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root/group/trunk/OOPSE/libmdtools/DumpWriter.cpp
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Comparing trunk/OOPSE/libmdtools/DumpWriter.cpp (file contents):
Revision 436 by chuckv, Fri Mar 28 21:45:03 2003 UTC vs.
Revision 951 by mmeineke, Fri Jan 16 21:51:51 2004 UTC

# Line 1 | Line 1
1 < #include <cstring>
1 > #define _FILE_OFFSET_BITS 64
2 >
3 > #include <string.h>
4   #include <iostream>
5   #include <fstream>
6 + #include <algorithm>
7 + #include <utility>
8  
9   #ifdef IS_MPI
10   #include <mpi.h>
7 – #include <mpi++.h>
11   #include "mpiSimulation.hpp"
12 < #define TAKE_THIS_TAG_CHAR 1
13 < #define TAKE_THIS_TAG_INT 2
12 >
13 > namespace dWrite{
14 >  void DieDieDie( void );
15 > }
16 >
17 > using namespace dWrite;
18   #endif //is_mpi
19  
20   #include "ReadWrite.hpp"
# Line 20 | 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 <    
28 <    outFile.open(outName, ios::out | ios::trunc );
29 <    
30 <    if( !outFile ){
31 <      
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      }
38 –  
39 –    //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 53 | 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";
79 <    
80 <  outFile << currentTime << "\t"
81 <          << entry_plug->box_x << "\t"
82 <          << entry_plug->box_y << "\t"
83 <          << entry_plug->box_z << "\n";
84 <    
85 <  for( i=0; i<nAtoms; i++ ){
86 <      
103 > }
104  
105 <    sprintf( tempBuffer,
89 <             "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
90 <             atoms[i]->getType(),
91 <             atoms[i]->getX(),
92 <             atoms[i]->getY(),
93 <             atoms[i]->getZ(),
94 <             atoms[i]->get_vx(),
95 <             atoms[i]->get_vy(),
96 <             atoms[i]->get_vz());
97 <    strcpy( writeLine, tempBuffer );
105 > #endif
106  
107 <    if( atoms[i]->isDirectional() ){
100 <        
101 <      dAtom = (DirectionalAtom *)atoms[i];
102 <      dAtom->getQ( q );
103 <        
104 <      sprintf( tempBuffer,
105 <               "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
106 <               q[0],
107 <               q[1],
108 <               q[2],
109 <               q[3],
110 <               dAtom->getJx(),
111 <               dAtom->getJy(),
112 <               dAtom->getJz());
113 <      strcat( writeLine, tempBuffer );
114 <    }
115 <    else
116 <      strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
117 <      
118 <    outFile << writeLine;
119 <  }
120 <  outFile.flush();
107 > void DumpWriter::writeDump(double currentTime){
108  
109 < #else // is_mpi
109 >  ofstream finalOut;
110 >  vector<ofstream*> fileStreams;
111  
112 <  MPI::Status istatus;
113 <  int *AtomToProcMap = mpiSim->getAtomToProcMap();
114 <  
115 <  // write out header and node 0's coordinates
128 <  
129 <  if( worldRank == 0 ){
130 <    outFile << mpiSim->getTotAtoms() << "\n";
112 > #ifdef IS_MPI
113 >  printf("Hello from node %d\n", worldRank);
114 >  sortByGlobalIndex();
115 >  if(worldRank == 0 ){
116      
117 <    outFile << currentTime << "\t"
118 <            << entry_plug->box_x << "\t"
119 <            << entry_plug->box_y << "\t"
120 <            << entry_plug->box_z << "\n";
121 <    outFile.flush();
122 <    for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) {
123 <      // Get the Node number which has this atom;
139 <      
140 <      which_node = AtomToProcMap[i];    
141 <      
142 <      if (which_node == 0 ) {
143 <        
144 <        which_atom = i;
145 <        local_index=-1;        
146 <        for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) {
147 <          if (atoms[j]->getGlobalIndex() == which_atom) local_index = j;
148 <        }
149 <        if (local_index != -1) {
150 <          //format the line
151 <          sprintf( tempBuffer,
152 <                   "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
153 <                   atoms[local_index]->getType(),
154 <                   atoms[local_index]->getX(),
155 <                   atoms[local_index]->getY(),
156 <                   atoms[local_index]->getZ(),
157 <                   atoms[local_index]->get_vx(),
158 <                   atoms[local_index]->get_vy(),
159 <                   atoms[local_index]->get_vz()); // check here.
