trisurf-ng.git - Gitblit

It seems that bondlip is debugged. Still, recommend testing

Samo Penic

2014-03-08 7efbb1dbd7c2c1368c429858a32fbeb9467420a8

commit \| author \| age
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;
314f2d	17
SP	18
7958e9	19
SP	20	ts_vesicle *vesicle=init_vesicle(no_vertices,ncmax1,ncmax2,ncmax3,stepsize);
314f2d	21
7958e9	22	vesicle->nshell=nshell;
SP	23	retval = vtx_set_global_values(vesicle);
	24	retval = pentagonal_dipyramid_vertex_distribution(vesicle->vlist);
	25	retval = init_vertex_neighbours(vesicle->vlist);
b01cc1	26	vesicle->vlist = init_sort_neighbours(vesicle->blist,vesicle->vlist);
SP	27	// retval = init_vesicle_bonds(vesicle); // bonds are created in sort_neigh
7958e9	28	retval = init_triangles(vesicle);
SP	29	retval = init_triangle_neighbours(vesicle);
	30	retval = init_common_vertex_triangle_neighbours(vesicle);
dac2e5	31	retval = init_normal_vectors(vesicle->tlist);
f74313	32	retval = mean_curvature_and_energy(vesicle);
7958e9	33	ts_fprintf(stderr,"initial_distribution finished!\n");
41a035	34	if(retval);
7958e9	35	return vesicle;
SP	36	}
	37
	38
	39	ts_bool pentagonal_dipyramid_vertex_distribution(ts_vertex_list *vlist){
	40	/* Some often used relations */
	41	const ts_double s1= sin(2.0*M_PI/5.0);
	42	const ts_double s2= sin(4.0*M_PI/5.0);
	43	const ts_double c1= cos(2.0*M_PI/5.0);
	44	const ts_double c2= cos(4.0*M_PI/5.0);
	45
	46	/* Calculates projection lenght of an edge bond to pentagram plane */
	47	const ts_double xl0=A0/(2.0*sin(M_PI/5.0));
	48	#ifdef TS_DOUBLE_DOUBLE
	49	const ts_double z0=sqrt(pow(A0,2)-pow(xl0,2));
	50	#endif
	51	#ifdef TS_DOUBLE_FLOAT
	52	const ts_double z0=sqrtf(powf(A0,2)-powf(xl0,2));
	53	#endif
	54	#ifdef TS_DOUBLE_LONGDOUBLE
	55	const ts_double z0=sqrtl(powl(A0,2)-powl(xl0,2));
	56	#endif
	57	// 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 */
	58
	59	/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!/
	60	ts_vertex **vtx=vlist->vtx -1 ;
	61
	62
	63	ts_uint nshell=(ts_uint)( sqrt((ts_double)(vlist->n-2)/5));
	64	// printf("nshell=%u\n",nshell);
	65	ts_uint i,n0; // some for loop prereq
	66	ts_int j,k;
	67	ts_double dx,dy; // end loop prereq
	68
	69	/* topmost vertex */
8f6a69	70	vtx[1]->x=0.0;
SP	71	vtx[1]->y=0.0;
	72	vtx[1]->z=z0*(ts_double)nshell;
7958e9	73
SP	74	/* starting from to in circular order on pentagrams */
	75	for(i=1;i<=nshell;i++){
	76	n0=2+5i(i-1)/2; //-1 would be for the reason that C index starts from 0
8f6a69	77	vtx[n0]->x=0.0;
SP	78	vtx[n0]->y=(ts_double)i*xl0;
	79	vtx[n0+i]->x=vtx[n0]->y*s1;
	80	vtx[n0+i]->y=vtx[n0]->y*c1;
	81	vtx[n0+2i]->x=vtx[n0]->ys2;
	82	vtx[n0+2i]->y=vtx[n0]->yc2;
	83	vtx[n0+3i]->x=-vtx[n0+2i]->x;
	84	vtx[n0+3i]->y=vtx[n0+2i]->y;
	85	vtx[n0+4*i]->x=-vtx[n0+i]->x;
	86	vtx[n0+4*i]->y=vtx[n0+i]->y;
7958e9	87	}
SP	88
	89	/* vertexes on the faces of the dipyramid */
	90	for(i=1;i<=nshell;i++){
	91	n0=2+5i(i-1)/2; // -1 would be because of C!
