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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 615 by tim, Tue Sep 20 21:22:38 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  
61 < #ifdef IS_MPI
62 <  if(worldRank == 0 ){
63 < #endif // is_mpi
31 <
32 <    dumpFile.open(entry_plug->sampleName.c_str(), ios::out | ios::trunc );
33 <
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();
61 >    if (needCompression_) {
62 >        filename_ += ".gz";
63 >        eorFilename_ += ".gz";
64      }
65 <
65 >    
66   #ifdef IS_MPI
44 –  }
67  
68 <  //sort the local atoms by global index
47 <  sortByGlobalIndex();
48 <  
49 <  sprintf( checkPointMsg,
50 <           "Sucessfully opened output file for dumping.\n");
51 <  MPIcheckPoint();
68 >      if (worldRank == 0) {
69   #endif // is_mpi
53 – }
70  
55 – DumpWriter::~DumpWriter( ){
71  
72 < #ifdef IS_MPI
58 <  if(worldRank == 0 ){
59 < #endif // is_mpi
72 >        dumpFile_ = createOStream(filename_);
73  
74 <    dumpFile.close();
74 >        if (!dumpFile_) {
75 >          sprintf(painCave.errMsg, "Could not open \"%s\" for dump output.\n",
76 >                  filename_.c_str());
77 >          painCave.isFatal = 1;
78 >          simError();
79 >        }
80  
81   #ifdef IS_MPI
64 –  }
65 – #endif // is_mpi
66 – }
82  
83 < #ifdef IS_MPI
83 >      }
84  
85 < /**
86 < * A hook function to load balancing
72 < */
85 >      sprintf(checkPointMsg, "Sucessfully opened output file for dumping.\n");
86 >      MPIcheckPoint();
87  
88 < 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 < }
88 > #endif // is_mpi
89  
90 < /**
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 < }
90 >    }
91  
100 – #endif
92  
93 < void DumpWriter::writeDump(double currentTime){
93 >  DumpWriter::DumpWriter(SimInfo* info, const std::string& filename)
94 >    : info_(info), filename_(filename){
95  
96 <  ofstream finalOut;
97 <  vector<ofstream*> fileStreams;
96 >    Globals* simParams = info->getSimParams();
97 >    eorFilename_ = filename_.substr(0, filename_.rfind(".")) + ".eor";    
98  
99 < #ifdef IS_MPI
100 <  if(worldRank == 0 ){
101 < #endif    
102 <    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();
99 >    needCompression_ = simParams->getCompressDumpFile();
100 >    if (needCompression_) {
101 >        filename_ += ".gz";
102 >        eorFilename_ += ".gz";
103      }
104 +    
105   #ifdef IS_MPI
106 <  }
106 >
107 >      if (worldRank == 0) {
108   #endif // is_mpi
109  
122 –  fileStreams.push_back(&finalOut);
123 –  fileStreams.push_back(&dumpFile);
110  
111 <  writeFrame(fileStreams, currentTime);
111 >        dumpFile_ = createOStream(filename_);
112  
113 +        if (!dumpFile_) {
114 +          sprintf(painCave.errMsg, "Could not open \"%s\" for dump output.\n",
115 +                  filename_.c_str());
116 +          painCave.isFatal = 1;
117 +          simError();
118 +        }
119 +
120   #ifdef IS_MPI
128 –  finalOut.close();
129 – #endif
130 –        
131 – }
121  
122 < void DumpWriter::writeFinal(double currentTime){
122 >      }
123  
124 <  ofstream finalOut;
125 <  vector<ofstream*> fileStreams;
124 >      sprintf(checkPointMsg, "Sucessfully opened output file for dumping.\n");
125 >      MPIcheckPoint();
126  
138 – #ifdef IS_MPI
139 –  if(worldRank == 0 ){
127   #endif // is_mpi
128  
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();
129      }
130  
131 < #ifdef IS_MPI
153 <  }
154 < #endif // is_mpi
155 <  
156 <  fileStreams.push_back(&finalOut);  
157 <  writeFrame(fileStreams, currentTime);
131 >  DumpWriter::~DumpWriter() {
