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Comparing trunk/src/io/DumpWriter.cpp (file contents):
Revision 507 by gezelter, Fri Apr 15 22:04:00 2005 UTC vs.
Revision 1025 by gezelter, Wed Aug 30 20:33:44 2006 UTC

# Line 43 | Line 43
43   #include "primitives/Molecule.hpp"
44   #include "utils/simError.h"
45   #include "io/basic_teebuf.hpp"
46 + #include "io/gzstream.hpp"
47 + #include "io/Globals.hpp"
48 +
49   #ifdef IS_MPI
50   #include <mpi.h>
51   #endif //is_mpi
# Line 51 | Line 54 | namespace oopse {
54  
55    DumpWriter::DumpWriter(SimInfo* info)
56      : info_(info), filename_(info->getDumpFileName()), eorFilename_(info->getFinalConfigFileName()){
57 +
58 +    Globals* simParams = info->getSimParams();
59 +    needCompression_ = simParams->getCompressDumpFile();
60 +    needForceVector_ = simParams->getOutputForceVector();
61 +    createDumpFile_ = true;
62 + #ifdef HAVE_LIBZ
63 +    if (needCompression_) {
64 +      filename_ += ".gz";
65 +      eorFilename_ += ".gz";
66 +    }
67 + #endif
68 +    
69   #ifdef IS_MPI
70  
71 <      if (worldRank == 0) {
71 >    if (worldRank == 0) {
72   #endif // is_mpi
73 +        
74 +      dumpFile_ = createOStream(filename_);
75  
76 <        dumpFile_.open(filename_.c_str(), std::ios::out | std::ios::trunc);
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  
61 –        if (!dumpFile_) {
62 –          sprintf(painCave.errMsg, "Could not open \"%s\" for dump output.\n",
63 –                  filename_.c_str());
64 –          painCave.isFatal = 1;
65 –          simError();
66 –        }
67 –
83   #ifdef IS_MPI
84  
85 <      }
85 >    }
86  
72 –      sprintf(checkPointMsg, "Sucessfully opened output file for dumping.\n");
73 –      MPIcheckPoint();
74 –
87   #endif // is_mpi
88  
89 <    }
89 >  }
90  
91  
92    DumpWriter::DumpWriter(SimInfo* info, const std::string& filename)
93      : info_(info), filename_(filename){
94 +
95 +    Globals* simParams = info->getSimParams();
96 +    eorFilename_ = filename_.substr(0, filename_.rfind(".")) + ".eor";    
97 +
98 +    needCompression_ = simParams->getCompressDumpFile();
99 +    needForceVector_ = simParams->getOutputForceVector();
100 +    createDumpFile_ = true;
101 + #ifdef HAVE_LIBZ
102 +    if (needCompression_) {
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 <        eorFilename_ = filename_.substr(0, filename_.rfind(".")) + ".eor";
114 <        dumpFile_.open(filename_.c_str(), std::ios::out | std::ios::trunc);
113 >      
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  
101 –      sprintf(checkPointMsg, "Sucessfully opened output file for dumping.\n");
102 –      MPIcheckPoint();
103 –
127   #endif // is_mpi
128  
129 +  }
130 +  
131 +  DumpWriter::DumpWriter(SimInfo* info, const std::string& filename, bool writeDumpFile)
132 +    : info_(info), filename_(filename){
133 +    
134 +    Globals* simParams = info->getSimParams();
135 +    eorFilename_ = filename_.substr(0, filename_.rfind(".")) + ".eor";    
136 +    
137 +    needCompression_ = simParams->getCompressDumpFile();
138 +    needForceVector_ = simParams->getOutputForceVector();
139 +    
140 + #ifdef HAVE_LIBZ
141 +    if (needCompression_) {
142 +      filename_ += ".gz";
143 +      eorFilename_ += ".gz";
144      }
145 + #endif
146 +    
147 + #ifdef IS_MPI
148 +    
149 +    if (worldRank == 0) {
150 + #endif // is_mpi
151 +      
152 +      createDumpFile_ = writeDumpFile;
153 +      if (createDumpFile_) {
154 +        dumpFile_ = createOStream(filename_);
155 +      
156 +        if (!dumpFile_) {
157 +          sprintf(painCave.errMsg, "Could not open \"%s\" for dump output.\n",
158 +                  filename_.c_str());
159 +          painCave.isFatal = 1;
160 +          simError();
161 +        }
162 +      }
