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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 1097 by gezelter, Mon Apr 12 20:32:20 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 +  Atom** atoms = entry_plug->atoms;
92 +  
93 +  indexArray.clear();
94 +  
95 +  for(int i = 0; i < mpiSim->getMyNlocal();i++)
96 +    indexArray.push_back(make_pair(i, atoms[i]->getGlobalIndex()));
97 +  
98 +  sort(indexArray.begin(), indexArray.end(), indexSortingCriterion);    
99 + }
100 +
101 + #endif
102 +
103 + void DumpWriter::writeDump(double currentTime){
104 +
105 +  ofstream finalOut;
106 +  vector<ofstream*> fileStreams;
107 +
108 + #ifdef IS_MPI
109 +  if(worldRank == 0 ){
110 + #endif    
111 +    finalOut.open( entry_plug->finalName, ios::out | ios::trunc );
112 +    if( !finalOut ){
113 +      sprintf( painCave.errMsg,
114 +               "Could not open \"%s\" for final dump output.\n",
115 +               entry_plug->finalName );
116 +      painCave.isFatal = 1;
117 +      simError();
118 +    }
119 + #ifdef IS_MPI
120 +  }
121 + #endif // is_mpi
122 +
123 +  fileStreams.push_back(&finalOut);
124 +  fileStreams.push_back(&dumpFile);
125 +
126 +  writeFrame(fileStreams, currentTime);
127 +
128 + #ifdef IS_MPI
129 +  finalOut.close();
130 + #endif
131 +        
132 + }
133 +
134 + void DumpWriter::writeFinal(double currentTime){
135 +
136 +  ofstream finalOut;
137 +  vector<ofstream*> fileStreams;
138 +
139 + #ifdef IS_MPI
140 +  if(worldRank == 0 ){
141 + #endif // is_mpi
142 +
143 +    finalOut.open( entry_plug->finalName, ios::out | ios::trunc );
144 +
145 +    if( !finalOut ){
146 +      sprintf( painCave.errMsg,
147 +               "Could not open \"%s\" for final dump output.\n",
148 +               entry_plug->finalName );
149 +      painCave.isFatal = 1;
150 +      simError();
151 +    }
152 +
153 + #ifdef IS_MPI
154 +  }
155 + #endif // is_mpi
156 +  
157 +  fileStreams.push_back(&finalOut);  
158 +  writeFrame(fileStreams, currentTime);
159 +
160 + #ifdef IS_MPI
161 +  finalOut.close();
162 + #endif
163 +  
164 + }
165 +
166 + void DumpWriter::writeFrame( vector<ofstream*>& outFile, double currentTime ){
167 +
168    const int BUFFERSIZE = 2000;
169    const int MINIBUFFERSIZE = 100;
170  
171 <  char tempBuffer[BUFFERSIZE];
171 >  char tempBuffer[BUFFERSIZE];  
172    char writeLine[BUFFERSIZE];
173  
174 <  int i;
174 >  int i, k;
175 >
176   #ifdef IS_MPI
177 <  int j, which_node, done, which_atom, local_index;
178 <  double atomTransData[6];
179 <  double atomOrientData[7];
177 >  
178 >  /*********************************************************************
179 >   * Documentation?  You want DOCUMENTATION?
180 >   *
181 >   * Why all the potatoes below?  
182 >   *
183 >   * To make a long story short, the original version of DumpWriter
184 >   * worked in the most inefficient way possible.  Node 0 would
185 >   * poke each of the node for an individual atom's formatted data
186 >   * as node 0 worked its way down the global index. This was particularly
187 >   * inefficient since the method blocked all processors at every atom
188 >   * (and did it twice!).
189 >   *
190 >   * An intermediate version of DumpWriter could be described from Node
191 >   * zero's perspective as follows:
192 >   *
193 >   *  1) Have 100 of your friends stand in a circle.
194 >   *  2) When you say go, have all of them start tossing potatoes at
195 >   *     you (one at a time).
196 >   *  3) Catch the potatoes.
