trisurf-ng.git - Gitblit

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

mihaf

2014-03-21 bcf4557ddd61890f130247430267feac5b05c5b7

commit \| author \| age
aec47d	1	#include<stdlib.h>
SP	2	#include<math.h>
	3	#include "general.h"
	4	#include "vertex.h"
	5	#include "bond.h"
	6	#include "triangle.h"
	7	#include "vesicle.h"
	8	#include "energy.h"
	9	#include "timestep.h"
	10	#include "cell.h"
30ee9c	11	#include "bondflip.h"
aec47d	12	//#include "io.h"
SP	13	#include<stdio.h>
2870ab	14	#include<string.h>
aec47d	15
SP	16	ts_bool single_bondflip_timestep(ts_vesicle vesicle, ts_bond bond, ts_double *rn){
	17	/*c Vertex and triangle (lm and lp) indexing for bond flip:
	18	c +----- k-------+ +----- k ------+
	19	c \|lm1 / \| \ lp1 \| \|lm1 / \ lp1 \|
	20	c \| / \| \ \| \| / \ \|
	21	c \|/ \| \ \| FLIP \|/ lm \ \|
	22	c km lm \| lp kp ---> km ---------- kp
	23	c \|\ \| / \| \|\ lp / \|
	24	c \| \ \| / \| \| \ / \|
	25	c \|lm2 \ \| / lp2 \| \|lm2 \ / lp2 \|
	26	c +------it------+ +----- it -----+
	27	c
	28	*/
	29	ts_vertex *it=bond->vtx1;
	30	ts_vertex *k=bond->vtx2;
	31	ts_uint nei,neip,neim;
b866cf	32	ts_uint i,j;
414b8a	33	ts_double oldenergy, delta_energy, dvol=0.0;
b866cf	34	ts_triangle lm=NULL,lp=NULL, lp1=NULL, lm2=NULL;
aec47d	35
SP	36	ts_vertex kp,km;
	37
	38	if(it->neigh_no< 3) return TS_FAIL;
	39	if(k->neigh_no< 3) return TS_FAIL;
	40	if(k==NULL \|\| it==NULL){
	41	fatal("In bondflip, number of neighbours of k or it is less than 3!",999);
	42	}
	43
30ee9c	44	nei=0;
aec47d	45	for(i=0;i<it->neigh_no;i++){ // Finds the nn of it, that is k
SP	46	if(it->neigh[i]==k){
	47	nei=i;
	48	break;
	49	}
	50	}
	51	neip=nei+1; // I don't like it.. Smells like I must have it in correct order
	52	neim=nei-1;
	53	if(neip>=it->neigh_no) neip=0;
	54	if((ts_int)neim<0) neim=it->neigh_no-1; /* casting is essential... If not
	55	there the neim is never <0 !!! */
	56	// fprintf(stderr,"The numbers are: %u %u\n",neip, neim);
	57	km=it->neigh[neim]; // We located km and kp
	58	kp=it->neigh[neip];
	59
	60	if(km==NULL \|\| kp==NULL){
	61	fatal("In bondflip, cannot determine km and kp!",999);
	62	}
	63
	64	// fprintf(stderr,"I WAS HERE! after the 4 vertices are known!\n");
	65
	66	/* test if the membrane is wrapped too much, so that kp is nearest neighbour of
	67	* km. If it is true, then don't flip! */
	68	for(i=0;i<km->neigh_no;i++){
	69	if(km->neigh[i] == kp) return TS_FAIL;
	70	}
	71	// fprintf(stderr,"Membrane didn't wrap too much.. Continue.\n");
	72	/* if bond would be too long, return... */
30ee9c	73	if(vtx_distance_sq(km,kp) > vesicle->dmax ) return TS_FAIL;
aec47d	74	// fprintf(stderr,"Bond will not be too long.. Continue.\n");
SP	75
	76	/* we make a bond flip. this is different than in original fortran */
b866cf	77	// find lm, lp
aec47d	78	// 1. step. We find lm and lp from k->tristar !