163 + #ifdef IS_MPI
164 +      
165 +    }
166  
167 +    
168 + #endif // is_mpi
169 +    
170 +  }
171 +
172    DumpWriter::~DumpWriter() {
173  
174   #ifdef IS_MPI
175  
176      if (worldRank == 0) {
177   #endif // is_mpi
178 <
179 <      dumpFile_.close();
180 <
178 >      if (createDumpFile_){
179 >        writeClosing(*dumpFile_);
180 >        delete dumpFile_;
181 >      }
182   #ifdef IS_MPI
183  
184      }
# Line 122 | Line 187 | namespace oopse {
187  
188    }
189  
190 <  void DumpWriter::writeCommentLine(std::ostream& os, Snapshot* s) {
190 >  void DumpWriter::writeFrameProperties(std::ostream& os, Snapshot* s) {
191  
192 <    double currentTime;
192 >    char buffer[1024];
193 >
194 >    os << "    <FrameData>\n";
195 >
196 >    RealType currentTime = s->getTime();
197 >    sprintf(buffer, "        Time: %.10g\n", currentTime);
198 >    os << buffer;
199 >
200      Mat3x3d hmat;
129 –    double chi;
130 –    double integralOfChiDt;
131 –    Mat3x3d eta;
132 –    
133 –    currentTime = s->getTime();
201      hmat = s->getHmat();
202 <    chi = s->getChi();
203 <    integralOfChiDt = s->getIntegralOfChiDt();
204 <    eta = s->getEta();
205 <    
206 <    os << currentTime << ";\t"
140 <       << hmat(0, 0) << "\t" << hmat(1, 0) << "\t" << hmat(2, 0) << ";\t"
141 <       << hmat(0, 1) << "\t" << hmat(1, 1) << "\t" << hmat(2, 1) << ";\t"
142 <       << hmat(0, 2) << "\t" << hmat(1, 2) << "\t" << hmat(2, 2) << ";\t";
202 >    sprintf(buffer, "        Hmat: {{ %.10g, %.10g, %.10g }, { %.10g, %.10g, %.10g }, { %.10g, %.10g, %.10g }}\n",
203 >            hmat(0, 0), hmat(1, 0), hmat(2, 0),
204 >            hmat(0, 1), hmat(1, 1), hmat(2, 1),
205 >            hmat(0, 2), hmat(1, 2), hmat(2, 2));
206 >    os << buffer;
207  
208 <    //write out additional parameters, such as chi and eta
208 >    RealType chi = s->getChi();
209 >    RealType integralOfChiDt = s->getIntegralOfChiDt();
210 >    sprintf(buffer, "  Thermostat: %.10g , %.10g\n", chi, integralOfChiDt);
211 >    os << buffer;
212  
213 <    os << chi << "\t" << integralOfChiDt << "\t;";
213 >    Mat3x3d eta;
214 >    eta = s->getEta();
215 >    sprintf(buffer, "    Barostat: {{ %.10g, %.10g, %.10g }, { %.10g, %.10g, %.10g }, { %.10g, %.10g, %.10g }}\n",
216 >            eta(0, 0), eta(1, 0), eta(2, 0),
217 >            eta(0, 1), eta(1, 1), eta(2, 1),
218 >            eta(0, 2), eta(1, 2), eta(2, 2));
219 >    os << buffer;
220  
221 <    os << eta(0, 0) << "\t" << eta(1, 0) << "\t" << eta(2, 0) << ";\t"
149 <       << eta(0, 1) << "\t" << eta(1, 1) << "\t" << eta(2, 1) << ";\t"
150 <       << eta(0, 2) << "\t" << eta(1, 2) << "\t" << eta(2, 2) << ";";
151 <        
152 <    os << "\n";
221 >    os << "    </FrameData>\n";
222    }
223  
224    void DumpWriter::writeFrame(std::ostream& os) {
156 –    const int BUFFERSIZE = 2000;
157 –    const int MINIBUFFERSIZE = 100;
225  
226 <    char tempBuffer[BUFFERSIZE];
227 <    char writeLine[BUFFERSIZE];
226 > #ifdef IS_MPI
227 >    MPI_Status istatus;
228 > #endif
229  
162 –    Quat4d q;
163 –    Vector3d ji;
164 –    Vector3d pos;
165 –    Vector3d vel;
166 –
230      Molecule* mol;
231      StuntDouble* integrableObject;
232      SimInfo::MoleculeIterator mi;
233      Molecule::IntegrableObjectIterator ii;
171 –  
172 –    int nTotObjects;    
173 –    nTotObjects = info_->getNGlobalIntegrableObjects();
234  
235   #ifndef IS_MPI
236 +    os << "  <Snapshot>\n";
237 +
238 +    writeFrameProperties(os, info_->getSnapshotManager()->getCurrentSnapshot());
239  
240 <
178 <    os << nTotObjects << "\n";
179 <        
180 <    writeCommentLine(os, info_->getSnapshotManager()->getCurrentSnapshot());
181 <
240 >    os << "    <StuntDoubles>\n";
241      for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
