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tape fixed, output has additional timestamp, ncurrent iteration is dumped a...

Samo Penic

2014-03-08 1ab449a2d9d4433794736566014f5c311d5a9317

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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"
7958e9	13
SP	14	ts_vesicle *initial_distribution_dipyramid(ts_uint nshell, ts_uint ncmax1, ts_uint ncmax2, ts_uint ncmax3, ts_double stepsize){
1ab449	15	ts_fprintf(stdout,"Starting initial_distribution on vesicle with %u shells!...\n",nshell);
7958e9	16	ts_bool retval;
1ab449	17	ts_uint no_vertices=5nshellnshell+2;
SP	18	ts_vesicle *vesicle=init_vesicle(no_vertices,ncmax1,ncmax2,ncmax3,stepsize);
	19	vesicle->nshell=nshell;
	20	//retval = vtx_set_global_values(vesicle);
	21	retval = pentagonal_dipyramid_vertex_distribution(vesicle->vlist);
	22	retval = init_vertex_neighbours(vesicle->vlist);
	23	vesicle->vlist = init_sort_neighbours(vesicle->blist,vesicle->vlist);
b01cc1	24	// retval = init_vesicle_bonds(vesicle); // bonds are created in sort_neigh
1ab449	25	retval = init_triangles(vesicle);
SP	26	retval = init_triangle_neighbours(vesicle);
	27	retval = init_common_vertex_triangle_neighbours(vesicle);
	28	retval = init_normal_vectors(vesicle->tlist);
	29	retval = mean_curvature_and_energy(vesicle);
	30	ts_fprintf(stdout,"initial_distribution finished!\n");
41a035	31	if(retval);
7958e9	32	return vesicle;
SP	33	}
	34
	35
1ab449	36
SP	37	ts_vesicle create_vesicle_from_tape(ts_tape tape){
	38	ts_vesicle *vesicle;
	39	vesicle=initial_distribution_dipyramid(tape->nshell,tape->ncxmax,tape->ncymax,tape->nczmax,tape->stepsize);
	40	vesicle->poly_list=init_poly_list(tape->npoly,tape->nmono, vesicle->vlist);
	41	vesicle->spring_constant=tape->kspring;
	42	poly_assign_spring_const(vesicle);
	43
	44	vesicle->nshell=tape->nshell;
	45	vesicle->dmax=tape->dmaxtape->dmax; / dmax^2 in the vesicle dmax variable */
	46	vesicle->bending_rigidity=tape->xk0;
	47	vtx_set_global_values(vesicle); /* make xk0 default value for every vertex */
	48	ts_fprintf(stdout, "Tape setting: xk0=%e\n",tape->xk0);
	49	vesicle->stepsize=tape->stepsize;
	50	vesicle->clist->ncmax[0]=tape->ncxmax;
	51	vesicle->clist->ncmax[1]=tape->ncymax;
	52	vesicle->clist->ncmax[2]=tape->nczmax;
	53	vesicle->clist->max_occupancy=8; /* hard coded max occupancy? */
	54
	55	vesicle->pressure= tape->pressure;
	56	vesicle->pswitch=tape->pswitch;
	57
	58	return vesicle;
	59
	60	}
	61
	62
	63
	64
	65
7958e9	66	ts_bool pentagonal_dipyramid_vertex_distribution(ts_vertex_list *vlist){
SP	67	/* Some often used relations */
	68	const ts_double s1= sin(2.0*M_PI/5.0);
	69	const ts_double s2= sin(4.0*M_PI/5.0);
	70	const ts_double c1= cos(2.0*M_PI/5.0);
	71	const ts_double c2= cos(4.0*M_PI/5.0);
	72
	73	/* Calculates projection lenght of an edge bond to pentagram plane */
	74	const ts_double xl0=A0/(2.0*sin(M_PI/5.0));
