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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 1097 by gezelter, Mon Apr 12 20:32:20 2004 UTC

# Line 1 | Line 1
1 + #define _LARGEFILE_SOURCE64
2   #define _FILE_OFFSET_BITS 64
3  
4   #include <string.h>
# Line 28 | Line 29 | DumpWriter::DumpWriter( SimInfo* the_entry_plug ){
29    if(worldRank == 0 ){
30   #endif // is_mpi
31  
31 –
32      dumpFile.open(entry_plug->sampleName, ios::out | ios::trunc );
33  
34      if( !dumpFile ){
# 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 94 | Line 92 | void DumpWriter::sortByGlobalIndex(){
92    
93    indexArray.clear();
94    
95 <  for(int i = 0; i < mpiSim->getMyNlocal();i++)
95 >  for(int i = 0; i < mpiSim->getMyNlocal();i++)
96      indexArray.push_back(make_pair(i, atoms[i]->getGlobalIndex()));
97    
98    sort(indexArray.begin(), indexArray.end(), indexSortingCriterion);    
99   }
100 +
101   #endif
102  
103   void DumpWriter::writeDump(double currentTime){
105 –  
106 – // write to eor file
107 –  writeFinal(currentTime);
104  
105 < //write to dump file
106 <  writeFrame(dumpFile, currentTime);
105 >  ofstream finalOut;
106 >  vector<ofstream*> fileStreams;
107 >
108 > #ifdef IS_MPI
109 >  if(worldRank == 0 ){
110 > #endif    
111 >    finalOut.open( entry_plug->finalName, ios::out | ios::trunc );
112 >    if( !finalOut ){
113 >      sprintf( painCave.errMsg,
114 >               "Could not open \"%s\" for final dump output.\n",
115 >               entry_plug->finalName );
116 >      painCave.isFatal = 1;
117 >      simError();
118 >    }
119 > #ifdef IS_MPI
120 >  }
121 > #endif // is_mpi
122 >
123 >  fileStreams.push_back(&finalOut);
124 >  fileStreams.push_back(&dumpFile);
125 >
126 >  writeFrame(fileStreams, currentTime);
127 >
128 > #ifdef IS_MPI
129 >  finalOut.close();
130 > #endif
131          
132   }
133  
134   void DumpWriter::writeFinal(double currentTime){
135  
136 <  ofstream finalOut;    
137 <  
138 <  //Open eor file
136 >  ofstream finalOut;
137 >  vector<ofstream*> fileStreams;
138 >
139   #ifdef IS_MPI
140    if(worldRank == 0 ){
141   #endif // is_mpi
142  
143      finalOut.open( entry_plug->finalName, ios::out | ios::trunc );
144 +
145      if( !finalOut ){
146        sprintf( painCave.errMsg,
147                 "Could not open \"%s\" for final dump output.\n",
# Line 128 | Line 149 | void DumpWriter::writeFinal(double currentTime){
149        painCave.isFatal = 1;
150        simError();
151      }
152 <    
152 >
153   #ifdef IS_MPI
154    }
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 –  }
155   #endif // is_mpi
156 +  
157 +  fileStreams.push_back(&finalOut);  
158 +  writeFrame(fileStreams, currentTime);
159  
160 + #ifdef IS_MPI
161 +  finalOut.close();
162 + #endif
163 +  
164   }
165  
166 < void DumpWriter::writeFrame( ofstream& outFile, double currentTime ){
166 > void DumpWriter::writeFrame( vector<ofstream*>& outFile, double currentTime ){
167  
168    const int BUFFERSIZE = 2000;
169    const int MINIBUFFERSIZE = 100;
170  
171 <  char tempBuffer[BUFFERSIZE];
171 >  char tempBuffer[BUFFERSIZE];  
172    char writeLine[BUFFERSIZE];
173  
174 <  int i;
174 >  int i, k;
175  
176   #ifdef IS_MPI
177    
178 +  /*********************************************************************
179 +   * Documentation?  You want DOCUMENTATION?
180 +   *
181 +   * Why all the potatoes below?  
182 +   *
183 +   * To make a long story short, the original version of DumpWriter
184 +   * worked in the most inefficient way possible.  Node 0 would
185 +   * poke each of the node for an individual atom's formatted data
186 +   * as node 0 worked its way down the global index. This was particularly
187 +   * inefficient since the method blocked all processors at every atom
188 +   * (and did it twice!).
