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root/group/trunk/OOPSE/libmdtools/DumpWriter.cpp
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Comparing trunk/OOPSE/libmdtools/DumpWriter.cpp (file contents):
Revision 919 by tim, Sat Jan 10 02:15:35 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 + /**
71 + * A hook function to load balancing
72 + */
73 +
74 + void DumpWriter::update(){
75 +  sortByGlobalIndex();          
76 + }
77 +  
78 + /**
79 + * Auxiliary sorting function
80 + */
81 +
82 + bool indexSortingCriterion(const pair<int, int>& p1, const pair<int, int>& p2){
83 +  return p1.second < p2.second;
84 + }
85 +
86 + /**
87 + * Sorting the local index by global index
88 + */
89 +
90 + void DumpWriter::sortByGlobalIndex(){
91 +  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 +  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 +  fileStreams.push_back(&finalOut);
123 +  fileStreams.push_back(&dumpFile);
124 +
125 +  writeFrame(fileStreams, currentTime);
126 +
127 + #ifdef IS_MPI
128 +  finalOut.close();
129 + #endif
130 +        
131 + }
132 +
133 + void DumpWriter::writeFinal(double currentTime){
134 +
135 +  ofstream finalOut;
136 +  vector<ofstream*> fileStreams;
137 +
138 + #ifdef IS_MPI
139 +  if(worldRank == 0 ){
140 + #endif // is_mpi
141 +
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 +
152 + #ifdef IS_MPI
153 +  }
154 + #endif // is_mpi
155 +  
156 +  fileStreams.push_back(&finalOut);  
157 +  writeFrame(fileStreams, currentTime);
158 +
159 + #ifdef IS_MPI
160 +  finalOut.close();
161 + #endif
162 +  
163 + }
164 +
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];
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;
220 <  double atomData6[6];
84 <  double atomData13[13];
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 <
225 < #else //is_mpi
90 <  int nAtoms = entry_plug->n_atoms;
224 >  int nObjects;
225 >  int msgLen; // the length of message actually recieved at master nodes
226   #endif //is_mpi
227  
228 <  double q[4];
228 >  double q[4], ji[3];
229    DirectionalAtom* dAtom;
95 –  Atom** atoms = entry_plug->atoms;
230    double pos[3], vel[3];
231 <
232 <  // write current frame to the eor file
233 <
234 <  this->writeFinal( currentTime );
235 <
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 << nAtoms << "\n";
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 <  outFile << currentTime << ";\t"
252 <          << entry_plug->Hmat[0][0] << "\t"
253 <          << entry_plug->Hmat[1][0] << "\t"
109 <          << entry_plug->Hmat[2][0] << ";\t"
251 >                     << entry_plug->Hmat[0][2] << "\t"
252 >                     << entry_plug->Hmat[1][2] << "\t"
253 >                     << entry_plug->Hmat[2][2] << ";";
254  
255 <          << entry_plug->Hmat[0][1] << "\t"
256 <          << entry_plug->Hmat[1][1] << "\t"
257 <          << entry_plug->Hmat[2][1] << ";\t"
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 <          << entry_plug->Hmat[0][2] << "\t"
262 <          << entry_plug->Hmat[1][2] << "\t"
263 <          << entry_plug->Hmat[2][2] << ";";
264 <  //write out additional parameters, such as chi and eta
265 <  outFile << entry_plug->the_integrator->getAdditionalParameters();
266 <  outFile << endl;
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 <  for( i=0; i<nAtoms; i++ ){
269 >      sprintf( 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 <    atoms[i]->getPos(pos);
125 <    atoms[i]->getVel(vel);
280 >      if( sd->isDirectional() ){
281  
282 <    sprintf( tempBuffer,
283 <             "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
129 <             atoms[i]->getType(),
130 <             pos[0],
131 <             pos[1],
132 <             pos[2],
133 <             vel[0],
134 <             vel[1],
135 <             vel[2]);
136 <    strcpy( writeLine, tempBuffer );
282 >        sd->getQ( q );
283 >        sd->getJ( ji );
284  
285 <    if( atoms[i]->isDirectional() ){
286 <
287 <      dAtom = (DirectionalAtom *)atoms[i];
288 <      dAtom->getQ( q );
289 <
290 <      sprintf( tempBuffer,
291 <               "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
292 <               q[0],
293 <               q[1],
294 <               q[2],
295 <               q[3],
