pyTEMlib 0.2020.11.1__py3-none-any.whl → 0.2024.9.0__py3-none-any.whl

pyTEMlib/structure_tools.py

@@ -1,316 +0,0 @@
-import numpy as np
-from math import gcd, ceil, atan
-from fractions import Fraction
-
-
-# SIGMA_SYMBOL = u'\u03A3'
-UNIMODULAR_MATRIX = np.array([np.identity(3),
-                              [[1, 0, 1],
-                               [0, 1, 0],
-                               [0, 1, 1]],
-                              [[1, 0, 1],
-                               [0, 1, 0],
-                               [0, 1, -1]],
-                              [[1, 0, 1],
-                               [0, 1, 0],
-                               [-1, 1, 0]],
-                              [[1, 0, 1],
-                               [1, 1, 0],
-                               [1, 1, 1]]])
-STRUCTURE_MATRIX = np.array([np.identity(3),
-                             [[0.5, -0.5, 0],
-                              [0.5, 0.5, 0],
-                              [0.5, 0.5, 1]],
-                             [[0.5, 0.5, 0],
-                              [0, 0.5, 0.5],
-                              [0.5, 0, 0.5]]])
-
-# 0 is coprime only with 1
-def coprime(a, b):
-    return gcd(a,b) in (0, 1)
-
-
-def get_cubic_sigma(hkl, m, n=1):
-    sqsum = np.inner(hkl, hkl)
-    sigma = m*m + n*n * sqsum
-    while sigma != 0 and sigma % 2 == 0:
-        sigma /= 2
-    return (sigma if sigma > 1 else None)
-
-def get_cubic_theta(hkl, m, n=1):
-    h,k,l = hkl
-    sqsum = h*h + k*k + l*l
-    assert sqsum > 0
-    if m > 0:
-        return 2 * atan(np.sqrt(sqsum) * n / m)
-    else:
-        return pi
-
-
-def get_theta_m_n_list(hkl, sigma, verbose=False):
-    if sigma == 1:
-        return [(0., 0, 0)]
-    thetas = []
-
-    # From Grimmer, Acta Cryst. (1984). A40, 108-112
-    #    S = m^2 + (u^2+v^2+w^2) n^2     (eq. 2)
-    #    S = alpha * Sigma               (eq. 4)
-    #   where alpha = 1, 2 or 4.
-    # Since (u^2+v^2+w^2) n^2 > 0,
-    # thus alpha * Sigma > m^2    =>   m^2 < 4 * Sigma
-    max_m = int(ceil(np.sqrt(4*sigma)))
-
-    for m in range(max_m):
-        for n in range(1, max_m):
-            if not coprime(m, n):
-                continue
-            s = get_cubic_sigma(hkl, m, n)
-            if s != sigma:
-                continue
-            theta = get_cubic_theta(hkl, m, n)
-            if verbose:
-                print("m=%i n=%i" % (m, n), "%.3f" % np.degrees(theta))
-            thetas.append((theta, m, n))
-    return np.array(thetas)
-
-
-def rodrigues(a, angle, verbose=False):
-    "use Rodrigues' rotation formula to get rotation matrix"
-    a = np.array(a, dtype=float)
-    a /= np.sqrt(np.inner(a, a)) # make unit vector
-    #assert abs(sin_angle - sin(acos(cos_angle))) < 1e-6
-    if verbose:
-        print ("rotation angle:", np.degrees(angle))
-        print ("rotation axis:", a)
-    omega = np.array([[   0., -a[2],  a[1]],
-                   [ a[2],    0., -a[0]],
-                   [-a[1],  a[0],    0.]])
-    rm = (np.identity(3) + omega * np.sin(angle)
-                            + np.dot(omega, omega) * (1 - np.cos(angle)))
-    if verbose:
-        print("rotation matrix:", rm)
-    return rm
-
-def is_integer(a, epsilon=1e-7):
-    "return true if numpy Float array consists off all integers"
-    return (np.abs(a - np.round(a)) < epsilon).all()
-
-def get_smallest_multiplier(a, max_n=1000):
-    """return the smallest positive integer n such that matrix a multiplied
-       by n is an integer matrix
-    """
-    for i in range(1, max_n):
-        if is_integer(i*a):
-            return i
-        
-def plus_minus_gen(start, end):
-    """
-    Generate a list of plus and minus alternating integers
-    """
-    for i in range(start, end):
-        yield i
-        yield -i
-def get_csl_matrix(sigma, rotate_matrix):
-    """\
-    Find matrix that determines the coincidence site lattice
-    for cubic structures.
