trisurf-ng.git - Gitblit

Samo Penic

2010-12-27 3131dcbf73ff8a0699a688119d57eaf386f49590

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7958e9	1	#include<stdlib.h>
SP	2	#include<math.h>
	3	#include<stdio.h>
	4	#include "general.h"
	5	#include "vertex.h"
	6	#include "bond.h"
	7	#include "vesicle.h"
	8	#include "vertex.h"
	9	#include "triangle.h"
	10	#include "initial_distribution.h"
f74313	11	#include "energy.h"
7958e9	12
SP	13	ts_vesicle *initial_distribution_dipyramid(ts_uint nshell, ts_uint ncmax1, ts_uint ncmax2, ts_uint ncmax3, ts_double stepsize){
	14	ts_fprintf(stderr,"Starting initial_distribution on vesicle with %u shells!...\n",nshell);
	15	ts_bool retval;
	16	ts_uint no_vertices=5nshellnshell+2;
	17
	18	ts_vesicle *vesicle=init_vesicle(no_vertices,ncmax1,ncmax2,ncmax3,stepsize);
	19	vesicle->nshell=nshell;
	20	retval = vtx_set_global_values(vesicle);
	21	retval = pentagonal_dipyramid_vertex_distribution(vesicle->vlist);
	22	retval = init_vertex_neighbours(vesicle->vlist);
b01cc1	23	vesicle->vlist = init_sort_neighbours(vesicle->blist,vesicle->vlist);
SP	24	// retval = init_vesicle_bonds(vesicle); // bonds are created in sort_neigh
7958e9	25	retval = init_triangles(vesicle);
SP	26	retval = init_triangle_neighbours(vesicle);
	27	retval = init_common_vertex_triangle_neighbours(vesicle);
f74313	28	retval = mean_curvature_and_energy(vesicle);
7958e9	29	ts_fprintf(stderr,"initial_distribution finished!\n");
SP	30	return vesicle;
	31	}
	32
	33
	34	ts_bool pentagonal_dipyramid_vertex_distribution(ts_vertex_list *vlist){
	35	/* Some often used relations */
	36	const ts_double s1= sin(2.0*M_PI/5.0);
	37	const ts_double s2= sin(4.0*M_PI/5.0);
	38	const ts_double c1= cos(2.0*M_PI/5.0);
	39	const ts_double c2= cos(4.0*M_PI/5.0);
	40
	41	/* Calculates projection lenght of an edge bond to pentagram plane */
	42	const ts_double xl0=A0/(2.0*sin(M_PI/5.0));
	43	#ifdef TS_DOUBLE_DOUBLE
	44	const ts_double z0=sqrt(pow(A0,2)-pow(xl0,2));
	45	#endif
	46	#ifdef TS_DOUBLE_FLOAT
	47	const ts_double z0=sqrtf(powf(A0,2)-powf(xl0,2));
	48	#endif
	49	#ifdef TS_DOUBLE_LONGDOUBLE
	50	const ts_double z0=sqrtl(powl(A0,2)-powl(xl0,2));
	51	#endif
	52	// const z0=sqrt(A0A0 -xl0xl0); /* 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 */
	53
	54	/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!/
	55	ts_vertex **vtx=vlist->vtx -1 ;
	56
	57
	58	ts_uint nshell=(ts_uint)( sqrt((ts_double)(vlist->n-2)/5));
	59	// printf("nshell=%u\n",nshell);
	60	ts_uint i,n0; // some for loop prereq
	61	ts_int j,k;
	62	ts_double dx,dy; // end loop prereq
	63
	64	/* topmost vertex */
	65	vtx[1]->data->x=0.0;
	66	vtx[1]->data->y=0.0;
	67	vtx[1]->data->z=z0*(ts_double)nshell;
	68
	69	/* starting from to in circular order on pentagrams */
	70	for(i=1;i<=nshell;i++){
	71	n0=2+5i(i-1)/2; //-1 would be for the reason that C index starts from 0
	72	vtx[n0]->data->x=0.0;
	73	vtx[n0]->data->y=(ts_double)i*xl0;
	74	vtx[n0+i]->data->x=vtx[n0]->data->y*s1;
	75	vtx[n0+i]->data->y=vtx[n0]->data->y*c1;
	76	vtx[n0+2i]->data->x=vtx[n0]->data->ys2;
	77	vtx[n0+2i]->data->y=vtx[n0]->data->yc2;
	78	vtx[n0+3i]->data->x=-vtx[n0+2i]->data->x;
	79	vtx[n0+3i]->data->y=vtx[n0+2i]->data->y;
	80	vtx[n0+4*i]->data->x=-vtx[n0+i]->data->x;
	81	vtx[n0+4*i]->data->y=vtx[n0+i]->data->y;
	82	}
	83
	84	/* vertexes on the faces of the dipyramid */
	85	for(i=1;i<=nshell;i++){
	86	n0=2+5i(i-1)/2; // -1 would be because of C!
