From d5d78a49c6b51fb1f6f0661d063034eaf65e02f7 Mon Sep 17 00:00:00 2001
From: Samo Penic <samo.penic@gmail.com>
Date: Wed, 25 Sep 2019 09:20:36 +0000
Subject: [PATCH] Constant volume and constant area fix. Removed spherical harmonics calculations in simulations. No ulm2.cvs and state.dat files are produced anymore
---
src/initial_distribution.c | 55 +++++++++++++++++++++++++++++++++++++++++++------------
1 files changed, 43 insertions(+), 12 deletions(-)
diff --git a/src/initial_distribution.c b/src/initial_distribution.c
index 7dfd23d..87cfb68 100644
--- a/src/initial_distribution.c
+++ b/src/initial_distribution.c
@@ -43,7 +43,10 @@
vesicle=initial_distribution_dipyramid(tape->nshell,tape->ncxmax,tape->ncymax,tape->nczmax,tape->stepsize);
vesicle->tape=tape;
+ vesicle->clist->dmin_interspecies = tape->dmin_interspecies*tape->dmin_interspecies;
+ vesicle->poly_list=init_poly_list(tape->npoly,tape->nmono, vesicle->vlist, vesicle);
set_vesicle_values_from_tape(vesicle);
+ initial_population_with_c0(vesicle,tape);
return vesicle;
}
@@ -52,11 +55,13 @@
ts_vertex *vtx;
ts_tape *tape=vesicle->tape;
vesicle->R_nucleus=tape->R_nucleus*tape->R_nucleus;
-
+ vesicle->R_nucleusX=tape->R_nucleusX*tape->R_nucleusX;
+ vesicle->R_nucleusY=tape->R_nucleusY*tape->R_nucleusY;
+ vesicle->R_nucleusZ=tape->R_nucleusZ*tape->R_nucleusZ;
vesicle->clist->dmin_interspecies = tape->dmin_interspecies*tape->dmin_interspecies;
//Initialize grafted polymers (brush):
- vesicle->poly_list=init_poly_list(tape->npoly,tape->nmono, vesicle->vlist, vesicle);
+ //vesicle->poly_list=init_poly_list(tape->npoly,tape->nmono, vesicle->vlist, vesicle);
vesicle->spring_constant=tape->kspring;
poly_assign_spring_const(vesicle);
@@ -93,12 +98,12 @@
vesicle->dmax=tape->dmax*tape->dmax; /* dmax^2 in the vesicle dmax variable */
vesicle->bending_rigidity=tape->xk0;
vtx_set_global_values(vesicle); /* make xk0 default value for every vertex */
- ts_fprintf(stdout, "Tape setting: xk0=%e\n",tape->xk0);
+// ts_fprintf(stdout, "Tape setting: xk0=%e\n",tape->xk0);
vesicle->stepsize=tape->stepsize;
vesicle->clist->ncmax[0]=tape->ncxmax;
vesicle->clist->ncmax[1]=tape->ncymax;
vesicle->clist->ncmax[2]=tape->nczmax;
- vesicle->clist->max_occupancy=8; /* hard coded max occupancy? */
+ vesicle->clist->max_occupancy=16; /* hard coded max occupancy? */
vesicle->pressure= tape->pressure;
vesicle->pswitch=tape->pswitch;
@@ -108,12 +113,38 @@
else {
vesicle->sphHarmonics=NULL;
}
+
+ vesicle->tlist->a0=sqrt(3)/4*pow((vesicle->tape->dmax+1.0)/2.0,2);
return TS_SUCCESS;
}
-
+ts_bool initial_population_with_c0(ts_vesicle *vesicle, ts_tape *tape){
+ int rndvtx,i,j;
+ if(tape->number_of_vertices_with_c0>0){
