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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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mmeineke |
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double boxX, boxY, boxZ; |
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mmeineke |
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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 |
515 |
int draw_box = 0; // boolean to draw the periodic Box |
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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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mmeineke |
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int startFrame = 1; |
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int endFrame; |
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int span = 0; |
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int currentCount = 0; |
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int haveEnd = 0; |
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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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mmeineke |
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mmeineke |
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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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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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mmeineke |
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case 'f': |
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// -f <#> => frame to render |
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i++; |
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startFrame = atoi( argv[i] ); |
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endFrame = startFrame; |
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haveEnd = 1; |
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done = 1; |
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break; |
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case 's': |
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// -s <#> => frame to start |
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i++; |
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startFrame = atoi( argv[i] ); |
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done = 1; |
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break; |
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case 'e': |
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// -e <#> => frame to end |
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i++; |
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endFrame = atoi( argv[i] ); |
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haveEnd = 1; |
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done = 1; |
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break; |
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mmeineke |
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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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case 'p': |
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// -r => draw periodic box |
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draw_box = 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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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 |
60 |
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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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mmeineke |
515 |
if( haveEnd ) span = endFrame - startFrame; |
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done = 0; |
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if( span < 0 ) done = 1; |
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while( (eof_test != NULL) && !done ){ |
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mmeineke |
60 |
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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); |
295 |
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if(eof_test == NULL){ |
296 |
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printf("error in reading file\n"); |
297 |
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exit(8); |
298 |
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} |
299 |
mmeineke |
515 |
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// unless we need to get the box size |
301 |
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302 |
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if( draw_box ){ |
303 |
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foo = strtok(read_buffer, " ,;\t"); |
304 |
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if(foo == NULL){ |
305 |
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printf("error in reading file\n"); |
306 |
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exit(8); |
307 |
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} |
308 |
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309 |
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foo = strtok(NULL, " ,;\t"); |
310 |
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if(foo == NULL){ |
311 |
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printf("error in reading file\n"); |
312 |
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exit(8); |
313 |
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} |
314 |
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current_frame->boxX = atof( foo ); |
315 |
mmeineke |
60 |
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316 |
mmeineke |
515 |
foo = strtok(NULL, " ,;\t"); |
317 |
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if(foo == NULL){ |
318 |
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printf("error in reading file\n"); |
319 |
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exit(8); |
320 |
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} |
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current_frame->boxY = atof( foo ); |
322 |
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323 |
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foo = strtok(NULL, " ,;\t"); |
324 |
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if(foo == NULL){ |
325 |
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printf("error in reading file\n"); |
326 |
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exit(8); |
327 |
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} |
328 |
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current_frame->boxZ = atof( foo ); |
329 |
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} |
330 |
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mmeineke |
60 |
for( i=0; i < n_atoms; i++){ |
332 |
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333 |
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eof_test = fgets(read_buffer, sizeof(read_buffer), in_file); |
334 |
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if(eof_test == NULL){ |
335 |
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printf("error in reading file\n"); |
336 |
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exit(8); |
337 |
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} |
338 |
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339 |
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foo = strtok(read_buffer, " ,;\t"); |
340 |
mmeineke |
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if(foo == NULL){ |
341 |
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printf("error in reading file\n"); |
