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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 "atom_parser.h" |
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#include "pov_writer.h" |
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#include "file_stuff.h" |
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#define POV_DIR "./pov" |
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struct linked_xyz{ |
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struct coords *r; |
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struct linked_xyz *next; |
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}; |
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char *program_name; /*the name of the program */ |
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int draw_bonds = 0; /* boolean to draw bonds or not */ |
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int draw_hydrogens = 1; /*boolean to draw hydrogens */ |
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int draw_atoms = 1; /*boolean to draw atoms */ |
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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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char out_name[500]; /*the output name */ |
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char temp_name[500]; |
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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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struct linked_xyz *current_frame; |
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struct linked_xyz *temp_frame; |
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unsigned int n_interpolate = 0; /* number of frames to interpolate */ |
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double dx, dy, dz; /* temp variables for interpolating distances */ |
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char pov_dir[500]; /* the pov_dir */ |
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program_name = argv[0]; /*save the program name in case we need it*/ |
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for( i = 0; i < argc; i++){ |
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if(argv[i][0] =='-'){ |
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/* argv[i][1] is the actual option character */ |
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switch(argv[i][1]){ |
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/* -H => generate header */ |
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case 'H': |
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generate_header = 1; |
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break; |
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/* -i # => the number of frames to interpolate. |
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* [i+1] actually starts the name |
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*/ |
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case 'i': |
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(void)sscanf(argv[i+1],"%d", &n_interpolate); |
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break; |
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/* -f <name> => the xyz input file |
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* [i+1] actually starts the name |
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*/ |
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case 'f': |
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in_name = argv[i+1]; |
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break; |
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/* -o <name> => the orientation file prefix |
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* [i+1] actually starts the name |
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*/ |
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case 'o': |
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out_prefix = argv[i+1]; |
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break; |
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default: |
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(void)fprintf(stderr, "Bad option %s\n", argv[i]); |
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usage(); |
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} |
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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(out_prefix == NULL){ |
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out_prefix = strtok(in_name, "."); |
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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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// start reading the first frame |
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eof_test = fgets(read_buffer, sizeof(read_buffer), in_file); |
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current_frame = (struct linked_xyz *)malloc(sizeof(struct linked_xyz)); |
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current_frame->next = NULL; |
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while(eof_test != NULL){ |
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(void)sscanf(read_buffer, "%d", &n_atoms); |
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current_frame->r = |
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(struct coords *)calloc(n_atoms, sizeof(struct coords)); |
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/*read and toss the comment line */ |
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eof_test = fgets(read_buffer, sizeof(read_buffer), in_file); |
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if(eof_test == NULL){ |
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printf("error in reading file\n"); |
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exit(8); |
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} |
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for( i=0; i < n_atoms; i++){ |
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eof_test = fgets(read_buffer, sizeof(read_buffer), in_file); |
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if(eof_test == NULL){ |
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printf("error in reading file\n"); |
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exit(8); |
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} |
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foo = strtok(read_buffer, " ,;\t"); |
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(void)strcpy(current_frame->r[i].name, foo); /*copy the atom name */ |
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/* next we grab the positions */ |
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foo = strtok(NULL, " ,;\t"); |
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if(foo == NULL){ |
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printf("error in reading file\n"); |
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exit(8); |
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} |
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(void)sscanf(foo, "%lf",¤t_frame->r[i].x); |
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if(current_frame->r[i].x > big_x) big_x = current_frame->r[i].x; |
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if(current_frame->r[i].x < small_x) small_x = current_frame->r[i].x; |
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foo = strtok(NULL, " ,;\t"); |
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if(foo == NULL){ |
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printf("error in reading file\n"); |
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exit(8); |
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} |
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(void)sscanf(foo, "%lf", ¤t_frame->r[i].y); |
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if(current_frame->r[i].y > big_y) big_y = current_frame->r[i].y; |
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if(current_frame->r[i].y < small_y) small_y = current_frame->r[i].y; |
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foo = strtok(NULL, " ,;\t"); |