296 <               dAtom->getJx(),
297 <               dAtom->getJy(),
298 <               dAtom->getJz());
299 <      strcat( writeLine, tempBuffer );
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      }
154 –    else
155 –      strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
302  
303 <    outFile << writeLine;
158 <  }
159 <  outFile.flush();
303 > }
304  
305   #else // is_mpi
306  
163 –  cout << "master" <<endl;
307    /* code to find maximum tag value */
308    
309 <  int tagub, flag, MAXTAG;
309 >  int *tagub, flag, MAXTAG;
310    MPI_Attr_get(MPI_COMM_WORLD, MPI_TAG_UB, &tagub, &flag);
311    if (flag) {
312 <    MAXTAG = tagub;
312 >    MAXTAG = *tagub;
313    } else {
314      MAXTAG = 32767;
315    }  
# Line 174 | Line 317 | void DumpWriter::writeDump( double currentTime ){
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  
# Line 182 | Line 326 | void DumpWriter::writeDump( double currentTime ){
326  
327      // Node 0 needs a list of the magic potatoes for each processor;
328  
329 <    nProc = mpiSim->getNumberProcessors();
329 >    nProc = mpiSim->getNProcessors();
330      potatoes = new int[nProc];
331  
332 +    //write out the comment lines
333      for (i = 0; i < nProc; i++)
334        potatoes[i] = 0;
335      
336 <    outFile << mpiSim->getTotAtoms() << "\n";
336 >      for(k = 0; k < outFile.size(); k++){
337 >        *outFile[k] << nTotObjects << "\n";
338  
339 <    outFile << currentTime << ";\t"
340 <            << entry_plug->Hmat[0][0] << "\t"
341 <            << entry_plug->Hmat[1][0] << "\t"
342 <            << entry_plug->Hmat[2][0] << ";\t"
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 <            << entry_plug->Hmat[0][1] << "\t"
345 <            << entry_plug->Hmat[1][1] << "\t"
346 <            << entry_plug->Hmat[2][1] << ";\t"
344 >                         << entry_plug->Hmat[0][1] << "\t"
345 >                         << entry_plug->Hmat[1][1] << "\t"
346 >                         << entry_plug->Hmat[2][1] << ";\t"
347  
348 <            << entry_plug->Hmat[0][2] << "\t"
349 <            << entry_plug->Hmat[1][2] << "\t"
350 <            << entry_plug->Hmat[2][2] << ";";
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 <    outFile << entry_plug->the_integrator->getAdditionalParameters();
207 <    outFile << endl;
208 <    outFile.flush();
355 >    currentIndex = 0;
356  
357 <    for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) {
357 >    for (i = 0 ; i < mpiSim->getNMolGlobal(); i++ ) {
358        
359        // Get the Node number which has this atom;
360        
361 <      which_node = AtomToProcMap[i];
361 >      which_node = MolToProcMap[i];
362        
363        if (which_node != 0) {
364 <
365 <        if (potatoes[which_node] + 3 >= MAXTAG) {
364 >        
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            potatoes[which_node] = 0;          
370 <          MPI_Send(0, 1, MPI_INT, which_node, 0, MPI_COMM_WORLD);
370 >          MPI_Send(&potatoes[which_node], 1, MPI_INT, which_node, 0, MPI_COMM_WORLD);
371            
372          }
373  
374          myPotato = potatoes[which_node];        
228 –        
229 –        MPI_Recv(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, which_node,
230 –                 myPotato, MPI_COMM_WORLD, &istatus);
231 –        
232 –        strncpy(atomTypeString, MPIatomTypeString, MINIBUFFERSIZE);
233 –        
234 –        // Null terminate the atomTypeString just in case:
375  
376 <        atomTypeString[strlen(atomTypeString) - 1] = '\0';
377 <
238 <        myPotato++;
239 <
240 <        MPI_Recv(&isDirectional, 1, MPI_INT, which_node,
376 >        //recieve the number of integrableObject in current molecule
377 >        MPI_Recv(&nCurObj, 1, MPI_INT, which_node,
378                   myPotato, MPI_COMM_WORLD, &istatus);
242 –              
379          myPotato++;
244 –
245 –        if (isDirectional) {          
246 –          MPI_Recv(atomData13, 13, MPI_DOUBLE, which_node,
247 –                   myPotato, MPI_COMM_WORLD, &istatus);
248 –        } else {
249 –          MPI_Recv(atomData6, 6, MPI_DOUBLE, which_node,
250 –                   myPotato, MPI_COMM_WORLD, &istatus);          
251 –        }
