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root/group/trunk/OOPSE/libmdtools/DumpWriter.cpp
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Comparing trunk/OOPSE/libmdtools/DumpWriter.cpp (file contents):
Revision 670 by mmeineke, Thu Aug 7 21:47:18 2003 UTC vs.
Revision 1108 by tim, Wed Apr 14 15:37:41 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;
70 > /**
71 > * A hook function to load balancing
72 > */
73  
74 <  double pos[3], vel[3];
75 <    
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 < #ifndef IS_MPI
87 <    
88 <  outFile << nAtoms << "\n";
89 <    
90 <  outFile << currentTime << ";\t"
91 <          << entry_plug->Hmat[0][0] << "\t"
92 <          << entry_plug->Hmat[1][0] << "\t"
93 <          << entry_plug->Hmat[2][0] << ";\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 < mpiSim->getMyNlocal();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[0][1] << "\t"
92 <          << entry_plug->Hmat[1][1] << "\t"
93 <          << entry_plug->Hmat[2][1] << ";\t"
100 > #endif
101  
102 <          << entry_plug->Hmat[0][2] << "\t"
96 <          << entry_plug->Hmat[1][2] << "\t"
97 <          << entry_plug->Hmat[2][2] << ";\n";
98 <    
99 <  for( i=0; i<nAtoms; i++ ){
100 <      
101 <    atoms[i]->getPos(pos);
102 <    atoms[i]->getVel(vel);
102 > void DumpWriter::writeDump(double currentTime){
103  
104 <    sprintf( tempBuffer,
105 <             "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
106 <             atoms[i]->getType(),
107 <             pos[0],
108 <             pos[1],
109 <             pos[2],
110 <             vel[0],
111 <             vel[1],
112 <             vel[2]);
113 <    strcpy( writeLine, tempBuffer );
104 >  ofstream finalOut;
105 >  vector<ofstream*> fileStreams;
106  
107 <    if( atoms[i]->isDirectional() ){
108 <        
109 <      dAtom = (DirectionalAtom *)atoms[i];
110 <      dAtom->getQ( q );
111 <        
112 <      sprintf( tempBuffer,
113 <               "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
114 <               q[0],
115 <               q[1],
116 <               q[2],
125 <               q[3],
126 <               dAtom->getJx(),
127 <               dAtom->getJy(),
128 <               dAtom->getJz());
129 <      strcat( writeLine, tempBuffer );
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
132 <      strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
133 <      
134 <    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.
141 <  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;
147 <  int *AtomToProcMap = mpiSim->getAtomToProcMap();
148 <  
149 <  // write out header and node 0's coordinates
150 <  
151 <  if( worldRank == 0 ){
152 <    outFile << mpiSim->getTotAtoms() << "\n";
153 <  
154 <    outFile << currentTime << ";\t"
155 <            << entry_plug->Hmat[0][0] << "\t"
156 <            << entry_plug->Hmat[1][0] << "\t"
157 <            << entry_plug->Hmat[2][0] << ";\t"
158 <      
159 <            << entry_plug->Hmat[0][1] << "\t"
160 <            << entry_plug->Hmat[1][1] << "\t"
161 <            << entry_plug->Hmat[2][1] << ";\t"
162 <      
163 <            << entry_plug->Hmat[0][2] << "\t"
164 <            << entry_plug->Hmat[1][2] << "\t"
165 <            << entry_plug->Hmat[2][2] << ";\n";
166 <    
167 <    outFile.flush();
168 <    for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) {
169 <      // Get the Node number which has this atom;
170 <      
171 <      which_node = AtomToProcMap[i];    
172 <      
173 <      if (which_node == 0 ) {
174 <        
175 <        haveError = 0;
176 <        which_atom = i;
177 <        local_index=-1;        
178 <        for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) {
179 <          if (atoms[j]->getGlobalIndex() == which_atom) local_index = j;
180 <        }
181 <        if (local_index != -1) {
182 <          //format the line
183 <          
184 <          atoms[local_index]->getPos(pos);
185 <          atoms[local_index]->getVel(vel);
133 > void DumpWriter::writeFinal(double currentTime){
134  
187 –          sprintf( tempBuffer,
188 –                   "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
189 –                   atoms[local_index]->getType(),
190 –                   pos[0],
191 –                   pos[1],
192 –                   pos[2],
193 –                   vel[0],
194 –                   vel[1],
195 –                   vel[2]); // check here.