	87	for(j=1;j<=i-1;j++){
	88	dx=(vtx[n0]->data->x-vtx[n0+4*i]->data->x)/(ts_double)i;
	89	dy=(vtx[n0]->data->y-vtx[n0+4*i]->data->y)/(ts_double)i;
	90	vtx[n0+4i+j]->data->x=(ts_double)jdx+vtx[n0+4*i]->data->x;
	91	vtx[n0+4i+j]->data->y=(ts_double)jdy+vtx[n0+4*i]->data->y;
	92	}
	93	for(k=0;k<=3;k++){ // I would be worried about zero starting of for
	94	dx=(vtx[n0+(k+1)i]->data->x - vtx[n0+ki]->data->x)/(ts_double) i;
	95	dy=(vtx[n0+(k+1)i]->data->y - vtx[n0+ki]->data->y)/(ts_double) i;
	96	for(j=1; j<=i-1;j++){
	97	vtx[n0+ki+j]->data->x= (ts_double)jdx+vtx[n0+k*i]->data->x;
	98	vtx[n0+ki+j]->data->y= (ts_double)jdy+vtx[n0+k*i]->data->y;
	99	}
	100	}
	101	}
	102
	103	for(i=1;i<=nshell;i++){
	104	n0= 2+ 5i(i-1)/2;
	105	for(j=0;j<=5*i-1;j++){
	106	vtx[n0+j]->data->z= z0*(ts_double)(nshell-i); // I would be worried about zero starting of for
	107	}
	108	}
	109
	110	/* for botom part of dipyramide we calculate the positions of vertices */
	111	for(i=2+5nshell(nshell+1)/2;i<=vlist->n;i++){
	112	vtx[i]->data->x=vtx[vlist->n - i +1]->data->x;
	113	vtx[i]->data->y=vtx[vlist->n - i +1]->data->y;
	114	vtx[i]->data->z=-vtx[vlist->n - i +1]->data->z;
	115	}
	116
	117	for(i=1;i<=vlist->n;i++){
	118	for(j=1;j<=vlist->n;j++){
	119	if(i!=j && vtx_distance_sq(vtx[i],vtx[j])<0.001){
	120	printf("Vertices %u and %u are the same!\n",i,j);
	121	}
	122	}
	123	}
	124	return TS_SUCCESS;
	125	}
	126
	127
	128
	129	ts_bool init_vertex_neighbours(ts_vertex_list *vlist){
	130	ts_vertex **vtx=vlist->vtx -1; // take a look at dipyramid function for comment.
	131	const ts_double eps=0.001; //TODO: find out if you can use EPS from math.h
	132	ts_uint i,j;
	133	ts_double dist2; // Square of distance of neighbours
	134	/this is not required if we zero all data in vertex structure at initialization /
	135	/if we force zeroing at initialization this for loop can safely be deleted /
	136	//for(i=1;i<=vlist->n;i++){
	137	// vtx[i].neigh_no=0;
	138	//}
	139	for(i=1;i<=vlist->n;i++){
	140	for(j=1;j<=vlist->n;j++){
	141	dist2=vtx_distance_sq(vtx[i],vtx[j]);
	142	if( (dist2>eps) && (dist2<(A0*A0+eps))){
	143	//if it is close enough, but not too much close (solves problem of comparing when i==j)
	144	vtx_add_neighbour(vtx[i],vtx[j]);
	145	}
	146	}
	147	// printf ("vertex %u ima %u sosedov!\n",i,vtx[i]->data->neigh_no);
	148	}
	149
	150	return TS_SUCCESS;
	151	}
	152
b01cc1	153	// TODO: with new datastructure can be rewritten. Partially it is done, but it is complicated.
