add example for Python with vector-style variable
This commit is contained in:
Steve Plimpton
@ -1,10 +1,10 @@
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LAMMPS (2 Apr 2025 - Development - patch_2Apr2025-266-gebfb94a717-modified)
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LAMMPS (2 Apr 2025 - Development - patch_2Apr2025-270-g2351418c94-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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variable x index 3
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variable y index 3
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variable z index 3
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units lj
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atom_style atomic
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@ -12,15 +12,15 @@ 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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region box block 0 3 0 $y 0 $z
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region box block 0 3 0 3 0 $z
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region box block 0 3 0 3 0 3
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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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Created orthogonal box = (0 0 0) to (5.0387886 5.0387886 5.0387886)
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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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Created 108 atoms
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using lattice units in orthogonal box = (0 0 0) to (5.0387886 5.0387886 5.0387886)
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create_atoms CPU = 0.000 seconds
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mass 1 1.0
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@ -34,24 +34,36 @@ neigh_modify delay 0 every 20 check no
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fix 1 all nve
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# define Python truncate() function
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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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# use in equal-style variable
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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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# use in atom-style variable
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# examine dump file to see truncated xyz coords of each atom
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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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# use in vector-style variable
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compute ke all temp
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variable ke vector c_ke
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variable ketrunc vector py_foo(v_ke)
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thermo_style custom step temp epair v_ketrunc[*6]
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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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@ -59,41 +71,46 @@ Neighbor list info ...
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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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binsize = 1.4, bins = 4 4 4
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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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Per MPI rank memory allocation (min/avg/max) = 2.598 | 2.598 | 2.598 Mbytes
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Step Temp E_pair v_ketrunc[1] v_ketrunc[2] v_ketrunc[3] v_ketrunc[4] v_ketrunc[5] v_ketrunc[6]
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0 1.44 -6.7733681 155 152 154 -10 -4 -6
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100 0.82217015 -5.8614684 113 65 84 7 -1 -12
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Loop time of 0.00278186 on 1 procs for 100 steps with 108 atoms
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Performance: 2953445.899 tau/day, 6836.680 timesteps/s, 3.418 Matom-step/s
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Performance: 15529161.573 tau/day, 35947.133 timesteps/s, 3.882 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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Pair | 0.0018161 | 0.0018161 | 0.0018161 | 0.0 | 65.29
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Neigh | 0.00057543 | 0.00057543 | 0.00057543 | 0.0 | 20.68
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Comm | 0.00019634 | 0.00019634 | 0.00019634 | 0.0 | 7.06
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Output | 0.00012056 | 0.00012056 | 0.00012056 | 0.0 | 4.33
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Modify | 4.8221e-05 | 4.8221e-05 | 4.8221e-05 | 0.0 | 1.73
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Other | | 2.516e-05 | | | 0.90
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Nlocal: 500 ave 500 max 500 min
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Nlocal: 108 ave 108 max 108 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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Nghost: 980 ave 980 max 980 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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Neighs: 4071 ave 4071 max 4071 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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Total # of neighbors = 4071
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Ave neighs/atom = 37.694444
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Neighbor list builds = 5
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Dangerous builds not checked
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print "KE TENSOR ${ketrunc}"
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KE TENSOR [113,65,84,7,-1,-12]
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Total wall time: 0:00:00
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