trisurf-ng.git - Gitblit

Fixed some bugs in cluster.c, added a line in cluster.h

Samo Penic

2016-07-05 8c91d2bcad7df7c647f1379483673183329ddfe8

commit \| author \| age
7f6076	1	/* vim: set ts=4 sts=4 sw=4 noet : */
aec47d	2	#include<stdlib.h>
SP	3	#include<math.h>
	4	#include "general.h"
	5	#include "vertex.h"
	6	#include "bond.h"
	7	#include "triangle.h"
	8	#include "vesicle.h"
	9	#include "energy.h"
	10	#include "timestep.h"
	11	#include "cell.h"
30ee9c	12	#include "bondflip.h"
aec47d	13	//#include "io.h"
SP	14	#include<stdio.h>
2870ab	15	#include<string.h>
fbcbdf	16	#include "constvol.h"
aec47d	17
SP	18	ts_bool single_bondflip_timestep(ts_vesicle vesicle, ts_bond bond, ts_double *rn){
	19	/*c Vertex and triangle (lm and lp) indexing for bond flip:
	20	c +----- k-------+ +----- k ------+
	21	c \|lm1 / \| \ lp1 \| \|lm1 / \ lp1 \|
	22	c \| / \| \ \| \| / \ \|
	23	c \|/ \| \ \| FLIP \|/ lm \ \|
	24	c km lm \| lp kp ---> km ---------- kp
	25	c \|\ \| / \| \|\ lp / \|
	26	c \| \ \| / \| \| \ / \|
	27	c \|lm2 \ \| / lp2 \| \|lm2 \ / lp2 \|
	28	c +------it------+ +----- it -----+
	29	c
	30	*/
	31	ts_vertex *it=bond->vtx1;
	32	ts_vertex *k=bond->vtx2;
	33	ts_uint nei,neip,neim;
b866cf	34	ts_uint i,j;
c0ae90	35	ts_double oldenergy, delta_energy, dvol=0.0, darea=0.0;
b866cf	36	ts_triangle lm=NULL,lp=NULL, lp1=NULL, lm2=NULL;
aec47d	37
SP	38	ts_vertex kp,km;
fbcbdf	39
SP	40	ts_double delta_energy_cv;
	41	ts_vertex constvol_vtx_moved, constvol_vtx_backup;
	42	ts_bool retval;
aec47d	43
SP	44	if(it->neigh_no< 3) return TS_FAIL;
	45	if(k->neigh_no< 3) return TS_FAIL;
	46	if(k==NULL \|\| it==NULL){
	47	fatal("In bondflip, number of neighbours of k or it is less than 3!",999);
	48	}
	49
30ee9c	50	nei=0;
aec47d	51	for(i=0;i<it->neigh_no;i++){ // Finds the nn of it, that is k
SP	52	if(it->neigh[i]==k){
	53	nei=i;
	54	break;
	55	}
	56	}
	57	neip=nei+1; // I don't like it.. Smells like I must have it in correct order
	58	neim=nei-1;
	59	if(neip>=it->neigh_no) neip=0;
	60	if((ts_int)neim<0) neim=it->neigh_no-1; /* casting is essential... If not
	61	there the neim is never <0 !!! */
	62	// fprintf(stderr,"The numbers are: %u %u\n",neip, neim);
	63	km=it->neigh[neim]; // We located km and kp
	64	kp=it->neigh[neip];
	65
	66	if(km==NULL \|\| kp==NULL){
	67	fatal("In bondflip, cannot determine km and kp!",999);
	68	}
	69
	70	// fprintf(stderr,"I WAS HERE! after the 4 vertices are known!\n");
	71
	72	/* test if the membrane is wrapped too much, so that kp is nearest neighbour of
	73	* km. If it is true, then don't flip! */
	74	for(i=0;i<km->neigh_no;i++){
	75	if(km->neigh[i] == kp) return TS_FAIL;
	76	}
	77	// fprintf(stderr,"Membrane didn't wrap too much.. Continue.\n");
	78	/* if bond would be too long, return... */
30ee9c	79	if(vtx_distance_sq(km,kp) > vesicle->dmax ) return TS_FAIL;
aec47d	80	// fprintf(stderr,"Bond will not be too long.. Continue.\n");
SP	81
	82	/* we make a bond flip. this is different than in original fortran */
b866cf	83	// find lm, lp
aec47d	84	// 1. step. We find lm and lp from k->tristar !
