1 |
mmeineke |
60 |
#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 |
508 |
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mmeineke |
60 |
struct linked_xyz{ |
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struct coords *r; |
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gezelter |
625 |
double Hmat[3][3]; |
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mmeineke |
60 |
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 |
508 |
int regenerateBonds = 0; // boolean to regenearate bonds each frame |
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mmeineke |
60 |
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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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gezelter |
625 |
int i,j,k; /* loop counters */ |
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mmeineke |
60 |
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 |
515 |
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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mmeineke |
60 |
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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gezelter |
625 |
double dm[3][3]; |
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mmeineke |
515 |
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mmeineke |
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|
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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 |
60 |
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 |
515 |
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 |
60 |
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 |
508 |
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 |
515 |
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 |
60 |
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 |
508 |
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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270 |
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if(!have_prefix){ |
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out_prefix = strtok(in_name, "."); |
272 |
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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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278 |
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eof_test = fgets(read_buffer, sizeof(read_buffer), in_file); |
279 |
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280 |
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current_frame = (struct linked_xyz *)malloc(sizeof(struct linked_xyz)); |
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current_frame->next = NULL; |
282 |
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283 |
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mmeineke |
515 |
if( haveEnd ) span = endFrame - startFrame; |
285 |
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done = 0; |
286 |
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if( span < 0 ) done = 1; |
287 |
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while( (eof_test != NULL) && !done ){ |
288 |
mmeineke |
60 |
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289 |
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(void)sscanf(read_buffer, "%d", &n_atoms); |
290 |
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current_frame->r = |
291 |
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(struct coords *)calloc(n_atoms, sizeof(struct coords)); |
292 |
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293 |
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/*read and toss the comment line */ |
294 |
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eof_test = fgets(read_buffer, sizeof(read_buffer), in_file); |
296 |
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if(eof_test == NULL){ |
297 |
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printf("error in reading file\n"); |
298 |
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exit(8); |
299 |
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} |
300 |
mmeineke |
515 |
|
301 |
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// unless we need to get the box size |
