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root/group/trunk/OOPSE/libmdtools/DumpWriter.cpp
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Comparing trunk/OOPSE/libmdtools/DumpWriter.cpp (file contents):
Revision 434 by chuckv, Fri Mar 28 19:30:59 2003 UTC vs.
Revision 952 by tim, Fri Jan 16 21:55:39 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>
7 – #include <mpi++.h>
11   #include "mpiSimulation.hpp"
12 < #define TAKE_THIS_TAG 1
12 >
13 > namespace dWrite{
14 >  void DieDieDie( void );
15 > }
16 >
17 > using namespace dWrite;
18   #endif //is_mpi
19  
20   #include "ReadWrite.hpp"
# Line 19 | Line 27 | DumpWriter::DumpWriter( SimInfo* the_entry_plug ){
27   #ifdef IS_MPI
28    if(worldRank == 0 ){
29   #endif // is_mpi
30 <    
31 <
32 <    
33 <    strcpy( outName, entry_plug->sampleName );
34 <    
27 <    outFile.open(outName, ios::out | ios::trunc );
28 <    
29 <    if( !outFile ){
30 <      
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      }
37 –  
38 –    //outFile.setf( ios::scientific );
41  
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 52 | 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, game_over, 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";
78 <    
79 <  outFile << currentTime << "\t"
80 <          << entry_plug->box_x << "\t"
81 <          << entry_plug->box_y << "\t"
82 <          << entry_plug->box_z << "\n";
83 <    
84 <  for( i=0; i<nAtoms; i++ ){
85 <      
103 > }
104  
105 <    sprintf( tempBuffer,
88 <             "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
89 <             atoms[i]->getType(),
90 <             atoms[i]->getX(),
91 <             atoms[i]->getY(),
92 <             atoms[i]->getZ(),
93 <             atoms[i]->get_vx(),
94 <             atoms[i]->get_vy(),
95 <             atoms[i]->get_vz());
96 <    strcpy( writeLine, tempBuffer );
105 > #endif
106  
107 <    if( atoms[i]->isDirectional() ){
108 <        
109 <      dAtom = (DirectionalAtom *)atoms[i];
110 <      dAtom->getQ( q );
111 <        
112 <      sprintf( tempBuffer,
113 <               "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
114 <               q[0],
115 <               q[1],
116 <               q[2],
117 <               q[3],
118 <               dAtom->getJx(),
119 <               dAtom->getJy(),
120 <               dAtom->getJz());
121 <      strcat( writeLine, tempBuffer );
107 > void DumpWriter::writeDump(double currentTime){
108 >
109 >  ofstream finalOut;
110 >  vector<ofstream*> fileStreams;
111 >
112 > #ifdef IS_MPI
113 >  if(worldRank == 0 ){
114 > #endif    
115 >    finalOut.open( entry_plug->finalName, ios::out | ios::trunc );
116 >    if( !finalOut ){
117 >      sprintf( painCave.errMsg,
118 >               "Could not open \"%s\" for final dump output.\n",
119 >               entry_plug->finalName );
120 >      painCave.isFatal = 1;
121 >      simError();
122      }
123 <    else
115 <      strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
116 <      
117 <    outFile << writeLine;
123 > #ifdef IS_MPI
124    }
125 <  outFile.flush();
125 > #endif // is_mpi
126  
127 < #else // is_mpi
127 >  fileStreams.push_back(&finalOut);
128 >  fileStreams.push_back(&dumpFile);
129  
130 <  MPI::Status istatus;
124 <  int *AtomToProcMap = mpiSim->getAtomToProcMap();
125 <  
126 <  // write out header and node 0's coordinates
127 <  
128 <  if( worldRank == 0 ){
129 <    outFile << mpiSim->getTotAtoms() << "\n";
130 <    
131 <    outFile << currentTime << "\t"
132 <            << entry_plug->box_x << "\t"
