renormalize line endings. add .gitattributes to configure them explicitly
This commit is contained in:
Axel Kohlmeyer
@ -1,56 +1,56 @@
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echo both
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units real
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atom_style atomic
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lattice fcc 5.405 origin 0.25 0.25 0.25
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region mdRegion block -12 12 -3 3 -3 3
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region mdInternal block -10 10 -3 3 -3 3
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# create atoms
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boundary f p p
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create_box 1 mdRegion
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create_atoms 1 region mdRegion
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mass 1 39.95
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pair_style lj/cut 13.5
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pair_coeff 1 1 .238 3.405 13.5
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# specify interal/ghost atoms
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group internal region mdInternal
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velocity internal create 40 87287 mom yes loop geom # <<< NOTE
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neighbor 5. bin
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neigh_modify every 10 delay 0 check no
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# ID group atc PhysicsType ParameterFile
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fix AtC internal atc two_temperature Ar_ttm.mat
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fix_modify AtC mesh read gaussianIC1d_hex.mesh
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# fix a temperature
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fix_modify AtC fix temperature all 20.0
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fix_modify AtC initial temperature all 20.0
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fix_modify AtC initial electron_temperature all gaussian 0 0 0 1 0 0 5 20 20
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fix_modify AtC fix electron_temperature all gaussian 0 0 0 1 0 0 5 20 20
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# turn on thermostat
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fix_modify AtC extrinsic exchange off
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fix_modify AtC control thermal rescale 10
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# equilibrate MD field
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timestep 5.0
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thermo 10
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#output
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fix_modify AtC output gaussianIC1d_hexFE 10 text
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# change thermostat
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fix_modify AtC unfix temperature all
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fix_modify AtC unfix electron_temperature all
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fix_modify AtC control thermal flux
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fix_modify AtC extrinsic exchange on
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fix_modify AtC extrinsic electron_integration explicit 10
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# run with FE
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thermo_style custom step temp pe f_AtC[2] f_AtC[4]
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reset_timestep 0
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run 100 # 400
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echo both
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units real
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atom_style atomic
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lattice fcc 5.405 origin 0.25 0.25 0.25
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region mdRegion block -12 12 -3 3 -3 3
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region mdInternal block -10 10 -3 3 -3 3
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# create atoms
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boundary f p p
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create_box 1 mdRegion
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create_atoms 1 region mdRegion
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mass 1 39.95
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pair_style lj/cut 13.5
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pair_coeff 1 1 .238 3.405 13.5
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# specify interal/ghost atoms
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group internal region mdInternal
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velocity internal create 40 87287 mom yes loop geom # <<< NOTE
