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root/group/trunk/OOPSE/libmdtools/DumpWriter.cpp
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Comparing trunk/OOPSE/libmdtools/DumpWriter.cpp (file contents):
Revision 907 by gezelter, Thu Jan 8 17:40:56 2004 UTC vs.
Revision 1097 by gezelter, Mon Apr 12 20:32:20 2004 UTC

# Line 1 | Line 1
1 + #define _LARGEFILE_SOURCE64
2   #define _FILE_OFFSET_BITS 64
3  
4   #include <string.h>
5   #include <iostream>
6   #include <fstream>
7 + #include <algorithm>
8 + #include <utility>
9  
10   #ifdef IS_MPI
11   #include <mpi.h>
# Line 26 | Line 29 | DumpWriter::DumpWriter( SimInfo* the_entry_plug ){
29    if(worldRank == 0 ){
30   #endif // is_mpi
31  
32 <    strcpy( outName, entry_plug->sampleName );
32 >    dumpFile.open(entry_plug->sampleName, ios::out | ios::trunc );
33  
34 <    outFile.open(outName, ios::out | ios::trunc );
34 >    if( !dumpFile ){
35  
33 –    if( !outFile ){
34 –
36        sprintf( painCave.errMsg,
37                 "Could not open \"%s\" for dump output.\n",
38 <               outName);
38 >               entry_plug->sampleName);
39        painCave.isFatal = 1;
40        simError();
41      }
42  
42 –    //outFile.setf( ios::scientific );
43 –
43   #ifdef IS_MPI
44    }
45  
46 +  //sort the local atoms by global index
47 +  sortByGlobalIndex();
48 +  
49    sprintf( checkPointMsg,
50             "Sucessfully opened output file for dumping.\n");
51    MPIcheckPoint();
# Line 56 | Line 58 | DumpWriter::~DumpWriter( ){
58    if(worldRank == 0 ){
59   #endif // is_mpi
60  
61 <    outFile.close();
61 >    dumpFile.close();
62  
63   #ifdef IS_MPI
64    }
65   #endif // is_mpi
66   }
67  
68 < void DumpWriter::writeDump( double currentTime ){
68 > #ifdef IS_MPI
69  
70 <  const int BUFFERSIZE = 2000;
71 <  const int MINIBUFFERSIZE = 10;
70 > /**
71 > * A hook function to load balancing
72 > */
73  
74 <  char tempBuffer[BUFFERSIZE];
75 <  char writeLine[BUFFERSIZE];
74 > void DumpWriter::update(){
75 >  sortByGlobalIndex();          
76 > }
77 >  
78 > /**
79 > * Auxiliary sorting function
80 > */
81 >
82 > bool indexSortingCriterion(const pair<int, int>& p1, const pair<int, int>& p2){
83 >  return p1.second < p2.second;
84 > }
85  
86 <  int i;
87 < #ifdef IS_MPI
88 <  int j, which_node, done, which_atom, local_index;
89 <  double atomTransData[6];
90 <  double atomOrientData[7];
79 <  int isDirectional;
80 <  char* atomTypeString;
81 <  int me;
82 <  int atomTypeTag;
83 <  int atomIsDirectionalTag;
84 <  int atomTransDataTag;
85 <  int atomOrientDataTag;
86 < #else //is_mpi
87 <  int nAtoms = entry_plug->n_atoms;
88 < #endif //is_mpi
89 <
90 <  double q[4];
91 <  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"
111 <
112 <          << entry_plug->Hmat[0][2] << "\t"
113 <          << entry_plug->Hmat[1][2] << "\t"
114 <          << entry_plug->Hmat[2][2] << ";";
115 <  //write out additional parameters, such as chi and eta
116 <  outFile << entry_plug->the_integrator->getAdditionalParameters();
117 <  outFile << endl;
118 <
119 <  for( i=0; i<nAtoms; i++ ){
120 <
121 <    atoms[i]->getPos(pos);
122 <    atoms[i]->getVel(vel);
123 <
124 <    sprintf( tempBuffer,
125 <             "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
126 <             atoms[i]->getType(),
127 <             pos[0],
128 <             pos[1],
129 <             pos[2],
130 <             vel[0],
131 <             vel[1],
132 <             vel[2]);
133 <    strcpy( writeLine, tempBuffer );
134 <
135 <    if( atoms[i]->isDirectional() ){
136 <
137 <      dAtom = (DirectionalAtom *)atoms[i];
138 <      dAtom->getQ( q );
139 <
140 <      sprintf( tempBuffer,
141 <               "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
142 <               q[0],
143 <               q[1],
144 <               q[2],
145 <               q[3],
146 <               dAtom->getJx(),
147 <               dAtom->getJy(),
148 <               dAtom->getJz());
149 <      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
152 <      strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
153 <
154 <    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 <  // first thing first, suspend fatalities.
