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root/group/trunk/OOPSE/libmdtools/DumpWriter.cpp
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Comparing trunk/OOPSE/libmdtools/DumpWriter.cpp (file contents):
Revision 378 by mmeineke, Fri Mar 21 17:42:12 2003 UTC vs.
Revision 1097 by gezelter, Mon Apr 12 20:32:20 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 <        
103 <      dAtom = (DirectionalAtom *)atoms[i];
104 <      dAtom->getQ( q );
105 <        
106 <      sprintf( tempBuffer,
107 <               "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
108 <               q[0],
109 <               q[1],
110 <               q[2],
111 <               q[3],
112 <               dAtom->getJx(),
113 <               dAtom->getJy(),
114 <               dAtom->getJz());
115 <      strcat( writeLine, tempBuffer );
116 <    }
117 <    else
118 <      strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
119 <      
120 <    outFile << writeLine;
121 <  }
122 <  outFile.flush();
105 >  ofstream finalOut;
106 >  vector<ofstream*> fileStreams;
107  
108 < #else // is_mpi
109 <
110 <  int masterIndex;
111 <  int nodeAtomsStart;
112 <  int nodeAtomsEnd;
113 <  int mpiErr;
114 <  int sendError;
115 <  int procIndex;
116 <    
117 <  MPI_Status istatus[MPI_STATUS_SIZE];
134 <
135 <    
136 <  // write out header and node 0's coordinates
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";
145 <
146 <    masterIndex = 0;
147 <    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++;
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 <    outFile.flush();
119 > #ifdef IS_MPI
120    }
121 + #endif // is_mpi
122  
123 <  sprintf( checkPointMsg,
124 <           "Sucessfully wrote node 0's dump configuration.\n");
187 <  MPIcheckPoint();
188 <    
189 <  for (procIndex = 1; procIndex < mpiSim->getNumberProcessors();
190 <       procIndex++){
191 <
192 <    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 <    }
123 >  fileStreams.push_back(&finalOut);
124 >  fileStreams.push_back(&dumpFile);
125  
126 <    else if( worldRank == procIndex ){
126 >  writeFrame(fileStreams, currentTime);
127  
128 <      nodeAtomsStart = mpiSim->getMyAtomStart();
129 <      nodeAtomsEnd = mpiSim->getMyAtomEnd();
128 > #ifdef IS_MPI
129 >  finalOut.close();
130 > #endif
131 >        
132 > }
133  
134 <      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);
134 > void DumpWriter::writeFinal(double currentTime){
135  
136 <      if (sendError) MPIcheckPoint();
136 >  ofstream finalOut;
137 >  vector<ofstream*> fileStreams;
138  
139 <      // send current node's configuration line by line.
139 > #ifdef IS_MPI
140 >  if(worldRank == 0 ){
141 > #endif // is_mpi
142  
143 <      for( i=0; i<nAtoms; i++ ){
143 >    finalOut.open( entry_plug->finalName, ios::out | ios::trunc );
144  
145 <        sprintf( tempBuffer,
146 <                 "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
147 <                 atoms[i]->getType(),
148 <                 atoms[i]->getX(),
149 <                 atoms[i]->getY(),
150 <                 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;
216 <  double q[4];
217 <  DirectionalAtom* dAtom;
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], ji[3];
231 +  DirectionalAtom* dAtom;
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 >      dAtom->getJ( ji );
278 >
279        sprintf( tempBuffer,
280                 "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
281                 q[0],
282                 q[1],
283                 q[2],
284                 q[3],
285 <               dAtom->getJx(),
286 <               dAtom->getJy(),
287 <               dAtom->getJz());
285 >               ji[0],
286 >               ji[1],
287 >               ji[2]);
288        strcat( writeLine, tempBuffer );
289      }
290      else
291        strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
292 <      
293 <    finalOut << writeLine;