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neighbor 5. bin
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neigh_modify every 10 delay 0 check no
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# ID group atc PhysicsType ParameterFile
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fix AtC internal atc two_temperature Ar_ttm.mat
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fix_modify AtC mesh read gaussianIC1d_hex.mesh
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# fix a temperature
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fix_modify AtC fix temperature all 20.0
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fix_modify AtC initial temperature all 20.0
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fix_modify AtC initial electron_temperature all gaussian 0 0 0 1 0 0 5 20 20
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fix_modify AtC fix electron_temperature all gaussian 0 0 0 1 0 0 5 20 20
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# turn on thermostat
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fix_modify AtC extrinsic exchange off
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fix_modify AtC control thermal rescale 10
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# equilibrate MD field
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timestep 5.0
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thermo 10
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#output
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fix_modify AtC output gaussianIC1d_hexFE 10 text
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# change thermostat
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fix_modify AtC unfix temperature all
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fix_modify AtC unfix electron_temperature all
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fix_modify AtC control thermal flux
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fix_modify AtC extrinsic exchange on
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fix_modify AtC extrinsic electron_integration explicit 10
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# run with FE
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thermo_style custom step temp pe f_AtC[2] f_AtC[4]
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reset_timestep 0
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run 100 # 400
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@ -1,69 +1,69 @@
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echo both
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units real
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atom_style atomic
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variable L equal 12
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variable l2 equal 6
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variable l equal 4
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variable w equal 2
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lattice fcc 5.405 origin 0.25 0.25 0.25
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region mdRegion cylinder z 0. 0. ${l2} -$w $w
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region mdInternal cylinder z 0. 0. $l -$w $w
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boundary f f f
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pair_style lj/cut 13.5
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read_data circle_temp.init
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fix ZWALLS all wall/reflect zlo EDGE zhi EDGE
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mass 1 39.95
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pair_coeff 1 1 .238 3.405 13.5
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group internal region mdInternal
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group ghost subtract all internal
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fix AtC internal atc two_temperature Ar_ttm.mat
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# computational geometry
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fix_modify AtC mesh read gaussianIC2d_hex.mesh
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#fix_modify AtC mesh read gaussianIC2d_hex.exo
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#fix_modify AtC mesh read gaussianIC2d_hex2.exo
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#fix_modify AtC mesh read gaussianIC2d_hex2.mesh
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fix_modify AtC mesh write parsed_gaussianIC2d_hex.mesh
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fix_modify AtC mesh output gaussianIC2d_hexMESH
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fix_modify AtC boundary ghost
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# numerical parameters
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fix_modify AtC time_integration fractional_step
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fix_modify AtC internal_quadrature off
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# initial conditions
