From 1153c110781fc3add2c22ab2d996e05b0e0b10de Mon Sep 17 00:00:00 2001
From: Samo Penic <samo.penic@gmail.com>
Date: Sat, 08 Mar 2014 11:56:00 +0000
Subject: [PATCH] Merged branches polyel with constant volume
---
src/vertexmove.c | 253 ++++++++++++++++++++++++++++++++++++--------------
1 files changed, 183 insertions(+), 70 deletions(-)
diff --git a/src/vertexmove.c b/src/vertexmove.c
index 54b4491..7f6391f 100644
--- a/src/vertexmove.c
+++ b/src/vertexmove.c
@@ -13,76 +13,105 @@
#include "vertexmove.h"
#include <string.h>
-ts_bool single_verticle_timestep(ts_vesicle *vesicle,ts_vertex *vtx,ts_double
-*rn){
+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 xold,yold,zold;
- ts_double delta_energy,oenergy;
- ts_vertex *ovtx;
- ts_vertex *tvtx=(ts_vertex *)calloc(1,sizeof(ts_vertex));
-
+ ts_double delta_energy,oenergy,dvol=0.0;
+ ts_double costheta,sintheta,phi,r;
//This will hold all the information of vtx and its neighbours
- ts_vertex **backupvtx=(ts_vertex **)calloc(vtx->neigh_no+1,sizeof(ts_vertex *));
+ ts_vertex backupvtx[20];
+ memcpy((void *)&backupvtx[0],(void *)vtx,sizeof(ts_vertex));
- //randomly we move the temporary vertex
- tvtx->x=vtx->x+vesicle->stepsize*(2.0*rn[0]-1.0);
- tvtx->y=vtx->y+vesicle->stepsize*(2.0*rn[1]-1.0);
- tvtx->z=vtx->z+vesicle->stepsize*(2.0*rn[2]-1.0);
- //check we if some length to neighbours are too much
+ //Some stupid tests for debugging cell occupation!
+/* cellidx=vertex_self_avoidance(vesicle, vtx);
+ if(vesicle->clist->cell[cellidx]==vtx->cell){
+ fprintf(stderr,"Idx match!\n");
+ } else {
+ fprintf(stderr,"***** Idx don't match!\n");
+ fatal("ENding.",1);
+ }
+*/
+
+ //temporarly moving the vertex
+// vtx->x=vtx->x+vesicle->stepsize*(2.0*rn[0]-1.0);
+// vtx->y=vtx->y+vesicle->stepsize*(2.0*rn[1]-1.0);
+// vtx->z=vtx->z+vesicle->stepsize*(2.0*rn[2]-1.0);
+
+ //random move in a sphere with radius stepsize:
+ r=vesicle->stepsize*rn[0];
+ phi=rn[1]*2*M_PI;
+ costheta=2*rn[2]-1;
+ sintheta=sqrt(1-pow(costheta,2));
+ vtx->x=vtx->x+r*sintheta*cos(phi);
+ vtx->y=vtx->y+r*sintheta*sin(phi);
+ vtx->z=vtx->z+r*costheta;
+
+
+ //distance with neighbours check
for(i=0;i<vtx->neigh_no;i++){
- dist=vtx_distance_sq(tvtx,vtx->neigh[i]);
+ dist=vtx_distance_sq(vtx,vtx->neigh[i]);
if(dist<1.0 || dist>vesicle->dmax) {
- vtx_free(tvtx);
-// fprintf(stderr,"Fail 1, dist=%f, vesicle->dmax=%f\n", dist, vesicle->dmax);
+ vtx=memcpy((void *)vtx,(void *)&backupvtx[0],sizeof(ts_vertex));
return TS_FAIL;
}
}
+
+// Distance with grafted poly-vertex check:
+ if(vtx->grafted_poly!=NULL){
+ dist=vtx_distance_sq(vtx,vtx->grafted_poly->vlist->vtx[0]);
+ if(dist<1.0 || dist>vesicle->dmax) {
+ vtx=memcpy((void *)vtx,(void *)&backupvtx[0],sizeof(ts_vertex));
+ return TS_FAIL;
+ }
+ }
+
//self avoidance check with distant vertices
- cellidx=vertex_self_avoidance(vesicle, tvtx);
+ cellidx=vertex_self_avoidance(vesicle, vtx);
//check occupation number
- retval=cell_occupation_number_and_internal_proximity(vesicle->clist,cellidx,vtx,tvtx);
+ retval=cell_occupation_number_and_internal_proximity(vesicle->clist,cellidx,vtx);
