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root/group/trunk/mdtools/md_code/InitializeFromFile.cpp
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Comparing trunk/mdtools/md_code/InitializeFromFile.cpp (file contents):
Revision 162 by mmeineke, Thu Oct 31 21:20:49 2002 UTC vs.
Revision 249 by chuckv, Mon Jan 27 21:28:19 2003 UTC

# Line 11 | Line 11
11   #include "ReadWrite.hpp"
12   #include "simError.h"
13  
14 + #ifdef IS_MPI
15 + #include "mpiSimulation.hpp"
16 + #endif // is_mpi
17  
18   InitializeFromFile :: InitializeFromFile( char *in_name ){
19 + #ifdef IS_MPI
20 +  if (worldRank == 0) {
21 + #endif
22  
23    c_in_file = fopen(in_name, "r");
24    if(c_in_file == NULL){
# Line 23 | Line 29 | InitializeFromFile :: InitializeFromFile( char *in_nam
29    }
30    
31    strcpy( c_in_name, in_name);
32 + #ifdef IS_MPI
33 +  }
34 + strcpy( checkPointMsg, "Infile opened for reading successfully." );
35 +  MPIcheckPoint();
36 + #endif
37    return;  
38   }
39  
40   InitializeFromFile :: ~InitializeFromFile( ){
41 <  
41 > #ifdef IS_MPI
42 >  if (worldRank == 0) {
43 > #endif
44    int error;
45    error = fclose( c_in_file );
46    if( error ){
# Line 35 | Line 48 | InitializeFromFile :: ~InitializeFromFile( ){
48               "Error closing %s\n", c_in_name );
49      simError();
50    }
51 + #ifdef IS_MPI
52 +  }
53 +  strcpy( checkPointMsg, "Infile closed successfully." );
54 +  MPIcheckPoint();
55 + #endif
56 +
57    return;
58   }
59  
60  
61 < void InitializeFromFile :: read_xyz( SimInfo* entry_plug ){
61 > void InitializeFromFile :: read_xyz( SimInfo* the_entry_plug ){
62  
63    int i; // loop counter
64  
65 +  const int BUFFERSIZE = 2000; // size of the read buffer
66    int n_atoms; // the number of atoms
67 <  char read_buffer[2000]; //the line buffer for reading
67 >  char read_buffer[BUFFERSIZE]; //the line buffer for reading
68 > #ifdef IS_MPI
69 >  char send_buffer[BUFFERSIZE];
70 > #endif
71 >
72    char *eof_test; // ptr to see when we reach the end of the file
73 <  char *foo; // the pointer to the current string token
73 >  char *parseErr;
74  
51 –  double rx, ry, rz; // position place holders
52 –  double vx, vy, vz; // velocity placeholders
53 –  double q[4]; // the quaternions
54 –  double jx, jy, jz; // angular velocity placeholders;
55 –  double qSqr, qLength; // needed to normalize the quaternion vector.
75  
76 +  entry_plug = the_entry_plug;
77 +
78 +
79 + #ifndef IS_MPI
80    eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file);
81    if( eof_test == NULL ){
82 <    std::cerr << "error reading 1st line of" << c_in_name << "\n";
82 >    sprintf( painCave.errMsg,
83 >             "InitializeFromFile error: error reading 1st line of \"%s\"\n",
84 >             c_in_name );
85 >    painCave.isFatal = 1;
86 >    simError();
87    }
88  
89 <  (void)sscanf(read_buffer, "%d", &n_atoms);
89 >  n_atoms = atoi( read_buffer );
90  
91    Atom **atoms = entry_plug->atoms;
92    DirectionalAtom* dAtom;
# Line 96 | Line 123 | void InitializeFromFile :: read_xyz( SimInfo* entry_pl
123        simError();
124      }
125  
99 –    foo = strtok(read_buffer, " ,;\t");
126      
127 <    // check the atom name to the current atom
128 <
129 <    if( strcmp( foo, atoms[i]->getType() ) ){
104 <      sprintf( painCave.errMsg,
105 <               "Initialize from file error. Atom %s at index %d "
106 <               "in file %s does not"
107 <               " match the BASS atom %s.\n",
108 <               foo, i, c_in_name, atoms[i]->getType() );
127 >    parseErr = parseDumpLine( read_buffer, i );
128 >    if( parseErr != NULL ){
129 >      strcpy( painCave.errMsg, parseErr );
