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root/group/trunk/OOPSE/libmdtools/DumpWriter.cpp
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Comparing trunk/OOPSE/libmdtools/DumpWriter.cpp (file contents):
Revision 907 by gezelter, Thu Jan 8 17:40:56 2004 UTC vs.
Revision 1129 by tim, Thu Apr 22 03:29:30 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 = 10;
168 >  const int MINIBUFFERSIZE = 100;
169  
170 <  char tempBuffer[BUFFERSIZE];
170 >  char tempBuffer[BUFFERSIZE];  
171    char writeLine[BUFFERSIZE];
172  
173 <  int i;
173 >  int i, k;
174 >
175   #ifdef IS_MPI
176 <  int j, which_node, done, which_atom, local_index;
177 <  double atomTransData[6];
178 <  double atomOrientData[7];
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 atomData6[6];
220 >  double atomData13[13];
221    int isDirectional;
222    char* atomTypeString;
223 <  int me;
224 <  int atomTypeTag;
83 <  int atomIsDirectionalTag;
84 <  int atomTransDataTag;
85 <  int atomOrientDataTag;
86 < #else //is_mpi
87 <  int nAtoms = entry_plug->n_atoms;
223 >  char MPIatomTypeString[MINIBUFFERSIZE];
224 >  int nObjects;
225   #endif //is_mpi
226  
227 <  double q[4];
227 >  double q[4], ji[3];
228    DirectionalAtom* dAtom;
92 –  Atom** atoms = entry_plug->atoms;
229    double pos[3], vel[3];
230 <
231 <  // write current frame to the eor file
232 <
233 <  this->writeFinal( currentTime );
234 <
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 << nAtoms << "\n";
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 <  outFile << currentTime << ";\t"
251 <          << entry_plug->Hmat[0][0] << "\t"
252 <          << entry_plug->Hmat[1][0] << "\t"
106 <          << entry_plug->Hmat[2][0] << ";\t"
250 >                     << entry_plug->Hmat[0][2] << "\t"
251 >                     << entry_plug->Hmat[1][2] << "\t"
252 >                     << entry_plug->Hmat[2][2] << ";";
253  
254 <          << entry_plug->Hmat[0][1] << "\t"
255 <          << entry_plug->Hmat[1][1] << "\t"
256 <          << entry_plug->Hmat[2][1] << ";\t"
254 >    //write out additional parameters, such as chi and eta
255 >    *outFile[k] << entry_plug->the_integrator->getAdditionalParameters() << endl;
256 >  }
257 >  
258 >  for( i=0; i< entry_plug->n_mol; i++ ){
259  
260 <          << entry_plug->Hmat[0][2] << "\t"
261 <          << entry_plug->Hmat[1][2] << "\t"
262 <          << entry_plug->Hmat[2][2] << ";";
263 <  //write out additional parameters, such as chi and eta
264 <  outFile << entry_plug->the_integrator->getAdditionalParameters();
265 <  outFile << endl;
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 <  for( i=0; i<nAtoms; i++ ){
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 <    atoms[i]->getPos(pos);
122 <    atoms[i]->getVel(vel);
279 >      if( sd->isDirectional() ){
280  
281 <    sprintf( tempBuffer,
282 <             "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
126 <             atoms[i]->getType(),
127 <             pos[0],
128 <             pos[1],
129 <             pos[2],
130 <             vel[0],
131 <             vel[1],
132 <             vel[2]);
133 <    strcpy( writeLine, tempBuffer );
281 >        sd->getQ( q );
282 >        sd->getJ( ji );
283  
284 <    if( atoms[i]->isDirectional() ){
285 <
286 <      dAtom = (DirectionalAtom *)atoms[i];
287 <      dAtom->getQ( q );
288 <
289 <      sprintf( tempBuffer,
290 <               "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
291 <               q[0],
292 <               q[1],
293 <               q[2],
294 <               q[3],
295 <               dAtom->getJx(),
296 <               dAtom->getJy(),
148 <               dAtom->getJz());
149 <      strcat( writeLine, tempBuffer );
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      }
151 –    else
152 –      strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
298  
299 <    outFile << writeLine;
300 <  }
301 <  outFile.flush();
299 >    
300 >    for(k = 0; k < outFile.size(); k++)
301 >      *outFile[k] << writeLine;
302 > }
303  
304   #else // is_mpi
305  
306 <  // first thing first, suspend fatalities.
