trisurf-ng.git - Gitblit

Constant volume in bondflip need lots of debugging

Samo Penic

2014-04-29 fbcbdf4093644e43688d9a44d6553d7153d8a2eb

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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>
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;
414b8a	34	ts_double oldenergy, delta_energy, dvol=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
fbcbdf	172	if(vesicle->pswitch == 1 \|\| vesicle->tape->constvolswitch==1){dvol = -lm->volume - lp->volume;}
414b8a	173
M	174	/* fix data structure for flipped bond */
	175	ts_flip_bond(k,it,km,kp, bond,lm, lp, lm2, lp1);
aec47d	176
SP	177
b866cf	178	/* Calculating the new energy */
M	179	delta_energy=0;
	180	delta_energy+=k->xk* k->energy;
	181	delta_energy+=kp->xk* kp->energy;
	182	delta_energy+=km->xk* km->energy;
	183	delta_energy+=it->xk* it->energy;
414b8a	184	//Neigbours of k, it, km, kp don't change its energy.
M	185
fbcbdf	186	delta_energy-=oldenergy;
SP	187	if(vesicle->pswitch == 1 \|\| vesicle->tape->constvolswitch==1){
414b8a	188	dvol = dvol + lm->volume + lp->volume;
fbcbdf	189	if(vesicle->pswitch==1) delta_energy-= vesicle->pressure*dvol;
414b8a	190	}
fbcbdf	191
SP	192	retval=TS_SUCCESS;
	193	if(vesicle->tape->constvolswitch == 1){
	194	retval=constvolume(vesicle, it, -dvol, &delta_energy_cv, &constvol_vtx_moved,&constvol_vtx_backup);
	195	if(retval==TS_FAIL){
	196	/* restoration procedure copied from few lines below */
	197	for(i=0;i<4;i++){
	198	// fprintf(stderr,"Restoring vtx neigh[%d] with neighbours %d\n",i, orig_vtx[i]->neigh_no );
	199	free(orig_vtx[i]->neigh);
	200	free(orig_vtx[i]->tristar);
	201	free(orig_vtx[i]->bond);
	202	free(orig_tria[i]->neigh);
	203	memcpy((void )orig_vtx[i],(void )bck_vtx[i],sizeof(ts_vertex));
	204	memcpy((void )orig_tria[i],(void )bck_tria[i],sizeof(ts_triangle));
	205	// fprintf(stderr,"Restored vtx neigh[%d] with neighbours %d\n",i, orig_vtx[i]->neigh_no );
	206	/* level 2 pointers are redirected*/
	207	}
	208	memcpy(bond,bck_bond,sizeof(ts_bond));
	209
	210	for(i=0;i<4;i++){
	211	free(bck_vtx[i]);
	212	free(bck_tria[i]);
	213	/* fprintf(stderr,"Restoring vtx neigh[%d] with neighbours %d =",i, orig_vtx[i]->neigh_no );
	214	for(j=0;j<orig_vtx[i]->neigh_no;j++) fprintf(stderr," %d", orig_vtx[i]->neigh[j]->idx);
	215	fprintf(stderr,"\n"); */
	216	}
	217
	218	free(bck_bond);
	219	return TS_FAIL;
	220
	221	}
	222
	223	delta_energy+=delta_energy_cv;
	224	}
	225
414b8a	226
b866cf	227	/* MONTE CARLO */
M	228	if(delta_energy>=0){
	229	#ifdef TS_DOUBLE_DOUBLE
fbcbdf	230	if(exp(-delta_energy)< drand48())
b866cf	231	#endif
M	232	#ifdef TS_DOUBLE_FLOAT
	233	if(expf(-delta_energy)< (ts_float)drand48())
	234	#endif
	235	#ifdef TS_DOUBLE_LONGDOUBLE
	236	if(expl(-delta_energy)< (ts_ldouble)drand48())
	237	#endif
	238	{
	239	//not accepted, reverting changes
7efbb1	240	//restore all backups
SP	241	// fprintf(stderr,"Restoring!!!\n");
aec47d	242
7efbb1	243	for(i=0;i<4;i++){
SP	244	// fprintf(stderr,"Restoring vtx neigh[%d] with neighbours %d\n",i, orig_vtx[i]->neigh_no );
	245	free(orig_vtx[i]->neigh);
	246	free(orig_vtx[i]->tristar);
	247	free(orig_vtx[i]->bond);
	248	free(orig_tria[i]->neigh);
	249	memcpy((void )orig_vtx[i],(void )bck_vtx[i],sizeof(ts_vertex));
	250	memcpy((void )orig_tria[i],(void )bck_tria[i],sizeof(ts_triangle));
	251	// fprintf(stderr,"Restored vtx neigh[%d] with neighbours %d\n",i, orig_vtx[i]->neigh_no );
	252	/* level 2 pointers are redirected*/
	253	}
	254	memcpy(bond,bck_bond,sizeof(ts_bond));
2870ab	255
7efbb1	256	for(i=0;i<4;i++){
SP	257	free(bck_vtx[i]);
	258	free(bck_tria[i]);
	259	/* fprintf(stderr,"Restoring vtx neigh[%d] with neighbours %d =",i, orig_vtx[i]->neigh_no );
	260	for(j=0;j<orig_vtx[i]->neigh_no;j++) fprintf(stderr," %d", orig_vtx[i]->neigh[j]->idx);
	261	fprintf(stderr,"\n"); */
	262	}
2870ab	263
