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root/group/trunk/OOPSE/libmdtools/DumpWriter.cpp
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Comparing trunk/OOPSE/libmdtools/DumpWriter.cpp (file contents):
Revision 929 by tim, Tue Jan 13 15:46:49 2004 UTC vs.
Revision 947 by gezelter, Thu Jan 15 14:22:16 2004 UTC

# Line 40 | Line 40 | DumpWriter::DumpWriter( SimInfo* the_entry_plug ){
40        simError();
41      }
42  
43 –    //outFile.setf( ios::scientific );
44 –
43   #ifdef IS_MPI
44    }
45  
# Line 102 | Line 100 | void DumpWriter::writeDump(double currentTime){
100   #endif
101  
102   void DumpWriter::writeDump(double currentTime){
105 –  
106 – // write to eor file
107 –  writeFinal(currentTime);
103  
104 < //write to dump file
105 <  writeFrame(dumpFile, currentTime);
104 >  ofstream finalOut;
105 >  vector<ofstream*> fileStreams;
106 >
107 > #ifdef IS_MPI
108 >  if(worldRank == 0 ){
109 >    
110 >    finalOut.open( entry_plug->finalName, ios::out | ios::trunc );
111 >    if( !finalOut ){
112 >      sprintf( painCave.errMsg,
113 >               "Could not open \"%s\" for final dump output.\n",
114 >               entry_plug->finalName );
115 >      painCave.isFatal = 1;
116 >      simError();
117 >    }
118 >  }
119 > #endif // is_mpi
120 >
121 >  fileStreams.push_back(&finalOut);
122 >  fileStreams.push_back(&dumpFile);
123 >
124 >  writeFrame(fileStreams, currentTime);
125 >
126 > #ifdef IS_MPI
127 >  finalOut.close();
128 > #endif
129          
130   }
131  
132   void DumpWriter::writeFinal(double currentTime){
133  
134 <  ofstream finalOut;    
135 <  
136 <  //Open eor file
134 >  ofstream finalOut;
135 >  vector<ofstream*> fileStreams;
136 >
137   #ifdef IS_MPI
138    if(worldRank == 0 ){
121 – #endif // is_mpi
139  
140      finalOut.open( entry_plug->finalName, ios::out | ios::trunc );
141 +
142      if( !finalOut ){
143        sprintf( painCave.errMsg,
144                 "Could not open \"%s\" for final dump output.\n",
# Line 128 | Line 146 | void DumpWriter::writeFinal(double currentTime){
146        painCave.isFatal = 1;
147        simError();
148      }
149 <    
132 < #ifdef IS_MPI
149 >
150    }
134 – #endif
135 –  
136 –  //write to eor file  
137 –  writeFrame(finalOut, currentTime);
138 –  
139 –  //close eor file      
140 – #ifdef IS_MPI
141 –  if(worldRank == 0 ){
142 –    finalOut.close();
143 –  }
151   #endif // is_mpi
152 +  
153 +  fileStreams.push_back(&finalOut);  
154 +  writeFrame(fileStreams, currentTime);
155  
156 + #ifdef IS_MPI
157 +  finalOut.close();
158 + #endif
159 +  
160   }
161  
162 < void DumpWriter::writeFrame( ofstream& outFile, double currentTime ){
162 > void DumpWriter::writeFrame( vector<ofstream*>& outFile, double currentTime ){
163  
164    const int BUFFERSIZE = 2000;
165    const int MINIBUFFERSIZE = 100;
166  
167 <  char tempBuffer[BUFFERSIZE];
167 >  char tempBuffer[BUFFERSIZE];  
168    char writeLine[BUFFERSIZE];
169  
170 <  int i;
170 >  int i, k;
171  
172   #ifdef IS_MPI
173    
174 +  /*********************************************************************
175 +   * Documentation?  You want DOCUMENTATION?
176 +   *
177 +   * Why all the potatoes below?  