197 >   *
198 >   * It was an improvement, but MPI has buffers and caches that could
199 >   * best be described in this analogy as "potato nets", so there's no
200 >   * need to block the processors atom-by-atom.
201 >   *
202 >   * This new and improved DumpWriter works in an even more efficient
203 >   * way:
204 >   *
205 >   *  1) Have 100 of your friend stand in a circle.
206 >   *  2) When you say go, have them start tossing 5-pound bags of
207 >   *     potatoes at you.
208 >   *  3) Once you've caught a friend's bag of potatoes,
209 >   *     toss them a spud to let them know they can toss another bag.
210 >   *
211 >   * How's THAT for documentation?
212 >   *
213 >   *********************************************************************/
214 >
215 >  int *potatoes;
216 >  int myPotato;
217 >
218 >  int nProc;
219 >  int j, which_node, done, which_atom, local_index, currentIndex;
220 >  double atomData6[6];
221 >  double atomData13[13];
222    int isDirectional;
223    char* atomTypeString;
224    char MPIatomTypeString[MINIBUFFERSIZE];
225 <  int me;
83 <  int atomTypeTag;
84 <  int atomIsDirectionalTag;
85 <  int atomTransDataTag;
86 <  int atomOrientDataTag;
225 >
226   #else //is_mpi
227    int nAtoms = entry_plug->n_atoms;
228   #endif //is_mpi
229  
230 <  double q[4];
230 >  double q[4], ji[3];
231    DirectionalAtom* dAtom;
232    Atom** atoms = entry_plug->atoms;
233    double pos[3], vel[3];
234  
96 –  // write current frame to the eor file
97 –
98 –  this->writeFinal( currentTime );
99 –
235   #ifndef IS_MPI
236 +  
237 +  for(k = 0; k < outFile.size(); k++){
238 +    *outFile[k] << nAtoms << "\n";
239  
240 <  outFile << nAtoms << "\n";
240 >    *outFile[k] << currentTime << ";\t"
241 >               << entry_plug->Hmat[0][0] << "\t"
242 >                     << entry_plug->Hmat[1][0] << "\t"
243 >                     << entry_plug->Hmat[2][0] << ";\t"
244 >              
245 >               << entry_plug->Hmat[0][1] << "\t"
246 >                     << entry_plug->Hmat[1][1] << "\t"
247 >                     << entry_plug->Hmat[2][1] << ";\t"
248  
249 <  outFile << currentTime << ";\t"
250 <          << entry_plug->Hmat[0][0] << "\t"
251 <          << entry_plug->Hmat[1][0] << "\t"
107 <          << entry_plug->Hmat[2][0] << ";\t"
249 >                     << entry_plug->Hmat[0][2] << "\t"
250 >                     << entry_plug->Hmat[1][2] << "\t"
251 >                     << entry_plug->Hmat[2][2] << ";";
252  
253 <          << entry_plug->Hmat[0][1] << "\t"
254 <          << entry_plug->Hmat[1][1] << "\t"
255 <          << entry_plug->Hmat[2][1] << ";\t"
256 <
113 <          << entry_plug->Hmat[0][2] << "\t"
114 <          << entry_plug->Hmat[1][2] << "\t"
115 <          << entry_plug->Hmat[2][2] << ";";
116 <  //write out additional parameters, such as chi and eta
117 <  outFile << entry_plug->the_integrator->getAdditionalParameters();
118 <  outFile << endl;
119 <
253 >    //write out additional parameters, such as chi and eta
254 >    *outFile[k] << entry_plug->the_integrator->getAdditionalParameters() << endl;
255 >  }
256 >  
257    for( i=0; i<nAtoms; i++ ){
258  
259      atoms[i]->getPos(pos);
# Line 137 | Line 274 | void DumpWriter::writeDump( double currentTime ){
274  
275        dAtom = (DirectionalAtom *)atoms[i];
276        dAtom->getQ( q );
277 +      dAtom->getJ( ji );
278  
279        sprintf( tempBuffer,
280                 "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
# Line 144 | Line 282 | void DumpWriter::writeDump( double currentTime ){
282                 q[1],
283                 q[2],
284                 q[3],
285 <               dAtom->getJx(),
286 <               dAtom->getJy(),
287 <               dAtom->getJz());
285 >               ji[0],
