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Comparing trunk/src/io/DumpWriter.cpp (file contents):
Revision 619 by tim, Wed Sep 21 20:59:31 2005 UTC vs.
Revision 1390 by gezelter, Wed Nov 25 20:02:06 2009 UTC

# Line 1 | Line 1
1   /*
2 < * Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
2 > * Copyright (c) 2009 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
9 > * 1. Redistributions of source code must retain the above copyright
10   *    notice, this list of conditions and the following disclaimer.
11   *
12 < * 3. Redistributions in binary form must reproduce the above copyright
12 > * 2. Redistributions in binary form must reproduce the above copyright
13   *    notice, this list of conditions and the following disclaimer in the
14   *    documentation and/or other materials provided with the
15   *    distribution.
# Line 37 | Line 28
28   * arising out of the use of or inability to use software, even if the
29   * University of Notre Dame has been advised of the possibility of
30   * such damages.
31 + *
32 + * SUPPORT OPEN SCIENCE!  If you use OpenMD or its source code in your
33 + * research, please cite the appropriate papers when you publish your
34 + * work.  Good starting points are:
35 + *                                                                      
36 + * [1]  Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).            
37 + * [2]  Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).          
38 + * [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008).          
39 + * [4]  Vardeman & Gezelter, in progress (2009).                        
40   */
41  
42   #include "io/DumpWriter.hpp"
# Line 50 | Line 50
50   #include <mpi.h>
51   #endif //is_mpi
52  
53 < namespace oopse {
53 > namespace OpenMD {
54  
55    DumpWriter::DumpWriter(SimInfo* info)
56      : info_(info), filename_(info->getDumpFileName()), eorFilename_(info->getFinalConfigFileName()){
57  
58      Globals* simParams = info->getSimParams();
59      needCompression_ = simParams->getCompressDumpFile();
60 <
60 >    needForceVector_ = simParams->getOutputForceVector();
61 >    createDumpFile_ = true;
62   #ifdef HAVE_LIBZ
63      if (needCompression_) {
64 <        filename_ += ".gz";
65 <        eorFilename_ += ".gz";
64 >      filename_ += ".gz";
65 >      eorFilename_ += ".gz";
66      }
67   #endif
68      
69   #ifdef IS_MPI
70  
71 <      if (worldRank == 0) {
71 >    if (worldRank == 0) {
72   #endif // is_mpi
73 +        
74 +      dumpFile_ = createOStream(filename_);
75  
76 +      if (!dumpFile_) {
77 +        sprintf(painCave.errMsg, "Could not open \"%s\" for dump output.\n",
78 +                filename_.c_str());
79 +        painCave.isFatal = 1;
80 +        simError();
81 +      }
82  
74 –        dumpFile_ = createOStream(filename_);
75 –
76 –        if (!dumpFile_) {
77 –          sprintf(painCave.errMsg, "Could not open \"%s\" for dump output.\n",
78 –                  filename_.c_str());
79 –          painCave.isFatal = 1;
80 –          simError();
81 –        }
82 –
83   #ifdef IS_MPI
84  
85 <      }
85 >    }
86  
87 –      sprintf(checkPointMsg, "Sucessfully opened output file for dumping.\n");
88 –      MPIcheckPoint();
89 –
87   #endif // is_mpi
88  
89 <    }
89 >  }
90  
91  