160 <          strcpy( writeLine, tempBuffer );
161 <          
162 <          if( atoms[local_index]->isDirectional() ){
163 <            
164 <            dAtom = (DirectionalAtom *)atoms[local_index];
165 <            dAtom->getQ( q );
166 <            
167 <            sprintf( tempBuffer,
168 <                     "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
169 <                     q[0],
170 <                     q[1],
171 <                     q[2],
172 <                     q[3],
173 <                     dAtom->getJx(),
174 <                     dAtom->getJy(),
175 <                     dAtom->getJz());
176 <            strcat( writeLine, tempBuffer );
177 <            
178 <          }
179 <          else
180 <            strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );      
181 <        }
182 <        else {
183 <          strcpy( writeLine, "ATOM NOT FOUND ON THIS PROCESSOR");
184 <        }
185 <      }
186 <      else {
187 <        
188 <        //std::cerr << "node 0: sending node " << which_node << " request for atom " << i << "\n";
189 <        MPI::COMM_WORLD.Send(&i, 1, MPI_INT, which_node, TAKE_THIS_TAG_INT);
190 <        //std::cerr << "node 0: sent!\n";
191 <        MPI::COMM_WORLD.Recv(writeLine, BUFFERSIZE, MPI_CHAR, which_node,
192 <                             TAKE_THIS_TAG_CHAR, istatus);
193 <        //std::cerr << "node 0: got this line: " << writeLine;
194 <      }
195 <      
196 <      outFile << writeLine;
197 <      outFile.flush();
117 >    finalOut.open( entry_plug->finalName, ios::out | ios::trunc );
118 >    if( !finalOut ){
119 >      sprintf( painCave.errMsg,
120 >               "Could not open \"%s\" for final dump output.\n",
121 >               entry_plug->finalName );
122 >      painCave.isFatal = 1;
123 >      simError();
124      }
125 <    
126 <    // kill everyone off:
201 <    game_over = -1;
202 <    for (j = 0; j < mpiSim->getNumberProcessors(); j++) {      
203 <      MPI::COMM_WORLD.Send(&game_over, 1, MPI_INT, j, TAKE_THIS_TAG_INT);
204 <    }
125 >  }
126 > #endif // is_mpi
127  
128 <  } else {
129 <    
130 <    done = 0;
131 <    while (!done) {
132 <      //std::cerr << "node: " << mpiSim->getMyNode() << " Waiting for receive \n";
133 <      MPI::COMM_WORLD.Recv(&which_atom, 1, MPI_INT, 0,
134 <                           TAKE_THIS_TAG_INT, istatus);
135 <      //std::cerr << "node: " << mpiSim->getMyNode() << " got request for atom " << which_atom << "\n";
136 <      if (which_atom == -1) {
215 <        done=1;
216 <        continue;
217 <      } else {
218 <        local_index=-1;        
219 <        for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) {
220 <          if (atoms[j]->getGlobalIndex() == which_atom) local_index = j;
221 <        }
222 <        if (local_index != -1) {
223 <          //format the line
224 <          sprintf( tempBuffer,
225 <                   "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
226 <                   atoms[local_index]->getType(),
227 <                   atoms[local_index]->getX(),
228 <                   atoms[local_index]->getY(),
229 <                   atoms[local_index]->getZ(),
230 <                   atoms[local_index]->get_vx(),
231 <                   atoms[local_index]->get_vy(),
232 <                   atoms[local_index]->get_vz()); // check here.
