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root/group/trunk/OOPSE/libmdtools/DumpWriter.cpp
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Comparing trunk/OOPSE/libmdtools/DumpWriter.cpp (file contents):
Revision 912 by gezelter, Thu Jan 8 18:59:36 2004 UTC vs.
Revision 1252 by gezelter, Mon Jun 7 14:26:33 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;
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 > #endif
101 >
102 > void DumpWriter::writeDump(double currentTime){
103 >
104 >  ofstream finalOut;
105 >  vector<ofstream*> fileStreams;
106 >
107   #ifdef IS_MPI
108 <  int j, which_node, done, which_atom, local_index;
109 <  double atomTransData[6];
110 <  double atomOrientData[7];
111 <  int isDirectional;
112 <  char* atomTypeString;
113 <  char MPIatomTypeString[MINIBUFFERSIZE];
114 <  int me;
115 <  int atomTypeTag;
116 <  int atomIsDirectionalTag;
117 <  int atomTransDataTag;
118 <  int atomOrientDataTag;
119 < #else //is_mpi
120 <  int nAtoms = entry_plug->n_atoms;
89 < #endif //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 <  double q[4];
123 <  DirectionalAtom* dAtom;
93 <  Atom** atoms = entry_plug->atoms;
94 <  double pos[3], vel[3];
122 >  fileStreams.push_back(&finalOut);
123 >  fileStreams.push_back(&dumpFile);
124  
125 <  // write current frame to the eor file
125 >  writeFrame(fileStreams, currentTime);
126  
127 <  this->writeFinal( currentTime );
127 > #ifdef IS_MPI
128 >  finalOut.close();
129 > #endif
130 >        
131 > }
132  
133 < #ifndef IS_MPI
133 > void DumpWriter::writeFinal(double currentTime){
134  
135 <  outFile << nAtoms << "\n";
135 >  ofstream finalOut;
136 >  vector<ofstream*> fileStreams;
137  
138 <  outFile << currentTime << ";\t"
139 <          << entry_plug->Hmat[0][0] << "\t"
140 <          << entry_plug->Hmat[1][0] << "\t"
107 <          << entry_plug->Hmat[2][0] << ";\t"
138 > #ifdef IS_MPI
139 >  if(worldRank == 0 ){
140 > #endif // is_mpi
141  
142 <          << entry_plug->Hmat[0][1] << "\t"
110 <          << entry_plug->Hmat[1][1] << "\t"
111 <          << entry_plug->Hmat[2][1] << ";\t"
142 >    finalOut.open( entry_plug->finalName, ios::out | ios::trunc );
143  
144 <          << entry_plug->Hmat[0][2] << "\t"
145 <          << entry_plug->Hmat[1][2] << "\t"
146 <          << entry_plug->Hmat[2][2] << ";";
147 <  //write out additional parameters, such as chi and eta
148 <  outFile << entry_plug->the_integrator->getAdditionalParameters();
149 <  outFile << endl;
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 <  for( i=0; i<nAtoms; i++ ){
152 > #ifdef IS_MPI
153 >  }
154 > #endif // is_mpi
155 >  
156 >  fileStreams.push_back(&finalOut);  
157 >  writeFrame(fileStreams, currentTime);
158  
159 <    atoms[i]->getPos(pos);
160 <    atoms[i]->getVel(vel);
159 > #ifdef IS_MPI
160 >  finalOut.close();
161 > #endif
162 >  
163 > }
164  
165 <    sprintf( tempBuffer,
126 <             "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
127 <             atoms[i]->getType(),
128 <             pos[0],
129 <             pos[1],
130 <             pos[2],
131 <             vel[0],
132 <             vel[1],
133 <             vel[2]);
134 <    strcpy( writeLine, tempBuffer );
165 > void DumpWriter::writeFrame( vector<ofstream*>& outFile, double currentTime ){
166  
167 <    if( atoms[i]->isDirectional() ){
167 >  const int BUFFERSIZE = 2000;
168 >  const int MINIBUFFERSIZE = 100;
169  
170 <      dAtom = (DirectionalAtom *)atoms[i];
171 <      dAtom->getQ( q );
170 >  char tempBuffer[BUFFERSIZE];  
171 >  char writeLine[BUFFERSIZE];
172 >
173 >  int i;
174 >  unsigned int k;
175 >
176 > #ifdef IS_MPI
177 >  
178 >  /*********************************************************************
179 >   * Documentation?  You want DOCUMENTATION?
180 >   *
181 >   * Why all the potatoes below?  
182 >   *
183 >   * To make a long story short, the original version of DumpWriter
184 >   * worked in the most inefficient way possible.  Node 0 would
185 >   * poke each of the node for an individual atom's formatted data
186 >   * as node 0 worked its way down the global index. This was particularly
187 >   * inefficient since the method blocked all processors at every atom
188 >   * (and did it twice!).
189 >   *
190 >   * An intermediate version of DumpWriter could be described from Node
191 >   * zero's perspective as follows:
192 >   *
193 >   *  1) Have 100 of your friends stand in a circle.
194 >   *  2) When you say go, have all of them start tossing potatoes at
195 >   *     you (one at a time).
196 >   *  3) Catch the potatoes.
197 >   *
198 >   * It was an improvement, but MPI has buffers and caches that could
199 >   * best be described in this analogy as "potato nets", so there's no
200 >   * need to block the processors atom-by-atom.
