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root/group/trunk/OOPSE/libmdtools/DumpWriter.cpp
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Comparing trunk/OOPSE/libmdtools/DumpWriter.cpp (file contents):
Revision 572 by mmeineke, Wed Jul 2 21:26:55 2003 UTC vs.
Revision 1129 by tim, Thu Apr 22 03:29:30 2004 UTC

# Line 1 | Line 1
1 < #include <cstring>
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>
12   #include "mpiSimulation.hpp"
8 – #define TAKE_THIS_TAG_CHAR 1
9 – #define TAKE_THIS_TAG_INT 2
13  
14   namespace dWrite{
15 <  void nodeZeroError( void );
13 <  void anonymousNodeDie( void );
15 >  void DieDieDie( void );
16   }
17  
18   using namespace dWrite;
# Line 26 | Line 28 | DumpWriter::DumpWriter( SimInfo* the_entry_plug ){
28   #ifdef IS_MPI
29    if(worldRank == 0 ){
30   #endif // is_mpi
31 <    
32 <    strcpy( outName, entry_plug->sampleName );
33 <    
34 <    outFile.open(outName, ios::out | ios::trunc );
35 <    
34 <    if( !outFile ){
35 <      
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  
43 –    //outFile.setf( ios::scientific );
44 –
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 57 | 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 <  
69 <  const int BUFFERSIZE = 2000;
70 <  char tempBuffer[BUFFERSIZE];
71 <  char writeLine[BUFFERSIZE];
68 > #ifdef IS_MPI
69  
70 <  int i, j, which_node, done, which_atom, local_index;
71 <  double q[4];
72 <  DirectionalAtom* dAtom;
76 <  int nAtoms = entry_plug->n_atoms;
77 <  Atom** atoms = entry_plug->atoms;
78 <    
70 > /**
71 > * A hook function to load balancing
72 > */
73  
74 < #ifndef IS_MPI
75 <    
76 <  outFile << nAtoms << "\n";
77 <    
78 <  outFile << currentTime << "\t"
79 <          << entry_plug->Hmat[0] << "\t"
80 <          << entry_plug->Hmat[1] << "\t"
81 <          << entry_plug->Hmat[2] << "\t"
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 <          << entry_plug->Hmat[3] << "\t"
87 <          << entry_plug->Hmat[4] << "\t"
88 <          << entry_plug->Hmat[5] << "\t"
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 <          << entry_plug->Hmat[6] << "\t"
94 <          << entry_plug->Hmat[7] << "\t"
95 <          << entry_plug->Hmat[8] << "\n";
96 <    
97 <  for( i=0; i<nAtoms; i++ ){
98 <      
100 > #endif
101  
102 <    sprintf( tempBuffer,
101 <             "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
102 <             atoms[i]->getType(),
103 <             atoms[i]->getX(),
104 <             atoms[i]->getY(),
105 <             atoms[i]->getZ(),
106 <             atoms[i]->get_vx(),
107 <             atoms[i]->get_vy(),
108 <             atoms[i]->get_vz());
109 <    strcpy( writeLine, tempBuffer );
102 > void DumpWriter::writeDump(double currentTime){
103  
104 <    if( atoms[i]->isDirectional() ){
105 <        
106 <      dAtom = (DirectionalAtom *)atoms[i];
107 <      dAtom->getQ( q );
108 <        
109 <      sprintf( tempBuffer,
110 <               "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
111 <               q[0],
112 <               q[1],
113 <               q[2],
114 <               q[3],
115 <               dAtom->getJx(),
116 <               dAtom->getJy(),
124 <               dAtom->getJz());
125 <      strcat( writeLine, tempBuffer );
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 <    else
128 <      strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
129 <      
130 <    outFile << writeLine;
118 > #ifdef IS_MPI
119    }
120 <  outFile.flush();
120 > #endif // is_mpi
121  
122 < #else // is_mpi
122 >  fileStreams.push_back(&finalOut);
123 >  fileStreams.push_back(&dumpFile);
124  
125 <  // first thing first, suspend fatalities.
