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root/group/trunk/OOPSE/libmdtools/DumpWriter.cpp
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Comparing trunk/OOPSE/libmdtools/DumpWriter.cpp (file contents):
Revision 916 by gezelter, Fri Jan 9 20:29:32 2004 UTC vs.
Revision 1108 by tim, Wed Apr 14 15:37:41 2004 UTC

# Line 1 | Line 1
1 + #define _LARGEFILE_SOURCE64
2   #define _FILE_OFFSET_BITS 64
3  
4   #include <string.h>
5   #include <iostream>
6   #include <fstream>
7 + #include <algorithm>
8 + #include <utility>
9  
10   #ifdef IS_MPI
11   #include <mpi.h>
# Line 26 | Line 29 | DumpWriter::DumpWriter( SimInfo* the_entry_plug ){
29    if(worldRank == 0 ){
30   #endif // is_mpi
31  
32 <    strcpy( outName, entry_plug->sampleName );
32 >    dumpFile.open(entry_plug->sampleName, ios::out | ios::trunc );
33  
34 <    outFile.open(outName, ios::out | ios::trunc );
34 >    if( !dumpFile ){
35  
33 –    if( !outFile ){
34 –
36        sprintf( painCave.errMsg,
37                 "Could not open \"%s\" for dump output.\n",
38 <               outName);
38 >               entry_plug->sampleName);
39        painCave.isFatal = 1;
40        simError();
41      }
42  
42 –    //outFile.setf( ios::scientific );
43 –
43   #ifdef IS_MPI
44    }
45  
46 +  //sort the local atoms by global index
47 +  sortByGlobalIndex();
48 +  
49    sprintf( checkPointMsg,
50             "Sucessfully opened output file for dumping.\n");
51    MPIcheckPoint();
# Line 56 | Line 58 | DumpWriter::~DumpWriter( ){
58    if(worldRank == 0 ){
59   #endif // is_mpi
60  
61 <    outFile.close();
61 >    dumpFile.close();
62  
63   #ifdef IS_MPI
64    }
65   #endif // is_mpi
66   }
67  
68 < void DumpWriter::writeDump( double currentTime ){
68 > #ifdef IS_MPI
69  
70 + /**
71 + * A hook function to load balancing
72 + */
73 +
74 + void DumpWriter::update(){
75 +  sortByGlobalIndex();          
76 + }
77 +  
78 + /**
79 + * Auxiliary sorting function
80 + */
81 +
82 + bool indexSortingCriterion(const pair<int, int>& p1, const pair<int, int>& p2){
83 +  return p1.second < p2.second;
84 + }
85 +
86 + /**
87 + * Sorting the local index by global index
88 + */
89 +
90 + void DumpWriter::sortByGlobalIndex(){
91 +  Molecule* mols = entry_plug->molecules;  
92 +  indexArray.clear();
93 +  
94 +  for(int i = 0; i < mpiSim->getMyNlocal();i++)
95 +    indexArray.push_back(make_pair(i, mols[i].getGlobalIndex()));
96 +  
97 +  sort(indexArray.begin(), indexArray.end(), indexSortingCriterion);    
98 + }
99 +
100 + #endif
101 +
102 + void DumpWriter::writeDump(double currentTime){
103 +
104 +  ofstream finalOut;
105 +  vector<ofstream*> fileStreams;
106 +
107 + #ifdef IS_MPI
108 +  if(worldRank == 0 ){
109 + #endif    
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 + #ifdef IS_MPI
119 +  }
120 + #endif // is_mpi
121 +
122 +  fileStreams.push_back(&finalOut);
123 +  fileStreams.push_back(&dumpFile);
124 +
125 +  writeFrame(fileStreams, currentTime);
126 +
127 + #ifdef IS_MPI
128 +  finalOut.close();
129 + #endif
130 +        
131 + }
132 +
133 + void DumpWriter::writeFinal(double currentTime){
134 +
135 +  ofstream finalOut;
136 +  vector<ofstream*> fileStreams;
137 +
138 + #ifdef IS_MPI
139 +  if(worldRank == 0 ){
140 + #endif // is_mpi
141 +
142 +    finalOut.open( entry_plug->finalName, ios::out | ios::trunc );
143 +
144 +    if( !finalOut ){
145 +      sprintf( painCave.errMsg,
146 +               "Could not open \"%s\" for final dump output.\n",
147 +               entry_plug->finalName );
148 +      painCave.isFatal = 1;
149 +      simError();
150 +    }
151 +
152 + #ifdef IS_MPI
153 +  }
154 + #endif // is_mpi
155 +  
156 +  fileStreams.push_back(&finalOut);  
157 +  writeFrame(fileStreams, currentTime);
158 +
159 + #ifdef IS_MPI
160 +  finalOut.close();
161 + #endif
162 +  
163 + }
164 +
165 + void DumpWriter::writeFrame( vector<ofstream*>& outFile, double currentTime ){
166 +
167    const int BUFFERSIZE = 2000;
168    const int MINIBUFFERSIZE = 100;
169  
170 <  char tempBuffer[BUFFERSIZE];
170 >  char tempBuffer[BUFFERSIZE];  
171    char writeLine[BUFFERSIZE];
172  
173 <  int i;
173 >  int i, k;
174  
175   #ifdef IS_MPI
176    
177 +  /*********************************************************************
178 +   * Documentation?  You want DOCUMENTATION?
179 +   *
180 +   * Why all the potatoes below?  
181 +   *
182 +   * To make a long story short, the original version of DumpWriter
183 +   * worked in the most inefficient way possible.  Node 0 would
184 +   * poke each of the node for an individual atom's formatted data
185 +   * as node 0 worked its way down the global index. This was particularly
186 +   * inefficient since the method blocked all processors at every atom
187 +   * (and did it twice!).
