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root/group/trunk/OOPSE/libmdtools/DumpWriter.cpp
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Comparing trunk/OOPSE/libmdtools/DumpWriter.cpp (file contents):
Revision 910 by gezelter, Thu Jan 8 18:05:37 2004 UTC vs.
Revision 1198 by tim, Thu May 27 00:48:12 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 atomData[13];
220    int isDirectional;
221    char* atomTypeString;
222    char MPIatomTypeString[MINIBUFFERSIZE];
223 <  int me;
224 <  int atomTypeTag;
84 <  int atomIsDirectionalTag;
85 <  int atomTransDataTag;
86 <  int atomOrientDataTag;
87 < #else //is_mpi
88 <  int nAtoms = entry_plug->n_atoms;
223 >  int nObjects;
224 >  int msgLen; // the length of message actually recieved at master nodes
225   #endif //is_mpi
226  
227 <  double q[4];
227 >  double q[4], ji[3];
228    DirectionalAtom* dAtom;
93 –  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"
107 <          << 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);
123 <    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",
127 <             atoms[i]->getType(),
128 <             pos[0],
129 <             pos[1],
130 <             pos[2],
131 <             vel[0],
132 <             vel[1],
133 <             vel[2]);
134 <    strcpy( writeLine, tempBuffer );
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(),
149 <               dAtom->getJz());
150 <      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      }
152 –    else
153 –      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  
164 –  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 ){
173 –    outFile << mpiSim->getTotAtoms() << "\n";
325  
326 <    outFile << currentTime << ";\t"
176 <            << entry_plug->Hmat[0][0] << "\t"
177 <            << entry_plug->Hmat[1][0] << "\t"
178 <            << 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"
182 <            << entry_plug->Hmat[2][1] << ";\t"
328 >    nProc = mpiSim->getNprocessors();
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++ ) {
192 <      // 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(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, which_node,
204 <                 atomTypeTag, MPI_COMM_WORLD, &istatus);
205 <        
206 <        strncpy(atomTypeString, MPIatomTypeString, MINIBUFFERSIZE);
354 >    currentIndex = 0;
355  
356 <        MPI_Recv(&isDirectional, 1, MPI_INT, which_node,
357 <                 atomIsDirectionalTag, MPI_COMM_WORLD, &istatus);
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 <        MPI_Recv(atomTransData, 6, MPI_DOUBLE, which_node,
365 <                 atomTransDataTag, MPI_COMM_WORLD, &istatus);
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 <        if (isDirectional) {
369 <
370 <          MPI_Recv(atomOrientData, 7, MPI_DOUBLE, which_node,
217 <                   atomOrientDataTag, MPI_COMM_WORLD, &istatus);
218 <
368 >          potatoes[which_node] = 0;          
369 >          MPI_Send(&potatoes[which_node], 1, MPI_INT, which_node, 0, MPI_COMM_WORLD);
370 >          
371          }
372  
373 <      } else {
373 >        myPotato = potatoes[which_node];        
374 >
375 >        //recieve the number of integrableObject in current molecule
376 >        MPI_Recv(&nCurObj, 1, MPI_INT, which_node,
377 >                 myPotato, MPI_COMM_WORLD, &istatus);
378 >        myPotato++;
379          
380 <        haveError = 0;
224 <        which_atom = i;
225 <        local_index=-1;
380 >        for(int l = 0; l < nCurObj; l++){
381  
382 <        for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) {
383 <          if (atoms[j]->getGlobalIndex() == which_atom) local_index = j;
384 <        }
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 <        if (local_index != -1) {
387 <
233 <          atomTypeString = atoms[local_index]->getType();
234 <
235 <          atoms[local_index]->getPos(pos);
236 <          atoms[local_index]->getVel(vel);
237 <
238 <          atomTransData[0] = pos[0];
239 <          atomTransData[1] = pos[1];
240 <          atomTransData[2] = pos[2];
241 <
242 <          atomTransData[3] = vel[0];
243 <          atomTransData[4] = vel[1];
244 <          atomTransData[5] = vel[2];
245 <          
246 <          isDirectional = 0;
247 <
248 <          if( atoms[local_index]->isDirectional() ){
249 <
250 <            isDirectional = 1;
386 >            potatoes[which_node] = 0;          
387 >            MPI_Send(&potatoes[which_node], 1, MPI_INT, which_node, 0, MPI_COMM_WORLD);
388              
252 –            dAtom = (DirectionalAtom *)atoms[local_index];
