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root/group/trunk/OOPSE/libmdtools/DumpWriter.cpp
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Comparing trunk/OOPSE/libmdtools/DumpWriter.cpp (file contents):
Revision 723 by mmeineke, Tue Aug 26 20:12:51 2003 UTC vs.
Revision 947 by gezelter, Thu Jan 15 14:22:16 2004 UTC

# Line 1 | Line 1
1   #define _FILE_OFFSET_BITS 64
2  
3 < #include <cstring>
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"
10 – #define TAKE_THIS_TAG_CHAR 1
11 – #define TAKE_THIS_TAG_INT 2
12  
13   namespace dWrite{
14 <  void nodeZeroError( void );
15 <  void anonymousNodeDie( void );
14 >  void DieDieDie( void );
15   }
16  
17   using namespace dWrite;
# Line 28 | 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 <    
35 <    if( !outFile ){
37 <      
30 >
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  
45 –    //outFile.setf( ios::scientific );
46 –
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 59 | 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 ){
70 <  
71 <  const int BUFFERSIZE = 2000;
72 <  char tempBuffer[BUFFERSIZE];
73 <  char writeLine[BUFFERSIZE];
68 > #ifdef IS_MPI
69  
70 <  int i, j, which_node, done, which_atom, local_index;
71 <  double q[4];
72 <  DirectionalAtom* dAtom;
78 <  int nAtoms = entry_plug->n_atoms;
79 <  Atom** atoms = entry_plug->atoms;
70 > /**
71 > * A hook function to load balancing
72 > */
73  
74 <  double pos[3], vel[3];
75 <    
74 > void DumpWriter::update(){
75 >  sortByGlobalIndex();          
76 > }
77 >  
78 > /**
79 > * Auxiliary sorting function
80 > */
81 >
82 > bool indexSortingCriterion(const pair<int, int>& p1, const pair<int, int>& p2){
83 >  return p1.second < p2.second;
84 > }
85  
86 < #ifndef IS_MPI
87 <    
88 <  outFile << nAtoms << "\n";
89 <    
90 <  outFile << currentTime << ";\t"
91 <          << entry_plug->Hmat[0][0] << "\t"
90 <          << entry_plug->Hmat[1][0] << "\t"
91 <          << entry_plug->Hmat[2][0] << ";\t"
92 <
93 <          << entry_plug->Hmat[0][1] << "\t"
94 <          << entry_plug->Hmat[1][1] << "\t"
95 <          << entry_plug->Hmat[2][1] << ";\t"
96 <
97 <          << entry_plug->Hmat[0][2] << "\t"
98 <          << entry_plug->Hmat[1][2] << "\t"
99 <          << entry_plug->Hmat[2][2] << ";\n";
100 <    
101 <  for( i=0; i<nAtoms; i++ ){
102 <      
103 <    atoms[i]->getPos(pos);
104 <    atoms[i]->getVel(vel);
105 <
106 <    sprintf( tempBuffer,
107 <             "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
108 <             atoms[i]->getType(),
109 <             pos[0],
110 <             pos[1],
111 <             pos[2],
112 <             vel[0],
113 <             vel[1],
114 <             vel[2]);
115 <    strcpy( writeLine, tempBuffer );
116 <
117 <    if( atoms[i]->isDirectional() ){
118 <        
119 <      dAtom = (DirectionalAtom *)atoms[i];
120 <      dAtom->getQ( q );
121 <        
122 <      sprintf( tempBuffer,
123 <               "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
124 <               q[0],
125 <               q[1],
126 <               q[2],
127 <               q[3],
128 <               dAtom->getJx(),
129 <               dAtom->getJy(),
130 <               dAtom->getJz());
131 <      strcat( writeLine, tempBuffer );
132 <    }
133 <    else
134 <      strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
135 <      
136 <    outFile << writeLine;
137 <  }
138 <  outFile.flush();
139 <
140 < #else // is_mpi
141 <
142 <  // first thing first, suspend fatalities.
