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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 1231 by tim, Thu Jun 3 21:06:51 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  
66 – void DumpWriter::writeDump( double currentTime ){
67 –
68 –  const int BUFFERSIZE = 2000;
69 –  const int MINIBUFFERSIZE = 10;
70 –
71 –  char tempBuffer[BUFFERSIZE];
72 –  char writeLine[BUFFERSIZE];
73 –
74 –  int i;
68   #ifdef IS_MPI
76 –  int j, which_node, done, which_atom, local_index;
77 –  double atomTransData[6];
78 –  double atomOrientData[7];
79 –  int isDirectional;
80 –  char* atomTypeString;
81 –  int me;
82 –  int atomTypeTag;
83 –  int atomIsDirectionalTag;
84 –  int atomTransDataTag;
85 –  int atomOrientDataTag;
86 – #else //is_mpi
87 –  int nAtoms = entry_plug->n_atoms;
88 – #endif //is_mpi
69  
70 <  double q[4];
71 <  DirectionalAtom* dAtom;
72 <  Atom** atoms = entry_plug->atoms;
93 <  double pos[3], vel[3];
70 > /**
71 > * A hook function to load balancing
72 > */
73  
74 <  // write current frame to the eor file
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 <  this->writeFinal( currentTime );
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 >  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 < #ifndef IS_MPI
100 > #endif
101  
102 <  outFile << nAtoms << "\n";
102 > void DumpWriter::writeDump(double currentTime){
103  
104 <  outFile << currentTime << ";\t"
105 <          << entry_plug->Hmat[0][0] << "\t"
105 <          << entry_plug->Hmat[1][0] << "\t"
106 <          << entry_plug->Hmat[2][0] << ";\t"
104 >  ofstream finalOut;
105 >  vector<ofstream*> fileStreams;
106  
107 <          << entry_plug->Hmat[0][1] << "\t"
108 <          << entry_plug->Hmat[1][1] << "\t"
109 <          << entry_plug->Hmat[2][1] << ";\t"
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 <          << entry_plug->Hmat[0][2] << "\t"
123 <          << 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;
122 >  fileStreams.push_back(&finalOut);
123 >  fileStreams.push_back(&dumpFile);
124  
125 <  for( i=0; i<nAtoms; i++ ){
125 >  writeFrame(fileStreams, currentTime);
126  
127 <    atoms[i]->getPos(pos);
128 <    atoms[i]->getVel(vel);
127 > #ifdef IS_MPI
128 >  finalOut.close();
129 > #endif
130 >        
131 > }
132  
133 <    sprintf( tempBuffer,
125 <             "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
126 <             atoms[i]->getType(),
127 <             pos[0],
128 <             pos[1],
129 <             pos[2],
130 <             vel[0],
131 <             vel[1],
132 <             vel[2]);
133 <    strcpy( writeLine, tempBuffer );
133 > void DumpWriter::writeFinal(double currentTime){
134  
135 <    if( atoms[i]->isDirectional() ){
135 >  ofstream finalOut;
136 >  vector<ofstream*> fileStreams;
137  
138 <      dAtom = (DirectionalAtom *)atoms[i];
139 <      dAtom->getQ( q );
138 > #ifdef IS_MPI
139 >  if(worldRank == 0 ){
140 > #endif // is_mpi
141  
142 <      sprintf( tempBuffer,
143 <               "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
144 <               q[0],
145 <               q[1],
146 <               q[2],
147 <               q[3],
148 <               dAtom->getJx(),
149 <               dAtom->getJy(),
148 <               dAtom->getJz());
149 <      strcat( writeLine, tempBuffer );
142 >    finalOut.open( entry_plug->finalName, ios::out | ios::trunc );
143 >
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 –    else
152 –      strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
151  
152 <    outFile << writeLine;
152 > #ifdef IS_MPI
153    }
154 <  outFile.flush();
154 > #endif // is_mpi
155 >  
156 >  fileStreams.push_back(&finalOut);  
157 >  writeFrame(fileStreams, currentTime);
158  
159 < #else // is_mpi
159 > #ifdef IS_MPI
160 >  finalOut.close();
161 > #endif
162 >  
163 > }
164  
165 <  // first thing first, suspend fatalities.