133 <            << entry_plug->box_y << "\t"
134 <            << entry_plug->box_z << "\n";
135 <    outFile.flush();
136 <    for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) {
137 <      // Get the Node number which has this atom;
138 <      
139 <      which_node = AtomToProcMap[i];    
140 <      
141 <      if (which_node == mpiSim->getMyNode()) {
142 <                sprintf( tempBuffer,
143 <                 "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
144 <                 atoms[i]->getType(),
145 <                 atoms[i]->getX(),
146 <                 atoms[i]->getY(),
147 <                 atoms[i]->getZ(),
148 <                 atoms[i]->get_vx(),
149 <                 atoms[i]->get_vy(),
150 <                 atoms[i]->get_vz());
151 <        strcpy( writeLine, tempBuffer );
152 <        
153 <        if( atoms[i]->isDirectional() ){
154 <          
155 <          dAtom = (DirectionalAtom *)atoms[i];
156 <          dAtom->getQ( q );
157 <          
158 <          sprintf( tempBuffer,
159 <                   "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
160 <                   q[0],
161 <                   q[1],
162 <                   q[2],
163 <                   q[3],
164 <                   dAtom->getJx(),
165 <                   dAtom->getJy(),
166 <                   dAtom->getJz());
167 <          strcat( writeLine, tempBuffer );
168 <        }
169 <        else
170 <          strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );      
171 <        
172 <      } else {
173 <        
174 <        std::cerr << "node 0: sending node " << which_node << " request for atom " << i << "\n";
175 <        MPI::COMM_WORLD.Send(&i, 1, MPI_INT, which_node, TAKE_THIS_TAG);
176 <        std::cerr << "node 0: sent!\n";
177 <        MPI::COMM_WORLD.Recv(writeLine, BUFFERSIZE, MPI_CHAR, which_node,
178 <                                TAKE_THIS_TAG, istatus);
179 <        std::cerr << "node 0: got this line: " << writeLine;
180 <      }
181 <      
182 <      outFile << writeLine;
183 <      outFile.flush();
184 <    }
185 <    
186 <    // kill everyone off:
187 <    game_over = -1;
188 <    for (j = 0; j < mpiSim->getNumberProcessors(); j++) {      
189 <      MPI::COMM_WORLD.Send(&game_over, 1, MPI_INT, j, TAKE_THIS_TAG);
190 <    }
130 >  writeFrame(fileStreams, currentTime);
131  
132 <  } else {
133 <    
134 <    done = 0;
135 <    while (!done) {
196 <      std::cerr << "node: " << mpiSim->getMyNode() << " Waiting for receive \n";
197 <      MPI::COMM_WORLD.Recv(&which_atom, 1, MPI_INT, 0,
198 <                           TAKE_THIS_TAG, istatus);
199 <      std::cerr << "node: " << mpiSim->getMyNode() << " got request for atom " << which_atom << "\n";
200 <      if (which_atom == -1) {
201 <        done=1;
202 <        continue;
203 <      } else {
204 <        local_index=-1;        
205 <        for (j=0; j < mpiSim->getMyNlocal(); j++) {
206 <          if (atoms[j]->getGlobalIndex() == which_atom) local_index = j;
207 <        }
208 <        if (local_index != -1) {
209 <          //format the line
210 <          sprintf( tempBuffer,
211 <                   "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
212 <                   atoms[local_index]->getType(),
213 <                   atoms[local_index]->getX(),
214 <                   atoms[local_index]->getY(),
215 <                   atoms[local_index]->getZ(),
216 <                   atoms[local_index]->get_vx(),
217 <                   atoms[local_index]->get_vy(),
218 <                   atoms[local_index]->get_vz()); // check here.
