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root/group/trunk/OOPSE/libmdtools/DumpWriter.cpp
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Comparing trunk/OOPSE/libmdtools/DumpWriter.cpp (file contents):
Revision 804 by mmeineke, Thu Oct 16 19:16:24 2003 UTC vs.
Revision 1000 by tim, Fri Jan 30 21:47:22 2004 UTC

# Line 1 | Line 1
1   #define _FILE_OFFSET_BITS 64
2  
3 < #include <cstring>
3 > #include <string.h>
4   #include <iostream>
5   #include <fstream>
6 + #include <algorithm>
7 + #include <utility>
8  
9   #ifdef IS_MPI
10   #include <mpi.h>
11   #include "mpiSimulation.hpp"
10 – #define TAKE_THIS_TAG_CHAR 1
11 – #define TAKE_THIS_TAG_INT 2
12  
13   namespace dWrite{
14 <  void nodeZeroError( void );
15 <  void anonymousNodeDie( void );
14 >  void DieDieDie( void );
15   }
16  
17   using namespace dWrite;
# Line 28 | Line 27 | DumpWriter::DumpWriter( SimInfo* the_entry_plug ){
27   #ifdef IS_MPI
28    if(worldRank == 0 ){
29   #endif // is_mpi
30 <    
31 <    strcpy( outName, entry_plug->sampleName );
32 <    
33 <    outFile.open(outName, ios::out | ios::trunc );
34 <    
36 <    if( !outFile ){
37 <      
30 >
31 >    dumpFile.open(entry_plug->sampleName, ios::out | ios::trunc );
32 >
33 >    if( !dumpFile ){
34 >
35        sprintf( painCave.errMsg,
36                 "Could not open \"%s\" for dump output.\n",
37 <               outName);
37 >               entry_plug->sampleName);
38        painCave.isFatal = 1;
39        simError();
40      }
41  
45 –    //outFile.setf( ios::scientific );
46 –
42   #ifdef IS_MPI
43    }
44  
45 +  //sort the local atoms by global index
46 +  sortByGlobalIndex();
47 +  
48    sprintf( checkPointMsg,
49             "Sucessfully opened output file for dumping.\n");
50    MPIcheckPoint();
# Line 59 | Line 57 | DumpWriter::~DumpWriter( ){
57    if(worldRank == 0 ){
58   #endif // is_mpi
59  
60 <    outFile.close();
60 >    dumpFile.close();
61  
62   #ifdef IS_MPI
63    }
64   #endif // is_mpi
65   }
66  
67 < void DumpWriter::writeDump( double currentTime ){
67 > #ifdef IS_MPI
68 >
69 > /**
70 > * A hook function to load balancing
71 > */
72 >
73 > void DumpWriter::update(){
74 >  sortByGlobalIndex();          
75 > }
76    
77 + /**
78 + * Auxiliary sorting function
79 + */
80 +
81 + bool indexSortingCriterion(const pair<int, int>& p1, const pair<int, int>& p2){
82 +  return p1.second < p2.second;
83 + }
84 +
85 + /**
86 + * Sorting the local index by global index
87 + */
88 +
89 + void DumpWriter::sortByGlobalIndex(){
90 +  Atom** atoms = entry_plug->atoms;
91 +  
92 +  indexArray.clear();
93 +  
94 +  for(int i = 0; i < mpiSim->getMyNlocal();i++)
95 +    indexArray.push_back(make_pair(i, atoms[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 <  char tempBuffer[BUFFERSIZE];
168 >  const int MINIBUFFERSIZE = 100;
169 >
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;
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 >  char MPIatomTypeString[MINIBUFFERSIZE];
224 >
225   #else //is_mpi
226    int nAtoms = entry_plug->n_atoms;
227   #endif //is_mpi
# Line 83 | Line 230 | void DumpWriter::writeDump( double currentTime ){
230    DirectionalAtom* dAtom;
231    Atom** atoms = entry_plug->atoms;
232    double pos[3], vel[3];
86 –    
87 –  
88 –  // write current frame to the eor file
233  
90 –  this->writeFinal( currentTime );
91 –
234   #ifndef IS_MPI
235 <    
236 <  outFile << nAtoms << "\n";
237 <    
96 <  outFile << currentTime << ";\t"
97 <          << entry_plug->Hmat[0][0] << "\t"
