trisurf-ng.git - Gitblit

Make changes in memory allocation. Memory reservation is done, but pointers...

Samo Penic

2014-02-11 23d807748be58e5178c04304d9cc788bf122eb12

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"
23d807	12	#include "memory.h"
7958e9	13
SP	14	ts_vesicle *initial_distribution_dipyramid(ts_uint nshell, ts_uint ncmax1, ts_uint ncmax2, ts_uint ncmax3, ts_double stepsize){
	15	ts_fprintf(stderr,"Starting initial_distribution on vesicle with %u shells!...\n",nshell);
	16	ts_bool retval;
	17	ts_uint no_vertices=5nshellnshell+2;
314f2d	18
23d807	19	ts_memory mem;
SP	20	mem.vertex_no=no_vertices;
	21	mem.ncmax[0]=ncmax1;
	22	mem.ncmax[1]=ncmax2;
	23	mem.ncmax[2]=ncmax3;
314f2d	24
23d807	25	init_memory_block(&mem);
7958e9	26	ts_vesicle *vesicle=init_vesicle(no_vertices,ncmax1,ncmax2,ncmax3,stepsize);
314f2d	27
SP	28	//TODO: debugging only. Please remove ASAP!
443ba1	29	vesicle->bending_rigidity=25.0;
314f2d	30
7958e9	31	vesicle->nshell=nshell;
SP	32	retval = vtx_set_global_values(vesicle);
	33	retval = pentagonal_dipyramid_vertex_distribution(vesicle->vlist);
	34	retval = init_vertex_neighbours(vesicle->vlist);
b01cc1	35	vesicle->vlist = init_sort_neighbours(vesicle->blist,vesicle->vlist);
SP	36	// retval = init_vesicle_bonds(vesicle); // bonds are created in sort_neigh
7958e9	37	retval = init_triangles(vesicle);
SP	38	retval = init_triangle_neighbours(vesicle);
	39	retval = init_common_vertex_triangle_neighbours(vesicle);
dac2e5	40	retval = init_normal_vectors(vesicle->tlist);
f74313	41	retval = mean_curvature_and_energy(vesicle);
7958e9	42	ts_fprintf(stderr,"initial_distribution finished!\n");
41a035	43	if(retval);
7958e9	44	return vesicle;
SP	45	}
	46
	47
	48	ts_bool pentagonal_dipyramid_vertex_distribution(ts_vertex_list *vlist){
	49	/* Some often used relations */
	50	const ts_double s1= sin(2.0*M_PI/5.0);
	51	const ts_double s2= sin(4.0*M_PI/5.0);
	52	const ts_double c1= cos(2.0*M_PI/5.0);
	53	const ts_double c2= cos(4.0*M_PI/5.0);
	54
	55	/* Calculates projection lenght of an edge bond to pentagram plane */
	56	const ts_double xl0=A0/(2.0*sin(M_PI/5.0));
	57	#ifdef TS_DOUBLE_DOUBLE
	58	const ts_double z0=sqrt(pow(A0,2)-pow(xl0,2));
	59	#endif
	60	#ifdef TS_DOUBLE_FLOAT
	61	const ts_double z0=sqrtf(powf(A0,2)-powf(xl0,2));
	62	#endif
	63	#ifdef TS_DOUBLE_LONGDOUBLE
	64	const ts_double z0=sqrtl(powl(A0,2)-powl(xl0,2));
	65	#endif
	66	// 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 */
	67
	68	/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!/
	69	ts_vertex **vtx=vlist->vtx -1 ;
	70
	71
	72	ts_uint nshell=(ts_uint)( sqrt((ts_double)(vlist->n-2)/5));
	73	// printf("nshell=%u\n",nshell);
	74	ts_uint i,n0; // some for loop prereq
	75	ts_int j,k;
	76	ts_double dx,dy; // end loop prereq
	77
	78	/* topmost vertex */
8f6a69	79	vtx[1]->x=0.0;
SP	80	vtx[1]->y=0.0;
	81	vtx[1]->z=z0*(ts_double)nshell;
7958e9	82
SP	83	/* starting from to in circular order on pentagrams */
	84	for(i=1;i<=nshell;i++){
	85	n0=2+5i(i-1)/2; //-1 would be for the reason that C index starts from 0
8f6a69	86	vtx[n0]->x=0.0;
SP	87	vtx[n0]->y=(ts_double)i*xl0;
	88	vtx[n0+i]->x=vtx[n0]->y*s1;
	89	vtx[n0+i]->y=vtx[n0]->y*c1;
	90	vtx[n0+2i]->x=vtx[n0]->ys2;
	91	vtx[n0+2i]->y=vtx[n0]->yc2;
	92	vtx[n0+3i]->x=-vtx[n0+2i]->x;
	93	vtx[n0+3i]->y=vtx[n0+2i]->y;
	94	vtx[n0+4*i]->x=-vtx[n0+i]->x;
	95	vtx[n0+4*i]->y=vtx[n0+i]->y;
7958e9	96	}
SP	97
	98	/* vertexes on the faces of the dipyramid */
	99	for(i=1;i<=nshell;i++){
	100	n0=2+5i(i-1)/2; // -1 would be because of C!