219 <          strcpy( writeLine, tempBuffer );
220 <          
221 <          if( atoms[local_index]->isDirectional() ){
222 <            
223 <            dAtom = (DirectionalAtom *)atoms[local_index];
224 <            dAtom->getQ( q );
225 <            
226 <            sprintf( tempBuffer,
227 <                     "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
228 <                     q[0],
229 <                     q[1],
230 <                     q[2],
231 <                     q[3],
232 <                     dAtom->getJx(),
233 <                     dAtom->getJy(),
234 <                     dAtom->getJz());
235 <            strcat( writeLine, tempBuffer );
236 <          }
237 <          else
238 <            strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
239 <          std::cerr << "node: " << mpiSim->getMyNode() << " sending this line" << writeLine;
240 <          MPI::COMM_WORLD.Send(writeLine, BUFFERSIZE, MPI_CHAR, 0,
241 <                               TAKE_THIS_TAG);
242 <        } else {
243 <          strcpy( writeLine, "ATOM NOT FOUND ON THIS PROCESSOR");
244 <          MPI::COMM_WORLD.Send(writeLine, BUFFERSIZE, MPI_CHAR, 0,
245 <                               TAKE_THIS_TAG);
246 <        }
247 <      }
248 <    }
249 <  }  
250 <  outFile.flush();
251 <  sprintf( checkPointMsg,
252 <           "Sucessfully took a dump.\n");
253 <  MPIcheckPoint();
254 < #endif // is_mpi
132 > #ifdef IS_MPI
133 >  finalOut.close();
134 > #endif
135 >        
136   }
137  
138 < void DumpWriter::writeFinal(){
138 > void DumpWriter::writeFinal(double currentTime){
139  
259 –  char finalName[500];
140    ofstream finalOut;
141 +  vector<ofstream*> fileStreams;
142  
262 –  const int BUFFERSIZE = 2000;
263 –  char tempBuffer[BUFFERSIZE];
264 –  char writeLine[BUFFERSIZE];  
265 –
266 –  double q[4];
267 –  DirectionalAtom* dAtom;
268 –  int nAtoms = entry_plug->n_atoms;
269 –  Atom** atoms = entry_plug->atoms;
270 –  int i, j, which_node, done, game_over, which_atom, local_index;
271 –  
272 –  
143   #ifdef IS_MPI
144    if(worldRank == 0 ){
145   #endif // is_mpi
146 <    
147 <    strcpy( finalName, entry_plug->finalName );
148 <    
279 <    finalOut.open( finalName, ios::out | ios::trunc );
146 >
147 >    finalOut.open( entry_plug->finalName, ios::out | ios::trunc );
148 >
149      if( !finalOut ){
150        sprintf( painCave.errMsg,
151                 "Could not open \"%s\" for final dump output.\n",
152 <               finalName );
152 >               entry_plug->finalName );
153        painCave.isFatal = 1;
154        simError();
155      }
156 <    
288 <    // finalOut.setf( ios::scientific );
289 <    
156 >
157   #ifdef IS_MPI
158    }
159 + #endif // is_mpi
160    
161 <  sprintf(checkPointMsg,"Opened file for final configuration\n");
162 <  MPIcheckPoint();  
161 >  fileStreams.push_back(&finalOut);  
162 >  writeFrame(fileStreams, currentTime);
163 >
164 > #ifdef IS_MPI
165 >  finalOut.close();
166 > #endif
167    
168 < #endif //is_mpi
168 > }
169  
170 + void DumpWriter::writeFrame( vector<ofstream*>& outFile, double currentTime ){
171 +
172 +  const int BUFFERSIZE = 2000;
173 +  const int MINIBUFFERSIZE = 100;
174 +
175 +  char tempBuffer[BUFFERSIZE];  
176 +  char writeLine[BUFFERSIZE];
177 +
178 +  int i, k;
179 +
180 + #ifdef IS_MPI
181    
182 +  /*********************************************************************
183 +   * Documentation?  You want DOCUMENTATION?
184 +   *
185 +   * Why all the potatoes below?  
186 +   *
187 +   * To make a long story short, the original version of DumpWriter
188 +   * worked in the most inefficient way possible.  Node 0 would
189 +   * poke each of the node for an individual atom's formatted data
190 +   * as node 0 worked its way down the global index. This was particularly
191 +   * inefficient since the method blocked all processors at every atom
192 +   * (and did it twice!).
193 +   *
194 +   * An intermediate version of DumpWriter could be described from Node
195 +   * zero's perspective as follows:
196 +   *
197 +   *  1) Have 100 of your friends stand in a circle.