92    DumpWriter::DumpWriter(SimInfo* info, const std::string& filename)
# Line 99 | Line 96 | namespace oopse {
96      eorFilename_ = filename_.substr(0, filename_.rfind(".")) + ".eor";    
97  
98      needCompression_ = simParams->getCompressDumpFile();
99 <
99 >    needForceVector_ = simParams->getOutputForceVector();
100 >    createDumpFile_ = true;
101   #ifdef HAVE_LIBZ
102      if (needCompression_) {
103 <        filename_ += ".gz";
104 <        eorFilename_ += ".gz";
103 >      filename_ += ".gz";
104 >      eorFilename_ += ".gz";
105      }
106   #endif
107      
108   #ifdef IS_MPI
109  
110 <      if (worldRank == 0) {
110 >    if (worldRank == 0) {
111   #endif // is_mpi
112  
113 +      
114 +      dumpFile_ = createOStream(filename_);
115  
116 <        dumpFile_ = createOStream(filename_);
116 >      if (!dumpFile_) {
117 >        sprintf(painCave.errMsg, "Could not open \"%s\" for dump output.\n",
118 >                filename_.c_str());
119 >        painCave.isFatal = 1;
120 >        simError();
121 >      }
122  
118 –        if (!dumpFile_) {
119 –          sprintf(painCave.errMsg, "Could not open \"%s\" for dump output.\n",
120 –                  filename_.c_str());
121 –          painCave.isFatal = 1;
122 –          simError();
123 –        }
124 –
123   #ifdef IS_MPI
124  
125 <      }
125 >    }
126  
129 –      sprintf(checkPointMsg, "Sucessfully opened output file for dumping.\n");
130 –      MPIcheckPoint();
131 –
127   #endif // is_mpi
128  
129 +  }
130 +  
131 +  DumpWriter::DumpWriter(SimInfo* info, const std::string& filename, bool writeDumpFile)
132 +    : info_(info), filename_(filename){
133 +    
134 +    Globals* simParams = info->getSimParams();
135 +    eorFilename_ = filename_.substr(0, filename_.rfind(".")) + ".eor";    
136 +    
137 +    needCompression_ = simParams->getCompressDumpFile();
138 +    needForceVector_ = simParams->getOutputForceVector();
139 +    
140 + #ifdef HAVE_LIBZ
141 +    if (needCompression_) {
142 +      filename_ += ".gz";
143 +      eorFilename_ += ".gz";
144      }
145 + #endif
146 +    
147 + #ifdef IS_MPI
148 +    
149 +    if (worldRank == 0) {
150 + #endif // is_mpi
151 +      
152 +      createDumpFile_ = writeDumpFile;
153 +      if (createDumpFile_) {
154 +        dumpFile_ = createOStream(filename_);
155 +      
156 +        if (!dumpFile_) {
157 +          sprintf(painCave.errMsg, "Could not open \"%s\" for dump output.\n",
158 +                  filename_.c_str());
159 +          painCave.isFatal = 1;
160 +          simError();
161 +        }
162 +      }
163 + #ifdef IS_MPI
164 +      
165 +    }
166  
167 +    
168 + #endif // is_mpi
169 +    
170 +  }
171 +
172    DumpWriter::~DumpWriter() {
173  
174   #ifdef IS_MPI
175  
176      if (worldRank == 0) {
177   #endif // is_mpi
178 <
179 <      delete dumpFile_;
180 <
178 >      if (createDumpFile_){
179 >        writeClosing(*dumpFile_);
180 >        delete dumpFile_;
181 >      }
182   #ifdef IS_MPI
183  
184      }
# Line 150 | Line 187 | namespace oopse {
187  
188    }
189  
190 <  void DumpWriter::writeCommentLine(std::ostream& os, Snapshot* s) {
190 >  void DumpWriter::writeFrameProperties(std::ostream& os, Snapshot* s) {
191  
192 <    double currentTime;
192 >    char buffer[1024];
193 >
194 >    os << "    <FrameData>\n";
195 >