132  
133   #ifdef IS_MPI
160 –  finalOut.close();
161 – #endif
162 –  
163 – }
134  
135 < void DumpWriter::writeFrame( vector<ofstream*>& outFile, double currentTime ){
135 >    if (worldRank == 0) {
136 > #endif // is_mpi
137  
138 <  const int BUFFERSIZE = 2000;
168 <  const int MINIBUFFERSIZE = 100;
138 >      delete dumpFile_;
139  
170 –  char tempBuffer[BUFFERSIZE];  
171 –  char writeLine[BUFFERSIZE];
172 –
173 –  int i;
174 –  unsigned int k;
175 –
140   #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 –   *********************************************************************/
141  
142 <  int *potatoes;
216 <  int myPotato;
142 >    }
143  
144 <  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
144 > #endif // is_mpi
145  
228 –  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";
241 –
242 –    *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"
250 –
251 –                     << entry_plug->Hmat[0][2] << "\t"
252 –                     << entry_plug->Hmat[1][2] << "\t"
253 –                     << entry_plug->Hmat[2][2] << ";";
254 –
255 –    //write out additional parameters, such as chi and eta
256 –    *outFile[k] << entry_plug->the_integrator->getAdditionalParameters() << endl;
146    }
258 –  
259 –  for( i=0; i< entry_plug->n_mol; i++ ){
147  
148 <    integrableObjects = entry_plug->molecules[i].getIntegrableObjects();
149 <    molName = (entry_plug->compStamps[entry_plug->molecules[i].getStampID()])->getID();
148 >  void DumpWriter::writeCommentLine(std::ostream& os, Snapshot* s) {
149 >
150 >    double currentTime;
151 >    Mat3x3d hmat;
152 >    double chi;
153 >    double integralOfChiDt;
154 >    Mat3x3d eta;
155      
156 <    for( iter = integrableObjects.begin();iter !=  integrableObjects.end(); ++iter){
157 <      sd = *iter;
158 <      sd->getPos(pos);
159 <      sd->getVel(vel);
156 >    currentTime = s->getTime();
157 >    hmat = s->getHmat();
158 >    chi = s->getChi();
159 >    integralOfChiDt = s->getIntegralOfChiDt();
160 >    eta = s->getEta();
161 >    
162 >    os << currentTime << ";\t"
163 >       << hmat(0, 0) << "\t" << hmat(1, 0) << "\t" << hmat(2, 0) << ";\t"
164 >       << hmat(0, 1) << "\t" << hmat(1, 1) << "\t" << hmat(2, 1) << ";\t"
165 >       << hmat(0, 2) << "\t" << hmat(1, 2) << "\t" << hmat(2, 2) << ";\t";
166  
167 <      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 );
167 >    //write out additional parameters, such as chi and eta
168  
169 <      if( sd->isDirectional() ){
169 >    os << chi << "\t" << integralOfChiDt << "\t;";
170  
171 <        sd->getQ( q );
172 <        sd->getJ( ji );
173 <
174 <        sprintf( tempBuffer,
175 <               "%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 <    
171 >    os << eta(0, 0) << "\t" << eta(1, 0) << "\t" << eta(2, 0) << ";\t"
172 >       << eta(0, 1) << "\t" << eta(1, 1) << "\t" << eta(2, 1) << ";\t"
173 >       << eta(0, 2) << "\t" << eta(1, 2) << "\t" << eta(2, 2) << ";";
174 >        
175 >    os << "\n";
176    }
177  
178 < #else // is_mpi
178 >  void DumpWriter::writeFrame(std::ostream& os) {
179 >    const int BUFFERSIZE = 2000;
180 >    const int MINIBUFFERSIZE = 100;
181  
182 <  /* code to find maximum tag value */
182 >    char tempBuffer[BUFFERSIZE];
183 >    char writeLine[BUFFERSIZE];
184 >
185 >    Quat4d q;
186 >    Vector3d ji;
187 >    Vector3d pos;
188 >    Vector3d vel;
189 >
190 >    Molecule* mol;
191 >    StuntDouble* integrableObject;
192 >    SimInfo::MoleculeIterator mi;
193 >    Molecule::IntegrableObjectIterator ii;
194    
195 <  int *tagub, flag, MAXTAG;
