From 6da644f98434d3eac8b4e19981754f6030a315a5 Mon Sep 17 00:00:00 2001 From: Samo Penic <samo.penic@gmail.com> Date: Wed, 27 Jun 2018 12:05:32 +0000 Subject: [PATCH] Resolving the issues with restoring vesicles from vtu and fixing the volume. Dump to vtu has been repaired. --- src/tape | 65 ++++++++++++++++++++++++++++---- 1 files changed, 57 insertions(+), 8 deletions(-) diff --git a/src/tape b/src/tape index 1c0d279..978e3c9 100644 --- a/src/tape +++ b/src/tape @@ -3,25 +3,55 @@ 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) +dmin_interspecies=1.2 # bending rigidity of the membrane (in units kT) -xk0=25.0 +xk0=10.0 # max step size (in units l_min) stepsize=0.15 # Pressure calculations # (pswitch=1: calc. p*dV energy contribution) -pswitch = 1 -# pressure difference: p_inside - p_outside (in units l_min^3/kT): -pressure=0.0 +pswitch = 0 +# pressure difference: p_inside - p_outside (in units kT/l_min^3): +pressure=10.0 -####### Polymer definitions ########### +#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 + + +#Stretching +stretchswitch=1 +xkA0=1.0 + +####### Polymer (brush) definitions ########### # npoly is a number of polymers attached to npoly distinct vertices on vesicle -npoly=30 +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=0 +# nfono is a number of monomers in each filament +nfono=3 +# Persistence lenght of the filaments (in units l_min) +xi=100 + +####### Nucleus (inside the vesicle) ########### +# Radius of an impenetrable hard sphere inside the vesicle +R_nucleus=0 +R_nucleusX=0 +R_nucleusY=0 +R_nucleusZ=0 ####### Cell definitions ############ nxmax=60 nymax=60 @@ -30,15 +60,24 @@ ####### Program Control ############ #how many MC sweeps between subsequent records of states to disk -mcsweeps=5000 +#200000 +mcsweeps=200 #how many initial mcsweeps*inititer MC sweeps before recording to disk? +#2 inititer=1 #how many records do you want on the disk iteration are there in a run? -iterations=2000 +#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. @@ -50,3 +89,13 @@ #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=0 +#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 -- Gitblit v1.9.3