302 |
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303 |
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if( draw_box ){ |
304 |
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foo = strtok(read_buffer, " ,;\t"); |
305 |
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if(foo == NULL){ |
306 |
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printf("error in reading file\n"); |
307 |
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exit(8); |
308 |
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} |
309 |
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310 |
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foo = strtok(NULL, " ,;\t"); |
311 |
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if(foo == NULL){ |
312 |
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printf("error in reading file\n"); |
313 |
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exit(8); |
314 |
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} |
315 |
gezelter |
625 |
current_frame->Hmat[0][0] = atof( foo ); |
316 |
mmeineke |
60 |
|
317 |
mmeineke |
515 |
foo = strtok(NULL, " ,;\t"); |
318 |
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if(foo == NULL){ |
319 |
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printf("error in reading file\n"); |
320 |
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exit(8); |
321 |
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} |
322 |
gezelter |
625 |
current_frame->Hmat[1][0] = atof( foo ); |
323 |
mmeineke |
515 |
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324 |
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foo = strtok(NULL, " ,;\t"); |
325 |
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if(foo == NULL){ |
326 |
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printf("error in reading file\n"); |
327 |
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exit(8); |
328 |
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} |
329 |
gezelter |
625 |
current_frame->Hmat[2][0] = atof( foo ); |
330 |
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331 |
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foo = strtok(NULL, " ,;\t"); |
332 |
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if(foo == NULL){ |
333 |
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printf("error in reading file\n"); |
334 |
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exit(8); |
335 |
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} |
336 |
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current_frame->Hmat[0][1] = atof( foo ); |
337 |
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338 |
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foo = strtok(NULL, " ,;\t"); |
339 |
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if(foo == NULL){ |
340 |
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printf("error in reading file\n"); |
341 |
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exit(8); |
342 |
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} |
343 |
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current_frame->Hmat[1][1] = atof( foo ); |
344 |
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345 |
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foo = strtok(NULL, " ,;\t"); |
346 |
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if(foo == NULL){ |
347 |
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printf("error in reading file\n"); |
348 |
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exit(8); |
349 |
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} |
350 |
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current_frame->Hmat[2][1] = atof( foo ); |
351 |
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352 |
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foo = strtok(NULL, " ,;\t"); |
353 |
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if(foo == NULL){ |
354 |
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printf("error in reading file\n"); |
355 |
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exit(8); |
356 |
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} |