161 <  painCave.isEventLoop = 1;
126 >  writeFrame(fileStreams, currentTime);
127  
128 <  int myStatus; // 1 = wakeup & success; 0 = error; -1 = AllDone
129 <  int haveError;
128 > #ifdef IS_MPI
129 >  finalOut.close();
130 > #endif
131 >        
132 > }
133  
134 <  MPI_Status istatus;
167 <  int *AtomToProcMap = mpiSim->getAtomToProcMap();
134 > void DumpWriter::writeFinal(double currentTime){
135  
169 –  // write out header and node 0's coordinates
170 –
171 –  if( worldRank == 0 ){
172 –    outFile << mpiSim->getTotAtoms() << "\n";
173 –
174 –    outFile << currentTime << ";\t"
175 –            << entry_plug->Hmat[0][0] << "\t"
176 –            << entry_plug->Hmat[1][0] << "\t"
177 –            << entry_plug->Hmat[2][0] << ";\t"
178 –
179 –            << entry_plug->Hmat[0][1] << "\t"
180 –            << entry_plug->Hmat[1][1] << "\t"
181 –            << entry_plug->Hmat[2][1] << ";\t"
182 –
183 –            << entry_plug->Hmat[0][2] << "\t"
184 –            << entry_plug->Hmat[1][2] << "\t"
185 –            << entry_plug->Hmat[2][2] << ";";
186 –
187 –    outFile << entry_plug->the_integrator->getAdditionalParameters();
188 –    outFile << endl;
189 –    outFile.flush();
190 –    for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) {
191 –      // Get the Node number which has this atom;
192 –
193 –      which_node = AtomToProcMap[i];
194 –
195 –      if (which_node != 0) {
196 –        
197 –        atomTypeTag          = 4*i;
198 –        atomIsDirectionalTag = 4*i + 1;
199 –        atomTransDataTag     = 4*i + 2;
200 –        atomOrientDataTag    = 4*i + 3;
201 –
202 –        MPI_Recv(atomTypeString, MINIBUFFERSIZE, MPI_CHAR, which_node,
203 –                 atomTypeTag, MPI_COMM_WORLD, &istatus);
204 –        
205 –        MPI_Recv(&isDirectional, 1, MPI_INT, which_node,
206 –                 atomIsDirectionalTag, MPI_COMM_WORLD, &istatus);
207 –        
208 –        MPI_Recv(atomTransData, 6, MPI_DOUBLE, which_node,
209 –                 atomTransDataTag, MPI_COMM_WORLD, &istatus);
210 –
211 –        if (isDirectional) {
212 –
213 –          MPI_Recv(atomOrientData, 7, MPI_DOUBLE, which_node,
214 –                   atomOrientDataTag, MPI_COMM_WORLD, &istatus);
215 –
216 –        }
217 –
218 –      } else {
219 –        
220 –        haveError = 0;
221 –        which_atom = i;
222 –        local_index=-1;
223 –
224 –        for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) {
225 –          if (atoms[j]->getGlobalIndex() == which_atom) local_index = j;
226 –        }
227 –
228 –        if (local_index != -1) {
229 –
230 –          atomTypeString = atoms[local_index]->getType();
231 –
232 –          atoms[local_index]->getPos(pos);
233 –          atoms[local_index]->getVel(vel);
234 –
235 –          atomTransData[0] = pos[0];
236 –          atomTransData[1] = pos[1];
237 –          atomTransData[2] = pos[2];
238 –
239 –          atomTransData[3] = vel[0];
240 –          atomTransData[4] = vel[1];
241 –          atomTransData[5] = vel[2];
242 –          
243 –          isDirectional = 0;
244 –
245 –          if( atoms[local_index]->isDirectional() ){
246 –
247 –            isDirectional = 1;
248 –            
249 –            dAtom = (DirectionalAtom *)atoms[local_index];
250 –            dAtom->getQ( q );
251 –            
252 –            atomOrientData[0] = q[0];
253 –            atomOrientData[1] = q[1];
254 –            atomOrientData[2] = q[2];
255 –            atomOrientData[3] = q[3];
256 –
257 –            atomOrientData[4] = dAtom->getJx();
258 –            atomOrientData[5] = dAtom->getJy();
259 –            atomOrientData[6] = dAtom->getJz();
