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Convert USER/lb/polymer files to UNIX line endings and remove trailing whitespace

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Richard Berger
2017-03-05 21:16:21 -05:00
parent 778a79b8ee
commit 17486a9319
3 changed files with 1252 additions and 1252 deletions
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2080
examples/USER/lb/polymer/data.polymer
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examples/USER/lb/polymer/in.polymer_default_gamma
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@ -1,107 +1,107 @@
#===========================================================================# #===========================================================================#
# polymer test # # polymer test #
# # # #
# Run consists of a lone 32-bead coarse-grained polymer # # Run consists of a lone 32-bead coarse-grained polymer #
# undergoing Brownian motion in thermal lattice-Boltzmann fluid. # # undergoing Brownian motion in thermal lattice-Boltzmann fluid. #
# # # #
# Here, gamma (used in the calculation of the monomer-fluid interaction # # Here, gamma (used in the calculation of the monomer-fluid interaction #
# force) is set by the user (gamma = 0.03 for this simulation...this # # force) is set by the user (gamma = 0.03 for this simulation...this #
# value has been calibrated a priori through simulations of the drag # # value has been calibrated a priori through simulations of the drag #
# force acting on a single particle of the same radius). # # force acting on a single particle of the same radius). #
# Sample output from this run can be found in the file: # # Sample output from this run can be found in the file: #
# 'dump.polymer.lammpstrj' # # 'dump.polymer.lammpstrj' #
# and viewed using, e.g., the VMD software. # # and viewed using, e.g., the VMD software. #
# # # #
#===========================================================================# #===========================================================================#
units nano units nano
dimension 3 dimension 3
boundary p p p boundary p p p
atom_style hybrid molecular atom_style hybrid molecular
special_bonds fene special_bonds fene
read_data data.polymer read_data data.polymer
#---------------------------------------------------------------------------- #----------------------------------------------------------------------------
# Need a neighbor bin size smaller than the lattice-Boltzmann grid spacing # Need a neighbor bin size smaller than the lattice-Boltzmann grid spacing
# to ensure that the particles belonging to a given processor remain inside # to ensure that the particles belonging to a given processor remain inside
# that processors lattice-Boltzmann grid. # that processors lattice-Boltzmann grid.
#---------------------------------------------------------------------------- #----------------------------------------------------------------------------
neighbor 0.5 bin neighbor 0.5 bin
neigh_modify delay 0 every 1 check yes neigh_modify delay 0 every 1 check yes
neigh_modify exclude type 2 2 neigh_modify exclude type 2 2
neigh_modify exclude type 2 1 neigh_modify exclude type 2 1
#---------------------------------------------------------------------------- #----------------------------------------------------------------------------
# Implement a hard-sphere interaction between the particles at the center of # Implement a hard-sphere interaction between the particles at the center of
# each monomer (use a truncated and shifted Lennard-Jones potential). # each monomer (use a truncated and shifted Lennard-Jones potential).
#---------------------------------------------------------------------------- #----------------------------------------------------------------------------
bond_style fene bond_style fene
bond_coeff 1 60.0 2.25 4.14195 1.5 bond_coeff 1 60.0 2.25 4.14195 1.5
pair_style lj/cut 1.68369 pair_style lj/cut 1.68369
pair_coeff 1 1 4.14195 1.5 1.68369 pair_coeff 1 1 4.14195 1.5 1.68369
pair_coeff 1 2 4.14195 1.5 1.68369 pair_coeff 1 2 4.14195 1.5 1.68369
pair_coeff 2 2 0 1.0 pair_coeff 2 2 0 1.0
mass * 0.000000771064 mass * 0.000000771064
timestep 0.00003 timestep 0.00003
#---------------------------------------------------------------------------- #----------------------------------------------------------------------------
# ForceAtoms are the particles at the center of each monomer which # ForceAtoms are the particles at the center of each monomer which
# do not interact with the fluid, but are used to implement the hard-sphere # do not interact with the fluid, but are used to implement the hard-sphere
# interactions. # interactions.
# FluidAtoms are the particles representing the surface of the monomer # FluidAtoms are the particles representing the surface of the monomer
# which do interact with the fluid. Monomer surface is shell of radius 0.7 # which do interact with the fluid. Monomer surface is shell of radius 0.7
#---------------------------------------------------------------------------- #----------------------------------------------------------------------------
group ForceAtoms type 1 group ForceAtoms type 1
group FluidAtoms type 2 group FluidAtoms type 2
#--------------------------------------------------------------------------- #---------------------------------------------------------------------------
# Create a lattice-Boltzmann fluid covering the simulation domain. # Create a lattice-Boltzmann fluid covering the simulation domain.
