qsym2/auxiliary/

molecule.rs

//! Molecular structures.

use std::collections::{HashMap, HashSet};
use std::fmt;
use std::fs;
use std::io::{BufWriter, Write};
use std::path::Path;
use std::process;

use anyhow;
use itertools::Itertools;
use log;
use nalgebra::{DVector, Matrix3, Point3, Vector3};
use ndarray::{Array2, ShapeBuilder};
use ndarray_linalg::{Eigh, UPLO};
use num_traits::ToPrimitive;
use serde::{Deserialize, Serialize};

use crate::auxiliary::atom::{Atom, AtomKind, ElementMap};
use crate::auxiliary::geometry::{self, ImproperRotationKind, Transform};
use crate::permutation::{PermutableCollection, Permutation, permute_inplace};

#[cfg(test)]
#[path = "sea_tests.rs"]
mod sea_tests;

#[cfg(test)]
#[path = "molecule_tests.rs"]
mod molecule_tests;

// ==================
// Struct definitions
// ==================

/// Structure containing the atoms constituting a molecule.
#[derive(Clone, Debug, Serialize, Deserialize)]
pub struct Molecule {
    /// The atoms constituting this molecule.
    pub atoms: Vec<Atom>,

    /// Optional special atom to represent the electric fields applied to this molecule.
    pub electric_atoms: Option<Vec<Atom>>,

    /// Optional special atoms to represent the magnetic fields applied to this molecule.
    pub magnetic_atoms: Option<Vec<Atom>>,

    /// A threshold for approximate equality comparisons.
    pub threshold: f64,
}

impl Molecule {
    /// Parses an XYZ file to construct a molecule.
    ///
    /// # Arguments
    ///
    /// * `filename` - The XYZ file to be parsed.
    ///
    /// # Returns
    ///
    /// The parsed [`Molecule`] structure.
    ///
    /// # Panics
    ///
    /// Panics when unable to parse the provided XYZ file.
    #[must_use]
    pub fn from_xyz<P: AsRef<Path>>(filename: P, thresh: f64) -> Self {
        let contents = fs::read_to_string(&filename).unwrap_or_else(|err| {
            log::error!("Unable to read file {}.", filename.as_ref().display());
            log::error!("{}", err);
            process::exit(1);
        });

        let mut atoms: Vec<Atom> = vec![];
        let emap = ElementMap::new();
        let mut n_atoms = 0usize;
        for (i, line) in contents.lines().enumerate() {
            if i == 0 {
                n_atoms = line.parse::<usize>().unwrap_or_else(|err| {
                    log::error!(
                        "Unable to read number of atoms in {}.",
                        filename.as_ref().display()
                    );
                    log::error!("{}", err);
                    process::exit(1);
                });
            } else if i == 1 {
                continue;
            } else {
                atoms.push(
                    Atom::from_xyz(line, &emap, thresh)
                        .unwrap_or_else(|| panic!("Unable to parse {line} to give an atom.")),
                );
            }
        }
        assert_eq!(
            atoms.len(),
            n_atoms,
            "Expected {} atoms, got {} instead.",
            n_atoms,
            atoms.len()
        );
        Molecule {
            atoms,
            electric_atoms: None,
            magnetic_atoms: None,
            threshold: thresh,
        }
    }

    /// Writes the ordinary atoms in the molecule to an XYZ file.
    ///
    /// # Arguments
    ///
    /// * `filename` - The XYZ file to be written.
    pub fn to_xyz<P: AsRef<Path>>(&self, filename: P) -> Result<(), anyhow::Error> {
        let mut f = BufWriter::new(fs::File::create(filename)?);
        writeln!(f, "{}", self.atoms.len())?;
        writeln!(f)?;
        for atom in self.atoms.iter() {
            writeln!(f, "{}", atom.to_xyz())?;
        }
        Ok(())
    }

