Welcome to Atomaton’s documentation!

Indices and tables

• Index

• Module Index

• Search Page

Contents

• Usage
  • Installation
  • Analyzer: atomaton.analyze
    • bin_data()
    • create_extended_cell()
    • create_extended_cell_minimal()
    • get_angle_properties()
    • get_bond_properties()
    • get_bonds_on_atom()
    • guess_angles()
    • guess_bonds()
    • guess_dihedrals_and_impropers()
    • remove_atoms_outside_cell()
    • remove_duplicate_atoms()
    • split_by_property()
    • wrap_atoms_outside_cell()
• Classes
  • Models: atomaton.models
    • Angle
    • Atoms
      • Atoms.bind_from_ase()
      • Atoms.bind_from_file()
      • Atoms.calculate_angles()
      • Atoms.calculate_bonds()
      • Atoms.calculate_bounding_box()
      • Atoms.calculate_dihedrals_and_impropers()
      • Atoms.center_in_cell()
      • Atoms.center_on_position()
      • Atoms.create_extended_cell_minimal()
      • Atoms.delete_atoms()
      • Atoms.get_bonds_metadata()
      • Atoms.get_center_of_positions()
      • Atoms.insert_atoms()
      • Atoms.overlap_at_point()
      • Atoms.shift_atoms()
      • Atoms.view()
    • Bond
    • Crystal
      • Crystal.build_supercell()
    • Improper
    • SimulationBox
      • SimulationBox.build_supercell()
      • SimulationBox.create_from_atoms()
      • SimulationBox.insert_atoms()
      • SimulationBox.overlap_at_point()
      • SimulationBox.view()
    • UnitCell
      • UnitCell.get_cart_to_frac_matrix()
      • UnitCell.get_center_of_cell()
      • UnitCell.get_corners()
      • UnitCell.get_frac_to_cart_matrix()
• LAMMPS
  • LAMMPS Input File Generation: atomaton.write_lammps_files
    • get_lammps_box_parameters()
    • get_masses()
    • write_angle_coeff_section()
    • write_angle_section()
    • write_atom_section()
    • write_bond_coeff_section()
    • write_bond_section()
    • write_box_info()
    • write_header()
    • write_header_comments()
    • write_lammps_data_file()
    • write_lammps_data_file_alt()
    • write_mass_section()
    • write_multibody_terms_header()
    • write_pair_coeff_section()
• Visualize
  • Visualizer: atomaton.visualize
    • bin_data()
    • convert_images_to_gif()
    • draw_atoms()
    • draw_bonds()
    • draw_unit_cell()
    • view_structure()

Check out the Usage section for further information, including how to install the project.

Learn about key classes!

View structures and generate movies!

Integrate with LAMMPS!