trisurf-ng.git - Gitblit

Samo Penic

2014-03-05 719c9febac2eaff9483fda487b57684afbb59bb2

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);
d335d9	35	retval = init_bond_triangles(vesicle->blist);
f74313	36	retval = mean_curvature_and_energy(vesicle);
7958e9	37	ts_fprintf(stderr,"initial_distribution finished!\n");
41a035	38	if(retval);
7958e9	39	return vesicle;
SP	40	}
	41
	42
	43	ts_bool pentagonal_dipyramid_vertex_distribution(ts_vertex_list *vlist){
	44	/* Some often used relations */
	45	const ts_double s1= sin(2.0*M_PI/5.0);
	46	const ts_double s2= sin(4.0*M_PI/5.0);
	47	const ts_double c1= cos(2.0*M_PI/5.0);
	48	const ts_double c2= cos(4.0*M_PI/5.0);
	49
	50	/* Calculates projection lenght of an edge bond to pentagram plane */
	51	const ts_double xl0=A0/(2.0*sin(M_PI/5.0));
	52	#ifdef TS_DOUBLE_DOUBLE
	53	const ts_double z0=sqrt(pow(A0,2)-pow(xl0,2));
	54	#endif
	55	#ifdef TS_DOUBLE_FLOAT
	56	const ts_double z0=sqrtf(powf(A0,2)-powf(xl0,2));
	57	#endif
	58	#ifdef TS_DOUBLE_LONGDOUBLE
	59	const ts_double z0=sqrtl(powl(A0,2)-powl(xl0,2));
	60	#endif
	61	// 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 */
	62
	63	/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!/
	64	ts_vertex **vtx=vlist->vtx -1 ;
	65
	66
	67	ts_uint nshell=(ts_uint)( sqrt((ts_double)(vlist->n-2)/5));
	68	// printf("nshell=%u\n",nshell);
	69	ts_uint i,n0; // some for loop prereq
	70	ts_int j,k;
	71	ts_double dx,dy; // end loop prereq
	72
	73	/* topmost vertex */
8f6a69	74	vtx[1]->x=0.0;
SP	75	vtx[1]->y=0.0;
	76	vtx[1]->z=z0*(ts_double)nshell;
7958e9	77
SP	78	/* starting from to in circular order on pentagrams */
	79	for(i=1;i<=nshell;i++){
	80	n0=2+5i(i-1)/2; //-1 would be for the reason that C index starts from 0
8f6a69	81	vtx[n0]->x=0.0;
SP	82	vtx[n0]->y=(ts_double)i*xl0;
	83	vtx[n0+i]->x=vtx[n0]->y*s1;
	84	vtx[n0+i]->y=vtx[n0]->y*c1;
	85	vtx[n0+2i]->x=vtx[n0]->ys2;
	86	vtx[n0+2i]->y=vtx[n0]->yc2;
	87	vtx[n0+3i]->x=-vtx[n0+2i]->x;
	88	vtx[n0+3i]->y=vtx[n0+2i]->y;
	89	vtx[n0+4*i]->x=-vtx[n0+i]->x;
	90	vtx[n0+4*i]->y=vtx[n0+i]->y;
7958e9	91	}
SP	92
	93	/* vertexes on the faces of the dipyramid */
	94	for(i=1;i<=nshell;i++){
	95	n0=2+5i(i-1)/2; // -1 would be because of C!