286 >               ji[1],
287 >               ji[2]);
288        strcat( writeLine, tempBuffer );
289      }
290      else
291        strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
292  
293 <    outFile << writeLine;
293 >    for(k = 0; k < outFile.size(); k++)
294 >      *outFile[k] << writeLine;
295    }
157 –  outFile.flush();
296  
297   #else // is_mpi
298  
299    /* code to find maximum tag value */
300 +  
301    int *tagub, flag, MAXTAG;
302    MPI_Attr_get(MPI_COMM_WORLD, MPI_TAG_UB, &tagub, &flag);
303    if (flag) {
304      MAXTAG = *tagub;
305    } else {
306      MAXTAG = 32767;
307 <  }
307 >  }  
308  
309    int haveError;
310  
# Line 175 | Line 314 | void DumpWriter::writeDump( double currentTime ){
314    // write out header and node 0's coordinates
315  
316    if( worldRank == 0 ){
178 –    outFile << mpiSim->getTotAtoms() << "\n";
317  
318 <    outFile << currentTime << ";\t"
181 <            << entry_plug->Hmat[0][0] << "\t"
182 <            << entry_plug->Hmat[1][0] << "\t"
183 <            << entry_plug->Hmat[2][0] << ";\t"
318 >    // Node 0 needs a list of the magic potatoes for each processor;
319  
320 <            << entry_plug->Hmat[0][1] << "\t"
321 <            << entry_plug->Hmat[1][1] << "\t"
187 <            << entry_plug->Hmat[2][1] << ";\t"
320 >    nProc = mpiSim->getNumberProcessors();
321 >    potatoes = new int[nProc];
322  
323 <            << entry_plug->Hmat[0][2] << "\t"
324 <            << entry_plug->Hmat[1][2] << "\t"
325 <            << entry_plug->Hmat[2][2] << ";";
323 >    //write out the comment lines
324 >    for (i = 0; i < nProc; i++)
325 >      potatoes[i] = 0;
326 >    
327 >      for(k = 0; k < outFile.size(); k++){
328 >        *outFile[k] << mpiSim->getTotAtoms() << "\n";
329  
330 <    outFile << entry_plug->the_integrator->getAdditionalParameters();
331 <    outFile << endl;
332 <    outFile.flush();
330 >        *outFile[k] << currentTime << ";\t"
331 >                         << entry_plug->Hmat[0][0] << "\t"
332 >                         << entry_plug->Hmat[1][0] << "\t"
333 >                         << entry_plug->Hmat[2][0] << ";\t"
334  
335 <    tag = 0;
335 >                         << entry_plug->Hmat[0][1] << "\t"
336 >                         << entry_plug->Hmat[1][1] << "\t"
337 >                         << entry_plug->Hmat[2][1] << ";\t"
338  
339 <    for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) {
339 >                         << entry_plug->Hmat[0][2] << "\t"
340 >                         << entry_plug->Hmat[1][2] << "\t"
341 >                         << entry_plug->Hmat[2][2] << ";";
342 >  
343 >        *outFile[k] << entry_plug->the_integrator->getAdditionalParameters() << endl;
344 >    }
345  
346 <      if (tag + 2 >= MAXTAG) {
347 <        // The tag was going to exceed the maximum value, so wrap around to 0:
348 <        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 <      }
346 >    currentIndex = 0;
347 >
348 >    for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) {
349        
350        // Get the Node number which has this atom;
351        
352        which_node = AtomToProcMap[i];
353        
354        if (which_node != 0) {
355 +
356 +        if (potatoes[which_node] + 3 >= MAXTAG) {
357 +          // The potato was going to exceed the maximum value,
358 +          // so wrap this processor potato back to 0:        
359 +
360 +          potatoes[which_node] = 0;          
361 +          MPI_Send(0, 1, MPI_INT, which_node, 0, MPI_COMM_WORLD);
362 +          
363 +        }
364 +
365 +        myPotato = potatoes[which_node];        
366          
367          MPI_Recv(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, which_node,
368 <                 atomTypeTag, MPI_COMM_WORLD, &istatus);
