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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 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>
12   #include "mpiSimulation.hpp"
13 < #define TAKE_THIS_TAG 0
13 >
14 > namespace dWrite{
15 >  void DieDieDie( void );
16 > }
17 >
18 > using namespace dWrite;
19   #endif //is_mpi
20  
21   #include "ReadWrite.hpp"
22   #include "simError.h"
23  
14 –
15 –
16 –
17 –
24   DumpWriter::DumpWriter( SimInfo* the_entry_plug ){
25  
26    entry_plug = the_entry_plug;
# Line 22 | 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 <    
30 <    outFile.open(outName, ios::out | ios::trunc );
31 <    
32 <    if( !outFile ){
33 <      
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      }
40 –  
41 –    //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 55 | 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;
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
79 <    
80 <  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 <      
101 > #endif
102  
103 <    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 );
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(),
114 <               dAtom->getJz());
115 <      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
118 <      strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
119 <      
120 <    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 <  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];
126 >  writeFrame(fileStreams, currentTime);
127  
128 <    
129 <  // write out header and node 0's coordinates
128 > #ifdef IS_MPI
129 >  finalOut.close();
130 > #endif
131 >        
132 > }
133  
134 <  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";
134 > void DumpWriter::writeFinal(double currentTime){
135  
136 <    masterIndex = 0;
137 <    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 <  }
136 >  ofstream finalOut;
137 >  vector<ofstream*> fileStreams;
138  
139 <  sprintf( checkPointMsg,
140 <           "Sucessfully wrote node 0's dump configuration.\n");
141 <  MPIcheckPoint();
188 <    
189 <  for (procIndex = 1; procIndex < mpiSim->getNumberProcessors();
190 <       procIndex++){
139 > #ifdef IS_MPI
140 >  if(worldRank == 0 ){
141 > #endif // is_mpi
142  
143 <    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 <    }
143 >    finalOut.open( entry_plug->finalName, ios::out | ios::trunc );
144  
145 <    else if( worldRank == procIndex ){
146 <
147 <      nodeAtomsStart = mpiSim->getMyAtomStart();
148 <      nodeAtomsEnd = mpiSim->getMyAtomEnd();
149 <
150 <      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 <      }
145 >    if( !finalOut ){
146 >      sprintf( painCave.errMsg,
147 >               "Could not open \"%s\" for final dump output.\n",
148 >               entry_plug->finalName );
149 >      painCave.isFatal = 1;
150 >      simError();
151      }
152 <      
153 <    sprintf(checkPointMsg,"Node %d sent dump configuration.",
287 <            procIndex);
288 <    MPIcheckPoint();
152 >
153 > #ifdef IS_MPI
154    }
290 –    
155   #endif // is_mpi
156 +  
157 +  fileStreams.push_back(&finalOut);  
158 +  writeFrame(fileStreams, currentTime);
159 +
160 + #ifdef IS_MPI
161 +  finalOut.close();
162 + #endif
163 +  
164   }
165  
166 + void DumpWriter::writeFrame( vector<ofstream*>& outFile, double currentTime ){
167  
168 +  const int BUFFERSIZE = 2000;
169 +  const int MINIBUFFERSIZE = 100;
170  
171 < void DumpWriter::writeFinal(){
171 >  char tempBuffer[BUFFERSIZE];  
172 >  char writeLine[BUFFERSIZE];
173  
174 +  int i, k;
175  
176 <  const int BUFFERSIZE = 2000;
300 <  char tempBuffer[500];
301 <  char writeLine[BUFFERSIZE];
176 > #ifdef IS_MPI
177    
178 <  char finalName[500];
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 i;
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;
308 –  int nAtoms = entry_plug->n_atoms;
232    Atom** atoms = entry_plug->atoms;
233 +  double pos[3], vel[3];
234 +
235 + #ifndef IS_MPI
236    
237 <  ofstream finalOut;
238 <  
239 < #ifdef IS_MPI
240 <  if(worldRank == 0 ){
241 < #endif // is_mpi
242 <    
