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root/group/trunk/xyz2pov/src/xyz2pov.c
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Comparing trunk/xyz2pov/src/xyz2pov.c (file contents):
Revision 649 by mmeineke, Thu Jul 24 15:50:41 2003 UTC vs.
Revision 864 by gezelter, Tue Nov 18 17:04:25 2003 UTC

# Line 24 | Line 24 | int draw_box = 0;  // boolean to draw the periodic Box
24   int draw_bonds = 0; /* boolean to draw bonds or not */
25   int draw_hydrogens = 0; /*boolean to draw hydrogens */
26   int draw_atoms = 0; /*boolean to draw atoms */
27 + int draw_vectors = 0; /*boolean to draw vectors */
28   int draw_box = 0;  // boolean to draw the periodic Box
29   int regenerateBonds = 0; // boolean to regenearate bonds each frame
30  
31   void usage(void);
32 + int count_tokens(char *line, char *delimiters);
33  
34   int main(argc, argv)
35       int argc;
# Line 47 | Line 49 | int main(argc, argv)
49    double small_x = 0;
50    double small_y = 0; /* lets me know the smallest x, y, z */
51    double small_z = 0;
52 +  int extremaSet = 0;
53    double rsqr; /* the square of the diagonal */
54    double diagonal; /* the diagonal length of the sim box */
55  
# Line 66 | Line 69 | int main(argc, argv)
69    char current_flag;
70    int nFrames;
71    int nZeroes;
72 +  int nTokens;
73    double count;
74  
75    int startFrame = 1;
# Line 180 | Line 184 | int main(argc, argv)
184              // -a => draw the atoms
185  
186              draw_atoms = 1;
187 +            break;
188 +
189 +          case 'v':
190 +            // -v => draw the vectors
191 +
192 +            draw_vectors = 1;
193              break;
194  
195            case 'r':
# Line 378 | Line 388 | int main(argc, argv)
388        if(eof_test == NULL){
389          printf("error in reading file line at atom %d\n", i);
390          exit(8);
391 +      }
392 +
393 +      nTokens = count_tokens(read_buffer, " ,;\t");
394 +
395 +      if (nTokens < 4) {
396 +        printf("Not enough tokens while parsing file at atom %d\n", i);
397 +        exit(8);
398        }
399  
400        foo = strtok(read_buffer, " ,;\t");
384 –      if(foo == NULL){
385 –        printf("error in reading atom %d name\n", i);
386 –        exit(8);
387 –      }
401        (void)strcpy(current_frame->r[i].name, foo); /*copy the atom name */
402  
390 –      /* next we grab the positions */
391 –      
403        foo = strtok(NULL, " ,;\t");
404 <      if(foo == NULL){
394 <        printf("error in reading atom %d position x\n", i);
395 <        exit(8);
396 <      }
397 <      (void)sscanf(foo, "%lf",&current_frame->r[i].x);
398 <      if(current_frame->r[i].x > big_x) big_x = current_frame->r[i].x;
399 <      if(current_frame->r[i].x < small_x) small_x = current_frame->r[i].x;
400 <            
401 <  
404 >      (void)sscanf(foo, "%lf",&current_frame->r[i].x);
405        foo = strtok(NULL, " ,;\t");
403 –      if(foo == NULL){
404 –        printf("error in reading atom %d position y\n", i);
405 –        exit(8);
406 –      }
406        (void)sscanf(foo, "%lf", &current_frame->r[i].y);
407 <      if(current_frame->r[i].y > big_y) big_y = current_frame->r[i].y;
408 <      if(current_frame->r[i].y < small_y) small_y = current_frame->r[i].y;
407 >      foo = strtok(NULL, " ,;\t");
408 >      (void)sscanf(foo, "%lf", &current_frame->r[i].z);
409  
410 +      if (extremaSet) {
411 +        if(current_frame->r[i].x > big_x) big_x = current_frame->r[i].x;
412 +        if(current_frame->r[i].x < small_x) small_x = current_frame->r[i].x;
413 +        
414 +        if(current_frame->r[i].y > big_y) big_y = current_frame->r[i].y;
415 +        if(current_frame->r[i].y < small_y) small_y = current_frame->r[i].y;
416 +        
417 +        if(current_frame->r[i].z > big_z) big_z = current_frame->r[i].z;
418 +        if(current_frame->r[i].z < small_z) small_z = current_frame->r[i].z;
419 +      } else {
420 +        big_x = current_frame->r[i].x;
421 +        small_x = current_frame->r[i].x;
422 +        
423 +        big_y = current_frame->r[i].y;
424 +        small_y = current_frame->r[i].y;
425 +        
426 +        big_z = current_frame->r[i].z;
427 +        small_z = current_frame->r[i].z;
428  
429 <      foo = strtok(NULL, " ,;\t");
430 <      if(foo == NULL){
414 <        printf("error in reading atom %d position z\n", i);
415 <        exit(8);
429 >        extremaSet = 1;
430 >
431        }
417 –      (void)sscanf(foo, "%lf", &current_frame->r[i].z);
418 –      if(current_frame->r[i].z > big_z) big_z = current_frame->r[i].z;
419 –      if(current_frame->r[i].z < small_z) small_z = current_frame->r[i].z;
432  
433 +      if (nTokens == 5 || nTokens > 7) {
434 +        foo = strtok(NULL, " ,;\t");
435 +        (void)sscanf(foo, "%lf", &current_frame->r[i].charge);
436 +        current_frame->r[i].hasCharge = 1;
437 +      } else {
438 +        current_frame->r[i].hasCharge = 0;
439 +      }
440 +
441 +      
442 +      if (nTokens >= 7) {
443 +        foo = strtok(NULL, " ,;\t");
444 +        (void)sscanf(foo, "%lf", &current_frame->r[i].ux);
