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root/group/trunk/xyz2pov/src/xyz2pov.c
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Comparing trunk/xyz2pov/src/xyz2pov.c (file contents):
Revision 515 by mmeineke, Thu May 1 17:36:33 2003 UTC vs.
Revision 2750 by tim, Fri May 12 19:24:30 2006 UTC

# Line 1 | Line 1
1 + #define _FILE_OFFSET_BITS 64
2 +
3   #include <stdio.h>
4   #include <stdlib.h>
5   #include <string.h>
# Line 16 | Line 18 | struct linked_xyz{
18  
19   struct linked_xyz{
20    struct coords *r;
21 <  double boxX, boxY, boxZ;
21 >  double Hmat[3][3];
22    struct linked_xyz *next;
23   };
24  
# Line 24 | Line 26 | int draw_atoms = 0; /*boolean to draw atoms */
26   int draw_bonds = 0; /* boolean to draw bonds or not */
27   int draw_hydrogens = 0; /*boolean to draw hydrogens */
28   int draw_atoms = 0; /*boolean to draw atoms */
29 + int draw_vectors = 0; /*boolean to draw vectors */
30   int draw_box = 0;  // boolean to draw the periodic Box
31   int regenerateBonds = 0; // boolean to regenearate bonds each frame
32  
33   void usage(void);
34 + int count_tokens(char *line, char *delimiters);
35  
36   int main(argc, argv)
37       int argc;
# Line 37 | Line 41 | int main(argc, argv)
41  
42    struct coords *out_coords;
43  
44 <  int i,j; /* loop counters */
44 >  int i,j,k; /* loop counters */
45    mode_t dir_mode = S_IRWXU;
46  
47    int generate_header = 0; /* boolean for generating the pov ray header */
# Line 47 | Line 51 | int main(argc, argv)
51    double small_x = 0;
52    double small_y = 0; /* lets me know the smallest x, y, z */
53    double small_z = 0;
54 +  int extremaSet = 0;
55    double rsqr; /* the square of the diagonal */
56    double diagonal; /* the diagonal length of the sim box */
57  
58    unsigned int n_atoms; /*the number of atoms in each time step */
59 <  char read_buffer[120]; /*the line buffer for reading */
59 >  char read_buffer[2000]; /*the line buffer for reading */
60    char *eof_test; /*ptr to see when we reach the end of the file */
61    char *foo; /*the pointer to the current string token */
62    FILE *in_file; /* the input file */
# Line 66 | Line 71 | int main(argc, argv)
71    char current_flag;
72    int nFrames;
73    int nZeroes;
74 +  int nTokens;
75    double count;
76  
77    int startFrame = 1;
# Line 79 | Line 85 | int main(argc, argv)
85    
86    unsigned int n_interpolate = 0; /* number of frames to interpolate */
87    double dx, dy, dz; /* temp variables for interpolating distances */
88 +  double dm[3][3];
89    
90  
91    char pov_dir[500]; /* the pov_dir */
# Line 181 | Line 188 | int main(argc, argv)
188              draw_atoms = 1;
189              break;
190  
191 +          case 'v':
192 +            // -v => draw the vectors
193 +
194 +            draw_vectors = 1;
195 +            break;
196 +
197            case 'r':
198              // -r => regenerate bonds
199  
# Line 270 | Line 283 | int main(argc, argv)
283      out_prefix = strtok(in_name, ".");
284    }
285  
286 <  sprintf( out_format, "%s%s%%0%dd.pov", pov_dir, out_prefix, nZeroes );
286 >  sprintf( out_format, "%s%s-%%0%dd.pov", pov_dir, out_prefix, nZeroes );
287  
288    // start reading the first frame
289  
# Line 302 | Line 315 | int main(argc, argv)
315      if( draw_box ){
316        foo = strtok(read_buffer, " ,;\t");
317        if(foo == NULL){
318 <        printf("error in reading file\n");
318 >        printf("error in reading file time\n");
319          exit(8);
320        }
321        
322        foo = strtok(NULL, " ,;\t");
323        if(foo == NULL){
324 <        printf("error in reading file\n");
324 >        printf("error in reading file h00\n");
325          exit(8);
326        }
327 <      current_frame->boxX = atof( foo );
327 >      current_frame->Hmat[0][0] = atof( foo );
328  
329        foo = strtok(NULL, " ,;\t");
330        if(foo == NULL){
331 <        printf("error in reading file\n");
331 >        printf("error in reading file h10\n");
332          exit(8);
333        }
334 <      current_frame->boxY = atof( foo );
334 >      current_frame->Hmat[1][0] = atof( foo );
335  
336        foo = strtok(NULL, " ,;\t");
337        if(foo == NULL){
338 <        printf("error in reading file\n");
338 >        printf("error in reading file h20\n");
339          exit(8);
340        }
341 <      current_frame->boxZ = atof( foo );
329 <    }
341 >      current_frame->Hmat[2][0] = atof( foo );
