trisurf-ng.git - Gitblit

Added option to include trisurf runtime arguments in the main configuration...

Samo Penic

2016-04-07 b122c46c95b96febda4ebf3c8ddfa79998d599f9

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;
414b8a	171	//Neigbours of k, it, km, kp don't change its energy.
aec47d	172
1121fa	173	if(vesicle->pswitch == 1 \|\| vesicle->tape->constvolswitch>0){dvol = -lm->volume - lp->volume;}
c0ae90	174	if(vesicle->tape->constareaswitch==2){darea=-lm->area-lp->area;}
dd5aca	175	/* vesicle_volume(vesicle);
SP	176	fprintf(stderr,"Volume in the beginning=%1.16e\n", vesicle->volume);
	177	*/
414b8a	178
M	179	/* fix data structure for flipped bond */
	180	ts_flip_bond(k,it,km,kp, bond,lm, lp, lm2, lp1);
aec47d	181
SP	182
b866cf	183	/* Calculating the new energy */
M	184	delta_energy=0;
	185	delta_energy+=k->xk* k->energy;
	186	delta_energy+=kp->xk* kp->energy;
	187	delta_energy+=km->xk* km->energy;
	188	delta_energy+=it->xk* it->energy;
414b8a	189	//Neigbours of k, it, km, kp don't change its energy.
M	190
fbcbdf	191	delta_energy-=oldenergy;
1121fa	192	if(vesicle->pswitch == 1 \|\| vesicle->tape->constvolswitch>0){
414b8a	193	dvol = dvol + lm->volume + lp->volume;
fbcbdf	194	if(vesicle->pswitch==1) delta_energy-= vesicle->pressure*dvol;
414b8a	195	}
c0ae90	196	if(vesicle->tape->constareaswitch==2){
SP	197	darea=darea+lm->area+lp->area;
	198	/check whether the dvol is gt than epsvol /
	199	if(fabs(vesicle->area+darea-A0)>epsarea){
	200	//restore old state.
	201	/* restoration procedure copied from few lines below */
	202	for(i=0;i<4;i++){
	203	// fprintf(stderr,"Restoring vtx neigh[%d] with neighbours %d\n",i, orig_vtx[i]->neigh_no );
	204	free(orig_vtx[i]->neigh);
	205	free(orig_vtx[i]->tristar);
	206	free(orig_vtx[i]->bond);
	207	free(orig_tria[i]->neigh);
	208	memcpy((void )orig_vtx[i],(void )bck_vtx[i],sizeof(ts_vertex));
	209	memcpy((void )orig_tria[i],(void )bck_tria[i],sizeof(ts_triangle));
	210	// fprintf(stderr,"Restored vtx neigh[%d] with neighbours %d\n",i, orig_vtx[i]->neigh_no );
	211	/* level 2 pointers are redirected*/
	212	}
	213	memcpy(bond,bck_bond,sizeof(ts_bond));
	214	for(i=0;i<4;i++){
	215	free(bck_vtx[i]);
	216	free(bck_tria[i]);
	217	/* fprintf(stderr,"Restoring vtx neigh[%d] with neighbours %d =",i, orig_vtx[i]->neigh_no );
	218	for(j=0;j<orig_vtx[i]->neigh_no;j++) fprintf(stderr," %d", orig_vtx[i]->neigh[j]->idx);
	219	fprintf(stderr,"\n"); */
	220	}
	221	free(bck_bond);
	222	return TS_FAIL;
	223
	224	}
	225	}
	226
	227
	228
fbcbdf	229
1121fa	230	if(vesicle->tape->constvolswitch == 2){
SP	231	/check whether the dvol is gt than epsvol /
	232	if(fabs(vesicle->volume+dvol-V0)>epsvol){
	233	//restore old state.