380          
381 <        myPotato++;
254 <        potatoes[which_node] = myPotato;
381 >        for(int l = 0; l < nCurObj; l++){
382  
383 <      } else {
384 <        
385 <        haveError = 0;
259 <        which_atom = i;
260 <        local_index=-1;
261 <        
262 <        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();
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 <          atoms[local_index]->getPos(pos);
388 <          atoms[local_index]->getVel(vel);          
387 >            potatoes[which_node] = 0;          
388 >            MPI_Send(&potatoes[which_node], 1, MPI_INT, which_node, 0, MPI_COMM_WORLD);
389 >            
390 >          }
391  
392 <          atomData6[0] = pos[0];
393 <          atomData6[1] = pos[1];
275 <          atomData6[2] = pos[2];
392 >          MPI_Recv(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, which_node,
393 >          myPotato, MPI_COMM_WORLD, &istatus);
394  
395 <          atomData6[3] = vel[0];
278 <          atomData6[4] = vel[1];
279 <          atomData6[5] = vel[2];
280 <          
281 <          isDirectional = 0;
395 >          atomTypeString = MPIatomTypeString;
396  
397 <          if( atoms[local_index]->isDirectional() ){
397 >          myPotato++;
398  
399 +          MPI_Recv(atomData, 13, MPI_DOUBLE, which_node, myPotato, MPI_COMM_WORLD, &istatus);
400 +          myPotato++;
401 +
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 );
413 <
414 <            for (int j = 0; j < 6 ; j++)
415 <              atomData13[j] = atomData6[j];            
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              
293 –            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();
445            }
446            
447 <        } else {
448 <          sprintf(painCave.errMsg,
305 <                  "Atom %d not found on processor %d\n",
306 <                  i, worldRank );
307 <          haveError= 1;
308 <          simError();
309 <        }
310 <        
311 <        if(haveError) DieDieDie();
312 <        
313 <        // If we've survived to here, format the line:
314 <        
315 <        if (!isDirectional) {
447 >          for(k = 0; k < outFile.size(); k++)
448 >            *outFile[k] << writeLine;            
449  
450 <          sprintf( tempBuffer,
451 <                   "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
319 <                   atomTypeString,
320 <                   atomData6[0],
321 <                   atomData6[1],
322 <                   atomData6[2],
323 <                   atomData6[3],
324 <                   atomData6[4],
325 <                   atomData6[5]);
326 <          
327 <          strcpy( writeLine, tempBuffer );
328 <          strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
450 >        }// end for(int l =0)
451 >        potatoes[which_node] = myPotato;
452  
330 –        } else {
331 –          
332 –          sprintf( tempBuffer,
333 –                   "%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",
334 –                   atomTypeString,
335 –                   atomData13[0],
336 –                   atomData13[1],
337 –                   atomData13[2],
338 –                   atomData13[3],
339 –                   atomData13[4],
340 –                   atomData13[5],
341 –                   atomData13[6],
342 –                   atomData13[7],
343 –                   atomData13[8],
344 –                   atomData13[9],
345 –                   atomData13[10],
346 –                   atomData13[11],
347 –                   atomData13[12]);
348 –          
349 –          strcat( writeLine, tempBuffer );
350 –          
351 –        }
352 –        
353 –        outFile << writeLine;
354 –        outFile.flush();
453        }
454 <    }
454 >      else {
455 >        
456 >        haveError = 0;
457 >        
458 >            local_index = indexArray[currentIndex].first;        
459  
460 <    outFile.flush();
359 <    sprintf( checkPointMsg,
360 <             "Sucessfully took a dump.\n");
361 <    MPIcheckPoint();        
362 <    delete[] potatoes;
363 <  } else {
460 >        integrableObjects = (entry_plug->molecules[local_index]).getIntegrableObjects();
461  
462 <    // worldRank != 0, so I'm a remote node.  
