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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 1097 by gezelter, Mon Apr 12 20:32:20 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 > #ifdef IS_MPI
69 >
70 > /**
71 > * A hook function to load balancing
72 > */
73 >
74 > void DumpWriter::update(){
75 >  sortByGlobalIndex();          
76 > }
77    
78 <  const int BUFFERSIZE = 2000;
79 <  char tempBuffer[BUFFERSIZE];
80 <  char writeLine[BUFFERSIZE];
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 <  int i, j, which_node, done, which_atom, local_index;
87 <  double q[4];
88 <  DirectionalAtom* dAtom;
89 <  int nAtoms = entry_plug->n_atoms;
86 > /**
87 > * Sorting the local index by global index
88 > */
89 >
90 > void DumpWriter::sortByGlobalIndex(){
91    Atom** atoms = entry_plug->atoms;
92 <    
92 >  
93 >  indexArray.clear();
94 >  
95 >  for(int i = 0; i < mpiSim->getMyNlocal();i++)
96 >    indexArray.push_back(make_pair(i, atoms[i]->getGlobalIndex()));
97 >  
98 >  sort(indexArray.begin(), indexArray.end(), indexSortingCriterion);    
99 > }
100  
101 < #ifndef IS_MPI
81 <    
82 <  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"
101 > #endif
102  
103 <          << entry_plug->Hmat[3] << "\t"
90 <          << entry_plug->Hmat[4] << "\t"
91 <          << entry_plug->Hmat[5] << ";\t"
103 > void DumpWriter::writeDump(double currentTime){
104  
105 <          << entry_plug->Hmat[6] << "\t"
106 <          << entry_plug->Hmat[7] << "\t"
95 <          << entry_plug->Hmat[8] << ";\n";
96 <    
97 <  for( i=0; i<nAtoms; i++ ){
98 <      
105 >  ofstream finalOut;
106 >  vector<ofstream*> fileStreams;
107  
108 <    sprintf( tempBuffer,
109 <             "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
110 <             atoms[i]->getType(),
111 <             atoms[i]->getX(),
112 <             atoms[i]->getY(),
113 <             atoms[i]->getZ(),
114 <             atoms[i]->get_vx(),
115 <             atoms[i]->get_vy(),
116 <             atoms[i]->get_vz());
117 <    strcpy( writeLine, tempBuffer );
110 <
111 <    if( atoms[i]->isDirectional() ){
112 <        
113 <      dAtom = (DirectionalAtom *)atoms[i];
114 <      dAtom->getQ( q );
115 <        
116 <      sprintf( tempBuffer,
117 <               "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
118 <               q[0],
119 <               q[1],
120 <               q[2],
121 <               q[3],
122 <               dAtom->getJx(),
123 <               dAtom->getJy(),
124 <               dAtom->getJz());
125 <      strcat( writeLine, tempBuffer );
108 > #ifdef IS_MPI
109 >  if(worldRank == 0 ){
110 > #endif    
111 >    finalOut.open( entry_plug->finalName, ios::out | ios::trunc );
112 >    if( !finalOut ){
113 >      sprintf( painCave.errMsg,
114 >               "Could not open \"%s\" for final dump output.\n",
115 >               entry_plug->finalName );
116 >      painCave.isFatal = 1;
117 >      simError();
118      }
119 <    else
128 <      strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
129 <      
130 <    outFile << writeLine;
119 > #ifdef IS_MPI
120    }
121 <  outFile.flush();
121 > #endif // is_mpi
122  
123 < #else // is_mpi
123 >  fileStreams.push_back(&finalOut);
124 >  fileStreams.push_back(&dumpFile);
125  
126 <  // first thing first, suspend fatalities.