307 <  painCave.isEventLoop = 1;
306 >  /* code to find maximum tag value */
307 >  
308 >  int *tagub, flag, MAXTAG;
309 >  MPI_Attr_get(MPI_COMM_WORLD, MPI_TAG_UB, &tagub, &flag);
310 >  if (flag) {
311 >    MAXTAG = *tagub;
312 >  } else {
313 >    MAXTAG = 32767;
314 >  }  
315  
163 –  int myStatus; // 1 = wakeup & success; 0 = error; -1 = AllDone
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  
324    if( worldRank == 0 ){
172 –    outFile << mpiSim->getTotAtoms() << "\n";
325  
326 <    outFile << currentTime << ";\t"
175 <            << entry_plug->Hmat[0][0] << "\t"
176 <            << entry_plug->Hmat[1][0] << "\t"
177 <            << entry_plug->Hmat[2][0] << ";\t"
326 >    // Node 0 needs a list of the magic potatoes for each processor;
327  
328 <            << entry_plug->Hmat[0][1] << "\t"
329 <            << entry_plug->Hmat[1][1] << "\t"
181 <            << entry_plug->Hmat[2][1] << ";\t"
328 >    nProc = mpiSim->getNumberProcessors();
329 >    potatoes = new int[nProc];
330  
331 <            << entry_plug->Hmat[0][2] << "\t"
332 <            << entry_plug->Hmat[1][2] << "\t"
333 <            << entry_plug->Hmat[2][2] << ";";
331 >    //write out the comment lines
332 >    for (i = 0; i < nProc; i++)
333 >      potatoes[i] = 0;
334 >    
335 >      for(k = 0; k < outFile.size(); k++){
336 >        *outFile[k] << nTotObjects << "\n";
337  
338 <    outFile << entry_plug->the_integrator->getAdditionalParameters();
339 <    outFile << endl;
340 <    outFile.flush();
341 <    for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) {
191 <      // Get the Node number which has this atom;
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 <      which_node = AtomToProcMap[i];
343 >                         << entry_plug->Hmat[0][1] << "\t"
344 >                         << entry_plug->Hmat[1][1] << "\t"
345 >                         << entry_plug->Hmat[2][1] << ";\t"
346  
347 <      if (which_node != 0) {
348 <        
349 <        atomTypeTag          = 4*i;
350 <        atomIsDirectionalTag = 4*i + 1;
351 <        atomTransDataTag     = 4*i + 2;
352 <        atomOrientDataTag    = 4*i + 3;
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 <        MPI_Recv(atomTypeString, MINIBUFFERSIZE, MPI_CHAR, which_node,
203 <                 atomTypeTag, MPI_COMM_WORLD, &istatus);
204 <        
205 <        MPI_Recv(&isDirectional, 1, MPI_INT, which_node,
206 <                 atomIsDirectionalTag, MPI_COMM_WORLD, &istatus);
207 <        
208 <        MPI_Recv(atomTransData, 6, MPI_DOUBLE, which_node,
209 <                 atomTransDataTag, MPI_COMM_WORLD, &istatus);
354 >    currentIndex = 0;
355  
356 <        if (isDirectional) {
357 <
358 <          MPI_Recv(atomOrientData, 7, MPI_DOUBLE, which_node,
359 <                   atomOrientDataTag, MPI_COMM_WORLD, &istatus);
360 <
361 <        }
362 <
218 <      } else {
356 >    for (i = 0 ; i < mpiSim->getTotNmol(); i++ ) {
357 >      
358 >      // Get the Node number which has this atom;
359 >      
360 >      which_node = MolToProcMap[i];
361 >      
362 >      if (which_node != 0) {
363          
364 <        haveError = 0;
365 <        which_atom = i;
366 <        local_index=-1;
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 <        for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) {
369 <          if (atoms[j]->getGlobalIndex() == which_atom) local_index = j;
368 >          potatoes[which_node] = 0;          
369 >          MPI_Send(&potatoes[which_node], 1, MPI_INT, which_node, 0, MPI_COMM_WORLD);
370 >          
371          }
372  
373 <        if (local_index != -1) {
373 >        myPotato = potatoes[which_node];        
374  
375 <          atomTypeString = atoms[local_index]->getType();
375 >        //recieve the number of integrableObject in current molecule
376 >        MPI_Recv(&nCurObj, 1, MPI_INT, which_node,
377 >                 myPotato, MPI_COMM_WORLD, &istatus);
378 >        myPotato++;
379 >        
380 >        for(int l = 0; l < nCurObj; l++){
381  