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 <    // Set my magic potato to 0:
473 >            atomData[3] = vel[0];
474 >            atomData[4] = vel[1];
475 >            atomData[5] = vel[2];
476 >              
477 >            isDirectional = 0;
478  
479 <    myPotato = 0;
370 <    
371 <    for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) {
372 <      
373 <      // Am I the node which has this atom?
374 <      
375 <      if (AtomToProcMap[i] == worldRank) {
479 >            if( sd->isDirectional() ){
480  
481 <        if (myPotato + 3 >= MAXTAG) {
481 >              isDirectional = 1;
482 >                
483 >              sd->getQ( q );
484 >              sd->getJ( ji );
485  
486 <          // The potato was going to exceed the maximum value,
487 <          // so wrap this processor potato back to 0 (and block until
488 <          // node 0 says we can go:
489 <
490 <          MPI_Recv(&myPotato, 1, MPI_INT, 0, 0, MPI_COMM_WORLD, &istatus);
491 <          
492 <        }
493 <        which_atom = i;
494 <        local_index=-1;
495 <        for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) {
496 <          if (atoms[j]->getGlobalIndex() == which_atom) local_index = j;
497 <        }
391 <        if (local_index != -1) {
392 <        
393 <          atomTypeString = atoms[local_index]->getType();
394 <
395 <          atoms[local_index]->getPos(pos);
396 <          atoms[local_index]->getVel(vel);
397 <
398 <          atomData6[0] = pos[0];
399 <          atomData6[1] = pos[1];
400 <          atomData6[2] = pos[2];
401 <
402 <          atomData6[3] = vel[0];
403 <          atomData6[4] = vel[1];
404 <          atomData6[5] = vel[2];
405 <          
406 <          isDirectional = 0;
407 <
408 <          if( atoms[local_index]->isDirectional() ){
409 <
410 <            isDirectional = 1;
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 <            dAtom = (DirectionalAtom *)atoms[local_index];
413 <            dAtom->getQ( q );
499 >            // If we've survived to here, format the line:
500              
501 <            for (int j = 0; j < 6 ; j++)
502 <              atomData13[j] = atomData6[j];
503 <            
504 <            atomData13[6] = q[0];
505 <            atomData13[7] = q[1];
506 <            atomData13[8] = q[2];
507 <            atomData13[9] = q[3];
508 <
509 <            atomData13[10] = dAtom->getJx();
510 <            atomData13[11] = dAtom->getJy();
511 <            atomData13[12] = dAtom->getJz();
512 <          }
513 <
514 <        } else {
515 <          sprintf(painCave.errMsg,
516 <                  "Atom %d not found on processor %d\n",
517 <                  i, worldRank );
518 <          haveError= 1;
519 <          simError();
520 <        }
521 <
522 <        strncpy(MPIatomTypeString, atomTypeString, MINIBUFFERSIZE);
523 <
524 <        // null terminate the string before sending (just in case):
525 <        MPIatomTypeString[MINIBUFFERSIZE-1] = '\0';
526 <
527 <        MPI_Send(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, 0,
528 <                 myPotato, MPI_COMM_WORLD);
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 <        myPotato++;
445 <
446 <        MPI_Send(&isDirectional, 1, MPI_INT, 0,
447 <                 myPotato, MPI_COMM_WORLD);
448 <        
449 <        myPotato++;
450 <        
451 <        if (isDirectional) {
452 <
453 <          MPI_Send(atomData13, 13, MPI_DOUBLE, 0,
454 <                   myPotato, MPI_COMM_WORLD);
455 <          
456 <        } else {
457 <
458 <          MPI_Send(atomData6, 6, MPI_DOUBLE, 0,
459 <                   myPotato, MPI_COMM_WORLD);
460 <        }
461 <
462 <        myPotato++;      
543 >      currentIndex++;
544        }
464 –    }
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 <  }
557 <  
558 < #endif // is_mpi
473 < }
556 >    delete[] potatoes;
557 >    
558 >  } else {
559  
560 < void DumpWriter::writeFinal(double finalTime){
560 >    // worldRank != 0, so I'm a remote node.  