137 <  painCave.isEventLoop = 1;
126 >  writeFrame(fileStreams, currentTime);
127  
128 <  int myStatus; // 1 = wakeup & success; 0 = error; -1 = AllDone
129 <  int haveError;
128 > #ifdef IS_MPI
129 >  finalOut.close();
130 > #endif
131 >        
132 > }
133  
134 <  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();
134 > void DumpWriter::writeFinal(double currentTime){
135  
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
325 – }
326 –
327 – void DumpWriter::writeFinal(double finalTime){
328 –
329 –  char finalName[500];
136    ofstream finalOut;
137 +  vector<ofstream*> fileStreams;
138  
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 –  
139   #ifdef IS_MPI
140    if(worldRank == 0 ){
141   #endif // is_mpi
142 <    
143 <    strcpy( finalName, entry_plug->finalName );
144 <    
349 <    finalOut.open( finalName, ios::out | ios::trunc );
142 >
143 >    finalOut.open( entry_plug->finalName, ios::out | ios::trunc );
144 >
145      if( !finalOut ){
146        sprintf( painCave.errMsg,
147                 "Could not open \"%s\" for final dump output.\n",
148 <               finalName );
148 >               entry_plug->finalName );
149        painCave.isFatal = 1;
150        simError();
151      }
152 <    
358 <    // finalOut.setf( ios::scientific );
359 <    
152 >
153   #ifdef IS_MPI
154    }
155 + #endif // is_mpi
156    
157 <  sprintf(checkPointMsg,"Opened file for final configuration\n");
158 <  MPIcheckPoint();  
157 >  fileStreams.push_back(&finalOut);  
158 >  writeFrame(fileStreams, currentTime);
159 >
160 > #ifdef IS_MPI
161 >  finalOut.close();
162 > #endif
163    
164 < #endif //is_mpi
164 > }
165  
166 + void DumpWriter::writeFrame( vector<ofstream*>& outFile, double currentTime ){
167 +
168 +  const int BUFFERSIZE = 2000;
169 +  const int MINIBUFFERSIZE = 100;
170 +
171 +  char tempBuffer[BUFFERSIZE];  
172 +  char writeLine[BUFFERSIZE];
173 +
174 +  int i, k;
175 +
176 + #ifdef IS_MPI
177    
178 +  /*********************************************************************
179 +   * Documentation?  You want DOCUMENTATION?
180 +   *
181 +   * Why all the potatoes below?  
182 +   *
183 +   * To make a long story short, the original version of DumpWriter
184 +   * worked in the most inefficient way possible.  Node 0 would
185 +   * poke each of the node for an individual atom's formatted data
186 +   * as node 0 worked its way down the global index. This was particularly
187 +   * inefficient since the method blocked all processors at every atom
188 +   * (and did it twice!).
189 +   *
190 +   * An intermediate version of DumpWriter could be described from Node
191 +   * zero's perspective as follows:
192 +   *
193 +   *  1) Have 100 of your friends stand in a circle.
194 +   *  2) When you say go, have all of them start tossing potatoes at
195 +   *     you (one at a time).
196 +   *  3) Catch the potatoes.
197 +   *
198 +   * It was an improvement, but MPI has buffers and caches that could
199 +   * best be described in this analogy as "potato nets", so there's no
200 +   * need to block the processors atom-by-atom.
201 +   *
202 +   * This new and improved DumpWriter works in an even more efficient
203 +   * way:
204 +   *
205 +   *  1) Have 100 of your friend stand in a circle.
206 +   *  2) When you say go, have them start tossing 5-pound bags of
207 +   *     potatoes at you.
208 +   *  3) Once you've caught a friend's bag of potatoes,
209 +   *     toss them a spud to let them know they can toss another bag.
210 +   *
211 +   * How's THAT for documentation?