260 –          }
261 –
262 –        } else {
263 –          sprintf(painCave.errMsg,
264 –                  "Atom %d not found on processor %d\n",
265 –                  i, worldRank );
266 –          haveError= 1;
267 –          simError();
268 –        }
269 –
270 –        if(haveError) DieDieDie();
271 –                              
272 –        // If we've survived to here, format the line:
273 –        
274 –        sprintf( tempBuffer,
275 –                 "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
276 –                 atomTypeString,
277 –                 atomTransData[0],
278 –                 atomTransData[1],
279 –                 atomTransData[2],
280 –                 atomTransData[3],
281 –                 atomTransData[4],
282 –                 atomTransData[5]);
283 –
284 –        strcpy( writeLine, tempBuffer );
285 –
286 –        if (isDirectional) {
287 –
288 –          sprintf( tempBuffer,
289 –                   "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
290 –                   atomOrientData[0],
291 –                   atomOrientData[1],
292 –                   atomOrientData[2],
293 –                   atomOrientData[3],
294 –                   atomOrientData[4],
295 –                   atomOrientData[5],
296 –                   atomOrientData[6]);
297 –          strcat( writeLine, tempBuffer );
298 –
299 –        } else {
300 –          strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
301 –        }
302 –
303 –        outFile << writeLine;
304 –        outFile.flush();
305 –      }
306 –    }
307 –
308 –    outFile.flush();
309 –    sprintf( checkPointMsg,
310 –             "Sucessfully took a dump.\n");
311 –    MPIcheckPoint();        
312 –    
313 –  } else {
314 –
315 –    // worldRank != 0, so I'm a remote node.  
316 –    
317 –    for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) {
318 –      
319 –      // Am I the node which has this atom?
320 –      
321 –      if (AtomToProcMap[i] == worldRank) {
322 –
323 –        local_index=-1;
324 –        for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) {
325 –          if (atoms[j]->getGlobalIndex() == which_atom) local_index = j;
326 –        }
327 –        if (local_index != -1) {
328 –        
329 –          atomTypeString = atoms[local_index]->getType();
330 –
331 –          atoms[local_index]->getPos(pos);
332 –          atoms[local_index]->getVel(vel);
333 –
334 –          atomTransData[0] = pos[0];
335 –          atomTransData[1] = pos[1];
336 –          atomTransData[2] = pos[2];
337 –
338 –          atomTransData[3] = vel[0];
339 –          atomTransData[4] = vel[1];
340 –          atomTransData[5] = vel[2];
341 –          
342 –          isDirectional = 0;
343 –
344 –          if( atoms[local_index]->isDirectional() ){
345 –
346 –            isDirectional = 1;
347 –            
348 –            dAtom = (DirectionalAtom *)atoms[local_index];
349 –            dAtom->getQ( q );
350 –            
351 –            atomOrientData[0] = q[0];
352 –            atomOrientData[1] = q[1];
353 –            atomOrientData[2] = q[2];
354 –            atomOrientData[3] = q[3];
355 –
356 –            atomOrientData[4] = dAtom->getJx();
357 –            atomOrientData[5] = dAtom->getJy();
358 –            atomOrientData[6] = dAtom->getJz();
359 –          }
360 –
361 –        } else {
362 –          sprintf(painCave.errMsg,
363 –                  "Atom %d not found on processor %d\n",
364 –                  i, worldRank );
365 –          haveError= 1;
366 –          simError();
367 –        }
368 –
369 –        // I've survived this far, so send off the data!
