trisurf-ng.git - Gitblit

Samo Penic

2014-04-30 fe5069cc3872b513f4715b0cfd303175ae80c468

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"
	11	//#include "io.h"
9166cb	12	#include "io.h"
aec47d	13	#include<stdio.h>
SP	14	#include "vertexmove.h"
1ad6d1	15	#include <string.h>
43c042	16	#include "constvol.h"
aec47d	17
fedf2b	18	ts_bool single_verticle_timestep(ts_vesicle vesicle,ts_vertex vtx,ts_double *rn){
aec47d	19	ts_uint i;
SP	20	ts_double dist;
	21	ts_bool retval;
	22	ts_uint cellidx;
fbcbdf	23	ts_double delta_energy, delta_energy_cv,oenergy,dvol=0.0;
ed31fe	24	ts_double costheta,sintheta,phi,r;
1ad6d1	25	//This will hold all the information of vtx and its neighbours
958e0e	26	ts_vertex backupvtx[20], constvol_vtx_moved=NULL, constvol_vtx_backup=NULL;
dcd350	27	memcpy((void )&backupvtx[0],(void )vtx,sizeof(ts_vertex));
a63f17	28
SP	29	//Some stupid tests for debugging cell occupation!
	30	/* cellidx=vertex_self_avoidance(vesicle, vtx);
	31	if(vesicle->clist->cell[cellidx]==vtx->cell){
	32	fprintf(stderr,"Idx match!\n");
	33	} else {
	34	fprintf(stderr,"***** Idx don't match!\n");
	35	fatal("ENding.",1);
	36	}
	37	*/
	38
352fad	39	//temporarly moving the vertex
672ae4	40	// vtx->x=vtx->x+vesicle->stepsize(2.0rn[0]-1.0);
SP	41	// vtx->y=vtx->y+vesicle->stepsize(2.0rn[1]-1.0);
	42	// vtx->z=vtx->z+vesicle->stepsize(2.0rn[2]-1.0);
	43
ed31fe	44	//random move in a sphere with radius stepsize:
M	45	r=vesicle->stepsize*rn[0];
	46	phi=rn[1]2M_PI;
	47	costheta=2*rn[2]-1;
	48	sintheta=sqrt(1-pow(costheta,2));
672ae4	49	vtx->x=vtx->x+rsinthetacos(phi);
SP	50	vtx->y=vtx->y+rsinthetasin(phi);
	51	vtx->z=vtx->z+r*costheta;
	52
	53
a63f17	54	//distance with neighbours check
8f6a69	55	for(i=0;i<vtx->neigh_no;i++){
352fad	56	dist=vtx_distance_sq(vtx,vtx->neigh[i]);
8f6a69	57	if(dist<1.0 \|\| dist>vesicle->dmax) {
dcd350	58	vtx=memcpy((void )vtx,(void )&backupvtx[0],sizeof(ts_vertex));
8f6a69	59	return TS_FAIL;
SP	60	}
aec47d	61	}
304510	62
M	63	// Distance with grafted poly-vertex check:
	64	if(vtx->grafted_poly!=NULL){
	65	dist=vtx_distance_sq(vtx,vtx->grafted_poly->vlist->vtx[0]);
	66	if(dist<1.0 \|\| dist>vesicle->dmax) {
	67	vtx=memcpy((void )vtx,(void )&backupvtx[0],sizeof(ts_vertex));
	68	return TS_FAIL;
	69	}
	70	}
	71
fe24d2	72	// TODO: Maybe faster if checks only nucleus-neighboring cells
M	73	// Nucleus penetration check:
	74	if (vtx->xvtx->x + vtx->yvtx->y + vtx->z*vtx->z < vesicle->R_nucleus){
	75	vtx=memcpy((void )vtx,(void )&backupvtx[0],sizeof(ts_vertex));
	76	return TS_FAIL;
	77	}
	78
	79	//self avoidance check with distant vertices
	80	cellidx=vertex_self_avoidance(vesicle, vtx);
	81	//check occupation number
	82	retval=cell_occupation_number_and_internal_proximity(vesicle->clist,cellidx,vtx);
	83
aec47d	84	if(retval==TS_FAIL){
dcd350	85	vtx=memcpy((void )vtx,(void )&backupvtx[0],sizeof(ts_vertex));
aec47d	86	return TS_FAIL;
SP	87	}
1ad6d1	88
SP	89
352fad	90	//if all the tests are successful, then energy for vtx and neighbours is calculated
1ad6d1	91	for(i=0;i<vtx->neigh_no;i++){
dcd350	92	memcpy((void )&backupvtx[i+1],(void )vtx->neigh[i],sizeof(ts_vertex));
1ad6d1	93	}
aec47d	94
fbcbdf	95	if(vesicle->pswitch == 1 \|\| vesicle->tape->constvolswitch==1){
414b8a	96	for(i=0;i<vtx->tristar_no;i++) dvol-=vtx->tristar[i]->volume;
M	97	};
a63f17	98
aec47d	99	delta_energy=0;
fe5069	100
SP	101	// vesicle_volume(vesicle);
	102	// fprintf(stderr,"Volume in the beginning=%1.16e\n", vesicle->volume);
43c042	103
aec47d	104	//update the normals of triangles that share bead i.
