trisurf-ng.git - Gitblit

Constant volume in bondflip need lots of debugging

Samo Penic

2014-04-29 fbcbdf4093644e43688d9a44d6553d7153d8a2eb

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;
43c042	100
fbcbdf	101
SP	102	// fprintf(stderr,"Success for now.\n");
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
fbcbdf	121	if(vesicle->tape->constvolswitch == 1){
SP	122	retval=constvolume(vesicle, vtx, -dvol, &delta_energy_cv, &constvol_vtx_moved,&constvol_vtx_backup);
	123	if(retval==TS_FAIL){ // if we couldn't move the vertex to assure constant volume
	124	vtx=memcpy((void )vtx,(void )&backupvtx[0],sizeof(ts_vertex));
	125	for(i=0;i<vtx->neigh_no;i++){
	126	vtx->neigh[i]=memcpy((void )vtx->neigh[i],(void )&backupvtx[i+1],sizeof(ts_vertex));
	127	}
	128	for(i=0;i<vtx->tristar_no;i++) triangle_normal_vector(vtx->tristar[i]);
	129	return TS_FAIL;
	130	}
	131	delta_energy+=delta_energy_cv;
	132	}
304510	133	/* No poly-bond energy for now!
fedf2b	134	if(vtx->grafted_poly!=NULL){
M	135	delta_energy+=
	136	(pow(sqrt(vtx_distance_sq(vtx, vtx->grafted_poly->vlist->vtx[0])-1),2)-
	137	pow(sqrt(vtx_distance_sq(&backupvtx[0], vtx->grafted_poly->vlist->vtx[0])-1),2)) *vtx->grafted_poly->k;
	138	}
304510	139	*/
314f2d	140	// fprintf(stderr, "DE=%f\n",delta_energy);
aec47d	141	//MONTE CARLOOOOOOOO
SP	142	if(delta_energy>=0){
	143	#ifdef TS_DOUBLE_DOUBLE
	144	if(exp(-delta_energy)< drand48() )
	145	#endif
	146	#ifdef TS_DOUBLE_FLOAT
	147	if(expf(-delta_energy)< (ts_float)drand48())
	148	#endif
	149	#ifdef TS_DOUBLE_LONGDOUBLE
	150	if(expl(-delta_energy)< (ts_ldouble)drand48())
	151	#endif
	152	{
	153	//not accepted, reverting changes
fbcbdf	154	// fprintf(stderr,"MC failed\n");
dcd350	155	vtx=memcpy((void )vtx,(void )&backupvtx[0],sizeof(ts_vertex));
1ad6d1	156	for(i=0;i<vtx->neigh_no;i++){
a63f17	157	vtx->neigh[i]=memcpy((void )vtx->neigh[i],(void )&backupvtx[i+1],sizeof(ts_vertex));
1ad6d1	158	}
SP	159
aec47d	160	//update the normals of triangles that share bead i.
dcd350	161	for(i=0;i<vtx->tristar_no;i++) triangle_normal_vector(vtx->tristar[i]);
1ad6d1	162
43c042	163	if(vesicle->tape->constvolswitch == 1){
958e0e	164	constvolumerestore(constvol_vtx_moved,constvol_vtx_backup);
43c042	165	}
aec47d	166	return TS_FAIL;
SP	167	}
	168	}
2b14da	169	//accepted
fbcbdf	170	// fprintf(stderr,"MC accepted\n");
a63f17	171	// oldcellidx=vertex_self_avoidance(vesicle, &backupvtx[0]);
SP	172	if(vtx->cell!=vesicle->clist->cell[cellidx]){
	173	retval=cell_add_vertex(vesicle->clist->cell[cellidx],vtx);
	174	// if(retval==TS_SUCCESS) cell_remove_vertex(vesicle->clist->cell[oldcellidx],vtx);
	175	if(retval==TS_SUCCESS) cell_remove_vertex(backupvtx[0].cell,vtx);
	176
	177	}
2b14da	178
43c042	179	if(vesicle->tape->constvolswitch == 1){
fbcbdf	180	constvolumeaccept(vesicle,constvol_vtx_moved,constvol_vtx_backup);
43c042	181	}
a63f17	182	// if(oldcellidx);
aec47d	183	//END MONTE CARLOOOOOOO
SP	184	return TS_SUCCESS;
	185	}
	186
fedf2b	187
M	188	ts_bool single_poly_vertex_move(ts_vesicle vesicle,ts_poly poly,ts_vertex vtx,ts_double rn){
	189	ts_uint i;
	190	ts_bool retval;
	191	ts_uint cellidx;
304510	192	// ts_double delta_energy;
fedf2b	193	ts_double costheta,sintheta,phi,r;
304510	194	ts_double dist;
fedf2b	195	//This will hold all the information of vtx and its neighbours
M	196	ts_vertex backupvtx;
304510	197	// ts_bond backupbond[2];
fedf2b	198	memcpy((void )&backupvtx,(void )vtx,sizeof(ts_vertex));