+// ts_fprintf(stderr,"Setting values for spontaneous curvature as defined in tape\n");
+ j=0;
+ for(i=0;i<tape->number_of_vertices_with_c0;i++){
+ rndvtx=rand() % vesicle->vlist->n;
+ if(fabs(vesicle->vlist->vtx[rndvtx]->c-tape->c0)<1e-15){
+ j++;
+ i--;
+ if(j>10*vesicle->vlist->n){
+ fatal("cannot populate vesicle with vertices with spontaneous curvature. Too many spontaneous curvature vertices?",100);
+ }
+ continue;
+ }
+ 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;
+}
ts_bool pentagonal_dipyramid_vertex_distribution(ts_vertex_list *vlist){
@@ -124,15 +155,15 @@
const ts_double c2= cos(4.0*M_PI/5.0);
/* Calculates projection lenght of an edge bond to pentagram plane */
- const ts_double xl0=A0/(2.0*sin(M_PI/5.0));
+ const ts_double xl0=DEF_A0/(2.0*sin(M_PI/5.0));
#ifdef TS_DOUBLE_DOUBLE
- const ts_double z0=sqrt(pow(A0,2)-pow(xl0,2));
+ const ts_double z0=sqrt(pow(DEF_A0,2)-pow(xl0,2));
#endif
#ifdef TS_DOUBLE_FLOAT
- const ts_double z0=sqrtf(powf(A0,2)-powf(xl0,2));
+ const ts_double z0=sqrtf(powf(DEF_A0,2)-powf(xl0,2));
#endif
#ifdef TS_DOUBLE_LONGDOUBLE
- const ts_double z0=sqrtl(powl(A0,2)-powl(xl0,2));
+ const ts_double z0=sqrtl(powl(DEF_A0,2)-powl(xl0,2));
#endif
// const z0=sqrt(A0*A0 -xl0*xl0); /* I could use pow function but if pow is used make a check on the float type. If float then powf, if long double use powl */
@@ -224,7 +255,7 @@
for(i=1;i<=vlist->n;i++){
for(j=1;j<=vlist->n;j++){
dist2=vtx_distance_sq(vtx[i],vtx[j]);
- if( (dist2>eps) && (dist2<(A0*A0+eps))){
+ if( (dist2>eps) && (dist2<(DEF_A0*DEF_A0+eps))){
//if it is close enough, but not too much close (solves problem of comparing when i==j)
vtx_add_neighbour(vtx[i],vtx[j]);
}
@@ -257,7 +288,7 @@
dist2=vtx_distance_sq(vtx[i]->neigh[j-1],vtx[i]->neigh[jj-1]);
direct=vtx_direct(vtx[i],vtx[i]->neigh[j-1],vtx[i]->neigh[jj-1]);
// TODO: check if fabs can be used with all floating point types!!
- if( (fabs(dist2-A0*A0)<=eps) && (direct>0.0) && (j!=jjj) ){
+ if( (fabs(dist2-DEF_A0*DEF_A0)<=eps) && (direct>0.0) && (j!=jjj) ){
vtx_add_cneighbour(blist,tvtx[k],tvtx[vtx[i]->neigh[j-1]->idx+1]);
jjj=jj;
jj=j;
@@ -323,7 +354,7 @@
dist=vtx_distance_sq(vtx[i]->neigh[j-1],vtx[i]->neigh[jj-1]);
direct=vtx_direct(vtx[i],vtx[i]->neigh[j-1],vtx[i]->neigh[jj-1]);
// TODO: same as above
- if(fabs(dist-A0*A0)<=eps && direct < 0.0 && vtx[i]->neigh[j-1]->idx+1 > i && vtx[i]->neigh[jj-1]->idx+1 >i){
+ if(fabs(dist-DEF_A0*DEF_A0)<=eps && direct < 0.0 && vtx[i]->neigh[j-1]->idx+1 > i && vtx[i]->neigh[jj-1]->idx+1 >i){
triangle_add(tlist,vtx[i],vtx[i]->neigh[j-1],vtx[i]->neigh[jj-1]);
}
}
--
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