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root/group/trunk/OOPSE/libmdtools/DumpWriter.cpp
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Comparing trunk/OOPSE/libmdtools/DumpWriter.cpp (file contents):
Revision 437 by chuckv, Fri Mar 28 22:34:02 2003 UTC vs.
Revision 929 by tim, Tue Jan 13 15:46:49 2004 UTC

# Line 1 | Line 1
1 < #include <cstring>
1 > #define _FILE_OFFSET_BITS 64
2 >
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>
7 – #include <mpi++.h>
11   #include "mpiSimulation.hpp"
12 < #define TAKE_THIS_TAG_CHAR 1
13 < #define TAKE_THIS_TAG_INT 2
12 >
13 > namespace dWrite{
14 >  void DieDieDie( void );
15 > }
16 >
17 > using namespace dWrite;
18   #endif //is_mpi
19  
20   #include "ReadWrite.hpp"
# Line 20 | Line 27 | DumpWriter::DumpWriter( SimInfo* the_entry_plug ){
27   #ifdef IS_MPI
28    if(worldRank == 0 ){
29   #endif // is_mpi
30 <    
31 <
32 <    
33 <    strcpy( outName, entry_plug->sampleName );
34 <    
35 <    outFile.open(outName, ios::out | ios::trunc );
29 <    
30 <    if( !outFile ){
31 <      
30 >
31 >
32 >    dumpFile.open(entry_plug->sampleName, ios::out | ios::trunc );
33 >
34 >    if( !dumpFile ){
35 >
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 >
43      //outFile.setf( ios::scientific );
44  
45   #ifdef IS_MPI
46    }
47  
48 +  //sort the local atoms by global index
49 +  sortByGlobalIndex();
50 +  
51    sprintf( checkPointMsg,
52             "Sucessfully opened output file for dumping.\n");
53    MPIcheckPoint();
# Line 53 | Line 60 | DumpWriter::~DumpWriter( ){
60    if(worldRank == 0 ){
61   #endif // is_mpi
62  
63 <    outFile.close();
63 >    dumpFile.close();
64  
65   #ifdef IS_MPI
66    }
67   #endif // is_mpi
68   }
69  
70 < void DumpWriter::writeDump( double currentTime ){
70 > #ifdef IS_MPI
71 >
72 > /**
73 > * A hook function to load balancing
74 > */
75 >
76 > void DumpWriter::update(){
77 >  sortByGlobalIndex();          
78 > }
79    
80 + /**
81 + * Auxiliary sorting function
82 + */
83 +
84 + bool indexSortingCriterion(const pair<int, int>& p1, const pair<int, int>& p2){
85 +  return p1.second < p2.second;
86 + }
87 +
88 + /**
89 + * Sorting the local index by global index
90 + */
91 +
92 + void DumpWriter::sortByGlobalIndex(){
93 +  Atom** atoms = entry_plug->atoms;
94 +  
95 +  indexArray.clear();
96 +  
97 +  for(int i = 0; i < mpiSim->getMyNlocal();i++)
98 +    indexArray.push_back(make_pair(i, atoms[i]->getGlobalIndex()));
99 +  
100 +  sort(indexArray.begin(), indexArray.end(), indexSortingCriterion);    
101 + }
102 + #endif
103 +
104 + void DumpWriter::writeDump(double currentTime){
105 +  
106 + // write to eor file
107 +  writeFinal(currentTime);
108 +
109 + //write to dump file
110 +  writeFrame(dumpFile, currentTime);
111 +        
112 + }
113 +
114 + void DumpWriter::writeFinal(double currentTime){
115 +
116 +  ofstream finalOut;    
117 +  
118 +  //Open eor file
119 + #ifdef IS_MPI
120 +  if(worldRank == 0 ){
121 + #endif // is_mpi
122 +
123 +    finalOut.open( entry_plug->finalName, ios::out | ios::trunc );
124 +    if( !finalOut ){
125 +      sprintf( painCave.errMsg,
126 +               "Could not open \"%s\" for final dump output.\n",
127 +               entry_plug->finalName );
128 +      painCave.isFatal = 1;
129 +      simError();
130 +    }
131 +    
132 + #ifdef IS_MPI
133 +  }
134 + #endif
135 +  
136 +  //write to eor file  
137 +  writeFrame(finalOut, currentTime);
138 +  
139 +  //close eor file      
140 + #ifdef IS_MPI
141 +  if(worldRank == 0 ){
142 +    finalOut.close();
143 +  }
144 + #endif // is_mpi
145 +
146 + }