130        painCave.isFatal = 1;
131        simError();
132 <    }
133 <    
113 <    // get the positions
132 >    }    
133 >  }
134  
115 –    foo = strtok(NULL, " ,;\t");
116 –    if(foo == NULL){
117 –      sprintf( painCave.errMsg,
118 –               "error in reading postition x from %s\n"
119 –               "natoms  = %d, index = %d\n",
120 –               c_in_name, n_atoms, i );
121 –      painCave.isFatal = 1;
122 –      simError();
123 –    }
124 –    (void)sscanf( foo, "%lf", &rx );
125 –  
126 –    foo = strtok(NULL, " ,;\t");
127 –    if(foo == NULL){
128 –      sprintf( painCave.errMsg,
129 –               "error in reading postition y from %s\n"
130 –               "natoms  = %d, index = %d\n",
131 –               c_in_name, n_atoms, i );
132 –      painCave.isFatal = 1;
133 –      simError();
134 –    }
135 –    (void)sscanf( foo, "%lf", &ry );
136 –    
137 –    foo = strtok(NULL, " ,;\t");
138 –    if(foo == NULL){
139 –      sprintf( painCave.errMsg,
140 –               "error in reading postition z from %s\n"
141 –               "natoms  = %d, index = %d\n",
142 –               c_in_name, n_atoms, i );
143 –      painCave.isFatal = 1;
144 –      simError();
145 –    }
146 –    (void)sscanf( foo, "%lf", &rz );
147 –    
148 –    // get the velocities
135  
136 <    foo = strtok(NULL, " ,;\t");
137 <    if(foo == NULL){
136 >  // MPI Section of code..........
137 > #else //IS_MPI
138 >
139 >  int masterIndex;
140 >  int nodeAtomsStart;
141 >  int nodeAtomsEnd;
142 >  int mpiErr;
143 >  int sendError;
144 >
145 >  MPI_Status istatus[MPI_STATUS_SIZE];
146 >
147 >  if (worldRank == 0) {
148 >    eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file);
149 >    if( eof_test == NULL ){
150        sprintf( painCave.errMsg,
151 <               "error in reading velocity x from %s\n"
154 <               "natoms  = %d, index = %d\n",
155 <               c_in_name, n_atoms, i );
151 >               "Error reading 1st line of %d \n ",c_in_name);
152        painCave.isFatal = 1;
153        simError();
154      }
159 –    (void)sscanf( foo, "%lf", &vx );
155      
156 <    foo = strtok(NULL, " ,;\t");
157 <    if(foo == NULL){
156 >    n_atoms = atoi( read_buffer );
157 >    
158 >    Atom **atoms = entry_plug->atoms;
159 >    DirectionalAtom* dAtom;
160 >
161 >    // Check to see that the number of atoms in the intial configuration file is the
162 >    // same as declared in simBass.
163 >    
164 >    if( n_atoms != mpiSim->getTotAtoms() ){
165        sprintf( painCave.errMsg,
166 <               "error in reading velocity y from %s\n"
167 <               "natoms  = %d, index = %d\n",
168 <               c_in_name, n_atoms, i );
166 >               "Initialize from File error. %s n_atoms, %d, "
167 >               "does not match the BASS file's n_atoms, %d.\n",
168 >               c_in_name, n_atoms, entry_plug->n_atoms );
169        painCave.isFatal = 1;
170        simError();
171      }
170 –    (void)sscanf( foo, "%lf", &vy );
172      
173 <    foo = strtok(NULL, " ,;\t");
174 <    if(foo == NULL){
173 >    //read and toss the comment line
174 >    
175 >    eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file);
176 >    if(eof_test == NULL){
177        sprintf( painCave.errMsg,
178 <               "error in reading velocity z from %s\n"
176 <               "natoms  = %d, index = %d\n",
177 <               c_in_name, n_atoms, i );
178 >               "error in reading commment in %s\n", c_in_name);
179        painCave.isFatal = 1;
180        simError();
181      }
182 <    (void)sscanf( foo, "%lf", &vz );
182 >  
183 >    // Read Proc 0 share of the xyz file...
