From fe5069cc3872b513f4715b0cfd303175ae80c468 Mon Sep 17 00:00:00 2001
From: Samo Penic <samo.penic@fe.uni-lj.si>
Date: Wed, 30 Apr 2014 10:23:50 +0000
Subject: [PATCH] Debugged vertexmove. testing bondflip.
---
src/constvol.c | 65 ++++++++++++++------------------
src/timestep.c | 7 ++-
src/tape | 2
src/vertexmove.c | 19 +++++++--
4 files changed, 49 insertions(+), 44 deletions(-)
diff --git a/src/constvol.c b/src/constvol.c
index 33922b4..be69edf 100644
--- a/src/constvol.c
+++ b/src/constvol.c
@@ -12,45 +12,36 @@
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=3;
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];
+ /* chosen vertex must not be a nearest neighbour. TODO: probably must
+ * 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!
+ //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);
//check for constraints
if(constvolConstraintCheck(vesicle, vtx_moved)==TS_FAIL){
vtx_moved=memcpy((void *)vtx_moved,(void *)&backupvtx[0],sizeof(ts_vertex));
continue;
}
-// fprintf(stderr,"Sprejet.\n");
-
// 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));
@@ -58,30 +49,35 @@
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));
@@ -94,41 +90,36 @@
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));
+ //also, restore normals
+ for(j=0;j<vtx_moved->tristar_no;j++) triangle_normal_vector(vtx_moved->tristar[j]);
continue;
}
- 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);
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;
}
@@ -171,6 +162,8 @@
for(j=0;j<vtx_moved->neigh_no;j++){
memcpy((void *)vtx_moved->neigh[j],(void *)&vtx_backup[j+1],sizeof(ts_vertex));
}
+ for(j=0;j<vtx_moved->tristar_no;j++) triangle_normal_vector(vtx_moved->tristar[j]);
+
free(vtx_backup);
return TS_SUCCESS;
}
diff --git a/src/tape b/src/tape
index 935bf18..3c6bcb7 100644
--- a/src/tape
+++ b/src/tape
@@ -18,7 +18,7 @@
#Constant volume constraint (0 disable constant volume, 1 enable)
constvolswitch=1
-constvolprecision=1e-3
+constvolprecision=1e-16
####### Polymer (brush) definitions ###########
diff --git a/src/timestep.c b/src/timestep.c
index 2ecc30b..9001639 100644
--- a/src/timestep.c
+++ b/src/timestep.c
@@ -27,6 +27,7 @@
fprintf(fd, "Epoch OuterLoop VertexMoveSucessRate BondFlipSuccessRate Volume Area lamdba1 lambda2 lambda3 Kc(2-9) Kc(6-9) Kc(2-end) Kc(3-6)\n");
centermass(vesicle);
cell_occupation(vesicle);
+ vesicle_volume(vesicle); //needed for constant volume at this moment
if(start_iteration<inititer) ts_fprintf(stdout, "Starting simulation (first %d x %d MC sweeps will not be recorded on disk)\n", inititer, mcsweeps);
for(i=start_iteration;i<inititer+iterations;i++){
vmsr=0.0;
@@ -88,7 +89,7 @@
ts_bool single_timestep(ts_vesicle *vesicle,ts_double *vmsr, ts_double *bfsr){
ts_bool retval;
ts_double rnvec[3];
- ts_uint i,j;//b;
+ ts_uint i,j, b;
ts_uint vmsrcnt=0;
for(i=0;i<vesicle->vlist->n;i++){
rnvec[0]=drand48();
@@ -100,10 +101,10 @@
ts_int bfsrcnt=0;
for(i=0;i<3*vesicle->vlist->n;i++){
-// b=rand() % vesicle->blist->n;
+ b=rand() % vesicle->blist->n;
//find a bond and return a pointer to a bond...
//call single_bondflip_timestep...
- // retval=single_bondflip_timestep(vesicle,vesicle->blist->bond[b],rnvec);
+ retval=single_bondflip_timestep(vesicle,vesicle->blist->bond[b],rnvec);
retval=TS_FAIL;
if(retval==TS_SUCCESS) bfsrcnt++;
}
diff --git a/src/vertexmove.c b/src/vertexmove.c
index 9f263c8..36cf993 100644
--- a/src/vertexmove.c
+++ b/src/vertexmove.c
@@ -97,9 +97,9 @@
};
delta_energy=0;
-
-
-// fprintf(stderr,"Success for now.\n");
+
+// vesicle_volume(vesicle);
+// fprintf(stderr,"Volume in the beginning=%1.16e\n", vesicle->volume);
//update the normals of triangles that share bead i.
for(i=0;i<vtx->tristar_no;i++) triangle_normal_vector(vtx->tristar[i]);
@@ -118,17 +118,26 @@
if(vesicle->pswitch==1) delta_energy-=vesicle->pressure*dvol;
};
+// vesicle_volume(vesicle);
+// fprintf(stderr,"Volume before=%1.16e\n", vesicle->volume);
if(vesicle->tape->constvolswitch == 1){
- retval=constvolume(vesicle, vtx, dvol, &delta_energy_cv, &constvol_vtx_moved,&constvol_vtx_backup);
+ 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]);
+ // fprintf(stderr,"fajlam!\n");
return TS_FAIL;
}
+// vesicle_volume(vesicle);
+// fprintf(stderr,"Volume after=%1.16e\n", vesicle->volume);
+// fprintf(stderr,"Volume after-dvol=%1.16e\n", vesicle->volume-dvol);
+// fprintf(stderr,"Denergy before=%e\n",delta_energy);
+
delta_energy+=delta_energy_cv;
+// fprintf(stderr,"Denergy after=%e\n",delta_energy);
}
/* No poly-bond energy for now!
if(vtx->grafted_poly!=NULL){
@@ -160,9 +169,11 @@
//update the normals of triangles that share bead i.
for(i=0;i<vtx->tristar_no;i++) triangle_normal_vector(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);
}
+// fprintf(stderr, "after vtx(x,y,z)=%e,%e,%e\n",constvol_vtx_moved->x, constvol_vtx_moved->y, constvol_vtx_moved->z);
return TS_FAIL;
}
}
--
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