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root/group/trunk/OOPSE/libmdtools/DumpWriter.cpp
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Comparing trunk/OOPSE/libmdtools/DumpWriter.cpp (file contents):
Revision 913 by chuckv, Thu Jan 8 22:25:52 2004 UTC vs.
Revision 1198 by tim, Thu May 27 00:48:12 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(),
149 <               dAtom->getJz());
150 <      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      }
152 –    else
153 –      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) {
311      MAXTAG = *tagub;
312    } else {
313      MAXTAG = 32767;
314 <  }
314 >  }  
315  
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 ){
178 –    outFile << mpiSim->getTotAtoms() << "\n";
325  
326 <    outFile << currentTime << ";\t"
181 <            << entry_plug->Hmat[0][0] << "\t"
182 <            << entry_plug->Hmat[1][0] << "\t"
183 <            << entry_plug->Hmat[2][0] << ";\t"
326 >    // Node 0 needs a list of the magic potatoes for each processor;
327  
328 <            << entry_plug->Hmat[0][1] << "\t"
329 <            << entry_plug->Hmat[1][1] << "\t"
187 <            << entry_plug->Hmat[2][1] << ";\t"
328 >    nProc = mpiSim->getNprocessors();
329 >    potatoes = new int[nProc];
330  
331 <            << entry_plug->Hmat[0][2] << "\t"
332 <            << entry_plug->Hmat[1][2] << "\t"
333 <            << entry_plug->Hmat[2][2] << ";";
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 <    outFile << entry_plug->the_integrator->getAdditionalParameters();
339 <    outFile << endl;
340 <    outFile.flush();
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 <    tag = 0;
343 >                         << entry_plug->Hmat[0][1] << "\t"
344 >                         << entry_plug->Hmat[1][1] << "\t"
345 >                         << entry_plug->Hmat[2][1] << ";\t"
346  
347 <    for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) {
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 <      if (tag + 2 >= MAXTAG) {
355 <        // The tag was going to exceed the maximum value, so wrap around to 0:
356 <        tag = 0;
204 <        // Send the newly zeroed tag on to the other nodes:
205 <        MPI_Bcast(&tag, 1, MPI_INT, 0, MPI_COMM_WORLD);
206 <      }
354 >    currentIndex = 0;
355 >
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 <        MPI_Recv(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, which_node,
365 <                 atomTypeTag, MPI_COMM_WORLD, &istatus);
366 <        
217 <        strncpy(atomTypeString, MPIatomTypeString, MINIBUFFERSIZE);
218 <        
219 <        // Null terminate the atomTypeString just in case:
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 <        atomTypeString[strlen(atomTypeString) - 1] = '\0';
369 <
370 <        MPI_Recv(&isDirectional, 1, MPI_INT, which_node,
224 <                 atomIsDirectionalTag, MPI_COMM_WORLD, &istatus);
225 <        
226 <        MPI_Recv(atomTransData, 6, MPI_DOUBLE, which_node,
227 <                 atomTransDataTag, MPI_COMM_WORLD, &istatus);
228 <
229 <        if (isDirectional) {
230 <
231 <          MPI_Recv(atomOrientData, 7, MPI_DOUBLE, which_node,
232 <                   atomOrientDataTag, MPI_COMM_WORLD, &istatus);
233 <
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;
239 <        which_atom = i;
240 <        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);
251 <          atoms[local_index]->getVel(vel);
394 >          atomTypeString = MPIatomTypeString;
395  
396 <          atomTransData[0] = pos[0];
254 <          atomTransData[1] = pos[1];
255 <          atomTransData[2] = pos[2];
396 >          myPotato++;
397  
398 <          atomTransData[3] = vel[0];
399 <          atomTransData[4] = vel[1];
259 <          atomTransData[5] = vel[2];
260 <          
261 <          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 <            dAtom = (DirectionalAtom *)atoms[local_index];
409 <            dAtom->getQ( q );
269 <            
270 <            atomOrientData[0] = q[0];
271 <            atomOrientData[1] = q[1];
272 <            atomOrientData[2] = q[2];
273 <            atomOrientData[3] = q[3];
408 >        }
409 >        potatoes[which_node] = myPotato;
410  
411 <            atomOrientData[4] = dAtom->getJx();
412 <            atomOrientData[5] = dAtom->getJy();
413 <            atomOrientData[6] = dAtom->getJz();
414 <          }
411 >      } else {
412 >        
413 >        haveError = 0;
414 >        
415 >            local_index = indexArray[currentIndex].first;        
416  
417 <        } else {