184 >    masterIndex = 0;
185 >    for( i=0; i <= mpiSim->getMyAtomEnd(); i++){
186      
187 <    
188 <    // get the quaternions
185 <    
186 <    if( atoms[i]->isDirectional() ){
187 <      
188 <      foo = strtok(NULL, " ,;\t");
189 <      if(foo == NULL){
187 >      eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file);
188 >      if(eof_test == NULL){
189          sprintf(painCave.errMsg,
190 <                "error in reading quaternion 0 from %s\n"
191 <                "natoms  = %d, index = %d\n",
190 >                "error in reading file %s\n"
191 >                "natoms  = %d; index = %d\n"
192 >                "error reading the line from the file.\n",
193                  c_in_name, n_atoms, i );
194          painCave.isFatal = 1;
195          simError();
196        }
197 <      (void)sscanf( foo, "%lf", &q[0] );
198 <      
199 <      foo = strtok(NULL, " ,;\t");
200 <      if(foo == NULL){
201 <        sprintf( painCave.errMsg,
202 <                 "error in reading quaternion 1 from %s\n"
203 <                 "natoms  = %d, index = %d\n",
204 <                 c_in_name, n_atoms, i );
197 >    
198 >      parseErr = parseDumpLine( read_buffer, i );
199 >      if( parseErr != NULL ){
200 >        strcpy( painCave.errMsg, parseErr );
201          painCave.isFatal = 1;
202          simError();
203 <      }
204 <      (void)sscanf( foo, "%lf", &q[1] );
205 <      
206 <      foo = strtok(NULL, " ,;\t");
207 <      if(foo == NULL){
208 <        sprintf( painCave.errMsg,
209 <                 "error in reading quaternion 2 from %s\n"
210 <                 "natoms  = %d, index = %d\n",
211 <                 c_in_name, n_atoms, i );
203 >      }    
204 >      masterIndex++;
205 >    }
206 >  }
207 >
208 >  sprintf(checkPointMsg,
209 >          "Node 0 has successfully read positions from input file.");
210 >  mpiCheckPoint();
211 >
212 >  for (procIndex = 1; procIndex < entryPlug->mpiSim->getNumberProcessors();
213 >         procIndex++){
214 >    if (worldRank == 0) {
215 >
216 >      mpiErr = MPI_Recv(&nodeAtomsStart,1,MPI_INT,procIndex,MPI_ANY_TAG,MPI_COMM_WORLD,
217 >               istatus);
218 >
219 >      mpiErr = MPI_Recv(&nodeAtomsEnd,1,MPI_INT,procIndex,MPI_ANY_TAG,MPI_COMM_WORLD,
220 >               istatus);
221 >      // Make sure where node 0 is reading from, matches where the receiving node
222 >      // expects it to be.
223 >
224 >      if (masterIndex != nodeAtomsStart){
225 >        sendError = 1;
226 >        mpiErr = MPI_Send(&sendError,1,MPI_INT,procIndex,MPI_ANY_TAG,MPI_COMM_WORLD);
227 >        sprintf(painCave.errMsg,
228 >                "Initialize from file error: atoms start index (%d) for "
229 >                "node %d not equal to master index (%d)",nodeAtomsStart,procIndex,masterIndex );
230          painCave.isFatal = 1;
231          simError();
232        }
233 <      (void)sscanf( foo, "%lf", &q[2] );
233 >      sendError = 0;
234 >      mpiErr = MPI_Send(&sendError,1,MPI_INT,procIndex,MPI_ANY_TAG,MPI_COMM_WORLD);
235        
236 <      foo = strtok(NULL, " ,;\t");
237 <      if(foo == NULL){
238 <        sprintf( painCave.errMsg,
239 <                 "error in reading quaternion 3 from %s\n"
240 <                 "natoms  = %d, index = %d\n",
241 <                 c_in_name, n_atoms, i );
242 <        painCave.isFatal = 1;
243 <        simError();
244 <      }
245 <      (void)sscanf( foo, "%lf", &q[3] );
246 <      
247 <      // get the angular velocities
248 <      
249 <      foo = strtok(NULL, " ,;\t");
250 <      if(foo == NULL){
251 <        sprintf( painCave.errMsg,
252 <                 "error in reading angular momentum jx from %s\n"
253 <                 "natoms  = %d, index = %d\n",
254 <                 c_in_name, n_atoms, i );
255 <        painCave.isFatal = 1;
241 <        simError();
242 <      }
243 <      (void)sscanf( foo, "%lf", &jx );
244 <      
245 <      foo = strtok(NULL, " ,;\t");
246 <      if(foo == NULL){
247 <        sprintf( painCave.errMsg,
248 <                 "error in reading angular momentum jy from %s\n"
