New file |
| | |
| | | #include<stdlib.h> |
| | | #include<math.h> |
| | | #include<stdio.h> |
| | | #include "general.h" |
| | | #include "vertex.h" |
| | | #include "bond.h" |
| | | #include "vesicle.h" |
| | | #include "vertex.h" |
| | | #include "triangle.h" |
| | | #include "initial_distribution.h" |
| | | |
| | | ts_vesicle *initial_distribution_dipyramid(ts_uint nshell, ts_uint ncmax1, ts_uint ncmax2, ts_uint ncmax3, ts_double stepsize){ |
| | | ts_fprintf(stderr,"Starting initial_distribution on vesicle with %u shells!...\n",nshell); |
| | | ts_bool retval; |
| | | ts_uint no_vertices=5*nshell*nshell+2; |
| | | |
| | | ts_vesicle *vesicle=init_vesicle(no_vertices,ncmax1,ncmax2,ncmax3,stepsize); |
| | | vesicle->nshell=nshell; |
| | | retval = vtx_set_global_values(vesicle); |
| | | retval = pentagonal_dipyramid_vertex_distribution(vesicle->vlist); |
| | | retval = init_vertex_neighbours(vesicle->vlist); |
| | | retval = init_sort_neighbours(vesicle->vlist); |
| | | retval = init_vesicle_bonds(vesicle); |
| | | retval = init_triangles(vesicle); |
| | | retval = init_triangle_neighbours(vesicle); |
| | | retval = init_common_vertex_triangle_neighbours(vesicle); |
| | | ts_fprintf(stderr,"initial_distribution finished!\n"); |
| | | return vesicle; |
| | | } |
| | | |
| | | |
| | | ts_bool pentagonal_dipyramid_vertex_distribution(ts_vertex_list *vlist){ |
| | | /* Some often used relations */ |
| | | const ts_double s1= sin(2.0*M_PI/5.0); |
| | | const ts_double s2= sin(4.0*M_PI/5.0); |
| | | const ts_double c1= cos(2.0*M_PI/5.0); |
| | | const ts_double c2= cos(4.0*M_PI/5.0); |
| | | |
| | | /* Calculates projection lenght of an edge bond to pentagram plane */ |
| | | const ts_double xl0=A0/(2.0*sin(M_PI/5.0)); |
| | | #ifdef TS_DOUBLE_DOUBLE |
| | | const ts_double z0=sqrt(pow(A0,2)-pow(xl0,2)); |
| | | #endif |
| | | #ifdef TS_DOUBLE_FLOAT |
| | | const ts_double z0=sqrtf(powf(A0,2)-powf(xl0,2)); |
| | | #endif |
| | | #ifdef TS_DOUBLE_LONGDOUBLE |
| | | const ts_double z0=sqrtl(powl(A0,2)-powl(xl0,2)); |
| | | #endif |
| | | // const z0=sqrt(A0*A0 -xl0*xl0); /* I could use pow function but if pow is used make a check on the float type. If float then powf, if long double use powl */ |
| | | |
| | | /*placeholder for the pointer to vertex datastructure list... DIRTY: actual pointer points towards invalid address, one position before actual beginning of the list... This is to solve the difference between 1 based indexing in original program in fortran and 0 based indexing in C. All algorithms remain unchanged because of this!*/ |
| | | ts_vertex **vtx=vlist->vtx -1 ; |
| | | |
| | | |
| | | ts_uint nshell=(ts_uint)( sqrt((ts_double)(vlist->n-2)/5)); |
| | | // printf("nshell=%u\n",nshell); |
| | | ts_uint i,n0; // some for loop prereq |
| | | ts_int j,k; |
| | | ts_double dx,dy; // end loop prereq |
| | | |
| | | /* topmost vertex */ |
| | | vtx[1]->data->x=0.0; |
| | | vtx[1]->data->y=0.0; |
| | | vtx[1]->data->z=z0*(ts_double)nshell; |
| | | |
| | | /* starting from to in circular order on pentagrams */ |
