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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 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 = 10;
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 <  int me;
184 <  int atomTypeTag;
83 <  int atomIsDirectionalTag;
84 <  int atomTransDataTag;
85 <  int atomOrientDataTag;
183 >  char MPIatomTypeString[MINIBUFFERSIZE];
184 >
185   #else //is_mpi
186    int nAtoms = entry_plug->n_atoms;
187   #endif //is_mpi
# Line 92 | Line 191 | void DumpWriter::writeDump( double currentTime ){
191    Atom** atoms = entry_plug->atoms;
192    double pos[3], vel[3];
193  
95 –  // write current frame to the eor file
96 –
97 –  this->writeFinal( currentTime );
98 –
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"
106 <          << 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 <
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 <
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 151 | 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    }
156 –  outFile.flush();
254  
255   #else // is_mpi
256  
257 <  // first thing first, suspend fatalities.
258 <  painCave.isEventLoop = 1;
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 >  }  
266  
163 –  int myStatus; // 1 = wakeup & success; 0 = error; -1 = AllDone
267    int haveError;
268  
269    MPI_Status istatus;
# Line 169 | Line 272 | void DumpWriter::writeDump( double currentTime ){
272    // write out header and node 0's coordinates
273  
274    if( worldRank == 0 ){
172 –    outFile << mpiSim->getTotAtoms() << "\n";
275  
276 <    outFile << currentTime << ";\t"
175 <            << entry_plug->Hmat[0][0] << "\t"
176 <            << entry_plug->Hmat[1][0] << "\t"
177 <            << 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"
181 <            << 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();
291 <    for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) {
191 <      // Get the Node number which has this atom;
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 <      which_node = AtomToProcMap[i];
293 >                         << entry_plug->Hmat[0][1] << "\t"
294 >                         << entry_plug->Hmat[1][1] << "\t"
295 >                         << entry_plug->Hmat[2][1] << ";\t"
296  
297 <      if (which_node != 0) {
298 <        
299 <        atomTypeTag          = 4*i;
300 <        atomIsDirectionalTag = 4*i + 1;
301 <        atomTransDataTag     = 4*i + 2;
302 <        atomOrientDataTag    = 4*i + 3;
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 <        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);
304 >    currentIndex = 0;
305  
306 <        if (isDirectional) {
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) {
313  
314 <          MPI_Recv(atomOrientData, 7, MPI_DOUBLE, which_node,
315 <                   atomOrientDataTag, 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 +          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;
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:
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,
277 <                 atomTransData[0],
278 <                 atomTransData[1],
279 <                 atomTransData[2],
280 <                 atomTransData[3],
281 <                 atomTransData[4],
282 <                 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,
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 <
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();        
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 <        
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 347 | Line 375 | void DumpWriter::writeDump( double currentTime ){
375              
376              dAtom = (DirectionalAtom *)atoms[local_index];
377              dAtom->getQ( q );
350 –            
351 –            atomOrientData[0] = q[0];
352 –            atomOrientData[1] = q[1];
353 –            atomOrientData[2] = q[2];
354 –            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 <        }
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);
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,
380 <                 atomIsDirectionalTag, MPI_COMM_WORLD);
400 >        if(haveError) DieDieDie();
401          
402 <        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 <      
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");
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];
409 <  ofstream finalOut;
410 <
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;
420 < #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
437 <  if(worldRank == 0 ){
438 < #endif // is_mpi
439 <
440 <    strcpy( finalName, entry_plug->finalName );
441 <
442 <    finalOut.open( finalName, ios::out | ios::trunc );
443 <    if( !finalOut ){
444 <      sprintf( painCave.errMsg,
445 <               "Could not open \"%s\" for final dump output.\n",
446 <               finalName );
447 <      painCave.isFatal = 1;
448 <      simError();
449 <    }
450 <
451 <    // finalOut.setf( ios::scientific );
452 <
453 < #ifdef IS_MPI
454 <  }
455 <
456 <  sprintf(checkPointMsg,"Opened file for final configuration\n");
457 <  MPIcheckPoint();
458 <
459 < #endif //is_mpi
460 <
461 <
462 < #ifndef IS_MPI
463 <
464 <  finalOut << nAtoms << "\n";
465 <
466 <  finalOut << finalTime << ";\t"
467 <           << entry_plug->Hmat[0][0] << "\t"
468 <           << entry_plug->Hmat[1][0] << "\t"
469 <           << entry_plug->Hmat[2][0] << ";\t"
470 <
471 <           << entry_plug->Hmat[0][1] << "\t"
472 <           << entry_plug->Hmat[1][1] << "\t"
473 <           << entry_plug->Hmat[2][1] << ";\t"
474 <
475 <           << entry_plug->Hmat[0][2] << "\t"
476 <           << entry_plug->Hmat[1][2] << "\t"
477 <           << entry_plug->Hmat[2][2] << ";";
478 <
479 <  //write out additional parameters, such as chi and eta
480 <  finalOut << entry_plug->the_integrator->getAdditionalParameters();
481 <  finalOut << endl;
482 <
483 <  for( i=0; i<nAtoms; i++ ){
484 <
485 <    atoms[i]->getPos(pos);
486 <    atoms[i]->getVel(vel);
487 <
488 <    sprintf( tempBuffer,
489 <             "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
490 <             atoms[i]->getType(),
491 <             pos[0],
492 <             pos[1],
493 <             pos[2],
494 <             vel[0],
495 <             vel[1],
496 <             vel[2]);
497 <    strcpy( writeLine, tempBuffer );
498 <
499 <    if( atoms[i]->isDirectional() ){
500 <
501 <      dAtom = (DirectionalAtom *)atoms[i];
502 <      dAtom->getQ( q );
503 <
504 <      sprintf( tempBuffer,
505 <               "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
506 <               q[0],
507 <               q[1],
508 <               q[2],
509 <               q[3],
510 <               dAtom->getJx(),
511 <               dAtom->getJy(),
512 <               dAtom->getJz());
513 <      strcat( writeLine, tempBuffer );
514 <    }
515 <    else
516 <      strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
517 <
518 <    finalOut << writeLine;
519 <  }
520 <  finalOut.flush();
521 <  finalOut.close();
522 <
523 < #else // is_mpi
524 <
525 <  // first thing first, suspend fatalities.
