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root/group/trunk/OOPSE/libmdtools/DumpWriter.cpp
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Comparing trunk/OOPSE/libmdtools/DumpWriter.cpp (file contents):
Revision 927 by tim, Mon Jan 12 22:54:42 2004 UTC vs.
Revision 1078 by tim, Tue Mar 2 20:32:40 2004 UTC

# Line 1 | Line 1
1 + #define _LARGEFILE_SOURCE64
2   #define _FILE_OFFSET_BITS 64
3  
4   #include <string.h>
5   #include <iostream>
6   #include <fstream>
7 + #include <algorithm>
8 + #include <utility>
9  
10   #ifdef IS_MPI
11   #include <mpi.h>
# Line 26 | Line 29 | DumpWriter::DumpWriter( SimInfo* the_entry_plug ){
29    if(worldRank == 0 ){
30   #endif // is_mpi
31  
32 <    strcpy( outName, entry_plug->sampleName );
32 >    dumpFile.open(entry_plug->sampleName, ios::out | ios::trunc );
33  
34 <    outFile.open(outName, ios::out | ios::trunc );
34 >    if( !dumpFile ){
35  
33 –    if( !outFile ){
34 –
36        sprintf( painCave.errMsg,
37                 "Could not open \"%s\" for dump output.\n",
38 <               outName);
38 >               entry_plug->sampleName);
39        painCave.isFatal = 1;
40        simError();
41      }
42  
42 –    //outFile.setf( ios::scientific );
43 –
43   #ifdef IS_MPI
44    }
45  
46 +  //sort the local atoms by global index
47 +  sortByGlobalIndex();
48 +  
49    sprintf( checkPointMsg,
50             "Sucessfully opened output file for dumping.\n");
51    MPIcheckPoint();
# Line 56 | Line 58 | DumpWriter::~DumpWriter( ){
58    if(worldRank == 0 ){
59   #endif // is_mpi
60  
61 <    outFile.close();
61 >    dumpFile.close();
62  
63   #ifdef IS_MPI
64    }
65   #endif // is_mpi
66   }
67  
68 < void DumpWriter::writeDump( double currentTime ){
68 > #ifdef IS_MPI
69  
70 <  const int BUFFERSIZE = 2000;
71 <  const int MINIBUFFERSIZE = 100;
70 > /**
71 > * A hook function to load balancing
72 > */
73  
74 <  char tempBuffer[BUFFERSIZE];
75 <  char writeLine[BUFFERSIZE];
76 <
74 <  int i;
75 <
76 < #ifdef IS_MPI
74 > void DumpWriter::update(){
75 >  sortByGlobalIndex();          
76 > }
77    
78 <  int *potatoes;
79 <  int myPotato;
78 > /**
79 > * Auxiliary sorting function
80 > */
81 >
82 > bool indexSortingCriterion(const pair<int, int>& p1, const pair<int, int>& p2){
83 >  return p1.second < p2.second;
84 > }
85  
86 <  int nProc;
87 <  int j, which_node, done, which_atom, local_index;
88 <  double atomData6[6];
89 <  double atomData13[13];
90 <  int isDirectional;
86 <  char* atomTypeString;
87 <  char MPIatomTypeString[MINIBUFFERSIZE];
88 <
89 < #else //is_mpi
90 <  int nAtoms = entry_plug->n_atoms;
91 < #endif //is_mpi
92 <
93 <  double q[4];
94 <  DirectionalAtom* dAtom;
86 > /**
87 > * Sorting the local index by global index
88 > */
89 >
90 > void DumpWriter::sortByGlobalIndex(){
91    Atom** atoms = entry_plug->atoms;
92 <  double pos[3], vel[3];
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 <  // write current frame to the eor file
101 > #endif
102  
103 <  this->writeFinal( currentTime );
103 > void DumpWriter::writeDump(double currentTime){
104  
105 < #ifndef IS_MPI
105 >  ofstream finalOut;
106 >  vector<ofstream*> fileStreams;
107  
108 <  outFile << nAtoms << "\n";
109 <
110 <  outFile << currentTime << ";\t"
111 <          << entry_plug->Hmat[0][0] << "\t"
112 <          << entry_plug->Hmat[1][0] << "\t"
113 <          << entry_plug->Hmat[2][0] << ";\t"
114 <
115 <          << entry_plug->Hmat[0][1] << "\t"
116 <          << entry_plug->Hmat[1][1] << "\t"
117 <          << entry_plug->Hmat[2][1] << ";\t"
114 <
115 <          << entry_plug->Hmat[0][2] << "\t"
