ViewVC Help
View File | Revision Log | Show Annotations | View Changeset | Root Listing
root/OpenMD/branches/development/src/io/DumpWriter.cpp
(Generate patch)

Comparing:
trunk/src/io/DumpWriter.cpp (file contents), Revision 507 by gezelter, Fri Apr 15 22:04:00 2005 UTC vs.
branches/development/src/io/DumpWriter.cpp (file contents), Revision 1875 by gezelter, Fri May 17 14:41:42 2013 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, 234107 (2008).          
39 + * [4]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
40 + * [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41   */
42  
43   #include "io/DumpWriter.hpp"
44   #include "primitives/Molecule.hpp"
45   #include "utils/simError.h"
46   #include "io/basic_teebuf.hpp"
47 + #ifdef HAVE_ZLIB
48 + #include "io/gzstream.hpp"
49 + #endif
50 + #include "io/Globals.hpp"
51 +
52 + #ifdef _MSC_VER
53 + #define isnan(x) _isnan((x))
54 + #define isinf(x) (!_finite(x) && !_isnan(x))
55 + #endif
56 +
57   #ifdef IS_MPI
58   #include <mpi.h>
59 < #endif //is_mpi
59 > #endif
60  
61 < namespace oopse {
61 > using namespace std;
62 > namespace OpenMD {
63  
64    DumpWriter::DumpWriter(SimInfo* info)
65      : info_(info), filename_(info->getDumpFileName()), eorFilename_(info->getFinalConfigFileName()){
54 #ifdef IS_MPI
66  
67 <      if (worldRank == 0) {
68 < #endif // is_mpi
67 >    Globals* simParams = info->getSimParams();
68 >    needCompression_   = simParams->getCompressDumpFile();
69 >    needForceVector_   = simParams->getOutputForceVector();
70 >    needParticlePot_   = simParams->getOutputParticlePotential();
71 >    needFlucQ_         = simParams->getOutputFluctuatingCharges();
72 >    needElectricField_ = simParams->getOutputElectricField();
73  
74 <        dumpFile_.open(filename_.c_str(), std::ios::out | std::ios::trunc);
74 >    if (needParticlePot_ || needFlucQ_ || needElectricField_) {
75 >      doSiteData_ = true;
76 >    } else {
77 >      doSiteData_ = false;
78 >    }
79  
80 <        if (!dumpFile_) {
81 <          sprintf(painCave.errMsg, "Could not open \"%s\" for dump output.\n",
82 <                  filename_.c_str());
83 <          painCave.isFatal = 1;
84 <          simError();
85 <        }
86 <
80 >    createDumpFile_ = true;
81 > #ifdef HAVE_LIBZ
82 >    if (needCompression_) {
83 >      filename_ += ".gz";
84 >      eorFilename_ += ".gz";
85 >    }
86 > #endif
87 >    
88   #ifdef IS_MPI
89  
90 +    if (worldRank == 0) {
91 + #endif // is_mpi
92 +        
93 +      dumpFile_ = createOStream(filename_);
94 +
95 +      if (!dumpFile_) {
96 +        sprintf(painCave.errMsg, "Could not open \"%s\" for dump output.\n",
97 +                filename_.c_str());
98 +        painCave.isFatal = 1;
99 +        simError();
100        }
101  
102 <      sprintf(checkPointMsg, "Sucessfully opened output file for dumping.\n");
73 <      MPIcheckPoint();
102 > #ifdef IS_MPI
103  
104 +    }
105 +
106   #endif // is_mpi
107  
108 <    }
108 >  }
109  
110  
111    DumpWriter::DumpWriter(SimInfo* info, const std::string& filename)
112      : info_(info), filename_(filename){
82 #ifdef IS_MPI
113  
114 <      if (worldRank == 0) {
115 < #endif // is_mpi
114 >    Globals* simParams = info->getSimParams();
115 >    eorFilename_ = filename_.substr(0, filename_.rfind(".")) + ".eor";    
116  
117 <        eorFilename_ = filename_.substr(0, filename_.rfind(".")) + ".eor";
118 <        dumpFile_.open(filename_.c_str(), std::ios::out | std::ios::trunc);
117 >    needCompression_   = simParams->getCompressDumpFile();
118 >    needForceVector_   = simParams->getOutputForceVector();
119 >    needParticlePot_   = simParams->getOutputParticlePotential();
120 >    needFlucQ_         = simParams->getOutputFluctuatingCharges();
121 >    needElectricField_ = simParams->getOutputElectricField();
122  
123 <        if (!dumpFile_) {
124 <          sprintf(painCave.errMsg, "Could not open \"%s\" for dump output.\n",
125 <                  filename_.c_str());
126 <          painCave.isFatal = 1;
127 <          simError();
95 <        }
123 >    if (needParticlePot_ || needFlucQ_ || needElectricField_) {
124 >      doSiteData_ = true;
125 >    } else {
126 >      doSiteData_ = false;
127 >    }
128  
129 +    createDumpFile_ = true;
130 + #ifdef HAVE_LIBZ
131 +    if (needCompression_) {
132 +      filename_ += ".gz";
133 +      eorFilename_ += ".gz";
134 +    }
135 + #endif
136 +    
137   #ifdef IS_MPI
138  
139 +    if (worldRank == 0) {
140 + #endif // is_mpi
141 +
142 +      
143 +      dumpFile_ = createOStream(filename_);
144 +
145 +      if (!dumpFile_) {
146 +        sprintf(painCave.errMsg, "Could not open \"%s\" for dump output.\n",
147 +                filename_.c_str());
148 +        painCave.isFatal = 1;
149 +        simError();
150        }
151  
152 <      sprintf(checkPointMsg, "Sucessfully opened output file for dumping.\n");
102 <      MPIcheckPoint();
152 > #ifdef IS_MPI
153  
154 +    }
155 +
156   #endif // is_mpi
157  
158 +  }
159 +  
160 +  DumpWriter::DumpWriter(SimInfo* info, const std::string& filename, bool writeDumpFile)
161 +    : info_(info), filename_(filename){
162 +    
163 +    Globals* simParams = info->getSimParams();
164 +    eorFilename_ = filename_.substr(0, filename_.rfind(".")) + ".eor";    
165 +    
166 +    needCompression_   = simParams->getCompressDumpFile();
167 +    needForceVector_   = simParams->getOutputForceVector();
168 +    needParticlePot_   = simParams->getOutputParticlePotential();
169 +    needFlucQ_         = simParams->getOutputFluctuatingCharges();
170 +    needElectricField_ = simParams->getOutputElectricField();
171 +
