in.intel.rhodo
81879899299dlammm-master-deprecated

in.intel.rhodo
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			# Rhodopsin model

			variable w index 10 # Warmup Timesteps
			variable t index 520 # Main Run Timesteps
			variable m index 1 # Main Run Timestep Multiplier
			variable n index 0 # Use NUMA Mapping for Multi-Node
			variable b index 3 # Neighbor binsize
			variable p index 0 # Use Power Measurement
			variable c index 0 # 1 to use collectives for PPPM
			variable d index 1 # 1 to use 'diff ad' for PPPM

			variable x index 4
			variable y index 2
			variable z index 2

			variable rr equal floor($t*$m)
			variable root getenv LMP_ROOT

			if "$n > 0" then "processors * * * grid numa"

			units real
			neigh_modify delay 5 every 1 binsize $b

			atom_style full
			bond_style harmonic
			angle_style charmm
			dihedral_style charmm
			improper_style harmonic
			pair_style lj/charmm/coul/long 8.0 10.0
			pair_modify mix arithmetic
			kspace_style pppm 1e-4

			if "$c > 0" then "kspace_modify collective yes"
			if "$d > 0" then "kspace_modify diff ad"

			read_data ${root}/bench/data.rhodo

			replicate $x $y $z

			fix 1 all shake 0.0001 5 0 m 1.0 a 232
			fix 2 all npt temp 300.0 300.0 100.0 &
			z 0.0 0.0 1000.0 mtk no pchain 0 tchain 1

			special_bonds charmm

			thermo 100
			thermo_style multi
			timestep 2.0

			if "$p > 0" then "run_style verlet/power"

			if "$w > 0" then "run $w"
			run ${rr}