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root/group/trunk/OOPSE/libmdtools/DumpWriter.cpp
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Comparing trunk/OOPSE/libmdtools/DumpWriter.cpp (file contents):
Revision 416 by gezelter, Wed Mar 26 23:14:02 2003 UTC vs.
Revision 1097 by gezelter, Mon Apr 12 20:32:20 2004 UTC

# Line 1 | Line 1
1 < #include <cstring>
1 > #define _LARGEFILE_SOURCE64
2 > #define _FILE_OFFSET_BITS 64
3 >
4 > #include <string.h>
5   #include <iostream>
6   #include <fstream>
7 + #include <algorithm>
8 + #include <utility>
9  
10   #ifdef IS_MPI
11   #include <mpi.h>
7 – #include <mpi++.h>
12   #include "mpiSimulation.hpp"
13 < #define TAKE_THIS_TAG 0
13 >
14 > namespace dWrite{
15 >  void DieDieDie( void );
16 > }
17 >
18 > using namespace dWrite;
19   #endif //is_mpi
20  
21   #include "ReadWrite.hpp"
# Line 19 | Line 28 | DumpWriter::DumpWriter( SimInfo* the_entry_plug ){
28   #ifdef IS_MPI
29    if(worldRank == 0 ){
30   #endif // is_mpi
31 <    
32 <
33 <    
34 <    strcpy( outName, entry_plug->sampleName );
35 <    
27 <    outFile.open(outName, ios::out | ios::trunc );
28 <    
29 <    if( !outFile ){
30 <      
31 >
32 >    dumpFile.open(entry_plug->sampleName, ios::out | ios::trunc );
33 >
34 >    if( !dumpFile ){
35 >
36        sprintf( painCave.errMsg,
37                 "Could not open \"%s\" for dump output.\n",
38 <               outName);
38 >               entry_plug->sampleName);
39        painCave.isFatal = 1;
40        simError();
41      }
37 –  
38 –    //outFile.setf( ios::scientific );
42  
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 52 | 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, game_over, which_atom;
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
76 <    
77 <  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 <      
101 > #endif
102  
103 <    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 );
103 > void DumpWriter::writeDump(double currentTime){
104  
105 <    if( atoms[i]->isDirectional() ){
106 <        
107 <      dAtom = (DirectionalAtom *)atoms[i];
108 <      dAtom->getQ( q );
109 <        
110 <      sprintf( tempBuffer,
111 <               "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
112 <               q[0],
113 <               q[1],
114 <               q[2],
115 <               q[3],
116 <               dAtom->getJx(),
117 <               dAtom->getJy(),
111 <               dAtom->getJz());
112 <      strcat( writeLine, tempBuffer );
105 >  ofstream finalOut;
106 >  vector<ofstream*> fileStreams;
107 >
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
115 <      strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
116 <      
117 <    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 <  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 <    
136 <    for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) {
137 <      // Get the Node number which has this molecule:
138 <      
139 <      which_node = AtomToProcMap[i];    
140 <      
141 <      if (which_node == mpiSim->getMyNode()) {
142 <        
143 <        sprintf( tempBuffer,
144 <                 "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
145 <                 atoms[i]->getType(),
146 <                 atoms[i]->getX(),
147 <                 atoms[i]->getY(),
148 <                 atoms[i]->getZ(),
149 <                 atoms[i]->get_vx(),
150 <                 atoms[i]->get_vy(),
151 <                 atoms[i]->get_vz());
152 <        strcpy( writeLine, tempBuffer );
153 <        
154 <        if( atoms[i]->isDirectional() ){
155 <          
156 <          dAtom = (DirectionalAtom *)atoms[i];
157 <          dAtom->getQ( q );
158 <          
159 <          sprintf( tempBuffer,
160 <                   "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
161 <                   q[0],
162 <                   q[1],
163 <                   q[2],
164 <                   q[3],
165 <                   dAtom->getJx(),
166 <                   dAtom->getJy(),
167 <                   dAtom->getJz());
168 <          strcat( writeLine, tempBuffer );
169 <        }
170 <        else
