in.deposit.molecule
627fd232e947lammm-master-deprecated

in.deposit.molecule
View Options

			# sample surface deposition script for molecules

			units lj
			atom_style bond
			boundary p p f

			lattice fcc 1.0
			region box block 0 5 0 5 0 10
			create_box 3 box "bond types" 1 "extra bond per atom" 1

			region substrate block INF INF INF INF INF 3
			create_atoms 1 region substrate

			pair_style lj/cut 2.5
			pair_coeff * * 1.0 1.0
			pair_coeff 1 2 1.0 1.0 5.0
			mass * 1.0

			bond_style harmonic
			bond_coeff 1 5.0 1.0

			neigh_modify delay 0

			group addatoms type 2
			region mobile block 0 5 0 5 2 INF
			group mobile region mobile

			compute add addatoms temp
			compute_modify add dynamic yes extra 0

			fix 1 addatoms nve
			fix 2 mobile langevin 0.1 0.1 0.1 587283
			fix 3 mobile nve

			molecule dimer molecule.dimer
			region slab block 0 5 0 5 8 9
			fix 4 addatoms deposit 100 2 100 12345 region slab near 1.0 &
			mol dimer vz -1.0 -1.0
			fix 5 addatoms wall/reflect zhi EDGE

			thermo_style custom step atoms temp epair etotal press
			thermo 100
			thermo_modify temp add lost/bond ignore lost warn

			#dump 1 all atom 50 dump.deposit.atom

			#dump 1 all movie 50 image.*.jpg type type &
			# axes yes 0.8 0.02 view 80 -30
			#dump_modify 1 pad 5

			#dump 1 all movie 50 movie.mpg type type &
			# axes yes 0.8 0.02 view 80 -30
			#dump_modify 1 pad 5

			run 10000