From fc6f3ef0a9822f3d5f06d38e556dbb5f2e985f4a Mon Sep 17 00:00:00 2001
From: Samo Penic <samo.penic@gmail.com>
Date: Wed, 13 Jul 2016 17:33:28 +0000
Subject: [PATCH] First attempt in solving an issue of dense packed internal pegs. They are recreated as many times as needed.
---
src/general.h | 82 ++++++++++++++++++++++++++++++++++++----
1 files changed, 73 insertions(+), 9 deletions(-)
diff --git a/src/general.h b/src/general.h
index e7e9545..4eab674 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
@@ -167,10 +170,11 @@
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;
@@ -213,12 +217,14 @@
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;
@@ -244,6 +250,44 @@
+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;
+ 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;
+} ts_tape;
+
+
+
typedef struct {
ts_vertex_list *vlist;
@@ -257,19 +301,32 @@
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;
- ts_double spring_constant;
-} ts_vesicle;
+// 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_vesicle;
/* GLOBAL VARIABLES */
int quiet;
-
-
+ts_double V0;
+ts_double A0;
+ts_double epsvol;
+ts_double epsarea;
/* FUNCTIONS */
/** Non-fatal error function handler:
@@ -290,4 +347,11 @@
#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);
#endif
--
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