trisurf-ng.git - Gitblit

Samo Penic

2014-11-12 43e534d0d6499cf47569787f2468a6941bd03721

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>
fbcbdf	15	#include "constvol.h"
aec47d	16
SP	17	ts_bool single_bondflip_timestep(ts_vesicle vesicle, ts_bond bond, ts_double *rn){
	18	/*c Vertex and triangle (lm and lp) indexing for bond flip:
	19	c +----- k-------+ +----- k ------+
	20	c \|lm1 / \| \ lp1 \| \|lm1 / \ lp1 \|
	21	c \| / \| \ \| \| / \ \|
	22	c \|/ \| \ \| FLIP \|/ lm \ \|
	23	c km lm \| lp kp ---> km ---------- kp
	24	c \|\ \| / \| \|\ lp / \|
	25	c \| \ \| / \| \| \ / \|
	26	c \|lm2 \ \| / lp2 \| \|lm2 \ / lp2 \|
	27	c +------it------+ +----- it -----+
	28	c
	29	*/
	30	ts_vertex *it=bond->vtx1;
	31	ts_vertex *k=bond->vtx2;
	32	ts_uint nei,neip,neim;
b866cf	33	ts_uint i,j;
c0ae90	34	ts_double oldenergy, delta_energy, dvol=0.0, darea=0.0;
b866cf	35	ts_triangle lm=NULL,lp=NULL, lp1=NULL, lm2=NULL;
aec47d	36
SP	37	ts_vertex kp,km;
fbcbdf	38
SP	39	ts_double delta_energy_cv;
	40	ts_vertex constvol_vtx_moved, constvol_vtx_backup;
	41	ts_bool retval;
aec47d	42
SP	43	if(it->neigh_no< 3) return TS_FAIL;
	44	if(k->neigh_no< 3) return TS_FAIL;
	45	if(k==NULL \|\| it==NULL){
	46	fatal("In bondflip, number of neighbours of k or it is less than 3!",999);
	47	}
	48
30ee9c	49	nei=0;
aec47d	50	for(i=0;i<it->neigh_no;i++){ // Finds the nn of it, that is k
SP	51	if(it->neigh[i]==k){
	52	nei=i;
	53	break;
	54	}
	55	}
	56	neip=nei+1; // I don't like it.. Smells like I must have it in correct order
	57	neim=nei-1;
	58	if(neip>=it->neigh_no) neip=0;
	59	if((ts_int)neim<0) neim=it->neigh_no-1; /* casting is essential... If not
	60	there the neim is never <0 !!! */
	61	// fprintf(stderr,"The numbers are: %u %u\n",neip, neim);
	62	km=it->neigh[neim]; // We located km and kp
	63	kp=it->neigh[neip];
	64
	65	if(km==NULL \|\| kp==NULL){
	66	fatal("In bondflip, cannot determine km and kp!",999);
	67	}
	68
	69	// fprintf(stderr,"I WAS HERE! after the 4 vertices are known!\n");
	70
	71	/* test if the membrane is wrapped too much, so that kp is nearest neighbour of
	72	* km. If it is true, then don't flip! */
	73	for(i=0;i<km->neigh_no;i++){
	74	if(km->neigh[i] == kp) return TS_FAIL;
	75	}
	76	// fprintf(stderr,"Membrane didn't wrap too much.. Continue.\n");
	77	/* if bond would be too long, return... */
30ee9c	78	if(vtx_distance_sq(km,kp) > vesicle->dmax ) return TS_FAIL;
aec47d	79	// fprintf(stderr,"Bond will not be too long.. Continue.\n");
SP	80
	81	/* we make a bond flip. this is different than in original fortran */
b866cf	82	// find lm, lp
aec47d	83	// 1. step. We find lm and lp from k->tristar !
