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root/group/trunk/OOPSE/libmdtools/DumpWriter.cpp
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Comparing trunk/OOPSE/libmdtools/DumpWriter.cpp (file contents):
Revision 590 by mmeineke, Thu Jul 10 22:15:53 2003 UTC vs.
Revision 1000 by tim, Fri Jan 30 21:47:22 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"
8 – #define TAKE_THIS_TAG_CHAR 1
9 – #define TAKE_THIS_TAG_INT 2
12  
13   namespace dWrite{
14 <  void nodeZeroError( void );
13 <  void anonymousNodeDie( void );
14 >  void DieDieDie( void );
15   }
16  
17   using namespace dWrite;
# Line 26 | Line 27 | DumpWriter::DumpWriter( SimInfo* the_entry_plug ){
27   #ifdef IS_MPI
28    if(worldRank == 0 ){
29   #endif // is_mpi
30 <    
31 <    strcpy( outName, entry_plug->sampleName );
32 <    
33 <    outFile.open(outName, ios::out | ios::trunc );
34 <    
34 <    if( !outFile ){
35 <      
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      }
41  
43 –    //outFile.setf( ios::scientific );
44 –
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 57 | 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, j, which_node, done, which_atom, local_index;
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  
100 < #ifndef IS_MPI
81 <    
82 <  outFile << nAtoms << "\n";
83 <    
84 <  outFile << currentTime << ";\t"
85 <          << entry_plug->Hmat[0][0] << "\t"
86 <          << entry_plug->Hmat[1][0] << "\t"
87 <          << entry_plug->Hmat[2][0] << ";\t"
100 > #endif
101  
102 <          << entry_plug->Hmat[0][1] << "\t"
90 <          << entry_plug->Hmat[1][1] << "\t"
91 <          << entry_plug->Hmat[2][1] << ";\t"
102 > void DumpWriter::writeDump(double currentTime){
103  
104 <          << entry_plug->Hmat[0][2] << "\t"
105 <          << entry_plug->Hmat[1][2] << "\t"
95 <          << entry_plug->Hmat[2][2] << ";\n";
96 <    
97 <  for( i=0; i<nAtoms; i++ ){
98 <      
104 >  ofstream finalOut;
105 >  vector<ofstream*> fileStreams;
106  
107 <    sprintf( tempBuffer,
108 <             "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
109 <             atoms[i]->getType(),
110 <             atoms[i]->getX(),
111 <             atoms[i]->getY(),
112 <             atoms[i]->getZ(),
113 <             atoms[i]->get_vx(),
114 <             atoms[i]->get_vy(),
115 <             atoms[i]->get_vz());
116 <    strcpy( writeLine, tempBuffer );
110 <
111 <    if( atoms[i]->isDirectional() ){
112 <        
113 <      dAtom = (DirectionalAtom *)atoms[i];
114 <      dAtom->getQ( q );
115 <        
116 <      sprintf( tempBuffer,
117 <               "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
118 <               q[0],
119 <               q[1],
120 <               q[2],
121 <               q[3],
122 <               dAtom->getJx(),
123 <               dAtom->getJy(),
124 <               dAtom->getJz());
125 <      strcat( writeLine, tempBuffer );
107 > #ifdef IS_MPI
108 >  if(worldRank == 0 ){
109 > #endif    
110 >    finalOut.open( entry_plug->finalName, ios::out | ios::trunc );
111 >    if( !finalOut ){
112 >      sprintf( painCave.errMsg,
113 >               "Could not open \"%s\" for final dump output.\n",
114 >               entry_plug->finalName );
115 >      painCave.isFatal = 1;
116 >      simError();
117      }
118 <    else
128 <      strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
129 <      
130 <    outFile << writeLine;
118 > #ifdef IS_MPI
119    }
120 <  outFile.flush();
120 > #endif // is_mpi
121  
122 < #else // is_mpi
122 >  fileStreams.push_back(&finalOut);
123 >  fileStreams.push_back(&dumpFile);
124  
125 <  // first thing first, suspend fatalities.
