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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 1078 by tim, Tue Mar 2 20:32:40 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  
136 <      }
137 <      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 <    }
136 >  ofstream finalOut;
137 >  vector<ofstream*> fileStreams;
138  
247 –  } else {
248 –    
249 –    done = 0;
250 –    while (!done) {
251 –      
252 –      MPI_Recv(&myStatus, 1, MPI_INT, 0,
253 –               TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus);
254 –
255 –      if(!myStatus) anonymousNodeDie();
256 –      
257 –      if(myStatus < 0) break;
258 –
259 –      MPI_Recv(&which_atom, 1, MPI_INT, 0,
260 –               TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus);
261 –      
262 –      myStatus = 1;
263 –      local_index=-1;        
264 –      for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) {
265 –        if (atoms[j]->getGlobalIndex() == which_atom) local_index = j;
266 –      }
267 –      if (local_index != -1) {
268 –        //format the line
269 –        sprintf( tempBuffer,
270 –                 "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
271 –                 atoms[local_index]->getType(),
272 –                 atoms[local_index]->getX(),
273 –                 atoms[local_index]->getY(),
274 –                 atoms[local_index]->getZ(),
275 –                 atoms[local_index]->get_vx(),
276 –                 atoms[local_index]->get_vy(),
277 –                 atoms[local_index]->get_vz()); // check here.
278 –        strcpy( writeLine, tempBuffer );
279 –        
280 –        if( atoms[local_index]->isDirectional() ){
281 –          
282 –          dAtom = (DirectionalAtom *)atoms[local_index];
283 –          dAtom->getQ( q );
284 –          
285 –          sprintf( tempBuffer,
286 –                   "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
287 –                   q[0],
288 –                   q[1],
289 –                   q[2],
290 –                   q[3],
291 –                   dAtom->getJx(),
292 –                   dAtom->getJy(),
293 –                   dAtom->getJz());
294 –          strcat( writeLine, tempBuffer );
295 –        }
296 –        else{
297 –          strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
298 –        }
299 –      }
300 –      else {
301 –        sprintf(painCave.errMsg,
302 –                "Atom %d not found on processor %d\n",
303 –                which_atom, worldRank );
304 –        myStatus = 0;
305 –        simError();
306 –
307 –        strcpy( writeLine, "Hello, I'm an error.\n");
308 –      }
309 –
310 –      MPI_Send(writeLine, BUFFERSIZE, MPI_CHAR, 0,
311 –               TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD);
312 –      MPI_Send( &myStatus, 1, MPI_INT, 0,
313 –                TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
314 –    }
315 –  }  
316 –  outFile.flush();
317 –  sprintf( checkPointMsg,
318 –           "Sucessfully took a dump.\n");
319 –  MPIcheckPoint();
320 –
321 – // last  thing last, enable  fatalities.
322 –  painCave.isEventLoop = 0;
323 –
324 – #endif // is_mpi
325 – }
326 –
327 – void DumpWriter::writeFinal(double finalTime){
328 –
329 –  char finalName[500];
330 –  ofstream finalOut;
331 –
332 –  const int BUFFERSIZE = 2000;
333 –  char tempBuffer[BUFFERSIZE];
334 –  char writeLine[BUFFERSIZE];  
335 –
336 –  double q[4];
337 –  DirectionalAtom* dAtom;
338 –  int nAtoms = entry_plug->n_atoms;
339 –  Atom** atoms = entry_plug->atoms;
340 –  int i, j, which_node, done, game_over, which_atom, local_index;
341 –  
342 –  
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];
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 >
278        sprintf( tempBuffer,
279                 "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
280                 q[0],
# Line 414 | Line 288 | void DumpWriter::writeFinal(double finalTime){
288      }
289      else
290        strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
291 <      
292 <    finalOut << writeLine;
291 >
292 >    for(k = 0; k < outFile.size(); k++)
293 >      *outFile[k] << writeLine;
294    }
420 –  finalOut.flush();
421 –  finalOut.close();
295  
296   #else // is_mpi
297 +
298 +  /* code to find maximum tag value */
299    
300 <  // first thing first, suspend fatalities.