SP	264	free(bck_bond);
fbcbdf	265
SP	266	if(vesicle->tape->constvolswitch == 1){
	267	constvolumerestore(constvol_vtx_moved,constvol_vtx_backup);
	268	}
7efbb1	269	// fprintf(stderr,"Restoration complete!!!\n");
2870ab	270
7efbb1	271	return TS_FAIL;
b866cf	272	}
M	273	}
	274	/* IF BONDFLIP ACCEPTED, THEN RETURN SUCCESS! */
fbcbdf	275	// fprintf(stderr,"SUCCESS!!!\n");
2870ab	276
SP	277	// delete all backups
	278	for(i=0;i<4;i++){
7efbb1	279	free(bck_vtx[i]->neigh);
SP	280	free(bck_vtx[i]->bond);
	281	free(bck_vtx[i]->tristar);
	282	free(bck_vtx[i]);
2870ab	283	free(bck_tria[i]->neigh);
SP	284	free(bck_tria[i]);
7efbb1	285	/* fprintf(stderr,"Afret backup deletion vtx neigh[%d]=",i);
SP	286	for(j=0;j<orig_vtx[i]->neigh_no;j++) fprintf(stderr," %d", orig_vtx[i]->neigh[j]->idx);
	287	fprintf(stderr,"\n");
	288	*/
2870ab	289	}
7efbb1	290	free(bck_bond);
fbcbdf	291	if(vesicle->tape->constvolswitch == 1){
SP	292	constvolumeaccept(vesicle,constvol_vtx_moved,constvol_vtx_backup);
	293	}
7efbb1	294
b866cf	295	return TS_SUCCESS;
aec47d	296	}
SP	297
	298
b866cf	299	ts_bool ts_flip_bond(ts_vertex k,ts_vertex it,ts_vertex km, ts_vertex kp,
M	300	ts_bond bond, ts_triangle lm, ts_triangle lp, ts_triangle lm2, ts_triangle *lp1){
	301
	302	ts_uint i; //lmidx, lpidx;
	303	if(k==NULL \|\| it==NULL \|\| km==NULL \|\| kp==NULL){
	304	fatal("ts_flip_bond: You called me with invalid pointers to vertices",999);
	305	}
aec47d	306	// 2. step. We change the triangle vertices... (actual bond flip)
SP	307	for(i=0;i<3;i++) if(lm->vertex[i]== it) lm->vertex[i]= kp;
	308	for(i=0;i<3;i++) if(lp->vertex[i]== k) lp->vertex[i]= km;
e19e79	309	//fprintf(stderr,"2. step: actual bondflip made\n");
aec47d	310	// 2a. step. If any changes in triangle calculations must be done, do it here!
SP	311	// * normals are recalculated here
	312	triangle_normal_vector(lp);
	313	triangle_normal_vector(lm);
e19e79	314	//fprintf(stderr,"2a. step: triangle normals recalculated\n");
aec47d	315	// 3. step. Correct neighbours in vertex_list
SP	316
	317
30ee9c	318	vtx_remove_neighbour(k,it);
306559	319	// vtx_remove_neighbour(it,k);
e19e79	320	//fprintf(stderr,"3. step (PROGRESS): removed k and it neighbours\n");
306559	321
aec47d	322	//Tukaj pa nastopi tezava... Kam dodati soseda?
30ee9c	323	vtx_insert_neighbour(km,kp,k);
SP	324	vtx_insert_neighbour(kp,km,it);
aec47d	325	// vertex_add_neighbour(km,kp); //pazi na vrstni red.
SP	326	// vertex_add_neighbour(kp,km);
e19e79	327	//fprintf(stderr,"3. step: vertex neighbours corrected\n");
aec47d	328
SP	329	// 3a. step. If any changes to ts_vertex, do it here!
	330	// bond_length calculatons not required for it is done in energy.c
	331
	332	// 4. step. Correct bond_list (don't know why I still have it!)
	333	bond->vtx1=km;
	334	bond->vtx2=kp;
	335	//fprintf(stderr,"4. step: bondlist corrected\n");
	336
	337
	338	// 5. step. Correct neighbouring triangles
	339
	340	triangle_remove_neighbour(lp,lp1);
e19e79	341	// fprintf(stderr,".\n");
aec47d	342	triangle_remove_neighbour(lp1,lp);
SP	343	// fprintf(stderr,".\n");
	344	triangle_remove_neighbour(lm,lm2);
	345	// fprintf(stderr,".\n");
	346	triangle_remove_neighbour(lm2,lm);
	347
	348	triangle_add_neighbour(lm,lp1);
	349	triangle_add_neighbour(lp1,lm);
	350	triangle_add_neighbour(lp,lm2); //Vrstni red?!
	351	triangle_add_neighbour(lm2,lp);
	352
	353	//fprintf(stderr,"5. step: triangle neigbours corrected\n");
	354
	355
	356	// 6. step. Correct tristar for vertices km, kp, k and it
	357	vertex_add_tristar(km,lp); // Preveri vrstni red!
	358	vertex_add_tristar(kp,lm);
30ee9c	359	vtx_remove_tristar(it,lm);
SP	360	vtx_remove_tristar(k,lp);
aec47d	361	//fprintf(stderr,"6. step: tristar corrected\n");
SP	362	energy_vertex(k);
	363	energy_vertex(kp);
	364	energy_vertex(km);
	365	energy_vertex(it);
	366	// END modifications to data structure!
	367	return TS_SUCCESS;
	368	}