249 <                 "natoms  = %d, index = %d\n",
250 <                 c_in_name, n_atoms, i );
251 <        painCave.isFatal = 1;
252 <        simError();
253 <      }
254 <      (void)sscanf( foo, "%lf", &jy );
255 <      
256 <      foo = strtok(NULL, " ,;\t");
257 <      if(foo == NULL){
258 <        sprintf( painCave.errMsg,
259 <                 "error in reading angular momentum jz from %s\n"
260 <                 "natoms  = %d, index = %d\n",
261 <                 c_in_name, n_atoms, i );
262 <        painCave.isFatal = 1;
263 <        simError();
264 <      }
265 <      (void)sscanf( foo, "%lf", &jz );
266 <      
267 <      dAtom = ( DirectionalAtom* )atoms[i];
268 <
269 <      // check that the quaternion vector is normalized
270 <
271 <      qSqr = (q[0] * q[0]) + (q[1] * q[1]) + (q[2] * q[2]) + (q[3] * q[3]);
272 <      
273 <      qLength = sqrt( qSqr );
274 <      q[0] = q[0] / qLength;
275 <      q[1] = q[1] / qLength;
276 <      q[2] = q[2] / qLength;
277 <      q[3] = q[3] / qLength;
278 <      
279 <      dAtom->setQ( q );
280 <      
281 <      // add the angular velocities
236 >      for ( i = nodeAtomStart; i <= nodeAtomEnd, i++){
237 >        eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file);
238 >        if(eof_test == NULL){
239 >          
240 >          sprintf(read_buffer,"ERROR");
241 >          mpiErr = MPI_Send(read_buffer,BUFFERSIZE,MPI_CHAR,procIndex,MPI_ANY_TAG,MPI_COMM_WORLD);
242 >          
243 >          sprintf(painCave.errMsg,
244 >                  "error in reading file %s\n"
245 >                  "natoms  = %d; index = %d\n"
246 >                  "error reading the line from the file.\n",
247 >                  c_in_name, n_atoms, i );
248 >          painCave.isFatal = 1;
249 >          simError();
250 >        }
251 >        
252 >        mpiErr = MPI_Send(read_buffer,BUFFERSIZE,MPI_CHAR,procIndex,MPI_ANY_TAG,MPI_COMM_WORLD);
253 >        mpiErr = MPI_Recv(&sendError,1,MPI_INT,procIndex,MPI_ANY_TAG,MPI_COMM_WORLD,
254 >                          istatus);
255 >        if (sendError) mpiCheckpoint();
256  
257 <      dAtom->setJx( jx );
258 <      dAtom->setJy( jy );
285 <      dAtom->setJz( jz );
257 >        masterIndex++;
258 >      }
259      }
260 +
261 +
262 +    else if(worldRank == procIndex){
263 +      nodeAtomStart = mpiSim->getMyAtomStart();
264 +      nodeAtomEnd = mpiSim->getMyAtomEnd();
265 +      mpiErr = MPI_Send(&nodeAtomsStart,1,MPI_INT,0,MPI_ANY_TAG,MPI_COMM_WORLD);
266 +      mpiErr = MPI_Send(&nodeAtomsEnd,1,MPI_INT,0,MPI_ANY_TAG,MPI_COMM_WORLD);
267 +      
268 +      mpiErr = MPI_Recv(&sendError,1,MPI_INT,0,MPI_ANY_TAG,MPI_COMM_WORLD,
269 +               istatus);
270 +      if (sendError) mpiCheckpoint();
271 +
272 +      for ( i = 0; i < entry_plug->n_atoms, i++){
273 +
274 +        mpiErr = MPI_Recv(&read_buffer,BUFFERSIZE,MPI_CHAR,0,MPI_ANY_TAG,MPI_COMM_WORLD,
275 +                          istatus);
276 +        
277 +        if(!strcmp(read_buffer, "ERROR")) mpiCheckPoint();
278 +        
279 +        parseErr = parseDumpLine( read_buffer, i );
280 +        if( parseErr != NULL ){
281 +          sendError = 1;
282 +          mpiErr = MPI_Send(&sendError,1,MPI_INT,0,MPI_ANY_TAG,MPI_COMM_WORLD);
283 +
284 +
285 +          strcpy( painCave.errMsg, parseErr );
286 +          painCave.isFatal = 1;
287 +          simError();
288 +        }
289 +        sendError = 0;
290 +        mpiErr = MPI_Send(&sendError,1,MPI_INT,0,MPI_ANY_TAG,MPI_COMM_WORLD);
291 +      }
292 +    }
293 +    sprintf(checkPointMsg,"Node %d received initial configuration.",procIndex);
294 +    mpiCheckPoint();
295 +  }
296 +
297 + #endif
298 + }
299 +
300 +
301 + char* InitializeFromFile::parseDumpLine(char* readLine, int atomIndex){
302 +
303 +  char *foo; // the pointer to the current string token
304 +  
305 +  double rx, ry, rz; // position place holders
306 +  double vx, vy, vz; // velocity placeholders
307 +  double q[4]; // the quaternions
308 +  double jx, jy, jz; // angular velocity placeholders;
309 +  double qSqr, qLength; // needed to normalize the quaternion vector.
