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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 936 by tim, Tue Jan 13 20:35:25 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  
29 –    strcpy( outName, entry_plug->sampleName );
31  
32 <    outFile.open(outName, ios::out | ios::trunc );
32 >    dumpFile.open(entry_plug->sampleName, ios::out | ios::trunc );
33  
34 <    if( !outFile ){
34 >    if( !dumpFile ){
35  
36        sprintf( painCave.errMsg,
37                 "Could not open \"%s\" for dump output.\n",
38 <               outName);
38 >               entry_plug->sampleName);
39        painCave.isFatal = 1;
40        simError();
41      }
42  
42 –    //outFile.setf( ios::scientific );
43 –
43   #ifdef IS_MPI
44    }
45  
46 +  //sort the local atoms by global index
47 +  sortByGlobalIndex();
48 +  
49    sprintf( checkPointMsg,
50             "Sucessfully opened output file for dumping.\n");
51    MPIcheckPoint();
# Line 56 | Line 58 | DumpWriter::~DumpWriter( ){
58    if(worldRank == 0 ){
59   #endif // is_mpi
60  
61 <    outFile.close();
61 >    dumpFile.close();
62  
63   #ifdef IS_MPI
64    }
65   #endif // is_mpi
66   }
67  
68 < void DumpWriter::writeDump( double currentTime ){
68 > #ifdef IS_MPI
69  
70 + /**
71 + * A hook function to load balancing
72 + */
73 +
74 + void DumpWriter::update(){
75 +  sortByGlobalIndex();          
76 + }
77 +  
78 + /**
79 + * Auxiliary sorting function
80 + */
81 +
82 + bool indexSortingCriterion(const pair<int, int>& p1, const pair<int, int>& p2){
83 +  return p1.second < p2.second;
84 + }
85 +
86 + /**
87 + * Sorting the local index by global index
88 + */
89 +
90 + void DumpWriter::sortByGlobalIndex(){
91 +  Atom** atoms = entry_plug->atoms;
92 +  
93 +  indexArray.clear();
94 +  
95 +  for(int i = 0; i < mpiSim->getMyNlocal();i++)
96 +    indexArray.push_back(make_pair(i, atoms[i]->getGlobalIndex()));
97 +  
98 +  sort(indexArray.begin(), indexArray.end(), indexSortingCriterion);    
99 + }
100 + #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 +    
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 +  }
119 + #endif // is_mpi
120 +
121 +  fileStreams.push_back(&finalOut);
122 +  fileStreams.push_back(&dumpFile);
123 +
124 +  writeFrame(fileStreams, currentTime);
125 +
126 + #ifdef IS_MPI
127 +  finalOut.close();
128 + #endif
129 +        
130 + }
131 +
132 + void DumpWriter::writeFinal(double currentTime){
133 +
134 +  ofstream finalOut;
135 +  vector<ofstream*> fileStreams;
136 +
137 + #ifdef IS_MPI
138 +  if(worldRank == 0 ){
139 +
140 +    finalOut.open( entry_plug->finalName, ios::out | ios::trunc );
141 +
142 +    if( !finalOut ){
143 +      sprintf( painCave.errMsg,
144 +               "Could not open \"%s\" for final dump output.\n",
145 +               entry_plug->finalName );
146 +      painCave.isFatal = 1;
147 +      simError();
148 +    }
149 +
150 +  }
151 + #endif // is_mpi
152 +  
153 +  fileStreams.push_back(&finalOut);  
154 +  writeFrame(fileStreams, currentTime);
155 +
156 + #ifdef IS_MPI
157 +  finalOut.close();
158 + #endif
159 +  
160 + }
161 +
162 + void DumpWriter::writeFrame( vector<ofstream*>& outFile, double currentTime ){
163 +
164    const int BUFFERSIZE = 2000;
165    const int MINIBUFFERSIZE = 100;
166  
167 <  char tempBuffer[BUFFERSIZE];
167 >  char tempBuffer[BUFFERSIZE];  
168    char writeLine[BUFFERSIZE];
169  
170 <  int i;
170 >  int i, k;
171 >
172   #ifdef IS_MPI
173 <  int j, which_node, done, which_atom, local_index;
174 <  double atomTransData[6];
175 <  double atomOrientData[7];
173 >  
174 >  int *potatoes;
175 >  int myPotato;
176 >
177 >  int nProc;
178 >  int j, which_node, done, which_atom, local_index, currentIndex;
179 >  double atomData6[6];
180 >  double atomData13[13];
181    int isDirectional;
182    char* atomTypeString;
183    char MPIatomTypeString[MINIBUFFERSIZE];
184 <  int me;
83 <  int atomTypeTag;
84 <  int atomIsDirectionalTag;
85 <  int atomTransDataTag;
86 <  int atomOrientDataTag;
