trisurf-ng.git - Gitblit

Samo Penic

2019-03-08 7522b886602380764ce76f1d2244fad11bd1054f

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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"
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"
51b4f0	17	#include "plugins.h"
aec47d	18
fedf2b	19	ts_bool single_verticle_timestep(ts_vesicle vesicle,ts_vertex vtx,ts_double *rn){
aec47d	20	ts_uint i;
SP	21	ts_bool retval;
	22	ts_uint cellidx;
7522b8	23	ts_double delta_energy, oenergy, darea=0.0, dstretchenergy=0.0;
ed31fe	24	ts_double costheta,sintheta,phi,r;
1ad6d1	25	//This will hold all the information of vtx and its neighbours
2afc2f	26	ts_vertex backupvtx[20]; // constvol_vtx_moved=NULL, constvol_vtx_backup=NULL;
b5cd8c	27	memcpy((void )&backupvtx[0],(void )vtx,sizeof(ts_vertex));
672ae4	28
b5cd8c	29	//random move in a sphere with radius stepsize:
SP	30	r=vesicle->stepsize*rn[0];
	31	phi=rn[1]2M_PI;
	32	costheta=2*rn[2]-1;
	33	sintheta=sqrt(1-pow(costheta,2));
	34	vtx->x=vtx->x+rsinthetacos(phi);
	35	vtx->y=vtx->y+rsinthetasin(phi);
	36	vtx->z=vtx->z+r*costheta;
672ae4	37
fe24d2	38
51b4f0	39	/* Entry point for plugin vm_hard_constraint() function */
77a2c7	40	vesicle->plist->pointer=vesicle->plist->chain->vm_hard_constraint;
SP	41	while(vesicle->plist->pointer!=NULL){
	42	retval = vesicle->plist->pointer->plugin->function->vm_hard_constraint(vesicle,vtx, &backupvtx[0]);
51b4f0	43	if(retval==TS_FAIL){
SP	44	vtx=memcpy((void )vtx,(void )&backupvtx[0],sizeof(ts_vertex));
	45	return TS_FAIL;
	46	}
77a2c7	47	vesicle->plist->pointer=vesicle->plist->pointer->next;
51b4f0	48	}
36dba8	49	/* End of vm_hard_constraint() */
51b4f0	50
36dba8	51	/* Backuping the neighbours */
1ad6d1	52	for(i=0;i<vtx->neigh_no;i++){
dcd350	53	memcpy((void )&backupvtx[i+1],(void )vtx->neigh[i],sizeof(ts_vertex));
1ad6d1	54	}
aec47d	55
36dba8	56	/* Entry point for plugin vm_energy_before_prepare() */
SP	57
	58	vesicle->plist->pointer=vesicle->plist->chain->vm_energy_before_prepare;
	59	while(vesicle->plist->pointer!=NULL){
	60	vesicle->plist->pointer->plugin->function->vm_energy_before_prepare(vesicle, vtx);
	61	vesicle->plist->pointer=vesicle->plist->pointer->next;
c0ae90	62	}
SP	63
	64	if(vesicle->tape->constareaswitch==2){
	65	for(i=0;i<vtx->tristar_no;i++) darea-=vtx->tristar[i]->area;
	66
	67	}
7ec6fb	68	//stretching energy 1 of 3
SP	69	if(vesicle->tape->stretchswitch==1){
699ac4	70	for(i=0;i<vtx->tristar_no;i++) dstretchenergy-=vtx->tristar[i]->energy;
7ec6fb	71	}
aec47d	72	delta_energy=0;
0dd5ba	73
SP	74
fe5069	75	// vesicle_volume(vesicle);
SP	76	// fprintf(stderr,"Volume in the beginning=%1.16e\n", vesicle->volume);
43c042	77
aec47d	78	//update the normals of triangles that share bead i.