-    Parameters:
-        sigma: CSL sigma
-        R: rotation matrix
-        centering: "f" for f.c.c., "b" for b.c.c. and None for p.c.
-    Return value:
-        matrix, which column vectors are the unit vectors of the CSL.
-    Based on H. Grimmer et al., Acta Cryst. (1974) A30, 197
-    https://doi.org/10.1107/S056773947400043X
-    """
-
-    s = STRUCTURE_MATRIX[0]
-    for u in UNIMODULAR_MATRIX:
-        t = np.eye(3) - np.dot(np.dot(np.dot(u, np.linalg.inv(s)),  np.linalg.inv(rotate_matrix)), s)
-        if abs( np.linalg.det(t)) > 1e-6:
-            break
-    o_lattice = np.round( np.linalg.inv(t), 12)
-    n = np.round(sigma /  np.linalg.det(o_lattice), 6)
-    csl_matrix = o_lattice_to_csl(o_lattice, n)
-    return csl_matrix
-    
-
-def o_lattice_to_csl(o_lattice, n):
-    """
-    The algorithm was borrowed from gosam project with slight changes.
-    Link to the project: https://github.com/wojdyr/gosam
-
-    There are two major steps: (1) Manipulate the columns of O-lattice to get
-    an integral basis matrix for CSL: make two columns become integers and
-    the remaining column can be multiplied by n whereby the determinant
-    becomes sigma. (2) Simplify CSL so its vectors acquire the shortest length:
-    decrease the integers in the matrix while keeping the determinant the same
-    by adding other column vectors (row vectors in the following example) to a
-    column vector. If after the addition or subtraction, the maximum value or
-    absolute summation of added or subtracted vector is smaller than the
-    original, then proceed the addition or subtraction.
-    0 0 -1      0 0 -1      0 0 -1      0 0 -1      0 0 -1
-    1 2 -1  ->  1 2 0   ->  1 2 0   ->  1 2 0   ->  1 2 0
-    1 -3 2      1 -3 2      1 -3 1      1 -3 0      2 -1 0
-
-    Args:
-     o_lattice (3x3 array): O-lattice in crystal coordinates
-     n (int): Number of O-lattice units per CSL unit
-
-    Returns:
-     CSL matrix (3x3 array) in crystal coordinates
-    """
-    csl = o_lattice.copy()
-    if n < 0:
-        csl[0] *= -1
-        n *= -1
-    while True:
-        m = [get_smallest_multiplier(i) for i in csl]
-        m_prod = np.prod(m)
-        if m_prod <= n:
-            for i in range(3):
-                csl[i] *= m[i]
-            if m_prod < n:
-                assert n % m_prod == 0
-                csl[0] *= n / m_prod
-            break
-        else:
-            changed = False
-            for i in range(3):
-                for j in range(3):
-                    if changed or i == j or m[i] == 1 or m[j] == 1:
-                        continue
-                    a, b = (i, j) if m[i] <= m[j] else (j, i)
-                    for k in plus_minus_gen(1, m[b]):
-                        handle = csl[a] + k * csl[b]
-                        if get_smallest_multiplier(handle) < m[a]:
-                            csl[a] += k * csl[b]
-                            changed = True
-                            break
-            if not changed:
-                # This situation rarely happens. Not sure if this solution is
-                # legit, as det not equals to sigma. E.g. Sigma 115[113]
-                for i in range(3):
-                    csl[i] *= m[i]
-                break
-    csl = csl.round().astype(int)
-
-    # Reshape CSL
-    def simplify(l1, l2):
-        x = abs(l1 + l2)
-        y = abs(l1)
-        changed = False
-        while max(x) < max(y) or (max(x) == max(y) and sum(x) < sum(y)):
-            l1 += l2
-            changed = True
-            x = abs(l1 + l2)
-            y = abs(l1)
-        return changed
-
-    while True:
-        changed = False
-        for i in range(3):
-            for j in range(3):
-                if i != j and not changed:
-                    changed = simplify(csl[i], csl[j]) or simplify(csl[i], -csl[j])
-                    if changed:
-                        break
-        if not changed:
-            break
-    return csl
-
-
-def orthogonalize_csl(csl, axis):
-    """
-    (1) Set the 3rd column of csl same as the rotation axis. The algorithm was
-    borrowed from gosam project with slight changes. Link to the project:
-    https://github.com/wojdyr/gosam
-    (2) Orthogonalize CSL, which is essentially a Gram-Schmidt process. At the
-    same time, we want to make sure the column vectors of orthogonalized csl
-    has the smallest value possible. That's why we compared two different ways.
