ViewVC Help
View File | Revision Log | Show Annotations | View Changeset | Root Listing
root/OpenMD/branches/development/src/io/DumpWriter.cpp
(Generate patch)

Comparing trunk/src/io/DumpWriter.cpp (file contents):
Revision 221 by chrisfen, Tue Nov 23 22:48:31 2004 UTC vs.
Revision 726 by chrisfen, Fri Nov 11 15:22:11 2005 UTC

# Line 1 | Line 1
1 < #define _LARGEFILE_SOURCE64
2 < #define _FILE_OFFSET_BITS 64
1 > /*
2 > * Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
3 > *
4 > * The University of Notre Dame grants you ("Licensee") a
5 > * non-exclusive, royalty free, license to use, modify and
6 > * redistribute this software in source and binary code form, provided
7 > * that the following conditions are met:
8 > *
9 > * 1. Acknowledgement of the program authors must be made in any
10 > *    publication of scientific results based in part on use of the
11 > *    program.  An acceptable form of acknowledgement is citation of
12 > *    the article in which the program was described (Matthew
13 > *    A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
14 > *    J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
15 > *    Parallel Simulation Engine for Molecular Dynamics,"
16 > *    J. Comput. Chem. 26, pp. 252-271 (2005))
17 > *
18 > * 2. Redistributions of source code must retain the above copyright
19 > *    notice, this list of conditions and the following disclaimer.
20 > *
21 > * 3. Redistributions in binary form must reproduce the above copyright
22 > *    notice, this list of conditions and the following disclaimer in the
23 > *    documentation and/or other materials provided with the
24 > *    distribution.
25 > *
26 > * This software is provided "AS IS," without a warranty of any
27 > * kind. All express or implied conditions, representations and
28 > * warranties, including any implied warranty of merchantability,
29 > * fitness for a particular purpose or non-infringement, are hereby
30 > * excluded.  The University of Notre Dame and its licensors shall not
31 > * be liable for any damages suffered by licensee as a result of
32 > * using, modifying or distributing the software or its
33 > * derivatives. In no event will the University of Notre Dame or its
34 > * licensors be liable for any lost revenue, profit or data, or for
35 > * direct, indirect, special, consequential, incidental or punitive
36 > * damages, however caused and regardless of the theory of liability,
37 > * arising out of the use of or inability to use software, even if the
38 > * University of Notre Dame has been advised of the possibility of
39 > * such damages.
40 > */
41 >
42 > #include "io/DumpWriter.hpp"
43 > #include "primitives/Molecule.hpp"
44 > #include "utils/simError.h"
45 > #include "io/basic_teebuf.hpp"
46 > #include "io/gzstream.hpp"
47 > #include "io/Globals.hpp"
48  
4 – #include <string.h>
5 – #include <iostream>
6 – #include <fstream>
7 – #include <algorithm>
8 – #include <utility>
9 –
49   #ifdef IS_MPI
50   #include <mpi.h>
12 – #include "brains/mpiSimulation.hpp"
13 –
14 – namespace dWrite{
15 –  void DieDieDie( void );
16 – }
17 –
18 – using namespace dWrite;
51   #endif //is_mpi
52  
53 < #include "io/ReadWrite.hpp"
22 < #include "utils/simError.h"
53 > namespace oopse {
54  
55 < DumpWriter::DumpWriter( SimInfo* the_entry_plug ){
55 >  DumpWriter::DumpWriter(SimInfo* info)
56 >    : info_(info), filename_(info->getDumpFileName()), eorFilename_(info->getFinalConfigFileName()){
57  
58 <  entry_plug = the_entry_plug;
58 >    Globals* simParams = info->getSimParams();
59 >    needCompression_ = simParams->getCompressDumpFile();
60 >    needForceVector_ = simParams->getOutputForceVector();
61  
62 + #ifdef HAVE_LIBZ
63 +    if (needCompression_) {
64 +        filename_ += ".gz";
65 +        eorFilename_ += ".gz";
66 +    }
67 + #endif
68 +    
69   #ifdef IS_MPI
70 <  if(worldRank == 0 ){
70 >
71 >      if (worldRank == 0) {
72   #endif // is_mpi
73  
32 –    dumpFile.open(entry_plug->sampleName.c_str(), ios::out | ios::trunc );
74  
75 <    if( !dumpFile ){
75 >        dumpFile_ = createOStream(filename_);
76  
77 <      sprintf( painCave.errMsg,
78 <               "Could not open \"%s\" for dump output.\n",
79 <               entry_plug->sampleName.c_str());
80 <      painCave.isFatal = 1;
81 <      simError();
82 <    }
77 >        if (!dumpFile_) {
78 >          sprintf(painCave.errMsg, "Could not open \"%s\" for dump output.\n",
79 >                  filename_.c_str());
80 >          painCave.isFatal = 1;
81 >          simError();
82 >        }
83  
84   #ifdef IS_MPI
44 –  }
85  
86 <  //sort the local atoms by global index
47 <  sortByGlobalIndex();
48 <  
49 <  sprintf( checkPointMsg,
50 <           "Sucessfully opened output file for dumping.\n");
51 <  MPIcheckPoint();
52 < #endif // is_mpi
53 < }
86 >      }
87  
88 < DumpWriter::~DumpWriter( ){
88 >      sprintf(checkPointMsg, "Sucessfully opened output file for dumping.\n");
89 >      MPIcheckPoint();
90  
57 – #ifdef IS_MPI
58 –  if(worldRank == 0 ){
91   #endif // is_mpi
92  
93 <    dumpFile.close();
93 >    }
94  
63 – #ifdef IS_MPI
64 –  }
65 – #endif // is_mpi
66 – }
95  
96 < #ifdef IS_MPI
96 >  DumpWriter::DumpWriter(SimInfo* info, const std::string& filename)
97 >    : info_(info), filename_(filename){