116 <          << entry_plug->Hmat[1][2] << "\t"
117 <          << entry_plug->Hmat[2][2] << ";";
118 <  //write out additional parameters, such as chi and eta
119 <  outFile << entry_plug->the_integrator->getAdditionalParameters();
120 <  outFile << endl;
121 <
122 <  for( i=0; i<nAtoms; i++ ){
123 <
124 <    atoms[i]->getPos(pos);
125 <    atoms[i]->getVel(vel);
126 <
127 <    sprintf( tempBuffer,
128 <             "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
129 <             atoms[i]->getType(),
130 <             pos[0],
131 <             pos[1],
132 <             pos[2],
133 <             vel[0],
134 <             vel[1],
135 <             vel[2]);
136 <    strcpy( writeLine, tempBuffer );
137 <
138 <    if( atoms[i]->isDirectional() ){
139 <
140 <      dAtom = (DirectionalAtom *)atoms[i];
141 <      dAtom->getQ( q );
142 <
143 <      sprintf( tempBuffer,
144 <               "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
145 <               q[0],
146 <               q[1],
147 <               q[2],
148 <               q[3],
149 <               dAtom->getJx(),
150 <               dAtom->getJy(),
151 <               dAtom->getJz());
152 <      strcat( writeLine, tempBuffer );
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 <    else
155 <      strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
156 <
157 <    outFile << writeLine;
119 > #ifdef IS_MPI
120    }
121 <  outFile.flush();
121 > #endif // is_mpi
122  
123 < #else // is_mpi
123 >  fileStreams.push_back(&finalOut);
124 >  fileStreams.push_back(&dumpFile);
125  
126 <  /* code to find maximum tag value */
164 <  
165 <  int *tagub, flag, MAXTAG;
166 <  MPI_Attr_get(MPI_COMM_WORLD, MPI_TAG_UB, &tagub, &flag);
167 <  if (flag) {
168 <    MAXTAG = *tagub;
169 <  } else {
170 <    MAXTAG = 32767;
171 <  }  
126 >  writeFrame(fileStreams, currentTime);
127  
128 <  int haveError;
128 > #ifdef IS_MPI
129 >  finalOut.close();
130 > #endif
131 >        
132 > }
133  
134 <  MPI_Status istatus;
176 <  int *AtomToProcMap = mpiSim->getAtomToProcMap();
134 > void DumpWriter::writeFinal(double currentTime){
135  
136 <  // write out header and node 0's coordinates
136 >  ofstream finalOut;
137 >  vector<ofstream*> fileStreams;
138  
139 <  if( worldRank == 0 ){
139 > #ifdef IS_MPI
140 >  if(worldRank == 0 ){
141 > #endif // is_mpi
142  
143 <    // Node 0 needs a list of the magic potatoes for each processor;
143 >    finalOut.open( entry_plug->finalName, ios::out | ios::trunc );
144  
145 <    nProc = mpiSim->getNumberProcessors();
146 <    potatoes = new int[nProc];
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 <    for (i = 0; i < nProc; i++)
154 <      potatoes[i] = 0;
155 <    
156 <    outFile << mpiSim->getTotAtoms() << "\n";
157 <
158 <    outFile << currentTime << ";\t"
193 <            << entry_plug->Hmat[0][0] << "\t"
194 <            << entry_plug->Hmat[1][0] << "\t"
195 <            << entry_plug->Hmat[2][0] << ";\t"
196 <
197 <            << entry_plug->Hmat[0][1] << "\t"
198 <            << entry_plug->Hmat[1][1] << "\t"
199 <            << entry_plug->Hmat[2][1] << ";\t"
200 <
201 <            << entry_plug->Hmat[0][2] << "\t"
202 <            << entry_plug->Hmat[1][2] << "\t"
203 <            << entry_plug->Hmat[2][2] << ";";
204 <
205 <    outFile << entry_plug->the_integrator->getAdditionalParameters();
206 <    outFile << endl;
207 <    outFile.flush();
208 <
209 <    for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) {
210 <      
211 <      // Get the Node number which has this atom;
212 <      