	92	for(j=1;j<=i-1;j++){
8f6a69	93	dx=(vtx[n0]->x-vtx[n0+4*i]->x)/(ts_double)i;
SP	94	dy=(vtx[n0]->y-vtx[n0+4*i]->y)/(ts_double)i;
	95	vtx[n0+4i+j]->x=(ts_double)jdx+vtx[n0+4*i]->x;
	96	vtx[n0+4i+j]->y=(ts_double)jdy+vtx[n0+4*i]->y;
7958e9	97	}
SP	98	for(k=0;k<=3;k++){ // I would be worried about zero starting of for
8f6a69	99	dx=(vtx[n0+(k+1)i]->x - vtx[n0+ki]->x)/(ts_double) i;
SP	100	dy=(vtx[n0+(k+1)i]->y - vtx[n0+ki]->y)/(ts_double) i;
7958e9	101	for(j=1; j<=i-1;j++){
8f6a69	102	vtx[n0+ki+j]->x= (ts_double)jdx+vtx[n0+k*i]->x;
SP	103	vtx[n0+ki+j]->y= (ts_double)jdy+vtx[n0+k*i]->y;
7958e9	104	}
SP	105	}
	106	}
	107
	108	for(i=1;i<=nshell;i++){
	109	n0= 2+ 5i(i-1)/2;
	110	for(j=0;j<=5*i-1;j++){
8f6a69	111	vtx[n0+j]->z= z0*(ts_double)(nshell-i); // I would be worried about zero starting of for
7958e9	112	}
SP	113	}
	114
	115	/* for botom part of dipyramide we calculate the positions of vertices */
	116	for(i=2+5nshell(nshell+1)/2;i<=vlist->n;i++){
8f6a69	117	vtx[i]->x=vtx[vlist->n - i +1]->x;
SP	118	vtx[i]->y=vtx[vlist->n - i +1]->y;
	119	vtx[i]->z=-vtx[vlist->n - i +1]->z;
7958e9	120	}
SP	121
	122	for(i=1;i<=vlist->n;i++){
	123	for(j=1;j<=vlist->n;j++){
	124	if(i!=j && vtx_distance_sq(vtx[i],vtx[j])<0.001){
	125	printf("Vertices %u and %u are the same!\n",i,j);
	126	}
	127	}
	128	}
	129	return TS_SUCCESS;
	130	}
	131
	132
	133
	134	ts_bool init_vertex_neighbours(ts_vertex_list *vlist){
	135	ts_vertex **vtx=vlist->vtx -1; // take a look at dipyramid function for comment.
	136	const ts_double eps=0.001; //TODO: find out if you can use EPS from math.h
	137	ts_uint i,j;
	138	ts_double dist2; // Square of distance of neighbours
	139	/this is not required if we zero all data in vertex structure at initialization /
	140	/if we force zeroing at initialization this for loop can safely be deleted /
	141	//for(i=1;i<=vlist->n;i++){
	142	// vtx[i].neigh_no=0;
	143	//}
	144	for(i=1;i<=vlist->n;i++){
	145	for(j=1;j<=vlist->n;j++){
	146	dist2=vtx_distance_sq(vtx[i],vtx[j]);
	147	if( (dist2>eps) && (dist2<(A0*A0+eps))){
	148	//if it is close enough, but not too much close (solves problem of comparing when i==j)
	149	vtx_add_neighbour(vtx[i],vtx[j]);
	150	}
	151	}
	152	// printf ("vertex %u ima %u sosedov!\n",i,vtx[i]->data->neigh_no);
	153	}
	154
	155	return TS_SUCCESS;
	156	}
	157
b01cc1	158	// TODO: with new datastructure can be rewritten. Partially it is done, but it is complicated.
SP	159	ts_vertex_list init_sort_neighbours(ts_bond_list blist,ts_vertex_list *vlist){
7958e9	160	ts_vertex **vtx=vlist->vtx -1; // take a look at dipyramid function for comment.
