68 lines
1.9 KiB
Plaintext
68 lines
1.9 KiB
Plaintext
# 3D overdamped active brownian dynamics with no interactions
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variable gamma_t string 3.0
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variable gamma_r string 1.0
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variable temp string 1.0
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variable seed equal 1974019
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variable fp string 4.0
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variable params string ${temp}_${gamma_t}_${gamma_r}_${fp}
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units lj
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atom_style hybrid dipole sphere
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dimension 3
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newton off
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lattice sc 0.4
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region box block -8 8 -8 8 -8 8
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create_box 1 box
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create_atoms 1 box
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mass * 1.0
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set type * dipole/random ${seed} 1.0
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velocity all create 1.0 1 loop geom
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pair_style none
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# overdamped brownian dynamics time-step
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fix step all brownian/sphere ${temp} ${seed} gamma_t ${gamma_t} gamma_r ${gamma_r}
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# self-propulsion force along the dipole direction
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fix activity all propel/self dipole ${fp}
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compute press all pressure NULL virial
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thermo_style custom step ke pe c_press
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#equilibration
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timestep 0.0000000001
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thermo 100
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run 5000
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reset_timestep 0
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# MSD to demonstrate expected diffusive behaviour for ideal active
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# brownian motion, which is
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#
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# MSD = (2*d*kb*T/gamma_t + 2*fp**2*gamma_r/(kb*T*gamma_t**2*(d-1)))*t
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# + 2*fp**2*gamma_r**2/(gamma_t**2*(d-1)**2*(kb*T)**2)*(e^(-(d-1)*t*kb*T/gamma_r)-1)
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#
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# with d being simulation dimension
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compute msd all msd
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thermo_style custom step ke pe c_msd[*] c_press
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timestep 0.00001
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thermo 1000
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# main run
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run 12000
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# if you want to check that rotational diffusion is behaving as expected,
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# uncomment next three lines for dump output and then plot <e(t).e(0)>,
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# which should decay exponentially with timescale (d-1)*D_r (with d
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# being simulation dimension)
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#dump 1 all custom 2000 dump_ideal_${params}_3d.lammpstrj id type &
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# x y xu yu mux muy muz fx fy fz
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#dump_modify 1 first yes sort id
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#run 120000
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