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root/group/trunk/OOPSE/libmdtools/DumpWriter.cpp
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Comparing trunk/OOPSE/libmdtools/DumpWriter.cpp (file contents):
Revision 590 by mmeineke, Thu Jul 10 22:15:53 2003 UTC vs.
Revision 951 by mmeineke, Fri Jan 16 21:51:51 2004 UTC

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

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