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root/group/trunk/OOPSE/libmdtools/DumpWriter.cpp
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Comparing:
branches/mmeineke/OOPSE/libmdtools/DumpWriter.cpp (file contents), Revision 377 by mmeineke, Fri Mar 21 17:42:12 2003 UTC vs.
trunk/OOPSE/libmdtools/DumpWriter.cpp (file contents), Revision 952 by tim, Fri Jan 16 21:55:39 2004 UTC

# Line 1 | Line 1
1 < #include <cstring>
1 > #define _FILE_OFFSET_BITS 64
2 >
3 > #include <string.h>
4   #include <iostream>
5   #include <fstream>
6 + #include <algorithm>
7 + #include <utility>
8  
9   #ifdef IS_MPI
10   #include <mpi.h>
11   #include "mpiSimulation.hpp"
12 < #define TAKE_THIS_TAG 0
12 >
13 > namespace dWrite{
14 >  void DieDieDie( void );
15 > }
16 >
17 > using namespace dWrite;
18   #endif //is_mpi
19  
20   #include "ReadWrite.hpp"
21   #include "simError.h"
22  
14 –
15 –
16 –
17 –
23   DumpWriter::DumpWriter( SimInfo* the_entry_plug ){
24  
25    entry_plug = the_entry_plug;
# Line 22 | 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 <    
30 <    outFile.open(outName, ios::out | ios::trunc );
31 <    
32 <    if( !outFile ){
33 <      
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      }
40 –  
41 –    //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 55 | 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;
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";
81 <    
82 <  outFile << currentTime << "\t"
83 <          << entry_plug->box_x << "\t"
84 <          << entry_plug->box_y << "\t"
85 <          << entry_plug->box_z << "\n";
86 <    
87 <  for( i=0; i<nAtoms; i++ ){
88 <      
103 > }
104  
105 <    sprintf( tempBuffer,
91 <             "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
92 <             atoms[i]->getType(),
93 <             atoms[i]->getX(),
94 <             atoms[i]->getY(),
95 <             atoms[i]->getZ(),
96 <             atoms[i]->get_vx(),
97 <             atoms[i]->get_vy(),
98 <             atoms[i]->get_vz());
99 <    strcpy( writeLine, tempBuffer );
105 > #endif
106  
107 <    if( atoms[i]->isDirectional() ){
108 <        
109 <      dAtom = (DirectionalAtom *)atoms[i];
110 <      dAtom->getQ( q );
111 <        
112 <      sprintf( tempBuffer,
113 <               "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
114 <               q[0],
115 <               q[1],
116 <               q[2],
117 <               q[3],
118 <               dAtom->getJx(),
119 <               dAtom->getJy(),
120 <               dAtom->getJz());
121 <      strcat( writeLine, tempBuffer );
107 > void DumpWriter::writeDump(double currentTime){
108 >
109 >  ofstream finalOut;
110 >  vector<ofstream*> fileStreams;
111 >
112 > #ifdef IS_MPI
113 >  if(worldRank == 0 ){
114 > #endif    
115 >    finalOut.open( entry_plug->finalName, ios::out | ios::trunc );
116 >    if( !finalOut ){
117 >      sprintf( painCave.errMsg,
118 >               "Could not open \"%s\" for final dump output.\n",
119 >               entry_plug->finalName );
120 >      painCave.isFatal = 1;
121 >      simError();
122      }
123 <    else
118 <      strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
119 <      
120 <    outFile << writeLine;
123 > #ifdef IS_MPI
124    }
125 <  outFile.flush();
125 > #endif // is_mpi
126  
127 < #else // is_mpi
127 >  fileStreams.push_back(&finalOut);
128 >  fileStreams.push_back(&dumpFile);
129  
130 <  int masterIndex;
127 <  int nodeAtomsStart;
128 <  int nodeAtomsEnd;
129 <  int mpiErr;
130 <  int sendError;
131 <  int procIndex;
132 <    
133 <  MPI_Status istatus[MPI_STATUS_SIZE];
130 >  writeFrame(fileStreams, currentTime);
131  
132 <    
133 <  // write out header and node 0's coordinates
132 > #ifdef IS_MPI
133 >  finalOut.close();
134 > #endif
135 >        
136 > }
137  
138 <  if( worldRank == 0 ){
139 <    outFile << mpiSim->getTotAtoms() << "\n";
140 <      
141 <    outFile << currentTime << "\t"
142 <            << entry_plug->box_x << "\t"
143 <            << entry_plug->box_y << "\t"