357 |
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current_frame->Hmat[0][2] = atof( foo ); |
358 |
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359 |
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foo = strtok(NULL, " ,;\t"); |
360 |
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if(foo == NULL){ |
361 |
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printf("error in reading file\n"); |
362 |
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exit(8); |
363 |
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} |
364 |
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current_frame->Hmat[1][2] = atof( foo ); |
365 |
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366 |
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foo = strtok(NULL, " ,;\t"); |
367 |
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if(foo == NULL){ |
368 |
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printf("error in reading file\n"); |
369 |
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exit(8); |
370 |
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} |
371 |
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current_frame->Hmat[2][2] = atof( foo ); |
372 |
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373 |
mmeineke |
515 |
} |
374 |
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375 |
mmeineke |
60 |
for( i=0; i < n_atoms; i++){ |
376 |
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377 |
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eof_test = fgets(read_buffer, sizeof(read_buffer), in_file); |
378 |
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if(eof_test == NULL){ |
379 |
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printf("error in reading file\n"); |
380 |
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exit(8); |
381 |
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} |
382 |
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383 |
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foo = strtok(read_buffer, " ,;\t"); |
384 |
mmeineke |
515 |
if(foo == NULL){ |
385 |
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printf("error in reading file\n"); |
386 |
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exit(8); |
387 |
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} |
388 |
mmeineke |
60 |
(void)strcpy(current_frame->r[i].name, foo); /*copy the atom name */ |
389 |
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390 |
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/* next we grab the positions */ |
391 |
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392 |
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foo = strtok(NULL, " ,;\t"); |
393 |
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if(foo == NULL){ |
394 |
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printf("error in reading file\n"); |
395 |
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exit(8); |
396 |
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} |
397 |
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(void)sscanf(foo, "%lf",¤t_frame->r[i].x); |
398 |
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if(current_frame->r[i].x > big_x) big_x = current_frame->r[i].x; |
399 |
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if(current_frame->r[i].x < small_x) small_x = current_frame->r[i].x; |
400 |
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401 |
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402 |
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foo = strtok(NULL, " ,;\t"); |
403 |
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if(foo == NULL){ |
404 |
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printf("error in reading file\n"); |
405 |
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exit(8); |
406 |
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} |
407 |
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(void)sscanf(foo, "%lf", ¤t_frame->r[i].y); |
408 |
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if(current_frame->r[i].y > big_y) big_y = current_frame->r[i].y; |
409 |
