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root/group/trunk/OOPSE/libmdtools/DumpWriter.cpp
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Comparing trunk/OOPSE/libmdtools/DumpWriter.cpp (file contents):
Revision 483 by gezelter, Wed Apr 9 04:06:43 2003 UTC vs.
Revision 949 by chuckv, Thu Jan 15 21:57:10 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 < #ifndef IS_MPI
99 >  //for (int i = 0; i < mpiSim->getMyNlocal(); i++) {
100 >  //  printf("node %d has global %d at local %d\n", worldRank, indexArray[i].second, indexArray[i].first);
101 >  //}
102      
103 <  outFile << nAtoms << "\n";
83 <    
84 <  outFile << currentTime << "\t"
85 <          << entry_plug->box_x << "\t"
86 <          << entry_plug->box_y << "\t"
87 <          << entry_plug->box_z << "\n";
88 <    
89 <  for( i=0; i<nAtoms; i++ ){
90 <      
103 > }
104  
105 <    sprintf( tempBuffer,
93 <             "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
94 <             atoms[i]->getType(),
95 <             atoms[i]->getX(),
96 <             atoms[i]->getY(),
97 <             atoms[i]->getZ(),
98 <             atoms[i]->get_vx(),
99 <             atoms[i]->get_vy(),
100 <             atoms[i]->get_vz());
101 <    strcpy( writeLine, tempBuffer );
105 > #endif
106  
107 <    if( atoms[i]->isDirectional() ){
104 <        
105 <      dAtom = (DirectionalAtom *)atoms[i];
106 <      dAtom->getQ( q );
107 <        
108 <      sprintf( tempBuffer,
109 <               "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
110 <               q[0],
111 <               q[1],
112 <               q[2],
113 <               q[3],
114 <               dAtom->getJx(),
115 <               dAtom->getJy(),
116 <               dAtom->getJz());
117 <      strcat( writeLine, tempBuffer );
118 <    }
119 <    else
120 <      strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
121 <      
122 <    outFile << writeLine;
123 <  }
124 <  outFile.flush();
107 > void DumpWriter::writeDump(double currentTime){
108  
109 < #else // is_mpi
109 >  ofstream finalOut;
110 >  vector<ofstream*> fileStreams;
111  
112 <  // first thing first, suspend fatalities.
113 <  painCave.isEventLoop = 1;
114 <
115 <  int myStatus; // 1 = wakeup & success; 0 = error; -1 = AllDone
132 <  int haveError;
133 <
134 <  MPI_Status istatus;
135 <  int *AtomToProcMap = mpiSim->getAtomToProcMap();
136 <  
137 <  // write out header and node 0's coordinates
138 <  
139 <  if( worldRank == 0 ){
140 <    outFile << mpiSim->getTotAtoms() << "\n";
112 > #ifdef IS_MPI
113 >  printf("Hello from node %d\n", worldRank);
114 >  sortByGlobalIndex();
115 >  if(worldRank == 0 ){
116      
117 <    outFile << currentTime << "\t"
118 <            << entry_plug->box_x << "\t"
119 <            << entry_plug->box_y << "\t"
120 <            << entry_plug->box_z << "\n";
121 <    outFile.flush();
122 <    for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) {
123 <      // Get the Node number which has this atom;
149 <      
150 <      which_node = AtomToProcMap[i];    
151 <      
152 <      if (which_node == 0 ) {
153 <        
154 <        haveError = 0;
155 <        which_atom = i;
156 <        local_index=-1;        
157 <        for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) {
158 <          if (atoms[j]->getGlobalIndex() == which_atom) local_index = j;
159 <        }
160 <        if (local_index != -1) {
161 <          //format the line
162 <          sprintf( tempBuffer,
163 <                   "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
164 <                   atoms[local_index]->getType(),
165 <                   atoms[local_index]->getX(),
166 <                   atoms[local_index]->getY(),
167 <                   atoms[local_index]->getZ(),
168 <                   atoms[local_index]->get_vx(),
169 <                   atoms[local_index]->get_vy(),
170 <                   atoms[local_index]->get_vz()); // check here.