301 <  painCave.isEventLoop = 1;
300 >  int *tagub, flag, MAXTAG;
301 >  MPI_Attr_get(MPI_COMM_WORLD, MPI_TAG_UB, &tagub, &flag);
302 >  if (flag) {
303 >    MAXTAG = *tagub;
304 >  } else {
305 >    MAXTAG = 32767;
306 >  }  
307  
428 –  int myStatus; // 1 = wakeup & success; 0 = error; -1 = AllDone
308    int haveError;
309  
310    MPI_Status istatus;
311    int *AtomToProcMap = mpiSim->getAtomToProcMap();
312  
313    // write out header and node 0's coordinates
314 <  
436 <  haveError = 0;
314 >
315    if( worldRank == 0 ){
316 <    finalOut << mpiSim->getTotAtoms() << "\n";
316 >
317 >    // Node 0 needs a list of the magic potatoes for each processor;
318 >
319 >    nProc = mpiSim->getNumberProcessors();
320 >    potatoes = new int[nProc];
321 >
322 >    //write out the comment lines
323 >    for (i = 0; i < nProc; i++)
324 >      potatoes[i] = 0;
325      
326 <    finalOut << finalTime << "\t"
327 <             << entry_plug->Hmat[0] << "\t"
328 <             << entry_plug->Hmat[1] << "\t"
329 <             << entry_plug->Hmat[2] << "\t"
330 <      
331 <             << entry_plug->Hmat[3] << "\t"
332 <             << entry_plug->Hmat[4] << "\t"
333 <             << entry_plug->Hmat[5] << "\t"
334 <      
335 <             << entry_plug->Hmat[6] << "\t"
336 <             << entry_plug->Hmat[7] << "\t"
337 <             << entry_plug->Hmat[8] << "\n";
338 <    
326 >      for(k = 0; k < outFile.size(); k++){
327 >        *outFile[k] << mpiSim->getTotAtoms() << "\n";
328 >
329 >        *outFile[k] << currentTime << ";\t"
330 >                         << entry_plug->Hmat[0][0] << "\t"
331 >                         << entry_plug->Hmat[1][0] << "\t"
332 >                         << entry_plug->Hmat[2][0] << ";\t"
333 >
334 >                         << entry_plug->Hmat[0][1] << "\t"
335 >                         << entry_plug->Hmat[1][1] << "\t"
336 >                         << entry_plug->Hmat[2][1] << ";\t"
337 >
338 >                         << entry_plug->Hmat[0][2] << "\t"
339 >                         << entry_plug->Hmat[1][2] << "\t"
340 >                         << entry_plug->Hmat[2][2] << ";";
341 >  
342 >        *outFile[k] << entry_plug->the_integrator->getAdditionalParameters() << endl;
343 >    }
344 >
345 >    currentIndex = 0;
346 >
347      for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) {
454 –      // Get the Node number which has this molecule:
348        
349 <      which_node = AtomToProcMap[i];    
349 >      // Get the Node number which has this atom;
350        
351 <      if (which_node == mpiSim->getMyNode()) {
351 >      which_node = AtomToProcMap[i];
352 >      
353 >      if (which_node != 0) {
354  
355 <        which_atom = i;
356 <        local_index=-1;        
357 <        for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) {
358 <          if (atoms[j]->getGlobalIndex() == which_atom) local_index = j;
355 >        if (potatoes[which_node] + 3 >= MAXTAG) {
356 >          // The potato was going to exceed the maximum value,
357 >          // so wrap this processor potato back to 0:        
358 >
359 >          potatoes[which_node] = 0;          
360 >          MPI_Send(0, 1, MPI_INT, which_node, 0, MPI_COMM_WORLD);
361 >          
362          }
363 <        if (local_index != -1) {        
364 <          sprintf( tempBuffer,
365 <                   "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
366 <                   atoms[local_index]->getType(),