171 <          strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );      
172 <        
173 <      } else {
174 <        
175 <        MPI::COMM_WORLD.Send(&i, 1, MPI_INT, which_node, TAKE_THIS_TAG);
176 <        MPI::COMM_WORLD.Recv(writeLine, BUFFERSIZE, MPI_CHAR, which_node,
177 <                                TAKE_THIS_TAG, istatus);
178 <      }
179 <      
180 <      outFile << writeLine;
181 <    }
182 <    
183 <    // kill everyone off:
184 <    game_over = -1;
185 <    for (j = 0; j < mpiSim->getNumberProcessors(); j++) {      
186 <      MPI::COMM_WORLD.Send(&game_over, 1, MPI_INT, j, TAKE_THIS_TAG);
187 <    }
188 <
189 <  } else {
190 <    
191 <    done = 0;
192 <    while (!done) {
193 <      MPI::COMM_WORLD.Recv(&which_atom, 1, MPI_INT, 0,
194 <                              TAKE_THIS_TAG, istatus);
195 <
196 <      if (which_atom == -1) {
197 <        done=1;
198 <        continue;
199 <      } else {
126 >  writeFrame(fileStreams, currentTime);
127  
128 <        //format the line
129 <        sprintf( tempBuffer,
130 <                 "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
131 <                 atoms[which_atom]->getType(),
205 <                 atoms[which_atom]->getX(),
206 <                 atoms[which_atom]->getY(),
207 <                 atoms[which_atom]->getZ(),
208 <                 atoms[which_atom]->get_vx(),
209 <                 atoms[which_atom]->get_vy(),
210 <                 atoms[which_atom]->get_vz()); // check here.
211 <        strcpy( writeLine, tempBuffer );
212 <          
213 <        if( atoms[which_atom]->isDirectional() ){
214 <            
215 <          dAtom = (DirectionalAtom *)atoms[which_atom];
216 <          dAtom->getQ( q );
217 <            
218 <          sprintf( tempBuffer,
219 <                   "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
220 <                   q[0],
221 <                   q[1],
222 <                   q[2],
223 <                   q[3],
224 <                   dAtom->getJx(),
225 <                   dAtom->getJy(),
226 <                   dAtom->getJz());
227 <          strcat( writeLine, tempBuffer );
228 <        }
229 <        else
230 <          strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
231 <        
232 <        MPI::COMM_WORLD.Send(writeLine, BUFFERSIZE, MPI_CHAR, 0,
233 <                             TAKE_THIS_TAG);
234 <      }
235 <    }
236 <  }  
237 <  outFile.flush();
238 <  sprintf( checkPointMsg,
239 <           "Sucessfully took a dump.\n");
240 <  MPIcheckPoint();
241 < #endif // is_mpi
128 > #ifdef IS_MPI
129 >  finalOut.close();
130 > #endif
131 >        
132   }
133  
134 < void DumpWriter::writeFinal(){
134 > void DumpWriter::writeFinal(double currentTime){
135  
246 –  char finalName[500];
136    ofstream finalOut;
137 +  vector<ofstream*> fileStreams;
138  
249 –  const int BUFFERSIZE = 2000;
250 –  char tempBuffer[BUFFERSIZE];
251 –  char writeLine[BUFFERSIZE];  
252 –
253 –  double q[4];
254 –  DirectionalAtom* dAtom;
255 –  int nAtoms = entry_plug->n_atoms;
256 –  Atom** atoms = entry_plug->atoms;
257 –  int i, j, which_node, done, game_over, which_atom;
258 –  
259 –  
139   #ifdef IS_MPI
140    if(worldRank == 0 ){
141   #endif // is_mpi
142 <    
143 <    strcpy( finalName, entry_plug->finalName );
144 <    
266 <    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 <    
275 <    // finalOut.setf( ios::scientific );
276 <    
152 >
153   #ifdef IS_MPI
154    }
155 + #endif // is_mpi
156    
157 <  sprintf(checkPointMsg,"Opened file for final configuration\n");
158 <  MPIcheckPoint();  
157 >  fileStreams.push_back(&finalOut);  
158 >  writeFrame(fileStreams, currentTime);
159 >
160 > #ifdef IS_MPI
161 >  finalOut.close();
162 > #endif
163    
164 < #endif //is_mpi
164 > }
165  
166 + void DumpWriter::writeFrame( vector<ofstream*>& outFile, double currentTime ){
167 +
168 +  const int BUFFERSIZE = 2000;
169 +  const int MINIBUFFERSIZE = 100;
170 +
171 +  char tempBuffer[BUFFERSIZE];  
172 +  char writeLine[BUFFERSIZE];
173 +
174 +  int i, k;
175 +
176 + #ifdef IS_MPI
177    
178 +  /*********************************************************************
179 +   * Documentation?  You want DOCUMENTATION?