171 <          strcpy( writeLine, tempBuffer );
172 <          
173 <          if( atoms[local_index]->isDirectional() ){
174 <            
175 <            dAtom = (DirectionalAtom *)atoms[local_index];
176 <            dAtom->getQ( q );
177 <            
178 <            sprintf( tempBuffer,
179 <                     "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
180 <                     q[0],
181 <                     q[1],
182 <                     q[2],
183 <                     q[3],
184 <                     dAtom->getJx(),
185 <                     dAtom->getJy(),
186 <                     dAtom->getJz());
187 <            strcat( writeLine, tempBuffer );
188 <            
189 <          }
190 <          else
191 <            strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );      
192 <        }
193 <        else {
194 <          sprintf(painCave.errMsg,
195 <                  "Atom %d not found on processor %d\n",
196 <                  i, worldRank );
197 <          haveError= 1;
198 <          simError();
199 <        }
200 <        
201 <        if(haveError) nodeZeroError();
202 <
203 <      }
204 <      else {
205 <        myStatus = 1;
206 <        MPI_Send(&myStatus, 1, MPI_INT, which_node,
207 <                 TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
208 <        MPI_Send(&i, 1, MPI_INT, which_node, TAKE_THIS_TAG_INT,
209 <                 MPI_COMM_WORLD);
210 <        MPI_Recv(writeLine, BUFFERSIZE, MPI_CHAR, which_node,
211 <                 TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD, &istatus);
212 <        MPI_Recv(&myStatus, 1, MPI_INT, which_node,
213 <                 TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus);
214 <        
215 <        if(!myStatus) nodeZeroError();
216 <
217 <      }
218 <      
219 <      outFile << writeLine;
220 <      outFile.flush();
117 >    finalOut.open( entry_plug->finalName, ios::out | ios::trunc );
118 >    if( !finalOut ){
119 >      sprintf( painCave.errMsg,
120 >               "Could not open \"%s\" for final dump output.\n",
121 >               entry_plug->finalName );
122 >      painCave.isFatal = 1;
123 >      simError();
124      }
125 <    
126 <    // kill everyone off:
224 <    myStatus = -1;
225 <    for (j = 0; j < mpiSim->getNumberProcessors(); j++) {      
226 <      MPI_Send(&myStatus, 1, MPI_INT, j,
227 <               TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
228 <    }
125 >  }
126 > #endif // is_mpi
127  
128 <  } else {
129 <    
232 <    done = 0;
233 <    while (!done) {
234 <      
235 <      MPI_Recv(&myStatus, 1, MPI_INT, 0,
236 <               TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus);
237 <
238 <      if(!myStatus) anonymousNodeDie();
239 <      
240 <      if(myStatus < 0) break;
128 >  fileStreams.push_back(&finalOut);
129 >  fileStreams.push_back(&dumpFile);
130  
131 <      MPI_Recv(&which_atom, 1, MPI_INT, 0,
243 <               TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus);
244 <      
245 <      myStatus = 1;
246 <      local_index=-1;        
247 <      for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) {
248 <        if (atoms[j]->getGlobalIndex() == which_atom) local_index = j;
249 <      }
250 <      if (local_index != -1) {
251 <        //format the line
252 <        sprintf( tempBuffer,
253 <                 "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
254 <                 atoms[local_index]->getType(),
255 <                 atoms[local_index]->getX(),
256 <                 atoms[local_index]->getY(),
257 <                 atoms[local_index]->getZ(),
258 <                 atoms[local_index]->get_vx(),
259 <                 atoms[local_index]->get_vy(),
260 <                 atoms[local_index]->get_vz()); // check here.
261 <        strcpy( writeLine, tempBuffer );
262 <        
263 <        if( atoms[local_index]->isDirectional() ){
264 <          
265 <          dAtom = (DirectionalAtom *)atoms[local_index];
266 <          dAtom->getQ( q );
267 <          
268 <          sprintf( tempBuffer,
269 <                   "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
270 <                   q[0],
271 <                   q[1],
272 <                   q[2],
273 <                   q[3],
274 <                   dAtom->getJx(),
275 <                   dAtom->getJy(),
276 <                   dAtom->getJz());
277 <          strcat( writeLine, tempBuffer );
278 <        }
279 <        else{
280 <          strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
281 <        }
282 <      }
283 <      else {
284 <        sprintf(painCave.errMsg,
285 <                "Atom %d not found on processor %d\n",
286 <                which_atom, worldRank );
287 <        myStatus = 0;
288 <        simError();
131 >  writeFrame(fileStreams, currentTime);
132  
133 <        strcpy( writeLine, "Hello, I'm an error.\n");
134 <      }
135 <
136 <      MPI_Send(writeLine, BUFFERSIZE, MPI_CHAR, 0,
294 <               TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD);
295 <      MPI_Send( &myStatus, 1, MPI_INT, 0,
296 <                TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
297 <    }
298 <  }  
299 <  outFile.flush();
300 <  sprintf( checkPointMsg,
301 <           "Sucessfully took a dump.\n");
302 <  MPIcheckPoint();
303 <
304 < // last  thing last, enable  fatalities.
