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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 206 by chuckv, Thu Dec 12 21:21:59 2002 UTC vs.
Revision 254 by chuckv, Thu Jan 30 20:03:37 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
# Line 59 | Line 62 | void InitializeFromFile :: read_xyz( SimInfo* the_entr
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[2000];
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 >  int procIndex;
75  
76 <  double rx, ry, rz; // position place holders
72 <  double vx, vy, vz; // velocity placeholders
73 <  double q[4]; // the quaternions
74 <  double jx, jy, jz; // angular velocity placeholders;
75 <  double qSqr, qLength; // needed to normalize the quaternion vector.
76 >  entry_plug = the_entry_plug;
77  
77 –  entry_plug = the_entry_plug
78  
79 –
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 120 | Line 123 | void InitializeFromFile :: read_xyz( SimInfo* the_entr
123        simError();
124      }
125  
123 –    foo = strtok(read_buffer, " ,;\t");
126      
127 <    // check the atom name to the current atom
128 <
129 <    if( strcmp( foo, atoms[i]->getType() ) ){
128 <      sprintf( painCave.errMsg,
129 <               "Initialize from file error. Atom %s at index %d "
130 <               "in file %s does not"
131 <               " match the BASS atom %s.\n",
132 <               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 <    }
136 <    
137 <    // get the positions
138 <
139 <    foo = strtok(NULL, " ,;\t");
140 <    if(foo == NULL){
141 <      sprintf( painCave.errMsg,
142 <               "error in reading postition x from %s\n"
143 <               "natoms  = %d, index = %d\n",
144 <               c_in_name, n_atoms, i );
145 <      painCave.isFatal = 1;
146 <      simError();
147 <    }
148 <    (void)sscanf( foo, "%lf", &rx );
149 <  
150 <    foo = strtok(NULL, " ,;\t");
151 <    if(foo == NULL){
152 <      sprintf( painCave.errMsg,
153 <               "error in reading postition y from %s\n"
154 <               "natoms  = %d, index = %d\n",
155 <               c_in_name, n_atoms, i );
156 <      painCave.isFatal = 1;
157 <      simError();
158 <    }
159 <    (void)sscanf( foo, "%lf", &ry );
160 <    
161 <    foo = strtok(NULL, " ,;\t");
162 <    if(foo == NULL){
163 <      sprintf( painCave.errMsg,
164 <               "error in reading postition z from %s\n"
165 <               "natoms  = %d, index = %d\n",
166 <               c_in_name, n_atoms, i );
167 <      painCave.isFatal = 1;
168 <      simError();
169 <    }
170 <    (void)sscanf( foo, "%lf", &rz );
171 <    
172 <    // get the velocities
173 <
174 <    foo = strtok(NULL, " ,;\t");
175 <    if(foo == NULL){
176 <      sprintf( painCave.errMsg,
177 <               "error in reading velocity x from %s\n"
178 <               "natoms  = %d, index = %d\n",
179 <               c_in_name, n_atoms, i );
180 <      painCave.isFatal = 1;
181 <      simError();
182 <    }
183 <    (void)sscanf( foo, "%lf", &vx );
184 <    
185 <    foo = strtok(NULL, " ,;\t");
186 <    if(foo == NULL){
187 <      sprintf( painCave.errMsg,
188 <               "error in reading velocity y from %s\n"
189 <               "natoms  = %d, index = %d\n",
190 <               c_in_name, n_atoms, i );
191 <      painCave.isFatal = 1;
192 <      simError();
193 <    }
194 <    (void)sscanf( foo, "%lf", &vy );
195 <    
196 <    foo = strtok(NULL, " ,;\t");
197 <    if(foo == NULL){
198 <      sprintf( painCave.errMsg,
199 <               "error in reading velocity z from %s\n"
200 <               "natoms  = %d, index = %d\n",
