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/bondflip.c | 97 ++++++++++++++++++++++++++++++++++++++++++++----
1 files changed, 89 insertions(+), 8 deletions(-)
diff --git a/src/bondflip.c b/src/bondflip.c
index 3a31a28..13ec263 100644
--- a/src/bondflip.c
+++ b/src/bondflip.c
@@ -1,3 +1,4 @@
+/* vim: set ts=4 sts=4 sw=4 noet : */
#include<stdlib.h>
#include<math.h>
#include "general.h"
@@ -31,7 +32,7 @@
ts_vertex *k=bond->vtx2;
ts_uint nei,neip,neim;
ts_uint i,j;
- ts_double oldenergy, delta_energy, dvol=0.0;
+ ts_double oldenergy, delta_energy, dvol=0.0, darea=0.0;
ts_triangle *lm=NULL,*lp=NULL, *lp1=NULL, *lm2=NULL;
ts_vertex *kp,*km;
@@ -167,16 +168,16 @@
oldenergy+=kp->xk* kp->energy;
oldenergy+=km->xk* km->energy;
oldenergy+=it->xk* it->energy;
+ oldenergy+=bond->energy; /* attraction with neighboring vertices, that have spontaneous curvature */
//Neigbours of k, it, km, kp don't change its energy.
- if(vesicle->pswitch == 1 || vesicle->tape->constvolswitch==1){dvol = -lm->volume - lp->volume;}
-
+ if(vesicle->pswitch == 1 || vesicle->tape->constvolswitch>0){dvol = -lm->volume - lp->volume;}
+ if(vesicle->tape->constareaswitch==2){darea=-lm->area-lp->area;}
/* 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);
+ ts_flip_bond(k,it,km,kp, bond,lm, lp, lm2, lp1, vesicle->tape->w);
/* Calculating the new energy */
@@ -185,14 +186,84 @@
delta_energy+=kp->xk* kp->energy;
delta_energy+=km->xk* km->energy;
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==1){
+ if(vesicle->pswitch == 1 || vesicle->tape->constvolswitch>0){
dvol = dvol + lm->volume + lp->volume;
if(vesicle->pswitch==1) delta_energy-= vesicle->pressure*dvol;
}
+ if(vesicle->tape->constareaswitch==2){
+ darea=darea+lm->area+lp->area;
+/*check whether the dvol is gt than epsvol */
+ if(fabs(vesicle->area+darea-A0)>epsarea){
+ //restore old state.
+ /* restoration procedure copied from few lines below */
+ for(i=0;i<4;i++){
+ // fprintf(stderr,"Restoring vtx neigh[%d] with neighbours %d\n",i, orig_vtx[i]->neigh_no );
+ free(orig_vtx[i]->neigh);
+ free(orig_vtx[i]->tristar);
+ free(orig_vtx[i]->bond);
+ free(orig_tria[i]->neigh);
+ memcpy((void *)orig_vtx[i],(void *)bck_vtx[i],sizeof(ts_vertex));
+ memcpy((void *)orig_tria[i],(void *)bck_tria[i],sizeof(ts_triangle));
+ // fprintf(stderr,"Restored vtx neigh[%d] with neighbours %d\n",i, orig_vtx[i]->neigh_no );
+ /* level 2 pointers are redirected*/
+ }
+ memcpy(bond,bck_bond,sizeof(ts_bond));
+ for(i=0;i<4;i++){
+ free(bck_vtx[i]);
+ free(bck_tria[i]);
+ /* fprintf(stderr,"Restoring vtx neigh[%d] with neighbours %d =",i, orig_vtx[i]->neigh_no );
+ for(j=0;j<orig_vtx[i]->neigh_no;j++) fprintf(stderr," %d", orig_vtx[i]->neigh[j]->idx);
+ fprintf(stderr,"\n"); */
+ }
+ free(bck_bond);
+ return TS_FAIL;
+ }
+ }
+
+
+
+
+ if(vesicle->tape->constvolswitch == 2){
+ /*check whether the dvol is gt than epsvol */
+ if(fabs(vesicle->volume+dvol-V0)>epsvol){
+ //restore old state.
+ /* restoration procedure copied from few lines below */
+ for(i=0;i<4;i++){
+ // fprintf(stderr,"Restoring vtx neigh[%d] with neighbours %d\n",i, orig_vtx[i]->neigh_no );
+ free(orig_vtx[i]->neigh);
+ free(orig_vtx[i]->tristar);
+ free(orig_vtx[i]->bond);
+ free(orig_tria[i]->neigh);
+ memcpy((void *)orig_vtx[i],(void *)bck_vtx[i],sizeof(ts_vertex));
+ memcpy((void *)orig_tria[i],(void *)bck_tria[i],sizeof(ts_triangle));
+ // fprintf(stderr,"Restored vtx neigh[%d] with neighbours %d\n",i, orig_vtx[i]->neigh_no );
+ /* level 2 pointers are redirected*/
+ }
+ memcpy(bond,bck_bond,sizeof(ts_bond));
+ for(i=0;i<4;i++){
+ free(bck_vtx[i]);
+ free(bck_tria[i]);
+ /* fprintf(stderr,"Restoring vtx neigh[%d] with neighbours %d =",i, orig_vtx[i]->neigh_no );
+ for(j=0;j<orig_vtx[i]->neigh_no;j++) fprintf(stderr," %d", orig_vtx[i]->neigh[j]->idx);
+ fprintf(stderr,"\n"); */
+ }
+ free(bck_bond);
+ return TS_FAIL;
+
+ }
+
+ } else
if(vesicle->tape->constvolswitch == 1){
retval=constvolume(vesicle, it, -dvol, &delta_energy_cv, &constvol_vtx_moved,&constvol_vtx_backup);
if(retval==TS_FAIL){
@@ -268,6 +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;
}
@@ -275,8 +350,13 @@
/* IF BONDFLIP ACCEPTED, THEN RETURN SUCCESS! */
// fprintf(stderr,"SUCCESS!!!\n");
- if(vesicle->tape->constvolswitch == 1){
+ if(vesicle->tape->constvolswitch == 2){
+ vesicle->volume+=dvol;
+ } else if(vesicle->tape->constvolswitch == 1){
constvolumeaccept(vesicle,constvol_vtx_moved,constvol_vtx_backup);
+ }
+ if(vesicle->tape->constareaswitch==2){
+ vesicle->area+=darea;
}
// delete all backups
for(i=0;i<4;i++){
@@ -300,7 +380,7 @@
ts_bool ts_flip_bond(ts_vertex *k,ts_vertex *it,ts_vertex *km, ts_vertex *kp,
-ts_bond *bond, ts_triangle *lm, ts_triangle *lp, ts_triangle *lm2, ts_triangle *lp1){
+ts_bond *bond, ts_triangle *lm, ts_triangle *lp, ts_triangle *lm2, ts_triangle *lp1, ts_double w_energy){
ts_uint i; //lmidx, lpidx;
if(k==NULL || it==NULL || km==NULL || kp==NULL){
@@ -366,6 +446,7 @@
energy_vertex(kp);
energy_vertex(km);
energy_vertex(it);
+ attraction_bond_energy(bond, w_energy);
// END modifications to data structure!
return TS_SUCCESS;
}
--
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