From 51b4f09bca802c4941700c78c5733ce968ddc7c6 Mon Sep 17 00:00:00 2001
From: Samo Penic <samo.penic@gmail.com>
Date: Wed, 27 Feb 2019 22:44:22 +0000
Subject: [PATCH] An attempt of adding hard constraints plugin to the simulator. It seems it does not work yet
---
src/general.h | 165 ++++++++++++++++++++++++++++++++++++++++++++++++++-----
1 files changed, 150 insertions(+), 15 deletions(-)
diff --git a/src/general.h b/src/general.h
index 5194460..d7c1ec7 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;
@@ -230,6 +240,7 @@
ts_vertex_list *vlist;
ts_bond_list *blist;
ts_vertex *grafted_vtx;
+ ts_double k;
};
typedef struct ts_poly ts_poly;
@@ -241,31 +252,147 @@
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)(int argc, char **argv);
+ 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_prepare)(void *vesicle, ts_vertex *vtx);
+ ts_double (*vm_energy_before_execute)(void *vesicle, ts_vertex *vtx);
+ ts_double (*vm_energy_after_prepare)(void *vesicle, ts_vertex *vtx);
+ ts_double (*vm_energy_after_execute)(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 {
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_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 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:
@@ -286,4 +413,12 @@
#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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