	96	for(j=1;j<=i-1;j++){
8f6a69	97	dx=(vtx[n0]->x-vtx[n0+4*i]->x)/(ts_double)i;
SP	98	dy=(vtx[n0]->y-vtx[n0+4*i]->y)/(ts_double)i;
	99	vtx[n0+4i+j]->x=(ts_double)jdx+vtx[n0+4*i]->x;
	100	vtx[n0+4i+j]->y=(ts_double)jdy+vtx[n0+4*i]->y;
7958e9	101	}
SP	102	for(k=0;k<=3;k++){ // I would be worried about zero starting of for
8f6a69	103	dx=(vtx[n0+(k+1)i]->x - vtx[n0+ki]->x)/(ts_double) i;
SP	104	dy=(vtx[n0+(k+1)i]->y - vtx[n0+ki]->y)/(ts_double) i;
7958e9	105	for(j=1; j<=i-1;j++){
8f6a69	106	vtx[n0+ki+j]->x= (ts_double)jdx+vtx[n0+k*i]->x;
SP	107	vtx[n0+ki+j]->y= (ts_double)jdy+vtx[n0+k*i]->y;
7958e9	108	}
SP	109	}
	110	}
	111
	112	for(i=1;i<=nshell;i++){
	113	n0= 2+ 5i(i-1)/2;
	114	for(j=0;j<=5*i-1;j++){
8f6a69	115	vtx[n0+j]->z= z0*(ts_double)(nshell-i); // I would be worried about zero starting of for
7958e9	116	}
SP	117	}
	118
	119	/* for botom part of dipyramide we calculate the positions of vertices */
	120	for(i=2+5nshell(nshell+1)/2;i<=vlist->n;i++){
8f6a69	121	vtx[i]->x=vtx[vlist->n - i +1]->x;
SP	122	vtx[i]->y=vtx[vlist->n - i +1]->y;
	123	vtx[i]->z=-vtx[vlist->n - i +1]->z;
7958e9	124	}
SP	125
	126	for(i=1;i<=vlist->n;i++){
	127	for(j=1;j<=vlist->n;j++){
	128	if(i!=j && vtx_distance_sq(vtx[i],vtx[j])<0.001){
	129	printf("Vertices %u and %u are the same!\n",i,j);
	130	}
	131	}
	132	}
	133	return TS_SUCCESS;
	134	}
	135
	136
	137
	138	ts_bool init_vertex_neighbours(ts_vertex_list *vlist){
	139	ts_vertex **vtx=vlist->vtx -1; // take a look at dipyramid function for comment.
	140	const ts_double eps=0.001; //TODO: find out if you can use EPS from math.h
	141	ts_uint i,j;
	142	ts_double dist2; // Square of distance of neighbours
	143	/this is not required if we zero all data in vertex structure at initialization /
	144	/if we force zeroing at initialization this for loop can safely be deleted /
	145	//for(i=1;i<=vlist->n;i++){
	146	// vtx[i].neigh_no=0;
	147	//}
	148	for(i=1;i<=vlist->n;i++){
	149	for(j=1;j<=vlist->n;j++){
	150	dist2=vtx_distance_sq(vtx[i],vtx[j]);
	151	if( (dist2>eps) && (dist2<(A0*A0+eps))){
	152	//if it is close enough, but not too much close (solves problem of comparing when i==j)
	153	vtx_add_neighbour(vtx[i],vtx[j]);
	154	}
	155	}
	156	// printf ("vertex %u ima %u sosedov!\n",i,vtx[i]->data->neigh_no);
	157	}
	158
	159	return TS_SUCCESS;
	160	}
	161
b01cc1	162	// TODO: with new datastructure can be rewritten. Partially it is done, but it is complicated.
SP	163	ts_vertex_list init_sort_neighbours(ts_bond_list blist,ts_vertex_list *vlist){
7958e9	164	ts_vertex **vtx=vlist->vtx -1; // take a look at dipyramid function for comment.
SP	165	ts_uint i,l,j,jj,jjj,k=0;
	166	ts_double eps=0.001; // Take a look if EPS from math.h can be used
	167
	168	/lets initialize memory for temporary vertex_list. Should we write a function instead /
b01cc1	169	ts_vertex_list *tvlist=vertex_list_copy(vlist);
7958e9	170	ts_vertex *tvtx=tvlist->vtx -1; / again to compensate for 0-indexing */
SP	171
	172	ts_double dist2; // Square of distance of neighbours
	173	ts_double direct; // Something, dont know what, but could be normal of some kind
	174	for(i=1;i<=vlist->n;i++){
	175	k++; // WHY i IS NOT GOOD??