196 >    RealType currentTime = s->getTime();
197 >    sprintf(buffer, "        Time: %.10g\n", currentTime);
198 >    os << buffer;
199 >
200      Mat3x3d hmat;
157 –    double chi;
158 –    double integralOfChiDt;
159 –    Mat3x3d eta;
160 –    
161 –    currentTime = s->getTime();
201      hmat = s->getHmat();
202 <    chi = s->getChi();
203 <    integralOfChiDt = s->getIntegralOfChiDt();
204 <    eta = s->getEta();
205 <    
206 <    os << currentTime << ";\t"
168 <       << hmat(0, 0) << "\t" << hmat(1, 0) << "\t" << hmat(2, 0) << ";\t"
169 <       << hmat(0, 1) << "\t" << hmat(1, 1) << "\t" << hmat(2, 1) << ";\t"
170 <       << hmat(0, 2) << "\t" << hmat(1, 2) << "\t" << hmat(2, 2) << ";\t";
202 >    sprintf(buffer, "        Hmat: {{ %.10g, %.10g, %.10g }, { %.10g, %.10g, %.10g }, { %.10g, %.10g, %.10g }}\n",
203 >            hmat(0, 0), hmat(1, 0), hmat(2, 0),
204 >            hmat(0, 1), hmat(1, 1), hmat(2, 1),
205 >            hmat(0, 2), hmat(1, 2), hmat(2, 2));
206 >    os << buffer;
207  
208 <    //write out additional parameters, such as chi and eta
208 >    RealType chi = s->getChi();
209 >    RealType integralOfChiDt = s->getIntegralOfChiDt();
210 >    sprintf(buffer, "  Thermostat: %.10g , %.10g\n", chi, integralOfChiDt);
211 >    os << buffer;
212  
213 <    os << chi << "\t" << integralOfChiDt << "\t;";
213 >    Mat3x3d eta;
214 >    eta = s->getEta();
215 >    sprintf(buffer, "    Barostat: {{ %.10g, %.10g, %.10g }, { %.10g, %.10g, %.10g }, { %.10g, %.10g, %.10g }}\n",
216 >            eta(0, 0), eta(1, 0), eta(2, 0),
217 >            eta(0, 1), eta(1, 1), eta(2, 1),
218 >            eta(0, 2), eta(1, 2), eta(2, 2));
219 >    os << buffer;
220  
221 <    os << eta(0, 0) << "\t" << eta(1, 0) << "\t" << eta(2, 0) << ";\t"
177 <       << eta(0, 1) << "\t" << eta(1, 1) << "\t" << eta(2, 1) << ";\t"
178 <       << eta(0, 2) << "\t" << eta(1, 2) << "\t" << eta(2, 2) << ";";
179 <        
180 <    os << "\n";
221 >    os << "    </FrameData>\n";
222    }
223  
224    void DumpWriter::writeFrame(std::ostream& os) {
184 –    const int BUFFERSIZE = 2000;
185 –    const int MINIBUFFERSIZE = 100;
225  
226 <    char tempBuffer[BUFFERSIZE];
227 <    char writeLine[BUFFERSIZE];
226 > #ifdef IS_MPI
227 >    MPI_Status istatus;
228 > #endif
229  
190 –    Quat4d q;
191 –    Vector3d ji;
192 –    Vector3d pos;
193 –    Vector3d vel;
194 –
230      Molecule* mol;
231      StuntDouble* integrableObject;
232      SimInfo::MoleculeIterator mi;
233      Molecule::IntegrableObjectIterator ii;
199 –  
200 –    int nTotObjects;    
201 –    nTotObjects = info_->getNGlobalIntegrableObjects();
234  
235   #ifndef IS_MPI
236 +    os << "  <Snapshot>\n";
237 +
238 +    writeFrameProperties(os, info_->getSnapshotManager()->getCurrentSnapshot());
239  
240 +    os << "    <StuntDoubles>\n";
241 +    for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
242  
243 <    os << nTotObjects << "\n";
244 <        
245 <    writeCommentLine(os, info_->getSnapshotManager()->getCurrentSnapshot());
243 >      
244 >      for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;  
245 >           integrableObject = mol->nextIntegrableObject(ii)) {  
246 >          os << prepareDumpLine(integrableObject);
247 >          
248 >      }
249 >    }    
250 >    os << "    </StuntDoubles>\n";