188 +   *
189 +   * An intermediate version of DumpWriter could be described from Node
190 +   * zero's perspective as follows:
191 +   *
192 +   *  1) Have 100 of your friends stand in a circle.
193 +   *  2) When you say go, have all of them start tossing potatoes at
194 +   *     you (one at a time).
195 +   *  3) Catch the potatoes.
196 +   *
197 +   * It was an improvement, but MPI has buffers and caches that could
198 +   * best be described in this analogy as "potato nets", so there's no
199 +   * need to block the processors atom-by-atom.
200 +   *
201 +   * This new and improved DumpWriter works in an even more efficient
202 +   * way:
203 +   *
204 +   *  1) Have 100 of your friend stand in a circle.
205 +   *  2) When you say go, have them start tossing 5-pound bags of
206 +   *     potatoes at you.
207 +   *  3) Once you've caught a friend's bag of potatoes,
208 +   *     toss them a spud to let them know they can toss another bag.
209 +   *
210 +   * How's THAT for documentation?
211 +   *
212 +   *********************************************************************/
213 +
214    int *potatoes;
215    int myPotato;
216  
217    int nProc;
218 <  int j, which_node, done, which_atom, local_index;
218 >  int j, which_node, done, which_atom, local_index, currentIndex;
219    double atomData6[6];
220    double atomData13[13];
221    int isDirectional;
222    char* atomTypeString;
223    char MPIatomTypeString[MINIBUFFERSIZE];
224 <
89 < #else //is_mpi
90 <  int nAtoms = entry_plug->n_atoms;
224 >  int nObjects;
225   #endif //is_mpi
226  
227 <  double q[4];
227 >  double q[4], ji[3];
228    DirectionalAtom* dAtom;
95 –  Atom** atoms = entry_plug->atoms;
229    double pos[3], vel[3];
230 <
231 <  // write current frame to the eor file
232 <
233 <  this->writeFinal( currentTime );
234 <
230 >  int nTotObjects;
231 >  StuntDouble* sd;
232 >  char* molName;
233 >  vector<StuntDouble*> integrableObjects;
234 >  vector<StuntDouble*>::iterator iter;
235 >  nTotObjects = entry_plug->getTotIntegrableObjects();
236   #ifndef IS_MPI
237 +  
238 +  for(k = 0; k < outFile.size(); k++){
239 +    *outFile[k] << nTotObjects << "\n";
240  
241 <  outFile << nAtoms << "\n";
241 >    *outFile[k] << currentTime << ";\t"
242 >               << entry_plug->Hmat[0][0] << "\t"
243 >                     << entry_plug->Hmat[1][0] << "\t"
244 >                     << entry_plug->Hmat[2][0] << ";\t"
245 >              
246 >               << entry_plug->Hmat[0][1] << "\t"
247 >                     << entry_plug->Hmat[1][1] << "\t"
248 >                     << entry_plug->Hmat[2][1] << ";\t"
249  
250 <  outFile << currentTime << ";\t"
251 <          << entry_plug->Hmat[0][0] << "\t"
252 <          << entry_plug->Hmat[1][0] << "\t"
109 <          << entry_plug->Hmat[2][0] << ";\t"
250 >                     << entry_plug->Hmat[0][2] << "\t"
251 >                     << entry_plug->Hmat[1][2] << "\t"
252 >                     << entry_plug->Hmat[2][2] << ";";
253  
254 <          << entry_plug->Hmat[0][1] << "\t"
255 <          << entry_plug->Hmat[1][1] << "\t"
256 <          << entry_plug->Hmat[2][1] << ";\t"
254 >    //write out additional parameters, such as chi and eta
255 >    *outFile[k] << entry_plug->the_integrator->getAdditionalParameters() << endl;
256 >  }
257 >  
258 >  for( i=0; i< entry_plug->n_mol; i++ ){
259  
260 <          << entry_plug->Hmat[0][2] << "\t"
261 <          << entry_plug->Hmat[1][2] << "\t"
262 <          << entry_plug->Hmat[2][2] << ";";
263 <  //write out additional parameters, such as chi and eta
264 <  outFile << entry_plug->the_integrator->getAdditionalParameters();
265 <  outFile << endl;
260 >    integrableObjects = entry_plug->molecules[i].getIntegrableObjects();
261 >    molName = (entry_plug->compStamps[entry_plug->molecules[i].getStampID()])->getID();
262 >    
263 >    for( iter = integrableObjects.begin();iter !=  integrableObjects.end(); ++iter){
264 >      sd = *iter;
265 >      sd->getPos(pos);
266 >      sd->getVel(vel);
267  
268 <  for( i=0; i<nAtoms; i++ ){
268 >      sprintf( tempBuffer,
269 >             "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
270 >             sd->getType(),
271 >             pos[0],
272 >             pos[1],
273 >             pos[2],
274 >             vel[0],
275 >             vel[1],
276 >             vel[2]);
277 >      strcpy( writeLine, tempBuffer );
278  
279 <    atoms[i]->getPos(pos);
125 <    atoms[i]->getVel(vel);
279 >      if( sd->isDirectional() ){
280  
281 <    sprintf( tempBuffer,
282 <             "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
129 <             atoms[i]->getType(),
130 <             pos[0],
131 <             pos[1],
132 <             pos[2],
133 <             vel[0],
134 <             vel[1],
135 <             vel[2]);
136 <    strcpy( writeLine, tempBuffer );
281 >        sd->getQ( q );
282 >        sd->getJ( ji );
283  
284 <    if( atoms[i]->isDirectional() ){
285 <
286 <      dAtom = (DirectionalAtom *)atoms[i];
287 <      dAtom->getQ( q );
288 <
289 <      sprintf( tempBuffer,
290 <               "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
291 <               q[0],
292 <               q[1],
293 <               q[2],
294 <               q[3],
295 <               dAtom->getJx(),
296 <               dAtom->getJy(),
151 <               dAtom->getJz());
152 <      strcat( writeLine, tempBuffer );
284 >        sprintf( tempBuffer,
285 >               "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
286 >               q[0],
287 >               q[1],
288 >               q[2],
289 >               q[3],
290 >                 ji[0],
291 >                 ji[1],
292 >                 ji[2]);
293 >        strcat( writeLine, tempBuffer );
294 >      }
295 >      else
296 >        strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
297      }
154 –    else
155 –      strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
298  
