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root/OpenMD/trunk/src/io/DumpWriter.cpp
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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 1437 by gezelter, Wed Apr 21 14:59:18 2010 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 46 | Line 46
46   #include "io/gzstream.hpp"
47   #include "io/Globals.hpp"
48  
49 +
50   #ifdef IS_MPI
51   #include <mpi.h>
52   #endif //is_mpi
53  
54 < namespace oopse {
54 > using namespace std;
55 > namespace OpenMD {
56  
57    DumpWriter::DumpWriter(SimInfo* info)
58      : info_(info), filename_(info->getDumpFileName()), eorFilename_(info->getFinalConfigFileName()){
# Line 61 | Line 63 | namespace oopse {
63      createDumpFile_ = true;
64   #ifdef HAVE_LIBZ
65      if (needCompression_) {
66 <        filename_ += ".gz";
67 <        eorFilename_ += ".gz";
66 >      filename_ += ".gz";
67 >      eorFilename_ += ".gz";
68      }
69   #endif
70      
71   #ifdef IS_MPI
72  
73 <      if (worldRank == 0) {
73 >    if (worldRank == 0) {
74   #endif // is_mpi
73 –
75          
76 <        dumpFile_ = createOStream(filename_);
76 >      dumpFile_ = createOStream(filename_);
77  
78 <        if (!dumpFile_) {
79 <          sprintf(painCave.errMsg, "Could not open \"%s\" for dump output.\n",
80 <                  filename_.c_str());
81 <          painCave.isFatal = 1;
82 <          simError();
83 <        }
78 >      if (!dumpFile_) {
79 >        sprintf(painCave.errMsg, "Could not open \"%s\" for dump output.\n",
80 >                filename_.c_str());
81 >        painCave.isFatal = 1;
82 >        simError();
83 >      }
84  
85   #ifdef IS_MPI
86  
87 <      }
87 >    }
88  
88 –      sprintf(checkPointMsg, "Sucessfully opened output file for dumping.\n");
89 –      MPIcheckPoint();
90 –
89   #endif // is_mpi
90  
91 <    }
91 >  }
92  
93  
94    DumpWriter::DumpWriter(SimInfo* info, const std::string& filename)
# Line 104 | Line 102 | namespace oopse {
102      createDumpFile_ = true;
103   #ifdef HAVE_LIBZ
104      if (needCompression_) {
105 <        filename_ += ".gz";
106 <        eorFilename_ += ".gz";
105 >      filename_ += ".gz";
106 >      eorFilename_ += ".gz";
107      }
108   #endif
109      
110   #ifdef IS_MPI
111  
112 <      if (worldRank == 0) {
112 >    if (worldRank == 0) {
113   #endif // is_mpi
114  
115        
116 <        dumpFile_ = createOStream(filename_);
116 >      dumpFile_ = createOStream(filename_);
117  
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 <        }
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  
125   #ifdef IS_MPI
126  
127 <      }
127 >    }
128  
131 –      sprintf(checkPointMsg, "Sucessfully opened output file for dumping.\n");
132 –      MPIcheckPoint();
133 –
129   #endif // is_mpi
130  
131 <    }
131 >  }
132    
133    DumpWriter::DumpWriter(SimInfo* info, const std::string& filename, bool writeDumpFile)
134 <  : info_(info), filename_(filename){
134 >    : info_(info), filename_(filename){
135      
136      Globals* simParams = info->getSimParams();
137      eorFilename_ = filename_.substr(0, filename_.rfind(".")) + ".eor";    
# Line 170 | Line 165 | namespace oopse {
165   #ifdef IS_MPI
166        
167      }
168 +
169      
174 –    sprintf(checkPointMsg, "Sucessfully opened output file for dumping.\n");
175 –    MPIcheckPoint();
176 –    
170   #endif // is_mpi
171      
172    }
180 –  
181 –  
182 –  
183 –  
184 –  
173  
174    DumpWriter::~DumpWriter() {
175  
# Line 190 | Line 178 | namespace oopse {
178      if (worldRank == 0) {