98  
99 < /**
100 < * A hook function to load balancing
72 < */
99 >    Globals* simParams = info->getSimParams();
100 >    eorFilename_ = filename_.substr(0, filename_.rfind(".")) + ".eor";    
101  
102 < void DumpWriter::update(){
103 <  sortByGlobalIndex();          
76 < }
77 <  
78 < /**
79 < * Auxiliary sorting function
80 < */
81 <
82 < bool indexSortingCriterion(const pair<int, int>& p1, const pair<int, int>& p2){
83 <  return p1.second < p2.second;
84 < }
102 >    needCompression_ = simParams->getCompressDumpFile();
103 >    needForceVector_ = simParams->getOutputForceVector();
104  
105 < /**
106 < * Sorting the local index by global index
107 < */
108 <
109 < void DumpWriter::sortByGlobalIndex(){
91 <  Molecule* mols = entry_plug->molecules;  
92 <  indexArray.clear();
93 <  
94 <  for(int i = 0; i < entry_plug->n_mol;i++)
95 <    indexArray.push_back(make_pair(i, mols[i].getGlobalIndex()));
96 <  
97 <  sort(indexArray.begin(), indexArray.end(), indexSortingCriterion);    
98 < }
99 <
105 > #ifdef HAVE_LIBZ
106 >    if (needCompression_) {
107 >        filename_ += ".gz";
108 >        eorFilename_ += ".gz";
109 >    }
110   #endif
111 <
102 < void DumpWriter::writeDump(double currentTime){
103 <
104 <  ofstream finalOut;
105 <  vector<ofstream*> fileStreams;
106 <
111 >    
112   #ifdef IS_MPI
113 <  if(worldRank == 0 ){
114 < #endif    
110 <    finalOut.open( entry_plug->finalName.c_str(), ios::out | ios::trunc );
111 <    if( !finalOut ){
112 <      sprintf( painCave.errMsg,
113 <               "Could not open \"%s\" for final dump output.\n",
114 <               entry_plug->finalName.c_str() );
115 <      painCave.isFatal = 1;
116 <      simError();
117 <    }
118 < #ifdef IS_MPI
119 <  }
113 >
114 >      if (worldRank == 0) {
115   #endif // is_mpi
116  
122 –  fileStreams.push_back(&finalOut);
123 –  fileStreams.push_back(&dumpFile);
117  
118 <  writeFrame(fileStreams, currentTime);
118 >        dumpFile_ = createOStream(filename_);
119  
120 +        if (!dumpFile_) {
121 +          sprintf(painCave.errMsg, "Could not open \"%s\" for dump output.\n",
122 +                  filename_.c_str());
123 +          painCave.isFatal = 1;
124 +          simError();
125 +        }
126 +
127   #ifdef IS_MPI
128 –  finalOut.close();
129 – #endif
130 –        
131 – }
128  
129 < void DumpWriter::writeFinal(double currentTime){
129 >      }
130  
131 <  ofstream finalOut;
132 <  vector<ofstream*> fileStreams;
131 >      sprintf(checkPointMsg, "Sucessfully opened output file for dumping.\n");
132 >      MPIcheckPoint();
133  
138 – #ifdef IS_MPI
139 –  if(worldRank == 0 ){
134   #endif // is_mpi
135  
142 –    finalOut.open( entry_plug->finalName.c_str(), ios::out | ios::trunc );
143 –
144 –    if( !finalOut ){
145 –      sprintf( painCave.errMsg,
146 –               "Could not open \"%s\" for final dump output.\n",
147 –               entry_plug->finalName.c_str() );
148 –      painCave.isFatal = 1;
149 –      simError();
136      }
137  
138 < #ifdef IS_MPI
153 <  }
154 < #endif // is_mpi
155 <  
156 <  fileStreams.push_back(&finalOut);  
157 <  writeFrame(fileStreams, currentTime);
138 >  DumpWriter::~DumpWriter() {
139  
140   #ifdef IS_MPI
160 –  finalOut.close();
161 – #endif
162 –  
163 – }
141  
142 < void DumpWriter::writeFrame( vector<ofstream*>& outFile, double currentTime ){
142 >    if (worldRank == 0) {
143 > #endif // is_mpi
144  
145 <  const int BUFFERSIZE = 2000;
168 <  const int MINIBUFFERSIZE = 100;
145 >      delete dumpFile_;
146  
170 –  char tempBuffer[BUFFERSIZE];  
171 –  char writeLine[BUFFERSIZE];
172 –
173 –  int i;
174 –  unsigned int k;
175 –
147   #ifdef IS_MPI
177 –  
178 –  /*********************************************************************
179 –   * Documentation?  You want DOCUMENTATION?
180 –   *
181 –   * Why all the potatoes below?  
182 –   *
183 –   * To make a long story short, the original version of DumpWriter
184 –   * worked in the most inefficient way possible.  Node 0 would
185 –   * poke each of the node for an individual atom's formatted data
186 –   * as node 0 worked its way down the global index. This was particularly
187 –   * inefficient since the method blocked all processors at every atom
188 –   * (and did it twice!).
189 –   *
190 –   * An intermediate version of DumpWriter could be described from Node
191 –   * zero's perspective as follows:
192 –   *
193 –   *  1) Have 100 of your friends stand in a circle.
194 –   *  2) When you say go, have all of them start tossing potatoes at
195 –   *     you (one at a time).
196 –   *  3) Catch the potatoes.
197 –   *
198 –   * It was an improvement, but MPI has buffers and caches that could
199 –   * best be described in this analogy as "potato nets", so there's no
200 –   * need to block the processors atom-by-atom.
201 –   *
202 –   * This new and improved DumpWriter works in an even more efficient
203 –   * way:
204 –   *
205 –   *  1) Have 100 of your friend stand in a circle.
206 –   *  2) When you say go, have them start tossing 5-pound bags of
207 –   *     potatoes at you.
208 –   *  3) Once you've caught a friend's bag of potatoes,
209 –   *     toss them a spud to let them know they can toss another bag.
210 –   *
211 –   * How's THAT for documentation?