98 <          << entry_plug->Hmat[1][0] << "\t"
99 <          << entry_plug->Hmat[2][0] << ";\t"
235 >  
236 >  for(k = 0; k < outFile.size(); k++){
237 >    *outFile[k] << nAtoms << "\n";
238  
239 <          << entry_plug->Hmat[0][1] << "\t"
240 <          << entry_plug->Hmat[1][1] << "\t"
241 <          << entry_plug->Hmat[2][1] << ";\t"
239 >    *outFile[k] << currentTime << ";\t"
240 >               << entry_plug->Hmat[0][0] << "\t"
241 >                     << entry_plug->Hmat[1][0] << "\t"
242 >                     << entry_plug->Hmat[2][0] << ";\t"
243 >              
244 >               << entry_plug->Hmat[0][1] << "\t"
245 >                     << entry_plug->Hmat[1][1] << "\t"
246 >                     << entry_plug->Hmat[2][1] << ";\t"
247  
248 <          << entry_plug->Hmat[0][2] << "\t"
249 <          << entry_plug->Hmat[1][2] << "\t"
250 <          << entry_plug->Hmat[2][2] << ";\n";
251 <    
248 >                     << entry_plug->Hmat[0][2] << "\t"
249 >                     << entry_plug->Hmat[1][2] << "\t"
250 >                     << entry_plug->Hmat[2][2] << ";";
251 >
252 >    //write out additional parameters, such as chi and eta
253 >    *outFile[k] << entry_plug->the_integrator->getAdditionalParameters() << endl;
254 >  }
255 >  
256    for( i=0; i<nAtoms; i++ ){
257 <      
257 >
258      atoms[i]->getPos(pos);
259      atoms[i]->getVel(vel);
260  
# Line 123 | Line 270 | void DumpWriter::writeDump( double currentTime ){
270      strcpy( writeLine, tempBuffer );
271  
272      if( atoms[i]->isDirectional() ){
273 <        
273 >
274        dAtom = (DirectionalAtom *)atoms[i];
275        dAtom->getQ( q );
276 <        
276 >
277        sprintf( tempBuffer,
278                 "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
279                 q[0],
# Line 140 | Line 287 | void DumpWriter::writeDump( double currentTime ){
287      }
288      else
289        strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
290 <      
291 <    outFile << writeLine;
290 >
291 >    for(k = 0; k < outFile.size(); k++)
292 >      *outFile[k] << writeLine;
293    }
146 –  outFile.flush();
294  
295   #else // is_mpi
296  
297 <  // first thing first, suspend fatalities.
298 <  painCave.isEventLoop = 1;
297 >  /* code to find maximum tag value */
298 >  
299 >  int *tagub, flag, MAXTAG;
300 >  MPI_Attr_get(MPI_COMM_WORLD, MPI_TAG_UB, &tagub, &flag);
301 >  if (flag) {
302 >    MAXTAG = *tagub;
303 >  } else {
304 >    MAXTAG = 32767;
305 >  }  
306  
153 –  int myStatus; // 1 = wakeup & success; 0 = error; -1 = AllDone
307    int haveError;
308  
309    MPI_Status istatus;
310    int *AtomToProcMap = mpiSim->getAtomToProcMap();
311 <  
311 >
312    // write out header and node 0's coordinates
313 <  
313 >
314    if( worldRank == 0 ){
315 <    outFile << mpiSim->getTotAtoms() << "\n";
316 <  
317 <    outFile << currentTime << ";\t"
318 <            << entry_plug->Hmat[0][0] << "\t"
319 <            << entry_plug->Hmat[1][0] << "\t"
320 <            << entry_plug->Hmat[2][0] << ";\t"
321 <      
322 <            << entry_plug->Hmat[0][1] << "\t"
323 <            << entry_plug->Hmat[1][1] << "\t"
171 <            << entry_plug->Hmat[2][1] << ";\t"
172 <      
173 <            << entry_plug->Hmat[0][2] << "\t"
174 <            << entry_plug->Hmat[1][2] << "\t"
175 <            << entry_plug->Hmat[2][2] << ";\n";
315 >
316 >    // Node 0 needs a list of the magic potatoes for each processor;
317 >
318 >    nProc = mpiSim->getNumberProcessors();
