trisurf-ng.git - Gitblit

Changed atan to atan2 for transfroming coordinates from cartesian to spheri...

Samo Penic

2014-04-17 e9c87efeb9235748e8d19a3f5a067ec442d8a500

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8db569	1	#include"general.h"
M	2	#include"poly.h"
	3	#include<stdlib.h>
	4	#include"vertex.h"
	5	#include"bond.h"
	6	#include<math.h>
fedf2b	7	#include"energy.h"
8db569	8
bcf455	9	ts_bool poly_assign_filament_xi(ts_vesicle vesicle, ts_tape tape){
M	10	ts_uint i;
	11
	12	for(i=0;i<vesicle->filament_list->n;i++){
	13	vesicle->filament_list->poly[i]->k = tape->xi;
	14	}
	15
	16	return TS_SUCCESS;
	17	}
	18
	19
48bb92	20	ts_bool poly_assign_spring_const(ts_vesicle *vesicle){
M	21	ts_uint i;
	22
	23	for(i=0;i<vesicle->poly_list->n;i++){
	24	vesicle->poly_list->poly[i]->k = vesicle->spring_constant;
	25	}
	26
	27	return TS_SUCCESS;
	28	}
8db569	29
1d5dff	30	ts_poly init_poly(ts_uint n, ts_vertex grafted_vtx){
M	31	ts_poly poly=(ts_poly )calloc(1,sizeof(ts_poly));
	32	poly->vlist = init_vertex_list(n);
	33	poly->blist = init_bond_list();
624f81	34	if (grafted_vtx!=NULL){
M	35	poly->grafted_vtx = grafted_vtx;
	36	grafted_vtx->grafted_poly = poly;
	37	}
1d5dff	38
M	39	ts_uint i;
8db569	40	for(i=0;i<n-1;i++){
1d5dff	41	vtx_add_cneighbour(poly->blist, poly->vlist->vtx[i], poly->vlist->vtx[i+1]);
8db569	42	vtx_add_neighbour(poly->vlist->vtx[i+1], poly->vlist->vtx[i]);
1d5dff	43	}
M	44
48bb92	45	for(i=0;i<poly->blist->n;i++){
M	46	poly->blist->bond[i]->bond_length=sqrt(vtx_distance_sq(poly->blist->bond[i]->vtx1,poly->blist->bond[i]->vtx2));
fedf2b	47	bond_energy(poly->blist->bond[i],poly);
48bb92	48	}
M	49
1d5dff	50	return poly;
M	51	}
	52
	53
624f81	54	ts_poly_list init_poly_list(ts_uint n_poly, ts_uint n_mono, ts_vertex_list vlist, ts_vesicle *vesicle){
1d5dff	55	ts_poly_list poly_list=(ts_poly_list )calloc(1,sizeof(ts_poly_list));
8db569	56	poly_list->poly = (ts_poly *)calloc(n_poly,sizeof(ts_poly ));
3c1ac1	57	ts_uint i=0,j=0; //idx;
8db569	58	ts_uint gvtxi;
M	59	ts_double xnorm,ynorm,znorm,normlength;
624f81	60	ts_double dphi,dh;
1d5dff	61
624f81	62	// Grafting polymers:
M	63	if (vlist!=NULL){
	64	if (n_poly > vlist->n){fatal("Number of polymers larger then numbero f vertices on a vesicle.",310);}
1d5dff	65
624f81	66	while(i<n_poly){
M	67	gvtxi = rand() % vlist->n;
	68	if (vlist->vtx[gvtxi]->grafted_poly == NULL){
	69	poly_list->poly[i] = init_poly(n_mono, vlist->vtx[gvtxi]);
	70	i++;
	71	}
1d5dff	72	}
M	73	}
624f81	74	else
M	75	{
	76	for(i=0;i<n_poly;i++){
	77	poly_list->poly[i] = init_poly(n_mono, NULL);
	78	}
	79	}
	80
1d5dff	81	poly_list->n = n_poly;
M	82
624f81	83	if (vlist!=NULL){
M	84	/* Make straight grafted poylmers normal to membrane (polymer brush). Dist. between poly vertices put to 1*/
	85	for (i=0;i<poly_list->n;i++){
	86
	87	xnorm=0.0;
	88	ynorm=0.0;