212 –   *
213 –   *********************************************************************/
148  
149 <  int *potatoes;
216 <  int myPotato;
149 >    }
150  
151 <  int nProc;
219 <  int j, which_node, done, which_atom, local_index, currentIndex;
220 <  double atomData[13];
221 <  int isDirectional;
222 <  char* atomTypeString;
223 <  char MPIatomTypeString[MINIBUFFERSIZE];
224 <  int nObjects;
225 <  int msgLen; // the length of message actually recieved at master nodes
226 < #endif //is_mpi
151 > #endif // is_mpi
152  
153 <  double q[4], ji[3];
229 <  DirectionalAtom* dAtom;
230 <  double pos[3], vel[3];
231 <  int nTotObjects;
232 <  StuntDouble* sd;
233 <  char* molName;
234 <  vector<StuntDouble*> integrableObjects;
235 <  vector<StuntDouble*>::iterator iter;
236 <  nTotObjects = entry_plug->getTotIntegrableObjects();
237 < #ifndef IS_MPI
238 <  
239 <  for(k = 0; k < outFile.size(); k++){
240 <    *outFile[k] << nTotObjects << "\n";
153 >  }
154  
155 <    *outFile[k] << currentTime << ";\t"
243 <               << entry_plug->Hmat[0][0] << "\t"
244 <                     << entry_plug->Hmat[1][0] << "\t"
245 <                     << entry_plug->Hmat[2][0] << ";\t"
246 <              
247 <               << entry_plug->Hmat[0][1] << "\t"
248 <                     << entry_plug->Hmat[1][1] << "\t"
249 <                     << entry_plug->Hmat[2][1] << ";\t"
155 >  void DumpWriter::writeCommentLine(std::ostream& os, Snapshot* s) {
156  
157 <                     << entry_plug->Hmat[0][2] << "\t"
158 <                     << entry_plug->Hmat[1][2] << "\t"
159 <                     << entry_plug->Hmat[2][2] << ";";
157 >    double currentTime;
158 >    Mat3x3d hmat;
159 >    double chi;
160 >    double integralOfChiDt;
161 >    Mat3x3d eta;
162 >    
163 >    currentTime = s->getTime();
164 >    hmat = s->getHmat();
165 >    chi = s->getChi();
166 >    integralOfChiDt = s->getIntegralOfChiDt();
167 >    eta = s->getEta();
168 >    
169 >    os << currentTime << ";\t"
170 >       << hmat(0, 0) << "\t" << hmat(1, 0) << "\t" << hmat(2, 0) << ";\t"
171 >       << hmat(0, 1) << "\t" << hmat(1, 1) << "\t" << hmat(2, 1) << ";\t"
172 >       << hmat(0, 2) << "\t" << hmat(1, 2) << "\t" << hmat(2, 2) << ";\t";
173  
174      //write out additional parameters, such as chi and eta
256 –    *outFile[k] << entry_plug->the_integrator->getAdditionalParameters() << endl;
257 –  }
258 –  
259 –  for( i=0; i< entry_plug->n_mol; i++ ){
175  
176 <    integrableObjects = entry_plug->molecules[i].getIntegrableObjects();
262 <    molName = (entry_plug->compStamps[entry_plug->molecules[i].getStampID()])->getID();
263 <    
264 <    for( iter = integrableObjects.begin();iter !=  integrableObjects.end(); ++iter){
265 <      sd = *iter;
266 <      sd->getPos(pos);
267 <      sd->getVel(vel);
268 <
269 <      sprintf( tempBuffer,
270 <             "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
271 <             sd->getType(),
272 <             pos[0],
273 <             pos[1],
274 <             pos[2],
275 <             vel[0],
276 <             vel[1],
277 <             vel[2]);
278 <      strcpy( writeLine, tempBuffer );
176 >    os << chi << "\t" << integralOfChiDt << "\t;";
177  
178 <      if( sd->isDirectional() ){
178 >    os << eta(0, 0) << "\t" << eta(1, 0) << "\t" << eta(2, 0) << ";\t"
179 >       << eta(0, 1) << "\t" << eta(1, 1) << "\t" << eta(2, 1) << ";\t"
180 >       << eta(0, 2) << "\t" << eta(1, 2) << "\t" << eta(2, 2) << ";";
181 >        
182 >    os << "\n";
183 >  }
184  
185 <        sd->getQ( q );
186 <        sd->getJ( ji );
185 >  void DumpWriter::writeFrame(std::ostream& os) {
186 >    const int BUFFERSIZE = 2000;
187 >    const int MINIBUFFERSIZE = 100;
188  
189 <        sprintf( tempBuffer,
190 <               "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
287 <               q[0],
288 <               q[1],
289 <               q[2],
290 <               q[3],
291 <                 ji[0],
292 <                 ji[1],
293 <                 ji[2]);
294 <        strcat( writeLine, tempBuffer );
295 <      }
296 <      else
297 <        strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
298 <    
299 <      for(k = 0; k < outFile.size(); k++)
300 <        *outFile[k] << writeLine;      
301 <    }
302 <    
303 <  }
189 >    char tempBuffer[BUFFERSIZE];
190 >    char writeLine[BUFFERSIZE];
191  
192 < #else // is_mpi
192 >    Quat4d q;
193 >    Vector3d ji;
194 >    Vector3d pos;
195 >    Vector3d vel;
196 >    Vector3d frc;
197 >    Vector3d trq;
198  
199 <  /* code to find maximum tag value */
199 >    Molecule* mol;
200 >    StuntDouble* integrableObject;
201 >    SimInfo::MoleculeIterator mi;
202 >    Molecule::IntegrableObjectIterator ii;
203    
204 <  int *tagub, flag, MAXTAG;
205 <  MPI_Attr_get(MPI_COMM_WORLD, MPI_TAG_UB, &tagub, &flag);
311 <  if (flag) {
312 <    MAXTAG = *tagub;
313 <  } else {
314 <    MAXTAG = 32767;
315 <  }  
204 >    int nTotObjects;    
205 >    nTotObjects = info_->getNGlobalIntegrableObjects();
206  
207 <  int haveError;
207 > #ifndef IS_MPI
208  
319 –  MPI_Status istatus;
320 –  int nCurObj;
321 –  int *MolToProcMap = mpiSim->getMolToProcMap();
209  
210 <  // write out header and node 0's coordinates
210 >    os << nTotObjects << "\n";
211 >        
212 >    writeCommentLine(os, info_->getSnapshotManager()->getCurrentSnapshot());
213  
214 <  if( worldRank == 0 ){
214 >    for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
215  
216 <    // Node 0 needs a list of the magic potatoes for each processor;
216 >      for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
217 >           integrableObject = mol->nextIntegrableObject(ii)) {
218 >                
219  
220 <    nProc = mpiSim->getNProcessors();
221 <    potatoes = new int[nProc];
220 >        pos = integrableObject->getPos();
221 >        vel = integrableObject->getVel();
222  
223 <    //write out the comment lines
224 <    for (i = 0; i < nProc; i++)
225 <      potatoes[i] = 0;
226 <    
227 <    for(k = 0; k < outFile.size(); k++){
228 <      *outFile[k] << nTotObjects << "\n";
229 <      
230 <      *outFile[k] << currentTime << ";\t"
231 <                  << entry_plug->Hmat[0][0] << "\t"
232 <                  << entry_plug->Hmat[1][0] << "\t"
233 <                  << entry_plug->Hmat[2][0] << ";\t"
223 >        sprintf(tempBuffer, "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
224 >                integrableObject->getType().c_str(),
225 >                pos[0], pos[1], pos[2],
226 >                vel[0], vel[1], vel[2]);
227 >
228 >        strcpy(writeLine, tempBuffer);
229 >
230 >        if (integrableObject->isDirectional()) {
231 >          q = integrableObject->getQ();
