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root/group/trunk/OOPSE/libmdtools/DumpWriter.cpp
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Comparing trunk/OOPSE/libmdtools/DumpWriter.cpp (file contents):
Revision 586 by mmeineke, Wed Jul 9 22:14:06 2003 UTC vs.
Revision 949 by chuckv, Thu Jan 15 21:57:10 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] << "\t"
86 <          << entry_plug->Hmat[1] << "\t"
87 <          << entry_plug->Hmat[2] << ";\t"
103 > }
104  
105 <          << entry_plug->Hmat[3] << "\t"
90 <          << entry_plug->Hmat[4] << "\t"
91 <          << entry_plug->Hmat[5] << ";\t"
105 > #endif
106  
107 <          << 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 <      
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],
122 <               q[3],
123 <               dAtom->getJx(),
123 <               dAtom->getJy(),
124 <               dAtom->getJz());
125 <      strcat( writeLine, tempBuffer );
112 > #ifdef IS_MPI
113 >  printf("Hello from node %d\n", worldRank);
114 >  sortByGlobalIndex();
115 >  if(worldRank == 0 ){
116 >    
117 >    finalOut.open( entry_plug->finalName, ios::out | ios::trunc );
118 >    if( !finalOut ){
119 >      sprintf( painCave.errMsg,
120 >               "Could not open \"%s\" for final dump output.\n",
121 >               entry_plug->finalName );
122 >      painCave.isFatal = 1;
123 >      simError();
124      }
127 –    else
128 –      strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
129 –      
130 –    outFile << writeLine;
125    }
126 <  outFile.flush();
126 > #endif // is_mpi
127  
128 < #else // is_mpi
128 >  fileStreams.push_back(&finalOut);
129 >  fileStreams.push_back(&dumpFile);
130  
131 <  // first thing first, suspend fatalities.
137 <  painCave.isEventLoop = 1;
131 >  writeFrame(fileStreams, currentTime);
132  
133 <  int myStatus; // 1 = wakeup & success; 0 = error; -1 = AllDone
134 <  int haveError;
135 <
136 <  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();
219 <
220 <      }
221 <      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();
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
133 > #ifdef IS_MPI
134 >  finalOut.close();
135 > #endif
136 >        
137   }
138  
139 < void DumpWriter::writeFinal(double finalTime){
139 > void DumpWriter::writeFinal(double currentTime){
140  
329 –  char finalName[500];
141    ofstream finalOut;
142 +  vector<ofstream*> fileStreams;
143  
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 –  
144   #ifdef IS_MPI
145    if(worldRank == 0 ){
146 < #endif // is_mpi
147 <    
148 <    strcpy( finalName, entry_plug->finalName );
348 <    
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 <    
360 < #ifdef IS_MPI
156 >
157    }
158 + #endif // is_mpi
159    
160 <  sprintf(checkPointMsg,"Opened file for final configuration\n");
161 <  MPIcheckPoint();  
160 >  fileStreams.push_back(&finalOut);  
161 >  writeFrame(fileStreams, currentTime);
162 >
163 > #ifdef IS_MPI
164 >  finalOut.close();
165 > #endif
166    
167 < #endif //is_mpi
167 > }
168  
169 + void DumpWriter::writeFrame( vector<ofstream*>& outFile, double currentTime ){
170 +
171 +  const int BUFFERSIZE = 2000;
172 +  const int MINIBUFFERSIZE = 100;
173 +
174 +  char tempBuffer[BUFFERSIZE];  
175 +  char writeLine[BUFFERSIZE];
176 +
177 +  int i, k;
178 +
179 + #ifdef IS_MPI
180    
181 +  /*********************************************************************
182 +   * Documentation?  You want DOCUMENTATION?
183 +   *
184 +   * Why all the potatoes below?  
185 +   *
186 +   * To make a long story short, the original version of DumpWriter
187 +   * worked in the most inefficient way possible.  Node 0 would
188 +   * poke each of the node for an individual atom's formatted data
189 +   * as node 0 worked its way down the global index. This was particularly
190 +   * inefficient since the method blocked all processors at every atom
191 +   * (and did it twice!).