172 +    if (needParticlePot_ || needFlucQ_ || needElectricField_) {
173 +      doSiteData_ = true;
174 +    } else {
175 +      doSiteData_ = false;
176      }
177  
178 + #ifdef HAVE_LIBZ
179 +    if (needCompression_) {
180 +      filename_ += ".gz";
181 +      eorFilename_ += ".gz";
182 +    }
183 + #endif
184 +    
185 + #ifdef IS_MPI
186 +    
187 +    if (worldRank == 0) {
188 + #endif // is_mpi
189 +      
190 +      createDumpFile_ = writeDumpFile;
191 +      if (createDumpFile_) {
192 +        dumpFile_ = createOStream(filename_);
193 +      
194 +        if (!dumpFile_) {
195 +          sprintf(painCave.errMsg, "Could not open \"%s\" for dump output.\n",
196 +                  filename_.c_str());
197 +          painCave.isFatal = 1;
198 +          simError();
199 +        }
200 +      }
201 + #ifdef IS_MPI
202 +      
203 +    }
204 +
205 +    
206 + #endif // is_mpi
207 +    
208 +  }
209 +
210    DumpWriter::~DumpWriter() {
211  
212   #ifdef IS_MPI
213  
214      if (worldRank == 0) {
215   #endif // is_mpi
216 <
217 <      dumpFile_.close();
218 <
216 >      if (createDumpFile_){
217 >        writeClosing(*dumpFile_);
218 >        delete dumpFile_;
219 >      }
220   #ifdef IS_MPI
221  
222      }
# Line 122 | Line 225 | namespace oopse {
225  
226    }
227  
228 <  void DumpWriter::writeCommentLine(std::ostream& os, Snapshot* s) {
228 >  void DumpWriter::writeFrameProperties(std::ostream& os, Snapshot* s) {
229  
230 <    double currentTime;
231 <    Mat3x3d hmat;
232 <    double chi;
233 <    double integralOfChiDt;
234 <    Mat3x3d eta;
230 >    char buffer[1024];
231 >
232 >    os << "    <FrameData>\n";
233 >
234 >    RealType currentTime = s->getTime();
235 >
236 >    if (isinf(currentTime) || isnan(currentTime)) {      
237 >      sprintf( painCave.errMsg,
238 >               "DumpWriter detected a numerical error writing the time");      
239 >      painCave.isFatal = 1;
240 >      simError();
241 >    }
242      
243 <    currentTime = s->getTime();
243 >    sprintf(buffer, "        Time: %.10g\n", currentTime);
244 >    os << buffer;
245 >
246 >    Mat3x3d hmat;
247      hmat = s->getHmat();
248 <    chi = s->getChi();
249 <    integralOfChiDt = s->getIntegralOfChiDt();
250 <    eta = s->getEta();
248 >
249 >    for (unsigned int i = 0; i < 3; i++) {
250 >      for (unsigned int j = 0; j < 3; j++) {
251 >        if (isinf(hmat(i,j)) || isnan(hmat(i,j))) {      
252 >          sprintf( painCave.errMsg,
253 >                   "DumpWriter detected a numerical error writing the box");
254 >          painCave.isFatal = 1;
255 >          simError();
256 >        }        
257 >      }
258 >    }
259      
260 <    os << currentTime << ";\t"
261 <       << hmat(0, 0) << "\t" << hmat(1, 0) << "\t" << hmat(2, 0) << ";\t"
262 <       << hmat(0, 1) << "\t" << hmat(1, 1) << "\t" << hmat(2, 1) << ";\t"
263 <       << hmat(0, 2) << "\t" << hmat(1, 2) << "\t" << hmat(2, 2) << ";\t";
260 >    sprintf(buffer, "        Hmat: {{ %.10g, %.10g, %.10g }, { %.10g, %.10g, %.10g }, { %.10g, %.10g, %.10g }}\n",
261 >            hmat(0, 0), hmat(1, 0), hmat(2, 0),
262 >            hmat(0, 1), hmat(1, 1), hmat(2, 1),
263 >            hmat(0, 2), hmat(1, 2), hmat(2, 2));
264 >    os << buffer;
265  
266 <    //write out additional parameters, such as chi and eta
266 >    pair<RealType, RealType> thermostat = s->getThermostat();
267  
268 <    os << chi << "\t" << integralOfChiDt << "\t;";
268 >    if (isinf(thermostat.first)  || isnan(thermostat.first) ||
269 >        isinf(thermostat.second) || isnan(thermostat.second)) {      
270 >      sprintf( painCave.errMsg,
271 >               "DumpWriter detected a numerical error writing the thermostat");
272 >      painCave.isFatal = 1;
273 >      simError();
274 >    }
275 >    sprintf(buffer, "  Thermostat: %.10g , %.10g\n", thermostat.first,
276 >            thermostat.second);
277 >    os << buffer;
278  
279 <    os << eta(0, 0) << "\t" << eta(1, 0) << "\t" << eta(2, 0) << ";\t"
280 <       << eta(0, 1) << "\t" << eta(1, 1) << "\t" << eta(2, 1) << ";\t"
281 <       << eta(0, 2) << "\t" << eta(1, 2) << "\t" << eta(2, 2) << ";";
282 <        
283 <    os << "\n";
279 >    Mat3x3d eta;
280 >    eta = s->getBarostat();
281 >
282 >    for (unsigned int i = 0; i < 3; i++) {
283 >      for (unsigned int j = 0; j < 3; j++) {
284 >        if (isinf(eta(i,j)) || isnan(eta(i,j))) {      
285 >          sprintf( painCave.errMsg,
286 >                   "DumpWriter detected a numerical error writing the barostat");
287 >          painCave.isFatal = 1;
288 >          simError();
289 >        }        
290 >      }
291 >    }
292 >
293 >    sprintf(buffer, "    Barostat: {{ %.10g, %.10g, %.10g }, { %.10g, %.10g, %.10g }, { %.10g, %.10g, %.10g }}\n",
294 >            eta(0, 0), eta(1, 0), eta(2, 0),
295 >            eta(0, 1), eta(1, 1), eta(2, 1),
296 >            eta(0, 2), eta(1, 2), eta(2, 2));
297 >    os << buffer;
298 >
299 >    os << "    </FrameData>\n";
300    }
301  
302    void DumpWriter::writeFrame(std::ostream& os) {
156    const int BUFFERSIZE = 2000;
157    const int MINIBUFFERSIZE = 100;
303  
304 <    char tempBuffer[BUFFERSIZE];
305 <    char writeLine[BUFFERSIZE];
304 > #ifdef IS_MPI
305 >    MPI::Status istatus;
306 > #endif
307  
162    Quat4d q;
163    Vector3d ji;
164    Vector3d pos;
165    Vector3d vel;
166
308      Molecule* mol;
309 <    StuntDouble* integrableObject;
309 >    StuntDouble* sd;
310      SimInfo::MoleculeIterator mi;
311      Molecule::IntegrableObjectIterator ii;
312 <  
172 <    int nTotObjects;    
173 <    nTotObjects = info_->getNGlobalIntegrableObjects();
312 >    RigidBody::AtomIterator ai;
313  