196 <  MPI_Attr_get(MPI_COMM_WORLD, MPI_TAG_UB, &tagub, &flag);
311 <  if (flag) {
312 <    MAXTAG = *tagub;
313 <  } else {
314 <    MAXTAG = 32767;
315 <  }  
195 >    int nTotObjects;    
196 >    nTotObjects = info_->getNGlobalIntegrableObjects();
197  
198 <  int haveError;
198 > #ifndef IS_MPI
199  
319 –  MPI_Status istatus;
320 –  int nCurObj;
321 –  int *MolToProcMap = mpiSim->getMolToProcMap();
200  
201 <  // write out header and node 0's coordinates
201 >    os << nTotObjects << "\n";
202 >        
203 >    writeCommentLine(os, info_->getSnapshotManager()->getCurrentSnapshot());
204  
205 <  if( worldRank == 0 ){
205 >    for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
206  
207 <    // Node 0 needs a list of the magic potatoes for each processor;
207 >      for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
208 >           integrableObject = mol->nextIntegrableObject(ii)) {
209 >                
210  
211 <    nProc = mpiSim->getNProcessors();
212 <    potatoes = new int[nProc];
211 >        pos = integrableObject->getPos();
212 >        vel = integrableObject->getVel();
213  
214 <    //write out the comment lines
215 <    for (i = 0; i < nProc; i++)
216 <      potatoes[i] = 0;
217 <    
218 <    for(k = 0; k < outFile.size(); k++){
219 <      *outFile[k] << nTotObjects << "\n";
220 <      
221 <      *outFile[k] << currentTime << ";\t"
222 <                  << entry_plug->Hmat[0][0] << "\t"
223 <                  << entry_plug->Hmat[1][0] << "\t"
224 <                  << entry_plug->Hmat[2][0] << ";\t"
225 <        
226 <                  << entry_plug->Hmat[0][1] << "\t"
227 <                  << entry_plug->Hmat[1][1] << "\t"
228 <                  << entry_plug->Hmat[2][1] << ";\t"
229 <        
230 <                  << entry_plug->Hmat[0][2] << "\t"
231 <                  << entry_plug->Hmat[1][2] << "\t"
232 <                  << entry_plug->Hmat[2][2] << ";";
233 <      
234 <      *outFile[k] << entry_plug->the_integrator->getAdditionalParameters()
235 <                  << endl;
214 >        sprintf(tempBuffer, "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
215 >                integrableObject->getType().c_str(),
216 >                pos[0], pos[1], pos[2],
217 >                vel[0], vel[1], vel[2]);
218 >
219 >        strcpy(writeLine, tempBuffer);
220 >
221 >        if (integrableObject->isDirectional()) {
222 >          q = integrableObject->getQ();
223 >          ji = integrableObject->getJ();
224 >
225 >          sprintf(tempBuffer, "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
226 >                  q[0], q[1], q[2], q[3],
227 >                  ji[0], ji[1], ji[2]);
228 >          strcat(writeLine, tempBuffer);
229 >        } else {
230 >          strcat(writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n");
231 >        }
232 >
233 >        os << writeLine;
234 >
235 >      }
236      }
237 +
238 +    os.flush();
239 + #else // is_mpi
240 +    /*********************************************************************
241 +     * Documentation?  You want DOCUMENTATION?
242 +     *
243 +     * Why all the potatoes below?  
244 +     *
245 +     * To make a long story short, the original version of DumpWriter
246 +     * worked in the most inefficient way possible.  Node 0 would
247 +     * poke each of the node for an individual atom's formatted data
248 +     * as node 0 worked its way down the global index. This was particularly
249 +     * inefficient since the method blocked all processors at every atom
250 +     * (and did it twice!).