253 –            dAtom->getQ( q );
254 –            
255 –            atomOrientData[0] = q[0];
256 –            atomOrientData[1] = q[1];
257 –            atomOrientData[2] = q[2];
258 –            atomOrientData[3] = q[3];
259 –
260 –            atomOrientData[4] = dAtom->getJx();
261 –            atomOrientData[5] = dAtom->getJy();
262 –            atomOrientData[6] = dAtom->getJz();
389            }
390  
391 <        } else {
392 <          sprintf(painCave.errMsg,
267 <                  "Atom %d not found on processor %d\n",
268 <                  i, worldRank );
269 <          haveError= 1;
270 <          simError();
271 <        }
391 >          MPI_Recv(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, which_node,
392 >          myPotato, MPI_COMM_WORLD, &istatus);
393  
394 <        if(haveError) DieDieDie();
274 <                              
275 <        // If we've survived to here, format the line:
276 <        
277 <        sprintf( tempBuffer,
278 <                 "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
279 <                 atomTypeString,
280 <                 atomTransData[0],
281 <                 atomTransData[1],
282 <                 atomTransData[2],
283 <                 atomTransData[3],
284 <                 atomTransData[4],
285 <                 atomTransData[5]);
394 >          atomTypeString = MPIatomTypeString;
395  
396 <        strcpy( writeLine, tempBuffer );
396 >          myPotato++;
397  
398 <        if (isDirectional) {
398 >          MPI_Recv(atomData, 13, MPI_DOUBLE, which_node, myPotato, MPI_COMM_WORLD, &istatus);
399 >          myPotato++;
400  
401 <          sprintf( tempBuffer,
292 <                   "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
293 <                   atomOrientData[0],
294 <                   atomOrientData[1],
295 <                   atomOrientData[2],
296 <                   atomOrientData[3],
297 <                   atomOrientData[4],
298 <                   atomOrientData[5],
299 <                   atomOrientData[6]);
300 <          strcat( writeLine, tempBuffer );
401 >          MPI_Get_count(&istatus, MPI_DOUBLE, &msgLen);
402  
403 <        } else {
303 <          strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
304 <        }
305 <
306 <        outFile << writeLine;
307 <        outFile.flush();
308 <      }
309 <    }
310 <
311 <    outFile.flush();
312 <    sprintf( checkPointMsg,
313 <             "Sucessfully took a dump.\n");
314 <    MPIcheckPoint();        
315 <    
316 <  } else {
317 <
318 <    // worldRank != 0, so I'm a remote node.  
319 <    
320 <    for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) {
321 <      
322 <      // Am I the node which has this atom?
323 <      
324 <      if (AtomToProcMap[i] == worldRank) {
325 <
326 <        local_index=-1;
327 <        for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) {
328 <          if (atoms[j]->getGlobalIndex() == which_atom) local_index = j;
329 <        }
330 <        if (local_index != -1) {
331 <        
332 <          atomTypeString = atoms[local_index]->getType();
333 <
334 <          atoms[local_index]->getPos(pos);
335 <          atoms[local_index]->getVel(vel);
336 <
337 <          atomTransData[0] = pos[0];
338 <          atomTransData[1] = pos[1];
339 <          atomTransData[2] = pos[2];
340 <
341 <          atomTransData[3] = vel[0];
342 <          atomTransData[4] = vel[1];
343 <          atomTransData[5] = vel[2];
344 <          
345 <          isDirectional = 0;
346 <
347 <          if( atoms[local_index]->isDirectional() ){
348 <
403 >          if(msgLen  == 13)
404              isDirectional = 1;
405 +          else
406 +            isDirectional = 0;
407              
408 <            dAtom = (DirectionalAtom *)atoms[local_index];
409 <            dAtom->getQ( q );
353 <            
354 <            atomOrientData[0] = q[0];
355 <            atomOrientData[1] = q[1];
356 <            atomOrientData[2] = q[2];
357 <            atomOrientData[3] = q[3];
408 >        }
409 >        potatoes[which_node] = myPotato;
410  
411 <            atomOrientData[4] = dAtom->getJx();
360 <            atomOrientData[5] = dAtom->getJy();
361 <            atomOrientData[6] = dAtom->getJz();
362 <          }
363 <
364 <        } else {
365 <          sprintf(painCave.errMsg,
366 <                  "Atom %d not found on processor %d\n",
367 <                  i, worldRank );
368 <          haveError= 1;
369 <          simError();
370 <        }
371 <
372 <        // I've survived this far, so send off the data!
