trisurf-ng.git - Gitblit

Added filaments inside the vesicle. TODO: tape etc.

mihaf

2014-03-14 624f819d40ca2204b0a128970dcd3d9ca7e17699

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"
1ab449	12	#include "poly.h"
8a6614	13	#include "io.h"
7958e9	14
SP	15	ts_vesicle *initial_distribution_dipyramid(ts_uint nshell, ts_uint ncmax1, ts_uint ncmax2, ts_uint ncmax3, ts_double stepsize){
1ab449	16	ts_fprintf(stdout,"Starting initial_distribution on vesicle with %u shells!...\n",nshell);
7958e9	17	ts_bool retval;
1ab449	18	ts_uint no_vertices=5nshellnshell+2;
SP	19	ts_vesicle *vesicle=init_vesicle(no_vertices,ncmax1,ncmax2,ncmax3,stepsize);
	20	vesicle->nshell=nshell;
	21	//retval = vtx_set_global_values(vesicle);
	22	retval = pentagonal_dipyramid_vertex_distribution(vesicle->vlist);
	23	retval = init_vertex_neighbours(vesicle->vlist);
	24	vesicle->vlist = init_sort_neighbours(vesicle->blist,vesicle->vlist);
b01cc1	25	// retval = init_vesicle_bonds(vesicle); // bonds are created in sort_neigh
1ab449	26	retval = init_triangles(vesicle);
SP	27	retval = init_triangle_neighbours(vesicle);
	28	retval = init_common_vertex_triangle_neighbours(vesicle);
	29	retval = init_normal_vectors(vesicle->tlist);
	30	retval = mean_curvature_and_energy(vesicle);
	31	ts_fprintf(stdout,"initial_distribution finished!\n");
41a035	32	if(retval);
7958e9	33	return vesicle;
SP	34	}
	35
	36
1ab449	37
SP	38	ts_vesicle create_vesicle_from_tape(ts_tape tape){
	39	ts_vesicle *vesicle;
	40	vesicle=initial_distribution_dipyramid(tape->nshell,tape->ncxmax,tape->ncymax,tape->nczmax,tape->stepsize);
624f81	41	vesicle->poly_list=init_poly_list(tape->npoly,tape->nmono, vesicle->vlist, vesicle);
1ab449	42	vesicle->spring_constant=tape->kspring;
SP	43	poly_assign_spring_const(vesicle);
	44
	45	vesicle->nshell=tape->nshell;
	46	vesicle->dmax=tape->dmaxtape->dmax; / dmax^2 in the vesicle dmax variable */
	47	vesicle->bending_rigidity=tape->xk0;
	48	vtx_set_global_values(vesicle); /* make xk0 default value for every vertex */
	49	ts_fprintf(stdout, "Tape setting: xk0=%e\n",tape->xk0);
	50	vesicle->stepsize=tape->stepsize;
	51	vesicle->clist->ncmax[0]=tape->ncxmax;
	52	vesicle->clist->ncmax[1]=tape->ncymax;
	53	vesicle->clist->ncmax[2]=tape->nczmax;
	54	vesicle->clist->max_occupancy=8; /* hard coded max occupancy? */
	55
	56	vesicle->pressure= tape->pressure;
	57	vesicle->pswitch=tape->pswitch;
	58
	59	return vesicle;
	60
	61	}
	62
	63
	64
	65
	66
7958e9	67	ts_bool pentagonal_dipyramid_vertex_distribution(ts_vertex_list *vlist){
SP	68	/* Some often used relations */
	69	const ts_double s1= sin(2.0*M_PI/5.0);
	70	const ts_double s2= sin(4.0*M_PI/5.0);
	71	const ts_double c1= cos(2.0*M_PI/5.0);
	72	const ts_double c2= cos(4.0*M_PI/5.0);
	73
	74	/* Calculates projection lenght of an edge bond to pentagram plane */
	75	const ts_double xl0=A0/(2.0*sin(M_PI/5.0));
	76	#ifdef TS_DOUBLE_DOUBLE