137 <  painCave.isEventLoop = 1;
125 >  writeFrame(fileStreams, currentTime);
126  
127 <  int myStatus; // 1 = wakeup & success; 0 = error; -1 = AllDone
128 <  int haveError;
127 > #ifdef IS_MPI
128 >  finalOut.close();
129 > #endif
130 >        
131 > }
132  
133 <  MPI_Status istatus;
143 <  int *AtomToProcMap = mpiSim->getAtomToProcMap();
144 <  
145 <  // write out header and node 0's coordinates
146 <  
147 <  if( worldRank == 0 ){
148 <    outFile << mpiSim->getTotAtoms() << "\n";
149 <  
150 <    outFile << currentTime << "\t"
151 <            << entry_plug->Hmat[0] << "\t"
152 <            << entry_plug->Hmat[1] << "\t"
153 <            << entry_plug->Hmat[2] << "\t"
154 <      
155 <            << entry_plug->Hmat[3] << "\t"
156 <            << entry_plug->Hmat[4] << "\t"
157 <            << entry_plug->Hmat[5] << "\t"
158 <      
159 <            << entry_plug->Hmat[6] << "\t"
160 <            << entry_plug->Hmat[7] << "\t"
161 <            << entry_plug->Hmat[8] << "\n";
162 <    ;
163 <    outFile.flush();
164 <    for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) {
165 <      // Get the Node number which has this atom;
166 <      
167 <      which_node = AtomToProcMap[i];    
168 <      
169 <      if (which_node == 0 ) {
170 <        
171 <        haveError = 0;
172 <        which_atom = i;
173 <        local_index=-1;        
174 <        for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) {
175 <          if (atoms[j]->getGlobalIndex() == which_atom) local_index = j;
176 <        }
177 <        if (local_index != -1) {
178 <          //format the line
179 <          sprintf( tempBuffer,
180 <                   "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
181 <                   atoms[local_index]->getType(),
182 <                   atoms[local_index]->getX(),
183 <                   atoms[local_index]->getY(),
184 <                   atoms[local_index]->getZ(),
185 <                   atoms[local_index]->get_vx(),
186 <                   atoms[local_index]->get_vy(),
187 <                   atoms[local_index]->get_vz()); // check here.
188 <          strcpy( writeLine, tempBuffer );
189 <          
190 <          if( atoms[local_index]->isDirectional() ){
191 <            
192 <            dAtom = (DirectionalAtom *)atoms[local_index];
193 <            dAtom->getQ( q );
194 <            
195 <            sprintf( tempBuffer,
196 <                     "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
197 <                     q[0],
198 <                     q[1],
199 <                     q[2],
200 <                     q[3],
201 <                     dAtom->getJx(),
202 <                     dAtom->getJy(),
203 <                     dAtom->getJz());
204 <            strcat( writeLine, tempBuffer );
205 <            
206 <          }
207 <          else
208 <            strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );      
209 <        }
210 <        else {
211 <          sprintf(painCave.errMsg,
212 <                  "Atom %d not found on processor %d\n",
213 <                  i, worldRank );
214 <          haveError= 1;
215 <          simError();
216 <        }
217 <        
218 <        if(haveError) nodeZeroError();
133 > void DumpWriter::writeFinal(double currentTime){
134  
135 <      }
136 <      else {
222 <        myStatus = 1;
223 <        MPI_Send(&myStatus, 1, MPI_INT, which_node,
224 <                 TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
225 <        MPI_Send(&i, 1, MPI_INT, which_node, TAKE_THIS_TAG_INT,
226 <                 MPI_COMM_WORLD);
227 <        MPI_Recv(writeLine, BUFFERSIZE, MPI_CHAR, which_node,
228 <                 TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD, &istatus);
229 <        MPI_Recv(&myStatus, 1, MPI_INT, which_node,
230 <                 TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus);
231 <        
232 <        if(!myStatus) nodeZeroError();
233 <
234 <      }
235 <      
236 <      outFile << writeLine;
237 <      outFile.flush();
238 <    }
239 <    
240 <    // kill everyone off:
241 <    myStatus = -1;
242 <    for (j = 0; j < mpiSim->getNumberProcessors(); j++) {      
243 <      MPI_Send(&myStatus, 1, MPI_INT, j,
244 <               TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
245 <    }
135 >  ofstream finalOut;
136 >  vector<ofstream*> fileStreams;
137  
247 –  } else {
248 –    
249 –    done = 0;
250 –    while (!done) {
251 –      
252 –      MPI_Recv(&myStatus, 1, MPI_INT, 0,
253 –               TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus);
254 –
255 –      if(!myStatus) anonymousNodeDie();
256 –      
257 –      if(myStatus < 0) break;
258 –
259 –      MPI_Recv(&which_atom, 1, MPI_INT, 0,
260 –               TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus);
261 –      
262 –      myStatus = 1;
263 –      local_index=-1;        
264 –      for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) {
265 –        if (atoms[j]->getGlobalIndex() == which_atom) local_index = j;
266 –      }
267 –      if (local_index != -1) {
268 –        //format the line
269 –        sprintf( tempBuffer,
270 –                 "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
271 –                 atoms[local_index]->getType(),
272 –                 atoms[local_index]->getX(),
273 –                 atoms[local_index]->getY(),
274 –                 atoms[local_index]->getZ(),
275 –                 atoms[local_index]->get_vx(),
276 –                 atoms[local_index]->get_vy(),
277 –                 atoms[local_index]->get_vz()); // check here.