179   #endif // is_mpi
180        if (createDumpFile_){
181 +        writeClosing(*dumpFile_);
182          delete dumpFile_;
183        }
184   #ifdef IS_MPI
# Line 200 | Line 189 | namespace oopse {
189  
190    }
191  
192 <  void DumpWriter::writeCommentLine(std::ostream& os, Snapshot* s) {
192 >  void DumpWriter::writeFrameProperties(std::ostream& os, Snapshot* s) {
193  
194 <    RealType currentTime;
206 <    Mat3x3d hmat;
207 <    RealType chi;
208 <    RealType integralOfChiDt;
209 <    Mat3x3d eta;
210 <    
211 <    currentTime = s->getTime();
212 <    hmat = s->getHmat();
213 <    chi = s->getChi();
214 <    integralOfChiDt = s->getIntegralOfChiDt();
215 <    eta = s->getEta();
216 <    
217 <    os << currentTime << ";\t"
218 <       << hmat(0, 0) << "\t" << hmat(1, 0) << "\t" << hmat(2, 0) << ";\t"
219 <       << hmat(0, 1) << "\t" << hmat(1, 1) << "\t" << hmat(2, 1) << ";\t"
220 <       << hmat(0, 2) << "\t" << hmat(1, 2) << "\t" << hmat(2, 2) << ";\t";
194 >    char buffer[1024];
195  
196 <    //write out additional parameters, such as chi and eta
196 >    os << "    <FrameData>\n";
197  
198 <    os << chi << "\t" << integralOfChiDt << ";\t";
198 >    RealType currentTime = s->getTime();
199  
200 <    os << eta(0, 0) << "\t" << eta(1, 0) << "\t" << eta(2, 0) << ";\t"
201 <       << eta(0, 1) << "\t" << eta(1, 1) << "\t" << eta(2, 1) << ";\t"
202 <       << eta(0, 2) << "\t" << eta(1, 2) << "\t" << eta(2, 2) << ";";
203 <        
204 <    os << "\n";
200 >    if (isinf(currentTime) || isnan(currentTime)) {      
201 >      sprintf( painCave.errMsg,
202 >               "DumpWriter detected a numerical error writing the time");      
203 >      painCave.isFatal = 1;
204 >      simError();
205 >    }
206 >    
207 >    sprintf(buffer, "        Time: %.10g\n", currentTime);
208 >    os << buffer;
209 >
210 >    Mat3x3d hmat;
211 >    hmat = s->getHmat();
212 >
213 >    for (unsigned int i = 0; i < 3; i++) {
214 >      for (unsigned int j = 0; j < 3; j++) {
215 >        if (isinf(hmat(i,j)) || isnan(hmat(i,j))) {      
216 >          sprintf( painCave.errMsg,
217 >                   "DumpWriter detected a numerical error writing the box");
218 >          painCave.isFatal = 1;
219 >          simError();
220 >        }        
221 >      }
222 >    }
223 >    
224 >    sprintf(buffer, "        Hmat: {{ %.10g, %.10g, %.10g }, { %.10g, %.10g, %.10g }, { %.10g, %.10g, %.10g }}\n",
225 >            hmat(0, 0), hmat(1, 0), hmat(2, 0),
226 >            hmat(0, 1), hmat(1, 1), hmat(2, 1),
227 >            hmat(0, 2), hmat(1, 2), hmat(2, 2));
228 >    os << buffer;
229 >
230 >    RealType chi = s->getChi();
231 >    RealType integralOfChiDt = s->getIntegralOfChiDt();
232 >    if (isinf(chi) || isnan(chi) ||
233 >        isinf(integralOfChiDt) || isnan(integralOfChiDt)) {      
234 >      sprintf( painCave.errMsg,
235 >               "DumpWriter detected a numerical error writing the thermostat");
236 >      painCave.isFatal = 1;
237 >      simError();
238 >    }
239 >    sprintf(buffer, "  Thermostat: %.10g , %.10g\n", chi, integralOfChiDt);
240 >    os << buffer;
241 >
242 >    Mat3x3d eta;
243 >    eta = s->getEta();
244 >
245 >    for (unsigned int i = 0; i < 3; i++) {
246 >      for (unsigned int j = 0; j < 3; j++) {
247 >        if (isinf(eta(i,j)) || isnan(eta(i,j))) {      
248 >          sprintf( painCave.errMsg,
249 >                   "DumpWriter detected a numerical error writing the barostat");
250 >          painCave.isFatal = 1;
