ViewVC Help
View File | Revision Log | Show Annotations | View Changeset | Root Listing
root/group/trunk/mdtools/md_code/InitializeFromFile.cpp
(Generate patch)

Comparing trunk/mdtools/md_code/InitializeFromFile.cpp (file contents):
Revision 206 by chuckv, Thu Dec 12 21:21:59 2002 UTC vs.
Revision 212 by chuckv, Fri Dec 13 21:17:00 2002 UTC

# Line 59 | Line 59 | void InitializeFromFile :: read_xyz( SimInfo* the_entr
59  
60    int i; // loop counter
61  
62 +  const int BUFFERSIZE = 2000; // size of the read buffer
63    int n_atoms; // the number of atoms
64 <  char read_buffer[2000]; //the line buffer for reading
64 >  char read_buffer[BUFFERSIZE]; //the line buffer for reading
65   #ifdef IS_MPI
66 <  char send_buffer[2000];
66 >  char send_buffer[BUFFERSIZE];
67   #endif
68  
69    char *eof_test; // ptr to see when we reach the end of the file
70 <  char *foo; // the pointer to the current string token
70 >  char *parseErr;
71  
71 –  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.
72  
73    entry_plug = the_entry_plug
74  
# Line 80 | Line 76 | void InitializeFromFile :: read_xyz( SimInfo* the_entr
76   #ifndef IS_MPI
77    eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file);
78    if( eof_test == NULL ){
79 <    std::cerr << "error reading 1st line of" << c_in_name << "\n";
79 >    sprintf( painCave.errMsg,
80 >             "InitializeFromFile error: error reading 1st line of \"%s\"\n",
81 >             c_in_name );
82 >    painCave.isFatal = 1;
83 >    simError();
84    }
85  
86 <  (void)sscanf(read_buffer, "%d", &n_atoms);
86 >  n_atoms = atoi( read_buffer );
87  
88    Atom **atoms = entry_plug->atoms;
89    DirectionalAtom* dAtom;
# Line 120 | Line 120 | void InitializeFromFile :: read_xyz( SimInfo* the_entr
120        simError();
121      }
122  
123 –    foo = strtok(read_buffer, " ,;\t");
123      
124 <    // check the atom name to the current atom
125 <
126 <    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() );
124 >    parseErr = parseDumpLine( read_buffer, i );
125 >    if( parseErr != NULL ){
126 >      strcpy( painCave.errMsg, parseErr );
127        painCave.isFatal = 1;
128        simError();
129 <    }
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 <    
129 >    }    
130    }
131  
132  
133    // MPI Section of code..........
134   #else //IS_MPI
135  
136 +  int masterIndex;
137 +  int nodeAtomsStart;
138 +  int nodeAtomsEnd;
139 +  int mpiErr;
140 +  int sendError;
141  
142 +  MPI_Status istatus[MPI_STATUS_SIZE];
143  
330 –
144    if (worldRank == 0) {
145      eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file);
146      if( eof_test == NULL ){
# Line 337 | Line 150 | void InitializeFromFile :: read_xyz( SimInfo* the_entr
150        simError();
151      }
152      
153 <    (void)sscanf(read_buffer, "%d", &n_atoms);
153 >    n_atoms = atoi( read_buffer );
154      
155      Atom **atoms = entry_plug->atoms;
156      DirectionalAtom* dAtom;
157 +
158 +    // Check to see that the number of atoms in the intial configuration file is the
159 +    // same as declared in simBass.
160      
161 <    if( n_atoms != entry_plug->n_atoms ){
161 >    if( n_atoms != entry_plug->mpiSim->getTotAtoms() ){
162        sprintf( painCave.errMsg,
163                 "Initialize from File error. %s n_atoms, %d, "
164                 "does not match the BASS file's n_atoms, %d.\n",
# Line 360 | Line 176 | void InitializeFromFile :: read_xyz( SimInfo* the_entr
176        painCave.isFatal = 1;
177        simError();
178      }
179 <  }
180 <  for( i=0; i < n_atoms; i++){
179 >  
180 >    // Read Proc 0 share of the xyz file...