198 +   *  2) When you say go, have all of them start tossing potatoes at
199 +   *     you (one at a time).
200 +   *  3) Catch the potatoes.
201 +   *
202 +   * It was an improvement, but MPI has buffers and caches that could
203 +   * best be described in this analogy as "potato nets", so there's no
204 +   * need to block the processors atom-by-atom.
205 +   *
206 +   * This new and improved DumpWriter works in an even more efficient
207 +   * way:
208 +   *
209 +   *  1) Have 100 of your friend stand in a circle.
210 +   *  2) When you say go, have them start tossing 5-pound bags of
211 +   *     potatoes at you.
212 +   *  3) Once you've caught a friend's bag of potatoes,
213 +   *     toss them a spud to let them know they can toss another bag.
214 +   *
215 +   * How's THAT for documentation?
216 +   *
217 +   *********************************************************************/
218 +
219 +  int *potatoes;
220 +  int myPotato;
221 +
222 +  int nProc;
223 +  int j, which_node, done, which_atom, local_index, currentIndex;
224 +  double atomData6[6];
225 +  double atomData13[13];
226 +  int isDirectional;
227 +  char* atomTypeString;
228 +  char MPIatomTypeString[MINIBUFFERSIZE];
229 +
230 + #else //is_mpi
231 +  int nAtoms = entry_plug->n_atoms;
232 + #endif //is_mpi
233 +
234 +  double q[4];
235 +  DirectionalAtom* dAtom;
236 +  Atom** atoms = entry_plug->atoms;
237 +  double pos[3], vel[3];
238 +
239   #ifndef IS_MPI
300 –    
301 –  finalOut << nAtoms << "\n";
302 –    
303 –  finalOut << entry_plug->box_x << "\t"
304 –           << entry_plug->box_y << "\t"
305 –           << entry_plug->box_z << "\n";
240    
241 +  for(k = 0; k < outFile.size(); k++){
242 +    *outFile[k] << nAtoms << "\n";
243 +
244 +    *outFile[k] << currentTime << ";\t"
245 +               << entry_plug->Hmat[0][0] << "\t"
246 +                     << entry_plug->Hmat[1][0] << "\t"
247 +                     << entry_plug->Hmat[2][0] << ";\t"
248 +              
249 +               << entry_plug->Hmat[0][1] << "\t"
250 +                     << entry_plug->Hmat[1][1] << "\t"
251 +                     << entry_plug->Hmat[2][1] << ";\t"
252 +
253 +                     << entry_plug->Hmat[0][2] << "\t"
254 +                     << entry_plug->Hmat[1][2] << "\t"
255 +                     << entry_plug->Hmat[2][2] << ";";
256 +
257 +    //write out additional parameters, such as chi and eta
258 +    *outFile[k] << entry_plug->the_integrator->getAdditionalParameters() << endl;
259 +  }
260 +  
261    for( i=0; i<nAtoms; i++ ){
262 <      
262 >
263 >    atoms[i]->getPos(pos);
264 >    atoms[i]->getVel(vel);
265 >
266      sprintf( tempBuffer,
267               "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
268               atoms[i]->getType(),
269 <             atoms[i]->getX(),
270 <             atoms[i]->getY(),
271 <             atoms[i]->getZ(),
272 <             atoms[i]->get_vx(),
273 <             atoms[i]->get_vy(),
274 <             atoms[i]->get_vz());
269 >             pos[0],
270 >             pos[1],
271 >             pos[2],
272 >             vel[0],
273 >             vel[1],
274 >             vel[2]);
275      strcpy( writeLine, tempBuffer );
276  
277      if( atoms[i]->isDirectional() ){
278 <        
278 >
279        dAtom = (DirectionalAtom *)atoms[i];
280        dAtom->getQ( q );
281 <        
281 >
282        sprintf( tempBuffer,
283                 "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
284                 q[0],
# Line 335 | Line 292 | void DumpWriter::writeFinal(){
292      }
293      else
294        strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
295 <      