314   #ifndef IS_MPI
315 +    os << "  <Snapshot>\n";
316 +
317 +    writeFrameProperties(os, info_->getSnapshotManager()->getCurrentSnapshot());
318  
319 +    os << "    <StuntDoubles>\n";
320 +    for (mol = info_->beginMolecule(mi); mol != NULL;
321 +         mol = info_->nextMolecule(mi)) {
322 +      
323 +      for (sd = mol->beginIntegrableObject(ii); sd != NULL;  
324 +           sd = mol->nextIntegrableObject(ii)) {        
325 +          os << prepareDumpLine(sd);
326 +          
327 +      }
328 +    }    
329 +    os << "    </StuntDoubles>\n";
330  
331 <    os << nTotObjects << "\n";
332 <        
333 <    writeCommentLine(os, info_->getSnapshotManager()->getCurrentSnapshot());
331 >    if (doSiteData_) {
332 >      os << "    <SiteData>\n";
333 >      for (mol = info_->beginMolecule(mi); mol != NULL;
334 >           mol = info_->nextMolecule(mi)) {
335 >              
336 >        for (sd = mol->beginIntegrableObject(ii); sd != NULL;  
337 >           sd = mol->nextIntegrableObject(ii)) {        
338  
339 <    for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
339 >          int ioIndex = sd->getGlobalIntegrableObjectIndex();
340 >          // do one for the IO itself
341 >          os << prepareSiteLine(sd, ioIndex, 0);
342  
343 <      for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
344 <           integrableObject = mol->nextIntegrableObject(ii)) {
345 <                
343 >          if (sd->isRigidBody()) {
344 >            
345 >            RigidBody* rb = static_cast<RigidBody*>(sd);
346 >            int siteIndex = 0;
347 >            for (Atom* atom = rb->beginAtom(ai); atom != NULL;  
348 >                 atom = rb->nextAtom(ai)) {                                            
349 >              os << prepareSiteLine(atom, ioIndex, siteIndex);
350 >              siteIndex++;
351 >            }
352 >          }
353 >        }
354 >      }    
355 >      os << "    </SiteData>\n";
356 >    }
357 >    os << "  </Snapshot>\n";
358  
359 <        pos = integrableObject->getPos();
360 <        vel = integrableObject->getVel();
359 >    os.flush();
360 > #else
361  
362 <        sprintf(tempBuffer, "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
363 <                integrableObject->getType().c_str(),
364 <                pos[0], pos[1], pos[2],
194 <                vel[0], vel[1], vel[2]);
362 >    const int masterNode = 0;
363 >    int worldRank = MPI::COMM_WORLD.Get_rank();
364 >    int nProc = MPI::COMM_WORLD.Get_size();
365  
366 <        strcpy(writeLine, tempBuffer);
366 >    if (worldRank == masterNode) {      
367 >      os << "  <Snapshot>\n";  
368 >      writeFrameProperties(os,
369 >                           info_->getSnapshotManager()->getCurrentSnapshot());
370 >      os << "    <StuntDoubles>\n";
371 >    }
372  
373 <        if (integrableObject->isDirectional()) {
374 <          q = integrableObject->getQ();
375 <          ji = integrableObject->getJ();
373 >    //every node prepares the dump lines for integrable objects belong to itself
374 >    std::string buffer;
375 >    for (mol = info_->beginMolecule(mi); mol != NULL;
376 >         mol = info_->nextMolecule(mi)) {
377 >      for (sd = mol->beginIntegrableObject(ii); sd != NULL;
378 >           sd = mol->nextIntegrableObject(ii)) {        
379 >        buffer += prepareDumpLine(sd);
380 >      }
381 >    }
382 >    
383 >    if (worldRank == masterNode) {      
384 >      os << buffer;
385 >      
386 >      for (int i = 1; i < nProc; ++i) {
387 >        // tell processor i to start sending us data:
388 >        MPI::COMM_WORLD.Bcast(&i, 1, MPI::INT, masterNode);
389  
390 <          sprintf(tempBuffer, "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
391 <                  q[0], q[1], q[2], q[3],
392 <                  ji[0], ji[1], ji[2]);
393 <          strcat(writeLine, tempBuffer);
394 <        } else {
207 <          strcat(writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n");
208 <        }
390 >        // receive the length of the string buffer that was
391 >        // prepared by processor i:        
392 >        int recvLength;
393 >        MPI::COMM_WORLD.Recv(&recvLength, 1, MPI::INT, i, MPI::ANY_TAG,
394 >                             istatus);
395  
396 <        os << writeLine;
396 >        // create a buffer to receive the data
397 >        char* recvBuffer = new char[recvLength];
398 >        if (recvBuffer == NULL) {
399 >        } else {
400 >          // receive the data:
401 >          MPI::COMM_WORLD.Recv(recvBuffer, recvLength, MPI::CHAR, i,
402 >                               MPI::ANY_TAG, istatus);
403 >          // send it to the file:
404 >          os << recvBuffer;
405 >          // get rid of the receive buffer:
406 >          delete [] recvBuffer;
407 >        }
408 >      }
409 >    } else {
410 >      int sendBufferLength = buffer.size() + 1;
411 >      int myturn = 0;
412 >      for (int i = 1; i < nProc; ++i){
413 >        // wait for the master node to call our number:
414 >        MPI::COMM_WORLD.Bcast(&myturn, 1, MPI::INT, masterNode);
415 >        if (myturn == worldRank){
416 >          // send the length of our buffer:
417 >          MPI::COMM_WORLD.Send(&sendBufferLength, 1, MPI::INT, masterNode, 0);
418  
419 +          // send our buffer:
420 +          MPI::COMM_WORLD.Send((void *)buffer.c_str(), sendBufferLength,
421 +                               MPI::CHAR, masterNode, 0);
422 +        }
423        }
424      }
214
215    os.flush();
216 #else // is_mpi
217    /*********************************************************************
218     * Documentation?  You want DOCUMENTATION?