143 <  painCave.isEventLoop = 1;
144 <
145 <  int myStatus; // 1 = wakeup & success; 0 = error; -1 = AllDone
146 <  int haveError;
147 <
148 <  MPI_Status istatus;
149 <  int *AtomToProcMap = mpiSim->getAtomToProcMap();
86 > /**
87 > * Sorting the local index by global index
88 > */
89 >
90 > void DumpWriter::sortByGlobalIndex(){
91 >  Atom** atoms = entry_plug->atoms;
92    
93 <  // write out header and node 0's coordinates
93 >  indexArray.clear();
94    
95 <  if( worldRank == 0 ){
96 <    outFile << mpiSim->getTotAtoms() << "\n";
95 >  for(int i = 0; i < mpiSim->getMyNlocal();i++)
96 >    indexArray.push_back(make_pair(i, atoms[i]->getGlobalIndex()));
97    
98 <    outFile << currentTime << ";\t"
99 <            << entry_plug->Hmat[0][0] << "\t"
100 <            << entry_plug->Hmat[1][0] << "\t"
159 <            << entry_plug->Hmat[2][0] << ";\t"
160 <      
161 <            << entry_plug->Hmat[0][1] << "\t"
162 <            << entry_plug->Hmat[1][1] << "\t"
163 <            << entry_plug->Hmat[2][1] << ";\t"
164 <      
165 <            << entry_plug->Hmat[0][2] << "\t"
166 <            << entry_plug->Hmat[1][2] << "\t"
167 <            << entry_plug->Hmat[2][2] << ";\n";
168 <    
169 <    outFile.flush();
170 <    for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) {
171 <      // Get the Node number which has this atom;
172 <      
173 <      which_node = AtomToProcMap[i];    
174 <      
175 <      if (which_node == 0 ) {
176 <        
177 <        haveError = 0;
178 <        which_atom = i;
179 <        local_index=-1;        
180 <        for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) {
181 <          if (atoms[j]->getGlobalIndex() == which_atom) local_index = j;
182 <        }
183 <        if (local_index != -1) {
184 <          //format the line
185 <          
186 <          atoms[local_index]->getPos(pos);
187 <          atoms[local_index]->getVel(vel);
98 >  sort(indexArray.begin(), indexArray.end(), indexSortingCriterion);    
99 > }
100 > #endif
101  
102 <          sprintf( tempBuffer,
190 <                   "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
191 <                   atoms[local_index]->getType(),
192 <                   pos[0],
193 <                   pos[1],
194 <                   pos[2],
195 <                   vel[0],
196 <                   vel[1],
197 <                   vel[2]); // check here.
198 <          strcpy( writeLine, tempBuffer );
199 <          
200 <          if( atoms[local_index]->isDirectional() ){
201 <            
202 <            dAtom = (DirectionalAtom *)atoms[local_index];
203 <            dAtom->getQ( q );
204 <            
205 <            sprintf( tempBuffer,
206 <                     "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
207 <                     q[0],
208 <                     q[1],
209 <                     q[2],
210 <                     q[3],
211 <                     dAtom->getJx(),
212 <                     dAtom->getJy(),
213 <                     dAtom->getJz());
214 <            strcat( writeLine, tempBuffer );
215 <            
216 <          }
217 <          else
218 <            strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );      
219 <        }
220 <        else {
221 <          sprintf(painCave.errMsg,
222 <                  "Atom %d not found on processor %d\n",
223 <                  i, worldRank );
224 <          haveError= 1;
225 <          simError();
226 <        }
227 <        
228 <        if(haveError) nodeZeroError();
102 > void DumpWriter::writeDump(double currentTime){
103  
104 <      }
105 <      else {
232 <        myStatus = 1;
233 <        MPI_Send(&myStatus, 1, MPI_INT, which_node,
234 <                 TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
235 <        MPI_Send(&i, 1, MPI_INT, which_node, TAKE_THIS_TAG_INT,
236 <                 MPI_COMM_WORLD);
237 <        MPI_Recv(writeLine, BUFFERSIZE, MPI_CHAR, which_node,
238 <                 TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD, &istatus);
239 <        MPI_Recv(&myStatus, 1, MPI_INT, which_node,
240 <                 TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus);
241 <        
242 <        if(!myStatus) nodeZeroError();
104 >  ofstream finalOut;
105 >  vector<ofstream*> fileStreams;
106  
107 <      }
108 <      
246 <      outFile << writeLine;
247 <      outFile.flush();
248 <    }
107 > #ifdef IS_MPI
108 >  if(worldRank == 0 ){
109      
110 <    // kill everyone off:
111 <    myStatus = -1;
112 <    for (j = 0; j < mpiSim->getNumberProcessors(); j++) {      
113 <      MPI_Send(&myStatus, 1, MPI_INT, j,
114 <               TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
110 >    finalOut.open( entry_plug->finalName, ios::out | ios::trunc );
111 >    if( !finalOut ){
112 >      sprintf( painCave.errMsg,
113 >               "Could not open \"%s\" for final dump output.\n",
114 >               entry_plug->finalName );
115 >      painCave.isFatal = 1;
116 >      simError();
117      }
118 +  }
119 + #endif // is_mpi
120  
121 <  } else {
122 <    
259 <    done = 0;
260 <    while (!done) {
261 <      
262 <      MPI_Recv(&myStatus, 1, MPI_INT, 0,
263 <               TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus);
121 >  fileStreams.push_back(&finalOut);
122 >  fileStreams.push_back(&dumpFile);
123  
124 <      if(!myStatus) anonymousNodeDie();
266 <      
267 <      if(myStatus < 0) break;
124 >  writeFrame(fileStreams, currentTime);
125  
126 <      MPI_Recv(&which_atom, 1, MPI_INT, 0,
127 <               TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus);
128 <      
129 <      myStatus = 1;
273 <      local_index=-1;        
274 <      for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) {
275 <        if (atoms[j]->getGlobalIndex() == which_atom) local_index = j;
276 <      }
277 <      if (local_index != -1) {
278 <        //format the line
279 <
280 <        atoms[local_index]->getPos(pos);
281 <        atoms[local_index]->getVel(vel);
282 <
283 <        sprintf( tempBuffer,
284 <                 "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
285 <                 atoms[local_index]->getType(),
286 <                 pos[0],
287 <                 pos[1],
288 <                 pos[2],
289 <                 vel[0],
290 <                 vel[1],
291 <                 vel[2]); // check here.
