# fmt: off

"""Bravais.py - class for generating Bravais lattices etc.

This is a base class for numerous classes setting up pieces of crystal.
"""

import math
from typing import Optional, Sequence

import numpy as np

import ase.data
from ase.atoms import Atoms


class Bravais:
    """Bravais lattice factory.

    This is a base class for the objects producing various lattices
    (SC, FCC, ...).
    """

    # The following methods are NOT defined here, but must be defined
    # in classes inhering from Bravais:
    #   get_lattice_constant
    #   make_crystal_basis
    # The following class attributes are NOT defined here, but must be defined
    # in classes inhering from Bravais:
    #   int_basis
    #   inverse_basis

    other = {0: (1, 2), 1: (2, 0), 2: (0, 1)}

    # For Bravais lattices with a basis, set the basis here.  Leave as
    # None if no basis is present.
    bravais_basis: Optional[Sequence[Sequence[float]]] = None

    # If more than one type of element appear in the crystal, give the
    # order here.  For example, if two elements appear in a 3:1 ratio,
    # bravais_basis could contain four vectors, and element_basis
    # could be (0,0,1,0) - the third atom in the basis is different
    # from the other three.  Leave as None if all atoms are of the
    # same type.
    element_basis: Optional[Sequence[int]] = None

    # How small numbers should be considered zero in the unit cell?
    chop_tolerance = 1e-10

    def __call__(self, symbol,
                 directions=(None, None, None), miller=(None, None, None),
                 size=(1, 1, 1), latticeconstant=None,
                 pbc=True, align=True, debug=0):
        "Create a lattice."
        self.size = size
        self.pbc = pbc
        self.debug = debug
        self.process_element(symbol)
        self.find_directions(directions, miller)
        if self.debug:
            self.print_directions_and_miller()
        self.convert_to_natural_basis()
        if self.debug >= 2:
            self.print_directions_and_miller(" (natural basis)")
        if latticeconstant is None:
            if self.element_basis is None:
                self.latticeconstant = self.get_lattice_constant()
            else:
                raise ValueError(
                    "A lattice constant must be specified for a compound")
        else:
            self.latticeconstant = latticeconstant
        if self.debug:
            print(
                "Expected number of atoms in unit cell:",
                self.calc_num_atoms())
        if self.debug >= 2:
            print("Bravais lattice basis:", self.bravais_basis)
            if self.bravais_basis is not None:
                print(" ... in natural basis:", self.natural_bravais_basis)
        self.make_crystal_basis()
        self.make_unit_cell()
        if align:
            self.align()
        return self.make_list_of_atoms()

    def align(self):
        "Align the first axis along x-axis and the second in the x-y plane."
        degree = 180 / np.pi
        if self.debug >= 2:
            print("Basis before alignment:")
            print(self.basis)
        if self.basis[0][0]**2 + \
                self.basis[0][2]**2 < 0.01 * self.basis[0][1]**2:
            # First basis vector along y axis - rotate 90 deg along z
            t = np.array([[0, -1, 0],
                          [1, 0, 0],
                          [0, 0, 1]], float)
            self.basis = np.dot(self.basis, t)
            transf = t
            if self.debug >= 2:
                print("Rotating -90 degrees around z axis for numerical "
                      "stability.")
                print(self.basis)
        else:
            transf = np.identity(3, float)
        assert abs(np.linalg.det(transf) - 1) < 1e-6
        # Rotate first basis vector into xy plane
        theta = math.atan2(self.basis[0, 2], self.basis[0, 0])
        t = np.array([[np.cos(theta), 0, -np.sin(theta)],
                      [0, 1, 0],
                      [np.sin(theta), 0, np.cos(theta)]])
        self.basis = np.dot(self.basis, t)
        transf = np.dot(transf, t)
        if self.debug >= 2:
            print(f"Rotating {-theta * degree:f} degrees around y axis.")
            print(self.basis)
        assert abs(np.linalg.det(transf) - 1) < 1e-6
        # Rotate first basis vector to point along x axis
        theta = math.atan2(self.basis[0, 1], self.basis[0, 0])
        t = np.array([[np.cos(theta), -np.sin(theta), 0],
                      [np.sin(theta), np.cos(theta), 0],
                      [0, 0, 1]])
        self.basis = np.dot(self.basis, t)
        transf = np.dot(transf, t)
        if self.debug >= 2:
            print(f"Rotating {-theta * degree:f} degrees around z axis.")
            print(self.basis)
        assert abs(np.linalg.det(transf) - 1) < 1e-6
        # Rotate second basis vector into xy plane
        theta = math.atan2(self.basis[1, 2], self.basis[1, 1])
        t = np.array([[1, 0, 0],
                      [0, np.cos(theta), -np.sin(theta)],
                      [0, np.sin(theta), np.cos(theta)]])
        self.basis = np.dot(self.basis, t)
        transf = np.dot(transf, t)
        if self.debug >= 2:
            print(f"Rotating {-theta * degree:f} degrees around x axis.")
            print(self.basis)
        assert abs(np.linalg.det(transf) - 1) < 1e-6
        # Now we better rotate the atoms as well
        self.atoms = np.dot(self.atoms, transf)
        # ... and rotate miller_basis
        self.miller_basis = np.dot(self.miller_basis, transf)

