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root/group/trunk/OOPSE/libmdtools/DumpWriter.cpp
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Comparing trunk/OOPSE/libmdtools/DumpWriter.cpp (file contents):
Revision 912 by gezelter, Thu Jan 8 18:59:36 2004 UTC vs.
Revision 1231 by tim, Thu Jun 3 21:06:51 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 = 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 <  int j, which_node, done, which_atom, local_index;
177 <  double atomTransData[6];
178 <  double atomOrientData[7];
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, currentIndex;
219 >  double atomData[13];
220    int isDirectional;
221    char* atomTypeString;
222    char MPIatomTypeString[MINIBUFFERSIZE];
223 <  int me;
224 <  int atomTypeTag;
84 <  int atomIsDirectionalTag;
85 <  int atomTransDataTag;
86 <  int atomOrientDataTag;
87 < #else //is_mpi
88 <  int nAtoms = entry_plug->n_atoms;
223 >  int nObjects;
224 >  int msgLen; // the length of message actually recieved at master nodes
225   #endif //is_mpi
226  
227 <  double q[4];
227 >  double q[4], ji[3];
228    DirectionalAtom* dAtom;
93 –  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"
107 <          << 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);
123 <    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",
127 <             atoms[i]->getType(),
128 <             pos[0],
129 <             pos[1],
130 <             pos[2],
131 <             vel[0],
132 <             vel[1],
133 <             vel[2]);
134 <    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(),
297 <               dAtom->getJz());
298 <      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 >    
298 >      for(k = 0; k < outFile.size(); k++)
299 >        *outFile[k] << writeLine;      
300      }
152 –    else
153 –      strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
301  
302 <    outFile << writeLine;
156 <  }
157 <  outFile.flush();
302 > }
303  
304   #else // is_mpi
305  
306 <  // first thing first, suspend fatalities.
307 <  painCave.isEventLoop = 1;
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) {
311 >    MAXTAG = *tagub;
312 >  } else {
313 >    MAXTAG = 32767;
314 >  }  
315  
164 –  int myStatus; // 1 = wakeup & success; 0 = error; -1 = AllDone
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  
324    if( worldRank == 0 ){
173 –    outFile << mpiSim->getTotAtoms() << "\n";
325  
326 <    outFile << currentTime << ";\t"
176 <            << entry_plug->Hmat[0][0] << "\t"
177 <            << entry_plug->Hmat[1][0] << "\t"
178 <            << entry_plug->Hmat[2][0] << ";\t"
179 <
180 <            << entry_plug->Hmat[0][1] << "\t"
181 <            << entry_plug->Hmat[1][1] << "\t"
182 <            << entry_plug->Hmat[2][1] << ";\t"
183 <
184 <            << entry_plug->Hmat[0][2] << "\t"
185 <            << entry_plug->Hmat[1][2] << "\t"
186 <            << entry_plug->Hmat[2][2] << ";";
326 >    // Node 0 needs a list of the magic potatoes for each processor;
327  
328 <    outFile << entry_plug->the_integrator->getAdditionalParameters();
329 <    outFile << endl;
190 <    outFile.flush();
191 <    for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) {
192 <      // Get the Node number which has this atom;
328 >    nProc = mpiSim->getNProcessors();
329 >    potatoes = new int[nProc];
330  
331 <      which_node = AtomToProcMap[i];
331 >    //write out the comment lines
332 >    for (i = 0; i < nProc; i++)
333 >      potatoes[i] = 0;
334 >    
335 >      for(k = 0; k < outFile.size(); k++){
336 >        *outFile[k] << nTotObjects << "\n";
337  
338 <      if (which_node != 0) {
339 <        
340 <        atomTypeTag          = 4*i;
341 <        atomIsDirectionalTag = 4*i + 1;
200 <        atomTransDataTag     = 4*i + 2;
201 <        atomOrientDataTag    = 4*i + 3;
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 <        MPI_Recv(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, which_node,
344 <                 atomTypeTag, MPI_COMM_WORLD, &istatus);
345 <        
206 <        strncpy(atomTypeString, MPIatomTypeString, MINIBUFFERSIZE);
207 <        
208 <        // Null terminate the atomTypeString just in case:
343 >                         << entry_plug->Hmat[0][1] << "\t"
344 >                         << entry_plug->Hmat[1][1] << "\t"
345 >                         << entry_plug->Hmat[2][1] << ";\t"
346  
347 <        atomTypeString[strlen(atomTypeString) - 1] = '\0';
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 <        MPI_Recv(&isDirectional, 1, MPI_INT, which_node,
355 <                 atomIsDirectionalTag, MPI_COMM_WORLD, &istatus);
354 >    currentIndex = 0;
355 >
356 >    for (i = 0 ; i < mpiSim->getNMolGlobal(); i++ ) {
357 >      
358 >      // Get the Node number which has this atom;
359 >      
360 >      which_node = MolToProcMap[i];
361 >      
