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root/group/trunk/OOPSE/libmdtools/InitializeFromFile.cpp
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Comparing trunk/OOPSE/libmdtools/InitializeFromFile.cpp (file contents):
Revision 911 by mmeineke, Thu Jan 8 18:13:30 2004 UTC vs.
Revision 1113 by tim, Thu Apr 15 16:18:26 2004 UTC

# Line 85 | Line 85 | void InitializeFromFile :: readInit( SimInfo* the_simn
85   #endif //is_mpi
86  
87    const int BUFFERSIZE = 2000; // size of the read buffer
88 <  int n_atoms; // the number of atoms
88 >  int nTotObjs; // the number of atoms
89    char read_buffer[BUFFERSIZE]; //the line buffer for reading
90  
91    char *eof_test; // ptr to see when we reach the end of the file
92    char *parseErr;
93  
94 +  vector<StuntDouble*> integrableObjects;
95 +
96    simnfo = the_simnfo;
97  
98  
# Line 104 | Line 106 | void InitializeFromFile :: readInit( SimInfo* the_simn
106      simError();
107    }
108  
109 <  n_atoms = atoi( read_buffer );
109 >  nTotObjs = atoi( read_buffer );
110  
111 <  if( n_atoms != simnfo->n_atoms ){
111 >  if( nTotObjs != simnfo->getTotIntegrableObjects() ){
112      sprintf( painCave.errMsg,
113               "Initialize from File error. %s n_atoms, %d, "
114               "does not match the BASS file's n_atoms, %d.\n",
115 <             c_in_name, n_atoms, simnfo->n_atoms );
115 >             c_in_name, nTotObjs, simnfo->getTotIntegrableObjects());
116      painCave.isFatal = 1;
117      simError();
118    }
# Line 125 | Line 127 | void InitializeFromFile :: readInit( SimInfo* the_simn
127      simError();
128    }
129  
128 –
129 –
130    parseErr = parseCommentLine( read_buffer, simnfo);
131    if( parseErr != NULL ){
132      strcpy( painCave.errMsg, parseErr );
# Line 136 | Line 136 | void InitializeFromFile :: readInit( SimInfo* the_simn
136  
137    //parse dump lines
138  
139 <  for( i=0; i < n_atoms; i++){
139 >  for( i=0; i < simnfo->n_mol; i++){
140  
141 <    eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file);
142 <    if(eof_test == NULL){
143 <      sprintf(painCave.errMsg,
144 <              "error in reading file %s\n"
145 <              "natoms  = %d; index = %d\n"
146 <              "error reading the line from the file.\n",
147 <              c_in_name, n_atoms, i );
148 <      painCave.isFatal = 1;
149 <      simError();
150 <    }
141 >    integrableObjects = (simnfo->molecules[i]).getIntegrableObjects();
142  
143 +    for(j = 0; j < integrableObjects.size(); j++){
144  
145 <    parseErr = parseDumpLine( read_buffer, i );
146 <    if( parseErr != NULL ){
147 <      strcpy( painCave.errMsg, parseErr );
148 <      painCave.isFatal = 1;
149 <      simError();
145 >      eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file);
146 >      if(eof_test == NULL){
147 >        sprintf(painCave.errMsg,
148 >              "error in reading file %s\n"
149 >              "natoms  = %d; index = %d\n"
150 >              "error reading the line from the file.\n",
151 >              c_in_name, nTotObjs, i );
152 >        painCave.isFatal = 1;
153 >        simError();
154 >      }
155 >      
156 >      parseErr = parseDumpLine( read_buffer, integrableObjects[j]);
157 >      if( parseErr != NULL ){
158 >        strcpy( painCave.errMsg, parseErr );
159 >        painCave.isFatal = 1;
160 >        simError();
161 >      }
162      }
163    }
164  
161 –
165    // MPI Section of code..........
166   #else //IS_MPI
167  
# Line 169 | Line 172 | void InitializeFromFile :: readInit( SimInfo* the_simn
172    int haveError;
173  
174    MPI_Status istatus;
175 <  int *AtomToProcMap = mpiSim->getAtomToProcMap();
175 >  int *MolToProcMap = mpiSim->getMolToProcMap();
176 >  int localIndex;
177 >  int nCurObj;
178  
174 –
179    haveError = 0;
180    if (worldRank == 0) {
181  
# Line 183 | Line 187 | void InitializeFromFile :: readInit( SimInfo* the_simn
187        simError();
188      }
189  
190 <    n_atoms = atoi( read_buffer );
190 >    nTotObjs = atoi( read_buffer );
191  
192 <    // Check to see that the number of atoms in the intial configuration file is the
192 >    // Check to see that the number of integrable objects  in the intial configuration file is the
193      // same as declared in simBass.
