From 6487a03362d35589c286d0660eba123a7ab00535 Mon Sep 17 00:00:00 2001
From: Samo Penic <samo.penic@gmail.com>
Date: Mon, 10 May 2021 11:14:04 +0000
Subject: [PATCH] Raj and Yoav session in making multiple protein species
---
src/energy.c | 61 +++++++++++++++++++++++++++++-
1 files changed, 59 insertions(+), 2 deletions(-)
diff --git a/src/energy.c b/src/energy.c
index 4f2b386..b182a87 100644
--- a/src/energy.c
+++ b/src/energy.c
@@ -44,9 +44,12 @@
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$c_{tn}\f$.
*
\begin{tikzpicture}{
@@ -181,7 +184,61 @@
#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->direct_interaction_force)<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;
+
+}
+
+void stretchenergy(ts_vesicle *vesicle, ts_triangle *triangle){
+ triangle->energy=vesicle->tape->xkA0/2.0*pow((triangle->area/vesicle->tlist->a0-1.0),2);
+}
--
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