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if(current_frame->r[i].y < small_y) small_y = current_frame->r[i].y; |
410 |
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411 |
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412 |
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foo = strtok(NULL, " ,;\t"); |
413 |
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if(foo == NULL){ |
414 |
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printf("error in reading file\n"); |
415 |
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exit(8); |
416 |
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} |
417 |
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(void)sscanf(foo, "%lf", ¤t_frame->r[i].z); |
418 |
|
|
if(current_frame->r[i].z > big_z) big_z = current_frame->r[i].z; |
419 |
|
|
if(current_frame->r[i].z < small_z) small_z = current_frame->r[i].z; |
420 |
|
|
|
421 |
|
|
} |
422 |
mmeineke |
515 |
currentCount++; |
423 |
mmeineke |
60 |
|
424 |
mmeineke |
515 |
|
425 |
|
|
if( currentCount >= startFrame ){ |
426 |
|
|
if(n_interpolate && current_frame->next != NULL){ |
427 |
mmeineke |
60 |
|
428 |
mmeineke |
515 |
temp_frame = current_frame->next; |
429 |
mmeineke |
60 |
|
430 |
mmeineke |
515 |
for(i = 0; i < n_interpolate; i++){ |
431 |
|
|
|
432 |
|
|
/* open the new output file */ |
433 |
|
|
|
434 |
|
|
sprintf(out_name, out_format, currentCount ); |
435 |
|
|
out_file = fopen(out_name, "w"); |
436 |
|
|
currentCount++; |
437 |
|
|
if(out_file == NULL){ |
438 |
|
|
printf("error opening output file: %s\n", out_name); |
439 |
|
|
exit(8); |
440 |
|
|
} |
441 |
|
|
(void)fprintf(out_file, |
442 |
|
|
"// The following script was automatically generated by:\n" |
443 |
|
|
"// xyz2pov Copyright 2001 by MATTHEW A. MEINEKE\n" |
444 |
|
|
"\n" |
445 |
|
|
"#include \"pov_header.pov\"\n" |
446 |
|
|
"\n"); |
447 |
|
|
if( draw_box ){ |
448 |
gezelter |
625 |
|
449 |
|
|
for (j = 0; j < 3; j++) { |
450 |
|
|
for (k = 0; k < 3; k++) { |
451 |
|
|
dm[j][k] = current_frame->Hmat[j][k] - temp_frame->Hmat[j][k]; |
452 |
|
|
dm[j][k] /= (double)(n_interpolate + 1); |
453 |
|
|
} |
454 |
|
|
} |
455 |
|
|
|
456 |
mmeineke |
515 |
fprintf( out_file, |
457 |
gezelter |
625 |
"makePeriodicBox( %lf, %lf, %lf, %lf, %lf, %lf, %lf, %lf, %lf)\n" |
458 |
mmeineke |
515 |
"\n", |
459 |
gezelter |
625 |
temp_frame->Hmat[0][0] + dm[0][0] * (i+1), |
460 |
|
|
temp_frame->Hmat[1][0] + dm[1][0] * (i+1), |
461 |
|
|
temp_frame->Hmat[2][0] + dm[2][0] * (i+1), |
462 |
|
|
temp_frame->Hmat[0][1] + dm[0][1] * (i+1), |
463 |
|
|
temp_frame->Hmat[1][1] + dm[1][1] * (i+1), |
464 |
|
|
temp_frame->Hmat[2][1] + dm[2][1] * (i+1), |
465 |
|
|
temp_frame->Hmat[0][2] + dm[0][2] * (i+1), |
466 |
|
|
temp_frame->Hmat[1][2] + dm[1][2] * (i+1), |
467 |
|
|
temp_frame->Hmat[2][2] + dm[2][2] * (i+1) ); |
468 |
mmeineke |
515 |
} |
469 |
|
|
|
470 |
|
|
|
471 |
|
|
out_coords = |
472 |
|
|
(struct coords *)calloc(n_atoms, sizeof(struct coords)); |
473 |
|
|
|
474 |
|
|
for(j=0; j < n_atoms; j++){ |
475 |
|
|
dx = current_frame->r[j].x - temp_frame->r[j].x; |
476 |
|
|
dy = current_frame->r[j].y - temp_frame->r[j].y; |
477 |
|
|
dz = current_frame->r[j].z - temp_frame->r[j].z; |
478 |
|
|
|
479 |
|
|
dx /= (double)(n_interpolate + 1); |
480 |
|
|
dy /= (double)(n_interpolate + 1); |
481 |
|
|
dz /= (double)(n_interpolate + 1); |
482 |
|
|
|
483 |
|
|
strcpy(out_coords[j].name, temp_frame->r[j].name); |
484 |
|
|
out_coords[j].x = temp_frame->r[j].x + dx * (i+1); |
485 |
|
|
out_coords[j].y = temp_frame->r[j].y + dy * (i+1); |
486 |
|
|
out_coords[j].z = temp_frame->r[j].z + dz * (i+1); |
487 |
|
|
} |
488 |
|
|
|
489 |
|
|
pov_write(out_file, out_coords, n_atoms, draw_hydrogens, draw_bonds, |
490 |
|
|
draw_atoms); |
491 |
|
|
free(out_coords); |
492 |
|
|
(void)fclose(out_file); |
493 |
mmeineke |
60 |
} |
494 |
mmeineke |
515 |
} |
495 |
|
|
|
496 |
|
|
/* open the new output file */ |
497 |
|
|
|
498 |
|
|
sprintf(out_name, out_format, currentCount ); |
499 |
|
|
out_file = fopen(out_name, "w"); |
500 |
|
|
if(out_file == NULL){ |
501 |
|
|
printf("error opening output file: %s\n", out_name); |
502 |
|
|
exit(8); |
503 |
|
|
} |
504 |
|
|
(void)fprintf(out_file, |
505 |
|
|
