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root/group/trunk/OOPSE/libmdtools/DumpWriter.cpp
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Comparing trunk/OOPSE/libmdtools/DumpWriter.cpp (file contents):
Revision 907 by gezelter, Thu Jan 8 17:40:56 2004 UTC vs.
Revision 1252 by gezelter, Mon Jun 7 14:26:33 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 < entry_plug->n_mol;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 = 10;
168 >  const int MINIBUFFERSIZE = 100;
169  
170 <  char tempBuffer[BUFFERSIZE];
170 >  char tempBuffer[BUFFERSIZE];  
171    char writeLine[BUFFERSIZE];
172  
173    int i;
174 +  unsigned int k;
175 +
176   #ifdef IS_MPI
177 <  int j, which_node, done, which_atom, local_index;
178 <  double atomTransData[6];
179 <  double atomOrientData[7];
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 >
218 >  int nProc;
219 >  int j, which_node, done, which_atom, local_index, currentIndex;
220 >  double atomData[13];
221    int isDirectional;
222    char* atomTypeString;
223 <  int me;
224 <  int atomTypeTag;
225 <  int atomIsDirectionalTag;
84 <  int atomTransDataTag;
85 <  int atomOrientDataTag;
86 < #else //is_mpi
87 <  int nAtoms = entry_plug->n_atoms;
223 >  char MPIatomTypeString[MINIBUFFERSIZE];
224 >  int nObjects;
225 >  int msgLen; // the length of message actually recieved at master nodes
226   #endif //is_mpi
227  
228 <  double q[4];
228 >  double q[4], ji[3];
229    DirectionalAtom* dAtom;
92 –  Atom** atoms = entry_plug->atoms;
230    double pos[3], vel[3];
231 <
232 <  // write current frame to the eor file
233 <
234 <  this->writeFinal( currentTime );
235 <
231 >  int nTotObjects;
232 >  StuntDouble* sd;
233 >  char* molName;
234 >  vector<StuntDouble*> integrableObjects;
235 >  vector<StuntDouble*>::iterator iter;
236 >  nTotObjects = entry_plug->getTotIntegrableObjects();
237   #ifndef IS_MPI
238 +  
239 +  for(k = 0; k < outFile.size(); k++){
240 +    *outFile[k] << nTotObjects << "\n";
241  
242 <  outFile << nAtoms << "\n";
242 >    *outFile[k] << currentTime << ";\t"
243 >               << entry_plug->Hmat[0][0] << "\t"
244 >                     << entry_plug->Hmat[1][0] << "\t"
245 >                     << entry_plug->Hmat[2][0] << ";\t"
246 >              
247 >               << entry_plug->Hmat[0][1] << "\t"
248 >                     << entry_plug->Hmat[1][1] << "\t"
249 >                     << entry_plug->Hmat[2][1] << ";\t"
250  
251 <  outFile << currentTime << ";\t"
252 <          << entry_plug->Hmat[0][0] << "\t"
253 <          << entry_plug->Hmat[1][0] << "\t"
106 <          << entry_plug->Hmat[2][0] << ";\t"
251 >                     << entry_plug->Hmat[0][2] << "\t"
252 >                     << entry_plug->Hmat[1][2] << "\t"
253 >                     << entry_plug->Hmat[2][2] << ";";
254  
255 <          << entry_plug->Hmat[0][1] << "\t"
256 <          << entry_plug->Hmat[1][1] << "\t"
257 <          << entry_plug->Hmat[2][1] << ";\t"
255 >    //write out additional parameters, such as chi and eta
256 >    *outFile[k] << entry_plug->the_integrator->getAdditionalParameters() << endl;
257 >  }
258 >  
259 >  for( i=0; i< entry_plug->n_mol; i++ ){
260  
261 <          << entry_plug->Hmat[0][2] << "\t"
262 <          << entry_plug->Hmat[1][2] << "\t"
263 <          << entry_plug->Hmat[2][2] << ";";
264 <  //write out additional parameters, such as chi and eta
265 <  outFile << entry_plug->the_integrator->getAdditionalParameters();
266 <  outFile << endl;
261 >    integrableObjects = entry_plug->molecules[i].getIntegrableObjects();
262 >    molName = (entry_plug->compStamps[entry_plug->molecules[i].getStampID()])->getID();
263 >    
264 >    for( iter = integrableObjects.begin();iter !=  integrableObjects.end(); ++iter){
265 >      sd = *iter;
266 >      sd->getPos(pos);
267 >      sd->getVel(vel);
268  
269 <  for( i=0; i<nAtoms; i++ ){
269 >      sprintf( tempBuffer,
270 >             "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
271 >             sd->getType(),
272 >             pos[0],
273 >             pos[1],
274 >             pos[2],
275 >             vel[0],
276 >             vel[1],
277 >             vel[2]);
278 >      strcpy( writeLine, tempBuffer );
279  
280 <    atoms[i]->getPos(pos);
122 <    atoms[i]->getVel(vel);
280 >      if( sd->isDirectional() ){
281  
282 <    sprintf( tempBuffer,
283 <             "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
126 <             atoms[i]->getType(),
127 <             pos[0],
128 <             pos[1],
129 <             pos[2],
130 <             vel[0],
131 <             vel[1],
132 <             vel[2]);
133 <    strcpy( writeLine, tempBuffer );
282 >        sd->getQ( q );
283 >        sd->getJ( ji );
284  
285 <    if( atoms[i]->isDirectional() ){
286 <
287 <      dAtom = (DirectionalAtom *)atoms[i];
288 <      dAtom->getQ( q );