213 <      which_node = AtomToProcMap[i];
214 <      
215 <      if (which_node != 0) {
216 <
217 <        if (potatoes[which_node] + 3 >= MAXTAG) {
218 <          // The potato was going to exceed the maximum value,
219 <          // so wrap this processor potato back to 0:        
220 <
221 <          potatoes[which_node] = 0;          
222 <          MPI_Send(0, 1, MPI_INT, which_node, 0, MPI_COMM_WORLD);
223 <          
224 <        }
225 <
226 <        myPotato = potatoes[which_node];        
227 <        
228 <        MPI_Recv(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, which_node,
229 <                 myPotato, MPI_COMM_WORLD, &istatus);
230 <        
231 <        //strncpy(atomTypeString, MPIatomTypeString, MINIBUFFERSIZE);
232 <        
233 <        // Null terminate the atomTypeString just in case:
234 <
235 <        //atomTypeString[strlen(atomTypeString) - 1] = '\0';
236 <        atomTypeString = MPIatomTypeString;
237 <        
238 <        myPotato++;
239 <
240 <        MPI_Recv(&isDirectional, 1, MPI_INT, which_node,
241 <                 myPotato, MPI_COMM_WORLD, &istatus);
242 <              
243 <        myPotato++;
244 <
245 <        if (isDirectional) {          
246 <          MPI_Recv(atomData13, 13, MPI_DOUBLE, which_node,
247 <                   myPotato, MPI_COMM_WORLD, &istatus);
248 <        } else {
249 <          MPI_Recv(atomData6, 6, MPI_DOUBLE, which_node,
250 <                   myPotato, MPI_COMM_WORLD, &istatus);          
251 <        }
252 <        
253 <        myPotato++;
254 <        potatoes[which_node] = myPotato;
255 <
256 <      } else {
257 <        
258 <        haveError = 0;
259 <        which_atom = i;
260 <        local_index=-1;
261 <        
262 <        for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) {
263 <          if (atoms[j]->getGlobalIndex() == which_atom) local_index = j;
264 <        }
265 <        
266 <        if (local_index != -1) {
267 <          
268 <          atomTypeString = atoms[local_index]->getType();
269 <
270 <          atoms[local_index]->getPos(pos);
271 <          atoms[local_index]->getVel(vel);          
272 <
273 <          atomData6[0] = pos[0];
274 <          atomData6[1] = pos[1];
275 <          atomData6[2] = pos[2];
276 <
277 <          atomData6[3] = vel[0];
278 <          atomData6[4] = vel[1];
279 <          atomData6[5] = vel[2];
280 <          
281 <          isDirectional = 0;
282 <
283 <          if( atoms[local_index]->isDirectional() ){
284 <
285 <            isDirectional = 1;
286 <            
287 <            dAtom = (DirectionalAtom *)atoms[local_index];
288 <            dAtom->getQ( q );
289 <
290 <            for (int j = 0; j < 6 ; j++)
291 <              atomData13[j] = atomData6[j];            
292 <            
293 <            atomData13[6] = q[0];
294 <            atomData13[7] = q[1];
295 <            atomData13[8] = q[2];
296 <            atomData13[9] = q[3];
297 <            
298 <            atomData13[10] = dAtom->getJx();
299 <            atomData13[11] = dAtom->getJy();
300 <            atomData13[12] = dAtom->getJz();
301 <          }
302 <          
303 <        } else {
304 <          sprintf(painCave.errMsg,
305 <                  "Atom %d not found on processor %d\n",
306 <                  i, worldRank );
307 <          haveError= 1;
308 <          simError();
309 <        }
310 <        
311 <        if(haveError) DieDieDie();
312 <        
313 <      }
314 <      // If we've survived to here, format the line:
315 <      
316 <      if (!isDirectional) {
317 <        
318 <        sprintf( tempBuffer,