305 <  painCave.isEventLoop = 0;
306 <
307 < #endif // is_mpi
133 > #ifdef IS_MPI
134 >  finalOut.close();
135 > #endif
136 >        
137   }
138  
139 < void DumpWriter::writeFinal(){
139 > void DumpWriter::writeFinal(double currentTime){
140  
312 –  char finalName[500];
141    ofstream finalOut;
142 +  vector<ofstream*> fileStreams;
143  
315 –  const int BUFFERSIZE = 2000;
316 –  char tempBuffer[BUFFERSIZE];
317 –  char writeLine[BUFFERSIZE];  
318 –
319 –  double q[4];
320 –  DirectionalAtom* dAtom;
321 –  int nAtoms = entry_plug->n_atoms;
322 –  Atom** atoms = entry_plug->atoms;
323 –  int i, j, which_node, done, game_over, which_atom, local_index;
324 –  
325 –  
144   #ifdef IS_MPI
145    if(worldRank == 0 ){
146 < #endif // is_mpi
147 <    
148 <    strcpy( finalName, entry_plug->finalName );
331 <    
332 <    finalOut.open( finalName, ios::out | ios::trunc );
146 >
147 >    finalOut.open( entry_plug->finalName, ios::out | ios::trunc );
148 >
149      if( !finalOut ){
150        sprintf( painCave.errMsg,
151                 "Could not open \"%s\" for final dump output.\n",
152 <               finalName );
152 >               entry_plug->finalName );
153        painCave.isFatal = 1;
154        simError();
155      }
156 <    
341 <    // finalOut.setf( ios::scientific );
342 <    
343 < #ifdef IS_MPI
156 >
157    }
158 + #endif // is_mpi
159    
160 <  sprintf(checkPointMsg,"Opened file for final configuration\n");
161 <  MPIcheckPoint();  
160 >  fileStreams.push_back(&finalOut);  
161 >  writeFrame(fileStreams, currentTime);
162 >
163 > #ifdef IS_MPI
164 >  finalOut.close();
165 > #endif
166    
167 < #endif //is_mpi
167 > }
168  
169 + void DumpWriter::writeFrame( vector<ofstream*>& outFile, double currentTime ){
170 +
171 +  const int BUFFERSIZE = 2000;
172 +  const int MINIBUFFERSIZE = 100;
173 +
174 +  char tempBuffer[BUFFERSIZE];  
175 +  char writeLine[BUFFERSIZE];
176 +
177 +  int i, k;
178 +
179 + #ifdef IS_MPI
180    
181 +  /*********************************************************************
182 +   * Documentation?  You want DOCUMENTATION?
183 +   *
184 +   * Why all the potatoes below?  
185 +   *
186 +   * To make a long story short, the original version of DumpWriter
187 +   * worked in the most inefficient way possible.  Node 0 would
188 +   * poke each of the node for an individual atom's formatted data
189 +   * as node 0 worked its way down the global index. This was particularly
190 +   * inefficient since the method blocked all processors at every atom
191 +   * (and did it twice!).
192 +   *
193 +   * An intermediate version of DumpWriter could be described from Node
194 +   * zero's perspective as follows:
195 +   *
196 +   *  1) Have 100 of your friends stand in a circle.
197 +   *  2) When you say go, have all of them start tossing potatoes at
198 +   *     you (one at a time).
199 +   *  3) Catch the potatoes.
200 +   *
201 +   * It was an improvement, but MPI has buffers and caches that could
202 +   * best be described in this analogy as "potato nets", so there's no
203 +   * need to block the processors atom-by-atom.
