From 1121faa13a2038facad22073f0fc610903d98691 Mon Sep 17 00:00:00 2001
From: Samo Penic <samo@CAE-linux.(none)>
Date: Fri, 05 Sep 2014 20:18:05 +0000
Subject: [PATCH] First variant of constant volume constrant (a new one proposed by Miha after reading his article). It seems to work, however there are still some things to be done, such as Miha's derivation of the epsvol (0.003% is used at the moment) and solving the problem of additional global variables.
---
src/vertexmove.c | 450 +++++++++++++++++++++++++++++++++++++++++++++++++-------
1 files changed, 394 insertions(+), 56 deletions(-)
diff --git a/src/vertexmove.c b/src/vertexmove.c
index 243463f..28a8880 100644
--- a/src/vertexmove.c
+++ b/src/vertexmove.c
@@ -9,66 +9,164 @@
#include "timestep.h"
#include "cell.h"
//#include "io.h"
+#include "io.h"
#include<stdio.h>
#include "vertexmove.h"
+#include <string.h>
+#include "constvol.h"
-ts_bool single_verticle_timestep(ts_vesicle *vesicle,ts_vertex *vtx,ts_double
-*rn){
+ts_bool single_verticle_timestep(ts_vesicle *vesicle,ts_vertex *vtx,ts_double *rn){
ts_uint i;
ts_double dist;
- ts_vertex *tvtx=(ts_vertex *)malloc(sizeof(ts_vertex));
- tvtx->data=init_vertex_data();
ts_bool retval;
ts_uint cellidx;
- ts_double xold,yold,zold;
- ts_double delta_energy,oenergy;
- ts_vertex *ovtx;
+ ts_double delta_energy, delta_energy_cv,oenergy,dvol=0.0;
+ ts_double costheta,sintheta,phi,r;
+ //This will hold all the information of vtx and its neighbours
+ ts_vertex backupvtx[20], *constvol_vtx_moved=NULL, *constvol_vtx_backup=NULL;
+ memcpy((void *)&backupvtx[0],(void *)vtx,sizeof(ts_vertex));
- //randomly we move the temporary vertex
- tvtx->data->x=vtx->data->x+vesicle->stepsize*(2.0*rn[0]-1.0);
- tvtx->data->y=vtx->data->y+vesicle->stepsize*(2.0*rn[1]-1.0);
- tvtx->data->z=vtx->data->z+vesicle->stepsize*(2.0*rn[2]-1.0);
- //check we if some length to neighbours are too much
- for(i=0;i<vtx->data->neigh_no;i++){
- dist=vtx_distance_sq(tvtx,vtx->data->neigh[i]);
- if(dist<1.0 || dist>vesicle->dmax) return TS_FAIL;
+ //Some stupid tests for debugging cell occupation!
+/* cellidx=vertex_self_avoidance(vesicle, vtx);
+ if(vesicle->clist->cell[cellidx]==vtx->cell){
+ fprintf(stderr,"Idx match!\n");
+ } else {
+ fprintf(stderr,"***** Idx don't match!\n");
+ fatal("ENding.",1);
+ }
+*/
+
+ //temporarly moving the vertex
+// vtx->x=vtx->x+vesicle->stepsize*(2.0*rn[0]-1.0);
+// vtx->y=vtx->y+vesicle->stepsize*(2.0*rn[1]-1.0);
+// vtx->z=vtx->z+vesicle->stepsize*(2.0*rn[2]-1.0);
+
+ //random move in a sphere with radius stepsize:
+ r=vesicle->stepsize*rn[0];
+ phi=rn[1]*2*M_PI;
+ costheta=2*rn[2]-1;
+ sintheta=sqrt(1-pow(costheta,2));
+ vtx->x=vtx->x+r*sintheta*cos(phi);
+ vtx->y=vtx->y+r*sintheta*sin(phi);
+ vtx->z=vtx->z+r*costheta;
+
+
+ //distance with neighbours check
+ for(i=0;i<vtx->neigh_no;i++){
+ dist=vtx_distance_sq(vtx,vtx->neigh[i]);
+ if(dist<1.0 || dist>vesicle->dmax) {
+ vtx=memcpy((void *)vtx,(void *)&backupvtx[0],sizeof(ts_vertex));
+ return TS_FAIL;
+ }
}
-fprintf(stderr,"Was here!\n");