289 <
290 <      sprintf( tempBuffer,
291 <               "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
292 <               q[0],
293 <               q[1],
294 <               q[2],
295 <               q[3],
296 <               dAtom->getJx(),
297 <               dAtom->getJy(),
298 <               dAtom->getJz());
299 <      strcat( writeLine, tempBuffer );
285 >        sprintf( tempBuffer,
286 >               "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
287 >               q[0],
288 >               q[1],
289 >               q[2],
290 >               q[3],
291 >                 ji[0],
292 >                 ji[1],
293 >                 ji[2]);
294 >        strcat( writeLine, tempBuffer );
295 >      }
296 >      else
297 >        strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
298 >    
299 >      for(k = 0; k < outFile.size(); k++)
300 >        *outFile[k] << writeLine;      
301      }
151 –    else
152 –      strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
302  
303 <    outFile << writeLine;
155 <  }
156 <  outFile.flush();
303 > }
304  
305   #else // is_mpi
306  
307 <  // first thing first, suspend fatalities.
308 <  painCave.isEventLoop = 1;
307 >  /* code to find maximum tag value */
308 >  
309 >  int *tagub, flag, MAXTAG;
310 >  MPI_Attr_get(MPI_COMM_WORLD, MPI_TAG_UB, &tagub, &flag);
311 >  if (flag) {
312 >    MAXTAG = *tagub;
313 >  } else {
314 >    MAXTAG = 32767;
315 >  }  
316  
163 –  int myStatus; // 1 = wakeup & success; 0 = error; -1 = AllDone
317    int haveError;
318  
319    MPI_Status istatus;
320 <  int *AtomToProcMap = mpiSim->getAtomToProcMap();
320 >  int nCurObj;
321 >  int *MolToProcMap = mpiSim->getMolToProcMap();
322  
323    // write out header and node 0's coordinates
324  
325    if( worldRank == 0 ){
172 –    outFile << mpiSim->getTotAtoms() << "\n";
326  
327 <    outFile << currentTime << ";\t"
175 <            << entry_plug->Hmat[0][0] << "\t"
176 <            << entry_plug->Hmat[1][0] << "\t"
177 <            << entry_plug->Hmat[2][0] << ";\t"
327 >    // Node 0 needs a list of the magic potatoes for each processor;
328  
329 <            << entry_plug->Hmat[0][1] << "\t"
330 <            << entry_plug->Hmat[1][1] << "\t"
181 <            << entry_plug->Hmat[2][1] << ";\t"
329 >    nProc = mpiSim->getNProcessors();
330 >    potatoes = new int[nProc];
331  
332 <            << entry_plug->Hmat[0][2] << "\t"
333 <            << entry_plug->Hmat[1][2] << "\t"
334 <            << entry_plug->Hmat[2][2] << ";";
332 >    //write out the comment lines
333 >    for (i = 0; i < nProc; i++)
334 >      potatoes[i] = 0;
335 >    
336 >      for(k = 0; k < outFile.size(); k++){
337 >        *outFile[k] << nTotObjects << "\n";
338  
339 <    outFile << entry_plug->the_integrator->getAdditionalParameters();
340 <    outFile << endl;
341 <    outFile.flush();
342 <    for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) {
191 <      // Get the Node number which has this atom;
339 >        *outFile[k] << currentTime << ";\t"
340 >                         << entry_plug->Hmat[0][0] << "\t"
341 >                         << entry_plug->Hmat[1][0] << "\t"
342 >                         << entry_plug->Hmat[2][0] << ";\t"
343  
344 <      which_node = AtomToProcMap[i];
344 >                         << entry_plug->Hmat[0][1] << "\t"
345 >                         << entry_plug->Hmat[1][1] << "\t"
346 >                         << entry_plug->Hmat[2][1] << ";\t"
347  
348 +                         << entry_plug->Hmat[0][2] << "\t"
349 +                         << entry_plug->Hmat[1][2] << "\t"
350 +                         << entry_plug->Hmat[2][2] << ";";
351 +  
352 +        *outFile[k] << entry_plug->the_integrator->getAdditionalParameters() << endl;
353 +    }
354 +
355 +    currentIndex = 0;
356 +
357 +    for (i = 0 ; i < mpiSim->getNMolGlobal(); i++ ) {
358 +      
359 +      // Get the Node number which has this atom;
360 +      
361 +      which_node = MolToProcMap[i];
362 +      
363        if (which_node != 0) {
364          
365 <        atomTypeTag          = 4*i;
366 <        atomIsDirectionalTag = 4*i + 1;
367 <        atomTransDataTag     = 4*i + 2;
200 <        atomOrientDataTag    = 4*i + 3;
365 >        if (potatoes[which_node] + 1 >= MAXTAG) {
366 >          // The potato was going to exceed the maximum value,
367 >          // so wrap this processor potato back to 0:        
368  
369 <        MPI_Recv(atomTypeString, MINIBUFFERSIZE, MPI_CHAR, which_node,
370 <                 atomTypeTag, MPI_COMM_WORLD, &istatus);
371 <        
205 <        MPI_Recv(&isDirectional, 1, MPI_INT, which_node,
206 <                 atomIsDirectionalTag, MPI_COMM_WORLD, &istatus);
207 <        
208 <        MPI_Recv(atomTransData, 6, MPI_DOUBLE, which_node,
209 <                 atomTransDataTag, MPI_COMM_WORLD, &istatus);