281 <          sprintf(painCave.errMsg,
282 <                  "Atom %d not found on processor %d\n",
283 <                  i, worldRank );
284 <          haveError= 1;
285 <          simError();
286 <        }
417 >        integrableObjects = (entry_plug->molecules[local_index]).getIntegrableObjects();
418  
419 <        if(haveError) DieDieDie();
420 <                              
421 <        // If we've survived to here, format the line:
422 <        
423 <        sprintf( tempBuffer,
424 <                 "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
425 <                 atomTypeString,
426 <                 atomTransData[0],
427 <                 atomTransData[1],
428 <                 atomTransData[2],
298 <                 atomTransData[3],
299 <                 atomTransData[4],
300 <                 atomTransData[5]);
419 >        for(iter= integrableObjects.begin(); iter != integrableObjects.end(); ++iter){    
420 >                sd = *iter;
421 >            atomTypeString = sd->getType();
422 >            
423 >            sd->getPos(pos);
424 >            sd->getVel(vel);          
425 >          
426 >            atomData[0] = pos[0];
427 >            atomData[1] = pos[1];
428 >            atomData[2] = pos[2];
429  
430 <        strcpy( writeLine, tempBuffer );
430 >            atomData[3] = vel[0];
431 >            atomData[4] = vel[1];
432 >            atomData[5] = vel[2];
433 >              
434 >            isDirectional = 0;
435  
436 <        if (isDirectional) {
436 >            if( sd->isDirectional() ){
437  
438 <          sprintf( tempBuffer,
439 <                   "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
440 <                   atomOrientData[0],
441 <                   atomOrientData[1],
310 <                   atomOrientData[2],
311 <                   atomOrientData[3],
312 <                   atomOrientData[4],
313 <                   atomOrientData[5],
314 <                   atomOrientData[6]);
315 <          strcat( writeLine, tempBuffer );
438 >              isDirectional = 1;
439 >                
440 >              sd->getQ( q );
441 >              sd->getJ( ji );
442  
443 <        } else {
444 <          strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
443 >              for (int j = 0; j < 6 ; j++)
444 >                atomData[j] = atomData[j];            
445 >              
446 >              atomData[6] = q[0];
447 >              atomData[7] = q[1];
448 >              atomData[8] = q[2];
449 >              atomData[9] = q[3];
450 >              
451 >              atomData[10] = ji[0];
452 >              atomData[11] = ji[1];
453 >              atomData[12] = ji[2];
454 >            }
455 >            
456          }
457 <
458 <        outFile << writeLine;
322 <        outFile.flush();
457 >        
458 >      currentIndex++;
459        }
460 +      // If we've survived to here, format the line:
461 +      
462 +      if (!isDirectional) {
463 +        
464 +        sprintf( writeLine,
465 +                 "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
466 +                 atomTypeString,
467 +                 atomData[0],
468 +                 atomData[1],
469 +                 atomData[2],
470 +                 atomData[3],
471 +                 atomData[4],
472 +                 atomData[5]);
473 +        
474 +        strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
475 +        
476 +      } else {
477 +        
478 +        sprintf( writeLine,
479 +                 "%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",
480 +                 atomTypeString,
481 +                 atomData[0],
482 +                 atomData[1],
483 +                 atomData[2],
484 +                 atomData[3],
485 +                 atomData[4],
486 +                 atomData[5],
487 +                 atomData[6],
488 +                 atomData[7],
489 +                 atomData[8],
490 +                 atomData[9],
491 +                 atomData[10],
492 +                 atomData[11],
493 +                 atomData[12]);
494 +        
495 +      }
496 +      
497 +      for(k = 0; k < outFile.size(); k++)
498 +        *outFile[k] << writeLine;
499      }
500 <
501 <    outFile.flush();
500 >    
501 >    for(k = 0; k < outFile.size(); k++)
502 >      outFile[k]->flush();
503 >    
504      sprintf( checkPointMsg,
505               "Sucessfully took a dump.\n");
506 +    
507      MPIcheckPoint();        
508      
509 +    delete[] potatoes;
510 +    
511    } else {
512  
513      // worldRank != 0, so I'm a remote node.  