204 +   *
205 +   * This new and improved DumpWriter works in an even more efficient
206 +   * way:
207 +   *
208 +   *  1) Have 100 of your friend stand in a circle.
209 +   *  2) When you say go, have them start tossing 5-pound bags of
210 +   *     potatoes at you.
211 +   *  3) Once you've caught a friend's bag of potatoes,
212 +   *     toss them a spud to let them know they can toss another bag.
213 +   *
214 +   * How's THAT for documentation?
215 +   *
216 +   *********************************************************************/
217 +
218 +  int *potatoes;
219 +  int myPotato;
220 +
221 +  int nProc;
222 +  int j, which_node, done, which_atom, local_index, currentIndex;
223 +  double atomData6[6];
224 +  double atomData13[13];
225 +  int isDirectional;
226 +  char* atomTypeString;
227 +  char MPIatomTypeString[MINIBUFFERSIZE];
228 +
229 + #else //is_mpi
230 +  int nAtoms = entry_plug->n_atoms;
231 + #endif //is_mpi
232 +
233 +  double q[4];
234 +  DirectionalAtom* dAtom;
235 +  Atom** atoms = entry_plug->atoms;
236 +  double pos[3], vel[3];
237 +
238   #ifndef IS_MPI
353 –    
354 –  finalOut << nAtoms << "\n";
355 –    
356 –  finalOut << entry_plug->box_x << "\t"
357 –           << entry_plug->box_y << "\t"
358 –           << entry_plug->box_z << "\n";
239    
240 +  for(k = 0; k < outFile.size(); k++){
241 +    *outFile[k] << nAtoms << "\n";
242 +
243 +    *outFile[k] << currentTime << ";\t"
244 +               << entry_plug->Hmat[0][0] << "\t"
245 +                     << entry_plug->Hmat[1][0] << "\t"
246 +                     << entry_plug->Hmat[2][0] << ";\t"
247 +              
248 +               << entry_plug->Hmat[0][1] << "\t"
249 +                     << entry_plug->Hmat[1][1] << "\t"
250 +                     << entry_plug->Hmat[2][1] << ";\t"
251 +
252 +                     << entry_plug->Hmat[0][2] << "\t"
253 +                     << entry_plug->Hmat[1][2] << "\t"
254 +                     << entry_plug->Hmat[2][2] << ";";
255 +
256 +    //write out additional parameters, such as chi and eta
257 +    *outFile[k] << entry_plug->the_integrator->getAdditionalParameters() << endl;
258 +  }
259 +  
260    for( i=0; i<nAtoms; i++ ){
261 <      
261 >
262 >    atoms[i]->getPos(pos);
263 >    atoms[i]->getVel(vel);
264 >
265      sprintf( tempBuffer,
266               "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
267               atoms[i]->getType(),
268 <             atoms[i]->getX(),
269 <             atoms[i]->getY(),
270 <             atoms[i]->getZ(),
271 <             atoms[i]->get_vx(),
272 <             atoms[i]->get_vy(),
273 <             atoms[i]->get_vz());
268 >             pos[0],
269 >             pos[1],
270 >             pos[2],
271 >             vel[0],
272 >             vel[1],
273 >             vel[2]);
274      strcpy( writeLine, tempBuffer );
275  
276      if( atoms[i]->isDirectional() ){
277 <        
277 >
278        dAtom = (DirectionalAtom *)atoms[i];
279        dAtom->getQ( q );
280 <        
280 >
281        sprintf( tempBuffer,
282                 "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
283                 q[0],
# Line 388 | Line 291 | void DumpWriter::writeFinal(){
291      }
292      else
293        strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
294 <      
295 <    finalOut << writeLine;
294 >
295 >    for(k = 0; k < outFile.size(); k++)
296 >      *outFile[k] << writeLine;
297    }
394 –  finalOut.flush();
395 –  finalOut.close();
298  
299   #else // is_mpi
300 +
301 +  /* code to find maximum tag value */
302    
303 <  // first thing first, suspend fatalities.
