trisurf-ng.git - Gitblit

Moved all global variables to separate file and defined extern keyword wher...

Samo Penic

2022-05-04 06afc729f9061c1cfa14c78728d61d518324c2f0

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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"
06afc7	17	#include "globals.h"
aec47d	18
SP	19	ts_bool single_bondflip_timestep(ts_vesicle vesicle, ts_bond bond, ts_double *rn){
	20	/*c Vertex and triangle (lm and lp) indexing for bond flip:
	21	c +----- k-------+ +----- k ------+
	22	c \|lm1 / \| \ lp1 \| \|lm1 / \ lp1 \|
	23	c \| / \| \ \| \| / \ \|
	24	c \|/ \| \ \| FLIP \|/ lm \ \|
	25	c km lm \| lp kp ---> km ---------- kp
	26	c \|\ \| / \| \|\ lp / \|
	27	c \| \ \| / \| \| \ / \|
	28	c \|lm2 \ \| / lp2 \| \|lm2 \ / lp2 \|
	29	c +------it------+ +----- it -----+
	30	c
	31	*/
	32	ts_vertex *it=bond->vtx1;
	33	ts_vertex *k=bond->vtx2;
	34	ts_uint nei,neip,neim;
b866cf	35	ts_uint i,j;
2a1e3d	36	ts_double oldenergy=0.0, delta_energy=0.0, dvol=0.0, darea=0.0;
b866cf	37	ts_triangle lm=NULL,lp=NULL, lp1=NULL, lm2=NULL;
aec47d	38
SP	39	ts_vertex kp,km;
fbcbdf	40
SP	41	ts_double delta_energy_cv;
	42	ts_vertex constvol_vtx_moved, constvol_vtx_backup;
	43	ts_bool retval;
aec47d	44
SP	45	if(it->neigh_no< 3) return TS_FAIL;
	46	if(k->neigh_no< 3) return TS_FAIL;
	47	if(k==NULL \|\| it==NULL){
	48	fatal("In bondflip, number of neighbours of k or it is less than 3!",999);
	49	}
	50
30ee9c	51	nei=0;
aec47d	52	for(i=0;i<it->neigh_no;i++){ // Finds the nn of it, that is k
SP	53	if(it->neigh[i]==k){
	54	nei=i;
	55	break;
	56	}
	57	}
	58	neip=nei+1; // I don't like it.. Smells like I must have it in correct order
	59	neim=nei-1;
	60	if(neip>=it->neigh_no) neip=0;
	61	if((ts_int)neim<0) neim=it->neigh_no-1; /* casting is essential... If not
	62	there the neim is never <0 !!! */
	63	// fprintf(stderr,"The numbers are: %u %u\n",neip, neim);
	64	km=it->neigh[neim]; // We located km and kp
	65	kp=it->neigh[neip];
	66
	67	if(km==NULL \|\| kp==NULL){
	68	fatal("In bondflip, cannot determine km and kp!",999);
	69	}
	70
	71	// fprintf(stderr,"I WAS HERE! after the 4 vertices are known!\n");
	72
	73	/* test if the membrane is wrapped too much, so that kp is nearest neighbour of
	74	* km. If it is true, then don't flip! */
	75	for(i=0;i<km->neigh_no;i++){
	76	if(km->neigh[i] == kp) return TS_FAIL;
	77	}
	78	// fprintf(stderr,"Membrane didn't wrap too much.. Continue.\n");
	79	/* if bond would be too long, return... */
30ee9c	80	if(vtx_distance_sq(km,kp) > vesicle->dmax ) return TS_FAIL;
aec47d	81	// fprintf(stderr,"Bond will not be too long.. Continue.\n");
SP	82
	83	/* we make a bond flip. this is different than in original fortran */
b866cf	84	// find lm, lp
aec47d	85	// 1. step. We find lm and lp from k->tristar !