310 +  
311 +  Atom **atoms = entry_plug->atoms;
312 +  DirectionalAtom* dAtom;
313 +  
314 +  int n_atoms;
315 +
316 + #ifdef IS_MPI
317 +  n_atoms = mpiSim->getTotAtoms();
318 + #else
319 +  n_atoms = entry_plug->n_atoms;
320 + #endif // is_mpi
321 +
322 +
323 +  // set the string tokenizer
324 +  
325 +  foo = strtok(readLine, " ,;\t");
326 +  
327 +  // check the atom name to the current atom
328 +  
329 +  if( strcmp( foo, atoms[atomIndex]->getType() ) ){
330 +    sprintf( painCave.errMsg,
331 +             "Initialize from file error. Atom %s at index %d "
332 +             "in file %s does not"
333 +             " match the BASS atom %s.\n",
334 +             foo, atomIndex, c_in_name, atoms[atomIndex]->getType() );
335 +    return strdup( painCave.errMsg );
336 +  }
337      
338 <    // add the positions and velocities to the atom
338 >  // get the positions
339 >
340 >  foo = strtok(NULL, " ,;\t");
341 >  if(foo == NULL){
342 >    sprintf( painCave.errMsg,
343 >             "error in reading postition x from %s\n"
344 >             "natoms  = %d, index = %d\n",
345 >             c_in_name, n_atoms, atomIndex );
346 >    return strdup( painCave.errMsg );
347 >  }
348 >  rx = atof( foo );
349 >  
350 >  foo = strtok(NULL, " ,;\t");
351 >  if(foo == NULL){
352 >    sprintf( painCave.errMsg,
353 >             "error in reading postition y from %s\n"
354 >             "natoms  = %d, index = %d\n",
355 >             c_in_name, n_atoms, atomIndex );
356 >    return strdup( painCave.errMsg );
357 >  }
358 >  ry = atof( foo );
359 >    
360 >  foo = strtok(NULL, " ,;\t");
361 >  if(foo == NULL){
362 >    sprintf( painCave.errMsg,
363 >             "error in reading postition z from %s\n"
364 >             "natoms  = %d, index = %d\n",
365 >             c_in_name, n_atoms, atomIndex );
366 >    return strdup( painCave.errMsg );
367 >  }
368 >  rz = atof( foo );    
369 >
370 >
371 >  // get the velocities
372 >
373 >  foo = strtok(NULL, " ,;\t");
374 >  if(foo == NULL){
375 >    sprintf( painCave.errMsg,
376 >             "error in reading velocity x from %s\n"
377 >             "natoms  = %d, index = %d\n",
378 >             c_in_name, n_atoms, atomIndex );
379 >    return strdup( painCave.errMsg );
380 >  }
381 >  vx = atof( foo );
382      
383 <    atoms[i]->setX( rx );
384 <    atoms[i]->setY( ry );
385 <    atoms[i]->setZ( rz );
383 >  foo = strtok(NULL, " ,;\t");
384 >  if(foo == NULL){
385 >    sprintf( painCave.errMsg,
386 >             "error in reading velocity y from %s\n"
387 >             "natoms  = %d, index = %d\n",
388 >             c_in_name, n_atoms, atomIndex );
389 >    return strdup( painCave.errMsg );
390 >  }
391 >  vy = atof( foo );
392      
393 <    atoms[i]->set_vx( vx );
394 <    atoms[i]->set_vy( vy );
395 <    atoms[i]->set_vz( vz );
393 >  foo = strtok(NULL, " ,;\t");
394 >  if(foo == NULL){
395 >    sprintf( painCave.errMsg,
396 >             "error in reading velocity z from %s\n"
397 >             "natoms  = %d, index = %d\n",
398 >             c_in_name, n_atoms, atomIndex );
399 >    return strdup( painCave.errMsg );
400 >  }
401 >  vz = atof( foo );
402      
403 +    
404 +  // get the quaternions
405 +    
406 +  if( atoms[atomIndex]->isDirectional() ){
407 +      
408 +    foo = strtok(NULL, " ,;\t");
409 +    if(foo == NULL){
410 +      sprintf(painCave.errMsg,
411 +              "error in reading quaternion 0 from %s\n"