181 >    masterIndex = 0;
182 >    for( i=0; i <= entry_plug->mpiSim->getMyAtomEnd(); i++){
183      
184 <    eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file);
185 <    if(eof_test == NULL){
186 <      sprintf(painCave.errMsg,
187 <              "error in reading file %s\n"
188 <              "natoms  = %d; index = %d\n"
189 <              "error reading the line from the file.\n",
190 <              c_in_name, n_atoms, i );
191 <      painCave.isFatal = 1;
192 <      simError();
184 >      eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file);
185 >      if(eof_test == NULL){
186 >        sprintf(painCave.errMsg,
187 >                "error in reading file %s\n"
188 >                "natoms  = %d; index = %d\n"
189 >                "error reading the line from the file.\n",
190 >                c_in_name, n_atoms, i );
191 >        painCave.isFatal = 1;
192 >        simError();
193 >      }
194 >    
195 >      parseErr = parseDumpLine( read_buffer, i );
196 >      if( parseErr != NULL ){
197 >        strcpy( painCave.errMsg, parseErr );
198 >        painCave.isFatal = 1;
199 >        simError();
200 >      }    
201 >      masterIndex++;
202      }
203 +  }
204  
205 <    foo = strtok(read_buffer, " ,;\t");
206 <    
207 <    // check the atom name to the current atom
205 >  sprintf(checkPointMsg,
206 >          "Node 0 has successfully read positions from input file.");
207 >  mpiCheckPoint();
208  
209 <    if( strcmp( foo, atoms[i]->getType() ) ){
210 <      sprintf( painCave.errMsg,
211 <               "Initialize from file error. Atom %s at index %d "
212 <               "in file %s does not"
213 <               " match the BASS atom %s.\n",
214 <               foo, i, c_in_name, atoms[i]->getType() );
215 <      painCave.isFatal = 1;
216 <      simError();
209 >  for (procIndex = 1; procIndex < entryPlug->mpiSim->getNumberProcessors();
210 >         procIndex++){
211 >    if (worldRank == 0) {
212 >
213 >      mpiErr = MPI_Recv(&nodeAtomsStart,1,MPI_INT,procIndex,MPI_ANY_TAG,MPI_COMM_WORLD,
214 >               istatus);
215 >
216 >      mpiErr = MPI_Recv(&nodeAtomsEnd,1,MPI_INT,procIndex,MPI_ANY_TAG,MPI_COMM_WORLD,
217 >               istatus);
218 >      // Make sure where node 0 is reading from, matches where the receiving node
219 >      // expects it to be.
220 >
221 >      if (masterIndex != nodeAtomsStart){
222 >        sendError = 1;
223 >        mpiErr = MPI_Send(&sendError,1,MPI_INT,procIndex,MPI_ANY_TAG,MPI_COMM_WORLD);
224 >        sprintf(painCave.errMsg,
225 >                "Initialize from file error: atoms start index (%d) for "
226 >                "node %d not equal to master index (%d)",nodeAtomsStart,procIndex,masterIndex );
227 >        painCave.isFatal = 1;
228 >        simError();
229 >      }
230 >      sendError = 0;
231 >      mpiErr = MPI_Send(&sendError,1,MPI_INT,procIndex,MPI_ANY_TAG,MPI_COMM_WORLD);
232 >      
233 >      for ( i = nodeAtomStart; i <= nodeAtomEnd, i++){
234 >        eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file);
235 >        if(eof_test == NULL){
236 >          
237 >          sprintf(read_buffer,"ERROR");
238 >          mpiErr = MPI_Send(read_buffer,BUFFERSIZE,MPI_CHAR,procIndex,MPI_ANY_TAG,MPI_COMM_WORLD);
239 >          
240 >          sprintf(painCave.errMsg,
241 >                  "error in reading file %s\n"
242 >                  "natoms  = %d; index = %d\n"
243 >                  "error reading the line from the file.\n",
244 >                  c_in_name, n_atoms, i );
245 >          painCave.isFatal = 1;
246 >          simError();
247 >        }
248 >        
249 >        mpiErr = MPI_Send(read_buffer,BUFFERSIZE,MPI_CHAR,procIndex,MPI_ANY_TAG,MPI_COMM_WORLD);