    /// Construct a molecule from an array of atoms.
    ///
    /// # Arguments
    ///
    /// * `all_atoms` - The atoms (of all types) constituting this molecule.
    /// * `threshold` - A threshold for approximate equality comparisons.
    ///
    /// # Returns
    ///
    /// The constructed [`Molecule`] struct.
    ///
    /// # Panics
    ///
    /// Panics when the numbers of fictitious special atoms, if any, are invalid. It is expected
    /// that, when present, there are two magnetic special atoms and/or one electric special atom.
    #[must_use]
    pub fn from_atoms(all_atoms: &[Atom], thresh: f64) -> Self {
        let mut atoms: Vec<Atom> = all_atoms
            .iter()
            .filter(|atom| matches!(atom.kind, AtomKind::Ordinary))
            .cloned()
            .collect();
        atoms.iter_mut().for_each(|atom| atom.threshold = thresh);

        let mut magnetic_atoms_vec: Vec<Atom> = all_atoms
            .iter()
            .filter(|atom| matches!(atom.kind, AtomKind::Magnetic(_)))
            .cloned()
            .collect();
        magnetic_atoms_vec
            .iter_mut()
            .for_each(|atom| atom.threshold = thresh);
        let magnetic_atoms = if magnetic_atoms_vec.is_empty() {
            None
        } else {
            Some(magnetic_atoms_vec)
        };

        let mut electric_atoms_vec: Vec<Atom> = all_atoms
            .iter()
            .filter(|atom| matches!(atom.kind, AtomKind::Electric(_)))
            .cloned()
            .collect();
        electric_atoms_vec
            .iter_mut()
            .for_each(|atom| atom.threshold = thresh);
        let electric_atoms = if electric_atoms_vec.is_empty() {
            None
        } else {
            Some(electric_atoms_vec)
        };

        Molecule {
            atoms,
            electric_atoms,
            magnetic_atoms,
            threshold: thresh,
        }
    }

    /// Constructs a new molecule containing only the ordinary atoms in this molecule.
    #[must_use]
    pub fn molecule_ordinary_atoms(&self) -> Self {
        Self::from_atoms(&self.atoms, self.threshold)
    }

    /// Constructs a new molecule containing only the fictitious magnetic atoms in this molecule,
    /// if any.
    ///
    /// # Returns
    ///
    /// Returns `None` if this molecule has no fictitious magnetic atoms.
    #[must_use]
    pub fn molecule_magnetic_atoms(&self) -> Option<Self> {
        Some(Self::from_atoms(
            self.magnetic_atoms.as_ref()?,
            self.threshold,
        ))
    }

    /// Constructs a new molecule containing only the fictitious electric atoms in this molecule,
    /// if any.
    ///
    /// # Returns
    ///
    /// Returns `None` if this molecule has no fictitious electric atoms.
    #[must_use]
    pub fn molecule_electric_atoms(&self) -> Option<Self> {
        Some(Self::from_atoms(
            self.electric_atoms.as_ref()?,
            self.threshold,
        ))
    }

    /// Retrieves a vector of references to all atoms in this molecule, including special ones, if
    /// any.
    ///
    /// # Returns
    ///
    /// All atoms in this molecule.
    #[must_use]
    pub fn get_all_atoms(&self) -> Vec<&Atom> {
        let mut atoms: Vec<&Atom> = vec![];
        for atom in &self.atoms {
            atoms.push(atom);
        }
        if let Some(magnetic_atoms) = &self.magnetic_atoms {
            for magnetic_atom in magnetic_atoms.iter() {
                atoms.push(magnetic_atom);
            }
        }
        if let Some(electric_atoms) = &self.electric_atoms {
            for electric_atom in electric_atoms.iter() {
                atoms.push(electric_atom);
            }
        }
        atoms
    }

    /// Retrieves a vector of mutable references to all atoms in this molecule, including special
    /// ones, if any.
    ///
    /// # Returns
    ///
    /// All atoms in this molecule.
    #[must_use]
    pub fn get_all_atoms_mut(&mut self) -> Vec<&mut Atom> {
        let mut atoms: Vec<&mut Atom> = vec![];
        for atom in &mut self.atoms {
            atoms.push(atom);
        }
        if let Some(magnetic_atoms) = &mut self.magnetic_atoms {
            for magnetic_atom in magnetic_atoms.iter_mut() {
                atoms.push(magnetic_atom);
            }
        }
        if let Some(electric_atoms) = &mut self.electric_atoms {
            for electric_atom in electric_atoms.iter_mut() {
                atoms.push(electric_atom);
            }
        }
        atoms
    }

    /// Calculates the centre of mass of the molecule.
    ///
    /// This does not take into account fictitious special atoms.
    ///
    /// # Returns
    ///
    /// The centre of mass.
    #[must_use]
    pub fn calc_com(&self) -> Point3<f64> {
        let atoms = &self.atoms;
        let mut com: Point3<f64> = Point3::origin();
        if atoms.is_empty() {
            return com;
        }
        let mut tot_m: f64 = 0.0;
        for atom in atoms.iter() {
            let m: f64 = atom.atomic_mass;
            com += atom.coordinates * m - Point3::origin();
            tot_m += m;
        }
        com *= 1.0 / tot_m;
        com
    }