	101	for(j=1;j<=i-1;j++){
8f6a69	102	dx=(vtx[n0]->x-vtx[n0+4*i]->x)/(ts_double)i;
SP	103	dy=(vtx[n0]->y-vtx[n0+4*i]->y)/(ts_double)i;
	104	vtx[n0+4i+j]->x=(ts_double)jdx+vtx[n0+4*i]->x;
	105	vtx[n0+4i+j]->y=(ts_double)jdy+vtx[n0+4*i]->y;
7958e9	106	}
SP	107	for(k=0;k<=3;k++){ // I would be worried about zero starting of for
8f6a69	108	dx=(vtx[n0+(k+1)i]->x - vtx[n0+ki]->x)/(ts_double) i;
SP	109	dy=(vtx[n0+(k+1)i]->y - vtx[n0+ki]->y)/(ts_double) i;
7958e9	110	for(j=1; j<=i-1;j++){
8f6a69	111	vtx[n0+ki+j]->x= (ts_double)jdx+vtx[n0+k*i]->x;
SP	112	vtx[n0+ki+j]->y= (ts_double)jdy+vtx[n0+k*i]->y;
7958e9	113	}
SP	114	}
	115	}
	116
	117	for(i=1;i<=nshell;i++){
	118	n0= 2+ 5i(i-1)/2;
	119	for(j=0;j<=5*i-1;j++){
8f6a69	120	vtx[n0+j]->z= z0*(ts_double)(nshell-i); // I would be worried about zero starting of for
7958e9	121	}
SP	122	}
	123
	124	/* for botom part of dipyramide we calculate the positions of vertices */
	125	for(i=2+5nshell(nshell+1)/2;i<=vlist->n;i++){
8f6a69	126	vtx[i]->x=vtx[vlist->n - i +1]->x;
SP	127	vtx[i]->y=vtx[vlist->n - i +1]->y;
	128	vtx[i]->z=-vtx[vlist->n - i +1]->z;
7958e9	129	}
SP	130
	131	for(i=1;i<=vlist->n;i++){
	132	for(j=1;j<=vlist->n;j++){
	133	if(i!=j && vtx_distance_sq(vtx[i],vtx[j])<0.001){
	134	printf("Vertices %u and %u are the same!\n",i,j);
	135	}
	136	}
	137	}
	138	return TS_SUCCESS;
	139	}
	140
	141
	142
	143	ts_bool init_vertex_neighbours(ts_vertex_list *vlist){
	144	ts_vertex **vtx=vlist->vtx -1; // take a look at dipyramid function for comment.
	145	const ts_double eps=0.001; //TODO: find out if you can use EPS from math.h
	146	ts_uint i,j;
	147	ts_double dist2; // Square of distance of neighbours
	148	/this is not required if we zero all data in vertex structure at initialization /
	149	/if we force zeroing at initialization this for loop can safely be deleted /
	150	//for(i=1;i<=vlist->n;i++){
	151	// vtx[i].neigh_no=0;
	152	//}
	153	for(i=1;i<=vlist->n;i++){
	154	for(j=1;j<=vlist->n;j++){
	155	dist2=vtx_distance_sq(vtx[i],vtx[j]);
	156	if( (dist2>eps) && (dist2<(A0*A0+eps))){
	157	//if it is close enough, but not too much close (solves problem of comparing when i==j)
	158	vtx_add_neighbour(vtx[i],vtx[j]);
	159	}
	160	}
	161	// printf ("vertex %u ima %u sosedov!\n",i,vtx[i]->data->neigh_no);
	162	}
	163
	164	return TS_SUCCESS;
	165	}
	166
b01cc1	167	// TODO: with new datastructure can be rewritten. Partially it is done, but it is complicated.
