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Samo Penic

2010-12-28 dac2e5020dc34c236b741ff5c4591244e73f56f2

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