319 >    potatoes = new int[nProc];
320 >
321 >    //write out the comment lines
322 >    for (i = 0; i < nProc; i++)
323 >      potatoes[i] = 0;
324      
325 <    outFile.flush();
325 >      for(k = 0; k < outFile.size(); k++){
326 >        *outFile[k] << mpiSim->getTotAtoms() << "\n";
327 >
328 >        *outFile[k] << currentTime << ";\t"
329 >                         << entry_plug->Hmat[0][0] << "\t"
330 >                         << entry_plug->Hmat[1][0] << "\t"
331 >                         << entry_plug->Hmat[2][0] << ";\t"
332 >
333 >                         << entry_plug->Hmat[0][1] << "\t"
334 >                         << entry_plug->Hmat[1][1] << "\t"
335 >                         << entry_plug->Hmat[2][1] << ";\t"
336 >
337 >                         << entry_plug->Hmat[0][2] << "\t"
338 >                         << entry_plug->Hmat[1][2] << "\t"
339 >                         << entry_plug->Hmat[2][2] << ";";
340 >  
341 >        *outFile[k] << entry_plug->the_integrator->getAdditionalParameters() << endl;
342 >    }
343 >
344 >    currentIndex = 0;
345 >
346      for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) {
347 +      
348        // Get the Node number which has this atom;
349        
350 <      which_node = AtomToProcMap[i];    
350 >      which_node = AtomToProcMap[i];
351        
352 <      if (which_node == 0 ) {
352 >      if (which_node != 0) {
353 >
354 >        if (potatoes[which_node] + 3 >= MAXTAG) {
355 >          // The potato was going to exceed the maximum value,
356 >          // so wrap this processor potato back to 0:        
357 >
358 >          potatoes[which_node] = 0;          
359 >          MPI_Send(0, 1, MPI_INT, which_node, 0, MPI_COMM_WORLD);
360 >          
361 >        }
362 >
363 >        myPotato = potatoes[which_node];        
364 >        
365 >        MPI_Recv(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, which_node,
366 >                 myPotato, MPI_COMM_WORLD, &istatus);
367 >        
368 >        atomTypeString = MPIatomTypeString;
369          
370 <        haveError = 0;
371 <        which_atom = i;
372 <        local_index=-1;        
373 <        for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) {
374 <          if (atoms[j]->getGlobalIndex() == which_atom) local_index = j;
370 >        myPotato++;
371 >
372 >        MPI_Recv(&isDirectional, 1, MPI_INT, which_node,
373 >                 myPotato, MPI_COMM_WORLD, &istatus);
374 >              
375 >        myPotato++;
376 >
377 >        if (isDirectional) {          
378 >          MPI_Recv(atomData13, 13, MPI_DOUBLE, which_node,
379 >                   myPotato, MPI_COMM_WORLD, &istatus);
380 >        } else {
381 >          MPI_Recv(atomData6, 6, MPI_DOUBLE, which_node,
382 >                   myPotato, MPI_COMM_WORLD, &istatus);          
383          }
384 <        if (local_index != -1) {
385 <          //format the line
386 <          
194 <          atoms[local_index]->getPos(pos);
195 <          atoms[local_index]->getVel(vel);
384 >        
385 >        myPotato++;
386 >        potatoes[which_node] = myPotato;
387  
388 <          sprintf( tempBuffer,
389 <                   "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
390 <                   atoms[local_index]->getType(),
391 <                   pos[0],
392 <                   pos[1],
393 <                   pos[2],
394 <                   vel[0],
395 <                   vel[1],
396 <                   vel[2]); // check here.
