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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 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 <  const int BUFFERSIZE = 2000;
71 <  const int MINIBUFFERSIZE = 100;
70 > /**
71 > * A hook function to load balancing
72 > */
73  
74 <  char tempBuffer[BUFFERSIZE];
75 <  char writeLine[BUFFERSIZE];
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 <  int i;
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 <  int j, which_node, done, which_atom, local_index;
109 <  double atomTransData[6];
110 <  double atomOrientData[7];
111 <  int isDirectional;
112 <  char* atomTypeString;
113 <  char MPIatomTypeString[MINIBUFFERSIZE];
114 <  int me;
115 <  int atomTypeTag;
116 <  int atomIsDirectionalTag;
117 <  int atomTransDataTag;
118 <  int atomOrientDataTag;
119 < #else //is_mpi
120 <  int nAtoms = entry_plug->n_atoms;
89 < #endif //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 <  double q[4];
123 <  DirectionalAtom* dAtom;
93 <  Atom** atoms = entry_plug->atoms;
94 <  double pos[3], vel[3];
122 >  fileStreams.push_back(&finalOut);
123 >  fileStreams.push_back(&dumpFile);
124  
125 <  // write current frame to the eor file
125 >  writeFrame(fileStreams, currentTime);
126  
127 <  this->writeFinal( currentTime );
127 > #ifdef IS_MPI
128 >  finalOut.close();
129 > #endif
130 >        
131 > }
132  
133 < #ifndef IS_MPI
133 > void DumpWriter::writeFinal(double currentTime){
134  
135 <  outFile << nAtoms << "\n";
135 >  ofstream finalOut;
136 >  vector<ofstream*> fileStreams;
137  
138 <  outFile << currentTime << ";\t"
139 <          << entry_plug->Hmat[0][0] << "\t"
140 <          << entry_plug->Hmat[1][0] << "\t"
107 <          << entry_plug->Hmat[2][0] << ";\t"
138 > #ifdef IS_MPI
139 >  if(worldRank == 0 ){
140 > #endif // is_mpi
141  
142 <          << entry_plug->Hmat[0][1] << "\t"
110 <          << entry_plug->Hmat[1][1] << "\t"
111 <          << entry_plug->Hmat[2][1] << ";\t"
142 >    finalOut.open( entry_plug->finalName, ios::out | ios::trunc );
143  
144 <          << entry_plug->Hmat[0][2] << "\t"
145 <          << entry_plug->Hmat[1][2] << "\t"
146 <          << entry_plug->Hmat[2][2] << ";";
147 <  //write out additional parameters, such as chi and eta
148 <  outFile << entry_plug->the_integrator->getAdditionalParameters();
149 <  outFile << endl;
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 <  for( i=0; i<nAtoms; i++ ){
152 > #ifdef IS_MPI
153 >  }
154 > #endif // is_mpi
155 >  
156 >  fileStreams.push_back(&finalOut);  
157 >  writeFrame(fileStreams, currentTime);
158  
159 <    atoms[i]->getPos(pos);
160 <    atoms[i]->getVel(vel);
159 > #ifdef IS_MPI
160 >  finalOut.close();
161 > #endif
162 >  
163 > }
164  
165 <    sprintf( tempBuffer,
126 <             "%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 );
165 > void DumpWriter::writeFrame( vector<ofstream*>& outFile, double currentTime ){
166  
167 <    if( atoms[i]->isDirectional() ){
167 >  const int BUFFERSIZE = 2000;
168 >  const int MINIBUFFERSIZE = 100;
169  
170 <      dAtom = (DirectionalAtom *)atoms[i];
171 <      dAtom->getQ( q );
170 >  char tempBuffer[BUFFERSIZE];  
171 >  char writeLine[BUFFERSIZE];
172 >
173 >  int i, k;
174 >
175 > #ifdef IS_MPI
176 >  
177 >  /*********************************************************************
178 >   * Documentation?  You want DOCUMENTATION?
179 >   *
180 >   * Why all the potatoes below?  
181 >   *
182 >   * To make a long story short, the original version of DumpWriter
183 >   * worked in the most inefficient way possible.  Node 0 would
184 >   * poke each of the node for an individual atom's formatted data
185 >   * as node 0 worked its way down the global index. This was particularly
186 >   * inefficient since the method blocked all processors at every atom
187 >   * (and did it twice!).
188 >   *
189 >   * An intermediate version of DumpWriter could be described from Node
190 >   * zero's perspective as follows:
191 >   *
192 >   *  1) Have 100 of your friends stand in a circle.
193 >   *  2) When you say go, have all of them start tossing potatoes at
194 >   *     you (one at a time).
195 >   *  3) Catch the potatoes.
196 >   *
197 >   * It was an improvement, but MPI has buffers and caches that could
198 >   * best be described in this analogy as "potato nets", so there's no
199 >   * need to block the processors atom-by-atom.
200 >   *
201 >   * This new and improved DumpWriter works in an even more efficient
202 >   * way:
203 >   *
204 >   *  1) Have 100 of your friend stand in a circle.
205 >   *  2) When you say go, have them start tossing 5-pound bags of
206 >   *     potatoes at you.