304 <  painCave.isEventLoop = 1;
303 >  int *tagub, flag, MAXTAG;
304 >  MPI_Attr_get(MPI_COMM_WORLD, MPI_TAG_UB, &tagub, &flag);
305 >  if (flag) {
306 >    MAXTAG = *tagub;
307 >  } else {
308 >    MAXTAG = 32767;
309 >  }  
310  
402 –  int myStatus; // 1 = wakeup & success; 0 = error; -1 = AllDone
311    int haveError;
312  
313    MPI_Status istatus;
314    int *AtomToProcMap = mpiSim->getAtomToProcMap();
315  
316    // write out header and node 0's coordinates
317 <  
410 <  haveError = 0;
317 >
318    if( worldRank == 0 ){
319 <    finalOut << mpiSim->getTotAtoms() << "\n";
319 >
320 >    // Node 0 needs a list of the magic potatoes for each processor;
321 >
322 >    nProc = mpiSim->getNumberProcessors();
323 >    potatoes = new int[nProc];
324 >
325 >    //write out the comment lines
326 >    for (i = 0; i < nProc; i++)
327 >      potatoes[i] = 0;
328      
329 <    finalOut << entry_plug->box_x << "\t"
330 <            << entry_plug->box_y << "\t"
331 <            << entry_plug->box_z << "\n";
332 <    
329 >      for(k = 0; k < outFile.size(); k++){
330 >        *outFile[k] << mpiSim->getTotAtoms() << "\n";
331 >
332 >        *outFile[k] << currentTime << ";\t"
333 >                         << entry_plug->Hmat[0][0] << "\t"
334 >                         << entry_plug->Hmat[1][0] << "\t"
335 >                         << entry_plug->Hmat[2][0] << ";\t"
336 >
337 >                         << entry_plug->Hmat[0][1] << "\t"
338 >                         << entry_plug->Hmat[1][1] << "\t"
339 >                         << entry_plug->Hmat[2][1] << ";\t"
340 >
341 >                         << entry_plug->Hmat[0][2] << "\t"
342 >                         << entry_plug->Hmat[1][2] << "\t"
343 >                         << entry_plug->Hmat[2][2] << ";";
344 >  
345 >        *outFile[k] << entry_plug->the_integrator->getAdditionalParameters() << endl;
346 >    }
347 >
348 >    currentIndex = 0;
349 >
350      for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) {
419 –      // Get the Node number which has this molecule:
351        
352 <      which_node = AtomToProcMap[i];    
352 >      // Get the Node number which has this atom;
353        
354 <      if (which_node == mpiSim->getMyNode()) {
354 >      which_node = AtomToProcMap[i];
355 >      
356 >      if (which_node != 0) {
357  
358 <        which_atom = i;
359 <        local_index=-1;        
360 <        for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) {
361 <          if (atoms[j]->getGlobalIndex() == which_atom) local_index = j;
358 >        if (potatoes[which_node] + 3 >= MAXTAG) {
359 >          // The potato was going to exceed the maximum value,
360 >          // so wrap this processor potato back to 0:        
361 >
362 >          potatoes[which_node] = 0;          
363 >          MPI_Send(0, 1, MPI_INT, which_node, 0, MPI_COMM_WORLD);
364 >          
365          }
366 <        if (local_index != -1) {        
367 <          sprintf( tempBuffer,
368 <                   "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
369 <                   atoms[local_index]->getType(),
370 <                   atoms[local_index]->getX(),
371 <                   atoms[local_index]->getY(),
372 <                   atoms[local_index]->getZ(),
373 <                   atoms[local_index]->get_vx(),
374 <                   atoms[local_index]->get_vy(),
375 <                   atoms[local_index]->get_vz());
376 <          strcpy( writeLine, tempBuffer );
366 >
367 >        myPotato = potatoes[which_node];        
368 >        
369 >        MPI_Recv(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, which_node,
370 >                 myPotato, MPI_COMM_WORLD, &istatus);
371 >        
372 >        atomTypeString = MPIatomTypeString;
373 >        
374 >        myPotato++;
375 >
376 >        MPI_Recv(&isDirectional, 1, MPI_INT, which_node,
377 >                 myPotato, MPI_COMM_WORLD, &istatus);
378 >              
379 >        myPotato++;
380 >
381 >        if (isDirectional) {          
382 >          MPI_Recv(atomData13, 13, MPI_DOUBLE, which_node,
383 >                   myPotato, MPI_COMM_WORLD, &istatus);
384 >        } else {
385 >          MPI_Recv(atomData6, 6, MPI_DOUBLE, which_node,
386 >                   myPotato, MPI_COMM_WORLD, &istatus);          
387 >        }