147 +
148 + void DumpWriter::writeFrame( ofstream& outFile, double currentTime ){
149 +
150    const int BUFFERSIZE = 2000;
151 +  const int MINIBUFFERSIZE = 100;
152 +
153    char tempBuffer[BUFFERSIZE];
154    char writeLine[BUFFERSIZE];
155  
156 <  int i, j, which_node, done, game_over, which_atom, local_index;
156 >  int i;
157 >
158 > #ifdef IS_MPI
159 >  
160 >  int *potatoes;
161 >  int myPotato;
162 >
163 >  int nProc;
164 >  int j, which_node, done, which_atom, local_index, currentIndex;
165 >  double atomData6[6];
166 >  double atomData13[13];
167 >  int isDirectional;
168 >  char* atomTypeString;
169 >  char MPIatomTypeString[MINIBUFFERSIZE];
170 >
171 > #else //is_mpi
172 >  int nAtoms = entry_plug->n_atoms;
173 > #endif //is_mpi
174 >
175    double q[4];
176    DirectionalAtom* dAtom;
72 –  int nAtoms = entry_plug->n_atoms;
177    Atom** atoms = entry_plug->atoms;
178 <    
178 >  double pos[3], vel[3];
179  
180   #ifndef IS_MPI
181 <    
181 >
182    outFile << nAtoms << "\n";
183 <    
184 <  outFile << currentTime << "\t"
185 <          << entry_plug->box_x << "\t"
186 <          << entry_plug->box_y << "\t"
187 <          << entry_plug->box_z << "\n";
188 <    
183 >
184 >  outFile << currentTime << ";\t"
185 >          << entry_plug->Hmat[0][0] << "\t"
186 >          << entry_plug->Hmat[1][0] << "\t"
187 >          << entry_plug->Hmat[2][0] << ";\t"
188 >
189 >          << entry_plug->Hmat[0][1] << "\t"
190 >          << entry_plug->Hmat[1][1] << "\t"
191 >          << entry_plug->Hmat[2][1] << ";\t"
192 >
193 >          << entry_plug->Hmat[0][2] << "\t"
194 >          << entry_plug->Hmat[1][2] << "\t"
195 >          << entry_plug->Hmat[2][2] << ";";
196 >  //write out additional parameters, such as chi and eta
197 >  outFile << entry_plug->the_integrator->getAdditionalParameters();
198 >  outFile << endl;
199 >
200    for( i=0; i<nAtoms; i++ ){
86 –      
201  
202 +    atoms[i]->getPos(pos);
203 +    atoms[i]->getVel(vel);
204 +
205      sprintf( tempBuffer,
206               "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
207               atoms[i]->getType(),
208 <             atoms[i]->getX(),
209 <             atoms[i]->getY(),
210 <             atoms[i]->getZ(),
211 <             atoms[i]->get_vx(),
212 <             atoms[i]->get_vy(),
213 <             atoms[i]->get_vz());
208 >             pos[0],
209 >             pos[1],
210 >             pos[2],
211 >             vel[0],
212 >             vel[1],
213 >             vel[2]);
214      strcpy( writeLine, tempBuffer );
215  
216      if( atoms[i]->isDirectional() ){
217 <        
217 >
218        dAtom = (DirectionalAtom *)atoms[i];
219        dAtom->getQ( q );
220 <        
220 >
221        sprintf( tempBuffer,
222                 "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
223                 q[0],
# Line 114 | Line 231 | void DumpWriter::writeDump( double currentTime ){
231      }
232      else
233        strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
234 <      
234 >
235      outFile << writeLine;
236    }
120 –  outFile.flush();
237  
238   #else // is_mpi
239  
240 <  MPI::Status istatus;
125 <  int *AtomToProcMap = mpiSim->getAtomToProcMap();
240 >  /* code to find maximum tag value */
241    
242 +  int *tagub, flag, MAXTAG;
243 +  MPI_Attr_get(MPI_COMM_WORLD, MPI_TAG_UB, &tagub, &flag);
244 +  if (flag) {
245 +    MAXTAG = *tagub;
246 +  } else {
247 +    MAXTAG = 32767;
248 +  }  
249 +
250 +  int haveError;
251 +
252 +  MPI_Status istatus;
253 +  int *AtomToProcMap = mpiSim->getAtomToProcMap();
254 +
