From e5858ff1dcf5cecfcfe81602f52d255de9d508f4 Mon Sep 17 00:00:00 2001
From: Samo Penic <samo.penic@fe.uni-lj.si>
Date: Tue, 21 Jun 2016 10:49:57 +0000
Subject: [PATCH] Change in location of setting spontaneous curvature. Now it is done in initial_distribution.c, in function set_vesicle_values_from_tape. Also, energy assigning function is done and sweeping of the whole vesicle aswell.

---
 src/tape |   38 +++++++++++++++++++++++++++++---------
 1 files changed, 29 insertions(+), 9 deletions(-)

diff --git a/src/tape b/src/tape
index 023bc27..206d649 100644
--- a/src/tape
+++ b/src/tape
@@ -14,16 +14,18 @@
 # (pswitch=1: calc. p*dV energy contribution)
 pswitch = 0
 # pressure difference: p_inside - p_outside (in units kT/l_min^3):
-pressure=0.0
+pressure=-10.0
 
-#Constant volume constraint (0 disable constant volume, 1 enable)
+#Constant volume constraint (0 disable constant volume, 1 enable wiht additional vertex move, 2 enable with epsvol)
 constvolswitch=0
 constvolprecision=1e-14
 
+#Constant area constraint (0 disable constant area, 2 enable constant area with epsarea)
+constareaswitch=0
 
 ####### Polymer (brush) definitions ###########
 # npoly is a number of polymers attached to npoly distinct vertices on vesicle
-npoly=0
+npoly=3
 # nmono is a number of monomers in each polymer
 nmono=10
 # Spring constant between monomers of the polymer
@@ -31,16 +33,18 @@
 
 ####### Filament (inside the vesicle) definitions ###########
 # nfil is a number of filaments inside the vesicle
-nfil=0
+nfil=2
 # nfono is a number of monomers in each filament
 nfono=300
 # 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
 #######  Cell definitions ############
 nxmax=60
 nymax=60
@@ -49,18 +53,24 @@
 
 ####### Program Control ############
 #how many MC sweeps between subsequent records of states to disk
-mcsweeps=2500
+#200000
+mcsweeps=200
 #how many initial mcsweeps*inititer MC sweeps before recording to disk?
-inititer=10
+#2
+inititer=0
 #how many records do you want on the disk iteration are there in a run?
-iterations=50010
+#10000
+iterations=100
 
 
 ###### Spherical harmonics ###########
+# If 0 then spherical harmonics are not calculated at all.
 spherical_harmonics_coefficients=21
 
 #shut up if we are using cluster!!!
 quiet=false
+ 
+
 
 #what type of multiprocessing? (*none, smp, cluster, distributed, cuda, auto)
 #currently only none makes sense.
@@ -72,3 +82,13 @@
 #max number of processes in distributed (voluntary) environment
 distributed_processes=50
 #cuda options???
+
+
+#NirGov branch only!
+#number of vertices with spontaneous curvature (integer)
+number_of_vertices_with_c0=200
+#spontaneous curvature (float)
+c0=2.0
+#energy of attraction of vertices with spontaneous curvature
+w=1.0
+

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