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root/OpenMD/trunk/src/io/DumpWriter.cpp
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Comparing trunk/src/io/DumpWriter.cpp (file contents):
Revision 221 by chrisfen, Tue Nov 23 22:48:31 2004 UTC vs.
Revision 854 by chuckv, Thu Jan 12 19:56:30 2006 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;
59 <
60 < #ifdef IS_MPI
61 <  if(worldRank == 0 ){
62 < #endif // is_mpi
63 <
64 <    dumpFile.open(entry_plug->sampleName.c_str(), ios::out | ios::trunc );
65 <
34 <    if( !dumpFile ){
35 <
36 <      sprintf( painCave.errMsg,
37 <               "Could not open \"%s\" for dump output.\n",
38 <               entry_plug->sampleName.c_str());
39 <      painCave.isFatal = 1;
40 <      simError();
58 >    Globals* simParams = info->getSimParams();
59 >    needCompression_ = simParams->getCompressDumpFile();
60 >    needForceVector_ = simParams->getOutputForceVector();
61 >    createDumpFile_ = true;
62 > #ifdef HAVE_LIBZ
63 >    if (needCompression_) {
64 >        filename_ += ".gz";
65 >        eorFilename_ += ".gz";
66      }
67 <
67 > #endif
68 >    
69   #ifdef IS_MPI
44 –  }
70  
71 <  //sort the local atoms by global index
47 <  sortByGlobalIndex();
48 <  
49 <  sprintf( checkPointMsg,
50 <           "Sucessfully opened output file for dumping.\n");
51 <  MPIcheckPoint();
71 >      if (worldRank == 0) {
72   #endif // is_mpi
53 – }
73  
74 < DumpWriter::~DumpWriter( ){
74 >        
75 >        dumpFile_ = createOStream(filename_);
76  
77 < #ifdef IS_MPI
78 <  if(worldRank == 0 ){
79 < #endif // is_mpi
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  
61 –    dumpFile.close();
62 –
84   #ifdef IS_MPI
64 –  }
65 – #endif // is_mpi
66 – }
85  
86 < #ifdef IS_MPI
86 >      }
87  
88 < /**
89 < * A hook function to load balancing
72 < */
88 >      sprintf(checkPointMsg, "Sucessfully opened output file for dumping.\n");
89 >      MPIcheckPoint();
90  
91 < void DumpWriter::update(){
75 <  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 < }
91 > #endif // is_mpi
92  
93 < /**
87 < * Sorting the local index by global index
88 < */
89 <
90 < 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 < }
93 >    }
94  
100 – #endif
95  
96 < void DumpWriter::writeDump(double currentTime){
96 >  DumpWriter::DumpWriter(SimInfo* info, const std::string& filename)
97 >    : info_(info), filename_(filename){
98  
99 <  ofstream finalOut;
100 <  vector<ofstream*> fileStreams;
99 >    Globals* simParams = info->getSimParams();
100 >    eorFilename_ = filename_.substr(0, filename_.rfind(".")) + ".eor";    
101  
102 < #ifdef IS_MPI
103 <  if(worldRank == 0 ){
104 < #endif    
105 <    finalOut.open( entry_plug->finalName.c_str(), ios::out | ios::trunc );
106 <    if( !finalOut ){
107 <      sprintf( painCave.errMsg,
108 <               "Could not open \"%s\" for final dump output.\n",
114 <               entry_plug->finalName.c_str() );
115 <      painCave.isFatal = 1;
116 <      simError();
102 >    needCompression_ = simParams->getCompressDumpFile();
103 >    needForceVector_ = simParams->getOutputForceVector();
104 >    createDumpFile_ = true;
105 > #ifdef HAVE_LIBZ
106 >    if (needCompression_) {
107 >        filename_ += ".gz";
108 >        eorFilename_ += ".gz";
109      }
110 + #endif
111 +    
112   #ifdef IS_MPI
113 <  }
113 >
114 >      if (worldRank == 0) {
115   #endif // is_mpi
116  
117 <  fileStreams.push_back(&finalOut);
118 <  fileStreams.push_back(&dumpFile);
117 >      
118 >        dumpFile_ = createOStream(filename_);
119  
120 <  writeFrame(fileStreams, currentTime);
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 <
137 >  
138 >  DumpWriter::DumpWriter(SimInfo* info, const std::string& filename, bool writeDumpFile)
139 >  : info_(info), filename_(filename){
140 >    
141 >    Globals* simParams = info->getSimParams();
142 >    eorFilename_ = filename_.substr(0, filename_.rfind(".")) + ".eor";    
143 >    
144 >    needCompression_ = simParams->getCompressDumpFile();
145 >    needForceVector_ = simParams->getOutputForceVector();
146 >    
