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root/group/trunk/OOPSE/libmdtools/InitializeFromFile.cpp
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Comparing trunk/OOPSE/libmdtools/InitializeFromFile.cpp (file contents):
Revision 440 by mmeineke, Tue Apr 1 16:49:17 2003 UTC vs.
Revision 643 by mmeineke, Mon Jul 21 21:27:40 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_CHAR 0
18   #define TAKE_THIS_TAG_INT 1
# Line 70 | 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 84 | 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 boxMat[9];
87 +  double theBoxMat3[3][3];
88  
89 <  entry_plug = the_entry_plug;
89 >  simnfo = the_simnfo;
90  
91  
92   #ifndef IS_MPI
# Line 100 | Line 101 | void InitializeFromFile :: read_xyz( SimInfo* the_entr
101  
102    n_atoms = atoi( read_buffer );
103  
104 <  Atom **atoms = entry_plug->atoms;
104 >  Atom **atoms = simnfo->atoms;
105    DirectionalAtom* dAtom;
106  
107 <  if( n_atoms != entry_plug->n_atoms ){
107 >  if( n_atoms != simnfo->n_atoms ){
108      sprintf( painCave.errMsg,
109               "Initialize from File error. %s n_atoms, %d, "
110               "does not match the BASS file's n_atoms, %d.\n",
111 <             c_in_name, n_atoms, entry_plug->n_atoms );
111 >             c_in_name, n_atoms, simnfo->n_atoms );
112      painCave.isFatal = 1;
113      simError();
114    }
115    
116 <  //read and toss the comment line
116 >  //read the box mat from the comment line
117    
118    eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file);
119    if(eof_test == NULL){
# Line 122 | Line 123 | void InitializeFromFile :: read_xyz( SimInfo* the_entr
123      simError();
124    }
125  
126 +  parseErr = parseBoxLine( read_buffer, boxMat );
127 +  if( parseErr != NULL ){
128 +    strcpy( painCave.errMsg, parseErr );
129 +    painCave.isFatal = 1;
130 +    simError();
131 +  }
132 +
133 +  for(i=0;i<3;i++)
134 +    for(j=0;j<3;j++) theBoxMat3[i][j] = boxMat[3*j+i];
135 +
136 +  simnfo->setBoxM( theBoxMat3 );
137 +
138 +
139    for( i=0; i < n_atoms; i++){
140      
141      eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file);
# Line 141 | Line 155 | void InitializeFromFile :: read_xyz( SimInfo* the_entr
155        strcpy( painCave.errMsg, parseErr );
156        painCave.isFatal = 1;
157        simError();
158 <    }    
158 >    }
159    }
160  
161  
# Line 154 | Line 168 | void InitializeFromFile :: read_xyz( SimInfo* the_entr
168    int myStatus; // 1 = wakeup & success; 0 = error; -1 = AllDone
169    int haveError;
170    
171 <  MPI::Status istatus;
171 >  MPI_Status istatus;
172    int *AtomToProcMap = mpiSim->getAtomToProcMap();
173  
174    
# Line 171 | Line 185 | void InitializeFromFile :: read_xyz( SimInfo* the_entr
185      
186      n_atoms = atoi( read_buffer );
187      
188 <    Atom **atoms = entry_plug->atoms;
188 >    Atom **atoms = simnfo->atoms;
189      DirectionalAtom* dAtom;
190  
191      // Check to see that the number of atoms in the intial configuration file is the
# Line 181 | Line 195 | void InitializeFromFile :: read_xyz( SimInfo* the_entr
195        sprintf( painCave.errMsg,
196                 "Initialize from File error. %s n_atoms, %d, "
197                 "does not match the BASS file's n_atoms, %d.\n",
198 <               c_in_name, n_atoms, entry_plug->n_atoms );
198 >               c_in_name, n_atoms, simnfo->n_atoms );
199        haveError= 1;
200        simError();
201      }
202      
203 <    //read and toss the comment line
203 >    //read the boxMat from the comment line
204      
205      eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file);
206      if(eof_test == NULL){
207        sprintf( painCave.errMsg,
208                 "error in reading commment in %s\n", c_in_name);
209 <      haveError= 1;
209 >      haveError = 1;
210        simError();
