trisurf-ng.git - Gitblit

backuping vtxes complete. debugging bondflip

Samo Penic

2014-03-08 2870ab279d5dce60c24e7a3e35d8a5e421003548

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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};
	129	ts_triangle *orig_tria[]={lm,lp, lm2,lp1};
	130
	131	fprintf(stderr,"Backuping!!!\n");
	132	for(i=0;i<4;i++){
	133	bck_vtx[i]=(ts_vertex *)malloc(sizeof(ts_vertex));
	134	bck_tria[i]=(ts_triangle *)malloc(sizeof(ts_triangle));
	135	bck_bond=(ts_bond *)malloc(sizeof(ts_bond));
	136	/* level 2 pointers */
	137	bck_vtx[i]->neigh=(ts_vertex *)malloc(orig_vtx[i]->neigh_nosizeof(ts_vertex *));
	138	bck_vtx[i]->tristar=(ts_triangle *)malloc(orig_vtx[i]->tristar_nosizeof(ts_triangle *));
	139	bck_vtx[i]->bond=(ts_bond *)malloc(orig_vtx[i]->bond_nosizeof(ts_bond *));
	140	bck_tria[i]->neigh=(ts_triangle *)malloc(orig_tria[i]->neigh_nosizeof(ts_triangle *));
	141
	142	bck_vtx[i]=memcpy(bck_vtx[i],orig_vtx[i],sizeof(ts_vertex));
	143	bck_vtx[i]->neigh=memcpy(bck_vtx[i]->neigh,orig_vtx[i]->neigh,orig_vtx[i]->neigh_nosizeof(ts_vertex ));
	144	bck_vtx[i]->tristar=memcpy(bck_vtx[i]->tristar,orig_vtx[i]->tristar,orig_vtx[i]->tristar_nosizeof(ts_triangle ));
	145	bck_vtx[i]->bond=memcpy(bck_vtx[i]->bond,orig_vtx[i]->bond,orig_vtx[i]->bond_nosizeof(ts_bond ));
	146
	147
	148	bck_tria[i]=memcpy(bck_tria[i],orig_tria[i],sizeof(ts_triangle));
	149	bck_tria[i]->neigh=memcpy(bck_tria[i]->neigh,orig_tria[i]->neigh,orig_tria[i]->neigh_nosizeof(ts_triangle ));
	150	}
	151	bck_bond=memcpy(bck_bond,bond,sizeof(ts_bond));
	152	fprintf(stderr,"Backup complete!!!\n");
	153	/* end backup vertex */
b866cf	154
414b8a	155	/* Save old energy */
b866cf	156	oldenergy=0;
M	157	oldenergy+=k->xk* k->energy;
	158	oldenergy+=kp->xk* kp->energy;
	159	oldenergy+=km->xk* km->energy;
	160	oldenergy+=it->xk* it->energy;
414b8a	161	//Neigbours of k, it, km, kp don't change its energy.
aec47d	162
414b8a	163	if(vesicle->pswitch == 1){dvol = -lm->volume - lp->volume;}
M	164
	165	/* fix data structure for flipped bond */
	166	ts_flip_bond(k,it,km,kp, bond,lm, lp, lm2, lp1);
aec47d	167
SP	168
b866cf	169	/* Calculating the new energy */
M	170	delta_energy=0;
	171	delta_energy+=k->xk* k->energy;
	172	delta_energy+=kp->xk* kp->energy;
	173	delta_energy+=km->xk* km->energy;
	174	delta_energy+=it->xk* it->energy;
414b8a	175	//Neigbours of k, it, km, kp don't change its energy.
M	176
b866cf	177	delta_energy-=oldenergy;
414b8a	178	if(vesicle->pswitch == 1){
M	179	dvol = dvol + lm->volume + lp->volume;
	180	delta_energy-= vesicle->pressure*dvol;
	181	}
	182
b866cf	183	/* MONTE CARLO */
M	184	if(delta_energy>=0){
	185	#ifdef TS_DOUBLE_DOUBLE
	186	if(exp(-delta_energy)< drand48() )
	187	#endif
	188	#ifdef TS_DOUBLE_FLOAT
	189	if(expf(-delta_energy)< (ts_float)drand48())
	190	#endif
	191	#ifdef TS_DOUBLE_LONGDOUBLE
	192	if(expl(-delta_energy)< (ts_ldouble)drand48())
	193	#endif
	194	{
	195	//not accepted, reverting changes
	196	// fprintf(stderr,"Failed to move, due to MC\n");
aec47d	197
2870ab	198	// ts_flip_bond(kp,km,k,it, bond, lm,lp,lm2,lp1);
b866cf	199	// fprintf(stderr,"%e, %e, %e\n", lp->xnorm, lp->ynorm, lp->znorm);
2870ab	200
SP	201	//restore all backups
	202	fprintf(stderr,"Restoring!!!\n");
	203
	204	for(i=0;i<4;i++){
	205	/* level 2 pointers */
	206	orig_vtx[i]=memcpy(orig_vtx[i],bck_vtx[i],sizeof(ts_vertex));
	207	orig_vtx[i]->neigh=memcpy(orig_vtx[i]->neigh,bck_vtx[i]->neigh,bck_vtx[i]->neigh_nosizeof(ts_vertex ));
	208	orig_vtx[i]->tristar=memcpy(orig_vtx[i]->tristar,bck_vtx[i]->tristar,bck_vtx[i]->tristar_nosizeof(ts_triangle ));
	209	orig_vtx[i]->bond=memcpy(orig_vtx[i]->bond,bck_vtx[i]->bond,bck_vtx[i]->bond_nosizeof(ts_bond ));