388 >        
389 >        myPotato++;
390 >        potatoes[which_node] = myPotato;
391 >
392 >      } else {
393 >        
394 >        haveError = 0;
395 >        which_atom = i;
396 >        
397 >        //local_index = -1;
398 >
399 >        //for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) {
400 >        //  if (atoms[j]->getGlobalIndex() == which_atom) local_index = j;
401 >        //}
402 >        
403 >        //if (local_index != -1) {
404            
405 <          if( atoms[local_index]->isDirectional() ){
405 >          local_index = indexArray[currentIndex].first;        
406 >          
407 >          if (which_atom == indexArray[currentIndex].second) {
408              
409 <            dAtom = (DirectionalAtom *)atoms[local_index];
445 <            dAtom->getQ( q );
409 >            atomTypeString = atoms[local_index]->getType();
410              
411 <            sprintf( tempBuffer,
412 <                     "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
413 <                     q[0],
414 <                     q[1],
415 <                     q[2],
416 <                     q[3],
417 <                     dAtom->getJx(),
418 <                     dAtom->getJy(),
419 <                     dAtom->getJz());
420 <            strcat( writeLine, tempBuffer );
421 <          }
422 <          else
423 <            strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );      
424 <        }
425 <        else {
411 >          atoms[local_index]->getPos(pos);
412 >          atoms[local_index]->getVel(vel);          
413 >          
414 >          atomData6[0] = pos[0];
415 >          atomData6[1] = pos[1];
416 >          atomData6[2] = pos[2];
417 >
418 >          atomData6[3] = vel[0];
419 >          atomData6[4] = vel[1];
420 >          atomData6[5] = vel[2];
421 >          
422 >          isDirectional = 0;
423 >
424 >          if( atoms[local_index]->isDirectional() ){
425 >
426 >            isDirectional = 1;
427 >            
428 >            dAtom = (DirectionalAtom *)atoms[local_index];
429 >            dAtom->getQ( q );
430 >
431 >            for (int j = 0; j < 6 ; j++)
432 >              atomData13[j] = atomData6[j];            
433 >            
434 >            atomData13[6] = q[0];
435 >            atomData13[7] = q[1];
436 >            atomData13[8] = q[2];
437 >            atomData13[9] = q[3];
438 >            
439 >            atomData13[10] = dAtom->getJx();
440 >            atomData13[11] = dAtom->getJy();
441 >            atomData13[12] = dAtom->getJz();
442 >          }
443 >          
444 >        } else {
445            sprintf(painCave.errMsg,
446 <                  "Atom %d not found on processor %d\n",
447 <                  i, worldRank );
446 >                  "Atom %d not found on processor %d, currentIndex = %d, local_index = %d\n",
447 >                  which_atom, worldRank, currentIndex, local_index );
448            haveError= 1;
449            simError();
450 <        }
468 <
469 <        if(haveError) nodeZeroError();
470 <    
471 <      }
472 <      else {
450 >        }
451          
452 <        myStatus = 1;
453 <        MPI_Send(&myStatus, 1, MPI_INT, which_node,
454 <                 TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
455 <        MPI_Send(&i, 1, MPI_INT, which_node, TAKE_THIS_TAG_INT,
456 <                 MPI_COMM_WORLD);
457 <        MPI_Recv(writeLine, BUFFERSIZE, MPI_CHAR, which_node,
458 <                 TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD, &istatus);
481 <        MPI_Recv(&myStatus, 1, MPI_INT, which_node,
482 <                 TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus);
452 >        if(haveError) DieDieDie();
453 >        
454 >        currentIndex++;
455 >      }
456 >      // If we've survived to here, format the line:
457 >      
458 >      if (!isDirectional) {
459          
460 <        if(!myStatus) nodeZeroError();
460 >        sprintf( writeLine,
461 >                 "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
462 >                 atomTypeString,
463 >                 atomData6[0],
464 >                 atomData6[1],
465 >                 atomData6[2],
466 >                 atomData6[3],
467 >                 atomData6[4],
468 >                 atomData6[5]);
469 >        
