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mmeineke |
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#include <stdio.h> |
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#include <stdlib.h> |
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#include <string.h> |
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#include <math.h> |
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#include <unistd.h> |
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#include <sys/types.h> |
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#include <sys/stat.h> |
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#include "frameCount.h" |
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#include "atom_parser.h" |
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#include "pov_writer.h" |
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#define POV_DIR "./pov" |
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mmeineke |
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mmeineke |
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struct linked_xyz{ |
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struct coords *r; |
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struct linked_xyz *next; |
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}; |
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char *program_name; /*the name of the program */ |
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int draw_bonds = 0; /* boolean to draw bonds or not */ |
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int draw_hydrogens = 0; /*boolean to draw hydrogens */ |
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int draw_atoms = 0; /*boolean to draw atoms */ |
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mmeineke |
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int regenerateBonds = 0; // boolean to regenearate bonds each frame |
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mmeineke |
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void usage(void); |
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int main(argc, argv) |
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int argc; |
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char *argv[]; |
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{ |
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struct coords *out_coords; |
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int i,j; /* loop counters */ |
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mode_t dir_mode = S_IRWXU; |
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int generate_header = 0; /* boolean for generating the pov ray header */ |
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double big_x = 0; |
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double big_y = 0; /* lets me know the biggest x y and z */ |
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double big_z = 0; |
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double small_x = 0; |
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double small_y = 0; /* lets me know the smallest x, y, z */ |
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double small_z = 0; |
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double rsqr; /* the square of the diagonal */ |
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double diagonal; /* the diagonal length of the sim box */ |
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unsigned int n_atoms; /*the number of atoms in each time step */ |
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char read_buffer[120]; /*the line buffer for reading */ |
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char *eof_test; /*ptr to see when we reach the end of the file */ |
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char *foo; /*the pointer to the current string token */ |
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FILE *in_file; /* the input file */ |
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FILE *out_file; /*the output file */ |
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char *out_prefix = NULL; /*the prefix of the output file */ |
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int have_prefix = 0; |
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char out_name[500]; /*the output name */ |
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char out_format[1000]; |
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char *in_name = NULL; /*the name of the input file */ |
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unsigned int n_out = 0; /*keeps track of which output file is being written*/ |
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int done; |
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char current_flag; |
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int nFrames; |
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int nZeroes; |
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double count; |
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struct linked_xyz *current_frame; |
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struct linked_xyz *temp_frame; |
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unsigned int n_interpolate = 0; /* number of frames to interpolate */ |
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double dx, dy, dz; /* temp variables for interpolating distances */ |
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char pov_dir[500]; /* the pov_dir */ |
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program_name = argv[0]; /*save the program name in case we need it*/ |
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mmeineke |
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mmeineke |
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for( i = 1; i < argc; i++){ |
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if(argv[i][0] =='-'){ |
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// parse the option |
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if(argv[i][1] == '-' ){ |
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// parse long word options |
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fprintf( stderr, |
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"Invalid option \"%s\"\n", argv[i] ); |
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usage(); |