	210
	211
	212	orig_tria[i]=memcpy(orig_tria[i],bck_tria[i],sizeof(ts_triangle));
	213	orig_tria[i]->neigh=memcpy(orig_tria[i]->neigh,bck_tria[i]->neigh,bck_tria[i]->neigh_nosizeof(ts_triangle ));
	214	}
	215	bond=memcpy(bond,bck_bond,sizeof(ts_bond));
	216
	217
	218	for(i=0;i<4;i++){
	219	vtx_free(bck_vtx[i]);
	220
	221	free(bck_tria[i]->neigh);
	222	free(bck_tria[i]);
	223
	224	}
	225	free(bck_bond);
	226
	227	fprintf(stderr,"Restoration complete!!!\n");
	228
b866cf	229	return TS_FAIL;
M	230	}
	231	}
	232	/* IF BONDFLIP ACCEPTED, THEN RETURN SUCCESS! */
2870ab	233	fprintf(stderr,"SUCCESS!!!\n");
SP	234
	235	// delete all backups
	236	for(i=0;i<4;i++){
	237	vtx_free(bck_vtx[i]);
	238
	239	free(bck_tria[i]->neigh);
	240	free(bck_tria[i]);
	241
	242	}
	243	free(bck_bond);
b866cf	244	return TS_SUCCESS;
aec47d	245	}
SP	246
	247
b866cf	248	ts_bool ts_flip_bond(ts_vertex k,ts_vertex it,ts_vertex km, ts_vertex kp,
M	249	ts_bond bond, ts_triangle lm, ts_triangle lp, ts_triangle lm2, ts_triangle *lp1){
	250
	251	ts_uint i; //lmidx, lpidx;
	252	if(k==NULL \|\| it==NULL \|\| km==NULL \|\| kp==NULL){
	253	fatal("ts_flip_bond: You called me with invalid pointers to vertices",999);
	254	}
aec47d	255	// 2. step. We change the triangle vertices... (actual bond flip)
SP	256	for(i=0;i<3;i++) if(lm->vertex[i]== it) lm->vertex[i]= kp;
	257	for(i=0;i<3;i++) if(lp->vertex[i]== k) lp->vertex[i]= km;
e19e79	258	//fprintf(stderr,"2. step: actual bondflip made\n");
aec47d	259	// 2a. step. If any changes in triangle calculations must be done, do it here!
SP	260	// * normals are recalculated here
	261	triangle_normal_vector(lp);
	262	triangle_normal_vector(lm);
e19e79	263	//fprintf(stderr,"2a. step: triangle normals recalculated\n");
aec47d	264	// 3. step. Correct neighbours in vertex_list
SP	265
	266
30ee9c	267	vtx_remove_neighbour(k,it);
306559	268	// vtx_remove_neighbour(it,k);
e19e79	269	//fprintf(stderr,"3. step (PROGRESS): removed k and it neighbours\n");
306559	270
aec47d	271	//Tukaj pa nastopi tezava... Kam dodati soseda?
30ee9c	272	vtx_insert_neighbour(km,kp,k);
SP	273	vtx_insert_neighbour(kp,km,it);
aec47d	274	// vertex_add_neighbour(km,kp); //pazi na vrstni red.
SP	275	// vertex_add_neighbour(kp,km);
e19e79	276	//fprintf(stderr,"3. step: vertex neighbours corrected\n");
aec47d	277
SP	278	// 3a. step. If any changes to ts_vertex, do it here!
	279	// bond_length calculatons not required for it is done in energy.c
	280
	281	// 4. step. Correct bond_list (don't know why I still have it!)
	282	bond->vtx1=km;
	283	bond->vtx2=kp;
	284	//fprintf(stderr,"4. step: bondlist corrected\n");
	285
	286
	287	// 5. step. Correct neighbouring triangles
	288
	289	triangle_remove_neighbour(lp,lp1);
e19e79	290	// fprintf(stderr,".\n");
aec47d	291	triangle_remove_neighbour(lp1,lp);
SP	292	// fprintf(stderr,".\n");
	293	triangle_remove_neighbour(lm,lm2);
	294	// fprintf(stderr,".\n");
	295	triangle_remove_neighbour(lm2,lm);
	296
	297	triangle_add_neighbour(lm,lp1);
	298	triangle_add_neighbour(lp1,lm);
	299	triangle_add_neighbour(lp,lm2); //Vrstni red?!
	300	triangle_add_neighbour(lm2,lp);
	301
	302	//fprintf(stderr,"5. step: triangle neigbours corrected\n");
	303
	304
	305	// 6. step. Correct tristar for vertices km, kp, k and it
	306	vertex_add_tristar(km,lp); // Preveri vrstni red!
	307	vertex_add_tristar(kp,lm);
30ee9c	308	vtx_remove_tristar(it,lm);
SP	309	vtx_remove_tristar(k,lp);
aec47d	310	//fprintf(stderr,"6. step: tristar corrected\n");
SP	311	energy_vertex(k);
	312	energy_vertex(kp);
	313	energy_vertex(km);
	314	energy_vertex(it);
	315	// END modifications to data structure!
	316	return TS_SUCCESS;
	317	}