143 lines
4.9 KiB
Groff
143 lines
4.9 KiB
Groff
LAMMPS (22 Dec 2022)
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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 2 by 2 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_coefficients.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: 1
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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: 150
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total number of descriptors for all potentials: 182
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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) = 3.062 | 3.062 | 3.062 Mbytes
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Step Temp E_pair E_mol TotEng Press
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0 300 -11.847697 0 -11.809222 13502.169
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10 296.47494 -11.847245 0 -11.809222 13529.584
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20 286.0918 -11.845913 0 -11.809222 13613.884
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30 269.42275 -11.843776 0 -11.809222 13759.746
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40 247.39423 -11.84095 0 -11.809222 13972.073
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50 221.23976 -11.837596 0 -11.809222 14253.202
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60 192.43252 -11.833901 0 -11.809222 14600.367
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70 162.59874 -11.830075 0 -11.809221 15004.156
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80 133.41531 -11.826332 0 -11.809221 15448.418
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90 106.49785 -11.82288 0 -11.809221 15911.638
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100 83.288219 -11.819903 0 -11.809221 16369.373
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Loop time of 0.427448 on 4 procs for 100 steps with 128 atoms
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Performance: 10.106 ns/day, 2.375 hours/ns, 233.947 timesteps/s, 29.945 katom-step/s
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97.9% 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 | 0.40622 | 0.40946 | 0.419 | 0.9 | 95.79
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Neigh | 0 | 0 | 0 | 0.0 | 0.00
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Comm | 0.0071192 | 0.016995 | 0.020439 | 4.4 | 3.98
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Output | 0.00012904 | 0.0002071 | 0.00043132 | 0.0 | 0.05
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Modify | 3.905e-05 | 4.8089e-05 | 5.5714e-05 | 0.0 | 0.01
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Other | | 0.0007341 | | | 0.17
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Nlocal: 32 ave 32 max 32 min
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Histogram: 4 0 0 0 0 0 0 0 0 0
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Nghost: 431 ave 431 max 431 min
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Histogram: 4 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: 4 0 0 0 0 0 0 0 0 0
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FullNghs: 1856 ave 1856 max 1856 min
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Histogram: 4 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: 0:00:00
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