trisurf-ng.git - Gitblit

Finished rewriting io.c. Output for paraview works. Tape parser doesn't wor...

Samo Penic

2010-12-04 a6b1b556b6c8c8da22c5f322b57ccc1528578e10

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"
	11
	12	ts_vesicle *initial_distribution_dipyramid(ts_uint nshell, ts_uint ncmax1, ts_uint ncmax2, ts_uint ncmax3, ts_double stepsize){
	13	ts_fprintf(stderr,"Starting initial_distribution on vesicle with %u shells!...\n",nshell);
	14	ts_bool retval;
	15	ts_uint no_vertices=5nshellnshell+2;
	16
	17	ts_vesicle *vesicle=init_vesicle(no_vertices,ncmax1,ncmax2,ncmax3,stepsize);
	18	vesicle->nshell=nshell;
	19	retval = vtx_set_global_values(vesicle);
	20	retval = pentagonal_dipyramid_vertex_distribution(vesicle->vlist);
	21	retval = init_vertex_neighbours(vesicle->vlist);
	22	retval = init_sort_neighbours(vesicle->vlist);
	23	retval = init_vesicle_bonds(vesicle);
	24	retval = init_triangles(vesicle);
	25	retval = init_triangle_neighbours(vesicle);
	26	retval = init_common_vertex_triangle_neighbours(vesicle);
	27	ts_fprintf(stderr,"initial_distribution finished!\n");
	28	return vesicle;
	29	}
	30
	31
	32	ts_bool pentagonal_dipyramid_vertex_distribution(ts_vertex_list *vlist){
	33	/* Some often used relations */
	34	const ts_double s1= sin(2.0*M_PI/5.0);
	35	const ts_double s2= sin(4.0*M_PI/5.0);
	36	const ts_double c1= cos(2.0*M_PI/5.0);
	37	const ts_double c2= cos(4.0*M_PI/5.0);
	38
	39	/* Calculates projection lenght of an edge bond to pentagram plane */
	40	const ts_double xl0=A0/(2.0*sin(M_PI/5.0));
	41	#ifdef TS_DOUBLE_DOUBLE
	42	const ts_double z0=sqrt(pow(A0,2)-pow(xl0,2));
	43	#endif
	44	#ifdef TS_DOUBLE_FLOAT
	45	const ts_double z0=sqrtf(powf(A0,2)-powf(xl0,2));
	46	#endif
	47	#ifdef TS_DOUBLE_LONGDOUBLE
	48	const ts_double z0=sqrtl(powl(A0,2)-powl(xl0,2));
	49	#endif
	50	// 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 */
	51
	52	/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!/
	53	ts_vertex **vtx=vlist->vtx -1 ;
	54
	55
	56	ts_uint nshell=(ts_uint)( sqrt((ts_double)(vlist->n-2)/5));
	57	// printf("nshell=%u\n",nshell);
	58	ts_uint i,n0; // some for loop prereq
	59	ts_int j,k;
	60	ts_double dx,dy; // end loop prereq
	61
	62	/* topmost vertex */
	63	vtx[1]->data->x=0.0;
	64	vtx[1]->data->y=0.0;
	65	vtx[1]->data->z=z0*(ts_double)nshell;
	66
	67	/* starting from to in circular order on pentagrams */
	68	for(i=1;i<=nshell;i++){
	69	n0=2+5i(i-1)/2; //-1 would be for the reason that C index starts from 0
	70	vtx[n0]->data->x=0.0;
	71	vtx[n0]->data->y=(ts_double)i*xl0;
	72	vtx[n0+i]->data->x=vtx[n0]->data->y*s1;
	73	vtx[n0+i]->data->y=vtx[n0]->data->y*c1;
	74	vtx[n0+2i]->data->x=vtx[n0]->data->ys2;
	75	vtx[n0+2i]->data->y=vtx[n0]->data->yc2;
	76	vtx[n0+3i]->data->x=-vtx[n0+2i]->data->x;
	77	vtx[n0+3i]->data->y=vtx[n0+2i]->data->y;
	78	vtx[n0+4*i]->data->x=-vtx[n0+i]->data->x;
	79	vtx[n0+4*i]->data->y=vtx[n0+i]->data->y;
	80	}
	81
	82	/* vertexes on the faces of the dipyramid */
	83	for(i=1;i<=nshell;i++){
	84	n0=2+5i(i-1)/2; // -1 would be because of C!