397 <          strcpy( writeLine, tempBuffer );
388 >      } else {
389 >        
390 >        haveError = 0;
391 >        which_atom = i;
392 >        
393 >          local_index = indexArray[currentIndex].first;        
394 >          
395 >          if (which_atom == indexArray[currentIndex].second) {
396 >            
397 >            atomTypeString = atoms[local_index]->getType();
398 >            
399 >          atoms[local_index]->getPos(pos);
400 >          atoms[local_index]->getVel(vel);          
401            
402 +          atomData6[0] = pos[0];
403 +          atomData6[1] = pos[1];
404 +          atomData6[2] = pos[2];
405 +
406 +          atomData6[3] = vel[0];
407 +          atomData6[4] = vel[1];
408 +          atomData6[5] = vel[2];
409 +          
410 +          isDirectional = 0;
411 +
412            if( atoms[local_index]->isDirectional() ){
413 +
414 +            isDirectional = 1;
415              
416              dAtom = (DirectionalAtom *)atoms[local_index];
417              dAtom->getQ( q );
418 +
419 +            for (int j = 0; j < 6 ; j++)
420 +              atomData13[j] = atomData6[j];            
421              
422 <            sprintf( tempBuffer,
423 <                     "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
424 <                     q[0],
425 <                     q[1],
426 <                     q[2],
427 <                     q[3],
428 <                     dAtom->getJx(),
429 <                     dAtom->getJy(),
430 <                     dAtom->getJz());
431 <            strcat( writeLine, tempBuffer );
432 <            
224 <          }
225 <          else
226 <            strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );      
227 <        }
228 <        else {
422 >            atomData13[6] = q[0];
423 >            atomData13[7] = q[1];
424 >            atomData13[8] = q[2];
425 >            atomData13[9] = q[3];
426 >            
427 >            atomData13[10] = dAtom->getJx();
428 >            atomData13[11] = dAtom->getJy();
429 >            atomData13[12] = dAtom->getJz();
430 >          }
431 >          
432 >        } else {
433            sprintf(painCave.errMsg,
434 <                  "Atom %d not found on processor %d\n",
435 <                  i, worldRank );
434 >                  "Atom %d not found on processor %d, currentIndex = %d, local_index = %d\n",
435 >                  which_atom, worldRank, currentIndex, local_index );
436            haveError= 1;
437            simError();
438 <        }
439 <        
440 <        if(haveError) nodeZeroError();
441 <
438 >        }
439 >        
440 >        if(haveError) DieDieDie();
441 >        
442 >        currentIndex++;
443        }
444 <      else {
445 <        myStatus = 1;
446 <        MPI_Send(&myStatus, 1, MPI_INT, which_node,
242 <                 TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
243 <        MPI_Send(&i, 1, MPI_INT, which_node, TAKE_THIS_TAG_INT,
244 <                 MPI_COMM_WORLD);
245 <        MPI_Recv(writeLine, BUFFERSIZE, MPI_CHAR, which_node,
246 <                 TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD, &istatus);
247 <        MPI_Recv(&myStatus, 1, MPI_INT, which_node,
248 <                 TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus);
444 >      // If we've survived to here, format the line:
445 >      
446 >      if (!isDirectional) {
447          
448 <        if(!myStatus) nodeZeroError();
449 <
448 >        sprintf( writeLine,
449 >                 "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
450 >                 atomTypeString,
451 >                 atomData6[0],
452 >                 atomData6[1],
453 >                 atomData6[2],
454 >                 atomData6[3],
455 >                 atomData6[4],
456 >                 atomData6[5]);
457 >        
458 >        strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
459 >        
460 >      } else {
461 >        
462 >        sprintf( writeLine,
463 >                 "%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",
464 >                 atomTypeString,
465 >                 atomData13[0],
466 >                 atomData13[1],
467 >                 atomData13[2],
468 >                 atomData13[3],
469 >                 atomData13[4],
470 >                 atomData13[5],
471 >                 atomData13[6],
472 >                 atomData13[7],
473 >                 atomData13[8],
474 >                 atomData13[9],
475 >                 atomData13[10],
476 >                 atomData13[11],
477 >                 atomData13[12]);
478 >        
479        }
480        
481 <      outFile << writeLine;
482 <      outFile.flush();
481 >      for(k = 0; k < outFile.size(); k++)
482 >        *outFile[k] << writeLine;
483      }
484      
485 <    // kill everyone off:
486 <    myStatus = -1;
260 <    for (j = 0; j < mpiSim->getNumberProcessors(); j++) {      
261 <      MPI_Send(&myStatus, 1, MPI_INT, j,
262 <               TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
263 <    }
264 <
265 <  } else {
485 >    for(k = 0; k < outFile.size(); k++)
486 >      outFile[k]->flush();
487      
488 <    done = 0;
489 <    while (!done) {
269 <      
270 <      MPI_Recv(&myStatus, 1, MPI_INT, 0,
271 <               TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus);
272 <
273 <      if(!myStatus) anonymousNodeDie();
274 <      
275 <      if(myStatus < 0) break;
276 <
277 <      MPI_Recv(&which_atom, 1, MPI_INT, 0,
278 <               TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus);
279 <      
280 <      myStatus = 1;
281 <      local_index=-1;        
282 <      for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) {
283 <        if (atoms[j]->getGlobalIndex() == which_atom) local_index = j;
284 <      }
285 <      if (local_index != -1) {
286 <        //format the line
287 <
288 <        atoms[local_index]->getPos(pos);
289 <        atoms[local_index]->getVel(vel);
290 <
291 <        sprintf( tempBuffer,
292 <                 "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
293 <                 atoms[local_index]->getType(),
294 <                 pos[0],
295 <                 pos[1],
296 <                 pos[2],
297 <                 vel[0],
298 <                 vel[1],
299 <                 vel[2]); // check here.