514 +
515 +    // Set my magic potato to 0:
516 +
517 +    myPotato = 0;
518 +    currentIndex = 0;
519      
520 <    for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) {
520 >    for (i = 0 ; i < mpiSim->getTotNmol(); i++ ) {
521        
522 <      // Am I the node which has this atom?
522 >      // Am I the node which has this integrableObject?
523        
524 <      if (AtomToProcMap[i] == worldRank) {
524 >      if (MolToProcMap[i] == worldRank) {
525  
526 <        local_index=-1;
527 <        for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) {
528 <          if (atoms[j]->getGlobalIndex() == which_atom) local_index = j;
526 >
527 >        if (myPotato + 1 >= MAXTAG) {
528 >          
529 >          // The potato was going to exceed the maximum value,
530 >          // so wrap this processor potato back to 0 (and block until
531 >          // node 0 says we can go:
532 >          
533 >          MPI_Recv(&myPotato, 1, MPI_INT, 0, 0, MPI_COMM_WORLD, &istatus);
534 >          
535          }
345 –        if (local_index != -1) {
346 –        
347 –          atomTypeString = atoms[local_index]->getType();
536  
537 <          atoms[local_index]->getPos(pos);
538 <          atoms[local_index]->getVel(vel);
351 <
352 <          atomTransData[0] = pos[0];
353 <          atomTransData[1] = pos[1];
354 <          atomTransData[2] = pos[2];
355 <
356 <          atomTransData[3] = vel[0];
357 <          atomTransData[4] = vel[1];
358 <          atomTransData[5] = vel[2];
537 >          local_index = indexArray[currentIndex].first;        
538 >          integrableObjects = entry_plug->molecules[local_index].getIntegrableObjects();
539            
540 <          isDirectional = 0;
540 >          nCurObj = integrableObjects.size();
541 >                      
542 >          MPI_Send(&nCurObj, 1, MPI_INT, 0,
543 >                             myPotato, MPI_COMM_WORLD);
544 >          myPotato++;
545  
546 <          if( atoms[local_index]->isDirectional() ){
546 >          for( iter = integrableObjects.begin(); iter  != integrableObjects.end(); iter++){
547  
548 <            isDirectional = 1;
548 >            if (myPotato + 2 >= MAXTAG) {
549 >          
550 >              // The potato was going to exceed the maximum value,
551 >              // so wrap this processor potato back to 0 (and block until
552 >              // node 0 says we can go:
553 >          
554 >              MPI_Recv(&myPotato, 1, MPI_INT, 0, 0, MPI_COMM_WORLD, &istatus);
555 >              
556 >            }
557              
558 <            dAtom = (DirectionalAtom *)atoms[local_index];
367 <            dAtom->getQ( q );
558 >            sd = *iter;
559              
560 <            atomOrientData[0] = q[0];
370 <            atomOrientData[1] = q[1];
371 <            atomOrientData[2] = q[2];
372 <            atomOrientData[3] = q[3];
560 >            atomTypeString = sd->getType();
561  
562 <            atomOrientData[4] = dAtom->getJx();
563 <            atomOrientData[5] = dAtom->getJy();
376 <            atomOrientData[6] = dAtom->getJz();
377 <          }
562 >            sd->getPos(pos);
563 >            sd->getVel(vel);
564  
565 <        } else {
566 <          sprintf(painCave.errMsg,
567 <                  "Atom %d not found on processor %d\n",
382 <                  i, worldRank );
383 <          haveError= 1;
384 <          simError();
385 <        }
565 >            atomData[0] = pos[0];
566 >            atomData[1] = pos[1];
567 >            atomData[2] = pos[2];
568  
569 <        // I've survived this far, so send off the data!