SP	161	ts_uint i,l,j,jj,jjj,k=0;
	162	ts_double eps=0.001; // Take a look if EPS from math.h can be used
	163
	164	/lets initialize memory for temporary vertex_list. Should we write a function instead /
b01cc1	165	ts_vertex_list *tvlist=vertex_list_copy(vlist);
7958e9	166	ts_vertex *tvtx=tvlist->vtx -1; / again to compensate for 0-indexing */
SP	167
	168	ts_double dist2; // Square of distance of neighbours
	169	ts_double direct; // Something, dont know what, but could be normal of some kind
	170	for(i=1;i<=vlist->n;i++){
	171	k++; // WHY i IS NOT GOOD??
8f6a69	172	vtx_add_cneighbour(blist,tvtx[k], tvtx[vtx[i]->neigh[0]->idx+1]); //always add 1st
7958e9	173	jjj=1;
SP	174	jj=1;
8f6a69	175	for(l=2;l<=vtx[i]->neigh_no;l++){
SP	176	for(j=2;j<=vtx[i]->neigh_no;j++){
	177	dist2=vtx_distance_sq(vtx[i]->neigh[j-1],vtx[i]->neigh[jj-1]);
	178	direct=vtx_direct(vtx[i],vtx[i]->neigh[j-1],vtx[i]->neigh[jj-1]);
	179	// TODO: check if fabs can be used with all floating point types!!
7958e9	180	if( (fabs(dist2-A0*A0)<=eps) && (direct>0.0) && (j!=jjj) ){
8f6a69	181	vtx_add_cneighbour(blist,tvtx[k],tvtx[vtx[i]->neigh[j-1]->idx+1]);
7958e9	182	jjj=jj;
SP	183	jj=j;
	184	break;
	185	}
	186	}
	187	}
	188	}
b01cc1	189	/* We use the temporary vertex for our main vertices and we abandon main
SP	190	* vertices, because their neighbours are not correctly ordered */
	191	// tvtx=vlist->vtx;
	192	// vlist->vtx=tvtx;
	193	// tvlist->vtx=vtx;
	194	vtx_list_free(vlist);
	195	/* Let's make a check if the number of bonds is correct */
	196	if((blist->n)!=3*(tvlist->n-2)){
	197	ts_fprintf(stderr,"Number of bonds is %u should be %u!\n", blist->n, 3*(tvlist->n-2));
	198	fatal("Number of bonds is not 3*(no_vertex-2).",4);
7958e9	199	}
SP	200
b01cc1	201	return tvlist;
7958e9	202	}
SP	203
	204
	205	ts_bool init_vesicle_bonds(ts_vesicle *vesicle){
	206	ts_vertex_list *vlist=vesicle->vlist;
	207	ts_bond_list *blist=vesicle->blist;
	208	ts_vertex **vtx=vesicle->vlist->vtx - 1; // Because of 0 indexing
	209	/* lets make correct clockwise ordering of in nearest neighbour list */
	210	ts_uint i,j,k;
	211	for(i=1;i<=vlist->n;i++){
	212	for(j=i+1;j<=vlist->n;j++){
8f6a69	213	for(k=0;k<vtx[i]->neigh_no;k++){ // has changed 0 to < instead of 1 and <=
SP	214	if(vtx[i]->neigh[k]==vtx[j]){ //if addresses matches it is the same
7958e9	215	bond_add(blist,vtx[i],vtx[j]);
SP	216	break;
	217	}
	218	}
	219	}
	220	}
	221	/* Let's make a check if the number of bonds is correct */
	222	if((blist->n)!=3*(vlist->n-2)){
	223	ts_fprintf(stderr,"Number of bonds is %u should be %u!\n", blist->n, 3*(vlist->n-2));
	224	fatal("Number of bonds is not 3*(no_vertex-2).",4);
	225	}
	226	return TS_SUCCESS;
	227	}
	228
	229
	230
	231	ts_bool init_triangles(ts_vesicle *vesicle){
	232	ts_uint i,j,jj,k;
	233	ts_vertex **vtx=vesicle->vlist->vtx -1; // difference between 0 indexing and 1 indexing
	234	ts_triangle_list *tlist=vesicle->tlist;
	235	ts_double dist, direct;
	236	ts_double eps=0.001; // can we use EPS from math.h?
