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

pyTEMlib/KinsCat.py

@@ -1,2758 +0,0 @@
-"""
-KinsCat
-Kinematic Scattering Theory
-Copyright by Gerd Duscher
-
-The University of Tennessee, Knoxville
-Department of Materials Science & Engineering
-
-Sources:
-   Scattering Theory:
-   Zuo and Spence, "Advanced TEM", 2017
-
-   Spence and Zuo, Electron Microdiffraction, Plenum 1992
-
-   Atomic Form Factor:
-       Kirkland: Advanced Computing in Electron Microscopy 2nd edition
-       Appendix C
-
-Units:
-    everything is in SI units, except length is given in nm.
-
-Usage:
-    See the notebooks for examples of these routines
-
-All the input and output is done through a dictionary
-"""
-# numerical packages used
-import numpy as np
-import scipy.constants as const
-import itertools
-from scipy import spatial
-
-import sidpy
-# plotting package used
-import matplotlib.pylab as plt  # basic plotting
-# import matplotlib as mpl
-# from mpl_toolkits.mplot3d import Axes3D  # 3D plotting
-from matplotlib.patches import Circle  # , Ellipse, Rectangle
-from matplotlib.collections import PatchCollection
-
-from ase.io import read  # , write
-import pyTEMlib.file_tools as ft
-import os
-
-
-_version_ = 0.5
-
-print('Using KinsCat library version ', _version_, ' by G.Duscher')
-_spglib_present = True
-try:
-    import spglib
-except ModuleNotFoundError:
-    _spglib_present = False
-    
-if _spglib_present:
-    print('Symmetry functions of spglib enabled')
-else:
-    print('spglib not installed; Symmetry functions of spglib disabled')
-
-
-def read_poscar():
-    """
-    Open file dialog to select a POSCAR file from VASP
-    """
-    file_name = ft.openfile_dialog('POSCAR (POSCAR*.txt);;All files (*)')
-    # use ase package to read file
-    
-    base = os.path.basename(file_name)
-    base_name = os.path.splitext(base)[0]
-    crystal = read(file_name, format='vasp', parallel=False)
-
-    # make dictionary and plot structure (not essential for further notebook)
-    tags = {'unit_cell': crystal.cell * 1e-1, 'elements': crystal.get_chemical_symbols(),
-            'base': crystal.get_scaled_positions(), 'max_bond_length': 0.23, 'name': base_name}
-
-    return tags
-
-# Some Structure Determination Routines
-
-
-def example():
-    """
-    same as Zuo_fig_3_18
-    """
-    return zuo_fig_3_18()
-
-
-def zuo_fig_3_18():
-    """
-    Input for Figure 3.18 in Zuo and Spence \"Advanced TEM\", 2017
-
-    This input acts as an example as well as a reference
-
-    Returns:
-        dictionary: tags is the dictionary of all input and output paramter needed to reproduce that figure.
-    """
-    # INPUT
-    # Create Silicon structure (Could be produced with Silicon routine)
-    print('Sample Input for Figure 3.18 in Zuo and Spence \"Advanced TEM\", 2017')
-    tags = {'crystal_name': 'Silicon'}
-    print('tags[\'crystal\'] = ', tags['crystal_name'])
-    a = 0.514  # nm
-    tags['lattice_parameter_nm'] = a
-    print('tags[\'lattice_parameter_nm\'] =', tags['lattice_parameter_nm'])
-    tags['unit_cell'] = [[a, 0, 0], [0, a, 0], [0, 0, a]]
-    print('tags[\'unit_cell\'] =', tags['unit_cell'])
-    tags['elements'] = list(itertools.repeat('Si', 8))
-    print('tags[\'elements\'] =', tags['elements'])
-    base = [(0., 0., 0.), (0.5, 0.0, 0.5), (0.5, 0.5, 0.), (0., 0.5, 0.5)]
-    tags['base'] = np.array(base + (np.array(base) + (.25, .25, .25)).tolist())
-    print('tags[\'base\'] =', tags['base'])
-
-    # Define Experimental Conditions
-    tags['convergence_angle_mrad'] = 7
- 
-    tags['acceleration_voltage_V'] = 101.6*1000.0  # V
-    print('tags[\'acceleration_voltage_V\'] =', tags['acceleration_voltage_V'])
-    
-    tags['convergence_angle_mrad'] = 7.1  # mrad;  0 is parallel illumination
-    print('tags[\'convergence_angle_mrad\'] =', tags['convergence_angle_mrad'])
-    
-    tags['zone_hkl'] = np.array([-2, 2, 1])  # incident neares zone axis: defines Laue Zones!!!!
-    print('tags[\'zone_hkl\'] =', tags['zone_hkl'])
-    tags['mistilt'] = np.array([0, 0, 0])  # mistilt in degrees
-    print('tags[\'mistilt\'] =', tags['mistilt'])
-    
-    # Define Simulation Parameters 
-
-    tags['Sg_max'] = .2  # 1/nm  maximum allowed excitation error
-    print('tags[\'Sg_max\'] =', tags['Sg_max'])
-    
-    tags['hkl_max'] = 9   # Highest evaluated Miller indices
-    print('tags[\'hkl_max\'] =', tags['hkl_max'])
-
-    print('##################')
-    print('# Output Options #')
-    print('##################')
-
-    # Output options
-
-    tags['background'] = 'black'  # 'white'  'grey'
-    print('tags[\'background\'] =', tags['background'], '# \'white\',  \'grey\' ')
-    tags['color map'] = 'plasma'
-    print('tags[\'color map\'] =', tags['color map'], '#,\'cubehelix\',\'Greys\',\'jet\' ')
-
-    tags['plot HOLZ'] = 1
-    print('tags[\'plot HOLZ\'] =', tags['plot HOLZ'])
-    tags['plot HOLZ excess'] = 1
-    print('tags[\'plot HOLZ excess\'] =', tags['plot HOLZ excess'])
-    tags['plot Kikuchi'] = 1
-    print('tags[\'plot Kikuchi\'] =', tags['plot Kikuchi'])
-    tags['plot reflections'] = 1
-    print('tags[\'plot reflections\'] =', tags['plot reflections'])
-    
-    tags['label HOLZ'] = 0
-    print('tags[\'label HOLZ\'] =', tags['label HOLZ'])
-    tags['label Kikuchi'] = 0
-    print('tags[\'label Kikuchi\'] =', tags['label Kikuchi'])
-    tags['label reflections'] = 0
-    print('tags[\'label reflections\'] =', tags['label reflections'])
-
-    tags['label color'] = 'black'
-    print('tags[\'label color\'] =', tags['label color'])
-    tags['label size'] = 10
-    print('tags[\'label size\'] =', tags['label size'])
-    
-    tags['color Laue Zones'] = ['red',  'blue', 'green', 'blue', 'green']   # , 'green', 'red'] #for OLZ give a sequence
-    print('tags[\'color Laue Zones\'] =', tags['color Laue Zones'], ' #[\'red\', \'blue\', \'lightblue\']')
-
-    tags['color Kikuchi'] = 'green'
-    print('tags[\'color Kikuchi\'] =', tags['color Kikuchi'])
-    tags['linewidth HOLZ'] = -1  # -1: linewidth according to intensity (structure factor F^2
-    print('tags[\'linewidth HOLZ\'] =', tags['linewidth HOLZ'], '# -1: linewidth according to intensity '
-                                                                '(structure factor F^2')
-    tags['linewidth Kikuchi'] = -1  # -1: linewidth according to intensity (structure factor F^2
-    print('tags[\'linewidth Kikuchi\'] =', tags['linewidth Kikuchi'], '# -1: linewidth according to intensity '
-                                                                      '(structure factor F^2')
-
-    tags['color reflections'] = 'intensity'  # 'Laue Zone'
-    print('tags[\'color reflections\'] =', tags['color reflections'], '#\'Laue Zone\' ')
-    tags['color zero'] = 'white'  # 'None', 'white', 'blue'
-    print('tags[\'color zero\'] =', tags['color zero'], '#\'None\', \'white\', \'blue\' ')
-    tags['color ring zero'] = 'None'  # 'Red' #'white' #, 'None'
-    print('tags[\'color ring zero\'] =', tags['color ring zero'], '#\'None\', \'white\', \'Red\' ')
-
-    print('########################')
-    print('# End of Example Input #')
-    print('########################\n\n')
-    
-    return tags
-
-
-def h5_add_crystal_structure(h5_file, crystal_tags):
-    """
-    Adds the basic crystal information to a pyNSID style hdf5 file.
-
-    example usage:
-    >> crystal_tags = ks.structure_by_name(h5_file, 'Graphite')
-    >> ks.add_crystal_structure(h5_file, crystal_tags)
-    """
-    structure_group = sidpy.hdf.prov_utils.create_indexed_group(h5_file, 'Structure')
-    
-    structure_group['unit_cell'] = crystal_tags['unit_cell']
-    structure_group['relative_positions'] = crystal_tags['base']
-    structure_group['title'] = str(crystal_tags['crystal_name'])
-    structure_group['_'+crystal_tags['crystal_name']] = str(crystal_tags['crystal_name'])
-    structure_group['elements'] = np.array(crystal_tags['elements'], dtype='S')
-    if 'zone_axis' in structure_group:
-        structure_group['zone_axis'] = np.array(crystal_tags['zone_axis'], dtype=float)
-    else:
-        structure_group['zone_axis'] = np.array([1., 1., 1.], dtype=float)
-
-    h5_file.flush()
-    
-    return structure_group
-
-
-def h5_add_to_structure(structure_group, crystal_tags):
-    for key in crystal_tags:
-        if key in structure_group.keys():
-            print(key, ' not written; use new name')
-        else:
-            structure_group[key] = crystal_tags[key]
-
-
-def cubic(a):
-    """ Cubic lattice of dimensions a x a x a. """
-    return np.identity(3)*a
-
-
-def from_parameters(a, b, c, alpha, beta, gamma):
-    """
-    Create a unit cell  using lengths and angles (in degrees).
-    """
-
-    alpha_r = np.radians(alpha)
-    beta_r = np.radians(beta)
-    gamma_r = np.radians(gamma)
-    val = (np.cos(alpha_r) * np.cos(beta_r) - np.cos(gamma_r)) / (np.sin(alpha_r) * np.sin(beta_r))
-    
-    # Sometimes rounding errors result in values slightly > 1.
-    if val > 1.:  
-        val = 1.
-    if val < -1.:  
-        val = -1.
-
-    gamma_star = np.arccos(val)
-    vector_a = [a * np.sin(beta_r), 0.0, a * np.cos(beta_r)]
-    vector_b = [-b * np.sin(alpha_r) * np.cos(gamma_star),
-                b * np.sin(alpha_r) * np.sin(gamma_star),
-                b * np.cos(alpha_r)]
-    vector_c = [0.0, 0.0, float(c)]
-    return np.array([vector_a, vector_b, vector_c])
-
-
-def tetragonal(a, c):
-    """
-    Tetragonal unit cell of dimensions a x a x c.
-    """
-    return from_parameters(a, a, c, 90, 90, 90)
-
-
-def bcc(lattice_parameter, elements):
-    """
-    BCC structure
-
-    Input:
-        lattice parameter in nm and
-        elements as a list or a string of a single element
-
-    Returns:
-        unit cell , base and relative atom positions
-    """
-    unit_cell = cubic(lattice_parameter)
-    base = np.array([(0., 0., 0.), (0.5, 0.5, 0.5)])
-    if len(elements) > 1:
-        atoms = [elements[0], elements[1]]
-    else:
-        atoms = [elements[0], elements[0]]
-    return unit_cell, base, atoms
-        
-   
-def fcc(lattice_parameter, elements):
-    """
-    FCC structure
-
-    Input:
-        lattice parameter in nm and
-        elements as a list or a string of a single element
-
-    Returns:
-        unit cell , base and relative atom positions
-    """
-    unit_cell = cubic(lattice_parameter)
-    base = np.array([(0., 0., 0.), (0.5, 0.0, 0.5), (0.5, 0.5, 0.0), (0., 0.5, 0.5)])
-    if len(elements) > 3:
-        atoms = [elements[0], elements[1], elements[2], elements[3]]
-    elif len(elements) > 1:
-        atoms = [elements[0], elements[1], elements[1], elements[1]]
-    else:
-        atoms = [elements[0]]*4
-    return unit_cell, base, atoms
-
-
-def dichalcogenide(a, c, u, elements):
-    """
-    Dichalcogenide structure
-
-    Input:
-        a, c: floats - lattice parameters
-        u: float - relative shift parameter
-        elements: string of element or list of strings of elements
-
-    Returns:
-        unit_cell, base, atoms
-    """
-    unit_cell = from_parameters(a, a, c, 90., 90., 120.)
-    base = [(1/3., 2/3., 1/4.), (2/3., 1/3., 3/4.),
-            (2/3., 1/3., 1/4.+u), (2/3., 1/3., 1/4.-u),
-            (1/3., 2/3., 3/4.+u), (1/3., 2/3., 3/4.-u)]
-    
-    if len(elements) > 1:
-        atoms = [elements[0]]*2 + [elements[1]]*4
-    else:
-        atoms = elements[0]*6
-    return unit_cell, base, atoms
-
-
-def wurzite(a, c, u, elements):
-    """
-    Wurzite structure
-
-    Input:
-        a, c: floats - lattice parameters in nm
-        elements: string of element or list of strings of elements
-
-    Returns:
-        unit_cell, base, atoms
-    """
-    unit_cell = from_parameters(a, a, c, 90., 90., 120.)
-    base = [(2./3., 1./3., .500), (1./3., 2./3., 0.000), (2./3., 1./3., 0.5+u), (1./3., 2./3., u)]
-    if len(elements) > 1:
-        atoms = [elements[0]]*2 + [elements[1]]*2
-    else:
-        atoms = [elements[0]]*4
-    return unit_cell, base, atoms
-
-
-def rocksalt(lattice_parameter, elements):
-    """
-        Rocksalt structure
-
-        Input:
-            lattice_parameter: float in nm
-            elements: string of element or list of strings of elements
-        Returns:
-            unit_cell, base, atoms
-        """
-    unit_cell = np.identity(3) * lattice_parameter
-    base = [(0., 0., 0.), (0.5, 0.0, 0.5), (0.5, 0.5, 0.), (0., 0.5, 0.5)]
-    base2 = np.array(base)+(0.5, 0.5, 0.5)
-    base2 = np.where(base2 == 1., 0, base2)
-    base = base + base2.tolist()
-    if len(elements) > 1:
-        atoms = [elements[0]]*4 + [elements[1]]*4
-    else:
-        atoms = [elements[0]]*8
-    return unit_cell, base, atoms
-
-
-def zinc_blende(lattice_parameter, elements):
-    """
-    Zinc blende structure
-
-    Input:
-        lattice_parameter: float in nm
-        elements: string of element or list of strings of elements
-
-    Returns:
-        unit_cell, base, atoms
-    """
-    unit_cell = np.identity(3) * lattice_parameter
-    base = [(0., 0., 0.), (0.5, 0.0, 0.5), (0.5, 0.5, 0.), (0., 0.5, 0.5)]
-    base = base + (np.array(base) + (.25, .25, .25)).tolist()
-    if len(elements) > 3:
-        atoms = [elements[0], elements[0], elements[1], elements[1], elements[2], elements[2], elements[3], elements[3]]
-        # Z = [electronFF[elements[0]][Z],
-    elif len(elements) > 1:
-        atoms = [elements[0]]*4 + [elements[1]]*4
-    else:
-        atoms = [elements[0]]*8
-    return unit_cell, base, atoms
-
-
-def perovskite(lattice_parameter, elements):
-    """
-    Perovskite structure
-
-    Input:
-        lattice_parameter: float in nm
-        elements: string of element or list of strings of elements
-
-    Returns:
-        unit_cell, base, atoms
-    """
-    unit_cell = cubic(lattice_parameter)
-    base = np.array([(0., 0., 0.), (0.5, 0.5, 0.5), (0.5, 0.0, 0.5), (0.5, 0.5, 0.), (0., 0.5, 0.5)])
-    if len(elements) > 2:
-        atoms = [elements[0], elements[1]] + [elements[2]]*3
-    elif len(elements) > 1:
-        atoms = [elements[0]] + [elements[1]]*4
-    else:
-        atoms = [elements[0]]*5
-    return unit_cell, base, atoms
-
-
-def zone_mistilt(zone, angles):
-    """
-    Rotation of zone axis by mistilt
-
-    Input:
-        zone: zone axis in Miller indices
-        angles: list of mistilt angles in degree
-
-    Returns:
-        rotation matrix (3x3)
-
-    """
-    alpha, beta, gamma = np.radians(angles)
-
-    # first we rotate alpha about x axis
-    c, s = np.cos(alpha), np.sin(alpha)
-    rotx = np.array([[1, 0, 0], [0, c, -s], [0, s, c]])
-    
-    # second we rotate beta about y axis
-    c, s = np.cos(beta), np.sin(beta)
-    roty = np.array([[c, 0, s], [0, 1, 0], [-s, 0, c]])
-    
-    # third we rotate gamma about z-axis
-    c, s = np.cos(gamma), np.sin(gamma)
-    rotz = np.array([[c, -s, 0], [s, c, 0], [0, 0, 1]])
-
-    return np.dot(np.dot(np.dot(zone, rotx), roty), rotz)
-
-
-def structure_by_name(crystal):
-    """
-        Provides unit cell as a structure matrix, the list of elements and the atom base
-        
-        Input:
-        ------
-            crystal name as string:
-            type "print(ks.crystal_data_base.keys())" for a list of pre-defined crystal structures
-
-            Please note that the chemical expressions are case sensitive.