255    // write out header and node 0's coordinates
256 <  
256 >
257    if( worldRank == 0 ){
258 <    outFile << mpiSim->getTotAtoms() << "\n";
258 >
259 >    // Node 0 needs a list of the magic potatoes for each processor;
260 >
261 >    nProc = mpiSim->getNumberProcessors();
262 >    potatoes = new int[nProc];
263 >
264 >    for (i = 0; i < nProc; i++)
265 >      potatoes[i] = 0;
266      
267 <    outFile << currentTime << "\t"
268 <            << entry_plug->box_x << "\t"
269 <            << entry_plug->box_y << "\t"
270 <            << entry_plug->box_z << "\n";
267 >    outFile << mpiSim->getTotAtoms() << "\n";
268 >
269 >    outFile << currentTime << ";\t"
270 >            << entry_plug->Hmat[0][0] << "\t"
271 >            << entry_plug->Hmat[1][0] << "\t"
272 >            << entry_plug->Hmat[2][0] << ";\t"
273 >
274 >            << entry_plug->Hmat[0][1] << "\t"
275 >            << entry_plug->Hmat[1][1] << "\t"
276 >            << entry_plug->Hmat[2][1] << ";\t"
277 >
278 >            << entry_plug->Hmat[0][2] << "\t"
279 >            << entry_plug->Hmat[1][2] << "\t"
280 >            << entry_plug->Hmat[2][2] << ";";
281 >
282 >    outFile << entry_plug->the_integrator->getAdditionalParameters();
283 >    outFile << endl;
284      outFile.flush();
285 +    
286 +    currentIndex = 0;
287      for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) {
288 +      
289        // Get the Node number which has this atom;
290        
291 <      which_node = AtomToProcMap[i];    
291 >      which_node = AtomToProcMap[i];
292        
293 <      if (which_node == 0 ) {
293 >      if (which_node != 0) {
294 >
295 >        if (potatoes[which_node] + 3 >= MAXTAG) {
296 >          // The potato was going to exceed the maximum value,
297 >          // so wrap this processor potato back to 0:        
298 >
299 >          potatoes[which_node] = 0;          
300 >          MPI_Send(0, 1, MPI_INT, which_node, 0, MPI_COMM_WORLD);
301 >          
302 >        }
303 >
304 >        myPotato = potatoes[which_node];        
305 >        
306 >        MPI_Recv(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, which_node,
307 >                 myPotato, MPI_COMM_WORLD, &istatus);
308 >        
309 >        atomTypeString = MPIatomTypeString;
310          
311 <        which_atom = i;
312 <        local_index=-1;        
313 <        for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) {
314 <          if (atoms[j]->getGlobalIndex() == which_atom) local_index = j;
311 >        myPotato++;
312 >
313 >        MPI_Recv(&isDirectional, 1, MPI_INT, which_node,
314 >                 myPotato, MPI_COMM_WORLD, &istatus);
315 >              
316 >        myPotato++;
317 >
318 >        if (isDirectional) {          
319 >          MPI_Recv(atomData13, 13, MPI_DOUBLE, which_node,
320 >                   myPotato, MPI_COMM_WORLD, &istatus);
321 >        } else {
322 >          MPI_Recv(atomData6, 6, MPI_DOUBLE, which_node,
323 >                   myPotato, MPI_COMM_WORLD, &istatus);          
324          }
325 <        if (local_index != -1) {
326 <          //format the line
327 <          sprintf( tempBuffer,
328 <                   "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
329 <                   atoms[local_index]->getType(),
330 <                   atoms[local_index]->getX(),
331 <                   atoms[local_index]->getY(),
332 <                   atoms[local_index]->getZ(),
333 <                   atoms[local_index]->get_vx(),
334 <                   atoms[local_index]->get_vy(),
335 <                   atoms[local_index]->get_vz()); // check here.