250 >        mpiErr = MPI_Recv(&sendError,1,MPI_INT,procIndex,MPI_ANY_TAG,MPI_COMM_WORLD,
251 >                          istatus);
252 >        if (sendError) mpiCheckpoint();
253 >
254 >        masterIndex++;
255 >      }
256      }
390 –    
391 –    // get the positions
257  
258 +
259 +    else if(worldRank == procIndex){
260 +      nodeAtomStart = entry_plug->mpiSim->getMyAtomStart();
261 +      nodeAtomEnd = entry_plug->mpiSim->getMyAtomEnd();
262 +      mpiErr = MPI_Send(&nodeAtomsStart,1,MPI_INT,0,MPI_ANY_TAG,MPI_COMM_WORLD);
263 +      mpiErr = MPI_Send(&nodeAtomsEnd,1,MPI_INT,0,MPI_ANY_TAG,MPI_COMM_WORLD);
264 +      
265 +      mpiErr = MPI_Recv(&sendError,1,MPI_INT,0,MPI_ANY_TAG,MPI_COMM_WORLD,
266 +               istatus);
267 +      if (sendError) mpiCheckpoint();
268 +
269 +      for ( i = 0; i < entry_plug->n_atoms, i++){
270 +
271 +        mpiErr = MPI_Recv(&read_buffer,BUFFERSIZE,MPI_CHAR,0,MPI_ANY_TAG,MPI_COMM_WORLD,
272 +                          istatus);
273 +        
274 +        if(!strcmp(read_buffer, "ERROR")) mpiCheckPoint();
275 +        
276 +        parseErr = parseDumpLine( read_buffer, i );
277 +        if( parseErr != NULL ){
278 +          sendError = 1;
279 +          mpiErr = MPI_Send(&sendError,1,MPI_INT,0,MPI_ANY_TAG,MPI_COMM_WORLD);
280 +
281 +
282 +          strcpy( painCave.errMsg, parseErr );
283 +          painCave.isFatal = 1;
284 +          simError();
285 +        }
286 +        sendError = 0;
287 +        mpiErr = MPI_Send(&sendError,1,MPI_INT,0,MPI_ANY_TAG,MPI_COMM_WORLD);
288 +      }
289 +    }
290 +    sprintf(checkPointMsg,"Node %d received initial configuration.",procIndex);
291 +    mpiCheckPoint();
292 +  }
293 +
294 + #endif
295 + }
296 +
297 +
298 + char* IntitializeFromFile::parseDumpLine(char* readLine, int atomIndex){
299 +
300 +  char *foo; // the pointer to the current string token
301 +  
302 +  double rx, ry, rz; // position place holders
303 +  double vx, vy, vz; // velocity placeholders
304 +  double q[4]; // the quaternions
305 +  double jx, jy, jz; // angular velocity placeholders;
306 +  double qSqr, qLength; // needed to normalize the quaternion vector.
307 +  
308 +  Atom **atoms = entry_plug->atoms;
309 +  DirectionalAtom* dAtom;
310 +  
311 +  int n_atoms;
312 +
313 + #ifdef IS_MPI
314 +  n_atoms = entry_plug->mpiSim->getTotAtoms();
315 + #else
316 +  n_atoms = entry_plug->n_atoms;
317 + #endi // is_mpi
318 +
319 +
320 +  // set the string tokenizer
321 +  
322 +  foo = strtok(readLine, " ,;\t");
323 +  
324 +  // check the atom name to the current atom
325 +  
326 +  if( strcmp( foo, atoms[atomIndex]->getType() ) ){
327 +    sprintf( painCave.errMsg,
328 +             "Initialize from file error. Atom %s at index %d "
329 +             "in file %s does not"
330 +             " match the BASS atom %s.\n",
331 +             foo, atomIndex, c_in_name, atoms[atomIndex]->getType() );
332 +    return strdup( painCave.errMsg );
333 +  }
334 +    
335 +  // get the positions
336 +
337 +  foo = strtok(NULL, " ,;\t");
338 +  if(foo == NULL){
339 +    sprintf( painCave.errMsg,
340 +             "error in reading postition x from %s\n"
341 +             "natoms  = %d, index = %d\n",
342 +             c_in_name, n_atoms, atomIndex );
343 +    return strdup( painCave.errMsg );
344 +  }
345 +  rx = atof( foo );
346 +  
347 +  foo = strtok(NULL, " ,;\t");
348 +  if(foo == NULL){
349 +    sprintf( painCave.errMsg,
350 +             "error in reading postition y from %s\n"
351 +             "natoms  = %d, index = %d\n",
352 +             c_in_name, n_atoms, atomIndex );
353 +    return strdup( painCave.errMsg );
354 +  }
355 +  ry = atof( foo );
356 +    