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} |
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else{ |
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// parse single character options |
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done = 0; |
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j = 1; |
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current_flag = argv[i][j]; |
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while( (current_flag != '\0') && (!done) ){ |
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switch(current_flag){ |
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case 'o': |
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// -o <prefix> => the output prefix. |
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i++; |
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out_prefix = argv[i]; |
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have_prefix = 1; |
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done = 1; |
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break; |
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case 'i': |
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// -i <#> => the number to interpolate |
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i++; |
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n_interpolate = atoi( argv[i] ); |
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done = 1; |
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break; |
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case 'H': |
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// -h => generate a pov-ray Header |
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generate_header = 1; |
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break; |
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case 'h': |
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// -h => draw Hydrogens |
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draw_hydrogens = 1; |
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break; |
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case 'b': |
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// -b => draw bonds |
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draw_bonds = 1; |
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break; |
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case 'a': |
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// -a => draw the atoms |
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draw_atoms = 1; |
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break; |
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mmeineke |
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case 'r': |
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// -r => regenerate bonds |
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regenerateBonds = 1; |
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break; |
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mmeineke |
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default: |
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(void)fprintf(stderr, "Bad option \"-%c\"\n", current_flag); |
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usage(); |
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} |
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j++; |
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current_flag = argv[i][j]; |
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} |
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} |
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} |
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else{ |
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if( in_name != NULL ){ |
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fprintf( stderr, |
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"Error at \"%s\", program does not currently support\n" |
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"more than one input file.\n" |
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"\n", |
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argv[i]); |
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usage(); |
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} |
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in_name = argv[i]; |
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} |
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} |
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if(in_name == NULL){ |
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usage(); |
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} |
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184 |
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in_file = fopen(in_name, "r"); |
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if(in_file == NULL){ |
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printf("Cannot open file: %s\n", in_name); |
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exit(8); |
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} |
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if(access(POV_DIR, F_OK)){ |
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/*create the pov directory*/ |
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mkdir(POV_DIR, dir_mode); |
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} |
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strcpy(pov_dir, POV_DIR); strcat(pov_dir, "/"); |
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// initialize atom type parser |
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initializeParser(); |
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mmeineke |
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initBondList(); |
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mmeineke |
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// count the number of frames |
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printf( "Counting the number of frames..." ); |
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fflush(stdout); |
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nFrames = frameCount( in_name ); |
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printf( "done.\n" |
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"%d frames found\n", |
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nFrames); |
