in.gaussianIC1d_hex
6297a32d9b46lammm-master-deprecated

in.gaussianIC1d_hex
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			echo both
			units real
			atom_style atomic

			lattice fcc 5.405 origin 0.25 0.25 0.25
			region mdRegion block -12 12 -3 3 -3 3
			region mdInternal block -10 10 -3 3 -3 3

			# create atoms
			boundary f p p
			create_box 1 mdRegion
			create_atoms 1 region mdRegion
			mass 1 39.95
			pair_style lj/cut 13.5
			pair_coeff 1 1 .238 3.405 13.5

			# specify interal/ghost atoms
			group internal region mdInternal
			velocity internal create 40 87287 mom yes loop geom # <<< NOTE

			neighbor 5. bin
			neigh_modify every 10 delay 0 check no

			# ID group atc PhysicsType ParameterFile
			fix AtC internal atc two_temperature Ar_ttm.mat

			fix_modify AtC mesh read gaussianIC1d_hex.mesh

			# fix a temperature
			fix_modify AtC fix temperature all 20.0
			fix_modify AtC initial temperature all 20.0
			fix_modify AtC initial electron_temperature all gaussian 0 0 0 1 0 0 5 20 20
			fix_modify AtC fix electron_temperature all gaussian 0 0 0 1 0 0 5 20 20

			# turn on thermostat
			fix_modify AtC extrinsic exchange off
			fix_modify AtC control thermal rescale 10

			# equilibrate MD field
			timestep 5.0
			thermo 10

			#output
			fix_modify AtC output gaussianIC1d_hexFE 10 text

			# change thermostat
			fix_modify AtC unfix temperature all
			fix_modify AtC unfix electron_temperature all
			fix_modify AtC control thermal flux
			fix_modify AtC extrinsic exchange on
			fix_modify AtC extrinsic electron_integration explicit 10

			# run with FE
			thermo_style custom step temp pe f_AtC[2] f_AtC[4]
			reset_timestep 0
			run 100 # 400