232 >          ji = integrableObject->getJ();
233 >
234 >          sprintf(tempBuffer, "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf",
235 >                  q[0], q[1], q[2], q[3],
236 >                  ji[0], ji[1], ji[2]);
237 >          strcat(writeLine, tempBuffer);
238 >        } else {
239 >          strcat(writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0");
240 >        }
241 >
242 >        if (needForceVector_) {
243 >          frc = integrableObject->getFrc();
244 >          trq = integrableObject->getTrq();
245 >          
246 >          sprintf(tempBuffer, "\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf",
247 >                  frc[0], frc[1], frc[2],
248 >                  trq[0], trq[1], trq[2]);
249 >          strcat(writeLine, tempBuffer);
250 >        }
251          
252 <                  << entry_plug->Hmat[0][1] << "\t"
253 <                  << entry_plug->Hmat[1][1] << "\t"
254 <                  << entry_plug->Hmat[2][1] << ";\t"
255 <        
348 <                  << entry_plug->Hmat[0][2] << "\t"
349 <                  << entry_plug->Hmat[1][2] << "\t"
350 <                  << entry_plug->Hmat[2][2] << ";";
351 <      
352 <      *outFile[k] << entry_plug->the_integrator->getAdditionalParameters()
353 <                  << endl;
252 >        strcat(writeLine, "\n");
253 >        os << writeLine;
254 >
255 >      }
256      }
257 +
258 +    os.flush();
259 + #else // is_mpi
260 +    /*********************************************************************
261 +     * Documentation?  You want DOCUMENTATION?
262 +     *
263 +     * Why all the potatoes below?  
264 +     *
265 +     * To make a long story short, the original version of DumpWriter
266 +     * worked in the most inefficient way possible.  Node 0 would
267 +     * poke each of the node for an individual atom's formatted data
268 +     * as node 0 worked its way down the global index. This was particularly
269 +     * inefficient since the method blocked all processors at every atom
270 +     * (and did it twice!).
271 +     *
272 +     * An intermediate version of DumpWriter could be described from Node
273 +     * zero's perspective as follows:
274 +     *
275 +     *  1) Have 100 of your friends stand in a circle.
276 +     *  2) When you say go, have all of them start tossing potatoes at
277 +     *     you (one at a time).
278 +     *  3) Catch the potatoes.
279 +     *
280 +     * It was an improvement, but MPI has buffers and caches that could
281 +     * best be described in this analogy as "potato nets", so there's no
282 +     * need to block the processors atom-by-atom.
283 +     *
284 +     * This new and improved DumpWriter works in an even more efficient
285 +     * way:
286 +     *
287 +     *  1) Have 100 of your friend stand in a circle.
288 +     *  2) When you say go, have them start tossing 5-pound bags of
289 +     *     potatoes at you.
290 +     *  3) Once you've caught a friend's bag of potatoes,
291 +     *     toss them a spud to let them know they can toss another bag.
292 +     *
293 +     * How's THAT for documentation?
294 +     *
295 +     *********************************************************************/
296 +    const int masterNode = 0;
297 +
298 +    int * potatoes;
299 +    int myPotato;
300 +    int nProc;
301 +    int which_node;
302 +    double atomData[19];
303 +    int isDirectional;
304 +    char MPIatomTypeString[MINIBUFFERSIZE];
305 +    int msgLen; // the length of message actually recieved at master nodes
306 +    int haveError;
307 +    MPI_Status istatus;
308 +    int nCurObj;
309      
310 <    currentIndex = 0;
311 <    
312 <    for (i = 0 ; i < mpiSim->getNMolGlobal(); i++ ) {
313 <      
314 <      // Get the Node number which has this atom;
361 <      
362 <      which_node = MolToProcMap[i];
363 <      
364 <      if (which_node != 0) {
365 <        
366 <        if (potatoes[which_node] + 1 >= MAXTAG) {
367 <          // The potato was going to exceed the maximum value,
368 <          // so wrap this processor potato back to 0:        
310 >    // code to find maximum tag value
311 >    int * tagub;
312 >    int flag;
313 >    int MAXTAG;
314 >    MPI_Attr_get(MPI_COMM_WORLD, MPI_TAG_UB, &tagub, &flag);
315  
316 <          potatoes[which_node] = 0;          
317 <          MPI_Send(&potatoes[which_node], 1, MPI_INT, which_node, 0,
318 <                   MPI_COMM_WORLD);
319 <          
320 <        }
316 >    if (flag) {
317 >      MAXTAG = *tagub;
318 >    } else {
319 >      MAXTAG = 32767;
320 >    }
321  
322 <        myPotato = potatoes[which_node];        
322 >    if (worldRank == masterNode) { //master node (node 0) is responsible for writing the dump file
323  
324 <        //recieve the number of integrableObject in current molecule
379 <        MPI_Recv(&nCurObj, 1, MPI_INT, which_node,
380 <                 myPotato, MPI_COMM_WORLD, &istatus);
381 <        myPotato++;
382 <        
383 <        for(int l = 0; l < nCurObj; l++){
324 >      // Node 0 needs a list of the magic potatoes for each processor;
325  
326 <          if (potatoes[which_node] + 2 >= MAXTAG) {
327 <            // The potato was going to exceed the maximum value,
387 <            // so wrap this processor potato back to 0:        
326 >      MPI_Comm_size(MPI_COMM_WORLD, &nProc);
327 >      potatoes = new int[nProc];
328  
329 <            potatoes[which_node] = 0;          
330 <            MPI_Send(&potatoes[which_node], 1, MPI_INT, which_node, 0, MPI_COMM_WORLD);
331 <            
332 <          }
329 >      //write out the comment lines
330 >      for(int i = 0; i < nProc; i++) {
331 >        potatoes[i] = 0;
332 >      }
333  
394 –          MPI_Recv(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, which_node,
395 –          myPotato, MPI_COMM_WORLD, &istatus);
334  
335 <          atomTypeString = MPIatomTypeString;
335 >      os << nTotObjects << "\n";
336 >      writeCommentLine(os, info_->getSnapshotManager()->getCurrentSnapshot());
337  
338 <          myPotato++;
338 >      for(int i = 0; i < info_->getNGlobalMolecules(); i++) {
339  
340 <          MPI_Recv(atomData, 13, MPI_DOUBLE, which_node, myPotato, MPI_COMM_WORLD, &istatus);
402 <          myPotato++;
340 >        // Get the Node number which has this atom;
341  
342 <          MPI_Get_count(&istatus, MPI_DOUBLE, &msgLen);
342 >        which_node = info_->getMolToProc(i);
343  
344 <          if(msgLen  == 13)
345 <            isDirectional = 1;
346 <          else
347 <            isDirectional = 0;
410 <          
411 <          // If we've survived to here, format the line:
412 <            
413 <          if (!isDirectional) {
414 <        
