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root/group/trunk/OOPSE/libmdtools/DumpWriter.cpp
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Comparing trunk/OOPSE/libmdtools/DumpWriter.cpp (file contents):
Revision 916 by gezelter, Fri Jan 9 20:29:32 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  
68 < void DumpWriter::writeDump( double currentTime ){
68 > #ifdef IS_MPI
69  
70 <  const int BUFFERSIZE = 2000;
71 <  const int MINIBUFFERSIZE = 100;
70 > /**
71 > * A hook function to load balancing
72 > */
73  
74 <  char tempBuffer[BUFFERSIZE];
75 <  char writeLine[BUFFERSIZE];
74 > void DumpWriter::update(){
75 >  sortByGlobalIndex();          
76 > }
77 >  
78 > /**
79 > * Auxiliary sorting function
80 > */
81 >
82 > bool indexSortingCriterion(const pair<int, int>& p1, const pair<int, int>& p2){
83 >  return p1.second < p2.second;
84 > }
85  
86 <  int i;
87 <
88 < #ifdef IS_MPI
86 > /**
87 > * Sorting the local index by global index
88 > */
89 >
90 > void DumpWriter::sortByGlobalIndex(){
91 >  Molecule* mols = entry_plug->molecules;  
92 >  indexArray.clear();
93    
94 <  int *potatoes;
95 <  int myPotato;
94 >  for(int i = 0; i < entry_plug->n_mol;i++)
95 >    indexArray.push_back(make_pair(i, mols[i].getGlobalIndex()));
96 >  
97 >  sort(indexArray.begin(), indexArray.end(), indexSortingCriterion);    
98 > }
99  
100 <  int nProc;
82 <  int j, which_node, done, which_atom, local_index;
83 <  double atomData6[6];
84 <  double atomData13[13];
85 <  int isDirectional;
86 <  char* atomTypeString;
87 <  char MPIatomTypeString[MINIBUFFERSIZE];
100 > #endif
101  
102 < #else //is_mpi
90 <  int nAtoms = entry_plug->n_atoms;
91 < #endif //is_mpi
102 > void DumpWriter::writeDump(double currentTime){
103  
104 <  double q[4];
105 <  DirectionalAtom* dAtom;
95 <  Atom** atoms = entry_plug->atoms;
96 <  double pos[3], vel[3];
104 >  ofstream finalOut;
105 >  vector<ofstream*> fileStreams;
106  
107 <  // write current frame to the eor file
107 > #ifdef IS_MPI
108 >  if(worldRank == 0 ){
109 > #endif    
110 >    finalOut.open( entry_plug->finalName, ios::out | ios::trunc );
111 >    if( !finalOut ){
112 >      sprintf( painCave.errMsg,
113 >               "Could not open \"%s\" for final dump output.\n",
114 >               entry_plug->finalName );
115 >      painCave.isFatal = 1;
116 >      simError();
117 >    }
118 > #ifdef IS_MPI
119 >  }
120 > #endif // is_mpi
121  
122 <  this->writeFinal( currentTime );
122 >  fileStreams.push_back(&finalOut);
123 >  fileStreams.push_back(&dumpFile);
124  
125 < #ifndef IS_MPI
125 >  writeFrame(fileStreams, currentTime);
126  
127 <  outFile << nAtoms << "\n";
127 > #ifdef IS_MPI
128 >  finalOut.close();
129 > #endif
130 >        
131 > }
132  
133 <  outFile << currentTime << ";\t"
107 <          << entry_plug->Hmat[0][0] << "\t"
108 <          << entry_plug->Hmat[1][0] << "\t"
109 <          << entry_plug->Hmat[2][0] << ";\t"
133 > void DumpWriter::writeFinal(double currentTime){
134  
135 <          << entry_plug->Hmat[0][1] << "\t"
136 <          << entry_plug->Hmat[1][1] << "\t"
113 <          << entry_plug->Hmat[2][1] << ";\t"
135 >  ofstream finalOut;
136 >  vector<ofstream*> fileStreams;
137  
138 <          << entry_plug->Hmat[0][2] << "\t"
139 <          << entry_plug->Hmat[1][2] << "\t"
140 <          << entry_plug->Hmat[2][2] << ";";
118 <  //write out additional parameters, such as chi and eta
119 <  outFile << entry_plug->the_integrator->getAdditionalParameters();
120 <  outFile << endl;
138 > #ifdef IS_MPI
139 >  if(worldRank == 0 ){
140 > #endif // is_mpi
141  
142 <  for( i=0; i<nAtoms; i++ ){
142 >    finalOut.open( entry_plug->finalName, ios::out | ios::trunc );
143  
144 <    atoms[i]->getPos(pos);
145 <    atoms[i]->getVel(vel);
144 >    if( !finalOut ){
145 >      sprintf( painCave.errMsg,
146 >               "Could not open \"%s\" for final dump output.\n",
147 >               entry_plug->finalName );
148 >      painCave.isFatal = 1;
149 >      simError();
150 >    }
151  
152 <    sprintf( tempBuffer,
153 <             "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
154 <             atoms[i]->getType(),
155 <             pos[0],
156 <             pos[1],
157 <             pos[2],
133 <             vel[0],
134 <             vel[1],
135 <             vel[2]);
136 <    strcpy( writeLine, tempBuffer );
152 > #ifdef IS_MPI
153 >  }
154 > #endif // is_mpi
155 >  
156 >  fileStreams.push_back(&finalOut);  
157 >  writeFrame(fileStreams, currentTime);
158  
159 <    if( atoms[i]->isDirectional() ){
159 > #ifdef IS_MPI
160 >  finalOut.close();
161 > #endif
162 >  
163 > }
164  
165 <      dAtom = (DirectionalAtom *)atoms[i];
141 <      dAtom->getQ( q );
165 > void DumpWriter::writeFrame( vector<ofstream*>& outFile, double currentTime ){
166  
167 <      sprintf( tempBuffer,
168 <               "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
145 <               q[0],
146 <               q[1],
147 <               q[2],
148 <               q[3],
149 <               dAtom->getJx(),
150 <               dAtom->getJy(),
151 <               dAtom->getJz());
152 <      strcat( writeLine, tempBuffer );
153 <    }
154 <    else
155 <      strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
167 >  const int BUFFERSIZE = 2000;
168 >  const int MINIBUFFERSIZE = 100;
169  
170 <    outFile << writeLine;
170 >  char tempBuffer[BUFFERSIZE];  
171 >  char writeLine[BUFFERSIZE];
172 >
173 >  int i, k;
174 >
175 > #ifdef IS_MPI
176 >  
177 >  /*********************************************************************
178 >   * Documentation?  You want DOCUMENTATION?