| | | for(i=1;i<=nshell;i++){ |
| | | n0=2+5*i*(i-1)/2; //-1 would be for the reason that C index starts from 0 |
| | | vtx[n0]->data->x=0.0; |
| | | vtx[n0]->data->y=(ts_double)i*xl0; |
| | | vtx[n0+i]->data->x=vtx[n0]->data->y*s1; |
| | | vtx[n0+i]->data->y=vtx[n0]->data->y*c1; |
| | | vtx[n0+2*i]->data->x=vtx[n0]->data->y*s2; |
| | | vtx[n0+2*i]->data->y=vtx[n0]->data->y*c2; |
| | | vtx[n0+3*i]->data->x=-vtx[n0+2*i]->data->x; |
| | | vtx[n0+3*i]->data->y=vtx[n0+2*i]->data->y; |
| | | vtx[n0+4*i]->data->x=-vtx[n0+i]->data->x; |
| | | vtx[n0+4*i]->data->y=vtx[n0+i]->data->y; |
| | | } |
| | | |
| | | /* vertexes on the faces of the dipyramid */ |
| | | for(i=1;i<=nshell;i++){ |
| | | n0=2+5*i*(i-1)/2; // -1 would be because of C! |
| | | for(j=1;j<=i-1;j++){ |
| | | dx=(vtx[n0]->data->x-vtx[n0+4*i]->data->x)/(ts_double)i; |
| | | dy=(vtx[n0]->data->y-vtx[n0+4*i]->data->y)/(ts_double)i; |
| | | vtx[n0+4*i+j]->data->x=(ts_double)j*dx+vtx[n0+4*i]->data->x; |
| | | vtx[n0+4*i+j]->data->y=(ts_double)j*dy+vtx[n0+4*i]->data->y; |
| | | } |
| | | for(k=0;k<=3;k++){ // I would be worried about zero starting of for |
| | | dx=(vtx[n0+(k+1)*i]->data->x - vtx[n0+k*i]->data->x)/(ts_double) i; |
| | | dy=(vtx[n0+(k+1)*i]->data->y - vtx[n0+k*i]->data->y)/(ts_double) i; |
| | | for(j=1; j<=i-1;j++){ |
| | | vtx[n0+k*i+j]->data->x= (ts_double)j*dx+vtx[n0+k*i]->data->x; |
| | | vtx[n0+k*i+j]->data->y= (ts_double)j*dy+vtx[n0+k*i]->data->y; |
| | | } |
| | | } |
| | | } |
| | | |
| | | for(i=1;i<=nshell;i++){ |
| | | n0= 2+ 5*i*(i-1)/2; |
| | | for(j=0;j<=5*i-1;j++){ |
| | | vtx[n0+j]->data->z= z0*(ts_double)(nshell-i); // I would be worried about zero starting of for |
| | | } |
| | | } |
| | | |
| | | /* for botom part of dipyramide we calculate the positions of vertices */ |
| | | for(i=2+5*nshell*(nshell+1)/2;i<=vlist->n;i++){ |
| | | vtx[i]->data->x=vtx[vlist->n - i +1]->data->x; |
| | | vtx[i]->data->y=vtx[vlist->n - i +1]->data->y; |
| | | vtx[i]->data->z=-vtx[vlist->n - i +1]->data->z; |
| | | } |
| | | |
| | | for(i=1;i<=vlist->n;i++){ |
| | | for(j=1;j<=vlist->n;j++){ |
| | | if(i!=j && vtx_distance_sq(vtx[i],vtx[j])<0.001){ |
| | | printf("Vertices %u and %u are the same!\n",i,j); |
| | | } |
| | | } |
| | | } |
| | | return TS_SUCCESS; |
| | | } |
| | | |
| | | |
| | | |
| | | ts_bool init_vertex_neighbours(ts_vertex_list *vlist){ |
| | | ts_vertex **vtx=vlist->vtx -1; // take a look at dipyramid function for comment. |
| | | const ts_double eps=0.001; //TODO: find out if you can use EPS from math.h |
| | | ts_uint i,j; |
| | | ts_double dist2; // Square of distance of neighbours |
| | | /*this is not required if we zero all data in vertex structure at initialization */ |
| | | /*if we force zeroing at initialization this for loop can safely be deleted */ |
| | | //for(i=1;i<=vlist->n;i++){ |
| | | // vtx[i].neigh_no=0; |
| | | //} |
| | | for(i=1;i<=vlist->n;i++){ |
| | | for(j=1;j<=vlist->n;j++){ |
| | | dist2=vtx_distance_sq(vtx[i],vtx[j]); |
| | | if( (dist2>eps) && (dist2<(A0*A0+eps))){ |
