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root/group/trunk/OOPSE/libmdtools/DumpWriter.cpp
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Comparing trunk/OOPSE/libmdtools/DumpWriter.cpp (file contents):
Revision 437 by chuckv, Fri Mar 28 22:34:02 2003 UTC vs.
Revision 1078 by tim, Tue Mar 2 20:32:40 2004 UTC

# Line 1 | Line 1
1 < #include <cstring>
1 > #define _LARGEFILE_SOURCE64
2 > #define _FILE_OFFSET_BITS 64
3 >
4 > #include <string.h>
5   #include <iostream>
6   #include <fstream>
7 + #include <algorithm>
8 + #include <utility>
9  
10   #ifdef IS_MPI
11   #include <mpi.h>
7 – #include <mpi++.h>
12   #include "mpiSimulation.hpp"
13 < #define TAKE_THIS_TAG_CHAR 1
14 < #define TAKE_THIS_TAG_INT 2
13 >
14 > namespace dWrite{
15 >  void DieDieDie( void );
16 > }
17 >
18 > using namespace dWrite;
19   #endif //is_mpi
20  
21   #include "ReadWrite.hpp"
# Line 20 | 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 <    
28 <    outFile.open(outName, ios::out | ios::trunc );
29 <    
30 <    if( !outFile ){
31 <      
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      }
38 –  
39 –    //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 53 | 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, local_index;
87 <  double q[4];
88 <  DirectionalAtom* dAtom;
89 <  int nAtoms = entry_plug->n_atoms;
86 > /**
87 > * Sorting the local index by global index
88 > */
89 >
90 > void DumpWriter::sortByGlobalIndex(){
91    Atom** atoms = entry_plug->atoms;
92 <    
92 >  
93 >  indexArray.clear();
94 >  
95 >  for(int i = 0; i < mpiSim->getMyNlocal();i++)
96 >    indexArray.push_back(make_pair(i, atoms[i]->getGlobalIndex()));
97 >  
98 >  sort(indexArray.begin(), indexArray.end(), indexSortingCriterion);    
99 > }
100  
101 < #ifndef IS_MPI
77 <    
78 <  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 <      
101 > #endif
102  
103 <    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 );
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(),
112 <               dAtom->getJz());
113 <      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
116 <      strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
117 <      
118 <    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;
125 <  int *AtomToProcMap = mpiSim->getAtomToProcMap();
126 <  
127 <  // write out header and node 0's coordinates
128 <  
129 <  if( worldRank == 0 ){
130 <    outFile << mpiSim->getTotAtoms() << "\n";
131 <    
132 <    outFile << currentTime << "\t"
133 <            << entry_plug->box_x << "\t"
134 <            << entry_plug->box_y << "\t"
135 <            << entry_plug->box_z << "\n";
136 <    outFile.flush();
137 <    for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) {
138 <      // 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();
198 <    }
199 <    
200 <    // 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 <    }
126 >  writeFrame(fileStreams, currentTime);
127  
128 <  } else {
129 <    
130 <    done = 0;
131 <    while (!done) {
210 <      //std::cerr << "node: " << mpiSim->getMyNode() << " Waiting for receive \n";
211 <      MPI::COMM_WORLD.Recv(&which_atom, 1, MPI_INT, 0,
212 <                           TAKE_THIS_TAG_INT, istatus);
213 <      //std::cerr << "node: " << mpiSim->getMyNode() << " got request for atom " << which_atom << "\n";
214 <      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 > #ifdef IS_MPI
129 >  finalOut.close();
130 > #endif
131 >        
132   }
133  
134 < void DumpWriter::writeFinal(){
134 > void DumpWriter::writeFinal(double currentTime){
135  
273 –  char finalName[500];
136    ofstream finalOut;
137 +  vector<ofstream*> fileStreams;
138  
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 –  
139   #ifdef IS_MPI
140    if(worldRank == 0 ){
141   #endif // is_mpi
142 <    
143 <    strcpy( finalName, entry_plug->finalName );
144 <    
293 <    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 <    
302 <    // finalOut.setf( ios::scientific );
303 <    
152 >
153   #ifdef IS_MPI
154    }
155 + #endif // is_mpi
156    
157 <  sprintf(checkPointMsg,"Opened file for final configuration\n");
158 <  MPIcheckPoint();  
157 >  fileStreams.push_back(&finalOut);  
158 >  writeFrame(fileStreams, currentTime);
159 >
160 > #ifdef IS_MPI
161 >  finalOut.close();
162 > #endif
163    
164 < #endif //is_mpi
164 > }
165  
166 + void DumpWriter::writeFrame( vector<ofstream*>& outFile, double currentTime ){
167 +
168 +  const int BUFFERSIZE = 2000;
169 +  const int MINIBUFFERSIZE = 100;
170 +
171 +  char tempBuffer[BUFFERSIZE];  
172 +  char writeLine[BUFFERSIZE];
173 +
174 +  int i, k;
175 +
176 + #ifdef IS_MPI
177    
178 +  /*********************************************************************
179 +   * Documentation?  You want DOCUMENTATION?