SP	168	ts_vertex_list init_sort_neighbours(ts_bond_list blist,ts_vertex_list *vlist){
7958e9	169	ts_vertex **vtx=vlist->vtx -1; // take a look at dipyramid function for comment.
SP	170	ts_uint i,l,j,jj,jjj,k=0;
	171	ts_double eps=0.001; // Take a look if EPS from math.h can be used
	172
	173	/lets initialize memory for temporary vertex_list. Should we write a function instead /
b01cc1	174	ts_vertex_list *tvlist=vertex_list_copy(vlist);
7958e9	175	ts_vertex *tvtx=tvlist->vtx -1; / again to compensate for 0-indexing */
SP	176
	177	ts_double dist2; // Square of distance of neighbours
	178	ts_double direct; // Something, dont know what, but could be normal of some kind
	179	for(i=1;i<=vlist->n;i++){
	180	k++; // WHY i IS NOT GOOD??
8f6a69	181	vtx_add_cneighbour(blist,tvtx[k], tvtx[vtx[i]->neigh[0]->idx+1]); //always add 1st
7958e9	182	jjj=1;
SP	183	jj=1;
8f6a69	184	for(l=2;l<=vtx[i]->neigh_no;l++){
SP	185	for(j=2;j<=vtx[i]->neigh_no;j++){
	186	dist2=vtx_distance_sq(vtx[i]->neigh[j-1],vtx[i]->neigh[jj-1]);
	187	direct=vtx_direct(vtx[i],vtx[i]->neigh[j-1],vtx[i]->neigh[jj-1]);
	188	// TODO: check if fabs can be used with all floating point types!!
7958e9	189	if( (fabs(dist2-A0*A0)<=eps) && (direct>0.0) && (j!=jjj) ){
8f6a69	190	vtx_add_cneighbour(blist,tvtx[k],tvtx[vtx[i]->neigh[j-1]->idx+1]);
7958e9	191	jjj=jj;
SP	192	jj=j;
	193	break;
	194	}
	195	}
	196	}
	197	}
b01cc1	198	/* We use the temporary vertex for our main vertices and we abandon main
SP	199	* vertices, because their neighbours are not correctly ordered */
	200	// tvtx=vlist->vtx;
	201	// vlist->vtx=tvtx;
	202	// tvlist->vtx=vtx;
	203	vtx_list_free(vlist);
	204	/* Let's make a check if the number of bonds is correct */
	205	if((blist->n)!=3*(tvlist->n-2)){
	206	ts_fprintf(stderr,"Number of bonds is %u should be %u!\n", blist->n, 3*(tvlist->n-2));
	207	fatal("Number of bonds is not 3*(no_vertex-2).",4);
7958e9	208	}
SP	209
b01cc1	210	return tvlist;
7958e9	211	}
SP	212
	213
	214	ts_bool init_vesicle_bonds(ts_vesicle *vesicle){
	215	ts_vertex_list *vlist=vesicle->vlist;
	216	ts_bond_list *blist=vesicle->blist;
	217	ts_vertex **vtx=vesicle->vlist->vtx - 1; // Because of 0 indexing
	218	/* lets make correct clockwise ordering of in nearest neighbour list */
	219	ts_uint i,j,k;
	220	for(i=1;i<=vlist->n;i++){
	221	for(j=i+1;j<=vlist->n;j++){
8f6a69	222	for(k=0;k<vtx[i]->neigh_no;k++){ // has changed 0 to < instead of 1 and <=
SP	223	if(vtx[i]->neigh[k]==vtx[j]){ //if addresses matches it is the same
7958e9	224	bond_add(blist,vtx[i],vtx[j]);
SP	225	break;
	226	}
	227	}
	228	}
	229	}
	230	/* Let's make a check if the number of bonds is correct */
	231	if((blist->n)!=3*(vlist->n-2)){
	232	ts_fprintf(stderr,"Number of bonds is %u should be %u!\n", blist->n, 3*(vlist->n-2));
	233	fatal("Number of bonds is not 3*(no_vertex-2).",4);
	234	}
	235	return TS_SUCCESS;
	236	}
	237
	238
	239
	240	ts_bool init_triangles(ts_vesicle *vesicle){
	241	ts_uint i,j,jj,k;
	242	ts_vertex **vtx=vesicle->vlist->vtx -1; // difference between 0 indexing and 1 indexing
	243	ts_triangle_list *tlist=vesicle->tlist;
	244	ts_double dist, direct;
	245	ts_double eps=0.001; // can we use EPS from math.h?
