--- trunk/OOPSE/libmdtools/DumpWriter.cpp 2003/03/21 17:42:12 378 +++ trunk/OOPSE/libmdtools/DumpWriter.cpp 2004/01/13 15:46:49 929 @@ -1,20 +1,25 @@ -#include +#define _FILE_OFFSET_BITS 64 + +#include #include #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; @@ -22,27 +27,27 @@ 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 ){ - + + + dumpFile.open(entry_plug->sampleName, ios::out | ios::trunc ); + + if( !dumpFile ){ + sprintf( painCave.errMsg, "Could not open \"%s\" for dump output.\n", - outName); + entry_plug->sampleName); painCave.isFatal = 1; simError(); } - + //outFile.setf( ios::scientific ); #ifdef IS_MPI } + //sort the local atoms by global index + sortByGlobalIndex(); + sprintf( checkPointMsg, "Sucessfully opened output file for dumping.\n"); MPIcheckPoint(); @@ -55,54 +60,164 @@ DumpWriter::~DumpWriter( ){ if(worldRank == 0 ){ #endif // is_mpi - outFile.close(); + dumpFile.close(); #ifdef IS_MPI } #endif // is_mpi } -void DumpWriter::writeDump( double currentTime ){ +#ifdef IS_MPI + +/** + * A hook function to load balancing + */ + +void DumpWriter::update(){ + sortByGlobalIndex(); +} +/** + * Auxiliary sorting function + */ + +bool indexSortingCriterion(const pair& p1, const pair& p2){ + return p1.second < p2.second; +} + +/** + * Sorting the local index by global index + */ + +void DumpWriter::sortByGlobalIndex(){ + Atom** atoms = entry_plug->atoms; + + indexArray.clear(); + + for(int i = 0; i < mpiSim->getMyNlocal();i++) + indexArray.push_back(make_pair(i, atoms[i]->getGlobalIndex())); + + sort(indexArray.begin(), indexArray.end(), indexSortingCriterion); +} +#endif + +void DumpWriter::writeDump(double currentTime){ + +// write to eor file + writeFinal(currentTime); + +//write to dump file + writeFrame(dumpFile, currentTime); + +} + +void DumpWriter::writeFinal(double currentTime){ + + ofstream finalOut; + + //Open eor file +#ifdef IS_MPI + if(worldRank == 0 ){ +#endif // is_mpi + + finalOut.open( entry_plug->finalName, ios::out | ios::trunc ); + if( !finalOut ){ + sprintf( painCave.errMsg, + "Could not open \"%s\" for final dump output.\n", + entry_plug->finalName ); + painCave.isFatal = 1; + simError(); + } + +#ifdef IS_MPI + } +#endif + + //write to eor file + writeFrame(finalOut, currentTime); + + //close eor file +#ifdef IS_MPI + if(worldRank == 0 ){ + finalOut.close(); + } +#endif // is_mpi + +} + +void DumpWriter::writeFrame( ofstream& outFile, double currentTime ){ + const int BUFFERSIZE = 2000; + const int MINIBUFFERSIZE = 100; + char tempBuffer[BUFFERSIZE]; char writeLine[BUFFERSIZE]; int i; + +#ifdef IS_MPI + + int *potatoes; + int myPotato; + + int nProc; + int j, which_node, done, which_atom, local_index, currentIndex; + double atomData6[6]; + double atomData13[13]; + int isDirectional; + char* atomTypeString; + char MPIatomTypeString[MINIBUFFERSIZE]; + +#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]; #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], @@ -116,436 +231,323 @@ 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]; + /* code to find maximum tag value */ + + int *tagub, flag, MAXTAG; + MPI_Attr_get(MPI_COMM_WORLD, MPI_TAG_UB, &tagub, &flag); + if (flag) { + MAXTAG = *tagub; + } else { + MAXTAG = 32767; + } - + int haveError; + + MPI_Status istatus; + int *AtomToProcMap = mpiSim->getAtomToProcMap(); + // write out header and node 0's coordinates if( worldRank == 0 ){ + + // Node 0 needs a list of the magic potatoes for each processor; + + nProc = mpiSim->getNumberProcessors(); + potatoes = new int[nProc]; + + for (i = 0; i < nProc; i++) + potatoes[i] = 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 ){ + << 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(); + + currentIndex = 0; + for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) { - mpiErr = MPI_Recv(&nodeAtomsStart,1,MPI_INT,procIndex, - TAKE_THIS_TAG,MPI_COMM_WORLD,istatus); + // Get the Node number which has this atom; - mpiErr = MPI_Recv(&nodeAtomsEnd,1,MPI_INT,procIndex, - TAKE_THIS_TAG,MPI_COMM_WORLD, istatus); + which_node = AtomToProcMap[i]; - // 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++; - } - } + if (which_node != 0) { - else if( worldRank == procIndex ){ + if (potatoes[which_node] + 3 >= MAXTAG) { + // The potato was going to exceed the maximum value, + // so wrap this processor potato back to 0: - nodeAtomsStart = mpiSim->getMyAtomStart(); - nodeAtomsEnd = mpiSim->getMyAtomEnd(); + potatoes[which_node] = 0; + MPI_Send(0, 1, MPI_INT, which_node, 0, MPI_COMM_WORLD); + + } - 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); + myPotato = potatoes[which_node]; + + MPI_Recv(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, which_node, + myPotato, MPI_COMM_WORLD, &istatus); + + atomTypeString = MPIatomTypeString; - sendError = -1; - mpiErr = MPI_Recv(&sendError,1,MPI_INT,0,TAKE_THIS_TAG, - MPI_COMM_WORLD, istatus); + myPotato++; - if (sendError) MPIcheckPoint(); + MPI_Recv(&isDirectional, 1, MPI_INT, which_node, + myPotato, MPI_COMM_WORLD, &istatus); + + myPotato++; - // send current node's configuration line by line. + if (isDirectional) { + MPI_Recv(atomData13, 13, MPI_DOUBLE, which_node, + myPotato, MPI_COMM_WORLD, &istatus); + } else { + MPI_Recv(atomData6, 6, MPI_DOUBLE, which_node, + myPotato, MPI_COMM_WORLD, &istatus); + } + + myPotato++; + potatoes[which_node] = myPotato; - for( i=0; igetType(); - 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()); // 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 ); - } - 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); - } - } - - sprintf(checkPointMsg,"Node %d sent dump configuration.", - procIndex); - MPIcheckPoint(); - } - -#endif // is_mpi -} + atoms[local_index]->getPos(pos); + atoms[local_index]->getVel(vel); + atomData6[0] = pos[0]; + atomData6[1] = pos[1]; + atomData6[2] = pos[2]; + atomData6[3] = vel[0]; + atomData6[4] = vel[1]; + atomData6[5] = vel[2]; + + isDirectional = 0; -void DumpWriter::writeFinal(){ + if( atoms[local_index]->isDirectional() ){ + + isDirectional = 1; + + dAtom = (DirectionalAtom *)atoms[local_index]; + dAtom->getQ( q ); - - const int BUFFERSIZE = 2000; - char tempBuffer[500]; - 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; - -#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, - "Could not open \"%s\" for final dump output.\n", - finalName ); - painCave.isFatal = 1; - simError(); - } - - // finalOut.setf( ios::scientific ); - -#ifdef IS_MPI - } - - sprintf(checkPointMsg,"Opened file for final configuration\n"); - 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"; - - for( i=0; igetJx(); + atomData13[11] = dAtom->getJy(); + atomData13[12] = dAtom->getJz(); + } + + } else { + sprintf(painCave.errMsg, + "Atom %d not found on processor %d\n", + i, worldRank ); + haveError= 1; + simError(); + } + + if(haveError) DieDieDie(); + + currentIndex ++; + } + // 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()); - strcpy( writeLine, tempBuffer ); + if (!isDirectional) { + + sprintf( writeLine, + "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", + atomTypeString, + atomData6[0], + atomData6[1], + atomData6[2], + atomData6[3], + atomData6[4], + atomData6[5]); - if( atoms[i]->isDirectional() ){ + strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" ); - dAtom = (DirectionalAtom *)atoms[i]; - dAtom->getQ( q ); + } else { - 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" ); + sprintf( writeLine, + "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n", + atomTypeString, + atomData13[0], + atomData13[1], + atomData13[2], + atomData13[3], + atomData13[4], + atomData13[5], + atomData13[6], + atomData13[7], + atomData13[8], + atomData13[9], + atomData13[10], + atomData13[11], + atomData13[12]); + + } - finalOut << writeLine; - } - finalOut.flush(); + outFile << writeLine; + } + -#else // is_mpi + outFile.flush(); + sprintf( checkPointMsg, + "Sucessfully took a dump.