#!/usr/bin/env python import ase.io from ase.utils import StringIO input = StringIO("""LAMMPS data file via write_data, version 7 Sep 2016, timestep = 1000000 8 atoms 1 atom types 6 bonds 1 bond types 4 angles 1 angle types -5.1188800000000001e+01 5.1188800000000001e+01 xlo xhi -5.1188800000000001e+01 5.1188800000000001e+01 ylo yhi -5.1188800000000001e+01 5.1188800000000001e+01 zlo zhi Masses 1 56 Atoms 1 1 1 0.0 -7.0654012878945753e+00 -4.7737244253442213e-01 -5.1102452666801824e+01 2 -1 6 2 1 1 0.0 -8.1237844371679362e+00 -1.3340695922796841e+00 4.7658302278206179e+01 2 -1 5 3 1 1 0.0 -1.2090525219882498e+01 -3.2315354021627760e+00 4.7363437099502839e+01 2 -1 5 4 1 1 0.0 -8.3272244953257601e+00 -4.8413162043515321e+00 4.5609055410298623e+01 2 -1 5 5 2 1 0.0 -5.3879618209198750e+00 4.9524635221072280e+01 3.0054862714858366e+01 6 -7 -2 6 2 1 0.0 -8.4950075933508273e+00 -4.9363297129348325e+01 3.2588925816534982e+01 6 -6 -2 7 2 1 0.0 -9.7544282093133940e+00 4.9869755980935565e+01 3.6362287886934432e+01 6 -7 -2 8 2 1 0.0 -5.5712437770663756e+00 4.7660225526197003e+01 3.8847235874270240e+01 6 -7 -2 Velocities 1 -1.2812627962466232e-02 -1.8102422526771818e-03 8.8697845357364469e-03 2 7.7087896348612683e-03 -5.6149199730983867e-04 1.3646724560472424e-02 3 -3.5128553734623657e-03 1.2368758037550581e-03 9.7460093657088121e-03 4 1.1626059392751346e-02 -1.1942908859710665e-05 8.7505240354339674e-03 5 1.0953500823880464e-02 -1.6710422557096375e-02 2.2322216388444985e-03 6 3.7515599452757294e-03 1.4091708517087744e-02 7.2963916249300454e-03 7 5.3953961772651359e-03 -8.2013715102925017e-03 2.0159609509813853e-02 8 7.5074008407567160e-03 5.9398495239242483e-03 7.3144909044607909e-03 Bonds 1 1 1 2 2 1 2 3 3 1 3 4 4 1 5 6 5 1 6 7 6 1 7 8 Angles 1 1 1 2 3 2 1 2 3 4 3 1 5 6 7 4 1 6 7 8 """) at = ase.io.read(input, format="lammps-data") expected_output = [line.strip() for line in """8 Lattice="102.3776 0.0 0.0 0.0 102.3776 0.0 0.0 0.0 102.3776" Properties=species:S:1:pos:R:3:bonds:S:1:masses:R:1:mol-id:I:1:Z:I:1:angles:S:1:momenta:R:3:type:I:1:id:I:1:travel:I:3 pbc="T T T" H -7.06540129 -0.47737244 -51.10245267 1(1) 56.00000000 1 1 _ -0.71750717 -0.10137357 0.49670793 1 1 2 -1 6 H -8.12378444 -1.33406959 47.65830228 2(1) 56.00000000 1 1 0-2(1) 0.43169222 -0.03144355 0.76421658 1 2 2 -1 5 H -12.09052522 -3.23153540 47.36343710 3(1) 56.00000000 1 1 1-3(1) -0.19671990 0.06926505 0.54577652 1 3 2 -1 5 H -8.32722450 -4.84131620 45.60905541 _ 56.00000000 1 1 _ 0.65105933 -0.00066880 0.49002935 1 4 2 -1 5 H -5.38796182 49.52463522 30.05486271 5(1) 56.00000000 2 1 _ 0.61339605 -0.93578366 0.12500441 1 5 6 -7 -2 H -8.49500759 -49.36329713 32.58892582 6(1) 56.00000000 2 1 4-6(1) 0.21008736 0.78913568 0.40859793 1 6 6 -6 -2 H -9.75442821 49.86975598 36.36228789 7(1) 56.00000000 2 1 5-7(1) 0.30214219 -0.45927680 1.12893813 1 7 6 -7 -2 H -5.57124378 47.66022553 38.84723587 _ 56.00000000 2 1 _ 0.42041445 0.33263157 0.40961149 1 8 6 -7 -2 """.split("\n")] buf = StringIO() ase.io.write(buf, at, format="extxyz", columns=["symbols", "positions", "bonds", "masses", "mol-id", "numbers", "angles", "momenta", "type", "id", "travel"], write_info=False) lines = [line.strip() for line in buf.getvalue().split("\n")] assert lines == expected_output