161 <  painCave.isEventLoop = 1;
165 > void DumpWriter::writeFrame( vector<ofstream*>& outFile, double currentTime ){
166  
167 <  int myStatus; // 1 = wakeup & success; 0 = error; -1 = AllDone
168 <  int haveError;
167 >  const int BUFFERSIZE = 2000;
168 >  const int MINIBUFFERSIZE = 100;
169  
170 <  MPI_Status istatus;
171 <  int *AtomToProcMap = mpiSim->getAtomToProcMap();
170 >  char tempBuffer[BUFFERSIZE];  
171 >  char writeLine[BUFFERSIZE];
172  
173 <  // write out header and node 0's coordinates
173 >  int i, k;
174  
175 <  if( worldRank == 0 ){
176 <    outFile << mpiSim->getTotAtoms() << "\n";
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 <    outFile << currentTime << ";\t"
215 <            << entry_plug->Hmat[0][0] << "\t"
176 <            << entry_plug->Hmat[1][0] << "\t"
177 <            << entry_plug->Hmat[2][0] << ";\t"
214 >  int *potatoes;
215 >  int myPotato;
216  
217 <            << entry_plug->Hmat[0][1] << "\t"
218 <            << entry_plug->Hmat[1][1] << "\t"
219 <            << entry_plug->Hmat[2][1] << ";\t"
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 <            << entry_plug->Hmat[0][2] << "\t"
228 <            << entry_plug->Hmat[1][2] << "\t"
229 <            << entry_plug->Hmat[2][2] << ";";
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 << entry_plug->the_integrator->getAdditionalParameters();
242 <    outFile << endl;
243 <    outFile.flush();
244 <    for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) {
245 <      // Get the Node number which has this atom;
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 <      which_node = AtomToProcMap[i];
250 >                     << entry_plug->Hmat[0][2] << "\t"
251 >                     << entry_plug->Hmat[1][2] << "\t"
252 >                     << entry_plug->Hmat[2][2] << ";";
253  
254 <      if (which_node != 0) {
255 <        
256 <        atomTypeTag          = 4*i;
257 <        atomIsDirectionalTag = 4*i + 1;
258 <        atomTransDataTag     = 4*i + 2;
200 <        atomOrientDataTag    = 4*i + 3;
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 <        MPI_Recv(atomTypeString, MINIBUFFERSIZE, MPI_CHAR, which_node,
261 <                 atomTypeTag, MPI_COMM_WORLD, &istatus);
262 <        
263 <        MPI_Recv(&isDirectional, 1, MPI_INT, which_node,
264 <                 atomIsDirectionalTag, MPI_COMM_WORLD, &istatus);
265 <        
266 <        MPI_Recv(atomTransData, 6, MPI_DOUBLE, which_node,
209 <                 atomTransDataTag, MPI_COMM_WORLD, &istatus);
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 <        if (isDirectional) {
268 >      sprintf( 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 <          MPI_Recv(atomOrientData, 7, MPI_DOUBLE, which_node,
214 <                   atomOrientDataTag, MPI_COMM_WORLD, &istatus);
215 <
216 <        }
217 <
218 <      } else {
219 <        
220 <        haveError = 0;
221 <        which_atom = i;
222 <        local_index=-1;
279 >      if( sd->isDirectional() ){
280  
281 <        for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) {
282 <          if (atoms[j]->getGlobalIndex() == which_atom) local_index = j;
226 <        }
281 >        sd->getQ( q );
282 >        sd->getJ( ji );
283  
284 <        if (local_index != -1) {
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 >    
298 >      for(k = 0; k < outFile.size(); k++)
299 >        *outFile[k] << writeLine;      
300 >    }
301  
302 <          atomTypeString = atoms[local_index]->getType();
302 > }
303  
304 <          atoms[local_index]->getPos(pos);
233 <          atoms[local_index]->getVel(vel);
304 > #else // is_mpi
305  
306 <          atomTransData[0] = pos[0];
307 <          atomTransData[1] = pos[1];
308 <          atomTransData[2] = pos[2];
306 >  /* code to find maximum tag value */
307 >  
308 >  int *tagub, flag, MAXTAG;
309 >  MPI_Attr_get(MPI_COMM_WORLD, MPI_TAG_UB, &tagub, &flag);
310 >  if (flag) {
311 >    MAXTAG = *tagub;
312 >  } else {
313 >    MAXTAG = 32767;
314 >  }  
315  
316 <          atomTransData[3] = vel[0];
317 <          atomTransData[4] = vel[1];
318 <          atomTransData[5] = vel[2];
316 >  int haveError;
317 >