299 <    outFile << writeLine;
300 <  }
301 <  outFile.flush();
299 >    
300 >    for(k = 0; k < outFile.size(); k++)
301 >      *outFile[k] << writeLine;
302 > }
303  
304   #else // is_mpi
305  
306    /* code to find maximum tag value */
307 +  
308    int *tagub, flag, MAXTAG;
309    MPI_Attr_get(MPI_COMM_WORLD, MPI_TAG_UB, &tagub, &flag);
310    if (flag) {
# Line 172 | Line 316 | void DumpWriter::writeDump( double currentTime ){
316    int haveError;
317  
318    MPI_Status istatus;
319 <  int *AtomToProcMap = mpiSim->getAtomToProcMap();
319 >  int nCurObj;
320 >  int *MolToProcMap = mpiSim->getMolToProcMap();
321  
322    // write out header and node 0's coordinates
323  
# Line 183 | Line 328 | void DumpWriter::writeDump( double currentTime ){
328      nProc = mpiSim->getNumberProcessors();
329      potatoes = new int[nProc];
330  
331 +    //write out the comment lines
332      for (i = 0; i < nProc; i++)
333        potatoes[i] = 0;
334      
335 <    outFile << mpiSim->getTotAtoms() << "\n";
335 >      for(k = 0; k < outFile.size(); k++){
336 >        *outFile[k] << nTotObjects << "\n";
337  
338 <    outFile << currentTime << ";\t"
339 <            << entry_plug->Hmat[0][0] << "\t"
340 <            << entry_plug->Hmat[1][0] << "\t"
341 <            << entry_plug->Hmat[2][0] << ";\t"
338 >        *outFile[k] << currentTime << ";\t"
339 >                         << entry_plug->Hmat[0][0] << "\t"
340 >                         << entry_plug->Hmat[1][0] << "\t"
341 >                         << entry_plug->Hmat[2][0] << ";\t"
342  
343 <            << entry_plug->Hmat[0][1] << "\t"
344 <            << entry_plug->Hmat[1][1] << "\t"
345 <            << entry_plug->Hmat[2][1] << ";\t"
343 >                         << entry_plug->Hmat[0][1] << "\t"
344 >                         << entry_plug->Hmat[1][1] << "\t"
345 >                         << entry_plug->Hmat[2][1] << ";\t"
346  
347 <            << entry_plug->Hmat[0][2] << "\t"
348 <            << entry_plug->Hmat[1][2] << "\t"
349 <            << entry_plug->Hmat[2][2] << ";";
347 >                         << entry_plug->Hmat[0][2] << "\t"
348 >                         << entry_plug->Hmat[1][2] << "\t"
349 >                         << entry_plug->Hmat[2][2] << ";";
350 >  
351 >        *outFile[k] << entry_plug->the_integrator->getAdditionalParameters() << endl;
352 >    }
353  
354 <    outFile << entry_plug->the_integrator->getAdditionalParameters();
205 <    outFile << endl;
206 <    outFile.flush();
354 >    currentIndex = 0;
355  
356 <    for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) {
356 >    for (i = 0 ; i < mpiSim->getTotNmol(); i++ ) {
357        
358        // Get the Node number which has this atom;
359        
360 <      which_node = AtomToProcMap[i];
360 >      which_node = MolToProcMap[i];
361        
362        if (which_node != 0) {
363 <
364 <        if (potatoes[which_node] + 3 >= MAXTAG) {
363 >        
364 >        if (potatoes[which_node] + 1 >= MAXTAG) {
365            // The potato was going to exceed the maximum value,
366            // so wrap this processor potato back to 0:        
367  
# Line 223 | Line 371 | void DumpWriter::writeDump( double currentTime ){
371          }
372  
373          myPotato = potatoes[which_node];        
374 <        
375 <        MPI_Recv(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, which_node,
374 >
375 >        //recieve the number of integrableObject in current molecule
376 >        MPI_Recv(&nCurObj, 1, MPI_INT, which_node,
377                   myPotato, MPI_COMM_WORLD, &istatus);
378          
379 <        strncpy(atomTypeString, MPIatomTypeString, MINIBUFFERSIZE);
231 <        
232 <        // Null terminate the atomTypeString just in case:
379 >        for(int l = 0; l < nCurObj; l++){
380  
381 <        atomTypeString[strlen(atomTypeString) - 1] = '\0';
381 >          if (potatoes[which_node] + 3 >= MAXTAG) {
382 >            // The potato was going to exceed the maximum value,
383 >            // so wrap this processor potato back to 0:        
384  
385 <        myPotato++;
385 >            potatoes[which_node] = 0;          
386 >            MPI_Send(0, 1, MPI_INT, which_node, 0, MPI_COMM_WORLD);
387 >            
388 >          }
389  
390 <        MPI_Recv(&isDirectional, 1, MPI_INT, which_node,
391 <                 myPotato, MPI_COMM_WORLD, &istatus);
390 >          MPI_Recv(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, which_node,
391 >          myPotato, MPI_COMM_WORLD, &istatus);
392 >
393 >          atomTypeString = MPIatomTypeString;
394 >
395 >          myPotato++;
396 >
397 >          MPI_Recv(&isDirectional, 1, MPI_INT, which_node,
398 >          myPotato, MPI_COMM_WORLD, &istatus);
399                
400 <        myPotato++;
400 >          myPotato++;
401  
402 <        if (isDirectional) {          
402 >          if (isDirectional) {          
403            MPI_Recv(atomData13, 13, MPI_DOUBLE, which_node,
404                     myPotato, MPI_COMM_WORLD, &istatus);
405 <        } else {
405 >          } else {
406            MPI_Recv(atomData6, 6, MPI_DOUBLE, which_node,
407                     myPotato, MPI_COMM_WORLD, &istatus);          
408 +          }
409 +
410 +          myPotato++;
411          }
250 –        
251 –        myPotato++;
412          potatoes[which_node] = myPotato;
413  
414        } else {
415          
416 <        haveError = 0;
257 <        which_atom = i;
258 <        local_index=-1;
416 >        haveError = 0;
417          
418 <        for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) {
261 <          if (atoms[j]->getGlobalIndex() == which_atom) local_index = j;
262 <        }
263 <        
264 <        if (local_index != -1) {
265 <          
266 <          atomTypeString = atoms[local_index]->getType();
418 >            local_index = indexArray[currentIndex].first;        
419  
420 <          atoms[local_index]->getPos(pos);
269 <          atoms[local_index]->getVel(vel);          