569 >            atomData[3] = vel[0];
570 >            atomData[4] = vel[1];
571 >            atomData[5] = vel[2];
572 >              
573 >            isDirectional = 0;
574  
575 <        atomTypeTag          = 4*i;
390 <        atomIsDirectionalTag = 4*i + 1;
391 <        atomTransDataTag     = 4*i + 2;
392 <        atomOrientDataTag    = 4*i + 3;
575 >            if( sd->isDirectional() ){
576  
577 <
578 <        strncpy(MPIatomTypeString, atomTypeString, MINIBUFFERSIZE);
579 <
580 <        // null terminate the string before sending (just in case):
581 <        MPIatomTypeString[MINIBUFFERSIZE-1] = '\0';
582 <
583 <        MPI_Send(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, 0,
584 <                 atomTypeTag, MPI_COMM_WORLD);
585 <        
586 <        MPI_Send(&isDirectional, 1, MPI_INT, 0,
404 <                 atomIsDirectionalTag, MPI_COMM_WORLD);
405 <        
406 <        MPI_Send(atomTransData, 6, MPI_DOUBLE, 0,
407 <                 atomTransDataTag, MPI_COMM_WORLD);
408 <
409 <        if (isDirectional) {
410 <
411 <          MPI_Send(atomOrientData, 7, MPI_DOUBLE, 0,
412 <                   atomOrientDataTag, MPI_COMM_WORLD);
413 <          
414 <        }
577 >                isDirectional = 1;
578 >                
579 >                sd->getQ( q );
580 >                sd->getJ( ji );
581 >                
582 >                
583 >                atomData[6] = q[0];
584 >                atomData[7] = q[1];
585 >                atomData[8] = q[2];
586 >                atomData[9] = q[3];
587        
588 <      }
589 <    }
588 >                atomData[10] = ji[0];
589 >                atomData[11] = ji[1];
590 >                atomData[12] = ji[2];
591 >              }
592  
593 <    sprintf( checkPointMsg,
594 <             "Sucessfully took a dump.\n");
421 <    MPIcheckPoint();        
422 <    
423 <  }
424 <  
425 <  painCave.isEventLoop = 0;
593 >            
594 >            strncpy(MPIatomTypeString, atomTypeString, MINIBUFFERSIZE);
595  
596 < #endif // is_mpi
597 < }
596 >            // null terminate the string before sending (just in case):
597 >            MPIatomTypeString[MINIBUFFERSIZE-1] = '\0';
598  
599 < void DumpWriter::writeFinal(double finalTime){
599 >            MPI_Send(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, 0,
600 >                             myPotato, MPI_COMM_WORLD);
601 >            
602 >            myPotato++;
603 >            
604 >            if (isDirectional) {
605  
606 <  char finalName[500];
607 <  ofstream finalOut;
606 >              MPI_Send(atomData, 13, MPI_DOUBLE, 0,
607 >                       myPotato, MPI_COMM_WORLD);
608 >              
609 >            } else {
610  
611 <  const int BUFFERSIZE = 2000;
612 <  const int MINIBUFFERSIZE = 100;
613 <  char tempBuffer[BUFFERSIZE];
438 <  char writeLine[BUFFERSIZE];
611 >              MPI_Send(atomData, 6, MPI_DOUBLE, 0,
612 >                       myPotato, MPI_COMM_WORLD);
613 >            }
614  
615 <  double q[4];
441 <  DirectionalAtom* dAtom;
442 <  Atom** atoms = entry_plug->atoms;
443 <  int i;
444 < #ifdef IS_MPI
