--- trunk/OOPSE/libmdtools/DumpWriter.cpp 2003/03/21 17:42:12 378 +++ trunk/OOPSE/libmdtools/DumpWriter.cpp 2004/01/08 18:05:37 910 @@ -1,20 +1,23 @@ -#include +#define _FILE_OFFSET_BITS 64 + +#include #include #include #ifdef IS_MPI #include #include "mpiSimulation.hpp" -#define TAKE_THIS_TAG 0 + +namespace dWrite{ + void DieDieDie( void ); +} + +using namespace dWrite; #endif //is_mpi #include "ReadWrite.hpp" #include "simError.h" - - - - DumpWriter::DumpWriter( SimInfo* the_entry_plug ){ entry_plug = the_entry_plug; @@ -22,22 +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 @@ -63,46 +64,80 @@ void DumpWriter::writeDump( double currentTime ){ } void DumpWriter::writeDump( double currentTime ){ - + const int BUFFERSIZE = 2000; + const int MINIBUFFERSIZE = 10; + char tempBuffer[BUFFERSIZE]; char writeLine[BUFFERSIZE]; 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], @@ -116,206 +151,301 @@ 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 - int masterIndex; - int nodeAtomsStart; - int nodeAtomsEnd; - int mpiErr; - int sendError; - int procIndex; - - MPI_Status istatus[MPI_STATUS_SIZE]; + // 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"; - masterIndex = 0; - for( i=0; igetType(), - atoms[i]->getX(), - atoms[i]->getY(), - atoms[i]->getZ(), - atoms[i]->get_vx(), - atoms[i]->get_vy(), - atoms[i]->get_vz()); - 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], - q[1], - q[2], - q[3], - dAtom->getJx(), - 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" ); - - outFile << writeLine; - masterIndex++; - } - outFile.flush(); - } + outFile << currentTime << ";\t" + << entry_plug->Hmat[0][0] << "\t" + << entry_plug->Hmat[1][0] << "\t" + << entry_plug->Hmat[2][0] << ";\t" - sprintf( checkPointMsg, - "Sucessfully wrote node 0's dump configuration.\n"); - MPIcheckPoint(); - - for (procIndex = 1; procIndex < mpiSim->getNumberProcessors(); - procIndex++){ + << entry_plug->Hmat[0][1] << "\t" + << entry_plug->Hmat[1][1] << "\t" + << entry_plug->Hmat[2][1] << ";\t" - if( worldRank == 0 ){ - - mpiErr = MPI_Recv(&nodeAtomsStart,1,MPI_INT,procIndex, - TAKE_THIS_TAG,MPI_COMM_WORLD,istatus); - - mpiErr = MPI_Recv(&nodeAtomsEnd,1,MPI_INT,procIndex, - TAKE_THIS_TAG,MPI_COMM_WORLD, istatus); - - // Make sure where node 0 is writing to, matches where the - // receiving node expects it to be. - - if (masterIndex != nodeAtomsStart){ - sendError = 1; - mpiErr = MPI_Send(&sendError,1,MPI_INT,procIndex,TAKE_THIS_TAG, - MPI_COMM_WORLD); - sprintf(painCave.errMsg, - "DumpWriter error: atoms start index (%d) for " - "node %d not equal to master index (%d)", - nodeAtomsStart,procIndex,masterIndex ); - painCave.isFatal = 1; - simError(); - } - - sendError = 0; - mpiErr = MPI_Send(&sendError,1,MPI_INT,procIndex,TAKE_THIS_TAG, - MPI_COMM_WORLD); - - // recieve the nodes writeLines - - for ( i = nodeAtomsStart; i <= nodeAtomsEnd; i++){ - - mpiErr = MPI_Recv(writeLine,BUFFERSIZE,MPI_CHAR,procIndex, - TAKE_THIS_TAG,MPI_COMM_WORLD,istatus ); - - outFile << writeLine; - masterIndex++; - } - } + << entry_plug->Hmat[0][2] << "\t" + << entry_plug->Hmat[1][2] << "\t" + << entry_plug->Hmat[2][2] << ";"; - else if( worldRank == procIndex ){ + 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; - nodeAtomsStart = mpiSim->getMyAtomStart(); - nodeAtomsEnd = mpiSim->getMyAtomEnd(); + which_node = AtomToProcMap[i]; - mpiErr = MPI_Send(&nodeAtomsStart,1,MPI_INT,0,TAKE_THIS_TAG, - MPI_COMM_WORLD); - mpiErr = MPI_Send(&nodeAtomsEnd,1,MPI_INT,0,TAKE_THIS_TAG, - MPI_COMM_WORLD); - - sendError = -1; - mpiErr = MPI_Recv(&sendError,1,MPI_INT,0,TAKE_THIS_TAG, - MPI_COMM_WORLD, istatus); + if (which_node != 0) { + + atomTypeTag = 4*i; + atomIsDirectionalTag = 4*i + 1; + atomTransDataTag = 4*i + 2; + atomOrientDataTag = 4*i + 3; - if (sendError) MPIcheckPoint(); + MPI_Recv(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, which_node, + atomTypeTag, MPI_COMM_WORLD, &istatus); + + strncpy(atomTypeString, MPIatomTypeString, MINIBUFFERSIZE); - // send current node's configuration line by line. + 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); - for( i=0; igetType(), - atoms[i]->getX(), - atoms[i]->getY(), - atoms[i]->getZ(), - atoms[i]->get_vx(), - atoms[i]->get_vy(), - atoms[i]->get_vz()); // check here. - 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], - q[1], - q[2], - q[3], - dAtom->getJx(), - dAtom->getJy(), - dAtom->getJz()); - strcat( writeLine, tempBuffer ); + 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(); } - else - strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" ); - - mpiErr = MPI_Send(writeLine,BUFFERSIZE,MPI_CHAR,0,TAKE_THIS_TAG, - MPI_COMM_WORLD); + + 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", + atomTypeString, + atomTransData[0], + atomTransData[1], + atomTransData[2], + atomTransData[3], + atomTransData[4], + atomTransData[5]); + + strcpy( writeLine, tempBuffer ); + + if (isDirectional) { + + sprintf( tempBuffer, + "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n", + 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" ); + } + + outFile << writeLine; + outFile.flush(); } } + + outFile.flush(); + sprintf( checkPointMsg, + "Sucessfully took a dump.\n"); + MPIcheckPoint(); + + } else { + + // worldRank != 0, so I'm a remote node. + + for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) { - sprintf(checkPointMsg,"Node %d sent dump configuration.", - procIndex); - MPIcheckPoint(); - } + // Am I the node which has this atom? + + if (AtomToProcMap[i] == worldRank) { + + 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(); + } + + // 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_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); + + } + + } + } + + sprintf( checkPointMsg, + "Sucessfully took a dump.\n"); + MPIcheckPoint(); + } + + painCave.isEventLoop = 0; + #endif // is_mpi } +void DumpWriter::writeFinal(double finalTime){ + char finalName[500]; + ofstream finalOut; -void DumpWriter::writeFinal(){ - - const int BUFFERSIZE = 2000; - char tempBuffer[500]; + const int MINIBUFFERSIZE = 10; + char tempBuffer[BUFFERSIZE]; char writeLine[BUFFERSIZE]; - - char finalName[500]; - int i; double q[4]; DirectionalAtom* dAtom; - int nAtoms = entry_plug->n_atoms; Atom** atoms = entry_plug->atoms; - - ofstream finalOut; - + 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, @@ -324,45 +454,60 @@ 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], @@ -376,176 +521,275 @@ 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 - int masterIndex; - int nodeAtomsStart; - int nodeAtomsEnd; - int mpiErr; - int sendError; - int procIndex; - - MPI_Status istatus[MPI_STATUS_SIZE]; + // 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"; - - masterIndex = 0; - - for( i=0; igetType(), - atoms[i]->getX(), - atoms[i]->getY(), - atoms[i]->getZ(), - atoms[i]->get_vx(), - atoms[i]->get_vy(), - atoms[i]->get_vz()); - 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], - q[1], - q[2], - q[3], - dAtom->getJx(), - 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" ); - - finalOut << writeLine; - masterIndex++; - } + + 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 (procIndex = 1; procIndex < mpiSim->getNumberProcessors(); - procIndex++){ + for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) { + // Get the Node number which has this atom; - if( worldRank == 0 ){ - - mpiErr = MPI_Recv(&nodeAtomsStart,1,MPI_INT,procIndex, - TAKE_THIS_TAG,MPI_COMM_WORLD,istatus); + which_node = AtomToProcMap[i]; - mpiErr = MPI_Recv(&nodeAtomsEnd,1,MPI_INT,procIndex, - TAKE_THIS_TAG,MPI_COMM_WORLD, istatus); - - // Make sure where node 0 is writing to, matches where the - // receiving node expects it to be. - - if (masterIndex != nodeAtomsStart){ - sendError = 1; - mpiErr = MPI_Send(&sendError,1,MPI_INT,procIndex,TAKE_THIS_TAG, - MPI_COMM_WORLD); - sprintf(painCave.errMsg, - "DumpWriter error: atoms start index (%d) for " - "node %d not equal to master index (%d)", - nodeAtomsStart,procIndex,masterIndex ); - painCave.isFatal = 1; - simError(); - } - - sendError = 0; - mpiErr = MPI_Send(&sendError,1,MPI_INT,procIndex,TAKE_THIS_TAG, - MPI_COMM_WORLD); + if (which_node != 0) { + + atomTypeTag = 4*i; + atomIsDirectionalTag = 4*i + 1; + atomTransDataTag = 4*i + 2; + atomOrientDataTag = 4*i + 3; - // recieve the nodes writeLines + MPI_Recv(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, which_node, + atomTypeTag, MPI_COMM_WORLD, &istatus); + + strncpy(atomTypeString, MPIatomTypeString, MINIBUFFERSIZE); - for ( i = nodeAtomsStart; i <= nodeAtomsEnd; i++){ - - mpiErr = MPI_Recv(writeLine,BUFFERSIZE,MPI_CHAR,procIndex, - TAKE_THIS_TAG,MPI_COMM_WORLD,istatus ); + 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); - finalOut << writeLine; - masterIndex++; - } + if (isDirectional) { - finalOut.flush(); - } + MPI_Recv(atomOrientData, 7, MPI_DOUBLE, which_node, + atomOrientDataTag, MPI_COMM_WORLD, &istatus); - else if( worldRank == procIndex ){ + } - nodeAtomsStart = mpiSim->getMyAtomStart(); - nodeAtomsEnd = mpiSim->getMyAtomEnd(); - - mpiErr = MPI_Send(&nodeAtomsStart,1,MPI_INT,0,TAKE_THIS_TAG, - MPI_COMM_WORLD); - mpiErr = MPI_Send(&nodeAtomsEnd,1,MPI_INT,0,TAKE_THIS_TAG, - MPI_COMM_WORLD); - - mpiErr = MPI_Recv(&sendError,1,MPI_INT,0,TAKE_THIS_TAG, - MPI_COMM_WORLD, istatus); - if (sendError) MPIcheckPoint(); + } else { + + haveError = 0; + which_atom = i; + local_index=-1; - // send current node's configuration line by line. + for (j=0; (jgetMyNlocal()) && (local_index < 0); j++) { + if (atoms[j]->getGlobalIndex() == which_atom) local_index = j; + } - for( i=0; igetType(), - atoms[i]->getX(), - atoms[i]->getY(), - atoms[i]->getZ(), - atoms[i]->get_vx(), - atoms[i]->get_vy(), - atoms[i]->get_vz()); - 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], - q[1], - q[2], - q[3], - dAtom->getJx(), - dAtom->getJy(), - dAtom->getJz()); - strcat( writeLine, tempBuffer ); + 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(); } - else - strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" ); - - mpiErr = MPI_Send(writeLine,BUFFERSIZE,MPI_CHAR,0,TAKE_THIS_TAG, - MPI_COMM_WORLD); + + 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", + atomTypeString, + atomTransData[0], + atomTransData[1], + atomTransData[2], + atomTransData[3], + atomTransData[4], + atomTransData[5]); + + strcpy( writeLine, tempBuffer ); + + if (isDirectional) { + + sprintf( tempBuffer, + "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n", + 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" ); + } + + finalOut << writeLine; + finalOut.flush(); } } + + finalOut.flush(); + sprintf( checkPointMsg, + "Sucessfully took a dump.\n"); + MPIcheckPoint(); + + } else { + + // worldRank != 0, so I'm a remote node. + + for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) { - sprintf(checkPointMsg,"Node %d sent dump configuration.", - procIndex); - MPIcheckPoint(); - } + // Am I the node which has this atom? + + if (AtomToProcMap[i] == worldRank) { - if( worldRank == 0 ) finalOut.close(); + 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(); + } + + // 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_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); + + } + + } + } + + 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