470 >        strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
471 >        
472 >      } else {
473 >        
474 >        sprintf( writeLine,
475 >                 "%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",
476 >                 atomTypeString,
477 >                 atomData13[0],
478 >                 atomData13[1],
479 >                 atomData13[2],
480 >                 atomData13[3],
481 >                 atomData13[4],
482 >                 atomData13[5],
483 >                 atomData13[6],
484 >                 atomData13[7],
485 >                 atomData13[8],
486 >                 atomData13[9],
487 >                 atomData13[10],
488 >                 atomData13[11],
489 >                 atomData13[12]);
490 >        
491        }
492        
493 <      finalOut << writeLine;
493 >      for(k = 0; k < outFile.size(); k++)
494 >        *outFile[k] << writeLine;
495      }
496      
497 <    // kill everyone off:
498 <    myStatus = -1;
492 <    for (j = 0; j < mpiSim->getNumberProcessors(); j++) {      
493 <      MPI_Send(&myStatus, 1, MPI_INT, j,
494 <               TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
495 <    }
496 <
497 <  } else {
497 >    for(k = 0; k < outFile.size(); k++)
498 >      outFile[k]->flush();
499      
500 <    done = 0;
501 <    while (!done) {
500 >    sprintf( checkPointMsg,
501 >             "Sucessfully took a dump.\n");
502 >    
503 >    MPIcheckPoint();        
504 >    
505 >    delete[] potatoes;
506 >    
507 >  } else {
508  
509 <      MPI_Recv(&myStatus, 1, MPI_INT, 0,
510 <               TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus);
509 >    // worldRank != 0, so I'm a remote node.  
510 >
511 >    // Set my magic potato to 0:
512 >
513 >    myPotato = 0;
514 >    currentIndex = 0;
515 >    
516 >    for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) {
517        
518 <      if(!myStatus) anonymousNodeDie();
518 >      // Am I the node which has this atom?
519        
520 <      if(myStatus < 0) break;
508 <      
509 <      MPI_Recv(&which_atom, 1, MPI_INT, 0,
510 <               TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus);
511 <      
512 <      myStatus = 1;
513 <      local_index=-1;        
514 <      for (j=0; j < mpiSim->getMyNlocal(); j++) {
515 <        if (atoms[j]->getGlobalIndex() == which_atom) local_index = j;
516 <      }
517 <      if (local_index != -1) {
520 >      if (AtomToProcMap[i] == worldRank) {
521  
522 <        //format the line
520 <        sprintf( tempBuffer,
521 <                 "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
522 <                 atoms[local_index]->getType(),
523 <                 atoms[local_index]->getX(),
524 <                 atoms[local_index]->getY(),
525 <                 atoms[local_index]->getZ(),
526 <                 atoms[local_index]->get_vx(),
527 <                 atoms[local_index]->get_vy(),
528 <                 atoms[local_index]->get_vz()); // check here.
529 <        strcpy( writeLine, tempBuffer );
530 <        
531 <        if( atoms[local_index]->isDirectional() ){
522 >        if (myPotato + 3 >= MAXTAG) {
523            
524 <          dAtom = (DirectionalAtom *)atoms[local_index];
525 <          dAtom->getQ( q );
524 >          // The potato was going to exceed the maximum value,
525 >          // so wrap this processor potato back to 0 (and block until
526 >          // node 0 says we can go:
527            
528 <          sprintf( tempBuffer,
529 <                   "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
530 <                   q[0],
531 <                   q[1],
532 <                   q[2],
533 <                   q[3],
534 <                   dAtom->getJx(),
535 <                   dAtom->getJy(),
536 <                   dAtom->getJz());
537 <          strcat( writeLine, tempBuffer );
528 >          MPI_Recv(&myPotato, 1, MPI_INT, 0, 0, MPI_COMM_WORLD, &istatus);
529 >          
530 >        }
531 >        which_atom = i;
532 >
533 >        //local_index = -1;
534 >
535 >        //for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) {
536 >        // if (atoms[j]->getGlobalIndex() == which_atom) local_index = j;
537 >        //}
538 >        
539 >        //if (local_index != -1) {
540 >
