trisurf-ng.git - Gitblit

First attempt to calculate points of cross-section

Samo Penic

2014-06-13 0af0cf6ac748ba9c135c9ca0a23cdd6cbf50caf1

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
3de289	153	if(exp(-delta_energy)< drand48())
aec47d	154	#endif
SP	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);
dd5aca	177	// vesicle_volume(vesicle);
SP	178	// fprintf(stderr,"Volume after fail=%1.16e\n", vesicle->volume);
aec47d	179	return TS_FAIL;
SP	180	}
	181	}
2b14da	182	//accepted
fbcbdf	183	// fprintf(stderr,"MC accepted\n");
a63f17	184	// oldcellidx=vertex_self_avoidance(vesicle, &backupvtx[0]);
SP	185	if(vtx->cell!=vesicle->clist->cell[cellidx]){
	186	retval=cell_add_vertex(vesicle->clist->cell[cellidx],vtx);
	187	// if(retval==TS_SUCCESS) cell_remove_vertex(vesicle->clist->cell[oldcellidx],vtx);
	188	if(retval==TS_SUCCESS) cell_remove_vertex(backupvtx[0].cell,vtx);
	189
	190	}
2b14da	191
43c042	192	if(vesicle->tape->constvolswitch == 1){
fbcbdf	193	constvolumeaccept(vesicle,constvol_vtx_moved,constvol_vtx_backup);
43c042	194	}
a63f17	195	// if(oldcellidx);
aec47d	196	//END MONTE CARLOOOOOOO
dd5aca	197	// vesicle_volume(vesicle);
SP	198	// fprintf(stderr,"Volume after success=%1.16e\n", vesicle->volume);
aec47d	199	return TS_SUCCESS;
SP	200	}
	201
fedf2b	202
M	203	ts_bool single_poly_vertex_move(ts_vesicle vesicle,ts_poly poly,ts_vertex vtx,ts_double rn){
	204	ts_uint i;
	205	ts_bool retval;
	206	ts_uint cellidx;
304510	207	// ts_double delta_energy;
fedf2b	208	ts_double costheta,sintheta,phi,r;
304510	209	ts_double dist;
fedf2b	210	//This will hold all the information of vtx and its neighbours
M	211	ts_vertex backupvtx;
304510	212	// ts_bond backupbond[2];
fedf2b	213	memcpy((void )&backupvtx,(void )vtx,sizeof(ts_vertex));
M	214
	215	//random move in a sphere with radius stepsize:
	216	r=vesicle->stepsize*rn[0];
	217	phi=rn[1]2M_PI;
	218	costheta=2*rn[2]-1;
	219	sintheta=sqrt(1-pow(costheta,2));
	220	vtx->x=vtx->x+rsinthetacos(phi);
	221	vtx->y=vtx->y+rsinthetasin(phi);
	222	vtx->z=vtx->z+r*costheta;
	223
	224
	225	//distance with neighbours check
304510	226	for(i=0;i<vtx->neigh_no;i++){
M	227	dist=vtx_distance_sq(vtx,vtx->neigh[i]);
	228	if(dist<1.0 \|\| dist>vesicle->dmax) {
	229	vtx=memcpy((void )vtx,(void )&backupvtx,sizeof(ts_vertex));
	230	return TS_FAIL;
	231	}
	232	}
	233
	234	// Distance with grafted vesicle-vertex check:
	235	if(vtx==poly->vlist->vtx[0]){
	236	dist=vtx_distance_sq(vtx,poly->grafted_vtx);
	237	if(dist<1.0 \|\| dist>vesicle->dmax) {
	238	vtx=memcpy((void )vtx,(void )&backupvtx,sizeof(ts_vertex));
	239	return TS_FAIL;
	240	}
	241	}
	242
fedf2b	243
M	244	//self avoidance check with distant vertices
	245	cellidx=vertex_self_avoidance(vesicle, vtx);
	246	//check occupation number
	247	retval=cell_occupation_number_and_internal_proximity(vesicle->clist,cellidx,vtx);
	248
	249	if(retval==TS_FAIL){
	250	vtx=memcpy((void )vtx,(void )&backupvtx,sizeof(ts_vertex));
	251	return TS_FAIL;
	252	}
	253
	254
	255	//if all the tests are successful, then energy for vtx and neighbours is calculated
304510	256	/* Energy ignored for now!
