--- trunk/src/io/DumpWriter.cpp 2004/09/24 16:27:58 3 +++ trunk/src/io/DumpWriter.cpp 2005/01/12 23:24:55 251 @@ -1,693 +1,551 @@ -#define _LARGEFILE_SOURCE64 -#define _FILE_OFFSET_BITS 64 + /* + * Copyright (c) 2005 The University of Notre Dame. All Rights Reserved. + * + * The University of Notre Dame grants you ("Licensee") a + * non-exclusive, royalty free, license to use, modify and + * redistribute this software in source and binary code form, provided + * that the following conditions are met: + * + * 1. Acknowledgement of the program authors must be made in any + * publication of scientific results based in part on use of the + * program. An acceptable form of acknowledgement is citation of + * the article in which the program was described (Matthew + * A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher + * J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented + * Parallel Simulation Engine for Molecular Dynamics," + * J. Comput. Chem. 26, pp. 252-271 (2005)) + * + * 2. Redistributions of source code must retain the above copyright + * notice, this list of conditions and the following disclaimer. + * + * 3. Redistributions in binary form must reproduce the above copyright + * notice, this list of conditions and the following disclaimer in the + * documentation and/or other materials provided with the + * distribution. + * + * This software is provided "AS IS," without a warranty of any + * kind. All express or implied conditions, representations and + * warranties, including any implied warranty of merchantability, + * fitness for a particular purpose or non-infringement, are hereby + * excluded. The University of Notre Dame and its licensors shall not + * be liable for any damages suffered by licensee as a result of + * using, modifying or distributing the software or its + * derivatives. In no event will the University of Notre Dame or its + * licensors be liable for any lost revenue, profit or data, or for + * direct, indirect, special, consequential, incidental or punitive + * damages, however caused and regardless of the theory of liability, + * arising out of the use of or inability to use software, even if the + * University of Notre Dame has been advised of the possibility of + * such damages. + */ + +#include "io/DumpWriter.hpp" +#include "primitives/Molecule.hpp" +#include "utils/simError.h" -#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" +namespace oopse { -DumpWriter::DumpWriter( SimInfo* the_entry_plug ){ - - entry_plug = the_entry_plug; - +DumpWriter::DumpWriter(SimInfo* info, const std::string& filename) + : info_(info), filename_(filename){ #ifdef IS_MPI - if(worldRank == 0 ){ + + if (worldRank == 0) { #endif // is_mpi - dumpFile.open(entry_plug->sampleName.c_str(), ios::out | ios::trunc ); + dumpFile_.open(filename_.c_str(), std::ios::out | std::ios::trunc); - if( !dumpFile ){ + if (!dumpFile_) { + sprintf(painCave.errMsg, "Could not open \"%s\" for dump output.\n", + filename_.c_str()); + painCave.isFatal = 1; + simError(); + } - sprintf( painCave.errMsg, - "Could not open \"%s\" for dump output.\n", - entry_plug->sampleName.c_str()); - painCave.isFatal = 1; - simError(); +#ifdef IS_MPI + } -#ifdef IS_MPI - } + sprintf(checkPointMsg, "Sucessfully opened output file for dumping.\n"); + MPIcheckPoint(); - //sort the local atoms by global index - sortByGlobalIndex(); - - sprintf( checkPointMsg, - "Sucessfully opened output file for dumping.\n"); - MPIcheckPoint(); #endif // is_mpi + } -DumpWriter::~DumpWriter( ){ +DumpWriter::~DumpWriter() { #ifdef IS_MPI - if(worldRank == 0 ){ + + if (worldRank == 0) { #endif // is_mpi - dumpFile.close(); + dumpFile_.close(); #ifdef IS_MPI - } + + } + #endif // is_mpi + } -#ifdef IS_MPI +void DumpWriter::writeCommentLine(std::ostream& os, Snapshot* s) { -/** - * A hook function to load balancing - */ + double currentTime; + Mat3x3d hmat; + double chi; + double integralOfChiDt; + Mat3x3d eta; + + currentTime = s->getTime(); + hmat = s->getHmat(); + chi = s->getChi(); + integralOfChiDt = s->getIntegralOfChiDt(); + eta = s->getEta(); + + os << currentTime << ";\t" + << hmat(0, 0) << "\t" << hmat(1, 0) << "\t" << hmat(2, 0) << ";\t" + << hmat(0, 