445 <  int j, which_node, done, which_atom, local_index;
446 <  double atomTransData[6];
447 <  double atomOrientData[7];
448 <  int isDirectional;
449 <  char* atomTypeString;
450 <  char MPIatomTypeString[MINIBUFFERSIZE];
451 <  int atomTypeTag;
452 <  int atomIsDirectionalTag;
453 <  int atomTransDataTag;
454 <  int atomOrientDataTag;
455 < #else //is_mpi
456 <  int nAtoms = entry_plug->n_atoms;
457 < #endif //is_mpi
458 <
459 <  double pos[3], vel[3];
460 <
461 < #ifdef IS_MPI
462 <  if(worldRank == 0 ){
463 < #endif // is_mpi
464 <
465 <    strcpy( finalName, entry_plug->finalName );
466 <
467 <    finalOut.open( finalName, ios::out | ios::trunc );
468 <    if( !finalOut ){
469 <      sprintf( painCave.errMsg,
470 <               "Could not open \"%s\" for final dump output.\n",
471 <               finalName );
472 <      painCave.isFatal = 1;
473 <      simError();
474 <    }
475 <
476 <    // finalOut.setf( ios::scientific );
477 <
478 < #ifdef IS_MPI
479 <  }
480 <
481 <  sprintf(checkPointMsg,"Opened file for final configuration\n");
482 <  MPIcheckPoint();
483 <
484 < #endif //is_mpi
485 <
486 <
487 < #ifndef IS_MPI
488 <
489 <  finalOut << nAtoms << "\n";
490 <
491 <  finalOut << finalTime << ";\t"
492 <           << entry_plug->Hmat[0][0] << "\t"
493 <           << entry_plug->Hmat[1][0] << "\t"
494 <           << entry_plug->Hmat[2][0] << ";\t"
495 <
496 <           << entry_plug->Hmat[0][1] << "\t"
497 <           << entry_plug->Hmat[1][1] << "\t"
498 <           << entry_plug->Hmat[2][1] << ";\t"
499 <
500 <           << entry_plug->Hmat[0][2] << "\t"
501 <           << entry_plug->Hmat[1][2] << "\t"
502 <           << entry_plug->Hmat[2][2] << ";";
503 <
504 <  //write out additional parameters, such as chi and eta
505 <  finalOut << entry_plug->the_integrator->getAdditionalParameters();
506 <  finalOut << endl;
507 <
508 <  for( i=0; i<nAtoms; i++ ){
509 <
510 <    atoms[i]->getPos(pos);
511 <    atoms[i]->getVel(vel);
512 <
513 <    sprintf( tempBuffer,
514 <             "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
515 <             atoms[i]->getType(),
516 <             pos[0],
517 <             pos[1],
518 <             pos[2],
519 <             vel[0],
520 <             vel[1],
521 <             vel[2]);
522 <    strcpy( writeLine, tempBuffer );
523 <
524 <    if( atoms[i]->isDirectional() ){
525 <
526 <      dAtom = (DirectionalAtom *)atoms[i];
527 <      dAtom->getQ( q );
528 <
529 <      sprintf( tempBuffer,
530 <               "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
531 <               q[0],
532 <               q[1],
533 <               q[2],
534 <               q[3],
535 <               dAtom->getJx(),
536 <               dAtom->getJy(),
537 <               dAtom->getJz());
538 <      strcat( writeLine, tempBuffer );
539 <    }
540 <    else
541 <      strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
615 >            myPotato++;  
616  
543 –    finalOut << writeLine;
544 –  }
545 –  finalOut.flush();
546 –  finalOut.close();
547 –
548 – #else // is_mpi
549 –
550 –  // first thing first, suspend fatalities.
