trisurf-ng.git - Gitblit

Filament inside the vesicle added and debugged. Testing time...

mihaf

2014-03-21 bcf4557ddd61890f130247430267feac5b05c5b7

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