fedf2b	257	delta_energy=0;
M	258	for(i=0;i<vtx->bond_no;i++){
	259	memcpy((void )&backupbond[i],(void )vtx->bond[i],sizeof(ts_bond));
	260
	261	vtx->bond[i]->bond_length=sqrt(vtx_distance_sq(vtx->bond[i]->vtx1,vtx->bond[i]->vtx2));
	262	bond_energy(vtx->bond[i],poly);
	263	delta_energy+= vtx->bond[i]->energy - backupbond[i].energy;
	264	}
	265
	266	if(vtx==poly->vlist->vtx[0]){
	267	delta_energy+=
	268	(pow(sqrt(vtx_distance_sq(vtx, poly->grafted_vtx)-1),2)-
	269	pow(sqrt(vtx_distance_sq(&backupvtx, poly->grafted_vtx)-1),2)) *poly->k;
	270
	271	}
	272
	273
	274	if(delta_energy>=0){
	275	#ifdef TS_DOUBLE_DOUBLE
	276	if(exp(-delta_energy)< drand48() )
	277	#endif
	278	#ifdef TS_DOUBLE_FLOAT
	279	if(expf(-delta_energy)< (ts_float)drand48())
	280	#endif
	281	#ifdef TS_DOUBLE_LONGDOUBLE
	282	if(expl(-delta_energy)< (ts_ldouble)drand48())
	283	#endif
	284	{
	285	//not accepted, reverting changes
	286	vtx=memcpy((void )vtx,(void )&backupvtx,sizeof(ts_vertex));
	287	for(i=0;i<vtx->bond_no;i++){
	288	vtx->bond[i]=memcpy((void )vtx->bond[i],(void )&backupbond[i],sizeof(ts_bond));
	289	}
	290
	291	return TS_FAIL;
	292	}
	293	}
304510	294	*/
fedf2b	295
M	296	// oldcellidx=vertex_self_avoidance(vesicle, &backupvtx[0]);
	297	if(vtx->cell!=vesicle->clist->cell[cellidx]){
	298	retval=cell_add_vertex(vesicle->clist->cell[cellidx],vtx);
	299	// if(retval==TS_SUCCESS) cell_remove_vertex(vesicle->clist->cell[oldcellidx],vtx);
	300	if(retval==TS_SUCCESS) cell_remove_vertex(backupvtx.cell,vtx);
	301	}
	302	// if(oldcellidx);
	303	//END MONTE CARLOOOOOOO
	304	return TS_SUCCESS;
	305	}
58230a	306
M	307
	308
	309
	310	ts_bool single_filament_vertex_move(ts_vesicle vesicle,ts_poly poly,ts_vertex vtx,ts_double rn){
	311	ts_uint i;
	312	ts_bool retval;
	313	ts_uint cellidx;
b30f45	314	ts_double delta_energy;
58230a	315	ts_double costheta,sintheta,phi,r;
M	316	ts_double dist[2];
	317	//This will hold all the information of vtx and its neighbours
b30f45	318	ts_vertex backupvtx,backupneigh[2];
58230a	319	ts_bond backupbond[2];
b30f45	320
M	321	//backup vertex:
58230a	322	memcpy((void )&backupvtx,(void )vtx,sizeof(ts_vertex));
M	323
	324	//random move in a sphere with radius stepsize:
	325	r=vesicle->stepsize*rn[0];
	326	phi=rn[1]2M_PI;
	327	costheta=2*rn[2]-1;
	328	sintheta=sqrt(1-pow(costheta,2));
	329	vtx->x=vtx->x+rsinthetacos(phi);
	330	vtx->y=vtx->y+rsinthetasin(phi);
	331	vtx->z=vtx->z+r*costheta;
	332
	333
	334	//distance with neighbours check
	335	for(i=0;i<vtx->bond_no;i++){
	336	dist[i]=vtx_distance_sq(vtx->bond[i]->vtx1,vtx->bond[i]->vtx2);
	337	if(dist[i]<1.0 \|\| dist[i]>vesicle->dmax) {
	338	vtx=memcpy((void )vtx,(void )&backupvtx,sizeof(ts_vertex));
	339	return TS_FAIL;
	340	}
	341	}
	342