551 –  painCave.isEventLoop = 1;
552 –
553 –  int myStatus; // 1 = wakeup & success; 0 = error; -1 = AllDone
554 –  int haveError;
555 –
556 –  MPI_Status istatus;
557 –  int *AtomToProcMap = mpiSim->getAtomToProcMap();
558 –
559 –  // write out header and node 0's coordinates
560 –
561 –  if( worldRank == 0 ){
562 –    finalOut << mpiSim->getTotAtoms() << "\n";
563 –
564 –    finalOut << finalTime << ";\t"
565 –            << entry_plug->Hmat[0][0] << "\t"
566 –            << entry_plug->Hmat[1][0] << "\t"
567 –            << entry_plug->Hmat[2][0] << ";\t"
568 –
569 –            << entry_plug->Hmat[0][1] << "\t"
570 –            << entry_plug->Hmat[1][1] << "\t"
571 –            << entry_plug->Hmat[2][1] << ";\t"
572 –
573 –            << entry_plug->Hmat[0][2] << "\t"
574 –            << entry_plug->Hmat[1][2] << "\t"
575 –            << entry_plug->Hmat[2][2] << ";";
576 –
577 –    finalOut << entry_plug->the_integrator->getAdditionalParameters();
578 –    finalOut << endl;
579 –    finalOut.flush();
580 –    for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) {
581 –      // Get the Node number which has this atom;
582 –
583 –      which_node = AtomToProcMap[i];
584 –
585 –      if (which_node != 0) {
586 –        
587 –        atomTypeTag          = 4*i;
588 –        atomIsDirectionalTag = 4*i + 1;
589 –        atomTransDataTag     = 4*i + 2;
590 –        atomOrientDataTag    = 4*i + 3;
591 –
592 –        MPI_Recv(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, which_node,
593 –                 atomTypeTag, MPI_COMM_WORLD, &istatus);
594 –        
595 –        strncpy(atomTypeString, MPIatomTypeString, MINIBUFFERSIZE);
596 –
597 –        MPI_Recv(&isDirectional, 1, MPI_INT, which_node,
598 –                 atomIsDirectionalTag, MPI_COMM_WORLD, &istatus);
599 –        
600 –        MPI_Recv(atomTransData, 6, MPI_DOUBLE, which_node,
601 –                 atomTransDataTag, MPI_COMM_WORLD, &istatus);
602 –
603 –        if (isDirectional) {
604 –
605 –          MPI_Recv(atomOrientData, 7, MPI_DOUBLE, which_node,
606 –                   atomOrientDataTag, MPI_COMM_WORLD, &istatus);
607 –
608 –        }
609 –
610 –      } else {
611 –        
612 –        haveError = 0;
613 –        which_atom = i;
614 –        local_index=-1;
615 –
616 –        for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) {
617 –          if (atoms[j]->getGlobalIndex() == which_atom) local_index = j;
618 –        }
619 –
620 –        if (local_index != -1) {
621 –
622 –          atomTypeString = atoms[local_index]->getType();
623 –
624 –          atoms[local_index]->getPos(pos);
625 –          atoms[local_index]->getVel(vel);
626 –
627 –          atomTransData[0] = pos[0];
628 –          atomTransData[1] = pos[1];
629 –          atomTransData[2] = pos[2];
630 –
631 –          atomTransData[3] = vel[0];
632 –          atomTransData[4] = vel[1];
633 –          atomTransData[5] = vel[2];
634 –          
635 –          isDirectional = 0;
636 –
637 –          if( atoms[local_index]->isDirectional() ){
638 –
639 –            isDirectional = 1;
640 –            
641 –            dAtom = (DirectionalAtom *)atoms[local_index];
642 –            dAtom->getQ( q );
643 –            
644 –            atomOrientData[0] = q[0];
645 –            atomOrientData[1] = q[1];
646 –            atomOrientData[2] = q[2];
647 –            atomOrientData[3] = q[3];
648 –
649 –            atomOrientData[4] = dAtom->getJx();
650 –            atomOrientData[5] = dAtom->getJy();
651 –            atomOrientData[6] = dAtom->getJz();
617            }
618  
619 <        } else {
620 <          sprintf(painCave.errMsg,
656 <                  "Atom %d not found on processor %d\n",
657 <                  i, worldRank );
658 <          haveError= 1;
659 <          simError();
660 <        }
661 <
662 <        if(haveError) DieDieDie();
663 <                              
664 <        // If we've survived to here, format the line:
665 <        
666 <        sprintf( tempBuffer,
667 <                 "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
668 <                 atomTypeString,
669 <                 atomTransData[0],
670 <                 atomTransData[1],
671 <                 atomTransData[2],
672 <                 atomTransData[3],
673 <                 atomTransData[4],
674 <                 atomTransData[5]);
675 <
676 <        strcpy( writeLine, tempBuffer );
677 <
678 <        if (isDirectional) {
679 <
680 <          sprintf( tempBuffer,
681 <                   "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
682 <                   atomOrientData[0],
683 <                   atomOrientData[1],
684 <                   atomOrientData[2],
685 <                   atomOrientData[3],
686 <                   atomOrientData[4],
687 <                   atomOrientData[5],
688 <                   atomOrientData[6]);
689 <          strcat( writeLine, tempBuffer );
690 <
691 <        } else {
692 <          strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
619 >          currentIndex++;    
620 >          
621          }
622 <
695 <        finalOut << writeLine;
696 <        finalOut.flush();
622 >      
623        }
698 –    }
624  
700 –    finalOut.flush();
625      sprintf( checkPointMsg,
626               "Sucessfully took a dump.\n");
627 <    MPIcheckPoint();        
627 >    MPIcheckPoint();                
628      
705 –  } else {
706 –
707 –    // worldRank != 0, so I'm a remote node.  