    /// Calculates the inertia tensor of the molecule.
    ///
    /// This *does* take into account fictitious special atoms.
    ///
    /// # Arguments
    ///
    /// * `origin` - An origin about which the inertia tensor is evaluated.
    ///
    /// # Returns
    ///
    /// The inertia tensor as a $`3 \times 3`$ matrix.
    #[must_use]
    pub fn calc_inertia_tensor(&self, origin: &Point3<f64>) -> Matrix3<f64> {
        let atoms = self.get_all_atoms();
        let mut inertia_tensor = Matrix3::zeros();
        for atom in &atoms {
            let rel_coordinates: Vector3<f64> = atom.coordinates - origin;
            for i in 0..3 {
                for j in 0..=i {
                    if i == j {
                        inertia_tensor[(i, j)] += atom.atomic_mass
                            * (rel_coordinates.norm_squared()
                                - rel_coordinates[i] * rel_coordinates[j]);
                    } else {
                        inertia_tensor[(i, j)] -=
                            atom.atomic_mass * rel_coordinates[i] * rel_coordinates[j];
                        inertia_tensor[(j, i)] -=
                            atom.atomic_mass * rel_coordinates[j] * rel_coordinates[i];
                    }
                }
            }
        }
        log::debug!("Origin for inertia tensor:");
        for component in origin.iter() {
            log::debug!("  {component:+.14}");
        }
        log::debug!("Inertia tensor:\n{}", inertia_tensor);
        inertia_tensor
    }

    /// Calculates the moments of inertia and the corresponding principal axes.
    ///
    /// This *does* take into account fictitious special atoms.
    ///
    /// # Returns
    ///
    /// * The moments of inertia in ascending order.
    /// * The corresponding principal axes.
    ///
    /// # Panics
    ///
    /// Panics when any of the moments of inertia cannot be compared.
    #[must_use]
    pub fn calc_moi(&self) -> ([f64; 3], [Vector3<f64>; 3]) {
        let inertia_tensor = Array2::from_shape_vec(
            (3, 3).f(),
            self.calc_inertia_tensor(&self.calc_com())
                .into_iter()
                .copied()
                .collect::<Vec<_>>(),
        )
        .expect("Unable to construct the inertia tensor.");
        let (eigvals, eigvecs) = inertia_tensor
            .eigh(UPLO::Lower)
            .expect("Unable to diagonalise the inertia tensor.");
        let eigenvalues: Vec<f64> = eigvals.into_iter().collect::<Vec<_>>();
        let eigenvectors = eigvecs
            .columns()
            .into_iter()
            .map(|col| Vector3::from_iterator(col.into_owned()))
            .collect::<Vec<_>>();
        let mut eigen_tuple: Vec<(f64, _)> = eigenvalues
            .iter()
            .copied()
            .zip(eigenvectors.iter().copied())
            .collect();
        eigen_tuple.sort_by(|(eigval0, _), (eigval1, _)| {
            eigval0
                .partial_cmp(eigval1)
                .unwrap_or_else(|| panic!("{eigval0} and {eigval1} cannot be compared."))
        });
        let (sorted_eigenvalues, sorted_eigenvectors): (Vec<f64>, Vec<_>) =
            eigen_tuple.into_iter().unzip();
        let result = (
            [
                sorted_eigenvalues[0],
                sorted_eigenvalues[1],
                sorted_eigenvalues[2],
            ],
            [
                geometry::get_standard_positive_pole(
                    &Vector3::new(
                        sorted_eigenvectors[0][(0, 0)],
                        sorted_eigenvectors[0][(1, 0)],
                        sorted_eigenvectors[0][(2, 0)],
                    ),
                    self.threshold,
                ),
                geometry::get_standard_positive_pole(
                    &Vector3::new(
                        sorted_eigenvectors[1][(0, 0)],
                        sorted_eigenvectors[1][(1, 0)],
                        sorted_eigenvectors[1][(2, 0)],
                    ),
                    self.threshold,
                ),
                geometry::get_standard_positive_pole(
                    &Vector3::new(
                        sorted_eigenvectors[2][(0, 0)],
                        sorted_eigenvectors[2][(1, 0)],
                        sorted_eigenvectors[2][(2, 0)],
                    ),
                    self.threshold,
                ),
            ],
        );
        result
            .0
            .iter()
            .zip(result.1.iter())
            .for_each(|(moi, axis)| {
                log::debug!("Principal moment of inertia: {moi:.14}");
                log::debug!("  -- Principal axis:\n{axis}");
            });
        result
    }