SP	84	for(i=0;i<it->tristar_no;i++){
	85	for(j=0;j<k->tristar_no;j++){
	86	if((it->tristar[i] == k->tristar[j])){ //ce gre za skupen trikotnik
	87	if((it->tristar[i]->vertex[0] == km \|\| it->tristar[i]->vertex[1]
	88	== km \|\| it->tristar[i]->vertex[2]== km )){
	89	lm=it->tristar[i];
	90	// lmidx=i;
	91	}
	92	else
	93	{
	94	lp=it->tristar[i];
	95	// lpidx=i;
	96	}
	97
	98	}
	99	}
	100	}
	101	if(lm==NULL \|\| lp==NULL) fatal("ts_flip_bond: Cannot find triangles lm and lp!",999);
	102
	103	//we look for important triangles lp1 and lm2.
	104
	105	for(i=0;i<k->tristar_no;i++){
	106	for(j=0;j<kp->tristar_no;j++){
	107	if((k->tristar[i] == kp->tristar[j]) && k->tristar[i]!=lp){ //ce gre za skupen trikotnik
	108	lp1=k->tristar[i];
	109	}
	110	}
	111	}
	112
	113	for(i=0;i<it->tristar_no;i++){
	114	for(j=0;j<km->tristar_no;j++){
	115	if((it->tristar[i] == km->tristar[j]) && it->tristar[i]!=lm){ //ce gre za skupen trikotnik
	116	lm2=it->tristar[i];
	117	}
	118	}
	119	}
	120
	121	if(lm2==NULL \|\| lp1==NULL) fatal("ts_flip_bond: Cannot find triangles lm2 and lp1!",999);
2870ab	122
SP	123
	124	/* backup old structure */
	125	/* need to backup:
	126	* vertices k, kp, km, it
	127	* triangles lm, lp, lm2, lp1
	128	* bond
	129	*/
	130	ts_vertex *bck_vtx[4];
	131	ts_triangle *bck_tria[4];
	132	ts_bond *bck_bond;
	133	ts_vertex *orig_vtx[]={k,it,kp,km};
7efbb1	134	ts_triangle *orig_tria[]={lm,lp,lm2,lp1};
2870ab	135
7efbb1	136	//fprintf(stderr,"Backuping!!!\n");
SP	137	bck_bond=(ts_bond *)malloc(sizeof(ts_bond));
2870ab	138	for(i=0;i<4;i++){
7efbb1	139	/* fprintf(stderr,"vtx neigh[%d]=",i);
SP	140	for(j=0;j<orig_vtx[i]->neigh_no;j++) fprintf(stderr," %d", orig_vtx[i]->neigh[j]->idx);
	141	fprintf(stderr,"\n");
	142	*/
2870ab	143	bck_vtx[i]=(ts_vertex *)malloc(sizeof(ts_vertex));
SP	144	bck_tria[i]=(ts_triangle *)malloc(sizeof(ts_triangle));
7efbb1	145	memcpy((void )bck_vtx[i],(void )orig_vtx[i],sizeof(ts_vertex));
SP	146	memcpy((void )bck_tria[i],(void )orig_tria[i],sizeof(ts_triangle));
2870ab	147	/* level 2 pointers */
7efbb1	148
2870ab	149	bck_vtx[i]->neigh=(ts_vertex *)malloc(orig_vtx[i]->neigh_nosizeof(ts_vertex *));
SP	150	bck_vtx[i]->tristar=(ts_triangle *)malloc(orig_vtx[i]->tristar_nosizeof(ts_triangle *));
	151	bck_vtx[i]->bond=(ts_bond *)malloc(orig_vtx[i]->bond_nosizeof(ts_bond *));
	152	bck_tria[i]->neigh=(ts_triangle *)malloc(orig_tria[i]->neigh_nosizeof(ts_triangle *));
	153
7efbb1	154	memcpy((void )bck_vtx[i]->neigh,(void )orig_vtx[i]->neigh,orig_vtx[i]->neigh_nosizeof(ts_vertex ));
SP	155	memcpy((void )bck_vtx[i]->tristar,(void )orig_vtx[i]->tristar,orig_vtx[i]->tristar_nosizeof(ts_triangle ));
	156	memcpy((void )bck_vtx[i]->bond,(void )orig_vtx[i]->bond,orig_vtx[i]->bond_nosizeof(ts_bond ));
b866cf	157
7efbb1	158	memcpy((void )bck_tria[i]->neigh,(void )orig_tria[i]->neigh,orig_tria[i]->neigh_nosizeof(ts_triangle ));
SP	159	}
	160	memcpy(bck_bond,bond,sizeof(ts_bond));
	161	//fprintf(stderr,"Backup complete!!!\n");
	162	/* end backup vertex */
	163
414b8a	164	/* Save old energy */
b866cf	165	oldenergy=0;
M	166	oldenergy+=k->xk* k->energy;
	167	oldenergy+=kp->xk* kp->energy;
	168	oldenergy+=km->xk* km->energy;
	169	oldenergy+=it->xk* it->energy;
414b8a	170	//Neigbours of k, it, km, kp don't change its energy.
