DATAData

class sknano.io.lammps_data.DATAData(fpath=None, **kwargs)[source] [edit on github][source]

Bases: sknano.io.lammps_data.DATAReader

Class for reading and writing StructureData in LAMMPS data format.

Parameters:fpath (str, optional) –

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.
delete(key)
formatter([atom_style]) Return DATAFormatter object.
get(section[, colnum, colname, colindex]) Return section with section.
make_supercell(scaling_matrix[, wrap_coords]) Make supercell.
map(*pairs)
maxbox()
maxtype()
newxyz()
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.
reorder(colname, *order)
replace(section, new_data[, colnum, ...]) Replace section data.
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.
viz(isnap)
write([datafile, atoms, comment_line]) Write data 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.

Methods Summary

delete(key)
formatter([atom_style]) Return DATAFormatter object.
map(*pairs)
maxbox()
maxtype()
newxyz()
reorder(colname, *order)
replace(section, new_data[, colnum, ...]) Replace section data.
viz(isnap)
write([datafile, atoms, comment_line]) Write data file.

Methods Documentation

delete(key)[source] [edit on github][source]
classmethod formatter(atom_style='full', **kwargs)[source] [edit on github][source]

Return DATAFormatter object.

map(*pairs)[source] [edit on github][source]
maxbox()[source] [edit on github][source]
maxtype()[source] [edit on github][source]
newxyz()[source] [edit on github][source]
reorder(colname, *order)[source] [edit on github][source]
replace(section, new_data, colnum=None, colname=None, colindex=None)[source] [edit on github][source]

Replace section data.

Parameters:
  • section (str) –
  • new_data (sequence) –
  • colnum (int, optional) –
  • colname (str, optional) –
  • colindex (int, optional) –
viz(isnap)[source] [edit on github][source]
write(datafile=None, atoms=None, comment_line=None, **kwargs)[source] [edit on github][source]

Write data file.

Parameters:
  • datafile (str, optional) –
  • atoms (Atoms, optional) –
  • comment_line (str, optional) – A string written to the first line of data file. If None, then it is the current version string of scikit-nano.