144 <            << entry_plug->box_z << "\n";
138 > void DumpWriter::writeFinal(double currentTime){
139  
140 <    masterIndex = 0;
141 <    for( i=0; i<nAtoms; i++ ){
148 <      
149 <      sprintf( tempBuffer,
150 <               "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
151 <               atoms[i]->getType(),
152 <               atoms[i]->getX(),
153 <               atoms[i]->getY(),
154 <               atoms[i]->getZ(),
155 <               atoms[i]->get_vx(),
156 <               atoms[i]->get_vy(),
157 <               atoms[i]->get_vz());
158 <      strcpy( writeLine, tempBuffer );
159 <        
160 <      if( atoms[i]->isDirectional() ){
161 <          
162 <        dAtom = (DirectionalAtom *)atoms[i];
163 <        dAtom->getQ( q );
164 <          
165 <        sprintf( tempBuffer,
166 <                 "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
167 <                 q[0],
168 <                 q[1],
169 <                 q[2],
170 <                 q[3],
171 <                 dAtom->getJx(),
172 <                 dAtom->getJy(),
173 <                 dAtom->getJz());
174 <        strcat( writeLine, tempBuffer );
175 <      }
176 <      else
177 <        strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
178 <        
179 <      outFile << writeLine;
180 <      masterIndex++;
181 <    }
182 <    outFile.flush();
183 <  }
140 >  ofstream finalOut;
141 >  vector<ofstream*> fileStreams;
142  
143 <  sprintf( checkPointMsg,
144 <           "Sucessfully wrote node 0's dump configuration.\n");
145 <  MPIcheckPoint();
188 <    
189 <  for (procIndex = 1; procIndex < mpiSim->getNumberProcessors();
190 <       procIndex++){
143 > #ifdef IS_MPI
144 >  if(worldRank == 0 ){
145 > #endif // is_mpi
146  
147 <    if( worldRank == 0 ){
193 <      
194 <      mpiErr = MPI_Recv(&nodeAtomsStart,1,MPI_INT,procIndex,
195 <                        TAKE_THIS_TAG,MPI_COMM_WORLD,istatus);
196 <      
197 <      mpiErr = MPI_Recv(&nodeAtomsEnd,1,MPI_INT,procIndex,
198 <                        TAKE_THIS_TAG,MPI_COMM_WORLD, istatus);
199 <      
200 <      // Make sure where node 0 is writing to, matches where the
201 <      // receiving node expects it to be.
202 <      
203 <      if (masterIndex != nodeAtomsStart){
204 <        sendError = 1;
205 <        mpiErr = MPI_Send(&sendError,1,MPI_INT,procIndex,TAKE_THIS_TAG,
206 <                          MPI_COMM_WORLD);
207 <        sprintf(painCave.errMsg,
208 <                "DumpWriter error: atoms start index (%d) for "
209 <                "node %d not equal to master index (%d)",
210 <                nodeAtomsStart,procIndex,masterIndex );
211 <        painCave.isFatal = 1;
212 <        simError();
213 <      }
214 <      
215 <      sendError = 0;
216 <      mpiErr = MPI_Send(&sendError,1,MPI_INT,procIndex,TAKE_THIS_TAG,
217 <                        MPI_COMM_WORLD);
218 <      
219 <      // recieve the nodes writeLines
220 <      
221 <      for ( i = nodeAtomsStart; i <= nodeAtomsEnd; i++){
222 <        
223 <        mpiErr = MPI_Recv(writeLine,BUFFERSIZE,MPI_CHAR,procIndex,
224 <                          TAKE_THIS_TAG,MPI_COMM_WORLD,istatus );
225 <        
226 <        outFile << writeLine;
227 <        masterIndex++;
228 <      }
229 <    }
147 >    finalOut.open( entry_plug->finalName, ios::out | ios::trunc );
148  
149 <    else if( worldRank == procIndex ){
150 <
151 <      nodeAtomsStart = mpiSim->getMyAtomStart();
152 <      nodeAtomsEnd = mpiSim->getMyAtomEnd();
153 <
154 <      mpiErr = MPI_Send(&nodeAtomsStart,1,MPI_INT,0,TAKE_THIS_TAG,
237 <                        MPI_COMM_WORLD);
238 <      mpiErr = MPI_Send(&nodeAtomsEnd,1,MPI_INT,0,TAKE_THIS_TAG,
239 <                        MPI_COMM_WORLD);
240 <        
241 <      sendError = -1;
242 <      mpiErr = MPI_Recv(&sendError,1,MPI_INT,0,TAKE_THIS_TAG,
243 <                        MPI_COMM_WORLD, istatus);
244 <
245 <      if (sendError) MPIcheckPoint();
246 <
247 <      // send current node's configuration line by line.