196 –          strcpy( writeLine, tempBuffer );
197 –          
198 –          if( atoms[local_index]->isDirectional() ){
199 –            
200 –            dAtom = (DirectionalAtom *)atoms[local_index];
201 –            dAtom->getQ( q );
202 –            
203 –            sprintf( tempBuffer,
204 –                     "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
205 –                     q[0],
206 –                     q[1],
207 –                     q[2],
208 –                     q[3],
209 –                     dAtom->getJx(),
210 –                     dAtom->getJy(),
211 –                     dAtom->getJz());
212 –            strcat( writeLine, tempBuffer );
213 –            
214 –          }
215 –          else
216 –            strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );      
217 –        }
218 –        else {
219 –          sprintf(painCave.errMsg,
220 –                  "Atom %d not found on processor %d\n",
221 –                  i, worldRank );
222 –          haveError= 1;
223 –          simError();
224 –        }
225 –        
226 –        if(haveError) nodeZeroError();
227 –
228 –      }
229 –      else {
230 –        myStatus = 1;
231 –        MPI_Send(&myStatus, 1, MPI_INT, which_node,
232 –                 TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
233 –        MPI_Send(&i, 1, MPI_INT, which_node, TAKE_THIS_TAG_INT,
234 –                 MPI_COMM_WORLD);
235 –        MPI_Recv(writeLine, BUFFERSIZE, MPI_CHAR, which_node,
236 –                 TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD, &istatus);
237 –        MPI_Recv(&myStatus, 1, MPI_INT, which_node,
238 –                 TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus);
239 –        
240 –        if(!myStatus) nodeZeroError();
241 –
242 –      }
243 –      
244 –      outFile << writeLine;
245 –      outFile.flush();
246 –    }
247 –    
248 –    // kill everyone off:
249 –    myStatus = -1;
250 –    for (j = 0; j < mpiSim->getNumberProcessors(); j++) {      
251 –      MPI_Send(&myStatus, 1, MPI_INT, j,
252 –               TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
253 –    }
254 –
255 –  } else {
256 –    
257 –    done = 0;
258 –    while (!done) {
259 –      
260 –      MPI_Recv(&myStatus, 1, MPI_INT, 0,
261 –               TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus);
262 –
263 –      if(!myStatus) anonymousNodeDie();
264 –      
265 –      if(myStatus < 0) break;
266 –
267 –      MPI_Recv(&which_atom, 1, MPI_INT, 0,
268 –               TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus);
269 –      
270 –      myStatus = 1;
271 –      local_index=-1;        
272 –      for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) {
273 –        if (atoms[j]->getGlobalIndex() == which_atom) local_index = j;
274 –      }
275 –      if (local_index != -1) {
276 –        //format the line
277 –
278 –        atoms[local_index]->getPos(pos);
279 –        atoms[local_index]->getVel(vel);
280 –
281 –        sprintf( tempBuffer,
282 –                 "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
283 –                 atoms[local_index]->getType(),
284 –                 pos[0],
285 –                 pos[1],
286 –                 pos[2],
287 –                 vel[0],
288 –                 vel[1],
289 –                 vel[2]); // check here.
