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root/group/trunk/OOPSE/libmdtools/InitializeFromFile.cpp
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Comparing trunk/OOPSE/libmdtools/InitializeFromFile.cpp (file contents):
Revision 906 by mmeineke, Thu Jan 8 15:44:47 2004 UTC vs.
Revision 1129 by tim, Thu Apr 22 03:29:30 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 >  int nItems;
179  
180 <
180 >  nTotObjs = simnfo->getTotIntegrableObjects();
181    haveError = 0;
182    if (worldRank == 0) {
183  
# Line 183 | Line 189 | void InitializeFromFile :: readInit( SimInfo* the_simn
189        simError();
190      }
191  
192 <    n_atoms = atoi( read_buffer );
192 >    nItems = atoi( read_buffer );
193  
194 <    // Check to see that the number of atoms in the intial configuration file is the
194 >    // Check to see that the number of integrable objects  in the intial configuration file is the
195      // same as declared in simBass.
196  
197 <    if( n_atoms != mpiSim->getTotAtoms() ){
197 >    if( nTotObjs != nItems){
198        sprintf( painCave.errMsg,
199                 "Initialize from File error. %s n_atoms, %d, "
200                 "does not match the BASS file's n_atoms, %d.\n",
201 <               c_in_name, n_atoms, simnfo->n_atoms );
201 >               c_in_name, nTotObjs, simnfo->getTotIntegrableObjects());
202        haveError= 1;
203        simError();
204      }
# Line 222 | Line 228 | void InitializeFromFile :: readInit( SimInfo* the_simn
228        simError();
229      }
230  
231 <    for (i=0 ; i < mpiSim->getTotAtoms(); i++) {
231 >    for (i=0 ; i < mpiSim->getTotNmol(); i++) {
232 >      which_node = MolToProcMap[i];
233 >      if(which_node == 0){
234 >       //molecules belong to master node
235  
236 <      eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file);
237 <      if(eof_test == NULL){
238 <        sprintf(painCave.errMsg,
239 <                "error in reading file %s\n"
240 <                "natoms  = %d; index = %d\n"
241 <                "error reading the line from the file.\n",
233 <                c_in_name, n_atoms, i );
234 <        haveError= 1;
235 <        simError();
236 >      localIndex = mpiSim->getGlobalToLocalMol(i);
237 >
238 >      if(localIndex == -1) {
239 >        strcpy(painCave.errMsg, "Molecule not found on node 0!");
240 >        haveError = 1;
241 >        simError();
242        }
243  
244 <      if(haveError) nodeZeroError();
244 >       integrableObjects = (simnfo->molecules[localIndex]).getIntegrableObjects();
245 >       for(j=0; j < integrableObjects.size(); j++){
246 >        
247 >          eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file);
248 >          if(eof_test == NULL){
249 >                sprintf(painCave.errMsg,
250 >                    "error in reading file %s\n"
251 >                    "natoms  = %d; index = %d\n"
252 >                    "error reading the line from the file.\n",
253 >                    c_in_name, nTotObjs, i );
254 >                haveError= 1;
255 >                simError();
256 >          }
257 >          
258 >          if(haveError) nodeZeroError();
259 >
260 >          parseDumpLine(read_buffer, integrableObjects[j]);
261 >          
262 >       }
263  
264 <      // Get the Node number which wants this atom:
241 <      which_node = AtomToProcMap[i];
242 <      if (which_node == 0) {
243 <        parseErr = parseDumpLine( read_buffer, i );
244 <        if( parseErr != NULL ){
245 <          strcpy( painCave.errMsg, parseErr );
246 <          haveError = 1;
247 <          simError();
248 <        }
249 <        if(haveError) nodeZeroError();
264 >
265        }
266 +      else{
267 +      //molecule belongs to slave nodes
268  
269 <      else {
269 >        MPI_Recv(&nCurObj, 1, MPI_INT, which_node,
270 >               TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus);
271 >      
272 >       for(j=0; j < integrableObjects.size(); j++){
273 >        
274 >          eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file);
275 >          if(eof_test == NULL){
276 >                sprintf(painCave.errMsg,
277 >                    "error in reading file %s\n"