147 > #ifdef HAVE_LIBZ
148 >    if (needCompression_) {
149 >      filename_ += ".gz";
150 >      eorFilename_ += ".gz";
151 >    }
152 > #endif
153 >    
154   #ifdef IS_MPI
155 <  }
155 >    
156 >    if (worldRank == 0) {
157   #endif // is_mpi
158 <  
159 <  fileStreams.push_back(&finalOut);  
160 <  writeFrame(fileStreams, currentTime);
161 <
158 >      
159 >      createDumpFile_ = writeDumpFile;
160 >      if (createDumpFile_) {
161 >        dumpFile_ = createOStream(filename_);
162 >      
163 >        if (!dumpFile_) {
164 >          sprintf(painCave.errMsg, "Could not open \"%s\" for dump output.\n",
165 >                  filename_.c_str());
166 >          painCave.isFatal = 1;
167 >          simError();
168 >        }
169 >      }
170   #ifdef IS_MPI
171 <  finalOut.close();
172 < #endif
171 >      
172 >    }
173 >    
174 >    sprintf(checkPointMsg, "Sucessfully opened output file for dumping.\n");
175 >    MPIcheckPoint();
176 >    
177 > #endif // is_mpi
178 >    
179 >  }
180    
181 < }
181 >  
182 >  
183 >  
184 >  
185  
186 < void DumpWriter::writeFrame( vector<ofstream*>& outFile, double currentTime ){
186 >  DumpWriter::~DumpWriter() {
187  
188 <  const int BUFFERSIZE = 2000;
168 <  const int MINIBUFFERSIZE = 100;
188 > #ifdef IS_MPI
189  
190 <  char tempBuffer[BUFFERSIZE];  
191 <  char writeLine[BUFFERSIZE];
192 <
193 <  int i;
194 <  unsigned int k;
175 <
190 >    if (worldRank == 0) {
191 > #endif // is_mpi
192 >      if (createDumpFile_){
193 >        delete dumpFile_;
194 >      }
195   #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 –   *********************************************************************/
196  
197 <  int *potatoes;
216 <  int myPotato;
197 >    }
198  
199 <  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
199 > #endif // is_mpi
200  
201 <  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";
201 >  }
202  
203 <    *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"
203 >  void DumpWriter::writeCommentLine(std::ostream& os, Snapshot* s) {
204  
205 <                     << entry_plug->Hmat[0][2] << "\t"
206 <                     << entry_plug->Hmat[1][2] << "\t"
207 <                     << entry_plug->Hmat[2][2] << ";";
205 >    double currentTime;
206 >    Mat3x3d hmat;
207 >    double chi;
208 >    double integralOfChiDt;
209 >    Mat3x3d eta;
210 >    
211 >    currentTime = s->getTime();
212 >    hmat = s->getHmat();
213 >    chi = s->getChi();
214 >    integralOfChiDt = s->getIntegralOfChiDt();
215 >    eta = s->getEta();
216 >    
217 >    os << currentTime << ";\t"
218 >       << hmat(0, 0) << "\t" << hmat(1, 0) << "\t" << hmat(2, 0) << ";\t"
219 >       << hmat(0, 1) << "\t" << hmat(1, 1) << "\t" << hmat(2, 1) << ";\t"
220 >       << hmat(0, 2) << "\t" << hmat(1, 2) << "\t" << hmat(2, 2) << ";\t";
221  
222      //write out additional parameters, such as chi and eta
223 <    *outFile[k] << entry_plug->the_integrator->getAdditionalParameters() << endl;
223 >
224 >    os << chi << "\t" << integralOfChiDt << ";\t";
225 >
226 >    os << eta(0, 0) << "\t" << eta(1, 0) << "\t" << eta(2, 0) << ";\t"
227 >       << eta(0, 1) << "\t" << eta(1, 1) << "\t" << eta(2, 1) << ";\t"
228 >       << eta(0, 2) << "\t" << eta(1, 2) << "\t" << eta(2, 2) << ";";
229 >        
230 >    os << "\n";
231    }
232 +
233 +  void DumpWriter::writeFrame(std::ostream& os) {
234 +    const int BUFFERSIZE = 2000;
235 +    const int MINIBUFFERSIZE = 100;
236 +
237 +    char tempBuffer[BUFFERSIZE];
238 +    char writeLine[BUFFERSIZE];
239 +
240 +    Quat4d q;
241 +    Vector3d ji;
242 +    Vector3d pos;
243 +    Vector3d vel;
244 +    Vector3d frc;
245 +    Vector3d trq;
246 +
247 +    Molecule* mol;
248 +    StuntDouble* integrableObject;
249 +    SimInfo::MoleculeIterator mi;
250 +    Molecule::IntegrableObjectIterator ii;
251    
252 <  for( i=0; i< entry_plug->n_mol; i++ ){
252 >    int nTotObjects;    
253 >    nTotObjects = info_->getNGlobalIntegrableObjects();
254  
255 <    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);
255 > #ifndef IS_MPI
256  