412 +              "natoms  = %d, index = %d\n",
413 +              c_in_name, n_atoms, atomIndex );
414 +      return strdup( painCave.errMsg );
415 +    }
416 +    q[0] = atof( foo );
417 +      
418 +    foo = strtok(NULL, " ,;\t");
419 +    if(foo == NULL){
420 +      sprintf( painCave.errMsg,
421 +               "error in reading quaternion 1 from %s\n"
422 +               "natoms  = %d, index = %d\n",
423 +               c_in_name, n_atoms, atomIndex );
424 +      return strdup( painCave.errMsg );
425 +    }
426 +    q[1] = atof( foo );
427 +      
428 +    foo = strtok(NULL, " ,;\t");
429 +    if(foo == NULL){
430 +      sprintf( painCave.errMsg,
431 +               "error in reading quaternion 2 from %s\n"
432 +               "natoms  = %d, index = %d\n",
433 +               c_in_name, n_atoms, atomIndex );
434 +      return strdup( painCave.errMsg );
435 +    }
436 +    q[2] = atof( foo );
437 +      
438 +    foo = strtok(NULL, " ,;\t");
439 +    if(foo == NULL){
440 +      sprintf( painCave.errMsg,
441 +               "error in reading quaternion 3 from %s\n"
442 +               "natoms  = %d, index = %d\n",
443 +               c_in_name, n_atoms, atomIndex );
444 +      return strdup( painCave.errMsg );
445 +    }
446 +    q[3] = atof( foo );
447 +      
448 +    // get the angular velocities
449 +      
450 +    foo = strtok(NULL, " ,;\t");
451 +    if(foo == NULL){
452 +      sprintf( painCave.errMsg,
453 +               "error in reading angular momentum jx from %s\n"
454 +               "natoms  = %d, index = %d\n",
455 +               c_in_name, n_atoms, atomIndex );
456 +      return strdup( painCave.errMsg );
457 +    }
458 +    jx = atof( foo );
459 +      
460 +    foo = strtok(NULL, " ,;\t");
461 +    if(foo == NULL){
462 +      sprintf( painCave.errMsg,
463 +               "error in reading angular momentum jy from %s\n"
464 +               "natoms  = %d, index = %d\n",
465 +               c_in_name, n_atoms, atomIndex );
466 +      return strdup( painCave.errMsg );
467 +    }
468 +    jy = atof(foo );
469 +      
470 +    foo = strtok(NULL, " ,;\t");
471 +    if(foo == NULL){
472 +      sprintf( painCave.errMsg,
473 +               "error in reading angular momentum jz from %s\n"
474 +               "natoms  = %d, index = %d\n",
475 +               c_in_name, n_atoms, atomIndex );
476 +      return strdup( painCave.errMsg );
477 +    }
478 +    jz = atof( foo );
479 +      
480 +    dAtom = ( DirectionalAtom* )atoms[atomIndex];
481 +
482 +    // check that the quaternion vector is normalized
483 +
484 +    qSqr = (q[0] * q[0]) + (q[1] * q[1]) + (q[2] * q[2]) + (q[3] * q[3]);
485 +      
486 +    qLength = sqrt( qSqr );
487 +    q[0] = q[0] / qLength;
488 +    q[1] = q[1] / qLength;
489 +    q[2] = q[2] / qLength;
490 +    q[3] = q[3] / qLength;
491 +      
492 +    dAtom->setQ( q );
493 +      
494 +    // add the angular velocities
495 +
496 +    dAtom->setJx( jx );
497 +    dAtom->setJy( jy );
498 +    dAtom->setJz( jz );
499    }
500 +    
501 +  // add the positions and velocities to the atom
502 +    
503 +  atoms[atomIndex]->setX( rx );
504 +  atoms[atomIndex]->setY( ry );
505 +  atoms[atomIndex]->setZ( rz );
506 +    
507 +  atoms[atomIndex]->set_vx( vx );
508 +  atoms[atomIndex]->set_vy( vy );
509 +  atoms[atomIndex]->set_vz( vz );
510 +
511 +  return NULL;
512   }

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