210 <
211 <        if (isDirectional) {
212 <
213 <          MPI_Recv(atomOrientData, 7, MPI_DOUBLE, which_node,
214 <                   atomOrientDataTag, MPI_COMM_WORLD, &istatus);
215 <
369 >          potatoes[which_node] = 0;          
370 >          MPI_Send(&potatoes[which_node], 1, MPI_INT, which_node, 0, MPI_COMM_WORLD);
371 >          
372          }
373  
374 <      } else {
374 >        myPotato = potatoes[which_node];        
375 >
376 >        //recieve the number of integrableObject in current molecule
377 >        MPI_Recv(&nCurObj, 1, MPI_INT, which_node,
378 >                 myPotato, MPI_COMM_WORLD, &istatus);
379 >        myPotato++;
380          
381 <        haveError = 0;
221 <        which_atom = i;
222 <        local_index=-1;
381 >        for(int l = 0; l < nCurObj; l++){
382  
383 <        for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) {
384 <          if (atoms[j]->getGlobalIndex() == which_atom) local_index = j;
385 <        }
383 >          if (potatoes[which_node] + 2 >= MAXTAG) {
384 >            // The potato was going to exceed the maximum value,
385 >            // so wrap this processor potato back to 0:        
386  
387 <        if (local_index != -1) {
387 >            potatoes[which_node] = 0;          
388 >            MPI_Send(&potatoes[which_node], 1, MPI_INT, which_node, 0, MPI_COMM_WORLD);
389 >            
390 >          }
391  
392 <          atomTypeString = atoms[local_index]->getType();
392 >          MPI_Recv(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, which_node,
393 >          myPotato, MPI_COMM_WORLD, &istatus);
394  
395 <          atoms[local_index]->getPos(pos);
233 <          atoms[local_index]->getVel(vel);
395 >          atomTypeString = MPIatomTypeString;
396  
397 <          atomTransData[0] = pos[0];
236 <          atomTransData[1] = pos[1];
237 <          atomTransData[2] = pos[2];
397 >          myPotato++;
398  
399 <          atomTransData[3] = vel[0];
400 <          atomTransData[4] = vel[1];
241 <          atomTransData[5] = vel[2];
242 <          
243 <          isDirectional = 0;
399 >          MPI_Recv(atomData, 13, MPI_DOUBLE, which_node, myPotato, MPI_COMM_WORLD, &istatus);
400 >          myPotato++;
401  
402 <          if( atoms[local_index]->isDirectional() ){
402 >          MPI_Get_count(&istatus, MPI_DOUBLE, &msgLen);
403  
404 +          if(msgLen  == 13)
405              isDirectional = 1;
406 +          else
407 +            isDirectional = 0;
408 +          
409 +          // If we've survived to here, format the line:
410              
411 <            dAtom = (DirectionalAtom *)atoms[local_index];
412 <            dAtom->getQ( q );
411 >          if (!isDirectional) {
412 >        
413 >            sprintf( writeLine,
414 >                 "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
415 >                 atomTypeString,
416 >                 atomData[0],
417 >                 atomData[1],
418 >                 atomData[2],
419 >                 atomData[3],
420 >                 atomData[4],
421 >                 atomData[5]);
422 >        
423 >           strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
424 >        
425 >          }
426 >          else {
427 >        
428 >                sprintf( writeLine,
429 >                         "%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",
430 >                         atomTypeString,
431 >                         atomData[0],
432 >                         atomData[1],
433 >                         atomData[2],
434 >                         atomData[3],
435 >                         atomData[4],
436 >                         atomData[5],
437 >                         atomData[6],
438 >                         atomData[7],
439 >                         atomData[8],
440 >                         atomData[9],
441 >                         atomData[10],
442 >                         atomData[11],
443 >                         atomData[12]);
444              
252 –            atomOrientData[0] = q[0];
253 –            atomOrientData[1] = q[1];
254 –            atomOrientData[2] = q[2];
255 –            atomOrientData[3] = q[3];
256 –
257 –            atomOrientData[4] = dAtom->getJx();
258 –            atomOrientData[5] = dAtom->getJy();
259 –            atomOrientData[6] = dAtom->getJz();
445            }
446 +          
447 +          for(k = 0; k < outFile.size(); k++)
448 +            *outFile[k] << writeLine;            
449  
450 <        } else {
451 <          sprintf(painCave.errMsg,
264 <                  "Atom %d not found on processor %d\n",
265 <                  i, worldRank );
266 <          haveError= 1;
267 <          simError();
268 <        }
450 >        }// end for(int l =0)
451 >        potatoes[which_node] = myPotato;
452  
453 <        if(haveError) DieDieDie();