342 |
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exit(8); |
343 |
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} |
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mmeineke |
60 |
(void)strcpy(current_frame->r[i].name, foo); /*copy the atom name */ |
345 |
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346 |
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/* next we grab the positions */ |
347 |
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348 |
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foo = strtok(NULL, " ,;\t"); |
349 |
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if(foo == NULL){ |
350 |
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printf("error in reading file\n"); |
351 |
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exit(8); |
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} |
353 |
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(void)sscanf(foo, "%lf",¤t_frame->r[i].x); |
354 |
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if(current_frame->r[i].x > big_x) big_x = current_frame->r[i].x; |
355 |
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if(current_frame->r[i].x < small_x) small_x = current_frame->r[i].x; |
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357 |
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358 |
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foo = strtok(NULL, " ,;\t"); |
359 |
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if(foo == NULL){ |
360 |
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printf("error in reading file\n"); |
361 |
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exit(8); |
362 |
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} |
363 |
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(void)sscanf(foo, "%lf", ¤t_frame->r[i].y); |
364 |
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if(current_frame->r[i].y > big_y) big_y = current_frame->r[i].y; |
365 |
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if(current_frame->r[i].y < small_y) small_y = current_frame->r[i].y; |
366 |
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367 |
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368 |
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foo = strtok(NULL, " ,;\t"); |
369 |
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if(foo == NULL){ |
370 |
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printf("error in reading file\n"); |
371 |
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exit(8); |
372 |
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} |
373 |
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(void)sscanf(foo, "%lf", ¤t_frame->r[i].z); |
374 |
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if(current_frame->r[i].z > big_z) big_z = current_frame->r[i].z; |
375 |
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if(current_frame->r[i].z < small_z) small_z = current_frame->r[i].z; |
376 |
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377 |
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} |
378 |
mmeineke |
515 |
currentCount++; |
379 |
mmeineke |
60 |
|
380 |
mmeineke |
515 |
|
381 |
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if( currentCount >= startFrame ){ |
382 |
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if(n_interpolate && current_frame->next != NULL){ |
383 |
mmeineke |
60 |
|
384 |
mmeineke |
515 |
temp_frame = current_frame->next; |
385 |
mmeineke |
60 |
|
386 |
mmeineke |
515 |
for(i = 0; i < n_interpolate; i++){ |
387 |
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388 |
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/* open the new output file */ |
389 |
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390 |
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sprintf(out_name, out_format, currentCount ); |
391 |