290 –        strcpy( writeLine, tempBuffer );
291 –        
292 –        if( atoms[local_index]->isDirectional() ){
293 –          
294 –          dAtom = (DirectionalAtom *)atoms[local_index];
295 –          dAtom->getQ( q );
296 –          
297 –          sprintf( tempBuffer,
298 –                   "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
299 –                   q[0],
300 –                   q[1],
301 –                   q[2],
302 –                   q[3],
303 –                   dAtom->getJx(),
304 –                   dAtom->getJy(),
305 –                   dAtom->getJz());
306 –          strcat( writeLine, tempBuffer );
307 –        }
308 –        else{
309 –          strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
310 –        }
311 –      }
312 –      else {
313 –        sprintf(painCave.errMsg,
314 –                "Atom %d not found on processor %d\n",
315 –                which_atom, worldRank );
316 –        myStatus = 0;
317 –        simError();
318 –
319 –        strcpy( writeLine, "Hello, I'm an error.\n");
320 –      }
321 –
322 –      MPI_Send(writeLine, BUFFERSIZE, MPI_CHAR, 0,
323 –               TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD);
324 –      MPI_Send( &myStatus, 1, MPI_INT, 0,
325 –                TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
326 –    }
327 –  }  
328 –  outFile.flush();
329 –  sprintf( checkPointMsg,
330 –           "Sucessfully took a dump.\n");
331 –  MPIcheckPoint();
332 –
333 – // last  thing last, enable  fatalities.
334 –  painCave.isEventLoop = 0;
335 –
336 – #endif // is_mpi
337 – }
338 –
339 – void DumpWriter::writeFinal(double finalTime){
340 –
341 –  char finalName[500];
135    ofstream finalOut;
136 +  vector<ofstream*> fileStreams;
137  
344 –  const int BUFFERSIZE = 2000;
345 –  char tempBuffer[BUFFERSIZE];
346 –  char writeLine[BUFFERSIZE];  
347 –
348 –  double q[4];
349 –  DirectionalAtom* dAtom;
350 –  int nAtoms = entry_plug->n_atoms;
351 –  Atom** atoms = entry_plug->atoms;
352 –  int i, j, which_node, done, game_over, which_atom, local_index;
353 –  
354 –  double pos[3], vel[3];
355 –  
138   #ifdef IS_MPI
139    if(worldRank == 0 ){
140   #endif // is_mpi
141 <    
142 <    strcpy( finalName, entry_plug->finalName );
143 <    
362 <    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 <    
371 <    // finalOut.setf( ios::scientific );
372 <    
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
383 –    
384 –  finalOut << nAtoms << "\n";
385 –    
386 –  finalOut << finalTime << ";\t"
387 –           << entry_plug->Hmat[0][0] << "\t"
388 –           << entry_plug->Hmat[1][0] << "\t"
389 –           << entry_plug->Hmat[2][0] << ";\t"
390 –    
391 –           << entry_plug->Hmat[0][1] << "\t"
392 –           << entry_plug->Hmat[1][1] << "\t"
393 –           << entry_plug->Hmat[2][1] << ";\t"
394 –    
395 –           << entry_plug->Hmat[0][2] << "\t"
396 –           << entry_plug->Hmat[1][2] << "\t"
397 –           << entry_plug->Hmat[2][2] << ";\n";
237    
238 <  for( i=0; i<nAtoms; i++ ){
239 <      
240 <    atoms[i]->getPos(pos);
241 <    atoms[i]->getVel(vel);
238 >  for(k = 0; k < outFile.size(); k++){
239 >    *outFile[k] << nTotObjects << "\n";
240 >
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 <    sprintf( tempBuffer,
264 <             "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
265 <             atoms[i]->getType(),
266 <             pos[0],
408 <             pos[1],
409 <             pos[2],
410 <             vel[0],
411 <             vel[1],
412 <             vel[2]);
413 <    strcpy( writeLine, tempBuffer );
263 >    for( iter = integrableObjects.begin();iter !=  integrableObjects.end(); ++iter){
264 >      sd = *iter;
265 >      sd->getPos(pos);
266 >      sd->getVel(vel);
267  
415 –    if( atoms[i]->isDirectional() ){
