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root/group/trunk/OOPSE/libmdtools/DumpWriter.cpp
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Comparing trunk/OOPSE/libmdtools/DumpWriter.cpp (file contents):
Revision 927 by tim, Mon Jan 12 22:54:42 2004 UTC vs.
Revision 1198 by tim, Thu May 27 00:48:12 2004 UTC

# Line 1 | Line 1
1 + #define _LARGEFILE_SOURCE64
2   #define _FILE_OFFSET_BITS 64
3  
4   #include <string.h>
5   #include <iostream>
6   #include <fstream>
7 + #include <algorithm>
8 + #include <utility>
9  
10   #ifdef IS_MPI
11   #include <mpi.h>
# Line 26 | Line 29 | DumpWriter::DumpWriter( SimInfo* the_entry_plug ){
29    if(worldRank == 0 ){
30   #endif // is_mpi
31  
32 <    strcpy( outName, entry_plug->sampleName );
32 >    dumpFile.open(entry_plug->sampleName, ios::out | ios::trunc );
33  
34 <    outFile.open(outName, ios::out | ios::trunc );
34 >    if( !dumpFile ){
35  
33 –    if( !outFile ){
34 –
36        sprintf( painCave.errMsg,
37                 "Could not open \"%s\" for dump output.\n",
38 <               outName);
38 >               entry_plug->sampleName);
39        painCave.isFatal = 1;
40        simError();
41      }
42  
42 –    //outFile.setf( ios::scientific );
43 –
43   #ifdef IS_MPI
44    }
45  
46 +  //sort the local atoms by global index
47 +  sortByGlobalIndex();
48 +  
49    sprintf( checkPointMsg,
50             "Sucessfully opened output file for dumping.\n");
51    MPIcheckPoint();
# Line 56 | Line 58 | DumpWriter::~DumpWriter( ){
58    if(worldRank == 0 ){
59   #endif // is_mpi
60  
61 <    outFile.close();
61 >    dumpFile.close();
62  
63   #ifdef IS_MPI
64    }
65   #endif // is_mpi
66   }
67  
68 < void DumpWriter::writeDump( double currentTime ){
68 > #ifdef IS_MPI
69  
70 <  const int BUFFERSIZE = 2000;
71 <  const int MINIBUFFERSIZE = 100;
70 > /**
71 > * A hook function to load balancing
72 > */
73  
74 <  char tempBuffer[BUFFERSIZE];
75 <  char writeLine[BUFFERSIZE];
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 <
88 < #ifdef IS_MPI
86 > /**
87 > * Sorting the local index by global index
88 > */
89 >
90 > void DumpWriter::sortByGlobalIndex(){
91 >  Molecule* mols = entry_plug->molecules;  
92 >  indexArray.clear();
93    
94 <  int *potatoes;
95 <  int myPotato;
94 >  for(int i = 0; i < entry_plug->n_mol;i++)
95 >    indexArray.push_back(make_pair(i, mols[i].getGlobalIndex()));
96 >  
97 >  sort(indexArray.begin(), indexArray.end(), indexSortingCriterion);    
98 > }
99  
100 <  int nProc;
82 <  int j, which_node, done, which_atom, local_index;
83 <  double atomData6[6];
84 <  double atomData13[13];
85 <  int isDirectional;
86 <  char* atomTypeString;
87 <  char MPIatomTypeString[MINIBUFFERSIZE];
100 > #endif
101  
102 < #else //is_mpi
90 <  int nAtoms = entry_plug->n_atoms;
91 < #endif //is_mpi
102 > void DumpWriter::writeDump(double currentTime){
103  
104 <  double q[4];
105 <  DirectionalAtom* dAtom;
95 <  Atom** atoms = entry_plug->atoms;
96 <  double pos[3], vel[3];
104 >  ofstream finalOut;
105 >  vector<ofstream*> fileStreams;
106  
107 <  // write current frame to the eor file
107 > #ifdef IS_MPI
108 >  if(worldRank == 0 ){
109 > #endif    
110 >    finalOut.open( entry_plug->finalName, ios::out | ios::trunc );
111 >    if( !finalOut ){
112 >      sprintf( painCave.errMsg,
113 >               "Could not open \"%s\" for final dump output.\n",
114 >               entry_plug->finalName );
115 >      painCave.isFatal = 1;
116 >      simError();
117 >    }
118 > #ifdef IS_MPI
119 >  }
120 > #endif // is_mpi
121  
122 <  this->writeFinal( currentTime );
122 >  fileStreams.push_back(&finalOut);
123 >  fileStreams.push_back(&dumpFile);
124  
125 < #ifndef IS_MPI
125 >  writeFrame(fileStreams, currentTime);
126  
127 <  outFile << nAtoms << "\n";
127 > #ifdef IS_MPI
128 >  finalOut.close();
129 > #endif
130 >        
131 > }
132  
133 <  outFile << currentTime << ";\t"
107 <          << entry_plug->Hmat[0][0] << "\t"
108 <          << entry_plug->Hmat[1][0] << "\t"
109 <          << entry_plug->Hmat[2][0] << ";\t"
133 > void DumpWriter::writeFinal(double currentTime){
134  
135 <          << entry_plug->Hmat[0][1] << "\t"
136 <          << entry_plug->Hmat[1][1] << "\t"
113 <          << entry_plug->Hmat[2][1] << ";\t"
135 >  ofstream finalOut;
136 >  vector<ofstream*> fileStreams;
137  
138 <          << entry_plug->Hmat[0][2] << "\t"
139 <          << entry_plug->Hmat[1][2] << "\t"
140 <          << entry_plug->Hmat[2][2] << ";";
118 <  //write out additional parameters, such as chi and eta
119 <  outFile << entry_plug->the_integrator->getAdditionalParameters();
120 <  outFile << endl;
138 > #ifdef IS_MPI
139 >  if(worldRank == 0 ){
140 > #endif // is_mpi
141  
142 <  for( i=0; i<nAtoms; i++ ){
142 >    finalOut.open( entry_plug->finalName, ios::out | ios::trunc );
143  
144 <    atoms[i]->getPos(pos);
145 <    atoms[i]->getVel(vel);
144 >    if( !finalOut ){
145 >      sprintf( painCave.errMsg,
146 >               "Could not open \"%s\" for final dump output.\n",
147 >               entry_plug->finalName );
148 >      painCave.isFatal = 1;
149 >      simError();
150 >    }
151  
152 <    sprintf( tempBuffer,
153 <             "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
154 <             atoms[i]->getType(),
155 <             pos[0],
156 <             pos[1],
157 <             pos[2],
133 <             vel[0],
134 <             vel[1],
135 <             vel[2]);
136 <    strcpy( writeLine, tempBuffer );
152 > #ifdef IS_MPI
153 >  }
154 > #endif // is_mpi
155 >  
156 >  fileStreams.push_back(&finalOut);  
157 >  writeFrame(fileStreams, currentTime);
158  
159 <    if( atoms[i]->isDirectional() ){
159 > #ifdef IS_MPI