251 >    
252 >    os << "  </Snapshot>\n";
253  
254 +    os.flush();
255 + #else
256 +    //every node prepares the dump lines for integrable objects belong to itself
257 +    std::string buffer;
258      for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
259  
212 –      for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
213 –           integrableObject = mol->nextIntegrableObject(ii)) {
214 –                
260  
261 <        pos = integrableObject->getPos();
262 <        vel = integrableObject->getVel();
263 <
219 <        sprintf(tempBuffer, "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
220 <                integrableObject->getType().c_str(),
221 <                pos[0], pos[1], pos[2],
222 <                vel[0], vel[1], vel[2]);
223 <
224 <        strcpy(writeLine, tempBuffer);
225 <
226 <        if (integrableObject->isDirectional()) {
227 <          q = integrableObject->getQ();
228 <          ji = integrableObject->getJ();
229 <
230 <          sprintf(tempBuffer, "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
231 <                  q[0], q[1], q[2], q[3],
232 <                  ji[0], ji[1], ji[2]);
233 <          strcat(writeLine, tempBuffer);
234 <        } else {
235 <          strcat(writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n");
236 <        }
237 <
238 <        os << writeLine;
239 <
261 >      for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
262 >           integrableObject = mol->nextIntegrableObject(ii)) {  
263 >          buffer += prepareDumpLine(integrableObject);
264        }
265      }
266 <
243 <    os.flush();
244 < #else // is_mpi
245 <    /*********************************************************************
246 <     * Documentation?  You want DOCUMENTATION?
247 <     *
248 <     * Why all the potatoes below?  
249 <     *
250 <     * To make a long story short, the original version of DumpWriter
251 <     * worked in the most inefficient way possible.  Node 0 would
252 <     * poke each of the node for an individual atom's formatted data
253 <     * as node 0 worked its way down the global index. This was particularly
254 <     * inefficient since the method blocked all processors at every atom
255 <     * (and did it twice!).
256 <     *
257 <     * An intermediate version of DumpWriter could be described from Node
258 <     * zero's perspective as follows:
259 <     *
260 <     *  1) Have 100 of your friends stand in a circle.
261 <     *  2) When you say go, have all of them start tossing potatoes at
262 <     *     you (one at a time).
263 <     *  3) Catch the potatoes.
264 <     *
265 <     * It was an improvement, but MPI has buffers and caches that could
266 <     * best be described in this analogy as "potato nets", so there's no
267 <     * need to block the processors atom-by-atom.
268 <     *
269 <     * This new and improved DumpWriter works in an even more efficient
270 <     * way:
271 <     *
272 <     *  1) Have 100 of your friend stand in a circle.
273 <     *  2) When you say go, have them start tossing 5-pound bags of
274 <     *     potatoes at you.
275 <     *  3) Once you've caught a friend's bag of potatoes,
276 <     *     toss them a spud to let them know they can toss another bag.
277 <     *
278 <     * How's THAT for documentation?