368 >                 myPotato, MPI_COMM_WORLD, &istatus);
369          
370 <        strncpy(atomTypeString, MPIatomTypeString, MINIBUFFERSIZE);
371 <        
372 <        // Null terminate the atomTypeString just in case:
370 >        atomTypeString = MPIatomTypeString;
371 >        
372 >        myPotato++;
373  
221 –        atomTypeString[strlen(atomTypeString) - 1] = '\0';
222 –
374          MPI_Recv(&isDirectional, 1, MPI_INT, which_node,
375 <                 atomIsDirectionalTag, MPI_COMM_WORLD, &istatus);
376 <        
377 <        MPI_Recv(atomTransData, 6, MPI_DOUBLE, which_node,
227 <                 atomTransDataTag, MPI_COMM_WORLD, &istatus);
375 >                 myPotato, MPI_COMM_WORLD, &istatus);
376 >              
377 >        myPotato++;
378  
379 <        if (isDirectional) {
380 <
381 <          MPI_Recv(atomOrientData, 7, MPI_DOUBLE, which_node,
382 <                   atomOrientDataTag, MPI_COMM_WORLD, &istatus);
383 <
379 >        if (isDirectional) {          
380 >          MPI_Recv(atomData13, 13, MPI_DOUBLE, which_node,
381 >                   myPotato, MPI_COMM_WORLD, &istatus);
382 >        } else {
383 >          MPI_Recv(atomData6, 6, MPI_DOUBLE, which_node,
384 >                   myPotato, MPI_COMM_WORLD, &istatus);          
385          }
386 +        
387 +        myPotato++;
388 +        potatoes[which_node] = myPotato;
389  
390        } else {
391          
392 <        haveError = 0;
392 >        haveError = 0;
393          which_atom = i;
394 <        local_index=-1;
395 <
396 <        for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) {
397 <          if (atoms[j]->getGlobalIndex() == which_atom) local_index = j;
398 <        }
399 <
400 <        if (local_index != -1) {
247 <
248 <          atomTypeString = atoms[local_index]->getType();
249 <
394 >        
395 >          local_index = indexArray[currentIndex].first;        
396 >          
397 >          if (which_atom == indexArray[currentIndex].second) {
398 >            
399 >            atomTypeString = atoms[local_index]->getType();
400 >            
401            atoms[local_index]->getPos(pos);
402 <          atoms[local_index]->getVel(vel);
402 >          atoms[local_index]->getVel(vel);          
403 >          
404 >          atomData6[0] = pos[0];
405 >          atomData6[1] = pos[1];
406 >          atomData6[2] = pos[2];
407  
408 <          atomTransData[0] = pos[0];
409 <          atomTransData[1] = pos[1];
410 <          atomTransData[2] = pos[2];
256 <
257 <          atomTransData[3] = vel[0];
258 <          atomTransData[4] = vel[1];
259 <          atomTransData[5] = vel[2];
408 >          atomData6[3] = vel[0];
409 >          atomData6[4] = vel[1];
410 >          atomData6[5] = vel[2];
411            
412            isDirectional = 0;
413  
# Line 266 | Line 417 | void DumpWriter::writeDump( double currentTime ){
417              
418              dAtom = (DirectionalAtom *)atoms[local_index];
419              dAtom->getQ( q );
420 <            
270 <            atomOrientData[0] = q[0];
271 <            atomOrientData[1] = q[1];
272 <            atomOrientData[2] = q[2];
273 <            atomOrientData[3] = q[3];
420 >            dAtom->getJ( ji );
421  
422 <            atomOrientData[4] = dAtom->getJx();
423 <            atomOrientData[5] = dAtom->getJy();
424 <            atomOrientData[6] = dAtom->getJz();
422 >            for (int j = 0; j < 6 ; j++)
423 >              atomData13[j] = atomData6[j];            
424 >            
425 >            atomData13[6] = q[0];
426 >            atomData13[7] = q[1];
427 >            atomData13[8] = q[2];
428 >            atomData13[9] = q[3];
429 >            
430 >            atomData13[10] = ji[0];
431 >            atomData13[11] = ji[1];
