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mihaf

2014-03-24 ea1cce4c80ddb68c0b46a6873ef3b64cc4a958a1

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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;
bcf455	40	ts_vertex *vtx;
M	41
1ab449	42	vesicle=initial_distribution_dipyramid(tape->nshell,tape->ncxmax,tape->ncymax,tape->nczmax,tape->stepsize);
58230a	43	// Nucleus:
M	44	vesicle->R_nucleus=tape->R_nucleus;
bcf455	45
58230a	46	//Initialize grafted polymers (brush):
624f81	47	vesicle->poly_list=init_poly_list(tape->npoly,tape->nmono, vesicle->vlist, vesicle);
1ab449	48	vesicle->spring_constant=tape->kspring;
SP	49	poly_assign_spring_const(vesicle);
bcf455	50
58230a	51	//Initialize filaments (polymers inside the vesicle):
M	52	vesicle->filament_list=init_poly_list(tape->nfil,tape->nfono, NULL, vesicle);
bcf455	53	poly_assign_filament_xi(vesicle,tape);
58230a	54
bcf455	55	ts_uint i,j;
M	56	for(i=0;i<vesicle->filament_list->n;i++){
	57	for(j=0;j<vesicle->filament_list->poly[i]->blist->n;j++){
	58	bond_vector(vesicle->filament_list->poly[i]->blist->bond[j]);
	59	vesicle->filament_list->poly[i]->blist->bond[j]->bond_length = sqrt(vtx_distance_sq(vesicle->filament_list->poly[i]->blist->bond[j]->vtx1,vesicle->filament_list->poly[i]->blist->bond[j]->vtx2));
	60	}
58230a	61	}
bcf455	62
M	63	for(i=0;i<vesicle->filament_list->n;i++){
	64	for(j=0;j<vesicle->filament_list->poly[i]->vlist->n;j++){
	65	vtx = vesicle->filament_list->poly[i]->vlist->vtx[j];
	66	if(vtx->bond_no == 2){
	67	vtx->energy = -(vtx->bond[0]->xvtx->bond[1]->x + vtx->bond[0]->yvtx->bond[1]->y + vtx->bond[0]->z*vtx->bond[1]->z)/vtx->bond[0]->bond_length/vtx->bond[1]->bond_length;
	68	}
	69	}
58230a	70	}
bcf455	71
ea1cce	72	for(i=0;i<vesicle->filament_list->n;i++){
M	73	vertex_list_assign_id(vesicle->filament_list->poly[i]->vlist,TS_ID_FILAMENT);
	74	}
bcf455	75
58230a	76	// vesicle->spring_constant=tape->kspring;
M	77	// poly_assign_spring_const(vesicle);
	78
1ab449	79
SP	80	vesicle->nshell=tape->nshell;
	81	vesicle->dmax=tape->dmaxtape->dmax; / dmax^2 in the vesicle dmax variable */
ea1cce	82	vesicle->clist->dmin_interspecies = tape->dmin_interspecies*tape->dmin_interspecies;
1ab449	83	vesicle->bending_rigidity=tape->xk0;
SP	84	vtx_set_global_values(vesicle); /* make xk0 default value for every vertex */
	85	ts_fprintf(stdout, "Tape setting: xk0=%e\n",tape->xk0);
	86	vesicle->stepsize=tape->stepsize;
	87	vesicle->clist->ncmax[0]=tape->ncxmax;
	88	vesicle->clist->ncmax[1]=tape->ncymax;
	89	vesicle->clist->ncmax[2]=tape->nczmax;
	90	vesicle->clist->max_occupancy=8; /* hard coded max occupancy? */
	91
	92	vesicle->pressure= tape->pressure;
	93	vesicle->pswitch=tape->pswitch;
	94
	95	return vesicle;
	96
	97	}
	98
	99
	100
	101
	102
7958e9	103	ts_bool pentagonal_dipyramid_vertex_distribution(ts_vertex_list *vlist){
SP	104	/* Some often used relations */
	105	const ts_double s1= sin(2.0*M_PI/5.0);
	106	const ts_double s2= sin(4.0*M_PI/5.0);
	107	const ts_double c1= cos(2.0*M_PI/5.0);
	108	const ts_double c2= cos(4.0*M_PI/5.0);
	109