8f6a69	79	for(i=0;i<vtx->tristar_no;i++) triangle_normal_vector(vtx->tristar[i]);
a63f17	80	oenergy=vtx->energy;
aec47d	81	energy_vertex(vtx);
a63f17	82	delta_energy=vtx->xk*(vtx->energy - oenergy);
aec47d	83	//the same is done for neighbouring vertices
8f6a69	84	for(i=0;i<vtx->neigh_no;i++){
SP	85	oenergy=vtx->neigh[i]->energy;
	86	energy_vertex(vtx->neigh[i]);
	87	delta_energy+=vtx->neigh[i]->xk*(vtx->neigh[i]->energy-oenergy);
aec47d	88	}
414b8a	89
77a2c7	90
SP	91	/* Entry point for plugin vm_energy_after_execute() */
	92
	93	vesicle->plist->pointer=vesicle->plist->chain->vm_energy_after_execute;
	94	while(vesicle->plist->pointer!=NULL){
	95	delta_energy+=vesicle->plist->pointer->plugin->function->vm_energy_after_execute(vesicle, vtx);
	96	vesicle->plist->pointer=vesicle->plist->pointer->next;
	97	}
	98
	99
43c042	100
c0ae90	101	if(vesicle->tape->constareaswitch==2){
SP	102	/* check whether the darea is gt epsarea */
	103	for(i=0;i<vtx->tristar_no;i++) darea+=vtx->tristar[i]->area;
	104	if(fabs(vesicle->area+darea-A0)>epsarea){
	105	//restore old state.
	106	vtx=memcpy((void )vtx,(void )&backupvtx[0],sizeof(ts_vertex));
	107	for(i=0;i<vtx->neigh_no;i++){
	108	vtx->neigh[i]=memcpy((void )vtx->neigh[i],(void )&backupvtx[i+1],sizeof(ts_vertex));
	109	}
	110	for(i=0;i<vtx->tristar_no;i++) triangle_normal_vector(vtx->tristar[i]);
	111	//fprintf(stderr,"fajlam!\n");
	112	return TS_FAIL;
	113	}
	114
	115
	116	}
1121fa	117
250de4	118	/* Vertices with spontaneous curvature may have spontaneous force perpendicular to the surface of the vesicle. additional delta energy is calculated in this function */
SP	119	delta_energy+=direct_force_energy(vesicle,vtx,backupvtx);
7ec6fb	120
SP	121	//stretching energy 2 of 3
	122	if(vesicle->tape->stretchswitch==1){
	123	for(i=0;i<vtx->tristar_no;i++){
	124	stretchenergy(vesicle, vtx->tristar[i]);
699ac4	125	dstretchenergy+=vtx->tristar[i]->energy;
7ec6fb	126	}
SP	127	}
	128
	129	delta_energy+=dstretchenergy;
	130
304510	131	/* No poly-bond energy for now!
fedf2b	132	if(vtx->grafted_poly!=NULL){
M	133	delta_energy+=
	134	(pow(sqrt(vtx_distance_sq(vtx, vtx->grafted_poly->vlist->vtx[0])-1),2)-
	135	pow(sqrt(vtx_distance_sq(&backupvtx[0], vtx->grafted_poly->vlist->vtx[0])-1),2)) *vtx->grafted_poly->k;
	136	}
304510	137	*/
0dd5ba	138
SP	139	// plane confinement energy due to compressing force
	140	if(vesicle->tape->plane_confinement_switch){
	141	if(vesicle->confinement_plane.force_switch){
	142	//substract old energy
	143	if(abs(vesicle->tape->plane_d/2.0-vesicle->confinement_plane.z_max)>1e-10) {
	144	delta_energy-=vesicle->tape->plane_F / pow(vesicle->confinement_plane.z_max-backupvtx[0].z,2);
	145	delta_energy+=vesicle->tape->plane_F / pow(vesicle->confinement_plane.z_max-vtx->z,2);
	146	}
