From 51f7fd23ba4e56dc198273eb795c8d1730cf4dbe Mon Sep 17 00:00:00 2001 From: Samo Penic <samo.penic@gmail.com> Date: Mon, 19 Apr 2021 13:54:45 +0000 Subject: [PATCH] Work in progress --- src/tape | 98 +++++++++++++++++++++++++++++++++++++++++-------- 1 files changed, 82 insertions(+), 16 deletions(-) diff --git a/src/tape b/src/tape index e0d0dee..41bd4da 100644 --- a/src/tape +++ b/src/tape @@ -1,36 +1,83 @@ ####### Vesicle definitions ########### # nshell is a number of divisions of dipyramid nshell=17 -# dmax is the square of the bond length -dmax=1.67 -# bending rigidity of the membrane -xk0=25.0 -# max step size +# 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=10.0 +# max step size (in units l_min) stepsize=0.15 -####### Polymer definitions ########### -# npoly is a number of polymers attached to npoly distinct vertices on vesicle -npoly=1000 -# nmono is a number of monomers in each polymere -nmono=15 +# Pressure calculations +# (pswitch=1: calc. p*dV energy contribution) +pswitch = 0 +# pressure difference: p_inside - p_outside (in units kT/l_min^3): +pressure=10000.0 +#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=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=20 +# 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 +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 -nzmax=60 +nxmax=100 +nymax=100 +nzmax=100 ####### Program Control ############ #how many MC sweeps between subsequent records of states to disk -mcsweeps=100 +#200000 +mcsweeps=200 #how many initial mcsweeps*inititer MC sweeps before recording to disk? -inititer=100 +#2 +inititer=0 #how many records do you want on the disk iteration are there in a run? -iterations=1000 +#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. @@ -42,3 +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=0 +#final plane distance (float in lmin) +plane_d=10 +#plane to vesicle repulsion force while closing +plane_F=10 -- Gitblit v1.9.3