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root/group/trunk/OOPSE/libmdtools/DumpWriter.cpp
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Comparing trunk/OOPSE/libmdtools/DumpWriter.cpp (file contents):
Revision 591 by gezelter, Fri Jul 11 01:15:28 2003 UTC vs.
Revision 952 by tim, Fri Jan 16 21:55:39 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>
11   #include "mpiSimulation.hpp"
8 – #define TAKE_THIS_TAG_CHAR 1
9 – #define TAKE_THIS_TAG_INT 2
12  
13   namespace dWrite{
14 <  void nodeZeroError( void );
13 <  void anonymousNodeDie( void );
14 >  void DieDieDie( void );
15   }
16  
17   using namespace dWrite;
# Line 26 | Line 27 | DumpWriter::DumpWriter( SimInfo* the_entry_plug ){
27   #ifdef IS_MPI
28    if(worldRank == 0 ){
29   #endif // is_mpi
30 <    
31 <    strcpy( outName, entry_plug->sampleName );
32 <    
33 <    outFile.open(outName, ios::out | ios::trunc );
34 <    
34 <    if( !outFile ){
35 <      
30 >
31 >    dumpFile.open(entry_plug->sampleName, ios::out | ios::trunc );
32 >
33 >    if( !dumpFile ){
34 >
35        sprintf( painCave.errMsg,
36                 "Could not open \"%s\" for dump output.\n",
37 <               outName);
37 >               entry_plug->sampleName);
38        painCave.isFatal = 1;
39        simError();
40      }
41  
43 –    //outFile.setf( ios::scientific );
44 –
42   #ifdef IS_MPI
43    }
44  
45 +  //sort the local atoms by global index
46 +  sortByGlobalIndex();
47 +  
48    sprintf( checkPointMsg,
49             "Sucessfully opened output file for dumping.\n");
50    MPIcheckPoint();
# Line 57 | Line 57 | DumpWriter::~DumpWriter( ){
57    if(worldRank == 0 ){
58   #endif // is_mpi
59  
60 <    outFile.close();
60 >    dumpFile.close();
61  
62   #ifdef IS_MPI
63    }
64   #endif // is_mpi
65   }
66  
67 < void DumpWriter::writeDump( double currentTime ){
67 > #ifdef IS_MPI
68 >
69 > /**
70 > * A hook function to load balancing
71 > */
72 >
73 > void DumpWriter::update(){
74 >  sortByGlobalIndex();          
75 > }
76    
77 <  const int BUFFERSIZE = 2000;
78 <  char tempBuffer[BUFFERSIZE];
79 <  char writeLine[BUFFERSIZE];
77 > /**
78 > * Auxiliary sorting function
79 > */
80 >
81 > bool indexSortingCriterion(const pair<int, int>& p1, const pair<int, int>& p2){
82 >  return p1.second < p2.second;
83 > }
84  
85 <  int i, j, which_node, done, which_atom, local_index;
86 <  double q[4];
87 <  DirectionalAtom* dAtom;
88 <  int nAtoms = entry_plug->n_atoms;
85 > /**
86 > * Sorting the local index by global index
87 > */
88 >
89 > void DumpWriter::sortByGlobalIndex(){
90    Atom** atoms = entry_plug->atoms;
91 <    
91 >  
92 >  indexArray.clear();
93 >  
94 >  for(int i = 0; i < mpiSim->getMyNlocal();i++)
95 >    indexArray.push_back(make_pair(i, atoms[i]->getGlobalIndex()));
96 >  
97 >  sort(indexArray.begin(), indexArray.end(), indexSortingCriterion);    
98  
99 < #ifndef IS_MPI
99 >  //for (int i = 0; i < mpiSim->getMyNlocal(); i++) {
100 >  //  printf("node %d has global %d at local %d\n", worldRank, indexArray[i].second, indexArray[i].first);
101 >  //}
102      
103 <  outFile << nAtoms << "\n";
83 <    
84 <  outFile << currentTime << ";\t"
85 <          << entry_plug->Hmat[0][0] << "\t"
