thylakoid.in
87e06310cb52lammm-master-deprecated

thylakoid.in
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			units lj
			dimension 3
			boundary f f p

			pair_style lj/cut 1.1225
			read_data thylakoid.data

			pair_coeff * * 1.0 1.0
			pair_modify shift yes

			# Makes about 100 particles type 2:
			region make_two sphere -29 0 0 6.25
			region everywhere block -25 25 -25 25 -25 25
			group two region make_two
			set group two type 2

			# And deletes some of type 1 to allow more movement:
			group one type 1
			set group one type 1
			delete_atoms porosity everywhere 0.2 123


			# Start run
			variable wB equal 5.0
			variable LB equal 10.0
			variable lB equal 3.0
			fix step all nve/manifold/rattle 1e-4 10 thylakoid ${wB} ${LB} ${lB}

			thermo_style custom time step pe ke etotal temp
			thermo 2500
			dump traj all custom 10000 thylakoid.dump id type x y z
			run 25000000