	246	k=0;
	247	for(i=1;i<=vesicle->vlist->n;i++){
8f6a69	248	for(j=1;j<=vtx[i]->neigh_no;j++){
SP	249	for(jj=1;jj<=vtx[i]->neigh_no;jj++){
7958e9	250	// ts_fprintf(stderr,"%u: (%u,%u) neigh_no=%u ",i,j,jj,vtx[i].neigh_no);
SP	251	// ts_fprintf(stderr,"%e, %e",vtx[i].neigh[j-1]->x,vtx[i].neigh[jj-1]->x);
8f6a69	252	dist=vtx_distance_sq(vtx[i]->neigh[j-1],vtx[i]->neigh[jj-1]);
SP	253	direct=vtx_direct(vtx[i],vtx[i]->neigh[j-1],vtx[i]->neigh[jj-1]);
	254	// TODO: same as above
	255	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){
	256	triangle_add(tlist,vtx[i],vtx[i]->neigh[j-1],vtx[i]->neigh[jj-1]);
7958e9	257	}
SP	258	}
	259	}
	260	}
	261	/* We check if all triangles have 3 vertices and if the number of triangles
	262	* matches the theoretical value.
	263	*/
	264	for(i=0;i<tlist->n;i++){
	265	k=0;
	266	for(j=0;j<3;j++){
41a035	267	if(tlist->tria[i]->vertex[j]!=NULL)
7958e9	268	k++;
SP	269	}
	270	if(k!=3){
8f6a69	271	fatal("Some triangles have less than 3 vertices..",4);
7958e9	272	}
SP	273	}
	274	if(tlist->n!=2*(vesicle->vlist->n -2)){
	275	ts_fprintf(stderr,"The number of triangles is %u but should be %u!\n",tlist->n,2*(vesicle->vlist->n -2));
	276	fatal("The number of triangles doesn't match 2*(no_vertex -2).",4);
	277	}
	278	return TS_SUCCESS;
	279	}
	280
	281
	282
	283	ts_bool init_triangle_neighbours(ts_vesicle *vesicle){
	284	ts_uint i,j,nobo;
	285	ts_vertex i1,i2,i3,j1,j2,j3;
	286	// ts_vertex **vtx=vesicle->vlist->vtx -1; // difference between 0 indexing and 1 indexing
	287	ts_triangle_list *tlist=vesicle->tlist;
	288	ts_triangle **tria=tlist->tria -1;
	289	nobo=0;
	290	for(i=1;i<=tlist->n;i++){
41a035	291	i1=tria[i]->vertex[0];
SP	292	i2=tria[i]->vertex[1];
	293	i3=tria[i]->vertex[2];
7958e9	294	for(j=1;j<=tlist->n;j++){
SP	295	if(j==i) continue;
41a035	296	j1=tria[j]->vertex[0];
SP	297	j2=tria[j]->vertex[1];
	298	j3=tria[j]->vertex[2];
7958e9	299	if((i1==j1 && i3==j2) \|\| (i1==j2 && i3==j3) \|\| (i1==j3 && i3==j1)){
SP	300	triangle_add_neighbour(tria[i],tria[j]);
	301	nobo++;
	302	}
	303	}
	304	}
	305	for(i=1;i<=tlist->n;i++){
41a035	306	i1=tria[i]->vertex[0];
SP	307	i2=tria[i]->vertex[1];
	308	i3=tria[i]->vertex[2];
7958e9	309	for(j=1;j<=tlist->n;j++){
SP	310	if(j==i) continue;
41a035	311	j1=tria[j]->vertex[0];
SP	312	j2=tria[j]->vertex[1];
	313	j3=tria[j]->vertex[2];
7958e9	314	if((i1==j1 && i2==j3) \|\| (i1==j3 && i2==j2) \|\| (i1==j2 && i2==j1)){
SP	315	triangle_add_neighbour(tria[i],tria[j]);
	316	nobo++;
	317	}