86 <          << entry_plug->Hmat[1][0] << "\t"
87 <          << entry_plug->Hmat[2][0] << ";\t"
103 > }
104  
105 <          << entry_plug->Hmat[0][1] << "\t"
90 <          << entry_plug->Hmat[1][1] << "\t"
91 <          << entry_plug->Hmat[2][1] << ";\t"
105 > #endif
106  
107 <          << entry_plug->Hmat[0][2] << "\t"
94 <          << entry_plug->Hmat[1][2] << "\t"
95 <          << entry_plug->Hmat[2][2] << ";\n";
96 <    
97 <  for( i=0; i<nAtoms; i++ ){
98 <      
107 > void DumpWriter::writeDump(double currentTime){
108  
109 <    sprintf( tempBuffer,
110 <             "%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 );
109 >  ofstream finalOut;
110 >  vector<ofstream*> fileStreams;
111  
112 <    if( atoms[i]->isDirectional() ){
113 <        
114 <      dAtom = (DirectionalAtom *)atoms[i];
115 <      dAtom->getQ( q );
116 <        
117 <      sprintf( tempBuffer,
118 <               "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
119 <               q[0],
120 <               q[1],
121 <               q[2],
121 <               q[3],
122 <               dAtom->getJx(),
123 <               dAtom->getJy(),
124 <               dAtom->getJz());
125 <      strcat( writeLine, tempBuffer );
112 > #ifdef IS_MPI
113 >  if(worldRank == 0 ){
114 > #endif    
115 >    finalOut.open( entry_plug->finalName, ios::out | ios::trunc );
116 >    if( !finalOut ){
117 >      sprintf( painCave.errMsg,
118 >               "Could not open \"%s\" for final dump output.\n",
119 >               entry_plug->finalName );
120 >      painCave.isFatal = 1;
121 >      simError();
122      }
123 <    else
128 <      strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
129 <      
130 <    outFile << writeLine;
123 > #ifdef IS_MPI
124    }
125 <  outFile.flush();
125 > #endif // is_mpi
126  
127 < #else // is_mpi
127 >  fileStreams.push_back(&finalOut);
128 >  fileStreams.push_back(&dumpFile);
129  
130 <  // first thing first, suspend fatalities.
137 <  painCave.isEventLoop = 1;
130 >  writeFrame(fileStreams, currentTime);
131  
132 <  int myStatus; // 1 = wakeup & success; 0 = error; -1 = AllDone
133 <  int haveError;
132 > #ifdef IS_MPI
133 >  finalOut.close();
134 > #endif
135 >        
136 > }
137  
138 <  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][0] << "\t"
152 <            << entry_plug->Hmat[1][0] << "\t"
153 <            << entry_plug->Hmat[2][0] << ";\t"
154 <      
155 <            << entry_plug->Hmat[0][1] << "\t"
156 <            << entry_plug->Hmat[1][1] << "\t"
157 <            << entry_plug->Hmat[2][1] << ";\t"
158 <      
159 <            << entry_plug->Hmat[0][2] << "\t"
160 <            << entry_plug->Hmat[1][2] << "\t"
161 <            << entry_plug->Hmat[2][2] << ";\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();
138 > void DumpWriter::writeFinal(double currentTime){
139  
140 <      }
141 <      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 <    }
140 >  ofstream finalOut;
141 >  vector<ofstream*> fileStreams;
142  
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();
306 –
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 –  
143   #ifdef IS_MPI
144    if(worldRank == 0 ){