561  
562 <  char finalName[500];
478 <  ofstream finalOut;
562 >    // Set my magic potato to 0:
563  
564 <  const int BUFFERSIZE = 2000;
565 <  const int MINIBUFFERSIZE = 100;
566 <  char tempBuffer[BUFFERSIZE];
567 <  char writeLine[BUFFERSIZE];
564 >    myPotato = 0;
565 >    currentIndex = 0;
566 >    
567 >    for (i = 0 ; i < mpiSim->getNMolGlobal(); i++ ) {
568 >      
569 >      // Am I the node which has this integrableObject?
570 >      
571 >      if (MolToProcMap[i] == worldRank) {
572  
485 –  double q[4];
486 –  DirectionalAtom* dAtom;
487 –  Atom** atoms = entry_plug->atoms;
488 –  int i;
489 – #ifdef IS_MPI
490 –  
491 –  int *potatoes;
492 –  int myPotato;
573  
574 <  int nProc;
575 <  int j, which_node, done, which_atom, local_index;
576 <  double atomData6[6];
577 <  double atomData13[13];
578 <  int isDirectional;
579 <  char* atomTypeString;
580 <  char MPIatomTypeString[MINIBUFFERSIZE];
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 >        }
583  
584 < #else //is_mpi
585 <  int nAtoms = entry_plug->n_atoms;
586 < #endif //is_mpi
584 >          local_index = indexArray[currentIndex].first;        
585 >          integrableObjects = entry_plug->molecules[local_index].getIntegrableObjects();
586 >          
587 >          nCurObj = integrableObjects.size();
588 >                      
589 >          MPI_Send(&nCurObj, 1, MPI_INT, 0,
590 >                             myPotato, MPI_COMM_WORLD);
591 >          myPotato++;
592  
593 <  double pos[3], vel[3];
593 >          for( iter = integrableObjects.begin(); iter  != integrableObjects.end(); iter++){
594  
595 < #ifdef IS_MPI
596 <  if(worldRank == 0 ){
597 < #endif // is_mpi
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 >            sd = *iter;
606 >            
607 >            atomTypeString = sd->getType();
608  
609 <    strcpy( finalName, entry_plug->finalName );
609 >            sd->getPos(pos);
610 >            sd->getVel(vel);
611  
612 <    finalOut.open( finalName, ios::out | ios::trunc );
613 <    if( !finalOut ){
614 <      sprintf( painCave.errMsg,
517 <               "Could not open \"%s\" for final dump output.\n",
518 <               finalName );
519 <      painCave.isFatal = 1;
520 <      simError();
521 <    }
612 >            atomData[0] = pos[0];
613 >            atomData[1] = pos[1];
614 >            atomData[2] = pos[2];
615  
616 <    // finalOut.setf( ios::scientific );
616 >            atomData[3] = vel[0];
617 >            atomData[4] = vel[1];
618 >            atomData[5] = vel[2];
619 >              
620 >            isDirectional = 0;
621  
622 < #ifdef IS_MPI
526 <  }
622 >            if( sd->isDirectional() ){
623  
624 <  sprintf(checkPointMsg,"Opened file for final configuration\n");
625 <  MPIcheckPoint();
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 >                atomData[10] = ji[0];
636 >                atomData[11] = ji[1];
637 >                atomData[12] = ji[2];
638 >              }
639  
640 < #endif //is_mpi
640 >            
641 >            strncpy(MPIatomTypeString, atomTypeString, MINIBUFFERSIZE);
642  
643 +            // null terminate the string before sending (just in case):
644 +            MPIatomTypeString[MINIBUFFERSIZE-1] = '\0';
645  
646 < #ifndef IS_MPI
646 >            MPI_Send(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, 0,
647 >                             myPotato, MPI_COMM_WORLD);
648 >            
649 >            myPotato++;
650 >            
651 >            if (isDirectional) {
652  
653 <  finalOut << nAtoms << "\n";
653 >              MPI_Send(atomData, 13, MPI_DOUBLE, 0,
654 >                       myPotato, MPI_COMM_WORLD);
655 >              
656 >            } else {
657  
658 <  finalOut << finalTime << ";\t"
659 <           << entry_plug->Hmat[0][0] << "\t"
