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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 952 by tim, Fri Jan 16 21:55:39 2004 UTC

# Line 3 | Line 3
3   #include <string.h>
4   #include <iostream>
5   #include <fstream>
6 + #include <algorithm>
7 + #include <utility>
8  
9   #ifdef IS_MPI
10   #include <mpi.h>
# Line 26 | Line 28 | DumpWriter::DumpWriter( SimInfo* the_entry_plug ){
28    if(worldRank == 0 ){
29   #endif // is_mpi
30  
31 <    strcpy( outName, entry_plug->sampleName );
31 >    dumpFile.open(entry_plug->sampleName, ios::out | ios::trunc );
32  
33 <    outFile.open(outName, ios::out | ios::trunc );
33 >    if( !dumpFile ){
34  
33    if( !outFile ){
34
35        sprintf( painCave.errMsg,
36                 "Could not open \"%s\" for dump output.\n",
37 <               outName);
37 >               entry_plug->sampleName);
38        painCave.isFatal = 1;
39        simError();
40      }
41  
42    //outFile.setf( ios::scientific );
43
42   #ifdef IS_MPI
43    }
44  
45 +  //sort the local atoms by global index
46 +  sortByGlobalIndex();
47 +  
48    sprintf( checkPointMsg,
49             "Sucessfully opened output file for dumping.\n");
50    MPIcheckPoint();
# Line 56 | Line 57 | DumpWriter::~DumpWriter( ){
57    if(worldRank == 0 ){
58   #endif // is_mpi
59  
60 <    outFile.close();
60 >    dumpFile.close();
61  
62   #ifdef IS_MPI
63    }
64   #endif // is_mpi
65   }
66  
67 < void DumpWriter::writeDump( double currentTime ){
67 > #ifdef IS_MPI
68  
69 + /**
70 + * A hook function to load balancing
71 + */
72 +
73 + void DumpWriter::update(){
74 +  sortByGlobalIndex();          
75 + }
76 +  
77 + /**
78 + * Auxiliary sorting function
79 + */
80 +
81 + bool indexSortingCriterion(const pair<int, int>& p1, const pair<int, int>& p2){
82 +  return p1.second < p2.second;
83 + }
84 +
85 + /**
86 + * Sorting the local index by global index
87 + */
88 +
89 + void DumpWriter::sortByGlobalIndex(){
90 +  Atom** atoms = entry_plug->atoms;
91 +  
92 +  indexArray.clear();
93 +  
94 +  for(int i = 0; i < mpiSim->getMyNlocal();i++)
95 +    indexArray.push_back(make_pair(i, atoms[i]->getGlobalIndex()));
96 +  
97 +  sort(indexArray.begin(), indexArray.end(), indexSortingCriterion);    
98 +
99 +  //for (int i = 0; i < mpiSim->getMyNlocal(); i++) {
100 +  //  printf("node %d has global %d at local %d\n", worldRank, indexArray[i].second, indexArray[i].first);
101 +  //}
102 +    
103 + }
104 +
105 + #endif
106 +
107 + void DumpWriter::writeDump(double currentTime){
108 +
109 +  ofstream finalOut;
110 +  vector<ofstream*> fileStreams;
111 +
112 + #ifdef IS_MPI
113 +  if(worldRank == 0 ){
114 + #endif    
115 +    finalOut.open( entry_plug->finalName, ios::out | ios::trunc );
116 +    if( !finalOut ){
117 +      sprintf( painCave.errMsg,
118 +               "Could not open \"%s\" for final dump output.\n",
119 +               entry_plug->finalName );
120 +      painCave.isFatal = 1;
121 +      simError();
122 +    }
123 + #ifdef IS_MPI
124 +  }
125 + #endif // is_mpi
126 +
127 +  fileStreams.push_back(&finalOut);
128 +  fileStreams.push_back(&dumpFile);
129 +
130 +  writeFrame(fileStreams, currentTime);
131 +
132 + #ifdef IS_MPI
133 +  finalOut.close();
134 + #endif
135 +        
136 + }
137 +
138 + void DumpWriter::writeFinal(double currentTime){
139 +
140 +  ofstream finalOut;
141 +  vector<ofstream*> fileStreams;
142 +
143 + #ifdef IS_MPI
144 +  if(worldRank == 0 ){
145 + #endif // is_mpi
146 +
147 +    finalOut.open( entry_plug->finalName, ios::out | ios::trunc );
148 +
149 +    if( !finalOut ){
150 +      sprintf( painCave.errMsg,
151 +               "Could not open \"%s\" for final dump output.\n",
152 +               entry_plug->finalName );
153 +      painCave.isFatal = 1;
154 +      simError();
155 +    }
156 +
157 + #ifdef IS_MPI
158 +  }
159 + #endif // is_mpi
160 +  
161 +  fileStreams.push_back(&finalOut);  
162 +  writeFrame(fileStreams, currentTime);
163 +
164 + #ifdef IS_MPI
165 +  finalOut.close();
166 + #endif
167 +  
168 + }
169 +
170 + void DumpWriter::writeFrame( vector<ofstream*>& outFile, double currentTime ){
171 +
172    const int BUFFERSIZE = 2000;
173    const int MINIBUFFERSIZE = 100;
174  
175 <  char tempBuffer[BUFFERSIZE];
175 >  char tempBuffer[BUFFERSIZE];  
176    char writeLine[BUFFERSIZE];
177  
178 <  int i;
178 >  int i, k;
179 >
180   #ifdef IS_MPI
181 <  int j, which_node, done, which_atom, local_index;
182 <  double atomTransData[6];
183 <  double atomOrientData[7];
181 >  
182 >  /*********************************************************************
183 >   * Documentation?  You want DOCUMENTATION?
