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root/group/trunk/OOPSE/libmdtools/InitializeFromFile.cpp
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Comparing trunk/OOPSE/libmdtools/InitializeFromFile.cpp (file contents):
Revision 419 by gezelter, Thu Mar 27 15:07:29 2003 UTC vs.
Revision 670 by mmeineke, Thu Aug 7 21:47:18 2003 UTC

# Line 13 | Line 13
13  
14   #ifdef IS_MPI
15   #include <mpi.h>
16 – #include <mpi++.h>
16   #include "mpiSimulation.hpp"
17 < #define TAKE_THIS_TAG 0
17 > #define TAKE_THIS_TAG_CHAR 0
18 > #define TAKE_THIS_TAG_INT 1
19 >
20 > namespace initFile{
21 >  void nodeZeroError( void );
22 >  void anonymousNodeDie( void );
23 > }
24 >
25 > using namespace initFile;
26 >
27   #endif // is_mpi
28  
29   InitializeFromFile :: InitializeFromFile( char *in_name ){
# Line 61 | Line 69 | void InitializeFromFile :: read_xyz( SimInfo* the_entr
69   }
70  
71  
72 < void InitializeFromFile :: read_xyz( SimInfo* the_entry_plug ){
72 > void InitializeFromFile :: readInit( SimInfo* the_simnfo ){
73  
74    int i, j, done, which_node, which_atom; // loop counter
75  
# Line 75 | Line 83 | void InitializeFromFile :: read_xyz( SimInfo* the_entr
83    char *eof_test; // ptr to see when we reach the end of the file
84    char *parseErr;
85    int procIndex;
86 +  double currTime;
87 +  double boxMat[9];
88 +  double theBoxMat3[3][3];
89  
90 <  entry_plug = the_entry_plug;
90 >  simnfo = the_simnfo;
91  
92  
93   #ifndef IS_MPI
# Line 91 | Line 102 | void InitializeFromFile :: read_xyz( SimInfo* the_entr
102  
103    n_atoms = atoi( read_buffer );
104  
105 <  Atom **atoms = entry_plug->atoms;
105 >  Atom **atoms = simnfo->atoms;
106    DirectionalAtom* dAtom;
107  
108 <  if( n_atoms != entry_plug->n_atoms ){
108 >  if( n_atoms != simnfo->n_atoms ){
109      sprintf( painCave.errMsg,
110               "Initialize from File error. %s n_atoms, %d, "
111               "does not match the BASS file's n_atoms, %d.\n",
112 <             c_in_name, n_atoms, entry_plug->n_atoms );
112 >             c_in_name, n_atoms, simnfo->n_atoms );
113      painCave.isFatal = 1;
114      simError();
115    }
116    
117 <  //read and toss the comment line
117 >  //read the box mat from the comment line
118    
119    eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file);
120    if(eof_test == NULL){
# Line 113 | Line 124 | void InitializeFromFile :: read_xyz( SimInfo* the_entr
124      simError();
125    }
126  
127 +  parseErr = parseBoxLine( read_buffer, boxMat, currTime );
128 +  if( parseErr != NULL ){
129 +    strcpy( painCave.errMsg, parseErr );
130 +    painCave.isFatal = 1;
131 +    simError();
132 +  }
133 +
134 +  for(i=0;i<3;i++)
135 +    for(j=0;j<3;j++) theBoxMat3[i][j] = boxMat[3*j+i];
136 +
137 +  simnfo->setBoxM( theBoxMat3 );
138 +  simnfo->setTime( currTime );
139 +
140 +
141    for( i=0; i < n_atoms; i++){
142      
143      eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file);
# Line 132 | Line 157 | void InitializeFromFile :: read_xyz( SimInfo* the_entr
157        strcpy( painCave.errMsg, parseErr );
158        painCave.isFatal = 1;
159        simError();
160 <    }    
160 >    }
161    }
162  
163  
164    // MPI Section of code..........
165   #else //IS_MPI
166  
167 <  MPI::Status istatus;
167 >  // first thing first, suspend fatalities.