201 >   *
202 >   * This new and improved DumpWriter works in an even more efficient
203 >   * way:
204 >   *
205 >   *  1) Have 100 of your friend stand in a circle.
206 >   *  2) When you say go, have them start tossing 5-pound bags of
207 >   *     potatoes at you.
208 >   *  3) Once you've caught a friend's bag of potatoes,
209 >   *     toss them a spud to let them know they can toss another bag.
210 >   *
211 >   * How's THAT for documentation?
212 >   *
213 >   *********************************************************************/
214  
215 +  int *potatoes;
216 +  int myPotato;
217 +
218 +  int nProc;
219 +  int j, which_node, done, which_atom, local_index, currentIndex;
220 +  double atomData[13];
221 +  int isDirectional;
222 +  char* atomTypeString;
223 +  char MPIatomTypeString[MINIBUFFERSIZE];
224 +  int nObjects;
225 +  int msgLen; // the length of message actually recieved at master nodes
226 + #endif //is_mpi
227 +
228 +  double q[4], ji[3];
229 +  DirectionalAtom* dAtom;
230 +  double pos[3], vel[3];
231 +  int nTotObjects;
232 +  StuntDouble* sd;
233 +  char* molName;
234 +  vector<StuntDouble*> integrableObjects;
235 +  vector<StuntDouble*>::iterator iter;
236 +  nTotObjects = entry_plug->getTotIntegrableObjects();
237 + #ifndef IS_MPI
238 +  
239 +  for(k = 0; k < outFile.size(); k++){
240 +    *outFile[k] << nTotObjects << "\n";
241 +
242 +    *outFile[k] << currentTime << ";\t"
243 +               << entry_plug->Hmat[0][0] << "\t"
244 +                     << entry_plug->Hmat[1][0] << "\t"
245 +                     << entry_plug->Hmat[2][0] << ";\t"
246 +              
247 +               << entry_plug->Hmat[0][1] << "\t"
248 +                     << entry_plug->Hmat[1][1] << "\t"
249 +                     << entry_plug->Hmat[2][1] << ";\t"
250 +
251 +                     << entry_plug->Hmat[0][2] << "\t"
252 +                     << entry_plug->Hmat[1][2] << "\t"
253 +                     << entry_plug->Hmat[2][2] << ";";
254 +
255 +    //write out additional parameters, such as chi and eta
256 +    *outFile[k] << entry_plug->the_integrator->getAdditionalParameters() << endl;
257 +  }
258 +  
259 +  for( i=0; i< entry_plug->n_mol; i++ ){
260 +
261 +    integrableObjects = entry_plug->molecules[i].getIntegrableObjects();
262 +    molName = (entry_plug->compStamps[entry_plug->molecules[i].getStampID()])->getID();
263 +    
264 +    for( iter = integrableObjects.begin();iter !=  integrableObjects.end(); ++iter){
265 +      sd = *iter;
266 +      sd->getPos(pos);
267 +      sd->getVel(vel);
268 +
269        sprintf( tempBuffer,
270 <               "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
271 <               q[0],
272 <               q[1],
273 <               q[2],
274 <               q[3],
275 <               dAtom->getJx(),
276 <               dAtom->getJy(),
277 <               dAtom->getJz());
278 <      strcat( writeLine, tempBuffer );
270 >             "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
271 >             sd->getType(),
272 >             pos[0],
273 >             pos[1],
274 >             pos[2],
275 >             vel[0],
276 >             vel[1],
277 >             vel[2]);
278 >      strcpy( writeLine, tempBuffer );
279 >
280 >      if( sd->isDirectional() ){
281 >
282 >        sd->getQ( q );
283 >        sd->getJ( ji );
284 >
285 >        sprintf( tempBuffer,
286 >               "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
287 >               q[0],
288 >               q[1],
289 >               q[2],
290 >               q[3],
291 >                 ji[0],
292 >                 ji[1],
293 >                 ji[2]);
294 >        strcat( writeLine, tempBuffer );
295 >      }
296 >      else
297 >        strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
298 >    
299 >      for(k = 0; k < outFile.size(); k++)
300 >        *outFile[k] << writeLine;      
301      }
152 –    else
153 –      strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
302  
303 <    outFile << writeLine;
156 <  }
157 <  outFile.flush();
303 > }
304  
305   #else // is_mpi
306  
307 <  // first thing first, suspend fatalities.