382 <          atoms[local_index]->getPos(pos);
383 <          atoms[local_index]->getVel(vel);
382 >          if (potatoes[which_node] + 3 >= MAXTAG) {
383 >            // The potato was going to exceed the maximum value,
384 >            // so wrap this processor potato back to 0:        
385  
386 <          atomTransData[0] = pos[0];
387 <          atomTransData[1] = pos[1];
237 <          atomTransData[2] = pos[2];
238 <
239 <          atomTransData[3] = vel[0];
240 <          atomTransData[4] = vel[1];
241 <          atomTransData[5] = vel[2];
242 <          
243 <          isDirectional = 0;
244 <
245 <          if( atoms[local_index]->isDirectional() ){
246 <
247 <            isDirectional = 1;
386 >            potatoes[which_node] = 0;          
387 >            MPI_Send(&potatoes[which_node], 1, MPI_INT, which_node, 0, MPI_COMM_WORLD);
388              
249 –            dAtom = (DirectionalAtom *)atoms[local_index];
250 –            dAtom->getQ( q );
251 –            
252 –            atomOrientData[0] = q[0];
253 –            atomOrientData[1] = q[1];
254 –            atomOrientData[2] = q[2];
255 –            atomOrientData[3] = q[3];
256 –
257 –            atomOrientData[4] = dAtom->getJx();
258 –            atomOrientData[5] = dAtom->getJy();
259 –            atomOrientData[6] = dAtom->getJz();
389            }
390  
391 <        } else {
392 <          sprintf(painCave.errMsg,
264 <                  "Atom %d not found on processor %d\n",
265 <                  i, worldRank );
266 <          haveError= 1;
267 <          simError();
268 <        }
391 >          MPI_Recv(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, which_node,
392 >          myPotato, MPI_COMM_WORLD, &istatus);
393  
394 <        if(haveError) DieDieDie();
271 <                              
272 <        // If we've survived to here, format the line:
273 <        
274 <        sprintf( tempBuffer,
275 <                 "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
276 <                 atomTypeString,
277 <                 atomTransData[0],
278 <                 atomTransData[1],
279 <                 atomTransData[2],
280 <                 atomTransData[3],
281 <                 atomTransData[4],
282 <                 atomTransData[5]);
394 >          atomTypeString = MPIatomTypeString;
395  
396 <        strcpy( writeLine, tempBuffer );
396 >          myPotato++;
397  
398 <        if (isDirectional) {
398 >          MPI_Recv(&isDirectional, 1, MPI_INT, which_node,
399 >          myPotato, MPI_COMM_WORLD, &istatus);
400 >              
401 >          myPotato++;
402  
403 <          sprintf( tempBuffer,
404 <                   "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
405 <                   atomOrientData[0],
406 <                   atomOrientData[1],
407 <                   atomOrientData[2],
408 <                   atomOrientData[3],
409 <                   atomOrientData[4],
295 <                   atomOrientData[5],
296 <                   atomOrientData[6]);
297 <          strcat( writeLine, tempBuffer );
403 >          if (isDirectional) {          
404 >          MPI_Recv(atomData13, 13, MPI_DOUBLE, which_node,
405 >                   myPotato, MPI_COMM_WORLD, &istatus);
406 >          } else {
407 >          MPI_Recv(atomData6, 6, MPI_DOUBLE, which_node,
408 >                   myPotato, MPI_COMM_WORLD, &istatus);          
409 >          }
410  
411 <        } else {
300 <          strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
411 >          myPotato++;
412          }
413 +        potatoes[which_node] = myPotato;
414  
415 <        outFile << writeLine;
304 <        outFile.flush();
305 <      }
306 <    }
307 <
308 <    outFile.flush();
309 <    sprintf( checkPointMsg,
310 <             "Sucessfully took a dump.\n");
311 <    MPIcheckPoint();        
312 <    
313 <  } else {
314 <
315 <    // worldRank != 0, so I'm a remote node.  
316 <    
317 <    for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) {
318 <      
319 <      // Am I the node which has this atom?