278 >                    "natoms  = %d; index = %d\n"
279 >                    "error reading the line from the file.\n",
280 >                    c_in_name, nTotObjs, i );
281 >                haveError= 1;
282 >                simError();
283 >          }
284 >          
285 >          if(haveError) nodeZeroError();
286  
287 <        myStatus = 1;
288 <        MPI_Send(&myStatus, 1, MPI_INT, which_node,
289 <                 TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
290 <        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);
287 >            MPI_Send(read_buffer, BUFFERSIZE, MPI_CHAR, which_node,
288 >                      TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD);
289 >          
290 >       }
291  
264 –        if(!myStatus) nodeZeroError();
292        }
293 +      
294      }
295 <    myStatus = -1;
296 <    for (j = 1; j < mpiSim->getNumberProcessors(); j++) {
297 <      MPI_Send( &myStatus, 1, MPI_INT, j,
298 <                TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
271 <    }
295 >    
296 >  }
297 >  else{
298 >  //actions taken at slave nodes
299  
273 –  } else {
274 –
300      MPI_Bcast(read_buffer, BUFFERSIZE, MPI_CHAR, 0, MPI_COMM_WORLD);
301  
302      parseErr = parseCommentLine( read_buffer, simnfo);
# Line 281 | Line 306 | void InitializeFromFile :: readInit( SimInfo* the_simn
306        haveError = 1;
307        simError();
308      }
309 +  
310 +    for (i=0 ; i < mpiSim->getTotNmol(); i++) {
311 +      which_node = MolToProcMap[i];
312 +      
313 +      if(which_node == worldRank){
314 +      //molecule with global index i belongs to this processor
315 +      
316 +        localIndex = mpiSim->getGlobalToLocalMol(i);
317  
318 +        if(localIndex == -1) {
319 +          sprintf(painCave.errMsg, "Molecule not found on node %d\n", worldRank);
320 +          haveError = 1;
321 +          simError();
322 +        }
323  
324 <    done = 0;
287 <    while (!done) {
324 >        integrableObjects = (simnfo->molecules[localIndex]).getIntegrableObjects();        
325  
326 <      MPI_Recv(&myStatus, 1, MPI_INT, 0,
327 <               TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus);
326 >        nCurObj = integrableObjects.size();
327 >        
328 >        MPI_Send(&nCurObj, 1, MPI_INT, 0,
329 >                        TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
330  
331 <      if(!myStatus) anonymousNodeDie();
331 >        for(j = 0; j < integrableObjects.size(); j++){
332  
333 <      if(myStatus < 0) break;
333 >          MPI_Recv(read_buffer, BUFFERSIZE, MPI_CHAR, 0,
334 >                              TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD, &istatus);
335  
336 <      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);
336 >          parseErr = parseDumpLine(read_buffer, integrableObjects[j]);
337  
338 <      myStatus = 1;
339 <      parseErr = parseDumpLine( read_buffer, which_atom );
340 <      if( parseErr != NULL ){
341 <        strcpy( painCave.errMsg, parseErr );
305 <        myStatus = 0;;
306 <        simError();
307 <      }
338 >          if( parseErr != NULL ){
339 >                strcpy( painCave.errMsg, parseErr );
340 >                simError();
341 >          }
342  
343 <      MPI_Send( &myStatus, 1, MPI_INT, 0,
344 <                TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
345 <
343 >        }
344 >          
345 >      }
346 >      
347      }
313 –  }
348  
349 < // last  thing last, enable  fatalities.
316 <  painCave.isEventLoop = 0;
317 <
318 <
319 <
349 >  }
350   #endif
351   }
352  
353 < char* InitializeFromFile::parseDumpLine(char* readLine, int globalIndex){
353 > char* InitializeFromFile::parseDumpLine(char* readLine, StuntDouble* sd){
354  
355    char *foo; // the pointer to the current string token
356  
357    double pos[3]; // position place holders
358    double vel[3]; // velocity placeholders
359    double q[4]; // the quaternions
360 <  double jx, jy, jz; // angular velocity placeholders;
360 >  double ji[3]; // angular velocity placeholders;
361    double qSqr, qLength; // needed to normalize the quaternion vector.