251 +     *
252 +     * An intermediate version of DumpWriter could be described from Node
253 +     * zero's perspective as follows:
254 +     *
255 +     *  1) Have 100 of your friends stand in a circle.
256 +     *  2) When you say go, have all of them start tossing potatoes at
257 +     *     you (one at a time).
258 +     *  3) Catch the potatoes.
259 +     *
260 +     * It was an improvement, but MPI has buffers and caches that could
261 +     * best be described in this analogy as "potato nets", so there's no
262 +     * need to block the processors atom-by-atom.
263 +     *
264 +     * This new and improved DumpWriter works in an even more efficient
265 +     * way:
266 +     *
267 +     *  1) Have 100 of your friend stand in a circle.
268 +     *  2) When you say go, have them start tossing 5-pound bags of
269 +     *     potatoes at you.
270 +     *  3) Once you've caught a friend's bag of potatoes,
271 +     *     toss them a spud to let them know they can toss another bag.
272 +     *
273 +     * How's THAT for documentation?
274 +     *
275 +     *********************************************************************/
276 +    const int masterNode = 0;
277 +
278 +    int * potatoes;
279 +    int myPotato;
280 +    int nProc;
281 +    int which_node;
282 +    double atomData[13];
283 +    int isDirectional;
284 +    char MPIatomTypeString[MINIBUFFERSIZE];
285 +    int msgLen; // the length of message actually recieved at master nodes
286 +    int haveError;
287 +    MPI_Status istatus;
288 +    int nCurObj;
289      
290 <    currentIndex = 0;
291 <    
292 <    for (i = 0 ; i < mpiSim->getNMolGlobal(); i++ ) {
293 <      
294 <      // 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:        
290 >    // code to find maximum tag value
291 >    int * tagub;
292 >    int flag;
293 >    int MAXTAG;
294 >    MPI_Attr_get(MPI_COMM_WORLD, MPI_TAG_UB, &tagub, &flag);
295  
296 <          potatoes[which_node] = 0;          
297 <          MPI_Send(&potatoes[which_node], 1, MPI_INT, which_node, 0,
298 <                   MPI_COMM_WORLD);
299 <          
300 <        }
296 >    if (flag) {
297 >      MAXTAG = *tagub;
298 >    } else {
299 >      MAXTAG = 32767;
300 >    }
301  
302 <        myPotato = potatoes[which_node];        
302 >    if (worldRank == masterNode) { //master node (node 0) is responsible for writing the dump file
303  
304 <        //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++){
304 >      // Node 0 needs a list of the magic potatoes for each processor;
305  
306 <          if (potatoes[which_node] + 2 >= MAXTAG) {
307 <            // The potato was going to exceed the maximum value,
387 <            // so wrap this processor potato back to 0:        
306 >      MPI_Comm_size(MPI_COMM_WORLD, &nProc);
307 >      potatoes = new int[nProc];
308  
309 <            potatoes[which_node] = 0;          
310 <            MPI_Send(&potatoes[which_node], 1, MPI_INT, which_node, 0, MPI_COMM_WORLD);
311 <            
312 <          }
309 >      //write out the comment lines
310 >      for(int i = 0; i < nProc; i++) {
311 >        potatoes[i] = 0;
312 >      }
313  
394 –          MPI_Recv(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, which_node,
395 –          myPotato, MPI_COMM_WORLD, &istatus);
314  
315 <          atomTypeString = MPIatomTypeString;
315 >      os << nTotObjects << "\n";
316 >      writeCommentLine(os, info_->getSnapshotManager()->getCurrentSnapshot());
317  
318 <          myPotato++;
318 >      for(int i = 0; i < info_->getNGlobalMolecules(); i++) {
319  
320 <          MPI_Recv(atomData, 13, MPI_DOUBLE, which_node, myPotato, MPI_COMM_WORLD, &istatus);
402 <          myPotato++;
320 >        // Get the Node number which has this atom;
321  
322 <          MPI_Get_count(&istatus, MPI_DOUBLE, &msgLen);
322 >        which_node = info_->getMolToProc(i);
323 >
324 >        if (which_node != masterNode) { //current molecule is in slave node
325 >          if (potatoes[which_node] + 1 >= MAXTAG) {
326 >            // The potato was going to exceed the maximum value,
327 >            // so wrap this processor potato back to 0:        
328 >
329 >            potatoes[which_node] = 0;
330 >            MPI_Send(&potatoes[which_node], 1, MPI_INT, which_node, 0,
331 >                     MPI_COMM_WORLD);
332 >          }
333 >
334 >          myPotato = potatoes[which_node];