aec47d	171
1121fa	172	if(vesicle->pswitch == 1 \|\| vesicle->tape->constvolswitch>0){dvol = -lm->volume - lp->volume;}
c0ae90	173	if(vesicle->tape->constareaswitch==2){darea=-lm->area-lp->area;}
dd5aca	174	/* vesicle_volume(vesicle);
SP	175	fprintf(stderr,"Volume in the beginning=%1.16e\n", vesicle->volume);
	176	*/
414b8a	177
M	178	/* fix data structure for flipped bond */
	179	ts_flip_bond(k,it,km,kp, bond,lm, lp, lm2, lp1);
aec47d	180
SP	181
b866cf	182	/* Calculating the new energy */
M	183	delta_energy=0;
	184	delta_energy+=k->xk* k->energy;
	185	delta_energy+=kp->xk* kp->energy;
	186	delta_energy+=km->xk* km->energy;
	187	delta_energy+=it->xk* it->energy;
414b8a	188	//Neigbours of k, it, km, kp don't change its energy.
M	189
fbcbdf	190	delta_energy-=oldenergy;
1121fa	191	if(vesicle->pswitch == 1 \|\| vesicle->tape->constvolswitch>0){
414b8a	192	dvol = dvol + lm->volume + lp->volume;
fbcbdf	193	if(vesicle->pswitch==1) delta_energy-= vesicle->pressure*dvol;
414b8a	194	}
c0ae90	195	if(vesicle->tape->constareaswitch==2){
SP	196	darea=darea+lm->area+lp->area;
	197	/check whether the dvol is gt than epsvol /
	198	if(fabs(vesicle->area+darea-A0)>epsarea){
	199	//restore old state.
	200	/* restoration procedure copied from few lines below */
	201	for(i=0;i<4;i++){
	202	// fprintf(stderr,"Restoring vtx neigh[%d] with neighbours %d\n",i, orig_vtx[i]->neigh_no );
	203	free(orig_vtx[i]->neigh);
	204	free(orig_vtx[i]->tristar);
	205	free(orig_vtx[i]->bond);
	206	free(orig_tria[i]->neigh);
	207	memcpy((void )orig_vtx[i],(void )bck_vtx[i],sizeof(ts_vertex));
	208	memcpy((void )orig_tria[i],(void )bck_tria[i],sizeof(ts_triangle));
	209	// fprintf(stderr,"Restored vtx neigh[%d] with neighbours %d\n",i, orig_vtx[i]->neigh_no );
	210	/* level 2 pointers are redirected*/
	211	}
	212	memcpy(bond,bck_bond,sizeof(ts_bond));
	213	for(i=0;i<4;i++){
	214	free(bck_vtx[i]);
	215	free(bck_tria[i]);
	216	/* fprintf(stderr,"Restoring vtx neigh[%d] with neighbours %d =",i, orig_vtx[i]->neigh_no );
	217	for(j=0;j<orig_vtx[i]->neigh_no;j++) fprintf(stderr," %d", orig_vtx[i]->neigh[j]->idx);
	218	fprintf(stderr,"\n"); */
	219	}
	220	free(bck_bond);
	221	return TS_FAIL;
	222
	223	}
	224	}
	225
	226
	227
fbcbdf	228
1121fa	229	if(vesicle->tape->constvolswitch == 2){
SP	230	/check whether the dvol is gt than epsvol /
	231	if(fabs(vesicle->volume+dvol-V0)>epsvol){
	232	//restore old state.
