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globals.h
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globals.h
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/*=================================================================*/
/*= globals.h =*/
/*= header file for global routines from treekin =*/
/*= --------------------------------------------------------- =*/
/*= Last changed Time-stamp: <2006-11-24 19:17:45 mtw> =*/
/*= $Id: globals.h,v 1.15 2006/11/24 18:24:11 mtw Exp $ =*/
/*= --------------------------------------------------------- =*/
/*= (c) Michael Thomas Wolfinger =*/
/*= mtw@tbi.univie.ac.at =*/
/*= treekin =*/
/*=================================================================*/
#ifndef _GLOBALS_H_
#define _GLOBALS_H_
#define TZERO 0.1
typedef enum { false = 0, true = 1 } bool;
typedef struct { /* command-line options */
char *basename; /* base name of processed file */
int absrb; /* make one lmin absorbing */
int real_abs; /* remember absorbing state */
int want_linear; /* logarithmic time-scale */
int want_verbose; /* verbose output */
int want_degenerate; /* consider degeneracy */
int dumpU; /* dump U to a binary file */
int dumpMathematica; /* dump U to a Mathematica-readable file */
int matexp; /* use matrix-exponent routines */
int binrates; /* assume binary rates file */
int rrecover; /* recover from previous diagonalization */
int wrecover; /* write recovery file */
int n; /* read only n lmins */
double T; /* Temperature */
double t0; /* start time */
double t8; /* stop time */
double tinc; /* time increment */
double *pini; /* start population at lmin xxx */
char method; /* method to build transition matrix */
FILE *INFILE; /* input file (usually bar-file) */
char *sequence; /* sequence */
int fpt; /* switch for fpt-related calculations */
int fpt_num; /* state to count ftp's to (-1 for all states)*/
char *rate_matrix; /* path to the file containing the rate matrix, if given */
char *fpt_file; /* output file for first passage times */
} treekin_options;
treekin_options opt;
int lmins; /* # of lmins in the barrier tree, needed in FULL process */
void parse_commandline(int argc, char **argv);
void free_gengetopt();
void MxFPrint(double *mx, char *name, char T, FILE *out);
void MxPrint(double *mx, char *name, char T);
#endif
/* End of file */