forked from lijiext/lammps
117 lines
3.8 KiB
Plaintext
117 lines
3.8 KiB
Plaintext
# needs description
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echo both
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units metal
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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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lattice fcc 5.405 origin 0.25 0.25 0.25
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# create atoms
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region simRegion block -12 12 -3 3 -3 3
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region atomRegion block -9 9 -3 3 -3 3
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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 simRegion
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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 leftghost block -8 -6 -3 3 -3 3
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region rightghost block 6 8 -3 3 -3 3
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group internal region mdInternal
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group Lghost region leftghost
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group Rghost region rightghost
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group ghosts union Lghost Rghost
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# velocities have Vcm = 0
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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 * * .238 3.405 13.5
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pair_coeff * * 0.010323166 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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# define layer
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# ID group atc PhysicsType ParameterFile
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fix AtC internal atc elastic Ar_damped.mat
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# ID part keywords nx ny nz region
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fix_modify AtC mesh create 12 1 1 simRegion f p p
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# initial conditions
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fix_modify AtC initial displacement x all 0.0
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fix_modify AtC initial displacement y all 0.0
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fix_modify AtC initial displacement z all 0.0
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fix_modify AtC initial velocity x all 0.0
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fix_modify AtC initial velocity y all 0.0
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fix_modify AtC initial velocity z all 0.0
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variable v equal 0.00000004e3
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variable n equal 1000
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variable dt equal 0.005
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variable u equal $v*$n*${dt}
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# set node sets and bcs
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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 -12.1 -11.9 -INF INF -INF INF
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fix_modify AtC mesh create_nodeset rbc 11.9 12.1 -INF INF -INF INF
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fix_modify AtC fix velocity x rbc $v
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fix_modify AtC fix displacement x lbc 0.
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fix_modify AtC fix velocity x lbc 0.
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# specify atom types
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fix_modify AtC boundary ghosts
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#fix_modify AtC output follow_ex.fe 50
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fix_modify AtC internal_quadrature off
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fix_modify AtC control localized_lambda on
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fix_modify AtC control momentum glc_velocity
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#fix_modify AtC filter type exponential
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#fix_modify AtC filter scale 1.0
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#fix_modify AtC filter on
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# run to extension
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timestep 0.005
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thermo 100
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thermo_style custom step cpu ke pe
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run 0
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variable pe0 equal pe
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variable pe equal pe-${pe0}
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thermo_style custom step cpu ke pe v_pe f_AtC[1] f_AtC[2] f_AtC[4] f_AtC[5]
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run $n
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fix_modify AtC output bar1d_dampedFE 500 text
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dump CONFIG all custom 500 bar1d_damped.dmp id type x y z vx vy vz
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# change nodes to fixed
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fix_modify AtC fix velocity x rbc 0.
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fix_modify AtC fix displacement x rbc $u
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# run to equilibrium
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thermo 100
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log bar1d_damped.log
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run 2000
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fix_modify AtC material all cubic # M damping
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run 2000
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fix_modify AtC material all damped # K damping
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run 2000
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# ATC: CB stiffness: 7.56717 Einstein freq: 0.355649 from Ar_CauchyBorn.mat
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# real to metal 1 kcal/mol = 0.04336 eV
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variable kCal2eV equal 0.04336
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variable fconv equal 1./0.000103643 # NOTE old routine was doing calculations in lammps units, not atc units, so this conversion is necessary for bmark to pass
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#variable k equal 1.e-3 # 7.56717*${kCal2eV} NOTE <<<
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#variable k equal 0.75*0.355649e3*${kCal2eV}
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variable k equal 0.5*39.95*${fconv} # NOTE it was set to above, should have been 2 above, but there was a bug so this value is here for bmark
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#variable g equal 0.75*0.355649e3*${kCal2eV}
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variable g equal 1.e-3*${fconv} # NOTE it should be above, but there was a bug so this value is here for bmark
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variable m equal 2. #0.5*39.95
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fix_modify AtC boundary_dynamics damped_harmonic $k $g $m
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run 2000
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