296 <    finalOut << writeLine;
295 >
296 >    for(k = 0; k < outFile.size(); k++)
297 >      *outFile[k] << writeLine;
298    }
341 –  finalOut.flush();
342 –  finalOut.close();
299  
300   #else // is_mpi
301 +
302 +  /* code to find maximum tag value */
303    
304 <  MPI::Status istatus;
304 >  int *tagub, flag, MAXTAG;
305 >  MPI_Attr_get(MPI_COMM_WORLD, MPI_TAG_UB, &tagub, &flag);
306 >  if (flag) {
307 >    MAXTAG = *tagub;
308 >  } else {
309 >    MAXTAG = 32767;
310 >  }  
311 >
312 >  int haveError;
313 >
314 >  MPI_Status istatus;
315    int *AtomToProcMap = mpiSim->getAtomToProcMap();
316  
317    // write out header and node 0's coordinates
318 <  
318 >
319    if( worldRank == 0 ){
320 <    finalOut << mpiSim->getTotAtoms() << "\n";
320 >
321 >    // Node 0 needs a list of the magic potatoes for each processor;
322 >
323 >    nProc = mpiSim->getNumberProcessors();
324 >    potatoes = new int[nProc];
325 >
326 >    //write out the comment lines
327 >    for (i = 0; i < nProc; i++)
328 >      potatoes[i] = 0;
329      
330 <    finalOut << entry_plug->box_x << "\t"
331 <            << entry_plug->box_y << "\t"
332 <            << entry_plug->box_z << "\n";
333 <    
330 >      for(k = 0; k < outFile.size(); k++){
331 >        *outFile[k] << mpiSim->getTotAtoms() << "\n";
332 >
333 >        *outFile[k] << currentTime << ";\t"
334 >                         << entry_plug->Hmat[0][0] << "\t"
335 >                         << entry_plug->Hmat[1][0] << "\t"
336 >                         << entry_plug->Hmat[2][0] << ";\t"
337 >
338 >                         << entry_plug->Hmat[0][1] << "\t"
339 >                         << entry_plug->Hmat[1][1] << "\t"
340 >                         << entry_plug->Hmat[2][1] << ";\t"
341 >
342 >                         << entry_plug->Hmat[0][2] << "\t"
343 >                         << entry_plug->Hmat[1][2] << "\t"
344 >                         << entry_plug->Hmat[2][2] << ";";
345 >  
346 >        *outFile[k] << entry_plug->the_integrator->getAdditionalParameters() << endl;
347 >    }
348 >
349 >    currentIndex = 0;
350 >
351      for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) {
359 –      // Get the Node number which has this molecule:
352        
353 <      which_node = AtomToProcMap[i];    
353 >      // Get the Node number which has this atom;
354        
355 <      if (which_node == mpiSim->getMyNode()) {
355 >      which_node = AtomToProcMap[i];
356 >      
357 >      if (which_node != 0) {
358 >
359 >        if (potatoes[which_node] + 3 >= MAXTAG) {
360 >          // The potato was going to exceed the maximum value,
361 >          // so wrap this processor potato back to 0:        
362 >
363 >          potatoes[which_node] = 0;          
364 >          MPI_Send(0, 1, MPI_INT, which_node, 0, MPI_COMM_WORLD);
365 >          
366 >        }
367 >
368 >        myPotato = potatoes[which_node];        
369          
370 <        sprintf( tempBuffer,
371 <                 "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
372 <                 atoms[i]->getType(),
373 <                 atoms[i]->getX(),
369 <                 atoms[i]->getY(),
370 <                 atoms[i]->getZ(),
371 <                 atoms[i]->get_vx(),
372 <                 atoms[i]->get_vy(),
373 <                 atoms[i]->get_vz());
374 <        strcpy( writeLine, tempBuffer );
370 >        MPI_Recv(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, which_node,
371 >                 myPotato, MPI_COMM_WORLD, &istatus);
372 >        
373 >        atomTypeString = MPIatomTypeString;
374          
375 <        if( atoms[i]->isDirectional() ){
375 >        myPotato++;