318 >  MPI_Status istatus;
319 >  int nCurObj;
320 >  int *MolToProcMap = mpiSim->getMolToProcMap();
321 >
322 >  // write out header and node 0's coordinates
323 >
324 >  if( worldRank == 0 ){
325 >
326 >    // Node 0 needs a list of the magic potatoes for each processor;
327 >
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 >      for(k = 0; k < outFile.size(); k++){
336 >        *outFile[k] << nTotObjects << "\n";
337 >
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"
346 >
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 >    currentIndex = 0;
355 >
356 >    for (i = 0 ; i < mpiSim->getNMolGlobal(); i++ ) {
357 >      
358 >      // Get the Node number which has this atom;
359 >      
360 >      which_node = MolToProcMap[i];
361 >      
362 >      if (which_node != 0) {
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(&potatoes[which_node], 1, MPI_INT, which_node, 0, MPI_COMM_WORLD);
370            
371 <          isDirectional = 0;
371 >        }
372  
373 <          if( atoms[local_index]->isDirectional() ){
373 >        myPotato = potatoes[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 +        for(int l = 0; l < nCurObj; l++){
381 +
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 +            potatoes[which_node] = 0;          
387 +            MPI_Send(&potatoes[which_node], 1, MPI_INT, which_node, 0, MPI_COMM_WORLD);
388 +            
389 +          }
390 +
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 +          // If we've survived to here, format the line:
409              
410 <            dAtom = (DirectionalAtom *)atoms[local_index];
411 <            dAtom->getQ( q );
410 >          if (!isDirectional) {
411 >        
412 >            sprintf( writeLine,
413 >                 "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
414 >                 atomTypeString,
415 >                 atomData[0],
416 >                 atomData[1],
417 >                 atomData[2],
418 >                 atomData[3],
419 >                 atomData[4],
420 >                 atomData[5]);
421 >        
422 >           strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
423 >        
424 >          }
425 >          else {
426 >        
427 >                sprintf( writeLine,
428 >                         "%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",
429 >                         atomTypeString,
430 >                         atomData[0],
431 >                         atomData[1],
432 >                         atomData[2],
433 >                         atomData[3],
434 >                         atomData[4],
435 >                         atomData[5],
436 >                         atomData[6],
437 >                         atomData[7],
438 >                         atomData[8],
439 >                         atomData[9],
440 >                         atomData[10],
441 >                         atomData[11],
442 >                         atomData[12]);
443              
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();
444            }
445 +          
446 +          for(k = 0; k < outFile.size(); k++)
447 +            *outFile[k] << writeLine;            
448  
449 <        } else {
450 <          sprintf(painCave.errMsg,
264 <                  "Atom %d not found on processor %d\n",
265 <                  i, worldRank );
266 <          haveError= 1;
267 <          simError();
268 <        }
449 >        }// end for(int l =0)
450 >        potatoes[which_node] = myPotato;
451  
452 <        if(haveError) DieDieDie();
453 <                              
272 <        // If we've survived to here, format the line:
452 >      }
453 >      else {
454          
455 <        sprintf( tempBuffer,
456 <                 "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
457 <                 atomTypeString,
277 <                 atomTransData[0],
278 <                 atomTransData[1],
279 <                 atomTransData[2],
280 <                 atomTransData[3],
281 <                 atomTransData[4],
282 <                 atomTransData[5]);
455 >        haveError = 0;
456 >        
457 >            local_index = indexArray[currentIndex].first;        
458  