	85	for(j=1;j<=i-1;j++){
	86	dx=(vtx[n0]->data->x-vtx[n0+4*i]->data->x)/(ts_double)i;
	87	dy=(vtx[n0]->data->y-vtx[n0+4*i]->data->y)/(ts_double)i;
	88	vtx[n0+4i+j]->data->x=(ts_double)jdx+vtx[n0+4*i]->data->x;
	89	vtx[n0+4i+j]->data->y=(ts_double)jdy+vtx[n0+4*i]->data->y;
	90	}
	91	for(k=0;k<=3;k++){ // I would be worried about zero starting of for
	92	dx=(vtx[n0+(k+1)i]->data->x - vtx[n0+ki]->data->x)/(ts_double) i;
	93	dy=(vtx[n0+(k+1)i]->data->y - vtx[n0+ki]->data->y)/(ts_double) i;
	94	for(j=1; j<=i-1;j++){
	95	vtx[n0+ki+j]->data->x= (ts_double)jdx+vtx[n0+k*i]->data->x;
	96	vtx[n0+ki+j]->data->y= (ts_double)jdy+vtx[n0+k*i]->data->y;
	97	}
	98	}
	99	}
	100
	101	for(i=1;i<=nshell;i++){
	102	n0= 2+ 5i(i-1)/2;
	103	for(j=0;j<=5*i-1;j++){
	104	vtx[n0+j]->data->z= z0*(ts_double)(nshell-i); // I would be worried about zero starting of for
	105	}
	106	}
	107
	108	/* for botom part of dipyramide we calculate the positions of vertices */
	109	for(i=2+5nshell(nshell+1)/2;i<=vlist->n;i++){
	110	vtx[i]->data->x=vtx[vlist->n - i +1]->data->x;
	111	vtx[i]->data->y=vtx[vlist->n - i +1]->data->y;
	112	vtx[i]->data->z=-vtx[vlist->n - i +1]->data->z;
	113	}
	114
	115	for(i=1;i<=vlist->n;i++){
	116	for(j=1;j<=vlist->n;j++){
	117	if(i!=j && vtx_distance_sq(vtx[i],vtx[j])<0.001){
	118	printf("Vertices %u and %u are the same!\n",i,j);
	119	}
	120	}
	121	}
	122	return TS_SUCCESS;
	123	}
	124
	125
	126
	127	ts_bool init_vertex_neighbours(ts_vertex_list *vlist){
	128	ts_vertex **vtx=vlist->vtx -1; // take a look at dipyramid function for comment.
	129	const ts_double eps=0.001; //TODO: find out if you can use EPS from math.h
	130	ts_uint i,j;
	131	ts_double dist2; // Square of distance of neighbours
	132	/this is not required if we zero all data in vertex structure at initialization /
	133	/if we force zeroing at initialization this for loop can safely be deleted /
	134	//for(i=1;i<=vlist->n;i++){
	135	// vtx[i].neigh_no=0;
	136	//}
	137	for(i=1;i<=vlist->n;i++){
	138	for(j=1;j<=vlist->n;j++){
	139	dist2=vtx_distance_sq(vtx[i],vtx[j]);
	140	if( (dist2>eps) && (dist2<(A0*A0+eps))){
	141	//if it is close enough, but not too much close (solves problem of comparing when i==j)
	142	vtx_add_neighbour(vtx[i],vtx[j]);
	143	}
	144	}
	145	// printf ("vertex %u ima %u sosedov!\n",i,vtx[i]->data->neigh_no);
	146	}
	147
	148	return TS_SUCCESS;
	149	}
	150
	151	// TODO: with new datastructure can be rewritten.
	152	ts_bool init_sort_neighbours(ts_vertex_list *vlist){
	153	ts_vertex **vtx=vlist->vtx -1; // take a look at dipyramid function for comment.
	154	ts_uint i,l,j,jj,jjj,k=0;
	155	ts_double eps=0.001; // Take a look if EPS from math.h can be used
	156
	157	/lets initialize memory for temporary vertex_list. Should we write a function instead /
	158	ts_vertex_list *tvlist=init_vertex_list(vlist->n);
	159	ts_vertex *tvtx=tvlist->vtx -1; / again to compensate for 0-indexing */
	160
	161	ts_double dist2; // Square of distance of neighbours
	162	ts_double direct; // Something, dont know what, but could be normal of some kind
	163	for(i=1;i<=vlist->n;i++){
	164	k++; // WHY i IS NOT GOOD??
