--- trunk/OOPSE/libmdtools/DumpWriter.cpp 2003/03/26 23:14:02 416 +++ trunk/OOPSE/libmdtools/DumpWriter.cpp 2004/01/08 18:59:36 912 @@ -1,12 +1,18 @@ -#include +#define _FILE_OFFSET_BITS 64 + +#include #include #include #ifdef IS_MPI #include -#include #include "mpiSimulation.hpp" -#define TAKE_THIS_TAG 0 + +namespace dWrite{ + void DieDieDie( void ); +} + +using namespace dWrite; #endif //is_mpi #include "ReadWrite.hpp" @@ -19,22 +25,20 @@ 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 @@ -60,46 +64,80 @@ void DumpWriter::writeDump( double currentTime ){ } void DumpWriter::writeDump( double currentTime ){ - + const int BUFFERSIZE = 2000; + const int MINIBUFFERSIZE = 100; + char tempBuffer[BUFFERSIZE]; char writeLine[BUFFERSIZE]; - int i, j, which_node, done, game_over, which_atom; + int i; +#ifdef IS_MPI + int j, which_node, done, which_atom, local_index; + double atomTransData[6]; + double atomOrientData[7]; + int isDirectional; + char* atomTypeString; + char MPIatomTypeString[MINIBUFFERSIZE]; + int me; + int atomTypeTag; + int atomIsDirectionalTag; + int atomTransDataTag; + int atomOrientDataTag; +#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], @@ -113,156 +151,308 @@ 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(); #else // is_mpi - MPI::Status istatus; + // first thing first, suspend fatalities. + painCave.isEventLoop = 1; + + int myStatus; // 1 = wakeup & success; 0 = error; -1 = AllDone + int haveError; + + 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 molecule: - - which_node = AtomToProcMap[i]; - - if (which_node == mpiSim->getMyNode()) { + // Get the Node number which has this atom; + + which_node = AtomToProcMap[i]; + + if (which_node != 0) { + atomTypeTag = 4*i; + atomIsDirectionalTag = 4*i + 1; + atomTransDataTag = 4*i + 2; + atomOrientDataTag = 4*i + 3; + + MPI_Recv(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, which_node, + atomTypeTag, MPI_COMM_WORLD, &istatus); + + strncpy(atomTypeString, MPIatomTypeString, MINIBUFFERSIZE); + + // Null terminate the atomTypeString just in case: + + atomTypeString[strlen(atomTypeString) - 1] = '\0'; + + MPI_Recv(&isDirectional, 1, MPI_INT, which_node, + atomIsDirectionalTag, MPI_COMM_WORLD, &istatus); + + MPI_Recv(atomTransData, 6, MPI_DOUBLE, which_node, + atomTransDataTag, MPI_COMM_WORLD, &istatus); + + if (isDirectional) { + + MPI_Recv(atomOrientData, 7, MPI_DOUBLE, which_node, + atomOrientDataTag, MPI_COMM_WORLD, &istatus); + + } + + } else { + + haveError = 0; + which_atom = i; + local_index=-1; + + for (j=0; (jgetMyNlocal()) && (local_index < 0); j++) { + if (atoms[j]->getGlobalIndex() == which_atom) local_index = j; + } + + if (local_index != -1) { + + atomTypeString = atoms[local_index]->getType(); + + atoms[local_index]->getPos(pos); + atoms[local_index]->getVel(vel); + + atomTransData[0] = pos[0]; + atomTransData[1] = pos[1]; + atomTransData[2] = pos[2]; + + atomTransData[3] = vel[0]; + atomTransData[4] = vel[1]; + atomTransData[5] = vel[2]; + + isDirectional = 0; + + if( atoms[local_index]->isDirectional() ){ + + isDirectional = 1; + + dAtom = (DirectionalAtom *)atoms[local_index]; + dAtom->getQ( q ); + + atomOrientData[0] = q[0]; + atomOrientData[1] = q[1]; + atomOrientData[2] = q[2]; + atomOrientData[3] = q[3]; + + atomOrientData[4] = dAtom->getJx(); + atomOrientData[5] = dAtom->getJy(); + atomOrientData[6] = dAtom->getJz(); + } + + } else { + sprintf(painCave.errMsg, + "Atom %d not found on processor %d\n", + i, worldRank ); + haveError= 1; + simError(); + } + + if(haveError) DieDieDie(); + + // If we've survived to here, format the line: + 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()); + atomTypeString, + atomTransData[0], + atomTransData[1], + atomTransData[2], + atomTransData[3], + atomTransData[4], + atomTransData[5]); + strcpy( writeLine, tempBuffer ); - - if( atoms[i]->isDirectional() ){ - - dAtom = (DirectionalAtom *)atoms[i]; - dAtom->getQ( q ); - + + if (isDirectional) { + sprintf( tempBuffer, "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n", - q[0], - q[1], - q[2], - q[3], - dAtom->getJx(), - dAtom->getJy(), - dAtom->getJz()); + atomOrientData[0], + atomOrientData[1], + atomOrientData[2], + atomOrientData[3], + atomOrientData[4], + atomOrientData[5], + atomOrientData[6]); strcat( writeLine, tempBuffer ); + + } else { + strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" ); } - else - strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" ); - - } else { - - MPI::COMM_WORLD.Send(&i, 1, MPI_INT, which_node, TAKE_THIS_TAG); - MPI::COMM_WORLD.Recv(writeLine, BUFFERSIZE, MPI_CHAR, which_node, - TAKE_THIS_TAG, istatus); + + outFile << writeLine; + outFile.flush(); } - - outFile << writeLine; } - - // kill everyone off: - game_over = -1; - for (j = 0; j < mpiSim->getNumberProcessors(); j++) { - MPI::COMM_WORLD.Send(&game_over, 1, MPI_INT, j, TAKE_THIS_TAG); - } + outFile.flush(); + sprintf( checkPointMsg, + "Sucessfully took a dump.\n"); + MPIcheckPoint(); + } else { + + // worldRank != 0, so I'm a remote node. - done = 0; - while (!done) { - MPI::COMM_WORLD.Recv(&which_atom, 1, MPI_INT, 0, - TAKE_THIS_TAG, istatus); + for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) { + + // Am I the node which has this atom? + + if (AtomToProcMap[i] == worldRank) { - if (which_atom == -1) { - done=1; - continue; - } else { + local_index=-1; + for (j=0; (jgetMyNlocal()) && (local_index < 0); j++) { + if (atoms[j]->getGlobalIndex() == which_atom) local_index = j; + } + if (local_index != -1) { + + atomTypeString = atoms[local_index]->getType(); - //format the line - sprintf( tempBuffer, - "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", - atoms[which_atom]->getType(), - atoms[which_atom]->getX(), - atoms[which_atom]->getY(), - atoms[which_atom]->getZ(), - atoms[which_atom]->get_vx(), - atoms[which_atom]->get_vy(), - atoms[which_atom]->get_vz()); // check here. - strcpy( writeLine, tempBuffer ); - - if( atoms[which_atom]->isDirectional() ){ - - dAtom = (DirectionalAtom *)atoms[which_atom]; - dAtom->getQ( q ); - - sprintf( tempBuffer, - "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n", - q[0], - q[1], - q[2], - q[3], - dAtom->getJx(), - dAtom->getJy(), - dAtom->getJz()); - strcat( writeLine, tempBuffer ); + atoms[local_index]->getPos(pos); + atoms[local_index]->getVel(vel); + + atomTransData[0] = pos[0]; + atomTransData[1] = pos[1]; + atomTransData[2] = pos[2]; + + atomTransData[3] = vel[0]; + atomTransData[4] = vel[1]; + atomTransData[5] = vel[2]; + + isDirectional = 0; + + if( atoms[local_index]->isDirectional() ){ + + isDirectional = 1; + + dAtom = (DirectionalAtom *)atoms[local_index]; + dAtom->getQ( q ); + + atomOrientData[0] = q[0]; + atomOrientData[1] = q[1]; + atomOrientData[2] = q[2]; + atomOrientData[3] = q[3]; + + atomOrientData[4] = dAtom->getJx(); + atomOrientData[5] = dAtom->getJy(); + atomOrientData[6] = dAtom->getJz(); + } + + } else { + sprintf(painCave.errMsg, + "Atom %d not found on processor %d\n", + i, worldRank ); + haveError= 1; + simError(); } - else - strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" ); + + // I've survived this far, so send off the data! + + atomTypeTag = 4*i; + atomIsDirectionalTag = 4*i + 1; + atomTransDataTag = 4*i + 2; + atomOrientDataTag = 4*i + 3; + + + strncpy(MPIatomTypeString, atomTypeString, MINIBUFFERSIZE); + + // null terminate the string before sending (just in case): + MPIatomTypeString[MINIBUFFERSIZE-1] = '\0'; + + MPI_Send(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, 0, + atomTypeTag, MPI_COMM_WORLD); - MPI::COMM_WORLD.Send(writeLine, BUFFERSIZE, MPI_CHAR, 0, - TAKE_THIS_TAG); + MPI_Send(&isDirectional, 1, MPI_INT, 0, + atomIsDirectionalTag, MPI_COMM_WORLD); + + MPI_Send(atomTransData, 6, MPI_DOUBLE, 0, + atomTransDataTag, MPI_COMM_WORLD); + + if (isDirectional) { + + MPI_Send(atomOrientData, 7, MPI_DOUBLE, 0, + atomOrientDataTag, MPI_COMM_WORLD); + + } + } } - } - outFile.flush(); - sprintf( checkPointMsg, - "Sucessfully took a dump.\n"); - MPIcheckPoint(); + + sprintf( checkPointMsg, + "Sucessfully took a dump.\n"); + MPIcheckPoint(); + + } + + painCave.isEventLoop = 0; + #endif // is_mpi } -void DumpWriter::writeFinal(){ +void DumpWriter::writeFinal(double finalTime){ char finalName[500]; ofstream finalOut; const int BUFFERSIZE = 2000; + const int MINIBUFFERSIZE = 100; 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; - - + int i; #ifdef IS_MPI + int j, which_node, done, which_atom, local_index; + double atomTransData[6]; + double atomOrientData[7]; + int isDirectional; + char* atomTypeString; + char MPIatomTypeString[MINIBUFFERSIZE]; + int atomTypeTag; + int atomIsDirectionalTag; + int atomTransDataTag; + int atomOrientDataTag; +#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, @@ -271,44 +461,60 @@ 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], @@ -322,132 +528,275 @@ 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 - - MPI::Status istatus; + + // first thing first, suspend fatalities. + painCave.isEventLoop = 1; + + int myStatus; // 1 = wakeup & success; 0 = error; -1 = AllDone + int haveError; + + MPI_Status istatus; int *AtomToProcMap = mpiSim->getAtomToProcMap(); // write out header and node 0's coordinates - + 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] << ";"; + + finalOut << entry_plug->the_integrator->getAdditionalParameters(); + finalOut << endl; + finalOut.flush(); for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) { - // Get the Node number which has this molecule: - - which_node = AtomToProcMap[i]; - - if (which_node == mpiSim->getMyNode()) { + // Get the Node number which has this atom; + + which_node = AtomToProcMap[i]; + + if (which_node != 0) { + atomTypeTag = 4*i; + atomIsDirectionalTag = 4*i + 1; + atomTransDataTag = 4*i + 2; + atomOrientDataTag = 4*i + 3; + + MPI_Recv(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, which_node, + atomTypeTag, MPI_COMM_WORLD, &istatus); + + strncpy(atomTypeString, MPIatomTypeString, MINIBUFFERSIZE); + + MPI_Recv(&isDirectional, 1, MPI_INT, which_node, + atomIsDirectionalTag, MPI_COMM_WORLD, &istatus); + + MPI_Recv(atomTransData, 6, MPI_DOUBLE, which_node, + atomTransDataTag, MPI_COMM_WORLD, &istatus); + + if (isDirectional) { + + MPI_Recv(atomOrientData, 7, MPI_DOUBLE, which_node, + atomOrientDataTag, MPI_COMM_WORLD, &istatus); + + } + + } else { + + haveError = 0; + which_atom = i; + local_index=-1; + + for (j=0; (jgetMyNlocal()) && (local_index < 0); j++) { + if (atoms[j]->getGlobalIndex() == which_atom) local_index = j; + } + + if (local_index != -1) { + + atomTypeString = atoms[local_index]->getType(); + + atoms[local_index]->getPos(pos); + atoms[local_index]->getVel(vel); + + atomTransData[0] = pos[0]; + atomTransData[1] = pos[1]; + atomTransData[2] = pos[2]; + + atomTransData[3] = vel[0]; + atomTransData[4] = vel[1]; + atomTransData[5] = vel[2]; + + isDirectional = 0; + + if( atoms[local_index]->isDirectional() ){ + + isDirectional = 1; + + dAtom = (DirectionalAtom *)atoms[local_index]; + dAtom->getQ( q ); + + atomOrientData[0] = q[0]; + atomOrientData[1] = q[1]; + atomOrientData[2] = q[2]; + atomOrientData[3] = q[3]; + + atomOrientData[4] = dAtom->getJx(); + atomOrientData[5] = dAtom->getJy(); + atomOrientData[6] = dAtom->getJz(); + } + + } else { + sprintf(painCave.errMsg, + "Atom %d not found on processor %d\n", + i, worldRank ); + haveError= 1; + simError(); + } + + if(haveError) DieDieDie(); + + // If we've survived to here, format the line: + 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()); + atomTypeString, + atomTransData[0], + atomTransData[1], + atomTransData[2], + atomTransData[3], + atomTransData[4], + atomTransData[5]); + strcpy( writeLine, tempBuffer ); - - if( atoms[i]->isDirectional() ){ - - dAtom = (DirectionalAtom *)atoms[i]; - dAtom->getQ( q ); - + + if (isDirectional) { + sprintf( tempBuffer, "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n", - q[0], - q[1], - q[2], - q[3], - dAtom->getJx(), - dAtom->getJy(), - dAtom->getJz()); + atomOrientData[0], + atomOrientData[1], + atomOrientData[2], + atomOrientData[3], + atomOrientData[4], + atomOrientData[5], + atomOrientData[6]); strcat( writeLine, tempBuffer ); + + } else { + strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" ); } - else - strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" ); - - } else { - - MPI::COMM_WORLD.Send(&i, 1, MPI_INT, which_node, TAKE_THIS_TAG); - MPI::COMM_WORLD.Recv(writeLine, BUFFERSIZE, MPI_CHAR, which_node, - TAKE_THIS_TAG, istatus); + + finalOut << writeLine; + finalOut.flush(); } - - finalOut << writeLine; } - - // kill everyone off: - game_over = -1; - for (j = 0; j < mpiSim->getNumberProcessors(); j++) { - MPI::COMM_WORLD.Send(&game_over, 1, MPI_INT, j, TAKE_THIS_TAG); - } + finalOut.flush(); + sprintf( checkPointMsg, + "Sucessfully took a dump.