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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 1000 by tim, Fri Jan 30 21:47:22 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 +
100 + #endif
101 +
102 + void DumpWriter::writeDump(double currentTime){
103 +
104 +  ofstream finalOut;
105 +  vector<ofstream*> fileStreams;
106 +
107 + #ifdef IS_MPI
108 +  if(worldRank == 0 ){
109 + #endif    
110 +    finalOut.open( entry_plug->finalName, ios::out | ios::trunc );
111 +    if( !finalOut ){
112 +      sprintf( painCave.errMsg,
113 +               "Could not open \"%s\" for final dump output.\n",
114 +               entry_plug->finalName );
115 +      painCave.isFatal = 1;
116 +      simError();
117 +    }
118 + #ifdef IS_MPI
119 +  }
120 + #endif // is_mpi
121 +
122 +  fileStreams.push_back(&finalOut);
123 +  fileStreams.push_back(&dumpFile);
124 +
125 +  writeFrame(fileStreams, currentTime);
126 +
127 + #ifdef IS_MPI
128 +  finalOut.close();
129 + #endif
130 +        
131 + }
132 +
133 + void DumpWriter::writeFinal(double currentTime){
134 +
135 +  ofstream finalOut;
136 +  vector<ofstream*> fileStreams;
137 +
138 + #ifdef IS_MPI
139 +  if(worldRank == 0 ){
140 + #endif // is_mpi
141 +
142 +    finalOut.open( entry_plug->finalName, ios::out | ios::trunc );
143 +
144 +    if( !finalOut ){
145 +      sprintf( painCave.errMsg,
146 +               "Could not open \"%s\" for final dump output.\n",
147 +               entry_plug->finalName );
148 +      painCave.isFatal = 1;
149 +      simError();
150 +    }
151 +
152 + #ifdef IS_MPI
153 +  }
154 + #endif // is_mpi
155 +  
156 +  fileStreams.push_back(&finalOut);  
157 +  writeFrame(fileStreams, currentTime);
158 +
159 + #ifdef IS_MPI
160 +  finalOut.close();
161 + #endif
162 +  
163 + }
164 +
165 + void DumpWriter::writeFrame( vector<ofstream*>& outFile, double currentTime ){
166 +
167    const int BUFFERSIZE = 2000;
168    const int MINIBUFFERSIZE = 100;
169  
170 <  char tempBuffer[BUFFERSIZE];
170 >  char tempBuffer[BUFFERSIZE];  
171    char writeLine[BUFFERSIZE];
172  
173 <  int i;
173 >  int i, k;
174 >
175   #ifdef IS_MPI
176 <  int j, which_node, done, which_atom, local_index;
177 <  double atomTransData[6];
178 <  double atomOrientData[7];
176 >  
177 >  /*********************************************************************
178 >   * Documentation?  You want DOCUMENTATION?
179 >   *
180 >   * Why all the potatoes below?  
181 >   *
182 >   * To make a long story short, the original version of DumpWriter
183 >   * worked in the most inefficient way possible.  Node 0 would
184 >   * poke each of the node for an individual atom's formatted data
185 >   * as node 0 worked its way down the global index. This was particularly
186 >   * inefficient since the method blocked all processors at every atom
187 >   * (and did it twice!).
188 >   *
189 >   * An intermediate version of DumpWriter could be described from Node
190 >   * zero's perspective as follows:
191 >   *
192 >   *  1) Have 100 of your friends stand in a circle.
193 >   *  2) When you say go, have all of them start tossing potatoes at
194 >   *     you (one at a time).
195 >   *  3) Catch the potatoes.
196 >   *
197 >   * It was an improvement, but MPI has buffers and caches that could
198 >   * best be described in this analogy as "potato nets", so there's no
199 >   * need to block the processors atom-by-atom.
200 >   *
201 >   * This new and improved DumpWriter works in an even more efficient
202 >   * way:
203 >   *
204 >   *  1) Have 100 of your friend stand in a circle.