194  
195 <    if( n_atoms != mpiSim->getTotAtoms() ){
195 >    if( nTotObjs != simnfo->getTotIntegrableObjects()){
196        sprintf( painCave.errMsg,
197                 "Initialize from File error. %s n_atoms, %d, "
198                 "does not match the BASS file's n_atoms, %d.\n",
199 <               c_in_name, n_atoms, simnfo->n_atoms );
199 >               c_in_name, nTotObjs, simnfo->getTotIntegrableObjects());
200        haveError= 1;
201        simError();
202      }
# Line 222 | Line 226 | void InitializeFromFile :: readInit( SimInfo* the_simn
226        simError();
227      }
228  
229 <    for (i=0 ; i < mpiSim->getTotAtoms(); i++) {
229 >    for (i=0 ; i < mpiSim->getTotNmol(); i++) {
230 >      which_node = MolToProcMap[i];
231 >      if(which_node == 0){
232 >       //molecules belong to master node
233  
234 <      eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file);
235 <      if(eof_test == NULL){
236 <        sprintf(painCave.errMsg,
237 <                "error in reading file %s\n"
238 <                "natoms  = %d; index = %d\n"
239 <                "error reading the line from the file.\n",
233 <                c_in_name, n_atoms, i );
234 <        haveError= 1;
235 <        simError();
234 >      localIndex = mpiSim->getGlobalToLocalMol(i);
235 >
236 >      if(localIndex == -1) {
237 >        strcpy(painCave.errMsg, "Molecule not found on node 0!");
238 >        haveError = 1;
239 >        simError();
240        }
241  
242 <      if(haveError) nodeZeroError();
242 >       integrableObjects = (simnfo->molecules[localIndex]).getIntegrableObjects();
243 >       for(j=0; j < integrableObjects.size(); j++){
244 >        
245 >          eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file);
246 >          if(eof_test == NULL){
247 >                sprintf(painCave.errMsg,
248 >                    "error in reading file %s\n"
249 >                    "natoms  = %d; index = %d\n"
250 >                    "error reading the line from the file.\n",
251 >                    c_in_name, nTotObjs, i );
252 >                haveError= 1;
253 >                simError();
254 >          }
255 >          
256 >          if(haveError) nodeZeroError();
257  
258 <      // Get the Node number which wants this atom:
259 <      which_node = AtomToProcMap[i];
260 <      if (which_node == 0) {
261 <        parseErr = parseDumpLine( read_buffer, i );
262 <        if( parseErr != NULL ){
245 <          strcpy( painCave.errMsg, parseErr );
246 <          haveError = 1;
247 <          simError();
248 <        }
249 <        if(haveError) nodeZeroError();
258 >          parseDumpLine(read_buffer, integrableObjects[i]);
259 >          
260 >       }
261 >
262 >
263        }
264 +      else{
265 +      //molecule belongs to slave nodes
266  
267 <      else {
267 >        MPI_Recv(&nCurObj, 1, MPI_INT, 0,
268 >               TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus);
269 >      
270 >       for(j=0; j < integrableObjects.size(); j++){
271 >        
272 >          eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file);
273 >          if(eof_test == NULL){
274 >                sprintf(painCave.errMsg,
275 >                    "error in reading file %s\n"
276 >                    "natoms  = %d; index = %d\n"
277 >                    "error reading the line from the file.\n",
278 >                    c_in_name, nTotObjs, i );
279 >                haveError= 1;
280 >                simError();
281 >          }
282 >          
283 >          if(haveError) nodeZeroError();
284  
285 <        myStatus = 1;
286 <        MPI_Send(&myStatus, 1, MPI_INT, which_node,
287 <                 TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
288 <        MPI_Send(read_buffer, BUFFERSIZE, MPI_CHAR, which_node,
258 <                 TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD);
259 <        MPI_Send(&i, 1, MPI_INT, which_node, TAKE_THIS_TAG_INT,