233 <          strcpy( writeLine, tempBuffer );
234 <          
235 <          if( atoms[local_index]->isDirectional() ){
236 <            
237 <            dAtom = (DirectionalAtom *)atoms[local_index];
238 <            dAtom->getQ( q );
239 <            
240 <            sprintf( tempBuffer,
241 <                     "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
242 <                     q[0],
243 <                     q[1],
244 <                     q[2],
245 <                     q[3],
246 <                     dAtom->getJx(),
247 <                     dAtom->getJy(),
248 <                     dAtom->getJz());
249 <            strcat( writeLine, tempBuffer );
250 <          }
251 <          else
252 <            strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
253 <          // std::cerr << "node: " << mpiSim->getMyNode() << " sending this line" << writeLine;
254 <          MPI::COMM_WORLD.Send(writeLine, BUFFERSIZE, MPI_CHAR, 0,
255 <                               TAKE_THIS_TAG_CHAR);
256 <        } else {
257 <          strcpy( writeLine, "ATOM NOT FOUND ON THIS PROCESSOR");
258 <          MPI::COMM_WORLD.Send(writeLine, BUFFERSIZE, MPI_CHAR, 0,
259 <                               TAKE_THIS_TAG_CHAR);
260 <        }
261 <      }
262 <    }
263 <  }  
264 <  outFile.flush();
265 <  sprintf( checkPointMsg,
266 <           "Sucessfully took a dump.\n");
267 <  MPIcheckPoint();
268 < #endif // is_mpi
128 >  fileStreams.push_back(&finalOut);
129 >  fileStreams.push_back(&dumpFile);
130 >
131 >  writeFrame(fileStreams, currentTime);
132 >
133 > #ifdef IS_MPI
134 >  finalOut.close();
135 > #endif
136 >        
137   }
138  
139 < void DumpWriter::writeFinal(){
139 > void DumpWriter::writeFinal(double currentTime){
140  
273 –  char finalName[500];
141    ofstream finalOut;
142 +  vector<ofstream*> fileStreams;
143  
276 –  const int BUFFERSIZE = 2000;
277 –  char tempBuffer[BUFFERSIZE];
278 –  char writeLine[BUFFERSIZE];  
279 –
280 –  double q[4];
281 –  DirectionalAtom* dAtom;
282 –  int nAtoms = entry_plug->n_atoms;
283 –  Atom** atoms = entry_plug->atoms;
284 –  int i, j, which_node, done, game_over, which_atom, local_index;
285 –  
286 –  
144   #ifdef IS_MPI
145    if(worldRank == 0 ){
146   #endif // is_mpi
147 <    
148 <    strcpy( finalName, entry_plug->finalName );
149 <    
293 <    finalOut.open( finalName, ios::out | ios::trunc );
147 >
148 >    finalOut.open( entry_plug->finalName, ios::out | ios::trunc );
149 >
150      if( !finalOut ){
151        sprintf( painCave.errMsg,
152                 "Could not open \"%s\" for final dump output.\n",
153 <               finalName );
153 >               entry_plug->finalName );
154        painCave.isFatal = 1;
155        simError();
156      }
157 <    
302 <    // finalOut.setf( ios::scientific );
303 <    
157 >
158   #ifdef IS_MPI
159    }
160 + #endif // is_mpi
161    
162 <  sprintf(checkPointMsg,"Opened file for final configuration\n");
163 <  MPIcheckPoint();  
162 >  fileStreams.push_back(&finalOut);  
163 >  writeFrame(fileStreams, currentTime);
164 >
165 > #ifdef IS_MPI
166 >  finalOut.close();
167 > #endif
168    
169 < #endif //is_mpi
169 > }
170  
171 + void DumpWriter::writeFrame( vector<ofstream*>& outFile, double currentTime ){
172 +
173 +  const int BUFFERSIZE = 2000;
174 +  const int MINIBUFFERSIZE = 100;
175 +
176 +  char tempBuffer[BUFFERSIZE];  
177 +  char writeLine[BUFFERSIZE];
178 +
179 +  int i, k;
180 +
181 + #ifdef IS_MPI
182    
183 +  /*********************************************************************
184 +   * Documentation?  You want DOCUMENTATION?
185 +   *
186 +   * Why all the potatoes below?  
