From eb7d7ef09dce79ec0c95f8e8779abe963c4043f2 Mon Sep 17 00:00:00 2001
From: Samo Penic <samo.penic@gmail.com>
Date: Tue, 25 Dec 2018 19:49:00 +0000
Subject: [PATCH] First working version of plugins
---
src/energy.c | 62 +++++++++++++++++++++++++++++--
1 files changed, 58 insertions(+), 4 deletions(-)
diff --git a/src/energy.c b/src/energy.c
index 695247c..4d27995 100644
--- a/src/energy.c
+++ b/src/energy.c
@@ -1,3 +1,4 @@
+/* vim: set ts=4 sts=4 sw=4 noet : */
#include<stdlib.h>
#include "general.h"
#include "energy.h"
@@ -43,12 +44,15 @@
return TS_SUCCESS;
};
-/** @brief Calculation of energy of the vertex
+/** @brief Calculation of the bending 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.
+ * Main function that calculates energy of the vertex \f$i\f$. Function returns \f$\frac{1}{2}(c_1+c_2-c)^2 s\f$, where \f$(c_1+c_2)/2\f$ is mean curvature,
+ * \f$c/2\f$ is spontaneous curvature and \f$s\f$ is area per 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}{
+\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);
@@ -74,7 +78,7 @@
\draw [fill=white] (jp) circle (0.1);
\draw [fill=white] (jm) circle (0.1);
%\node[draw,circle,fill=white] at (i) {};
-\f}
+\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).
*
@@ -180,7 +184,57 @@
#endif
// c is forced curvature energy for each vertex. Should be set to zero for
// normal circumstances.
+/* the following statement is an expression for $\frac{1}{2}\int(c_1+c_2-c_0^\prime)^2\mathrm{d}A$, where $c_0^\prime=2c_0$ (twice the spontaneous curvature) */
vtx->energy=0.5*s*(vtx->curvature/s-vtx->c)*(vtx->curvature/s-vtx->c);
return TS_SUCCESS;
}
+
+
+
+ts_bool sweep_attraction_bond_energy(ts_vesicle *vesicle){
+ int i;
+ for(i=0;i<vesicle->blist->n;i++){
+ attraction_bond_energy(vesicle->blist->bond[i], vesicle->tape->w);
+ }
+ return TS_SUCCESS;
+}
+
+
+inline ts_bool attraction_bond_energy(ts_bond *bond, ts_double w){
+
+ if(fabs(bond->vtx1->c)>1e-16 && fabs(bond->vtx2->c)>1e-16){
+ bond->energy=-w;
+ }
+ else {
+ bond->energy=0.0;
+ }
+ return TS_SUCCESS;
+}
+
+ts_double direct_force_energy(ts_vesicle *vesicle, ts_vertex *vtx, ts_vertex *vtx_old){
+ if(fabs(vtx->c)<1e-15) return 0.0;
+// printf("was here");
+ if(fabs(vesicle->tape->F)<1e-15) return 0.0;
+
+ ts_double norml,ddp=0.0;
+ ts_uint i;
+ ts_double xnorm=0.0,ynorm=0.0,znorm=0.0;
+ /*find normal of the vertex as sum of all the normals of the triangles surrounding it. */
+ for(i=0;i<vtx->tristar_no;i++){
+ xnorm+=vtx->tristar[i]->xnorm;
+ ynorm+=vtx->tristar[i]->ynorm;
+ znorm+=vtx->tristar[i]->znorm;
+ }
+ /*normalize*/
+ norml=sqrt(xnorm*xnorm+ynorm*ynorm+znorm*znorm);
+ xnorm/=norml;
+ ynorm/=norml;
+ znorm/=norml;
+ /*calculate ddp, perpendicular displacement*/
+ ddp=xnorm*(vtx->x-vtx_old->x)+ynorm*(vtx->y-vtx_old->y)+znorm*(vtx->z-vtx_old->z);
+ /*calculate dE*/
+// printf("ddp=%e",ddp);
+ return vesicle->tape->F*ddp;
+
+}
--
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