211      }
212 +    
213 +    parseErr = parseBoxLine( read_buffer, boxMat );
214 +    if( parseErr != NULL ){
215 +      strcpy( painCave.errMsg, parseErr );
216 +      haveError = 1;
217 +      simError();
218 +    }
219 +
220 +    MPI_Bcast(boxMat, 9, MPI_DOUBLE, 0, MPI_COMM_WORLD );
221    
222      if(haveError) nodeZeroError();
223  
# Line 228 | Line 251 | void InitializeFromFile :: read_xyz( SimInfo* the_entr
251        else {
252        
253          myStatus = 1;
254 <        MPI::COMM_WORLD.Send(&myStatus, 1, MPI_INT, which_node,
255 <                             TAKE_THIS_TAG_INT);
256 <        MPI::COMM_WORLD.Send(read_buffer, BUFFERSIZE, MPI_CHAR, which_node,
257 <                             TAKE_THIS_TAG_CHAR);
258 <        MPI::COMM_WORLD.Send(&i, 1, MPI_INT, which_node, TAKE_THIS_TAG_INT);
259 <        MPI::COMM_WORLD.Recv(&myStatus, 1, MPI_INT, which_node, TAKE_THIS_TAG_INT, istatus);
254 >        MPI_Send(&myStatus, 1, MPI_INT, which_node,
255 >                 TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
256 >        MPI_Send(read_buffer, BUFFERSIZE, MPI_CHAR, which_node,
257 >                 TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD);
258 >        MPI_Send(&i, 1, MPI_INT, which_node, TAKE_THIS_TAG_INT,
259 >                 MPI_COMM_WORLD);
260 >        MPI_Recv(&myStatus, 1, MPI_INT, which_node, TAKE_THIS_TAG_INT,
261 >                 MPI_COMM_WORLD, &istatus);
262          
263          if(!myStatus) nodeZeroError();
264        }
265      }
266      myStatus = -1;
267      for (j = 0; j < mpiSim->getNumberProcessors(); j++) {      
268 <      MPI::COMM_WORLD.Send( &myStatus, 1, MPI_INT, j,
269 <                            TAKE_THIS_TAG_INT);
268 >      MPI_Send( &myStatus, 1, MPI_INT, j,
269 >                TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
270      }
271      
272    } else {
273      
274 +    MPI_Bcast(boxMat, 9, MPI_DOUBLE, 0, MPI_COMM_WORLD);
275 +
276      done = 0;
277      while (!done) {
278  
279 <      MPI::COMM_WORLD.Recv(&myStatus, 1, MPI_INT, 0,
280 <                           TAKE_THIS_TAG_INT, istatus);
279 >      MPI_Recv(&myStatus, 1, MPI_INT, 0,
280 >               TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus);
281        
282        if(!myStatus) anonymousNodeDie();
283        
284        if(myStatus < 0) break;
285  
286 <      MPI::COMM_WORLD.Recv(read_buffer, BUFFERSIZE, MPI_CHAR, 0,
287 <                           TAKE_THIS_TAG_CHAR, istatus);
288 <      MPI::COMM_WORLD.Recv(&which_atom, 1, MPI_INT, 0,
289 <                           TAKE_THIS_TAG_INT, istatus);
286 >      MPI_Recv(read_buffer, BUFFERSIZE, MPI_CHAR, 0,
287 >               TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD, &istatus);
288 >      MPI_Recv(&which_atom, 1, MPI_INT, 0,
289 >               TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus);
290        
291        myStatus = 1;
292        parseErr = parseDumpLine( read_buffer, which_atom );
# Line 269 | Line 296 | void InitializeFromFile :: read_xyz( SimInfo* the_entr
296          simError();
297        }
298        
299 <      MPI::COMM_WORLD.Send( &myStatus, 1, MPI_INT, 0,
300 <                            TAKE_THIS_TAG_INT);
299 >      MPI_Send( &myStatus, 1, MPI_INT, 0,
300 >                TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
301        
302      }
303    }
304      
305   // last  thing last, enable  fatalities.
306    painCave.isEventLoop = 0;
307 +
308 +  for(i=0;i<3;i++)
309 +    for(j=0;j<3;j++) theBoxMat3[i][j] = boxMat[3*j+i];
310 +
311 +  simnfo->setBoxM( theBoxMat3 );
312 +
313    
314   #endif
315   }
# Line 291 | Line 324 | char* InitializeFromFile::parseDumpLine(char* readLine
324    double jx, jy, jz; // angular velocity placeholders;
325    double qSqr, qLength; // needed to normalize the quaternion vector.