187 +   *
188 +   * To make a long story short, the original version of DumpWriter
189 +   * worked in the most inefficient way possible.  Node 0 would
190 +   * poke each of the node for an individual atom's formatted data
191 +   * as node 0 worked its way down the global index. This was particularly
192 +   * inefficient since the method blocked all processors at every atom
193 +   * (and did it twice!).
194 +   *
195 +   * An intermediate version of DumpWriter could be described from Node
196 +   * zero's perspective as follows:
197 +   *
198 +   *  1) Have 100 of your friends stand in a circle.
199 +   *  2) When you say go, have all of them start tossing potatoes at
200 +   *     you (one at a time).
201 +   *  3) Catch the potatoes.
202 +   *
203 +   * It was an improvement, but MPI has buffers and caches that could
204 +   * best be described in this analogy as "potato nets", so there's no
205 +   * need to block the processors atom-by-atom.
206 +   *
207 +   * This new and improved DumpWriter works in an even more efficient
208 +   * way:
209 +   *
210 +   *  1) Have 100 of your friend stand in a circle.
211 +   *  2) When you say go, have them start tossing 5-pound bags of
212 +   *     potatoes at you.
213 +   *  3) Once you've caught a friend's bag of potatoes,
214 +   *     toss them a spud to let them know they can toss another bag.
215 +   *
216 +   * How's THAT for documentation?
217 +   *
218 +   *********************************************************************/
219 +
220 +  int *potatoes;
221 +  int myPotato;
222 +
223 +  int nProc;
224 +  int j, which_node, done, which_atom, local_index, currentIndex;
225 +  double atomData6[6];
226 +  double atomData13[13];
227 +  int isDirectional;
228 +  char* atomTypeString;
229 +  char MPIatomTypeString[MINIBUFFERSIZE];
230 +
231 + #else //is_mpi
232 +  int nAtoms = entry_plug->n_atoms;
233 + #endif //is_mpi
234 +
235 +  double q[4];
236 +  DirectionalAtom* dAtom;
237 +  Atom** atoms = entry_plug->atoms;
238 +  double pos[3], vel[3];
239 +
240   #ifndef IS_MPI
314 –    
315 –  finalOut << nAtoms << "\n";
316 –    
317 –  finalOut << entry_plug->box_x << "\t"
318 –           << entry_plug->box_y << "\t"
319 –           << entry_plug->box_z << "\n";
241    
242 +  for(k = 0; k < outFile.size(); k++){
243 +    *outFile[k] << nAtoms << "\n";
244 +
245 +    *outFile[k] << currentTime << ";\t"
246 +               << entry_plug->Hmat[0][0] << "\t"
247 +                     << entry_plug->Hmat[1][0] << "\t"
248 +                     << entry_plug->Hmat[2][0] << ";\t"
249 +              
250 +               << entry_plug->Hmat[0][1] << "\t"
251 +                     << entry_plug->Hmat[1][1] << "\t"
252 +                     << entry_plug->Hmat[2][1] << ";\t"
253 +
254 +                     << entry_plug->Hmat[0][2] << "\t"
255 +                     << entry_plug->Hmat[1][2] << "\t"
256 +                     << entry_plug->Hmat[2][2] << ";";
257 +
258 +    //write out additional parameters, such as chi and eta
259 +    *outFile[k] << entry_plug->the_integrator->getAdditionalParameters() << endl;
260 +  }
261 +  
262    for( i=0; i<nAtoms; i++ ){
263 <      
263 >
264 >    atoms[i]->getPos(pos);
265 >    atoms[i]->getVel(vel);
266 >
267      sprintf( tempBuffer,
268               "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
269               atoms[i]->getType(),
270 <             atoms[i]->getX(),
271 <             atoms[i]->getY(),
272 <             atoms[i]->getZ(),
273 <             atoms[i]->get_vx(),
274 <             atoms[i]->get_vy(),
275 <             atoms[i]->get_vz());
270 >             pos[0],
271 >             pos[1],
272 >             pos[2],
273 >             vel[0],
274 >             vel[1],
275 >             vel[2]);
276      strcpy( writeLine, tempBuffer );
277  