308 <  painCave.isEventLoop = 1;
307 >  /* code to find maximum tag value */
308 >  
309 >  int *tagub, flag, MAXTAG;
310 >  MPI_Attr_get(MPI_COMM_WORLD, MPI_TAG_UB, &tagub, &flag);
311 >  if (flag) {
312 >    MAXTAG = *tagub;
313 >  } else {
314 >    MAXTAG = 32767;
315 >  }  
316  
164 –  int myStatus; // 1 = wakeup & success; 0 = error; -1 = AllDone
317    int haveError;
318  
319    MPI_Status istatus;
320 <  int *AtomToProcMap = mpiSim->getAtomToProcMap();
320 >  int nCurObj;
321 >  int *MolToProcMap = mpiSim->getMolToProcMap();
322  
323    // write out header and node 0's coordinates
324  
325    if( worldRank == 0 ){
173 –    outFile << mpiSim->getTotAtoms() << "\n";
326  
327 <    outFile << currentTime << ";\t"
176 <            << entry_plug->Hmat[0][0] << "\t"
177 <            << entry_plug->Hmat[1][0] << "\t"
178 <            << entry_plug->Hmat[2][0] << ";\t"
179 <
180 <            << entry_plug->Hmat[0][1] << "\t"
181 <            << entry_plug->Hmat[1][1] << "\t"
182 <            << entry_plug->Hmat[2][1] << ";\t"
183 <
184 <            << entry_plug->Hmat[0][2] << "\t"
185 <            << entry_plug->Hmat[1][2] << "\t"
186 <            << entry_plug->Hmat[2][2] << ";";
327 >    // Node 0 needs a list of the magic potatoes for each processor;
328  
329 <    outFile << entry_plug->the_integrator->getAdditionalParameters();
330 <    outFile << endl;
190 <    outFile.flush();
191 <    for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) {
192 <      // Get the Node number which has this atom;
329 >    nProc = mpiSim->getNProcessors();
330 >    potatoes = new int[nProc];
331  
332 <      which_node = AtomToProcMap[i];
332 >    //write out the comment lines
333 >    for (i = 0; i < nProc; i++)
334 >      potatoes[i] = 0;
335 >    
336 >      for(k = 0; k < outFile.size(); k++){
337 >        *outFile[k] << nTotObjects << "\n";
338  
339 <      if (which_node != 0) {
340 <        
341 <        atomTypeTag          = 4*i;
342 <        atomIsDirectionalTag = 4*i + 1;
200 <        atomTransDataTag     = 4*i + 2;
201 <        atomOrientDataTag    = 4*i + 3;
339 >        *outFile[k] << currentTime << ";\t"
340 >                         << entry_plug->Hmat[0][0] << "\t"
341 >                         << entry_plug->Hmat[1][0] << "\t"
342 >                         << entry_plug->Hmat[2][0] << ";\t"
343  
344 <        MPI_Recv(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, which_node,
345 <                 atomTypeTag, MPI_COMM_WORLD, &istatus);
346 <        
206 <        strncpy(atomTypeString, MPIatomTypeString, MINIBUFFERSIZE);
207 <        
208 <        // Null terminate the atomTypeString just in case:
344 >                         << entry_plug->Hmat[0][1] << "\t"
345 >                         << entry_plug->Hmat[1][1] << "\t"
346 >                         << entry_plug->Hmat[2][1] << ";\t"
347  
348 <        atomTypeString[strlen(atomTypeString) - 1] = '\0';
348 >                         << entry_plug->Hmat[0][2] << "\t"
349 >                         << entry_plug->Hmat[1][2] << "\t"
350 >                         << entry_plug->Hmat[2][2] << ";";
351 >  
352 >        *outFile[k] << entry_plug->the_integrator->getAdditionalParameters() << endl;
353 >    }
354  
355 <        MPI_Recv(&isDirectional, 1, MPI_INT, which_node,
356 <                 atomIsDirectionalTag, MPI_COMM_WORLD, &istatus);
355 >    currentIndex = 0;
356 >
357 >    for (i = 0 ; i < mpiSim->getNMolGlobal(); i++ ) {
358 >      
359 >      // Get the Node number which has this atom;
360 >      
361 >      which_node = MolToProcMap[i];
362 >      
363 >      if (which_node != 0) {
364          
365 <        MPI_Recv(atomTransData, 6, MPI_DOUBLE, which_node,
366 <                 atomTransDataTag, MPI_COMM_WORLD, &istatus);
365 >        if (potatoes[which_node] + 1 >= MAXTAG) {
366 >          // The potato was going to exceed the maximum value,
367 >          // so wrap this processor potato back to 0:        
368  
369 <        if (isDirectional) {
370 <
371 <          MPI_Recv(atomOrientData, 7, MPI_DOUBLE, which_node,
221 <                   atomOrientDataTag, MPI_COMM_WORLD, &istatus);
222 <
369 >          potatoes[which_node] = 0;          
370 >          MPI_Send(&potatoes[which_node], 1, MPI_INT, which_node, 0, MPI_COMM_WORLD);
371 >          
372          }
373  
374 <      } else {
374 >        myPotato = potatoes[which_node];        
375 >
376 >        //recieve the number of integrableObject in current molecule
377 >        MPI_Recv(&nCurObj, 1, MPI_INT, which_node,
378 >                 myPotato, MPI_COMM_WORLD, &istatus);
379 >        myPotato++;
380          
381 <        haveError = 0;
228 <        which_atom = i;
229 <        local_index=-1;
381 >        for(int l = 0; l < nCurObj; l++){
382  
383 <        for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) {
384 <          if (atoms[j]->getGlobalIndex() == which_atom) local_index = j;
385 <        }
383 >          if (potatoes[which_node] + 2 >= MAXTAG) {
384 >            // The potato was going to exceed the maximum value,
385 >            // so wrap this processor potato back to 0:        
386  
387 <        if (local_index != -1) {
387 >            potatoes[which_node] = 0;          
388 >            MPI_Send(&potatoes[which_node], 1, MPI_INT, which_node, 0, MPI_COMM_WORLD);
389 >            
390 >          }
391  
392 <          atomTypeString = atoms[local_index]->getType();
392 >          MPI_Recv(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, which_node,
393 >          myPotato, MPI_COMM_WORLD, &istatus);
394  
395 <          atoms[local_index]->getPos(pos);
240 <          atoms[local_index]->getVel(vel);
395 >          atomTypeString = MPIatomTypeString;
396  
397 <          atomTransData[0] = pos[0];
243 <          atomTransData[1] = pos[1];
244 <          atomTransData[2] = pos[2];
397 >          myPotato++;
398  
399 <          atomTransData[3] = vel[0];
400 <          atomTransData[4] = vel[1];
248 <          atomTransData[5] = vel[2];
249 <          
250 <          isDirectional = 0;
399 >          MPI_Recv(atomData, 13, MPI_DOUBLE, which_node, myPotato, MPI_COMM_WORLD, &istatus);
400 >          myPotato++;
401  
402 <          if( atoms[local_index]->isDirectional() ){
402 >          MPI_Get_count(&istatus, MPI_DOUBLE, &msgLen);
403  
404 +          if(msgLen  == 13)
405              isDirectional = 1;
406 +          else
407 +            isDirectional = 0;
408 +          
409 +          // If we've survived to here, format the line:
410              
411 <            dAtom = (DirectionalAtom *)atoms[local_index];
412 <            dAtom->getQ( q );
411 >          if (!isDirectional) {
412 >        
413 >            sprintf( writeLine,
414 >                 "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
415 >                 atomTypeString,