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fix_modify AtC fix temperature all 20.0
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# NOTE this is only gaussian in x
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fix_modify AtC fix electron_temperature all gaussian 0 0 0 1 0 0 5 20 20
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# thermostat
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fix_modify AtC control thermal rescale 10
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fix_modify AtC extrinsic exchange off
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# run to equilibrate
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thermo_style custom step temp pe f_AtC[2] f_AtC[4]
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timestep 1.0
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thermo 10
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run 400
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# boundary conditions
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fix_modify AtC unfix temperature all
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fix_modify AtC unfix electron_temperature all
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fix_modify AtC fix temperature 11 20.0
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fix_modify AtC fix temperature 12 20.0
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# numerical parameters
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fix_modify AtC extrinsic electron_integration explicit 10
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# thermostat
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fix_modify AtC control thermal flux
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fix_modify AtC extrinsic exchange on
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# output
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fix_modify AtC output gaussianIC2d_hexFE 10 full_text binary
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dump D1 all atom 10 gaussianIC2d_hex.dmp
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# relax the system
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run 1000
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echo both
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units real
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atom_style atomic
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||||
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variable L equal 12
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variable l2 equal 6
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variable l equal 4
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variable w equal 2
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lattice fcc 5.405 origin 0.25 0.25 0.25
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region mdRegion cylinder z 0. 0. ${l2} -$w $w
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region mdInternal cylinder z 0. 0. $l -$w $w
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boundary f f f
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pair_style lj/cut 13.5
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read_data circle_temp.init
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fix ZWALLS all wall/reflect zlo EDGE zhi EDGE
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mass 1 39.95
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pair_coeff 1 1 .238 3.405 13.5
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group internal region mdInternal
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group ghost subtract all internal
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fix AtC internal atc two_temperature Ar_ttm.mat
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# computational geometry
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fix_modify AtC mesh read gaussianIC2d_hex.mesh
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#fix_modify AtC mesh read gaussianIC2d_hex.exo
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#fix_modify AtC mesh read gaussianIC2d_hex2.exo
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#fix_modify AtC mesh read gaussianIC2d_hex2.mesh
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fix_modify AtC mesh write parsed_gaussianIC2d_hex.mesh
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fix_modify AtC mesh output gaussianIC2d_hexMESH
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fix_modify AtC boundary ghost
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# numerical parameters
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fix_modify AtC time_integration fractional_step
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fix_modify AtC internal_quadrature off
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# initial conditions
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fix_modify AtC fix temperature all 20.0
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# NOTE this is only gaussian in x
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fix_modify AtC fix electron_temperature all gaussian 0 0 0 1 0 0 5 20 20