180 +   *
181 +   * Why all the potatoes below?  
182 +   *
183 +   * To make a long story short, the original version of DumpWriter
184 +   * worked in the most inefficient way possible.  Node 0 would
185 +   * poke each of the node for an individual atom's formatted data
186 +   * as node 0 worked its way down the global index. This was particularly
187 +   * inefficient since the method blocked all processors at every atom
188 +   * (and did it twice!).
189 +   *
190 +   * An intermediate version of DumpWriter could be described from Node
191 +   * zero's perspective as follows:
192 +   *
193 +   *  1) Have 100 of your friends stand in a circle.
194 +   *  2) When you say go, have all of them start tossing potatoes at
195 +   *     you (one at a time).
196 +   *  3) Catch the potatoes.
197 +   *
198 +   * It was an improvement, but MPI has buffers and caches that could
199 +   * best be described in this analogy as "potato nets", so there's no
200 +   * need to block the processors atom-by-atom.
201 +   *
202 +   * This new and improved DumpWriter works in an even more efficient
203 +   * way:
204 +   *
205 +   *  1) Have 100 of your friend stand in a circle.
206 +   *  2) When you say go, have them start tossing 5-pound bags of
207 +   *     potatoes at you.
208 +   *  3) Once you've caught a friend's bag of potatoes,
209 +   *     toss them a spud to let them know they can toss another bag.
210 +   *
211 +   * How's THAT for documentation?
212 +   *
213 +   *********************************************************************/
214 +
215 +  int *potatoes;
216 +  int myPotato;
217 +
218 +  int nProc;
219 +  int j, which_node, done, which_atom, local_index, currentIndex;
220 +  double atomData6[6];
221 +  double atomData13[13];
222 +  int isDirectional;
223 +  char* atomTypeString;
224 +  char MPIatomTypeString[MINIBUFFERSIZE];
225 +
226 + #else //is_mpi
227 +  int nAtoms = entry_plug->n_atoms;
228 + #endif //is_mpi
229 +
230 +  double q[4], ji[3];
231 +  DirectionalAtom* dAtom;
232 +  Atom** atoms = entry_plug->atoms;
233 +  double pos[3], vel[3];
234 +
235   #ifndef IS_MPI
287 –    
288 –  finalOut << nAtoms << "\n";
289 –    
290 –  finalOut << entry_plug->box_x << "\t"
291 –           << entry_plug->box_y << "\t"
292 –           << entry_plug->box_z << "\n";
236    
237 +  for(k = 0; k < outFile.size(); k++){
238 +    *outFile[k] << nAtoms << "\n";
239 +
240 +    *outFile[k] << currentTime << ";\t"
241 +               << entry_plug->Hmat[0][0] << "\t"
242 +                     << entry_plug->Hmat[1][0] << "\t"
243 +                     << entry_plug->Hmat[2][0] << ";\t"
244 +              
245 +               << entry_plug->Hmat[0][1] << "\t"
246 +                     << entry_plug->Hmat[1][1] << "\t"
247 +                     << entry_plug->Hmat[2][1] << ";\t"
248 +
249 +                     << entry_plug->Hmat[0][2] << "\t"
250 +                     << entry_plug->Hmat[1][2] << "\t"
251 +                     << entry_plug->Hmat[2][2] << ";";
252 +
253 +    //write out additional parameters, such as chi and eta
254 +    *outFile[k] << entry_plug->the_integrator->getAdditionalParameters() << endl;
255 +  }
256 +  
257    for( i=0; i<nAtoms; i++ ){
258 <      
258 >
259 >    atoms[i]->getPos(pos);
260 >    atoms[i]->getVel(vel);
261 >
262      sprintf( tempBuffer,
263               "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
264               atoms[i]->getType(),
265 <             atoms[i]->getX(),
266 <             atoms[i]->getY(),
267 <             atoms[i]->getZ(),
268 <             atoms[i]->get_vx(),
269 <             atoms[i]->get_vy(),
270 <             atoms[i]->get_vz());
265 >             pos[0],
266 >             pos[1],
267 >             pos[2],
268 >             vel[0],
