From 60c2b879f26c5f008af0df7d7f159d33077225ac Mon Sep 17 00:00:00 2001
From: Samo Penic <samo.penic@gmail.com>
Date: Sat, 09 Mar 2019 19:47:16 +0000
Subject: [PATCH] Cleanup of stretching energy plugin

---
 src/tape |   27 ++++++++++++++++++++-------
 1 files changed, 20 insertions(+), 7 deletions(-)

diff --git a/src/tape b/src/tape
index f2edf02..42e22ea 100644
--- a/src/tape
+++ b/src/tape
@@ -12,9 +12,9 @@
 
 # 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
+pressure=-10.0
 
 #Constant volume constraint (0 disable constant volume, 1 enable wiht additional vertex move, 2 enable with epsvol)
 constvolswitch=0
@@ -23,9 +23,14 @@
 #Constant area constraint (0 disable constant area, 2 enable constant area with epsarea)
 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=400
+npoly=0
 # nmono is a number of monomers in each polymer
 nmono=10
 # Spring constant between monomers of the polymer
@@ -56,10 +61,10 @@
 ####### Program Control ############
 #how many MC sweeps between subsequent records of states to disk
 #200000
-mcsweeps=2000
+mcsweeps=200
 #how many initial mcsweeps*inititer MC sweeps before recording to disk?
 #2
-inititer=1
+inititer=0
 #how many records do you want on the disk iteration are there in a run?
 #10000
 iterations=100
@@ -86,12 +91,20 @@
 #cuda options???
 
 
-#NirGov branch only!
 #number of vertices with spontaneous curvature (integer)
 number_of_vertices_with_c0=100
-#spontaneous curvature (float)
+#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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