	147	if(abs(-vesicle->tape->plane_d/2.0-vesicle->confinement_plane.z_min)>1e-10) {
	148	delta_energy-=vesicle->tape->plane_F / pow(vesicle->confinement_plane.z_min-backupvtx[0].z,2);
	149	delta_energy+=vesicle->tape->plane_F / pow(vesicle->confinement_plane.z_min-vtx->z,2);
	150	}
	151	}
	152	}
	153
77a2c7	154
SP	155	/* Entry point for plugin vm_before_montecarlo_constraint() function */
	156	vesicle->plist->pointer=vesicle->plist->chain->vm_before_montecarlo_constraint;
	157	while(vesicle->plist->pointer!=NULL){
	158	retval = vesicle->plist->pointer->plugin->function->vm_before_montecarlo_constraint(vesicle,vtx, &backupvtx[0]);
	159	if(retval==TS_FAIL){
	160	vtx=memcpy((void )vtx,(void )&backupvtx[0],sizeof(ts_vertex));
	161	for(i=0;i<vtx->neigh_no;i++){
	162	vtx->neigh[i]=memcpy((void )vtx->neigh[i],(void )&backupvtx[i+1],sizeof(ts_vertex));
	163	}
	164	for(i=0;i<vtx->tristar_no;i++) triangle_normal_vector(vtx->tristar[i]);
	165	return TS_FAIL;
	166	}
	167	vesicle->plist->pointer=vesicle->plist->pointer->next;
	168	}
	169	/* End of vm_before_montecarlo_constraint() */
	170
	171
	172
	173
	174
314f2d	175	// fprintf(stderr, "DE=%f\n",delta_energy);
aec47d	176	//MONTE CARLOOOOOOOO
SP	177	if(delta_energy>=0){
	178	#ifdef TS_DOUBLE_DOUBLE
3de289	179	if(exp(-delta_energy)< drand48())
aec47d	180	#endif
SP	181	#ifdef TS_DOUBLE_FLOAT
	182	if(expf(-delta_energy)< (ts_float)drand48())
	183	#endif
	184	#ifdef TS_DOUBLE_LONGDOUBLE
	185	if(expl(-delta_energy)< (ts_ldouble)drand48())
	186	#endif
	187	{
7522b8	188	/************************************************* MC step rejected ************************************************************/
dcd350	189	vtx=memcpy((void )vtx,(void )&backupvtx[0],sizeof(ts_vertex));
1ad6d1	190	for(i=0;i<vtx->neigh_no;i++){
a63f17	191	vtx->neigh[i]=memcpy((void )vtx->neigh[i],(void )&backupvtx[i+1],sizeof(ts_vertex));
1ad6d1	192	}
SP	193
7522b8	194	//update the normals of triangles that share bead i.
SP	195	for(i=0;i<vtx->tristar_no;i++) triangle_normal_vector(vtx->tristar[i]);
	196
7ec6fb	197	//stretching energy 3 of 3
SP	198	if(vesicle->tape->stretchswitch==1){
	199	for(i=0;i<vtx->tristar_no;i++){
	200	stretchenergy(vesicle,vtx->tristar[i]);
	201	}
	202	}
1ad6d1	203
7522b8	204
SP	205
	206	/* Entry point for plugin vm_before_montecarlo_constraint() function */
	207	vesicle->plist->pointer=vesicle->plist->chain->vm_new_state_rejected;
	208	while(vesicle->plist->pointer!=NULL){
	209	vesicle->plist->pointer->plugin->function->vm_new_state_rejected(vesicle,vtx, &backupvtx[0]);
	210	vesicle->plist->pointer=vesicle->plist->pointer->next;
	211	}
	212	/* End of vm_before_montecarlo_constraint() */
	213
	214
aec47d	215	return TS_FAIL;
SP	216	}
	217	}
7522b8	218	/************************************************* MC step accepted ************************************************************/