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# thermostat
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fix_modify AtC control thermal rescale 10
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fix_modify AtC extrinsic exchange off
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# run to equilibrate
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thermo_style custom step temp pe f_AtC[2] f_AtC[4]
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timestep 1.0
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thermo 10
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run 400
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# boundary conditions
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fix_modify AtC unfix temperature all
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fix_modify AtC unfix electron_temperature all
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fix_modify AtC fix temperature 11 20.0
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fix_modify AtC fix temperature 12 20.0
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# numerical parameters
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fix_modify AtC extrinsic electron_integration explicit 10
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# thermostat
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fix_modify AtC control thermal flux
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fix_modify AtC extrinsic exchange on
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# output
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fix_modify AtC output gaussianIC2d_hexFE 10 full_text binary
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dump D1 all atom 10 gaussianIC2d_hex.dmp
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# relax the system
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run 1000
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@ -1,37 +1,37 @@
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echo both
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units real
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atom_style atomic
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variable L equal 12
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variable l2 equal 6
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variable l equal 4
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variable w equal 2
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lattice fcc 5.405 origin 0.25 0.25 0.25
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region mdInternal block -$l $l -$l $l -$w $w
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||||
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boundary f f f # p
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pair_style lj/cut 13.5
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read_data temp.init
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fix ZWALLS all wall/reflect zlo EDGE zhi EDGE
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mass 1 39.95
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||||
pair_coeff 1 1 .238 3.405 13.5
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group internal region mdInternal
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||||
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||||
fix AtC internal atc two_temperature Ar_ttm.mat
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fix_modify AtC mesh read gaussianIC2d_hex20_uniform.mesh
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fix_modify AtC output gaussianIC2d_hex20_uniformFE 10 full_text
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||||
fix_modify AtC initial temperature all 20.0
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||||
# NOTE this is only gaussian in x
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fix_modify AtC initial electron_temperature all gaussian 0 0 0 1 0 0 5 20 20
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||||
fix_modify AtC fix temperature 11 20.0
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||||
fix_modify AtC fix temperature 12 20.0
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||||
fix_modify AtC control thermal flux
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||||
fix_modify AtC extrinsic exchange on
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||||
fix_modify AtC extrinsic electron_integration explicit 10
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||||
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||||
thermo_style custom step temp pe f_AtC[2] f_AtC[4]
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||||
timestep 1.0
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||||
thermo 10
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run 100
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||||
echo both
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units real
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||||
atom_style atomic
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||||