260 <                 MPI_COMM_WORLD);
261 <        MPI_Recv(&myStatus, 1, MPI_INT, which_node, TAKE_THIS_TAG_INT,
262 <                 MPI_COMM_WORLD, &istatus);
285 >            MPI_Send(read_buffer, BUFFERSIZE, MPI_CHAR, which_node,
286 >                      TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD);
287 >          
288 >       }
289  
264 –        if(!myStatus) nodeZeroError();
290        }
291 +      
292      }
293 <    myStatus = -1;
294 <    for (j = 1; j < mpiSim->getNumberProcessors(); j++) {
295 <      MPI_Send( &myStatus, 1, MPI_INT, j,
296 <                TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
297 <    }
293 >    
294 >  }
295 >  else{
296 >  //actions taken at slave nodes
297 >    for (i=0 ; i < mpiSim->getTotNmol(); i++) {
298 >      which_node = MolToProcMap[i];
299 >      
300 >      if(which_node == worldRank){
301 >      //molecule with global index i belongs to this processor
302 >      
303 >        localIndex = mpiSim->getGlobalToLocalMol(i);
304  
305 <  } else {
305 >        if(localIndex == -1) {
306 >          sprintf(painCave.errMsg, "Molecule not found on node %d\n", worldRank);
307 >          haveError = 1;
308 >          simError();
309 >        }
310  
311 <    MPI_Bcast(read_buffer, BUFFERSIZE, MPI_CHAR, 0, MPI_COMM_WORLD);
311 >        integrableObjects = (simnfo->molecules[localIndex]).getIntegrableObjects();        
312  
313 <    parseErr = parseCommentLine( read_buffer, simnfo);
313 >        nCurObj = integrableObjects.size();
314 >        
315 >        MPI_Recv(&nCurObj, 1, MPI_INT, 0,
316 >                        TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus);
317  
318 <    if( parseErr != NULL ){
319 <      strcpy( painCave.errMsg, parseErr );
320 <      haveError = 1;
321 <      simError();
283 <    }
318 >        for(j = 0; j < integrableObjects.size(); j++){
319 >
320 >          MPI_Recv(read_buffer, BUFFERSIZE, MPI_CHAR, 0,
321 >                              TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD, &istatus);
322  
323 +          parseErr = parseDumpLine(read_buffer, integrableObjects[j]);
324  
325 <    done = 0;
326 <    while (!done) {
325 >          if( parseErr != NULL ){
326 >                strcpy( painCave.errMsg, parseErr );
327 >                simError();
328 >          }
329  
330 <      MPI_Recv(&myStatus, 1, MPI_INT, 0,
331 <               TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus);
291 <
292 <      if(!myStatus) anonymousNodeDie();
293 <
294 <      if(myStatus < 0) break;
295 <
296 <      MPI_Recv(read_buffer, BUFFERSIZE, MPI_CHAR, 0,
297 <               TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD, &istatus);
298 <      MPI_Recv(&which_atom, 1, MPI_INT, 0,
299 <               TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus);
300 <
301 <      myStatus = 1;
302 <      parseErr = parseDumpLine( read_buffer, which_atom );
303 <      if( parseErr != NULL ){
304 <        strcpy( painCave.errMsg, parseErr );
305 <        myStatus = 0;;
306 <        simError();
330 >        }
331 >          
332        }
333 <
309 <      MPI_Send( &myStatus, 1, MPI_INT, 0,
310 <                TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
311 <
333 >      
334      }
313 –  }
335  
336 < // last  thing last, enable  fatalities.
316 <  painCave.isEventLoop = 0;
317 <
318 <
319 <
336 >  }
337   #endif
338   }
339  
340 < char* InitializeFromFile::parseDumpLine(char* readLine, int globalIndex){
340 > char* InitializeFromFile::parseDumpLine(char* readLine, StuntDouble* sd){
341  
342    char *foo; // the pointer to the current string token
343  
344    double pos[3]; // position place holders
345    double vel[3]; // velocity placeholders
346    double q[4]; // the quaternions
347 <  double jx, jy, jz; // angular velocity placeholders;
347 >  double ji[3]; // angular velocity placeholders;
348    double qSqr, qLength; // needed to normalize the quaternion vector.