242  
243        for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
244 <           integrableObject = mol->nextIntegrableObject(ii)) {
245 <                
244 >           integrableObject = mol->nextIntegrableObject(ii)) {  
245 >        os << prepareDumpLine(integrableObject);
246  
247 <        pos = integrableObject->getPos();
248 <        vel = integrableObject->getVel();
247 >      }
248 >    }    
249 >    os << "    </StuntDoubles>\n";
250  
251 <        sprintf(tempBuffer, "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
192 <                integrableObject->getType().c_str(),
193 <                pos[0], pos[1], pos[2],
194 <                vel[0], vel[1], vel[2]);
251 >    os << "  </Snapshot>\n";
252  
253 <        strcpy(writeLine, tempBuffer);
254 <
255 <        if (integrableObject->isDirectional()) {
256 <          q = integrableObject->getQ();
257 <          ji = integrableObject->getJ();
258 <
259 <          sprintf(tempBuffer, "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
260 <                  q[0], q[1], q[2], q[3],
261 <                  ji[0], ji[1], ji[2]);
205 <          strcat(writeLine, tempBuffer);
206 <        } else {
207 <          strcat(writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n");
208 <        }
209 <
210 <        os << writeLine;
211 <
253 >    os.flush();
254 > #else
255 >    //every node prepares the dump lines for integrable objects belong to itself
256 >    std::string buffer;
257 >    for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
258 >      
259 >      for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
260 >           integrableObject = mol->nextIntegrableObject(ii)) {  
261 >        buffer += prepareDumpLine(integrableObject);
262        }
263      }
264 <
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 <     *********************************************************************/
264 >    
265      const int masterNode = 0;
266  
267 <    int * potatoes;
268 <    int myPotato;
269 <    int nProc;
270 <    int which_node;
271 <    double atomData[13];
272 <    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;
266 <    
267 <    // code to find maximum tag value
268 <    int * tagub;
269 <    int flag;
270 <    int MAXTAG;
271 <    MPI_Attr_get(MPI_COMM_WORLD, MPI_TAG_UB, &tagub, &flag);
267 >    if (worldRank == masterNode) {      
268 >      os << "  <Snapshot>\n";  
269 >      writeFrameProperties(os, info_->getSnapshotManager()->getCurrentSnapshot());
270 >      os << "    <StuntDoubles>\n";
271 >        
272 >      os << buffer;
273  
274 <    if (flag) {
274 <      MAXTAG = *tagub;
275 <    } else {
276 <      MAXTAG = 32767;
277 <    }
278 <
279 <    if (worldRank == masterNode) { //master node (node 0) is responsible for writing the dump file
280 <
281 <      // Node 0 needs a list of the magic potatoes for each processor;
282 <
274 >      int nProc;
275        MPI_Comm_size(MPI_COMM_WORLD, &nProc);
276 <      potatoes = new int[nProc];
276 >      for (int i = 1; i < nProc; ++i) {
277  
278 <      //write out the comment lines
279 <      for(int i = 0; i < nProc; i++) {
288 <        potatoes[i] = 0;
289 <      }
278 >        // receive the length of the string buffer that was
279 >        // prepared by processor i
280  
281 +        int recvLength;
282 +        MPI_Recv(&recvLength, 1, MPI_INT, i, 0, MPI_COMM_WORLD, &istatus);
283 +        char* recvBuffer = new char[recvLength];
284 +        if (recvBuffer == NULL) {
285 +        } else {
286 +          MPI_Recv(recvBuffer, recvLength, MPI_CHAR, i, 0, MPI_COMM_WORLD, &istatus);
287 +          os << recvBuffer;
288 +          delete recvBuffer;
289 +        }
290 +      }
291 +      os << "    </StuntDoubles>\n";
292 +      
293 +      os << "  </Snapshot>\n";
