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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 830 by gezelter, Tue Oct 28 16:20:28 2003 UTC

# Line 1 | Line 1
1 + #define _FILE_OFFSET_BITS 64
2   #include <iostream>
3 < #include <cmath>
3 > #include <math.h>
4  
5   #include <stdio.h>
6   #include <stdlib.h>
# Line 26 | Line 27 | InitializeFromFile :: InitializeFromFile( char *in_nam
27  
28   #endif // is_mpi
29  
30 < InitializeFromFile :: InitializeFromFile( char *in_name ){
30 > InitializeFromFile::InitializeFromFile( char *in_name ){
31 >
32   #ifdef IS_MPI
33    if (worldRank == 0) {
34   #endif
# Line 48 | Line 50 | InitializeFromFile :: ~InitializeFromFile( ){
50    return;  
51   }
52  
53 < InitializeFromFile :: ~InitializeFromFile( ){
53 > InitializeFromFile::~InitializeFromFile( ){
54   #ifdef IS_MPI
55    if (worldRank == 0) {
56   #endif
# Line 69 | Line 71 | void InitializeFromFile :: read_xyz( SimInfo* the_entr
71   }
72  
73  
74 < void InitializeFromFile :: read_xyz( SimInfo* the_entry_plug ){
74 > void InitializeFromFile :: readInit( SimInfo* the_simnfo ){
75  
76 <  int i, j, done, which_node, which_atom; // loop counter
76 >  int i, j;
77 >  
78 > #ifdef IS_MPI
79 >  int done, which_node, which_atom; // loop counter
80 > #endif //is_mpi
81  
82    const int BUFFERSIZE = 2000; // size of the read buffer
83    int n_atoms; // the number of atoms
84    char read_buffer[BUFFERSIZE]; //the line buffer for reading
79 – #ifdef IS_MPI
80 –  char send_buffer[BUFFERSIZE];
81 – #endif
85  
86    char *eof_test; // ptr to see when we reach the end of the file
87    char *parseErr;
85 –  int procIndex;
88  
89 <  entry_plug = the_entry_plug;
89 >  double currTime;
90 >  double boxMat[9];
91 >  double theBoxMat3[3][3];
92  
93 +  simnfo = the_simnfo;
94  
95 +
96   #ifndef IS_MPI
97    eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file);
98    if( eof_test == NULL ){
# Line 99 | Line 105 | void InitializeFromFile :: read_xyz( SimInfo* the_entr
105  
106    n_atoms = atoi( read_buffer );
107  
108 <  Atom **atoms = entry_plug->atoms;
103 <  DirectionalAtom* dAtom;
104 <
105 <  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 163 | Line 180 | void InitializeFromFile :: read_xyz( SimInfo* the_entr
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);
183 >               "Error reading 1st line of %s \n ",c_in_name);
184        haveError = 1;
185        simError();
186      }
187      
188      n_atoms = atoi( read_buffer );
189      
173 –    Atom **atoms = entry_plug->atoms;
174 –    DirectionalAtom* dAtom;
175 –
190      // Check to see that the number of atoms in the intial configuration file is the
191      // same as declared in simBass.
192      
# Line 180 | Line 194 | void InitializeFromFile :: read_xyz( SimInfo* the_entr
194        sprintf( painCave.errMsg,
195                 "Initialize from File error. %s n_atoms, %d, "
196                 "does not match the BASS file's n_atoms, %d.\n",
197 <               c_in_name, n_atoms, entry_plug->n_atoms );
197 >               c_in_name, n_atoms, simnfo->n_atoms );
198        haveError= 1;
199        simError();
200      }
201      
202 <    //read and toss the comment line
202 >    //read the boxMat from the comment line
203      
204      eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file);
205      if(eof_test == NULL){
206        sprintf( painCave.errMsg,
207                 "error in reading commment in %s\n", c_in_name);
208 <      haveError= 1;
208 >      haveError = 1;
209        simError();
210      }
211 +    
212 +    parseErr = parseBoxLine( read_buffer, boxMat, currTime );
213 +    if( parseErr != NULL ){
214 +      strcpy( painCave.errMsg, parseErr );
215 +      haveError = 1;
216 +      simError();
217 +    }
218 +
219 +    MPI_Bcast(boxMat, 9, MPI_DOUBLE, 0, MPI_COMM_WORLD );
220 +    MPI_Bcast(&currTime, 1, MPI_DOUBLE, 0, MPI_COMM_WORLD );
221    
222      if(haveError) nodeZeroError();
223  
# Line 247 | Line 271 | void InitializeFromFile :: read_xyz( SimInfo* the_entr
271      
272    } else {
273      
274 +    MPI_Bcast(boxMat, 9, MPI_DOUBLE, 0, MPI_COMM_WORLD);
275 +    MPI_Bcast(&currTime, 1, MPI_DOUBLE, 0, MPI_COMM_WORLD);
276 +
277      done = 0;
278      while (!done) {
279  
# Line 278 | Line 305 | void InitializeFromFile :: read_xyz( SimInfo* the_entr
305      
306   // last  thing last, enable  fatalities.