278 –        strcpy( writeLine, tempBuffer );
279 –        
280 –        if( atoms[local_index]->isDirectional() ){
281 –          
282 –          dAtom = (DirectionalAtom *)atoms[local_index];
283 –          dAtom->getQ( q );
284 –          
285 –          sprintf( tempBuffer,
286 –                   "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
287 –                   q[0],
288 –                   q[1],
289 –                   q[2],
290 –                   q[3],
291 –                   dAtom->getJx(),
292 –                   dAtom->getJy(),
293 –                   dAtom->getJz());
294 –          strcat( writeLine, tempBuffer );
295 –        }
296 –        else{
297 –          strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
298 –        }
299 –      }
300 –      else {
301 –        sprintf(painCave.errMsg,
302 –                "Atom %d not found on processor %d\n",
303 –                which_atom, worldRank );
304 –        myStatus = 0;
305 –        simError();
306 –
307 –        strcpy( writeLine, "Hello, I'm an error.\n");
308 –      }
309 –
310 –      MPI_Send(writeLine, BUFFERSIZE, MPI_CHAR, 0,
311 –               TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD);
312 –      MPI_Send( &myStatus, 1, MPI_INT, 0,
313 –                TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
314 –    }
315 –  }  
316 –  outFile.flush();
317 –  sprintf( checkPointMsg,
318 –           "Sucessfully took a dump.\n");
319 –  MPIcheckPoint();
320 –
321 – // last  thing last, enable  fatalities.
322 –  painCave.isEventLoop = 0;
323 –
324 – #endif // is_mpi
325 – }
326 –
327 – void DumpWriter::writeFinal(double finalTime){
328 –
329 –  char finalName[500];
330 –  ofstream finalOut;
331 –
332 –  const int BUFFERSIZE = 2000;
333 –  char tempBuffer[BUFFERSIZE];
334 –  char writeLine[BUFFERSIZE];  
335 –
336 –  double q[4];
337 –  DirectionalAtom* dAtom;
338 –  int nAtoms = entry_plug->n_atoms;
339 –  Atom** atoms = entry_plug->atoms;
340 –  int i, j, which_node, done, game_over, which_atom, local_index;
341 –  
342 –  
138   #ifdef IS_MPI
139    if(worldRank == 0 ){
140   #endif // is_mpi
141 <    
142 <    strcpy( finalName, entry_plug->finalName );
143 <    
349 <    finalOut.open( finalName, ios::out | ios::trunc );
141 >
142 >    finalOut.open( entry_plug->finalName, ios::out | ios::trunc );
143 >
144      if( !finalOut ){
145        sprintf( painCave.errMsg,
146                 "Could not open \"%s\" for final dump output.\n",
147 <               finalName );
147 >               entry_plug->finalName );
148        painCave.isFatal = 1;
149        simError();
150      }
151 <    
358 <    // finalOut.setf( ios::scientific );
359 <    
151 >
152   #ifdef IS_MPI
153    }
154 + #endif // is_mpi
155    
156 <  sprintf(checkPointMsg,"Opened file for final configuration\n");
157 <  MPIcheckPoint();  
156 >  fileStreams.push_back(&finalOut);  
157 >  writeFrame(fileStreams, currentTime);
158 >
159 > #ifdef IS_MPI
160 >  finalOut.close();
161 > #endif
162    
163 < #endif //is_mpi
163 > }
164  
165 + void DumpWriter::writeFrame( vector<ofstream*>& outFile, double currentTime ){
166 +
167 +  const int BUFFERSIZE = 2000;
168 +  const int MINIBUFFERSIZE = 100;
169 +
170 +  char tempBuffer[BUFFERSIZE];  
171 +  char writeLine[BUFFERSIZE];
172 +
173 +  int i, k;
174 +
175 + #ifdef IS_MPI
176    
177 +  /*********************************************************************
178 +   * Documentation?  You want DOCUMENTATION?
179 +   *
180 +   * Why all the potatoes below?  