160 >  finalOut.close();
161 > #endif
162 >  
163 > }
164  
165 <      dAtom = (DirectionalAtom *)atoms[i];
166 <      dAtom->getQ( q );
165 > void DumpWriter::writeFrame( vector<ofstream*>& outFile, double currentTime ){
166 >
167 >  const int BUFFERSIZE = 2000;
168 >  const int MINIBUFFERSIZE = 100;
169 >
170 >  char tempBuffer[BUFFERSIZE];  
171 >  char writeLine[BUFFERSIZE];
172  
173 +  int i, k;
174 +
175 + #ifdef IS_MPI
176 +  
177 +  /*********************************************************************
178 +   * Documentation?  You want DOCUMENTATION?
179 +   *
180 +   * Why all the potatoes below?  
181 +   *
182 +   * To make a long story short, the original version of DumpWriter
183 +   * worked in the most inefficient way possible.  Node 0 would
184 +   * poke each of the node for an individual atom's formatted data
185 +   * as node 0 worked its way down the global index. This was particularly
186 +   * inefficient since the method blocked all processors at every atom
187 +   * (and did it twice!).
188 +   *
189 +   * An intermediate version of DumpWriter could be described from Node
190 +   * zero's perspective as follows:
191 +   *
192 +   *  1) Have 100 of your friends stand in a circle.
193 +   *  2) When you say go, have all of them start tossing potatoes at
194 +   *     you (one at a time).
195 +   *  3) Catch the potatoes.
196 +   *
197 +   * It was an improvement, but MPI has buffers and caches that could
198 +   * best be described in this analogy as "potato nets", so there's no
199 +   * need to block the processors atom-by-atom.
200 +   *
201 +   * This new and improved DumpWriter works in an even more efficient
202 +   * way:
203 +   *
204 +   *  1) Have 100 of your friend stand in a circle.
205 +   *  2) When you say go, have them start tossing 5-pound bags of
206 +   *     potatoes at you.
207 +   *  3) Once you've caught a friend's bag of potatoes,
208 +   *     toss them a spud to let them know they can toss another bag.
209 +   *
210 +   * How's THAT for documentation?
211 +   *
212 +   *********************************************************************/
213 +
214 +  int *potatoes;
215 +  int myPotato;
216 +
217 +  int nProc;
218 +  int j, which_node, done, which_atom, local_index, currentIndex;
219 +  double atomData[13];
220 +  int isDirectional;
221 +  char* atomTypeString;
222 +  char MPIatomTypeString[MINIBUFFERSIZE];
223 +  int nObjects;
224 +  int msgLen; // the length of message actually recieved at master nodes
225 + #endif //is_mpi
226 +
227 +  double q[4], ji[3];
228 +  DirectionalAtom* dAtom;
229 +  double pos[3], vel[3];
230 +  int nTotObjects;
231 +  StuntDouble* sd;
232 +  char* molName;
233 +  vector<StuntDouble*> integrableObjects;
234 +  vector<StuntDouble*>::iterator iter;
235 +  nTotObjects = entry_plug->getTotIntegrableObjects();
236 + #ifndef IS_MPI
237 +  
238 +  for(k = 0; k < outFile.size(); k++){
239 +    *outFile[k] << nTotObjects << "\n";
240 +
241 +    *outFile[k] << currentTime << ";\t"
242 +               << entry_plug->Hmat[0][0] << "\t"
243 +                     << entry_plug->Hmat[1][0] << "\t"
244 +                     << entry_plug->Hmat[2][0] << ";\t"
245 +              
246 +               << entry_plug->Hmat[0][1] << "\t"
247 +                     << entry_plug->Hmat[1][1] << "\t"
248 +                     << entry_plug->Hmat[2][1] << ";\t"
249 +
250 +                     << entry_plug->Hmat[0][2] << "\t"
251 +                     << entry_plug->Hmat[1][2] << "\t"
252 +                     << entry_plug->Hmat[2][2] << ";";
253 +
254 +    //write out additional parameters, such as chi and eta
255 +    *outFile[k] << entry_plug->the_integrator->getAdditionalParameters() << endl;
256 +  }
257 +  
258 +  for( i=0; i< entry_plug->n_mol; i++ ){
259 +
260 +    integrableObjects = entry_plug->molecules[i].getIntegrableObjects();
261 +    molName = (entry_plug->compStamps[entry_plug->molecules[i].getStampID()])->getID();
262 +    
263 +    for( iter = integrableObjects.begin();iter !=  integrableObjects.end(); ++iter){
264 +      sd = *iter;
265 +      sd->getPos(pos);
266 +      sd->getVel(vel);
267 +
268        sprintf( tempBuffer,
269 <               "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
270 <               q[0],
271 <               q[1],
272 <               q[2],
273 <               q[3],
274 <               dAtom->getJx(),
275 <               dAtom->getJy(),
276 <               dAtom->getJz());
277 <      strcat( writeLine, tempBuffer );
269 >             "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
270 >             sd->getType(),
271 >             pos[0],
272 >             pos[1],
273 >             pos[2],
274 >             vel[0],
275 >             vel[1],
276 >             vel[2]);
277 >      strcpy( writeLine, tempBuffer );
278 >
279 >      if( sd->isDirectional() ){
280 >
281 >        sd->getQ( q );
282 >        sd->getJ( ji );
283 >
284 >        sprintf( tempBuffer,
285 >               "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
286 >               q[0],
287 >               q[1],
288 >               q[2],
289 >               q[3],
290 >                 ji[0],
291 >                 ji[1],
292 >                 ji[2]);
293 >        strcat( writeLine, tempBuffer );
294 >      }
295 >      else
296 >        strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
297      }
154 –    else
155 –      strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
298  
299 <    outFile << writeLine;
300 <  }
301 <  outFile.flush();
299 >    
300 >    for(k = 0; k < outFile.size(); k++)
301 >      *outFile[k] << writeLine;
302 > }
303  
304   #else // is_mpi
305  