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out_file = fopen(out_name, "w"); |
392 |
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currentCount++; |
393 |
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if(out_file == NULL){ |
394 |
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printf("error opening output file: %s\n", out_name); |
395 |
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exit(8); |
396 |
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} |
397 |
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(void)fprintf(out_file, |
398 |
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"// The following script was automatically generated by:\n" |
399 |
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"// xyz2pov Copyright 2001 by MATTHEW A. MEINEKE\n" |
400 |
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"\n" |
401 |
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"#include \"pov_header.pov\"\n" |
402 |
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"\n"); |
403 |
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if( draw_box ){ |
404 |
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dx = current_frame->boxX - temp_frame->boxX; |
405 |
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dy = current_frame->boxY - temp_frame->boxY; |
406 |
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dz = current_frame->boxZ - temp_frame->boxZ; |
407 |
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408 |
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dx /= (double)(n_interpolate + 1); |
409 |
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dy /= (double)(n_interpolate + 1); |
410 |
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dz /= (double)(n_interpolate + 1); |
411 |
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412 |
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fprintf( out_file, |
413 |
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"makePeriodicBox( %lf, %lf, %lf )\n" |
414 |
|
|
"\n", |
415 |
|
|
temp_frame->boxX + dx * (i+1), |
416 |
|
|
temp_frame->boxZ + dz * (i+1), |
417 |
|
|
temp_frame->boxY + dy * (i+1) ); |
418 |
|
|
} |
419 |
|
|
|
420 |
|
|
|
421 |
|
|
out_coords = |
422 |
|
|
(struct coords *)calloc(n_atoms, sizeof(struct coords)); |
423 |
|
|
|
424 |
|
|
for(j=0; j < n_atoms; j++){ |
425 |
|
|
dx = current_frame->r[j].x - temp_frame->r[j].x; |
426 |
|
|
dy = current_frame->r[j].y - temp_frame->r[j].y; |
427 |
|
|
dz = current_frame->r[j].z - temp_frame->r[j].z; |
428 |
|
|
|
429 |
|
|
dx /= (double)(n_interpolate + 1); |
430 |
|
|
dy /= (double)(n_interpolate + 1); |
431 |
|
|
dz /= (double)(n_interpolate + 1); |
432 |
|
|
|
433 |
|
|
strcpy(out_coords[j].name, temp_frame->r[j].name); |
434 |
|
|
out_coords[j].x = temp_frame->r[j].x + dx * (i+1); |
435 |
|
|
out_coords[j].y = temp_frame->r[j].y + dy * (i+1); |
436 |
|
|
out_coords[j].z = temp_frame->r[j].z + dz * (i+1); |
437 |
|
|
} |
438 |
|
|
|
439 |
|
|
pov_write(out_file, out_coords, n_atoms, draw_hydrogens, draw_bonds, |
440 |
|
|
draw_atoms); |
441 |
|
|
free(out_coords); |
442 |
|
|
(void)fclose(out_file); |
443 |
mmeineke |
60 |
} |
444 |
mmeineke |
515 |
} |
445 |
|
|
|
446 |
|
|
/* open the new output file */ |
447 |
|
|
|
448 |
|
|
sprintf(out_name, out_format, currentCount ); |
449 |
|
|
out_file = fopen(out_name, "w"); |
450 |
|
|
if(out_file == NULL){ |
451 |
|
|
printf("error opening output file: %s\n", out_name); |
452 |
|
|
exit(8); |
453 |
|
|
} |
454 |
|
|
(void)fprintf(out_file, |
455 |
|
|
"// The following script was automatically generated by:\n" |
456 |
|
|
"// xyz2pov Copyright 2001 by MATTHEW A. MEINEKE\n" |
457 |
|
|
"\n" |
458 |
|
|
"#include \"pov_header.pov\"\n" |
459 |
|
|
"\n"); |
460 |
|
|
|
461 |
|
|
if( draw_box ){ |
462 |
mmeineke |
60 |
|
463 |
mmeineke |
515 |
fprintf( out_file, |
464 |
|
|