181 +   *
182 +   * To make a long story short, the original version of DumpWriter
183 +   * worked in the most inefficient way possible.  Node 0 would
184 +   * poke each of the node for an individual atom's formatted data
185 +   * as node 0 worked its way down the global index. This was particularly
186 +   * inefficient since the method blocked all processors at every atom
187 +   * (and did it twice!).
188 +   *
189 +   * An intermediate version of DumpWriter could be described from Node
190 +   * zero's perspective as follows:
191 +   *
192 +   *  1) Have 100 of your friends stand in a circle.
193 +   *  2) When you say go, have all of them start tossing potatoes at
194 +   *     you (one at a time).
195 +   *  3) Catch the potatoes.
196 +   *
197 +   * It was an improvement, but MPI has buffers and caches that could
198 +   * best be described in this analogy as "potato nets", so there's no
199 +   * need to block the processors atom-by-atom.
200 +   *
201 +   * This new and improved DumpWriter works in an even more efficient
202 +   * way:
203 +   *
204 +   *  1) Have 100 of your friend stand in a circle.
205 +   *  2) When you say go, have them start tossing 5-pound bags of
206 +   *     potatoes at you.
207 +   *  3) Once you've caught a friend's bag of potatoes,
208 +   *     toss them a spud to let them know they can toss another bag.
209 +   *
210 +   * How's THAT for documentation?
211 +   *
212 +   *********************************************************************/
213 +
214 +  int *potatoes;
215 +  int myPotato;
216 +
217 +  int nProc;
218 +  int j, which_node, done, which_atom, local_index, currentIndex;
219 +  double atomData6[6];
220 +  double atomData13[13];
221 +  int isDirectional;
222 +  char* atomTypeString;
223 +  char MPIatomTypeString[MINIBUFFERSIZE];
224 +
225 + #else //is_mpi
226 +  int nAtoms = entry_plug->n_atoms;
227 + #endif //is_mpi
228 +
229 +  double q[4];
230 +  DirectionalAtom* dAtom;
231 +  Atom** atoms = entry_plug->atoms;
232 +  double pos[3], vel[3];
233 +
234   #ifndef IS_MPI
370 –    
371 –  finalOut << nAtoms << "\n";
372 –    
373 –  finalOut << finalTime << "\t"
374 –           << entry_plug->Hmat[0][0] << "\t"
375 –           << entry_plug->Hmat[1][0] << "\t"
376 –           << entry_plug->Hmat[2][0] << "\t"
377 –    
378 –           << entry_plug->Hmat[0][1] << "\t"
379 –           << entry_plug->Hmat[1][1] << "\t"
380 –           << entry_plug->Hmat[2][1] << "\t"
381 –    
382 –           << entry_plug->Hmat[0][2] << "\t"
383 –           << entry_plug->Hmat[1][2] << "\t"
384 –           << entry_plug->Hmat[2][2] << "\n";
235    
236 +  for(k = 0; k < outFile.size(); k++){
237 +    *outFile[k] << nAtoms << "\n";
238 +
239 +    *outFile[k] << currentTime << ";\t"
240 +               << entry_plug->Hmat[0][0] << "\t"
241 +                     << entry_plug->Hmat[1][0] << "\t"
242 +                     << entry_plug->Hmat[2][0] << ";\t"
243 +              
244 +               << entry_plug->Hmat[0][1] << "\t"
245 +                     << entry_plug->Hmat[1][1] << "\t"
246 +                     << entry_plug->Hmat[2][1] << ";\t"
247 +
248 +                     << entry_plug->Hmat[0][2] << "\t"
249 +                     << entry_plug->Hmat[1][2] << "\t"
250 +                     << entry_plug->Hmat[2][2] << ";";
251 +
252 +    //write out additional parameters, such as chi and eta
253 +    *outFile[k] << entry_plug->the_integrator->getAdditionalParameters() << endl;
254 +  }
255 +  
256    for( i=0; i<nAtoms; i++ ){
257 <      
257 >
258 >    atoms[i]->getPos(pos);
259 >    atoms[i]->getVel(vel);
260 >
261      sprintf( tempBuffer,
262               "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
263               atoms[i]->getType(),
264 <             atoms[i]->getX(),
265 <             atoms[i]->getY(),
266 <             atoms[i]->getZ(),
267 <             atoms[i]->get_vx(),
268 <             atoms[i]->get_vy(),
269 <             atoms[i]->get_vz());
264 >             pos[0],
265 >             pos[1],
266 >             pos[2],
267 >             vel[0],
268 >             vel[1],
269 >             vel[2]);
270      strcpy( writeLine, tempBuffer );
271  
272      if( atoms[i]->isDirectional() ){
273 <        
273 >
274        dAtom = (DirectionalAtom *)atoms[i];
275        dAtom->getQ( q );
276 <        
276 >
277        sprintf( tempBuffer,
278                 "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
279                 q[0],
# Line 414 | Line 287 | void DumpWriter::writeFinal(double finalTime){
287      }
288      else
289        strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
290 <      
291 <    finalOut << writeLine;
290 >
291 >    for(k = 0; k < outFile.size(); k++)
292 >      *outFile[k] << writeLine;
293    }
420 –  finalOut.flush();
421 –  finalOut.close();
294  
295   #else // is_mpi
296 +
297 +  /* code to find maximum tag value */
298    
299 <  // first thing first, suspend fatalities.