335 >
336 >          //recieve the number of integrableObject in current molecule
337 >          MPI_Recv(&nCurObj, 1, MPI_INT, which_node, myPotato,
338 >                   MPI_COMM_WORLD, &istatus);
339 >          myPotato++;
340 >
341 >          for(int l = 0; l < nCurObj; l++) {
342 >            if (potatoes[which_node] + 2 >= MAXTAG) {
343 >              // The potato was going to exceed the maximum value,
344 >              // so wrap this processor potato back to 0:        
345 >
346 >              potatoes[which_node] = 0;
347 >              MPI_Send(&potatoes[which_node], 1, MPI_INT, which_node,
348 >                       0, MPI_COMM_WORLD);
349 >            }
350 >
351 >            MPI_Recv(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR,
352 >                     which_node, myPotato, MPI_COMM_WORLD,
353 >                     &istatus);
354  
355 <          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;            
355 >            myPotato++;
356  
357 <        }// end for(int l =0)
358 <        potatoes[which_node] = myPotato;
359 <        
455 <      }
456 <      else {
457 <        
458 <        haveError = 0;
459 <        
460 <            local_index = indexArray[currentIndex].first;        
461 <            
462 <            integrableObjects = (entry_plug->molecules[local_index]).getIntegrableObjects();
357 >            MPI_Recv(atomData, 13, MPI_DOUBLE, which_node, myPotato,
358 >                     MPI_COMM_WORLD, &istatus);
359 >            myPotato++;
360  
361 <        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];
361 >            MPI_Get_count(&istatus, MPI_DOUBLE, &msgLen);
362  
363 <            atomData[3] = vel[0];
364 <            atomData[4] = vel[1];
365 <            atomData[5] = vel[2];
366 <              
479 <            isDirectional = 0;
363 >            if (msgLen == 13)
364 >              isDirectional = 1;
365 >            else
366 >              isDirectional = 0;
367  
368 <            if( sd->isDirectional() ){
368 >            // If we've survived to here, format the line:
369  
370 <              isDirectional = 1;
371 <                
372 <              sd->getQ( q );
373 <              sd->getJ( ji );
370 >            if (!isDirectional) {
371 >              sprintf(writeLine, "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
372 >                      MPIatomTypeString, atomData[0],
373 >                      atomData[1], atomData[2],
374 >                      atomData[3], atomData[4],
375 >                      atomData[5]);
376  
377 <              for (int j = 0; j < 6 ; j++)
378 <                atomData[j] = atomData[j];            
379 <              
380 <              atomData[6] = q[0];
381 <              atomData[7] = q[1];
382 <              atomData[8] = q[2];
383 <              atomData[9] = q[3];
384 <              
385 <              atomData[10] = ji[0];
386 <              atomData[11] = ji[1];
387 <              atomData[12] = ji[2];
388 <            }
389 <            
390 <            // If we've survived to here, format the line:
391 <            
392 <            if (!isDirectional) {
393 <        
394 <              sprintf( writeLine,
395 <                 "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
396 <                 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 >              strcat(writeLine,
378 >                     "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n");
379 >            } else {
380 >              sprintf(writeLine,
381 >                      "%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",
382 >                      MPIatomTypeString,
383 >                      atomData[0],
384 >                      atomData[1],
385 >                      atomData[2],
386 >                      atomData[3],
387 >                      atomData[4],
388 >                      atomData[5],
389 >                      atomData[6],
390 >                      atomData[7],
391 >                      atomData[8],
392 >                      atomData[9],
393 >                      atomData[10],
394 >                      atomData[11],
395 >                      atomData[12]);
396 >            }
397  
398 <    }//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 {
398 >            os << writeLine;
399  
400 <    // worldRank != 0, so I'm a remote node.  
