From b2fa8c6b55c420c079f285224f8d56ed03939767 Mon Sep 17 00:00:00 2001
From: Samo Penic <samo.penic@fe.uni-lj.si>
Date: Tue, 29 Apr 2014 18:13:26 +0000
Subject: [PATCH] Bondflip doesnt segfaults anymore. Bondflip is disabled, debugging vertexmove
---
src/vertexmove.c | 64 ++++++++++++++++++++++++++------
1 files changed, 52 insertions(+), 12 deletions(-)
diff --git a/src/vertexmove.c b/src/vertexmove.c
index da8e70f..9f263c8 100644
--- a/src/vertexmove.c
+++ b/src/vertexmove.c
@@ -9,19 +9,21 @@
#include "timestep.h"
#include "cell.h"
//#include "io.h"
+#include "io.h"
#include<stdio.h>
#include "vertexmove.h"
#include <string.h>
+#include "constvol.h"
ts_bool single_verticle_timestep(ts_vesicle *vesicle,ts_vertex *vtx,ts_double *rn){
ts_uint i;
ts_double dist;
ts_bool retval;
ts_uint cellidx;
- ts_double delta_energy,oenergy,dvol=0.0;
+ ts_double delta_energy, delta_energy_cv,oenergy,dvol=0.0;
ts_double costheta,sintheta,phi,r;
//This will hold all the information of vtx and its neighbours
- ts_vertex backupvtx[20];
+ ts_vertex backupvtx[20], *constvol_vtx_moved=NULL, *constvol_vtx_backup=NULL;
memcpy((void *)&backupvtx[0],(void *)vtx,sizeof(ts_vertex));
//Some stupid tests for debugging cell occupation!
@@ -67,11 +69,18 @@
}
}
- //self avoidance check with distant vertices
- cellidx=vertex_self_avoidance(vesicle, vtx);
- //check occupation number
- retval=cell_occupation_number_and_internal_proximity(vesicle->clist,cellidx,vtx);
-
+// 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){
+ vtx=memcpy((void *)vtx,(void *)&backupvtx[0],sizeof(ts_vertex));
+ return TS_FAIL;
+ }
+
+//self avoidance check with distant vertices
+ cellidx=vertex_self_avoidance(vesicle, vtx);
+ //check occupation number
+ retval=cell_occupation_number_and_internal_proximity(vesicle->clist,cellidx,vtx);
+
if(retval==TS_FAIL){
vtx=memcpy((void *)vtx,(void *)&backupvtx[0],sizeof(ts_vertex));
return TS_FAIL;
@@ -83,11 +92,15 @@
memcpy((void *)&backupvtx[i+1],(void *)vtx->neigh[i],sizeof(ts_vertex));
}
- if(vesicle->pswitch == 1){
+ if(vesicle->pswitch == 1 || vesicle->tape->constvolswitch==1){
for(i=0;i<vtx->tristar_no;i++) dvol-=vtx->tristar[i]->volume;
};
delta_energy=0;
+
+
+// fprintf(stderr,"Success for now.\n");
+
//update the normals of triangles that share bead i.
for(i=0;i<vtx->tristar_no;i++) triangle_normal_vector(vtx->tristar[i]);
oenergy=vtx->energy;
@@ -100,11 +113,23 @@
delta_energy+=vtx->neigh[i]->xk*(vtx->neigh[i]->energy-oenergy);
}
- if(vesicle->pswitch == 1){
+ if(vesicle->pswitch == 1 || vesicle->tape->constvolswitch == 1){
for(i=0;i<vtx->tristar_no;i++) dvol+=vtx->tristar[i]->volume;
- delta_energy-=vesicle->pressure*dvol;
+ if(vesicle->pswitch==1) delta_energy-=vesicle->pressure*dvol;
};
+ if(vesicle->tape->constvolswitch == 1){
+ retval=constvolume(vesicle, vtx, dvol, &delta_energy_cv, &constvol_vtx_moved,&constvol_vtx_backup);
+ if(retval==TS_FAIL){ // if we couldn't move the vertex to assure constant volume
+ vtx=memcpy((void *)vtx,(void *)&backupvtx[0],sizeof(ts_vertex));
+ for(i=0;i<vtx->neigh_no;i++){
+ 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]);
+ return TS_FAIL;
+ }
+ delta_energy+=delta_energy_cv;
+ }
/* No poly-bond energy for now!
if(vtx->grafted_poly!=NULL){
delta_energy+=
@@ -126,6 +151,7 @@
#endif
{
//not accepted, reverting changes
+ // fprintf(stderr,"MC failed\n");
vtx=memcpy((void *)vtx,(void *)&backupvtx[0],sizeof(ts_vertex));
for(i=0;i<vtx->neigh_no;i++){
vtx->neigh[i]=memcpy((void *)vtx->neigh[i],(void *)&backupvtx[i+1],sizeof(ts_vertex));
@@ -134,10 +160,14 @@
//update the normals of triangles that share bead i.
for(i=0;i<vtx->tristar_no;i++) triangle_normal_vector(vtx->tristar[i]);
+ if(vesicle->tape->constvolswitch == 1){
+ constvolumerestore(constvol_vtx_moved,constvol_vtx_backup);
+ }
return TS_FAIL;
}
}
-
+ //accepted
+ // fprintf(stderr,"MC accepted\n");
// oldcellidx=vertex_self_avoidance(vesicle, &backupvtx[0]);
if(vtx->cell!=vesicle->clist->cell[cellidx]){
retval=cell_add_vertex(vesicle->clist->cell[cellidx],vtx);
@@ -145,6 +175,10 @@
if(retval==TS_SUCCESS) cell_remove_vertex(backupvtx[0].cell,vtx);
}
+
+ if(vesicle->tape->constvolswitch == 1){
+ constvolumeaccept(vesicle,constvol_vtx_moved,constvol_vtx_backup);
+ }
// if(oldcellidx);
//END MONTE CARLOOOOOOO
return TS_SUCCESS;
@@ -291,12 +325,18 @@
}
}
+// 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){
+ vtx=memcpy((void *)vtx,(void *)&backupvtx,sizeof(ts_vertex));
+ return TS_FAIL;
+ }
+
//self avoidance check with distant vertices
cellidx=vertex_self_avoidance(vesicle, vtx);
//check occupation number
retval=cell_occupation_number_and_internal_proximity(vesicle->clist,cellidx,vtx);
-
if(retval==TS_FAIL){
vtx=memcpy((void *)vtx,(void *)&backupvtx,sizeof(ts_vertex));
return TS_FAIL;
--
Gitblit v1.9.3