416 >                 atomData[0],
417 >                 atomData[1],
418 >                 atomData[2],
419 >                 atomData[3],
420 >                 atomData[4],
421 >                 atomData[5]);
422 >        
423 >           strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
424 >        
425 >          }
426 >          else {
427 >        
428 >                sprintf( writeLine,
429 >                         "%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",
430 >                         atomTypeString,
431 >                         atomData[0],
432 >                         atomData[1],
433 >                         atomData[2],
434 >                         atomData[3],
435 >                         atomData[4],
436 >                         atomData[5],
437 >                         atomData[6],
438 >                         atomData[7],
439 >                         atomData[8],
440 >                         atomData[9],
441 >                         atomData[10],
442 >                         atomData[11],
443 >                         atomData[12]);
444              
259 –            atomOrientData[0] = q[0];
260 –            atomOrientData[1] = q[1];
261 –            atomOrientData[2] = q[2];
262 –            atomOrientData[3] = q[3];
263 –
264 –            atomOrientData[4] = dAtom->getJx();
265 –            atomOrientData[5] = dAtom->getJy();
266 –            atomOrientData[6] = dAtom->getJz();
445            }
446 +          
447 +          for(k = 0; k < outFile.size(); k++)
448 +            *outFile[k] << writeLine;            
449  
450 <        } else {
451 <          sprintf(painCave.errMsg,
271 <                  "Atom %d not found on processor %d\n",
272 <                  i, worldRank );
273 <          haveError= 1;
274 <          simError();
275 <        }
450 >        }// end for(int l =0)
451 >        potatoes[which_node] = myPotato;
452  
453 <        if(haveError) DieDieDie();
454 <                              
279 <        // If we've survived to here, format the line:
453 >      }
454 >      else {
455          
456 <        sprintf( tempBuffer,
457 <                 "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
458 <                 atomTypeString,
284 <                 atomTransData[0],
285 <                 atomTransData[1],
286 <                 atomTransData[2],
287 <                 atomTransData[3],
288 <                 atomTransData[4],
289 <                 atomTransData[5]);
456 >        haveError = 0;
457 >        
458 >            local_index = indexArray[currentIndex].first;        
459  
460 <        strcpy( writeLine, tempBuffer );
460 >        integrableObjects = (entry_plug->molecules[local_index]).getIntegrableObjects();
461  
462 <        if (isDirectional) {
462 >        for(iter= integrableObjects.begin(); iter != integrableObjects.end(); ++iter){    
463 >                sd = *iter;
464 >            atomTypeString = sd->getType();
465 >            
466 >            sd->getPos(pos);
467 >            sd->getVel(vel);          
468 >          
469 >            atomData[0] = pos[0];
470 >            atomData[1] = pos[1];
471 >            atomData[2] = pos[2];
472  
473 <          sprintf( tempBuffer,
474 <                   "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
475 <                   atomOrientData[0],
476 <                   atomOrientData[1],
477 <                   atomOrientData[2],
300 <                   atomOrientData[3],
301 <                   atomOrientData[4],
302 <                   atomOrientData[5],
303 <                   atomOrientData[6]);
304 <          strcat( writeLine, tempBuffer );
473 >            atomData[3] = vel[0];
474 >            atomData[4] = vel[1];
475 >            atomData[5] = vel[2];
476 >              
477 >            isDirectional = 0;
478  
479 <        } else {
307 <          strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
308 <        }
479 >            if( sd->isDirectional() ){
480  
481 <        outFile << writeLine;
482 <        outFile.flush();
483 <      }
484 <    }
481 >              isDirectional = 1;
482 >                
483 >              sd->getQ( q );
484 >              sd->getJ( ji );
485  
486 <    outFile.flush();
486 >              for (int j = 0; j < 6 ; j++)
487 >                atomData[j] = atomData[j];            
488 >              
489 >              atomData[6] = q[0];
490 >              atomData[7] = q[1];
491 >              atomData[8] = q[2];
492 >              atomData[9] = q[3];
493 >              
494 >              atomData[10] = ji[0];
495 >              atomData[11] = ji[1];
496 >              atomData[12] = ji[2];
497 >            }
498 >            
499 >            // If we've survived to here, format the line:
500 >            
501 >            if (!isDirectional) {
502 >        
503 >              sprintf( writeLine,
504 >                 "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
505 >                 atomTypeString,
506 >                 atomData[0],
507 >                 atomData[1],
508 >                 atomData[2],
509 >                 atomData[3],
510 >                 atomData[4],
511 >                 atomData[5]);
512 >        
513 >             strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
514 >        
515 >            }
516 >            else {
517 >        
518 >                sprintf( writeLine,
519 >                         "%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",
520 >                         atomTypeString,
521 >                         atomData[0],
522 >                         atomData[1],
523 >                         atomData[2],
524 >                         atomData[3],
525 >                         atomData[4],
526 >                         atomData[5],
527 >                         atomData[6],
528 >                         atomData[7],
529 >                         atomData[8],
530 >                         atomData[9],
531 >                         atomData[10],
532 >                         atomData[11],
533 >                         atomData[12]);
534 >              
535 >            }
536 >            
537 >            for(k = 0; k < outFile.size(); k++)
538 >              *outFile[k] << writeLine;
539 >            
540 >            
541 >        }//end for(iter = integrableObject.begin())
542 >        
543 >      currentIndex++;
544 >      }
545 >
546 >    }//end for(i = 0; i < mpiSim->getNmol())
547 >    
548 >    for(k = 0; k < outFile.size(); k++)
549 >      outFile[k]->flush();
550 >    
551      sprintf( checkPointMsg,
552               "Sucessfully took a dump.\n");
553 +    
554      MPIcheckPoint();        
555      
556 +    delete[] potatoes;
557 +    
558    } else {
559  
560      // worldRank != 0, so I'm a remote node.  