    /// Determines the interatomic distance matrix and the indices of symmetry-equivalent atoms.
    ///
    /// This *does* take into account fictitious special atoms.
    ///
    /// # Returns
    ///
    /// * The interatomic distance matrix where the distances in each column are sorted in ascending
    ///   order. Column $`j`$ contains the interatomic distances from atom $`j`$ to all other atoms
    ///   (both ordinary and fictitious) in the molecule. Also note that all atoms (both ordinary and
    ///   fictitious) are included here, so the matrix is square.
    /// * A vector of vectors of symmetry-equivalent atom indices. Each inner vector contains
    ///   indices of atoms in one SEA group.
    pub fn calc_interatomic_distance_matrix(&self) -> (Array2<f64>, Vec<Vec<usize>>) {
        let all_atoms = &self.get_all_atoms();
        let all_coords: Vec<_> = all_atoms.iter().map(|atm| atm.coordinates).collect();
        let mut dist_columns: Vec<DVector<f64>> = vec![];
        let mut sorted_dist_columns: Vec<DVector<f64>> = vec![];

        // Determine indices of symmetry-equivalent atoms
        let mut equiv_indicess: Vec<Vec<usize>> = vec![vec![0]];
        for (j, coord_j) in all_coords.iter().enumerate() {
            // column_j is the j-th column in the interatomic distance matrix. This column contains
            // distances from ordinary atom j to all other atoms (both ordinary and fictitious) in
            // the molecule.
            let column_j = all_coords
                .iter()
                .map(|coord_i| (coord_j - coord_i).norm())
                .collect_vec();
            let mut sorted_column_j = column_j.clone();
            dist_columns.push(DVector::from_vec(column_j));

            sorted_column_j.sort_by(|a, b| {
                a.partial_cmp(b).unwrap_or_else(|| {
                    panic!("Mass-weighted interatomic distances {a} and {b} cannot be compared.")
                })
            });
            let sorted_column_j_vec = DVector::from_vec(sorted_column_j);
            if j == 0 {
                sorted_dist_columns.push(sorted_column_j_vec);
            } else {
                let equiv_set_search = equiv_indicess.iter().position(|equiv_indices| {
                    sorted_dist_columns[equiv_indices[0]].relative_eq(
                        &sorted_column_j_vec,
                        self.threshold,
                        self.threshold,
                    ) && match (&all_atoms[j].kind, &all_atoms[equiv_indices[0]].kind) {
                        (AtomKind::Ordinary, AtomKind::Ordinary) => {
                            all_atoms[j].atomic_number == all_atoms[equiv_indices[0]].atomic_number
                        }
                        (AtomKind::Magnetic(_), AtomKind::Magnetic(_))
                        | (AtomKind::Electric(_), AtomKind::Electric(_)) => true,
                        _ => false,
                    }
                });
                sorted_dist_columns.push(sorted_column_j_vec);
                if let Some(index) = equiv_set_search {
                    equiv_indicess[index].push(j);
                } else {
                    equiv_indicess.push(vec![j]);
                };
            }
        }

        let dist_elements_f = dist_columns.iter().flatten().cloned().collect::<Vec<_>>();
        let n_atoms = all_atoms.len();
        let dist_matrix = Array2::<f64>::from_shape_vec((n_atoms, n_atoms).f(), dist_elements_f)
            .expect("Unable to collect the interatomic distances into a square matrix.");

        (dist_matrix, equiv_indicess)
    }

    /// Determines the sets of symmetry-equivalent atoms.
    ///
    /// This *does* take into account fictitious special atoms.
    ///
    /// # Returns
    ///
    /// * Copies of the atoms in the molecule, grouped into symmetry-equivalent
    ///   groups.
    ///
    /// # Panics
    ///
    /// Panics when the any of the mass-weighted interatomic distances cannot be compared.
    #[must_use]
    pub fn calc_sea_groups(&self) -> Vec<Vec<Atom>> {
        let all_atoms = &self.get_all_atoms();
        let (_, equiv_indicess) = self.calc_interatomic_distance_matrix();
        let sea_groups: Vec<Vec<Atom>> = equiv_indicess
            .iter()
            .map(|equiv_indices| {
                equiv_indices
                    .iter()
                    .map(|index| all_atoms[*index].clone())
                    .collect()
            })
            .collect();

        log::debug!("Number of SEA groups: {}", sea_groups.len());
        sea_groups
    }