137 <  painCave.isEventLoop = 1;
125 >  writeFrame(fileStreams, currentTime);
126  
127 <  int myStatus; // 1 = wakeup & success; 0 = error; -1 = AllDone
128 <  int haveError;
127 > #ifdef IS_MPI
128 >  finalOut.close();
129 > #endif
130 >        
131 > }
132  
133 <  MPI_Status istatus;
143 <  int *AtomToProcMap = mpiSim->getAtomToProcMap();
144 <  
145 <  // write out header and node 0's coordinates
146 <  
147 <  if( worldRank == 0 ){
148 <    outFile << mpiSim->getTotAtoms() << "\n";
149 <  
150 <    outFile << currentTime << "\t"
151 <            << entry_plug->Hmat[0] << "\t"
152 <            << entry_plug->Hmat[1] << "\t"
153 <            << entry_plug->Hmat[2] << "\t"
154 <      
155 <            << entry_plug->Hmat[3] << "\t"
156 <            << entry_plug->Hmat[4] << "\t"
157 <            << entry_plug->Hmat[5] << "\t"
158 <      
159 <            << entry_plug->Hmat[6] << "\t"
160 <            << entry_plug->Hmat[7] << "\t"
161 <            << entry_plug->Hmat[8] << "\n";
162 <    ;
163 <    outFile.flush();
164 <    for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) {
165 <      // Get the Node number which has this atom;
166 <      
167 <      which_node = AtomToProcMap[i];    
168 <      
169 <      if (which_node == 0 ) {
170 <        
171 <        haveError = 0;
172 <        which_atom = i;
173 <        local_index=-1;        
174 <        for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) {
175 <          if (atoms[j]->getGlobalIndex() == which_atom) local_index = j;
176 <        }
177 <        if (local_index != -1) {
178 <          //format the line
179 <          sprintf( tempBuffer,
180 <                   "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
181 <                   atoms[local_index]->getType(),
182 <                   atoms[local_index]->getX(),
183 <                   atoms[local_index]->getY(),
184 <                   atoms[local_index]->getZ(),
185 <                   atoms[local_index]->get_vx(),
186 <                   atoms[local_index]->get_vy(),
187 <                   atoms[local_index]->get_vz()); // check here.
188 <          strcpy( writeLine, tempBuffer );
189 <          
190 <          if( atoms[local_index]->isDirectional() ){
191 <            
192 <            dAtom = (DirectionalAtom *)atoms[local_index];
193 <            dAtom->getQ( q );
194 <            
195 <            sprintf( tempBuffer,
196 <                     "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
197 <                     q[0],
198 <                     q[1],
199 <                     q[2],
200 <                     q[3],
201 <                     dAtom->getJx(),
202 <                     dAtom->getJy(),
203 <                     dAtom->getJz());
204 <            strcat( writeLine, tempBuffer );
205 <            
206 <          }
207 <          else
208 <            strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );      
209 <        }
210 <        else {
211 <          sprintf(painCave.errMsg,
212 <                  "Atom %d not found on processor %d\n",
213 <                  i, worldRank );
214 <          haveError= 1;
215 <          simError();
216 <        }
217 <        
218 <        if(haveError) nodeZeroError();
133 > void DumpWriter::writeFinal(double currentTime){
134  
135 <      }
136 <      else {
222 <        myStatus = 1;
223 <        MPI_Send(&myStatus, 1, MPI_INT, which_node,
224 <                 TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
225 <        MPI_Send(&i, 1, MPI_INT, which_node, TAKE_THIS_TAG_INT,
226 <                 MPI_COMM_WORLD);
227 <        MPI_Recv(writeLine, BUFFERSIZE, MPI_CHAR, which_node,
228 <                 TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD, &istatus);
229 <        MPI_Recv(&myStatus, 1, MPI_INT, which_node,
230 <                 TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus);
231 <        
232 <        if(!myStatus) nodeZeroError();
233 <
234 <      }
235 <      
236 <      outFile << writeLine;
237 <      outFile.flush();
238 <    }
239 <    
240 <    // kill everyone off:
241 <    myStatus = -1;
242 <    for (j = 0; j < mpiSim->getNumberProcessors(); j++) {      
243 <      MPI_Send(&myStatus, 1, MPI_INT, j,
244 <               TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
245 <    }
246 <
247 <  } else {
248 <    
249 <    done = 0;
250 <    while (!done) {
251 <      
252 <      MPI_Recv(&myStatus, 1, MPI_INT, 0,
253 <               TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus);
254 <
255 <      if(!myStatus) anonymousNodeDie();
256 <      
257 <      if(myStatus < 0) break;
258 <
259 <      MPI_Recv(&which_atom, 1, MPI_INT, 0,
260 <               TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus);
261 <      
262 <      myStatus = 1;
263 <      local_index=-1;        
264 <      for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) {
265 <        if (atoms[j]->getGlobalIndex() == which_atom) local_index = j;
266 <      }
267 <      if (local_index != -1) {
268 <        //format the line
269 <        sprintf( tempBuffer,
270 <                 "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
271 <                 atoms[local_index]->getType(),
272 <                 atoms[local_index]->getX(),
273 <                 atoms[local_index]->getY(),
274 <                 atoms[local_index]->getZ(),
275 <                 atoms[local_index]->get_vx(),
276 <                 atoms[local_index]->get_vy(),
277 <                 atoms[local_index]->get_vz()); // check here.
