From e984829db39b2778e4f66c34524329ad09749c45 Mon Sep 17 00:00:00 2001
From: Samo Penic <samo.penic@gmail.com>
Date: Mon, 11 Jul 2016 19:29:21 +0000
Subject: [PATCH] Added possibility of internal pegs. It can break the system however
---
src/poly.c | 4 ++++
src/io.c | 1 +
src/tape | 10 ++++++----
src/general.h | 1 +
4 files changed, 12 insertions(+), 4 deletions(-)
diff --git a/src/general.h b/src/general.h
index a6f5114..4eab674 100644
--- a/src/general.h
+++ b/src/general.h
@@ -257,6 +257,7 @@
long int nczmax;
long int npoly;
long int nmono;
+ long int internal_poly;
long int nfil;
long int nfono;
long int R_nucleus;
diff --git a/src/io.c b/src/io.c
index 147b655..f488ebe 100644
--- a/src/io.c
+++ b/src/io.c
@@ -1066,6 +1066,7 @@
CFG_SIMPLE_INT("nmono", &tape->nmono),
CFG_SIMPLE_INT("nfil",&tape->nfil),
CFG_SIMPLE_INT("nfono",&tape->nfono),
+ CFG_SIMPLE_INT("internal_poly",&tape->internal_poly),
CFG_SIMPLE_INT("R_nucleus",&tape->R_nucleus),
CFG_SIMPLE_FLOAT("R_nucleusX",&tape->R_nucleusX),
CFG_SIMPLE_FLOAT("R_nucleusY",&tape->R_nucleusY),
diff --git a/src/poly.c b/src/poly.c
index 3c93d0c..252b1c6 100644
--- a/src/poly.c
+++ b/src/poly.c
@@ -83,6 +83,7 @@
if (vlist!=NULL){
/* Make straight grafted poylmers normal to membrane (polymer brush). Dist. between poly vertices put to 1*/
+ ts_int intpoly=vesicle->tape->internal_poly;
for (i=0;i<poly_list->n;i++){
xnorm=0.0;
@@ -94,6 +95,9 @@
znorm-=poly_list->poly[i]->grafted_vtx->tristar[j]->znorm;
}
normlength=sqrt(xnorm*xnorm+ynorm*ynorm+znorm*znorm);
+ if(intpoly && i%2){
+ normlength=-normlength;
+ }
xnorm=xnorm/normlength;
ynorm=ynorm/normlength;
znorm=znorm/normlength;
diff --git a/src/tape b/src/tape
index 50b4272..69fd056 100644
--- a/src/tape
+++ b/src/tape
@@ -1,6 +1,6 @@
####### Vesicle definitions ###########
# nshell is a number of divisions of dipyramid
-nshell=5
+nshell=17
# dmax is the max. bond length (in units l_min)
dmax=1.7
# dmin_interspecies in the min. dist. between different vertex species (in units l_min)
@@ -14,7 +14,7 @@
# (pswitch=1: calc. p*dV energy contribution)
pswitch = 0
# pressure difference: p_inside - p_outside (in units kT/l_min^3):
-pressure=-10.0
+pressure=10.0
#Constant volume constraint (0 disable constant volume, 1 enable wiht additional vertex move, 2 enable with epsvol)
constvolswitch=0
@@ -25,11 +25,13 @@
####### Polymer (brush) definitions ###########
# npoly is a number of polymers attached to npoly distinct vertices on vesicle
-npoly=0
+npoly=800
# nmono is a number of monomers in each polymer
-nmono=2
+nmono=6
# Spring constant between monomers of the polymer
k_spring=800
+#set to 1 if half of the polymeres are inside the vesicle
+internal_poly=1
####### Filament (inside the vesicle) definitions ###########
# nfil is a number of filaments inside the vesicle
--
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