708 –    
709 –    for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) {
710 –      
711 –      // Am I the node which has this atom?
712 –      
713 –      if (AtomToProcMap[i] == worldRank) {
714 –
715 –        local_index=-1;
716 –        for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) {
717 –          if (atoms[j]->getGlobalIndex() == which_atom) local_index = j;
718 –        }
719 –        if (local_index != -1) {
720 –        
721 –          atomTypeString = atoms[local_index]->getType();
722 –
723 –          atoms[local_index]->getPos(pos);
724 –          atoms[local_index]->getVel(vel);
725 –
726 –          atomTransData[0] = pos[0];
727 –          atomTransData[1] = pos[1];
728 –          atomTransData[2] = pos[2];
729 –
730 –          atomTransData[3] = vel[0];
731 –          atomTransData[4] = vel[1];
732 –          atomTransData[5] = vel[2];
733 –          
734 –          isDirectional = 0;
735 –
736 –          if( atoms[local_index]->isDirectional() ){
737 –
738 –            isDirectional = 1;
739 –            
740 –            dAtom = (DirectionalAtom *)atoms[local_index];
741 –            dAtom->getQ( q );
742 –            
743 –            atomOrientData[0] = q[0];
744 –            atomOrientData[1] = q[1];
745 –            atomOrientData[2] = q[2];
746 –            atomOrientData[3] = q[3];
747 –
748 –            atomOrientData[4] = dAtom->getJx();
749 –            atomOrientData[5] = dAtom->getJy();
750 –            atomOrientData[6] = dAtom->getJz();
751 –          }
752 –
753 –        } else {
754 –          sprintf(painCave.errMsg,
755 –                  "Atom %d not found on processor %d\n",
756 –                  i, worldRank );
757 –          haveError= 1;
758 –          simError();
759 –        }
760 –
761 –        // I've survived this far, so send off the data!
762 –
763 –        atomTypeTag          = 4*i;
764 –        atomIsDirectionalTag = 4*i + 1;
765 –        atomTransDataTag     = 4*i + 2;
766 –        atomOrientDataTag    = 4*i + 3;
767 –
768 –        strncpy(MPIatomTypeString, atomTypeString, MINIBUFFERSIZE);
769 –
770 –        MPI_Send(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, 0,
771 –                 atomTypeTag, MPI_COMM_WORLD);
772 –        
773 –        MPI_Send(&isDirectional, 1, MPI_INT, 0,
774 –                 atomIsDirectionalTag, MPI_COMM_WORLD);
775 –        
776 –        MPI_Send(atomTransData, 6, MPI_DOUBLE, 0,
777 –                 atomTransDataTag, MPI_COMM_WORLD);
778 –
779 –        if (isDirectional) {
780 –
781 –          MPI_Send(atomOrientData, 7, MPI_DOUBLE, 0,
782 –                   atomOrientDataTag, MPI_COMM_WORLD);
783 –          
784 –        }
785 –      
786 –      }
629      }
630  
789 –    sprintf( checkPointMsg,
790 –             "Sucessfully wrote final file.\n");
791 –    MPIcheckPoint();        
792 –    
793 –  }
794 –  
795 –  painCave.isEventLoop = 0;
631  
632 <  if( worldRank == 0 ) finalOut.close();
632 >  
633   #endif // is_mpi
634   }
635  
801 –
802 –
636   #ifdef IS_MPI
637  
638   // a couple of functions to let us escape the write loop

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