248 <
249 <      for( i=0; i<nAtoms; i++ ){
250 <
251 <        sprintf( tempBuffer,
252 <                 "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
253 <                 atoms[i]->getType(),
254 <                 atoms[i]->getX(),
255 <                 atoms[i]->getY(),
256 <                 atoms[i]->getZ(),
257 <                 atoms[i]->get_vx(),
258 <                 atoms[i]->get_vy(),
259 <                 atoms[i]->get_vz()); // check here.
260 <        strcpy( writeLine, tempBuffer );
261 <          
262 <        if( atoms[i]->isDirectional() ){
263 <            
264 <          dAtom = (DirectionalAtom *)atoms[i];
265 <          dAtom->getQ( q );
266 <            
267 <          sprintf( tempBuffer,
268 <                   "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
269 <                   q[0],
270 <                   q[1],
271 <                   q[2],
272 <                   q[3],
273 <                   dAtom->getJx(),
274 <                   dAtom->getJy(),
275 <                   dAtom->getJz());
276 <          strcat( writeLine, tempBuffer );
277 <        }
278 <        else
279 <          strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
280 <          
281 <        mpiErr = MPI_Send(writeLine,BUFFERSIZE,MPI_CHAR,0,TAKE_THIS_TAG,
282 <                          MPI_COMM_WORLD);
283 <      }
149 >    if( !finalOut ){
150 >      sprintf( painCave.errMsg,
151 >               "Could not open \"%s\" for final dump output.\n",
152 >               entry_plug->finalName );
153 >      painCave.isFatal = 1;
154 >      simError();
155      }
156 <      
157 <    sprintf(checkPointMsg,"Node %d sent dump configuration.",
287 <            procIndex);
288 <    MPIcheckPoint();
156 >
157 > #ifdef IS_MPI
158    }
290 –    
159   #endif // is_mpi
160 +  
161 +  fileStreams.push_back(&finalOut);  
162 +  writeFrame(fileStreams, currentTime);
163 +
164 + #ifdef IS_MPI
165 +  finalOut.close();
166 + #endif
167 +  
168   }
169  
170 + void DumpWriter::writeFrame( vector<ofstream*>& outFile, double currentTime ){
171  
172 +  const int BUFFERSIZE = 2000;
173 +  const int MINIBUFFERSIZE = 100;
174  
175 < void DumpWriter::writeFinal(){
175 >  char tempBuffer[BUFFERSIZE];  
176 >  char writeLine[BUFFERSIZE];
177  
178 +  int i, k;
179  
180 <  const int BUFFERSIZE = 2000;
300 <  char tempBuffer[500];
301 <  char writeLine[BUFFERSIZE];
180 > #ifdef IS_MPI
181    
182 <  char finalName[500];
182 >  /*********************************************************************
183 >   * Documentation?  You want DOCUMENTATION?
184 >   *
185 >   * Why all the potatoes below?  
186 >   *
187 >   * To make a long story short, the original version of DumpWriter
188 >   * worked in the most inefficient way possible.  Node 0 would
189 >   * poke each of the node for an individual atom's formatted data
190 >   * as node 0 worked its way down the global index. This was particularly
191 >   * inefficient since the method blocked all processors at every atom
192 >   * (and did it twice!).
193 >   *
194 >   * An intermediate version of DumpWriter could be described from Node
195 >   * zero's perspective as follows:
196 >   *
197 >   *  1) Have 100 of your friends stand in a circle.
198 >   *  2) When you say go, have all of them start tossing potatoes at
199 >   *     you (one at a time).
200 >   *  3) Catch the potatoes.
201 >   *
202 >   * It was an improvement, but MPI has buffers and caches that could
203 >   * best be described in this analogy as "potato nets", so there's no
204 >   * need to block the processors atom-by-atom.
205 >   *
206 >   * This new and improved DumpWriter works in an even more efficient
207 >   * way:
208 >   *
209 >   *  1) Have 100 of your friend stand in a circle.
210 >   *  2) When you say go, have them start tossing 5-pound bags of
211 >   *     potatoes at you.