357 +  foo = strtok(NULL, " ,;\t");
358 +  if(foo == NULL){
359 +    sprintf( painCave.errMsg,
360 +             "error in reading postition z from %s\n"
361 +             "natoms  = %d, index = %d\n",
362 +             c_in_name, n_atoms, atomIndex );
363 +    return strdup( painCave.errMsg );
364 +  }
365 +  rz = atof( foo );    
366 +
367 +
368 +  // get the velocities
369 +
370 +  foo = strtok(NULL, " ,;\t");
371 +  if(foo == NULL){
372 +    sprintf( painCave.errMsg,
373 +             "error in reading velocity x from %s\n"
374 +             "natoms  = %d, index = %d\n",
375 +             c_in_name, n_atoms, atomIndex );
376 +    return strdup( painCave.errMsg );
377 +  }
378 +  vx = atof( foo );
379 +    
380 +  foo = strtok(NULL, " ,;\t");
381 +  if(foo == NULL){
382 +    sprintf( painCave.errMsg,
383 +             "error in reading velocity y from %s\n"
384 +             "natoms  = %d, index = %d\n",
385 +             c_in_name, n_atoms, atomIndex );
386 +    return strdup( painCave.errMsg );
387 +  }
388 +  vy = atof( foo );
389 +    
390 +  foo = strtok(NULL, " ,;\t");
391 +  if(foo == NULL){
392 +    sprintf( painCave.errMsg,
393 +             "error in reading velocity z from %s\n"
394 +             "natoms  = %d, index = %d\n",
395 +             c_in_name, n_atoms, atomIndex );
396 +    return strdup( painCave.errMsg );
397 +  }
398 +  vz = atof( foo );
399 +    
400 +    
401 +  // get the quaternions
402 +    
403 +  if( atoms[atomIndex]->isDirectional() ){
404 +      
405      foo = strtok(NULL, " ,;\t");
406      if(foo == NULL){
407 +      sprintf(painCave.errMsg,
408 +              "error in reading quaternion 0 from %s\n"
409 +              "natoms  = %d, index = %d\n",
410 +              c_in_name, n_atoms, atomIndex );
411 +      return strdup( painCave.errMsg );
412 +    }
413 +    q[0] = atof( foo );
414 +      
415 +    foo = strtok(NULL, " ,;\t");
416 +    if(foo == NULL){
417        sprintf( painCave.errMsg,
418 <               "error in reading postition x from %s\n"
418 >               "error in reading quaternion 1 from %s\n"
419                 "natoms  = %d, index = %d\n",
420 <               c_in_name, n_atoms, i );
421 <      painCave.isFatal = 1;
400 <      simError();
420 >               c_in_name, n_atoms, atomIndex );
421 >      return strdup( painCave.errMsg );
422      }
423 <    (void)sscanf( foo, "%lf", &rx );
424 <  
423 >    q[1] = atof( foo );
424 >      
425      foo = strtok(NULL, " ,;\t");
426      if(foo == NULL){
427        sprintf( painCave.errMsg,
428 <               "error in reading postition y from %s\n"
428 >               "error in reading quaternion 2 from %s\n"
429                 "natoms  = %d, index = %d\n",
430 <               c_in_name, n_atoms, i );
431 <      painCave.isFatal = 1;
411 <      simError();
430 >               c_in_name, n_atoms, atomIndex );
431 >      return strdup( painCave.errMsg );
432      }
433 <    (void)sscanf( foo, "%lf", &ry );
434 <    
433 >    q[2] = atof( foo );
434 >      
435      foo = strtok(NULL, " ,;\t");
436      if(foo == NULL){
437        sprintf( painCave.errMsg,
438 <               "error in reading postition z from %s\n"
438 >               "error in reading quaternion 3 from %s\n"
439                 "natoms  = %d, index = %d\n",
440 <               c_in_name, n_atoms, i );
441 <      painCave.isFatal = 1;
422 <      simError();
440 >               c_in_name, n_atoms, atomIndex );
441 >      return strdup( painCave.errMsg );
442      }
443 <    (void)sscanf( foo, "%lf", &rz );
444 <    
445 <    // get the velocities
446 <
443 >    q[3] = atof( foo );
444 >      
445 >    // get the angular velocities
446 >      
447      foo = strtok(NULL, " ,;\t");
