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root/group/trunk/OOPSE/libmdtools/DumpWriter.cpp
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Comparing trunk/OOPSE/libmdtools/DumpWriter.cpp (file contents):
Revision 905 by tim, Wed Jan 7 19:26:12 2004 UTC vs.
Revision 1129 by tim, Thu Apr 22 03:29:30 2004 UTC

# Line 1 | Line 1
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"
10 – #define TAKE_THIS_TAG_CHAR 15
11 – #define TAKE_THIS_TAG_INT 20
13  
14   namespace dWrite{
15 <  void nodeZeroError( void );
15 <  void anonymousNodeDie( void );
15 >  void DieDieDie( void );
16   }
17  
18   using namespace dWrite;
# Line 29 | Line 29 | DumpWriter::DumpWriter( SimInfo* the_entry_plug ){
29    if(worldRank == 0 ){
30   #endif // is_mpi
31  
32 <    strcpy( outName, entry_plug->sampleName );
32 >    dumpFile.open(entry_plug->sampleName, ios::out | ios::trunc );
33  
34 <    outFile.open(outName, ios::out | ios::trunc );
34 >    if( !dumpFile ){
35  
36 –    if( !outFile ){
37 –
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      }
42  
45 –    //outFile.setf( ios::scientific );
46 –
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 59 | 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  
69 – void DumpWriter::writeDump( double currentTime ){
70 –
71 –  const int BUFFERSIZE = 2000;
72 –  char tempBuffer[BUFFERSIZE];
73 –  char writeLine[BUFFERSIZE];
74 –
75 –  int i;
68   #ifdef IS_MPI
77 –  int j, which_node, done, which_atom, local_index;
78 – #else //is_mpi
79 –  int nAtoms = entry_plug->n_atoms;
80 – #endif //is_mpi
69  
70 <  double q[4];
71 <  DirectionalAtom* dAtom;
72 <  Atom** atoms = entry_plug->atoms;
85 <  double pos[3], vel[3];
70 > /**
71 > * A hook function to load balancing
72 > */
73  
74 + void DumpWriter::update(){
75 +  sortByGlobalIndex();          
76 + }
77 +  
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 <  // write current frame to the eor file
86 > /**
87 > * Sorting the local index by global index
88 > */
89 >
90 > void DumpWriter::sortByGlobalIndex(){
91 >  Molecule* mols = entry_plug->molecules;  
92 >  indexArray.clear();
93 >  
94 >  for(int i = 0; i < entry_plug->n_mol;i++)
95 >    indexArray.push_back(make_pair(i, mols[i].getGlobalIndex()));
96 >  
97 >  sort(indexArray.begin(), indexArray.end(), indexSortingCriterion);    
98 > }
99  
100 <  this->writeFinal( currentTime );
100 > #endif
101  
102 < #ifndef IS_MPI
102 > void DumpWriter::writeDump(double currentTime){
103  
104 <  outFile << nAtoms << "\n";
104 >  ofstream finalOut;
105 >  vector<ofstream*> fileStreams;
106  
107 <  outFile << currentTime << ";\t"
108 <          << entry_plug->Hmat[0][0] << "\t"
109 <          << entry_plug->Hmat[1][0] << "\t"
110 <          << entry_plug->Hmat[2][0] << ";\t"
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 > #ifdef IS_MPI
119 >  }
120 > #endif // is_mpi
121  
122 <          << entry_plug->Hmat[0][1] << "\t"
123 <          << entry_plug->Hmat[1][1] << "\t"
103 <          << entry_plug->Hmat[2][1] << ";\t"
122 >  fileStreams.push_back(&finalOut);
123 >  fileStreams.push_back(&dumpFile);
124  
125 <          << entry_plug->Hmat[0][2] << "\t"
106 <          << entry_plug->Hmat[1][2] << "\t"
107 <          << entry_plug->Hmat[2][2] << ";";
108 <  //write out additional parameters, such as chi and eta
109 <  outFile << entry_plug->the_integrator->getAdditionalParameters();
110 <  outFile << endl;
125 >  writeFrame(fileStreams, currentTime);
126  
127 <  for( i=0; i<nAtoms; i++ ){
127 > #ifdef IS_MPI
128 >  finalOut.close();
129 > #endif
130 >        
131 > }
132  
133 <    atoms[i]->getPos(pos);
115 <    atoms[i]->getVel(vel);
133 > void DumpWriter::writeFinal(double currentTime){
134  
135 <    sprintf( tempBuffer,
136 <             "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
119 <             atoms[i]->getType(),
120 <             pos[0],
121 <             pos[1],
122 <             pos[2],
123 <             vel[0],
124 <             vel[1],
125 <             vel[2]);
126 <    strcpy( writeLine, tempBuffer );
135 >  ofstream finalOut;
136 >  vector<ofstream*> fileStreams;
137  
138 <    if( atoms[i]->isDirectional() ){
138 > #ifdef IS_MPI
139 >  if(worldRank == 0 ){
140 > #endif // is_mpi
141  
142 <      dAtom = (DirectionalAtom *)atoms[i];
131 <      dAtom->getQ( q );
142 >    finalOut.open( entry_plug->finalName, ios::out | ios::trunc );
143  
144 <      sprintf( tempBuffer,
145 <               "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
146 <               q[0],
147 <               q[1],
148 <               q[2],
149 <               q[3],
139 <               dAtom->getJx(),
140 <               dAtom->getJy(),
141 <               dAtom->getJz());
142 <      strcat( writeLine, tempBuffer );
144 >    if( !finalOut ){
145 >      sprintf( painCave.errMsg,
146 >               "Could not open \"%s\" for final dump output.\n",
147 >               entry_plug->finalName );
148 >      painCave.isFatal = 1;
149 >      simError();
150      }
144 –    else
145 –      strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
151  
152 <    outFile << writeLine;
152 > #ifdef IS_MPI
153    }
154 <  outFile.flush();
154 > #endif // is_mpi
155 >  
156 >  fileStreams.push_back(&finalOut);  
157 >  writeFrame(fileStreams, currentTime);
158  
159 < #else // is_mpi
159 > #ifdef IS_MPI
160 >  finalOut.close();
161 > #endif
162 >  
163 > }
164  
165 <  // first thing first, suspend fatalities.