561 +
562 +    // Set my magic potato to 0:
563 +
564 +    myPotato = 0;
565 +    currentIndex = 0;
566      
567 <    for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) {
567 >    for (i = 0 ; i < mpiSim->getNMolGlobal(); i++ ) {
568        
569 <      // Am I the node which has this atom?
569 >      // Am I the node which has this integrableObject?
570        
571 <      if (AtomToProcMap[i] == worldRank) {
571 >      if (MolToProcMap[i] == worldRank) {
572  
573 <        local_index=-1;
574 <        for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) {
575 <          if (atoms[j]->getGlobalIndex() == which_atom) local_index = j;
573 >
574 >        if (myPotato + 1 >= MAXTAG) {
575 >          
576 >          // The potato was going to exceed the maximum value,
577 >          // so wrap this processor potato back to 0 (and block until
578 >          // node 0 says we can go:
579 >          
580 >          MPI_Recv(&myPotato, 1, MPI_INT, 0, 0, MPI_COMM_WORLD, &istatus);
581 >          
582          }
334 –        if (local_index != -1) {
335 –        
336 –          atomTypeString = atoms[local_index]->getType();
583  
584 <          atoms[local_index]->getPos(pos);
585 <          atoms[local_index]->getVel(vel);
340 <
341 <          atomTransData[0] = pos[0];
342 <          atomTransData[1] = pos[1];
343 <          atomTransData[2] = pos[2];
344 <
345 <          atomTransData[3] = vel[0];
346 <          atomTransData[4] = vel[1];
347 <          atomTransData[5] = vel[2];
584 >          local_index = indexArray[currentIndex].first;        
585 >          integrableObjects = entry_plug->molecules[local_index].getIntegrableObjects();
586            
587 <          isDirectional = 0;
587 >          nCurObj = integrableObjects.size();
588 >                      
589 >          MPI_Send(&nCurObj, 1, MPI_INT, 0,
590 >                             myPotato, MPI_COMM_WORLD);
591 >          myPotato++;
592  
593 <          if( atoms[local_index]->isDirectional() ){
593 >          for( iter = integrableObjects.begin(); iter  != integrableObjects.end(); iter++){
594  
595 <            isDirectional = 1;
595 >            if (myPotato + 2 >= MAXTAG) {
596 >          
597 >              // The potato was going to exceed the maximum value,
598 >              // so wrap this processor potato back to 0 (and block until
599 >              // node 0 says we can go:
600 >          
601 >              MPI_Recv(&myPotato, 1, MPI_INT, 0, 0, MPI_COMM_WORLD, &istatus);
602 >              
603 >            }
604              
605 <            dAtom = (DirectionalAtom *)atoms[local_index];
356 <            dAtom->getQ( q );
605 >            sd = *iter;
606              
607 <            atomOrientData[0] = q[0];
359 <            atomOrientData[1] = q[1];
360 <            atomOrientData[2] = q[2];
361 <            atomOrientData[3] = q[3];
607 >            atomTypeString = sd->getType();
608  
609 <            atomOrientData[4] = dAtom->getJx();
610 <            atomOrientData[5] = dAtom->getJy();
365 <            atomOrientData[6] = dAtom->getJz();
366 <          }
609 >            sd->getPos(pos);
610 >            sd->getVel(vel);
611  
612 <        } else {
613 <          sprintf(painCave.errMsg,
614 <                  "Atom %d not found on processor %d\n",
371 <                  i, worldRank );
372 <          haveError= 1;
373 <          simError();
374 <        }
612 >            atomData[0] = pos[0];
613 >            atomData[1] = pos[1];
614 >            atomData[2] = pos[2];
615  
616 <        // I've survived this far, so send off the data!