180 +   *
181 +   * Why all the potatoes below?  
182 +   *
183 +   * To make a long story short, the original version of DumpWriter
184 +   * worked in the most inefficient way possible.  Node 0 would
185 +   * poke each of the node for an individual atom's formatted data
186 +   * as node 0 worked its way down the global index. This was particularly
187 +   * inefficient since the method blocked all processors at every atom
188 +   * (and did it twice!).
189 +   *
190 +   * An intermediate version of DumpWriter could be described from Node
191 +   * zero's perspective as follows:
192 +   *
193 +   *  1) Have 100 of your friends stand in a circle.
194 +   *  2) When you say go, have all of them start tossing potatoes at
195 +   *     you (one at a time).
196 +   *  3) Catch the potatoes.
197 +   *
198 +   * It was an improvement, but MPI has buffers and caches that could
199 +   * best be described in this analogy as "potato nets", so there's no
200 +   * need to block the processors atom-by-atom.
201 +   *
202 +   * This new and improved DumpWriter works in an even more efficient
203 +   * way:
204 +   *
205 +   *  1) Have 100 of your friend stand in a circle.
206 +   *  2) When you say go, have them start tossing 5-pound bags of
207 +   *     potatoes at you.
208 +   *  3) Once you've caught a friend's bag of potatoes,
209 +   *     toss them a spud to let them know they can toss another bag.
210 +   *
211 +   * How's THAT for documentation?
212 +   *
213 +   *********************************************************************/
214 +
215 +  int *potatoes;
216 +  int myPotato;
217 +
218 +  int nProc;
219 +  int j, which_node, done, which_atom, local_index, currentIndex;
220 +  double atomData6[6];
221 +  double atomData13[13];
222 +  int isDirectional;
223 +  char* atomTypeString;
224 +  char MPIatomTypeString[MINIBUFFERSIZE];
225 +
226 + #else //is_mpi
227 +  int nAtoms = entry_plug->n_atoms;
228 + #endif //is_mpi
229 +
230 +  double q[4];
231 +  DirectionalAtom* dAtom;
232 +  Atom** atoms = entry_plug->atoms;
233 +  double pos[3], vel[3];
234 +
235   #ifndef IS_MPI
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";
236    
237 +  for(k = 0; k < outFile.size(); k++){
238 +    *outFile[k] << nAtoms << "\n";
239 +
240 +    *outFile[k] << currentTime << ";\t"
241 +               << entry_plug->Hmat[0][0] << "\t"
242 +                     << entry_plug->Hmat[1][0] << "\t"
243 +                     << entry_plug->Hmat[2][0] << ";\t"
244 +              
245 +               << entry_plug->Hmat[0][1] << "\t"
246 +                     << entry_plug->Hmat[1][1] << "\t"
247 +                     << entry_plug->Hmat[2][1] << ";\t"
248 +
249 +                     << entry_plug->Hmat[0][2] << "\t"
250 +                     << entry_plug->Hmat[1][2] << "\t"
251 +                     << entry_plug->Hmat[2][2] << ";";
252 +
253 +    //write out additional parameters, such as chi and eta
254 +    *outFile[k] << entry_plug->the_integrator->getAdditionalParameters() << endl;
255 +  }
256 +  
257    for( i=0; i<nAtoms; i++ ){
258 <      
258 >
259 >    atoms[i]->getPos(pos);
260 >    atoms[i]->getVel(vel);
261 >
262      sprintf( tempBuffer,
263               "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
264               atoms[i]->getType(),
265 <             atoms[i]->getX(),
266 <             atoms[i]->getY(),
267 <             atoms[i]->getZ(),
268 <             atoms[i]->get_vx(),
269 <             atoms[i]->get_vy(),
270 <             atoms[i]->get_vz());
265 >             pos[0],
266 >             pos[1],
267 >             pos[2],
268 >             vel[0],
269 >             vel[1],
270 >             vel[2]);
271      strcpy( writeLine, tempBuffer );
272  
273      if( atoms[i]->isDirectional() ){
274 <        
274 >
275        dAtom = (DirectionalAtom *)atoms[i];
276        dAtom->getQ( q );