279 <     *
280 <     *********************************************************************/
266 >    
267      const int masterNode = 0;
268  
269 <    int * potatoes;
270 <    int myPotato;
271 <    int nProc;
272 <    int which_node;
273 <    double atomData[13];
274 <    int isDirectional;
289 <    char MPIatomTypeString[MINIBUFFERSIZE];
290 <    int msgLen; // the length of message actually recieved at master nodes
291 <    int haveError;
292 <    MPI_Status istatus;
293 <    int nCurObj;
294 <    
295 <    // code to find maximum tag value
296 <    int * tagub;
297 <    int flag;
298 <    int MAXTAG;
299 <    MPI_Attr_get(MPI_COMM_WORLD, MPI_TAG_UB, &tagub, &flag);
269 >    if (worldRank == masterNode) {      
270 >      os << "  <Snapshot>\n";  
271 >      writeFrameProperties(os, info_->getSnapshotManager()->getCurrentSnapshot());
272 >      os << "    <StuntDoubles>\n";
273 >        
274 >      os << buffer;
275  
276 <    if (flag) {
302 <      MAXTAG = *tagub;
303 <    } else {
304 <      MAXTAG = 32767;
305 <    }
306 <
307 <    if (worldRank == masterNode) { //master node (node 0) is responsible for writing the dump file
308 <
309 <      // Node 0 needs a list of the magic potatoes for each processor;
310 <
276 >      int nProc;
277        MPI_Comm_size(MPI_COMM_WORLD, &nProc);
278 <      potatoes = new int[nProc];
278 >      for (int i = 1; i < nProc; ++i) {
279  
280 <      //write out the comment lines
281 <      for(int i = 0; i < nProc; i++) {
316 <        potatoes[i] = 0;
317 <      }
318 <
319 <
320 <      os << nTotObjects << "\n";
321 <      writeCommentLine(os, info_->getSnapshotManager()->getCurrentSnapshot());
322 <
323 <      for(int i = 0; i < info_->getNGlobalMolecules(); i++) {
324 <
325 <        // Get the Node number which has this atom;
326 <
327 <        which_node = info_->getMolToProc(i);
328 <
329 <        if (which_node != masterNode) { //current molecule is in slave node
330 <          if (potatoes[which_node] + 1 >= MAXTAG) {
331 <            // The potato was going to exceed the maximum value,
332 <            // so wrap this processor potato back to 0:        
333 <
334 <            potatoes[which_node] = 0;
335 <            MPI_Send(&potatoes[which_node], 1, MPI_INT, which_node, 0,
336 <                     MPI_COMM_WORLD);
337 <          }
338 <
339 <          myPotato = potatoes[which_node];
280 >        // receive the length of the string buffer that was
281 >        // prepared by processor i
282  
283 <          //recieve the number of integrableObject in current molecule
284 <          MPI_Recv(&nCurObj, 1, MPI_INT, which_node, myPotato,
285 <                   MPI_COMM_WORLD, &istatus);
286 <          myPotato++;
287 <
288 <          for(int l = 0; l < nCurObj; l++) {
289 <            if (potatoes[which_node] + 2 >= MAXTAG) {
290 <              // The potato was going to exceed the maximum value,
291 <              // so wrap this processor potato back to 0:        
292 <
293 <              potatoes[which_node] = 0;
294 <              MPI_Send(&potatoes[which_node], 1, MPI_INT, which_node,
295 <                       0, MPI_COMM_WORLD);
354 <            }
355 <
356 <            MPI_Recv(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR,
357 <                     which_node, myPotato, MPI_COMM_WORLD,
358 <                     &istatus);
359 <
360 <            myPotato++;
361 <
362 <            MPI_Recv(atomData, 13, MPI_DOUBLE, which_node, myPotato,
363 <                     MPI_COMM_WORLD, &istatus);
364 <            myPotato++;
365 <
366 <            MPI_Get_count(&istatus, MPI_DOUBLE, &msgLen);
367 <
368 <            if (msgLen == 13)
369 <              isDirectional = 1;
370 <            else
371 <              isDirectional = 0;
372 <
373 <            // If we've survived to here, format the line:
374 <
375 <            if (!isDirectional) {
376 <              sprintf(writeLine, "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
377 <                      MPIatomTypeString, atomData[0],
378 <                      atomData[1], atomData[2],
379 <                      atomData[3], atomData[4],
380 <                      atomData[5]);
381 <
382 <              strcat(writeLine,
383 <                     "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n");
384 <            } else {
385 <              sprintf(writeLine,
386 <                      "%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",
387 <                      MPIatomTypeString,
388 <                      atomData[0],
389 <                      atomData[1],
390 <                      atomData[2],
