DataFileReader

class pylimer_tools_cpp.DataFileReader(self: pylimer_tools_cpp.DataFileReader)

Bases: pybind11_object

A reader for LAMMPS’s write_data files.

Initialize a new data file parser.

Methods Summary

get_atom_ids(self)	Get all atom IDs from the data file.
get_atom_nx(self)	Get periodic image flags in x direction for all atoms.
get_atom_ny(self)	Get periodic image flags in y direction for all atoms.
get_atom_nz(self)	Get periodic image flags in z direction for all atoms.
get_atom_types(self)	Get all atom types from the data file.
get_atom_x(self)	Get x coordinates of all atoms.
get_atom_y(self)	Get y coordinates of all atoms.
get_atom_z(self)	Get z coordinates of all atoms.
get_bond_from(self)	Get starting atom IDs for all bonds.
get_bond_to(self)	Get ending atom IDs for all bonds.
get_bond_types(self)	Get all bond types from the data file.
get_high_x(self)	Get the upper bound of the box in x direction.
get_high_y(self)	Get the upper bound of the box in y direction.
get_high_z(self)	Get the upper bound of the box in z direction.
get_low_x(self)	Get the lower bound of the box in x direction.
get_low_y(self)	Get the lower bound of the box in y direction.
get_low_z(self)	Get the lower bound of the box in z direction.
get_lx(self)	Get the box length in x direction.
get_ly(self)	Get the box length in y direction.
get_lz(self)	Get the box length in z direction.
get_masses(self)	Get the mass values for each atom type.
get_molecule_ids(self)	Get all molecule IDs from the data file.
get_nr_of_atom_types(self)	Get the number of atom types in the data file.
get_nr_of_atoms(self)	Get the number of atoms in the data file.
get_nr_of_bond_types(self)	Get the number of bond types in the data file.
get_nr_of_bonds(self)	Get the number of bonds in the data file.
read(self, path_of_file_to_read, atom_style, ...)	Actually read a LAMMPS's write_data file.

Methods Documentation

get_atom_ids(self: pylimer_tools_cpp.DataFileReader) → list[int]

Get all atom IDs from the data file.

Returns:

Vector of atom IDs

get_atom_nx(self: pylimer_tools_cpp.DataFileReader) → list[int]

Get periodic image flags in x direction for all atoms.

Returns:

Vector of nx values (image flags)

get_atom_ny(self: pylimer_tools_cpp.DataFileReader) → list[int]

Get periodic image flags in y direction for all atoms.

Returns:

Vector of ny values (image flags)

get_atom_nz(self: pylimer_tools_cpp.DataFileReader) → list[int]

Get periodic image flags in z direction for all atoms.

Returns:

Vector of nz values (image flags)

get_atom_types(self: pylimer_tools_cpp.DataFileReader) → list[int]

Get all atom types from the data file.

Returns:

Vector of atom types

get_atom_x(self: pylimer_tools_cpp.DataFileReader) → list[float]

Get x coordinates of all atoms.

Returns:

Vector of x coordinates

get_atom_y(self: pylimer_tools_cpp.DataFileReader) → list[float]

Get y coordinates of all atoms.

Returns:

Vector of y coordinates

get_atom_z(self: pylimer_tools_cpp.DataFileReader) → list[float]

Get z coordinates of all atoms.

Returns:

Vector of z coordinates

get_bond_from(self: pylimer_tools_cpp.DataFileReader) → list[int]

Get starting atom IDs for all bonds.

Returns:

Vector of starting atom IDs for bonds

get_bond_to(self: pylimer_tools_cpp.DataFileReader) → list[int]

Get ending atom IDs for all bonds.

Returns:

Vector of ending atom IDs for bonds

get_bond_types(self: pylimer_tools_cpp.DataFileReader) → list[int]

Get all bond types from the data file.

Returns:

Vector of bond types

get_high_x(self: pylimer_tools_cpp.DataFileReader) → float

Get the upper bound of the box in x direction.

Returns:

Upper x boundary

get_high_y(self: pylimer_tools_cpp.DataFileReader) → float

Get the upper bound of the box in y direction.

Returns:

Upper y boundary

get_high_z(self: pylimer_tools_cpp.DataFileReader) → float

Get the upper bound of the box in z direction.

Returns:

Upper z boundary

get_low_x(self: pylimer_tools_cpp.DataFileReader) → float

Get the lower bound of the box in x direction.

Returns:

Lower x boundary

get_low_y(self: pylimer_tools_cpp.DataFileReader) → float

Get the lower bound of the box in y direction.

Returns:

Lower y boundary

get_low_z(self: pylimer_tools_cpp.DataFileReader) → float

Get the lower bound of the box in z direction.

Returns:

Lower z boundary

get_lx(self: pylimer_tools_cpp.DataFileReader) → float

Get the box length in x direction.

Returns:

Box length in x direction

get_ly(self: pylimer_tools_cpp.DataFileReader) → float

Get the box length in y direction.

Returns:

Box length in y direction

get_lz(self: pylimer_tools_cpp.DataFileReader) → float

Get the box length in z direction.

Returns:

Box length in z direction

get_masses(self: pylimer_tools_cpp.DataFileReader) → dict[int, float]

Get the mass values for each atom type.

Returns:

Map of atom types to their masses

get_molecule_ids(self: pylimer_tools_cpp.DataFileReader) → list[int]

Get all molecule IDs from the data file.

Returns:

Vector of molecule IDs

get_nr_of_atom_types(self: pylimer_tools_cpp.DataFileReader) → int

Get the number of atom types in the data file.

Returns:

Number of atom types

get_nr_of_atoms(self: pylimer_tools_cpp.DataFileReader) → int

Get the number of atoms in the data file.

Returns:

Number of atoms

get_nr_of_bond_types(self: pylimer_tools_cpp.DataFileReader) → int

Get the number of bond types in the data file.

Returns:

Number of bond types

get_nr_of_bonds(self: pylimer_tools_cpp.DataFileReader) → int

Get the number of bonds in the data file.

Returns:

Number of bonds

read(self: pylimer_tools_cpp.DataFileReader, path_of_file_to_read: str, atom_style: pylimer_tools_cpp.AtomStyle = <AtomStyle.ANGLE: 1>, atom_style2: pylimer_tools_cpp.AtomStyle = <AtomStyle.NONE: 0>, atom_style_3: pylimer_tools_cpp.AtomStyle = <AtomStyle.NONE: 0>) → None

Actually read a LAMMPS’s write_data file.

Parameters:

• path_of_file_to_read – The path to the file to read

• atom_style – The format of the “Atoms” section, see https://docs.lammps.org/read_data.html

• atom_style2 – The format of the “Atoms” section if the previous parameter is equal to AtomStyle::HYBRID

• atom_style_3 – The format of the “Atoms” section if the second to last parameter is equal to AtomStyle::HYBRID