251 >          simError();
252 >        }        
253 >      }
254 >    }
255 >
256 >    sprintf(buffer, "    Barostat: {{ %.10g, %.10g, %.10g }, { %.10g, %.10g, %.10g }, { %.10g, %.10g, %.10g }}\n",
257 >            eta(0, 0), eta(1, 0), eta(2, 0),
258 >            eta(0, 1), eta(1, 1), eta(2, 1),
259 >            eta(0, 2), eta(1, 2), eta(2, 2));
260 >    os << buffer;
261 >
262 >    os << "    </FrameData>\n";
263    }
264  
265    void DumpWriter::writeFrame(std::ostream& os) {
234 –    const int BUFFERSIZE = 2000;
235 –    const int MINIBUFFERSIZE = 100;
266  
267 <    char tempBuffer[BUFFERSIZE];
268 <    char writeLine[BUFFERSIZE];
267 > #ifdef IS_MPI
268 >    MPI_Status istatus;
269 > #endif
270  
240 –    Quat4d q;
241 –    Vector3d ji;
242 –    Vector3d pos;
243 –    Vector3d vel;
244 –    Vector3d frc;
245 –    Vector3d trq;
246 –
271      Molecule* mol;
272      StuntDouble* integrableObject;
273      SimInfo::MoleculeIterator mi;
274      Molecule::IntegrableObjectIterator ii;
251 –  
252 –    int nTotObjects;    
253 –    nTotObjects = info_->getNGlobalIntegrableObjects();
275  
276   #ifndef IS_MPI
277 +    os << "  <Snapshot>\n";
278 +
279 +    writeFrameProperties(os, info_->getSnapshotManager()->getCurrentSnapshot());
280  
281 +    os << "    <StuntDoubles>\n";
282 +    for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
283  
284 <    os << nTotObjects << "\n";
285 <        
286 <    writeCommentLine(os, info_->getSnapshotManager()->getCurrentSnapshot());
284 >      
285 >      for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;  
286 >           integrableObject = mol->nextIntegrableObject(ii)) {  
287 >          os << prepareDumpLine(integrableObject);
288 >          
289 >      }
290 >    }    
291 >    os << "    </StuntDoubles>\n";
292 >    
293 >    os << "  </Snapshot>\n";
294  
295 +    os.flush();
296 + #else
297 +    //every node prepares the dump lines for integrable objects belong to itself
298 +    std::string buffer;
299      for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
300  
301 +
302        for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
303 <           integrableObject = mol->nextIntegrableObject(ii)) {
304 <                
303 >           integrableObject = mol->nextIntegrableObject(ii)) {  
304 >          buffer += prepareDumpLine(integrableObject);
305 >      }
306 >    }
307 >    
308 >    const int masterNode = 0;
309  
310 <        pos = integrableObject->getPos();
311 <        vel = integrableObject->getVel();
310 >    if (worldRank == masterNode) {      
311 >      os << "  <Snapshot>\n";  
312 >      writeFrameProperties(os, info_->getSnapshotManager()->getCurrentSnapshot());
313 >      os << "    <StuntDoubles>\n";
314 >        
315 >      os << buffer;
316  
317 <        sprintf(tempBuffer, "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
318 <                integrableObject->getType().c_str(),
319 <                pos[0], pos[1], pos[2],
274 <                vel[0], vel[1], vel[2]);
317 >      int nProc;
318 >      MPI_Comm_size(MPI_COMM_WORLD, &nProc);
319 >      for (int i = 1; i < nProc; ++i) {
320  
321 <        strcpy(writeLine, tempBuffer);
321 >        // receive the length of the string buffer that was
322 >        // prepared by processor i
323  
324 <        if (integrableObject->isDirectional()) {
325 <          q = integrableObject->getQ();
326 <          ji = integrableObject->getJ();
324 >        int recvLength;
325 >        MPI_Recv(&recvLength, 1, MPI_INT, i, 0, MPI_COMM_WORLD, &istatus);
