--- trunk/OOPSE/libmdtools/DumpWriter.cpp 2003/04/03 21:12:51 450 +++ trunk/OOPSE/libmdtools/DumpWriter.cpp 2003/10/29 00:19:10 837 @@ -1,4 +1,6 @@ -#include +#define _FILE_OFFSET_BITS 64 + +#include #include #include @@ -26,22 +28,20 @@ DumpWriter::DumpWriter( SimInfo* the_entry_plug ){ #ifdef IS_MPI if(worldRank == 0 ){ #endif // is_mpi - - - + strcpy( outName, entry_plug->sampleName ); - + outFile.open(outName, ios::out | ios::trunc ); - + if( !outFile ){ - + sprintf( painCave.errMsg, "Could not open \"%s\" for dump output.\n", outName); painCave.isFatal = 1; simError(); } - + //outFile.setf( ios::scientific ); #ifdef IS_MPI @@ -67,46 +67,69 @@ void DumpWriter::writeDump( double currentTime ){ } void DumpWriter::writeDump( double currentTime ){ - + const int BUFFERSIZE = 2000; char tempBuffer[BUFFERSIZE]; char writeLine[BUFFERSIZE]; - int i, j, which_node, done, which_atom, local_index; + int i; +#ifdef IS_MPI + int j, which_node, done, which_atom, local_index; +#else //is_mpi + int nAtoms = entry_plug->n_atoms; +#endif //is_mpi + double q[4]; DirectionalAtom* dAtom; - int nAtoms = entry_plug->n_atoms; Atom** atoms = entry_plug->atoms; - + double pos[3], vel[3]; + + // write current frame to the eor file + + this->writeFinal( currentTime ); + #ifndef IS_MPI - + outFile << nAtoms << "\n"; - - outFile << currentTime << "\t" - << entry_plug->box_x << "\t" - << entry_plug->box_y << "\t" - << entry_plug->box_z << "\n"; - + + outFile << currentTime << ";\t" + << entry_plug->Hmat[0][0] << "\t" + << entry_plug->Hmat[1][0] << "\t" + << entry_plug->Hmat[2][0] << ";\t" + + << entry_plug->Hmat[0][1] << "\t" + << entry_plug->Hmat[1][1] << "\t" + << entry_plug->Hmat[2][1] << ";\t" + + << entry_plug->Hmat[0][2] << "\t" + << entry_plug->Hmat[1][2] << "\t" + << entry_plug->Hmat[2][2] << ";"; + //write out additional parameters, such as chi and eta + outFile << entry_plug->the_integrator->getAdditionalParameters(); + outFile << endl; + for( i=0; igetPos(pos); + atoms[i]->getVel(vel); + sprintf( tempBuffer, "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", atoms[i]->getType(), - atoms[i]->getX(), - atoms[i]->getY(), - atoms[i]->getZ(), - atoms[i]->get_vx(), - atoms[i]->get_vy(), - atoms[i]->get_vz()); + pos[0], + pos[1], + pos[2], + vel[0], + vel[1], + vel[2]); strcpy( writeLine, tempBuffer ); if( atoms[i]->isDirectional() ){ - + dAtom = (DirectionalAtom *)atoms[i]; dAtom->getQ( q ); - + sprintf( tempBuffer, "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n", q[0], @@ -120,7 +143,7 @@ void DumpWriter::writeDump( double currentTime ){ } else strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" ); - + outFile << writeLine; } outFile.flush(); @@ -135,48 +158,63 @@ void DumpWriter::writeDump( double currentTime ){ MPI_Status istatus; int *AtomToProcMap = mpiSim->getAtomToProcMap(); - + // write out header and node 0's coordinates - + if( worldRank == 0 ){ outFile << mpiSim->getTotAtoms() << "\n"; - - outFile << currentTime << "\t" - << entry_plug->box_x << "\t" - << entry_plug->box_y << "\t" - << entry_plug->box_z << "\n"; + + outFile << currentTime << ";\t" + << entry_plug->Hmat[0][0] << "\t" + << entry_plug->Hmat[1][0] << "\t" + << entry_plug->Hmat[2][0] << ";\t" + + << entry_plug->Hmat[0][1] << "\t" + << entry_plug->Hmat[1][1] << "\t" + << entry_plug->Hmat[2][1] << ";\t" + + << entry_plug->Hmat[0][2] << "\t" + << entry_plug->Hmat[1][2] << "\t" + << entry_plug->Hmat[2][2] << ";"; + + outFile << entry_plug->the_integrator->getAdditionalParameters(); + outFile << endl; outFile.flush(); for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) { // Get the Node number which has this atom; - - which_node = AtomToProcMap[i]; - + + which_node = AtomToProcMap[i]; + if (which_node == 0 ) { - + haveError = 0; which_atom = i; - local_index=-1; + local_index=-1; for (j=0; (jgetMyNlocal()) && (local_index < 0); j++) { if (atoms[j]->getGlobalIndex() == which_atom) local_index = j; } if (local_index != -1) { //format the line + + atoms[local_index]->getPos(pos); + atoms[local_index]->getVel(vel); + sprintf( tempBuffer, "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", atoms[local_index]->getType(), - atoms[local_index]->getX(), - atoms[local_index]->getY(), - atoms[local_index]->getZ(), - atoms[local_index]->get_vx(), - atoms[local_index]->get_vy(), - atoms[local_index]->get_vz()); // check here. - strcpy( writeLine, tempBuffer ); - + pos[0], + pos[1], + pos[2], + vel[0], + vel[1], + vel[2]); // check here. + strcpy( writeLine, tempBuffer ); + if( atoms[local_index]->isDirectional() ){ - + dAtom = (DirectionalAtom *)atoms[local_index]; dAtom->getQ( q ); - + sprintf( tempBuffer, "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n", q[0], @@ -187,10 +225,10 @@ void DumpWriter::writeDump( double currentTime ){ dAtom->getJy(), dAtom->getJz()); strcat( writeLine, tempBuffer ); - + } else - strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" ); + strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" ); } else { sprintf(painCave.errMsg, @@ -198,75 +236,79 @@ void DumpWriter::writeDump( double currentTime ){ i, worldRank ); haveError= 1; simError(); - } - + } + if(haveError) nodeZeroError(); } else { myStatus = 1; - MPI_Send(&myStatus, 1, MPI_INT, which_node, + MPI_Send(&myStatus, 1, MPI_INT, which_node, TAKE_THIS_TAG_INT, MPI_COMM_WORLD); - MPI_Send(&i, 1, MPI_INT, which_node, TAKE_THIS_TAG_INT, + MPI_Send(&i, 1, MPI_INT, which_node, TAKE_THIS_TAG_INT, MPI_COMM_WORLD); MPI_Recv(writeLine, BUFFERSIZE, MPI_CHAR, which_node, TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD, &istatus); - MPI_Recv(&myStatus, 1, MPI_INT, which_node, + MPI_Recv(&myStatus, 1, MPI_INT, which_node, TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus); - + if(!myStatus) nodeZeroError(); } - + outFile << writeLine; outFile.flush(); } - + // kill everyone off: myStatus = -1; - for (j = 0; j < mpiSim->getNumberProcessors(); j++) { - MPI_Send(&myStatus, 1, MPI_INT, j, + for (j = 0; j < mpiSim->getNumberProcessors(); j++) { + MPI_Send(&myStatus, 1, MPI_INT, j, TAKE_THIS_TAG_INT, MPI_COMM_WORLD); } } else { - + done = 0; while (!done) { - - MPI_Recv(&myStatus, 1, MPI_INT, 0, + + MPI_Recv(&myStatus, 1, MPI_INT, 0, TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus); if(!myStatus) anonymousNodeDie(); - + if(myStatus < 0) break; - MPI_Recv(&which_atom, 1, MPI_INT, 0, + MPI_Recv(&which_atom, 1, MPI_INT, 0, TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus); - + myStatus = 1; - local_index=-1; + local_index=-1; for (j=0; (jgetMyNlocal()) && (local_index < 0); j++) { if (atoms[j]->getGlobalIndex() == which_atom) local_index = j; } if (local_index != -1) { //format the line + + atoms[local_index]->getPos(pos); + atoms[local_index]->getVel(vel); + sprintf( tempBuffer, "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", atoms[local_index]->getType(), - atoms[local_index]->getX(), - atoms[local_index]->getY(), - atoms[local_index]->getZ(), - atoms[local_index]->get_vx(), - atoms[local_index]->get_vy(), - atoms[local_index]->get_vz()); // check here. + pos[0], + pos[1], + pos[2], + vel[0], + vel[1], + vel[2]); // check here. strcpy( writeLine, tempBuffer ); - + if( atoms[local_index]->isDirectional() ){ - + dAtom = (DirectionalAtom *)atoms[local_index]; dAtom->getQ( q ); - + sprintf( tempBuffer, "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n", q[0], @@ -281,7 +323,7 @@ void DumpWriter::writeDump( double currentTime ){ else{ strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" ); } - } + } else { sprintf(painCave.errMsg, "Atom %d not found on processor %d\n", @@ -292,12 +334,12 @@ void DumpWriter::writeDump( double currentTime ){ strcpy( writeLine, "Hello, I'm an error.\n"); } - MPI_Send(writeLine, BUFFERSIZE, MPI_CHAR, 0, + MPI_Send(writeLine, BUFFERSIZE, MPI_CHAR, 0, TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD); - MPI_Send( &myStatus, 1, MPI_INT, 0, + MPI_Send( &myStatus, 1, MPI_INT, 0, TAKE_THIS_TAG_INT, MPI_COMM_WORLD); } - } + } outFile.flush(); sprintf( checkPointMsg, "Sucessfully took a dump.\n"); @@ -309,28 +351,33 @@ void DumpWriter::writeDump( double currentTime ){ #endif // is_mpi } -void DumpWriter::writeFinal(){ +void DumpWriter::writeFinal(double finalTime){ char finalName[500]; ofstream finalOut; const int BUFFERSIZE = 2000; char tempBuffer[BUFFERSIZE]; - char writeLine[BUFFERSIZE]; + char writeLine[BUFFERSIZE]; double q[4]; DirectionalAtom* dAtom; - int nAtoms = entry_plug->n_atoms; Atom** atoms = entry_plug->atoms; - int i, j, which_node, done, game_over, which_atom, local_index; - - + int i; #ifdef IS_MPI + int j, which_node, done, which_atom, local_index; +#else //is_mpi + int nAtoms = entry_plug->n_atoms; +#endif //is_mpi + + double pos[3], vel[3]; + +#ifdef IS_MPI if(worldRank == 0 ){ #endif // is_mpi - + strcpy( finalName, entry_plug->finalName ); - + finalOut.open( finalName, ios::out | ios::trunc ); if( !finalOut ){ sprintf( painCave.errMsg, @@ -339,44 +386,60 @@ void DumpWriter::writeFinal(){ painCave.isFatal = 1; simError(); } - + // finalOut.setf( ios::scientific ); - + #ifdef IS_MPI } - + sprintf(checkPointMsg,"Opened file for final configuration\n"); - MPIcheckPoint(); - + MPIcheckPoint(); + #endif //is_mpi - + #ifndef IS_MPI - + finalOut << nAtoms << "\n"; - - finalOut << entry_plug->box_x << "\t" - << entry_plug->box_y << "\t" - << entry_plug->box_z << "\n"; - + + finalOut << finalTime << ";\t" + << entry_plug->Hmat[0][0] << "\t" + << entry_plug->Hmat[1][0] << "\t" + << entry_plug->Hmat[2][0] << ";\t" + + << entry_plug->Hmat[0][1] << "\t" + << entry_plug->Hmat[1][1] << "\t" + << entry_plug->Hmat[2][1] << ";\t" + + << entry_plug->Hmat[0][2] << "\t" + << entry_plug->Hmat[1][2] << "\t" + << entry_plug->Hmat[2][2] << ";"; + + //write out additional parameters, such as chi and eta + finalOut << entry_plug->the_integrator->getAdditionalParameters(); + finalOut << endl; + for( i=0; igetPos(pos); + atoms[i]->getVel(vel); + sprintf( tempBuffer, "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", atoms[i]->getType(), - atoms[i]->getX(), - atoms[i]->getY(), - atoms[i]->getZ(), - atoms[i]->get_vx(), - atoms[i]->get_vy(), - atoms[i]->get_vz()); + pos[0], + pos[1], + pos[2], + vel[0], + vel[1], + vel[2]); strcpy( writeLine, tempBuffer ); if( atoms[i]->isDirectional() ){ - + dAtom = (DirectionalAtom *)atoms[i]; dAtom->getQ( q ); - + sprintf( tempBuffer, "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n", q[0], @@ -390,14 +453,14 @@ void DumpWriter::writeFinal(){ } else strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" ); - + finalOut << writeLine; } finalOut.flush(); finalOut.close(); #else // is_mpi - + // first thing first, suspend fatalities. painCave.isEventLoop = 1; @@ -408,44 +471,61 @@ void DumpWriter::writeFinal(){ int *AtomToProcMap = mpiSim->getAtomToProcMap(); // write out header and node 0's coordinates - + haveError = 0; if( worldRank == 0 ){ finalOut << mpiSim->getTotAtoms() << "\n"; - - finalOut << entry_plug->box_x << "\t" - << entry_plug->box_y << "\t" - << entry_plug->box_z << "\n"; - + + finalOut << finalTime << ";\t" + << entry_plug->Hmat[0][0] << "\t" + << entry_plug->Hmat[1][0] << "\t" + << entry_plug->Hmat[2][0] << ";\t" + + << entry_plug->Hmat[0][1] << "\t" + << entry_plug->Hmat[1][1] << "\t" + << entry_plug->Hmat[2][1] << ";\t" + + << entry_plug->Hmat[0][2] << "\t" + << entry_plug->Hmat[1][2] << "\t" + << entry_plug->Hmat[2][2] << ";"; + + //write out additional parameters, such as chi and eta + finalOut << entry_plug->the_integrator->getAdditionalParameters(); + finalOut << endl; + for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) { // Get the Node number which has this molecule: - - which_node = AtomToProcMap[i]; - + + which_node = AtomToProcMap[i]; + if (which_node == mpiSim->getMyNode()) { which_atom = i; - local_index=-1; + local_index=-1; for (j=0; (jgetMyNlocal()) && (local_index < 0); j++) { if (atoms[j]->getGlobalIndex() == which_atom) local_index = j; } - if (local_index != -1) { + if (local_index != -1) { + + atoms[local_index]->getPos(pos); + atoms[local_index]->getVel(vel); + sprintf( tempBuffer, "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", atoms[local_index]->getType(), - atoms[local_index]->getX(), - atoms[local_index]->getY(), - atoms[local_index]->getZ(), - atoms[local_index]->get_vx(), - atoms[local_index]->get_vy(), - atoms[local_index]->get_vz()); + pos[0], + pos[1], + pos[2], + vel[0], + vel[1], + vel[2]); strcpy( writeLine, tempBuffer ); - + if( atoms[local_index]->isDirectional() ){ - + dAtom = (DirectionalAtom *)atoms[local_index]; dAtom->getQ( q ); - + sprintf( tempBuffer, "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n", q[0], @@ -458,7 +538,7 @@ void DumpWriter::writeFinal(){ strcat( writeLine, tempBuffer ); } else - strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" ); + strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" ); } else { sprintf(painCave.errMsg, @@ -466,75 +546,78 @@ void DumpWriter::writeFinal(){ i, worldRank ); haveError= 1; simError(); - } + } if(haveError) nodeZeroError(); - - } + + } else { - + myStatus = 1; - MPI_Send(&myStatus, 