189 +   *
190 +   * An intermediate version of DumpWriter could be described from Node
191 +   * zero's perspective as follows:
192 +   *
193 +   *  1) Have 100 of your friends stand in a circle.
194 +   *  2) When you say go, have all of them start tossing potatoes at
195 +   *     you (one at a time).
196 +   *  3) Catch the potatoes.
197 +   *
198 +   * It was an improvement, but MPI has buffers and caches that could
199 +   * best be described in this analogy as "potato nets", so there's no
200 +   * need to block the processors atom-by-atom.
201 +   *
202 +   * This new and improved DumpWriter works in an even more efficient
203 +   * way:
204 +   *
205 +   *  1) Have 100 of your friend stand in a circle.
206 +   *  2) When you say go, have them start tossing 5-pound bags of
207 +   *     potatoes at you.
208 +   *  3) Once you've caught a friend's bag of potatoes,
209 +   *     toss them a spud to let them know they can toss another bag.
210 +   *
211 +   * How's THAT for documentation?
212 +   *
213 +   *********************************************************************/
214 +
215    int *potatoes;
216    int myPotato;
217  
# Line 172 | Line 227 | void DumpWriter::writeFrame( ofstream& outFile, double
227    int nAtoms = entry_plug->n_atoms;
228   #endif //is_mpi
229  
230 <  double q[4];
230 >  double q[4], ji[3];
231    DirectionalAtom* dAtom;
232    Atom** atoms = entry_plug->atoms;
233    double pos[3], vel[3];
234  
235   #ifndef IS_MPI
236 +  
237 +  for(k = 0; k < outFile.size(); k++){
238 +    *outFile[k] << nAtoms << "\n";
239  
240 <  outFile << nAtoms << "\n";
240 >    *outFile[k] << currentTime << ";\t"
241 >               << entry_plug->Hmat[0][0] << "\t"
242 >                     << entry_plug->Hmat[1][0] << "\t"
243 >                     << entry_plug->Hmat[2][0] << ";\t"
244 >              
245 >               << entry_plug->Hmat[0][1] << "\t"
246 >                     << entry_plug->Hmat[1][1] << "\t"
247 >                     << entry_plug->Hmat[2][1] << ";\t"
248  
249 <  outFile << currentTime << ";\t"
250 <          << entry_plug->Hmat[0][0] << "\t"
251 <          << entry_plug->Hmat[1][0] << "\t"
187 <          << entry_plug->Hmat[2][0] << ";\t"
249 >                     << entry_plug->Hmat[0][2] << "\t"
250 >                     << entry_plug->Hmat[1][2] << "\t"
251 >                     << entry_plug->Hmat[2][2] << ";";
252  
253 <          << entry_plug->Hmat[0][1] << "\t"
254 <          << entry_plug->Hmat[1][1] << "\t"
255 <          << entry_plug->Hmat[2][1] << ";\t"
256 <
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 <
253 >    //write out additional parameters, such as chi and eta
254 >    *outFile[k] << entry_plug->the_integrator->getAdditionalParameters() << endl;
255 >  }
256 >  
257    for( i=0; i<nAtoms; i++ ){
258  
259      atoms[i]->getPos(pos);
# Line 217 | Line 274 | void DumpWriter::writeFrame( ofstream& outFile, double
274  
275        dAtom = (DirectionalAtom *)atoms[i];
276        dAtom->getQ( q );
277 +      dAtom->getJ( ji );
278  
279        sprintf( tempBuffer,
280                 "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
# Line 224 | Line 282 | void DumpWriter::writeFrame( ofstream& outFile, double
282                 q[1],
283                 q[2],
284                 q[3],
285 <               dAtom->getJx(),
286 <               dAtom->getJy(),
287 <               dAtom->getJz());
285 >               ji[0],
286 >               ji[1],
287 >               ji[2]);
288        strcat( writeLine, tempBuffer );
289      }
290      else
291        strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
292  
293 <    outFile << writeLine;
293 >    for(k = 0; k < outFile.size(); k++)
294 >      *outFile[k] << writeLine;
295    }
296  
297   #else // is_mpi
# Line 261 | Line 320 | void DumpWriter::writeFrame( ofstream& outFile, double
320      nProc = mpiSim->getNumberProcessors();
321      potatoes = new int[nProc];
322  
323 +    //write out the comment lines
324      for (i = 0; i < nProc; i++)
325        potatoes[i] = 0;
326      
327 <    outFile << mpiSim->getTotAtoms() << "\n";
327 >      for(k = 0; k < outFile.size(); k++){
328 >        *outFile[k] << mpiSim->getTotAtoms() << "\n";
329  
330 <    outFile << currentTime << ";\t"
331 <            << entry_plug->Hmat[0][0] << "\t"
332 <            << entry_plug->Hmat[1][0] << "\t"
333 <            << entry_plug->Hmat[2][0] << ";\t"
330 >        *outFile[k] << currentTime << ";\t"
331 >                         << entry_plug->Hmat[0][0] << "\t"
332 >                         << entry_plug->Hmat[1][0] << "\t"
333 >                         << entry_plug->Hmat[2][0] << ";\t"
334  
335 <            << entry_plug->Hmat[0][1] << "\t"
