5fd323fe32
- flatten directory structure - remove CPU time and reduce excess precision from output - delete redundant and unused files - regenerate reference outputs
57 lines
2.1 KiB
Plaintext
57 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 different molecule ids for each layer of hBN
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# so that inter- and intra-layer
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# interactions can be specified separately
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read_data hBN_AA_prime_stack_2L_noH.data
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mass 1 10.8110 # boron mass (g/mole) | membrane
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mass 2 14.0067 # nitrogen mass (g/mole) | adsorbate
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mass 3 10.8110 # boron mass (g/mole) | membrane
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mass 4 14.0067 # nitrogen mass (g/mole) | adsorbate
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# Separate atom groups
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group layer1 molecule 1
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group layer2 molecule 2
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######################## Potential defition ########################
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pair_style hybrid/overlay tersoff ilp/graphene/hbn 16.0 coul/shield 16.0 1
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####################################################################
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pair_coeff * * tersoff BNC.tersoff B N B N # chemical
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pair_coeff * * ilp/graphene/hbn BNCH.ILP B N B N # long range
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pair_coeff 1 3 coul/shield 0.70
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pair_coeff 1 4 coul/shield 0.69498201415576216335
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pair_coeff 2 3 coul/shield 0.69498201415576216335
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pair_coeff 2 4 coul/shield 0.69
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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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#### Simulation settings ####
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timestep 0.001
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velocity all create 300.0 12345 dist gaussian mom yes rot yes
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fix thermostat all nve
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compute 0 all pair tersoff
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compute 1 all pair coul/shield ecoul
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compute 2 all pair ilp/graphene/hbn
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variable Tersoff equal c_0 # Tersoff energy
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variable Ecoul equal c_1 # Coulomb energy
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variable EILP equal c_2 # total interlayer energy
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variable Evdw equal c_2[1] # attractive energy
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variable Erep equal c_2[2] # repulsive energy
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############# Output ###############
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thermo 100
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thermo_style custom step etotal pe ke v_Evdw v_Tersoff v_EILP v_Erep v_Evdw v_Ecoul temp
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thermo_modify lost warn
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###### Run molecular dynamics ######
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run 1000
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