SP	85	for(i=0;i<it->tristar_no;i++){
	86	for(j=0;j<k->tristar_no;j++){
	87	if((it->tristar[i] == k->tristar[j])){ //ce gre za skupen trikotnik
	88	if((it->tristar[i]->vertex[0] == km \|\| it->tristar[i]->vertex[1]
	89	== km \|\| it->tristar[i]->vertex[2]== km )){
	90	lm=it->tristar[i];
	91	// lmidx=i;
	92	}
	93	else
	94	{
	95	lp=it->tristar[i];
	96	// lpidx=i;
	97	}
	98
	99	}
	100	}
	101	}
	102	if(lm==NULL \|\| lp==NULL) fatal("ts_flip_bond: Cannot find triangles lm and lp!",999);
	103
	104	//we look for important triangles lp1 and lm2.
	105
	106	for(i=0;i<k->tristar_no;i++){
	107	for(j=0;j<kp->tristar_no;j++){
	108	if((k->tristar[i] == kp->tristar[j]) && k->tristar[i]!=lp){ //ce gre za skupen trikotnik
	109	lp1=k->tristar[i];
	110	}
	111	}
	112	}
	113
	114	for(i=0;i<it->tristar_no;i++){
	115	for(j=0;j<km->tristar_no;j++){
	116	if((it->tristar[i] == km->tristar[j]) && it->tristar[i]!=lm){ //ce gre za skupen trikotnik
	117	lm2=it->tristar[i];
	118	}
	119	}
	120	}
	121
	122	if(lm2==NULL \|\| lp1==NULL) fatal("ts_flip_bond: Cannot find triangles lm2 and lp1!",999);
2870ab	123
SP	124
	125	/* backup old structure */
	126	/* need to backup:
	127	* vertices k, kp, km, it
	128	* triangles lm, lp, lm2, lp1
	129	* bond
	130	*/
	131	ts_vertex *bck_vtx[4];
	132	ts_triangle *bck_tria[4];
	133	ts_bond *bck_bond;
	134	ts_vertex *orig_vtx[]={k,it,kp,km};
7efbb1	135	ts_triangle *orig_tria[]={lm,lp,lm2,lp1};
2870ab	136
7efbb1	137	//fprintf(stderr,"Backuping!!!\n");
SP	138	bck_bond=(ts_bond *)malloc(sizeof(ts_bond));
2870ab	139	for(i=0;i<4;i++){
7efbb1	140	/* fprintf(stderr,"vtx neigh[%d]=",i);
SP	141	for(j=0;j<orig_vtx[i]->neigh_no;j++) fprintf(stderr," %d", orig_vtx[i]->neigh[j]->idx);
	142	fprintf(stderr,"\n");
	143	*/
2870ab	144	bck_vtx[i]=(ts_vertex *)malloc(sizeof(ts_vertex));
SP	145	bck_tria[i]=(ts_triangle *)malloc(sizeof(ts_triangle));
7efbb1	146	memcpy((void )bck_vtx[i],(void )orig_vtx[i],sizeof(ts_vertex));
SP	147	memcpy((void )bck_tria[i],(void )orig_tria[i],sizeof(ts_triangle));
2870ab	148	/* level 2 pointers */
7efbb1	149
2870ab	150	bck_vtx[i]->neigh=(ts_vertex *)malloc(orig_vtx[i]->neigh_nosizeof(ts_vertex *));
SP	151	bck_vtx[i]->tristar=(ts_triangle *)malloc(orig_vtx[i]->tristar_nosizeof(ts_triangle *));
	152	bck_vtx[i]->bond=(ts_bond *)malloc(orig_vtx[i]->bond_nosizeof(ts_bond *));
	153	bck_tria[i]->neigh=(ts_triangle *)malloc(orig_tria[i]->neigh_nosizeof(ts_triangle *));
	154
7efbb1	155	memcpy((void )bck_vtx[i]->neigh,(void )orig_vtx[i]->neigh,orig_vtx[i]->neigh_nosizeof(ts_vertex ));
SP	156	memcpy((void )bck_vtx[i]->tristar,(void )orig_vtx[i]->tristar,orig_vtx[i]->tristar_nosizeof(ts_triangle ));
	157	memcpy((void )bck_vtx[i]->bond,(void )orig_vtx[i]->bond,orig_vtx[i]->bond_nosizeof(ts_bond ));
b866cf	158
7efbb1	159	memcpy((void )bck_tria[i]->neigh,(void )orig_tria[i]->neigh,orig_tria[i]->neigh_nosizeof(ts_triangle ));