	75	#ifdef TS_DOUBLE_DOUBLE
	76	const ts_double z0=sqrt(pow(A0,2)-pow(xl0,2));
	77	#endif
	78	#ifdef TS_DOUBLE_FLOAT
	79	const ts_double z0=sqrtf(powf(A0,2)-powf(xl0,2));
	80	#endif
	81	#ifdef TS_DOUBLE_LONGDOUBLE
	82	const ts_double z0=sqrtl(powl(A0,2)-powl(xl0,2));
	83	#endif
	84	// 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 */
	85
	86	/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!/
	87	ts_vertex **vtx=vlist->vtx -1 ;
	88
	89
	90	ts_uint nshell=(ts_uint)( sqrt((ts_double)(vlist->n-2)/5));
	91	// printf("nshell=%u\n",nshell);
	92	ts_uint i,n0; // some for loop prereq
	93	ts_int j,k;
	94	ts_double dx,dy; // end loop prereq
	95
	96	/* topmost vertex */
8f6a69	97	vtx[1]->x=0.0;
SP	98	vtx[1]->y=0.0;
	99	vtx[1]->z=z0*(ts_double)nshell;
7958e9	100
SP	101	/* starting from to in circular order on pentagrams */
	102	for(i=1;i<=nshell;i++){
	103	n0=2+5i(i-1)/2; //-1 would be for the reason that C index starts from 0
8f6a69	104	vtx[n0]->x=0.0;
SP	105	vtx[n0]->y=(ts_double)i*xl0;
	106	vtx[n0+i]->x=vtx[n0]->y*s1;
	107	vtx[n0+i]->y=vtx[n0]->y*c1;
	108	vtx[n0+2i]->x=vtx[n0]->ys2;
	109	vtx[n0+2i]->y=vtx[n0]->yc2;
	110	vtx[n0+3i]->x=-vtx[n0+2i]->x;
	111	vtx[n0+3i]->y=vtx[n0+2i]->y;
	112	vtx[n0+4*i]->x=-vtx[n0+i]->x;
	113	vtx[n0+4*i]->y=vtx[n0+i]->y;
7958e9	114	}
SP	115
	116	/* vertexes on the faces of the dipyramid */
	117	for(i=1;i<=nshell;i++){
	118	n0=2+5i(i-1)/2; // -1 would be because of C!
	119	for(j=1;j<=i-1;j++){
8f6a69	120	dx=(vtx[n0]->x-vtx[n0+4*i]->x)/(ts_double)i;
SP	121	dy=(vtx[n0]->y-vtx[n0+4*i]->y)/(ts_double)i;
	122	vtx[n0+4i+j]->x=(ts_double)jdx+vtx[n0+4*i]->x;
	123	vtx[n0+4i+j]->y=(ts_double)jdy+vtx[n0+4*i]->y;
7958e9	124	}
SP	125	for(k=0;k<=3;k++){ // I would be worried about zero starting of for
8f6a69	126	dx=(vtx[n0+(k+1)i]->x - vtx[n0+ki]->x)/(ts_double) i;
SP	127	dy=(vtx[n0+(k+1)i]->y - vtx[n0+ki]->y)/(ts_double) i;
7958e9	128	for(j=1; j<=i-1;j++){
8f6a69	129	vtx[n0+ki+j]->x= (ts_double)jdx+vtx[n0+k*i]->x;
SP	130	vtx[n0+ki+j]->y= (ts_double)jdy+vtx[n0+k*i]->y;
7958e9	131	}
SP	132	}
	133	}
	134
	135	for(i=1;i<=nshell;i++){
	136	n0= 2+ 5i(i-1)/2;
	137	for(j=0;j<=5*i-1;j++){
8f6a69	138	vtx[n0+j]->z= z0*(ts_double)(nshell-i); // I would be worried about zero starting of for
7958e9	139	}
SP	140	}
	141
	142	/* for botom part of dipyramide we calculate the positions of vertices */
	143	for(i=2+5nshell(nshell+1)/2;i<=vlist->n;i++){
8f6a69	144	vtx[i]->x=vtx[vlist->n - i +1]->x;
SP	145	vtx[i]->y=vtx[vlist->n - i +1]->y;
	146	vtx[i]->z=-vtx[vlist->n - i +1]->z;
7958e9	147	}
SP	148
	149	for(i=1;i<=vlist->n;i++){
	150	for(j=1;j<=vlist->n;j++){
	151	if(i!=j && vtx_distance_sq(vtx[i],vtx[j])<0.001){
	152	printf("Vertices %u and %u are the same!\n",i,j);
	153	}
	154	}
	155	}
	156	return TS_SUCCESS;
	157	}
	158
	159
	160
	161	ts_bool init_vertex_neighbours(ts_vertex_list *vlist){
	162	ts_vertex **vtx=vlist->vtx -1; // take a look at dipyramid function for comment.