319 <                 "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
320 <                 atomTypeString,
321 <                 atomData6[0],
322 <                 atomData6[1],
323 <                 atomData6[2],
324 <                 atomData6[3],
325 <                 atomData6[4],
326 <                 atomData6[5]);
327 <        
328 <        strcpy( writeLine, tempBuffer );
329 <        strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
330 <        
331 <      } else {
332 <        
333 <        sprintf( tempBuffer,
334 <                 "%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",
335 <                 atomTypeString,
336 <                 atomData13[0],
337 <                 atomData13[1],
338 <                 atomData13[2],
339 <                 atomData13[3],
340 <                 atomData13[4],
341 <                 atomData13[5],
342 <                 atomData13[6],
343 <                 atomData13[7],
344 <                 atomData13[8],
345 <                 atomData13[9],
346 <                 atomData13[10],
347 <                 atomData13[11],
348 <                 atomData13[12]);
349 <        
350 <        strcpy( writeLine, tempBuffer );
351 <        
352 <      }
353 <      
354 <      outFile << writeLine;
355 <      outFile.flush();
356 <    }
357 <    
358 <
359 <    outFile.flush();
360 <    sprintf( checkPointMsg,
361 <             "Sucessfully took a dump.\n");
362 <    MPIcheckPoint();        
363 <    delete[] potatoes;
364 <  } else {
365 <
366 <    // worldRank != 0, so I'm a remote node.  
367 <
368 <    // Set my magic potato to 0:
369 <
370 <    myPotato = 0;
371 <    
372 <    for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) {
373 <      
374 <      // Am I the node which has this atom?
375 <      
376 <      if (AtomToProcMap[i] == worldRank) {
153 > #ifdef IS_MPI
154 >  }
155 > #endif // is_mpi
156 >  
157 >  fileStreams.push_back(&finalOut);  
158 >  writeFrame(fileStreams, currentTime);
159  
160 <        if (myPotato + 3 >= MAXTAG) {
161 <
162 <          // The potato was going to exceed the maximum value,
381 <          // so wrap this processor potato back to 0 (and block until
382 <          // node 0 says we can go:
383 <
384 <          MPI_Recv(&myPotato, 1, MPI_INT, 0, 0, MPI_COMM_WORLD, &istatus);
385 <          
386 <        }
387 <        which_atom = i;
388 <        local_index=-1;
389 <        for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) {
390 <          if (atoms[j]->getGlobalIndex() == which_atom) local_index = j;
391 <        }
392 <        if (local_index != -1) {
393 <        
394 <          atomTypeString = atoms[local_index]->getType();
395 <
396 <          atoms[local_index]->getPos(pos);
397 <          atoms[local_index]->getVel(vel);
398 <
399 <          atomData6[0] = pos[0];
400 <          atomData6[1] = pos[1];
401 <          atomData6[2] = pos[2];
402 <
403 <          atomData6[3] = vel[0];
404 <          atomData6[4] = vel[1];
405 <          atomData6[5] = vel[2];
406 <          
407 <          isDirectional = 0;
408 <
409 <          if( atoms[local_index]->isDirectional() ){
410 <
411 <            isDirectional = 1;
412 <            
413 <            dAtom = (DirectionalAtom *)atoms[local_index];
414 <            dAtom->getQ( q );
415 <            
416 <            for (int j = 0; j < 6 ; j++)
417 <              atomData13[j] = atomData6[j];
418 <            
419 <            atomData13[6] = q[0];
420 <            atomData13[7] = q[1];
421 <            atomData13[8] = q[2];
422 <            atomData13[9] = q[3];