292 <        strcpy( writeLine, tempBuffer );
293 <        
294 <        if( atoms[local_index]->isDirectional() ){
295 <          
296 <          dAtom = (DirectionalAtom *)atoms[local_index];
297 <          dAtom->getQ( q );
298 <          
299 <          sprintf( tempBuffer,
300 <                   "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
301 <                   q[0],
302 <                   q[1],
303 <                   q[2],
304 <                   q[3],
305 <                   dAtom->getJx(),
306 <                   dAtom->getJy(),
307 <                   dAtom->getJz());
308 <          strcat( writeLine, tempBuffer );
309 <        }
310 <        else{
311 <          strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
312 <        }
313 <      }
314 <      else {
315 <        sprintf(painCave.errMsg,
316 <                "Atom %d not found on processor %d\n",
317 <                which_atom, worldRank );
318 <        myStatus = 0;
319 <        simError();
320 <
321 <        strcpy( writeLine, "Hello, I'm an error.\n");
322 <      }
323 <
324 <      MPI_Send(writeLine, BUFFERSIZE, MPI_CHAR, 0,
325 <               TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD);
326 <      MPI_Send( &myStatus, 1, MPI_INT, 0,
327 <                TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
328 <    }
329 <  }  
330 <  outFile.flush();
331 <  sprintf( checkPointMsg,
332 <           "Sucessfully took a dump.\n");
333 <  MPIcheckPoint();
334 <
335 < // last  thing last, enable  fatalities.
336 <  painCave.isEventLoop = 0;
337 <
338 < #endif // is_mpi
126 > #ifdef IS_MPI
127 >  finalOut.close();
128 > #endif
129 >        
130   }
131  
132 < void DumpWriter::writeFinal(double finalTime){
132 > void DumpWriter::writeFinal(double currentTime){
133  
343 –  char finalName[500];
134    ofstream finalOut;
135 +  vector<ofstream*> fileStreams;
136  
346 –  const int BUFFERSIZE = 2000;
347 –  char tempBuffer[BUFFERSIZE];
348 –  char writeLine[BUFFERSIZE];  
349 –
350 –  double q[4];
351 –  DirectionalAtom* dAtom;
352 –  int nAtoms = entry_plug->n_atoms;
353 –  Atom** atoms = entry_plug->atoms;
354 –  int i, j, which_node, done, game_over, which_atom, local_index;
355 –  
356 –  double pos[3], vel[3];
357 –  
137   #ifdef IS_MPI
138    if(worldRank == 0 ){
139 < #endif // is_mpi
140 <    
141 <    strcpy( finalName, entry_plug->finalName );
363 <    
364 <    finalOut.open( finalName, ios::out | ios::trunc );
139 >
140 >    finalOut.open( entry_plug->finalName, ios::out | ios::trunc );
141 >
142      if( !finalOut ){
143        sprintf( painCave.errMsg,
144                 "Could not open \"%s\" for final dump output.\n",
145 <               finalName );
145 >               entry_plug->finalName );
146        painCave.isFatal = 1;
147        simError();
148      }
149 <    
373 <    // finalOut.setf( ios::scientific );
374 <    
375 < #ifdef IS_MPI
149 >
150    }
151 + #endif // is_mpi
152    
153 <  sprintf(checkPointMsg,"Opened file for final configuration\n");
154 <  MPIcheckPoint();  
153 >  fileStreams.push_back(&finalOut);  
154 >  writeFrame(fileStreams, currentTime);
155 >
156 > #ifdef IS_MPI
157 >  finalOut.close();
158 > #endif
159    
160 < #endif //is_mpi
160 > }
161  
162 + void DumpWriter::writeFrame( vector<ofstream*>& outFile, double currentTime ){
163 +
164 +  const int BUFFERSIZE = 2000;
165 +  const int MINIBUFFERSIZE = 100;
166 +
167 +  char tempBuffer[BUFFERSIZE];  
168 +  char writeLine[BUFFERSIZE];
169 +
170 +  int i, k;
171 +
172 + #ifdef IS_MPI
173    
174 +  /*********************************************************************
175 +   * Documentation?  You want DOCUMENTATION?