278 <        strcpy( writeLine, tempBuffer );
279 <        
280 <        if( atoms[local_index]->isDirectional() ){
281 <          
282 <          dAtom = (DirectionalAtom *)atoms[local_index];
283 <          dAtom->getQ( q );
284 <          
285 <          sprintf( tempBuffer,
286 <                   "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
287 <                   q[0],
288 <                   q[1],
289 <                   q[2],
290 <                   q[3],
291 <                   dAtom->getJx(),
292 <                   dAtom->getJy(),
293 <                   dAtom->getJz());
294 <          strcat( writeLine, tempBuffer );
295 <        }
296 <        else{
297 <          strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
298 <        }
299 <      }
300 <      else {
301 <        sprintf(painCave.errMsg,
302 <                "Atom %d not found on processor %d\n",
303 <                which_atom, worldRank );
304 <        myStatus = 0;
305 <        simError();
135 >  ofstream finalOut;
136 >  vector<ofstream*> fileStreams;
137  
307 –        strcpy( writeLine, "Hello, I'm an error.\n");
308 –      }
309 –
310 –      MPI_Send(writeLine, BUFFERSIZE, MPI_CHAR, 0,
311 –               TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD);
312 –      MPI_Send( &myStatus, 1, MPI_INT, 0,
313 –                TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
314 –    }
315 –  }  
316 –  outFile.flush();
317 –  sprintf( checkPointMsg,
318 –           "Sucessfully took a dump.\n");
319 –  MPIcheckPoint();
320 –
321 – // last  thing last, enable  fatalities.
322 –  painCave.isEventLoop = 0;
323 –
324 – #endif // is_mpi
325 – }
326 –
327 – void DumpWriter::writeFinal(double finalTime){
328 –
329 –  char finalName[500];
330 –  ofstream finalOut;
331 –
332 –  const int BUFFERSIZE = 2000;
333 –  char tempBuffer[BUFFERSIZE];
334 –  char writeLine[BUFFERSIZE];  
335 –
336 –  double q[4];
337 –  DirectionalAtom* dAtom;
338 –  int nAtoms = entry_plug->n_atoms;
339 –  Atom** atoms = entry_plug->atoms;
340 –  int i, j, which_node, done, game_over, which_atom, local_index;
341 –  
342 –  
138   #ifdef IS_MPI
139    if(worldRank == 0 ){
140   #endif // is_mpi
141 <    
142 <    strcpy( finalName, entry_plug->finalName );
143 <    
349 <    finalOut.open( finalName, ios::out | ios::trunc );
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 <               finalName );
147 >               entry_plug->finalName );
148        painCave.isFatal = 1;
149        simError();
150      }
151 <    
358 <    // finalOut.setf( ios::scientific );
359 <    
151 >
152   #ifdef IS_MPI
153    }
154 + #endif // is_mpi
155    
156 <  sprintf(checkPointMsg,"Opened file for final configuration\n");
157 <  MPIcheckPoint();  
156 >  fileStreams.push_back(&finalOut);  
157 >  writeFrame(fileStreams, currentTime);
158 >
159 > #ifdef IS_MPI
160 >  finalOut.close();
161 > #endif
162    
163 < #endif //is_mpi
163 > }
164  
165 + void DumpWriter::writeFrame( vector<ofstream*>& outFile, double currentTime ){
166 +
167 +  const int BUFFERSIZE = 2000;
168 +  const int MINIBUFFERSIZE = 100;
169 +
170 +  char tempBuffer[BUFFERSIZE];  
171 +  char writeLine[BUFFERSIZE];
172 +
173 +  int i, k;
174 +
175 + #ifdef IS_MPI
176    
177 +  /*********************************************************************
178 +   * Documentation?  You want DOCUMENTATION?
179 +   *
180 +   * Why all the potatoes below?  
181 +   *
182 +   * To make a long story short, the original version of DumpWriter
183 +   * worked in the most inefficient way possible.  Node 0 would
184 +   * poke each of the node for an individual atom's formatted data
185 +   * as node 0 worked its way down the global index. This was particularly
186 +   * inefficient since the method blocked all processors at every atom
187 +   * (and did it twice!).
188 +   *
189 +   * An intermediate version of DumpWriter could be described from Node
190 +   * zero's perspective as follows:
191 +   *
192 +   *  1) Have 100 of your friends stand in a circle.