370 –
371 –        atomTypeTag          = 4*i;
372 –        atomIsDirectionalTag = 4*i + 1;
373 –        atomTransDataTag     = 4*i + 2;
374 –        atomOrientDataTag    = 4*i + 3;
375 –
376 –        MPI_Send(atomTypeString, MINIBUFFERSIZE, MPI_CHAR, 0,
377 –                 atomTypeTag, MPI_COMM_WORLD);
378 –        
379 –        MPI_Send(&isDirectional, 1, MPI_INT, 0,
380 –                 atomIsDirectionalTag, MPI_COMM_WORLD);
381 –        
382 –        MPI_Send(atomTransData, 6, MPI_DOUBLE, 0,
383 –                 atomTransDataTag, MPI_COMM_WORLD);
384 –
385 –        if (isDirectional) {
386 –
387 –          MPI_Send(atomOrientData, 7, MPI_DOUBLE, 0,
388 –                   atomOrientDataTag, MPI_COMM_WORLD);
389 –          
390 –        }
391 –      
392 –      }
393 –    }
394 –
395 –    sprintf( checkPointMsg,
396 –             "Sucessfully took a dump.\n");
397 –    MPIcheckPoint();        
398 –    
399 –  }
400 –  
401 –  painCave.isEventLoop = 0;
402 –
403 – #endif // is_mpi
404 – }
405 –
406 – void DumpWriter::writeFinal(double finalTime){
407 –
408 –  char finalName[500];
136    ofstream finalOut;
137 +  vector<ofstream*> fileStreams;
138  
411 –  const int BUFFERSIZE = 2000;
412 –  const int MINIBUFFERSIZE = 10;
413 –  char tempBuffer[BUFFERSIZE];
414 –  char writeLine[BUFFERSIZE];
415 –
416 –  double q[4];
417 –  DirectionalAtom* dAtom;
418 –  Atom** atoms = entry_plug->atoms;
419 –  int i;
139   #ifdef IS_MPI
421 –  int j, which_node, done, which_atom, local_index;
422 –  double atomTransData[6];
423 –  double atomOrientData[7];
424 –  int isDirectional;
425 –  char* atomTypeString;
426 –  int atomTypeTag;
427 –  int atomIsDirectionalTag;
428 –  int atomTransDataTag;
429 –  int atomOrientDataTag;
430 – #else //is_mpi
431 –  int nAtoms = entry_plug->n_atoms;
432 – #endif //is_mpi
433 –
434 –  double pos[3], vel[3];
435 –
436 – #ifdef IS_MPI
140    if(worldRank == 0 ){
141   #endif // is_mpi
142  
143 <    strcpy( finalName, entry_plug->finalName );
143 >    finalOut.open( entry_plug->finalName, ios::out | ios::trunc );
144  
442 –    finalOut.open( finalName, ios::out | ios::trunc );
145      if( !finalOut ){
146        sprintf( painCave.errMsg,
147                 "Could not open \"%s\" for final dump output.\n",
148 <               finalName );
148 >               entry_plug->finalName );
149        painCave.isFatal = 1;
150        simError();
151      }
152  
451 –    // finalOut.setf( ios::scientific );
452 –
153   #ifdef IS_MPI
154    }
155 + #endif // is_mpi
156 +  
157 +  fileStreams.push_back(&finalOut);  
158 +  writeFrame(fileStreams, currentTime);
159  
160 <  sprintf(checkPointMsg,"Opened file for final configuration\n");
161 <  MPIcheckPoint();
160 > #ifdef IS_MPI
161 >  finalOut.close();
162 > #endif
163 >  
164 > }
165  
166 < #endif //is_mpi
166 > void DumpWriter::writeFrame( vector<ofstream*>& outFile, double currentTime ){
167  
168 +  const int BUFFERSIZE = 2000;
169 +  const int MINIBUFFERSIZE = 100;
170  
171 < #ifndef IS_MPI
171 >  char tempBuffer[BUFFERSIZE];  
172 >  char writeLine[BUFFERSIZE];
173  
174 <  finalOut << nAtoms << "\n";
174 >  int i, k;
175  
176 <  finalOut << finalTime << ";\t"
177 <           << entry_plug->Hmat[0][0] << "\t"
178 <           << entry_plug->Hmat[1][0] << "\t"
179 <           << entry_plug->Hmat[2][0] << ";\t"
180 <
181 <           << entry_plug->Hmat[0][1] << "\t"
182 <           << entry_plug->Hmat[1][1] << "\t"
183 <           << entry_plug->Hmat[2][1] << ";\t"
184 <
185 <           << entry_plug->Hmat[0][2] << "\t"
186 <           << entry_plug->Hmat[1][2] << "\t"
187 <           << entry_plug->Hmat[2][2] << ";";
188 <
189 <  //write out additional parameters, such as chi and eta
190 <  finalOut << entry_plug->the_integrator->getAdditionalParameters();
191 <  finalOut << endl;
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, currentIndex;
220 +  double atomData6[6];
221 +  double atomData13[13];
222 +  int isDirectional;
223 +  char* atomTypeString;
224 +  char MPIatomTypeString[MINIBUFFERSIZE];
225 +
226 + #else //is_mpi
227 +  int nAtoms = entry_plug->n_atoms;
228 + #endif //is_mpi
229 +
230 +  double q[4], ji[3];