219     *
220     * Why all the potatoes below?  
221     *
222     * To make a long story short, the original version of DumpWriter
223     * worked in the most inefficient way possible.  Node 0 would
224     * poke each of the node for an individual atom's formatted data
225     * as node 0 worked its way down the global index. This was particularly
226     * inefficient since the method blocked all processors at every atom
227     * (and did it twice!).
228     *
229     * An intermediate version of DumpWriter could be described from Node
230     * zero's perspective as follows:
231     *
232     *  1) Have 100 of your friends stand in a circle.
233     *  2) When you say go, have all of them start tossing potatoes at
234     *     you (one at a time).
235     *  3) Catch the potatoes.
236     *
237     * It was an improvement, but MPI has buffers and caches that could
238     * best be described in this analogy as "potato nets", so there's no
239     * need to block the processors atom-by-atom.
240     *
241     * This new and improved DumpWriter works in an even more efficient
242     * way:
243     *
244     *  1) Have 100 of your friend stand in a circle.
245     *  2) When you say go, have them start tossing 5-pound bags of
246     *     potatoes at you.
247     *  3) Once you've caught a friend's bag of potatoes,
248     *     toss them a spud to let them know they can toss another bag.
249     *
250     * How's THAT for documentation?
251     *
252     *********************************************************************/
253    const int masterNode = 0;
254
255    int * potatoes;
256    int myPotato;
257    int nProc;
258    int which_node;
259    double atomData[13];
260    int isDirectional;
261    char MPIatomTypeString[MINIBUFFERSIZE];
262    int msgLen; // the length of message actually recieved at master nodes
263    int haveError;
264    MPI_Status istatus;
265    int nCurObj;
425      
426 <    // code to find maximum tag value
427 <    int * tagub;
269 <    int flag;
270 <    int MAXTAG;
271 <    MPI_Attr_get(MPI_COMM_WORLD, MPI_TAG_UB, &tagub, &flag);
272 <
273 <    if (flag) {
274 <      MAXTAG = *tagub;
275 <    } else {
276 <      MAXTAG = 32767;
426 >    if (worldRank == masterNode) {      
427 >      os << "    </StuntDoubles>\n";
428      }
429  
430 <    if (worldRank == masterNode) { //master node (node 0) is responsible for writing the dump file
430 >    if (doSiteData_) {
431 >      if (worldRank == masterNode) {
432 >        os << "    <SiteData>\n";
433 >      }
434 >      buffer.clear();
435 >      for (mol = info_->beginMolecule(mi); mol != NULL;
436 >           mol = info_->nextMolecule(mi)) {
437 >              
438 >        for (sd = mol->beginIntegrableObject(ii); sd != NULL;  
439 >             sd = mol->nextIntegrableObject(ii)) {      
440 >          
441 >          int ioIndex = sd->getGlobalIntegrableObjectIndex();
442 >          // do one for the IO itself
443 >          buffer += prepareSiteLine(sd, ioIndex, 0);
444  
445 <      // Node 0 needs a list of the magic potatoes for each processor;
445 >          if (sd->isRigidBody()) {
446 >            
447 >            RigidBody* rb = static_cast<RigidBody*>(sd);
448 >            int siteIndex = 0;
449 >            for (Atom* atom = rb->beginAtom(ai); atom != NULL;  
450 >                 atom = rb->nextAtom(ai)) {                                            
451 >              buffer += prepareSiteLine(atom, ioIndex, siteIndex);
452 >              siteIndex++;
453 >            }
454 >          }
455 >        }
456 >      }
457  
458 <      MPI_Comm_size(MPI_COMM_WORLD, &nProc);
459 <      potatoes = new int[nProc];
460 <
461 <      //write out the comment lines
462 <      for(int i = 0; i < nProc; i++) {
463 <        potatoes[i] = 0;
464 <      }
458 >      if (worldRank == masterNode) {    
459 >        os << buffer;
460 >        
461 >        for (int i = 1; i < nProc; ++i) {
462 >          
463 >          // tell processor i to start sending us data:
464 >          MPI::COMM_WORLD.Bcast(&i, 1, MPI::INT, masterNode);
465 >          
466 >          // receive the length of the string buffer that was
467 >          // prepared by processor i:        
468 >          int recvLength;
469 >          MPI::COMM_WORLD.Recv(&recvLength, 1, MPI::INT, i, MPI::ANY_TAG,
470 >                               istatus);
471 >          
472 >          // create a buffer to receive the data
473 >          char* recvBuffer = new char[recvLength];
474 >          if (recvBuffer == NULL) {
475 >          } else {
476 >            // receive the data:
477 >            MPI::COMM_WORLD.Recv(recvBuffer, recvLength, MPI::CHAR, i,
478 >                                 MPI::ANY_TAG, istatus);
479 >            // send it to the file:
480 >            os << recvBuffer;
481 >            // get rid of the receive buffer:
482 >            delete [] recvBuffer;
483 >          }
484 >        }      
485 >      } else {
486 >        int sendBufferLength = buffer.size() + 1;
487 >        int myturn = 0;
488 >        for (int i = 1; i < nProc; ++i){
489 >          // wait for the master node to call our number:
490 >          MPI::COMM_WORLD.Bcast(&myturn, 1, MPI::INT, masterNode);
491 >          if (myturn == worldRank){
492 >            // send the length of our buffer:
493 >            MPI::COMM_WORLD.Send(&sendBufferLength, 1, MPI::INT, masterNode, 0);