184 >   *
185 >   * Why all the potatoes below?  
186 >   *
187 >   * To make a long story short, the original version of DumpWriter
188 >   * worked in the most inefficient way possible.  Node 0 would
189 >   * poke each of the node for an individual atom's formatted data
190 >   * as node 0 worked its way down the global index. This was particularly
191 >   * inefficient since the method blocked all processors at every atom
192 >   * (and did it twice!).
193 >   *
194 >   * An intermediate version of DumpWriter could be described from Node
195 >   * zero's perspective as follows:
196 >   *
197 >   *  1) Have 100 of your friends stand in a circle.
198 >   *  2) When you say go, have all of them start tossing potatoes at
199 >   *     you (one at a time).
200 >   *  3) Catch the potatoes.
201 >   *
202 >   * It was an improvement, but MPI has buffers and caches that could
203 >   * best be described in this analogy as "potato nets", so there's no
204 >   * need to block the processors atom-by-atom.
205 >   *
206 >   * This new and improved DumpWriter works in an even more efficient
207 >   * way:
208 >   *
209 >   *  1) Have 100 of your friend stand in a circle.
210 >   *  2) When you say go, have them start tossing 5-pound bags of
211 >   *     potatoes at you.
212 >   *  3) Once you've caught a friend's bag of potatoes,
213 >   *     toss them a spud to let them know they can toss another bag.
214 >   *
215 >   * How's THAT for documentation?
216 >   *
217 >   *********************************************************************/
218 >
219 >  int *potatoes;
220 >  int myPotato;
221 >
222 >  int nProc;
223 >  int j, which_node, done, which_atom, local_index, currentIndex;
224 >  double atomData6[6];
225 >  double atomData13[13];
226    int isDirectional;
227    char* atomTypeString;
228    char MPIatomTypeString[MINIBUFFERSIZE];
229 <  int me;
83 <  int atomTypeTag;
84 <  int atomIsDirectionalTag;
85 <  int atomTransDataTag;
86 <  int atomOrientDataTag;
229 >
230   #else //is_mpi
231    int nAtoms = entry_plug->n_atoms;
232   #endif //is_mpi
# Line 93 | Line 236 | void DumpWriter::writeDump( double currentTime ){
236    Atom** atoms = entry_plug->atoms;
237    double pos[3], vel[3];
238  
96  // write current frame to the eor file
97
98  this->writeFinal( currentTime );
99
239   #ifndef IS_MPI
240 +  
241 +  for(k = 0; k < outFile.size(); k++){
242 +    *outFile[k] << nAtoms << "\n";
243  
244 <  outFile << nAtoms << "\n";
244 >    *outFile[k] << currentTime << ";\t"
245 >               << entry_plug->Hmat[0][0] << "\t"
246 >                     << entry_plug->Hmat[1][0] << "\t"
247 >                     << entry_plug->Hmat[2][0] << ";\t"
248 >              
249 >               << entry_plug->Hmat[0][1] << "\t"
250 >                     << entry_plug->Hmat[1][1] << "\t"
251 >                     << entry_plug->Hmat[2][1] << ";\t"
252  
253 <  outFile << currentTime << ";\t"
254 <          << entry_plug->Hmat[0][0] << "\t"
255 <          << entry_plug->Hmat[1][0] << "\t"
107 <          << entry_plug->Hmat[2][0] << ";\t"
253 >                     << entry_plug->Hmat[0][2] << "\t"
254 >                     << entry_plug->Hmat[1][2] << "\t"
255 >                     << entry_plug->Hmat[2][2] << ";";
256  
257 <          << entry_plug->Hmat[0][1] << "\t"
258 <          << entry_plug->Hmat[1][1] << "\t"
259 <          << entry_plug->Hmat[2][1] << ";\t"
260 <
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 <
257 >    //write out additional parameters, such as chi and eta
258 >    *outFile[k] << entry_plug->the_integrator->getAdditionalParameters() << endl;
259 >  }
260 >  
261    for( i=0; i<nAtoms; i++ ){
262  
263      atoms[i]->getPos(pos);
# Line 152 | Line 293 | void DumpWriter::writeDump( double currentTime ){
293      else
294        strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
295  
296 <    outFile << writeLine;
296 >    for(k = 0; k < outFile.size(); k++)
297 >      *outFile[k] << writeLine;
298    }
157  outFile.flush();
299  
300   #else // is_mpi
301  
302    /* code to find maximum tag value */
303 +  
304    int *tagub, flag, MAXTAG;
305    MPI_Attr_get(MPI_COMM_WORLD, MPI_TAG_UB, &tagub, &flag);