| | | //if it is close enough, but not too much close (solves problem of comparing when i==j) |
| | | vtx_add_neighbour(vtx[i],vtx[j]); |
| | | } |
| | | } |
| | | // printf ("vertex %u ima %u sosedov!\n",i,vtx[i]->data->neigh_no); |
| | | } |
| | | |
| | | return TS_SUCCESS; |
| | | } |
| | | |
| | | // TODO: with new datastructure can be rewritten. |
| | | ts_bool init_sort_neighbours(ts_vertex_list *vlist){ |
| | | ts_vertex **vtx=vlist->vtx -1; // take a look at dipyramid function for comment. |
| | | ts_uint i,l,j,jj,jjj,k=0; |
| | | ts_double eps=0.001; // Take a look if EPS from math.h can be used |
| | | |
| | | /*lets initialize memory for temporary vertex_list. Should we write a function instead */ |
| | | ts_vertex_list *tvlist=init_vertex_list(vlist->n); |
| | | ts_vertex **tvtx=tvlist->vtx -1; /* again to compensate for 0-indexing */ |
| | | |
| | | ts_double dist2; // Square of distance of neighbours |
| | | ts_double direct; // Something, dont know what, but could be normal of some kind |
| | | for(i=1;i<=vlist->n;i++){ |
| | | k++; // WHY i IS NOT GOOD?? |
| | | vtx_add_neighbour(tvtx[k], tvtx[vtx[i]->data->neigh[0]->idx+1]); //always add 1st |
| | | jjj=1; |
| | | jj=1; |
| | | for(l=2;l<=vtx[i]->data->neigh_no;l++){ |
| | | for(j=2;j<=vtx[i]->data->neigh_no;j++){ |
| | | dist2=vtx_distance_sq(vtx[i]->data->neigh[j-1],vtx[i]->data->neigh[jj-1]); |
| | | direct=vtx_direct(vtx[i],vtx[i]->data->neigh[j-1],vtx[i]->data->neigh[jj-1]); |
| | | if( (fabs(dist2-A0*A0)<=eps) && (direct>0.0) && (j!=jjj) ){ |
| | | vtx_add_neighbour(tvtx[k],tvtx[vtx[i]->data->neigh[j-1]->idx+1]); |
| | | jjj=jj; |
| | | jj=j; |
| | | break; |
| | | } |
| | | } |
| | | } |
| | | } |
| | | |
| | | for(i=1;i<=vlist->n;i++){ |
| | | for(j=1;j<=vtx[i]->data->neigh_no;j++){ |
| | | if(vtx[i]->data->neigh_no!=tvtx[i]->data->neigh_no){ //doesn't work with nshell=1! |
| | | // fprintf(stderr,"data1=%u data2=%u\n",vtx[i]->data->neigh_no,tvtx[i]->data->neigh_no); |
| | | fatal("Number of neighbours not the same in init_sort_neighbours.",4); |
| | | } |
| | | //we must correct the pointers in original to point to their |
| | | //neighbours according to indexes. Must be sure not to do it any |
| | | //other way! Also, we need to repair the collection of bonds... |
| | | vtx[i]->data->neigh[j-1]=vtx[tvtx[i]->data->neigh[j-1]->idx+1]; |
| | | } |
| | | } |
| | | |
| | | // Must free memory for temporary vertex array to avoid memory leak! HERE! NOW! |
| | | // free_vertex(tvlist.vertex,tvlist.n); |
| | | vtx_list_free(tvlist); |
| | | return TS_SUCCESS; |
| | | } |
| | | |
| | | |
| | | ts_bool init_vesicle_bonds(ts_vesicle *vesicle){ |
| | | ts_vertex_list *vlist=vesicle->vlist; |
| | | ts_bond_list *blist=vesicle->blist; |
| | | ts_vertex **vtx=vesicle->vlist->vtx - 1; // Because of 0 indexing |
| | | /* lets make correct clockwise ordering of in nearest neighbour list */ |
| | | ts_uint i,j,k; |
| | | for(i=1;i<=vlist->n;i++){ |
| | | for(j=i+1;j<=vlist->n;j++){ |
| | | for(k=0;k<vtx[i]->data->neigh_no;k++){ // has changed 0 to < instead of 1 and <= |