	110	/* Calculates projection lenght of an edge bond to pentagram plane */
	111	const ts_double xl0=A0/(2.0*sin(M_PI/5.0));
	112	#ifdef TS_DOUBLE_DOUBLE
	113	const ts_double z0=sqrt(pow(A0,2)-pow(xl0,2));
	114	#endif
	115	#ifdef TS_DOUBLE_FLOAT
	116	const ts_double z0=sqrtf(powf(A0,2)-powf(xl0,2));
	117	#endif
	118	#ifdef TS_DOUBLE_LONGDOUBLE
	119	const ts_double z0=sqrtl(powl(A0,2)-powl(xl0,2));
	120	#endif
	121	// 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 */
	122
	123	/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!/
	124	ts_vertex **vtx=vlist->vtx -1 ;
	125
	126
	127	ts_uint nshell=(ts_uint)( sqrt((ts_double)(vlist->n-2)/5));
	128	// printf("nshell=%u\n",nshell);
	129	ts_uint i,n0; // some for loop prereq
	130	ts_int j,k;
	131	ts_double dx,dy; // end loop prereq
	132
	133	/* topmost vertex */
8f6a69	134	vtx[1]->x=0.0;
SP	135	vtx[1]->y=0.0;
	136	vtx[1]->z=z0*(ts_double)nshell;
7958e9	137
SP	138	/* starting from to in circular order on pentagrams */
	139	for(i=1;i<=nshell;i++){
	140	n0=2+5i(i-1)/2; //-1 would be for the reason that C index starts from 0
8f6a69	141	vtx[n0]->x=0.0;
SP	142	vtx[n0]->y=(ts_double)i*xl0;
	143	vtx[n0+i]->x=vtx[n0]->y*s1;
	144	vtx[n0+i]->y=vtx[n0]->y*c1;
	145	vtx[n0+2i]->x=vtx[n0]->ys2;
	146	vtx[n0+2i]->y=vtx[n0]->yc2;
	147	vtx[n0+3i]->x=-vtx[n0+2i]->x;
	148	vtx[n0+3i]->y=vtx[n0+2i]->y;
	149	vtx[n0+4*i]->x=-vtx[n0+i]->x;
	150	vtx[n0+4*i]->y=vtx[n0+i]->y;
7958e9	151	}
SP	152
	153	/* vertexes on the faces of the dipyramid */
	154	for(i=1;i<=nshell;i++){
	155	n0=2+5i(i-1)/2; // -1 would be because of C!
	156	for(j=1;j<=i-1;j++){
8f6a69	157	dx=(vtx[n0]->x-vtx[n0+4*i]->x)/(ts_double)i;
SP	158	dy=(vtx[n0]->y-vtx[n0+4*i]->y)/(ts_double)i;
	159	vtx[n0+4i+j]->x=(ts_double)jdx+vtx[n0+4*i]->x;
	160	vtx[n0+4i+j]->y=(ts_double)jdy+vtx[n0+4*i]->y;
7958e9	161	}
SP	162	for(k=0;k<=3;k++){ // I would be worried about zero starting of for
8f6a69	163	dx=(vtx[n0+(k+1)i]->x - vtx[n0+ki]->x)/(ts_double) i;
SP	164	dy=(vtx[n0+(k+1)i]->y - vtx[n0+ki]->y)/(ts_double) i;
7958e9	165	for(j=1; j<=i-1;j++){
8f6a69	166	vtx[n0+ki+j]->x= (ts_double)jdx+vtx[n0+k*i]->x;
SP	167	vtx[n0+ki+j]->y= (ts_double)jdy+vtx[n0+k*i]->y;
7958e9	168	}
SP	169	}
	170	}
	171
	172	for(i=1;i<=nshell;i++){
	173	n0= 2+ 5i(i-1)/2;
	174	for(j=0;j<=5*i-1;j++){
8f6a69	175	vtx[n0+j]->z= z0*(ts_double)(nshell-i); // I would be worried about zero starting of for
7958e9	176	}
SP	177	}
	178
	179	/* for botom part of dipyramide we calculate the positions of vertices */
	180	for(i=2+5nshell(nshell+1)/2;i<=vlist->n;i++){
8f6a69	181	vtx[i]->x=vtx[vlist->n - i +1]->x;
SP	182	vtx[i]->y=vtx[vlist->n - i +1]->y;
	183	vtx[i]->z=-vtx[vlist->n - i +1]->z;
7958e9	184	}
SP	185
	186	for(i=1;i<=vlist->n;i++){
	187	for(j=1;j<=vlist->n;j++){
	188	if(i!=j && vtx_distance_sq(vtx[i],vtx[j])<0.001){
	189	printf("Vertices %u and %u are the same!\n",i,j);
	190	}
	191	}
	192	}
	193	return TS_SUCCESS;
	194	}
	195
	196
	197
	198	ts_bool init_vertex_neighbours(ts_vertex_list *vlist){
	199	ts_vertex **vtx=vlist->vtx -1; // take a look at dipyramid function for comment.
