From 3197854e89eb9ffe5ff3137e274d16806c2028a5 Mon Sep 17 00:00:00 2001
From: Samo Penic <samo.penic@gmail.com>
Date: Tue, 27 Jul 2021 12:51:09 +0000
Subject: [PATCH] Found one bug in the code when calculating mprod. Fixed.

---
 src/general.h |   60 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++----
 1 files changed, 56 insertions(+), 4 deletions(-)

diff --git a/src/general.h b/src/general.h
index 24c5f89..4388e2c 100644
--- a/src/general.h
+++ b/src/general.h
@@ -156,7 +156,12 @@
         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 edge_x[14];
+	ts_double edge_y[14];
+	ts_double edge_z[14];
+
 };
 typedef struct ts_vertex ts_vertex;
 
@@ -194,11 +199,13 @@
 	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 +223,7 @@
     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 +256,11 @@
 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;
@@ -257,12 +269,18 @@
 	long int nczmax;
 	long int npoly;
 	long int nmono;
+	long int internal_poly;
 	long int nfil;
 	long int nfono;
 	long int R_nucleus;
+	ts_double R_nucleusX;
+	ts_double R_nucleusY;
+	ts_double R_nucleusZ;
 	long int pswitch;
     long int constvolswitch;
     long int constareaswitch;
+	long int stretchswitch;
+	ts_double xkA0;
     ts_double constvolprecision;
     	char *multiprocessing;
    	long int brezveze0;
@@ -280,6 +298,13 @@
 	long int mcsweeps;
 	long int quiet;
 	long int shc;
+	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;
 
 
@@ -305,11 +330,30 @@
 	ts_double spring_constant;
 	ts_double pressure;
 	ts_int pswitch;
-    ts_tape *tape;
+ 	ts_tape *tape;
 	ts_double R_nucleus;
-    ts_double area;
+	ts_double R_nucleusX;
+	ts_double R_nucleusY;
+	ts_double R_nucleusZ;
+	ts_double nucleus_center[3];
+	ts_double area;
+	ts_confinement_plane confinement_plane;
 } ts_vesicle;
 
+
+
+struct ts_cluster{
+	ts_uint nvtx;
+	ts_uint idx;
+	ts_vertex **vtx;
+};
+
+typedef struct ts_cluster ts_cluster;
+
+typedef struct{
+	ts_uint n;
+	ts_cluster **cluster;
+} ts_cluster_list;
 
 
 /* GLOBAL VARIABLES */
@@ -339,4 +383,12 @@
 #define VTX(n) &(vlist->vtx[n])
 #define VTX_DATA(n) vlist->vtx[n].data
 
+
+/* FOR PID GENERATION ROUTINE */
+#define CPF_CLOEXEC 1
+
+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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