420 >        integrableObjects = (entry_plug->molecules[local_index]).getIntegrableObjects();
421  
422 <          atomData6[0] = pos[0];
423 <          atomData6[1] = pos[1];
424 <          atomData6[2] = pos[2];
422 >        for(iter= integrableObjects.begin(); iter != integrableObjects.end(); ++iter){    
423 >                sd = *iter;
424 >            atomTypeString = sd->getType();
425 >            
426 >            sd->getPos(pos);
427 >            sd->getVel(vel);          
428 >          
429 >            atomData6[0] = pos[0];
430 >            atomData6[1] = pos[1];
431 >            atomData6[2] = pos[2];
432  
433 <          atomData6[3] = vel[0];
434 <          atomData6[4] = vel[1];
435 <          atomData6[5] = vel[2];
436 <          
437 <          isDirectional = 0;
433 >            atomData6[3] = vel[0];
434 >            atomData6[4] = vel[1];
435 >            atomData6[5] = vel[2];
436 >              
437 >            isDirectional = 0;
438  
439 <          if( atoms[local_index]->isDirectional() ){
439 >            if( sd->isDirectional() ){
440  
441 <            isDirectional = 1;
442 <            
443 <            dAtom = (DirectionalAtom *)atoms[local_index];
444 <            dAtom->getQ( q );
441 >              isDirectional = 1;
442 >                
443 >              sd->getQ( q );
444 >              sd->getJ( ji );
445  
446 <            for (int j = 0; j < 6 ; j++)
447 <              atomData13[j] = atomData6[j];            
446 >              for (int j = 0; j < 6 ; j++)
447 >                atomData13[j] = atomData6[j];            
448 >              
449 >              atomData13[6] = q[0];
450 >              atomData13[7] = q[1];
451 >              atomData13[8] = q[2];
452 >              atomData13[9] = q[3];
453 >              
454 >              atomData13[10] = ji[0];
455 >              atomData13[11] = ji[1];
456 >              atomData13[12] = ji[2];
457 >            }
458              
291 –            atomData13[6] = q[0];
292 –            atomData13[7] = q[1];
293 –            atomData13[8] = q[2];
294 –            atomData13[9] = q[3];
295 –            
296 –            atomData13[10] = dAtom->getJx();
297 –            atomData13[11] = dAtom->getJy();
298 –            atomData13[12] = dAtom->getJz();
299 –          }
300 –          
301 –        } else {
302 –          sprintf(painCave.errMsg,
303 –                  "Atom %d not found on processor %d\n",
304 –                  i, worldRank );
305 –          haveError= 1;
306 –          simError();
307 –        }
308 –        
309 –        if(haveError) DieDieDie();
310 –        
311 –        // If we've survived to here, format the line:
312 –        
313 –        if (!isDirectional) {
314 –
315 –          sprintf( tempBuffer,
316 –                   "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
317 –                   atomTypeString,
318 –                   atomData6[0],
319 –                   atomData6[1],
320 –                   atomData6[2],
321 –                   atomData6[3],
322 –                   atomData6[4],
323 –                   atomData6[5]);
324 –          
325 –          strcpy( writeLine, tempBuffer );
326 –          strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
327 –
328 –        } else {
329 –          
330 –          sprintf( tempBuffer,
331 –                   "%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",
332 –                   atomTypeString,
333 –                   atomData13[0],
334 –                   atomData13[1],
335 –                   atomData13[2],
336 –                   atomData13[3],
337 –                   atomData13[4],
338 –                   atomData13[5],
339 –                   atomData13[6],
340 –                   atomData13[7],
341 –                   atomData13[8],
342 –                   atomData13[9],
343 –                   atomData13[10],
344 –                   atomData13[11],
345 –                   atomData13[12]);
346 –          
347 –          strcat( writeLine, tempBuffer );
348 –          
459          }
460          
461 <        outFile << writeLine;
352 <        outFile.flush();
461 >      currentIndex++;
462        }
463 +      // If we've survived to here, format the line:
464 +      
465 +      if (!isDirectional) {
466 +        
467 +        sprintf( writeLine,
468 +                 "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
469 +                 atomTypeString,
470 +                 atomData6[0],
471 +                 atomData6[1],
472 +                 atomData6[2],
473 +                 atomData6[3],
474 +                 atomData6[4],
475 +                 atomData6[5]);
476 +        
477 +        strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
478 +        
479 +      } else {
480 +        
481 +        sprintf( writeLine,
482 +                 "%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",
483 +                 atomTypeString,
484 +                 atomData13[0],
485 +                 atomData13[1],
486 +                 atomData13[2],
487 +                 atomData13[3],
488 +                 atomData13[4],
489 +                 atomData13[5],
490 +                 atomData13[6],
491 +                 atomData13[7],
492 +                 atomData13[8],
493 +                 atomData13[9],
494 +                 atomData13[10],
495 +                 atomData13[11],
496 +                 atomData13[12]);
497 +        
498 +      }
499 +      
500 +      for(k = 0; k < outFile.size(); k++)
501 +        *outFile[k] << writeLine;
502      }
503 <
504 <    outFile.flush();
503 >    
504 >    for(k = 0; k < outFile.size(); k++)
505 >      outFile[k]->flush();
506 >    
507      sprintf( checkPointMsg,
508               "Sucessfully took a dump.\n");
509 +    
510      MPIcheckPoint();        
511      
512 +    delete[] potatoes;
513 +    
514    } else {
515  
516      // worldRank != 0, so I'm a remote node.  
