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root/group/trunk/OOPSE/libmdtools/InitializeFromFile.cpp
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Comparing trunk/OOPSE/libmdtools/InitializeFromFile.cpp (file contents):
Revision 447 by mmeineke, Thu Apr 3 20:21:54 2003 UTC vs.
Revision 644 by mmeineke, Tue Jul 22 16:41:08 2003 UTC

# Line 69 | Line 69 | InitializeFromFile :: ~InitializeFromFile( ){
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 83 | 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 99 | 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 121 | 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 140 | 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  
# Line 170 | Line 187 | void InitializeFromFile :: read_xyz( SimInfo* the_entr
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 180 | 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 );
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 <      haveError= 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  
# Line 247 | Line 274 | void InitializeFromFile :: read_xyz( SimInfo* the_entr
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  
# Line 278 | Line 308 | void InitializeFromFile :: read_xyz( SimInfo* the_entr
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   }
# Line 292 | Line 329 | char* InitializeFromFile::parseDumpLine(char* readLine
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 311 | 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 505 | Line 542 | char* InitializeFromFile::parseDumpLine(char* readLine
542  
543    return NULL;
544   }
545 +
546 +
547 + char* InitializeFromFile::parseBoxLine(char* readLine, double boxMat[9],
548 +                                       double &time ){
549  
550 +  char *foo; // the pointer to the current string token
551 +  int j;
552  
553 +  // set the string tokenizer
554 +  
555 +  foo = strtok(readLine, " ,;\t");
556 +  // set the timeToken.
557 +
558 +  if(foo == NULL){
559 +    sprintf( painCave.errMsg,
560 +             "error in reading Time from %s\n",
561 +             c_in_name );
562 +    return strdup( painCave.errMsg );
563 +  }
564 +  time = atof( foo );
565 +
566 +  // get the Hx vector
567 +
568 +  foo = strtok(NULL, " ,;\t");
569 +  if(foo == NULL){
570 +    sprintf( painCave.errMsg,
571 +             "error in reading Hx[0] from %s\n",
572 +             c_in_name );
573 +    return strdup( painCave.errMsg );
574 +  }
575 +  boxMat[0] = atof( foo );
576 +  
577 +  foo = strtok(NULL, " ,;\t");
578 +  if(foo == NULL){
579 +    sprintf( painCave.errMsg,
580 +             "error in reading Hx[1] from %s\n",
581 +             c_in_name );
582 +    return strdup( painCave.errMsg );
583 +  }
584 +  boxMat[1] = atof( foo );
585 +    
586 +  foo = strtok(NULL, " ,;\t");
587 +  if(foo == NULL){
588 +    sprintf( painCave.errMsg,
589 +             "error in reading Hx[2] from %s\n",
590 +             c_in_name );
591 +    return strdup( painCave.errMsg );
592 +  }
593 +  boxMat[2] = atof( foo );    
594 +
595 +  // get the Hy vector
596 +
597 +  foo = strtok(NULL, " ,;\t");
598 +  if(foo == NULL){
599 +    sprintf( painCave.errMsg,
600 +             "error in reading Hy[0] from %s\n",
601 +             c_in_name );
602 +    return strdup( painCave.errMsg );
603 +  }
604 +  boxMat[3] = atof( foo );
605 +  
606 +  foo = strtok(NULL, " ,;\t");
607 +  if(foo == NULL){
608 +    sprintf( painCave.errMsg,
609 +             "error in reading Hy[1] from %s\n",
610 +             c_in_name );
611 +    return strdup( painCave.errMsg );
612 +  }
613 +  boxMat[4] = atof( foo );
614 +    
615 +  foo = strtok(NULL, " ,;\t");
616 +  if(foo == NULL){
617 +    sprintf( painCave.errMsg,
618 +             "error in reading Hy[2] from %s\n",
619 +             c_in_name );
620 +    return strdup( painCave.errMsg );
621 +  }
622 +  boxMat[5] = atof( foo );    
623 +
624 +  // get the Hz vector
625 +
626 +  foo = strtok(NULL, " ,;\t");
627 +  if(foo == NULL){
628 +    sprintf( painCave.errMsg,
629 +             "error in reading Hz[0] from %s\n",
630 +             c_in_name );
631 +    return strdup( painCave.errMsg );
632 +  }
633 +  boxMat[6] = atof( foo );
634 +  
635 +  foo = strtok(NULL, " ,;\t");
636 +  if(foo == NULL){
637 +    sprintf( painCave.errMsg,
638 +             "error in reading Hz[1] from %s\n",
639 +             c_in_name );
640 +    return strdup( painCave.errMsg );
641 +  }
642 +  boxMat[7] = atof( foo );
643 +    
644 +  foo = strtok(NULL, " ,;\t");
645 +  if(foo == NULL){
646 +    sprintf( painCave.errMsg,
647 +             "error in reading Hz[2] from %s\n",
648 +             c_in_name );
649 +    return strdup( painCave.errMsg );
650 +  }
651 +  boxMat[8] = atof( foo );    
652 +
653 +  return NULL;
654 + }
655 +
656 +
657   #ifdef IS_MPI
658  
659   // a couple of functions to let us escape the read loop

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