"// The following script was automatically generated by:\n" |
506 |
|
|
"// xyz2pov Copyright 2001 by MATTHEW A. MEINEKE\n" |
507 |
|
|
"\n" |
508 |
|
|
"#include \"pov_header.pov\"\n" |
509 |
|
|
"\n"); |
510 |
|
|
|
511 |
|
|
if( draw_box ){ |
512 |
mmeineke |
60 |
|
513 |
mmeineke |
515 |
fprintf( out_file, |
514 |
gezelter |
625 |
"makePeriodicBox( %lf, %lf, %lf, %lf, %lf, %lf, %lf, %lf %lf )\n" |
515 |
mmeineke |
515 |
"\n", |
516 |
gezelter |
625 |
current_frame->Hmat[0][0], |
517 |
|
|
current_frame->Hmat[1][0], |
518 |
|
|
current_frame->Hmat[2][0], |
519 |
|
|
current_frame->Hmat[0][1], |
520 |
|
|
current_frame->Hmat[1][1], |
521 |
|
|
current_frame->Hmat[2][1], |
522 |
|
|
current_frame->Hmat[0][2], |
523 |
|
|
current_frame->Hmat[1][2], |
524 |
|
|
current_frame->Hmat[2][2] ); |
525 |
mmeineke |
60 |
} |
526 |
mmeineke |
515 |
|
527 |
|
|
|
528 |
|
|
|
529 |
|
|
out_coords = |
530 |
|
|
(struct coords *)calloc(n_atoms, sizeof(struct coords)); |
531 |
|
|
|
532 |
|
|
for(i = 0; i < n_atoms; i++){ |
533 |
|
|
strcpy(out_coords[i].name, current_frame->r[i].name); |
534 |
|
|
out_coords[i].x = current_frame->r[i].x; |
535 |
|
|
out_coords[i].y = current_frame->r[i].y; |
536 |
|
|
out_coords[i].z = current_frame->r[i].z; |
537 |
|
|
} |
538 |
|
|
pov_write(out_file, out_coords, n_atoms, draw_hydrogens, draw_bonds, |
539 |
|
|
draw_atoms); |
540 |
|
|
free(out_coords); |
541 |
|
|
|
542 |
|
|
(void)fclose(out_file); |
543 |
mmeineke |
60 |
} |
544 |
|
|
|
545 |
|
|
/*free up memory */ |
546 |
|
|
|
547 |
|
|
temp_frame = current_frame->next; |
548 |
|
|
current_frame->next = NULL; |
549 |
|
|
|
550 |
|
|
if(temp_frame != NULL){ |
551 |
|
|
|
552 |
|
|
free(temp_frame->r); |
553 |
|
|
free(temp_frame); |
554 |
|
|
} |
555 |
|
|
|
556 |
|
|
/* make a new frame */ |
557 |
|
|
|
558 |
|
|
temp_frame = (struct linked_xyz *)malloc(sizeof(struct linked_xyz)); |
559 |
|
|
temp_frame->next = current_frame; |
560 |
|
|
current_frame = temp_frame; |
561 |
|
|
|
562 |
|
|
eof_test = fgets(read_buffer, sizeof(read_buffer), in_file); |
563 |
|
|
|
564 |
mmeineke |
515 |
if( haveEnd ){ |
565 |
|
|
if( currentCount >= (endFrame + n_interpolate * span) ) done = 1; |
566 |
|
|
} |
567 |
mmeineke |
60 |
} |
568 |
|
|
|
569 |
|
|
(void)fclose(in_file); |
570 |
|
|
|
571 |
|
|
|
572 |
|
|
if(generate_header){ |
573 |
|
|
|
574 |
|
|
dx = big_x - small_x; |
575 |
|
|
dy = big_y - small_y; |
576 |
|
|
dz = big_z - small_z; |
577 |
|
|
|
578 |
|
|
rsqr = dx * dx + dy * dy + dz * dz; |
579 |
|
|
diagonal = sqrt(rsqr); |
580 |
|
|
diagonal *= 0.5; |
581 |
|
|
|
582 |
mmeineke |
515 |
// calculate the center |
583 |
|
|
|
584 |
|
|
dx = big_x + small_x; |
585 |
|
|
dy = big_y + small_y; |
586 |
|
|
dz = big_z + small_z; |
587 |
|
|
|
588 |
mmeineke |
60 |
dx /= 2.0; |
589 |
|
|
dy /= 2.0; |
590 |
|
|
dz /= 2.0; |
591 |
mmeineke |
515 |
|
592 |
mmeineke |
60 |
|
593 |
|
|
/*note the y and z axis is exchanged for the different coordinate |
594 |
|
|
system in pov-ray*/ |
595 |
|
|
|
596 |
|
|
|
597 |
|
|
out_file = fopen("pov_header.pov", "w"); |
598 |
|
|
|
599 |
|
|
fprintf(out_file, |
600 |
|
|
"// The following script was automatically generated by:\n" |
601 |
|
|
"// xyz2pov Copyright 2001 by MATTHEW A. MEINEKE\n" |
602 |
|
|
"\n" |
603 |
|
|
"\n" |
604 |
|
|
"background { rgb <1.0, 1.0, 1.0> }\n" |
605 |
|
|
"\n" |
606 |
|
|
"\n" |
607 |
|
|
); |
608 |
|
|
|
609 |
|
|
fprintf(out_file, |
610 |
|
|
"//******************************************************\n" |
611 |
|
|
"// Declare the resolution, camera, and light sources.\n" |
612 |
|
|
"//******************************************************\n" |
613 |
|
|
"\n" |
614 |
|
|
"// NOTE: if you plan to render at a different resoltion,\n" |
615 |
|
|
"// be sure to update the following two lines to maintain\n" |
616 |
|
|
"// the correct aspect ratio.\n" |
617 |
|
|
"\n" |
618 |
|
|
"#declare Width = 640.0;\n" |
619 |
|
|
"#declare Height = 480.0;\n" |
620 |
|
|
"#declare Ratio = Width / Height;\n" |
621 |
|
|
"\n" |
622 |
|
|
"#declare ATOM_SPHERE_FACTOR = 0.2;\n" |
623 |
|
|
"#declare BOND_RADIUS = 0.1;\n" |
624 |
|
|
"\n" |
625 |
mmeineke |
515 |
"// declare camera, light, and system variables\n" |
626 |