459 <        strcpy( writeLine, tempBuffer );
459 >        integrableObjects = (entry_plug->molecules[local_index]).getIntegrableObjects();
460  
461 <        if (isDirectional) {
461 >        for(iter= integrableObjects.begin(); iter != integrableObjects.end(); ++iter){    
462 >                sd = *iter;
463 >            atomTypeString = sd->getType();
464 >            
465 >            sd->getPos(pos);
466 >            sd->getVel(vel);          
467 >          
468 >            atomData[0] = pos[0];
469 >            atomData[1] = pos[1];
470 >            atomData[2] = pos[2];
471  
472 <          sprintf( tempBuffer,
473 <                   "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
474 <                   atomOrientData[0],
475 <                   atomOrientData[1],
476 <                   atomOrientData[2],
293 <                   atomOrientData[3],
294 <                   atomOrientData[4],
295 <                   atomOrientData[5],
296 <                   atomOrientData[6]);
297 <          strcat( writeLine, tempBuffer );
472 >            atomData[3] = vel[0];
473 >            atomData[4] = vel[1];
474 >            atomData[5] = vel[2];
475 >              
476 >            isDirectional = 0;
477  
478 <        } else {
300 <          strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
301 <        }
478 >            if( sd->isDirectional() ){
479  
480 <        outFile << writeLine;
481 <        outFile.flush();
482 <      }
483 <    }
480 >              isDirectional = 1;
481 >                
482 >              sd->getQ( q );
483 >              sd->getJ( ji );
484  
485 <    outFile.flush();
485 >              for (int j = 0; j < 6 ; j++)
486 >                atomData[j] = atomData[j];            
487 >              
488 >              atomData[6] = q[0];
489 >              atomData[7] = q[1];
490 >              atomData[8] = q[2];
491 >              atomData[9] = q[3];
492 >              
493 >              atomData[10] = ji[0];
494 >              atomData[11] = ji[1];
495 >              atomData[12] = ji[2];
496 >            }
497 >            
498 >            // If we've survived to here, format the line:
499 >            
500 >            if (!isDirectional) {
501 >        
502 >              sprintf( writeLine,
503 >                 "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
504 >                 atomTypeString,
505 >                 atomData[0],
506 >                 atomData[1],
507 >                 atomData[2],
508 >                 atomData[3],
509 >                 atomData[4],
510 >                 atomData[5]);
511 >        
512 >             strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
513 >        
514 >            }
515 >            else {
516 >        
517 >                sprintf( writeLine,
518 >                         "%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",
519 >                         atomTypeString,
520 >                         atomData[0],
521 >                         atomData[1],
522 >                         atomData[2],
523 >                         atomData[3],
524 >                         atomData[4],
525 >                         atomData[5],
526 >                         atomData[6],
527 >                         atomData[7],
528 >                         atomData[8],
529 >                         atomData[9],
530 >                         atomData[10],
531 >                         atomData[11],
532 >                         atomData[12]);
533 >              
534 >            }
535 >            
536 >            for(k = 0; k < outFile.size(); k++)
537 >              *outFile[k] << writeLine;
538 >            
539 >            
540 >        }//end for(iter = integrableObject.begin())
541 >        
542 >      currentIndex++;
543 >      }
544 >
545 >    }//end for(i = 0; i < mpiSim->getNmol())
546 >    
547 >    for(k = 0; k < outFile.size(); k++)
548 >      outFile[k]->flush();
549 >    
550      sprintf( checkPointMsg,
551               "Sucessfully took a dump.\n");
552 +    
553      MPIcheckPoint();        
554      
555 +    delete[] potatoes;
556 +    
557    } else {
558  
559      // worldRank != 0, so I'm a remote node.  