300 <        strcpy( writeLine, tempBuffer );
301 <        
302 <        if( atoms[local_index]->isDirectional() ){
303 <          
304 <          dAtom = (DirectionalAtom *)atoms[local_index];
305 <          dAtom->getQ( q );
306 <          
307 <          sprintf( tempBuffer,
308 <                   "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
309 <                   q[0],
310 <                   q[1],
311 <                   q[2],
312 <                   q[3],
313 <                   dAtom->getJx(),
314 <                   dAtom->getJy(),
315 <                   dAtom->getJz());
316 <          strcat( writeLine, tempBuffer );
317 <        }
318 <        else{
319 <          strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
320 <        }
321 <      }
322 <      else {
323 <        sprintf(painCave.errMsg,
324 <                "Atom %d not found on processor %d\n",
325 <                which_atom, worldRank );
326 <        myStatus = 0;
327 <        simError();
328 <
329 <        strcpy( writeLine, "Hello, I'm an error.\n");
330 <      }
331 <
332 <      MPI_Send(writeLine, BUFFERSIZE, MPI_CHAR, 0,
333 <               TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD);
334 <      MPI_Send( &myStatus, 1, MPI_INT, 0,
335 <                TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
336 <    }
337 <  }  
338 <  outFile.flush();
339 <  sprintf( checkPointMsg,
340 <           "Sucessfully took a dump.\n");
341 <  MPIcheckPoint();
342 <
343 < // last  thing last, enable  fatalities.
344 <  painCave.isEventLoop = 0;
345 <
346 < #endif // is_mpi
347 < }
348 <
349 < void DumpWriter::writeFinal(double finalTime){
350 <
351 <  char finalName[500];
352 <  ofstream finalOut;
353 <
354 <  const int BUFFERSIZE = 2000;
355 <  char tempBuffer[BUFFERSIZE];
356 <  char writeLine[BUFFERSIZE];  
357 <
358 <  double q[4];
359 <  DirectionalAtom* dAtom;
360 <  Atom** atoms = entry_plug->atoms;
361 <  int i;
362 < #ifdef IS_MPI
363 <  int j, which_node, done, which_atom, local_index;
364 < #else //is_mpi
365 <  int nAtoms = entry_plug->n_atoms;
366 < #endif //is_mpi
367 <  
368 <  double pos[3], vel[3];
369 <  
370 < #ifdef IS_MPI
371 <  if(worldRank == 0 ){
372 < #endif // is_mpi
488 >    sprintf( checkPointMsg,
489 >             "Sucessfully took a dump.\n");
490      
491 <    strcpy( finalName, entry_plug->finalName );
491 >    MPIcheckPoint();        
492      
493 <    finalOut.open( finalName, ios::out | ios::trunc );
377 <    if( !finalOut ){
378 <      sprintf( painCave.errMsg,
379 <               "Could not open \"%s\" for final dump output.\n",
380 <               finalName );
381 <      painCave.isFatal = 1;
382 <      simError();
383 <    }
493 >    delete[] potatoes;
494      
495 <    // finalOut.setf( ios::scientific );
386 <    
387 < #ifdef IS_MPI
388 <  }
389 <  
390 <  sprintf(checkPointMsg,"Opened file for final configuration\n");
391 <  MPIcheckPoint();  
392 <  
393 < #endif //is_mpi
495 >  } else {
496  
497 <  
396 < #ifndef IS_MPI
397 <    
398 <  finalOut << nAtoms << "\n";
399 <    