145   #endif // is_mpi
146 <    
147 <    strcpy( finalName, entry_plug->finalName );
148 <    
349 <    finalOut.open( finalName, ios::out | ios::trunc );
146 >
147 >    finalOut.open( entry_plug->finalName, ios::out | ios::trunc );
148 >
149      if( !finalOut ){
150        sprintf( painCave.errMsg,
151                 "Could not open \"%s\" for final dump output.\n",
152 <               finalName );
152 >               entry_plug->finalName );
153        painCave.isFatal = 1;
154        simError();
155      }
156 <    
358 <    // finalOut.setf( ios::scientific );
359 <    
156 >
157   #ifdef IS_MPI
158    }
159 + #endif // is_mpi
160    
161 <  sprintf(checkPointMsg,"Opened file for final configuration\n");
162 <  MPIcheckPoint();  
161 >  fileStreams.push_back(&finalOut);  
162 >  writeFrame(fileStreams, currentTime);
163 >
164 > #ifdef IS_MPI
165 >  finalOut.close();
166 > #endif
167    
168 < #endif //is_mpi
168 > }
169  
170 + void DumpWriter::writeFrame( vector<ofstream*>& outFile, double currentTime ){
171 +
172 +  const int BUFFERSIZE = 2000;
173 +  const int MINIBUFFERSIZE = 100;
174 +
175 +  char tempBuffer[BUFFERSIZE];  
176 +  char writeLine[BUFFERSIZE];
177 +
178 +  int i, k;
179 +
180 + #ifdef IS_MPI
181    
182 +  /*********************************************************************
183 +   * Documentation?  You want DOCUMENTATION?
184 +   *
185 +   * Why all the potatoes below?  
186 +   *
187 +   * To make a long story short, the original version of DumpWriter
188 +   * worked in the most inefficient way possible.  Node 0 would
189 +   * poke each of the node for an individual atom's formatted data
190 +   * as node 0 worked its way down the global index. This was particularly
191 +   * inefficient since the method blocked all processors at every atom
192 +   * (and did it twice!).
193 +   *
194 +   * An intermediate version of DumpWriter could be described from Node
195 +   * zero's perspective as follows:
196 +   *
197 +   *  1) Have 100 of your friends stand in a circle.
198 +   *  2) When you say go, have all of them start tossing potatoes at
199 +   *     you (one at a time).
200 +   *  3) Catch the potatoes.
201 +   *
202 +   * It was an improvement, but MPI has buffers and caches that could
203 +   * best be described in this analogy as "potato nets", so there's no
204 +   * need to block the processors atom-by-atom.
205 +   *
206 +   * This new and improved DumpWriter works in an even more efficient
207 +   * way:
208 +   *
209 +   *  1) Have 100 of your friend stand in a circle.
210 +   *  2) When you say go, have them start tossing 5-pound bags of
211 +   *     potatoes at you.
212 +   *  3) Once you've caught a friend's bag of potatoes,
213 +   *     toss them a spud to let them know they can toss another bag.
214 +   *
215 +   * How's THAT for documentation?
216 +   *
217 +   *********************************************************************/
218 +
219 +  int *potatoes;
220 +  int myPotato;
221 +
222 +  int nProc;
223 +  int j, which_node, done, which_atom, local_index, currentIndex;
224 +  double atomData6[6];
225 +  double atomData13[13];
226 +  int isDirectional;
227 +  char* atomTypeString;