231 +  DirectionalAtom* dAtom;
232 +  Atom** atoms = entry_plug->atoms;
233 +  double pos[3], vel[3];
234 +
235 + #ifndef IS_MPI
236 +  
237 +  for(k = 0; k < outFile.size(); k++){
238 +    *outFile[k] << nAtoms << "\n";
239 +
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 +                     << entry_plug->Hmat[0][2] << "\t"
250 +                     << entry_plug->Hmat[1][2] << "\t"
251 +                     << entry_plug->Hmat[2][2] << ";";
252 +
253 +    //write out additional parameters, such as chi and eta
254 +    *outFile[k] << entry_plug->the_integrator->getAdditionalParameters() << endl;
255 +  }
256 +  
257    for( i=0; i<nAtoms; i++ ){
258  
259      atoms[i]->getPos(pos);
# Line 500 | Line 274 | void DumpWriter::writeFinal(double finalTime){
274  
275        dAtom = (DirectionalAtom *)atoms[i];
276        dAtom->getQ( q );
277 +      dAtom->getJ( ji );
278  
279        sprintf( tempBuffer,
280                 "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
# Line 507 | Line 282 | void DumpWriter::writeFinal(double finalTime){
282                 q[1],
283                 q[2],
284                 q[3],
285 <               dAtom->getJx(),
286 <               dAtom->getJy(),
287 <               dAtom->getJz());
285 >               ji[0],
286 >               ji[1],
287 >               ji[2]);
288        strcat( writeLine, tempBuffer );
289      }
290      else
291        strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
292  
293 <    finalOut << writeLine;
293 >    for(k = 0; k < outFile.size(); k++)
294 >      *outFile[k] << writeLine;
295    }
520 –  finalOut.flush();
521 –  finalOut.close();
296  
297   #else // is_mpi
298  
299 <  // first thing first, suspend fatalities.
300 <  painCave.isEventLoop = 1;
299 >  /* code to find maximum tag value */
300 >  
301 >  int *tagub, flag, MAXTAG;
302 >  MPI_Attr_get(MPI_COMM_WORLD, MPI_TAG_UB, &tagub, &flag);
303 >  if (flag) {
304 >    MAXTAG = *tagub;
305 >  } else {
306 >    MAXTAG = 32767;
307 >  }  
308  
528 –  int myStatus; // 1 = wakeup & success; 0 = error; -1 = AllDone
309    int haveError;
310  
311    MPI_Status istatus;
# Line 534 | Line 314 | void DumpWriter::writeFinal(double finalTime){
314    // write out header and node 0's coordinates
315  
316    if( worldRank == 0 ){
537 –    finalOut << mpiSim->getTotAtoms() << "\n";
317  
318 <    finalOut << finalTime << ";\t"
540 <            << entry_plug->Hmat[0][0] << "\t"
541 <            << entry_plug->Hmat[1][0] << "\t"
542 <            << entry_plug->Hmat[2][0] << ";\t"
318 >    // Node 0 needs a list of the magic potatoes for each processor;
319  
320 <            << entry_plug->Hmat[0][1] << "\t"
321 <            << entry_plug->Hmat[1][1] << "\t"
546 <            << entry_plug->Hmat[2][1] << ";\t"
320 >    nProc = mpiSim->getNumberProcessors();
321 >    potatoes = new int[nProc];
322  
323 <            << entry_plug->Hmat[0][2] << "\t"
324 <            << entry_plug->Hmat[1][2] << "\t"
325 <            << entry_plug->Hmat[2][2] << ";";
323 >    //write out the comment lines
324 >    for (i = 0; i < nProc; i++)
325 >      potatoes[i] = 0;
326 >    
327 >      for(k = 0; k < outFile.size(); k++){
328 >        *outFile[k] << mpiSim->getTotAtoms() << "\n";
329  
330 <    finalOut << entry_plug->the_integrator->getAdditionalParameters();
331 <    finalOut << endl;
332 <    finalOut.flush();
330 >        *outFile[k] << currentTime << ";\t"
331 >                         << entry_plug->Hmat[0][0] << "\t"
332 >                         << entry_plug->Hmat[1][0] << "\t"
333 >                         << entry_plug->Hmat[2][0] << ";\t"
334 >
335 >                         << entry_plug->Hmat[0][1] << "\t"
336 >                         << entry_plug->Hmat[1][1] << "\t"
337 >                         << entry_plug->Hmat[2][1] << ";\t"
338 >
339 >                         << entry_plug->Hmat[0][2] << "\t"
340 >                         << entry_plug->Hmat[1][2] << "\t"
341 >                         << entry_plug->Hmat[2][2] << ";";
342 >  
343 >        *outFile[k] << entry_plug->the_integrator->getAdditionalParameters() << endl;
344 >    }
345 >
346 >    currentIndex = 0;
