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root/group/trunk/xyz2pov/src/xyz2pov.c
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Comparing trunk/xyz2pov/src/xyz2pov.c (file contents):
Revision 625 by gezelter, Wed Jul 16 19:29:54 2003 UTC vs.
Revision 864 by gezelter, Tue Nov 18 17:04:25 2003 UTC

# Line 24 | Line 24 | int draw_atoms = 0; /*boolean to draw atoms */
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  
56    unsigned int n_atoms; /*the number of atoms in each time step */
57 <  char read_buffer[120]; /*the line buffer for reading */
57 >  char read_buffer[2000]; /*the line buffer for reading */
58    char *eof_test; /*ptr to see when we reach the end of the file */
59    char *foo; /*the pointer to the current string token */
60    FILE *in_file; /* the input file */
# 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 271 | Line 281 | int main(argc, argv)
281      out_prefix = strtok(in_name, ".");
282    }
283  
284 <  sprintf( out_format, "%s%s%%0%dd.pov", pov_dir, out_prefix, nZeroes );
284 >  sprintf( out_format, "%s%s-%%0%dd.pov", pov_dir, out_prefix, nZeroes );
285  
286    // start reading the first frame
287  
# Line 303 | Line 313 | int main(argc, argv)
313      if( draw_box ){
314        foo = strtok(read_buffer, " ,;\t");
315        if(foo == NULL){
316 <        printf("error in reading file\n");
316 >        printf("error in reading file time\n");
317          exit(8);
318        }
319        
320        foo = strtok(NULL, " ,;\t");
321        if(foo == NULL){
322 <        printf("error in reading file\n");
322 >        printf("error in reading file h00\n");
323          exit(8);
324        }
325        current_frame->Hmat[0][0] = atof( foo );
326  
327        foo = strtok(NULL, " ,;\t");
328        if(foo == NULL){
329 <        printf("error in reading file\n");
329 >        printf("error in reading file h10\n");
330          exit(8);
331        }
332        current_frame->Hmat[1][0] = atof( foo );
333  
334        foo = strtok(NULL, " ,;\t");
335        if(foo == NULL){
336 <        printf("error in reading file\n");
336 >        printf("error in reading file h20\n");
337          exit(8);
338        }
339        current_frame->Hmat[2][0] = atof( foo );
340  
341        foo = strtok(NULL, " ,;\t");
342        if(foo == NULL){
343 <        printf("error in reading file\n");
343 >        printf("error in reading file h01\n");
344          exit(8);
345        }
346        current_frame->Hmat[0][1] = atof( foo );
347  
348        foo = strtok(NULL, " ,;\t");
349        if(foo == NULL){
350 <        printf("error in reading file\n");
350 >        printf("error in reading file h11\n");
351          exit(8);
352        }
353        current_frame->Hmat[1][1] = atof( foo );
354  
355        foo = strtok(NULL, " ,;\t");
356        if(foo == NULL){
357 <        printf("error in reading file\n");
357 >        printf("error in reading file h21\n");
358          exit(8);
359        }
360        current_frame->Hmat[2][1] = atof( foo );
361  
362        foo = strtok(NULL, " ,;\t");
363        if(foo == NULL){
364 <        printf("error in reading file\n");
364 >        printf("error in reading file h02\n");
365          exit(8);
366        }
367        current_frame->Hmat[0][2] = atof( foo );
368  
369        foo = strtok(NULL, " ,;\t");
370        if(foo == NULL){
371 <        printf("error in reading file\n");
371 >        printf("error in reading file h12\n");
372          exit(8);
373        }
374        current_frame->Hmat[1][2] = atof( foo );
375  
