From e6efc61995516174081e923004477e3ff0853515 Mon Sep 17 00:00:00 2001
From: Samo Penic <samo.penic@gmail.com>
Date: Tue, 19 Sep 2017 12:35:28 +0000
Subject: [PATCH] Added comments for spontaneous curvature in energy.c and tape
---
src/constvol.c | 135 ++++++++++++++++++++++++++++----------------
1 files changed, 85 insertions(+), 50 deletions(-)
diff --git a/src/constvol.c b/src/constvol.c
index da07add..63c07e0 100644
--- a/src/constvol.c
+++ b/src/constvol.c
@@ -1,3 +1,4 @@
+/* vim: set ts=4 sts=4 sw=4 noet : */
#include<stdlib.h>
#include<stdio.h>
#include<string.h>
@@ -9,69 +10,84 @@
#include "vertex.h"
#include "cell.h"
-ts_bool constvolume(ts_vesicle *vesicle, ts_vertex *vtx_avoid, ts_double Vol, ts_double *retEnergy, ts_vertex *vtx_moved, ts_vertex *vtx_backup){
-
+ts_bool constvolume(ts_vesicle *vesicle, ts_vertex *vtx_avoid, ts_double Vol, ts_double *retEnergy, ts_vertex **vtx_moved_retval, ts_vertex **vtx_backup){
+ ts_vertex *vtx_moved;
ts_uint vtxind,i,j;
- ts_uint Ntries=20;
+ ts_uint Ntries=100;
ts_vertex *backupvtx;
- ts_double Rv, dh, dvol, voldiff, oenergy,delta_energy;
-
+ ts_double Rv, dh, dvol, volFirst, voldiff, oenergy,delta_energy;
backupvtx=(ts_vertex *)calloc(sizeof(ts_vertex),10);
-
+ ts_double l0 = (1.0 + sqrt(vesicle->dmax))/2.0; //make this a global constant if necessary
for(i=0;i<Ntries;i++){
vtxind=rand() % vesicle->vlist->n;
vtx_moved=vesicle->vlist->vtx[vtxind];
- if(vtx_moved==vtx_avoid) continue;
-
+ /* chosen vertex must not be a nearest neighbour. WASTODO: probably must.
+ * DONE: solved below, when using different algorithm.
+ * extend search in case of bondflip */
+/* if(vtx_moved==vtx_avoid) continue;
for(j=0;j<vtx_moved->neigh_no;j++){
if(vtx_moved->neigh[j]==vtx_avoid) continue;
}
-
- memcpy((void *)&backupvtx[0],(void *)vtx_moved,sizeof(ts_vertex));
- //move vertex in specified direction. first try, test move!
+*/
+/* different check of nearest neighbour (and second nearest neighbour) check.
+ * Checking the distance between vertex and vertex to be moved to assure
+ * constant volume. Solves upper todo problem. */
- Rv=sqrt(pow(vtx_moved->x,2)+pow(vtx_moved->y,2)+pow(vtx_moved->z,2));
- dh=2*Rv*vesicle->dmax/sqrt(3);
- vtx_moved->x=vtx_moved->x*(1-dh/Rv);
- vtx_moved->y=vtx_moved->y*(1-dh/Rv);
- vtx_moved->z=vtx_moved->z*(1-dh/Rv);
-
- //check for constraints
- if(constvolConstraintCheck(vesicle, vtx_moved)==TS_FAIL){
- vtx_moved=memcpy((void *)vtx_moved,(void *)&backupvtx[0],sizeof(ts_vertex));
+ if(vtx_distance_sq(vtx_moved,vtx_avoid)<16.0*vesicle->dmax){
continue;
}
+
+ memcpy((void *)&backupvtx[0],(void *)vtx_moved,sizeof(ts_vertex));
+ //move vertex in specified direction. first try, test move!
+ Rv=sqrt(pow(vtx_moved->x,2)+pow(vtx_moved->y,2)+pow(vtx_moved->z,2));
+ dh=2.0*Vol/(sqrt(3.0)*l0*l0);
+ vtx_moved->x=vtx_moved->x*(1.0-dh/Rv);
+ vtx_moved->y=vtx_moved->y*(1.0-dh/Rv);
+ vtx_moved->z=vtx_moved->z*(1.0-dh/Rv);
+
+
+//SKIPPING FIRST CHECK of CONSTRAINTS. This is not a final move.
+ //check for constraints
+/* if(constvolConstraintCheck(vesicle, vtx_moved)==TS_FAIL){
+ vtx_moved=memcpy((void *)vtx_moved,(void *)&backupvtx[0],sizeof(ts_vertex));
+// continue;
+ break;
+ } */
// All checks OK!
- // doing second and final move.
- for(j=0;j<vtx_moved->neigh_no;j++){
- memcpy((void *)&backupvtx[j+1],(void *)vtx_moved->neigh[j],sizeof(ts_vertex));
- }
dvol=0.0;
for(j=0;j<vtx_moved->tristar_no;j++){
dvol-=vtx_moved->tristar[j]->volume;
+ }
+ volFirst=dvol;
+ for(j=0;j<vtx_moved->tristar_no;j++){
triangle_normal_vector(vtx_moved->tristar[j]);
dvol+=vtx_moved->tristar[j]->volume;
}
-
- voldiff=dvol-Vol;
-
+//TODO: here there is a bug. Don't know where, but preliminary success can
+//happen sometimes. And when I do this checks, constant value is not achieved
+//anymore
+/* voldiff=dvol-Vol;
if(fabs(voldiff)/vesicle->volume < vesicle->tape->constvolprecision){
//calculate energy, return change in energy...