307    painCave.isEventLoop = 0;
308 +
309 +  for(i=0;i<3;i++)
310 +    for(j=0;j<3;j++) theBoxMat3[i][j] = boxMat[3*j+i];
311 +
312 +  simnfo->setBoxM( theBoxMat3 );
313 +  simnfo->setTime( currTime );
314 +
315    
316   #endif
317   }
# Line 286 | Line 320 | char* InitializeFromFile::parseDumpLine(char* readLine
320  
321    char *foo; // the pointer to the current string token
322    
323 <  double rx, ry, rz; // position place holders
324 <  double vx, vy, vz; // velocity placeholders
323 >  double pos[3]; // position place holders
324 >  double vel[3]; // velocity placeholders
325    double q[4]; // the quaternions
326    double jx, jy, jz; // angular velocity placeholders;
327    double qSqr, qLength; // needed to normalize the quaternion vector.
328    
329 <  Atom **atoms = entry_plug->atoms;
329 >  Atom **atoms = simnfo->atoms;
330    DirectionalAtom* dAtom;
331    
332 <  int j, n_atoms, atomIndex;
332 >  int n_atoms, atomIndex;
333  
334   #ifdef IS_MPI
335 +  int j;
336 +
337    n_atoms = mpiSim->getTotAtoms();
338    atomIndex=-1;        
339    for (j=0; j < mpiSim->getMyNlocal(); j++) {
# Line 311 | Line 347 | char* InitializeFromFile::parseDumpLine(char* readLine
347      return strdup( painCave.errMsg );
348    }  
349   #else
350 <  n_atoms = entry_plug->n_atoms;
350 >  n_atoms = simnfo->n_atoms;
351    atomIndex = globalIndex;
352   #endif // is_mpi
353  
# Line 340 | Line 376 | char* InitializeFromFile::parseDumpLine(char* readLine
376               c_in_name, n_atoms, atomIndex );
377      return strdup( painCave.errMsg );
378    }
379 <  rx = atof( foo );
379 >  pos[0] = atof( foo );
380    
381    foo = strtok(NULL, " ,;\t");
382    if(foo == NULL){
# Line 350 | Line 386 | char* InitializeFromFile::parseDumpLine(char* readLine
386               c_in_name, n_atoms, atomIndex );
387      return strdup( painCave.errMsg );
388    }
389 <  ry = atof( foo );
389 >  pos[1] = atof( foo );
390      
391    foo = strtok(NULL, " ,;\t");
392    if(foo == NULL){
# Line 360 | Line 396 | char* InitializeFromFile::parseDumpLine(char* readLine
396               c_in_name, n_atoms, atomIndex );
397      return strdup( painCave.errMsg );
398    }
399 <  rz = atof( foo );    
399 >  pos[2] = atof( foo );    
400  
401  
402    // get the velocities
# Line 373 | Line 409 | char* InitializeFromFile::parseDumpLine(char* readLine
409               c_in_name, n_atoms, atomIndex );
410      return strdup( painCave.errMsg );
411    }
412 <  vx = atof( foo );
412 >  vel[0] = atof( foo );
413      
414    foo = strtok(NULL, " ,;\t");
415    if(foo == NULL){
# Line 383 | Line 419 | char* InitializeFromFile::parseDumpLine(char* readLine
419               c_in_name, n_atoms, atomIndex );
420      return strdup( painCave.errMsg );
421    }
422 <  vy = atof( foo );
422 >  vel[1] = atof( foo );
423      
424    foo = strtok(NULL, " ,;\t");
425    if(foo == NULL){
# Line 393 | Line 429 | char* InitializeFromFile::parseDumpLine(char* readLine
429               c_in_name, n_atoms, atomIndex );
430      return strdup( painCave.errMsg );
431    }
432 <  vz = atof( foo );
432 >  vel[2] = atof( foo );
433      
434      
435    // get the quaternions
# Line 495 | Line 531 | char* InitializeFromFile::parseDumpLine(char* readLine
531      
532    // add the positions and velocities to the atom
533      
534 <  atoms[atomIndex]->setX( rx );
535 <  atoms[atomIndex]->setY( ry );
500 <  atoms[atomIndex]->setZ( rz );
501 <    
502 <  atoms[atomIndex]->set_vx( vx );
503 <  atoms[atomIndex]->set_vy( vy );
504 <  atoms[atomIndex]->set_vz( vz );
534 >  atoms[atomIndex]->setPos( pos );
535 >  atoms[atomIndex]->setVel( vel );
536  
537    return NULL;
538   }
539  
540  
541 + char* InitializeFromFile::parseBoxLine(char* readLine, double boxMat[9],
542 +                                       double &time ){
543 +
544 +  char *foo; // the pointer to the current string token
545 +
546 +  // set the string tokenizer
547 +  
548 +  foo = strtok(readLine, " ,;\t");
549 +  // set the timeToken.