300 <  painCave.isEventLoop = 1;
299 >  int *tagub, flag, MAXTAG;
300 >  MPI_Attr_get(MPI_COMM_WORLD, MPI_TAG_UB, &tagub, &flag);
301 >  if (flag) {
302 >    MAXTAG = *tagub;
303 >  } else {
304 >    MAXTAG = 32767;
305 >  }  
306  
428 –  int myStatus; // 1 = wakeup & success; 0 = error; -1 = AllDone
307    int haveError;
308  
309    MPI_Status istatus;
310    int *AtomToProcMap = mpiSim->getAtomToProcMap();
311  
312    // write out header and node 0's coordinates
313 <  
436 <  haveError = 0;
313 >
314    if( worldRank == 0 ){
315 <    finalOut << mpiSim->getTotAtoms() << "\n";
315 >
316 >    // Node 0 needs a list of the magic potatoes for each processor;
317 >
318 >    nProc = mpiSim->getNumberProcessors();
319 >    potatoes = new int[nProc];
320 >
321 >    //write out the comment lines
322 >    for (i = 0; i < nProc; i++)
323 >      potatoes[i] = 0;
324      
325 <    finalOut << finalTime << "\t"
326 <             << entry_plug->Hmat[0] << "\t"
327 <             << entry_plug->Hmat[1] << "\t"
328 <             << entry_plug->Hmat[2] << "\t"
329 <      
330 <             << entry_plug->Hmat[3] << "\t"
331 <             << entry_plug->Hmat[4] << "\t"
332 <             << entry_plug->Hmat[5] << "\t"
333 <      
334 <             << entry_plug->Hmat[6] << "\t"
335 <             << entry_plug->Hmat[7] << "\t"
336 <             << entry_plug->Hmat[8] << "\n";
337 <    
325 >      for(k = 0; k < outFile.size(); k++){
326 >        *outFile[k] << mpiSim->getTotAtoms() << "\n";
327 >
328 >        *outFile[k] << currentTime << ";\t"
329 >                         << entry_plug->Hmat[0][0] << "\t"
330 >                         << entry_plug->Hmat[1][0] << "\t"
331 >                         << entry_plug->Hmat[2][0] << ";\t"
332 >
333 >                         << entry_plug->Hmat[0][1] << "\t"
334 >                         << entry_plug->Hmat[1][1] << "\t"
335 >                         << entry_plug->Hmat[2][1] << ";\t"
336 >
337 >                         << entry_plug->Hmat[0][2] << "\t"
338 >                         << entry_plug->Hmat[1][2] << "\t"
339 >                         << entry_plug->Hmat[2][2] << ";";
340 >  
341 >        *outFile[k] << entry_plug->the_integrator->getAdditionalParameters() << endl;
342 >    }
343 >
344 >    currentIndex = 0;
345 >
346      for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) {
454 –      // Get the Node number which has this molecule:
347        
348 <      which_node = AtomToProcMap[i];    
348 >      // Get the Node number which has this atom;
349        
350 <      if (which_node == mpiSim->getMyNode()) {
350 >      which_node = AtomToProcMap[i];
351 >      
352 >      if (which_node != 0) {
353  
354 <        which_atom = i;
355 <        local_index=-1;        
356 <        for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) {
357 <          if (atoms[j]->getGlobalIndex() == which_atom) local_index = j;
354 >        if (potatoes[which_node] + 3 >= MAXTAG) {
355 >          // The potato was going to exceed the maximum value,
356 >          // so wrap this processor potato back to 0:        
357 >
358 >          potatoes[which_node] = 0;          
359 >          MPI_Send(0, 1, MPI_INT, which_node, 0, MPI_COMM_WORLD);
360 >          
361          }
362 <        if (local_index != -1) {        
363 <          sprintf( tempBuffer,
364 <                   "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
365 <                   atoms[local_index]->getType(),
366 <                   atoms[local_index]->getX(),
367 <                   atoms[local_index]->getY(),
368 <                   atoms[local_index]->getZ(),
369 <                   atoms[local_index]->get_vx(),
370 <                   atoms[local_index]->get_vy(),
371 <                   atoms[local_index]->get_vz());
372 <          strcpy( writeLine, tempBuffer );
373 <          
374 <          if( atoms[local_index]->isDirectional() ){