"makePeriodicBox( %lf, %lf, %lf )\n" |
465 |
|
|
"\n", |
466 |
|
|
current_frame->boxX, |
467 |
|
|
current_frame->boxZ, |
468 |
|
|
current_frame->boxY ); |
469 |
mmeineke |
60 |
} |
470 |
mmeineke |
515 |
|
471 |
|
|
|
472 |
|
|
|
473 |
|
|
out_coords = |
474 |
|
|
(struct coords *)calloc(n_atoms, sizeof(struct coords)); |
475 |
|
|
|
476 |
|
|
for(i = 0; i < n_atoms; i++){ |
477 |
|
|
strcpy(out_coords[i].name, current_frame->r[i].name); |
478 |
|
|
out_coords[i].x = current_frame->r[i].x; |
479 |
|
|
out_coords[i].y = current_frame->r[i].y; |
480 |
|
|
out_coords[i].z = current_frame->r[i].z; |
481 |
|
|
} |
482 |
|
|
pov_write(out_file, out_coords, n_atoms, draw_hydrogens, draw_bonds, |
483 |
|
|
draw_atoms); |
484 |
|
|
free(out_coords); |
485 |
|
|
|
486 |
|
|
(void)fclose(out_file); |
487 |
mmeineke |
60 |
} |
488 |
|
|
|
489 |
|
|
/*free up memory */ |
490 |
|
|
|
491 |
|
|
temp_frame = current_frame->next; |
492 |
|
|
current_frame->next = NULL; |
493 |
|
|
|
494 |
|
|
if(temp_frame != NULL){ |
495 |
|
|
|
496 |
|
|
free(temp_frame->r); |
497 |
|
|
free(temp_frame); |
498 |
|
|
} |
499 |
|
|
|
500 |
|
|
/* make a new frame */ |
501 |
|
|
|
502 |
|
|
temp_frame = (struct linked_xyz *)malloc(sizeof(struct linked_xyz)); |
503 |
|
|
temp_frame->next = current_frame; |
504 |
|
|
current_frame = temp_frame; |
505 |
|
|
|
506 |
|
|
eof_test = fgets(read_buffer, sizeof(read_buffer), in_file); |
507 |
|
|
|
508 |
mmeineke |
515 |
if( haveEnd ){ |
509 |
|
|
if( currentCount >= (endFrame + n_interpolate * span) ) done = 1; |
510 |
|
|
} |
511 |
mmeineke |
60 |
} |
512 |
|
|
|
513 |
|
|
(void)fclose(in_file); |
514 |
|
|
|
515 |
|
|
|
516 |
|
|
if(generate_header){ |
517 |
|
|
|
518 |
|
|
dx = big_x - small_x; |
519 |
|
|
dy = big_y - small_y; |
520 |
|
|
dz = big_z - small_z; |
521 |
|
|
|
522 |
|
|
rsqr = dx * dx + dy * dy + dz * dz; |
523 |
|
|
diagonal = sqrt(rsqr); |
524 |
|
|
diagonal *= 0.5; |
525 |
|
|
|
526 |
mmeineke |
515 |
// calculate the center |
527 |
|
|
|
528 |
|
|
dx = big_x + small_x; |
529 |
|
|
dy = big_y + small_y; |
530 |
|
|
dz = big_z + small_z; |
531 |
|
|
|
532 |
mmeineke |
60 |
dx /= 2.0; |
533 |
|
|
dy /= 2.0; |
534 |
|
|
dz /= 2.0; |
535 |
mmeineke |
515 |
|
536 |
mmeineke |
60 |
|
537 |
|
|
/*note the y and z axis is exchanged for the different coordinate |
538 |
|
|
system in pov-ray*/ |
539 |
|
|
|
540 |
|
|
|
541 |
|
|
out_file = fopen("pov_header.pov", "w"); |
542 |
|
|
|
543 |
|
|
fprintf(out_file, |
544 |
|
|
"// The following script was automatically generated by:\n" |
545 |
|
|
"// xyz2pov Copyright 2001 by MATTHEW A. MEINEKE\n" |
546 |
|
|
"\n" |
547 |
|
|
"\n" |
548 |
|
|
"background { rgb <1.0, 1.0, 1.0> }\n" |
549 |
|
|
"\n" |
550 |
|
|
"\n" |
551 |
|
|
); |
552 |
|
|
|
553 |
|
|
fprintf(out_file, |
554 |
|
|
"//******************************************************\n" |
555 |
|
|
"// Declare the resolution, camera, and light sources.\n" |
556 |
|
|
"//******************************************************\n" |
557 |
|
|
"\n" |
558 |
|
|
"// NOTE: if you plan to render at a different resoltion,\n" |
559 |
|
|
"// be sure to update the following two lines to maintain\n" |
560 |
|
|
"// the correct aspect ratio.\n" |
561 |
|
|
"\n" |
562 |
|
|
"#declare Width = 640.0;\n" |
563 |
|
|
"#declare Height = 480.0;\n" |
564 |
|
|
"#declare Ratio = Width / Height;\n" |
565 |
|
|
"\n" |
566 |
|
|
"#declare ATOM_SPHERE_FACTOR = 0.2;\n" |
567 |
|
|
"#declare BOND_RADIUS = 0.1;\n" |
568 |
|
|
"\n" |
569 |
mmeineke |
515 |
"// declare camera, light, and system variables\n" |
570 |
|
|
"\n" |
571 |
|
|
"#declare sysCenterX = %lf;\n" |
572 |
|
|
"#declare sysCenterY = %lf;\n" |
573 |
|
|
"#declare sysCenterZ = %lf;\n" |
574 |
|
|
"\n" |
575 |
|
|
"#declare zoom = %lf;\n" |
576 |
|
|
"\n", |
577 |
|
|
dx, dz, dy, |
578 |
|
|
diagonal ); |
579 |
|
|
|
580 |
|
|
fprintf(out_file, |
581 |
|
|
"#declare cameraLookX = sysCenterX;\n" |