SP	79	for(i=0;i<it->tristar_no;i++){
	80	for(j=0;j<k->tristar_no;j++){
	81	if((it->tristar[i] == k->tristar[j])){ //ce gre za skupen trikotnik
	82	if((it->tristar[i]->vertex[0] == km \|\| it->tristar[i]->vertex[1]
	83	== km \|\| it->tristar[i]->vertex[2]== km )){
	84	lm=it->tristar[i];
	85	// lmidx=i;
	86	}
	87	else
	88	{
	89	lp=it->tristar[i];
	90	// lpidx=i;
	91	}
	92
	93	}
	94	}
	95	}
	96	if(lm==NULL \|\| lp==NULL) fatal("ts_flip_bond: Cannot find triangles lm and lp!",999);
	97
	98	//we look for important triangles lp1 and lm2.
	99
	100	for(i=0;i<k->tristar_no;i++){
	101	for(j=0;j<kp->tristar_no;j++){
	102	if((k->tristar[i] == kp->tristar[j]) && k->tristar[i]!=lp){ //ce gre za skupen trikotnik
	103	lp1=k->tristar[i];
	104	}
	105	}
	106	}
	107
	108	for(i=0;i<it->tristar_no;i++){
	109	for(j=0;j<km->tristar_no;j++){
	110	if((it->tristar[i] == km->tristar[j]) && it->tristar[i]!=lm){ //ce gre za skupen trikotnik
	111	lm2=it->tristar[i];
	112	}
	113	}
	114	}
	115
	116	if(lm2==NULL \|\| lp1==NULL) fatal("ts_flip_bond: Cannot find triangles lm2 and lp1!",999);
2870ab	117
SP	118
	119	/* backup old structure */
	120	/* need to backup:
	121	* vertices k, kp, km, it
	122	* triangles lm, lp, lm2, lp1
	123	* bond
	124	*/
	125	ts_vertex *bck_vtx[4];
	126	ts_triangle *bck_tria[4];
	127	ts_bond *bck_bond;
	128	ts_vertex *orig_vtx[]={k,it,kp,km};
7efbb1	129	ts_triangle *orig_tria[]={lm,lp,lm2,lp1};
2870ab	130
7efbb1	131	//fprintf(stderr,"Backuping!!!\n");
SP	132	bck_bond=(ts_bond *)malloc(sizeof(ts_bond));
2870ab	133	for(i=0;i<4;i++){
7efbb1	134	/* fprintf(stderr,"vtx neigh[%d]=",i);
SP	135	for(j=0;j<orig_vtx[i]->neigh_no;j++) fprintf(stderr," %d", orig_vtx[i]->neigh[j]->idx);
	136	fprintf(stderr,"\n");
	137	*/
2870ab	138	bck_vtx[i]=(ts_vertex *)malloc(sizeof(ts_vertex));
SP	139	bck_tria[i]=(ts_triangle *)malloc(sizeof(ts_triangle));
7efbb1	140	memcpy((void )bck_vtx[i],(void )orig_vtx[i],sizeof(ts_vertex));
SP	141	memcpy((void )bck_tria[i],(void )orig_tria[i],sizeof(ts_triangle));
2870ab	142	/* level 2 pointers */
7efbb1	143
2870ab	144	bck_vtx[i]->neigh=(ts_vertex *)malloc(orig_vtx[i]->neigh_nosizeof(ts_vertex *));
SP	145	bck_vtx[i]->tristar=(ts_triangle *)malloc(orig_vtx[i]->tristar_nosizeof(ts_triangle *));
	146	bck_vtx[i]->bond=(ts_bond *)malloc(orig_vtx[i]->bond_nosizeof(ts_bond *));
	147	bck_tria[i]->neigh=(ts_triangle *)malloc(orig_tria[i]->neigh_nosizeof(ts_triangle *));
	148
7efbb1	149	memcpy((void )bck_vtx[i]->neigh,(void )orig_vtx[i]->neigh,orig_vtx[i]->neigh_nosizeof(ts_vertex ));
SP	150	memcpy((void )bck_vtx[i]->tristar,(void )orig_vtx[i]->tristar,orig_vtx[i]->tristar_nosizeof(ts_triangle ));
	151	memcpy((void )bck_vtx[i]->bond,(void )orig_vtx[i]->bond,orig_vtx[i]->bond_nosizeof(ts_bond ));
b866cf	152
7efbb1	153	memcpy((void )bck_tria[i]->neigh,(void )orig_tria[i]->neigh,orig_tria[i]->neigh_nosizeof(ts_triangle ));
SP	154	}
	155	memcpy(bck_bond,bond,sizeof(ts_bond));
	156	//fprintf(stderr,"Backup complete!!!\n");
	157	/* end backup vertex */
	158
414b8a	159	/* Save old energy */
b866cf	160	oldenergy=0;
M	161	oldenergy+=k->xk* k->energy;
	162	oldenergy+=kp->xk* kp->energy;
	163	oldenergy+=km->xk* km->energy;
	164	oldenergy+=it->xk* it->energy;
414b8a	165	//Neigbours of k, it, km, kp don't change its energy.