205 >   *  2) When you say go, have them start tossing 5-pound bags of
206 >   *     potatoes at you.
207 >   *  3) Once you've caught a friend's bag of potatoes,
208 >   *     toss them a spud to let them know they can toss another bag.
209 >   *
210 >   * How's THAT for documentation?
211 >   *
212 >   *********************************************************************/
213 >
214 >  int *potatoes;
215 >  int myPotato;
216 >
217 >  int nProc;
218 >  int j, which_node, done, which_atom, local_index, currentIndex;
219 >  double atomData6[6];
220 >  double atomData13[13];
221    int isDirectional;
222    char* atomTypeString;
223    char MPIatomTypeString[MINIBUFFERSIZE];
224 <  int me;
83 <  int atomTypeTag;
84 <  int atomIsDirectionalTag;
85 <  int atomTransDataTag;
86 <  int atomOrientDataTag;
224 >
225   #else //is_mpi
226    int nAtoms = entry_plug->n_atoms;
227   #endif //is_mpi
# Line 93 | Line 231 | void DumpWriter::writeDump( double currentTime ){
231    Atom** atoms = entry_plug->atoms;
232    double pos[3], vel[3];
233  
96 –  // write current frame to the eor file
97 –
98 –  this->writeFinal( currentTime );
99 –
234   #ifndef IS_MPI
235 +  
236 +  for(k = 0; k < outFile.size(); k++){
237 +    *outFile[k] << nAtoms << "\n";
238  
239 <  outFile << nAtoms << "\n";
239 >    *outFile[k] << currentTime << ";\t"
240 >               << entry_plug->Hmat[0][0] << "\t"
241 >                     << entry_plug->Hmat[1][0] << "\t"
242 >                     << entry_plug->Hmat[2][0] << ";\t"
243 >              
244 >               << entry_plug->Hmat[0][1] << "\t"
245 >                     << entry_plug->Hmat[1][1] << "\t"
246 >                     << entry_plug->Hmat[2][1] << ";\t"
247  
248 <  outFile << currentTime << ";\t"
249 <          << entry_plug->Hmat[0][0] << "\t"
250 <          << entry_plug->Hmat[1][0] << "\t"
107 <          << entry_plug->Hmat[2][0] << ";\t"
248 >                     << entry_plug->Hmat[0][2] << "\t"
249 >                     << entry_plug->Hmat[1][2] << "\t"
250 >                     << entry_plug->Hmat[2][2] << ";";
251  
252 <          << entry_plug->Hmat[0][1] << "\t"
253 <          << entry_plug->Hmat[1][1] << "\t"
254 <          << entry_plug->Hmat[2][1] << ";\t"
255 <
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 <
252 >    //write out additional parameters, such as chi and eta
253 >    *outFile[k] << entry_plug->the_integrator->getAdditionalParameters() << endl;
254 >  }
255 >  
256    for( i=0; i<nAtoms; i++ ){
257  
258      atoms[i]->getPos(pos);
# Line 152 | Line 288 | void DumpWriter::writeDump( double currentTime ){
288      else
289        strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
290  
291 <    outFile << writeLine;
291 >    for(k = 0; k < outFile.size(); k++)
292 >      *outFile[k] << writeLine;
293    }
157 –  outFile.flush();
294  
295   #else // is_mpi
296  
297    /* code to find maximum tag value */
298 +  
299    int *tagub, flag, MAXTAG;
300    MPI_Attr_get(MPI_COMM_WORLD, MPI_TAG_UB, &tagub, &flag);
301    if (flag) {
302      MAXTAG = *tagub;
303    } else {
304      MAXTAG = 32767;
305 <  }
305 >  }  
306  
307    int haveError;
308  
# Line 175 | Line 312 | void DumpWriter::writeDump( double currentTime ){
312    // write out header and node 0's coordinates
313  
314    if( worldRank == 0 ){
178 –    outFile << mpiSim->getTotAtoms() << "\n";
315  
316 <    outFile << currentTime << ";\t"
181 <            << entry_plug->Hmat[0][0] << "\t"
182 <            << entry_plug->Hmat[1][0] << "\t"
183 <            << entry_plug->Hmat[2][0] << ";\t"
316 >    // Node 0 needs a list of the magic potatoes for each processor;
317  
318 <            << entry_plug->Hmat[0][1] << "\t"