-
-        Output:
-        ------
-            new dictionary with the following keys:
-            
-            ['unit_cell']: the structure matrix
-            ['base']:      relative coordinates of atoms
-            ['elements']:     name of elements in same order as base
-
-            an empty dictionary will be returned if the name is not recognized.
-    """
-
-    # Check whether name is in the crystal_data_base
-    
-    if crystal in cdb:
-        tags = cdb[crystal].copy()
-    else:
-        print('Crystal name not defined')
-        return {}   
-    print(tags['elements'])
-    unit_cell = np.identity(3)
-    atoms = ''
-    base = []
-    # Make crystal structure dictionary based on symmetry 
-    if 'symmetry' in tags:
-        if tags['symmetry'] == 'BCC':
-            unit_cell, base, atoms = bcc(tags['a'], tags['elements'])
-         
-        elif tags['symmetry'] == 'FCC':
-            unit_cell, base, atoms = fcc(tags['a'], tags['elements'])
-
-        elif tags['symmetry'] == 'perovskite':
-            unit_cell, base, atoms = perovskite(tags['a'], tags['elements'])
-
-        elif tags['symmetry'] == 'zinc_blende':
-            unit_cell, base, atoms = zinc_blende(tags['a'], tags['elements'])
-            
-        elif tags['symmetry'] == 'wurzite':
-            unit_cell, base, atoms = wurzite(tags['a'], tags['c'], tags['u'], tags['elements'])
-
-        elif tags['symmetry'] == 'rocksalt':
-            unit_cell, base, atoms = rocksalt(tags['a'], tags['elements'])
-
-        elif tags['symmetry'] == 'dichalcogenide':
-            unit_cell, base, atoms = dichalcogenide(tags['a'], tags['c'], tags['u'], tags['elements'])
-           
-        tags['unit_cell'] = unit_cell
-        tags['elements'] = atoms
-        tags['base'] = base
-    
-    return tags
-
-
-def get_symmetry(unit_cell, base, atoms):
-    """
-    Symmetry analysis with spglib
-
-    spglib must be installed
-    """
-    if _spglib_present:
-
-        print('#####################')
-        print('# Symmetry Analysis #')
-        print('#####################')
-        
-        atomic_number = []
-        for i in range(len(atoms)):
-            a = atoms[i]
-            atomic_number.append(electronFF[a]['Z'])
-            print(f'{i+1}: {atomic_number[i]} = {2} : [{base[i][0]:.2f}, {base[i][1]:.2f}, {base[i][2]:.2f}]')
-                  
-        lattice = (unit_cell, base, atomic_number)
-        spgroup = spglib.get_spacegroup(lattice)
-        sym = spglib.get_symmetry(lattice)
-
-        print("  Spacegroup  is %s." % spgroup)
-        print('  Crystal has {0} symmetry operation'.format(sym['rotations'].shape[0]))
-
-        p_lattice, p_positions, p_numbers = spglib.find_primitive(lattice, symprec=1e-5)
-        print("\n########################\n #Basis vectors of primitive Cell:")
-        for i in range(3):
-            print('[{0:.4f}, {1:.4f}, {2:.4f}]'.format(p_lattice[i][0], p_lattice[i][1], p_lattice[i][2]))
-
-        print('There {0} atoms and {1} species in primitive unit cell:'.format(len(p_positions), p_numbers))
-    else:
-        print('spglib is not installed')
-
-
-def ball_and_stick(tags, extend=1, max_bond_length=0.):
-    
-    """
-    Calculates the data to plot a ball and stick model
-    
-    Input:
-        tags: dictionary containing the 'unit_cell', 'base' and 'elements' tags.
-
-        extend: 1 or 3 integers
-            The *extend* argument scales the effective cell in which atoms
-            will be included. It must either be a list of three integers or a single
-            integer scaling all 3 directions.  By setting this value to one,
-            all  corner and edge atoms will be included in the returned cell.
-            This will of cause make the returned cell non-repeatable, but this is
-            very useful for visualisation.
-
-        max_bond_length: 1 float
-            The max_bond_length argument defines the distance for which a bond will be shown.
-            If max_bond_length is zero, the tabulated atom radii will be used.
-
-    Output:
-
-        corners,balls, Z, bonds: lists
-            These lists can be used to plot the
-            unit cell:
-                for x, y, z in corners:
-                    l=mlab.plot3d( x,y,z, tube_radius=0.002)
-            bonds:
-                for x, y, z in bonds:
-                    mlab.plot3d( x,y,z, tube_radius=0.02)
-            and atoms:
-                for i,atom in enumerate(balls):
-                    mlab.points3d(atom[0],atom[1],atom[2],
-                                  scale_factor=0.1,##ks.vdw_radii[Z[i]]/5,
-                                  resolution=20,
-                                  color=tuple(ks.jmol_colors [Z[i]]),
-                                  scale_mode='none')
-                              
-        Please note that you'll need the *Z* list for coloring, or for radii that depend on elements
-    
-    """
-    # Check in which form extend is given
-    if isinstance(extend, int):
-        extend = [extend]*3
-        
-    extend = np.array(extend, dtype=int)
-    
-    # Make the x,y, and z multiplicators
-    if len(extend) == 3:
-        x = np.linspace(0, extend[0], extend[0]+1)  
-        y = np.linspace(0, extend[1], extend[1]+1)  
-        z = np.linspace(0, extend[2], extend[2]+1)  
-    else:
-        print('wrong extend parameter')
-        return   
-    
-    # Check whether this is the right kind of dictionary                  
-    if 'unit_cell' not in tags:
-        return
-    cell = tags['unit_cell']
-    
-    # Corners and Outline of unit cell
-    h = (0, 1)
-    corner_vectors = np.dot(np.array(list(itertools.product(h, h, h))), cell)
-    trace = [[0, 1], [1, 3], [3, 2], [2, 0], [0, 4], [4, 5], [5, 7], [6, 7], [6, 4], [1, 5], [2, 6], [3, 7]]
-    corners = []
-    for s, e in trace:
-        corners.append([*zip(corner_vectors[s], corner_vectors[e])])
-    
-    # ball position and elements in supercell
-    super_cell = np.array(list(itertools.product(x, y, z)))  # all evaluated Miller indices
-
-    pos = np.add(super_cell, np.array(tags['base'])[:, np.newaxis])
-    
-    atomic_number = []
-    for i in range(len(tags['elements'])):
-        atomic_number.append(electronFF[tags['elements'][i]]['Z'])
-
-    # List of bond lengths taken from electronFF database below
-    bond_lengths = []
-    for atom in tags['elements']:
-        bond_lengths.append(electronFF[atom]['bond_length'][0])
-        
-    # extend list of atomic numbers
-    zpp = []
-    for z in atomic_number:
-        zpp.append([z]*pos.shape[1]) 
-    zpp = np.array(zpp).flatten()
-
-    # reshape supercell atom positions
-    pos = pos.reshape((pos.shape[0]*pos.shape[1], pos.shape[2]))
-    
-    # Make a mask that excludes all atoms outside of super cell
-    maskz = pos[:, 2] <= extend[2]
-    masky = pos[:, 1] <= extend[1]
-    maskx = pos[:, 0] <= extend[0]
-    mask = np.logical_and(maskx, np.logical_and(masky, maskz))   # , axis=1)
-    
-    # Only use balls and elements inside super cell
-    balls = np.dot(pos[mask], cell)
-    atomic_number = zpp[mask]
-
-    # Get maximum bond length from list of bond -lengths taken from electronFF database 
-    if max_bond_length == 0:
-        max_bond_length = np.median(bond_lengths)/5
-    # Check nearest neighbours within max_bond_length
-    tree = spatial.KDTree(balls)
-    nearest_neighbours = np.array(tree.query(balls, k=8, distance_upper_bound=max_bond_length))
-
-    # Calculate bonds
-    bonds = []
-    bond_indices = []
-    for i in range(nearest_neighbours.shape[1]):
-        for j in range(nearest_neighbours.shape[2]):
-            if nearest_neighbours[0, i, j] < max_bond_length:
-                if nearest_neighbours[0, i, j] > 0:
-                    # print(atoms[i],atoms[int(bonds[1,i,j])],bonds[:,i,j])
-                    bonds.append([*zip(balls[i], balls[int(nearest_neighbours[1, i, j])])])
-                    bond_indices.append([i, int(nearest_neighbours[1, i, j])])
-        
-    return corners, balls, atomic_number, bonds
-
-
-def plot_unitcell_mayavi(tags):
-    """
-        Makes a 3D plot of crystal structure
-
-        Input:
-
-            Dictionary with tags: 'unit_cell, 'elements', 'base'
-
-        Output:
-
-            3D plot
-
-        Dependencies:
-
-            ball_and_stick function of KinsCat
-            mlab of mayavi 
-    """
-    from mayavi import mlab
-
-    # Make sure "max_bond_length" and "extend" variables are initialized
-    if 'max_bond_length' not in tags:
-        max_bond_length = 0.
-    else:
-        max_bond_length = tags['max_bond_length']
-
-    if 'extend' not in tags:
-        extend = 1
-    else:
-        extend = tags['extend']
-
-    # get balls, sticks and atomic numbers for colors and sizes
-    corners, balls, atomic_number, bonds = ball_and_stick(tags, extend=extend, max_bond_length=max_bond_length)
-
-    print('Now plotting')
-    fig = mlab.figure(1, bgcolor=(0, 0, 0), size=(350, 350))
-
-    mlab.clf()  # clear figure
-
-    # parallel projection
-    mlab.gcf().scene.parallel_projection = True
-    mlab.gcf().scene.camera.parallel_scale = 5
-
-    # plot unit cell 
-    for x, y, z in corners:
-        ll = mlab.plot3d(x, y, z, tube_radius=0.002)
-
-    # plot bonds as sticks
-    for x, y, z in bonds:
-        mlab.plot3d(x, y, z, tube_radius=0.02)
-
-    # plot atoms
-    for i, atom in enumerate(balls):
-        mlab.points3d(atom[0], atom[1], atom[2],
-                      scale_factor=0.1,  # ks.vdw_radii[Z[i]]/50,
-                      resolution=20,
-                      color=tuple(jmol_colors[atomic_number[i]]),
-                      scale_mode='none')
-
-    # parallel projection    
-    mlab.gcf().scene.parallel_projection = True
-    mlab.gcf().scene.camera.parallel_scale = 5
-    # show plot
-    mlab.show()
-    
-
-def plot_unitcell(tags):
-    """
-    Simple plot of unit cell
-    """
-
-    if 'max_bond_length' not in tags:
-        max_bond_length = 0.
-    else:
-        max_bond_length = tags['max_bond_length']
-
-    if 'extend' not in tags:
-        extend = 1
-    else:
-        extend = tags['extend']
-
-    corners, balls, atomic_number, bonds = ball_and_stick(tags, extend=extend, max_bond_length=max_bond_length)
-
-    maximum_position = balls.max()*1.05
-    maximum_x = balls[:, 0].max()
-    maximum_y = balls[:, 1].max()
-    maximum_z = balls[:, 2].max()
-
-    balls = balls - [maximum_x/2, maximum_y/2, maximum_z/2]
-
-    fig = plt.figure()
-    ax = fig.add_subplot(111, projection='3d')
-    # draw unit_cell
-    for x, y, z in corners:
-        ax.plot3D(x-maximum_x/2, y-maximum_y/2, z-maximum_z/2, color="blue")
-
-    # draw bonds
-    for x, y, z in bonds:
-        ax.plot3D(x-maximum_x/2, y-maximum_y/2, z-maximum_z/2, color="black", linewidth=4)  # , tube_radius=0.02)
-
-    # draw atoms
-    for i, atom in enumerate(balls):
-        ax.scatter(atom[0], atom[1], atom[2],
-                   color=tuple(jmol_colors[atomic_number[i]]),
-                   alpha=1.0, s=50)
-    maximum_position = balls.max()*1.05
-    ax.set_proj_type('ortho')
-
-    ax.set_zlim(-maximum_position/2, maximum_position/2)
-    ax.set_ylim(-maximum_position/2, maximum_position/2)
-    ax.set_xlim(-maximum_position/2, maximum_position/2)
-
-    if 'name' in tags:
-        ax.set_title(tags['name'])
-
-    ax.set_xlabel('x [nm]')
-    ax.set_ylabel('y [nm]')
-    ax.set_zlabel('z [nm]')
-    
-    
-# The metric tensor of the lattice.
-def metric_tensor(matrix):
-    """
-    The metric tensor of the lattice.
-
-    Usage:
-        metric_tensor(unit_cell)
-    """
-    metric_tensor2 = np.dot(matrix, matrix.T)
-    return metric_tensor2
-
-
-def vector_norm(g):
-    """
-    Length of vector
-    """
-    return np.sqrt(g[:, 0]**2+g[:, 1]**2+g[:, 2]**2)
-
-
-def make_pretty_labels(hkls, hex_label=False):
-    """
-    Make pretty labels
-
-    Input:
-        hkls: a numpy array with all the Miller indices to be labeled
-
-    Optional:
-        hex_label: if True this will make for Miller indices.
-
-    Output:
-        list of labels in Latex format
-    """
-    hkl_label = []
-    for i in range(len(hkls)):
-        h, k, l = np.array(hkls)[i]
-        
-        if h < 0:
-            h_string = r'[$\bar {'+str(int(-h))+'},'
-        else:
-            h_string = r'[$\bar {'+str(int(h))+'},'
-        if k < 0:
-            k_string = r'\bar {'+str(int(-k))+'},'
-        else:
-            k_string = str(int(k))+','
-        if hex_label:
-            ii = -(h+k)
-            if ii < 0:
-                k_string = k_string + r'\bar {'+str(int(-ii))+'},'
-            else:
-                k_string = k_string + str(int(ii))+','
-        if l < 0:
-            l_string = r'\bar {'+str(int(-l))+'} $]'
-        else:
-            l_string = str(int(l))+'} $]'
-        label = h_string+k_string+l_string
-        hkl_label.append(label)
-    return hkl_label
-
-
-# Wavelength in 1/nm
-def get_wavelength(e0):
-    """
-    Calculates the relativistic corrected de Broglie wave length of an electron
-
-    Input:
-    ------
-        acceleration voltage in volt
-    Output:
-    -------
-        wave length in nm
-    """
-
-    eV = const.e * e0 
-    return const.h/np.sqrt(2*const.m_e*eV*(1+eV/(2*const.m_e*const.c**2)))*10**9
-    
-
-# Determine rotation matrix to tilt zone axis onto z-axis
-# We determine spherical coordinates to do that
-def get_rotation_matrix(zone, verbose=False):
-    """
-     Calculates the rotation matrix to rotate the zone axis parallel to the cartasian z-axis.
-     
-     We use spherical coordinates to first rotate around the z-axis and then around the y-axis.
-     This makes it easier to apply additional tilts, than to use the cross product to determine a single rotation 
-     axis (Rodrigues Formula)
-
-     INPUT:
-     ------
-      - zone axis has to be in cartesian coordinates also. 
-     The dot product of zone axis  and unit cell will accomplish that.
-
-    Output:
-    -------
-     - rotation_matrix
-     - theta (degrees)
-     - phi (degrees)
-    """
-    # spherical coordinates of zone
-    r = np.sqrt((zone*zone).sum())
-    theta = np.arccos(zone[2]/r)
-    if zone[0] < 0:
-        theta = -theta
-    if zone[0] == 0:
-        phi = np.pi/2
-    else: 
-        phi = (np.arctan(zone[1]/zone[0]))
-
-    if verbose:
-        print('Rotation theta ', np.degrees(theta), ' phi ', np.degrees(phi))
-    # unit = np.array([[1, 0, 0],[0,1, 0],[0, 0,1]])
-
-    # first we rotate phi about z-axis
-    c, s = np.cos(phi), np.sin(phi)
-    rotz = np.array([[c, -s, 0], [s, c, 0], [0, 0, 1]])
-
-    # second we rotate theta about y axis
-    c, s = np.cos(theta), np.sin(theta)
-    roty = np.array([[c, 0, s], [0, 1, 0], [-s, 0, c]])
-    
-    # the rotation now makes zone-axis coincide with plane normal
-    return np.dot(rotz, roty), np.degrees(theta), np.degrees(phi)
-
-
-def check_sanity(tags):
-    """
-    Check sanity of input parameters
-    """
-    stop = False
-    if 'unit_cell' not in tags:
-        print(' No unit_cell defined')
-        stop = True
-    if 'base' not in tags:
-        print(' No base defined')
-        stop = True
-    if 'elements' not in tags:
-        print(' No atoms defined')
-        stop = True
-    if 'acceleration_voltage_V' not in tags:
-        print(' No acceleration_voltage_V defined')
-        stop = True
-    if 'zone_hkl' not in tags:
-        print(' No zone_hkl defined')
-        stop = True
-    if 'Sg_max' not in tags:
-        print(' No Sg_max defined')
-        stop = True
-    if 'hkl_max' not in tags:
-        print(' No hkl_max defined')
-        stop = True
-    
-    if 'crystal_name' not in tags:
-        tags['crystal_name'] = 'undefined'
-        print('tags[\'crystal\'] = \'undefined\'')
-    if 'mistilt' not in tags:
-        tags['mistilt'] = [0., 0., 0.]
-        print('tags[\'mistilt\'] = [0., 0., 0.]')
-    if 'convergence_angle_mrad' not in tags:
-        tags['convergence_angle_mrad'] = 0. 