306    if (flag) {
307      MAXTAG = *tagub;
308    } else {
309      MAXTAG = 32767;
310 <  }
310 >  }  
311  
312    int haveError;
313  
# Line 175 | Line 317 | void DumpWriter::writeDump( double currentTime ){
317    // write out header and node 0's coordinates
318  
319    if( worldRank == 0 ){
178    outFile << mpiSim->getTotAtoms() << "\n";
320  
321 <    outFile << currentTime << ";\t"
181 <            << entry_plug->Hmat[0][0] << "\t"
182 <            << entry_plug->Hmat[1][0] << "\t"
183 <            << entry_plug->Hmat[2][0] << ";\t"
321 >    // Node 0 needs a list of the magic potatoes for each processor;
322  
323 <            << entry_plug->Hmat[0][1] << "\t"
324 <            << entry_plug->Hmat[1][1] << "\t"
187 <            << entry_plug->Hmat[2][1] << ";\t"
323 >    nProc = mpiSim->getNumberProcessors();
324 >    potatoes = new int[nProc];
325  
326 <            << entry_plug->Hmat[0][2] << "\t"
327 <            << entry_plug->Hmat[1][2] << "\t"
328 <            << entry_plug->Hmat[2][2] << ";";
326 >    //write out the comment lines
327 >    for (i = 0; i < nProc; i++)
328 >      potatoes[i] = 0;
329 >    
330 >      for(k = 0; k < outFile.size(); k++){
331 >        *outFile[k] << mpiSim->getTotAtoms() << "\n";
332  
333 <    outFile << entry_plug->the_integrator->getAdditionalParameters();
334 <    outFile << endl;
335 <    outFile.flush();
333 >        *outFile[k] << currentTime << ";\t"
334 >                         << entry_plug->Hmat[0][0] << "\t"
335 >                         << entry_plug->Hmat[1][0] << "\t"
336 >                         << entry_plug->Hmat[2][0] << ";\t"
337  
338 <    tag = 0;
338 >                         << entry_plug->Hmat[0][1] << "\t"
339 >                         << entry_plug->Hmat[1][1] << "\t"
340 >                         << entry_plug->Hmat[2][1] << ";\t"
341  
342 <    for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) {
342 >                         << entry_plug->Hmat[0][2] << "\t"
343 >                         << entry_plug->Hmat[1][2] << "\t"
344 >                         << entry_plug->Hmat[2][2] << ";";
345 >  
346 >        *outFile[k] << entry_plug->the_integrator->getAdditionalParameters() << endl;
347 >    }
348  
349 <      if (tag + 2 >= MAXTAG) {
350 <        // The tag was going to exceed the maximum value, so wrap around to 0:
351 <        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 <      }
349 >    currentIndex = 0;
350 >
351 >    for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) {
352        
353        // Get the Node number which has this atom;
354        
355        which_node = AtomToProcMap[i];
356        
357        if (which_node != 0) {
358 +
359 +        if (potatoes[which_node] + 3 >= MAXTAG) {
360 +          // The potato was going to exceed the maximum value,
361 +          // so wrap this processor potato back to 0:        
362 +
363 +          potatoes[which_node] = 0;          
364 +          MPI_Send(0, 1, MPI_INT, which_node, 0, MPI_COMM_WORLD);
365 +          
366 +        }
367 +
368 +        myPotato = potatoes[which_node];        
369          
370          MPI_Recv(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, which_node,
371 <                 atomTypeTag, MPI_COMM_WORLD, &istatus);
371 >                 myPotato, MPI_COMM_WORLD, &istatus);
372          
373 <        strncpy(atomTypeString, MPIatomTypeString, MINIBUFFERSIZE);
374 <        
375 <        // Null terminate the atomTypeString just in case:
373 >        atomTypeString = MPIatomTypeString;
374 >        
375 >        myPotato++;
376  
221        atomTypeString[strlen(atomTypeString) - 1] = '\0';
222
377          MPI_Recv(&isDirectional, 1, MPI_INT, which_node,
378 <                 atomIsDirectionalTag, MPI_COMM_WORLD, &istatus);
379 <        
380 <        MPI_Recv(atomTransData, 6, MPI_DOUBLE, which_node,
227 <                 atomTransDataTag, MPI_COMM_WORLD, &istatus);
378 >                 myPotato, MPI_COMM_WORLD, &istatus);
379 >              
380 >        myPotato++;
381  
382 <        if (isDirectional) {
383 <
384 <          MPI_Recv(atomOrientData, 7, MPI_DOUBLE, which_node,
385 <                   atomOrientDataTag, MPI_COMM_WORLD, &istatus);
