From d2f3609e9ecec5ec8dc02a992a6ec98e28ca9c6d Mon Sep 17 00:00:00 2001
From: Samo Penic <samo.penic@gmail.com>
Date: Wed, 27 Feb 2019 18:37:32 +0000
Subject: [PATCH] Merge branch 'master' into plugins

---
 src/general.h |  148 ++++++++++++++++++++++++++++++++++++++++++++++---
 1 files changed, 139 insertions(+), 9 deletions(-)

diff --git a/src/general.h b/src/general.h
index 0372e7a..6756149 100644
--- a/src/general.h
+++ b/src/general.h
@@ -1,9 +1,10 @@
+/* vim: set ts=4 sts=4 sw=4 noet : */
 #ifndef _GENERAL_H
 #define _GENERAL_H
 
 #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
@@ -48,6 +49,8 @@
 #define TS_FAIL 1
 
 /* CONSTANTS */
+
+#define TS_ID_FILAMENT 1
 
 /* DATA TYPES */
 /** @brief Sets the default datatype for ts_double
@@ -153,7 +156,8 @@
         ts_double projArea;
         ts_double relR;
         ts_double solAngle;
-	struct ts_poly *grafted_poly;
+		struct ts_poly *grafted_poly;
+		struct ts_cluster *cluster;
 };
 typedef struct ts_vertex ts_vertex;
 
@@ -164,12 +168,14 @@
 } 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_bool tainted;
+    	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;
 
@@ -189,11 +195,13 @@
 	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;
@@ -212,12 +220,14 @@
     ts_double dcell;
     ts_double shift;
     ts_double max_occupancy;
+	ts_double dmin_interspecies;
 } ts_cell_list;
 
 
 typedef struct {
     ts_uint l;
     ts_double **ulm;
+    gsl_complex **ulmComplex;
     ts_double **sumUlm2;
     ts_uint N;
     ts_double **co;
@@ -242,6 +252,89 @@
 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;
+	long int ncxmax;
+	long int ncymax;
+	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;
+    	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;
+	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;
+
+
+/* plugins */
+typedef struct {
+	void (*at_start)(void);
+	void (*after_vesicle_init)(void *vesicle);
+	ts_bool (*vm_hard_constraint)(void *vesicle, ts_vertex *vtx, ts_vertex *odl_vtx);
+	ts_double (*vm_energy_before)(void *vesicle, ts_vertex *vtx);
+	ts_double (*vm_energy_after)(void *vesicle, ts_vertex *vtx);
+	ts_double (*vm_new_state_accepted)(void *vesicle, ts_vertex *vtx);
+	ts_double (*vm_new_state_rejected)(void *vesicle, ts_vertex *vtx);
+	void (*cleanup)(void);
+} ts_plugin_function;
+
+typedef struct {
+	ts_char *name;
+	ts_char *description;
+	ts_char *author;
+} ts_plugin_details;
+
+typedef struct {
+	ts_plugin_details *details;
+	ts_plugin_function *function;
+	ts_char *filename;
+	void *libhandle;
+} ts_plugin;
+
+typedef struct {
+	ts_uint n;
+	ts_plugin **plugin;
+} ts_plugin_list;
+
+/* end plugins */
 
 
 typedef struct {
@@ -256,19 +349,48 @@
    	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 R_nucleusX;
+	ts_double R_nucleusY;
+	ts_double R_nucleusZ;
+	ts_double nucleus_center[3];
+	ts_double area;
+	ts_confinement_plane confinement_plane;
+	ts_plugin_list plist;
 } 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 */
 
 int quiet;
-
-
+ts_double V0;
+ts_double A0;
+ts_double epsvol;
+ts_double epsarea;
 /* FUNCTIONS */
 
 /** Non-fatal error function handler:
@@ -289,4 +411,12 @@
 #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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