342  
343 <    for( i=0; i < n_atoms; i++){
344 <      
345 <      eof_test = fgets(read_buffer, sizeof(read_buffer), in_file);
334 <      if(eof_test == NULL){
335 <        printf("error in reading file\n");
343 >      foo = strtok(NULL, " ,;\t");
344 >      if(foo == NULL){
345 >        printf("error in reading file h01\n");
346          exit(8);
347        }
348 +      current_frame->Hmat[0][1] = atof( foo );
349  
350 <      foo = strtok(read_buffer, " ,;\t");
350 >      foo = strtok(NULL, " ,;\t");
351        if(foo == NULL){
352 <        printf("error in reading file\n");
352 >        printf("error in reading file h11\n");
353          exit(8);
354        }
355 <      (void)strcpy(current_frame->r[i].name, foo); /*copy the atom name */
355 >      current_frame->Hmat[1][1] = atof( foo );
356  
346 –      /* next we grab the positions */
347 –      
357        foo = strtok(NULL, " ,;\t");
358        if(foo == NULL){
359 <        printf("error in reading file\n");
359 >        printf("error in reading file h21\n");
360          exit(8);
361        }
362 <      (void)sscanf(foo, "%lf",&current_frame->r[i].x);
363 <      if(current_frame->r[i].x > big_x) big_x = current_frame->r[i].x;
355 <      if(current_frame->r[i].x < small_x) small_x = current_frame->r[i].x;
356 <            
357 <  
362 >      current_frame->Hmat[2][1] = atof( foo );
363 >
364        foo = strtok(NULL, " ,;\t");
365        if(foo == NULL){
366 <        printf("error in reading file\n");
366 >        printf("error in reading file h02\n");
367          exit(8);
368        }
369 <      (void)sscanf(foo, "%lf", &current_frame->r[i].y);
364 <      if(current_frame->r[i].y > big_y) big_y = current_frame->r[i].y;
365 <      if(current_frame->r[i].y < small_y) small_y = current_frame->r[i].y;
369 >      current_frame->Hmat[0][2] = atof( foo );
370  
371 +      foo = strtok(NULL, " ,;\t");
372 +      if(foo == NULL){
373 +        printf("error in reading file h12\n");
374 +        exit(8);
375 +      }
376 +      current_frame->Hmat[1][2] = atof( foo );
377  
378        foo = strtok(NULL, " ,;\t");
379        if(foo == NULL){
380 <        printf("error in reading file\n");
380 >        printf("error in reading file h22\n");
381          exit(8);
382        }
383 +      current_frame->Hmat[2][2] = atof( foo );
384 +
385 +    }
386 +
387 +    for( i=0; i < n_atoms; i++){
388 +      
389 +      eof_test = fgets(read_buffer, sizeof(read_buffer), in_file);
390 +      if(eof_test == NULL){
391 +        printf("error in reading file line at atom %d\n", i);
392 +        exit(8);
393 +      }
394 +
395 +      nTokens = count_tokens(read_buffer, " ,;\t");
396 +
397 +      if (nTokens < 4) {
398 +        printf("Not enough tokens while parsing file at atom %d\n", i);
399 +        exit(8);
400 +      }
401 +
402 +      foo = strtok(read_buffer, " ,;\t");
403 +      (void)strcpy(current_frame->r[i].name, foo); /*copy the atom name */
404 +
405 +      foo = strtok(NULL, " ,;\t");
406 +      (void)sscanf(foo, "%lf",&current_frame->r[i].x);
407 +      foo = strtok(NULL, " ,;\t");
408 +      (void)sscanf(foo, "%lf", &current_frame->r[i].y);
409 +      foo = strtok(NULL, " ,;\t");
410        (void)sscanf(foo, "%lf", &current_frame->r[i].z);
374 –      if(current_frame->r[i].z > big_z) big_z = current_frame->r[i].z;
375 –      if(current_frame->r[i].z < small_z) small_z = current_frame->r[i].z;
411  
412 +      if (extremaSet) {
413 +        if(current_frame->r[i].x > big_x) big_x = current_frame->r[i].x;
414 +        if(current_frame->r[i].x < small_x) small_x = current_frame->r[i].x;
415 +        
416 +        if(current_frame->r[i].y > big_y) big_y = current_frame->r[i].y;
417 +        if(current_frame->r[i].y < small_y) small_y = current_frame->r[i].y;
418 +        
419 +        if(current_frame->r[i].z > big_z) big_z = current_frame->r[i].z;
420 +        if(current_frame->r[i].z < small_z) small_z = current_frame->r[i].z;
421 +      } else {
422 +        big_x = current_frame->r[i].x;
423 +        small_x = current_frame->r[i].x;
424 +        
425 +        big_y = current_frame->r[i].y;
426 +        small_y = current_frame->r[i].y;
427 +        
428 +        big_z = current_frame->r[i].z;
429 +        small_z = current_frame->r[i].z;
430 +
431 +        extremaSet = 1;
432 +
433 +      }
434 +
435 +      if (nTokens == 5 || nTokens > 7) {
436 +        foo = strtok(NULL, " ,;\t");
