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lammps.py errors #4458

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merged 9 commits into from
Apr 1, 2024
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lammps.py errors #4458

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lammps.py_initial_commit
nataliyah123 Feb 15, 2024
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nataliyah123 Feb 15, 2024
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nataliyah123 Feb 17, 2024
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fixed lammps.py
nataliyah123 Feb 17, 2024
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nataliyah123 Feb 20, 2024
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nataliyah123 Mar 22, 2024
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nataliyah123 Mar 31, 2024
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32 changes: 23 additions & 9 deletions package/MDAnalysis/coordinates/LAMMPS.py
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Original file line number Diff line number Diff line change
Expand Up @@ -66,22 +66,36 @@
:class:`~MDAnalysis.topology.LAMMPSParser.DATAParser`) together with a
LAMMPS DCD with "*real*" provide the keyword *format="LAMMPS*"::

>>> u = MDAnalysis.Universe("lammps.data", "lammps_real.dcd", format="LAMMPS")
..testsetup::
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This code block should be placed right after the title level Example: Loading xxx


>>> import MDAnalysis
>>> from MDAnalysis.tests.datafiles import LAMMPSdata2, LAMMPSdcd2

..doctest::
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Suggested change
..doctest::
.. doctest::


>>> u = MDAnalysis.Universe(LAMMPSdata2, LAMMPSdcd2, format="LAMMPS")

If the trajectory uses *units nano* then use ::
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Suggested change
If the trajectory uses *units nano* then use ::
If the trajectory uses *units nano* then use


>>> u = MDAnalysis.Universe("lammps.data", "lammps_nano.dcd", format="LAMMPS",
... lengthunit="nm", timeunit="ns")
.. doctest::

>>> u = MDAnalysis.Universe(LAMMPSdata2, LAMMPSdcd2, format="LAMMPS",
... lengthunit="nm", timeunit="ns")

To scan through a trajectory to find a desirable frame and write to a LAMMPS
data file,

>>> for ts in u.trajectory:
... # analyze frame
... if take_this_frame == True:
... with mda.Writer('frame.data') as W:
... W.write(u.atoms)
... break
>>> u = MDAnalysis.Universe(LAMMPSdata2, LAMMPSdcd2, format="LAMMPS",
... lengthunit="nm", timeunit="ns")
>>> take_this_frame = False
>>> for ts in u.trajectory:
... # analyze frame
... if ts.frame == 4:
... take_this_frame = True
... if take_this_frame == True:
... with MDAnalysis.Writer('frame.data') as W:
... W.write(u.atoms)
... break

Note
----
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