From 055dd7840f6926f3b4b41a04a86b7fac0a8fec26 Mon Sep 17 00:00:00 2001
From: Samo Penic <samo.penic@fe.uni-lj.si>
Date: Tue, 08 Jul 2014 14:13:54 +0000
Subject: [PATCH] Fixed cell from dump with new tape. Take 2.
---
src/vertexmove.c | 124 +++++++++++++++++++++++++++++++----------
1 files changed, 94 insertions(+), 30 deletions(-)
diff --git a/src/vertexmove.c b/src/vertexmove.c
index 04325ef..af578e2 100644
--- a/src/vertexmove.c
+++ b/src/vertexmove.c
@@ -9,19 +9,21 @@
#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_uint i;
ts_double dist;
ts_bool retval;
ts_uint cellidx;
- ts_double delta_energy,oenergy,dvol=0.0;
+ 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];
+ ts_vertex backupvtx[20], *constvol_vtx_moved=NULL, *constvol_vtx_backup=NULL;
memcpy((void *)&backupvtx[0],(void *)vtx,sizeof(ts_vertex));
//Some stupid tests for debugging cell occupation!
@@ -67,11 +69,18 @@
}
}
- //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);
-
+// 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;
@@ -83,11 +92,15 @@
memcpy((void *)&backupvtx[i+1],(void *)vtx->neigh[i],sizeof(ts_vertex));
}
- if(vesicle->pswitch == 1){
+ if(vesicle->pswitch == 1 || vesicle->tape->constvolswitch==1){
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->tristar_no;i++) triangle_normal_vector(vtx->tristar[i]);
oenergy=vtx->energy;
@@ -100,11 +113,32 @@
delta_energy+=vtx->neigh[i]->xk*(vtx->neigh[i]->energy-oenergy);
}
- if(vesicle->pswitch == 1){
+ if(vesicle->pswitch == 1 || vesicle->tape->constvolswitch == 1){
for(i=0;i<vtx->tristar_no;i++) dvol+=vtx->tristar[i]->volume;
- delta_energy-=vesicle->pressure*dvol;
+ if(vesicle->pswitch==1) delta_energy-=vesicle->pressure*dvol;
};
+// 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+=
@@ -116,7 +150,7 @@
//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())
@@ -126,6 +160,7 @@
#endif
{
//not accepted, reverting changes
+ // 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));
@@ -134,10 +169,18 @@
//update the normals of triangles that share bead i.
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);
@@ -145,8 +188,14 @@
if(retval==TS_SUCCESS) cell_remove_vertex(backupvtx[0].cell,vtx);
}
+
+ if(vesicle->tape->constvolswitch == 1){
+ constvolumeaccept(vesicle,constvol_vtx_moved,constvol_vtx_backup);
+ }
// if(oldcellidx);
//END MONTE CARLOOOOOOO
+// vesicle_volume(vesicle);
+// fprintf(stderr,"Volume after success=%1.16e\n", vesicle->volume);
return TS_SUCCESS;
}
@@ -262,12 +311,14 @@
ts_uint i;
ts_bool retval;
ts_uint cellidx;
-// ts_double delta_energy;
+ 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;
+ 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:
@@ -289,12 +340,18 @@
}
}
+// 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;
@@ -305,26 +362,30 @@
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;
-/* for(i=0;i<vtx->neigh_no;i++){
-// memcpy((void *)&backupbond[i],(void *)vtx->bond[i],sizeof(ts_bond));
- xp = vtx->neigh[i]
- 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;
+ 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;
}
- 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;
-
+ 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
@@ -339,15 +400,18 @@
{
//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));
+ 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);
--
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