319 <            << entry_plug->Hmat[1][1] << "\t"
187 <            << entry_plug->Hmat[2][1] << ";\t"
318 >    nProc = mpiSim->getNumberProcessors();
319 >    potatoes = new int[nProc];
320  
321 <            << entry_plug->Hmat[0][2] << "\t"
322 <            << entry_plug->Hmat[1][2] << "\t"
323 <            << entry_plug->Hmat[2][2] << ";";
321 >    //write out the comment lines
322 >    for (i = 0; i < nProc; i++)
323 >      potatoes[i] = 0;
324 >    
325 >      for(k = 0; k < outFile.size(); k++){
326 >        *outFile[k] << mpiSim->getTotAtoms() << "\n";
327  
328 <    outFile << entry_plug->the_integrator->getAdditionalParameters();
329 <    outFile << endl;
330 <    outFile.flush();
328 >        *outFile[k] << currentTime << ";\t"
329 >                         << entry_plug->Hmat[0][0] << "\t"
330 >                         << entry_plug->Hmat[1][0] << "\t"
331 >                         << entry_plug->Hmat[2][0] << ";\t"
332  
333 <    tag = 0;
333 >                         << entry_plug->Hmat[0][1] << "\t"
334 >                         << entry_plug->Hmat[1][1] << "\t"
335 >                         << entry_plug->Hmat[2][1] << ";\t"
336  
337 <    for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) {
337 >                         << entry_plug->Hmat[0][2] << "\t"
338 >                         << entry_plug->Hmat[1][2] << "\t"
339 >                         << entry_plug->Hmat[2][2] << ";";
340 >  
341 >        *outFile[k] << entry_plug->the_integrator->getAdditionalParameters() << endl;
342 >    }
343  
344 <      if (tag + 2 >= MAXTAG) {
345 <        // The tag was going to exceed the maximum value, so wrap around to 0:
346 <        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 <      }
344 >    currentIndex = 0;
345 >
346 >    for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) {
347        
348        // Get the Node number which has this atom;
349        
350        which_node = AtomToProcMap[i];
351        
352        if (which_node != 0) {
353 +
354 +        if (potatoes[which_node] + 3 >= MAXTAG) {
355 +          // The potato was going to exceed the maximum value,
356 +          // so wrap this processor potato back to 0:        
357 +
358 +          potatoes[which_node] = 0;          
359 +          MPI_Send(0, 1, MPI_INT, which_node, 0, MPI_COMM_WORLD);
360 +          
361 +        }
362 +
363 +        myPotato = potatoes[which_node];        
364          
365          MPI_Recv(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, which_node,
366 <                 atomTypeTag, MPI_COMM_WORLD, &istatus);
366 >                 myPotato, MPI_COMM_WORLD, &istatus);
367          
368 <        strncpy(atomTypeString, MPIatomTypeString, MINIBUFFERSIZE);
369 <        
370 <        // Null terminate the atomTypeString just in case:
368 >        atomTypeString = MPIatomTypeString;
369 >        
370 >        myPotato++;
371  
221 –        atomTypeString[strlen(atomTypeString) - 1] = '\0';
222 –
372          MPI_Recv(&isDirectional, 1, MPI_INT, which_node,
373 <                 atomIsDirectionalTag, MPI_COMM_WORLD, &istatus);
374 <        
375 <        MPI_Recv(atomTransData, 6, MPI_DOUBLE, which_node,
227 <                 atomTransDataTag, MPI_COMM_WORLD, &istatus);
373 >                 myPotato, MPI_COMM_WORLD, &istatus);
374 >              
375 >        myPotato++;
376  
377 <        if (isDirectional) {
378 <
379 <          MPI_Recv(atomOrientData, 7, MPI_DOUBLE, which_node,
380 <                   atomOrientDataTag, MPI_COMM_WORLD, &istatus);
381 <
377 >        if (isDirectional) {          
378 >          MPI_Recv(atomData13, 13, MPI_DOUBLE, which_node,
379 >                   myPotato, MPI_COMM_WORLD, &istatus);
380 >        } else {