51b4f0	219	cellidx=vertex_self_avoidance(vesicle, vtx);
a63f17	220	if(vtx->cell!=vesicle->clist->cell[cellidx]){
SP	221	retval=cell_add_vertex(vesicle->clist->cell[cellidx],vtx);
7522b8	222	if(retval==TS_SUCCESS) cell_remove_vertex(backupvtx[0].cell,vtx);
a63f17	223	}
2afc2f	224
c0ae90	225
SP	226	if(vesicle->tape->constareaswitch==2){
	227	vesicle->area+=darea;
	228	}
2afc2f	229
SP	230
	231	/* Entry point for plugin vm_before_montecarlo_constraint() function */
	232	vesicle->plist->pointer=vesicle->plist->chain->vm_new_state_accepted;
	233	while(vesicle->plist->pointer!=NULL){
	234	vesicle->plist->pointer->plugin->function->vm_new_state_accepted(vesicle,vtx, &backupvtx[0]);
	235	vesicle->plist->pointer=vesicle->plist->pointer->next;
	236	}
	237	/* End of vm_before_montecarlo_constraint() */
	238
aec47d	239	return TS_SUCCESS;
SP	240	}
	241
fedf2b	242
7522b8	243
SP	244
	245
fedf2b	246	ts_bool single_poly_vertex_move(ts_vesicle vesicle,ts_poly poly,ts_vertex vtx,ts_double rn){
M	247	ts_uint i;
	248	ts_bool retval;
	249	ts_uint cellidx;
304510	250	// ts_double delta_energy;
fedf2b	251	ts_double costheta,sintheta,phi,r;
304510	252	ts_double dist;
fedf2b	253	//This will hold all the information of vtx and its neighbours
M	254	ts_vertex backupvtx;
304510	255	// ts_bond backupbond[2];
fedf2b	256	memcpy((void )&backupvtx,(void )vtx,sizeof(ts_vertex));
M	257
	258	//random move in a sphere with radius stepsize:
	259	r=vesicle->stepsize*rn[0];
	260	phi=rn[1]2M_PI;
	261	costheta=2*rn[2]-1;
	262	sintheta=sqrt(1-pow(costheta,2));
	263	vtx->x=vtx->x+rsinthetacos(phi);
	264	vtx->y=vtx->y+rsinthetasin(phi);
	265	vtx->z=vtx->z+r*costheta;
	266
	267
	268	//distance with neighbours check
304510	269	for(i=0;i<vtx->neigh_no;i++){
M	270	dist=vtx_distance_sq(vtx,vtx->neigh[i]);
	271	if(dist<1.0 \|\| dist>vesicle->dmax) {
	272	vtx=memcpy((void )vtx,(void )&backupvtx,sizeof(ts_vertex));
	273	return TS_FAIL;
	274	}
	275	}
	276
	277	// Distance with grafted vesicle-vertex check:
	278	if(vtx==poly->vlist->vtx[0]){
	279	dist=vtx_distance_sq(vtx,poly->grafted_vtx);
	280	if(dist<1.0 \|\| dist>vesicle->dmax) {
	281	vtx=memcpy((void )vtx,(void )&backupvtx,sizeof(ts_vertex));
	282	return TS_FAIL;
	283	}
	284	}
	285
fedf2b	286
M	287	//self avoidance check with distant vertices
	288	cellidx=vertex_self_avoidance(vesicle, vtx);
	289	//check occupation number
	290	retval=cell_occupation_number_and_internal_proximity(vesicle->clist,cellidx,vtx);
	291
	292	if(retval==TS_FAIL){
	293	vtx=memcpy((void )vtx,(void )&backupvtx,sizeof(ts_vertex));
	294	return TS_FAIL;
	295	}
	296
	297
	298	//if all the tests are successful, then energy for vtx and neighbours is calculated
304510	299	/* Energy ignored for now!
