trisurf-ng.git - Gitblit

Added nucleus. Better initial configuration of filaments.

mihaf

2014-03-25 fe24d29b3c8684f08dccd01f5785aa48b7137322

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;
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:
fe24d2	44	vesicle->R_nucleus=tape->R_nucleus*tape->R_nucleus;
M	45
	46	vesicle->clist->dmin_interspecies = tape->dmin_interspecies*tape->dmin_interspecies;
bcf455	47
58230a	48	//Initialize grafted polymers (brush):
624f81	49	vesicle->poly_list=init_poly_list(tape->npoly,tape->nmono, vesicle->vlist, vesicle);
1ab449	50	vesicle->spring_constant=tape->kspring;
SP	51	poly_assign_spring_const(vesicle);
bcf455	52
58230a	53	//Initialize filaments (polymers inside the vesicle):
M	54	vesicle->filament_list=init_poly_list(tape->nfil,tape->nfono, NULL, vesicle);
bcf455	55	poly_assign_filament_xi(vesicle,tape);
58230a	56
bcf455	57	ts_uint i,j;
M	58	for(i=0;i<vesicle->filament_list->n;i++){
	59	for(j=0;j<vesicle->filament_list->poly[i]->blist->n;j++){
	60	bond_vector(vesicle->filament_list->poly[i]->blist->bond[j]);
	61	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));
	62	}
58230a	63	}
bcf455	64
M	65	for(i=0;i<vesicle->filament_list->n;i++){
	66	for(j=0;j<vesicle->filament_list->poly[i]->vlist->n;j++){
	67	vtx = vesicle->filament_list->poly[i]->vlist->vtx[j];
	68	if(vtx->bond_no == 2){
	69	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;
	70	}
	71	}
58230a	72	}
bcf455	73
ea1cce	74	for(i=0;i<vesicle->filament_list->n;i++){
M	75	vertex_list_assign_id(vesicle->filament_list->poly[i]->vlist,TS_ID_FILAMENT);
	76	}
bcf455	77
58230a	78	// vesicle->spring_constant=tape->kspring;
M	79	// poly_assign_spring_const(vesicle);
	80
1ab449	81
SP	82	vesicle->nshell=tape->nshell;
	83	vesicle->dmax=tape->dmaxtape->dmax; / dmax^2 in the vesicle dmax variable */
	84	vesicle->bending_rigidity=tape->xk0;
	85	vtx_set_global_values(vesicle); /* make xk0 default value for every vertex */
	86	ts_fprintf(stdout, "Tape setting: xk0=%e\n",tape->xk0);
	87	vesicle->stepsize=tape->stepsize;
	88	vesicle->clist->ncmax[0]=tape->ncxmax;
	89	vesicle->clist->ncmax[1]=tape->ncymax;
	90	vesicle->clist->ncmax[2]=tape->nczmax;
	91	vesicle->clist->max_occupancy=8; /* hard coded max occupancy? */
	92
	93	vesicle->pressure= tape->pressure;
	94	vesicle->pswitch=tape->pswitch;
	95
	96	return vesicle;
	97
	98	}
	99
	100
	101
	102
	103
7958e9	104	ts_bool pentagonal_dipyramid_vertex_distribution(ts_vertex_list *vlist){
SP	105	/* Some often used relations */
	106	const ts_double s1= sin(2.0*M_PI/5.0);
	107	const ts_double s2= sin(4.0*M_PI/5.0);
	108	const ts_double c1= cos(2.0*M_PI/5.0);
	109	const ts_double c2= cos(4.0*M_PI/5.0);
	110
	111	/* Calculates projection lenght of an edge bond to pentagram plane */
	112	const ts_double xl0=A0/(2.0*sin(M_PI/5.0));
	113	#ifdef TS_DOUBLE_DOUBLE
	114	const ts_double z0=sqrt(pow(A0,2)-pow(xl0,2));