269 >             vel[1],
270 >             vel[2]);
271      strcpy( writeLine, tempBuffer );
272  
273      if( atoms[i]->isDirectional() ){
274 <        
274 >
275        dAtom = (DirectionalAtom *)atoms[i];
276        dAtom->getQ( q );
277 <        
277 >      dAtom->getJ( ji );
278 >
279        sprintf( tempBuffer,
280                 "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
281                 q[0],
282                 q[1],
283                 q[2],
284                 q[3],
285 <               dAtom->getJx(),
286 <               dAtom->getJy(),
287 <               dAtom->getJz());
285 >               ji[0],
286 >               ji[1],
287 >               ji[2]);
288        strcat( writeLine, tempBuffer );
289      }
290      else
291        strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
292 <      
293 <    finalOut << writeLine;
292 >
293 >    for(k = 0; k < outFile.size(); k++)
294 >      *outFile[k] << writeLine;
295    }
328 –  finalOut.flush();
329 –  finalOut.close();
296  
297   #else // is_mpi
298 +
299 +  /* code to find maximum tag value */
300    
301 <  MPI::Status istatus;
301 >  int *tagub, flag, MAXTAG;
302 >  MPI_Attr_get(MPI_COMM_WORLD, MPI_TAG_UB, &tagub, &flag);
303 >  if (flag) {
304 >    MAXTAG = *tagub;
305 >  } else {
306 >    MAXTAG = 32767;
307 >  }  
308 >
309 >  int haveError;
310 >
311 >  MPI_Status istatus;
312    int *AtomToProcMap = mpiSim->getAtomToProcMap();
313  
314    // write out header and node 0's coordinates
315 <  
315 >
316    if( worldRank == 0 ){
317 <    finalOut << mpiSim->getTotAtoms() << "\n";
317 >
318 >    // Node 0 needs a list of the magic potatoes for each processor;
319 >
320 >    nProc = mpiSim->getNumberProcessors();
321 >    potatoes = new int[nProc];
322 >
323 >    //write out the comment lines
324 >    for (i = 0; i < nProc; i++)
325 >      potatoes[i] = 0;
326      
327 <    finalOut << entry_plug->box_x << "\t"
328 <            << entry_plug->box_y << "\t"
329 <            << entry_plug->box_z << "\n";
330 <    
327 >      for(k = 0; k < outFile.size(); k++){
328 >        *outFile[k] << mpiSim->getTotAtoms() << "\n";
329 >
330 >        *outFile[k] << currentTime << ";\t"
331 >                         << entry_plug->Hmat[0][0] << "\t"
332 >                         << entry_plug->Hmat[1][0] << "\t"
333 >                         << entry_plug->Hmat[2][0] << ";\t"
334 >
335 >                         << entry_plug->Hmat[0][1] << "\t"
336 >                         << entry_plug->Hmat[1][1] << "\t"
337 >                         << entry_plug->Hmat[2][1] << ";\t"
338 >
339 >                         << entry_plug->Hmat[0][2] << "\t"
340 >                         << entry_plug->Hmat[1][2] << "\t"
341 >                         << entry_plug->Hmat[2][2] << ";";
342 >  
343 >        *outFile[k] << entry_plug->the_integrator->getAdditionalParameters() << endl;
344 >    }
345 >
346 >    currentIndex = 0;
347 >
348      for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) {
346 –      // Get the Node number which has this molecule:
349        
350 <      which_node = AtomToProcMap[i];    
350 >      // Get the Node number which has this atom;
351        
352 <      if (which_node == mpiSim->getMyNode()) {
352 >      which_node = AtomToProcMap[i];
353 >      
354 >      if (which_node != 0) {
355 >
356 >        if (potatoes[which_node] + 3 >= MAXTAG) {
357 >          // The potato was going to exceed the maximum value,
358 >          // so wrap this processor potato back to 0:        
359 >
360 >          potatoes[which_node] = 0;          
361 >          MPI_Send(0, 1, MPI_INT, which_node, 0, MPI_COMM_WORLD);
362 >          
363 >        }
364 >
365 >        myPotato = potatoes[which_node];        
366          