212 >   *  3) Once you've caught a friend's bag of potatoes,
213 >   *     toss them a spud to let them know they can toss another bag.
214 >   *
215 >   * How's THAT for documentation?
216 >   *
217 >   *********************************************************************/
218  
219 <  int i;
219 >  int *potatoes;
220 >  int myPotato;
221 >
222 >  int nProc;
223 >  int j, which_node, done, which_atom, local_index, currentIndex;
224 >  double atomData6[6];
225 >  double atomData13[13];
226 >  int isDirectional;
227 >  char* atomTypeString;
228 >  char MPIatomTypeString[MINIBUFFERSIZE];
229 >
230 > #else //is_mpi
231 >  int nAtoms = entry_plug->n_atoms;
232 > #endif //is_mpi
233 >
234    double q[4];
235    DirectionalAtom* dAtom;
308 –  int nAtoms = entry_plug->n_atoms;
236    Atom** atoms = entry_plug->atoms;
237 +  double pos[3], vel[3];
238 +
239 + #ifndef IS_MPI
240    
241 <  ofstream finalOut;
242 <  
243 < #ifdef IS_MPI
244 <  if(worldRank == 0 ){
245 < #endif // is_mpi
246 <    
247 <    strcpy( finalName, entry_plug->finalName );
248 <    
249 <    finalOut.open( finalName, ios::out | ios::trunc );
250 <    if( !finalOut ){
251 <      sprintf( painCave.errMsg,
252 <               "Could not open \"%s\" for final dump output.\n",
253 <               finalName );
254 <      painCave.isFatal = 1;
255 <      simError();
256 <    }
257 <    
258 <    // finalOut.setf( ios::scientific );
329 <    
330 < #ifdef IS_MPI
241 >  for(k = 0; k < outFile.size(); k++){
242 >    *outFile[k] << nAtoms << "\n";
243 >
244 >    *outFile[k] << currentTime << ";\t"
245 >               << entry_plug->Hmat[0][0] << "\t"
246 >                     << entry_plug->Hmat[1][0] << "\t"
247 >                     << entry_plug->Hmat[2][0] << ";\t"
248 >              
249 >               << entry_plug->Hmat[0][1] << "\t"
250 >                     << entry_plug->Hmat[1][1] << "\t"
251 >                     << entry_plug->Hmat[2][1] << ";\t"
252 >
253 >                     << entry_plug->Hmat[0][2] << "\t"
254 >                     << entry_plug->Hmat[1][2] << "\t"
255 >                     << entry_plug->Hmat[2][2] << ";";
256 >
257 >    //write out additional parameters, such as chi and eta
258 >    *outFile[k] << entry_plug->the_integrator->getAdditionalParameters() << endl;
259    }
260    
261 <  sprintf(checkPointMsg,"Opened file for final configuration\n");
334 <  MPIcheckPoint();  
335 <  
336 < #endif //is_mpi
261 >  for( i=0; i<nAtoms; i++ ){
262  
263 <    
263 >    atoms[i]->getPos(pos);
264 >    atoms[i]->getVel(vel);
265  
340 – #ifndef IS_MPI
341 –    
342 –  finalOut << nAtoms << "\n";
343 –    
344 –  finalOut << entry_plug->box_x << "\t"
345 –           << entry_plug->box_y << "\t"
346 –           << entry_plug->box_z << "\n";
347 –    
348 –  for( i=0; i<nAtoms; i++ ){
349 –      
266      sprintf( tempBuffer,
267               "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
268               atoms[i]->getType(),
269 <             atoms[i]->getX(),
270 <             atoms[i]->getY(),
271 <             atoms[i]->getZ(),
272 <             atoms[i]->get_vx(),
273 <             atoms[i]->get_vy(),
274 <             atoms[i]->get_vz());
269 >             pos[0],
270 >             pos[1],
271 >             pos[2],
272 >             vel[0],
273 >             vel[1],
274 >             vel[2]);
275      strcpy( writeLine, tempBuffer );
276  
277      if( atoms[i]->isDirectional() ){
278 <        
278 >
279        dAtom = (DirectionalAtom *)atoms[i];
280        dAtom->getQ( q );
281 <        
281 >
282        sprintf( tempBuffer,
283                 "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
284                 q[0],
# Line 376 | Line 292 | void DumpWriter::writeFinal(){
292      }
293      else
294        strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
295 <      
296 <    finalOut << writeLine;
295 >
296 >    for(k = 0; k < outFile.size(); k++)
297 >      *outFile[k] << writeLine;
298    }
382 –  finalOut.flush();
299  
300   #else // is_mpi
301  
302 <  int masterIndex;
303 <  int nodeAtomsStart;
304 <  int nodeAtomsEnd;
305 <  int mpiErr;
306 <  int sendError;
307 <  int procIndex;
308 <    
309 <  MPI_Status istatus[MPI_STATUS_SIZE];
302 >  /* code to find maximum tag value */
303 >  
304 >  int *tagub, flag, MAXTAG;
