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lammps/examples/USER/atc/thermal/in.bar1d_all_atoms
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#AtC Thermal Coupling
# This benchmark tests thermostats applied in all atom simulations. The
# temperature is initially 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 all_atoms.init
lattice fcc 5.405 origin 0.25 0.25 0.25
region simRegion block -7 7 -3 3 -3 3
# create atoms, NOTE commented out for restart
#boundary f p p
#create_box 1 simRegion
#create_atoms 1 region simRegion
#mass 1 39.95
# specify interal/ghost atoms
region mdInternal block -6 6 -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
#write_restart all_atoms.init
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 mesh create 6 1 1 mdInternal f p p
fix_modify AtC mesh create_faceset obndy box -6.0 6.0 -INF INF -INF INF outward
fix_modify AtC mesh create_faceset lbndy box -6.0 16.0 -INF INF -INF INF outward
fix_modify AtC mesh create_faceset rbndy box -16.0 6.0 -INF INF -INF INF outward
# fix a temperature
fix_modify AtC fix temperature all 20.
# turn on thermostat
fix_modify AtC control thermal rescale 10
fix_modify AtC internal_quadrature off
# equilibrate MD field
#dump D1 all atom 100 dump.bar1d
#fix_modify AtC output bar1dfe 100
#fix_modify AtC time_integration frac_step
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
# change thermostat to hoover
fix_modify AtC control thermal hoover
#fix_modify AtC thermal control flux interpolate
#fix_modify AtC thermal control flux faceset obndy
fix_modify AtC filter scale 1000.0
#fix_modify AtC filter equilibrate
#fix_modify AtC filter on
#fix_modify AtC localized_lambda on
fix_modify AtC boundary_faceset is obndy
# initialize filter
#fix_modify AtC output bar1d_all_atoms_preqFE 1
reset_timestep 0
thermo 1
#run 5000
# add nodesets and ramp temperature
# ID mesh create_nodeset tag xmin xmax ymin ymax zmin zmax
#fix_modify AtC mesh create_nodeset lbc -6.1 -5.9 -INF INF -INF INF
#fix_modify AtC mesh create_nodeset rbc 5.9 6.1 -INF INF -INF INF
#fix_modify AtC fix temperature lbc temporal_ramp 20. 40. 25000.
#fix_modify AtC fix temperature rbc 20.
# initialize filter
#fix_modify AtC output bar1d_all_atoms_eqFE 200
reset_timestep 0
fix_modify AtC reset_time
#run 5000
# release and let run
#fix_modify AtC filter on
fix_modify AtC unfix temperature all
#fix_modify AtC localized_lambda on
fix_modify AtC control lumped_lambda_solve on
# dirichlet boundaries
#fix_modify AtC fix temperature lbc 40.
#fix_modify AtC fix temperature rbc 20.
# neumann boundaries
fix_modify AtC control thermal flux no_boundary
fix_modify AtC fix_flux temperature lbndy 0.0000000001
fix_modify AtC fix_flux temperature rbndy -0.0000000001
# set up output, should be before a "run"
fix_modify AtC output bar1d_all_atomsFE 200 text binary
# ouput command
#dump D1 all atom 1000 dump.bar1d
# run with FE
reset_timestep 0
thermo 200
run 5000
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