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fflush(stdout); |
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// create the output string |
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nZeroes = 1; |
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count = (double)( nFrames * (n_interpolate+1) ); |
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while( count >= 10.0 ){ |
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count /= 10.0; |
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nZeroes++; |
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} |
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if(!have_prefix){ |
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out_prefix = strtok(in_name, "."); |
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} |
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sprintf( out_format, "%s%s%%0%dd.pov", pov_dir, out_prefix, nZeroes ); |
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// start reading the first frame |
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eof_test = fgets(read_buffer, sizeof(read_buffer), in_file); |
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current_frame = (struct linked_xyz *)malloc(sizeof(struct linked_xyz)); |
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current_frame->next = NULL; |
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while(eof_test != NULL){ |
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(void)sscanf(read_buffer, "%d", &n_atoms); |
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current_frame->r = |
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(struct coords *)calloc(n_atoms, sizeof(struct coords)); |
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/*read and toss the comment line */ |
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eof_test = fgets(read_buffer, sizeof(read_buffer), in_file); |
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if(eof_test == NULL){ |
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printf("error in reading file\n"); |
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exit(8); |
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} |
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for( i=0; i < n_atoms; i++){ |
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eof_test = fgets(read_buffer, sizeof(read_buffer), in_file); |
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if(eof_test == NULL){ |
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printf("error in reading file\n"); |
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exit(8); |
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} |
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foo = strtok(read_buffer, " ,;\t"); |
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(void)strcpy(current_frame->r[i].name, foo); /*copy the atom name */ |
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/* next we grab the positions */ |
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foo = strtok(NULL, " ,;\t"); |
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if(foo == NULL){ |
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printf("error in reading file\n"); |
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exit(8); |
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} |
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(void)sscanf(foo, "%lf",¤t_frame->r[i].x); |
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if(current_frame->r[i].x > big_x) big_x = current_frame->r[i].x; |
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if(current_frame->r[i].x < small_x) small_x = current_frame->r[i].x; |
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277 |
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278 |
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foo = strtok(NULL, " ,;\t"); |
279 |
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if(foo == NULL){ |
280 |
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printf("error in reading file\n"); |
281 |
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exit(8); |
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} |
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(void)sscanf(foo, "%lf", ¤t_frame->r[i].y); |
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if(current_frame->r[i].y > big_y) big_y = current_frame->r[i].y; |
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if(current_frame->r[i].y < small_y) small_y = current_frame->r[i].y; |
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287 |
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288 |
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foo = strtok(NULL, " ,;\t"); |
289 |
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if(foo == NULL){ |
290 |
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printf("error in reading file\n"); |
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exit(8); |
292 |
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} |
293 |
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(void)sscanf(foo, "%lf", ¤t_frame->r[i].z); |
294 |
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if(current_frame->r[i].z > big_z) big_z = current_frame->r[i].z; |
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if(current_frame->r[i].z < small_z) small_z = current_frame->r[i].z; |
296 |
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297 |
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} |
298 |
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299 |
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if(n_interpolate && current_frame->next != NULL){ |
300 |
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301 |
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temp_frame = current_frame->next; |
302 |
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303 |
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for(i = 0; i < n_interpolate; i++){ |
304 |
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305 |
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/* open the new output file */ |
306 |
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sprintf(out_name, out_format, n_out ); |
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out_file = fopen(out_name, "w"); |
309 |
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n_out++; |
310 |
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if(out_file == NULL){ |