154 <  painCave.isEventLoop = 1;
165 > void DumpWriter::writeFrame( vector<ofstream*>& outFile, double currentTime ){
166  
167 <  int myStatus; // 1 = wakeup & success; 0 = error; -1 = AllDone
168 <  int haveError;
167 >  const int BUFFERSIZE = 2000;
168 >  const int MINIBUFFERSIZE = 100;
169  
170 <  MPI_Status istatus;
171 <  int *AtomToProcMap = mpiSim->getAtomToProcMap();
170 >  char tempBuffer[BUFFERSIZE];  
171 >  char writeLine[BUFFERSIZE];
172  
173 <  // write out header and node 0's coordinates
173 >  int i, k;
174  
175 <  if( worldRank == 0 ){
176 <    outFile << mpiSim->getTotAtoms() << "\n";
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 <    outFile << currentTime << ";\t"
215 <            << entry_plug->Hmat[0][0] << "\t"
169 <            << entry_plug->Hmat[1][0] << "\t"
170 <            << entry_plug->Hmat[2][0] << ";\t"
214 >  int *potatoes;
215 >  int myPotato;
216  
217 <            << entry_plug->Hmat[0][1] << "\t"
218 <            << entry_plug->Hmat[1][1] << "\t"
219 <            << entry_plug->Hmat[2][1] << ";\t"
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 >  int nObjects;
225 > #endif //is_mpi
226  
227 <            << entry_plug->Hmat[0][2] << "\t"
228 <            << entry_plug->Hmat[1][2] << "\t"
229 <            << entry_plug->Hmat[2][2] << ";";
227 >  double q[4], ji[3];
228 >  DirectionalAtom* dAtom;
229 >  double pos[3], vel[3];
230 >  int nTotObjects;
231 >  StuntDouble* sd;
232 >  char* molName;
233 >  vector<StuntDouble*> integrableObjects;
234 >  vector<StuntDouble*>::iterator iter;
235 >  nTotObjects = entry_plug->getTotIntegrableObjects();
236 > #ifndef IS_MPI
237 >  
238 >  for(k = 0; k < outFile.size(); k++){
239 >    *outFile[k] << nTotObjects << "\n";
240  
241 <    outFile << entry_plug->the_integrator->getAdditionalParameters();
242 <    outFile << endl;
243 <    outFile.flush();
244 <    for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) {
245 <      // Get the Node number which has this atom;
241 >    *outFile[k] << currentTime << ";\t"
242 >               << entry_plug->Hmat[0][0] << "\t"
243 >                     << entry_plug->Hmat[1][0] << "\t"
244 >                     << entry_plug->Hmat[2][0] << ";\t"
245 >              
246 >               << entry_plug->Hmat[0][1] << "\t"
247 >                     << entry_plug->Hmat[1][1] << "\t"
248 >                     << entry_plug->Hmat[2][1] << ";\t"
249  
250 <      which_node = AtomToProcMap[i];
250 >                     << entry_plug->Hmat[0][2] << "\t"
251 >                     << entry_plug->Hmat[1][2] << "\t"
252 >                     << entry_plug->Hmat[2][2] << ";";
253  
254 <      if (which_node == 0 ) {
254 >    //write out additional parameters, such as chi and eta
255 >    *outFile[k] << entry_plug->the_integrator->getAdditionalParameters() << endl;
256 >  }
257 >  
258 >  for( i=0; i< entry_plug->n_mol; i++ ){
259  
260 <        haveError = 0;
261 <        which_atom = i;
262 <        local_index=-1;
263 <        for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) {
264 <          if (atoms[j]->getGlobalIndex() == which_atom) local_index = j;
265 <        }
266 <        if (local_index != -1) {
197 <          //format the line
260 >    integrableObjects = entry_plug->molecules[i].getIntegrableObjects();
261 >    molName = (entry_plug->compStamps[entry_plug->molecules[i].getStampID()])->getID();
262 >    
263 >    for( iter = integrableObjects.begin();iter !=  integrableObjects.end(); ++iter){
264 >      sd = *iter;
265 >      sd->getPos(pos);
266 >      sd->getVel(vel);
267  
268 <          atoms[local_index]->getPos(pos);
269 <          atoms[local_index]->getVel(vel);
268 >      sprintf( tempBuffer,
269 >             "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
270 >             sd->getType(),
271 >             pos[0],
272 >             pos[1],
273 >             pos[2],
274 >             vel[0],
275 >             vel[1],
276 >             vel[2]);
277 >      strcpy( writeLine, tempBuffer );
278  
279 <          sprintf( tempBuffer,
203 <                   "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
204 <                   atoms[local_index]->getType(),
205 <                   pos[0],
206 <                   pos[1],
207 <                   pos[2],
208 <                   vel[0],
209 <                   vel[1],
210 <                   vel[2]); // check here.