373 <
374 <        atomTypeTag          = 4*i;
375 <        atomIsDirectionalTag = 4*i + 1;
376 <        atomTransDataTag     = 4*i + 2;
377 <        atomOrientDataTag    = 4*i + 3;
378 <
379 <
380 <        strncpy(MPIatomTypeString, atomTypeString, MINIBUFFERSIZE);
381 <
382 <        MPI_Send(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, 0,
383 <                 atomTypeTag, MPI_COMM_WORLD);
411 >      } else {
412          
413 <        MPI_Send(&isDirectional, 1, MPI_INT, 0,
386 <                 atomIsDirectionalTag, MPI_COMM_WORLD);
413 >        haveError = 0;
414          
415 <        MPI_Send(atomTransData, 6, MPI_DOUBLE, 0,
389 <                 atomTransDataTag, MPI_COMM_WORLD);
415 >            local_index = indexArray[currentIndex].first;        
416  
417 <        if (isDirectional) {
417 >        integrableObjects = (entry_plug->molecules[local_index]).getIntegrableObjects();
418  
419 <          MPI_Send(atomOrientData, 7, MPI_DOUBLE, 0,
420 <                   atomOrientDataTag, MPI_COMM_WORLD);
421 <          
419 >        for(iter= integrableObjects.begin(); iter != integrableObjects.end(); ++iter){    
420 >                sd = *iter;
421 >            atomTypeString = sd->getType();
422 >            
423 >            sd->getPos(pos);
424 >            sd->getVel(vel);          
425 >          
426 >            atomData[0] = pos[0];
427 >            atomData[1] = pos[1];
428 >            atomData[2] = pos[2];
429 >
430 >            atomData[3] = vel[0];
431 >            atomData[4] = vel[1];
432 >            atomData[5] = vel[2];
433 >              
434 >            isDirectional = 0;
435 >
436 >            if( sd->isDirectional() ){
437 >
438 >              isDirectional = 1;
439 >                
440 >              sd->getQ( q );
441 >              sd->getJ( ji );
442 >
443 >              for (int j = 0; j < 6 ; j++)
444 >                atomData[j] = atomData[j];            
445 >              
446 >              atomData[6] = q[0];
447 >              atomData[7] = q[1];
448 >              atomData[8] = q[2];
449 >              atomData[9] = q[3];
450 >              
451 >              atomData[10] = ji[0];
452 >              atomData[11] = ji[1];
453 >              atomData[12] = ji[2];
454 >            }
455 >            
456          }
457 +        
458 +      currentIndex++;
459 +      }
460 +      // If we've survived to here, format the line:
461        
462 +      if (!isDirectional) {
463 +        
464 +        sprintf( writeLine,
465 +                 "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
466 +                 atomTypeString,
467 +                 atomData[0],
468 +                 atomData[1],
469 +                 atomData[2],
470 +                 atomData[3],
471 +                 atomData[4],
472 +                 atomData[5]);
473 +        
474 +        strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
475 +        
476 +      } else {
477 +        
478 +        sprintf( writeLine,
479 +                 "%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",
480 +                 atomTypeString,
481 +                 atomData[0],
482 +                 atomData[1],
483 +                 atomData[2],
484 +                 atomData[3],
485 +                 atomData[4],
486 +                 atomData[5],
487 +                 atomData[6],
488 +                 atomData[7],
489 +                 atomData[8],
490 +                 atomData[9],
491 +                 atomData[10],
492 +                 atomData[11],
493 +                 atomData[12]);
494 +        
495        }
496 +      
497 +      for(k = 0; k < outFile.size(); k++)
498 +        *outFile[k] << writeLine;
499      }
500 <
500 >    
501 >    for(k = 0; k < outFile.size(); k++)
502 >      outFile[k]->flush();
503 >    
504      sprintf( checkPointMsg,
505               "Sucessfully took a dump.\n");
506 +    
507      MPIcheckPoint();        
508      
509 <  }
510 <  
511 <  painCave.isEventLoop = 0;
509 >    delete[] potatoes;
510 >    
511 >  } else {
512  
513 < #endif // is_mpi
410 < }
513 >    // worldRank != 0, so I'm a remote node.  