	115	#endif
	116	#ifdef TS_DOUBLE_FLOAT
	117	const ts_double z0=sqrtf(powf(A0,2)-powf(xl0,2));
	118	#endif
	119	#ifdef TS_DOUBLE_LONGDOUBLE
	120	const ts_double z0=sqrtl(powl(A0,2)-powl(xl0,2));
	121	#endif
	122	// 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 */
	123
	124	/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!/
	125	ts_vertex **vtx=vlist->vtx -1 ;
	126
	127
	128	ts_uint nshell=(ts_uint)( sqrt((ts_double)(vlist->n-2)/5));
	129	// printf("nshell=%u\n",nshell);
	130	ts_uint i,n0; // some for loop prereq
	131	ts_int j,k;
	132	ts_double dx,dy; // end loop prereq
	133
	134	/* topmost vertex */
8f6a69	135	vtx[1]->x=0.0;
SP	136	vtx[1]->y=0.0;
	137	vtx[1]->z=z0*(ts_double)nshell;
7958e9	138
SP	139	/* starting from to in circular order on pentagrams */
	140	for(i=1;i<=nshell;i++){
	141	n0=2+5i(i-1)/2; //-1 would be for the reason that C index starts from 0
8f6a69	142	vtx[n0]->x=0.0;
SP	143	vtx[n0]->y=(ts_double)i*xl0;
	144	vtx[n0+i]->x=vtx[n0]->y*s1;
	145	vtx[n0+i]->y=vtx[n0]->y*c1;
	146	vtx[n0+2i]->x=vtx[n0]->ys2;
	147	vtx[n0+2i]->y=vtx[n0]->yc2;
	148	vtx[n0+3i]->x=-vtx[n0+2i]->x;
	149	vtx[n0+3i]->y=vtx[n0+2i]->y;
	150	vtx[n0+4*i]->x=-vtx[n0+i]->x;
	151	vtx[n0+4*i]->y=vtx[n0+i]->y;
7958e9	152	}
SP	153
	154	/* vertexes on the faces of the dipyramid */
	155	for(i=1;i<=nshell;i++){
	156	n0=2+5i(i-1)/2; // -1 would be because of C!
	157	for(j=1;j<=i-1;j++){
8f6a69	158	dx=(vtx[n0]->x-vtx[n0+4*i]->x)/(ts_double)i;
SP	159	dy=(vtx[n0]->y-vtx[n0+4*i]->y)/(ts_double)i;
	160	vtx[n0+4i+j]->x=(ts_double)jdx+vtx[n0+4*i]->x;
	161	vtx[n0+4i+j]->y=(ts_double)jdy+vtx[n0+4*i]->y;
7958e9	162	}
SP	163	for(k=0;k<=3;k++){ // I would be worried about zero starting of for
8f6a69	164	dx=(vtx[n0+(k+1)i]->x - vtx[n0+ki]->x)/(ts_double) i;
SP	165	dy=(vtx[n0+(k+1)i]->y - vtx[n0+ki]->y)/(ts_double) i;
7958e9	166	for(j=1; j<=i-1;j++){
8f6a69	167	vtx[n0+ki+j]->x= (ts_double)jdx+vtx[n0+k*i]->x;
SP	168	vtx[n0+ki+j]->y= (ts_double)jdy+vtx[n0+k*i]->y;
7958e9	169	}
SP	170	}
	171	}
	172
	173	for(i=1;i<=nshell;i++){
	174	n0= 2+ 5i(i-1)/2;
	175	for(j=0;j<=5*i-1;j++){
8f6a69	176	vtx[n0+j]->z= z0*(ts_double)(nshell-i); // I would be worried about zero starting of for
7958e9	177	}
SP	178	}
	179
	180	/* for botom part of dipyramide we calculate the positions of vertices */
	181	for(i=2+5nshell(nshell+1)/2;i<=vlist->n;i++){
8f6a69	182	vtx[i]->x=vtx[vlist->n - i +1]->x;
SP	183	vtx[i]->y=vtx[vlist->n - i +1]->y;
	184	vtx[i]->z=-vtx[vlist->n - i +1]->z;
7958e9	185	}
SP	186
	187	for(i=1;i<=vlist->n;i++){
	188	for(j=1;j<=vlist->n;j++){
	189	if(i!=j && vtx_distance_sq(vtx[i],vtx[j])<0.001){
	190	printf("Vertices %u and %u are the same!\n",i,j);
	191	}
	192	}
	193	}
	194	return TS_SUCCESS;
	195	}
	196
	197
	198
	199	ts_bool init_vertex_neighbours(ts_vertex_list *vlist){
	200	ts_vertex **vtx=vlist->vtx -1; // take a look at dipyramid function for comment.