362 >
363 >        myPotato = potatoes[which_node];        
364 >        
365 >        MPI_Recv(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, which_node,
366 >                 myPotato, MPI_COMM_WORLD, &istatus);
367 >        
368 >        atomTypeString = MPIatomTypeString;
369 >        
370 >        myPotato++;
371 >
372 >        MPI_Recv(&isDirectional, 1, MPI_INT, which_node,
373 >                 myPotato, MPI_COMM_WORLD, &istatus);
374 >              
375 >        myPotato++;
376 >
377 >        if (isDirectional) {          
378 >          MPI_Recv(atomData13, 13, MPI_DOUBLE, which_node,
379 >                   myPotato, MPI_COMM_WORLD, &istatus);
380 >        } else {
381 >          MPI_Recv(atomData6, 6, MPI_DOUBLE, which_node,
382 >                   myPotato, MPI_COMM_WORLD, &istatus);          
383 >        }
384 >        
385 >        myPotato++;
386 >        potatoes[which_node] = myPotato;
387 >
388 >      } else {
389 >        
390 >        haveError = 0;
391 >        which_atom = i;
392 >        
393 >          local_index = indexArray[currentIndex].first;        
394 >          
395 >          if (which_atom == indexArray[currentIndex].second) {
396              
397 <            dAtom = (DirectionalAtom *)atoms[local_index];
480 <            dAtom->getQ( q );
397 >            atomTypeString = atoms[local_index]->getType();
398              
399 <            sprintf( tempBuffer,
400 <                     "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
401 <                     q[0],
402 <                     q[1],
403 <                     q[2],
404 <                     q[3],
405 <                     dAtom->getJx(),
406 <                     dAtom->getJy(),
407 <                     dAtom->getJz());
408 <            strcat( writeLine, tempBuffer );
409 <          }
410 <          else
411 <            strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );      
412 <        }
413 <        else {
399 >          atoms[local_index]->getPos(pos);
400 >          atoms[local_index]->getVel(vel);          
401 >          
402 >          atomData6[0] = pos[0];
403 >          atomData6[1] = pos[1];
404 >          atomData6[2] = pos[2];
405 >
406 >          atomData6[3] = vel[0];
407 >          atomData6[4] = vel[1];
408 >          atomData6[5] = vel[2];
409 >          
410 >          isDirectional = 0;
411 >
412 >          if( atoms[local_index]->isDirectional() ){
413 >
414 >            isDirectional = 1;
415 >            
416 >            dAtom = (DirectionalAtom *)atoms[local_index];
417 >            dAtom->getQ( q );
418 >
419 >            for (int j = 0; j < 6 ; j++)
420 >              atomData13[j] = atomData6[j];            
421 >            
422 >            atomData13[6] = q[0];
423 >            atomData13[7] = q[1];
424 >            atomData13[8] = q[2];
425 >            atomData13[9] = q[3];
426 >            
427 >            atomData13[10] = dAtom->getJx();
428 >            atomData13[11] = dAtom->getJy();
429 >            atomData13[12] = dAtom->getJz();
430 >          }
431 >          
432 >        } else {
433            sprintf(painCave.errMsg,
434 <                  "Atom %d not found on processor %d\n",
435 <                  i, worldRank );
434 >                  "Atom %d not found on processor %d, currentIndex = %d, local_index = %d\n",
435 >                  which_atom, worldRank, currentIndex, local_index );
436            haveError= 1;
437            simError();
438 <        }
503 <
504 <        if(haveError) nodeZeroError();
505 <    
506 <      }
507 <      else {
438 >        }
439          
440 <        myStatus = 1;
441 <        MPI_Send(&myStatus, 1, MPI_INT, which_node,
442 <                 TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
443 <        MPI_Send(&i, 1, MPI_INT, which_node, TAKE_THIS_TAG_INT,
444 <                 MPI_COMM_WORLD);
