5.11. LAMMPSParser

Parses data or dump files produced by LAMMPS.

Note

By default, masses will be guessed on Universe creation if they are not read from the input file. This may change in release 3.0. See Guesser modules for more information.

Changed in version 1.0.0: Deprecated LAMMPSDataConverter has now been removed.

5.11.1. Atom styles

By default parsers and readers for Lammps data files expect either an atomic or full atom_style. This can be customised by passing the atom_style keyword argument. This should be a space separated string indicating the position of the id, type, resid, charge, x, y and z fields. The resid and charge fields are optional and any other specified field will be ignored.

For example to read a file with the following format, where there is no resid:

Atoms # atomic

1 1 3.7151744275286681e+01 1.8684434743140471e+01 1.9285127961842125e+01 0 0 0

The following code could be used:

>>> import MDAnalysis as mda
>>>
>>> u = mda.Universe('myfile.data', atom_style='id type x y z')

5.11.2. Classes

class MDAnalysis.topology.LAMMPSParser.DATAParser(filename)[source]

Parse a LAMMPS DATA file for topology and coordinates.

Note that LAMMPS DATA files can be used standalone.

Both topology and coordinate parsing functionality is kept in this class as the topology and coordinate reader share many common functions

By default the parser expects either atomic or full atom_style however this can be by passing an atom_style keyword argument, see Atom styles.

Added in version 0.9.0.

Changed in version 2.8.0: Removed mass guessing (attributes guessing takes place now through universe.guess_TopologyAttrs() API).

close()

Close the trajectory file.

convert_forces_from_native(force, inplace=True)

Conversion of forces array force from native to base units

Parameters:

  • force (array_like) – Forces to transform

  • inplace (bool (optional)) – Whether to modify the array inplace, overwriting previous data

Note

By default, the input force is modified in place and also returned. In-place operations improve performance because allocating new arrays is avoided.

Added in version 0.7.7.

convert_forces_to_native(force, inplace=True)

Conversion of force array force from base to native units.

Parameters:

  • force (array_like) – Forces to transform

  • inplace (bool (optional)) – Whether to modify the array inplace, overwriting previous data

Note

By default, the input force is modified in place and also returned. In-place operations improve performance because allocating new arrays is avoided.

Added in version 0.7.7.

convert_pos_from_native(x, inplace=True)

Conversion of coordinate array x from native units to base units.

Parameters:

  • x (array_like) – Positions to transform

  • inplace (bool (optional)) – Whether to modify the array inplace, overwriting previous data

Note

By default, the input x is modified in place and also returned. In-place operations improve performance because allocating new arrays is avoided.

Changed in version 0.7.5: Keyword inplace can be set to False so that a modified copy is returned unless no conversion takes place, in which case the reference to the unmodified x is returned.

convert_pos_to_native(x, inplace=True)

Conversion of coordinate array x from base units to native units.

Parameters:

  • x (array_like) – Positions to transform

  • inplace (bool (optional)) – Whether to modify the array inplace, overwriting previous data

Note

By default, the input x is modified in place and also returned. In-place operations improve performance because allocating new arrays is avoided.

Changed in version 0.7.5: Keyword inplace can be set to False so that a modified copy is returned unless no conversion takes place, in which case the reference to the unmodified x is returned.

convert_time_from_native(t, inplace=True)

Convert time t from native units to base units.

Parameters:

  • t (array_like) – Time values to transform

  • inplace (bool (optional)) – Whether to modify the array inplace, overwriting previous data

Note

By default, the input t is modified in place and also returned (although note that scalar values t are passed by value in Python and hence an in-place modification has no effect on the caller.) In-place operations improve performance because allocating new arrays is avoided.

Changed in version 0.7.5: Keyword inplace can be set to False so that a modified copy is returned unless no conversion takes place, in which case the reference to the unmodified x is returned.

convert_time_to_native(t, inplace=True)

Convert time t from base units to native units.

Parameters:

  • t (array_like) – Time values to transform

  • inplace (bool, optional) – Whether to modify the array inplace, overwriting previous data

Note

By default, the input t is modified in place and also returned. (Also note that scalar values t are passed by value in Python and hence an in-place modification has no effect on the caller.)

Changed in version 0.7.5: Keyword inplace can be set to False so that a modified copy is returned unless no conversion takes place, in which case the reference to the unmodified x is returned.

convert_velocities_from_native(v, inplace=True)

Conversion of velocities array v from native to base units

Parameters:

  • v (array_like) – Velocities to transform

  • inplace (bool (optional)) – Whether to modify the array inplace, overwriting previous data

Note

By default, the input v is modified in place and also returned. In-place operations improve performance because allocating new arrays is avoided.

Added in version 0.7.5.

convert_velocities_to_native(v, inplace=True)

Conversion of coordinate array v from base to native units

Parameters:

  • v (array_like) – Velocities to transform

  • inplace (bool (optional)) – Whether to modify the array inplace, overwriting previous data

Note

By default, the input v is modified in place and also returned. In-place operations improve performance because allocating new arrays is avoided.

Added in version 0.7.5.

grab_datafile()[source]

Split a data file into dict of header and sections

Returns:

  • header - dict of header section (value)

  • sections - dict of section name (content)

parse(**kwargs)[source]

Parses a LAMMPS DATA file.

Return type:

MDAnalysis Topology object.

read_DATA_timestep(n_atoms, TS_class, TS_kwargs, atom_style=None)[source]

Read a DATA file and try and extract x, v, box.

  • positions

  • velocities (optional)

  • box information

Fills this into the Timestep object and returns it

Added in version 0.9.0.

Changed in version 0.18.0: Added atom_style kwarg

units = {'length': None, 'time': None, 'velocity': None}

dict with units of of time and length (and velocity, force, … for formats that support it)

class MDAnalysis.topology.LAMMPSParser.LammpsDumpParser(filename)[source]

Parses Lammps ascii dump files in ‘atom’ format.

Sets all masses to 1.0.

Changed in version 2.0.0.

Added in version 0.19.0.