From a00f10fd48a1de31c3ac923c2106969f84e831e0 Mon Sep 17 00:00:00 2001
From: Samo Penic <samo.penic@fe.uni-lj.si>
Date: Mon, 09 Mar 2015 11:09:31 +0000
Subject: [PATCH] Documented energy.c
---
src/energy.c | 61 +++++++++++++++++++++++++++---
1 files changed, 55 insertions(+), 6 deletions(-)
diff --git a/src/energy.c b/src/energy.c
index 440f319..695247c 100644
--- a/src/energy.c
+++ b/src/energy.c
@@ -4,6 +4,15 @@
#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;
@@ -19,7 +28,14 @@
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;
@@ -27,11 +43,46 @@
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$c_{tn}\f$.
+ *
+ \f{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) {};
+\f}
+
+ * 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_vertex_data *data=vtx->data;
ts_uint jj;
ts_uint jjp,jjm;
ts_vertex *j,*jp, *jm;
@@ -47,7 +98,6 @@
j=vtx->neigh[jj-1];
jp=vtx->neigh[jjp-1];
jm=vtx->neigh[jjm-1];
-// printf("tristar_no=%u, neigh_no=%u, jj=%u\n",data->tristar_no,data->neigh_no,jj);
jt=vtx->tristar[jj-1];
x1=vtx_distance_sq(vtx,jp); //shouldn't be zero!
x2=vtx_distance_sq(j,jp); // shouldn't be zero!
@@ -128,7 +178,6 @@
vtx->curvature=-sqrtl(h);
}
#endif
-// What is vtx->c?????????????? Here it is 0!
// 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);
--
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