400 >          } // end for(int l =0)
401  
402 <    // Set my magic potato to 0:
402 >          potatoes[which_node] = myPotato;
403 >        } else { //master node has current molecule
404  
405 <    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) {
405 >          mol = info_->getMoleculeByGlobalIndex(i);
406  
407 +          if (mol == NULL) {
408 +            sprintf(painCave.errMsg, "Molecule not found on node %d!", worldRank);
409 +            painCave.isFatal = 1;
410 +            simError();
411 +          }
412 +                
413 +          for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
414 +               integrableObject = mol->nextIntegrableObject(ii)) {      
415  
416 <        if (myPotato + 1 >= MAXTAG) {
417 <          
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 <        }
416 >            pos = integrableObject->getPos();
417 >            vel = integrableObject->getVel();
418  
419 <          local_index = indexArray[currentIndex].first;        
420 <          integrableObjects = entry_plug->molecules[local_index].getIntegrableObjects();
421 <          
589 <          nCurObj = integrableObjects.size();
590 <                      
591 <          MPI_Send(&nCurObj, 1, MPI_INT, 0,
592 <                   myPotato, MPI_COMM_WORLD);
593 <          myPotato++;
419 >            atomData[0] = pos[0];
420 >            atomData[1] = pos[1];
421 >            atomData[2] = pos[2];
422  
423 <          for( iter = integrableObjects.begin(); iter  != integrableObjects.end(); iter++){
423 >            atomData[3] = vel[0];
424 >            atomData[4] = vel[1];
425 >            atomData[5] = vel[2];
426  
427 <            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();
427 >            isDirectional = 0;
428  
429 <            sd->getPos(pos);
430 <            sd->getVel(vel);
429 >            if (integrableObject->isDirectional()) {
430 >              isDirectional = 1;
431  
432 <            atomData[0] = pos[0];
433 <            atomData[1] = pos[1];
616 <            atomData[2] = pos[2];
432 >              q = integrableObject->getQ();
433 >              ji = integrableObject->getJ();
434  
435 <            atomData[3] = vel[0];
436 <            atomData[4] = vel[1];
437 <            atomData[5] = vel[2];
621 <              
622 <            isDirectional = 0;
435 >              for(int j = 0; j < 6; j++) {
436 >                atomData[j] = atomData[j];
437 >              }
438  
439 <            if( sd->isDirectional() ){
439 >              atomData[6] = q[0];
440 >              atomData[7] = q[1];
441 >              atomData[8] = q[2];
442 >              atomData[9] = q[3];
443  
444 <                isDirectional = 1;
445 <                
446 <                sd->getQ( q );
447 <                sd->getJ( ji );
448 <                
444 >              atomData[10] = ji[0];
445 >              atomData[11] = ji[1];
446 >              atomData[12] = ji[2];
447 >            }
448 >
449 >            // If we've survived to here, format the line:
450 >
451 >            if (!isDirectional) {
452 >              sprintf(writeLine, "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
453 >                      integrableObject->getType().c_str(), atomData[0],
454 >                      atomData[1], atomData[2],
455 >                      atomData[3], atomData[4],
456 >                      atomData[5]);
457 >
458 >              strcat(writeLine,
459 >                     "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n");
460 >            } else {
461 >              sprintf(writeLine,
462 >                      "%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",
463 >                      integrableObject->getType().c_str(),
464 >                      atomData[0],
465 >                      atomData[1],
466 >                      atomData[2],
467 >                      atomData[3],
468 >                      atomData[4],
469 >                      atomData[5],
470 >                      atomData[6],
471 >                      atomData[7],
472 >                      atomData[8],
473 >                      atomData[9],
474 >                      atomData[10],
475 >                      atomData[11],
476 >                      atomData[12]);
477 >            }
478 >
479 >
480 >            os << writeLine;
481 >
482 >          } //end for(iter = integrableObject.begin())
483 >        }
484 >      } //end for(i = 0; i < mpiSim->getNmol())
485 >
486 >      os.flush();
487 >        
488 >      sprintf(checkPointMsg, "Sucessfully took a dump.\n");
489 >      MPIcheckPoint();
490 >
491 >      delete [] potatoes;
492 >    } else {
493 >
494 >      // worldRank != 0, so I'm a remote node.  