560 +
561 +    // Set my magic potato to 0:
562 +
563 +    myPotato = 0;
564 +    currentIndex = 0;
565      
566 <    for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) {
566 >    for (i = 0 ; i < mpiSim->getNMolGlobal(); i++ ) {
567        
568 <      // Am I the node which has this atom?
568 >      // Am I the node which has this integrableObject?
569        
570 <      if (AtomToProcMap[i] == worldRank) {
570 >      if (MolToProcMap[i] == worldRank) {
571  
572 <        local_index=-1;
573 <        for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) {
574 <          if (atoms[j]->getGlobalIndex() == which_atom) local_index = j;
572 >
573 >        if (myPotato + 1 >= MAXTAG) {
574 >          
575 >          // The potato was going to exceed the maximum value,
576 >          // so wrap this processor potato back to 0 (and block until
577 >          // node 0 says we can go:
578 >          
579 >          MPI_Recv(&myPotato, 1, MPI_INT, 0, 0, MPI_COMM_WORLD, &istatus);
580 >          
581          }
327 –        if (local_index != -1) {
328 –        
329 –          atomTypeString = atoms[local_index]->getType();
582  
583 <          atoms[local_index]->getPos(pos);
584 <          atoms[local_index]->getVel(vel);
333 <
334 <          atomTransData[0] = pos[0];
335 <          atomTransData[1] = pos[1];
336 <          atomTransData[2] = pos[2];
337 <
338 <          atomTransData[3] = vel[0];
339 <          atomTransData[4] = vel[1];
340 <          atomTransData[5] = vel[2];
583 >          local_index = indexArray[currentIndex].first;        
584 >          integrableObjects = entry_plug->molecules[local_index].getIntegrableObjects();
585            
586 <          isDirectional = 0;
586 >          nCurObj = integrableObjects.size();
587 >                      
588 >          MPI_Send(&nCurObj, 1, MPI_INT, 0,
589 >                             myPotato, MPI_COMM_WORLD);
590 >          myPotato++;
591  
592 <          if( atoms[local_index]->isDirectional() ){
592 >          for( iter = integrableObjects.begin(); iter  != integrableObjects.end(); iter++){
593  
594 <            isDirectional = 1;
594 >            if (myPotato + 2 >= MAXTAG) {
595 >          
596 >              // The potato was going to exceed the maximum value,
597 >              // so wrap this processor potato back to 0 (and block until
598 >              // node 0 says we can go:
599 >          
600 >              MPI_Recv(&myPotato, 1, MPI_INT, 0, 0, MPI_COMM_WORLD, &istatus);
601 >              
602 >            }
603              
604 <            dAtom = (DirectionalAtom *)atoms[local_index];
349 <            dAtom->getQ( q );
604 >            sd = *iter;
605              
606 <            atomOrientData[0] = q[0];
352 <            atomOrientData[1] = q[1];
353 <            atomOrientData[2] = q[2];
354 <            atomOrientData[3] = q[3];
606 >            atomTypeString = sd->getType();
607  
608 <            atomOrientData[4] = dAtom->getJx();
609 <            atomOrientData[5] = dAtom->getJy();
358 <            atomOrientData[6] = dAtom->getJz();
359 <          }
608 >            sd->getPos(pos);
609 >            sd->getVel(vel);
610  
611 <        } else {
612 <          sprintf(painCave.errMsg,
613 <                  "Atom %d not found on processor %d\n",
364 <                  i, worldRank );
365 <          haveError= 1;
366 <          simError();
367 <        }
611 >            atomData[0] = pos[0];
612 >            atomData[1] = pos[1];
613 >            atomData[2] = pos[2];
614  
615 <        // I've survived this far, so send off the data!