212 +   *
213 +   *********************************************************************/
214 +
215 +  int *potatoes;
216 +  int myPotato;
217 +
218 +  int nProc;
219 +  int j, which_node, done, which_atom, local_index, currentIndex;
220 +  double atomData6[6];
221 +  double atomData13[13];
222 +  int isDirectional;
223 +  char* atomTypeString;
224 +  char MPIatomTypeString[MINIBUFFERSIZE];
225 +
226 + #else //is_mpi
227 +  int nAtoms = entry_plug->n_atoms;
228 + #endif //is_mpi
229 +
230 +  double q[4], ji[3];
231 +  DirectionalAtom* dAtom;
232 +  Atom** atoms = entry_plug->atoms;
233 +  double pos[3], vel[3];
234 +
235   #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";
236    
237 +  for(k = 0; k < outFile.size(); k++){
238 +    *outFile[k] << nAtoms << "\n";
239 +
240 +    *outFile[k] << currentTime << ";\t"
241 +               << entry_plug->Hmat[0][0] << "\t"
242 +                     << entry_plug->Hmat[1][0] << "\t"
243 +                     << entry_plug->Hmat[2][0] << ";\t"
244 +              
245 +               << entry_plug->Hmat[0][1] << "\t"
246 +                     << entry_plug->Hmat[1][1] << "\t"
247 +                     << entry_plug->Hmat[2][1] << ";\t"
248 +
249 +                     << entry_plug->Hmat[0][2] << "\t"
250 +                     << entry_plug->Hmat[1][2] << "\t"
251 +                     << entry_plug->Hmat[2][2] << ";";
252 +
253 +    //write out additional parameters, such as chi and eta
254 +    *outFile[k] << entry_plug->the_integrator->getAdditionalParameters() << endl;
255 +  }
256 +  
257    for( i=0; i<nAtoms; i++ ){
258 <      
258 >
259 >    atoms[i]->getPos(pos);
260 >    atoms[i]->getVel(vel);
261 >
262      sprintf( tempBuffer,
263               "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
264               atoms[i]->getType(),
265 <             atoms[i]->getX(),
266 <             atoms[i]->getY(),
267 <             atoms[i]->getZ(),
268 <             atoms[i]->get_vx(),
269 <             atoms[i]->get_vy(),
270 <             atoms[i]->get_vz());
265 >             pos[0],
266 >             pos[1],
267 >             pos[2],
268 >             vel[0],
269 >             vel[1],
270 >             vel[2]);
271      strcpy( writeLine, tempBuffer );
272  
273      if( atoms[i]->isDirectional() ){
274 <        
274 >
275        dAtom = (DirectionalAtom *)atoms[i];
276        dAtom->getQ( q );
277 <        
277 >      dAtom->getJ( ji );
278 >
279        sprintf( tempBuffer,
280                 "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
281                 q[0],
282                 q[1],
283                 q[2],
284                 q[3],
285 <               dAtom->getJx(),
286 <               dAtom->getJy(),
287 <               dAtom->getJz());
285 >               ji[0],
286 >               ji[1],
287 >               ji[2]);
288        strcat( writeLine, tempBuffer );
289      }
290      else
291        strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
292 <      
293 <    finalOut << writeLine;
292 >
293 >    for(k = 0; k < outFile.size(); k++)
294 >      *outFile[k] << writeLine;
295    }
420 –  finalOut.flush();
421 –  finalOut.close();
296  
297   #else // is_mpi
298 +
299 +  /* code to find maximum tag value */
300    
301 <  // first thing first, suspend fatalities.
302 <  painCave.isEventLoop = 1;
301 >  int *tagub, flag, MAXTAG;
302 >  MPI_Attr_get(MPI_COMM_WORLD, MPI_TAG_UB, &tagub, &flag);
303 >  if (flag) {
304 >    MAXTAG = *tagub;
305 >  } else {
306 >    MAXTAG = 32767;
307 >  }  
308  
428 –  int myStatus; // 1 = wakeup & success; 0 = error; -1 = AllDone
309    int haveError;
310  
311    MPI_Status istatus;
312    int *AtomToProcMap = mpiSim->getAtomToProcMap();
313  
314    // write out header and node 0's coordinates
315 <  
436 <  haveError = 0;
315 >
316    if( worldRank == 0 ){
317 <    finalOut << mpiSim->getTotAtoms() << "\n";
317 >
318 >    // Node 0 needs a list of the magic potatoes for each processor;
319 >
320 >    nProc = mpiSim->getNumberProcessors();
321 >    potatoes = new int[nProc];
322 >
323 >    //write out the comment lines
324 >    for (i = 0; i < nProc; i++)
325 >      potatoes[i] = 0;
326      
327 <    finalOut << finalTime << "\t"
328 <             << entry_plug->Hmat[0] << "\t"
329 <             << entry_plug->Hmat[1] << "\t"
330 <             << entry_plug->Hmat[2] << "\t"
331 <      