	201	const ts_double eps=0.001; //TODO: find out if you can use EPS from math.h
	202	ts_uint i,j;
	203	ts_double dist2; // Square of distance of neighbours
	204	/this is not required if we zero all data in vertex structure at initialization /
	205	/if we force zeroing at initialization this for loop can safely be deleted /
	206	//for(i=1;i<=vlist->n;i++){
	207	// vtx[i].neigh_no=0;
	208	//}
	209	for(i=1;i<=vlist->n;i++){
	210	for(j=1;j<=vlist->n;j++){
	211	dist2=vtx_distance_sq(vtx[i],vtx[j]);
	212	if( (dist2>eps) && (dist2<(A0*A0+eps))){
	213	//if it is close enough, but not too much close (solves problem of comparing when i==j)
	214	vtx_add_neighbour(vtx[i],vtx[j]);
	215	}
	216	}
	217	// printf ("vertex %u ima %u sosedov!\n",i,vtx[i]->data->neigh_no);
	218	}
	219
	220	return TS_SUCCESS;
	221	}
	222
b01cc1	223	// TODO: with new datastructure can be rewritten. Partially it is done, but it is complicated.
SP	224	ts_vertex_list init_sort_neighbours(ts_bond_list blist,ts_vertex_list *vlist){
7958e9	225	ts_vertex **vtx=vlist->vtx -1; // take a look at dipyramid function for comment.
SP	226	ts_uint i,l,j,jj,jjj,k=0;
	227	ts_double eps=0.001; // Take a look if EPS from math.h can be used
	228
	229	/lets initialize memory for temporary vertex_list. Should we write a function instead /
b01cc1	230	ts_vertex_list *tvlist=vertex_list_copy(vlist);
7958e9	231	ts_vertex *tvtx=tvlist->vtx -1; / again to compensate for 0-indexing */
SP	232
	233	ts_double dist2; // Square of distance of neighbours
	234	ts_double direct; // Something, dont know what, but could be normal of some kind
	235	for(i=1;i<=vlist->n;i++){
	236	k++; // WHY i IS NOT GOOD??
8f6a69	237	vtx_add_cneighbour(blist,tvtx[k], tvtx[vtx[i]->neigh[0]->idx+1]); //always add 1st
7958e9	238	jjj=1;
SP	239	jj=1;
8f6a69	240	for(l=2;l<=vtx[i]->neigh_no;l++){
SP	241	for(j=2;j<=vtx[i]->neigh_no;j++){
	242	dist2=vtx_distance_sq(vtx[i]->neigh[j-1],vtx[i]->neigh[jj-1]);
	243	direct=vtx_direct(vtx[i],vtx[i]->neigh[j-1],vtx[i]->neigh[jj-1]);
	244	// TODO: check if fabs can be used with all floating point types!!
7958e9	245	if( (fabs(dist2-A0*A0)<=eps) && (direct>0.0) && (j!=jjj) ){
8f6a69	246	vtx_add_cneighbour(blist,tvtx[k],tvtx[vtx[i]->neigh[j-1]->idx+1]);
7958e9	247	jjj=jj;
SP	248	jj=j;
	249	break;
	250	}
	251	}
	252	}
	253	}
b01cc1	254	/* We use the temporary vertex for our main vertices and we abandon main
SP	255	* vertices, because their neighbours are not correctly ordered */
	256	// tvtx=vlist->vtx;
	257	// vlist->vtx=tvtx;
	258	// tvlist->vtx=vtx;
	259	vtx_list_free(vlist);
	260	/* Let's make a check if the number of bonds is correct */
	261	if((blist->n)!=3*(tvlist->n-2)){
	262	ts_fprintf(stderr,"Number of bonds is %u should be %u!\n", blist->n, 3*(tvlist->n-2));
	263	fatal("Number of bonds is not 3*(no_vertex-2).",4);
7958e9	264	}
SP	265
b01cc1	266	return tvlist;
7958e9	267	}
SP	268
	269
	270	ts_bool init_vesicle_bonds(ts_vesicle *vesicle){
	271	ts_vertex_list *vlist=vesicle->vlist;
	272	ts_bond_list *blist=vesicle->blist;
	273	ts_vertex **vtx=vesicle->vlist->vtx - 1; // Because of 0 indexing
	274	/* lets make correct clockwise ordering of in nearest neighbour list */
	275	ts_uint i,j,k;
	276	for(i=1;i<=vlist->n;i++){
	277	for(j=i+1;j<=vlist->n;j++){
8f6a69	278	for(k=0;k<vtx[i]->neigh_no;k++){ // has changed 0 to < instead of 1 and <=
SP	279	if(vtx[i]->neigh[k]==vtx[j]){ //if addresses matches it is the same
7958e9	280	bond_add(blist,vtx[i],vtx[j]);
SP	281	break;
	282	}
	283	}
	284	}
	285	}
	286	/* Let's make a check if the number of bonds is correct */
	287	if((blist->n)!=3*(vlist->n-2)){
	288	ts_fprintf(stderr,"Number of bonds is %u should be %u!\n", blist->n, 3*(vlist->n-2));
	289	fatal("Number of bonds is not 3*(no_vertex-2).",4);
	290	}
	291	return TS_SUCCESS;
	292	}
	293
	294
	295
	296	ts_bool init_triangles(ts_vesicle *vesicle){
	297	ts_uint i,j,jj,k;
	298	ts_vertex **vtx=vesicle->vlist->vtx -1; // difference between 0 indexing and 1 indexing
	299	ts_triangle_list *tlist=vesicle->tlist;
	300	ts_double dist, direct;
	301	ts_double eps=0.001; // can we use EPS from math.h?