# This fluid feels a force due to the particles specified through FluidAtoms # 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 # (however, this fix does not explicitly apply a force back on to these
# particles. This is accomplished through the use of the lb/viscous # particles. This is accomplished through the use of the lb/viscous
# fix). # fix).
# Uses the standard LB integration scheme, fluid viscosity = 0.023333333, # Uses the standard LB integration scheme, fluid viscosity = 0.023333333,
# fluid density= 0.0000166368, lattice spacing dx=1.0, and mass unit, # fluid density= 0.0000166368, lattice spacing dx=1.0, and mass unit,
# dm=0.0000166368. # dm=0.0000166368.
# Use the default method to calculate the interaction force between the # Use the default method to calculate the interaction force between the
# particles and the fluid. This calculation requires the surface area # particles and the fluid. This calculation requires the surface area
# of the composite object represented by each particle node. By default # 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 # 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 # here, it is input through the setArea keyword (i.e. particles of type 2
# correspond to a surface area of 0.2025=4 Pi R^2/N ). # correspond to a surface area of 0.2025=4 Pi R^2/N ).
# Use the trilinear interpolation stencil to distribute the force from # Use the trilinear interpolation stencil to distribute the force from
# a given particle onto the fluid mesh (results in a smaller hydrodynamic # a given particle onto the fluid mesh (results in a smaller hydrodynamic
# radius than if the Peskin stencil is used). # radius than if the Peskin stencil is used).
# Use a thermal lattice-Boltzmann fluid (temperature 300K, random number # Use a thermal lattice-Boltzmann fluid (temperature 300K, random number
# seed=15003). This enables the particles to undergo Brownian motion in # seed=15003). This enables the particles to undergo Brownian motion in
# the fluid. # the fluid.
#---------------------------------------------------------------------------- #----------------------------------------------------------------------------
fix 1 FluidAtoms lb/fluid 3 1 0.023333333 0.0000166368 setArea 2 0.20525 dx 1.0 dm 0.0000166368 noise 300.0 15003 fix 1 FluidAtoms lb/fluid 3 1 0.023333333 0.0000166368 setArea 2 0.20525 dx 1.0 dm 0.0000166368 noise 300.0 15003
#---------------------------------------------------------------------------- #----------------------------------------------------------------------------
# Apply the force from the fluid to the particles, and integrate their # Apply the force from the fluid to the particles, and integrate their
# motion, constraining them to move and rotate together as a single rigid # motion, constraining them to move and rotate together as a single rigid
# spherical object. # spherical object.
# Since both the ForceAtoms (central atoms), and the FluidAtoms (spherical # Since both the ForceAtoms (central atoms), and the FluidAtoms (spherical
# shell) should move and rotate together, this fix is applied to all of # shell) should move and rotate together, this fix is applied to all of
# the atoms in the system. However, since the central atoms should not # the atoms in the system. However, since the central atoms should not
# feel a force due to the fluid, they are excluded from the fluid force # feel a force due to the fluid, they are excluded from the fluid force
# calculation. # calculation.
#---------------------------------------------------------------------------- #----------------------------------------------------------------------------
fix 2 FluidAtoms lb/viscous fix 2 FluidAtoms lb/viscous
fix 3 all rigid molecule fix 3 all rigid molecule
#---------------------------------------------------------------------------- #----------------------------------------------------------------------------
# To ensure that numerical errors do not lead to a buildup of momentum in the # 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 # system, the momentum_lb fix is used every 10000 timesteps to zero out the
# total (particle plus fluid) momentum in the system. # total (particle plus fluid) momentum in the system.
#---------------------------------------------------------------------------- #----------------------------------------------------------------------------
fix 4 all lb/momentum 10000 linear 1 1 1 fix 4 all lb/momentum 10000 linear 1 1 1
#---------------------------------------------------------------------------- #----------------------------------------------------------------------------
# Write position and velocity coordinates into a file every 2000 time steps. # Write position and velocity coordinates into a file every 2000 time steps.