	77	const ts_double z0=sqrt(pow(A0,2)-pow(xl0,2));
	78	#endif
	79	#ifdef TS_DOUBLE_FLOAT
	80	const ts_double z0=sqrtf(powf(A0,2)-powf(xl0,2));
	81	#endif
	82	#ifdef TS_DOUBLE_LONGDOUBLE
	83	const ts_double z0=sqrtl(powl(A0,2)-powl(xl0,2));
	84	#endif
	85	// 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 */
	86
	87	/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!/
	88	ts_vertex **vtx=vlist->vtx -1 ;
	89
	90
	91	ts_uint nshell=(ts_uint)( sqrt((ts_double)(vlist->n-2)/5));
	92	// printf("nshell=%u\n",nshell);
	93	ts_uint i,n0; // some for loop prereq
	94	ts_int j,k;
	95	ts_double dx,dy; // end loop prereq
	96
	97	/* topmost vertex */
8f6a69	98	vtx[1]->x=0.0;
SP	99	vtx[1]->y=0.0;
	100	vtx[1]->z=z0*(ts_double)nshell;
7958e9	101
SP	102	/* starting from to in circular order on pentagrams */
	103	for(i=1;i<=nshell;i++){
	104	n0=2+5i(i-1)/2; //-1 would be for the reason that C index starts from 0
8f6a69	105	vtx[n0]->x=0.0;
SP	106	vtx[n0]->y=(ts_double)i*xl0;
	107	vtx[n0+i]->x=vtx[n0]->y*s1;
	108	vtx[n0+i]->y=vtx[n0]->y*c1;
	109	vtx[n0+2i]->x=vtx[n0]->ys2;
	110	vtx[n0+2i]->y=vtx[n0]->yc2;
	111	vtx[n0+3i]->x=-vtx[n0+2i]->x;
	112	vtx[n0+3i]->y=vtx[n0+2i]->y;
	113	vtx[n0+4*i]->x=-vtx[n0+i]->x;
	114	vtx[n0+4*i]->y=vtx[n0+i]->y;
7958e9	115	}
SP	116
	117	/* vertexes on the faces of the dipyramid */
	118	for(i=1;i<=nshell;i++){
	119	n0=2+5i(i-1)/2; // -1 would be because of C!
	120	for(j=1;j<=i-1;j++){
8f6a69	121	dx=(vtx[n0]->x-vtx[n0+4*i]->x)/(ts_double)i;
SP	122	dy=(vtx[n0]->y-vtx[n0+4*i]->y)/(ts_double)i;
	123	vtx[n0+4i+j]->x=(ts_double)jdx+vtx[n0+4*i]->x;
	124	vtx[n0+4i+j]->y=(ts_double)jdy+vtx[n0+4*i]->y;
7958e9	125	}
SP	126	for(k=0;k<=3;k++){ // I would be worried about zero starting of for
8f6a69	127	dx=(vtx[n0+(k+1)i]->x - vtx[n0+ki]->x)/(ts_double) i;
SP	128	dy=(vtx[n0+(k+1)i]->y - vtx[n0+ki]->y)/(ts_double) i;
7958e9	129	for(j=1; j<=i-1;j++){
8f6a69	130	vtx[n0+ki+j]->x= (ts_double)jdx+vtx[n0+k*i]->x;
SP	131	vtx[n0+ki+j]->y= (ts_double)jdy+vtx[n0+k*i]->y;
7958e9	132	}
SP	133	}
	134	}
	135
	136	for(i=1;i<=nshell;i++){
	137	n0= 2+ 5i(i-1)/2;
	138	for(j=0;j<=5*i-1;j++){
8f6a69	139	vtx[n0+j]->z= z0*(ts_double)(nshell-i); // I would be worried about zero starting of for
7958e9	140	}
SP	141	}
	142
	143	/* for botom part of dipyramide we calculate the positions of vertices */
	144	for(i=2+5nshell(nshell+1)/2;i<=vlist->n;i++){
8f6a69	145	vtx[i]->x=vtx[vlist->n - i +1]->x;
SP	146	vtx[i]->y=vtx[vlist->n - i +1]->y;
	147	vtx[i]->z=-vtx[vlist->n - i +1]->z;
7958e9	148	}
SP	149
	150	for(i=1;i<=vlist->n;i++){
	151	for(j=1;j<=vlist->n;j++){
	152	if(i!=j && vtx_distance_sq(vtx[i],vtx[j])<0.001){
	153	printf("Vertices %u and %u are the same!\n",i,j);
	154	}
	155	}
	156	}
	157	return TS_SUCCESS;
	158	}
	159
	160
	161
	162	ts_bool init_vertex_neighbours(ts_vertex_list *vlist){
	163	ts_vertex **vtx=vlist->vtx -1; // take a look at dipyramid function for comment.