495 >
496 >      // Set my magic potato to 0:
497 >
498 >      myPotato = 0;
499 >
500 >      for(int i = 0; i < info_->getNGlobalMolecules(); i++) {
501 >
502 >        // Am I the node which has this integrableObject?
503 >        int whichNode = info_->getMolToProc(i);
504 >        if (whichNode == worldRank) {
505 >          if (myPotato + 1 >= MAXTAG) {
506 >
507 >            // The potato was going to exceed the maximum value,
508 >            // so wrap this processor potato back to 0 (and block until
509 >            // node 0 says we can go:
510 >
511 >            MPI_Recv(&myPotato, 1, MPI_INT, 0, 0, MPI_COMM_WORLD,
512 >                     &istatus);
513 >          }
514 >
515 >          mol = info_->getMoleculeByGlobalIndex(i);
516 >
517                  
518 <                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 <              }
518 >          nCurObj = mol->getNIntegrableObjects();
519  
520 <            
521 <            strncpy(MPIatomTypeString, atomTypeString, MINIBUFFERSIZE);
520 >          MPI_Send(&nCurObj, 1, MPI_INT, 0, myPotato, MPI_COMM_WORLD);
521 >          myPotato++;
522  
523 <            // null terminate the string before sending (just in case):
524 <            MPIatomTypeString[MINIBUFFERSIZE-1] = '\0';
523 >          for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
524 >               integrableObject = mol->nextIntegrableObject(ii)) {
525  
526 <            MPI_Send(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, 0,
649 <                             myPotato, MPI_COMM_WORLD);
650 <            
651 <            myPotato++;
652 <            
653 <            if (isDirectional) {
526 >            if (myPotato + 2 >= MAXTAG) {
527  
528 <              MPI_Send(atomData, 13, MPI_DOUBLE, 0,
529 <                       myPotato, MPI_COMM_WORLD);
530 <              
658 <            } else {
528 >              // The potato was going to exceed the maximum value,
529 >              // so wrap this processor potato back to 0 (and block until
530 >              // node 0 says we can go:
531  
532 <              MPI_Send(atomData, 6, MPI_DOUBLE, 0,
533 <                       myPotato, MPI_COMM_WORLD);
534 <            }
532 >              MPI_Recv(&myPotato, 1, MPI_INT, 0, 0, MPI_COMM_WORLD,
533 >                       &istatus);
534 >            }
535  
536 <            myPotato++;  
536 >            pos = integrableObject->getPos();
537 >            vel = integrableObject->getVel();
538  
539 <          }
539 >            atomData[0] = pos[0];
540 >            atomData[1] = pos[1];
541 >            atomData[2] = pos[2];
542  
543 <          currentIndex++;    
544 <          
545 <        }
546 <      
543 >            atomData[3] = vel[0];
544 >            atomData[4] = vel[1];
545 >            atomData[5] = vel[2];
546 >
547 >            isDirectional = 0;
548 >
549 >            if (integrableObject->isDirectional()) {
550 >              isDirectional = 1;
551 >
552 >              q = integrableObject->getQ();
553 >              ji = integrableObject->getJ();
554 >
555 >              atomData[6] = q[0];
556 >              atomData[7] = q[1];
557 >              atomData[8] = q[2];
558 >              atomData[9] = q[3];
559 >
