/* vim: set ts=4 sts=4 sw=4 noet : */
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#ifndef _GENERAL_H
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#define _GENERAL_H
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#include<stdarg.h>
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#include<stdio.h>
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#include<gsl/gsl_complex.h>
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/* @brief This is a header file, defining general constants and structures.
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* @file header.h
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* @author Samo Penic
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* @date 5.3.2001
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*
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* Header file for general inclusion in all the code, defining data structures
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* and general constans. All datatypes used in the code is also defined here.
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*
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* Miha: branch trisurf-polyel
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*/
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/* Defines */
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/** @brief Return value of type bz_bool that indiceates successful function finish
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*
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* Function usualy return some value, which are the result of certain operation. Functions that don't
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* return any parameters can return value, that indicates if the function call finished successfully.
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* In case of successful function run, the functions should return TS_SUCCESS to the caller. This define
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* is set here to get uniformity among all the functions used in program.
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*
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* Example of usage:
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* ts_boot somefunction(ts_int param1, ....){
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* ...
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* return TS_SUCCESS;
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* }
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*/
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#define TS_SUCCESS 0
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/** @brief Return value of type bz_bool that indicates unsuccessful function finish
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*
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* Function usualy return some value, which are the result of certain operation. Functions that don't
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* return any parameters can return value, that indicates if the function call finished successfully.
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* In case of unsuccessful function run, the functions should return TS_FAIL to the caller. This define
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* is set here to get uniformity among all the functions used in program.
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*
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* Example of usage:
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*
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* ts_boot somefunction(ts_int param1, ....){
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* ...
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* return TS_FAIL;
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* }
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*/
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#define TS_FAIL 1
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/* CONSTANTS */
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#define TS_ID_FILAMENT 1
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/* DATA TYPES */
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/** @brief Sets the default datatype for ts_double
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*
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* Requred for some functions to work, like "pow" from math.h. If ts_double is defined as
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* float program must run with "powf". Where type dependant function is used it checks this
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* define directive to decide which version to compile in. Available options
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*
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* TS_DOUBLE_FLOAT
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* TS_DOUBLE_DOUBLE
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* TS_DOUBLE_LONGDOUBLE
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*/
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#define TS_DOUBLE_DOUBLE
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/** For the purpose of greater flexibility all data types used in the program
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* shouldn't use standard C types, but should use types defined here.
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* ts_int (uses int)
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*/
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typedef int ts_int;
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/** For the purpose of greater flexibility all data types used in the program
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* shouldn't use standard C types, but should use types defined here.
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* ts_uint (uses unsigned int)
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*/
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typedef unsigned int ts_uint;
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/** For the purpose of greater flexibility all data types used in the program
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* shouldn't use standard C types, but should use types defined here.
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* ts_long (uses long)
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*/
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typedef long ts_long;
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/** For the purpose of greater flexibility all data types used in the program
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* shouldn't use standard C types, but should use types defined here.
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* ts_ulong (uses unsigned long)
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*/
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typedef unsigned long ts_ulong;
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/** For the purpose of greater flexibility all data types used in the program
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* shouldn't use standard C types, but should use types defined here.
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* ts_float (uses float)
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*/
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typedef float ts_float;
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/** For the purpose of greater flexibility all data types used in the program
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* shouldn't use standard C types, but should use types defined here.
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* ts_double (uses double)
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*/
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typedef double ts_double;
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/** For the purpose of greater flexibility all data types used in the program
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* shouldn't use standard C types, but should use types defined here.
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* ts_char (uses char)
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*/
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typedef char ts_char;
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/** For the purpose of greater flexibility all data types used in the program
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* shouldn't use standard C types, but should use types defined here.
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* ts_uchar (uses unsigned char)
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*/
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typedef unsigned char ts_uchar;
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/** For the purpose of greater flexibility all data types used in the program
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* shouldn't use standard C types, but should use types defined here.