294 +      os.flush();
295 +    } else {
296 +      int sendBufferLength = buffer.size() + 1;
297 +      MPI_Send(&sendBufferLength, 1, MPI_INT, masterNode, 0, MPI_COMM_WORLD);
298 +      MPI_Send((void *)buffer.c_str(), sendBufferLength, MPI_CHAR, masterNode, 0, MPI_COMM_WORLD);
299 +    }
300  
301 <      os << nTotObjects << "\n";
293 <      writeCommentLine(os, info_->getSnapshotManager()->getCurrentSnapshot());
301 > #endif // is_mpi
302  
303 <      for(int i = 0; i < info_->getNGlobalMolecules(); i++) {
303 >  }
304  
305 <        // Get the Node number which has this atom;
305 >  std::string DumpWriter::prepareDumpLine(StuntDouble* integrableObject) {
306 >        
307 >    int index = integrableObject->getGlobalIntegrableObjectIndex();
308 >    std::string type("pv");
309 >    std::string line;
310 >    char tempBuffer[4096];
311  
312 <        which_node = info_->getMolToProc(i);
312 >    Vector3d pos;
313 >    Vector3d vel;
314 >    pos = integrableObject->getPos();
315 >    vel = integrableObject->getVel();          
316 >    sprintf(tempBuffer, "%18.10g %18.10g %18.10g %13e %13e %13e",
317 >            pos[0], pos[1], pos[2],
318 >            vel[0], vel[1], vel[2]);                    
319 >    line += tempBuffer;
320  
321 <        if (which_node != masterNode) { //current molecule is in slave node
322 <          if (potatoes[which_node] + 1 >= MAXTAG) {
323 <            // The potato was going to exceed the maximum value,
324 <            // so wrap this processor potato back to 0:        
325 <
326 <            potatoes[which_node] = 0;
327 <            MPI_Send(&potatoes[which_node], 1, MPI_INT, which_node, 0,
328 <                     MPI_COMM_WORLD);
329 <          }
330 <
311 <          myPotato = potatoes[which_node];
312 <
313 <          //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++;
317 <
318 <          for(int l = 0; l < nCurObj; l++) {
319 <            if (potatoes[which_node] + 2 >= MAXTAG) {
320 <              // The potato was going to exceed the maximum value,
321 <              // so wrap this processor potato back to 0:        
322 <
323 <              potatoes[which_node] = 0;
324 <              MPI_Send(&potatoes[which_node], 1, MPI_INT, which_node,
325 <                       0, MPI_COMM_WORLD);
326 <            }
327 <
328 <            MPI_Recv(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR,
329 <                     which_node, myPotato, MPI_COMM_WORLD,
330 <                     &istatus);
331 <
332 <            myPotato++;
333 <
334 <            MPI_Recv(atomData, 13, MPI_DOUBLE, which_node, myPotato,
335 <                     MPI_COMM_WORLD, &istatus);
336 <            myPotato++;
337 <
338 <            MPI_Get_count(&istatus, MPI_DOUBLE, &msgLen);
339 <
340 <            if (msgLen == 13)
341 <              isDirectional = 1;
342 <            else
343 <              isDirectional = 0;
344 <
345 <            // If we've survived to here, format the line:
346 <
347 <            if (!isDirectional) {
348 <              sprintf(writeLine, "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
349 <                      MPIatomTypeString, atomData[0],
350 <                      atomData[1], atomData[2],
351 <                      atomData[3], atomData[4],
352 <                      atomData[5]);
353 <
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 <            }
374 <
375 <            os << writeLine;
376 <
377 <          } // end for(int l =0)
378 <
379 <          potatoes[which_node] = myPotato;
380 <        } else { //master node has current molecule
381 <
382 <          mol = info_->getMoleculeByGlobalIndex(i);
383 <
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 <            
565 <      }
566 <      sprintf(checkPointMsg, "Sucessfully took a dump.\n");