168 >  painCave.isEventLoop = 1;
169 >
170 >  int myStatus; // 1 = wakeup & success; 0 = error; -1 = AllDone
171 >  int haveError;
172 >  
173 >  MPI_Status istatus;
174    int *AtomToProcMap = mpiSim->getAtomToProcMap();
175  
176 +  
177 +  haveError = 0;
178    if (worldRank == 0) {
179 +
180      eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file);
181      if( eof_test == NULL ){
182        sprintf( painCave.errMsg,
183                 "Error reading 1st line of %d \n ",c_in_name);
184 <      painCave.isFatal = 1;
184 >      haveError = 1;
185        simError();
186      }
187      
188      n_atoms = atoi( read_buffer );
189      
190 <    Atom **atoms = entry_plug->atoms;
190 >    Atom **atoms = simnfo->atoms;
191      DirectionalAtom* dAtom;
192  
193      // Check to see that the number of atoms in the intial configuration file is the
# Line 163 | Line 197 | void InitializeFromFile :: read_xyz( SimInfo* the_entr
197        sprintf( painCave.errMsg,
198                 "Initialize from File error. %s n_atoms, %d, "
199                 "does not match the BASS file's n_atoms, %d.\n",
200 <               c_in_name, n_atoms, entry_plug->n_atoms );
201 <      painCave.isFatal = 1;
200 >               c_in_name, n_atoms, simnfo->n_atoms );
201 >      haveError= 1;
202        simError();
203      }
204      
205 <    //read and toss the comment line
205 >    //read the boxMat from the comment line
206      
207      eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file);
208      if(eof_test == NULL){
209        sprintf( painCave.errMsg,
210                 "error in reading commment in %s\n", c_in_name);
211 <      painCave.isFatal = 1;
211 >      haveError = 1;
212        simError();
213      }
214 +    
215 +    parseErr = parseBoxLine( read_buffer, boxMat, currTime );
216 +    if( parseErr != NULL ){
217 +      strcpy( painCave.errMsg, parseErr );
218 +      haveError = 1;
219 +      simError();
220 +    }
221 +
222 +    MPI_Bcast(boxMat, 9, MPI_DOUBLE, 0, MPI_COMM_WORLD );
223 +    MPI_Bcast(&currTime, 1, MPI_DOUBLE, 0, MPI_COMM_WORLD );
224    
225 +    if(haveError) nodeZeroError();
226  
227      for (i=0 ; i < mpiSim->getTotAtoms(); i++) {
228        
# Line 188 | Line 233 | void InitializeFromFile :: read_xyz( SimInfo* the_entr
233                  "natoms  = %d; index = %d\n"
234                  "error reading the line from the file.\n",
235                  c_in_name, n_atoms, i );
236 <        painCave.isFatal = 1;
236 >        haveError= 1;
237          simError();
238        }
239      
240 +      if(haveError) nodeZeroError();
241 +
242        // Get the Node number which wants this atom:
243        which_node = AtomToProcMap[i];    
244 <      if (which_node == mpiSim->getMyNode()) {
244 >      if (which_node == 0) {
245          parseErr = parseDumpLine( read_buffer, i );
246          if( parseErr != NULL ){
247            strcpy( painCave.errMsg, parseErr );
248 <          painCave.isFatal = 1;
248 >          haveError = 1;
249            simError();
250          }    
251 <      } else {
252 <        MPI::COMM_WORLD.Send(read_buffer, BUFFERSIZE, MPI_CHAR, which_node,
253 <                             TAKE_THIS_TAG);
254 <        MPI::COMM_WORLD.Send(&i, 1, MPI_INT, which_node, TAKE_THIS_TAG);
251 >        if(haveError) nodeZeroError();
252 >      }
253 >      
254 >      else {
255 >      
256 >        myStatus = 1;
257 >        MPI_Send(&myStatus, 1, MPI_INT, which_node,