# Line 365 | Line 518 | void DumpWriter::writeDump( double currentTime ){
518      // Set my magic potato to 0:
519  
520      myPotato = 0;
521 +    currentIndex = 0;
522      
523 <    for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) {
523 >    for (i = 0 ; i < mpiSim->getTotNmol(); i++ ) {
524        
525 <      // Am I the node which has this atom?
525 >      // Am I the node which has this integrableObject?
526        
527 <      if (AtomToProcMap[i] == worldRank) {
527 >      if (MolToProcMap[i] == worldRank) {
528  
375 –        if (myPotato + 3 >= MAXTAG) {
529  
530 +        if (myPotato + 1 >= MAXTAG) {
531 +          
532            // The potato was going to exceed the maximum value,
533            // so wrap this processor potato back to 0 (and block until
534            // node 0 says we can go:
535 <
535 >          
536            MPI_Recv(&myPotato, 1, MPI_INT, 0, 0, MPI_COMM_WORLD, &istatus);
537            
538          }
539  
540 <        local_index=-1;
541 <        for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) {
542 <          if (atoms[j]->getGlobalIndex() == which_atom) local_index = j;
543 <        }
544 <        if (local_index != -1) {
545 <        
546 <          atomTypeString = atoms[local_index]->getType();
540 >          local_index = indexArray[currentIndex].first;        
541 >          integrableObjects = entry_plug->molecules[local_index].getIntegrableObjects();
542 >          
543 >          nCurObj = integrableObjects.size();
544 >                      
545 >          MPI_Send(&nCurObj, 1, MPI_INT, 0,
546 >                             myPotato, MPI_COMM_WORLD);
547  
548 <          atoms[local_index]->getPos(pos);
394 <          atoms[local_index]->getVel(vel);
395 <
396 <          atomData6[0] = pos[0];
397 <          atomData6[1] = pos[1];
398 <          atomData6[2] = pos[2];
548 >          for( iter = integrableObjects.begin(); iter  != integrableObjects.end(); iter++){
549  
550 <          atomData6[3] = vel[0];
551 <          atomData6[4] = vel[1];
552 <          atomData6[5] = vel[2];
553 <          
554 <          isDirectional = 0;
555 <
556 <          if( atoms[local_index]->isDirectional() ){
557 <
558 <            isDirectional = 1;
550 >            if (myPotato + 3 >= MAXTAG) {
551 >          
552 >              // The potato was going to exceed the maximum value,
553 >              // so wrap this processor potato back to 0 (and block until
554 >              // node 0 says we can go:
555 >          
556 >              MPI_Recv(&myPotato, 1, MPI_INT, 0, 0, MPI_COMM_WORLD, &istatus);
557 >              
558 >            }
559              
560 <            dAtom = (DirectionalAtom *)atoms[local_index];
411 <            dAtom->getQ( q );
560 >            sd = *iter;
561              
562 <            for (int j = 0; j < 6 ; j++)
414 <              atomData13[j] = atomData6[j];
415 <            
416 <            atomData13[6] = q[0];
417 <            atomData13[7] = q[1];
418 <            atomData13[8] = q[2];
419 <            atomData13[9] = q[3];
562 >            atomTypeString = sd->getType();
563  
564 <            atomData13[10] = dAtom->getJx();
565 <            atomData13[11] = dAtom->getJy();
423 <            atomData13[12] = dAtom->getJz();
424 <          }
564 >            sd->getPos(pos);
565 >            sd->getVel(vel);
566  
567 <        } else {
568 <          sprintf(painCave.errMsg,
569 <                  "Atom %d not found on processor %d\n",
429 <                  i, worldRank );
430 <          haveError= 1;
431 <          simError();
432 <        }
567 >            atomData6[0] = pos[0];
568 >            atomData6[1] = pos[1];
569 >            atomData6[2] = pos[2];
570  
571 <        strncpy(MPIatomTypeString, atomTypeString, MINIBUFFERSIZE);
571 >            atomData6[3] = vel[0];
572 >            atomData6[4] = vel[1];
573 >            atomData6[5] = vel[2];
574 >              
575 >            isDirectional = 0;
576  
577 <        // null terminate the string before sending (just in case):
437 <        MPIatomTypeString[MINIBUFFERSIZE-1] = '\0';
577 >            if( sd->isDirectional() ){
578  
579 <        MPI_Send(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, 0,
580 <                 myPotato, MPI_COMM_WORLD);
581 <        
582 <        myPotato++;
579 >                isDirectional = 1;
580 >                
581 >                sd->getQ( q );
582 >                sd->getJ( ji );
583 >                
584 >                for (int j = 0; j < 6 ; j++)
585 >                  atomData13[j] = atomData6[j];
586 >                
587 >                atomData13[6] = q[0];
588 >                atomData13[7] = q[1];
589 >                atomData13[8] = q[2];
590 >                atomData13[9] = q[3];
591 >      
592 >                atomData13[10] = ji[0];
593 >                atomData13[11] = ji[1];
594 >                atomData13[12] = ji[2];
595 >              }
596  
597 <        MPI_Send(&isDirectional, 1, MPI_INT, 0,
598 <                 myPotato, MPI_COMM_WORLD);
446 <        
447 <        myPotato++;