8f6a69	105	for(i=0;i<vtx->tristar_no;i++) triangle_normal_vector(vtx->tristar[i]);
a63f17	106	oenergy=vtx->energy;
aec47d	107	energy_vertex(vtx);
a63f17	108	delta_energy=vtx->xk*(vtx->energy - oenergy);
aec47d	109	//the same is done for neighbouring vertices
8f6a69	110	for(i=0;i<vtx->neigh_no;i++){
SP	111	oenergy=vtx->neigh[i]->energy;
	112	energy_vertex(vtx->neigh[i]);
	113	delta_energy+=vtx->neigh[i]->xk*(vtx->neigh[i]->energy-oenergy);
aec47d	114	}
414b8a	115
fbcbdf	116	if(vesicle->pswitch == 1 \|\| vesicle->tape->constvolswitch == 1){
414b8a	117	for(i=0;i<vtx->tristar_no;i++) dvol+=vtx->tristar[i]->volume;
fbcbdf	118	if(vesicle->pswitch==1) delta_energy-=vesicle->pressure*dvol;
414b8a	119	};
43c042	120
fe5069	121	// vesicle_volume(vesicle);
SP	122	// fprintf(stderr,"Volume before=%1.16e\n", vesicle->volume);
fbcbdf	123	if(vesicle->tape->constvolswitch == 1){
fe5069	124	retval=constvolume(vesicle, vtx, -dvol, &delta_energy_cv, &constvol_vtx_moved,&constvol_vtx_backup);
fbcbdf	125	if(retval==TS_FAIL){ // if we couldn't move the vertex to assure constant volume
SP	126	vtx=memcpy((void )vtx,(void )&backupvtx[0],sizeof(ts_vertex));
	127	for(i=0;i<vtx->neigh_no;i++){
	128	vtx->neigh[i]=memcpy((void )vtx->neigh[i],(void )&backupvtx[i+1],sizeof(ts_vertex));
	129	}
	130	for(i=0;i<vtx->tristar_no;i++) triangle_normal_vector(vtx->tristar[i]);
fe5069	131	// fprintf(stderr,"fajlam!\n");
fbcbdf	132	return TS_FAIL;
SP	133	}
fe5069	134	// vesicle_volume(vesicle);
SP	135	// fprintf(stderr,"Volume after=%1.16e\n", vesicle->volume);
	136	// fprintf(stderr,"Volume after-dvol=%1.16e\n", vesicle->volume-dvol);
	137	// fprintf(stderr,"Denergy before=%e\n",delta_energy);
	138
fbcbdf	139	delta_energy+=delta_energy_cv;
fe5069	140	// fprintf(stderr,"Denergy after=%e\n",delta_energy);
fbcbdf	141	}
304510	142	/* No poly-bond energy for now!
fedf2b	143	if(vtx->grafted_poly!=NULL){
M	144	delta_energy+=
	145	(pow(sqrt(vtx_distance_sq(vtx, vtx->grafted_poly->vlist->vtx[0])-1),2)-
	146	pow(sqrt(vtx_distance_sq(&backupvtx[0], vtx->grafted_poly->vlist->vtx[0])-1),2)) *vtx->grafted_poly->k;
	147	}
304510	148	*/
314f2d	149	// fprintf(stderr, "DE=%f\n",delta_energy);
aec47d	150	//MONTE CARLOOOOOOOO
SP	151	if(delta_energy>=0){
	152	#ifdef TS_DOUBLE_DOUBLE
	153	if(exp(-delta_energy)< drand48() )
	154	#endif
	155	#ifdef TS_DOUBLE_FLOAT
	156	if(expf(-delta_energy)< (ts_float)drand48())
	157	#endif
	158	#ifdef TS_DOUBLE_LONGDOUBLE
	159	if(expl(-delta_energy)< (ts_ldouble)drand48())
	160	#endif
	161	{
	162	//not accepted, reverting changes
fbcbdf	163	// fprintf(stderr,"MC failed\n");
dcd350	164	vtx=memcpy((void )vtx,(void )&backupvtx[0],sizeof(ts_vertex));
1ad6d1	165	for(i=0;i<vtx->neigh_no;i++){
a63f17	166	vtx->neigh[i]=memcpy((void )vtx->neigh[i],(void )&backupvtx[i+1],sizeof(ts_vertex));
1ad6d1	167	}
SP	168
aec47d	169	//update the normals of triangles that share bead i.