526 <  painCave.isEventLoop = 1;
527 <
528 <  int myStatus; // 1 = wakeup & success; 0 = error; -1 = AllDone
529 <  int haveError;
530 <
531 <  MPI_Status istatus;
532 <  int *AtomToProcMap = mpiSim->getAtomToProcMap();
533 <
534 <  // write out header and node 0's coordinates
535 <
536 <  if( worldRank == 0 ){
537 <    finalOut << mpiSim->getTotAtoms() << "\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 <    finalOut << entry_plug->the_integrator->getAdditionalParameters();
553 <    finalOut << endl;
554 <    finalOut.flush();
555 <    for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) {
556 <      // Get the Node number which has this atom;
557 <
558 <      which_node = AtomToProcMap[i];
559 <
560 <      if (which_node != 0) {
561 <        
562 <        atomTypeTag          = 4*i;
563 <        atomIsDirectionalTag = 4*i + 1;
564 <        atomTransDataTag     = 4*i + 2;
565 <        atomOrientDataTag    = 4*i + 3;
566 <
567 <        MPI_Recv(atomTypeString, MINIBUFFERSIZE, MPI_CHAR, which_node,
568 <                 atomTypeTag, MPI_COMM_WORLD, &istatus);
569 <        
570 <        MPI_Recv(&isDirectional, 1, MPI_INT, which_node,
571 <                 atomIsDirectionalTag, MPI_COMM_WORLD, &istatus);
572 <        
573 <        MPI_Recv(atomTransData, 6, MPI_DOUBLE, which_node,
574 <                 atomTransDataTag, MPI_COMM_WORLD, &istatus);
575 <
576 <        if (isDirectional) {
577 <
578 <          MPI_Recv(atomOrientData, 7, MPI_DOUBLE, which_node,
579 <                   atomOrientDataTag, MPI_COMM_WORLD, &istatus);
580 <
581 <        }
582 <
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];
601 <          atomTransData[1] = pos[1];
602 <          atomTransData[2] = pos[2];
603 <
604 <          atomTransData[3] = vel[0];
605 <          atomTransData[4] = vel[1];
606 <          atomTransData[5] = vel[2];
607 <          
608 <          isDirectional = 0;
609 <
610 <          if( atoms[local_index]->isDirectional() ){
611 <
612 <            isDirectional = 1;
613 <            
614 <            dAtom = (DirectionalAtom *)atoms[local_index];
615 <            dAtom->getQ( q );
616 <            
617 <            atomOrientData[0] = q[0];
618 <            atomOrientData[1] = q[1];
619 <            atomOrientData[2] = q[2];
620 <            atomOrientData[3] = q[3];
621 <
622 <            atomOrientData[4] = dAtom->getJx();
623 <            atomOrientData[5] = dAtom->getJy();
624 <            atomOrientData[6] = dAtom->getJz();
625 <          }
626 <
627 <        } else {
628 <          sprintf(painCave.errMsg,
629 <                  "Atom %d not found on processor %d\n",
630 <                  i, worldRank );
631 <          haveError= 1;
632 <          simError();
633 <        }
634 <
635 <        if(haveError) DieDieDie();
636 <                              
637 <        // 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          
639 –        sprintf( tempBuffer,
640 –                 "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
641 –                 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();
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 685 | 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 713 | 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  
527 <        // I've survived this far, so send off the data!
527 >        strncpy(MPIatomTypeString, atomTypeString, MINIBUFFERSIZE);
528  
529 <        atomTypeTag          = 4*i;
530 <        atomIsDirectionalTag = 4*i + 1;
738 <        atomTransDataTag     = 4*i + 2;
739 <        atomOrientDataTag    = 4*i + 3;
529 >        // null terminate the string before sending (just in case):
530 >        MPIatomTypeString[MINIBUFFERSIZE-1] = '\0';
531  
532 <        MPI_Send(atomTypeString, MINIBUFFERSIZE, MPI_CHAR, 0,
533 <                 atomTypeTag, MPI_COMM_WORLD);
532 >        MPI_Send(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, 0,
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);
749 <
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    
766 –  painCave.isEventLoop = 0;
767 –
768 –  if( worldRank == 0 ) finalOut.close();
564   #endif // is_mpi
565   }
566  
772 –
773 –
567   #ifdef IS_MPI
568  
569   // a couple of functions to let us escape the write loop

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