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 );
257  
258 <      if( sd->isDirectional() ){
258 >    os << nTotObjects << "\n";
259 >        
260 >    writeCommentLine(os, info_->getSnapshotManager()->getCurrentSnapshot());
261  
262 <        sd->getQ( q );
283 <        sd->getJ( ji );
262 >    for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
263  
264 <        sprintf( tempBuffer,
265 <               "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
266 <               q[0],
267 <               q[1],
268 <               q[2],
269 <               q[3],
270 <                 ji[0],
271 <                 ji[1],
272 <                 ji[2]);
273 <        strcat( writeLine, tempBuffer );
264 >      for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
265 >           integrableObject = mol->nextIntegrableObject(ii)) {
266 >                
267 >
268 >        pos = integrableObject->getPos();
269 >        vel = integrableObject->getVel();
270 >
271 >        sprintf(tempBuffer, "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
272 >                integrableObject->getType().c_str(),
273 >                pos[0], pos[1], pos[2],
274 >                vel[0], vel[1], vel[2]);
275 >
276 >        strcpy(writeLine, tempBuffer);
277 >
278 >        if (integrableObject->isDirectional()) {
279 >          q = integrableObject->getQ();
280 >          ji = integrableObject->getJ();
281 >
282 >          sprintf(tempBuffer, "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf",
283 >                  q[0], q[1], q[2], q[3],
284 >                  ji[0], ji[1], ji[2]);
285 >          strcat(writeLine, tempBuffer);
286 >        } else {
287 >          strcat(writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0");
288 >        }
289 >
290 >        if (needForceVector_) {
291 >          frc = integrableObject->getFrc();
292 >          trq = integrableObject->getTrq();
293 >          
294 >          sprintf(tempBuffer, "\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf",
295 >                  frc[0], frc[1], frc[2],
296 >                  trq[0], trq[1], trq[2]);
297 >          strcat(writeLine, tempBuffer);
298 >        }
299 >        
300 >        strcat(writeLine, "\n");
301 >        os << writeLine;
302 >
303        }
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;      
304      }
302 –    
303 –  }
305  
306 +    os.flush();
307   #else // is_mpi
308 +    /*********************************************************************
309 +     * Documentation?  You want DOCUMENTATION?
310 +     *
311 +     * Why all the potatoes below?  
312 +     *
313 +     * To make a long story short, the original version of DumpWriter
314 +     * worked in the most inefficient way possible.  Node 0 would
315 +     * poke each of the node for an individual atom's formatted data
316 +     * as node 0 worked its way down the global index. This was particularly
317 +     * inefficient since the method blocked all processors at every atom
318 +     * (and did it twice!).
319 +     *
320 +     * An intermediate version of DumpWriter could be described from Node
321 +     * zero's perspective as follows:
322 +     *
323 +     *  1) Have 100 of your friends stand in a circle.
324 +     *  2) When you say go, have all of them start tossing potatoes at
325 +     *     you (one at a time).
326 +     *  3) Catch the potatoes.
327 +     *
328 +     * It was an improvement, but MPI has buffers and caches that could
329 +     * best be described in this analogy as "potato nets", so there's no
330 +     * need to block the processors atom-by-atom.
331 +     *
332 +     * This new and improved DumpWriter works in an even more efficient
333 +     * way:
334 +     *
335 +     *  1) Have 100 of your friend stand in a circle.
336 +     *  2) When you say go, have them start tossing 5-pound bags of
337 +     *     potatoes at you.
338 +     *  3) Once you've caught a friend's bag of potatoes,
339 +     *     toss them a spud to let them know they can toss another bag.
340 +     *
341 +     * How's THAT for documentation?
