From e87e4e4fcbba57d36dfd17b92f413ccf2c1b322a Mon Sep 17 00:00:00 2001
From: Samo Penic <samo.penic@fe.uni-lj.si>
Date: Mon, 29 Feb 2016 08:20:59 +0000
Subject: [PATCH] Fixed restoration (partially)
---
src/energy.c | 100 +++++++++++++++++++++++++++++++++++++++++---------
1 files changed, 82 insertions(+), 18 deletions(-)
diff --git a/src/energy.c b/src/energy.c
index 61720ee..3173f67 100644
--- a/src/energy.c
+++ b/src/energy.c
@@ -4,30 +4,90 @@
#include "vertex.h"
#include<math.h>
#include<stdio.h>
+
+
+/** @brief Wrapper that calculates energy of every vertex in vesicle
+ *
+ * Function calculated energy of every vertex in vesicle. It can be used in
+ * initialization procedure or in recalculation of the energy after non-MCsweep * operations. However, when random move of vertex or flip of random bond occur * call to this function is not necessary nor recommended.
+ * @param *vesicle is a pointer to vesicle.
+ * @returns TS_SUCCESS on success.
+*/
ts_bool mean_curvature_and_energy(ts_vesicle *vesicle){
- ts_uint i, jj, jjp;
+ ts_uint i;
- ts_vertex_list *vlist=&vesicle->vlist;
- ts_vertex *vtx=vlist->vertex;
+ ts_vertex_list *vlist=vesicle->vlist;
+ ts_vertex **vtx=vlist->vtx;
for(i=0;i<vlist->n;i++){
- //should call with zero index!!!
- energy_vertex(&vtx[i]);
+ energy_vertex(vtx[i]);
+
}
return TS_SUCCESS;
}
+/** @brief Calculate energy of a bond (in models where energy is bond related)
+ *
+ * This function is experimental and currently only used in polymeres calculation (PEGs or polymeres inside the vesicle).
+ *
+ * @param *bond is a pointer to a bond between two vertices in polymere
+ * @param *poly is a pointer to polymere in which we calculate te energy of the bond
+ * @returns TS_SUCCESS on successful calculation
+*/
+inline ts_bool bond_energy(ts_bond *bond,ts_poly *poly){
+//TODO: This value to be changed and implemented in data structure:
+ ts_double d_relaxed=1.0;
+ bond->energy=poly->k*pow(bond->bond_length-d_relaxed,2);
+ return TS_SUCCESS;
+};
+/** @brief Calculation of energy of the vertex
+ *
+ * Main function that calculates energy of the vertex \f$i\f$. Nearest neighbors (NN) must be ordered in counterclockwise direction for this function to work.
+ * Firstly NNs that form two neighboring triangles are found (\f$j_m\f$, \f$j_p\f$ and common \f$j\f$). Later, the scalar product of vectors \f$x_1=(\mathbf{i}-\mathbf{j_p})\cdot (\mathbf{i}-\mathbf{j_p})(\mathbf{i}-\mathbf{j_p})\f$, \f$x_2=(\mathbf{j}-\mathbf{j_p})\cdot (\mathbf{j}-\mathbf{j_p})\f$ and \f$x_3=(\mathbf{j}-\mathbf{j_p})\cdot (\mathbf{i}-\mathbf{j_p})\f$ are calculated. From these three vectors the \f$c_{tp}=\frac{1}{\tan(\varphi_p)}\f$ is calculated, where \f$\varphi_p\f$ is the inner angle at vertex \f$j_p\f$. The procedure is repeated for \f$j_m\f$ instead of \f$j_p\f$ resulting in \f$c_{tn}\f$.
+ *
+\begin{tikzpicture}{
+\coordinate[label=below:$i$] (i) at (2,0);
+\coordinate[label=left:$j_m$] (jm) at (0,3.7);
+\coordinate[label=above:$j$] (j) at (2.5,6.4);
+\coordinate[label=right:$j_p$] (jp) at (4,2.7);
+
+\draw (i) -- (jm) -- (j) -- (jp) -- (i) -- (j);
+
+\begin{scope}
+\path[clip] (jm)--(i)--(j);
+\draw (jm) circle (0.8);
+\node[right] at (jm) {$\varphi_m$};
+\end{scope}
+
+\begin{scope}
+\path[clip] (jp)--(i)--(j);
+\draw (jp) circle (0.8);
+\node[left] at (jp) {$\varphi_p$};
+\end{scope}
+
+%%vertices
+\draw [fill=gray] (i) circle (0.1);
+\draw [fill=white] (j) circle (0.1);
+\draw [fill=white] (jp) circle (0.1);
+\draw [fill=white] (jm) circle (0.1);
+%\node[draw,circle,fill=white] at (i) {};
+\end{tikzpicture}
+
+ * The curvature is then calculated as \f$\mathbf{h}=\frac{1}{2}\Sigma_{k=0}^{\mathrm{neigh\_no}} c_{tp}^{(k)}+c_{tm}^{(k)} (\mathbf{j_k}-\mathbf{i})\f$, where \f$c_{tp}^{(k)}+c_{tm}^k=2\sigma^{(k)}\f$ (length in dual lattice?) and the previous equation can be written as \f$\mathbf{h}=\Sigma_{k=0}^{\mathrm{neigh\_no}}\sigma^{(k)}\cdot(\mathbf{j}-\mathbf{i})\f$ (See Kroll, p. 384, eq 70).