178 +   *
179 +   * To make a long story short, the original version of DumpWriter
180 +   * worked in the most inefficient way possible.  Node 0 would
181 +   * poke each of the node for an individual atom's formatted data
182 +   * as node 0 worked its way down the global index. This was particularly
183 +   * inefficient since the method blocked all processors at every atom
184 +   * (and did it twice!).
185 +   *
186 +   * An intermediate version of DumpWriter could be described from Node
187 +   * zero's perspective as follows:
188 +   *
189 +   *  1) Have 100 of your friends stand in a circle.
190 +   *  2) When you say go, have all of them start tossing potatoes at
191 +   *     you (one at a time).
192 +   *  3) Catch the potatoes.
193 +   *
194 +   * It was an improvement, but MPI has buffers and caches that could
195 +   * best be described in this analogy as "potato nets", so there's no
196 +   * need to block the processors atom-by-atom.
197 +   *
198 +   * This new and improved DumpWriter works in an even more efficient
199 +   * way:
200 +   *
201 +   *  1) Have 100 of your friend stand in a circle.
202 +   *  2) When you say go, have them start tossing 5-pound bags of
203 +   *     potatoes at you.
204 +   *  3) Once you've caught a friend's bag of potatoes,
205 +   *     toss them a spud to let them know they can toss another bag.
206 +   *
207 +   * How's THAT for documentation?
208 +   *
209 +   *********************************************************************/
210 +
211    int *potatoes;
212    int myPotato;
213  
# Line 178 | Line 229 | void DumpWriter::writeFrame( ofstream& outFile, double
229    double pos[3], vel[3];
230  
231   #ifndef IS_MPI
232 +  
233 +  for(k = 0; k < outFile.size(); k++){
234 +    *outFile[k] << nAtoms << "\n";
235  
236 <  outFile << nAtoms << "\n";
236 >    *outFile[k] << currentTime << ";\t"
237 >               << entry_plug->Hmat[0][0] << "\t"
238 >                     << entry_plug->Hmat[1][0] << "\t"
239 >                     << entry_plug->Hmat[2][0] << ";\t"
240 >              
241 >               << entry_plug->Hmat[0][1] << "\t"
242 >                     << entry_plug->Hmat[1][1] << "\t"
243 >                     << entry_plug->Hmat[2][1] << ";\t"
244  
245 <  outFile << currentTime << ";\t"
246 <          << entry_plug->Hmat[0][0] << "\t"
247 <          << entry_plug->Hmat[1][0] << "\t"
187 <          << entry_plug->Hmat[2][0] << ";\t"
245 >                     << entry_plug->Hmat[0][2] << "\t"
246 >                     << entry_plug->Hmat[1][2] << "\t"
247 >                     << entry_plug->Hmat[2][2] << ";";
248  
249 <          << entry_plug->Hmat[0][1] << "\t"
250 <          << entry_plug->Hmat[1][1] << "\t"
251 <          << entry_plug->Hmat[2][1] << ";\t"
252 <
193 <          << entry_plug->Hmat[0][2] << "\t"
194 <          << entry_plug->Hmat[1][2] << "\t"
195 <          << entry_plug->Hmat[2][2] << ";";
196 <  //write out additional parameters, such as chi and eta
197 <  outFile << entry_plug->the_integrator->getAdditionalParameters();
198 <  outFile << endl;
199 <
249 >    //write out additional parameters, such as chi and eta
250 >    *outFile[k] << entry_plug->the_integrator->getAdditionalParameters() << endl;
251 >  }
252 >  
253    for( i=0; i<nAtoms; i++ ){
254  
255      atoms[i]->getPos(pos);
# Line 232 | Line 285 | void DumpWriter::writeFrame( ofstream& outFile, double
285      else
286        strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
287  
288 <    outFile << writeLine;
288 >    for(k = 0; k < outFile.size(); k++)
289 >      *outFile[k] << writeLine;
290    }
291  
292   #else // is_mpi
# Line 261 | Line 315 | void DumpWriter::writeFrame( ofstream& outFile, double
315      nProc = mpiSim->getNumberProcessors();
316      potatoes = new int[nProc];
317  
318 +    //write out the comment lines
319      for (i = 0; i < nProc; i++)
320        potatoes[i] = 0;
321      
322 <    outFile << mpiSim->getTotAtoms() << "\n";
322 >      for(k = 0; k < outFile.size(); k++){
323 >        *outFile[k] << mpiSim->getTotAtoms() << "\n";
324  
325 <    outFile << currentTime << ";\t"