415 <            sprintf( writeLine,
416 <                 "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
417 <                 atomTypeString,
418 <                 atomData[0],
419 <                 atomData[1],
420 <                 atomData[2],
421 <                 atomData[3],
422 <                 atomData[4],
423 <                 atomData[5]);
424 <        
425 <           strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
426 <        
427 <          }
428 <          else {
429 <        
430 <                sprintf( writeLine,
431 <                         "%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",
432 <                         atomTypeString,
433 <                         atomData[0],
434 <                         atomData[1],
435 <                         atomData[2],
436 <                         atomData[3],
437 <                         atomData[4],
438 <                         atomData[5],
439 <                         atomData[6],
440 <                         atomData[7],
441 <                         atomData[8],
442 <                         atomData[9],
443 <                         atomData[10],
444 <                         atomData[11],
445 <                         atomData[12]);
446 <            
447 <          }
448 <          
449 <          for(k = 0; k < outFile.size(); k++)
450 <            *outFile[k] << writeLine;            
344 >        if (which_node != masterNode) { //current molecule is in slave node
345 >          if (potatoes[which_node] + 1 >= MAXTAG) {
346 >            // The potato was going to exceed the maximum value,
347 >            // so wrap this processor potato back to 0:        
348  
349 <        }// end for(int l =0)
350 <        potatoes[which_node] = myPotato;
351 <        
352 <      }
353 <      else {
354 <        
355 <        haveError = 0;
356 <        
357 <            local_index = indexArray[currentIndex].first;        
358 <            
359 <            integrableObjects = (entry_plug->molecules[local_index]).getIntegrableObjects();
349 >            potatoes[which_node] = 0;
350 >            MPI_Send(&potatoes[which_node], 1, MPI_INT, which_node, 0,
351 >                     MPI_COMM_WORLD);
352 >          }
353 >
354 >          myPotato = potatoes[which_node];
355 >
356 >          //recieve the number of integrableObject in current molecule
357 >          MPI_Recv(&nCurObj, 1, MPI_INT, which_node, myPotato,
358 >                   MPI_COMM_WORLD, &istatus);
359 >          myPotato++;
360  
361 <        for(iter= integrableObjects.begin(); iter != integrableObjects.end(); ++iter){    
362 <                sd = *iter;
363 <            atomTypeString = sd->getType();
364 <            
468 <            sd->getPos(pos);
469 <            sd->getVel(vel);          
470 <          
471 <            atomData[0] = pos[0];
472 <            atomData[1] = pos[1];
473 <            atomData[2] = pos[2];
361 >          for(int l = 0; l < nCurObj; l++) {
362 >            if (potatoes[which_node] + 2 >= MAXTAG) {
363 >              // The potato was going to exceed the maximum value,
364 >              // so wrap this processor potato back to 0:        
365  
366 <            atomData[3] = vel[0];
367 <            atomData[4] = vel[1];
368 <            atomData[5] = vel[2];
369 <              
479 <            isDirectional = 0;
366 >              potatoes[which_node] = 0;
367 >              MPI_Send(&potatoes[which_node], 1, MPI_INT, which_node,
368 >                       0, MPI_COMM_WORLD);
369 >            }
370  
371 <            if( sd->isDirectional() ){
371 >            MPI_Recv(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR,
372 >                     which_node, myPotato, MPI_COMM_WORLD,
373 >                     &istatus);
374  
375 <              isDirectional = 1;
484 <                
485 <              sd->getQ( q );
486 <              sd->getJ( ji );
375 >            myPotato++;
376  
377 <              for (int j = 0; j < 6 ; j++)
378 <                atomData[j] = atomData[j];            
379 <              
491 <              atomData[6] = q[0];
492 <              atomData[7] = q[1];
493 <              atomData[8] = q[2];
494 <              atomData[9] = q[3];
495 <              
496 <              atomData[10] = ji[0];
497 <              atomData[11] = ji[1];
498 <              atomData[12] = ji[2];
499 <            }
500 <            
501 <            // If we've survived to here, format the line:
502 <            
503 <            if (!isDirectional) {
504 <        
505 <              sprintf( writeLine,
506 <                 "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
507 <                 atomTypeString,
508 <                 atomData[0],
509 <                 atomData[1],
510 <                 atomData[2],
511 <                 atomData[3],
512 <                 atomData[4],
513 <                 atomData[5]);
514 <        
515 <             strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
516 <        
517 <            }
518 <            else {
519 <        
520 <                sprintf( writeLine,
521 <                         "%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",
522 <                         atomTypeString,
523 <                         atomData[0],
524 <                         atomData[1],
525 <                         atomData[2],
526 <                         atomData[3],
527 <                         atomData[4],
528 <                         atomData[5],
529 <                         atomData[6],
530 <                         atomData[7],
531 <                         atomData[8],
532 <                         atomData[9],
533 <                         atomData[10],
534 <                         atomData[11],
535 <                         atomData[12]);
536 <              
537 <            }
538 <            
539 <            for(k = 0; k < outFile.size(); k++)
540 <              *outFile[k] << writeLine;
541 <            
542 <            
543 <        }//end for(iter = integrableObject.begin())
544 <        
545 <      currentIndex++;
546 <      }
377 >            MPI_Recv(atomData, 19, MPI_DOUBLE, which_node, myPotato,
378 >                     MPI_COMM_WORLD, &istatus);
379 >            myPotato++;
380  
381 <    }//end for(i = 0; i < mpiSim->getNmol())
549 <    
550 <    for(k = 0; k < outFile.size(); k++)
551 <      outFile[k]->flush();
552 <    
553 <    sprintf( checkPointMsg,
554 <             "Sucessfully took a dump.\n");
555 <    
556 <    MPIcheckPoint();        
557 <    
558 <    delete[] potatoes;
559 <    
560 <  } else {
381 >            MPI_Get_count(&istatus, MPI_DOUBLE, &msgLen);
382  
383 <    // worldRank != 0, so I'm a remote node.  