258 >                 TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
259 >        MPI_Send(read_buffer, BUFFERSIZE, MPI_CHAR, which_node,
260 >                 TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD);
261 >        MPI_Send(&i, 1, MPI_INT, which_node, TAKE_THIS_TAG_INT,
262 >                 MPI_COMM_WORLD);
263 >        MPI_Recv(&myStatus, 1, MPI_INT, which_node, TAKE_THIS_TAG_INT,
264 >                 MPI_COMM_WORLD, &istatus);
265 >        
266 >        if(!myStatus) nodeZeroError();
267        }
268      }
269 <    sprintf(read_buffer, "GAMEOVER");
269 >    myStatus = -1;
270      for (j = 0; j < mpiSim->getNumberProcessors(); j++) {      
271 <      MPI::COMM_WORLD.Send(read_buffer, BUFFERSIZE, MPI_CHAR, j,
272 <                           TAKE_THIS_TAG);
271 >      MPI_Send( &myStatus, 1, MPI_INT, j,
272 >                TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
273      }
274      
275    } else {
276      
277 +    MPI_Bcast(boxMat, 9, MPI_DOUBLE, 0, MPI_COMM_WORLD);
278 +    MPI_Bcast(&currTime, 1, MPI_DOUBLE, 0, MPI_COMM_WORLD);
279 +
280      done = 0;
281      while (!done) {
282 <      MPI::COMM_WORLD.Recv(read_buffer, BUFFERSIZE, MPI_CHAR, 0,
283 <                           TAKE_THIS_TAG, istatus);
284 <      if (strcmp(read_buffer, "GAMEOVER")) {
285 <        done = 1;
286 <        continue;
287 <      } else {
288 <        MPI::COMM_WORLD.Recv(&which_atom, 1, MPI_INT, 0,
289 <                             TAKE_THIS_TAG, istatus);
290 <        
291 <        parseErr = parseDumpLine( read_buffer, which_atom );
292 <        if( parseErr != NULL ){
293 <          strcpy( painCave.errMsg, parseErr );
294 <          painCave.isFatal = 1;
295 <          simError();
296 <        }
282 >
283 >      MPI_Recv(&myStatus, 1, MPI_INT, 0,
284 >               TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus);
285 >      
286 >      if(!myStatus) anonymousNodeDie();
287 >      
288 >      if(myStatus < 0) break;
289 >
290 >      MPI_Recv(read_buffer, BUFFERSIZE, MPI_CHAR, 0,
291 >               TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD, &istatus);
292 >      MPI_Recv(&which_atom, 1, MPI_INT, 0,
293 >               TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus);
294 >      
295 >      myStatus = 1;
296 >      parseErr = parseDumpLine( read_buffer, which_atom );
297 >      if( parseErr != NULL ){
298 >        strcpy( painCave.errMsg, parseErr );
299 >        myStatus = 0;;
300 >        simError();
301        }
302 +      
303 +      MPI_Send( &myStatus, 1, MPI_INT, 0,
304 +                TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
305 +      
306      }
307    }
308 <        
308 >    
309 > // last  thing last, enable  fatalities.
310 >  painCave.isEventLoop = 0;
311 >
312 >  for(i=0;i<3;i++)
313 >    for(j=0;j<3;j++) theBoxMat3[i][j] = boxMat[3*j+i];
314 >
315 >  simnfo->setBoxM( theBoxMat3 );
316 >  simnfo->setTime( currTime );
317 >
318 >  
319   #endif
320   }
321  
# Line 243 | Line 323 | char* InitializeFromFile::parseDumpLine(char* readLine
323  
324    char *foo; // the pointer to the current string token
325    
326 <  double rx, ry, rz; // position place holders
327 <  double vx, vy, vz; // velocity placeholders
326 >  double pos[3]; // position place holders
327 >  double vel[3]; // velocity placeholders
328    double q[4]; // the quaternions
329    double jx, jy, jz; // angular velocity placeholders;
330    double qSqr, qLength; // needed to normalize the quaternion vector.