dcd350	170	for(i=0;i<vtx->tristar_no;i++) triangle_normal_vector(vtx->tristar[i]);
1ad6d1	171
fe5069	172	// fprintf(stderr, "before vtx(x,y,z)=%e,%e,%e\n",constvol_vtx_moved->x, constvol_vtx_moved->y, constvol_vtx_moved->z);
43c042	173	if(vesicle->tape->constvolswitch == 1){
958e0e	174	constvolumerestore(constvol_vtx_moved,constvol_vtx_backup);
43c042	175	}
fe5069	176	// fprintf(stderr, "after vtx(x,y,z)=%e,%e,%e\n",constvol_vtx_moved->x, constvol_vtx_moved->y, constvol_vtx_moved->z);
aec47d	177	return TS_FAIL;
SP	178	}
	179	}
2b14da	180	//accepted
fbcbdf	181	// fprintf(stderr,"MC accepted\n");
a63f17	182	// oldcellidx=vertex_self_avoidance(vesicle, &backupvtx[0]);
SP	183	if(vtx->cell!=vesicle->clist->cell[cellidx]){
	184	retval=cell_add_vertex(vesicle->clist->cell[cellidx],vtx);
	185	// if(retval==TS_SUCCESS) cell_remove_vertex(vesicle->clist->cell[oldcellidx],vtx);
	186	if(retval==TS_SUCCESS) cell_remove_vertex(backupvtx[0].cell,vtx);
	187
	188	}
2b14da	189
43c042	190	if(vesicle->tape->constvolswitch == 1){
fbcbdf	191	constvolumeaccept(vesicle,constvol_vtx_moved,constvol_vtx_backup);
43c042	192	}
a63f17	193	// if(oldcellidx);
aec47d	194	//END MONTE CARLOOOOOOO
SP	195	return TS_SUCCESS;
	196	}
	197
fedf2b	198
M	199	ts_bool single_poly_vertex_move(ts_vesicle vesicle,ts_poly poly,ts_vertex vtx,ts_double rn){
	200	ts_uint i;
	201	ts_bool retval;
	202	ts_uint cellidx;
304510	203	// ts_double delta_energy;
fedf2b	204	ts_double costheta,sintheta,phi,r;
304510	205	ts_double dist;
fedf2b	206	//This will hold all the information of vtx and its neighbours
M	207	ts_vertex backupvtx;
304510	208	// ts_bond backupbond[2];
fedf2b	209	memcpy((void )&backupvtx,(void )vtx,sizeof(ts_vertex));
M	210
	211	//random move in a sphere with radius stepsize:
	212	r=vesicle->stepsize*rn[0];
	213	phi=rn[1]2M_PI;
	214	costheta=2*rn[2]-1;
	215	sintheta=sqrt(1-pow(costheta,2));
	216	vtx->x=vtx->x+rsinthetacos(phi);
	217	vtx->y=vtx->y+rsinthetasin(phi);
	218	vtx->z=vtx->z+r*costheta;
	219
	220
	221	//distance with neighbours check
304510	222	for(i=0;i<vtx->neigh_no;i++){
M	223	dist=vtx_distance_sq(vtx,vtx->neigh[i]);
	224	if(dist<1.0 \|\| dist>vesicle->dmax) {
	225	vtx=memcpy((void )vtx,(void )&backupvtx,sizeof(ts_vertex));
	226	return TS_FAIL;
	227	}
	228	}
	229
	230	// Distance with grafted vesicle-vertex check:
	231	if(vtx==poly->vlist->vtx[0]){
	232	dist=vtx_distance_sq(vtx,poly->grafted_vtx);
	233	if(dist<1.0 \|\| dist>vesicle->dmax) {
	234	vtx=memcpy((void )vtx,(void )&backupvtx,sizeof(ts_vertex));
	235	return TS_FAIL;
	236	}
	237	}
	238
fedf2b	239
M	240	//self avoidance check with distant vertices
	241	cellidx=vertex_self_avoidance(vesicle, vtx);
	242	//check occupation number
	243	retval=cell_occupation_number_and_internal_proximity(vesicle->clist,cellidx,vtx);
	244
	245	if(retval==TS_FAIL){
	246	vtx=memcpy((void )vtx,(void )&backupvtx,sizeof(ts_vertex));
	247	return TS_FAIL;
	248	}
	249
	250
	251	//if all the tests are successful, then energy for vtx and neighbours is calculated
304510	252	/* Energy ignored for now!