454 <                              
272 <        // If we've survived to here, format the line:
453 >      }
454 >      else {
455          
456 <        sprintf( tempBuffer,
457 <                 "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
458 <                 atomTypeString,
277 <                 atomTransData[0],
278 <                 atomTransData[1],
279 <                 atomTransData[2],
280 <                 atomTransData[3],
281 <                 atomTransData[4],
282 <                 atomTransData[5]);
456 >        haveError = 0;
457 >        
458 >            local_index = indexArray[currentIndex].first;        
459  
460 <        strcpy( writeLine, tempBuffer );
460 >        integrableObjects = (entry_plug->molecules[local_index]).getIntegrableObjects();
461  
462 <        if (isDirectional) {
462 >        for(iter= integrableObjects.begin(); iter != integrableObjects.end(); ++iter){    
463 >                sd = *iter;
464 >            atomTypeString = sd->getType();
465 >            
466 >            sd->getPos(pos);
467 >            sd->getVel(vel);          
468 >          
469 >            atomData[0] = pos[0];
470 >            atomData[1] = pos[1];
471 >            atomData[2] = pos[2];
472  
473 <          sprintf( tempBuffer,
474 <                   "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
475 <                   atomOrientData[0],
476 <                   atomOrientData[1],
477 <                   atomOrientData[2],
293 <                   atomOrientData[3],
294 <                   atomOrientData[4],
295 <                   atomOrientData[5],
296 <                   atomOrientData[6]);
297 <          strcat( writeLine, tempBuffer );
473 >            atomData[3] = vel[0];
474 >            atomData[4] = vel[1];
475 >            atomData[5] = vel[2];
476 >              
477 >            isDirectional = 0;
478  
479 <        } else {
300 <          strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
301 <        }
479 >            if( sd->isDirectional() ){
480  
481 <        outFile << writeLine;
482 <        outFile.flush();
483 <      }
484 <    }
481 >              isDirectional = 1;
482 >                
483 >              sd->getQ( q );
484 >              sd->getJ( ji );
485  
486 <    outFile.flush();
486 >              for (int j = 0; j < 6 ; j++)
487 >                atomData[j] = atomData[j];            
488 >              
489 >              atomData[6] = q[0];
490 >              atomData[7] = q[1];
491 >              atomData[8] = q[2];
492 >              atomData[9] = q[3];
493 >              
494 >              atomData[10] = ji[0];
495 >              atomData[11] = ji[1];
496 >              atomData[12] = ji[2];
497 >            }
498 >            
499 >            // If we've survived to here, format the line:
500 >            
501 >            if (!isDirectional) {
502 >        
503 >              sprintf( writeLine,
504 >                 "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
505 >                 atomTypeString,
506 >                 atomData[0],
507 >                 atomData[1],
508 >                 atomData[2],
509 >                 atomData[3],
510 >                 atomData[4],
511 >                 atomData[5]);
512 >        
513 >             strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
514 >        
515 >            }
516 >            else {
517 >        
518 >                sprintf( writeLine,
519 >                         "%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",
520 >                         atomTypeString,
521 >                         atomData[0],
522 >                         atomData[1],
523 >                         atomData[2],
524 >                         atomData[3],
525 >                         atomData[4],
526 >                         atomData[5],
527 >                         atomData[6],
528 >                         atomData[7],
529 >                         atomData[8],
530 >                         atomData[9],
531 >                         atomData[10],
532 >                         atomData[11],
533 >                         atomData[12]);
534 >              
535 >            }
536 >            
537 >            for(k = 0; k < outFile.size(); k++)
538 >              *outFile[k] << writeLine;
539 >            
540 >            
541 >        }//end for(iter = integrableObject.begin())
542 >        
543 >      currentIndex++;
544 >      }
545 >
546 >    }//end for(i = 0; i < mpiSim->getNmol())
547 >    
548 >    for(k = 0; k < outFile.size(); k++)
549 >      outFile[k]->flush();
550 >    
551      sprintf( checkPointMsg,
552               "Sucessfully took a dump.\n");
553 +    
554      MPIcheckPoint();        
555      
556 +    delete[] potatoes;
557 +    
558    } else {
559  
560      // worldRank != 0, so I'm a remote node.  