400 <  finalOut << finalTime << ";\t"
401 <           << entry_plug->Hmat[0][0] << "\t"
402 <           << entry_plug->Hmat[1][0] << "\t"
403 <           << entry_plug->Hmat[2][0] << ";\t"
404 <    
405 <           << entry_plug->Hmat[0][1] << "\t"
406 <           << entry_plug->Hmat[1][1] << "\t"
407 <           << entry_plug->Hmat[2][1] << ";\t"
408 <    
409 <           << entry_plug->Hmat[0][2] << "\t"
410 <           << entry_plug->Hmat[1][2] << "\t"
411 <           << entry_plug->Hmat[2][2] << ";\n";
412 <  
413 <  for( i=0; i<nAtoms; i++ ){
414 <      
415 <    atoms[i]->getPos(pos);
416 <    atoms[i]->getVel(vel);
417 <    
418 <    sprintf( tempBuffer,
419 <             "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
420 <             atoms[i]->getType(),
421 <             pos[0],
422 <             pos[1],
423 <             pos[2],
424 <             vel[0],
425 <             vel[1],
426 <             vel[2]);
427 <    strcpy( writeLine, tempBuffer );
497 >    // worldRank != 0, so I'm a remote node.  
498  
499 <    if( atoms[i]->isDirectional() ){
430 <        
431 <      dAtom = (DirectionalAtom *)atoms[i];
432 <      dAtom->getQ( q );
433 <        
434 <      sprintf( tempBuffer,
435 <               "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
436 <               q[0],
437 <               q[1],
438 <               q[2],
439 <               q[3],
440 <               dAtom->getJx(),
441 <               dAtom->getJy(),
442 <               dAtom->getJz());
443 <      strcat( writeLine, tempBuffer );
444 <    }
445 <    else
446 <      strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
447 <      
448 <    finalOut << writeLine;
449 <  }
450 <  finalOut.flush();
451 <  finalOut.close();
499 >    // Set my magic potato to 0:
500  
501 < #else // is_mpi
502 <  
455 <  // first thing first, suspend fatalities.
456 <  painCave.isEventLoop = 1;
457 <
458 <  int myStatus; // 1 = wakeup & success; 0 = error; -1 = AllDone
459 <  int haveError;
460 <
461 <  MPI_Status istatus;
462 <  int *AtomToProcMap = mpiSim->getAtomToProcMap();
463 <
464 <  // write out header and node 0's coordinates
465 <  
466 <  haveError = 0;
467 <  if( worldRank == 0 ){
468 <    finalOut << mpiSim->getTotAtoms() << "\n";
501 >    myPotato = 0;
502 >    currentIndex = 0;
503      
470 –    finalOut << finalTime << ";\t"
471 –             << entry_plug->Hmat[0][0] << "\t"
472 –             << entry_plug->Hmat[1][0] << "\t"
473 –             << entry_plug->Hmat[2][0] << ";\t"
474 –      
475 –             << entry_plug->Hmat[0][1] << "\t"
476 –             << entry_plug->Hmat[1][1] << "\t"
477 –             << entry_plug->Hmat[2][1] << ";\t"
478 –      
479 –             << entry_plug->Hmat[0][2] << "\t"
480 –             << entry_plug->Hmat[1][2] << "\t"
481 –             << entry_plug->Hmat[2][2] << ";\n";
482 –    
504      for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) {
484 –      // Get the Node number which has this molecule:
505        
506 <      which_node = AtomToProcMap[i];    
506 >      // Am I the node which has this atom?