416 –        
417 –      dAtom = (DirectionalAtom *)atoms[i];
418 –      dAtom->getQ( q );
419 –        
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      }
431 –    else
432 –      strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
433 –      
434 –    finalOut << writeLine;
435 –  }
436 –  finalOut.flush();
437 –  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  
444 –  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 <  
452 <  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][0] << "\t"
337 <             << entry_plug->Hmat[1][0] << "\t"
338 <             << entry_plug->Hmat[2][0] << ";\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[0][1] << "\t"
462 <             << entry_plug->Hmat[1][1] << "\t"
463 <             << entry_plug->Hmat[2][1] << ";\t"
358 >      // Get the Node number which has this atom;
359        
360 <             << entry_plug->Hmat[0][2] << "\t"
466 <             << entry_plug->Hmat[1][2] << "\t"
467 <             << entry_plug->Hmat[2][2] << ";\n";
468 <    
469 <    for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) {
470 <      // 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++) {
479 <          if (atoms[j]->getGlobalIndex() == which_atom) local_index = j;
368 >          potatoes[which_node] = 0;          
369 >          MPI_Send(0, 1, MPI_INT, which_node, 0, MPI_COMM_WORLD);
370 >          
371          }
481 –        if (local_index != -1) {    
372  
373 <          atoms[local_index]->getPos(pos);
484 <          atoms[local_index]->getVel(vel);
485 <          
486 <          sprintf( tempBuffer,
487 <                   "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
488 <                   atoms[local_index]->getType(),
489 <                   pos[0],
490 <                   pos[1],
491 <                   pos[2],
492 <                   vel[0],
493 <                   vel[1],
494 <                   vel[2]);
495 <          strcpy( writeLine, tempBuffer );
496 <          
497 <          if( atoms[local_index]->isDirectional() ){
498 <            
499 <            dAtom = (DirectionalAtom *)atoms[local_index];
500 <            dAtom->getQ( q );
501 <            
502 <            sprintf( tempBuffer,
503 <                     "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
504 <                     q[0],
505 <                     q[1],
506 <                     q[2],
507 <                     q[3],
508 <                     dAtom->getJx(),
509 <                     dAtom->getJy(),
510 <                     dAtom->getJz());
511 <            strcat( writeLine, tempBuffer );
512 <          }
513 <          else
514 <            strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );      
515 <        }
516 <        else {
517 <          sprintf(painCave.errMsg,
518 <                  "Atom %d not found on processor %d\n",
519 <                  i, worldRank );
520 <          haveError= 1;
521 <          simError();
522 <        }
373 >        myPotato = potatoes[which_node];        
374  
375 <        if(haveError) nodeZeroError();
376 <    
377 <      }
527 <      else {
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          
379 <        myStatus = 1;
530 <        MPI_Send(&myStatus, 1, MPI_INT, which_node,
531 <                 TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
532 <        MPI_Send(&i, 1, MPI_INT, which_node, TAKE_THIS_TAG_INT,
533 <                 MPI_COMM_WORLD);
534 <        MPI_Recv(writeLine, BUFFERSIZE, MPI_CHAR, which_node,
535 <                 TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD, &istatus);
536 <        MPI_Recv(&myStatus, 1, MPI_INT, which_node,
537 <                 TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus);
538 <        
539 <        if(!myStatus) nodeZeroError();