    def make_list_of_atoms(self):
        "Repeat the unit cell."
        nrep = self.size[0] * self.size[1] * self.size[2]
        if nrep <= 0:
            raise ValueError(
                "Cannot create a non-positive number of unit cells")
        # Now the unit cells must be merged.
        a2 = []
        e2 = []
        for i in range(self.size[0]):
            offset = self.basis[0] * i
            a2.append(self.atoms + offset[np.newaxis, :])
            e2.append(self.elements)
        atoms = np.concatenate(a2)
        elements = np.concatenate(e2)
        a2 = []
        e2 = []
        for j in range(self.size[1]):
            offset = self.basis[1] * j
            a2.append(atoms + offset[np.newaxis, :])
            e2.append(elements)
        atoms = np.concatenate(a2)
        elements = np.concatenate(e2)
        a2 = []
        e2 = []
        for k in range(self.size[2]):
            offset = self.basis[2] * k
            a2.append(atoms + offset[np.newaxis, :])
            e2.append(elements)
        atoms = np.concatenate(a2)
        elements = np.concatenate(e2)
        del a2, e2
        assert len(atoms) == nrep * len(self.atoms)
        basis = np.array([[self.size[0], 0, 0],
                          [0, self.size[1], 0],
                          [0, 0, self.size[2]]])
        basis = np.dot(basis, self.basis)

        # Tiny elements should be replaced by zero.  The cutoff is
        # determined by chop_tolerance which is a class attribute.
        basis = np.where(np.abs(basis) < self.chop_tolerance,
                         0.0, basis)

        # None should be replaced, and memory should be freed.
        lattice = Lattice(positions=atoms, cell=basis, numbers=elements,
                          pbc=self.pbc)
        lattice.millerbasis = self.miller_basis
        # Add info for lattice.surface.AddAdsorbate
        lattice._addsorbate_info_size = np.array(self.size[:2])
        return lattice

    def process_element(self, element):
        "Extract atomic number from element"
        # The types that can be elements: integers and strings
        if self.element_basis is None:
            if isinstance(element, str):
                self.atomicnumber = ase.data.atomic_numbers[element]
            elif isinstance(element, int):
                self.atomicnumber = element
            else:
                raise TypeError(
                    "The symbol argument must be a string or an atomic number.")
        else:
            atomicnumber = []
            try:
                if len(element) != max(self.element_basis) + 1:
                    oops = True
                else:
                    oops = False
            except TypeError:
                oops = True
            if oops:
                raise TypeError(
                    ("The symbol argument must be a sequence of length %d"
                     + " (one for each kind of lattice position")
                    % (max(self.element_basis) + 1,))
            for e in element:
                if isinstance(e, str):
                    atomicnumber.append(ase.data.atomic_numbers[e])
                elif isinstance(e, int):
                    atomicnumber.append(e)
                else:
                    raise TypeError(
                        "The symbols argument must be a sequence of strings "
                        "or atomic numbers.")
            self.atomicnumber = [atomicnumber[i] for i in self.element_basis]
            assert len(self.atomicnumber) == len(self.bravais_basis)

