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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 947 by gezelter, Thu Jan 15 14:22:16 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 <    
35 <    outFile.open(outName, ios::out | ios::trunc );
29 <    
30 <    if( !outFile ){
31 <      
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      }
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 > #endif
101  
102 < #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 <      
102 > void DumpWriter::writeDump(double currentTime){
103  
104 <    sprintf( tempBuffer,
105 <             "%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 );
104 >  ofstream finalOut;
105 >  vector<ofstream*> fileStreams;
106  
107 <    if( atoms[i]->isDirectional() ){
108 <        
109 <      dAtom = (DirectionalAtom *)atoms[i];
110 <      dAtom->getQ( q );
111 <        
112 <      sprintf( tempBuffer,
113 <               "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
114 <               q[0],
115 <               q[1],
116 <               q[2],
109 <               q[3],
110 <               dAtom->getJx(),
111 <               dAtom->getJy(),
112 <               dAtom->getJz());
113 <      strcat( writeLine, tempBuffer );
107 > #ifdef IS_MPI
108 >  if(worldRank == 0 ){
109 >    
110 >    finalOut.open( entry_plug->finalName, ios::out | ios::trunc );
111 >    if( !finalOut ){
112 >      sprintf( painCave.errMsg,
113 >               "Could not open \"%s\" for final dump output.\n",
114 >               entry_plug->finalName );
115 >      painCave.isFatal = 1;
116 >      simError();
117      }
115 –    else
116 –      strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
117 –      
118 –    outFile << writeLine;
118    }
119 <  outFile.flush();
119 > #endif // is_mpi
120  
121 < #else // is_mpi
121 >  fileStreams.push_back(&finalOut);
122 >  fileStreams.push_back(&dumpFile);
123  
124 <  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 <    }
124 >  writeFrame(fileStreams, currentTime);
125  
126 <  } else {
127 <    
128 <    done = 0;
129 <    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
126 > #ifdef IS_MPI
127 >  finalOut.close();
128 > #endif
129 >        
130   }
131  
132 < void DumpWriter::writeFinal(){
132 > void DumpWriter::writeFinal(double currentTime){
133  
273 –  char finalName[500];
134    ofstream finalOut;
135 +  vector<ofstream*> fileStreams;
136  
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 –  
137   #ifdef IS_MPI
138    if(worldRank == 0 ){
139 < #endif // is_mpi
140 <    
141 <    strcpy( finalName, entry_plug->finalName );
292 <    
293 <    finalOut.open( finalName, ios::out | ios::trunc );
139 >
140 >    finalOut.open( entry_plug->finalName, ios::out | ios::trunc );
141 >
142      if( !finalOut ){
143        sprintf( painCave.errMsg,
144                 "Could not open \"%s\" for final dump output.\n",
145 <               finalName );
145 >               entry_plug->finalName );
146        painCave.isFatal = 1;
147        simError();
148      }
149 <    
302 <    // finalOut.setf( ios::scientific );
303 <    
304 < #ifdef IS_MPI
149 >
150    }
151 + #endif // is_mpi
152    
153 <  sprintf(checkPointMsg,"Opened file for final configuration\n");
154 <  MPIcheckPoint();  
153 >  fileStreams.push_back(&finalOut);  
154 >  writeFrame(fileStreams, currentTime);
155 >
156 > #ifdef IS_MPI
157 >  finalOut.close();
158 > #endif
159    
160 < #endif //is_mpi
160 > }
161  
162 + void DumpWriter::writeFrame( vector<ofstream*>& outFile, double currentTime ){
163 +
164 +  const int BUFFERSIZE = 2000;
165 +  const int MINIBUFFERSIZE = 100;
166 +
167 +  char tempBuffer[BUFFERSIZE];  
168 +  char writeLine[BUFFERSIZE];
169 +
170 +  int i, k;
171 +
172 + #ifdef IS_MPI
173    
174 +  /*********************************************************************
175 +   * Documentation?  You want DOCUMENTATION?