|
|
"\n" |
627 |
|
|
"#declare sysCenterX = %lf;\n" |
628 |
|
|
"#declare sysCenterY = %lf;\n" |
629 |
|
|
"#declare sysCenterZ = %lf;\n" |
630 |
|
|
"\n" |
631 |
|
|
"#declare zoom = %lf;\n" |
632 |
|
|
"\n", |
633 |
|
|
dx, dz, dy, |
634 |
|
|
diagonal ); |
635 |
|
|
|
636 |
|
|
fprintf(out_file, |
637 |
|
|
"#declare cameraLookX = sysCenterX;\n" |
638 |
|
|
"#declare cameraLookY = sysCenterY;\n" |
639 |
|
|
"#declare cameraLookZ = sysCenterZ;\n" |
640 |
|
|
"\n" |
641 |
|
|
"#declare cameraX = cameraLookX;\n" |
642 |
|
|
"#declare cameraY = cameraLookY;\n" |
643 |
|
|
"#declare cameraZ = cameraLookZ - zoom;\n" |
644 |
|
|
"\n" |
645 |
|
|
"#declare lightAx = cameraX;\n" |
646 |
|
|
"#declare lightAy = cameraY;\n" |
647 |
|
|
"#declare lightAz = cameraZ;\n" |
648 |
|
|
"\n" |
649 |
|
|
"#declare lightBx = cameraX - zoom;\n" |
650 |
|
|
"#declare lightBy = cameraY + zoom;\n" |
651 |
|
|
"#declare lightBz = cameraZ;\n" |
652 |
|
|
"\n" |
653 |
|
|
"#declare boxCenterX = cameraLookX;\n" |
654 |
|
|
"#declare boxCenterY = cameraLookY;\n" |
655 |
|
|
"#declare boxCenterZ = cameraLookZ;\n" |
656 |
|
|
"\n" |
657 |
|
|
"// declare the cameras and the light sources\n" |
658 |
|
|
"\n" |
659 |
mmeineke |
60 |
"camera{\n" |
660 |
mmeineke |
515 |
" location < cameraX, cameraY, cameraZ>\n" |
661 |
mmeineke |
60 |
" right < Ratio , 0, 0>\n" |
662 |
mmeineke |
515 |
" look_at < cameraLookX, cameraLookY, cameraLookZ >\n" |
663 |
mmeineke |
60 |
"}\n" |
664 |
mmeineke |
515 |
"\n" |
665 |
mmeineke |
60 |
"light_source{\n" |
666 |
mmeineke |
515 |
" < lightAx, lightAy, lightAz >\n" |
667 |
|
|
" rgb < 1.0, 1.0, 1.0 > }\n" |
668 |
|
|
"\n" |
669 |
mmeineke |
60 |
"light_source{\n" |
670 |
mmeineke |
515 |
" < lightBx, lightBy, lightBz >\n" |
671 |
mmeineke |
60 |
" rgb < 1.0, 1.0, 1.0 > }\n" |
672 |
|
|
"\n" |
673 |
mmeineke |
515 |
"\n" |
674 |
mmeineke |
60 |
"//************************************************************\n" |
675 |
|
|
"// Set whether or not to rotate the system.\n" |
676 |
|
|
"//\n" |
677 |
|
|
"// To Rotate, set ROTATE to 1.0 (true),\n" |
678 |
|
|
"// Then set the Euler Angles PHI, THETA, and PSI in degrees.\n" |
679 |
|
|
"//************************************************************\n" |
680 |
|
|
"\n" |
681 |
|
|
"#declare ROTATE = 0.0;\n" |
682 |
|
|
"#declare PHI = 0.0;\n" |
683 |
|
|
"#declare THETA = 0.0;\n" |
684 |
|
|
"#declare PSI = 0.0;\n" |
685 |
|
|
"\n" |
686 |
|
|
"#if(ROTATE)\n" |
687 |
|
|
" #declare phi_r = radians(PHI);\n" |
688 |
|
|
" #declare theta_r = radians(THETA);\n" |
689 |
|
|
" #declare psi_r = radians(PSI);\n" |
690 |
|
|
"\n" |
691 |
|
|
" #declare A11 = cos(phi_r) * cos(psi_r) - sin(phi_r) * cos(theta_r) * sin(psi_r);\n" |
692 |
|
|
" #declare A12 = sin(phi_r) * cos(psi_r) + cos(phi_r) * cos(theta_r) * sin(psi_r);\n" |
693 |
|
|
" #declare A13 = sin(theta_r) * sin(psi_r);\n" |
694 |
|
|
"\n" |
695 |
|
|
" #declare A21 = -cos(phi_r) * sin(psi_r) - sin(phi_r) * cos(theta_r) * cos(psi_r);\n" |
696 |
|
|
" #declare A22 = -sin(phi_r) * sin(psi_r) + cos(phi_r) * cos(theta_r) * cos(psi_r);\n" |
697 |
|
|
" #declare A23 = sin(theta_r) * cos(psi_r);\n" |
698 |
|
|
"\n" |
699 |
|
|
" #declare A31 = sin(phi_r) * sin(theta_r);\n" |
700 |
|
|
" #declare A32 = -cos(phi_r) * sin(theta_r);\n" |
701 |
|
|
" #declare A33 = cos(theta_r);\n" |
702 |
|
|
"\n" |
703 |
|
|
"#end\n" |
704 |
mmeineke |
515 |
"\n" |
705 |
|
|
"\n" |
706 |
|
|
"//************************************************************\n" |
707 |
|
|
"// declare the periodic box macro\n" |
708 |
|
|
"//************************************************************\n" |
709 |
|
|
"\n" |
710 |
gezelter |
625 |
"#macro makePeriodicBox( bx1, by1, bz1, bx2, by2, bz2, bx3, by3, bz3 )\n" |
711 |
mmeineke |
515 |
"\n" |
712 |
gezelter |
625 |
" #local pAx = -boxCenterX;\n" |
713 |
|
|
" #local pAy = -boxCenterY;\n" |
714 |
|
|
" #local pAz = -boxCenterZ;\n" |
715 |
|
|
" #local pBx = bx1 - boxCenterX;\n" |
716 |
|
|
" #local pBy = by1 - boxCenterY;\n" |
717 |
|
|
" #local pBz = bz1 - boxCenterZ;\n" |
718 |
|
|
" #local pCx = bx2 - boxCenterX;\n" |
719 |
|
|
" #local pCy = by2 - boxCenterY;\n" |
720 |
|
|
" #local pCz = bz2 - boxCenterZ;\n" |
721 |
|
|