305 >  MPI_Attr_get(MPI_COMM_WORLD, MPI_TAG_UB, &tagub, &flag);
306 >  if (flag) {
307 >    MAXTAG = *tagub;
308 >  } else {
309 >    MAXTAG = 32767;
310 >  }  
311  
312 <    
312 >  int haveError;
313 >
314 >  MPI_Status istatus;
315 >  int *AtomToProcMap = mpiSim->getAtomToProcMap();
316 >
317    // write out header and node 0's coordinates
318  
319    if( worldRank == 0 ){
320 <    finalOut << mpiSim->getTotAtoms() << "\n";
321 <      
322 <    finalOut << entry_plug->box_x << "\t"
323 <             << entry_plug->box_y << "\t"
324 <             << entry_plug->box_z << "\n";
320 >
321 >    // Node 0 needs a list of the magic potatoes for each processor;
322 >
323 >    nProc = mpiSim->getNumberProcessors();
324 >    potatoes = new int[nProc];
325 >
326 >    //write out the comment lines
327 >    for (i = 0; i < nProc; i++)
328 >      potatoes[i] = 0;
329      
330 <    masterIndex = 0;
331 <    
332 <    for( i=0; i<nAtoms; i++ ){
330 >      for(k = 0; k < outFile.size(); k++){
331 >        *outFile[k] << mpiSim->getTotAtoms() << "\n";
332 >
333 >        *outFile[k] << currentTime << ";\t"
334 >                         << entry_plug->Hmat[0][0] << "\t"
335 >                         << entry_plug->Hmat[1][0] << "\t"
336 >                         << entry_plug->Hmat[2][0] << ";\t"
337 >
338 >                         << entry_plug->Hmat[0][1] << "\t"
339 >                         << entry_plug->Hmat[1][1] << "\t"
340 >                         << entry_plug->Hmat[2][1] << ";\t"
341 >
342 >                         << entry_plug->Hmat[0][2] << "\t"
343 >                         << entry_plug->Hmat[1][2] << "\t"
344 >                         << entry_plug->Hmat[2][2] << ";";
345 >  
346 >        *outFile[k] << entry_plug->the_integrator->getAdditionalParameters() << endl;
347 >    }
348 >
349 >    currentIndex = 0;
350 >
351 >    for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) {
352        
353 <      sprintf( tempBuffer,
354 <               "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
355 <               atoms[i]->getType(),
356 <               atoms[i]->getX(),
357 <               atoms[i]->getY(),
358 <               atoms[i]->getZ(),
359 <               atoms[i]->get_vx(),
360 <               atoms[i]->get_vy(),
361 <               atoms[i]->get_vz());
362 <      strcpy( writeLine, tempBuffer );
353 >      // Get the Node number which has this atom;
354 >      
355 >      which_node = AtomToProcMap[i];
356 >      
357 >      if (which_node != 0) {
358 >
359 >        if (potatoes[which_node] + 3 >= MAXTAG) {
360 >          // The potato was going to exceed the maximum value,
361 >          // so wrap this processor potato back to 0:        
362 >
363 >          potatoes[which_node] = 0;          
364 >          MPI_Send(0, 1, MPI_INT, which_node, 0, MPI_COMM_WORLD);
365 >          
366 >        }
367 >
368 >        myPotato = potatoes[which_node];        
369 >        
370 >        MPI_Recv(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, which_node,
371 >                 myPotato, MPI_COMM_WORLD, &istatus);
372 >        
373 >        atomTypeString = MPIatomTypeString;
374          
375 <      if( atoms[i]->isDirectional() ){
375 >        myPotato++;
376 >
377 >        MPI_Recv(&isDirectional, 1, MPI_INT, which_node,
378 >                 myPotato, MPI_COMM_WORLD, &istatus);
379 >              
380 >        myPotato++;
381 >
382 >        if (isDirectional) {          
383 >          MPI_Recv(atomData13, 13, MPI_DOUBLE, which_node,
384 >                   myPotato, MPI_COMM_WORLD, &istatus);
385 >        } else {
386 >          MPI_Recv(atomData6, 6, MPI_DOUBLE, which_node,
387 >                   myPotato, MPI_COMM_WORLD, &istatus);          
388 >        }
389 >        
390 >        myPotato++;
391 >        potatoes[which_node] = myPotato;
392 >
393 >      } else {
394 >        
395 >        haveError = 0;
396 >        which_atom = i;
397 >        
398 >        //local_index = -1;
399 >
400 >        //for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) {
401 >        //  if (atoms[j]->getGlobalIndex() == which_atom) local_index = j;
402 >        //}
403 >        
404 >        //if (local_index != -1) {
405            
406 <        dAtom = (DirectionalAtom *)atoms[i];
