| | |
|---|
| | | # (pswitch=1: calc. p*dV energy contribution) |
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| | | pswitch = 1 |
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| | | # pressure difference: p_inside - p_outside (in units kT/l_min^3): |
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| | | pressure=0.0 |
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| | | pressure=-10.0 |
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| | | |
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| | | #Constant volume constraint (0 disable constant volume, 1 enable wiht additional vertex move, 2 enable with epsvol) |
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| | | constvolswitch=0 |
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| | | constvolprecision=1e-14 |
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| | | |
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| | | #Constant area constraint (0 disable constant area, 2 enable constant area with epsarea) |
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| | | constareaswitch=0 |
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| | | |
|---|
| | | |
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| | | #Stretching |
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| | | stretchswitch=1 |
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| | | xkA0=1.0 |
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| | | |
|---|
| | | ####### Polymer (brush) definitions ########### |
|---|
| | | # npoly is a number of polymers attached to npoly distinct vertices on vesicle |
|---|
| | |
|---|
| | | nmono=10 |
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| | | # Spring constant between monomers of the polymer |
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| | | k_spring=800 |
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| | | #set to 1 if half of the polymeres are inside the vesicle |
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| | | internal_poly=1 |
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| | | |
|---|
| | | ####### Filament (inside the vesicle) definitions ########### |
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| | | # nfil is a number of filaments inside the vesicle |
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| | | nfil=2 |
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| | | nfil=0 |
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| | | # nfono is a number of monomers in each filament |
|---|
| | | nfono=300 |
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| | | nfono=3 |
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| | | # Persistence lenght of the filaments (in units l_min) |
|---|
| | | xi=0 |
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| | | xi=100 |
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| | | |
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| | | ####### Nucleus (inside the vesicle) ########### |
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| | | # Radius of an impenetrable hard sphere inside the vesicle |
|---|
| | | R_nucleus=5 |
|---|
| | | |
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| | | R_nucleus=0 |
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| | | R_nucleusX=0 |
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| | | R_nucleusY=0 |
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| | | R_nucleusZ=0 |
|---|
| | | ####### Cell definitions ############ |
|---|
| | | nxmax=60 |
|---|
| | | nymax=60 |
|---|
| | |
|---|
| | | |
|---|
| | | ####### Program Control ############ |
|---|
| | | #how many MC sweeps between subsequent records of states to disk |
|---|
| | | mcsweeps=250 |
|---|
| | | #200000 |
|---|
| | | mcsweeps=200 |
|---|
| | | #how many initial mcsweeps*inititer MC sweeps before recording to disk? |
|---|
| | | #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 ########### |
|---|
| | | spherical_harmonics_coefficients=15 |
|---|
| | | # 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. |
|---|
| | |
|---|
| | | #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 |
|---|