SP	86	for(i=0;i<it->tristar_no;i++){
	87	for(j=0;j<k->tristar_no;j++){
	88	if((it->tristar[i] == k->tristar[j])){ //ce gre za skupen trikotnik
	89	if((it->tristar[i]->vertex[0] == km \|\| it->tristar[i]->vertex[1]
	90	== km \|\| it->tristar[i]->vertex[2]== km )){
	91	lm=it->tristar[i];
	92	// lmidx=i;
	93	}
	94	else
	95	{
	96	lp=it->tristar[i];
	97	// lpidx=i;
	98	}
	99
	100	}
	101	}
	102	}
	103	if(lm==NULL \|\| lp==NULL) fatal("ts_flip_bond: Cannot find triangles lm and lp!",999);
	104
	105	//we look for important triangles lp1 and lm2.
	106
	107	for(i=0;i<k->tristar_no;i++){
	108	for(j=0;j<kp->tristar_no;j++){
	109	if((k->tristar[i] == kp->tristar[j]) && k->tristar[i]!=lp){ //ce gre za skupen trikotnik
	110	lp1=k->tristar[i];
	111	}
	112	}
	113	}
	114
	115	for(i=0;i<it->tristar_no;i++){
	116	for(j=0;j<km->tristar_no;j++){
	117	if((it->tristar[i] == km->tristar[j]) && it->tristar[i]!=lm){ //ce gre za skupen trikotnik
	118	lm2=it->tristar[i];
	119	}
	120	}
	121	}
	122
	123	if(lm2==NULL \|\| lp1==NULL) fatal("ts_flip_bond: Cannot find triangles lm2 and lp1!",999);
2870ab	124
SP	125
	126	/* backup old structure */
	127	/* need to backup:
	128	* vertices k, kp, km, it
	129	* triangles lm, lp, lm2, lp1
	130	* bond
	131	*/
	132	ts_vertex *bck_vtx[4];
	133	ts_triangle *bck_tria[4];
	134	ts_bond *bck_bond;
	135	ts_vertex *orig_vtx[]={k,it,kp,km};
7efbb1	136	ts_triangle *orig_tria[]={lm,lp,lm2,lp1};
2870ab	137
7efbb1	138	//fprintf(stderr,"Backuping!!!\n");
SP	139	bck_bond=(ts_bond *)malloc(sizeof(ts_bond));
2870ab	140	for(i=0;i<4;i++){
7efbb1	141	/* fprintf(stderr,"vtx neigh[%d]=",i);
SP	142	for(j=0;j<orig_vtx[i]->neigh_no;j++) fprintf(stderr," %d", orig_vtx[i]->neigh[j]->idx);
	143	fprintf(stderr,"\n");
	144	*/
2870ab	145	bck_vtx[i]=(ts_vertex *)malloc(sizeof(ts_vertex));
SP	146	bck_tria[i]=(ts_triangle *)malloc(sizeof(ts_triangle));
7efbb1	147	memcpy((void )bck_vtx[i],(void )orig_vtx[i],sizeof(ts_vertex));
SP	148	memcpy((void )bck_tria[i],(void )orig_tria[i],sizeof(ts_triangle));
2870ab	149	/* level 2 pointers */
7efbb1	150
2870ab	151	bck_vtx[i]->neigh=(ts_vertex *)malloc(orig_vtx[i]->neigh_nosizeof(ts_vertex *));
SP	152	bck_vtx[i]->tristar=(ts_triangle *)malloc(orig_vtx[i]->tristar_nosizeof(ts_triangle *));
	153	bck_vtx[i]->bond=(ts_bond *)malloc(orig_vtx[i]->bond_nosizeof(ts_bond *));
	154	bck_tria[i]->neigh=(ts_triangle *)malloc(orig_tria[i]->neigh_nosizeof(ts_triangle *));
	155
7efbb1	156	memcpy((void )bck_vtx[i]->neigh,(void )orig_vtx[i]->neigh,orig_vtx[i]->neigh_nosizeof(ts_vertex ));
SP	157	memcpy((void )bck_vtx[i]->tristar,(void )orig_vtx[i]->tristar,orig_vtx[i]->tristar_nosizeof(ts_triangle ));
	158	memcpy((void )bck_vtx[i]->bond,(void )orig_vtx[i]->bond,orig_vtx[i]->bond_nosizeof(ts_bond ));
b866cf	159
7efbb1	160	memcpy((void )bck_tria[i]->neigh,(void )orig_tria[i]->neigh,orig_tria[i]->neigh_nosizeof(ts_triangle ));
SP	161	}