448 <        
449 <        if (isDirectional) {
597 >            
598 >            strncpy(MPIatomTypeString, atomTypeString, MINIBUFFERSIZE);
599  
600 <          MPI_Send(atomData13, 13, MPI_DOUBLE, 0,
601 <                   myPotato, MPI_COMM_WORLD);
453 <          
454 <        } else {
600 >            // null terminate the string before sending (just in case):
601 >            MPIatomTypeString[MINIBUFFERSIZE-1] = '\0';
602  
603 <          MPI_Send(atomData6, 6, MPI_DOUBLE, 0,
604 <                   myPotato, MPI_COMM_WORLD);
605 <        }
603 >            MPI_Send(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, 0,
604 >                             myPotato, MPI_COMM_WORLD);
605 >            
606 >            myPotato++;
607  
608 <        myPotato++;      
609 <      }
610 <    }
608 >            MPI_Send(&isDirectional, 1, MPI_INT, 0,
609 >                             myPotato, MPI_COMM_WORLD);
610 >            
611 >            myPotato++;
612 >            
613 >            if (isDirectional) {
614  
615 <    sprintf( checkPointMsg,
616 <             "Sucessfully took a dump.\n");
617 <    MPIcheckPoint();        
618 <    
468 <  }
469 <  
470 < #endif // is_mpi
471 < }
615 >              MPI_Send(atomData13, 13, MPI_DOUBLE, 0,
616 >                       myPotato, MPI_COMM_WORLD);
617 >              
618 >            } else {
619  
620 < void DumpWriter::writeFinal(double finalTime){
620 >              MPI_Send(atomData6, 6, MPI_DOUBLE, 0,
621 >                       myPotato, MPI_COMM_WORLD);
622 >            }
623  
624 <  char finalName[500];
476 <  ofstream finalOut;
624 >            myPotato++;  
625  
626 <  const int BUFFERSIZE = 2000;
479 <  const int MINIBUFFERSIZE = 100;
480 <  char tempBuffer[BUFFERSIZE];
481 <  char writeLine[BUFFERSIZE];
626 >          }
627  
628 <  double q[4];
484 <  DirectionalAtom* dAtom;
485 <  Atom** atoms = entry_plug->atoms;
486 <  int i;
487 < #ifdef IS_MPI
488 <  
489 <  int *potatoes;
490 <  int myPotato;
491 <
492 <  int nProc;
493 <  int j, which_node, done, which_atom, local_index;
494 <  double atomData6[6];
495 <  double atomData13[13];
496 <  int isDirectional;
497 <  char* atomTypeString;
498 <  char MPIatomTypeString[MINIBUFFERSIZE];
499 <
500 < #else //is_mpi
501 <  int nAtoms = entry_plug->n_atoms;
502 < #endif //is_mpi
503 <
504 <  double pos[3], vel[3];
505 <
506 < #ifdef IS_MPI
507 <  if(worldRank == 0 ){
508 < #endif // is_mpi
509 <
510 <    strcpy( finalName, entry_plug->finalName );
511 <
512 <    finalOut.open( finalName, ios::out | ios::trunc );
513 <    if( !finalOut ){
514 <      sprintf( painCave.errMsg,
515 <               "Could not open \"%s\" for final dump output.\n",
516 <               finalName );
517 <      painCave.isFatal = 1;
518 <      simError();
519 <    }
520 <
521 <    // finalOut.setf( ios::scientific );
522 <
523 < #ifdef IS_MPI
524 <  }
525 <
526 <  sprintf(checkPointMsg,"Opened file for final configuration\n");
527 <  MPIcheckPoint();
528 <
529 < #endif //is_mpi
530 <
531 <
532 < #ifndef IS_MPI
533 <
534 <  finalOut << nAtoms << "\n";
535 <
536 <  finalOut << finalTime << ";\t"
537 <           << entry_plug->Hmat[0][0] << "\t"
538 <           << entry_plug->Hmat[1][0] << "\t"
539 <           << entry_plug->Hmat[2][0] << ";\t"
540 <
541 <           << entry_plug->Hmat[0][1] << "\t"
542 <           << entry_plug->Hmat[1][1] << "\t"
543 <           << entry_plug->Hmat[2][1] << ";\t"
544 <
545 <           << entry_plug->Hmat[0][2] << "\t"
546 <           << entry_plug->Hmat[1][2] << "\t"
547 <           << entry_plug->Hmat[2][2] << ";";
548 <
549 <  //write out additional parameters, such as chi and eta
550 <  finalOut << entry_plug->the_integrator->getAdditionalParameters();
551 <  finalOut << endl;
552 <
553 <  for( i=0; i<nAtoms; i++ ){
554 <
555 <    atoms[i]->getPos(pos);
556 <    atoms[i]->getVel(vel);
557 <
558 <    sprintf( tempBuffer,
559 <             "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
560 <             atoms[i]->getType(),
561 <             pos[0],
562 <             pos[1],
563 <             pos[2],
564 <             vel[0],
565 <             vel[1],
566 <             vel[2]);
567 <    strcpy( writeLine, tempBuffer );
568 <
569 <    if( atoms[i]->isDirectional() ){
570 <
571 <      dAtom = (DirectionalAtom *)atoms[i];
572 <      dAtom->getQ( q );
573 <
574 <      sprintf( tempBuffer,
575 <               "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
576 <               q[0],
577 <               q[1],
578 <               q[2],
579 <               q[3],
580 <               dAtom->getJx(),
581 <               dAtom->getJy(),
582 <               dAtom->getJz());
583 <      strcat( writeLine, tempBuffer );
584 <    }
585 <    else
586 <      strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
587 <
588 <    finalOut << writeLine;
589 <  }
590 <  finalOut.flush();
591 <  finalOut.close();
592 <
593 < #else // is_mpi
594 <
595 <  /* code to find maximum tag value */
596 <  int *tagub, flag, MAXTAG;
597 <  MPI_Attr_get(MPI_COMM_WORLD, MPI_TAG_UB, &tagub, &flag);