228 +  char MPIatomTypeString[MINIBUFFERSIZE];
229 +
230 + #else //is_mpi
231 +  int nAtoms = entry_plug->n_atoms;
232 + #endif //is_mpi
233 +
234 +  double q[4];
235 +  DirectionalAtom* dAtom;
236 +  Atom** atoms = entry_plug->atoms;
237 +  double pos[3], vel[3];
238 +
239   #ifndef IS_MPI
370 –    
371 –  finalOut << nAtoms << "\n";
372 –    
373 –  finalOut << finalTime << ";\t"
374 –           << entry_plug->Hmat[0][0] << "\t"
375 –           << entry_plug->Hmat[1][0] << "\t"
376 –           << entry_plug->Hmat[2][0] << ";\t"
377 –    
378 –           << entry_plug->Hmat[0][1] << "\t"
379 –           << entry_plug->Hmat[1][1] << "\t"
380 –           << entry_plug->Hmat[2][1] << ";\t"
381 –    
382 –           << entry_plug->Hmat[0][2] << "\t"
383 –           << entry_plug->Hmat[1][2] << "\t"
384 –           << entry_plug->Hmat[2][2] << ";\n";
240    
241 +  for(k = 0; k < outFile.size(); k++){
242 +    *outFile[k] << nAtoms << "\n";
243 +
244 +    *outFile[k] << currentTime << ";\t"
245 +               << entry_plug->Hmat[0][0] << "\t"
246 +                     << entry_plug->Hmat[1][0] << "\t"
247 +                     << entry_plug->Hmat[2][0] << ";\t"
248 +              
249 +               << entry_plug->Hmat[0][1] << "\t"
250 +                     << entry_plug->Hmat[1][1] << "\t"
251 +                     << entry_plug->Hmat[2][1] << ";\t"
252 +
253 +                     << entry_plug->Hmat[0][2] << "\t"
254 +                     << entry_plug->Hmat[1][2] << "\t"
255 +                     << entry_plug->Hmat[2][2] << ";";
256 +
257 +    //write out additional parameters, such as chi and eta
258 +    *outFile[k] << entry_plug->the_integrator->getAdditionalParameters() << endl;
259 +  }
260 +  
261    for( i=0; i<nAtoms; i++ ){
262 <      
262 >
263 >    atoms[i]->getPos(pos);
264 >    atoms[i]->getVel(vel);
265 >
266      sprintf( tempBuffer,
267               "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
268               atoms[i]->getType(),
269 <             atoms[i]->getX(),
270 <             atoms[i]->getY(),
271 <             atoms[i]->getZ(),
272 <             atoms[i]->get_vx(),
273 <             atoms[i]->get_vy(),
274 <             atoms[i]->get_vz());
269 >             pos[0],
270 >             pos[1],
271 >             pos[2],
272 >             vel[0],
273 >             vel[1],
274 >             vel[2]);
275      strcpy( writeLine, tempBuffer );
276  
277      if( atoms[i]->isDirectional() ){
278 <        
278 >
279        dAtom = (DirectionalAtom *)atoms[i];
280        dAtom->getQ( q );
281 <        
281 >
282        sprintf( tempBuffer,
283                 "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
284                 q[0],
# Line 414 | Line 292 | void DumpWriter::writeFinal(double finalTime){
292      }
293      else
294        strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
295 <      
296 <    finalOut << writeLine;
295 >
296 >    for(k = 0; k < outFile.size(); k++)
297 >      *outFile[k] << writeLine;
298    }
420 –  finalOut.flush();
421 –  finalOut.close();
299  
300   #else // is_mpi
301 +
302 +  /* code to find maximum tag value */
303    
304 <  // first thing first, suspend fatalities.