432 >            atomData13[12] = ji[2];
433            }
434 <
434 >          
435          } else {
436            sprintf(painCave.errMsg,
437 <                  "Atom %d not found on processor %d\n",
438 <                  i, worldRank );
437 >                  "Atom %d not found on processor %d, currentIndex = %d, local_index = %d\n",
438 >                  which_atom, worldRank, currentIndex, local_index );
439            haveError= 1;
440            simError();
441          }
287 –
288 –        if(haveError) DieDieDie();
289 –                              
290 –        // If we've survived to here, format the line:
442          
443 <        sprintf( tempBuffer,
444 <                 "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
445 <                 atomTypeString,
295 <                 atomTransData[0],
296 <                 atomTransData[1],
297 <                 atomTransData[2],
298 <                 atomTransData[3],
299 <                 atomTransData[4],
300 <                 atomTransData[5]);
301 <
302 <        strcpy( writeLine, tempBuffer );
303 <
304 <        if (isDirectional) {
305 <
306 <          sprintf( tempBuffer,
307 <                   "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
308 <                   atomOrientData[0],
309 <                   atomOrientData[1],
310 <                   atomOrientData[2],
311 <                   atomOrientData[3],
312 <                   atomOrientData[4],
313 <                   atomOrientData[5],
314 <                   atomOrientData[6]);
315 <          strcat( writeLine, tempBuffer );
316 <
317 <        } else {
318 <          strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
319 <        }
320 <
321 <        outFile << writeLine;
322 <        outFile.flush();
443 >        if(haveError) DieDieDie();
444 >        
445 >        currentIndex++;
446        }
447 <    }
325 <
326 <    outFile.flush();
327 <    sprintf( checkPointMsg,
328 <             "Sucessfully took a dump.\n");
329 <    MPIcheckPoint();        
330 <    
331 <  } else {
332 <
333 <    // worldRank != 0, so I'm a remote node.  
334 <    
335 <    for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) {
447 >      // If we've survived to here, format the line:
448        
449 <      // Am I the node which has this atom?
450 <      
451 <      if (AtomToProcMap[i] == worldRank) {
452 <
453 <        local_index=-1;
454 <        for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) {
455 <          if (atoms[j]->getGlobalIndex() == which_atom) local_index = j;
456 <        }
457 <        if (local_index != -1) {
458 <        
459 <          atomTypeString = atoms[local_index]->getType();
460 <
461 <          atoms[local_index]->getPos(pos);
462 <          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];
359 <          
360 <          isDirectional = 0;
361 <
362 <          if( atoms[local_index]->isDirectional() ){
363 <
364 <            isDirectional = 1;
365 <            
366 <            dAtom = (DirectionalAtom *)atoms[local_index];
367 <            dAtom->getQ( q );
368 <            
369 <            atomOrientData[0] = q[0];
370 <            atomOrientData[1] = q[1];
371 <            atomOrientData[2] = q[2];
372 <            atomOrientData[3] = q[3];
373 <
374 <            atomOrientData[4] = dAtom->getJx();
375 <            atomOrientData[5] = dAtom->getJy();
376 <            atomOrientData[6] = dAtom->getJz();
377 <          }
378 <
379 <        } else {
380 <          sprintf(painCave.errMsg,
381 <                  "Atom %d not found on processor %d\n",
382 <                  i, worldRank );
383 <          haveError= 1;
384 <          simError();
385 <        }
386 <
387 <        // I've survived this far, so send off the data!