598 <  if (flag) {
599 <    MAXTAG = *tagub;
600 <  } else {
601 <    MAXTAG = 32767;
602 <  }  
603 <
604 <  int haveError;
605 <
606 <  MPI_Status istatus;
607 <  int *AtomToProcMap = mpiSim->getAtomToProcMap();
608 <
609 <  // write out header and node 0's coordinates
610 <
611 <  if( worldRank == 0 ){
612 <
613 <    // Node 0 needs a list of the magic potatoes for each processor;
614 <
615 <    nProc = mpiSim->getNumberProcessors();
616 <    potatoes = new int[nProc];
617 <
618 <    for (i = 0; i < nProc; i++)
619 <      potatoes[i] = 0;
620 <    
621 <    finalOut << mpiSim->getTotAtoms() << "\n";
622 <
623 <    finalOut << finalTime << ";\t"
624 <            << entry_plug->Hmat[0][0] << "\t"
625 <            << entry_plug->Hmat[1][0] << "\t"
626 <            << entry_plug->Hmat[2][0] << ";\t"
627 <
628 <            << entry_plug->Hmat[0][1] << "\t"
629 <            << entry_plug->Hmat[1][1] << "\t"
630 <            << entry_plug->Hmat[2][1] << ";\t"
631 <
632 <            << entry_plug->Hmat[0][2] << "\t"
633 <            << entry_plug->Hmat[1][2] << "\t"
634 <            << entry_plug->Hmat[2][2] << ";";
635 <
636 <    finalOut << entry_plug->the_integrator->getAdditionalParameters();
637 <    finalOut << endl;
638 <    finalOut.flush();
639 <
640 <    for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) {
641 <      
642 <      // Get the Node number which has this atom;
643 <      
644 <      which_node = AtomToProcMap[i];
645 <      
646 <      if (which_node != 0) {
647 <
648 <        if (potatoes[which_node] + 3 >= MAXTAG) {
649 <          // The potato was going to exceed the maximum value,
650 <          // so wrap this processor potato back to 0:        
651 <
652 <          potatoes[which_node] = 0;          
653 <          MPI_Send(0, 1, MPI_INT, which_node, 0, MPI_COMM_WORLD);
628 >          currentIndex++;    
629            
630          }
656 –
657 –        myPotato = potatoes[which_node];        
658 –        
659 –        MPI_Recv(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, which_node,
660 –                 myPotato, MPI_COMM_WORLD, &istatus);
661 –        
662 –        strncpy(atomTypeString, MPIatomTypeString, MINIBUFFERSIZE);
663 –        
664 –        // Null terminate the atomTypeString just in case:
665 –
666 –        atomTypeString[strlen(atomTypeString) - 1] = '\0';
667 –
668 –        myPotato++;
669 –
670 –        MPI_Recv(&isDirectional, 1, MPI_INT, which_node,
671 –                 myPotato, MPI_COMM_WORLD, &istatus);
672 –              
673 –        myPotato++;
674 –
675 –        if (isDirectional) {          
676 –          MPI_Recv(atomData13, 13, MPI_DOUBLE, which_node,
677 –                   myPotato, MPI_COMM_WORLD, &istatus);
678 –        } else {
679 –          MPI_Recv(atomData6, 6, MPI_DOUBLE, which_node,
680 –                   myPotato, MPI_COMM_WORLD, &istatus);          
681 –        }
682 –        
683 –        myPotato++;
684 –        potatoes[which_node] = myPotato;
685 –
686 –      } else {
687 –        
688 –        haveError = 0;
689 –        which_atom = i;
690 –        local_index=-1;
691 –        
692 –        for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) {
693 –          if (atoms[j]->getGlobalIndex() == which_atom) local_index = j;
694 –        }
695 –        
696 –        if (local_index != -1) {
697 –          
698 –          atomTypeString = atoms[local_index]->getType();
699 –
700 –          atoms[local_index]->getPos(pos);
701 –          atoms[local_index]->getVel(vel);          
702 –
703 –          atomData6[0] = pos[0];
704 –          atomData6[1] = pos[1];
705 –          atomData6[2] = pos[2];
706 –
707 –          atomData6[3] = vel[0];
708 –          atomData6[4] = vel[1];
709 –          atomData6[5] = vel[2];
710 –          
711 –          isDirectional = 0;
712 –
713 –          if( atoms[local_index]->isDirectional() ){
714 –
715 –            isDirectional = 1;
716 –            
717 –            dAtom = (DirectionalAtom *)atoms[local_index];
718 –            dAtom->getQ( q );
719 –
720 –            for (int j = 0; j < 6 ; j++)
721 –              atomData13[j] = atomData6[j];            
722 –            
723 –            atomData13[6] = q[0];
724 –            atomData13[7] = q[1];
725 –            atomData13[8] = q[2];
726 –            atomData13[9] = q[3];
727 –            
728 –            atomData13[10] = dAtom->getJx();
729 –            atomData13[11] = dAtom->getJy();
730 –            atomData13[12] = dAtom->getJz();
731 –          }
732 –          
733 –        } else {
734 –          sprintf(painCave.errMsg,
735 –                  "Atom %d not found on processor %d\n",
736 –                  i, worldRank );
737 –          haveError= 1;
738 –          simError();
739 –        }
740 –        
741 –        if(haveError) DieDieDie();
742 –        
743 –        // If we've survived to here, format the line:
744 –        
745 –        if (!isDirectional) {
746 –
747 –          sprintf( tempBuffer,
748 –                   "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
749 –                   atomTypeString,
