From 3197854e89eb9ffe5ff3137e274d16806c2028a5 Mon Sep 17 00:00:00 2001
From: Samo Penic <samo.penic@gmail.com>
Date: Tue, 27 Jul 2021 12:51:09 +0000
Subject: [PATCH] Found one bug in the code when calculating mprod. Fixed.
---
src/energy.c | 383 ++++++++++++++++++++++++++++++++++++++++--------------
1 files changed, 285 insertions(+), 98 deletions(-)
diff --git a/src/energy.c b/src/energy.c
index 3173f67..85a4fb4 100644
--- a/src/energy.c
+++ b/src/energy.c
@@ -1,9 +1,24 @@
+/* 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>
+#include <gsl/gsl_vector_complex.h>
+#include <gsl/gsl_matrix.h>
+#include <gsl/gsl_eigen.h>
+
+
+
+int cmpfunc(const void *x, const void *y)
+{
+ double diff= fabs(*(double*)x) - fabs(*(double*)y);
+ if(diff<0) return 1;
+ else return -1;
+}
+
/** @brief Wrapper that calculates energy of every vertex in vesicle
@@ -43,9 +58,12 @@
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}{
@@ -83,104 +101,273 @@
* @returns TS_SUCCESS on successful calculation.
*/
inline ts_bool energy_vertex(ts_vertex *vtx){
- ts_uint jj;
- ts_uint jjp,jjm;
- ts_vertex *j,*jp, *jm;
- ts_triangle *jt;
- 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<=vtx->neigh_no;jj++){
- jjp=jj+1;
- if(jjp>vtx->neigh_no) jjp=1;
- jjm=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->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);
-#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->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
-#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;
+ 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};
- xlen=vtx_distance_sq(j,vtx);
-/*
-#ifdef TS_DOUBLE_DOUBLE
- vtx->bond[jj-1]->bond_length=sqrt(xlen);
-#endif
-#ifdef TS_DOUBLE_FLOAT
- vtx->bond[jj-1]->bond_length=sqrtf(xlen);
-#endif
-#ifdef TS_DOUBLE_LONGDOUBLE
- vtx->bond[jj-1]->bond_length=sqrtl(xlen);
-#endif
+ ts_uint nei,neip,neim;
+ ts_vertex *it, *k, *kp,*km;
+ ts_triangle *lm=NULL, *lp=NULL;
+ ts_double sumnorm;
+ ts_double temp_length;
- vtx->bond[jj-1]->bond_length_dual=tot*vtx->bond[jj-1]->bond_length;
+
+ ts_double Se11, Se21, Se22, Se31, Se32, Se33;
+ ts_double Pv11, Pv21, Pv22, Pv31, Pv32, Pv33;
+ ts_double We;
+ ts_double Av, We_Av;
+
+ ts_double eigenval[3];
+
+ gsl_matrix *gsl_Sv=gsl_matrix_alloc(3,3);
+ gsl_vector *Sv_eigen=gsl_vector_alloc(3);
+ gsl_eigen_symm_workspace *workspace=gsl_eigen_symm_alloc(3);
+
+ ts_double mprod[7], phi[7], he[7];
+ ts_double Sv[3][3]={{0,0,0},{0,0,0},{0,0,0}};
+ // Here edge vector is calculated
+// fprintf(stderr, "Vertex has neighbours=%d\n", vtx->neigh_no);
+
+
+
+
+ Av=0;
+ 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);
+ Av+=vtx->tristar[i]->area/3;
+ }
+ temp_length=sqrt(pow(vertex_normal_x,2)+pow(vertex_normal_y,2)+pow(vertex_normal_z,2));
+ vertex_normal_x=vertex_normal_x/temp_length;
+ vertex_normal_y=vertex_normal_y/temp_length;
+ vertex_normal_z=vertex_normal_z/temp_length;
+
+ Pv11=1-vertex_normal_x*vertex_normal_x;
+ Pv22=1-vertex_normal_y*vertex_normal_y;
+ Pv33=1-vertex_normal_z*vertex_normal_z;