	163	const ts_double eps=0.001; //TODO: find out if you can use EPS from math.h
	164	ts_uint i,j;
	165	ts_double dist2; // Square of distance of neighbours
	166	/this is not required if we zero all data in vertex structure at initialization /
	167	/if we force zeroing at initialization this for loop can safely be deleted /
	168	//for(i=1;i<=vlist->n;i++){
	169	// vtx[i].neigh_no=0;
	170	//}
	171	for(i=1;i<=vlist->n;i++){
	172	for(j=1;j<=vlist->n;j++){
	173	dist2=vtx_distance_sq(vtx[i],vtx[j]);
	174	if( (dist2>eps) && (dist2<(A0*A0+eps))){
	175	//if it is close enough, but not too much close (solves problem of comparing when i==j)
	176	vtx_add_neighbour(vtx[i],vtx[j]);
	177	}
	178	}
	179	// printf ("vertex %u ima %u sosedov!\n",i,vtx[i]->data->neigh_no);
	180	}
	181
	182	return TS_SUCCESS;
	183	}
	184
b01cc1	185	// TODO: with new datastructure can be rewritten. Partially it is done, but it is complicated.
SP	186	ts_vertex_list init_sort_neighbours(ts_bond_list blist,ts_vertex_list *vlist){
7958e9	187	ts_vertex **vtx=vlist->vtx -1; // take a look at dipyramid function for comment.
SP	188	ts_uint i,l,j,jj,jjj,k=0;
	189	ts_double eps=0.001; // Take a look if EPS from math.h can be used
	190
	191	/lets initialize memory for temporary vertex_list. Should we write a function instead /
b01cc1	192	ts_vertex_list *tvlist=vertex_list_copy(vlist);
7958e9	193	ts_vertex *tvtx=tvlist->vtx -1; / again to compensate for 0-indexing */
SP	194
	195	ts_double dist2; // Square of distance of neighbours
	196	ts_double direct; // Something, dont know what, but could be normal of some kind
	197	for(i=1;i<=vlist->n;i++){
	198	k++; // WHY i IS NOT GOOD??
8f6a69	199	vtx_add_cneighbour(blist,tvtx[k], tvtx[vtx[i]->neigh[0]->idx+1]); //always add 1st
7958e9	200	jjj=1;
SP	201	jj=1;
8f6a69	202	for(l=2;l<=vtx[i]->neigh_no;l++){
SP	203	for(j=2;j<=vtx[i]->neigh_no;j++){
	204	dist2=vtx_distance_sq(vtx[i]->neigh[j-1],vtx[i]->neigh[jj-1]);
	205	direct=vtx_direct(vtx[i],vtx[i]->neigh[j-1],vtx[i]->neigh[jj-1]);
	206	// TODO: check if fabs can be used with all floating point types!!
7958e9	207	if( (fabs(dist2-A0*A0)<=eps) && (direct>0.0) && (j!=jjj) ){
8f6a69	208	vtx_add_cneighbour(blist,tvtx[k],tvtx[vtx[i]->neigh[j-1]->idx+1]);
7958e9	209	jjj=jj;
SP	210	jj=j;
	211	break;
	212	}
	213	}
	214	}
	215	}
b01cc1	216	/* We use the temporary vertex for our main vertices and we abandon main
SP	217	* vertices, because their neighbours are not correctly ordered */
	218	// tvtx=vlist->vtx;
	219	// vlist->vtx=tvtx;
	220	// tvlist->vtx=vtx;
	221	vtx_list_free(vlist);
	222	/* Let's make a check if the number of bonds is correct */
	223	if((blist->n)!=3*(tvlist->n-2)){
	224	ts_fprintf(stderr,"Number of bonds is %u should be %u!\n", blist->n, 3*(tvlist->n-2));
	225	fatal("Number of bonds is not 3*(no_vertex-2).",4);
7958e9	226	}
SP	227
b01cc1	228	return tvlist;
7958e9	229	}
SP	230
	231
	232	ts_bool init_vesicle_bonds(ts_vesicle *vesicle){
	233	ts_vertex_list *vlist=vesicle->vlist;
	234	ts_bond_list *blist=vesicle->blist;
	235	ts_vertex **vtx=vesicle->vlist->vtx - 1; // Because of 0 indexing
	236	/* lets make correct clockwise ordering of in nearest neighbour list */
	237	ts_uint i,j,k;
	238	for(i=1;i<=vlist->n;i++){
	239	for(j=i+1;j<=vlist->n;j++){
8f6a69	240	for(k=0;k<vtx[i]->neigh_no;k++){ // has changed 0 to < instead of 1 and <=
SP	241	if(vtx[i]->neigh[k]==vtx[j]){ //if addresses matches it is the same
7958e9	242	bond_add(blist,vtx[i],vtx[j]);
SP	243	break;
	244	}
	245	}
	246	}
	247	}
	248	/* Let's make a check if the number of bonds is correct */
	249	if((blist->n)!=3*(vlist->n-2)){
	250	ts_fprintf(stderr,"Number of bonds is %u should be %u!\n", blist->n, 3*(vlist->n-2));
	251	fatal("Number of bonds is not 3*(no_vertex-2).",4);
	252	}
	253	return TS_SUCCESS;
	254	}
	255
	256
	257
	258	ts_bool init_triangles(ts_vesicle *vesicle){
	259	ts_uint i,j,jj,k;
	260	ts_vertex **vtx=vesicle->vlist->vtx -1; // difference between 0 indexing and 1 indexing
	261	ts_triangle_list *tlist=vesicle->tlist;
	262	ts_double dist, direct;
	263	ts_double eps=0.001; // can we use EPS from math.h?