305 <  painCave.isEventLoop = 1;
304 >  int *tagub, flag, MAXTAG;
305 >  MPI_Attr_get(MPI_COMM_WORLD, MPI_TAG_UB, &tagub, &flag);
306 >  if (flag) {
307 >    MAXTAG = *tagub;
308 >  } else {
309 >    MAXTAG = 32767;
310 >  }  
311  
428 –  int myStatus; // 1 = wakeup & success; 0 = error; -1 = AllDone
312    int haveError;
313  
314    MPI_Status istatus;
315    int *AtomToProcMap = mpiSim->getAtomToProcMap();
316  
317    // write out header and node 0's coordinates
318 <  
436 <  haveError = 0;
318 >
319    if( worldRank == 0 ){
320 <    finalOut << mpiSim->getTotAtoms() << "\n";
320 >
321 >    // Node 0 needs a list of the magic potatoes for each processor;
322 >
323 >    nProc = mpiSim->getNumberProcessors();
324 >    potatoes = new int[nProc];
325 >
326 >    //write out the comment lines
327 >    for (i = 0; i < nProc; i++)
328 >      potatoes[i] = 0;
329      
330 <    finalOut << finalTime << ";\t"
331 <             << entry_plug->Hmat[0][0] << "\t"
332 <             << entry_plug->Hmat[1][0] << "\t"
333 <             << entry_plug->Hmat[2][0] << ";\t"
334 <      
335 <             << entry_plug->Hmat[0][1] << "\t"
336 <             << entry_plug->Hmat[1][1] << "\t"
337 <             << entry_plug->Hmat[2][1] << ";\t"
338 <      
339 <             << entry_plug->Hmat[0][2] << "\t"
340 <             << entry_plug->Hmat[1][2] << "\t"
341 <             << entry_plug->Hmat[2][2] << ";\n";
342 <    
330 >      for(k = 0; k < outFile.size(); k++){
331 >        *outFile[k] << mpiSim->getTotAtoms() << "\n";
332 >
333 >        *outFile[k] << currentTime << ";\t"
334 >                         << entry_plug->Hmat[0][0] << "\t"
335 >                         << entry_plug->Hmat[1][0] << "\t"
336 >                         << entry_plug->Hmat[2][0] << ";\t"
337 >
338 >                         << entry_plug->Hmat[0][1] << "\t"
339 >                         << entry_plug->Hmat[1][1] << "\t"
340 >                         << entry_plug->Hmat[2][1] << ";\t"
341 >
342 >                         << entry_plug->Hmat[0][2] << "\t"
343 >                         << entry_plug->Hmat[1][2] << "\t"
344 >                         << entry_plug->Hmat[2][2] << ";";
345 >  
346 >        *outFile[k] << entry_plug->the_integrator->getAdditionalParameters() << endl;
347 >    }
348 >
349 >    currentIndex = 0;
350 >
351      for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) {
454 –      // Get the Node number which has this molecule:
352        
353 <      which_node = AtomToProcMap[i];    
353 >      // Get the Node number which has this atom;
354        
355 <      if (which_node == mpiSim->getMyNode()) {
355 >      which_node = AtomToProcMap[i];
356 >      
357 >      if (which_node != 0) {
358  
359 <        which_atom = i;
360 <        local_index=-1;        
361 <        for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) {
362 <          if (atoms[j]->getGlobalIndex() == which_atom) local_index = j;
359 >        if (potatoes[which_node] + 3 >= MAXTAG) {
360 >          // The potato was going to exceed the maximum value,
361 >          // so wrap this processor potato back to 0:        
362 >
363 >          potatoes[which_node] = 0;          
364 >          MPI_Send(0, 1, MPI_INT, which_node, 0, MPI_COMM_WORLD);
365 >          
366          }
367 <        if (local_index != -1) {        
368 <          sprintf( tempBuffer,
369 <                   "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
370 <                   atoms[local_index]->getType(),
371 <                   atoms[local_index]->getX(),
372 <                   atoms[local_index]->getY(),
373 <                   atoms[local_index]->getZ(),
374 <                   atoms[local_index]->get_vx(),
375 <                   atoms[local_index]->get_vy(),
376 <                   atoms[local_index]->get_vz());
377 <          strcpy( writeLine, tempBuffer );
367 >
368 >        myPotato = potatoes[which_node];        
369 >        
370 >        MPI_Recv(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, which_node,
371 >                 myPotato, MPI_COMM_WORLD, &istatus);
372 >        
373 >        atomTypeString = MPIatomTypeString;
