| | |
|---|
| | | ####### Vesicle definitions ########### |
|---|
| | | # nshell is a number of divisions of dipyramid |
|---|
| | | nshell=20 |
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| | | # dmax is the square of the bond length |
|---|
| | | dmax=1.67 |
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| | | # bending rigidity of the membrane |
|---|
| | | 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) |
|---|
| | | 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) |
|---|
| | | stepsize=0.15 |
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| | | |
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| | | # Pressure calculations |
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| | | # (pswitch=1: calc. p*dV energy contribution) |
|---|
| | | pswitch = 0 |
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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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| | | |
|---|
| | | #Constant volume constraint (0 disable constant volume, 1 enable) |
|---|
| | | constvolswitch=0 |
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| | | constvolprecision=1e-14 |
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| | | |
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| | | |
|---|
| | | ####### Polymer (brush) definitions ########### |
|---|
| | | # npoly is a number of polymers attached to npoly distinct vertices on vesicle |
|---|
| | | npoly=0 |
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| | | # nmono is a number of monomers in each polymer |
|---|
| | | nmono=10 |
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| | | # Spring constant between monomers of the polymer |
|---|
| | | k_spring=800 |
|---|
| | | |
|---|
| | | ####### Filament (inside the vesicle) definitions ########### |
|---|
| | | # nfil is a number of filaments inside the vesicle |
|---|
| | | nfil=0 |
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| | | # nfono is a number of monomers in each filament |
|---|
| | | nfono=300 |
|---|
| | | # Persistence lenght of the filaments (in units l_min) |
|---|
| | | xi=0 |
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| | | |
|---|
| | | ####### Nucleus (inside the vesicle) ########### |
|---|
| | | # Radius of an impenetrable hard sphere inside the vesicle |
|---|
| | | R_nucleus=0 |
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| | | |
|---|
| | | ####### Cell definitions ############ |
|---|
| | | nxmax=60 |
|---|
| | |
|---|
| | | |
|---|
| | | |
|---|
| | | ####### Program Control ############ |
|---|
| | | #how many iteration are there in a run? |
|---|
| | | iterations=20000 |
|---|
| | | #how many MC sweeps between subsequent records of states to disk |
|---|
| | | mcsweeps=2500 |
|---|
| | | #how many initial mcsweeps*inititer MC sweeps before recording to disk? |
|---|
| | | inititer=10 |
|---|
| | | #how many records do you want on the disk iteration are there in a run? |
|---|
| | | iterations=50010 |
|---|
| | | |
|---|
| | | |
|---|
| | | ###### Spherical harmonics ########### |
|---|
| | | 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. |
|---|
| | | multiprocessing=none |
|---|
| | | #how many cores are allowed to process in SMP? |
|---|
| | | smp_cores=2 |
|---|
| | | #how many nodes in cluster? |
|---|
| | | cluster_nodes=50 |
|---|
| | | #max number of processes in distributed (voluntary) environment |
|---|
| | | distributed_processes=50 |
|---|
| | | #cuda options??? |
|---|