362 >      if (which_node != 0) {
363          
364 <        MPI_Recv(atomTransData, 6, MPI_DOUBLE, which_node,
365 <                 atomTransDataTag, MPI_COMM_WORLD, &istatus);
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  
368 <        if (isDirectional) {
369 <
370 <          MPI_Recv(atomOrientData, 7, MPI_DOUBLE, which_node,
221 <                   atomOrientDataTag, MPI_COMM_WORLD, &istatus);
222 <
368 >          potatoes[which_node] = 0;          
369 >          MPI_Send(&potatoes[which_node], 1, MPI_INT, which_node, 0, MPI_COMM_WORLD);
370 >          
371          }
372  
373 <      } else {
373 >        myPotato = potatoes[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 >        myPotato++;
379          
380 <        haveError = 0;
228 <        which_atom = i;
229 <        local_index=-1;
380 >        for(int l = 0; l < nCurObj; l++){
381  
382 <        for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) {
383 <          if (atoms[j]->getGlobalIndex() == which_atom) local_index = j;
384 <        }
382 >          if (potatoes[which_node] + 2 >= MAXTAG) {
383 >            // The potato was going to exceed the maximum value,
384 >            // so wrap this processor potato back to 0:        
385  
386 <        if (local_index != -1) {
386 >            potatoes[which_node] = 0;          
387 >            MPI_Send(&potatoes[which_node], 1, MPI_INT, which_node, 0, MPI_COMM_WORLD);
388 >            
389 >          }
390  
391 <          atomTypeString = atoms[local_index]->getType();
391 >          MPI_Recv(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, which_node,
392 >          myPotato, MPI_COMM_WORLD, &istatus);
393  
394 <          atoms[local_index]->getPos(pos);
240 <          atoms[local_index]->getVel(vel);
394 >          atomTypeString = MPIatomTypeString;
395  
396 <          atomTransData[0] = pos[0];
243 <          atomTransData[1] = pos[1];
244 <          atomTransData[2] = pos[2];
396 >          myPotato++;
397  
398 <          atomTransData[3] = vel[0];
399 <          atomTransData[4] = vel[1];
248 <          atomTransData[5] = vel[2];
249 <          
250 <          isDirectional = 0;
398 >          MPI_Recv(atomData, 13, MPI_DOUBLE, which_node, myPotato, MPI_COMM_WORLD, &istatus);
399 >          myPotato++;
400  
401 <          if( atoms[local_index]->isDirectional() ){
401 >          MPI_Get_count(&istatus, MPI_DOUBLE, &msgLen);
402  
403 +          if(msgLen  == 13)
404              isDirectional = 1;
405 +          else
406 +            isDirectional = 0;
407 +          
408 +          // If we've survived to here, format the line:
409              
410 <            dAtom = (DirectionalAtom *)atoms[local_index];
411 <            dAtom->getQ( q );
410 >          if (!isDirectional) {
411 >        
412 >            sprintf( writeLine,
413 >                 "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
414 >                 atomTypeString,
415 >                 atomData[0],
416 >                 atomData[1],
417 >                 atomData[2],
418 >                 atomData[3],
419 >                 atomData[4],
420 >                 atomData[5]);
421 >        
422 >           strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
423 >        
424 >          }
425 >          else {
426 >        
427 >                sprintf( writeLine,
428 >                         "%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",
429 >                         atomTypeString,
430 >                         atomData[0],
431 >                         atomData[1],
432 >                         atomData[2],
433 >                         atomData[3],
434 >                         atomData[4],
435 >                         atomData[5],
436 >                         atomData[6],
437 >                         atomData[7],
438 >                         atomData[8],
439 >                         atomData[9],
440 >                         atomData[10],
441 >                         atomData[11],
442 >                         atomData[12]);
443              
259 –            atomOrientData[0] = q[0];
260 –            atomOrientData[1] = q[1];
261 –            atomOrientData[2] = q[2];
262 –            atomOrientData[3] = q[3];
263 –
264 –            atomOrientData[4] = dAtom->getJx();
265 –            atomOrientData[5] = dAtom->getJy();
266 –            atomOrientData[6] = dAtom->getJz();
444            }
445 +          
446 +          for(k = 0; k < outFile.size(); k++)
447 +            *outFile[k] << writeLine;            
448  
449 <        } else {
450 <          sprintf(painCave.errMsg,
271 <                  "Atom %d not found on processor %d\n",
272 <                  i, worldRank );
273 <          haveError= 1;
274 <          simError();
275 <        }
449 >        }// end for(int l =0)
450 >        potatoes[which_node] = myPotato;
451  