" #local pDx = bx3 - boxCenterX;\n" |
722 |
|
|
" #local pDy = by3 - boxCenterY;\n" |
723 |
|
|
" #local pDz = bz3 - boxCenterZ;\n" |
724 |
|
|
" #local pEx = bx1 + bx2 - boxCenterX;\n" |
725 |
|
|
" #local pEy = by1 + by2 - boxCenterY;\n" |
726 |
|
|
" #local pEz = bz1 + bz2 - boxCenterZ;\n" |
727 |
|
|
" #local pFx = bx1 + bx3 - boxCenterX;\n" |
728 |
|
|
" #local pFy = by1 + by3 - boxCenterY;\n" |
729 |
|
|
" #local pFz = bz1 + bz3 - boxCenterZ;\n" |
730 |
|
|
" #local pGx = bx2 + bx3 - boxCenterX;\n" |
731 |
|
|
" #local pGy = by2 + by3 - boxCenterY;\n" |
732 |
|
|
" #local pGz = bz2 + bz3 - boxCenterZ;\n" |
733 |
|
|
" #local pHx = bx1 + bx2 + bx3 - boxCenterX;\n" |
734 |
|
|
" #local pHy = by1 + by2 + by3 - boxCenterY;\n" |
735 |
|
|
" #local pHz = bz1 + bz2 + bz3 - boxCenterZ;\n" |
736 |
mmeineke |
515 |
"\n" |
737 |
|
|
" #local colorR = 0.90;\n" |
738 |
|
|
" #local colorG = 0.91;\n" |
739 |
|
|
" #local colorB = 0.98;\n" |
740 |
|
|
"\n" |
741 |
|
|
" #local pipeWidth = 0.4;\n" |
742 |
|
|
"\n" |
743 |
|
|
" // 1\n" |
744 |
|
|
" cylinder{\n" |
745 |
gezelter |
625 |
" < pAx, pAy, pAz >,\n" |
746 |
|
|
" < pBx, pBy, pBz >,\n" |
747 |
mmeineke |
515 |
" pipeWidth\n" |
748 |
|
|
" texture{\n" |
749 |
|
|
" pigment{ rgb < colorR, colorG, colorB > }\n" |
750 |
|
|
" finish{\n" |
751 |
|
|
" ambient .2\n" |
752 |
|
|
" diffuse .6\n" |
753 |
|
|
" specular 1\n" |
754 |
|
|
" roughness .001\n" |
755 |
|
|
" metallic\n" |
756 |
|
|
" }\n" |
757 |
|
|
" }\n" |
758 |
|
|
" }\n" |
759 |
|
|
"\n" |
760 |
|
|
" // 2\n" |
761 |
|
|
" cylinder{\n" |
762 |
gezelter |
625 |
" < pAx, pAy, pAz >,\n" |
763 |
|
|
" < pCx, pCy, pCz >,\n" |
764 |
mmeineke |
515 |
" pipeWidth\n" |
765 |
|
|
" texture{\n" |
766 |
|
|
" pigment{ rgb < colorR, colorG, colorB > }\n" |
767 |
|
|
" finish{\n" |
768 |
|
|
" ambient .2\n" |
769 |
|
|
" diffuse .6\n" |
770 |
|
|
" specular 1\n" |
771 |
|
|
" roughness .001\n" |
772 |
|
|
" metallic\n" |
773 |
|
|
" }\n" |
774 |
|
|
" }\n" |
775 |
|
|
" }\n" |
776 |
|
|
"\n" |
777 |
|
|
" // 3\n" |
778 |
|
|
" cylinder{\n" |
779 |
gezelter |
625 |
" < pAx, pAy, pAz >,\n" |
780 |
|
|
" < pDx, pDy, pDz >,\n" |
781 |
mmeineke |
515 |
" pipeWidth\n" |
782 |
|
|
" texture{\n" |
783 |
|
|
" pigment{ rgb < colorR, colorG, colorB > }\n" |
784 |
|
|
" finish{\n" |
785 |
|
|
" ambient .2\n" |
786 |
|
|
" diffuse .6\n" |
787 |
|
|
" specular 1\n" |
788 |
|
|
" roughness .001\n" |
789 |
|
|
" metallic\n" |
790 |
|
|
" }\n" |
791 |
|
|
" }\n" |
792 |
|
|
" }\n" |
793 |
|
|
"\n" |
794 |
|
|
" // 4\n" |
795 |
|
|
" cylinder{\n" |
796 |
gezelter |
625 |
" < pBx, pBy, pBz >,\n" |
797 |
|
|
" < pEx, pEy, pEz >,\n" |
798 |
mmeineke |
515 |
" pipeWidth\n" |
799 |
|
|
" texture{\n" |
800 |
|
|
" pigment{ rgb < colorR, colorG, colorB > }\n" |
801 |
|
|
" finish{\n" |
802 |
|
|
" ambient .2\n" |
803 |
|
|
" diffuse .6\n" |
804 |
|
|
" specular 1\n" |
805 |
|
|
" roughness .001\n" |
806 |
|
|
" metallic\n" |
807 |
|
|
" }\n" |
808 |
|
|
" }\n" |
809 |
|
|
" }\n" |
810 |
|
|
"\n" |
811 |
|
|
" // 5\n" |
812 |
|
|
" cylinder{\n" |
813 |
gezelter |
625 |
" < pCx, pCy, pCz >,\n" |
814 |
|
|
" < pEx, pEy, pEz >,\n" |
815 |
mmeineke |
515 |
" pipeWidth\n" |
816 |
|
|
" texture{\n" |
817 |
|
|
" pigment{ rgb < colorR, colorG, colorB > }\n" |
818 |
|
|
" finish{\n" |
819 |
|
|
" ambient .2\n" |
820 |
|
|
" diffuse .6\n" |
821 |
|
|
" specular 1\n" |
822 |
|
|
" roughness .001\n" |
823 |
|
|
" metallic\n" |
824 |
|
|
" }\n" |
825 |
|
|
" }\n" |
826 |
|
|
" }\n" |
827 |
|
|
"\n" |
828 |
|
|
" // 6\n" |
829 |
|
|
" cylinder{\n" |
830 |
gezelter |
625 |
" < pBx, pBy, pBz >,\n" |
831 |
|
|
" < pFx, pFy, pFz >,\n" |
832 |
mmeineke |
515 |
" pipeWidth\n" |
833 |
|
|
" texture{\n" |
834 |
|
|
" pigment{ rgb < colorR, colorG, colorB > }\n" |
835 |
|
|
" finish{\n" |
836 |
|
|
" ambient .2\n" |
837 |
|
|
" diffuse .6\n" |
838 |
|
|
" specular 1\n" |
839 |
|
|
" roughness .001\n" |
840 |
|
|
" metallic\n" |
841 |
|
|
" }\n" |
842 |
|
|
" }\n" |
843 |
|
|
" }\n" |
844 |
|
|
"\n" |
845 |
|
|
" // 7\n" |
846 |
|
|
" cylinder{\n" |
847 |
gezelter |
625 |
" < pCx, pCy, pCz >,\n" |
848 |
|
|
" < pGx, pGy, pGz >,\n" |
849 |
mmeineke |
515 |
" pipeWidth\n" |
850 |
|
|
" texture{\n" |