391 <                      atomData[3],
392 <                      atomData[4],
393 <                      atomData[5],
394 <                      atomData[6],
395 <                      atomData[7],
396 <                      atomData[8],
397 <                      atomData[9],
398 <                      atomData[10],
399 <                      atomData[11],
400 <                      atomData[12]);
401 <            }
402 <
403 <            os << writeLine;
404 <
405 <          } // end for(int l =0)
406 <
407 <          potatoes[which_node] = myPotato;
408 <        } else { //master node has current molecule
409 <
410 <          mol = info_->getMoleculeByGlobalIndex(i);
411 <
412 <          if (mol == NULL) {
413 <            sprintf(painCave.errMsg, "Molecule not found on node %d!", worldRank);
414 <            painCave.isFatal = 1;
415 <            simError();
416 <          }
417 <                
418 <          for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
419 <               integrableObject = mol->nextIntegrableObject(ii)) {      
420 <
421 <            pos = integrableObject->getPos();
422 <            vel = integrableObject->getVel();
423 <
424 <            atomData[0] = pos[0];
425 <            atomData[1] = pos[1];
426 <            atomData[2] = pos[2];
427 <
428 <            atomData[3] = vel[0];
429 <            atomData[4] = vel[1];
430 <            atomData[5] = vel[2];
431 <
432 <            isDirectional = 0;
433 <
434 <            if (integrableObject->isDirectional()) {
435 <              isDirectional = 1;
436 <
437 <              q = integrableObject->getQ();
438 <              ji = integrableObject->getJ();
439 <
440 <              for(int j = 0; j < 6; j++) {
441 <                atomData[j] = atomData[j];
442 <              }
443 <
444 <              atomData[6] = q[0];
445 <              atomData[7] = q[1];
446 <              atomData[8] = q[2];
447 <              atomData[9] = q[3];
448 <
449 <              atomData[10] = ji[0];
450 <              atomData[11] = ji[1];
451 <              atomData[12] = ji[2];
452 <            }
453 <
454 <            // If we've survived to here, format the line:
455 <
456 <            if (!isDirectional) {
457 <              sprintf(writeLine, "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
458 <                      integrableObject->getType().c_str(), atomData[0],
459 <                      atomData[1], atomData[2],
460 <                      atomData[3], atomData[4],
461 <                      atomData[5]);
462 <
463 <              strcat(writeLine,
464 <                     "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n");
465 <            } else {
466 <              sprintf(writeLine,
467 <                      "%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",
468 <                      integrableObject->getType().c_str(),
469 <                      atomData[0],
470 <                      atomData[1],
471 <                      atomData[2],
472 <                      atomData[3],
473 <                      atomData[4],
474 <                      atomData[5],
475 <                      atomData[6],
476 <                      atomData[7],
477 <                      atomData[8],
478 <                      atomData[9],
479 <                      atomData[10],
480 <                      atomData[11],
481 <                      atomData[12]);
482 <            }
483 <
484 <
485 <            os << writeLine;
486 <
487 <          } //end for(iter = integrableObject.begin())
488 <        }
489 <      } //end for(i = 0; i < mpiSim->getNmol())
490 <
283 >        int recvLength;
284 >        MPI_Recv(&recvLength, 1, MPI_INT, i, 0, MPI_COMM_WORLD, &istatus);
285 >        char* recvBuffer = new char[recvLength];
286 >        if (recvBuffer == NULL) {
287 >        } else {
288 >          MPI_Recv(recvBuffer, recvLength, MPI_CHAR, i, 0, MPI_COMM_WORLD, &istatus);
289 >          os << recvBuffer;
290 >          delete [] recvBuffer;
291 >        }
292 >      }
293 >      os << "    </StuntDoubles>\n";
294 >      
295 >      os << "  </Snapshot>\n";
296        os.flush();
492 –        
493 –      sprintf(checkPointMsg, "Sucessfully took a dump.\n");
494 –      MPIcheckPoint();
495 –
496 –      delete [] potatoes;
297      } else {
298 +      int sendBufferLength = buffer.size() + 1;
299 +      MPI_Send(&sendBufferLength, 1, MPI_INT, masterNode, 0, MPI_COMM_WORLD);
300 +      MPI_Send((void *)buffer.c_str(), sendBufferLength, MPI_CHAR, masterNode, 0, MPI_COMM_WORLD);
301 +    }
302  
303 <      // worldRank != 0, so I'm a remote node.  