	164	const ts_double eps=0.001; //TODO: find out if you can use EPS from math.h
	165	ts_uint i,j;
	166	ts_double dist2; // Square of distance of neighbours
	167	/this is not required if we zero all data in vertex structure at initialization /
	168	/if we force zeroing at initialization this for loop can safely be deleted /
	169	//for(i=1;i<=vlist->n;i++){
	170	// vtx[i].neigh_no=0;
	171	//}
	172	for(i=1;i<=vlist->n;i++){
	173	for(j=1;j<=vlist->n;j++){
	174	dist2=vtx_distance_sq(vtx[i],vtx[j]);
	175	if( (dist2>eps) && (dist2<(A0*A0+eps))){
	176	//if it is close enough, but not too much close (solves problem of comparing when i==j)
	177	vtx_add_neighbour(vtx[i],vtx[j]);
	178	}
	179	}
	180	// printf ("vertex %u ima %u sosedov!\n",i,vtx[i]->data->neigh_no);
	181	}
	182
	183	return TS_SUCCESS;
	184	}
	185
b01cc1	186	// TODO: with new datastructure can be rewritten. Partially it is done, but it is complicated.
SP	187	ts_vertex_list init_sort_neighbours(ts_bond_list blist,ts_vertex_list *vlist){
7958e9	188	ts_vertex **vtx=vlist->vtx -1; // take a look at dipyramid function for comment.
SP	189	ts_uint i,l,j,jj,jjj,k=0;
	190	ts_double eps=0.001; // Take a look if EPS from math.h can be used
	191
	192	/lets initialize memory for temporary vertex_list. Should we write a function instead /
b01cc1	193	ts_vertex_list *tvlist=vertex_list_copy(vlist);
7958e9	194	ts_vertex *tvtx=tvlist->vtx -1; / again to compensate for 0-indexing */
SP	195
	196	ts_double dist2; // Square of distance of neighbours
	197	ts_double direct; // Something, dont know what, but could be normal of some kind
	198	for(i=1;i<=vlist->n;i++){
	199	k++; // WHY i IS NOT GOOD??
8f6a69	200	vtx_add_cneighbour(blist,tvtx[k], tvtx[vtx[i]->neigh[0]->idx+1]); //always add 1st
7958e9	201	jjj=1;
SP	202	jj=1;
8f6a69	203	for(l=2;l<=vtx[i]->neigh_no;l++){
SP	204	for(j=2;j<=vtx[i]->neigh_no;j++){
	205	dist2=vtx_distance_sq(vtx[i]->neigh[j-1],vtx[i]->neigh[jj-1]);
	206	direct=vtx_direct(vtx[i],vtx[i]->neigh[j-1],vtx[i]->neigh[jj-1]);
	207	// TODO: check if fabs can be used with all floating point types!!
7958e9	208	if( (fabs(dist2-A0*A0)<=eps) && (direct>0.0) && (j!=jjj) ){
8f6a69	209	vtx_add_cneighbour(blist,tvtx[k],tvtx[vtx[i]->neigh[j-1]->idx+1]);
7958e9	210	jjj=jj;
SP	211	jj=j;
	212	break;
	213	}
	214	}
	215	}
	216	}
b01cc1	217	/* We use the temporary vertex for our main vertices and we abandon main
SP	218	* vertices, because their neighbours are not correctly ordered */
	219	// tvtx=vlist->vtx;
	220	// vlist->vtx=tvtx;
	221	// tvlist->vtx=vtx;
	222	vtx_list_free(vlist);
	223	/* Let's make a check if the number of bonds is correct */
	224	if((blist->n)!=3*(tvlist->n-2)){
	225	ts_fprintf(stderr,"Number of bonds is %u should be %u!\n", blist->n, 3*(tvlist->n-2));
	226	fatal("Number of bonds is not 3*(no_vertex-2).",4);
7958e9	227	}
SP	228
b01cc1	229	return tvlist;
7958e9	230	}
SP	231
	232
	233	ts_bool init_vesicle_bonds(ts_vesicle *vesicle){
	234	ts_vertex_list *vlist=vesicle->vlist;
	235	ts_bond_list *blist=vesicle->blist;
	236	ts_vertex **vtx=vesicle->vlist->vtx - 1; // Because of 0 indexing
	237	/* lets make correct clockwise ordering of in nearest neighbour list */
	238	ts_uint i,j,k;
	239	for(i=1;i<=vlist->n;i++){
	240	for(j=i+1;j<=vlist->n;j++){
8f6a69	241	for(k=0;k<vtx[i]->neigh_no;k++){ // has changed 0 to < instead of 1 and <=
SP	242	if(vtx[i]->neigh[k]==vtx[j]){ //if addresses matches it is the same
7958e9	243	bond_add(blist,vtx[i],vtx[j]);
SP	244	break;
	245	}
	246	}
	247	}
	248	}
	249	/* Let's make a check if the number of bonds is correct */
	250	if((blist->n)!=3*(vlist->n-2)){
	251	ts_fprintf(stderr,"Number of bonds is %u should be %u!\n", blist->n, 3*(vlist->n-2));
	252	fatal("Number of bonds is not 3*(no_vertex-2).",4);
	253	}
	254	return TS_SUCCESS;
	255	}
	256
	257
	258
	259	ts_bool init_triangles(ts_vesicle *vesicle){
	260	ts_uint i,j,jj,k;
	261	ts_vertex **vtx=vesicle->vlist->vtx -1; // difference between 0 indexing and 1 indexing
	262	ts_triangle_list *tlist=vesicle->tlist;
	263	ts_double dist, direct;
	264	ts_double eps=0.001; // can we use EPS from math.h?