192 +   *
193 +   * An intermediate version of DumpWriter could be described from Node
194 +   * zero's perspective as follows:
195 +   *
196 +   *  1) Have 100 of your friends stand in a circle.
197 +   *  2) When you say go, have all of them start tossing potatoes at
198 +   *     you (one at a time).
199 +   *  3) Catch the potatoes.
200 +   *
201 +   * It was an improvement, but MPI has buffers and caches that could
202 +   * best be described in this analogy as "potato nets", so there's no
203 +   * need to block the processors atom-by-atom.
204 +   *
205 +   * This new and improved DumpWriter works in an even more efficient
206 +   * way:
207 +   *
208 +   *  1) Have 100 of your friend stand in a circle.
209 +   *  2) When you say go, have them start tossing 5-pound bags of
210 +   *     potatoes at you.
211 +   *  3) Once you've caught a friend's bag of potatoes,
212 +   *     toss them a spud to let them know they can toss another bag.
213 +   *
214 +   * How's THAT for documentation?
215 +   *
216 +   *********************************************************************/
217 +
218 +  int *potatoes;
219 +  int myPotato;
220 +
221 +  int nProc;
222 +  int j, which_node, done, which_atom, local_index, currentIndex;
223 +  double atomData6[6];
224 +  double atomData13[13];
225 +  int isDirectional;
226 +  char* atomTypeString;
227 +  char MPIatomTypeString[MINIBUFFERSIZE];
228 +
229 + #else //is_mpi
230 +  int nAtoms = entry_plug->n_atoms;
231 + #endif //is_mpi
232 +
233 +  double q[4];
234 +  DirectionalAtom* dAtom;
235 +  Atom** atoms = entry_plug->atoms;
236 +  double pos[3], vel[3];
237 +
238   #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";
239    
240 +  for(k = 0; k < outFile.size(); k++){
241 +    *outFile[k] << nAtoms << "\n";
242 +
243 +    *outFile[k] << currentTime << ";\t"
244 +               << entry_plug->Hmat[0][0] << "\t"
245 +                     << entry_plug->Hmat[1][0] << "\t"
246 +                     << entry_plug->Hmat[2][0] << ";\t"
247 +              
248 +               << entry_plug->Hmat[0][1] << "\t"
249 +                     << entry_plug->Hmat[1][1] << "\t"
250 +                     << entry_plug->Hmat[2][1] << ";\t"
251 +
252 +                     << entry_plug->Hmat[0][2] << "\t"
253 +                     << entry_plug->Hmat[1][2] << "\t"
254 +                     << entry_plug->Hmat[2][2] << ";";
255 +
256 +    //write out additional parameters, such as chi and eta
257 +    *outFile[k] << entry_plug->the_integrator->getAdditionalParameters() << endl;
258 +  }
259 +  
260    for( i=0; i<nAtoms; i++ ){
261 <      
261 >
262 >    atoms[i]->getPos(pos);
263 >    atoms[i]->getVel(vel);
264 >
265      sprintf( tempBuffer,
266               "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
267               atoms[i]->getType(),
268 <             atoms[i]->getX(),
269 <             atoms[i]->getY(),
270 <             atoms[i]->getZ(),
271 <             atoms[i]->get_vx(),
272 <             atoms[i]->get_vy(),
273 <             atoms[i]->get_vz());
268 >             pos[0],
269 >             pos[1],
270 >             pos[2],
271 >             vel[0],
272 >             vel[1],
273 >             vel[2]);
274      strcpy( writeLine, tempBuffer );
275  
276      if( atoms[i]->isDirectional() ){
277 <        
277 >
278        dAtom = (DirectionalAtom *)atoms[i];
279        dAtom->getQ( q );
280 <        
280 >
281        sprintf( tempBuffer,
282                 "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
283                 q[0],
# Line 414 | Line 291 | void DumpWriter::writeFinal(double finalTime){
291      }
292      else
293        strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
294 <      
295 <    finalOut << writeLine;
294 >
295 >    for(k = 0; k < outFile.size(); k++)
296 >      *outFile[k] << writeLine;
297    }
420 –  finalOut.flush();
421 –  finalOut.close();
298  
299   #else // is_mpi
300 +
301 +  /* code to find maximum tag value */
302    
303 <  // first thing first, suspend fatalities.
