forked from lijiext/lammps
106 lines
4.9 KiB
Groff
106 lines
4.9 KiB
Groff
LAMMPS (28 Mar 2023 - Development)
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using 1 OpenMP thread(s) per MPI task
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#Carbon SNAP example: 216 atom diamond unit cell simulated NVT at ~1,000GPa and 5,000K
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units metal
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atom_style atomic
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boundary p p p
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#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~#
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# Crystal orientation and MD box creation #
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#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~#
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lattice diamond 2.845
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Lattice spacing in x,y,z = 2.845 2.845 2.845
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region Bbox block 0 3 0 3 0 3
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create_box 1 Bbox
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Created orthogonal box = (0 0 0) to (8.535 8.535 8.535)
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1 by 1 by 1 MPI processor grid
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create_atoms 1 region Bbox basis 1 1
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Created 216 atoms
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using lattice units in orthogonal box = (0 0 0) to (8.535 8.535 8.535)
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create_atoms CPU = 0.000 seconds
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#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~#
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# Interatomic potential parameters #
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#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~#
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# Specify hybrid with SNAP, ZBL, and long-range C_SNAP_2021.10.15.quadratic.ulomb
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pair_style hybrid/overlay zbl 0.1 0.2 snap
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pair_coeff 1 1 zbl 10 10
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pair_coeff * * snap C_SNAP_2021.10.15.quadratic.snapcoeff C_SNAP_2021.10.15.quadratic.snapparam C
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SNAP Element = C, Radius 0.5, Weight 1
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SNAP keyword rcutfac 2.7
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SNAP keyword twojmax 8
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SNAP keyword rfac0 0.99363
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SNAP keyword rmin0 0.0
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SNAP keyword bzeroflag 0
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SNAP keyword quadraticflag 1
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mass * 12.01
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velocity all create 8000.0 3412461 loop geom
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fix NVE all nve
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fix NVT all langevin 5000.0 5000.0 0.1 3216548
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thermo 50
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thermo_style custom step temp ke pe etotal press pxx pyy pzz
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run 500
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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 = 4.7
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ghost atom cutoff = 4.7
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binsize = 2.35, bins = 4 4 4
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2 neighbor lists, perpetual/occasional/extra = 2 0 0
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(1) pair zbl, perpetual, half/full trim from (2)
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attributes: half, newton on, cut 2.2
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pair build: halffull/newton/trim
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stencil: none
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bin: none
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(2) pair snap, 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) = 4.835 | 4.835 | 4.835 Mbytes
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Step Temp KinEng PotEng TotEng Press Pxx Pyy Pzz
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0 8000 222.32745 -846.66062 -624.33318 10234249 10210805 10267435 10224506
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50 4199.4229 116.70587 -723.2423 -606.53643 10256033 10157803 10280166 10330129
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100 3820.2509 106.16833 -710.43537 -604.26704 10232872 10216484 10241309 10240825
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150 4413.2948 122.64957 -710.09702 -587.44745 10254093 10323013 10265454 10173810
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200 4688.024 130.28455 -702.26198 -571.97742 10306186 10281632 10342390 10294536
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250 4997.165 138.87587 -720.58476 -581.70889 10284438 10220856 10360231 10272226
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300 4640.4911 128.96357 -710.75063 -581.78706 10263301 10264007 10290526 10235369
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350 4929.5117 136.99572 -707.2526 -570.25688 10290742 10359920 10284236 10228071
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400 4700.9354 130.64337 -697.90277 -567.2594 10250682 10277287 10246032 10228729
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450 5108.4971 141.96989 -700.57144 -558.60155 10289765 10323648 10306588 10239058
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500 5146.7039 143.03169 -700.33221 -557.30052 10334303 10349736 10358785 10294387
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Loop time of 36.7771 on 1 procs for 500 steps with 216 atoms
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Performance: 1.175 ns/day, 20.432 hours/ns, 13.595 timesteps/s, 2.937 katom-step/s
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99.8% CPU use with 1 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 | 36.766 | 36.766 | 36.766 | 0.0 | 99.97
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Neigh | 0.0010226 | 0.0010226 | 0.0010226 | 0.0 | 0.00
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Comm | 0.0033205 | 0.0033205 | 0.0033205 | 0.0 | 0.01
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Output | 0.00020657 | 0.00020657 | 0.00020657 | 0.0 | 0.00
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Modify | 0.0047621 | 0.0047621 | 0.0047621 | 0.0 | 0.01
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Other | | 0.001464 | | | 0.00
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Nlocal: 216 ave 216 max 216 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Nghost: 1746 ave 1746 max 1746 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Neighs: 1767 ave 1767 max 1767 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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FullNghs: 32846 ave 32846 max 32846 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Total # of neighbors = 32846
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Ave neighs/atom = 152.06481
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Neighbor list builds = 1
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Dangerous builds = 0
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Total wall time: 0:00:36
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