342 +     *
343 +     *********************************************************************/
344 +    const int masterNode = 0;
345  
346 <  /* code to find maximum tag value */
347 <  
348 <  int *tagub, flag, MAXTAG;
349 <  MPI_Attr_get(MPI_COMM_WORLD, MPI_TAG_UB, &tagub, &flag);
350 <  if (flag) {
351 <    MAXTAG = *tagub;
352 <  } else {
353 <    MAXTAG = 32767;
354 <  }  
346 >    int * potatoes;
347 >    int myPotato;
348 >    int nProc;
349 >    int which_node;
350 >    double atomData[19];
351 >    int isDirectional;
352 >    char MPIatomTypeString[MINIBUFFERSIZE];
353 >    int msgLen; // the length of message actually recieved at master nodes
354 >    int haveError;
355 >    MPI_Status istatus;
356 >    int nCurObj;
357 >    
358 >    // code to find maximum tag value
359 >    int * tagub;
360 >    int flag;
361 >    int MAXTAG;
362 >    MPI_Attr_get(MPI_COMM_WORLD, MPI_TAG_UB, &tagub, &flag);
363  
364 <  int haveError;
364 >    if (flag) {
365 >      MAXTAG = *tagub;
366 >    } else {
367 >      MAXTAG = 32767;
368 >    }
369  
370 <  MPI_Status istatus;
320 <  int nCurObj;
321 <  int *MolToProcMap = mpiSim->getMolToProcMap();
370 >    if (worldRank == masterNode) { //master node (node 0) is responsible for writing the dump file
371  
372 <  // write out header and node 0's coordinates
372 >      // Node 0 needs a list of the magic potatoes for each processor;
373  
374 <  if( worldRank == 0 ){
374 >      MPI_Comm_size(MPI_COMM_WORLD, &nProc);
375 >      potatoes = new int[nProc];
376  
377 <    // Node 0 needs a list of the magic potatoes for each processor;
377 >      //write out the comment lines
378 >      for(int i = 0; i < nProc; i++) {
379 >        potatoes[i] = 0;
380 >      }
381  
329 –    nProc = mpiSim->getNProcessors();
330 –    potatoes = new int[nProc];
382  
383 <    //write out the comment lines
384 <    for (i = 0; i < nProc; i++)
334 <      potatoes[i] = 0;
335 <    
336 <    for(k = 0; k < outFile.size(); k++){
337 <      *outFile[k] << nTotObjects << "\n";
338 <      
339 <      *outFile[k] << currentTime << ";\t"
340 <                  << entry_plug->Hmat[0][0] << "\t"
341 <                  << entry_plug->Hmat[1][0] << "\t"
342 <                  << entry_plug->Hmat[2][0] << ";\t"
343 <        
344 <                  << entry_plug->Hmat[0][1] << "\t"
345 <                  << entry_plug->Hmat[1][1] << "\t"
346 <                  << entry_plug->Hmat[2][1] << ";\t"
347 <        
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;
354 <    }
355 <    
356 <    currentIndex = 0;
357 <    
358 <    for (i = 0 ; i < mpiSim->getNMolGlobal(); i++ ) {
359 <      
360 <      // 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:        
383 >      os << nTotObjects << "\n";
384 >      writeCommentLine(os, info_->getSnapshotManager()->getCurrentSnapshot());
385  
386 <          potatoes[which_node] = 0;          
371 <          MPI_Send(&potatoes[which_node], 1, MPI_INT, which_node, 0,
372 <                   MPI_COMM_WORLD);
373 <          
374 <        }
386 >      for(int i = 0; i < info_->getNGlobalMolecules(); i++) {
387  
388 <        myPotato = potatoes[which_node];        
388 >        // Get the Node number which has this atom;
389  
390 <        //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++){
390 >        which_node = info_->getMolToProc(i);
391  
392 <          if (potatoes[which_node] + 2 >= MAXTAG) {
393 <            // The potato was going to exceed the maximum value,
394 <            // so wrap this processor potato back to 0:        
392 >        if (which_node != masterNode) { //current molecule is in slave node
393 >          if (potatoes[which_node] + 1 >= MAXTAG) {
394 >            // The potato was going to exceed the maximum value,
395 >            // so wrap this processor potato back to 0:        
396  
397 <            potatoes[which_node] = 0;          
398 <            MPI_Send(&potatoes[which_node], 1, MPI_INT, which_node, 0, MPI_COMM_WORLD);
399 <            
400 <          }
397 >            potatoes[which_node] = 0;
398 >            MPI_Send(&potatoes[which_node], 1, MPI_INT, which_node, 0,
399 >                     MPI_COMM_WORLD);
400 >          }
401  
402 <          MPI_Recv(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, which_node,
395 <          myPotato, MPI_COMM_WORLD, &istatus);
402 >          myPotato = potatoes[which_node];
403  
404 <          atomTypeString = MPIatomTypeString;
404 >          //recieve the number of integrableObject in current molecule
405 >          MPI_Recv(&nCurObj, 1, MPI_INT, which_node, myPotato,
406 >                   MPI_COMM_WORLD, &istatus);
407 >          myPotato++;
408  
409 <          myPotato++;
409 >          for(int l = 0; l < nCurObj; l++) {
410 >            if (potatoes[which_node] + 2 >= MAXTAG) {
411 >              // The potato was going to exceed the maximum value,
412 >              // so wrap this processor potato back to 0:        
413  
414 <          MPI_Recv(atomData, 13, MPI_DOUBLE, which_node, myPotato, MPI_COMM_WORLD, &istatus);
415 <          myPotato++;
414 >              potatoes[which_node] = 0;
415 >              MPI_Send(&potatoes[which_node], 1, MPI_INT, which_node,
416 >                       0, MPI_COMM_WORLD);
417 >            }
418  
419 <          MPI_Get_count(&istatus, MPI_DOUBLE, &msgLen);
419 >            MPI_Recv(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR,
420 >                     which_node, myPotato, MPI_COMM_WORLD,
421 >                     &istatus);
422  
423 <          if(msgLen  == 13)
407 <            isDirectional = 1;