374 >        
375 >        myPotato++;
376 >
377 >        MPI_Recv(&isDirectional, 1, MPI_INT, which_node,
378 >                 myPotato, MPI_COMM_WORLD, &istatus);
379 >              
380 >        myPotato++;
381 >
382 >        if (isDirectional) {          
383 >          MPI_Recv(atomData13, 13, MPI_DOUBLE, which_node,
384 >                   myPotato, MPI_COMM_WORLD, &istatus);
385 >        } else {
386 >          MPI_Recv(atomData6, 6, MPI_DOUBLE, which_node,
387 >                   myPotato, MPI_COMM_WORLD, &istatus);          
388 >        }
389 >        
390 >        myPotato++;
391 >        potatoes[which_node] = myPotato;
392 >
393 >      } else {
394 >        
395 >        haveError = 0;
396 >        which_atom = i;
397 >        
398 >        //local_index = -1;
399 >
400 >        //for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) {
401 >        //  if (atoms[j]->getGlobalIndex() == which_atom) local_index = j;
402 >        //}
403 >        
404 >        //if (local_index != -1) {
405            
406 <          if( atoms[local_index]->isDirectional() ){
406 >          local_index = indexArray[currentIndex].first;        
407 >          
408 >          if (which_atom == indexArray[currentIndex].second) {
409              
410 <            dAtom = (DirectionalAtom *)atoms[local_index];
480 <            dAtom->getQ( q );
410 >            atomTypeString = atoms[local_index]->getType();
411              
412 <            sprintf( tempBuffer,
413 <                     "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
414 <                     q[0],
415 <                     q[1],
416 <                     q[2],
417 <                     q[3],
418 <                     dAtom->getJx(),
419 <                     dAtom->getJy(),
420 <                     dAtom->getJz());
421 <            strcat( writeLine, tempBuffer );
422 <          }
423 <          else
424 <            strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );      
425 <        }
426 <        else {
412 >          atoms[local_index]->getPos(pos);
413 >          atoms[local_index]->getVel(vel);          
414 >          
415 >          atomData6[0] = pos[0];
416 >          atomData6[1] = pos[1];
417 >          atomData6[2] = pos[2];
418 >
419 >          atomData6[3] = vel[0];
420 >          atomData6[4] = vel[1];
421 >          atomData6[5] = vel[2];
422 >          
423 >          isDirectional = 0;
424 >
425 >          if( atoms[local_index]->isDirectional() ){
426 >
427 >            isDirectional = 1;
428 >            
429 >            dAtom = (DirectionalAtom *)atoms[local_index];
430 >            dAtom->getQ( q );
431 >
432 >            for (int j = 0; j < 6 ; j++)
433 >              atomData13[j] = atomData6[j];            
434 >            
435 >            atomData13[6] = q[0];
436 >            atomData13[7] = q[1];
437 >            atomData13[8] = q[2];
438 >            atomData13[9] = q[3];
439 >            
440 >            atomData13[10] = dAtom->getJx();
441 >            atomData13[11] = dAtom->getJy();
442 >            atomData13[12] = dAtom->getJz();
443 >          }
444 >          
445 >        } else {
446            sprintf(painCave.errMsg,
447 <                  "Atom %d not found on processor %d\n",
448 <                  i, worldRank );
447 >                  "Atom %d not found on processor %d, currentIndex = %d, local_index = %d\n",
448 >                  which_atom, worldRank, currentIndex, local_index );
449            haveError= 1;
450            simError();
451 <        }
503 <
504 <        if(haveError) nodeZeroError();
505 <    
506 <      }
507 <      else {
451 >        }
452          
453 <        myStatus = 1;
454 <        MPI_Send(&myStatus, 1, MPI_INT, which_node,
455 <                 TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
456 <        MPI_Send(&i, 1, MPI_INT, which_node, TAKE_THIS_TAG_INT,
457 <                 MPI_COMM_WORLD);
458 <        MPI_Recv(writeLine, BUFFERSIZE, MPI_CHAR, which_node,
459 <                 TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD, &istatus);