540 <      }
541 <      
542 <      finalOut << writeLine;
543 <    }
544 <    
545 <    // kill everyone off:
546 <    myStatus = -1;
547 <    for (j = 0; j < mpiSim->getNumberProcessors(); j++) {      
548 <      MPI_Send(&myStatus, 1, MPI_INT, j,
549 <               TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
550 <    }
379 >        for(int l = 0; l < nCurObj; l++){
380  
381 <  } else {
382 <    
383 <    done = 0;
555 <    while (!done) {
381 >          if (potatoes[which_node] + 3 >= MAXTAG) {
382 >            // The potato was going to exceed the maximum value,
383 >            // so wrap this processor potato back to 0:        
384  
385 <      MPI_Recv(&myStatus, 1, MPI_INT, 0,
386 <               TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus);
387 <      
388 <      if(!myStatus) anonymousNodeDie();
561 <      
562 <      if(myStatus < 0) break;
563 <      
564 <      MPI_Recv(&which_atom, 1, MPI_INT, 0,
565 <               TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus);
566 <      
567 <      myStatus = 1;
568 <      local_index=-1;        
569 <      for (j=0; j < mpiSim->getMyNlocal(); j++) {
570 <        if (atoms[j]->getGlobalIndex() == which_atom) local_index = j;
571 <      }
572 <      if (local_index != -1) {
385 >            potatoes[which_node] = 0;          
386 >            MPI_Send(0, 1, MPI_INT, which_node, 0, MPI_COMM_WORLD);
387 >            
388 >          }
389  
390 <        atoms[local_index]->getPos(pos);
391 <        atoms[local_index]->getVel(vel);
390 >          MPI_Recv(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, which_node,
391 >          myPotato, MPI_COMM_WORLD, &istatus);
392  
393 <        //format the line
394 <        sprintf( tempBuffer,
395 <                 "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
396 <                 atoms[local_index]->getType(),
397 <                 pos[0],
398 <                 pos[1],
399 <                 pos[2],
400 <                 vel[0],
401 <                 vel[1],
402 <                 vel[2]); // check here.
403 <        strcpy( writeLine, tempBuffer );
404 <        
405 <        if( atoms[local_index]->isDirectional() ){
406 <          
407 <          dAtom = (DirectionalAtom *)atoms[local_index];
408 <          dAtom->getQ( q );
409 <          
410 <          sprintf( tempBuffer,
411 <                   "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
412 <                   q[0],
413 <                   q[1],
414 <                   q[2],
415 <                   q[3],
416 <                   dAtom->getJx(),
417 <                   dAtom->getJy(),
418 <                   dAtom->getJz());
419 <          strcat( writeLine, tempBuffer );
420 <        }
421 <        else{
422 <          strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
423 <        }
424 <      }
425 <      else {
426 <        sprintf(painCave.errMsg,
427 <                "Atom %d not found on processor %d\n",
428 <                which_atom, worldRank );
429 <        myStatus = 0;
430 <        simError();
393 >          atomTypeString = MPIatomTypeString;
394 >
395 >          myPotato++;
396 >
397 >          MPI_Recv(&isDirectional, 1, MPI_INT, which_node,
398 >          myPotato, MPI_COMM_WORLD, &istatus);
399 >              
400 >          myPotato++;
401 >
402 >          if (isDirectional) {          
403 >          MPI_Recv(atomData13, 13, MPI_DOUBLE, which_node,
404 >                   myPotato, MPI_COMM_WORLD, &istatus);
405 >          } else {
406 >          MPI_Recv(atomData6, 6, MPI_DOUBLE, which_node,
407 >                   myPotato, MPI_COMM_WORLD, &istatus);          
408 >          }
409 >
410 >          myPotato++;
411 >        }
412 >        potatoes[which_node] = myPotato;
413 >
414 >      } else {
415 >        