408 <          else
409 <            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;            
423 >            myPotato++;
424  
425 <        }// end for(int l =0)
426 <        potatoes[which_node] = myPotato;
427 <        
455 <      }
456 <      else {
457 <        
458 <        haveError = 0;
459 <        
460 <            local_index = indexArray[currentIndex].first;        
461 <            
462 <            integrableObjects = (entry_plug->molecules[local_index]).getIntegrableObjects();
425 >            MPI_Recv(atomData, 19, MPI_DOUBLE, which_node, myPotato,
426 >                     MPI_COMM_WORLD, &istatus);
427 >            myPotato++;
428  
429 <        for(iter= integrableObjects.begin(); iter != integrableObjects.end(); ++iter){    
465 <                sd = *iter;
466 <            atomTypeString = sd->getType();
467 <            
468 <            sd->getPos(pos);
469 <            sd->getVel(vel);          
470 <          
471 <            atomData[0] = pos[0];
472 <            atomData[1] = pos[1];
473 <            atomData[2] = pos[2];
429 >            MPI_Get_count(&istatus, MPI_DOUBLE, &msgLen);
430  
431 <            atomData[3] = vel[0];
432 <            atomData[4] = vel[1];
433 <            atomData[5] = vel[2];
434 <              
479 <            isDirectional = 0;
431 >            if (msgLen == 13 || msgLen == 19)
432 >              isDirectional = 1;
433 >            else
434 >              isDirectional = 0;
435  
436 <            if( sd->isDirectional() ){
436 >            // If we've survived to here, format the line:
437  
438 <              isDirectional = 1;
439 <                
440 <              sd->getQ( q );
441 <              sd->getJ( ji );
438 >            if (!isDirectional) {
439 >              sprintf(writeLine, "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
440 >                      MPIatomTypeString, atomData[0],
441 >                      atomData[1], atomData[2],
442 >                      atomData[3], atomData[4],
443 >                      atomData[5]);
444  
445 <              for (int j = 0; j < 6 ; j++)
446 <                atomData[j] = atomData[j];            
447 <              
448 <              atomData[6] = q[0];
449 <              atomData[7] = q[1];
450 <              atomData[8] = q[2];
451 <              atomData[9] = q[3];
452 <              
453 <              atomData[10] = ji[0];
454 <              atomData[11] = ji[1];
455 <              atomData[12] = ji[2];
456 <            }
457 <            
458 <            // If we've survived to here, format the line:
459 <            
460 <            if (!isDirectional) {
461 <        
462 <              sprintf( writeLine,
463 <                 "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
464 <                 atomTypeString,
465 <                 atomData[0],
466 <                 atomData[1],
467 <                 atomData[2],
468 <                 atomData[3],
469 <                 atomData[4],
470 <                 atomData[5]);
471 <        
472 <             strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
473 <        
474 <            }
475 <            else {
476 <        
477 <                sprintf( writeLine,
478 <                         "%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",
479 <                         atomTypeString,
480 <                         atomData[0],
481 <                         atomData[1],
482 <                         atomData[2],
483 <                         atomData[3],
484 <                         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 <      }
445 >              strcat(writeLine,
446 >                     "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0");
447 >            } else {
448 >              sprintf(writeLine,
449 >                      "%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",
450 >                      MPIatomTypeString,
451 >                      atomData[0],
452 >                      atomData[1],
453 >                      atomData[2],
454 >                      atomData[3],
455 >                      atomData[4],
456 >                      atomData[5],
457 >                      atomData[6],
458 >                      atomData[7],
459 >                      atomData[8],
460 >                      atomData[9],
461 >                      atomData[10],
462 >                      atomData[11],
463 >                      atomData[12]);
464 >            }
465 >            
466 >            if (needForceVector_) {
467 >              if (!isDirectional) {
468 >                sprintf(writeLine, "\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf",
469 >                        atomData[6],
470 >                        atomData[7],
471 >                        atomData[8],
472 >                        atomData[9],
473 >                        atomData[10],
474 >                        atomData[11]);
475 >              } else {
476 >                sprintf(writeLine, "\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf",
477 >                        atomData[13],
478 >                        atomData[14],
479 >                        atomData[15],
480 >                        atomData[16],
481 >                        atomData[17],
482 >                        atomData[18]);
483 >              }
484 >            }
485  
486 <    }//end for(i = 0; i < mpiSim->getNmol())
487 <    
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 {
486 >            sprintf(writeLine, "\n");
487 >            os << writeLine;
488  
489 <    // worldRank != 0, so I'm a remote node.  