	162	memcpy(bck_bond,bond,sizeof(ts_bond));
	163	//fprintf(stderr,"Backup complete!!!\n");
	164	/* end backup vertex */
	165
414b8a	166	/* Save old energy */
2a1e3d	167	oldenergy=0.0;
b866cf	168	oldenergy+=k->xk* k->energy;
M	169	oldenergy+=kp->xk* kp->energy;
	170	oldenergy+=km->xk* km->energy;
	171	oldenergy+=it->xk* it->energy;
032273	172	oldenergy+=bond->energy; /* attraction with neighboring vertices, that have spontaneous curvature */
414b8a	173	//Neigbours of k, it, km, kp don't change its energy.
aec47d	174
1121fa	175	if(vesicle->pswitch == 1 \|\| vesicle->tape->constvolswitch>0){dvol = -lm->volume - lp->volume;}
c0ae90	176	if(vesicle->tape->constareaswitch==2){darea=-lm->area-lp->area;}
dd5aca	177	/* vesicle_volume(vesicle);
SP	178	fprintf(stderr,"Volume in the beginning=%1.16e\n", vesicle->volume);
	179	*/
414b8a	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 */
2a1e3d	185	delta_energy=0.0;
b866cf	186	delta_energy+=k->xk* k->energy;
M	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.
7ec6fb	192	if(vesicle->tape->stretchswitch==1){
SP	193	oldenergy+=lm->energy+lp->energy;
	194	stretchenergy(vesicle,lm);
	195	stretchenergy(vesicle,lp);
	196	delta_energy+=lm->energy+lp->energy;
	197	}
414b8a	198
fbcbdf	199	delta_energy-=oldenergy;
1121fa	200	if(vesicle->pswitch == 1 \|\| vesicle->tape->constvolswitch>0){
414b8a	201	dvol = dvol + lm->volume + lp->volume;
fbcbdf	202	if(vesicle->pswitch==1) delta_energy-= vesicle->pressure*dvol;
414b8a	203	}
c0ae90	204	if(vesicle->tape->constareaswitch==2){
SP	205	darea=darea+lm->area+lp->area;
	206	/check whether the dvol is gt than epsvol /
	207	if(fabs(vesicle->area+darea-A0)>epsarea){
	208	//restore old state.
	209	/* restoration procedure copied from few lines below */
	210	for(i=0;i<4;i++){
	211	// fprintf(stderr,"Restoring vtx neigh[%d] with neighbours %d\n",i, orig_vtx[i]->neigh_no );
	212	free(orig_vtx[i]->neigh);
	213	free(orig_vtx[i]->tristar);
	214	free(orig_vtx[i]->bond);
	215	free(orig_tria[i]->neigh);
	216	memcpy((void )orig_vtx[i],(void )bck_vtx[i],sizeof(ts_vertex));
	217	memcpy((void )orig_tria[i],(void )bck_tria[i],sizeof(ts_triangle));
	218	// fprintf(stderr,"Restored vtx neigh[%d] with neighbours %d\n",i, orig_vtx[i]->neigh_no );
	219	/* level 2 pointers are redirected*/
	220	}
	221	memcpy(bond,bck_bond,sizeof(ts_bond));
	222	for(i=0;i<4;i++){
	223	free(bck_vtx[i]);
	224	free(bck_tria[i]);
	225	/* fprintf(stderr,"Restoring vtx neigh[%d] with neighbours %d =",i, orig_vtx[i]->neigh_no );
	226	for(j=0;j<orig_vtx[i]->neigh_no;j++) fprintf(stderr," %d", orig_vtx[i]->neigh[j]->idx);
	227	fprintf(stderr,"\n"); */
	228	}
	229	free(bck_bond);
	230	return TS_FAIL;
	231
	232	}
	233	}
	234
	235
	236
fbcbdf	237
1121fa	238	if(vesicle->tape->constvolswitch == 2){
SP	239	/check whether the dvol is gt than epsvol /
	240	if(fabs(vesicle->volume+dvol-V0)>epsvol){
	241	//restore old state.