SP	154	ts_vertex_list init_sort_neighbours(ts_bond_list blist,ts_vertex_list *vlist){
7958e9	155	ts_vertex **vtx=vlist->vtx -1; // take a look at dipyramid function for comment.
SP	156	ts_uint i,l,j,jj,jjj,k=0;
	157	ts_double eps=0.001; // Take a look if EPS from math.h can be used
	158
	159	/lets initialize memory for temporary vertex_list. Should we write a function instead /
b01cc1	160	ts_vertex_list *tvlist=vertex_list_copy(vlist);
7958e9	161	ts_vertex *tvtx=tvlist->vtx -1; / again to compensate for 0-indexing */
SP	162
	163	ts_double dist2; // Square of distance of neighbours
	164	ts_double direct; // Something, dont know what, but could be normal of some kind
	165	for(i=1;i<=vlist->n;i++){
	166	k++; // WHY i IS NOT GOOD??
b01cc1	167	vtx_add_cneighbour(blist,tvtx[k], tvtx[vtx[i]->data->neigh[0]->idx+1]); //always add 1st
7958e9	168	jjj=1;
SP	169	jj=1;
	170	for(l=2;l<=vtx[i]->data->neigh_no;l++){
	171	for(j=2;j<=vtx[i]->data->neigh_no;j++){
	172	dist2=vtx_distance_sq(vtx[i]->data->neigh[j-1],vtx[i]->data->neigh[jj-1]);
	173	direct=vtx_direct(vtx[i],vtx[i]->data->neigh[j-1],vtx[i]->data->neigh[jj-1]);
	174	if( (fabs(dist2-A0*A0)<=eps) && (direct>0.0) && (j!=jjj) ){
b01cc1	175	vtx_add_cneighbour(blist,tvtx[k],tvtx[vtx[i]->data->neigh[j-1]->idx+1]);
7958e9	176	jjj=jj;
SP	177	jj=j;
	178	break;
	179	}
	180	}
	181	}
	182	}
b01cc1	183	/* We use the temporary vertex for our main vertices and we abandon main
SP	184	* vertices, because their neighbours are not correctly ordered */
	185	// tvtx=vlist->vtx;
	186	// vlist->vtx=tvtx;
	187	// tvlist->vtx=vtx;
	188	vtx_list_free(vlist);
	189	/* Let's make a check if the number of bonds is correct */
	190	if((blist->n)!=3*(tvlist->n-2)){
	191	ts_fprintf(stderr,"Number of bonds is %u should be %u!\n", blist->n, 3*(tvlist->n-2));
	192	fatal("Number of bonds is not 3*(no_vertex-2).",4);
7958e9	193	}
SP	194
b01cc1	195	return tvlist;
7958e9	196	}
SP	197
	198
	199	ts_bool init_vesicle_bonds(ts_vesicle *vesicle){
	200	ts_vertex_list *vlist=vesicle->vlist;
	201	ts_bond_list *blist=vesicle->blist;
	202	ts_vertex **vtx=vesicle->vlist->vtx - 1; // Because of 0 indexing
	203	/* lets make correct clockwise ordering of in nearest neighbour list */
	204	ts_uint i,j,k;
	205	for(i=1;i<=vlist->n;i++){
	206	for(j=i+1;j<=vlist->n;j++){
	207	for(k=0;k<vtx[i]->data->neigh_no;k++){ // has changed 0 to < instead of 1 and <=
	208	if(vtx[i]->data->neigh[k]==vtx[j]){ //if addresses matches it is the same
	209	bond_add(blist,vtx[i],vtx[j]);
	210	break;
	211	}
	212	}
	213	}
	214	}
	215	/* Let's make a check if the number of bonds is correct */
	216	if((blist->n)!=3*(vlist->n-2)){
	217	ts_fprintf(stderr,"Number of bonds is %u should be %u!\n", blist->n, 3*(vlist->n-2));
	218	fatal("Number of bonds is not 3*(no_vertex-2).",4);
	219	}
	220	return TS_SUCCESS;
	221	}
	222
	223
	224
	225	ts_bool init_triangles(ts_vesicle *vesicle){
	226	ts_uint i,j,jj,k;
	227	ts_vertex **vtx=vesicle->vlist->vtx -1; // difference between 0 indexing and 1 indexing
	228	ts_triangle_list *tlist=vesicle->tlist;
	229	ts_double dist, direct;
	230	ts_double eps=0.001; // can we use EPS from math.h?