311 |
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printf("error opening output file: %s\n", out_name); |
312 |
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exit(8); |
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} |
314 |
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(void)fprintf(out_file, |
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"// The following script was automatically generated by:\n" |
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"// xyz2pov Copyright 2001 by MATTHEW A. MEINEKE\n" |
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"\n" |
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"#include \"pov_header.pov\"\n" |
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"\n"); |
320 |
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321 |
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out_coords = |
322 |
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(struct coords *)calloc(n_atoms, sizeof(struct coords)); |
323 |
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324 |
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for(j=0; j < n_atoms; j++){ |
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dx = current_frame->r[j].x - temp_frame->r[j].x; |
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dy = current_frame->r[j].y - temp_frame->r[j].y; |
327 |
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dz = current_frame->r[j].z - temp_frame->r[j].z; |
328 |
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329 |
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dx /= (double)(n_interpolate + 1); |
330 |
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dy /= (double)(n_interpolate + 1); |
331 |
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dz /= (double)(n_interpolate + 1); |
332 |
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333 |
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strcpy(out_coords[j].name, temp_frame->r[j].name); |
334 |
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out_coords[j].x = temp_frame->r[j].x + dx * (i+1); |
335 |
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out_coords[j].y = temp_frame->r[j].y + dy * (i+1); |
336 |
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out_coords[j].z = temp_frame->r[j].z + dz * (i+1); |
337 |
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} |
338 |
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339 |
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pov_write(out_file, out_coords, n_atoms, draw_hydrogens, draw_bonds, |
340 |
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draw_atoms); |
341 |
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free(out_coords); |
342 |
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(void)fclose(out_file); |
343 |
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} |
344 |
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} |
345 |
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346 |
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/* open the new output file */ |
347 |
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348 |
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sprintf(out_name, out_format, n_out ); |
349 |
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out_file = fopen(out_name, "w"); |
350 |
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n_out++; |
351 |
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if(out_file == NULL){ |
352 |
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printf("error opening output file: %s\n", out_name); |
353 |
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exit(8); |
354 |
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} |
355 |
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(void)fprintf(out_file, |
356 |
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"// The following script was automatically generated by:\n" |
357 |
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"// xyz2pov Copyright 2001 by MATTHEW A. MEINEKE\n" |
358 |
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"\n" |
359 |
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"#include \"pov_header.pov\"\n" |
360 |
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"\n"); |
361 |
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362 |
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out_coords = |
363 |
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(struct coords *)calloc(n_atoms, sizeof(struct coords)); |
364 |
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365 |
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for(i = 0; i < n_atoms; i++){ |
366 |
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strcpy(out_coords[i].name, current_frame->r[i].name); |
367 |
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out_coords[i].x = current_frame->r[i].x; |
368 |
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out_coords[i].y = current_frame->r[i].y; |
369 |
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out_coords[i].z = current_frame->r[i].z; |
370 |
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} |
371 |
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pov_write(out_file, out_coords, n_atoms, draw_hydrogens, draw_bonds, |
372 |
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draw_atoms); |
373 |
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free(out_coords); |
374 |
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375 |
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(void)fclose(out_file); |
376 |
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377 |
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/*free up memory */ |
378 |
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379 |
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temp_frame = current_frame->next; |
380 |
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current_frame->next = NULL; |
381 |
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382 |
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if(temp_frame != NULL){ |
383 |
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384 |
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free(temp_frame->r); |
385 |
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free(temp_frame); |
386 |
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} |
387 |
