trisurf-ng.git - Gitblit

Structures for grafted polymers (Samo&Miha)

mihaf

2013-11-29 1d5dff5a3576a028f691608ef9369844efdfe82b

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
SP	22	//TODO: debugging only. Please remove ASAP!
443ba1	23	vesicle->bending_rigidity=25.0;
314f2d	24
7958e9	25	vesicle->nshell=nshell;
SP	26	retval = vtx_set_global_values(vesicle);
	27	retval = pentagonal_dipyramid_vertex_distribution(vesicle->vlist);
	28	retval = init_vertex_neighbours(vesicle->vlist);
b01cc1	29	vesicle->vlist = init_sort_neighbours(vesicle->blist,vesicle->vlist);
SP	30	// retval = init_vesicle_bonds(vesicle); // bonds are created in sort_neigh
7958e9	31	retval = init_triangles(vesicle);
SP	32	retval = init_triangle_neighbours(vesicle);
	33	retval = init_common_vertex_triangle_neighbours(vesicle);
dac2e5	34	retval = init_normal_vectors(vesicle->tlist);
f74313	35	retval = mean_curvature_and_energy(vesicle);
7958e9	36	ts_fprintf(stderr,"initial_distribution finished!\n");
41a035	37	if(retval);
7958e9	38	return vesicle;
SP	39	}
	40
	41
	42	ts_bool pentagonal_dipyramid_vertex_distribution(ts_vertex_list *vlist){
	43	/* Some often used relations */
	44	const ts_double s1= sin(2.0*M_PI/5.0);
	45	const ts_double s2= sin(4.0*M_PI/5.0);
	46	const ts_double c1= cos(2.0*M_PI/5.0);
	47	const ts_double c2= cos(4.0*M_PI/5.0);
	48
	49	/* Calculates projection lenght of an edge bond to pentagram plane */
	50	const ts_double xl0=A0/(2.0*sin(M_PI/5.0));
	51	#ifdef TS_DOUBLE_DOUBLE
	52	const ts_double z0=sqrt(pow(A0,2)-pow(xl0,2));
	53	#endif
	54	#ifdef TS_DOUBLE_FLOAT
	55	const ts_double z0=sqrtf(powf(A0,2)-powf(xl0,2));
	56	#endif
	57	#ifdef TS_DOUBLE_LONGDOUBLE
	58	const ts_double z0=sqrtl(powl(A0,2)-powl(xl0,2));
	59	#endif
	60	// 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 */
	61
	62	/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!/
	63	ts_vertex **vtx=vlist->vtx -1 ;
	64
	65
	66	ts_uint nshell=(ts_uint)( sqrt((ts_double)(vlist->n-2)/5));
	67	// printf("nshell=%u\n",nshell);
	68	ts_uint i,n0; // some for loop prereq
	69	ts_int j,k;
	70	ts_double dx,dy; // end loop prereq
	71
	72	/* topmost vertex */
8f6a69	73	vtx[1]->x=0.0;
SP	74	vtx[1]->y=0.0;
	75	vtx[1]->z=z0*(ts_double)nshell;
7958e9	76
SP	77	/* starting from to in circular order on pentagrams */
	78	for(i=1;i<=nshell;i++){
	79	n0=2+5i(i-1)/2; //-1 would be for the reason that C index starts from 0
8f6a69	80	vtx[n0]->x=0.0;
SP	81	vtx[n0]->y=(ts_double)i*xl0;
	82	vtx[n0+i]->x=vtx[n0]->y*s1;
	83	vtx[n0+i]->y=vtx[n0]->y*c1;
	84	vtx[n0+2i]->x=vtx[n0]->ys2;
	85	vtx[n0+2i]->y=vtx[n0]->yc2;
	86	vtx[n0+3i]->x=-vtx[n0+2i]->x;
	87	vtx[n0+3i]->y=vtx[n0+2i]->y;
	88	vtx[n0+4*i]->x=-vtx[n0+i]->x;
	89	vtx[n0+4*i]->y=vtx[n0+i]->y;
7958e9	90	}
SP	91
	92	/* vertexes on the faces of the dipyramid */
	93	for(i=1;i<=nshell;i++){
	94	n0=2+5i(i-1)/2; // -1 would be because of C!