386 <
382 >        if (isDirectional) {          
383 >          MPI_Recv(atomData13, 13, MPI_DOUBLE, which_node,
384 >                   myPotato, MPI_COMM_WORLD, &istatus);
385 >        } else {
386 >          MPI_Recv(atomData6, 6, MPI_DOUBLE, which_node,
387 >                   myPotato, MPI_COMM_WORLD, &istatus);          
388          }
389 +        
390 +        myPotato++;
391 +        potatoes[which_node] = myPotato;
392  
393        } else {
394          
395 <        haveError = 0;
395 >        haveError = 0;
396          which_atom = i;
397 <        local_index=-1;
397 >        
398 >        //local_index = -1;
399  
400 <        for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) {
401 <          if (atoms[j]->getGlobalIndex() == which_atom) local_index = j;
402 <        }
403 <
404 <        if (local_index != -1) {
405 <
406 <          atomTypeString = atoms[local_index]->getType();
407 <
400 >        //for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) {
401 >        //  if (atoms[j]->getGlobalIndex() == which_atom) local_index = j;
402 >        //}
403 >        
404 >        //if (local_index != -1) {
405 >          
406 >          local_index = indexArray[currentIndex].first;        
407 >          
408 >          if (which_atom == indexArray[currentIndex].second) {
409 >            
410 >            atomTypeString = atoms[local_index]->getType();
411 >            
412            atoms[local_index]->getPos(pos);
413 <          atoms[local_index]->getVel(vel);
413 >          atoms[local_index]->getVel(vel);          
414 >          
415 >          atomData6[0] = pos[0];
416 >          atomData6[1] = pos[1];
417 >          atomData6[2] = pos[2];
418  
419 <          atomTransData[0] = pos[0];
420 <          atomTransData[1] = pos[1];
421 <          atomTransData[2] = pos[2];
256 <
257 <          atomTransData[3] = vel[0];
258 <          atomTransData[4] = vel[1];
259 <          atomTransData[5] = vel[2];
419 >          atomData6[3] = vel[0];
420 >          atomData6[4] = vel[1];
421 >          atomData6[5] = vel[2];
422            
423            isDirectional = 0;
424  
# Line 266 | Line 428 | void DumpWriter::writeDump( double currentTime ){
428              
429              dAtom = (DirectionalAtom *)atoms[local_index];
430              dAtom->getQ( q );
269            
270            atomOrientData[0] = q[0];
271            atomOrientData[1] = q[1];
272            atomOrientData[2] = q[2];
273            atomOrientData[3] = q[3];
431  
432 <            atomOrientData[4] = dAtom->getJx();
433 <            atomOrientData[5] = dAtom->getJy();
434 <            atomOrientData[6] = dAtom->getJz();
432 >            for (int j = 0; j < 6 ; j++)
433 >              atomData13[j] = atomData6[j];            
434 >            
435 >            atomData13[6] = q[0];
436 >            atomData13[7] = q[1];
437 >            atomData13[8] = q[2];
438 >            atomData13[9] = q[3];
439 >            
440 >            atomData13[10] = dAtom->getJx();
441 >            atomData13[11] = dAtom->getJy();
442 >            atomData13[12] = dAtom->getJz();
443            }
444 <
444 >          
445          } else {
446            sprintf(painCave.errMsg,
447 <                  "Atom %d not found on processor %d\n",
448 <                  i, worldRank );
447 >                  "Atom %d not found on processor %d, currentIndex = %d, local_index = %d\n",
448 >                  which_atom, worldRank, currentIndex, local_index );
449            haveError= 1;
450            simError();
451          }
287
288        if(haveError) DieDieDie();
289                              
290        // If we've survived to here, format the line:
452          
453 <        sprintf( tempBuffer,
454 <                 "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
455 <                 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();
453 >        if(haveError) DieDieDie();
454 >        
455 >        currentIndex++;
456        }
457 <    }
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++ ) {
457 >      // If we've survived to here, format the line:
458        
459 <      // Am I the node which has this atom?