+ Pv21=vertex_normal_x*vertex_normal_y;
+ Pv31=vertex_normal_x*vertex_normal_z;
+ Pv32=vertex_normal_y*vertex_normal_z;
+
+/* if(vtx->idx==0){
+ printf("Vertex normal for vertex %d: %f, %f, %f\n",vtx->idx,vertex_normal_x, vertex_normal_y, vertex_normal_z);
+ }
*/
- s+=tot*xlen;
- 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;
- ht=txn*xh+tyn*yh + tzn*zh;
- s=s/4.0;
-#ifdef TS_DOUBLE_DOUBLE
- if(ht>=0.0) {
- vtx->curvature=sqrt(h);
- } else {
- vtx->curvature=-sqrt(h);
- }
-#endif
-#ifdef TS_DOUBLE_FLOAT
- if(ht>=0.0) {
- vtx->curvature=sqrtf(h);
- } else {
- vtx->curvature=-sqrtf(h);
- }
-#endif
-#ifdef TS_DOUBLE_LONGDOUBLE
- if(ht>=0.0) {
- vtx->curvature=sqrtl(h);
- } else {
- vtx->curvature=-sqrtl(h);
- }
-#endif
-// 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);
+ 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;
+ //Here we calculate normalized edge vector
+
+ temp_length=sqrt(edge_vector_x[jj]*edge_vector_x[jj]+edge_vector_y[jj]*edge_vector_y[jj]+edge_vector_z[jj]*edge_vector_z[jj]);
+ edge_vector_x[jj]=edge_vector_x[jj]/temp_length;
+ edge_vector_y[jj]=edge_vector_y[jj]/temp_length;
+ edge_vector_z[jj]=edge_vector_z[jj]/temp_length;
+
+ //end normalization
+// printf("(%f %f %f)\n", vertex_normal_x, vertex_normal_y, vertex_normal_z);
+/*
+ if(vtx->idx==0){
+ printf("Edge vector for vertex %d (vector %d): %f, %f, %f\n",vtx->idx,jj,edge_vector_x[jj], edge_vector_y[jj], edge_vector_z[jj]);
+ }
+*/
+ 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("energy_vertex: cannot determine km and kp!",233);
+ }
+
+ 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("energy_vertex: Cannot find triangles lm and lp!",233);
+
+ //Triangle normals are NORMALIZED!
+
+ 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]);
+
+
+ mprod[jj]=lm->xnorm*(lp->ynorm*edge_vector_z[jj]-lp->znorm*edge_vector_y[jj]) - lm->ynorm*(lp->xnorm*edge_vector_z[jj]-lp->znorm*edge_vector_x[jj])+ lm->znorm*(lp->xnorm*edge_vector_y[jj]-lp->ynorm*edge_vector_x[jj]);
+
+ phi[jj]=-copysign(acos(lm->xnorm*lp->xnorm+lm->ynorm*lp->ynorm+lm->znorm*lp->znorm),mprod[jj])+M_PI;
+/* if(vtx->idx==0){
+ printf("Angle PHI vertex %d (angle %d): %f\n",vtx->idx,jj,phi[jj]);
+ }
+*/
+// printf("ACOS arg=%e\n", lm->xnorm*lp->xnorm+lm->ynorm*lp->ynorm+lm->znorm*lp->znorm);
+ //he was multiplied with 2 before...
+// he[jj]=sqrt( pow((edge_vector_x[jj]),2) + pow((edge_vector_y[jj]), 2) + pow((edge_vector_z[jj]), 2))*cos(phi[jj]/2.0);
+ he[jj]=temp_length*cos(phi[jj]/2.0);
+// printf("phi[%d]=%f\n", jj,phi[jj]);
+/*
+ if(vtx->idx==0){
+ printf("H operator of edge vertex %d (edge %d): %f\n",vtx->idx,jj,he[jj]);
+ }
+*/
+ Se11=-edge_binormal_x[jj]*edge_binormal_x[jj]*he[jj];
+ Se21=-edge_binormal_x[jj]*edge_binormal_y[jj]*he[jj];
+ Se22=-edge_binormal_y[jj]*edge_binormal_y[jj]*he[jj];
+ Se31=-edge_binormal_x[jj]*edge_binormal_z[jj]*he[jj];
+ Se32=-edge_binormal_y[jj]*edge_binormal_z[jj]*he[jj];
+ Se33=-edge_binormal_z[jj]*edge_binormal_z[jj]*he[jj];
+