326 <            << entry_plug->Hmat[0][0] << "\t"
327 <            << entry_plug->Hmat[1][0] << "\t"
328 <            << entry_plug->Hmat[2][0] << ";\t"
325 >        *outFile[k] << currentTime << ";\t"
326 >                         << entry_plug->Hmat[0][0] << "\t"
327 >                         << entry_plug->Hmat[1][0] << "\t"
328 >                         << entry_plug->Hmat[2][0] << ";\t"
329  
330 <            << entry_plug->Hmat[0][1] << "\t"
331 <            << entry_plug->Hmat[1][1] << "\t"
332 <            << entry_plug->Hmat[2][1] << ";\t"
330 >                         << entry_plug->Hmat[0][1] << "\t"
331 >                         << entry_plug->Hmat[1][1] << "\t"
332 >                         << entry_plug->Hmat[2][1] << ";\t"
333  
334 <            << entry_plug->Hmat[0][2] << "\t"
335 <            << entry_plug->Hmat[1][2] << "\t"
336 <            << entry_plug->Hmat[2][2] << ";";
334 >                         << entry_plug->Hmat[0][2] << "\t"
335 >                         << entry_plug->Hmat[1][2] << "\t"
336 >                         << entry_plug->Hmat[2][2] << ";";
337 >  
338 >        *outFile[k] << entry_plug->the_integrator->getAdditionalParameters() << endl;
339 >    }
340  
282 –    outFile << entry_plug->the_integrator->getAdditionalParameters();
283 –    outFile << endl;
284 –    outFile.flush();
285 –    
341      currentIndex = 0;
342 +
343      for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) {
344        
345        // Get the Node number which has this atom;
# Line 328 | Line 384 | void DumpWriter::writeFrame( ofstream& outFile, double
384  
385        } else {
386          
387 <        haveError = 0;
388 <        which_atom = i;
387 >        haveError = 0;
388 >              which_atom = i;
389          
390          local_index = indexArray[currentIndex].first;        
391                  
# Line 337 | Line 393 | void DumpWriter::writeFrame( ofstream& outFile, double
393            
394            atomTypeString = atoms[local_index]->getType();
395  
396 <          atoms[local_index]->getPos(pos);
397 <          atoms[local_index]->getVel(vel);          
396 >                atoms[local_index]->getPos(pos);
397 >                atoms[local_index]->getVel(vel);          
398  
399            atomData6[0] = pos[0];
400            atomData6[1] = pos[1];
# Line 371 | Line 427 | void DumpWriter::writeFrame( ofstream& outFile, double
427            }
428            
429          } else {
430 <          sprintf(painCave.errMsg,
431 <                  "Atom %d not found on processor %d\n",
432 <                  i, worldRank );
433 <          haveError= 1;
434 <          simError();
435 <        }
430 >          sprintf(painCave.errMsg,
431 >                              "Atom %d not found on processor %d\n",
432 >                              i, worldRank );
433 >                haveError= 1;
434 >                simError();
435 >              }
436          
437 <        if(haveError) DieDieDie();
437 >        if(haveError) DieDieDie();
438          
439          currentIndex ++;
440        }
# Line 386 | Line 442 | void DumpWriter::writeFrame( ofstream& outFile, double
442        
443        if (!isDirectional) {
444          
445 <        sprintf( writeLine,
446 <                 "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
447 <                 atomTypeString,
448 <                 atomData6[0],
449 <                 atomData6[1],
450 <                 atomData6[2],
451 <                 atomData6[3],
452 <                 atomData6[4],
453 <                 atomData6[5]);
445 >        sprintf( writeLine,
446 >                             "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
447 >                             atomTypeString,
448 >                             atomData6[0],
449 >                             atomData6[1],
450 >                             atomData6[2],
451 >                             atomData6[3],
452 >                             atomData6[4],
453 >                             atomData6[5]);
454  
455 <        strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