	302	k=0;
	303	for(i=1;i<=vesicle->vlist->n;i++){
8f6a69	304	for(j=1;j<=vtx[i]->neigh_no;j++){
SP	305	for(jj=1;jj<=vtx[i]->neigh_no;jj++){
7958e9	306	// ts_fprintf(stderr,"%u: (%u,%u) neigh_no=%u ",i,j,jj,vtx[i].neigh_no);
SP	307	// ts_fprintf(stderr,"%e, %e",vtx[i].neigh[j-1]->x,vtx[i].neigh[jj-1]->x);
8f6a69	308	dist=vtx_distance_sq(vtx[i]->neigh[j-1],vtx[i]->neigh[jj-1]);
SP	309	direct=vtx_direct(vtx[i],vtx[i]->neigh[j-1],vtx[i]->neigh[jj-1]);
	310	// TODO: same as above
	311	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){
	312	triangle_add(tlist,vtx[i],vtx[i]->neigh[j-1],vtx[i]->neigh[jj-1]);
7958e9	313	}
SP	314	}
	315	}
	316	}
	317	/* We check if all triangles have 3 vertices and if the number of triangles
	318	* matches the theoretical value.
	319	*/
	320	for(i=0;i<tlist->n;i++){
	321	k=0;
	322	for(j=0;j<3;j++){
41a035	323	if(tlist->tria[i]->vertex[j]!=NULL)
7958e9	324	k++;
SP	325	}
	326	if(k!=3){
8f6a69	327	fatal("Some triangles have less than 3 vertices..",4);
7958e9	328	}
SP	329	}
	330	if(tlist->n!=2*(vesicle->vlist->n -2)){
	331	ts_fprintf(stderr,"The number of triangles is %u but should be %u!\n",tlist->n,2*(vesicle->vlist->n -2));
	332	fatal("The number of triangles doesn't match 2*(no_vertex -2).",4);
	333	}
	334	return TS_SUCCESS;
	335	}
	336
	337
	338
	339	ts_bool init_triangle_neighbours(ts_vesicle *vesicle){
	340	ts_uint i,j,nobo;
	341	ts_vertex i1,i2,i3,j1,j2,j3;
	342	// ts_vertex **vtx=vesicle->vlist->vtx -1; // difference between 0 indexing and 1 indexing
	343	ts_triangle_list *tlist=vesicle->tlist;
	344	ts_triangle **tria=tlist->tria -1;
	345	nobo=0;
	346	for(i=1;i<=tlist->n;i++){
41a035	347	i1=tria[i]->vertex[0];
SP	348	i2=tria[i]->vertex[1];
	349	i3=tria[i]->vertex[2];
7958e9	350	for(j=1;j<=tlist->n;j++){
SP	351	if(j==i) continue;
41a035	352	j1=tria[j]->vertex[0];
SP	353	j2=tria[j]->vertex[1];
	354	j3=tria[j]->vertex[2];
7958e9	355	if((i1==j1 && i3==j2) \|\| (i1==j2 && i3==j3) \|\| (i1==j3 && i3==j1)){
SP	356	triangle_add_neighbour(tria[i],tria[j]);
	357	nobo++;
	358	}
	359	}
	360	}
	361	for(i=1;i<=tlist->n;i++){
41a035	362	i1=tria[i]->vertex[0];
SP	363	i2=tria[i]->vertex[1];
	364	i3=tria[i]->vertex[2];
7958e9	365	for(j=1;j<=tlist->n;j++){
SP	366	if(j==i) continue;
41a035	367	j1=tria[j]->vertex[0];
SP	368	j2=tria[j]->vertex[1];
	369	j3=tria[j]->vertex[2];
7958e9	370	if((i1==j1 && i2==j3) \|\| (i1==j3 && i2==j2) \|\| (i1==j2 && i2==j1)){
SP	371	triangle_add_neighbour(tria[i],tria[j]);
	372	nobo++;
	373	}