452 <        if(haveError) DieDieDie();
453 <                              
279 <        // If we've survived to here, format the line:
452 >      }
453 >      else {
454          
455 <        sprintf( tempBuffer,
456 <                 "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
457 <                 atomTypeString,
284 <                 atomTransData[0],
285 <                 atomTransData[1],
286 <                 atomTransData[2],
287 <                 atomTransData[3],
288 <                 atomTransData[4],
289 <                 atomTransData[5]);
455 >        haveError = 0;
456 >        
457 >            local_index = indexArray[currentIndex].first;        
458  
459 <        strcpy( writeLine, tempBuffer );
459 >        integrableObjects = (entry_plug->molecules[local_index]).getIntegrableObjects();
460  
461 <        if (isDirectional) {
461 >        for(iter= integrableObjects.begin(); iter != integrableObjects.end(); ++iter){    
462 >                sd = *iter;
463 >            atomTypeString = sd->getType();
464 >            
465 >            sd->getPos(pos);
466 >            sd->getVel(vel);          
467 >          
468 >            atomData[0] = pos[0];
469 >            atomData[1] = pos[1];
470 >            atomData[2] = pos[2];
471  
472 <          sprintf( tempBuffer,
473 <                   "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
474 <                   atomOrientData[0],
475 <                   atomOrientData[1],
476 <                   atomOrientData[2],
300 <                   atomOrientData[3],
301 <                   atomOrientData[4],
302 <                   atomOrientData[5],
303 <                   atomOrientData[6]);
304 <          strcat( writeLine, tempBuffer );
472 >            atomData[3] = vel[0];
473 >            atomData[4] = vel[1];
474 >            atomData[5] = vel[2];
475 >              
476 >            isDirectional = 0;
477  
478 <        } else {
307 <          strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
308 <        }
478 >            if( sd->isDirectional() ){
479  
480 <        outFile << writeLine;
481 <        outFile.flush();
482 <      }
483 <    }
480 >              isDirectional = 1;
481 >                
482 >              sd->getQ( q );
483 >              sd->getJ( ji );
484  
485 <    outFile.flush();
485 >              for (int j = 0; j < 6 ; j++)
486 >                atomData[j] = atomData[j];            
487 >              
488 >              atomData[6] = q[0];
489 >              atomData[7] = q[1];
490 >              atomData[8] = q[2];
491 >              atomData[9] = q[3];
492 >              
493 >              atomData[10] = ji[0];
494 >              atomData[11] = ji[1];
495 >              atomData[12] = ji[2];
496 >            }
497 >            
498 >            // If we've survived to here, format the line:
499 >            
500 >            if (!isDirectional) {
501 >        
502 >              sprintf( writeLine,
503 >                 "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
504 >                 atomTypeString,
505 >                 atomData[0],
506 >                 atomData[1],
507 >                 atomData[2],
508 >                 atomData[3],
509 >                 atomData[4],
510 >                 atomData[5]);
511 >        
512 >             strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
513 >        
514 >            }
515 >            else {
516 >        
517 >                sprintf( writeLine,
518 >                         "%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",
519 >                         atomTypeString,
520 >                         atomData[0],
521 >                         atomData[1],
522 >                         atomData[2],
523 >                         atomData[3],
524 >                         atomData[4],
525 >                         atomData[5],
526 >                         atomData[6],
527 >                         atomData[7],
528 >                         atomData[8],
529 >                         atomData[9],
530 >                         atomData[10],
531 >                         atomData[11],
532 >                         atomData[12]);
533 >              
534 >            }
535 >            
536 >            for(k = 0; k < outFile.size(); k++)
537 >              *outFile[k] << writeLine;
538 >            
539 >            
540 >        }//end for(iter = integrableObject.begin())
541 >        
542 >      currentIndex++;
543 >      }
544 >
545 >    }//end for(i = 0; i < mpiSim->getNmol())
546 >    
547 >    for(k = 0; k < outFile.size(); k++)
548 >      outFile[k]->flush();
549 >    
550      sprintf( checkPointMsg,
551               "Sucessfully took a dump.\n");
552 +    
553      MPIcheckPoint();        
554      
555 +    delete[] potatoes;
556 +    
557    } else {
558  
559      // worldRank != 0, so I'm a remote node.  