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||||
variable L equal 12
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||||
variable l2 equal 6
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||||
variable l equal 4
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||||
variable w equal 2
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||||
|
||||
lattice fcc 5.405 origin 0.25 0.25 0.25
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||||
region mdInternal block -$l $l -$l $l -$w $w
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||||
|
||||
boundary f f f # p
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||||
pair_style lj/cut 13.5
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||||
read_data temp.init
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||||
fix ZWALLS all wall/reflect zlo EDGE zhi EDGE
|
||||
mass 1 39.95
|
||||
pair_coeff 1 1 .238 3.405 13.5
|
||||
group internal region mdInternal
|
||||
|
||||
fix AtC internal atc two_temperature Ar_ttm.mat
|
||||
fix_modify AtC mesh read gaussianIC2d_hex20_uniform.mesh
|
||||
fix_modify AtC output gaussianIC2d_hex20_uniformFE 10 full_text
|
||||
|
||||
fix_modify AtC initial temperature all 20.0
|
||||
# NOTE this is only gaussian in x
|
||||
fix_modify AtC initial electron_temperature all gaussian 0 0 0 1 0 0 5 20 20
|
||||
fix_modify AtC fix temperature 11 20.0
|
||||
fix_modify AtC fix temperature 12 20.0
|
||||
fix_modify AtC control thermal flux
|
||||
fix_modify AtC extrinsic exchange on
|
||||
fix_modify AtC extrinsic electron_integration explicit 10
|
||||
|
||||
thermo_style custom step temp pe f_AtC[2] f_AtC[4]
|
||||
timestep 1.0
|
||||
thermo 10
|
||||
run 100
|
||||
|
||||
@ -1,37 +1,37 @@
|
||||
echo both
|
||||
units real
|
||||
atom_style atomic
|
||||
|
||||
variable L equal 12
|
||||
variable l2 equal 6
|
||||
variable l equal 4
|
||||
variable w equal 2
|
||||
|
||||
lattice fcc 5.405 origin 0.25 0.25 0.25
|
||||
region mdInternal block -$l $l -$l $l -$w $w
|
||||
|
||||
boundary f f f # p
|
||||
pair_style lj/cut 13.5
|
||||
read_data temp.init
|
||||
fix ZWALLS all wall/reflect zlo EDGE zhi EDGE
|
||||
mass 1 39.95
|
||||
pair_coeff 1 1 .238 3.405 13.5
|
||||
group internal region mdInternal
|
||||
|
||||
fix AtC internal atc two_temperature Ar_ttm.mat
|
||||
fix_modify AtC mesh read gaussianIC2d_hex27_uniform.mesh
|
||||
fix_modify AtC output gaussianIC2d_hex27_uniformFE 10 full_text
|
||||
|
||||
fix_modify AtC initial temperature all 20.0
|
||||
# NOTE this is only gaussian in x
|
||||
fix_modify AtC initial electron_temperature all gaussian 0 0 0 1 0 0 5 20 20
|
||||
fix_modify AtC fix temperature 11 20.0
|
||||
fix_modify AtC fix temperature 12 20.0
|
||||
fix_modify AtC control thermal flux
|
||||
fix_modify AtC extrinsic exchange on
|
||||
fix_modify AtC extrinsic electron_integration explicit 10
|
||||
|
||||
thermo_style custom step temp pe f_AtC[2] f_AtC[4]
|
||||
timestep 1.0
|
||||
thermo 10
|
||||
run 100
|
||||
echo both
|
||||
units real
|
||||
atom_style atomic
|
||||
|
||||
variable L equal 12
|
||||
variable l2 equal 6
|
||||
variable l equal 4
|
||||
variable w equal 2
|
||||
|
||||
lattice fcc 5.405 origin 0.25 0.25 0.25
|
||||
region mdInternal block -$l $l -$l $l -$w $w
|
||||
|
||||
boundary f f f # p
|
||||
pair_style lj/cut 13.5
|
||||
read_data temp.init
|
||||
fix ZWALLS all wall/reflect zlo EDGE zhi EDGE
|
||||
mass 1 39.95
|
||||
pair_coeff 1 1 .238 3.405 13.5
|
||||
group internal region mdInternal
|
||||
|
||||
fix AtC internal atc two_temperature Ar_ttm.mat
|
||||
fix_modify AtC mesh read gaussianIC2d_hex27_uniform.mesh
|
||||
fix_modify AtC output gaussianIC2d_hex27_uniformFE 10 full_text
|
||||
|
||||
fix_modify AtC initial temperature all 20.0
|
||||
# NOTE this is only gaussian in x
|
||||
fix_modify AtC initial electron_temperature all gaussian 0 0 0 1 0 0 5 20 20
|
||||
fix_modify AtC fix temperature 11 20.0
|
||||
fix_modify AtC fix temperature 12 20.0
|
||||
fix_modify AtC control thermal flux
|
||||
fix_modify AtC extrinsic exchange on
|
||||
fix_modify AtC extrinsic electron_integration explicit 10
|
||||
|
||||
thermo_style custom step temp pe f_AtC[2] f_AtC[4]
|
||||
timestep 1.0
|
||||
thermo 10
|
||||
run 100
|
||||
|
||||
@ -1,40 +1,40 @@
|
||||
echo both
|
||||
units real
|
||||
atom_style atomic
|
||||
|
||||
variable L equal 12
|
||||
variable l2 equal 6
|
||||
variable l equal 4
|
||||
variable w equal 2
|
||||
|
||||
lattice fcc 5.405 origin 0.25 0.25 0.25
|
||||
region mdInternal block -$l $l -$l $l -$w $w
|
||||
|
||||
boundary f f f # p
|
||||
pair_style lj/cut 13.5
|
||||
read_data temp.init
|
||||
fix ZWALLS all wall/reflect zlo EDGE zhi EDGE
|
||||
mass 1 39.95
|
||||
pair_coeff 1 1 .238 3.405 13.5
|
||||
group internal region mdInternal
|
||||
|
||||
fix AtC internal atc two_temperature Ar_ttm.mat
|
||||
fix_modify AtC mesh read gaussianIC2d_tet.mesh
|
||||
#fix_modify AtC mesh read gaussianIC2d_tet.exo
|
||||
fix_modify AtC mesh write parsed_gaussianIC2d_tet.mesh
|
||||
fix_modify AtC mesh output parsed_gaussianIC2d_tetMESH
|
||||
fix_modify AtC output gaussianIC2d_tetFE 10 full_text
