DataFileWriter

class pylimer_tools_cpp.DataFileWriter(self: pylimer_tools_cpp.DataFileWriter, universe: pylimer_tools_cpp.Universe)

Bases: pybind11_object

A class to write a LAMMPS data file from a universe.

Attention

The resulting file is not guaranteed to be a completely valid LAMMPS file. In particular, this writer does not force you to set masses for all atom types, and it does not have limits on the image flags. You can use set_masses() to set the masses for all atom types, and either set_vertex_property() or config_attempt_image_reset() and config_move_into_box() to ensure that the image flags are correct.

Initialize the writer with the universe to write.

Parameters:

universe – The universe to write to the data file

Methods Summary

config_atom_style(self, atom_style)	Set the (LAMMPS) atom style to use for writing the atoms.
config_attempt_image_reset(self[, ...])	Set whether to attempt to reset image flags so that output coordinates lie in the box.
config_crosslinker_type(self[, crosslinker_type])	Set which atom type represents crosslinkers.
config_include_angles(self[, include_angles])	Set whether to include the angles from the universe in the file or not.
config_include_dihedral_angles(self[, ...])	Set whether to include the dihedral angles from the universe in the file or not.
config_include_velocities(self[, ...])	Set whether to include the velocities from the universe (if any) in the file or not.
config_molecule_idx_for_swap(self[, ...])	Swappable chains implies that their moleculeIdx in the LAMMPS data file is not identical per chain, but identical per position in the chain.
config_move_into_box(self[, move_into_box])	Set whether to change the output coordinates to lie in the box or not.
config_reindex_atoms(self[, reindex_atoms])	Set whether to reindex the atoms or not.
set_custom_atom_format(self[, atom_format])	Specify a custom format for the atom section.
set_universe_to_write(self, universe)	Re-set the universe to write.
write_to_file(self, file)	Actually do the writing to the disk.

Methods Documentation

config_atom_style(self: pylimer_tools_cpp.DataFileWriter, atom_style: pylimer_tools_cpp.AtomStyle = <AtomStyle.ANGLE: 1>) → None

Set the (LAMMPS) atom style to use for writing the atoms.

Parameters:

atom_style – The LAMMPS atom style to use (default: AtomStyle.ANGLE)

config_attempt_image_reset(self: pylimer_tools_cpp.DataFileWriter, attempt_image_reset: bool = False) → None

Set whether to attempt to reset image flags so that output coordinates lie in the box.

Parameters:

attempt_image_reset – Whether to attempt image flag reset (default: False)

config_crosslinker_type(self: pylimer_tools_cpp.DataFileWriter, crosslinker_type: int = 2) → None

Set which atom type represents crosslinkers. Needed in case the moleculeIdx in the output file should have any meaning. (e.g. with config_molecule_idx_for_swap()).

Parameters:

crosslinker_type – The atom type representing crosslinkers (default: 2)

config_include_angles(self: pylimer_tools_cpp.DataFileWriter, include_angles: bool = True) → None

Set whether to include the angles from the universe in the file or not.

Parameters:

include_angles – Whether to include angles (default: True)

config_include_dihedral_angles(self: pylimer_tools_cpp.DataFileWriter, include_dihedral_angles: bool = True) → None

Set whether to include the dihedral angles from the universe in the file or not.

Parameters:

include_dihedral_angles – Whether to include dihedral angles (default: True)

config_include_velocities(self: pylimer_tools_cpp.DataFileWriter, include_velocities: bool = True) → None

Set whether to include the velocities from the universe (if any) in the file or not.

Parameters:

include_velocities – Whether to include velocities (default: True)

config_molecule_idx_for_swap(self: pylimer_tools_cpp.DataFileWriter, enable_swappability: bool = False) → None

Swappable chains implies that their moleculeIdx in the LAMMPS data file is not identical per chain, but identical per position in the chain. That’s how you can have bond swapping with constant chain length distribution.

Parameters:

enable_swappability – Whether to enable molecule index swappability (default: False)

config_move_into_box(self: pylimer_tools_cpp.DataFileWriter, move_into_box: bool = False) → None

Set whether to change the output coordinates to lie in the box or not.

Parameters:

move_into_box – Whether to move coordinates into box (default: False)

config_reindex_atoms(self: pylimer_tools_cpp.DataFileWriter, reindex_atoms: bool = False) → None

Set whether to reindex the atoms or not. Re-indexing leads to atom IDs being in the range of 1 to the number of atoms.

Parameters:

reindex_atoms – Whether to reindex atoms (default: False)

set_custom_atom_format(self: pylimer_tools_cpp.DataFileWriter, atom_format: str = '\t$atomId\t$moleculeId\t$atomType\t$x\t$y\t$z\t$nx\t$ny\t$nz') → None

Specify a custom format for the atom section.

Placeholder options are:

• $atomId

• $moleculeId

• $atomType

• $x

• $y

• $z

• $nx

• $ny

• $nz

Additionally, you can use the keys used in set_property_value() as placeholders (as long as they are alphanumeric only; prefix in the format with ‘$’ as well). Other placeholders are available if the universe was read from a LAMMPS data file with an atom style with additional data.

This method is specifically useful if you need a different (or hybrid) atom style in LAMMPS.

Be sure to still call config_atom_style(), so that the file can be read correctly again.

Parameters:

atom_format – Custom format string for atoms (default: tab-separated standard format)

set_universe_to_write(self: pylimer_tools_cpp.DataFileWriter, universe: pylimer_tools_cpp.Universe) → None

Re-set the universe to write.

Parameters:

universe – The new universe to write to the data file

write_to_file(self: pylimer_tools_cpp.DataFileWriter, file: str) → None

Actually do the writing to the disk.

Parameters:

file – The path and file name to write to