	242	/* restoration procedure copied from few lines below */
	243	for(i=0;i<4;i++){
	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));
	255	for(i=0;i<4;i++){
	256	free(bck_vtx[i]);
	257	free(bck_tria[i]);
	258	/* fprintf(stderr,"Restoring vtx neigh[%d] with neighbours %d =",i, orig_vtx[i]->neigh_no );
	259	for(j=0;j<orig_vtx[i]->neigh_no;j++) fprintf(stderr," %d", orig_vtx[i]->neigh[j]->idx);
	260	fprintf(stderr,"\n"); */
	261	}
	262	free(bck_bond);
	263	return TS_FAIL;
	264
	265	}
	266
	267	} else
fbcbdf	268	if(vesicle->tape->constvolswitch == 1){
dd5aca	269	retval=constvolume(vesicle, it, -dvol, &delta_energy_cv, &constvol_vtx_moved,&constvol_vtx_backup);
fbcbdf	270	if(retval==TS_FAIL){
SP	271	/* restoration procedure copied from few lines below */
dd5aca	272	for(i=0;i<4;i++){
SP	273	// fprintf(stderr,"Restoring vtx neigh[%d] with neighbours %d\n",i, orig_vtx[i]->neigh_no );
	274	free(orig_vtx[i]->neigh);
	275	free(orig_vtx[i]->tristar);
	276	free(orig_vtx[i]->bond);
	277	free(orig_tria[i]->neigh);
	278	memcpy((void )orig_vtx[i],(void )bck_vtx[i],sizeof(ts_vertex));
	279	memcpy((void )orig_tria[i],(void )bck_tria[i],sizeof(ts_triangle));
	280	// fprintf(stderr,"Restored vtx neigh[%d] with neighbours %d\n",i, orig_vtx[i]->neigh_no );
	281	/* level 2 pointers are redirected*/
	282	}
	283	memcpy(bond,bck_bond,sizeof(ts_bond));
	284	for(i=0;i<4;i++){
	285	free(bck_vtx[i]);
	286	free(bck_tria[i]);
	287	/* fprintf(stderr,"Restoring vtx neigh[%d] with neighbours %d =",i, orig_vtx[i]->neigh_no );
	288	for(j=0;j<orig_vtx[i]->neigh_no;j++) fprintf(stderr," %d", orig_vtx[i]->neigh[j]->idx);
	289	fprintf(stderr,"\n"); */
	290	}
	291	free(bck_bond);
	292	return TS_FAIL;
fbcbdf	293	}
b2fa8c	294	delta_energy+=delta_energy_cv;
fbcbdf	295	}
SP	296
414b8a	297
b866cf	298	/* MONTE CARLO */
M	299	if(delta_energy>=0){
	300	#ifdef TS_DOUBLE_DOUBLE
fbcbdf	301	if(exp(-delta_energy)< drand48())
b866cf	302	#endif
M	303	#ifdef TS_DOUBLE_FLOAT
	304	if(expf(-delta_energy)< (ts_float)drand48())
	305	#endif
	306	#ifdef TS_DOUBLE_LONGDOUBLE
	307	if(expl(-delta_energy)< (ts_ldouble)drand48())
	308	#endif
	309	{
	310	//not accepted, reverting changes
7efbb1	311	//restore all backups
SP	312	// fprintf(stderr,"Restoring!!!\n");
b2fa8c	313	if(vesicle->tape->constvolswitch == 1){
SP	314	constvolumerestore(constvol_vtx_moved,constvol_vtx_backup);
	315	}
aec47d	316
7efbb1	317	for(i=0;i<4;i++){
SP	318	// fprintf(stderr,"Restoring vtx neigh[%d] with neighbours %d\n",i, orig_vtx[i]->neigh_no );
	319	free(orig_vtx[i]->neigh);
	320	free(orig_vtx[i]->tristar);
	321	free(orig_vtx[i]->bond);
	322	free(orig_tria[i]->neigh);
	323	memcpy((void )orig_vtx[i],(void )bck_vtx[i],sizeof(ts_vertex));
	324	memcpy((void )orig_tria[i],(void )bck_tria[i],sizeof(ts_triangle));