582 |
|
|
"#declare cameraLookY = sysCenterY;\n" |
583 |
|
|
"#declare cameraLookZ = sysCenterZ;\n" |
584 |
|
|
"\n" |
585 |
|
|
"#declare cameraX = cameraLookX;\n" |
586 |
|
|
"#declare cameraY = cameraLookY;\n" |
587 |
|
|
"#declare cameraZ = cameraLookZ - zoom;\n" |
588 |
|
|
"\n" |
589 |
|
|
"#declare lightAx = cameraX;\n" |
590 |
|
|
"#declare lightAy = cameraY;\n" |
591 |
|
|
"#declare lightAz = cameraZ;\n" |
592 |
|
|
"\n" |
593 |
|
|
"#declare lightBx = cameraX - zoom;\n" |
594 |
|
|
"#declare lightBy = cameraY + zoom;\n" |
595 |
|
|
"#declare lightBz = cameraZ;\n" |
596 |
|
|
"\n" |
597 |
|
|
"#declare boxCenterX = cameraLookX;\n" |
598 |
|
|
"#declare boxCenterY = cameraLookY;\n" |
599 |
|
|
"#declare boxCenterZ = cameraLookZ;\n" |
600 |
|
|
"\n" |
601 |
|
|
"// declare the cameras and the light sources\n" |
602 |
|
|
"\n" |
603 |
mmeineke |
60 |
"camera{\n" |
604 |
mmeineke |
515 |
" location < cameraX, cameraY, cameraZ>\n" |
605 |
mmeineke |
60 |
" right < Ratio , 0, 0>\n" |
606 |
mmeineke |
515 |
" look_at < cameraLookX, cameraLookY, cameraLookZ >\n" |
607 |
mmeineke |
60 |
"}\n" |
608 |
mmeineke |
515 |
"\n" |
609 |
mmeineke |
60 |
"light_source{\n" |
610 |
mmeineke |
515 |
" < lightAx, lightAy, lightAz >\n" |
611 |
|
|
" rgb < 1.0, 1.0, 1.0 > }\n" |
612 |
|
|
"\n" |
613 |
mmeineke |
60 |
"light_source{\n" |
614 |
mmeineke |
515 |
" < lightBx, lightBy, lightBz >\n" |
615 |
mmeineke |
60 |
" rgb < 1.0, 1.0, 1.0 > }\n" |
616 |
|
|
"\n" |
617 |
mmeineke |
515 |
"\n" |
618 |
mmeineke |
60 |
"//************************************************************\n" |
619 |
|
|
"// Set whether or not to rotate the system.\n" |
620 |
|
|
"//\n" |
621 |
|
|
"// To Rotate, set ROTATE to 1.0 (true),\n" |
622 |
|
|
"// Then set the Euler Angles PHI, THETA, and PSI in degrees.\n" |
623 |
|
|
"//************************************************************\n" |
624 |
|
|
"\n" |
625 |
|
|
"#declare ROTATE = 0.0;\n" |
626 |
|
|
"#declare PHI = 0.0;\n" |
627 |
|
|
"#declare THETA = 0.0;\n" |
628 |
|
|
"#declare PSI = 0.0;\n" |
629 |
|
|
"\n" |
630 |
|
|
"#if(ROTATE)\n" |
631 |
|
|
" #declare phi_r = radians(PHI);\n" |
632 |
|
|
" #declare theta_r = radians(THETA);\n" |
633 |
|
|
" #declare psi_r = radians(PSI);\n" |
634 |
|
|
"\n" |
635 |
|
|
" #declare A11 = cos(phi_r) * cos(psi_r) - sin(phi_r) * cos(theta_r) * sin(psi_r);\n" |
636 |
|
|
" #declare A12 = sin(phi_r) * cos(psi_r) + cos(phi_r) * cos(theta_r) * sin(psi_r);\n" |
637 |
|
|
" #declare A13 = sin(theta_r) * sin(psi_r);\n" |
638 |
|
|
"\n" |
639 |
|
|
" #declare A21 = -cos(phi_r) * sin(psi_r) - sin(phi_r) * cos(theta_r) * cos(psi_r);\n" |
640 |
|
|
" #declare A22 = -sin(phi_r) * sin(psi_r) + cos(phi_r) * cos(theta_r) * cos(psi_r);\n" |
641 |
|
|
" #declare A23 = sin(theta_r) * cos(psi_r);\n" |
642 |
|
|
"\n" |
643 |
|
|
" #declare A31 = sin(phi_r) * sin(theta_r);\n" |
644 |
|
|
" #declare A32 = -cos(phi_r) * sin(theta_r);\n" |
645 |
|
|
" #declare A33 = cos(theta_r);\n" |
646 |
|
|
"\n" |
647 |
|
|
"#end\n" |
648 |
mmeineke |
515 |
"\n" |
649 |
|
|
"\n" |
650 |
|
|
"//************************************************************\n" |
651 |
|
|
"// declare the periodic box macro\n" |
652 |
|
|
"//************************************************************\n" |
653 |
|
|
"\n" |
654 |
|
|
"#macro makePeriodicBox( lengthX, lengthY, lengthZ )\n" |
655 |
|
|
"\n" |
656 |
|
|
" #local addX = lengthX / 2.0;\n" |
657 |
|
|
" #local addY = lengthY / 2.0;\n" |
658 |
|
|
" #local addZ = lengthZ / 2.0;\n" |
659 |
|
|
"\n" |
660 |
|
|
" #local colorR = 0.90;\n" |
661 |
|
|
" #local colorG = 0.91;\n" |
662 |
|
|
" #local colorB = 0.98;\n" |
663 |
|
|
"\n" |
664 |
|
|
" #local pipeWidth = 0.4;\n" |
665 |
|
|
"\n" |
666 |
|
|
" // 1\n" |
667 |
|
|
" cylinder{\n" |
668 |
|
|
" < boxCenterX-addX, boxCenterY-addY, boxCenterZ-addZ >,\n" |
669 |
|
|
" < boxCenterX-addX, boxCenterY+addY, boxCenterZ-addZ >,\n" |