+ *
+ * From the curvature the enery is calculated by equation \f$E=\frac{1}{2}\mathbf{h}\cdot\mathbf{h}\f$.
+ * @param *vtx is a pointer to vertex at which we want to calculate the energy
+ * @returns TS_SUCCESS on successful calculation.
+*/
inline ts_bool energy_vertex(ts_vertex *vtx){
-// ts_vertex *vtx=&vlist->vertex[n]-1; // Caution! 0 Indexed value!
-// ts_triangle *tristar=vtx->tristar-1;
ts_uint jj;
ts_uint jjp,jjm;
ts_vertex *j,*jp, *jm;
ts_triangle *jt;
- ts_double s=0,xh=0,yh=0,zh=0,txn=0,tyn=0,tzn=0;
+ ts_double s=0.0,xh=0.0,yh=0.0,zh=0.0,txn=0.0,tyn=0.0,tzn=0.0;
ts_double x1,x2,x3,ctp,ctm,tot,xlen;
ts_double h,ht;
for(jj=1; jj<=vtx->neigh_no;jj++){
@@ -39,8 +99,8 @@
jp=vtx->neigh[jjp-1];
jm=vtx->neigh[jjm-1];
jt=vtx->tristar[jj-1];
- x1=vertex_distance_sq(vtx,jp); //shouldn't be zero!
- x2=vertex_distance_sq(j,jp); // shouldn't be zero!
+ x1=vtx_distance_sq(vtx,jp); //shouldn't be zero!
+ x2=vtx_distance_sq(j,jp); // shouldn't be zero!
x3=(j->x-jp->x)*(vtx->x-jp->x)+
(j->y-jp->y)*(vtx->y-jp->y)+
(j->z-jp->z)*(vtx->z-jp->z);
@@ -54,8 +114,8 @@
#ifdef TS_DOUBLE_LONGDOUBLE
ctp=x3/sqrtl(x1*x2-x3*x3);
#endif
- x1=vertex_distance_sq(vtx,jm);
- x2=vertex_distance_sq(j,jm);
+ x1=vtx_distance_sq(vtx,jm);
+ x2=vtx_distance_sq(j,jm);
x3=(j->x-jm->x)*(vtx->x-jm->x)+
(j->y-jm->y)*(vtx->y-jm->y)+
(j->z-jm->z)*(vtx->z-jm->z);
@@ -70,19 +130,21 @@
#endif
tot=ctp+ctm;
tot=0.5*tot;
- xlen=vertex_distance_sq(j,vtx);
+
+ xlen=vtx_distance_sq(j,vtx);
+/*
#ifdef TS_DOUBLE_DOUBLE
- vtx->bond_length[jj-1]=sqrt(xlen);
+ vtx->bond[jj-1]->bond_length=sqrt(xlen);
#endif
#ifdef TS_DOUBLE_FLOAT
- vtx->bond_length[jj-1]=sqrtf(xlen);
+ vtx->bond[jj-1]->bond_length=sqrtf(xlen);
#endif
#ifdef TS_DOUBLE_LONGDOUBLE
- vtx->bond_length[jj-1]=sqrtl(xlen);
+ vtx->bond[jj-1]->bond_length=sqrtl(xlen);
#endif
- vtx->bond_length_dual[jj-1]=tot*vtx->bond_length[jj-1];
-
+ vtx->bond[jj-1]->bond_length_dual=tot*vtx->bond[jj-1]->bond_length;
+*/
s+=tot*xlen;
xh+=tot*(j->x - vtx->x);
yh+=tot*(j->y - vtx->y);
@@ -116,6 +178,8 @@
vtx->curvature=-sqrtl(h);
}
#endif
+// c is forced curvature energy for each vertex. Should be set to zero for
+// normal circumstances.
vtx->energy=0.5*s*(vtx->curvature/s-vtx->c)*(vtx->curvature/s-vtx->c);
return TS_SUCCESS;
--
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