184 >
185   #else //is_mpi
186    int nAtoms = entry_plug->n_atoms;
187   #endif //is_mpi
# Line 93 | Line 191 | void DumpWriter::writeDump( double currentTime ){
191    Atom** atoms = entry_plug->atoms;
192    double pos[3], vel[3];
193  
96 –  // write current frame to the eor file
97 –
98 –  this->writeFinal( currentTime );
99 –
194   #ifndef IS_MPI
195 +  
196 +  for(k = 0; k < outFile.size(); k++){
197 +    *outFile[k] << nAtoms << "\n";
198  
199 <  outFile << nAtoms << "\n";
199 >    *outFile[k] << currentTime << ";\t"
200 >               << entry_plug->Hmat[0][0] << "\t"
201 >                     << entry_plug->Hmat[1][0] << "\t"
202 >                     << entry_plug->Hmat[2][0] << ";\t"
203 >              
204 >               << entry_plug->Hmat[0][1] << "\t"
205 >                     << entry_plug->Hmat[1][1] << "\t"
206 >                     << entry_plug->Hmat[2][1] << ";\t"
207  
208 <  outFile << currentTime << ";\t"
209 <          << entry_plug->Hmat[0][0] << "\t"
210 <          << entry_plug->Hmat[1][0] << "\t"
107 <          << entry_plug->Hmat[2][0] << ";\t"
208 >                     << entry_plug->Hmat[0][2] << "\t"
209 >                     << entry_plug->Hmat[1][2] << "\t"
210 >                     << entry_plug->Hmat[2][2] << ";";
211  
212 <          << entry_plug->Hmat[0][1] << "\t"
213 <          << entry_plug->Hmat[1][1] << "\t"
214 <          << entry_plug->Hmat[2][1] << ";\t"
215 <
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 <
212 >    //write out additional parameters, such as chi and eta
213 >    *outFile[k] << entry_plug->the_integrator->getAdditionalParameters() << endl;
214 >  }
215 >  
216    for( i=0; i<nAtoms; i++ ){
217  
218      atoms[i]->getPos(pos);
# Line 152 | Line 248 | void DumpWriter::writeDump( double currentTime ){
248      else
249        strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
250  
251 <    outFile << writeLine;
251 >    for(k = 0; k < outFile.size(); k++)
252 >      *outFile[k] << writeLine;
253    }
157 –  outFile.flush();
254  
255   #else // is_mpi
256  
257    /* code to find maximum tag value */
258 +  
259    int *tagub, flag, MAXTAG;
260    MPI_Attr_get(MPI_COMM_WORLD, MPI_TAG_UB, &tagub, &flag);
261    if (flag) {
262      MAXTAG = *tagub;
263    } else {
264      MAXTAG = 32767;
265 <  }
265 >  }  
266  
267    int haveError;
268  
# Line 175 | Line 272 | void DumpWriter::writeDump( double currentTime ){
272    // write out header and node 0's coordinates
273  
274    if( worldRank == 0 ){
178 –    outFile << mpiSim->getTotAtoms() << "\n";
275  
276 <    outFile << currentTime << ";\t"
181 <            << entry_plug->Hmat[0][0] << "\t"
182 <            << entry_plug->Hmat[1][0] << "\t"
183 <            << entry_plug->Hmat[2][0] << ";\t"
276 >    // Node 0 needs a list of the magic potatoes for each processor;
277  
278 <            << entry_plug->Hmat[0][1] << "\t"
279 <            << entry_plug->Hmat[1][1] << "\t"
187 <            << entry_plug->Hmat[2][1] << ";\t"
278 >    nProc = mpiSim->getNumberProcessors();
279 >    potatoes = new int[nProc];
280  
281 <            << entry_plug->Hmat[0][2] << "\t"
282 <            << entry_plug->Hmat[1][2] << "\t"
283 <            << entry_plug->Hmat[2][2] << ";";
281 >    //write out the comment lines
282 >    for (i = 0; i < nProc; i++)
283 >      potatoes[i] = 0;
284 >    
285 >      for(k = 0; k < outFile.size(); k++){
286 >        *outFile[k] << mpiSim->getTotAtoms() << "\n";
287  
288 <    outFile << entry_plug->the_integrator->getAdditionalParameters();
289 <    outFile << endl;
290 <    outFile.flush();
288 >        *outFile[k] << currentTime << ";\t"
289 >                         << entry_plug->Hmat[0][0] << "\t"
290 >                         << entry_plug->Hmat[1][0] << "\t"
291 >                         << entry_plug->Hmat[2][0] << ";\t"
292  
293 <    tag = 0;
293 >                         << entry_plug->Hmat[0][1] << "\t"
294 >                         << entry_plug->Hmat[1][1] << "\t"