	231	k=0;
	232	for(i=1;i<=vesicle->vlist->n;i++){
	233	for(j=1;j<=vtx[i]->data->neigh_no;j++){
	234	for(jj=1;jj<=vtx[i]->data->neigh_no;jj++){
	235	// ts_fprintf(stderr,"%u: (%u,%u) neigh_no=%u ",i,j,jj,vtx[i].neigh_no);
	236	// ts_fprintf(stderr,"%e, %e",vtx[i].neigh[j-1]->x,vtx[i].neigh[jj-1]->x);
	237	dist=vtx_distance_sq(vtx[i]->data->neigh[j-1],vtx[i]->data->neigh[jj-1]);
	238	direct=vtx_direct(vtx[i],vtx[i]->data->neigh[j-1],vtx[i]->data->neigh[jj-1]);
	239	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){
	240	triangle_add(tlist,vtx[i],vtx[i]->data->neigh[j-1],vtx[i]->data->neigh[jj-1]);
	241	}
	242	}
	243	}
	244	}
	245	/* We check if all triangles have 3 vertices and if the number of triangles
	246	* matches the theoretical value.
	247	*/
	248	for(i=0;i<tlist->n;i++){
	249	k=0;
	250	for(j=0;j<3;j++){
	251	if(tlist->tria[i]->data->vertex[j]!=NULL)
	252	k++;
	253	}
	254	if(k!=3){
	255	fatal("Some triangles has less than 3 vertices..",4);
	256	}
	257	}
	258	if(tlist->n!=2*(vesicle->vlist->n -2)){
	259	ts_fprintf(stderr,"The number of triangles is %u but should be %u!\n",tlist->n,2*(vesicle->vlist->n -2));
	260	fatal("The number of triangles doesn't match 2*(no_vertex -2).",4);
	261	}
	262	return TS_SUCCESS;
	263	}
	264
	265
	266
	267	ts_bool init_triangle_neighbours(ts_vesicle *vesicle){
	268	ts_uint i,j,nobo;
	269	ts_vertex i1,i2,i3,j1,j2,j3;
	270	// ts_vertex **vtx=vesicle->vlist->vtx -1; // difference between 0 indexing and 1 indexing
	271	ts_triangle_list *tlist=vesicle->tlist;
	272	ts_triangle **tria=tlist->tria -1;
	273	nobo=0;
	274	for(i=1;i<=tlist->n;i++){
	275	i1=tria[i]->data->vertex[0];
	276	i2=tria[i]->data->vertex[1];
	277	i3=tria[i]->data->vertex[2];
	278	for(j=1;j<=tlist->n;j++){
	279	if(j==i) continue;
	280	j1=tria[j]->data->vertex[0];
	281	j2=tria[j]->data->vertex[1];
	282	j3=tria[j]->data->vertex[2];
	283	if((i1==j1 && i3==j2) \|\| (i1==j2 && i3==j3) \|\| (i1==j3 && i3==j1)){
	284	triangle_add_neighbour(tria[i],tria[j]);
	285	nobo++;
	286	}
	287	}
	288	}
	289	for(i=1;i<=tlist->n;i++){
	290	i1=tria[i]->data->vertex[0];
	291	i2=tria[i]->data->vertex[1];
	292	i3=tria[i]->data->vertex[2];
	293	for(j=1;j<=tlist->n;j++){
	294	if(j==i) continue;
	295	j1=tria[j]->data->vertex[0];
	296	j2=tria[j]->data->vertex[1];
	297	j3=tria[j]->data->vertex[2];
	298	if((i1==j1 && i2==j3) \|\| (i1==j3 && i2==j2) \|\| (i1==j2 && i2==j1)){
	299	triangle_add_neighbour(tria[i],tria[j]);
	300	nobo++;
	301	}
	302	}
	303	}