560 +
561 +    // Set my magic potato to 0:
562 +
563 +    myPotato = 0;
564 +    currentIndex = 0;
565      
566 <    for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) {
566 >    for (i = 0 ; i < mpiSim->getNMolGlobal(); i++ ) {
567        
568 <      // Am I the node which has this atom?
568 >      // Am I the node which has this integrableObject?
569        
570 <      if (AtomToProcMap[i] == worldRank) {
570 >      if (MolToProcMap[i] == worldRank) {
571  
572 <        local_index=-1;
573 <        for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) {
574 <          if (atoms[j]->getGlobalIndex() == which_atom) local_index = j;
572 >
573 >        if (myPotato + 1 >= MAXTAG) {
574 >          
575 >          // The potato was going to exceed the maximum value,
576 >          // so wrap this processor potato back to 0 (and block until
577 >          // node 0 says we can go:
578 >          
579 >          MPI_Recv(&myPotato, 1, MPI_INT, 0, 0, MPI_COMM_WORLD, &istatus);
580 >          
581          }
334 –        if (local_index != -1) {
335 –        
336 –          atomTypeString = atoms[local_index]->getType();
582  
583 <          atoms[local_index]->getPos(pos);
584 <          atoms[local_index]->getVel(vel);
340 <
341 <          atomTransData[0] = pos[0];
342 <          atomTransData[1] = pos[1];
343 <          atomTransData[2] = pos[2];
344 <
345 <          atomTransData[3] = vel[0];
346 <          atomTransData[4] = vel[1];
347 <          atomTransData[5] = vel[2];
583 >          local_index = indexArray[currentIndex].first;        
584 >          integrableObjects = entry_plug->molecules[local_index].getIntegrableObjects();
585            
586 <          isDirectional = 0;
586 >          nCurObj = integrableObjects.size();
587 >                      
588 >          MPI_Send(&nCurObj, 1, MPI_INT, 0,
589 >                             myPotato, MPI_COMM_WORLD);
590 >          myPotato++;
591  
592 <          if( atoms[local_index]->isDirectional() ){
592 >          for( iter = integrableObjects.begin(); iter  != integrableObjects.end(); iter++){
593  
594 <            isDirectional = 1;
594 >            if (myPotato + 2 >= MAXTAG) {
595 >          
596 >              // The potato was going to exceed the maximum value,
597 >              // so wrap this processor potato back to 0 (and block until
598 >              // node 0 says we can go:
599 >          
600 >              MPI_Recv(&myPotato, 1, MPI_INT, 0, 0, MPI_COMM_WORLD, &istatus);
601 >              
602 >            }
603              
604 <            dAtom = (DirectionalAtom *)atoms[local_index];
356 <            dAtom->getQ( q );
604 >            sd = *iter;
605              
606 <            atomOrientData[0] = q[0];
359 <            atomOrientData[1] = q[1];
360 <            atomOrientData[2] = q[2];
361 <            atomOrientData[3] = q[3];
606 >            atomTypeString = sd->getType();
607  
608 <            atomOrientData[4] = dAtom->getJx();
609 <            atomOrientData[5] = dAtom->getJy();
365 <            atomOrientData[6] = dAtom->getJz();
366 <          }
608 >            sd->getPos(pos);
609 >            sd->getVel(vel);
610  
611 <        } else {
612 <          sprintf(painCave.errMsg,
613 <                  "Atom %d not found on processor %d\n",
371 <                  i, worldRank );
372 <          haveError= 1;
373 <          simError();
374 <        }
611 >            atomData[0] = pos[0];
612 >            atomData[1] = pos[1];
613 >            atomData[2] = pos[2];
614  
615 <        // I've survived this far, so send off the data!