    /// Adds two fictitious magnetic atoms to represent the magnetic field.
    ///
    /// # Arguments
    ///
    /// * `magnetic_field` - The magnetic field vector. If zero or `None`, any magnetic
    ///   field present will be removed.
    ///
    /// # Panics
    ///
    /// Panics when the number of atoms cannot be represented as an `f64` value.
    pub fn set_magnetic_field(&mut self, magnetic_field: Option<Vector3<f64>>) {
        if let Some(b_vec) = magnetic_field {
            if approx::relative_ne!(b_vec.norm(), 0.0) {
                let com = self.calc_com();
                let ave_mag = {
                    let average_distance = self
                        .atoms
                        .iter()
                        .fold(0.0, |acc, atom| acc + (atom.coordinates - com).magnitude())
                        / self.atoms.len().to_f64().unwrap_or_else(|| {
                            panic!("Unable to convert `{}` to `f64`.", self.atoms.len())
                        });
                    if average_distance > 0.0 {
                        average_distance
                    } else {
                        0.5
                    }
                };
                let b_vec_norm = b_vec.normalize() * ave_mag * 0.5;
                self.magnetic_atoms = Some(vec![
                    Atom::new_special(AtomKind::Magnetic(true), com + b_vec_norm, self.threshold)
                        .expect("Unable to construct a special magnetic atom."),
                    Atom::new_special(AtomKind::Magnetic(false), com - b_vec_norm, self.threshold)
                        .expect("Unable to construct a special magnetic atom."),
                ]);
            } else {
                self.magnetic_atoms = None;
            }
        } else {
            self.magnetic_atoms = None;
        }
    }

    /// Adds one fictitious electric atom to represent the electric field.
    ///
    /// # Arguments
    ///
    /// * `electric_field` - The electric field vector. If zero or `None`, any electric
    ///   field present will be removed.
    ///
    /// # Panics
    ///
    /// Panics when the number of atoms cannot be represented as an `f64` value.
    pub fn set_electric_field(&mut self, electric_field: Option<Vector3<f64>>) {
        if let Some(e_vec) = electric_field {
            if approx::relative_ne!(e_vec.norm(), 0.0) {
                let com = self.calc_com();
                let ave_mag = {
                    let average_distance = self
                        .atoms
                        .iter()
                        .fold(0.0, |acc, atom| acc + (atom.coordinates - com).magnitude())
                        / self.atoms.len().to_f64().unwrap_or_else(|| {
                            panic!("Unable to convert `{}` to `f64`.", self.atoms.len())
                        });
                    if average_distance > 0.0 {
                        average_distance
                    } else {
                        0.5
                    }
                };
                let e_vec_norm = e_vec.normalize() * ave_mag * 0.5;
                self.electric_atoms = Some(vec![
                    Atom::new_special(AtomKind::Electric(true), com + e_vec_norm, self.threshold)
                        .expect("Unable to construct an electric special atom."),
                ]);
            } else {
                self.electric_atoms = None;
            }
        } else {
            self.electric_atoms = None;
        }
    }

    /// Clones this molecule and adjusts all comparison thresholds to that specified by `thresh`.
    ///
    /// # Arguments
    ///
    /// * `thresh` - The new threshold to be assigned to the cloned molecule.
    ///
    /// # Returns
    ///
    /// A cloned copy of the molecule wit the adjusted threshold.
    pub fn adjust_threshold(&self, thresh: f64) -> Self {
        Self::from_atoms(
            &self
                .get_all_atoms()
                .into_iter()
                .cloned()
                .collect::<Vec<_>>(),
            thresh,
        )
    }

    /// Reorientates the molecule in-place into a canonical alignment with the space-fixed axes of
    /// the coordinate system.
    ///
    /// Fictitious special atoms are also moved during the reorientation.
    ///
    /// If the molecule has a unique principal axis, then this axis becomes aligned with the
    /// $`z`$-axis and the other two degenerate axes become aligned with the $`x`$- and $`y`$-axes
    /// of the coordinate system. If the molecule has no unique principal axes, then the axes are
    /// aligned with $`x`$-, $`y`$-,  and $`z`$-axes in ascending order of moments of inertia.
    ///
    /// # Arguments
    ///
    /// * `moi_thresh` - Threshold for comparing moments of inertia.
    pub fn reorientate_mut(&mut self, moi_thresh: f64) {
        let (moi, principal_axes) = self.calc_moi();
        let rotmat = if approx::relative_ne!(
            moi[0],
            moi[1],
            max_relative = moi_thresh,
            epsilon = moi_thresh
        ) && approx::relative_eq!(
            moi[1],
            moi[2],
            max_relative = moi_thresh,
            epsilon = moi_thresh
        ) {
            // principal_axes[0] is unique.
            Matrix3::from_columns(&[principal_axes[1], principal_axes[2], principal_axes[0]])
                .transpose()
        } else {
            // principal_axes[2] is unique, or no unique axis, or isotropic.
            Matrix3::from_columns(&[principal_axes[0], principal_axes[1], principal_axes[2]])
                .transpose()
        };
        let com = self.calc_com();
        self.recentre_mut();
        self.transform_mut(&rotmat);
        self.translate_mut(&(com - Point3::origin()));
    }