176 +   *
177 +   * Why all the potatoes below?  
178 +   *
179 +   * To make a long story short, the original version of DumpWriter
180 +   * worked in the most inefficient way possible.  Node 0 would
181 +   * poke each of the node for an individual atom's formatted data
182 +   * as node 0 worked its way down the global index. This was particularly
183 +   * inefficient since the method blocked all processors at every atom
184 +   * (and did it twice!).
185 +   *
186 +   * An intermediate version of DumpWriter could be described from Node
187 +   * zero's perspective as follows:
188 +   *
189 +   *  1) Have 100 of your friends stand in a circle.
190 +   *  2) When you say go, have all of them start tossing potatoes at
191 +   *     you (one at a time).
192 +   *  3) Catch the potatoes.
193 +   *
194 +   * It was an improvement, but MPI has buffers and caches that could
195 +   * best be described in this analogy as "potato nets", so there's no
196 +   * need to block the processors atom-by-atom.
197 +   *
198 +   * This new and improved DumpWriter works in an even more efficient
199 +   * way:
200 +   *
201 +   *  1) Have 100 of your friend stand in a circle.
202 +   *  2) When you say go, have them start tossing 5-pound bags of
203 +   *     potatoes at you.
204 +   *  3) Once you've caught a friend's bag of potatoes,
205 +   *     toss them a spud to let them know they can toss another bag.
206 +   *
207 +   * How's THAT for documentation?
208 +   *
209 +   *********************************************************************/
210 +
211 +  int *potatoes;
212 +  int myPotato;
213 +
214 +  int nProc;
215 +  int j, which_node, done, which_atom, local_index, currentIndex;
216 +  double atomData6[6];
217 +  double atomData13[13];
218 +  int isDirectional;
219 +  char* atomTypeString;
220 +  char MPIatomTypeString[MINIBUFFERSIZE];
221 +
222 + #else //is_mpi
223 +  int nAtoms = entry_plug->n_atoms;
224 + #endif //is_mpi
225 +
226 +  double q[4];
227 +  DirectionalAtom* dAtom;
228 +  Atom** atoms = entry_plug->atoms;
229 +  double pos[3], vel[3];
230 +
231   #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";
232    
233 +  for(k = 0; k < outFile.size(); k++){
234 +    *outFile[k] << nAtoms << "\n";
235 +
236 +    *outFile[k] << currentTime << ";\t"
237 +               << entry_plug->Hmat[0][0] << "\t"
238 +                     << entry_plug->Hmat[1][0] << "\t"
239 +                     << entry_plug->Hmat[2][0] << ";\t"
240 +              
241 +               << entry_plug->Hmat[0][1] << "\t"
242 +                     << entry_plug->Hmat[1][1] << "\t"
243 +                     << entry_plug->Hmat[2][1] << ";\t"
244 +
245 +                     << entry_plug->Hmat[0][2] << "\t"
246 +                     << entry_plug->Hmat[1][2] << "\t"
247 +                     << entry_plug->Hmat[2][2] << ";";
248 +
249 +    //write out additional parameters, such as chi and eta
250 +    *outFile[k] << entry_plug->the_integrator->getAdditionalParameters() << endl;
251 +  }
252 +  
253    for( i=0; i<nAtoms; i++ ){
254 <      
254 >
255 >    atoms[i]->getPos(pos);
256 >    atoms[i]->getVel(vel);
257 >
258      sprintf( tempBuffer,
259               "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
260               atoms[i]->getType(),
261 <             atoms[i]->getX(),
262 <             atoms[i]->getY(),
263 <             atoms[i]->getZ(),
264 <             atoms[i]->get_vx(),
265 <             atoms[i]->get_vy(),
266 <             atoms[i]->get_vz());
261 >             pos[0],
262 >             pos[1],
263 >             pos[2],
264 >             vel[0],
265 >             vel[1],
266 >             vel[2]);
267      strcpy( writeLine, tempBuffer );
268  
269      if( atoms[i]->isDirectional() ){
270 <        
270 >