437 +        (void)sscanf(foo, "%lf", &current_frame->r[i].charge);
438 +        current_frame->r[i].hasCharge = 1;
439 +      } else {
440 +        current_frame->r[i].hasCharge = 0;
441 +      }
442 +
443 +      
444 +      if (nTokens >= 7) {
445 +        foo = strtok(NULL, " ,;\t");
446 +        (void)sscanf(foo, "%lf", &current_frame->r[i].ux);
447 +        foo = strtok(NULL, " ,;\t");
448 +        (void)sscanf(foo, "%lf", &current_frame->r[i].uy);
449 +        foo = strtok(NULL, " ,;\t");
450 +        (void)sscanf(foo, "%lf", &current_frame->r[i].uz);
451 +        current_frame->r[i].hasVector = 1;
452 +      } else {
453 +        current_frame->r[i].hasVector = 0;
454 +      }
455 +
456 +      if (nTokens >= 10) {
457 +        foo = strtok(NULL, " ,;\t");
458 +        (void)sscanf(foo, "%lf", &current_frame->r[i].vx);
459 +        foo = strtok(NULL, " ,;\t");
460 +        (void)sscanf(foo, "%lf", &current_frame->r[i].vy);
461 +        foo = strtok(NULL, " ,;\t");
462 +        (void)sscanf(foo, "%lf", &current_frame->r[i].vz);
463 +        current_frame->r[i].hasSecondVector = 1;
464 +      } else {
465 +        current_frame->r[i].hasSecondVector = 0;
466 +      }
467 +
468 +
469 +
470      }
471      currentCount++;
472      
# Line 401 | Line 494 | int main(argc, argv)
494                          "#include \"pov_header.pov\"\n"
495                          "\n");
496            if( draw_box ){
497 <            dx = current_frame->boxX - temp_frame->boxX;
498 <            dy = current_frame->boxY - temp_frame->boxY;
499 <            dz = current_frame->boxZ - temp_frame->boxZ;
500 <            
501 <            dx /= (double)(n_interpolate + 1);
502 <            dy /= (double)(n_interpolate + 1);
503 <            dz /= (double)(n_interpolate + 1);
504 <            
497 >
498 >            for (j = 0; j < 3; j++) {
499 >              for (k = 0; k < 3; k++) {
500 >                dm[j][k] = current_frame->Hmat[j][k] - temp_frame->Hmat[j][k];
501 >                dm[j][k] /= (double)(n_interpolate + 1);
502 >              }
503 >            }
504 >                            
505              fprintf( out_file,
506 <                     "makePeriodicBox( %lf, %lf, %lf )\n"
506 >                     "makePeriodicBox( %lf, %lf, %lf, %lf, %lf, %lf, %lf, %lf, %lf)\n"
507                       "\n",
508 <                     temp_frame->boxX + dx * (i+1),
509 <                     temp_frame->boxZ + dz * (i+1),
510 <                     temp_frame->boxY + dy * (i+1) );
508 >                     temp_frame->Hmat[0][0] + dm[0][0] * (i+1),
509 >                     temp_frame->Hmat[2][0] + dm[2][0] * (i+1),
510 >                     temp_frame->Hmat[1][0] + dm[1][0] * (i+1),
511 >                     temp_frame->Hmat[0][1] + dm[0][1] * (i+1),
512 >                     temp_frame->Hmat[2][1] + dm[2][1] * (i+1),
513 >                     temp_frame->Hmat[1][1] + dm[1][1] * (i+1),
514 >                     temp_frame->Hmat[0][2] + dm[0][2] * (i+1),
515 >                     temp_frame->Hmat[2][2] + dm[2][2] * (i+1),
516 >                     temp_frame->Hmat[1][2] + dm[1][2] * (i+1) );
517            }
518            
519            
# Line 434 | Line 533 | int main(argc, argv)
533              out_coords[j].x = temp_frame->r[j].x + dx * (i+1);
534              out_coords[j].y = temp_frame->r[j].y + dy * (i+1);
535              out_coords[j].z = temp_frame->r[j].z + dz * (i+1);
536 +
537 +            if (current_frame->r[j].hasVector) {              
538 +              dx = current_frame->r[j].ux - temp_frame->r[j].ux;
539 +              dy = current_frame->r[j].uy - temp_frame->r[j].uy;
540 +              dz = current_frame->r[j].uz - temp_frame->r[j].uz;
541 +              
542 +              dx /= (double)(n_interpolate + 1);
543 +              dy /= (double)(n_interpolate + 1);
544 +              dz /= (double)(n_interpolate + 1);
545 +              
546 +              out_coords[j].hasVector = current_frame->r[j].hasVector;
547 +              out_coords[j].ux = temp_frame->r[j].ux + dx * (i+1);
548 +              out_coords[j].uy = temp_frame->r[j].uy + dy * (i+1);
549 +              out_coords[j].uz = temp_frame->r[j].uz + dz * (i+1);
550 +            }
551 +
552 +            if (current_frame->r[j].hasSecondVector) {              
553 +              dx = current_frame->r[j].vx - temp_frame->r[j].vx;
554 +              dy = current_frame->r[j].vy - temp_frame->r[j].vy;