326    
327 <  Atom **atoms = entry_plug->atoms;
327 >  Atom **atoms = simnfo->atoms;
328    DirectionalAtom* dAtom;
329    
330    int j, n_atoms, atomIndex;
# Line 310 | Line 343 | char* InitializeFromFile::parseDumpLine(char* readLine
343      return strdup( painCave.errMsg );
344    }  
345   #else
346 <  n_atoms = entry_plug->n_atoms;
346 >  n_atoms = simnfo->n_atoms;
347    atomIndex = globalIndex;
348   #endif // is_mpi
349  
# Line 501 | Line 534 | char* InitializeFromFile::parseDumpLine(char* readLine
534    atoms[atomIndex]->set_vx( vx );
535    atoms[atomIndex]->set_vy( vy );
536    atoms[atomIndex]->set_vz( vz );
537 +
538 +  return NULL;
539 + }
540 +
541 +
542 + char* InitializeFromFile::parseBoxLine(char* readLine, double boxMat[9]){
543 +
544 +  char *foo; // the pointer to the current string token
545 +  int j;
546 +
547 +  // set the string tokenizer
548 +  
549 +  foo = strtok(readLine, " ,;\t");
550 +  // set the timeToken.
551  
552 +  if(foo == NULL){
553 +    sprintf( painCave.errMsg,
554 +             "error in reading Time from %s\n",
555 +             c_in_name );
556 +    return strdup( painCave.errMsg );
557 +  }
558 +  simnfo->setTime( atof( foo ) );
559 +
560 +  // get the Hx vector
561 +
562 +  foo = strtok(NULL, " ,;\t");
563 +  if(foo == NULL){
564 +    sprintf( painCave.errMsg,
565 +             "error in reading Hx[0] from %s\n",
566 +             c_in_name );
567 +    return strdup( painCave.errMsg );
568 +  }
569 +  boxMat[0] = atof( foo );
570 +  
571 +  foo = strtok(NULL, " ,;\t");
572 +  if(foo == NULL){
573 +    sprintf( painCave.errMsg,
574 +             "error in reading Hx[1] from %s\n",
575 +             c_in_name );
576 +    return strdup( painCave.errMsg );
577 +  }
578 +  boxMat[1] = atof( foo );
579 +    
580 +  foo = strtok(NULL, " ,;\t");
581 +  if(foo == NULL){
582 +    sprintf( painCave.errMsg,
583 +             "error in reading Hx[2] from %s\n",
584 +             c_in_name );
585 +    return strdup( painCave.errMsg );
586 +  }
587 +  boxMat[2] = atof( foo );    
588 +
589 +  // get the Hy vector
590 +
591 +  foo = strtok(NULL, " ,;\t");
592 +  if(foo == NULL){
593 +    sprintf( painCave.errMsg,
594 +             "error in reading Hy[0] from %s\n",
595 +             c_in_name );
596 +    return strdup( painCave.errMsg );
597 +  }
598 +  boxMat[3] = atof( foo );
599 +  
600 +  foo = strtok(NULL, " ,;\t");
601 +  if(foo == NULL){
602 +    sprintf( painCave.errMsg,
603 +             "error in reading Hy[1] from %s\n",
604 +             c_in_name );
605 +    return strdup( painCave.errMsg );
606 +  }
607 +  boxMat[4] = atof( foo );
608 +    
609 +  foo = strtok(NULL, " ,;\t");
610 +  if(foo == NULL){
611 +    sprintf( painCave.errMsg,
612 +             "error in reading Hy[2] from %s\n",
613 +             c_in_name );
614 +    return strdup( painCave.errMsg );
615 +  }
616 +  boxMat[5] = atof( foo );    
617 +
618 +  // get the Hz vector
619 +
620 +  foo = strtok(NULL, " ,;\t");
621 +  if(foo == NULL){
622 +    sprintf( painCave.errMsg,
623 +             "error in reading Hz[0] from %s\n",
624 +             c_in_name );
625 +    return strdup( painCave.errMsg );
626 +  }
627 +  boxMat[6] = atof( foo );
628 +  
629 +  foo = strtok(NULL, " ,;\t");
630 +  if(foo == NULL){
631 +    sprintf( painCave.errMsg,
632 +             "error in reading Hz[1] from %s\n",
633 +             c_in_name );
634 +    return strdup( painCave.errMsg );
635 +  }
636 +  boxMat[7] = atof( foo );
637 +    
638 +  foo = strtok(NULL, " ,;\t");
639 +  if(foo == NULL){
640 +    sprintf( painCave.errMsg,
641 +             "error in reading Hz[2] from %s\n",
642 +             c_in_name );
643 +    return strdup( painCave.errMsg );
644 +  }
645 +  boxMat[8] = atof( foo );    
646 +
647    return NULL;
648   }
649  
# Line 515 | Line 657 | void initFile::nodeZeroError( void ){
657    
658    myStatus = 0;
659    for (j = 0; j < mpiSim->getNumberProcessors(); j++) {      
660 <    MPI::COMM_WORLD.Send( &myStatus, 1, MPI_INT, j,
661 <                          TAKE_THIS_TAG_INT);
660 >    MPI_Send( &myStatus, 1, MPI_INT, j,
661 >              TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
662    }  
663    
664  

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