416 >        haveError = 0;
417 >        
418 >            local_index = indexArray[currentIndex].first;        
419 >
420 >        integrableObjects = (entry_plug->molecules[local_index]).getIntegrableObjects();
421 >
422 >        for(iter= integrableObjects.begin(); iter != integrableObjects.end(); ++iter){    
423 >                sd = *iter;
424 >            atomTypeString = sd->getType();
425 >            
426 >            sd->getPos(pos);
427 >            sd->getVel(vel);          
428 >          
429 >            atomData6[0] = pos[0];
430 >            atomData6[1] = pos[1];
431 >            atomData6[2] = pos[2];
432 >
433 >            atomData6[3] = vel[0];
434 >            atomData6[4] = vel[1];
435 >            atomData6[5] = vel[2];
436 >              
437 >            isDirectional = 0;
438 >
439 >            if( sd->isDirectional() ){
440 >
441 >              isDirectional = 1;
442 >                
443 >              sd->getQ( q );
444 >              sd->getJ( ji );
445 >
446 >              for (int j = 0; j < 6 ; j++)
447 >                atomData13[j] = atomData6[j];            
448 >              
449 >              atomData13[6] = q[0];
450 >              atomData13[7] = q[1];
451 >              atomData13[8] = q[2];
452 >              atomData13[9] = q[3];
453 >              
454 >              atomData13[10] = ji[0];
455 >              atomData13[11] = ji[1];
456 >              atomData13[12] = ji[2];
457 >            }
458 >            
459 >        }
460 >        
461 >      currentIndex++;
462 >      }
463 >      // If we've survived to here, format the line:
464 >      
465 >      if (!isDirectional) {
466          
467 <        strcpy( writeLine, "Hello, I'm an error.\n");
467 >        sprintf( writeLine,
468 >                 "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
469 >                 atomTypeString,
470 >                 atomData6[0],
471 >                 atomData6[1],
472 >                 atomData6[2],
473 >                 atomData6[3],
474 >                 atomData6[4],
475 >                 atomData6[5]);
476 >        
477 >        strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
478 >        
479 >      } else {
480 >        
481 >        sprintf( writeLine,
482 >                 "%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",
483 >                 atomTypeString,
484 >                 atomData13[0],
485 >                 atomData13[1],
486 >                 atomData13[2],
487 >                 atomData13[3],
488 >                 atomData13[4],
489 >                 atomData13[5],
490 >                 atomData13[6],
491 >                 atomData13[7],
492 >                 atomData13[8],
493 >                 atomData13[9],
494 >                 atomData13[10],
495 >                 atomData13[11],
496 >                 atomData13[12]);
497 >        
498        }
499 +      
500 +      for(k = 0; k < outFile.size(); k++)
501 +        *outFile[k] << writeLine;
502 +    }
503 +    
504 +    for(k = 0; k < outFile.size(); k++)
505 +      outFile[k]->flush();
506 +    
507 +    sprintf( checkPointMsg,
508 +             "Sucessfully took a dump.\n");
509 +    
510 +    MPIcheckPoint();        
511 +    
512 +    delete[] potatoes;
513 +    
514 +  } else {
515  
516 <      MPI_Send(writeLine, BUFFERSIZE, MPI_CHAR, 0,
517 <               TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD);
518 <      MPI_Send( &myStatus, 1, MPI_INT, 0,
519 <                TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
516 >    // worldRank != 0, so I'm a remote node.  
517 >
518 >    // Set my magic potato to 0:
519 >
520 >    myPotato = 0;
521 >    currentIndex = 0;
522 >    
523 >    for (i = 0 ; i < mpiSim->getTotNmol(); i++ ) {
524 >      
525 >      // Am I the node which has this integrableObject?