176 +   *
177 +   * Why all the potatoes below?  
178 +   *
179 +   * To make a long story short, the original version of DumpWriter
180 +   * worked in the most inefficient way possible.  Node 0 would
181 +   * poke each of the node for an individual atom's formatted data
182 +   * as node 0 worked its way down the global index. This was particularly
183 +   * inefficient since the method blocked all processors at every atom
184 +   * (and did it twice!).
185 +   *
186 +   * An intermediate version of DumpWriter could be described from Node
187 +   * zero's perspective as follows:
188 +   *
189 +   *  1) Have 100 of your friends stand in a circle.
190 +   *  2) When you say go, have all of them start tossing potatoes at
191 +   *     you (one at a time).
192 +   *  3) Catch the potatoes.
193 +   *
194 +   * It was an improvement, but MPI has buffers and caches that could
195 +   * best be described in this analogy as "potato nets", so there's no
196 +   * need to block the processors atom-by-atom.
197 +   *
198 +   * This new and improved DumpWriter works in an even more efficient
199 +   * way:
200 +   *
201 +   *  1) Have 100 of your friend stand in a circle.
202 +   *  2) When you say go, have them start tossing 5-pound bags of
203 +   *     potatoes at you.
204 +   *  3) Once you've caught a friend's bag of potatoes,
205 +   *     toss them a spud to let them know they can toss another bag.
206 +   *
207 +   * How's THAT for documentation?
208 +   *
209 +   *********************************************************************/
210 +
211 +  int *potatoes;
212 +  int myPotato;
213 +
214 +  int nProc;
215 +  int j, which_node, done, which_atom, local_index, currentIndex;
216 +  double atomData6[6];
217 +  double atomData13[13];
218 +  int isDirectional;
219 +  char* atomTypeString;
220 +  char MPIatomTypeString[MINIBUFFERSIZE];
221 +
222 + #else //is_mpi
223 +  int nAtoms = entry_plug->n_atoms;
224 + #endif //is_mpi
225 +
226 +  double q[4];
227 +  DirectionalAtom* dAtom;
228 +  Atom** atoms = entry_plug->atoms;
229 +  double pos[3], vel[3];
230 +
231   #ifndef IS_MPI
385 –    
386 –  finalOut << nAtoms << "\n";
387 –    
388 –  finalOut << finalTime << ";\t"
389 –           << entry_plug->Hmat[0][0] << "\t"
390 –           << entry_plug->Hmat[1][0] << "\t"
391 –           << entry_plug->Hmat[2][0] << ";\t"
392 –    
393 –           << entry_plug->Hmat[0][1] << "\t"
394 –           << entry_plug->Hmat[1][1] << "\t"
395 –           << entry_plug->Hmat[2][1] << ";\t"
396 –    
397 –           << entry_plug->Hmat[0][2] << "\t"
398 –           << entry_plug->Hmat[1][2] << "\t"
399 –           << entry_plug->Hmat[2][2] << ";\n";
232    
233 +  for(k = 0; k < outFile.size(); k++){
234 +    *outFile[k] << nAtoms << "\n";
235 +
236 +    *outFile[k] << currentTime << ";\t"
237 +               << entry_plug->Hmat[0][0] << "\t"
238 +                     << entry_plug->Hmat[1][0] << "\t"
239 +                     << entry_plug->Hmat[2][0] << ";\t"
240 +              
241 +               << entry_plug->Hmat[0][1] << "\t"
242 +                     << entry_plug->Hmat[1][1] << "\t"
243 +                     << entry_plug->Hmat[2][1] << ";\t"
244 +
245 +                     << entry_plug->Hmat[0][2] << "\t"
246 +                     << entry_plug->Hmat[1][2] << "\t"
247 +                     << entry_plug->Hmat[2][2] << ";";
248 +
249 +    //write out additional parameters, such as chi and eta
250 +    *outFile[k] << entry_plug->the_integrator->getAdditionalParameters() << endl;
251 +  }
252 +  
253    for( i=0; i<nAtoms; i++ ){
254 <      
254 >
255      atoms[i]->getPos(pos);
256      atoms[i]->getVel(vel);
257 <    
257 >
258      sprintf( tempBuffer,
259               "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
260               atoms[i]->getType(),
# Line 415 | Line 267 | void DumpWriter::writeFinal(double finalTime){
267      strcpy( writeLine, tempBuffer );
268  
269      if( atoms[i]->isDirectional() ){
270 <        
270 >
271        dAtom = (DirectionalAtom *)atoms[i];
272        dAtom->getQ( q );
273 <        
273 >
274        sprintf( tempBuffer,
275                 "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
276                 q[0],
# Line 432 | Line 284 | void DumpWriter::writeFinal(double finalTime){
284      }
285      else
286        strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
287 <      
288 <    finalOut << writeLine;
287 >
288 >    for(k = 0; k < outFile.size(); k++)
289 >      *outFile[k] << writeLine;
290    }
438 –  finalOut.flush();
439 –  finalOut.close();
291  
292   #else // is_mpi
293 +
294 +  /* code to find maximum tag value */
295    
296 <  // first thing first, suspend fatalities.