295 >                         << entry_plug->Hmat[2][1] << ";\t"
296  
297 <    for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) {
297 >                         << entry_plug->Hmat[0][2] << "\t"
298 >                         << entry_plug->Hmat[1][2] << "\t"
299 >                         << entry_plug->Hmat[2][2] << ";";
300 >  
301 >        *outFile[k] << entry_plug->the_integrator->getAdditionalParameters() << endl;
302 >    }
303  
304 <      if (tag + 2 >= MAXTAG) {
305 <        // The tag was going to exceed the maximum value, so wrap around to 0:
306 <        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 <      }
304 >    currentIndex = 0;
305 >
306 >    for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) {
307        
308        // Get the Node number which has this atom;
309        
310        which_node = AtomToProcMap[i];
311        
312        if (which_node != 0) {
213 –        
214 –        MPI_Recv(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, which_node,
215 –                 atomTypeTag, MPI_COMM_WORLD, &istatus);
216 –        
217 –        strncpy(atomTypeString, MPIatomTypeString, MINIBUFFERSIZE);
218 –        
219 –        // Null terminate the atomTypeString just in case:
313  
314 <        atomTypeString[strlen(atomTypeString) - 1] = '\0';
315 <
316 <        MPI_Recv(&isDirectional, 1, MPI_INT, which_node,
224 <                 atomIsDirectionalTag, MPI_COMM_WORLD, &istatus);
225 <        
226 <        MPI_Recv(atomTransData, 6, MPI_DOUBLE, which_node,
227 <                 atomTransDataTag, MPI_COMM_WORLD, &istatus);
314 >        if (potatoes[which_node] + 3 >= MAXTAG) {
315 >          // The potato was going to exceed the maximum value,
316 >          // so wrap this processor potato back to 0:        
317  
318 <        if (isDirectional) {
319 <
320 <          MPI_Recv(atomOrientData, 7, MPI_DOUBLE, which_node,
232 <                   atomOrientDataTag, MPI_COMM_WORLD, &istatus);
233 <
318 >          potatoes[which_node] = 0;          
319 >          MPI_Send(0, 1, MPI_INT, which_node, 0, MPI_COMM_WORLD);
320 >          
321          }
322  
323 <      } else {
323 >        myPotato = potatoes[which_node];        
324          
325 <        haveError = 0;
326 <        which_atom = i;
240 <        local_index=-1;
241 <
242 <        for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) {
243 <          if (atoms[j]->getGlobalIndex() == which_atom) local_index = j;
244 <        }
245 <
246 <        if (local_index != -1) {
247 <
248 <          atomTypeString = atoms[local_index]->getType();
249 <
250 <          atoms[local_index]->getPos(pos);
251 <          atoms[local_index]->getVel(vel);
252 <
253 <          atomTransData[0] = pos[0];
254 <          atomTransData[1] = pos[1];
255 <          atomTransData[2] = pos[2];
256 <
257 <          atomTransData[3] = vel[0];
258 <          atomTransData[4] = vel[1];
259 <          atomTransData[5] = vel[2];
260 <          
261 <          isDirectional = 0;
262 <
263 <          if( atoms[local_index]->isDirectional() ){
264 <
265 <            isDirectional = 1;
266 <            
267 <            dAtom = (DirectionalAtom *)atoms[local_index];
268 <            dAtom->getQ( q );
269 <            
270 <            atomOrientData[0] = q[0];
271 <            atomOrientData[1] = q[1];
272 <            atomOrientData[2] = q[2];
273 <            atomOrientData[3] = q[3];
274 <
275 <            atomOrientData[4] = dAtom->getJx();
276 <            atomOrientData[5] = dAtom->getJy();
277 <            atomOrientData[6] = dAtom->getJz();
278 <          }
279 <
280 <        } else {
281 <          sprintf(painCave.errMsg,
282 <                  "Atom %d not found on processor %d\n",
283 <                  i, worldRank );
284 <          haveError= 1;
285 <          simError();
286 <        }
287 <
288 <        if(haveError) DieDieDie();
289 <                              
290 <        // If we've survived to here, format the line:
325 >        MPI_Recv(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, which_node,
326 >                 myPotato, MPI_COMM_WORLD, &istatus);
327          
328 <        sprintf( tempBuffer,
329 <                 "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
330 <                 atomTypeString,
295 <                 atomTransData[0],
296 <                 atomTransData[1],
297 <                 atomTransData[2],
298 <                 atomTransData[3],
299 <                 atomTransData[4],
300 <                 atomTransData[5]);
328 >        atomTypeString = MPIatomTypeString;
329 >        
330 >        myPotato++;
331  
332 <        strcpy( writeLine, tempBuffer );
332 >        MPI_Recv(&isDirectional, 1, MPI_INT, which_node,
333 >                 myPotato, MPI_COMM_WORLD, &istatus);
334 >              
335 >        myPotato++;
336  
337 <        if (isDirectional) {
338 <
339 <          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 <
337 >        if (isDirectional) {          
338 >          MPI_Recv(atomData13, 13, MPI_DOUBLE, which_node,
339 >                   myPotato, MPI_COMM_WORLD, &istatus);
340          } else {
341 <          strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
341 >          MPI_Recv(atomData6, 6, MPI_DOUBLE, which_node,
342 >                   myPotato, MPI_COMM_WORLD, &istatus);          
343          }
344 +        
345 +        myPotato++;
346 +        potatoes[which_node] = myPotato;
347  
348 <        outFile << writeLine;
349 <        outFile.flush();
350 <      }
351 <    }
352 <
353 <    outFile.flush();
354 <    sprintf( checkPointMsg,
355 <             "Sucessfully took a dump.\n");
356 <    MPIcheckPoint();        
330 <    
331 <  } else {
332 <
333 <    // worldRank != 0, so I'm a remote node.  
334 <    
335 <    for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) {
336 <      
337 <      // Am I the node which has this atom?
338 <      
339 <      if (AtomToProcMap[i] == worldRank) {
340 <
341 <        local_index=-1;
342 <        for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) {
343 <          if (atoms[j]->getGlobalIndex() == which_atom) local_index = j;
344 <        }
345 <        if (local_index != -1) {
346 <        
348 >      } else {
349 >        
350 >        haveError = 0;
351 >              which_atom = i;
352 >        
353 >        local_index = indexArray[currentIndex].first;        
354 >                
355 >        if (which_atom == indexArray[currentIndex].second) {
356 >          
357            atomTypeString = atoms[local_index]->getType();
358  
359 <          atoms[local_index]->getPos(pos);
360 <          atoms[local_index]->getVel(vel);
359 >                atoms[local_index]->getPos(pos);
360 >                atoms[local_index]->getVel(vel);          
361  
362 <          atomTransData[0] = pos[0];
363 <          atomTransData[1] = pos[1];
364 <          atomTransData[2] = pos[2];
362 >          atomData6[0] = pos[0];
363 >          atomData6[1] = pos[1];
364 >          atomData6[2] = pos[2];
365  
366 <          atomTransData[3] = vel[0];
367 <          atomTransData[4] = vel[1];
368 <          atomTransData[5] = vel[2];
366 >          atomData6[3] = vel[0];
367 >          atomData6[4] = vel[1];
368 >          atomData6[5] = vel[2];
369            
370            isDirectional = 0;
371  
# Line 365 | Line 375 | void DumpWriter::writeDump( double currentTime ){
375              
376              dAtom = (DirectionalAtom *)atoms[local_index];
377              dAtom->getQ( q );
368 –            
369 –            atomOrientData[0] = q[0];
370 –            atomOrientData[1] = q[1];
371 –            atomOrientData[2] = q[2];
372 –            atomOrientData[3] = q[3];
378  
379 <            atomOrientData[4] = dAtom->getJx();
380 <            atomOrientData[5] = dAtom->getJy();
381 <            atomOrientData[6] = dAtom->getJz();
379 >            for (int j = 0; j < 6 ; j++)
380 >              atomData13[j] = atomData6[j];            