567 <      MPIcheckPoint();
321 >    if (integrableObject->isDirectional()) {
322 >      type += "qj";
323 >      Quat4d q;
324 >      Vector3d ji;
325 >      q = integrableObject->getQ();
326 >      ji = integrableObject->getJ();
327 >      sprintf(tempBuffer, " %13e %13e %13e %13e %13e %13e %13e",
328 >              q[0], q[1], q[2], q[3],
329 >              ji[0], ji[1], ji[2]);
330 >      line += tempBuffer;
331      }
332  
333 < #endif // is_mpi
334 <
333 >    if (needForceVector_) {
334 >      type += "ft";
335 >      Vector3d frc;
336 >      Vector3d trq;
337 >      frc = integrableObject->getFrc();
338 >      trq = integrableObject->getTrq();
339 >              
340 >      sprintf(tempBuffer, " %13e %13e %13e %13e %13e %13e",
341 >              frc[0], frc[1], frc[2],
342 >              trq[0], trq[1], trq[2]);
343 >      line += tempBuffer;
344 >    }
345 >        
346 >    sprintf(tempBuffer, "%10d %7s %s\n", index, type.c_str(), line.c_str());
347 >    return std::string(tempBuffer);
348    }
349  
350    void DumpWriter::writeDump() {
351 <    writeFrame(dumpFile_);
576 <
351 >    writeFrame(*dumpFile_);
352    }
353  
354    void DumpWriter::writeEor() {
355 <    std::ofstream eorStream;
355 >    std::ostream* eorStream;
356      
357   #ifdef IS_MPI
358      if (worldRank == 0) {
359   #endif // is_mpi
360  
361 <      eorStream.open(eorFilename_.c_str());
587 <      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 <      }
361 >      eorStream = createOStream(eorFilename_);
362  
363   #ifdef IS_MPI
364      }
365   #endif // is_mpi    
366  
367 <    writeFrame(eorStream);
367 >    writeFrame(*eorStream);
368 >
369 > #ifdef IS_MPI
370 >    if (worldRank == 0) {
371 > #endif // is_mpi
372 >      writeClosing(*eorStream);
373 >      delete eorStream;
374 > #ifdef IS_MPI
375 >    }
376 > #endif // is_mpi  
377 >
378    }
379  
380  
381    void DumpWriter::writeDumpAndEor() {
603 –    std::ofstream eorStream;
382      std::vector<std::streambuf*> buffers;
383 +    std::ostream* eorStream;
384   #ifdef IS_MPI
385      if (worldRank == 0) {
386   #endif // is_mpi
387  
388 <      buffers.push_back(dumpFile_.rdbuf());
388 >      buffers.push_back(dumpFile_->rdbuf());
389  
390 <      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 <      }
390 >      eorStream = createOStream(eorFilename_);
391  
392 <      buffers.push_back(eorStream.rdbuf());
392 >      buffers.push_back(eorStream->rdbuf());
393          
394   #ifdef IS_MPI
395      }
# Line 626 | Line 399 | namespace oopse {
399      std::ostream os(&tbuf);
400  
401      writeFrame(os);
402 +
403 + #ifdef IS_MPI
404 +    if (worldRank == 0) {
405 + #endif // is_mpi
406 +      writeClosing(*eorStream);
407 +      delete eorStream;
408 + #ifdef IS_MPI
409 +    }
410 + #endif // is_mpi  
411      
412    }
413  
414 +  std::ostream* DumpWriter::createOStream(const std::string& filename) {
415  
416 +    std::ostream* newOStream;
417 + #ifdef HAVE_LIBZ
418 +    if (needCompression_) {
419 +      newOStream = new ogzstream(filename.c_str());
420 +    } else {
421 +      newOStream = new std::ofstream(filename.c_str());
422 +    }
423 + #else
424 +    newOStream = new std::ofstream(filename.c_str());
425 + #endif
426 +    //write out MetaData first
427 +    (*newOStream) << "<OOPSE version=4>" << std::endl;
428 +    (*newOStream) << "  <MetaData>" << std::endl;
429 +    (*newOStream) << info_->getRawMetaData();
430 +    (*newOStream) << "  </MetaData>" << std::endl;
431 +    return newOStream;
432 +  }
433  
434 +  void DumpWriter::writeClosing(std::ostream& os) {
435 +
436 +    os << "</OOPSE>\n";
437 +    os.flush();
438 +  }
439 +
440   }//end namespace oopse

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