336 <          strcpy( writeLine, tempBuffer );
337 <          
325 >        
326 >        myPotato++;
327 >        potatoes[which_node] = myPotato;
328 >
329 >      } else {
330 >        
331 >        haveError = 0;
332 >        which_atom = i;
333 >        
334 >        local_index = indexArray[currentIndex].first;        
335 >                
336 >        if (which_atom == indexArray[currentIndex].second) {
337 >          
338 >          atomTypeString = atoms[local_index]->getType();
339 >
340 >          atoms[local_index]->getPos(pos);
341 >          atoms[local_index]->getVel(vel);          
342 >
343 >          atomData6[0] = pos[0];
344 >          atomData6[1] = pos[1];
345 >          atomData6[2] = pos[2];
346 >
347 >          atomData6[3] = vel[0];
348 >          atomData6[4] = vel[1];
349 >          atomData6[5] = vel[2];
350 >          
351 >          isDirectional = 0;
352 >
353            if( atoms[local_index]->isDirectional() ){
354 +
355 +            isDirectional = 1;
356              
357              dAtom = (DirectionalAtom *)atoms[local_index];
358              dAtom->getQ( q );
359 +
360 +            for (int j = 0; j < 6 ; j++)
361 +              atomData13[j] = atomData6[j];            
362              
363 <            sprintf( tempBuffer,
364 <                     "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
365 <                     q[0],
366 <                     q[1],
367 <                     q[2],
368 <                     q[3],
369 <                     dAtom->getJx(),
370 <                     dAtom->getJy(),
371 <                     dAtom->getJz());
372 <            strcat( writeLine, tempBuffer );
373 <            
374 <          }
375 <          else
376 <            strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );      
363 >            atomData13[6] = q[0];
364 >            atomData13[7] = q[1];
365 >            atomData13[8] = q[2];
366 >            atomData13[9] = q[3];
367 >            
368 >            atomData13[10] = dAtom->getJx();
369 >            atomData13[11] = dAtom->getJy();
370 >            atomData13[12] = dAtom->getJz();
371 >          }
372 >          
373 >        } else {
374 >          sprintf(painCave.errMsg,
375 >                  "Atom %d not found on processor %d\n",
376 >                  i, worldRank );
377 >          haveError= 1;
378 >          simError();
379          }
182 –        else {
183 –          strcpy( writeLine, "ATOM NOT FOUND ON THIS PROCESSOR");
184 –        }
185 –      }
186 –      else {
380          
381 <        //std::cerr << "node 0: sending node " << which_node << " request for atom " << i << "\n";
382 <        MPI::COMM_WORLD.Send(&i, 1, MPI_INT, which_node, TAKE_THIS_TAG_INT);
383 <        //std::cerr << "node 0: sent!\n";
384 <        MPI::COMM_WORLD.Recv(writeLine, BUFFERSIZE, MPI_CHAR, which_node,
385 <                             TAKE_THIS_TAG_CHAR, istatus);
386 <        //std::cerr << "node 0: got this line: " << writeLine;
381 >        if(haveError) DieDieDie();
382 >        
383 >        currentIndex ++;
384 >      }
385 >      // If we've survived to here, format the line:
386 >      
387 >      if (!isDirectional) {
388 >        
389 >        sprintf( writeLine,
390 >                 "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
391 >                 atomTypeString,
392 >                 atomData6[0],
393 >                 atomData6[1],
394 >                 atomData6[2],
395 >                 atomData6[3],
396 >                 atomData6[4],
397 >                 atomData6[5]);
398 >
399 >        strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
400 >        
401 >      } else {
402 >        
403 >        sprintf( writeLine,
404 >                 "%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",