SP	160	}
	161	memcpy(bck_bond,bond,sizeof(ts_bond));
	162	//fprintf(stderr,"Backup complete!!!\n");
	163	/* end backup vertex */
	164
414b8a	165	/* Save old energy */
b866cf	166	oldenergy=0;
M	167	oldenergy+=k->xk* k->energy;
	168	oldenergy+=kp->xk* kp->energy;
	169	oldenergy+=km->xk* km->energy;
	170	oldenergy+=it->xk* it->energy;
032273	171	oldenergy+=bond->energy; /* attraction with neighboring vertices, that have spontaneous curvature */
414b8a	172	//Neigbours of k, it, km, kp don't change its energy.
aec47d	173
1121fa	174	if(vesicle->pswitch == 1 \|\| vesicle->tape->constvolswitch>0){dvol = -lm->volume - lp->volume;}
c0ae90	175	if(vesicle->tape->constareaswitch==2){darea=-lm->area-lp->area;}
dd5aca	176	/* vesicle_volume(vesicle);
SP	177	fprintf(stderr,"Volume in the beginning=%1.16e\n", vesicle->volume);
	178	*/
414b8a	179
M	180	/* fix data structure for flipped bond */
032273	181	ts_flip_bond(k,it,km,kp, bond,lm, lp, lm2, lp1, vesicle->tape->w);
aec47d	182
SP	183
b866cf	184	/* Calculating the new energy */
M	185	delta_energy=0;
	186	delta_energy+=k->xk* k->energy;
	187	delta_energy+=kp->xk* kp->energy;
	188	delta_energy+=km->xk* km->energy;
	189	delta_energy+=it->xk* it->energy;
032273	190	delta_energy+=bond->energy; /* attraction with neighboring vertices, that have spontaneous curvature */
414b8a	191	//Neigbours of k, it, km, kp don't change its energy.
M	192
fbcbdf	193	delta_energy-=oldenergy;
1121fa	194	if(vesicle->pswitch == 1 \|\| vesicle->tape->constvolswitch>0){
414b8a	195	dvol = dvol + lm->volume + lp->volume;
fbcbdf	196	if(vesicle->pswitch==1) delta_energy-= vesicle->pressure*dvol;
414b8a	197	}
c0ae90	198	if(vesicle->tape->constareaswitch==2){
SP	199	darea=darea+lm->area+lp->area;
	200	/check whether the dvol is gt than epsvol /
	201	if(fabs(vesicle->area+darea-A0)>epsarea){
	202	//restore old state.
	203	/* restoration procedure copied from few lines below */
	204	for(i=0;i<4;i++){
	205	// fprintf(stderr,"Restoring vtx neigh[%d] with neighbours %d\n",i, orig_vtx[i]->neigh_no );
	206	free(orig_vtx[i]->neigh);
	207	free(orig_vtx[i]->tristar);
	208	free(orig_vtx[i]->bond);
	209	free(orig_tria[i]->neigh);
	210	memcpy((void )orig_vtx[i],(void )bck_vtx[i],sizeof(ts_vertex));
	211	memcpy((void )orig_tria[i],(void )bck_tria[i],sizeof(ts_triangle));
	212	// fprintf(stderr,"Restored vtx neigh[%d] with neighbours %d\n",i, orig_vtx[i]->neigh_no );
	213	/* level 2 pointers are redirected*/
	214	}
	215	memcpy(bond,bck_bond,sizeof(ts_bond));
	216	for(i=0;i<4;i++){
	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	}
	223	free(bck_bond);
	224	return TS_FAIL;
	225
	226	}
	227	}
	228
	229
	230
fbcbdf	231
1121fa	232	if(vesicle->tape->constvolswitch == 2){
SP	233	/check whether the dvol is gt than epsvol /
	234	if(fabs(vesicle->volume+dvol-V0)>epsvol){
	235	//restore old state.