+ We=vertex_normal_x*edge_normal_x[jj]+vertex_normal_y*edge_normal_y[jj]+vertex_normal_z*edge_normal_z[jj];
+ We_Av=We/Av;
+
+ Sv[0][0]+=We_Av* ( Pv11*(Pv11*Se11+Pv21*Se21+Pv31*Se31)+Pv21*(Pv11*Se21+Pv21*Se22+Pv31*Se32)+Pv31*(Pv11*Se31+Pv21*Se32+Pv31*Se33) );
+ Sv[0][1]+=We_Av* (Pv21*(Pv11*Se11+Pv21*Se21+Pv31*Se31)+Pv22*(Pv11*Se21+Pv21*Se22+Pv31*Se32)+Pv32*(Pv11*Se31+Pv21*Se32+Pv31*Se33));
+ Sv[0][2]+=We_Av* (Pv31*(Pv11*Se11+Pv21*Se21+Pv31*Se31)+Pv32*(Pv11*Se21+Pv21*Se22+Pv31*Se32)+Pv33*(Pv11*Se31+Pv21*Se32+Pv31*Se33));
+
+ Sv[1][0]+=We_Av* (Pv11*(Pv21*Se11+Pv22*Se21+Pv32*Se31)+Pv21*(Pv21*Se21+Pv22*Se22+Pv32*Se32)+Pv31*(Pv21*Se31+Pv22*Se32+Pv32*Se33));
+ Sv[1][1]+=We_Av* (Pv21*(Pv21*Se11+Pv22*Se21+Pv32*Se31)+Pv22*(Pv21*Se21+Pv22*Se22+Pv32*Se32)+Pv32*(Pv21*Se31+Pv22*Se32+Pv32*Se33));
+ Sv[1][2]+=We_Av* (Pv31*(Pv21*Se11+Pv22*Se21+Pv32*Se31)+Pv32*(Pv21*Se21+Pv22*Se22+Pv32*Se32)+Pv33*(Pv21*Se31+Pv22*Se32+Pv32*Se33));
+
+ Sv[2][0]+=We_Av* (Pv11*(Pv31*Se11+Pv32*Se21+Pv33*Se31)+Pv21*(Pv31*Se21+Pv32*Se22+Pv33*Se32)+Pv31*(Pv31*Se31+Pv32*Se32+Pv33*Se33));
+ Sv[2][1]+=We_Av* (Pv21*(Pv31*Se11+Pv32*Se21+Pv33*Se31)+Pv22*(Pv31*Se21+Pv32*Se22+Pv33*Se32)+Pv32*(Pv31*Se31+Pv32*Se32+Pv33*Se33));
+ Sv[2][2]+=We_Av* (Pv31*(Pv31*Se11+Pv32*Se21+Pv33*Se31)+Pv32*(Pv31*Se21+Pv32*Se22+Pv33*Se32)+Pv33*(Pv31*Se31+Pv32*Se32+Pv33*Se33));
+// 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]);
+
+ } // END FOR JJ
+ gsl_matrix_set(gsl_Sv, 0,0, Sv[0][0]);
+ gsl_matrix_set(gsl_Sv, 0,1, Sv[0][1]);
+ gsl_matrix_set(gsl_Sv, 0,2, Sv[0][2]);
+ gsl_matrix_set(gsl_Sv, 1,0, Sv[1][0]);
+ gsl_matrix_set(gsl_Sv, 1,1, Sv[1][1]);
+ gsl_matrix_set(gsl_Sv, 1,2, Sv[1][2]);
+ gsl_matrix_set(gsl_Sv, 2,0, Sv[2][0]);
+ gsl_matrix_set(gsl_Sv, 2,1, Sv[2][1]);
+ gsl_matrix_set(gsl_Sv, 2,2, Sv[2][2]);
+
+// printf("Se= %f, %f, %f\n %f, %f, %f\n %f, %f, %f\n", Se11, Se21, Se31, Se21, Se22, Se32, Se31, Se32, Se33);
+// printf("Pv= %f, %f, %f\n %f, %f, %f\n %f, %f, %f\n", Pv11, Pv21, Pv31, Pv21, Pv22, Pv32, Pv31, Pv32, Pv33);
+// printf("Sv= %f, %f, %f\n %f, %f, %f\n %f, %f, %f\n", Sv[0][0], Sv[0][1], Sv[0][2], Sv[1][0], Sv[1][1], Sv[1][2], Sv[2][0], Sv[2][1], Sv[2][2]);
+
+
+ gsl_eigen_symm(gsl_Sv, Sv_eigen, workspace);
+
+// printf("Eigenvalues: %f, %f, %f\n", gsl_vector_get(Sv_eigen, 0),gsl_vector_get(Sv_eigen, 1), gsl_vector_get(Sv_eigen, 2) );
+// printf("Eigenvalues: %f, %f, %f\n", gsl_matrix_get(evec, 0,0),gsl_matrix_get(evec, 0,1), gsl_matrix_get(evec, 0,2) );
+
+
+ eigenval[0]= gsl_vector_get(Sv_eigen, 0);
+ eigenval[1]= gsl_vector_get(Sv_eigen, 1);
+ eigenval[2]= gsl_vector_get(Sv_eigen, 2);
+
+ qsort(eigenval, 3, sizeof(ts_double), cmpfunc);
+
+/* if(vtx->idx==1){
+ printf("Eigenvalues: %f, %f, %f\n", eigenval[0], eigenval[1], eigenval[2] );
+ exit(0);
+ }
+*/
+ vtx->energy=0.5*(eigenval[0]+eigenval[1])*(eigenval[0]+eigenval[1])*Av;
+
+ gsl_matrix_free(gsl_Sv);
+ gsl_vector_free(Sv_eigen);
+// gsl_matrix_free(evec);
+ gsl_eigen_symm_free(workspace);
+ 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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