fedf2b	253	delta_energy=0;
M	254	for(i=0;i<vtx->bond_no;i++){
	255	memcpy((void )&backupbond[i],(void )vtx->bond[i],sizeof(ts_bond));
	256
	257	vtx->bond[i]->bond_length=sqrt(vtx_distance_sq(vtx->bond[i]->vtx1,vtx->bond[i]->vtx2));
	258	bond_energy(vtx->bond[i],poly);
	259	delta_energy+= vtx->bond[i]->energy - backupbond[i].energy;
	260	}
	261
	262	if(vtx==poly->vlist->vtx[0]){
	263	delta_energy+=
	264	(pow(sqrt(vtx_distance_sq(vtx, poly->grafted_vtx)-1),2)-
	265	pow(sqrt(vtx_distance_sq(&backupvtx, poly->grafted_vtx)-1),2)) *poly->k;
	266
	267	}
	268
	269
	270	if(delta_energy>=0){
	271	#ifdef TS_DOUBLE_DOUBLE
	272	if(exp(-delta_energy)< drand48() )
	273	#endif
	274	#ifdef TS_DOUBLE_FLOAT
	275	if(expf(-delta_energy)< (ts_float)drand48())
	276	#endif
	277	#ifdef TS_DOUBLE_LONGDOUBLE
	278	if(expl(-delta_energy)< (ts_ldouble)drand48())
	279	#endif
	280	{
	281	//not accepted, reverting changes
	282	vtx=memcpy((void )vtx,(void )&backupvtx,sizeof(ts_vertex));
	283	for(i=0;i<vtx->bond_no;i++){
	284	vtx->bond[i]=memcpy((void )vtx->bond[i],(void )&backupbond[i],sizeof(ts_bond));
	285	}
	286
	287	return TS_FAIL;
	288	}
	289	}
304510	290	*/
fedf2b	291
M	292	// oldcellidx=vertex_self_avoidance(vesicle, &backupvtx[0]);
	293	if(vtx->cell!=vesicle->clist->cell[cellidx]){
	294	retval=cell_add_vertex(vesicle->clist->cell[cellidx],vtx);
	295	// if(retval==TS_SUCCESS) cell_remove_vertex(vesicle->clist->cell[oldcellidx],vtx);
	296	if(retval==TS_SUCCESS) cell_remove_vertex(backupvtx.cell,vtx);
	297	}
	298	// if(oldcellidx);
	299	//END MONTE CARLOOOOOOO
	300	return TS_SUCCESS;
	301	}
58230a	302
M	303
	304
	305
	306	ts_bool single_filament_vertex_move(ts_vesicle vesicle,ts_poly poly,ts_vertex vtx,ts_double rn){
	307	ts_uint i;
	308	ts_bool retval;
	309	ts_uint cellidx;
b30f45	310	ts_double delta_energy;
58230a	311	ts_double costheta,sintheta,phi,r;
M	312	ts_double dist[2];
	313	//This will hold all the information of vtx and its neighbours
b30f45	314	ts_vertex backupvtx,backupneigh[2];
58230a	315	ts_bond backupbond[2];
b30f45	316
M	317	//backup vertex:
58230a	318	memcpy((void )&backupvtx,(void )vtx,sizeof(ts_vertex));
M	319
	320	//random move in a sphere with radius stepsize:
	321	r=vesicle->stepsize*rn[0];
	322	phi=rn[1]2M_PI;
	323	costheta=2*rn[2]-1;
	324	sintheta=sqrt(1-pow(costheta,2));
	325	vtx->x=vtx->x+rsinthetacos(phi);
	326	vtx->y=vtx->y+rsinthetasin(phi);
	327	vtx->z=vtx->z+r*costheta;
	328
	329
	330	//distance with neighbours check
	331	for(i=0;i<vtx->bond_no;i++){
	332	dist[i]=vtx_distance_sq(vtx->bond[i]->vtx1,vtx->bond[i]->vtx2);
	333	if(dist[i]<1.0 \|\| dist[i]>vesicle->dmax) {
	334	vtx=memcpy((void )vtx,(void )&backupvtx,sizeof(ts_vertex));
	335	return TS_FAIL;
	336	}
	337	}
	338
fe24d2	339	// TODO: Maybe faster if checks only nucleus-neighboring cells
M	340	// Nucleus penetration check:
	341	if (vtx->xvtx->x + vtx->yvtx->y + vtx->z*vtx->z < vesicle->R_nucleus){
