From bbe7df469c40beb309542c01f25c262340978629 Mon Sep 17 00:00:00 2001
From: Samo Penic <samo.penic@fe.uni-lj.si>
Date: Thu, 15 Sep 2016 08:04:34 +0000
Subject: [PATCH] Merge branch 'pegs'
---
src/main.c | 3
src/poly.c | 162 +++++++++++++++++++++++++++++++++++++++++------------
src/io.c | 2
src/tape | 6 +-
src/initial_distribution.c | 2
src/frame.c | 5 +
6 files changed, 135 insertions(+), 45 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 596d4a5..cb6dd05 100644
--- a/src/main.c
+++ b/src/main.c
@@ -127,7 +127,8 @@
}
}
//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 7c7450b..bcf01e5 100644
--- a/src/poly.c
+++ b/src/poly.c
@@ -6,7 +6,8 @@
#include"bond.h"
#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;
@@ -47,45 +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; //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;
- for (i=0;i<poly_list->n;i++){
-
+ ts_int cellidx;
+ ts_double posX,posY,posZ,prevPosX,prevPosY,prevPosZ, phi,costheta,sintheta;
+ ts_bool retval;
+ ts_int j,k,l,m;
xnorm=0.0;
ynorm=0.0;
znorm=0.0;
@@ -101,13 +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++){
- poly_list->poly[i]->vlist->vtx[j]->x = poly_list->poly[i]->grafted_vtx->x + xnorm*(ts_double)(j+1);
- poly_list->poly[i]->vlist->vtx[j]->y = poly_list->poly[i]->grafted_vtx->y + ynorm*(ts_double)(j+1);
- poly_list->poly[i]->vlist->vtx[j]->z = poly_list->poly[i]->grafted_vtx->z + znorm*(ts_double)(j+1);
+ //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
+ k=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]);
+ 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 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;
+
+ } 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
+ printf("was here\n");
+ break;
+ }
+ }
+ 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
{
@@ -149,7 +235,7 @@
}
}
*/
-
+
return poly_list;
}
diff --git a/src/tape b/src/tape
index a7baa73..93e42d7 100644
--- a/src/tape
+++ b/src/tape
@@ -25,9 +25,9 @@
####### Polymer (brush) definitions ###########
# npoly is a number of polymers attached to npoly distinct vertices on vesicle
-npoly=800
+npoly=400
# nmono is a number of monomers in each polymer
-nmono=6
+nmono=10
# Spring constant between monomers of the polymer
k_spring=800
#set to 1 if half of the polymeres are inside the vesicle
@@ -59,7 +59,7 @@
mcsweeps=200
#how many initial mcsweeps*inititer MC sweeps before recording to disk?
#2
-inititer=10
+inititer=1
#how many records do you want on the disk iteration are there in a run?
#10000
iterations=100
--
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