489 >          } // end for(int l =0)
490  
491 <    // Set my magic potato to 0:
491 >          potatoes[which_node] = myPotato;
492 >        } else { //master node has current molecule
493  
494 <    myPotato = 0;
567 <    currentIndex = 0;
568 <    
569 <    for (i = 0 ; i < mpiSim->getNMolGlobal(); i++ ) {
570 <      
571 <      // Am I the node which has this integrableObject?
572 <      
573 <      if (MolToProcMap[i] == worldRank) {
494 >          mol = info_->getMoleculeByGlobalIndex(i);
495  
496 +          if (mol == NULL) {
497 +            sprintf(painCave.errMsg, "Molecule not found on node %d!", worldRank);
498 +            painCave.isFatal = 1;
499 +            simError();
500 +          }
501 +                
502 +          for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
503 +               integrableObject = mol->nextIntegrableObject(ii)) {      
504  
505 <        if (myPotato + 1 >= MAXTAG) {
506 <          
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 <        }
505 >            pos = integrableObject->getPos();
506 >            vel = integrableObject->getVel();
507  
508 <          local_index = indexArray[currentIndex].first;        
509 <          integrableObjects = entry_plug->molecules[local_index].getIntegrableObjects();
510 <          
589 <          nCurObj = integrableObjects.size();
590 <                      
591 <          MPI_Send(&nCurObj, 1, MPI_INT, 0,
592 <                   myPotato, MPI_COMM_WORLD);
593 <          myPotato++;
508 >            atomData[0] = pos[0];
509 >            atomData[1] = pos[1];
510 >            atomData[2] = pos[2];
511  
512 <          for( iter = integrableObjects.begin(); iter  != integrableObjects.end(); iter++){
512 >            atomData[3] = vel[0];
513 >            atomData[4] = vel[1];
514 >            atomData[5] = vel[2];
515  
516 <            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();
516 >            isDirectional = 0;
517  
518 <            sd->getPos(pos);
519 <            sd->getVel(vel);
518 >            if (integrableObject->isDirectional()) {
519 >              isDirectional = 1;
520  
521 <            atomData[0] = pos[0];
522 <            atomData[1] = pos[1];
616 <            atomData[2] = pos[2];
521 >              q = integrableObject->getQ();
522 >              ji = integrableObject->getJ();
523  
524 <            atomData[3] = vel[0];
525 <            atomData[4] = vel[1];
526 <            atomData[5] = vel[2];
621 <              
622 <            isDirectional = 0;
524 >              for(int j = 0; j < 6; j++) {
525 >                atomData[j] = atomData[j];
526 >              }
527  
528 <            if( sd->isDirectional() ){
528 >              atomData[6] = q[0];
529 >              atomData[7] = q[1];
530 >              atomData[8] = q[2];
531 >              atomData[9] = q[3];
532  
533 <                isDirectional = 1;
534 <                
535 <                sd->getQ( q );
536 <                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 <              }
533 >              atomData[10] = ji[0];
534 >              atomData[11] = ji[1];
535 >              atomData[12] = ji[2];
536 >            }
537  
538 <            
539 <            strncpy(MPIatomTypeString, atomTypeString, MINIBUFFERSIZE);
538 >            if (needForceVector_) {
539 >              frc = integrableObject->getFrc();
540 >              trq = integrableObject->getTrq();
541  
542 <            // null terminate the string before sending (just in case):
543 <            MPIatomTypeString[MINIBUFFERSIZE-1] = '\0';
544 <
545 <            MPI_Send(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, 0,
546 <                             myPotato, MPI_COMM_WORLD);
547 <            
548 <            myPotato++;
549 <            
550 <            if (isDirectional) {
542 >              if (!isDirectional) {
543 >                atomData[6] = frc[0];
544 >                atomData[7] = frc[1];
545 >                atomData[8] = frc[2];
546 >                atomData[9] = trq[0];
547 >                atomData[10] = trq[1];
548 >                atomData[11] = trq[2];
549 >              } else {
550 >                atomData[13] = frc[0];
551 >                atomData[14] = frc[1];
552 >                atomData[15] = frc[2];
553 >                atomData[16] = trq[0];
554 >                atomData[17] = trq[1];
555 >                atomData[18] = trq[2];
556 >              }
557 >            }
558  
559 <              MPI_Send(atomData, 13, MPI_DOUBLE, 0,
656 <                       myPotato, MPI_COMM_WORLD);
657 <              
658 <            } else {
559 >            // If we've survived to here, format the line:
560  
561 <              MPI_Send(atomData, 6, MPI_DOUBLE, 0,
