DATAReader

class sknano.io.lammps_data.DATAReader(fpath, atom_style='full', bond_style=None, angle_style=None, dihedral_style=None, improper_style=None, pair_style=None, formatter=None, **kwargs)

Bases: sknano.io.StructureIO

StructureData class for reading LAMMPS data file format.

Parameters:

• fpath (str) – LAMMPS data file path
• atom_style ({'full', 'atomic'}, optional) –
• bond_style ({None, 'class2', 'fene', 'fene/expand', 'harmonic', 'morse', 'nonlinear', 'quartic'}) –
• angle_style (str, optional) –
• dihedral_style (str, optional) –
• improper_style (str, optional) –
• pair_style (str, optional) –

domain

sknano.core.crystallography.Domain

Attributes

atoms	Structure Atoms.
basis	Structure BasisAtoms.
comment_line	Comment line.
crystal_cell	Structure CrystalCell.
fmtstr	Format string.
headers	Alias for header_data.
lattice	Structure Crystal3DLattice.
lattice_shift	Lattice displacement vector.
scaling_matrix	CrystalCell.scaling_matrix.
sections	Alias for section_data.
structure	An alias to self.
unit_cell	Structure UnitCell.

Methods

clear()	Clear list of StructureMixin.atoms.
get(section[, colnum, colname, colindex])	Return section with section.
make_supercell(scaling_matrix[, wrap_coords])	Make supercell.
read()	Read data file.
read_data(*args, **kwargs)	Read LAMMPS Data file.
read_dump(*args, **kwargs)	Read LAMMPS Dump file.
read_pdb(*args, **kwargs)	Read PDB file.
read_xyz(*args, **kwargs)	Read XYZ file.
rotate(**kwargs)	Rotate crystal cell lattice, basis, and unit cell.
todict()	Return dict of constructor parameters.
transform_lattice(scaling_matrix[, ...])	Transform structure lattice.
translate(t[, fix_anchor_points])	Translate crystal cell lattice, basis, and unit cell.
write(*args, **kwargs)	Write structure data to file.
write_data(**kwargs)	Write LAMMPS data file.
write_dump(**kwargs)	Write LAMMPS dump file.
write_pdb(**kwargs)	Write pdb file.
write_xyz(**kwargs)	Write xyz file.

Attributes Summary

headers	Alias for header_data.
sections	Alias for section_data.

Methods Summary

get(section[, colnum, colname, colindex])	Return section with section.
read()	Read data file.
todict()	Return dict of constructor parameters.

Attributes Documentation

headers

Alias for header_data.

Returns:dict of dump file header values Return type:dict

sections

Alias for section_data.

Returns:dict of dump file section data Return type:dict

Methods Documentation

get(section, colnum=None, colname=None, colindex=None)

Return section with section.

Parameters:

• section (str) –
• colnum (int, optional) –
• colname (str, optional) –
• colindex (int, optional) –

Returns:

Return type:

sequence

read()

Read data file.

todict()

Return dict of constructor parameters.