# Line 173 | Line 316 | void DumpWriter::writeDump( double currentTime ){
316    int haveError;
317  
318    MPI_Status istatus;
319 <  int *AtomToProcMap = mpiSim->getAtomToProcMap();
319 >  int nCurObj;
320 >  int *MolToProcMap = mpiSim->getMolToProcMap();
321  
322    // write out header and node 0's coordinates
323  
# Line 181 | Line 325 | void DumpWriter::writeDump( double currentTime ){
325  
326      // Node 0 needs a list of the magic potatoes for each processor;
327  
328 <    nProc = mpiSim->getNumberProcessors();
328 >    nProc = mpiSim->getNprocessors();
329      potatoes = new int[nProc];
330  
331 +    //write out the comment lines
332      for (i = 0; i < nProc; i++)
333        potatoes[i] = 0;
334      
335 <    outFile << mpiSim->getTotAtoms() << "\n";
335 >      for(k = 0; k < outFile.size(); k++){
336 >        *outFile[k] << nTotObjects << "\n";
337  
338 <    outFile << currentTime << ";\t"
339 <            << entry_plug->Hmat[0][0] << "\t"
340 <            << entry_plug->Hmat[1][0] << "\t"
341 <            << entry_plug->Hmat[2][0] << ";\t"
338 >        *outFile[k] << currentTime << ";\t"
339 >                         << entry_plug->Hmat[0][0] << "\t"
340 >                         << entry_plug->Hmat[1][0] << "\t"
341 >                         << entry_plug->Hmat[2][0] << ";\t"
342  
343 <            << entry_plug->Hmat[0][1] << "\t"
344 <            << entry_plug->Hmat[1][1] << "\t"
345 <            << entry_plug->Hmat[2][1] << ";\t"
343 >                         << entry_plug->Hmat[0][1] << "\t"
344 >                         << entry_plug->Hmat[1][1] << "\t"
345 >                         << entry_plug->Hmat[2][1] << ";\t"
346  
347 <            << entry_plug->Hmat[0][2] << "\t"
348 <            << entry_plug->Hmat[1][2] << "\t"
349 <            << entry_plug->Hmat[2][2] << ";";
347 >                         << entry_plug->Hmat[0][2] << "\t"
348 >                         << entry_plug->Hmat[1][2] << "\t"
349 >                         << entry_plug->Hmat[2][2] << ";";
350 >  
351 >        *outFile[k] << entry_plug->the_integrator->getAdditionalParameters() << endl;
352 >    }
353  
354 <    outFile << entry_plug->the_integrator->getAdditionalParameters();
206 <    outFile << endl;
207 <    outFile.flush();
354 >    currentIndex = 0;
355  
356 <    for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) {
356 >    for (i = 0 ; i < mpiSim->getTotNmol(); i++ ) {
357        
358        // Get the Node number which has this atom;
359        
360 <      which_node = AtomToProcMap[i];
360 >      which_node = MolToProcMap[i];
361        
362        if (which_node != 0) {
363 <
364 <        if (potatoes[which_node] + 3 >= MAXTAG) {
363 >        
364 >        if (potatoes[which_node] + 1 >= MAXTAG) {
365            // The potato was going to exceed the maximum value,
366            // so wrap this processor potato back to 0:        
367  
368            potatoes[which_node] = 0;          
369 <          MPI_Send(0, 1, MPI_INT, which_node, 0, MPI_COMM_WORLD);
369 >          MPI_Send(&potatoes[which_node], 1, MPI_INT, which_node, 0, MPI_COMM_WORLD);
370            
371          }
372  
373          myPotato = potatoes[which_node];        
374 <        
375 <        MPI_Recv(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, which_node,
374 >
375 >        //recieve the number of integrableObject in current molecule
376 >        MPI_Recv(&nCurObj, 1, MPI_INT, which_node,
377                   myPotato, MPI_COMM_WORLD, &istatus);
378 +        myPotato++;
379          
380 <        //strncpy(atomTypeString, MPIatomTypeString, MINIBUFFERSIZE);
232 <        
233 <        // Null terminate the atomTypeString just in case:
380 >        for(int l = 0; l < nCurObj; l++){
381  
382 <        //atomTypeString[strlen(atomTypeString) - 1] = '\0';
383 <        atomTypeString = MPIatomTypeString;
384 <        
238 <        myPotato++;
382 >          if (potatoes[which_node] + 2 >= MAXTAG) {
383 >            // The potato was going to exceed the maximum value,
384 >            // so wrap this processor potato back to 0:        
385  
386 <        MPI_Recv(&isDirectional, 1, MPI_INT, which_node,
387 <                 myPotato, MPI_COMM_WORLD, &istatus);
388 <              
389 <        myPotato++;
386 >            potatoes[which_node] = 0;          
387 >            MPI_Send(&potatoes[which_node], 1, MPI_INT, which_node, 0, MPI_COMM_WORLD);
388 >            
389 >          }
390  
391 <        if (isDirectional) {          
392 <          MPI_Recv(atomData13, 13, MPI_DOUBLE, which_node,
393 <                   myPotato, MPI_COMM_WORLD, &istatus);
394 <        } else {
395 <          MPI_Recv(atomData6, 6, MPI_DOUBLE, which_node,
396 <                   myPotato, MPI_COMM_WORLD, &istatus);          
391 >          MPI_Recv(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, which_node,
392 >          myPotato, MPI_COMM_WORLD, &istatus);
393 >
394 >          atomTypeString = MPIatomTypeString;
395 >
396 >          myPotato++;
397 >
398 >          MPI_Recv(atomData, 13, MPI_DOUBLE, which_node, myPotato, MPI_COMM_WORLD, &istatus);
399 >          myPotato++;
400 >
401 >          MPI_Get_count(&istatus, MPI_DOUBLE, &msgLen);
402 >
403 >          if(msgLen  == 13)
404 >            isDirectional = 1;
405 >          else
406 >            isDirectional = 0;
407 >            
408          }
252 –        
253 –        myPotato++;
409          potatoes[which_node] = myPotato;
410  
411        } else {
412          
413 <        haveError = 0;
259 <        which_atom = i;
260 <        local_index=-1;
413 >        haveError = 0;
414          
415 <        for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) {