	264	k=0;
	265	for(i=1;i<=vesicle->vlist->n;i++){
8f6a69	266	for(j=1;j<=vtx[i]->neigh_no;j++){
SP	267	for(jj=1;jj<=vtx[i]->neigh_no;jj++){
7958e9	268	// ts_fprintf(stderr,"%u: (%u,%u) neigh_no=%u ",i,j,jj,vtx[i].neigh_no);
SP	269	// ts_fprintf(stderr,"%e, %e",vtx[i].neigh[j-1]->x,vtx[i].neigh[jj-1]->x);
8f6a69	270	dist=vtx_distance_sq(vtx[i]->neigh[j-1],vtx[i]->neigh[jj-1]);
SP	271	direct=vtx_direct(vtx[i],vtx[i]->neigh[j-1],vtx[i]->neigh[jj-1]);
	272	// TODO: same as above
	273	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){
	274	triangle_add(tlist,vtx[i],vtx[i]->neigh[j-1],vtx[i]->neigh[jj-1]);
7958e9	275	}
SP	276	}
	277	}
	278	}
	279	/* We check if all triangles have 3 vertices and if the number of triangles
	280	* matches the theoretical value.
	281	*/
	282	for(i=0;i<tlist->n;i++){
	283	k=0;
	284	for(j=0;j<3;j++){
41a035	285	if(tlist->tria[i]->vertex[j]!=NULL)
7958e9	286	k++;
SP	287	}
	288	if(k!=3){
8f6a69	289	fatal("Some triangles have less than 3 vertices..",4);
7958e9	290	}
SP	291	}
	292	if(tlist->n!=2*(vesicle->vlist->n -2)){
	293	ts_fprintf(stderr,"The number of triangles is %u but should be %u!\n",tlist->n,2*(vesicle->vlist->n -2));
	294	fatal("The number of triangles doesn't match 2*(no_vertex -2).",4);
	295	}
	296	return TS_SUCCESS;
	297	}
	298
	299
	300
	301	ts_bool init_triangle_neighbours(ts_vesicle *vesicle){
	302	ts_uint i,j,nobo;
	303	ts_vertex i1,i2,i3,j1,j2,j3;
	304	// ts_vertex **vtx=vesicle->vlist->vtx -1; // difference between 0 indexing and 1 indexing
	305	ts_triangle_list *tlist=vesicle->tlist;
	306	ts_triangle **tria=tlist->tria -1;
	307	nobo=0;
	308	for(i=1;i<=tlist->n;i++){
41a035	309	i1=tria[i]->vertex[0];
SP	310	i2=tria[i]->vertex[1];
	311	i3=tria[i]->vertex[2];
7958e9	312	for(j=1;j<=tlist->n;j++){
SP	313	if(j==i) continue;
41a035	314	j1=tria[j]->vertex[0];
SP	315	j2=tria[j]->vertex[1];
	316	j3=tria[j]->vertex[2];
7958e9	317	if((i1==j1 && i3==j2) \|\| (i1==j2 && i3==j3) \|\| (i1==j3 && i3==j1)){
SP	318	triangle_add_neighbour(tria[i],tria[j]);
	319	nobo++;
	320	}
	321	}
	322	}
	323	for(i=1;i<=tlist->n;i++){
41a035	324	i1=tria[i]->vertex[0];
SP	325	i2=tria[i]->vertex[1];
	326	i3=tria[i]->vertex[2];
7958e9	327	for(j=1;j<=tlist->n;j++){
SP	328	if(j==i) continue;
41a035	329	j1=tria[j]->vertex[0];
SP	330	j2=tria[j]->vertex[1];
	331	j3=tria[j]->vertex[2];
7958e9	332	if((i1==j1 && i2==j3) \|\| (i1==j3 && i2==j2) \|\| (i1==j2 && i2==j1)){
SP	333	triangle_add_neighbour(tria[i],tria[j]);
	334	nobo++;
	335	}
