From 608cbe1dd70feed73f702459c52876bf62f276b7 Mon Sep 17 00:00:00 2001
From: Samo Penic <samo.penic@gmail.com>
Date: Mon, 06 Jul 2020 07:44:11 +0000
Subject: [PATCH] Triangles are in right order.
---
src/energy.c | 321 ++++++++++++++++++++++++++++++++++++----------------
1 files changed, 221 insertions(+), 100 deletions(-)
diff --git a/src/energy.c b/src/energy.c
index 97e7315..1f2bd1c 100644
--- a/src/energy.c
+++ b/src/energy.c
@@ -1,9 +1,20 @@
+/* vim: set ts=4 sts=4 sw=4 noet : */
#include<stdlib.h>
#include "general.h"
#include "energy.h"
#include "vertex.h"
+#include "bond.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;
@@ -19,109 +30,219 @@
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 x1,x2,x3,ctp,ctm,tot,xlen;
- ts_double h,ht;
- for(jj=1; jj<=data->neigh_no;jj++){
- jjp=jj+1;
- if(jjp>data->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];
-// printf("tristar_no=%u, neigh_no=%u, jj=%u\n",data->tristar_no,data->neigh_no,jj);
- jt=data->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);
-
-#ifdef TS_DOUBLE_DOUBLE
- ctp=x3/sqrt(x1*x2-x3*x3);
-#endif
-#ifdef TS_DOUBLE_FLOAT
- ctp=x3/sqrtf(x1*x2-x3*x3);
-#endif
-#ifdef TS_DOUBLE_LONGDOUBLE
- ctp=x3/sqrtl(x1*x2-x3*x3);
-#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);
-#ifdef TS_DOUBLE_DOUBLE
- ctm=x3/sqrt(x1*x2-x3*x3);
-#endif
-#ifdef TS_DOUBLE_FLOAT
- ctm=x3/sqrtf(x1*x2-x3*x3);
-#endif
-#ifdef TS_DOUBLE_LONGDOUBLE
- ctm=x3/sqrtl(x1*x2-x3*x3);
-#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);
-#endif
-#ifdef TS_DOUBLE_FLOAT
- data->bond[jj-1]->data->bond_length=sqrtf(xlen);
-#endif
-#ifdef TS_DOUBLE_LONGDOUBLE
- data->bond[jj-1]->data->bond_length=sqrtl(xlen);
-#endif
+ ts_uint jj, i, j;
+ ts_double edge_vector_x[7]={0,0,0,0,0,0,0};
+ ts_double edge_vector_y[7]={0,0,0,0,0,0,0};
+ ts_double edge_vector_z[7]={0,0,0,0,0,0,0};
+ ts_double edge_normal_x[7]={0,0,0,0,0,0,0};
+ ts_double edge_normal_y[7]={0,0,0,0,0,0,0};
+ ts_double edge_normal_z[7]={0,0,0,0,0,0,0};
+ ts_double edge_binormal_x[7]={0,0,0,0,0,0,0};
+ ts_double edge_binormal_y[7]={0,0,0,0,0,0,0};
+ ts_double edge_binormal_z[7]={0,0,0,0,0,0,0};
+ ts_double vertex_normal_x=0.0;
+ ts_double vertex_normal_y=0.0;
+ ts_double vertex_normal_z=0.0;
+// ts_triangle *triedge[2]={NULL,NULL};
- data->bond[jj-1]->data->bond_length_dual=tot*data->bond[jj-1]->data->bond_length;
+ ts_uint nei,neip,neim;
+ ts_vertex *it, *k, *kp,*km;
+ ts_triangle *lm=NULL, *lp=NULL;
+ ts_double sumnorm;
- 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->xnorm;
- tyn+=jt->ynorm;
- tzn+=jt->znorm;
- }
-
- h=xh*xh+yh*yh+zh*zh;
- ht=txn*xh+tyn*yh + tzn*zh;
- s=s/4.0;
-#ifdef TS_DOUBLE_DOUBLE
- if(ht>=0.0) {
- data->curvature=sqrt(h);
- } else {
- data->curvature=-sqrt(h);
- }
-#endif
-#ifdef TS_DOUBLE_FLOAT
- if(ht>=0.0) {
- data->curvature=sqrtf(h);
- } else {
- data->curvature=-sqrtf(h);
- }
-#endif
-#ifdef TS_DOUBLE_LONGDOUBLE
- if(ht>=0.0) {
- data->curvature=sqrtl(h);
- } else {
- data->curvature=-sqrtl(h);
- }
-#endif
-// What is vtx->data->c?????????????? Here it is 0!
-// c is forced curvature energy for each vertex. Should be set to zero for
-// norman circumstances.
