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lammps/examples/USER/atc/elastic/in.bar1d_damped
1ca6fb0f8160lammm-master

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in.bar1d_damped
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# needs description
echo both
units metal
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)
lattice fcc 5.405 origin 0.25 0.25 0.25
# create atoms
region simRegion block -12 12 -3 3 -3 3
region atomRegion block -9 9 -3 3 -3 3
region mdRegion block -8 8 -3 3 -3 3
boundary f p p
create_box 2 simRegion
create_atoms 1 region mdRegion
mass * 39.95
# specify interal/ghost atoms
region mdInternal block -6 6 -3 3 -3 3
region leftghost block -8 -6 -3 3 -3 3
region rightghost block 6 8 -3 3 -3 3
group internal region mdInternal
group Lghost region leftghost
group Rghost region rightghost
group ghosts union Lghost Rghost
# velocities have Vcm = 0
#velocity internal create 40. 87287 mom yes loop geom
pair_style lj/cut 13.5
#pair_coeff * * .238 3.405 13.5
pair_coeff * * 0.010323166 3.405 13.5
neighbor 5. bin
neigh_modify every 10 delay 0 check no
# define layer
# ID group atc PhysicsType ParameterFile
fix AtC internal atc elastic Ar_damped.mat
# ID part keywords nx ny nz region
fix_modify AtC mesh create 12 1 1 simRegion f p p
# initial conditions
fix_modify AtC initial displacement x all 0.0
fix_modify AtC initial displacement y all 0.0
fix_modify AtC initial displacement z all 0.0
fix_modify AtC initial velocity x all 0.0
fix_modify AtC initial velocity y all 0.0
fix_modify AtC initial velocity z all 0.0
variable v equal 0.00000004e3
variable n equal 1000
variable dt equal 0.005
variable u equal $v*$n*${dt}
# set node sets and bcs
# ID mesh create_nodeset tag xmin xmax ymin ymax zmin zmax
fix_modify AtC mesh create_nodeset lbc -12.1 -11.9 -INF INF -INF INF
fix_modify AtC mesh create_nodeset rbc 11.9 12.1 -INF INF -INF INF
fix_modify AtC fix velocity x rbc $v
fix_modify AtC fix displacement x lbc 0.
fix_modify AtC fix velocity x lbc 0.
# specify atom types
fix_modify AtC boundary ghosts
#fix_modify AtC output follow_ex.fe 50
fix_modify AtC internal_quadrature off
fix_modify AtC control localized_lambda on
fix_modify AtC control momentum glc_velocity
#fix_modify AtC filter type exponential
#fix_modify AtC filter scale 1.0
#fix_modify AtC filter on
# run to extension
timestep 0.005
thermo 100
thermo_style custom step cpu ke pe
run 0
variable pe0 equal pe
variable pe equal pe-${pe0}
thermo_style custom step cpu ke pe v_pe f_AtC[1] f_AtC[2] f_AtC[4] f_AtC[5]
run $n
fix_modify AtC output bar1d_dampedFE 500 text
dump CONFIG all custom 500 bar1d_damped.dmp id type x y z vx vy vz
# change nodes to fixed
fix_modify AtC fix velocity x rbc 0.
fix_modify AtC fix displacement x rbc $u
# run to equilibrium
thermo 100
log bar1d_damped.log
run 2000
fix_modify AtC material all cubic # M damping
run 2000
fix_modify AtC material all damped # K damping
run 2000
# ATC: CB stiffness: 7.56717 Einstein freq: 0.355649 from Ar_CauchyBorn.mat
# real to metal 1 kcal/mol = 0.04336 eV
variable kCal2eV equal 0.04336
variable fconv equal 1./0.000103643 # NOTE old routine was doing calculations in lammps units, not atc units, so this conversion is necessary for bmark to pass
#variable k equal 1.e-3 # 7.56717*${kCal2eV} NOTE <<<
#variable k equal 0.75*0.355649e3*${kCal2eV}
variable k equal 0.5*39.95*${fconv} # NOTE it was set to above, should have been 2 above, but there was a bug so this value is here for bmark
#variable g equal 0.75*0.355649e3*${kCal2eV}
variable g equal 1.e-3*${fconv} # NOTE it should be above, but there was a bug so this value is here for bmark
variable m equal 2. #0.5*39.95
fix_modify AtC boundary_dynamics damped_harmonic $k $g $m
run 2000
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