526 >      
527 >      if (MolToProcMap[i] == worldRank) {
528 >
529 >
530 >        if (myPotato + 1 >= MAXTAG) {
531 >          
532 >          // The potato was going to exceed the maximum value,
533 >          // so wrap this processor potato back to 0 (and block until
534 >          // node 0 says we can go:
535 >          
536 >          MPI_Recv(&myPotato, 1, MPI_INT, 0, 0, MPI_COMM_WORLD, &istatus);
537 >          
538 >        }
539 >
540 >          local_index = indexArray[currentIndex].first;        
541 >          integrableObjects = entry_plug->molecules[local_index].getIntegrableObjects();
542 >          
543 >          nCurObj = integrableObjects.size();
544 >                      
545 >          MPI_Send(&nCurObj, 1, MPI_INT, 0,
546 >                             myPotato, MPI_COMM_WORLD);
547 >
548 >          for( iter = integrableObjects.begin(); iter  != integrableObjects.end(); iter++){
549 >
550 >            if (myPotato + 3 >= MAXTAG) {
551 >          
552 >              // The potato was going to exceed the maximum value,
553 >              // so wrap this processor potato back to 0 (and block until
554 >              // node 0 says we can go:
555 >          
556 >              MPI_Recv(&myPotato, 1, MPI_INT, 0, 0, MPI_COMM_WORLD, &istatus);
557 >              
558 >            }
559 >            
560 >            sd = *iter;
561 >            
562 >            atomTypeString = sd->getType();
563 >
564 >            sd->getPos(pos);
565 >            sd->getVel(vel);
566 >
567 >            atomData6[0] = pos[0];
568 >            atomData6[1] = pos[1];
569 >            atomData6[2] = pos[2];
570 >
571 >            atomData6[3] = vel[0];
572 >            atomData6[4] = vel[1];
573 >            atomData6[5] = vel[2];
574 >              
575 >            isDirectional = 0;
576 >
577 >            if( sd->isDirectional() ){
578 >
579 >                isDirectional = 1;
580 >                
581 >                sd->getQ( q );
582 >                sd->getJ( ji );
583 >                
584 >                for (int j = 0; j < 6 ; j++)
585 >                  atomData13[j] = atomData6[j];
586 >                
587 >                atomData13[6] = q[0];
588 >                atomData13[7] = q[1];
589 >                atomData13[8] = q[2];
590 >                atomData13[9] = q[3];
591 >      
592 >                atomData13[10] = ji[0];
593 >                atomData13[11] = ji[1];
594 >                atomData13[12] = ji[2];
595 >              }
596 >
597 >            
598 >            strncpy(MPIatomTypeString, atomTypeString, MINIBUFFERSIZE);
599 >
600 >            // null terminate the string before sending (just in case):
601 >            MPIatomTypeString[MINIBUFFERSIZE-1] = '\0';
602 >
603 >            MPI_Send(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, 0,
604 >                             myPotato, MPI_COMM_WORLD);
605 >            
606 >            myPotato++;
607 >
608 >            MPI_Send(&isDirectional, 1, MPI_INT, 0,
609 >                             myPotato, MPI_COMM_WORLD);
610 >            
611 >            myPotato++;
612 >            
613 >            if (isDirectional) {
614 >
615 >              MPI_Send(atomData13, 13, MPI_DOUBLE, 0,
616 >                       myPotato, MPI_COMM_WORLD);
617 >              
618 >            } else {
619 >
620 >              MPI_Send(atomData6, 6, MPI_DOUBLE, 0,
621 >                       myPotato, MPI_COMM_WORLD);
622 >            }
623 >
624 >            myPotato++;  
625 >
626 >          }
627 >
628 >          currentIndex++;    
629 >          
630 >        }
631 >      
632 >      }
633 >    
634      }
635 <  }
636 <  finalOut.flush();
637 <  sprintf( checkPointMsg,
638 <           "Sucessfully took a dump.\n");
639 <  MPIcheckPoint();
635 >
636 >    sprintf( checkPointMsg,
637 >             "Sucessfully took a dump.\n");
638 >    MPIcheckPoint();        
639 >    
640    
630 –  if( worldRank == 0 ) finalOut.close();    
641   #endif // is_mpi
642   }
643  
634 –
635 –
644   #ifdef IS_MPI
645  
646   // a couple of functions to let us escape the write loop
647  
648 < void dWrite::nodeZeroError( void ){
641 <  int j, myStatus;
642 <  
643 <  myStatus = 0;
644 <  for (j = 0; j < mpiSim->getNumberProcessors(); j++) {      
645 <    MPI_Send( &myStatus, 1, MPI_INT, j,
646 <              TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
647 <  }  
648 <  
648 > void dWrite::DieDieDie( void ){
649  
650    MPI_Finalize();
651    exit (0);
652 –  
652   }
653  
655 – void dWrite::anonymousNodeDie( void ){
656 –
657 –  MPI_Finalize();
658 –  exit (0);
659 – }
660 –
654   #endif //is_mpi

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