+
if(retval==TS_FAIL){
- vtx_free(tvtx);
-// fprintf(stderr,"Fail 2\n");
+ vtx=memcpy((void *)vtx,(void *)&backupvtx[0],sizeof(ts_vertex));
return TS_FAIL;
}
- //if all the tests are successful, then we update the vertex position
- backupvtx[0]=(ts_vertex *)malloc(sizeof(ts_vertex));
- backupvtx[0]=(ts_vertex *)memcpy((void *)backupvtx[0],(void *)vtx,sizeof(ts_vertex));
-
+ //if all the tests are successful, then energy for vtx and neighbours is calculated
for(i=0;i<vtx->neigh_no;i++){
- backupvtx[i+1]=(ts_vertex *)malloc(sizeof(ts_vertex));
- backupvtx[i+1]=memcpy((void *)backupvtx[i+1],(void *)vtx->neigh[i],sizeof(ts_vertex));
+ memcpy((void *)&backupvtx[i+1],(void *)vtx->neigh[i],sizeof(ts_vertex));
}
-// fprintf(stderr,"CREATED\n");
-
- // xold=vtx->x;
- // yold=vtx->y;
- // zold=vtx->z;
- ovtx=malloc(sizeof(ts_vertex));
- vtx_copy(ovtx,vtx);
- vtx->x=tvtx->x;
- vtx->y=tvtx->y;
- vtx->z=tvtx->z;
+ if(vesicle->pswitch == 1){
+ for(i=0;i<vtx->tristar_no;i++) dvol-=vtx->tristar[i]->volume;
+ };
delta_energy=0;
//update the normals of triangles that share bead i.
for(i=0;i<vtx->tristar_no;i++) triangle_normal_vector(vtx->tristar[i]);
- //energy and curvature
+ oenergy=vtx->energy;
energy_vertex(vtx);
- delta_energy=vtx->xk*(vtx->energy - ovtx->energy);
+ delta_energy=vtx->xk*(vtx->energy - oenergy);
//the same is done for neighbouring vertices
for(i=0;i<vtx->neigh_no;i++){
oenergy=vtx->neigh[i]->energy;
energy_vertex(vtx->neigh[i]);
delta_energy+=vtx->neigh[i]->xk*(vtx->neigh[i]->energy-oenergy);
}
+
+ if(vesicle->pswitch == 1){
+ for(i=0;i<vtx->tristar_no;i++) dvol+=vtx->tristar[i]->volume;
+ delta_energy-=vesicle->pressure*dvol;
+ };
+
+/* No poly-bond energy for now!
+ if(vtx->grafted_poly!=NULL){
+ delta_energy+=
+ (pow(sqrt(vtx_distance_sq(vtx, vtx->grafted_poly->vlist->vtx[0])-1),2)-
+ pow(sqrt(vtx_distance_sq(&backupvtx[0], vtx->grafted_poly->vlist->vtx[0])-1),2)) *vtx->grafted_poly->k;
+ }
+*/
// fprintf(stderr, "DE=%f\n",delta_energy);
//MONTE CARLOOOOOOOO
if(delta_energy>=0){
@@ -97,47 +126,131 @@
#endif
{
//not accepted, reverting changes
- // vtx->x=xold;
- // vtx->y=yold;
- // vtx->z=zold;
-
- vtx=memcpy((void *)vtx,(void *)backupvtx[0],sizeof(ts_vertex));
- free(backupvtx[0]);
+ 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));
- free(backupvtx[i+1]);
+ vtx->neigh[i]=memcpy((void *)vtx->neigh[i],(void *)&backupvtx[i+1],sizeof(ts_vertex));
}
- free(backupvtx);
-// fprintf(stderr,"Reverted\n");
//update the normals of triangles that share bead i.
- for(i=0;i<vtx->tristar_no;i++) triangle_normal_vector(vtx->tristar[i]);
- //energy and curvature
- // energy_vertex(vtx);
- //the same is done for neighbouring vertices
-// for(i=0;i<vtx->neigh_no;i++) energy_vertex(vtx->neigh[i]);
-// free(ovtx->bond_length);
- free(ovtx->bond_length_dual);
- free(ovtx);
- vtx_free(tvtx);
+ for(i=0;i<vtx->tristar_no;i++) triangle_normal_vector(vtx->tristar[i]);
return TS_FAIL;
}
}
- //END MONTE CARLOOOOOOO
-
- //TODO: change cell occupation if necessary!