- //self avoidance check with distant vertices
- cellidx=vertex_self_avoidance(vesicle, tvtx);
- //check occupation number
- retval=cell_occupation_number_and_internal_proximity(vesicle->clist,cellidx,vtx,tvtx);
+
+// Distance with grafted poly-vertex check:
+ if(vtx->grafted_poly!=NULL){
+ dist=vtx_distance_sq(vtx,vtx->grafted_poly->vlist->vtx[0]);
+ if(dist<1.0 || dist>vesicle->dmax) {
+ vtx=memcpy((void *)vtx,(void *)&backupvtx[0],sizeof(ts_vertex));
+ return TS_FAIL;
+ }
+ }
+
+// TODO: Maybe faster if checks only nucleus-neighboring cells
+// Nucleus penetration check:
+ if (vtx->x*vtx->x + vtx->y*vtx->y + vtx->z*vtx->z < vesicle->R_nucleus){
+ vtx=memcpy((void *)vtx,(void *)&backupvtx[0],sizeof(ts_vertex));
+ return TS_FAIL;
+ }
+
+//self avoidance check with distant vertices
+ cellidx=vertex_self_avoidance(vesicle, vtx);
+ //check occupation number
+ retval=cell_occupation_number_and_internal_proximity(vesicle->clist,cellidx,vtx);
+
if(retval==TS_FAIL){
+ vtx=memcpy((void *)vtx,(void *)&backupvtx[0],sizeof(ts_vertex));
return TS_FAIL;
}
-
- //if all the tests are successful, then we update the vertex position
- xold=vtx->data->x;
- yold=vtx->data->y;
- zold=vtx->data->z;
- ovtx=malloc(sizeof(ts_vertex));
- vtx_copy(ovtx,vtx);
- vtx->data->x=tvtx->data->x;
- vtx->data->y=tvtx->data->y;
- vtx->data->z=tvtx->data->z;
+
+
+ //if all the tests are successful, then energy for vtx and neighbours is calculated
+ for(i=0;i<vtx->neigh_no;i++){
+ memcpy((void *)&backupvtx[i+1],(void *)vtx->neigh[i],sizeof(ts_vertex));
+ }
+
+ if(vesicle->pswitch == 1 || vesicle->tape->constvolswitch>0){
+ for(i=0;i<vtx->tristar_no;i++) dvol-=vtx->tristar[i]->volume;
+ };
delta_energy=0;
+
+// vesicle_volume(vesicle);
+// fprintf(stderr,"Volume in the beginning=%1.16e\n", vesicle->volume);
+
//update the normals of triangles that share bead i.
- for(i=0;i<vtx->data->tristar_no;i++) triangle_normal_vector(vtx->data->tristar[i]);
- //energy and curvature
+ for(i=0;i<vtx->tristar_no;i++) triangle_normal_vector(vtx->tristar[i]);
+ oenergy=vtx->energy;
energy_vertex(vtx);
- delta_energy=vtx->data->xk*(vtx->data->energy - ovtx->data->energy);
+ delta_energy=vtx->xk*(vtx->energy - oenergy);
//the same is done for neighbouring vertices
- for(i=0;i<vtx->data->neigh_no;i++){
- oenergy=vtx->data->neigh[i]->data->energy;
- energy_vertex(vtx->data->neigh[i]);
- delta_energy+=vtx->data->neigh[i]->data->xk*(vtx->data->neigh[i]->data->energy-oenergy);
+ for(i=0;i<vtx->neigh_no;i++){
+ oenergy=vtx->neigh[i]->energy;
+ energy_vertex(vtx->neigh[i]);
+ delta_energy+=vtx->neigh[i]->xk*(vtx->neigh[i]->energy-oenergy);
}
- fprintf(stderr, "DE=%f\n",delta_energy);
+
+ if(vesicle->pswitch == 1 || vesicle->tape->constvolswitch >0){
+ for(i=0;i<vtx->tristar_no;i++) dvol+=vtx->tristar[i]->volume;
+ if(vesicle->pswitch==1) delta_energy-=vesicle->pressure*dvol;
+ };
+
+
+ if(vesicle->tape->constvolswitch==2){
+ /*check whether the dvol is gt than epsvol */
+ //fprintf(stderr,"DVOL=%1.16e\n",dvol);
+ if(fabs(vesicle->volume+dvol-V0)>epsvol){
+ //restore old state.