263 <          if (atoms[j]->getGlobalIndex() == which_atom) local_index = j;
264 <        }
265 <        
266 <        if (local_index != -1) {
267 <          
268 <          atomTypeString = atoms[local_index]->getType();
415 >            local_index = indexArray[currentIndex].first;        
416  
417 <          atoms[local_index]->getPos(pos);
271 <          atoms[local_index]->getVel(vel);          
417 >        integrableObjects = (entry_plug->molecules[local_index]).getIntegrableObjects();
418  
419 <          atomData6[0] = pos[0];
420 <          atomData6[1] = pos[1];
421 <          atomData6[2] = pos[2];
419 >        for(iter= integrableObjects.begin(); iter != integrableObjects.end(); ++iter){    
420 >                sd = *iter;
421 >            atomTypeString = sd->getType();
422 >            
423 >            sd->getPos(pos);
424 >            sd->getVel(vel);          
425 >          
426 >            atomData[0] = pos[0];
427 >            atomData[1] = pos[1];
428 >            atomData[2] = pos[2];
429  
430 <          atomData6[3] = vel[0];
431 <          atomData6[4] = vel[1];
432 <          atomData6[5] = vel[2];
433 <          
434 <          isDirectional = 0;
430 >            atomData[3] = vel[0];
431 >            atomData[4] = vel[1];
432 >            atomData[5] = vel[2];
433 >              
434 >            isDirectional = 0;
435  
436 <          if( atoms[local_index]->isDirectional() ){
436 >            if( sd->isDirectional() ){
437  
438 <            isDirectional = 1;
439 <            
440 <            dAtom = (DirectionalAtom *)atoms[local_index];
441 <            dAtom->getQ( q );
438 >              isDirectional = 1;
439 >                
440 >              sd->getQ( q );
441 >              sd->getJ( ji );
442  
443 <            for (int j = 0; j < 6 ; j++)
444 <              atomData13[j] = atomData6[j];            
443 >              for (int j = 0; j < 6 ; j++)
444 >                atomData[j] = atomData[j];            
445 >              
446 >              atomData[6] = q[0];
447 >              atomData[7] = q[1];
448 >              atomData[8] = q[2];
449 >              atomData[9] = q[3];
450 >              
451 >              atomData[10] = ji[0];
452 >              atomData[11] = ji[1];
453 >              atomData[12] = ji[2];
454 >            }
455              
456 <            atomData13[6] = q[0];
294 <            atomData13[7] = q[1];
295 <            atomData13[8] = q[2];
296 <            atomData13[9] = q[3];
297 <            
298 <            atomData13[10] = dAtom->getJx();
299 <            atomData13[11] = dAtom->getJy();
300 <            atomData13[12] = dAtom->getJz();
301 <          }
302 <          
303 <        } else {
304 <          sprintf(painCave.errMsg,
305 <                  "Atom %d not found on processor %d\n",
306 <                  i, worldRank );
307 <          haveError= 1;
308 <          simError();
309 <        }
456 >        }
457          
458 <        if(haveError) DieDieDie();
312 <        
458 >      currentIndex++;
459        }
460        // If we've survived to here, format the line:
461        
462        if (!isDirectional) {
463          
464 <        sprintf( tempBuffer,
464 >        sprintf( writeLine,
465                   "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
466                   atomTypeString,
467 <                 atomData6[0],
468 <                 atomData6[1],
469 <                 atomData6[2],
470 <                 atomData6[3],
471 <                 atomData6[4],
472 <                 atomData6[5]);
467 >                 atomData[0],
468 >                 atomData[1],
469 >                 atomData[2],
470 >                 atomData[3],
471 >                 atomData[4],
472 >                 atomData[5]);
473          
328 –        strcpy( writeLine, tempBuffer );
474          strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
475          
476        } else {
477          
478 <        sprintf( tempBuffer,
478 >        sprintf( writeLine,
479                   "%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",
480                   atomTypeString,
481 <                 atomData13[0],
482 <                 atomData13[1],
483 <                 atomData13[2],
484 <                 atomData13[3],
485 <                 atomData13[4],
486 <                 atomData13[5],
487 <                 atomData13[6],
488 <                 atomData13[7],
489 <                 atomData13[8],
490 <                 atomData13[9],
491 <                 atomData13[10],
492 <                 atomData13[11],
493 <                 atomData13[12]);
349 <        
350 <        strcpy( writeLine, tempBuffer );
481 >                 atomData[0],
482 >                 atomData[1],
483 >                 atomData[2],
484 >                 atomData[3],
485 >                 atomData[4],
486 >                 atomData[5],
487 >                 atomData[6],
488 >                 atomData[7],
489 >                 atomData[8],
490 >                 atomData[9],
491 >                 atomData[10],
492 >                 atomData[11],
493 >                 atomData[12]);
494          
495        }
496        
497 <      outFile << writeLine;
498 <      outFile.flush();
497 >      for(k = 0; k < outFile.size(); k++)
498 >        *outFile[k] << writeLine;
499      }
500      
501 <
502 <    outFile.flush();
501 >    for(k = 0; k < outFile.size(); k++)
502 >      outFile[k]->flush();
503 >    
504      sprintf( checkPointMsg,
505               "Sucessfully took a dump.\n");
506 +    
507      MPIcheckPoint();        
508 +    
509      delete[] potatoes;
510 +    
511    } else {
512  
513      // worldRank != 0, so I'm a remote node.  