750 –                   atomData6[0],
751 –                   atomData6[1],
752 –                   atomData6[2],
753 –                   atomData6[3],
754 –                   atomData6[4],
755 –                   atomData6[5]);
756 –          
757 –          strcpy( writeLine, tempBuffer );
758 –          strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
759 –
760 –        } else {
761 –          
762 –          sprintf( tempBuffer,
763 –                   "%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",
764 –                   atomTypeString,
765 –                   atomData13[0],
766 –                   atomData13[1],
767 –                   atomData13[2],
768 –                   atomData13[3],
769 –                   atomData13[4],
770 –                   atomData13[5],
771 –                   atomData13[6],
772 –                   atomData13[7],
773 –                   atomData13[8],
774 –                   atomData13[9],
775 –                   atomData13[10],
776 –                   atomData13[11],
777 –                   atomData13[12]);
778 –          
779 –          strcat( writeLine, tempBuffer );
780 –          
781 –        }
782 –        
783 –        finalOut << writeLine;
784 –        finalOut.flush();
785 –      }
786 –    }
787 –
788 –    finalOut.flush();
789 –    sprintf( checkPointMsg,
790 –             "Sucessfully took a dump.\n");
791 –    MPIcheckPoint();        
792 –    
793 –  } else {
794 –
795 –    // worldRank != 0, so I'm a remote node.  
796 –
797 –    // Set my magic potato to 0:
798 –
799 –    myPotato = 0;
800 –    
801 –    for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) {
631        
803 –      // Am I the node which has this atom?
804 –      
805 –      if (AtomToProcMap[i] == worldRank) {
806 –
807 –        if (myPotato + 3 >= MAXTAG) {
808 –
809 –          // The potato was going to exceed the maximum value,
810 –          // so wrap this processor potato back to 0 (and block until
811 –          // node 0 says we can go:
812 –
813 –          MPI_Recv(&myPotato, 1, MPI_INT, 0, 0, MPI_COMM_WORLD, &istatus);
814 –          
815 –        }
816 –
817 –        local_index=-1;
818 –        for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) {
819 –          if (atoms[j]->getGlobalIndex() == which_atom) local_index = j;
820 –        }
821 –        if (local_index != -1) {
822 –        
823 –          atomTypeString = atoms[local_index]->getType();
824 –
825 –          atoms[local_index]->getPos(pos);
826 –          atoms[local_index]->getVel(vel);
827 –
828 –          atomData6[0] = pos[0];
829 –          atomData6[1] = pos[1];
830 –          atomData6[2] = pos[2];
831 –
832 –          atomData6[3] = vel[0];
833 –          atomData6[4] = vel[1];
834 –          atomData6[5] = vel[2];
835 –          
836 –          isDirectional = 0;
837 –
838 –          if( atoms[local_index]->isDirectional() ){
839 –
840 –            isDirectional = 1;
841 –            
842 –            dAtom = (DirectionalAtom *)atoms[local_index];
843 –            dAtom->getQ( q );
844 –            
845 –            for (int j = 0; j < 6 ; j++)
846 –              atomData13[j] = atomData6[j];
847 –            
848 –            atomData13[6] = q[0];
849 –            atomData13[7] = q[1];
850 –            atomData13[8] = q[2];
851 –            atomData13[9] = q[3];
852 –
853 –            atomData13[10] = dAtom->getJx();
854 –            atomData13[11] = dAtom->getJy();
855 –            atomData13[12] = dAtom->getJz();
856 –          }
857 –
858 –        } else {
859 –          sprintf(painCave.errMsg,
860 –                  "Atom %d not found on processor %d\n",
861 –                  i, worldRank );
862 –          haveError= 1;
863 –          simError();
864 –        }
865 –
866 –        strncpy(MPIatomTypeString, atomTypeString, MINIBUFFERSIZE);
867 –
868 –        // null terminate the string before sending (just in case):
869 –        MPIatomTypeString[MINIBUFFERSIZE-1] = '\0';
870 –
871 –        MPI_Send(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, 0,
872 –                 myPotato, MPI_COMM_WORLD);
873 –        
874 –        myPotato++;
875 –
876 –        MPI_Send(&isDirectional, 1, MPI_INT, 0,
877 –                 myPotato, MPI_COMM_WORLD);
878 –        
879 –        myPotato++;
880 –        
881 –        if (isDirectional) {
882 –
883 –          MPI_Send(atomData13, 13, MPI_DOUBLE, 0,
884 –                   myPotato, MPI_COMM_WORLD);
885 –          
886 –        } else {
887 –
888 –          MPI_Send(atomData6, 6, MPI_DOUBLE, 0,
889 –                   myPotato, MPI_COMM_WORLD);
890 –        }
891 –
892 –        myPotato++;      
632        }
633 +    
634      }
635  
636      sprintf( checkPointMsg,
637               "Sucessfully took a dump.\n");
638      MPIcheckPoint();        
639      
900 –  }
640    
902 –  if( worldRank == 0 ) finalOut.close();
641   #endif // is_mpi
642   }
643  
906 –
907 –
644   #ifdef IS_MPI
645  
646   // a couple of functions to let us escape the write loop

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