423 <
424 <            atomData13[10] = dAtom->getJx();
425 <            atomData13[11] = dAtom->getJy();
426 <            atomData13[12] = dAtom->getJz();
427 <          }
428 <
429 <        } else {
430 <          sprintf(painCave.errMsg,
431 <                  "Atom %d not found on processor %d\n",
432 <                  i, worldRank );
433 <          haveError= 1;
434 <          simError();
435 <        }
436 <
437 <        strncpy(MPIatomTypeString, atomTypeString, MINIBUFFERSIZE);
438 <
439 <        // null terminate the string before sending (just in case):
440 <        MPIatomTypeString[MINIBUFFERSIZE-1] = '\0';
441 <
442 <        MPI_Send(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, 0,
443 <                 myPotato, MPI_COMM_WORLD);
444 <        
445 <        myPotato++;
446 <
447 <        MPI_Send(&isDirectional, 1, MPI_INT, 0,
448 <                 myPotato, MPI_COMM_WORLD);
449 <        
450 <        myPotato++;
451 <        
452 <        if (isDirectional) {
453 <
454 <          MPI_Send(atomData13, 13, MPI_DOUBLE, 0,
455 <                   myPotato, MPI_COMM_WORLD);
456 <          
457 <        } else {
458 <
459 <          MPI_Send(atomData6, 6, MPI_DOUBLE, 0,
460 <                   myPotato, MPI_COMM_WORLD);
461 <        }
462 <
463 <        myPotato++;      
464 <      }
465 <    }
466 <
467 <    sprintf( checkPointMsg,
468 <             "Sucessfully took a dump.\n");
469 <    MPIcheckPoint();        
470 <    
471 <  }
160 > #ifdef IS_MPI
161 >  finalOut.close();
162 > #endif
163    
473 – #endif // is_mpi
164   }
165  
166 < void DumpWriter::writeFinal(double finalTime){
166 > void DumpWriter::writeFrame( vector<ofstream*>& outFile, double currentTime ){
167  
478 –  char finalName[500];
479 –  ofstream finalOut;
480 –
168    const int BUFFERSIZE = 2000;
169    const int MINIBUFFERSIZE = 100;
170 <  char tempBuffer[BUFFERSIZE];
170 >
171 >  char tempBuffer[BUFFERSIZE];  
172    char writeLine[BUFFERSIZE];
173  
174 <  double q[4];
175 <  DirectionalAtom* dAtom;
488 <  Atom** atoms = entry_plug->atoms;
489 <  int i;
174 >  int i, k;
175 >
176   #ifdef IS_MPI
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;
219 >  int j, which_node, done, which_atom, local_index, currentIndex;
220    double atomData6[6];
221    double atomData13[13];
222    int isDirectional;
# Line 504 | Line 227 | void DumpWriter::writeFinal(double finalTime){
227    int nAtoms = entry_plug->n_atoms;
228   #endif //is_mpi
229  
230 +  double q[4];
231 +  DirectionalAtom* dAtom;
232 +  Atom** atoms = entry_plug->atoms;
233    double pos[3], vel[3];
234  
235 < #ifdef IS_MPI
236 <  if(worldRank == 0 ){
237 < #endif // is_mpi
235 > #ifndef IS_MPI
236 >  
237 >  for(k = 0; k < outFile.size(); k++){
238 >    *outFile[k] << nAtoms << "\n";
239  
240 <    strcpy( finalName, entry_plug->finalName );
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 <    finalOut.open( finalName, ios::out | ios::trunc );
250 <    if( !finalOut ){
251 <      sprintf( painCave.errMsg,
518 <               "Could not open \"%s\" for final dump output.\n",
519 <               finalName );
520 <      painCave.isFatal = 1;
521 <      simError();
522 <    }
249 >                     << entry_plug->Hmat[0][2] << "\t"
250 >                     << entry_plug->Hmat[1][2] << "\t"
251 >                     << entry_plug->Hmat[2][2] << ";";
252  
253 <    // finalOut.setf( ios::scientific );
254 <
526 < #ifdef IS_MPI
253 >    //write out additional parameters, such as chi and eta
254 >    *outFile[k] << entry_plug->the_integrator->getAdditionalParameters() << endl;