-        print('tags[\'convergence_angle_mrad\'] = 0')
-    
-    return stop
-
-
-def ring_pattern_calculation(tags, verbose=False):
-    """
-    Calculate the ring diffraction pattern of a crystal structure
-
-    Input:
-        tags: dictionary of crystal structure
-    Output:
-        tags: dictionary with diffraction information added
-
-    """
-    # Reciprocal Lattice 
-    # We use the linear algebra package of numpy to invert the unit_cell "matrix"
-    reciprocal_unit_cell = np.linalg.inv(tags['unit_cell']).T  # transposed of inverted unit_cell
-    
-    # INPUT
-    hkl_max = 7   # maximum allowed Miller index
-    
-    acceleration_voltage = 200.0*1000.0  # V
-    wave_length = get_wavelength(acceleration_voltage)
-    
-    h = np.linspace(-hkl_max, hkl_max, 2*hkl_max+1)    # all to be evaluated single Miller Index
-    hkl = np.array(list(itertools.product(h, h, h)))  # all to be evaluated Miller indices
-    g_hkl = np.dot(hkl, reciprocal_unit_cell)  
-    
-    # Calculate Structure Factors
-    
-    structure_factors = []
-    
-    base = np.dot(tags['base'], tags['unit_cell'])  # transformation from relative to Cartesian coordinates
-    for j in range(len(g_hkl)):
-        F = 0
-        for b in range(len(base)):
-            # Atomic formfactor for element and momentum change (g vector)
-            f = feq(tags['elements'][b], np.linalg.norm(g_hkl[j]))  
-            F += f * np.exp(-2*np.pi*1j*(g_hkl[j]*base[b]).sum())        
-        structure_factors.append(F)
-    F = structure_factors = np.array(structure_factors)
-    
-    # Allowed reflections have a non zero structure factor F (with a  bit of numerical error)
-    allowed = np.absolute(structure_factors) > 0.001
-    
-    distances = np.linalg.norm(g_hkl, axis=1)
-    
-    if verbose:
-        print(f' Of the evaluated {hkl.shape[0]} Miller indices {allowed.sum()} are allowed. ')
-    # We select now all the 
-    zero = distances == 0.
-    allowed = np.logical_and(allowed, np.logical_not(zero))
-    
-    F = F[allowed]
-    g_hkl = g_hkl[allowed]
-    hkl = hkl[allowed]
-    distances = distances[allowed]
-    
-    sorted_allowed = np.argsort(distances)
-    
-    distances = distances[sorted_allowed]
-    hkl = hkl[sorted_allowed]
-    F = F[sorted_allowed]
-    
-    # How many have unique distances and what is their multiplicity
-    
-    unique, indices = np.unique(distances, return_index=True)
-    
-    if verbose:
-        print(f' Of the {allowed.sum()} allowed Bragg reflections there are {len(unique)} families of reflections.')
-    
-    intensity = np.absolute(F[indices]**2*(np.roll(indices, -1)-indices))
-    if verbose:
-        print('\n index \t  hkl \t      1/d [1/nm]       d [pm]     F     multip.  intensity')
-    family = []
-    out_tags = {}
-    for j in range(len(unique)-1):
-        i = indices[j]    
-        i2 = indices[j+1]   
-        family.append(hkl[i+np.argmax(hkl[i:i2].sum(axis=1))])
-        index = '{'+f'{family[j][0]:.0f} {family[j][1]:.0f} {family[j][2]:.0f}'+'}'
-        if verbose:
-            print(f'{i:3g}\t {index} \t  {distances[i]:.2f}  \t {1/distances[i]*1000:.0f} \t {np.absolute(F[i]):.2f},'
-                  f' \t  {indices[j+1]-indices[j]:3g} \t {intensity[j]:.2f}') 
-        out_tags[index] = {}
-        out_tags[index]['reciprocal_distance'] = distances[i]
-        out_tags[index]['real_distance'] = 1/distances[i]
-        out_tags[index]['F'] = np.absolute(F[i])
-        out_tags[index]['multiplicity'] = indices[j+1]-indices[j]
-        out_tags[index]['intensity'] = intensity[j]
-    return out_tags  
-        
-            
-def kinematic_scattering(tags, verbose=False):
-    """
-        All kinematic scattering calculation
-
-        Calculates Bragg spots, Kikuchi lines, excess, and deficient HOLZ lines
-
-        Input:
-            a dictionary with crystal structure:
-                'unit_cell', 'base' 'elements'
-            and with experimental parameters:
-                'acceleration_voltage_V', 'zone_hkl', 'Sg_max', 'hkl_max'
-            Optional parameters are:
-                'mistilt', convergence_angle_mrad', and 'crystal_name'
-            vebose = True will give extended output of the calculation
-        Output to dictionary:
-            There are three sub_dictionaries:
-                ['allowed'], ['forbidden'], and ['HOLZ']
-                ['allowed'] and ['forbidden'] dictionaries contain:
-                    ['Sg'], ['hkl'], ['g'], ['structure factor'], ['intensities'],
-                    ['ZOLZ'], ['FOLZ'], ['SOLZ'], ['HOLZ'], ['HHOLZ'], ['label'], and ['Laue_zone']
-                the ['HOLZ'] dictionary contains:
-                    ['slope'], ['distance'], ['theta'], ['g deficient'], ['g excess'], ['hkl'], ['intensities'],
-                    ['ZOLZ'], ['FOLZ'], ['SOLZ'], ['HOLZ'], and  ['HHOLZ']
-                Please note that the Kikuchi lines are the HOLZ lines of ZOLZ
-
-                There are also a few parameters stored in the main dictionary:
-                    ['wave_length_nm'], ['reciprocal_unit_cell'], ['inner_potential_V'], ['incident_wave_vector'],
-                    ['volume'], ['theta'], ['phi'], and ['incident_wave_vector_vacuum']
-    """
-
-    if check_sanity(tags):
-        print('Input is not complete, stopping')
-        print('Try \'example()\' for example input')
-        return
-
-    tags['wave_length_nm'] = get_wavelength(tags['acceleration_voltage_V'])
-    
-    # ###########################################
-    # reciprocal_unit_cell 
-    # ###########################################
-    unit_cell = np.array(tags['unit_cell'])
-    # We use the linear algebra package of numpy to invert the unit_cell "matrix"
-    reciprocal_unit_cell = np.linalg.inv(unit_cell).T  # transposed of inverted unit_cell
-    tags['reciprocal_unit_cell'] = reciprocal_unit_cell
-    
-    if verbose:
-        print('reciprocal_unit_cell')
-        print(np.round(reciprocal_unit_cell, 3))
-        
-    # ###########################################
-    # Incident wave vector K0 in vacuum and material 
-    # ###########################################
-
-    # Incident wave vector K0 in vacuum and material 
-    u0 = 0
-    for i in range(len(tags['elements'])):
-        a = tags['elements'][i]
-        u0 += feq(a, 0)*0.023933754
-
-    tags['volume'] = float(np.linalg.det(tags['unit_cell']))
-    volume = tags['volume']*1000.0  # Needs to be in Angstrom for form factors
-    angstrom_conversion = 1.0e10  # So [1A (in m)] * angstrom_conversion = 1
-    # NanometerConversion = 1.0e9
-
-    scatt_factor_to_volts = (const.h**2)*(angstrom_conversion**2)/(2*np.pi*const.m_e*const.e)*float(volume)
-    u0 = u0*scatt_factor_to_volts
-    tags['inner_potential_A'] = u0   
-    tags['inner_potential_V'] = u0*scatt_factor_to_volts
-    if verbose:
-        print('The inner potential is {0:.3f}kV'.format(tags['inner_potential_V']/1000))
-
-    # Calculating incident wave vector magnitude 'K0' in material
-    wl = tags['wave_length_nm']
-    tags['incident_wave_vector_vacuum'] = 1/wl
-    
-    k_0 = tags['incident_wave_vector'] = np.sqrt(1/wl**2 - (u0/volume*100.))  # 1/nm
-
-    tags['convergence_angle_nm-1'] = k_0*np.sin(tags['convergence_angle_mrad']/1000.)
-
-    if verbose:
-        print('Magnitude of incident wave vector in material {0:.1f} 1/nm and vacuum {1:.1f} 1/nm'.format(k_0, 1/wl))
-        print('The convergence angle of {0}mrad = {1:.2f} 1/nm'.format(tags['convergence_angle_mrad'], 
-                                                                       tags['convergence_angle_nm-1']))
-
-    # ############
-    # Rotate
-    # ############
-    
-    # first we take care of mistilt: zone axis is then in fractional Miller indices
-    zone = tags['zone'] = zone_mistilt(tags['zone_hkl'], tags['mistilt'])
-
-    # zone axis in global coordinate system
-    zone_vector = np.dot(zone, reciprocal_unit_cell)
-
-    rotation_matrix, theta, phi = get_rotation_matrix(zone_vector, verbose=False)
-    
-    if verbose:
-        print('Rotation angles are {0:.1f} deg and {1:.1f} deg'.format(theta, phi))
-    tags['theta'] = theta
-    tags['phi'] = phi
-    
-    # rotate incident wave vector 
-    w_vector = np.dot(zone_vector, rotation_matrix)
-    k0_unit_vector = w_vector / np.linalg.norm(w_vector)  # incident unit wave vector 
-    k0_vector = k0_unit_vector*k_0                         # incident  wave vector 
-       
-    if verbose:
-        print('Center of Ewald sphere ', k0_vector)
-
-    # #######################
-    # Find all Miller indices whose reciprocal point lays near the Ewald sphere with radius k_0 
-    # within a maximum excitation error Sg
-    # #######################
-    
-    hkl_max = tags['hkl_max']
-    Sg_max = tags['Sg_max']  # 1/nm  maximum allowed excitation error
-    
-    h = np.linspace(-hkl_max, hkl_max, 2*hkl_max+1)  # all evaluated single Miller Indices
-    hkl = np.array(list(itertools.product(h, h, h)))  # all evaluated Miller indices
-    g = np.dot(hkl, reciprocal_unit_cell)  # all evaluated reciprocal_unit_cell points
-    g_norm = np.linalg.norm(g, axis=1)   # length of all vectors
-    not_zero = g_norm > 0
-    g = g[not_zero]  # zero reflection will make problems further on, so we exclude it.
-    g_norm = g_norm[not_zero]
-    hkl = hkl[not_zero]
-    g_non_rot = g
-    g = np.dot(g, rotation_matrix)
-    
-    # #######################
-    # Calculate excitation errors for all reciprocal_unit_cell points
-    # #######################
-    
-    # Zuo and Spence, 'Adv TEM', 2017 -- Eq 3:14
-    # S=(k_0**2-np.linalg.norm(g - k0_vector, axis=1)**2)/(2*k_0)
-    g_mz = g - k0_vector
-
-    in_sqrt = g_mz[:, 2]**2 + np.linalg.norm(g_mz, axis=1)**2 - k_0**2
-    in_sqrt[in_sqrt < 0] = 0.
-    S = -g_mz[:, 2] - np.sqrt(in_sqrt)
-    
-    # #######################
-    # Determine reciprocal_unit_cell points with excitation error less than the maximum allowed one: Sg_max
-    # #######################
-    
-    reflections = abs(S) < Sg_max   # This is now a boolean array with True for all possible reflections
-    
-    Sg = S[reflections]
-    g_hkl = g[reflections]
-    g_hkl_non_rot = g_non_rot[reflections]
-    hkl = hkl[reflections]
-    g_norm = g_norm[reflections]
-
-    if verbose:
-        print('Of the {0} tested reciprocal_unit_cell points, {1} have an excitation error less than {2:.2f} 1/nm'.
-              format(len(g), len(g_hkl), Sg_max))
-        
-    # #################################
-    # Calculate Structure Factors
-    # ################################
-    
-    structure_factors = []
-    """for j  in range(len(g_hkl)):
-        F = 0
-        for b in range(len(tags['base'])):
-            f = feq(tags['elements'][b],np.linalg.norm(g_hkl[j]))
-            #F += f * np.exp(-2*np.pi*1j*(hkl*tags['base'][b]).sum()) # may only work for cubic Gerd
-            F += f * np.exp(-2*np.pi*1j*(g_hkl_non_rot*np.dot(tags['base'][b],unit_cell)).sum())
-            
-
-        structure_factors.append(F)
-    
-    F = structure_factors = np.array(structure_factors)
-    """
-    base = np.dot(tags['base'], tags['unit_cell'])  # transformation from relative to Cartesian coordinates
-    for j in range(len(g_hkl)):
-        F = 0
-        for b in range(len(base)):
-            f = feq(tags['elements'][b], g_norm[j])  # Atomic form factor for element and momentum change (g vector)
-            F += f * np.exp(-2*np.pi*1j*(g_hkl_non_rot[j]*base[b]).sum())        
-        structure_factors.append(F)
-    F = structure_factors = np.array(structure_factors)
-    
-    # ###########################################
-    # Sort reflection in allowed and forbidden #
-    # ###########################################
-    
-    allowed = np.absolute(F) > 0.000001    # allowed within numerical error 
-
-    if verbose:
-        print('Of the {0} possible reflection {1} are allowed.'.format(hkl.shape[0], allowed.sum()))
-        
-    # information of allowed reflections
-    Sg_allowed = Sg[allowed]
-    hkl_allowed = hkl[allowed][:]
-    g_allowed = g_hkl[allowed, :]
-    F_allowed = F[allowed]
-    g_norm_allowed = g_norm[allowed]
-    
-    tags['allowed'] = {}
-    tags['allowed']['Sg'] = Sg_allowed
-    tags['allowed']['hkl'] = hkl_allowed
-    tags['allowed']['g'] = g_allowed
-    tags['allowed']['structure factor'] = F_allowed
-    
-    # information of forbidden reflections
-    forbidden = np.logical_not(allowed)
-    Sg_forbidden = Sg[forbidden]
-    hkl_forbidden = hkl[forbidden]
-    g_forbidden = g_hkl[forbidden]
-    
-    tags['forbidden'] = {}
-    tags['forbidden']['Sg'] = Sg_forbidden
-    tags['forbidden']['hkl'] = hkl_forbidden
-    tags['forbidden']['g'] = g_forbidden
-
-    # ##########################
-    # Make pretty labels
-    # ##########################
-    hkl_label = make_pretty_labels(hkl_allowed)
-    tags['allowed']['label'] = hkl_label
-    
-    # hkl_label = make_pretty_labels(hkl_forbidden)
-    # tags['forbidden']['label'] = hkl_label
-    
-    # ###########################
-    # Calculate Intensities (of allowed reflections)
-    # ###########################
-    
-    intensities = np.absolute(F_allowed)**2
-    
-    tags['allowed']['intensities'] = intensities
-    
-    # ###########################
-    # Calculate Laue Zones (of allowed reflections)
-    # ###########################
-    # Below is the expression given in most books.
-    # However, that would only work for orthogonal crystal systems
-    # Laue_Zone = abs(np.dot(hkl_allowed,tags['zone_hkl']))  # works only for orthogonal systems
-
-    # This expression works for all crystal systems
-    # Remember we have already tilted, and so the dot product is trivial and gives only the z-component.
-    length_zone_axis = np.linalg.norm(np.dot(tags['zone_hkl'], tags['unit_cell']))
-    laue_zone = abs(np.floor(g_allowed[:, 2]*length_zone_axis+0.5))
-    
-    tags['allowed']['Laue_Zone'] = laue_zone
-
-    ZOLZ_forbidden = abs(np.floor(g_forbidden[:, 2]*length_zone_axis+0.5)) == 0
-    
-    tags['forbidden']['Laue_Zone'] = ZOLZ_forbidden
-    ZOLZ = laue_zone == 0
-    FOLZ = laue_zone == 1
-    SOLZ = laue_zone == 2
-    HOLZ = laue_zone > 0
-    HOLZp = laue_zone > 2
-
-    tags['allowed']['ZOLZ'] = ZOLZ
-    tags['allowed']['FOLZ'] = FOLZ
-    tags['allowed']['SOLZ'] = SOLZ
-    tags['allowed']['HOLZ'] = HOLZ
-    tags['allowed']['HOLZ_plus'] = tags['allowed']['HHOLZ'] = HOLZp
-    
-    if verbose:
-        print(' There are {0} allowed reflections in the zero order Laue Zone'.format(ZOLZ.sum()))
-        print(' There are {0} allowed reflections in the first order Laue Zone'.format((laue_zone == 1).sum()))
-        print(' There are {0} allowed reflections in the second order Laue Zone'.format((laue_zone == 2).sum()))
-        print(' There are {0} allowed reflections in the other higher order Laue Zones'.format((laue_zone > 2).sum()))
-        
-    if verbose == 2:
-        print(' hkl  \t Laue zone \t Intensity (*1 and \t log) \t length \n')
-        for i in range(len(hkl_allowed)):
-            print(' {0} \t {1} \t {2:.3f} \t  {3:.3f} \t  {4:.3f}   '.format(hkl_allowed[i], g_allowed[i], 
-                                                                             intensities[i], np.log(intensities[i]+1), 
-                                                                             g_norm_allowed[i]))  
-   
-    # ##########################
-    # Dynamically Activated forbidden reflections
-    # ##########################
-   
-    double_diffraction = (np.sum(np.array(list(itertools.combinations(hkl_allowed[ZOLZ], 2))), axis=1))
-    
-    dynamical_allowed = []
-    still_forbidden = []
-    for i, hkl in enumerate(hkl_forbidden):
-        if ZOLZ_forbidden[i]:
-            if hkl.tolist() in double_diffraction.tolist():
-                dynamical_allowed.append(i)
-            else:
-                still_forbidden.append(i)
-    tags['forbidden']['dynamically_activated'] = dynamical_allowed
-    tags['forbidden']['forbidden'] = dynamical_allowed
-    if verbose:
-        print('Length of zone axis vector in real space {0} nm'.format(np.round(length_zone_axis, 3)))
-        print(f'There are {len(dynamical_allowed)} forbidden but dynamical activated diffraction spots:')
-        # print(tags['forbidden']['hkl'][dynamical_allowed])
-
-    # ###################################
-    # Calculate HOLZ and Kikuchi Lines #
-    # ###################################
-
-    # Dynamic Correction
-
-    # Equation Spence+Zuo 3.86a
-    gamma_1 = - 1./(2.*k_0) * (intensities / (2.*k_0*Sg_allowed)).sum()
-    # print('gamma_1',gamma_1)
-
-    # Equation Spence+Zuo 3.84
-    Kg = k_0 - k_0*gamma_1/(g_allowed[:, 2]+1e-15)
-    Kg[ZOLZ] = k_0
-    
-    # print(Kg, Kg.shape)
-
-    # Calculate angle between K0 and deficient cone vector
-    # For dynamic calculations K0 is replaced by Kg
-    Kg[:] = k_0
-    d_theta = np.arcsin(g_norm_allowed/Kg/2.)-np.arcsin(np.abs(g_allowed[:, 2])/g_norm_allowed)
-
-    # calculate length of distance of deficient cone to K0 in ZOLZ plane
-    gd_length = 2*np.sin(d_theta/2)*k_0
-    
-    # Calculate nearest point of HOLZ and Kikuchi lines
-    g_closest = g_allowed.copy()
-    g_closest = g_closest*(gd_length/np.linalg.norm(g_closest, axis=1))[:, np.newaxis]
-    
-    g_closest[:, 2] = 0.