243 <    strcpy( finalName, entry_plug->finalName );
244 <    
245 <    finalOut.open( finalName, ios::out | ios::trunc );
246 <    if( !finalOut ){
247 <      sprintf( painCave.errMsg,
248 <               "Could not open \"%s\" for final dump output.\n",
249 <               finalName );
250 <      painCave.isFatal = 1;
251 <      simError();
252 <    }
253 <    
254 <    // finalOut.setf( ios::scientific );
329 <    
330 < #ifdef IS_MPI
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 <  sprintf(checkPointMsg,"Opened file for final configuration\n");
334 <  MPIcheckPoint();  
335 <  
336 < #endif //is_mpi
257 >  for( i=0; i<nAtoms; i++ ){
258  
259 <    
259 >    atoms[i]->getPos(pos);
260 >    atoms[i]->getVel(vel);
261  
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 –      
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 376 | 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    }
382 –  finalOut.flush();
295  
296   #else // is_mpi
297  
298 <  int masterIndex;
299 <  int nodeAtomsStart;
300 <  int nodeAtomsEnd;
301 <  int mpiErr;
302 <  int sendError;
303 <  int procIndex;
304 <    
305 <  MPI_Status istatus[MPI_STATUS_SIZE];
298 >  /* code to find maximum tag value */
299 >  
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 <    
308 >  int haveError;
309 >
310 >  MPI_Status istatus;
311 >  int *AtomToProcMap = mpiSim->getAtomToProcMap();
312 >
313    // write out header and node 0's coordinates
314  
315    if( worldRank == 0 ){
399 –    finalOut << mpiSim->getTotAtoms() << "\n";
400 –      
401 –    finalOut << entry_plug->box_x << "\t"
402 –             << entry_plug->box_y << "\t"
403 –             << entry_plug->box_z << "\n";
404 –    
405 –    masterIndex = 0;
406 –    
407 –    for( i=0; i<nAtoms; i++ ){
408 –      
409 –      sprintf( tempBuffer,
410 –               "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
411 –               atoms[i]->getType(),
412 –               atoms[i]->getX(),
413 –               atoms[i]->getY(),
414 –               atoms[i]->getZ(),
415 –               atoms[i]->get_vx(),
416 –               atoms[i]->get_vy(),
417 –               atoms[i]->get_vz());
418 –      strcpy( writeLine, tempBuffer );
419 –        
420 –      if( atoms[i]->isDirectional() ){
421 –          
422 –        dAtom = (DirectionalAtom *)atoms[i];
423 –        dAtom->getQ( q );
424 –          
425 –        sprintf( tempBuffer,
426 –                 "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
427 –                 q[0],
428 –                 q[1],
429 –                 q[2],
430 –                 q[3],
431 –                 dAtom->getJx(),
432 –                 dAtom->getJy(),
433 –                 dAtom->getJz());
434 –        strcat( writeLine, tempBuffer );
435 –      }
436 –      else
437 –        strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
438 –        
439 –      finalOut << writeLine;
440 –      masterIndex++;
441 –    }
442 –    finalOut.flush();
443 –  }
444 –    
445 –  for (procIndex = 1; procIndex < mpiSim->getNumberProcessors();
446 –       procIndex++){
316  
317 <    if( worldRank == 0 ){
449 <        
450 <      mpiErr = MPI_Recv(&nodeAtomsStart,1,MPI_INT,procIndex,
451 <                        TAKE_THIS_TAG,MPI_COMM_WORLD,istatus);
317 >    // Node 0 needs a list of the magic potatoes for each processor;
318  
319 <      mpiErr = MPI_Recv(&nodeAtomsEnd,1,MPI_INT,procIndex,
320 <                        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);
319 >    nProc = mpiSim->getNumberProcessors();
320 >    potatoes = new int[nProc];
321  
322 <      // recieve the nodes writeLines
322 >    //write out the comment lines
323 >    for (i = 0; i < nProc; i++)
324 >      potatoes[i] = 0;
325 >    
326 >      for(k = 0; k < outFile.size(); k++){
327 >        *outFile[k] << mpiSim->getTotAtoms() << "\n";
328  
329 <      for ( i = nodeAtomsStart; i <= nodeAtomsEnd; i++){
330 <          
331 <        mpiErr = MPI_Recv(writeLine,BUFFERSIZE,MPI_CHAR,procIndex,
332 <                          TAKE_THIS_TAG,MPI_COMM_WORLD,istatus );
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 <        finalOut << writeLine;