336 <            << entry_plug->Hmat[1][1] << "\t"
337 <            << entry_plug->Hmat[2][1] << ";\t"
335 >                         << entry_plug->Hmat[0][1] << "\t"
336 >                         << entry_plug->Hmat[1][1] << "\t"
337 >                         << entry_plug->Hmat[2][1] << ";\t"
338  
339 <            << entry_plug->Hmat[0][2] << "\t"
340 <            << entry_plug->Hmat[1][2] << "\t"
341 <            << entry_plug->Hmat[2][2] << ";";
339 >                         << entry_plug->Hmat[0][2] << "\t"
340 >                         << entry_plug->Hmat[1][2] << "\t"
341 >                         << entry_plug->Hmat[2][2] << ";";
342 >  
343 >        *outFile[k] << entry_plug->the_integrator->getAdditionalParameters() << endl;
344 >    }
345  
282 –    outFile << entry_plug->the_integrator->getAdditionalParameters();
283 –    outFile << endl;
284 –    outFile.flush();
285 –    
346      currentIndex = 0;
347 +
348      for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) {
349        
350        // Get the Node number which has this atom;
# Line 328 | Line 389 | void DumpWriter::writeFrame( ofstream& outFile, double
389  
390        } else {
391          
392 <        haveError = 0;
392 >        haveError = 0;
393          which_atom = i;
394          
395 <        local_index = indexArray[currentIndex].first;        
335 <                
336 <        if (which_atom == indexArray[currentIndex].second) {
395 >          local_index = indexArray[currentIndex].first;        
396            
397 <          atomTypeString = atoms[local_index]->getType();
398 <
397 >          if (which_atom == indexArray[currentIndex].second) {
398 >            
399 >            atomTypeString = atoms[local_index]->getType();
400 >            
401            atoms[local_index]->getPos(pos);
402            atoms[local_index]->getVel(vel);          
403 <
403 >          
404            atomData6[0] = pos[0];
405            atomData6[1] = pos[1];
406            atomData6[2] = pos[2];
# Line 356 | Line 417 | void DumpWriter::writeFrame( ofstream& outFile, double
417              
418              dAtom = (DirectionalAtom *)atoms[local_index];
419              dAtom->getQ( q );
420 +            dAtom->getJ( ji );
421  
422              for (int j = 0; j < 6 ; j++)
423                atomData13[j] = atomData6[j];            
# Line 365 | Line 427 | void DumpWriter::writeFrame( ofstream& outFile, double
427              atomData13[8] = q[2];
428              atomData13[9] = q[3];
429              
430 <            atomData13[10] = dAtom->getJx();
431 <            atomData13[11] = dAtom->getJy();
432 <            atomData13[12] = dAtom->getJz();
430 >            atomData13[10] = ji[0];
431 >            atomData13[11] = ji[1];
432 >            atomData13[12] = ji[2];
433            }
434            
435          } else {
436            sprintf(painCave.errMsg,
437 <                  "Atom %d not found on processor %d\n",
438 <                  i, worldRank );
437 >                  "Atom %d not found on processor %d, currentIndex = %d, local_index = %d\n",
438 >                  which_atom, worldRank, currentIndex, local_index );
439            haveError= 1;
440            simError();
441          }
442          
443 <        if(haveError) DieDieDie();
443 >        if(haveError) DieDieDie();
444          
445 <        currentIndex ++;
445 >        currentIndex++;
446        }
447        // If we've survived to here, format the line:
448        
449        if (!isDirectional) {
450          
451 <        sprintf( writeLine,
451 >        sprintf( writeLine,
452                   "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
453                   atomTypeString,
454                   atomData6[0],
# Line 395 | Line 457 | void DumpWriter::writeFrame( ofstream& outFile, double
457                   atomData6[3],
458                   atomData6[4],
459                   atomData6[5]);
460 <
460 >        
461          strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
462          
463        } else {
# Line 419 | Line 481 | void DumpWriter::writeFrame( ofstream& outFile, double
481          
482        }
483        
484 <      outFile << writeLine;
484 >      for(k = 0; k < outFile.size(); k++)
485 >        *outFile[k] << writeLine;
486      }
487      
488 <
489 <    outFile.flush();
488 >    for(k = 0; k < outFile.size(); k++)
489 >      outFile[k]->flush();
490 >    
491      sprintf( checkPointMsg,
492               "Sucessfully took a dump.\n");
493 +    
494      MPIcheckPoint();        
495 +    
496      delete[] potatoes;
497 +    
498    } else {
499  
500      // worldRank != 0, so I'm a remote node.  