304 <  painCave.isEventLoop = 1;
303 >  int *tagub, flag, MAXTAG;
304 >  MPI_Attr_get(MPI_COMM_WORLD, MPI_TAG_UB, &tagub, &flag);
305 >  if (flag) {
306 >    MAXTAG = *tagub;
307 >  } else {
308 >    MAXTAG = 32767;
309 >  }  
310  
428 –  int myStatus; // 1 = wakeup & success; 0 = error; -1 = AllDone
311    int haveError;
312  
313    MPI_Status istatus;
314    int *AtomToProcMap = mpiSim->getAtomToProcMap();
315  
316    // write out header and node 0's coordinates
317 <  
436 <  haveError = 0;
317 >
318    if( worldRank == 0 ){
319 <    finalOut << mpiSim->getTotAtoms() << "\n";
319 >
320 >    // Node 0 needs a list of the magic potatoes for each processor;
321 >
322 >    nProc = mpiSim->getNumberProcessors();
323 >    potatoes = new int[nProc];
324 >
325 >    //write out the comment lines
326 >    for (i = 0; i < nProc; i++)
327 >      potatoes[i] = 0;
328      
329 <    finalOut << finalTime << "\t"
330 <             << entry_plug->Hmat[0] << "\t"
331 <             << entry_plug->Hmat[1] << "\t"
332 <             << entry_plug->Hmat[2] << "\t"
333 <      
334 <             << entry_plug->Hmat[3] << "\t"
335 <             << entry_plug->Hmat[4] << "\t"
336 <             << entry_plug->Hmat[5] << "\t"
337 <      
338 <             << entry_plug->Hmat[6] << "\t"
339 <             << entry_plug->Hmat[7] << "\t"
340 <             << entry_plug->Hmat[8] << "\n";
341 <    
329 >      for(k = 0; k < outFile.size(); k++){
330 >        *outFile[k] << mpiSim->getTotAtoms() << "\n";
331 >
332 >        *outFile[k] << currentTime << ";\t"
333 >                         << entry_plug->Hmat[0][0] << "\t"
334 >                         << entry_plug->Hmat[1][0] << "\t"
335 >                         << entry_plug->Hmat[2][0] << ";\t"
336 >
337 >                         << entry_plug->Hmat[0][1] << "\t"
338 >                         << entry_plug->Hmat[1][1] << "\t"
339 >                         << entry_plug->Hmat[2][1] << ";\t"
340 >
341 >                         << entry_plug->Hmat[0][2] << "\t"
342 >                         << entry_plug->Hmat[1][2] << "\t"
343 >                         << entry_plug->Hmat[2][2] << ";";
344 >  
345 >        *outFile[k] << entry_plug->the_integrator->getAdditionalParameters() << endl;
346 >    }
347 >
348 >    currentIndex = 0;
349 >
350      for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) {
454 –      // Get the Node number which has this molecule:
351        
352 <      which_node = AtomToProcMap[i];    
352 >      // Get the Node number which has this atom;
353        
354 <      if (which_node == mpiSim->getMyNode()) {
354 >      which_node = AtomToProcMap[i];
355 >      
356 >      if (which_node != 0) {
357  
358 <        which_atom = i;
359 <        local_index=-1;        
360 <        for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) {
361 <          if (atoms[j]->getGlobalIndex() == which_atom) local_index = j;
358 >        if (potatoes[which_node] + 3 >= MAXTAG) {
359 >          // The potato was going to exceed the maximum value,
360 >          // so wrap this processor potato back to 0:        
361 >
362 >          potatoes[which_node] = 0;          
363 >          MPI_Send(0, 1, MPI_INT, which_node, 0, MPI_COMM_WORLD);
364 >          
365          }
366 <        if (local_index != -1) {        
367 <          sprintf( tempBuffer,
368 <                   "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
369 <                   atoms[local_index]->getType(),
370 <                   atoms[local_index]->getX(),
371 <                   atoms[local_index]->getY(),
372 <                   atoms[local_index]->getZ(),
373 <                   atoms[local_index]->get_vx(),
374 <                   atoms[local_index]->get_vy(),
375 <                   atoms[local_index]->get_vz());
376 <          strcpy( writeLine, tempBuffer );
366 >
367 >        myPotato = potatoes[which_node];        
368 >        
369 >        MPI_Recv(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, which_node,