+ vtx=memcpy((void *)vtx,(void *)&backupvtx[0],sizeof(ts_vertex));
+ for(i=0;i<vtx->neigh_no;i++){
+ vtx->neigh[i]=memcpy((void *)vtx->neigh[i],(void *)&backupvtx[i+1],sizeof(ts_vertex));
+ }
+ for(i=0;i<vtx->tristar_no;i++) triangle_normal_vector(vtx->tristar[i]);
+ //fprintf(stderr,"fajlam!\n");
+ return TS_FAIL;
+ }
+
+ } else
+// vesicle_volume(vesicle);
+// fprintf(stderr,"Volume before=%1.16e\n", vesicle->volume);
+ if(vesicle->tape->constvolswitch == 1){
+ retval=constvolume(vesicle, vtx, -dvol, &delta_energy_cv, &constvol_vtx_moved,&constvol_vtx_backup);
+ if(retval==TS_FAIL){ // if we couldn't move the vertex to assure constant volume
+ vtx=memcpy((void *)vtx,(void *)&backupvtx[0],sizeof(ts_vertex));
+ for(i=0;i<vtx->neigh_no;i++){
+ vtx->neigh[i]=memcpy((void *)vtx->neigh[i],(void *)&backupvtx[i+1],sizeof(ts_vertex));
+ }
+ for(i=0;i<vtx->tristar_no;i++) triangle_normal_vector(vtx->tristar[i]);
+ // fprintf(stderr,"fajlam!\n");
+ return TS_FAIL;
+ }
+// vesicle_volume(vesicle);
+// fprintf(stderr,"Volume after=%1.16e\n", vesicle->volume);
+// fprintf(stderr,"Volume after-dvol=%1.16e\n", vesicle->volume-dvol);
+// fprintf(stderr,"Denergy before=%e\n",delta_energy);
+
+ delta_energy+=delta_energy_cv;
+// fprintf(stderr,"Denergy after=%e\n",delta_energy);
+ }
+/* No poly-bond energy for now!
+ if(vtx->grafted_poly!=NULL){
+ delta_energy+=
+ (pow(sqrt(vtx_distance_sq(vtx, vtx->grafted_poly->vlist->vtx[0])-1),2)-
+ pow(sqrt(vtx_distance_sq(&backupvtx[0], vtx->grafted_poly->vlist->vtx[0])-1),2)) *vtx->grafted_poly->k;
+ }
+*/
+// fprintf(stderr, "DE=%f\n",delta_energy);
//MONTE CARLOOOOOOOO
if(delta_energy>=0){
#ifdef TS_DOUBLE_DOUBLE
- if(exp(-delta_energy)< drand48() )
+ if(exp(-delta_energy)< drand48())
#endif
#ifdef TS_DOUBLE_FLOAT
if(expf(-delta_energy)< (ts_float)drand48())
@@ -78,28 +176,268 @@
#endif
{
//not accepted, reverting changes
- vtx->data->x=xold;
- vtx->data->y=yold;
- vtx->data->z=zold;
+ // fprintf(stderr,"MC failed\n");
+ vtx=memcpy((void *)vtx,(void *)&backupvtx[0],sizeof(ts_vertex));
+ for(i=0;i<vtx->neigh_no;i++){
+ vtx->neigh[i]=memcpy((void *)vtx->neigh[i],(void *)&backupvtx[i+1],sizeof(ts_vertex));
+ }
+
//update the normals of triangles that share bead i.