278      if( atoms[i]->isDirectional() ){
279 <        
279 >
280        dAtom = (DirectionalAtom *)atoms[i];
281        dAtom->getQ( q );
282 <        
282 >
283        sprintf( tempBuffer,
284                 "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
285                 q[0],
# Line 349 | Line 293 | void DumpWriter::writeFinal(){
293      }
294      else
295        strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
296 <      
297 <    finalOut << writeLine;
296 >
297 >    for(k = 0; k < outFile.size(); k++)
298 >      *outFile[k] << writeLine;
299    }
355 –  finalOut.flush();
356 –  finalOut.close();
300  
301   #else // is_mpi
302 +
303 +  /* code to find maximum tag value */
304    
305 <  MPI::Status istatus;
305 >  int *tagub, flag, MAXTAG;
306 >  MPI_Attr_get(MPI_COMM_WORLD, MPI_TAG_UB, &tagub, &flag);
307 >  if (flag) {
308 >    MAXTAG = *tagub;
309 >  } else {
310 >    MAXTAG = 32767;
311 >  }  
312 >
313 >  int haveError;
314 >
315 >  MPI_Status istatus;
316    int *AtomToProcMap = mpiSim->getAtomToProcMap();
317  
318    // write out header and node 0's coordinates
319 <  
319 >
320    if( worldRank == 0 ){
321 <    finalOut << mpiSim->getTotAtoms() << "\n";
321 >
322 >    // Node 0 needs a list of the magic potatoes for each processor;
323 >
324 >    nProc = mpiSim->getNumberProcessors();
325 >    potatoes = new int[nProc];
326 >
327 >    //write out the comment lines
328 >    for (i = 0; i < nProc; i++)
329 >      potatoes[i] = 0;
330      
331 <    finalOut << entry_plug->box_x << "\t"
332 <            << entry_plug->box_y << "\t"
333 <            << entry_plug->box_z << "\n";
334 <    
331 >      for(k = 0; k < outFile.size(); k++){
332 >        *outFile[k] << mpiSim->getTotAtoms() << "\n";
333 >
334 >        *outFile[k] << currentTime << ";\t"
335 >                         << entry_plug->Hmat[0][0] << "\t"
336 >                         << entry_plug->Hmat[1][0] << "\t"
337 >                         << entry_plug->Hmat[2][0] << ";\t"
338 >
339 >                         << entry_plug->Hmat[0][1] << "\t"
340 >                         << entry_plug->Hmat[1][1] << "\t"
341 >                         << entry_plug->Hmat[2][1] << ";\t"
342 >
343 >                         << entry_plug->Hmat[0][2] << "\t"
344 >                         << entry_plug->Hmat[1][2] << "\t"
345 >                         << entry_plug->Hmat[2][2] << ";";
346 >  
347 >        *outFile[k] << entry_plug->the_integrator->getAdditionalParameters() << endl;
348 >    }
349 >
350 >    currentIndex = 0;
351 >
352      for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) {
373 –      // Get the Node number which has this molecule:
353        
354 <      which_node = AtomToProcMap[i];    
354 >      // Get the Node number which has this atom;
355        
356 <      if (which_node == mpiSim->getMyNode()) {
356 >      which_node = AtomToProcMap[i];
357 >      
358 >      if (which_node != 0) {
359 >
360 >        if (potatoes[which_node] + 3 >= MAXTAG) {
361 >          // The potato was going to exceed the maximum value,
362 >          // so wrap this processor potato back to 0:        
363 >
364 >          potatoes[which_node] = 0;          
365 >          MPI_Send(0, 1, MPI_INT, which_node, 0, MPI_COMM_WORLD);
366 >          
367 >        }
368 >
369 >        myPotato = potatoes[which_node];        
370          
371 <        sprintf( tempBuffer,
372 <                 "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
373 <                 atoms[i]->getType(),
374 <                 atoms[i]->getX(),
383 <                 atoms[i]->getY(),
384 <                 atoms[i]->getZ(),
385 <                 atoms[i]->get_vx(),
386 <                 atoms[i]->get_vy(),
387 <                 atoms[i]->get_vz());
388 <        strcpy( writeLine, tempBuffer );
