forked from lijiext/lammps
81 lines
3.3 KiB
Plaintext
81 lines
3.3 KiB
Plaintext
#AtC Thermal Coupling
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# This benchmark tests heat conducting into and out of the MD region. The
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# temperature is initially 20 everywhere and the left boundary BC is fixed at
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# 40.# The result should show heat diffusing through the FEM to the MD and back
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# out # to the FEM on the right. Insufficient time is captured to reach the
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# linear # steady state, but heat crossing both boundaries should be observed.
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units real
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atom_style atomic
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# create domain
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#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)
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# NOTE following 3 lines added for restart
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boundary f p p
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pair_style lj/cut 13.5
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read_data temp.init
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lattice fcc 5.405 origin 0.25 0.25 0.25
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region simRegion block -12 12 -3 3 -3 3
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# create atoms, NOTE commented out for restart
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#region mdRegion block -5 5 -3 3 -3 3
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#boundary f p p
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#create_box 1 mdRegion
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#create_atoms 1 region mdRegion
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#mass 1 39.95
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# specify interal/ghost atoms
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region mdInternal block -4 4 -3 3 -3 3
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group internal region mdInternal
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group ghost subtract all internal
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# velocities have Vcm = 0, NOTE next four lines commented out for restart
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#velocity internal create 40. 87287 mom yes loop geom
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#pair_style lj/cut 13.5
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##pair_coeff 1 1 0.010323166 3.405 13.5
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#pair_coeff 1 1 .238 3.405 13.5
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neighbor 5. bin
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neigh_modify every 10 delay 0 check no
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# ID group atc PhysicsType ParameterFile
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fix AtC internal atc thermal Ar_thermal.mat
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# ID part keywords nx ny nz region
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fix_modify AtC mesh create 4 1 1 mdInternal f p p
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fix_modify AtC time_integration fractional_step
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fix_modify AtC internal_atom_integrate off
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fix iNVE internal nve
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fix_modify AtC internal_quadrature off
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# fix a temperature
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fix_modify AtC fix temperature all 20.
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# add nodesets
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# ID mesh create_nodeset tag xmin xmax ymin ymax zmin zmax
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fix_modify AtC mesh create_nodeset lbc -4.1 -3.9 -INF INF -INF INF
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fix_modify AtC mesh create_nodeset rbc 3.9 4.1 -INF INF -INF INF
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fix_modify AtC fix temperature lbc 40.
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fix_modify AtC fix temperature rbc 20.
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# turn on thermostat
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fix_modify AtC control thermal rescale 10
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# equilibrate MD field
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#dump D1 all atom 100 dump.bar1d
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#fix_modify AtC output bar1dfe 100 text
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timestep 5
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variable xdof equal 3*count(ghost)
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compute_modify thermo_temp extra ${xdof}
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thermo_style custom step cpu etotal pe f_AtC[1] temp f_AtC[2]
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thermo_modify format 1 %6i format 2 %7.2g
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thermo 100
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run 400
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# change thermostat to hoover
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fix_modify AtC unfix temperature all
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fix_modify AtC fix temperature lbc 40.
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fix_modify AtC fix temperature rbc 20.
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fix_modify AtC control thermal flux no_boundary
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fix_modify AtC control tolerance 1.e-9 # this is to remove looser benchmark tolerance because the lambda solution was reacting to numerical noise, but it results in a slight drift in the constraints
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#fix_modify AtC thermal control none
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fix_modify AtC control localized_lambda on
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fix_modify AtC filter type exponential
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fix_modify AtC filter scale 1000.0
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fix_modify AtC filter on
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# set up output, should be before a "run"
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fix_modify AtC output bar1d_frac_stepFE 200 text
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# ouput command
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#dump D1 all atom 1000 dump.bar1d
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# run with FE
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reset_timestep 0
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thermo 100
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run 10000
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