326 >        char* recvBuffer = new char[recvLength];
327 >        if (recvBuffer == NULL) {
328 >        } else {
329 >          MPI_Recv(recvBuffer, recvLength, MPI_CHAR, i, 0, MPI_COMM_WORLD, &istatus);
330 >          os << recvBuffer;
331 >          delete [] recvBuffer;
332 >        }
333 >      }
334 >      os << "    </StuntDoubles>\n";
335 >      
336 >      os << "  </Snapshot>\n";
337 >      os.flush();
338 >    } else {
339 >      int sendBufferLength = buffer.size() + 1;
340 >      MPI_Send(&sendBufferLength, 1, MPI_INT, masterNode, 0, MPI_COMM_WORLD);
341 >      MPI_Send((void *)buffer.c_str(), sendBufferLength, MPI_CHAR, masterNode, 0, MPI_COMM_WORLD);
342 >    }
343  
344 <          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 <        }
344 > #endif // is_mpi
345  
346 <        if (needForceVector_) {
347 <          frc = integrableObject->getFrc();
348 <          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 <        }
346 >  }
347 >
348 >  std::string DumpWriter::prepareDumpLine(StuntDouble* integrableObject) {
349          
350 <        strcat(writeLine, "\n");
351 <        os << writeLine;
350 >    int index = integrableObject->getGlobalIntegrableObjectIndex();
351 >    std::string type("pv");
352 >    std::string line;
353 >    char tempBuffer[4096];
354  
355 <      }
355 >    Vector3d pos;
356 >    Vector3d vel;
357 >    pos = integrableObject->getPos();
358 >
359 >    if (isinf(pos[0]) || isnan(pos[0]) ||
360 >        isinf(pos[1]) || isnan(pos[1]) ||
361 >        isinf(pos[2]) || isnan(pos[2]) ) {      
362 >      sprintf( painCave.errMsg,
363 >               "DumpWriter detected a numerical error writing the position"
364 >               " for object %d", index);      
365 >      painCave.isFatal = 1;
366 >      simError();
367      }
368  
369 <    os.flush();
307 < #else // is_mpi
308 <    /*********************************************************************
309 <     * Documentation?  You want DOCUMENTATION?
310 <     *
311 <     * Why all the potatoes below?  
312 <     *
313 <     * To make a long story short, the original version of DumpWriter
314 <     * worked in the most inefficient way possible.  Node 0 would
315 <     * poke each of the node for an individual atom's formatted data
316 <     * as node 0 worked its way down the global index. This was particularly
317 <     * inefficient since the method blocked all processors at every atom
318 <     * (and did it twice!).
319 <     *
320 <     * An intermediate version of DumpWriter could be described from Node
321 <     * zero's perspective as follows:
322 <     *
323 <     *  1) Have 100 of your friends stand in a circle.
324 <     *  2) When you say go, have all of them start tossing potatoes at
325 <     *     you (one at a time).
326 <     *  3) Catch the potatoes.
327 <     *
328 <     * It was an improvement, but MPI has buffers and caches that could
329 <     * best be described in this analogy as "potato nets", so there's no
330 <     * need to block the processors atom-by-atom.
331 <     *
332 <     * This new and improved DumpWriter works in an even more efficient
333 <     * way:
334 <     *
335 <     *  1) Have 100 of your friend stand in a circle.
336 <     *  2) When you say go, have them start tossing 5-pound bags of
337 <     *     potatoes at you.
338 <     *  3) Once you've caught a friend's bag of potatoes,
339 <     *     toss them a spud to let them know they can toss another bag.
340 <     *
341 <     * How's THAT for documentation?