367 <                   atoms[local_index]->getX(),
368 <                   atoms[local_index]->getY(),
369 <                   atoms[local_index]->getZ(),
370 <                   atoms[local_index]->get_vx(),
371 <                   atoms[local_index]->get_vy(),
372 <                   atoms[local_index]->get_vz());
373 <          strcpy( writeLine, tempBuffer );
374 <          
375 <          if( atoms[local_index]->isDirectional() ){
363 >
364 >        myPotato = potatoes[which_node];        
365 >        
366 >        MPI_Recv(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, which_node,
367 >                 myPotato, MPI_COMM_WORLD, &istatus);
368 >        
369 >        atomTypeString = MPIatomTypeString;
370 >        
371 >        myPotato++;
372 >
373 >        MPI_Recv(&isDirectional, 1, MPI_INT, which_node,
374 >                 myPotato, MPI_COMM_WORLD, &istatus);
375 >              
376 >        myPotato++;
377 >
378 >        if (isDirectional) {          
379 >          MPI_Recv(atomData13, 13, MPI_DOUBLE, which_node,
380 >                   myPotato, MPI_COMM_WORLD, &istatus);
381 >        } else {
382 >          MPI_Recv(atomData6, 6, MPI_DOUBLE, which_node,
383 >                   myPotato, MPI_COMM_WORLD, &istatus);          
384 >        }
385 >        
386 >        myPotato++;
387 >        potatoes[which_node] = myPotato;
388 >
389 >      } else {
390 >        
391 >        haveError = 0;
392 >        which_atom = i;
393 >        
394 >          local_index = indexArray[currentIndex].first;        
395 >          
396 >          if (which_atom == indexArray[currentIndex].second) {
397              
398 <            dAtom = (DirectionalAtom *)atoms[local_index];
480 <            dAtom->getQ( q );
398 >            atomTypeString = atoms[local_index]->getType();
399              
400 <            sprintf( tempBuffer,
401 <                     "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
402 <                     q[0],
403 <                     q[1],
404 <                     q[2],
405 <                     q[3],
406 <                     dAtom->getJx(),
407 <                     dAtom->getJy(),
408 <                     dAtom->getJz());
409 <            strcat( writeLine, tempBuffer );
410 <          }
411 <          else
412 <            strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );      
413 <        }
414 <        else {
400 >          atoms[local_index]->getPos(pos);
401 >          atoms[local_index]->getVel(vel);          
402 >          
403 >          atomData6[0] = pos[0];
404 >          atomData6[1] = pos[1];
405 >          atomData6[2] = pos[2];
406 >
407 >          atomData6[3] = vel[0];
408 >          atomData6[4] = vel[1];
409 >          atomData6[5] = vel[2];
410 >          
411 >          isDirectional = 0;
412 >
413 >          if( atoms[local_index]->isDirectional() ){
414 >
415 >            isDirectional = 1;
416 >            
417 >            dAtom = (DirectionalAtom *)atoms[local_index];
418 >            dAtom->getQ( q );
419 >
420 >            for (int j = 0; j < 6 ; j++)
421 >              atomData13[j] = atomData6[j];            
422 >            
423 >            atomData13[6] = q[0];
424 >            atomData13[7] = q[1];
425 >            atomData13[8] = q[2];
426 >            atomData13[9] = q[3];
427 >            
428 >            atomData13[10] = dAtom->getJx();
429 >            atomData13[11] = dAtom->getJy();