	237	k=0;
	238	for(i=1;i<=vesicle->vlist->n;i++){
8f6a69	239	for(j=1;j<=vtx[i]->neigh_no;j++){
SP	240	for(jj=1;jj<=vtx[i]->neigh_no;jj++){
7958e9	241	// ts_fprintf(stderr,"%u: (%u,%u) neigh_no=%u ",i,j,jj,vtx[i].neigh_no);
SP	242	// ts_fprintf(stderr,"%e, %e",vtx[i].neigh[j-1]->x,vtx[i].neigh[jj-1]->x);
8f6a69	243	dist=vtx_distance_sq(vtx[i]->neigh[j-1],vtx[i]->neigh[jj-1]);
SP	244	direct=vtx_direct(vtx[i],vtx[i]->neigh[j-1],vtx[i]->neigh[jj-1]);
	245	// TODO: same as above
	246	if(fabs(dist-A0*A0)<=eps && direct < 0.0 && vtx[i]->neigh[j-1]->idx+1 > i && vtx[i]->neigh[jj-1]->idx+1 >i){
	247	triangle_add(tlist,vtx[i],vtx[i]->neigh[j-1],vtx[i]->neigh[jj-1]);
7958e9	248	}
SP	249	}
	250	}
	251	}
	252	/* We check if all triangles have 3 vertices and if the number of triangles
	253	* matches the theoretical value.
	254	*/
	255	for(i=0;i<tlist->n;i++){
	256	k=0;
	257	for(j=0;j<3;j++){
41a035	258	if(tlist->tria[i]->vertex[j]!=NULL)
7958e9	259	k++;
SP	260	}
	261	if(k!=3){
8f6a69	262	fatal("Some triangles have less than 3 vertices..",4);
7958e9	263	}
SP	264	}
	265	if(tlist->n!=2*(vesicle->vlist->n -2)){
	266	ts_fprintf(stderr,"The number of triangles is %u but should be %u!\n",tlist->n,2*(vesicle->vlist->n -2));
	267	fatal("The number of triangles doesn't match 2*(no_vertex -2).",4);
	268	}
	269	return TS_SUCCESS;
	270	}
	271
	272
	273
	274	ts_bool init_triangle_neighbours(ts_vesicle *vesicle){
	275	ts_uint i,j,nobo;
	276	ts_vertex i1,i2,i3,j1,j2,j3;
	277	// ts_vertex **vtx=vesicle->vlist->vtx -1; // difference between 0 indexing and 1 indexing
	278	ts_triangle_list *tlist=vesicle->tlist;
	279	ts_triangle **tria=tlist->tria -1;
	280	nobo=0;
	281	for(i=1;i<=tlist->n;i++){
41a035	282	i1=tria[i]->vertex[0];
SP	283	i2=tria[i]->vertex[1];
	284	i3=tria[i]->vertex[2];
7958e9	285	for(j=1;j<=tlist->n;j++){
SP	286	if(j==i) continue;
41a035	287	j1=tria[j]->vertex[0];
SP	288	j2=tria[j]->vertex[1];
	289	j3=tria[j]->vertex[2];
7958e9	290	if((i1==j1 && i3==j2) \|\| (i1==j2 && i3==j3) \|\| (i1==j3 && i3==j1)){
SP	291	triangle_add_neighbour(tria[i],tria[j]);
	292	nobo++;
	293	}
	294	}
	295	}
	296	for(i=1;i<=tlist->n;i++){
41a035	297	i1=tria[i]->vertex[0];
SP	298	i2=tria[i]->vertex[1];
	299	i3=tria[i]->vertex[2];
7958e9	300	for(j=1;j<=tlist->n;j++){
SP	301	if(j==i) continue;
41a035	302	j1=tria[j]->vertex[0];
SP	303	j2=tria[j]->vertex[1];
	304	j3=tria[j]->vertex[2];
7958e9	305	if((i1==j1 && i2==j3) \|\| (i1==j3 && i2==j2) \|\| (i1==j2 && i2==j1)){
SP	306	triangle_add_neighbour(tria[i],tria[j]);