561 +
562 +    // Set my magic potato to 0:
563 +
564 +    myPotato = 0;
565 +    currentIndex = 0;
566      
567 <    for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) {
567 >    for (i = 0 ; i < mpiSim->getNMolGlobal(); i++ ) {
568        
569 <      // Am I the node which has this atom?
569 >      // Am I the node which has this integrableObject?
570        
571 <      if (AtomToProcMap[i] == worldRank) {
571 >      if (MolToProcMap[i] == worldRank) {
572  
573 <        local_index=-1;
574 <        for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) {
575 <          if (atoms[j]->getGlobalIndex() == which_atom) local_index = j;
573 >
574 >        if (myPotato + 1 >= MAXTAG) {
575 >          
576 >          // The potato was going to exceed the maximum value,
577 >          // so wrap this processor potato back to 0 (and block until
578 >          // node 0 says we can go:
579 >          
580 >          MPI_Recv(&myPotato, 1, MPI_INT, 0, 0, MPI_COMM_WORLD, &istatus);
581 >          
582          }
327 –        if (local_index != -1) {
328 –        
329 –          atomTypeString = atoms[local_index]->getType();
583  
584 <          atoms[local_index]->getPos(pos);
585 <          atoms[local_index]->getVel(vel);
333 <
334 <          atomTransData[0] = pos[0];
335 <          atomTransData[1] = pos[1];
336 <          atomTransData[2] = pos[2];
337 <
338 <          atomTransData[3] = vel[0];
339 <          atomTransData[4] = vel[1];
340 <          atomTransData[5] = vel[2];
584 >          local_index = indexArray[currentIndex].first;        
585 >          integrableObjects = entry_plug->molecules[local_index].getIntegrableObjects();
586            
587 <          isDirectional = 0;
587 >          nCurObj = integrableObjects.size();
588 >                      
589 >          MPI_Send(&nCurObj, 1, MPI_INT, 0,
590 >                             myPotato, MPI_COMM_WORLD);
591 >          myPotato++;
592  
593 <          if( atoms[local_index]->isDirectional() ){
593 >          for( iter = integrableObjects.begin(); iter  != integrableObjects.end(); iter++){
594  
595 <            isDirectional = 1;
595 >            if (myPotato + 2 >= MAXTAG) {
596 >          
597 >              // The potato was going to exceed the maximum value,
598 >              // so wrap this processor potato back to 0 (and block until
599 >              // node 0 says we can go:
600 >          
601 >              MPI_Recv(&myPotato, 1, MPI_INT, 0, 0, MPI_COMM_WORLD, &istatus);
602 >              
603 >            }
604              
605 <            dAtom = (DirectionalAtom *)atoms[local_index];
349 <            dAtom->getQ( q );
605 >            sd = *iter;
606              
607 <            atomOrientData[0] = q[0];
352 <            atomOrientData[1] = q[1];
353 <            atomOrientData[2] = q[2];
354 <            atomOrientData[3] = q[3];
607 >            atomTypeString = sd->getType();
608  
609 <            atomOrientData[4] = dAtom->getJx();
610 <            atomOrientData[5] = dAtom->getJy();
358 <            atomOrientData[6] = dAtom->getJz();
359 <          }
609 >            sd->getPos(pos);
610 >            sd->getVel(vel);
611  
612 <        } else {
613 <          sprintf(painCave.errMsg,
614 <                  "Atom %d not found on processor %d\n",
364 <                  i, worldRank );
365 <          haveError= 1;
366 <          simError();
367 <        }
612 >            atomData[0] = pos[0];
613 >            atomData[1] = pos[1];
614 >            atomData[2] = pos[2];
615  
616 <        // I've survived this far, so send off the data!