376        foo = strtok(NULL, " ,;\t");
377        if(foo == NULL){
378 <        printf("error in reading file\n");
378 >        printf("error in reading file h22\n");
379          exit(8);
380        }
381        current_frame->Hmat[2][2] = atof( foo );
# Line 376 | Line 386 | int main(argc, argv)
386        
387        eof_test = fgets(read_buffer, sizeof(read_buffer), in_file);
388        if(eof_test == NULL){
389 <        printf("error in reading file\n");
389 >        printf("error in reading file line at atom %d\n", i);
390          exit(8);
391        }
392  
393 <      foo = strtok(read_buffer, " ,;\t");
394 <      if(foo == NULL){
395 <        printf("error in reading file\n");
396 <        exit(8);
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");
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");
393 –      if(foo == NULL){
394 –        printf("error in reading file\n");
395 –        exit(8);
396 –      }
404        (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 –  
405        foo = strtok(NULL, " ,;\t");
403 –      if(foo == NULL){
404 –        printf("error in reading file\n");
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 file\n");
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 457 | Line 489 | int main(argc, argv)
489                       "makePeriodicBox( %lf, %lf, %lf, %lf, %lf, %lf, %lf, %lf, %lf)\n"
490                       "\n",
491                       temp_frame->Hmat[0][0] + dm[0][0] * (i+1),
460 –                     temp_frame->Hmat[1][0] + dm[1][0] * (i+1),
492                       temp_frame->Hmat[2][0] + dm[2][0] * (i+1),
493 +                     temp_frame->Hmat[1][0] + dm[1][0] * (i+1),
494                       temp_frame->Hmat[0][1] + dm[0][1] * (i+1),
463 –                     temp_frame->Hmat[1][1] + dm[1][1] * (i+1),
495                       temp_frame->Hmat[2][1] + dm[2][1] * (i+1),
496 +                     temp_frame->Hmat[1][1] + dm[1][1] * (i+1),
497                       temp_frame->Hmat[0][2] + dm[0][2] * (i+1),
498 <                     temp_frame->Hmat[1][2] + dm[1][2] * (i+1),
499 <                     temp_frame->Hmat[2][2] + dm[2][2] * (i+1) );
498 >                     temp_frame->Hmat[2][2] + dm[2][2] * (i+1),
499 >                     temp_frame->Hmat[1][2] + dm[1][2] * (i+1) );
500            }
501            
502            
# 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 511 | Line 568 | int main(argc, argv)
568        if( draw_box ){
569          
570          fprintf( out_file,
571 <                 "makePeriodicBox( %lf, %lf, %lf, %lf, %lf, %lf, %lf, %lf %lf )\n"
571 >                 "makePeriodicBox( %lf, %lf, %lf, %lf, %lf, %lf, %lf, %lf, %lf )\n"
572                   "\n",
573                   current_frame->Hmat[0][0],
517 –                 current_frame->Hmat[1][0],
574                   current_frame->Hmat[2][0],
575 +                 current_frame->Hmat[1][0],
576                   current_frame->Hmat[0][1],
520 –                 current_frame->Hmat[1][1],
577                   current_frame->Hmat[2][1],
578 +                 current_frame->Hmat[1][1],
579                   current_frame->Hmat[0][2],
580 <                 current_frame->Hmat[1][2],
581 <                 current_frame->Hmat[2][2] );
580 >                 current_frame->Hmat[2][2],
581 >                 current_frame->Hmat[1][2] );
582        }
583        
584        
# 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 709 | Line 782 | int main(argc, argv)
782              "\n"