    /// Clones and reorientates the molecule into a canonical alignment with the space-fixed axes
    /// of the coordinate system.
    ///
    /// Fictitious special atoms are also moved during the reorientation.
    ///
    /// If the molecule has a unique principal axis, then this axis becomes aligned with the
    /// $`z`$-axis and the other two degenerate axes become aligned with the $`x`$- and $`y`$-axes
    /// of the coordinate system. If the molecule has no unique principal axes, then the axes are
    /// aligned with $`x`$-, $`y`$-,  and $`z`$-axes in ascending order of moments of inertia.
    ///
    /// # Arguments
    ///
    /// * `moi_thresh` - Threshold for comparing moments of inertia.
    ///
    /// # Returns
    ///
    /// A reoriented copy of the molecule.
    pub fn reorientate(&self, moi_thresh: f64) -> Self {
        let mut reoriented_mol = self.clone();
        reoriented_mol.reorientate_mut(moi_thresh);
        reoriented_mol
    }
}

// =====================
// Trait implementations
// =====================

impl fmt::Display for Molecule {
    fn fmt(&self, f: &mut fmt::Formatter<'_>) -> fmt::Result {
        writeln!(f, "Molecule consisting of")?;
        for atom in self.get_all_atoms().iter() {
            writeln!(f, "  {atom}")?;
        }
        Ok(())
    }
}

impl Transform for Molecule {
    fn transform_mut(&mut self, mat: &Matrix3<f64>) {
        for atom in &mut self.atoms {
            atom.transform_mut(mat);
        }
        if let Some(ref mut mag_atoms) = self.magnetic_atoms {
            for atom in mag_atoms.iter_mut() {
                atom.transform_mut(mat);
            }
        }
        if let Some(ref mut ele_atoms) = self.electric_atoms {
            for atom in ele_atoms.iter_mut() {
                atom.transform_mut(mat);
            }
        }
    }

    fn rotate_mut(&mut self, angle: f64, axis: &Vector3<f64>) {
        for atom in &mut self.atoms {
            atom.rotate_mut(angle, axis);
        }
        if let Some(ref mut mag_atoms) = self.magnetic_atoms {
            for atom in mag_atoms.iter_mut() {
                atom.rotate_mut(angle, axis);
            }
        }
        if let Some(ref mut ele_atoms) = self.electric_atoms {
            for atom in ele_atoms.iter_mut() {
                atom.rotate_mut(angle, axis);
            }
        }
    }

    fn improper_rotate_mut(
        &mut self,
        angle: f64,
        axis: &Vector3<f64>,
        kind: &ImproperRotationKind,
    ) {
        for atom in &mut self.atoms {
            atom.improper_rotate_mut(angle, axis, kind);
        }
        if let Some(ref mut mag_atoms) = self.magnetic_atoms {
            for atom in mag_atoms.iter_mut() {
                atom.improper_rotate_mut(angle, axis, kind);
            }
        }
        if let Some(ref mut ele_atoms) = self.electric_atoms {
            for atom in ele_atoms.iter_mut() {
                atom.improper_rotate_mut(angle, axis, kind);
            }
        }
    }

    fn translate_mut(&mut self, tvec: &Vector3<f64>) {
        for atom in &mut self.atoms {
            atom.translate_mut(tvec);
        }
        if let Some(ref mut mag_atoms) = self.magnetic_atoms {
            for atom in mag_atoms.iter_mut() {
                atom.translate_mut(tvec);
            }
        }
        if let Some(ref mut ele_atoms) = self.electric_atoms {
            for atom in ele_atoms.iter_mut() {
                atom.translate_mut(tvec);
            }
        }
    }