405 >                 atomTypeString,
406 >                 atomData13[0],
407 >                 atomData13[1],
408 >                 atomData13[2],
409 >                 atomData13[3],
410 >                 atomData13[4],
411 >                 atomData13[5],
412 >                 atomData13[6],
413 >                 atomData13[7],
414 >                 atomData13[8],
415 >                 atomData13[9],
416 >                 atomData13[10],
417 >                 atomData13[11],
418 >                 atomData13[12]);
419 >        
420        }
421        
422        outFile << writeLine;
197 –      outFile.flush();
423      }
424      
200 –    // kill everyone off:
201 –    game_over = -1;
202 –    for (j = 0; j < mpiSim->getNumberProcessors(); j++) {      
203 –      MPI::COMM_WORLD.Send(&game_over, 1, MPI_INT, j, TAKE_THIS_TAG_INT);
204 –    }
425  
426 +    outFile.flush();
427 +    sprintf( checkPointMsg,
428 +             "Sucessfully took a dump.\n");
429 +    MPIcheckPoint();        
430 +    delete[] potatoes;
431    } else {
207 –    
208 –    done = 0;
209 –    while (!done) {
210 –      //std::cerr << "node: " << mpiSim->getMyNode() << " Waiting for receive \n";
211 –      MPI::COMM_WORLD.Recv(&which_atom, 1, MPI_INT, 0,
212 –                           TAKE_THIS_TAG_INT, istatus);
213 –      //std::cerr << "node: " << mpiSim->getMyNode() << " got request for atom " << which_atom << "\n";
214 –      if (which_atom == -1) {
215 –        done=1;
216 –        continue;
217 –      } else {
218 –        local_index=-1;        
219 –        for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) {
220 –          if (atoms[j]->getGlobalIndex() == which_atom) local_index = j;
221 –        }
222 –        if (local_index != -1) {
223 –          //format the line
224 –          sprintf( tempBuffer,
225 –                   "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
226 –                   atoms[local_index]->getType(),
227 –                   atoms[local_index]->getX(),
228 –                   atoms[local_index]->getY(),
229 –                   atoms[local_index]->getZ(),
230 –                   atoms[local_index]->get_vx(),
231 –                   atoms[local_index]->get_vy(),
232 –                   atoms[local_index]->get_vz()); // check here.
233 –          strcpy( writeLine, tempBuffer );
234 –          
235 –          if( atoms[local_index]->isDirectional() ){
236 –            
237 –            dAtom = (DirectionalAtom *)atoms[local_index];
238 –            dAtom->getQ( q );
239 –            
240 –            sprintf( tempBuffer,
241 –                     "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
242 –                     q[0],
243 –                     q[1],
244 –                     q[2],
245 –                     q[3],
246 –                     dAtom->getJx(),
247 –                     dAtom->getJy(),
248 –                     dAtom->getJz());
249 –            strcat( writeLine, tempBuffer );
250 –          }
251 –          else
252 –            strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
253 –          // std::cerr << "node: " << mpiSim->getMyNode() << " sending this line" << writeLine;
254 –          MPI::COMM_WORLD.Send(writeLine, BUFFERSIZE, MPI_CHAR, 0,
255 –                               TAKE_THIS_TAG_CHAR);
256 –        } else {
257 –          strcpy( writeLine, "ATOM NOT FOUND ON THIS PROCESSOR");
258 –          MPI::COMM_WORLD.Send(writeLine, BUFFERSIZE, MPI_CHAR, 0,
259 –                               TAKE_THIS_TAG_CHAR);
260 –        }
261 –      }
262 –    }
263 –  }  
264 –  outFile.flush();
265 –  sprintf( checkPointMsg,
266 –           "Sucessfully took a dump.\n");
267 –  MPIcheckPoint();
268 – #endif // is_mpi
269 – }
432  
433 < void DumpWriter::writeFinal(){
433 >    // worldRank != 0, so I'm a remote node.  