514  
515 < void DumpWriter::writeFinal(double finalTime){
515 >    // Set my magic potato to 0:
516  
517 <  char finalName[500];
518 <  ofstream finalOut;
517 >    myPotato = 0;
518 >    currentIndex = 0;
519 >    
520 >    for (i = 0 ; i < mpiSim->getTotNmol(); i++ ) {
521 >      
522 >      // Am I the node which has this integrableObject?
523 >      
524 >      if (MolToProcMap[i] == worldRank) {
525  
417 –  const int BUFFERSIZE = 2000;
418 –  const int MINIBUFFERSIZE = 10;
419 –  char tempBuffer[BUFFERSIZE];
420 –  char writeLine[BUFFERSIZE];
526  
527 <  double q[4];
528 <  DirectionalAtom* dAtom;
529 <  Atom** atoms = entry_plug->atoms;
530 <  int i;
531 < #ifdef IS_MPI
532 <  int j, which_node, done, which_atom, local_index;
533 <  double atomTransData[6];
534 <  double atomOrientData[7];
535 <  int isDirectional;
431 <  char* atomTypeString;
432 <  char MPIatomTypeString[MINIBUFFERSIZE];
433 <  int atomTypeTag;
434 <  int atomIsDirectionalTag;
435 <  int atomTransDataTag;
436 <  int atomOrientDataTag;
437 < #else //is_mpi
438 <  int nAtoms = entry_plug->n_atoms;
439 < #endif //is_mpi
527 >        if (myPotato + 1 >= MAXTAG) {
528 >          
529 >          // The potato was going to exceed the maximum value,
530 >          // so wrap this processor potato back to 0 (and block until
531 >          // node 0 says we can go:
532 >          
533 >          MPI_Recv(&myPotato, 1, MPI_INT, 0, 0, MPI_COMM_WORLD, &istatus);
534 >          
535 >        }
536  
537 <  double pos[3], vel[3];
537 >          local_index = indexArray[currentIndex].first;        
538 >          integrableObjects = entry_plug->molecules[local_index].getIntegrableObjects();
539 >          
540 >          nCurObj = integrableObjects.size();
541 >                      
542 >          MPI_Send(&nCurObj, 1, MPI_INT, 0,
543 >                             myPotato, MPI_COMM_WORLD);
544 >          myPotato++;
545  
546 < #ifdef IS_MPI
444 <  if(worldRank == 0 ){
445 < #endif // is_mpi
546 >          for( iter = integrableObjects.begin(); iter  != integrableObjects.end(); iter++){
547  
548 <    strcpy( finalName, entry_plug->finalName );
548 >            if (myPotato + 2 >= MAXTAG) {
549 >          
550 >              // The potato was going to exceed the maximum value,
551 >              // so wrap this processor potato back to 0 (and block until
552 >              // node 0 says we can go:
553 >          
554 >              MPI_Recv(&myPotato, 1, MPI_INT, 0, 0, MPI_COMM_WORLD, &istatus);
555 >              
556 >            }
557 >            
558 >            sd = *iter;
559 >            
560 >            atomTypeString = sd->getType();
561  
562 <    finalOut.open( finalName, ios::out | ios::trunc );
563 <    if( !finalOut ){
451 <      sprintf( painCave.errMsg,
452 <               "Could not open \"%s\" for final dump output.\n",
453 <               finalName );
454 <      painCave.isFatal = 1;
455 <      simError();
456 <    }
562 >            sd->getPos(pos);
563 >            sd->getVel(vel);
564  
565 <    // finalOut.setf( ios::scientific );
565 >            atomData[0] = pos[0];
566 >            atomData[1] = pos[1];
567 >            atomData[2] = pos[2];
568  
569 < #ifdef IS_MPI
570 <  }
569 >            atomData[3] = vel[0];
570 >            atomData[4] = vel[1];
571 >            atomData[5] = vel[2];
572 >              
573 >            isDirectional = 0;
574  
