--- trunk/OOPSE/libmdtools/DumpWriter.cpp 2004/01/07 19:26:12 905 +++ trunk/OOPSE/libmdtools/DumpWriter.cpp 2004/01/09 20:29:32 916 @@ -7,12 +7,9 @@ #ifdef IS_MPI #include #include "mpiSimulation.hpp" -#define TAKE_THIS_TAG_CHAR 15 -#define TAKE_THIS_TAG_INT 20 namespace dWrite{ - void nodeZeroError( void ); - void anonymousNodeDie( void ); + void DieDieDie( void ); } using namespace dWrite; @@ -69,12 +66,26 @@ 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; + #ifdef IS_MPI + + int *potatoes; + int myPotato; + + int nProc; int j, which_node, done, which_atom, local_index; + 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 @@ -84,7 +95,6 @@ void DumpWriter::writeDump( double currentTime ){ Atom** atoms = entry_plug->atoms; double pos[3], vel[3]; - // write current frame to the eor file this->writeFinal( currentTime ); @@ -150,10 +160,15 @@ void DumpWriter::writeDump( double currentTime ){ #else // is_mpi - // first thing first, suspend fatalities. - painCave.isEventLoop = 1; + /* 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 myStatus; // 1 = wakeup & success; 0 = error; -1 = AllDone int haveError; MPI_Status istatus; @@ -162,6 +177,15 @@ void DumpWriter::writeDump( double currentTime ){ // 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" @@ -180,174 +204,269 @@ void DumpWriter::writeDump( double currentTime ){ 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]; + + if (which_node != 0) { - if (which_node == 0 ) { + if (potatoes[which_node] + 3 >= MAXTAG) { + // The potato was going to exceed the maximum value, + // so wrap this processor potato back to 0: + potatoes[which_node] = 0; + MPI_Send(0, 1, MPI_INT, which_node, 0, MPI_COMM_WORLD); + + } + + myPotato = potatoes[which_node]; + + MPI_Recv(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, which_node, + myPotato, MPI_COMM_WORLD, &istatus); + + strncpy(atomTypeString, MPIatomTypeString, MINIBUFFERSIZE); + + // Null terminate the atomTypeString just in case: + + atomTypeString[strlen(atomTypeString) - 1] = '\0'; + + myPotato++; + + MPI_Recv(&isDirectional, 1, MPI_INT, which_node, + myPotato, MPI_COMM_WORLD, &istatus); + + myPotato++; + + 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; + + } 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) { - //format the line + + atomTypeString = atoms[local_index]->getType(); atoms[local_index]->getPos(pos); - atoms[local_index]->getVel(vel); + 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(), - pos[0], - pos[1], - pos[2], - vel[0], - vel[1], - vel[2]); // check here. - strcpy( writeLine, tempBuffer ); + 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; + if( atoms[local_index]->isDirectional() ){ + isDirectional = 1; + 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], - 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" ); - } - else { + 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]; + + atomData13[10] = dAtom->getJx(); + 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(); + + // If we've survived to here, format the line: + + if (!isDirectional) { - if(haveError) nodeZeroError(); + sprintf( tempBuffer, + "%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]); + + strcpy( writeLine, tempBuffer ); + strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" ); + } else { + + sprintf( tempBuffer, + "%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]); + + strcat( writeLine, tempBuffer ); + + } + + outFile << writeLine; + outFile.flush(); } - else { - myStatus = 1; - 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, - TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus); - - if(!myStatus) nodeZeroError(); - - } - - outFile << writeLine; - outFile.flush(); } - // kill everyone off: - myStatus = -1; - for (j = 1; j < mpiSim->getNumberProcessors(); j++) { - MPI_Send(&myStatus, 1, MPI_INT, j, - TAKE_THIS_TAG_INT, MPI_COMM_WORLD); - } - + outFile.flush(); + sprintf( checkPointMsg, + "Sucessfully took a dump.