forked from lijiext/lammps
85 lines
3.1 KiB
Plaintext
85 lines
3.1 KiB
Plaintext
#AtC Mechanical Coupling
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# This benchmark tests momentum flux as a BC to the MD region to generate shear flow.
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# Currently heat will be generated as it will have no where to go.
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log shear_flow.log
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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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read_data post_eq.init
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lattice fcc 5.405 origin 0.25 0.25 0.25
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# create atoms, NOTE commented out for restart
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#region mdRegion block -8 8 -3 3 -3 3
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#boundary f p p
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#create_box 2 mdRegion
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#create_atoms 1 region mdRegion
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#mass * 39.95
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# specify interal/ghost atoms
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#region mdInternal block -6 6 -3 3 -3 3
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#region mdGhost block -6 6 -3 3 -3 3 side out
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#create_atoms 1 region mdGhost
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#lattice fcc 6.5 origin 0.25 0.25 0.25
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#create_atoms 2 region mdInternal
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group internal type 2
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group ghost type 1
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# velocities have Vcm = 0, NOTE next four lines commented out for restart
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#velocity internal create 100. 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 * * .238 3.405 13.5
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#write_restart tinit.dat
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neighbor 5. bin
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neigh_modify every 10 delay 0 check no
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# equilibrate MD field
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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 temp
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thermo_modify format 1 %6i format 2 %7.2g
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#fix NVT internal nvt temp 100 100 10 drag 0.2
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#dump D1 all atom 200 shear_flow_init.dmp
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timestep 2
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#thermo 200
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#run 2000
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#write_restart post_eq.dat
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# ID group atc PhysicsType ParameterFile
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lattice fcc 5.405 origin 0.25 0.25 0.25
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region atcRegion block -6.25 6.25 -3 3 -3 3
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fix AtC internal atc shear Ar_viscosity.mat
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# ID part keywords nx ny nz region periodicity
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fix_modify AtC mesh create 6 1 1 atcRegion f p p
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#fix_modify AtC time_integration fractional_step
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##fix_modify AtC atom_element_map eulerian 10 # NOTE this introduces a minor amount of time integration error tracking the atomic temperature
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fix_modify AtC internal_quadrature off
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#fix_modify AtC mass_matrix fe
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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_elementset rbc 4.12 6.3 -INF INF -INF INF
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#used for restarting
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fix_modify AtC consistent_fe_initialization on
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#fix_modify AtC initial velocity x all 0.
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# turn on kinetostat
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reset_timestep 0
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fix_modify AtC reset_time
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fix_modify AtC source velocity y rbc .0000001
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fix_modify AtC control momentum flux no_boundary
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fix_modify AtC control tolerance 1.e-14
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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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# ouput commands
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fix_modify AtC output shear_flowFE 100 text #binary
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#undump D1
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#dump D1 all custom 100 shear_flow.dmp id type xs ys zs vx vy vz
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# set-up non-equilibrium IC
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thermo 100
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run 2000
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