370 >                 myPotato, MPI_COMM_WORLD, &istatus);
371 >        
372 >        atomTypeString = MPIatomTypeString;
373 >        
374 >        myPotato++;
375 >
376 >        MPI_Recv(&isDirectional, 1, MPI_INT, which_node,
377 >                 myPotato, MPI_COMM_WORLD, &istatus);
378 >              
379 >        myPotato++;
380 >
381 >        if (isDirectional) {          
382 >          MPI_Recv(atomData13, 13, MPI_DOUBLE, which_node,
383 >                   myPotato, MPI_COMM_WORLD, &istatus);
384 >        } else {
385 >          MPI_Recv(atomData6, 6, MPI_DOUBLE, which_node,
386 >                   myPotato, MPI_COMM_WORLD, &istatus);          
387 >        }
388 >        
389 >        myPotato++;
390 >        potatoes[which_node] = myPotato;
391 >
392 >      } else {
393 >        
394 >        haveError = 0;
395 >        which_atom = i;
396 >        
397 >        //local_index = -1;
398 >
399 >        //for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) {
400 >        //  if (atoms[j]->getGlobalIndex() == which_atom) local_index = j;
401 >        //}
402 >        
403 >        //if (local_index != -1) {
404            
405 <          if( atoms[local_index]->isDirectional() ){
405 >          local_index = indexArray[currentIndex].first;        
406 >          
407 >          if (which_atom == indexArray[currentIndex].second) {
408              
409 <            dAtom = (DirectionalAtom *)atoms[local_index];
480 <            dAtom->getQ( q );
409 >            atomTypeString = atoms[local_index]->getType();
410              
411 <            sprintf( tempBuffer,
412 <                     "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
413 <                     q[0],
414 <                     q[1],
415 <                     q[2],
416 <                     q[3],
417 <                     dAtom->getJx(),
418 <                     dAtom->getJy(),
419 <                     dAtom->getJz());
420 <            strcat( writeLine, tempBuffer );
421 <          }
422 <          else
423 <            strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );      
424 <        }
425 <        else {
411 >          atoms[local_index]->getPos(pos);
412 >          atoms[local_index]->getVel(vel);          
413 >          
414 >          atomData6[0] = pos[0];
415 >          atomData6[1] = pos[1];
416 >          atomData6[2] = pos[2];
417 >
418 >          atomData6[3] = vel[0];
419 >          atomData6[4] = vel[1];
420 >          atomData6[5] = vel[2];
421 >          
422 >          isDirectional = 0;
423 >
424 >          if( atoms[local_index]->isDirectional() ){
425 >
426 >            isDirectional = 1;
427 >            
428 >            dAtom = (DirectionalAtom *)atoms[local_index];
429 >            dAtom->getQ( q );
430 >
431 >            for (int j = 0; j < 6 ; j++)
432 >              atomData13[j] = atomData6[j];            
433 >            
434 >            atomData13[6] = q[0];
435 >            atomData13[7] = q[1];
436 >            atomData13[8] = q[2];
437 >            atomData13[9] = q[3];
438 >            
439 >            atomData13[10] = dAtom->getJx();
440 >            atomData13[11] = dAtom->getJy();
441 >            atomData13[12] = dAtom->getJz();
442 >          }
443 >          
444 >        } else {
445            sprintf(painCave.errMsg,
446 <                  "Atom %d not found on processor %d\n",
447 <                  i, worldRank );
446 >                  "Atom %d not found on processor %d, currentIndex = %d, local_index = %d\n",
447 >                  which_atom, worldRank, currentIndex, local_index );
448            haveError= 1;
449            simError();
450 <        }
503 <
504 <        if(haveError) nodeZeroError();
505 <    
506 <      }
507 <      else {
450 >        }
451          
452 <        myStatus = 1;
453 <        MPI_Send(&myStatus, 1, MPI_INT, which_node,
454 <                 TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
