forked from lijiext/lammps
61 lines
2.1 KiB
Plaintext
61 lines
2.1 KiB
Plaintext
# Initialization
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units metal
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boundary p p p
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atom_style full
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processors * * 1 # domain decomposition over x and y
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# System and atom definition
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# we use 2 atom types so that inter- and intra-layer
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# interactions can be specified separately
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# read lammps data file
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read_data Bi_gr_AB_stack_2L_noH_300K.data
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mass 1 12.0107 # carbon mass (g/mole) | membrane
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mass 2 12.0107 # carbon mass (g/mole) | adsorbate
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# Separate atom groups
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group membrane type 1
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group adsorbate type 2
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######################## Potential defition ########################
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pair_style hybrid/overlay rebo kolmogorov/crespi/full 16.0
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####################################################################
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pair_coeff * * rebo CH.airebo NULL C # chemical
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pair_coeff * * kolmogorov/crespi/full CC.KC-full C C # long range
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####################################################################
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# Neighbor update settings
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neighbor 2.0 bin
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neigh_modify every 1
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neigh_modify delay 0
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neigh_modify check yes
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# calculate the COM
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variable adsxcom equal xcm(adsorbate,x)
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variable adsycom equal xcm(adsorbate,y)
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variable adszcom equal xcm(adsorbate,z)
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variable adsvxcom equal vcm(adsorbate,x)
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variable adsvycom equal vcm(adsorbate,y)
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variable adsvzcom equal vcm(adsorbate,z)
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#### Simulation settings ####
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timestep 0.001
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fix subf membrane setforce 0.0 0.0 0.0
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fix thermostat all nve
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compute 0 all pair rebo
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compute 1 all pair kolmogorov/crespi/full
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variable REBO equal c_0
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variable KC equal c_1
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############################
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# Output
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thermo 100
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thermo_style custom step etotal pe ke v_REBO v_KC temp v_adsxcom v_adsycom v_adszcom v_adsvxcom v_adsvycom v_adsvzcom
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thermo_modify line one format float %.10f
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thermo_modify flush yes norm no lost warn #ignore
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#dump 1 all custom 1000 traj.lammpstrj id mol type xu yu zu
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#dump_modify 1 format line "%7d %3d %3d %15.10g %15.10g %15.10g" flush yes
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###### Run molecular dynamics ######
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run 1000
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