434  
435 <  char finalName[500];
274 <  ofstream finalOut;
435 >    // Set my magic potato to 0:
436  
437 <  const int BUFFERSIZE = 2000;
438 <  char tempBuffer[BUFFERSIZE];
278 <  char writeLine[BUFFERSIZE];  
279 <
280 <  double q[4];
281 <  DirectionalAtom* dAtom;
282 <  int nAtoms = entry_plug->n_atoms;
283 <  Atom** atoms = entry_plug->atoms;
284 <  int i, j, which_node, done, game_over, which_atom, local_index;
285 <  
286 <  
287 < #ifdef IS_MPI
288 <  if(worldRank == 0 ){
289 < #endif // is_mpi
437 >    myPotato = 0;
438 >    currentIndex = 0;
439      
440 <    strcpy( finalName, entry_plug->finalName );
292 <    
293 <    finalOut.open( finalName, ios::out | ios::trunc );
294 <    if( !finalOut ){
295 <      sprintf( painCave.errMsg,
296 <               "Could not open \"%s\" for final dump output.\n",
297 <               finalName );
298 <      painCave.isFatal = 1;
299 <      simError();
300 <    }
301 <    
302 <    // finalOut.setf( ios::scientific );
303 <    
304 < #ifdef IS_MPI
305 <  }
306 <  
307 <  sprintf(checkPointMsg,"Opened file for final configuration\n");
308 <  MPIcheckPoint();  
309 <  
310 < #endif //is_mpi
311 <
312 <  
313 < #ifndef IS_MPI
314 <    
315 <  finalOut << nAtoms << "\n";
316 <    
317 <  finalOut << entry_plug->box_x << "\t"
318 <           << entry_plug->box_y << "\t"
319 <           << entry_plug->box_z << "\n";
320 <  
321 <  for( i=0; i<nAtoms; i++ ){
440 >    for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) {
441        
442 <    sprintf( tempBuffer,
324 <             "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
325 <             atoms[i]->getType(),
326 <             atoms[i]->getX(),
327 <             atoms[i]->getY(),
328 <             atoms[i]->getZ(),
329 <             atoms[i]->get_vx(),
330 <             atoms[i]->get_vy(),
331 <             atoms[i]->get_vz());
332 <    strcpy( writeLine, tempBuffer );
333 <
334 <    if( atoms[i]->isDirectional() ){
335 <        
336 <      dAtom = (DirectionalAtom *)atoms[i];
337 <      dAtom->getQ( q );
338 <        
339 <      sprintf( tempBuffer,
340 <               "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
341 <               q[0],
342 <               q[1],
343 <               q[2],
344 <               q[3],
345 <               dAtom->getJx(),
346 <               dAtom->getJy(),
347 <               dAtom->getJz());
348 <      strcat( writeLine, tempBuffer );
349 <    }
350 <    else
351 <      strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
442 >      // Am I the node which has this atom?