407 <        dAtom->getQ( q );
406 >          local_index = indexArray[currentIndex].first;        
407 >          
408 >          if (which_atom == indexArray[currentIndex].second) {
409 >            
410 >            atomTypeString = atoms[local_index]->getType();
411 >            
412 >          atoms[local_index]->getPos(pos);
413 >          atoms[local_index]->getVel(vel);          
414            
415 <        sprintf( tempBuffer,
416 <                 "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
417 <                 q[0],
418 <                 q[1],
419 <                 q[2],
420 <                 q[3],
421 <                 dAtom->getJx(),
422 <                 dAtom->getJy(),
423 <                 dAtom->getJz());
424 <        strcat( writeLine, tempBuffer );
415 >          atomData6[0] = pos[0];
416 >          atomData6[1] = pos[1];
417 >          atomData6[2] = pos[2];
418 >
419 >          atomData6[3] = vel[0];
420 >          atomData6[4] = vel[1];
421 >          atomData6[5] = vel[2];
422 >          
423 >          isDirectional = 0;
424 >
425 >          if( atoms[local_index]->isDirectional() ){
426 >
427 >            isDirectional = 1;
428 >            
429 >            dAtom = (DirectionalAtom *)atoms[local_index];
430 >            dAtom->getQ( q );
431 >
432 >            for (int j = 0; j < 6 ; j++)
433 >              atomData13[j] = atomData6[j];            
434 >            
435 >            atomData13[6] = q[0];
436 >            atomData13[7] = q[1];
437 >            atomData13[8] = q[2];
438 >            atomData13[9] = q[3];
439 >            
440 >            atomData13[10] = dAtom->getJx();
441 >            atomData13[11] = dAtom->getJy();
442 >            atomData13[12] = dAtom->getJz();
443 >          }
444 >          
445 >        } else {
446 >          sprintf(painCave.errMsg,
447 >                  "Atom %d not found on processor %d, currentIndex = %d, local_index = %d\n",
448 >                  which_atom, worldRank, currentIndex, local_index );
449 >          haveError= 1;
450 >          simError();
451 >        }
452 >        
453 >        if(haveError) DieDieDie();
454 >        
455 >        currentIndex++;
456        }
457 <      else
457 >      // If we've survived to here, format the line:
458 >      
459 >      if (!isDirectional) {
460 >        
461 >        sprintf( writeLine,
462 >                 "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
463 >                 atomTypeString,
464 >                 atomData6[0],
465 >                 atomData6[1],
466 >                 atomData6[2],
467 >                 atomData6[3],
468 >                 atomData6[4],
469 >                 atomData6[5]);
470 >        
471          strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
472          
473 <      finalOut << writeLine;
474 <      masterIndex++;
473 >      } else {
474 >        
475 >        sprintf( writeLine,
476 >                 "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
477 >                 atomTypeString,
478 >                 atomData13[0],
479 >                 atomData13[1],
480 >                 atomData13[2],
481 >                 atomData13[3],
482 >                 atomData13[4],
483 >                 atomData13[5],
484 >                 atomData13[6],
485 >                 atomData13[7],
486 >                 atomData13[8],
487 >                 atomData13[9],
488 >                 atomData13[10],
489 >                 atomData13[11],
490 >                 atomData13[12]);
491 >        
492 >      }
493 >      
494 >      for(k = 0; k < outFile.size(); k++)
495 >        *outFile[k] << writeLine;
496      }
442 –    finalOut.flush();
443 –  }
497      
498 <  for (procIndex = 1; procIndex < mpiSim->getNumberProcessors();
499 <       procIndex++){
498 >    for(k = 0; k < outFile.size(); k++)
499 >      outFile[k]->flush();
500 >    
501 >    sprintf( checkPointMsg,
502 >             "Sucessfully took a dump.\n");
503 >    
504 >    MPIcheckPoint();        
505 >    
506 >    delete[] potatoes;
507 >    
508 >  } else {
509  
510 <    if( worldRank == 0 ){
449 <        
450 <      mpiErr = MPI_Recv(&nodeAtomsStart,1,MPI_INT,procIndex,
451 <                        TAKE_THIS_TAG,MPI_COMM_WORLD,istatus);
510 >    // worldRank != 0, so I'm a remote node.  
