Some friday hacking

Samo Penic

2020-07-03 7d84ef2a0c3f672007317882a2d93487009d668b

Some friday hacking

 src/bond.c

@@ -47,6 +47,19 @@
}


ts_bool bond_get_edge_vector(ts_double *vector, ts_bond *bond, ts_vertex *vtx){
    if(vtx==bond->vtx2){
        vector[0]=bond->x;
        vector[1]=bond->y;
        vector[2]=bond->z;
    } else {
        vector[0]=-bond->x;
        vector[1]=-bond->y;
        vector[2]=-bond->z;
    }
    return TS_SUCCESS;
}

ts_bool bond_list_free(ts_bond_list *blist){
    ts_uint i;
    for(i=0;i<blist->n;i++){

 src/bond.h

@@ -22,6 +22,7 @@
ts_bond *bond_add(ts_bond_list *blist, ts_vertex *vtx1, ts_vertex *vtx2);

ts_bool bond_vector(ts_bond *bond);
ts_bool bond_get_edge_vector(ts_double *vector, ts_bond *bond, ts_vertex *vtx);
ts_bool bond_list_free(ts_bond_list *blist);



 src/energy.c

@@ -3,6 +3,7 @@
#include "general.h"
#include "energy.h"
#include "vertex.h"
#include "bond.h"
#include<math.h>
#include<stdio.h>

@@ -87,110 +88,63 @@
 * @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);
    ts_uint jj, i, j, cnt=0;
    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};
        
#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_double sumnorm;

        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

        vtx->bond[jj-1]->bond_length_dual=tot*vtx->bond[jj-1]->bond_length;
*/
        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;
    // 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;
    // 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((triedge[0]->xnorm + triedge[1]->xnorm),2) + pow((triedge[0]->ynorm + triedge[1]->ynorm), 2) + pow((triedge[0]->znorm + triedge[1]->znorm), 2));
    
    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.
/* 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);
    edge_normal_x[jj]=(triedge[0]->xnorm+ triedge[1]->xnorm)/sumnorm;
    edge_normal_y[jj]=(triedge[0]->ynorm+ triedge[1]->ynorm)/sumnorm;
    edge_normal_z[jj]=(triedge[0]->znorm+ triedge[1]->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), %d\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],triedge[0]->idx);

    }
    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;

 src/general.h

@@ -158,6 +158,10 @@
        ts_double solAngle;
        struct ts_poly *grafted_poly;
        struct ts_cluster *cluster;
    ts_double edge_x[14];
    ts_double edge_y[14];
    ts_double edge_z[14];

};
typedef struct ts_vertex ts_vertex;