560 >              atomData[10] = ji[0];
561 >              atomData[11] = ji[1];
562 >              atomData[12] = ji[2];
563 >            }
564 >
565 >            strncpy(MPIatomTypeString, integrableObject->getType().c_str(), MINIBUFFERSIZE);
566 >
567 >            // null terminate the  std::string before sending (just in case):
568 >            MPIatomTypeString[MINIBUFFERSIZE - 1] = '\0';
569 >
570 >            MPI_Send(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, 0,
571 >                     myPotato, MPI_COMM_WORLD);
572 >
573 >            myPotato++;
574 >
575 >            if (isDirectional) {
576 >              MPI_Send(atomData, 13, MPI_DOUBLE, 0, myPotato,
577 >                       MPI_COMM_WORLD);
578 >            } else {
579 >              MPI_Send(atomData, 6, MPI_DOUBLE, 0, myPotato,
580 >                       MPI_COMM_WORLD);
581 >            }
582 >
583 >            myPotato++;
584 >          }
585 >                    
586 >        }
587 >            
588        }
589 +      sprintf(checkPointMsg, "Sucessfully took a dump.\n");
590 +      MPIcheckPoint();
591 +    }
592  
593 <    sprintf( checkPointMsg,
594 <             "Successfully took a dump.\n");
595 <    MPIcheckPoint();                
593 > #endif // is_mpi
594 >
595 >  }
596 >
597 >  void DumpWriter::writeDump() {
598 >    writeFrame(*dumpFile_);
599 >  }
600 >
601 >  void DumpWriter::writeEor() {
602 >    std::ostream* eorStream;
603      
604 + #ifdef IS_MPI
605 +    if (worldRank == 0) {
606 + #endif // is_mpi
607 +
608 +      eorStream = createOStream(eorFilename_);
609 +
610 + #ifdef IS_MPI
611 +    }
612 + #endif // is_mpi    
613 +
614 +    writeFrame(*eorStream);
615 +
616 + #ifdef IS_MPI
617 +    if (worldRank == 0) {
618 + #endif // is_mpi
619 +    delete eorStream;
620 +
621 + #ifdef IS_MPI
622 +    }
623 + #endif // is_mpi  
624 +
625    }
626 <  
626 >
627 >
628 >  void DumpWriter::writeDumpAndEor() {
629 >    std::vector<std::streambuf*> buffers;
630 >    std::ostream* eorStream;
631 > #ifdef IS_MPI
632 >    if (worldRank == 0) {
633   #endif // is_mpi
681 – }
634  
635 +      buffers.push_back(dumpFile_->rdbuf());
636 +
637 +      eorStream = createOStream(eorFilename_);
638 +
639 +      buffers.push_back(eorStream->rdbuf());
640 +        
641   #ifdef IS_MPI
642 +    }
643 + #endif // is_mpi    
644  
645 < // a couple of functions to let us escape the write loop
645 >    TeeBuf tbuf(buffers.begin(), buffers.end());
646 >    std::ostream os(&tbuf);
647  
648 < void dWrite::DieDieDie( void ){
648 >    writeFrame(os);
649  
650 <  MPI_Finalize();
651 <  exit (0);
650 > #ifdef IS_MPI
651 >    if (worldRank == 0) {
652 > #endif // is_mpi
653 >    delete eorStream;
654 >
655 > #ifdef IS_MPI
656 >    }
657 > #endif // is_mpi  
658 >    
659 >  }
660 >
661 > std::ostream* DumpWriter::createOStream(const std::string& filename) {
662 >    std::ostream* newOStream;
663 >    if (needCompression_) {
664 >        newOStream = new ogzstream(filename.c_str());
665 >    } else {
666 >        newOStream = new std::ofstream(filename.c_str());
667 >    }
668 >    return newOStream;
669   }
670  
671 < #endif //is_mpi
671 > }//end namespace oopse

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