1, MPI_INT, which_node, + MPI_Send(&myStatus, 1, MPI_INT, which_node, TAKE_THIS_TAG_INT, MPI_COMM_WORLD); MPI_Send(&i, 1, MPI_INT, which_node, TAKE_THIS_TAG_INT, MPI_COMM_WORLD); MPI_Recv(writeLine, BUFFERSIZE, MPI_CHAR, which_node, TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD, &istatus); - MPI_Recv(&myStatus, 1, MPI_INT, which_node, + MPI_Recv(&myStatus, 1, MPI_INT, which_node, TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus); - + if(!myStatus) nodeZeroError(); } - + finalOut << writeLine; } - + // kill everyone off: myStatus = -1; - for (j = 0; j < mpiSim->getNumberProcessors(); j++) { - MPI_Send(&myStatus, 1, MPI_INT, j, + for (j = 0; j < mpiSim->getNumberProcessors(); j++) { + MPI_Send(&myStatus, 1, MPI_INT, j, TAKE_THIS_TAG_INT, MPI_COMM_WORLD); } } else { - + done = 0; while (!done) { - MPI_Recv(&myStatus, 1, MPI_INT, 0, + MPI_Recv(&myStatus, 1, MPI_INT, 0, TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus); - + if(!myStatus) anonymousNodeDie(); - + if(myStatus < 0) break; - - MPI_Recv(&which_atom, 1, MPI_INT, 0, + + MPI_Recv(&which_atom, 1, MPI_INT, 0, TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus); - + myStatus = 1; - local_index=-1; + local_index=-1; for (j=0; j < mpiSim->getMyNlocal(); j++) { if (atoms[j]->getGlobalIndex() == which_atom) local_index = j; } if (local_index != -1) { + atoms[local_index]->getPos(pos); + atoms[local_index]->getVel(vel); + //format the line sprintf( tempBuffer, "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", atoms[local_index]->getType(), - atoms[local_index]->getX(), - atoms[local_index]->getY(), - atoms[local_index]->getZ(), - atoms[local_index]->get_vx(), - atoms[local_index]->get_vy(), - atoms[local_index]->get_vz()); // check here. + pos[0], + pos[1], + pos[2], + vel[0], + vel[1], + vel[2]); // check here. strcpy( writeLine, tempBuffer ); - + if( atoms[local_index]->isDirectional() ){ - + dAtom = (DirectionalAtom *)atoms[local_index]; dAtom->getQ( q ); - + sprintf( tempBuffer, "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n", q[0], @@ -549,20 +632,20 @@ void DumpWriter::writeFinal(){ else{ strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" ); } - } + } else { sprintf(painCave.errMsg, "Atom %d not found on processor %d\n", which_atom, worldRank ); myStatus = 0; simError(); - + strcpy( writeLine, "Hello, I'm an error.\n"); } - MPI_Send(writeLine, BUFFERSIZE, MPI_CHAR, 0, + MPI_Send(writeLine, BUFFERSIZE, MPI_CHAR, 0, TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD); - MPI_Send( &myStatus, 1, MPI_INT, 0, + MPI_Send( &myStatus, 1, MPI_INT, 0, TAKE_THIS_TAG_INT, MPI_COMM_WORLD); } } @@ -570,8 +653,8 @@ void DumpWriter::writeFinal(){ sprintf( checkPointMsg, "Sucessfully took a dump.\n"); MPIcheckPoint(); - - if( worldRank == 0 ) finalOut.close(); + + if( worldRank == 0 ) finalOut.close(); #endif // is_mpi } @@ -583,17 +666,17 @@ void dWrite::nodeZeroError( void ){ void dWrite::nodeZeroError( void ){ int j, myStatus; - + myStatus = 0; - for (j = 0; j < mpiSim->getNumberProcessors(); j++) { - MPI_Send( &myStatus, 1, MPI_INT, j, + for (j = 0; j < mpiSim->getNumberProcessors(); j++) { + MPI_Send( &myStatus, 1, MPI_INT, j, TAKE_THIS_TAG_INT, MPI_COMM_WORLD); - } - + } + MPI_Finalize(); exit (0); - + } void dWrite::anonymousNodeDie( void ){