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/tape |   36 ++++++++++++++++++++++++++----------
 1 files changed, 26 insertions(+), 10 deletions(-)

diff --git a/src/tape b/src/tape
index 0e4f777..1e96bcb 100644
--- a/src/tape
+++ b/src/tape
@@ -6,7 +6,7 @@
 # dmin_interspecies in the min. dist. between different vertex species (in units l_min)
 dmin_interspecies=1.2
 # bending rigidity of the membrane (in units kT)
-xk0=10.0
+xk0=20.0
 # max step size (in units l_min)
 stepsize=0.15
 
@@ -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
@@ -23,13 +23,20 @@
 #Constant area constraint (0 disable constant area, 2 enable constant area with epsarea)
 constareaswitch=0
 
+
+#Stretching
+stretchswitch=0
+xkA0=1.0
+
 ####### Polymer (brush) definitions ###########
 # npoly is a number of polymers attached to npoly distinct vertices on vesicle
 npoly=0
 # nmono is a number of monomers in each polymer
-nmono=2
+nmono=0
 # Spring constant between monomers of the polymer
 k_spring=800
+#set to 1 if half of the polymeres are inside the vesicle
+internal_poly=0
 
 ####### Filament (inside the vesicle) definitions ###########
 # nfil is a number of filaments inside the vesicle
@@ -46,9 +53,9 @@
 R_nucleusY=0
 R_nucleusZ=0
 #######  Cell definitions ############
-nxmax=60
-nymax=60
-nzmax=60
+nxmax=100
+nymax=100
+nzmax=100
 
 
 ####### Program Control ############
@@ -84,11 +91,20 @@
 #cuda options???
 
 
-#NirGov branch only!
 #number of vertices with spontaneous curvature (integer)
-number_of_vertices_with_c0=30
-#spontaneous curvature (float)
+number_of_vertices_with_c0=400
+#c0/2 is spontaneous curvature. c0 is used as (c1+c1-c0)^2 in energy term (float)
 c0=0.5
 #energy of attraction of vertices with spontaneous curvature (float, positive value for attraction)
-w=100.0
+w=10.0
+#direct force on vesicles with spontaneous curvature (float)
+F=0.0
 
+
+
+#plane confinement
+plane_confinement_switch=0
+#final plane distance (float in lmin)
+plane_d=10
+#plane to vesicle repulsion force while closing
+plane_F=10

--
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