	325	// fprintf(stderr,"Restored vtx neigh[%d] with neighbours %d\n",i, orig_vtx[i]->neigh_no );
	326	/* level 2 pointers are redirected*/
	327	}
	328	memcpy(bond,bck_bond,sizeof(ts_bond));
2870ab	329
7efbb1	330	for(i=0;i<4;i++){
SP	331	free(bck_vtx[i]);
	332	free(bck_tria[i]);
	333	/* fprintf(stderr,"Restoring vtx neigh[%d] with neighbours %d =",i, orig_vtx[i]->neigh_no );
	334	for(j=0;j<orig_vtx[i]->neigh_no;j++) fprintf(stderr," %d", orig_vtx[i]->neigh[j]->idx);
	335	fprintf(stderr,"\n"); */
	336	}
2870ab	337
SP	338	free(bck_bond);
fbcbdf	339
7efbb1	340	// fprintf(stderr,"Restoration complete!!!\n");
dd5aca	341	// vesicle_volume(vesicle);
SP	342	// fprintf(stderr,"Volume after fail=%1.16e\n", vesicle->volume);
7ec6fb	343	if(vesicle->tape->stretchswitch==1){
SP	344	stretchenergy(vesicle,lm);
	345	stretchenergy(vesicle,lp);
	346	}
2870ab	347
7efbb1	348	return TS_FAIL;
b866cf	349	}
M	350	}
	351	/* IF BONDFLIP ACCEPTED, THEN RETURN SUCCESS! */
fbcbdf	352	// fprintf(stderr,"SUCCESS!!!\n");
2870ab	353
c0ae90	354	if(vesicle->tape->constvolswitch == 2){
SP	355	vesicle->volume+=dvol;
	356	} else if(vesicle->tape->constvolswitch == 1){
b2fa8c	357	constvolumeaccept(vesicle,constvol_vtx_moved,constvol_vtx_backup);
SP	358	}
c0ae90	359	if(vesicle->tape->constareaswitch==2){
SP	360	vesicle->area+=darea;
	361	}
2870ab	362	// delete all backups
SP	363	for(i=0;i<4;i++){
7efbb1	364	free(bck_vtx[i]->neigh);
SP	365	free(bck_vtx[i]->bond);
	366	free(bck_vtx[i]->tristar);
	367	free(bck_vtx[i]);
2870ab	368	free(bck_tria[i]->neigh);
SP	369	free(bck_tria[i]);
7efbb1	370	/* fprintf(stderr,"Afret backup deletion vtx neigh[%d]=",i);
SP	371	for(j=0;j<orig_vtx[i]->neigh_no;j++) fprintf(stderr," %d", orig_vtx[i]->neigh[j]->idx);
	372	fprintf(stderr,"\n");
	373	*/
2870ab	374	}
7efbb1	375	free(bck_bond);
SP	376
dd5aca	377	// vesicle_volume(vesicle);
SP	378	// fprintf(stderr,"Volume after success=%1.16e\n", vesicle->volume);
b866cf	379	return TS_SUCCESS;
aec47d	380	}
SP	381
	382
b866cf	383	ts_bool ts_flip_bond(ts_vertex k,ts_vertex it,ts_vertex km, ts_vertex kp,
032273	384	ts_bond bond, ts_triangle lm, ts_triangle lp, ts_triangle lm2, ts_triangle *lp1, ts_double w_energy){
b866cf	385
M	386	ts_uint i; //lmidx, lpidx;
	387	if(k==NULL \|\| it==NULL \|\| km==NULL \|\| kp==NULL){
	388	fatal("ts_flip_bond: You called me with invalid pointers to vertices",999);
	389	}
aec47d	390	// 2. step. We change the triangle vertices... (actual bond flip)
SP	391	for(i=0;i<3;i++) if(lm->vertex[i]== it) lm->vertex[i]= kp;
	392	for(i=0;i<3;i++) if(lp->vertex[i]== k) lp->vertex[i]= km;
e19e79	393	//fprintf(stderr,"2. step: actual bondflip made\n");
aec47d	394	// 2a. step. If any changes in triangle calculations must be done, do it here!