	233	/* restoration procedure copied from few lines below */
	234	for(i=0;i<4;i++){
	235	// fprintf(stderr,"Restoring vtx neigh[%d] with neighbours %d\n",i, orig_vtx[i]->neigh_no );
	236	free(orig_vtx[i]->neigh);
	237	free(orig_vtx[i]->tristar);
	238	free(orig_vtx[i]->bond);
	239	free(orig_tria[i]->neigh);
	240	memcpy((void )orig_vtx[i],(void )bck_vtx[i],sizeof(ts_vertex));
	241	memcpy((void )orig_tria[i],(void )bck_tria[i],sizeof(ts_triangle));
	242	// fprintf(stderr,"Restored vtx neigh[%d] with neighbours %d\n",i, orig_vtx[i]->neigh_no );
	243	/* level 2 pointers are redirected*/
	244	}
	245	memcpy(bond,bck_bond,sizeof(ts_bond));
	246	for(i=0;i<4;i++){
	247	free(bck_vtx[i]);
	248	free(bck_tria[i]);
	249	/* fprintf(stderr,"Restoring vtx neigh[%d] with neighbours %d =",i, orig_vtx[i]->neigh_no );
	250	for(j=0;j<orig_vtx[i]->neigh_no;j++) fprintf(stderr," %d", orig_vtx[i]->neigh[j]->idx);
	251	fprintf(stderr,"\n"); */
	252	}
	253	free(bck_bond);
	254	return TS_FAIL;
	255
	256	}
	257
	258	} else
fbcbdf	259	if(vesicle->tape->constvolswitch == 1){
dd5aca	260	retval=constvolume(vesicle, it, -dvol, &delta_energy_cv, &constvol_vtx_moved,&constvol_vtx_backup);
fbcbdf	261	if(retval==TS_FAIL){
SP	262	/* restoration procedure copied from few lines below */
dd5aca	263	for(i=0;i<4;i++){
SP	264	// fprintf(stderr,"Restoring vtx neigh[%d] with neighbours %d\n",i, orig_vtx[i]->neigh_no );
	265	free(orig_vtx[i]->neigh);
	266	free(orig_vtx[i]->tristar);
	267	free(orig_vtx[i]->bond);
	268	free(orig_tria[i]->neigh);
	269	memcpy((void )orig_vtx[i],(void )bck_vtx[i],sizeof(ts_vertex));
	270	memcpy((void )orig_tria[i],(void )bck_tria[i],sizeof(ts_triangle));
	271	// fprintf(stderr,"Restored vtx neigh[%d] with neighbours %d\n",i, orig_vtx[i]->neigh_no );
	272	/* level 2 pointers are redirected*/
	273	}
	274	memcpy(bond,bck_bond,sizeof(ts_bond));
	275	for(i=0;i<4;i++){
	276	free(bck_vtx[i]);
	277	free(bck_tria[i]);
	278	/* fprintf(stderr,"Restoring vtx neigh[%d] with neighbours %d =",i, orig_vtx[i]->neigh_no );
	279	for(j=0;j<orig_vtx[i]->neigh_no;j++) fprintf(stderr," %d", orig_vtx[i]->neigh[j]->idx);
	280	fprintf(stderr,"\n"); */
	281	}
	282	free(bck_bond);
	283	return TS_FAIL;
fbcbdf	284	}
b2fa8c	285	delta_energy+=delta_energy_cv;
fbcbdf	286	}
SP	287
414b8a	288
b866cf	289	/* MONTE CARLO */
M	290	if(delta_energy>=0){
	291	#ifdef TS_DOUBLE_DOUBLE
fbcbdf	292	if(exp(-delta_energy)< drand48())
b866cf	293	#endif
M	294	#ifdef TS_DOUBLE_FLOAT
	295	if(expf(-delta_energy)< (ts_float)drand48())
	296	#endif
	297	#ifdef TS_DOUBLE_LONGDOUBLE
	298	if(expl(-delta_energy)< (ts_ldouble)drand48())
	299	#endif
	300	{
	301	//not accepted, reverting changes
7efbb1	302	//restore all backups
SP	303	// fprintf(stderr,"Restoring!!!\n");
b2fa8c	304	if(vesicle->tape->constvolswitch == 1){
SP	305	constvolumerestore(constvol_vtx_moved,constvol_vtx_backup);
	306	}
aec47d	307
7efbb1	308	for(i=0;i<4;i++){
