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Comparing trunk/src/io/DumpWriter.cpp (file contents):
Revision 963 by tim, Wed May 17 21:51:42 2006 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()){
# Line 61 | Line 61 | namespace oopse {
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 –
73          
74 <        dumpFile_ = createOStream(filename_);
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 <        }
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  
88 –      sprintf(checkPointMsg, "Sucessfully opened output file for dumping.\n");
89 –      MPIcheckPoint();
90 –
87   #endif // is_mpi
88  
89 <    }
89 >  }
90  
91  
92    DumpWriter::DumpWriter(SimInfo* info, const std::string& filename)
# Line 104 | Line 100 | namespace oopse {
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_);
114 >      dumpFile_ = createOStream(filename_);
115  
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 <        }
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  
123   #ifdef IS_MPI
124  
125 <      }
125 >    }
126  
131 –      sprintf(checkPointMsg, "Sucessfully opened output file for dumping.\n");
132 –      MPIcheckPoint();
133 –
127   #endif // is_mpi
128  
129 <    }
129 >  }
130    
131    DumpWriter::DumpWriter(SimInfo* info, const std::string& filename, bool writeDumpFile)
132 <  : info_(info), filename_(filename){
132 >    : info_(info), filename_(filename){
133      
134      Globals* simParams = info->getSimParams();
135      eorFilename_ = filename_.substr(0, filename_.rfind(".")) + ".eor";    
# Line 170 | Line 163 | namespace oopse {
163   #ifdef IS_MPI
164        
165      }
166 +
167      
174 –    sprintf(checkPointMsg, "Sucessfully opened output file for dumping.\n");
175 –    MPIcheckPoint();
176 –    
168   #endif // is_mpi
169      
170    }
180 –  
181 –  
182 –  
183 –  
184 –  
171  
172    DumpWriter::~DumpWriter() {
173  
# Line 190 | Line 176 | namespace oopse {
176      if (worldRank == 0) {
177   #endif // is_mpi
178        if (createDumpFile_){
179 +        writeClosing(*dumpFile_);
180          delete dumpFile_;
181        }
182   #ifdef IS_MPI
# Line 200 | 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 <    RealType 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;
201 <    RealType chi;
202 <    RealType integralOfChiDt;
201 >    hmat = s->getHmat();
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 >    RealType chi = s->getChi();
209 >    RealType integralOfChiDt = s->getIntegralOfChiDt();
210 >    sprintf(buffer, "  Thermostat: %.10g , %.10g\n", chi, integralOfChiDt);
211 >    os << buffer;
212 >
213      Mat3x3d eta;
210 –    
211 –    currentTime = s->getTime();
212 –    hmat = s->getHmat();
213 –    chi = s->getChi();
214 –    integralOfChiDt = s->getIntegralOfChiDt();
214      eta = s->getEta();
215 <    
216 <    os << currentTime << ";\t"
217 <       << hmat(0, 0) << "\t" << hmat(1, 0) << "\t" << hmat(2, 0) << ";\t"
218 <       << hmat(0, 1) << "\t" << hmat(1, 1) << "\t" << hmat(2, 1) << ";\t"
219 <       << hmat(0, 2) << "\t" << hmat(1, 2) << "\t" << hmat(2, 2) << ";\t";
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 <    //write out additional parameters, such as chi and eta
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";
221 >    os << "    </FrameData>\n";
222    }
223  
224    void DumpWriter::writeFrame(std::ostream& os) {
234 –    const int BUFFERSIZE = 2000;
235 –    const int MINIBUFFERSIZE = 100;
225  
226 <    char tempBuffer[BUFFERSIZE];
227 <    char writeLine[BUFFERSIZE];
226 > #ifdef IS_MPI
227 >    MPI_Status istatus;
228 > #endif
229  
240 –    Quat4d q;
241 –    Vector3d ji;
242 –    Vector3d pos;
243 –    Vector3d vel;
244 –    Vector3d frc;
245 –    Vector3d trq;
246 –
230      Molecule* mol;
231      StuntDouble* integrableObject;
232      SimInfo::MoleculeIterator mi;
233      Molecule::IntegrableObjectIterator ii;
251 –  
252 –    int nTotObjects;    
253 –    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  
260 +
261        for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
262 <           integrableObject = mol->nextIntegrableObject(ii)) {
263 <                
262 >           integrableObject = mol->nextIntegrableObject(ii)) {  
263 >          buffer += prepareDumpLine(integrableObject);
264 >      }
265 >    }
266 >    
267 >    const int masterNode = 0;
268  
269 <        pos = integrableObject->getPos();
270 <        vel = integrableObject->getVel();
271 <
272 <        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 <        }
269 >    if (worldRank == masterNode) {      
270 >      os << "  <Snapshot>\n";  
271 >      writeFrameProperties(os, info_->getSnapshotManager()->getCurrentSnapshot());
272 >      os << "    <StuntDoubles>\n";
273          
274 <        strcat(writeLine, "\n");
301 <        os << writeLine;
274 >      os << buffer;
275  
276 <      }
277 <    }
276 >      int nProc;
277 >      MPI_Comm_size(MPI_COMM_WORLD, &nProc);
278 >      for (int i = 1; i < nProc; ++i) {
279  
280 <    os.flush();
281 < #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;
280 >        // receive the length of the string buffer that was
281 >        // prepared by processor i
282  
283 <    int * potatoes;