455 <        MPI_Send(&i, 1, MPI_INT, which_node, TAKE_THIS_TAG_INT,
456 <                 MPI_COMM_WORLD);
457 <        MPI_Recv(writeLine, BUFFERSIZE, MPI_CHAR, which_node,
458 <                 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);
452 >        if(haveError) DieDieDie();
453 >        
454 >        currentIndex++;
455 >      }
456 >      // If we've survived to here, format the line:
457 >      
458 >      if (!isDirectional) {
459          
460 <        if(!myStatus) nodeZeroError();
460 >        sprintf( writeLine,
461 >                 "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
462 >                 atomTypeString,
463 >                 atomData6[0],
464 >                 atomData6[1],
465 >                 atomData6[2],
466 >                 atomData6[3],
467 >                 atomData6[4],
468 >                 atomData6[5]);
469 >        
470 >        strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
471 >        
472 >      } else {
473 >        
474 >        sprintf( writeLine,
475 >                 "%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",
476 >                 atomTypeString,
477 >                 atomData13[0],
478 >                 atomData13[1],
479 >                 atomData13[2],
480 >                 atomData13[3],
481 >                 atomData13[4],
482 >                 atomData13[5],
483 >                 atomData13[6],
484 >                 atomData13[7],
485 >                 atomData13[8],
486 >                 atomData13[9],
487 >                 atomData13[10],
488 >                 atomData13[11],
489 >                 atomData13[12]);
490 >        
491        }
492        
493 <      finalOut << writeLine;
493 >      for(k = 0; k < outFile.size(); k++)
494 >        *outFile[k] << writeLine;
495      }
496      
497 <    // kill everyone off:
498 <    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 {
497 >    for(k = 0; k < outFile.size(); k++)
498 >      outFile[k]->flush();
499      
500 <    done = 0;
501 <    while (!done) {
500 >    sprintf( checkPointMsg,
501 >             "Sucessfully took a dump.\n");
502 >    
503 >    MPIcheckPoint();        
504 >    
505 >    delete[] potatoes;
506 >    
507 >  } else {
508  
509 <      MPI_Recv(&myStatus, 1, MPI_INT, 0,
510 <               TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus);
509 >    // worldRank != 0, so I'm a remote node.  
510 >
511 >    // Set my magic potato to 0:
512 >
513 >    myPotato = 0;
514 >    currentIndex = 0;
515 >    
516 >    for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) {
517        
518 <      if(!myStatus) anonymousNodeDie();
518 >      // Am I the node which has this atom?
519        
520 <      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) {
520 >      if (AtomToProcMap[i] == worldRank) {
521  
522 <        //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() ){
522 >        if (myPotato + 3 >= MAXTAG) {
523            
524 <          dAtom = (DirectionalAtom *)atoms[local_index];
525 <          dAtom->getQ( q );
524 >          // The potato was going to exceed the maximum value,
525 >          // so wrap this processor potato back to 0 (and block until
526 >          // node 0 says we can go:
527            
528 <          sprintf( tempBuffer,
529 <                   "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
530 <                   q[0],
531 <                   q[1],
532 <                   q[2],
533 <                   q[3],
534 <                   dAtom->getJx(),
535 <                   dAtom->getJy(),
536 <                   dAtom->getJz());
537 <          strcat( writeLine, tempBuffer );
528 >          MPI_Recv(&myPotato, 1, MPI_INT, 0, 0, MPI_COMM_WORLD, &istatus);
529 >          
530 >        }
531 >        which_atom = i;
532 >
533 >        //local_index = -1;
534 >
535 >        //for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) {