616 >            atomData[3] = vel[0];
617 >            atomData[4] = vel[1];
618 >            atomData[5] = vel[2];
619 >              
620 >            isDirectional = 0;
621  
622 <        atomTypeTag          = 4*i;
372 <        atomIsDirectionalTag = 4*i + 1;
373 <        atomTransDataTag     = 4*i + 2;
374 <        atomOrientDataTag    = 4*i + 3;
622 >            if( sd->isDirectional() ){
623  
624 <        MPI_Send(atomTypeString, MINIBUFFERSIZE, MPI_CHAR, 0,
625 <                 atomTypeTag, MPI_COMM_WORLD);
626 <        
627 <        MPI_Send(&isDirectional, 1, MPI_INT, 0,
628 <                 atomIsDirectionalTag, MPI_COMM_WORLD);
629 <        
630 <        MPI_Send(atomTransData, 6, MPI_DOUBLE, 0,
631 <                 atomTransDataTag, MPI_COMM_WORLD);
632 <
633 <        if (isDirectional) {
386 <
387 <          MPI_Send(atomOrientData, 7, MPI_DOUBLE, 0,
388 <                   atomOrientDataTag, MPI_COMM_WORLD);
389 <          
390 <        }
624 >                isDirectional = 1;
625 >                
626 >                sd->getQ( q );
627 >                sd->getJ( ji );
628 >                
629 >                
630 >                atomData[6] = q[0];
631 >                atomData[7] = q[1];
632 >                atomData[8] = q[2];
633 >                atomData[9] = q[3];
634        
635 <      }
636 <    }
635 >                atomData[10] = ji[0];
636 >                atomData[11] = ji[1];
637 >                atomData[12] = ji[2];
638 >              }
639  
640 <    sprintf( checkPointMsg,
641 <             "Sucessfully took a dump.\n");
397 <    MPIcheckPoint();        
398 <    
399 <  }
400 <  
401 <  painCave.isEventLoop = 0;
640 >            
641 >            strncpy(MPIatomTypeString, atomTypeString, MINIBUFFERSIZE);
642  
643 < #endif // is_mpi
644 < }
643 >            // null terminate the string before sending (just in case):
644 >            MPIatomTypeString[MINIBUFFERSIZE-1] = '\0';
645  
646 < void DumpWriter::writeFinal(double finalTime){
646 >            MPI_Send(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, 0,
647 >                             myPotato, MPI_COMM_WORLD);
648 >            
649 >            myPotato++;
650 >            
651 >            if (isDirectional) {
652  
653 <  char finalName[500];
654 <  ofstream finalOut;
653 >              MPI_Send(atomData, 13, MPI_DOUBLE, 0,
654 >                       myPotato, MPI_COMM_WORLD);
655 >              
656 >            } else {
657  
658 <  const int BUFFERSIZE = 2000;
659 <  const int MINIBUFFERSIZE = 10;
660 <  char tempBuffer[BUFFERSIZE];
414 <  char writeLine[BUFFERSIZE];
415 <
416 <  double q[4];
417 <  DirectionalAtom* dAtom;
418 <  Atom** atoms = entry_plug->atoms;
419 <  int i;
420 < #ifdef IS_MPI
421 <  int j, which_node, done, which_atom, local_index;
422 <  double atomTransData[6];
423 <  double atomOrientData[7];
424 <  int isDirectional;
425 <  char* atomTypeString;
426 <  int atomTypeTag;
427 <  int atomIsDirectionalTag;
428 <  int atomTransDataTag;
429 <  int atomOrientDataTag;
430 < #else //is_mpi
431 <  int nAtoms = entry_plug->n_atoms;
432 < #endif //is_mpi
433 <
434 <  double pos[3], vel[3];
435 <
436 < #ifdef IS_MPI
437 <  if(worldRank == 0 ){
438 < #endif // is_mpi
439 <
440 <    strcpy( finalName, entry_plug->finalName );
441 <
442 <    finalOut.open( finalName, ios::out | ios::trunc );
443 <    if( !finalOut ){
444 <      sprintf( painCave.errMsg,
445 <               "Could not open \"%s\" for final dump output.\n",
446 <               finalName );
447 <      painCave.isFatal = 1;
448 <      simError();
449 <    }
450 <
451 <    // finalOut.setf( ios::scientific );
452 <
453 < #ifdef IS_MPI
454 <  }
455 <
456 <  sprintf(checkPointMsg,"Opened file for final configuration\n");
457 <  MPIcheckPoint();
458 <
459 < #endif //is_mpi
460 <
461 <
462 < #ifndef IS_MPI
463 <
464 <  finalOut << nAtoms << "\n";
465 <
466 <  finalOut << finalTime << ";\t"
467 <           << entry_plug->Hmat[0][0] << "\t"
468 <           << entry_plug->Hmat[1][0] << "\t"
469 <           << entry_plug->Hmat[2][0] << ";\t"
470 <
471 <           << entry_plug->Hmat[0][1] << "\t"
472 <           << entry_plug->Hmat[1][1] << "\t"
473 <           << entry_plug->Hmat[2][1] << ";\t"
474 <
475 <           << entry_plug->Hmat[0][2] << "\t"
476 <           << entry_plug->Hmat[1][2] << "\t"
477 <           << entry_plug->Hmat[2][2] << ";";
478 <
479 <  //write out additional parameters, such as chi and eta
480 <  finalOut << entry_plug->the_integrator->getAdditionalParameters();
481 <  finalOut << endl;
482 <
483 <  for( i=0; i<nAtoms; i++ ){
484 <
485 <    atoms[i]->getPos(pos);
486 <    atoms[i]->getVel(vel);
487 <
488 <    sprintf( tempBuffer,
489 <             "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
490 <             atoms[i]->getType(),
491 <             pos[0],
492 <             pos[1],
493 <             pos[2],
494 <             vel[0],
495 <             vel[1],
496 <             vel[2]);
497 <    strcpy( writeLine, tempBuffer );
658 >              MPI_Send(atomData, 6, MPI_DOUBLE, 0,
659 >                       myPotato, MPI_COMM_WORLD);
660 >            }
661  
662 <    if( atoms[i]->isDirectional() ){
662 >            myPotato++;  
663  
501 –      dAtom = (DirectionalAtom *)atoms[i];
502 –      dAtom->getQ( q );
503 –
504 –      sprintf( tempBuffer,
505 –               "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
506 –               q[0],
507 –               q[1],
508 –               q[2],
509 –               q[3],
510 –               dAtom->getJx(),
511 –               dAtom->getJy(),
512 –               dAtom->getJz());
513 –      strcat( writeLine, tempBuffer );
514 –    }
515 –    else
516 –      strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
517 –
518 –    finalOut << writeLine;
519 –  }
520 –  finalOut.flush();
521 –  finalOut.close();
522 –
523 – #else // is_mpi
524 –
525 –  // first thing first, suspend fatalities.
