143 lines
6.2 KiB
Groff
143 lines
6.2 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 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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orthogonal box = (0 0 0) to (43.38 42.5773 100)
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2 by 2 by 1 MPI processor grid
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reading atoms ...
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1360 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 = 0.000224352 secs
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read_data CPU = 0.00160909 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) | 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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680 atoms in group layer1
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group layer2 molecule 2
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680 atoms in group layer2
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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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Reading potential file BNC.tersoff with DATE: 2013-03-21
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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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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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4 neighbor lists, perpetual/occasional/extra = 4 0 0
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(1) pair tersoff, perpetual
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attributes: full, newton on
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pair build: full/bin
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stencil: full/bin/3d
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bin: standard
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(2) 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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(3) pair coul/shield, perpetual, skip from (4)
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attributes: half, 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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(4) neighbor class addition, perpetual, half/full from (1)
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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) = 18.99 | 18.99 | 18.99 Mbytes
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Step TotEng PotEng KinEng v_Evdw v_Tersoff v_EILP v_Erep v_Evdw v_Ecoul Temp
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0 -10193.138 -10245.837 52.699361 -77.557069 -10208.73 -36.776483 40.780586 -77.557069 -0.33075117 300
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100 -10192.814 -10215.193 22.37957 -80.997619 -10177.878 -36.967736 44.029884 -80.997619 -0.34809915 127.39947
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200 -10192.922 -10221.807 28.884855 -86.370319 -10184.251 -37.168986 49.201334 -86.370319 -0.38644764 164.43191
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300 -10192.878 -10219.029 26.151464 -83.063924 -10182.349 -36.30412 46.759804 -83.063924 -0.37660157 148.87162
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400 -10192.892 -10218.834 25.942229 -78.394242 -10181.398 -37.110968 41.283274 -78.394242 -0.32494569 147.68051
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500 -10192.909 -10221.331 28.422213 -81.768531 -10184.03 -36.946226 44.822304 -81.768531 -0.35489965 161.79824
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600 -10192.886 -10219.371 26.48495 -86.278335 -10182.669 -36.29515 49.983185 -86.278335 -0.40636253 150.77004
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700 -10192.902 -10220.95 28.048108 -82.28873 -10183.208 -37.39374 44.89499 -82.28873 -0.34777958 159.66859
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800 -10192.88 -10218.51 25.630186 -78.011019 -10181.427 -36.754209 41.256811 -78.011019 -0.32904942 145.90415
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900 -10192.894 -10220.56 27.665437 -82.474379 -10183.801 -36.381157 46.093222 -82.474379 -0.37703328 157.49017
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1000 -10192.897 -10219.01 26.11313 -87.125683 -10181.252 -37.361898 49.763785 -87.125683 -0.39607952 148.65339
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Loop time of 68.3631 on 4 procs for 1000 steps with 1360 atoms
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Performance: 1.264 ns/day, 18.990 hours/ns, 14.628 timesteps/s
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98.5% 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 | 64.58 | 66.38 | 67.402 | 13.2 | 97.10
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Bond | 0.0001719 | 0.00021869 | 0.00024033 | 0.0 | 0.00
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Neigh | 0 | 0 | 0 | 0.0 | 0.00
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Comm | 0.93767 | 1.9601 | 3.76 | 77.0 | 2.87
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Output | 0.00033593 | 0.00061601 | 0.0014501 | 0.0 | 0.00
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Modify | 0.0085733 | 0.0089303 | 0.0093236 | 0.4 | 0.01
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Other | | 0.01285 | | | 0.02
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Nlocal: 340 ave 340 max 340 min
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Histogram: 4 0 0 0 0 0 0 0 0 0
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Nghost: 4536 ave 4536 max 4536 min
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Histogram: 4 0 0 0 0 0 0 0 0 0
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Neighs: 62390 ave 62390 max 62390 min
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Histogram: 4 0 0 0 0 0 0 0 0 0
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FullNghs: 251260 ave 251260 max 251260 min
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Histogram: 4 0 0 0 0 0 0 0 0 0
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Total # of neighbors = 1005040
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Ave neighs/atom = 739
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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: 0:01:08
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