320 <      
321 <      if (AtomToProcMap[i] == worldRank) {
322 <
323 <        local_index=-1;
324 <        for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) {
325 <          if (atoms[j]->getGlobalIndex() == which_atom) local_index = j;
326 <        }
327 <        if (local_index != -1) {
328 <        
329 <          atomTypeString = atoms[local_index]->getType();
330 <
331 <          atoms[local_index]->getPos(pos);
332 <          atoms[local_index]->getVel(vel);
333 <
334 <          atomTransData[0] = pos[0];
335 <          atomTransData[1] = pos[1];
336 <          atomTransData[2] = pos[2];
337 <
338 <          atomTransData[3] = vel[0];
339 <          atomTransData[4] = vel[1];
340 <          atomTransData[5] = vel[2];
341 <          
342 <          isDirectional = 0;
343 <
344 <          if( atoms[local_index]->isDirectional() ){
345 <
346 <            isDirectional = 1;
347 <            
348 <            dAtom = (DirectionalAtom *)atoms[local_index];
349 <            dAtom->getQ( q );
350 <            
351 <            atomOrientData[0] = q[0];
352 <            atomOrientData[1] = q[1];
353 <            atomOrientData[2] = q[2];
354 <            atomOrientData[3] = q[3];
355 <
356 <            atomOrientData[4] = dAtom->getJx();
357 <            atomOrientData[5] = dAtom->getJy();
358 <            atomOrientData[6] = dAtom->getJz();
359 <          }
360 <
361 <        } else {
362 <          sprintf(painCave.errMsg,
363 <                  "Atom %d not found on processor %d\n",
364 <                  i, worldRank );
365 <          haveError= 1;
366 <          simError();
367 <        }
368 <
369 <        // I've survived this far, so send off the data!
370 <
371 <        atomTypeTag          = 4*i;
372 <        atomIsDirectionalTag = 4*i + 1;
373 <        atomTransDataTag     = 4*i + 2;
374 <        atomOrientDataTag    = 4*i + 3;
375 <
376 <        MPI_Send(atomTypeString, MINIBUFFERSIZE, MPI_CHAR, 0,
377 <                 atomTypeTag, MPI_COMM_WORLD);
415 >      } else {
416          
417 <        MPI_Send(&isDirectional, 1, MPI_INT, 0,
380 <                 atomIsDirectionalTag, MPI_COMM_WORLD);
417 >        haveError = 0;
418          
419 <        MPI_Send(atomTransData, 6, MPI_DOUBLE, 0,
383 <                 atomTransDataTag, MPI_COMM_WORLD);
419 >            local_index = indexArray[currentIndex].first;        
420  
421 <        if (isDirectional) {
421 >        integrableObjects = (entry_plug->molecules[local_index]).getIntegrableObjects();
422  
423 <          MPI_Send(atomOrientData, 7, MPI_DOUBLE, 0,
424 <                   atomOrientDataTag, MPI_COMM_WORLD);
425 <          
423 >        for(iter= integrableObjects.begin(); iter != integrableObjects.end(); ++iter){    
424 >                sd = *iter;
425 >            atomTypeString = sd->getType();
426 >            
427 >            sd->getPos(pos);
428 >            sd->getVel(vel);          
429 >          
430 >            atomData6[0] = pos[0];
431 >            atomData6[1] = pos[1];
432 >            atomData6[2] = pos[2];
433 >
434 >            atomData6[3] = vel[0];
435 >            atomData6[4] = vel[1];
436 >            atomData6[5] = vel[2];
437 >              
438 >            isDirectional = 0;
439 >
440 >            if( sd->isDirectional() ){
441 >
442 >              isDirectional = 1;
443 >                
444 >              sd->getQ( q );
445 >              sd->getJ( ji );
446 >
447 >              for (int j = 0; j < 6 ; j++)
448 >                atomData13[j] = atomData6[j];            
449 >              
450 >              atomData13[6] = q[0];
451 >              atomData13[7] = q[1];
452 >              atomData13[8] = q[2];
453 >              atomData13[9] = q[3];
454 >              
455 >              atomData13[10] = ji[0];
456 >              atomData13[11] = ji[1];
457 >              atomData13[12] = ji[2];
458 >            }
459 >            
460          }
461 +        
462 +      currentIndex++;
463 +      }
464 +      // If we've survived to here, format the line:
465        
466 +      if (!isDirectional) {
467 +        
468 +        sprintf( writeLine,
469 +                 "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
470 +                 atomTypeString,
471 +                 atomData6[0],
472 +                 atomData6[1],
473 +                 atomData6[2],
474 +                 atomData6[3],
475 +                 atomData6[4],
476 +                 atomData6[5]);
477 +        
478 +        strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
479 +        
480 +      } else {
481 +        
482 +        sprintf( writeLine,
483 +                 "%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",
484 +                 atomTypeString,
485 +                 atomData13[0],
486 +                 atomData13[1],
487 +                 atomData13[2],
488 +                 atomData13[3],
489 +                 atomData13[4],
490 +                 atomData13[5],
491 +                 atomData13[6],
492 +                 atomData13[7],
493 +                 atomData13[8],
494 +                 atomData13[9],
495 +                 atomData13[10],
496 +                 atomData13[11],
497 +                 atomData13[12]);
498 +        
499        }
500 +      
501 +      for(k = 0; k < outFile.size(); k++)
502 +        *outFile[k] << writeLine;
503      }
504 <
504 >    
505 >    for(k = 0; k < outFile.size(); k++)
506 >      outFile[k]->flush();
507 >    
508      sprintf( checkPointMsg,
509               "Sucessfully took a dump.\n");
510 +    
511      MPIcheckPoint();        
512      
513 <  }
514 <  
515 <  painCave.isEventLoop = 0;
513 >    delete[] potatoes;
514 >    
515 >  } else {
516  
517 < #endif // is_mpi
404 < }
517 >    // worldRank != 0, so I'm a remote node.  