526 –  painCave.isEventLoop = 1;
527 –
528 –  int myStatus; // 1 = wakeup & success; 0 = error; -1 = AllDone
529 –  int haveError;
530 –
531 –  MPI_Status istatus;
532 –  int *AtomToProcMap = mpiSim->getAtomToProcMap();
533 –
534 –  // write out header and node 0's coordinates
535 –
536 –  if( worldRank == 0 ){
537 –    finalOut << mpiSim->getTotAtoms() << "\n";
538 –
539 –    finalOut << finalTime << ";\t"
540 –            << entry_plug->Hmat[0][0] << "\t"
541 –            << entry_plug->Hmat[1][0] << "\t"
542 –            << entry_plug->Hmat[2][0] << ";\t"
543 –
544 –            << entry_plug->Hmat[0][1] << "\t"
545 –            << entry_plug->Hmat[1][1] << "\t"
546 –            << entry_plug->Hmat[2][1] << ";\t"
547 –
548 –            << entry_plug->Hmat[0][2] << "\t"
549 –            << entry_plug->Hmat[1][2] << "\t"
550 –            << entry_plug->Hmat[2][2] << ";";
551 –
552 –    finalOut << entry_plug->the_integrator->getAdditionalParameters();
553 –    finalOut << endl;
554 –    finalOut.flush();
555 –    for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) {
556 –      // Get the Node number which has this atom;
557 –
558 –      which_node = AtomToProcMap[i];
559 –
560 –      if (which_node != 0) {
561 –        
562 –        atomTypeTag          = 4*i;
563 –        atomIsDirectionalTag = 4*i + 1;
564 –        atomTransDataTag     = 4*i + 2;
565 –        atomOrientDataTag    = 4*i + 3;
566 –
567 –        MPI_Recv(atomTypeString, MINIBUFFERSIZE, MPI_CHAR, which_node,
568 –                 atomTypeTag, MPI_COMM_WORLD, &istatus);
569 –        
570 –        MPI_Recv(&isDirectional, 1, MPI_INT, which_node,
571 –                 atomIsDirectionalTag, MPI_COMM_WORLD, &istatus);
572 –        
573 –        MPI_Recv(atomTransData, 6, MPI_DOUBLE, which_node,
574 –                 atomTransDataTag, MPI_COMM_WORLD, &istatus);
575 –
576 –        if (isDirectional) {
577 –
578 –          MPI_Recv(atomOrientData, 7, MPI_DOUBLE, which_node,
579 –                   atomOrientDataTag, MPI_COMM_WORLD, &istatus);
580 –
581 –        }
582 –
583 –      } else {
584 –        
585 –        haveError = 0;
586 –        which_atom = i;
587 –        local_index=-1;
588 –
589 –        for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) {
590 –          if (atoms[j]->getGlobalIndex() == which_atom) local_index = j;
591 –        }
592 –
593 –        if (local_index != -1) {
594 –
595 –          atomTypeString = atoms[local_index]->getType();
596 –
597 –          atoms[local_index]->getPos(pos);
598 –          atoms[local_index]->getVel(vel);
599 –
600 –          atomTransData[0] = pos[0];
601 –          atomTransData[1] = pos[1];
602 –          atomTransData[2] = pos[2];
603 –
604 –          atomTransData[3] = vel[0];
605 –          atomTransData[4] = vel[1];
606 –          atomTransData[5] = vel[2];
607 –          
608 –          isDirectional = 0;
609 –
610 –          if( atoms[local_index]->isDirectional() ){
611 –
612 –            isDirectional = 1;
613 –            
614 –            dAtom = (DirectionalAtom *)atoms[local_index];
615 –            dAtom->getQ( q );
616 –            
617 –            atomOrientData[0] = q[0];
618 –            atomOrientData[1] = q[1];
619 –            atomOrientData[2] = q[2];
620 –            atomOrientData[3] = q[3];
621 –
622 –            atomOrientData[4] = dAtom->getJx();
623 –            atomOrientData[5] = dAtom->getJy();
624 –            atomOrientData[6] = dAtom->getJz();
664            }
665  
666 <        } else {
667 <          sprintf(painCave.errMsg,
629 <                  "Atom %d not found on processor %d\n",
630 <                  i, worldRank );
631 <          haveError= 1;
632 <          simError();
633 <        }
634 <
635 <        if(haveError) DieDieDie();
636 <                              
637 <        // If we've survived to here, format the line:
638 <        
639 <        sprintf( tempBuffer,
640 <                 "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
641 <                 atomTypeString,
642 <                 atomTransData[0],
643 <                 atomTransData[1],
644 <                 atomTransData[2],
645 <                 atomTransData[3],
646 <                 atomTransData[4],