670 |
|
|
" pipeWidth\n" |
671 |
|
|
" texture{\n" |
672 |
|
|
" pigment{ rgb < colorR, colorG, colorB > }\n" |
673 |
|
|
" finish{\n" |
674 |
|
|
" ambient .2\n" |
675 |
|
|
" diffuse .6\n" |
676 |
|
|
" specular 1\n" |
677 |
|
|
" roughness .001\n" |
678 |
|
|
" metallic\n" |
679 |
|
|
" }\n" |
680 |
|
|
" }\n" |
681 |
|
|
" }\n" |
682 |
|
|
"\n" |
683 |
|
|
" // 2\n" |
684 |
|
|
" cylinder{\n" |
685 |
|
|
" < boxCenterX-addX, boxCenterY-addY, boxCenterZ+addZ >,\n" |
686 |
|
|
" < boxCenterX-addX, boxCenterY+addY, boxCenterZ+addZ >,\n" |
687 |
|
|
" pipeWidth\n" |
688 |
|
|
" texture{\n" |
689 |
|
|
" pigment{ rgb < colorR, colorG, colorB > }\n" |
690 |
|
|
" finish{\n" |
691 |
|
|
" ambient .2\n" |
692 |
|
|
" diffuse .6\n" |
693 |
|
|
" specular 1\n" |
694 |
|
|
" roughness .001\n" |
695 |
|
|
" metallic\n" |
696 |
|
|
" }\n" |
697 |
|
|
" }\n" |
698 |
|
|
" }\n" |
699 |
|
|
"\n" |
700 |
|
|
" // 3\n" |
701 |
|
|
" cylinder{\n" |
702 |
|
|
" < boxCenterX+addX, boxCenterY-addY, boxCenterZ-addZ >,\n" |
703 |
|
|
" < boxCenterX+addX, boxCenterY+addY, boxCenterZ-addZ >,\n" |
704 |
|
|
" pipeWidth\n" |
705 |
|
|
" texture{\n" |
706 |
|
|
" pigment{ rgb < colorR, colorG, colorB > }\n" |
707 |
|
|
" finish{\n" |
708 |
|
|
" ambient .2\n" |
709 |
|
|
" diffuse .6\n" |
710 |
|
|
" specular 1\n" |
711 |
|
|
" roughness .001\n" |
712 |
|
|
" metallic\n" |
713 |
|
|
" }\n" |
714 |
|
|
" }\n" |
715 |
|
|
" }\n" |
716 |
|
|
"\n" |
717 |
|
|
" // 4\n" |
718 |
|
|
" cylinder{\n" |
719 |
|
|
" < boxCenterX+addX, boxCenterY-addY, boxCenterZ+addZ >,\n" |
720 |
|
|
" < boxCenterX+addX, boxCenterY+addY, boxCenterZ+addZ >,\n" |
721 |
|
|
" pipeWidth\n" |
722 |
|
|
" texture{\n" |
723 |
|
|
" pigment{ rgb < colorR, colorG, colorB > }\n" |
724 |
|
|
" finish{\n" |
725 |
|
|
" ambient .2\n" |
726 |
|
|
" diffuse .6\n" |
727 |
|
|
" specular 1\n" |
728 |
|
|
" roughness .001\n" |
729 |
|
|
" metallic\n" |
730 |
|
|
" }\n" |
731 |
|
|
" }\n" |
732 |
|
|
" }\n" |
733 |
|
|
"\n" |
734 |
|
|
" // 5\n" |
735 |
|
|
" cylinder{\n" |
736 |
|
|
" < boxCenterX-addX, boxCenterY-addY, boxCenterZ-addZ >,\n" |
737 |
|
|
" < boxCenterX-addX, boxCenterY-addY, boxCenterZ+addZ >,\n" |
738 |
|
|
" pipeWidth\n" |
739 |
|
|
" texture{\n" |
740 |
|
|
" pigment{ rgb < colorR, colorG, colorB > }\n" |
741 |
|
|
" finish{\n" |
742 |
|
|
" ambient .2\n" |
743 |
|
|
" diffuse .6\n" |
744 |
|
|
" specular 1\n" |
745 |
|
|
" roughness .001\n" |
746 |
|
|
" metallic\n" |
747 |
|
|
" }\n" |
748 |
|
|
" }\n" |
749 |
|
|
" }\n" |
750 |
|
|
"\n" |
751 |
|
|
" // 6\n" |
752 |
|
|
" cylinder{\n" |
753 |
|
|
" < boxCenterX-addX, boxCenterY-addY, boxCenterZ+addZ >,\n" |
754 |
|
|
" < boxCenterX+addX, boxCenterY-addY, boxCenterZ+addZ >,\n" |
755 |
|
|
" pipeWidth\n" |
756 |
|
|
" texture{\n" |
757 |
|
|
" pigment{ rgb < colorR, colorG, colorB > }\n" |
758 |
|
|
" finish{\n" |
759 |
|
|
" ambient .2\n" |
760 |
|
|
" diffuse .6\n" |
761 |
|
|
" specular 1\n" |
762 |
|
|
" roughness .001\n" |
763 |
|
|
" metallic\n" |
764 |
|
|
" }\n" |
765 |
|
|
" }\n" |
766 |
|
|
" }\n" |
767 |
|
|
"\n" |
768 |
|
|
" // 7\n" |
769 |
|
|
" cylinder{\n" |
770 |
|
|
" < boxCenterX+addX, boxCenterY-addY, boxCenterZ+addZ >,\n" |
771 |
|
|
" < boxCenterX+addX, boxCenterY-addY, boxCenterZ-addZ >,\n" |
772 |
|
|
" pipeWidth\n" |
773 |
|
|
" texture{\n" |
774 |
|
|
" pigment{ rgb < colorR, colorG, colorB > }\n" |
775 |
|
|
" finish{\n" |
776 |
|
|
" ambient .2\n" |
777 |
|
|
" diffuse .6\n" |
778 |
|
|
" specular 1\n" |
779 |
|
|
" roughness .001\n" |
780 |
|
|
" metallic\n" |
781 |
|
|
" }\n" |
782 |
|
|
" }\n" |
783 |
|
|
" }\n" |
784 |
|
|
"\n" |
785 |
|
|
" // 8\n" |
786 |
|
|
" cylinder{\n" |
787 |
|
|
" < boxCenterX+addX, boxCenterY-addY, boxCenterZ-addZ >,\n" |
788 |
|
|
" < boxCenterX-addX, boxCenterY-addY, boxCenterZ-addZ >,\n" |
789 |
|
|
" pipeWidth\n" |
790 |
|
|
" texture{\n" |