SP	309	// fprintf(stderr,"Restoring vtx neigh[%d] with neighbours %d\n",i, orig_vtx[i]->neigh_no );
	310	free(orig_vtx[i]->neigh);
	311	free(orig_vtx[i]->tristar);
	312	free(orig_vtx[i]->bond);
	313	free(orig_tria[i]->neigh);
	314	memcpy((void )orig_vtx[i],(void )bck_vtx[i],sizeof(ts_vertex));
	315	memcpy((void )orig_tria[i],(void )bck_tria[i],sizeof(ts_triangle));
	316	// fprintf(stderr,"Restored vtx neigh[%d] with neighbours %d\n",i, orig_vtx[i]->neigh_no );
	317	/* level 2 pointers are redirected*/
	318	}
	319	memcpy(bond,bck_bond,sizeof(ts_bond));
2870ab	320
7efbb1	321	for(i=0;i<4;i++){
SP	322	free(bck_vtx[i]);
	323	free(bck_tria[i]);
	324	/* fprintf(stderr,"Restoring vtx neigh[%d] with neighbours %d =",i, orig_vtx[i]->neigh_no );
	325	for(j=0;j<orig_vtx[i]->neigh_no;j++) fprintf(stderr," %d", orig_vtx[i]->neigh[j]->idx);
	326	fprintf(stderr,"\n"); */
	327	}
2870ab	328
SP	329	free(bck_bond);
fbcbdf	330
7efbb1	331	// fprintf(stderr,"Restoration complete!!!\n");
dd5aca	332	// vesicle_volume(vesicle);
SP	333	// fprintf(stderr,"Volume after fail=%1.16e\n", vesicle->volume);
2870ab	334
7efbb1	335	return TS_FAIL;
b866cf	336	}
M	337	}
	338	/* IF BONDFLIP ACCEPTED, THEN RETURN SUCCESS! */
fbcbdf	339	// fprintf(stderr,"SUCCESS!!!\n");
2870ab	340
c0ae90	341	if(vesicle->tape->constvolswitch == 2){
SP	342	vesicle->volume+=dvol;
	343	} else if(vesicle->tape->constvolswitch == 1){
b2fa8c	344	constvolumeaccept(vesicle,constvol_vtx_moved,constvol_vtx_backup);
SP	345	}
c0ae90	346	if(vesicle->tape->constareaswitch==2){
SP	347	vesicle->area+=darea;
	348	}
2870ab	349	// delete all backups
SP	350	for(i=0;i<4;i++){
7efbb1	351	free(bck_vtx[i]->neigh);
SP	352	free(bck_vtx[i]->bond);
	353	free(bck_vtx[i]->tristar);
	354	free(bck_vtx[i]);
2870ab	355	free(bck_tria[i]->neigh);
SP	356	free(bck_tria[i]);
7efbb1	357	/* fprintf(stderr,"Afret backup deletion vtx neigh[%d]=",i);
SP	358	for(j=0;j<orig_vtx[i]->neigh_no;j++) fprintf(stderr," %d", orig_vtx[i]->neigh[j]->idx);
	359	fprintf(stderr,"\n");
	360	*/
2870ab	361	}
7efbb1	362	free(bck_bond);
SP	363
dd5aca	364	// vesicle_volume(vesicle);
SP	365	// fprintf(stderr,"Volume after success=%1.16e\n", vesicle->volume);
b866cf	366	return TS_SUCCESS;
aec47d	367	}
SP	368
	369
b866cf	370	ts_bool ts_flip_bond(ts_vertex k,ts_vertex it,ts_vertex km, ts_vertex kp,
M	371	ts_bond bond, ts_triangle lm, ts_triangle lp, ts_triangle lm2, ts_triangle *lp1){
	372
	373	ts_uint i; //lmidx, lpidx;
	374	if(k==NULL \|\| it==NULL \|\| km==NULL \|\| kp==NULL){
	375	fatal("ts_flip_bond: You called me with invalid pointers to vertices",999);
	376	}
aec47d	377	// 2. step. We change the triangle vertices... (actual bond flip)
SP	378	for(i=0;i<3;i++) if(lm->vertex[i]== it) lm->vertex[i]= kp;
	379	for(i=0;i<3;i++) if(lp->vertex[i]== k) lp->vertex[i]= km;
e19e79	380	//fprintf(stderr,"2. step: actual bondflip made\n");
aec47d	381	// 2a. step. If any changes in triangle calculations must be done, do it here!