	336	}
	337	}
	338	for(i=1;i<=tlist->n;i++){
41a035	339	i1=tria[i]->vertex[0];
SP	340	i2=tria[i]->vertex[1];
	341	i3=tria[i]->vertex[2];
7958e9	342	for(j=1;j<=tlist->n;j++){
SP	343	if(j==i) continue;
41a035	344	j1=tria[j]->vertex[0];
SP	345	j2=tria[j]->vertex[1];
	346	j3=tria[j]->vertex[2];
7958e9	347	if((i2==j1 && i3==j3) \|\| (i2==j3 && i3==j2) \|\| (i2==j2 && i3==j1)){
SP	348	triangle_add_neighbour(tria[i],tria[j]);
	349	nobo++;
	350	}
	351	}
	352	}
	353	if(nobo != vesicle->blist->n*2) {
	354	ts_fprintf(stderr,"Number of triangles= %u, number of bonds= %u\n",nobo/2, vesicle->blist->n);
	355	fatal("Number of triangle neighbour pairs differs from double the number of bonds!",4);
	356	}
	357	return TS_SUCCESS;
	358	}
	359
	360
	361	ts_bool init_common_vertex_triangle_neighbours(ts_vesicle *vesicle){
	362	ts_uint i,j,jp,k;
	363	ts_vertex k1,k2,k3,k4,*k5;
	364	ts_vertex **vtx=vesicle->vlist->vtx -1; // difference between 0 indexing and 1 indexing
	365	ts_triangle_list *tlist=vesicle->tlist;
	366	ts_triangle **tria=tlist->tria -1;
	367
	368	for(i=1;i<=vesicle->vlist->n;i++){
8f6a69	369	for(j=1;j<=vtx[i]->neigh_no;j++){
SP	370	k1=vtx[i]->neigh[j-1];
7958e9	371	jp=j+1;
8f6a69	372	if(j == vtx[i]->neigh_no) jp=1;
SP	373	k2=vtx[i]->neigh[jp-1];
7958e9	374	for(k=1;k<=tlist->n;k++){ // VERY NON-OPTIMAL!!! too many loops (vlist.n * vtx.neigh * tlist.n )!
41a035	375	k3=tria[k]->vertex[0];
SP	376	k4=tria[k]->vertex[1];
	377	k5=tria[k]->vertex[2];
7958e9	378	// ts_fprintf(stderr,"%u %u: k=(%u %u %u)\n",k1,k2,k3,k4,k5);
SP	379	if((vtx[i]==k3 && k1==k4 && k2==k5) \|\|
	380	(vtx[i]==k4 && k1==k5 && k2==k3) \|\|
	381	(vtx[i]==k5 && k1==k3 && k2==k4)){
b01cc1	382
SP	383	//TODO: probably something wrong with neighbour distribution.
	384	// if(vtx[i]==k3 \|\| vtx[i]==k4 \|\| vtx[i]==k5){
dac2e5	385	// if(i==6) ts_fprintf(stdout, "Vtx[%u] > Added to tristar!\n",i);
7958e9	386	vertex_add_tristar(vtx[i],tria[k]);
SP	387	}
	388	}
	389	}
	390	/* ts_fprintf(stderr,"TRISTAR for %u (%u):",i-1,vtx[i].tristar_no);
	391	for(j=0;j<vtx[i].tristar_no;j++){
	392	ts_fprintf(stderr," %u,",vtx[i].tristar[j]->idx);
	393	}
	394	ts_fprintf(stderr,"\n"); */
	395	}
	396	return TS_SUCCESS;
	397	}
	398
	399
	400	ts_bool init_normal_vectors(ts_triangle_list *tlist){
	401	/* Normals point INSIDE vesicle */
	402	ts_uint k;
	403	ts_triangle **tria=tlist->tria -1; //for 0 indexing
	404	for(k=1;k<=tlist->n;k++){
	405	triangle_normal_vector(tria[k]);
	406	}
	407	return TS_SUCCESS;
	408	}