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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 <ctype.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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|
| 10 |
#include "atom_parser.h" |
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#include "pov_writer.h" |
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#include "file_stuff.h" |
| 13 |
#define POV_DIR "./pov" |
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|
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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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|
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|
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struct linked_coords{ |
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struct coords r; |
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struct linked_coords *next; |
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}; |
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|
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|
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char *program_name; /*the name of the program */ |
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int draw_bonds = 1; /* 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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|
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void usage(void); |
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|
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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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|
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char name_foo[10]; |
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char *token; |
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struct coords *out_coords; |
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struct linked_coords *lc_head; |
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struct linked_coords *lc_temp; |
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struct linked_coords *lc_temp2; |
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int i; /* loop counters */ |
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mode_t dir_mode = S_IRWXU; |
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|
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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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|
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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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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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|
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struct linked_xyz *current_frame; |
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|
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double dx, dy, dz; /* temp variables for interpolating distances */ |
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|
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char pov_dir[500]; /* the pov_dir */ |
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|
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program_name = argv[0]; /*save the program name in case we need it*/ |
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|
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for( i = 0; i < argc; i++){ |
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|
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if(argv[i][0] =='-'){ |
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|
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/* argv[i][1] is the actual option character */ |
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|
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switch(argv[i][1]){ |
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|
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/* -H => generate header */ |
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|
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case 'H': |
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generate_header = 1; |
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break; |
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|
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|
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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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|
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case 'f': |
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in_name = argv[i+1]; |
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break; |
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|
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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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|
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case 'o': |
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out_prefix = argv[i+1]; |
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break; |
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|
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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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|
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if(in_name == NULL){ |
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usage(); |
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} |
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|
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|
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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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|
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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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|
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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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|
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|
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// initialize atom type parser |
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|
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initializeParser(); |
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|
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// start reading the frame |
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|
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lc_head = (struct linked_coords *)malloc(sizeof(struct linked_coords)); |
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lc_head->next = NULL; |
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|
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eof_test = fgets(read_buffer, sizeof(read_buffer), in_file); |
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|
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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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|
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|
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while(eof_test != NULL){ |
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|
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token = strtok(read_buffer, "\t "); |
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token = strtok(NULL, "\t "); |
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|
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(void)sscanf(token, "%d", &n_atoms); |
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|
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token = strtok(NULL, "\t "); |
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|
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(void)sscanf(token, "%s", &name_foo); |
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|
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i=0; |
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while( isalpha( name_foo[i] ) ){ |
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|
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lc_head->r.name[i] = name_foo[i]; |
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i++; |
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} |
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lc_head->r.name[i] = '\0'; |
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|
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token = strtok(NULL, "\t "); |
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token = strtok(NULL, "\t "); |
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|
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token = strtok(NULL, "\t "); |
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(void)sscanf(token, "%lf", &lc_head->r.x); |
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|
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token = strtok(NULL, "\t "); |
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(void)sscanf(token, "%lf", &lc_head->r.y); |
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|
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token = strtok(NULL, "\t "); |
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(void)sscanf(token, "%lf", &lc_head->r.z); |
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|
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lc_temp = (struct linked_coords *)malloc(sizeof(struct linked_coords)); |
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|
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lc_temp->next = lc_head; |
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lc_head = lc_temp; |
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|
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eof_test = fgets(read_buffer, sizeof(read_buffer), in_file); |
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} |
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|
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current_frame->r = |
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(struct coords *)calloc(n_atoms, sizeof(struct coords)); |
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|
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lc_temp = lc_head->next; |
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|
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for( i=0; i < n_atoms; i++ ){ |