297 <  painCave.isEventLoop = 1;
296 >  int *tagub, flag, MAXTAG;
297 >  MPI_Attr_get(MPI_COMM_WORLD, MPI_TAG_UB, &tagub, &flag);
298 >  if (flag) {
299 >    MAXTAG = *tagub;
300 >  } else {
301 >    MAXTAG = 32767;
302 >  }  
303  
446 –  int myStatus; // 1 = wakeup & success; 0 = error; -1 = AllDone
304    int haveError;
305  
306    MPI_Status istatus;
307    int *AtomToProcMap = mpiSim->getAtomToProcMap();
308  
309    // write out header and node 0's coordinates
310 <  
454 <  haveError = 0;
310 >
311    if( worldRank == 0 ){
312 <    finalOut << mpiSim->getTotAtoms() << "\n";
312 >
313 >    // Node 0 needs a list of the magic potatoes for each processor;
314 >
315 >    nProc = mpiSim->getNumberProcessors();
316 >    potatoes = new int[nProc];
317 >
318 >    //write out the comment lines
319 >    for (i = 0; i < nProc; i++)
320 >      potatoes[i] = 0;
321      
322 <    finalOut << finalTime << ";\t"
323 <             << entry_plug->Hmat[0][0] << "\t"
460 <             << entry_plug->Hmat[1][0] << "\t"
461 <             << entry_plug->Hmat[2][0] << ";\t"
462 <      
463 <             << entry_plug->Hmat[0][1] << "\t"
464 <             << entry_plug->Hmat[1][1] << "\t"
465 <             << entry_plug->Hmat[2][1] << ";\t"
466 <      
467 <             << entry_plug->Hmat[0][2] << "\t"
468 <             << entry_plug->Hmat[1][2] << "\t"
469 <             << entry_plug->Hmat[2][2] << ";\n";
470 <    
471 <    for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) {
472 <      // Get the Node number which has this molecule:
473 <      
474 <      which_node = AtomToProcMap[i];    
475 <      
476 <      if (which_node == mpiSim->getMyNode()) {
322 >      for(k = 0; k < outFile.size(); k++){
323 >        *outFile[k] << mpiSim->getTotAtoms() << "\n";
324  
325 <        which_atom = i;
326 <        local_index=-1;        
327 <        for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) {
328 <          if (atoms[j]->getGlobalIndex() == which_atom) local_index = j;
482 <        }
483 <        if (local_index != -1) {    
325 >        *outFile[k] << currentTime << ";\t"
326 >                         << entry_plug->Hmat[0][0] << "\t"
327 >                         << entry_plug->Hmat[1][0] << "\t"
328 >                         << entry_plug->Hmat[2][0] << ";\t"
329  
330 <          atoms[local_index]->getPos(pos);
331 <          atoms[local_index]->getVel(vel);
332 <          
488 <          sprintf( tempBuffer,
489 <                   "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
490 <                   atoms[local_index]->getType(),
491 <                   pos[0],
492 <                   pos[1],
493 <                   pos[2],
494 <                   vel[0],
495 <                   vel[1],
496 <                   vel[2]);
497 <          strcpy( writeLine, tempBuffer );
498 <          
499 <          if( atoms[local_index]->isDirectional() ){
500 <            
501 <            dAtom = (DirectionalAtom *)atoms[local_index];
502 <            dAtom->getQ( q );
503 <            
504 <            sprintf( tempBuffer,
505 <                     "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
506 <                     q[0],
507 <                     q[1],
508 <                     q[2],
509 <                     q[3],
510 <                     dAtom->getJx(),
511 <                     dAtom->getJy(),
512 <                     dAtom->getJz());
513 <            strcat( writeLine, tempBuffer );
514 <          }
515 <          else