277 <        
277 >
278        sprintf( tempBuffer,
279                 "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
280                 q[0],
# Line 349 | Line 288 | void DumpWriter::writeFinal(){
288      }
289      else
290        strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
291 <      
292 <    finalOut << writeLine;
291 >
292 >    for(k = 0; k < outFile.size(); k++)
293 >      *outFile[k] << writeLine;
294    }
355 –  finalOut.flush();
356 –  finalOut.close();
295  
296   #else // is_mpi
297 +
298 +  /* code to find maximum tag value */
299    
300 <  MPI::Status istatus;
300 >  int *tagub, flag, MAXTAG;
301 >  MPI_Attr_get(MPI_COMM_WORLD, MPI_TAG_UB, &tagub, &flag);
302 >  if (flag) {
303 >    MAXTAG = *tagub;
304 >  } else {
305 >    MAXTAG = 32767;
306 >  }  
307 >
308 >  int haveError;
309 >
310 >  MPI_Status istatus;
311    int *AtomToProcMap = mpiSim->getAtomToProcMap();
312  
313    // write out header and node 0's coordinates
314 <  
314 >
315    if( worldRank == 0 ){
316 <    finalOut << mpiSim->getTotAtoms() << "\n";
316 >
317 >    // Node 0 needs a list of the magic potatoes for each processor;
318 >
319 >    nProc = mpiSim->getNumberProcessors();
320 >    potatoes = new int[nProc];
321 >
322 >    //write out the comment lines
323 >    for (i = 0; i < nProc; i++)
324 >      potatoes[i] = 0;
325      
326 <    finalOut << entry_plug->box_x << "\t"
327 <            << entry_plug->box_y << "\t"
328 <            << entry_plug->box_z << "\n";
329 <    
326 >      for(k = 0; k < outFile.size(); k++){
327 >        *outFile[k] << mpiSim->getTotAtoms() << "\n";
328 >
329 >        *outFile[k] << currentTime << ";\t"
330 >                         << entry_plug->Hmat[0][0] << "\t"
331 >                         << entry_plug->Hmat[1][0] << "\t"
332 >                         << entry_plug->Hmat[2][0] << ";\t"
333 >
334 >                         << entry_plug->Hmat[0][1] << "\t"
335 >                         << entry_plug->Hmat[1][1] << "\t"
336 >                         << entry_plug->Hmat[2][1] << ";\t"
337 >
338 >                         << entry_plug->Hmat[0][2] << "\t"
339 >                         << entry_plug->Hmat[1][2] << "\t"
340 >                         << entry_plug->Hmat[2][2] << ";";
341 >  
342 >        *outFile[k] << entry_plug->the_integrator->getAdditionalParameters() << endl;
343 >    }
344 >
345 >    currentIndex = 0;
346 >
347      for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) {
373 –      // Get the Node number which has this molecule:
348        
349 <      which_node = AtomToProcMap[i];    
349 >      // Get the Node number which has this atom;
350        
351 <      if (which_node == mpiSim->getMyNode()) {
351 >      which_node = AtomToProcMap[i];
352 >      
353 >      if (which_node != 0) {
354  
355 <        which_atom = i;
356 <        local_index=-1;        
357 <        for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) {
358 <          if (atoms[j]->getGlobalIndex() == which_atom) local_index = j;
355 >        if (potatoes[which_node] + 3 >= MAXTAG) {
356 >          // The potato was going to exceed the maximum value,
357 >          // so wrap this processor potato back to 0:        
358 >
359 >          potatoes[which_node] = 0;          
360 >          MPI_Send(0, 1, MPI_INT, which_node, 0, MPI_COMM_WORLD);
361 >          
362          }
363 <        if (local_index != -1) {        
364 <          sprintf( tempBuffer,
365 <                   "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
366 <                   atoms[local_index]->getType(),
367 <                   atoms[local_index]->getX(),
368 <                   atoms[local_index]->getY(),
369 <                   atoms[local_index]->getZ(),
370 <                   atoms[local_index]->get_vx(),
371 <                   atoms[local_index]->get_vy(),