616 >            atomData[3] = vel[0];
617 >            atomData[4] = vel[1];
618 >            atomData[5] = vel[2];
619 >              
620 >            isDirectional = 0;
621  
622 <        atomTypeTag          = 4*i;
379 <        atomIsDirectionalTag = 4*i + 1;
380 <        atomTransDataTag     = 4*i + 2;
381 <        atomOrientDataTag    = 4*i + 3;
622 >            if( sd->isDirectional() ){
623  
624 <
625 <        strncpy(MPIatomTypeString, atomTypeString, MINIBUFFERSIZE);
626 <
627 <        // null terminate the string before sending (just in case):
628 <        MPIatomTypeString[MINIBUFFERSIZE-1] = '\0';
629 <
630 <        MPI_Send(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, 0,
631 <                 atomTypeTag, MPI_COMM_WORLD);
632 <        
633 <        MPI_Send(&isDirectional, 1, MPI_INT, 0,
393 <                 atomIsDirectionalTag, MPI_COMM_WORLD);
394 <        
395 <        MPI_Send(atomTransData, 6, MPI_DOUBLE, 0,
396 <                 atomTransDataTag, MPI_COMM_WORLD);
397 <
398 <        if (isDirectional) {
399 <
400 <          MPI_Send(atomOrientData, 7, MPI_DOUBLE, 0,
401 <                   atomOrientDataTag, MPI_COMM_WORLD);
402 <          
403 <        }
624 >                isDirectional = 1;
625 >                
626 >                sd->getQ( q );
627 >                sd->getJ( ji );
628 >                
629 >                
630 >                atomData[6] = q[0];
631 >                atomData[7] = q[1];
632 >                atomData[8] = q[2];
633 >                atomData[9] = q[3];
634        
635 <      }
636 <    }
635 >                atomData[10] = ji[0];
636 >                atomData[11] = ji[1];
637 >                atomData[12] = ji[2];
638 >              }
639  
640 <    sprintf( checkPointMsg,
641 <             "Sucessfully took a dump.\n");
410 <    MPIcheckPoint();        
411 <    
412 <  }
413 <  
414 <  painCave.isEventLoop = 0;
640 >            
641 >            strncpy(MPIatomTypeString, atomTypeString, MINIBUFFERSIZE);
642  
643 < #endif // is_mpi
644 < }
643 >            // null terminate the string before sending (just in case):
644 >            MPIatomTypeString[MINIBUFFERSIZE-1] = '\0';
645  
646 < void DumpWriter::writeFinal(double finalTime){
646 >            MPI_Send(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, 0,
647 >                             myPotato, MPI_COMM_WORLD);
648 >            
649 >            myPotato++;
650 >            
651 >            if (isDirectional) {
652  
653 <  char finalName[500];
654 <  ofstream finalOut;
653 >              MPI_Send(atomData, 13, MPI_DOUBLE, 0,
654 >                       myPotato, MPI_COMM_WORLD);
655 >              
656 >            } else {
657  
658 <  const int BUFFERSIZE = 2000;
659 <  const int MINIBUFFERSIZE = 100;
660 <  char tempBuffer[BUFFERSIZE];
427 <  char writeLine[BUFFERSIZE];
428 <
429 <  double q[4];
430 <  DirectionalAtom* dAtom;
431 <  Atom** atoms = entry_plug->atoms;
432 <  int i;
433 < #ifdef IS_MPI
434 <  int j, which_node, done, which_atom, local_index;
435 <  double atomTransData[6];
436 <  double atomOrientData[7];
437 <  int isDirectional;
438 <  char* atomTypeString;
439 <  char MPIatomTypeString[MINIBUFFERSIZE];
440 <  int atomTypeTag;
441 <  int atomIsDirectionalTag;
442 <  int atomTransDataTag;
443 <  int atomOrientDataTag;
444 < #else //is_mpi
445 <  int nAtoms = entry_plug->n_atoms;
446 < #endif //is_mpi
447 <
448 <  double pos[3], vel[3];
449 <
450 < #ifdef IS_MPI
451 <  if(worldRank == 0 ){
452 < #endif // is_mpi
453 <
454 <    strcpy( finalName, entry_plug->finalName );
455 <
456 <    finalOut.open( finalName, ios::out | ios::trunc );
457 <    if( !finalOut ){
458 <      sprintf( painCave.errMsg,
459 <               "Could not open \"%s\" for final dump output.\n",
460 <               finalName );
461 <      painCave.isFatal = 1;
462 <      simError();
463 <    }
464 <
465 <    // finalOut.setf( ios::scientific );
466 <
467 < #ifdef IS_MPI
468 <  }
469 <
470 <  sprintf(checkPointMsg,"Opened file for final configuration\n");
471 <  MPIcheckPoint();
472 <
473 < #endif //is_mpi
474 <
475 <
476 < #ifndef IS_MPI
477 <
478 <  finalOut << nAtoms << "\n";
479 <
480 <  finalOut << finalTime << ";\t"
481 <           << entry_plug->Hmat[0][0] << "\t"
482 <           << entry_plug->Hmat[1][0] << "\t"
483 <           << entry_plug->Hmat[2][0] << ";\t"
484 <
485 <           << entry_plug->Hmat[0][1] << "\t"
486 <           << entry_plug->Hmat[1][1] << "\t"
487 <           << entry_plug->Hmat[2][1] << ";\t"
488 <
489 <           << entry_plug->Hmat[0][2] << "\t"
490 <           << entry_plug->Hmat[1][2] << "\t"
491 <           << entry_plug->Hmat[2][2] << ";";
492 <
493 <  //write out additional parameters, such as chi and eta
494 <  finalOut << entry_plug->the_integrator->getAdditionalParameters();
495 <  finalOut << endl;
496 <
497 <  for( i=0; i<nAtoms; i++ ){
498 <
499 <    atoms[i]->getPos(pos);
500 <    atoms[i]->getVel(vel);
501 <
502 <    sprintf( tempBuffer,
503 <             "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
504 <             atoms[i]->getType(),
505 <             pos[0],
506 <             pos[1],
507 <             pos[2],
508 <             vel[0],
509 <             vel[1],
510 <             vel[2]);
511 <    strcpy( writeLine, tempBuffer );
512 <
513 <    if( atoms[i]->isDirectional() ){
658 >              MPI_Send(atomData, 6, MPI_DOUBLE, 0,
659 >                       myPotato, MPI_COMM_WORLD);
660 >            }
661  
662 <      dAtom = (DirectionalAtom *)atoms[i];
516 <      dAtom->getQ( q );
662 >            myPotato++;  
663  
518 –      sprintf( tempBuffer,
519 –               "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
520 –               q[0],
521 –               q[1],
522 –               q[2],
523 –               q[3],
524 –               dAtom->getJx(),
525 –               dAtom->getJy(),
526 –               dAtom->getJz());
527 –      strcat( writeLine, tempBuffer );
528 –    }
529 –    else
530 –      strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
531 –
532 –    finalOut << writeLine;
533 –  }
534 –  finalOut.flush();
535 –  finalOut.close();
536 –
537 – #else // is_mpi
538 –
539 –  // first thing first, suspend fatalities.