388 <
389 <        atomTypeTag          = 4*i;
390 <        atomIsDirectionalTag = 4*i + 1;
391 <        atomTransDataTag     = 4*i + 2;
392 <        atomOrientDataTag    = 4*i + 3;
393 <
394 <
395 <        strncpy(MPIatomTypeString, atomTypeString, MINIBUFFERSIZE);
396 <
397 <        // null terminate the string before sending (just in case):
398 <        MPIatomTypeString[MINIBUFFERSIZE-1] = '\0';
399 <
400 <        MPI_Send(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, 0,
401 <                 atomTypeTag, MPI_COMM_WORLD);
402 <        
403 <        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 <        }
415 <      
416 <      }
417 <    }
418 <
419 <    sprintf( checkPointMsg,
420 <             "Sucessfully took a dump.\n");
421 <    MPIcheckPoint();        
422 <    
423 <  }
424 <  
425 <  painCave.isEventLoop = 0;
426 <
427 < #endif // is_mpi
428 < }
429 <
430 < void DumpWriter::writeFinal(double finalTime){
431 <
432 <  char finalName[500];
433 <  ofstream finalOut;
434 <
435 <  const int BUFFERSIZE = 2000;
436 <  const int MINIBUFFERSIZE = 100;
437 <  char tempBuffer[BUFFERSIZE];
438 <  char writeLine[BUFFERSIZE];
439 <
440 <  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" );
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 <
449 >      if (!isDirectional) {
450 >        
451 >        sprintf( writeLine,
452 >                 "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
453 >                 atomTypeString,
454 >                 atomData6[0],
455 >                 atomData6[1],
456 >                 atomData6[2],
457 >                 atomData6[3],
458 >                 atomData6[4],
459 >                 atomData6[5]);
460 >        
461 >        strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
462 >        
463        } else {
464 +        
465 +        sprintf( writeLine,
466 +                 "%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",
467 +                 atomTypeString,
468 +                 atomData13[0],
469 +                 atomData13[1],
470 +                 atomData13[2],
471 +                 atomData13[3],
472 +                 atomData13[4],
473 +                 atomData13[5],
474 +                 atomData13[6],
475 +                 atomData13[7],
476 +                 atomData13[8],
477 +                 atomData13[9],
478 +                 atomData13[10],
479 +                 atomData13[11],
480 +                 atomData13[12]);
481          
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();
652 –          }
653 –
654 –        } else {
655 –          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" );
693 –        }
694 –
695 –        finalOut << writeLine;
696 –        finalOut.flush();
482        }
483 +      
484 +      for(k = 0; k < outFile.size(); k++)
485 +        *outFile[k] << writeLine;
486      }
487 <
488 <    finalOut.flush();
487 >    
488 >    for(k = 0; k < outFile.size(); k++)
489 >      outFile[k]->flush();
490 >    
491      sprintf( checkPointMsg,
492               "Sucessfully took a dump.\n");
493 +    
494      MPIcheckPoint();        
495      
496 +    delete[] potatoes;
497 +    
498    } else {
499  
500      // worldRank != 0, so I'm a remote node.  
501 +
502 +    // Set my magic potato to 0:
503 +
504 +    myPotato = 0;
505 +    currentIndex = 0;
506      
507      for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) {
508        
# Line 712 | Line 510 | void DumpWriter::writeFinal(double finalTime){
510        
511        if (AtomToProcMap[i] == worldRank) {
512  
513 <        local_index=-1;
514 <        for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) {
515 <          if (atoms[j]->getGlobalIndex() == which_atom) local_index = j;
513 >        if (myPotato + 3 >= MAXTAG) {
514 >          
515 >          // The potato was going to exceed the maximum value,
516 >          // so wrap this processor potato back to 0 (and block until
517 >          // node 0 says we can go:
518 >          
519 >          MPI_Recv(&myPotato, 1, MPI_INT, 0, 0, MPI_COMM_WORLD, &istatus);
520 >          
521          }
522 <        if (local_index != -1) {
522 >        which_atom = i;
523 >