536 >        // if (atoms[j]->getGlobalIndex() == which_atom) local_index = j;
537 >        //}
538 >        
539 >        //if (local_index != -1) {
540 >
541 >        local_index = indexArray[currentIndex].first;        
542 >                
543 >        if (which_atom == indexArray[currentIndex].second) {
544 >        
545 >          atomTypeString = atoms[local_index]->getType();
546 >          
547 >          atoms[local_index]->getPos(pos);
548 >          atoms[local_index]->getVel(vel);
549 >          
550 >          atomData6[0] = pos[0];
551 >          atomData6[1] = pos[1];
552 >          atomData6[2] = pos[2];
553 >
554 >          atomData6[3] = vel[0];
555 >          atomData6[4] = vel[1];
556 >          atomData6[5] = vel[2];
557 >          
558 >          isDirectional = 0;
559 >
560 >          if( atoms[local_index]->isDirectional() ){
561 >
562 >            isDirectional = 1;
563 >            
564 >            dAtom = (DirectionalAtom *)atoms[local_index];
565 >            dAtom->getQ( q );
566 >            
567 >            for (int j = 0; j < 6 ; j++)
568 >              atomData13[j] = atomData6[j];
569 >            
570 >            atomData13[6] = q[0];
571 >            atomData13[7] = q[1];
572 >            atomData13[8] = q[2];
573 >            atomData13[9] = q[3];
574 >  
575 >            atomData13[10] = dAtom->getJx();
576 >            atomData13[11] = dAtom->getJy();
577 >            atomData13[12] = dAtom->getJz();
578 >          }
579 >
580 >        } else {
581 >          sprintf(painCave.errMsg,
582 >                  "Atom %d not found on processor %d, currentIndex = %d, local_index = %d\n",
583 >                  which_atom, worldRank, currentIndex, local_index );
584 >          haveError= 1;
585 >          simError();
586          }
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();
587          
588 <        strcpy( writeLine, "Hello, I'm an error.\n");
594 <      }
588 >        strncpy(MPIatomTypeString, atomTypeString, MINIBUFFERSIZE);
589  
590 <      MPI_Send(writeLine, BUFFERSIZE, MPI_CHAR, 0,
591 <               TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD);
592 <      MPI_Send( &myStatus, 1, MPI_INT, 0,
593 <                TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
590 >        // null terminate the string before sending (just in case):
591 >        MPIatomTypeString[MINIBUFFERSIZE-1] = '\0';
592 >
593 >        MPI_Send(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, 0,
594 >                             myPotato, MPI_COMM_WORLD);
595 >        
596 >        myPotato++;
597 >
598 >        MPI_Send(&isDirectional, 1, MPI_INT, 0,
599 >                             myPotato, MPI_COMM_WORLD);
600 >        
601 >        myPotato++;
602 >        
603 >        if (isDirectional) {
604 >
605 >          MPI_Send(atomData13, 13, MPI_DOUBLE, 0,
606 >                   myPotato, MPI_COMM_WORLD);
607 >          
608 >        } else {
609 >
610 >          MPI_Send(atomData6, 6, MPI_DOUBLE, 0,
611 >                   myPotato, MPI_COMM_WORLD);
612 >        }
613 >
614 >        myPotato++;  
615 >        currentIndex++;    
616 >      }
617      }
618 <  }
619 <  finalOut.flush();
620 <  sprintf( checkPointMsg,
621 <           "Sucessfully took a dump.\n");
622 <  MPIcheckPoint();
618 >
619 >    sprintf( checkPointMsg,
620 >             "Sucessfully took a dump.\n");
621 >    MPIcheckPoint();        
622 >    
623 >  }
624    
607 –  if( worldRank == 0 ) finalOut.close();    
625   #endif // is_mpi
626   }
627  
611 –
612 –
628   #ifdef IS_MPI
629  
630   // a couple of functions to let us escape the write loop
631  
632 < 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 <  
632 > void dWrite::DieDieDie( void ){
633  
634    MPI_Finalize();
635    exit (0);
629 –  
636   }
637  
632 – void dWrite::anonymousNodeDie( void ){
633 –
634 –  MPI_Finalize();
635 –  exit (0);
636 – }
637 –
638   #endif //is_mpi

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