fedf2b	300	delta_energy=0;
M	301	for(i=0;i<vtx->bond_no;i++){
	302	memcpy((void )&backupbond[i],(void )vtx->bond[i],sizeof(ts_bond));
	303
	304	vtx->bond[i]->bond_length=sqrt(vtx_distance_sq(vtx->bond[i]->vtx1,vtx->bond[i]->vtx2));
	305	bond_energy(vtx->bond[i],poly);
	306	delta_energy+= vtx->bond[i]->energy - backupbond[i].energy;
	307	}
	308
	309	if(vtx==poly->vlist->vtx[0]){
	310	delta_energy+=
	311	(pow(sqrt(vtx_distance_sq(vtx, poly->grafted_vtx)-1),2)-
	312	pow(sqrt(vtx_distance_sq(&backupvtx, poly->grafted_vtx)-1),2)) *poly->k;
	313
	314	}
	315
	316
	317	if(delta_energy>=0){
	318	#ifdef TS_DOUBLE_DOUBLE
	319	if(exp(-delta_energy)< drand48() )
	320	#endif
	321	#ifdef TS_DOUBLE_FLOAT
	322	if(expf(-delta_energy)< (ts_float)drand48())
	323	#endif
	324	#ifdef TS_DOUBLE_LONGDOUBLE
	325	if(expl(-delta_energy)< (ts_ldouble)drand48())
	326	#endif
	327	{
	328	//not accepted, reverting changes
	329	vtx=memcpy((void )vtx,(void )&backupvtx,sizeof(ts_vertex));
	330	for(i=0;i<vtx->bond_no;i++){
	331	vtx->bond[i]=memcpy((void )vtx->bond[i],(void )&backupbond[i],sizeof(ts_bond));
	332	}
	333
	334	return TS_FAIL;
	335	}
	336	}
304510	337	*/
fedf2b	338
M	339	// oldcellidx=vertex_self_avoidance(vesicle, &backupvtx[0]);
	340	if(vtx->cell!=vesicle->clist->cell[cellidx]){
	341	retval=cell_add_vertex(vesicle->clist->cell[cellidx],vtx);
	342	// if(retval==TS_SUCCESS) cell_remove_vertex(vesicle->clist->cell[oldcellidx],vtx);
	343	if(retval==TS_SUCCESS) cell_remove_vertex(backupvtx.cell,vtx);
	344	}
	345	// if(oldcellidx);
	346	//END MONTE CARLOOOOOOO
	347	return TS_SUCCESS;
	348	}
58230a	349
M	350
	351
	352
	353	ts_bool single_filament_vertex_move(ts_vesicle vesicle,ts_poly poly,ts_vertex vtx,ts_double rn){
	354	ts_uint i;
	355	ts_bool retval;
	356	ts_uint cellidx;
b30f45	357	ts_double delta_energy;
58230a	358	ts_double costheta,sintheta,phi,r;
M	359	ts_double dist[2];
	360	//This will hold all the information of vtx and its neighbours
b30f45	361	ts_vertex backupvtx,backupneigh[2];
58230a	362	ts_bond backupbond[2];
b30f45	363
M	364	//backup vertex:
58230a	365	memcpy((void )&backupvtx,(void )vtx,sizeof(ts_vertex));
M	366
	367	//random move in a sphere with radius stepsize:
	368	r=vesicle->stepsize*rn[0];
	369	phi=rn[1]2M_PI;
	370	costheta=2*rn[2]-1;
	371	sintheta=sqrt(1-pow(costheta,2));
	372	vtx->x=vtx->x+rsinthetacos(phi);
	373	vtx->y=vtx->y+rsinthetasin(phi);
	374	vtx->z=vtx->z+r*costheta;
	375
	376
	377	//distance with neighbours check
	378	for(i=0;i<vtx->bond_no;i++){
	379	dist[i]=vtx_distance_sq(vtx->bond[i]->vtx1,vtx->bond[i]->vtx2);
	380	if(dist[i]<1.0 \|\| dist[i]>vesicle->dmax) {
	381	vtx=memcpy((void )vtx,(void )&backupvtx,sizeof(ts_vertex));
	382	return TS_FAIL;
	383	}
	384	}
	385