383 >            if (msgLen == 13 || msgLen == 19)
384 >              isDirectional = 1;
385 >            else
386 >              isDirectional = 0;
387  
388 <    // Set my magic potato to 0:
388 >            // If we've survived to here, format the line:
389  
390 <    myPotato = 0;
391 <    currentIndex = 0;
392 <    
393 <    for (i = 0 ; i < mpiSim->getNMolGlobal(); i++ ) {
394 <      
395 <      // Am I the node which has this integrableObject?
572 <      
573 <      if (MolToProcMap[i] == worldRank) {
390 >            if (!isDirectional) {
391 >              sprintf(writeLine, "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
392 >                      MPIatomTypeString, atomData[0],
393 >                      atomData[1], atomData[2],
394 >                      atomData[3], atomData[4],
395 >                      atomData[5]);
396  
397 +              strcat(writeLine,
398 +                     "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0");
399 +            } else {
400 +              sprintf(writeLine,
401 +                      "%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",
402 +                      MPIatomTypeString,
403 +                      atomData[0],
404 +                      atomData[1],
405 +                      atomData[2],
406 +                      atomData[3],
407 +                      atomData[4],
408 +                      atomData[5],
409 +                      atomData[6],
410 +                      atomData[7],
411 +                      atomData[8],
412 +                      atomData[9],
413 +                      atomData[10],
414 +                      atomData[11],
415 +                      atomData[12]);
416 +            }
417 +            
418 +            if (needForceVector_) {
419 +              if (!isDirectional) {
420 +                sprintf(writeLine, "\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf",
421 +                        atomData[6],
422 +                        atomData[7],
423 +                        atomData[8],
424 +                        atomData[9],
425 +                        atomData[10],
426 +                        atomData[11]);
427 +              } else {
428 +                sprintf(writeLine, "\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf",
429 +                        atomData[13],
430 +                        atomData[14],
431 +                        atomData[15],
432 +                        atomData[16],
433 +                        atomData[17],
434 +                        atomData[18]);
435 +              }
436 +            }
437  
438 <        if (myPotato + 1 >= MAXTAG) {
439 <          
578 <          // The potato was going to exceed the maximum value,
579 <          // so wrap this processor potato back to 0 (and block until
580 <          // node 0 says we can go:
581 <          
582 <          MPI_Recv(&myPotato, 1, MPI_INT, 0, 0, MPI_COMM_WORLD, &istatus);
583 <          
584 <        }
438 >            sprintf(writeLine, "\n");
439 >            os << writeLine;
440  
441 <          local_index = indexArray[currentIndex].first;        
587 <          integrableObjects = entry_plug->molecules[local_index].getIntegrableObjects();
588 <          
589 <          nCurObj = integrableObjects.size();
590 <                      
591 <          MPI_Send(&nCurObj, 1, MPI_INT, 0,
592 <                   myPotato, MPI_COMM_WORLD);
593 <          myPotato++;
441 >          } // end for(int l =0)
442  
443 <          for( iter = integrableObjects.begin(); iter  != integrableObjects.end(); iter++){
443 >          potatoes[which_node] = myPotato;
444 >        } else { //master node has current molecule
445  
446 <            if (myPotato + 2 >= MAXTAG) {
598 <          
599 <              // The potato was going to exceed the maximum value,
600 <              // so wrap this processor potato back to 0 (and block until
601 <              // node 0 says we can go:
602 <          
603 <              MPI_Recv(&myPotato, 1, MPI_INT, 0, 0, MPI_COMM_WORLD, &istatus);
604 <              
605 <            }
606 <            
607 <            sd = *iter;
608 <            
609 <            atomTypeString = sd->getType();
446 >          mol = info_->getMoleculeByGlobalIndex(i);
447  
448 <            sd->getPos(pos);
449 <            sd->getVel(vel);
448 >          if (mol == NULL) {
449 >            sprintf(painCave.errMsg, "Molecule not found on node %d!", worldRank);
450 >            painCave.isFatal = 1;
451 >            simError();
452 >          }
453 >                
454 >          for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
455 >               integrableObject = mol->nextIntegrableObject(ii)) {      
456  
457 <            atomData[0] = pos[0];
458 <            atomData[1] = pos[1];
616 <            atomData[2] = pos[2];
457 >            pos = integrableObject->getPos();
458 >            vel = integrableObject->getVel();
459  
460 <            atomData[3] = vel[0];
461 <            atomData[4] = vel[1];
462 <            atomData[5] = vel[2];
621 <              
622 <            isDirectional = 0;
460 >            atomData[0] = pos[0];
461 >            atomData[1] = pos[1];
462 >            atomData[2] = pos[2];
463  
464 <            if( sd->isDirectional() ){
464 >            atomData[3] = vel[0];
465 >            atomData[4] = vel[1];
466 >            atomData[5] = vel[2];
467  
468 <                isDirectional = 1;
627 <                
628 <                sd->getQ( q );
629 <                sd->getJ( ji );
630 <                
