndex, |
560 |
< |
TAKE_THIS_TAG,MPI_COMM_WORLD, istatus); |
561 |
< |
|
562 |
< |
// Make sure where node 0 is writing to, matches where the |
563 |
< |
// receiving node expects it to be. |
564 |
< |
|
565 |
< |
if (masterIndex != nodeAtomsStart){ |
566 |
< |
sendError = 1; |
567 |
< |
mpiErr = MPI_Send(&sendError,1,MPI_INT,procIndex,TAKE_THIS_TAG, |
568 |
< |
MPI_COMM_WORLD); |
569 |
< |
sprintf(painCave.errMsg, |
570 |
< |
"DumpWriter error: atoms start index (%d) for " |
571 |
< |
"node %d not equal to master index (%d)", |
572 |
< |
nodeAtomsStart,procIndex,masterIndex ); |
467 |
< |
painCave.isFatal = 1; |
468 |
< |
simError(); |
559 |
> |
MPI_Recv(&myStatus, 1, MPI_INT, 0, |
560 |
> |
TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus); |
561 |
> |
|
562 |
> |
if(!myStatus) anonymousNodeDie(); |
563 |
> |
|
564 |
> |
if(myStatus < 0) break; |
565 |
> |
|
566 |
> |
MPI_Recv(&which_atom, 1, MPI_INT, 0, |
567 |
> |
TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus); |
568 |
> |
|
569 |
> |
myStatus = 1; |
570 |
> |
local_index=-1; |
571 |
> |
for (j=0; j < mpiSim->getMyNlocal(); j++) { |
572 |
> |
if (atoms[j]->getGlobalIndex() == which_atom) local_index = j; |
573 |
|
} |
574 |
< |
|
471 |
< |
sendError = 0; |
472 |
< |
mpiErr = MPI_Send(&sendError,1,MPI_INT,procIndex,TAKE_THIS_TAG, |
473 |
< |
MPI_COMM_WORLD); |
574 |
> |
if (local_index != -1) { |
575 |
|
|
576 |
< |
// recieve the nodes writeLines |
576 |
> |
atoms[local_index]->getPos(pos); |
577 |
> |
atoms[local_index]->getVel(vel); |
578 |
|
|
579 |
< |
for ( i = nodeAtomsStart; i <= nodeAtomsEnd; i++){ |
478 |
< |
|
479 |
< |
mpiErr = MPI_Recv(writeLine,BUFFERSIZE,MPI_CHAR,procIndex, |
480 |
< |
TAKE_THIS_TAG,MPI_COMM_WORLD,istatus ); |
481 |
< |
|
482 |
< |
finalOut << writeLine; |
483 |
< |
masterIndex++; |
484 |
< |
} |
485 |
< |
|
486 |
< |
finalOut.flush(); |
487 |
< |
} |
488 |
< |
|
489 |
< |
else if( worldRank == procIndex ){ |
490 |
< |
|
491 |
< |
nodeAtomsStart = mpiSim->getMyAtomStart(); |
492 |
< |
nodeAtomsEnd = mpiSim->getMyAtomEnd(); |
493 |
< |
|
494 |
< |
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(); |
502 |
< |
|
503 |
< |
// send current node's configuration line by line. |
504 |
< |
|
505 |
< |
for( i=0; i<nAtoms; i++ ){ |
506 |
< |
|
579 |
> |
//format the line |
580 |
|
sprintf( tempBuffer, |
581 |
|
"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", |
582 |
< |
atoms[i]->getType(), |
583 |
< |
atoms[i]->getX(), |
584 |
< |
atoms[i]->getY(), |
585 |
< |
atoms[i]->getZ(), |
586 |
< |
atoms[i]->get_vx(), |
587 |
< |
atoms[i]->get_vy(), |
588 |
< |
atoms[i]->get_vz()); |
582 |
> |
atoms[local_index]->getType(), |