443        
444 <    finalOut << writeLine;
354 <  }
355 <  finalOut.flush();
356 <  finalOut.close();
444 >      if (AtomToProcMap[i] == worldRank) {
445  
446 < #else // is_mpi
359 <  
360 <  MPI::Status istatus;
361 <  int *AtomToProcMap = mpiSim->getAtomToProcMap();
446 >        if (myPotato + 3 >= MAXTAG) {
447  
448 <  // write out header and node 0's coordinates
449 <  
450 <  if( worldRank == 0 ){
366 <    finalOut << mpiSim->getTotAtoms() << "\n";
367 <    
368 <    finalOut << entry_plug->box_x << "\t"
369 <            << entry_plug->box_y << "\t"
370 <            << entry_plug->box_z << "\n";
371 <    
372 <    for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) {
373 <      // Get the Node number which has this molecule:
374 <      
375 <      which_node = AtomToProcMap[i];    
376 <      
377 <      if (which_node == mpiSim->getMyNode()) {
448 >          // The potato was going to exceed the maximum value,
449 >          // so wrap this processor potato back to 0 (and block until
450 >          // node 0 says we can go:
451  
452 <        which_atom = i;
453 <        local_index=-1;        
381 <        for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) {
382 <          if (atoms[j]->getGlobalIndex() == which_atom) local_index = j;
452 >          MPI_Recv(&myPotato, 1, MPI_INT, 0, 0, MPI_COMM_WORLD, &istatus);
453 >          
454          }
455 <        if (local_index != -1) {        
456 <          sprintf( tempBuffer,
457 <                   "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
458 <                   atoms[local_index]->getType(),
459 <                   atoms[local_index]->getX(),
460 <                   atoms[local_index]->getY(),
390 <                   atoms[local_index]->getZ(),
391 <                   atoms[local_index]->get_vx(),
392 <                   atoms[local_index]->get_vy(),
393 <                   atoms[local_index]->get_vz());
394 <          strcpy( writeLine, tempBuffer );
395 <          
396 <          if( atoms[local_index]->isDirectional() ){
397 <            
398 <            dAtom = (DirectionalAtom *)atoms[local_index];
399 <            dAtom->getQ( q );
400 <            
401 <            sprintf( tempBuffer,
402 <                     "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
403 <                     q[0],
404 <                     q[1],
405 <                     q[2],
406 <                     q[3],
407 <                     dAtom->getJx(),
408 <                     dAtom->getJy(),
409 <                     dAtom->getJz());
410 <            strcat( writeLine, tempBuffer );
411 <          }
412 <          else
413 <            strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );      
414 <        }
415 <        else {
416 <          strcpy( writeLine, "ATOM NOT FOUND ON THIS PROCESSOR");
417 <        }
418 <    
419 <      } else {
420 <        
421 <        MPI::COMM_WORLD.Send(&i, 1, MPI_INT, which_node, TAKE_THIS_TAG_INT);
422 <        MPI::COMM_WORLD.Recv(writeLine, BUFFERSIZE, MPI_CHAR, which_node,
423 <                                TAKE_THIS_TAG_CHAR, istatus);
424 <      }
425 <      
426 <      finalOut << writeLine;
427 <    }
428 <    
429 <    // kill everyone off:
430 <    game_over = -1;
431 <    for (j = 0; j < mpiSim->getNumberProcessors(); j++) {
432 <      MPI::COMM_WORLD.Send(&game_over, 1, MPI_INT, j, TAKE_THIS_TAG_INT);
433 <    }
455 >        which_atom = i;
456 >        local_index = indexArray[currentIndex].first;        
457 >                
458 >        if (which_atom == indexArray[currentIndex].second) {
459 >        
460 >          atomTypeString = atoms[local_index]->getType();
461  
462 <  } else {
463 <    
437 <    done = 0;
438 <    while (!done) {
439 <      MPI::COMM_WORLD.Recv(&which_atom, 1, MPI_INT, 0,
440 <                           TAKE_THIS_TAG_INT, istatus);
462 >          atoms[local_index]->getPos(pos);
463 >          atoms[local_index]->getVel(vel);
464  
465 <      if (which_atom == -1) {
466 <        done=1;
467 <        continue;
445 <      } else {
465 >          atomData6[0] = pos[0];
466 >          atomData6[1] = pos[1];
467 >          atomData6[2] = pos[2];
468  
469 <        local_index=-1;        
470 <        for (j=0; j < mpiSim->getMyNlocal(); j++) {
471 <          if (atoms[j]->getGlobalIndex() == which_atom) local_index = j;
472 <        }
473 <        if (local_index != -1) {
469 >          atomData6[3] = vel[0];
470 >          atomData6[4] = vel[1];
471 >          atomData6[5] = vel[2];
472 >          
473 >          isDirectional = 0;
474  
453 –          //format the line
454 –          sprintf( tempBuffer,
455 –                   "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
456 –                   atoms[local_index]->getType(),
457 –                   atoms[local_index]->getX(),
458 –                   atoms[local_index]->getY(),
459 –                   atoms[local_index]->getZ(),
460 –                   atoms[local_index]->get_vx(),
461 –                   atoms[local_index]->get_vy(),
462 –                   atoms[local_index]->get_vz()); // check here.