	265	k=0;
	266	for(i=1;i<=vesicle->vlist->n;i++){
8f6a69	267	for(j=1;j<=vtx[i]->neigh_no;j++){
SP	268	for(jj=1;jj<=vtx[i]->neigh_no;jj++){
7958e9	269	// ts_fprintf(stderr,"%u: (%u,%u) neigh_no=%u ",i,j,jj,vtx[i].neigh_no);
SP	270	// ts_fprintf(stderr,"%e, %e",vtx[i].neigh[j-1]->x,vtx[i].neigh[jj-1]->x);
8f6a69	271	dist=vtx_distance_sq(vtx[i]->neigh[j-1],vtx[i]->neigh[jj-1]);
SP	272	direct=vtx_direct(vtx[i],vtx[i]->neigh[j-1],vtx[i]->neigh[jj-1]);
	273	// TODO: same as above
	274	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){
	275	triangle_add(tlist,vtx[i],vtx[i]->neigh[j-1],vtx[i]->neigh[jj-1]);
7958e9	276	}
SP	277	}
	278	}
	279	}
	280	/* We check if all triangles have 3 vertices and if the number of triangles
	281	* matches the theoretical value.
	282	*/
	283	for(i=0;i<tlist->n;i++){
	284	k=0;
	285	for(j=0;j<3;j++){
41a035	286	if(tlist->tria[i]->vertex[j]!=NULL)
7958e9	287	k++;
SP	288	}
	289	if(k!=3){
8f6a69	290	fatal("Some triangles have less than 3 vertices..",4);
7958e9	291	}
SP	292	}
	293	if(tlist->n!=2*(vesicle->vlist->n -2)){
	294	ts_fprintf(stderr,"The number of triangles is %u but should be %u!\n",tlist->n,2*(vesicle->vlist->n -2));
	295	fatal("The number of triangles doesn't match 2*(no_vertex -2).",4);
	296	}
	297	return TS_SUCCESS;
	298	}
	299
	300
	301
	302	ts_bool init_triangle_neighbours(ts_vesicle *vesicle){
	303	ts_uint i,j,nobo;
	304	ts_vertex i1,i2,i3,j1,j2,j3;
	305	// ts_vertex **vtx=vesicle->vlist->vtx -1; // difference between 0 indexing and 1 indexing
	306	ts_triangle_list *tlist=vesicle->tlist;
	307	ts_triangle **tria=tlist->tria -1;
	308	nobo=0;
	309	for(i=1;i<=tlist->n;i++){
41a035	310	i1=tria[i]->vertex[0];
SP	311	i2=tria[i]->vertex[1];
	312	i3=tria[i]->vertex[2];
7958e9	313	for(j=1;j<=tlist->n;j++){
SP	314	if(j==i) continue;
41a035	315	j1=tria[j]->vertex[0];
SP	316	j2=tria[j]->vertex[1];
	317	j3=tria[j]->vertex[2];
7958e9	318	if((i1==j1 && i3==j2) \|\| (i1==j2 && i3==j3) \|\| (i1==j3 && i3==j1)){
SP	319	triangle_add_neighbour(tria[i],tria[j]);
	320	nobo++;
	321	}
	322	}
	323	}
	324	for(i=1;i<=tlist->n;i++){
41a035	325	i1=tria[i]->vertex[0];
SP	326	i2=tria[i]->vertex[1];
	327	i3=tria[i]->vertex[2];
7958e9	328	for(j=1;j<=tlist->n;j++){
SP	329	if(j==i) continue;
41a035	330	j1=tria[j]->vertex[0];
SP	331	j2=tria[j]->vertex[1];
	332	j3=tria[j]->vertex[2];
7958e9	333	if((i1==j1 && i2==j3) \|\| (i1==j3 && i2==j2) \|\| (i1==j2 && i2==j1)){
SP	334	triangle_add_neighbour(tria[i],tria[j]);
	335	nobo++;
	336	}
