Debugging, but not finished yet! There are still problems in vertex move an...

Samo Penic

2012-02-23 314f2dd60176b0f378baa66f5a5514fb15dddabc

Debugging, but not finished yet! There are still problems in vertex move and extreme points that remain sharp edged.

 src/initial_distribution.c

@@ -14,8 +14,14 @@
    ts_fprintf(stderr,"Starting initial_distribution on vesicle with %u shells!...\n",nshell);
    ts_bool retval;
    ts_uint no_vertices=5*nshell*nshell+2;


    
    ts_vesicle *vesicle=init_vesicle(no_vertices,ncmax1,ncmax2,ncmax3,stepsize);

//TODO: debugging only. Please remove ASAP!
    vesicle->bending_rigidity=25.0;

    vesicle->nshell=nshell;
    retval = vtx_set_global_values(vesicle);
    retval = pentagonal_dipyramid_vertex_distribution(vesicle->vlist);

 src/io.c

@@ -296,6 +296,8 @@

ts_bool parsetape(ts_vesicle *vesicle,ts_uint *iterations){
    long int nshell=17,ncxmax=60, ncymax=60, nczmax=60;  // THIS IS DUE TO CONFUSE BUG!
    char buf[255];
    long int brezveze=1;
    ts_double xk0=25.0, dmax=1.67,stepsize=0.15;
    *iterations=1000;
    cfg_opt_t opts[] = {
@@ -308,6 +310,10 @@
        CFG_SIMPLE_INT("nzmax", &nczmax),
        CFG_SIMPLE_INT("iterations",iterations),
        CFG_SIMPLE_BOOL("quiet",&quiet),
        CFG_SIMPLE_STR("multiprocessing",buf),
        CFG_SIMPLE_INT("smp_cores",&brezveze),
        CFG_SIMPLE_INT("cluster_nodes",&brezveze),
        CFG_SIMPLE_INT("distributed_processes",&brezveze),
        CFG_END()
    };
    cfg_t *cfg;    

 src/main.c

@@ -60,13 +60,23 @@

vtx_list_free(vlist1);
printf("Tests complete.\n");
vesicle=initial_distribution_dipyramid(17,60,60,60,0.15);
vesicle=initial_distribution_dipyramid(8,60,60,60,0.15);
//parsetape(vesicle,&i);

//these four must come from parsetype!
vesicle->dmax=1.67;
vesicle->stepsize=0.15;
vesicle->clist->max_occupancy=8;
vesicle->bending_rigidity=25.0;
fprintf(stderr,"xk=%f",vesicle->bending_rigidity);

centermass(vesicle);
cell_occupation(vesicle);
for(i=0;i<100;i++){
for(i=0;i<10000;i++){
single_timestep(vesicle);
write_vertex_xml_file(vesicle,i);
if(i%100==0){
write_vertex_xml_file(vesicle,i/100);
}
}
write_master_xml_file("test.pvd");
write_dout_fcompat_file(vesicle,"dout");

 src/vertexmove.c

@@ -16,16 +16,15 @@
*rn){
    ts_uint i;
    ts_double dist;
    ts_vertex *tvtx=(ts_vertex *)calloc(1,sizeof(ts_vertex));
//    tvtx->data=init_vertex_data();
    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));

    //randomly we move the temporary vertex
    tvtx->x=vtx->x+vesicle->stepsize*(2.0*rn[0]-1.0);
    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
@@ -33,16 +32,17 @@
        dist=vtx_distance_sq(tvtx,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);
        return TS_FAIL;
        }
    }
//fprintf(stderr,"Was here!\n");
    //self avoidance check with distant vertices
     cellidx=vertex_self_avoidance(vesicle, tvtx);
    //check occupation number
     retval=cell_occupation_number_and_internal_proximity(vesicle->clist,cellidx,vtx,tvtx);
    if(retval==TS_FAIL){
    vtx_free(tvtx);
//    fprintf(stderr,"Fail 2\n");
        return TS_FAIL;
    } 
    
@@ -68,7 +68,7 @@
        energy_vertex(vtx->neigh[i]);
        delta_energy+=vtx->neigh[i]->xk*(vtx->neigh[i]->energy-oenergy);
    }
//    fprintf(stderr, "DE=%f\n",delta_energy);
//   fprintf(stderr, "DE=%f\n",delta_energy);
    //MONTE CARLOOOOOOOO
    if(delta_energy>=0){
#ifdef TS_DOUBLE_DOUBLE
@@ -101,7 +101,7 @@
    //END MONTE CARLOOOOOOO

    //TODO: change cell occupation if necessary!

//    fprintf(stderr,"Success!!\n");
    free(ovtx->bond_length);
    free(ovtx->bond_length_dual);
    free(ovtx);