367 <        sprintf( tempBuffer,
368 <                 "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
369 <                 atoms[i]->getType(),
370 <                 atoms[i]->getX(),
356 <                 atoms[i]->getY(),
357 <                 atoms[i]->getZ(),
358 <                 atoms[i]->get_vx(),
359 <                 atoms[i]->get_vy(),
360 <                 atoms[i]->get_vz());
361 <        strcpy( writeLine, tempBuffer );
367 >        MPI_Recv(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, which_node,
368 >                 myPotato, MPI_COMM_WORLD, &istatus);
369 >        
370 >        atomTypeString = MPIatomTypeString;
371          
372 <        if( atoms[i]->isDirectional() ){
373 <          
374 <          dAtom = (DirectionalAtom *)atoms[i];
375 <          dAtom->getQ( q );
376 <          
377 <          sprintf( tempBuffer,
378 <                   "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
379 <                   q[0],
380 <                   q[1],
381 <                   q[2],
382 <                   q[3],
383 <                   dAtom->getJx(),
384 <                   dAtom->getJy(),
376 <                   dAtom->getJz());
377 <          strcat( writeLine, tempBuffer );
372 >        myPotato++;
373 >
374 >        MPI_Recv(&isDirectional, 1, MPI_INT, which_node,
375 >                 myPotato, MPI_COMM_WORLD, &istatus);
376 >              
377 >        myPotato++;
378 >
379 >        if (isDirectional) {          
380 >          MPI_Recv(atomData13, 13, MPI_DOUBLE, which_node,
381 >                   myPotato, MPI_COMM_WORLD, &istatus);
382 >        } else {
383 >          MPI_Recv(atomData6, 6, MPI_DOUBLE, which_node,
384 >                   myPotato, MPI_COMM_WORLD, &istatus);          
385          }
379 –        else
380 –          strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );      
386          
387 +        myPotato++;
388 +        potatoes[which_node] = myPotato;
389 +
390        } else {
391          
392 <        MPI::COMM_WORLD.Send(&i, 1, MPI_INT, which_node, TAKE_THIS_TAG);
393 <        MPI::COMM_WORLD.Recv(writeLine, BUFFERSIZE, MPI_CHAR, which_node,
394 <                                TAKE_THIS_TAG, istatus);
392 >        haveError = 0;
393 >        which_atom = i;
394 >        
395 >          local_index = indexArray[currentIndex].first;        
396 >          
397 >          if (which_atom == indexArray[currentIndex].second) {
398 >            
399 >            atomTypeString = atoms[local_index]->getType();
400 >            
401 >          atoms[local_index]->getPos(pos);
402 >          atoms[local_index]->getVel(vel);          
403 >          
404 >          atomData6[0] = pos[0];
405 >          atomData6[1] = pos[1];
406 >          atomData6[2] = pos[2];
407 >
408 >          atomData6[3] = vel[0];
409 >          atomData6[4] = vel[1];
410 >          atomData6[5] = vel[2];
411 >          
412 >          isDirectional = 0;
413 >
414 >          if( atoms[local_index]->isDirectional() ){
415 >
416 >            isDirectional = 1;
417 >            
418 >            dAtom = (DirectionalAtom *)atoms[local_index];
419 >            dAtom->getQ( q );
420 >            dAtom->getJ( ji );
421 >
422 >            for (int j = 0; j < 6 ; j++)
423 >              atomData13[j] = atomData6[j];            
424 >            
425 >            atomData13[6] = q[0];
426 >            atomData13[7] = q[1];
427 >            atomData13[8] = q[2];
428 >            atomData13[9] = q[3];
429 >            
430 >            atomData13[10] = ji[0];
431 >            atomData13[11] = ji[1];
432 >            atomData13[12] = ji[2];
433 >          }
434 >          
435 >        } else {
436 >          sprintf(painCave.errMsg,