562 <                       myPotato, MPI_COMM_WORLD);
563 <            }
561 >            if (!isDirectional) {
562 >              sprintf(writeLine, "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
563 >                      integrableObject->getType().c_str(), atomData[0],
564 >                      atomData[1], atomData[2],
565 >                      atomData[3], atomData[4],
566 >                      atomData[5]);
567  
568 <            myPotato++;  
568 >              strcat(writeLine,
569 >                     "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0");
570 >            } else {
571 >              sprintf(writeLine,
572 >                      "%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",
573 >                      integrableObject->getType().c_str(),
574 >                      atomData[0],
575 >                      atomData[1],
576 >                      atomData[2],
577 >                      atomData[3],
578 >                      atomData[4],
579 >                      atomData[5],
580 >                      atomData[6],
581 >                      atomData[7],
582 >                      atomData[8],
583 >                      atomData[9],
584 >                      atomData[10],
585 >                      atomData[11],
586 >                      atomData[12]);
587 >            }
588  
589 <          }
589 >            if (needForceVector_) {
590 >              if (!isDirectional) {
591 >              sprintf(writeLine, "\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf",
592 >                      atomData[6],
593 >                      atomData[7],
594 >                      atomData[8],
595 >                      atomData[9],
596 >                      atomData[10],
597 >                      atomData[11]);
598 >              } else {
599 >                sprintf(writeLine, "\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf",
600 >                        atomData[13],
601 >                        atomData[14],
602 >                        atomData[15],
603 >                        atomData[16],
604 >                        atomData[17],
605 >                        atomData[18]);
606 >              }
607 >            }
608  
609 <          currentIndex++;    
610 <          
611 <        }
612 <      
609 >            sprintf(writeLine, "\n");
610 >            os << writeLine;
611 >
612 >          } //end for(iter = integrableObject.begin())
613 >        }
614 >      } //end for(i = 0; i < mpiSim->getNmol())
615 >
616 >      os.flush();
617 >        
618 >      sprintf(checkPointMsg, "Sucessfully took a dump.\n");
619 >      MPIcheckPoint();
620 >
621 >      delete [] potatoes;
622 >    } else {
623 >
624 >      // worldRank != 0, so I'm a remote node.  
625 >
626 >      // Set my magic potato to 0:
627 >
628 >      myPotato = 0;
629 >
630 >      for(int i = 0; i < info_->getNGlobalMolecules(); i++) {
631 >
632 >        // Am I the node which has this integrableObject?
633 >        int whichNode = info_->getMolToProc(i);
634 >        if (whichNode == worldRank) {
635 >          if (myPotato + 1 >= MAXTAG) {
636 >
637 >            // The potato was going to exceed the maximum value,
638 >            // so wrap this processor potato back to 0 (and block until
639 >            // node 0 says we can go:
640 >
641 >            MPI_Recv(&myPotato, 1, MPI_INT, 0, 0, MPI_COMM_WORLD,
642 >                     &istatus);
643 >          }
644 >
645 >          mol = info_->getMoleculeByGlobalIndex(i);
646 >
647 >                
648 >          nCurObj = mol->getNIntegrableObjects();
649 >
650 >          MPI_Send(&nCurObj, 1, MPI_INT, 0, myPotato, MPI_COMM_WORLD);
651 >          myPotato++;
652 >
653 >          for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
654 >               integrableObject = mol->nextIntegrableObject(ii)) {
655 >
656 >            if (myPotato + 2 >= MAXTAG) {
657 >
658 >              // The potato was going to exceed the maximum value,
659 >              // so wrap this processor potato back to 0 (and block until
660 >              // node 0 says we can go:
661 >
662 >              MPI_Recv(&myPotato, 1, MPI_INT, 0, 0, MPI_COMM_WORLD,
663 >                       &istatus);
664 >            }
665 >
666 >            pos = integrableObject->getPos();
667 >            vel = integrableObject->getVel();
668 >
669 >            atomData[0] = pos[0];
670 >            atomData[1] = pos[1];
671 >            atomData[2] = pos[2];
672 >
673 >            atomData[3] = vel[0];
674 >            atomData[4] = vel[1];
675 >            atomData[5] = vel[2];
676 >
677 >            isDirectional = 0;
678 >
679 >            if (integrableObject->isDirectional()) {
680 >              isDirectional = 1;
681 >
682 >              q = integrableObject->getQ();