575 <  sprintf(checkPointMsg,"Opened file for final configuration\n");
464 <  MPIcheckPoint();
575 >            if( sd->isDirectional() ){
576  
577 < #endif //is_mpi
577 >                isDirectional = 1;
578 >                
579 >                sd->getQ( q );
580 >                sd->getJ( ji );
581 >                
582 >                
583 >                atomData[6] = q[0];
584 >                atomData[7] = q[1];
585 >                atomData[8] = q[2];
586 >                atomData[9] = q[3];
587 >      
588 >                atomData[10] = ji[0];
589 >                atomData[11] = ji[1];
590 >                atomData[12] = ji[2];
591 >              }
592  
593 +            
594 +            strncpy(MPIatomTypeString, atomTypeString, MINIBUFFERSIZE);
595  
596 < #ifndef IS_MPI
596 >            // null terminate the string before sending (just in case):
597 >            MPIatomTypeString[MINIBUFFERSIZE-1] = '\0';
598  
599 <  finalOut << nAtoms << "\n";
599 >            MPI_Send(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, 0,
600 >                             myPotato, MPI_COMM_WORLD);
601 >            
602 >            myPotato++;
603 >            
604 >            if (isDirectional) {
605  
606 <  finalOut << finalTime << ";\t"
607 <           << entry_plug->Hmat[0][0] << "\t"
608 <           << entry_plug->Hmat[1][0] << "\t"
609 <           << entry_plug->Hmat[2][0] << ";\t"
606 >              MPI_Send(atomData, 13, MPI_DOUBLE, 0,
607 >                       myPotato, MPI_COMM_WORLD);
608 >              
609 >            } else {
610  
611 <           << entry_plug->Hmat[0][1] << "\t"
612 <           << entry_plug->Hmat[1][1] << "\t"
613 <           << entry_plug->Hmat[2][1] << ";\t"
611 >              MPI_Send(atomData, 6, MPI_DOUBLE, 0,
612 >                       myPotato, MPI_COMM_WORLD);
613 >            }
614  
615 <           << entry_plug->Hmat[0][2] << "\t"
483 <           << entry_plug->Hmat[1][2] << "\t"
484 <           << entry_plug->Hmat[2][2] << ";";
485 <
486 <  //write out additional parameters, such as chi and eta
487 <  finalOut << entry_plug->the_integrator->getAdditionalParameters();
488 <  finalOut << endl;
489 <
490 <  for( i=0; i<nAtoms; i++ ){
491 <
492 <    atoms[i]->getPos(pos);
493 <    atoms[i]->getVel(vel);
494 <
495 <    sprintf( tempBuffer,
496 <             "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
497 <             atoms[i]->getType(),
498 <             pos[0],
499 <             pos[1],
500 <             pos[2],
501 <             vel[0],
502 <             vel[1],
503 <             vel[2]);
504 <    strcpy( writeLine, tempBuffer );
505 <
506 <    if( atoms[i]->isDirectional() ){
507 <
508 <      dAtom = (DirectionalAtom *)atoms[i];
509 <      dAtom->getQ( q );
510 <
511 <      sprintf( tempBuffer,
512 <               "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
513 <               q[0],
514 <               q[1],
515 <               q[2],
516 <               q[3],
517 <               dAtom->getJx(),
518 <               dAtom->getJy(),
519 <               dAtom->getJz());
520 <      strcat( writeLine, tempBuffer );
521 <    }
522 <    else
523 <      strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
615 >            myPotato++;  
616  
525 –    finalOut << writeLine;
526 –  }
527 –  finalOut.flush();
528 –  finalOut.close();
529 –
530 – #else // is_mpi
531 –
532 –  // first thing first, suspend fatalities.