211 <          strcpy( writeLine, tempBuffer );
279 >      if( sd->isDirectional() ){
280  
281 <          if( atoms[local_index]->isDirectional() ){
281 >        sd->getQ( q );
282 >        sd->getJ( ji );
283  
284 <            dAtom = (DirectionalAtom *)atoms[local_index];
285 <            dAtom->getQ( q );
284 >        sprintf( tempBuffer,
285 >               "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
286 >               q[0],
287 >               q[1],
288 >               q[2],
289 >               q[3],
290 >                 ji[0],
291 >                 ji[1],
292 >                 ji[2]);
293 >        strcat( writeLine, tempBuffer );
294 >      }
295 >      else
296 >        strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
297 >    }
298  
299 <            sprintf( tempBuffer,
300 <                     "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
301 <                     q[0],
302 <                     q[1],
222 <                     q[2],
223 <                     q[3],
224 <                     dAtom->getJx(),
225 <                     dAtom->getJy(),
226 <                     dAtom->getJz());
227 <            strcat( writeLine, tempBuffer );
299 >    
300 >    for(k = 0; k < outFile.size(); k++)
301 >      *outFile[k] << writeLine;
302 > }
303  
304 <          }
230 <          else
231 <            strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
232 <        }
233 <        else {
234 <          sprintf(painCave.errMsg,
235 <                  "Atom %d not found on processor %d\n",
236 <                  i, worldRank );
237 <          haveError= 1;
238 <          simError();
239 <        }
304 > #else // is_mpi
305  
306 <        if(haveError) nodeZeroError();
306 >  /* code to find maximum tag value */
307 >  
308 >  int *tagub, flag, MAXTAG;
309 >  MPI_Attr_get(MPI_COMM_WORLD, MPI_TAG_UB, &tagub, &flag);
310 >  if (flag) {
311 >    MAXTAG = *tagub;
312 >  } else {
313 >    MAXTAG = 32767;
314 >  }  
315  
316 <      }
244 <      else {
245 <        myStatus = 1;
246 <        MPI_Send(&myStatus, 1, MPI_INT, which_node,
247 <                 TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
248 <        MPI_Send(&i, 1, MPI_INT, which_node, TAKE_THIS_TAG_INT,
249 <                 MPI_COMM_WORLD);
250 <        MPI_Recv(writeLine, BUFFERSIZE, MPI_CHAR, which_node,
251 <                 TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD, &istatus);
252 <        MPI_Recv(&myStatus, 1, MPI_INT, which_node,
253 <                 TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus);
316 >  int haveError;
317  
318 <        if(!myStatus) nodeZeroError();
318 >  MPI_Status istatus;
319 >  int nCurObj;
320 >  int *MolToProcMap = mpiSim->getMolToProcMap();
321  
322 <      }
322 >  // write out header and node 0's coordinates
323  
324 <      outFile << writeLine;
260 <      outFile.flush();
261 <    }
324 >  if( worldRank == 0 ){
325  
326 <    // kill everyone off:
264 <    myStatus = -1;
265 <    for (j = 1; j < mpiSim->getNumberProcessors(); j++) {
266 <      MPI_Send(&myStatus, 1, MPI_INT, j,
267 <               TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
268 <    }
326 >    // Node 0 needs a list of the magic potatoes for each processor;
327  
328 <  } else {
328 >    nProc = mpiSim->getNumberProcessors();
329 >    potatoes = new int[nProc];
330  
331 <    done = 0;
332 <    while (!done) {
331 >    //write out the comment lines
332 >    for (i = 0; i < nProc; i++)
333 >      potatoes[i] = 0;
334 >    
335 >      for(k = 0; k < outFile.size(); k++){
336 >        *outFile[k] << nTotObjects << "\n";
337  
338 <      MPI_Recv(&myStatus, 1, MPI_INT, 0,
339 <               TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus);
338 >        *outFile[k] << currentTime << ";\t"
339 >                         << entry_plug->Hmat[0][0] << "\t"
340 >                         << entry_plug->Hmat[1][0] << "\t"
341 >                         << entry_plug->Hmat[2][0] << ";\t"
342  
343 <      if(!myStatus) anonymousNodeDie();
343 >                         << entry_plug->Hmat[0][1] << "\t"
344 >                         << entry_plug->Hmat[1][1] << "\t"
345 >                         << entry_plug->Hmat[2][1] << ";\t"
346  