M	199
	200	//random move in a sphere with radius stepsize:
	201	r=vesicle->stepsize*rn[0];
	202	phi=rn[1]2M_PI;
	203	costheta=2*rn[2]-1;
	204	sintheta=sqrt(1-pow(costheta,2));
	205	vtx->x=vtx->x+rsinthetacos(phi);
	206	vtx->y=vtx->y+rsinthetasin(phi);
	207	vtx->z=vtx->z+r*costheta;
	208
	209
	210	//distance with neighbours check
304510	211	for(i=0;i<vtx->neigh_no;i++){
M	212	dist=vtx_distance_sq(vtx,vtx->neigh[i]);
	213	if(dist<1.0 \|\| dist>vesicle->dmax) {
	214	vtx=memcpy((void )vtx,(void )&backupvtx,sizeof(ts_vertex));
	215	return TS_FAIL;
	216	}
	217	}
	218
	219	// Distance with grafted vesicle-vertex check:
	220	if(vtx==poly->vlist->vtx[0]){
	221	dist=vtx_distance_sq(vtx,poly->grafted_vtx);
	222	if(dist<1.0 \|\| dist>vesicle->dmax) {
	223	vtx=memcpy((void )vtx,(void )&backupvtx,sizeof(ts_vertex));
	224	return TS_FAIL;
	225	}
	226	}
	227
fedf2b	228
M	229	//self avoidance check with distant vertices
	230	cellidx=vertex_self_avoidance(vesicle, vtx);
	231	//check occupation number
	232	retval=cell_occupation_number_and_internal_proximity(vesicle->clist,cellidx,vtx);
	233
	234	if(retval==TS_FAIL){
	235	vtx=memcpy((void )vtx,(void )&backupvtx,sizeof(ts_vertex));
	236	return TS_FAIL;
	237	}
	238
	239
	240	//if all the tests are successful, then energy for vtx and neighbours is calculated
304510	241	/* Energy ignored for now!
fedf2b	242	delta_energy=0;
M	243	for(i=0;i<vtx->bond_no;i++){
	244	memcpy((void )&backupbond[i],(void )vtx->bond[i],sizeof(ts_bond));
	245
	246	vtx->bond[i]->bond_length=sqrt(vtx_distance_sq(vtx->bond[i]->vtx1,vtx->bond[i]->vtx2));
	247	bond_energy(vtx->bond[i],poly);
	248	delta_energy+= vtx->bond[i]->energy - backupbond[i].energy;
	249	}
	250
	251	if(vtx==poly->vlist->vtx[0]){
	252	delta_energy+=
	253	(pow(sqrt(vtx_distance_sq(vtx, poly->grafted_vtx)-1),2)-
	254	pow(sqrt(vtx_distance_sq(&backupvtx, poly->grafted_vtx)-1),2)) *poly->k;
	255
	256	}
	257
	258
	259	if(delta_energy>=0){
	260	#ifdef TS_DOUBLE_DOUBLE
	261	if(exp(-delta_energy)< drand48() )
	262	#endif
	263	#ifdef TS_DOUBLE_FLOAT
	264	if(expf(-delta_energy)< (ts_float)drand48())
	265	#endif
	266	#ifdef TS_DOUBLE_LONGDOUBLE
	267	if(expl(-delta_energy)< (ts_ldouble)drand48())
	268	#endif
	269	{
	270	//not accepted, reverting changes
	271	vtx=memcpy((void )vtx,(void )&backupvtx,sizeof(ts_vertex));
	272	for(i=0;i<vtx->bond_no;i++){
	273	vtx->bond[i]=memcpy((void )vtx->bond[i],(void )&backupbond[i],sizeof(ts_bond));
	274	}
	275
	276	return TS_FAIL;
	277	}
	278	}
304510	279	*/
fedf2b	280
M	281	// oldcellidx=vertex_self_avoidance(vesicle, &backupvtx[0]);
	282	if(vtx->cell!=vesicle->clist->cell[cellidx]){
	283	retval=cell_add_vertex(vesicle->clist->cell[cellidx],vtx);
	284	// if(retval==TS_SUCCESS) cell_remove_vertex(vesicle->clist->cell[oldcellidx],vtx);
	285	if(retval==TS_SUCCESS) cell_remove_vertex(backupvtx.cell,vtx);
	286	}
	287	// if(oldcellidx);
	288	//END MONTE CARLOOOOOOO
	289	return TS_SUCCESS;
	290	}
58230a	291
M	292
	293
	294
	295	ts_bool single_filament_vertex_move(ts_vesicle vesicle,ts_poly poly,ts_vertex vtx,ts_double rn){
	296	ts_uint i;
	297	ts_bool retval;
	298	ts_uint cellidx;
b30f45	299	ts_double delta_energy;
58230a	300	ts_double costheta,sintheta,phi,r;
M	301	ts_double dist[2];
	302	//This will hold all the information of vtx and its neighbours
b30f45	303	ts_vertex backupvtx,backupneigh[2];
58230a	304	ts_bond backupbond[2];
b30f45	305
M	306	//backup vertex:
