Now it works after remake! However, some crossection segments are in the li...

Samo Penic

2014-06-13 ad4e7069f10b80446be8d13eba28a03c2c642a3b

Now it works after remake! However, some crossection segments are in the list multiple times.

 src/cross-section.c

@@ -12,13 +12,11 @@
ts_coord_list *get_crossection_with_plane(ts_vesicle *vesicle,ts_double a,ts_double b,ts_double c, ts_double d){


    ts_uint i, j,k;
    ts_uint i, j,k,l;
    ts_double pp,Dsq; // distance from the plane squared
    ts_double ppn1,ppn2; // distance from the plane squared of a neighbor
    ts_double u; //factor to scale vector from first vector to the second to get intersection
    ts_double ppn1; // distance from the plane squared of a neighbor
    ts_vertex *vtx;
    ts_uint ntria=0; // number triangles
    ts_uint cnt=0;
    ts_triangle *tria[2]; // list of triangles
    ts_coord_list *pts=init_coord_list();
    for(i=0;i<vesicle->vlist->n;i++){
@@ -30,18 +28,10 @@
            for(j=0;j<vtx->neigh_no;j++){
                ppn1=vtx->neigh[j]->x*a+vtx->neigh[j]->y*b+vtx->neigh[j]->z*c+d;
                if(pp*ppn1<=0){ //the combination of vertices are good candidates for a crossection
/*                    u=pp/(a*(vtx->x-vtx->neigh[j]->x)+b*(vtx->y-vtx->neigh[j]->y)+c*(vtx->z-vtx->neigh[j]->z));
                    add_coord(pts, vtx->x+u*(vtx->neigh[j]->x - vtx->x),
                            vtx->y+u*(vtx->neigh[j]->y - vtx->y),		
                            vtx->z+u*(vtx->neigh[j]->z - vtx->z),
                            TS_COORD_CARTESIAN);		

*/
                    //find triangle that belongs to the two vertices
                    cnt=0;
                    ntria=0;
                    for(k=0;k<vtx->tristar_no;k++){
                        if(vtx->tristar[k]->vertex[1]==vtx->neigh[j] && vtx->tristar[k]->vertex[0]==vtx){ 
                        if(vtx->tristar[k]->vertex[0]==vtx && ( vtx->tristar[k]->vertex[1]==vtx->neigh[j] || vtx->tristar[k]->vertex[2]==vtx->neigh[j]) ){ 
                            //triangle found.
                            tria[ntria]=vtx->tristar[k];
                            ntria++;
@@ -49,45 +39,17 @@
                    }
                    // if ntria !=1 there is probably something wrong I would say...
                    if(ntria==0) continue;
                    if(ntria!=1) {
                /*    if(ntria!=1) { //there should be 2 triangles. of course, all some of them will be doubled.
                        fprintf(stderr,"ntria=%u\n",ntria);
                        fatal ("Error in mesh. 1 triangle not found",123123);
                    }
                        fatal ("Error in mesh. 2 triangles not found",123123);
                    } */
                    //find the two intersections (in general) to form a intersection line
                    /* we dont know which vertex is which, so we need to recalculate all previously calculated values*/
                    pp=vtx->x*a+vtx->y*b+vtx->z*c+d;
                    ppn1=vtx->neigh[j]->x*a+vtx->neigh[j]->y*b+vtx->neigh[j]->z*c+d;
                    for(l=0;l<ntria;l++){
                    //we add intersection line between two points for each of the triangles found above.
                        add_crosssection_point(pts,a,b,c,d,tria[l]->vertex[0], tria[l]->vertex[1]);
                        add_crosssection_point(pts,a,b,c,d,tria[l]->vertex[0], tria[l]->vertex[2]);
                        add_crosssection_point(pts,a,b,c,d,tria[l]->vertex[1], tria[l]->vertex[2]);

                    u=pp/(a*(vtx->x-vtx->neigh[j]->x)+b*(vtx->y-vtx->neigh[j]->y)+c*(vtx->z-vtx->neigh[j]->z));
                    add_coord(pts, vtx->x+u*(vtx->neigh[j]->x - vtx->x),
                            vtx->y+u*(vtx->neigh[j]->y - vtx->y),		
                            vtx->z+u*(vtx->neigh[j]->z - vtx->z),
                            TS_COORD_CARTESIAN);
                    ppn2=tria[0]->vertex[2]->x*a+tria[0]->vertex[2]->y*b+tria[0]->vertex[2]->z*c+d;	
                    cnt++;
                    //two more tries to find anothen pair of vertices, one above and one below the intersection plane */	
                    if(pp*ppn2<=0) {
                        u=pp/(a*(vtx->x-tria[0]->vertex[2]->x)+b*(vtx->y-tria[0]->vertex[2]->y)+c*(vtx->z-tria[0]->vertex[2]->z));
                        add_coord(pts, vtx->x+u*(tria[0]->vertex[2]->x - vtx->x),
                            vtx->y+u*(tria[0]->vertex[2]->y - vtx->y),		
                            vtx->z+u*(tria[0]->vertex[2]->z - vtx->z),
                            TS_COORD_CARTESIAN);	
                        cnt++;
                    }