201 <               c_in_name, n_atoms, i );
202 <      painCave.isFatal = 1;
203 <      simError();
204 <    }
205 <    (void)sscanf( foo, "%lf", &vz );
206 <    
207 <    
208 <    // get the quaternions
209 <    
210 <    if( atoms[i]->isDirectional() ){
211 <      
212 <      foo = strtok(NULL, " ,;\t");
213 <      if(foo == NULL){
214 <        sprintf(painCave.errMsg,
215 <                "error in reading quaternion 0 from %s\n"
216 <                "natoms  = %d, index = %d\n",
217 <                c_in_name, n_atoms, i );
218 <        painCave.isFatal = 1;
219 <        simError();
220 <      }
221 <      (void)sscanf( foo, "%lf", &q[0] );
222 <      
223 <      foo = strtok(NULL, " ,;\t");
224 <      if(foo == NULL){
225 <        sprintf( painCave.errMsg,
226 <                 "error in reading quaternion 1 from %s\n"
227 <                 "natoms  = %d, index = %d\n",
228 <                 c_in_name, n_atoms, i );
229 <        painCave.isFatal = 1;
230 <        simError();
231 <      }
232 <      (void)sscanf( foo, "%lf", &q[1] );
233 <      
234 <      foo = strtok(NULL, " ,;\t");
235 <      if(foo == NULL){
236 <        sprintf( painCave.errMsg,
237 <                 "error in reading quaternion 2 from %s\n"
238 <                 "natoms  = %d, index = %d\n",
239 <                 c_in_name, n_atoms, i );
240 <        painCave.isFatal = 1;
241 <        simError();
242 <      }
243 <      (void)sscanf( foo, "%lf", &q[2] );
244 <      
245 <      foo = strtok(NULL, " ,;\t");
246 <      if(foo == NULL){
247 <        sprintf( painCave.errMsg,
248 <                 "error in reading quaternion 3 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", &q[3] );
255 <      
256 <      // get the angular velocities
257 <      
258 <      foo = strtok(NULL, " ,;\t");
259 <      if(foo == NULL){
260 <        sprintf( painCave.errMsg,
261 <                 "error in reading angular momentum jx from %s\n"
262 <                 "natoms  = %d, index = %d\n",
263 <                 c_in_name, n_atoms, i );
264 <        painCave.isFatal = 1;
265 <        simError();
266 <      }
267 <      (void)sscanf( foo, "%lf", &jx );
268 <      
269 <      foo = strtok(NULL, " ,;\t");
270 <      if(foo == NULL){
271 <        sprintf( painCave.errMsg,
272 <                 "error in reading angular momentum jy from %s\n"
273 <                 "natoms  = %d, index = %d\n",
274 <                 c_in_name, n_atoms, i );
275 <        painCave.isFatal = 1;
276 <        simError();
277 <      }
278 <      (void)sscanf( foo, "%lf", &jy );
279 <      
280 <      foo = strtok(NULL, " ,;\t");
281 <      if(foo == NULL){
282 <        sprintf( painCave.errMsg,
283 <                 "error in reading angular momentum jz from %s\n"
284 <                 "natoms  = %d, index = %d\n",
285 <                 c_in_name, n_atoms, i );
286 <        painCave.isFatal = 1;
287 <        simError();
288 <      }
289 <      (void)sscanf( foo, "%lf", &jz );
290 <      
291 <      dAtom = ( DirectionalAtom* )atoms[i];
292 <
293 <      // check that the quaternion vector is normalized
294 <
295 <      qSqr = (q[0] * q[0]) + (q[1] * q[1]) + (q[2] * q[2]) + (q[3] * q[3]);
296 <      
297 <      qLength = sqrt( qSqr );
298 <      q[0] = q[0] / qLength;
299 <      q[1] = q[1] / qLength;
300 <      q[2] = q[2] / qLength;
301 <      q[3] = q[3] / qLength;
302 <      
303 <      dAtom->setQ( q );
304 <      
305 <      // add the angular velocities
306 <
307 <      dAtom->setJx( jx );
308 <      dAtom->setJy( jy );
309 <      dAtom->setJz( jz );
310 <    }
311 <    