58230a	307	memcpy((void )&backupvtx,(void )vtx,sizeof(ts_vertex));
M	308
	309	//random move in a sphere with radius stepsize:
	310	r=vesicle->stepsize*rn[0];
	311	phi=rn[1]2M_PI;
	312	costheta=2*rn[2]-1;
	313	sintheta=sqrt(1-pow(costheta,2));
	314	vtx->x=vtx->x+rsinthetacos(phi);
	315	vtx->y=vtx->y+rsinthetasin(phi);
	316	vtx->z=vtx->z+r*costheta;
	317
	318
	319	//distance with neighbours check
	320	for(i=0;i<vtx->bond_no;i++){
	321	dist[i]=vtx_distance_sq(vtx->bond[i]->vtx1,vtx->bond[i]->vtx2);
	322	if(dist[i]<1.0 \|\| dist[i]>vesicle->dmax) {
	323	vtx=memcpy((void )vtx,(void )&backupvtx,sizeof(ts_vertex));
	324	return TS_FAIL;
	325	}
	326	}
	327
fe24d2	328	// TODO: Maybe faster if checks only nucleus-neighboring cells
M	329	// Nucleus penetration check:
	330	if (vtx->xvtx->x + vtx->yvtx->y + vtx->z*vtx->z < vesicle->R_nucleus){
	331	vtx=memcpy((void )vtx,(void )&backupvtx,sizeof(ts_vertex));
	332	return TS_FAIL;
	333	}
	334
58230a	335
M	336	//self avoidance check with distant vertices
	337	cellidx=vertex_self_avoidance(vesicle, vtx);
	338	//check occupation number
	339	retval=cell_occupation_number_and_internal_proximity(vesicle->clist,cellidx,vtx);
	340	if(retval==TS_FAIL){
	341	vtx=memcpy((void )vtx,(void )&backupvtx,sizeof(ts_vertex));
	342	return TS_FAIL;
	343	}
	344
	345	//backup bonds
	346	for(i=0;i<vtx->bond_no;i++){
	347	memcpy(&backupbond[i],vtx->bond[i], sizeof(ts_bond));
	348	vtx->bond[i]->bond_length=sqrt(dist[i]);
	349	bond_vector(vtx->bond[i]);
b30f45	350	}
M	351
	352	//backup neighboring vertices:
	353	for(i=0;i<vtx->neigh_no;i++){
	354	memcpy(&backupneigh[i],vtx->neigh[i], sizeof(ts_vertex));
58230a	355	}
M	356
	357	//if all the tests are successful, then energy for vtx and neighbours is calculated
b30f45	358	delta_energy=0;
M	359
	360	if(vtx->bond_no == 2){
	361	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;
	362	delta_energy += vtx->energy - backupvtx.energy;
58230a	363	}
M	364
b30f45	365	for(i=0;i<vtx->neigh_no;i++){
M	366	if(vtx->neigh[i]->bond_no == 2){
	367	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;
	368	delta_energy += vtx->neigh[i]->energy - backupneigh[i].energy;
	369	}
58230a	370	}
M	371
b30f45	372	// poly->k is filament persistence length (in units l_min)
M	373	delta_energy *= poly->k;
58230a	374
M	375	if(delta_energy>=0){
	376	#ifdef TS_DOUBLE_DOUBLE
	377	if(exp(-delta_energy)< drand48() )
	378	#endif
	379	#ifdef TS_DOUBLE_FLOAT
	380	if(expf(-delta_energy)< (ts_float)drand48())
	381	#endif
	382	#ifdef TS_DOUBLE_LONGDOUBLE
	383	if(expl(-delta_energy)< (ts_ldouble)drand48())
	384	#endif
	385	{
	386	//not accepted, reverting changes
	387	vtx=memcpy((void )vtx,(void )&backupvtx,sizeof(ts_vertex));
b30f45	388	for(i=0;i<vtx->neigh_no;i++){
M	389	memcpy(vtx->neigh[i],&backupneigh[i],sizeof(ts_vertex));
	390	}
58230a	391	for(i=0;i<vtx->bond_no;i++){
b30f45	392	vtx->bond[i]=memcpy((void )vtx->bond[i],(void )&backupbond[i],sizeof(ts_bond));
58230a	393	}
M	394
	395	return TS_FAIL;
	396	}
	397	}
	398
b30f45	399
58230a	400	// oldcellidx=vertex_self_avoidance(vesicle, &backupvtx[0]);
M	401	if(vtx->cell!=vesicle->clist->cell[cellidx]){
	402	retval=cell_add_vertex(vesicle->clist->cell[cellidx],vtx);
	403	// if(retval==TS_SUCCESS) cell_remove_vertex(vesicle->clist->cell[oldcellidx],vtx);
	404	if(retval==TS_SUCCESS) cell_remove_vertex(backupvtx.cell,vtx);
	405	}
	406	// if(oldcellidx);
	407	//END MONTE CARLOOOOOOO
	408	return TS_SUCCESS;
	409	}