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if(foo == NULL){ |
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printf("error in reading file\n"); |
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exit(8); |
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} |
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(void)sscanf(foo, "%lf", ¤t_frame->r[i].z); |
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if(current_frame->r[i].z > big_z) big_z = current_frame->r[i].z; |
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if(current_frame->r[i].z < small_z) small_z = current_frame->r[i].z; |
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} |
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if(n_interpolate && current_frame->next != NULL){ |
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temp_frame = current_frame->next; |
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for(i = 0; i < n_interpolate; i++){ |
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/* open the new output file */ |
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strcpy(out_name, pov_dir); |
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make_filename(temp_name, out_prefix, n_out); |
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strcat(out_name, temp_name); strcat(out_name, ".pov"); |
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out_file = fopen(out_name, "w"); |
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n_out++; |
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if(out_file == NULL){ |
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printf("error opening output file: %s\n", out_name); |
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exit(8); |
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} |
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(void)fprintf(out_file, |
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"// The following script was automatically generated by:\n" |
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"// xyz2pov Copyright 2001 by MATTHEW A. MEINEKE\n" |
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"\n" |
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"#include \"pov_header.pov\"\n" |
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"\n"); |
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out_coords = |
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(struct coords *)calloc(n_atoms, sizeof(struct coords)); |
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for(j=0; j < n_atoms; j++){ |
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dx = current_frame->r[j].x - temp_frame->r[j].x; |
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dy = current_frame->r[j].y - temp_frame->r[j].y; |
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dz = current_frame->r[j].z - temp_frame->r[j].z; |
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dx /= (double)(n_interpolate + 1); |
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dy /= (double)(n_interpolate + 1); |
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dz /= (double)(n_interpolate + 1); |
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strcpy(out_coords[j].name, temp_frame->r[j].name); |
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out_coords[j].x = temp_frame->r[j].x + dx * (i+1); |
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out_coords[j].y = temp_frame->r[j].y + dy * (i+1); |
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out_coords[j].z = temp_frame->r[j].z + dz * (i+1); |
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} |
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pov_write(out_file, out_coords, n_atoms, draw_hydrogens, draw_bonds, |
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draw_atoms); |
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free(out_coords); |
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(void)fclose(out_file); |
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} |
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} |
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/* open the new output file */ |
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strcpy(out_name, pov_dir); |
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make_filename(temp_name, out_prefix, n_out); |
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strcat(out_name, temp_name); strcat(out_name, ".pov"); |
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out_file = fopen(out_name, "w"); |
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n_out++; |
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if(out_file == NULL){ |
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printf("error opening output file: %s\n", out_name); |
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exit(8); |
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} |
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(void)fprintf(out_file, |
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"// The following script was automatically generated by:\n" |
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"// xyz2pov Copyright 2001 by MATTHEW A. MEINEKE\n" |
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"\n" |
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"#include \"pov_header.pov\"\n" |
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"\n"); |
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out_coords = |
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(struct coords *)calloc(n_atoms, sizeof(struct coords)); |
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for(i = 0; i < n_atoms; i++){ |
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strcpy(out_coords[i].name, current_frame->r[i].name); |
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out_coords[i].x = current_frame->r[i].x; |
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out_coords[i].y = current_frame->r[i].y; |
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out_coords[i].z = current_frame->r[i].z; |
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} |
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pov_write(out_file, out_coords, n_atoms, draw_hydrogens, draw_bonds, |
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draw_atoms); |
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free(out_coords); |
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(void)fclose(out_file); |
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/*free up memory */ |
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temp_frame = current_frame->next; |
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current_frame->next = NULL; |
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294 |
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if(temp_frame != NULL){ |
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free(temp_frame->r); |
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free(temp_frame); |
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} |
299 |
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300 |
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/* make a new frame */ |
301 |
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temp_frame = (struct linked_xyz *)malloc(sizeof(struct linked_xyz)); |
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temp_frame->next = current_frame; |
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current_frame = temp_frame; |
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eof_test = fgets(read_buffer, sizeof(read_buffer), in_file); |
307 |
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308 |
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} |
309 |
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310 |
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(void)fclose(in_file); |
311 |
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312 |
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313 |
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if(generate_header){ |
314 |
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dx = big_x - small_x; |
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dy = big_y - small_y; |
317 |