2f8ee7	176	vtx_add_cneighbour(blist,tvtx[k], tvtx[vtx[i]->neigh->vtx[0]->idx+1]); //always add 1st
7958e9	177	jjj=1;
SP	178	jj=1;
2f8ee7	179	for(l=2;l<=vtx[i]->neigh->n;l++){
SP	180	for(j=2;j<=vtx[i]->neigh->n;j++){
	181	dist2=vtx_distance_sq(vtx[i]->neigh->vtx[j-1],vtx[i]->neigh->vtx[jj-1]);
	182	direct=vtx_direct(vtx[i],vtx[i]->neigh->vtx[j-1],vtx[i]->neigh->vtx[jj-1]);
8f6a69	183	// TODO: check if fabs can be used with all floating point types!!
7958e9	184	if( (fabs(dist2-A0*A0)<=eps) && (direct>0.0) && (j!=jjj) ){
2f8ee7	185	vtx_add_cneighbour(blist,tvtx[k],tvtx[vtx[i]->neigh->vtx[j-1]->idx+1]);
7958e9	186	jjj=jj;
SP	187	jj=j;
	188	break;
	189	}
	190	}
	191	}
	192	}
b01cc1	193	/* We use the temporary vertex for our main vertices and we abandon main
SP	194	* vertices, because their neighbours are not correctly ordered */
	195	// tvtx=vlist->vtx;
	196	// vlist->vtx=tvtx;
	197	// tvlist->vtx=vtx;
	198	vtx_list_free(vlist);
	199	/* Let's make a check if the number of bonds is correct */
	200	if((blist->n)!=3*(tvlist->n-2)){
	201	ts_fprintf(stderr,"Number of bonds is %u should be %u!\n", blist->n, 3*(tvlist->n-2));
	202	fatal("Number of bonds is not 3*(no_vertex-2).",4);
7958e9	203	}
SP	204
b01cc1	205	return tvlist;
7958e9	206	}
SP	207
	208
	209	ts_bool init_vesicle_bonds(ts_vesicle *vesicle){
	210	ts_vertex_list *vlist=vesicle->vlist;
	211	ts_bond_list *blist=vesicle->blist;
	212	ts_vertex **vtx=vesicle->vlist->vtx - 1; // Because of 0 indexing
	213	/* lets make correct clockwise ordering of in nearest neighbour list */
	214	ts_uint i,j,k;
	215	for(i=1;i<=vlist->n;i++){
	216	for(j=i+1;j<=vlist->n;j++){
2f8ee7	217	for(k=0;k<vtx[i]->neigh->n;k++){ // has changed 0 to < instead of 1 and <=
SP	218	if(vtx[i]->neigh->vtx[k]==vtx[j]){ //if addresses matches it is the same
7958e9	219	bond_add(blist,vtx[i],vtx[j]);
SP	220	break;
	221	}
	222	}
	223	}
	224	}
	225	/* Let's make a check if the number of bonds is correct */
	226	if((blist->n)!=3*(vlist->n-2)){
	227	ts_fprintf(stderr,"Number of bonds is %u should be %u!\n", blist->n, 3*(vlist->n-2));
	228	fatal("Number of bonds is not 3*(no_vertex-2).",4);
	229	}
	230	return TS_SUCCESS;
	231	}
	232
	233
	234
	235	ts_bool init_triangles(ts_vesicle *vesicle){
	236	ts_uint i,j,jj,k;
	237	ts_vertex **vtx=vesicle->vlist->vtx -1; // difference between 0 indexing and 1 indexing
	238	ts_triangle_list *tlist=vesicle->tlist;
	239	ts_double dist, direct;
	240	ts_double eps=0.001; // can we use EPS from math.h?