631 <                
632 <                atomData[6] = q[0];
633 <                atomData[7] = q[1];
634 <                atomData[8] = q[2];
635 <                atomData[9] = q[3];
636 <      
637 <                atomData[10] = ji[0];
638 <                atomData[11] = ji[1];
639 <                atomData[12] = ji[2];
640 <              }
468 >            isDirectional = 0;
469  
470 <            
471 <            strncpy(MPIatomTypeString, atomTypeString, MINIBUFFERSIZE);
470 >            if (integrableObject->isDirectional()) {
471 >              isDirectional = 1;
472  
473 <            // null terminate the string before sending (just in case):
474 <            MPIatomTypeString[MINIBUFFERSIZE-1] = '\0';
473 >              q = integrableObject->getQ();
474 >              ji = integrableObject->getJ();
475  
476 <            MPI_Send(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, 0,
477 <                             myPotato, MPI_COMM_WORLD);
478 <            
651 <            myPotato++;
652 <            
653 <            if (isDirectional) {
476 >              for(int j = 0; j < 6; j++) {
477 >                atomData[j] = atomData[j];
478 >              }
479  
480 <              MPI_Send(atomData, 13, MPI_DOUBLE, 0,
481 <                       myPotato, MPI_COMM_WORLD);
482 <              
483 <            } else {
480 >              atomData[6] = q[0];
481 >              atomData[7] = q[1];
482 >              atomData[8] = q[2];
483 >              atomData[9] = q[3];
484  
485 <              MPI_Send(atomData, 6, MPI_DOUBLE, 0,
486 <                       myPotato, MPI_COMM_WORLD);
487 <            }
485 >              atomData[10] = ji[0];
486 >              atomData[11] = ji[1];
487 >              atomData[12] = ji[2];
488 >            }
489  
490 <            myPotato++;  
490 >            if (needForceVector_) {
491 >              frc = integrableObject->getFrc();
492 >              trq = integrableObject->getTrq();
493  
494 <          }
494 >              if (!isDirectional) {
495 >                atomData[6] = frc[0];
496 >                atomData[7] = frc[1];
497 >                atomData[8] = frc[2];
498 >                atomData[9] = trq[0];
499 >                atomData[10] = trq[1];
500 >                atomData[11] = trq[2];
501 >              } else {
502 >                atomData[13] = frc[0];
503 >                atomData[14] = frc[1];
504 >                atomData[15] = frc[2];
505 >                atomData[16] = trq[0];
506 >                atomData[17] = trq[1];
507 >                atomData[18] = trq[2];
508 >              }
509 >            }
510  
511 <          currentIndex++;    
512 <          
513 <        }
514 <      
511 >            // If we've survived to here, format the line:
512 >
513 >            if (!isDirectional) {
514 >              sprintf(writeLine, "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
515 >                      integrableObject->getType().c_str(), atomData[0],
516 >                      atomData[1], atomData[2],
517 >                      atomData[3], atomData[4],
518 >                      atomData[5]);
519 >
520 >              strcat(writeLine,
521 >                     "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0");
522 >            } else {
523 >              sprintf(writeLine,
524 >                      "%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",
525 >                      integrableObject->getType().c_str(),
526 >                      atomData[0],
527 >                      atomData[1],
528 >                      atomData[2],
529 >                      atomData[3],
530 >                      atomData[4],
531 >                      atomData[5],
532 >                      atomData[6],
533 >                      atomData[7],
534 >                      atomData[8],
535 >                      atomData[9],
536 >                      atomData[10],
537 >                      atomData[11],
538 >                      atomData[12]);
539 >            }
540 >
541 >            if (needForceVector_) {
542 >              if (!isDirectional) {
543 >              sprintf(writeLine, "\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf",
544 >                      atomData[6],
545 >                      atomData[7],
546 >                      atomData[8],
547 >                      atomData[9],
548 >                      atomData[10],
549 >                      atomData[11]);
550 >              } else {
551 >                sprintf(writeLine, "\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf",
552 >                        atomData[13],
553 >                        atomData[14],
554 >                        atomData[15],
555 >                        atomData[16],
556 >                        atomData[17],
557 >                        atomData[18]);
558 >              }
559 >            }
560 >
561 >            sprintf(writeLine, "\n");
562 >            os << writeLine;
563 >
564 >          } //end for(iter = integrableObject.begin())
565 >        }
566 >      } //end for(i = 0; i < mpiSim->getNmol())
567 >
568 >      os.flush();
569 >        
570 >      sprintf(checkPointMsg, "Sucessfully took a dump.\n");
571 >      MPIcheckPoint();
572 >
573 >      delete [] potatoes;
574 >    } else {
575 >
576 >      // worldRank != 0, so I'm a remote node.  
577 >
578 >      // Set my magic potato to 0:
579 >
580 >      myPotato = 0;
581 >
582 >      for(int i = 0; i < info_->getNGlobalMolecules(); i++) {
583 >
584 >        // Am I the node which has this integrableObject?