494 >            // send our buffer:
495 >            MPI::COMM_WORLD.Send((void *)buffer.c_str(), sendBufferLength,
496 >                                 MPI::CHAR, masterNode, 0);
497 >          }
498 >        }
499 >      }
500 >      
501 >      if (worldRank == masterNode) {    
502 >        os << "    </SiteData>\n";
503 >      }
504 >    }
505 >    
506 >    if (worldRank == masterNode) {
507 >      os << "  </Snapshot>\n";
508 >      os.flush();
509 >    }
510 >    
511 > #endif // is_mpi
512 >    
513 >  }
514  
515 +  std::string DumpWriter::prepareDumpLine(StuntDouble* sd) {
516 +        
517 +    int index = sd->getGlobalIntegrableObjectIndex();
518 +    std::string type("pv");
519 +    std::string line;
520 +    char tempBuffer[4096];
521  
522 <      os << nTotObjects << "\n";
523 <      writeCommentLine(os, info_->getSnapshotManager()->getCurrentSnapshot());
522 >    Vector3d pos;
523 >    Vector3d vel;
524 >    pos = sd->getPos();
525  
526 <      for(int i = 0; i < info_->getNGlobalMolecules(); i++) {
526 >    if (isinf(pos[0]) || isnan(pos[0]) ||
527 >        isinf(pos[1]) || isnan(pos[1]) ||
528 >        isinf(pos[2]) || isnan(pos[2]) ) {      
529 >      sprintf( painCave.errMsg,
530 >               "DumpWriter detected a numerical error writing the position"
531 >               " for object %d", index);      
532 >      painCave.isFatal = 1;
533 >      simError();
534 >    }
535  
536 <        // Get the Node number which has this atom;
536 >    vel = sd->getVel();        
537  
538 <        which_node = info_->getMolToProc(i);
538 >    if (isinf(vel[0]) || isnan(vel[0]) ||
539 >        isinf(vel[1]) || isnan(vel[1]) ||
540 >        isinf(vel[2]) || isnan(vel[2]) ) {      
541 >      sprintf( painCave.errMsg,
542 >               "DumpWriter detected a numerical error writing the velocity"
543 >               " for object %d", index);      
544 >      painCave.isFatal = 1;
545 >      simError();
546 >    }
547  
548 <        if (which_node != masterNode) { //current molecule is in slave node
549 <          if (potatoes[which_node] + 1 >= MAXTAG) {
550 <            // The potato was going to exceed the maximum value,
551 <            // so wrap this processor potato back to 0:        
548 >    sprintf(tempBuffer, "%18.10g %18.10g %18.10g %13e %13e %13e",
549 >            pos[0], pos[1], pos[2],
550 >            vel[0], vel[1], vel[2]);                    
551 >    line += tempBuffer;
552  
553 <            potatoes[which_node] = 0;
554 <            MPI_Send(&potatoes[which_node], 1, MPI_INT, which_node, 0,
555 <                     MPI_COMM_WORLD);
556 <          }
553 >    if (sd->isDirectional()) {
554 >      type += "qj";
555 >      Quat4d q;
556 >      Vector3d ji;
557 >      q = sd->getQ();
558  
559 <          myPotato = potatoes[which_node];
559 >      if (isinf(q[0]) || isnan(q[0]) ||
560 >          isinf(q[1]) || isnan(q[1]) ||
561 >          isinf(q[2]) || isnan(q[2]) ||
562 >          isinf(q[3]) || isnan(q[3]) ) {      
563 >        sprintf( painCave.errMsg,
564 >                 "DumpWriter detected a numerical error writing the quaternion"
565 >                 " for object %d", index);      
566 >        painCave.isFatal = 1;
567 >        simError();
568 >      }
569  
570 <          //recieve the number of integrableObject in current molecule
314 <          MPI_Recv(&nCurObj, 1, MPI_INT, which_node, myPotato,
315 <                   MPI_COMM_WORLD, &istatus);
316 <          myPotato++;
570 >      ji = sd->getJ();
571  
572 <          for(int l = 0; l < nCurObj; l++) {
573 <            if (potatoes[which_node] + 2 >= MAXTAG) {
574 <              // The potato was going to exceed the maximum value,
575 <              // so wrap this processor potato back to 0:        
572 >      if (isinf(ji[0]) || isnan(ji[0]) ||
573 >          isinf(ji[1]) || isnan(ji[1]) ||
574 >          isinf(ji[2]) || isnan(ji[2]) ) {      
575 >        sprintf( painCave.errMsg,
576 >                 "DumpWriter detected a numerical error writing the angular"
577 >                 " momentum for object %d", index);      
578 >        painCave.isFatal = 1;
579 >        simError();
580 >      }
581  
582 <              potatoes[which_node] = 0;
583 <              MPI_Send(&potatoes[which_node], 1, MPI_INT, which_node,
584 <                       0, MPI_COMM_WORLD);
585 <            }
582 >      sprintf(tempBuffer, " %13e %13e %13e %13e %13e %13e %13e",
583 >              q[0], q[1], q[2], q[3],
584 >              ji[0], ji[1], ji[2]);
585 >      line += tempBuffer;
586 >    }
587  
588 <            MPI_Recv(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR,
589 <                     which_node, myPotato, MPI_COMM_WORLD,
590 <                     &istatus);
588 >    if (needForceVector_) {
589 >      type += "f";
590 >      Vector3d frc = sd->getFrc();
591 >      if (isinf(frc[0]) || isnan(frc[0]) ||
592 >          isinf(frc[1]) || isnan(frc[1]) ||
593 >          isinf(frc[2]) || isnan(frc[2]) ) {      
594 >        sprintf( painCave.errMsg,
595 >                 "DumpWriter detected a numerical error writing the force"
596 >                 " for object %d", index);      
597 >        painCave.isFatal = 1;
598 >        simError();
599 >      }
600 >      sprintf(tempBuffer, " %13e %13e %13e",
601 >              frc[0], frc[1], frc[2]);
602 >      line += tempBuffer;
