From 06afc729f9061c1cfa14c78728d61d518324c2f0 Mon Sep 17 00:00:00 2001
From: Samo Penic <samo.penic@gmail.com>
Date: Wed, 04 May 2022 05:46:43 +0000
Subject: [PATCH] Moved all global variables to separate file and defined extern keyword where appropriate

---
 src/general.h |   44 ++++++++++++++++++++++++++++++++++----------
 1 files changed, 34 insertions(+), 10 deletions(-)

diff --git a/src/general.h b/src/general.h
index 31de50a..2f15c50 100644
--- a/src/general.h
+++ b/src/general.h
@@ -156,7 +156,9 @@
         ts_double projArea;
         ts_double relR;
         ts_double solAngle;
-	struct ts_poly *grafted_poly;
+		struct ts_poly *grafted_poly;
+		struct ts_cluster *cluster;
+	ts_double direct_interaction_force;
 };
 typedef struct ts_vertex ts_vertex;
 
@@ -194,11 +196,13 @@
 	ts_double znorm;
     ts_double area; // firstly needed for sh.c
     ts_double volume; // firstly needed for sh.c
+	ts_double energy;
 };
 typedef struct ts_triangle ts_triangle;
 
 struct ts_triangle_list{
     ts_uint n;
+	ts_double a0;
     ts_triangle **tria;
 };
 typedef struct ts_triangle_list ts_triangle_list;
@@ -216,7 +220,7 @@
     ts_cell **cell;
     ts_double dcell;
     ts_double shift;
-    ts_double max_occupancy;
+    ts_uint max_occupancy;
 	ts_double dmin_interspecies;
 } ts_cell_list;
 
@@ -249,6 +253,11 @@
 typedef struct ts_poly_list ts_poly_list;
 
 
+typedef struct{
+	ts_float z_max;
+	ts_float z_min;
+	ts_int force_switch;
+} ts_confinement_plane;
 
 typedef struct {
 	long int nshell;
@@ -257,6 +266,7 @@
 	long int nczmax;
 	long int npoly;
 	long int nmono;
+	long int internal_poly;
 	long int nfil;
 	long int nfono;
 	long int R_nucleus;
@@ -266,6 +276,8 @@
 	long int pswitch;
     long int constvolswitch;
     long int constareaswitch;
+	long int stretchswitch;
+	ts_double xkA0;
     ts_double constvolprecision;
     	char *multiprocessing;
    	long int brezveze0;
@@ -286,6 +298,10 @@
 	long int number_of_vertices_with_c0;
 	ts_double c0;
 	ts_double w;
+	ts_double F;
+	long int plane_confinement_switch;
+	ts_double plane_d;
+	ts_double plane_F;
 } ts_tape;
 
 
@@ -311,24 +327,31 @@
 	ts_double spring_constant;
 	ts_double pressure;
 	ts_int pswitch;
-    ts_tape *tape;
+ 	ts_tape *tape;
 	ts_double R_nucleus;
 	ts_double R_nucleusX;
 	ts_double R_nucleusY;
 	ts_double R_nucleusZ;
 	ts_double nucleus_center[3];
-    ts_double area;
+	ts_double area;
+	ts_confinement_plane confinement_plane;
 } ts_vesicle;
 
 
 
-/* GLOBAL VARIABLES */
+struct ts_cluster{
+	ts_uint nvtx;
+	ts_uint idx;
+	ts_vertex **vtx;
+};
 
-int quiet;
-ts_double V0;
-ts_double A0;
-ts_double epsvol;
-ts_double epsarea;
+typedef struct ts_cluster ts_cluster;
+
+typedef struct{
+	ts_uint n;
+	ts_cluster **cluster;
+} ts_cluster_list;
+
 /* FUNCTIONS */
 
 /** Non-fatal error function handler:
@@ -356,4 +379,5 @@
 int createPidFile(const char *progName, const char *pidFile, int flags);
 
 int lockRegion(int fd, int type, int whence, int start, int len);
+char *libVersion();
 #endif

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