#---------------------------------------------------------------------------- #----------------------------------------------------------------------------
dump 1 ForceAtoms custom 2000 dump.polymer_default_gamma.lammpstrj id x y z vx vy vz dump 1 ForceAtoms custom 2000 dump.polymer_default_gamma.lammpstrj id x y z vx vy vz
run 2000001 run 2000001

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examples/USER/lb/polymer/in.polymer_setgamma
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@ -1,105 +1,105 @@
#===========================================================================# #===========================================================================#
# polymer test # # polymer test #
# # # #
# Run consists of a lone 32-bead coarse-grained polymer # # Run consists of a lone 32-bead coarse-grained polymer #
# undergoing Brownian motion in thermal lattice-Boltzmann fluid. # # undergoing Brownian motion in thermal lattice-Boltzmann fluid. #
# # # #
# Here, gamma (used in the calculation of the monomer-fluid interaction # # Here, gamma (used in the calculation of the monomer-fluid interaction #
# force) is set by the user (gamma = 0.03 for this simulation...this # # force) is set by the user (gamma = 0.03 for this simulation...this #
# value has been calibrated a priori through simulations of the drag # # value has been calibrated a priori through simulations of the drag #
# force acting on a single particle of the same radius). # # force acting on a single particle of the same radius). #
# Sample output from this run can be found in the file: # # Sample output from this run can be found in the file: #
# 'dump.polymer.lammpstrj' # # 'dump.polymer.lammpstrj' #
# and viewed using, e.g., the VMD software. # # and viewed using, e.g., the VMD software. #
# # # #
# Santtu Ollila # # Santtu Ollila #
# santtu.ollila@aalto.fi # # santtu.ollila@aalto.fi #
# Aalto University # # Aalto University #
# August 14, 2013 # # August 14, 2013 #
#===========================================================================# #===========================================================================#
units nano units nano
dimension 3 dimension 3
boundary p p p boundary p p p
atom_style hybrid molecular atom_style hybrid molecular
special_bonds fene special_bonds fene
read_data data.polymer read_data data.polymer
#---------------------------------------------------------------------------- #----------------------------------------------------------------------------
# Need a neighbor bin size smaller than the lattice-Boltzmann grid spacing # Need a neighbor bin size smaller than the lattice-Boltzmann grid spacing
# to ensure that the particles belonging to a given processor remain inside # to ensure that the particles belonging to a given processor remain inside
# that processors lattice-Boltzmann grid. # that processors lattice-Boltzmann grid.
#---------------------------------------------------------------------------- #----------------------------------------------------------------------------
neighbor 0.5 bin neighbor 0.5 bin
neigh_modify delay 0 every 1 check yes neigh_modify delay 0 every 1 check yes
neigh_modify exclude type 2 2 neigh_modify exclude type 2 2
neigh_modify exclude type 2 1 neigh_modify exclude type 2 1
#---------------------------------------------------------------------------- #----------------------------------------------------------------------------
# Implement a hard-sphere interaction between the particles at the center of # Implement a hard-sphere interaction between the particles at the center of
# each monomer (use a truncated and shifted Lennard-Jones potential). # each monomer (use a truncated and shifted Lennard-Jones potential).
#---------------------------------------------------------------------------- #----------------------------------------------------------------------------
bond_style fene bond_style fene
bond_coeff 1 60.0 2.25 4.14195 1.5 bond_coeff 1 60.0 2.25 4.14195 1.5
pair_style lj/cut 1.68369 pair_style lj/cut 1.68369
pair_coeff 1 1 4.14195 1.5 1.68369 pair_coeff 1 1 4.14195 1.5 1.68369
pair_coeff 1 2 4.14195 1.5 1.68369 pair_coeff 1 2 4.14195 1.5 1.68369
pair_coeff 2 2 0 1.0 pair_coeff 2 2 0 1.0
mass * 0.000000771064 mass * 0.000000771064
timestep 0.00003 timestep 0.00003
#---------------------------------------------------------------------------- #----------------------------------------------------------------------------
# ForceAtoms are the particles at the center of each monomer which # ForceAtoms are the particles at the center of each monomer which
# do not interact with the fluid, but are used to implement the hard-sphere # do not interact with the fluid, but are used to implement the hard-sphere
# interactions. # interactions.
# FluidAtoms are the particles representing the surface of the monomer # FluidAtoms are the particles representing the surface of the monomer
# which do interact with the fluid. # which do interact with the fluid.
#---------------------------------------------------------------------------- #----------------------------------------------------------------------------
group ForceAtoms type 1 group ForceAtoms type 1
group FluidAtoms type 2 group FluidAtoms type 2
#--------------------------------------------------------------------------- #---------------------------------------------------------------------------
# Create a lattice-Boltzmann fluid covering the simulation domain. # Create a lattice-Boltzmann fluid covering the simulation domain.