- for(i=0;i<vtx->data->tristar_no;i++) triangle_normal_vector(vtx->data->tristar[i]);
- //energy and curvature
- energy_vertex(vtx);
- //the same is done for neighbouring vertices
- for(i=0;i<vtx->data->neigh_no;i++) energy_vertex(vtx->data->neigh[i]);
- free(ovtx->data->bond_length);
- free(ovtx->data->bond_length_dual);
- free(ovtx);
+ for(i=0;i<vtx->tristar_no;i++) triangle_normal_vector(vtx->tristar[i]);
+
+// fprintf(stderr, "before vtx(x,y,z)=%e,%e,%e\n",constvol_vtx_moved->x, constvol_vtx_moved->y, constvol_vtx_moved->z);
+ if(vesicle->tape->constvolswitch == 1){
+ constvolumerestore(constvol_vtx_moved,constvol_vtx_backup);
+ }
+// fprintf(stderr, "after vtx(x,y,z)=%e,%e,%e\n",constvol_vtx_moved->x, constvol_vtx_moved->y, constvol_vtx_moved->z);
+// vesicle_volume(vesicle);
+// fprintf(stderr,"Volume after fail=%1.16e\n", vesicle->volume);
return TS_FAIL;
}
}
+ //accepted
+ // fprintf(stderr,"MC accepted\n");
+// oldcellidx=vertex_self_avoidance(vesicle, &backupvtx[0]);
+ if(vtx->cell!=vesicle->clist->cell[cellidx]){
+ retval=cell_add_vertex(vesicle->clist->cell[cellidx],vtx);
+// if(retval==TS_SUCCESS) cell_remove_vertex(vesicle->clist->cell[oldcellidx],vtx);
+ if(retval==TS_SUCCESS) cell_remove_vertex(backupvtx[0].cell,vtx);
+
+ }
+
+ if(vesicle->tape->constvolswitch == 2){
+ vesicle->volume+=dvol;
+ } else
+ if(vesicle->tape->constvolswitch == 1){
+ constvolumeaccept(vesicle,constvol_vtx_moved,constvol_vtx_backup);
+ }
+// if(oldcellidx);
//END MONTE CARLOOOOOOO
-
- //TODO: change cell occupation if necessary!
-
- free(ovtx->data->bond_length);
- free(ovtx->data->bond_length_dual);
- free(ovtx);
+// vesicle_volume(vesicle);
+// fprintf(stderr,"Volume after success=%1.16e\n", vesicle->volume);
return TS_SUCCESS;
}
+
+ts_bool single_poly_vertex_move(ts_vesicle *vesicle,ts_poly *poly,ts_vertex *vtx,ts_double *rn){
+ ts_uint i;
+ ts_bool retval;
+ ts_uint cellidx;
+// ts_double delta_energy;
+ ts_double costheta,sintheta,phi,r;
+ ts_double dist;
+ //This will hold all the information of vtx and its neighbours
+ ts_vertex backupvtx;
+// ts_bond backupbond[2];
+ memcpy((void *)&backupvtx,(void *)vtx,sizeof(ts_vertex));
+
+ //random move in a sphere with radius stepsize:
+ r=vesicle->stepsize*rn[0];
+ phi=rn[1]*2*M_PI;
+ costheta=2*rn[2]-1;
+ sintheta=sqrt(1-pow(costheta,2));
+ vtx->x=vtx->x+r*sintheta*cos(phi);
+ vtx->y=vtx->y+r*sintheta*sin(phi);
+ vtx->z=vtx->z+r*costheta;
+
+
+ //distance with neighbours check
+ for(i=0;i<vtx->neigh_no;i++){
+ dist=vtx_distance_sq(vtx,vtx->neigh[i]);
+ if(dist<1.0 || dist>vesicle->dmax) {
+ vtx=memcpy((void *)vtx,(void *)&backupvtx,sizeof(ts_vertex));
+ return TS_FAIL;
+ }
+ }
+
+// Distance with grafted vesicle-vertex check:
+ if(vtx==poly->vlist->vtx[0]){
+ dist=vtx_distance_sq(vtx,poly->grafted_vtx);
+ if(dist<1.0 || dist>vesicle->dmax) {
+ vtx=memcpy((void *)vtx,(void *)&backupvtx,sizeof(ts_vertex));
+ return TS_FAIL;
+ }
+ }
+
+
+ //self avoidance check with distant vertices
+ cellidx=vertex_self_avoidance(vesicle, vtx);
+ //check occupation number
+ retval=cell_occupation_number_and_internal_proximity(vesicle->clist,cellidx,vtx);
+
+ if(retval==TS_FAIL){
+ vtx=memcpy((void *)vtx,(void *)&backupvtx,sizeof(ts_vertex));
+ return TS_FAIL;
+ }
+
+
+ //if all the tests are successful, then energy for vtx and neighbours is calculated
+/* Energy ignored for now!