583 |
> |
pos[0], |
584 |
> |
pos[1], |
585 |
> |
pos[2], |
586 |
> |
vel[0], |
587 |
> |
vel[1], |
588 |
> |
vel[2]); // check here. |
589 |
|
strcpy( writeLine, tempBuffer ); |
590 |
+ |
|
591 |
+ |
if( atoms[local_index]->isDirectional() ){ |
592 |
|
|
593 |
< |
if( atoms[i]->isDirectional() ){ |
519 |
< |
|
520 |
< |
dAtom = (DirectionalAtom *)atoms[i]; |
593 |
> |
dAtom = (DirectionalAtom *)atoms[local_index]; |
594 |
|
dAtom->getQ( q ); |
595 |
< |
|
595 |
> |
|
596 |
|
sprintf( tempBuffer, |
597 |
|
"%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n", |
598 |
|
q[0], |
604 |
|
dAtom->getJz()); |
605 |
|
strcat( writeLine, tempBuffer ); |
606 |
|
} |
607 |
< |
else |
607 |
> |
else{ |
608 |
|
strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" ); |
609 |
< |
|
610 |
< |
mpiErr = MPI_Send(writeLine,BUFFERSIZE,MPI_CHAR,0,TAKE_THIS_TAG, |
611 |
< |
MPI_COMM_WORLD); |
609 |
> |
} |
610 |
> |
} |
611 |
> |
else { |
612 |
> |
sprintf(painCave.errMsg, |
613 |
> |
"Atom %d not found on processor %d\n", |
614 |
> |
which_atom, worldRank ); |
615 |
> |
myStatus = 0; |
616 |
> |
simError(); |
617 |
> |
|
618 |
> |
strcpy( writeLine, "Hello, I'm an error.\n"); |
619 |
|
} |
620 |
+ |
|
621 |
+ |
MPI_Send(writeLine, BUFFERSIZE, MPI_CHAR, 0, |
622 |
+ |
TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD); |
623 |
+ |
MPI_Send( &myStatus, 1, MPI_INT, 0, |
624 |
+ |
TAKE_THIS_TAG_INT, MPI_COMM_WORLD); |
625 |
|
} |
541 |
– |
|
542 |
– |
sprintf(checkPointMsg,"Node %d sent dump configuration.", |
543 |
– |
procIndex); |
544 |
– |
MPIcheckPoint(); |
626 |
|
} |
627 |
+ |
finalOut.flush(); |
628 |
+ |
sprintf( checkPointMsg, |
629 |
+ |
"Sucessfully took a dump.\n"); |
630 |
+ |
MPIcheckPoint(); |
631 |
+ |
|
632 |
+ |
if( worldRank == 0 ) finalOut.close(); |
633 |
+ |
#endif // is_mpi |
634 |
+ |
} |
635 |
|
|
547 |
– |
if( worldRank == 0 ) finalOut.close(); |
636 |
|
|
637 |
< |
|
638 |
< |
#endif // is_mpi |
637 |
> |
|
638 |
> |
#ifdef IS_MPI |
639 |
> |
|
640 |
> |
// a couple of functions to let us escape the write loop |
641 |
> |
|
642 |
> |
void dWrite::nodeZeroError( void ){ |
643 |
> |
int j, myStatus; |
644 |
> |
|
645 |
> |
myStatus = 0; |
646 |
> |
for (j = 0; j < mpiSim->getNumberProcessors(); j++) { |
647 |
> |
MPI_Send( &myStatus, 1, MPI_INT, j, |
648 |
> |
TAKE_THIS_TAG_INT, MPI_COMM_WORLD); |
649 |
> |
} |
650 |
> |
|
651 |
> |
|
652 |
> |
MPI_Finalize(); |
653 |
> |
exit (0); |
654 |
> |
|
655 |
|
} |
656 |
+ |
|
657 |
+ |
void dWrite::anonymousNodeDie( void ){ |
658 |
+ |
|
659 |
+ |
MPI_Finalize(); |
660 |
+ |
exit (0); |
661 |
+ |
} |
662 |
+ |
|
663 |
+ |
#endif //is_mpi |