From fedf2b217113800a15f367e111e2dbcad4a3c92c Mon Sep 17 00:00:00 2001
From: Miha <mihaf@hapi.(none)>
Date: Thu, 06 Feb 2014 17:39:37 +0000
Subject: [PATCH] Polymers thermicaly move now! HArmonic potential added.
---
src/timestep.c | 20 +++++-
src/poly.c | 2
src/vertexmove.h | 1
src/tape | 6 +-
src/energy.c | 9 ++-
src/general.h | 3
src/energy.h | 1
src/vertexmove.c | 103 +++++++++++++++++++++++++++++++++
8 files changed, 132 insertions(+), 13 deletions(-)
diff --git a/src/energy.c b/src/energy.c
index 3b1779c..1e37e08 100644
--- a/src/energy.c
+++ b/src/energy.c
@@ -19,9 +19,12 @@
return TS_SUCCESS;
}
-inline ts_bool energy_poly_vertex(ts_vertex *vtx,ts_poly *poly){
-
-}
+
+inline ts_bool bond_energy(ts_bond *bond,ts_poly *poly){
+ bond->energy=poly->k*pow(bond->bond_length-1,2);
+ return TS_SUCCESS;
+};
+
inline ts_bool energy_vertex(ts_vertex *vtx){
// ts_vertex *vtx=&vlist->vertex[n]-1; // Caution! 0 Indexed value!
diff --git a/src/energy.h b/src/energy.h
index 90463d8..8a37b85 100644
--- a/src/energy.h
+++ b/src/energy.h
@@ -2,4 +2,5 @@
#define _ENERGY_H
ts_bool mean_curvature_and_energy(ts_vesicle *vesicle);
inline ts_bool energy_vertex(ts_vertex *vtx);
+inline ts_bool bond_energy(ts_bond *bond,ts_poly *poly);
#endif
diff --git a/src/general.h b/src/general.h
index 0372e7a..e7e9545 100644
--- a/src/general.h
+++ b/src/general.h
@@ -164,12 +164,13 @@
} ts_vertex_list;
struct ts_bond {
- ts_uint idx;
+ ts_uint idx;
ts_vertex *vtx1;
ts_vertex *vtx2;
ts_double bond_length;
ts_double bond_length_dual;
ts_bool tainted;
+ ts_double energy;
};
typedef struct ts_bond ts_bond;
diff --git a/src/poly.c b/src/poly.c
index edab18f..1ddcec7 100644
--- a/src/poly.c
+++ b/src/poly.c
@@ -4,6 +4,7 @@
#include"vertex.h"
#include"bond.h"
#include<math.h>
+#include"energy.h"
ts_bool poly_assign_spring_const(ts_vesicle *vesicle){
ts_uint i;
@@ -30,6 +31,7 @@
for(i=0;i<poly->blist->n;i++){
poly->blist->bond[i]->bond_length=sqrt(vtx_distance_sq(poly->blist->bond[i]->vtx1,poly->blist->bond[i]->vtx2));
+ bond_energy(poly->blist->bond[i],poly);
}
return poly;
diff --git a/src/tape b/src/tape
index c8c8cdb..02c85b8 100644
--- a/src/tape
+++ b/src/tape
@@ -1,8 +1,8 @@
####### Vesicle definitions ###########
# nshell is a number of divisions of dipyramid
nshell=17
-# dmax is the square of the bond length
-dmax=1.67
+# dmax is the max. bond length
+dmax=1.7
# bending rigidity of the membrane
xk0=25.0
# max step size
@@ -10,7 +10,7 @@
####### Polymer definitions ###########
# npoly is a number of polymers attached to npoly distinct vertices on vesicle
-npoly=10
+npoly=20
# nmono is a number of monomers in each polymer
nmono=15
# Spring constant between monomers of the polymer
diff --git a/src/timestep.c b/src/timestep.c
index 9e5e61c..0ce9372 100644
--- a/src/timestep.c
+++ b/src/timestep.c
@@ -8,6 +8,7 @@
#include "bondflip.h"
#include "frame.h"
#include "io.h"
+
ts_bool run_simulation(ts_vesicle *vesicle, ts_uint mcsweeps, ts_uint inititer, ts_uint iterations){
ts_uint i, j;
@@ -30,7 +31,7 @@
ts_bool single_timestep(ts_vesicle *vesicle){
ts_bool retval;
ts_double rnvec[3];
- ts_uint i, b;
+ ts_uint i,j,b;
for(i=0;i<vesicle->vlist->n;i++){
rnvec[0]=drand48();
rnvec[1]=drand48();
@@ -39,7 +40,7 @@
}
// ts_int cnt=0;
- for(i=0;i<vesicle->vlist->n;i++){
+ for(i=0;i<3*vesicle->vlist->n;i++){
//why is rnvec needed in bondflip?
/* rnvec[0]=drand48();
rnvec[1]=drand48();
@@ -50,8 +51,19 @@
//call single_bondflip_timestep...
retval=single_bondflip_timestep(vesicle,vesicle->blist->bond[b],rnvec);
// if(retval==TS_SUCCESS) cnt++;
- }
-// printf("Bondflip success rate in one sweep: %d/%d=%e\n", cnt,vesicle->blist->n,(double)cnt/(double)vesicle->blist->n);
+ }
+
+ for(i=0;i<vesicle->poly_list->n;i++){
+ for(j=0;j<vesicle->poly_list->poly[i]->vlist->n;j++){
+ rnvec[0]=drand48();
+ rnvec[1]=drand48();
+ rnvec[2]=drand48();
+ retval=single_poly_vertex_move(vesicle,vesicle->poly_list->poly[i],vesicle->poly_list->poly[i]->vlist->vtx[j],rnvec);
+ }
+
+ }
+
+// printf("Bondflip success rate in one sweep: %d/%d=%e\n", cnt,3*vesicle->blist->n,(double)cnt/(double)vesicle->blist->n/3.0);
if(retval);
return TS_SUCCESS;
}
diff --git a/src/vertexmove.c b/src/vertexmove.c
index a79b2f0..f78fd61 100644
--- a/src/vertexmove.c
+++ b/src/vertexmove.c
@@ -13,8 +13,7 @@
#include "vertexmove.h"
#include <string.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_bool retval;
@@ -88,6 +87,15 @@
energy_vertex(vtx->neigh[i]);
delta_energy+=vtx->neigh[i]->xk*(vtx->neigh[i]->energy-oenergy);
}
+
+ 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){
@@ -126,3 +134,94 @@
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;
+ //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[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,sizeof(ts_vertex));
+ return TS_FAIL;
+ }
+
+
+ //if all the tests are successful, then energy for vtx and neighbours is calculated
+ 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;
+}
diff --git a/src/vertexmove.h b/src/vertexmove.h
index 0c24d54..6387ab8 100644
--- a/src/vertexmove.h
+++ b/src/vertexmove.h
@@ -1,3 +1,4 @@
ts_bool single_verticle_timestep(ts_vesicle *vesicle,ts_vertex *vtx,ts_double *rn);
+ts_bool single_poly_vertex_move(ts_vesicle *vesicle,ts_poly *poly,ts_vertex *vtx,ts_double *rn);
--
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