| | | if(vtx[i]->data->neigh[k]==vtx[j]){ //if addresses matches it is the same |
| | | bond_add(blist,vtx[i],vtx[j]); |
| | | break; |
| | | } |
| | | } |
| | | } |
| | | } |
| | | /* Let's make a check if the number of bonds is correct */ |
| | | if((blist->n)!=3*(vlist->n-2)){ |
| | | ts_fprintf(stderr,"Number of bonds is %u should be %u!\n", blist->n, 3*(vlist->n-2)); |
| | | fatal("Number of bonds is not 3*(no_vertex-2).",4); |
| | | } |
| | | return TS_SUCCESS; |
| | | } |
| | | |
| | | |
| | | |
| | | ts_bool init_triangles(ts_vesicle *vesicle){ |
| | | ts_uint i,j,jj,k; |
| | | ts_vertex **vtx=vesicle->vlist->vtx -1; // difference between 0 indexing and 1 indexing |
| | | ts_triangle_list *tlist=vesicle->tlist; |
| | | ts_double dist, direct; |
| | | ts_double eps=0.001; // can we use EPS from math.h? |
| | | k=0; |
| | | for(i=1;i<=vesicle->vlist->n;i++){ |
| | | for(j=1;j<=vtx[i]->data->neigh_no;j++){ |
| | | for(jj=1;jj<=vtx[i]->data->neigh_no;jj++){ |
| | | // ts_fprintf(stderr,"%u: (%u,%u) neigh_no=%u ",i,j,jj,vtx[i].neigh_no); |
| | | // ts_fprintf(stderr,"%e, %e",vtx[i].neigh[j-1]->x,vtx[i].neigh[jj-1]->x); |
| | | dist=vtx_distance_sq(vtx[i]->data->neigh[j-1],vtx[i]->data->neigh[jj-1]); |
| | | direct=vtx_direct(vtx[i],vtx[i]->data->neigh[j-1],vtx[i]->data->neigh[jj-1]); |
| | | if(fabs(dist-A0*A0)<=eps && direct < 0.0 && vtx[i]->data->neigh[j-1]->idx+1 > i && vtx[i]->data->neigh[jj-1]->idx+1 >i){ |
| | | triangle_add(tlist,vtx[i],vtx[i]->data->neigh[j-1],vtx[i]->data->neigh[jj-1]); |
| | | } |
| | | } |
| | | } |
| | | } |
| | | /* We check if all triangles have 3 vertices and if the number of triangles |
| | | * matches the theoretical value. |
| | | */ |
| | | for(i=0;i<tlist->n;i++){ |
| | | k=0; |
| | | for(j=0;j<3;j++){ |
| | | if(tlist->tria[i]->data->vertex[j]!=NULL) |
| | | k++; |
| | | } |
| | | if(k!=3){ |
| | | fatal("Some triangles has less than 3 vertices..",4); |
| | | } |
| | | } |
| | | if(tlist->n!=2*(vesicle->vlist->n -2)){ |
| | | ts_fprintf(stderr,"The number of triangles is %u but should be %u!\n",tlist->n,2*(vesicle->vlist->n -2)); |
| | | fatal("The number of triangles doesn't match 2*(no_vertex -2).",4); |
| | | } |
| | | return TS_SUCCESS; |
| | | } |
| | | |
| | | |
| | | |
| | | ts_bool init_triangle_neighbours(ts_vesicle *vesicle){ |
| | | ts_uint i,j,nobo; |
| | | ts_vertex *i1,*i2,*i3,*j1,*j2,*j3; |
| | | // ts_vertex **vtx=vesicle->vlist->vtx -1; // difference between 0 indexing and 1 indexing |
| | | ts_triangle_list *tlist=vesicle->tlist; |
| | | ts_triangle **tria=tlist->tria -1; |
| | | nobo=0; |
| | | for(i=1;i<=tlist->n;i++){ |
| | | i1=tria[i]->data->vertex[0]; |
| | | i2=tria[i]->data->vertex[1]; |
| | | i3=tria[i]->data->vertex[2]; |
| | | for(j=1;j<=tlist->n;j++){ |
| | | if(j==i) continue; |
| | | j1=tria[j]->data->vertex[0]; |
| | | j2=tria[j]->data->vertex[1]; |
| | | j3=tria[j]->data->vertex[2]; |
| | | if((i1==j1 && i3==j2) || (i1==j2 && i3==j3) || (i1==j3 && i3==j1)){ |
| | | triangle_add_neighbour(tria[i],tria[j]); |