445 <        MPI_Recv(writeLine, BUFFERSIZE, MPI_CHAR, which_node,
446 <                 TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD, &istatus);
516 <        MPI_Recv(&myStatus, 1, MPI_INT, which_node,
517 <                 TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus);
440 >        if(haveError) DieDieDie();
441 >        
442 >        currentIndex++;
443 >      }
444 >      // If we've survived to here, format the line:
445 >      
446 >      if (!isDirectional) {
447          
448 <        if(!myStatus) nodeZeroError();
448 >        sprintf( writeLine,
449 >                 "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
450 >                 atomTypeString,
451 >                 atomData6[0],
452 >                 atomData6[1],
453 >                 atomData6[2],
454 >                 atomData6[3],
455 >                 atomData6[4],
456 >                 atomData6[5]);
457 >        
458 >        strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
459 >        
460 >      } else {
461 >        
462 >        sprintf( writeLine,
463 >                 "%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",
464 >                 atomTypeString,
465 >                 atomData13[0],
466 >                 atomData13[1],
467 >                 atomData13[2],
468 >                 atomData13[3],
469 >                 atomData13[4],
470 >                 atomData13[5],
471 >                 atomData13[6],
472 >                 atomData13[7],
473 >                 atomData13[8],
474 >                 atomData13[9],
475 >                 atomData13[10],
476 >                 atomData13[11],
477 >                 atomData13[12]);
478 >        
479        }
480        
481 <      finalOut << writeLine;
481 >      for(k = 0; k < outFile.size(); k++)
482 >        *outFile[k] << writeLine;
483      }
484      
485 <    // kill everyone off:
486 <    myStatus = -1;
527 <    for (j = 0; j < mpiSim->getNumberProcessors(); j++) {      
528 <      MPI_Send(&myStatus, 1, MPI_INT, j,
529 <               TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
530 <    }
531 <
532 <  } else {
485 >    for(k = 0; k < outFile.size(); k++)
486 >      outFile[k]->flush();
487      
488 <    done = 0;
489 <    while (!done) {
488 >    sprintf( checkPointMsg,
489 >             "Sucessfully took a dump.\n");
490 >    
491 >    MPIcheckPoint();        
492 >    
493 >    delete[] potatoes;
494 >    
495 >  } else {
496  
497 <      MPI_Recv(&myStatus, 1, MPI_INT, 0,
498 <               TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus);
497 >    // worldRank != 0, so I'm a remote node.  
498 >
499 >    // Set my magic potato to 0:
500 >
501 >    myPotato = 0;
502 >    currentIndex = 0;
503 >    
504 >    for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) {
505        
506 <      if(!myStatus) anonymousNodeDie();
506 >      // Am I the node which has this atom?
507        
508 <      if(myStatus < 0) break;
543 <      
544 <      MPI_Recv(&which_atom, 1, MPI_INT, 0,
545 <               TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus);
546 <      
547 <      myStatus = 1;
548 <      local_index=-1;        
549 <      for (j=0; j < mpiSim->getMyNlocal(); j++) {
550 <        if (atoms[j]->getGlobalIndex() == which_atom) local_index = j;
551 <      }
552 <      if (local_index != -1) {
508 >      if (AtomToProcMap[i] == worldRank) {
509  
510 <        //format the line
555 <        sprintf( tempBuffer,
556 <                 "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
557 <                 atoms[local_index]->getType(),
558 <                 atoms[local_index]->getX(),
559 <                 atoms[local_index]->getY(),
560 <                 atoms[local_index]->getZ(),
561 <                 atoms[local_index]->get_vx(),
562 <                 atoms[local_index]->get_vy(),
563 <                 atoms[local_index]->get_vz()); // check here.