518  
519 < void DumpWriter::writeFinal(double finalTime){
519 >    // Set my magic potato to 0:
520  
521 <  char finalName[500];
522 <  ofstream finalOut;
521 >    myPotato = 0;
522 >    currentIndex = 0;
523 >    
524 >    for (i = 0 ; i < mpiSim->getTotNmol(); i++ ) {
525 >      
526 >      // Am I the node which has this integrableObject?
527 >      
528 >      if (MolToProcMap[i] == worldRank) {
529  
411 –  const int BUFFERSIZE = 2000;
412 –  const int MINIBUFFERSIZE = 10;
413 –  char tempBuffer[BUFFERSIZE];
414 –  char writeLine[BUFFERSIZE];
530  
531 <  double q[4];
532 <  DirectionalAtom* dAtom;
533 <  Atom** atoms = entry_plug->atoms;
534 <  int i;
535 < #ifdef IS_MPI
536 <  int j, which_node, done, which_atom, local_index;
537 <  double atomTransData[6];
538 <  double atomOrientData[7];
539 <  int isDirectional;
425 <  char* atomTypeString;
426 <  int atomTypeTag;
427 <  int atomIsDirectionalTag;
428 <  int atomTransDataTag;
429 <  int atomOrientDataTag;
430 < #else //is_mpi
431 <  int nAtoms = entry_plug->n_atoms;
432 < #endif //is_mpi
531 >        if (myPotato + 1 >= MAXTAG) {
532 >          
533 >          // The potato was going to exceed the maximum value,
534 >          // so wrap this processor potato back to 0 (and block until
535 >          // node 0 says we can go:
536 >          
537 >          MPI_Recv(&myPotato, 1, MPI_INT, 0, 0, MPI_COMM_WORLD, &istatus);
538 >          
539 >        }
540  
541 <  double pos[3], vel[3];
541 >          local_index = indexArray[currentIndex].first;        
542 >          integrableObjects = entry_plug->molecules[local_index].getIntegrableObjects();
543 >          
544 >          nCurObj = integrableObjects.size();
545 >                      
546 >          MPI_Send(&nCurObj, 1, MPI_INT, 0,
547 >                             myPotato, MPI_COMM_WORLD);
548 >          myPotato++;
549  
550 < #ifdef IS_MPI
437 <  if(worldRank == 0 ){
438 < #endif // is_mpi
550 >          for( iter = integrableObjects.begin(); iter  != integrableObjects.end(); iter++){
551  
552 <    strcpy( finalName, entry_plug->finalName );
552 >            if (myPotato + 3 >= MAXTAG) {
553 >          
554 >              // The potato was going to exceed the maximum value,
555 >              // so wrap this processor potato back to 0 (and block until
556 >              // node 0 says we can go:
557 >          
558 >              MPI_Recv(&myPotato, 1, MPI_INT, 0, 0, MPI_COMM_WORLD, &istatus);
559 >              
560 >            }
561 >            
562 >            sd = *iter;
563 >            
564 >            atomTypeString = sd->getType();
565  
566 <    finalOut.open( finalName, ios::out | ios::trunc );
567 <    if( !finalOut ){
444 <      sprintf( painCave.errMsg,
445 <               "Could not open \"%s\" for final dump output.\n",
446 <               finalName );
447 <      painCave.isFatal = 1;
448 <      simError();
449 <    }
566 >            sd->getPos(pos);
567 >            sd->getVel(vel);
568  
569 <    // finalOut.setf( ios::scientific );
569 >            atomData6[0] = pos[0];
570 >            atomData6[1] = pos[1];
571 >            atomData6[2] = pos[2];
572  
573 < #ifdef IS_MPI
574 <  }
573 >            atomData6[3] = vel[0];
574 >            atomData6[4] = vel[1];
575 >            atomData6[5] = vel[2];
576 >              
577 >            isDirectional = 0;
578  
579 <  sprintf(checkPointMsg,"Opened file for final configuration\n");
457 <  MPIcheckPoint();
579 >            if( sd->isDirectional() ){
580  
581 < #endif //is_mpi