347 <      if(myStatus < 0) break;
347 >                         << entry_plug->Hmat[0][2] << "\t"
348 >                         << entry_plug->Hmat[1][2] << "\t"
349 >                         << entry_plug->Hmat[2][2] << ";";
350 >  
351 >        *outFile[k] << entry_plug->the_integrator->getAdditionalParameters() << endl;
352 >    }
353  
354 <      MPI_Recv(&which_atom, 1, MPI_INT, 0,
283 <               TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus);
354 >    currentIndex = 0;
355  
356 <      myStatus = 1;
357 <      local_index=-1;
358 <      for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) {
359 <        if (atoms[j]->getGlobalIndex() == which_atom) local_index = j;
360 <      }
361 <      if (local_index != -1) {
362 <        //format the line
356 >    for (i = 0 ; i < mpiSim->getTotNmol(); i++ ) {
357 >      
358 >      // Get the Node number which has this atom;
359 >      
360 >      which_node = MolToProcMap[i];
361 >      
362 >      if (which_node != 0) {
363 >        
364 >        if (potatoes[which_node] + 1 >= MAXTAG) {
365 >          // The potato was going to exceed the maximum value,
366 >          // so wrap this processor potato back to 0:        
367  
368 <        atoms[local_index]->getPos(pos);
369 <        atoms[local_index]->getVel(vel);
368 >          potatoes[which_node] = 0;          
369 >          MPI_Send(&potatoes[which_node], 1, MPI_INT, which_node, 0, MPI_COMM_WORLD);
370 >          
371 >        }
372  
373 <        sprintf( tempBuffer,
297 <                 "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
298 <                 atoms[local_index]->getType(),
299 <                 pos[0],
300 <                 pos[1],
301 <                 pos[2],
302 <                 vel[0],
303 <                 vel[1],
304 <                 vel[2]); // check here.
305 <        strcpy( writeLine, tempBuffer );
373 >        myPotato = potatoes[which_node];        
374  
375 <        if( atoms[local_index]->isDirectional() ){
375 >        //recieve the number of integrableObject in current molecule
376 >        MPI_Recv(&nCurObj, 1, MPI_INT, which_node,
377 >                 myPotato, MPI_COMM_WORLD, &istatus);
378 >        myPotato++;
379 >        
380 >        for(int l = 0; l < nCurObj; l++){
381  
382 <          dAtom = (DirectionalAtom *)atoms[local_index];
383 <          dAtom->getQ( q );
382 >          if (potatoes[which_node] + 3 >= MAXTAG) {
383 >            // The potato was going to exceed the maximum value,
384 >            // so wrap this processor potato back to 0:        
385  
386 <          sprintf( tempBuffer,
387 <                   "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
388 <                   q[0],
389 <                   q[1],
316 <                   q[2],
317 <                   q[3],
318 <                   dAtom->getJx(),
319 <                   dAtom->getJy(),
320 <                   dAtom->getJz());
321 <          strcat( writeLine, tempBuffer );
322 <        }
323 <        else{
324 <          strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
325 <        }
326 <      }
327 <      else {
328 <        sprintf(painCave.errMsg,
329 <                "Atom %d not found on processor %d\n",
330 <                which_atom, worldRank );
331 <        myStatus = 0;
332 <        simError();
386 >            potatoes[which_node] = 0;          
387 >            MPI_Send(&potatoes[which_node], 1, MPI_INT, which_node, 0, MPI_COMM_WORLD);
388 >            
389 >          }
390  
391 <        strcpy( writeLine, "Hello, I'm an error.\n");
392 <      }
391 >          MPI_Recv(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, which_node,
392 >          myPotato, MPI_COMM_WORLD, &istatus);
393  
394 <      MPI_Send(writeLine, BUFFERSIZE, MPI_CHAR, 0,
338 <               TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD);
339 <      MPI_Send( &myStatus, 1, MPI_INT, 0,
340 <                TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
341 <    }
342 <  }
343 <  outFile.flush();
344 <  sprintf( checkPointMsg,
345 <           "Sucessfully took a dump.\n");
346 <  MPIcheckPoint();
394 >          atomTypeString = MPIatomTypeString;
395  
396 < // last  thing last, enable  fatalities.