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388 |
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/* make a new frame */ |
389 |
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390 |
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temp_frame = (struct linked_xyz *)malloc(sizeof(struct linked_xyz)); |
391 |
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temp_frame->next = current_frame; |
392 |
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current_frame = temp_frame; |
393 |
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394 |
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eof_test = fgets(read_buffer, sizeof(read_buffer), in_file); |
395 |
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396 |
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} |
397 |
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398 |
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(void)fclose(in_file); |
399 |
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400 |
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401 |
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if(generate_header){ |
402 |
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403 |
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dx = big_x - small_x; |
404 |
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dy = big_y - small_y; |
405 |
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dz = big_z - small_z; |
406 |
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407 |
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rsqr = dx * dx + dy * dy + dz * dz; |
408 |
|
|
diagonal = sqrt(rsqr); |
409 |
|
|
diagonal *= 0.5; |
410 |
|
|
|
411 |
|
|
dx /= 2.0; |
412 |
|
|
dy /= 2.0; |
413 |
|
|
dz /= 2.0; |
414 |
|
|
|
415 |
|
|
dx += small_x; |
416 |
|
|
dy += small_y; |
417 |
|
|
dz += small_z; |
418 |
|
|
|
419 |
|
|
|
420 |
|
|
/*note the y and z axis is exchanged for the different coordinate |
421 |
|
|
system in pov-ray*/ |
422 |
|
|
|
423 |
|
|
|
424 |
|
|
out_file = fopen("pov_header.pov", "w"); |
425 |
|
|
|
426 |
|
|
fprintf(out_file, |
427 |
|
|
"// The following script was automatically generated by:\n" |
428 |
|
|
"// xyz2pov Copyright 2001 by MATTHEW A. MEINEKE\n" |
429 |
|
|
"\n" |
430 |
|
|
"\n" |
431 |
|
|
"background { rgb <1.0, 1.0, 1.0> }\n" |
432 |
|
|
"\n" |
433 |
|
|
"\n" |
434 |
|
|
); |
435 |
|
|
|
436 |
|
|
fprintf(out_file, |
437 |
|
|
"//******************************************************\n" |
438 |
|
|
"// Declare the resolution, camera, and light sources.\n" |
439 |
|
|
"//******************************************************\n" |
440 |
|
|
"\n" |
441 |
|
|
"// NOTE: if you plan to render at a different resoltion,\n" |
442 |
|
|
"// be sure to update the following two lines to maintain\n" |
443 |
|
|
"// the correct aspect ratio.\n" |
444 |
|
|
"\n" |
445 |
|
|
"#declare Width = 640.0;\n" |
446 |
|
|
"#declare Height = 480.0;\n" |
447 |
|
|
"#declare Ratio = Width / Height;\n" |
448 |
|
|
"\n" |
449 |
|
|
"#declare zoom = %lf;\n" |
450 |
|
|
"\n" |
451 |
|
|
"#declare ATOM_SPHERE_FACTOR = 0.2;\n" |
452 |
|
|
"#declare BOND_RADIUS = 0.1;\n" |
453 |
|
|
"\n" |
454 |
|
|
"camera{\n" |
455 |
|
|
" location < %lf, %lf, %lf - zoom>\n" |
456 |
|
|
" right < Ratio , 0, 0>\n" |
457 |
|
|
" look_at < %lf, %lf, %lf >\n" |
458 |
|
|
"}\n" |
459 |
|
|
"\n", |
460 |
|
|
diagonal, |
461 |
|
|
dx, dz, dy, |
462 |
|
|
dx, dz, dy); |
463 |
|
|
|
464 |
|
|
fprintf(out_file, |
465 |
|
|
"light_source{\n" |
466 |
|
|
" < %lf, %lf, %lf - zoom >\n" |
467 |
|
|
" rgb < 1.0, 1.0, 1.0 > }\n", |
468 |
|
|
dx, dz, dy); |
469 |
|
|
|
470 |
|
|
fprintf(out_file, |
471 |
|
|
"light_source{\n" |
472 |
|
|
" < %lf - zoom , %lf + zoom, %lf - zoom >\n" |
473 |
|
|
" rgb < 1.0, 1.0, 1.0 > }\n" |
474 |
|
|
"\n" |
475 |
|
|
"\n", |
476 |
|
|
dx, dz, dy); |
477 |
|
|
|
478 |
|
|
fprintf(out_file, |
479 |
|
|
"//************************************************************\n" |
480 |
|
|
"// Set whether or not to rotate the system.\n" |
481 |
|
|
"//\n" |
482 |
|
|
"// To Rotate, set ROTATE to 1.0 (true),\n" |
483 |
|
|
"// Then set the Euler Angles PHI, THETA, and PSI in degrees.\n" |
484 |
|
|
"//************************************************************\n" |
485 |
|
|
"\n" |
486 |
|
|
"#declare ROTATE = 0.0;\n" |
487 |
|
|
"#declare PHI = 0.0;\n" |
488 |
|
|
"#declare THETA = 0.0;\n" |
489 |
|
|
"#declare PSI = 0.0;\n" |
490 |
|
|
"\n" |
491 |
|
|
"#if(ROTATE)\n" |
492 |
|
|
" #declare phi_r = radians(PHI);\n" |
493 |
|
|
" #declare theta_r = radians(THETA);\n" |
494 |
|
|
" #declare psi_r = radians(PSI);\n" |
495 |
|
|
"\n" |
496 |
|
|
" #declare A11 = cos(phi_r) * cos(psi_r) - sin(phi_r) * cos(theta_r) * sin(psi_r);\n" |
497 |
|
|
" #declare A12 = sin(phi_r) * cos(psi_r) + cos(phi_r) * cos(theta_r) * sin(psi_r);\n" |
498 |
|
|
" #declare A13 = sin(theta_r) * sin(psi_r);\n" |
499 |
|
|
"\n" |
500 |
|
|
" #declare A21 = -cos(phi_r) * sin(psi_r) - sin(phi_r) * cos(theta_r) * cos(psi_r);\n" |
501 |
|
|
" #declare A22 = -sin(phi_r) * sin(psi_r) + cos(phi_r) * cos(theta_r) * cos(psi_r);\n" |
502 |
|
|
" #declare A23 = sin(theta_r) * cos(psi_r);\n" |
503 |
|
|
"\n" |
504 |
|
|
" #declare A31 = sin(phi_r) * sin(theta_r);\n" |
505 |
|
|
" #declare A32 = -cos(phi_r) * sin(theta_r);\n" |
506 |
|
|
" #declare A33 = cos(theta_r);\n" |
507 |
|
|
"\n" |
508 |
|
|
"#end\n" |
509 |
|
|
"\n"); |
510 |
|
|
|
511 |
|
|
|
512 |
|
|
make_header_macros(out_file); |
513 |
|
|
|
514 |
|
|
fclose(out_file); |
515 |
|
|
} |
516 |
|
|
|
517 |
|
|
return 0; |
518 |
|
|
|
519 |
|
|
} |
520 |
|
|
|
521 |
|
|
|
522 |
|
|
|
523 |
|
|
/*************************************************************************** |
524 |
|
|
* prints out the usage for the command line arguments, then exits. |
525 |
|
|
***************************************************************************/ |
526 |
|
|
|
527 |
|
|
void usage(){ |
528 |
|
|
(void)fprintf(stderr, |
529 |
|
|
"The proper usage is: %s [options] <xyz_file>\n" |
530 |
|
|
"\n" |
531 |
|
|
"Options:\n" |
532 |
|
|
"\n" |
533 |
|
|
" -o <prefix> the output file prefix\n" |
534 |
|
|
" -H generate a pov-ray header file\n" |
535 |
|
|
" -i <#> number of frames to interpolate\n" |
536 |
|
|
" -h draw hydrogens\n" |
537 |
|
|
" -b draw bonds\n" |
538 |
|
|
" -a draw atoms\n" |
539 |
mmeineke |
508 |
" -r regenerate bond\n" |
540 |
mmeineke |
60 |
"\n", |
541 |
|
|
program_name); |
542 |
|
|
exit(8); |
543 |
|
|
} |