603 >      
604 >      if (sd->isDirectional()) {
605 >        type += "t";
606 >        Vector3d trq = sd->getTrq();        
607 >        if (isinf(trq[0]) || isnan(trq[0]) ||
608 >            isinf(trq[1]) || isnan(trq[1]) ||
609 >            isinf(trq[2]) || isnan(trq[2]) ) {      
610 >          sprintf( painCave.errMsg,
611 >                   "DumpWriter detected a numerical error writing the torque"
612 >                   " for object %d", index);      
613 >          painCave.isFatal = 1;
614 >          simError();
615 >        }        
616 >        sprintf(tempBuffer, " %13e %13e %13e",
617 >                trq[0], trq[1], trq[2]);
618 >        line += tempBuffer;
619 >      }      
620 >    }
621  
622 <            myPotato++;
622 >    sprintf(tempBuffer, "%10d %7s %s\n", index, type.c_str(), line.c_str());
623 >    return std::string(tempBuffer);
624 >  }
625  
626 <            MPI_Recv(atomData, 13, MPI_DOUBLE, which_node, myPotato,
627 <                     MPI_COMM_WORLD, &istatus);
336 <            myPotato++;
626 >  std::string DumpWriter::prepareSiteLine(StuntDouble* sd, int ioIndex, int siteIndex) {
627 >        
628  
629 <            MPI_Get_count(&istatus, MPI_DOUBLE, &msgLen);
629 >    std::string id;
630 >    std::string type;
631 >    std::string line;
632 >    char tempBuffer[4096];
633  
634 <            if (msgLen == 13)
635 <              isDirectional = 1;
636 <            else
637 <              isDirectional = 0;
634 >    if (sd->isRigidBody()) {
635 >      sprintf(tempBuffer, "%10d           ", ioIndex);
636 >      id = std::string(tempBuffer);
637 >    } else {
638 >      sprintf(tempBuffer, "%10d %10d", ioIndex, siteIndex);
639 >      id = std::string(tempBuffer);
640 >    }
641 >              
642 >    if (needFlucQ_) {
643 >      type += "cw";
644 >      RealType fqPos = sd->getFlucQPos();
645 >      if (isinf(fqPos) || isnan(fqPos) ) {      
646 >        sprintf( painCave.errMsg,
647 >                 "DumpWriter detected a numerical error writing the"
648 >                 " fluctuating charge for object %s", id.c_str());      
649 >        painCave.isFatal = 1;
650 >        simError();
651 >      }
652 >      sprintf(tempBuffer, " %13e ", fqPos);
653 >      line += tempBuffer;
654 >    
655 >      RealType fqVel = sd->getFlucQVel();
656 >      if (isinf(fqVel) || isnan(fqVel) ) {      
657 >        sprintf( painCave.errMsg,
658 >                 "DumpWriter detected a numerical error writing the"
659 >                 " fluctuating charge velocity for object %s", id.c_str());      
660 >        painCave.isFatal = 1;
661 >        simError();
662 >      }
663 >      sprintf(tempBuffer, " %13e ", fqVel);
664 >      line += tempBuffer;
665  
666 <            // If we've survived to here, format the line:
666 >      if (needForceVector_) {
667 >        type += "g";
668 >        RealType fqFrc = sd->getFlucQFrc();        
669 >        if (isinf(fqFrc) || isnan(fqFrc) ) {      
670 >          sprintf( painCave.errMsg,
671 >                   "DumpWriter detected a numerical error writing the"
672 >                   " fluctuating charge force for object %s", id.c_str());      
673 >          painCave.isFatal = 1;
674 >          simError();
675 >        }
676 >        sprintf(tempBuffer, " %13e ", fqFrc);        
677 >        line += tempBuffer;
678 >      }
679 >    }
680  
681 <            if (!isDirectional) {
682 <              sprintf(writeLine, "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
683 <                      MPIatomTypeString, atomData[0],
684 <                      atomData[1], atomData[2],
685 <                      atomData[3], atomData[4],
686 <                      atomData[5]);
681 >    if (needElectricField_) {
682 >      type += "e";
683 >      Vector3d eField= sd->getElectricField();
684 >      if (isinf(eField[0]) || isnan(eField[0]) ||
685 >          isinf(eField[1]) || isnan(eField[1]) ||
686 >          isinf(eField[2]) || isnan(eField[2]) ) {      
687 >        sprintf( painCave.errMsg,
688 >                 "DumpWriter detected a numerical error writing the electric"
689 >                 " field for object %s", id.c_str());      
690 >        painCave.isFatal = 1;
691 >        simError();
692 >      }
693 >      sprintf(tempBuffer, " %13e %13e %13e",
694 >              eField[0], eField[1], eField[2]);
695 >      line += tempBuffer;
696 >    }
697  
354              strcat(writeLine,
355                     "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n");
356            } else {
357              sprintf(writeLine,
358                      "%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",
359                      MPIatomTypeString,
360                      atomData[0],
361                      atomData[1],
362                      atomData[2],
363                      atomData[3],
364                      atomData[4],
365                      atomData[5],
366                      atomData[6],
367                      atomData[7],
368                      atomData[8],
369                      atomData[9],
370                      atomData[10],
371                      atomData[11],
372                      atomData[12]);
373            }
698  
699 <            os << writeLine;
700 <
701 <          } // end for(int l =0)
702 <
703 <          potatoes[which_node] = myPotato;
704 <        } else { //master node has current molecule