349 <  painCave.isEventLoop = 0;
396 >          myPotato++;
397  
398 < #endif // is_mpi
399 < }
398 >          MPI_Recv(&isDirectional, 1, MPI_INT, which_node,
399 >          myPotato, MPI_COMM_WORLD, &istatus);
400 >              
401 >          myPotato++;
402  
403 < void DumpWriter::writeFinal(double finalTime){
403 >          if (isDirectional) {          
404 >          MPI_Recv(atomData13, 13, MPI_DOUBLE, which_node,
405 >                   myPotato, MPI_COMM_WORLD, &istatus);
406 >          } else {
407 >          MPI_Recv(atomData6, 6, MPI_DOUBLE, which_node,
408 >                   myPotato, MPI_COMM_WORLD, &istatus);          
409 >          }
410  
411 <  char finalName[500];
412 <  ofstream finalOut;
413 <
359 <  const int BUFFERSIZE = 2000;
360 <  char tempBuffer[BUFFERSIZE];
361 <  char writeLine[BUFFERSIZE];
411 >          myPotato++;
412 >        }
413 >        potatoes[which_node] = myPotato;
414  
415 <  double q[4];
416 <  DirectionalAtom* dAtom;
417 <  Atom** atoms = entry_plug->atoms;
418 <  int i;
419 < #ifdef IS_MPI
368 <  int j, which_node, done, which_atom, local_index;
369 < #else //is_mpi
370 <  int nAtoms = entry_plug->n_atoms;
371 < #endif //is_mpi
415 >      } else {
416 >        
417 >        haveError = 0;
418 >        
419 >            local_index = indexArray[currentIndex].first;        
420  
421 <  double pos[3], vel[3];
421 >        integrableObjects = (entry_plug->molecules[local_index]).getIntegrableObjects();
422  
423 < #ifdef IS_MPI
424 <  if(worldRank == 0 ){
425 < #endif // is_mpi
423 >        for(iter= integrableObjects.begin(); iter != integrableObjects.end(); ++iter){    
424 >                sd = *iter;
425 >            atomTypeString = sd->getType();
426 >            
427 >            sd->getPos(pos);
428 >            sd->getVel(vel);          
429 >          
430 >            atomData6[0] = pos[0];
431 >            atomData6[1] = pos[1];
432 >            atomData6[2] = pos[2];
433  
434 <    strcpy( finalName, entry_plug->finalName );
434 >            atomData6[3] = vel[0];
435 >            atomData6[4] = vel[1];
436 >            atomData6[5] = vel[2];
437 >              
438 >            isDirectional = 0;
439  
440 <    finalOut.open( finalName, ios::out | ios::trunc );
382 <    if( !finalOut ){
383 <      sprintf( painCave.errMsg,
384 <               "Could not open \"%s\" for final dump output.\n",
385 <               finalName );
386 <      painCave.isFatal = 1;
387 <      simError();
388 <    }
440 >            if( sd->isDirectional() ){
441  
442 <    // finalOut.setf( ios::scientific );
442 >              isDirectional = 1;
443 >                
444 >              sd->getQ( q );
445 >              sd->getJ( ji );
446  
447 < #ifdef IS_MPI
448 <  }
447 >              for (int j = 0; j < 6 ; j++)
448 >                atomData13[j] = atomData6[j];            
449 >              
450 >              atomData13[6] = q[0];
451 >              atomData13[7] = q[1];
452 >              atomData13[8] = q[2];
453 >              atomData13[9] = q[3];
454 >              
455 >              atomData13[10] = ji[0];
456 >              atomData13[11] = ji[1];
457 >              atomData13[12] = ji[2];
458 >            }
459 >            
460 >        }
461 >        
462 >      currentIndex++;
463 >      }
464 >      // If we've survived to here, format the line:
465 >      
466 >      if (!isDirectional) {
467 >        
468 >        sprintf( writeLine,
469 >                 "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
470 >                 atomTypeString,
471 >                 atomData6[0],
472 >                 atomData6[1],
473 >                 atomData6[2],
474 >                 atomData6[3],
475 >                 atomData6[4],
476 >                 atomData6[5]);
477 >        
478 >        strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
479 >        
480 >      } else {
481 >        
482 >        sprintf( writeLine,
483 >                 "%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",
484 >                 atomTypeString,
485 >                 atomData13[0],
486 >                 atomData13[1],
487 >                 atomData13[2],
488 >                 atomData13[3],
489 >                 atomData13[4],
490 >                 atomData13[5],
491 >                 atomData13[6],
492 >                 atomData13[7],
493 >                 atomData13[8],
494 >                 atomData13[9],
495 >                 atomData13[10],
496 >                 atomData13[11],
497 >                 atomData13[12]);
498 >        
499 >      }
500 >      
501 >      for(k = 0; k < outFile.size(); k++)
502 >        *outFile[k] << writeLine;
503 >    }
504 >    
505 >    for(k = 0; k < outFile.size(); k++)
506 >      outFile[k]->flush();
507 >    
508 >    sprintf( checkPointMsg,
509 >             "Sucessfully took a dump.\n");
510 >    
511 >    MPIcheckPoint();        
512 >    
513 >    delete[] potatoes;
514 >    
515 >  } else {
516  
517 <  sprintf(checkPointMsg,"Opened file for final configuration\n");
396 <  MPIcheckPoint();
517 >    // worldRank != 0, so I'm a remote node.  