555 +              dz = current_frame->r[j].vz - temp_frame->r[j].vz;
556 +              
557 +              dx /= (double)(n_interpolate + 1);
558 +              dy /= (double)(n_interpolate + 1);
559 +              dz /= (double)(n_interpolate + 1);
560 +              
561 +              out_coords[j].hasVector = current_frame->r[j].hasSecondVector;
562 +              out_coords[j].vx = temp_frame->r[j].vx + dx * (i+1);
563 +              out_coords[j].vy = temp_frame->r[j].vy + dy * (i+1);
564 +              out_coords[j].vz = temp_frame->r[j].vz + dz * (i+1);
565 +            }
566 +
567 +            if (current_frame->r[j].hasCharge) {              
568 +              dx = current_frame->r[j].charge - temp_frame->r[j].charge;
569 +              
570 +              dx /= (double)(n_interpolate + 1);
571 +              
572 +              out_coords[j].hasCharge = current_frame->r[j].hasCharge;
573 +              out_coords[j].charge = temp_frame->r[j].charge + dx * (i+1);
574 +            }
575 +
576            }
577            
578            pov_write(out_file, out_coords, n_atoms, draw_hydrogens, draw_bonds,
579 <                    draw_atoms);
579 >                    draw_atoms, draw_vectors);
580            free(out_coords);
581            (void)fclose(out_file);
582          }
# Line 461 | Line 600 | int main(argc, argv)
600        if( draw_box ){
601          
602          fprintf( out_file,
603 <                 "makePeriodicBox( %lf, %lf, %lf )\n"
603 >                 "makePeriodicBox( %lf, %lf, %lf, %lf, %lf, %lf, %lf, %lf, %lf )\n"
604                   "\n",
605 <                 current_frame->boxX,
606 <                 current_frame->boxZ,
607 <                 current_frame->boxY );
605 >                 current_frame->Hmat[0][0],
606 >                 current_frame->Hmat[2][0],
607 >                 current_frame->Hmat[1][0],
608 >                 current_frame->Hmat[0][1],
609 >                 current_frame->Hmat[2][1],
610 >                 current_frame->Hmat[1][1],
611 >                 current_frame->Hmat[0][2],
612 >                 current_frame->Hmat[2][2],
613 >                 current_frame->Hmat[1][2] );
614        }
615        
616        
# Line 478 | Line 623 | int main(argc, argv)
623          out_coords[i].x = current_frame->r[i].x;
624          out_coords[i].y = current_frame->r[i].y;
625          out_coords[i].z = current_frame->r[i].z;
626 +
627 +        if (current_frame->r[i].hasVector) {              
628 +          out_coords[i].hasVector = current_frame->r[i].hasVector;
629 +          out_coords[i].ux = current_frame->r[i].ux;
630 +          out_coords[i].uy = current_frame->r[i].uy;
631 +          out_coords[i].uz = current_frame->r[i].uz;
632 +        }
633 +
634 +        if (current_frame->r[i].hasSecondVector) {              
635 +          out_coords[i].hasSecondVector = current_frame->r[i].hasSecondVector;
636 +          out_coords[i].vx = current_frame->r[i].vx;
637 +          out_coords[i].vy = current_frame->r[i].vy;
638 +          out_coords[i].vz = current_frame->r[i].vz;
639 +        }
640 +
641 +        if (current_frame->r[i].hasCharge) {              
642 +          out_coords[i].hasCharge = current_frame->r[i].hasCharge;
643 +          out_coords[i].charge = current_frame->r[i].charge;
644 +        }
645        }
646        pov_write(out_file, out_coords, n_atoms, draw_hydrogens, draw_bonds,
647 <                draw_atoms);
647 >                draw_atoms, draw_vectors);
648        free(out_coords);
649        
650        (void)fclose(out_file);
# Line 543 | Line 707 | int main(argc, argv)
707      fprintf(out_file,
708              "// The following script was automatically generated by:\n"
709              "// xyz2pov Copyright 2001 by MATTHEW A. MEINEKE\n"
710 +            "#include \"colors.inc\"\n"
711 +            "#include \"math.inc\"\n"
712              "\n"
713              "\n"
714              "background { rgb <1.0, 1.0, 1.0> }\n"
# Line 565 | Line 731 | int main(argc, argv)
731              "\n"
732              "#declare ATOM_SPHERE_FACTOR = 0.2;\n"
733              "#declare BOND_RADIUS = 0.1;\n"
734 +            "#declare VECTOR_SCALE = 1.0;\n"    
735 +            "#declare STICK_RADIUS = 0.5 * BOND_RADIUS;\n"
736 +            "#declare CONE_RADIUS = 2.0 * STICK_RADIUS;\n"
737 +            "#declare CONE_FRACTION = 0.15;\n"
738              "\n"
739              "// declare camera, light, and system variables\n"
