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lammps/examples/USER/atc/fluids/in.bar1d_fluids
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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.
log bar1d_fluids.log
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
#read_restart post_eq.dat
lattice fcc 5.405 origin 0.25 0.25 0.25
# create atoms, NOTE commented out for restart
#region mdRegion block -7 7 -3 3 -3 3
#boundary f p p
#create_box 2 mdRegion
#create_atoms 1 region mdRegion
#mass * 39.95
# specify interal/ghost atoms
#region mdInternal block -6 6 -3 3 -3 3
#region mdGhost block -6 6 -3 3 -3 3 side out
#create_atoms 1 region mdGhost
#lattice fcc 6.5 origin 0.25 0.25 0.25
#create_atoms 2 region mdInternal
group internal type 2
group ghost type 1
# velocities have Vcm = 0, NOTE next four lines commented out for restart
#velocity internal create 100. 87287 mom yes loop geom
#pair_style lj/cut 13.5
##pair_coeff 1 1 0.010323166 3.405 13.5
#pair_coeff * * .238 3.405 13.5
neighbor 5. bin
neigh_modify every 10 delay 0 check no
#write_restart tinit.dat
# ID group atc PhysicsType ParameterFile
lattice fcc 5.405 origin 0.25 0.25 0.25
region atcRegion block -6.25 6.25 -3 3 -3 3
fix AtC internal atc thermal Ar_thermal.mat
# ID part keywords nx ny nz region periodicity
fix_modify AtC mesh create 6 1 1 atcRegion f p p
fix_modify AtC time_integration fractional_step
fix_modify AtC atom_element_map eulerian 10 # NOTE this introduces a minor amount of time integration error tracking the atomic temperature
fix_modify AtC internal_quadrature off
#fix_modify AtC mass_matrix fe
# fix a temperature
fix_modify AtC fix temperature all 100.
# add nodesets
# ID mesh create_nodeset tag xmin xmax ymin ymax zmin zmax
fix_modify AtC mesh create_nodeset lbc -6.3 -6.2 -INF INF -INF INF
fix_modify AtC mesh create_nodeset rbc 6.2 6.3 -INF INF -INF INF
#fix_modify AtC fix temperature lbc 120.
#fix_modify AtC fix temperature rbc 100.
#used for restarting
#fix_modify AtC consistent_fe_initialization on
#fix_modify AtC initial temperature all 100.
# turn on thermostat
fix_modify AtC control thermal rescale 10
# equilibrate MD field
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
#fix_modify AtC output bar1d_fluids_eqFE 200 text binary
#dump D1 all atom 200 dump_eq.bar1d
timestep 2
thermo 200
run 2000
#write_restart post_eq.dat
# change thermostat to hoover
reset_timestep 0
fix_modify AtC reset_time
fix_modify AtC unfix temperature all
variable deltaT equal 2.*2000.
fix_modify AtC fix temperature lbc temporal_ramp 100. 120. ${deltaT}
#fix_modify AtC fix temperature lbc 100.
fix_modify AtC fix temperature rbc 100.
fix_modify AtC control thermal flux no_boundary
fix_modify AtC control tolerance 1.e-14
fix_modify AtC control localized_lambda on
fix_modify AtC filter type exponential
fix_modify AtC filter scale 1000.0
fix_modify AtC filter on
# ouput commands
fix_modify AtC output bar1d_fluidsFE 100 text
#undump D1
#dump D2 all atom 200 dump.bar1d
#dump D2 all custom 200 dump.bar1d id type xs ys zs vx vy vz
# set-up non-equilibrium IC
thermo 100
run 2000
# run non-equilibrium condition
fix_modify AtC fix temperature lbc 120.
run 4000
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