oenergy=vtx_moved->energy;
energy_vertex(vtx_moved);
delta_energy=vtx_moved->xk*(vtx_moved->energy - oenergy);
//the same is done for neighbouring vertices
- for(i=0;i<vtx_moved->neigh_no;i++){
- oenergy=vtx_moved->neigh[i]->energy;
- energy_vertex(vtx_moved->neigh[i]);
- delta_energy+=vtx_moved->neigh[i]->xk*(vtx_moved->neigh[i]->energy-oenergy);
+ for(j=0;j<vtx_moved->neigh_no;j++){
+ oenergy=vtx_moved->neigh[j]->energy;
+ energy_vertex(vtx_moved->neigh[j]);
+ delta_energy+=vtx_moved->neigh[j]->xk*(vtx_moved->neigh[j]->energy-oenergy);
}
*retEnergy=delta_energy;
- vtx_backup=backupvtx;
+ *vtx_backup=backupvtx;
+ *vtx_moved_retval=vtx_moved;
+ fprintf(stderr, "Preliminary success\n");
return TS_SUCCESS;
- }
+ } */
+
+// fprintf(stderr, "Step 2 success\n");
//do it again ;)
dh=Vol*dh/dvol;
vtx_moved=memcpy((void *)vtx_moved,(void *)&backupvtx[0],sizeof(ts_vertex));
@@ -80,31 +96,40 @@
vtx_moved->z=vtx_moved->z*(1-dh/Rv);
//check for constraints
if(constvolConstraintCheck(vesicle, vtx_moved)==TS_FAIL){
- for(j=0;j<vtx_moved->neigh_no;j++){
- memcpy((void *)vtx_moved->neigh[j],(void *)&backupvtx[j+1],sizeof(ts_vertex));
- }
vtx_moved=memcpy((void *)vtx_moved,(void *)&backupvtx[0],sizeof(ts_vertex));
- continue;
+ //also, restore normals
+ for(j=0;j<vtx_moved->tristar_no;j++) triangle_normal_vector(vtx_moved->tristar[j]);
+// continue;
+ break;
}
+ dvol=volFirst;
+ for(j=0;j<vtx_moved->tristar_no;j++){
+ triangle_normal_vector(vtx_moved->tristar[j]);
+ dvol+=vtx_moved->tristar[j]->volume;
+ }
voldiff=dvol-Vol;
if(fabs(voldiff)/vesicle->volume < vesicle->tape->constvolprecision){
//calculate energy, return change in energy...
+// fprintf(stderr, "Constvol success! %e\n",voldiff);
+ for(j=0;j<vtx_moved->neigh_no;j++){
+ memcpy((void *)&backupvtx[j+1],(void *)vtx_moved->neigh[j],sizeof(ts_vertex));
+ }
+
oenergy=vtx_moved->energy;
energy_vertex(vtx_moved);
delta_energy=vtx_moved->xk*(vtx_moved->energy - oenergy);
//the same is done for neighbouring vertices
- for(i=0;i<vtx_moved->neigh_no;i++){
- oenergy=vtx_moved->neigh[i]->energy;
- energy_vertex(vtx_moved->neigh[i]);
- delta_energy+=vtx_moved->neigh[i]->xk*(vtx_moved->neigh[i]->energy-oenergy);
+ for(j=0;j<vtx_moved->neigh_no;j++){
+ oenergy=vtx_moved->neigh[j]->energy;
+ energy_vertex(vtx_moved->neigh[j]);
+ delta_energy+=vtx_moved->neigh[j]->xk*(vtx_moved->neigh[j]->energy-oenergy);
}
*retEnergy=delta_energy;
- vtx_backup=backupvtx;
+ *vtx_backup=backupvtx;
+ *vtx_moved_retval=vtx_moved;
return TS_SUCCESS;
}
-
-
}
free(backupvtx);
return TS_FAIL;
@@ -145,16 +170,26 @@
ts_bool constvolumerestore(ts_vertex *vtx_moved,ts_vertex *vtx_backup){
ts_uint j;
- for(j=0;j<vtx_moved->neigh_no;j++){
- memcpy((void *)vtx_moved->neigh[j],(void *)&vtx_backup[j+1],sizeof(ts_vertex));
- }
- vtx_moved=memcpy((void *)vtx_moved,(void *)&vtx_backup[0],sizeof(ts_vertex));
+ memcpy((void *)vtx_moved,(void *)&vtx_backup[0],sizeof(ts_vertex));
+ for(j=0;j<vtx_moved->tristar_no;j++) triangle_normal_vector(vtx_moved->tristar[j]);
+ for(j=0;j<vtx_moved->neigh_no;j++){
+ // memcpy((void *)vtx_moved->neigh[j],(void *)&vtx_backup[j+1],sizeof(ts_vertex));
+ energy_vertex(vtx_moved->neigh[j]);
+ }
+ free(vtx_backup);
return TS_SUCCESS;
}
-ts_bool constvolumeaccept(ts_vertex *vtx_moved, ts_vertex *vtx_backup){
-
+ts_bool constvolumeaccept(ts_vesicle *vesicle,ts_vertex *vtx_moved, ts_vertex *vtx_backup){
+ ts_bool retval;
+ ts_uint cellidx=vertex_self_avoidance(vesicle, vtx_moved);
+ if(vtx_moved->cell!=vesicle->clist->cell[cellidx]){
+ retval=cell_add_vertex(vesicle->clist->cell[cellidx],vtx_moved);
+ if(retval==TS_SUCCESS) cell_remove_vertex(vtx_backup[0].cell,vtx_moved);
+
+ }
+ free(vtx_backup);
return TS_SUCCESS;
}
--
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