740              "\n"
# Line 582 | Line 752 | int main(argc, argv)
752              "#declare cameraLookY = sysCenterY;\n"
753              "#declare cameraLookZ = sysCenterZ;\n"
754              "\n"
755 +            "#declare rotatePointX = cameraLookX;\n"
756 +            "#declare rotatePointY = cameraLookY;\n"
757 +            "#declare rotatePointZ = cameraLookZ;\n"
758 +            "\n"
759              "#declare cameraX = cameraLookX;\n"
760              "#declare cameraY = cameraLookY;\n"
761              "#declare cameraZ = cameraLookZ - zoom;\n"
# Line 597 | Line 771 | int main(argc, argv)
771              "#declare boxCenterX = cameraLookX;\n"
772              "#declare boxCenterY = cameraLookY;\n"
773              "#declare boxCenterZ = cameraLookZ;\n"
774 +            "#declare fn = function(x,y,z) {(y+1)/2}\n"
775 +            "#declare grad1 = pigment { function { fn(x, y, z) } color_map {[0.0 rgb <0,0,0>] [1.0 rgb <3,0,0>]}  };\n"
776 +            "#declare grad2 = pigment { function { fn(x, y, z) } rotate 120*z color_map {[0.0 rgb <0,0,0>] [1.0 rgb <0,3,0>]}  };\n"
777 +            "#declare grad3 = pigment { function { fn(x, y, z) } rotate 240*z color_map {[0.0 rgb <0,0,0>] [1.0 rgb <0,0,3>]}  };\n"
778 +            "#declare fnz = function(x,y,z) {(z+1)/2}\n"
779 +            "#declare gradz = pigment { function { fnz(x, y, z) } color_map {[0.0 rgb <0,0,0>] [1.0 rgb <1,1,1>]}  };\n"
780              "\n"
781              "// declare the cameras and the light sources\n"
782              "\n"
# Line 651 | Line 831 | int main(argc, argv)
831              "// declare the periodic box macro\n"
832              "//************************************************************\n"
833              "\n"
834 <            "#macro makePeriodicBox( lengthX, lengthY, lengthZ )\n"
834 >            "#macro makePeriodicBox( bx1, by1, bz1, bx2, by2, bz2, bx3, by3, bz3 )\n"
835              "\n"
836 <            "  #local addX = lengthX / 2.0;\n"
837 <            "  #local addY = lengthY / 2.0;\n"
838 <            "  #local addZ = lengthZ / 2.0;\n"
836 >            "  #local bcx = (bx1 + bx2 + bx3) / 2.0;\n"
837 >            "  #local bcy = (by1 + by2 + by3) / 2.0;\n"
838 >            "  #local bcz = (bz1 + bz2 + bz3) / 2.0;\n"
839              "\n"
840 +            "  #local pAx = boxCenterX - bcx;\n"
841 +            "  #local pAy = boxCenterY - bcy;\n"
842 +            "  #local pAz = boxCenterZ - bcz;\n"
843 +            "  #local pBx = boxCenterX + bx1 - bcx;\n"
844 +            "  #local pBy = boxCenterY + by1 - bcy;\n"
845 +            "  #local pBz = boxCenterZ + bz1 - bcz;\n"
846 +            "  #local pCx = boxCenterX + bx2 - bcx;\n"
847 +            "  #local pCy = boxCenterY + by2 - bcy;\n"
848 +            "  #local pCz = boxCenterZ + bz2 - bcz;\n"
849 +            "  #local pDx = boxCenterX + bx3 - bcx;\n"
850 +            "  #local pDy = boxCenterY + by3 - bcy;\n"
851 +            "  #local pDz = boxCenterZ + bz3 - bcz;\n"
852 +            "  #local pEx = boxCenterX + bx1 + bx2 - bcx;\n"
853 +            "  #local pEy = boxCenterY + by1 + by2 - bcy;\n"
854 +            "  #local pEz = boxCenterZ + bz1 + bz2 - bcz;\n"
855 +            "  #local pFx = boxCenterX + bx1 + bx3 - bcx;\n"
856 +            "  #local pFy = boxCenterY + by1 + by3 - bcy;\n"
857 +            "  #local pFz = boxCenterZ + bz1 + bz3 - bcz;\n"
858 +            "  #local pGx = boxCenterX + bx2 + bx3 - bcx;\n"
859 +            "  #local pGy = boxCenterY + by2 + by3 - bcy;\n"
860 +            "  #local pGz = boxCenterZ + bz2 + bz3 - bcz;\n"
861 +            "  #local pHx = boxCenterX + bx1 + bx2 + bx3 - bcx;\n"
862 +            "  #local pHy = boxCenterY + by1 + by2 + by3 - bcy;\n"
863 +            "  #local pHz = boxCenterZ + bz1 + bz2 + bz3 - bcz;\n"
864 +            "\n"
865 +            "  #if(ROTATE)\n"
866 +            "    #local pAx_new = rotatePointX + A11 * (pAx-rotatePointX) + A12 * (pAy-rotatePointY) + A13 * (pAz-rotatePointZ);\n"
867 +            "    #local pAy_new = rotatePointY + A21 * (pAx-rotatePointX) + A22 * (pAy-rotatePointY) + A23 * (pAz-rotatePointZ);\n"
868 +            "    #local pAz_new = rotatePointZ + A31 * (pAx-rotatePointX) + A32 * (pAy-rotatePointY) + A33 * (pAz-rotatePointZ);\n"
869 +            "\n"
870 +            "    #local pBx_new = rotatePointX + A11 * (pBx-rotatePointX) + A12 * (pBy-rotatePointY) + A13 * (pBz-rotatePointZ);\n"