	234	/* restoration procedure copied from few lines below */
	235	for(i=0;i<4;i++){
	236	// fprintf(stderr,"Restoring vtx neigh[%d] with neighbours %d\n",i, orig_vtx[i]->neigh_no );
	237	free(orig_vtx[i]->neigh);
	238	free(orig_vtx[i]->tristar);
	239	free(orig_vtx[i]->bond);
	240	free(orig_tria[i]->neigh);
	241	memcpy((void )orig_vtx[i],(void )bck_vtx[i],sizeof(ts_vertex));
	242	memcpy((void )orig_tria[i],(void )bck_tria[i],sizeof(ts_triangle));
	243	// fprintf(stderr,"Restored vtx neigh[%d] with neighbours %d\n",i, orig_vtx[i]->neigh_no );
	244	/* level 2 pointers are redirected*/
	245	}
	246	memcpy(bond,bck_bond,sizeof(ts_bond));
	247	for(i=0;i<4;i++){
	248	free(bck_vtx[i]);
	249	free(bck_tria[i]);
	250	/* fprintf(stderr,"Restoring vtx neigh[%d] with neighbours %d =",i, orig_vtx[i]->neigh_no );
	251	for(j=0;j<orig_vtx[i]->neigh_no;j++) fprintf(stderr," %d", orig_vtx[i]->neigh[j]->idx);
	252	fprintf(stderr,"\n"); */
	253	}
	254	free(bck_bond);
	255	return TS_FAIL;
	256
	257	}
	258
	259	} else
fbcbdf	260	if(vesicle->tape->constvolswitch == 1){
dd5aca	261	retval=constvolume(vesicle, it, -dvol, &delta_energy_cv, &constvol_vtx_moved,&constvol_vtx_backup);
fbcbdf	262	if(retval==TS_FAIL){
SP	263	/* restoration procedure copied from few lines below */
dd5aca	264	for(i=0;i<4;i++){
SP	265	// fprintf(stderr,"Restoring vtx neigh[%d] with neighbours %d\n",i, orig_vtx[i]->neigh_no );
	266	free(orig_vtx[i]->neigh);
	267	free(orig_vtx[i]->tristar);
	268	free(orig_vtx[i]->bond);
	269	free(orig_tria[i]->neigh);
	270	memcpy((void )orig_vtx[i],(void )bck_vtx[i],sizeof(ts_vertex));
	271	memcpy((void )orig_tria[i],(void )bck_tria[i],sizeof(ts_triangle));
	272	// fprintf(stderr,"Restored vtx neigh[%d] with neighbours %d\n",i, orig_vtx[i]->neigh_no );
	273	/* level 2 pointers are redirected*/
	274	}
	275	memcpy(bond,bck_bond,sizeof(ts_bond));
	276	for(i=0;i<4;i++){
	277	free(bck_vtx[i]);
	278	free(bck_tria[i]);
	279	/* fprintf(stderr,"Restoring vtx neigh[%d] with neighbours %d =",i, orig_vtx[i]->neigh_no );
	280	for(j=0;j<orig_vtx[i]->neigh_no;j++) fprintf(stderr," %d", orig_vtx[i]->neigh[j]->idx);
	281	fprintf(stderr,"\n"); */
	282	}
	283	free(bck_bond);
	284	return TS_FAIL;
fbcbdf	285	}
b2fa8c	286	delta_energy+=delta_energy_cv;
fbcbdf	287	}
SP	288
414b8a	289
b866cf	290	/* MONTE CARLO */
M	291	if(delta_energy>=0){
	292	#ifdef TS_DOUBLE_DOUBLE
fbcbdf	293	if(exp(-delta_energy)< drand48())
b866cf	294	#endif
M	295	#ifdef TS_DOUBLE_FLOAT
	296	if(expf(-delta_energy)< (ts_float)drand48())
	297	#endif
	298	#ifdef TS_DOUBLE_LONGDOUBLE
	299	if(expl(-delta_energy)< (ts_ldouble)drand48())
	300	#endif
	301	{
	302	//not accepted, reverting changes
7efbb1	303	//restore all backups
SP	304	// fprintf(stderr,"Restoring!!!\n");
b2fa8c	305	if(vesicle->tape->constvolswitch == 1){
SP	306	constvolumerestore(constvol_vtx_moved,constvol_vtx_backup);
	307	}
aec47d	308
7efbb1	309	for(i=0;i<4;i++){
SP	310	// fprintf(stderr,"Restoring vtx neigh[%d] with neighbours %d\n",i, orig_vtx[i]->neigh_no );
	311	free(orig_vtx[i]->neigh);
	312	free(orig_vtx[i]->tristar);
	313	free(orig_vtx[i]->bond);
	314	free(orig_tria[i]->neigh);
	315	memcpy((void )orig_vtx[i],(void )bck_vtx[i],sizeof(ts_vertex));
	316	memcpy((void )orig_tria[i],(void )bck_tria[i],sizeof(ts_triangle));
	317	// fprintf(stderr,"Restored vtx neigh[%d] with neighbours %d\n",i, orig_vtx[i]->neigh_no );
	318	/* level 2 pointers are redirected*/
	319	}
	320	memcpy(bond,bck_bond,sizeof(ts_bond));
2870ab	321
7efbb1	322	for(i=0;i<4;i++){
SP	323	free(bck_vtx[i]);
	324	free(bck_tria[i]);
	325	/* fprintf(stderr,"Restoring vtx neigh[%d] with neighbours %d =",i, orig_vtx[i]->neigh_no );
	326	for(j=0;j<orig_vtx[i]->neigh_no;j++) fprintf(stderr," %d", orig_vtx[i]->neigh[j]->idx);
	327	fprintf(stderr,"\n"); */
	328	}
2870ab	329
SP	330	free(bck_bond);
fbcbdf	331
7efbb1	332	// fprintf(stderr,"Restoration complete!!!\n");
dd5aca	333	// vesicle_volume(vesicle);
SP	334	// fprintf(stderr,"Volume after fail=%1.16e\n", vesicle->volume);