1) << "\t" << hmat(1, 1) << "\t" << hmat(2, 1) << ";\t" + << hmat(0, 2) << "\t" << hmat(1, 2) << "\t" << hmat(2, 2) << ";\t"; -void DumpWriter::update(){ - sortByGlobalIndex(); -} - -/** - * Auxiliary sorting function - */ - -bool indexSortingCriterion(const pair& p1, const pair& p2){ - return p1.second < p2.second; -} + //write out additional parameters, such as chi and eta -/** - * 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); + os << chi << "\t" << integralOfChiDt << "\t;"; + + os << eta(0, 0) << "\t" << eta(1, 0) << "\t" << eta(2, 0) << ";\t" + << eta(0, 1) << "\t" << eta(1, 1) << "\t" << eta(2, 1) << ";\t" + << eta(0, 2) << "\t" << eta(1, 2) << "\t" << eta(2, 2) << ";"; + + os << std::endl; } -#endif +void DumpWriter::writeFrame(std::ostream& os) { + const int BUFFERSIZE = 2000; + const int MINIBUFFERSIZE = 100; -void DumpWriter::writeDump(double currentTime){ + char tempBuffer[BUFFERSIZE]; + char writeLine[BUFFERSIZE]; - ofstream finalOut; - vector fileStreams; + Quat4d q; + Vector3d ji; + Vector3d pos; + Vector3d vel; -#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 + Molecule* mol; + StuntDouble* integrableObject; + SimInfo::MoleculeIterator mi; + Molecule::IntegrableObjectIterator ii; + + int nTotObjects; + nTotObjects = info_->getNGlobalIntegrableObjects(); - fileStreams.push_back(&finalOut); - fileStreams.push_back(&dumpFile); +#ifndef IS_MPI - writeFrame(fileStreams, currentTime); -#ifdef IS_MPI - finalOut.close(); -#endif - -} + os << nTotObjects << "\n"; + + writeCommentLine(os, info_->getSnapshotManager()->getCurrentSnapshot()); -void DumpWriter::writeFinal(double currentTime){ + for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) { - ofstream finalOut; - vector fileStreams; + for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL; + integrableObject = mol->nextIntegrableObject(ii)) { + -#ifdef IS_MPI - if(worldRank == 0 ){ -#endif // is_mpi + pos = integrableObject->getPos(); + vel = integrableObject->getVel(); - finalOut.open( entry_plug->finalName.c_str(), ios::out | ios::trunc ); + sprintf(tempBuffer, "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", + integrableObject->getType().c_str(), + pos[0], pos[1], pos[2], + vel[0], vel[1], vel[2]); - if( !finalOut ){ - sprintf( painCave.errMsg, - "Could not open \"%s\" for final dump output.\n", - entry_plug->finalName.c_str() ); - painCave.isFatal = 1; - simError(); - } + strcpy(writeLine, tempBuffer); -#ifdef IS_MPI - } -#endif // is_mpi - - fileStreams.push_back(&finalOut); - writeFrame(fileStreams, currentTime); + if (integrableObject->isDirectional()) { + q = integrableObject->getQ(); + ji = integrableObject->getJ(); -#ifdef IS_MPI - finalOut.close(); -#endif - -} + 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"); + } -void DumpWriter::writeFrame( vector& outFile, double currentTime ){ + os << writeLine; - const int BUFFERSIZE = 2000; - const int MINIBUFFERSIZE = 100; + } + } - char tempBuffer[BUFFERSIZE]; - char writeLine[BUFFERSIZE]; - - int i; - unsigned int k; +#else // 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? + * + *********************************************************************/ + const int masterNode = 0; -#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(); + int * potatoes; + int myPotato; + int nProc; + int which_node; + double atomData[13]; + int isDirectional; + const char * atomTypeString; + char MPIatomTypeString[MINIBUFFERSIZE]; + int msgLen; // the length of message actually recieved at master nodes + int haveError; + MPI_Status istatus; + int nCurObj; - for( iter = integrableObjects.begin();iter != integrableObjects.end(); ++iter){ - sd = *iter; - sd->getPos(pos); - sd->getVel(vel); + // code to find maximum tag value + int * tagub; + int flag; + int MAXTAG; + MPI_Attr_get(MPI_COMM_WORLD, MPI_TAG_UB, &tagub, &flag); - 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 (flag) { + MAXTAG = *tagub; + } else { + MAXTAG = 32767; + } - if( sd->isDirectional() ){ + if (worldRank == masterNode) { //master node (node 0) is responsible for writing the dump file - sd->getQ( q ); - sd->getJ( ji ); + // Node 0 needs a list of the magic potatoes for each processor; - 