871 +            "    #local pBy_new = rotatePointY + A21 * (pBx-rotatePointX) + A22 * (pBy-rotatePointY) + A23 * (pBz-rotatePointZ);\n"
872 +            "    #local pBz_new = rotatePointZ + A31 * (pBx-rotatePointX) + A32 * (pBy-rotatePointY) + A33 * (pBz-rotatePointZ);\n"
873 +            "\n"
874 +            "    #local pCx_new = rotatePointX + A11 * (pCx-rotatePointX) + A12 * (pCy-rotatePointY) + A13 * (pCz-rotatePointZ);\n"
875 +            "    #local pCy_new = rotatePointY + A21 * (pCx-rotatePointX) + A22 * (pCy-rotatePointY) + A23 * (pCz-rotatePointZ);\n"
876 +            "    #local pCz_new = rotatePointZ + A31 * (pCx-rotatePointX) + A32 * (pCy-rotatePointY) + A33 * (pCz-rotatePointZ);\n"
877 +            "\n"
878 +            "    #local pDx_new = rotatePointX + A11 * (pDx-rotatePointX) + A12 * (pDy-rotatePointY) + A13 * (pDz-rotatePointZ);\n"
879 +            "    #local pDy_new = rotatePointY + A21 * (pDx-rotatePointX) + A22 * (pDy-rotatePointY) + A23 * (pDz-rotatePointZ);\n"
880 +            "    #local pDz_new = rotatePointZ + A31 * (pDx-rotatePointX) + A32 * (pDy-rotatePointY) + A33 * (pDz-rotatePointZ);\n"
881 +            "\n"
882 +            "    #local pEx_new = rotatePointX + A11 * (pEx-rotatePointX) + A12 * (pEy-rotatePointY) + A13 * (pEz-rotatePointZ);\n"
883 +            "    #local pEy_new = rotatePointY + A21 * (pEx-rotatePointX) + A22 * (pEy-rotatePointY) + A23 * (pEz-rotatePointZ);\n"
884 +            "    #local pEz_new = rotatePointZ + A31 * (pEx-rotatePointX) + A32 * (pEy-rotatePointY) + A33 * (pEz-rotatePointZ);\n"
885 +            "\n"
886 +            "    #local pFx_new = rotatePointX + A11 * (pFx-rotatePointX) + A12 * (pFy-rotatePointY) + A13 * (pFz-rotatePointZ);\n"
887 +            "    #local pFy_new = rotatePointY + A21 * (pFx-rotatePointX) + A22 * (pFy-rotatePointY) + A23 * (pFz-rotatePointZ);\n"
888 +            "    #local pFz_new = rotatePointZ + A31 * (pFx-rotatePointX) + A32 * (pFy-rotatePointY) + A33 * (pFz-rotatePointZ);\n"
889 +            "\n"
890 +            "    #local pGx_new = rotatePointX + A11 * (pGx-rotatePointX) + A12 * (pGy-rotatePointY) + A13 * (pGz-rotatePointZ);\n"
891 +            "    #local pGy_new = rotatePointY + A21 * (pGx-rotatePointX) + A22 * (pGy-rotatePointY) + A23 * (pGz-rotatePointZ);\n"
892 +            "    #local pGz_new = rotatePointZ + A31 * (pGx-rotatePointX) + A32 * (pGy-rotatePointY) + A33 * (pGz-rotatePointZ);\n"
893 +            "\n"
894 +            "    #local pHx_new = rotatePointX + A11 * (pHx-rotatePointX) + A12 * (pHy-rotatePointY) + A13 * (pHz-rotatePointZ);\n"
895 +            "    #local pHy_new = rotatePointY + A21 * (pHx-rotatePointX) + A22 * (pHy-rotatePointY) + A23 * (pHz-rotatePointZ);\n"
896 +            "    #local pHz_new = rotatePointZ + A31 * (pHx-rotatePointX) + A32 * (pHy-rotatePointY) + A33 * (pHz-rotatePointZ);\n"
897 +            "\n"
898 +            "  #else\n"
899 +            "    #local pAx_new = pAx;"
900 +            "    #local pAy_new = pAy;"
901 +            "    #local pAz_new = pAz;"
902 +            "\n"
903 +            "    #local pBx_new = pBx;"
904 +            "    #local pBy_new = pBy;"
905 +            "    #local pBz_new = pBz;"
906 +            "\n"
907 +            "    #local pCx_new = pCx;"
908 +            "    #local pCy_new = pCy;"
909 +            "    #local pCz_new = pCz;"
910 +            "\n"
911 +            "    #local pDx_new = pDx;"
912 +            "    #local pDy_new = pDy;"
913 +            "    #local pDz_new = pDz;"
914 +            "\n"
915 +            "    #local pEx_new = pEx;"
916 +            "    #local pEy_new = pEy;"
917 +            "    #local pEz_new = pEz;"
918 +            "\n"
919 +            "    #local pFx_new = pFx;"
920 +            "    #local pFy_new = pFy;"
921 +            "    #local pFz_new = pFz;"
922 +            "\n"
923 +            "    #local pGx_new = pGx;"
924 +            "    #local pGy_new = pGy;"
925 +            "    #local pGz_new = pGz;"
926 +            "\n"
927 +            "    #local pHx_new = pHx;"
928 +            "    #local pHy_new = pHy;"
929 +            "    #local pHz_new = pHz;"
930 +            "\n"
931 +            "  #end\n"
932 +            "  #local pAx = pAx_new;"
933 +            "  #local pAy = pAy_new;"
934 +            "  #local pAz = pAz_new;"
935 +            "\n"                    
936 +            "  #local pBx = pBx_new;"