511  
512 <      mpiErr = MPI_Recv(&nodeAtomsEnd,1,MPI_INT,procIndex,
454 <                        TAKE_THIS_TAG,MPI_COMM_WORLD, istatus);
455 <        
456 <      // Make sure where node 0 is writing to, matches where the
457 <      // receiving node expects it to be.
458 <        
459 <      if (masterIndex != nodeAtomsStart){
460 <        sendError = 1;
461 <        mpiErr = MPI_Send(&sendError,1,MPI_INT,procIndex,TAKE_THIS_TAG,
462 <                          MPI_COMM_WORLD);
463 <        sprintf(painCave.errMsg,
464 <                "DumpWriter error: atoms start index (%d) for "
465 <                "node %d not equal to master index (%d)",
466 <                nodeAtomsStart,procIndex,masterIndex );
467 <        painCave.isFatal = 1;
468 <        simError();
469 <      }
470 <        
471 <      sendError = 0;
472 <      mpiErr = MPI_Send(&sendError,1,MPI_INT,procIndex,TAKE_THIS_TAG,
473 <                        MPI_COMM_WORLD);
512 >    // Set my magic potato to 0:
513  
514 <      // recieve the nodes writeLines
514 >    myPotato = 0;
515 >    currentIndex = 0;
516 >    
517 >    for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) {
518 >      
519 >      // Am I the node which has this atom?
520 >      
521 >      if (AtomToProcMap[i] == worldRank) {
522  
523 <      for ( i = nodeAtomsStart; i <= nodeAtomsEnd; i++){
523 >        if (myPotato + 3 >= MAXTAG) {
524            
525 <        mpiErr = MPI_Recv(writeLine,BUFFERSIZE,MPI_CHAR,procIndex,
526 <                          TAKE_THIS_TAG,MPI_COMM_WORLD,istatus );
525 >          // The potato was going to exceed the maximum value,
526 >          // so wrap this processor potato back to 0 (and block until
527 >          // node 0 says we can go:
528 >          
529 >          MPI_Recv(&myPotato, 1, MPI_INT, 0, 0, MPI_COMM_WORLD, &istatus);
530 >          
531 >        }
532 >        which_atom = i;
533  
534 <        finalOut << writeLine;
483 <        masterIndex++;
484 <      }
534 >        //local_index = -1;
535  
536 <      finalOut.flush();
537 <    }
536 >        //for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) {
537 >        // if (atoms[j]->getGlobalIndex() == which_atom) local_index = j;
538 >        //}
539 >        
540 >        //if (local_index != -1) {
541  
542 <    else if( worldRank == procIndex ){
542 >        local_index = indexArray[currentIndex].first;        
543 >                
544 >        if (which_atom == indexArray[currentIndex].second) {
545 >        
546 >          atomTypeString = atoms[local_index]->getType();
547 >          
548 >          atoms[local_index]->getPos(pos);
549 >          atoms[local_index]->getVel(vel);
550 >          
551 >          atomData6[0] = pos[0];
552 >          atomData6[1] = pos[1];
553 >          atomData6[2] = pos[2];
554  
555 <      nodeAtomsStart = mpiSim->getMyAtomStart();
556 <      nodeAtomsEnd = mpiSim->getMyAtomEnd();
557 <        
558 <      mpiErr = MPI_Send(&nodeAtomsStart,1,MPI_INT,0,TAKE_THIS_TAG,
559 <                        MPI_COMM_WORLD);
496 <      mpiErr = MPI_Send(&nodeAtomsEnd,1,MPI_INT,0,TAKE_THIS_TAG,
497 <                        MPI_COMM_WORLD);
498 <        
499 <      mpiErr = MPI_Recv(&sendError,1,MPI_INT,0,TAKE_THIS_TAG,
500 <                        MPI_COMM_WORLD, istatus);
501 <      if (sendError) MPIcheckPoint();
555 >          atomData6[3] = vel[0];
556 >          atomData6[4] = vel[1];
557 >          atomData6[5] = vel[2];
558 >          
559 >          isDirectional = 0;
560  
561 <      // send current node's configuration line by line.
