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lammps/examples/USER/atc/thermal/in.bar1d_hoover
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# AtC Thermal Coupling
# This benchmark tests thermostats applied in all atom simulations. 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
log bar1d_hoover.log
# 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
#atom_modify sort 0 0
# 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
# switch depending on application of BCs or coupling
#variable nEls equal 6 # for boundary conditions
variable nEls equal 12 # for coupling
fix_modify AtC boundary ghost # for coupling
region atcRegion block -${nEls} ${nEls} -3 3 -3 3
fix_modify AtC mesh create ${nEls} 1 1 atcRegion 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
variable tol equal 0.1
variable uBnd equal ${nEls}+${tol}
variable lBnd equal ${nEls}-${tol}
fix_modify AtC mesh create_nodeset lbc -${uBnd} -${lBnd} -INF INF -INF INF
fix_modify AtC mesh create_nodeset rbc ${lBnd} ${uBnd} -INF INF -INF INF
# fix a temperature
fix_modify AtC fix temperature all 20.
#fix_modify AtC initial temperature all 20.
#fix_modify AtC consistent_fe_initialization on
# 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_hoover_init
#fix_modify AtC output bar1d_hoover_init 100 text binary
fix_modify AtC time_integration fractional_step
fix_modify AtC temperature_definition total
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
fix_modify AtC unfix temperature all
fix_modify AtC filter type exponential
fix_modify AtC filter scale 1000.0
fix_modify AtC filter on
# boundary conditions------------------------
# dirichlet with ramp (unstable when filtered due to instantaneous change in rate)
#fix_modify AtC fix temperature lbc temporal_ramp 20. 40. 25000.
#fix_modify AtC fix temperature rbc 20.
#fix_modify AtC localized_lambda on
#fix_modify AtC control thermal flux no_boundary
#fix_modify AtC output test_rampFE 200 text binary
#dump D1 all atom 200 dump.test_ramp
#reset_timestep 0
#fix_modify AtC reset_time
#thermo 100
#run 5000
#fix_modify AtC fix temperature lbc 40.
# dirichlet with rescaling
#fix_modify AtC filter off
#fix_modify AtC fix temperature all 20.
#fix_modify AtC fix temperature lbc 40.
#fix_modify AtC output test_rampFE 200 text binary
#dump D1 all atom 200 dump.test_ramp
#reset_timestep 0
#fix_modify AtC reset_time
#thermo 100
#run 1000
#fix_modify AtC unfix temperature all
#fix_modify AtC fix temperature lbc 40.
#fix_modify AtC fix temperature rbc 20.
#fix_modify AtC control thermal flux no_boundary
#fix_modify AtC localized_lambda on
#fix_modify AtC filter on
# neumann
#fix_modify AtC fix_flux temperature lbndy 0.0000000005
#fix_modify AtC fix_flux temperature rbndy -0.0000000005
#fix_modify AtC control thermal flux no_boundary
#fix_modify AtC lumped_lambda_solve on
# coupling------------------------------------
fix_modify AtC fix temperature lbc 40.
fix_modify AtC fix temperature rbc 20.
# flux
#fix_modify AtC control thermal flux interpolate
#fix_modify AtC control thermal flux faceset obndy
#fix_modify AtC lumped_lambda_solve on
# hoover
fix_modify AtC control thermal hoover
fix_modify AtC control localized_lambda on
fix_modify AtC control tolerance 1.e-14
fix_modify AtC output bar1d_hooverFE 200 text binary
#dump D1 all atom 200 dump.bar1d_hoover
reset_timestep 0
fix_modify AtC reset_time
thermo 100
run 5000
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