445 +        foo = strtok(NULL, " ,;\t");
446 +        (void)sscanf(foo, "%lf", &current_frame->r[i].uy);
447 +        foo = strtok(NULL, " ,;\t");
448 +        (void)sscanf(foo, "%lf", &current_frame->r[i].uz);
449 +        current_frame->r[i].hasVector = 1;
450 +      } else {
451 +        current_frame->r[i].hasVector = 0;
452 +      }
453      }
454      currentCount++;
455      
# Line 484 | Line 516 | int main(argc, argv)
516              out_coords[j].x = temp_frame->r[j].x + dx * (i+1);
517              out_coords[j].y = temp_frame->r[j].y + dy * (i+1);
518              out_coords[j].z = temp_frame->r[j].z + dz * (i+1);
519 +
520 +            if (current_frame->r[j].hasVector) {              
521 +              dx = current_frame->r[j].ux - temp_frame->r[j].ux;
522 +              dy = current_frame->r[j].uy - temp_frame->r[j].uy;
523 +              dz = current_frame->r[j].uz - temp_frame->r[j].uz;
524 +              
525 +              dx /= (double)(n_interpolate + 1);
526 +              dy /= (double)(n_interpolate + 1);
527 +              dz /= (double)(n_interpolate + 1);
528 +              
529 +              out_coords[j].hasVector = current_frame->r[j].hasVector;
530 +              out_coords[j].ux = temp_frame->r[j].ux + dx * (i+1);
531 +              out_coords[j].uy = temp_frame->r[j].uy + dy * (i+1);
532 +              out_coords[j].uz = temp_frame->r[j].uz + dz * (i+1);
533 +            }
534 +
535 +            if (current_frame->r[j].hasCharge) {              
536 +              dx = current_frame->r[j].charge - temp_frame->r[j].charge;
537 +              
538 +              dx /= (double)(n_interpolate + 1);
539 +              
540 +              out_coords[j].hasCharge = current_frame->r[j].hasCharge;
541 +              out_coords[j].charge = temp_frame->r[j].charge + dx * (i+1);
542 +            }
543 +
544            }
545            
546            pov_write(out_file, out_coords, n_atoms, draw_hydrogens, draw_bonds,
547 <                    draw_atoms);
547 >                    draw_atoms, draw_vectors);
548            free(out_coords);
549            (void)fclose(out_file);
550          }
# Line 534 | Line 591 | int main(argc, argv)
591          out_coords[i].x = current_frame->r[i].x;
592          out_coords[i].y = current_frame->r[i].y;
593          out_coords[i].z = current_frame->r[i].z;
594 +
595 +        if (current_frame->r[i].hasVector) {              
596 +          out_coords[i].hasVector = current_frame->r[i].hasVector;
597 +          out_coords[i].ux = current_frame->r[i].ux;
598 +          out_coords[i].uy = current_frame->r[i].uy;
599 +          out_coords[i].uz = current_frame->r[i].uz;
600 +        }
601 +
602 +        if (current_frame->r[i].hasCharge) {              
603 +          out_coords[i].hasCharge = current_frame->r[i].hasCharge;
604 +          out_coords[i].charge = current_frame->r[i].charge;
605 +        }
606        }
607        pov_write(out_file, out_coords, n_atoms, draw_hydrogens, draw_bonds,
608 <                draw_atoms);
608 >                draw_atoms, draw_vectors);
609        free(out_coords);
610        
611        (void)fclose(out_file);
# Line 621 | Line 690 | int main(argc, argv)
690              "\n"
691              "#declare ATOM_SPHERE_FACTOR = 0.2;\n"
692              "#declare BOND_RADIUS = 0.1;\n"
693 +            "#declare VECTOR_SCALE = 1.0;\n"    
694 +            "#declare STICK_RADIUS = 0.5 * BOND_RADIUS;\n"
695 +            "#declare CONE_RADIUS = 2.0 * STICK_RADIUS;\n"
696 +            "#declare CONE_FRACTION = 0.15;\n"
697              "\n"
698              "// declare camera, light, and system variables\n"
699              "\n"
# Line 982 | Line 1055 | void usage(){
1055                  "   -h            draw hydrogens\n"
1056                  "   -b            draw bonds\n"
1057                  "   -a            draw atoms\n"
1058 +                "   -v            draw vectors\n"
1059                  "   -p            draw periodic box\n"
1060                  "   -r            regenerate bond\n"
1061                  "   -f <#>        render frame <#> only\n"
# Line 991 | Line 1065 | void usage(){
1065                  program_name);
1066    exit(8);
1067   }
1068 +
1069 + int count_tokens(line, delimiters)
1070 +     /* PURPOSE: RETURN A COUNT OF THE NUMBER OF TOKENS ON THE LINE. */
1071 +     char *line;                /* LINE CONTAINING TOKENS. */
1072 +     char *delimiters;  /* POSSIBLE TOKEN DELIMITERS TO USE. */
1073 + {
1074 +  char *working_line;   /* WORKING COPY OF LINE. */
1075 +  int ntokens;          /* NUMBER OF TOKENS FOUND IN LINE. */
1076 +  char *strtok_ptr;     /* POINTER FOR STRTOK. */
1077 +  
1078 +  strtok_ptr= working_line= strdup(line);
1079 +  
1080 +  ntokens=0;
1081 +  while (strtok(strtok_ptr,delimiters)!=NULL)
1082 +    {
1083 +      ntokens++;
1084 +      strtok_ptr=NULL;
1085 +    }
1086 +  
1087 +  free(working_line);
1088 +  return(ntokens);
1089 + }

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