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|
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strcpy(current_frame->r[i].name, lc_temp->r.name); |
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|
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current_frame->r[i].x = lc_temp->r.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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|
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current_frame->r[i].y = lc_temp->r.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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|
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current_frame->r[i].z = lc_temp->r.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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lc_temp = lc_temp->next; |
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} |
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|
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|
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/*clean up the memory */ |
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|
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lc_temp = lc_head->next; |
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|
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while(lc_temp != NULL){ |
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lc_temp2 = lc_temp->next; |
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free(lc_temp); |
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lc_temp = lc_temp2; |
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} |
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|
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|
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/* open the new output file */ |
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|
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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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|
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out_coords = |
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(struct coords *)calloc(n_atoms, sizeof(struct coords)); |
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|
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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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|
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(void)fclose(out_file); |
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|
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(void)fclose(in_file); |
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|
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|
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if(generate_header){ |
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|
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dx = big_x - small_x; |
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dy = big_y - small_y; |
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dz = big_z - small_z; |
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|
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rsqr = dx * dx + dy * dy + dz * dz; |
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diagonal = sqrt(rsqr); |
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diagonal *= 0.5; |
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|
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dx /= 2.0; |
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dy /= 2.0; |
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dz /= 2.0; |
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|
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dx += small_x; |
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dy += small_y; |
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dz += small_z; |
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|
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|
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/*note the y and z axis is exchanged for the different coordinate |
| 284 |
system in pov-ray*/ |
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|
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|
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out_file = fopen("pov_header.pov", "w"); |
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|
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fprintf(out_file, |
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"// The following script was automatically generated by:\n" |
| 291 |
"// xyz2pov Copyright 2001 by MATTHEW A. MEINEKE\n" |
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"\n" |
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"\n" |
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"background { rgb <1.0, 1.0, 1.0> }\n" |
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"\n" |
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"\n" |
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); |
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|
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fprintf(out_file, |
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"//******************************************************\n" |
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"// Declare the resolution, camera, and light sources.\n" |
| 302 |
"//******************************************************\n" |
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"\n" |
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"// NOTE: if you plan to render at a different resoltion,\n" |
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"// be sure to update the following two lines to maintain\n" |
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"// the correct aspect ratio.\n" |
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"\n" |
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"#declare Width = 640.0;\n" |
| 309 |
"#declare Height = 480.0;\n" |
| 310 |
"#declare Ratio = Width / Height;\n" |
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"\n" |
| 312 |
"#declare zoom = %lf;\n" |
| 313 |
"\n" |
| 314 |
"#declare ATOM_SPHERE_FACTOR = 0.2;\n" |
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"#declare BOND_RADIUS = 0.1;\n" |
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"\n" |
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"camera{\n" |
| 318 |
" location < %lf, %lf, %lf - zoom>\n" |
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" right < Ratio , 0, 0>\n" |
| 320 |
" look_at < %lf, %lf, %lf >\n" |
| 321 |
"}\n" |
| 322 |
"\n", |
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diagonal, |
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dx, dz, dy, |
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dx, dz, dy); |
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|
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fprintf(out_file, |
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"light_source{\n" |
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" < %lf, %lf, %lf - zoom >\n" |
| 330 |
" rgb < 1.0, 1.0, 1.0 > }\n", |
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dx, dz, dy); |
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|
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fprintf(out_file, |
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"light_source{\n" |
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" < %lf - zoom , %lf + zoom, %lf - zoom >\n" |
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" rgb < 1.0, 1.0, 1.0 > }\n" |
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"\n" |
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"\n", |
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dx, dz, dy); |
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|
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fprintf(out_file, |
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"//************************************************************\n" |
| 343 |
"// Set whether or not to rotate the system.\n" |
| 344 |
"//\n" |
| 345 |
"// To Rotate, set ROTATE to 1.0 (true),\n" |
| 346 |
"// Then set the Euler Angles PHI, THETA, and PSI in degrees.\n" |
| 347 |
"//************************************************************\n" |
| 348 |
"\n" |
| 349 |
"#declare ROTATE = 0.0;\n" |
| 350 |
"#declare PHI = 0.0;\n" |
| 351 |
"#declare THETA = 0.0;\n" |
| 352 |
"#declare PSI = 0.0;\n" |
| 353 |
"\n" |
| 354 |
"#if(ROTATE)\n" |
| 355 |
" #declare phi_r = radians(PHI);\n" |
| 356 |
" #declare theta_r = radians(THETA);\n" |
| 357 |
" #declare psi_r = radians(PSI);\n" |
| 358 |
"\n" |
| 359 |
" #declare A11 = cos(phi_r) * cos(psi_r) - sin(phi_r) * cos(theta_r) * sin(psi_r);\n" |
| 360 |
" #declare A12 = sin(phi_r) * cos(psi_r) + cos(phi_r) * cos(theta_r) * sin(psi_r);\n" |
| 361 |
" #declare A13 = sin(theta_r) * sin(psi_r);\n" |
| 362 |
"\n" |
| 363 |
" #declare A21 = -cos(phi_r) * sin(psi_r) - sin(phi_r) * cos(theta_r) * cos(psi_r);\n" |
| 364 |
" #declare A22 = -sin(phi_r) * sin(psi_r) + cos(phi_r) * cos(theta_r) * cos(psi_r);\n" |
| 365 |
" #declare A23 = sin(theta_r) * cos(psi_r);\n" |
| 366 |
"\n" |
| 367 |
" #declare A31 = sin(phi_r) * sin(theta_r);\n" |
| 368 |
" #declare A32 = -cos(phi_r) * sin(theta_r);\n" |
| 369 |
" #declare A33 = cos(theta_r);\n" |
| 370 |
"\n" |
| 371 |
"#end\n" |
| 372 |
"\n"); |
| 373 |
|
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|
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make_header_macros(out_file); |
| 376 |
|
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fclose(out_file); |
| 378 |
} |
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|
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return 0; |
| 381 |
|
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} |
| 383 |
|
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|
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|
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/*************************************************************************** |
| 387 |
* prints out the usage for the command line arguments, then exits. |
| 388 |
***************************************************************************/ |
| 389 |
|
| 390 |
void usage(){ |
| 391 |
(void)fprintf(stderr, |
| 392 |
"The proper usage is: %s [options] -f <xyz_file>\n\n" |
| 393 |
"Options:\n" |
| 394 |
" -o <name> the output file prefix\n" |
| 395 |
" -H generate a pov-ray header file\n", |
| 396 |
program_name); |
| 397 |
exit(8); |
| 398 |
} |
