101 lines
3.8 KiB
Groff
101 lines
3.8 KiB
Groff
LAMMPS (30 Nov 2020)
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OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:94)
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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 charge
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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-momolayer-5nm.data
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Reading data file ...
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orthogonal box = (0.0000000 0.0000000 0.0000000) to (46.152980 48.443364 100.00000)
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2 by 2 by 1 MPI processor grid
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reading atoms ...
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880 atoms
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read_data CPU = 0.007 seconds
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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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######################## Potential defition ########################
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pair_style tersoff shift 0.0
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pair_coeff * * BNC.tersoff B N
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Reading tersoff potential file BNC.tersoff with DATE: 2013-03-21
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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 loop geom
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fix thermostat all nve
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############# Output ###############
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thermo 100
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thermo_style custom step etotal pe ke 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 = 4.1
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ghost atom cutoff = 4.1
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binsize = 2.05, bins = 23 24 49
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1 neighbor lists, perpetual/occasional/extra = 1 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/atomonly
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stencil: full/bin/3d
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bin: standard
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Per MPI rank memory allocation (min/avg/max) = 3.297 | 3.297 | 3.297 Mbytes
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Step TotEng PotEng KinEng Temp
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0 -6517.7517 -6551.8376 34.0859 300
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100 -6517.5918 -6540.7795 23.187734 204.08204
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200 -6517.5423 -6546.3342 28.791974 253.4066
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300 -6517.547 -6552.0178 34.47074 303.38708
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400 -6517.5499 -6554.1682 36.618359 322.28891
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500 -6517.5482 -6553.3948 35.846598 315.49641
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600 -6517.5438 -6557.8044 40.260609 354.34542
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700 -6517.5489 -6554.8963 37.3474 328.70542
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800 -6517.5426 -6557.376 39.833345 350.58494
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900 -6517.5508 -6557.1115 39.560726 348.18554
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1000 -6517.5427 -6559.2989 41.756142 367.50804
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Loop time of 0.398907 on 4 procs for 1000 steps with 880 atoms
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Performance: 216.592 ns/day, 0.111 hours/ns, 2506.850 timesteps/s
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99.1% 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 | 0.32415 | 0.32873 | 0.33831 | 1.0 | 82.41
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Neigh | 0.003216 | 0.0032905 | 0.003397 | 0.1 | 0.82
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Comm | 0.050126 | 0.059974 | 0.064634 | 2.4 | 15.03
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Output | 0.0001 | 0.000131 | 0.000221 | 0.0 | 0.03
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Modify | 0.002423 | 0.0024955 | 0.002658 | 0.2 | 0.63
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Other | | 0.004282 | | | 1.07
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Nlocal: 220.000 ave 231 max 210 min
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Histogram: 1 0 0 1 0 1 0 0 0 1
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Nghost: 578.500 ave 590 max 572 min
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Histogram: 1 1 1 0 0 0 0 0 0 1
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Neighs: 0.00000 ave 0 max 0 min
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Histogram: 4 0 0 0 0 0 0 0 0 0
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FullNghs: 3965.00 ave 4169 max 3784 min
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Histogram: 1 0 0 1 0 1 0 0 0 1
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Total # of neighbors = 15860
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Ave neighs/atom = 18.022727
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Neighbor list builds = 15
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Dangerous builds = 0
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Total wall time: 0:00:00
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