From 620ba72765eda244ca3f3806b8ad709929e74b3c Mon Sep 17 00:00:00 2001
From: Samo Penic <samo.penic@gmail.com>
Date: Thu, 21 Jun 2018 10:50:23 +0000
Subject: [PATCH] Isak's proposal for stretching energy calculation, take 1
---
src/timestep.c | 2 +-
src/bondflip.c | 17 ++++++++++++++---
src/energy.c | 5 +++++
src/energy.h | 1 +
src/vertexmove.c | 25 +++++++++++++++++++------
5 files changed, 40 insertions(+), 10 deletions(-)
diff --git a/src/bondflip.c b/src/bondflip.c
index 13ec263..d48413f 100644
--- a/src/bondflip.c
+++ b/src/bondflip.c
@@ -40,6 +40,7 @@
ts_double delta_energy_cv;
ts_vertex *constvol_vtx_moved, *constvol_vtx_backup;
ts_bool retval;
+ ts_double temp_area=0.0;
if(it->neigh_no< 3) return TS_FAIL;
if(k->neigh_no< 3) return TS_FAIL;
@@ -176,6 +177,9 @@
/* vesicle_volume(vesicle);
fprintf(stderr,"Volume in the beginning=%1.16e\n", vesicle->volume);
*/
+ if(vesicle->tape->stretchswitch==1){
+ temp_area=vesicle->area-lm->area-lp->area;
+ }
/* fix data structure for flipped bond */
ts_flip_bond(k,it,km,kp, bond,lm, lp, lm2, lp1, vesicle->tape->w);
@@ -189,10 +193,13 @@
delta_energy+=bond->energy; /* attraction with neighboring vertices, that have spontaneous curvature */
//Neigbours of k, it, km, kp don't change its energy.
if(vesicle->tape->stretchswitch==1){
- oldenergy+=lm->energy+lp->energy;
+/* oldenergy+=lm->energy+lp->energy;
stretchenergy(vesicle,lm);
stretchenergy(vesicle,lp);
delta_energy+=lm->energy+lp->energy;
+ */
+ temp_area=temp_area+lm->area+lp->area;
+ delta_energy+=stretchenergy2(temp_area,vesicle->tlist->a0*vesicle->tlist->n)-stretchenergy2(vesicle->area,vesicle->tlist->a0*vesicle->tlist->n);
}
delta_energy-=oldenergy;
@@ -339,11 +346,11 @@
// fprintf(stderr,"Restoration complete!!!\n");
// vesicle_volume(vesicle);
// fprintf(stderr,"Volume after fail=%1.16e\n", vesicle->volume);
- if(vesicle->tape->stretchswitch==1){
+/* if(vesicle->tape->stretchswitch==1){
stretchenergy(vesicle,lm);
stretchenergy(vesicle,lp);
}
-
+*/
return TS_FAIL;
}
}
@@ -358,6 +365,10 @@
if(vesicle->tape->constareaswitch==2){
vesicle->area+=darea;
}
+ if(vesicle->tape->stretchswitch==1){
+ vesicle->area=temp_area;
+ }
+
// delete all backups
for(i=0;i<4;i++){
free(bck_vtx[i]->neigh);
diff --git a/src/energy.c b/src/energy.c
index 1dae415..e9db3a4 100644
--- a/src/energy.c
+++ b/src/energy.c
@@ -242,3 +242,8 @@
void stretchenergy(ts_vesicle *vesicle, ts_triangle *triangle){
triangle->energy=vesicle->tape->xkA0/2.0*pow((triangle->area/vesicle->tlist->a0-1.0),2);
}
+
+ts_double stretchenergy2(ts_double current_area,ts_double tensionless_area){
+ return pow((current_area*tensionless_area),2)/tensionless_area;
+
+}
diff --git a/src/energy.h b/src/energy.h
index 9d1f47c..ad3a01b 100644
--- a/src/energy.h
+++ b/src/energy.h
@@ -10,4 +10,5 @@
ts_double direct_force_energy(ts_vesicle *vesicle, ts_vertex *vtx, ts_vertex *vtx_old);
void stretchenergy(ts_vesicle *vesicle, ts_triangle *triangle);
+ts_double stretchenergy2(ts_double current_area,ts_double tensionless_area);
#endif
diff --git a/src/timestep.c b/src/timestep.c
index 27400e7..d4748e6 100644
--- a/src/timestep.c
+++ b/src/timestep.c
@@ -62,7 +62,7 @@
centermass(vesicle);
cell_occupation(vesicle);
vesicle_volume(vesicle); //needed for constant volume at this moment
- vesicle_area(vesicle); //needed for constant area at this moment
+ vesicle_area(vesicle); //needed for constant area and stretching energy at this moment
if(V0<0.000001)
V0=vesicle->volume;
ts_fprintf(stdout,"Setting volume V0=%.17f\n",V0);
diff --git a/src/vertexmove.c b/src/vertexmove.c
index 45a4b33..1d5d7fa 100644
--- a/src/vertexmove.c
+++ b/src/vertexmove.c
@@ -22,6 +22,7 @@
ts_bool retval;
ts_uint cellidx;
ts_double delta_energy, delta_energy_cv,oenergy,dvol=0.0, darea=0.0, dstretchenergy=0.0;
+ ts_double temp_area=0.0; //for stretching
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;
@@ -115,7 +116,13 @@
}
//stretching energy 1 of 3
if(vesicle->tape->stretchswitch==1){
- for(i=0;i<vtx->tristar_no;i++) dstretchenergy-=vtx->tristar[i]->energy;
+ temp_area=vesicle->area;
+ dstretchenergy-=stretchenergy2(vesicle->area,vesicle->tlist->a0*vesicle->tlist->n);
+ for(i=0;i<vtx->tristar_no;i++){
+ temp_area-=vtx->tristar[i]->area;
+ }
+ //0.5*vesicle->tape->xkA0*pow((vesicle->area-vesicle->tlist->a0*vesicle->tlist->n),2)/(vesicle->tlist->a0*vesicle->tlist->n);
+ //for(i=0;i<vtx->tristar_no;i++) dstretchenergy-=vtx->tristar[i]->energy;
}
delta_energy=0;
@@ -197,10 +204,12 @@
//stretching energy 2 of 3
if(vesicle->tape->stretchswitch==1){
- for(i=0;i<vtx->tristar_no;i++){
- stretchenergy(vesicle, vtx->tristar[i]);
- dstretchenergy+=vtx->tristar[i]->energy;
+ for(i=0;i<vtx->tristar_no;i++){
+ temp_area+=vtx->tristar[i]->area;
}
+ dstretchenergy+=stretchenergy2(temp_area,vesicle->tlist->a0*vesicle->tlist->n);
+ dstretchenergy=0.5*vesicle->tape->xkA0*dstretchenergy;
+
}
delta_energy+=dstretchenergy;
@@ -235,13 +244,13 @@
//update the normals of triangles that share bead i.
for(i=0;i<vtx->tristar_no;i++) triangle_normal_vector(vtx->tristar[i]);
- //stretching energy 3 of 3
+/* //stretching energy 3 of 3
if(vesicle->tape->stretchswitch==1){
for(i=0;i<vtx->tristar_no;i++){
stretchenergy(vesicle,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);
@@ -272,6 +281,10 @@
if(vesicle->tape->constareaswitch==2){
vesicle->area+=darea;
}
+ //stretching energy 3 of 3
+ if(vesicle->tape->stretchswitch==1){
+ vesicle->area=temp_area;
+ }
// if(oldcellidx);
//END MONTE CARLOOOOOOO
// vesicle_volume(vesicle);
--
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