615 >            atomData[3] = vel[0];
616 >            atomData[4] = vel[1];
617 >            atomData[5] = vel[2];
618 >              
619 >            isDirectional = 0;
620  
621 <        atomTypeTag          = 4*i;
379 <        atomIsDirectionalTag = 4*i + 1;
380 <        atomTransDataTag     = 4*i + 2;
381 <        atomOrientDataTag    = 4*i + 3;
621 >            if( sd->isDirectional() ){
622  
623 <
624 <        strncpy(MPIatomTypeString, atomTypeString, MINIBUFFERSIZE);
625 <
626 <        // null terminate the string before sending (just in case):
627 <        MPIatomTypeString[MINIBUFFERSIZE-1] = '\0';
628 <
629 <        MPI_Send(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, 0,
630 <                 atomTypeTag, MPI_COMM_WORLD);
631 <        
632 <        MPI_Send(&isDirectional, 1, MPI_INT, 0,
393 <                 atomIsDirectionalTag, MPI_COMM_WORLD);
394 <        
395 <        MPI_Send(atomTransData, 6, MPI_DOUBLE, 0,
396 <                 atomTransDataTag, MPI_COMM_WORLD);
397 <
398 <        if (isDirectional) {
399 <
400 <          MPI_Send(atomOrientData, 7, MPI_DOUBLE, 0,
401 <                   atomOrientDataTag, MPI_COMM_WORLD);
402 <          
403 <        }
623 >                isDirectional = 1;
624 >                
625 >                sd->getQ( q );
626 >                sd->getJ( ji );
627 >                
628 >                
629 >                atomData[6] = q[0];
630 >                atomData[7] = q[1];
631 >                atomData[8] = q[2];
632 >                atomData[9] = q[3];
633        
634 <      }
635 <    }
634 >                atomData[10] = ji[0];
635 >                atomData[11] = ji[1];
636 >                atomData[12] = ji[2];
637 >              }
638  
639 <    sprintf( checkPointMsg,
640 <             "Sucessfully took a dump.\n");
410 <    MPIcheckPoint();        
411 <    
412 <  }
413 <  
414 <  painCave.isEventLoop = 0;
639 >            
640 >            strncpy(MPIatomTypeString, atomTypeString, MINIBUFFERSIZE);
641  
642 < #endif // is_mpi
643 < }
642 >            // null terminate the string before sending (just in case):
643 >            MPIatomTypeString[MINIBUFFERSIZE-1] = '\0';
644  
645 < void DumpWriter::writeFinal(double finalTime){
645 >            MPI_Send(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, 0,
646 >                             myPotato, MPI_COMM_WORLD);
647 >            
648 >            myPotato++;
649 >            
650 >            if (isDirectional) {
651  
652 <  char finalName[500];
653 <  ofstream finalOut;
652 >              MPI_Send(atomData, 13, MPI_DOUBLE, 0,
653 >                       myPotato, MPI_COMM_WORLD);
654 >              
655 >            } else {
656  
657 <  const int BUFFERSIZE = 2000;
658 <  const int MINIBUFFERSIZE = 100;
659 <  char tempBuffer[BUFFERSIZE];
427 <  char writeLine[BUFFERSIZE];
428 <
429 <  double q[4];
430 <  DirectionalAtom* dAtom;
431 <  Atom** atoms = entry_plug->atoms;
432 <  int i;
433 < #ifdef IS_MPI
434 <  int j, which_node, done, which_atom, local_index;
435 <  double atomTransData[6];
436 <  double atomOrientData[7];