	95	for(j=1;j<=i-1;j++){
8f6a69	96	dx=(vtx[n0]->x-vtx[n0+4*i]->x)/(ts_double)i;
SP	97	dy=(vtx[n0]->y-vtx[n0+4*i]->y)/(ts_double)i;
	98	vtx[n0+4i+j]->x=(ts_double)jdx+vtx[n0+4*i]->x;
	99	vtx[n0+4i+j]->y=(ts_double)jdy+vtx[n0+4*i]->y;
7958e9	100	}
SP	101	for(k=0;k<=3;k++){ // I would be worried about zero starting of for
8f6a69	102	dx=(vtx[n0+(k+1)i]->x - vtx[n0+ki]->x)/(ts_double) i;
SP	103	dy=(vtx[n0+(k+1)i]->y - vtx[n0+ki]->y)/(ts_double) i;
7958e9	104	for(j=1; j<=i-1;j++){
8f6a69	105	vtx[n0+ki+j]->x= (ts_double)jdx+vtx[n0+k*i]->x;
SP	106	vtx[n0+ki+j]->y= (ts_double)jdy+vtx[n0+k*i]->y;
7958e9	107	}
SP	108	}
	109	}
	110
	111	for(i=1;i<=nshell;i++){
	112	n0= 2+ 5i(i-1)/2;
	113	for(j=0;j<=5*i-1;j++){
8f6a69	114	vtx[n0+j]->z= z0*(ts_double)(nshell-i); // I would be worried about zero starting of for
7958e9	115	}
SP	116	}
	117
	118	/* for botom part of dipyramide we calculate the positions of vertices */
	119	for(i=2+5nshell(nshell+1)/2;i<=vlist->n;i++){
8f6a69	120	vtx[i]->x=vtx[vlist->n - i +1]->x;
SP	121	vtx[i]->y=vtx[vlist->n - i +1]->y;
	122	vtx[i]->z=-vtx[vlist->n - i +1]->z;
7958e9	123	}
SP	124
	125	for(i=1;i<=vlist->n;i++){
	126	for(j=1;j<=vlist->n;j++){
	127	if(i!=j && vtx_distance_sq(vtx[i],vtx[j])<0.001){
	128	printf("Vertices %u and %u are the same!\n",i,j);
	129	}
	130	}
	131	}
	132	return TS_SUCCESS;
	133	}
	134
	135
	136
	137	ts_bool init_vertex_neighbours(ts_vertex_list *vlist){
	138	ts_vertex **vtx=vlist->vtx -1; // take a look at dipyramid function for comment.
	139	const ts_double eps=0.001; //TODO: find out if you can use EPS from math.h
	140	ts_uint i,j;
	141	ts_double dist2; // Square of distance of neighbours
	142	/this is not required if we zero all data in vertex structure at initialization /
	143	/if we force zeroing at initialization this for loop can safely be deleted /
	144	//for(i=1;i<=vlist->n;i++){
	145	// vtx[i].neigh_no=0;
	146	//}
	147	for(i=1;i<=vlist->n;i++){
	148	for(j=1;j<=vlist->n;j++){
	149	dist2=vtx_distance_sq(vtx[i],vtx[j]);
	150	if( (dist2>eps) && (dist2<(A0*A0+eps))){
	151	//if it is close enough, but not too much close (solves problem of comparing when i==j)
	152	vtx_add_neighbour(vtx[i],vtx[j]);
	153	}
	154	}
	155	// printf ("vertex %u ima %u sosedov!\n",i,vtx[i]->data->neigh_no);
	156	}
	157
	158	return TS_SUCCESS;
	159	}
	160
b01cc1	161	// TODO: with new datastructure can be rewritten. Partially it is done, but it is complicated.
SP	162	ts_vertex_list init_sort_neighbours(ts_bond_list blist,ts_vertex_list *vlist){
7958e9	163	ts_vertex **vtx=vlist->vtx -1; // take a look at dipyramid function for comment.