312 <    // add the positions and velocities to the atom
313 <    
314 <    atoms[i]->setX( rx );
315 <    atoms[i]->setY( ry );
316 <    atoms[i]->setZ( rz );
317 <    
318 <    atoms[i]->set_vx( vx );
319 <    atoms[i]->set_vy( vy );
320 <    atoms[i]->set_vz( vz );
321 <    
132 >    }    
133    }
134  
135  
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  
330 –
147    if (worldRank == 0) {
148      eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file);
149      if( eof_test == NULL ){
# Line 337 | Line 153 | void InitializeFromFile :: read_xyz( SimInfo* the_entr
153        simError();
154      }
155      
156 <    (void)sscanf(read_buffer, "%d", &n_atoms);
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 != entry_plug->n_atoms ){
164 >    if( n_atoms != mpiSim->getTotAtoms() ){
165        sprintf( painCave.errMsg,
166                 "Initialize from File error. %s n_atoms, %d, "
167                 "does not match the BASS file's n_atoms, %d.\n",
# Line 360 | Line 179 | void InitializeFromFile :: read_xyz( SimInfo* the_entr
179        painCave.isFatal = 1;
180        simError();
181      }
182 <  }
183 <  for( i=0; i < n_atoms; i++){
182 >  
183 >    // Read Proc 0 share of the xyz file...
184 >    masterIndex = 0;
185 >    for( i=0; i <= mpiSim->getMyAtomEnd(); i++){
186      
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 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();
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 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 >    
198 >      parseErr = parseDumpLine( read_buffer, i );
199 >      if( parseErr != NULL ){
200 >        strcpy( painCave.errMsg, parseErr );
201 >        painCave.isFatal = 1;
202 >        simError();
203 >      }    
204 >      masterIndex++;
205      }
206 +  }
207  
208 <    foo = strtok(read_buffer, " ,;\t");
209 <    
210 <    // check the atom name to the current atom
208 >  sprintf(checkPointMsg,
209 >          "Node 0 has successfully read positions from input file.");
210 >  MPIcheckPoint();
211  
212 <    if( strcmp( foo, atoms[i]->getType() ) ){
213 <      sprintf( painCave.errMsg,
214 <               "Initialize from file error. Atom %s at index %d "
215 <               "in file %s does not"
216 <               " match the BASS atom %s.\n",
217 <               foo, i, c_in_name, atoms[i]->getType() );
218 <      painCave.isFatal = 1;
219 <      simError();
212 >  for (procIndex = 1; procIndex < 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 >      sendError = 0;
234 >      mpiErr = MPI_Send(&sendError,1,MPI_INT,procIndex,MPI_ANY_TAG,MPI_COMM_WORLD);
235 >      
236 >      for ( i = nodeAtomsStart; i <= nodeAtomsEnd; 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 >        masterIndex++;
258 >      }
259      }
260 <    
261 <    // get the positions
260 >
261 >
262 >    else if(worldRank == procIndex){
263 >      nodeAtomsStart = mpiSim->getMyAtomStart();
264 >      nodeAtomsEnd = 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 +  // 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 +  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 +  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 postition x from %s\n"
421 >               "error in reading quaternion 1 from %s\n"
422                 "natoms  = %d, index = %d\n",
423 <               c_in_name, n_atoms, i );
424 <      painCave.isFatal = 1;
400 <      simError();
423 >               c_in_name, n_atoms, atomIndex );
424 >      return strdup( painCave.errMsg );
425      }
426 <    (void)sscanf( foo, "%lf", &rx );
427 <  
426 >    q[1] = atof( foo );
