Removed harmonic potential between poly-monomers for now. Added min and max...

Miha

2014-02-21 304510886da7e3969efd6d506e68652b533c0975

Removed harmonic potential between poly-monomers for now. Added min and max distance between neighboring poly-vertices.

 src/energy.c

@@ -21,7 +21,9 @@


inline ts_bool bond_energy(ts_bond *bond,ts_poly *poly){
    bond->energy=poly->k*pow(bond->bond_length-1,2);
//TODO: This value to be changed and implemented in data structure:
    ts_double d_relaxed=1.0;
    bond->energy=poly->k*pow(bond->bond_length-d_relaxed,2);
    return TS_SUCCESS;
};


 src/tape

@@ -2,7 +2,7 @@
# nshell is a number of divisions of dipyramid
nshell=17
# dmax is the max. bond length 
dmax=1.4
dmax=1.7
# bending rigidity of the membrane 
xk0=25.0
# max step size 

 src/vertexmove.c

@@ -57,6 +57,16 @@
        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, vtx);
    //check occupation number
@@ -87,15 +97,13 @@
        energy_vertex(vtx->neigh[i]);
        delta_energy+=vtx->neigh[i]->xk*(vtx->neigh[i]->energy-oenergy);
    }

/* 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){
@@ -139,11 +147,12 @@
    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;
    //This will hold all the information of vtx and its neighbours
    ts_vertex backupvtx;
    ts_bond backupbond[2];
//    ts_bond backupbond[2];
    memcpy((void *)&backupvtx,(void *)vtx,sizeof(ts_vertex));

    //random move in a sphere with radius stepsize:
@@ -157,13 +166,23 @@


    //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[0],sizeof(ts_vertex));
//    return TS_FAIL;
//        }
//    }
    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);
@@ -177,6 +196,7 @@


    //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));
@@ -214,6 +234,7 @@
    return TS_FAIL; 
    }
    }
*/
        
//    oldcellidx=vertex_self_avoidance(vesicle, &backupvtx[0]);
    if(vtx->cell!=vesicle->clist->cell[cellidx]){