349  
333 –  Atom **atoms = simnfo->atoms;
334 –  DirectionalAtom* dAtom;
350  
336 –  int n_atoms, atomIndex;
337 –
338 – #ifdef IS_MPI
339 –  int j;
340 –
341 –  n_atoms = mpiSim->getTotAtoms();
342 –  atomIndex=-1;
343 –  for (j=0; j < mpiSim->getMyNlocal(); j++) {
344 –    if (atoms[j]->getGlobalIndex() == globalIndex) atomIndex = j;
345 –  }
346 –  if (atomIndex == -1) {
347 –    sprintf( painCave.errMsg,
348 –             "Initialize from file error. Atom at index %d "
349 –             "in file %s does not exist on processor %d .\n",
350 –             globalIndex, c_in_name, mpiSim->getMyNode() );
351 –    return strdup( painCave.errMsg );
352 –  }
353 – #else
354 –  n_atoms = simnfo->n_atoms;
355 –  atomIndex = globalIndex;
356 – #endif // is_mpi
357 –
351    // set the string tokenizer
352  
353    foo = strtok(readLine, " ,;\t");
354  
355    // check the atom name to the current atom
356  
357 <  if( strcmp( foo, atoms[atomIndex]->getType() ) ){
357 >  if( strcmp( foo, sd->getType() ) ){
358      sprintf( painCave.errMsg,
359 <             "Initialize from file error. Atom %s at index %d "
367 <             "in file %s does not"
359 >             "Initialize from file error.  Does not"
360               " match the BASS atom %s.\n",
361 <             foo, atomIndex, c_in_name, atoms[atomIndex]->getType() );
361 >             sd->getType() );
362      return strdup( painCave.errMsg );
363    }
364  
# Line 375 | Line 367 | char* InitializeFromFile::parseDumpLine(char* readLine
367    foo = strtok(NULL, " ,;\t");
368    if(foo == NULL){
369      sprintf( painCave.errMsg,
370 <             "error in reading postition x from %s\n"
371 <             "natoms  = %d, index = %d\n",
380 <             c_in_name, n_atoms, atomIndex );
370 >             "error in reading postition x from %s\n",
371 >             c_in_name);
372      return strdup( painCave.errMsg );
373    }
374    pos[0] = atof( foo );
# Line 385 | Line 376 | char* InitializeFromFile::parseDumpLine(char* readLine
376    foo = strtok(NULL, " ,;\t");
377    if(foo == NULL){
378      sprintf( painCave.errMsg,
379 <             "error in reading postition y from %s\n"
380 <             "natoms  = %d, index = %d\n",
390 <             c_in_name, n_atoms, atomIndex );
379 >             "error in reading postition y from %s\n",
380 >             c_in_name);
381      return strdup( painCave.errMsg );
382    }
383    pos[1] = atof( foo );
# Line 395 | Line 385 | char* InitializeFromFile::parseDumpLine(char* readLine
385    foo = strtok(NULL, " ,;\t");
386    if(foo == NULL){
387      sprintf( painCave.errMsg,
388 <             "error in reading postition z from %s\n"
389 <             "natoms  = %d, index = %d\n",
400 <             c_in_name, n_atoms, atomIndex );
388 >             "error in reading postition z from %s\n",
389 >             c_in_name);
390      return strdup( painCave.errMsg );
391    }
392    pos[2] = atof( foo );
# Line 408 | Line 397 | char* InitializeFromFile::parseDumpLine(char* readLine
397    foo = strtok(NULL, " ,;\t");
398    if(foo == NULL){
399      sprintf( painCave.errMsg,
400 <             "error in reading velocity x from %s\n"
401 <             "natoms  = %d, index = %d\n",
413 <             c_in_name, n_atoms, atomIndex );
400 >             "error in reading velocity x from %s\n",
401 >             c_in_name );
402      return strdup( painCave.errMsg );
403    }
404    vel[0] = atof( foo );
# Line 418 | Line 406 | char* InitializeFromFile::parseDumpLine(char* readLine
406    foo = strtok(NULL, " ,;\t");
407    if(foo == NULL){
408      sprintf( painCave.errMsg,
409 <             "error in reading velocity y from %s\n"
410 <             "natoms  = %d, index = %d\n",
423 <             c_in_name, n_atoms, atomIndex );
409 >             "error in reading velocity x from %s\n",
410 >             c_in_name );
411      return strdup( painCave.errMsg );
412    }
413    vel[1] = atof( foo );
# Line 428 | Line 415 | char* InitializeFromFile::parseDumpLine(char* readLine
415    foo = strtok(NULL, " ,;\t");
416    if(foo == NULL){
417      sprintf( painCave.errMsg,
418 <             "error in reading velocity z from %s\n"
419 <             "natoms  = %d, index = %d\n",
433 <             c_in_name, n_atoms, atomIndex );
418 >             "error in reading velocity x from %s\n",
419 >             c_in_name );
420      return strdup( painCave.errMsg );
421    }
422    vel[2] = atof( foo );
423  
424  
425 +  // add the positions and velocities to the atom
426 +
427 +  sd->setPos( pos );
428 +  sd->setVel( vel );
429 +
430 +  if (!sd->isDirectional())
