From 7ec6fb63c690080d0624c7bf138d0fd84fe7664e Mon Sep 17 00:00:00 2001
From: Samo Penic <samo.penic@gmail.com>
Date: Tue, 15 May 2018 16:11:14 +0000
Subject: [PATCH] First working version, not debugged and energy assigned to vesicles on timesteps
---
src/io.c | 32 +++++++++++++++
src/tape | 4 +-
src/bondflip.c | 11 +++++
src/energy.c | 4 ++
src/initial_distribution.c | 2
src/general.h | 1
src/energy.h | 2 +
src/vertexmove.c | 24 +++++++++++-
8 files changed, 73 insertions(+), 7 deletions(-)
diff --git a/src/bondflip.c b/src/bondflip.c
index 66c40f7..13ec263 100644
--- a/src/bondflip.c
+++ b/src/bondflip.c
@@ -176,7 +176,6 @@
/* vesicle_volume(vesicle);
fprintf(stderr,"Volume in the beginning=%1.16e\n", vesicle->volume);
*/
-
/* fix data structure for flipped bond */
ts_flip_bond(k,it,km,kp, bond,lm, lp, lm2, lp1, vesicle->tape->w);
@@ -189,6 +188,12 @@
delta_energy+=it->xk* it->energy;
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;
+ stretchenergy(vesicle,lm);
+ stretchenergy(vesicle,lp);
+ delta_energy+=lm->energy+lp->energy;
+ }
delta_energy-=oldenergy;
if(vesicle->pswitch == 1 || vesicle->tape->constvolswitch>0){
@@ -334,6 +339,10 @@
// fprintf(stderr,"Restoration complete!!!\n");
// vesicle_volume(vesicle);
// fprintf(stderr,"Volume after fail=%1.16e\n", vesicle->volume);
+ if(vesicle->tape->stretchswitch==1){
+ stretchenergy(vesicle,lm);
+ stretchenergy(vesicle,lp);
+ }
return TS_FAIL;
}
diff --git a/src/energy.c b/src/energy.c
index 4d27995..810edd1 100644
--- a/src/energy.c
+++ b/src/energy.c
@@ -238,3 +238,7 @@
return vesicle->tape->F*ddp;
}
+
+void stretchenergy(ts_vesicle *vesicle, ts_triangle *triangle){
+ triangle->energy=vesicle->tape->xkA0/vesicle->tlist->n*pow((triangle->area/vesicle->tlist->a0-1),2);
+}
diff --git a/src/energy.h b/src/energy.h
index 1b97fa9..9d1f47c 100644
--- a/src/energy.h
+++ b/src/energy.h
@@ -8,4 +8,6 @@
ts_bool sweep_attraction_bond_energy(ts_vesicle *vesicle);
inline ts_bool attraction_bond_energy(ts_bond *bond, ts_double w);
ts_double direct_force_energy(ts_vesicle *vesicle, ts_vertex *vtx, ts_vertex *vtx_old);
+
+void stretchenergy(ts_vesicle *vesicle, ts_triangle *triangle);
#endif
diff --git a/src/general.h b/src/general.h
index 9a8feab..7676000 100644
--- a/src/general.h
+++ b/src/general.h
@@ -201,6 +201,7 @@
struct ts_triangle_list{
ts_uint n;
+ ts_double a0;
ts_triangle **tria;
};
typedef struct ts_triangle_list ts_triangle_list;
diff --git a/src/initial_distribution.c b/src/initial_distribution.c
index 0274038..59bf808 100644
--- a/src/initial_distribution.c
+++ b/src/initial_distribution.c
@@ -112,7 +112,7 @@
vesicle->sphHarmonics=NULL;
}
-
+ vesicle->tlist->a0=sqrt(3)/2*pow((vesicle->tape->dmax+1.0),2);
return TS_SUCCESS;
}
diff --git a/src/io.c b/src/io.c
index f513501..83bb26d 100644
--- a/src/io.c
+++ b/src/io.c
@@ -826,6 +826,7 @@
ts_bond_list *blist=vesicle->blist;
ts_vertex **vtx=vlist->vtx;