284 <    int myPotato;
285 <    int nProc;
286 <    int which_node;
287 <    RealType atomData[19];
288 <    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;
360 <    int flag;
361 <    int MAXTAG;
362 <    MPI_Attr_get(MPI_COMM_WORLD, MPI_TAG_UB, &tagub, &flag);
363 <
364 <    if (flag) {
365 <      MAXTAG = *tagub;
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();
297      } else {
298 <      MAXTAG = 32767;
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 <    if (worldRank == masterNode) { //master node (node 0) is responsible for writing the dump file
303 > #endif // is_mpi
304  
305 <      // Node 0 needs a list of the magic potatoes for each processor;
305 >  }
306  
307 <      MPI_Comm_size(MPI_COMM_WORLD, &nProc);
308 <      potatoes = new int[nProc];
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 <      //write out the comment lines
315 <      for(int i = 0; i < nProc; i++) {
316 <        potatoes[i] = 0;
317 <      }
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 <
324 <      os << nTotObjects << "\n";
325 <      writeCommentLine(os, info_->getSnapshotManager()->getCurrentSnapshot());
326 <
327 <      for(int i = 0; i < info_->getNGlobalMolecules(); i++) {
328 <
329 <        // Get the Node number which has this atom;
330 <
331 <        which_node = info_->getMolToProc(i);
332 <
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,
399 <                     MPI_COMM_WORLD);
400 <          }
401 <
402 <          myPotato = potatoes[which_node];
403 <
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 <          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 <              potatoes[which_node] = 0;
415 <              MPI_Send(&potatoes[which_node], 1, MPI_INT, which_node,
416 <                       0, MPI_COMM_WORLD);
417 <            }
418 <
419 <            MPI_Recv(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR,
420 <                     which_node, myPotato, MPI_COMM_WORLD,
421 <                     &istatus);
422 <
423 <            myPotato++;
424 <
425 <            MPI_Recv(atomData, 19, MPI_REALTYPE, which_node, myPotato,
426 <                     MPI_COMM_WORLD, &istatus);
427 <            myPotato++;
428 <
429 <            MPI_Get_count(&istatus, MPI_REALTYPE, &msgLen);
430 <
431 <            if (msgLen == 13 || msgLen == 19)
432 <              isDirectional = 1;
433 <            else
434 <              isDirectional = 0;
435 <
436 <            // If we've survived to here, format the line:
437 <
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 <              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 <            sprintf(writeLine, "\n");
487 <            os << writeLine;
488 <
489 <          } // end for(int l =0)
490 <
491 <          potatoes[which_node] = myPotato;
492 <        } else { //master node has current molecule
493 <
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 <            pos = integrableObject->getPos();
506 <            vel = integrableObject->getVel();
507 <
508 <            atomData[0] = pos[0];
509 <            atomData[1] = pos[1];
510 <            atomData[2] = pos[2];
511 <
512 <            atomData[3] = vel[0];
513 <            atomData[4] = vel[1];
514 <            atomData[5] = vel[2];
515 <
516 <            isDirectional = 0;
517 <
518 <            if (integrableObject->isDirectional()) {
519 <              isDirectional = 1;
520 <
521 <              q = integrableObject->getQ();
522 <              ji = integrableObject->getJ();
523 <
524 <              for(int j = 0; j < 6; j++) {
525 <                atomData[j] = atomData[j];
526 <              }
527 <
528 <              atomData[6] = q[0];
529 <              atomData[7] = q[1];
530 <              atomData[8] = q[2];
531 <              atomData[9] = q[3];
532 <
533 <              atomData[10] = ji[0];
534 <              atomData[11] = ji[1];
535 <              atomData[12] = ji[2];
536 <            }
537 <
538 <            if (needForceVector_) {
539 <              frc = integrableObject->getFrc();
540 <              trq = integrableObject->getTrq();
541 <
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 <            // If we've survived to here, format the line:
560 <
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 <              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 <            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 <            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_REALTYPE, 0, myPotato,
730 <                       MPI_COMM_WORLD);
731 <            } else if (isDirectional) {
732 <              MPI_Send(atomData, 13, MPI_REALTYPE, 0, myPotato,
733 <                       MPI_COMM_WORLD);
734 <            } else if (needForceVector_) {
735 <              MPI_Send(atomData, 12, MPI_REALTYPE, 0, myPotato,
736 <                       MPI_COMM_WORLD);
737 <            } else {
738 <              MPI_Send(atomData, 6, MPI_REALTYPE, 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();
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 775 | 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 809 | 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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