From a00f10fd48a1de31c3ac923c2106969f84e831e0 Mon Sep 17 00:00:00 2001
From: Samo Penic <samo.penic@fe.uni-lj.si>
Date: Mon, 09 Mar 2015 11:09:31 +0000
Subject: [PATCH] Documented energy.c
---
src/general.h | 111 ++++++++++++++++++++++++++++++++++++++++++++++---------
1 files changed, 92 insertions(+), 19 deletions(-)
diff --git a/src/general.h b/src/general.h
index 2fe0ee2..393eafe 100644
--- a/src/general.h
+++ b/src/general.h
@@ -3,15 +3,16 @@
#include<stdarg.h>
#include<stdio.h>
-
+#include<gsl/gsl_complex.h>
/* @brief This is a header file, defining general constants and structures.
* @file header.h
* @author Samo Penic
* @date 5.3.2001
- *
+ *
* Header file for general inclusion in all the code, defining data structures
* and general constans. All datatypes used in the code is also defined here.
*
+ * Miha: branch trisurf-polyel
*/
/* Defines */
@@ -47,6 +48,8 @@
#define TS_FAIL 1
/* CONSTANTS */
+
+#define TS_ID_FILAMENT 1
/* DATA TYPES */
/** @brief Sets the default datatype for ts_double
@@ -125,8 +128,6 @@
ts_uint coord_type;
} ts_coord;
-
-
/** @brief Data structure of all data connected to a vertex
*
* ts_vertex holds the data for one single point (bead, vertex). To understand how to use it
@@ -151,10 +152,10 @@
ts_double xk;
ts_double c;
ts_uint id;
- ts_double **Ylm;
ts_double projArea;
ts_double relR;
ts_double solAngle;
+ struct ts_poly *grafted_poly;
};
typedef struct ts_vertex ts_vertex;
@@ -165,11 +166,14 @@
} ts_vertex_list;
struct ts_bond {
- ts_uint idx;
+ ts_uint idx;
ts_vertex *vtx1;
ts_vertex *vtx2;
- ts_double bond_length;
- ts_double bond_length_dual;
+ ts_double bond_length;
+ ts_double bond_length_dual;
+ ts_bool tainted; //TODO: remove
+ ts_double energy;
+ ts_double x,y,z;
};
typedef struct ts_bond ts_bond;
@@ -188,6 +192,7 @@
ts_double ynorm;
ts_double znorm;
ts_double area; // firstly needed for sh.c
+ ts_double volume; // firstly needed for sh.c
};
typedef struct ts_triangle ts_triangle;
@@ -211,15 +216,71 @@
ts_double dcell;
ts_double shift;
ts_double max_occupancy;
+ ts_double dmin_interspecies;
} ts_cell_list;
typedef struct {
ts_uint l;
- ts_uint i;
ts_double **ulm;
+ gsl_complex **ulmComplex;
+ ts_double **sumUlm2;
+ ts_uint N;
ts_double **co;
+ ts_double ***Ylmi;
} ts_spharm;
+
+
+
+struct ts_poly {
+ ts_vertex_list *vlist;
+ ts_bond_list *blist;
+ ts_vertex *grafted_vtx;
+ ts_double k;
+};
+typedef struct ts_poly ts_poly;
+
+
+struct ts_poly_list {
+ ts_uint n;
+ ts_poly **poly;
+};
+typedef struct ts_poly_list ts_poly_list;
+
+
+
+typedef struct {
+ long int nshell;
+ long int ncxmax;
+ long int ncymax;
+ long int nczmax;
+ long int npoly;
+ long int nmono;
+ long int nfil;
+ long int nfono;
+ long int R_nucleus;
+ long int pswitch;
+ long int constvolswitch;
+ long int constareaswitch;
+ ts_double constvolprecision;
+ char *multiprocessing;
+ long int brezveze0;
+ long int brezveze1;
+ long int brezveze2;
+ ts_double xk0;
+ ts_double dmax;
+ ts_double dmin_interspecies;
+ ts_double stepsize;
+ ts_double kspring;
+ ts_double xi;
+ ts_double pressure;
+ long int iterations;
+ long int inititer;
+ long int mcsweeps;
+ long int quiet;
+ long int shc;
+} ts_tape;
+
@@ -227,24 +288,36 @@
ts_vertex_list *vlist;
ts_bond_list *blist;
ts_triangle_list *tlist;
- ts_cell_list *clist;
+ ts_cell_list *clist;
ts_uint nshell;
- ts_double bending_rigidity;
- ts_double dmax;
- ts_double stepsize;
- ts_double cm[3];
- ts_double volume;
- ts_spharm *sphHarmonics;
-} ts_vesicle;
+ ts_double bending_rigidity;
+ ts_double dmax;
+ ts_double stepsize;
+ ts_double cm[3];
+ ts_double volume;
+ ts_spharm *sphHarmonics;
+// Polymers outside the vesicle and attached to the vesicle membrane (polymer brush):
+ ts_poly_list *poly_list;
+// Filaments inside the vesicle (not attached to the vesicel membrane:
+ ts_poly_list *filament_list;
+ ts_double spring_constant;
+ ts_double pressure;
+ ts_int pswitch;
+ ts_tape *tape;
+ ts_double R_nucleus;
+ ts_double area;
+} ts_vesicle;
/* GLOBAL VARIABLES */
int quiet;
-
-
+ts_double V0;
+ts_double A0;
+ts_double epsvol;
+ts_double epsarea;
/* FUNCTIONS */
/** Non-fatal error function handler:
--
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