	374	}
	375	}
	376	for(i=1;i<=tlist->n;i++){
41a035	377	i1=tria[i]->vertex[0];
SP	378	i2=tria[i]->vertex[1];
	379	i3=tria[i]->vertex[2];
7958e9	380	for(j=1;j<=tlist->n;j++){
SP	381	if(j==i) continue;
41a035	382	j1=tria[j]->vertex[0];
SP	383	j2=tria[j]->vertex[1];
	384	j3=tria[j]->vertex[2];
7958e9	385	if((i2==j1 && i3==j3) \|\| (i2==j3 && i3==j2) \|\| (i2==j2 && i3==j1)){
SP	386	triangle_add_neighbour(tria[i],tria[j]);
	387	nobo++;
	388	}
	389	}
	390	}
	391	if(nobo != vesicle->blist->n*2) {
	392	ts_fprintf(stderr,"Number of triangles= %u, number of bonds= %u\n",nobo/2, vesicle->blist->n);
	393	fatal("Number of triangle neighbour pairs differs from double the number of bonds!",4);
	394	}
	395	return TS_SUCCESS;
	396	}
	397
	398
	399	ts_bool init_common_vertex_triangle_neighbours(ts_vesicle *vesicle){
	400	ts_uint i,j,jp,k;
	401	ts_vertex k1,k2,k3,k4,*k5;
	402	ts_vertex **vtx=vesicle->vlist->vtx -1; // difference between 0 indexing and 1 indexing
	403	ts_triangle_list *tlist=vesicle->tlist;
	404	ts_triangle **tria=tlist->tria -1;
	405
	406	for(i=1;i<=vesicle->vlist->n;i++){
8f6a69	407	for(j=1;j<=vtx[i]->neigh_no;j++){
SP	408	k1=vtx[i]->neigh[j-1];
7958e9	409	jp=j+1;
8f6a69	410	if(j == vtx[i]->neigh_no) jp=1;
SP	411	k2=vtx[i]->neigh[jp-1];
7958e9	412	for(k=1;k<=tlist->n;k++){ // VERY NON-OPTIMAL!!! too many loops (vlist.n * vtx.neigh * tlist.n )!
41a035	413	k3=tria[k]->vertex[0];
SP	414	k4=tria[k]->vertex[1];
	415	k5=tria[k]->vertex[2];
7958e9	416	// ts_fprintf(stderr,"%u %u: k=(%u %u %u)\n",k1,k2,k3,k4,k5);
SP	417	if((vtx[i]==k3 && k1==k4 && k2==k5) \|\|
	418	(vtx[i]==k4 && k1==k5 && k2==k3) \|\|
	419	(vtx[i]==k5 && k1==k3 && k2==k4)){
b01cc1	420
SP	421	//TODO: probably something wrong with neighbour distribution.
	422	// if(vtx[i]==k3 \|\| vtx[i]==k4 \|\| vtx[i]==k5){
dac2e5	423	// if(i==6) ts_fprintf(stdout, "Vtx[%u] > Added to tristar!\n",i);
7958e9	424	vertex_add_tristar(vtx[i],tria[k]);
SP	425	}
	426	}
	427	}
	428	/* ts_fprintf(stderr,"TRISTAR for %u (%u):",i-1,vtx[i].tristar_no);
	429	for(j=0;j<vtx[i].tristar_no;j++){
	430	ts_fprintf(stderr," %u,",vtx[i].tristar[j]->idx);
	431	}
	432	ts_fprintf(stderr,"\n"); */
	433	}
	434	return TS_SUCCESS;
	435	}
	436
	437
	438	ts_bool init_normal_vectors(ts_triangle_list *tlist){
	439	/* Normals point INSIDE vesicle */
	440	ts_uint k;
	441	ts_triangle **tria=tlist->tria -1; //for 0 indexing
	442	for(k=1;k<=tlist->n;k++){
	443	triangle_normal_vector(tria[k]);
	444	}
	445	return TS_SUCCESS;
	446	}