    def convert_to_natural_basis(self):
        "Convert directions and miller indices to the natural basis."
        self.directions = np.dot(self.directions, self.inverse_basis)
        if self.bravais_basis is not None:
            self.natural_bravais_basis = np.dot(self.bravais_basis,
                                                self.inverse_basis)
        for i in (0, 1, 2):
            self.directions[i] = reduceindex(self.directions[i])
        for i in (0, 1, 2):
            (j, k) = self.other[i]
            self.miller[i] = reduceindex(self.handedness *
                                         cross(self.directions[j],
                                               self.directions[k]))

    def calc_num_atoms(self):
        v = int(round(abs(np.linalg.det(self.directions))))
        if self.bravais_basis is None:
            return v
        else:
            return v * len(self.bravais_basis)

    def make_unit_cell(self):
        "Make the unit cell."
        # Make three loops, and find the positions in the integral
        # lattice.  Each time a position is found, the atom is placed
        # in the real unit cell by put_atom().
        self.natoms = self.calc_num_atoms()
        self.nput = 0
        self.atoms = np.zeros((self.natoms, 3), float)
        self.elements = np.zeros(self.natoms, int)
        self.farpoint = sum(self.directions)
        # printprogress = self.debug and (len(self.atoms) > 250)
        # Find the radius of the sphere containing the whole system
        sqrad = 0
        for i in (0, 1):
            for j in (0, 1):
                for k in (0, 1):
                    vect = (i * self.directions[0] +
                            j * self.directions[1] +
                            k * self.directions[2])
                    if np.dot(vect, vect) > sqrad:
                        sqrad = np.dot(vect, vect)
        del i, j, k
        # Loop along first crystal axis (i)
        for (istart, istep) in ((0, 1), (-1, -1)):
            i = istart
            icont = True
            while icont:
                nj = 0
                for (jstart, jstep) in ((0, 1), (-1, -1)):
                    j = jstart
                    jcont = True
                    while jcont:
                        nk = 0
                        for (kstart, kstep) in ((0, 1), (-1, -1)):
                            k = kstart
                            kcont = True
                            while kcont:
                                # Now (i,j,k) loops over Z^3, except that
                                # the loops can be cut off when we get outside
                                # the unit cell.
                                point = np.array((i, j, k))
                                if self.inside(point):
                                    self.put_atom(point)
                                    nk += 1
                                    nj += 1
                                # Is k too high?
                                if np.dot(point, point) > sqrad:
                                    assert not self.inside(point)
                                    kcont = False
                                k += kstep
                        # Is j too high?
                        if i * i + j * j > sqrad:
                            jcont = False
                        j += jstep
                # Is i too high?
                if i * i > sqrad:
                    icont = False
                i += istep
                # if printprogress:
                #    perce = int(100*self.nput / len(self.atoms))
                #    if perce > percent + 10:
                #        print ("%d%%" % perce),
                #        percent = perce
        assert self.nput == self.natoms

    def inside(self, point):
        "Is a point inside the unit cell?"
        return (np.dot(self.miller[0], point) >= 0 and
                np.dot(self.miller[0], point - self.farpoint) < 0 and
                np.dot(self.miller[1], point) >= 0 and
                np.dot(self.miller[1], point - self.farpoint) < 0 and
                np.dot(self.miller[2], point) >= 0 and
                np.dot(self.miller[2], point - self.farpoint) < 0)

    def put_atom(self, point):
        "Place an atom given its integer coordinates."
        if self.bravais_basis is None:
            # No basis - just place a single atom
            pos = np.dot(point, self.crystal_basis)
            if self.debug >= 2:
                print('Placing an atom at (%d,%d,%d) ~ (%.3f, %.3f, %.3f).' %
                      (tuple(point) + tuple(pos)))
            self.atoms[self.nput] = pos
            self.elements[self.nput] = self.atomicnumber
            self.nput += 1
        else:
            for i, offset in enumerate(self.natural_bravais_basis):
                pos = np.dot(point + offset, self.crystal_basis)
                if self.debug >= 2:
                    print('Placing an atom at (%d+%f, %d+%f, %d+%f) ~ '
                          '(%.3f, %.3f, %.3f).' %
                          (point[0], offset[0], point[1], offset[1],
                           point[2], offset[2], pos[0], pos[1], pos[2]))
                self.atoms[self.nput] = pos
                if self.element_basis is None:
                    self.elements[self.nput] = self.atomicnumber
                else:
                    self.elements[self.nput] = self.atomicnumber[i]
                self.nput += 1

