in.harmonic_bonds
9dd1fd29b218lammm-master-deprecated

in.harmonic_bonds
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			# run018 <017/tolammps.py -> input.lammps
			# T->0.3 harmonic->quartic
			# Np=900
			# f=6
			# dens = 0.80
			# rigid wall: none

			log harmonic_bonds.log
			echo both
			units lj
			lattice sc 1.0
			boundary p p p
			neighbor 1.0 bin
			neigh_modify every 5 delay 0 check yes

			atom_style full
			bond_style quartic
			#angle_style harmonic
			pair_style lj/cut 2.5
			pair_modify table 0
			special_bonds lj 1.0 1.0 1.0

			read_data harmonic_bonds.init

			# k b1 b2 rc U0
			bond_coeff 1 1434.3 -0.7589 0.00 1.5 67.2234
			pair_coeff * * 1.0 1.0 2.5

			timestep 0.005
			fix 1 all npt temp 0.3 0.3 1.0 iso 0.1 0.1 10.0
			thermo_style custom step temp etotal evdwl ebond pxx pyy pzz lz
			thermo_modify flush yes
			thermo 100
			reset_timestep 0


			########################################################################
			variable l equal xhi
			#region MESH block xlo xhi ylo yhi zlo zhi
			region MESH block -$l $l -$l $l -$l $l
			group MESH region MESH
			# ID group atc PhysicsType ParameterFile
			fix ATC all atc field
			fix_modify ATC fields add mass_density energy stress heat_flux
			# ID part keywords nx ny nz region
			fix_modify ATC mesh create 4 4 1 MESH p p p
			fix_modify ATC bond_interactions on
			fix_modify ATC pair_interactions off
			fix_modify ATC output nodeset all average energy
			fix_modify ATC output nodeset all average stress
			fix_modify ATC output harmonic_bondsFE 100 full_text binary tensor_components
			########################################################################

			dump d1 all custom 1000 config.dmp id type mol x y z ix iy iz
			run 1000