937 +            "  #local pBy = pBy_new;"
938 +            "  #local pBz = pBz_new;"
939 +            "\n"                    
940 +            "  #local pCx = pCx_new;"
941 +            "  #local pCy = pCy_new;"
942 +            "  #local pCz = pCz_new;"
943 +            "\n"                    
944 +            "  #local pDx = pDx_new;"
945 +            "  #local pDy = pDy_new;"
946 +            "  #local pDz = pDz_new;"
947 +            "\n"                    
948 +            "  #local pEx = pEx_new;"
949 +            "  #local pEy = pEy_new;"
950 +            "  #local pEz = pEz_new;"
951 +            "\n"                    
952 +            "  #local pFx = pFx_new;"
953 +            "  #local pFy = pFy_new;"
954 +            "  #local pFz = pFz_new;"
955 +            "\n"                    
956 +            "  #local pGx = pGx_new;"
957 +            "  #local pGy = pGy_new;"
958 +            "  #local pGz = pGz_new;"
959 +            "\n"                    
960 +            "  #local pHx = pHx_new;"
961 +            "  #local pHy = pHy_new;"
962 +            "  #local pHz = pHz_new;"
963 +            "\n"
964              "  #local colorR = 0.90;\n"
965              "  #local colorG = 0.91;\n"
966              "  #local colorB = 0.98;\n"
# Line 665 | Line 969 | int main(argc, argv)
969              "\n"
970              "  // 1\n"
971              "  cylinder{\n"
972 <            "    < boxCenterX-addX, boxCenterY-addY, boxCenterZ-addZ >,\n"
973 <            "    < boxCenterX-addX, boxCenterY+addY, boxCenterZ-addZ >,\n"
972 >            "    < pAx, pAy, pAz >,\n"
973 >            "    < pBx, pBy, pBz >,\n"
974              "    pipeWidth\n"
975              "    texture{\n"
976              "      pigment{ rgb < colorR, colorG, colorB > }\n"
# Line 682 | Line 986 | int main(argc, argv)
986              "\n"
987              "  // 2\n"
988              "  cylinder{\n"
989 <            "    < boxCenterX-addX, boxCenterY-addY, boxCenterZ+addZ >,\n"
990 <            "    < boxCenterX-addX, boxCenterY+addY, boxCenterZ+addZ >,\n"
989 >            "    < pAx, pAy, pAz >,\n"
990 >            "    < pCx, pCy, pCz >,\n"
991              "    pipeWidth\n"
992              "    texture{\n"
993              "      pigment{ rgb < colorR, colorG, colorB > }\n"
# Line 699 | Line 1003 | int main(argc, argv)
1003              "\n"
1004              "  // 3\n"
1005              "  cylinder{\n"
1006 <            "    < boxCenterX+addX, boxCenterY-addY, boxCenterZ-addZ >,\n"
1007 <            "    < boxCenterX+addX, boxCenterY+addY, boxCenterZ-addZ >,\n"
1006 >            "    < pAx, pAy, pAz >,\n"
1007 >            "    < pDx, pDy, pDz >,\n"
1008              "    pipeWidth\n"
1009              "    texture{\n"
1010              "      pigment{ rgb < colorR, colorG, colorB > }\n"
# Line 716 | Line 1020 | int main(argc, argv)
1020              "\n"
1021              "  // 4\n"
1022              "  cylinder{\n"
1023 <            "    < boxCenterX+addX, boxCenterY-addY, boxCenterZ+addZ >,\n"
1024 <            "    < boxCenterX+addX, boxCenterY+addY, boxCenterZ+addZ >,\n"
1023 >            "    < pBx, pBy, pBz >,\n"
1024 >            "    < pEx, pEy, pEz >,\n"
1025              "    pipeWidth\n"
1026              "    texture{\n"
1027              "      pigment{ rgb < colorR, colorG, colorB > }\n"
# Line 733 | Line 1037 | int main(argc, argv)
1037              "\n"
1038              "  // 5\n"
1039              "  cylinder{\n"
1040 <            "    < boxCenterX-addX, boxCenterY-addY, boxCenterZ-addZ >,\n"
1041 <            "    < boxCenterX-addX, boxCenterY-addY, boxCenterZ+addZ >,\n"
1040 >            "    < pCx, pCy, pCz >,\n"
1041 >            "    < pEx, pEy, pEz >,\n"
1042              "    pipeWidth\n"
1043              "    texture{\n"
1044              "      pigment{ rgb < colorR, colorG, colorB > }\n"
# Line 750 | Line 1054 | int main(argc, argv)
1054              "\n"
1055              "  // 6\n"
1056              "  cylinder{\n"
1057 <            "    < boxCenterX-addX, boxCenterY-addY, boxCenterZ+addZ >,\n"
1058 <            "    < boxCenterX+addX, boxCenterY-addY, boxCenterZ+addZ >,\n"
1057 >            "    < pBx, pBy, pBz >,\n"
1058 >            "    < pFx, pFy, pFz >,\n"
1059              "    pipeWidth\n"
1060              "    texture{\n"
1061              "      pigment{ rgb < colorR, colorG, colorB > }\n"
# Line 767 | Line 1071 | int main(argc, argv)
1071              "\n"