|
||||
|
||||
fix_modify AtC initial temperature all 20.0
|
||||
# NOTE this is only gaussian in x
|
||||
fix_modify AtC initial electron_temperature all gaussian 0 0 0 1 0 0 5 20 20
|
||||
fix_modify AtC fix temperature 11 20.0
|
||||
fix_modify AtC fix temperature 12 20.0
|
||||
fix_modify AtC control thermal flux
|
||||
fix_modify AtC extrinsic exchange on
|
||||
fix_modify AtC extrinsic electron_integration explicit 10
|
||||
|
||||
thermo_style custom step temp pe f_AtC[2] f_AtC[4]
|
||||
timestep 1.0
|
||||
thermo 10
|
||||
run 100
|
||||
echo both
|
||||
units real
|
||||
atom_style atomic
|
||||
|
||||
variable L equal 12
|
||||
variable l2 equal 6
|
||||
variable l equal 4
|
||||
variable w equal 2
|
||||
|
||||
lattice fcc 5.405 origin 0.25 0.25 0.25
|
||||
region mdInternal block -$l $l -$l $l -$w $w
|
||||
|
||||
boundary f f f # p
|
||||
pair_style lj/cut 13.5
|
||||
read_data temp.init
|
||||
fix ZWALLS all wall/reflect zlo EDGE zhi EDGE
|
||||
mass 1 39.95
|
||||
pair_coeff 1 1 .238 3.405 13.5
|
||||
group internal region mdInternal
|
||||
|
||||
fix AtC internal atc two_temperature Ar_ttm.mat
|
||||
fix_modify AtC mesh read gaussianIC2d_tet.mesh
|
||||
#fix_modify AtC mesh read gaussianIC2d_tet.exo
|
||||
fix_modify AtC mesh write parsed_gaussianIC2d_tet.mesh
|
||||
fix_modify AtC mesh output parsed_gaussianIC2d_tetMESH
|
||||
fix_modify AtC output gaussianIC2d_tetFE 10 full_text
|
||||
|
||||
fix_modify AtC initial temperature all 20.0
|
||||
# NOTE this is only gaussian in x
|
||||
fix_modify AtC initial electron_temperature all gaussian 0 0 0 1 0 0 5 20 20
|
||||
fix_modify AtC fix temperature 11 20.0
|
||||
fix_modify AtC fix temperature 12 20.0
|
||||
fix_modify AtC control thermal flux
|
||||
fix_modify AtC extrinsic exchange on
|
||||
fix_modify AtC extrinsic electron_integration explicit 10
|
||||
|
||||
thermo_style custom step temp pe f_AtC[2] f_AtC[4]
|
||||
timestep 1.0
|
||||
thermo 10
|
||||
run 100
|
||||
|
||||
@ -1,32 +1,32 @@
|
||||
echo both
|
||||
units real
|
||||
atom_style atomic
|
||||
|
||||
# correct mass density = 1.0120
|
||||
# NOTE the mesh is not currently periodic, so the density estimate is off by a factor of 2
|
||||
|
||||
variable L equal 6
|
||||
variable w equal 2
|
||||
|
||||
lattice fcc 5.405 origin 0.25 0.25 0.25
|
||||
region BOX block -$L $L -$L $L -$w $w
|
||||
|
||||
boundary f f p
|
||||
create_box 1 BOX
|
||||
create_atoms 1 region BOX
|
||||
mass 1 39.95
|
||||
pair_style lj/cut 13.5
|
||||
pair_coeff 1 1 .238 3.405 13.5
|
||||
group internal region BOX
|
||||
|
||||
fix AtC internal atc hardy
|
||||
fix_modify AtC kernel quartic_cylinder 5.0
|
||||
fix_modify AtC mesh read gaussianIC2d_hex.mesh
|
||||
fix_modify AtC fields add mass_density
|
||||
fix_modify AtC output kernel2d_hexFE 1 full_text binary
|
||||
#dump CONFIG all custom 1 kernel2d_hexMD.dmp id type x y z
|
||||
|
||||
thermo_style custom step cpu temp
|
||||
timestep 0.0
|
||||
thermo 1
|
||||
run 2
|
||||
echo both
|
||||
units real
|
||||
atom_style atomic
|
||||
|
||||
# correct mass density = 1.0120
|
||||
# NOTE the mesh is not currently periodic, so the density estimate is off by a factor of 2
|
||||
|
||||
variable L equal 6
|
||||
variable w equal 2
|
||||
|
||||
lattice fcc 5.405 origin 0.25 0.25 0.25
|
||||
region BOX block -$L $L -$L $L -$w $w
|
||||
|
||||
boundary f f p
|
||||
create_box 1 BOX
|
||||
create_atoms 1 region BOX
|
||||
mass 1 39.95
|
||||
pair_style lj/cut 13.5
|
||||
pair_coeff 1 1 .238 3.405 13.5
|
||||
group internal region BOX
|
||||
|
||||
fix AtC internal atc hardy
|
||||
fix_modify AtC kernel quartic_cylinder 5.0
|
||||
fix_modify AtC mesh read gaussianIC2d_hex.mesh
|
||||
fix_modify AtC fields add mass_density
|
||||
fix_modify AtC output kernel2d_hexFE 1 full_text binary
|
||||
#dump CONFIG all custom 1 kernel2d_hexMD.dmp id type x y z
|
||||
|
||||
thermo_style custom step cpu temp
|
||||
timestep 0.0
|
||||
thermo 1
|
||||
run 2
|
||||
|
||||
@ -1,28 +1,28 @@
|
||||
echo both
|
||||
units real
|
||||
atom_style atomic
|
||||
|
||||
variable L equal 6
|
||||
variable w equal 2
|
||||
|
||||
lattice fcc 5.405 origin 0.25 0.25 0.25
|
||||
region BOX block -$L $L -$L $L -$w $w
|
||||
|
||||
boundary f f p
|
||||
create_box 1 BOX
|
||||
create_atoms 1 region BOX
|
||||
mass 1 39.95
|
||||
pair_style lj/cut 13.5
|
||||
pair_coeff 1 1 .238 3.405 13.5
|
||||
group internal region BOX
|
||||
|
||||
fix AtC internal atc hardy
|
||||
fix_modify AtC kernel quartic_sphere 5.0
|
||||
fix_modify AtC mesh read gaussianIC2d_tet.mesh
|
||||
fix_modify AtC fields add mass_density
|
||||
fix_modify AtC output kernel2d_tetFE 1 full_text binary
|
||||
|
||||
thermo_style custom step cpu temp
|
||||
timestep 0.0
|
||||
thermo 1
|
||||
run 2
|
||||
echo both
|
||||
units real
|
||||
atom_style atomic
|
||||
|
||||
variable L equal 6
|
||||
variable w equal 2
|
||||
|
||||
lattice fcc 5.405 origin 0.25 0.25 0.25
|
||||
region BOX block -$L $L -$L $L -$w $w
|
||||
|
||||
boundary f f p
|
||||
create_box 1 BOX
|
||||
create_atoms 1 region BOX
|
||||
mass 1 39.95
|
||||
pair_style lj/cut 13.5
|
||||
pair_coeff 1 1 .238 3.405 13.5