660 <           << entry_plug->Hmat[1][0] << "\t"
541 <           << entry_plug->Hmat[2][0] << ";\t"
658 >              MPI_Send(atomData, 6, MPI_DOUBLE, 0,
659 >                       myPotato, MPI_COMM_WORLD);
660 >            }
661  
662 <           << entry_plug->Hmat[0][1] << "\t"
544 <           << entry_plug->Hmat[1][1] << "\t"
545 <           << entry_plug->Hmat[2][1] << ";\t"
662 >            myPotato++;  
663  
547 –           << entry_plug->Hmat[0][2] << "\t"
548 –           << entry_plug->Hmat[1][2] << "\t"
549 –           << entry_plug->Hmat[2][2] << ";";
550 –
551 –  //write out additional parameters, such as chi and eta
552 –  finalOut << entry_plug->the_integrator->getAdditionalParameters();
553 –  finalOut << endl;
554 –
555 –  for( i=0; i<nAtoms; i++ ){
556 –
557 –    atoms[i]->getPos(pos);
558 –    atoms[i]->getVel(vel);
559 –
560 –    sprintf( tempBuffer,
561 –             "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
562 –             atoms[i]->getType(),
563 –             pos[0],
564 –             pos[1],
565 –             pos[2],
566 –             vel[0],
567 –             vel[1],
568 –             vel[2]);
569 –    strcpy( writeLine, tempBuffer );
570 –
571 –    if( atoms[i]->isDirectional() ){
572 –
573 –      dAtom = (DirectionalAtom *)atoms[i];
574 –      dAtom->getQ( q );
575 –
576 –      sprintf( tempBuffer,
577 –               "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
578 –               q[0],
579 –               q[1],
580 –               q[2],
581 –               q[3],
582 –               dAtom->getJx(),
583 –               dAtom->getJy(),
584 –               dAtom->getJz());
585 –      strcat( writeLine, tempBuffer );
586 –    }
587 –    else
588 –      strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
589 –
590 –    finalOut << writeLine;
591 –  }
592 –  finalOut.flush();
593 –  finalOut.close();
594 –
595 – #else // is_mpi
596 –
597 –  /* code to find maximum tag value */
598 –  int *tagub, flag, MAXTAG;
599 –  MPI_Attr_get(MPI_COMM_WORLD, MPI_TAG_UB, &tagub, &flag);
600 –  if (flag) {
601 –    MAXTAG = *tagub;
602 –  } else {
603 –    MAXTAG = 32767;
604 –  }  
605 –
606 –  int haveError;
607 –
608 –  MPI_Status istatus;
609 –  int *AtomToProcMap = mpiSim->getAtomToProcMap();
610 –
611 –  // write out header and node 0's coordinates
612 –
613 –  if( worldRank == 0 ){
614 –
615 –    // Node 0 needs a list of the magic potatoes for each processor;
616 –
617 –    nProc = mpiSim->getNumberProcessors();
618 –    potatoes = new int[nProc];
619 –
620 –    for (i = 0; i < nProc; i++)
621 –      potatoes[i] = 0;
622 –    
623 –    finalOut << mpiSim->getTotAtoms() << "\n";
624 –
625 –    finalOut << finalTime << ";\t"
626 –            << entry_plug->Hmat[0][0] << "\t"
627 –            << entry_plug->Hmat[1][0] << "\t"
628 –            << entry_plug->Hmat[2][0] << ";\t"
629 –
630 –            << entry_plug->Hmat[0][1] << "\t"
631 –            << entry_plug->Hmat[1][1] << "\t"
632 –            << entry_plug->Hmat[2][1] << ";\t"
633 –
634 –            << entry_plug->Hmat[0][2] << "\t"
635 –            << entry_plug->Hmat[1][2] << "\t"
636 –            << entry_plug->Hmat[2][2] << ";";
637 –
638 –    finalOut << entry_plug->the_integrator->getAdditionalParameters();
639 –    finalOut << endl;
640 –    finalOut.flush();
641 –
642 –    for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) {
643 –      
644 –      // Get the Node number which has this atom;
645 –      
646 –      which_node = AtomToProcMap[i];
647 –      
648 –      if (which_node != 0) {
649 –
650 –        if (potatoes[which_node] + 3 >= MAXTAG) {
651 –          // The potato was going to exceed the maximum value,
652 –          // so wrap this processor potato back to 0:        
653 –
654 –          potatoes[which_node] = 0;          