SP	164	ts_uint i,l,j,jj,jjj,k=0;
	165	ts_double eps=0.001; // Take a look if EPS from math.h can be used
	166
	167	/lets initialize memory for temporary vertex_list. Should we write a function instead /
b01cc1	168	ts_vertex_list *tvlist=vertex_list_copy(vlist);
7958e9	169	ts_vertex *tvtx=tvlist->vtx -1; / again to compensate for 0-indexing */
SP	170
	171	ts_double dist2; // Square of distance of neighbours
	172	ts_double direct; // Something, dont know what, but could be normal of some kind
	173	for(i=1;i<=vlist->n;i++){
	174	k++; // WHY i IS NOT GOOD??
8f6a69	175	vtx_add_cneighbour(blist,tvtx[k], tvtx[vtx[i]->neigh[0]->idx+1]); //always add 1st
7958e9	176	jjj=1;
SP	177	jj=1;
8f6a69	178	for(l=2;l<=vtx[i]->neigh_no;l++){
SP	179	for(j=2;j<=vtx[i]->neigh_no;j++){
	180	dist2=vtx_distance_sq(vtx[i]->neigh[j-1],vtx[i]->neigh[jj-1]);
	181	direct=vtx_direct(vtx[i],vtx[i]->neigh[j-1],vtx[i]->neigh[jj-1]);
	182	// TODO: check if fabs can be used with all floating point types!!
7958e9	183	if( (fabs(dist2-A0*A0)<=eps) && (direct>0.0) && (j!=jjj) ){
8f6a69	184	vtx_add_cneighbour(blist,tvtx[k],tvtx[vtx[i]->neigh[j-1]->idx+1]);
7958e9	185	jjj=jj;
SP	186	jj=j;
	187	break;
	188	}
	189	}
	190	}
	191	}
b01cc1	192	/* We use the temporary vertex for our main vertices and we abandon main
SP	193	* vertices, because their neighbours are not correctly ordered */
	194	// tvtx=vlist->vtx;
	195	// vlist->vtx=tvtx;
	196	// tvlist->vtx=vtx;
	197	vtx_list_free(vlist);
	198	/* Let's make a check if the number of bonds is correct */
	199	if((blist->n)!=3*(tvlist->n-2)){
	200	ts_fprintf(stderr,"Number of bonds is %u should be %u!\n", blist->n, 3*(tvlist->n-2));
	201	fatal("Number of bonds is not 3*(no_vertex-2).",4);
7958e9	202	}
SP	203
b01cc1	204	return tvlist;
7958e9	205	}
SP	206
	207
	208	ts_bool init_vesicle_bonds(ts_vesicle *vesicle){
	209	ts_vertex_list *vlist=vesicle->vlist;
	210	ts_bond_list *blist=vesicle->blist;
	211	ts_vertex **vtx=vesicle->vlist->vtx - 1; // Because of 0 indexing
	212	/* lets make correct clockwise ordering of in nearest neighbour list */
	213	ts_uint i,j,k;
	214	for(i=1;i<=vlist->n;i++){
	215	for(j=i+1;j<=vlist->n;j++){
8f6a69	216	for(k=0;k<vtx[i]->neigh_no;k++){ // has changed 0 to < instead of 1 and <=
SP	217	if(vtx[i]->neigh[k]==vtx[j]){ //if addresses matches it is the same
7958e9	218	bond_add(blist,vtx[i],vtx[j]);
SP	219	break;
	220	}
	221	}
	222	}
	223	}
	224	/* Let's make a check if the number of bonds is correct */
	225	if((blist->n)!=3*(vlist->n-2)){
	226	ts_fprintf(stderr,"Number of bonds is %u should be %u!\n", blist->n, 3*(vlist->n-2));
	227	fatal("Number of bonds is not 3*(no_vertex-2).",4);
	228	}
	229	return TS_SUCCESS;
	230	}
	231
	232
	233
	234	ts_bool init_triangles(ts_vesicle *vesicle){
	235	ts_uint i,j,jj,k;
	236	ts_vertex **vtx=vesicle->vlist->vtx -1; // difference between 0 indexing and 1 indexing
	237	ts_triangle_list *tlist=vesicle->tlist;
	238	ts_double dist, direct;
	239	ts_double eps=0.001; // can we use EPS from math.h?
