154 lines
6.7 KiB
Groff
154 lines
6.7 KiB
Groff
LAMMPS (31 Jul 2019)
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using 1 OpenMP thread(s) per MPI task
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# 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
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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 gr_hBN_Cstack_2L_noH.data
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orthogonal box = (0 0 0) to (44.583 42.9 100)
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2 by 2 by 1 MPI processor grid
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reading atoms ...
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1440 atoms
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0 = max # of 1-2 neighbors
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0 = max # of 1-3 neighbors
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0 = max # of 1-4 neighbors
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1 = max # of special neighbors
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special bonds CPU = 0.00012207 secs
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read_data CPU = 0.00357461 secs
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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) | membrane
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mass 3 12.0107 # carbon mass (g/mole) | adsorbate
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# Separate atom groups
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group hBN molecule 1
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720 atoms in group hBN
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group gr molecule 2
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720 atoms in group gr
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######################## Potential defition ########################
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pair_style hybrid/overlay rebo tersoff ilp/graphene/hbn 16.0 coul/shield 16.0
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####################################################################
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pair_coeff * * rebo CH.rebo NULL NULL C # chemical
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Reading potential file CH.rebo with DATE: 2018-7-3
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pair_coeff * * tersoff BNC.tersoff B N NULL # chemical
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Reading potential file BNC.tersoff with DATE: 2013-03-21
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pair_coeff * * ilp/graphene/hbn BNCH.ILP B N C # long range
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pair_coeff 1 1 coul/shield 0.70
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pair_coeff 1 2 coul/shield 0.69498201415576216335
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pair_coeff 2 2 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 rebo
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compute 1 all pair tersoff
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compute 2 all pair ilp/graphene/hbn
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compute 3 all pair coul/shield
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variable REBO equal c_0
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variable Tersoff equal c_1
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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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variable Ecoul equal c_3
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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_REBO v_EILP v_Erep v_Evdw v_Ecoul temp
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###### Run molecular dynamics ######
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run 1000
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Neighbor list info ...
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update every 1 steps, delay 0 steps, check yes
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max neighbors/atom: 2000, page size: 100000
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master list distance cutoff = 18
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ghost atom cutoff = 18
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binsize = 9, bins = 5 5 12
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6 neighbor lists, perpetual/occasional/extra = 6 0 0
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(1) pair rebo, perpetual, skip from (3)
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attributes: full, newton on, ghost
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pair build: skip/ghost
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stencil: none
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bin: none
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(2) pair tersoff, perpetual, skip from (5)
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attributes: full, newton on
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pair build: skip
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stencil: none
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bin: none
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(3) pair ilp/graphene/hbn, perpetual
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attributes: full, newton on, ghost
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pair build: full/bin/ghost
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stencil: full/ghost/bin/3d
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bin: standard
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(4) pair coul/shield, perpetual, half/full from (2)
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attributes: half, newton on
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pair build: halffull/newton/skip
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stencil: none
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bin: none
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(5) neighbor class addition, perpetual, copy from (3)
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attributes: full, newton on
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pair build: copy
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stencil: none
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bin: none
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(6) neighbor class addition, perpetual, half/full from (5)
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attributes: half, newton on
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pair build: halffull/newton
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stencil: none
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bin: none
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Per MPI rank memory allocation (min/avg/max) = 12.45 | 12.45 | 12.45 Mbytes
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Step TotEng PotEng KinEng v_Evdw v_Tersoff v_REBO v_EILP v_Erep v_Evdw v_Ecoul Temp
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0 -10707.284 -10763.085 55.801605 -75.247726 -5401.7348 -5322.2781 -39.072409 36.175318 -75.247726 0 300
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100 -10707.074 -10737.127 30.05353 -73.217322 -5389.9568 -5309.2004 -37.970102 35.24722 -73.217322 0 161.57347
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200 -10707.016 -10734.932 27.91576 -71.603097 -5389.1294 -5307.7455 -38.056875 33.546222 -71.603097 0 150.08042
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300 -10707.013 -10734.987 27.973705 -75.082134 -5388.9196 -5308.1165 -37.950947 37.131186 -75.082134 0 150.39194
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400 -10707.012 -10735.498 28.486171 -76.339871 -5389.1657 -5308.153 -38.179442 38.160429 -76.339871 0 153.14706
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500 -10707.007 -10734.681 27.674101 -73.312354 -5388.7261 -5307.7384 -38.216944 35.09541 -73.312354 0 148.78121
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600 -10707.018 -10735.833 28.815132 -71.927763 -5389.0798 -5308.596 -38.157333 33.77043 -71.927763 0 154.91561
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700 -10707.02 -10735.656 28.635377 -74.679371 -5389.2971 -5308.1866 -38.172002 36.507368 -74.679371 0 153.94921
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800 -10707.004 -10734.352 27.347425 -76.371288 -5388.5923 -5307.7206 -38.038736 38.332552 -76.371288 0 147.02494
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900 -10707.014 -10735.832 28.817405 -73.699332 -5388.9674 -5308.7964 -38.068078 35.631254 -73.699332 0 154.92783
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1000 -10706.995 -10733.562 26.56615 -71.439868 -5388.0186 -5307.4414 -38.101452 33.338415 -71.439868 0 142.82466
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Loop time of 54.095 on 4 procs for 1000 steps with 1440 atoms
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Performance: 1.597 ns/day, 15.026 hours/ns, 18.486 timesteps/s
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84.8% CPU use with 4 MPI tasks x 1 OpenMP threads
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MPI task timing breakdown:
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Section | min time | avg time | max time |%varavg| %total
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---------------------------------------------------------------
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Pair | 42.138 | 45.531 | 49.106 | 42.0 | 84.17
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Bond | 0.0003159 | 0.00037384 | 0.000489 | 0.0 | 0.00
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Neigh | 0 | 0 | 0 | 0.0 | 0.00
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Comm | 4.71 | 8.2803 | 11.682 | 98.3 | 15.31
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Output | 0.0021999 | 0.0055975 | 0.013382 | 6.0 | 0.01
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Modify | 0.0092845 | 0.010981 | 0.012538 | 1.3 | 0.02
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Other | | 0.2673 | | | 0.49
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Nlocal: 360 ave 380 max 340 min
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Histogram: 2 0 0 0 0 0 0 0 0 2
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Nghost: 4716 ave 4736 max 4696 min
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Histogram: 2 0 0 0 0 0 0 0 0 2
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Neighs: 35100 ave 37050 max 33150 min
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Histogram: 2 0 0 0 0 0 0 0 0 2
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FullNghs: 70200 ave 74100 max 66300 min
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Histogram: 2 0 0 0 0 0 0 0 0 2
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Total # of neighbors = 280800
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Ave neighs/atom = 195
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Ave special neighs/atom = 0
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Neighbor list builds = 0
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Dangerous builds = 0
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Total wall time: 0:00:54
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