aec47d	166
414b8a	167	if(vesicle->pswitch == 1){dvol = -lm->volume - lp->volume;}
M	168
	169	/* fix data structure for flipped bond */
	170	ts_flip_bond(k,it,km,kp, bond,lm, lp, lm2, lp1);
aec47d	171
SP	172
b866cf	173	/* Calculating the new energy */
M	174	delta_energy=0;
	175	delta_energy+=k->xk* k->energy;
	176	delta_energy+=kp->xk* kp->energy;
	177	delta_energy+=km->xk* km->energy;
	178	delta_energy+=it->xk* it->energy;
414b8a	179	//Neigbours of k, it, km, kp don't change its energy.
M	180
b866cf	181	delta_energy-=oldenergy;
414b8a	182	if(vesicle->pswitch == 1){
M	183	dvol = dvol + lm->volume + lp->volume;
	184	delta_energy-= vesicle->pressure*dvol;
	185	}
	186
b866cf	187	/* MONTE CARLO */
M	188	if(delta_energy>=0){
	189	#ifdef TS_DOUBLE_DOUBLE
	190	if(exp(-delta_energy)< drand48() )
	191	#endif
	192	#ifdef TS_DOUBLE_FLOAT
	193	if(expf(-delta_energy)< (ts_float)drand48())
	194	#endif
	195	#ifdef TS_DOUBLE_LONGDOUBLE
	196	if(expl(-delta_energy)< (ts_ldouble)drand48())
	197	#endif
	198	{
	199	//not accepted, reverting changes
7efbb1	200	//restore all backups
SP	201	// fprintf(stderr,"Restoring!!!\n");
aec47d	202
7efbb1	203	for(i=0;i<4;i++){
SP	204	// fprintf(stderr,"Restoring vtx neigh[%d] with neighbours %d\n",i, orig_vtx[i]->neigh_no );
	205	free(orig_vtx[i]->neigh);
	206	free(orig_vtx[i]->tristar);
	207	free(orig_vtx[i]->bond);
	208	free(orig_tria[i]->neigh);
	209	memcpy((void )orig_vtx[i],(void )bck_vtx[i],sizeof(ts_vertex));
	210	memcpy((void )orig_tria[i],(void )bck_tria[i],sizeof(ts_triangle));
	211	// fprintf(stderr,"Restored vtx neigh[%d] with neighbours %d\n",i, orig_vtx[i]->neigh_no );
	212	/* level 2 pointers are redirected*/
	213	}
	214	memcpy(bond,bck_bond,sizeof(ts_bond));
2870ab	215
7efbb1	216	for(i=0;i<4;i++){
SP	217	free(bck_vtx[i]);
	218	free(bck_tria[i]);
	219	/* fprintf(stderr,"Restoring vtx neigh[%d] with neighbours %d =",i, orig_vtx[i]->neigh_no );
	220	for(j=0;j<orig_vtx[i]->neigh_no;j++) fprintf(stderr," %d", orig_vtx[i]->neigh[j]->idx);
	221	fprintf(stderr,"\n"); */
	222	}
2870ab	223
SP	224	free(bck_bond);
7efbb1	225	// fprintf(stderr,"Restoration complete!!!\n");
2870ab	226
7efbb1	227	return TS_FAIL;
b866cf	228	}
M	229	}
	230	/* IF BONDFLIP ACCEPTED, THEN RETURN SUCCESS! */
7efbb1	231	// fprintf(stderr,"SUCCESS!!!\n");
2870ab	232
SP	233	// delete all backups
	234	for(i=0;i<4;i++){
7efbb1	235	free(bck_vtx[i]->neigh);
SP	236	free(bck_vtx[i]->bond);
	237	free(bck_vtx[i]->tristar);
	238	free(bck_vtx[i]);
2870ab	239	free(bck_tria[i]->neigh);
SP	240	free(bck_tria[i]);
7efbb1	241	/* fprintf(stderr,"Afret backup deletion vtx neigh[%d]=",i);
SP	242	for(j=0;j<orig_vtx[i]->neigh_no;j++) fprintf(stderr," %d", orig_vtx[i]->neigh[j]->idx);
	243	fprintf(stderr,"\n");
	244	*/
2870ab	245	}
7efbb1	246	free(bck_bond);
SP	247
b866cf	248	return TS_SUCCESS;
aec47d	249	}