	236	/* restoration procedure copied from few lines below */
	237	for(i=0;i<4;i++){
	238	// fprintf(stderr,"Restoring vtx neigh[%d] with neighbours %d\n",i, orig_vtx[i]->neigh_no );
	239	free(orig_vtx[i]->neigh);
	240	free(orig_vtx[i]->tristar);
	241	free(orig_vtx[i]->bond);
	242	free(orig_tria[i]->neigh);
	243	memcpy((void )orig_vtx[i],(void )bck_vtx[i],sizeof(ts_vertex));
	244	memcpy((void )orig_tria[i],(void )bck_tria[i],sizeof(ts_triangle));
	245	// fprintf(stderr,"Restored vtx neigh[%d] with neighbours %d\n",i, orig_vtx[i]->neigh_no );
	246	/* level 2 pointers are redirected*/
	247	}
	248	memcpy(bond,bck_bond,sizeof(ts_bond));
	249	for(i=0;i<4;i++){
	250	free(bck_vtx[i]);
	251	free(bck_tria[i]);
	252	/* fprintf(stderr,"Restoring vtx neigh[%d] with neighbours %d =",i, orig_vtx[i]->neigh_no );
	253	for(j=0;j<orig_vtx[i]->neigh_no;j++) fprintf(stderr," %d", orig_vtx[i]->neigh[j]->idx);
	254	fprintf(stderr,"\n"); */
	255	}
	256	free(bck_bond);
	257	return TS_FAIL;
	258
	259	}
	260
	261	} else
fbcbdf	262	if(vesicle->tape->constvolswitch == 1){
dd5aca	263	retval=constvolume(vesicle, it, -dvol, &delta_energy_cv, &constvol_vtx_moved,&constvol_vtx_backup);
fbcbdf	264	if(retval==TS_FAIL){
SP	265	/* restoration procedure copied from few lines below */
dd5aca	266	for(i=0;i<4;i++){
SP	267	// fprintf(stderr,"Restoring vtx neigh[%d] with neighbours %d\n",i, orig_vtx[i]->neigh_no );
	268	free(orig_vtx[i]->neigh);
	269	free(orig_vtx[i]->tristar);
	270	free(orig_vtx[i]->bond);
	271	free(orig_tria[i]->neigh);
	272	memcpy((void )orig_vtx[i],(void )bck_vtx[i],sizeof(ts_vertex));
	273	memcpy((void )orig_tria[i],(void )bck_tria[i],sizeof(ts_triangle));
	274	// fprintf(stderr,"Restored vtx neigh[%d] with neighbours %d\n",i, orig_vtx[i]->neigh_no );
	275	/* level 2 pointers are redirected*/
	276	}
	277	memcpy(bond,bck_bond,sizeof(ts_bond));
	278	for(i=0;i<4;i++){
	279	free(bck_vtx[i]);
	280	free(bck_tria[i]);
	281	/* fprintf(stderr,"Restoring vtx neigh[%d] with neighbours %d =",i, orig_vtx[i]->neigh_no );
	282	for(j=0;j<orig_vtx[i]->neigh_no;j++) fprintf(stderr," %d", orig_vtx[i]->neigh[j]->idx);
	283	fprintf(stderr,"\n"); */
	284	}
	285	free(bck_bond);
	286	return TS_FAIL;
fbcbdf	287	}
b2fa8c	288	delta_energy+=delta_energy_cv;
fbcbdf	289	}
SP	290
414b8a	291
b866cf	292	/* MONTE CARLO */
M	293	if(delta_energy>=0){
	294	#ifdef TS_DOUBLE_DOUBLE
fbcbdf	295	if(exp(-delta_energy)< drand48())
b866cf	296	#endif
M	297	#ifdef TS_DOUBLE_FLOAT
	298	if(expf(-delta_energy)< (ts_float)drand48())
	299	#endif
	300	#ifdef TS_DOUBLE_LONGDOUBLE
	301	if(expl(-delta_energy)< (ts_ldouble)drand48())
	302	#endif
	303	{
	304	//not accepted, reverting changes
7efbb1	305	//restore all backups
SP	306	// fprintf(stderr,"Restoring!!!\n");
b2fa8c	307	if(vesicle->tape->constvolswitch == 1){
SP	308	constvolumerestore(constvol_vtx_moved,constvol_vtx_backup);
	309	}
aec47d	310
7efbb1	311	for(i=0;i<4;i++){