507        
508 <      if (which_node == mpiSim->getMyNode()) {
508 >      if (AtomToProcMap[i] == worldRank) {
509  
510 <        which_atom = i;
511 <        local_index=-1;        
512 <        for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) {
513 <          if (atoms[j]->getGlobalIndex() == which_atom) local_index = j;
510 >        if (myPotato + 3 >= MAXTAG) {
511 >          
512 >          // The potato was going to exceed the maximum value,
513 >          // so wrap this processor potato back to 0 (and block until
514 >          // node 0 says we can go:
515 >          
516 >          MPI_Recv(&myPotato, 1, MPI_INT, 0, 0, MPI_COMM_WORLD, &istatus);
517 >          
518          }
519 <        if (local_index != -1) {    
519 >        which_atom = i;
520  
521 +        local_index = indexArray[currentIndex].first;        
522 +                
523 +        if (which_atom == indexArray[currentIndex].second) {
524 +        
525 +          atomTypeString = atoms[local_index]->getType();
526 +          
527            atoms[local_index]->getPos(pos);
528            atoms[local_index]->getVel(vel);
529            
530 <          sprintf( tempBuffer,
531 <                   "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
532 <                   atoms[local_index]->getType(),
533 <                   pos[0],
534 <                   pos[1],
535 <                   pos[2],
536 <                   vel[0],
537 <                   vel[1],
538 <                   vel[2]);
539 <          strcpy( writeLine, tempBuffer );
540 <          
541 <          if( atoms[local_index]->isDirectional() ){
542 <            
543 <            dAtom = (DirectionalAtom *)atoms[local_index];
544 <            dAtom->getQ( q );
545 <            
546 <            sprintf( tempBuffer,
547 <                     "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
548 <                     q[0],
549 <                     q[1],
550 <                     q[2],
551 <                     q[3],
552 <                     dAtom->getJx(),
553 <                     dAtom->getJy(),
554 <                     dAtom->getJz());
555 <            strcat( writeLine, tempBuffer );
556 <          }
557 <          else
558 <            strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );      
559 <        }
560 <        else {
530 >          atomData6[0] = pos[0];
531 >          atomData6[1] = pos[1];
532 >          atomData6[2] = pos[2];
533 >
534 >          atomData6[3] = vel[0];
535 >          atomData6[4] = vel[1];
536 >          atomData6[5] = vel[2];
537 >          
538 >          isDirectional = 0;
539 >
540 >          if( atoms[local_index]->isDirectional() ){
541 >
542 >            isDirectional = 1;
543 >            
544 >            dAtom = (DirectionalAtom *)atoms[local_index];
545 >            dAtom->getQ( q );
546 >            
547 >            for (int j = 0; j < 6 ; j++)
548 >              atomData13[j] = atomData6[j];
549 >            
550 >            atomData13[6] = q[0];
551 >            atomData13[7] = q[1];
552 >            atomData13[8] = q[2];
553 >            atomData13[9] = q[3];
554 >  
555 >            atomData13[10] = dAtom->getJx();
556 >            atomData13[11] = dAtom->getJy();
557 >            atomData13[12] = dAtom->getJz();
558 >          }
559 >
560 >        } else {
561            sprintf(painCave.errMsg,
562 <                  "Atom %d not found on processor %d\n",
563 <                  i, worldRank );
562 >                  "Atom %d not found on processor %d, currentIndex = %d, local_index = %d\n",
563 >                  which_atom, worldRank, currentIndex, local_index );
564            haveError= 1;
565            simError();
566 <        }
566 >        }
567 >        
568 >        strncpy(MPIatomTypeString, atomTypeString, MINIBUFFERSIZE);
569  
570 <        if(haveError) nodeZeroError();
571 <    
572 <      }
573 <      else {
570 >        // null terminate the string before sending (just in case):
571 >        MPIatomTypeString[MINIBUFFERSIZE-1] = '\0';
572 >
573 >        MPI_Send(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, 0,
574 >                             myPotato, MPI_COMM_WORLD);
575          
576 <        myStatus = 1;
544 <        MPI_Send(&myStatus, 1, MPI_INT, which_node,
545 <                 TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
546 <        MPI_Send(&i, 1, MPI_INT, which_node, TAKE_THIS_TAG_INT,
547 <                 MPI_COMM_WORLD);
548 <        MPI_Recv(writeLine, BUFFERSIZE, MPI_CHAR, which_node,
549 <                 TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD, &istatus);
550 <        MPI_Recv(&myStatus, 1, MPI_INT, which_node,
