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in.bar1d_hoover
31b31f0a6ae6efficient_neuronet

in.bar1d_hoover
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			# AtC Thermal Coupling
			# This benchmark tests thermostats applied in all atom simulations. The
			# temperature is intially 20 everywhere and the left boundary BC is fixed at
			# 40.# The result should show heat diffusing through the FEM to the MD and back
			# out # to the FEM on the right. Insufficient time is captured to reach the
			# linear # steady state, but heat crossing both boundaries should be observed.
			units real
			atom_style atomic
			log bar1d_hoover.log
			# 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)
			# NOTE following 3 lines added for restart
			boundary f p p
			pair_style lj/cut 13.5
			read_data all_atoms.init
			lattice fcc 5.405 origin 0.25 0.25 0.25
			region simRegion block -7 7 -3 3 -3 3
			# create atoms, NOTE commented out for restart
			#boundary f p p
			#create_box 1 simRegion
			#create_atoms 1 region simRegion
			#mass 1 39.95
			#atom_modify sort 0 0
			# specify interal/ghost atoms
			region mdInternal block -6 6 -3 3 -3 3
			group internal region mdInternal
			group ghost subtract all internal
			# velocities have Vcm = 0, NOTE next four lines commented out for restart
			#velocity internal create 40. 87287 mom yes loop geom
			#pair_style lj/cut 13.5
			##pair_coeff 1 1 0.010323166 3.405 13.5
			#pair_coeff 1 1 .238 3.405 13.5
			#write_restart all_atoms.init
			neighbor 5. bin
			neigh_modify every 10 delay 0 check no
			# ID group atc PhysicsType ParameterFile
			fix AtC internal atc thermal Ar_thermal.mat
			# ID part keywords nx ny nz region

			# switch depending on application of BCs or coupling
			#variable nEls equal 6 # for boundary conditions
			variable nEls equal 12 # for coupling
			fix_modify AtC boundary ghost # for coupling

			region atcRegion block -${nEls} ${nEls} -3 3 -3 3
			fix_modify AtC mesh create ${nEls} 1 1 atcRegion f p p
			fix_modify AtC mesh create_faceset obndy box -6.0 6.0 -INF INF -INF INF outward
			fix_modify AtC mesh create_faceset lbndy box -6.0 16.0 -INF INF -INF INF outward
			fix_modify AtC mesh create_faceset rbndy box -16.0 6.0 -INF INF -INF INF outward
			variable tol equal 0.1
			variable uBnd equal ${nEls}+${tol}
			variable lBnd equal ${nEls}-${tol}
			fix_modify AtC mesh create_nodeset lbc -${uBnd} -${lBnd} -INF INF -INF INF
			fix_modify AtC mesh create_nodeset rbc ${lBnd} ${uBnd} -INF INF -INF INF
			# fix a temperature
			fix_modify AtC fix temperature all 20.
			#fix_modify AtC initial temperature all 20.
			#fix_modify AtC consistent_fe_initialization on
			# turn on thermostat
			fix_modify AtC control thermal rescale 10
			fix_modify AtC internal_quadrature off
			# equilibrate MD field
			#dump D1 all atom 100 dump.bar1d_hoover_init
			#fix_modify AtC output bar1d_hoover_init 100 text binary
			fix_modify AtC time_integration fractional_step
			fix_modify AtC temperature_definition total
			timestep 5
			variable xdof equal 3*count(ghost)
			compute_modify thermo_temp extra ${xdof}
			thermo_style custom step cpu etotal pe f_AtC[1] temp f_AtC[2]
			thermo_modify format 1 %6i format 2 %7.2g
			thermo 100
			run 400

			fix_modify AtC unfix temperature all

			fix_modify AtC filter type exponential
			fix_modify AtC filter scale 1000.0
			fix_modify AtC filter on


			# boundary conditions------------------------
			# dirichlet with ramp (unstable when filtered due to instantaneous change in rate)
			#fix_modify AtC fix temperature lbc temporal_ramp 20. 40. 25000.
			#fix_modify AtC fix temperature rbc 20.
			#fix_modify AtC localized_lambda on
			#fix_modify AtC control thermal flux no_boundary
			#fix_modify AtC output test_rampFE 200 text binary
			#dump D1 all atom 200 dump.test_ramp
			#reset_timestep 0
			#fix_modify AtC reset_time
			#thermo 100
			#run 5000
			#fix_modify AtC fix temperature lbc 40.

			# dirichlet with rescaling
			#fix_modify AtC filter off
			#fix_modify AtC fix temperature all 20.
			#fix_modify AtC fix temperature lbc 40.
			#fix_modify AtC output test_rampFE 200 text binary
			#dump D1 all atom 200 dump.test_ramp
			#reset_timestep 0
			#fix_modify AtC reset_time
			#thermo 100
			#run 1000
			#fix_modify AtC unfix temperature all
			#fix_modify AtC fix temperature lbc 40.
			#fix_modify AtC fix temperature rbc 20.
			#fix_modify AtC control thermal flux no_boundary
			#fix_modify AtC localized_lambda on
			#fix_modify AtC filter on

			# neumann
			#fix_modify AtC fix_flux temperature lbndy 0.0000000005
			#fix_modify AtC fix_flux temperature rbndy -0.0000000005
			#fix_modify AtC control thermal flux no_boundary
			#fix_modify AtC lumped_lambda_solve on

			# coupling------------------------------------
			fix_modify AtC fix temperature lbc 40.
			fix_modify AtC fix temperature rbc 20.

			# flux
			#fix_modify AtC control thermal flux interpolate
			#fix_modify AtC control thermal flux faceset obndy
			#fix_modify AtC lumped_lambda_solve on

			# hoover
			fix_modify AtC control thermal hoover
			fix_modify AtC control localized_lambda on

			fix_modify AtC control tolerance 1.e-14
			fix_modify AtC output bar1d_hooverFE 200 text binary
			#dump D1 all atom 200 dump.bar1d_hoover
			reset_timestep 0
			fix_modify AtC reset_time
			thermo 100
			run 5000

lammps/examples/USER/atc/thermal/in.bar1d_hoover31b31f0a6ae6efficient_neuronet

in.bar1d_hooverView Options

lammps/examples/USER/atc/thermal/in.bar1d_hoover
31b31f0a6ae6efficient_neuronet

in.bar1d_hoover
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