851 |
|
|
" pigment{ rgb < colorR, colorG, colorB > }\n" |
852 |
|
|
" finish{\n" |
853 |
|
|
" ambient .2\n" |
854 |
|
|
" diffuse .6\n" |
855 |
|
|
" specular 1\n" |
856 |
|
|
" roughness .001\n" |
857 |
|
|
" metallic\n" |
858 |
|
|
" }\n" |
859 |
|
|
" }\n" |
860 |
|
|
" }\n" |
861 |
|
|
"\n" |
862 |
|
|
" // 8\n" |
863 |
|
|
" cylinder{\n" |
864 |
gezelter |
625 |
" < pDx, pDy, pDz >,\n" |
865 |
|
|
" < pGx, pGy, pGz >,\n" |
866 |
mmeineke |
515 |
" pipeWidth\n" |
867 |
|
|
" texture{\n" |
868 |
|
|
" pigment{ rgb < colorR, colorG, colorB > }\n" |
869 |
|
|
" finish{\n" |
870 |
|
|
" ambient .2\n" |
871 |
|
|
" diffuse .6\n" |
872 |
|
|
" specular 1\n" |
873 |
|
|
" roughness .001\n" |
874 |
|
|
" metallic\n" |
875 |
|
|
" }\n" |
876 |
|
|
" }\n" |
877 |
|
|
" }\n" |
878 |
|
|
"\n" |
879 |
|
|
" // 9\n" |
880 |
|
|
" cylinder{\n" |
881 |
gezelter |
625 |
" < pDx, pDy, pDz >,\n" |
882 |
|
|
" < pFx, pFy, pFz >,\n" |
883 |
mmeineke |
515 |
" pipeWidth\n" |
884 |
|
|
" texture{\n" |
885 |
|
|
" pigment{ rgb < colorR, colorG, colorB > }\n" |
886 |
|
|
" finish{\n" |
887 |
|
|
" ambient .2\n" |
888 |
|
|
" diffuse .6\n" |
889 |
|
|
" specular 1\n" |
890 |
|
|
" roughness .001\n" |
891 |
|
|
" metallic\n" |
892 |
|
|
" }\n" |
893 |
|
|
" }\n" |
894 |
|
|
" }\n" |
895 |
|
|
"\n" |
896 |
|
|
" // 10\n" |
897 |
|
|
" cylinder{\n" |
898 |
gezelter |
625 |
" < pEx, pEy, pEz >,\n" |
899 |
|
|
" < pHx, pHy, pHz >,\n" |
900 |
mmeineke |
515 |
" pipeWidth\n" |
901 |
|
|
" texture{\n" |
902 |
|
|
" pigment{ rgb < colorR, colorG, colorB > }\n" |
903 |
|
|
" finish{\n" |
904 |
|
|
" ambient .2\n" |
905 |
|
|
" diffuse .6\n" |
906 |
|
|
" specular 1\n" |
907 |
|
|
" roughness .001\n" |
908 |
|
|
" metallic\n" |
909 |
|
|
" }\n" |
910 |
|
|
" }\n" |
911 |
|
|
" }\n" |
912 |
|
|
"\n" |
913 |
|
|
" // 11\n" |
914 |
|
|
" cylinder{\n" |
915 |
gezelter |
625 |
" < pFx, pFy, pFz >,\n" |
916 |
|
|
" < pHx, pHy, pHz >,\n" |
917 |
mmeineke |
515 |
" pipeWidth\n" |
918 |
|
|
" texture{\n" |
919 |
|
|
" pigment{ rgb < colorR, colorG, colorB > }\n" |
920 |
|
|
" finish{\n" |
921 |
|
|
" ambient .2\n" |
922 |
|
|
" diffuse .6\n" |
923 |
|
|
" specular 1\n" |
924 |
|
|
" roughness .001\n" |
925 |
|
|
" metallic\n" |
926 |
|
|
" }\n" |
927 |
|
|
" }\n" |
928 |
|
|
" }\n" |
929 |
|
|
"\n" |
930 |
|
|
" // 12\n" |
931 |
|
|
" cylinder{\n" |
932 |
gezelter |
625 |
" < pGx, pGy, pGz >,\n" |
933 |
|
|
" < pHx, pHy, pHz >,\n" |
934 |
mmeineke |
515 |
" pipeWidth\n" |
935 |
|
|
" texture{\n" |
936 |
|
|
" pigment{ rgb < colorR, colorG, colorB > }\n" |
937 |
|
|
" finish{\n" |
938 |
|
|
" ambient .2\n" |
939 |
|
|
" diffuse .6\n" |
940 |
|
|
" specular 1\n" |
941 |
|
|
" roughness .001\n" |
942 |
|
|
" metallic\n" |
943 |
|
|
" }\n" |
944 |
|
|
" }\n" |
945 |
|
|
" }\n" |
946 |
|
|
"\n" |
947 |
|
|
"#end\n" |
948 |
|
|
"\n" |
949 |
mmeineke |
60 |
"\n"); |
950 |
mmeineke |
515 |
|
951 |
|
|
|
952 |
|
|
|
953 |
|
|
|
954 |
mmeineke |
60 |
make_header_macros(out_file); |
955 |
|
|
|
956 |
|
|
fclose(out_file); |
957 |
|
|
} |
958 |
|
|
|
959 |
|
|
return 0; |
960 |
|
|
|
961 |
|
|
} |
962 |
|
|
|
963 |
|
|
|
964 |
|
|
|
965 |
|
|
/*************************************************************************** |
966 |
|
|
* prints out the usage for the command line arguments, then exits. |
967 |
|
|
***************************************************************************/ |
968 |
|
|
|
969 |
|
|
void usage(){ |
970 |
|
|
(void)fprintf(stderr, |
971 |
|
|
"The proper usage is: %s [options] <xyz_file>\n" |
972 |
|
|
"\n" |
973 |
|
|
"Options:\n" |
974 |
|
|
"\n" |
975 |
|
|
" -o <prefix> the output file prefix\n" |
976 |
|
|
" -H generate a pov-ray header file\n" |
977 |
|
|
" -i <#> number of frames to interpolate\n" |
978 |
|
|
" -h draw hydrogens\n" |
979 |
|
|
" -b draw bonds\n" |
980 |
|
|
" -a draw atoms\n" |
981 |
mmeineke |
515 |
" -p draw periodic box\n" |
982 |
mmeineke |
508 |
" -r regenerate bond\n" |
983 |
mmeineke |
515 |
" -f <#> render frame <#> only\n" |
984 |
|
|
" -s <#> begin at frame <#> (inclusive)\n" |
985 |
|
|
" -e <#> end at frame <#> (inclusive)\n" |
986 |
mmeineke |
60 |
"\n", |
987 |
|
|
program_name); |
988 |
|
|
exit(8); |
989 |
|
|
} |