DUMPData

class sknano.io.lammps_dump.DUMPData(*args, **kwargs)

Bases: sknano.io.lammps_dump.DUMPReader

Class for reading and writing structure data in LAMMPS dump format.

Parameters:

• *args –
• **kwargs –

Attributes

atoms	Structure Atoms.
basis	Structure BasisAtoms.
comment_line	Comment line.
crystal_cell	Structure CrystalCell.
fmtstr	Format string.
lattice	Structure Crystal3DLattice.
lattice_shift	Lattice displacement vector.
reference_index	Reference snapshot index.
reference_timestep	Reference snapshot timestep.
scaling_matrix	CrystalCell.scaling_matrix.
structure	An alias to self.
unit_cell	Structure UnitCell.

Methods

clear()	Clear list of StructureMixin.atoms.
make_supercell(scaling_matrix[, wrap_coords])	Make supercell.
map(*pairs)	Update dumpattrs2index mapping.
new_dumpattr(attr[, values])	Add new dump attr to snapshots.
newcolumn(name)	An alias for DUMPReader.new_dumpattr for compatibility LAMMPS pizza.py dump module.
read()	Read all snapshots from each dump 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_snapshot(f)	Read snapshot from file.
read_xyz(*args, **kwargs)	Read XYZ file.
rotate(**kwargs)	Rotate crystal cell lattice, basis, and unit cell.
scale()	Scale cartesian coordinates to fractional coordinates.
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.
unscale()	Unscale fractional coordinates to cartesian coordinates.
unwrap()	Unwrap coordinates from inside box to outside.
update_dumpattr(attr[, values])	Add new dump attr to snapshots.
wrap()	Wrap coordinates from outside box to inside.
write([dumpfile, atoms, snapshot, ...])	Write dump 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

write([dumpfile, atoms, snapshot, ...])

Write dump file.

Methods Documentation

write(dumpfile=None, atoms=None, snapshot=None, trajectory=None, write_header=True, mode='w', N=None, **kwargs)

Write dump file.

Parameters:

• dumpfile ({None, str}, optional) –
• atoms (Atoms, optional) –
• snapshot (Snapshot, optional) –
• trajectory (trajectory, optional) –
• write_header (bool, optional) –
• mode ({'w', 'a'}, optional) –
• N (int, optional) –