From 6da644f98434d3eac8b4e19981754f6030a315a5 Mon Sep 17 00:00:00 2001
From: Samo Penic <samo.penic@gmail.com>
Date: Wed, 27 Jun 2018 12:05:32 +0000
Subject: [PATCH] Resolving the issues with restoring vesicles from vtu and fixing the volume. Dump to vtu has been repaired.
---
src/vertexmove.c | 61 +++++++++++++++++++++++++++---
1 files changed, 55 insertions(+), 6 deletions(-)
diff --git a/src/vertexmove.c b/src/vertexmove.c
index b065cbb..3483965 100644
--- a/src/vertexmove.c
+++ b/src/vertexmove.c
@@ -21,7 +21,8 @@
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 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;
@@ -72,11 +73,23 @@
// 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){
+//#define SQ(x) x*x
+if(vesicle->R_nucleus>0.0){
+ if ((vtx->x-vesicle->nucleus_center[0])*(vtx->x-vesicle->nucleus_center[0])+ (vtx->y-vesicle->nucleus_center[1])*(vtx->y-vesicle->nucleus_center[1]) + (vtx->z-vesicle->nucleus_center[2])*(vtx->z-vesicle->nucleus_center[2]) < vesicle->R_nucleus){
+ vtx=memcpy((void *)vtx,(void *)&backupvtx[0],sizeof(ts_vertex));
+ return TS_FAIL;
+ }
+} else if(vesicle->R_nucleusX>0.0){
+// fprintf(stderr,"DEBUG, (Rx, Ry,Rz)^2=(%f,%f,%f)\n",vesicle->R_nucleusX, vesicle->R_nucleusY, vesicle->R_nucleusZ);
+// if (SQ(vtx->x-vesicle->nucleus_center[0])/vesicle->R_nucleusX + SQ(vtx->y-vesicle->nucleus_center[1])/vesicle->R_nucleusY + SQ(vtx->z-vesicle->nucleus_center[2])/vesicle->R_nucleusZ < 1.0){
+ if ((vtx->x-vesicle->nucleus_center[0])*(vtx->x-vesicle->nucleus_center[0])/vesicle->R_nucleusX + (vtx->y-vesicle->nucleus_center[1])*(vtx->y-vesicle->nucleus_center[1])/vesicle->R_nucleusY + (vtx->z-vesicle->nucleus_center[2])*(vtx->z-vesicle->nucleus_center[2])/vesicle->R_nucleusZ < 1.0){
+// if (SQ(vtx->x)/vesicle->R_nucleusX + SQ(vtx->y)/vesicle->R_nucleusY + SQ(vtx->z)/vesicle->R_nucleusZ < 1.0){
vtx=memcpy((void *)vtx,(void *)&backupvtx[0],sizeof(ts_vertex));
return TS_FAIL;
}
+}
+//#undef SQ
//self avoidance check with distant vertices
cellidx=vertex_self_avoidance(vesicle, vtx);
//check occupation number
@@ -101,7 +114,16 @@
for(i=0;i<vtx->tristar_no;i++) darea-=vtx->tristar[i]->area;
}
-
+ //stretching energy 1 of 3
+ if(vesicle->tape->stretchswitch==1){
+ 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;
// vesicle_volume(vesicle);
@@ -143,7 +165,7 @@
if(vesicle->tape->constvolswitch==2){
/*check whether the dvol is gt than epsvol */
- //fprintf(stderr,"DVOL=%1.16e\n",dvol);
+ //fprintf(stderr,"DVOL=%1.16e, V0=%1.16e, vesicleVolume=%1.16e, |volume+dvol-V0|=%1.16e\n",dvol, V0, vesicle->volume, fabs(vesicle->volume+dvol-V0));
if(fabs(vesicle->volume+dvol-V0)>epsvol){
//restore old state.
vtx=memcpy((void *)vtx,(void *)&backupvtx[0],sizeof(ts_vertex));
@@ -151,11 +173,12 @@
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");
+ // fprintf(stderr,"fajlam!\n");
return TS_FAIL;
}
} else
+ //fprintf(stderr, "success\n");
// vesicle_volume(vesicle);
// fprintf(stderr,"Volume before=%1.16e\n", vesicle->volume);
if(vesicle->tape->constvolswitch == 1){
@@ -177,6 +200,21 @@
delta_energy+=delta_energy_cv;
// fprintf(stderr,"Denergy after=%e\n",delta_energy);
}
+/* 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++){
+ 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;
+
/* No poly-bond energy for now!
if(vtx->grafted_poly!=NULL){
delta_energy+=
@@ -186,6 +224,7 @@
*/
// fprintf(stderr, "DE=%f\n",delta_energy);
//MONTE CARLOOOOOOOO
+// if(vtx->c!=0.0) printf("DE=%f\n",delta_energy);
if(delta_energy>=0){
#ifdef TS_DOUBLE_DOUBLE
if(exp(-delta_energy)< drand48())
@@ -206,7 +245,13 @@
//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
+ 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);
@@ -237,6 +282,10 @@
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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