	337	}
	338	}
	339	for(i=1;i<=tlist->n;i++){
41a035	340	i1=tria[i]->vertex[0];
SP	341	i2=tria[i]->vertex[1];
	342	i3=tria[i]->vertex[2];
7958e9	343	for(j=1;j<=tlist->n;j++){
SP	344	if(j==i) continue;
41a035	345	j1=tria[j]->vertex[0];
SP	346	j2=tria[j]->vertex[1];
	347	j3=tria[j]->vertex[2];
7958e9	348	if((i2==j1 && i3==j3) \|\| (i2==j3 && i3==j2) \|\| (i2==j2 && i3==j1)){
SP	349	triangle_add_neighbour(tria[i],tria[j]);
	350	nobo++;
	351	}
	352	}
	353	}
	354	if(nobo != vesicle->blist->n*2) {
	355	ts_fprintf(stderr,"Number of triangles= %u, number of bonds= %u\n",nobo/2, vesicle->blist->n);
	356	fatal("Number of triangle neighbour pairs differs from double the number of bonds!",4);
	357	}
	358	return TS_SUCCESS;
	359	}
	360
	361
	362	ts_bool init_common_vertex_triangle_neighbours(ts_vesicle *vesicle){
	363	ts_uint i,j,jp,k;
	364	ts_vertex k1,k2,k3,k4,*k5;
	365	ts_vertex **vtx=vesicle->vlist->vtx -1; // difference between 0 indexing and 1 indexing
	366	ts_triangle_list *tlist=vesicle->tlist;
	367	ts_triangle **tria=tlist->tria -1;
	368
	369	for(i=1;i<=vesicle->vlist->n;i++){
8f6a69	370	for(j=1;j<=vtx[i]->neigh_no;j++){
SP	371	k1=vtx[i]->neigh[j-1];
7958e9	372	jp=j+1;
8f6a69	373	if(j == vtx[i]->neigh_no) jp=1;
SP	374	k2=vtx[i]->neigh[jp-1];
7958e9	375	for(k=1;k<=tlist->n;k++){ // VERY NON-OPTIMAL!!! too many loops (vlist.n * vtx.neigh * tlist.n )!
41a035	376	k3=tria[k]->vertex[0];
SP	377	k4=tria[k]->vertex[1];
	378	k5=tria[k]->vertex[2];
7958e9	379	// ts_fprintf(stderr,"%u %u: k=(%u %u %u)\n",k1,k2,k3,k4,k5);
SP	380	if((vtx[i]==k3 && k1==k4 && k2==k5) \|\|
	381	(vtx[i]==k4 && k1==k5 && k2==k3) \|\|
	382	(vtx[i]==k5 && k1==k3 && k2==k4)){
b01cc1	383
SP	384	//TODO: probably something wrong with neighbour distribution.
	385	// if(vtx[i]==k3 \|\| vtx[i]==k4 \|\| vtx[i]==k5){
dac2e5	386	// if(i==6) ts_fprintf(stdout, "Vtx[%u] > Added to tristar!\n",i);
7958e9	387	vertex_add_tristar(vtx[i],tria[k]);
SP	388	}
	389	}
	390	}
	391	/* ts_fprintf(stderr,"TRISTAR for %u (%u):",i-1,vtx[i].tristar_no);
	392	for(j=0;j<vtx[i].tristar_no;j++){
	393	ts_fprintf(stderr," %u,",vtx[i].tristar[j]->idx);
	394	}
	395	ts_fprintf(stderr,"\n"); */
	396	}
	397	return TS_SUCCESS;
	398	}
	399
	400
	401	ts_bool init_normal_vectors(ts_triangle_list *tlist){
	402	/* Normals point INSIDE vesicle */
	403	ts_uint k;
	404	ts_triangle **tria=tlist->tria -1; //for 0 indexing
	405	for(k=1;k<=tlist->n;k++){
	406	triangle_normal_vector(tria[k]);
	407	}
	408	return TS_SUCCESS;
	409	}