	307	nobo++;
	308	}
	309	}
	310	}
	311	for(i=1;i<=tlist->n;i++){
41a035	312	i1=tria[i]->vertex[0];
SP	313	i2=tria[i]->vertex[1];
	314	i3=tria[i]->vertex[2];
7958e9	315	for(j=1;j<=tlist->n;j++){
SP	316	if(j==i) continue;
41a035	317	j1=tria[j]->vertex[0];
SP	318	j2=tria[j]->vertex[1];
	319	j3=tria[j]->vertex[2];
7958e9	320	if((i2==j1 && i3==j3) \|\| (i2==j3 && i3==j2) \|\| (i2==j2 && i3==j1)){
SP	321	triangle_add_neighbour(tria[i],tria[j]);
	322	nobo++;
	323	}
	324	}
	325	}
	326	if(nobo != vesicle->blist->n*2) {
	327	ts_fprintf(stderr,"Number of triangles= %u, number of bonds= %u\n",nobo/2, vesicle->blist->n);
	328	fatal("Number of triangle neighbour pairs differs from double the number of bonds!",4);
	329	}
	330	return TS_SUCCESS;
	331	}
	332
	333
	334	ts_bool init_common_vertex_triangle_neighbours(ts_vesicle *vesicle){
	335	ts_uint i,j,jp,k;
	336	ts_vertex k1,k2,k3,k4,*k5;
	337	ts_vertex **vtx=vesicle->vlist->vtx -1; // difference between 0 indexing and 1 indexing
	338	ts_triangle_list *tlist=vesicle->tlist;
	339	ts_triangle **tria=tlist->tria -1;
	340
	341	for(i=1;i<=vesicle->vlist->n;i++){
8f6a69	342	for(j=1;j<=vtx[i]->neigh_no;j++){
SP	343	k1=vtx[i]->neigh[j-1];
7958e9	344	jp=j+1;
8f6a69	345	if(j == vtx[i]->neigh_no) jp=1;
SP	346	k2=vtx[i]->neigh[jp-1];
7958e9	347	for(k=1;k<=tlist->n;k++){ // VERY NON-OPTIMAL!!! too many loops (vlist.n * vtx.neigh * tlist.n )!
41a035	348	k3=tria[k]->vertex[0];
SP	349	k4=tria[k]->vertex[1];
	350	k5=tria[k]->vertex[2];
7958e9	351	// ts_fprintf(stderr,"%u %u: k=(%u %u %u)\n",k1,k2,k3,k4,k5);
SP	352	if((vtx[i]==k3 && k1==k4 && k2==k5) \|\|
	353	(vtx[i]==k4 && k1==k5 && k2==k3) \|\|
	354	(vtx[i]==k5 && k1==k3 && k2==k4)){
b01cc1	355
SP	356	//TODO: probably something wrong with neighbour distribution.
	357	// if(vtx[i]==k3 \|\| vtx[i]==k4 \|\| vtx[i]==k5){
dac2e5	358	// if(i==6) ts_fprintf(stdout, "Vtx[%u] > Added to tristar!\n",i);
7958e9	359	vertex_add_tristar(vtx[i],tria[k]);
SP	360	}
	361	}
	362	}
	363	/* ts_fprintf(stderr,"TRISTAR for %u (%u):",i-1,vtx[i].tristar_no);
	364	for(j=0;j<vtx[i].tristar_no;j++){
	365	ts_fprintf(stderr," %u,",vtx[i].tristar[j]->idx);
	366	}
	367	ts_fprintf(stderr,"\n"); */
	368	}
	369	return TS_SUCCESS;
	370	}
	371
	372
	373	ts_bool init_normal_vectors(ts_triangle_list *tlist){
	374	/* Normals point INSIDE vesicle */
	375	ts_uint k;
	376	ts_triangle **tria=tlist->tria -1; //for 0 indexing
	377	for(k=1;k<=tlist->n;k++){
	378	triangle_normal_vector(tria[k]);
	379	}
	380	return TS_SUCCESS;
	381	}