463 –          strcpy( writeLine, tempBuffer );
464 –          
475            if( atoms[local_index]->isDirectional() ){
476 +
477 +            isDirectional = 1;
478              
479              dAtom = (DirectionalAtom *)atoms[local_index];
480              dAtom->getQ( q );
481 <            
482 <            sprintf( tempBuffer,
483 <                     "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
484 <                     q[0],
485 <                     q[1],
486 <                     q[2],
487 <                     q[3],
488 <                     dAtom->getJx(),
489 <                     dAtom->getJy(),
490 <                     dAtom->getJz());
491 <            strcat( writeLine, tempBuffer );
481 >            
482 >            for (int j = 0; j < 6 ; j++)
483 >              atomData13[j] = atomData6[j];
484 >            
485 >            atomData13[6] = q[0];
486 >            atomData13[7] = q[1];
487 >            atomData13[8] = q[2];
488 >            atomData13[9] = q[3];
489 >
490 >            atomData13[10] = dAtom->getJx();
491 >            atomData13[11] = dAtom->getJy();
492 >            atomData13[12] = dAtom->getJz();
493            }
494 <          else
495 <            strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
494 >
495 >        } else {
496 >          sprintf(painCave.errMsg,
497 >                  "Atom %d not found on processor %d\n",
498 >                  i, worldRank );
499 >          haveError= 1;
500 >          simError();
501 >        }
502 >
503 >        strncpy(MPIatomTypeString, atomTypeString, MINIBUFFERSIZE);
504 >
505 >        // null terminate the string before sending (just in case):
506 >        MPIatomTypeString[MINIBUFFERSIZE-1] = '\0';
507 >
508 >        MPI_Send(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, 0,
509 >                 myPotato, MPI_COMM_WORLD);
510 >        
511 >        myPotato++;
512 >
513 >        MPI_Send(&isDirectional, 1, MPI_INT, 0,
514 >                 myPotato, MPI_COMM_WORLD);
515 >        
516 >        myPotato++;
517 >        
518 >        if (isDirectional) {
519 >
520 >          MPI_Send(atomData13, 13, MPI_DOUBLE, 0,
521 >                   myPotato, MPI_COMM_WORLD);
522            
484 –          MPI::COMM_WORLD.Send(writeLine, BUFFERSIZE, MPI_CHAR, 0,
485 –                               TAKE_THIS_TAG_CHAR);
523          } else {
524 <          strcpy( writeLine, "ATOM NOT FOUND ON THIS PROCESSOR");
525 <          MPI::COMM_WORLD.Send(writeLine, BUFFERSIZE, MPI_CHAR, 0,
526 <                               TAKE_THIS_TAG_CHAR);
524 >
525 >          MPI_Send(atomData6, 6, MPI_DOUBLE, 0,
526 >                   myPotato, MPI_COMM_WORLD);
527          }
528 +
529 +        myPotato++;  
530 +        currentIndex++;    
531        }
532      }
493 –  }
494 –  finalOut.flush();
495 –  sprintf( checkPointMsg,
496 –           "Sucessfully took a dump.\n");
497 –  MPIcheckPoint();
533  
534 <  if( worldRank == 0 ) finalOut.close();    
534 >    sprintf( checkPointMsg,
535 >             "Sucessfully took a dump.\n");
536 >    MPIcheckPoint();        
537 >    
538 >  }
539 >  
540   #endif // is_mpi
541   }
542 +
543 + #ifdef IS_MPI
544 +
545 + // a couple of functions to let us escape the write loop
546 +
547 + void dWrite::DieDieDie( void ){
548 +
549 +  MPI_Finalize();
550 +  exit (0);
551 + }
552 +
553 + #endif //is_mpi

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