430 >            atomData13[12] = dAtom->getJz();
431 >          }
432 >          
433 >        } else {
434            sprintf(painCave.errMsg,
435 <                  "Atom %d not found on processor %d\n",
436 <                  i, worldRank );
435 >                  "Atom %d not found on processor %d, currentIndex = %d, local_index = %d\n",
436 >                  which_atom, worldRank, currentIndex, local_index );
437            haveError= 1;
438            simError();
439 <        }
503 <
504 <        if(haveError) nodeZeroError();
505 <    
506 <      }
507 <      else {
439 >        }
440          
441 <        myStatus = 1;
442 <        MPI_Send(&myStatus, 1, MPI_INT, which_node,
443 <                 TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
444 <        MPI_Send(&i, 1, MPI_INT, which_node, TAKE_THIS_TAG_INT,
445 <                 MPI_COMM_WORLD);
446 <        MPI_Recv(writeLine, BUFFERSIZE, MPI_CHAR, which_node,
447 <                 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);
441 >        if(haveError) DieDieDie();
442 >        
443 >        currentIndex++;
444 >      }
445 >      // If we've survived to here, format the line:
446 >      
447 >      if (!isDirectional) {
448          
449 <        if(!myStatus) nodeZeroError();
449 >        sprintf( writeLine,
450 >                 "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
451 >                 atomTypeString,
452 >                 atomData6[0],
453 >                 atomData6[1],
454 >                 atomData6[2],
455 >                 atomData6[3],
456 >                 atomData6[4],
457 >                 atomData6[5]);
458 >        
459 >        strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
460 >        
461 >      } else {
462 >        
463 >        sprintf( writeLine,
464 >                 "%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",
465 >                 atomTypeString,
466 >                 atomData13[0],
467 >                 atomData13[1],
468 >                 atomData13[2],
469 >                 atomData13[3],
470 >                 atomData13[4],
471 >                 atomData13[5],
472 >                 atomData13[6],
473 >                 atomData13[7],
474 >                 atomData13[8],
475 >                 atomData13[9],
476 >                 atomData13[10],
477 >                 atomData13[11],
478 >                 atomData13[12]);
479 >        
480        }
481        
482 <      finalOut << writeLine;
482 >      for(k = 0; k < outFile.size(); k++)
483 >        *outFile[k] << writeLine;
484      }
485      
486 <    // kill everyone off:
487 <    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 {
486 >    for(k = 0; k < outFile.size(); k++)
487 >      outFile[k]->flush();
488      
489 <    done = 0;
490 <    while (!done) {
489 >    sprintf( checkPointMsg,
490 >             "Sucessfully took a dump.\n");
491 >    
492 >    MPIcheckPoint();        
493 >    
494 >    delete[] potatoes;
495 >    
496 >  } else {
497  
498 <      MPI_Recv(&myStatus, 1, MPI_INT, 0,
499 <               TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus);
498 >    // worldRank != 0, so I'm a remote node.  
499 >
500 >    // Set my magic potato to 0:
501 >
502 >    myPotato = 0;
503 >    currentIndex = 0;
504 >    
505 >    for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) {
506        
507 <      if(!myStatus) anonymousNodeDie();
507 >      // Am I the node which has this atom?