655 –          MPI_Send(0, 1, MPI_INT, which_node, 0, MPI_COMM_WORLD);
656 –          
657 –        }
658 –
659 –        myPotato = potatoes[which_node];        
660 –        
661 –        MPI_Recv(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, which_node,
662 –                 myPotato, MPI_COMM_WORLD, &istatus);
663 –        
664 –        strncpy(atomTypeString, MPIatomTypeString, MINIBUFFERSIZE);
665 –        
666 –        // Null terminate the atomTypeString just in case:
667 –
668 –        atomTypeString[strlen(atomTypeString) - 1] = '\0';
669 –
670 –        myPotato++;
671 –
672 –        MPI_Recv(&isDirectional, 1, MPI_INT, which_node,
673 –                 myPotato, MPI_COMM_WORLD, &istatus);
674 –              
675 –        myPotato++;
676 –
677 –        if (isDirectional) {          
678 –          MPI_Recv(atomData13, 13, MPI_DOUBLE, which_node,
679 –                   myPotato, MPI_COMM_WORLD, &istatus);
680 –        } else {
681 –          MPI_Recv(atomData6, 6, MPI_DOUBLE, which_node,
682 –                   myPotato, MPI_COMM_WORLD, &istatus);          
683 –        }
684 –        
685 –        myPotato++;
686 –        potatoes[which_node] = myPotato;
687 –
688 –      } else {
689 –        
690 –        haveError = 0;
691 –        which_atom = i;
692 –        local_index=-1;
693 –        
694 –        for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) {
695 –          if (atoms[j]->getGlobalIndex() == which_atom) local_index = j;
696 –        }
697 –        
698 –        if (local_index != -1) {
699 –          
700 –          atomTypeString = atoms[local_index]->getType();
701 –
702 –          atoms[local_index]->getPos(pos);
703 –          atoms[local_index]->getVel(vel);          
704 –
705 –          atomData6[0] = pos[0];
706 –          atomData6[1] = pos[1];
707 –          atomData6[2] = pos[2];
708 –
709 –          atomData6[3] = vel[0];
710 –          atomData6[4] = vel[1];
711 –          atomData6[5] = vel[2];
712 –          
713 –          isDirectional = 0;
714 –
715 –          if( atoms[local_index]->isDirectional() ){
716 –
717 –            isDirectional = 1;
718 –            
719 –            dAtom = (DirectionalAtom *)atoms[local_index];
720 –            dAtom->getQ( q );
721 –
722 –            for (int j = 0; j < 6 ; j++)
723 –              atomData13[j] = atomData6[j];            
724 –            
725 –            atomData13[6] = q[0];
726 –            atomData13[7] = q[1];
727 –            atomData13[8] = q[2];
728 –            atomData13[9] = q[3];
729 –            
730 –            atomData13[10] = dAtom->getJx();
731 –            atomData13[11] = dAtom->getJy();
732 –            atomData13[12] = dAtom->getJz();
664            }
734 –          
735 –        } else {
736 –          sprintf(painCave.errMsg,
737 –                  "Atom %d not found on processor %d\n",
738 –                  i, worldRank );
739 –          haveError= 1;
740 –          simError();
741 –        }
742 –        
743 –        if(haveError) DieDieDie();
744 –        
745 –        // If we've survived to here, format the line:
746 –        
747 –        if (!isDirectional) {
665  
666 <          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]);
666 >          currentIndex++;    
667            
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 –          strcat( writeLine, tempBuffer );
782 –          
668          }
669 <        
785 <        finalOut << writeLine;
786 <        finalOut.flush();
669 >      
670        }
788 –    }
671  
790 –    finalOut.flush();
672      sprintf( checkPointMsg,
673               "Sucessfully took a dump.\n");
674 <    delete[] potatoes;
794 <      
795 <    MPIcheckPoint();        
674 >    MPIcheckPoint();                
675      
797 –  } else {
798 –
799 –    // worldRank != 0, so I'm a remote node.  
