--- trunk/OOPSE-3.0/src/io/DumpWriter.cpp 2004/09/24 04:16:43 1490 +++ branches/new_design/OOPSE-3.0/src/io/DumpWriter.cpp 2004/11/01 22:52:57 1695 @@ -1,693 +1,696 @@ -#define _LARGEFILE_SOURCE64 -#define _FILE_OFFSET_BITS 64 - -#include -#include -#include -#include -#include - -#ifdef IS_MPI -#include -#include "mpiSimulation.hpp" - -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; - -#ifdef IS_MPI - if(worldRank == 0 ){ -#endif // is_mpi - - dumpFile.open(entry_plug->sampleName.c_str(), ios::out | ios::trunc ); - - if( !dumpFile ){ - - sprintf( painCave.errMsg, - "Could not open \"%s\" for dump output.\n", - entry_plug->sampleName.c_str()); - painCave.isFatal = 1; - simError(); - } - -#ifdef IS_MPI - } - - //sort the local atoms by global index - sortByGlobalIndex(); - - sprintf( checkPointMsg, - "Sucessfully opened output file for dumping.\n"); - MPIcheckPoint(); -#endif // is_mpi -} - -DumpWriter::~DumpWriter( ){ - -#ifdef IS_MPI - if(worldRank == 0 ){ -#endif // is_mpi - - dumpFile.close(); - -#ifdef IS_MPI - } -#endif // is_mpi -} - -#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(){ - Molecule* mols = entry_plug->molecules; - indexArray.clear(); - - for(int i = 0; i < entry_plug->n_mol;i++) - indexArray.push_back(make_pair(i, mols[i].getGlobalIndex())); - - sort(indexArray.begin(), indexArray.end(), indexSortingCriterion); -} - -#endif - -void DumpWriter::writeDump(double currentTime){ - - ofstream finalOut; - vector fileStreams; - -#ifdef IS_MPI - if(worldRank == 0 ){ -#endif - finalOut.open( entry_plug->finalName.c_str(), ios::out | ios::trunc ); - if( !finalOut ){ - sprintf( painCave.errMsg, - "Could not open \"%s\" for final dump output.\n", - entry_plug->finalName.c_str() ); - painCave.isFatal = 1; - simError(); - } -#ifdef IS_MPI - } -#endif // is_mpi - - fileStreams.push_back(&finalOut); - fileStreams.push_back(&dumpFile); - - writeFrame(fileStreams, currentTime); - -#ifdef IS_MPI - finalOut.close(); -#endif - -} - -void DumpWriter::writeFinal(double currentTime){ - - ofstream finalOut; - vector fileStreams; - -#ifdef IS_MPI - if(worldRank == 0 ){ -#endif // is_mpi - - finalOut.open( entry_plug->finalName.c_str(), ios::out | ios::trunc ); - - if( !finalOut ){ - sprintf( painCave.errMsg, - "Could not open \"%s\" for final dump output.\n", - entry_plug->finalName.c_str() ); - painCave.isFatal = 1; - simError(); - } - -#ifdef IS_MPI - } -#endif // is_mpi - - fileStreams.push_back(&finalOut); - writeFrame(fileStreams, currentTime); - -#ifdef IS_MPI - finalOut.close(); -#endif - -} - -void DumpWriter::writeFrame( vector& outFile, double currentTime ){ - - const int BUFFERSIZE = 2000; - const int MINIBUFFERSIZE = 100; - - char tempBuffer[BUFFERSIZE]; - char writeLine[BUFFERSIZE]; - - int i; - unsigned int k; - -#ifdef IS_MPI - - /********************************************************************* - * Documentation? You want DOCUMENTATION? - * - * Why all the potatoes below? - * - * To make a long story short, the original version of DumpWriter - * worked in the most inefficient way possible. Node 0 would - * poke each of the node for an individual atom's formatted data - * as node 0 worked its way down the global index. This was particularly - * inefficient since the method blocked all processors at every atom - * (and did it twice!). - * - * An intermediate version of DumpWriter could be described from Node - * zero's perspective as follows: - * - * 1) Have 100 of your friends stand in a circle. - * 2) When you say