| | | nobo++; |
| | | } |
| | | } |
| | | } |
| | | for(i=1;i<=tlist->n;i++){ |
| | | i1=tria[i]->data->vertex[0]; |
| | | i2=tria[i]->data->vertex[1]; |
| | | i3=tria[i]->data->vertex[2]; |
| | | for(j=1;j<=tlist->n;j++){ |
| | | if(j==i) continue; |
| | | j1=tria[j]->data->vertex[0]; |
| | | j2=tria[j]->data->vertex[1]; |
| | | j3=tria[j]->data->vertex[2]; |
| | | if((i1==j1 && i2==j3) || (i1==j3 && i2==j2) || (i1==j2 && i2==j1)){ |
| | | triangle_add_neighbour(tria[i],tria[j]); |
| | | nobo++; |
| | | } |
| | | } |
| | | } |
| | | for(i=1;i<=tlist->n;i++){ |
| | | i1=tria[i]->data->vertex[0]; |
| | | i2=tria[i]->data->vertex[1]; |
| | | i3=tria[i]->data->vertex[2]; |
| | | for(j=1;j<=tlist->n;j++){ |
| | | if(j==i) continue; |
| | | j1=tria[j]->data->vertex[0]; |
| | | j2=tria[j]->data->vertex[1]; |
| | | j3=tria[j]->data->vertex[2]; |
| | | if((i2==j1 && i3==j3) || (i2==j3 && i3==j2) || (i2==j2 && i3==j1)){ |
| | | triangle_add_neighbour(tria[i],tria[j]); |
| | | nobo++; |
| | | } |
| | | } |
| | | } |
| | | if(nobo != vesicle->blist->n*2) { |
| | | ts_fprintf(stderr,"Number of triangles= %u, number of bonds= %u\n",nobo/2, vesicle->blist->n); |
| | | fatal("Number of triangle neighbour pairs differs from double the number of bonds!",4); |
| | | } |
| | | return TS_SUCCESS; |
| | | } |
| | | |
| | | |
| | | ts_bool init_common_vertex_triangle_neighbours(ts_vesicle *vesicle){ |
| | | ts_uint i,j,jp,k; |
| | | ts_vertex *k1,*k2,*k3,*k4,*k5; |
| | | ts_vertex **vtx=vesicle->vlist->vtx -1; // difference between 0 indexing and 1 indexing |
| | | ts_triangle_list *tlist=vesicle->tlist; |
| | | ts_triangle **tria=tlist->tria -1; |
| | | |
| | | for(i=1;i<=vesicle->vlist->n;i++){ |
| | | for(j=1;j<=vtx[i]->data->neigh_no;j++){ |
| | | k1=vtx[i]->data->neigh[j-1]; |
| | | jp=j+1; |
| | | if(j == vtx[i]->data->neigh_no) jp=1; |
| | | k2=vtx[i]->data->neigh[jp-1]; |
| | | for(k=1;k<=tlist->n;k++){ // VERY NON-OPTIMAL!!! too many loops (vlist.n * vtx.neigh * tlist.n )! |
| | | k3=tria[k]->data->vertex[0]; |
| | | k4=tria[k]->data->vertex[1]; |
| | | k5=tria[k]->data->vertex[2]; |
| | | // ts_fprintf(stderr,"%u %u: k=(%u %u %u)\n",k1,k2,k3,k4,k5); |
| | | if((vtx[i]==k3 && k1==k4 && k2==k5) || |
| | | (vtx[i]==k4 && k1==k5 && k2==k3) || |
| | | (vtx[i]==k5 && k1==k3 && k2==k4)){ |
| | | // ts_fprintf(stderr, "Added to tristar! "); |
| | | vertex_add_tristar(vtx[i],tria[k]); |
| | | } |
| | | } |
| | | } |
| | | /* ts_fprintf(stderr,"TRISTAR for %u (%u):",i-1,vtx[i].tristar_no); |
| | | for(j=0;j<vtx[i].tristar_no;j++){ |
| | | ts_fprintf(stderr," %u,",vtx[i].tristar[j]->idx); |
| | | } |
| | | ts_fprintf(stderr,"\n"); */ |
| | | } |
| | | return TS_SUCCESS; |
| | | } |
| | | |
| | | |
| | | ts_bool init_normal_vectors(ts_triangle_list *tlist){ |
| | | /* Normals point INSIDE vesicle */ |
| | | ts_uint k; |
| | | ts_triangle **tria=tlist->tria -1; //for 0 indexing |
| | | for(k=1;k<=tlist->n;k++){ |
| | | triangle_normal_vector(tria[k]); |
| | | } |
| | | return TS_SUCCESS; |
| | | } |