	318	}
	319	}
	320	for(i=1;i<=tlist->n;i++){
41a035	321	i1=tria[i]->vertex[0];
SP	322	i2=tria[i]->vertex[1];
	323	i3=tria[i]->vertex[2];
7958e9	324	for(j=1;j<=tlist->n;j++){
SP	325	if(j==i) continue;
41a035	326	j1=tria[j]->vertex[0];
SP	327	j2=tria[j]->vertex[1];
	328	j3=tria[j]->vertex[2];
7958e9	329	if((i2==j1 && i3==j3) \|\| (i2==j3 && i3==j2) \|\| (i2==j2 && i3==j1)){
SP	330	triangle_add_neighbour(tria[i],tria[j]);
	331	nobo++;
	332	}
	333	}
	334	}
	335	if(nobo != vesicle->blist->n*2) {
	336	ts_fprintf(stderr,"Number of triangles= %u, number of bonds= %u\n",nobo/2, vesicle->blist->n);
	337	fatal("Number of triangle neighbour pairs differs from double the number of bonds!",4);
	338	}
	339	return TS_SUCCESS;
	340	}
	341
	342
	343	ts_bool init_common_vertex_triangle_neighbours(ts_vesicle *vesicle){
	344	ts_uint i,j,jp,k;
	345	ts_vertex k1,k2,k3,k4,*k5;
	346	ts_vertex **vtx=vesicle->vlist->vtx -1; // difference between 0 indexing and 1 indexing
	347	ts_triangle_list *tlist=vesicle->tlist;
	348	ts_triangle **tria=tlist->tria -1;
	349
	350	for(i=1;i<=vesicle->vlist->n;i++){
8f6a69	351	for(j=1;j<=vtx[i]->neigh_no;j++){
SP	352	k1=vtx[i]->neigh[j-1];
7958e9	353	jp=j+1;
8f6a69	354	if(j == vtx[i]->neigh_no) jp=1;
SP	355	k2=vtx[i]->neigh[jp-1];
7958e9	356	for(k=1;k<=tlist->n;k++){ // VERY NON-OPTIMAL!!! too many loops (vlist.n * vtx.neigh * tlist.n )!
41a035	357	k3=tria[k]->vertex[0];
SP	358	k4=tria[k]->vertex[1];
	359	k5=tria[k]->vertex[2];
7958e9	360	// ts_fprintf(stderr,"%u %u: k=(%u %u %u)\n",k1,k2,k3,k4,k5);
SP	361	if((vtx[i]==k3 && k1==k4 && k2==k5) \|\|
	362	(vtx[i]==k4 && k1==k5 && k2==k3) \|\|
	363	(vtx[i]==k5 && k1==k3 && k2==k4)){
b01cc1	364
SP	365	//TODO: probably something wrong with neighbour distribution.
	366	// if(vtx[i]==k3 \|\| vtx[i]==k4 \|\| vtx[i]==k5){
dac2e5	367	// if(i==6) ts_fprintf(stdout, "Vtx[%u] > Added to tristar!\n",i);
7958e9	368	vertex_add_tristar(vtx[i],tria[k]);
SP	369	}
	370	}
	371	}
	372	/* ts_fprintf(stderr,"TRISTAR for %u (%u):",i-1,vtx[i].tristar_no);
	373	for(j=0;j<vtx[i].tristar_no;j++){
	374	ts_fprintf(stderr," %u,",vtx[i].tristar[j]->idx);
	375	}
	376	ts_fprintf(stderr,"\n"); */
	377	}
	378	return TS_SUCCESS;
	379	}
	380
	381
	382	ts_bool init_normal_vectors(ts_triangle_list *tlist){
	383	/* Normals point INSIDE vesicle */
	384	ts_uint k;
	385	ts_triangle **tria=tlist->tria -1; //for 0 indexing
	386	for(k=1;k<=tlist->n;k++){
	387	triangle_normal_vector(tria[k]);
	388	}
	389	return TS_SUCCESS;
	390	}