427 >      
428      foo = strtok(NULL, " ,;\t");
429      if(foo == NULL){
430        sprintf( painCave.errMsg,
431 <               "error in reading postition y from %s\n"
431 >               "error in reading quaternion 2 from %s\n"
432                 "natoms  = %d, index = %d\n",
433 <               c_in_name, n_atoms, i );
434 <      painCave.isFatal = 1;
411 <      simError();
433 >               c_in_name, n_atoms, atomIndex );
434 >      return strdup( painCave.errMsg );
435      }
436 <    (void)sscanf( foo, "%lf", &ry );
437 <    
436 >    q[2] = atof( foo );
437 >      
438      foo = strtok(NULL, " ,;\t");
439      if(foo == NULL){
440        sprintf( painCave.errMsg,
441 <               "error in reading postition z from %s\n"
441 >               "error in reading quaternion 3 from %s\n"
442                 "natoms  = %d, index = %d\n",
443 <               c_in_name, n_atoms, i );
444 <      painCave.isFatal = 1;
422 <      simError();
443 >               c_in_name, n_atoms, atomIndex );
444 >      return strdup( painCave.errMsg );
445      }
446 <    (void)sscanf( foo, "%lf", &rz );
447 <    
448 <    // get the velocities
449 <
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 velocity x from %s\n"
453 >               "error in reading angular momentum jx from %s\n"
454                 "natoms  = %d, index = %d\n",
455 <               c_in_name, n_atoms, i );
456 <      painCave.isFatal = 1;
435 <      simError();
455 >               c_in_name, n_atoms, atomIndex );
456 >      return strdup( painCave.errMsg );
457      }
458 <    (void)sscanf( foo, "%lf", &vx );
459 <    
458 >    jx = atof( foo );
459 >      
460      foo = strtok(NULL, " ,;\t");
461      if(foo == NULL){
462        sprintf( painCave.errMsg,
463 <               "error in reading velocity y from %s\n"
463 >               "error in reading angular momentum jy from %s\n"
464                 "natoms  = %d, index = %d\n",
465 <               c_in_name, n_atoms, i );
466 <      painCave.isFatal = 1;
446 <      simError();
465 >               c_in_name, n_atoms, atomIndex );
466 >      return strdup( painCave.errMsg );
467      }
468 <    (void)sscanf( foo, "%lf", &vy );
469 <    
468 >    jy = atof(foo );
469 >      
470      foo = strtok(NULL, " ,;\t");
471      if(foo == NULL){
472        sprintf( painCave.errMsg,
473 <               "error in reading velocity z from %s\n"
473 >               "error in reading angular momentum jz from %s\n"
474                 "natoms  = %d, index = %d\n",
475 <               c_in_name, n_atoms, i );
476 <      painCave.isFatal = 1;
457 <      simError();
475 >               c_in_name, n_atoms, atomIndex );
476 >      return strdup( painCave.errMsg );
477      }
478 <    (void)sscanf( foo, "%lf", &vz );
460 <    
461 <    
462 <    // get the quaternions
463 <    
464 <    if( atoms[i]->isDirectional() ){
478 >    jz = atof( foo );
479        
480 <      foo = strtok(NULL, " ,;\t");
467 <      if(foo == NULL){
468 <        sprintf(painCave.errMsg,
469 <                "error in reading quaternion 0 from %s\n"
470 <                "natoms  = %d, index = %d\n",
471 <                c_in_name, n_atoms, i );
472 <        painCave.isFatal = 1;
473 <        simError();
474 <      }
475 <      (void)sscanf( foo, "%lf", &q[0] );
476 <      
477 <      foo = strtok(NULL, " ,;\t");
478 <      if(foo == NULL){
479 <        sprintf( painCave.errMsg,
480 <                 "error in reading quaternion 1 from %s\n"
481 <                 "natoms  = %d, index = %d\n",
482 <                 c_in_name, n_atoms, i );
483 <        painCave.isFatal = 1;
