From 90882f51387b945bc0f660d8b12200b2f48e80fa Mon Sep 17 00:00:00 2001
From: Samo Penic <samo.penic@gmail.com>
Date: Wed, 13 Jul 2016 20:22:12 +0000
Subject: [PATCH] Many changes to the code to allow internal pegs
---
src/main.c | 3
src/poly.c | 123 +++++++++++++++++++++-------------------
src/io.c | 2
src/tape | 2
src/initial_distribution.c | 2
src/frame.c | 5 +
6 files changed, 73 insertions(+), 64 deletions(-)
diff --git a/src/frame.c b/src/frame.c
index d81ba7e..68b8a84 100644
--- a/src/frame.c
+++ b/src/frame.c
@@ -72,20 +72,23 @@
}
//Add all polymers to cells
+if(vesicle->poly_list!=NULL){
for(i=0;i<vesicle->poly_list->n;i++){
for(j=0;j<vesicle->poly_list->poly[i]->vlist->n;j++){
cellidx=vertex_self_avoidance(vesicle, vesicle->poly_list->poly[i]->vlist->vtx[j]);
cell_add_vertex(vesicle->clist->cell[cellidx],vesicle->poly_list->poly[i]->vlist->vtx[j]);
}
}
+}
//Add all filaments to cells
+if(vesicle->filament_list!=NULL){
for(i=0;i<vesicle->filament_list->n;i++){
for(j=0;j<vesicle->filament_list->poly[i]->vlist->n;j++){
cellidx=vertex_self_avoidance(vesicle, vesicle->filament_list->poly[i]->vlist->vtx[j]);
cell_add_vertex(vesicle->clist->cell[cellidx],vesicle->filament_list->poly[i]->vlist->vtx[j]);
}
}
-
+}
return TS_SUCCESS;
}
diff --git a/src/initial_distribution.c b/src/initial_distribution.c
index 45a4124..71a2c4f 100644
--- a/src/initial_distribution.c
+++ b/src/initial_distribution.c
@@ -100,7 +100,7 @@
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;
diff --git a/src/io.c b/src/io.c
index 2c76fd2..a478ca0 100644
--- a/src/io.c
+++ b/src/io.c
@@ -423,7 +423,7 @@
vesicle->tape=parsetape(command_line_args.tape_fullfilename);
// recreating space for cells //
vesicle->clist=init_cell_list(vesicle->tape->ncxmax, vesicle->tape->ncymax, vesicle->tape->nczmax, vesicle->tape->stepsize);
- vesicle->clist->max_occupancy=8;
+ vesicle->clist->max_occupancy=16;
// vesicle->tape=(ts_tape *)malloc(sizeof(ts_tape));
// retval=fread(vesicle->tape, sizeof(ts_tape),1,fh);
retval=fread(iteration,sizeof(ts_uint),1,fh);
diff --git a/src/main.c b/src/main.c
index c2e51af..085e09f 100644
--- a/src/main.c
+++ b/src/main.c
@@ -126,7 +126,8 @@
}
}
//printf("nucleus coords: %.17e %.17e %.17e\n",vesicle->nucleus_center[0], vesicle->nucleus_center[1], vesicle->nucleus_center[2]);
-
+// write_vertex_xml_file(vesicle,0);
+// exit(1);
run_simulation(vesicle, tape->mcsweeps, tape->inititer, tape->iterations, start_iteration);
write_master_xml_file(command_line_args.output_fullfilename);
write_dout_fcompat_file(vesicle,"dout");
diff --git a/src/poly.c b/src/poly.c
index cfaa354..9f66c0f 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;
@@ -47,7 +48,7 @@
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;
}
@@ -59,7 +60,7 @@
ts_uint gvtxi;
ts_double xnorm,ynorm,znorm,normlength;
ts_double dphi,dh;
-
+ cell_occupation(vesicle); //needed for evading the membrane
// Grafting polymers:
if (vlist!=NULL){
if (n_poly > vlist->n){fatal("Number of polymers larger than numbero f vertices on a vesicle.",310);}
@@ -85,7 +86,7 @@
/* Make straight grafted poylmers normal to membrane (polymer brush). Dist. between poly vertices put to 1*/
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++){
@@ -111,10 +112,16 @@
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){
@@ -122,31 +129,37 @@
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]);
+ //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.
+ // printf("%d %d Cannot put the vertex here. Finding another position\n",i,j);
+ //randomly change the direction.
+ 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 bipytamid 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;
+
+
+ } 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;
+ }
+ // if(j>0) break;
+ // if((xnorm*sintheta*cos(phi)+ynorm*sintheta*sin(phi)+znorm*costheta)<0.0 && j==0) break;
+ }
+ // while(j==0);
+ //we must move first vertex into the vesicle if the normal is in or out of the vesicle if the normal is out
+ 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){
@@ -160,37 +173,29 @@
vesicle->vlist->vtx[gvtxi]->grafted_poly = poly_list->poly[i];
l++;
k=0;
-
-
-
-
- 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;
-
-
-
-
-
-
+ 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;
+ prevPosX=poly_list->poly[i]->grafted_vtx->x;
+ prevPosY=poly_list->poly[i]->grafted_vtx->y;
+ prevPosZ=poly_list->poly[i]->grafted_vtx->z;
+ //prepare starting position for building the polymeres
+ posX=prevPosX+xnorm*(vesicle->clist->dmin_interspecies);
+ posY=prevPosY+ynorm*(vesicle->clist->dmin_interspecies);
+ posZ=prevPosZ+znorm*(vesicle->clist->dmin_interspecies);
break;
}
}
@@ -244,7 +249,7 @@
}
}
*/
-
+
return poly_list;
}
diff --git a/src/tape b/src/tape
index 93e42d7..4350284 100644
--- a/src/tape
+++ b/src/tape
@@ -25,7 +25,7 @@
####### Polymer (brush) definitions ###########
# npoly is a number of polymers attached to npoly distinct vertices on vesicle
-npoly=400
+npoly=30
# nmono is a number of monomers in each polymer
nmono=10
# Spring constant between monomers of the polymer
--
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