179 >   *
180 >   * Why all the potatoes below?  
181 >   *
182 >   * To make a long story short, the original version of DumpWriter
183 >   * worked in the most inefficient way possible.  Node 0 would
184 >   * poke each of the node for an individual atom's formatted data
185 >   * as node 0 worked its way down the global index. This was particularly
186 >   * inefficient since the method blocked all processors at every atom
187 >   * (and did it twice!).
188 >   *
189 >   * An intermediate version of DumpWriter could be described from Node
190 >   * zero's perspective as follows:
191 >   *
192 >   *  1) Have 100 of your friends stand in a circle.
193 >   *  2) When you say go, have all of them start tossing potatoes at
194 >   *     you (one at a time).
195 >   *  3) Catch the potatoes.
196 >   *
197 >   * It was an improvement, but MPI has buffers and caches that could
198 >   * best be described in this analogy as "potato nets", so there's no
199 >   * need to block the processors atom-by-atom.
200 >   *
201 >   * This new and improved DumpWriter works in an even more efficient
202 >   * way:
203 >   *
204 >   *  1) Have 100 of your friend stand in a circle.
205 >   *  2) When you say go, have them start tossing 5-pound bags of
206 >   *     potatoes at you.
207 >   *  3) Once you've caught a friend's bag of potatoes,
208 >   *     toss them a spud to let them know they can toss another bag.
209 >   *
210 >   * How's THAT for documentation?
211 >   *
212 >   *********************************************************************/
213 >
214 >  int *potatoes;
215 >  int myPotato;
216 >
217 >  int nProc;
218 >  int j, which_node, done, which_atom, local_index, currentIndex;
219 >  double atomData[13];
220 >  int isDirectional;
221 >  char* atomTypeString;
222 >  char MPIatomTypeString[MINIBUFFERSIZE];
223 >  int nObjects;
224 >  int msgLen; // the length of message actually recieved at master nodes
225 > #endif //is_mpi
226 >
227 >  double q[4], ji[3];
228 >  DirectionalAtom* dAtom;
229 >  double pos[3], vel[3];
230 >  int nTotObjects;
231 >  StuntDouble* sd;
232 >  char* molName;
233 >  vector<StuntDouble*> integrableObjects;
234 >  vector<StuntDouble*>::iterator iter;
235 >  nTotObjects = entry_plug->getTotIntegrableObjects();
236 > #ifndef IS_MPI
237 >  
238 >  for(k = 0; k < outFile.size(); k++){
239 >    *outFile[k] << nTotObjects << "\n";
240 >
241 >    *outFile[k] << currentTime << ";\t"
242 >               << entry_plug->Hmat[0][0] << "\t"
243 >                     << entry_plug->Hmat[1][0] << "\t"
244 >                     << entry_plug->Hmat[2][0] << ";\t"
245 >              
246 >               << entry_plug->Hmat[0][1] << "\t"
247 >                     << entry_plug->Hmat[1][1] << "\t"
248 >                     << entry_plug->Hmat[2][1] << ";\t"
249 >
250 >                     << entry_plug->Hmat[0][2] << "\t"
251 >                     << entry_plug->Hmat[1][2] << "\t"
252 >                     << entry_plug->Hmat[2][2] << ";";
253 >
254 >    //write out additional parameters, such as chi and eta
255 >    *outFile[k] << entry_plug->the_integrator->getAdditionalParameters() << endl;
256    }
257 <  outFile.flush();
257 >  
258 >  for( i=0; i< entry_plug->n_mol; i++ ){
259  
260 +    integrableObjects = entry_plug->molecules[i].getIntegrableObjects();
261 +    molName = (entry_plug->compStamps[entry_plug->molecules[i].getStampID()])->getID();
262 +    
263 +    for( iter = integrableObjects.begin();iter !=  integrableObjects.end(); ++iter){
264 +      sd = *iter;
265 +      sd->getPos(pos);
266 +      sd->getVel(vel);
267 +
268 +      sprintf( tempBuffer,
269 +             "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
270 +             sd->getType(),
271 +             pos[0],
272 +             pos[1],
273 +             pos[2],
274 +             vel[0],
275 +             vel[1],
276 +             vel[2]);
277 +      strcpy( writeLine, tempBuffer );
278 +
279 +      if( sd->isDirectional() ){
280 +
281 +        sd->getQ( q );
282 +        sd->getJ( ji );
283 +
284 +        sprintf( tempBuffer,
285 +               "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
286 +               q[0],
287 +               q[1],
288 +               q[2],
289 +               q[3],
290 +                 ji[0],
291 +                 ji[1],
292 +                 ji[2]);
293 +        strcat( writeLine, tempBuffer );
294 +      }
295 +      else
296 +        strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
297 +    
298 +      for(k = 0; k < outFile.size(); k++)
299 +        *outFile[k] << writeLine;      
300 +    }
301 +
302 + }
303 +
304   #else // is_mpi
305  