\n"); + MPIcheckPoint(); + } else { - done = 0; - while (!done) { + // worldRank != 0, so I'm a remote node. - MPI_Recv(&myStatus, 1, MPI_INT, 0, - TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus); + // Set my magic potato to 0: - if(!myStatus) anonymousNodeDie(); + myPotato = 0; + + for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) { + + // Am I the node which has this atom? + + if (AtomToProcMap[i] == worldRank) { - if(myStatus < 0) break; + if (myPotato + 3 >= MAXTAG) { - MPI_Recv(&which_atom, 1, MPI_INT, 0, - TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus); + // 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: - myStatus = 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 + MPI_Recv(&myPotato, 1, MPI_INT, 0, 0, MPI_COMM_WORLD, &istatus); + + } - atoms[local_index]->getPos(pos); - atoms[local_index]->getVel(vel); + 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(); - sprintf( tempBuffer, - "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", - atoms[local_index]->getType(), - pos[0], - pos[1], - pos[2], - vel[0], - vel[1], - vel[2]); // check here. - strcpy( writeLine, tempBuffer ); + atoms[local_index]->getPos(pos); + atoms[local_index]->getVel(vel); - if( atoms[local_index]->isDirectional() ){ + atomData6[0] = pos[0]; + atomData6[1] = pos[1]; + atomData6[2] = pos[2]; - dAtom = (DirectionalAtom *)atoms[local_index]; - dAtom->getQ( q ); + atomData6[3] = vel[0]; + atomData6[4] = vel[1]; + atomData6[5] = vel[2]; + + isDirectional = 0; - 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( atoms[local_index]->isDirectional() ){ + + 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]; + + atomData13[10] = dAtom->getJx(); + 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(); } - 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"); - } + strncpy(MPIatomTypeString, atomTypeString, MINIBUFFERSIZE); - MPI_Send(writeLine, BUFFERSIZE, MPI_CHAR, 0, - TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD); - MPI_Send( &myStatus, 1, MPI_INT, 0, - TAKE_THIS_TAG_INT, MPI_COMM_WORLD); - } - } - outFile.flush(); - sprintf( checkPointMsg, - "Sucessfully took a dump.\n"); - MPIcheckPoint(); + // null terminate the string before sending (just in case): + MPIatomTypeString[MINIBUFFERSIZE-1] = '\0'; - // last thing last, enable fatalities. - painCave.isEventLoop = 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++; + } + } + + sprintf( checkPointMsg, + "Sucessfully took a dump.\n"); + MPIcheckPoint(); + + } + #endif // is_mpi } @@ -357,6 +476,7 @@ void DumpWriter::writeFinal(double finalTime){ ofstream finalOut; const int BUFFERSIZE = 2000; + const int MINIBUFFERSIZE = 100; char tempBuffer[BUFFERSIZE]; char writeLine[BUFFERSIZE]; @@ -365,7 +485,18 @@ void DumpWriter::writeFinal(double finalTime){ Atom** atoms = entry_plug->atoms; int i; #ifdef IS_MPI + + int *potatoes; + int myPotato; + + int nProc; int j, which_node, done, which_atom, local_index; + 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 @@ -461,10 +592,15 @@ void DumpWriter::writeFinal(double finalTime){ #else // is_mpi - // first thing first, suspend fatalities. - painCave.isEventLoop = 1; + /* 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 myStatus; // 1 = wakeup & success; 0 = error; -1 = AllDone int haveError; MPI_Status istatus; @@ -472,188 +608,297 @@ void DumpWriter::writeFinal(double finalTime){ // write out header and node 0's coordinates - haveError = 0; 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; + finalOut << mpiSim->getTotAtoms() << "\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][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][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] << ";"; + << 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; + finalOut.flush(); for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) { - // Get the Node number which has this molecule: - + + // Get the Node number which has this atom; + which_node = AtomToProcMap[i]; + + if (which_node != 0) { - if (which_node == mpiSim->getMyNode()) { + if (potatoes[which_node] + 3 >= MAXTAG) { + // The potato was going to exceed the maximum value, + // so wrap this processor potato back to 0: + potatoes[which_node] = 0; + MPI_Send(0, 1, MPI_INT, which_node, 0, MPI_COMM_WORLD); + + } + + myPotato = potatoes[which_node]; + + MPI_Recv(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, which_node, + myPotato, MPI_COMM_WORLD, &istatus); + + strncpy(atomTypeString, MPIatomTypeString, MINIBUFFERSIZE); + + // Null terminate the atomTypeString just in case: + + atomTypeString[strlen(atomTypeString) - 1] = '\0'; + + myPotato++; + + MPI_Recv(&isDirectional, 1, MPI_INT, which_node, + myPotato, MPI_COMM_WORLD, &istatus); + + myPotato++; + + 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; + + } 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); + 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(), - pos[0], - pos[1], - pos[2], - vel[0], - vel[1], - vel[2]); - strcpy( writeLine, tempBuffer ); + atomData6[0] = pos[0]; + atomData6[1] = pos[1]; + atomData6[2] = pos[2]; - if( atoms[local_index]->isDirectional() ){ + atomData6[3] = vel[0]; + atomData6[4] = vel[1]; + atomData6[5] = vel[2]; + + isDirectional = 0; - dAtom = (DirectionalAtom *)atoms[local_index]; - dAtom->getQ( q ); + if( atoms[local_index]->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()); - strcat( writeLine, tempBuffer ); - } - else - strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" ); - } - else { + 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]; + + atomData13[10] = dAtom->getJx(); + 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(); + + // If we've survived to here, format the line: + + if (!isDirectional) { - if(haveError) nodeZeroError(); + sprintf( tempBuffer, + "%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]); + + strcpy( writeLine, tempBuffer ); + strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" ); + } else { + + sprintf( tempBuffer, + "%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]); + + strcat( writeLine, tempBuffer ); + + } + + finalOut << writeLine; + finalOut.flush(); } - else { + } - myStatus = 1; - 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, - TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus); + finalOut.flush(); + sprintf( checkPointMsg, + "Sucessfully took a dump.\n"); + MPIcheckPoint(); + + } else { - if(!myStatus) nodeZeroError(); - } + // worldRank != 0, so I'm a remote node. - finalOut << writeLine; - } + // Set my magic potato to 0: - // kill everyone off: - myStatus = -1; - for (j = 1; j < mpiSim->getNumberProcessors(); j++) { - MPI_Send(&myStatus, 1, MPI_INT, j, - TAKE_THIS_TAG_INT, MPI_COMM_WORLD); - } + myPotato = 0; + + for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) { + + // Am I the node which has this atom? + + if (AtomToProcMap[i] == worldRank) { - } else { + if (myPotato + 3 >= MAXTAG) { - done = 0; - while (!done) { + // 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: - MPI_Recv(&myStatus, 1, MPI_INT, 0, - TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus); + MPI_Recv(&myPotato, 1, MPI_INT, 0, 0, MPI_COMM_WORLD, &istatus); + + } - if(!myStatus) anonymousNodeDie(); + 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(); - if(myStatus < 0) break; + atoms[local_index]->getPos(pos); + atoms[local_index]->getVel(vel); - MPI_Recv(&which_atom, 1, MPI_INT, 0, - TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus); + atomData6[0] = pos[0]; + atomData6[1] = pos[1]; + atomData6[2] = pos[2]; - myStatus = 1; - local_index=-1; - for (j=0; j < mpiSim->getMyNlocal(); j++) { - if (atoms[j]->getGlobalIndex() == which_atom) local_index = j; - } - if (local_index != -1) { + atomData6[3] = vel[0]; + atomData6[4] = vel[1]; + atomData6[5] = vel[2]; + + isDirectional = 0; - atoms[local_index]->getPos(pos); - atoms[local_index]->getVel(vel); + if( atoms[local_index]->isDirectional() ){ - //format the line - sprintf( tempBuffer, - "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", - atoms[local_index]->getType(), - pos[0], - pos[1], - pos[2], - vel[0], - vel[1], - vel[2]); // check here. - strcpy( writeLine, tempBuffer ); + 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]; - if( atoms[local_index]->isDirectional() ){ + atomData13[10] = dAtom->getJx(); + atomData13[11] = dAtom->getJy(); + atomData13[12] = dAtom->getJz(); + } - 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], - 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" ); - } - } - 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"); - } + strncpy(MPIatomTypeString, atomTypeString, MINIBUFFERSIZE); - MPI_Send(writeLine, BUFFERSIZE, MPI_CHAR, 0, - TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD); - MPI_Send( &myStatus, 1, MPI_INT, 0, - TAKE_THIS_TAG_INT, MPI_COMM_WORLD); + // 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++; + } } - } - finalOut.flush(); - sprintf( checkPointMsg, - "Sucessfully took a dump.\n"); - MPIcheckPoint(); + sprintf( checkPointMsg, + "Sucessfully took a dump.\n"); + MPIcheckPoint(); + + } + if( worldRank == 0 ) finalOut.close(); #endif // is_mpi } @@ -664,25 +909,10 @@ void dWrite::nodeZeroError( void ){ // a couple of functions to let us escape the write loop -void dWrite::nodeZeroError( void ){ - int j, myStatus; +void dWrite::DieDieDie( void ){ - myStatus = 0; - 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 ){ - - MPI_Finalize(); - exit (0); -} - #endif //is_mpi