#### NOTE [Go to the end](#sphx-glr-download-auto-examples-readers-writers-plot-data-file-writer-py) to download the full example code. # Data File Writer The [`DataFileWriter`](../../api/pylimer_tools_cpp.DataFileWriter.html.md#pylimer_tools_cpp.DataFileWriter) generates LAMMPS-compatible data files. ```Python import os import random from pylimer_tools_cpp import AtomStyle, DataFileWriter, Universe # create folder generated_structures/ if not os.path.exists("generated_structures"): os.makedirs("generated_structures") # Generate a universe to write universe = Universe(10.0, 10.0, 10.0) universe.add_atoms( list(range(100)), [1 for _ in range(100)], [random.random() * 10.0 for _ in range(100)], [random.random() * 10.0 for _ in range(100)], [random.random() * 10.0 for _ in range(100)], [0 for _ in range(100)], [0 for _ in range(100)], [0 for _ in range(100)], ) # universe.add_bonds( # … # ) # Create writer for a universe writer = DataFileWriter(universe) # Basic output writer.write_to_file("generated_structures/output.structure.dat") ``` ## Advanced Configuration ```Python # Configure output options writer = DataFileWriter(universe) # Include topology information writer.config_include_angles(True) writer.config_include_dihedral_angles(True) # Control atom numbering writer.config_reindex_atoms(True) writer.config_crosslinker_type(2) # Handle periodic boundaries writer.config_move_into_box(True) writer.config_attempt_image_reset(True) # Include velocities writer.config_include_velocities(True) # Write configured output writer.write_to_file("generated_structures/configured_output.data") ``` ## Custom Atom Styles You can specify custom atom styles and formats using the following format: ```Python # Set predefined atom style writer.config_atom_style(AtomStyle.FULL) # Or define custom format custom_format = "$atomId $moleculeId $atomType $charge $x $y $z" writer.set_custom_atom_format(custom_format) ``` Note that currently, the atom styles `tdpd` and `hybrid` are not supported without you specifying this custom format. ## Molecule Indexing Control Control how molecules are numbered in the output ```Python # Standard molecular indexing: sets the molecule index for each atom # based on the decomposition at the junctions writer.config_molecule_idx_for_swap(False) # Optimize for LAMMPS' ``bond/swap`` operations # Sets the molecule index for each atom based on the distance from the # next junction writer.config_molecule_idx_for_swap(True) writer.config_molecule_idx_for_swap(True) ``` **Total running time of the script:** (0 minutes 0.004 seconds) [`Download Jupyter notebook: plot_data_file_writer.ipynb`](_downloads/0631f75f6838d78a5faf4611c88f7bcd/plot_data_file_writer.ipynb) [`Download Python source code: plot_data_file_writer.py`](_downloads/748057cfd1b0bb073a3921a395a9c7f8/plot_data_file_writer.py) [`Download zipped: plot_data_file_writer.zip`](_downloads/fd35ff0298534bb5f09a37f322230ad0/plot_data_file_writer.zip) [Gallery generated by Sphinx-Gallery](https://sphinx-gallery.github.io)