705 <
706 <          mol = info_->getMoleculeByGlobalIndex(i);
707 <
384 <          if (mol == NULL) {
385 <            sprintf(painCave.errMsg, "Molecule not found on node %d!", worldRank);
386 <            painCave.isFatal = 1;
387 <            simError();
388 <          }
389 <                
390 <          for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
391 <               integrableObject = mol->nextIntegrableObject(ii)) {      
392 <
393 <            pos = integrableObject->getPos();
394 <            vel = integrableObject->getVel();
395 <
396 <            atomData[0] = pos[0];
397 <            atomData[1] = pos[1];
398 <            atomData[2] = pos[2];
399 <
400 <            atomData[3] = vel[0];
401 <            atomData[4] = vel[1];
402 <            atomData[5] = vel[2];
403 <
404 <            isDirectional = 0;
405 <
406 <            if (integrableObject->isDirectional()) {
407 <              isDirectional = 1;
408 <
409 <              q = integrableObject->getQ();
410 <              ji = integrableObject->getJ();
411 <
412 <              for(int j = 0; j < 6; j++) {
413 <                atomData[j] = atomData[j];
414 <              }
415 <
416 <              atomData[6] = q[0];
417 <              atomData[7] = q[1];
418 <              atomData[8] = q[2];
419 <              atomData[9] = q[3];
420 <
421 <              atomData[10] = ji[0];
422 <              atomData[11] = ji[1];
423 <              atomData[12] = ji[2];
424 <            }
425 <
426 <            // If we've survived to here, format the line:
427 <
428 <            if (!isDirectional) {
429 <              sprintf(writeLine, "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
430 <                      integrableObject->getType().c_str(), atomData[0],
431 <                      atomData[1], atomData[2],
432 <                      atomData[3], atomData[4],
433 <                      atomData[5]);
434 <
435 <              strcat(writeLine,
436 <                     "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n");
437 <            } else {
438 <              sprintf(writeLine,
439 <                      "%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",
440 <                      integrableObject->getType().c_str(),
441 <                      atomData[0],
442 <                      atomData[1],
443 <                      atomData[2],
444 <                      atomData[3],
445 <                      atomData[4],
446 <                      atomData[5],
447 <                      atomData[6],
448 <                      atomData[7],
449 <                      atomData[8],
450 <                      atomData[9],
451 <                      atomData[10],
452 <                      atomData[11],
453 <                      atomData[12]);
454 <            }
455 <
456 <
457 <            os << writeLine;
458 <
459 <          } //end for(iter = integrableObject.begin())
460 <        }
461 <      } //end for(i = 0; i < mpiSim->getNmol())
462 <
463 <      os.flush();
464 <        
465 <      sprintf(checkPointMsg, "Sucessfully took a dump.\n");
466 <      MPIcheckPoint();
467 <
468 <      delete [] potatoes;
469 <    } else {
470 <
471 <      // worldRank != 0, so I'm a remote node.  
472 <
473 <      // Set my magic potato to 0:
474 <
475 <      myPotato = 0;
476 <
477 <      for(int i = 0; i < info_->getNGlobalMolecules(); i++) {
478 <
479 <        // Am I the node which has this integrableObject?
480 <        int whichNode = info_->getMolToProc(i);
481 <        if (whichNode == worldRank) {
482 <          if (myPotato + 1 >= MAXTAG) {
483 <
484 <            // The potato was going to exceed the maximum value,
485 <            // so wrap this processor potato back to 0 (and block until
486 <            // node 0 says we can go:
487 <
488 <            MPI_Recv(&myPotato, 1, MPI_INT, 0, 0, MPI_COMM_WORLD,
489 <                     &istatus);
490 <          }
491 <
492 <          mol = info_->getMoleculeByGlobalIndex(i);
493 <
494 <                
495 <          nCurObj = mol->getNIntegrableObjects();
496 <
497 <          MPI_Send(&nCurObj, 1, MPI_INT, 0, myPotato, MPI_COMM_WORLD);
498 <          myPotato++;
499 <
500 <          for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
501 <               integrableObject = mol->nextIntegrableObject(ii)) {
502 <
503 <            if (myPotato + 2 >= MAXTAG) {
504 <
505 <              // The potato was going to exceed the maximum value,
506 <              // so wrap this processor potato back to 0 (and block until
507 <              // node 0 says we can go:
508 <
509 <              MPI_Recv(&myPotato, 1, MPI_INT, 0, 0, MPI_COMM_WORLD,
510 <                       &istatus);
511 <            }
512 <
513 <            pos = integrableObject->getPos();
514 <            vel = integrableObject->getVel();
515 <
516 <            atomData[0] = pos[0];
517 <            atomData[1] = pos[1];
518 <            atomData[2] = pos[2];
519 <
520 <            atomData[3] = vel[0];
521 <            atomData[4] = vel[1];
522 <            atomData[5] = vel[2];
523 <
524 <            isDirectional = 0;
525 <
526 <            if (integrableObject->isDirectional()) {
527 <              isDirectional = 1;
528 <
529 <              q = integrableObject->getQ();
530 <              ji = integrableObject->getJ();
531 <
532 <              atomData[6] = q[0];