647 <                 atomTransData[5]);
648 <
649 <        strcpy( writeLine, tempBuffer );
650 <
651 <        if (isDirectional) {
652 <
653 <          sprintf( tempBuffer,
654 <                   "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
655 <                   atomOrientData[0],
656 <                   atomOrientData[1],
657 <                   atomOrientData[2],
658 <                   atomOrientData[3],
659 <                   atomOrientData[4],
660 <                   atomOrientData[5],
661 <                   atomOrientData[6]);
662 <          strcat( writeLine, tempBuffer );
663 <
664 <        } else {
665 <          strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
666 >          currentIndex++;    
667 >          
668          }
669 <
668 <        finalOut << writeLine;
669 <        finalOut.flush();
669 >      
670        }
671 –    }
671  
673 –    finalOut.flush();
672      sprintf( checkPointMsg,
673               "Sucessfully took a dump.\n");
674 <    MPIcheckPoint();        
674 >    MPIcheckPoint();                
675      
678 –  } else {
679 –
680 –    // worldRank != 0, so I'm a remote node.  
681 –    
682 –    for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) {
683 –      
684 –      // Am I the node which has this atom?
685 –      
686 –      if (AtomToProcMap[i] == worldRank) {
687 –
688 –        local_index=-1;
689 –        for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) {
690 –          if (atoms[j]->getGlobalIndex() == which_atom) local_index = j;
691 –        }
692 –        if (local_index != -1) {
693 –        
694 –          atomTypeString = atoms[local_index]->getType();
695 –
696 –          atoms[local_index]->getPos(pos);
697 –          atoms[local_index]->getVel(vel);
698 –
699 –          atomTransData[0] = pos[0];
700 –          atomTransData[1] = pos[1];
701 –          atomTransData[2] = pos[2];
702 –
703 –          atomTransData[3] = vel[0];
704 –          atomTransData[4] = vel[1];
705 –          atomTransData[5] = vel[2];
706 –          
707 –          isDirectional = 0;
708 –
709 –          if( atoms[local_index]->isDirectional() ){
710 –
711 –            isDirectional = 1;
712 –            
713 –            dAtom = (DirectionalAtom *)atoms[local_index];
714 –            dAtom->getQ( q );
715 –            
716 –            atomOrientData[0] = q[0];
717 –            atomOrientData[1] = q[1];
718 –            atomOrientData[2] = q[2];
719 –            atomOrientData[3] = q[3];
720 –
721 –            atomOrientData[4] = dAtom->getJx();
722 –            atomOrientData[5] = dAtom->getJy();
723 –            atomOrientData[6] = dAtom->getJz();
724 –          }
725 –
726 –        } else {
727 –          sprintf(painCave.errMsg,
728 –                  "Atom %d not found on processor %d\n",
729 –                  i, worldRank );
730 –          haveError= 1;
731 –          simError();
732 –        }
733 –
734 –        // I've survived this far, so send off the data!
735 –
736 –        atomTypeTag          = 4*i;
737 –        atomIsDirectionalTag = 4*i + 1;
738 –        atomTransDataTag     = 4*i + 2;
739 –        atomOrientDataTag    = 4*i + 3;
740 –
741 –        MPI_Send(atomTypeString, MINIBUFFERSIZE, MPI_CHAR, 0,
742 –                 atomTypeTag, MPI_COMM_WORLD);
743 –        
744 –        MPI_Send(&isDirectional, 1, MPI_INT, 0,
745 –                 atomIsDirectionalTag, MPI_COMM_WORLD);
746 –        
747 –        MPI_Send(atomTransData, 6, MPI_DOUBLE, 0,
748 –                 atomTransDataTag, MPI_COMM_WORLD);
749 –
750 –        if (isDirectional) {
751 –
752 –          MPI_Send(atomOrientData, 7, MPI_DOUBLE, 0,
753 –                   atomOrientDataTag, MPI_COMM_WORLD);
754 –          
755 –        }
756 –      
757 –      }
676      }
677  
760 –    sprintf( checkPointMsg,
761 –             "Sucessfully wrote final file.\n");
762 –    MPIcheckPoint();        
763 –    
764 –  }
765 –  
766 –  painCave.isEventLoop = 0;
678  
679 <  if( worldRank == 0 ) finalOut.close();
679 >  
680   #endif // is_mpi
681   }
682  
772 –
773 –
683   #ifdef IS_MPI
684  
685   // a couple of functions to let us escape the write loop

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