    fn recentre_mut(&mut self) {
        let com = self.calc_com();
        let tvec = -Vector3::new(com[0], com[1], com[2]);
        self.translate_mut(&tvec);
    }

    fn reverse_time_mut(&mut self) {
        if let Some(ref mut mag_atoms) = self.magnetic_atoms {
            for atom in mag_atoms.iter_mut() {
                atom.reverse_time_mut();
            }
        }
    }

    fn transform(&self, mat: &Matrix3<f64>) -> Self {
        let mut transformed_mol = self.clone();
        transformed_mol.transform_mut(mat);
        transformed_mol
    }

    fn rotate(&self, angle: f64, axis: &Vector3<f64>) -> Self {
        let mut rotated_mol = self.clone();
        rotated_mol.rotate_mut(angle, axis);
        rotated_mol
    }

    fn improper_rotate(
        &self,
        angle: f64,
        axis: &Vector3<f64>,
        kind: &ImproperRotationKind,
    ) -> Self {
        let mut improper_rotated_mol = self.clone();
        improper_rotated_mol.improper_rotate_mut(angle, axis, kind);
        improper_rotated_mol
    }

    fn translate(&self, tvec: &Vector3<f64>) -> Self {
        let mut translated_mol = self.clone();
        translated_mol.translate_mut(tvec);
        translated_mol
    }

    fn recentre(&self) -> Self {
        let mut recentred_mol = self.clone();
        recentred_mol.recentre_mut();
        recentred_mol
    }

    fn reverse_time(&self) -> Self {
        let mut time_reversed_mol = self.clone();
        time_reversed_mol.reverse_time_mut();
        time_reversed_mol
    }
}

impl PartialEq for Molecule {
    fn eq(&self, other: &Self) -> bool {
        if self.atoms.len() != other.atoms.len() {
            return false;
        };
        let thresh = self
            .atoms
            .iter()
            .chain(other.atoms.iter())
            .fold(0.0_f64, |acc, atom| acc.max(atom.threshold));

        let mut other_atoms_ref: HashSet<_> = other.atoms.iter().collect();
        for s_atom in &self.atoms {
            let o_atom = other
                .atoms
                .iter()
                .find(|o_atm| (s_atom.coordinates - o_atm.coordinates).norm() < thresh);
            match o_atom {
                Some(atm) => {
                    other_atoms_ref.remove(atm);
                }
                None => {
                    break;
                }
            }
        }
        if !other_atoms_ref.is_empty() {
            return false;
        }

        if let Some(self_mag_atoms) = &self.magnetic_atoms {
            if let Some(other_mag_atoms) = &other.magnetic_atoms {
                let mut other_mag_atoms_ref: HashSet<_> = other_mag_atoms.iter().collect();
                for s_atom in self_mag_atoms.iter() {
                    let o_atom = other_mag_atoms.iter().find(|o_atm| {
                        (s_atom.coordinates - o_atm.coordinates).norm() < thresh
                            && s_atom.kind == o_atm.kind
                    });
                    match o_atom {
                        Some(atm) => {
                            other_mag_atoms_ref.remove(atm);
                        }
                        None => {
                            break;
                        }
                    }
                }
                if !other_mag_atoms_ref.is_empty() {
                    return false;
                }
            } else {
                return false;
            }
        } else if other.magnetic_atoms.is_some() {
            return false;
        };

        if let Some(self_ele_atoms) = &self.electric_atoms {
            if let Some(other_ele_atoms) = &other.electric_atoms {
                let mut other_ele_atoms_ref: HashSet<_> = other_ele_atoms.iter().collect();
                for s_atom in self_ele_atoms.iter() {
                    let o_atom = other_ele_atoms.iter().find(|o_atm| {
                        (s_atom.coordinates - o_atm.coordinates).norm() < thresh
                            && s_atom.kind == o_atm.kind
                    });
                    match o_atom {
                        Some(atm) => {
                            other_ele_atoms_ref.remove(atm);
                        }
                        None => {
                            break;
                        }
                    }
                }
                if !other_ele_atoms_ref.is_empty() {
                    return false;
                }
            } else {
                return false;
            }
        } else if other.electric_atoms.is_some() {
            return false;
        };
        true
    }
}

impl PermutableCollection for Molecule {
    type Rank = usize;