-    
-    # calculate and save line in Hough space coordinates (distance and theta)
-    slope = g_closest[:, 0]/(g_closest[:, 1]+1e-10)
-    distance = gd_length
-    theta = np.arctan2(g_allowed[:, 0], g_allowed[:, 1])
-    
-    tags['HOLZ'] = {}
-    tags['HOLZ']['slope'] = slope
-    # a line is now given by
-    
-    tags['HOLZ']['distance'] = distance
-    tags['HOLZ']['theta'] = theta
-    
-    tags['HOLZ']['g deficient'] = g_closest
-    tags['HOLZ']['g excess'] = g_closest+g_allowed
-    
-    tags['HOLZ']['ZOLZ'] = ZOLZ
-    tags['HOLZ']['HOLZ'] = HOLZ
-    tags['HOLZ']['FOLZ'] = FOLZ
-    tags['HOLZ']['SOLZ'] = SOLZ
-    tags['HOLZ']['HHOLZ'] = HOLZp  # even higher HOLZ
-    
-    tags['HOLZ']['hkl'] = tags['allowed']['hkl']
-    tags['HOLZ']['intensities'] = intensities
-    
-    if verbose:
-        print('KinsCat\'s  \"Kinematic_Scattering\" finished')
-
-
-def plotSAED(tags, gray=False):
-    """
-    Plot SAED Pattern of single crystal
-    """
-
-    saed = tags.copy()
-    saed['convergence_angle_nm-1'] = 0
-    
-    saed['background'] = 'white'   # 'white'  'grey'
-    saed['color map'] = 'plasma'  # ,'cubehelix'#'Greys'#'plasma'
-    saed['color reflections'] = 'ZOLZ'
-    
-    if gray:
-        saed['color map'] = 'gray'
-        saed['background'] = '#303030'  # 'darkgray'
-        saed['color reflections'] = 'intensity'
-    saed['plot HOLZ'] = 0
-    saed['plot HOLZ excess'] = 0
-    saed['plot Kikuchi'] = 0
-    saed['plot reflections'] = 1
-
-    saed['label HOLZ'] = 0
-    saed['label Kikuchi'] = 0
-    saed['label reflections'] = 0
-
-    saed['label color'] = 'white'
-    saed['label size'] = 10
-
-    saed['color Laue Zones'] = ['red',  'blue', 'green', 'blue', 'green']  # , 'green', 'red'] #for OLZ give a sequence
-    saed['color zero'] = 'red'  # 'None' #'white'
-    saed['color ring zero'] = 'None'  # 'Red' #'white' #, 'None'
-    saed['width ring zero'] = 2
-    
-    plot_diffraction_pattern(saed, True)
-
-
-def plotKikuchi(tags, grey=False):
-    """
-    Plot Kikuchi Pattern
-    """
-    Kikuchi = tags.copy()
-    
-    Kikuchi['background'] = 'black'   # 'white'  'grey'
-    Kikuchi['color map'] = 'plasma'   # ,'cubehelix'#'Greys'#'plasma'
-    Kikuchi['color reflections'] = 'intensity'
-
-    Kikuchi['plot HOLZ'] = 0
-    Kikuchi['plot HOLZ excess'] = 0
-    Kikuchi['plot Kikuchi'] = 1
-    Kikuchi['plot reflections'] = 1
-
-    Kikuchi['label HOLZ'] = 0
-    Kikuchi['label Kikuchi'] = 0
-    Kikuchi['label reflections'] = 0
-
-    Kikuchi['label color'] = 'white'
-    Kikuchi['label size'] = 10
-
-    Kikuchi['color Kikuchi'] = 'green'
-    Kikuchi['linewidth HOLZ'] = -1  # -1: linewidth according to intensity (structure factor F^2
-    Kikuchi['linewidth Kikuchi'] = -1  # -1: linewidth according to intensity (structure factor F^2
-    
-    Kikuchi['color Laue Zones'] = ['red',  'blue', 'green', 'blue', 'green']  # , 'green', 'red']
-    # #for OLZ give a sequence
-    Kikuchi['color zero'] = 'white'  # 'None' #'white'
-    Kikuchi['color ring zero'] = 'None'  # 'Red' #'white' #, 'None'
-    Kikuchi['width ring zero'] = 2
-    
-    plot_diffraction_pattern(Kikuchi, True)
-
-
-def plotHOLZ(tags, grey=False):
-    """
-    Plot HOLZ Pattern
-    """
-    holz = tags.copy()
-    
-    holz['background'] = 'black'   # 'white'  'grey'
-    holz['color map'] = 'plasma'   # ,'cubehelix'#'Greys'#'plasma'
-    holz['color reflections'] = 'intensity'
-
-    holz['plot HOLZ'] = 1
-    holz['plot HOLZ excess'] = 0
-    holz['plot Kikuchi'] = 1
-    holz['plot reflections'] = 0
-
-    holz['label HOLZ'] = 0
-    holz['label Kikuchi'] = 0
-    holz['label reflections'] = 0
-
-    holz['label color'] = 'white'
-    holz['label size'] = 10
-
-    holz['color Kikuchi'] = 'green'
-    holz['linewidth HOLZ'] = -1  # -1: linewidth according to intensity (structure factor F^2
-    holz['linewidth Kikuchi'] = -1  # -1: linewidth according to intensity (structure factor F^2
-    
-    holz['color Laue Zones'] = ['red',  'blue', 'green']  # , 'green', 'red'] #for OLZ give a sequence
-    holz['color zero'] = 'white'   # 'None' #'white'
-    holz['color ring zero'] = 'Red'  # 'Red' #'white' #, 'None'
-    holz['width ring zero'] = 2
-    
-    plot_diffraction_pattern(holz, True)
-
-
-def plotCBED(tags, grey=False):
-    """
-    Plot CBED Pattern
-    """
-    cbed = tags.copy()
-    
-    cbed['background'] = 'black'   # 'white'  'grey'
-    cbed['color map'] = 'plasma'   # ,'cubehelix'#'Greys'#'plasma'
-    cbed['color reflections'] = 'intensity'
-
-    cbed['plot HOLZ'] = 1
-    cbed['plot HOLZ excess'] = 1
-    cbed['plot Kikuchi'] = 1
-    cbed['plot reflections'] = 1
-
-    cbed['label HOLZ'] = 0
-    cbed['label Kikuchi'] = 0
-    cbed['label reflections'] = 0
-
-    cbed['label color'] = 'white'
-    cbed['label size'] = 10
-
-    cbed['color Kikuchi'] = 'green'
-    cbed['linewidth HOLZ'] = -1  # -1: linewidth according to intensity (structure factor F^2
-    cbed['linewidth Kikuchi'] = -1  # -1: linewidth according to intensity (structure factor F^2
-
-    cbed['color reflections'] = 'intensity'
-
-    cbed['color Laue Zones'] = ['red',  'blue', 'green']   # , 'green', 'red'] #for OLZ give a sequence
-    cbed['color zero'] = 'white'  # 'None' #'white'
-    cbed['color ring zero'] = 'Red'  # 'Red' #'white' #, 'None'
-    cbed['width ring zero'] = 2
-    
-    plot_diffraction_pattern(cbed, True)
-
-    
-# #######################
-# Plot HOLZ Pattern #
-# #######################
-def circles(x, y, s, c='b', v_min=None, v_max=None, **kwargs):
-    """
-    Make a scatter plot of circles.
-
-    Similar to plt.scatter, but the size of circles are in data scale.
-
-    Parameters
-
-        x, y : scalar or array_like, shape (n, )
-            Input data
-        s : scalar or array_like, shape (n, )
-            Radius of circles.
-        c : color or sequence of color, optional, default : 'b'
-            `c` can be a single color format string, or a sequence of color
-            specifications of length `N`, or a sequence of `N` numbers to be
-            mapped to colors using the `cmap` and `norm` specified via kwargs.
-            Note that `c` should not be a single numeric RGB or RGBA sequence
-            because that is indistinguishable from an array of values
-            to be colormapped. (If you insist, use `color` instead.)
-            `c` can be a 2-D array in which the rows are RGB or RGBA, however.
-        v_min, v_max : scalar, optional, default: None
-            `v_min` and `v_max` are used in conjunction with `norm` to normalize
-            luminance data.  If either are `None`, the min and max of the
-            color array is used.
-        kwargs : `~matplotlib.collections.Collection` properties
-            Eg. alpha, edgecolor(ec), facecolor(fc), linewidth(lw), linestyle(ls),
-            norm, cmap, transform, etc.
-    Returns
-
-        paths : `~matplotlib.collections.PathCollection`
-    Examples
-        a = np.arange(11)
-        circles(a, a, s=a*0.2, c=a, alpha=0.5, ec='none')
-        plt.colorbar()
-    License
-        This code is under [The BSD 3-Clause License]
-        (http://opensource.org/licenses/BSD-3-Clause)
-    """
-
-    if np.isscalar(c):
-        kwargs.setdefault('color', c)
-        c = None
-
-    if 'fc' in kwargs:
-        kwargs.setdefault('facecolor', kwargs.pop('fc'))
-    if 'ec' in kwargs:
-        kwargs.setdefault('edgecolor', kwargs.pop('ec'))
-    if 'ls' in kwargs:
-        kwargs.setdefault('linestyle', kwargs.pop('ls'))
-    if 'lw' in kwargs:
-        kwargs.setdefault('linewidth', kwargs.pop('lw'))
-    # You can set `facecolor` with an array for each patch,
-    # while you can only set `facecolors` with a value for all.
-
-    zipped = np.broadcast(x, y, s)
-    patches = [Circle((x_, y_), s_)
-               for x_, y_, s_ in zipped]
-    collection = PatchCollection(patches, **kwargs)
-    if c is not None:
-        c = np.broadcast_to(c, zipped.shape).ravel()
-        collection.set_array(c)
-        collection.set_clim(v_min, v_max)
-
-    ax = plt.gca()
-    ax.add_collection(collection)
-    ax.autoscale_view()
-    plt.draw_if_interactive()
-    if c is not None:
-        plt.sci(collection)
-    return collection
-
-
-def plot_diffraction_pattern(tags, grey=False):
-    """
-    Plot any diffraction pattern based on content in dictionary
-    """
-    if 'plot_rotation' not in tags:
-        tags['plot_rotation'] = 0.
-
-    if 'new_plot' not in tags:
-        tags['new_plot'] = True
-
-    if tags['new_plot']:
-        fig = plt.figure()
-        ax = fig.add_subplot(111, facecolor=tags['background'])
-        
-        diffraction_pattern(tags, grey)
-            
-        plt.axis('equal')
-        if 'plot FOV' in tags:
-            x = tags['plot FOV']  # in 1/nm
-            plt.xlim(-x, x)
-            plt.ylim(-x, x)
-        plt.title(tags['crystal_name'])
-        plt.show()
-    else:
-        diffraction_pattern(tags, grey)
-
-
-def diffraction_pattern(tags, grey=False):
-    """
-    Determines how to plot diffraction pattern from kinematic scattering data.