381 >            
382 >            atomData13[6] = q[0];
383 >            atomData13[7] = q[1];
384 >            atomData13[8] = q[2];
385 >            atomData13[9] = q[3];
386 >            
387 >            atomData13[10] = dAtom->getJx();
388 >            atomData13[11] = dAtom->getJy();
389 >            atomData13[12] = dAtom->getJz();
390            }
391 <
391 >          
392          } else {
393 <          sprintf(painCave.errMsg,
394 <                  "Atom %d not found on processor %d\n",
395 <                  i, worldRank );
396 <          haveError= 1;
397 <          simError();
398 <        }
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);
393 >          sprintf(painCave.errMsg,
394 >                              "Atom %d not found on processor %d\n",
395 >                              i, worldRank );
396 >                haveError= 1;
397 >                simError();
398 >              }
399          
400 <        MPI_Send(&isDirectional, 1, MPI_INT, 0,
404 <                 atomIsDirectionalTag, MPI_COMM_WORLD);
400 >        if(haveError) DieDieDie();
401          
402 <        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 <      
402 >        currentIndex ++;
403        }
404 <    }
404 >      // If we've survived to here, format the line:
405 >      
406 >      if (!isDirectional) {
407 >        
408 >        sprintf( writeLine,
409 >                             "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
410 >                             atomTypeString,
411 >                             atomData6[0],
412 >                             atomData6[1],
413 >                             atomData6[2],
414 >                             atomData6[3],
415 >                             atomData6[4],
416 >                             atomData6[5]);
417  
418 <    sprintf( checkPointMsg,
419 <             "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 <
418 >              strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
419 >        
420        } else {
421 <        
422 <        haveError = 0;
423 <        which_atom = i;
424 <        local_index=-1;
425 <
426 <        for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) {
427 <          if (atoms[j]->getGlobalIndex() == which_atom) local_index = j;
428 <        }
429 <
430 <        if (local_index != -1) {
431 <
432 <          atomTypeString = atoms[local_index]->getType();
433 <
434 <          atoms[local_index]->getPos(pos);
435 <          atoms[local_index]->getVel(vel);
436 <
437 <          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:
421 >        
422 >              sprintf( writeLine,
423 >                             "%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",
424 >                             atomTypeString,
425 >                             atomData13[0],
426 >                             atomData13[1],
427 >                             atomData13[2],
428 >                             atomData13[3],
429 >                             atomData13[4],
430 >                             atomData13[5],
431 >                             atomData13[6],
432 >                             atomData13[7],
433 >                             atomData13[8],
434 >                             atomData13[9],
435 >                             atomData13[10],
436 >                             atomData13[11],
437 >                             atomData13[12]);
438          
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();
439        }
440 +      
441 +      for(k = 0; k < outFile.size(); k++)
442 +        *outFile[k] << writeLine;
443      }
444 <
445 <    finalOut.flush();
444 >    
445 >    for(k = 0; k < outFile.size(); k++)
446 >      outFile[k]->flush();
447 >    
448      sprintf( checkPointMsg,
449               "Sucessfully took a dump.\n");
450 +
451      MPIcheckPoint();        
452 <    
452 >
453 >    delete[] potatoes;
454 >
455    } else {
456  
457      // worldRank != 0, so I'm a remote node.  
