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lammps.py errors #4458

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lammps.py errors #4458

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32 changes: 22 additions & 10 deletions package/MDAnalysis/coordinates/LAMMPS.py
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Original file line number Diff line number Diff line change
Expand Up @@ -61,27 +61,39 @@

Example: Loading a LAMMPS simulation
------------------------------------
.. testsetup::
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You can just remove this, what testsetup does is that the code right below it runs without showing it in the documentation.


To load a LAMMPS simulation from a LAMMPS data file (using the
: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")
>>> import MDAnalysis
>>> from MDAnalysis.tests.datafiles import LAMMPSdata2, LAMMPSdcd2
>>> u = MDAnalysis.Universe(LAMMPSdata2, LAMMPSdcd2, format="LAMMPS")

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