|
||||
group internal region BOX
|
||||
|
||||
fix AtC internal atc hardy
|
||||
fix_modify AtC kernel quartic_sphere 5.0
|
||||
fix_modify AtC mesh read gaussianIC2d_tet.mesh
|
||||
fix_modify AtC fields add mass_density
|
||||
fix_modify AtC output kernel2d_tetFE 1 full_text binary
|
||||
|
||||
thermo_style custom step cpu temp
|
||||
timestep 0.0
|
||||
thermo 1
|
||||
run 2
|
||||
|
||||
@ -1,29 +1,29 @@
|
||||
echo both
|
||||
units real
|
||||
atom_style atomic
|
||||
|
||||
variable L equal 6
|
||||
variable w equal 2
|
||||
|
||||
lattice fcc 5.405 origin 0.25 0.25 0.25
|
||||
region BOX block -$L $L -$L $L -$w $w
|
||||
|
||||
boundary f f p
|
||||
create_box 1 BOX
|
||||
create_atoms 1 region BOX
|
||||
mass 1 39.95
|
||||
pair_style lj/cut 13.5
|
||||
pair_coeff 1 1 .238 3.405 13.5
|
||||
group internal region BOX
|
||||
|
||||
fix AtC internal atc field
|
||||
fix_modify AtC mesh read gaussianIC2d_tet.mesh
|
||||
fix_modify AtC fields add mass_density
|
||||
fix_modify AtC output mesh2d_tetFE 1 full_text binary
|
||||
|
||||
dump CONFIG all custom 10 mesh2d_tet.dmp id type x y z
|
||||
|
||||
thermo_style custom step cpu temp
|
||||
timestep 0.0
|
||||
thermo 1
|
||||
run 2
|
||||
echo both
|
||||
units real
|
||||
atom_style atomic
|
||||
|
||||
variable L equal 6
|
||||
variable w equal 2
|
||||
|
||||
lattice fcc 5.405 origin 0.25 0.25 0.25
|
||||
region BOX block -$L $L -$L $L -$w $w
|
||||
|
||||
boundary f f p
|
||||
create_box 1 BOX
|
||||
create_atoms 1 region BOX
|
||||
mass 1 39.95
|
||||
pair_style lj/cut 13.5
|
||||
pair_coeff 1 1 .238 3.405 13.5
|
||||
group internal region BOX
|
||||
|
||||
fix AtC internal atc field
|
||||
fix_modify AtC mesh read gaussianIC2d_tet.mesh
|
||||
fix_modify AtC fields add mass_density
|
||||
fix_modify AtC output mesh2d_tetFE 1 full_text binary
|
||||
|
||||
dump CONFIG all custom 10 mesh2d_tet.dmp id type x y z
|
||||
|
||||
thermo_style custom step cpu temp
|
||||
timestep 0.0
|
||||
thermo 1
|
||||
run 2
|
||||
|
||||
@ -1,101 +1,101 @@
|
||||
# this input can be used to generate the benchmark for in.gaussianIC2d_hex_uniform
|
||||
echo both
|
||||
units real
|
||||
atom_style atomic
|
||||
|
||||
variable l equal 8
|
||||
variable g equal 2
|
||||
variable lg equal $l+$g
|
||||
variable w equal 2
|
||||
|
||||
lattice fcc 5.405 origin 0.25 0.25 0.25
|
||||
boundary f f f
|
||||
|
||||
# region to create atoms
|
||||
region bigCyl cylinder z 0. 0. ${lg} -$w $w
|
||||
region offsetPlane block -${lg} $g -${lg} ${lg} -$w $w
|
||||
region mdRegion intersect 2 bigCyl offsetPlane
|
||||
#create_box 1 mdRegion
|
||||
pair_style lj/cut 13.5
|
||||
read_data semicircle.init
|
||||
|
||||
# region for internal atoms
|
||||
region mdInternalCyl cylinder z 0. 0. $l -$w $w
|
||||
region leftHalfPlane block INF 0. INF INF INF INF
|
||||
region mdInternal intersect 2 mdInternalCyl leftHalfPlane
|
||||
|
||||
# region for coupling ghosts
|
||||
region rightHalfPlane block 0. INF INF INF INF INF
|
||||
region mdGhost union 2 rightHalfPlane mdInternal side out
|
||||
|
||||
#create_atoms 1 region mdRegion
|
||||
#create_atoms 1 region mdInternal
|
||||
#create_atoms 2 region mdGhost
|
||||
#region outerGhost intersect 2 rightHalfPlane mdRegion
|
||||
#create_atoms 3 region outerGhost
|
||||
|
||||
#pair_style lj/cut 13.5
|
||||
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 region mdGhost
|
||||
#velocity internal create 40 102486 mom yes rot yes dist gaussian
|
||||
#write_restart semicircle_init.rst
|
||||
|
||||
# ATC commands
|
||||
fix AtC internal atc thermal Ar_ttm.mat
|
||||
fix_modify AtC boundary ghost
|
||||
fix_modify AtC mesh read semicircle.mesh f f p
|
||||
fix_modify AtC mesh nodeset_to_elementset 2 hole min
|
||||
fix_modify AtC internal_quadrature off
|
||||
fix_modify AtC time_integration fractional_step
|
||||
|
||||
# initial conditions
|
||||
fix_modify AtC fix temperature all 20.
|
||||
fix_modify AtC control thermal rescale 10
|
||||
fix_modify AtC control tolerance 1.e-14 # tolerance needed to produce consistent parallel and serial results
|
||||
|
||||
# initial output
|
||||
#fix_modify AtC mesh output semicircle_mesh
|
||||
#fix_modify AtC output semicircle_init 100 text binary
|
||||
#dump D1 all atom 100 semicircle_init.dmp
|
||||
|
||||
# run
|
||||
timestep 5.0
|
||||
thermo 100
|
||||
run 500
|
||||
|
||||
# boundary conditions
|
||||
fix_modify AtC unfix temperature all
|
||||
fix_modify AtC fix temperature 1 20.
|
||||
fix_modify AtC control thermal flux
|
||||
fix_modify AtC control localized_lambda on
|
||||
|
||||
# NOTE appears to be a problem with the temporal ramp function
|
||||
variable delta_t equal 1000*5.
|
||||
fix_modify AtC source temperature hole temporal_ramp 0. 0.0000000001 ${delta_t}
|
||||
|
||||
# equilibrate filter
|
||||
fix_modify AtC filter type exponential
|
||||
fix_modify AtC filter scale 1000.
|
||||
fix_modify AtC filter on
|
||||
|
||||
# equilibration output
|
||||
fix_modify AtC output semicircleFE 100 full_text #binary
|
||||
#undump D1
|
||||
#dump D1 all atom 100 semicircle_equil.dmp
|
||||
|
||||
# run
|
||||
fix_modify AtC reset_time 0.