    /// Determines the permutation of *all* atoms to map `self` to `other`. Special fictitious
    /// atoms are included after ordinary atoms, with magnetic atoms before electric atoms.
    ///
    /// # Arguments
    ///
    /// * `other` - Another molecule to be compared with `self`.
    ///
    /// # Returns
    ///
    /// Returns a permutation that permutes *all* atoms of `self` to give `other`, or `None` if no
    /// such permutation exists.
    fn get_perm_of(&self, other: &Self) -> Option<Permutation<Self::Rank>> {
        let self_recentred = self.recentre();
        let other_recentred = other.recentre();
        let o_atoms: HashMap<Atom, usize> = other_recentred
            .atoms
            .into_iter()
            .chain(other_recentred.magnetic_atoms.unwrap_or_default())
            .chain(other_recentred.electric_atoms.unwrap_or_default())
            .enumerate()
            .map(|(i, atom)| (atom, i))
            .collect();
        let image_opt: Option<Vec<Self::Rank>> = self_recentred
            .atoms
            .iter()
            .chain(self_recentred.magnetic_atoms.unwrap_or_default().iter())
            .chain(self_recentred.electric_atoms.unwrap_or_default().iter())
            .map(|s_atom| {
                o_atoms
                    .get(s_atom)
                    .or_else(|| {
                        let thresh = s_atom.threshold;
                        log::debug!("Unable to retrieve matching original atom by hash. Falling back on distance comparisons with threshold {thresh:.3e}...");
                        o_atoms.iter().find_map(|(o_atom, o_atom_idx)| {
                            if s_atom.atomic_number == o_atom.atomic_number
                                && s_atom.kind == o_atom.kind
                                && (s_atom.coordinates - o_atom.coordinates).norm() < thresh
                            {
                                Some(o_atom_idx)
                            } else {
                                None
                            }
                        })
                    })
                    .copied()
            })
            .collect();
        image_opt.and_then(|image| Permutation::from_image(image).ok())
    }

    /// Permutes *all* atoms in this molecule (including special fictitious atoms) and places them
    /// in a new molecule to be returned.
    ///
    /// # Arguments
    ///
    /// * `perm` - A permutation for the atoms. Special fictitious atoms are included after
    ///   ordinary atoms, with magnetic atoms before electric atoms.
    ///
    /// # Returns
    ///
    /// A new molecule with the permuted atoms.
    ///
    /// # Panics
    ///
    /// Panics if the rank of `perm` does not match the number of atoms in this molecule, or if the
    /// permutation results in atoms of different kind (*e.g.* ordinary and magnetic) are permuted
    /// into each other.
    fn permute(&self, perm: &Permutation<Self::Rank>) -> Result<Self, anyhow::Error> {
        let mut p_mol = self.clone();
        p_mol.permute_mut(perm)?;
        Ok(p_mol)
    }

    /// Permutes in-place *all* atoms in this molecule (including special fictitious atoms).
    ///
    /// The in-place rearrangement implementation is taken from
    /// [here](https://stackoverflow.com/a/69774341/5112668).
    ///
    /// # Arguments
    ///
    /// * `perm` - A permutation for the atoms. Special fictitious atoms are included after
    ///   ordinary atoms, with magnetic atoms before electric atoms.
    ///
    /// # Panics
    ///
    /// Panics if the rank of `perm` does not match the number of atoms in this molecule, or if the
    /// permutation results in atoms of different kind (*e.g.* ordinary and magnetic) are permuted
    /// into each other.
    fn permute_mut(&mut self, perm: &Permutation<Self::Rank>) -> Result<(), anyhow::Error> {
        let n_ordinary = self.atoms.len();
        let perm_ordinary = Permutation::from_image(perm.image()[0..n_ordinary].to_vec())?;
        permute_inplace(&mut self.atoms, &perm_ordinary);

        let n_last = if let Some(mag_atoms) = self.magnetic_atoms.as_mut() {
            let n_magnetic = mag_atoms.len();
            let perm_magnetic = Permutation::from_image(
                perm.image()[n_ordinary..(n_ordinary + n_magnetic)]
                    .iter()
                    .map(|x| x - n_ordinary)
                    .collect::<Vec<_>>(),
            )?;
            permute_inplace(mag_atoms, &perm_magnetic);
            n_ordinary + n_magnetic
        } else {
            n_ordinary
        };

        if let Some(elec_atoms) = self.electric_atoms.as_mut() {
            let n_electric = elec_atoms.len();
            let perm_electric = Permutation::from_image(
                perm.image()[n_last..(n_last + n_electric)]
                    .iter()
                    .map(|x| x - n_last)
                    .collect::<Vec<_>>(),
            )?;
            permute_inplace(elec_atoms, &perm_electric);
        }
        Ok(())
    }
}