484 <        simError();
485 <      }
486 <      (void)sscanf( foo, "%lf", &q[1] );
487 <      
488 <      foo = strtok(NULL, " ,;\t");
489 <      if(foo == NULL){
490 <        sprintf( painCave.errMsg,
491 <                 "error in reading quaternion 2 from %s\n"
492 <                 "natoms  = %d, index = %d\n",
493 <                 c_in_name, n_atoms, i );
494 <        painCave.isFatal = 1;
495 <        simError();
496 <      }
497 <      (void)sscanf( foo, "%lf", &q[2] );
498 <      
499 <      foo = strtok(NULL, " ,;\t");
500 <      if(foo == NULL){
501 <        sprintf( painCave.errMsg,
502 <                 "error in reading quaternion 3 from %s\n"
503 <                 "natoms  = %d, index = %d\n",
504 <                 c_in_name, n_atoms, i );
505 <        painCave.isFatal = 1;
506 <        simError();
507 <      }
508 <      (void)sscanf( foo, "%lf", &q[3] );
509 <      
510 <      // get the angular velocities
511 <      
512 <      foo = strtok(NULL, " ,;\t");
513 <      if(foo == NULL){
514 <        sprintf( painCave.errMsg,
515 <                 "error in reading angular momentum jx from %s\n"
516 <                 "natoms  = %d, index = %d\n",
517 <                 c_in_name, n_atoms, i );
518 <        painCave.isFatal = 1;
519 <        simError();
520 <      }
521 <      (void)sscanf( foo, "%lf", &jx );
522 <      
523 <      foo = strtok(NULL, " ,;\t");
524 <      if(foo == NULL){
525 <        sprintf( painCave.errMsg,
526 <                 "error in reading angular momentum jy from %s\n"
527 <                 "natoms  = %d, index = %d\n",
528 <                 c_in_name, n_atoms, i );
529 <        painCave.isFatal = 1;
530 <        simError();
531 <      }
532 <      (void)sscanf( foo, "%lf", &jy );
533 <      
534 <      foo = strtok(NULL, " ,;\t");
535 <      if(foo == NULL){
536 <        sprintf( painCave.errMsg,
537 <                 "error in reading angular momentum jz from %s\n"
538 <                 "natoms  = %d, index = %d\n",
539 <                 c_in_name, n_atoms, i );
540 <        painCave.isFatal = 1;
541 <        simError();
542 <      }
543 <      (void)sscanf( foo, "%lf", &jz );
544 <      
545 <      dAtom = ( DirectionalAtom* )atoms[i];
480 >    dAtom = ( DirectionalAtom* )atoms[atomIndex];
481  
482 <      // check that the quaternion vector is normalized
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]);
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;
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 );
492 >    dAtom->setQ( q );
493        
494 <      // add the angular velocities
494 >    // add the angular velocities
495  
496 <      dAtom->setJx( jx );
497 <      dAtom->setJy( jy );
498 <      dAtom->setJz( jz );
499 <    }
496 >    dAtom->setJx( jx );
497 >    dAtom->setJy( jy );
498 >    dAtom->setJz( jz );
499 >  }
500      
501 <    // add the positions and velocities to the atom
501 >  // add the positions and velocities to the atom
502      
503 <    atoms[i]->setX( rx );
504 <    atoms[i]->setY( ry );
505 <    atoms[i]->setZ( rz );
503 >  atoms[atomIndex]->setX( rx );
504 >  atoms[atomIndex]->setY( ry );
505 >  atoms[atomIndex]->setZ( rz );
506      
507 <    atoms[i]->set_vx( vx );
508 <    atoms[i]->set_vy( vy );
509 <    atoms[i]->set_vz( vz );
575 <    
576 <  }
577 < #endif
578 < }
507 >  atoms[atomIndex]->set_vx( vx );
508 >  atoms[atomIndex]->set_vy( vy );
509 >  atoms[atomIndex]->set_vz( vz );
510  
511 < char* IntitializeFromFile::parseDumpLine(char* readLine);
511 >  return NULL;
512 > }

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