564 <        strcpy( writeLine, tempBuffer );
565 <        
566 <        if( atoms[local_index]->isDirectional() ){
510 >        if (myPotato + 3 >= MAXTAG) {
511            
512 <          dAtom = (DirectionalAtom *)atoms[local_index];
513 <          dAtom->getQ( q );
512 >          // The potato was going to exceed the maximum value,
513 >          // so wrap this processor potato back to 0 (and block until
514 >          // node 0 says we can go:
515            
516 <          sprintf( tempBuffer,
517 <                   "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
518 <                   q[0],
519 <                   q[1],
520 <                   q[2],
521 <                   q[3],
522 <                   dAtom->getJx(),
523 <                   dAtom->getJy(),
524 <                   dAtom->getJz());
525 <          strcat( writeLine, tempBuffer );
516 >          MPI_Recv(&myPotato, 1, MPI_INT, 0, 0, MPI_COMM_WORLD, &istatus);
517 >          
518 >        }
519 >        which_atom = i;
520 >
521 >        local_index = indexArray[currentIndex].first;        
522 >                
523 >        if (which_atom == indexArray[currentIndex].second) {
524 >        
525 >          atomTypeString = atoms[local_index]->getType();
526 >          
527 >          atoms[local_index]->getPos(pos);
528 >          atoms[local_index]->getVel(vel);
529 >          
530 >          atomData6[0] = pos[0];
531 >          atomData6[1] = pos[1];
532 >          atomData6[2] = pos[2];
533 >
534 >          atomData6[3] = vel[0];
535 >          atomData6[4] = vel[1];
536 >          atomData6[5] = vel[2];
537 >          
538 >          isDirectional = 0;
539 >
540 >          if( atoms[local_index]->isDirectional() ){
541 >
542 >            isDirectional = 1;
543 >            
544 >            dAtom = (DirectionalAtom *)atoms[local_index];
545 >            dAtom->getQ( q );
546 >            
547 >            for (int j = 0; j < 6 ; j++)
548 >              atomData13[j] = atomData6[j];
549 >            
550 >            atomData13[6] = q[0];
551 >            atomData13[7] = q[1];
552 >            atomData13[8] = q[2];
553 >            atomData13[9] = q[3];
554 >  
555 >            atomData13[10] = dAtom->getJx();
556 >            atomData13[11] = dAtom->getJy();
557 >            atomData13[12] = dAtom->getJz();
558 >          }
559 >
560 >        } else {
561 >          sprintf(painCave.errMsg,
562 >                  "Atom %d not found on processor %d, currentIndex = %d, local_index = %d\n",
563 >                  which_atom, worldRank, currentIndex, local_index );
564 >          haveError= 1;
565 >          simError();
566          }
582 –        else{
583 –          strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
584 –        }
585 –      }
586 –      else {
587 –        sprintf(painCave.errMsg,
588 –                "Atom %d not found on processor %d\n",
589 –                which_atom, worldRank );
590 –        myStatus = 0;
591 –        simError();
567          
568 <        strcpy( writeLine, "Hello, I'm an error.\n");
594 <      }
568 >        strncpy(MPIatomTypeString, atomTypeString, MINIBUFFERSIZE);
569  
570 <      MPI_Send(writeLine, BUFFERSIZE, MPI_CHAR, 0,
571 <               TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD);
572 <      MPI_Send( &myStatus, 1, MPI_INT, 0,
573 <                TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
570 >        // null terminate the string before sending (just in case):
571 >        MPIatomTypeString[MINIBUFFERSIZE-1] = '\0';
572 >
573 >        MPI_Send(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, 0,
574 >                             myPotato, MPI_COMM_WORLD);
575 >        
576 >        myPotato++;
577 >
578 >        MPI_Send(&isDirectional, 1, MPI_INT, 0,
579 >                             myPotato, MPI_COMM_WORLD);
580 >        
581 >        myPotato++;
582 >        
583 >        if (isDirectional) {
584 >
585 >          MPI_Send(atomData13, 13, MPI_DOUBLE, 0,
586 >                   myPotato, MPI_COMM_WORLD);
587 >          
588 >        } else {
589 >
590 >          MPI_Send(atomData6, 6, MPI_DOUBLE, 0,
591 >                   myPotato, MPI_COMM_WORLD);
592 >        }
593 >
594 >        myPotato++;  
595 >        currentIndex++;    
596 >      }
597      }
598 <  }
599 <  finalOut.flush();
600 <  sprintf( checkPointMsg,
601 <           "Sucessfully took a dump.\n");
602 <  MPIcheckPoint();
598 >
599 >    sprintf( checkPointMsg,
600 >             "Sucessfully took a dump.\n");
601 >    MPIcheckPoint();        
602 >    
603 >  }
604    
607 –  if( worldRank == 0 ) finalOut.close();    
605   #endif // is_mpi
606   }
607  
611 –
612 –
608   #ifdef IS_MPI
609  
610   // a couple of functions to let us escape the write loop
611  
612 < void dWrite::nodeZeroError( void ){
618 <  int j, myStatus;
619 <  
620 <  myStatus = 0;
621 <  for (j = 0; j < mpiSim->getNumberProcessors(); j++) {      
622 <    MPI_Send( &myStatus, 1, MPI_INT, j,
623 <              TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
624 <  }  
625 <  
612 > void dWrite::DieDieDie( void ){
613  
614    MPI_Finalize();
615    exit (0);
629 –  
616   }
617  
632 – void dWrite::anonymousNodeDie( void ){
633 –
634 –  MPI_Finalize();
635 –  exit (0);
636 – }
637 –
618   #endif //is_mpi

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