ts_uint i,j;
+ ts_double senergy=0.0;
char filename[10000];
char just_name[255];
FILE *fh;
@@ -973,7 +974,36 @@
}
}
fprintf(fh,"</DataArray>\n");
-
+ if(vesicle->tape->stretchswitch==1){
+ fprintf(fh,"<DataArray type=\"Float64\" Name=\"stretching_energy\" format=\"ascii\">");
+ for(i=0;i<vlist->n;i++){
+ senergy=0.0;
+ for(j=0;j<vtx[i]->tristar_no;j++){
+ senergy+=vtx[i]->tristar[j]->energy;
+ }
+ fprintf(fh,"%.17e ",senergy);
+ }
+ //polymeres
+ if(poly){
+ poly_idx=vlist->n;
+ for(i=0;i<vesicle->poly_list->n;i++){
+ for(j=0;j<vesicle->poly_list->poly[i]->vlist->n;j++,poly_idx++){
+ fprintf(fh,"%.17e ", 0.0);
+ }
+ }
+ }
+ //filaments
+ if(fil){
+ poly_idx=vlist->n+monono*polyno;
+ for(i=0;i<vesicle->filament_list->n;i++){
+ for(j=0;j<vesicle->filament_list->poly[i]->vlist->n;j++,poly_idx++){
+ // fprintf(stderr,"was here\n");
+ fprintf(fh,"%.17e ", 0.0);
+ }
+ }
+ }
+ fprintf(fh,"</DataArray>\n");
+ }
fprintf(fh,"</PointData>\n<CellData>\n</CellData>\n<Points>\n<DataArray type=\"Float64\" Name=\"Koordinate tock\" NumberOfComponents=\"3\" format=\"ascii\">\n");
diff --git a/src/tape b/src/tape
index 70f526a..9e81e14 100644
--- a/src/tape
+++ b/src/tape
@@ -26,7 +26,7 @@
#Stretching
stretchswitch=1
-xkA0=10.0
+xkA0=1.0
####### Polymer (brush) definitions ###########
# npoly is a number of polymers attached to npoly distinct vertices on vesicle
@@ -61,7 +61,7 @@
####### Program Control ############
#how many MC sweeps between subsequent records of states to disk
#200000
-mcsweeps=2000
+mcsweeps=200
#how many initial mcsweeps*inititer MC sweeps before recording to disk?
#2
inititer=1
diff --git a/src/vertexmove.c b/src/vertexmove.c
index 2517f69..401dddf 100644
--- a/src/vertexmove.c
+++ b/src/vertexmove.c
@@ -21,7 +21,7 @@
ts_double dist;
ts_bool retval;
ts_uint cellidx;
- ts_double delta_energy, delta_energy_cv,oenergy,dvol=0.0, darea=0.0;
+ ts_double delta_energy, delta_energy_cv,oenergy,dvol=0.0, darea=0.0, dstretchenergy=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;
@@ -113,7 +113,10 @@
for(i=0;i<vtx->tristar_no;i++) darea-=vtx->tristar[i]->area;
}
-
+ //stretching energy 1 of 3
+ if(vesicle->tape->stretchswitch==1){
+ for(i=0;i<vtx->tristar_no;i++) dstretchenergy-=vtx->tristar[i]->energy/3.0;
+ }
delta_energy=0;
// vesicle_volume(vesicle);
@@ -191,6 +194,17 @@
}
/* Vertices with spontaneous curvature may have spontaneous force perpendicular to the surface of the vesicle. additional delta energy is calculated in this function */
delta_energy+=direct_force_energy(vesicle,vtx,backupvtx);
+
+ //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/3.0;
+ }
+ }
+
+ delta_energy+=dstretchenergy;
+
/* No poly-bond energy for now!
if(vtx->grafted_poly!=NULL){
delta_energy+=
@@ -221,6 +235,12 @@
//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
+ 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){
--
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