From 6487a03362d35589c286d0660eba123a7ab00535 Mon Sep 17 00:00:00 2001
From: Samo Penic <samo.penic@gmail.com>
Date: Mon, 10 May 2021 11:14:04 +0000
Subject: [PATCH] Raj and Yoav session in making multiple protein species
---
src/initial_distribution.c | 166 ++++++++++++++++++++++++++++++++++++++++++++++---------
1 files changed, 138 insertions(+), 28 deletions(-)
diff --git a/src/initial_distribution.c b/src/initial_distribution.c
index 382750b..756fdae 100644
--- a/src/initial_distribution.c
+++ b/src/initial_distribution.c
@@ -1,3 +1,4 @@
+/* vim: set ts=4 sts=4 sw=4 noet : */
#include<stdlib.h>
#include<math.h>
#include<stdio.h>
@@ -9,34 +10,143 @@
#include "triangle.h"
#include "initial_distribution.h"
#include "energy.h"
+#include "poly.h"
+#include "io.h"
+#include "sh.h"
+#include "shcomplex.h"
ts_vesicle *initial_distribution_dipyramid(ts_uint nshell, ts_uint ncmax1, ts_uint ncmax2, ts_uint ncmax3, ts_double stepsize){
- ts_fprintf(stderr,"Starting initial_distribution on vesicle with %u shells!...\n",nshell);
+ ts_fprintf(stdout,"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);
- retval = init_vertex_neighbours(vesicle->vlist);
- vesicle->vlist = init_sort_neighbours(vesicle->blist,vesicle->vlist);
+ ts_uint no_vertices=5*nshell*nshell+2;
+ ts_vesicle *vesicle=init_vesicle(no_vertices,ncmax1,ncmax2,ncmax3,stepsize);
+ vesicle->nshell=nshell;
+ //retval = vtx_set_global_values(vesicle);
+ retval = pentagonal_dipyramid_vertex_distribution(vesicle->vlist);
+ retval = init_vertex_neighbours(vesicle->vlist);
+ vesicle->vlist = init_sort_neighbours(vesicle->blist,vesicle->vlist);
// retval = init_vesicle_bonds(vesicle); // bonds are created in sort_neigh
- retval = init_triangles(vesicle);
- retval = init_triangle_neighbours(vesicle);
- retval = init_common_vertex_triangle_neighbours(vesicle);
- retval = init_normal_vectors(vesicle->tlist);
- retval = mean_curvature_and_energy(vesicle);
- ts_fprintf(stderr,"initial_distribution finished!\n");
+ retval = init_triangles(vesicle);
+ retval = init_triangle_neighbours(vesicle);
+ retval = init_common_vertex_triangle_neighbours(vesicle);
+ retval = init_normal_vectors(vesicle->tlist);
+ retval = mean_curvature_and_energy(vesicle);
+ ts_fprintf(stdout,"initial_distribution finished!\n");
if(retval);
return vesicle;
}
+
+
+
+ts_vesicle *create_vesicle_from_tape(ts_tape *tape){
+ ts_vesicle *vesicle;
+
+ 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;
+}
+
+ts_bool set_vesicle_values_from_tape(ts_vesicle *vesicle){
+ // Nucleus:
+ 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->spring_constant=tape->kspring;
+ poly_assign_spring_const(vesicle);
+
+ //Initialize filaments (polymers inside the vesicle):
+ vesicle->filament_list=init_poly_list(tape->nfil,tape->nfono, NULL, vesicle);
+ poly_assign_filament_xi(vesicle,tape);
+
+ ts_uint i,j;
+ for(i=0;i<vesicle->filament_list->n;i++){
+ for(j=0;j<vesicle->filament_list->poly[i]->blist->n;j++){
+ bond_vector(vesicle->filament_list->poly[i]->blist->bond[j]);
+ vesicle->filament_list->poly[i]->blist->bond[j]->bond_length = sqrt(vtx_distance_sq(vesicle->filament_list->poly[i]->blist->bond[j]->vtx1,vesicle->filament_list->poly[i]->blist->bond[j]->vtx2));
+ }
+ }
+
+ for(i=0;i<vesicle->filament_list->n;i++){
+ for(j=0;j<vesicle->filament_list->poly[i]->vlist->n;j++){
+ vtx = vesicle->filament_list->poly[i]->vlist->vtx[j];
+ if(vtx->bond_no == 2){
+ vtx->energy = -(vtx->bond[0]->x*vtx->bond[1]->x + vtx->bond[0]->y*vtx->bond[1]->y + vtx->bond[0]->z*vtx->bond[1]->z)/vtx->bond[0]->bond_length/vtx->bond[1]->bond_length;
+ }
+ }
+ }
+
+ for(i=0;i<vesicle->filament_list->n;i++){
+ vertex_list_assign_id(vesicle->filament_list->poly[i]->vlist,TS_ID_FILAMENT);
+ }
+
+// vesicle->spring_constant=tape->kspring;
+// poly_assign_spring_const(vesicle);
+
+
+ vesicle->nshell=tape->nshell;
+ 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);
+ vesicle->stepsize=tape->stepsize;
+ vesicle->clist->ncmax[0]=tape->ncxmax;
+ vesicle->clist->ncmax[1]=tape->ncymax;
+ vesicle->clist->ncmax[2]=tape->nczmax;
+//THIS IS NOW HARDCODED IN CELL.C
+// vesicle->clist->max_occupancy=16; /* hard coded max occupancy? */
+
+ vesicle->pressure= tape->pressure;
+ vesicle->pswitch=tape->pswitch;
+ if(tape->shc>0){
+ vesicle->sphHarmonics=complex_sph_init(vesicle->vlist,tape->shc);
+ }
+ 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;
+ vesicle->vlist->vtx[rndvtx]->direct_interaction_force=tape->F;
+ }
+ 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){
@@ -47,15 +157,15 @@
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 */
@@ -147,7 +257,7 @@
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]);
}
@@ -180,7 +290,7 @@
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;
@@ -246,7 +356,7 @@
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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