SP	250
	251
b866cf	252	ts_bool ts_flip_bond(ts_vertex k,ts_vertex it,ts_vertex km, ts_vertex kp,
M	253	ts_bond bond, ts_triangle lm, ts_triangle lp, ts_triangle lm2, ts_triangle *lp1){
	254
	255	ts_uint i; //lmidx, lpidx;
	256	if(k==NULL \|\| it==NULL \|\| km==NULL \|\| kp==NULL){
	257	fatal("ts_flip_bond: You called me with invalid pointers to vertices",999);
	258	}
aec47d	259	// 2. step. We change the triangle vertices... (actual bond flip)
SP	260	for(i=0;i<3;i++) if(lm->vertex[i]== it) lm->vertex[i]= kp;
	261	for(i=0;i<3;i++) if(lp->vertex[i]== k) lp->vertex[i]= km;
e19e79	262	//fprintf(stderr,"2. step: actual bondflip made\n");
aec47d	263	// 2a. step. If any changes in triangle calculations must be done, do it here!
SP	264	// * normals are recalculated here
	265	triangle_normal_vector(lp);
	266	triangle_normal_vector(lm);
e19e79	267	//fprintf(stderr,"2a. step: triangle normals recalculated\n");
aec47d	268	// 3. step. Correct neighbours in vertex_list
SP	269
	270
30ee9c	271	vtx_remove_neighbour(k,it);
306559	272	// vtx_remove_neighbour(it,k);
e19e79	273	//fprintf(stderr,"3. step (PROGRESS): removed k and it neighbours\n");
306559	274
aec47d	275	//Tukaj pa nastopi tezava... Kam dodati soseda?
30ee9c	276	vtx_insert_neighbour(km,kp,k);
SP	277	vtx_insert_neighbour(kp,km,it);
aec47d	278	// vertex_add_neighbour(km,kp); //pazi na vrstni red.
SP	279	// vertex_add_neighbour(kp,km);
e19e79	280	//fprintf(stderr,"3. step: vertex neighbours corrected\n");
aec47d	281
SP	282	// 3a. step. If any changes to ts_vertex, do it here!
	283	// bond_length calculatons not required for it is done in energy.c
	284
	285	// 4. step. Correct bond_list (don't know why I still have it!)
	286	bond->vtx1=km;
	287	bond->vtx2=kp;
	288	//fprintf(stderr,"4. step: bondlist corrected\n");
	289
	290
	291	// 5. step. Correct neighbouring triangles
	292
	293	triangle_remove_neighbour(lp,lp1);
e19e79	294	// fprintf(stderr,".\n");
aec47d	295	triangle_remove_neighbour(lp1,lp);
SP	296	// fprintf(stderr,".\n");
	297	triangle_remove_neighbour(lm,lm2);
	298	// fprintf(stderr,".\n");
	299	triangle_remove_neighbour(lm2,lm);
	300
	301	triangle_add_neighbour(lm,lp1);
	302	triangle_add_neighbour(lp1,lm);
	303	triangle_add_neighbour(lp,lm2); //Vrstni red?!
	304	triangle_add_neighbour(lm2,lp);
	305
	306	//fprintf(stderr,"5. step: triangle neigbours corrected\n");
	307
	308
	309	// 6. step. Correct tristar for vertices km, kp, k and it
	310	vertex_add_tristar(km,lp); // Preveri vrstni red!
	311	vertex_add_tristar(kp,lm);
30ee9c	312	vtx_remove_tristar(it,lm);
SP	313	vtx_remove_tristar(k,lp);
aec47d	314	//fprintf(stderr,"6. step: tristar corrected\n");
SP	315	energy_vertex(k);
	316	energy_vertex(kp);
	317	energy_vertex(km);
	318	energy_vertex(it);
	319	// END modifications to data structure!
	320	return TS_SUCCESS;
	321	}