372 <                   atoms[local_index]->get_vz());
373 <          strcpy( writeLine, tempBuffer );
374 <          
375 <          if( atoms[local_index]->isDirectional() ){
363 >
364 >        myPotato = potatoes[which_node];        
365 >        
366 >        MPI_Recv(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, which_node,
367 >                 myPotato, MPI_COMM_WORLD, &istatus);
368 >        
369 >        atomTypeString = MPIatomTypeString;
370 >        
371 >        myPotato++;
372 >
373 >        MPI_Recv(&isDirectional, 1, MPI_INT, which_node,
374 >                 myPotato, MPI_COMM_WORLD, &istatus);
375 >              
376 >        myPotato++;
377 >
378 >        if (isDirectional) {          
379 >          MPI_Recv(atomData13, 13, MPI_DOUBLE, which_node,
380 >                   myPotato, MPI_COMM_WORLD, &istatus);
381 >        } else {
382 >          MPI_Recv(atomData6, 6, MPI_DOUBLE, which_node,
383 >                   myPotato, MPI_COMM_WORLD, &istatus);          
384 >        }
385 >        
386 >        myPotato++;
387 >        potatoes[which_node] = myPotato;
388 >
389 >      } else {
390 >        
391 >        haveError = 0;
392 >        which_atom = i;
393 >        
394 >          local_index = indexArray[currentIndex].first;        
395 >          
396 >          if (which_atom == indexArray[currentIndex].second) {
397              
398 <            dAtom = (DirectionalAtom *)atoms[local_index];
399 <            dAtom->getQ( q );
398 >            atomTypeString = atoms[local_index]->getType();
399              
400 <            sprintf( tempBuffer,
401 <                     "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
402 <                     q[0],
403 <                     q[1],
404 <                     q[2],
405 <                     q[3],
406 <                     dAtom->getJx(),
407 <                     dAtom->getJy(),
408 <                     dAtom->getJz());
409 <            strcat( writeLine, tempBuffer );
410 <          }
411 <          else
412 <            strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );      
413 <        }
414 <        else {
415 <          strcpy( writeLine, "ATOM NOT FOUND ON THIS PROCESSOR");
416 <        }
417 <    
400 >          atoms[local_index]->getPos(pos);
401 >          atoms[local_index]->getVel(vel);          
402 >          
403 >          atomData6[0] = pos[0];
404 >          atomData6[1] = pos[1];
405 >          atomData6[2] = pos[2];
406 >
407 >          atomData6[3] = vel[0];
408 >          atomData6[4] = vel[1];
409 >          atomData6[5] = vel[2];
410 >          
411 >          isDirectional = 0;
412 >
413 >          if( atoms[local_index]->isDirectional() ){
414 >
415 >            isDirectional = 1;
416 >            
417 >            dAtom = (DirectionalAtom *)atoms[local_index];
418 >            dAtom->getQ( q );
419 >
420 >            for (int j = 0; j < 6 ; j++)
421 >              atomData13[j] = atomData6[j];            
422 >            
423 >            atomData13[6] = q[0];
424 >            atomData13[7] = q[1];
425 >            atomData13[8] = q[2];
426 >            atomData13[9] = q[3];
427 >            
428 >            atomData13[10] = dAtom->getJx();
429 >            atomData13[11] = dAtom->getJy();
430 >            atomData13[12] = dAtom->getJz();
431 >          }
432 >          
433 >        } else {
434 >          sprintf(painCave.errMsg,
435 >                  "Atom %d not found on processor %d, currentIndex = %d, local_index = %d\n",
436 >                  which_atom, worldRank, currentIndex, local_index );
437 >          haveError= 1;
438 >          simError();
439 >        }
440 >        
441 >        if(haveError) DieDieDie();
442 >        
443 >        currentIndex++;
444 >      }
445 >      // If we've survived to here, format the line:
446 >      