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* ts_bool (uses char)
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*/
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typedef char ts_bool;
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/* STRUCTURES */
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/** @brief Data structure for keeping the coordinates in selected coordinate
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* system
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*/
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#define TS_COORD_CARTESIAN 0
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#define TS_COORD_SPHERICAL 1
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#define TS_COORD_CYLINDRICAL 2
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typedef struct {
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ts_double e1;
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ts_double e2;
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ts_double e3;
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ts_uint coord_type;
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} ts_coord;
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/** @brief Data structure of all data connected to a vertex
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*
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* ts_vertex holds the data for one single point (bead, vertex). To understand how to use it
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* here is a detailed description of the fields in the data structure. */
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struct ts_vertex {
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ts_uint idx;
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ts_double x; /**< The x coordinate of vertex. */
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ts_double y; /**< The y coordinate of vertex. */
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ts_double z; /**< The z coordinate of vertex. */
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ts_uint neigh_no; /**< The number of neighbours. */
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struct ts_vertex **neigh; /**< The pointer that holds neigh_no pointers to this structure. */
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ts_double *bond_length; /**< Obsolete! The bond lenght is moved to ts_bond */
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ts_double *bond_length_dual; /**< Obsolete! Bond length in dual lattice is moved to ts_bond! */
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ts_double curvature;
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ts_double energy;
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ts_double energy_h;
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ts_uint tristar_no;
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struct ts_triangle **tristar; /**< The list of triangles this vertex belongs to. This is an array of pointers to ts_triangle structure of tristar_no length */
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ts_uint bond_no;
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struct ts_bond **bond; /**< Array of pointers of lenght bond_no that stores information on bonds. */
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struct ts_cell *cell; /**< Which cell do we belong to? */
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ts_double xk;
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ts_double c;
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ts_uint id;
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ts_double projArea;
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ts_double relR;
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ts_double solAngle;
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struct ts_poly *grafted_poly;
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struct ts_cluster *cluster;
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};
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typedef struct ts_vertex ts_vertex;
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typedef struct {
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ts_uint n;
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ts_vertex **vtx;
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} ts_vertex_list;
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struct ts_bond {
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ts_uint idx;
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ts_vertex *vtx1;
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ts_vertex *vtx2;
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ts_double bond_length;
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ts_double bond_length_dual;
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ts_bool tainted; //TODO: remove
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ts_double energy;
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ts_double x,y,z;
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};
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typedef struct ts_bond ts_bond;
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struct ts_bond_list {
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ts_uint n;
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ts_bond **bond;
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};
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typedef struct ts_bond_list ts_bond_list;
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struct ts_triangle {
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ts_uint idx;
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ts_vertex *vertex[3];
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ts_uint neigh_no;
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struct ts_triangle **neigh;
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ts_double xnorm;
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ts_double ynorm;
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ts_double znorm;
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ts_double area; // firstly needed for sh.c
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ts_double volume; // firstly needed for sh.c
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ts_double energy;
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};
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typedef struct ts_triangle ts_triangle;
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struct ts_triangle_list{
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ts_uint n;
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ts_double a0;
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ts_triangle **tria;
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};
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typedef struct ts_triangle_list ts_triangle_list;
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typedef struct ts_cell {
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ts_uint idx;
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ts_vertex **vertex;
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ts_uint nvertex;
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} ts_cell;
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typedef struct ts_cell_list{
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ts_uint ncmax[3];
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ts_uint cellno;
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ts_cell **cell;
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ts_double dcell;
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ts_double shift;
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ts_double max_occupancy;
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ts_double dmin_interspecies;
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} ts_cell_list;
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typedef struct {
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ts_uint l;
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ts_double **ulm;
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gsl_complex **ulmComplex;
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ts_double **sumUlm2;
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ts_uint N;
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ts_double **co;
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ts_double ***Ylmi;
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} ts_spharm;
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struct ts_poly {
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ts_vertex_list *vlist;
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ts_bond_list *blist;
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ts_vertex *grafted_vtx;
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ts_double k;
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};
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typedef struct ts_poly ts_poly;
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struct ts_poly_list {
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ts_uint n;
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ts_poly **poly;
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};
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typedef struct ts_poly_list ts_poly_list;
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typedef struct{
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ts_float z_max;
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ts_float z_min;
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ts_int force_switch;
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} ts_confinement_plane;
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typedef struct {
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long int nshell;
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long int ncxmax;
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long int ncymax;
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long int nczmax;
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long int npoly;
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long int nmono;
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long int internal_poly;
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long int nfil;
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long int nfono;
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long int R_nucleus;
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ts_double R_nucleusX;
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ts_double R_nucleusY;
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ts_double R_nucleusZ;
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long int pswitch;
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long int constvolswitch;
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long int constareaswitch;
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long int stretchswitch;
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ts_double xkA0;
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ts_double constvolprecision;