516 <        MPI_Recv(&myStatus, 1, MPI_INT, which_node,
517 <                 TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus);
453 >        if(haveError) DieDieDie();
454 >        
455 >        currentIndex++;
456 >      }
457 >      // If we've survived to here, format the line:
458 >      
459 >      if (!isDirectional) {
460          
461 <        if(!myStatus) nodeZeroError();
461 >        sprintf( writeLine,
462 >                 "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
463 >                 atomTypeString,
464 >                 atomData6[0],
465 >                 atomData6[1],
466 >                 atomData6[2],
467 >                 atomData6[3],
468 >                 atomData6[4],
469 >                 atomData6[5]);
470 >        
471 >        strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
472 >        
473 >      } else {
474 >        
475 >        sprintf( writeLine,
476 >                 "%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",
477 >                 atomTypeString,
478 >                 atomData13[0],
479 >                 atomData13[1],
480 >                 atomData13[2],
481 >                 atomData13[3],
482 >                 atomData13[4],
483 >                 atomData13[5],
484 >                 atomData13[6],
485 >                 atomData13[7],
486 >                 atomData13[8],
487 >                 atomData13[9],
488 >                 atomData13[10],
489 >                 atomData13[11],
490 >                 atomData13[12]);
491 >        
492        }
493        
494 <      finalOut << writeLine;
494 >      for(k = 0; k < outFile.size(); k++)
495 >        *outFile[k] << writeLine;
496      }
497      
498 <    // kill everyone off:
499 <    myStatus = -1;
527 <    for (j = 0; j < mpiSim->getNumberProcessors(); j++) {      
528 <      MPI_Send(&myStatus, 1, MPI_INT, j,
529 <               TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
530 <    }
531 <
532 <  } else {
498 >    for(k = 0; k < outFile.size(); k++)
499 >      outFile[k]->flush();
500      
501 <    done = 0;
502 <    while (!done) {
501 >    sprintf( checkPointMsg,
502 >             "Sucessfully took a dump.\n");
503 >    
504 >    MPIcheckPoint();        
505 >    
506 >    delete[] potatoes;
507 >    
508 >  } else {
509  
510 <      MPI_Recv(&myStatus, 1, MPI_INT, 0,
511 <               TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus);
510 >    // worldRank != 0, so I'm a remote node.  
511 >
512 >    // Set my magic potato to 0:
513 >
514 >    myPotato = 0;
515 >    currentIndex = 0;
516 >    
517 >    for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) {
518        
519 <      if(!myStatus) anonymousNodeDie();
519 >      // Am I the node which has this atom?
520        
521 <      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) {
521 >      if (AtomToProcMap[i] == worldRank) {
522  
523 <        //format the line
555 <        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() ){
523 >        if (myPotato + 3 >= MAXTAG) {
524            
525 <          dAtom = (DirectionalAtom *)atoms[local_index];
526 <          dAtom->getQ( q );
525 >          // The potato was going to exceed the maximum value,
526 >          // so wrap this processor potato back to 0 (and block until
527 >          // node 0 says we can go:
528            
529 <          sprintf( tempBuffer,
530 <                   "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
531 <                   q[0],
532 <                   q[1],
533 <                   q[2],
534 <                   q[3],
535 <                   dAtom->getJx(),
536 <                   dAtom->getJy(),
537 <                   dAtom->getJz());
538 <          strcat( writeLine, tempBuffer );
529 >          MPI_Recv(&myPotato, 1, MPI_INT, 0, 0, MPI_COMM_WORLD, &istatus);
530 >          
531 >        }
532 >        which_atom = i;
533 >
534 >        //local_index = -1;
535 >
536 >        //for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) {
537 >        // if (atoms[j]->getGlobalIndex() == which_atom) local_index = j;
538 >        //}
539 >        
540 >        //if (local_index != -1) {