516 <            strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );      
517 <        }
518 <        else {
519 <          sprintf(painCave.errMsg,
520 <                  "Atom %d not found on processor %d\n",
521 <                  i, worldRank );
522 <          haveError= 1;
523 <          simError();
524 <        }
330 >                         << entry_plug->Hmat[0][1] << "\t"
331 >                         << entry_plug->Hmat[1][1] << "\t"
332 >                         << entry_plug->Hmat[2][1] << ";\t"
333  
334 <        if(haveError) nodeZeroError();
335 <    
336 <      }
337 <      else {
338 <        
531 <        myStatus = 1;
532 <        MPI_Send(&myStatus, 1, MPI_INT, which_node,
533 <                 TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
534 <        MPI_Send(&i, 1, MPI_INT, which_node, TAKE_THIS_TAG_INT,
535 <                 MPI_COMM_WORLD);
536 <        MPI_Recv(writeLine, BUFFERSIZE, MPI_CHAR, which_node,
537 <                 TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD, &istatus);
538 <        MPI_Recv(&myStatus, 1, MPI_INT, which_node,
539 <                 TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus);
540 <        
541 <        if(!myStatus) nodeZeroError();
542 <      }
543 <      
544 <      finalOut << writeLine;
334 >                         << entry_plug->Hmat[0][2] << "\t"
335 >                         << entry_plug->Hmat[1][2] << "\t"
336 >                         << entry_plug->Hmat[2][2] << ";";
337 >  
338 >        *outFile[k] << entry_plug->the_integrator->getAdditionalParameters() << endl;
339      }
546 –    
547 –    // kill everyone off:
548 –    myStatus = -1;
549 –    for (j = 0; j < mpiSim->getNumberProcessors(); j++) {      
550 –      MPI_Send(&myStatus, 1, MPI_INT, j,
551 –               TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
552 –    }
340  
341 <  } else {
555 <    
556 <    done = 0;
557 <    while (!done) {
341 >    currentIndex = 0;
342  
343 <      MPI_Recv(&myStatus, 1, MPI_INT, 0,
560 <               TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus);
343 >    for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) {
344        
345 <      if(!myStatus) anonymousNodeDie();
345 >      // Get the Node number which has this atom;
346        
347 <      if(myStatus < 0) break;
347 >      which_node = AtomToProcMap[i];
348        
349 <      MPI_Recv(&which_atom, 1, MPI_INT, 0,
567 <               TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus);
568 <      
569 <      myStatus = 1;
570 <      local_index=-1;        
571 <      for (j=0; j < mpiSim->getMyNlocal(); j++) {
572 <        if (atoms[j]->getGlobalIndex() == which_atom) local_index = j;
573 <      }
574 <      if (local_index != -1) {
349 >      if (which_node != 0) {
350  
351 <        atoms[local_index]->getPos(pos);
352 <        atoms[local_index]->getVel(vel);
351 >        if (potatoes[which_node] + 3 >= MAXTAG) {
352 >          // The potato was going to exceed the maximum value,
353 >          // so wrap this processor potato back to 0:        
354  
355 <        //format the line
356 <        sprintf( tempBuffer,
357 <                 "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
358 <                 atoms[local_index]->getType(),
359 <                 pos[0],
360 <                 pos[1],
361 <                 pos[2],
362 <                 vel[0],
363 <                 vel[1],
364 <                 vel[2]); // check here.