271        dAtom = (DirectionalAtom *)atoms[i];
272        dAtom->getQ( q );
273 <        
273 >
274        sprintf( tempBuffer,
275                 "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
276                 q[0],
# Line 349 | Line 284 | void DumpWriter::writeFinal(){
284      }
285      else
286        strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
287 <      
288 <    finalOut << writeLine;
287 >
288 >    for(k = 0; k < outFile.size(); k++)
289 >      *outFile[k] << writeLine;
290    }
355 –  finalOut.flush();
356 –  finalOut.close();
291  
292   #else // is_mpi
293 +
294 +  /* code to find maximum tag value */
295    
296 <  MPI::Status istatus;
296 >  int *tagub, flag, MAXTAG;
297 >  MPI_Attr_get(MPI_COMM_WORLD, MPI_TAG_UB, &tagub, &flag);
298 >  if (flag) {
299 >    MAXTAG = *tagub;
300 >  } else {
301 >    MAXTAG = 32767;
302 >  }  
303 >
304 >  int haveError;
305 >
306 >  MPI_Status istatus;
307    int *AtomToProcMap = mpiSim->getAtomToProcMap();
308  
309    // write out header and node 0's coordinates
310 <  
310 >
311    if( worldRank == 0 ){
312 <    finalOut << mpiSim->getTotAtoms() << "\n";
312 >
313 >    // Node 0 needs a list of the magic potatoes for each processor;
314 >
315 >    nProc = mpiSim->getNumberProcessors();
316 >    potatoes = new int[nProc];
317 >
318 >    //write out the comment lines
319 >    for (i = 0; i < nProc; i++)
320 >      potatoes[i] = 0;
321      
322 <    finalOut << entry_plug->box_x << "\t"
323 <            << entry_plug->box_y << "\t"
324 <            << entry_plug->box_z << "\n";
325 <    
322 >      for(k = 0; k < outFile.size(); k++){
323 >        *outFile[k] << mpiSim->getTotAtoms() << "\n";
324 >
325 >        *outFile[k] << currentTime << ";\t"
326 >                         << entry_plug->Hmat[0][0] << "\t"
327 >                         << entry_plug->Hmat[1][0] << "\t"
328 >                         << entry_plug->Hmat[2][0] << ";\t"
329 >
330 >                         << entry_plug->Hmat[0][1] << "\t"
331 >                         << entry_plug->Hmat[1][1] << "\t"
332 >                         << entry_plug->Hmat[2][1] << ";\t"
333 >
334 >                         << entry_plug->Hmat[0][2] << "\t"
335 >                         << entry_plug->Hmat[1][2] << "\t"
336 >                         << entry_plug->Hmat[2][2] << ";";
337 >  
338 >        *outFile[k] << entry_plug->the_integrator->getAdditionalParameters() << endl;
339 >    }
340 >
341 >    currentIndex = 0;
342 >
343      for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) {
373 –      // Get the Node number which has this molecule:
344        
345 <      which_node = AtomToProcMap[i];    
345 >      // Get the Node number which has this atom;
346        
347 <      if (which_node == mpiSim->getMyNode()) {
347 >      which_node = AtomToProcMap[i];
348 >      
349 >      if (which_node != 0) {
350 >
351 >        if (potatoes[which_node] + 3 >= MAXTAG) {
352 >          // The potato was going to exceed the maximum value,
353 >          // so wrap this processor potato back to 0:        
354 >
355 >          potatoes[which_node] = 0;          
356 >          MPI_Send(0, 1, MPI_INT, which_node, 0, MPI_COMM_WORLD);
357 >          
358 >        }
359 >
360 >        myPotato = potatoes[which_node];        
361          
362 <        sprintf( tempBuffer,
363 <                 "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
364 <                 atoms[i]->getType(),
365 <                 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 );
362 >        MPI_Recv(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, which_node,
363 >                 myPotato, MPI_COMM_WORLD, &istatus);
364 >        
365 >        atomTypeString = MPIatomTypeString;
366          