	241	k=0;
	242	for(i=1;i<=vesicle->vlist->n;i++){
2f8ee7	243	for(j=1;j<=vtx[i]->neigh->n;j++){
SP	244	for(jj=1;jj<=vtx[i]->neigh->n;jj++){
7958e9	245	// ts_fprintf(stderr,"%u: (%u,%u) neigh_no=%u ",i,j,jj,vtx[i].neigh_no);
SP	246	// ts_fprintf(stderr,"%e, %e",vtx[i].neigh[j-1]->x,vtx[i].neigh[jj-1]->x);
2f8ee7	247	dist=vtx_distance_sq(vtx[i]->neigh->vtx[j-1],vtx[i]->neigh->vtx[jj-1]);
SP	248	direct=vtx_direct(vtx[i],vtx[i]->neigh->vtx[j-1],vtx[i]->neigh->vtx[jj-1]);
8f6a69	249	// TODO: same as above
2f8ee7	250	if(fabs(dist-A0*A0)<=eps && direct < 0.0 && vtx[i]->neigh->vtx[j-1]->idx+1 > i && vtx[i]->neigh->vtx[jj-1]->idx+1 >i){
SP	251	triangle_add(tlist,vtx[i],vtx[i]->neigh->vtx[j-1],vtx[i]->neigh->vtx[jj-1]);
7958e9	252	}
SP	253	}
	254	}
	255	}
	256	/* We check if all triangles have 3 vertices and if the number of triangles
	257	* matches the theoretical value.
	258	*/
	259	for(i=0;i<tlist->n;i++){
	260	k=0;
	261	for(j=0;j<3;j++){
41a035	262	if(tlist->tria[i]->vertex[j]!=NULL)
7958e9	263	k++;
SP	264	}
	265	if(k!=3){
8f6a69	266	fatal("Some triangles have less than 3 vertices..",4);
7958e9	267	}
SP	268	}
	269	if(tlist->n!=2*(vesicle->vlist->n -2)){
	270	ts_fprintf(stderr,"The number of triangles is %u but should be %u!\n",tlist->n,2*(vesicle->vlist->n -2));
	271	fatal("The number of triangles doesn't match 2*(no_vertex -2).",4);
	272	}
	273	return TS_SUCCESS;
	274	}
	275
	276
	277
	278	ts_bool init_triangle_neighbours(ts_vesicle *vesicle){
	279	ts_uint i,j,nobo;
	280	ts_vertex i1,i2,i3,j1,j2,j3;
	281	// ts_vertex **vtx=vesicle->vlist->vtx -1; // difference between 0 indexing and 1 indexing
	282	ts_triangle_list *tlist=vesicle->tlist;
	283	ts_triangle **tria=tlist->tria -1;
	284	nobo=0;
	285	for(i=1;i<=tlist->n;i++){
41a035	286	i1=tria[i]->vertex[0];
SP	287	i2=tria[i]->vertex[1];
	288	i3=tria[i]->vertex[2];
7958e9	289	for(j=1;j<=tlist->n;j++){
SP	290	if(j==i) continue;
41a035	291	j1=tria[j]->vertex[0];
SP	292	j2=tria[j]->vertex[1];
	293	j3=tria[j]->vertex[2];
7958e9	294	if((i1==j1 && i3==j2) \|\| (i1==j2 && i3==j3) \|\| (i1==j3 && i3==j1)){
SP	295	triangle_add_neighbour(tria[i],tria[j]);
	296	nobo++;
	297	}
	298	}
	299	}
	300	for(i=1;i<=tlist->n;i++){
41a035	301	i1=tria[i]->vertex[0];
SP	302	i2=tria[i]->vertex[1];
	303	i3=tria[i]->vertex[2];
7958e9	304	for(j=1;j<=tlist->n;j++){
SP	305	if(j==i) continue;
41a035	306	j1=tria[j]->vertex[0];
SP	307	j2=tria[j]->vertex[1];
	308	j3=tria[j]->vertex[2];
7958e9	309	if((i1==j1 && i2==j3) \|\| (i1==j3 && i2==j2) \|\| (i1==j2 && i2==j1)){
SP	310	triangle_add_neighbour(tria[i],tria[j]);
	311	nobo++;
	312	}
	313	}
	314	}
	315	for(i=1;i<=tlist->n;i++){
41a035	316	i1=tria[i]->vertex[0];
SP	317	i2=tria[i]->vertex[1];
	318	i3=tria[i]->vertex[2];