-// fprintf(stderr,"Success!!\n");
- free(ovtx->bond_length);
- free(ovtx->bond_length_dual);
- free(ovtx);
- vtx_free(tvtx);
- free(backupvtx[0]);
- for(i=0;i<vtx->neigh_no;i++){
- free(backupvtx[i+1]);
+
+// oldcellidx=vertex_self_avoidance(vesicle, &backupvtx[0]);
+ if(vtx->cell!=vesicle->clist->cell[cellidx]){
+ retval=cell_add_vertex(vesicle->clist->cell[cellidx],vtx);
+// if(retval==TS_SUCCESS) cell_remove_vertex(vesicle->clist->cell[oldcellidx],vtx);
+ if(retval==TS_SUCCESS) cell_remove_vertex(backupvtx[0].cell,vtx);
+
}
- free(backupvtx);
-// fprintf(stderr,"Accepted\n");
+// if(oldcellidx);
+ //END MONTE CARLOOOOOOO
return TS_SUCCESS;
}
+
+ts_bool single_poly_vertex_move(ts_vesicle *vesicle,ts_poly *poly,ts_vertex *vtx,ts_double *rn){
+ ts_uint i;
+ ts_bool retval;
+ ts_uint cellidx;
+// ts_double delta_energy;
+ ts_double costheta,sintheta,phi,r;
+ ts_double dist;
+ //This will hold all the information of vtx and its neighbours
+ ts_vertex backupvtx;
+// ts_bond backupbond[2];
+ memcpy((void *)&backupvtx,(void *)vtx,sizeof(ts_vertex));
+
+ //random move in a sphere with radius stepsize:
+ r=vesicle->stepsize*rn[0];
+ phi=rn[1]*2*M_PI;
+ costheta=2*rn[2]-1;
+ sintheta=sqrt(1-pow(costheta,2));
+ vtx->x=vtx->x+r*sintheta*cos(phi);
+ vtx->y=vtx->y+r*sintheta*sin(phi);
+ vtx->z=vtx->z+r*costheta;
+
+
+ //distance with neighbours check
+ for(i=0;i<vtx->neigh_no;i++){
+ dist=vtx_distance_sq(vtx,vtx->neigh[i]);
+ if(dist<1.0 || dist>vesicle->dmax) {
+ vtx=memcpy((void *)vtx,(void *)&backupvtx,sizeof(ts_vertex));
+ return TS_FAIL;
+ }
+ }
+
+// Distance with grafted vesicle-vertex check:
+ if(vtx==poly->vlist->vtx[0]){
+ dist=vtx_distance_sq(vtx,poly->grafted_vtx);
+ if(dist<1.0 || dist>vesicle->dmax) {
+ 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;
+ }
+
+
+ //if all the tests are successful, then energy for vtx and neighbours is calculated
+/* Energy ignored for now!
+ delta_energy=0;
+ for(i=0;i<vtx->bond_no;i++){
+ memcpy((void *)&backupbond[i],(void *)vtx->bond[i],sizeof(ts_bond));
+
+ vtx->bond[i]->bond_length=sqrt(vtx_distance_sq(vtx->bond[i]->vtx1,vtx->bond[i]->vtx2));
+ bond_energy(vtx->bond[i],poly);
+ delta_energy+= vtx->bond[i]->energy - backupbond[i].energy;
+ }
+
+ if(vtx==poly->vlist->vtx[0]){
+ delta_energy+=
+ (pow(sqrt(vtx_distance_sq(vtx, poly->grafted_vtx)-1),2)-
+ pow(sqrt(vtx_distance_sq(&backupvtx, poly->grafted_vtx)-1),2)) *poly->k;
+
+ }
+
+
+ if(delta_energy>=0){
+#ifdef TS_DOUBLE_DOUBLE
+ if(exp(-delta_energy)< drand48() )
+#endif
+#ifdef TS_DOUBLE_FLOAT
+ if(expf(-delta_energy)< (ts_float)drand48())
+#endif
+#ifdef TS_DOUBLE_LONGDOUBLE
+ if(expl(-delta_energy)< (ts_ldouble)drand48())
+#endif
+ {
+ //not accepted, reverting changes
+ vtx=memcpy((void *)vtx,(void *)&backupvtx,sizeof(ts_vertex));
+ for(i=0;i<vtx->bond_no;i++){
+ vtx->bond[i]=memcpy((void *)vtx->bond[i],(void *)&backupbond[i],sizeof(ts_bond));
+ }
+
+ return TS_FAIL;
+ }
+ }
+*/
+
+// oldcellidx=vertex_self_avoidance(vesicle, &backupvtx[0]);
+ if(vtx->cell!=vesicle->clist->cell[cellidx]){
+ retval=cell_add_vertex(vesicle->clist->cell[cellidx],vtx);
+// if(retval==TS_SUCCESS) cell_remove_vertex(vesicle->clist->cell[oldcellidx],vtx);
+ if(retval==TS_SUCCESS) cell_remove_vertex(backupvtx.cell,vtx);
+ }
+// if(oldcellidx);
+ //END MONTE CARLOOOOOOO
+ return TS_SUCCESS;
+}
--
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