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) {
# Line 172 | Line 316 | void DumpWriter::writeDump( double currentTime ){
316    int haveError;
317  
318    MPI_Status istatus;
319 <  int *AtomToProcMap = mpiSim->getAtomToProcMap();
319 >  int nCurObj;
320 >  int *MolToProcMap = mpiSim->getMolToProcMap();
321  
322    // write out header and node 0's coordinates
323  
# Line 180 | Line 325 | void DumpWriter::writeDump( double currentTime ){
325  
326      // Node 0 needs a list of the magic potatoes for each processor;
327  
328 <    nProc = mpiSim->getNumberProcessors();
328 >    nProc = mpiSim->getNProcessors();
329      potatoes = new int[nProc];
330  
331 +    //write out the comment lines
332      for (i = 0; i < nProc; i++)
333        potatoes[i] = 0;
334      
335 <    outFile << mpiSim->getTotAtoms() << "\n";
335 >      for(k = 0; k < outFile.size(); k++){
336 >        *outFile[k] << nTotObjects << "\n";
337  
338 <    outFile << currentTime << ";\t"
339 <            << entry_plug->Hmat[0][0] << "\t"
340 <            << entry_plug->Hmat[1][0] << "\t"
341 <            << entry_plug->Hmat[2][0] << ";\t"
338 >        *outFile[k] << currentTime << ";\t"
339 >                         << entry_plug->Hmat[0][0] << "\t"
340 >                         << entry_plug->Hmat[1][0] << "\t"
341 >                         << entry_plug->Hmat[2][0] << ";\t"
342  
343 <            << entry_plug->Hmat[0][1] << "\t"
344 <            << entry_plug->Hmat[1][1] << "\t"
345 <            << entry_plug->Hmat[2][1] << ";\t"
343 >                         << entry_plug->Hmat[0][1] << "\t"
344 >                         << entry_plug->Hmat[1][1] << "\t"
345 >                         << entry_plug->Hmat[2][1] << ";\t"
346  
347 <            << entry_plug->Hmat[0][2] << "\t"
348 <            << entry_plug->Hmat[1][2] << "\t"
349 <            << entry_plug->Hmat[2][2] << ";";
347 >                         << entry_plug->Hmat[0][2] << "\t"
348 >                         << entry_plug->Hmat[1][2] << "\t"
349 >                         << entry_plug->Hmat[2][2] << ";";
350 >  
351 >        *outFile[k] << entry_plug->the_integrator->getAdditionalParameters() << endl;
352 >    }
353  
354 <    outFile << entry_plug->the_integrator->getAdditionalParameters();
205 <    outFile << endl;
206 <    outFile.flush();
354 >    currentIndex = 0;
355  
356 <    for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) {
356 >    for (i = 0 ; i < mpiSim->getNMolGlobal(); i++ ) {
357        
358        // Get the Node number which has this atom;
359        
360 <      which_node = AtomToProcMap[i];
360 >      which_node = MolToProcMap[i];
361        
362        if (which_node != 0) {
363 <
364 <        if (potatoes[which_node] + 3 >= MAXTAG) {
363 >        
364 >        if (potatoes[which_node] + 1 >= MAXTAG) {
365            // The potato was going to exceed the maximum value,
366            // so wrap this processor potato back to 0:        
367  
368            potatoes[which_node] = 0;          
369 <          MPI_Send(0, 1, MPI_INT, which_node, 0, MPI_COMM_WORLD);
369 >          MPI_Send(&potatoes[which_node], 1, MPI_INT, which_node, 0, MPI_COMM_WORLD);
370            
371          }
372  
373          myPotato = potatoes[which_node];        
226 –        
227 –        MPI_Recv(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, which_node,
228 –                 myPotato, MPI_COMM_WORLD, &istatus);
229 –        
230 –        strncpy(atomTypeString, MPIatomTypeString, MINIBUFFERSIZE);
231 –        
232 –        // Null terminate the atomTypeString just in case:
374  
375 <        atomTypeString[strlen(atomTypeString) - 1] = '\0';
376 <
236 <        myPotato++;
237 <
238 <        MPI_Recv(&isDirectional, 1, MPI_INT, which_node,
375 >        //recieve the number of integrableObject in current molecule
376 >        MPI_Recv(&nCurObj, 1, MPI_INT, which_node,
377                   myPotato, MPI_COMM_WORLD, &istatus);
240 –              
378          myPotato++;
242 –
243 –        if (isDirectional) {          
244 –          MPI_Recv(atomData13, 13, MPI_DOUBLE, which_node,
245 –                   myPotato, MPI_COMM_WORLD, &istatus);
246 –        } else {
247 –          MPI_Recv(atomData6, 6, MPI_DOUBLE, which_node,
248 –                   myPotato, MPI_COMM_WORLD, &istatus);          
249 –        }
379          
380 <        myPotato++;
252 <        potatoes[which_node] = myPotato;
380 >        for(int l = 0; l < nCurObj; l++){
381  
382 <      } else {
383 <        
384 <        haveError = 0;
257 <        which_atom = i;
258 <        local_index=-1;
259 <        
260 <        for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) {