255    }
256 <
529 <  sprintf(checkPointMsg,"Opened file for final configuration\n");
530 <  MPIcheckPoint();
531 <
532 < #endif //is_mpi
533 <
534 <
535 < #ifndef IS_MPI
536 <
537 <  finalOut << nAtoms << "\n";
538 <
539 <  finalOut << finalTime << ";\t"
540 <           << entry_plug->Hmat[0][0] << "\t"
541 <           << entry_plug->Hmat[1][0] << "\t"
542 <           << entry_plug->Hmat[2][0] << ";\t"
543 <
544 <           << entry_plug->Hmat[0][1] << "\t"
545 <           << entry_plug->Hmat[1][1] << "\t"
546 <           << entry_plug->Hmat[2][1] << ";\t"
547 <
548 <           << entry_plug->Hmat[0][2] << "\t"
549 <           << entry_plug->Hmat[1][2] << "\t"
550 <           << entry_plug->Hmat[2][2] << ";";
551 <
552 <  //write out additional parameters, such as chi and eta
553 <  finalOut << entry_plug->the_integrator->getAdditionalParameters();
554 <  finalOut << endl;
555 <
256 >  
257    for( i=0; i<nAtoms; i++ ){
258  
259      atoms[i]->getPos(pos);
# Line 588 | Line 289 | void DumpWriter::writeFinal(double finalTime){
289      else
290        strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
291  
292 <    finalOut << writeLine;
292 >    for(k = 0; k < outFile.size(); k++)
293 >      *outFile[k] << writeLine;
294    }
593 –  finalOut.flush();
594 –  finalOut.close();
295  
296   #else // is_mpi
297  
298    /* code to find maximum tag value */
299 +  
300    int *tagub, flag, MAXTAG;
301    MPI_Attr_get(MPI_COMM_WORLD, MPI_TAG_UB, &tagub, &flag);
302    if (flag) {
# Line 618 | Line 319 | void DumpWriter::writeFinal(double finalTime){
319      nProc = mpiSim->getNumberProcessors();
320      potatoes = new int[nProc];
321  
322 +    //write out the comment lines
323      for (i = 0; i < nProc; i++)
324        potatoes[i] = 0;
325      
326 <    finalOut << mpiSim->getTotAtoms() << "\n";
326 >      for(k = 0; k < outFile.size(); k++){
327 >        *outFile[k] << mpiSim->getTotAtoms() << "\n";
328  
329 <    finalOut << finalTime << ";\t"
330 <            << entry_plug->Hmat[0][0] << "\t"
331 <            << entry_plug->Hmat[1][0] << "\t"
332 <            << entry_plug->Hmat[2][0] << ";\t"
329 >        *outFile[k] << currentTime << ";\t"
330 >                         << entry_plug->Hmat[0][0] << "\t"
331 >                         << entry_plug->Hmat[1][0] << "\t"
332 >                         << entry_plug->Hmat[2][0] << ";\t"
333  
334 <            << entry_plug->Hmat[0][1] << "\t"
335 <            << entry_plug->Hmat[1][1] << "\t"
336 <            << entry_plug->Hmat[2][1] << ";\t"
334 >                         << entry_plug->Hmat[0][1] << "\t"
335 >                         << entry_plug->Hmat[1][1] << "\t"
336 >                         << entry_plug->Hmat[2][1] << ";\t"
337  
338 <            << entry_plug->Hmat[0][2] << "\t"
339 <            << entry_plug->Hmat[1][2] << "\t"
340 <            << entry_plug->Hmat[2][2] << ";";
338 >                         << entry_plug->Hmat[0][2] << "\t"
339 >                         << entry_plug->Hmat[1][2] << "\t"
340 >                         << entry_plug->Hmat[2][2] << ";";
341 >  
342 >        *outFile[k] << entry_plug->the_integrator->getAdditionalParameters() << endl;
343 >    }
344  
345 <    finalOut << entry_plug->the_integrator->getAdditionalParameters();
640 <    finalOut << endl;
641 <    finalOut.flush();
345 >    currentIndex = 0;
346  
347      for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) {
348        
# Line 663 | Line 367 | void DumpWriter::writeFinal(double finalTime){
367                   myPotato, MPI_COMM_WORLD, &istatus);
368          