	304	for(i=1;i<=tlist->n;i++){
	305	i1=tria[i]->data->vertex[0];
	306	i2=tria[i]->data->vertex[1];
	307	i3=tria[i]->data->vertex[2];
	308	for(j=1;j<=tlist->n;j++){
	309	if(j==i) continue;
	310	j1=tria[j]->data->vertex[0];
	311	j2=tria[j]->data->vertex[1];
	312	j3=tria[j]->data->vertex[2];
	313	if((i2==j1 && i3==j3) \|\| (i2==j3 && i3==j2) \|\| (i2==j2 && i3==j1)){
	314	triangle_add_neighbour(tria[i],tria[j]);
	315	nobo++;
	316	}
	317	}
	318	}
	319	if(nobo != vesicle->blist->n*2) {
	320	ts_fprintf(stderr,"Number of triangles= %u, number of bonds= %u\n",nobo/2, vesicle->blist->n);
	321	fatal("Number of triangle neighbour pairs differs from double the number of bonds!",4);
	322	}
	323	return TS_SUCCESS;
	324	}
	325
	326
	327	ts_bool init_common_vertex_triangle_neighbours(ts_vesicle *vesicle){
	328	ts_uint i,j,jp,k;
	329	ts_vertex k1,k2,k3,k4,*k5;
	330	ts_vertex **vtx=vesicle->vlist->vtx -1; // difference between 0 indexing and 1 indexing
	331	ts_triangle_list *tlist=vesicle->tlist;
	332	ts_triangle **tria=tlist->tria -1;
	333
	334	for(i=1;i<=vesicle->vlist->n;i++){
	335	for(j=1;j<=vtx[i]->data->neigh_no;j++){
	336	k1=vtx[i]->data->neigh[j-1];
	337	jp=j+1;
	338	if(j == vtx[i]->data->neigh_no) jp=1;
	339	k2=vtx[i]->data->neigh[jp-1];
	340	for(k=1;k<=tlist->n;k++){ // VERY NON-OPTIMAL!!! too many loops (vlist.n * vtx.neigh * tlist.n )!
	341	k3=tria[k]->data->vertex[0];
	342	k4=tria[k]->data->vertex[1];
	343	k5=tria[k]->data->vertex[2];
	344	// ts_fprintf(stderr,"%u %u: k=(%u %u %u)\n",k1,k2,k3,k4,k5);
	345	if((vtx[i]==k3 && k1==k4 && k2==k5) \|\|
	346	(vtx[i]==k4 && k1==k5 && k2==k3) \|\|
	347	(vtx[i]==k5 && k1==k3 && k2==k4)){
b01cc1	348
SP	349	//TODO: probably something wrong with neighbour distribution.
	350	// if(vtx[i]==k3 \|\| vtx[i]==k4 \|\| vtx[i]==k5){
3131dc	351	// if(i==6) ts_fprintf(stdout, "Vtx[%u] > Added to tristar!\n",i);
7958e9	352	vertex_add_tristar(vtx[i],tria[k]);
SP	353	}
	354	}
	355	}
	356	/* ts_fprintf(stderr,"TRISTAR for %u (%u):",i-1,vtx[i].tristar_no);
	357	for(j=0;j<vtx[i].tristar_no;j++){
	358	ts_fprintf(stderr," %u,",vtx[i].tristar[j]->idx);
	359	}
	360	ts_fprintf(stderr,"\n"); */
	361	}
	362	return TS_SUCCESS;
	363	}
	364
	365
	366	ts_bool init_normal_vectors(ts_triangle_list *tlist){
	367	/* Normals point INSIDE vesicle */
	368	ts_uint k;
	369	ts_triangle **tria=tlist->tria -1; //for 0 indexing
	370	for(k=1;k<=tlist->n;k++){
	371	triangle_normal_vector(tria[k]);
	372	}
	373	return TS_SUCCESS;
	374	}