581 >                isDirectional = 1;
582 >                
583 >                sd->getQ( q );
584 >                sd->getJ( ji );
585 >                
586 >                for (int j = 0; j < 6 ; j++)
587 >                  atomData13[j] = atomData6[j];
588 >                
589 >                atomData13[6] = q[0];
590 >                atomData13[7] = q[1];
591 >                atomData13[8] = q[2];
592 >                atomData13[9] = q[3];
593 >      
594 >                atomData13[10] = ji[0];
595 >                atomData13[11] = ji[1];
596 >                atomData13[12] = ji[2];
597 >              }
598  
599 +            
600 +            strncpy(MPIatomTypeString, atomTypeString, MINIBUFFERSIZE);
601  
602 < #ifndef IS_MPI
602 >            // null terminate the string before sending (just in case):
603 >            MPIatomTypeString[MINIBUFFERSIZE-1] = '\0';
604  
605 <  finalOut << nAtoms << "\n";
605 >            MPI_Send(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, 0,
606 >                             myPotato, MPI_COMM_WORLD);
607 >            
608 >            myPotato++;
609  
610 <  finalOut << finalTime << ";\t"
611 <           << entry_plug->Hmat[0][0] << "\t"
612 <           << entry_plug->Hmat[1][0] << "\t"
613 <           << entry_plug->Hmat[2][0] << ";\t"
610 >            MPI_Send(&isDirectional, 1, MPI_INT, 0,
611 >                             myPotato, MPI_COMM_WORLD);
612 >            
613 >            myPotato++;
614 >            
615 >            if (isDirectional) {
616  
617 <           << entry_plug->Hmat[0][1] << "\t"
618 <           << entry_plug->Hmat[1][1] << "\t"
619 <           << entry_plug->Hmat[2][1] << ";\t"
617 >              MPI_Send(atomData13, 13, MPI_DOUBLE, 0,
618 >                       myPotato, MPI_COMM_WORLD);
619 >              
620 >            } else {
621  
622 <           << entry_plug->Hmat[0][2] << "\t"
623 <           << entry_plug->Hmat[1][2] << "\t"
624 <           << entry_plug->Hmat[2][2] << ";";
622 >              MPI_Send(atomData6, 6, MPI_DOUBLE, 0,
623 >                       myPotato, MPI_COMM_WORLD);
624 >            }
625  
626 <  //write out additional parameters, such as chi and eta
480 <  finalOut << entry_plug->the_integrator->getAdditionalParameters();
481 <  finalOut << endl;
626 >            myPotato++;  
627  
483 –  for( i=0; i<nAtoms; i++ ){
484 –
485 –    atoms[i]->getPos(pos);
486 –    atoms[i]->getVel(vel);
487 –
488 –    sprintf( tempBuffer,
489 –             "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
490 –             atoms[i]->getType(),
491 –             pos[0],
492 –             pos[1],
493 –             pos[2],
494 –             vel[0],
495 –             vel[1],
496 –             vel[2]);
497 –    strcpy( writeLine, tempBuffer );
498 –
499 –    if( atoms[i]->isDirectional() ){
500 –
501 –      dAtom = (DirectionalAtom *)atoms[i];
502 –      dAtom->getQ( q );
503 –
504 –      sprintf( tempBuffer,
505 –               "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
506 –               q[0],
507 –               q[1],
508 –               q[2],
509 –               q[3],
510 –               dAtom->getJx(),
511 –               dAtom->getJy(),
512 –               dAtom->getJz());
513 –      strcat( writeLine, tempBuffer );
514 –    }
515 –    else
516 –      strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
517 –
518 –    finalOut << writeLine;
519 –  }
520 –  finalOut.flush();
521 –  finalOut.close();
522 –
523 – #else // is_mpi
524 –
525 –  // first thing first, suspend fatalities.
