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lammps/examples/USER/lb/microrheology/in.microrheology_default_gamma
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in.microrheology_default_gamma
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#===========================================================================#
# 2 particle microrheology test #
# #
# Run consists of 2 colloidal particles undergoing Brownian motion in a #
# thermal lattice-Boltzmann fluid. #
# #
# Here, gamma (used in the calculation of the particle-fluid interaction #
# force) is calculated by default. Thus, the colloidal objects will have #
# a slightly larger "hydrodynamic" radii than given by the placement of #
# the particle nodes. #
# #
# Sample output from this run can be found in the file: #
# 'microrheology_setgamma.out' #
#===========================================================================#
units nano
dimension 3
boundary p p p
atom_style molecular
read_data data.two
#----------------------------------------------------------------------------
# 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 0.3 bin
neigh_modify delay 0 every 1
neigh_modify exclude type 2 2
neigh_modify exclude type 2 1
#----------------------------------------------------------------------------
# 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 5.88
pair_coeff * * 0.0 0.0 5.88
pair_coeff 1 1 100.0 5.238484463 5.88
pair_modify shift yes
mass * 0.0002398
timestep 0.00025
#----------------------------------------------------------------------------
# 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.
# FluidAtoms are the particles representing the surface of the colloidal
# object which do interact with the fluid.
#----------------------------------------------------------------------------
group ForceAtoms type 1
group FluidAtoms type 2
#---------------------------------------------------------------------------
# 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 explicitly 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 viscosity = 1.0, fluid
# density= 0.0009982071, lattice spacing dx=1.2, and mass unit, dm=0.003.
# Use the default method to calculate the interaction force between the
# particles and the fluid. This calculation requires the surface area
# of the composite object represented by each particle node. By default
# this area is assumed equal to dx*dx; however, since this is not the case
# here, it is input through the setArea keyword (i.e. particles of type 2
# correspond to a surface area of 0.3015928947).
# Use the trilinear interpolation stencil to distribute the force from
# a given particle onto the fluid mesh.
# Use a thermal lattice-Boltzmann fluid (temperature 300K, random number
# seed=2762). This enables the particles to undergo Brownian motion in
# the fluid.
#----------------------------------------------------------------------------
fix 1 FluidAtoms lb/fluid 1 1 1.0 0.0009982071 setArea 2 0.3015928947 dx 1.2 dm 0.003 trilinear noise 300.0 2762
#----------------------------------------------------------------------------
# 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 these sets of particles as rigid objects
# which each move and rotate together.
#----------------------------------------------------------------------------
fix 3 all rigid molecule
#----------------------------------------------------------------------------
# To ensure that numerical errors do not lead to a buildup of momentum in the
# system, the momentum_lb fix is used every 10000 timesteps to zero out the
# total (particle plus fluid) momentum in the system.
#----------------------------------------------------------------------------
fix 4 all lb/momentum 10000 linear 1 1 1
#----------------------------------------------------------------------------
# Create variables containing the positions of the central atoms (these
# values should correspond to the center of mass of each composite
# colloidal particle), and output these quantities to the screen.
#----------------------------------------------------------------------------
variable x1 equal x[1]
variable y1 equal y[1]
variable z1 equal z[1]
variable x2 equal x[242]
variable y2 equal y[242]
variable z2 equal z[242]
thermo_style custom v_x1 v_y1 v_z1 v_x2 v_y2 v_z2
thermo 1
run 2000000000
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