	165	vtx_add_neighbour(tvtx[k], tvtx[vtx[i]->data->neigh[0]->idx+1]); //always add 1st
	166	jjj=1;
	167	jj=1;
	168	for(l=2;l<=vtx[i]->data->neigh_no;l++){
	169	for(j=2;j<=vtx[i]->data->neigh_no;j++){
	170	dist2=vtx_distance_sq(vtx[i]->data->neigh[j-1],vtx[i]->data->neigh[jj-1]);
	171	direct=vtx_direct(vtx[i],vtx[i]->data->neigh[j-1],vtx[i]->data->neigh[jj-1]);
	172	if( (fabs(dist2-A0*A0)<=eps) && (direct>0.0) && (j!=jjj) ){
	173	vtx_add_neighbour(tvtx[k],tvtx[vtx[i]->data->neigh[j-1]->idx+1]);
	174	jjj=jj;
	175	jj=j;
	176	break;
	177	}
	178	}
	179	}
	180	}
	181
	182	for(i=1;i<=vlist->n;i++){
	183	for(j=1;j<=vtx[i]->data->neigh_no;j++){
	184	if(vtx[i]->data->neigh_no!=tvtx[i]->data->neigh_no){ //doesn't work with nshell=1!
	185	// fprintf(stderr,"data1=%u data2=%u\n",vtx[i]->data->neigh_no,tvtx[i]->data->neigh_no);
	186	fatal("Number of neighbours not the same in init_sort_neighbours.",4);
	187	}
	188	//we must correct the pointers in original to point to their
	189	//neighbours according to indexes. Must be sure not to do it any
	190	//other way! Also, we need to repair the collection of bonds...
	191	vtx[i]->data->neigh[j-1]=vtx[tvtx[i]->data->neigh[j-1]->idx+1];
	192	}
	193	}
	194
	195	// Must free memory for temporary vertex array to avoid memory leak! HERE! NOW!
	196	// free_vertex(tvlist.vertex,tvlist.n);
	197	vtx_list_free(tvlist);
	198	return TS_SUCCESS;
	199	}
	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++){
	210	for(k=0;k<vtx[i]->data->neigh_no;k++){ // has changed 0 to < instead of 1 and <=
	211	if(vtx[i]->data->neigh[k]==vtx[j]){ //if addresses matches it is the same
	212	bond_add(blist,vtx[i],vtx[j]);
	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++){
	236	for(j=1;j<=vtx[i]->data->neigh_no;j++){
	237	for(jj=1;jj<=vtx[i]->data->neigh_no;jj++){
	238	// ts_fprintf(stderr,"%u: (%u,%u) neigh_no=%u ",i,j,jj,vtx[i].neigh_no);
	239	// ts_fprintf(stderr,"%e, %e",vtx[i].neigh[j-1]->x,vtx[i].neigh[jj-1]->x);
	240	dist=vtx_distance_sq(vtx[i]->data->neigh[j-1],vtx[i]->data->neigh[jj-1]);
	241	direct=vtx_direct(vtx[i],vtx[i]->data->neigh[j-1],vtx[i]->data->neigh[jj-1]);
	242	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){
	243	triangle_add(tlist,vtx[i],vtx[i]->data->neigh[j-1],vtx[i]->data->neigh[jj-1]);
	244	}
	245	}
	246	}
	247	}
	248	/* We check if all triangles have 3 vertices and if the number of triangles
	249	* matches the theoretical value.
	250	*/
	251	for(i=0;i<tlist->n;i++){
	252	k=0;
	253	for(j=0;j<3;j++){
	254	if(tlist->tria[i]->data->vertex[j]!=NULL)
	255	k++;
	256	}
	257	if(k!=3){
	258	fatal("Some triangles has less than 3 vertices..",4);
	259	}
	260	}
	261	if(tlist->n!=2*(vesicle->vlist->n -2)){
	262	ts_fprintf(stderr,"The number of triangles is %u but should be %u!\n",tlist->n,2*(vesicle->vlist->n -2));
	263	fatal("The number of triangles doesn't match 2*(no_vertex -2).",4);
	264	}
	265	return TS_SUCCESS;
	266	}
	267
	268
	269
	270	ts_bool init_triangle_neighbours(ts_vesicle *vesicle){
	271	ts_uint i,j,nobo;
	272	ts_vertex i1,i2,i3,j1,j2,j3;
	273	// ts_vertex **vtx=vesicle->vlist->vtx -1; // difference between 0 indexing and 1 indexing
	274	ts_triangle_list *tlist=vesicle->tlist;
	275	ts_triangle **tria=tlist->tria -1;