193 +   *  2) When you say go, have all of them start tossing potatoes at
194 +   *     you (one at a time).
195 +   *  3) Catch the potatoes.
196 +   *
197 +   * It was an improvement, but MPI has buffers and caches that could
198 +   * best be described in this analogy as "potato nets", so there's no
199 +   * need to block the processors atom-by-atom.
200 +   *
201 +   * This new and improved DumpWriter works in an even more efficient
202 +   * way:
203 +   *
204 +   *  1) Have 100 of your friend stand in a circle.
205 +   *  2) When you say go, have them start tossing 5-pound bags of
206 +   *     potatoes at you.
207 +   *  3) Once you've caught a friend's bag of potatoes,
208 +   *     toss them a spud to let them know they can toss another bag.
209 +   *
210 +   * How's THAT for documentation?
211 +   *
212 +   *********************************************************************/
213 +
214 +  int *potatoes;
215 +  int myPotato;
216 +
217 +  int nProc;
218 +  int j, which_node, done, which_atom, local_index, currentIndex;
219 +  double atomData6[6];
220 +  double atomData13[13];
221 +  int isDirectional;
222 +  char* atomTypeString;
223 +  char MPIatomTypeString[MINIBUFFERSIZE];
224 +  int nObjects;
225 + #endif //is_mpi
226 +
227 +  double q[4], ji[3];
228 +  DirectionalAtom* dAtom;
229 +  double pos[3], vel[3];
230 +  int nTotObjects;
231 +  StuntDouble* sd;
232 +  char* molName;
233 +  vector<StuntDouble*> integrableObjects;
234 +  vector<StuntDouble*>::iterator iter;
235 +  nTotObjects = entry_plug->getTotIntegrableObjects();
236   #ifndef IS_MPI
370 –    
371 –  finalOut << nAtoms << "\n";
372 –    
373 –  finalOut << finalTime << "\t"
374 –           << entry_plug->Hmat[0] << "\t"
375 –           << entry_plug->Hmat[1] << "\t"
376 –           << entry_plug->Hmat[2] << "\t"
377 –    
378 –           << entry_plug->Hmat[3] << "\t"
379 –           << entry_plug->Hmat[4] << "\t"
380 –           << entry_plug->Hmat[5] << "\t"
381 –    
382 –           << entry_plug->Hmat[6] << "\t"
383 –           << entry_plug->Hmat[7] << "\t"
384 –           << entry_plug->Hmat[8] << "\n";
237    
238 <  for( i=0; i<nAtoms; i++ ){
239 <      
388 <    sprintf( tempBuffer,
389 <             "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
390 <             atoms[i]->getType(),
391 <             atoms[i]->getX(),
392 <             atoms[i]->getY(),
393 <             atoms[i]->getZ(),
394 <             atoms[i]->get_vx(),
395 <             atoms[i]->get_vy(),
396 <             atoms[i]->get_vz());
397 <    strcpy( writeLine, tempBuffer );
238 >  for(k = 0; k < outFile.size(); k++){
239 >    *outFile[k] << nTotObjects << "\n";
240  
241 <    if( atoms[i]->isDirectional() ){
242 <        
243 <      dAtom = (DirectionalAtom *)atoms[i];
244 <      dAtom->getQ( q );
245 <        
241 >    *outFile[k] << currentTime << ";\t"
242 >               << entry_plug->Hmat[0][0] << "\t"
243 >                     << entry_plug->Hmat[1][0] << "\t"
244 >                     << entry_plug->Hmat[2][0] << ";\t"
245 >              
246 >               << entry_plug->Hmat[0][1] << "\t"
247 >                     << entry_plug->Hmat[1][1] << "\t"
248 >                     << entry_plug->Hmat[2][1] << ";\t"
249 >
250 >                     << entry_plug->Hmat[0][2] << "\t"
251 >                     << entry_plug->Hmat[1][2] << "\t"
252 >                     << entry_plug->Hmat[2][2] << ";";
253 >
254 >    //write out additional parameters, such as chi and eta
255 >    *outFile[k] << entry_plug->the_integrator->getAdditionalParameters() << endl;
256 >  }
257 >  
258 >  for( i=0; i< entry_plug->n_mol; i++ ){
259 >
260 >    integrableObjects = entry_plug->molecules[i].getIntegrableObjects();
261 >    molName = (entry_plug->compStamps[entry_plug->molecules[i].getStampID()])->getID();
262 >    
263 >    for( iter = integrableObjects.begin();iter !=  integrableObjects.end(); ++iter){
264 >      sd = *iter;
265 >      sd->getPos(pos);
266 >      sd->getVel(vel);
267 >
268        sprintf( tempBuffer,
269 <               "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
270 <               q[0],
271 <               q[1],
272 <               q[2],
273 <               q[3],
274 <               dAtom->getJx(),
275 <               dAtom->getJy(),
276 <               dAtom->getJz());
277 <      strcat( writeLine, tempBuffer );
269 >             "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
270 >             sd->getType(),
271 >             pos[0],
272 >             pos[1],