371 >        MPI_Recv(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, which_node,
372 >                 myPotato, MPI_COMM_WORLD, &istatus);
373 >        
374 >        atomTypeString = MPIatomTypeString;
375          
376 <        if( atoms[i]->isDirectional() ){
376 >        myPotato++;
377 >
378 >        MPI_Recv(&isDirectional, 1, MPI_INT, which_node,
379 >                 myPotato, MPI_COMM_WORLD, &istatus);
380 >              
381 >        myPotato++;
382 >
383 >        if (isDirectional) {          
384 >          MPI_Recv(atomData13, 13, MPI_DOUBLE, which_node,
385 >                   myPotato, MPI_COMM_WORLD, &istatus);
386 >        } else {
387 >          MPI_Recv(atomData6, 6, MPI_DOUBLE, which_node,
388 >                   myPotato, MPI_COMM_WORLD, &istatus);          
389 >        }
390 >        
391 >        myPotato++;
392 >        potatoes[which_node] = myPotato;
393 >
394 >      } else {
395 >        
396 >        haveError = 0;
397 >        which_atom = i;
398 >        
399 >        //local_index = -1;
400 >
401 >        //for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) {
402 >        //  if (atoms[j]->getGlobalIndex() == which_atom) local_index = j;
403 >        //}
404 >        
405 >        //if (local_index != -1) {
406            
407 <          dAtom = (DirectionalAtom *)atoms[i];
408 <          dAtom->getQ( q );
407 >          local_index = indexArray[currentIndex].first;        
408 >          
409 >          if (which_atom == indexArray[currentIndex].second) {
410 >            
411 >            atomTypeString = atoms[local_index]->getType();
412 >            
413 >          atoms[local_index]->getPos(pos);
414 >          atoms[local_index]->getVel(vel);          
415            
416 <          sprintf( tempBuffer,
417 <                   "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
418 <                   q[0],
419 <                   q[1],
420 <                   q[2],
421 <                   q[3],
422 <                   dAtom->getJx(),
423 <                   dAtom->getJy(),
424 <                   dAtom->getJz());
425 <          strcat( writeLine, tempBuffer );
426 <        }
427 <        else
428 <          strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );      
416 >          atomData6[0] = pos[0];
417 >          atomData6[1] = pos[1];
418 >          atomData6[2] = pos[2];
419 >
420 >          atomData6[3] = vel[0];
421 >          atomData6[4] = vel[1];
422 >          atomData6[5] = vel[2];
423 >          
424 >          isDirectional = 0;
425 >
426 >          if( atoms[local_index]->isDirectional() ){
427 >
428 >            isDirectional = 1;
429 >            
430 >            dAtom = (DirectionalAtom *)atoms[local_index];
431 >            dAtom->getQ( q );
432 >
433 >            for (int j = 0; j < 6 ; j++)
434 >              atomData13[j] = atomData6[j];            
435 >            
436 >            atomData13[6] = q[0];
437 >            atomData13[7] = q[1];
438 >            atomData13[8] = q[2];
439 >            atomData13[9] = q[3];
440 >            
441 >            atomData13[10] = dAtom->getJx();
442 >            atomData13[11] = dAtom->getJy();
443 >            atomData13[12] = dAtom->getJz();
444 >          }
445 >          
446 >        } else {
447 >          sprintf(painCave.errMsg,
448 >                  "Atom %d not found on processor %d, currentIndex = %d, local_index = %d\n",
449 >                  which_atom, worldRank, currentIndex, local_index );
450 >          haveError= 1;
451 >          simError();
452 >        }
453          
454 +        if(haveError) DieDieDie();
455 +        
456 +        currentIndex++;
457 +      }
458 +      // If we've survived to here, format the line:
459 +      
460 +      if (!isDirectional) {
461 +        
