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in.bar1d_frac_step
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Sat, Nov 23, 23:09

in.bar1d_frac_step
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#AtC Thermal Coupling
# This benchmark tests heat conducting into and out of the MD region. The
# temperature is intially 20 everywhere and the left boundary BC is fixed at
# 40.# The result should show heat diffusing through the FEM to the MD and back
# out # to the FEM on the right. Insufficient time is captured to reach the
# linear # steady state, but heat crossing both boundaries should be observed.
units real
atom_style atomic
# create domain
#lattice type reduced density rho* = 4*(sigma/a)^3, where N=4 for fcc, s = 3.405 A (Wagner) and a = 5.25 A (Ashcroft & Mermin, p. 70)
# NOTE following 3 lines added for restart
boundary f p p
pair_style lj/cut 13.5
read_data temp.init
lattice fcc 5.405 origin 0.25 0.25 0.25
region simRegion block -12 12 -3 3 -3 3
# create atoms, NOTE commented out for restart
#region mdRegion block -5 5 -3 3 -3 3
#boundary f p p
#create_box 1 mdRegion
#create_atoms 1 region mdRegion
#mass 1 39.95
# specify interal/ghost atoms
region mdInternal block -4 4 -3 3 -3 3
group internal region mdInternal
group ghost subtract all internal
# velocities have Vcm = 0, NOTE next four lines commented out for restart
#velocity internal create 40. 87287 mom yes loop geom
#pair_style lj/cut 13.5
##pair_coeff 1 1 0.010323166 3.405 13.5
#pair_coeff 1 1 .238 3.405 13.5
neighbor 5. bin
neigh_modify every 10 delay 0 check no
# ID group atc PhysicsType ParameterFile
fix AtC internal atc thermal Ar_thermal.mat
# ID part keywords nx ny nz region
#fix_modify AtC fem create mesh 12 2 2 simRegion f p p
fix_modify AtC fem create mesh 4 1 1 mdInternal f p p
#fix_modify AtC mesh create_faceset ibndy box -4.0 4.0 -12 12 -12 12 in
#fix_modify AtC mesh create_faceset obndy box -4.0 4.0 -12 12 -12 12 outward
# specify atom types
#fix_modify AtC transfer internal type internal
#fix_modify AtC transfer boundary type ghost
# fix a temperature
fix_modify AtC transfer fix temperature all 20.
# turn on thermostat
fix_modify AtC transfer thermal control rescale 10
# equilibrate MD field
#dump D1 all atom 100 dump.bar1d
#fix_modify AtC transfer output bar1dfe 100
timestep 5
variable xdof equal 3*count(ghost)
compute_modify thermo_temp extra ${xdof}
thermo_style custom step cpu etotal pe f_AtC[1] temp f_AtC[2]
thermo_modify format 1 %6i format 2 %7.2g
thermo 100
run 400
# add nodesets
# ID mesh create_nodeset tag xmin xmax ymin ymax zmin zmax
fix_modify AtC mesh create_nodeset lbc -4.1 -3.9 -12 12 -12 12
fix_modify AtC mesh create_nodeset rbc 3.9 4.1 -12 12 -12 12
fix_modify AtC transfer fix temperature lbc 40.
fix_modify AtC transfer fix temperature rbc 20.
# initialize filter
#timestep 0.5
#fix_modify AtC transfer output bar1d_frac_stepFE 1
#thermo 1
run 400
# change thermostat to hoover
fix_modify AtC transfer pmfc
fix_modify AtC transfer unfix temperature all
fix_modify AtC transfer fix temperature lbc 40.
fix_modify AtC transfer fix temperature rbc 20.
# fix_modify AtC transfer thermal control none
#fix_modify AtC transfer thermal control hoover
fix_modify AtC transfer thermal control flux no_boundary
# #fix_modify AtC transfer thermal control flux interpolate
# #fix_modify AtC transfer thermal control flux faceset obndy
fix_modify AtC transfer filter type exponential
fix_modify AtC transfer filter scale 10000.0
#fix_modify AtC transfer filter on
fix_modify AtC transfer internal_quadrature off
# #fix_modify AtC transfer localized_lambda on
# set up output, should be before a "run"
fix_modify AtC transfer output bar1d_frac_stepFE 100 text
# ouput command
#dump D1 all atom 1000 dump.bar1d
fix_modify AtC transfer atomic_output bar1d_frac_stepMD 100
# run with FE
reset_timestep 0
thermo 100
run 10000

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