261 <          if (atoms[j]->getGlobalIndex() == which_atom) local_index = j;
262 <        }
263 <        
264 <        if (local_index != -1) {
265 <          
266 <          atomTypeString = atoms[local_index]->getType();
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 <          atoms[local_index]->getPos(pos);
387 <          atoms[local_index]->getVel(vel);          
386 >            potatoes[which_node] = 0;          
387 >            MPI_Send(&potatoes[which_node], 1, MPI_INT, which_node, 0, MPI_COMM_WORLD);
388 >            
389 >          }
390  
391 <          atomData6[0] = pos[0];
392 <          atomData6[1] = pos[1];
273 <          atomData6[2] = pos[2];
391 >          MPI_Recv(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, which_node,
392 >          myPotato, MPI_COMM_WORLD, &istatus);
393  
394 <          atomData6[3] = vel[0];
276 <          atomData6[4] = vel[1];
277 <          atomData6[5] = vel[2];
278 <          
279 <          isDirectional = 0;
394 >          atomTypeString = MPIatomTypeString;
395  
396 <          if( atoms[local_index]->isDirectional() ){
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 );
412 <
413 <            for (int j = 0; j < 6 ; j++)
414 <              atomData13[j] = atomData6[j];            
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              
291 –            atomData13[6] = q[0];
292 –            atomData13[7] = q[1];
293 –            atomData13[8] = q[2];
294 –            atomData13[9] = q[3];
295 –            
296 –            atomData13[10] = dAtom->getJx();
297 –            atomData13[11] = dAtom->getJy();
298 –            atomData13[12] = dAtom->getJz();
444            }
445            
446 <        } else {
447 <          sprintf(painCave.errMsg,
303 <                  "Atom %d not found on processor %d\n",
304 <                  i, worldRank );
305 <          haveError= 1;
306 <          simError();
307 <        }
308 <        
309 <        if(haveError) DieDieDie();
310 <        
311 <        // If we've survived to here, format the line:
312 <        
313 <        if (!isDirectional) {
446 >          for(k = 0; k < outFile.size(); k++)
447 >            *outFile[k] << writeLine;            
448  
449 <          sprintf( tempBuffer,
450 <                   "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
317 <                   atomTypeString,
318 <                   atomData6[0],
319 <                   atomData6[1],
320 <                   atomData6[2],
321 <                   atomData6[3],
322 <                   atomData6[4],
323 <                   atomData6[5]);
324 <          
325 <          strcpy( writeLine, tempBuffer );
326 <          strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
449 >        }// end for(int l =0)
450 >        potatoes[which_node] = myPotato;
451  
328 –        } else {
329 –          
330 –          sprintf( tempBuffer,
331 –                   "%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",
332 –                   atomTypeString,
333 –                   atomData13[0],
334 –                   atomData13[1],
335 –                   atomData13[2],
336 –                   atomData13[3],
337 –                   atomData13[4],
338 –                   atomData13[5],
339 –                   atomData13[6],
340 –                   atomData13[7],
341 –                   atomData13[8],
342 –                   atomData13[9],
343 –                   atomData13[10],
344 –                   atomData13[11],
345 –                   atomData13[12]);
346 –          
347 –          strcat( writeLine, tempBuffer );
348 –          
349 –        }
350 –        
351 –        outFile << writeLine;
352 –        outFile.flush();
452        }
453 <    }
453 >      else {
454 >        
455 >        haveError = 0;
456 >        
457 >            local_index = indexArray[currentIndex].first;        
458  
459 <    outFile.flush();
357 <    sprintf( checkPointMsg,
358 <             "Sucessfully took a dump.\n");
359 <    MPIcheckPoint();        
360 <    
361 <  } else {
459 >        integrableObjects = (entry_plug->molecules[local_index]).getIntegrableObjects();
460  
461 <    // worldRank != 0, so I'm a remote node.  
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 <    // Set my magic potato to 0:
472 >            atomData[3] = vel[0];
473 >            atomData[4] = vel[1];
474 >            atomData[5] = vel[2];
475 >              
476 >            isDirectional = 0;
477  
478 <    myPotato = 0;
368 <    
369 <    for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) {
370 <      
371 <      // Am I the node which has this atom?