365 <        strcpy( writeLine, tempBuffer );
355 >          potatoes[which_node] = 0;          
356 >          MPI_Send(0, 1, MPI_INT, which_node, 0, MPI_COMM_WORLD);
357 >          
358 >        }
359 >
360 >        myPotato = potatoes[which_node];        
361 >        
362 >        MPI_Recv(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, which_node,
363 >                 myPotato, MPI_COMM_WORLD, &istatus);
364 >        
365 >        atomTypeString = MPIatomTypeString;
366          
367 <        if( atoms[local_index]->isDirectional() ){
368 <          
369 <          dAtom = (DirectionalAtom *)atoms[local_index];
370 <          dAtom->getQ( q );
371 <          
372 <          sprintf( tempBuffer,
373 <                   "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
374 <                   q[0],
375 <                   q[1],
376 <                   q[2],
377 <                   q[3],
378 <                   dAtom->getJx(),
379 <                   dAtom->getJy(),
380 <                   dAtom->getJz());
381 <          strcat( writeLine, tempBuffer );
382 <        }
383 <        else{
384 <          strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
385 <        }
386 <      }
387 <      else {
388 <        sprintf(painCave.errMsg,
389 <                "Atom %d not found on processor %d\n",
390 <                which_atom, worldRank );
391 <        myStatus = 0;
392 <        simError();
393 <        
394 <        strcpy( writeLine, "Hello, I'm an error.\n");
367 >        myPotato++;
368 >
369 >        MPI_Recv(&isDirectional, 1, MPI_INT, which_node,
370 >                 myPotato, MPI_COMM_WORLD, &istatus);
371 >              
372 >        myPotato++;
373 >
374 >        if (isDirectional) {          
375 >          MPI_Recv(atomData13, 13, MPI_DOUBLE, which_node,
376 >                   myPotato, MPI_COMM_WORLD, &istatus);
377 >        } else {
378 >          MPI_Recv(atomData6, 6, MPI_DOUBLE, which_node,
379 >                   myPotato, MPI_COMM_WORLD, &istatus);          
380 >        }
381 >        
382 >        myPotato++;
383 >        potatoes[which_node] = myPotato;
384 >
385 >      } else {
386 >        
387 >        haveError = 0;
388 >              which_atom = i;
389 >        
390 >        local_index = indexArray[currentIndex].first;        
391 >                
392 >        if (which_atom == indexArray[currentIndex].second) {
393 >          
394 >          atomTypeString = atoms[local_index]->getType();
395 >
396 >                atoms[local_index]->getPos(pos);
397 >                atoms[local_index]->getVel(vel);          
398 >
399 >          atomData6[0] = pos[0];
400 >          atomData6[1] = pos[1];
401 >          atomData6[2] = pos[2];
402 >
403 >          atomData6[3] = vel[0];
404 >          atomData6[4] = vel[1];
405 >          atomData6[5] = vel[2];
406 >          
407 >          isDirectional = 0;
408 >
409 >          if( atoms[local_index]->isDirectional() ){
410 >
411 >            isDirectional = 1;
412 >            
413 >            dAtom = (DirectionalAtom *)atoms[local_index];
414 >            dAtom->getQ( q );
415 >
416 >            for (int j = 0; j < 6 ; j++)
417 >              atomData13[j] = atomData6[j];            
418 >            
419 >            atomData13[6] = q[0];
420 >            atomData13[7] = q[1];
421 >            atomData13[8] = q[2];
422 >            atomData13[9] = q[3];
423 >            
424 >            atomData13[10] = dAtom->getJx();
425 >            atomData13[11] = dAtom->getJy();
426 >            atomData13[12] = dAtom->getJz();
427 >          }
428 >          
429 >        } else {
430 >          sprintf(painCave.errMsg,
431 >                              "Atom %d not found on processor %d\n",
432 >                              i, worldRank );
433 >                haveError= 1;
434 >                simError();
435 >              }
436 >        
437 >        if(haveError) DieDieDie();
438 >        
439 >        currentIndex ++;
440        }
441 +      // If we've survived to here, format the line:
442 +      
443 +      if (!isDirectional) {
444 +        
445 +        sprintf( writeLine,
446 +                             "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
447 +                             atomTypeString,
448 +                             atomData6[0],
449 +                             atomData6[1],
450 +                             atomData6[2],
451 +                             atomData6[3],
452 +                             atomData6[4],
453 +                             atomData6[5]);
454  
455 <      MPI_Send(writeLine, BUFFERSIZE, MPI_CHAR, 0,
456 <               TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD);
457 <      MPI_Send( &myStatus, 1, MPI_INT, 0,
458 <                TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
455 >              strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
456 >        
457 >      } else {
458 >        
459 >              sprintf( writeLine,
460 >                             "%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",
461 >                             atomTypeString,
462 >                             atomData13[0],
463 >                             atomData13[1],
464 >                             atomData13[2],
465 >                             atomData13[3],
466 >                             atomData13[4],
467 >                             atomData13[5],
468 >                             atomData13[6],
469 >                             atomData13[7],
470 >                             atomData13[8],
471 >                             atomData13[9],
472 >                             atomData13[10],
473 >                             atomData13[11],
474 >                             atomData13[12]);
475 >        
476 >      }
477 >      
478 >      for(k = 0; k < outFile.size(); k++)
479 >        *outFile[k] << writeLine;
480      }
481 <  }
482 <  finalOut.flush();
483 <  sprintf( checkPointMsg,
484 <           "Sucessfully took a dump.\n");
485 <  MPIcheckPoint();
486 <  
632 <  if( worldRank == 0 ) finalOut.close();    
633 < #endif // is_mpi
634 < }
481 >    
482 >    for(k = 0; k < outFile.size(); k++)
483 >      outFile[k]->flush();
484 >    
485 >    sprintf( checkPointMsg,
486 >             "Sucessfully took a dump.\n");
487  
488 +    MPIcheckPoint();        
489  
490 +    delete[] potatoes;
491  
492 < #ifdef IS_MPI
492 >  } else {
493  
494 < // a couple of functions to let us escape the write loop
494 >    // worldRank != 0, so I'm a remote node.  