508        
509 <      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) {
509 >      if (AtomToProcMap[i] == worldRank) {
510  
511 <        //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() ){
511 >        if (myPotato + 3 >= MAXTAG) {
512            
513 <          dAtom = (DirectionalAtom *)atoms[local_index];
514 <          dAtom->getQ( q );
513 >          // The potato was going to exceed the maximum value,
514 >          // so wrap this processor potato back to 0 (and block until
515 >          // node 0 says we can go:
516            
517 <          sprintf( tempBuffer,
518 <                   "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
519 <                   q[0],
520 <                   q[1],
521 <                   q[2],
522 <                   q[3],
523 <                   dAtom->getJx(),
524 <                   dAtom->getJy(),
525 <                   dAtom->getJz());
526 <          strcat( writeLine, tempBuffer );
517 >          MPI_Recv(&myPotato, 1, MPI_INT, 0, 0, MPI_COMM_WORLD, &istatus);
518 >          
519 >        }
520 >        which_atom = i;
521 >
522 >        local_index = indexArray[currentIndex].first;        
523 >                
524 >        if (which_atom == indexArray[currentIndex].second) {
525 >        
526 >          atomTypeString = atoms[local_index]->getType();
527 >          
528 >          atoms[local_index]->getPos(pos);
529 >          atoms[local_index]->getVel(vel);
530 >          
531 >          atomData6[0] = pos[0];
532 >          atomData6[1] = pos[1];
533 >          atomData6[2] = pos[2];
534 >
535 >          atomData6[3] = vel[0];
536 >          atomData6[4] = vel[1];
537 >          atomData6[5] = vel[2];
538 >          
539 >          isDirectional = 0;
540 >
541 >          if( atoms[local_index]->isDirectional() ){
542 >
543 >            isDirectional = 1;
544 >            
545 >            dAtom = (DirectionalAtom *)atoms[local_index];
546 >            dAtom->getQ( q );
547 >            
548 >            for (int j = 0; j < 6 ; j++)
549 >              atomData13[j] = atomData6[j];
550 >            
551 >            atomData13[6] = q[0];
552 >            atomData13[7] = q[1];
553 >            atomData13[8] = q[2];
554 >            atomData13[9] = q[3];
555 >  
556 >            atomData13[10] = dAtom->getJx();
557 >            atomData13[11] = dAtom->getJy();
558 >            atomData13[12] = dAtom->getJz();
559 >          }
560 >
561 >        } else {
562 >          sprintf(painCave.errMsg,
563 >                  "Atom %d not found on processor %d, currentIndex = %d, local_index = %d\n",
564 >                  which_atom, worldRank, currentIndex, local_index );
565 >          haveError= 1;
566 >          simError();
567          }
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();
568          
569 <        strcpy( writeLine, "Hello, I'm an error.\n");
594 <      }
569 >        strncpy(MPIatomTypeString, atomTypeString, MINIBUFFERSIZE);
570  
571 <      MPI_Send(writeLine, BUFFERSIZE, MPI_CHAR, 0,
572 <               TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD);
573 <      MPI_Send( &myStatus, 1, MPI_INT, 0,
574 <                TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
571 >        // null terminate the string before sending (just in case):
572 >        MPIatomTypeString[MINIBUFFERSIZE-1] = '\0';
573 >
574 >        MPI_Send(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, 0,
575 >                             myPotato, MPI_COMM_WORLD);
576 >        
577 >        myPotato++;
578 >
579 >        MPI_Send(&isDirectional, 1, MPI_INT, 0,
580 >                             myPotato, MPI_COMM_WORLD);
581 >        
582 >        myPotato++;
583 >        
584 >        if (isDirectional) {
585 >
586 >          MPI_Send(atomData13, 13, MPI_DOUBLE, 0,
587 >                   myPotato, MPI_COMM_WORLD);
588 >          
589 >        } else {
590 >
591 >          MPI_Send(atomData6, 6, MPI_DOUBLE, 0,
592 >                   myPotato, MPI_COMM_WORLD);
593 >        }
594 >
595 >        myPotato++;  
596 >        currentIndex++;    
597 >      }
598      }
599 <  }
600 <  finalOut.flush();
601 <  sprintf( checkPointMsg,
602 <           "Sucessfully took a dump.\n");
603 <  MPIcheckPoint();
599 >
600 >    sprintf( checkPointMsg,
601 >             "Sucessfully took a dump.\n");
602 >    MPIcheckPoint();        
603 >    
604 >  }
605    
607 –  if( worldRank == 0 ) finalOut.close();    
606   #endif // is_mpi
607   }
608  
611 –
612 –
609   #ifdef IS_MPI
610  
611   // a couple of functions to let us escape the write loop
612  
613 < 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 <  
613 > void dWrite::DieDieDie( void ){
614  
615    MPI_Finalize();
616    exit (0);
629 –  
617   }
618  
632 – void dWrite::anonymousNodeDie( void ){
633 –
634 –  MPI_Finalize();
635 –  exit (0);
636 – }
637 –
619   #endif //is_mpi

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