fe24d2	386	// TODO: Maybe faster if checks only nucleus-neighboring cells
M	387	// Nucleus penetration check:
	388	if (vtx->xvtx->x + vtx->yvtx->y + vtx->z*vtx->z < vesicle->R_nucleus){
	389	vtx=memcpy((void )vtx,(void )&backupvtx,sizeof(ts_vertex));
	390	return TS_FAIL;
	391	}
	392
58230a	393
M	394	//self avoidance check with distant vertices
	395	cellidx=vertex_self_avoidance(vesicle, vtx);
	396	//check occupation number
	397	retval=cell_occupation_number_and_internal_proximity(vesicle->clist,cellidx,vtx);
	398	if(retval==TS_FAIL){
	399	vtx=memcpy((void )vtx,(void )&backupvtx,sizeof(ts_vertex));
	400	return TS_FAIL;
	401	}
	402
	403	//backup bonds
	404	for(i=0;i<vtx->bond_no;i++){
	405	memcpy(&backupbond[i],vtx->bond[i], sizeof(ts_bond));
	406	vtx->bond[i]->bond_length=sqrt(dist[i]);
	407	bond_vector(vtx->bond[i]);
b30f45	408	}
M	409
	410	//backup neighboring vertices:
	411	for(i=0;i<vtx->neigh_no;i++){
	412	memcpy(&backupneigh[i],vtx->neigh[i], sizeof(ts_vertex));
58230a	413	}
M	414
	415	//if all the tests are successful, then energy for vtx and neighbours is calculated
b30f45	416	delta_energy=0;
M	417
	418	if(vtx->bond_no == 2){
	419	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;
	420	delta_energy += vtx->energy - backupvtx.energy;
58230a	421	}
M	422
b30f45	423	for(i=0;i<vtx->neigh_no;i++){
M	424	if(vtx->neigh[i]->bond_no == 2){
	425	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;
	426	delta_energy += vtx->neigh[i]->energy - backupneigh[i].energy;
	427	}
58230a	428	}
M	429
b30f45	430	// poly->k is filament persistence length (in units l_min)
M	431	delta_energy *= poly->k;
58230a	432
M	433	if(delta_energy>=0){
	434	#ifdef TS_DOUBLE_DOUBLE
	435	if(exp(-delta_energy)< drand48() )
	436	#endif
	437	#ifdef TS_DOUBLE_FLOAT
	438	if(expf(-delta_energy)< (ts_float)drand48())
	439	#endif
	440	#ifdef TS_DOUBLE_LONGDOUBLE
	441	if(expl(-delta_energy)< (ts_ldouble)drand48())
	442	#endif
	443	{
	444	//not accepted, reverting changes
	445	vtx=memcpy((void )vtx,(void )&backupvtx,sizeof(ts_vertex));
b30f45	446	for(i=0;i<vtx->neigh_no;i++){
M	447	memcpy(vtx->neigh[i],&backupneigh[i],sizeof(ts_vertex));
	448	}
58230a	449	for(i=0;i<vtx->bond_no;i++){
b30f45	450	vtx->bond[i]=memcpy((void )vtx->bond[i],(void )&backupbond[i],sizeof(ts_bond));
58230a	451	}
M	452
	453	return TS_FAIL;
	454	}
	455	}
	456
b30f45	457
58230a	458	// oldcellidx=vertex_self_avoidance(vesicle, &backupvtx[0]);
M	459	if(vtx->cell!=vesicle->clist->cell[cellidx]){
	460	retval=cell_add_vertex(vesicle->clist->cell[cellidx],vtx);
	461	// if(retval==TS_SUCCESS) cell_remove_vertex(vesicle->clist->cell[oldcellidx],vtx);
	462	if(retval==TS_SUCCESS) cell_remove_vertex(backupvtx.cell,vtx);
	463	}
	464	// if(oldcellidx);
	465	//END MONTE CARLOOOOOOO
	466	return TS_SUCCESS;
	467	}