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This commit is contained in:
Stefan Paquay
2019-08-29 09:00:36 -04:00
committed by Pierre de Buyl
parent 8c7890b6df
commit 074dfd8651
5 changed files with 16 additions and 189 deletions
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61
examples/USER/misc/active/active_langevin.in
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# Uses a combnation of fix active and fix langevin to achieve
# self-propelled particles.
dimension 3
boundary p p p
units lj
# Fix active uses quaternions to orient the active force so you need
# ellipsoidal particles, even if you do not care about asymmetric shape
atom_style ellipsoid
# Set up box and particles:
variable L equal 10
region total block -$L $L -$L $L -$L $L
create_box 1 total
variable N equal 1000
create_atoms 1 random $N 123456 total
# Set particle shape:
set group all shape 1 1 1
set group all quat/random 18238
variable V equal "4.0*PI"
variable rho equal "1.0 / v_V"
# Density so that mass = 1
set group all density ${rho}
# Simple repulsive LJ
pair_style lj/cut 1.1225
pair_coeff * * 1.0 1.0
pair_modify shift yes
# Remove initial overlap:
minimize 1e-4 1e-6 1000 10000
reset_timestep 0
# Fixes for time integration
fix step all nve/asphere
fix active all active 1.0
fix temp all langevin 1.0 1.0 1.0 12341 angmom 3.333333333333
variable DUMP_OUT string "active_langevin.dump"
variable MSD_OUT string "active_langevin_msd.dat"
# Compute temperature and orientation
compute T all temp/asphere
compute quat all property/atom quatw quati quatj quatk
compute msd all msd
compute vacf all vacf
# Some output:
thermo_style custom time step pe ke etotal temp c_T
thermo 1000
dump traj all custom 100 ${DUMP_OUT} id type x y z &
c_quat[1] c_quat[2] c_quat[3] c_quat[4]
fix msd all ave/time 1 10 50 c_msd[4] c_vacf[1] c_vacf[2] c_vacf[3] c_vacf[4] file ${MSD_OUT}
timestep 0.001
run 10000

66
examples/USER/misc/active/active_viscous.in
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@ -1,66 +0,0 @@
# Uses a combnation of fix active and fix langevin to achieve
# self-propelled particles.
dimension 3
boundary p p p
units lj
# Fix active uses quaternions to orient the active force so you need
# ellipsoidal particles, even if you do not care about asymmetric shape
atom_style ellipsoid
# Set up box and particles:
variable L equal 10
region total block -$L $L -$L $L -$L $L
create_box 1 total
variable N equal 1000
create_atoms 1 random $N 123456 total
# Set particle shape:
set group all shape 1 1 1
set group all quat/random 18238
variable V equal "4.0*PI"
variable rho equal "1.0 / v_V"
# Density so that mass = 1
set group all density ${rho}
# Simple repulsive LJ
pair_style lj/cut 1.1225
pair_coeff * * 1.0 1.0
pair_modify shift yes
# Remove initial overlap:
minimize 1e-4 1e-6 1000 10000
reset_timestep 0
# Fixes for time integration
fix step all nve/asphere
# Should lead to constant velocity of 10 per particle
fix active all active 1.0
fix visc all viscous 0.1
# Initial velocities:
velocity all create 1.0 1234
variable DUMP_OUT string "active_viscous.dump"
variable MSD_OUT string "active_viscous_msd.dat"
# Compute temperature and orientation
compute T all temp/asphere
compute quat all property/atom quatw quati quatj quatk
compute msd all msd
compute vacf all vacf
# Some output:
thermo_style custom time step pe ke etotal temp c_T
thermo 1000
dump traj all custom 100 ${DUMP_OUT} id type x y z &
c_quat[1] c_quat[2] c_quat[3] c_quat[4]
fix msd all ave/time 1 10 50 c_msd[4] c_vacf[1] c_vacf[2] c_vacf[3] c_vacf[4] file ${MSD_OUT}
timestep 0.001
run 100000