362  
333 –  Atom **atoms = simnfo->atoms;
334 –  DirectionalAtom* dAtom;
363  
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 –
364    // set the string tokenizer
365  
366    foo = strtok(readLine, " ,;\t");
367  
368    // check the atom name to the current atom
369  
370 <  if( strcmp( foo, atoms[atomIndex]->getType() ) ){
370 >  if( strcmp( foo, sd->getType() ) ){
371      sprintf( painCave.errMsg,
372 <             "Initialize from file error. Atom %s at index %d "
367 <             "in file %s does not"
372 >             "Initialize from file error.  Does not"
373               " match the BASS atom %s.\n",
374 <             foo, atomIndex, c_in_name, atoms[atomIndex]->getType() );
374 >             sd->getType() );
375      return strdup( painCave.errMsg );
376    }
377  
# Line 375 | Line 380 | char* InitializeFromFile::parseDumpLine(char* readLine
380    foo = strtok(NULL, " ,;\t");
381    if(foo == NULL){
382      sprintf( painCave.errMsg,
383 <             "error in reading postition x from %s\n"
384 <             "natoms  = %d, index = %d\n",
380 <             c_in_name, n_atoms, atomIndex );
383 >             "error in reading postition x from %s\n",
384 >             c_in_name);
385      return strdup( painCave.errMsg );
386    }
387    pos[0] = atof( foo );
# Line 385 | Line 389 | char* InitializeFromFile::parseDumpLine(char* readLine
389    foo = strtok(NULL, " ,;\t");
390    if(foo == NULL){
391      sprintf( painCave.errMsg,
392 <             "error in reading postition y from %s\n"
393 <             "natoms  = %d, index = %d\n",
390 <             c_in_name, n_atoms, atomIndex );
392 >             "error in reading postition y from %s\n",
393 >             c_in_name);
394      return strdup( painCave.errMsg );
395    }
396    pos[1] = atof( foo );
# Line 395 | Line 398 | char* InitializeFromFile::parseDumpLine(char* readLine
398    foo = strtok(NULL, " ,;\t");
399    if(foo == NULL){
400      sprintf( painCave.errMsg,
401 <             "error in reading postition z from %s\n"
402 <             "natoms  = %d, index = %d\n",
400 <             c_in_name, n_atoms, atomIndex );
401 >             "error in reading postition z from %s\n",
402 >             c_in_name);
403      return strdup( painCave.errMsg );
404    }
405    pos[2] = atof( foo );
# Line 408 | Line 410 | char* InitializeFromFile::parseDumpLine(char* readLine
410    foo = strtok(NULL, " ,;\t");
411    if(foo == NULL){
412      sprintf( painCave.errMsg,
413 <             "error in reading velocity x from %s\n"
414 <             "natoms  = %d, index = %d\n",
413 <             c_in_name, n_atoms, atomIndex );
413 >             "error in reading velocity x from %s\n",
414 >             c_in_name );
415      return strdup( painCave.errMsg );
416    }
417    vel[0] = atof( foo );
# Line 418 | Line 419 | char* InitializeFromFile::parseDumpLine(char* readLine
419    foo = strtok(NULL, " ,;\t");
420    if(foo == NULL){
421      sprintf( painCave.errMsg,
422 <             "error in reading velocity y from %s\n"
423 <             "natoms  = %d, index = %d\n",
423 <             c_in_name, n_atoms, atomIndex );
422 >             "error in reading velocity x from %s\n",
423 >             c_in_name );
424      return strdup( painCave.errMsg );
425    }
426    vel[1] = atof( foo );
# Line 428 | Line 428 | char* InitializeFromFile::parseDumpLine(char* readLine
428    foo = strtok(NULL, " ,;\t");
429    if(foo == NULL){
430      sprintf( painCave.errMsg,
431 <             "error in reading velocity z from %s\n"
432 <             "natoms  = %d, index = %d\n",
433 <             c_in_name, n_atoms, atomIndex );
431 >             "error in reading velocity x from %s\n",
432 >             c_in_name );
433      return strdup( painCave.errMsg );
434    }
435    vel[2] = atof( foo );
436  
437  
438 +  // add the positions and velocities to the atom
439 +
440 +  sd->setPos( pos );
441 +  sd->setVel( vel );
442 +
443 +  if (!sd->isDirectional())
444 +    return NULL;
445 +
446    // get the quaternions
447  
448 <  if( atoms[atomIndex]->isDirectional() ){
448 >  if( sd->isDirectional() ){
449  
450      foo = strtok(NULL, " ,;\t");
451      if(foo == NULL){
452 <      sprintf(painCave.errMsg,
453 <              "error in reading quaternion 0 from %s\n"
454 <              "natoms  = %d, index = %d\n",
448 <              c_in_name, n_atoms, atomIndex );
452 >      sprintf( painCave.errMsg,
453 >                     "error in reading velocity x from %s\n",
454 >                      c_in_name );
455        return strdup( painCave.errMsg );
456      }
457      q[0] = atof( foo );
# Line 453 | Line 459 | char* InitializeFromFile::parseDumpLine(char* readLine
459      foo = strtok(NULL, " ,;\t");
460      if(foo == NULL){
461        sprintf( painCave.errMsg,
462 <               "error in reading quaternion 1 from %s\n"
463 <               "natoms  = %d, index = %d\n",