541 >        local_index = indexArray[currentIndex].first;        
542 >                
543 >        if (which_atom == indexArray[currentIndex].second) {
544 >        
545 >          atomTypeString = atoms[local_index]->getType();
546 >          
547 >          atoms[local_index]->getPos(pos);
548 >          atoms[local_index]->getVel(vel);
549 >          
550 >          atomData6[0] = pos[0];
551 >          atomData6[1] = pos[1];
552 >          atomData6[2] = pos[2];
553 >
554 >          atomData6[3] = vel[0];
555 >          atomData6[4] = vel[1];
556 >          atomData6[5] = vel[2];
557 >          
558 >          isDirectional = 0;
559 >
560 >          if( atoms[local_index]->isDirectional() ){
561 >
562 >            isDirectional = 1;
563 >            
564 >            dAtom = (DirectionalAtom *)atoms[local_index];
565 >            dAtom->getQ( q );
566 >            
567 >            for (int j = 0; j < 6 ; j++)
568 >              atomData13[j] = atomData6[j];
569 >            
570 >            atomData13[6] = q[0];
571 >            atomData13[7] = q[1];
572 >            atomData13[8] = q[2];
573 >            atomData13[9] = q[3];
574 >  
575 >            atomData13[10] = dAtom->getJx();
576 >            atomData13[11] = dAtom->getJy();
577 >            atomData13[12] = dAtom->getJz();
578 >          }
579 >
580 >        } else {
581 >          sprintf(painCave.errMsg,
582 >                  "Atom %d not found on processor %d, currentIndex = %d, local_index = %d\n",
583 >                  which_atom, worldRank, currentIndex, local_index );
584 >          haveError= 1;
585 >          simError();
586          }
547 –        else{
548 –          strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
549 –        }
550 –      }
551 –      else {
552 –        sprintf(painCave.errMsg,
553 –                "Atom %d not found on processor %d\n",
554 –                which_atom, worldRank );
555 –        myStatus = 0;
556 –        simError();
587          
588 <        strcpy( writeLine, "Hello, I'm an error.\n");
559 <      }
588 >        strncpy(MPIatomTypeString, atomTypeString, MINIBUFFERSIZE);
589  
590 <      MPI_Send(writeLine, BUFFERSIZE, MPI_CHAR, 0,
591 <               TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD);
592 <      MPI_Send( &myStatus, 1, MPI_INT, 0,
593 <                TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
590 >        // null terminate the string before sending (just in case):
591 >        MPIatomTypeString[MINIBUFFERSIZE-1] = '\0';
592 >
593 >        MPI_Send(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, 0,
594 >                             myPotato, MPI_COMM_WORLD);
595 >        
596 >        myPotato++;
597 >
598 >        MPI_Send(&isDirectional, 1, MPI_INT, 0,
599 >                             myPotato, MPI_COMM_WORLD);
600 >        
601 >        myPotato++;
602 >        
603 >        if (isDirectional) {
604 >
605 >          MPI_Send(atomData13, 13, MPI_DOUBLE, 0,
606 >                   myPotato, MPI_COMM_WORLD);
607 >          
608 >        } else {
609 >
610 >          MPI_Send(atomData6, 6, MPI_DOUBLE, 0,
611 >                   myPotato, MPI_COMM_WORLD);
612 >        }
613 >
614 >        myPotato++;  
615 >        currentIndex++;    
616 >      }
617      }
618 <  }
619 <  finalOut.flush();
620 <  sprintf( checkPointMsg,
621 <           "Sucessfully took a dump.\n");
622 <  MPIcheckPoint();
618 >
619 >    sprintf( checkPointMsg,
620 >             "Sucessfully took a dump.\n");
621 >    MPIcheckPoint();        
622 >    
623 >  }
624    
572 –  if( worldRank == 0 ) finalOut.close();    
625   #endif // is_mpi
626   }
627  
576 –
577 –
628   #ifdef IS_MPI
629  
630   // a couple of functions to let us escape the write loop
631  
632 < void dWrite::nodeZeroError( void ){
583 <  int j, myStatus;
584 <  
585 <  myStatus = 0;
586 <  for (j = 0; j < mpiSim->getNumberProcessors(); j++) {      
587 <    MPI_Send( &myStatus, 1, MPI_INT, j,
588 <              TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
589 <  }  
590 <  
632 > void dWrite::DieDieDie( void ){
633  
634    MPI_Finalize();
635    exit (0);
594 –  
636   }
637  
597 – void dWrite::anonymousNodeDie( void ){
598 –
599 –  MPI_Finalize();
600 –  exit (0);
601 – }
602 –
638   #endif //is_mpi

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