go, have all of them start tossing potatoes at - * you (one at a time). - * 3) Catch the potatoes. - * - * It was an improvement, but MPI has buffers and caches that could - * best be described in this analogy as "potato nets", so there's no - * need to block the processors atom-by-atom. - * - * This new and improved DumpWriter works in an even more efficient - * way: - * - * 1) Have 100 of your friend stand in a circle. - * 2) When you say go, have them start tossing 5-pound bags of - * potatoes at you. - * 3) Once you've caught a friend's bag of potatoes, - * toss them a spud to let them know they can toss another bag. - * - * How's THAT for documentation? - * - *********************************************************************/ - - int *potatoes; - int myPotato; - - int nProc; - int j, which_node, done, which_atom, local_index, currentIndex; - double atomData[13]; - int isDirectional; - char* atomTypeString; - char MPIatomTypeString[MINIBUFFERSIZE]; - int nObjects; - int msgLen; // the length of message actually recieved at master nodes -#endif //is_mpi - - double q[4], ji[3]; - DirectionalAtom* dAtom; - double pos[3], vel[3]; - int nTotObjects; - StuntDouble* sd; - char* molName; - vector integrableObjects; - vector::iterator iter; - nTotObjects = entry_plug->getTotIntegrableObjects(); -#ifndef IS_MPI - - for(k = 0; k < outFile.size(); k++){ - *outFile[k] << nTotObjects << "\n"; - - *outFile[k] << 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[k] << entry_plug->the_integrator->getAdditionalParameters() << endl; - } - - for( i=0; i< entry_plug->n_mol; i++ ){ - - integrableObjects = entry_plug->molecules[i].getIntegrableObjects(); - molName = (entry_plug->compStamps[entry_plug->molecules[i].getStampID()])->getID(); - - for( iter = integrableObjects.begin();iter != integrableObjects.end(); ++iter){ - sd = *iter; - sd->getPos(pos); - sd->getVel(vel); - - sprintf( tempBuffer, - "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", - sd->getType(), - pos[0], - pos[1], - pos[2], - vel[0], - vel[1], - vel[2]); - strcpy( writeLine, tempBuffer ); - - if( sd->isDirectional() ){ - - sd->getQ( q ); - sd->getJ( ji ); - - sprintf( tempBuffer, - "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n", - q[0], - q[1], - q[2], - q[3], - ji[0], - ji[1], - ji[2]); - strcat( writeLine, tempBuffer ); - } - else - strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" ); - - for(k = 0; k < outFile.size(); k++) - *outFile[k] << writeLine; - } - -} - -#else // is_mpi - - /* 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 nCurObj; - int *MolToProcMap = mpiSim->getMolToProcMap(); - - // 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->getNProcessors(); - potatoes = new int[nProc]; - - //write out the comment lines - for (i = 0; i < nProc; i++) - potatoes[i] = 0; - - for(k = 0; k < outFile.size(); k++){ - *outFile[k] << nTotObjects << "\n"; - - *outFile[k] << 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[k] << entry_plug->the_integrator->getAdditionalParameters() << endl; - } - - currentIndex = 0; - - for (i = 0 ; i < mpiSim->getNMolGlobal(); i++ ) { - - // Get the Node number which has this atom; - - which_node = MolToProcMap[i]; - - if (which_node != 0) { - - if (potatoes[which_node] + 1 >= MAXTAG) { - // The potato was going to exceed the maximum value, - // so wrap this processor potato back to 0: - - potatoes[which_node] = 0; - MPI_Send(&potatoes[which_node], 1, MPI_INT, which_node, 0, MPI_COMM_WORLD); - - } - - myPotato = potatoes[which_node]; - - //recieve the number of integrableObject in current molecule - MPI_Recv(&nCurObj, 1, MPI_INT, which_node, - myPotato, MPI_COMM_WORLD, &istatus); - myPotato++; - - for(int l = 0; l < nCurObj; l++){ - - if (potatoes[which_node] + 2 >= MAXTAG) { - // The potato was going to exceed the maximum value, - // so wrap this processor potato back to 0: - - potatoes[which_node] = 0; - MPI_Send(&potatoes[which_node], 1, MPI_INT, which_node, 0, MPI_COMM_WORLD); - - } - - MPI_Recv(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, which_node, - myPotato, MPI_COMM_WORLD, &istatus); - - atomTypeString = MPIatomTypeString; - - myPotato++; - - MPI_Recv(atomData, 13, MPI_DOUBLE, which_node, myPotato, MPI_COMM_WORLD, &istatus); - myPotato++; - - MPI_Get_count(&istatus, MPI_DOUBLE, &msgLen); - - if(msgLen == 13) - isDirectional = 1; - else - isDirectional = 0; - - // If we've survived to here, format the line: - - if (!isDirectional) { - - sprintf( writeLine, - "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", - atomTypeString, - atomData[0], - atomData[1], - atomData[2], - atomData[3], - atomData[4], - atomData[5]); - - strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" ); - - } - else { - - 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, - atomData[0], - atomData[1], - atomData[2], - atomData[3], - atomData[4], - atomData[5], - atomData[6], - atomData[7], - atomData[8], - atomData[9], - atomData[10], - atomData[11], - atomData[12]); - - } - - for(k = 0; k < outFile.size(); k++) - *outFile[k] << writeLine; - - }// end for(int l =0) - potatoes[which_node] = myPotato; - - } - else { - - haveError = 0; - - local_index = indexArray[currentIndex].first; - - integrableObjects = (entry_plug->molecules[local_index]).getIntegrableObjects(); - - for(iter= integrableObjects.begin(); iter != integrableObjects.end(); ++iter){ - sd = *iter; - atomTypeString = sd->getType(); - - sd->getPos(pos); - sd->getVel(vel); - - atomData[0] = pos[0]; - atomData[1] = pos[1]; - atomData[2] = pos[2]; - - atomData[3] = vel[0]; - atomData[4] = vel[1]; - atomData[5] = vel[2]; - - isDirectional = 0; - - if( sd->isDirectional() ){ - - isDirectional = 1; - - sd->getQ( q ); - sd->getJ( ji ); - - for (int j = 0; j < 6 ; j++) - atomData[j] = atomData[j]; - - atomData[6] = q[0]; - atomData[7] = q[1]; - atomData[8] = q[2]; - atomData[9] = q[3]; - - atomData[10] = ji[0]; - atomData[11] = ji[1]; - atomData[12] = ji[2]; - } - - // If we've survived to here, format the line: - - if (!isDirectional) { - - sprintf( writeLine, - "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", - atomTypeString, - atomData[0], - atomData[1], - atomData[2], - atomData[3], - atomData[4], - atomData[5]); - - strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" ); - - } - else { - - 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, - atomData[0], - atomData[1], - atomData[2], - atomData[3], - atomData[4], - atomData[5], - atomData[6], - atomData[7], - atomData[8], - atomData[9], - atomData[10], - atomData[11], - atomData[12]); - - } - - for(k = 0; k < outFile.size(); k++) - *outFile[k] << writeLine; - - - }//end for(iter = integrableObject.begin()) - - currentIndex++; - } - - }//end for(i = 0; i < mpiSim->getNmol()) - - for(k = 0; k < outFile.size(); k++) - outFile[k]->flush(); - - sprintf( checkPointMsg, - "Sucessfully took a dump.