376 >
377 >        MPI_Recv(&isDirectional, 1, MPI_INT, which_node,
378 >                 myPotato, MPI_COMM_WORLD, &istatus);
379 >              
380 >        myPotato++;
381 >
382 >        if (isDirectional) {          
383 >          MPI_Recv(atomData13, 13, MPI_DOUBLE, which_node,
384 >                   myPotato, MPI_COMM_WORLD, &istatus);
385 >        } else {
386 >          MPI_Recv(atomData6, 6, MPI_DOUBLE, which_node,
387 >                   myPotato, MPI_COMM_WORLD, &istatus);          
388 >        }
389 >        
390 >        myPotato++;
391 >        potatoes[which_node] = myPotato;
392 >
393 >      } else {
394 >        
395 >        haveError = 0;
396 >        which_atom = i;
397 >        
398 >        //local_index = -1;
399 >
400 >        //for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) {
401 >        //  if (atoms[j]->getGlobalIndex() == which_atom) local_index = j;
402 >        //}
403 >        
404 >        //if (local_index != -1) {
405            
406 <          dAtom = (DirectionalAtom *)atoms[i];
407 <          dAtom->getQ( q );
406 >          local_index = indexArray[currentIndex].first;        
407 >          
408 >          if (which_atom == indexArray[currentIndex].second) {
409 >            
410 >            atomTypeString = atoms[local_index]->getType();
411 >            
412 >          atoms[local_index]->getPos(pos);
413 >          atoms[local_index]->getVel(vel);          
414            
415 <          sprintf( tempBuffer,
416 <                   "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
417 <                   q[0],
418 <                   q[1],
419 <                   q[2],
420 <                   q[3],
421 <                   dAtom->getJx(),
422 <                   dAtom->getJy(),
423 <                   dAtom->getJz());
424 <          strcat( writeLine, tempBuffer );
425 <        }
426 <        else
427 <          strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );      
415 >          atomData6[0] = pos[0];
416 >          atomData6[1] = pos[1];
417 >          atomData6[2] = pos[2];
418 >
419 >          atomData6[3] = vel[0];
420 >          atomData6[4] = vel[1];
421 >          atomData6[5] = vel[2];
422 >          
423 >          isDirectional = 0;
424 >
425 >          if( atoms[local_index]->isDirectional() ){
426 >
427 >            isDirectional = 1;
428 >            
429 >            dAtom = (DirectionalAtom *)atoms[local_index];
430 >            dAtom->getQ( q );
431 >
432 >            for (int j = 0; j < 6 ; j++)
433 >              atomData13[j] = atomData6[j];            
434 >            
435 >            atomData13[6] = q[0];
436 >            atomData13[7] = q[1];
437 >            atomData13[8] = q[2];
438 >            atomData13[9] = q[3];
439 >            
440 >            atomData13[10] = dAtom->getJx();
441 >            atomData13[11] = dAtom->getJy();
442 >            atomData13[12] = dAtom->getJz();
443 >          }
444 >          
445 >        } else {
446 >          sprintf(painCave.errMsg,
447 >                  "Atom %d not found on processor %d, currentIndex = %d, local_index = %d\n",
448 >                  which_atom, worldRank, currentIndex, local_index );
449 >          haveError= 1;
450 >          simError();
451 >        }
452          
453 +        if(haveError) DieDieDie();
454 +        
455 +        currentIndex++;
456 +      }
457 +      // If we've survived to here, format the line:
458 +      
459 +      if (!isDirectional) {
460 +        
461 +        sprintf( writeLine,
462 +                 "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
463 +                 atomTypeString,