292 >
293 >    for(k = 0; k < outFile.size(); k++)
294 >      *outFile[k] << writeLine;
295    }
382 –  finalOut.flush();
296  
297   #else // is_mpi
298  
299 <  int masterIndex;
300 <  int nodeAtomsStart;
301 <  int nodeAtomsEnd;
302 <  int mpiErr;
303 <  int sendError;
304 <  int procIndex;
305 <    
306 <  MPI_Status istatus[MPI_STATUS_SIZE];
299 >  /* code to find maximum tag value */
300 >  
301 >  int *tagub, flag, MAXTAG;
302 >  MPI_Attr_get(MPI_COMM_WORLD, MPI_TAG_UB, &tagub, &flag);
303 >  if (flag) {
304 >    MAXTAG = *tagub;
305 >  } else {
306 >    MAXTAG = 32767;
307 >  }  
308  
309 <    
309 >  int haveError;
310 >
311 >  MPI_Status istatus;
312 >  int *AtomToProcMap = mpiSim->getAtomToProcMap();
313 >
314    // write out header and node 0's coordinates
315  
316    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++){
317  
318 <    if( worldRank == 0 ){
449 <        
450 <      mpiErr = MPI_Recv(&nodeAtomsStart,1,MPI_INT,procIndex,
451 <                        TAKE_THIS_TAG,MPI_COMM_WORLD,istatus);
318 >    // Node 0 needs a list of the magic potatoes for each processor;
319  
320 <      mpiErr = MPI_Recv(&nodeAtomsEnd,1,MPI_INT,procIndex,
321 <                        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);
320 >    nProc = mpiSim->getNumberProcessors();
321 >    potatoes = new int[nProc];
322  
323 <      // recieve the nodes writeLines
323 >    //write out the comment lines
324 >    for (i = 0; i < nProc; i++)
325 >      potatoes[i] = 0;
326 >    
327 >      for(k = 0; k < outFile.size(); k++){
328 >        *outFile[k] << mpiSim->getTotAtoms() << "\n";
329  
330 <      for ( i = nodeAtomsStart; i <= nodeAtomsEnd; i++){
331 <          
332 <        mpiErr = MPI_Recv(writeLine,BUFFERSIZE,MPI_CHAR,procIndex,
333 <                          TAKE_THIS_TAG,MPI_COMM_WORLD,istatus );
330 >        *outFile[k] << currentTime << ";\t"
331 >                         << entry_plug->Hmat[0][0] << "\t"
332 >                         << entry_plug->Hmat[1][0] << "\t"
333 >                         << entry_plug->Hmat[2][0] << ";\t"
334  
335 <        finalOut << writeLine;
336 <        masterIndex++;
337 <      }
335 >                         << entry_plug->Hmat[0][1] << "\t"
336 >                         << entry_plug->Hmat[1][1] << "\t"
337 >                         << entry_plug->Hmat[2][1] << ";\t"
338  
339 <      finalOut.flush();
339 >                         << entry_plug->Hmat[0][2] << "\t"
340 >                         << entry_plug->Hmat[1][2] << "\t"
341 >                         << entry_plug->Hmat[2][2] << ";";
342 >  
343 >        *outFile[k] << entry_plug->the_integrator->getAdditionalParameters() << endl;
344      }
345  
346 <    else if( worldRank == procIndex ){
346 >    currentIndex = 0;
347  
348 <      nodeAtomsStart = mpiSim->getMyAtomStart();
349 <      nodeAtomsEnd = mpiSim->getMyAtomEnd();
348 >    for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) {
349 >      
350 >      // Get the Node number which has this atom;
351 >      
352 >      which_node = AtomToProcMap[i];
353 >      
354 >      if (which_node != 0) {
355 >
356 >        if (potatoes[which_node] + 3 >= MAXTAG) {
357 >          // The potato was going to exceed the maximum value,
358 >          // so wrap this processor potato back to 0:        
359 >
360 >          potatoes[which_node] = 0;          
361 >          MPI_Send(0, 1, MPI_INT, which_node, 0, MPI_COMM_WORLD);
362 >          
363 >        }
364 >
365 >        myPotato = potatoes[which_node];        
366 >        
367 >        MPI_Recv(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, which_node,
368 >                 myPotato, MPI_COMM_WORLD, &istatus);
369 >        
370 >        atomTypeString = MPIatomTypeString;
371          
372 <      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();
372 >        myPotato++;
373  
374 <      // send current node's configuration line by line.
