102 lines
4.2 KiB
Groff
102 lines
4.2 KiB
Groff
LAMMPS (24 Dec 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-monolayer-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 = 0.010 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 0.05
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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 4928459 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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thermo_modify line one format float %20.16g 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 -6570.525999324095 -6604.611899560595 34.08590023650001 300.0000000000001
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100 -6570.310828576847 -6584.788128201208 14.47729962436078 127.4189579026416
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200 -6570.372315727983 -6587.981402302948 17.60908657496569 154.9827329140874
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300 -6570.341402414288 -6587.005611017607 16.66420860331862 146.6665849019371
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400 -6570.373381655087 -6587.81207434018 17.43869268509319 153.4830463396659
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500 -6570.357279692746 -6587.139105628339 16.78182593559348 147.7017695219013
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600 -6570.364533408483 -6588.199043380885 17.83450997240217 156.9667503160549
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700 -6570.362000654081 -6587.514376495217 17.15237584113621 150.9630878644276
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800 -6570.358394689017 -6587.200486866481 16.84209217746396 148.2321903831871
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900 -6570.372035122433 -6588.096861613309 17.72482649087623 156.001393842279
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1000 -6570.355748883587 -6587.399428461678 17.0436795780913 150.0064201898988
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Loop time of 0.32051 on 4 procs for 1000 steps with 880 atoms
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Performance: 269.571 ns/day, 0.089 hours/ns, 3120.030 timesteps/s
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97.8% 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 | 0.24483 | 0.26461 | 0.28741 | 2.9 | 82.56
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Neigh | 0 | 0 | 0 | 0.0 | 0.00
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Comm | 0.026425 | 0.049039 | 0.068616 | 6.8 | 15.30
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Output | 0.000126 | 0.00016475 | 0.000248 | 0.0 | 0.05
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Modify | 0.002472 | 0.002794 | 0.002933 | 0.4 | 0.87
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Other | | 0.003905 | | | 1.22
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Nlocal: 220.000 ave 241 max 199 min
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Histogram: 1 0 0 0 1 1 0 0 0 1
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Nghost: 563.000 ave 583 max 543 min
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Histogram: 1 0 0 0 1 1 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: 3960.00 ave 4338 max 3582 min
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Histogram: 1 0 0 0 1 1 0 0 0 1
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Total # of neighbors = 15840
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Ave neighs/atom = 18.000000
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Neighbor list builds = 0
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Dangerous builds = 0
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Total wall time: 0:00:00
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