2870ab	335
7efbb1	336	return TS_FAIL;
b866cf	337	}
M	338	}
	339	/* IF BONDFLIP ACCEPTED, THEN RETURN SUCCESS! */
fbcbdf	340	// fprintf(stderr,"SUCCESS!!!\n");
2870ab	341
c0ae90	342	if(vesicle->tape->constvolswitch == 2){
SP	343	vesicle->volume+=dvol;
	344	} else if(vesicle->tape->constvolswitch == 1){
b2fa8c	345	constvolumeaccept(vesicle,constvol_vtx_moved,constvol_vtx_backup);
SP	346	}
c0ae90	347	if(vesicle->tape->constareaswitch==2){
SP	348	vesicle->area+=darea;
	349	}
2870ab	350	// delete all backups
SP	351	for(i=0;i<4;i++){
7efbb1	352	free(bck_vtx[i]->neigh);
SP	353	free(bck_vtx[i]->bond);
	354	free(bck_vtx[i]->tristar);
	355	free(bck_vtx[i]);
2870ab	356	free(bck_tria[i]->neigh);
SP	357	free(bck_tria[i]);
7efbb1	358	/* fprintf(stderr,"Afret backup deletion vtx neigh[%d]=",i);
SP	359	for(j=0;j<orig_vtx[i]->neigh_no;j++) fprintf(stderr," %d", orig_vtx[i]->neigh[j]->idx);
	360	fprintf(stderr,"\n");
	361	*/
2870ab	362	}
7efbb1	363	free(bck_bond);
SP	364
dd5aca	365	// vesicle_volume(vesicle);
SP	366	// fprintf(stderr,"Volume after success=%1.16e\n", vesicle->volume);
b866cf	367	return TS_SUCCESS;
aec47d	368	}
SP	369
	370
b866cf	371	ts_bool ts_flip_bond(ts_vertex k,ts_vertex it,ts_vertex km, ts_vertex kp,
M	372	ts_bond bond, ts_triangle lm, ts_triangle lp, ts_triangle lm2, ts_triangle *lp1){
	373
	374	ts_uint i; //lmidx, lpidx;
	375	if(k==NULL \|\| it==NULL \|\| km==NULL \|\| kp==NULL){
	376	fatal("ts_flip_bond: You called me with invalid pointers to vertices",999);
	377	}
aec47d	378	// 2. step. We change the triangle vertices... (actual bond flip)
SP	379	for(i=0;i<3;i++) if(lm->vertex[i]== it) lm->vertex[i]= kp;
	380	for(i=0;i<3;i++) if(lp->vertex[i]== k) lp->vertex[i]= km;
e19e79	381	//fprintf(stderr,"2. step: actual bondflip made\n");
aec47d	382	// 2a. step. If any changes in triangle calculations must be done, do it here!
SP	383	// * normals are recalculated here
	384	triangle_normal_vector(lp);
	385	triangle_normal_vector(lm);
e19e79	386	//fprintf(stderr,"2a. step: triangle normals recalculated\n");
aec47d	387	// 3. step. Correct neighbours in vertex_list
SP	388
	389
30ee9c	390	vtx_remove_neighbour(k,it);
306559	391	// vtx_remove_neighbour(it,k);
e19e79	392	//fprintf(stderr,"3. step (PROGRESS): removed k and it neighbours\n");
306559	393
aec47d	394	//Tukaj pa nastopi tezava... Kam dodati soseda?
30ee9c	395	vtx_insert_neighbour(km,kp,k);
SP	396	vtx_insert_neighbour(kp,km,it);
aec47d	397	// vertex_add_neighbour(km,kp); //pazi na vrstni red.
SP	398	// vertex_add_neighbour(kp,km);
e19e79	399	//fprintf(stderr,"3. step: vertex neighbours corrected\n");
aec47d	400
SP	401	// 3a. step. If any changes to ts_vertex, do it here!
	402	// bond_length calculatons not required for it is done in energy.c
	403
	404	// 4. step. Correct bond_list (don't know why I still have it!)
	405	bond->vtx1=km;
	406	bond->vtx2=kp;
	407	//fprintf(stderr,"4. step: bondlist corrected\n");
	408
	409
	410	// 5. step. Correct neighbouring triangles
	411
	412	triangle_remove_neighbour(lp,lp1);
e19e79	413	// fprintf(stderr,".\n");
aec47d	414	triangle_remove_neighbour(lp1,lp);
SP	415	// fprintf(stderr,".\n");
	416	triangle_remove_neighbour(lm,lm2);
	417	// fprintf(stderr,".\n");
	418	triangle_remove_neighbour(lm2,lm);
	419
	420	triangle_add_neighbour(lm,lp1);
	421	triangle_add_neighbour(lp1,lm);
	422	triangle_add_neighbour(lp,lm2); //Vrstni red?!
	423	triangle_add_neighbour(lm2,lp);
	424
	425	//fprintf(stderr,"5. step: triangle neigbours corrected\n");
	426
	427
	428	// 6. step. Correct tristar for vertices km, kp, k and it
	429	vertex_add_tristar(km,lp); // Preveri vrstni red!
	430	vertex_add_tristar(kp,lm);
30ee9c	431	vtx_remove_tristar(it,lm);
SP	432	vtx_remove_tristar(k,lp);
aec47d	433	//fprintf(stderr,"6. step: tristar corrected\n");
SP	434	energy_vertex(k);
	435	energy_vertex(kp);
	436	energy_vertex(km);
	437	energy_vertex(it);
	438	// END modifications to data structure!
	439	return TS_SUCCESS;
	440	}