526 –  painCave.isEventLoop = 1;
527 –
528 –  int myStatus; // 1 = wakeup & success; 0 = error; -1 = AllDone
529 –  int haveError;
530 –
531 –  MPI_Status istatus;
532 –  int *AtomToProcMap = mpiSim->getAtomToProcMap();
533 –
534 –  // write out header and node 0's coordinates
535 –
536 –  if( worldRank == 0 ){
537 –    finalOut << mpiSim->getTotAtoms() << "\n";
538 –
539 –    finalOut << finalTime << ";\t"
540 –            << entry_plug->Hmat[0][0] << "\t"
541 –            << entry_plug->Hmat[1][0] << "\t"
542 –            << entry_plug->Hmat[2][0] << ";\t"
543 –
544 –            << entry_plug->Hmat[0][1] << "\t"
545 –            << entry_plug->Hmat[1][1] << "\t"
546 –            << entry_plug->Hmat[2][1] << ";\t"
547 –
548 –            << entry_plug->Hmat[0][2] << "\t"
549 –            << entry_plug->Hmat[1][2] << "\t"
550 –            << entry_plug->Hmat[2][2] << ";";
551 –
552 –    finalOut << entry_plug->the_integrator->getAdditionalParameters();
553 –    finalOut << endl;
554 –    finalOut.flush();
555 –    for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) {
556 –      // Get the Node number which has this atom;
557 –
558 –      which_node = AtomToProcMap[i];
559 –
560 –      if (which_node != 0) {
561 –        
562 –        atomTypeTag          = 4*i;
563 –        atomIsDirectionalTag = 4*i + 1;
564 –        atomTransDataTag     = 4*i + 2;
565 –        atomOrientDataTag    = 4*i + 3;
566 –
567 –        MPI_Recv(atomTypeString, MINIBUFFERSIZE, MPI_CHAR, which_node,
568 –                 atomTypeTag, MPI_COMM_WORLD, &istatus);
569 –        
570 –        MPI_Recv(&isDirectional, 1, MPI_INT, which_node,
571 –                 atomIsDirectionalTag, MPI_COMM_WORLD, &istatus);
572 –        
573 –        MPI_Recv(atomTransData, 6, MPI_DOUBLE, which_node,
574 –                 atomTransDataTag, MPI_COMM_WORLD, &istatus);
575 –
576 –        if (isDirectional) {
577 –
578 –          MPI_Recv(atomOrientData, 7, MPI_DOUBLE, which_node,
579 –                   atomOrientDataTag, MPI_COMM_WORLD, &istatus);
580 –
581 –        }
582 –
583 –      } else {
584 –        
585 –        haveError = 0;
586 –        which_atom = i;
587 –        local_index=-1;
588 –
589 –        for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) {
590 –          if (atoms[j]->getGlobalIndex() == which_atom) local_index = j;
591 –        }
592 –
593 –        if (local_index != -1) {
594 –
595 –          atomTypeString = atoms[local_index]->getType();
596 –
597 –          atoms[local_index]->getPos(pos);
598 –          atoms[local_index]->getVel(vel);
599 –
600 –          atomTransData[0] = pos[0];
601 –          atomTransData[1] = pos[1];
602 –          atomTransData[2] = pos[2];
603 –
604 –          atomTransData[3] = vel[0];
605 –          atomTransData[4] = vel[1];
606 –          atomTransData[5] = vel[2];
607 –          
608 –          isDirectional = 0;
609 –
610 –          if( atoms[local_index]->isDirectional() ){
611 –
612 –            isDirectional = 1;
613 –            
614 –            dAtom = (DirectionalAtom *)atoms[local_index];
615 –            dAtom->getQ( q );
616 –            
617 –            atomOrientData[0] = q[0];
618 –            atomOrientData[1] = q[1];
619 –            atomOrientData[2] = q[2];
620 –            atomOrientData[3] = q[3];
621 –
622 –            atomOrientData[4] = dAtom->getJx();
623 –            atomOrientData[5] = dAtom->getJy();
624 –            atomOrientData[6] = dAtom->getJz();
628            }
629  
630 <        } else {
631 <          sprintf(painCave.errMsg,
629 <                  "Atom %d not found on processor %d\n",
630 <                  i, worldRank );
631 <          haveError= 1;
632 <          simError();
633 <        }
634 <
635 <        if(haveError) DieDieDie();
636 <                              
637 <        // If we've survived to here, format the line:
638 <        
639 <        sprintf( tempBuffer,
640 <                 "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
641 <                 atomTypeString,
642 <                 atomTransData[0],
643 <                 atomTransData[1],
644 <                 atomTransData[2],
645 <                 atomTransData[3],
646 <                 atomTransData[4],
647 <                 atomTransData[5]);
648 <
649 <        strcpy( writeLine, tempBuffer );
650 <
651 <        if (isDirectional) {
652 <
653 <          sprintf( tempBuffer,
654 <                   "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
655 <                   atomOrientData[0],
656 <                   atomOrientData[1],
657 <                   atomOrientData[2],
658 <                   atomOrientData[3],
659 <                   atomOrientData[4],
660 <                   atomOrientData[5],
661 <                   atomOrientData[6]);
662 <          strcat( writeLine, tempBuffer );
663 <
664 <        } else {
665 <          strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
630 >          currentIndex++;    
631 >          
632          }
633 <
668 <        finalOut << writeLine;
669 <        finalOut.flush();
633 >      
634        }
671 –    }
635  
673 –    finalOut.flush();
636      sprintf( checkPointMsg,
637               "Sucessfully took a dump.\n");
638 <    MPIcheckPoint();        
638 >    MPIcheckPoint();                
639      
678 –  } else {
679 –
680 –    // worldRank != 0, so I'm a remote node.  