369          atomTypeString = MPIatomTypeString;
370 <                
370 >        
371          myPotato++;
372  
373          MPI_Recv(&isDirectional, 1, MPI_INT, which_node,
# Line 684 | Line 388 | void DumpWriter::writeFinal(double finalTime){
388  
389        } else {
390          
391 <        haveError = 0;
391 >        haveError = 0;
392          which_atom = i;
689 –        local_index=-1;
393          
394 <        for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) {
692 <          if (atoms[j]->getGlobalIndex() == which_atom) local_index = j;
693 <        }
694 <        
695 <        if (local_index != -1) {
394 >          local_index = indexArray[currentIndex].first;        
395            
396 <          atomTypeString = atoms[local_index]->getType();
397 <
396 >          if (which_atom == indexArray[currentIndex].second) {
397 >            
398 >            atomTypeString = atoms[local_index]->getType();
399 >            
400            atoms[local_index]->getPos(pos);
401            atoms[local_index]->getVel(vel);          
402 <
402 >          
403            atomData6[0] = pos[0];
404            atomData6[1] = pos[1];
405            atomData6[2] = pos[2];
# Line 731 | Line 432 | void DumpWriter::writeFinal(double finalTime){
432            
433          } else {
434            sprintf(painCave.errMsg,
435 <                  "Atom %d not found on processor %d\n",
436 <                  i, worldRank );
435 >                  "Atom %d not found on processor %d, currentIndex = %d, local_index = %d\n",
436 >                  which_atom, worldRank, currentIndex, local_index );
437            haveError= 1;
438            simError();
439          }
440          
441 <        if(haveError) DieDieDie();
441 >        if(haveError) DieDieDie();
442          
443 +        currentIndex++;
444        }
743 –
744 –
445        // If we've survived to here, format the line:
446        
447        if (!isDirectional) {
448          
449 <        sprintf( tempBuffer,
449 >        sprintf( writeLine,
450                   "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
451                   atomTypeString,
452                   atomData6[0],
# Line 756 | Line 456 | void DumpWriter::writeFinal(double finalTime){
456                   atomData6[4],
457                   atomData6[5]);
458          
759 –        strcpy( writeLine, tempBuffer );
459          strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
460          
461        } else {
462          
463 <        sprintf( tempBuffer,
463 >        sprintf( writeLine,
464                   "%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",
465                   atomTypeString,
466                   atomData13[0],
# Line 777 | Line 476 | void DumpWriter::writeFinal(double finalTime){
476                   atomData13[10],
477                   atomData13[11],
478                   atomData13[12]);
780 –        
781 –        strcpy( writeLine, tempBuffer );
479          
480        }
481 <        
482 <      finalOut << writeLine;
483 <      finalOut.flush();
481 >      
482 >      for(k = 0; k < outFile.size(); k++)
483 >        *outFile[k] << writeLine;
484      }
485 <  
486 <    finalOut.flush();
485 >    
486 >    for(k = 0; k < outFile.size(); k++)
487 >      outFile[k]->flush();
488 >    
489      sprintf( checkPointMsg,
490               "Sucessfully took a dump.\n");
792 –    delete[] potatoes;
491      
492      MPIcheckPoint();        
493      
494 +    delete[] potatoes;
495 +    
496    } else {
497  
498      // worldRank != 0, so I'm a remote node.  