335 <        masterIndex++;
336 <      }
334 >                         << entry_plug->Hmat[0][1] << "\t"
335 >                         << entry_plug->Hmat[1][1] << "\t"
336 >                         << entry_plug->Hmat[2][1] << ";\t"
337  
338 <      finalOut.flush();
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 <    else if( worldRank == procIndex ){
345 >    currentIndex = 0;
346  
347 <      nodeAtomsStart = mpiSim->getMyAtomStart();
348 <      nodeAtomsEnd = mpiSim->getMyAtomEnd();
347 >    for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) {
348 >      
349 >      // Get the Node number which has this atom;
350 >      
351 >      which_node = AtomToProcMap[i];
352 >      
353 >      if (which_node != 0) {
354 >
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 >
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 <      mpiErr = MPI_Send(&nodeAtomsStart,1,MPI_INT,0,TAKE_THIS_TAG,
495 <                        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();
371 >        myPotato++;
372  
373 <      // send current node's configuration line by line.
373 >        MPI_Recv(&isDirectional, 1, MPI_INT, which_node,
374 >                 myPotato, MPI_COMM_WORLD, &istatus);
375 >              
376 >        myPotato++;
377  
378 <      for( i=0; i<nAtoms; i++ ){
379 <          
380 <        sprintf( tempBuffer,
381 <                 "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
382 <                 atoms[i]->getType(),
383 <                 atoms[i]->getX(),
384 <                 atoms[i]->getY(),
385 <                 atoms[i]->getZ(),
386 <                 atoms[i]->get_vx(),
387 <                 atoms[i]->get_vy(),
388 <                 atoms[i]->get_vz());
389 <        strcpy( writeLine, tempBuffer );
390 <          
391 <        if( atoms[i]->isDirectional() ){
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[i];
521 <          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",
525 <                   q[0],
526 <                   q[1],
527 <                   q[2],
528 <                   q[3],
529 <                   dAtom->getJx(),
530 <                   dAtom->getJy(),
531 <                   dAtom->getJz());
532 <          strcat( writeLine, tempBuffer );
533 <        }
534 <        else
535 <          strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
400 >          atoms[local_index]->getPos(pos);
401 >          atoms[local_index]->getVel(vel);          
402            
403 <        mpiErr = MPI_Send(writeLine,BUFFERSIZE,MPI_CHAR,0,TAKE_THIS_TAG,
404 <                          MPI_COMM_WORLD);
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 +        
480 +      }
481 +      
482 +      for(k = 0; k < outFile.size(); k++)
483 +        *outFile[k] << writeLine;
484      }
485 +    
486 +    for(k = 0; k < outFile.size(); k++)
487 +      outFile[k]->flush();
488 +    
489 +    sprintf( checkPointMsg,
490 +             "Sucessfully took a dump.\n");
491 +    
492 +    MPIcheckPoint();        
493 +    
494 +    delete[] potatoes;
495 +    
496 +  } else {
497 +
498 +    // worldRank != 0, so I'm a remote node.  
499 +
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 <    sprintf(checkPointMsg,"Node %d sent dump configuration.",
508 <            procIndex);
509 <    MPIcheckPoint();
545 <  }
507 >      // Am I the node which has this atom?
508 >      
509 >      if (AtomToProcMap[i] == worldRank) {
510  
511 <  if( worldRank == 0 ) finalOut.close();
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 >        which_atom = i;
521  
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 +            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 +
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 +          
589 +        } else {
590 +
591 +          MPI_Send(atomData6, 6, MPI_DOUBLE, 0,
592 +                   myPotato, MPI_COMM_WORLD);
593 +        }
594 +
595 +        myPotato++;  
596 +        currentIndex++;    
597 +      }
598 +    }
599 +
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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