381 >          MPI_Recv(atomData6, 6, MPI_DOUBLE, which_node,
382 >                   myPotato, MPI_COMM_WORLD, &istatus);          
383          }
384 +        
385 +        myPotato++;
386 +        potatoes[which_node] = myPotato;
387  
388        } else {
389          
390 <        haveError = 0;
390 >        haveError = 0;
391          which_atom = i;
392 <        local_index=-1;
393 <
394 <        for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) {
395 <          if (atoms[j]->getGlobalIndex() == which_atom) local_index = j;
396 <        }
397 <
398 <        if (local_index != -1) {
247 <
248 <          atomTypeString = atoms[local_index]->getType();
249 <
392 >        
393 >          local_index = indexArray[currentIndex].first;        
394 >          
395 >          if (which_atom == indexArray[currentIndex].second) {
396 >            
397 >            atomTypeString = atoms[local_index]->getType();
398 >            
399            atoms[local_index]->getPos(pos);
400 <          atoms[local_index]->getVel(vel);
400 >          atoms[local_index]->getVel(vel);          
401 >          
402 >          atomData6[0] = pos[0];
403 >          atomData6[1] = pos[1];
404 >          atomData6[2] = pos[2];
405  
406 <          atomTransData[0] = pos[0];
407 <          atomTransData[1] = pos[1];
408 <          atomTransData[2] = pos[2];
256 <
257 <          atomTransData[3] = vel[0];
258 <          atomTransData[4] = vel[1];
259 <          atomTransData[5] = vel[2];
406 >          atomData6[3] = vel[0];
407 >          atomData6[4] = vel[1];
408 >          atomData6[5] = vel[2];
409            
410            isDirectional = 0;
411  
# Line 266 | Line 415 | void DumpWriter::writeDump( double currentTime ){
415              
416              dAtom = (DirectionalAtom *)atoms[local_index];
417              dAtom->getQ( q );
269 –            
270 –            atomOrientData[0] = q[0];
271 –            atomOrientData[1] = q[1];
272 –            atomOrientData[2] = q[2];
273 –            atomOrientData[3] = q[3];
418  
419 <            atomOrientData[4] = dAtom->getJx();
420 <            atomOrientData[5] = dAtom->getJy();
421 <            atomOrientData[6] = dAtom->getJz();
419 >            for (int j = 0; j < 6 ; j++)
420 >              atomData13[j] = atomData6[j];            
421 >            
422 >            atomData13[6] = q[0];
423 >            atomData13[7] = q[1];
424 >            atomData13[8] = q[2];
425 >            atomData13[9] = q[3];
426 >            
427 >            atomData13[10] = dAtom->getJx();
428 >            atomData13[11] = dAtom->getJy();
429 >            atomData13[12] = dAtom->getJz();
430            }
431 <
431 >          
432          } else {
433            sprintf(painCave.errMsg,
434 <                  "Atom %d not found on processor %d\n",
435 <                  i, worldRank );
434 >                  "Atom %d not found on processor %d, currentIndex = %d, local_index = %d\n",
435 >                  which_atom, worldRank, currentIndex, local_index );
436            haveError= 1;
437            simError();
438          }
287 –
288 –        if(haveError) DieDieDie();
289 –                              
290 –        // If we've survived to here, format the line:
439          
440 <        sprintf( tempBuffer,
441 <                 "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
442 <                 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();
440 >        if(haveError) DieDieDie();
441 >        
442 >        currentIndex++;
443        }
444 <    }
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++ ) {
444 >      // If we've survived to here, format the line:
445        
446 <      // Am I the node which has this atom?