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dz = big_z - small_z; |
318 |
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rsqr = dx * dx + dy * dy + dz * dz; |
320 |
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diagonal = sqrt(rsqr); |
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diagonal *= 0.5; |
322 |
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323 |
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dx /= 2.0; |
324 |
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dy /= 2.0; |
325 |
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dz /= 2.0; |
326 |
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327 |
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dx += small_x; |
328 |
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dy += small_y; |
329 |
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dz += small_z; |
330 |
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331 |
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332 |
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/*note the y and z axis is exchanged for the different coordinate |
333 |
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system in pov-ray*/ |
334 |
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335 |
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336 |
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out_file = fopen("pov_header.pov", "w"); |
337 |
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338 |
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fprintf(out_file, |
339 |
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"// The following script was automatically generated by:\n" |
340 |
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"// xyz2pov Copyright 2001 by MATTHEW A. MEINEKE\n" |
341 |
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"\n" |
342 |
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"\n" |
343 |
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"background { rgb <1.0, 1.0, 1.0> }\n" |
344 |
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"\n" |
345 |
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"\n" |
346 |
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); |
347 |
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348 |
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fprintf(out_file, |
349 |
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"//******************************************************\n" |
350 |
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"// Declare the resolution, camera, and light sources.\n" |
351 |
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"//******************************************************\n" |
352 |
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"\n" |
353 |
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"// NOTE: if you plan to render at a different resoltion,\n" |
354 |
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"// be sure to update the following two lines to maintain\n" |
355 |
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"// the correct aspect ratio.\n" |
356 |
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"\n" |
357 |
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"#declare Width = 640.0;\n" |
358 |
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"#declare Height = 480.0;\n" |
359 |
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"#declare Ratio = Width / Height;\n" |
360 |
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"\n" |
361 |
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"#declare zoom = %lf;\n" |
362 |
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"\n" |
363 |
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"#declare ATOM_SPHERE_FACTOR = 0.2;\n" |
364 |
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"#declare BOND_RADIUS = 0.1;\n" |
365 |
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"\n" |
366 |
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"camera{\n" |
367 |
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" location < %lf, %lf, %lf - zoom>\n" |
368 |
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" right < Ratio , 0, 0>\n" |
369 |
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" look_at < %lf, %lf, %lf >\n" |
370 |
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"}\n" |
371 |
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"\n", |
372 |
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diagonal, |
373 |
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dx, dz, dy, |
374 |
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dx, dz, dy); |
375 |
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376 |
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fprintf(out_file, |
377 |
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"light_source{\n" |
378 |
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" < %lf, %lf, %lf - zoom >\n" |
379 |
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" rgb < 1.0, 1.0, 1.0 > }\n", |
380 |
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dx, dz, dy); |
381 |
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382 |
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fprintf(out_file, |
383 |
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"light_source{\n" |
384 |
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" < %lf - zoom , %lf + zoom, %lf - zoom >\n" |
385 |
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" rgb < 1.0, 1.0, 1.0 > }\n" |
386 |
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"\n" |
387 |
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"\n", |
388 |
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dx, dz, dy); |
389 |
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390 |
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fprintf(out_file, |
391 |
|
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"//************************************************************\n" |
392 |
|
|
"// Set whether or not to rotate the system.\n" |
393 |
|
|
"//\n" |
394 |
|
|
"// To Rotate, set ROTATE to 1.0 (true),\n" |
395 |
|
|
"// Then set the Euler Angles PHI, THETA, and PSI in degrees.\n" |
396 |
|
|
"//************************************************************\n" |
397 |
|
|
"\n" |
398 |
|
|
"#declare ROTATE = 0.0;\n" |
399 |
|
|
"#declare PHI = 0.0;\n" |
400 |
|
|
"#declare THETA = 0.0;\n" |
401 |
|
|
"#declare PSI = 0.0;\n" |
402 |
|
|
"\n" |
403 |
|
|
"#if(ROTATE)\n" |
404 |
|
|
" #declare phi_r = radians(PHI);\n" |
405 |
|
|
" #declare theta_r = radians(THETA);\n" |
406 |
|
|
" #declare psi_r = radians(PSI);\n" |
407 |
|
|
"\n" |
408 |
|
|
" #declare A11 = cos(phi_r) * cos(psi_r) - sin(phi_r) * cos(theta_r) * sin(psi_r);\n" |
409 |
|
|
" #declare A12 = sin(phi_r) * cos(psi_r) + cos(phi_r) * cos(theta_r) * sin(psi_r);\n" |
410 |
|
|
" #declare A13 = sin(theta_r) * sin(psi_r);\n" |
411 |
|
|
"\n" |
412 |
|
|
" #declare A21 = -cos(phi_r) * sin(psi_r) - sin(phi_r) * cos(theta_r) * cos(psi_r);\n" |
413 |
|
|
" #declare A22 = -sin(phi_r) * sin(psi_r) + cos(phi_r) * cos(theta_r) * cos(psi_r);\n" |
414 |
|
|
" #declare A23 = sin(theta_r) * cos(psi_r);\n" |
415 |
|
|
"\n" |
416 |
|
|
" #declare A31 = sin(phi_r) * sin(theta_r);\n" |
417 |
|
|
" #declare A32 = -cos(phi_r) * sin(theta_r);\n" |
418 |
|
|
" #declare A33 = cos(theta_r);\n" |
419 |
|
|
"\n" |
420 |
|
|
"#end\n" |
421 |
|
|
"\n"); |
422 |
|
|
|
423 |
|
|
|
424 |
|
|
make_header_macros(out_file); |
425 |
|
|
|
426 |
|
|
fclose(out_file); |
427 |
|
|
} |
428 |
|
|
|
429 |
|
|
return 0; |
430 |
|
|
|
431 |
|
|
} |
432 |
|
|
|
433 |
|
|
|
434 |
|
|
|
435 |
|
|
/*************************************************************************** |
436 |
|
|
* prints out the usage for the command line arguments, then exits. |
437 |
|
|
***************************************************************************/ |
438 |
|
|
|
439 |
|
|
void usage(){ |
440 |
|
|
(void)fprintf(stderr, |
441 |
|
|
"The proper usage is: %s [options] -f <xyz_file>\n\n" |
442 |
|
|
"Options:\n" |
443 |
|
|
" -o <name> the output file prefix\n" |
444 |
|
|
" -H generate a pov-ray header file\n" |
445 |
|
|
" -i # number of frames to interpolate\n", |
446 |
|
|
program_name); |
447 |
|
|
exit(8); |
448 |
|
|
} |