683 >              ji = integrableObject->getJ();
684 >
685 >              atomData[6] = q[0];
686 >              atomData[7] = q[1];
687 >              atomData[8] = q[2];
688 >              atomData[9] = q[3];
689 >
690 >              atomData[10] = ji[0];
691 >              atomData[11] = ji[1];
692 >              atomData[12] = ji[2];
693 >            }
694 >
695 >            if (needForceVector_) {
696 >              frc = integrableObject->getFrc();
697 >              trq = integrableObject->getTrq();
698 >              
699 >              if (!isDirectional) {
700 >                atomData[6] = frc[0];
701 >                atomData[7] = frc[1];
702 >                atomData[8] = frc[2];
703 >                
704 >                atomData[9] = trq[0];
705 >                atomData[10] = trq[1];
706 >                atomData[11] = trq[2];
707 >              } else {
708 >                atomData[13] = frc[0];
709 >                atomData[14] = frc[1];
710 >                atomData[15] = frc[2];
711 >                
712 >                atomData[16] = trq[0];
713 >                atomData[17] = trq[1];
714 >                atomData[18] = trq[2];
715 >              }
716 >            }
717 >
718 >            strncpy(MPIatomTypeString, integrableObject->getType().c_str(), MINIBUFFERSIZE);
719 >
720 >            // null terminate the  std::string before sending (just in case):
721 >            MPIatomTypeString[MINIBUFFERSIZE - 1] = '\0';
722 >
723 >            MPI_Send(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, 0,
724 >                     myPotato, MPI_COMM_WORLD);
725 >
726 >            myPotato++;
727 >
728 >            if (isDirectional && needForceVector_) {
729 >              MPI_Send(atomData, 19, MPI_DOUBLE, 0, myPotato,
730 >                       MPI_COMM_WORLD);
731 >            } else if (isDirectional) {
732 >              MPI_Send(atomData, 13, MPI_DOUBLE, 0, myPotato,
733 >                       MPI_COMM_WORLD);
734 >            } else if (needForceVector_) {
735 >              MPI_Send(atomData, 12, MPI_DOUBLE, 0, myPotato,
736 >                       MPI_COMM_WORLD);
737 >            } else {
738 >              MPI_Send(atomData, 6, MPI_DOUBLE, 0, myPotato,
739 >                       MPI_COMM_WORLD);
740 >            }
741 >
742 >            myPotato++;
743 >          }
744 >                    
745 >        }
746 >            
747        }
748 +      sprintf(checkPointMsg, "Sucessfully took a dump.\n");
749 +      MPIcheckPoint();
750 +    }
751  
752 <    sprintf( checkPointMsg,
753 <             "Successfully took a dump.\n");
754 <    MPIcheckPoint();                
752 > #endif // is_mpi
753 >
754 >  }
755 >
756 >  void DumpWriter::writeDump() {
757 >    writeFrame(*dumpFile_);
758 >  }
759 >
760 >  void DumpWriter::writeEor() {
761 >    std::ostream* eorStream;
762      
763 + #ifdef IS_MPI
764 +    if (worldRank == 0) {
765 + #endif // is_mpi
766 +
767 +      eorStream = createOStream(eorFilename_);
768 +
769 + #ifdef IS_MPI
770 +    }
771 + #endif // is_mpi    
772 +
773 +    writeFrame(*eorStream);
774 +
775 + #ifdef IS_MPI
776 +    if (worldRank == 0) {
777 + #endif // is_mpi
778 +    delete eorStream;
779 +
780 + #ifdef IS_MPI
781 +    }
782 + #endif // is_mpi  
783 +
784    }
785 <  
785 >
786 >
787 >  void DumpWriter::writeDumpAndEor() {
788 >    std::vector<std::streambuf*> buffers;
789 >    std::ostream* eorStream;
790 > #ifdef IS_MPI
791 >    if (worldRank == 0) {
792   #endif // is_mpi
681 – }
793  
794 +      buffers.push_back(dumpFile_->rdbuf());
795 +
796 +      eorStream = createOStream(eorFilename_);
797 +
798 +      buffers.push_back(eorStream->rdbuf());
799 +        
800   #ifdef IS_MPI
801 +    }
802 + #endif // is_mpi    
803  
804 < // a couple of functions to let us escape the write loop
804 >    TeeBuf tbuf(buffers.begin(), buffers.end());
805 >    std::ostream os(&tbuf);
806  
807 < void dWrite::DieDieDie( void ){
807 >    writeFrame(os);
808  
809 <  MPI_Finalize();
810 <  exit (0);
809 > #ifdef IS_MPI
810 >    if (worldRank == 0) {
811 > #endif // is_mpi
812 >    delete eorStream;
813 >
814 > #ifdef IS_MPI
815 >    }
816 > #endif // is_mpi  
817 >    
818 >  }
819 >
820 > std::ostream* DumpWriter::createOStream(const std::string& filename) {
821 >
822 >    std::ostream* newOStream;
823 > #ifdef HAVE_LIBZ
824 >    if (needCompression_) {
825 >        newOStream = new ogzstream(filename.c_str());
826 >    } else {
827 >        newOStream = new std::ofstream(filename.c_str());
828 >    }
829 > #else
830 >    newOStream = new std::ofstream(filename.c_str());
831 > #endif
832 >    return newOStream;
833   }
834  
835 < #endif //is_mpi
835 > }//end namespace oopse

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