	200	const ts_double eps=0.001; //TODO: find out if you can use EPS from math.h
	201	ts_uint i,j;
	202	ts_double dist2; // Square of distance of neighbours
	203	/this is not required if we zero all data in vertex structure at initialization /
	204	/if we force zeroing at initialization this for loop can safely be deleted /
	205	//for(i=1;i<=vlist->n;i++){
	206	// vtx[i].neigh_no=0;
	207	//}
	208	for(i=1;i<=vlist->n;i++){
	209	for(j=1;j<=vlist->n;j++){
	210	dist2=vtx_distance_sq(vtx[i],vtx[j]);
	211	if( (dist2>eps) && (dist2<(A0*A0+eps))){
	212	//if it is close enough, but not too much close (solves problem of comparing when i==j)
	213	vtx_add_neighbour(vtx[i],vtx[j]);
	214	}
	215	}
	216	// printf ("vertex %u ima %u sosedov!\n",i,vtx[i]->data->neigh_no);
	217	}
	218
	219	return TS_SUCCESS;
	220	}
	221
b01cc1	222	// TODO: with new datastructure can be rewritten. Partially it is done, but it is complicated.
SP	223	ts_vertex_list init_sort_neighbours(ts_bond_list blist,ts_vertex_list *vlist){
7958e9	224	ts_vertex **vtx=vlist->vtx -1; // take a look at dipyramid function for comment.
SP	225	ts_uint i,l,j,jj,jjj,k=0;
	226	ts_double eps=0.001; // Take a look if EPS from math.h can be used
	227
	228	/lets initialize memory for temporary vertex_list. Should we write a function instead /
b01cc1	229	ts_vertex_list *tvlist=vertex_list_copy(vlist);
7958e9	230	ts_vertex *tvtx=tvlist->vtx -1; / again to compensate for 0-indexing */
SP	231
	232	ts_double dist2; // Square of distance of neighbours
	233	ts_double direct; // Something, dont know what, but could be normal of some kind
	234	for(i=1;i<=vlist->n;i++){
	235	k++; // WHY i IS NOT GOOD??
8f6a69	236	vtx_add_cneighbour(blist,tvtx[k], tvtx[vtx[i]->neigh[0]->idx+1]); //always add 1st
7958e9	237	jjj=1;
SP	238	jj=1;
8f6a69	239	for(l=2;l<=vtx[i]->neigh_no;l++){
SP	240	for(j=2;j<=vtx[i]->neigh_no;j++){
	241	dist2=vtx_distance_sq(vtx[i]->neigh[j-1],vtx[i]->neigh[jj-1]);
	242	direct=vtx_direct(vtx[i],vtx[i]->neigh[j-1],vtx[i]->neigh[jj-1]);
	243	// TODO: check if fabs can be used with all floating point types!!
7958e9	244	if( (fabs(dist2-A0*A0)<=eps) && (direct>0.0) && (j!=jjj) ){
8f6a69	245	vtx_add_cneighbour(blist,tvtx[k],tvtx[vtx[i]->neigh[j-1]->idx+1]);
7958e9	246	jjj=jj;
SP	247	jj=j;
	248	break;
	249	}
	250	}
	251	}
	252	}
b01cc1	253	/* We use the temporary vertex for our main vertices and we abandon main
SP	254	* vertices, because their neighbours are not correctly ordered */
	255	// tvtx=vlist->vtx;
	256	// vlist->vtx=tvtx;
	257	// tvlist->vtx=vtx;
	258	vtx_list_free(vlist);
	259	/* Let's make a check if the number of bonds is correct */
	260	if((blist->n)!=3*(tvlist->n-2)){
	261	ts_fprintf(stderr,"Number of bonds is %u should be %u!\n", blist->n, 3*(tvlist->n-2));
	262	fatal("Number of bonds is not 3*(no_vertex-2).",4);
7958e9	263	}
SP	264
b01cc1	265	return tvlist;
7958e9	266	}
SP	267
	268
	269	ts_bool init_vesicle_bonds(ts_vesicle *vesicle){
	270	ts_vertex_list *vlist=vesicle->vlist;