fe24d2	343	// TODO: Maybe faster if checks only nucleus-neighboring cells
M	344	// Nucleus penetration check:
	345	if (vtx->xvtx->x + vtx->yvtx->y + vtx->z*vtx->z < vesicle->R_nucleus){
	346	vtx=memcpy((void )vtx,(void )&backupvtx,sizeof(ts_vertex));
	347	return TS_FAIL;
	348	}
	349
58230a	350
M	351	//self avoidance check with distant vertices
	352	cellidx=vertex_self_avoidance(vesicle, vtx);
	353	//check occupation number
	354	retval=cell_occupation_number_and_internal_proximity(vesicle->clist,cellidx,vtx);
	355	if(retval==TS_FAIL){
	356	vtx=memcpy((void )vtx,(void )&backupvtx,sizeof(ts_vertex));
	357	return TS_FAIL;
	358	}
	359
	360	//backup bonds
	361	for(i=0;i<vtx->bond_no;i++){
	362	memcpy(&backupbond[i],vtx->bond[i], sizeof(ts_bond));
	363	vtx->bond[i]->bond_length=sqrt(dist[i]);
	364	bond_vector(vtx->bond[i]);
b30f45	365	}
M	366
	367	//backup neighboring vertices:
	368	for(i=0;i<vtx->neigh_no;i++){
	369	memcpy(&backupneigh[i],vtx->neigh[i], sizeof(ts_vertex));
58230a	370	}
M	371
	372	//if all the tests are successful, then energy for vtx and neighbours is calculated
b30f45	373	delta_energy=0;
M	374
	375	if(vtx->bond_no == 2){
	376	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;
	377	delta_energy += vtx->energy - backupvtx.energy;
58230a	378	}
M	379
b30f45	380	for(i=0;i<vtx->neigh_no;i++){
M	381	if(vtx->neigh[i]->bond_no == 2){
	382	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;
	383	delta_energy += vtx->neigh[i]->energy - backupneigh[i].energy;
	384	}
58230a	385	}
M	386
b30f45	387	// poly->k is filament persistence length (in units l_min)
M	388	delta_energy *= poly->k;
58230a	389
M	390	if(delta_energy>=0){
	391	#ifdef TS_DOUBLE_DOUBLE
	392	if(exp(-delta_energy)< drand48() )
	393	#endif
	394	#ifdef TS_DOUBLE_FLOAT
	395	if(expf(-delta_energy)< (ts_float)drand48())
	396	#endif
	397	#ifdef TS_DOUBLE_LONGDOUBLE
	398	if(expl(-delta_energy)< (ts_ldouble)drand48())
	399	#endif
	400	{
	401	//not accepted, reverting changes
	402	vtx=memcpy((void )vtx,(void )&backupvtx,sizeof(ts_vertex));
b30f45	403	for(i=0;i<vtx->neigh_no;i++){
M	404	memcpy(vtx->neigh[i],&backupneigh[i],sizeof(ts_vertex));
	405	}
58230a	406	for(i=0;i<vtx->bond_no;i++){
b30f45	407	vtx->bond[i]=memcpy((void )vtx->bond[i],(void )&backupbond[i],sizeof(ts_bond));
58230a	408	}
M	409
	410	return TS_FAIL;
	411	}
	412	}
	413
b30f45	414
58230a	415	// oldcellidx=vertex_self_avoidance(vesicle, &backupvtx[0]);
M	416	if(vtx->cell!=vesicle->clist->cell[cellidx]){
	417	retval=cell_add_vertex(vesicle->clist->cell[cellidx],vtx);
	418	// if(retval==TS_SUCCESS) cell_remove_vertex(vesicle->clist->cell[oldcellidx],vtx);
	419	if(retval==TS_SUCCESS) cell_remove_vertex(backupvtx.cell,vtx);
	420	}
	421	// if(oldcellidx);
	422	//END MONTE CARLOOOOOOO
	423	return TS_SUCCESS;
	424	}