374 >        MPI_Recv(&isDirectional, 1, MPI_INT, which_node,
375 >                 myPotato, MPI_COMM_WORLD, &istatus);
376 >              
377 >        myPotato++;
378  
379 <      for( i=0; i<nAtoms; i++ ){
380 <          
381 <        sprintf( tempBuffer,
382 <                 "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
383 <                 atoms[i]->getType(),
384 <                 atoms[i]->getX(),
385 <                 atoms[i]->getY(),
386 <                 atoms[i]->getZ(),
387 <                 atoms[i]->get_vx(),
388 <                 atoms[i]->get_vy(),
389 <                 atoms[i]->get_vz());
390 <        strcpy( writeLine, tempBuffer );
391 <          
392 <        if( atoms[i]->isDirectional() ){
379 >        if (isDirectional) {          
380 >          MPI_Recv(atomData13, 13, MPI_DOUBLE, which_node,
381 >                   myPotato, MPI_COMM_WORLD, &istatus);
382 >        } else {
383 >          MPI_Recv(atomData6, 6, MPI_DOUBLE, which_node,
384 >                   myPotato, MPI_COMM_WORLD, &istatus);          
385 >        }
386 >        
387 >        myPotato++;
388 >        potatoes[which_node] = myPotato;
389 >
390 >      } else {
391 >        
392 >        haveError = 0;
393 >        which_atom = i;
394 >        
395 >          local_index = indexArray[currentIndex].first;        
396 >          
397 >          if (which_atom == indexArray[currentIndex].second) {
398              
399 <          dAtom = (DirectionalAtom *)atoms[i];
521 <          dAtom->getQ( q );
399 >            atomTypeString = atoms[local_index]->getType();
400              
401 <          sprintf( tempBuffer,
402 <                   "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
403 <                   q[0],
404 <                   q[1],
405 <                   q[2],
406 <                   q[3],
407 <                   dAtom->getJx(),
408 <                   dAtom->getJy(),
409 <                   dAtom->getJz());
410 <          strcat( writeLine, tempBuffer );
401 >          atoms[local_index]->getPos(pos);
402 >          atoms[local_index]->getVel(vel);          
403 >          
404 >          atomData6[0] = pos[0];
405 >          atomData6[1] = pos[1];
406 >          atomData6[2] = pos[2];
407 >
408 >          atomData6[3] = vel[0];
409 >          atomData6[4] = vel[1];
410 >          atomData6[5] = vel[2];
411 >          
412 >          isDirectional = 0;
413 >
414 >          if( atoms[local_index]->isDirectional() ){
415 >
416 >            isDirectional = 1;
417 >            
418 >            dAtom = (DirectionalAtom *)atoms[local_index];
419 >            dAtom->getQ( q );
420 >            dAtom->getJ( ji );
421 >
422 >            for (int j = 0; j < 6 ; j++)
423 >              atomData13[j] = atomData6[j];            
424 >            
425 >            atomData13[6] = q[0];
426 >            atomData13[7] = q[1];
427 >            atomData13[8] = q[2];
428 >            atomData13[9] = q[3];
429 >            
430 >            atomData13[10] = ji[0];
431 >            atomData13[11] = ji[1];
432 >            atomData13[12] = ji[2];
433 >          }
434 >          
435 >        } else {
436 >          sprintf(painCave.errMsg,
437 >                  "Atom %d not found on processor %d, currentIndex = %d, local_index = %d\n",
438 >                  which_atom, worldRank, currentIndex, local_index );
439 >          haveError= 1;
440 >          simError();
441          }
442 <        else
443 <          strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
444 <          
445 <        mpiErr = MPI_Send(writeLine,BUFFERSIZE,MPI_CHAR,0,TAKE_THIS_TAG,
538 <                          MPI_COMM_WORLD);
442 >        
443 >        if(haveError) DieDieDie();
444 >        
445 >        currentIndex++;
446        }
447 +      // If we've survived to here, format the line:
448 +      
449 +      if (!isDirectional) {
450 +        
451 +        sprintf( writeLine,
452 +                 "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
453 +                 atomTypeString,
454 +                 atomData6[0],
455 +                 atomData6[1],
456 +                 atomData6[2],
457 +                 atomData6[3],
458 +                 atomData6[4],
459 +                 atomData6[5]);
460 +        
461 +        strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
462 +        
463 +      } else {
464 +        
465 +        sprintf( writeLine,
466 +                 "%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",
467 +                 atomTypeString,
468 +                 atomData13[0],
469 +                 atomData13[1],
470 +                 atomData13[2],
471 +                 atomData13[3],
472 +                 atomData13[4],
473 +                 atomData13[5],
474 +                 atomData13[6],
475 +                 atomData13[7],
476 +                 atomData13[8],
477 +                 atomData13[9],
478 +                 atomData13[10],
479 +                 atomData13[11],
480 +                 atomData13[12]);
481 +        
482 +      }
483 +      
484 +      for(k = 0; k < outFile.size(); k++)
485 +        *outFile[k] << writeLine;
486      }
487 +    
488 +    for(k = 0; k < outFile.size(); k++)
489 +      outFile[k]->flush();
490 +    
491 +    sprintf( checkPointMsg,
492 +             "Sucessfully took a dump.\n");
493 +    
494 +    MPIcheckPoint();        
495 +    
496 +    delete[] potatoes;
497 +    
498 +  } else {
499 +
500 +    // worldRank != 0, so I'm a remote node.  