7958e9	319	for(j=1;j<=tlist->n;j++){
SP	320	if(j==i) continue;
41a035	321	j1=tria[j]->vertex[0];
SP	322	j2=tria[j]->vertex[1];
	323	j3=tria[j]->vertex[2];
7958e9	324	if((i2==j1 && i3==j3) \|\| (i2==j3 && i3==j2) \|\| (i2==j2 && i3==j1)){
SP	325	triangle_add_neighbour(tria[i],tria[j]);
	326	nobo++;
	327	}
	328	}
	329	}
	330	if(nobo != vesicle->blist->n*2) {
	331	ts_fprintf(stderr,"Number of triangles= %u, number of bonds= %u\n",nobo/2, vesicle->blist->n);
	332	fatal("Number of triangle neighbour pairs differs from double the number of bonds!",4);
	333	}
	334	return TS_SUCCESS;
	335	}
	336
	337
	338	ts_bool init_common_vertex_triangle_neighbours(ts_vesicle *vesicle){
	339	ts_uint i,j,jp,k;
	340	ts_vertex k1,k2,k3,k4,*k5;
	341	ts_vertex **vtx=vesicle->vlist->vtx -1; // difference between 0 indexing and 1 indexing
	342	ts_triangle_list *tlist=vesicle->tlist;
	343	ts_triangle **tria=tlist->tria -1;
	344
	345	for(i=1;i<=vesicle->vlist->n;i++){
2f8ee7	346	for(j=1;j<=vtx[i]->neigh->n;j++){
SP	347	k1=vtx[i]->neigh->vtx[j-1];
7958e9	348	jp=j+1;
2f8ee7	349	if(j == vtx[i]->neigh->n) jp=1;
SP	350	k2=vtx[i]->neigh->vtx[jp-1];
7958e9	351	for(k=1;k<=tlist->n;k++){ // VERY NON-OPTIMAL!!! too many loops (vlist.n * vtx.neigh * tlist.n )!
41a035	352	k3=tria[k]->vertex[0];
SP	353	k4=tria[k]->vertex[1];
	354	k5=tria[k]->vertex[2];
7958e9	355	// ts_fprintf(stderr,"%u %u: k=(%u %u %u)\n",k1,k2,k3,k4,k5);
SP	356	if((vtx[i]==k3 && k1==k4 && k2==k5) \|\|
	357	(vtx[i]==k4 && k1==k5 && k2==k3) \|\|
	358	(vtx[i]==k5 && k1==k3 && k2==k4)){
b01cc1	359
SP	360	//TODO: probably something wrong with neighbour distribution.
	361	// if(vtx[i]==k3 \|\| vtx[i]==k4 \|\| vtx[i]==k5){
dac2e5	362	// if(i==6) ts_fprintf(stdout, "Vtx[%u] > Added to tristar!\n",i);
7958e9	363	vertex_add_tristar(vtx[i],tria[k]);
SP	364	}
	365	}
	366	}
	367	/* ts_fprintf(stderr,"TRISTAR for %u (%u):",i-1,vtx[i].tristar_no);
	368	for(j=0;j<vtx[i].tristar_no;j++){
	369	ts_fprintf(stderr," %u,",vtx[i].tristar[j]->idx);
	370	}
	371	ts_fprintf(stderr,"\n"); */
	372	}
	373	return TS_SUCCESS;
	374	}
	375
	376
	377	ts_bool init_normal_vectors(ts_triangle_list *tlist){
	378	/* Normals point INSIDE vesicle */
	379	ts_uint k;
	380	ts_triangle **tria=tlist->tria -1; //for 0 indexing
	381	for(k=1;k<=tlist->n;k++){
	382	triangle_normal_vector(tria[k]);
	383	}
	384	return TS_SUCCESS;
	385	}
d335d9	386
SP	387	ts_bool init_bond_triangles(ts_bond_list *blist){
	388
	389	ts_uint i;
	390	ts_bool retval;
	391	for(i=0;i<blist->n;i++){
	392	retval=bond_assign_triangles(blist->bond[i]);
	393	if(retval==TS_FAIL){
	394	fatal("Bond %u does not have 2 triangles. Possible error in structure.",156);
	395	}
	396	}
	397	return TS_SUCCESS;
	398	}