273 >             pos[2],
274 >             vel[0],
275 >             vel[1],
276 >             vel[2]);
277 >      strcpy( writeLine, tempBuffer );
278 >
279 >      if( sd->isDirectional() ){
280 >
281 >        sd->getQ( q );
282 >        sd->getJ( ji );
283 >
284 >        sprintf( tempBuffer,
285 >               "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
286 >               q[0],
287 >               q[1],
288 >               q[2],
289 >               q[3],
290 >                 ji[0],
291 >                 ji[1],
292 >                 ji[2]);
293 >        strcat( writeLine, tempBuffer );
294 >      }
295 >      else
296 >        strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
297      }
415 –    else
416 –      strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
417 –      
418 –    finalOut << writeLine;
419 –  }
420 –  finalOut.flush();
421 –  finalOut.close();
298  
299 +    
300 +    for(k = 0; k < outFile.size(); k++)
301 +      *outFile[k] << writeLine;
302 + }
303 +
304   #else // is_mpi
305 +
306 +  /* code to find maximum tag value */
307    
308 <  // first thing first, suspend fatalities.
309 <  painCave.isEventLoop = 1;
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  
428 –  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 <  
436 <  haveError = 0;
323 >
324    if( worldRank == 0 ){
325 <    finalOut << mpiSim->getTotAtoms() << "\n";
325 >
326 >    // Node 0 needs a list of the magic potatoes for each processor;
327 >
328 >    nProc = mpiSim->getNumberProcessors();
329 >    potatoes = new int[nProc];
330 >
331 >    //write out the comment lines
332 >    for (i = 0; i < nProc; i++)
333 >      potatoes[i] = 0;
334      
335 <    finalOut << finalTime << "\t"
336 <             << entry_plug->Hmat[0] << "\t"
337 <             << entry_plug->Hmat[1] << "\t"
338 <             << entry_plug->Hmat[2] << "\t"
335 >      for(k = 0; k < outFile.size(); k++){
336 >        *outFile[k] << nTotObjects << "\n";
337 >
338 >        *outFile[k] << currentTime << ";\t"
339 >                         << entry_plug->Hmat[0][0] << "\t"
340 >                         << entry_plug->Hmat[1][0] << "\t"
341 >                         << entry_plug->Hmat[2][0] << ";\t"
342 >
343 >                         << entry_plug->Hmat[0][1] << "\t"
344 >                         << entry_plug->Hmat[1][1] << "\t"
345 >                         << entry_plug->Hmat[2][1] << ";\t"
346 >
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 >    currentIndex = 0;
355 >
356 >    for (i = 0 ; i < mpiSim->getTotNmol(); i++ ) {
357        
358 <             << entry_plug->Hmat[3] << "\t"
446 <             << entry_plug->Hmat[4] << "\t"
447 <             << entry_plug->Hmat[5] << "\t"
358 >      // Get the Node number which has this atom;
359        
360 <             << entry_plug->Hmat[6] << "\t"
450 <             << entry_plug->Hmat[7] << "\t"
451 <             << entry_plug->Hmat[8] << "\n";
452 <    
453 <    for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) {
454 <      // Get the Node number which has this molecule:
360 >      which_node = MolToProcMap[i];
361        
362 <      which_node = AtomToProcMap[i];    
363 <      
364 <      if (which_node == mpiSim->getMyNode()) {
362 >      if (which_node != 0) {
363 >        
364 >        if (potatoes[which_node] + 1 >= MAXTAG) {
365 >          // The potato was going to exceed the maximum value,
366 >          // so wrap this processor potato back to 0:        
367  
368 <        which_atom = i;
369 <        local_index=-1;        
370 <        for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) {
463 <          if (atoms[j]->getGlobalIndex() == which_atom) local_index = j;
368 >          potatoes[which_node] = 0;          
369 >          MPI_Send(&potatoes[which_node], 1, MPI_INT, which_node, 0, MPI_COMM_WORLD);
370 >          
371          }
465 –        if (local_index != -1) {        
466 –          sprintf( tempBuffer,
467 –                   "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
468 –                   atoms[local_index]->getType(),
469 –                   atoms[local_index]->getX(),
470 –                   atoms[local_index]->getY(),
471 –                   atoms[local_index]->getZ(),
472 –                   atoms[local_index]->get_vx(),
473 –                   atoms[local_index]->get_vy(),
474 –                   atoms[local_index]->get_vz());
475 –          strcpy( writeLine, tempBuffer );
476 –          
477 –          if( atoms[local_index]->isDirectional() ){