447 <      
448 <      if (AtomToProcMap[i] == worldRank) {
449 <
450 <        local_index=-1;
451 <        for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) {
452 <          if (atoms[j]->getGlobalIndex() == which_atom) local_index = j;
453 <        }
454 <        if (local_index != -1) {
455 <        
456 <          atomTypeString = atoms[local_index]->getType();
457 <
458 <          atoms[local_index]->getPos(pos);
459 <          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 <
446 >      if (!isDirectional) {
447 >        
448 >        sprintf( writeLine,
449 >                 "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
450 >                 atomTypeString,
451 >                 atomData6[0],
452 >                 atomData6[1],
453 >                 atomData6[2],
454 >                 atomData6[3],
455 >                 atomData6[4],
456 >                 atomData6[5]);
457 >        
458 >        strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
459 >        
460        } else {
461 +        
462 +        sprintf( writeLine,
463 +                 "%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",
464 +                 atomTypeString,
465 +                 atomData13[0],
466 +                 atomData13[1],
467 +                 atomData13[2],
468 +                 atomData13[3],
469 +                 atomData13[4],
470 +                 atomData13[5],
471 +                 atomData13[6],
472 +                 atomData13[7],
473 +                 atomData13[8],
474 +                 atomData13[9],
475 +                 atomData13[10],
476 +                 atomData13[11],
477 +                 atomData13[12]);
478          
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();
479        }
480 +      
481 +      for(k = 0; k < outFile.size(); k++)
482 +        *outFile[k] << writeLine;
483      }
484 <
485 <    finalOut.flush();
484 >    
485 >    for(k = 0; k < outFile.size(); k++)
486 >      outFile[k]->flush();
487 >    
488      sprintf( checkPointMsg,
489               "Sucessfully took a dump.\n");
490 +    
491      MPIcheckPoint();        
492      
493 +    delete[] potatoes;
494 +    
495    } else {
496  
497      // worldRank != 0, so I'm a remote node.  
498 +
499 +    // Set my magic potato to 0:
500 +
501 +    myPotato = 0;
502 +    currentIndex = 0;
503      
504      for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) {
505        
# Line 712 | Line 507 | void DumpWriter::writeFinal(double finalTime){
507        
508        if (AtomToProcMap[i] == worldRank) {
509  
510 <        local_index=-1;
511 <        for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) {
512 <          if (atoms[j]->getGlobalIndex() == which_atom) local_index = j;
510 >        if (myPotato + 3 >= MAXTAG) {
511 >          
512 >          // The potato was going to exceed the maximum value,
513 >          // so wrap this processor potato back to 0 (and block until
514 >          // node 0 says we can go:
515 >          
516 >          MPI_Recv(&myPotato, 1, MPI_INT, 0, 0, MPI_COMM_WORLD, &istatus);
517 >          
518          }
519 <        if (local_index != -1) {
519 >        which_atom = i;
520 >
521 >        local_index = indexArray[currentIndex].first;        
522 >                
523 >        if (which_atom == indexArray[currentIndex].second) {
524          
525            atomTypeString = atoms[local_index]->getType();
526 <
526 >          
527            atoms[local_index]->getPos(pos);
528            atoms[local_index]->getVel(vel);
529 +          
530 +          atomData6[0] = pos[0];
531 +          atomData6[1] = pos[1];
532 +          atomData6[2] = pos[2];
533  