533 <              atomData[7] = q[1];
534 <              atomData[8] = q[2];
535 <              atomData[9] = q[3];
536 <
537 <              atomData[10] = ji[0];
538 <              atomData[11] = ji[1];
539 <              atomData[12] = ji[2];
540 <            }
541 <
542 <            strncpy(MPIatomTypeString, integrableObject->getType().c_str(), MINIBUFFERSIZE);
543 <
544 <            // null terminate the  std::string before sending (just in case):
545 <            MPIatomTypeString[MINIBUFFERSIZE - 1] = '\0';
546 <
547 <            MPI_Send(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, 0,
548 <                     myPotato, MPI_COMM_WORLD);
549 <
550 <            myPotato++;
551 <
552 <            if (isDirectional) {
553 <              MPI_Send(atomData, 13, MPI_DOUBLE, 0, myPotato,
554 <                       MPI_COMM_WORLD);
555 <            } else {
556 <              MPI_Send(atomData, 6, MPI_DOUBLE, 0, myPotato,
557 <                       MPI_COMM_WORLD);
558 <            }
559 <
560 <            myPotato++;
561 <          }
562 <                    
563 <        }
564 <            
699 >    if (needParticlePot_) {
700 >      type += "u";
701 >      RealType particlePot = sd->getParticlePot();
702 >      if (isinf(particlePot) || isnan(particlePot)) {      
703 >        sprintf( painCave.errMsg,
704 >                 "DumpWriter detected a numerical error writing the particle "
705 >                 " potential for object %s", id.c_str());      
706 >        painCave.isFatal = 1;
707 >        simError();
708        }
709 <      sprintf(checkPointMsg, "Sucessfully took a dump.\n");
710 <      MPIcheckPoint();
709 >      sprintf(tempBuffer, " %13e", particlePot);
710 >      line += tempBuffer;
711      }
712 +    
713  
714 < #endif // is_mpi
715 <
714 >    sprintf(tempBuffer, "%s %7s %s\n", id.c_str(), type.c_str(), line.c_str());
715 >    return std::string(tempBuffer);
716    }
717  
718    void DumpWriter::writeDump() {
719 <    writeFrame(dumpFile_);
576 <
719 >    writeFrame(*dumpFile_);
720    }
721  
722    void DumpWriter::writeEor() {
723 <    std::ofstream eorStream;
723 >    std::ostream* eorStream;
724      
725   #ifdef IS_MPI
726      if (worldRank == 0) {
727   #endif // is_mpi
728 +      
729 +      eorStream = createOStream(eorFilename_);
730 +      writeFrame(*eorStream);
731 +      
732 + #ifdef IS_MPI
733 +    }
734 +    if (worldRank == 0) {
735 + #endif // is_mpi
736  
737 <      eorStream.open(eorFilename_.c_str());
738 <      if (!eorStream.is_open()) {
588 <        sprintf(painCave.errMsg, "DumpWriter : Could not open \"%s\" for writing.\n",
589 <                eorFilename_.c_str());
590 <        painCave.isFatal = 1;
591 <        simError();
592 <      }
737 >      writeClosing(*eorStream);
738 >      delete eorStream;
739  
740   #ifdef IS_MPI
741      }
742 < #endif // is_mpi    
742 > #endif // is_mpi  
743  
598    writeFrame(eorStream);
744    }
745  
746  
747    void DumpWriter::writeDumpAndEor() {
603    std::ofstream eorStream;
748      std::vector<std::streambuf*> buffers;
749 +    std::ostream* eorStream;
750   #ifdef IS_MPI
751      if (worldRank == 0) {
752   #endif // is_mpi
753  
754 <      buffers.push_back(dumpFile_.rdbuf());
754 >      buffers.push_back(dumpFile_->rdbuf());
755  
756 <      eorStream.open(eorFilename_.c_str());
612 <      if (!eorStream.is_open()) {
613 <        sprintf(painCave.errMsg, "DumpWriter : Could not open \"%s\" for writing.\n",
614 <                eorFilename_.c_str());
615 <        painCave.isFatal = 1;
616 <        simError();
617 <      }
756 >      eorStream = createOStream(eorFilename_);
757  
758 <      buffers.push_back(eorStream.rdbuf());
758 >      buffers.push_back(eorStream->rdbuf());
759          
760   #ifdef IS_MPI
761      }
# Line 626 | Line 765 | namespace oopse {
765      std::ostream os(&tbuf);
766  
767      writeFrame(os);
768 +
769 + #ifdef IS_MPI
770 +    if (worldRank == 0) {
771 + #endif // is_mpi
772 +      writeClosing(*eorStream);
773 +      delete eorStream;
774 + #ifdef IS_MPI
775 +    }
776 + #endif // is_mpi  
777      
778    }
779  
780 +  std::ostream* DumpWriter::createOStream(const std::string& filename) {
781  
782 +    std::ostream* newOStream;
783 + #ifdef HAVE_ZLIB
784 +    if (needCompression_) {
785 +      newOStream = new ogzstream(filename.c_str());
786 +    } else {
787 +      newOStream = new std::ofstream(filename.c_str());
788 +    }
789 + #else
790 +    newOStream = new std::ofstream(filename.c_str());
791 + #endif
792 +    //write out MetaData first
793 +    (*newOStream) << "<OpenMD version=2>" << std::endl;
794 +    (*newOStream) << "  <MetaData>" << std::endl;
795 +    (*newOStream) << info_->getRawMetaData();
796 +    (*newOStream) << "  </MetaData>" << std::endl;
797 +    return newOStream;
798 +  }
799  
800 < }//end namespace oopse
800 >  void DumpWriter::writeClosing(std::ostream& os) {
801 >
802 >    os << "</OpenMD>\n";
803 >    os.flush();
804 >  }
805 >
806 > }//end namespace OpenMD

Comparing:
trunk/src/io/DumpWriter.cpp (property svn:keywords), Revision 507 by gezelter, Fri Apr 15 22:04:00 2005 UTC vs.
branches/development/src/io/DumpWriter.cpp (property svn:keywords), Revision 1875 by gezelter, Fri May 17 14:41:42 2013 UTC

# Line 0 | Line 1
1 + Author Id Revision Date

Diff Legend

Removed lines
+ Added lines
< Changed lines
> Changed lines