458 +
459 +    // Set my magic potato to 0:
460 +
461 +    myPotato = 0;
462 +    currentIndex = 0;
463      
464      for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) {
465        
# Line 712 | Line 467 | void DumpWriter::writeFinal(double finalTime){
467        
468        if (AtomToProcMap[i] == worldRank) {
469  
470 <        local_index=-1;
471 <        for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) {
472 <          if (atoms[j]->getGlobalIndex() == which_atom) local_index = j;
470 >        if (myPotato + 3 >= MAXTAG) {
471 >
472 >          // The potato was going to exceed the maximum value,
473 >          // so wrap this processor potato back to 0 (and block until
474 >          // node 0 says we can go:
475 >
476 >          MPI_Recv(&myPotato, 1, MPI_INT, 0, 0, MPI_COMM_WORLD, &istatus);
477 >          
478          }
479 <        if (local_index != -1) {
479 >        which_atom = i;
480 >        local_index = indexArray[currentIndex].first;        
481 >                
482 >        if (which_atom == indexArray[currentIndex].second) {
483          
484            atomTypeString = atoms[local_index]->getType();
485  
486 <          atoms[local_index]->getPos(pos);
487 <          atoms[local_index]->getVel(vel);
486 >                atoms[local_index]->getPos(pos);
487 >                atoms[local_index]->getVel(vel);
488  
489 <          atomTransData[0] = pos[0];
490 <          atomTransData[1] = pos[1];
491 <          atomTransData[2] = pos[2];
489 >          atomData6[0] = pos[0];
490 >          atomData6[1] = pos[1];
491 >          atomData6[2] = pos[2];
492  
493 <          atomTransData[3] = vel[0];
494 <          atomTransData[4] = vel[1];
495 <          atomTransData[5] = vel[2];
493 >          atomData6[3] = vel[0];
494 >          atomData6[4] = vel[1];
495 >          atomData6[5] = vel[2];
496            
497            isDirectional = 0;
498  
# Line 740 | Line 503 | void DumpWriter::writeFinal(double finalTime){
503              dAtom = (DirectionalAtom *)atoms[local_index];
504              dAtom->getQ( q );
505              
506 <            atomOrientData[0] = q[0];
507 <            atomOrientData[1] = q[1];
508 <            atomOrientData[2] = q[2];
509 <            atomOrientData[3] = q[3];
510 <
511 <            atomOrientData[4] = dAtom->getJx();
512 <            atomOrientData[5] = dAtom->getJy();
513 <            atomOrientData[6] = dAtom->getJz();
506 >            for (int j = 0; j < 6 ; j++)
507 >              atomData13[j] = atomData6[j];
508 >            
509 >            atomData13[6] = q[0];
510 >            atomData13[7] = q[1];
511 >            atomData13[8] = q[2];
512 >            atomData13[9] = q[3];
513 >  
514 >            atomData13[10] = dAtom->getJx();
515 >            atomData13[11] = dAtom->getJy();
516 >            atomData13[12] = dAtom->getJz();
517            }
518  
519          } else {
520 <          sprintf(painCave.errMsg,
521 <                  "Atom %d not found on processor %d\n",
522 <                  i, worldRank );
523 <          haveError= 1;
524 <          simError();
525 <        }
520 >                sprintf(painCave.errMsg,
521 >                              "Atom %d not found on processor %d\n",
522 >                              i, worldRank );
523 >                haveError= 1;
524 >                simError();
525 >              }
526  
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 –
527          strncpy(MPIatomTypeString, atomTypeString, MINIBUFFERSIZE);
528  
529 +        // null terminate the string before sending (just in case):
530 +        MPIatomTypeString[MINIBUFFERSIZE-1] = '\0';
531 +
532          MPI_Send(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, 0,
533 <                 atomTypeTag, MPI_COMM_WORLD);
533 >                             myPotato, MPI_COMM_WORLD);
534          
535 +        myPotato++;
536 +
537          MPI_Send(&isDirectional, 1, MPI_INT, 0,
538 <                 atomIsDirectionalTag, MPI_COMM_WORLD);
538 >                             myPotato, MPI_COMM_WORLD);
539          
540 <        MPI_Send(atomTransData, 6, MPI_DOUBLE, 0,
541 <                 atomTransDataTag, MPI_COMM_WORLD);
778 <
540 >        myPotato++;
541 >        
542          if (isDirectional) {
543  
544 <          MPI_Send(atomOrientData, 7, MPI_DOUBLE, 0,
545 <                   atomOrientDataTag, MPI_COMM_WORLD);
544 >          MPI_Send(atomData13, 13, MPI_DOUBLE, 0,
545 >                   myPotato, MPI_COMM_WORLD);
546            
547 +        } else {
548 +
549 +          MPI_Send(atomData6, 6, MPI_DOUBLE, 0,
550 +                   myPotato, MPI_COMM_WORLD);
551          }
552 <      
552 >
553 >        myPotato++;  
554 >        currentIndex++;    
555        }
556      }
557  
558      sprintf( checkPointMsg,
559 <             "Sucessfully wrote final file.\n");
559 >             "Sucessfully took a dump.\n");
560      MPIcheckPoint();        
561      
562 <  }
562 >  }
563    
795 –  painCave.isEventLoop = 0;
796 –
797 –  if( worldRank == 0 ) finalOut.close();
564   #endif // is_mpi
565   }
566  
801 –
802 –
567   #ifdef IS_MPI
568  
569   // a couple of functions to let us escape the write loop

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