533 –  painCave.isEventLoop = 1;
534 –
535 –  int myStatus; // 1 = wakeup & success; 0 = error; -1 = AllDone
536 –  int haveError;
537 –
538 –  MPI_Status istatus;
539 –  int *AtomToProcMap = mpiSim->getAtomToProcMap();
540 –
541 –  // write out header and node 0's coordinates
542 –
543 –  if( worldRank == 0 ){
544 –    finalOut << mpiSim->getTotAtoms() << "\n";
545 –
546 –    finalOut << finalTime << ";\t"
547 –            << entry_plug->Hmat[0][0] << "\t"
548 –            << entry_plug->Hmat[1][0] << "\t"
549 –            << entry_plug->Hmat[2][0] << ";\t"
550 –
551 –            << entry_plug->Hmat[0][1] << "\t"
552 –            << entry_plug->Hmat[1][1] << "\t"
553 –            << entry_plug->Hmat[2][1] << ";\t"
554 –
555 –            << entry_plug->Hmat[0][2] << "\t"
556 –            << entry_plug->Hmat[1][2] << "\t"
557 –            << entry_plug->Hmat[2][2] << ";";
558 –
559 –    finalOut << entry_plug->the_integrator->getAdditionalParameters();
560 –    finalOut << endl;
561 –    finalOut.flush();
562 –    for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) {
563 –      // Get the Node number which has this atom;
564 –
565 –      which_node = AtomToProcMap[i];
566 –
567 –      if (which_node != 0) {
568 –        
569 –        atomTypeTag          = 4*i;
570 –        atomIsDirectionalTag = 4*i + 1;
571 –        atomTransDataTag     = 4*i + 2;
572 –        atomOrientDataTag    = 4*i + 3;
573 –
574 –        MPI_Recv(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, which_node,
575 –                 atomTypeTag, MPI_COMM_WORLD, &istatus);
576 –        
577 –        strncpy(atomTypeString, MPIatomTypeString, MINIBUFFERSIZE);
578 –
579 –        MPI_Recv(&isDirectional, 1, MPI_INT, which_node,
580 –                 atomIsDirectionalTag, MPI_COMM_WORLD, &istatus);
581 –        
582 –        MPI_Recv(atomTransData, 6, MPI_DOUBLE, which_node,
583 –                 atomTransDataTag, MPI_COMM_WORLD, &istatus);
584 –
585 –        if (isDirectional) {
586 –
587 –          MPI_Recv(atomOrientData, 7, MPI_DOUBLE, which_node,
588 –                   atomOrientDataTag, MPI_COMM_WORLD, &istatus);
589 –
590 –        }
591 –
592 –      } else {
593 –        
594 –        haveError = 0;
595 –        which_atom = i;
596 –        local_index=-1;
597 –
598 –        for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) {
599 –          if (atoms[j]->getGlobalIndex() == which_atom) local_index = j;
600 –        }
601 –
602 –        if (local_index != -1) {
603 –
604 –          atomTypeString = atoms[local_index]->getType();
605 –
606 –          atoms[local_index]->getPos(pos);
607 –          atoms[local_index]->getVel(vel);
608 –
609 –          atomTransData[0] = pos[0];
610 –          atomTransData[1] = pos[1];
611 –          atomTransData[2] = pos[2];
612 –
613 –          atomTransData[3] = vel[0];
614 –          atomTransData[4] = vel[1];
615 –          atomTransData[5] = vel[2];
616 –          
617 –          isDirectional = 0;
618 –
619 –          if( atoms[local_index]->isDirectional() ){
620 –
621 –            isDirectional = 1;
622 –            
623 –            dAtom = (DirectionalAtom *)atoms[local_index];
624 –            dAtom->getQ( q );
625 –            
626 –            atomOrientData[0] = q[0];
627 –            atomOrientData[1] = q[1];
628 –            atomOrientData[2] = q[2];
629 –            atomOrientData[3] = q[3];
630 –
631 –            atomOrientData[4] = dAtom->getJx();
632 –            atomOrientData[5] = dAtom->getJy();
633 –            atomOrientData[6] = dAtom->getJz();
617            }
618  
619 <        } else {
620 <          sprintf(painCave.errMsg,
638 <                  "Atom %d not found on processor %d\n",
639 <                  i, worldRank );
640 <          haveError= 1;
641 <          simError();
642 <        }
643 <
644 <        if(haveError) DieDieDie();
645 <                              
646 <        // If we've survived to here, format the line:
647 <        
648 <        sprintf( tempBuffer,
649 <                 "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
650 <                 atomTypeString,
651 <                 atomTransData[0],
652 <                 atomTransData[1],
653 <                 atomTransData[2],
654 <                 atomTransData[3],
655 <                 atomTransData[4],
656 <                 atomTransData[5]);
657 <
658 <        strcpy( writeLine, tempBuffer );
659 <
660 <        if (isDirectional) {
661 <
662 <          sprintf( tempBuffer,
663 <                   "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
664 <                   atomOrientData[0],
665 <                   atomOrientData[1],
666 <                   atomOrientData[2],
667 <                   atomOrientData[3],
668 <                   atomOrientData[4],
669 <                   atomOrientData[5],
670 <                   atomOrientData[6]);
671 <          strcat( writeLine, tempBuffer );
672 <
673 <        } else {
674 <          strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
619 >          currentIndex++;    
620 >          
621          }
622 <
677 <        finalOut << writeLine;
678 <        finalOut.flush();
622 >      
623        }
680 –    }
624  
682 –    finalOut.flush();
625      sprintf( checkPointMsg,
626               "Sucessfully took a dump.\n");
627 <    MPIcheckPoint();        
627 >    MPIcheckPoint();                
628      
687 –  } else {
688 –
689 –    // worldRank != 0, so I'm a remote node.  