207 >   *  3) Once you've caught a friend's bag of potatoes,
208 >   *     toss them a spud to let them know they can toss another bag.
209 >   *
210 >   * How's THAT for documentation?
211 >   *
212 >   *********************************************************************/
213  
214 +  int *potatoes;
215 +  int myPotato;
216 +
217 +  int nProc;
218 +  int j, which_node, done, which_atom, local_index, currentIndex;
219 +  double atomData[13];
220 +  int isDirectional;
221 +  char* atomTypeString;
222 +  char MPIatomTypeString[MINIBUFFERSIZE];
223 +  int nObjects;
224 +  int msgLen; // the length of message actually recieved at master nodes
225 + #endif //is_mpi
226 +
227 +  double q[4], ji[3];
228 +  DirectionalAtom* dAtom;
229 +  double pos[3], vel[3];
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[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 +                     << entry_plug->Hmat[0][2] << "\t"
251 +                     << entry_plug->Hmat[1][2] << "\t"
252 +                     << entry_plug->Hmat[2][2] << ";";
253 +
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 +    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        sprintf( tempBuffer,
269 <               "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
270 <               q[0],
271 <               q[1],
272 <               q[2],
273 <               q[3],
274 <               dAtom->getJx(),
275 <               dAtom->getJy(),
276 <               dAtom->getJz());
277 <      strcat( writeLine, 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 >      if( sd->isDirectional() ){
280 >
281 >        sd->getQ( q );
282 >        sd->getJ( ji );
283 >
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    /* 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->getNMolGlobal(); 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 +          // 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              
270 –            atomOrientData[0] = q[0];
271 –            atomOrientData[1] = q[1];
272 –            atomOrientData[2] = q[2];
273 –            atomOrientData[3] = q[3];
274 –
275 –            atomOrientData[4] = dAtom->getJx();
276 –            atomOrientData[5] = dAtom->getJy();
277 –            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,
282 <                  "Atom %d not found on processor %d\n",
283 <                  i, worldRank );
284 <          haveError= 1;
285 <          simError();
286 <        }
449 >        }// end for(int l =0)
450 >        potatoes[which_node] = myPotato;
451  
452 <        if(haveError) DieDieDie();
453 <                              
290 <        // 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,
295 <                 atomTransData[0],
296 <                 atomTransData[1],
297 <                 atomTransData[2],
298 <                 atomTransData[3],
299 <                 atomTransData[4],
300 <                 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],
311 <                   atomOrientData[3],
312 <                   atomOrientData[4],
313 <                   atomOrientData[5],
314 <                   atomOrientData[6]);
315 <          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 {
318 <          strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
319 <        }
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          }
345 –        if (local_index != -1) {
346 –        
347 –          atomTypeString = atoms[local_index]->getType();
582  
583 <          atoms[local_index]->getPos(pos);
584 <          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];
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];
367 <            dAtom->getQ( q );
604 >            sd = *iter;
605              
606 <            atomOrientData[0] = q[0];
370 <            atomOrientData[1] = q[1];
371 <            atomOrientData[2] = q[2];
372 <            atomOrientData[3] = q[3];
606 >            atomTypeString = sd->getType();
607  
608 <            atomOrientData[4] = dAtom->getJx();
609 <            atomOrientData[5] = dAtom->getJy();
376 <            atomOrientData[6] = dAtom->getJz();
377 <          }
608 >            sd->getPos(pos);
609 >            sd->getVel(vel);
610  
611 <        } else {
612 <          sprintf(painCave.errMsg,
613 <                  "Atom %d not found on processor %d\n",
382 <                  i, worldRank );
383 <          haveError= 1;
384 <          simError();
385 <        }
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;
390 <        atomIsDirectionalTag = 4*i + 1;
391 <        atomTransDataTag     = 4*i + 2;
392 <        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,
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 <        }
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");
421 <    MPIcheckPoint();        
422 <    
423 <  }
424 <  
425 <  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];
438 <  char writeLine[BUFFERSIZE];
657 >              MPI_Send(atomData, 6, MPI_DOUBLE, 0,
658 >                       myPotato, MPI_COMM_WORLD);
659 >            }
660  
661 <  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 );
661 >            myPotato++;  
662  
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" );
542 –
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();
663            }
664  
665 <        } else {
666 <          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" );
665 >          currentIndex++;    
666 >          
667          }
668 <
695 <        finalOut << writeLine;
696 <        finalOut.flush();
668 >      
669        }
698 –    }
670  
700 –    finalOut.flush();
671      sprintf( checkPointMsg,
672               "Sucessfully took a dump.\n");
673 <    MPIcheckPoint();        
673 >    MPIcheckPoint();                
674      
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 –      }
675      }
676  
789 –    sprintf( checkPointMsg,
790 –             "Sucessfully wrote final file.\n");
791 –    MPIcheckPoint();        
792 –    
793 –  }
794 –  
795 –  painCave.isEventLoop = 0;
677  
678 <  if( worldRank == 0 ) finalOut.close();
678 >  
679   #endif // is_mpi
680   }
681  
801 –
802 –
682   #ifdef IS_MPI
683  
684   // a couple of functions to let us escape the write loop

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