SP	312	// fprintf(stderr,"Restoring vtx neigh[%d] with neighbours %d\n",i, orig_vtx[i]->neigh_no );
	313	free(orig_vtx[i]->neigh);
	314	free(orig_vtx[i]->tristar);
	315	free(orig_vtx[i]->bond);
	316	free(orig_tria[i]->neigh);
	317	memcpy((void )orig_vtx[i],(void )bck_vtx[i],sizeof(ts_vertex));
	318	memcpy((void )orig_tria[i],(void )bck_tria[i],sizeof(ts_triangle));
	319	// fprintf(stderr,"Restored vtx neigh[%d] with neighbours %d\n",i, orig_vtx[i]->neigh_no );
	320	/* level 2 pointers are redirected*/
	321	}
	322	memcpy(bond,bck_bond,sizeof(ts_bond));
2870ab	323
7efbb1	324	for(i=0;i<4;i++){
SP	325	free(bck_vtx[i]);
	326	free(bck_tria[i]);
	327	/* fprintf(stderr,"Restoring vtx neigh[%d] with neighbours %d =",i, orig_vtx[i]->neigh_no );
	328	for(j=0;j<orig_vtx[i]->neigh_no;j++) fprintf(stderr," %d", orig_vtx[i]->neigh[j]->idx);
	329	fprintf(stderr,"\n"); */
	330	}
2870ab	331
SP	332	free(bck_bond);
fbcbdf	333
7efbb1	334	// fprintf(stderr,"Restoration complete!!!\n");
dd5aca	335	// vesicle_volume(vesicle);
SP	336	// fprintf(stderr,"Volume after fail=%1.16e\n", vesicle->volume);
2870ab	337
7efbb1	338	return TS_FAIL;
b866cf	339	}
M	340	}
	341	/* IF BONDFLIP ACCEPTED, THEN RETURN SUCCESS! */
fbcbdf	342	// fprintf(stderr,"SUCCESS!!!\n");
2870ab	343
c0ae90	344	if(vesicle->tape->constvolswitch == 2){
SP	345	vesicle->volume+=dvol;
	346	} else if(vesicle->tape->constvolswitch == 1){
b2fa8c	347	constvolumeaccept(vesicle,constvol_vtx_moved,constvol_vtx_backup);
SP	348	}
c0ae90	349	if(vesicle->tape->constareaswitch==2){
SP	350	vesicle->area+=darea;
	351	}
2870ab	352	// delete all backups
SP	353	for(i=0;i<4;i++){
7efbb1	354	free(bck_vtx[i]->neigh);
SP	355	free(bck_vtx[i]->bond);
	356	free(bck_vtx[i]->tristar);
	357	free(bck_vtx[i]);
2870ab	358	free(bck_tria[i]->neigh);
SP	359	free(bck_tria[i]);
7efbb1	360	/* fprintf(stderr,"Afret backup deletion vtx neigh[%d]=",i);
SP	361	for(j=0;j<orig_vtx[i]->neigh_no;j++) fprintf(stderr," %d", orig_vtx[i]->neigh[j]->idx);
	362	fprintf(stderr,"\n");
	363	*/
2870ab	364	}
7efbb1	365	free(bck_bond);
SP	366
dd5aca	367	// vesicle_volume(vesicle);
SP	368	// fprintf(stderr,"Volume after success=%1.16e\n", vesicle->volume);
b866cf	369	return TS_SUCCESS;
aec47d	370	}
SP	371
	372
b866cf	373	ts_bool ts_flip_bond(ts_vertex k,ts_vertex it,ts_vertex km, ts_vertex kp,
032273	374	ts_bond bond, ts_triangle lm, ts_triangle lp, ts_triangle lm2, ts_triangle *lp1, ts_double w_energy){
b866cf	375
M	376	ts_uint i; //lmidx, lpidx;
	377	if(k==NULL \|\| it==NULL \|\| km==NULL \|\| kp==NULL){
	378	fatal("ts_flip_bond: You called me with invalid pointers to vertices",999);
	379	}
aec47d	380	// 2. step. We change the triangle vertices... (actual bond flip)
SP	381	for(i=0;i<3;i++) if(lm->vertex[i]== it) lm->vertex[i]= kp;
	382	for(i=0;i<3;i++) if(lp->vertex[i]== k) lp->vertex[i]= km;
e19e79	383	//fprintf(stderr,"2. step: actual bondflip made\n");
aec47d	384	// 2a. step. If any changes in triangle calculations must be done, do it here!