+ delta_energy=0;
+ for(i=0;i<vtx->bond_no;i++){
+ memcpy((void *)&backupbond[i],(void *)vtx->bond[i],sizeof(ts_bond));
+
+ vtx->bond[i]->bond_length=sqrt(vtx_distance_sq(vtx->bond[i]->vtx1,vtx->bond[i]->vtx2));
+ bond_energy(vtx->bond[i],poly);
+ delta_energy+= vtx->bond[i]->energy - backupbond[i].energy;
+ }
+
+ if(vtx==poly->vlist->vtx[0]){
+ delta_energy+=
+ (pow(sqrt(vtx_distance_sq(vtx, poly->grafted_vtx)-1),2)-
+ pow(sqrt(vtx_distance_sq(&backupvtx, poly->grafted_vtx)-1),2)) *poly->k;
+
+ }
+
+
+ if(delta_energy>=0){
+#ifdef TS_DOUBLE_DOUBLE
+ if(exp(-delta_energy)< drand48() )
+#endif
+#ifdef TS_DOUBLE_FLOAT
+ if(expf(-delta_energy)< (ts_float)drand48())
+#endif
+#ifdef TS_DOUBLE_LONGDOUBLE
+ if(expl(-delta_energy)< (ts_ldouble)drand48())
+#endif
+ {
+ //not accepted, reverting changes
+ vtx=memcpy((void *)vtx,(void *)&backupvtx,sizeof(ts_vertex));
+ for(i=0;i<vtx->bond_no;i++){
+ vtx->bond[i]=memcpy((void *)vtx->bond[i],(void *)&backupbond[i],sizeof(ts_bond));
+ }
+
+ return TS_FAIL;
+ }
+ }
+*/
+
+// oldcellidx=vertex_self_avoidance(vesicle, &backupvtx[0]);
+ if(vtx->cell!=vesicle->clist->cell[cellidx]){
+ retval=cell_add_vertex(vesicle->clist->cell[cellidx],vtx);
+// if(retval==TS_SUCCESS) cell_remove_vertex(vesicle->clist->cell[oldcellidx],vtx);
+ if(retval==TS_SUCCESS) cell_remove_vertex(backupvtx.cell,vtx);
+ }
+// if(oldcellidx);
+ //END MONTE CARLOOOOOOO
+ return TS_SUCCESS;
+}
+
+
+
+
+ts_bool single_filament_vertex_move(ts_vesicle *vesicle,ts_poly *poly,ts_vertex *vtx,ts_double *rn){
+ ts_uint i;
+ ts_bool retval;
+ ts_uint cellidx;
+ ts_double delta_energy;
+ ts_double costheta,sintheta,phi,r;
+ ts_double dist[2];
+ //This will hold all the information of vtx and its neighbours
+ ts_vertex backupvtx,backupneigh[2];
+ ts_bond backupbond[2];
+
+ //backup vertex:
+ memcpy((void *)&backupvtx,(void *)vtx,sizeof(ts_vertex));
+
+ //random move in a sphere with radius stepsize:
+ r=vesicle->stepsize*rn[0];
+ phi=rn[1]*2*M_PI;
+ costheta=2*rn[2]-1;
+ sintheta=sqrt(1-pow(costheta,2));
+ vtx->x=vtx->x+r*sintheta*cos(phi);
+ vtx->y=vtx->y+r*sintheta*sin(phi);
+ vtx->z=vtx->z+r*costheta;
+
+
+ //distance with neighbours check
+ for(i=0;i<vtx->bond_no;i++){
+ dist[i]=vtx_distance_sq(vtx->bond[i]->vtx1,vtx->bond[i]->vtx2);
+ if(dist[i]<1.0 || dist[i]>vesicle->dmax) {
+ vtx=memcpy((void *)vtx,(void *)&backupvtx,sizeof(ts_vertex));
+ return TS_FAIL;
+ }
+ }
+
+// TODO: Maybe faster if checks only nucleus-neighboring cells
+// Nucleus penetration check:
+ if (vtx->x*vtx->x + vtx->y*vtx->y + vtx->z*vtx->z < vesicle->R_nucleus){