SP	395	// * normals are recalculated here
	396	triangle_normal_vector(lp);
	397	triangle_normal_vector(lm);
e19e79	398	//fprintf(stderr,"2a. step: triangle normals recalculated\n");
aec47d	399	// 3. step. Correct neighbours in vertex_list
SP	400
	401
30ee9c	402	vtx_remove_neighbour(k,it);
306559	403	// vtx_remove_neighbour(it,k);
e19e79	404	//fprintf(stderr,"3. step (PROGRESS): removed k and it neighbours\n");
306559	405
aec47d	406	//Tukaj pa nastopi tezava... Kam dodati soseda?
30ee9c	407	vtx_insert_neighbour(km,kp,k);
SP	408	vtx_insert_neighbour(kp,km,it);
aec47d	409	// vertex_add_neighbour(km,kp); //pazi na vrstni red.
SP	410	// vertex_add_neighbour(kp,km);
e19e79	411	//fprintf(stderr,"3. step: vertex neighbours corrected\n");
aec47d	412
SP	413	// 3a. step. If any changes to ts_vertex, do it here!
	414	// bond_length calculatons not required for it is done in energy.c
	415
	416	// 4. step. Correct bond_list (don't know why I still have it!)
	417	bond->vtx1=km;
	418	bond->vtx2=kp;
	419	//fprintf(stderr,"4. step: bondlist corrected\n");
	420
	421
	422	// 5. step. Correct neighbouring triangles
	423
	424	triangle_remove_neighbour(lp,lp1);
e19e79	425	// fprintf(stderr,".\n");
aec47d	426	triangle_remove_neighbour(lp1,lp);
SP	427	// fprintf(stderr,".\n");
	428	triangle_remove_neighbour(lm,lm2);
	429	// fprintf(stderr,".\n");
	430	triangle_remove_neighbour(lm2,lm);
	431
	432	triangle_add_neighbour(lm,lp1);
	433	triangle_add_neighbour(lp1,lm);
	434	triangle_add_neighbour(lp,lm2); //Vrstni red?!
	435	triangle_add_neighbour(lm2,lp);
	436
	437	//fprintf(stderr,"5. step: triangle neigbours corrected\n");
	438
	439
	440	// 6. step. Correct tristar for vertices km, kp, k and it
	441	vertex_add_tristar(km,lp); // Preveri vrstni red!
	442	vertex_add_tristar(kp,lm);
30ee9c	443	vtx_remove_tristar(it,lm);
SP	444	vtx_remove_tristar(k,lp);
aec47d	445	//fprintf(stderr,"6. step: tristar corrected\n");
SP	446	energy_vertex(k);
	447	energy_vertex(kp);
	448	energy_vertex(km);
	449	energy_vertex(it);
032273	450	attraction_bond_energy(bond, w_energy);
aec47d	451	// END modifications to data structure!
SP	452	return TS_SUCCESS;
	453	}