448      if(foo == NULL){
449        sprintf( painCave.errMsg,
450 <               "error in reading velocity x from %s\n"
450 >               "error in reading angular momentum jx from %s\n"
451                 "natoms  = %d, index = %d\n",
452 <               c_in_name, n_atoms, i );
453 <      painCave.isFatal = 1;
435 <      simError();
452 >               c_in_name, n_atoms, atomIndex );
453 >      return strdup( painCave.errMsg );
454      }
455 <    (void)sscanf( foo, "%lf", &vx );
456 <    
455 >    jx = atof( foo );
456 >      
457      foo = strtok(NULL, " ,;\t");
458      if(foo == NULL){
459        sprintf( painCave.errMsg,
460 <               "error in reading velocity y from %s\n"
460 >               "error in reading angular momentum jy from %s\n"
461                 "natoms  = %d, index = %d\n",
462 <               c_in_name, n_atoms, i );
463 <      painCave.isFatal = 1;
446 <      simError();
462 >               c_in_name, n_atoms, atomIndex );
463 >      return strdup( painCave.errMsg );
464      }
465 <    (void)sscanf( foo, "%lf", &vy );
466 <    
465 >    jy = atof(foo );
466 >      
467      foo = strtok(NULL, " ,;\t");
468      if(foo == NULL){
469        sprintf( painCave.errMsg,
470 <               "error in reading velocity z from %s\n"
470 >               "error in reading angular momentum jz from %s\n"
471                 "natoms  = %d, index = %d\n",
472 <               c_in_name, n_atoms, i );
473 <      painCave.isFatal = 1;
457 <      simError();
472 >               c_in_name, n_atoms, atomIndex );
473 >      return strdup( painCave.errMsg );
474      }
475 <    (void)sscanf( foo, "%lf", &vz );
460 <    
461 <    
462 <    // get the quaternions
463 <    
464 <    if( atoms[i]->isDirectional() ){
475 >    jz = atof( foo );
476        
477 <      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];
477 >    dAtom = ( DirectionalAtom* )atoms[atomIndex];
478  
479 <      // check that the quaternion vector is normalized
479 >    // check that the quaternion vector is normalized
480  
481 <      qSqr = (q[0] * q[0]) + (q[1] * q[1]) + (q[2] * q[2]) + (q[3] * q[3]);
481 >    qSqr = (q[0] * q[0]) + (q[1] * q[1]) + (q[2] * q[2]) + (q[3] * q[3]);
482        
483 <      qLength = sqrt( qSqr );
484 <      q[0] = q[0] / qLength;
485 <      q[1] = q[1] / qLength;
486 <      q[2] = q[2] / qLength;
487 <      q[3] = q[3] / qLength;
483 >    qLength = sqrt( qSqr );
484 >    q[0] = q[0] / qLength;
485 >    q[1] = q[1] / qLength;
486 >    q[2] = q[2] / qLength;
487 >    q[3] = q[3] / qLength;
488        
489 <      dAtom->setQ( q );
489 >    dAtom->setQ( q );
490        
491 <      // add the angular velocities
491 >    // add the angular velocities
492  
493 <      dAtom->setJx( jx );
494 <      dAtom->setJy( jy );
495 <      dAtom->setJz( jz );
496 <    }
493 >    dAtom->setJx( jx );
494 >    dAtom->setJy( jy );
495 >    dAtom->setJz( jz );
496 >  }
497      
498 <    // add the positions and velocities to the atom
498 >  // add the positions and velocities to the atom
499      
500 <    atoms[i]->setX( rx );
501 <    atoms[i]->setY( ry );
502 <    atoms[i]->setZ( rz );
500 >  atoms[atomIndex]->setX( rx );
501 >  atoms[atomIndex]->setY( ry );
502 >  atoms[atomIndex]->setZ( rz );
503      
504 <    atoms[i]->set_vx( vx );
505 <    atoms[i]->set_vy( vy );
506 <    atoms[i]->set_vz( vz );
575 <    
576 <  }
577 < #endif
578 < }
504 >  atoms[atomIndex]->set_vx( vx );
505 >  atoms[atomIndex]->set_vy( vy );
506 >  atoms[atomIndex]->set_vz( vz );
507  
508 < char* IntitializeFromFile::parseDumpLine(char* readLine);
508 >  return NULL;
509 > }

Diff Legend

– Removed lines
+ Added lines
< Changed lines
> Changed lines