SP	385	// * normals are recalculated here
	386	triangle_normal_vector(lp);
	387	triangle_normal_vector(lm);
e19e79	388	//fprintf(stderr,"2a. step: triangle normals recalculated\n");
aec47d	389	// 3. step. Correct neighbours in vertex_list
SP	390
	391
30ee9c	392	vtx_remove_neighbour(k,it);
306559	393	// vtx_remove_neighbour(it,k);
e19e79	394	//fprintf(stderr,"3. step (PROGRESS): removed k and it neighbours\n");
306559	395
aec47d	396	//Tukaj pa nastopi tezava... Kam dodati soseda?
30ee9c	397	vtx_insert_neighbour(km,kp,k);
SP	398	vtx_insert_neighbour(kp,km,it);
aec47d	399	// vertex_add_neighbour(km,kp); //pazi na vrstni red.
SP	400	// vertex_add_neighbour(kp,km);
e19e79	401	//fprintf(stderr,"3. step: vertex neighbours corrected\n");
aec47d	402
SP	403	// 3a. step. If any changes to ts_vertex, do it here!
	404	// bond_length calculatons not required for it is done in energy.c
	405
	406	// 4. step. Correct bond_list (don't know why I still have it!)
	407	bond->vtx1=km;
	408	bond->vtx2=kp;
	409	//fprintf(stderr,"4. step: bondlist corrected\n");
	410
	411
	412	// 5. step. Correct neighbouring triangles
	413
	414	triangle_remove_neighbour(lp,lp1);
e19e79	415	// fprintf(stderr,".\n");
aec47d	416	triangle_remove_neighbour(lp1,lp);
SP	417	// fprintf(stderr,".\n");
	418	triangle_remove_neighbour(lm,lm2);
	419	// fprintf(stderr,".\n");
	420	triangle_remove_neighbour(lm2,lm);
	421
	422	triangle_add_neighbour(lm,lp1);
	423	triangle_add_neighbour(lp1,lm);
	424	triangle_add_neighbour(lp,lm2); //Vrstni red?!
	425	triangle_add_neighbour(lm2,lp);
	426
	427	//fprintf(stderr,"5. step: triangle neigbours corrected\n");
	428
	429
	430	// 6. step. Correct tristar for vertices km, kp, k and it
	431	vertex_add_tristar(km,lp); // Preveri vrstni red!
	432	vertex_add_tristar(kp,lm);
30ee9c	433	vtx_remove_tristar(it,lm);
SP	434	vtx_remove_tristar(k,lp);
aec47d	435	//fprintf(stderr,"6. step: tristar corrected\n");
SP	436	energy_vertex(k);
	437	energy_vertex(kp);
	438	energy_vertex(km);
	439	energy_vertex(it);
032273	440	attraction_bond_energy(bond, w_energy);
aec47d	441	// END modifications to data structure!
SP	442	return TS_SUCCESS;
	443	}