From 3006183b769f2e126b1a96e6bf697c2b7f657df7 Mon Sep 17 00:00:00 2001
From: Samo Penic <samo.penic@gmail.com>
Date: Sun, 26 Apr 2020 17:35:26 +0000
Subject: [PATCH] Code for incremental adding of inclusions done
---
src/poly.c | 222 ++++++++++++++++++++++++++++---------------------------
1 files changed, 113 insertions(+), 109 deletions(-)
diff --git a/src/poly.c b/src/poly.c
index cfaa354..cf416b5 100644
--- a/src/poly.c
+++ b/src/poly.c
@@ -7,6 +7,7 @@
#include<math.h>
#include"energy.h"
#include"cell.h"
+#include"frame.h"
ts_bool poly_assign_filament_xi(ts_vesicle *vesicle, ts_tape *tape){
ts_uint i;
@@ -47,49 +48,20 @@
poly->blist->bond[i]->bond_length=sqrt(vtx_distance_sq(poly->blist->bond[i]->vtx1,poly->blist->bond[i]->vtx2));
bond_energy(poly->blist->bond[i],poly);
}
-
+ vertex_list_assign_id(poly->vlist,TS_ID_FILAMENT);
return poly;
}
-ts_poly_list *init_poly_list(ts_uint n_poly, ts_uint n_mono, ts_vertex_list *vlist, ts_vesicle *vesicle){
- ts_poly_list *poly_list=(ts_poly_list *)calloc(1,sizeof(ts_poly_list));
- poly_list->poly = (ts_poly **)calloc(n_poly,sizeof(ts_poly *));
- ts_uint i=0,j=0,k; //idx;
- ts_uint gvtxi;
- ts_double xnorm,ynorm,znorm,normlength;
- ts_double dphi,dh;
- // Grafting polymers:
- if (vlist!=NULL){
- if (n_poly > vlist->n){fatal("Number of polymers larger than numbero f vertices on a vesicle.",310);}
-
- while(i<n_poly){
- gvtxi = rand() % vlist->n;
- if (vlist->vtx[gvtxi]->grafted_poly == NULL){
- poly_list->poly[i] = init_poly(n_mono, vlist->vtx[gvtxi]);
- i++;
- }
- }
- }
- else
- {
- for(i=0;i<n_poly;i++){
- poly_list->poly[i] = init_poly(n_mono, NULL);
- }
- }
-
- poly_list->n = n_poly;
-
- if (vlist!=NULL){
+ts_bool poly_initial_distribution(ts_poly_list *poly_list, ts_int i, ts_vesicle *vesicle){
/* Make straight grafted poylmers normal to membrane (polymer brush). Dist. between poly vertices put to 1*/
+ ts_double xnorm,ynorm,znorm,normlength;
ts_int intpoly=vesicle->tape->internal_poly;
ts_int cellidx;
- ts_double posX,posY,posZ,prevPosX,prevPosY,prevPosZ, phi,theta;
+ ts_double posX,posY,posZ,prevPosX,prevPosY,prevPosZ, phi,costheta,sintheta;
ts_bool retval;
- ts_int l;
- for (i=0;i<poly_list->n;i++){
-
+ ts_int j,k,l,m;
xnorm=0.0;
ynorm=0.0;
znorm=0.0;
@@ -105,104 +77,123 @@
xnorm=xnorm/normlength;
ynorm=ynorm/normlength;
znorm=znorm/normlength;
-
//prepare starting position for building the polymeres
prevPosX=poly_list->poly[i]->grafted_vtx->x;
prevPosY=poly_list->poly[i]->grafted_vtx->y;
prevPosZ=poly_list->poly[i]->grafted_vtx->z;
for (j=0;j<poly_list->poly[i]->vlist->n;j++){
+ //if(j==0){
+ posX=prevPosX+xnorm*(vesicle->clist->dmin_interspecies);
+ posY=prevPosY+ynorm*(vesicle->clist->dmin_interspecies);
+ posZ=prevPosZ+znorm*(vesicle->clist->dmin_interspecies);
+ //}else{
+ // posX=prevPosX+xnorm;
+ // posY=prevPosY+ynorm;
+ // posZ=prevPosZ+znorm;
+ //}
//trying to go towards normal
- posX=prevPosX+(ts_double)xnorm;
- posY=prevPosY+(ts_double)ynorm;
- posZ=prevPosZ+(ts_double)znorm;
k=0;
- l=0;
while(1){
poly_list->poly[i]->vlist->vtx[j]->x = posX;