551 <                 TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus);
552 <        
553 <        if(!myStatus) nodeZeroError();
554 <      }
555 <      
556 <      finalOut << writeLine;
557 <    }
558 <    
559 <    // kill everyone off:
560 <    myStatus = -1;
561 <    for (j = 0; j < mpiSim->getNumberProcessors(); j++) {      
562 <      MPI_Send(&myStatus, 1, MPI_INT, j,
563 <               TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
564 <    }
576 >        myPotato++;
577  
578 <  } else {
579 <    
580 <    done = 0;
581 <    while (!done) {
578 >        MPI_Send(&isDirectional, 1, MPI_INT, 0,
579 >                             myPotato, MPI_COMM_WORLD);
580 >        
581 >        myPotato++;
582 >        
583 >        if (isDirectional) {
584  
585 <      MPI_Recv(&myStatus, 1, MPI_INT, 0,
586 <               TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus);
587 <      
588 <      if(!myStatus) anonymousNodeDie();
575 <      
576 <      if(myStatus < 0) break;
577 <      
578 <      MPI_Recv(&which_atom, 1, MPI_INT, 0,
579 <               TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus);
580 <      
581 <      myStatus = 1;
582 <      local_index=-1;        
583 <      for (j=0; j < mpiSim->getMyNlocal(); j++) {
584 <        if (atoms[j]->getGlobalIndex() == which_atom) local_index = j;
585 <      }
586 <      if (local_index != -1) {
585 >          MPI_Send(atomData13, 13, MPI_DOUBLE, 0,
586 >                   myPotato, MPI_COMM_WORLD);
587 >          
588 >        } else {
589  
590 <        atoms[local_index]->getPos(pos);
591 <        atoms[local_index]->getVel(vel);
590 >          MPI_Send(atomData6, 6, MPI_DOUBLE, 0,
591 >                   myPotato, MPI_COMM_WORLD);
592 >        }
593  
594 <        //format the line
595 <        sprintf( tempBuffer,
593 <                 "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
594 <                 atoms[local_index]->getType(),
595 <                 pos[0],
596 <                 pos[1],
597 <                 pos[2],
598 <                 vel[0],
599 <                 vel[1],
600 <                 vel[2]); // check here.
601 <        strcpy( writeLine, tempBuffer );
602 <        
603 <        if( atoms[local_index]->isDirectional() ){
604 <          
605 <          dAtom = (DirectionalAtom *)atoms[local_index];
606 <          dAtom->getQ( q );
607 <          
608 <          sprintf( tempBuffer,
609 <                   "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
610 <                   q[0],
611 <                   q[1],
612 <                   q[2],
613 <                   q[3],
614 <                   dAtom->getJx(),
615 <                   dAtom->getJy(),
616 <                   dAtom->getJz());
617 <          strcat( writeLine, tempBuffer );
618 <        }
619 <        else{
620 <          strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
621 <        }
622 <      }
623 <      else {
624 <        sprintf(painCave.errMsg,
625 <                "Atom %d not found on processor %d\n",
626 <                which_atom, worldRank );
627 <        myStatus = 0;
628 <        simError();
629 <        
630 <        strcpy( writeLine, "Hello, I'm an error.\n");
594 >        myPotato++;  
595 >        currentIndex++;    
596        }
632 –
633 –      MPI_Send(writeLine, BUFFERSIZE, MPI_CHAR, 0,
634 –               TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD);
635 –      MPI_Send( &myStatus, 1, MPI_INT, 0,
636 –                TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
597      }
598 <  }
599 <  finalOut.flush();
600 <  sprintf( checkPointMsg,
601 <           "Sucessfully took a dump.\n");
602 <  MPIcheckPoint();
598 >
599 >    sprintf( checkPointMsg,
600 >             "Sucessfully took a dump.\n");
601 >    MPIcheckPoint();        
602 >    
603 >  }
604    
644 –  if( worldRank == 0 ) finalOut.close();    
605   #endif // is_mpi
606   }
607  
648 –
649 –
608   #ifdef IS_MPI
609  
610   // a couple of functions to let us escape the write loop
611  
612 < void dWrite::nodeZeroError( void ){
655 <  int j, myStatus;
656 <  
657 <  myStatus = 0;
658 <  for (j = 0; j < mpiSim->getNumberProcessors(); j++) {      
659 <    MPI_Send( &myStatus, 1, MPI_INT, j,
660 <              TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
661 <  }  
662 <  
612 > void dWrite::DieDieDie( void ){
613  
614    MPI_Finalize();
615    exit (0);
666 –  
616   }
617  
669 – void dWrite::anonymousNodeDie( void ){
670 –
671 –  MPI_Finalize();
672 –  exit (0);
673 – }
674 –
618   #endif //is_mpi

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