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 );
492 –          }
493 –          else
494 –            strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );      
495 –        }
496 –        else {
497 –          sprintf(painCave.errMsg,
498 –                  "Atom %d not found on processor %d\n",
499 –                  i, worldRank );
500 –          haveError= 1;
501 –          simError();
502 –        }
372  
373 <        if(haveError) nodeZeroError();
374 <    
375 <      }
376 <      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 <        myStatus = 1;
381 <        MPI_Send(&myStatus, 1, MPI_INT, which_node,
382 <                 TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
383 <        MPI_Send(&i, 1, MPI_INT, which_node, TAKE_THIS_TAG_INT,
384 <                 MPI_COMM_WORLD);
385 <        MPI_Recv(writeLine, BUFFERSIZE, MPI_CHAR, which_node,
386 <                 TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD, &istatus);
387 <        MPI_Recv(&myStatus, 1, MPI_INT, which_node,
388 <                 TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus);
389 <        
390 <        if(!myStatus) nodeZeroError();
380 >        for(int l = 0; l < nCurObj; l++){
381 >
382 >          if (potatoes[which_node] + 3 >= MAXTAG) {
383 >            // The potato was going to exceed the maximum value,
384 >            // so wrap this processor potato back to 0:        
385 >
386 >            potatoes[which_node] = 0;          
387 >            MPI_Send(&potatoes[which_node], 1, MPI_INT, which_node, 0, MPI_COMM_WORLD);
388 >            
389 >          }
390 >
391 >          MPI_Recv(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, which_node,
392 >          myPotato, MPI_COMM_WORLD, &istatus);
393 >
394 >          atomTypeString = MPIatomTypeString;
395 >
396 >          myPotato++;
397 >
398 >          MPI_Recv(&isDirectional, 1, MPI_INT, which_node,
399 >          myPotato, MPI_COMM_WORLD, &istatus);
400 >              
401 >          myPotato++;
402 >
403 >          if (isDirectional) {          
404 >          MPI_Recv(atomData13, 13, MPI_DOUBLE, which_node,
405 >                   myPotato, MPI_COMM_WORLD, &istatus);
406 >          } else {
407 >          MPI_Recv(atomData6, 6, MPI_DOUBLE, which_node,
408 >                   myPotato, MPI_COMM_WORLD, &istatus);          
409 >          }
410 >
411 >          myPotato++;
412 >        }
413 >        potatoes[which_node] = myPotato;
414 >
415 >      } else {
416 >        
417 >        haveError = 0;
418 >        
419 >            local_index = indexArray[currentIndex].first;        
420 >
421 >        integrableObjects = (entry_plug->molecules[local_index]).getIntegrableObjects();
422 >
423 >        for(iter= integrableObjects.begin(); iter != integrableObjects.end(); ++iter){    
424 >                sd = *iter;
425 >            atomTypeString = sd->getType();
426 >            
427 >            sd->getPos(pos);
428 >            sd->getVel(vel);          
429 >          
430 >            atomData6[0] = pos[0];
431 >            atomData6[1] = pos[1];
432 >            atomData6[2] = pos[2];
433 >
434 >            atomData6[3] = vel[0];
435 >            atomData6[4] = vel[1];
436 >            atomData6[5] = vel[2];
437 >              
438 >            isDirectional = 0;
439 >
440 >            if( sd->isDirectional() ){
441 >
442 >              isDirectional = 1;
443 >                
444 >              sd->getQ( q );
445 >              sd->getJ( ji );
446 >
447 >              for (int j = 0; j < 6 ; j++)
448 >                atomData13[j] = atomData6[j];            
449 >              
450 >              atomData13[6] = q[0];
451 >              atomData13[7] = q[1];
452 >              atomData13[8] = q[2];
453 >              atomData13[9] = q[3];
454 >              
455 >              atomData13[10] = ji[0];
456 >              atomData13[11] = ji[1];
457 >              atomData13[12] = ji[2];
458 >            }
459 >            
460 >        }
461 >        
462 >      currentIndex++;
463        }
464 +      // If we've survived to here, format the line:
465        
466 <      finalOut << writeLine;
467 <    }
468 <    
469 <    // kill everyone off:
470 <    myStatus = -1;
471 <    for (j = 0; j < mpiSim->getNumberProcessors(); j++) {      
472 <      MPI_Send(&myStatus, 1, MPI_INT, j,
473 <               TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
466 >      if (!isDirectional) {
467 >        
468 >        sprintf( writeLine,