501 +
502 +    // Set my magic potato to 0:
503 +
504 +    myPotato = 0;
505 +    currentIndex = 0;
506 +    
507 +    for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) {
508        
509 <    sprintf(checkPointMsg,"Node %d sent dump configuration.",
510 <            procIndex);
511 <    MPIcheckPoint();
545 <  }
509 >      // Am I the node which has this atom?
510 >      
511 >      if (AtomToProcMap[i] == worldRank) {
512  
513 <  if( worldRank == 0 ) finalOut.close();
513 >        if (myPotato + 3 >= MAXTAG) {
514 >          
515 >          // The potato was going to exceed the maximum value,
516 >          // so wrap this processor potato back to 0 (and block until
517 >          // node 0 says we can go:
518 >          
519 >          MPI_Recv(&myPotato, 1, MPI_INT, 0, 0, MPI_COMM_WORLD, &istatus);
520 >          
521 >        }
522 >        which_atom = i;
523  
524 +        local_index = indexArray[currentIndex].first;        
525 +                
526 +        if (which_atom == indexArray[currentIndex].second) {
527 +        
528 +          atomTypeString = atoms[local_index]->getType();
529 +          
530 +          atoms[local_index]->getPos(pos);
531 +          atoms[local_index]->getVel(vel);
532 +          
533 +          atomData6[0] = pos[0];
534 +          atomData6[1] = pos[1];
535 +          atomData6[2] = pos[2];
536 +
537 +          atomData6[3] = vel[0];
538 +          atomData6[4] = vel[1];
539 +          atomData6[5] = vel[2];
540 +          
541 +          isDirectional = 0;
542 +
543 +          if( atoms[local_index]->isDirectional() ){
544 +
545 +            isDirectional = 1;
546 +            
547 +            dAtom = (DirectionalAtom *)atoms[local_index];
548 +            dAtom->getQ( q );
549 +            dAtom->getJ( ji );
550 +            
551 +            for (int j = 0; j < 6 ; j++)
552 +              atomData13[j] = atomData6[j];
553 +            
554 +            atomData13[6] = q[0];
555 +            atomData13[7] = q[1];
556 +            atomData13[8] = q[2];
557 +            atomData13[9] = q[3];
558 +  
559 +            atomData13[10] = ji[0];
560 +            atomData13[11] = ji[1];
561 +            atomData13[12] = ji[2];
562 +          }
563 +
564 +        } else {
565 +          sprintf(painCave.errMsg,
566 +                  "Atom %d not found on processor %d, currentIndex = %d, local_index = %d\n",
567 +                  which_atom, worldRank, currentIndex, local_index );
568 +          haveError= 1;
569 +          simError();
570 +        }
571 +        
572 +        strncpy(MPIatomTypeString, atomTypeString, MINIBUFFERSIZE);
573 +
574 +        // null terminate the string before sending (just in case):
575 +        MPIatomTypeString[MINIBUFFERSIZE-1] = '\0';
576 +
577 +        MPI_Send(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, 0,
578 +                             myPotato, MPI_COMM_WORLD);
579 +        
580 +        myPotato++;
581 +
582 +        MPI_Send(&isDirectional, 1, MPI_INT, 0,
583 +                             myPotato, MPI_COMM_WORLD);
584 +        
585 +        myPotato++;
586 +        
587 +        if (isDirectional) {
588 +
589 +          MPI_Send(atomData13, 13, MPI_DOUBLE, 0,
590 +                   myPotato, MPI_COMM_WORLD);
591 +          
592 +        } else {
593 +
594 +          MPI_Send(atomData6, 6, MPI_DOUBLE, 0,
595 +                   myPotato, MPI_COMM_WORLD);
596 +        }
597 +
598 +        myPotato++;  
599 +        currentIndex++;    
600 +      }
601 +    }
602 +
603 +    sprintf( checkPointMsg,
604 +             "Sucessfully took a dump.\n");
605 +    MPIcheckPoint();        
606      
607 +  }
608 +  
609   #endif // is_mpi
610   }
611 +
612 + #ifdef IS_MPI
613 +
614 + // a couple of functions to let us escape the write loop
615 +
616 + void dWrite::DieDieDie( void ){
617 +
618 +  MPI_Finalize();
619 +  exit (0);
620 + }
621 +
622 + #endif //is_mpi

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