	271	ts_bond_list *blist=vesicle->blist;
	272	ts_vertex **vtx=vesicle->vlist->vtx - 1; // Because of 0 indexing
	273	/* lets make correct clockwise ordering of in nearest neighbour list */
	274	ts_uint i,j,k;
	275	for(i=1;i<=vlist->n;i++){
	276	for(j=i+1;j<=vlist->n;j++){
8f6a69	277	for(k=0;k<vtx[i]->neigh_no;k++){ // has changed 0 to < instead of 1 and <=
SP	278	if(vtx[i]->neigh[k]==vtx[j]){ //if addresses matches it is the same
7958e9	279	bond_add(blist,vtx[i],vtx[j]);
SP	280	break;
	281	}
	282	}
	283	}
	284	}
	285	/* Let's make a check if the number of bonds is correct */
	286	if((blist->n)!=3*(vlist->n-2)){
	287	ts_fprintf(stderr,"Number of bonds is %u should be %u!\n", blist->n, 3*(vlist->n-2));
	288	fatal("Number of bonds is not 3*(no_vertex-2).",4);
	289	}
	290	return TS_SUCCESS;
	291	}
	292
	293
	294
	295	ts_bool init_triangles(ts_vesicle *vesicle){
	296	ts_uint i,j,jj,k;
	297	ts_vertex **vtx=vesicle->vlist->vtx -1; // difference between 0 indexing and 1 indexing
	298	ts_triangle_list *tlist=vesicle->tlist;
	299	ts_double dist, direct;
	300	ts_double eps=0.001; // can we use EPS from math.h?
	301	k=0;
	302	for(i=1;i<=vesicle->vlist->n;i++){
8f6a69	303	for(j=1;j<=vtx[i]->neigh_no;j++){
SP	304	for(jj=1;jj<=vtx[i]->neigh_no;jj++){
7958e9	305	// ts_fprintf(stderr,"%u: (%u,%u) neigh_no=%u ",i,j,jj,vtx[i].neigh_no);
SP	306	// ts_fprintf(stderr,"%e, %e",vtx[i].neigh[j-1]->x,vtx[i].neigh[jj-1]->x);
8f6a69	307	dist=vtx_distance_sq(vtx[i]->neigh[j-1],vtx[i]->neigh[jj-1]);
SP	308	direct=vtx_direct(vtx[i],vtx[i]->neigh[j-1],vtx[i]->neigh[jj-1]);
	309	// TODO: same as above
	310	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){
	311	triangle_add(tlist,vtx[i],vtx[i]->neigh[j-1],vtx[i]->neigh[jj-1]);
7958e9	312	}
SP	313	}
	314	}
	315	}
	316	/* We check if all triangles have 3 vertices and if the number of triangles
	317	* matches the theoretical value.
	318	*/
	319	for(i=0;i<tlist->n;i++){
	320	k=0;
	321	for(j=0;j<3;j++){
41a035	322	if(tlist->tria[i]->vertex[j]!=NULL)
7958e9	323	k++;
SP	324	}
	325	if(k!=3){
8f6a69	326	fatal("Some triangles have less than 3 vertices..",4);
7958e9	327	}
SP	328	}
	329	if(tlist->n!=2*(vesicle->vlist->n -2)){
	330	ts_fprintf(stderr,"The number of triangles is %u but should be %u!\n",tlist->n,2*(vesicle->vlist->n -2));
	331	fatal("The number of triangles doesn't match 2*(no_vertex -2).",4);
	332	}
	333	return TS_SUCCESS;
	334	}
	335
	336
	337
	338	ts_bool init_triangle_neighbours(ts_vesicle *vesicle){
	339	ts_uint i,j,nobo;
	340	ts_vertex i1,i2,i3,j1,j2,j3;
	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	nobo=0;
	345	for(i=1;i<=tlist->n;i++){
41a035	346	i1=tria[i]->vertex[0];
SP	347	i2=tria[i]->vertex[1];
	348	i3=tria[i]->vertex[2];
7958e9	349	for(j=1;j<=tlist->n;j++){
SP	350	if(j==i) continue;
41a035	351	j1=tria[j]->vertex[0];
SP	352	j2=tria[j]->vertex[1];
	353	j3=tria[j]->vertex[2];
7958e9	354	if((i1==j1 && i3==j2) \|\| (i1==j2 && i3==j3) \|\| (i1==j3 && i3==j1)){