372 <      
373 <      if (AtomToProcMap[i] == worldRank) {
478 >            if( sd->isDirectional() ){
479  
480 <        if (myPotato + 3 >= MAXTAG) {
480 >              isDirectional = 1;
481 >                
482 >              sd->getQ( q );
483 >              sd->getJ( ji );
484  
485 <          // The potato was going to exceed the maximum value,
486 <          // so wrap this processor potato back to 0 (and block until
487 <          // node 0 says we can go:
488 <
489 <          MPI_Recv(&myPotato, 1, MPI_INT, 0, 0, MPI_COMM_WORLD, &istatus);
490 <          
491 <        }
492 <
493 <        local_index=-1;
494 <        for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) {
495 <          if (atoms[j]->getGlobalIndex() == which_atom) local_index = j;
496 <        }
389 <        if (local_index != -1) {
390 <        
391 <          atomTypeString = atoms[local_index]->getType();
392 <
393 <          atoms[local_index]->getPos(pos);
394 <          atoms[local_index]->getVel(vel);
395 <
396 <          atomData6[0] = pos[0];
397 <          atomData6[1] = pos[1];
398 <          atomData6[2] = pos[2];
399 <
400 <          atomData6[3] = vel[0];
401 <          atomData6[4] = vel[1];
402 <          atomData6[5] = vel[2];
403 <          
404 <          isDirectional = 0;
405 <
406 <          if( atoms[local_index]->isDirectional() ){
407 <
408 <            isDirectional = 1;
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 <            dAtom = (DirectionalAtom *)atoms[local_index];
411 <            dAtom->getQ( q );
498 >            // If we've survived to here, format the line:
499              
500 <            for (int j = 0; j < 6 ; j++)
501 <              atomData13[j] = atomData6[j];
502 <            
503 <            atomData13[6] = q[0];
504 <            atomData13[7] = q[1];
505 <            atomData13[8] = q[2];
506 <            atomData13[9] = q[3];
507 <
508 <            atomData13[10] = dAtom->getJx();
509 <            atomData13[11] = dAtom->getJy();
510 <            atomData13[12] = dAtom->getJz();
511 <          }
512 <
513 <        } else {
514 <          sprintf(painCave.errMsg,
515 <                  "Atom %d not found on processor %d\n",
516 <                  i, worldRank );
517 <          haveError= 1;
518 <          simError();
519 <        }
520 <
521 <        strncpy(MPIatomTypeString, atomTypeString, MINIBUFFERSIZE);
522 <
523 <        // null terminate the string before sending (just in case):
524 <        MPIatomTypeString[MINIBUFFERSIZE-1] = '\0';
525 <
526 <        MPI_Send(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, 0,
527 <                 myPotato, MPI_COMM_WORLD);
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 <        myPotato++;
443 <
444 <        MPI_Send(&isDirectional, 1, MPI_INT, 0,
445 <                 myPotato, MPI_COMM_WORLD);
446 <        
447 <        myPotato++;
448 <        
449 <        if (isDirectional) {
450 <
451 <          MPI_Send(atomData13, 13, MPI_DOUBLE, 0,
452 <                   myPotato, MPI_COMM_WORLD);
453 <          
454 <        } else {
455 <
456 <          MPI_Send(atomData6, 6, MPI_DOUBLE, 0,
457 <                   myPotato, MPI_COMM_WORLD);
458 <        }
459 <
460 <        myPotato++;      
542 >      currentIndex++;
543        }
462 –    }
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 <  }
556 <  
557 < #endif // is_mpi
471 < }
555 >    delete[] potatoes;
556 >    
557 >  } else {
558  
559 < void DumpWriter::writeFinal(double finalTime){
559 >    // worldRank != 0, so I'm a remote node.  
560  
561 <  char finalName[500];
476 <  ofstream finalOut;
561 >    // Set my magic potato to 0:
562  
563 <  const int BUFFERSIZE = 2000;
564 <  const int MINIBUFFERSIZE = 100;
565 <  char tempBuffer[BUFFERSIZE];
566 <  char writeLine[BUFFERSIZE];
563 >    myPotato = 0;
564 >    currentIndex = 0;
565 >    
566 >    for (i = 0 ; i < mpiSim->getNMolGlobal(); i++ ) {
567 >      
568 >      // Am I the node which has this integrableObject?