# Line 368 | Line 515 | void DumpWriter::writeDump( double currentTime ){
515      // Set my magic potato to 0:
516  
517      myPotato = 0;
518 +    currentIndex = 0;
519      
520 <    for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) {
520 >    for (i = 0 ; i < mpiSim->getTotNmol(); i++ ) {
521        
522 <      // Am I the node which has this atom?
522 >      // Am I the node which has this integrableObject?
523        
524 <      if (AtomToProcMap[i] == worldRank) {
524 >      if (MolToProcMap[i] == worldRank) {
525  
378 –        if (myPotato + 3 >= MAXTAG) {
526  
527 +        if (myPotato + 1 >= MAXTAG) {
528 +          
529            // The potato was going to exceed the maximum value,
530            // so wrap this processor potato back to 0 (and block until
531            // node 0 says we can go:
532 <
532 >          
533            MPI_Recv(&myPotato, 1, MPI_INT, 0, 0, MPI_COMM_WORLD, &istatus);
534            
535          }
387 –        which_atom = i;
388 –        local_index=-1;
389 –        for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) {
390 –          if (atoms[j]->getGlobalIndex() == which_atom) local_index = j;
391 –        }
392 –        if (local_index != -1) {
393 –        
394 –          atomTypeString = atoms[local_index]->getType();
536  
537 <          atoms[local_index]->getPos(pos);
538 <          atoms[local_index]->getVel(vel);
398 <
399 <          atomData6[0] = pos[0];
400 <          atomData6[1] = pos[1];
401 <          atomData6[2] = pos[2];
402 <
403 <          atomData6[3] = vel[0];
404 <          atomData6[4] = vel[1];
405 <          atomData6[5] = vel[2];
537 >          local_index = indexArray[currentIndex].first;        
538 >          integrableObjects = entry_plug->molecules[local_index].getIntegrableObjects();
539            
540 <          isDirectional = 0;
540 >          nCurObj = integrableObjects.size();
541 >                      
542 >          MPI_Send(&nCurObj, 1, MPI_INT, 0,
543 >                             myPotato, MPI_COMM_WORLD);
544 >          myPotato++;
545  
546 <          if( atoms[local_index]->isDirectional() ){
546 >          for( iter = integrableObjects.begin(); iter  != integrableObjects.end(); iter++){
547  
548 <            isDirectional = 1;
548 >            if (myPotato + 2 >= MAXTAG) {
549 >          
550 >              // The potato was going to exceed the maximum value,
551 >              // so wrap this processor potato back to 0 (and block until
552 >              // node 0 says we can go:
553 >          
554 >              MPI_Recv(&myPotato, 1, MPI_INT, 0, 0, MPI_COMM_WORLD, &istatus);
555 >              
556 >            }
557              
558 <            dAtom = (DirectionalAtom *)atoms[local_index];
414 <            dAtom->getQ( q );
558 >            sd = *iter;
559              
560 <            for (int j = 0; j < 6 ; j++)
417 <              atomData13[j] = atomData6[j];
418 <            
419 <            atomData13[6] = q[0];
420 <            atomData13[7] = q[1];
421 <            atomData13[8] = q[2];
422 <            atomData13[9] = q[3];
560 >            atomTypeString = sd->getType();
561  
562 <            atomData13[10] = dAtom->getJx();
563 <            atomData13[11] = dAtom->getJy();
426 <            atomData13[12] = dAtom->getJz();
427 <          }
562 >            sd->getPos(pos);
563 >            sd->getVel(vel);
564  
565 <        } else {
566 <          sprintf(painCave.errMsg,
567 <                  "Atom %d not found on processor %d\n",
432 <                  i, worldRank );
433 <          haveError= 1;
434 <          simError();
435 <        }
565 >            atomData[0] = pos[0];
566 >            atomData[1] = pos[1];
567 >            atomData[2] = pos[2];
568  
569 <        strncpy(MPIatomTypeString, atomTypeString, MINIBUFFERSIZE);
569 >            atomData[3] = vel[0];
570 >            atomData[4] = vel[1];
571 >            atomData[5] = vel[2];
572 >              
573 >            isDirectional = 0;
574  
575 <        // null terminate the string before sending (just in case):
440 <        MPIatomTypeString[MINIBUFFERSIZE-1] = '\0';
575 >            if( sd->isDirectional() ){
576  
577 <        MPI_Send(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, 0,
578 <                 myPotato, MPI_COMM_WORLD);
579 <        
580 <        myPotato++;
577 >                isDirectional = 1;
578 >                
579 >                sd->getQ( q );
580 >                sd->getJ( ji );
581 >                
582 >                
583 >                atomData[6] = q[0];
584 >                atomData[7] = q[1];
585 >                atomData[8] = q[2];
586 >                atomData[9] = q[3];
587 >      
588 >                atomData[10] = ji[0];
589 >                atomData[11] = ji[1];
590 >                atomData[12] = ji[2];
591 >              }
592  
593 <        MPI_Send(&isDirectional, 1, MPI_INT, 0,
594 <                 myPotato, MPI_COMM_WORLD);
449 <        
450 <        myPotato++;
