From d43116b7d609fa9cabae4068d037c1af3a20dae8 Mon Sep 17 00:00:00 2001
From: Samo Penic <samo.penic@gmail.com>
Date: Thu, 08 Aug 2019 17:42:46 +0000
Subject: [PATCH] An attempt to fix polymer error while recreating vesicle from vtu.
---
src/constvol.c | 106 ++++++++++++++++++++++++++++-------------------------
1 files changed, 56 insertions(+), 50 deletions(-)
diff --git a/src/constvol.c b/src/constvol.c
index 33922b4..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>
@@ -12,76 +13,81 @@
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;
-/* for(k=0;k<vtx_moved->neigh[j]->neigh_no;k++){
- if(vtx_moved->neigh[j]->neigh[k]==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. */
+ 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);
-// fprintf(stderr,"Prej (x,y,z)=(%e,%e,%e).\n",vtx_moved->x,vtx_moved->y,vtx_moved->z);
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);
-// fprintf(stderr,"Potem (x,y,z)=(%e,%e,%e). Vol=%e\n",vtx_moved->x,vtx_moved->y,vtx_moved->z,Vol);
+
+//SKIPPING FIRST CHECK of CONSTRAINTS. This is not a final move.
//check for constraints
- if(constvolConstraintCheck(vesicle, vtx_moved)==TS_FAIL){
+/* if(constvolConstraintCheck(vesicle, vtx_moved)==TS_FAIL){
vtx_moved=memcpy((void *)vtx_moved,(void *)&backupvtx[0],sizeof(ts_vertex));
- continue;
- }
-// fprintf(stderr,"Sprejet.\n");
-
+// continue;
+ break;
+ } */
// All checks OK!
- fprintf(stderr, "Step 1 success\n");
- 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_moved_retval=vtx_moved;
fprintf(stderr, "Preliminary success\n");
return TS_SUCCESS;
- }
- fprintf(stderr, "Step 2 success\n");
+ } */
+
+// 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));
@@ -90,45 +96,42 @@
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=0.0;
+ dvol=volFirst;
for(j=0;j<vtx_moved->tristar_no;j++){
- dvol-=vtx_moved->tristar[j]->volume;
triangle_normal_vector(vtx_moved->tristar[j]);
dvol+=vtx_moved->tristar[j]->volume;
}
-
- fprintf(stderr, "Step 3a success voldiff=%e\n",voldiff);
voldiff=dvol-Vol;
- fprintf(stderr, "Step 3b success voldiff=%e\n",voldiff);
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_moved_retval=vtx_moved;
- fprintf(stderr, "DVOL=%e\n",voldiff);
return TS_SUCCESS;
}
-
-
}
free(backupvtx);
- fprintf(stderr, "fail\n");
return TS_FAIL;
}
@@ -168,9 +171,12 @@
ts_bool constvolumerestore(ts_vertex *vtx_moved,ts_vertex *vtx_backup){
ts_uint j;
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));
+ // 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;
}
--
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