| | |
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| | | ####### Vesicle definitions ########### |
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| | | # nshell is a number of divisions of dipyramid |
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| | | nshell=20 |
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| | | # dmax is the square of the bond length |
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| | | dmax=1.67 |
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| | | # bending rigidity of the membrane |
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| | | xk0=25.0 |
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| | | # max step size |
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| | | nshell=17 |
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| | | # dmax is the max. bond length (in units l_min) |
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| | | dmax=1.7 |
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| | | # dmin_interspecies in the min. dist. between different vertex species (in units l_min) |
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| | | dmin_interspecies=1.2 |
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| | | # bending rigidity of the membrane (in units kT) |
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| | | xk0=10.0 |
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| | | # max step size (in units l_min) |
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| | | stepsize=0.15 |
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| | | |
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| | | # Pressure calculations |
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| | | # (pswitch=1: calc. p*dV energy contribution) |
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| | | pswitch = 0 |
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| | | # pressure difference: p_inside - p_outside (in units kT/l_min^3): |
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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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| | | |
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| | | #Stretching |
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| | | stretchswitch=1 |
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| | | xkA0=1.0 |
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| | | |
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| | | ####### Polymer (brush) definitions ########### |
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| | | # npoly is a number of polymers attached to npoly distinct vertices on vesicle |
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| | | npoly=0 |
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| | | # nmono is a number of monomers in each polymer |
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| | | nmono=20 |
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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=0 |
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| | | |
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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=0 |
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| | | # nfono is a number of monomers in each filament |
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| | | nfono=3 |
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| | | # Persistence lenght of the filaments (in units l_min) |
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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 |
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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 |
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| | | ####### Cell definitions ############ |
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| | | nxmax=60 |
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| | | nymax=60 |
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| | | nzmax=60 |
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| | | nxmax=100 |
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| | | nymax=100 |
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| | | nzmax=100 |
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| | | |
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| | | |
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| | | ####### Program Control ############ |
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| | | #how many iteration are there in a run? |
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| | | iterations=20000 |
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| | | #how many MC sweeps between subsequent records of states to disk |
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| | | #200000 |
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| | | mcsweeps=200 |
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| | | #how many initial mcsweeps*inititer MC sweeps before recording to disk? |
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| | | #2 |
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| | | inititer=0 |
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| | | #how many records do you want on the disk iteration are there in a run? |
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| | | #10000 |
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| | | iterations=100 |
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| | | |
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| | | |
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| | | ###### Spherical harmonics ########### |
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| | | # If 0 then spherical harmonics are not calculated at all. |
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| | | spherical_harmonics_coefficients=21 |
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| | | |
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| | | #shut up if we are using cluster!!! |
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| | | quiet=false |
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| | | |
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| | | |
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| | | |
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| | | #what type of multiprocessing? (*none, smp, cluster, distributed, cuda, auto) |
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| | | #currently only none makes sense. |
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| | | multiprocessing=none |
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| | | #how many cores are allowed to process in SMP? |
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| | | smp_cores=2 |
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| | | #how many nodes in cluster? |
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| | | cluster_nodes=50 |
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| | | #max number of processes in distributed (voluntary) environment |
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| | | distributed_processes=50 |
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| | | #cuda options??? |
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| | | |
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| | | |
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| | | #number of vertices with spontaneous curvature (integer) |
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| | | number_of_vertices_with_c0=100 |
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| | | #c0/2 is spontaneous curvature. c0 is used as (c1+c1-c0)^2 in energy term (float) |
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| | | c0=0.5 |
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| | | #energy of attraction of vertices with spontaneous curvature (float, positive value for attraction) |
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| | | w=10.0 |
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| | | #direct force on vesicles with spontaneous curvature (float) |
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| | | F=2.0 |
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| | | |
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| | | |
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| | | |
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| | | #plane confinement |
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| | | plane_confinement_switch=1 |
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| | | #final plane distance (float in lmin) |
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| | | plane_d=10 |
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| | | #plane to vesicle repulsion force while closing |
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| | | plane_F=10 |
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