342 <     *
343 <     *********************************************************************/
344 <    const int masterNode = 0;
369 >    vel = integrableObject->getVel();          
370  
371 <    int * potatoes;
372 <    int myPotato;
373 <    int nProc;
374 <    int which_node;
375 <    RealType atomData[19];
376 <    int isDirectional;
377 <    char MPIatomTypeString[MINIBUFFERSIZE];
378 <    int msgLen; // the length of message actually recieved at master nodes
354 <    int haveError;
355 <    MPI_Status istatus;
356 <    int nCurObj;
357 <    
358 <    // code to find maximum tag value
359 <    int * tagub;
360 <    int flag;
361 <    int MAXTAG;
362 <    MPI_Attr_get(MPI_COMM_WORLD, MPI_TAG_UB, &tagub, &flag);
363 <
364 <    if (flag) {
365 <      MAXTAG = *tagub;
366 <    } else {
367 <      MAXTAG = 32767;
371 >    if (isinf(vel[0]) || isnan(vel[0]) ||
372 >        isinf(vel[1]) || isnan(vel[1]) ||
373 >        isinf(vel[2]) || isnan(vel[2]) ) {      
374 >      sprintf( painCave.errMsg,
375 >               "DumpWriter detected a numerical error writing the velocity"
376 >               " for object %d", index);      
377 >      painCave.isFatal = 1;
378 >      simError();
379      }
380  
381 <    if (worldRank == masterNode) { //master node (node 0) is responsible for writing the dump file
381 >    sprintf(tempBuffer, "%18.10g %18.10g %18.10g %13e %13e %13e",
382 >            pos[0], pos[1], pos[2],
383 >            vel[0], vel[1], vel[2]);                    
384 >    line += tempBuffer;
385  
386 <      // Node 0 needs a list of the magic potatoes for each processor;
386 >    if (integrableObject->isDirectional()) {
387 >      type += "qj";
388 >      Quat4d q;
389 >      Vector3d ji;
390 >      q = integrableObject->getQ();
391  
392 <      MPI_Comm_size(MPI_COMM_WORLD, &nProc);
393 <      potatoes = new int[nProc];
394 <
395 <      //write out the comment lines
396 <      for(int i = 0; i < nProc; i++) {
397 <        potatoes[i] = 0;
392 >      if (isinf(q[0]) || isnan(q[0]) ||
393 >          isinf(q[1]) || isnan(q[1]) ||
394 >          isinf(q[2]) || isnan(q[2]) ||
395 >          isinf(q[3]) || isnan(q[3]) ) {      
396 >        sprintf( painCave.errMsg,
397 >                 "DumpWriter detected a numerical error writing the quaternion"
398 >                 " for object %d", index);      
399 >        painCave.isFatal = 1;
400 >        simError();
401        }
402  
403 +      ji = integrableObject->getJ();
404  
405 <      os << nTotObjects << "\n";
406 <      writeCommentLine(os, info_->getSnapshotManager()->getCurrentSnapshot());
405 >      if (isinf(ji[0]) || isnan(ji[0]) ||
406 >          isinf(ji[1]) || isnan(ji[1]) ||
407 >          isinf(ji[2]) || isnan(ji[2]) ) {      
408 >        sprintf( painCave.errMsg,
409 >                 "DumpWriter detected a numerical error writing the angular"
410 >                 " momentum for object %d", index);      
411 >        painCave.isFatal = 1;
412 >        simError();
413 >      }
414  
415 <      for(int i = 0; i < info_->getNGlobalMolecules(); i++) {
415 >      sprintf(tempBuffer, " %13e %13e %13e %13e %13e %13e %13e",
416 >              q[0], q[1], q[2], q[3],
417 >              ji[0], ji[1], ji[2]);
418 >      line += tempBuffer;
419 >    }
420  
421 <        // Get the Node number which has this atom;
421 >    if (needForceVector_) {
422 >      type += "f";
423 >      Vector3d frc;
424  
425 <        which_node = info_->getMolToProc(i);
425 >      frc = integrableObject->getFrc();
426  
427 <        if (which_node != masterNode) { //current molecule is in slave node
428 <          if (potatoes[which_node] + 1 >= MAXTAG) {