447 >      if (!isDirectional) {
448 >        
449 >        sprintf( writeLine,
450 >                 "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
451 >                 atomTypeString,
452 >                 atomData6[0],
453 >                 atomData6[1],
454 >                 atomData6[2],
455 >                 atomData6[3],
456 >                 atomData6[4],
457 >                 atomData6[5]);
458 >        
459 >        strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
460 >        
461        } else {
462 +        
463 +        sprintf( writeLine,
464 +                 "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
465 +                 atomTypeString,
466 +                 atomData13[0],
467 +                 atomData13[1],
468 +                 atomData13[2],
469 +                 atomData13[3],
470 +                 atomData13[4],
471 +                 atomData13[5],
472 +                 atomData13[6],
473 +                 atomData13[7],
474 +                 atomData13[8],
475 +                 atomData13[9],
476 +                 atomData13[10],
477 +                 atomData13[11],
478 +                 atomData13[12]);
479          
421 –        MPI::COMM_WORLD.Send(&i, 1, MPI_INT, which_node, TAKE_THIS_TAG_INT);
422 –        MPI::COMM_WORLD.Recv(writeLine, BUFFERSIZE, MPI_CHAR, which_node,
423 –                                TAKE_THIS_TAG_CHAR, istatus);
480        }
481        
482 <      finalOut << writeLine;
482 >      for(k = 0; k < outFile.size(); k++)
483 >        *outFile[k] << writeLine;
484      }
485      
486 <    // kill everyone off:
487 <    game_over = -1;
431 <    for (j = 0; j < mpiSim->getNumberProcessors(); j++) {
432 <      MPI::COMM_WORLD.Send(&game_over, 1, MPI_INT, j, TAKE_THIS_TAG_INT);
433 <    }
434 <
435 <  } else {
486 >    for(k = 0; k < outFile.size(); k++)
487 >      outFile[k]->flush();
488      
489 <    done = 0;
490 <    while (!done) {
491 <      MPI::COMM_WORLD.Recv(&which_atom, 1, MPI_INT, 0,
492 <                           TAKE_THIS_TAG_INT, istatus);
489 >    sprintf( checkPointMsg,
490 >             "Sucessfully took a dump.\n");
491 >    
492 >    MPIcheckPoint();        
493 >    
494 >    delete[] potatoes;
495 >    
496 >  } else {
497  
498 <      if (which_atom == -1) {
443 <        done=1;
444 <        continue;
445 <      } else {
498 >    // worldRank != 0, so I'm a remote node.  
499  
500 <        local_index=-1;        
501 <        for (j=0; j < mpiSim->getMyNlocal(); j++) {
502 <          if (atoms[j]->getGlobalIndex() == which_atom) local_index = j;
500 >    // Set my magic potato to 0:
501 >
502 >    myPotato = 0;
503 >    currentIndex = 0;
504 >    
505 >    for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) {
506 >      
507 >      // Am I the node which has this atom?
508 >      
509 >      if (AtomToProcMap[i] == worldRank) {
510 >
511 >        if (myPotato + 3 >= MAXTAG) {
512 >          
513 >          // The potato was going to exceed the maximum value,
514 >          // so wrap this processor potato back to 0 (and block until
515 >          // node 0 says we can go:
516 >          
517 >          MPI_Recv(&myPotato, 1, MPI_INT, 0, 0, MPI_COMM_WORLD, &istatus);
518 >          
519          }
520 <        if (local_index != -1) {
520 >        which_atom = i;
521  
522 <          //format the line
523 <          sprintf( tempBuffer,
524 <                   "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
525 <                   atoms[local_index]->getType(),
526 <                   atoms[local_index]->getX(),
458 <                   atoms[local_index]->getY(),
459 <                   atoms[local_index]->getZ(),
460 <                   atoms[local_index]->get_vx(),
461 <                   atoms[local_index]->get_vy(),
462 <                   atoms[local_index]->get_vz()); // check here.
