Homec4science
Diffusion lammps (efficient_neuronet) Browse

lammps/examples/USER/lb/confined_colloid/in.confined_colloids
576c6315c7f1efficient_neuronet

Last Change
Raw File

in.confined_colloids
View Options

#===========================================================================#
# System of colloidal particles under shear. #
# #
# Run consists of 10x12x4 particles, each composed of 3613 particle nodes #
# (3612 particles forming a spherical shell, and 1 central particle). #
# 280 x 280 x 101 lattice-Boltzmann grid sites. #
# #
# This simulation is used to illustrate the simulation time of a realistic #
# implementation of the lb_fluid fix. #
# The data file "confinedcolloids.dat" is quite large and so is not #
# included here. It can be obtained from: #
# http://www.apmaths.uwo.ca/~cdennist/confinedcolloids.dat.gz #
# #
# Sample output from this run can be found in the file: #
# results64.out #
#===========================================================================#
units micro
dimension 3
boundary p p f
atom_style molecular
read_data confinedcolloids.dat
mass * 0.00010287
#----------------------------------------------------------------------------
# Need a neighbor bin size smaller than the lattice-Boltzmann grid spacing
# to ensure that the particles belonging to a given processor remain inside
# that processors lattice-Boltzmann grid.
# The arguments for neigh_modify have been set to "delay 0 every 1", again
# to ensure that the particles belonging to a given processor remain inside
# that processors lattice-Boltzmann grid. However, these values can likely
# be somewhat increased without issue. If a problem does arise (a particle
# is outside of its processors LB grid) an error message is printed and
# the simulation is terminated.
#----------------------------------------------------------------------------
neighbor 0.03 bin
neigh_modify delay 0 every 1
neigh_modify exclude type 2 2
neigh_modify exclude type 2 1
#----------------------------------------------------------------------------
# ForceAtoms are the particles at the center of each colloidal object which
# do not interact with the fluid, but are used to implement the hard-sphere
# interactions.
#----------------------------------------------------------------------------
group ForceAtoms type 1
#----------------------------------------------------------------------------
# FluidAtoms are the particles representing the surface of the colloidal
# object which do interact with the fluid.
#----------------------------------------------------------------------------
group FluidAtoms type 2
#----------------------------------------------------------------------------
# Implement a hard-sphere interaction between the particles at the center of
# each colloidal object (use a truncated and shifted Lennard-Jones
# potential).
#----------------------------------------------------------------------------
pair_style lj/cut 1.572
pair_coeff * * 0.0 0.0 1.572
pair_coeff 1 1 10.0 1.400492785 1.572
pair_modify shift yes
timestep 0.0006
#---------------------------------------------------------------------------
# Create a lattice-Boltzmann fluid covering the simulation domain.
# This fluid feels a force due to the particles specified through FluidAtoms
# (however, this fix does not explicity apply a force back on to these
# particles...this is accomplished through the use of the viscous_lb fix).
# Use the standard LB integration scheme, a fluid density = 1.0,
# fluid viscosity = 1.0, lattice spacing dx=0.06, and mass unit, dm=0.00003.
# Use the default method to calculate the interaction force between the
# particles and the fluid. This calculation makes use of the surface area
# of the composite object represented by each particle node. Since this is
# not equal to dx*dx, it is input through the setArea keyword (i.e.
# particles of type 2 correspond to a surface area of 0.0018337299).
# Implement walls moving at speeds of 20.0 in opposite directions.
#----------------------------------------------------------------------------
fix 1 FluidAtoms lb/fluid 1 1 1.0 1.0 dx 0.06 dm 0.00003 setArea 2 0.0018337299 zwall_velocity -20.0 20.0
#----------------------------------------------------------------------------
# Apply the force due to the fluid onto the FluidAtoms particles (again,
# these atoms represent the surface of the colloidal object, which should
# interact with the fluid).
#----------------------------------------------------------------------------
fix 2 FluidAtoms lb/viscous
#----------------------------------------------------------------------------
# Each colloidal object (spherical shell of particles and central particle)
# is specified as a separate molecule in the confinedcolloids.dat data
# file. Integrate the motion of each of these sets of particles as rigid
# objects which move and rotate together.
#----------------------------------------------------------------------------
fix 3 all rigid molecule
#----------------------------------------------------------------------------
# Implement a repulsive interaction between the ForceAtoms particles, and the
# upper and lower z-walls. (A truncated and shifted Lennard-Jones potential
# is used).
#----------------------------------------------------------------------------
fix wallhi ForceAtoms wall/lj126 zhi 5.88 20.0 0.8071542386 0.906 units box
fix walllo ForceAtoms wall/lj126 zlo 0.0 20.0 0.8071542386 0.906 units box
#dump ParticleTracking ForceAtoms custom 50 test.track id mol x y z vx vy vz
run 400
c4science · Help