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char *multiprocessing;
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long int brezveze0;
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long int brezveze1;
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long int brezveze2;
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ts_double xk0;
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ts_double dmax;
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ts_double dmin_interspecies;
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ts_double stepsize;
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ts_double kspring;
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ts_double xi;
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ts_double pressure;
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long int iterations;
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long int inititer;
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long int mcsweeps;
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long int quiet;
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long int shc;
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long int number_of_vertices_with_c0;
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ts_double c0;
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ts_double w;
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ts_double F;
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long int plane_confinement_switch;
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ts_double plane_d;
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ts_double plane_F;
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} ts_tape;
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/* plugins */
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typedef struct {
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void (*at_start)(int argc, char **argv);
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void *(*after_vesicle_init)(void *vesicle);
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ts_bool (*vm_hard_constraint)(void *vesicle, ts_vertex *vtx, ts_vertex *odl_vtx);
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void (*vm_energy_before_prepare)(void *vesicle, ts_vertex *vtx);
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ts_double (*vm_energy_before_execute)(void *vesicle, ts_vertex *vtx);
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ts_double (*vm_energy_after_prepare)(void *vesicle, ts_vertex *vtx);
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ts_double (*vm_energy_after_execute)(void *vesicle, ts_vertex *vtx);
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ts_double (*vm_before_montecarlo_constraint)(void *vesicle, ts_vertex *vtx, ts_vertex *old_vtx);
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ts_double (*vm_new_state_accepted)(void *vesicle, ts_vertex *vtx, ts_vertex *old_vtx);
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ts_double (*vm_new_state_rejected)(void *vesicle, ts_vertex *vtx, ts_vertex *old_vtx);
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void (*cleanup)(void);
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} ts_plugin_function;
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typedef struct {
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ts_char *name;
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ts_char *description;
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ts_char *author;
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void *data;
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} ts_plugin_details;
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typedef struct {
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ts_plugin_details *details;
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ts_plugin_function *function;
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ts_char *filename;
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void *libhandle;
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} ts_plugin;
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struct ts_plugin_chain {
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ts_plugin *plugin;
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struct ts_plugin_chain *next;
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};
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typedef struct ts_plugin_chain ts_plugin_chain;
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typedef struct {
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ts_plugin_chain *at_start;
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ts_plugin_chain *after_vesicle_init;
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ts_plugin_chain *vm_hard_constraint;
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ts_plugin_chain *vm_energy_before_prepare;
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ts_plugin_chain *vm_energy_after_execute;
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ts_plugin_chain *vm_before_montecarlo_constraint;
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ts_plugin_chain *vm_new_state_accepted;
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ts_plugin_chain *vm_new_state_rejected;
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ts_plugin_chain *cleanup;
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} ts_plugin_chains;
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typedef struct {
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ts_uint n;
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ts_plugin **plugin;
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ts_plugin_chains *chain;
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ts_plugin_chain *pointer;
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} ts_plugin_list;
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/* end plugins */
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typedef struct {
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ts_vertex_list *vlist;
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ts_bond_list *blist;
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ts_triangle_list *tlist;
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ts_cell_list *clist;
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ts_uint nshell;
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ts_double bending_rigidity;
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ts_double dmax;
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ts_double stepsize;
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ts_double cm[3];
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ts_double volume;
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ts_spharm *sphHarmonics;
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// Polymers outside the vesicle and attached to the vesicle membrane (polymer brush):
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ts_poly_list *poly_list;
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// Filaments inside the vesicle (not attached to the vesicel membrane:
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ts_poly_list *filament_list;
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ts_double spring_constant;
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ts_double pressure;
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ts_int pswitch;
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ts_tape *tape;
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ts_double R_nucleus;
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ts_double R_nucleusX;
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ts_double R_nucleusY;
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ts_double R_nucleusZ;
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ts_double nucleus_center[3];
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ts_double area;
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ts_confinement_plane confinement_plane;
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ts_plugin_list *plist;
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} ts_vesicle;
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struct ts_cluster{
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ts_uint nvtx;
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ts_uint idx;
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ts_vertex **vtx;
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};
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typedef struct ts_cluster ts_cluster;
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typedef struct{
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ts_uint n;
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ts_cluster **cluster;
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} ts_cluster_list;
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/* GLOBAL VARIABLES */
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int quiet;
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ts_double V0;
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ts_double A0;
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ts_double epsvol;
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ts_double epsarea;
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/* FUNCTIONS */
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/** Non-fatal error function handler:
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* @param text is a description of an error
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* @returns doesn't return anything
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*/
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void err(char *text);
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/** Fatal error function handler:
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* @param text is a description of an error
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* @param errcode is a (non-zero) error code
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* @returns terminates the execution of program with errcode set
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*/
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void fatal(char *text, ts_int errcode);
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ts_uint ts_fprintf(FILE *fd, char *fmt, ...);
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#define VTX(n) &(vlist->vtx[n])
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#define VTX_DATA(n) vlist->vtx[n].data
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/* FOR PID GENERATION ROUTINE */
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#define CPF_CLOEXEC 1
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int createPidFile(const char *progName, const char *pidFile, int flags);
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int lockRegion(int fd, int type, int whence, int start, int len);
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char *libVersion();
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#endif
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