From 17fe35ccc428e18dd226e07d5517c4816ef6be44 Mon Sep 17 00:00:00 2001
From: Samo Penic <samo.penic@gmail.com>
Date: Mon, 19 Apr 2021 12:23:07 +0000
Subject: [PATCH] Work done previously
---
src/energy.c | 159 ++++++++++++++++++++++++++++++++++++++++++++--------
1 files changed, 134 insertions(+), 25 deletions(-)
diff --git a/src/energy.c b/src/energy.c
index 1f2bd1c..5913863 100644
--- a/src/energy.c
+++ b/src/energy.c
@@ -6,6 +6,19 @@
#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
@@ -107,13 +120,64 @@
ts_vertex *it, *k, *kp,*km;
ts_triangle *lm=NULL, *lp=NULL;
ts_double sumnorm;
+ ts_double temp_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;
+
+
+
+
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;
+
+ //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);
it=vtx;
@@ -135,7 +199,7 @@
kp=it->neigh[neip];
if(km==NULL || kp==NULL){
- fatal("In bondflip, cannot determine km and kp!",999);
+ fatal("energy_vertex: cannot determine km and kp!",233);
}
for(i=0;i<it->tristar_no;i++){
@@ -155,22 +219,9 @@
}
}
}
-if(lm==NULL || lp==NULL) fatal("ts_flip_bond: Cannot find triangles lm and lp!",999);
+if(lm==NULL || lp==NULL) fatal("energy_vertex: Cannot find triangles lm and lp!",233);
-
-/*
- // 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);
-*/
+ //Triangle normals are NORMALIZED!
sumnorm=sqrt( pow((lm->xnorm + lp->xnorm),2) + pow((lm->ynorm + lp->ynorm), 2) + pow((lm->znorm + lp->znorm), 2));
@@ -183,16 +234,74 @@
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;
+ mprod[jj]=it->x*(k->y*edge_vector_z[jj]-edge_vector_y[jj]*k->z)-it->y*(k->x*edge_vector_z[jj]-k->z*edge_vector_x[jj])+it->z*(k->x*edge_vector_y[jj]-k->y*edge_vector_x[jj]);
+ phi[jj]=copysign(acos(lm->xnorm*lp->xnorm+lm->ynorm*lp->ynorm+lm->znorm*lp->znorm-1e-15),mprod[jj])+M_PI;
+// 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);
+// printf("phi[%d]=%f\n", jj,phi[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);
+// printf("Eigenvalues: %f, %f, %f\n", eigenval[0], eigenval[1], eigenval[2] );
+
+
+ vtx->energy=(pow(eigenval[0]+eigenval[1],2))*Av;
+
+ gsl_matrix_free(gsl_Sv);
+ gsl_vector_free(Sv_eigen);
+// gsl_matrix_free(evec);
+ gsl_eigen_symm_free(workspace);
return TS_SUCCESS;
}
--
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