460 <      
461 <      if (AtomToProcMap[i] == worldRank) {
462 <
463 <        local_index=-1;
464 <        for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) {
465 <          if (atoms[j]->getGlobalIndex() == which_atom) local_index = j;
466 <        }
467 <        if (local_index != -1) {
468 <        
469 <          atomTypeString = atoms[local_index]->getType();
470 <
471 <          atoms[local_index]->getPos(pos);
472 <          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 <
459 >      if (!isDirectional) {
460 >        
461 >        sprintf( writeLine,
462 >                 "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
463 >                 atomTypeString,
464 >                 atomData6[0],
465 >                 atomData6[1],
466 >                 atomData6[2],
467 >                 atomData6[3],
468 >                 atomData6[4],
469 >                 atomData6[5]);
470 >        
471 >        strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
472 >        
473        } else {
474 +        
475 +        sprintf( writeLine,
476 +                 "%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",
477 +                 atomTypeString,
478 +                 atomData13[0],
479 +                 atomData13[1],
480 +                 atomData13[2],
481 +                 atomData13[3],
482 +                 atomData13[4],
483 +                 atomData13[5],
484 +                 atomData13[6],
485 +                 atomData13[7],
486 +                 atomData13[8],
487 +                 atomData13[9],
488 +                 atomData13[10],
489 +                 atomData13[11],
490 +                 atomData13[12]);
491          
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();
492        }
493 +      
494 +      for(k = 0; k < outFile.size(); k++)
495 +        *outFile[k] << writeLine;
496      }
497 <
498 <    finalOut.flush();
497 >    
498 >    for(k = 0; k < outFile.size(); k++)
499 >      outFile[k]->flush();
500 >    
501      sprintf( checkPointMsg,
502               "Sucessfully took a dump.\n");
503 +    
504      MPIcheckPoint();        
505      
506 +    delete[] potatoes;
507 +    
508    } else {
509  
510      // worldRank != 0, so I'm a remote node.  