550 +
551 +  if(foo == NULL){
552 +    sprintf( painCave.errMsg,
553 +             "error in reading Time from %s\n",
554 +             c_in_name );
555 +    return strdup( painCave.errMsg );
556 +  }
557 +  time = atof( foo );
558 +
559 +  // get the Hx vector
560 +
561 +  foo = strtok(NULL, " ,;\t");
562 +  if(foo == NULL){
563 +    sprintf( painCave.errMsg,
564 +             "error in reading Hx[0] from %s\n",
565 +             c_in_name );
566 +    return strdup( painCave.errMsg );
567 +  }
568 +  boxMat[0] = atof( foo );
569 +  
570 +  foo = strtok(NULL, " ,;\t");
571 +  if(foo == NULL){
572 +    sprintf( painCave.errMsg,
573 +             "error in reading Hx[1] from %s\n",
574 +             c_in_name );
575 +    return strdup( painCave.errMsg );
576 +  }
577 +  boxMat[1] = atof( foo );
578 +    
579 +  foo = strtok(NULL, " ,;\t");
580 +  if(foo == NULL){
581 +    sprintf( painCave.errMsg,
582 +             "error in reading Hx[2] from %s\n",
583 +             c_in_name );
584 +    return strdup( painCave.errMsg );
585 +  }
586 +  boxMat[2] = atof( foo );    
587 +
588 +  // get the Hy vector
589 +
590 +  foo = strtok(NULL, " ,;\t");
591 +  if(foo == NULL){
592 +    sprintf( painCave.errMsg,
593 +             "error in reading Hy[0] from %s\n",
594 +             c_in_name );
595 +    return strdup( painCave.errMsg );
596 +  }
597 +  boxMat[3] = atof( foo );
598 +  
599 +  foo = strtok(NULL, " ,;\t");
600 +  if(foo == NULL){
601 +    sprintf( painCave.errMsg,
602 +             "error in reading Hy[1] from %s\n",
603 +             c_in_name );
604 +    return strdup( painCave.errMsg );
605 +  }
606 +  boxMat[4] = atof( foo );
607 +    
608 +  foo = strtok(NULL, " ,;\t");
609 +  if(foo == NULL){
610 +    sprintf( painCave.errMsg,
611 +             "error in reading Hy[2] from %s\n",
612 +             c_in_name );
613 +    return strdup( painCave.errMsg );
614 +  }
615 +  boxMat[5] = atof( foo );    
616 +
617 +  // get the Hz vector
618 +
619 +  foo = strtok(NULL, " ,;\t");
620 +  if(foo == NULL){
621 +    sprintf( painCave.errMsg,
622 +             "error in reading Hz[0] from %s\n",
623 +             c_in_name );
624 +    return strdup( painCave.errMsg );
625 +  }
626 +  boxMat[6] = atof( foo );
627 +  
628 +  foo = strtok(NULL, " ,;\t");
629 +  if(foo == NULL){
630 +    sprintf( painCave.errMsg,
631 +             "error in reading Hz[1] from %s\n",
632 +             c_in_name );
633 +    return strdup( painCave.errMsg );
634 +  }
635 +  boxMat[7] = atof( foo );
636 +    
637 +  foo = strtok(NULL, " ,;\t");
638 +  if(foo == NULL){
639 +    sprintf( painCave.errMsg,
640 +             "error in reading Hz[2] from %s\n",
641 +             c_in_name );
642 +    return strdup( painCave.errMsg );
643 +  }
644 +  boxMat[8] = atof( foo );    
645 +
646 +  return NULL;
647 + }
648 +
649 +
650   #ifdef IS_MPI
651  
652   // a couple of functions to let us escape the read loop

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