-    csl = [v1, v2, v3], vi is the column vector
-    u1 = v3/||v3||, y2 = v1 - (v1 . u1)u1
-    u2 = y2/||y2||, y3 = v3 - [(v3 . u1)u1 + (v3 . u2)u2]
-    u3 = y3/||y3||
-    """
-    axis = np.array(axis)
-    c = np.linalg.solve(csl.transpose(), axis)
-    if not is_integer(c):
-        mult = get_smallest_multiplier(c)
-        c *= mult
-    c = c.round().astype(int)
-    ind = min([(i, v) for i, v in enumerate(c) if not np.allclose(v, 0)],
-              key=lambda x: abs(x[1]))[0]
-    if ind != 2:
-        csl[ind], csl[2] = csl[2].copy(), -csl[ind]
-        c[ind], c[2] = c[2], -c[ind]
-
-    csl[2] = np.dot(c, csl)
-    if c[2] < 0:
-        csl[1] *= -1
-
-    def get_integer(vec):
-        # Used vec = np.array(vec, dtype=float) before, but does not work for
-        # [5.00000000e-01, -5.00000000e-01,  2.22044605e-16] in Sigma3[112]
-        vec = np.round(vec, 12)
-        vec_sign = np.array([1 if abs(i) == i else -1 for i in vec])
-        vec = list(abs(vec))
-        new_vec = []
-        if 0.0 in vec:
-            zero_ind = vec.index(0)
-            vec.pop(zero_ind)
-            if 0.0 in vec:
-                new_vec = [get_smallest_multiplier(vec) * i for i in vec]
-            else:
-                frac = Fraction(vec[0] / vec[1]).limit_denominator()
-                new_vec = [frac.numerator, frac.denominator]
-            new_vec.insert(zero_ind, 0)
-        else:
-            for i in range(len(vec) - 1):
-                frac = Fraction(vec[i] / vec[i + 1]).limit_denominator()
-                new_vec.extend([frac.numerator, frac.denominator])
-            if new_vec[1] == new_vec[2]:
-                new_vec = [new_vec[0], new_vec[1], new_vec[3]]
-            else:
-                new_vec = reduce_vector([new_vec[0] * new_vec[2],
-                                         new_vec[1] * new_vec[2],
-                                         new_vec[3] * new_vec[1]])
-        assert is_integer(new_vec)
-        return new_vec * vec_sign
-
-    u1 = csl[2] / np.linalg.norm(csl[2])
-    y2_1 = csl[1] - np.dot(csl[1], u1) * u1
-    c0_1 = get_integer(y2_1)
-    y2_2 = csl[0] - np.dot(csl[0], u1) * u1
-    c0_2 = get_integer(y2_2)
-    if sum(abs(c0_1)) > sum(abs(c0_2)):
-        u2 = y2_2 / np.linalg.norm(y2_2)
-        y3 = csl[1] - np.dot(csl[1], u1) * u1 - np.dot(csl[1], u2) * u2
-        csl[1] = get_integer(y3)
-        csl[0] = c0_2
-    else:
-        u2 = y2_1 / np.linalg.norm(y2_1)
-        y3 = csl[0] - np.dot(csl[0], u1) * u1 - np.dot(csl[0], u2) * u2
-        csl[1] = c0_1
-        csl[0] = get_integer(y3)
-    for i in range(3):
-        for j in range(i + 1, 3):
-            if not np.allclose(np.dot(csl[i], csl[j]), 0):
-                raise ValueError("Non-orthogonal basis: %s" % csl)
-    return csl.round().astype(int)
-
-def find_smallest_real_multiplier(a, max_n=1000):
-    """return the smallest positive real f such that matrix `a' multiplied
-       by f is an integer matrix
-    """
-    # |the smallest non-zero element|
-    m = min(abs(i) for i in a if abs(i) > 1e-9)
-    for i in range(1, max_n):
-        t = i / float(m)
-        if is_integer(t * a):
-            return t
-    raise ValueError("Sorry, we can't make this matrix integer:\n%s" % a)
-
-def scale_to_integers(v):
-    return np.array(v * find_smallest_real_multiplier(v)).round().astype(int)
-