451 <        
452 <        if (isDirectional) {
593 >            
594 >            strncpy(MPIatomTypeString, atomTypeString, MINIBUFFERSIZE);
595  
596 <          MPI_Send(atomData13, 13, MPI_DOUBLE, 0,
597 <                   myPotato, MPI_COMM_WORLD);
456 <          
457 <        } else {
596 >            // null terminate the string before sending (just in case):
597 >            MPIatomTypeString[MINIBUFFERSIZE-1] = '\0';
598  
599 <          MPI_Send(atomData6, 6, MPI_DOUBLE, 0,
600 <                   myPotato, MPI_COMM_WORLD);
601 <        }
599 >            MPI_Send(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, 0,
600 >                             myPotato, MPI_COMM_WORLD);
601 >            
602 >            myPotato++;
603 >            
604 >            if (isDirectional) {
605  
606 <        myPotato++;      
607 <      }
608 <    }
606 >              MPI_Send(atomData, 13, MPI_DOUBLE, 0,
607 >                       myPotato, MPI_COMM_WORLD);
608 >              
609 >            } else {
610  
611 <    sprintf( checkPointMsg,
612 <             "Sucessfully took a dump.\n");
613 <    MPIcheckPoint();        
470 <    
471 <  }
472 <  
473 < #endif // is_mpi
474 < }
611 >              MPI_Send(atomData, 6, MPI_DOUBLE, 0,
612 >                       myPotato, MPI_COMM_WORLD);
613 >            }
614  
615 < void DumpWriter::writeFinal(double finalTime){
615 >            myPotato++;  
616  
617 <  char finalName[500];
479 <  ofstream finalOut;
617 >          }
618  
619 <  const int BUFFERSIZE = 2000;
482 <  const int MINIBUFFERSIZE = 100;
483 <  char tempBuffer[BUFFERSIZE];
484 <  char writeLine[BUFFERSIZE];
485 <
486 <  double q[4];
487 <  DirectionalAtom* dAtom;
488 <  Atom** atoms = entry_plug->atoms;
489 <  int i;
490 < #ifdef IS_MPI
491 <  
492 <  int *potatoes;
493 <  int myPotato;
494 <
495 <  int nProc;
496 <  int j, which_node, done, which_atom, local_index;
497 <  double atomData6[6];
498 <  double atomData13[13];
499 <  int isDirectional;
500 <  char* atomTypeString;
501 <  char MPIatomTypeString[MINIBUFFERSIZE];
502 <
503 < #else //is_mpi
504 <  int nAtoms = entry_plug->n_atoms;
505 < #endif //is_mpi
506 <
507 <  double pos[3], vel[3];
508 <
509 < #ifdef IS_MPI
510 <  if(worldRank == 0 ){
511 < #endif // is_mpi
512 <
513 <    strcpy( finalName, entry_plug->finalName );
514 <
515 <    finalOut.open( finalName, ios::out | ios::trunc );
516 <    if( !finalOut ){
517 <      sprintf( painCave.errMsg,
518 <               "Could not open \"%s\" for final dump output.\n",
519 <               finalName );
520 <      painCave.isFatal = 1;
521 <      simError();
522 <    }
523 <
524 <    // finalOut.setf( ios::scientific );
525 <
526 < #ifdef IS_MPI
527 <  }
528 <
529 <  sprintf(checkPointMsg,"Opened file for final configuration\n");
530 <  MPIcheckPoint();
531 <
532 < #endif //is_mpi
533 <
534 <
535 < #ifndef IS_MPI
536 <
537 <  finalOut << nAtoms << "\n";
538 <
539 <  finalOut << finalTime << ";\t"
540 <           << entry_plug->Hmat[0][0] << "\t"
541 <           << entry_plug->Hmat[1][0] << "\t"
542 <           << entry_plug->Hmat[2][0] << ";\t"
543 <
544 <           << entry_plug->Hmat[0][1] << "\t"
545 <           << entry_plug->Hmat[1][1] << "\t"
546 <           << entry_plug->Hmat[2][1] << ";\t"
547 <
548 <           << entry_plug->Hmat[0][2] << "\t"
549 <           << entry_plug->Hmat[1][2] << "\t"
550 <           << entry_plug->Hmat[2][2] << ";";
551 <
552 <  //write out additional parameters, such as chi and eta
553 <  finalOut << entry_plug->the_integrator->getAdditionalParameters();
554 <  finalOut << endl;
555 <
556 <  for( i=0; i<nAtoms; i++ ){
557 <
558 <    atoms[i]->getPos(pos);
559 <    atoms[i]->getVel(vel);
560 <
561 <    sprintf( tempBuffer,
562 <             "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
563 <             atoms[i]->getType(),
564 <             pos[0],
565 <             pos[1],
566 <             pos[2],
567 <             vel[0],
568 <             vel[1],
569 <             vel[2]);
570 <    strcpy( writeLine, tempBuffer );
571 <
572 <    if( atoms[i]->isDirectional() ){
573 <
574 <      dAtom = (DirectionalAtom *)atoms[i];
575 <      dAtom->getQ( q );
576 <
577 <      sprintf( tempBuffer,
578 <               "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
579 <               q[0],
580 <               q[1],
581 <               q[2],
582 <               q[3],
583 <               dAtom->getJx(),
584 <               dAtom->getJy(),
585 <               dAtom->getJz());
586 <      strcat( writeLine, tempBuffer );
587 <    }
588 <    else
589 <      strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
590 <
591 <    finalOut << writeLine;
592 <  }
593 <  finalOut.flush();
594 <  finalOut.close();
595 <
596 < #else // is_mpi
597 <
598 <  /* code to find maximum tag value */
599 <  int *tagub, flag, MAXTAG;
600 <  MPI_Attr_get(MPI_COMM_WORLD, MPI_TAG_UB, &tagub, &flag);
601 <  if (flag) {
602 <    MAXTAG = *tagub;
603 <  } else {
604 <    MAXTAG = 32767;
