5fd323fe32
- flatten directory structure - remove CPU time and reduce excess precision from output - delete redundant and unused files - regenerate reference outputs
52 lines
1.6 KiB
Plaintext
52 lines
1.6 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 Bi_gr_AB_stack_2L_noH.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 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 rebo ilp/graphene/hbn 16.0
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####################################################################
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pair_coeff * * rebo CH.rebo C C # chemical
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pair_coeff * * ilp/graphene/hbn BNCH.ILP 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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#### Simulation settings ####
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timestep 0.001
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velocity all create 300.0 12345
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compute 0 all pair rebo
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compute 1 all pair ilp/graphene/hbn
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variable REBO equal c_0 # REBO energy
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variable ILP equal c_1 # total interlayer energy
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variable Evdw equal c_1[1] # attractive energy
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variable Erep equal c_1[2] # repulsive energy
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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_ILP v_Erep v_Evdw temp
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thermo_modify lost warn
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###### Run molecular dynamics ######
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fix thermostat all nve
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run 1000
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