615 >            atomData[3] = vel[0];
616 >            atomData[4] = vel[1];
617 >            atomData[5] = vel[2];
618 >              
619 >            isDirectional = 0;
620  
621 <        atomTypeTag          = 4*i;
372 <        atomIsDirectionalTag = 4*i + 1;
373 <        atomTransDataTag     = 4*i + 2;
374 <        atomOrientDataTag    = 4*i + 3;
621 >            if( sd->isDirectional() ){
622  
623 <        MPI_Send(atomTypeString, MINIBUFFERSIZE, MPI_CHAR, 0,
624 <                 atomTypeTag, MPI_COMM_WORLD);
625 <        
626 <        MPI_Send(&isDirectional, 1, MPI_INT, 0,
627 <                 atomIsDirectionalTag, MPI_COMM_WORLD);
628 <        
629 <        MPI_Send(atomTransData, 6, MPI_DOUBLE, 0,
630 <                 atomTransDataTag, MPI_COMM_WORLD);
631 <
632 <        if (isDirectional) {
386 <
387 <          MPI_Send(atomOrientData, 7, MPI_DOUBLE, 0,
388 <                   atomOrientDataTag, MPI_COMM_WORLD);
389 <          
390 <        }
623 >                isDirectional = 1;
624 >                
625 >                sd->getQ( q );
626 >                sd->getJ( ji );
627 >                
628 >                
629 >                atomData[6] = q[0];
630 >                atomData[7] = q[1];
631 >                atomData[8] = q[2];
632 >                atomData[9] = q[3];
633        
634 <      }
635 <    }
634 >                atomData[10] = ji[0];
635 >                atomData[11] = ji[1];
636 >                atomData[12] = ji[2];
637 >              }
638  
639 <    sprintf( checkPointMsg,
640 <             "Sucessfully took a dump.\n");
397 <    MPIcheckPoint();        
398 <    
399 <  }
400 <  
401 <  painCave.isEventLoop = 0;
639 >            
640 >            strncpy(MPIatomTypeString, atomTypeString, MINIBUFFERSIZE);
641  
642 < #endif // is_mpi
643 < }
642 >            // null terminate the string before sending (just in case):
643 >            MPIatomTypeString[MINIBUFFERSIZE-1] = '\0';
644  
645 < void DumpWriter::writeFinal(double finalTime){
645 >            MPI_Send(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, 0,
646 >                             myPotato, MPI_COMM_WORLD);
647 >            
648 >            myPotato++;
649 >            
650 >            if (isDirectional) {
651  
652 <  char finalName[500];
653 <  ofstream finalOut;
652 >              MPI_Send(atomData, 13, MPI_DOUBLE, 0,
653 >                       myPotato, MPI_COMM_WORLD);
654 >              
655 >            } else {
656  
657 <  const int BUFFERSIZE = 2000;
658 <  const int MINIBUFFERSIZE = 10;
659 <  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 );
657 >              MPI_Send(atomData, 6, MPI_DOUBLE, 0,
658 >                       myPotato, MPI_COMM_WORLD);
659 >            }
660  
661 <    if( atoms[i]->isDirectional() ){
661 >            myPotato++;  
662  
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 –
583 –      } else {
584 –        
585 –        haveError = 0;
586 –        which_atom = i;
587 –        local_index=-1;
588 –
589 –        for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) {
590 –          if (atoms[j]->getGlobalIndex() == which_atom) local_index = j;
591 –        }
592 –
593 –        if (local_index != -1) {
594 –
595 –          atomTypeString = atoms[local_index]->getType();
596 –
597 –          atoms[local_index]->getPos(pos);
598 –          atoms[local_index]->getVel(vel);
599 –
600 –          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();
663            }
664  
665 <        } else {
666 <          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:
638 <        
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" );
665 >          currentIndex++;    
666 >          
667          }
668 <
668 <        finalOut << writeLine;
669 <        finalOut.flush();
668 >      
669        }
671 –    }
670  
673 –    finalOut.flush();
671      sprintf( checkPointMsg,
672               "Sucessfully took a dump.\n");
673 <    MPIcheckPoint();        
673 >    MPIcheckPoint();                
674      
678 –  } else {
679 –
680 –    // worldRank != 0, so I'm a remote node.  
