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 1 by 1 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) = 2.644 | 2.644 | 2.644 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 0.014627 on 1 procs for 100 steps with 500 atoms
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Performance: 2953445.899 tau/day, 6836.680 timesteps/s, 3.418 Matom-step/s
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100.0% 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 | 0.010546 | 0.010546 | 0.010546 | 0.0 | 72.10
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Neigh | 0.0027775 | 0.0027775 | 0.0027775 | 0.0 | 18.99
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Comm | 0.00044818 | 0.00044818 | 0.00044818 | 0.0 | 3.06
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Output | 0.00060601 | 0.00060601 | 0.00060601 | 0.0 | 4.14
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Modify | 0.00018516 | 0.00018516 | 0.00018516 | 0.0 | 1.27
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Other | | 6.39e-05 | | | 0.44
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Nlocal: 500 ave 500 max 500 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Nghost: 1941 ave 1941 max 1941 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Neighs: 18766 ave 18766 max 18766 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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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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