800 –
801 –    // Set my magic potato to 0:
802 –
803 –    myPotato = 0;
804 –    
805 –    for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) {
806 –      
807 –      // Am I the node which has this atom?
808 –      
809 –      if (AtomToProcMap[i] == worldRank) {
810 –
811 –        if (myPotato + 3 >= MAXTAG) {
812 –
813 –          // The potato was going to exceed the maximum value,
814 –          // so wrap this processor potato back to 0 (and block until
815 –          // node 0 says we can go:
816 –
817 –          MPI_Recv(&myPotato, 1, MPI_INT, 0, 0, MPI_COMM_WORLD, &istatus);
818 –          
819 –        }
820 –        which_atom = i;  
821 –        local_index=-1;
822 –        for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) {
823 –          if (atoms[j]->getGlobalIndex() == which_atom) local_index = j;
824 –        }
825 –        if (local_index != -1) {
826 –        
827 –          atomTypeString = atoms[local_index]->getType();
828 –
829 –          atoms[local_index]->getPos(pos);
830 –          atoms[local_index]->getVel(vel);
831 –
832 –          atomData6[0] = pos[0];
833 –          atomData6[1] = pos[1];
834 –          atomData6[2] = pos[2];
835 –
836 –          atomData6[3] = vel[0];
837 –          atomData6[4] = vel[1];
838 –          atomData6[5] = vel[2];
839 –          
840 –          isDirectional = 0;
841 –
842 –          if( atoms[local_index]->isDirectional() ){
843 –
844 –            isDirectional = 1;
845 –            
846 –            dAtom = (DirectionalAtom *)atoms[local_index];
847 –            dAtom->getQ( q );
848 –            
849 –            for (int j = 0; j < 6 ; j++)
850 –              atomData13[j] = atomData6[j];
851 –            
852 –            atomData13[6] = q[0];
853 –            atomData13[7] = q[1];
854 –            atomData13[8] = q[2];
855 –            atomData13[9] = q[3];
856 –
857 –            atomData13[10] = dAtom->getJx();
858 –            atomData13[11] = dAtom->getJy();
859 –            atomData13[12] = dAtom->getJz();
860 –          }
861 –
862 –        } else {
863 –          sprintf(painCave.errMsg,
864 –                  "Atom %d not found on processor %d\n",
865 –                  i, worldRank );
866 –          haveError= 1;
867 –          simError();
868 –        }
869 –
870 –        strncpy(MPIatomTypeString, atomTypeString, MINIBUFFERSIZE);
871 –
872 –        // null terminate the string before sending (just in case):
873 –        MPIatomTypeString[MINIBUFFERSIZE-1] = '\0';
874 –
875 –        MPI_Send(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, 0,
876 –                 myPotato, MPI_COMM_WORLD);
877 –        
878 –        myPotato++;
879 –
880 –        MPI_Send(&isDirectional, 1, MPI_INT, 0,
881 –                 myPotato, MPI_COMM_WORLD);
882 –        
883 –        myPotato++;
884 –        
885 –        if (isDirectional) {
886 –
887 –          MPI_Send(atomData13, 13, MPI_DOUBLE, 0,
888 –                   myPotato, MPI_COMM_WORLD);
889 –          
890 –        } else {
891 –
892 –          MPI_Send(atomData6, 6, MPI_DOUBLE, 0,
893 –                   myPotato, MPI_COMM_WORLD);
894 –        }
895 –
896 –        myPotato++;      
897 –      }
676      }
677  
678 <    sprintf( checkPointMsg,
901 <             "Sucessfully took a dump.\n");
902 <    MPIcheckPoint();        
903 <    
904 <  }
678 >
679    
906 –  if( worldRank == 0 ) finalOut.close();
680   #endif // is_mpi
681   }
682  
910 –
911 –
683   #ifdef IS_MPI
684  
685   // a couple of functions to let us escape the write loop

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