Many fixes, before changing bondflip. triangles are still calculated in ts_...

mihaf

2014-03-07 e86357faa6caf28f5032c624fa0cba24e5dc4686

Many fixes, before changing bondflip. triangles are still calculated in ts_bond_flip

 src/bondflip.c

@@ -79,10 +79,7 @@
  oldenergy+=kp->xk* kp->energy;
  oldenergy+=km->xk* km->energy;
  oldenergy+=it->xk* it->energy;
//  for(i=0;i<k->neigh_no;i++) oldenergy+=k->neigh[i]->xk*k->neigh[i]->energy;
//  for(i=0;i<kp->neigh_no;i++) oldenergy+=kp->neigh[i]->xk*kp->neigh[i]->energy;
//  for(i=0;i<km->neigh_no;i++) oldenergy+=km->neigh[i]->xk*km->neigh[i]->energy;
//  for(i=0;i<it->neigh_no;i++) oldenergy+=it->neigh[i]->xk*it->neigh[i]->energy;
    //Neigbours don't change its energy.
/*
fprintf(stderr,"*** Naslov k=%ld\n",(long)k);
fprintf(stderr,"*** Naslov it=%ld\n",(long)it);
@@ -107,18 +104,34 @@

/* Calculating the new energy */
  delta_energy=0;
  for(i=0;i<k->neigh_no;i++) energy_vertex(k->neigh[i]);
  for(i=0;i<kp->neigh_no;i++) energy_vertex(kp->neigh[i]);
  for(i=0;i<km->neigh_no;i++) energy_vertex(km->neigh[i]);
  for(i=0;i<it->neigh_no;i++) energy_vertex(it->neigh[i]);
/*    ts_double dbg_energy=0.0;
  for(i=0;i<k->neigh_no;i++) {
    dbg_energy=k->neigh[i]->energy;
    energy_vertex(k->neigh[i]);
    if(abs(dbg_energy-k->neigh[i]->energy)>1e-100) fatal("Energy changes!",1);
  }
  for(i=0;i<kp->neigh_no;i++) {
    dbg_energy=kp->neigh[i]->energy;
    energy_vertex(kp->neigh[i]);
    if(abs(dbg_energy-kp->neigh[i]->energy)>1e-100) fatal("Energy changes!",1);
  }
  for(i=0;i<km->neigh_no;i++){
    dbg_energy=km->neigh[i]->energy;
     energy_vertex(km->neigh[i]);
    if(abs(dbg_energy-km->neigh[i]->energy)>1e-100) fatal("Energy changes!",1);
  }

  for(i=0;i<it->neigh_no;i++){
    dbg_energy=it->neigh[i]->energy;
     energy_vertex(it->neigh[i]);
    if(abs(dbg_energy-it->neigh[i]->energy)>1e-100) fatal("Energy changes!",1);
  }
*/
  delta_energy+=k->xk* k->energy;
  delta_energy+=kp->xk* kp->energy;
  delta_energy+=km->xk* km->energy;
  delta_energy+=it->xk* it->energy;
//  for(i=0;i<k->neigh_no;i++) delta_energy+=k->neigh[i]->xk*k->neigh[i]->energy;
//  for(i=0;i<kp->neigh_no;i++) delta_energy+=kp->neigh[i]->xk*kp->neigh[i]->energy;
//  for(i=0;i<km->neigh_no;i++) delta_energy+=km->neigh[i]->xk*km->neigh[i]->energy;
//  for(i=0;i<it->neigh_no;i++) delta_energy+=it->neigh[i]->xk*it->neigh[i]->energy;
    //Neigbours don't change its energy.
  delta_energy-=oldenergy;
 // fprintf(stderr,"I WAS HERE! Got energy!\n");
/* MONTE CARLO */

 src/general.h

@@ -260,6 +260,7 @@

    ts_poly_list *poly_list;
    ts_double spring_constant;
    ts_double pressure;
} ts_vesicle;



 src/initial_distribution.c

@@ -19,9 +19,6 @@
    
    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

@@ -341,7 +341,7 @@
    long int brezveze0=1;
    long int brezveze1=1;
    long int brezveze2=1;
    ts_double xk0=25.0, dmax=1.67,stepsize=0.15,kspring=800.0;
    ts_double xk0=25.0, dmax=1.67,stepsize=0.15,kspring=800.0,pressure=0.0;
    long int iter=1000, init=1000, mcsw=1000;


@@ -351,7 +351,8 @@
        CFG_SIMPLE_INT("nmono", &nmono),
        CFG_SIMPLE_FLOAT("dmax", &dmax),
        CFG_SIMPLE_FLOAT("xk0",&xk0),
        CFG_SIMPLE_FLOAT("k_spring",&kspring),
    CFG_SIMPLE_FLOAT("pressure",&pressure),
    CFG_SIMPLE_FLOAT("k_spring",&kspring),
        CFG_SIMPLE_FLOAT("stepsize",&stepsize),
        CFG_SIMPLE_INT("nxmax", &ncxmax),
        CFG_SIMPLE_INT("nymax", &ncymax),
@@ -389,11 +390,15 @@
    vesicle->nshell=nshell;
    vesicle->dmax=dmax*dmax;
    vesicle->bending_rigidity=xk0;
    vtx_set_global_values(vesicle); //copies xk0 to every vertex


    vesicle->stepsize=stepsize;
    vesicle->clist->ncmax[0]=ncxmax;
    vesicle->clist->ncmax[1]=ncymax;
    vesicle->clist->ncmax[2]=nczmax;
    vesicle->clist->max_occupancy=8;
    vesicle->pressure=pressure/vesicle->bending_rigidity;    //all energy contributions need to be divided by bending_rigidity!

    cfg_free(cfg);
    free(buf);

 src/tape

@@ -1,12 +1,18 @@
####### Vesicle definitions ###########
# nshell is a number of divisions of dipyramid
nshell=17
# dmax is the max. bond length 
# dmax is the max. bond length (in units l_min)
dmax=1.7
# bending rigidity of the membrane 
# bending rigidity of the membrane (in units kT)
xk0=25.0
# max step size 
# max step size (in units l_min)
stepsize=0.15

# Pressure calculations
# (pswitch=1: calc. p*dV energy contribution)
pswitch = 1
# pressure difference: p_inside - p_outside (in units l_min^3/kT):
pressure=0.0

####### Polymer definitions ###########
# npoly is a number of polymers attached to npoly distinct vertices on vesicle
@@ -28,7 +34,7 @@
#how many initial mcsweeps*inititer MC sweeps before recording to disk?
inititer=1
#how many records do you want on the disk iteration are there in a run?
iterations=10000
iterations=2000


#shut up if we are using cluster!!!