437 >                  "Atom %d not found on processor %d, currentIndex = %d, local_index = %d\n",
438 >                  which_atom, worldRank, currentIndex, local_index );
439 >          haveError= 1;
440 >          simError();
441 >        }
442 >        
443 >        if(haveError) DieDieDie();
444 >        
445 >        currentIndex++;
446        }
447 +      // If we've survived to here, format the line:
448        
449 <      finalOut << writeLine;
449 >      if (!isDirectional) {
450 >        
451 >        sprintf( writeLine,
452 >                 "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
453 >                 atomTypeString,
454 >                 atomData6[0],
455 >                 atomData6[1],
456 >                 atomData6[2],
457 >                 atomData6[3],
458 >                 atomData6[4],
459 >                 atomData6[5]);
460 >        
461 >        strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
462 >        
463 >      } else {
464 >        
465 >        sprintf( writeLine,
466 >                 "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
467 >                 atomTypeString,
468 >                 atomData13[0],
469 >                 atomData13[1],
470 >                 atomData13[2],
471 >                 atomData13[3],
472 >                 atomData13[4],
473 >                 atomData13[5],
474 >                 atomData13[6],
475 >                 atomData13[7],
476 >                 atomData13[8],
477 >                 atomData13[9],
478 >                 atomData13[10],
479 >                 atomData13[11],
480 >                 atomData13[12]);
481 >        
482 >      }
483 >      
484 >      for(k = 0; k < outFile.size(); k++)
485 >        *outFile[k] << writeLine;
486      }
487      
488 <    // kill everyone off:
489 <    game_over = -1;
490 <    for (j = 0; j < mpiSim->getNumberProcessors(); j++) {
491 <      MPI::COMM_WORLD.Send(&game_over, 1, MPI_INT, j, TAKE_THIS_TAG);
492 <    }
493 <
488 >    for(k = 0; k < outFile.size(); k++)
489 >      outFile[k]->flush();
490 >    
491 >    sprintf( checkPointMsg,
492 >             "Sucessfully took a dump.\n");
493 >    
494 >    MPIcheckPoint();        
495 >    
496 >    delete[] potatoes;
497 >    
498    } else {
499 +
500 +    // worldRank != 0, so I'm a remote node.  
501 +
502 +    // Set my magic potato to 0:
503 +
504 +    myPotato = 0;
505 +    currentIndex = 0;
506      
507 <    done = 0;
508 <    while (!done) {
509 <      MPI::COMM_WORLD.Recv(&which_atom, 1, MPI_INT, 0,
510 <                           TAKE_THIS_TAG, istatus);
507 >    for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) {
508 >      
509 >      // Am I the node which has this atom?
510 >      
511 >      if (AtomToProcMap[i] == worldRank) {
512  
513 <      if (which_atom == -1) {
514 <        done=1;
515 <        continue;
516 <      } else {
513 >        if (myPotato + 3 >= MAXTAG) {
514 >          
515 >          // The potato was going to exceed the maximum value,
516 >          // so wrap this processor potato back to 0 (and block until
517 >          // node 0 says we can go:
518 >          
519 >          MPI_Recv(&myPotato, 1, MPI_INT, 0, 0, MPI_COMM_WORLD, &istatus);
520 >          
521 >        }
522 >        which_atom = i;
523  
524 <        //format the line
525 <        sprintf( tempBuffer,
526 <                 "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
527 <                 atoms[which_atom]->getType(),
528 <                 atoms[which_atom]->getX(),
415 <                 atoms[which_atom]->getY(),
416 <                 atoms[which_atom]->getZ(),
417 <                 atoms[which_atom]->get_vx(),
418 <                 atoms[which_atom]->get_vy(),
419 <                 atoms[which_atom]->get_vz()); // check here.
