From d43116b7d609fa9cabae4068d037c1af3a20dae8 Mon Sep 17 00:00:00 2001
From: Samo Penic <samo.penic@gmail.com>
Date: Thu, 08 Aug 2019 17:42:46 +0000
Subject: [PATCH] An attempt to fix polymer error while recreating vesicle from vtu.
---
src/energy.c | 193 +++++++++++++++++++++++++++++++++++++++---------
1 files changed, 157 insertions(+), 36 deletions(-)
diff --git a/src/energy.c b/src/energy.c
index 540686b..1dae415 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;
@@ -13,37 +23,91 @@
for(i=0;i<vlist->n;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 the bending energy of the vertex.
+ *
+ * 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}{
+\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;
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<=data->neigh_no;jj++){
+ for(jj=1; jj<=vtx->neigh_no;jj++){
jjp=jj+1;
- if(jjp>data->neigh_no) jjp=1;
+ if(jjp>vtx->neigh_no) jjp=1;
jjm=jj-1;
- if(jjm<1) jjm=data->neigh_no;
- j=data->neigh[jj-1];
- jp=data->neigh[jjp-1];
- jm=data->neigh[jjm-1];
- jt=data->tristar[jj-1];
+ if(jjm<1) jjm=vtx->neigh_no;
+ j=vtx->neigh[jj-1];
+ jp=vtx->neigh[jjp-1];
+ jm=vtx->neigh[jjm-1];
+ 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!
- x3=(j->data->x-jp->data->x)*(data->x-jp->data->x)+
- (j->data->y-jp->data->y)*(data->y-jp->data->y)+
- (j->data->z-jp->data->z)*(data->z-jp->data->z);
+ 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);
#ifdef TS_DOUBLE_DOUBLE
ctp=x3/sqrt(x1*x2-x3*x3);
@@ -56,9 +120,9 @@
#endif
x1=vtx_distance_sq(vtx,jm);
x2=vtx_distance_sq(j,jm);
- x3=(j->data->x-jm->data->x)*(data->x-jm->data->x)+
- (j->data->y-jm->data->y)*(data->y-jm->data->y)+
- (j->data->z-jm->data->z)*(data->z-jm->data->z);
+ 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);
#ifdef TS_DOUBLE_DOUBLE
ctm=x3/sqrt(x1*x2-x3*x3);
#endif
@@ -70,26 +134,28 @@
#endif
tot=ctp+ctm;
tot=0.5*tot;
+
xlen=vtx_distance_sq(j,vtx);
+/*
#ifdef TS_DOUBLE_DOUBLE
- data->bond[jj-1]->data->bond_length=sqrt(xlen);
+ vtx->bond[jj-1]->bond_length=sqrt(xlen);
#endif
#ifdef TS_DOUBLE_FLOAT
- data->bond[jj-1]->data->bond_length=sqrtf(xlen);
+ vtx->bond[jj-1]->bond_length=sqrtf(xlen);
#endif
#ifdef TS_DOUBLE_LONGDOUBLE
- data->bond[jj-1]->data->bond_length=sqrtl(xlen);
+ vtx->bond[jj-1]->bond_length=sqrtl(xlen);
#endif
- data->bond[jj-1]->data->bond_length_dual=tot*data->bond[jj-1]->data->bond_length;
-
+ vtx->bond[jj-1]->bond_length_dual=tot*vtx->bond[jj-1]->bond_length;
+*/
s+=tot*xlen;
- xh+=tot*(j->data->x - data->x);
- yh+=tot*(j->data->y - data->y);
- zh+=tot*(j->data->z - data->z);
- txn+=jt->data->xnorm;
- tyn+=jt->data->ynorm;
- tzn+=jt->data->znorm;
+ xh+=tot*(j->x - vtx->x);
+ yh+=tot*(j->y - vtx->y);
+ zh+=tot*(j->z - vtx->z);
+ txn+=jt->xnorm;
+ tyn+=jt->ynorm;
+ tzn+=jt->znorm;
}
h=xh*xh+yh*yh+zh*zh;
@@ -97,27 +163,82 @@
s=s/4.0;
#ifdef TS_DOUBLE_DOUBLE
if(ht>=0.0) {
- data->curvature=sqrt(h);
+ vtx->curvature=sqrt(h);
} else {
- data->curvature=-sqrt(h);
+ vtx->curvature=-sqrt(h);
}
#endif
#ifdef TS_DOUBLE_FLOAT
if(ht>=0.0) {
- data->curvature=sqrtf(h);
+ vtx->curvature=sqrtf(h);
} else {
- data->curvature=-sqrtf(h);
+ vtx->curvature=-sqrtf(h);
}
#endif
#ifdef TS_DOUBLE_LONGDOUBLE
if(ht>=0.0) {
- data->curvature=sqrtl(h);
+ vtx->curvature=sqrtl(h);
} else {
- data->curvature=-sqrtl(h);
+ vtx->curvature=-sqrtl(h);
}
#endif
-//TODO: MAJOR!!!! What is vtx->data->c?????????????? Here it is 0!
- data->energy=0.5*s*(data->curvature/s-data->c)*(data->curvature/s-data->c);
+// 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;
+
+}
+
+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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