# Line 444 | Line 511 | void DumpWriter::writeFrame( ofstream& outFile, double
511        if (AtomToProcMap[i] == worldRank) {
512  
513          if (myPotato + 3 >= MAXTAG) {
514 <
514 >          
515            // The potato was going to exceed the maximum value,
516            // so wrap this processor potato back to 0 (and block until
517            // node 0 says we can go:
518 <
518 >          
519            MPI_Recv(&myPotato, 1, MPI_INT, 0, 0, MPI_COMM_WORLD, &istatus);
520            
521          }
522          which_atom = i;
523 <        local_index = indexArray[currentIndex].first;        
523 >
524 >        local_index = indexArray[currentIndex].first;        
525                  
526 <        if (which_atom == indexArray[currentIndex].second) {
526 >        if (which_atom == indexArray[currentIndex].second) {
527          
528            atomTypeString = atoms[local_index]->getType();
529 <
529 >          
530            atoms[local_index]->getPos(pos);
531            atoms[local_index]->getVel(vel);
532 <
532 >          
533            atomData6[0] = pos[0];
534            atomData6[1] = pos[1];
535            atomData6[2] = pos[2];
# Line 478 | Line 546 | void DumpWriter::writeFrame( ofstream& outFile, double
546              
547              dAtom = (DirectionalAtom *)atoms[local_index];
548              dAtom->getQ( q );
549 +            dAtom->getJ( ji );
550              
551              for (int j = 0; j < 6 ; j++)
552                atomData13[j] = atomData6[j];
# Line 486 | Line 555 | void DumpWriter::writeFrame( ofstream& outFile, double
555              atomData13[7] = q[1];
556              atomData13[8] = q[2];
557              atomData13[9] = q[3];
558 <
559 <            atomData13[10] = dAtom->getJx();
560 <            atomData13[11] = dAtom->getJy();
561 <            atomData13[12] = dAtom->getJz();
558 >  
559 >            atomData13[10] = ji[0];
560 >            atomData13[11] = ji[1];
561 >            atomData13[12] = ji[2];
562            }
563  
564          } else {
565            sprintf(painCave.errMsg,
566 <                  "Atom %d not found on processor %d\n",
567 <                  i, worldRank );
566 >                  "Atom %d not found on processor %d, currentIndex = %d, local_index = %d\n",
567 >                  which_atom, worldRank, currentIndex, local_index );
568            haveError= 1;
569            simError();
570          }
571 <
571 >        
572          strncpy(MPIatomTypeString, atomTypeString, MINIBUFFERSIZE);
573  
574          // null terminate the string before sending (just in case):
575          MPIatomTypeString[MINIBUFFERSIZE-1] = '\0';
576  
577          MPI_Send(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, 0,
578 <                 myPotato, MPI_COMM_WORLD);
578 >                             myPotato, MPI_COMM_WORLD);
579          
580          myPotato++;
581  
582          MPI_Send(&isDirectional, 1, MPI_INT, 0,
583 <                 myPotato, MPI_COMM_WORLD);
583 >                             myPotato, MPI_COMM_WORLD);
584          
585          myPotato++;
586          

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