trisurf-ng.git - Gitblit

Adding ending energy to filaments. In progress. Continue in single_filament...

mihaf

2014-03-18 58230a2591414fb38b9ec8d3a76439b290cb0a6f

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