495  
496 < void dWrite::nodeZeroError( void ){
497 <  int j, myStatus;
496 >    // Set my magic potato to 0:
497 >
498 >    myPotato = 0;
499 >    currentIndex = 0;
500 >    
501 >    for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) {
502 >      
503 >      // Am I the node which has this atom?
504 >      
505 >      if (AtomToProcMap[i] == worldRank) {
506 >
507 >        if (myPotato + 3 >= MAXTAG) {
508 >
509 >          // The potato was going to exceed the maximum value,
510 >          // so wrap this processor potato back to 0 (and block until
511 >          // node 0 says we can go:
512 >
513 >          MPI_Recv(&myPotato, 1, MPI_INT, 0, 0, MPI_COMM_WORLD, &istatus);
514 >          
515 >        }
516 >        which_atom = i;
517 >        local_index = indexArray[currentIndex].first;        
518 >                
519 >        if (which_atom == indexArray[currentIndex].second) {
520 >        
521 >          atomTypeString = atoms[local_index]->getType();
522 >
523 >                atoms[local_index]->getPos(pos);
524 >                atoms[local_index]->getVel(vel);
525 >
526 >          atomData6[0] = pos[0];
527 >          atomData6[1] = pos[1];
528 >          atomData6[2] = pos[2];
529 >
530 >          atomData6[3] = vel[0];
531 >          atomData6[4] = vel[1];
532 >          atomData6[5] = vel[2];
533 >          
534 >          isDirectional = 0;
535 >
536 >          if( atoms[local_index]->isDirectional() ){
537 >
538 >            isDirectional = 1;
539 >            
540 >            dAtom = (DirectionalAtom *)atoms[local_index];
541 >            dAtom->getQ( q );
542 >            
543 >            for (int j = 0; j < 6 ; j++)
544 >              atomData13[j] = atomData6[j];
545 >            
546 >            atomData13[6] = q[0];
547 >            atomData13[7] = q[1];
548 >            atomData13[8] = q[2];
549 >            atomData13[9] = q[3];
550    
551 <  myStatus = 0;
552 <  for (j = 0; j < mpiSim->getNumberProcessors(); j++) {      
553 <    MPI_Send( &myStatus, 1, MPI_INT, j,
554 <              TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
649 <  }  
650 <  
551 >            atomData13[10] = dAtom->getJx();
552 >            atomData13[11] = dAtom->getJy();
553 >            atomData13[12] = dAtom->getJz();
554 >          }
555  
556 <  MPI_Finalize();
557 <  exit (0);
556 >        } else {
557 >                sprintf(painCave.errMsg,
558 >                              "Atom %d not found on processor %d\n",
559 >                              i, worldRank );
560 >                haveError= 1;
561 >                simError();
562 >              }
563 >
564 >        strncpy(MPIatomTypeString, atomTypeString, MINIBUFFERSIZE);
565 >
566 >        // null terminate the string before sending (just in case):
567 >        MPIatomTypeString[MINIBUFFERSIZE-1] = '\0';
568 >
569 >        MPI_Send(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, 0,
570 >                             myPotato, MPI_COMM_WORLD);
571 >        
572 >        myPotato++;
573 >
574 >        MPI_Send(&isDirectional, 1, MPI_INT, 0,
575 >                             myPotato, MPI_COMM_WORLD);
576 >        
577 >        myPotato++;
578 >        
579 >        if (isDirectional) {
580 >
581 >          MPI_Send(atomData13, 13, MPI_DOUBLE, 0,
582 >                   myPotato, MPI_COMM_WORLD);
583 >          
584 >        } else {
585 >
586 >          MPI_Send(atomData6, 6, MPI_DOUBLE, 0,
587 >                   myPotato, MPI_COMM_WORLD);
588 >        }
589 >
590 >        myPotato++;  
591 >        currentIndex++;    
592 >      }
593 >    }
594 >
595 >    sprintf( checkPointMsg,
596 >             "Sucessfully took a dump.\n");
597 >    MPIcheckPoint();        
598 >    
599 >  }
600    
601 + #endif // is_mpi
602   }
603  
604 < void dWrite::anonymousNodeDie( void ){
604 > #ifdef IS_MPI
605  
606 + // a couple of functions to let us escape the write loop
607 +
608 + void dWrite::DieDieDie( void ){
609 +
610    MPI_Finalize();
611    exit (0);
612   }

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