5.11. LAMMPSParser
Parses data or dump files produced by LAMMPS.
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.
New in version 0.9.0.
- 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.
New 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.
New 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
Falseso 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
Falseso 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
Falseso 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
Falseso 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.
New 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.
New 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)
- 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
New 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)