-
-    Input:
-        tags : dictionary of kinematic scattering data
-
-    Returns:
-        tags: dictionary that now contains all information of how to plot any diffraction pattern
-        plot
-    """
-    
-    # Get information from dictionary
-    HOLZ = tags['allowed']['HOLZ']
-    ZOLZ = tags['allowed']['ZOLZ']
-    
-    laue_zone = tags['allowed']['Laue_Zone']
-
-    if 'label' in tags['allowed']:
-        label = tags['allowed']['label']
-
-    angle = np.radians(tags['plot_rotation'])  # mrad
-    c = np.cos(angle)
-    s = np.sin(angle)
-    r_mat = np.array([[c, -s, 0], [s, c, 0], [0, 0, 1]])
-    
-    # HOLZ and Kikuchi lines coordinates in Hough space
-    gd = np.dot(tags['HOLZ']['g deficient'], r_mat)
-    ge = np.dot(tags['HOLZ']['g excess'], r_mat)
-
-    points = np.dot(tags['allowed']['g'], r_mat)
-    
-    theta = tags['HOLZ']['theta']+angle
-    
-    intensity = tags['allowed']['intensities']
-    radius = tags['convergence_angle_nm-1']
-    tags['Bragg'] = {}
-    tags['Bragg']['points'] = points
-    tags['Bragg']['intensity'] = intensity
-    tags['Bragg']['radius'] = radius
-    
-    if radius < 0.1:
-        radius_i = 2
-    else:
-        radius_i = radius
-    # Beginning and ends of HOLZ lines
-    max_length = radius_i * 1.3
-    h_xp = gd[:, 0] + max_length * np.cos(np.pi-theta)
-    h_yp = gd[:, 1] + max_length * np.sin(np.pi-theta)
-    h_xm = gd[:, 0] - max_length * np.cos(np.pi-theta)
-    h_ym = gd[:, 1] - max_length * np.sin(np.pi-theta)
-    tags['HOLZ lines'] = {}
-    tags['HOLZ lines']['Hxp'] = h_xp
-    tags['HOLZ lines']['Hyp'] = h_yp
-    tags['HOLZ lines']['Hxm'] = h_xm
-    tags['HOLZ lines']['Hym'] = h_ym
-
-    # Beginning and ends of excess HOLZ lines
-    max_length = radius_i * 0.8
-    e_xp = ge[:, 0] + max_length * np.cos(np.pi-theta)
-    e_yp = ge[:, 1] + max_length * np.sin(np.pi-theta)
-    e_xm = ge[:, 0] - max_length * np.cos(np.pi-theta)
-    e_ym = ge[:, 1] - max_length * np.sin(np.pi-theta)
-    tags['excess HOLZ lines'] = {}
-    tags['excess HOLZ lines']['Exp'] = e_xp
-    tags['excess HOLZ lines']['Eyp'] = e_yp
-    tags['excess HOLZ lines']['Exm'] = e_xm
-    tags['excess HOLZ lines']['Eym'] = e_ym
-
-    # Beginning and ends of HOLZ lines
-    max_length = 20
-    k_xp = gd[:, 0] + max_length * np.cos(np.pi-theta)
-    k_yp = gd[:, 1] + max_length * np.sin(np.pi-theta)
-    k_xm = gd[:, 0] - max_length * np.cos(np.pi-theta)
-    k_ym = gd[:, 1] - max_length * np.sin(np.pi-theta)
-    tags['Kikuchi lines'] = {}
-    tags['Kikuchi lines']['Kxp'] = k_xp
-    tags['Kikuchi lines']['Kyp'] = k_yp
-    tags['Kikuchi lines']['Kxm'] = k_xm
-    tags['Kikuchi lines']['Kym'] = k_ym
-    
-    intensity_Kikuchi = intensity*4./intensity[ZOLZ].max()
-    if len(intensity[tags['HOLZ']['HOLZ']]) > 1:
-        intensity_HOLZ = intensity*4./intensity[tags['HOLZ']['HOLZ']].max()*.75
-        tags['HOLZ lines']['intensity_HOLZ'] = intensity_HOLZ
-    tags['Kikuchi lines']['intensity_Kikuchi'] = intensity_Kikuchi
-    # #######
-    # Plot #
-    # #######
-    # cms = mpl.cm
-    # cm = cms.plasma#jet#, cms.gray, cms.autumn]
-    cm = plt.get_cmap(tags['color map']) 
-
-    fig = plt.gcf()
-    
-    ax = plt.gca()
- 
-    if 'plot image' in tags:
-        l = -tags['plot image FOV']/2+tags['plot shift x']
-        r = tags['plot image FOV']/2+tags['plot shift x']
-        t = -tags['plot image FOV']/2+tags['plot shift y']
-        b = tags['plot image FOV']/2+tags['plot shift y']
-        ax.imshow(tags['plot image'], extent=(l, r, t, b))
-        print('image') 
-    
-    ix = np.argsort((points**2).sum(axis=1))
-    # print(tags['allowed']['hkl'][ix])
-    p = points[ix]
-    inten = intensity[ix]
-    tags['Bragg']['points'] = p
-    tags['Bragg']['intensity'] = inten
-
-    laue_color = []
-    for i in range(int(laue_zone.max())+1):
-        if i < len(tags['color Laue Zones']):
-            laue_color.append(tags['color Laue Zones'][i])
-        else:
-            laue_color.append(tags['color Laue Zones'][-1])
-    
-    if tags['plot reflections']:
-        if radius < 0.1:
-            if tags['color reflections'] == 'intensity':
-                ax.scatter(points[:, 0], points[:, 1], c=np.log(intensity), cmap=cm, s=20)
-            else:
-                for i in range(len(laue_zone)):
-                    color = laue_color[int(laue_zone[i])]
-                    ax.scatter(points[i, 0], points[i, 1], c=color, cmap=cm, s=20)
-                
-            ax.scatter(0, 0, c=tags['color zero'], s=100)
-            radius = 2
-        else:
-            ix = np.argsort((points**2).sum(axis=1))
-            p = points[ix]
-            inten = intensity[ix]
-            if tags['color reflections'] == 'intensity':
-                circles(p[:, 0], p[:, 1], s=radius, c=np.log(inten+1), cmap=cm, alpha=0.9, edgecolor='') 
-            else:
-                for i in range(len(laue_zone)):
-                    color = laue_color[int(laue_zone[i])]
-                    circles(p[i, 0], p[i, 1], s=radius, c=color, cmap=cm, alpha=0.9, edgecolor='')          
-    
-    if not tags['color zero'] == 'None':
-        circle = plt.Circle((0, 0), radius, color=tags['color zero'])
-        ax.add_artist(circle)
-
-    for i in range(len(h_xp)):
-        if tags['HOLZ']['HOLZ'][i]:
-            color = laue_color[int(laue_zone[i])]
-            if tags['plot HOLZ']:
-                # plot HOLZ lines
-                ax.plot((h_xp[i], h_xm[i]), (h_yp[i], h_ym[i]), c=color, linewidth=intensity_HOLZ[i])
-            if tags['plot HOLZ excess']:
-                ax.plot((e_xp[i], e_xm[i]), (e_yp[i], e_ym[i]), c=color, linewidth=intensity_HOLZ[i])
-            
-                if tags['label HOLZ']:  # Add indices
-                    ax.text(h_xp[i], h_yp[i], label[i], fontsize=10) 
-                    ax.text(e_xp[i], e_yp[i], label[i], fontsize=10) 
-        else:
-            # Plot Kikuchi lines
-            if tags['plot Kikuchi']:
-                ax.plot((k_xp[i], k_xm[i]), (k_yp[i], k_ym[i]), c=tags['color Kikuchi'], linewidth=intensity_Kikuchi[i]) 
-                if tags['label Kikuchi']:  # Add indices
-                    ax.text(k_xp[i], k_yp[i], label[i], fontsize=tags['label size'], color=tags['label color']) 
-                # tags['Kikuchi lines']
-
-    if not (tags['color ring zero'] == 'None'):
-        ring = plt.Circle((0, 0), radius, color=tags['color ring zero'], fill=False, linewidth=2)
-        ax.add_artist(ring)
-        print(ring)
-
-    return tags    
-    
-    
-electronFF = {
-    # form factor coefficients
-    # Z= 6, chisq= 0.143335
-    # a1 b1 a2 b2
-    # a3 b3 c1 d1
-    # c2 d2 c3 d3
-
-    # name of the file:  feKirkland.txt
-    # converted with program sortFF.py
-    # form factor parametrized in 1/Angstrom
-    # bond_length as a list of atom Sizes, bond radii, angle radii, H-bond radii
-
-    'H': {'Z': 1, 'chisq': 0.170190,
-          'bond_length': [0.98, 0.78, 1.20, 0],
-          'fa': [4.20298324e-003, 6.27762505e-002, 3.00907347e-002],
-          'fb': [2.25350888e-001, 2.25366950e-001, 2.25331756e-001],
-          'fc': [6.77756695e-002, 3.56609237e-003, 2.76135815e-002],
-          'fd': [4.38854001e+000, 4.03884823e-001, 1.44490166e+000]},
-    'He': {'Z':  2,   'chisq': 0.396634,
-           'bond_length': [1.45, 1.25, 1.40, 0],
-           'fa': [1.87543704e-005, 4.10595800e-004, 1.96300059e-001],
-           'fb': [2.12427997e-001, 3.32212279e-001, 5.17325152e-001],
-           'fc': [8.36015738e-003, 2.95102022e-002, 4.65928982e-007],
-           'fd': [3.66668239e-001, 1.37171827e+000, 3.75768025e+004]},
-    'Li': {'Z':  3,   'chisq': 0.286232,
-           'bond_length': [1.76,  1.56, 1.82, 0],
-           'fa': [7.45843816e-002, 7.15382250e-002, 1.45315229e-001],
-           'fb': [8.81151424e-001, 4.59142904e-002, 8.81301714e-001],
-           'fc': [1.12125769e+000, 2.51736525e-003, 3.58434971e-001],
-           'fd': [1.88483665e+001, 1.59189995e-001, 6.12371000e+000]},
-    'Be': {'Z':  4,   'chisq': 0.195442,
-           'bond_length': [1.33,  1.13, 1.70, 0],
-           'fa': [6.11642897e-002, 1.25755034e-001, 2.00831548e-001],
-           'fb': [9.90182132e-002, 9.90272412e-002, 1.87392509e+000],
-           'fc': [7.87242876e-001, 1.58847850e-003, 2.73962031e-001],
-           'fd': [9.32794929e+000, 8.91900236e-002, 3.20687658e+000]},
-    'B': {'Z':  5,   'chisq': 0.146989,
-          'bond_length': [1.18,  0.98, 2.08, 0],
-          'fa': [1.25716066e-001, 1.73314452e-001, 1.84774811e-001],
-          'fb': [1.48258830e-001, 1.48257216e-001, 3.34227311e+000],
-          'fc': [1.95250221e-001, 5.29642075e-001, 1.08230500e-003],
-          'fd': [1.97339463e+000, 5.70035553e+000, 5.64857237e-002]},
-    'C': {'Z':  6,   'chisq': 0.102440,
-          'bond_length': [1.12,  0.92, 1.95, 0],
-          'fa': [2.12080767e-001, 1.99811865e-001, 1.68254385e-001],
-          'fb': [2.08605417e-001, 2.08610186e-001, 5.57870773e+000],
-          'fc': [1.42048360e-001, 3.63830672e-001, 8.35012044e-004],
-          'fd': [1.33311887e+000, 3.80800263e+000, 4.03982620e-002]},
-    'N': {'Z':  7,   'chisq': 0.060249,
-          'bond_length': [1.08,  0.88, 1.85, 1.30],
-          'fa': [5.33015554e-001, 5.29008883e-002, 9.24159648e-002],
-          'fb': [2.90952515e-001, 1.03547896e+001, 1.03540028e+001],
-          'fc': [2.61799101e-001, 8.80262108e-004, 1.10166555e-001],
-          'fd': [2.76252723e+000, 3.47681236e-002, 9.93421736e-001]},
-    'O': {'Z':  8,   'chisq': 0.039944,
-          'bond_length': [1.09,  0.89, 1.70, 1.40],
-          'fa': [3.39969204e-001, 3.07570172e-001, 1.30369072e-001],
-          'fb': [3.81570280e-001, 3.81571436e-001, 1.91919745e+001],
-          'fc': [8.83326058e-002, 1.96586700e-001, 9.96220028e-004],
-          'fd': [7.60635525e-001, 2.07401094e+000, 3.03266869e-002]},
-    'F': {'Z':  9,   'chisq': 0.027866,
-          'bond_length': [1.30,  1.10, 1.73, 0],
-          'fa': [2.30560593e-001, 5.26889648e-001, 1.24346755e-001],
-          'fb': [4.80754213e-001, 4.80763895e-001, 3.95306720e+001],
-          'fc': [1.24616894e-003, 7.20452555e-002, 1.53075777e-001],
-          'fd': [2.62181803e-002, 5.92495593e-001, 1.59127671e+000]},
-    'Ne': {'Z':  10,   'chisq': 0.021836,
-           'bond_length': [1.50,  1.30, 1.54, 0],
-           'fa': [4.08371771e-001, 4.54418858e-001, 1.44564923e-001],
-           'fb': [5.88228627e-001, 5.88288655e-001, 1.21246013e+002],
-           'fc': [5.91531395e-002, 1.24003718e-001, 1.64986037e-003],
-           'fd': [4.63963540e-001, 1.23413025e+000, 2.05869217e-002]},
-    'Na': {'Z':  11,   'chisq': 0.064136,
-           'bond_length': [2.10,  1.91, 2.27, 0],
-           'fa': [1.36471662e-001, 7.70677865e-001, 1.56862014e-001],
-           'fb': [4.99965301e-002, 8.81899664e-001, 1.61768579e+001],
-           'fc': [9.96821513e-001, 3.80304670e-002, 1.27685089e-001],
-           'fd': [2.00132610e+001, 2.60516254e-001, 6.99559329e-001]},
-    'Mg': {'Z':  12,   'chisq': 0.051303,
-           'bond_length': [1.80,  1.60, 1.73, 0], 
-           'fa': [3.04384121e-001, 7.56270563e-001, 1.01164809e-001],
-           'fb': [8.42014377e-002, 1.64065598e+000, 2.97142975e+001],
-           'fc': [3.45203403e-002, 9.71751327e-001, 1.20593012e-001],
-           'fd': [2.16596094e-001, 1.21236852e+001, 5.60865838e-001]},
-    'Al': {'Z':  13,   'chisq': 0.049529,
-           'bond_length': [1.60,  1.43, 2.05, 0],
-           'fa': [7.77419424e-001, 5.78312036e-002, 4.26386499e-001],
-           'fb': [2.71058227e+000, 7.17532098e+001, 9.13331555e-002],
-           'fc': [1.13407220e-001, 7.90114035e-001, 3.23293496e-002],
-           'fd': [4.48867451e-001, 8.66366718e+000, 1.78503463e-001]},
-    'Si': {'Z':  14,   'chisq': 0.071667,
-           'bond_length': [1.52,  1.32, 2.10, 0],
-           'fa': [1.06543892e+000, 1.20143691e-001, 1.80915263e-001],
-           'fb': [1.04118455e+000, 6.87113368e+001, 8.87533926e-002],
-           'fc': [1.12065620e+000, 3.05452816e-002, 1.59963502e+000],
-           'fd': [3.70062619e+000, 2.14097897e-001, 9.99096638e+000]},
-    'P': {'Z':  15,   'chisq': 0.047673,
-          'bond_length': [1.48,  1.28, 2.08, 0],
-          'fa': [1.05284447e+000, 2.99440284e-001, 1.17460748e-001],
-          'fb': [1.31962590e+000, 1.28460520e-001, 1.02190163e+002],
-          'fc': [9.60643452e-001, 2.63555748e-002, 1.38059330e+000],
-          'fd': [2.87477555e+000, 1.82076844e-001, 7.49165526e+000]},
-    'S': {'Z':  16,   'chisq': 0.033482,
-          'bond_length': [1.47,  1.27, 2.00, 0],
-          'fa': [1.01646916e+000, 4.41766748e-001, 1.21503863e-001],
-          'fb': [1.69181965e+000, 1.74180288e-001, 1.67011091e+002],
-          'fc': [8.27966670e-001, 2.33022533e-002, 1.18302846e+000],
-          'fd': [2.30342810e+000, 1.56954150e-001, 5.85782891e+000]},
-    'Cl': {'Z':  17,   'chisq': 0.206186,
-           'bond_length': [1.70,  1.50, 1.97, 0],
-           'fa': [9.44221116e-001, 4.37322049e-001, 2.54547926e-001],
-           'fb': [2.40052374e-001, 9.30510439e+000, 9.30486346e+000],
-           'fc': [5.47763323e-002, 8.00087488e-001, 1.07488641e-002],
-           'fd': [1.68655688e-001, 2.97849774e+000, 6.84240646e-002]},
-    'Ar': {'Z':  18,   'chisq': 0.263904,
-           'bond_length': [2.00,  1.80, 1.88, 0],
-           'fa': [1.06983288e+000, 4.24631786e-001, 2.43897949e-001],
-           'fb': [2.87791022e-001, 1.24156957e+001, 1.24158868e+001],
-           'fc': [4.79446296e-002, 7.64958952e-001, 8.23128431e-003],
-           'fd': [1.36979796e-001, 2.43940729e+000, 5.27258749e-002]},
-    'K': {'Z':  19,   'chisq': 0.161900,
-          'bond_length': [2.58,  2.38, 2.75, 0],
-          'fa': [6.92717865e-001, 9.65161085e-001, 1.48466588e-001],
-          'fb': [7.10849990e+000, 3.57532901e-001, 3.93763275e-002],
-          'fc': [2.64645027e-002, 1.80883768e+000, 5.43900018e-001],
-          'fd': [1.03591321e-001, 3.22845199e+001, 1.67791374e+000]},
-    'Ca': {'Z':  20,   'chisq': 0.085209,
-           'bond_length': [2.17,  1.97, 1.97, 0],
-           'fa': [3.66902871e-001, 8.66378999e-001, 6.67203300e-001],
-           'fb': [6.14274129e-002, 5.70881727e-001, 7.82965639e+000],
-           'fc': [4.87743636e-001, 1.82406314e+000, 2.20248453e-002],
-           'fd': [1.32531318e+000, 2.10056032e+001, 9.11853450e-002]},
-    'Sc': {'Z':  21,   'chisq': 0.052352,
-           'bond_length': [1.84,  1.64, 1.70, 0],
-           'fa': [3.78871777e-001, 9.00022505e-001, 7.15288914e-001],
-           'fb': [6.98910162e-002, 5.21061541e-001, 7.87707920e+000],