SP	382	// * normals are recalculated here
	383	triangle_normal_vector(lp);
	384	triangle_normal_vector(lm);
e19e79	385	//fprintf(stderr,"2a. step: triangle normals recalculated\n");
aec47d	386	// 3. step. Correct neighbours in vertex_list
SP	387
	388
30ee9c	389	vtx_remove_neighbour(k,it);
306559	390	// vtx_remove_neighbour(it,k);
e19e79	391	//fprintf(stderr,"3. step (PROGRESS): removed k and it neighbours\n");
306559	392
aec47d	393	//Tukaj pa nastopi tezava... Kam dodati soseda?
30ee9c	394	vtx_insert_neighbour(km,kp,k);
SP	395	vtx_insert_neighbour(kp,km,it);
aec47d	396	// vertex_add_neighbour(km,kp); //pazi na vrstni red.
SP	397	// vertex_add_neighbour(kp,km);
e19e79	398	//fprintf(stderr,"3. step: vertex neighbours corrected\n");
aec47d	399
SP	400	// 3a. step. If any changes to ts_vertex, do it here!
	401	// bond_length calculatons not required for it is done in energy.c
	402
	403	// 4. step. Correct bond_list (don't know why I still have it!)
	404	bond->vtx1=km;
	405	bond->vtx2=kp;
	406	//fprintf(stderr,"4. step: bondlist corrected\n");
	407
	408
	409	// 5. step. Correct neighbouring triangles
	410
	411	triangle_remove_neighbour(lp,lp1);
e19e79	412	// fprintf(stderr,".\n");
aec47d	413	triangle_remove_neighbour(lp1,lp);
SP	414	// fprintf(stderr,".\n");
	415	triangle_remove_neighbour(lm,lm2);
	416	// fprintf(stderr,".\n");
	417	triangle_remove_neighbour(lm2,lm);
	418
	419	triangle_add_neighbour(lm,lp1);
	420	triangle_add_neighbour(lp1,lm);
	421	triangle_add_neighbour(lp,lm2); //Vrstni red?!
	422	triangle_add_neighbour(lm2,lp);
	423
	424	//fprintf(stderr,"5. step: triangle neigbours corrected\n");
	425
	426
	427	// 6. step. Correct tristar for vertices km, kp, k and it
	428	vertex_add_tristar(km,lp); // Preveri vrstni red!
	429	vertex_add_tristar(kp,lm);
30ee9c	430	vtx_remove_tristar(it,lm);
SP	431	vtx_remove_tristar(k,lp);
aec47d	432	//fprintf(stderr,"6. step: tristar corrected\n");
SP	433	energy_vertex(k);
	434	energy_vertex(kp);
	435	energy_vertex(km);
	436	energy_vertex(it);
	437	// END modifications to data structure!
	438	return TS_SUCCESS;
	439	}