# Line 800 | Line 500 | void DumpWriter::writeFinal(double finalTime){
500      // Set my magic potato to 0:
501  
502      myPotato = 0;
503 +    currentIndex = 0;
504      
505      for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) {
506        
# Line 808 | Line 509 | void DumpWriter::writeFinal(double finalTime){
509        if (AtomToProcMap[i] == worldRank) {
510  
511          if (myPotato + 3 >= MAXTAG) {
512 <
512 >          
513            // The potato was going to exceed the maximum value,
514            // so wrap this processor potato back to 0 (and block until
515            // node 0 says we can go:
516 <
516 >          
517            MPI_Recv(&myPotato, 1, MPI_INT, 0, 0, MPI_COMM_WORLD, &istatus);
518            
519          }
520 <        which_atom = i;  
521 <        local_index=-1;
522 <        for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) {
523 <          if (atoms[j]->getGlobalIndex() == which_atom) local_index = j;
524 <        }
824 <        if (local_index != -1) {
520 >        which_atom = i;
521 >
522 >        local_index = indexArray[currentIndex].first;        
523 >                
524 >        if (which_atom == indexArray[currentIndex].second) {
525          
526            atomTypeString = atoms[local_index]->getType();
527 <
527 >          
528            atoms[local_index]->getPos(pos);
529            atoms[local_index]->getVel(vel);
530 <
530 >          
531            atomData6[0] = pos[0];
532            atomData6[1] = pos[1];
533            atomData6[2] = pos[2];
# Line 852 | Line 552 | void DumpWriter::writeFinal(double finalTime){
552              atomData13[7] = q[1];
553              atomData13[8] = q[2];
554              atomData13[9] = q[3];
555 <
555 >  
556              atomData13[10] = dAtom->getJx();
557              atomData13[11] = dAtom->getJy();
558              atomData13[12] = dAtom->getJz();
# Line 860 | Line 560 | void DumpWriter::writeFinal(double finalTime){
560  
561          } else {
562            sprintf(painCave.errMsg,
563 <                  "Atom %d not found on processor %d\n",
564 <                  i, worldRank );
563 >                  "Atom %d not found on processor %d, currentIndex = %d, local_index = %d\n",
564 >                  which_atom, worldRank, currentIndex, local_index );
565            haveError= 1;
566            simError();
567          }
568 <
568 >        
569          strncpy(MPIatomTypeString, atomTypeString, MINIBUFFERSIZE);
570  
571          // null terminate the string before sending (just in case):
572          MPIatomTypeString[MINIBUFFERSIZE-1] = '\0';
573  
574          MPI_Send(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, 0,
575 <                 myPotato, MPI_COMM_WORLD);
575 >                             myPotato, MPI_COMM_WORLD);
576          
577          myPotato++;
578  
579          MPI_Send(&isDirectional, 1, MPI_INT, 0,
580 <                 myPotato, MPI_COMM_WORLD);
580 >                             myPotato, MPI_COMM_WORLD);
581          
582          myPotato++;
583          
# Line 892 | Line 592 | void DumpWriter::writeFinal(double finalTime){
592                     myPotato, MPI_COMM_WORLD);
593          }
594  
595 <        myPotato++;      
595 >        myPotato++;  
596 >        currentIndex++;    
597        }
598      }
599  
# Line 902 | Line 603 | void DumpWriter::writeFinal(double finalTime){
603      
604    }
605    
905 –  if( worldRank == 0 ) finalOut.close();
606   #endif // is_mpi
607   }
608  
909 –
910 –
609   #ifdef IS_MPI
610  
611   // a couple of functions to let us escape the write loop

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