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echo both
units real
atom_style atomic
variable L equal 12
variable l2 equal 6
variable l equal 4
variable w equal 2
lattice fcc 5.405 origin 0.25 0.25 0.25
region mdRegion cylinder z 0. 0. ${l2} -$w $w
region mdInternal cylinder z 0. 0. $l -$w $w
boundary f f f
pair_style lj/cut 13.5
read_data circle_temp.init
fix ZWALLS all wall/reflect zlo EDGE zhi EDGE
mass 1 39.95
pair_coeff 1 1 .238 3.405 13.5
group internal region mdInternal
group ghost subtract all internal
fix AtC internal atc two_temperature Ar_ttm.mat
# computational geometry
fix_modify AtC mesh read gaussianIC2d_hex.mesh
#fix_modify AtC mesh read gaussianIC2d_hex.exo
#fix_modify AtC mesh read gaussianIC2d_hex2.exo
#fix_modify AtC mesh read gaussianIC2d_hex2.mesh
fix_modify AtC mesh write parsed_gaussianIC2d_hex.mesh
fix_modify AtC mesh output gaussianIC2d_hexMESH
fix_modify AtC boundary ghost
# numerical parameters
fix_modify AtC time_integration fractional_step
fix_modify AtC internal_quadrature off
# initial conditions
fix_modify AtC fix temperature all 20.0
# NOTE this is only gaussian in x
fix_modify AtC fix electron_temperature all gaussian 0 0 0 1 0 0 5 20 20
# thermostat
fix_modify AtC control thermal rescale 10
fix_modify AtC extrinsic exchange off
# run to equilibrate
thermo_style custom step temp pe f_AtC[2] f_AtC[4]
timestep 1.0
thermo 10
run 400
# boundary conditions
fix_modify AtC unfix temperature all
fix_modify AtC unfix electron_temperature all
fix_modify AtC fix temperature 11 20.0
fix_modify AtC fix temperature 12 20.0
# numerical parameters
fix_modify AtC extrinsic electron_integration explicit 10
# thermostat
fix_modify AtC control thermal flux
fix_modify AtC extrinsic exchange on
# output
fix_modify AtC output gaussianIC2d_hexFE 10 full_text binary
dump D1 all atom 10 gaussianIC2d_hex.dmp
# relax the system
run 1000
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