    def find_directions(self, directions, miller):
        """
        Find missing directions and miller indices from the specified ones.
        """
        directions = np.asarray(directions).tolist()
        miller = list(miller)  # np.asarray(miller).tolist()
        # If no directions etc are specified, use a sensible default.
        if directions == [None, None, None] and miller == [None, None, None]:
            directions = [[1, 0, 0], [0, 1, 0], [0, 0, 1]]
        # Now fill in missing directions and miller indices.  This is an
        # iterative process.
        change = 1
        while change:
            change = False
            missing = 0
            for i in (0, 1, 2):
                j, k = self.other[i]
                if directions[i] is None:
                    missing += 1
                    if miller[j] is not None and miller[k] is not None:
                        directions[i] = reduceindex(cross(miller[j],
                                                          miller[k]))
                        change = True
                        if self.debug >= 2:
                            print(
                                "Calculating directions[%d] from miller "
                                "indices" % i)
                if miller[i] is None:
                    missing += 1
                    if directions[j] is not None and directions[k] is not None:
                        miller[i] = reduceindex(cross(directions[j],
                                                      directions[k]))
                        change = True
                        if self.debug >= 2:
                            print("Calculating miller[%d] from directions" % i)
        if missing:
            raise ValueError(
                "Specification of directions and miller indices is incomplete.")
        # Make sure that everything is Numeric arrays
        self.directions = np.array(directions)
        self.miller = np.array(miller)
        # Check for zero-volume unit cell
        if abs(np.linalg.det(self.directions)) < 1e-10:
            raise ValueError(
                "The direction vectors are linearly dependent "
                "(unit cell volume would be zero)")
        # Check for left-handed coordinate system
        if np.linalg.det(self.directions) < 0:
            print("WARNING: Creating a left-handed coordinate system!")
            self.miller = -self.miller
            self.handedness = -1
        else:
            self.handedness = 1
        # Now check for consistency
        for i in (0, 1, 2):
            (j, k) = self.other[i]
            m = reduceindex(self.handedness *
                            cross(self.directions[j], self.directions[k]))
            if sum(np.not_equal(m, self.miller[i])):
                print(
                    "ERROR: Miller index %s is inconsisten with "
                    "directions %d and %d" % (i, j, k))
                print("Miller indices:")
                print(str(self.miller))
                print("Directions:")
                print(str(self.directions))
                raise ValueError(
                    "Inconsistent specification of miller indices and "
                    "directions.")

    def print_directions_and_miller(self, txt=""):
        "Print direction vectors and Miller indices."
        print(f"Direction vectors of unit cell{txt}:")
        for i in (0, 1, 2):
            print("   ", self.directions[i])
        print(f"Miller indices of surfaces{txt}:")
        for i in (0, 1, 2):
            print("   ", self.miller[i])


class MillerInfo:
    """Mixin class to provide information about Miller indices."""

    def miller_to_direction(self, miller):
        """Returns the direction corresponding to a given Miller index."""
        return np.dot(miller, self.millerbasis)


class Lattice(Atoms, MillerInfo):
    """List of atoms initially containing a regular lattice of atoms.

    A part from the usual list of atoms methods this list of atoms type
    also has a method, `miller_to_direction`, used to convert from Miller
    indices to directions in the coordinate system of the lattice.
    """


# Helper functions
def cross(a, b):
    """The cross product of two vectors."""
    return np.array((a[1] * b[2] - b[1] * a[2],
                     a[2] * b[0] - b[2] * a[0],
                     a[0] * b[1] - b[0] * a[1]))


def reduceindex(M):
    """Reduce Miller index to the lowest equivalent integers."""
    oldM = M
    g = math.gcd(M[0], M[1])
    h = math.gcd(g, M[2])
    while h != 1:
        if h == 0:
            raise ValueError(
                "Division by zero: Are the miller indices linearly dependent?")
        M = M // h
        g = math.gcd(M[0], M[1])
        h = math.gcd(g, M[2])
    if np.dot(oldM, M) > 0:
        return M
    else:
        return -M