331    
332 <  Atom **atoms = entry_plug->atoms;
332 >  Atom **atoms = simnfo->atoms;
333    DirectionalAtom* dAtom;
334    
335    int j, n_atoms, atomIndex;
# Line 268 | Line 348 | char* InitializeFromFile::parseDumpLine(char* readLine
348      return strdup( painCave.errMsg );
349    }  
350   #else
351 <  n_atoms = entry_plug->n_atoms;
351 >  n_atoms = simnfo->n_atoms;
352    atomIndex = globalIndex;
353   #endif // is_mpi
354  
# Line 297 | Line 377 | char* InitializeFromFile::parseDumpLine(char* readLine
377               c_in_name, n_atoms, atomIndex );
378      return strdup( painCave.errMsg );
379    }
380 <  rx = atof( foo );
380 >  pos[0] = atof( foo );
381    
382    foo = strtok(NULL, " ,;\t");
383    if(foo == NULL){
# Line 307 | Line 387 | char* InitializeFromFile::parseDumpLine(char* readLine
387               c_in_name, n_atoms, atomIndex );
388      return strdup( painCave.errMsg );
389    }
390 <  ry = atof( foo );
390 >  pos[1] = atof( foo );
391      
392    foo = strtok(NULL, " ,;\t");
393    if(foo == NULL){
# Line 317 | Line 397 | char* InitializeFromFile::parseDumpLine(char* readLine
397               c_in_name, n_atoms, atomIndex );
398      return strdup( painCave.errMsg );
399    }
400 <  rz = atof( foo );    
400 >  pos[2] = atof( foo );    
401  
402  
403    // get the velocities
# Line 330 | Line 410 | char* InitializeFromFile::parseDumpLine(char* readLine
410               c_in_name, n_atoms, atomIndex );
411      return strdup( painCave.errMsg );
412    }
413 <  vx = atof( foo );
413 >  vel[0] = atof( foo );
414      
415    foo = strtok(NULL, " ,;\t");
416    if(foo == NULL){
# Line 340 | Line 420 | char* InitializeFromFile::parseDumpLine(char* readLine
420               c_in_name, n_atoms, atomIndex );
421      return strdup( painCave.errMsg );
422    }
423 <  vy = atof( foo );
423 >  vel[1] = atof( foo );
424      
425    foo = strtok(NULL, " ,;\t");
426    if(foo == NULL){
# Line 350 | Line 430 | char* InitializeFromFile::parseDumpLine(char* readLine
430               c_in_name, n_atoms, atomIndex );
431      return strdup( painCave.errMsg );
432    }
433 <  vz = atof( foo );
433 >  vel[2] = atof( foo );
434      
435      
436    // get the quaternions
# Line 452 | Line 532 | char* InitializeFromFile::parseDumpLine(char* readLine
532      
533    // add the positions and velocities to the atom
534      
535 <  atoms[atomIndex]->setX( rx );
536 <  atoms[atomIndex]->setY( ry );
457 <  atoms[atomIndex]->setZ( rz );
458 <    
459 <  atoms[atomIndex]->set_vx( vx );
460 <  atoms[atomIndex]->set_vy( vy );
461 <  atoms[atomIndex]->set_vz( vz );
535 >  atoms[atomIndex]->setPos( pos );
536 >  atoms[atomIndex]->setVel( vel );
537  
538    return NULL;
539   }
540 +
541 +
542 + char* InitializeFromFile::parseBoxLine(char* readLine, double boxMat[9],
543 +                                       double &time ){
544 +
545 +  char *foo; // the pointer to the current string token
546 +  int j;
547 +
548 +  // set the string tokenizer
549 +  
550 +  foo = strtok(readLine, " ,;\t");
551 +  // set the timeToken.
