100 lines
3.5 KiB
Groff
100 lines
3.5 KiB
Groff
LAMMPS (2 Apr 2025 - Development - patch_2Apr2025-266-gebfb94a717-modified)
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# 3d Lennard-Jones melt with equal- and atom-style variables which
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# use a Python function wrapper in their formulas
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variable x index 5
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variable y index 5
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variable z index 5
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units lj
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atom_style atomic
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lattice fcc 0.8442
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Lattice spacing in x,y,z = 1.6795962 1.6795962 1.6795962
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region box block 0 $x 0 $y 0 $z
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region box block 0 5 0 $y 0 $z
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region box block 0 5 0 5 0 $z
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region box block 0 5 0 5 0 5
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create_box 1 box
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Created orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981)
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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 500 atoms
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using lattice units in orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981)
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create_atoms CPU = 0.000 seconds
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mass 1 1.0
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velocity all create 1.44 87287 loop geom
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pair_style lj/cut 2.5
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pair_coeff 1 1 1.0 1.0 2.5
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neighbor 0.3 bin
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neigh_modify delay 0 every 20 check no
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fix 1 all nve
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variable foo python truncate
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python truncate return v_foo input 1 iv_arg format fi here """
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def truncate(x):
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return int(x)
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"""
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variable scalar equal py_foo(4.5)
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print "TRUNCATE ${scalar}"
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TRUNCATE 4
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variable xtrunc atom py_foo(x)
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variable ytrunc atom py_foo(y)
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variable ztrunc atom py_foo(z)
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# examine dump file to see truncated xyz coords of each atom
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dump 1 all custom 100 tmp.dump id x y z v_xtrunc v_ytrunc v_ztrunc
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run 100
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Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
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Neighbor list info ...
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update: every = 20 steps, delay = 0 steps, check = no
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max neighbors/atom: 2000, page size: 100000
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master list distance cutoff = 2.8
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ghost atom cutoff = 2.8
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binsize = 1.4, bins = 6 6 6
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1 neighbor lists, perpetual/occasional/extra = 1 0 0
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(1) pair lj/cut, perpetual
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attributes: half, newton on
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pair build: half/bin/atomonly/newton
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stencil: half/bin/3d
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bin: standard
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Per MPI rank memory allocation (min/avg/max) = 2.609 | 2.609 | 2.609 Mbytes
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Step Temp E_pair E_mol TotEng Press
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0 1.44 -6.7733681 0 -4.6176881 -5.0221006
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100 0.75627408 -5.7580082 0 -4.6258659 0.21870071
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Loop time of 0.0062374 on 4 procs for 100 steps with 500 atoms
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Performance: 6925957.189 tau/day, 16032.308 timesteps/s, 8.016 Matom-step/s
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74.7% CPU use with 4 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 | 0.0027648 | 0.0028431 | 0.0029465 | 0.1 | 45.58
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Neigh | 0.00084567 | 0.00086563 | 0.00088168 | 0.0 | 13.88
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Comm | 0.0020822 | 0.0021609 | 0.0022418 | 0.1 | 34.64
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Output | 0.00021567 | 0.00022125 | 0.00022624 | 0.0 | 3.55
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Modify | 6.2567e-05 | 6.4105e-05 | 6.63e-05 | 0.0 | 1.03
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Other | | 8.241e-05 | | | 1.32
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Nlocal: 125 ave 126 max 123 min
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Histogram: 1 0 0 0 0 0 1 0 0 2
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Nghost: 1085.75 ave 1090 max 1082 min
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Histogram: 1 0 1 0 0 0 1 0 0 1
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Neighs: 4691.5 ave 4969 max 4368 min
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Histogram: 1 0 0 0 1 0 0 1 0 1
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Total # of neighbors = 18766
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Ave neighs/atom = 37.532
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Neighbor list builds = 5
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Dangerous builds not checked
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Total wall time: 0:00:00
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