From bd826de2f539f2e48c8c01d2d7f9f34c7e97104a Mon Sep 17 00:00:00 2001
From: Samo Penic <samo.penic@gmail.com>
Date: Fri, 13 May 2016 07:43:27 +0000
Subject: [PATCH] Fix in trisurf output, inhibiting print of successful reconstruction. Multiple fixes and improvements in python module. Added symlinking of tapes into the running directories and dumping tapes from snapshots into tape files.
---
src/energy.c | 68 +++++++++++++++++++++++++++++++--
1 files changed, 63 insertions(+), 5 deletions(-)
diff --git a/src/energy.c b/src/energy.c
index abbb8e7..4f2b386 100644
--- a/src/energy.c
+++ b/src/energy.c
@@ -1,9 +1,19 @@
+/* vim: set ts=4 sts=4 sw=4 noet : */
#include<stdlib.h>
#include "general.h"
#include "energy.h"
#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;
@@ -19,11 +29,61 @@
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_vertex_data *data=vtx->data;
ts_uint jj;
ts_uint jjp,jjm;
ts_vertex *j,*jp, *jm;
@@ -39,7 +99,6 @@
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!
@@ -120,7 +179,6 @@
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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