303 > #endif // is_mpi
304  
305 <      // Set my magic potato to 0:
305 >  }
306  
307 <      myPotato = 0;
307 >  std::string DumpWriter::prepareDumpLine(StuntDouble* integrableObject) {
308 >        
309 >    int index = integrableObject->getGlobalIntegrableObjectIndex();
310 >    std::string type("pv");
311 >    std::string line;
312 >    char tempBuffer[4096];
313  
314 <      for(int i = 0; i < info_->getNGlobalMolecules(); i++) {
314 >    Vector3d pos;
315 >    Vector3d vel;
316 >    pos = integrableObject->getPos();
317 >    vel = integrableObject->getVel();          
318 >    sprintf(tempBuffer, "%18.10g %18.10g %18.10g %13e %13e %13e",
319 >            pos[0], pos[1], pos[2],
320 >            vel[0], vel[1], vel[2]);                    
321 >    line += tempBuffer;
322  
323 <        // Am I the node which has this integrableObject?
324 <        int whichNode = info_->getMolToProc(i);
325 <        if (whichNode == worldRank) {
326 <          if (myPotato + 1 >= MAXTAG) {
327 <
328 <            // The potato was going to exceed the maximum value,
329 <            // so wrap this processor potato back to 0 (and block until
330 <            // node 0 says we can go:
331 <
332 <            MPI_Recv(&myPotato, 1, MPI_INT, 0, 0, MPI_COMM_WORLD,
517 <                     &istatus);
518 <          }
519 <
520 <          mol = info_->getMoleculeByGlobalIndex(i);
521 <
522 <                
523 <          nCurObj = mol->getNIntegrableObjects();
524 <
525 <          MPI_Send(&nCurObj, 1, MPI_INT, 0, myPotato, MPI_COMM_WORLD);
526 <          myPotato++;
527 <
528 <          for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
529 <               integrableObject = mol->nextIntegrableObject(ii)) {
530 <
531 <            if (myPotato + 2 >= MAXTAG) {
532 <
533 <              // The potato was going to exceed the maximum value,
534 <              // so wrap this processor potato back to 0 (and block until
535 <              // node 0 says we can go:
536 <
537 <              MPI_Recv(&myPotato, 1, MPI_INT, 0, 0, MPI_COMM_WORLD,
538 <                       &istatus);
539 <            }
540 <
541 <            pos = integrableObject->getPos();
542 <            vel = integrableObject->getVel();
543 <
544 <            atomData[0] = pos[0];
545 <            atomData[1] = pos[1];
546 <            atomData[2] = pos[2];
547 <
548 <            atomData[3] = vel[0];
549 <            atomData[4] = vel[1];
550 <            atomData[5] = vel[2];
551 <
552 <            isDirectional = 0;
553 <
554 <            if (integrableObject->isDirectional()) {
555 <              isDirectional = 1;
556 <
557 <              q = integrableObject->getQ();
558 <              ji = integrableObject->getJ();
559 <
560 <              atomData[6] = q[0];
561 <              atomData[7] = q[1];
562 <              atomData[8] = q[2];
563 <              atomData[9] = q[3];
564 <
565 <              atomData[10] = ji[0];
566 <              atomData[11] = ji[1];
567 <              atomData[12] = ji[2];
568 <            }
569 <
570 <            strncpy(MPIatomTypeString, integrableObject->getType().c_str(), MINIBUFFERSIZE);
571 <
572 <            // null terminate the  std::string before sending (just in case):
573 <            MPIatomTypeString[MINIBUFFERSIZE - 1] = '\0';
574 <
575 <            MPI_Send(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, 0,