464 +                 atomData6[0],
465 +                 atomData6[1],
466 +                 atomData6[2],
467 +                 atomData6[3],
468 +                 atomData6[4],
469 +                 atomData6[5]);
470 +        
471 +        strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
472 +        
473        } else {
474 +        
475 +        sprintf( writeLine,
476 +                 "%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",
477 +                 atomTypeString,
478 +                 atomData13[0],
479 +                 atomData13[1],
480 +                 atomData13[2],
481 +                 atomData13[3],
482 +                 atomData13[4],
483 +                 atomData13[5],
484 +                 atomData13[6],
485 +                 atomData13[7],
486 +                 atomData13[8],
487 +                 atomData13[9],
488 +                 atomData13[10],
489 +                 atomData13[11],
490 +                 atomData13[12]);
491          
397 –        MPI::COMM_WORLD.Send(&i, 1, MPI_INT, which_node, TAKE_THIS_TAG);
398 –        MPI::COMM_WORLD.Recv(writeLine, BUFFERSIZE, MPI_CHAR, which_node,
399 –                                TAKE_THIS_TAG, istatus);
492        }
493        
494 <      finalOut << writeLine;
494 >      for(k = 0; k < outFile.size(); k++)
495 >        *outFile[k] << writeLine;
496      }
497      
498 <    // kill everyone off:
499 <    game_over = -1;
407 <    for (j = 0; j < mpiSim->getNumberProcessors(); j++) {
408 <      MPI::COMM_WORLD.Send(&game_over, 1, MPI_INT, j, TAKE_THIS_TAG);
409 <    }
410 <
411 <  } else {
498 >    for(k = 0; k < outFile.size(); k++)
499 >      outFile[k]->flush();
500      
501 <    done = 0;
502 <    while (!done) {
503 <      MPI::COMM_WORLD.Recv(&which_atom, 1, MPI_INT, 0,
504 <                           TAKE_THIS_TAG, istatus);
501 >    sprintf( checkPointMsg,
502 >             "Sucessfully took a dump.\n");
503 >    
504 >    MPIcheckPoint();        
505 >    
506 >    delete[] potatoes;
507 >    
508 >  } else {
509  
510 <      if (which_atom == -1) {
419 <        done=1;
420 <        continue;
421 <      } else {
510 >    // worldRank != 0, so I'm a remote node.  
511  
512 <        local_index=-1;        
513 <        for (j=0; j < mpiSim->getMyNlocal(); j++) {
514 <          if (atoms[j]->getGlobalIndex() == which_atom) local_index = j;
512 >    // Set my magic potato to 0:
513 >
514 >    myPotato = 0;
515 >    currentIndex = 0;
516 >    
517 >    for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) {
518 >      
519 >      // Am I the node which has this atom?
520 >      
521 >      if (AtomToProcMap[i] == worldRank) {
522 >
523 >        if (myPotato + 3 >= MAXTAG) {
524 >          
525 >          // The potato was going to exceed the maximum value,
526 >          // so wrap this processor potato back to 0 (and block until
527 >          // node 0 says we can go:
528 >          
529 >          MPI_Recv(&myPotato, 1, MPI_INT, 0, 0, MPI_COMM_WORLD, &istatus);
530 >          
531          }
532 <        if (local_index != -1) {
532 >        which_atom = i;
533  
534 <          //format the line
535 <          sprintf( tempBuffer,
536 <                   "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
537 <                   atoms[local_index]->getType(),
538 <                   atoms[local_index]->getX(),
539 <                   atoms[local_index]->getY(),
540 <                   atoms[local_index]->getZ(),
541 <                   atoms[local_index]->get_vx(),
542 <                   atoms[local_index]->get_vy(),
543 <                   atoms[local_index]->get_vz()); // check here.