552 +
553 +  if(foo == NULL){
554 +    sprintf( painCave.errMsg,
555 +             "error in reading Time from %s\n",
556 +             c_in_name );
557 +    return strdup( painCave.errMsg );
558 +  }
559 +  time = atof( foo );
560 +
561 +  // get the Hx vector
562 +
563 +  foo = strtok(NULL, " ,;\t");
564 +  if(foo == NULL){
565 +    sprintf( painCave.errMsg,
566 +             "error in reading Hx[0] from %s\n",
567 +             c_in_name );
568 +    return strdup( painCave.errMsg );
569 +  }
570 +  boxMat[0] = atof( foo );
571 +  
572 +  foo = strtok(NULL, " ,;\t");
573 +  if(foo == NULL){
574 +    sprintf( painCave.errMsg,
575 +             "error in reading Hx[1] from %s\n",
576 +             c_in_name );
577 +    return strdup( painCave.errMsg );
578 +  }
579 +  boxMat[1] = atof( foo );
580 +    
581 +  foo = strtok(NULL, " ,;\t");
582 +  if(foo == NULL){
583 +    sprintf( painCave.errMsg,
584 +             "error in reading Hx[2] from %s\n",
585 +             c_in_name );
586 +    return strdup( painCave.errMsg );
587 +  }
588 +  boxMat[2] = atof( foo );    
589 +
590 +  // get the Hy vector
591 +
592 +  foo = strtok(NULL, " ,;\t");
593 +  if(foo == NULL){
594 +    sprintf( painCave.errMsg,
595 +             "error in reading Hy[0] from %s\n",
596 +             c_in_name );
597 +    return strdup( painCave.errMsg );
598 +  }
599 +  boxMat[3] = atof( foo );
600 +  
601 +  foo = strtok(NULL, " ,;\t");
602 +  if(foo == NULL){
603 +    sprintf( painCave.errMsg,
604 +             "error in reading Hy[1] from %s\n",
605 +             c_in_name );
606 +    return strdup( painCave.errMsg );
607 +  }
608 +  boxMat[4] = atof( foo );
609 +    
610 +  foo = strtok(NULL, " ,;\t");
611 +  if(foo == NULL){
612 +    sprintf( painCave.errMsg,
613 +             "error in reading Hy[2] from %s\n",
614 +             c_in_name );
615 +    return strdup( painCave.errMsg );
616 +  }
617 +  boxMat[5] = atof( foo );    
618 +
619 +  // get the Hz vector
620 +
621 +  foo = strtok(NULL, " ,;\t");
622 +  if(foo == NULL){
623 +    sprintf( painCave.errMsg,
624 +             "error in reading Hz[0] from %s\n",
625 +             c_in_name );
626 +    return strdup( painCave.errMsg );
627 +  }
628 +  boxMat[6] = atof( foo );
629 +  
630 +  foo = strtok(NULL, " ,;\t");
631 +  if(foo == NULL){
632 +    sprintf( painCave.errMsg,
633 +             "error in reading Hz[1] from %s\n",
634 +             c_in_name );
635 +    return strdup( painCave.errMsg );
636 +  }
637 +  boxMat[7] = atof( foo );
638 +    
639 +  foo = strtok(NULL, " ,;\t");
640 +  if(foo == NULL){
641 +    sprintf( painCave.errMsg,
642 +             "error in reading Hz[2] from %s\n",
643 +             c_in_name );
644 +    return strdup( painCave.errMsg );
645 +  }
646 +  boxMat[8] = atof( foo );    
647 +
648 +  return NULL;
649 + }
650 +
651 +
652 + #ifdef IS_MPI
653 +
654 + // a couple of functions to let us escape the read loop
655 +
656 + void initFile::nodeZeroError( void ){
657 +  int j, myStatus;
658 +  
659 +  myStatus = 0;
660 +  for (j = 0; j < mpiSim->getNumberProcessors(); j++) {      
661 +    MPI_Send( &myStatus, 1, MPI_INT, j,
662 +              TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
663 +  }  
664 +  
665 +
666 +  MPI_Finalize();
667 +  exit (0);
668 +  
669 + }
670 +
671 + void initFile::anonymousNodeDie( void ){
672 +
673 +  MPI_Finalize();
674 +  exit (0);
675 + }
676 +
677 + #endif //is_mpi

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