469 >                 "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
470 >                 atomTypeString,
471 >                 atomData6[0],
472 >                 atomData6[1],
473 >                 atomData6[2],
474 >                 atomData6[3],
475 >                 atomData6[4],
476 >                 atomData6[5]);
477 >        
478 >        strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
479 >        
480 >      } else {
481 >        
482 >        sprintf( writeLine,
483 >                 "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
484 >                 atomTypeString,
485 >                 atomData13[0],
486 >                 atomData13[1],
487 >                 atomData13[2],
488 >                 atomData13[3],
489 >                 atomData13[4],
490 >                 atomData13[5],
491 >                 atomData13[6],
492 >                 atomData13[7],
493 >                 atomData13[8],
494 >                 atomData13[9],
495 >                 atomData13[10],
496 >                 atomData13[11],
497 >                 atomData13[12]);
498 >        
499 >      }
500 >      
501 >      for(k = 0; k < outFile.size(); k++)
502 >        *outFile[k] << writeLine;
503      }
531 –
532 –  } else {
504      
505 <    done = 0;
506 <    while (!done) {
505 >    for(k = 0; k < outFile.size(); k++)
506 >      outFile[k]->flush();
507 >    
508 >    sprintf( checkPointMsg,
509 >             "Sucessfully took a dump.\n");
510 >    
511 >    MPIcheckPoint();        
512 >    
513 >    delete[] potatoes;
514 >    
515 >  } else {
516  
517 <      MPI_Recv(&myStatus, 1, MPI_INT, 0,
518 <               TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus);
517 >    // worldRank != 0, so I'm a remote node.  
518 >
519 >    // Set my magic potato to 0:
520 >
521 >    myPotato = 0;
522 >    currentIndex = 0;
523 >    
524 >    for (i = 0 ; i < mpiSim->getTotNmol(); i++ ) {
525        
526 <      if(!myStatus) anonymousNodeDie();
526 >      // Am I the node which has this integrableObject?
527        
528 <      if(myStatus < 0) break;
543 <      
544 <      MPI_Recv(&which_atom, 1, MPI_INT, 0,
545 <               TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus);
546 <      
547 <      myStatus = 1;
548 <      local_index=-1;        
549 <      for (j=0; j < mpiSim->getMyNlocal(); j++) {
550 <        if (atoms[j]->getGlobalIndex() == which_atom) local_index = j;
551 <      }
552 <      if (local_index != -1) {
528 >      if (MolToProcMap[i] == worldRank) {
529  
530 <        //format the line
531 <        sprintf( tempBuffer,
556 <                 "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
557 <                 atoms[local_index]->getType(),
558 <                 atoms[local_index]->getX(),
559 <                 atoms[local_index]->getY(),
560 <                 atoms[local_index]->getZ(),
561 <                 atoms[local_index]->get_vx(),
562 <                 atoms[local_index]->get_vy(),
563 <                 atoms[local_index]->get_vz()); // check here.
564 <        strcpy( writeLine, tempBuffer );
565 <        
566 <        if( atoms[local_index]->isDirectional() ){
530 >
531 >        if (myPotato + 1 >= MAXTAG) {
532            
533 <          dAtom = (DirectionalAtom *)atoms[local_index];
534 <          dAtom->getQ( q );
533 >          // The potato was going to exceed the maximum value,
534 >          // so wrap this processor potato back to 0 (and block until
535 >          // node 0 says we can go:
536            
537 <          sprintf( tempBuffer,
538 <                   "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
539 <                   q[0],
540 <                   q[1],
541 <                   q[2],
542 <                   q[3],
543 <                   dAtom->getJx(),
544 <                   dAtom->getJy(),
545 <                   dAtom->getJz());
546 <          strcat( writeLine, tempBuffer );
547 <        }
548 <        else{
549 <          strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
550 <        }
551 <      }
552 <      else {
553 <        sprintf(painCave.errMsg,
554 <                "Atom %d not found on processor %d\n",
555 <                which_atom, worldRank );
556 <        myStatus = 0;
557 <        simError();
558 <        
559 <        strcpy( writeLine, "Hello, I'm an error.\n");
537 >          MPI_Recv(&myPotato, 1, MPI_INT, 0, 0, MPI_COMM_WORLD, &istatus);
538 >          
539 >        }
540 >
