From 7522b886602380764ce76f1d2244fad11bd1054f Mon Sep 17 00:00:00 2001
From: Samo Penic <samo.penic@gmail.com>
Date: Fri, 08 Mar 2019 19:56:03 +0000
Subject: [PATCH] Full write of constant volume plugin

---
 src/tape |   46 +++++++++++++++++++++++++++++++++++++---------
 1 files changed, 37 insertions(+), 9 deletions(-)

diff --git a/src/tape b/src/tape
index 59cc09c..42e22ea 100644
--- a/src/tape
+++ b/src/tape
@@ -12,7 +12,7 @@
 
 # Pressure calculations
 # (pswitch=1: calc. p*dV energy contribution)
-pswitch = 0
+pswitch = 1
 # pressure difference: p_inside - p_outside (in units kT/l_min^3):
 pressure=-10.0
 
@@ -21,30 +21,37 @@
 constvolprecision=1e-14
 
 #Constant area constraint (0 disable constant area, 2 enable constant area with epsarea)
-constareaswitch=2
+constareaswitch=0
+
+
+#Stretching
+stretchswitch=1
+xkA0=1.0
 
 ####### Polymer (brush) definitions ###########
 # npoly is a number of polymers attached to npoly distinct vertices on vesicle
-npoly=3
+npoly=0
 # nmono is a number of monomers in each polymer
 nmono=10
 # 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
-nfil=2
+nfil=0
 # nfono is a number of monomers in each filament
-nfono=300
+nfono=3
 # Persistence lenght of the filaments (in units l_min)
-xi=0
+xi=100
 
 ####### Nucleus (inside the vesicle) ###########
 # Radius of an impenetrable hard sphere inside the vesicle
 R_nucleus=0
-R_nucleusX=6.0
-R_nucleusY=12.0
-R_nucleusZ=6.0
+R_nucleusX=0
+R_nucleusY=0
+R_nucleusZ=0
 #######  Cell definitions ############
 nxmax=60
 nymax=60
@@ -69,6 +76,8 @@
 
 #shut up if we are using cluster!!!
 quiet=false
+ 
+
 
 #what type of multiprocessing? (*none, smp, cluster, distributed, cuda, auto)
 #currently only none makes sense.
@@ -80,3 +89,22 @@
 #max number of processes in distributed (voluntary) environment
 distributed_processes=50
 #cuda options???
+
+
+#number of vertices with spontaneous curvature (integer)
+number_of_vertices_with_c0=100
+#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=10.0
+#direct force on vesicles with spontaneous curvature (float)
+F=2.0
+
+
+
+#plane confinement
+plane_confinement_switch=1
+#final plane distance (float in lmin)
+plane_d=10
+#plane to vesicle repulsion force while closing
+plane_F=10

--
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