783              "#macro makePeriodicBox( bx1, by1, bz1, bx2, by2, bz2, bx3, by3, bz3 )\n"
784              "\n"
785 <            "  #local pAx = -boxCenterX;\n"
786 <            "  #local pAy = -boxCenterY;\n"
787 <            "  #local pAz = -boxCenterZ;\n"
715 <            "  #local pBx = bx1 - boxCenterX;\n"
716 <            "  #local pBy = by1 - boxCenterY;\n"
717 <            "  #local pBz = bz1 - boxCenterZ;\n"
718 <            "  #local pCx = bx2 - boxCenterX;\n"
719 <            "  #local pCy = by2 - boxCenterY;\n"
720 <            "  #local pCz = bz2 - boxCenterZ;\n"
721 <            "  #local pDx = bx3 - boxCenterX;\n"
722 <            "  #local pDy = by3 - boxCenterY;\n"
723 <            "  #local pDz = bz3 - boxCenterZ;\n"
724 <            "  #local pEx = bx1 + bx2 - boxCenterX;\n"
725 <            "  #local pEy = by1 + by2 - boxCenterY;\n"
726 <            "  #local pEz = bz1 + bz2 - boxCenterZ;\n"
727 <            "  #local pFx = bx1 + bx3 - boxCenterX;\n"
728 <            "  #local pFy = by1 + by3 - boxCenterY;\n"
729 <            "  #local pFz = bz1 + bz3 - boxCenterZ;\n"
730 <            "  #local pGx = bx2 + bx3 - boxCenterX;\n"
731 <            "  #local pGy = by2 + by3 - boxCenterY;\n"
732 <            "  #local pGz = bz2 + bz3 - boxCenterZ;\n"
733 <            "  #local pHx = bx1 + bx2 + bx3 - boxCenterX;\n"
734 <            "  #local pHy = by1 + by2 + by3 - boxCenterY;\n"
735 <            "  #local pHz = bz1 + bz2 + bz3 - boxCenterZ;\n"
785 >            "  #local bcx = (bx1 + bx2 + bx3) / 2.0;\n"
786 >            "  #local bcy = (by1 + by2 + by3) / 2.0;\n"
787 >            "  #local bcz = (bz1 + bz2 + bz3) / 2.0;\n"
788              "\n"
789 +            "  #local pAx = boxCenterX - bcx;\n"
790 +            "  #local pAy = boxCenterY - bcy;\n"
791 +            "  #local pAz = boxCenterZ - bcz;\n"
792 +            "  #local pBx = boxCenterX + bx1 - bcx;\n"
793 +            "  #local pBy = boxCenterY + by1 - bcy;\n"
794 +            "  #local pBz = boxCenterZ + bz1 - bcz;\n"
795 +            "  #local pCx = boxCenterX + bx2 - bcx;\n"
796 +            "  #local pCy = boxCenterY + by2 - bcy;\n"
797 +            "  #local pCz = boxCenterZ + bz2 - bcz;\n"
798 +            "  #local pDx = boxCenterX + bx3 - bcx;\n"
799 +            "  #local pDy = boxCenterY + by3 - bcy;\n"
800 +            "  #local pDz = boxCenterZ + bz3 - bcz;\n"
801 +            "  #local pEx = boxCenterX + bx1 + bx2 - bcx;\n"
802 +            "  #local pEy = boxCenterY + by1 + by2 - bcy;\n"
803 +            "  #local pEz = boxCenterZ + bz1 + bz2 - bcz;\n"
804 +            "  #local pFx = boxCenterX + bx1 + bx3 - bcx;\n"
805 +            "  #local pFy = boxCenterY + by1 + by3 - bcy;\n"
806 +            "  #local pFz = boxCenterZ + bz1 + bz3 - bcz;\n"
807 +            "  #local pGx = boxCenterX + bx2 + bx3 - bcx;\n"
808 +            "  #local pGy = boxCenterY + by2 + by3 - bcy;\n"
809 +            "  #local pGz = boxCenterZ + bz2 + bz3 - bcz;\n"
810 +            "  #local pHx = boxCenterX + bx1 + bx2 + bx3 - bcx;\n"
811 +            "  #local pHy = boxCenterY + by1 + by2 + by3 - bcy;\n"
812 +            "  #local pHz = boxCenterZ + bz1 + bz2 + bz3 - bcz;\n"
813 +            "\n"
814              "  #local colorR = 0.90;\n"
815              "  #local colorG = 0.91;\n"
816              "  #local colorB = 0.98;\n"
# Line 978 | 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 986 | Line 1064 | void usage(){
1064                  "\n",
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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