437 <  int isDirectional;
438 <  char* atomTypeString;
439 <  char MPIatomTypeString[MINIBUFFERSIZE];
440 <  int atomTypeTag;
441 <  int atomIsDirectionalTag;
442 <  int atomTransDataTag;
443 <  int atomOrientDataTag;
444 < #else //is_mpi
445 <  int nAtoms = entry_plug->n_atoms;
446 < #endif //is_mpi
447 <
448 <  double pos[3], vel[3];
449 <
450 < #ifdef IS_MPI
451 <  if(worldRank == 0 ){
452 < #endif // is_mpi
453 <
454 <    strcpy( finalName, entry_plug->finalName );
455 <
456 <    finalOut.open( finalName, ios::out | ios::trunc );
457 <    if( !finalOut ){
458 <      sprintf( painCave.errMsg,
459 <               "Could not open \"%s\" for final dump output.\n",
460 <               finalName );
461 <      painCave.isFatal = 1;
462 <      simError();
463 <    }
464 <
465 <    // finalOut.setf( ios::scientific );
466 <
467 < #ifdef IS_MPI
468 <  }
469 <
470 <  sprintf(checkPointMsg,"Opened file for final configuration\n");
471 <  MPIcheckPoint();
472 <
473 < #endif //is_mpi
474 <
475 <
476 < #ifndef IS_MPI
477 <
478 <  finalOut << nAtoms << "\n";
479 <
480 <  finalOut << finalTime << ";\t"
481 <           << entry_plug->Hmat[0][0] << "\t"
482 <           << entry_plug->Hmat[1][0] << "\t"
483 <           << entry_plug->Hmat[2][0] << ";\t"
484 <
485 <           << entry_plug->Hmat[0][1] << "\t"
486 <           << entry_plug->Hmat[1][1] << "\t"
487 <           << entry_plug->Hmat[2][1] << ";\t"
488 <
489 <           << entry_plug->Hmat[0][2] << "\t"
490 <           << entry_plug->Hmat[1][2] << "\t"
491 <           << entry_plug->Hmat[2][2] << ";";
492 <
493 <  //write out additional parameters, such as chi and eta
494 <  finalOut << entry_plug->the_integrator->getAdditionalParameters();
495 <  finalOut << endl;
496 <
497 <  for( i=0; i<nAtoms; i++ ){
498 <
499 <    atoms[i]->getPos(pos);
500 <    atoms[i]->getVel(vel);
501 <
502 <    sprintf( tempBuffer,
503 <             "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
504 <             atoms[i]->getType(),
505 <             pos[0],
506 <             pos[1],
507 <             pos[2],
508 <             vel[0],
509 <             vel[1],
510 <             vel[2]);
511 <    strcpy( writeLine, tempBuffer );
512 <
513 <    if( atoms[i]->isDirectional() ){
657 >              MPI_Send(atomData, 6, MPI_DOUBLE, 0,
658 >                       myPotato, MPI_COMM_WORLD);
659 >            }
660  
661 <      dAtom = (DirectionalAtom *)atoms[i];
516 <      dAtom->getQ( q );
661 >            myPotato++;  
662  
518 –      sprintf( tempBuffer,
519 –               "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
520 –               q[0],
521 –               q[1],
522 –               q[2],
523 –               q[3],
524 –               dAtom->getJx(),
525 –               dAtom->getJy(),
526 –               dAtom->getJz());
527 –      strcat( writeLine, tempBuffer );
528 –    }
529 –    else
530 –      strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
531 –
532 –    finalOut << writeLine;
533 –  }
534 –  finalOut.flush();
535 –  finalOut.close();
536 –
537 – #else // is_mpi
538 –
539 –  // first thing first, suspend fatalities.