+ vtx=memcpy((void *)vtx,(void *)&backupvtx,sizeof(ts_vertex));
+ return TS_FAIL;
+ }
+
+
+ //self avoidance check with distant vertices
+ cellidx=vertex_self_avoidance(vesicle, vtx);
+ //check occupation number
+ retval=cell_occupation_number_and_internal_proximity(vesicle->clist,cellidx,vtx);
+ if(retval==TS_FAIL){
+ vtx=memcpy((void *)vtx,(void *)&backupvtx,sizeof(ts_vertex));
+ return TS_FAIL;
+ }
+
+ //backup bonds
+ for(i=0;i<vtx->bond_no;i++){
+ memcpy(&backupbond[i],vtx->bond[i], sizeof(ts_bond));
+ vtx->bond[i]->bond_length=sqrt(dist[i]);
+ bond_vector(vtx->bond[i]);
+ }
+
+ //backup neighboring vertices:
+ for(i=0;i<vtx->neigh_no;i++){
+ memcpy(&backupneigh[i],vtx->neigh[i], sizeof(ts_vertex));
+ }
+
+ //if all the tests are successful, then energy for vtx and neighbours is calculated
+ delta_energy=0;
+
+ if(vtx->bond_no == 2){
+ vtx->energy = -(vtx->bond[0]->x*vtx->bond[1]->x + vtx->bond[0]->y*vtx->bond[1]->y + vtx->bond[0]->z*vtx->bond[1]->z)/vtx->bond[0]->bond_length/vtx->bond[1]->bond_length;
+ delta_energy += vtx->energy - backupvtx.energy;
+ }
+
+ for(i=0;i<vtx->neigh_no;i++){
+ if(vtx->neigh[i]->bond_no == 2){
+ vtx->neigh[i]->energy = -(vtx->neigh[i]->bond[0]->x*vtx->neigh[i]->bond[1]->x + vtx->neigh[i]->bond[0]->y*vtx->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;
+ delta_energy += vtx->neigh[i]->energy - backupneigh[i].energy;
+ }
+ }
+
+ // poly->k is filament persistence length (in units l_min)
+ delta_energy *= poly->k;
+
+ if(delta_energy>=0){
+#ifdef TS_DOUBLE_DOUBLE
+ if(exp(-delta_energy)< drand48() )
+#endif
+#ifdef TS_DOUBLE_FLOAT
+ if(expf(-delta_energy)< (ts_float)drand48())
+#endif
+#ifdef TS_DOUBLE_LONGDOUBLE
+ if(expl(-delta_energy)< (ts_ldouble)drand48())
+#endif
+ {
+ //not accepted, reverting changes
+ vtx=memcpy((void *)vtx,(void *)&backupvtx,sizeof(ts_vertex));
+ for(i=0;i<vtx->neigh_no;i++){
+ memcpy(vtx->neigh[i],&backupneigh[i],sizeof(ts_vertex));
+ }
+ for(i=0;i<vtx->bond_no;i++){
+ vtx->bond[i]=memcpy((void *)vtx->bond[i],(void *)&backupbond[i],sizeof(ts_bond));
+ }
+
+ return TS_FAIL;
+ }
+ }
+
+
+// oldcellidx=vertex_self_avoidance(vesicle, &backupvtx[0]);
+ if(vtx->cell!=vesicle->clist->cell[cellidx]){
+ retval=cell_add_vertex(vesicle->clist->cell[cellidx],vtx);
+// if(retval==TS_SUCCESS) cell_remove_vertex(vesicle->clist->cell[oldcellidx],vtx);
+ if(retval==TS_SUCCESS) cell_remove_vertex(backupvtx.cell,vtx);
+ }
+// if(oldcellidx);
+ //END MONTE CARLOOOOOOO
+ return TS_SUCCESS;
+}
--
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