	240	k=0;
	241	for(i=1;i<=vesicle->vlist->n;i++){
8f6a69	242	for(j=1;j<=vtx[i]->neigh_no;j++){
SP	243	for(jj=1;jj<=vtx[i]->neigh_no;jj++){
7958e9	244	// ts_fprintf(stderr,"%u: (%u,%u) neigh_no=%u ",i,j,jj,vtx[i].neigh_no);
SP	245	// ts_fprintf(stderr,"%e, %e",vtx[i].neigh[j-1]->x,vtx[i].neigh[jj-1]->x);
8f6a69	246	dist=vtx_distance_sq(vtx[i]->neigh[j-1],vtx[i]->neigh[jj-1]);
SP	247	direct=vtx_direct(vtx[i],vtx[i]->neigh[j-1],vtx[i]->neigh[jj-1]);
	248	// TODO: same as above
	249	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){
	250	triangle_add(tlist,vtx[i],vtx[i]->neigh[j-1],vtx[i]->neigh[jj-1]);
7958e9	251	}
SP	252	}
	253	}
	254	}
	255	/* We check if all triangles have 3 vertices and if the number of triangles
	256	* matches the theoretical value.
	257	*/
	258	for(i=0;i<tlist->n;i++){
	259	k=0;
	260	for(j=0;j<3;j++){
41a035	261	if(tlist->tria[i]->vertex[j]!=NULL)
7958e9	262	k++;
SP	263	}
	264	if(k!=3){
8f6a69	265	fatal("Some triangles have less than 3 vertices..",4);
7958e9	266	}
SP	267	}
	268	if(tlist->n!=2*(vesicle->vlist->n -2)){
	269	ts_fprintf(stderr,"The number of triangles is %u but should be %u!\n",tlist->n,2*(vesicle->vlist->n -2));
	270	fatal("The number of triangles doesn't match 2*(no_vertex -2).",4);
	271	}
	272	return TS_SUCCESS;
	273	}
	274
	275
	276
	277	ts_bool init_triangle_neighbours(ts_vesicle *vesicle){
	278	ts_uint i,j,nobo;
	279	ts_vertex i1,i2,i3,j1,j2,j3;
	280	// ts_vertex **vtx=vesicle->vlist->vtx -1; // difference between 0 indexing and 1 indexing
	281	ts_triangle_list *tlist=vesicle->tlist;
	282	ts_triangle **tria=tlist->tria -1;
	283	nobo=0;
	284	for(i=1;i<=tlist->n;i++){
41a035	285	i1=tria[i]->vertex[0];
SP	286	i2=tria[i]->vertex[1];
	287	i3=tria[i]->vertex[2];
7958e9	288	for(j=1;j<=tlist->n;j++){
SP	289	if(j==i) continue;
41a035	290	j1=tria[j]->vertex[0];
SP	291	j2=tria[j]->vertex[1];
	292	j3=tria[j]->vertex[2];
7958e9	293	if((i1==j1 && i3==j2) \|\| (i1==j2 && i3==j3) \|\| (i1==j3 && i3==j1)){
SP	294	triangle_add_neighbour(tria[i],tria[j]);
	295	nobo++;
	296	}
	297	}
	298	}
	299	for(i=1;i<=tlist->n;i++){
41a035	300	i1=tria[i]->vertex[0];
SP	301	i2=tria[i]->vertex[1];
	302	i3=tria[i]->vertex[2];
7958e9	303	for(j=1;j<=tlist->n;j++){
SP	304	if(j==i) continue;
41a035	305	j1=tria[j]->vertex[0];
SP	306	j2=tria[j]->vertex[1];
	307	j3=tria[j]->vertex[2];
7958e9	308	if((i1==j1 && i2==j3) \|\| (i1==j3 && i2==j2) \|\| (i1==j2 && i2==j1)){
SP	309	triangle_add_neighbour(tria[i],tria[j]);
	310	nobo++;
	311	}