420 <        strcpy( writeLine, tempBuffer );
524 >        local_index = indexArray[currentIndex].first;        
525 >                
526 >        if (which_atom == indexArray[currentIndex].second) {
527 >        
528 >          atomTypeString = atoms[local_index]->getType();
529            
530 <        if( atoms[which_atom]->isDirectional() ){
531 <            
532 <          dAtom = (DirectionalAtom *)atoms[which_atom];
533 <          dAtom->getQ( q );
534 <            
535 <          sprintf( tempBuffer,
536 <                   "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
537 <                   q[0],
538 <                   q[1],
539 <                   q[2],
540 <                   q[3],
541 <                   dAtom->getJx(),
542 <                   dAtom->getJy(),
543 <                   dAtom->getJz());
544 <          strcat( writeLine, tempBuffer );
530 >          atoms[local_index]->getPos(pos);
531 >          atoms[local_index]->getVel(vel);
532 >          
533 >          atomData6[0] = pos[0];
534 >          atomData6[1] = pos[1];
535 >          atomData6[2] = pos[2];
536 >
537 >          atomData6[3] = vel[0];
538 >          atomData6[4] = vel[1];
539 >          atomData6[5] = vel[2];
540 >          
541 >          isDirectional = 0;
542 >
543 >          if( atoms[local_index]->isDirectional() ){
544 >
545 >            isDirectional = 1;
546 >            
547 >            dAtom = (DirectionalAtom *)atoms[local_index];
548 >            dAtom->getQ( q );
549 >            dAtom->getJ( ji );
550 >            
551 >            for (int j = 0; j < 6 ; j++)
552 >              atomData13[j] = atomData6[j];
553 >            
554 >            atomData13[6] = q[0];
555 >            atomData13[7] = q[1];
556 >            atomData13[8] = q[2];
557 >            atomData13[9] = q[3];
558 >  
559 >            atomData13[10] = ji[0];
560 >            atomData13[11] = ji[1];
561 >            atomData13[12] = ji[2];
562 >          }
563 >
564 >        } else {
565 >          sprintf(painCave.errMsg,
566 >                  "Atom %d not found on processor %d, currentIndex = %d, local_index = %d\n",
567 >                  which_atom, worldRank, currentIndex, local_index );
568 >          haveError= 1;
569 >          simError();
570          }
571 <        else
572 <          strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
571 >        
572 >        strncpy(MPIatomTypeString, atomTypeString, MINIBUFFERSIZE);
573 >
574 >        // null terminate the string before sending (just in case):
575 >        MPIatomTypeString[MINIBUFFERSIZE-1] = '\0';
576 >
577 >        MPI_Send(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, 0,
578 >                             myPotato, MPI_COMM_WORLD);
579          
580 <        MPI::COMM_WORLD.Send(writeLine, BUFFERSIZE, MPI_CHAR, 0,
581 <                             TAKE_THIS_TAG);
580 >        myPotato++;
581 >
582 >        MPI_Send(&isDirectional, 1, MPI_INT, 0,
583 >                             myPotato, MPI_COMM_WORLD);
584 >        
585 >        myPotato++;
586 >        
587 >        if (isDirectional) {
588 >
589 >          MPI_Send(atomData13, 13, MPI_DOUBLE, 0,
590 >                   myPotato, MPI_COMM_WORLD);
591 >          
592 >        } else {
593 >
594 >          MPI_Send(atomData6, 6, MPI_DOUBLE, 0,
595 >                   myPotato, MPI_COMM_WORLD);
596 >        }
597 >
598 >        myPotato++;  
599 >        currentIndex++;    
600        }
601      }
445 –  }  
446 –  finalOut.flush();
447 –  sprintf( checkPointMsg,
448 –           "Sucessfully took a dump.\n");
449 –  MPIcheckPoint();
602  
603 <  if( worldRank == 0 ) finalOut.close();    
603 >    sprintf( checkPointMsg,
604 >             "Sucessfully took a dump.\n");
605 >    MPIcheckPoint();        
606 >    
607 >  }
608 >  
609   #endif // is_mpi
610   }
611 +
612 + #ifdef IS_MPI
613 +
614 + // a couple of functions to let us escape the write loop
615 +
616 + void dWrite::DieDieDie( void ){
617 +
618 +  MPI_Finalize();
619 +  exit (0);
620 + }
621 +
622 + #endif //is_mpi

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