569 >      
570 >      if (MolToProcMap[i] == worldRank) {
571  
483 –  double q[4];
484 –  DirectionalAtom* dAtom;
485 –  Atom** atoms = entry_plug->atoms;
486 –  int i;
487 – #ifdef IS_MPI
488 –  
489 –  int *potatoes;
490 –  int myPotato;
572  
573 <  int nProc;
574 <  int j, which_node, done, which_atom, local_index;
575 <  double atomData6[6];
576 <  double atomData13[13];
577 <  int isDirectional;
578 <  char* atomTypeString;
579 <  char MPIatomTypeString[MINIBUFFERSIZE];
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 >        }
582  
583 < #else //is_mpi
584 <  int nAtoms = entry_plug->n_atoms;
585 < #endif //is_mpi
583 >          local_index = indexArray[currentIndex].first;        
584 >          integrableObjects = entry_plug->molecules[local_index].getIntegrableObjects();
585 >          
586 >          nCurObj = integrableObjects.size();
587 >                      
588 >          MPI_Send(&nCurObj, 1, MPI_INT, 0,
589 >                             myPotato, MPI_COMM_WORLD);
590 >          myPotato++;
591  
592 <  double pos[3], vel[3];
592 >          for( iter = integrableObjects.begin(); iter  != integrableObjects.end(); iter++){
593  
594 < #ifdef IS_MPI
595 <  if(worldRank == 0 ){
596 < #endif // is_mpi
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 >            sd = *iter;
605 >            
606 >            atomTypeString = sd->getType();
607  
608 <    strcpy( finalName, entry_plug->finalName );
608 >            sd->getPos(pos);
609 >            sd->getVel(vel);
610  
611 <    finalOut.open( finalName, ios::out | ios::trunc );
612 <    if( !finalOut ){
613 <      sprintf( painCave.errMsg,
515 <               "Could not open \"%s\" for final dump output.\n",
516 <               finalName );
517 <      painCave.isFatal = 1;
518 <      simError();
519 <    }
611 >            atomData[0] = pos[0];
612 >            atomData[1] = pos[1];
613 >            atomData[2] = pos[2];
614  
615 <    // finalOut.setf( ios::scientific );
615 >            atomData[3] = vel[0];
616 >            atomData[4] = vel[1];
617 >            atomData[5] = vel[2];
618 >              
619 >            isDirectional = 0;
620  
621 < #ifdef IS_MPI
524 <  }
621 >            if( sd->isDirectional() ){
622  
623 <  sprintf(checkPointMsg,"Opened file for final configuration\n");
624 <  MPIcheckPoint();
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 >                atomData[10] = ji[0];
635 >                atomData[11] = ji[1];
636 >                atomData[12] = ji[2];
637 >              }
638  
639 < #endif //is_mpi
639 >            
640 >            strncpy(MPIatomTypeString, atomTypeString, MINIBUFFERSIZE);
641  
642 +            // null terminate the string before sending (just in case):
643 +            MPIatomTypeString[MINIBUFFERSIZE-1] = '\0';
644  
645 < #ifndef IS_MPI
645 >            MPI_Send(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, 0,
646 >                             myPotato, MPI_COMM_WORLD);
647 >            
648 >            myPotato++;
649 >            
650 >            if (isDirectional) {
651  
652 <  finalOut << nAtoms << "\n";
652 >              MPI_Send(atomData, 13, MPI_DOUBLE, 0,
653 >                       myPotato, MPI_COMM_WORLD);
654 >              
655 >            } else {
656  
657 <  finalOut << finalTime << ";\t"
658 <           << entry_plug->Hmat[0][0] << "\t"
659 <           << entry_plug->Hmat[1][0] << "\t"
539 <           << entry_plug->Hmat[2][0] << ";\t"
540 <
541 <           << entry_plug->Hmat[0][1] << "\t"
542 <           << entry_plug->Hmat[1][1] << "\t"
543 <           << entry_plug->Hmat[2][1] << ";\t"
544 <
545 <           << entry_plug->Hmat[0][2] << "\t"
546 <           << entry_plug->Hmat[1][2] << "\t"
547 <           << entry_plug->Hmat[2][2] << ";";
548 <
549 <  //write out additional parameters, such as chi and eta
550 <  finalOut << entry_plug->the_integrator->getAdditionalParameters();
551 <  finalOut << endl;
552 <
553 <  for( i=0; i<nAtoms; i++ ){
554 <
555 <    atoms[i]->getPos(pos);
556 <    atoms[i]->getVel(vel);
557 <
558 <    sprintf( tempBuffer,
559 <             "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
560 <             atoms[i]->getType(),
561 <             pos[0],
562 <             pos[1],
563 <             pos[2],
564 <             vel[0],
565 <             vel[1],
566 <             vel[2]);
567 <    strcpy( writeLine, tempBuffer );
568 <
569 <    if( atoms[i]->isDirectional() ){
570 <
571 <      dAtom = (DirectionalAtom *)atoms[i];
572 <      dAtom->getQ( q );
573 <
574 <      sprintf( tempBuffer,
575 <               "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
576 <               q[0],
577 <               q[1],
578 <               q[2],
579 <               q[3],
580 <               dAtom->getJx(),
581 <               dAtom->getJy(),
582 <               dAtom->getJz());
583 <      strcat( writeLine, tempBuffer );
584 <    }
585 <    else
586 <      strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
587 <
588 <    finalOut << writeLine;
589 <  }
590 <  finalOut.flush();
591 <  finalOut.close();
592 <
593 < #else // is_mpi
594 <
595 <  /* code to find maximum tag value */
596 <  int *tagub, flag, MAXTAG;
597 <  MPI_Attr_get(MPI_COMM_WORLD, MPI_TAG_UB, &tagub, &flag);
598 <  if (flag) {
599 <    MAXTAG = *tagub;
600 <  } else {
601 <    MAXTAG = 32767;
602 <  }  
603 <
604 <  int haveError;
605 <
606 <  MPI_Status istatus;
607 <  int *AtomToProcMap = mpiSim->getAtomToProcMap();
657 >              MPI_Send(atomData, 6, MPI_DOUBLE, 0,
658 >                       myPotato, MPI_COMM_WORLD);
659 >            }
660  
661 <  // write out header and node 0's coordinates
661 >            myPotato++;  
662  
611 –  if( worldRank == 0 ){
612 –
613 –    // Node 0 needs a list of the magic potatoes for each processor;
614 –
615 –    nProc = mpiSim->getNumberProcessors();
616 –    potatoes = new int[nProc];
617 –
618 –    for (i = 0; i < nProc; i++)
619 –      potatoes[i] = 0;
620 –    
621 –    finalOut << mpiSim->getTotAtoms() << "\n";
622 –