\n"); - - MPIcheckPoint(); - - delete[] potatoes; - - } else { - - // worldRank != 0, so I'm a remote node. - - // Set my magic potato to 0: - - myPotato = 0; - currentIndex = 0; - - for (i = 0 ; i < mpiSim->getNMolGlobal(); i++ ) { - - // Am I the node which has this integrableObject? - - if (MolToProcMap[i] == worldRank) { - - - if (myPotato + 1 >= MAXTAG) { - - // 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(&myPotato, 1, MPI_INT, 0, 0, MPI_COMM_WORLD, &istatus); - - } - - local_index = indexArray[currentIndex].first; - integrableObjects = entry_plug->molecules[local_index].getIntegrableObjects(); - - nCurObj = integrableObjects.size(); - - MPI_Send(&nCurObj, 1, MPI_INT, 0, - myPotato, MPI_COMM_WORLD); - myPotato++; - - for( iter = integrableObjects.begin(); iter != integrableObjects.end(); iter++){ - - if (myPotato + 2 >= MAXTAG) { - - // 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(&myPotato, 1, MPI_INT, 0, 0, MPI_COMM_WORLD, &istatus); - - } - - sd = *iter; - - atomTypeString = sd->getType(); - - sd->getPos(pos); - sd->getVel(vel); - - atomData[0] = pos[0]; - atomData[1] = pos[1]; - atomData[2] = pos[2]; - - atomData[3] = vel[0]; - atomData[4] = vel[1]; - atomData[5] = vel[2]; - - isDirectional = 0; - - if( sd->isDirectional() ){ - - isDirectional = 1; - - sd->getQ( q ); - sd->getJ( ji ); - - - atomData[6] = q[0]; - atomData[7] = q[1]; - atomData[8] = q[2]; - atomData[9] = q[3]; - - atomData[10] = ji[0]; - atomData[11] = ji[1]; - atomData[12] = ji[2]; - } - - - 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++; - - if (isDirectional) { - - MPI_Send(atomData, 13, MPI_DOUBLE, 0, - myPotato, MPI_COMM_WORLD); - - } else { - - MPI_Send(atomData, 6, MPI_DOUBLE, 0, - myPotato, MPI_COMM_WORLD); - } - - myPotato++; - - } - - currentIndex++; - - } - - } - - 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 +#define _LARGEFILE_SOURCE64 +#define _FILE_OFFSET_BITS 64 + +#include +#include +#include +#include +#include + +#ifdef IS_MPI +#include +#include "brains/mpiSimulation.hpp" + +namespace dWrite{ + void DieDieDie( void ); +} + +using namespace dWrite; +#endif //is_mpi + +#include "io/ReadWrite.hpp" +#include "utils/simError.h" + +DumpWriter::DumpWriter( SimInfo* the_entry_plug ){ + + entry_plug = the_entry_plug; + +#ifdef IS_MPI + if(worldRank == 0 ){ +#endif // is_mpi + + dumpFile.open(entry_plug->sampleName.c_str(), ios::out | ios::trunc ); + + if( !dumpFile ){ + + sprintf( painCave.errMsg, + "Could not open \"%s\" for dump output.\n", + entry_plug->sampleName.c_str()); + painCave.isFatal = 1; + simError(); + } + +#ifdef IS_MPI + } + + //sort the local atoms by global index + sortByGlobalIndex(); + + sprintf( checkPointMsg, + "Sucessfully opened output file for dumping.\n"); + MPIcheckPoint(); +#endif // is_mpi +} + +DumpWriter::~DumpWriter( ){ + +#ifdef IS_MPI + if(worldRank == 0 ){ +#endif // is_mpi + + dumpFile.close(); + +#ifdef IS_MPI + } +#endif // is_mpi +} + +#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(){ + Molecule* mols = entry_plug->molecules; + indexArray.clear(); + + for(int i = 0; i < entry_plug->n_mol;i++) + indexArray.push_back(make_pair(i, mols[i].getGlobalIndex())); + + sort(indexArray.begin(), indexArray.end(), indexSortingCriterion); +} + +#endif + +void DumpWriter::writeDump(double currentTime){ + + ofstream finalOut; + vector fileStreams; + +#ifdef IS_MPI + if(worldRank == 0 ){ +#endif + finalOut.open( entry_plug->finalName.c_str(), ios::out | ios::trunc ); + if( !finalOut ){ + sprintf( painCave.errMsg, + "Could not open \"%s\" for final dump output.