347 >
348      for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) {
349 +      
350        // Get the Node number which has this atom;
351 <
351 >      
352        which_node = AtomToProcMap[i];
353 <
353 >      
354        if (which_node != 0) {
561 –        
562 –        atomTypeTag          = 4*i;
563 –        atomIsDirectionalTag = 4*i + 1;
564 –        atomTransDataTag     = 4*i + 2;
565 –        atomOrientDataTag    = 4*i + 3;
355  
356 <        MPI_Recv(atomTypeString, MINIBUFFERSIZE, MPI_CHAR, which_node,
357 <                 atomTypeTag, MPI_COMM_WORLD, &istatus);
356 >        if (potatoes[which_node] + 3 >= MAXTAG) {
357 >          // The potato was going to exceed the maximum value,
358 >          // so wrap this processor potato back to 0:        
359 >
360 >          potatoes[which_node] = 0;          
361 >          MPI_Send(0, 1, MPI_INT, which_node, 0, MPI_COMM_WORLD);
362 >          
363 >        }
364 >
365 >        myPotato = potatoes[which_node];        
366          
367 <        MPI_Recv(&isDirectional, 1, MPI_INT, which_node,
368 <                 atomIsDirectionalTag, MPI_COMM_WORLD, &istatus);
367 >        MPI_Recv(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, which_node,
368 >                 myPotato, MPI_COMM_WORLD, &istatus);
369          
370 <        MPI_Recv(atomTransData, 6, MPI_DOUBLE, which_node,
371 <                 atomTransDataTag, MPI_COMM_WORLD, &istatus);
370 >        atomTypeString = MPIatomTypeString;
371 >        
372 >        myPotato++;
373  
374 <        if (isDirectional) {
374 >        MPI_Recv(&isDirectional, 1, MPI_INT, which_node,
375 >                 myPotato, MPI_COMM_WORLD, &istatus);
376 >              
377 >        myPotato++;
378  
379 <          MPI_Recv(atomOrientData, 7, MPI_DOUBLE, which_node,
380 <                   atomOrientDataTag, MPI_COMM_WORLD, &istatus);
381 <
379 >        if (isDirectional) {          
380 >          MPI_Recv(atomData13, 13, MPI_DOUBLE, which_node,
381 >                   myPotato, MPI_COMM_WORLD, &istatus);
382 >        } else {
383 >          MPI_Recv(atomData6, 6, MPI_DOUBLE, which_node,
384 >                   myPotato, MPI_COMM_WORLD, &istatus);          
385          }
386 +        
387 +        myPotato++;
388 +        potatoes[which_node] = myPotato;
389  
390        } else {
391          
392 <        haveError = 0;
392 >        haveError = 0;
393          which_atom = i;
394 <        local_index=-1;
395 <
396 <        for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) {
397 <          if (atoms[j]->getGlobalIndex() == which_atom) local_index = j;
398 <        }
399 <
400 <        if (local_index != -1) {
594 <
595 <          atomTypeString = atoms[local_index]->getType();
596 <
394 >        
395 >          local_index = indexArray[currentIndex].first;        
396 >          
397 >          if (which_atom == indexArray[currentIndex].second) {
398 >            
399 >            atomTypeString = atoms[local_index]->getType();
400 >            
401            atoms[local_index]->getPos(pos);
402 <          atoms[local_index]->getVel(vel);
402 >          atoms[local_index]->getVel(vel);          
403 >          
404 >          atomData6[0] = pos[0];
405 >          atomData6[1] = pos[1];
406 >          atomData6[2] = pos[2];
407  
408 <          atomTransData[0] = pos[0];
409 <          atomTransData[1] = pos[1];
410 <          atomTransData[2] = pos[2];
603 <
604 <          atomTransData[3] = vel[0];
605 <          atomTransData[4] = vel[1];
606 <          atomTransData[5] = vel[2];
408 >          atomData6[3] = vel[0];
409 >          atomData6[4] = vel[1];
410 >          atomData6[5] = vel[2];
411            
412            isDirectional = 0;
413  
# Line 613 | Line 417 | void DumpWriter::writeFinal(double finalTime){
417              
418              dAtom = (DirectionalAtom *)atoms[local_index];
419              dAtom->getQ( q );
420 +            dAtom->getJ( ji );
421 +
422 +            for (int j = 0; j < 6 ; j++)
423 +              atomData13[j] = atomData6[j];            
424              
425 <            atomOrientData[0] = q[0];
426 <            atomOrientData[1] = q[1];
