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# Computes elastic waves propagating in and out of a finite temperature region
#AtC ThermoElastic Coupling
echo both
units real
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 5.2582305 origin 0.25 0.25 0.25
# NOTE following 3 lines added for restart
boundary f p p
pair_style lj/cut 13.
read_data temp.init
region simRegion block -12 12 -3 3 -3 3
# create atoms, NOTE commented out for restart
#region mdRegion block -8 8 -3 3 -3 3
#boundary f p p
#region mdBox block -9 9 -3 3 -3 3
#create_box 1 mdBox
#create_atoms 1 region mdRegion
#mass 1 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, NOTE next for lines commented out for restart
#velocity internal create 40. 87287 mom yes loop geom
#pair_style lj/cut 13.
##pair_coeff 1 1 0.010323166 3.405 13.
#pair_coeff 1 1 .2381 3.405 13.
neighbor 5. bin
neigh_modify every 10 delay 0 check no
#write_restart tinit.dat
# zero initial momentum
fix AtC internal atc elastic Ar_thermo_elastic.mat
# ID part keywords nx ny nz region
fix_modify AtC mesh create 12 1 1 simRegion f p p
fix_modify AtC mesh create_faceset obndy box -6.0 6.0 -INF INF -INF INF outward
fix_modify AtC internal_quadrature off
fix_modify AtC fix displacement x all 0.
fix_modify AtC fix displacement y all 0.
fix_modify AtC fix displacement z all 0.
fix_modify AtC fix velocity x all 0.
fix_modify AtC fix velocity y all 0.
fix_modify AtC fix velocity z all 0.
fix_modify AtC control momentum glc_velocity
#fix_modify AtC output bar1d_thermo_elastic_initializeFE 1 text #binary
timestep 0
thermo 1
run 1
unfix AtC
# define layer
# ID group atc PhysicsType ParameterFile
fix AtC internal atc thermo_elastic Ar_thermo_elastic.mat
fix_modify AtC boundary ghosts
# ID part keywords nx ny nz region
fix_modify AtC mesh create 12 1 1 simRegion f p p
fix_modify AtC mesh create_faceset obndy box -6.0 6.0 -INF INF -INF INF outward
fix_modify AtC internal_quadrature off
# initial conditions
fix_modify AtC initial displacement x all 0.0
fix_modify AtC fix displacement y all 0.0
fix_modify AtC fix displacement z all 0.0
fix_modify AtC initial velocity x all 0.0
fix_modify AtC fix velocity y all 0.0
fix_modify AtC fix velocity z all 0.0
fix_modify AtC fix temperature all 20.
# 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 0.
#fix_modify AtC fix displacement x rbc 0.
fix_modify AtC fix displacement x lbc 0.
fix_modify AtC fix velocity x lbc 0.
# rescale thermostat for initial atomic temperatures
fix_modify AtC control thermal rescale 10
fix_modify AtC control momentum ghost_flux
fix_modify AtC output bar1d_thermo_elasticFE 100 text #binary
timestep 5
thermo 100
run 1000
# free all nodes
#fix_modify AtC unfix displacement x all
#fix_modify AtC unfix velocity x all
fix_modify AtC unfix temperature all
# new boundary conditions
fix_modify AtC fix velocity x rbc 0.00000004
fix_modify AtC fix temperature lbc 20.
#fix_modify AtC output follow_ex.fe 50
#fix_modify AtC localized_lambda on
#fix_modify AtC momentum control glc_velocity
#fix_modify AtC momentum control flux faceset obndy
#fix_modify AtC control momentum flux
#fix_modify AtC control momentum ghost_flux
fix_modify AtC control thermal flux
#fix_modify AtC filter scale 1000.0
# run to extension
compute myTemp internal temp
compute atomStress internal stress/atom NULL
compute avgStress internal reduce sum c_atomStress[1] c_atomStress[2] c_atomStress[3]
variable myPres equal -(c_avgStress[1]+c_avgStress[2]+c_avgStress[3])/(3*vol)
thermo_style custom step c_myTemp v_myPres pe
fix_modify AtC output bar1d_thermo_elasticFE 500 text
#dump D1 all custom 100 bar1d_thermo_elastic.dmp id type x y z vx vy vz
timestep 5
thermo 100
run 1000
# change nodes to fixed
fix_modify AtC unfix velocity x rbc 0.
#fix_modify AtC fix displacement x rbc 0.0002
#fix_modify AtC output bar1d_fluxFE 500 text binary
# run to equilibrium
timestep 5
thermo 100
run 3000
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