\n", + entry_plug->finalName.c_str() ); + painCave.isFatal = 1; + simError(); + } +#ifdef IS_MPI + } +#endif // is_mpi + + fileStreams.push_back(&finalOut); + fileStreams.push_back(&dumpFile); + + writeFrame(fileStreams, currentTime); + +#ifdef IS_MPI + finalOut.close(); +#endif + +} + +void DumpWriter::writeFinal(double currentTime){ + + ofstream finalOut; + vector fileStreams; + +#ifdef IS_MPI + if(worldRank == 0 ){ +#endif // is_mpi + + finalOut.open( entry_plug->finalName.c_str(), ios::out | ios::trunc ); + + if( !finalOut ){ + sprintf( painCave.errMsg, + "Could not open \"%s\" for final dump output.\n", + entry_plug->finalName.c_str() ); + painCave.isFatal = 1; + simError(); + } + +#ifdef IS_MPI + } +#endif // is_mpi + + fileStreams.push_back(&finalOut); + writeFrame(fileStreams, currentTime); + +#ifdef IS_MPI + finalOut.close(); +#endif + +} + +void DumpWriter::writeFrame( vector& outFile, double currentTime ){ + + const int BUFFERSIZE = 2000; + const int MINIBUFFERSIZE = 100; + + char tempBuffer[BUFFERSIZE]; + char writeLine[BUFFERSIZE]; + + int i; + unsigned int k; + +#ifdef IS_MPI + + /********************************************************************* + * Documentation? You want DOCUMENTATION? + * + * Why all the potatoes below? + * + * To make a long story short, the original version of DumpWriter + * worked in the most inefficient way possible. Node 0 would + * poke each of the node for an individual atom's formatted data + * as node 0 worked its way down the global index. This was particularly + * inefficient since the method blocked all processors at every atom + * (and did it twice!). + * + * An intermediate version of DumpWriter could be described from Node + * zero's perspective as follows: + * + * 1) Have 100 of your friends stand in a circle. + * 2) When you say go, have all of them start tossing potatoes at + * you (one at a time). + * 3) Catch the potatoes. + * + * It was an improvement, but MPI has buffers and caches that could + * best be described in this analogy as "potato nets", so there's no + * need to block the processors atom-by-atom. + * + * This new and improved DumpWriter works in an even more efficient + * way: + * + * 1) Have 100 of your friend stand in a circle. + * 2) When you say go, have them start tossing 5-pound bags of + * potatoes at you. + * 3) Once you've caught a friend's bag of potatoes, + * toss them a spud to let them know they can toss another bag. + * + * How's THAT for documentation? + * + *********************************************************************/ + + int *potatoes; + int myPotato; + + int nProc; + int j, which_node, done, which_atom, local_index, currentIndex; + double atomData[13]; + int isDirectional; + char* atomTypeString; + char MPIatomTypeString[MINIBUFFERSIZE]; + int nObjects; + int msgLen; // the length of message actually recieved at master nodes +#endif //is_mpi + + Quat4d q; + Vector3d ji; + DirectionalAtom* dAtom; + Vector3d pos; + Vector3d vel; + + int nTotObjects; + StuntDouble* sd; + char* molName; + vector integrableObjects; + vector::iterator iter; + nTotObjects = entry_plug->getTotIntegrableObjects(); +#ifndef IS_MPI + + for(k = 0; k < outFile.size(); k++){ + *outFile[k] << nTotObjects << "\n"; + + *outFile[k] << 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[k] << entry_plug->the_integrator->getAdditionalParameters() << endl; + } + + for( i=0; i< entry_plug->n_mol; i++ ){ + + integrableObjects = entry_plug->molecules[i].getIntegrableObjects(); + molName = (entry_plug->compStamps[entry_plug->molecules[i].getStampID()])->getID(); + + for( iter = integrableObjects.begin();iter != integrableObjects.end(); ++iter){ + sd = *iter; + pos = sd->getPos(); + vel = sd->getVel(); + + sprintf( tempBuffer, + "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", + sd->getType(), + pos[0], + pos[1], + pos[2], + vel[0], + vel[1], + vel[2]); + strcpy( writeLine, tempBuffer ); + + if( sd->isDirectional() ){ + + q = sd->getQ(); + ji = sd->getJ(); + + sprintf( tempBuffer, + "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n", + q[0], + q[1], + q[2], + q[3], + ji[0], + ji[1], + ji[2]); + strcat( writeLine, tempBuffer ); + } + else + strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" ); + + for(k = 0; k < outFile.size(); k++) + *outFile[k] << writeLine; + } + +} + +#else // is_mpi + + /* 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 nCurObj; + int *MolToProcMap = mpiSim->getMolToProcMap(); + + // 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->getNProcessors(); + potatoes = new int[nProc]; + + //write out the comment lines + for (i = 0; i < nProc; i++) + potatoes[i] = 0; + + for(k = 0; k < outFile.size(); k++){ + *outFile[k] << nTotObjects << "\n"; + + *outFile[k] << 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[k] << entry_plug->the_integrator->getAdditionalParameters() << endl; + } + + currentIndex = 0; + + for (i = 0 ; i < mpiSim->getNMolGlobal(); i++ ) { + + // Get the Node number which has this atom; + + which_node = MolToProcMap[i]; + + if (which_node != 0) { + + if (potatoes[which_node] + 1 >= MAXTAG) { + // The potato was going to exceed the maximum value, + // so wrap this processor potato back to 0: + + potatoes[which_node] = 0; + MPI_Send(&potatoes[which_node], 1, MPI_INT, which_node, 0, MPI_COMM_WORLD); + + } + + myPotato = potatoes[which_node]; + + //recieve the number of integrableObject in current molecule + MPI_Recv(&nCurObj, 1, MPI_INT, which_node, + myPotato, MPI_COMM_WORLD, &istatus); + myPotato++; + + for(int l = 0; l < nCurObj; l++){ + + if (potatoes[which_node] + 2 >= MAXTAG) { + // The potato was going to exceed the maximum value, + // so wrap this processor potato back to 0: + + potatoes[which_node] = 0; + MPI_Send(&potatoes[which_node], 1, MPI_INT, which_node, 0, MPI_COMM_WORLD); + + } + + MPI_Recv(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, which_node, + myPotato, MPI_COMM_WORLD, &istatus); + + atomTypeString = MPIatomTypeString; + + myPotato++; + + MPI_Recv(atomData, 13, MPI_DOUBLE, which_node, myPotato, MPI_COMM_WORLD, &istatus); + myPotato++; + + MPI_Get_count(&istatus, MPI_DOUBLE, &msgLen); + + if(msgLen == 13) + isDirectional = 1; + else + isDirectional = 0; + + // If we've survived to here, format the line: + + if (!isDirectional) { + + sprintf( writeLine, + "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", + atomTypeString, + atomData[0], + atomData[1], + atomData[2], + atomData[3], + atomData[4], + atomData[5]); + + strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" ); + + } + else { + + 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, + atomData[0], + atomData[1], + atomData[2], + atomData[3], + atomData[4], + atomData[5], + atomData[6], + atomData[7], + atomData[8], + atomData[9], + atomData[10], + atomData[11], + atomData[12]); + + } + + for(k = 0; k < outFile.size(); k++) + *outFile[k] << writeLine; + + }// end for(int l =0) + potatoes[which_node] = myPotato; + + } + else { + + haveError = 0; + + local_index = indexArray[currentIndex].first; + + integrableObjects = (entry_plug->molecules[local_index]).getIntegrableObjects(); + + for(iter= integrableObjects.begin(); iter != integrableObjects.end(); ++iter){ + sd = *iter; + atomTypeString = sd->getType(); + + pos = sd->getPos(); + vel = sd->getVel(); + + atomData[0] = pos[0]; + atomData[1] = pos[1]; + atomData[2] = pos[2]; + + atomData[3] = vel[0]; + atomData[4] = vel[1]; + atomData[5] = vel[2]; + + isDirectional = 0; + + if( sd->isDirectional() ){ + + isDirectional = 1; + + q = sd->getQ(); + ji = sd->getJ(); + + for (int j = 0; j < 6 ; j++) + atomData[j] = atomData[j]; + + atomData[6] = q[0]; + atomData[7] = q[1]; + atomData[8] = q[2]; + atomData[9] = q[3]; + + atomData[10] = ji[0]; + atomData[11] = ji[1]; + atomData[12] = ji[2]; + } + + // If we've survived to here, format the line: + + if (!isDirectional) { + + sprintf( writeLine, + "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", + atomTypeString, + atomData[0], + atomData[1], + atomData[2], + atomData[3], + atomData[4], + atomData[5]); + + strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" ); + + } + else { + + 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, + atomData[0], + atomData[1], + atomData[2], + atomData[3], + atomData[4], + atomData[5], + atomData[6], + atomData[7], + atomData[8], + atomData[9], + atomData[10], + atomData[11], + atomData[12]); + + } + + for(k = 0; k < outFile.size(); k++) + *outFile[k] << writeLine; + + + }//end for(iter = integrableObject.begin()) + + currentIndex++; + } + + }//end for(i = 0; i < mpiSim->getNmol()) + + for(k = 0; k < outFile.size(); k++) + outFile[k]->flush(); + + sprintf( checkPointMsg, + "Sucessfully took a dump.\n"); + + MPIcheckPoint(); + + delete[] potatoes; + + } else { + + // worldRank != 0, so I'm a remote node. + + // Set my magic potato to 0: + + myPotato = 0; + currentIndex = 0; + + for (i = 0 ; i < mpiSim->getNMolGlobal(); i++ ) { + + // Am I the node which has this integrableObject? + + if (MolToProcMap[i] == worldRank) { + + + if (myPotato + 1 >= MAXTAG) { + + // 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(&myPotato, 1, MPI_INT, 0, 0, MPI_COMM_WORLD, &istatus); + + } + + local_index = indexArray[currentIndex].first; + integrableObjects = entry_plug->molecules[local_index].getIntegrableObjects(); + + nCurObj = integrableObjects.size(); + + MPI_Send(&nCurObj, 1, MPI_INT, 0, + myPotato, MPI_COMM_WORLD); + myPotato++; + + for( iter = integrableObjects.begin(); iter != integrableObjects.end(); iter++){ + + if (myPotato + 2 >= MAXTAG) { + + // 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(&myPotato, 1, MPI_INT, 0, 0, MPI_COMM_WORLD, &istatus); + + } + + sd = *iter; + + atomTypeString = sd->getType(); + + pos = sd->getPos(); + vel = sd->getVel(); + + atomData[0] = pos[0]; + atomData[1] = pos[1]; + atomData[2] = pos[2]; + + atomData[3] = vel[0]; + atomData[4] = vel[1]; + atomData[5] = vel[2]; + + isDirectional = 0; + + if( sd->isDirectional() ){ + + isDirectional = 1; + + q = sd->getQ(); + ji = sd->getJ(); + + + atomData[6] = q[0]; + atomData[7] = q[1]; + atomData[8] = q[2]; + atomData[9] = q[3]; + + atomData[10] = ji[0]; + atomData[11] = ji[1]; + atomData[12] = ji[2]; + } + + + 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++; + + if (isDirectional) { + + MPI_Send(atomData, 13, MPI_DOUBLE, 0, + myPotato, MPI_COMM_WORLD); + + } else { + + MPI_Send(atomData, 6, MPI_DOUBLE, 0, + myPotato, MPI_COMM_WORLD); + } + + myPotato++; + + } + + currentIndex++; + + } + + } + + 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