	312	}
	313	}
	314	for(i=1;i<=tlist->n;i++){
41a035	315	i1=tria[i]->vertex[0];
SP	316	i2=tria[i]->vertex[1];
	317	i3=tria[i]->vertex[2];
7958e9	318	for(j=1;j<=tlist->n;j++){
SP	319	if(j==i) continue;
41a035	320	j1=tria[j]->vertex[0];
SP	321	j2=tria[j]->vertex[1];
	322	j3=tria[j]->vertex[2];
7958e9	323	if((i2==j1 && i3==j3) \|\| (i2==j3 && i3==j2) \|\| (i2==j2 && i3==j1)){
SP	324	triangle_add_neighbour(tria[i],tria[j]);
	325	nobo++;
	326	}
	327	}
	328	}
	329	if(nobo != vesicle->blist->n*2) {
	330	ts_fprintf(stderr,"Number of triangles= %u, number of bonds= %u\n",nobo/2, vesicle->blist->n);
	331	fatal("Number of triangle neighbour pairs differs from double the number of bonds!",4);
	332	}
	333	return TS_SUCCESS;
	334	}
	335
	336
	337	ts_bool init_common_vertex_triangle_neighbours(ts_vesicle *vesicle){
	338	ts_uint i,j,jp,k;
	339	ts_vertex k1,k2,k3,k4,*k5;
	340	ts_vertex **vtx=vesicle->vlist->vtx -1; // difference between 0 indexing and 1 indexing
	341	ts_triangle_list *tlist=vesicle->tlist;
	342	ts_triangle **tria=tlist->tria -1;
	343
	344	for(i=1;i<=vesicle->vlist->n;i++){
8f6a69	345	for(j=1;j<=vtx[i]->neigh_no;j++){
SP	346	k1=vtx[i]->neigh[j-1];
7958e9	347	jp=j+1;
8f6a69	348	if(j == vtx[i]->neigh_no) jp=1;
SP	349	k2=vtx[i]->neigh[jp-1];
7958e9	350	for(k=1;k<=tlist->n;k++){ // VERY NON-OPTIMAL!!! too many loops (vlist.n * vtx.neigh * tlist.n )!
41a035	351	k3=tria[k]->vertex[0];
SP	352	k4=tria[k]->vertex[1];
	353	k5=tria[k]->vertex[2];
7958e9	354	// ts_fprintf(stderr,"%u %u: k=(%u %u %u)\n",k1,k2,k3,k4,k5);
SP	355	if((vtx[i]==k3 && k1==k4 && k2==k5) \|\|
	356	(vtx[i]==k4 && k1==k5 && k2==k3) \|\|
	357	(vtx[i]==k5 && k1==k3 && k2==k4)){
b01cc1	358
SP	359	//TODO: probably something wrong with neighbour distribution.
	360	// if(vtx[i]==k3 \|\| vtx[i]==k4 \|\| vtx[i]==k5){
dac2e5	361	// if(i==6) ts_fprintf(stdout, "Vtx[%u] > Added to tristar!\n",i);
7958e9	362	vertex_add_tristar(vtx[i],tria[k]);
SP	363	}
	364	}
	365	}
	366	/* ts_fprintf(stderr,"TRISTAR for %u (%u):",i-1,vtx[i].tristar_no);
	367	for(j=0;j<vtx[i].tristar_no;j++){
	368	ts_fprintf(stderr," %u,",vtx[i].tristar[j]->idx);
	369	}
	370	ts_fprintf(stderr,"\n"); */
	371	}
	372	return TS_SUCCESS;
	373	}
	374
	375
	376	ts_bool init_normal_vectors(ts_triangle_list *tlist){
	377	/* Normals point INSIDE vesicle */
	378	ts_uint k;
	379	ts_triangle **tria=tlist->tria -1; //for 0 indexing
	380	for(k=1;k<=tlist->n;k++){
	381	triangle_normal_vector(tria[k]);
	382	}
	383	return TS_SUCCESS;
	384	}