518  
519 < #endif //is_mpi
519 >    // Set my magic potato to 0:
520  
521 +    myPotato = 0;
522 +    currentIndex = 0;
523 +    
524 +    for (i = 0 ; i < mpiSim->getTotNmol(); i++ ) {
525 +      
526 +      // Am I the node which has this integrableObject?
527 +      
528 +      if (MolToProcMap[i] == worldRank) {
529  
401 – #ifndef IS_MPI
530  
531 <  finalOut << nAtoms << "\n";
531 >        if (myPotato + 1 >= MAXTAG) {
532 >          
533 >          // The potato was going to exceed the maximum value,
534 >          // so wrap this processor potato back to 0 (and block until
535 >          // node 0 says we can go:
536 >          
537 >          MPI_Recv(&myPotato, 1, MPI_INT, 0, 0, MPI_COMM_WORLD, &istatus);
538 >          
539 >        }
540  
541 <  finalOut << finalTime << ";\t"
542 <           << entry_plug->Hmat[0][0] << "\t"
543 <           << entry_plug->Hmat[1][0] << "\t"
544 <           << entry_plug->Hmat[2][0] << ";\t"
541 >          local_index = indexArray[currentIndex].first;        
542 >          integrableObjects = entry_plug->molecules[local_index].getIntegrableObjects();
543 >          
544 >          nCurObj = integrableObjects.size();
545 >                      
546 >          MPI_Send(&nCurObj, 1, MPI_INT, 0,
547 >                             myPotato, MPI_COMM_WORLD);
548 >          myPotato++;
549  
550 <           << entry_plug->Hmat[0][1] << "\t"
411 <           << entry_plug->Hmat[1][1] << "\t"
412 <           << entry_plug->Hmat[2][1] << ";\t"
550 >          for( iter = integrableObjects.begin(); iter  != integrableObjects.end(); iter++){
551  
552 <           << entry_plug->Hmat[0][2] << "\t"
553 <           << entry_plug->Hmat[1][2] << "\t"
554 <           << entry_plug->Hmat[2][2] << ";";
552 >            if (myPotato + 3 >= MAXTAG) {
553 >          
554 >              // The potato was going to exceed the maximum value,
555 >              // so wrap this processor potato back to 0 (and block until
556 >              // node 0 says we can go:
557 >          
558 >              MPI_Recv(&myPotato, 1, MPI_INT, 0, 0, MPI_COMM_WORLD, &istatus);
559 >              
560 >            }
561 >            
562 >            sd = *iter;
563 >            
564 >            atomTypeString = sd->getType();
565  
566 <  //write out additional parameters, such as chi and eta
567 <  finalOut << entry_plug->the_integrator->getAdditionalParameters();
420 <  finalOut << endl;
566 >            sd->getPos(pos);
567 >            sd->getVel(vel);
568  
569 <  for( i=0; i<nAtoms; i++ ){
569 >            atomData6[0] = pos[0];
570 >            atomData6[1] = pos[1];
571 >            atomData6[2] = pos[2];
572  
573 <    atoms[i]->getPos(pos);
574 <    atoms[i]->getVel(vel);
573 >            atomData6[3] = vel[0];
574 >            atomData6[4] = vel[1];
575 >            atomData6[5] = vel[2];
576 >              
577 >            isDirectional = 0;
578  
579 <    sprintf( tempBuffer,
428 <             "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
429 <             atoms[i]->getType(),
430 <             pos[0],
431 <             pos[1],
432 <             pos[2],
433 <             vel[0],
434 <             vel[1],
435 <             vel[2]);
436 <    strcpy( writeLine, tempBuffer );
579 >            if( sd->isDirectional() ){
580  
581 <    if( atoms[i]->isDirectional() ){
581 >                isDirectional = 1;
582 >                
583 >                sd->getQ( q );
584 >                sd->getJ( ji );
585 >                
586 >                for (int j = 0; j < 6 ; j++)
587 >                  atomData13[j] = atomData6[j];
588 >                
589 >                atomData13[6] = q[0];
590 >                atomData13[7] = q[1];
591 >                atomData13[8] = q[2];
592 >                atomData13[9] = q[3];
593 >      
594 >                atomData13[10] = ji[0];
595 >                atomData13[11] = ji[1];
596 >                atomData13[12] = ji[2];
597 >              }
598  
599 <      dAtom = (DirectionalAtom *)atoms[i];
600 <      dAtom->getQ( q );
599 >            
600 >            strncpy(MPIatomTypeString, atomTypeString, MINIBUFFERSIZE);
601  
602 <      sprintf( tempBuffer,
603 <               "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
445 <               q[0],
446 <               q[1],
447 <               q[2],
448 <               q[3],
449 <               dAtom->getJx(),
450 <               dAtom->getJy(),
451 <               dAtom->getJz());
452 <      strcat( writeLine, tempBuffer );
453 <    }
454 <    else
455 <      strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
456 <
457 <    finalOut << writeLine;
458 <  }
459 <  finalOut.flush();
460 <  finalOut.close();
602 >            // null terminate the string before sending (just in case):
603 >            MPIatomTypeString[MINIBUFFERSIZE-1] = '\0';
604  
605 < #else // is_mpi
605 >            MPI_Send(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, 0,
606 >                             myPotato, MPI_COMM_WORLD);
607 >            
608 >            myPotato++;
609  
610 <  // first thing first, suspend fatalities.