429 <            // The potato was going to exceed the maximum value,
430 <            // so wrap this processor potato back to 0:        
431 <
432 <            potatoes[which_node] = 0;
433 <            MPI_Send(&potatoes[which_node], 1, MPI_INT, which_node, 0,
434 <                     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 <            
427 >      if (isinf(frc[0]) || isnan(frc[0]) ||
428 >          isinf(frc[1]) || isnan(frc[1]) ||
429 >          isinf(frc[2]) || isnan(frc[2]) ) {      
430 >        sprintf( painCave.errMsg,
431 >                 "DumpWriter detected a numerical error writing the force"
432 >                 " for object %d", index);      
433 >        painCave.isFatal = 1;
434 >        simError();
435        }
436 <      sprintf(checkPointMsg, "Sucessfully took a dump.\n");
437 <      MPIcheckPoint();
436 >      sprintf(tempBuffer, " %13e %13e %13e",
437 >              frc[0], frc[1], frc[2]);
438 >      line += tempBuffer;
439 >      
440 >      if (integrableObject->isDirectional()) {
441 >        type += "t";
442 >        Vector3d trq;
443 >        
444 >        trq = integrableObject->getTrq();
445 >        
446 >        if (isinf(trq[0]) || isnan(trq[0]) ||
447 >            isinf(trq[1]) || isnan(trq[1]) ||
448 >            isinf(trq[2]) || isnan(trq[2]) ) {      
449 >          sprintf( painCave.errMsg,
450 >                   "DumpWriter detected a numerical error writing the torque"
451 >                   " for object %d", index);      
452 >          painCave.isFatal = 1;
453 >          simError();
454 >        }
455 >        
456 >        sprintf(tempBuffer, " %13e %13e %13e",
457 >                trq[0], trq[1], trq[2]);
458 >        line += tempBuffer;
459 >      }      
460      }
461 <
462 < #endif // is_mpi
463 <
461 >    
462 >    sprintf(tempBuffer, "%10d %7s %s\n", index, type.c_str(), line.c_str());
463 >    return std::string(tempBuffer);
464    }
465  
466    void DumpWriter::writeDump() {
# Line 775 | Line 485 | namespace oopse {
485   #ifdef IS_MPI
486      if (worldRank == 0) {
487   #endif // is_mpi
488 <    delete eorStream;
489 <
488 >      writeClosing(*eorStream);
489 >      delete eorStream;
490   #ifdef IS_MPI
491      }
492   #endif // is_mpi  
# Line 809 | Line 519 | namespace oopse {
519   #ifdef IS_MPI
520      if (worldRank == 0) {
521   #endif // is_mpi
522 <    delete eorStream;
523 <
522 >      writeClosing(*eorStream);
523 >      delete eorStream;
524   #ifdef IS_MPI
525      }
526   #endif // is_mpi  
527      
528    }
529  
530 < std::ostream* DumpWriter::createOStream(const std::string& filename) {
530 >  std::ostream* DumpWriter::createOStream(const std::string& filename) {
531  
532      std::ostream* newOStream;
533   #ifdef HAVE_LIBZ
534      if (needCompression_) {
535 <        newOStream = new ogzstream(filename.c_str());
535 >      newOStream = new ogzstream(filename.c_str());
536      } else {
537 <        newOStream = new std::ofstream(filename.c_str());
537 >      newOStream = new std::ofstream(filename.c_str());
538      }
539   #else
540      newOStream = new std::ofstream(filename.c_str());
541   #endif
542 +    //write out MetaData first
543 +    (*newOStream) << "<OpenMD version=1>" << std::endl;
544 +    (*newOStream) << "  <MetaData>" << std::endl;
545 +    (*newOStream) << info_->getRawMetaData();
546 +    (*newOStream) << "  </MetaData>" << std::endl;
547      return newOStream;
548 < }
548 >  }
549  
550 < }//end namespace oopse
550 >  void DumpWriter::writeClosing(std::ostream& os) {
551 >
552 >    os << "</OpenMD>\n";
553 >    os.flush();
554 >  }
555 >
556 > }//end namespace OpenMD

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