605 <  }  
606 <
607 <  int haveError;
608 <
609 <  MPI_Status istatus;
610 <  int *AtomToProcMap = mpiSim->getAtomToProcMap();
611 <
612 <  // write out header and node 0's coordinates
613 <
614 <  if( worldRank == 0 ){
615 <
616 <    // Node 0 needs a list of the magic potatoes for each processor;
617 <
618 <    nProc = mpiSim->getNumberProcessors();
619 <    potatoes = new int[nProc];
620 <
621 <    for (i = 0; i < nProc; i++)
622 <      potatoes[i] = 0;
623 <    
624 <    finalOut << mpiSim->getTotAtoms() << "\n";
625 <
626 <    finalOut << finalTime << ";\t"
627 <            << entry_plug->Hmat[0][0] << "\t"
628 <            << entry_plug->Hmat[1][0] << "\t"
629 <            << entry_plug->Hmat[2][0] << ";\t"
630 <
631 <            << entry_plug->Hmat[0][1] << "\t"
632 <            << entry_plug->Hmat[1][1] << "\t"
633 <            << entry_plug->Hmat[2][1] << ";\t"
634 <
635 <            << entry_plug->Hmat[0][2] << "\t"
636 <            << entry_plug->Hmat[1][2] << "\t"
637 <            << entry_plug->Hmat[2][2] << ";";
638 <
639 <    finalOut << entry_plug->the_integrator->getAdditionalParameters();
640 <    finalOut << endl;
641 <    finalOut.flush();
642 <
643 <    for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) {
644 <      
645 <      // Get the Node number which has this atom;
646 <      
647 <      which_node = AtomToProcMap[i];
648 <      
649 <      if (which_node != 0) {
650 <
651 <        if (potatoes[which_node] + 3 >= MAXTAG) {
652 <          // The potato was going to exceed the maximum value,
653 <          // so wrap this processor potato back to 0:        
654 <
655 <          potatoes[which_node] = 0;          
656 <          MPI_Send(0, 1, MPI_INT, which_node, 0, MPI_COMM_WORLD);
619 >          currentIndex++;    
620            
621          }
659 –
660 –        myPotato = potatoes[which_node];        
661 –        
662 –        MPI_Recv(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, which_node,
663 –                 myPotato, MPI_COMM_WORLD, &istatus);
664 –        
665 –        atomTypeString = MPIatomTypeString;
666 –                
667 –        myPotato++;
668 –
669 –        MPI_Recv(&isDirectional, 1, MPI_INT, which_node,
670 –                 myPotato, MPI_COMM_WORLD, &istatus);
671 –              
672 –        myPotato++;
673 –
674 –        if (isDirectional) {          
675 –          MPI_Recv(atomData13, 13, MPI_DOUBLE, which_node,
676 –                   myPotato, MPI_COMM_WORLD, &istatus);
677 –        } else {
678 –          MPI_Recv(atomData6, 6, MPI_DOUBLE, which_node,
679 –                   myPotato, MPI_COMM_WORLD, &istatus);          
680 –        }
681 –        
682 –        myPotato++;
683 –        potatoes[which_node] = myPotato;
684 –
685 –      } else {
686 –        
687 –        haveError = 0;
688 –        which_atom = i;
689 –        local_index=-1;
690 –        
691 –        for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) {
692 –          if (atoms[j]->getGlobalIndex() == which_atom) local_index = j;
693 –        }
694 –        
695 –        if (local_index != -1) {
696 –          
697 –          atomTypeString = atoms[local_index]->getType();
698 –
699 –          atoms[local_index]->getPos(pos);
700 –          atoms[local_index]->getVel(vel);          
701 –
702 –          atomData6[0] = pos[0];
703 –          atomData6[1] = pos[1];
704 –          atomData6[2] = pos[2];
705 –
706 –          atomData6[3] = vel[0];
707 –          atomData6[4] = vel[1];
708 –          atomData6[5] = vel[2];
709 –          
710 –          isDirectional = 0;
711 –
712 –          if( atoms[local_index]->isDirectional() ){
713 –
714 –            isDirectional = 1;
715 –            
716 –            dAtom = (DirectionalAtom *)atoms[local_index];
717 –            dAtom->getQ( q );
718 –
719 –            for (int j = 0; j < 6 ; j++)
720 –              atomData13[j] = atomData6[j];            
721 –            
722 –            atomData13[6] = q[0];
723 –            atomData13[7] = q[1];
724 –            atomData13[8] = q[2];
725 –            atomData13[9] = q[3];
726 –            
727 –            atomData13[10] = dAtom->getJx();
728 –            atomData13[11] = dAtom->getJy();
729 –            atomData13[12] = dAtom->getJz();
730 –          }
731 –          
732 –        } else {
733 –          sprintf(painCave.errMsg,
734 –                  "Atom %d not found on processor %d\n",
735 –                  i, worldRank );
736 –          haveError= 1;
737 –          simError();
738 –        }
739 –        
740 –        if(haveError) DieDieDie();
741 –        
742 –      }
743 –
744 –
745 –      // If we've survived to here, format the line:
622        
747 –      if (!isDirectional) {
748 –        
749 –        sprintf( tempBuffer,
750 –                 "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
751 –                 atomTypeString,
752 –                 atomData6[0],
753 –                 atomData6[1],
754 –                 atomData6[2],