462 +        sprintf( writeLine,
463 +                 "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
464 +                 atomTypeString,
465 +                 atomData6[0],
466 +                 atomData6[1],
467 +                 atomData6[2],
468 +                 atomData6[3],
469 +                 atomData6[4],
470 +                 atomData6[5]);
471 +        
472 +        strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
473 +        
474        } else {
475 +        
476 +        sprintf( writeLine,
477 +                 "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
478 +                 atomTypeString,
479 +                 atomData13[0],
480 +                 atomData13[1],
481 +                 atomData13[2],
482 +                 atomData13[3],
483 +                 atomData13[4],
484 +                 atomData13[5],
485 +                 atomData13[6],
486 +                 atomData13[7],
487 +                 atomData13[8],
488 +                 atomData13[9],
489 +                 atomData13[10],
490 +                 atomData13[11],
491 +                 atomData13[12]);
492          
411 –        MPI::COMM_WORLD.Send(&i, 1, MPI_INT, which_node, TAKE_THIS_TAG_INT);
412 –        MPI::COMM_WORLD.Recv(writeLine, BUFFERSIZE, MPI_CHAR, which_node,
413 –                                TAKE_THIS_TAG_CHAR, istatus);
493        }
494        
495 <      finalOut << writeLine;
495 >      for(k = 0; k < outFile.size(); k++)
496 >        *outFile[k] << writeLine;
497      }
498      
499 <    // kill everyone off:
500 <    game_over = -1;
421 <    for (j = 0; j < mpiSim->getNumberProcessors(); j++) {
422 <      MPI::COMM_WORLD.Send(&game_over, 1, MPI_INT, j, TAKE_THIS_TAG_INT);
423 <    }
424 <
425 <  } else {
499 >    for(k = 0; k < outFile.size(); k++)
500 >      outFile[k]->flush();
501      
502 <    done = 0;
503 <    while (!done) {
504 <      MPI::COMM_WORLD.Recv(&which_atom, 1, MPI_INT, 0,
505 <                           TAKE_THIS_TAG_INT, istatus);
502 >    sprintf( checkPointMsg,
503 >             "Sucessfully took a dump.\n");
504 >    
505 >    MPIcheckPoint();        
506 >    
507 >    delete[] potatoes;
508 >    
509 >  } else {
510  
511 <      if (which_atom == -1) {
433 <        done=1;
434 <        continue;
435 <      } else {
511 >    // worldRank != 0, so I'm a remote node.  
512  
513 <        local_index=-1;        
514 <        for (j=0; j < mpiSim->getMyNlocal(); j++) {
515 <          if (atoms[j]->getGlobalIndex() == which_atom) local_index = j;
513 >    // Set my magic potato to 0:
514 >
515 >    myPotato = 0;
516 >    currentIndex = 0;
517 >    
518 >    for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) {
519 >      
520 >      // Am I the node which has this atom?
521 >      
522 >      if (AtomToProcMap[i] == worldRank) {
523 >
524 >        if (myPotato + 3 >= MAXTAG) {
525 >          
526 >          // The potato was going to exceed the maximum value,
527 >          // so wrap this processor potato back to 0 (and block until
528 >          // node 0 says we can go:
529 >          
530 >          MPI_Recv(&myPotato, 1, MPI_INT, 0, 0, MPI_COMM_WORLD, &istatus);
531 >          
532          }
533 <        if (local_index != -1) {
533 >        which_atom = i;
534  
535 <          //format the line
536 <          sprintf( tempBuffer,
537 <                   "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
538 <                   atoms[local_index]->getType(),
539 <                   atoms[local_index]->getX(),
540 <                   atoms[local_index]->getY(),
541 <                   atoms[local_index]->getZ(),
542 <                   atoms[local_index]->get_vx(),
543 <                   atoms[local_index]->get_vy(),
544 <                   atoms[local_index]->get_vz()); // check here.
