From 2c4278db6ead5c27e30a3000097ed898c968534e Mon Sep 17 00:00:00 2001
From: Samo Penic <samo.penic@gmail.com>
Date: Sat, 09 Mar 2019 19:45:22 +0000
Subject: [PATCH] Added direct force plugin and fixes in stretching energy
---
src/general.h | 89 ++++++++++++++++++++++++++++++++++++++++++--
1 files changed, 84 insertions(+), 5 deletions(-)
diff --git a/src/general.h b/src/general.h
index 5189c23..ab0c257 100644
--- a/src/general.h
+++ b/src/general.h
@@ -156,7 +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;
@@ -194,11 +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;
@@ -249,6 +252,11 @@
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 +265,7 @@
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 +275,8 @@
long int pswitch;
long int constvolswitch;
long int constareaswitch;
+ long int stretchswitch;
+ ts_double xkA0;
ts_double constvolprecision;
char *multiprocessing;
long int brezveze0;
@@ -283,9 +294,72 @@
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);
+ void (*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_vertex *backup_vertices);
+ ts_double (*vm_before_montecarlo_constraint)(void *vesicle, ts_vertex *vtx, ts_vertex *old_vtx);
+ ts_double (*vm_new_state_accepted)(void *vesicle, ts_vertex *vtx, ts_vertex *old_vtx);
+ ts_double (*vm_new_state_rejected)(void *vesicle, ts_vertex *vtx, ts_vertex *old_vtx);
+ void (*cleanup)(void);
+} ts_plugin_function;
+
+typedef struct {
+ ts_char *name;
+ ts_char *description;
+ ts_char *author;
+ void *data;
+} ts_plugin_details;
+
+typedef struct {
+ ts_plugin_details *details;
+ ts_plugin_function *function;
+ ts_char *filename;
+ void *libhandle;
+} ts_plugin;
+
+struct ts_plugin_chain {
+ ts_plugin *plugin;
+ struct ts_plugin_chain *next;
+};
+typedef struct ts_plugin_chain ts_plugin_chain;
+
+typedef struct {
+ ts_plugin_chain *at_start;
+ ts_plugin_chain *after_vesicle_init;
+ ts_plugin_chain *vm_hard_constraint;
+ ts_plugin_chain *vm_energy_before_prepare;
+ ts_plugin_chain *vm_energy_after_execute;
+ ts_plugin_chain *vm_before_montecarlo_constraint;
+ ts_plugin_chain *vm_new_state_accepted;
+ ts_plugin_chain *vm_new_state_rejected;
+ ts_plugin_chain *cleanup;
+} ts_plugin_chains;
+
+
+typedef struct {
+ ts_uint n;
+ ts_plugin **plugin;
+ ts_plugin_chains *chain;
+ ts_plugin_chain *pointer;
+} ts_plugin_list;
+
+/* end plugins */
typedef struct {
@@ -308,22 +382,26 @@
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_plugin_list *plist;
} ts_vesicle;
-typedef struct{
+struct ts_cluster{
ts_uint nvtx;
ts_uint idx;
ts_vertex **vtx;
-} ts_cluster;
+};
+
+typedef struct ts_cluster ts_cluster;
typedef struct{
ts_uint n;
@@ -365,4 +443,5 @@
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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