	89	znorm=0.0;
	90	for (j=0;j<poly_list->poly[i]->grafted_vtx->tristar_no;j++){
	91	xnorm-=poly_list->poly[i]->grafted_vtx->tristar[j]->xnorm;
	92	ynorm-=poly_list->poly[i]->grafted_vtx->tristar[j]->ynorm;
	93	znorm-=poly_list->poly[i]->grafted_vtx->tristar[j]->znorm;
	94	}
	95	normlength=sqrt(xnormxnorm+ynormynorm+znorm*znorm);
	96	xnorm=xnorm/normlength;
	97	ynorm=ynorm/normlength;
	98	znorm=znorm/normlength;
8db569	99
624f81	100	for (j=0;j<poly_list->poly[i]->vlist->n;j++){
M	101	poly_list->poly[i]->vlist->vtx[j]->x = poly_list->poly[i]->grafted_vtx->x + xnorm*(ts_double)(j+1);
	102	poly_list->poly[i]->vlist->vtx[j]->y = poly_list->poly[i]->grafted_vtx->y + ynorm*(ts_double)(j+1);
	103	poly_list->poly[i]->vlist->vtx[j]->z = poly_list->poly[i]->grafted_vtx->z + znorm*(ts_double)(j+1);
	104	}
8db569	105	}
624f81	106	}
M	107	else
	108	{
	109	/* Make filaments inside the vesicle. Helix with radius... Dist. between poly vertices put to 1*/
fe24d2	110	ts_double a,R,H,tantheta,h,r,phi,A0=1.2;
M	111
	112	a = A0*(ts_double)vesicle->nshell;
	113	R = A0((ts_double)vesicle->nshell)/(2.0sin(M_PI/5.0));
	114	H = sqrt(aa - RR);
	115	tantheta = sqrt(RR - aa/4.0)/H;
	116
	117	h = -H + sqrt(vesicle->clist->dmin_interspecies)*1.5;
	118	r = (H-fabs(h))tantheta - sqrt(vesicle->clist->dmin_interspecies)1.5;
	119	dphi = 2.0asin(1.0/2.0/r)1.001;
402e8f	120	dh = dphi/2.0/M_PI*1.001;
fe24d2	121	phi=0.0;
624f81	122	for(i=0;i<poly_list->n;i++){
M	123	for (j=0;j<poly_list->poly[i]->vlist->n;j++){
fe24d2	124	h = h + dh;
M	125	r = (H-fabs(h))tantheta - sqrt(vesicle->clist->dmin_interspecies)1.5;
	126	dphi = 2.0asin(1.0/2.0/r)1.001;
	127	dh = dphi/2.0/M_PI*1.001;
	128	phi+=dphi;
	129	//ji = j + i*poly_list->poly[i]->vlist->n;
	130	poly_list->poly[i]->vlist->vtx[j]->x = r*cos(phi);
	131	poly_list->poly[i]->vlist->vtx[j]->y = r*sin(phi);
	132	poly_list->poly[i]->vlist->vtx[j]->z = h;// jidh - (dhpoly_list->n*poly_list->poly[i]->vlist->n/2.0);
624f81	133	}
8db569	134	}
M	135	}
	136
40aa5b	137	//index correction for polymeres. Important, since each vtx has to have unique id
3c1ac1	138	/* idx=vlist->n;
40aa5b	139	for(i=0;i<n_poly;i++){
SP	140	for(j=0;j<n_mono;j++,idx++){
	141
	142	poly_list->poly[i]->vlist->vtx[j]->idx=idx;
	143
	144	}
	145	}
3c1ac1	146	*/
40aa5b	147
1d5dff	148	return poly_list;
M	149	}
	150
8db569	151
M	152	ts_bool poly_free(ts_poly *poly){
	153
	154	if (poly->grafted_vtx!=NULL){
	155	poly->grafted_vtx->grafted_poly=NULL;
	156	}
	157	vtx_list_free(poly->vlist);
	158	bond_list_free(poly->blist);
	159	free(poly);
	160
	161	return TS_SUCCESS;
	162	}
	163
	164	ts_bool poly_list_free(ts_poly_list *poly_list){
	165	ts_uint i;
	166
	167	for(i=0;i<poly_list->n;i++){
	168	poly_free(poly_list->poly[i]);
	169	}
	170	free(poly_list->poly);
	171	free(poly_list);
	172
	173	return TS_SUCCESS;
	174	}