690 –    
691 –    for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) {
692 –      
693 –      // Am I the node which has this atom?
694 –      
695 –      if (AtomToProcMap[i] == worldRank) {
696 –
697 –        local_index=-1;
698 –        for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) {
699 –          if (atoms[j]->getGlobalIndex() == which_atom) local_index = j;
700 –        }
701 –        if (local_index != -1) {
702 –        
703 –          atomTypeString = atoms[local_index]->getType();
704 –
705 –          atoms[local_index]->getPos(pos);
706 –          atoms[local_index]->getVel(vel);
707 –
708 –          atomTransData[0] = pos[0];
709 –          atomTransData[1] = pos[1];
710 –          atomTransData[2] = pos[2];
711 –
712 –          atomTransData[3] = vel[0];
713 –          atomTransData[4] = vel[1];
714 –          atomTransData[5] = vel[2];
715 –          
716 –          isDirectional = 0;
717 –
718 –          if( atoms[local_index]->isDirectional() ){
719 –
720 –            isDirectional = 1;
721 –            
722 –            dAtom = (DirectionalAtom *)atoms[local_index];
723 –            dAtom->getQ( q );
724 –            
725 –            atomOrientData[0] = q[0];
726 –            atomOrientData[1] = q[1];
727 –            atomOrientData[2] = q[2];
728 –            atomOrientData[3] = q[3];
729 –
730 –            atomOrientData[4] = dAtom->getJx();
731 –            atomOrientData[5] = dAtom->getJy();
732 –            atomOrientData[6] = dAtom->getJz();
733 –          }
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 –        // I've survived this far, so send off the data!
744 –
745 –        atomTypeTag          = 4*i;
746 –        atomIsDirectionalTag = 4*i + 1;
747 –        atomTransDataTag     = 4*i + 2;
748 –        atomOrientDataTag    = 4*i + 3;
749 –
750 –        strncpy(MPIatomTypeString, atomTypeString, MINIBUFFERSIZE);
751 –
752 –        MPI_Send(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, 0,
753 –                 atomTypeTag, MPI_COMM_WORLD);
754 –        
755 –        MPI_Send(&isDirectional, 1, MPI_INT, 0,
756 –                 atomIsDirectionalTag, MPI_COMM_WORLD);
757 –        
758 –        MPI_Send(atomTransData, 6, MPI_DOUBLE, 0,
759 –                 atomTransDataTag, MPI_COMM_WORLD);
760 –
761 –        if (isDirectional) {
762 –
763 –          MPI_Send(atomOrientData, 7, MPI_DOUBLE, 0,
764 –                   atomOrientDataTag, MPI_COMM_WORLD);
765 –          
766 –        }
767 –      
768 –      }
629      }
630  
771 –    sprintf( checkPointMsg,
772 –             "Sucessfully wrote final file.\n");
773 –    MPIcheckPoint();        
774 –    
775 –  }
776 –  
777 –  painCave.isEventLoop = 0;
631  
632 <  if( worldRank == 0 ) finalOut.close();
632 >  
633   #endif // is_mpi
634   }
635  
783 –
784 –
636   #ifdef IS_MPI
637  
638   // a couple of functions to let us escape the write loop

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