trisurf-ng.git - Gitblit

vertex data removed and memory leaks fixed

Samo Penic

2012-02-23 8f6a69d8fddcae6b54d25cf02dd56f0afce6a075

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