524 >        local_index = indexArray[currentIndex].first;        
525 >                
526 >        if (which_atom == indexArray[currentIndex].second) {
527          
528            atomTypeString = atoms[local_index]->getType();
529 <
529 >          
530            atoms[local_index]->getPos(pos);
531            atoms[local_index]->getVel(vel);
532 +          
533 +          atomData6[0] = pos[0];
534 +          atomData6[1] = pos[1];
535 +          atomData6[2] = pos[2];
536  
537 <          atomTransData[0] = pos[0];
538 <          atomTransData[1] = pos[1];
539 <          atomTransData[2] = pos[2];
729 <
730 <          atomTransData[3] = vel[0];
731 <          atomTransData[4] = vel[1];
732 <          atomTransData[5] = vel[2];
537 >          atomData6[3] = vel[0];
538 >          atomData6[4] = vel[1];
539 >          atomData6[5] = vel[2];
540            
541            isDirectional = 0;
542  
# Line 739 | Line 546 | void DumpWriter::writeFinal(double finalTime){
546              
547              dAtom = (DirectionalAtom *)atoms[local_index];
548              dAtom->getQ( q );
549 +            dAtom->getJ( ji );
550              
551 <            atomOrientData[0] = q[0];
552 <            atomOrientData[1] = q[1];
553 <            atomOrientData[2] = q[2];
554 <            atomOrientData[3] = q[3];
555 <
556 <            atomOrientData[4] = dAtom->getJx();
557 <            atomOrientData[5] = dAtom->getJy();
558 <            atomOrientData[6] = dAtom->getJz();
551 >            for (int j = 0; j < 6 ; j++)
552 >              atomData13[j] = atomData6[j];
553 >            
554 >            atomData13[6] = q[0];
555 >            atomData13[7] = q[1];
556 >            atomData13[8] = q[2];
557 >            atomData13[9] = q[3];
558 >  
559 >            atomData13[10] = ji[0];
560 >            atomData13[11] = ji[1];
561 >            atomData13[12] = ji[2];
562            }
563  
564          } else {
565            sprintf(painCave.errMsg,
566 <                  "Atom %d not found on processor %d\n",
567 <                  i, worldRank );
566 >                  "Atom %d not found on processor %d, currentIndex = %d, local_index = %d\n",
567 >                  which_atom, worldRank, currentIndex, local_index );
568            haveError= 1;
569            simError();
570          }
571 <
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 <
571 >        
572          strncpy(MPIatomTypeString, atomTypeString, MINIBUFFERSIZE);
573  
574 +        // null terminate the string before sending (just in case):
575 +        MPIatomTypeString[MINIBUFFERSIZE-1] = '\0';
576 +
577          MPI_Send(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, 0,
578 <                 atomTypeTag, MPI_COMM_WORLD);
578 >                             myPotato, MPI_COMM_WORLD);
579          
580 +        myPotato++;
581 +
582          MPI_Send(&isDirectional, 1, MPI_INT, 0,
583 <                 atomIsDirectionalTag, MPI_COMM_WORLD);
583 >                             myPotato, MPI_COMM_WORLD);
584          
585 <        MPI_Send(atomTransData, 6, MPI_DOUBLE, 0,
586 <                 atomTransDataTag, MPI_COMM_WORLD);
778 <
585 >        myPotato++;
586 >        
587          if (isDirectional) {
588  
589 <          MPI_Send(atomOrientData, 7, MPI_DOUBLE, 0,
590 <                   atomOrientDataTag, MPI_COMM_WORLD);
589 >          MPI_Send(atomData13, 13, MPI_DOUBLE, 0,
590 >                   myPotato, MPI_COMM_WORLD);
591            
592 +        } else {
593 +
594 +          MPI_Send(atomData6, 6, MPI_DOUBLE, 0,
595 +                   myPotato, MPI_COMM_WORLD);
596          }
597 <      
597 >
598 >        myPotato++;  
599 >        currentIndex++;    
600        }
601      }
602  
603      sprintf( checkPointMsg,
604 <             "Sucessfully wrote final file.\n");
604 >             "Sucessfully took a dump.\n");
605      MPIcheckPoint();        
606      
607 <  }
607 >  }
608    
795 –  painCave.isEventLoop = 0;
796 –
797 –  if( worldRank == 0 ) finalOut.close();
609   #endif // is_mpi
610   }
611  
801 –
802 –
612   #ifdef IS_MPI
613  
614   // a couple of functions to let us escape the write loop

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