144 lines
5.0 KiB
Groff
144 lines
5.0 KiB
Groff
LAMMPS (3 Nov 2022)
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OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
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using 1 OpenMP thread(s) per MPI task
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# Demonstrate POD Ta potential
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# Initialize simulation
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variable nsteps index 100
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variable nrep equal 4
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variable a equal 3.316
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units metal
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# generate the box and atom positions using a BCC lattice
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variable nx equal ${nrep}
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variable nx equal 4
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variable ny equal ${nrep}
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variable ny equal 4
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variable nz equal ${nrep}
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variable nz equal 4
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boundary p p p
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lattice bcc $a
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lattice bcc 3.316
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Lattice spacing in x,y,z = 3.316 3.316 3.316
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region box block 0 ${nx} 0 ${ny} 0 ${nz}
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region box block 0 4 0 ${ny} 0 ${nz}
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region box block 0 4 0 4 0 ${nz}
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region box block 0 4 0 4 0 4
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create_box 1 box
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Created orthogonal box = (0 0 0) to (13.264 13.264 13.264)
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1 by 1 by 1 MPI processor grid
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create_atoms 1 box
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Created 128 atoms
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using lattice units in orthogonal box = (0 0 0) to (13.264 13.264 13.264)
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create_atoms CPU = 0.000 seconds
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mass 1 180.88
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# POD potential
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pair_style pod
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pair_coeff * * Ta_param.pod Ta_coeff.pod Ta
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Reading potential file Ta_param.pod with DATE: 2022-11-30
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**************** Begin of POD Potentials ****************
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species: Ta
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periodic boundary conditions: 1 1 1
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inner cut-off radius: 1
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outer cut-off radius: 5
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bessel polynomial degree: 3
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inverse polynomial degree: 6
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one-body potential: 1
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two-body potential: 3 6 6
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three-body potential: 3 6 5 5
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four-body SNAP potential: 0 0
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quadratic POD potential: 0
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number of basis functions for one-body potential: 1
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number of basis functions for two-body potential: 6
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number of basis functions for three-body potential: 25
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number of basis functions for four-body potential: 0
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number of descriptors for one-body potential: 1
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number of descriptors for two-body potential: 6
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number of descriptors for three-body potential: 25
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number of descriptors for four-body potential: 0
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number of descriptors for quadratic POD potential: 0
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total number of descriptors for all potentials: 32
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**************** End of POD Potentials ****************
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# Setup output
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thermo 10
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thermo_modify norm yes
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# Set up NVE run
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timestep 0.5e-3
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neighbor 1.0 bin
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neigh_modify once no every 1 delay 0 check yes
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# Run MD
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velocity all create 300.0 4928459 loop geom
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fix 1 all nve
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run ${nsteps}
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run 100
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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 = 6
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ghost atom cutoff = 6
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binsize = 3, bins = 5 5 5
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1 neighbor lists, perpetual/occasional/extra = 1 0 0
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(1) pair pod, 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) = 3.082 | 3.082 | 3.082 Mbytes
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Step Temp E_pair E_mol TotEng Press
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0 300 -11.841663 0 -11.803187 -15932.591
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10 296.91628 -11.841267 0 -11.803187 -15691.074
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20 287.83196 -11.840102 0 -11.803187 -14982.728
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30 273.24816 -11.838231 0 -11.803187 -13854.078
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40 253.9759 -11.83576 0 -11.803187 -12377.181
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50 231.08957 -11.832824 0 -11.803187 -10642.643
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60 205.86327 -11.829589 0 -11.803187 -8751.1586
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70 179.69223 -11.826232 0 -11.803187 -6804.6274
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80 154.00272 -11.822938 0 -11.803187 -4898.0969
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90 130.15562 -11.819879 0 -11.803187 -3113.551
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100 109.35031 -11.817211 0 -11.803187 -1516.0292
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Loop time of 1.54901 on 1 procs for 100 steps with 128 atoms
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Performance: 2.789 ns/day, 8.606 hours/ns, 64.557 timesteps/s, 8.263 katom-step/s
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98.0% CPU use with 1 MPI tasks x no 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 | 1.5472 | 1.5472 | 1.5472 | 0.0 | 99.88
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Neigh | 0 | 0 | 0 | 0.0 | 0.00
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Comm | 0.00056946 | 0.00056946 | 0.00056946 | 0.0 | 0.04
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Output | 0.00029755 | 0.00029755 | 0.00029755 | 0.0 | 0.02
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Modify | 0.0004159 | 0.0004159 | 0.0004159 | 0.0 | 0.03
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Other | | 0.0005638 | | | 0.04
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Nlocal: 128 ave 128 max 128 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Nghost: 727 ave 727 max 727 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Neighs: 0 ave 0 max 0 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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FullNghs: 7424 ave 7424 max 7424 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Total # of neighbors = 7424
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Ave neighs/atom = 58
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Neighbor list builds = 0
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Dangerous builds = 0
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Total wall time: 0:00:01
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