585 >        int whichNode = info_->getMolToProc(i);
586 >        if (whichNode == worldRank) {
587 >          if (myPotato + 1 >= MAXTAG) {
588 >
589 >            // The potato was going to exceed the maximum value,
590 >            // so wrap this processor potato back to 0 (and block until
591 >            // node 0 says we can go:
592 >
593 >            MPI_Recv(&myPotato, 1, MPI_INT, 0, 0, MPI_COMM_WORLD,
594 >                     &istatus);
595 >          }
596 >
597 >          mol = info_->getMoleculeByGlobalIndex(i);
598 >
599 >                
600 >          nCurObj = mol->getNIntegrableObjects();
601 >
602 >          MPI_Send(&nCurObj, 1, MPI_INT, 0, myPotato, MPI_COMM_WORLD);
603 >          myPotato++;
604 >
605 >          for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
606 >               integrableObject = mol->nextIntegrableObject(ii)) {
607 >
608 >            if (myPotato + 2 >= MAXTAG) {
609 >
610 >              // The potato was going to exceed the maximum value,
611 >              // so wrap this processor potato back to 0 (and block until
612 >              // node 0 says we can go:
613 >
614 >              MPI_Recv(&myPotato, 1, MPI_INT, 0, 0, MPI_COMM_WORLD,
615 >                       &istatus);
616 >            }
617 >
618 >            pos = integrableObject->getPos();
619 >            vel = integrableObject->getVel();
620 >
621 >            atomData[0] = pos[0];
622 >            atomData[1] = pos[1];
623 >            atomData[2] = pos[2];
624 >
625 >            atomData[3] = vel[0];
626 >            atomData[4] = vel[1];
627 >            atomData[5] = vel[2];
628 >
629 >            isDirectional = 0;
630 >
631 >            if (integrableObject->isDirectional()) {
632 >              isDirectional = 1;
633 >
634 >              q = integrableObject->getQ();
635 >              ji = integrableObject->getJ();
636 >
637 >              atomData[6] = q[0];
638 >              atomData[7] = q[1];
639 >              atomData[8] = q[2];
640 >              atomData[9] = q[3];
641 >
642 >              atomData[10] = ji[0];
643 >              atomData[11] = ji[1];
644 >              atomData[12] = ji[2];
645 >            }
646 >
647 >            if (needForceVector_) {
648 >              frc = integrableObject->getFrc();
649 >              trq = integrableObject->getTrq();
650 >              
651 >              if (!isDirectional) {
652 >                atomData[6] = frc[0];
653 >                atomData[7] = frc[1];
654 >                atomData[8] = frc[2];
655 >                
656 >                atomData[9] = trq[0];
657 >                atomData[10] = trq[1];
658 >                atomData[11] = trq[2];
659 >              } else {
660 >                atomData[13] = frc[0];
661 >                atomData[14] = frc[1];
662 >                atomData[15] = frc[2];
663 >                
664 >                atomData[16] = trq[0];
665 >                atomData[17] = trq[1];
666 >                atomData[18] = trq[2];
667 >              }
668 >            }
669 >
670 >            strncpy(MPIatomTypeString, integrableObject->getType().c_str(), MINIBUFFERSIZE);
671 >
672 >            // null terminate the  std::string before sending (just in case):
673 >            MPIatomTypeString[MINIBUFFERSIZE - 1] = '\0';
674 >
675 >            MPI_Send(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, 0,
676 >                     myPotato, MPI_COMM_WORLD);
677 >
678 >            myPotato++;
679 >
680 >            if (isDirectional && needForceVector_) {
681 >              MPI_Send(atomData, 19, MPI_DOUBLE, 0, myPotato,
682 >                       MPI_COMM_WORLD);
683 >            } else if (isDirectional) {
684 >              MPI_Send(atomData, 13, MPI_DOUBLE, 0, myPotato,
685 >                       MPI_COMM_WORLD);
686 >            } else if (needForceVector_) {
687 >              MPI_Send(atomData, 12, MPI_DOUBLE, 0, myPotato,
688 >                       MPI_COMM_WORLD);
689 >            } else {
690 >              MPI_Send(atomData, 6, MPI_DOUBLE, 0, myPotato,
691 >                       MPI_COMM_WORLD);
692 >            }
693 >
694 >            myPotato++;
695 >          }
696 >                    
697 >        }
698 >            
699        }
700 +      sprintf(checkPointMsg, "Sucessfully took a dump.\n");
701 +      MPIcheckPoint();
702 +    }
703  
704 <    sprintf( checkPointMsg,
705 <             "Successfully took a dump.\n");
706 <    MPIcheckPoint();                
704 > #endif // is_mpi
705 >
706 >  }
707 >
708 >  void DumpWriter::writeDump() {
709 >    writeFrame(*dumpFile_);
710 >  }
711 >
712 >  void DumpWriter::writeEor() {
713 >    std::ostream* eorStream;
714      
715 + #ifdef IS_MPI
716 +    if (worldRank == 0) {
717 + #endif // is_mpi
718 +
719 +      eorStream = createOStream(eorFilename_);
720 +
721 + #ifdef IS_MPI
722 +    }
723 + #endif // is_mpi    
724 +
725 +    writeFrame(*eorStream);
726 +
727 + #ifdef IS_MPI
728 +    if (worldRank == 0) {
729 + #endif // is_mpi
730 +    delete eorStream;
731 +
732 + #ifdef IS_MPI
733 +    }
734 + #endif // is_mpi  
735 +
736    }
737 <  
737 >
738 >
739 >  void DumpWriter::writeDumpAndEor() {
740 >    std::vector<std::streambuf*> buffers;
741 >    std::ostream* eorStream;
742 > #ifdef IS_MPI
743 >    if (worldRank == 0) {
744   #endif // is_mpi
681 – }
745  
746 +      buffers.push_back(dumpFile_->rdbuf());
747 +
748 +      eorStream = createOStream(eorFilename_);
749 +
750 +      buffers.push_back(eorStream->rdbuf());
751 +        
752   #ifdef IS_MPI
753 +    }
754 + #endif // is_mpi    
755  
756 < // a couple of functions to let us escape the write loop
756 >    TeeBuf tbuf(buffers.begin(), buffers.end());
757 >    std::ostream os(&tbuf);
758  
759 < void dWrite::DieDieDie( void ){
759 >    writeFrame(os);
760  
761 <  MPI_Finalize();
762 <  exit (0);
761 > #ifdef IS_MPI
762 >    if (worldRank == 0) {
763 > #endif // is_mpi
764 >    delete eorStream;
765 >
766 > #ifdef IS_MPI
767 >    }
768 > #endif // is_mpi  
769 >    
770 >  }
771 >
772 > std::ostream* DumpWriter::createOStream(const std::string& filename) {
773 >
774 >    std::ostream* newOStream;
775 > #ifdef HAVE_LIBZ
776 >    if (needCompression_) {
777 >        newOStream = new ogzstream(filename.c_str());
778 >    } else {
779 >        newOStream = new std::ofstream(filename.c_str());
780 >    }
781 > #else
782 >    newOStream = new std::ofstream(filename.c_str());
783 > #endif
784 >    return newOStream;
785   }
786  
787 < #endif //is_mpi
787 > }//end namespace oopse

Diff Legend

– Removed lines
+ Added lines
< Changed lines
> Changed lines