-           'fc': [1.88640973e-002, 4.07945949e-001, 1.61786540e+000],
-           'fd': [8.17512708e-002, 1.11141388e+000, 1.80840759e+001]},
-    'Ti': {'Z':  22,   'chisq': 0.035298,
-           'bond_length': [1.66,  1.46, 1.70, 0],
-           'fa': [3.62383267e-001, 9.84232966e-001, 7.41715642e-001],
-           'fb': [7.54707114e-002, 4.97757309e-001, 8.17659391e+000],
-           'fc': [3.62555269e-001, 1.49159390e+000, 1.61659509e-002],
-           'fd': [9.55524906e-001, 1.62221677e+001, 7.33140839e-002]},
-    'V': {'Z':  23,   'chisq': 0.030745,
-          'bond_length': [1.55,  1.35, 1.70, 0],
-          'fa': [3.52961378e-001, 7.46791014e-001, 1.08364068e+000],
-          'fb': [8.19204103e-002, 8.81189511e+000, 5.10646075e-001],
-          'fc': [1.39013610e+000, 3.31273356e-001, 1.40422612e-002],
-          'fd': [1.48901841e+001, 8.38543079e-001, 6.57432678e-002]},
-    'Cr': {'Z':  24,   'chisq': 0.015287,
-           'bond_length': [1.56,  1.36, 1.70, 0],
-           'fa': [1.34348379e+000, 5.07040328e-001, 4.26358955e-001],
-           'fb': [1.25814353e+000, 1.15042811e+001, 8.53660389e-002],
-           'fc': [1.17241826e-002, 5.11966516e-001, 3.38285828e-001],
-           'fd': [6.00177061e-002, 1.53772451e+000, 6.62418319e-001]},
-    'Mn': {'Z':  25,   'chisq': 0.031274,
-           'bond_length': [1.54,  1.30, 1.70, 0],
-           'fa': [3.26697613e-001, 7.17297000e-001, 1.33212464e+000],
-           'fb': [8.88813083e-002, 1.11300198e+001, 5.82141104e-001],
-           'fc': [2.80801702e-001, 1.15499241e+000, 1.11984488e-002],
-           'fd': [6.71583145e-001, 1.26825395e+001, 5.32334467e-002]},
-    'Fe': {'Z':  26,   'chisq': 0.031315,
-           'bond_length': [1.47,  1.27, 1.70, 0],
-           'fa': [3.13454847e-001, 6.89290016e-001, 1.47141531e+000],
-           'fb': [8.99325756e-002, 1.30366038e+001, 6.33345291e-001],
-           'fc': [1.03298688e+000, 2.58280285e-001, 1.03460690e-002],
-           'fd': [1.16783425e+001, 6.09116446e-001, 4.81610627e-002]},
-    'Co': {'Z':  27,   'chisq': 0.031643,
-           'bond_length': [1.45,  1.25, 1.70, 0],
-           'fa': [3.15878278e-001, 1.60139005e+000, 6.56394338e-001],
-           'fb': [9.46683246e-002, 6.99436449e-001, 1.56954403e+001],
-           'fc': [9.36746624e-001, 9.77562646e-003, 2.38378578e-001],
-           'fd': [1.09392410e+001, 4.37446816e-002, 5.56286483e-001]},
-    'Ni': {'Z':  28,   'chisq': 0.032245,
-           'bond_length': [1.45,  1.25, 1.63, 0],
-           'fa': [1.72254630e+000, 3.29543044e-001, 6.23007200e-001],
-           'fb': [7.76606908e-001, 1.02262360e-001, 1.94156207e+001],
-           'fc': [9.43496513e-003, 8.54063515e-001, 2.21073515e-001],
-           'fd': [3.98684596e-002, 1.04078166e+001, 5.10869330e-001]},
-    'Cu': {'Z':  29,   'chisq': 0.010467,
-           'bond_length': [1.48,  1.28, 1.40, 0],
-           'fa': [3.58774531e-001, 1.76181348e+000, 6.36905053e-001],
-           'fb': [1.06153463e-001, 1.01640995e+000, 1.53659093e+001],
-           'fc': [7.44930667e-003, 1.89002347e-001, 2.29619589e-001],
-           'fd': [3.85345989e-002, 3.98427790e-001, 9.01419843e-001]},
-    'Zn': {'Z':  30,   'chisq': 0.026698,
-           'bond_length': [1.59,  1.39, 1.39, 0],
-           'fa': [5.70893973e-001, 1.98908856e+000, 3.06060585e-001],
-           'fb': [1.26534614e-001, 2.17781965e+000, 3.78619003e+001],
-           'fc': [2.35600223e-001, 3.97061102e-001, 6.85657228e-003],
-           'fd': [3.67019041e-001, 8.66419596e-001, 3.35778823e-002]},
-    'Ga': {'Z':  31,   'chisq': 0.008110,
-           'bond_length': [1.61,  1.41, 1.87, 0],
-           'fa': [6.25528464e-001, 2.05302901e+000, 2.89608120e-001],
-           'fb': [1.10005650e-001, 2.41095786e+000, 4.78685736e+001],
-           'fc': [2.07910594e-001, 3.45079617e-001, 6.55634298e-003],
-           'fd': [3.27807224e-001, 7.43139061e-001, 3.09411369e-002]},
-    'Ge': {'Z':  32,   'chisq': 0.032198,
-           'bond_length': [1.57,  1.37, 1.70, 0],
-           'fa': [5.90952690e-001, 5.39980660e-001, 2.00626188e+000],
-           'fb': [1.18375976e-001, 7.18937433e+001, 1.39304889e+000],
-           'fc': [7.49705041e-001, 1.83581347e-001, 9.52190743e-003],
-           'fd': [6.89943350e+000, 3.64667232e-001, 2.69888650e-002]},
-    'As': {'Z':  33,   'chisq': 0.034014,
-           'bond_length': [1.59,  1.39, 1.85, 0],
-           'fa': [7.77875218e-001, 5.93848150e-001, 1.95918751e+000],
-           'fb': [1.50733157e-001, 1.42882209e+002, 1.74750339e+000],
-           'fc': [1.79880226e-001, 8.63267222e-001, 9.59053427e-003],
-           'fd': [3.31800852e-001, 5.85490274e+000, 2.33777569e-002]},
-    'Se': {'Z':  34,   'chisq': 0.035703,
-           'bond_length': [1.60,  1.40, 1.90, 0],
-           'fa': [9.58390681e-001, 6.03851342e-001, 1.90828931e+000],
-           'fb': [1.83775557e-001, 1.96819224e+002, 2.15082053e+000],
-           'fc': [1.73885956e-001, 9.35265145e-001, 8.62254658e-003],
-           'fd': [3.00006024e-001, 4.92471215e+000, 2.12308108e-002]},
-    'Br': {'Z':  35,   'chisq': 0.039250,
-           'bond_length': [1.80,  1.60, 2.10, 0],
-           'fa': [1.14136170e+000, 5.18118737e-001, 1.85731975e+000],
-           'fb': [2.18708710e-001, 1.93916682e+002, 2.65755396e+000],
-           'fc': [1.68217399e-001, 9.75705606e-001, 7.24187871e-003],
-           'fd': [2.71719918e-001, 4.19482500e+000, 1.99325718e-002]},
-    'Kr': {'Z':  36,   'chisq': 0.045421,
-           'bond_length': [2.10,  1.90, 2.02, 0],
-           'fa': [3.24386970e-001, 1.31732163e+000, 1.79912614e+000],
-           'fb': [6.31317973e+001, 2.54706036e-001, 3.23668394e+000],
-           'fc': [4.29961425e-003, 1.00429433e+000, 1.62188197e-001],
-           'fd': [1.98965610e-002, 3.61094513e+000, 2.45583672e-001]},
-    'Rb': {'Z':  37,   'chisq': 0.130044,
-           'bond_length': [2.75,  2.55, 1.70, 0],
-           'fa': [2.90445351e-001, 2.44201329e+000, 7.69435449e-001],
-           'fb': [3.68420227e-002, 1.16013332e+000, 1.69591472e+001],
-           'fc': [1.58687000e+000, 2.81617593e-003, 1.28663830e-001],
-           'fd': [2.53082574e+000, 1.88577417e-002, 2.10753969e-001]},
-    'Sr': {'Z':  38,   'chisq': 0.188055,
-           'bond_length': [2.35,  2.15, 1.70, 0],
-           'fa': [1.37373086e-002, 1.97548672e+000, 1.59261029e+000],
-           'fb': [1.87469061e-002, 6.36079230e+000, 2.21992482e-001],
-           'fc': [1.73263882e-001, 4.66280378e+000, 1.61265063e-003],
-           'fd': [2.01624958e-001, 2.53027803e+001, 1.53610568e-002]},
-    'Y': {'Z':  39,   'chisq': 0.174927,
-          'bond_length': [2.00,  1.80, 1.70, 0],
-          'fa': [6.75302747e-001, 4.70286720e-001, 2.63497677e+000],
-          'fb': [6.54331847e-002, 1.06108709e+002, 2.06643540e+000],
-          'fc': [1.09621746e-001, 9.60348773e-001, 5.28921555e-003],
-          'fd': [1.93131925e-001, 1.63310938e+000, 1.66083821e-002]},
-    'Zr': {'Z':  40,   'chisq': 0.072078,
-           'bond_length': [1.80,  1.60, 1.70, 0],
-           'fa': [2.64365505e+000, 5.54225147e-001, 7.61376625e-001],
-           'fb': [2.20202699e+000, 1.78260107e+002, 7.67218745e-002],
-           'fc': [6.02946891e-003, 9.91630530e-002, 9.56782020e-001],
-           'fd': [1.55143296e-002, 1.76175995e-001, 1.54330682e+000]},
-    'Nb': {'Z':  41,   'chisq': 0.011800,
-           'bond_length': [1.67,  1.47, 1.70, 0],
-           'fa': [6.59532875e-001, 1.84545854e+000, 1.25584405e+000],
-           'fb': [8.66145490e-002, 5.94774398e+000, 6.40851475e-001],
-           'fc': [1.22253422e-001, 7.06638328e-001, 2.62381591e-003],
-           'fd': [1.66646050e-001, 1.62853268e+000, 8.26257859e-003]},
-    'Mo': {'Z':  42,   'chisq': 0.008976,
-           'bond_length': [1.60,  1.40, 1.70, 0],
-           'fa': [6.10160120e-001, 1.26544000e+000, 1.97428762e+000],
-           'fb': [9.11628054e-002, 5.06776025e-001, 5.89590381e+000],
-           'fc': [6.48028962e-001, 2.60380817e-003, 1.13887493e-001],
-           'fd': [1.46634108e+000, 7.84336311e-003, 1.55114340e-001]},
-    'Tc': {'Z':  43,   'chisq': 0.023771,
-           'bond_length': [1.56,  1.36, 1.70, 0],
-           'fa': [8.55189183e-001, 1.66219641e+000, 1.45575475e+000],
-           'fb': [1.02962151e-001, 7.64907000e+000, 1.01639987e+000],
-           'fc': [1.05445664e-001, 7.71657112e-001, 2.20992635e-003],
-           'fd': [1.42303338e-001, 1.34659349e+000, 7.90358976e-003]},
-    'Ru': {'Z':  44,   'chisq': 0.010613,
-           'bond_length': [1.54,  1.34, 1.70, 0],
-           'fa': [4.70847093e-001, 1.58180781e+000, 2.02419818e+000],
-           'fb': [9.33029874e-002, 4.52831347e-001, 7.11489023e+000],
-           'fc': [1.97036257e-003, 6.26912639e-001, 1.02641320e-001],
-           'fd': [7.56181595e-003, 1.25399858e+000, 1.33786087e-001]},
-    'Rh': {'Z':  45,   'chisq': 0.012895,
-           'bond_length': [1.54,  1.34, 1.70, 0],
-           'fa': [4.20051553e-001, 1.76266507e+000, 2.02735641e+000],
-           'fb': [9.38882628e-002, 4.64441687e-001, 8.19346046e+000],
-           'fc': [1.45487176e-003, 6.22809600e-001, 9.91529915e-002],
-           'fd': [7.82704517e-003, 1.17194153e+000, 1.24532839e-001]},
-    'Pd': {'Z':  46,   'chisq': 0.009172,
-           'bond_length': [1.58,  1.38, 1.63, 0],
-           'fa': [2.10475155e+000, 2.03884487e+000, 1.82067264e-001],
-           'fb': [8.68606470e+000, 3.78924449e-001, 1.42921634e-001],
-           'fc': [9.52040948e-002, 5.91445248e-001, 1.13328676e-003],
-           'fd': [1.17125900e-001, 1.07843808e+000, 7.80252092e-003]},
-    'Ag': {'Z':  47,   'chisq': 0.006648,
-           'bond_length': [1.64,  1.44, 1.72, 0],
-           'fa': [2.07981390e+000, 4.43170726e-001, 1.96515215e+000],
-           'fb': [9.92540297e+000, 1.04920104e-001, 6.40103839e-001],
-           'fc': [5.96130591e-001, 4.78016333e-001, 9.46458470e-002],
-           'fd': [8.89594790e-001, 1.98509407e+000, 1.12744464e-001]},
-    'Cd': {'Z':  48,   'chisq': 0.005588,
-           'bond_length': [1.77,  1.57, 1.58, 0],
-           'fa': [1.63657549e+000, 2.17927989e+000, 7.71300690e-001],
-           'fb': [1.24540381e+001, 1.45134660e+000, 1.26695757e-001],
-           'fc': [6.64193880e-001, 7.64563285e-001, 8.61126689e-002],
-           'fd': [7.77659202e-001, 1.66075210e+000, 1.05728357e-001]},
-    'In': {'Z':  49,   'chisq': 0.002569,
-           'bond_length': [1.86,  1.66, 1.93, 0],
-           'fa': [2.24820632e+000, 1.64706864e+000, 7.88679265e-001],
-           'fb': [1.51913507e+000, 1.30113424e+001, 1.06128184e-001],
-           'fc': [8.12579069e-002, 6.68280346e-001, 6.38467475e-001],
-           'fd': [9.94045620e-002, 1.49742063e+000, 7.18422635e-001]},
-    'Sn': {'Z':  50,   'chisq': 0.005051,
-           'bond_length': [1.82,  1.62, 2.17, 0],
-           'fa': [2.16644620e+000, 6.88691021e-001, 1.92431751e+000],
-           'fb': [1.13174909e+001, 1.10131285e-001, 6.74464853e-001],
-           'fc': [5.65359888e-001, 9.18683861e-001, 7.80542213e-002],
-           'fd': [7.33564610e-001, 1.02310312e+001, 9.31104308e-002]},
-    'Sb': {'Z':  51,   'chisq': 0.004383,
-           'bond_length': [1.79,  1.59, 2.20, 0],
-           'fa': [1.73662114e+000, 9.99871380e-001, 2.13972409e+000],
-           'fb': [8.84334719e-001, 1.38462121e-001, 1.19666432e+001],
-           'fc': [5.60566526e-001, 9.93772747e-001, 7.37374982e-002],
-           'fd': [6.72672880e-001, 8.72330411e+000, 8.78577715e-002]},
-    'Te': {'Z':  52,   'chisq': 0.004105,
-           'bond_length': [1.80,  1.60, 2.06, 0],
-           'fa': [2.09383882e+000, 1.56940519e+000, 1.30941993e+000],
-           'fb': [1.26856869e+001, 1.21236537e+000, 1.66633292e-001],
-           'fc': [6.98067804e-002, 1.04969537e+000, 5.55594354e-001],
-           'fd': [8.30817576e-002, 7.43147857e+000, 6.17487676e-001]},
-    'I': {'Z':  53,   'chisq': 0.004068,
-          'bond_length': [1.90,  1.70, 2.15, 0],
-          'fa': [1.60186925e+000, 1.98510264e+000, 1.48226200e+000],
-          'fb': [1.95031538e-001, 1.36976183e+001, 1.80304795e+000],
-          'fc': [5.53807199e-001, 1.11728722e+000, 6.60720847e-002],
-          'fd': [5.67912340e-001, 6.40879878e+000, 7.86615429e-002]},
-    'Xe': {'Z':  54,   'chisq': 0.004381,
-           'bond_length': [2.30,  2.10, 2.16, 0],
-           'fa': [1.60015487e+000, 1.71644581e+000, 1.84968351e+000],
-           'fb': [2.92913354e+000, 1.55882990e+001, 2.22525983e-001],
-           'fc': [6.23813648e-002, 1.21387555e+000, 5.54051946e-001],
-           'fd': [7.45581223e-002, 5.56013271e+000, 5.21994521e-001]},
-    'Cs': {'Z':  55,   'chisq': 0.042676,
-           'bond_length': [2.93,  2.73, 1.70, 0],
-           'fa': [2.95236854e+000, 4.28105721e-001, 1.89599233e+000],
-           'fb': [6.01461952e+000, 4.64151246e+001, 1.80109756e-001],
-           'fc': [5.48012938e-002, 4.70838600e+000, 5.90356719e-001],
-           'fd': [7.12799633e-002, 4.56702799e+001, 4.70236310e-001]},
-    'Ba': {'Z':  56,   'chisq': 0.043267,
-           'bond_length': [2.44,  2.24, 1.70, 0],
-           'fa': [3.19434243e+000, 1.98289586e+000, 1.55121052e-001],
-           'fb': [9.27352241e+000, 2.28741632e-001, 3.82000231e-002],
-           'fc': [6.73222354e-002, 4.48474211e+000, 5.42674414e-001],
-           'fd': [7.30961745e-002, 2.95703565e+001, 4.08647015e-001]},
-    'La': {'Z':  57,   'chisq': 0.033249,
-           'bond_length': [2.08,  1.88, 1.70, 0],
-           'fa': [2.05036425e+000, 1.42114311e-001, 3.23538151e+000],
-           'fb': [2.20348417e-001, 3.96438056e-002, 9.56979169e+000],
-           'fc': [6.34683429e-002, 3.97960586e+000, 5.20116711e-001],
-           'fd': [6.92443091e-002, 2.53178406e+001, 3.83614098e-001]},
-    'Ce': {'Z':  58,   'chisq': 0.029355,
-           'bond_length': [2.02,  1.82, 1.70, 0],
-           'fa': [3.22990759e+000, 1.57618307e-001, 2.13477838e+000],
-           'fb': [9.94660135e+000, 4.15378676e-002, 2.40480572e-001],
-           'fc': [5.01907609e-001, 3.80889010e+000, 5.96625028e-002],
-           'fd': [3.66252019e-001, 2.43275968e+001, 6.59653503e-002]},
-    'Pr': {'Z':  59,   'chisq': 0.029725,
-           'bond_length': [2.03,  1.83, 1.70, 0],
-           'fa': [1.58189324e-001, 3.18141995e+000, 2.27622140e+000],
-           'fb': [3.91309056e-002, 1.04139545e+001, 2.81671757e-001],
-           'fc': [3.97705472e+000, 5.58448277e-002, 4.85207954e-001],
-           'fd': [2.61872978e+001, 6.30921695e-002, 3.54234369e-001]},
-    'Nd': {'Z':  60,   'chisq': 0.027597,
-           'bond_length': [2.02,  1.82, 1.70, 0],
-           'fa': [1.81379417e-001, 3.17616396e+000, 2.35221519e+000],