541 >          local_index = indexArray[currentIndex].first;        
542 >          integrableObjects = entry_plug->molecules[local_index].getIntegrableObjects();
543 >          
544 >          nCurObj = integrableObjects.size();
545 >                      
546 >          MPI_Send(&nCurObj, 1, MPI_INT, 0,
547 >                             myPotato, MPI_COMM_WORLD);
548 >          myPotato++;
549 >
550 >          for( iter = integrableObjects.begin(); iter  != integrableObjects.end(); iter++){
551 >
552 >            if (myPotato + 3 >= MAXTAG) {
553 >          
554 >              // The potato was going to exceed the maximum value,
555 >              // so wrap this processor potato back to 0 (and block until
556 >              // node 0 says we can go:
557 >          
558 >              MPI_Recv(&myPotato, 1, MPI_INT, 0, 0, MPI_COMM_WORLD, &istatus);
559 >              
560 >            }
561 >            
562 >            sd = *iter;
563 >            
564 >            atomTypeString = sd->getType();
565 >
566 >            sd->getPos(pos);
567 >            sd->getVel(vel);
568 >
569 >            atomData6[0] = pos[0];
570 >            atomData6[1] = pos[1];
571 >            atomData6[2] = pos[2];
572 >
573 >            atomData6[3] = vel[0];
574 >            atomData6[4] = vel[1];
575 >            atomData6[5] = vel[2];
576 >              
577 >            isDirectional = 0;
578 >
579 >            if( sd->isDirectional() ){
580 >
581 >                isDirectional = 1;
582 >                
583 >                sd->getQ( q );
584 >                sd->getJ( ji );
585 >                
586 >                for (int j = 0; j < 6 ; j++)
587 >                  atomData13[j] = atomData6[j];
588 >                
589 >                atomData13[6] = q[0];
590 >                atomData13[7] = q[1];
591 >                atomData13[8] = q[2];
592 >                atomData13[9] = q[3];
593 >      
594 >                atomData13[10] = ji[0];
595 >                atomData13[11] = ji[1];
596 >                atomData13[12] = ji[2];
597 >              }
598 >
599 >            
600 >            strncpy(MPIatomTypeString, atomTypeString, MINIBUFFERSIZE);
601 >
602 >            // null terminate the string before sending (just in case):
603 >            MPIatomTypeString[MINIBUFFERSIZE-1] = '\0';
604 >
605 >            MPI_Send(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, 0,
606 >                             myPotato, MPI_COMM_WORLD);
607 >            
608 >            myPotato++;
609 >
610 >            MPI_Send(&isDirectional, 1, MPI_INT, 0,
611 >                             myPotato, MPI_COMM_WORLD);
612 >            
613 >            myPotato++;
614 >            
615 >            if (isDirectional) {
616 >
617 >              MPI_Send(atomData13, 13, MPI_DOUBLE, 0,
618 >                       myPotato, MPI_COMM_WORLD);
619 >              
620 >            } else {
621 >
622 >              MPI_Send(atomData6, 6, MPI_DOUBLE, 0,
623 >                       myPotato, MPI_COMM_WORLD);
624 >            }
625 >
626 >            myPotato++;  
627 >
628 >          }
629 >
630 >          currentIndex++;    
631 >          
632 >        }
633 >      
634        }
635  
636 <      MPI_Send(writeLine, BUFFERSIZE, MPI_CHAR, 0,
637 <               TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD);
638 <      MPI_Send( &myStatus, 1, MPI_INT, 0,
639 <                TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
636 >    sprintf( checkPointMsg,
637 >             "Sucessfully took a dump.\n");
638 >    MPIcheckPoint();                
639 >    
640      }
641 <  }
642 <  finalOut.flush();
603 <  sprintf( checkPointMsg,
604 <           "Sucessfully took a dump.\n");
605 <  MPIcheckPoint();
641 >
642 >
643    
607 –  if( worldRank == 0 ) finalOut.close();    
644   #endif // is_mpi
645   }
646  
611 –
612 –
647   #ifdef IS_MPI
648  
649   // a couple of functions to let us escape the write loop
650  
651 < void dWrite::nodeZeroError( void ){
618 <  int j, myStatus;
619 <  
620 <  myStatus = 0;
621 <  for (j = 0; j < mpiSim->getNumberProcessors(); j++) {      
622 <    MPI_Send( &myStatus, 1, MPI_INT, j,
623 <              TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
624 <  }  
625 <  
651 > void dWrite::DieDieDie( void ){
652  
653    MPI_Finalize();
654    exit (0);
629 –  
655   }
656  
632 – void dWrite::anonymousNodeDie( void ){
633 –
634 –  MPI_Finalize();
635 –  exit (0);
636 – }
637 –
657   #endif //is_mpi

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