- data->energy=0.5*s*(data->curvature/s-data->c)*(data->curvature/s-data->c);
+ // Here edge vector is calculated
+// fprintf(stderr, "Vertex has neighbours=%d\n", vtx->neigh_no);
+ for(jj=0;jj<vtx->neigh_no;jj++){
+ edge_vector_x[jj]=vtx->neigh[jj]->x-vtx->x;
+ edge_vector_y[jj]=vtx->neigh[jj]->y-vtx->y;
+ edge_vector_z[jj]=vtx->neigh[jj]->z-vtx->z;
- return TS_SUCCESS;
+
+ it=vtx;
+ k=vtx->neigh[jj];
+ nei=0;
+ for(i=0;i<it->neigh_no;i++){ // Finds the nn of it, that is k
+ if(it->neigh[i]==k){
+ nei=i;
+ break;
+ }
+ }
+ neip=nei+1; // I don't like it.. Smells like I must have it in correct order
+ neim=nei-1;
+ if(neip>=it->neigh_no) neip=0;
+ if((ts_int)neim<0) neim=it->neigh_no-1; /* casting is essential... If not
+there the neim is never <0 !!! */
+ // fprintf(stderr,"The numbers are: %u %u\n",neip, neim);
+ km=it->neigh[neim]; // We located km and kp
+ kp=it->neigh[neip];
+
+ if(km==NULL || kp==NULL){
+ fatal("In bondflip, cannot determine km and kp!",999);
+ }
+
+ for(i=0;i<it->tristar_no;i++){
+ for(j=0;j<k->tristar_no;j++){
+ if((it->tristar[i] == k->tristar[j])){ //ce gre za skupen trikotnik
+ if((it->tristar[i]->vertex[0] == km || it->tristar[i]->vertex[1]
+== km || it->tristar[i]->vertex[2]== km )){
+ lm=it->tristar[i];
+ // lmidx=i;
+ }
+ else
+ {
+ lp=it->tristar[i];
+ // lpidx=i;
+ }
+
+ }
+ }
+ }
+if(lm==NULL || lp==NULL) fatal("ts_flip_bond: Cannot find triangles lm and lp!",999);
+
+
+/*
+ // We find lm and lp from k->tristar !
+ cnt=0;
+ for(i=0;i<vtx->tristar_no;i++){
+ for(j=0;j<vtx->neigh[jj]->tristar_no;j++){
+ if((vtx->tristar[i] == vtx->neigh[jj]->tristar[j])){ //ce gre za skupen trikotnik
+ triedge[cnt]=vtx->tristar[i];
+ cnt++;
+ }
+ }
+ }
+ if(cnt!=2) fatal("ts_energy_vertex: both triangles not found!", 133);
+*/
+
+ sumnorm=sqrt( pow((lm->xnorm + lp->xnorm),2) + pow((lm->ynorm + lp->ynorm), 2) + pow((lm->znorm + lp->znorm), 2));
+
+ edge_normal_x[jj]=(lm->xnorm+ lp->xnorm)/sumnorm;
+ edge_normal_y[jj]=(lm->ynorm+ lp->ynorm)/sumnorm;
+ edge_normal_z[jj]=(lm->znorm+ lp->znorm)/sumnorm;
+
+
+ edge_binormal_x[jj]=(edge_normal_y[jj]*edge_vector_z[jj])-(edge_normal_z[jj]*edge_vector_y[jj]);
+ edge_binormal_y[jj]=-(edge_normal_x[jj]*edge_vector_z[jj])+(edge_normal_z[jj]*edge_vector_x[jj]);
+ edge_binormal_z[jj]=(edge_normal_x[jj]*edge_vector_y[jj])-(edge_normal_y[jj]*edge_vector_x[jj]);
+
+ printf("(%f %f %f); (%f %f %f); (%f %f %f)\n", edge_vector_x[jj], edge_vector_y[jj], edge_vector_z[jj], edge_normal_x[jj], edge_normal_y[jj], edge_normal_z[jj], edge_binormal_x[jj], edge_binormal_y[jj], edge_binormal_z[jj]);
+
+ }
+ for(i=0; i<vtx->tristar_no; i++){
+ vertex_normal_x=vertex_normal_x + vtx->tristar[i]->xnorm*vtx->tristar[i]->area;
+ vertex_normal_y=vertex_normal_y + vtx->tristar[i]->ynorm*vtx->tristar[i]->area;
+ vertex_normal_z=vertex_normal_z + vtx->tristar[i]->znorm*vtx->tristar[i]->area;
+ }
+ printf("(%f %f %f)\n", vertex_normal_x, vertex_normal_y, vertex_normal_z);
+ vtx->energy=0.0;
+ 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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