544 <          strcpy( writeLine, tempBuffer );
534 >        //local_index = -1;
535 >
536 >        //for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) {
537 >        // if (atoms[j]->getGlobalIndex() == which_atom) local_index = j;
538 >        //}
539 >        
540 >        //if (local_index != -1) {
541 >
542 >        local_index = indexArray[currentIndex].first;        
543 >                
544 >        if (which_atom == indexArray[currentIndex].second) {
545 >        
546 >          atomTypeString = atoms[local_index]->getType();
547            
548 +          atoms[local_index]->getPos(pos);
549 +          atoms[local_index]->getVel(vel);
550 +          
551 +          atomData6[0] = pos[0];
552 +          atomData6[1] = pos[1];
553 +          atomData6[2] = pos[2];
554 +
555 +          atomData6[3] = vel[0];
556 +          atomData6[4] = vel[1];
557 +          atomData6[5] = vel[2];
558 +          
559 +          isDirectional = 0;
560 +
561            if( atoms[local_index]->isDirectional() ){
562 +
563 +            isDirectional = 1;
564              
565              dAtom = (DirectionalAtom *)atoms[local_index];
566              dAtom->getQ( q );
567 <            
568 <            sprintf( tempBuffer,
569 <                     "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
570 <                     q[0],
571 <                     q[1],
572 <                     q[2],
573 <                     q[3],
574 <                     dAtom->getJx(),
575 <                     dAtom->getJy(),
576 <                     dAtom->getJz());
577 <            strcat( writeLine, tempBuffer );
567 >            
568 >            for (int j = 0; j < 6 ; j++)
569 >              atomData13[j] = atomData6[j];
570 >            
571 >            atomData13[6] = q[0];
572 >            atomData13[7] = q[1];
573 >            atomData13[8] = q[2];
574 >            atomData13[9] = q[3];
575 >  
576 >            atomData13[10] = dAtom->getJx();
577 >            atomData13[11] = dAtom->getJy();
578 >            atomData13[12] = dAtom->getJz();
579            }
580 <          else
581 <            strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
580 >
581 >        } else {
582 >          sprintf(painCave.errMsg,
583 >                  "Atom %d not found on processor %d, currentIndex = %d, local_index = %d\n",
584 >                  which_atom, worldRank, currentIndex, local_index );
585 >          haveError= 1;
586 >          simError();
587 >        }
588 >        
589 >        strncpy(MPIatomTypeString, atomTypeString, MINIBUFFERSIZE);
590 >
591 >        // null terminate the string before sending (just in case):
592 >        MPIatomTypeString[MINIBUFFERSIZE-1] = '\0';
593 >
594 >        MPI_Send(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, 0,
595 >                             myPotato, MPI_COMM_WORLD);
596 >        
597 >        myPotato++;
598 >
599 >        MPI_Send(&isDirectional, 1, MPI_INT, 0,
600 >                             myPotato, MPI_COMM_WORLD);
601 >        
602 >        myPotato++;
603 >        
604 >        if (isDirectional) {
605 >
606 >          MPI_Send(atomData13, 13, MPI_DOUBLE, 0,
607 >                   myPotato, MPI_COMM_WORLD);
608            
460 –          MPI::COMM_WORLD.Send(writeLine, BUFFERSIZE, MPI_CHAR, 0,
461 –                               TAKE_THIS_TAG);
609          } else {
610 <          strcpy( writeLine, "ATOM NOT FOUND ON THIS PROCESSOR");
611 <          MPI::COMM_WORLD.Send(writeLine, BUFFERSIZE, MPI_CHAR, 0,
612 <                               TAKE_THIS_TAG);
610 >
611 >          MPI_Send(atomData6, 6, MPI_DOUBLE, 0,
612 >                   myPotato, MPI_COMM_WORLD);
613          }
614 +
615 +        myPotato++;  
616 +        currentIndex++;    
617        }
618      }
469 –  }
470 –  finalOut.flush();
471 –  sprintf( checkPointMsg,
472 –           "Sucessfully took a dump.\n");
473 –  MPIcheckPoint();
619  
620 <  if( worldRank == 0 ) finalOut.close();    
620 >    sprintf( checkPointMsg,
621 >             "Sucessfully took a dump.\n");
622 >    MPIcheckPoint();        
623 >    
624 >  }
625 >  
626   #endif // is_mpi
627   }
628 +
629 + #ifdef IS_MPI
630 +
631 + // a couple of functions to let us escape the write loop
632 +
633 + void dWrite::DieDieDie( void ){
634 +
635 +  MPI_Finalize();
636 +  exit (0);
637 + }
638 +
639 + #endif //is_mpi

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