540 –  painCave.isEventLoop = 1;
541 –
542 –  int myStatus; // 1 = wakeup & success; 0 = error; -1 = AllDone
543 –  int haveError;
544 –
545 –  MPI_Status istatus;
546 –  int *AtomToProcMap = mpiSim->getAtomToProcMap();
547 –
548 –  // write out header and node 0's coordinates
549 –
550 –  if( worldRank == 0 ){
551 –    finalOut << mpiSim->getTotAtoms() << "\n";
552 –
553 –    finalOut << finalTime << ";\t"
554 –            << entry_plug->Hmat[0][0] << "\t"
555 –            << entry_plug->Hmat[1][0] << "\t"
556 –            << entry_plug->Hmat[2][0] << ";\t"
557 –
558 –            << entry_plug->Hmat[0][1] << "\t"
559 –            << entry_plug->Hmat[1][1] << "\t"
560 –            << entry_plug->Hmat[2][1] << ";\t"
561 –
562 –            << entry_plug->Hmat[0][2] << "\t"
563 –            << entry_plug->Hmat[1][2] << "\t"
564 –            << entry_plug->Hmat[2][2] << ";";
565 –
566 –    finalOut << entry_plug->the_integrator->getAdditionalParameters();
567 –    finalOut << endl;
568 –    finalOut.flush();
569 –    for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) {
570 –      // Get the Node number which has this atom;
571 –
572 –      which_node = AtomToProcMap[i];
573 –
574 –      if (which_node != 0) {
575 –        
576 –        atomTypeTag          = 4*i;
577 –        atomIsDirectionalTag = 4*i + 1;
578 –        atomTransDataTag     = 4*i + 2;
579 –        atomOrientDataTag    = 4*i + 3;
580 –
581 –        MPI_Recv(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, which_node,
582 –                 atomTypeTag, MPI_COMM_WORLD, &istatus);
583 –        
584 –        strncpy(atomTypeString, MPIatomTypeString, MINIBUFFERSIZE);
585 –
586 –        MPI_Recv(&isDirectional, 1, MPI_INT, which_node,
587 –                 atomIsDirectionalTag, MPI_COMM_WORLD, &istatus);
588 –        
589 –        MPI_Recv(atomTransData, 6, MPI_DOUBLE, which_node,
590 –                 atomTransDataTag, MPI_COMM_WORLD, &istatus);
591 –
592 –        if (isDirectional) {
593 –
594 –          MPI_Recv(atomOrientData, 7, MPI_DOUBLE, which_node,
595 –                   atomOrientDataTag, MPI_COMM_WORLD, &istatus);
596 –
597 –        }
598 –
599 –      } else {
600 –        
601 –        haveError = 0;
602 –        which_atom = i;
603 –        local_index=-1;
604 –
605 –        for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) {
606 –          if (atoms[j]->getGlobalIndex() == which_atom) local_index = j;
607 –        }
608 –
609 –        if (local_index != -1) {
610 –
611 –          atomTypeString = atoms[local_index]->getType();
612 –
613 –          atoms[local_index]->getPos(pos);
614 –          atoms[local_index]->getVel(vel);
615 –
616 –          atomTransData[0] = pos[0];
617 –          atomTransData[1] = pos[1];
618 –          atomTransData[2] = pos[2];
619 –
620 –          atomTransData[3] = vel[0];
621 –          atomTransData[4] = vel[1];
622 –          atomTransData[5] = vel[2];
623 –          
624 –          isDirectional = 0;
625 –
626 –          if( atoms[local_index]->isDirectional() ){
627 –
628 –            isDirectional = 1;
629 –            
630 –            dAtom = (DirectionalAtom *)atoms[local_index];
631 –            dAtom->getQ( q );
632 –            
633 –            atomOrientData[0] = q[0];
634 –            atomOrientData[1] = q[1];
635 –            atomOrientData[2] = q[2];
636 –            atomOrientData[3] = q[3];
637 –
638 –            atomOrientData[4] = dAtom->getJx();
639 –            atomOrientData[5] = dAtom->getJy();
640 –            atomOrientData[6] = dAtom->getJz();
663            }
664  
665 <        } else {
666 <          sprintf(painCave.errMsg,
645 <                  "Atom %d not found on processor %d\n",
646 <                  i, worldRank );
647 <          haveError= 1;
648 <          simError();
649 <        }
650 <
651 <        if(haveError) DieDieDie();
652 <                              
653 <        // If we've survived to here, format the line:
654 <        
655 <        sprintf( tempBuffer,
656 <                 "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
657 <                 atomTypeString,
658 <                 atomTransData[0],
659 <                 atomTransData[1],
660 <                 atomTransData[2],
661 <                 atomTransData[3],
662 <                 atomTransData[4],
663 <                 atomTransData[5]);
664 <
665 <        strcpy( writeLine, tempBuffer );
666 <
667 <        if (isDirectional) {
668 <
669 <          sprintf( tempBuffer,
670 <                   "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
671 <                   atomOrientData[0],
672 <                   atomOrientData[1],
673 <                   atomOrientData[2],
674 <                   atomOrientData[3],
675 <                   atomOrientData[4],
676 <                   atomOrientData[5],
677 <                   atomOrientData[6]);
678 <          strcat( writeLine, tempBuffer );
679 <
680 <        } else {
681 <          strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
665 >          currentIndex++;    
666 >          
667          }
668 <
684 <        finalOut << writeLine;
685 <        finalOut.flush();
668 >      
669        }
687 –    }
670  
689 –    finalOut.flush();
671      sprintf( checkPointMsg,
672               "Sucessfully took a dump.\n");
673 <    MPIcheckPoint();        
673 >    MPIcheckPoint();                
674      
694 –  } else {
695 –
696 –    // worldRank != 0, so I'm a remote node.  