332 <             << entry_plug->Hmat[3] << "\t"
333 <             << entry_plug->Hmat[4] << "\t"
334 <             << entry_plug->Hmat[5] << "\t"
335 <      
336 <             << entry_plug->Hmat[6] << "\t"
337 <             << entry_plug->Hmat[7] << "\t"
338 <             << entry_plug->Hmat[8] << "\n";
339 <    
327 >      for(k = 0; k < outFile.size(); k++){
328 >        *outFile[k] << mpiSim->getTotAtoms() << "\n";
329 >
330 >        *outFile[k] << currentTime << ";\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] << ";";
342 >  
343 >        *outFile[k] << entry_plug->the_integrator->getAdditionalParameters() << endl;
344 >    }
345 >
346 >    currentIndex = 0;
347 >
348      for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) {
454 –      // Get the Node number which has this molecule:
349        
350 <      which_node = AtomToProcMap[i];    
350 >      // Get the Node number which has this atom;
351        
352 <      if (which_node == mpiSim->getMyNode()) {
352 >      which_node = AtomToProcMap[i];
353 >      
354 >      if (which_node != 0) {
355  
356 <        which_atom = i;
357 <        local_index=-1;        
358 <        for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) {
359 <          if (atoms[j]->getGlobalIndex() == which_atom) local_index = j;
356 >        if (potatoes[which_node] + 3 >= MAXTAG) {
357 >          // The potato was going to exceed the maximum value,
358 >          // so wrap this processor potato back to 0:        
359 >
360 >          potatoes[which_node] = 0;          
361 >          MPI_Send(0, 1, MPI_INT, which_node, 0, MPI_COMM_WORLD);
362 >          
363          }
364 <        if (local_index != -1) {        
365 <          sprintf( tempBuffer,
366 <                   "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
367 <                   atoms[local_index]->getType(),
368 <                   atoms[local_index]->getX(),
369 <                   atoms[local_index]->getY(),
370 <                   atoms[local_index]->getZ(),
371 <                   atoms[local_index]->get_vx(),
372 <                   atoms[local_index]->get_vy(),
373 <                   atoms[local_index]->get_vz());
374 <          strcpy( writeLine, tempBuffer );
375 <          
376 <          if( atoms[local_index]->isDirectional() ){
364 >
365 >        myPotato = potatoes[which_node];        
366 >        
367 >        MPI_Recv(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, which_node,
368 >                 myPotato, MPI_COMM_WORLD, &istatus);
369 >        
370 >        atomTypeString = MPIatomTypeString;
371 >        
372 >        myPotato++;
373 >
374 >        MPI_Recv(&isDirectional, 1, MPI_INT, which_node,
375 >                 myPotato, MPI_COMM_WORLD, &istatus);
376 >              
377 >        myPotato++;
378 >
379 >        if (isDirectional) {          
380 >          MPI_Recv(atomData13, 13, MPI_DOUBLE, which_node,
381 >                   myPotato, MPI_COMM_WORLD, &istatus);
382 >        } else {
383 >          MPI_Recv(atomData6, 6, MPI_DOUBLE, which_node,
384 >                   myPotato, MPI_COMM_WORLD, &istatus);          
385 >        }
386 >        
387 >        myPotato++;
388 >        potatoes[which_node] = myPotato;
389 >
390 >      } else {
391 >        
392 >        haveError = 0;
393 >        which_atom = i;
394 >        
395 >          local_index = indexArray[currentIndex].first;        
396 >          
397 >          if (which_atom == indexArray[currentIndex].second) {
398              
399 <            dAtom = (DirectionalAtom *)atoms[local_index];
480 <            dAtom->getQ( q );
399 >            atomTypeString = atoms[local_index]->getType();
400              
401 <            sprintf( tempBuffer,
402 <                     "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
403 <                     q[0],
404 <                     q[1],
405 <                     q[2],
406 <                     q[3],
407 <                     dAtom->getJx(),
408 <                     dAtom->getJy(),
409 <                     dAtom->getJz());
410 <            strcat( writeLine, tempBuffer );
411 <          }
412 <          else
413 <            strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );      
414 <        }
415 <        else {
401 >          atoms[local_index]->getPos(pos);
402 >          atoms[local_index]->getVel(vel);          
403 >          