534 <          atomTransData[0] = pos[0];
535 <          atomTransData[1] = pos[1];
536 <          atomTransData[2] = pos[2];
729 <
730 <          atomTransData[3] = vel[0];
731 <          atomTransData[4] = vel[1];
732 <          atomTransData[5] = vel[2];
534 >          atomData6[3] = vel[0];
535 >          atomData6[4] = vel[1];
536 >          atomData6[5] = vel[2];
537            
538            isDirectional = 0;
539  
# Line 740 | Line 544 | void DumpWriter::writeFinal(double finalTime){
544              dAtom = (DirectionalAtom *)atoms[local_index];
545              dAtom->getQ( q );
546              
547 <            atomOrientData[0] = q[0];
548 <            atomOrientData[1] = q[1];
549 <            atomOrientData[2] = q[2];
550 <            atomOrientData[3] = q[3];
551 <
552 <            atomOrientData[4] = dAtom->getJx();
553 <            atomOrientData[5] = dAtom->getJy();
554 <            atomOrientData[6] = dAtom->getJz();
547 >            for (int j = 0; j < 6 ; j++)
548 >              atomData13[j] = atomData6[j];
549 >            
550 >            atomData13[6] = q[0];
551 >            atomData13[7] = q[1];
552 >            atomData13[8] = q[2];
553 >            atomData13[9] = q[3];
554 >  
555 >            atomData13[10] = dAtom->getJx();
556 >            atomData13[11] = dAtom->getJy();
557 >            atomData13[12] = dAtom->getJz();
558            }
559  
560          } else {
561            sprintf(painCave.errMsg,
562 <                  "Atom %d not found on processor %d\n",
563 <                  i, worldRank );
562 >                  "Atom %d not found on processor %d, currentIndex = %d, local_index = %d\n",
563 >                  which_atom, worldRank, currentIndex, local_index );
564            haveError= 1;
565            simError();
566          }
567 <
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 <
567 >        
568          strncpy(MPIatomTypeString, atomTypeString, MINIBUFFERSIZE);
569  
570 +        // null terminate the string before sending (just in case):
571 +        MPIatomTypeString[MINIBUFFERSIZE-1] = '\0';
572 +
573          MPI_Send(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, 0,
574 <                 atomTypeTag, MPI_COMM_WORLD);
574 >                             myPotato, MPI_COMM_WORLD);
575          
576 +        myPotato++;
577 +
578          MPI_Send(&isDirectional, 1, MPI_INT, 0,
579 <                 atomIsDirectionalTag, MPI_COMM_WORLD);
579 >                             myPotato, MPI_COMM_WORLD);
580          
581 <        MPI_Send(atomTransData, 6, MPI_DOUBLE, 0,
582 <                 atomTransDataTag, MPI_COMM_WORLD);
778 <
581 >        myPotato++;
582 >        
583          if (isDirectional) {
584  
585 <          MPI_Send(atomOrientData, 7, MPI_DOUBLE, 0,
586 <                   atomOrientDataTag, MPI_COMM_WORLD);
585 >          MPI_Send(atomData13, 13, MPI_DOUBLE, 0,
586 >                   myPotato, MPI_COMM_WORLD);
587            
588 +        } else {
589 +
590 +          MPI_Send(atomData6, 6, MPI_DOUBLE, 0,
591 +                   myPotato, MPI_COMM_WORLD);
592          }
593 <      
593 >
594 >        myPotato++;  
595 >        currentIndex++;    
596        }
597      }
598  
599      sprintf( checkPointMsg,
600 <             "Sucessfully wrote final file.\n");
600 >             "Sucessfully took a dump.\n");
601      MPIcheckPoint();        
602      
603 <  }
603 >  }
604    
795 –  painCave.isEventLoop = 0;
796 –
797 –  if( worldRank == 0 ) finalOut.close();
605   #endif // is_mpi
606   }
607  
801 –
802 –
608   #ifdef IS_MPI
609  
610   // a couple of functions to let us escape the write loop

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