697 –    
698 –    for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) {
699 –      
700 –      // Am I the node which has this atom?
701 –      
702 –      if (AtomToProcMap[i] == worldRank) {
703 –
704 –        local_index=-1;
705 –        for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) {
706 –          if (atoms[j]->getGlobalIndex() == which_atom) local_index = j;
707 –        }
708 –        if (local_index != -1) {
709 –        
710 –          atomTypeString = atoms[local_index]->getType();
711 –
712 –          atoms[local_index]->getPos(pos);
713 –          atoms[local_index]->getVel(vel);
714 –
715 –          atomTransData[0] = pos[0];
716 –          atomTransData[1] = pos[1];
717 –          atomTransData[2] = pos[2];
718 –
719 –          atomTransData[3] = vel[0];
720 –          atomTransData[4] = vel[1];
721 –          atomTransData[5] = vel[2];
722 –          
723 –          isDirectional = 0;
724 –
725 –          if( atoms[local_index]->isDirectional() ){
726 –
727 –            isDirectional = 1;
728 –            
729 –            dAtom = (DirectionalAtom *)atoms[local_index];
730 –            dAtom->getQ( q );
731 –            
732 –            atomOrientData[0] = q[0];
733 –            atomOrientData[1] = q[1];
734 –            atomOrientData[2] = q[2];
735 –            atomOrientData[3] = q[3];
736 –
737 –            atomOrientData[4] = dAtom->getJx();
738 –            atomOrientData[5] = dAtom->getJy();
739 –            atomOrientData[6] = dAtom->getJz();
740 –          }
741 –
742 –        } else {
743 –          sprintf(painCave.errMsg,
744 –                  "Atom %d not found on processor %d\n",
745 –                  i, worldRank );
746 –          haveError= 1;
747 –          simError();
748 –        }
749 –
750 –        // I've survived this far, so send off the data!
751 –
752 –        atomTypeTag          = 4*i;
753 –        atomIsDirectionalTag = 4*i + 1;
754 –        atomTransDataTag     = 4*i + 2;
755 –        atomOrientDataTag    = 4*i + 3;
756 –
757 –        strncpy(MPIatomTypeString, atomTypeString, MINIBUFFERSIZE);
758 –
759 –        MPI_Send(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, 0,
760 –                 atomTypeTag, MPI_COMM_WORLD);
761 –        
762 –        MPI_Send(&isDirectional, 1, MPI_INT, 0,
763 –                 atomIsDirectionalTag, MPI_COMM_WORLD);
764 –        
765 –        MPI_Send(atomTransData, 6, MPI_DOUBLE, 0,
766 –                 atomTransDataTag, MPI_COMM_WORLD);
767 –
768 –        if (isDirectional) {
769 –
770 –          MPI_Send(atomOrientData, 7, MPI_DOUBLE, 0,
771 –                   atomOrientDataTag, MPI_COMM_WORLD);
772 –          
773 –        }
774 –      
775 –      }
675      }
676  
778 –    sprintf( checkPointMsg,
779 –             "Sucessfully wrote final file.\n");
780 –    MPIcheckPoint();        
781 –    
782 –  }
783 –  
784 –  painCave.isEventLoop = 0;
677  
678 <  if( worldRank == 0 ) finalOut.close();
678 >  
679   #endif // is_mpi
680   }
681  
790 –
791 –
682   #ifdef IS_MPI
683  
684   // a couple of functions to let us escape the write loop

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