                    if(ppn2*ppn1<=0) {
                        u=ppn1/(a*(vtx->neigh[j]->x-tria[0]->vertex[2]->x)+b*(vtx->neigh[j]->y-tria[0]->vertex[2]->y)+c*(vtx->neigh[j]->z-tria[0]->vertex[2]->z));
                        add_coord(pts, vtx->neigh[j]->x+u*(tria[0]->vertex[2]->x - vtx->neigh[j]->x),
                            vtx->neigh[j]->y+u*(tria[0]->vertex[2]->y - vtx->neigh[j]->y),		
                            vtx->neigh[j]->z+u*(tria[0]->vertex[2]->z - vtx->neigh[j]->z),
                            TS_COORD_CARTESIAN);	
                        cnt++;

                    }


                    if(cnt!=2){
                        fprintf(stderr,"Hey, cnt=%u",cnt);
                    }
                }
            }
@@ -97,13 +59,30 @@
}



ts_bool add_crosssection_point(ts_coord_list *pts, ts_double a, ts_double b, ts_double c, ts_double d, ts_vertex *vtx1, ts_vertex *vtx2){
    ts_double pp=vtx1->x*a+vtx1->y*b+vtx1->z*c+d;
    ts_double pp2=vtx2->x*a+vtx1->y*b+vtx2->z*c+d;
    if(pp*pp2<=0){
    ts_double u=pp/(a*(vtx1->x-vtx2->x)+b*(vtx1->y-vtx2->y)+c*(vtx1->z-vtx2->z));
    add_coord(pts, vtx1->x+u*(vtx2->x - vtx1->x),
        vtx1->y+u*(vtx2->y - vtx1->y),		
        vtx1->z+u*(vtx2->z - vtx1->z),
        TS_COORD_CARTESIAN);
	
    return TS_SUCCESS;
    } else {
    return TS_FAIL;
    }
}

/** Saves calculated crossection as a png image */
ts_bool crossection_to_png(ts_coord_list *pts, char *filename){

    cairo_surface_t *surface;
    cairo_t *cr;
    ts_uint i;
    surface = cairo_image_surface_create (CAIRO_FORMAT_ARGB32, 1800, 1800);
    surface = cairo_image_surface_create (CAIRO_FORMAT_RGB24, 1800, 1800);
    cr = cairo_create (surface);
    cairo_rectangle(cr, 0.0, 0.0, 1800,1800);
    cairo_set_source_rgb(cr, 0.3, 0.3, 0.3);
@@ -122,3 +101,11 @@
    cairo_surface_finish (surface);    
    return TS_SUCCESS;
}


ts_bool save_crossection_snapshot(ts_coord_list *pts, ts_uint timestepno){
    char filename[255];
        sprintf(filename,"timestep_%.6u.png",timestepno);
    crossection_to_png(pts,filename);
    return TS_SUCCESS;
}

 src/cross-section.h

@@ -1,5 +1,8 @@
#ifndef _H_CROSS_SECTION
#define _H_CROSS_SECTION
ts_coord_list *get_crossection_with_plane(ts_vesicle *vesicle,ts_double a,ts_double b,ts_double c, ts_double d);

ts_bool add_crosssection_point(ts_coord_list *pts,  ts_double a, ts_double b, ts_double c, ts_double d, ts_vertex *vtx1, ts_vertex *vtx2);
ts_bool crossection_to_png(ts_coord_list *pts, char *filename);
ts_bool save_crossection_snapshot(ts_coord_list *pts, ts_uint timestepno);
#endif

 src/tape

@@ -12,9 +12,9 @@

# Pressure calculations
# (pswitch=1: calc. p*dV energy contribution)
pswitch = 0
pswitch = 1
# pressure difference: p_inside - p_outside (in units kT/l_min^3):
pressure=0.0
pressure=1.0

#Constant volume constraint (0 disable constant volume, 1 enable)
constvolswitch=0

 src/timestep.c

@@ -25,7 +25,6 @@
//     char filename[255];
    FILE *fd=fopen("statistics.csv","w");

    FILE *fdx;
    ts_coord_list *pts;
    if(fd==NULL){
        fatal("Cannot open statistics.csv file for writing",1);
@@ -71,13 +70,8 @@
        if(i>=inititer){
            write_vertex_xml_file(vesicle,i-inititer);
            write_master_xml_file("test.pvd");
            fdx= fopen("test.txt","w");
            pts=get_crossection_with_plane(vesicle, 0.0,0.0,1.0,0.0);
            for(k=0;k<pts->n;k++){
                fprintf(fdx,"%e, %e, %e\n",pts->coord[k]->e1, pts->coord[k]->e2, pts->coord[k]->e3);
            }
            crossection_to_png(pts, "test.png");
            fclose(fdx);
            save_crossection_snapshot(pts,i-inititer);
            free(pts);
            epochtime=get_epoch();            
            gyration_eigen(vesicle, &l1, &l2, &l3);