\n"); + MPIcheckPoint(); + } else { + + // worldRank != 0, so I'm a remote node. - done = 0; - while (!done) { - MPI::COMM_WORLD.Recv(&which_atom, 1, MPI_INT, 0, - TAKE_THIS_TAG, istatus); + for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) { + + // Am I the node which has this atom? + + if (AtomToProcMap[i] == worldRank) { - if (which_atom == -1) { - done=1; - continue; - } else { + local_index=-1; + for (j=0; (jgetMyNlocal()) && (local_index < 0); j++) { + if (atoms[j]->getGlobalIndex() == which_atom) local_index = j; + } + if (local_index != -1) { + + atomTypeString = atoms[local_index]->getType(); - //format the line - sprintf( tempBuffer, - "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", - atoms[which_atom]->getType(), - atoms[which_atom]->getX(), - atoms[which_atom]->getY(), - atoms[which_atom]->getZ(), - atoms[which_atom]->get_vx(), - atoms[which_atom]->get_vy(), - atoms[which_atom]->get_vz()); // check here. - strcpy( writeLine, tempBuffer ); - - if( atoms[which_atom]->isDirectional() ){ - - dAtom = (DirectionalAtom *)atoms[which_atom]; - dAtom->getQ( q ); - - sprintf( tempBuffer, - "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n", - q[0], - q[1], - q[2], - q[3], - dAtom->getJx(), - dAtom->getJy(), - dAtom->getJz()); - strcat( writeLine, tempBuffer ); + atoms[local_index]->getPos(pos); + atoms[local_index]->getVel(vel); + + atomTransData[0] = pos[0]; + atomTransData[1] = pos[1]; + atomTransData[2] = pos[2]; + + atomTransData[3] = vel[0]; + atomTransData[4] = vel[1]; + atomTransData[5] = vel[2]; + + isDirectional = 0; + + if( atoms[local_index]->isDirectional() ){ + + isDirectional = 1; + + dAtom = (DirectionalAtom *)atoms[local_index]; + dAtom->getQ( q ); + + atomOrientData[0] = q[0]; + atomOrientData[1] = q[1]; + atomOrientData[2] = q[2]; + atomOrientData[3] = q[3]; + + atomOrientData[4] = dAtom->getJx(); + atomOrientData[5] = dAtom->getJy(); + atomOrientData[6] = dAtom->getJz(); + } + + } else { + sprintf(painCave.errMsg, + "Atom %d not found on processor %d\n", + i, worldRank ); + haveError= 1; + simError(); } - else - strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" ); + + // I've survived this far, so send off the data! + + atomTypeTag = 4*i; + atomIsDirectionalTag = 4*i + 1; + atomTransDataTag = 4*i + 2; + atomOrientDataTag = 4*i + 3; + + strncpy(MPIatomTypeString, atomTypeString, MINIBUFFERSIZE); + + MPI_Send(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, 0, + atomTypeTag, MPI_COMM_WORLD); - MPI::COMM_WORLD.Send(writeLine, BUFFERSIZE, MPI_CHAR, 0, - TAKE_THIS_TAG); + MPI_Send(&isDirectional, 1, MPI_INT, 0, + atomIsDirectionalTag, MPI_COMM_WORLD); + + MPI_Send(atomTransData, 6, MPI_DOUBLE, 0, + atomTransDataTag, MPI_COMM_WORLD); + + if (isDirectional) { + + MPI_Send(atomOrientData, 7, MPI_DOUBLE, 0, + atomOrientDataTag, MPI_COMM_WORLD); + + } + } } - } - finalOut.flush(); - sprintf( checkPointMsg, - "Sucessfully took a dump.\n"); - MPIcheckPoint(); - if( worldRank == 0 ) finalOut.close(); + sprintf( checkPointMsg, + "Sucessfully wrote final file.\n"); + MPIcheckPoint(); + + } + + painCave.isEventLoop = 0; + + if( worldRank == 0 ) finalOut.close(); #endif // is_mpi } + + + +#ifdef IS_MPI + +// a couple of functions to let us escape the write loop + +void dWrite::DieDieDie( void ){ + + MPI_Finalize(); + exit (0); +} + +#endif //is_mpi