755 –                 atomData6[3],
756 –                 atomData6[4],
757 –                 atomData6[5]);
758 –        
759 –        strcpy( writeLine, tempBuffer );
760 –        strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
761 –        
762 –      } else {
763 –        
764 –        sprintf( tempBuffer,
765 –                 "%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",
766 –                 atomTypeString,
767 –                 atomData13[0],
768 –                 atomData13[1],
769 –                 atomData13[2],
770 –                 atomData13[3],
771 –                 atomData13[4],
772 –                 atomData13[5],
773 –                 atomData13[6],
774 –                 atomData13[7],
775 –                 atomData13[8],
776 –                 atomData13[9],
777 –                 atomData13[10],
778 –                 atomData13[11],
779 –                 atomData13[12]);
780 –        
781 –        strcpy( writeLine, tempBuffer );
782 –        
623        }
624 <        
785 <      finalOut << writeLine;
786 <      finalOut.flush();
787 <    }
788 <  
789 <    finalOut.flush();
624 >
625      sprintf( checkPointMsg,
626               "Sucessfully took a dump.\n");
627 <    delete[] potatoes;
627 >    MPIcheckPoint();                
628      
794 –    MPIcheckPoint();        
795 –    
796 –  } else {
797 –
798 –    // worldRank != 0, so I'm a remote node.  
799 –
800 –    // Set my magic potato to 0:
801 –
802 –    myPotato = 0;
803 –    
804 –    for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) {
805 –      
806 –      // Am I the node which has this atom?
807 –      
808 –      if (AtomToProcMap[i] == worldRank) {
809 –
810 –        if (myPotato + 3 >= MAXTAG) {
811 –
812 –          // The potato was going to exceed the maximum value,
813 –          // so wrap this processor potato back to 0 (and block until
814 –          // node 0 says we can go:
815 –
816 –          MPI_Recv(&myPotato, 1, MPI_INT, 0, 0, MPI_COMM_WORLD, &istatus);
817 –          
818 –        }
819 –        which_atom = i;  
820 –        local_index=-1;
821 –        for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) {
822 –          if (atoms[j]->getGlobalIndex() == which_atom) local_index = j;
823 –        }
824 –        if (local_index != -1) {
825 –        
826 –          atomTypeString = atoms[local_index]->getType();
827 –
828 –          atoms[local_index]->getPos(pos);
829 –          atoms[local_index]->getVel(vel);
830 –
831 –          atomData6[0] = pos[0];
832 –          atomData6[1] = pos[1];
833 –          atomData6[2] = pos[2];
834 –
835 –          atomData6[3] = vel[0];
836 –          atomData6[4] = vel[1];
837 –          atomData6[5] = vel[2];
838 –          
839 –          isDirectional = 0;
840 –
841 –          if( atoms[local_index]->isDirectional() ){
842 –
843 –            isDirectional = 1;
844 –            
845 –            dAtom = (DirectionalAtom *)atoms[local_index];
846 –            dAtom->getQ( q );
847 –            
848 –            for (int j = 0; j < 6 ; j++)
849 –              atomData13[j] = atomData6[j];
850 –            
851 –            atomData13[6] = q[0];
852 –            atomData13[7] = q[1];
853 –            atomData13[8] = q[2];
854 –            atomData13[9] = q[3];
855 –
856 –            atomData13[10] = dAtom->getJx();
857 –            atomData13[11] = dAtom->getJy();
858 –            atomData13[12] = dAtom->getJz();
859 –          }
860 –
861 –        } else {
862 –          sprintf(painCave.errMsg,
863 –                  "Atom %d not found on processor %d\n",
864 –                  i, worldRank );
865 –          haveError= 1;
866 –          simError();
867 –        }
868 –
869 –        strncpy(MPIatomTypeString, atomTypeString, MINIBUFFERSIZE);
870 –
871 –        // null terminate the string before sending (just in case):
872 –        MPIatomTypeString[MINIBUFFERSIZE-1] = '\0';
873 –
874 –        MPI_Send(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, 0,
875 –                 myPotato, MPI_COMM_WORLD);
876 –        
877 –        myPotato++;
878 –
879 –        MPI_Send(&isDirectional, 1, MPI_INT, 0,
880 –                 myPotato, MPI_COMM_WORLD);
881 –        
882 –        myPotato++;
883 –        
884 –        if (isDirectional) {
885 –
886 –          MPI_Send(atomData13, 13, MPI_DOUBLE, 0,
887 –                   myPotato, MPI_COMM_WORLD);
888 –          
889 –        } else {
890 –
891 –          MPI_Send(atomData6, 6, MPI_DOUBLE, 0,
892 –                   myPotato, MPI_COMM_WORLD);
893 –        }
894 –
895 –        myPotato++;      
896 –      }
629      }
630  
631 <    sprintf( checkPointMsg,
900 <             "Sucessfully took a dump.\n");
901 <    MPIcheckPoint();        
902 <    
903 <  }
631 >
632    
905 –  if( worldRank == 0 ) finalOut.close();
633   #endif // is_mpi
634   }
635  
909 –
910 –
636   #ifdef IS_MPI
637  
638   // a couple of functions to let us escape the write loop

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