455 >              strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
456          
457        } else {
458          
459 <        sprintf( writeLine,
460 <                 "%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",
461 <                 atomTypeString,
462 <                 atomData13[0],
463 <                 atomData13[1],
464 <                 atomData13[2],
465 <                 atomData13[3],
466 <                 atomData13[4],
467 <                 atomData13[5],
468 <                 atomData13[6],
469 <                 atomData13[7],
470 <                 atomData13[8],
471 <                 atomData13[9],
472 <                 atomData13[10],
473 <                 atomData13[11],
474 <                 atomData13[12]);
459 >              sprintf( writeLine,
460 >                             "%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",
461 >                             atomTypeString,
462 >                             atomData13[0],
463 >                             atomData13[1],
464 >                             atomData13[2],
465 >                             atomData13[3],
466 >                             atomData13[4],
467 >                             atomData13[5],
468 >                             atomData13[6],
469 >                             atomData13[7],
470 >                             atomData13[8],
471 >                             atomData13[9],
472 >                             atomData13[10],
473 >                             atomData13[11],
474 >                             atomData13[12]);
475          
476        }
477        
478 <      outFile << writeLine;
478 >      for(k = 0; k < outFile.size(); k++)
479 >        *outFile[k] << writeLine;
480      }
481      
482 <
483 <    outFile.flush();
482 >    for(k = 0; k < outFile.size(); k++)
483 >      outFile[k]->flush();
484 >    
485      sprintf( checkPointMsg,
486               "Sucessfully took a dump.\n");
487 +
488      MPIcheckPoint();        
489 +
490      delete[] potatoes;
491 +
492    } else {
493  
494      // worldRank != 0, so I'm a remote node.  
# Line 459 | Line 520 | void DumpWriter::writeFrame( ofstream& outFile, double
520          
521            atomTypeString = atoms[local_index]->getType();
522  
523 <          atoms[local_index]->getPos(pos);
524 <          atoms[local_index]->getVel(vel);
523 >                atoms[local_index]->getPos(pos);
524 >                atoms[local_index]->getVel(vel);
525  
526            atomData6[0] = pos[0];
527            atomData6[1] = pos[1];
# Line 486 | Line 547 | void DumpWriter::writeFrame( ofstream& outFile, double
547              atomData13[7] = q[1];
548              atomData13[8] = q[2];
549              atomData13[9] = q[3];
550 <
550 >  
551              atomData13[10] = dAtom->getJx();
552              atomData13[11] = dAtom->getJy();
553              atomData13[12] = dAtom->getJz();
554            }
555  
556          } else {
557 <          sprintf(painCave.errMsg,
558 <                  "Atom %d not found on processor %d\n",
559 <                  i, worldRank );
560 <          haveError= 1;
561 <          simError();
562 <        }
557 >                sprintf(painCave.errMsg,
558 >                              "Atom %d not found on processor %d\n",
559 >                              i, worldRank );
560 >                haveError= 1;
561 >                simError();
562 >              }
563  
564          strncpy(MPIatomTypeString, atomTypeString, MINIBUFFERSIZE);
565  
# Line 506 | Line 567 | void DumpWriter::writeFrame( ofstream& outFile, double
567          MPIatomTypeString[MINIBUFFERSIZE-1] = '\0';
568  
569          MPI_Send(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, 0,
570 <                 myPotato, MPI_COMM_WORLD);
570 >                             myPotato, MPI_COMM_WORLD);
571          
572          myPotato++;
573  
574          MPI_Send(&isDirectional, 1, MPI_INT, 0,
575 <                 myPotato, MPI_COMM_WORLD);
575 >                             myPotato, MPI_COMM_WORLD);
576          
577          myPotato++;
578          

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