681 –    
682 –    for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) {
683 –      
684 –      // Am I the node which has this atom?
685 –      
686 –      if (AtomToProcMap[i] == worldRank) {
687 –
688 –        local_index=-1;
689 –        for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) {
690 –          if (atoms[j]->getGlobalIndex() == which_atom) local_index = j;
691 –        }
692 –        if (local_index != -1) {
693 –        
694 –          atomTypeString = atoms[local_index]->getType();
695 –
696 –          atoms[local_index]->getPos(pos);
697 –          atoms[local_index]->getVel(vel);
698 –
699 –          atomTransData[0] = pos[0];
700 –          atomTransData[1] = pos[1];
701 –          atomTransData[2] = pos[2];
702 –
703 –          atomTransData[3] = vel[0];
704 –          atomTransData[4] = vel[1];
705 –          atomTransData[5] = vel[2];
706 –          
707 –          isDirectional = 0;
708 –
709 –          if( atoms[local_index]->isDirectional() ){
710 –
711 –            isDirectional = 1;
712 –            
713 –            dAtom = (DirectionalAtom *)atoms[local_index];
714 –            dAtom->getQ( q );
715 –            
716 –            atomOrientData[0] = q[0];
717 –            atomOrientData[1] = q[1];
718 –            atomOrientData[2] = q[2];
719 –            atomOrientData[3] = q[3];
720 –
721 –            atomOrientData[4] = dAtom->getJx();
722 –            atomOrientData[5] = dAtom->getJy();
723 –            atomOrientData[6] = dAtom->getJz();
724 –          }
725 –
726 –        } else {
727 –          sprintf(painCave.errMsg,
728 –                  "Atom %d not found on processor %d\n",
729 –                  i, worldRank );
730 –          haveError= 1;
731 –          simError();
732 –        }
733 –
734 –        // I've survived this far, so send off the data!
735 –
736 –        atomTypeTag          = 4*i;
737 –        atomIsDirectionalTag = 4*i + 1;
738 –        atomTransDataTag     = 4*i + 2;
739 –        atomOrientDataTag    = 4*i + 3;
740 –
741 –        MPI_Send(atomTypeString, MINIBUFFERSIZE, MPI_CHAR, 0,
742 –                 atomTypeTag, MPI_COMM_WORLD);
743 –        
744 –        MPI_Send(&isDirectional, 1, MPI_INT, 0,
745 –                 atomIsDirectionalTag, MPI_COMM_WORLD);
746 –        
747 –        MPI_Send(atomTransData, 6, MPI_DOUBLE, 0,
748 –                 atomTransDataTag, MPI_COMM_WORLD);
749 –
750 –        if (isDirectional) {
751 –
752 –          MPI_Send(atomOrientData, 7, MPI_DOUBLE, 0,
753 –                   atomOrientDataTag, MPI_COMM_WORLD);
754 –          
755 –        }
756 –      
757 –      }
640      }
641  
760 –    sprintf( checkPointMsg,
761 –             "Sucessfully wrote final file.\n");
762 –    MPIcheckPoint();        
763 –    
764 –  }
765 –  
766 –  painCave.isEventLoop = 0;
642  
643 <  if( worldRank == 0 ) finalOut.close();
643 >  
644   #endif // is_mpi
645   }
646  
772 –
773 –
647   #ifdef IS_MPI
648  
649   // a couple of functions to let us escape the write loop

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