	342	vtx=memcpy((void )vtx,(void )&backupvtx,sizeof(ts_vertex));
	343	return TS_FAIL;
	344	}
	345
58230a	346
M	347	//self avoidance check with distant vertices
	348	cellidx=vertex_self_avoidance(vesicle, vtx);
	349	//check occupation number
	350	retval=cell_occupation_number_and_internal_proximity(vesicle->clist,cellidx,vtx);
	351	if(retval==TS_FAIL){
	352	vtx=memcpy((void )vtx,(void )&backupvtx,sizeof(ts_vertex));
	353	return TS_FAIL;
	354	}
	355
	356	//backup bonds
	357	for(i=0;i<vtx->bond_no;i++){
	358	memcpy(&backupbond[i],vtx->bond[i], sizeof(ts_bond));
	359	vtx->bond[i]->bond_length=sqrt(dist[i]);
	360	bond_vector(vtx->bond[i]);
b30f45	361	}
M	362
	363	//backup neighboring vertices:
	364	for(i=0;i<vtx->neigh_no;i++){
	365	memcpy(&backupneigh[i],vtx->neigh[i], sizeof(ts_vertex));
58230a	366	}
M	367
	368	//if all the tests are successful, then energy for vtx and neighbours is calculated
b30f45	369	delta_energy=0;
M	370
	371	if(vtx->bond_no == 2){
	372	vtx->energy = -(vtx->bond[0]->xvtx->bond[1]->x + vtx->bond[0]->yvtx->bond[1]->y + vtx->bond[0]->z*vtx->bond[1]->z)/vtx->bond[0]->bond_length/vtx->bond[1]->bond_length;
	373	delta_energy += vtx->energy - backupvtx.energy;
58230a	374	}
M	375
b30f45	376	for(i=0;i<vtx->neigh_no;i++){
M	377	if(vtx->neigh[i]->bond_no == 2){
	378	vtx->neigh[i]->energy = -(vtx->neigh[i]->bond[0]->xvtx->neigh[i]->bond[1]->x + vtx->neigh[i]->bond[0]->yvtx->neigh[i]->bond[1]->y + vtx->neigh[i]->bond[0]->z*vtx->neigh[i]->bond[1]->z)/vtx->neigh[i]->bond[0]->bond_length/vtx->neigh[i]->bond[1]->bond_length;
	379	delta_energy += vtx->neigh[i]->energy - backupneigh[i].energy;
	380	}
58230a	381	}
M	382
b30f45	383	// poly->k is filament persistence length (in units l_min)
M	384	delta_energy *= poly->k;
58230a	385
M	386	if(delta_energy>=0){
	387	#ifdef TS_DOUBLE_DOUBLE
	388	if(exp(-delta_energy)< drand48() )
	389	#endif
	390	#ifdef TS_DOUBLE_FLOAT
	391	if(expf(-delta_energy)< (ts_float)drand48())
	392	#endif
	393	#ifdef TS_DOUBLE_LONGDOUBLE
	394	if(expl(-delta_energy)< (ts_ldouble)drand48())
	395	#endif
	396	{
	397	//not accepted, reverting changes
	398	vtx=memcpy((void )vtx,(void )&backupvtx,sizeof(ts_vertex));
b30f45	399	for(i=0;i<vtx->neigh_no;i++){
M	400	memcpy(vtx->neigh[i],&backupneigh[i],sizeof(ts_vertex));
	401	}
58230a	402	for(i=0;i<vtx->bond_no;i++){
b30f45	403	vtx->bond[i]=memcpy((void )vtx->bond[i],(void )&backupbond[i],sizeof(ts_bond));
58230a	404	}
M	405
	406	return TS_FAIL;
	407	}
	408	}
	409
b30f45	410
58230a	411	// oldcellidx=vertex_self_avoidance(vesicle, &backupvtx[0]);
M	412	if(vtx->cell!=vesicle->clist->cell[cellidx]){
	413	retval=cell_add_vertex(vesicle->clist->cell[cellidx],vtx);
	414	// if(retval==TS_SUCCESS) cell_remove_vertex(vesicle->clist->cell[oldcellidx],vtx);
	415	if(retval==TS_SUCCESS) cell_remove_vertex(backupvtx.cell,vtx);
	416	}
	417	// if(oldcellidx);
	418	//END MONTE CARLOOOOOOO
	419	return TS_SUCCESS;
	420	}