367 <        if( atoms[i]->isDirectional() ){
368 <          
369 <          dAtom = (DirectionalAtom *)atoms[i];
370 <          dAtom->getQ( q );
371 <          
372 <          sprintf( tempBuffer,
373 <                   "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
374 <                   q[0],
375 <                   q[1],
376 <                   q[2],
377 <                   q[3],
378 <                   dAtom->getJx(),
379 <                   dAtom->getJy(),
403 <                   dAtom->getJz());
404 <          strcat( writeLine, tempBuffer );
367 >        myPotato++;
368 >
369 >        MPI_Recv(&isDirectional, 1, MPI_INT, which_node,
370 >                 myPotato, MPI_COMM_WORLD, &istatus);
371 >              
372 >        myPotato++;
373 >
374 >        if (isDirectional) {          
375 >          MPI_Recv(atomData13, 13, MPI_DOUBLE, which_node,
376 >                   myPotato, MPI_COMM_WORLD, &istatus);
377 >        } else {
378 >          MPI_Recv(atomData6, 6, MPI_DOUBLE, which_node,
379 >                   myPotato, MPI_COMM_WORLD, &istatus);          
380          }
406 –        else
407 –          strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );      
381          
382 +        myPotato++;
383 +        potatoes[which_node] = myPotato;
384 +
385        } else {
386          
387 <        MPI::COMM_WORLD.Send(&i, 1, MPI_INT, which_node, TAKE_THIS_TAG_INT);
388 <        MPI::COMM_WORLD.Recv(writeLine, BUFFERSIZE, MPI_CHAR, which_node,
389 <                                TAKE_THIS_TAG_CHAR, istatus);
387 >        haveError = 0;
388 >              which_atom = i;
389 >        
390 >        local_index = indexArray[currentIndex].first;        
391 >                
392 >        if (which_atom == indexArray[currentIndex].second) {
393 >          
394 >          atomTypeString = atoms[local_index]->getType();
395 >
396 >                atoms[local_index]->getPos(pos);
397 >                atoms[local_index]->getVel(vel);          
398 >
399 >          atomData6[0] = pos[0];
400 >          atomData6[1] = pos[1];
401 >          atomData6[2] = pos[2];
402 >
403 >          atomData6[3] = vel[0];
404 >          atomData6[4] = vel[1];
405 >          atomData6[5] = vel[2];
406 >          
407 >          isDirectional = 0;
408 >
409 >          if( atoms[local_index]->isDirectional() ){
410 >
411 >            isDirectional = 1;
412 >            
413 >            dAtom = (DirectionalAtom *)atoms[local_index];
414 >            dAtom->getQ( q );
415 >
416 >            for (int j = 0; j < 6 ; j++)
417 >              atomData13[j] = atomData6[j];            
418 >            
419 >            atomData13[6] = q[0];
420 >            atomData13[7] = q[1];
421 >            atomData13[8] = q[2];
422 >            atomData13[9] = q[3];
423 >            
424 >            atomData13[10] = dAtom->getJx();
425 >            atomData13[11] = dAtom->getJy();
426 >            atomData13[12] = dAtom->getJz();
427 >          }
428 >          
429 >        } else {
430 >          sprintf(painCave.errMsg,
431 >                              "Atom %d not found on processor %d\n",
432 >                              i, worldRank );
433 >                haveError= 1;
434 >                simError();
435 >              }
436 >        
437 >        if(haveError) DieDieDie();
438 >        
439 >        currentIndex ++;
440        }
441 +      // If we've survived to here, format the line:
442        
443 <      finalOut << writeLine;
443 >      if (!isDirectional) {
444 >        
445 >        sprintf( writeLine,
446 >                             "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
447 >                             atomTypeString,
448 >                             atomData6[0],
449 >                             atomData6[1],