427 <            atomOrientData[2] = q[2];
428 <            atomOrientData[3] = q[3];
429 <
430 <            atomOrientData[4] = dAtom->getJx();
431 <            atomOrientData[5] = dAtom->getJy();
432 <            atomOrientData[6] = dAtom->getJz();
425 >            atomData13[6] = q[0];
426 >            atomData13[7] = q[1];
427 >            atomData13[8] = q[2];
428 >            atomData13[9] = q[3];
429 >            
430 >            atomData13[10] = ji[0];
431 >            atomData13[11] = ji[1];
432 >            atomData13[12] = ji[2];
433            }
434 <
434 >          
435          } else {
436            sprintf(painCave.errMsg,
437 <                  "Atom %d not found on processor %d\n",
438 <                  i, worldRank );
437 >                  "Atom %d not found on processor %d, currentIndex = %d, local_index = %d\n",
438 >                  which_atom, worldRank, currentIndex, local_index );
439            haveError= 1;
440            simError();
441          }
634 –
635 –        if(haveError) DieDieDie();
636 –                              
637 –        // If we've survived to here, format the line:
442          
443 <        sprintf( tempBuffer,
444 <                 "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
445 <                 atomTypeString,
642 <                 atomTransData[0],
643 <                 atomTransData[1],
644 <                 atomTransData[2],
645 <                 atomTransData[3],
646 <                 atomTransData[4],
647 <                 atomTransData[5]);
648 <
649 <        strcpy( writeLine, tempBuffer );
650 <
651 <        if (isDirectional) {
652 <
653 <          sprintf( tempBuffer,
654 <                   "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
655 <                   atomOrientData[0],
656 <                   atomOrientData[1],
657 <                   atomOrientData[2],
658 <                   atomOrientData[3],
659 <                   atomOrientData[4],
660 <                   atomOrientData[5],
661 <                   atomOrientData[6]);
662 <          strcat( writeLine, tempBuffer );
663 <
664 <        } else {
665 <          strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
666 <        }
667 <
668 <        finalOut << writeLine;
669 <        finalOut.flush();
443 >        if(haveError) DieDieDie();
444 >        
445 >        currentIndex++;
446        }
447 +      // If we've survived to here, format the line:
448 +      
449 +      if (!isDirectional) {
450 +        
451 +        sprintf( writeLine,
452 +                 "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
453 +                 atomTypeString,
454 +                 atomData6[0],
455 +                 atomData6[1],
456 +                 atomData6[2],
457 +                 atomData6[3],
458 +                 atomData6[4],
459 +                 atomData6[5]);
460 +        
461 +        strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
462 +        
463 +      } else {
464 +        
465 +        sprintf( writeLine,
466 +                 "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
467 +                 atomTypeString,
468 +                 atomData13[0],
469 +                 atomData13[1],
470 +                 atomData13[2],
471 +                 atomData13[3],
472 +                 atomData13[4],
473 +                 atomData13[5],
474 +                 atomData13[6],
475 +                 atomData13[7],
476 +                 atomData13[8],
477 +                 atomData13[9],
478 +                 atomData13[10],
479 +                 atomData13[11],
480 +                 atomData13[12]);
481 +        
482 +      }
483 +      
484 +      for(k = 0; k < outFile.size(); k++)
485 +        *outFile[k] << writeLine;
486      }
487 <
488 <    finalOut.flush();
487 >    
488 >    for(k = 0; k < outFile.size(); k++)
489 >      outFile[k]->flush();
490 >    
491      sprintf( checkPointMsg,
492               "Sucessfully took a dump.\n");
493 +    
494      MPIcheckPoint();        
495      
496 +    delete[] potatoes;
497 +    
498    } else {
499  
500      // worldRank != 0, so I'm a remote node.  