511 +
512 +    // Set my magic potato to 0:
513 +
514 +    myPotato = 0;
515 +    currentIndex = 0;
516      
517      for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) {
518        
# Line 712 | Line 520 | void DumpWriter::writeFinal(double finalTime){
520        
521        if (AtomToProcMap[i] == worldRank) {
522  
523 <        local_index=-1;
524 <        for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) {
525 <          if (atoms[j]->getGlobalIndex() == which_atom) local_index = j;
523 >        if (myPotato + 3 >= MAXTAG) {
524 >          
525 >          // The potato was going to exceed the maximum value,
526 >          // so wrap this processor potato back to 0 (and block until
527 >          // node 0 says we can go:
528 >          
529 >          MPI_Recv(&myPotato, 1, MPI_INT, 0, 0, MPI_COMM_WORLD, &istatus);
530 >          
531          }
532 <        if (local_index != -1) {
532 >        which_atom = i;
533 >
534 >        //local_index = -1;
535 >
536 >        //for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) {
537 >        // if (atoms[j]->getGlobalIndex() == which_atom) local_index = j;
538 >        //}
539 >        
540 >        //if (local_index != -1) {
541 >
542 >        local_index = indexArray[currentIndex].first;        
543 >                
544 >        if (which_atom == indexArray[currentIndex].second) {
545          
546            atomTypeString = atoms[local_index]->getType();
547 <
547 >          
548            atoms[local_index]->getPos(pos);
549            atoms[local_index]->getVel(vel);
550 +          
551 +          atomData6[0] = pos[0];
552 +          atomData6[1] = pos[1];
553 +          atomData6[2] = pos[2];
554  
555 <          atomTransData[0] = pos[0];
556 <          atomTransData[1] = pos[1];
557 <          atomTransData[2] = pos[2];
729 <
730 <          atomTransData[3] = vel[0];
731 <          atomTransData[4] = vel[1];
732 <          atomTransData[5] = vel[2];
555 >          atomData6[3] = vel[0];
556 >          atomData6[4] = vel[1];
557 >          atomData6[5] = vel[2];
558            
559            isDirectional = 0;
560  
# Line 740 | Line 565 | void DumpWriter::writeFinal(double finalTime){
565              dAtom = (DirectionalAtom *)atoms[local_index];
566              dAtom->getQ( q );
567              
568 <            atomOrientData[0] = q[0];
569 <            atomOrientData[1] = q[1];
570 <            atomOrientData[2] = q[2];
571 <            atomOrientData[3] = q[3];
572 <
573 <            atomOrientData[4] = dAtom->getJx();
574 <            atomOrientData[5] = dAtom->getJy();
575 <            atomOrientData[6] = dAtom->getJz();
568 >            for (int j = 0; j < 6 ; j++)
569 >              atomData13[j] = atomData6[j];
570 >            
571 >            atomData13[6] = q[0];
572 >            atomData13[7] = q[1];
573 >            atomData13[8] = q[2];
574 >            atomData13[9] = q[3];
575 >  
576 >            atomData13[10] = dAtom->getJx();
577 >            atomData13[11] = dAtom->getJy();
578 >            atomData13[12] = dAtom->getJz();
579            }
580  
581          } else {
582            sprintf(painCave.errMsg,
583 <                  "Atom %d not found on processor %d\n",
584 <                  i, worldRank );
583 >                  "Atom %d not found on processor %d, currentIndex = %d, local_index = %d\n",
584 >                  which_atom, worldRank, currentIndex, local_index );
585            haveError= 1;
586            simError();
587          }
588 <
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 <
588 >        
589          strncpy(MPIatomTypeString, atomTypeString, MINIBUFFERSIZE);
590  
591 +        // null terminate the string before sending (just in case):
592 +        MPIatomTypeString[MINIBUFFERSIZE-1] = '\0';
593 +
594          MPI_Send(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, 0,
595 <                 atomTypeTag, MPI_COMM_WORLD);
595 >                             myPotato, MPI_COMM_WORLD);
596          
597 +        myPotato++;
598 +
599          MPI_Send(&isDirectional, 1, MPI_INT, 0,
600 <                 atomIsDirectionalTag, MPI_COMM_WORLD);
600 >                             myPotato, MPI_COMM_WORLD);
601          
602 <        MPI_Send(atomTransData, 6, MPI_DOUBLE, 0,
603 <                 atomTransDataTag, MPI_COMM_WORLD);
778 <
602 >        myPotato++;
603 >        
604          if (isDirectional) {
605  
606 <          MPI_Send(atomOrientData, 7, MPI_DOUBLE, 0,
607 <                   atomOrientDataTag, MPI_COMM_WORLD);
606 >          MPI_Send(atomData13, 13, MPI_DOUBLE, 0,
607 >                   myPotato, MPI_COMM_WORLD);
608            
609 +        } else {
610 +
611 +          MPI_Send(atomData6, 6, MPI_DOUBLE, 0,
612 +                   myPotato, MPI_COMM_WORLD);
613          }
614 <      
614 >
615 >        myPotato++;  
616 >        currentIndex++;    
617        }
618      }
619  
620      sprintf( checkPointMsg,
621 <             "Sucessfully wrote final file.\n");
621 >             "Sucessfully took a dump.\n");
622      MPIcheckPoint();        
623      
624 <  }
624 >  }
625    
795  painCave.isEventLoop = 0;
796
797  if( worldRank == 0 ) finalOut.close();
626   #endif // is_mpi
627   }
628  
801
802
629   #ifdef IS_MPI
630  
631   // a couple of functions to let us escape the write loop

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