450 >                             atomData6[2],
451 >                             atomData6[3],
452 >                             atomData6[4],
453 >                             atomData6[5]);
454 >
455 >              strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
456 >        
457 >      } else {
458 >        
459 >              sprintf( writeLine,
460 >                             "%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",
461 >                             atomTypeString,
462 >                             atomData13[0],
463 >                             atomData13[1],
464 >                             atomData13[2],
465 >                             atomData13[3],
466 >                             atomData13[4],
467 >                             atomData13[5],
468 >                             atomData13[6],
469 >                             atomData13[7],
470 >                             atomData13[8],
471 >                             atomData13[9],
472 >                             atomData13[10],
473 >                             atomData13[11],
474 >                             atomData13[12]);
475 >        
476 >      }
477 >      
478 >      for(k = 0; k < outFile.size(); k++)
479 >        *outFile[k] << writeLine;
480      }
481      
482 <    // kill everyone off:
483 <    game_over = -1;
484 <    for (j = 0; j < mpiSim->getNumberProcessors(); j++) {
485 <      MPI::COMM_WORLD.Send(&game_over, 1, MPI_INT, j, TAKE_THIS_TAG_INT);
486 <    }
482 >    for(k = 0; k < outFile.size(); k++)
483 >      outFile[k]->flush();
484 >    
485 >    sprintf( checkPointMsg,
486 >             "Sucessfully took a dump.\n");
487  
488 +    MPIcheckPoint();        
489 +
490 +    delete[] potatoes;
491 +
492    } else {
493 +
494 +    // worldRank != 0, so I'm a remote node.  
495 +
496 +    // Set my magic potato to 0:
497 +
498 +    myPotato = 0;
499 +    currentIndex = 0;
500      
501 <    done = 0;
502 <    while (!done) {
503 <      MPI::COMM_WORLD.Recv(&which_atom, 1, MPI_INT, 0,
504 <                           TAKE_THIS_TAG_INT, istatus);
501 >    for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) {
502 >      
503 >      // Am I the node which has this atom?
504 >      
505 >      if (AtomToProcMap[i] == worldRank) {
506  
507 <      if (which_atom == -1) {
433 <        done=1;
434 <        continue;
435 <      } else {
507 >        if (myPotato + 3 >= MAXTAG) {
508  
509 <        local_index=-1;        
510 <        for (j=0; j < mpiSim->getMyNlocal(); j++) {
511 <          if (atoms[j]->getGlobalIndex() == which_atom) local_index = j;
509 >          // The potato was going to exceed the maximum value,
510 >          // so wrap this processor potato back to 0 (and block until
511 >          // node 0 says we can go:
512 >
513 >          MPI_Recv(&myPotato, 1, MPI_INT, 0, 0, MPI_COMM_WORLD, &istatus);
514 >          
515          }
516 <        if (local_index != -1) {
516 >        which_atom = i;
517 >        local_index = indexArray[currentIndex].first;        
518 >                
519 >        if (which_atom == indexArray[currentIndex].second) {
520 >        
521 >          atomTypeString = atoms[local_index]->getType();
522  
523 <          //format the line
524 <          sprintf( tempBuffer,
525 <                   "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
526 <                   atoms[local_index]->getType(),
527 <                   atoms[local_index]->getX(),
528 <                   atoms[local_index]->getY(),
529 <                   atoms[local_index]->getZ(),
530 <                   atoms[local_index]->get_vx(),
531 <                   atoms[local_index]->get_vy(),
532 <                   atoms[local_index]->get_vz()); // check here.