791 |
|
|
" pigment{ rgb < colorR, colorG, colorB > }\n" |
792 |
|
|
" finish{\n" |
793 |
|
|
" ambient .2\n" |
794 |
|
|
" diffuse .6\n" |
795 |
|
|
" specular 1\n" |
796 |
|
|
" roughness .001\n" |
797 |
|
|
" metallic\n" |
798 |
|
|
" }\n" |
799 |
|
|
" }\n" |
800 |
|
|
" }\n" |
801 |
|
|
"\n" |
802 |
|
|
" // 9\n" |
803 |
|
|
" cylinder{\n" |
804 |
|
|
" < boxCenterX-addX, boxCenterY+addY, boxCenterZ-addZ >,\n" |
805 |
|
|
" < boxCenterX-addX, boxCenterY+addY, boxCenterZ+addZ >,\n" |
806 |
|
|
" pipeWidth\n" |
807 |
|
|
" texture{\n" |
808 |
|
|
" pigment{ rgb < colorR, colorG, colorB > }\n" |
809 |
|
|
" finish{\n" |
810 |
|
|
" ambient .2\n" |
811 |
|
|
" diffuse .6\n" |
812 |
|
|
" specular 1\n" |
813 |
|
|
" roughness .001\n" |
814 |
|
|
" metallic\n" |
815 |
|
|
" }\n" |
816 |
|
|
" }\n" |
817 |
|
|
" }\n" |
818 |
|
|
"\n" |
819 |
|
|
" // 10\n" |
820 |
|
|
" cylinder{\n" |
821 |
|
|
" < boxCenterX-addX, boxCenterY+addY, boxCenterZ+addZ >,\n" |
822 |
|
|
" < boxCenterX+addX, boxCenterY+addY, boxCenterZ+addZ >,\n" |
823 |
|
|
" pipeWidth\n" |
824 |
|
|
" texture{\n" |
825 |
|
|
" pigment{ rgb < colorR, colorG, colorB > }\n" |
826 |
|
|
" finish{\n" |
827 |
|
|
" ambient .2\n" |
828 |
|
|
" diffuse .6\n" |
829 |
|
|
" specular 1\n" |
830 |
|
|
" roughness .001\n" |
831 |
|
|
" metallic\n" |
832 |
|
|
" }\n" |
833 |
|
|
" }\n" |
834 |
|
|
" }\n" |
835 |
|
|
"\n" |
836 |
|
|
" // 11\n" |
837 |
|
|
" cylinder{\n" |
838 |
|
|
" < boxCenterX+addX, boxCenterY+addY, boxCenterZ+addZ >,\n" |
839 |
|
|
" < boxCenterX+addX, boxCenterY+addY, boxCenterZ-addZ >,\n" |
840 |
|
|
" pipeWidth\n" |
841 |
|
|
" texture{\n" |
842 |
|
|
" pigment{ rgb < colorR, colorG, colorB > }\n" |
843 |
|
|
" finish{\n" |
844 |
|
|
" ambient .2\n" |
845 |
|
|
" diffuse .6\n" |
846 |
|
|
" specular 1\n" |
847 |
|
|
" roughness .001\n" |
848 |
|
|
" metallic\n" |
849 |
|
|
" }\n" |
850 |
|
|
" }\n" |
851 |
|
|
" }\n" |
852 |
|
|
"\n" |
853 |
|
|
" // 12\n" |
854 |
|
|
" cylinder{\n" |
855 |
|
|
" < boxCenterX+addX, boxCenterY+addY, boxCenterZ-addZ >,\n" |
856 |
|
|
" < boxCenterX-addX, boxCenterY+addY, boxCenterZ-addZ >,\n" |
857 |
|
|
" pipeWidth\n" |
858 |
|
|
" texture{\n" |
859 |
|
|
" pigment{ rgb < colorR, colorG, colorB > }\n" |
860 |
|
|
" finish{\n" |
861 |
|
|
" ambient .2\n" |
862 |
|
|
" diffuse .6\n" |
863 |
|
|
" specular 1\n" |
864 |
|
|
" roughness .001\n" |
865 |
|
|
" metallic\n" |
866 |
|
|
" }\n" |
867 |
|
|
" }\n" |
868 |
|
|
" }\n" |
869 |
|
|
"\n" |
870 |
|
|
"#end\n" |
871 |
|
|
"\n" |
872 |
mmeineke |
60 |
"\n"); |
873 |
mmeineke |
515 |
|
874 |
|
|
|
875 |
|
|
|
876 |
|
|
|
877 |
mmeineke |
60 |
make_header_macros(out_file); |
878 |
|
|
|
879 |
|
|
fclose(out_file); |
880 |
|
|
} |
881 |
|
|
|
882 |
|
|
return 0; |
883 |
|
|
|
884 |
|
|
} |
885 |
|
|
|
886 |
|
|
|
887 |
|
|
|
888 |
|
|
/*************************************************************************** |
889 |
|
|
* prints out the usage for the command line arguments, then exits. |
890 |
|
|
***************************************************************************/ |
891 |
|
|
|
892 |
|
|
void usage(){ |
893 |
|
|
(void)fprintf(stderr, |
894 |
|
|
"The proper usage is: %s [options] <xyz_file>\n" |
895 |
|
|
"\n" |
896 |
|
|
"Options:\n" |
897 |
|
|
"\n" |
898 |
|
|
" -o <prefix> the output file prefix\n" |
899 |
|
|
" -H generate a pov-ray header file\n" |
900 |
|
|
" -i <#> number of frames to interpolate\n" |
901 |
|
|
" -h draw hydrogens\n" |
902 |
|
|
" -b draw bonds\n" |
903 |
|
|
" -a draw atoms\n" |
904 |
mmeineke |
515 |
" -p draw periodic box\n" |
905 |
mmeineke |
508 |
" -r regenerate bond\n" |
906 |
mmeineke |
515 |
" -f <#> render frame <#> only\n" |
907 |
|
|
" -s <#> begin at frame <#> (inclusive)\n" |
908 |
|
|
" -e <#> end at frame <#> (inclusive)\n" |
909 |
mmeineke |
60 |
"\n", |
910 |
|
|
program_name); |
911 |
|
|
exit(8); |
912 |
|
|
} |