541 >
542 >        local_index = indexArray[currentIndex].first;        
543 >                
544 >        if (which_atom == indexArray[currentIndex].second) {
545 >        
546 >          atomTypeString = atoms[local_index]->getType();
547 >          
548 >          atoms[local_index]->getPos(pos);
549 >          atoms[local_index]->getVel(vel);
550 >          
551 >          atomData6[0] = pos[0];
552 >          atomData6[1] = pos[1];
553 >          atomData6[2] = pos[2];
554 >
555 >          atomData6[3] = vel[0];
556 >          atomData6[4] = vel[1];
557 >          atomData6[5] = vel[2];
558 >          
559 >          isDirectional = 0;
560 >
561 >          if( atoms[local_index]->isDirectional() ){
562 >
563 >            isDirectional = 1;
564 >            
565 >            dAtom = (DirectionalAtom *)atoms[local_index];
566 >            dAtom->getQ( q );
567 >            
568 >            for (int j = 0; j < 6 ; j++)
569 >              atomData13[j] = atomData6[j];
570 >            
571 >            atomData13[6] = q[0];
572 >            atomData13[7] = q[1];
573 >            atomData13[8] = q[2];
574 >            atomData13[9] = q[3];
575 >  
576 >            atomData13[10] = dAtom->getJx();
577 >            atomData13[11] = dAtom->getJy();
578 >            atomData13[12] = dAtom->getJz();
579 >          }
580 >
581 >        } else {
582 >          sprintf(painCave.errMsg,
583 >                  "Atom %d not found on processor %d, currentIndex = %d, local_index = %d\n",
584 >                  which_atom, worldRank, currentIndex, local_index );
585 >          haveError= 1;
586 >          simError();
587          }
582 –        else{
583 –          strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
584 –        }
585 –      }
586 –      else {
587 –        sprintf(painCave.errMsg,
588 –                "Atom %d not found on processor %d\n",
589 –                which_atom, worldRank );
590 –        myStatus = 0;
591 –        simError();
588          
589 <        strcpy( writeLine, "Hello, I'm an error.\n");
594 <      }
589 >        strncpy(MPIatomTypeString, atomTypeString, MINIBUFFERSIZE);
590  
591 <      MPI_Send(writeLine, BUFFERSIZE, MPI_CHAR, 0,
592 <               TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD);
593 <      MPI_Send( &myStatus, 1, MPI_INT, 0,
594 <                TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
591 >        // null terminate the string before sending (just in case):
592 >        MPIatomTypeString[MINIBUFFERSIZE-1] = '\0';
593 >
594 >        MPI_Send(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, 0,
595 >                             myPotato, MPI_COMM_WORLD);
596 >        
597 >        myPotato++;
598 >
599 >        MPI_Send(&isDirectional, 1, MPI_INT, 0,
600 >                             myPotato, MPI_COMM_WORLD);
601 >        
602 >        myPotato++;
603 >        
604 >        if (isDirectional) {
605 >
606 >          MPI_Send(atomData13, 13, MPI_DOUBLE, 0,
607 >                   myPotato, MPI_COMM_WORLD);
608 >          
609 >        } else {
610 >
611 >          MPI_Send(atomData6, 6, MPI_DOUBLE, 0,
612 >                   myPotato, MPI_COMM_WORLD);
613 >        }
614 >
615 >        myPotato++;  
616 >        currentIndex++;    
617 >      }
618      }
619 <  }
620 <  finalOut.flush();
621 <  sprintf( checkPointMsg,
622 <           "Sucessfully took a dump.\n");
623 <  MPIcheckPoint();
619 >
620 >    sprintf( checkPointMsg,
621 >             "Sucessfully took a dump.\n");
622 >    MPIcheckPoint();        
623 >    
624 >  }
625    
607 –  if( worldRank == 0 ) finalOut.close();    
626   #endif // is_mpi
627   }
628  
611 –
612 –
629   #ifdef IS_MPI
630  
631   // a couple of functions to let us escape the write loop
632  
633 < 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 <  
633 > void dWrite::DieDieDie( void ){
634  
635    MPI_Finalize();
636    exit (0);
629 –  
637   }
638  
632 – void dWrite::anonymousNodeDie( void ){
633 –
634 –  MPI_Finalize();
635 –  exit (0);
636 – }
637 –
639   #endif //is_mpi

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