540 –  painCave.isEventLoop = 1;
541 –
542 –  int myStatus; // 1 = wakeup & success; 0 = error; -1 = AllDone
543 –  int haveError;
544 –
545 –  MPI_Status istatus;
546 –  int *AtomToProcMap = mpiSim->getAtomToProcMap();
547 –
548 –  // write out header and node 0's coordinates
549 –
550 –  if( worldRank == 0 ){
551 –    finalOut << mpiSim->getTotAtoms() << "\n";
552 –
553 –    finalOut << finalTime << ";\t"
554 –            << entry_plug->Hmat[0][0] << "\t"
555 –            << entry_plug->Hmat[1][0] << "\t"
556 –            << entry_plug->Hmat[2][0] << ";\t"
557 –
558 –            << entry_plug->Hmat[0][1] << "\t"
559 –            << entry_plug->Hmat[1][1] << "\t"
560 –            << entry_plug->Hmat[2][1] << ";\t"
561 –
562 –            << entry_plug->Hmat[0][2] << "\t"
563 –            << entry_plug->Hmat[1][2] << "\t"
564 –            << entry_plug->Hmat[2][2] << ";";
565 –
566 –    finalOut << entry_plug->the_integrator->getAdditionalParameters();
567 –    finalOut << endl;
568 –    finalOut.flush();
569 –    for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) {
570 –      // Get the Node number which has this atom;
571 –
572 –      which_node = AtomToProcMap[i];
573 –
574 –      if (which_node != 0) {
575 –        
576 –        atomTypeTag          = 4*i;
577 –        atomIsDirectionalTag = 4*i + 1;
578 –        atomTransDataTag     = 4*i + 2;
579 –        atomOrientDataTag    = 4*i + 3;
580 –
581 –        MPI_Recv(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, which_node,
582 –                 atomTypeTag, MPI_COMM_WORLD, &istatus);
583 –        
584 –        strncpy(atomTypeString, MPIatomTypeString, MINIBUFFERSIZE);
585 –
586 –        MPI_Recv(&isDirectional, 1, MPI_INT, which_node,
587 –                 atomIsDirectionalTag, MPI_COMM_WORLD, &istatus);
588 –        
589 –        MPI_Recv(atomTransData, 6, MPI_DOUBLE, which_node,
590 –                 atomTransDataTag, MPI_COMM_WORLD, &istatus);
591 –
592 –        if (isDirectional) {
593 –
594 –          MPI_Recv(atomOrientData, 7, MPI_DOUBLE, which_node,
595 –                   atomOrientDataTag, MPI_COMM_WORLD, &istatus);
596 –
597 –        }
598 –
599 –      } else {
600 –        
601 –        haveError = 0;
602 –        which_atom = i;
603 –        local_index=-1;
604 –
605 –        for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) {
606 –          if (atoms[j]->getGlobalIndex() == which_atom) local_index = j;
607 –        }
608 –
609 –        if (local_index != -1) {
610 –
611 –          atomTypeString = atoms[local_index]->getType();
612 –
613 –          atoms[local_index]->getPos(pos);
614 –          atoms[local_index]->getVel(vel);
615 –
616 –          atomTransData[0] = pos[0];
617 –          atomTransData[1] = pos[1];
618 –          atomTransData[2] = pos[2];
619 –
620 –          atomTransData[3] = vel[0];
621 –          atomTransData[4] = vel[1];
622 –          atomTransData[5] = vel[2];
623 –          
624 –          isDirectional = 0;
625 –
626 –          if( atoms[local_index]->isDirectional() ){
627 –
628 –            isDirectional = 1;
629 –            
630 –            dAtom = (DirectionalAtom *)atoms[local_index];
631 –            dAtom->getQ( q );
632 –            
633 –            atomOrientData[0] = q[0];
634 –            atomOrientData[1] = q[1];
635 –            atomOrientData[2] = q[2];
636 –            atomOrientData[3] = q[3];
637 –
638 –            atomOrientData[4] = dAtom->getJx();
639 –            atomOrientData[5] = dAtom->getJy();
640 –            atomOrientData[6] = dAtom->getJz();
664            }
665  
666 <        } else {
667 <          sprintf(painCave.errMsg,
645 <                  "Atom %d not found on processor %d\n",
646 <                  i, worldRank );
647 <          haveError= 1;
648 <          simError();
649 <        }
650 <
651 <        if(haveError) DieDieDie();
652 <                              
653 <        // If we've survived to here, format the line:
654 <        
655 <        sprintf( tempBuffer,
656 <                 "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
657 <                 atomTypeString,
658 <                 atomTransData[0],
659 <                 atomTransData[1],
660 <                 atomTransData[2],
661 <                 atomTransData[3],
662 <                 atomTransData[4],