545 <          strcpy( writeLine, tempBuffer );
535 >        //local_index = -1;
536 >
537 >        //for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) {
538 >        // if (atoms[j]->getGlobalIndex() == which_atom) local_index = j;
539 >        //}
540 >        
541 >        //if (local_index != -1) {
542 >
543 >        local_index = indexArray[currentIndex].first;        
544 >                
545 >        if (which_atom == indexArray[currentIndex].second) {
546 >        
547 >          atomTypeString = atoms[local_index]->getType();
548            
549 +          atoms[local_index]->getPos(pos);
550 +          atoms[local_index]->getVel(vel);
551 +          
552 +          atomData6[0] = pos[0];
553 +          atomData6[1] = pos[1];
554 +          atomData6[2] = pos[2];
555 +
556 +          atomData6[3] = vel[0];
557 +          atomData6[4] = vel[1];
558 +          atomData6[5] = vel[2];
559 +          
560 +          isDirectional = 0;
561 +
562            if( atoms[local_index]->isDirectional() ){
563 +
564 +            isDirectional = 1;
565              
566              dAtom = (DirectionalAtom *)atoms[local_index];
567              dAtom->getQ( q );
568 <            
569 <            sprintf( tempBuffer,
570 <                     "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
571 <                     q[0],
572 <                     q[1],
573 <                     q[2],
574 <                     q[3],
575 <                     dAtom->getJx(),
576 <                     dAtom->getJy(),
577 <                     dAtom->getJz());
578 <            strcat( writeLine, tempBuffer );
568 >            
569 >            for (int j = 0; j < 6 ; j++)
570 >              atomData13[j] = atomData6[j];
571 >            
572 >            atomData13[6] = q[0];
573 >            atomData13[7] = q[1];
574 >            atomData13[8] = q[2];
575 >            atomData13[9] = q[3];
576 >  
577 >            atomData13[10] = dAtom->getJx();
578 >            atomData13[11] = dAtom->getJy();
579 >            atomData13[12] = dAtom->getJz();
580            }
581 <          else
582 <            strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
581 >
582 >        } else {
583 >          sprintf(painCave.errMsg,
584 >                  "Atom %d not found on processor %d, currentIndex = %d, local_index = %d\n",
585 >                  which_atom, worldRank, currentIndex, local_index );
586 >          haveError= 1;
587 >          simError();
588 >        }
589 >        
590 >        strncpy(MPIatomTypeString, atomTypeString, MINIBUFFERSIZE);
591 >
592 >        // null terminate the string before sending (just in case):
593 >        MPIatomTypeString[MINIBUFFERSIZE-1] = '\0';
594 >
595 >        MPI_Send(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, 0,
596 >                             myPotato, MPI_COMM_WORLD);
597 >        
598 >        myPotato++;
599 >
600 >        MPI_Send(&isDirectional, 1, MPI_INT, 0,
601 >                             myPotato, MPI_COMM_WORLD);
602 >        
603 >        myPotato++;
604 >        
605 >        if (isDirectional) {
606 >
607 >          MPI_Send(atomData13, 13, MPI_DOUBLE, 0,
608 >                   myPotato, MPI_COMM_WORLD);
609            
474 –          MPI::COMM_WORLD.Send(writeLine, BUFFERSIZE, MPI_CHAR, 0,
475 –                               TAKE_THIS_TAG_CHAR);
610          } else {
611 <          strcpy( writeLine, "ATOM NOT FOUND ON THIS PROCESSOR");
612 <          MPI::COMM_WORLD.Send(writeLine, BUFFERSIZE, MPI_CHAR, 0,
613 <                               TAKE_THIS_TAG_CHAR);
611 >
612 >          MPI_Send(atomData6, 6, MPI_DOUBLE, 0,
613 >                   myPotato, MPI_COMM_WORLD);
614          }
615 +
616 +        myPotato++;  
617 +        currentIndex++;    
618        }
619      }
483 –  }
484 –  finalOut.flush();
485 –  sprintf( checkPointMsg,
486 –           "Sucessfully took a dump.\n");
487 –  MPIcheckPoint();
620  
621 <  if( worldRank == 0 ) finalOut.close();    
621 >    sprintf( checkPointMsg,
622 >             "Sucessfully took a dump.\n");
623 >    MPIcheckPoint();        
624 >    
625 >  }
626 >  
627   #endif // is_mpi
628   }
629 +
630 + #ifdef IS_MPI
631 +
632 + // a couple of functions to let us escape the write loop
633 +
634 + void dWrite::DieDieDie( void ){
635 +
636 +  MPI_Finalize();
637 +  exit (0);
638 + }
639 +
640 + #endif //is_mpi

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