463 <          strcpy( writeLine, tempBuffer );
522 >        local_index = indexArray[currentIndex].first;        
523 >                
524 >        if (which_atom == indexArray[currentIndex].second) {
525 >        
526 >          atomTypeString = atoms[local_index]->getType();
527            
528 +          atoms[local_index]->getPos(pos);
529 +          atoms[local_index]->getVel(vel);
530 +          
531 +          atomData6[0] = pos[0];
532 +          atomData6[1] = pos[1];
533 +          atomData6[2] = pos[2];
534 +
535 +          atomData6[3] = vel[0];
536 +          atomData6[4] = vel[1];
537 +          atomData6[5] = vel[2];
538 +          
539 +          isDirectional = 0;
540 +
541            if( atoms[local_index]->isDirectional() ){
542 +
543 +            isDirectional = 1;
544              
545              dAtom = (DirectionalAtom *)atoms[local_index];
546              dAtom->getQ( q );
547 <            
548 <            sprintf( tempBuffer,
549 <                     "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
550 <                     q[0],
551 <                     q[1],
552 <                     q[2],
553 <                     q[3],
554 <                     dAtom->getJx(),
555 <                     dAtom->getJy(),
556 <                     dAtom->getJz());
557 <            strcat( writeLine, tempBuffer );
547 >            
548 >            for (int j = 0; j < 6 ; j++)
549 >              atomData13[j] = atomData6[j];
550 >            
551 >            atomData13[6] = q[0];
552 >            atomData13[7] = q[1];
553 >            atomData13[8] = q[2];
554 >            atomData13[9] = q[3];
555 >  
556 >            atomData13[10] = dAtom->getJx();
557 >            atomData13[11] = dAtom->getJy();
558 >            atomData13[12] = dAtom->getJz();
559            }
560 <          else
561 <            strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
560 >
561 >        } else {
562 >          sprintf(painCave.errMsg,
563 >                  "Atom %d not found on processor %d, currentIndex = %d, local_index = %d\n",
564 >                  which_atom, worldRank, currentIndex, local_index );
565 >          haveError= 1;
566 >          simError();
567 >        }
568 >        
569 >        strncpy(MPIatomTypeString, atomTypeString, MINIBUFFERSIZE);
570 >
571 >        // null terminate the string before sending (just in case):
572 >        MPIatomTypeString[MINIBUFFERSIZE-1] = '\0';
573 >
574 >        MPI_Send(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, 0,
575 >                             myPotato, MPI_COMM_WORLD);
576 >        
577 >        myPotato++;
578 >
579 >        MPI_Send(&isDirectional, 1, MPI_INT, 0,
580 >                             myPotato, MPI_COMM_WORLD);
581 >        
582 >        myPotato++;
583 >        
584 >        if (isDirectional) {
585 >
586 >          MPI_Send(atomData13, 13, MPI_DOUBLE, 0,
587 >                   myPotato, MPI_COMM_WORLD);
588            
484 –          MPI::COMM_WORLD.Send(writeLine, BUFFERSIZE, MPI_CHAR, 0,
485 –                               TAKE_THIS_TAG_CHAR);
589          } else {
590 <          strcpy( writeLine, "ATOM NOT FOUND ON THIS PROCESSOR");
591 <          MPI::COMM_WORLD.Send(writeLine, BUFFERSIZE, MPI_CHAR, 0,
592 <                               TAKE_THIS_TAG_CHAR);
590 >
591 >          MPI_Send(atomData6, 6, MPI_DOUBLE, 0,
592 >                   myPotato, MPI_COMM_WORLD);
593          }
594 +
595 +        myPotato++;  
596 +        currentIndex++;    
597        }
598      }
493 –  }
494 –  finalOut.flush();
495 –  sprintf( checkPointMsg,
496 –           "Sucessfully took a dump.\n");
497 –  MPIcheckPoint();
599  
600 <  if( worldRank == 0 ) finalOut.close();    
600 >    sprintf( checkPointMsg,
601 >             "Sucessfully took a dump.\n");
602 >    MPIcheckPoint();        
603 >    
604 >  }
605 >  
606   #endif // is_mpi
607   }
608 +
609 + #ifdef IS_MPI
610 +
611 + // a couple of functions to let us escape the write loop
612 +
613 + void dWrite::DieDieDie( void ){
614 +
615 +  MPI_Finalize();
616 +  exit (0);
617 + }
618 +
619 + #endif //is_mpi

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