561 >          if( atoms[local_index]->isDirectional() ){
562  
563 <      for( i=0; i<nAtoms; i++ ){
564 <          
565 <        sprintf( tempBuffer,
566 <                 "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
567 <                 atoms[i]->getType(),
568 <                 atoms[i]->getX(),
569 <                 atoms[i]->getY(),
570 <                 atoms[i]->getZ(),
571 <                 atoms[i]->get_vx(),
572 <                 atoms[i]->get_vy(),
573 <                 atoms[i]->get_vz());
574 <        strcpy( writeLine, tempBuffer );
575 <          
576 <        if( atoms[i]->isDirectional() ){
577 <            
578 <          dAtom = (DirectionalAtom *)atoms[i];
579 <          dAtom->getQ( q );
580 <            
581 <          sprintf( tempBuffer,
582 <                   "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
583 <                   q[0],
584 <                   q[1],
585 <                   q[2],
586 <                   q[3],
529 <                   dAtom->getJx(),
530 <                   dAtom->getJy(),
531 <                   dAtom->getJz());
532 <          strcat( writeLine, tempBuffer );
563 >            isDirectional = 1;
564 >            
565 >            dAtom = (DirectionalAtom *)atoms[local_index];
566 >            dAtom->getQ( q );
567 >            
568 >            for (int j = 0; j < 6 ; j++)
569 >              atomData13[j] = atomData6[j];
570 >            
571 >            atomData13[6] = q[0];
572 >            atomData13[7] = q[1];
573 >            atomData13[8] = q[2];
574 >            atomData13[9] = q[3];
575 >  
576 >            atomData13[10] = dAtom->getJx();
577 >            atomData13[11] = dAtom->getJy();
578 >            atomData13[12] = dAtom->getJz();
579 >          }
580 >
581 >        } else {
582 >          sprintf(painCave.errMsg,
583 >                  "Atom %d not found on processor %d, currentIndex = %d, local_index = %d\n",
584 >                  which_atom, worldRank, currentIndex, local_index );
585 >          haveError= 1;
586 >          simError();
587          }
588 <        else
589 <          strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
590 <          
591 <        mpiErr = MPI_Send(writeLine,BUFFERSIZE,MPI_CHAR,0,TAKE_THIS_TAG,
592 <                          MPI_COMM_WORLD);
588 >        
589 >        strncpy(MPIatomTypeString, atomTypeString, MINIBUFFERSIZE);
590 >
591 >        // null terminate the string before sending (just in case):
592 >        MPIatomTypeString[MINIBUFFERSIZE-1] = '\0';
593 >
594 >        MPI_Send(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, 0,
595 >                             myPotato, MPI_COMM_WORLD);
596 >        
597 >        myPotato++;
598 >
599 >        MPI_Send(&isDirectional, 1, MPI_INT, 0,
600 >                             myPotato, MPI_COMM_WORLD);
601 >        
602 >        myPotato++;
603 >        
604 >        if (isDirectional) {
605 >
606 >          MPI_Send(atomData13, 13, MPI_DOUBLE, 0,
607 >                   myPotato, MPI_COMM_WORLD);
608 >          
609 >        } else {
610 >
611 >          MPI_Send(atomData6, 6, MPI_DOUBLE, 0,
612 >                   myPotato, MPI_COMM_WORLD);
613 >        }
614 >
615 >        myPotato++;  
616 >        currentIndex++;    
617        }
618      }
541 –      
542 –    sprintf(checkPointMsg,"Node %d sent dump configuration.",
543 –            procIndex);
544 –    MPIcheckPoint();
545 –  }
619  
620 <  if( worldRank == 0 ) finalOut.close();
621 <
620 >    sprintf( checkPointMsg,
621 >             "Sucessfully took a dump.\n");
622 >    MPIcheckPoint();        
623      
624 +  }
625 +  
626   #endif // is_mpi
627   }
628 +
629 + #ifdef IS_MPI
630 +
631 + // a couple of functions to let us escape the write loop
632 +
633 + void dWrite::DieDieDie( void ){
634 +
635 +  MPI_Finalize();
636 +  exit (0);
637 + }
638 +
639 + #endif //is_mpi

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