SP	355	triangle_add_neighbour(tria[i],tria[j]);
	356	nobo++;
	357	}
	358	}
	359	}
	360	for(i=1;i<=tlist->n;i++){
41a035	361	i1=tria[i]->vertex[0];
SP	362	i2=tria[i]->vertex[1];
	363	i3=tria[i]->vertex[2];
7958e9	364	for(j=1;j<=tlist->n;j++){
SP	365	if(j==i) continue;
41a035	366	j1=tria[j]->vertex[0];
SP	367	j2=tria[j]->vertex[1];
	368	j3=tria[j]->vertex[2];
7958e9	369	if((i1==j1 && i2==j3) \|\| (i1==j3 && i2==j2) \|\| (i1==j2 && i2==j1)){
SP	370	triangle_add_neighbour(tria[i],tria[j]);
	371	nobo++;
	372	}
	373	}
	374	}
	375	for(i=1;i<=tlist->n;i++){
41a035	376	i1=tria[i]->vertex[0];
SP	377	i2=tria[i]->vertex[1];
	378	i3=tria[i]->vertex[2];
7958e9	379	for(j=1;j<=tlist->n;j++){
SP	380	if(j==i) continue;
41a035	381	j1=tria[j]->vertex[0];
SP	382	j2=tria[j]->vertex[1];
	383	j3=tria[j]->vertex[2];
7958e9	384	if((i2==j1 && i3==j3) \|\| (i2==j3 && i3==j2) \|\| (i2==j2 && i3==j1)){
SP	385	triangle_add_neighbour(tria[i],tria[j]);
	386	nobo++;
	387	}
	388	}
	389	}
	390	if(nobo != vesicle->blist->n*2) {
	391	ts_fprintf(stderr,"Number of triangles= %u, number of bonds= %u\n",nobo/2, vesicle->blist->n);
	392	fatal("Number of triangle neighbour pairs differs from double the number of bonds!",4);
	393	}
	394	return TS_SUCCESS;
	395	}
	396
	397
	398	ts_bool init_common_vertex_triangle_neighbours(ts_vesicle *vesicle){
	399	ts_uint i,j,jp,k;
	400	ts_vertex k1,k2,k3,k4,*k5;
	401	ts_vertex **vtx=vesicle->vlist->vtx -1; // difference between 0 indexing and 1 indexing
	402	ts_triangle_list *tlist=vesicle->tlist;
	403	ts_triangle **tria=tlist->tria -1;
	404
	405	for(i=1;i<=vesicle->vlist->n;i++){
8f6a69	406	for(j=1;j<=vtx[i]->neigh_no;j++){
SP	407	k1=vtx[i]->neigh[j-1];
7958e9	408	jp=j+1;
8f6a69	409	if(j == vtx[i]->neigh_no) jp=1;
SP	410	k2=vtx[i]->neigh[jp-1];
7958e9	411	for(k=1;k<=tlist->n;k++){ // VERY NON-OPTIMAL!!! too many loops (vlist.n * vtx.neigh * tlist.n )!
41a035	412	k3=tria[k]->vertex[0];
SP	413	k4=tria[k]->vertex[1];
	414	k5=tria[k]->vertex[2];
7958e9	415	// ts_fprintf(stderr,"%u %u: k=(%u %u %u)\n",k1,k2,k3,k4,k5);
SP	416	if((vtx[i]==k3 && k1==k4 && k2==k5) \|\|
	417	(vtx[i]==k4 && k1==k5 && k2==k3) \|\|
	418	(vtx[i]==k5 && k1==k3 && k2==k4)){
b01cc1	419
SP	420	//TODO: probably something wrong with neighbour distribution.
	421	// if(vtx[i]==k3 \|\| vtx[i]==k4 \|\| vtx[i]==k5){
dac2e5	422	// if(i==6) ts_fprintf(stdout, "Vtx[%u] > Added to tristar!\n",i);
7958e9	423	vertex_add_tristar(vtx[i],tria[k]);
SP	424	}
	425	}
	426	}
	427	/* ts_fprintf(stderr,"TRISTAR for %u (%u):",i-1,vtx[i].tristar_no);
	428	for(j=0;j<vtx[i].tristar_no;j++){
	429	ts_fprintf(stderr," %u,",vtx[i].tristar[j]->idx);
	430	}
	431	ts_fprintf(stderr,"\n"); */
	432	}
	433	return TS_SUCCESS;
	434	}
	435
	436
	437	ts_bool init_normal_vectors(ts_triangle_list *tlist){
	438	/* Normals point INSIDE vesicle */
	439	ts_uint k;
	440	ts_triangle **tria=tlist->tria -1; //for 0 indexing
	441	for(k=1;k<=tlist->n;k++){
	442	triangle_normal_vector(tria[k]);
	443	}
	444	return TS_SUCCESS;
	445	}