576 <                     myPotato, MPI_COMM_WORLD);
577 <
578 <            myPotato++;
579 <
580 <            if (isDirectional) {
581 <              MPI_Send(atomData, 13, MPI_DOUBLE, 0, myPotato,
582 <                       MPI_COMM_WORLD);
583 <            } else {
584 <              MPI_Send(atomData, 6, MPI_DOUBLE, 0, myPotato,
585 <                       MPI_COMM_WORLD);
586 <            }
587 <
588 <            myPotato++;
589 <          }
590 <                    
591 <        }
592 <            
593 <      }
594 <      sprintf(checkPointMsg, "Sucessfully took a dump.\n");
595 <      MPIcheckPoint();
323 >    if (integrableObject->isDirectional()) {
324 >      type += "qj";
325 >      Quat4d q;
326 >      Vector3d ji;
327 >      q = integrableObject->getQ();
328 >      ji = integrableObject->getJ();
329 >      sprintf(tempBuffer, " %13e %13e %13e %13e %13e %13e %13e",
330 >              q[0], q[1], q[2], q[3],
331 >              ji[0], ji[1], ji[2]);
332 >      line += tempBuffer;
333      }
334  
335 < #endif // is_mpi
336 <
335 >    if (needForceVector_) {
336 >      type += "ft";
337 >      Vector3d frc;
338 >      Vector3d trq;
339 >      frc = integrableObject->getFrc();
340 >      trq = integrableObject->getTrq();
341 >              
342 >      sprintf(tempBuffer, " %13e %13e %13e %13e %13e %13e",
343 >              frc[0], frc[1], frc[2],
344 >              trq[0], trq[1], trq[2]);
345 >      line += tempBuffer;
346 >    }
347 >        
348 >    sprintf(tempBuffer, "%10d %7s %s\n", index, type.c_str(), line.c_str());
349 >    return std::string(tempBuffer);
350    }
351  
352    void DumpWriter::writeDump() {
# Line 621 | Line 371 | namespace oopse {
371   #ifdef IS_MPI
372      if (worldRank == 0) {
373   #endif // is_mpi
374 <    delete eorStream;
375 <
374 >      writeClosing(*eorStream);
375 >      delete eorStream;
376   #ifdef IS_MPI
377      }
378   #endif // is_mpi  
# Line 655 | Line 405 | namespace oopse {
405   #ifdef IS_MPI
406      if (worldRank == 0) {
407   #endif // is_mpi
408 <    delete eorStream;
409 <
408 >      writeClosing(*eorStream);
409 >      delete eorStream;
410   #ifdef IS_MPI
411      }
412   #endif // is_mpi  
413      
414    }
415  
416 < std::ostream* DumpWriter::createOStream(const std::string& filename) {
416 >  std::ostream* DumpWriter::createOStream(const std::string& filename) {
417  
418      std::ostream* newOStream;
419   #ifdef HAVE_LIBZ
420      if (needCompression_) {
421 <        newOStream = new ogzstream(filename.c_str());
421 >      newOStream = new ogzstream(filename.c_str());
422      } else {
423 <        newOStream = new std::ofstream(filename.c_str());
423 >      newOStream = new std::ofstream(filename.c_str());
424      }
425   #else
426      newOStream = new std::ofstream(filename.c_str());
427   #endif
428 +    //write out MetaData first
429 +    (*newOStream) << "<OpenMD version=1>" << std::endl;
430 +    (*newOStream) << "  <MetaData>" << std::endl;
431 +    (*newOStream) << info_->getRawMetaData();
432 +    (*newOStream) << "  </MetaData>" << std::endl;
433      return newOStream;
434 < }
434 >  }
435  
436 < }//end namespace oopse
436 >  void DumpWriter::writeClosing(std::ostream& os) {
437 >
438 >    os << "</OpenMD>\n";
439 >    os.flush();
440 >  }
441 >
442 > }//end namespace OpenMD

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