611 <  painCave.isEventLoop = 1;
610 >            MPI_Send(&isDirectional, 1, MPI_INT, 0,
611 >                             myPotato, MPI_COMM_WORLD);
612 >            
613 >            myPotato++;
614 >            
615 >            if (isDirectional) {
616  
617 <  int myStatus; // 1 = wakeup & success; 0 = error; -1 = AllDone
618 <  int haveError;
617 >              MPI_Send(atomData13, 13, MPI_DOUBLE, 0,
618 >                       myPotato, MPI_COMM_WORLD);
619 >              
620 >            } else {
621  
622 <  MPI_Status istatus;
623 <  int *AtomToProcMap = mpiSim->getAtomToProcMap();
622 >              MPI_Send(atomData6, 6, MPI_DOUBLE, 0,
623 >                       myPotato, MPI_COMM_WORLD);
624 >            }
625  
626 <  // write out header and node 0's coordinates
626 >            myPotato++;  
627  
628 <  haveError = 0;
476 <  if( worldRank == 0 ){
477 <    finalOut << mpiSim->getTotAtoms() << "\n";
628 >          }
629  
630 <    finalOut << finalTime << ";\t"
631 <             << entry_plug->Hmat[0][0] << "\t"
481 <             << entry_plug->Hmat[1][0] << "\t"
482 <             << entry_plug->Hmat[2][0] << ";\t"
483 <
484 <             << entry_plug->Hmat[0][1] << "\t"
485 <             << entry_plug->Hmat[1][1] << "\t"
486 <             << entry_plug->Hmat[2][1] << ";\t"
487 <
488 <             << entry_plug->Hmat[0][2] << "\t"
489 <             << entry_plug->Hmat[1][2] << "\t"
490 <             << entry_plug->Hmat[2][2] << ";";
491 <
492 <    //write out additional parameters, such as chi and eta
493 <    finalOut << entry_plug->the_integrator->getAdditionalParameters();
494 <    finalOut << endl;
495 <
496 <    for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) {
497 <      // Get the Node number which has this molecule:
498 <
499 <      which_node = AtomToProcMap[i];
500 <
501 <      if (which_node == mpiSim->getMyNode()) {
502 <
503 <        which_atom = i;
504 <        local_index=-1;
505 <        for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) {
506 <          if (atoms[j]->getGlobalIndex() == which_atom) local_index = j;
630 >          currentIndex++;    
631 >          
632          }
633 <        if (local_index != -1) {
509 <
510 <          atoms[local_index]->getPos(pos);
511 <          atoms[local_index]->getVel(vel);
512 <
513 <          sprintf( tempBuffer,
514 <                   "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
515 <                   atoms[local_index]->getType(),
516 <                   pos[0],
517 <                   pos[1],
518 <                   pos[2],
519 <                   vel[0],
520 <                   vel[1],
521 <                   vel[2]);
522 <          strcpy( writeLine, tempBuffer );
523 <
524 <          if( atoms[local_index]->isDirectional() ){
525 <
526 <            dAtom = (DirectionalAtom *)atoms[local_index];
527 <            dAtom->getQ( q );
528 <
529 <            sprintf( tempBuffer,
530 <                     "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
531 <                     q[0],
532 <                     q[1],
533 <                     q[2],
534 <                     q[3],
535 <                     dAtom->getJx(),
536 <                     dAtom->getJy(),
537 <                     dAtom->getJz());
538 <            strcat( writeLine, tempBuffer );
539 <          }
540 <          else
541 <            strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
542 <        }
543 <        else {
544 <          sprintf(painCave.errMsg,
545 <                  "Atom %d not found on processor %d\n",
546 <                  i, worldRank );
547 <          haveError= 1;
548 <          simError();
549 <        }
550 <
551 <        if(haveError) nodeZeroError();
552 <
633 >      
634        }
554 –      else {
635  
636 <        myStatus = 1;
637 <        MPI_Send(&myStatus, 1, MPI_INT, which_node,
638 <                 TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
639 <        MPI_Send(&i, 1, MPI_INT, which_node, TAKE_THIS_TAG_INT,
560 <                 MPI_COMM_WORLD);
561 <        MPI_Recv(writeLine, BUFFERSIZE, MPI_CHAR, which_node,