404 >          atomData6[0] = pos[0];
405 >          atomData6[1] = pos[1];
406 >          atomData6[2] = pos[2];
407 >
408 >          atomData6[3] = vel[0];
409 >          atomData6[4] = vel[1];
410 >          atomData6[5] = vel[2];
411 >          
412 >          isDirectional = 0;
413 >
414 >          if( atoms[local_index]->isDirectional() ){
415 >
416 >            isDirectional = 1;
417 >            
418 >            dAtom = (DirectionalAtom *)atoms[local_index];
419 >            dAtom->getQ( q );
420 >            dAtom->getJ( ji );
421 >
422 >            for (int j = 0; j < 6 ; j++)
423 >              atomData13[j] = atomData6[j];            
424 >            
425 >            atomData13[6] = q[0];
426 >            atomData13[7] = q[1];
427 >            atomData13[8] = q[2];
428 >            atomData13[9] = q[3];
429 >            
430 >            atomData13[10] = ji[0];
431 >            atomData13[11] = ji[1];
432 >            atomData13[12] = ji[2];
433 >          }
434 >          
435 >        } else {
436            sprintf(painCave.errMsg,
437 <                  "Atom %d not found on processor %d\n",
438 <                  i, worldRank );
437 >                  "Atom %d not found on processor %d, currentIndex = %d, local_index = %d\n",
438 >                  which_atom, worldRank, currentIndex, local_index );
439            haveError= 1;
440            simError();
441 <        }
503 <
504 <        if(haveError) nodeZeroError();
505 <    
506 <      }
507 <      else {
441 >        }
442          
443 <        myStatus = 1;
444 <        MPI_Send(&myStatus, 1, MPI_INT, which_node,
445 <                 TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
446 <        MPI_Send(&i, 1, MPI_INT, which_node, TAKE_THIS_TAG_INT,
447 <                 MPI_COMM_WORLD);
448 <        MPI_Recv(writeLine, BUFFERSIZE, MPI_CHAR, which_node,
449 <                 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);
443 >        if(haveError) DieDieDie();
444 >        
445 >        currentIndex++;
446 >      }
447 >      // If we've survived to here, format the line:
448 >      
449 >      if (!isDirectional) {
450          
451 <        if(!myStatus) nodeZeroError();
451 >        sprintf( writeLine,
452 >                 "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
453 >                 atomTypeString,
454 >                 atomData6[0],
455 >                 atomData6[1],
456 >                 atomData6[2],
457 >                 atomData6[3],
458 >                 atomData6[4],
459 >                 atomData6[5]);
460 >        
461 >        strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
462 >        
463 >      } else {
464 >        
465 >        sprintf( writeLine,
466 >                 "%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",
467 >                 atomTypeString,
468 >                 atomData13[0],
469 >                 atomData13[1],
470 >                 atomData13[2],
471 >                 atomData13[3],
472 >                 atomData13[4],
473 >                 atomData13[5],
474 >                 atomData13[6],
475 >                 atomData13[7],
476 >                 atomData13[8],
477 >                 atomData13[9],
478 >                 atomData13[10],
479 >                 atomData13[11],
480 >                 atomData13[12]);
481 >        
482        }
483        
484 <      finalOut << writeLine;
484 >      for(k = 0; k < outFile.size(); k++)
485 >        *outFile[k] << writeLine;
486      }
487      
488 <    // kill everyone off:
489 <    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 {
488 >    for(k = 0; k < outFile.size(); k++)
489 >      outFile[k]->flush();
490      
491 <    done = 0;
492 <    while (!done) {
491 >    sprintf( checkPointMsg,
492 >             "Sucessfully took a dump.\n");
493 >    
494 >    MPIcheckPoint();        
495 >    
496 >    delete[] potatoes;
497 >    
498 >  } else {
499  
500 <      MPI_Recv(&myStatus, 1, MPI_INT, 0,
501 <               TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus);
500 >    // worldRank != 0, so I'm a remote node.  
501 >
502 >    // Set my magic potato to 0:
503 >
504 >    myPotato = 0;
505 >    currentIndex = 0;
506 >    
507 >    for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) {
508        
509 <      if(!myStatus) anonymousNodeDie();
509 >      // Am I the node which has this atom?