poly_list->poly[i]->vlist->vtx[j]->y = posY;
poly_list->poly[i]->vlist->vtx[j]->z = posZ;
cellidx=vertex_self_avoidance(vesicle, poly_list->poly[i]->vlist->vtx[j]);
- //distance from neighbors
- //retval=TS_SUCCESS;
- /*for(k=0;k<poly_list->poly[i]->vlist->vtx[j]->neigh_no;k++){
- dist=vtx_distance_sq(poly_list->poly[i]->vlist->vtx[j],poly_list->poly[i]->vlist->vtx[j]->neigh[k]);
- if(dist<1.0 || dist>vesicle->dmax){
- retval=TS_FAIL;
- printf("dist_fail! %e\n", dist);
- }
- }*/
- //if(retval!=TS_FAIL){
- //check occupation number
- retval=cell_occupation_number_and_internal_proximity(vesicle->clist,cellidx,poly_list->poly[i]->vlist->vtx[j]);
- //}
+ retval=cell_occupation_number_and_internal_proximity(vesicle->clist,cellidx,poly_list->poly[i]->vlist->vtx[j]);
if(retval==TS_SUCCESS){
retval=cell_add_vertex(vesicle->clist->cell[cellidx],poly_list->poly[i]->vlist->vtx[j]);
break;
}
else{
- // printf("%d %d Cannot put the vesicle here. Finding another position\n",i,j);
- theta=drand48()*M_PI-M_PI/2;
- phi=drand48()*2*M_PI;
- posX=prevPosX+sin(phi)*cos(theta);
- posY=prevPosY+sin(phi)*sin(theta);
- posZ=prevPosZ+cos(theta);
- //randomly change the normal.
- }
- k++;
- if(k>1000){
- //lets choose another grafting vertex;
- while(1){
- gvtxi = rand() % vesicle->vlist->n;
- if (vesicle->vlist->vtx[gvtxi]->grafted_poly == NULL){
- ts_fprintf(stdout,"Found new potential grafting vertex %d for poly %d\n",gvtxi,i);
- poly_list->poly[i]->grafted_vtx->grafted_poly=NULL;
- poly_list->poly[i]->grafted_vtx = vesicle->vlist->vtx[gvtxi];
- vesicle->vlist->vtx[gvtxi]->grafted_poly = poly_list->poly[i];
- l++;
- k=0;
+ // printf("%d %d Cannot put the vertex here. Finding another position\n",i,j);
+ //randomly change the direction.
+ m=0;
+ //we must move first vertex into the vesicle if the normal is in or out of the vesicle if the normal is out
+ do{
+ costheta=2.0*drand48()-1.0;
+ sintheta=sqrt(1-pow(costheta,2));
+ phi=drand48()*2.0*M_PI;
+ if(j==0){
+ //for special cases, when we are on the edge of bipyramid the distance od dmin_interspecies is not enough
+ posX=prevPosX+vesicle->dmax*sintheta*cos(phi);
+ posY=prevPosY+vesicle->dmax*sintheta*sin(phi);
+ posZ=prevPosZ+vesicle->dmax*costheta;
-
-
-
- xnorm=0.0;
- ynorm=0.0;
- znorm=0.0;
- int o;
- for (o=0;o<poly_list->poly[i]->grafted_vtx->tristar_no;o++){
- xnorm-=poly_list->poly[i]->grafted_vtx->tristar[o]->xnorm;
- ynorm-=poly_list->poly[i]->grafted_vtx->tristar[o]->ynorm;
- znorm-=poly_list->poly[i]->grafted_vtx->tristar[o]->znorm;
- }
- normlength=sqrt(xnorm*xnorm+ynorm*ynorm+znorm*znorm);
- if(intpoly && i%2){
- normlength=-normlength;
- }
- xnorm=xnorm/normlength;
- ynorm=ynorm/normlength;
- znorm=znorm/normlength;
-
- //prepare starting position for building the polymeres
- posX=poly_list->poly[i]->grafted_vtx->x+xnorm;
- posY=poly_list->poly[i]->grafted_vtx->y+ynorm;
- posZ=poly_list->poly[i]->grafted_vtx->z+znorm;
-
-
-
-
-
-
+ } else {
+ posX=prevPosX+vesicle->clist->dmin_interspecies*sintheta*cos(phi);
+ posY=prevPosY+vesicle->clist->dmin_interspecies*sintheta*sin(phi);