623 –    finalOut << finalTime << ";\t"
624 –            << entry_plug->Hmat[0][0] << "\t"
625 –            << entry_plug->Hmat[1][0] << "\t"
626 –            << entry_plug->Hmat[2][0] << ";\t"
627 –
628 –            << entry_plug->Hmat[0][1] << "\t"
629 –            << entry_plug->Hmat[1][1] << "\t"
630 –            << entry_plug->Hmat[2][1] << ";\t"
631 –
632 –            << entry_plug->Hmat[0][2] << "\t"
633 –            << entry_plug->Hmat[1][2] << "\t"
634 –            << entry_plug->Hmat[2][2] << ";";
635 –
636 –    finalOut << entry_plug->the_integrator->getAdditionalParameters();
637 –    finalOut << endl;
638 –    finalOut.flush();
639 –
640 –    for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) {
641 –      
642 –      // Get the Node number which has this atom;
643 –      
644 –      which_node = AtomToProcMap[i];
645 –      
646 –      if (which_node != 0) {
647 –
648 –        if (potatoes[which_node] + 3 >= MAXTAG) {
649 –          // The potato was going to exceed the maximum value,
650 –          // so wrap this processor potato back to 0:        
651 –
652 –          potatoes[which_node] = 0;          
653 –          MPI_Send(0, 1, MPI_INT, which_node, 0, MPI_COMM_WORLD);
654 –          
655 –        }
656 –
657 –        myPotato = potatoes[which_node];        
658 –        
659 –        MPI_Recv(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, which_node,
660 –                 myPotato, MPI_COMM_WORLD, &istatus);
661 –        
662 –        strncpy(atomTypeString, MPIatomTypeString, MINIBUFFERSIZE);
663 –        
664 –        // Null terminate the atomTypeString just in case:
665 –
666 –        atomTypeString[strlen(atomTypeString) - 1] = '\0';
667 –
668 –        myPotato++;
669 –
670 –        MPI_Recv(&isDirectional, 1, MPI_INT, which_node,
671 –                 myPotato, MPI_COMM_WORLD, &istatus);
672 –              
673 –        myPotato++;
674 –
675 –        if (isDirectional) {          
676 –          MPI_Recv(atomData13, 13, MPI_DOUBLE, which_node,
677 –                   myPotato, MPI_COMM_WORLD, &istatus);
678 –        } else {
679 –          MPI_Recv(atomData6, 6, MPI_DOUBLE, which_node,
680 –                   myPotato, MPI_COMM_WORLD, &istatus);          
681 –        }
682 –        
683 –        myPotato++;
684 –        potatoes[which_node] = myPotato;
685 –
686 –      } else {
687 –        
688 –        haveError = 0;
689 –        which_atom = i;
690 –        local_index=-1;
691 –        
692 –        for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) {
693 –          if (atoms[j]->getGlobalIndex() == which_atom) local_index = j;
694 –        }
695 –        
696 –        if (local_index != -1) {
697 –          
698 –          atomTypeString = atoms[local_index]->getType();
699 –
700 –          atoms[local_index]->getPos(pos);
701 –          atoms[local_index]->getVel(vel);          
702 –
703 –          atomData6[0] = pos[0];
704 –          atomData6[1] = pos[1];
705 –          atomData6[2] = pos[2];
706 –
707 –          atomData6[3] = vel[0];
708 –          atomData6[4] = vel[1];
709 –          atomData6[5] = vel[2];
710 –          
711 –          isDirectional = 0;
712 –
713 –          if( atoms[local_index]->isDirectional() ){
714 –
715 –            isDirectional = 1;
716 –            
717 –            dAtom = (DirectionalAtom *)atoms[local_index];
718 –            dAtom->getQ( q );
719 –
720 –            for (int j = 0; j < 6 ; j++)
721 –              atomData13[j] = atomData6[j];            
722 –            
723 –            atomData13[6] = q[0];
724 –            atomData13[7] = q[1];
725 –            atomData13[8] = q[2];
726 –            atomData13[9] = q[3];
727 –            
728 –            atomData13[10] = dAtom->getJx();
729 –            atomData13[11] = dAtom->getJy();
730 –            atomData13[12] = dAtom->getJz();
663            }
732 –          
733 –        } else {
734 –          sprintf(painCave.errMsg,
735 –                  "Atom %d not found on processor %d\n",
736 –                  i, worldRank );
737 –          haveError= 1;
738 –          simError();
739 –        }
740 –        
741 –        if(haveError) DieDieDie();
742 –        
743 –        // If we've survived to here, format the line:
744 –        
745 –        if (!isDirectional) {
664  
665 <          sprintf( tempBuffer,
748 <                   "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
749 <                   atomTypeString,
750 <                   atomData6[0],
751 <                   atomData6[1],
752 <                   atomData6[2],
753 <                   atomData6[3],
754 <                   atomData6[4],
755 <                   atomData6[5]);
665 >          currentIndex++;    
666            
757 –          strcpy( writeLine, tempBuffer );
758 –          strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
759 –
760 –        } else {
761 –          
762 –          sprintf( tempBuffer,
763 –                   "%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",
764 –                   atomTypeString,
765 –                   atomData13[0],
766 –                   atomData13[1],
767 –                   atomData13[2],
768 –                   atomData13[3],
769 –                   atomData13[4],
770 –                   atomData13[5],
771 –                   atomData13[6],
772 –                   atomData13[7],
773 –                   atomData13[8],
774 –                   atomData13[9],
775 –                   atomData13[10],
776 –                   atomData13[11],
777 –                   atomData13[12]);
778 –          
779 –          strcat( writeLine, tempBuffer );
780 –          
667          }
668 <        
783 <        finalOut << writeLine;
784 <        finalOut.flush();
668 >      
669        }
786 –    }
670  
788 –    finalOut.flush();
671      sprintf( checkPointMsg,
672               "Sucessfully took a dump.\n");
673 <    MPIcheckPoint();        
673 >    MPIcheckPoint();                
674      
793 –  } else {
794 –
795 –    // worldRank != 0, so I'm a remote node.  
