From 9166cbcd0e28d61a69646911af35bb7895ff9203 Mon Sep 17 00:00:00 2001 From: Samo Penic <samo.penic@fe.uni-lj.si> Date: Mon, 28 Apr 2014 11:16:45 +0000 Subject: [PATCH] Did major change in vesicle datastructure. Added tape information into vesicle. This means the dump files will be broken each time tape structure changes. Beware. --- src/vertexmove.c | 75 ++++++++++++++++++++++++------------- 1 files changed, 49 insertions(+), 26 deletions(-) diff --git a/src/vertexmove.c b/src/vertexmove.c index 04325ef..7b099e4 100644 --- a/src/vertexmove.c +++ b/src/vertexmove.c @@ -9,6 +9,7 @@ #include "timestep.h" #include "cell.h" //#include "io.h" +#include "io.h" #include<stdio.h> #include "vertexmove.h" #include <string.h> @@ -67,11 +68,18 @@ } } - //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; @@ -83,7 +91,7 @@ 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; }; @@ -100,9 +108,9 @@ 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; }; /* No poly-bond energy for now! @@ -262,12 +270,14 @@ ts_uint i; ts_bool retval; ts_uint cellidx; -// ts_double delta_energy; + ts_double delta_energy; ts_double costheta,sintheta,phi,r; ts_double dist[2]; //This will hold all the information of vtx and its neighbours - ts_vertex backupvtx; + ts_vertex backupvtx,backupneigh[2]; ts_bond backupbond[2]; + + //backup vertex: memcpy((void *)&backupvtx,(void *)vtx,sizeof(ts_vertex)); //random move in a sphere with radius stepsize: @@ -289,12 +299,18 @@ } } +// 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; @@ -305,26 +321,30 @@ memcpy(&backupbond[i],vtx->bond[i], sizeof(ts_bond)); vtx->bond[i]->bond_length=sqrt(dist[i]); bond_vector(vtx->bond[i]); - + } + + //backup neighboring vertices: + for(i=0;i<vtx->neigh_no;i++){ + memcpy(&backupneigh[i],vtx->neigh[i], sizeof(ts_vertex)); } //if all the tests are successful, then energy for vtx and neighbours is calculated -// delta_energy=0; -/* for(i=0;i<vtx->neigh_no;i++){ -// memcpy((void *)&backupbond[i],(void *)vtx->bond[i],sizeof(ts_bond)); - xp = vtx->neigh[i] - 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; + delta_energy=0; + + if(vtx->bond_no == 2){ + vtx->energy = -(vtx->bond[0]->x*vtx->bond[1]->x + vtx->bond[0]->y*vtx->bond[1]->y + vtx->bond[0]->z*vtx->bond[1]->z)/vtx->bond[0]->bond_length/vtx->bond[1]->bond_length; + delta_energy += vtx->energy - backupvtx.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; - + for(i=0;i<vtx->neigh_no;i++){ + if(vtx->neigh[i]->bond_no == 2){ + vtx->neigh[i]->energy = -(vtx->neigh[i]->bond[0]->x*vtx->neigh[i]->bond[1]->x + vtx->neigh[i]->bond[0]->y*vtx->neigh[i]->bond[1]->y + vtx->neigh[i]->bond[0]->z*vtx->neigh[i]->bond[1]->z)/vtx->neigh[i]->bond[0]->bond_length/vtx->neigh[i]->bond[1]->bond_length; + delta_energy += vtx->neigh[i]->energy - backupneigh[i].energy; + } } + // poly->k is filament persistence length (in units l_min) + delta_energy *= poly->k; if(delta_energy>=0){ #ifdef TS_DOUBLE_DOUBLE @@ -339,15 +359,18 @@ { //not accepted, reverting changes vtx=memcpy((void *)vtx,(void *)&backupvtx,sizeof(ts_vertex)); + for(i=0;i<vtx->neigh_no;i++){ + memcpy(vtx->neigh[i],&backupneigh[i],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)); + 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); -- Gitblit v1.9.3