|
||||
reset_timestep 0
|
||||
thermo 100
|
||||
run 1000
|
||||
|
||||
# heat source
|
||||
# NOTE second run omitted as it causes diffs in parallel execution after just one timestep, not sure why
|
||||
#fix_modify AtC source temperature hole 0.0000000001
|
||||
#fix_modify AtC output semicircleFE 1 full_text #binary
|
||||
#undump D1
|
||||
#dump D1 all atom 100 semicircle.dmp
|
||||
#run 1#000
|
||||
# this input can be used to generate the benchmark for in.gaussianIC2d_hex_uniform
|
||||
echo both
|
||||
units real
|
||||
atom_style atomic
|
||||
|
||||
variable l equal 8
|
||||
variable g equal 2
|
||||
variable lg equal $l+$g
|
||||
variable w equal 2
|
||||
|
||||
lattice fcc 5.405 origin 0.25 0.25 0.25
|
||||
boundary f f f
|
||||
|
||||
# region to create atoms
|
||||
region bigCyl cylinder z 0. 0. ${lg} -$w $w
|
||||
region offsetPlane block -${lg} $g -${lg} ${lg} -$w $w
|
||||
region mdRegion intersect 2 bigCyl offsetPlane
|
||||
#create_box 1 mdRegion
|
||||
pair_style lj/cut 13.5
|
||||
read_data semicircle.init
|
||||
|
||||
# region for internal atoms
|
||||
region mdInternalCyl cylinder z 0. 0. $l -$w $w
|
||||
region leftHalfPlane block INF 0. INF INF INF INF
|
||||
region mdInternal intersect 2 mdInternalCyl leftHalfPlane
|
||||
|
||||
# region for coupling ghosts
|
||||
region rightHalfPlane block 0. INF INF INF INF INF
|
||||
region mdGhost union 2 rightHalfPlane mdInternal side out
|
||||
|
||||
#create_atoms 1 region mdRegion
|
||||
#create_atoms 1 region mdInternal
|
||||
#create_atoms 2 region mdGhost
|
||||
#region outerGhost intersect 2 rightHalfPlane mdRegion
|
||||
#create_atoms 3 region outerGhost
|
||||
|
||||
#pair_style lj/cut 13.5
|
||||
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 region mdGhost
|
||||
#velocity internal create 40 102486 mom yes rot yes dist gaussian
|
||||
#write_restart semicircle_init.rst
|
||||
|
||||
# ATC commands
|
||||
fix AtC internal atc thermal Ar_ttm.mat
|
||||
fix_modify AtC boundary ghost
|
||||
fix_modify AtC mesh read semicircle.mesh f f p
|
||||
fix_modify AtC mesh nodeset_to_elementset 2 hole min
|
||||
fix_modify AtC internal_quadrature off
|
||||
fix_modify AtC time_integration fractional_step
|
||||
|
||||
# initial conditions
|
||||
fix_modify AtC fix temperature all 20.
|
||||
fix_modify AtC control thermal rescale 10
|
||||
fix_modify AtC control tolerance 1.e-14 # tolerance needed to produce consistent parallel and serial results
|
||||
|
||||
# initial output
|
||||
#fix_modify AtC mesh output semicircle_mesh
|
||||
#fix_modify AtC output semicircle_init 100 text binary
|
||||
#dump D1 all atom 100 semicircle_init.dmp
|
||||
|
||||
# run
|
||||
timestep 5.0
|
||||
thermo 100
|
||||
run 500
|
||||
|
||||
# boundary conditions
|
||||
fix_modify AtC unfix temperature all
|
||||
fix_modify AtC fix temperature 1 20.
|
||||
fix_modify AtC control thermal flux
|
||||
fix_modify AtC control localized_lambda on
|
||||
|
||||
# NOTE appears to be a problem with the temporal ramp function
|
||||
variable delta_t equal 1000*5.
|
||||
fix_modify AtC source temperature hole temporal_ramp 0. 0.0000000001 ${delta_t}
|
||||
|
||||
# equilibrate filter
|
||||
fix_modify AtC filter type exponential
|
||||
fix_modify AtC filter scale 1000.
|
||||
fix_modify AtC filter on
|
||||
|
||||
# equilibration output
|
||||
fix_modify AtC output semicircleFE 100 full_text #binary
|
||||
#undump D1
|
||||
#dump D1 all atom 100 semicircle_equil.dmp
|
||||
|
||||
# run
|
||||
fix_modify AtC reset_time 0.
|
||||
reset_timestep 0
|
||||
thermo 100
|
||||
run 1000
|
||||
|
||||
# heat source
|
||||
# NOTE second run omitted as it causes diffs in parallel execution after just one timestep, not sure why
|
||||
#fix_modify AtC source temperature hole 0.0000000001
|
||||
#fix_modify AtC output semicircleFE 1 full_text #binary
|
||||
#undump D1
|
||||
#dump D1 all atom 100 semicircle.dmp
|
||||
#run 1#000
|
||||
|
||||
Reference in New Issue
Block a user