Change in location of setting spontaneous curvature. Now it is done in init...

Samo Penic

2016-06-21 e5858ff1dcf5cecfcfe81602f52d255de9d508f4

Change in location of setting spontaneous curvature. Now it is done in initial_distribution.c, in function set_vesicle_values_from_tape. Also, energy assigning function is done and sweeping of the whole vesicle aswell.

 src/energy.c

@@ -185,3 +185,25 @@

    return TS_SUCCESS;
}



ts_bool sweep_attraction_bond_energy(ts_vesicle *vesicle){
    int i;
    for(i=0;i<vesicle->blist->n;i++){
        attraction_bond_energy(vesicle->blist->bond[i], vesicle->tape->w);
    }
    return TS_SUCCESS;
}


inline ts_bool attraction_bond_energy(ts_bond *bond, ts_double w){

    if(fabs(bond->vtx1->c)>1e-16 && fabs(bond->vtx2->c)>1e-16){
        bond->energy=w;
    }
    else {
        bond->energy=0.0;
    }
    return TS_SUCCESS;
}

 src/energy.h

@@ -4,4 +4,8 @@
ts_bool mean_curvature_and_energy(ts_vesicle *vesicle);
inline ts_bool energy_vertex(ts_vertex *vtx);
inline ts_bool bond_energy(ts_bond *bond,ts_poly *poly);

ts_bool sweep_attraction_bond_energy(ts_vesicle *vesicle);
inline ts_bool attraction_bond_energy(ts_bond *bond, ts_double w);

#endif

 src/general.h

@@ -283,6 +283,9 @@
    long int mcsweeps;
    long int quiet;
    long int shc;
    long int number_of_vertices_with_c0;
    ts_double c0;
    ts_double w;
} ts_tape;



 src/initial_distribution.c

@@ -110,6 +110,21 @@
    else {
        vesicle->sphHarmonics=NULL;
    }

    int rndvtx;
    if(tape->number_of_vertices_with_c0>0){
        ts_fprintf(stderr,"Setting values for spontaneous curvature as defined in tape\n");
        for(i=0;i<tape->number_of_vertices_with_c0;i++){
            rndvtx=rand() % vesicle->vlist->n;
            vesicle->vlist->vtx[rndvtx]->c=tape->c0;
        }
        mean_curvature_and_energy(vesicle);
        if(fabs(tape->w)>1e-16){ //if nonzero energy
            ts_fprintf(stderr,"Setting attraction between vertices with spontaneous curvature\n");
            sweep_attraction_bond_energy(vesicle);
        }
    }
    
    return TS_SUCCESS;

}

 src/io.c

@@ -1140,6 +1140,9 @@
        CFG_SIMPLE_INT("cluster_nodes",&tape->brezveze1),
        CFG_SIMPLE_INT("distributed_processes",&tape->brezveze2),
    CFG_SIMPLE_INT("spherical_harmonics_coefficients",&tape->shc),
    CFG_SIMPLE_INT("number_of_vertices_with_c0", &tape->number_of_vertices_with_c0),
    CFG_SIMPLE_FLOAT("c0",&tape->c0),
    CFG_SIMPLE_FLOAT("w",&tape->w),
        CFG_END()
    };
    cfg_t *cfg;    

 src/tape

@@ -82,3 +82,13 @@
#max number of processes in distributed (voluntary) environment
distributed_processes=50
#cuda options???


#NirGov branch only!
#number of vertices with spontaneous curvature (integer)
number_of_vertices_with_c0=200
#spontaneous curvature (float)
c0=2.0
#energy of attraction of vertices with spontaneous curvature
w=1.0


 src/timestep.c

@@ -60,11 +60,6 @@
/* RANDOM SEED SET BY CURRENT TIME */
    epochtime=get_epoch();            
    srand48(epochtime);
/*Nir Gov: randomly add spontaneous curvature for some vertices */
    for(i=0;i<20;i++){
        int b=rand() % vesicle->vlist->n;
        vesicle->vlist->vtx[b]->c=-0.5;
    }
    centermass(vesicle);
    cell_occupation(vesicle);
    vesicle_volume(vesicle); //needed for constant volume at this moment

 src/vertexmove.c

@@ -198,6 +198,7 @@
*/
//   fprintf(stderr, "DE=%f\n",delta_energy);
    //MONTE CARLOOOOOOOO
//    if(vtx->c!=0.0) printf("DE=%f\n",delta_energy);
    if(delta_energy>=0){
#ifdef TS_DOUBLE_DOUBLE
        if(exp(-delta_energy)< drand48())