533 <          strcpy( writeLine, tempBuffer );
534 <          
523 >                atoms[local_index]->getPos(pos);
524 >                atoms[local_index]->getVel(vel);
525 >
526 >          atomData6[0] = pos[0];
527 >          atomData6[1] = pos[1];
528 >          atomData6[2] = pos[2];
529 >
530 >          atomData6[3] = vel[0];
531 >          atomData6[4] = vel[1];
532 >          atomData6[5] = vel[2];
533 >          
534 >          isDirectional = 0;
535 >
536            if( atoms[local_index]->isDirectional() ){
537 +
538 +            isDirectional = 1;
539              
540              dAtom = (DirectionalAtom *)atoms[local_index];
541              dAtom->getQ( q );
542 <            
543 <            sprintf( tempBuffer,
544 <                     "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
545 <                     q[0],
546 <                     q[1],
547 <                     q[2],
548 <                     q[3],
549 <                     dAtom->getJx(),
550 <                     dAtom->getJy(),
551 <                     dAtom->getJz());
552 <            strcat( writeLine, tempBuffer );
542 >            
543 >            for (int j = 0; j < 6 ; j++)
544 >              atomData13[j] = atomData6[j];
545 >            
546 >            atomData13[6] = q[0];
547 >            atomData13[7] = q[1];
548 >            atomData13[8] = q[2];
549 >            atomData13[9] = q[3];
550 >  
551 >            atomData13[10] = dAtom->getJx();
552 >            atomData13[11] = dAtom->getJy();
553 >            atomData13[12] = dAtom->getJz();
554            }
555 <          else
556 <            strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
555 >
556 >        } else {
557 >                sprintf(painCave.errMsg,
558 >                              "Atom %d not found on processor %d\n",
559 >                              i, worldRank );
560 >                haveError= 1;
561 >                simError();
562 >              }
563 >
564 >        strncpy(MPIatomTypeString, atomTypeString, MINIBUFFERSIZE);
565 >
566 >        // null terminate the string before sending (just in case):
567 >        MPIatomTypeString[MINIBUFFERSIZE-1] = '\0';
568 >
569 >        MPI_Send(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, 0,
570 >                             myPotato, MPI_COMM_WORLD);
571 >        
572 >        myPotato++;
573 >
574 >        MPI_Send(&isDirectional, 1, MPI_INT, 0,
575 >                             myPotato, MPI_COMM_WORLD);
576 >        
577 >        myPotato++;
578 >        
579 >        if (isDirectional) {
580 >
581 >          MPI_Send(atomData13, 13, MPI_DOUBLE, 0,
582 >                   myPotato, MPI_COMM_WORLD);
583            
474 –          MPI::COMM_WORLD.Send(writeLine, BUFFERSIZE, MPI_CHAR, 0,
475 –                               TAKE_THIS_TAG_CHAR);
584          } else {
585 <          strcpy( writeLine, "ATOM NOT FOUND ON THIS PROCESSOR");
586 <          MPI::COMM_WORLD.Send(writeLine, BUFFERSIZE, MPI_CHAR, 0,
587 <                               TAKE_THIS_TAG_CHAR);
585 >
586 >          MPI_Send(atomData6, 6, MPI_DOUBLE, 0,
587 >                   myPotato, MPI_COMM_WORLD);
588          }
589 +
590 +        myPotato++;  
591 +        currentIndex++;    
592        }
593      }
483 –  }
484 –  finalOut.flush();
485 –  sprintf( checkPointMsg,
486 –           "Sucessfully took a dump.\n");
487 –  MPIcheckPoint();
594  
595 <  if( worldRank == 0 ) finalOut.close();    
595 >    sprintf( checkPointMsg,
596 >             "Sucessfully took a dump.\n");
597 >    MPIcheckPoint();        
598 >    
599 >  }
600 >  
601   #endif // is_mpi
602   }
603 +
604 + #ifdef IS_MPI
605 +
606 + // a couple of functions to let us escape the write loop
607 +
608 + void dWrite::DieDieDie( void ){
609 +
610 +  MPI_Finalize();
611 +  exit (0);
612 + }
613 +
614 + #endif //is_mpi

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