# This fluid feels a force due to the particles specified through FluidAtoms # 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 # (however, this fix does not explicitly apply a force back on to these
# particles. This is accomplished through the use of the rigid_pc_sphere # particles. This is accomplished through the use of the rigid_pc_sphere
# fix). # fix).
# Use the LB integration scheme of Ollila et. al. (for stability reasons, # Use the LB integration scheme of Ollila et. al. (for stability reasons,
# this integration scheme should be used when a large user set value for # this integration scheme should be used when a large user set value for
# gamma is specified), a fluid viscosity = 0.023333333, # gamma is specified), a fluid viscosity = 0.023333333,
# fluid density= 0.0000166368, # fluid density= 0.0000166368,
# value for gamma=0.03, lattice spacing dx=1.0, and mass unit, dm=0.0000166368. # value for gamma=0.03, lattice spacing dx=1.0, and mass unit, dm=0.0000166368.
# Use a thermal lattice-Boltzmann fluid (temperature 300K, random number # Use a thermal lattice-Boltzmann fluid (temperature 300K, random number
# seed=15003). This enables the particles to undergo Brownian motion in # seed=15003). This enables the particles to undergo Brownian motion in
# the fluid. # the fluid.
#---------------------------------------------------------------------------- #----------------------------------------------------------------------------
fix 1 FluidAtoms lb/fluid 5 1 0.023333333 0.0000166368 setGamma 0.03 dx 1.0 dm 0.0000166368 noise 300.0 15003 fix 1 FluidAtoms lb/fluid 5 1 0.023333333 0.0000166368 setGamma 0.03 dx 1.0 dm 0.0000166368 noise 300.0 15003
#---------------------------------------------------------------------------- #----------------------------------------------------------------------------
# Apply the force from the fluid to the particles, and integrate their # Apply the force from the fluid to the particles, and integrate their
# motion, constraining them to move and rotate together as a single rigid # motion, constraining them to move and rotate together as a single rigid
# spherical object. # spherical object.
# Since both the ForceAtoms (central atoms), and the FluidAtoms (spherical # Since both the ForceAtoms (central atoms), and the FluidAtoms (spherical
# shell) should move and rotate together, this fix is applied to all of # shell) should move and rotate together, this fix is applied to all of
# the atoms in the system. However, since the central atoms should not # the atoms in the system. However, since the central atoms should not
# feel a force due to the fluid, they are excluded from the force # feel a force due to the fluid, they are excluded from the force
# calculation through the use of the 'innerNodes' keyword. # calculation through the use of the 'innerNodes' keyword.
# NOTE: This fix should only be used when the user specifies a value for # NOTE: This fix should only be used when the user specifies a value for
# gamma (through the setGamma keyword) in the lb_fluid fix. # gamma (through the setGamma keyword) in the lb_fluid fix.
#---------------------------------------------------------------------------- #----------------------------------------------------------------------------
fix 2 all lb/rigid/pc/sphere molecule innerNodes ForceAtoms fix 2 all lb/rigid/pc/sphere molecule innerNodes ForceAtoms
#---------------------------------------------------------------------------- #----------------------------------------------------------------------------
# To ensure that numerical errors do not lead to a buildup of momentum in the # 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 # system, the momentum_lb fix is used every 10000 timesteps to zero out the
# total (particle plus fluid) momentum in the system. # total (particle plus fluid) momentum in the system.
#---------------------------------------------------------------------------- #----------------------------------------------------------------------------
fix 3 all lb/momentum 10000 linear 1 1 1 fix 3 all lb/momentum 10000 linear 1 1 1
#---------------------------------------------------------------------------- #----------------------------------------------------------------------------
# Write position and velocity coordinates into a file every 2000 time steps. # Write position and velocity coordinates into a file every 2000 time steps.
#---------------------------------------------------------------------------- #----------------------------------------------------------------------------
dump 1 ForceAtoms custom 2000 dump.polymer_setgamma.lammpstrj id x y z vx vy vz dump 1 ForceAtoms custom 2000 dump.polymer_setgamma.lammpstrj id x y z vx vy vz
run 2000001 run 2000001