501 +
502 +    // Set my magic potato to 0:
503 +
504 +    myPotato = 0;
505 +    currentIndex = 0;
506      
507      for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) {
508        
# Line 685 | Line 510 | void DumpWriter::writeFinal(double finalTime){
510        
511        if (AtomToProcMap[i] == worldRank) {
512  
513 <        local_index=-1;
514 <        for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) {
515 <          if (atoms[j]->getGlobalIndex() == which_atom) local_index = j;
513 >        if (myPotato + 3 >= MAXTAG) {
514 >          
515 >          // The potato was going to exceed the maximum value,
516 >          // so wrap this processor potato back to 0 (and block until
517 >          // node 0 says we can go:
518 >          
519 >          MPI_Recv(&myPotato, 1, MPI_INT, 0, 0, MPI_COMM_WORLD, &istatus);
520 >          
521          }
522 <        if (local_index != -1) {
522 >        which_atom = i;
523 >
524 >        local_index = indexArray[currentIndex].first;        
525 >                
526 >        if (which_atom == indexArray[currentIndex].second) {
527          
528            atomTypeString = atoms[local_index]->getType();
529 <
529 >          
530            atoms[local_index]->getPos(pos);
531            atoms[local_index]->getVel(vel);
532 +          
533 +          atomData6[0] = pos[0];
534 +          atomData6[1] = pos[1];
535 +          atomData6[2] = pos[2];
536  
537 <          atomTransData[0] = pos[0];
538 <          atomTransData[1] = pos[1];
539 <          atomTransData[2] = pos[2];
702 <
703 <          atomTransData[3] = vel[0];
704 <          atomTransData[4] = vel[1];
705 <          atomTransData[5] = vel[2];
537 >          atomData6[3] = vel[0];
538 >          atomData6[4] = vel[1];
539 >          atomData6[5] = vel[2];
540            
541            isDirectional = 0;
542  
# Line 712 | Line 546 | void DumpWriter::writeFinal(double finalTime){
546              
547              dAtom = (DirectionalAtom *)atoms[local_index];
548              dAtom->getQ( q );
549 +            dAtom->getJ( ji );
550              
551 <            atomOrientData[0] = q[0];
552 <            atomOrientData[1] = q[1];
553 <            atomOrientData[2] = q[2];
554 <            atomOrientData[3] = q[3];
555 <
556 <            atomOrientData[4] = dAtom->getJx();
557 <            atomOrientData[5] = dAtom->getJy();
558 <            atomOrientData[6] = dAtom->getJz();
551 >            for (int j = 0; j < 6 ; j++)
552 >              atomData13[j] = atomData6[j];
553 >            
554 >            atomData13[6] = q[0];
555 >            atomData13[7] = q[1];
556 >            atomData13[8] = q[2];
557 >            atomData13[9] = q[3];
558 >  
559 >            atomData13[10] = ji[0];
560 >            atomData13[11] = ji[1];
561 >            atomData13[12] = ji[2];
562            }
563  
564          } else {
565            sprintf(painCave.errMsg,
566 <                  "Atom %d not found on processor %d\n",
567 <                  i, worldRank );
566 >                  "Atom %d not found on processor %d, currentIndex = %d, local_index = %d\n",
567 >                  which_atom, worldRank, currentIndex, local_index );
568            haveError= 1;
569            simError();
570          }
571 +        
572 +        strncpy(MPIatomTypeString, atomTypeString, MINIBUFFERSIZE);
573  
574 <        // I've survived this far, so send off the data!
574 >        // null terminate the string before sending (just in case):
575 >        MPIatomTypeString[MINIBUFFERSIZE-1] = '\0';
576  
577 <        atomTypeTag          = 4*i;
578 <        atomIsDirectionalTag = 4*i + 1;
738 <        atomTransDataTag     = 4*i + 2;
739 <        atomOrientDataTag    = 4*i + 3;
740 <
741 <        MPI_Send(atomTypeString, MINIBUFFERSIZE, MPI_CHAR, 0,
742 <                 atomTypeTag, MPI_COMM_WORLD);
577 >        MPI_Send(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, 0,
578 >                             myPotato, MPI_COMM_WORLD);
579          
580 +        myPotato++;
581 +
582          MPI_Send(&isDirectional, 1, MPI_INT, 0,
583 <                 atomIsDirectionalTag, MPI_COMM_WORLD);
583 >                             myPotato, MPI_COMM_WORLD);
584          
585 <        MPI_Send(atomTransData, 6, MPI_DOUBLE, 0,
586 <                 atomTransDataTag, MPI_COMM_WORLD);
749 <
585 >        myPotato++;
586 >        
587          if (isDirectional) {
588  
589 <          MPI_Send(atomOrientData, 7, MPI_DOUBLE, 0,
590 <                   atomOrientDataTag, MPI_COMM_WORLD);
589 >          MPI_Send(atomData13, 13, MPI_DOUBLE, 0,
590 >                   myPotato, MPI_COMM_WORLD);
591            
592 +        } else {
593 +
594 +          MPI_Send(atomData6, 6, MPI_DOUBLE, 0,
595 +                   myPotato, MPI_COMM_WORLD);
596          }
597 <      
597 >
598 >        myPotato++;  
599 >        currentIndex++;    
600        }
601      }
602  
603      sprintf( checkPointMsg,
604 <             "Sucessfully wrote final file.\n");
604 >             "Sucessfully took a dump.\n");
605      MPIcheckPoint();        
606      
607 <  }
607 >  }
608    
766 –  painCave.isEventLoop = 0;
767 –
768 –  if( worldRank == 0 ) finalOut.close();
609   #endif // is_mpi
610   }
611  
772 –
773 –
612   #ifdef IS_MPI
613  
614   // a couple of functions to let us escape the write loop

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