\n"); + MPIcheckPoint(); + delete[] potatoes; + } else { - int masterIndex; - int nodeAtomsStart; - int nodeAtomsEnd; - int mpiErr; - int sendError; - int procIndex; - - MPI_Status istatus[MPI_STATUS_SIZE]; + // worldRank != 0, so I'm a remote node. - - // write out header and node 0's coordinates + // Set my magic potato to 0: - if( worldRank == 0 ){ - finalOut << mpiSim->getTotAtoms() << "\n"; - - finalOut << entry_plug->box_x << "\t" - << entry_plug->box_y << "\t" - << entry_plug->box_z << "\n"; + myPotato = 0; + currentIndex = 0; - masterIndex = 0; - - for( i=0; igetTotAtoms(); i++ ) { - 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()); - 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.flush(); - } - - for (procIndex = 1; procIndex < mpiSim->getNumberProcessors(); - procIndex++){ + // Am I the node which has this atom? + + if (AtomToProcMap[i] == worldRank) { - if( worldRank == 0 ){ - - mpiErr = MPI_Recv(&nodeAtomsStart,1,MPI_INT,procIndex, - TAKE_THIS_TAG,MPI_COMM_WORLD,istatus); + if (myPotato + 3 >= MAXTAG) { - 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); + // The potato was going to exceed the maximum value, + // so wrap this processor potato back to 0 (and block until + // node 0 says we can go: - // recieve the nodes writeLines + MPI_Recv(&myPotato, 1, MPI_INT, 0, 0, MPI_COMM_WORLD, &istatus); + + } + which_atom = i; + local_index = indexArray[currentIndex].first; + + if (which_atom == indexArray[currentIndex].second) { + + atomTypeString = atoms[local_index]->getType(); - for ( i = nodeAtomsStart; i <= nodeAtomsEnd; i++){ - - mpiErr = MPI_Recv(writeLine,BUFFERSIZE,MPI_CHAR,procIndex, - TAKE_THIS_TAG,MPI_COMM_WORLD,istatus ); + atoms[local_index]->getPos(pos); + atoms[local_index]->getVel(vel); - finalOut << writeLine; - masterIndex++; - } + atomData6[0] = pos[0]; + atomData6[1] = pos[1]; + atomData6[2] = pos[2]; - finalOut.flush(); - } + atomData6[3] = vel[0]; + atomData6[4] = vel[1]; + atomData6[5] = vel[2]; + + isDirectional = 0; - else if( worldRank == procIndex ){ + if( atoms[local_index]->isDirectional() ){ - 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(); + isDirectional = 1; + + dAtom = (DirectionalAtom *)atoms[local_index]; + dAtom->getQ( q ); + + for (int j = 0; j < 6 ; j++) + atomData13[j] = atomData6[j]; + + atomData13[6] = q[0]; + atomData13[7] = q[1]; + atomData13[8] = q[2]; + atomData13[9] = q[3]; - // send current node's configuration line by line. + atomData13[10] = dAtom->getJx(); + atomData13[11] = dAtom->getJy(); + atomData13[12] = dAtom->getJz(); + } - 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 { + 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); + + strncpy(MPIatomTypeString, atomTypeString, MINIBUFFERSIZE); + + // null terminate the string before sending (just in case): + MPIatomTypeString[MINIBUFFERSIZE-1] = '\0'; + + MPI_Send(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, 0, + myPotato, MPI_COMM_WORLD); + + myPotato++; + + MPI_Send(&isDirectional, 1, MPI_INT, 0, + myPotato, MPI_COMM_WORLD); + + myPotato++; + + if (isDirectional) { + + MPI_Send(atomData13, 13, MPI_DOUBLE, 0, + myPotato, MPI_COMM_WORLD); + + } else { + + MPI_Send(atomData6, 6, MPI_DOUBLE, 0, + myPotato, MPI_COMM_WORLD); + } + + myPotato++; + currentIndex++; } } - - sprintf(checkPointMsg,"Node %d sent dump configuration.", - procIndex); - MPIcheckPoint(); - } - if( worldRank == 0 ) finalOut.close(); - + sprintf( checkPointMsg, + "Sucessfully took a dump.\n"); + MPIcheckPoint(); + } + #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