	276	nobo=0;
	277	for(i=1;i<=tlist->n;i++){
	278	i1=tria[i]->data->vertex[0];
	279	i2=tria[i]->data->vertex[1];
	280	i3=tria[i]->data->vertex[2];
	281	for(j=1;j<=tlist->n;j++){
	282	if(j==i) continue;
	283	j1=tria[j]->data->vertex[0];
	284	j2=tria[j]->data->vertex[1];
	285	j3=tria[j]->data->vertex[2];
	286	if((i1==j1 && i3==j2) \|\| (i1==j2 && i3==j3) \|\| (i1==j3 && i3==j1)){
	287	triangle_add_neighbour(tria[i],tria[j]);
	288	nobo++;
	289	}
	290	}
	291	}
	292	for(i=1;i<=tlist->n;i++){
	293	i1=tria[i]->data->vertex[0];
	294	i2=tria[i]->data->vertex[1];
	295	i3=tria[i]->data->vertex[2];
	296	for(j=1;j<=tlist->n;j++){
	297	if(j==i) continue;
	298	j1=tria[j]->data->vertex[0];
	299	j2=tria[j]->data->vertex[1];
	300	j3=tria[j]->data->vertex[2];
	301	if((i1==j1 && i2==j3) \|\| (i1==j3 && i2==j2) \|\| (i1==j2 && i2==j1)){
	302	triangle_add_neighbour(tria[i],tria[j]);
	303	nobo++;
	304	}
	305	}
	306	}
	307	for(i=1;i<=tlist->n;i++){
	308	i1=tria[i]->data->vertex[0];
	309	i2=tria[i]->data->vertex[1];
	310	i3=tria[i]->data->vertex[2];
	311	for(j=1;j<=tlist->n;j++){
	312	if(j==i) continue;
	313	j1=tria[j]->data->vertex[0];
	314	j2=tria[j]->data->vertex[1];
	315	j3=tria[j]->data->vertex[2];
	316	if((i2==j1 && i3==j3) \|\| (i2==j3 && i3==j2) \|\| (i2==j2 && i3==j1)){
	317	triangle_add_neighbour(tria[i],tria[j]);
	318	nobo++;
	319	}
	320	}
	321	}
	322	if(nobo != vesicle->blist->n*2) {
	323	ts_fprintf(stderr,"Number of triangles= %u, number of bonds= %u\n",nobo/2, vesicle->blist->n);
	324	fatal("Number of triangle neighbour pairs differs from double the number of bonds!",4);
	325	}
	326	return TS_SUCCESS;
	327	}
	328
	329
	330	ts_bool init_common_vertex_triangle_neighbours(ts_vesicle *vesicle){
	331	ts_uint i,j,jp,k;
	332	ts_vertex k1,k2,k3,k4,*k5;
	333	ts_vertex **vtx=vesicle->vlist->vtx -1; // difference between 0 indexing and 1 indexing
	334	ts_triangle_list *tlist=vesicle->tlist;
	335	ts_triangle **tria=tlist->tria -1;
	336
	337	for(i=1;i<=vesicle->vlist->n;i++){
	338	for(j=1;j<=vtx[i]->data->neigh_no;j++){
	339	k1=vtx[i]->data->neigh[j-1];
	340	jp=j+1;
	341	if(j == vtx[i]->data->neigh_no) jp=1;
	342	k2=vtx[i]->data->neigh[jp-1];
	343	for(k=1;k<=tlist->n;k++){ // VERY NON-OPTIMAL!!! too many loops (vlist.n * vtx.neigh * tlist.n )!
	344	k3=tria[k]->data->vertex[0];
	345	k4=tria[k]->data->vertex[1];
	346	k5=tria[k]->data->vertex[2];
	347	// ts_fprintf(stderr,"%u %u: k=(%u %u %u)\n",k1,k2,k3,k4,k5);
	348	if((vtx[i]==k3 && k1==k4 && k2==k5) \|\|
	349	(vtx[i]==k4 && k1==k5 && k2==k3) \|\|
	350	(vtx[i]==k5 && k1==k3 && k2==k4)){
	351	// ts_fprintf(stderr, "Added to tristar! ");
	352	vertex_add_tristar(vtx[i],tria[k]);
	353	}
	354	}
	355	}
	356	/* ts_fprintf(stderr,"TRISTAR for %u (%u):",i-1,vtx[i].tristar_no);
	357	for(j=0;j<vtx[i].tristar_no;j++){
	358	ts_fprintf(stderr," %u,",vtx[i].tristar[j]->idx);
	359	}
	360	ts_fprintf(stderr,"\n"); */
	361	}
	362	return TS_SUCCESS;
	363	}
	364
	365
	366	ts_bool init_normal_vectors(ts_triangle_list *tlist){
	367	/* Normals point INSIDE vesicle */
	368	ts_uint k;
	369	ts_triangle **tria=tlist->tria -1; //for 0 indexing
	370	for(k=1;k<=tlist->n;k++){
	371	triangle_normal_vector(tria[k]);
	372	}
	373	return TS_SUCCESS;
	374	}