681 –    
682 –    for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) {
683 –      
684 –      // Am I the node which has this atom?
685 –      
686 –      if (AtomToProcMap[i] == worldRank) {
687 –
688 –        local_index=-1;
689 –        for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) {
690 –          if (atoms[j]->getGlobalIndex() == which_atom) local_index = j;
691 –        }
692 –        if (local_index != -1) {
693 –        
694 –          atomTypeString = atoms[local_index]->getType();
695 –
696 –          atoms[local_index]->getPos(pos);
697 –          atoms[local_index]->getVel(vel);
698 –
699 –          atomTransData[0] = pos[0];
700 –          atomTransData[1] = pos[1];
701 –          atomTransData[2] = pos[2];
702 –
703 –          atomTransData[3] = vel[0];
704 –          atomTransData[4] = vel[1];
705 –          atomTransData[5] = vel[2];
706 –          
707 –          isDirectional = 0;
708 –
709 –          if( atoms[local_index]->isDirectional() ){
710 –
711 –            isDirectional = 1;
712 –            
713 –            dAtom = (DirectionalAtom *)atoms[local_index];
714 –            dAtom->getQ( q );
715 –            
716 –            atomOrientData[0] = q[0];
717 –            atomOrientData[1] = q[1];
718 –            atomOrientData[2] = q[2];
719 –            atomOrientData[3] = q[3];
720 –
721 –            atomOrientData[4] = dAtom->getJx();
722 –            atomOrientData[5] = dAtom->getJy();
723 –            atomOrientData[6] = dAtom->getJz();
724 –          }
725 –
726 –        } else {
727 –          sprintf(painCave.errMsg,
728 –                  "Atom %d not found on processor %d\n",
729 –                  i, worldRank );
730 –          haveError= 1;
731 –          simError();
732 –        }
733 –
734 –        // I've survived this far, so send off the data!
735 –
736 –        atomTypeTag          = 4*i;
737 –        atomIsDirectionalTag = 4*i + 1;
738 –        atomTransDataTag     = 4*i + 2;
739 –        atomOrientDataTag    = 4*i + 3;
740 –
741 –        MPI_Send(atomTypeString, MINIBUFFERSIZE, MPI_CHAR, 0,
742 –                 atomTypeTag, MPI_COMM_WORLD);
743 –        
744 –        MPI_Send(&isDirectional, 1, MPI_INT, 0,
745 –                 atomIsDirectionalTag, MPI_COMM_WORLD);
746 –        
747 –        MPI_Send(atomTransData, 6, MPI_DOUBLE, 0,
748 –                 atomTransDataTag, MPI_COMM_WORLD);
749 –
750 –        if (isDirectional) {
751 –
752 –          MPI_Send(atomOrientData, 7, MPI_DOUBLE, 0,
753 –                   atomOrientDataTag, MPI_COMM_WORLD);
754 –          
755 –        }
756 –      
757 –      }
675      }
676  
760 –    sprintf( checkPointMsg,
761 –             "Sucessfully wrote final file.\n");
762 –    MPIcheckPoint();        
763 –    
764 –  }
765 –  
766 –  painCave.isEventLoop = 0;
677  
678 <  if( worldRank == 0 ) finalOut.close();
678 >  
679   #endif // is_mpi
680   }
681  
772 –
773 –
682   #ifdef IS_MPI
683  
684   // a couple of functions to let us escape the write loop

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