796 –
797 –    // Set my magic potato to 0:
798 –
799 –    myPotato = 0;
800 –    
801 –    for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) {
802 –      
803 –      // Am I the node which has this atom?
804 –      
805 –      if (AtomToProcMap[i] == worldRank) {
806 –
807 –        if (myPotato + 3 >= MAXTAG) {
808 –
809 –          // The potato was going to exceed the maximum value,
810 –          // so wrap this processor potato back to 0 (and block until
811 –          // node 0 says we can go:
812 –
813 –          MPI_Recv(&myPotato, 1, MPI_INT, 0, 0, MPI_COMM_WORLD, &istatus);
814 –          
815 –        }
816 –
817 –        local_index=-1;
818 –        for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) {
819 –          if (atoms[j]->getGlobalIndex() == which_atom) local_index = j;
820 –        }
821 –        if (local_index != -1) {
822 –        
823 –          atomTypeString = atoms[local_index]->getType();
824 –
825 –          atoms[local_index]->getPos(pos);
826 –          atoms[local_index]->getVel(vel);
827 –
828 –          atomData6[0] = pos[0];
829 –          atomData6[1] = pos[1];
830 –          atomData6[2] = pos[2];
831 –
832 –          atomData6[3] = vel[0];
833 –          atomData6[4] = vel[1];
834 –          atomData6[5] = vel[2];
835 –          
836 –          isDirectional = 0;
837 –
838 –          if( atoms[local_index]->isDirectional() ){
839 –
840 –            isDirectional = 1;
841 –            
842 –            dAtom = (DirectionalAtom *)atoms[local_index];
843 –            dAtom->getQ( q );
844 –            
845 –            for (int j = 0; j < 6 ; j++)
846 –              atomData13[j] = atomData6[j];
847 –            
848 –            atomData13[6] = q[0];
849 –            atomData13[7] = q[1];
850 –            atomData13[8] = q[2];
851 –            atomData13[9] = q[3];
852 –
853 –            atomData13[10] = dAtom->getJx();
854 –            atomData13[11] = dAtom->getJy();
855 –            atomData13[12] = dAtom->getJz();
856 –          }
857 –
858 –        } else {
859 –          sprintf(painCave.errMsg,
860 –                  "Atom %d not found on processor %d\n",
861 –                  i, worldRank );
862 –          haveError= 1;
863 –          simError();
864 –        }
865 –
866 –        strncpy(MPIatomTypeString, atomTypeString, MINIBUFFERSIZE);
867 –
868 –        // null terminate the string before sending (just in case):
869 –        MPIatomTypeString[MINIBUFFERSIZE-1] = '\0';
870 –
871 –        MPI_Send(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, 0,
872 –                 myPotato, MPI_COMM_WORLD);
873 –        
874 –        myPotato++;
875 –
876 –        MPI_Send(&isDirectional, 1, MPI_INT, 0,
877 –                 myPotato, MPI_COMM_WORLD);
878 –        
879 –        myPotato++;
880 –        
881 –        if (isDirectional) {
882 –
883 –          MPI_Send(atomData13, 13, MPI_DOUBLE, 0,
884 –                   myPotato, MPI_COMM_WORLD);
885 –          
886 –        } else {
887 –
888 –          MPI_Send(atomData6, 6, MPI_DOUBLE, 0,
889 –                   myPotato, MPI_COMM_WORLD);
890 –        }
891 –
892 –        myPotato++;      
893 –      }
675      }
676  
677 <    sprintf( checkPointMsg,
897 <             "Sucessfully took a dump.\n");
898 <    MPIcheckPoint();        
899 <    
900 <  }
677 >
678    
902 –  if( worldRank == 0 ) finalOut.close();
679   #endif // is_mpi
680   }
681  
906 –
907 –
682   #ifdef IS_MPI
683  
684   // a couple of functions to let us escape the write loop

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