663 <                 atomTransData[5]);
664 <
665 <        strcpy( writeLine, tempBuffer );
666 <
667 <        if (isDirectional) {
668 <
669 <          sprintf( tempBuffer,
670 <                   "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
671 <                   atomOrientData[0],
672 <                   atomOrientData[1],
673 <                   atomOrientData[2],
674 <                   atomOrientData[3],
675 <                   atomOrientData[4],
676 <                   atomOrientData[5],
677 <                   atomOrientData[6]);
678 <          strcat( writeLine, tempBuffer );
679 <
680 <        } else {
681 <          strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
666 >          currentIndex++;    
667 >          
668          }
669 <
684 <        finalOut << writeLine;
685 <        finalOut.flush();
669 >      
670        }
687 –    }
671  
689 –    finalOut.flush();
672      sprintf( checkPointMsg,
673               "Sucessfully took a dump.\n");
674 <    MPIcheckPoint();        
674 >    MPIcheckPoint();                
675      
694 –  } else {
695 –
696 –    // worldRank != 0, so I'm a remote node.  
697 –    
698 –    for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) {
699 –      
700 –      // Am I the node which has this atom?
701 –      
702 –      if (AtomToProcMap[i] == worldRank) {
703 –
704 –        local_index=-1;
705 –        for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) {
706 –          if (atoms[j]->getGlobalIndex() == which_atom) local_index = j;
707 –        }
708 –        if (local_index != -1) {
709 –        
710 –          atomTypeString = atoms[local_index]->getType();
711 –
712 –          atoms[local_index]->getPos(pos);
713 –          atoms[local_index]->getVel(vel);
714 –
715 –          atomTransData[0] = pos[0];
716 –          atomTransData[1] = pos[1];
717 –          atomTransData[2] = pos[2];
718 –
719 –          atomTransData[3] = vel[0];
720 –          atomTransData[4] = vel[1];
721 –          atomTransData[5] = vel[2];
722 –          
723 –          isDirectional = 0;
724 –
725 –          if( atoms[local_index]->isDirectional() ){
726 –
727 –            isDirectional = 1;
728 –            
729 –            dAtom = (DirectionalAtom *)atoms[local_index];
730 –            dAtom->getQ( q );
731 –            
732 –            atomOrientData[0] = q[0];
733 –            atomOrientData[1] = q[1];
734 –            atomOrientData[2] = q[2];
735 –            atomOrientData[3] = q[3];
736 –
737 –            atomOrientData[4] = dAtom->getJx();
738 –            atomOrientData[5] = dAtom->getJy();
739 –            atomOrientData[6] = dAtom->getJz();
740 –          }
741 –
742 –        } else {
743 –          sprintf(painCave.errMsg,
744 –                  "Atom %d not found on processor %d\n",
745 –                  i, worldRank );
746 –          haveError= 1;
747 –          simError();
748 –        }
749 –
750 –        // I've survived this far, so send off the data!
751 –
752 –        atomTypeTag          = 4*i;
753 –        atomIsDirectionalTag = 4*i + 1;
754 –        atomTransDataTag     = 4*i + 2;
755 –        atomOrientDataTag    = 4*i + 3;
756 –
757 –        strncpy(MPIatomTypeString, atomTypeString, MINIBUFFERSIZE);
758 –
759 –        MPI_Send(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, 0,
760 –                 atomTypeTag, MPI_COMM_WORLD);
761 –        
762 –        MPI_Send(&isDirectional, 1, MPI_INT, 0,
763 –                 atomIsDirectionalTag, MPI_COMM_WORLD);
764 –        
765 –        MPI_Send(atomTransData, 6, MPI_DOUBLE, 0,
766 –                 atomTransDataTag, MPI_COMM_WORLD);
767 –
768 –        if (isDirectional) {
769 –
770 –          MPI_Send(atomOrientData, 7, MPI_DOUBLE, 0,
771 –                   atomOrientDataTag, MPI_COMM_WORLD);
772 –          
773 –        }
774 –      
775 –      }
676      }
677  
778 –    sprintf( checkPointMsg,
779 –             "Sucessfully wrote final file.\n");
780 –    MPIcheckPoint();        
781 –    
782 –  }
783 –  
784 –  painCave.isEventLoop = 0;
678  
679 <  if( worldRank == 0 ) finalOut.close();
679 >  
680   #endif // is_mpi
681   }
682  
790 –
791 –
683   #ifdef IS_MPI
684  
685   // a couple of functions to let us escape the write loop

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