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; - } + MPI_Comm_size(MPI_COMM_WORLD, &nProc); + potatoes = new int[nProc]; -} + //write out the comment lines + for(int i = 0; i < nProc; i++) { + potatoes[i] = 0; + } -#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; - } + os << nTotObjects << "\n"; + writeCommentLine(os, info_->getSnapshotManager()->getCurrentSnapshot()); - int haveError; + for(int i = 0; i < info_->getNGlobalMolecules(); i++) { - MPI_Status istatus; - int nCurObj; - int *MolToProcMap = mpiSim->getMolToProcMap(); + // Get the Node number which has this atom; - // write out header and node 0's coordinates + which_node = info_->getMolToProc(i); - if( worldRank == 0 ){ + if (which_node != masterNode) { //current molecule is in slave node + if (potatoes[which_node] + 1 >= MAXTAG) { + // The potato was going to exceed the maximum value, + // so wrap this processor potato back to 0: - // Node 0 needs a list of the magic potatoes for each processor; + potatoes[which_node] = 0; + MPI_Send(&potatoes[which_node], 1, MPI_INT, which_node, 0, + MPI_COMM_WORLD); + } - nProc = mpiSim->getNProcessors(); - potatoes = new int[nProc]; + myPotato = potatoes[which_node]; - //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"; + //recieve the number of integrableObject in current molecule + MPI_Recv(&nCurObj, 1, MPI_INT, which_node, myPotato, + MPI_COMM_WORLD, &istatus); + myPotato++; - *outFile[k] << currentTime << ";\t" - << entry_plug->Hmat[0][0] << "\t" - << entry_plug->Hmat[1][0] << "\t" - << entry_plug->Hmat[2][0] << ";\t" + 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: - << entry_plug->Hmat[0][1] << "\t" - << entry_plug->Hmat[1][1] << "\t" - << entry_plug->Hmat[2][1] << ";\t" + potatoes[which_node] = 0; + MPI_Send(&potatoes[which_node], 1, MPI_INT, which_node, + 0, MPI_COMM_WORLD); + } - << 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; - } + MPI_Recv(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, + which_node, myPotato, MPI_COMM_WORLD, + &istatus); - currentIndex = 0; + atomTypeString = MPIatomTypeString; - 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: + myPotato++; - potatoes[which_node] = 0; - MPI_Send(&potatoes[which_node], 1, MPI_INT, which_node, 0, MPI_COMM_WORLD); - - } + MPI_Recv(atomData, 13, MPI_DOUBLE, which_node, myPotato, + MPI_COMM_WORLD, &istatus); + myPotato++; - myPotato = potatoes[which_node]; + MPI_Get_count(&istatus, MPI_DOUBLE, &msgLen); - //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 (msgLen == 13) + isDirectional = 1; + else + isDirectional = 0; - if (potatoes[which_node] + 2 >= MAXTAG) { - // The potato was going to exceed the maximum value, - // so wrap this processor potato back to 0: + // If we've survived to here, format the line: - potatoes[which_node] = 0; - MPI_Send(&potatoes[which_node], 1, MPI_INT, which_node, 0, MPI_COMM_WORLD); - - } + 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]); - MPI_Recv(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, which_node, - myPotato, MPI_COMM_WORLD, &istatus); + 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]); + } - atomTypeString = MPIatomTypeString; + os << writeLine; - myPotato++; + } // end for(int l =0) - MPI_Recv(atomData, 13, MPI_DOUBLE, which_node, myPotato, MPI_COMM_WORLD, &istatus); - myPotato++; + potatoes[which_node] = myPotato; + } else { //master node has current molecule - MPI_Get_count(&istatus, MPI_DOUBLE, &msgLen); + mol = info_->getMoleculeByGlobalIndex(i); - 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; + if (mol == NULL) { + sprintf(painCave.errMsg, "Molecule not found on node %d!", worldRank); + painCave.isFatal = 1; + simError(); + } + + for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL; + integrableObject = mol->nextIntegrableObject(ii)) { + + atomTypeString = integrableObject->getType().c_str(); - }// end for(int l =0) - potatoes[which_node] = myPotato; + pos = integrableObject->getPos(); + vel = integrableObject->getVel(); - } - else { - - haveError = 0; - - local_index = indexArray[currentIndex].first; + atomData[0] = pos[0]; + atomData[1] = pos[1]; + atomData[2] = pos[2]; - integrableObjects = (entry_plug->molecules[local_index]).getIntegrableObjects(); + atomData[3] = vel[0]; + atomData[4] = vel[1]; + atomData[5] = vel[2]; - 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]; + isDirectional = 0; - atomData[3] = vel[0]; - atomData[4] = vel[1]; - atomData[5] = vel[2]; - - isDirectional = 0; + if (integrableObject->isDirectional()) { + isDirectional = 1; - if( sd->isDirectional() ){ + q = integrableObject->getQ(); + ji = integrableObject->getJ(); - isDirectional = 1; - - sd->getQ( q ); - sd->getJ( ji ); + for(int j = 0; j < 6; j++) { + atomData[j] = atomData[j]; + } - 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++; - } + atomData[6] = q[0]; + atomData[7] = q[1]; + atomData[8] = q[2]; + atomData[9] = q[3]; - }//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 { + atomData[10] = ji[0]; + atomData[11] = ji[1]; + atomData[12] = ji[2]; + } - // worldRank != 0, so I'm a remote node. + // If we've survived to here, format the line: - // 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 (!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]); + } - 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++; + os << writeLine; - 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); - + } //end for(iter = integrableObject.begin()) } - - sd = *iter; - - atomTypeString = sd->getType(); + } //end for(i = 0; i < mpiSim->getNmol()) - sd->getPos(pos); - sd->getVel(vel); + os.flush(); + + sprintf(checkPointMsg, "Sucessfully took a dump.\n"); + MPIcheckPoint(); - atomData[0] = pos[0]; - atomData[1] = pos[1]; - atomData[2] = pos[2]; + delete [] potatoes; + } else { - atomData[3] = vel[0]; - atomData[4] = vel[1]; - atomData[5] = vel[2]; - - isDirectional = 0; + // worldRank != 0, so I'm a remote node. - if( sd->isDirectional() ){ + // Set my magic potato to 0: - isDirectional = 1; + myPotato = 0; + + for(int i = 0; i < info_->getNGlobalMolecules(); i++) { + + // Am I the node which has this integrableObject? + int whichNode = info_->getMolToProc(i); + if (whichNode == 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); + } + + mol = info_->getMoleculeByGlobalIndex(i); + - 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]; - } + nCurObj = mol->getNIntegrableObjects(); - - strncpy(MPIatomTypeString, atomTypeString, MINIBUFFERSIZE); + MPI_Send(&nCurObj, 1, MPI_INT, 0, myPotato, MPI_COMM_WORLD); + myPotato++; - // null terminate the string before sending (just in case): - MPIatomTypeString[MINIBUFFERSIZE-1] = '\0'; + for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL; + integrableObject = mol->nextIntegrableObject(ii)) { - MPI_Send(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, 0, - myPotato, MPI_COMM_WORLD); - - myPotato++; - - if (isDirectional) { + if (myPotato + 2 >= MAXTAG) { - MPI_Send(atomData, 13, MPI_DOUBLE, 0, - myPotato, MPI_COMM_WORLD); - - } else { + // 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_Send(atomData, 6, MPI_DOUBLE, 0, - myPotato, MPI_COMM_WORLD); - } + MPI_Recv(&myPotato, 1, MPI_INT, 0, 0, MPI_COMM_WORLD, + &istatus); + } - myPotato++; + atomTypeString = integrableObject->getType().c_str(); - } + pos = integrableObject->getPos(); + vel = integrableObject->getVel(); - currentIndex++; - - } - - } + atomData[0] = pos[0]; + atomData[1] = pos[1]; + atomData[2] = pos[2]; - sprintf( checkPointMsg, - "Sucessfully took a dump.\n"); - MPIcheckPoint(); - - } + atomData[3] = vel[0]; + atomData[4] = vel[1]; + atomData[5] = vel[2]; + isDirectional = 0; - -#endif // is_mpi -} + if (integrableObject->isDirectional()) { + isDirectional = 1; -#ifdef IS_MPI + q = integrableObject->getQ(); + ji = integrableObject->getJ(); -// a couple of functions to let us escape the write loop + atomData[6] = q[0]; + atomData[7] = q[1]; + atomData[8] = q[2]; + atomData[9] = q[3]; -void dWrite::DieDieDie( void ){ + atomData[10] = ji[0]; + atomData[11] = ji[1]; + atomData[12] = ji[2]; + } - MPI_Finalize(); - exit (0); + strncpy(MPIatomTypeString, atomTypeString, MINIBUFFERSIZE); + + // null terminate the std::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++; + } + + } + + } + sprintf(checkPointMsg, "Sucessfully took a dump.\n"); + MPIcheckPoint(); + } + +#endif // is_mpi + } -#endif //is_mpi +}//end namespace oopse