-           'fb': [4.37324793e-002, 1.07842572e+001, 3.05571833e-001],
-           'fc': [3.83125763e+000, 5.25889976e-002, 4.70090742e-001],
-           'fd': [2.54745408e+001, 6.02676073e-002, 3.39017003e-001]},
-    'Pm': {'Z':  61,   'chisq': 0.025208,
-           'bond_length': [2.01,  1.81, 1.70, 0],
-           'fa': [1.92986811e-001, 2.43756023e+000, 3.17248504e+000],
-           'fb': [4.37785970e-002, 3.29336996e-001, 1.11259996e+001],
-           'fc': [3.58105414e+000, 4.56529394e-001, 4.94812177e-002],
-           'fd': [2.46709586e+001, 3.24990282e-001, 5.76553100e-002]},
-    'Sm': {'Z':  62,   'chisq': 0.023540,
-           'bond_length': [2.00,  1.80, 1.70, 0],
-           'fa': [2.12002595e-001, 3.16891754e+000, 2.51503494e+000],
-           'fb': [4.57703608e-002, 1.14536599e+001, 3.55561054e-001],
-           'fc': [4.44080845e-001, 3.36742101e+000, 4.65652543e-002],
-           'fd': [3.11953363e-001, 2.40291435e+001, 5.52266819e-002]},
-    'Eu': {'Z':  63,   'chisq': 0.022204,
-           'bond_length': [2.24,  2.04, 1.70, 0],
-           'fa': [2.59355002e+000, 3.16557522e+000, 2.29402652e-001],
-           'fb': [3.82452612e-001, 1.17675155e+001, 4.76642249e-002],
-           'fc': [4.32257780e-001, 3.17261920e+000, 4.37958317e-002],
-           'fd': [2.99719833e-001, 2.34462738e+001, 5.29440680e-002]},
-    'Gd': {'Z':  64,   'chisq': 0.017492,
-           'bond_length': [2.00,  1.80, 1.70, 0],
-           'fa': [3.19144939e+000, 2.55766431e+000, 3.32681934e-001],
-           'fb': [1.20224655e+001, 4.08338876e-001, 5.85819814e-002],
-           'fc': [4.14243130e-002, 2.61036728e+000, 4.20526863e-001],
-           'fd': [5.06771477e-002, 1.99344244e+001, 2.85686240e-001]},
-    'Tb': {'Z':  65,   'chisq': 0.020036,
-           'bond_length': [1.98,  1.78, 1.70, 0],
-           'fa': [2.59407462e-001, 3.16177855e+000, 2.75095751e+000],
-           'fb': [5.04689354e-002, 1.23140183e+001, 4.38337626e-001],
-           'fc': [2.79247686e+000, 3.85931001e-002, 4.10881708e-001],
-           'fd': [2.23797309e+001, 4.87920992e-002, 2.77622892e-001]},
-    'Dy': {'Z':  66,   'chisq': 0.019351,
-           'bond_length': [1.97,  1.77, 1.70, 0],
-           'fa': [3.16055396e+000, 2.82751709e+000, 2.75140255e-001],
-           'fb': [1.25470414e+001, 4.67899094e-001, 5.23226982e-002],
-           'fc': [4.00967160e-001, 2.63110834e+000, 3.61333817e-002],
-           'fd': [2.67614884e-001, 2.19498166e+001, 4.68871497e-002]},
-    'Ho': {'Z':  67,   'chisq': 0.018720,
-           'bond_length': [1.98,  1.78, 1.70, 0],
-           'fa': [2.88642467e-001, 2.90567296e+000, 3.15960159e+000],
-           'fb': [5.40507687e-002, 4.97581077e-001, 1.27599505e+001],
-           'fc': [3.91280259e-001, 2.48596038e+000, 3.37664478e-002],
-           'fd': [2.58151831e-001, 2.15400972e+001, 4.50664323e-002]},
-    'Er': {'Z':  68,   'chisq': 0.018677,
-           'bond_length': [1.96,  1.76, 1.70, 0],
-           'fa': [3.15573213e+000, 3.11519560e-001, 2.97722406e+000],
-           'fb': [1.29729009e+001, 5.81399387e-002, 5.31213394e-001],
-           'fc': [3.81563854e-001, 2.40247532e+000, 3.15224214e-002],
-           'fd': [2.49195776e-001, 2.13627616e+001, 4.33253257e-002]},
-    'Tm': {'Z':  69,   'chisq': 0.018176,
-           'bond_length': [1.95,  1.75, 1.70, 0],
-           'fa': [3.15591970e+000, 3.22544710e-001, 3.05569053e+000],
-           'fb': [1.31232407e+001, 5.97223323e-002, 5.61876773e-001],
-           'fc': [2.92845100e-002, 3.72487205e-001, 2.27833695e+000],
-           'fd': [4.16534255e-002, 2.40821967e-001, 2.10034185e+001]},
-    'Yb': {'Z':  70,   'chisq': 0.018460,
-           'bond_length': [2.10,  1.90, 1.70, 0],
-           'fa': [3.10794704e+000, 3.14091221e+000, 3.75660454e-001],
-           'fb': [6.06347847e-001, 1.33705269e+001, 7.29814740e-002],
-           'fc': [3.61901097e-001, 2.45409082e+000, 2.72383990e-002],
-           'fd': [2.32652051e-001, 2.12695209e+001, 3.99969597e-002]},
-    'Lu': {'Z':  71,   'chisq': 0.015021,
-           'bond_length': [1.93,  1.73, 1.70, 0],
-           'fa': [3.11446863e+000, 5.39634353e-001, 3.06460915e+000],
-           'fb': [1.38968881e+001, 8.91708508e-002, 6.79919563e-001],
-           'fc': [2.58563745e-002, 2.13983556e+000, 3.47788231e-001],
-           'fd': [3.82808522e-002, 1.80078788e+001, 2.22706591e-001]},
-    'Hf': {'Z':  72,   'chisq': 0.012070,
-           'bond_length': [1.78,  1.58, 1.70, 0],
-           'fa': [3.01166899e+000, 3.16284788e+000, 6.33421771e-001],
-           'fb': [7.10401889e-001, 1.38262192e+001, 9.48486572e-002],
-           'fc': [3.41417198e-001, 1.53566013e+000, 2.40723773e-002],
-           'fd': [2.14129678e-001, 1.55298698e+001, 3.67833690e-002]},
-    'Ta': {'Z':  73,   'chisq': 0.010775,
-           'bond_length': [1.67,  1.47, 1.70, 0],
-           'fa': [3.20236821e+000, 8.30098413e-001, 2.86552297e+000],
-           'fb': [1.38446369e+001, 1.18381581e-001, 7.66369118e-001],
-           'fc': [2.24813887e-002, 1.40165263e+000, 3.33740596e-001],
-           'fd': [3.52934622e-002, 1.46148877e+001, 2.05704486e-001]},
-    'W': {'Z':  74,   'chisq': 0.009479,
-          'bond_length': [1.61,  1.41, 1.70, 0],
-          'fa': [9.24906855e-001, 2.75554557e+000, 3.30440060e+000],
-          'fb': [1.28663377e-001, 7.65826479e-001, 1.34471170e+001],
-          'fc': [3.29973862e-001, 1.09916444e+000, 2.06498883e-002],
-          'fd': [1.98218895e-001, 1.35087534e+001, 3.38918459e-002]},
-    'Re': {'Z':  75,   'chisq': 0.004620,
-           'bond_length': [1.58,  1.38, 1.70, 0],
-           'fa': [1.96952105e+000, 1.21726619e+000, 4.10391685e+000],
-           'fb': [4.98830620e+001, 1.33243809e-001, 1.84396916e+000],
-           'fc': [2.90791978e-002, 2.30696669e-001, 6.08840299e-001],
-           'fd': [2.84192813e-002, 1.90968784e-001, 1.37090356e+000]},
-    'Os': {'Z':  76,   'chisq': 0.003085,
-           'bond_length': [1.55,  1.35, 1.70, 0],
-           'fa': [2.06385867e+000, 1.29603406e+000, 3.96920673e+000],
-           'fb': [4.05671697e+001, 1.46559047e-001, 1.82561596e+000],
-           'fc': [2.69835487e-002, 2.31083999e-001, 6.30466774e-001],
-           'fd': [2.84172045e-002, 1.79765184e-001, 1.38911543e+000]},
-    'Ir': {'Z':  77,   'chisq': 0.003924,
-           'bond_length': [1.56,  1.36, 1.70, 0],
-           'fa': [2.21522726e+000, 1.37573155e+000, 3.78244405e+000],
-           'fb': [3.24464090e+001, 1.60920048e-001, 1.78756553e+000],
-           'fc': [2.44643240e-002, 2.36932016e-001, 6.48471412e-001],
-           'fd': [2.82909938e-002, 1.70692368e-001, 1.37928390e+000]},
-    'Pt': {'Z':  78,   'chisq': 0.003817,
-           'bond_length': [1.59,  1.39, 1.72, 0],
-           'fa': [9.84697940e-001, 2.73987079e+000, 3.61696715e+000],
-           'fb': [1.60910839e-001, 7.18971667e-001, 1.29281016e+001],
-           'fc': [3.02885602e-001, 2.78370726e-001, 1.52124129e-002],
-           'fd': [1.70134854e-001, 1.49862703e+000, 2.83510822e-002]},
-    'Au': {'Z':  79,   'chisq': 0.003143,
-           'bond_length': [1.64,  1.44, 1.66, 0],
-           'fa': [9.61263398e-001, 3.69581030e+000, 2.77567491e+000],
-           'fb': [1.70932277e-001, 1.29335319e+001, 6.89997070e-001],
-           'fc': [2.95414176e-001, 3.11475743e-001, 1.43237267e-002],
-           'fd': [1.63525510e-001, 1.39200901e+000, 2.71265337e-002]},
-    'Hg': {'Z':  80,   'chisq': 0.002717,
-           'bond_length': [1.77,  1.57, 1.55, 0],
-           'fa': [1.29200491e+000, 2.75161478e+000, 3.49387949e+000],
-           'fb': [1.83432865e-001, 9.42368371e-001, 1.46235654e+001],
-           'fc': [2.77304636e-001, 4.30232810e-001, 1.48294351e-002],
-           'fd': [1.55110144e-001, 1.28871670e+000, 2.61903834e-002]},
-    'Tl': {'Z':  81,   'chisq': 0.003492,
-           'bond_length': [1.92,  1.72, 1.96, 0],
-           'fa': [3.75964730e+000, 3.21195904e+000, 6.47767825e-001],
-           'fb': [1.35041513e+001, 6.66330993e-001, 9.22518234e-002],
-           'fc': [2.76123274e-001, 3.18838810e-001, 1.31668419e-002],
-           'fd': [1.50312897e-001, 1.12565588e+000, 2.48879842e-002]},
-    'Pb': {'Z':  82,   'chisq': 0.001158,
-           'bond_length': [1.95,  1.75, 2.02, 0],
-           'fa': [1.00795975e+000, 3.09796153e+000, 3.61296864e+000],
-           'fb': [1.17268427e-001, 8.80453235e-001, 1.47325812e+001],
-           'fc': [2.62401476e-001, 4.05621995e-001, 1.31812509e-002],
-           'fd': [1.43491014e-001, 1.04103506e+000, 2.39575415e-002]},
-    'Bi': {'Z':  83,   'chisq': 0.026436,
-           'bond_length': [1.90,  1.70, 1.70, 0],
-           'fa': [1.59826875e+000, 4.38233925e+000, 2.06074719e+000],
-           'fb': [1.56897471e-001, 2.47094692e+000, 5.72438972e+001],
-           'fc': [1.94426023e-001, 8.22704978e-001, 2.33226953e-002],
-           'fd': [1.32979109e-001, 9.56532528e-001, 2.23038435e-002]},
-    'Po': {'Z':  84,   'chisq': 0.008962,
-           'bond_length': [1.96,  1.76, 1.70, 0],
-           'fa': [1.71463223e+000, 2.14115960e+000, 4.37512413e+000],
-           'fb': [9.79262841e+001, 2.10193717e-001, 3.66948812e+000],
-           'fc': [2.16216680e-002, 1.97843837e-001, 6.52047920e-001],
-           'fd': [1.98456144e-002, 1.33758807e-001, 7.80432104e-001]},
-    'At': {'Z':  85,   'chisq': 0.033776,
-           'bond_length': [2.00,  1.80, 1.70, 0],
-           'fa': [1.48047794e+000, 2.09174630e+000, 4.75246033e+000],
-           'fb': [1.25943919e+002, 1.83803008e-001, 4.19890596e+000],
-           'fc': [1.85643958e-002, 2.05859375e-001, 7.13540948e-001],
-           'fd': [1.81383503e-002, 1.33035404e-001, 7.03031938e-001]},
-    'Rn': {'Z':  86,   'chisq': 0.050132,
-           'bond_length': [2.40,  2.20, 1.70, 0],
-           'fa': [6.30022295e-001, 3.80962881e+000, 3.89756067e+000],
-           'fb': [1.40909762e-001, 3.08515540e+001, 6.51559763e-001],
-           'fc': [2.40755100e-001, 2.62868577e+000, 3.14285931e-002],
-           'fd': [1.08899672e-001, 6.42383261e+000, 2.42346699e-002]},
-    'Fr': {'Z':  87,   'chisq': 0.056720,
-           'bond_length': [3.00,  2.80, 1.70, 0],
-           'fa': [5.23288135e+000, 2.48604205e+000, 3.23431354e-001],
-           'fb': [8.60599536e+000, 3.04543982e-001, 3.87759096e-002],
-           'fc': [2.55403596e-001, 5.53607228e-001, 5.75278889e-003],
-           'fd': [1.28717724e-001, 5.36977452e-001, 1.29417790e-002]},
-    'Ra': {'Z':  88,   'chisq': 0.081498,
-           'bond_length': [2.46,  2.26, 1.70, 0],
-           'fa': [1.44192685e+000, 3.55291725e+000, 3.91259586e+000],
-           'fb': [1.18740873e-001, 1.01739750e+000, 6.31814783e+001],
-           'fc': [2.16173519e-001, 3.94191605e+000, 4.60422605e-002],
-           'fd': [9.55806441e-002, 3.50602732e+001, 2.20850385e-002]},
-    'Ac': {'Z':  89,   'chisq': 0.077643,
-           'bond_length': [2.09,  1.88, 1.70, 0],
-           'fa': [1.45864127e+000, 4.18945405e+000, 3.65866182e+000],
-           'fb': [1.07760494e-001, 8.89090649e+001, 1.05088931e+000],
-           'fc': [2.08479229e-001, 3.16528117e+000, 5.23892556e-002],
-           'fd': [9.09335557e-002, 3.13297788e+001, 2.08807697e-002]},
-    'Th': {'Z':  90,   'chisq': 0.048096,
-           'bond_length': [2.00,  1.80, 1.70, 0],
-           'fa': [1.19014064e+000, 2.55380607e+000, 4.68110181e+000],
-           'fb': [7.73468729e-002, 6.59693681e-001, 1.28013896e+001],
-           'fc': [2.26121303e-001, 3.58250545e-001, 7.82263950e-003],
-           'fd': [1.08632194e-001, 4.56765664e-001, 1.62623474e-002]},
-    'Pa': {'Z':  91,   'chisq': 0.070186,
-           'bond_length': [1.83,  1.63, 1.70, 0],
-           'fa': [4.68537504e+000, 2.98413708e+000, 8.91988061e-001],
-           'fb': [1.44503632e+001, 5.56438592e-001, 6.69512914e-002],
-           'fc': [2.24825384e-001, 3.04444846e-001, 9.48162708e-003],
-           'fd': [1.03235396e-001, 4.27255647e-001, 1.77730611e-002]},
-    'U': {'Z':  92,   'chisq': 0.072478,
-          'bond_length': [1.76,  1.56, 1.86, 0],
-          'fa': [4.63343606e+000, 3.18157056e+000, 8.76455075e-001],
-          'fb': [1.63377267e+001, 5.69517868e-001, 6.88860012e-002],
-          'fc': [2.21685477e-001, 2.72917100e-001, 1.11737298e-002],
-          'fd': [9.84254550e-002, 4.09470917e-001, 1.86215410e-002]},
-    'Np': {'Z':  93,   'chisq': 0.074792,
-           'bond_length': [1.80,  1.60, 1.70, 0],
-           'fa': [4.56773888e+000, 3.40325179e+000, 8.61841923e-001],
-           'fb': [1.90992795e+001, 5.90099634e-001, 7.03204851e-002],
-           'fc': [2.19728870e-001, 2.38176903e-001, 1.38306499e-002],
-           'fd': [9.36334280e-002, 3.93554882e-001, 1.94437286e-002]},
-    'Pu': {'Z':  94,   'chisq': 0.071877,
-           'bond_length': [1.84,  1.64, 1.70, 0],
-           'fa': [5.45671123e+000, 1.11687906e-001, 3.30260343e+000],
-           'fb': [1.01892720e+001, 3.98131313e-002, 3.14622212e-001],
-           'fc': [1.84568319e-001, 4.93644263e-001, 3.57484743e+000],
-           'fd': [1.04220860e-001, 4.63080540e-001, 2.19369542e+001]},
-    'Am': {'Z':  95,   'chisq': 0.062156,
-           'bond_length': [2.01,  1.81, 1.70, 0],
-           'fa': [5.38321999e+000, 1.23343236e-001, 3.46469090e+000],
-           'fb': [1.07289857e+001, 4.15137806e-002, 3.39326208e-001],
-           'fc': [1.75437132e-001, 3.39800073e+000, 4.69459519e-001],
-           'fd': [9.98932346e-002, 2.11601535e+001, 4.51996970e-001]},
-    'Cm': {'Z':  96,   'chisq': 0.050111,
-           'bond_length': [2.20,  2.00, 1.70, 0],
-           'fa': [5.38402377e+000, 3.49861264e+000, 1.88039547e-001],
-           'fb': [1.11211419e+001, 3.56750210e-001, 5.39853583e-002],
-           'fc': [1.69143137e-001, 3.19595016e+000, 4.64393059e-001],
-           'fd': [9.60082633e-002, 1.80694389e+001, 4.36318197e-001]},
-    'Bk': {'Z':  97,   'chisq': 0.044081,
-           'bond_length': [2.20,  2.00, 1.70, 0],
-           'fa': [3.66090688e+000, 2.03054678e-001, 5.30697515e+000],
-           'fb': [3.84420906e-001, 5.48547131e-002, 1.17150262e+001],
-           'fc': [1.60934046e-001, 3.04808401e+000, 4.43610295e-001],
-           'fd': [9.21020329e-002, 1.73525367e+001, 4.27132359e-001]},
-    'Cf': {'Z':  98,   'chisq': 0.041053,
-           'bond_length': [2.20,  2.00, 1.70, 0],
-           'fa': [3.94150390e+000, 5.16915345e+000, 1.61941074e-001],
-           'fb': [4.18246722e-001, 1.25201788e+001, 4.81540117e-002],
-           'fc': [4.15299561e-001, 2.91761325e+000, 1.51474927e-001],
-           'fd': [4.24913856e-001, 1.90899693e+001, 8.81568925e-002]}
-    }
-
-
-# From Appendix C of Kirkland, "Advanced Computing in Electron Microscopy", 2nd ed.