1072              "  // 7\n"
1073              "  cylinder{\n"
1074 <            "    < boxCenterX+addX, boxCenterY-addY, boxCenterZ+addZ >,\n"
1075 <            "    < boxCenterX+addX, boxCenterY-addY, boxCenterZ-addZ >,\n"
1074 >            "    < pCx, pCy, pCz >,\n"
1075 >            "    < pGx, pGy, pGz >,\n"
1076              "    pipeWidth\n"
1077              "    texture{\n"
1078              "      pigment{ rgb < colorR, colorG, colorB > }\n"
# Line 784 | Line 1088 | int main(argc, argv)
1088              "\n"
1089              "  // 8\n"
1090              "  cylinder{\n"
1091 <            "    < boxCenterX+addX, boxCenterY-addY, boxCenterZ-addZ >,\n"
1092 <            "    < boxCenterX-addX, boxCenterY-addY, boxCenterZ-addZ >,\n"
1091 >            "    < pDx, pDy, pDz >,\n"
1092 >            "    < pGx, pGy, pGz >,\n"
1093              "    pipeWidth\n"
1094              "    texture{\n"
1095              "      pigment{ rgb < colorR, colorG, colorB > }\n"
# Line 801 | Line 1105 | int main(argc, argv)
1105              "\n"
1106              "  // 9\n"
1107              "  cylinder{\n"
1108 <            "    < boxCenterX-addX, boxCenterY+addY, boxCenterZ-addZ >,\n"
1109 <            "    < boxCenterX-addX, boxCenterY+addY, boxCenterZ+addZ >,\n"
1108 >            "    < pDx, pDy, pDz >,\n"
1109 >            "    < pFx, pFy, pFz >,\n"
1110              "    pipeWidth\n"
1111              "    texture{\n"
1112              "      pigment{ rgb < colorR, colorG, colorB > }\n"
# Line 818 | Line 1122 | int main(argc, argv)
1122              "\n"
1123              "  // 10\n"
1124              "  cylinder{\n"
1125 <            "    < boxCenterX-addX, boxCenterY+addY, boxCenterZ+addZ >,\n"
1126 <            "    < boxCenterX+addX, boxCenterY+addY, boxCenterZ+addZ >,\n"
1125 >            "    < pEx, pEy, pEz >,\n"
1126 >            "    < pHx, pHy, pHz >,\n"
1127              "    pipeWidth\n"
1128              "    texture{\n"
1129              "      pigment{ rgb < colorR, colorG, colorB > }\n"
# Line 835 | Line 1139 | int main(argc, argv)
1139              "\n"
1140              "  // 11\n"
1141              "  cylinder{\n"
1142 <            "    < boxCenterX+addX, boxCenterY+addY, boxCenterZ+addZ >,\n"
1143 <            "    < boxCenterX+addX, boxCenterY+addY, boxCenterZ-addZ >,\n"
1142 >            "    < pFx, pFy, pFz >,\n"
1143 >            "    < pHx, pHy, pHz >,\n"
1144              "    pipeWidth\n"
1145              "    texture{\n"
1146              "      pigment{ rgb < colorR, colorG, colorB > }\n"
# Line 852 | Line 1156 | int main(argc, argv)
1156              "\n"
1157              "  // 12\n"
1158              "  cylinder{\n"
1159 <            "    < boxCenterX+addX, boxCenterY+addY, boxCenterZ-addZ >,\n"
1160 <            "    < boxCenterX-addX, boxCenterY+addY, boxCenterZ-addZ >,\n"
1159 >            "    < pGx, pGy, pGz >,\n"
1160 >            "    < pHx, pHy, pHz >,\n"
1161              "    pipeWidth\n"
1162              "    texture{\n"
1163              "      pigment{ rgb < colorR, colorG, colorB > }\n"
# Line 901 | Line 1205 | void usage(){
1205                  "   -h            draw hydrogens\n"
1206                  "   -b            draw bonds\n"
1207                  "   -a            draw atoms\n"
1208 +                "   -v            draw vectors\n"
1209                  "   -p            draw periodic box\n"
1210                  "   -r            regenerate bond\n"
1211                  "   -f <#>        render frame <#> only\n"
# Line 910 | Line 1215 | void usage(){
1215                  program_name);
1216    exit(8);
1217   }
1218 +
1219 + int count_tokens(line, delimiters)
1220 +     /* PURPOSE: RETURN A COUNT OF THE NUMBER OF TOKENS ON THE LINE. */
1221 +     char *line;                /* LINE CONTAINING TOKENS. */
1222 +     char *delimiters;  /* POSSIBLE TOKEN DELIMITERS TO USE. */
1223 + {
1224 +  char *working_line;   /* WORKING COPY OF LINE. */
1225 +  int ntokens;          /* NUMBER OF TOKENS FOUND IN LINE. */
1226 +  char *strtok_ptr;     /* POINTER FOR STRTOK. */
1227 +  
1228 +  strtok_ptr= working_line= strdup(line);
1229 +  
1230 +  ntokens=0;
1231 +  while (strtok(strtok_ptr,delimiters)!=NULL)
1232 +    {
1233 +      ntokens++;
1234 +      strtok_ptr=NULL;
1235 +    }
1236 +  
1237 +  free(working_line);
1238 +  return(ntokens);
1239 + }

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