458 <               c_in_name, n_atoms, atomIndex );
462 >                     "error in reading velocity x from %s\n",
463 >                      c_in_name );
464        return strdup( painCave.errMsg );
465      }
466      q[1] = atof( foo );
# Line 463 | Line 468 | char* InitializeFromFile::parseDumpLine(char* readLine
468      foo = strtok(NULL, " ,;\t");
469      if(foo == NULL){
470        sprintf( painCave.errMsg,
471 <               "error in reading quaternion 2 from %s\n"
472 <               "natoms  = %d, index = %d\n",
468 <               c_in_name, n_atoms, atomIndex );
471 >                     "error in reading velocity x from %s\n",
472 >                      c_in_name );
473        return strdup( painCave.errMsg );
474      }
475      q[2] = atof( foo );
# Line 473 | Line 477 | char* InitializeFromFile::parseDumpLine(char* readLine
477      foo = strtok(NULL, " ,;\t");
478      if(foo == NULL){
479        sprintf( painCave.errMsg,
480 <               "error in reading quaternion 3 from %s\n"
481 <               "natoms  = %d, index = %d\n",
478 <               c_in_name, n_atoms, atomIndex );
480 >                     "error in reading velocity x from %s\n",
481 >                      c_in_name );
482        return strdup( painCave.errMsg );
483      }
484      q[3] = atof( foo );
# Line 485 | Line 488 | char* InitializeFromFile::parseDumpLine(char* readLine
488      foo = strtok(NULL, " ,;\t");
489      if(foo == NULL){
490        sprintf( painCave.errMsg,
491 <               "error in reading angular momentum jx from %s\n"
492 <               "natoms  = %d, index = %d\n",
490 <               c_in_name, n_atoms, atomIndex );
491 >                     "error in reading velocity x from %s\n",
492 >                      c_in_name );
493        return strdup( painCave.errMsg );
494      }
495 <    jx = atof( foo );
495 >    ji[0] = atof( foo );
496  
497      foo = strtok(NULL, " ,;\t");
498      if(foo == NULL){
499        sprintf( painCave.errMsg,
500 <               "error in reading angular momentum jy from %s\n"
501 <               "natoms  = %d, index = %d\n",
500 <               c_in_name, n_atoms, atomIndex );
500 >                     "error in reading velocity x from %s\n",
501 >                      c_in_name );
502        return strdup( painCave.errMsg );
503      }
504 <    jy = atof(foo );
504 >    ji[1] = atof(foo );
505  
506      foo = strtok(NULL, " ,;\t");
507      if(foo == NULL){
508        sprintf( painCave.errMsg,
509 <               "error in reading angular momentum jz from %s\n"
510 <               "natoms  = %d, index = %d\n",
510 <               c_in_name, n_atoms, atomIndex );
509 >                     "error in reading velocity x from %s\n",
510 >                      c_in_name );
511        return strdup( painCave.errMsg );
512      }
513 <    jz = atof( foo );
513 >    ji[2] = atof( foo );
514  
515 –    dAtom = ( DirectionalAtom* )atoms[atomIndex];
515  
516      // check that the quaternion vector is normalized
517  
# Line 524 | Line 523 | char* InitializeFromFile::parseDumpLine(char* readLine
523      q[2] = q[2] / qLength;
524      q[3] = q[3] / qLength;
525  
526 <    dAtom->setQ( q );
526 >    // add quaternion and angular velocities
527  
528 <    // add the angular velocities
529 <
531 <    dAtom->setJx( jx );
532 <    dAtom->setJy( jy );
533 <    dAtom->setJz( jz );
528 >    sd->setQ( q );
529 >    sd->setJ( ji );
530    }
531  
536 –  // add the positions and velocities to the atom
532  
538 –  atoms[atomIndex]->setPos( pos );
539 –  atoms[atomIndex]->setVel( vel );
533  
534    return NULL;
535   }
# Line 618 | Line 611 | char* InitializeFromFile::parseCommentLine(char* readL
611        return NULL;
612      
613      //get eta
614 <    for(int i = 0 ; i < 9; i++){
615 <      foo = strtok(NULL, " ,;\t");
616 <      if(foo == NULL){
617 <        sprintf( painCave.errMsg,
618 <                 "error in reading eta[%d] from %s\n", i, c_in_name );
619 <        return strdup( painCave.errMsg );
614 >    foo = strtok(NULL, " ,;\t\n");
615 >    if(foo != NULL ){
616 >  
617 >      for(int i = 0 ; i < 9; i++){
618 >        
619 >        if(foo == NULL){
620 >          sprintf( painCave.errMsg,
621 >                   "error in reading eta[%d] from %s\n", i, c_in_name );
622 >          return strdup( painCave.errMsg );
623 >        }
624 >        eta[i] = atof( foo );
625 >        foo = strtok(NULL, " ,;\t\n");
626        }
628 –      eta[i] = atof( foo );
627      }
628 +    else
629 +      return NULL;
630      
631      //push eta into SimInfo::properties which can be
632      //retrieved by integrator later
633 <    //entry_plug->setBoxM( theBoxMat3 );
633 >    
634      DoubleArrayData* etaValue = new DoubleArrayData();
635      etaValue->setID(ETAVALUE_ID);
636      etaValue->setData(eta, 9);

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