562 <                 TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD, &istatus);
563 <        MPI_Recv(&myStatus, 1, MPI_INT, which_node,
564 <                 TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus);
565 <
566 <        if(!myStatus) nodeZeroError();
567 <      }
568 <
569 <      finalOut << writeLine;
636 >    sprintf( checkPointMsg,
637 >             "Sucessfully took a dump.\n");
638 >    MPIcheckPoint();                
639 >    
640      }
641  
572 –    // kill everyone off:
573 –    myStatus = -1;
574 –    for (j = 1; j < mpiSim->getNumberProcessors(); j++) {
575 –      MPI_Send(&myStatus, 1, MPI_INT, j,
576 –               TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
577 –    }
642  
643 <  } else {
580 <
581 <    done = 0;
582 <    while (!done) {
583 <
584 <      MPI_Recv(&myStatus, 1, MPI_INT, 0,
585 <               TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus);
586 <
587 <      if(!myStatus) anonymousNodeDie();
588 <
589 <      if(myStatus < 0) break;
590 <
591 <      MPI_Recv(&which_atom, 1, MPI_INT, 0,
592 <               TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus);
593 <
594 <      myStatus = 1;
595 <      local_index=-1;
596 <      for (j=0; j < mpiSim->getMyNlocal(); j++) {
597 <        if (atoms[j]->getGlobalIndex() == which_atom) local_index = j;
598 <      }
599 <      if (local_index != -1) {
600 <
601 <        atoms[local_index]->getPos(pos);
602 <        atoms[local_index]->getVel(vel);
603 <
604 <        //format the line
605 <        sprintf( tempBuffer,
606 <                 "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
607 <                 atoms[local_index]->getType(),
608 <                 pos[0],
609 <                 pos[1],
610 <                 pos[2],
611 <                 vel[0],
612 <                 vel[1],
613 <                 vel[2]); // check here.
614 <        strcpy( writeLine, tempBuffer );
615 <
616 <        if( atoms[local_index]->isDirectional() ){
617 <
618 <          dAtom = (DirectionalAtom *)atoms[local_index];
619 <          dAtom->getQ( q );
620 <
621 <          sprintf( tempBuffer,
622 <                   "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
623 <                   q[0],
624 <                   q[1],
625 <                   q[2],
626 <                   q[3],
627 <                   dAtom->getJx(),
628 <                   dAtom->getJy(),
629 <                   dAtom->getJz());
630 <          strcat( writeLine, tempBuffer );
631 <        }
632 <        else{
633 <          strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
634 <        }
635 <      }
636 <      else {
637 <        sprintf(painCave.errMsg,
638 <                "Atom %d not found on processor %d\n",
639 <                which_atom, worldRank );
640 <        myStatus = 0;
641 <        simError();
642 <
643 <        strcpy( writeLine, "Hello, I'm an error.\n");
644 <      }
645 <
646 <      MPI_Send(writeLine, BUFFERSIZE, MPI_CHAR, 0,
647 <               TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD);
648 <      MPI_Send( &myStatus, 1, MPI_INT, 0,
649 <                TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
650 <    }
651 <  }
652 <  finalOut.flush();
653 <  sprintf( checkPointMsg,
654 <           "Sucessfully took a dump.\n");
655 <  MPIcheckPoint();
656 <
657 <  if( worldRank == 0 ) finalOut.close();
643 >  
644   #endif // is_mpi
645   }
646  
661 –
662 –
647   #ifdef IS_MPI
648  
649   // a couple of functions to let us escape the write loop
650  
651 < void dWrite::nodeZeroError( void ){
668 <  int j, myStatus;
651 > void dWrite::DieDieDie( void ){
652  
670 –  myStatus = 0;
671 –  for (j = 0; j < mpiSim->getNumberProcessors(); j++) {
672 –    MPI_Send( &myStatus, 1, MPI_INT, j,
673 –              TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
674 –  }
675 –
676 –
653    MPI_Finalize();
654    exit (0);
679 –
655   }
656  
682 – void dWrite::anonymousNodeDie( void ){
683 –
684 –  MPI_Finalize();
685 –  exit (0);
686 – }
687 –
657   #endif //is_mpi

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