510        
511 <      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) {
511 >      if (AtomToProcMap[i] == worldRank) {
512  
513 <        //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() ){
513 >        if (myPotato + 3 >= MAXTAG) {
514            
515 <          dAtom = (DirectionalAtom *)atoms[local_index];
516 <          dAtom->getQ( q );
515 >          // The potato was going to exceed the maximum value,
516 >          // so wrap this processor potato back to 0 (and block until
517 >          // node 0 says we can go:
518            
519 <          sprintf( tempBuffer,
520 <                   "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
521 <                   q[0],
522 <                   q[1],
523 <                   q[2],
524 <                   q[3],
525 <                   dAtom->getJx(),
526 <                   dAtom->getJy(),
527 <                   dAtom->getJz());
528 <          strcat( writeLine, tempBuffer );
519 >          MPI_Recv(&myPotato, 1, MPI_INT, 0, 0, MPI_COMM_WORLD, &istatus);
520 >          
521 >        }
522 >        which_atom = i;
523 >
524 >        local_index = indexArray[currentIndex].first;        
525 >                
526 >        if (which_atom == indexArray[currentIndex].second) {
527 >        
528 >          atomTypeString = atoms[local_index]->getType();
529 >          
530 >          atoms[local_index]->getPos(pos);
531 >          atoms[local_index]->getVel(vel);
532 >          
533 >          atomData6[0] = pos[0];
534 >          atomData6[1] = pos[1];
535 >          atomData6[2] = pos[2];
536 >
537 >          atomData6[3] = vel[0];
538 >          atomData6[4] = vel[1];
539 >          atomData6[5] = vel[2];
540 >          
541 >          isDirectional = 0;
542 >
543 >          if( atoms[local_index]->isDirectional() ){
544 >
545 >            isDirectional = 1;
546 >            
547 >            dAtom = (DirectionalAtom *)atoms[local_index];
548 >            dAtom->getQ( q );
549 >            dAtom->getJ( ji );
550 >            
551 >            for (int j = 0; j < 6 ; j++)
552 >              atomData13[j] = atomData6[j];
553 >            
554 >            atomData13[6] = q[0];
555 >            atomData13[7] = q[1];
556 >            atomData13[8] = q[2];
557 >            atomData13[9] = q[3];
558 >  
559 >            atomData13[10] = ji[0];
560 >            atomData13[11] = ji[1];
561 >            atomData13[12] = ji[2];
562 >          }
563 >
564 >        } else {
565 >          sprintf(painCave.errMsg,
566 >                  "Atom %d not found on processor %d, currentIndex = %d, local_index = %d\n",
567 >                  which_atom, worldRank, currentIndex, local_index );
568 >          haveError= 1;
569 >          simError();
570          }
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();
571          
572 <        strcpy( writeLine, "Hello, I'm an error.\n");
594 <      }
572 >        strncpy(MPIatomTypeString, atomTypeString, MINIBUFFERSIZE);
573  
574 <      MPI_Send(writeLine, BUFFERSIZE, MPI_CHAR, 0,
575 <               TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD);
576 <      MPI_Send( &myStatus, 1, MPI_INT, 0,
577 <                TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
574 >        // null terminate the string before sending (just in case):
575 >        MPIatomTypeString[MINIBUFFERSIZE-1] = '\0';
576 >
577 >        MPI_Send(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, 0,
578 >                             myPotato, MPI_COMM_WORLD);
579 >        
580 >        myPotato++;
581 >
582 >        MPI_Send(&isDirectional, 1, MPI_INT, 0,
583 >                             myPotato, MPI_COMM_WORLD);
584 >        
585 >        myPotato++;
586 >        
587 >        if (isDirectional) {
588 >
589 >          MPI_Send(atomData13, 13, MPI_DOUBLE, 0,
590 >                   myPotato, MPI_COMM_WORLD);
591 >          
592 >        } else {
593 >
594 >          MPI_Send(atomData6, 6, MPI_DOUBLE, 0,
595 >                   myPotato, MPI_COMM_WORLD);
596 >        }
597 >
598 >        myPotato++;  
599 >        currentIndex++;    
600 >      }
601      }
602 <  }
603 <  finalOut.flush();
604 <  sprintf( checkPointMsg,
605 <           "Sucessfully took a dump.\n");
606 <  MPIcheckPoint();
602 >
603 >    sprintf( checkPointMsg,
604 >             "Sucessfully took a dump.\n");
605 >    MPIcheckPoint();        
606 >    
607 >  }
608    
607 –  if( worldRank == 0 ) finalOut.close();    
609   #endif // is_mpi
610   }
611  
611 –
612 –
612   #ifdef IS_MPI
613  
614   // a couple of functions to let us escape the write loop
615  
616 < 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 <  
616 > void dWrite::DieDieDie( void ){
617  
618    MPI_Finalize();
619    exit (0);
629 –  
620   }
621  
632 – void dWrite::anonymousNodeDie( void ){
633 –
634 –  MPI_Finalize();
635 –  exit (0);
636 – }
637 –
622   #endif //is_mpi

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