+ posZ=prevPosZ+vesicle->clist->dmin_interspecies*costheta;
+ }
+ m++;
+ if(m>1000) {
+ k=9999; //break also ot of the outer loop
break;
}
}
- if(l>1000)
- fatal("Cannot make internal polymeres. No space inside the vesicle?",1001);
+ while((xnorm*(poly_list->poly[i]->grafted_vtx->x-posX)+ynorm*(poly_list->poly[i]->grafted_vtx->y-posY)+znorm*(poly_list->poly[i]->grafted_vtx->z-posZ))>0.0 && j==0);
+ }
+ k++;
+ if(k>1000){
+ //undo changes to the cell
+ for(l=0;l<j;l++){
+ cellidx=vertex_self_avoidance(vesicle, poly_list->poly[i]->vlist->vtx[l]);
+ cell_remove_vertex(vesicle->clist->cell[cellidx],poly_list->poly[i]->vlist->vtx[l]);
+ }
+ return TS_FAIL;
}
}
prevPosX=posX;
prevPosY=posY;
prevPosZ=posZ;
}
+ printf("did it\n");
+ return TS_SUCCESS;
+
+}
+
+
+ts_poly_list *init_poly_list(ts_uint n_poly, ts_uint n_mono, ts_vertex_list *vlist, ts_vesicle *vesicle){
+ ts_poly_list *poly_list=(ts_poly_list *)calloc(1,sizeof(ts_poly_list));
+ poly_list->poly = (ts_poly **)calloc(n_poly,sizeof(ts_poly *));
+ ts_uint i=0,j=0; //idx;
+ ts_uint gvtxi;
+ ts_bool retval;
+ ts_double dphi,dh;
+
+ cell_occupation(vesicle); //needed for evading the membrane
+ // Grafting polymers:
+ int tries=0;
+ if (vlist!=NULL){
+ if (n_poly > vlist->n){fatal("Number of polymers larger than numbero f vertices on a vesicle.",310);}
+ while(i<n_poly){
+ gvtxi = rand() % vlist->n;
+ if (vlist->vtx[gvtxi]->grafted_poly == NULL){
+ poly_list->poly[i] = init_poly(n_mono, vlist->vtx[gvtxi]);
+ retval=poly_initial_distribution(poly_list, i, vesicle);
+ if(retval==TS_FAIL){
+ ts_fprintf(stdout,"Found new potential grafting vertex %d for poly %d\n",gvtxi,i);
+ poly_free(poly_list->poly[i]);
+ tries++;
+ }
+ else {
+ tries=0;
+ i++;
+ }
+ if(tries>5000){
+ fatal("Cannot find space for inner polymeres",1001);
+ }
+ }
}
+ }
+ else
+ {
+ for(i=0;i<n_poly;i++){
+ poly_list->poly[i] = init_poly(n_mono, NULL);
+ }
+ }
+
+ poly_list->n = n_poly;
+
+ if (vlist!=NULL){
}
else
{
@@ -244,16 +235,16 @@
}
}
*/
-
+
return poly_list;
}
ts_bool poly_free(ts_poly *poly){
- if (poly->grafted_vtx!=NULL){
- poly->grafted_vtx->grafted_poly=NULL;
- }
+// if (poly->grafted_vtx!=NULL){
+// poly->grafted_vtx->grafted_poly=NULL;
+// }
vtx_list_free(poly->vlist);
bond_list_free(poly->blist);
free(poly);
@@ -263,8 +254,9 @@
ts_bool poly_list_free(ts_poly_list *poly_list){
ts_uint i;
-
+ //fprintf(stderr,"no. of polys=%d\n", poly_list->n);
for(i=0;i<poly_list->n;i++){
+ // fprintf(stderr,"%d poly address in mem=%ld\n",i+1,(long)&(poly_list->poly[i]));
poly_free(poly_list->poly[i]);
}
free(poly_list->poly);
@@ -311,3 +303,15 @@
return TS_SUCCESS;
}
+
+
+ts_poly_list *init_empty_poly_list(ts_uint n_poly, ts_uint n_mono){
+ ts_poly_list *poly_list=(ts_poly_list *)calloc(1,sizeof(ts_poly_list));
+ poly_list->poly=(ts_poly **)calloc(n_poly,sizeof(ts_poly *));
+ ts_uint i;
+ for (i=0; i<n_poly;i++){
+ poly_list->poly[i]=init_poly(n_mono, NULL);
+ }
+ poly_list->n = n_poly;
+ return poly_list;
+}
--
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