-# Calculation of electron form factor for specific q:
-# Using equation Kirkland C.15
-
-def feq(element, q):
-    """
-    Atomic form factor parametrized in 1/Angstrom but converted to 1/nm
-
-    The atomic form factor is from Kirkland: Advanced Computing in Electron Microscopy 2nd edition, Appendix C.
-
-    Input:
-        element: string of element name
-        q:  now magnitude of scattering vector in 1/nm -- (=> exp(-i*g.r), physics negative convention)
-
-
-    """
-
-    q = q/10
-    # q is now magnitude of scattering vector in 1/A -- (=> exp(-i*g.r), physics negative convention)
-    param = electronFF[element]
-    f_l = 0
-    f_g = 0
-    for i in range(3):
-        f_l += param['fa'][i]/(q**2 + param['fb'][i])
-        f_g += param['fc'][i]*np.exp(-q**2 * param['fd'][i])
-
-    # Conversion factor from scattering factors to volts. h^2/(2pi*m0*e), see e.g. Kirkland eqn. C.5
-    # !NB RVolume is already in A unlike RPlanckConstant
-    # scatt_factor_to_volts=(PlanckConstant**2)*(angstrom_conversion**2)/(2*np.pi*ElectronMass*ElectronCharge)
-    return f_l+f_g  # * scatt_factor_to_volts
-
-
-# Jmol colors.  See: http://jmol.sourceforge.net/jscolors/#color_U
-jmol_colors = np.array([
-    (1.000, 0.000, 0.000),  # None1.000,1.000,1.000),  # H
-    (0.851, 1.000, 1.000),  # He
-    (0.800, 0.502, 1.000),  # Li
-    (0.761, 1.000, 0.000),  # Be
-    (1.000, 0.710, 0.710),  # B
-    (0.565, 0.565, 0.565),  # C
-    (0.188, 0.314, 0.973),  # N
-    (1.000, 0.051, 0.051),  # O
-    (0.565, 0.878, 0.314),  # F
-    (0.702, 0.890, 0.961),  # Ne
-    (0.671, 0.361, 0.949),  # Na
-    (0.541, 1.000, 0.000),  # Mg
-    (0.749, 0.651, 0.651),  # Al
-    (0.941, 0.784, 0.627),  # Si
-    (1.000, 0.502, 0.000),  # P
-    (1.000, 1.000, 0.188),  # S
-    (0.122, 0.941, 0.122),  # Cl
-    (0.502, 0.820, 0.890),  # Ar
-    (0.561, 0.251, 0.831),  # K
-    (0.239, 1.000, 0.000),  # Ca
-    (0.902, 0.902, 0.902),  # Sc
-    (0.749, 0.761, 0.780),  # Ti
-    (0.651, 0.651, 0.671),  # V
-    (0.541, 0.600, 0.780),  # Cr
-    (0.612, 0.478, 0.780),  # Mn
-    (0.878, 0.400, 0.200),  # Fe
-    (0.941, 0.565, 0.627),  # Co
-    (0.314, 0.816, 0.314),  # Ni
-    (0.784, 0.502, 0.200),  # Cu
-    (0.490, 0.502, 0.690),  # Zn
-    (0.761, 0.561, 0.561),  # Ga
-    (0.400, 0.561, 0.561),  # Ge
-    (0.741, 0.502, 0.890),  # As
-    (1.000, 0.631, 0.000),  # Se
-    (0.651, 0.161, 0.161),  # Br
-    (0.361, 0.722, 0.820),  # Kr
-    (0.439, 0.180, 0.690),  # Rb
-    (0.000, 1.000, 0.000),  # Sr
-    (0.580, 1.000, 1.000),  # Y
-    (0.580, 0.878, 0.878),  # Zr
-    (0.451, 0.761, 0.788),  # Nb
-    (0.329, 0.710, 0.710),  # Mo
-    (0.231, 0.620, 0.620),  # Tc
-    (0.141, 0.561, 0.561),  # Ru
-    (0.039, 0.490, 0.549),  # Rh
-    (0.000, 0.412, 0.522),  # Pd
-    (0.753, 0.753, 0.753),  # Ag
-    (1.000, 0.851, 0.561),  # Cd
-    (0.651, 0.459, 0.451),  # In
-    (0.400, 0.502, 0.502),  # Sn
-    (0.620, 0.388, 0.710),  # Sb
-    (0.831, 0.478, 0.000),  # Te
-    (0.580, 0.000, 0.580),  # I
-    (0.259, 0.620, 0.690),  # Xe
-    (0.341, 0.090, 0.561),  # Cs
-    (0.000, 0.788, 0.000),  # Ba
-    (0.439, 0.831, 1.000),  # La
-    (1.000, 1.000, 0.780),  # Ce
-    (0.851, 1.000, 0.780),  # Pr
-    (0.780, 1.000, 0.780),  # Nd
-    (0.639, 1.000, 0.780),  # Pm
-    (0.561, 1.000, 0.780),  # Sm
-    (0.380, 1.000, 0.780),  # Eu
-    (0.271, 1.000, 0.780),  # Gd
-    (0.188, 1.000, 0.780),  # Tb
-    (0.122, 1.000, 0.780),  # Dy
-    (0.000, 1.000, 0.612),  # Ho
-    (0.000, 0.902, 0.459),  # Er
-    (0.000, 0.831, 0.322),  # Tm
-    (0.000, 0.749, 0.220),  # Yb
-    (0.000, 0.671, 0.141),  # Lu
-    (0.302, 0.761, 1.000),  # Hf
-    (0.302, 0.651, 1.000),  # Ta
-    (0.129, 0.580, 0.839),  # W
-    (0.149, 0.490, 0.671),  # Re
-    (0.149, 0.400, 0.588),  # Os
-    (0.090, 0.329, 0.529),  # Ir
-    (0.816, 0.816, 0.878),  # Pt
-    (1.000, 0.820, 0.137),  # Au
-    (0.722, 0.722, 0.816),  # Hg
-    (0.651, 0.329, 0.302),  # Tl
-    (0.341, 0.349, 0.380),  # Pb
-    (0.620, 0.310, 0.710),  # Bi
-    (0.671, 0.361, 0.000),  # Po
-    (0.459, 0.310, 0.271),  # At
-    (0.259, 0.510, 0.588),  # Rn
-    (0.259, 0.000, 0.400),  # Fr
-    (0.000, 0.490, 0.000),  # Ra
-    (0.439, 0.671, 0.980),  # Ac
-    (0.000, 0.729, 1.000),  # Th
-    (0.000, 0.631, 1.000),  # Pa
-    (0.000, 0.561, 1.000),  # U
-    (0.000, 0.502, 1.000),  # Np
-    (0.000, 0.420, 1.000),  # Pu
-    (0.329, 0.361, 0.949),  # Am
-    (0.471, 0.361, 0.890),  # Cm
-    (0.541, 0.310, 0.890),  # Bk
-    (0.631, 0.212, 0.831),  # Cf
-    (0.702, 0.122, 0.831),  # Es
-    (0.702, 0.122, 0.729),  # Fm
-    (0.702, 0.051, 0.651),  # Md
-    (0.741, 0.051, 0.529),  # No
-    (0.780, 0.000, 0.400),  # Lr
-    (0.800, 0.000, 0.349),  # Rf
-    (0.820, 0.000, 0.310),  # Db
-    (0.851, 0.000, 0.271),  # Sg
-    (0.878, 0.000, 0.220),  # Bh
-    (0.902, 0.000, 0.180),  # Hs
-    (0.922, 0.000, 0.149),  # Mt
-])
-
-# encoding: utf-8
-# crystal data base cbd
-cdb = {'aluminum': {'crystal_name': 'aluminum',
-                    'symmetry': 'FCC',
-                    'elements': ['Al'],
-                    'a': 0.405,  # nm
-                    'reference': 'W. Witt, Z. Naturforsch. A, 1967, 22A, 92',
-                    'link': 'http://doi.org/10.1515/zna-1967-0115'}}
-cdb['Al'] = cdb['Aluminum'] = cdb['aluminum']
-
-cdb['gold'] = {'crystal_name': 'gold',
-               'symmetry': 'FCC',
-               'elements': ['Au'],
-               'a': 0.40782,  # nm
-               'reference': '',
-               'link': ''}
-cdb['Au'] = cdb['Gold'] = cdb['gold']
-
-cdb['silver'] = {'crystal_name': 'silver',
-                 'symmetry': 'FCC',
-                 'elements': ['Ag'],
-                 'a': 0.40853, # nm
-                 'reference': '', 'link': ''}
-cdb['Ag'] = cdb['Silver'] = cdb['silver']
-
-cdb['diamond'] = {'crystal_name': 'diamond',
-                  'symmetry': 'zinc_blende',
-                  'elements': ['C'],
-                  'a': 0.35668,  # nm
-                  'reference': '', 'link': ''}
-cdb['Diamond'] = cdb['diamond']
-
-cdb['germanium'] = {'crystal_name': 'germanium',
-                    'symmetry': 'zinc_blende',
-                    'elements': ['Ge'],
-                    'a': 0.566806348,   # nm for 300K
-                    'reference': 'H. P. Singh, Acta Crystallogr., 1968, 24A, 469',
-                    'link': 'https://doi.org/10.1107/S056773946800094X'}
-cdb['Ge'] = cdb['Germanium'] = cdb['germanium']
-
-cdb['silicon'] = {'crystal_name': 'silicon',
-                  'symmetry': 'zinc_blende',
-                  'elements': ['Si'],
-                  'a': 0.566806348,   # nm for 300K
-                  'reference': 'C. R. Hubbard, H. E. Swanson, and F. A. Mauer, J. Appl. Crystallogr., 1975, 8, 45',
-                  'link': 'https://doi.org/10.1107/S0021889875009508'}
-cdb['Si'] = cdb['Silicon'] = cdb['silicon']  
-
-cdb['GaAs'] = {'crystal_name': 'GaAs',
-               'symmetry': 'zinc_blende',
-               'elements': ['Ga', 'As'],
-               'a': 0.565325,   # nm for 300K
-               'reference': 'J.F.C. Baker, M. Hart, M.A.G. Halliwell, R. Heckingbottom, Solid-State Electronics, 19, '
-                           '1976, 331-334,',
-               'link': 'https://doi.org/10.1016/0038-1101(76)90031-9'}
-    
-cdb['FCC Fe'] = {'crystal_name': 'FCC Fe',
-                 'symmetry': 'FCC',
-                 'elements': ['Fe'],
-                 'a': 0.3571,   # nm
-                 'reference': 'R. Kohlhaas, P. Donner, and N. Schmitz-Pranghe, Z. Angew. Phys., 1967, 23, 245',
-                 'link': ''}
-cdb['fcc fe'] = cdb['FCC Fe']
-
-
-cdb['BCC Fe'] = {'crystal_name': 'BCC Fe',
-                 'symmetry': 'BCC',
-                 'elements': ['Fe'],
-                 'a': 0.2866,   # nm 
-                 'reference': 'Z. S. Basinski, W. Hume-Rothery and A. L. Sutton, Proceedings of the Royal Society of '
-                              'London. Series A, Mathematical and Physical Sciences Vol. 229, No. 1179 '
-                              '(May 24, 1955), pp. 459-467',
-                 'link': 'http://www.jstor.org/stable/99693'}
-cdb['bcc fe'] = cdb['BCC Fe']
-                        
-cdb['SrTiO3'] = {'crystal_name': 'SrTiO3',
-                 'symmetry': 'perovskite',
-                 'elements': ['Sr', 'Ti', 'O'],
-                 'a': 0.3905268,   # nm
-                 'reference': 'M. Schmidbauer, A. Kwasniewski and J. Schwarzkopf, Acta Cryst. (2012). B68, 8-14',
-                 'link': 'http://doi.org/10.1107/S0108768111046738'}
-
-cdb['ZnO Wurzite'] = {'crystal_name': 'ZnO Wurzite',
-                      'symmetry': 'wurzite',
-                      'elements': ['Zn', 'O'],
-                      'a': 0.3278,   # nm
-                      'c': 0.5292,   # nm
-                      'u': 0.382,   # nm
-                      'reference': '', 'link': ''}
-cdb['ZnO'] = cdb['ZnO wurzite'] = cdb['wZnO'] = cdb['ZnO Wurzite']
-
-cdb['GaN'] = {'crystal_name': 'GaN Wurzite',
-              'symmetry': 'wurzite',
-              'elements': ['Ga', 'N'],
-              'a': 0.3186,   # nm
-              'c': 0.5186,   # nm
-              'u': 0.376393,   # nm
-              'reference': '', 'link': ''}
-cdb['GaN wurzite'] = cdb['wGaN'] = cdb['GaN Wurzite'] = cdb['GaN']
-
-cdb['MgO'] = {'crystal_name': 'MgO',
-              'symmetry': 'rocksalt',
-              'elements': ['Mg', 'O'],
-              'a': 0.4256483,   # nm
-              'reference': '', 'link': ''}
-
-cdb['TiN'] = {'crystal_name': 'TiN',
-              'symmetry': 'rocksalt',
-              'elements': ['Ti', 'N'],
-              'a': 0.425353445,   # nm
-              'reference': '', 'link': '',
-              'space_group': 225,
-              'symmetry_name': 'Fm-3m'}
-
-cdb['MoS2'] = {'crystal_name': 'MoS2',
-               'symmetry': 'dichalcogenide',
-               'elements': ['Mo', 'S'],
-               'a': 0.319031573,  # nm
-               'c': 1.487900430,  # nm
-               'u': 0.105174,    # nm
-               'reference': '', 'link': ''}
-
-cdb['WS2'] = {'crystal_name': 'WS2',
-              'symmetry': 'dichalcogenide',
-              'elements': ['W', 'S'],
-              'a': 0.319073051,  # nm
-              'c': 1.420240204,  # nm
-              'u': 0.110759,     # nm
-              'reference': '', 'link': ''}
-
-cdb['WSe2'] = {'crystal_name': 'WSe2',
-               'symmetry': 'dichalcogenide',
-               'elements': ['W', 'Se'],
-               'a': 0.332706918,   # nm
-               'c': 1.506895072,   # nm
-               'u': 0.111569 ,     # nm
-               'reference': '', 'link': ''}
-
-cdb['MoSe2'] = {'crystal_name': 'MoSe2',
-                'elements': ['Mo', 'Se'],
-                'a': 0.332694913,  # nm
-                'c': 1.545142322,  # nm
-                'u': 0.108249,     # nm
-                'reference': '', 'link': ''}
-a_l = 0.3336
-c_l = 0.4754
-cdb['ZnO hexagonal'] = {'crystal_name': 'ZnO hexagonal',
-                        'symmetry': 'hexagonal',
-                        'a': a_l,   # nm
-                        'c': c_l,    # not np.sqrt(8/3)*1
-                        'elements': ['Zn', 'Zn', 'O', 'O'],
-                        'unit_cell': [[a_l, 0., 0.],
-                                     [np.cos(120/180*np.pi)*a_l, np.sin(120/180*np.pi)*a_l, 0.],
-                                     [0., 0., c_l]]}
-                        
-base_l = [(2./3., 1./3., .5), (1./3., 2./3., 0.), (2./3., 1./3., 0.), (1./3., 2./3., .5)]
-cdb['ZnO hexagonal']['base'] = np.array(base_l)
-
-a_l = b_l = 0.2464  # nm
-c_l = 0.6711  # nm
-cdb['Graphite'] = {'crystal_name': 'Graphite',
-                   'symmetry': 'hexagonal',
-                   'a': a_l,  
-                   'c': c_l}
-gamma_l = 60
-alpha_l = beta_l = 90
-cdb['Graphite']['unit_cell'] = from_parameters(a_l, b_l, c_l, alpha_l, beta_l, gamma_l)
-
-# ### Create graphite atom base
-# Elements of base
-cdb['Graphite']['elements'] = ['C']*4
-# atom positions in relative coordinates
-base_l = np.array([(.0, .0, .0), (.0, .0, 0.5), (1./3., 1./3., .0), (2./3., 2./3., 0.5)])
-cdb['Graphite']['base'] = np.array(base_l)
-cdb['Graphite']['reference'] = 'P. Trucano and R. Chen, Nature, 1975, 258, 136'
-cdb['Graphite']['link'] = 'https://doi.org/10.1038/258136a0'
-
-cdb['graphite'] = cdb['Graphite'] 
-
-# Create CsCl structure
-a_l = 0.4209
-cdb['CsCl'] = {'crystal_name': 'CsCl',
-               'a': a_l,  # nm
-               'unit_cell': np.identity(3)*a_l,
-               'elements': ['Cs', 'Cl'],
-               'base': np.array([[0, 0, 0], [0.5, 0.5, 0.5]]),
-               'reference': '', 'link': ''}
-
-cdb['PdSe2'] = {'crystal_name': 'PdSe2',
-                'unit_cell': (np.identity(3)*(.579441832, 0.594542204, 0.858506072)),
-                'elements': ['Pd']*4 + ['Se']*8,
-                'base': np.array([[.5, .0, .0], [.0, 0.5, 0.0], 
-                                  [.5, 0.5, 0.5], [.0, 0.5, 0.5],
-                                  [0.611300,  0.119356,  0.585891],
-                                  [0.111300,  0.380644,  0.414109],
-                                  [0.388700,  0.619356,  0.914109],
-                                  [0.888700,  0.880644,  0.085891],
-                                  [0.111300,  0.119356,  0.914109],
-                                  [0.611300,  0.380644,  0.085891],
-                                  [0.888700,  0.619356,  0.585891],
-                                  [0.388700,  0.880644,  0.414109]]),
-                'reference': '', 'link': ''}
-
-crystal_data_base = cdb