431 +    return NULL;
432 +
433    // get the quaternions
434  
435 <  if( atoms[atomIndex]->isDirectional() ){
435 >  if( sd->isDirectional() ){
436  
437      foo = strtok(NULL, " ,;\t");
438      if(foo == NULL){
439 <      sprintf(painCave.errMsg,
440 <              "error in reading quaternion 0 from %s\n"
441 <              "natoms  = %d, index = %d\n",
448 <              c_in_name, n_atoms, atomIndex );
439 >      sprintf( painCave.errMsg,
440 >                     "error in reading velocity x from %s\n",
441 >                      c_in_name );
442        return strdup( painCave.errMsg );
443      }
444      q[0] = atof( foo );
# Line 453 | Line 446 | char* InitializeFromFile::parseDumpLine(char* readLine
446      foo = strtok(NULL, " ,;\t");
447      if(foo == NULL){
448        sprintf( painCave.errMsg,
449 <               "error in reading quaternion 1 from %s\n"
450 <               "natoms  = %d, index = %d\n",
458 <               c_in_name, n_atoms, atomIndex );
449 >                     "error in reading velocity x from %s\n",
450 >                      c_in_name );
451        return strdup( painCave.errMsg );
452      }
453      q[1] = atof( foo );
# Line 463 | Line 455 | char* InitializeFromFile::parseDumpLine(char* readLine
455      foo = strtok(NULL, " ,;\t");
456      if(foo == NULL){
457        sprintf( painCave.errMsg,
458 <               "error in reading quaternion 2 from %s\n"
459 <               "natoms  = %d, index = %d\n",
468 <               c_in_name, n_atoms, atomIndex );
458 >                     "error in reading velocity x from %s\n",
459 >                      c_in_name );
460        return strdup( painCave.errMsg );
461      }
462      q[2] = atof( foo );
# Line 473 | Line 464 | char* InitializeFromFile::parseDumpLine(char* readLine
464      foo = strtok(NULL, " ,;\t");
465      if(foo == NULL){
466        sprintf( painCave.errMsg,
467 <               "error in reading quaternion 3 from %s\n"
468 <               "natoms  = %d, index = %d\n",
478 <               c_in_name, n_atoms, atomIndex );
467 >                     "error in reading velocity x from %s\n",
468 >                      c_in_name );
469        return strdup( painCave.errMsg );
470      }
471      q[3] = atof( foo );
# Line 485 | Line 475 | char* InitializeFromFile::parseDumpLine(char* readLine
475      foo = strtok(NULL, " ,;\t");
476      if(foo == NULL){
477        sprintf( painCave.errMsg,
478 <               "error in reading angular momentum jx from %s\n"
479 <               "natoms  = %d, index = %d\n",
490 <               c_in_name, n_atoms, atomIndex );
478 >                     "error in reading velocity x from %s\n",
479 >                      c_in_name );
480        return strdup( painCave.errMsg );
481      }
482 <    jx = atof( foo );
482 >    ji[0] = atof( foo );
483  
484      foo = strtok(NULL, " ,;\t");
485      if(foo == NULL){
486        sprintf( painCave.errMsg,
487 <               "error in reading angular momentum jy from %s\n"
488 <               "natoms  = %d, index = %d\n",
500 <               c_in_name, n_atoms, atomIndex );
487 >                     "error in reading velocity x from %s\n",
488 >                      c_in_name );
489        return strdup( painCave.errMsg );
490      }
491 <    jy = atof(foo );
491 >    ji[1] = atof(foo );
492  
493      foo = strtok(NULL, " ,;\t");
494      if(foo == NULL){
495        sprintf( painCave.errMsg,
496 <               "error in reading angular momentum jz from %s\n"
497 <               "natoms  = %d, index = %d\n",
510 <               c_in_name, n_atoms, atomIndex );
496 >                     "error in reading velocity x from %s\n",
497 >                      c_in_name );
498        return strdup( painCave.errMsg );
499      }
500 <    jz = atof( foo );
500 >    ji[2] = atof( foo );
501  
515 –    dAtom = ( DirectionalAtom* )atoms[atomIndex];
502  
503      // check that the quaternion vector is normalized
504  
# Line 524 | Line 510 | char* InitializeFromFile::parseDumpLine(char* readLine
510      q[2] = q[2] / qLength;
511      q[3] = q[3] / qLength;
512  
513 <    dAtom->setQ( q );
513 >    // add quaternion and angular velocities
514  
515 <    // add the angular velocities
516 <
531 <    dAtom->setJx( jx );
532 <    dAtom->setJy( jy );
533 <    dAtom->setJz( jz );
515 >    sd->setQ( q );
516 >    sd->setJ( ji );
517    }
518  
536 –  // add the positions and velocities to the atom
519  
538 –  atoms[atomIndex]->setPos( pos );
539 –  atoms[atomIndex]->setVel( vel );
520  
521    return NULL;
522   }

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