<filename>pyxtal/crystal.py
#Standard Libraries
import sys
import os
import random

#External Libraries
from pymatgen.core.structure import Structure
from pymatgen.core.structure import Molecule
from pymatgen.io.cif import CifWriter

#PyXtal imports
from pyxtal.symmetry import *
from pyxtal.database.element import Element
import pyxtal.database.hall as hall

#Constants
#------------------------------
tol_m = 0.3 #seperation tolerance in Angstroms
max1 = 40 #Attempts for generating lattices
max2 = 10 #Attempts for a given lattice
max3 = 20 #Attempts for a given Wyckoff position
minvec = 1.0 #minimum vector length

#Define functions
#------------------------------
class Tol_matrix():
    """
    Class for variable distance tolerance checking. Used within random_crystal and
    molecular_crystal to verify whether atoms are too close. Stores a matrix of atom-
    atom pair tolerances. Note that the matrix's indices correspond to atomic numbers,
    with the 0th entries being 0 (there is no atomic number 0).

    Args:
        prototype: a string representing the type of radii to use
            ("atomic", "molecular", or "metallic")
        factor: a float to scale the distances by. A smaller value means a smaller
            tolerance for distance checking
        tuples: a list or tuple of tuples, which define custom tolerance values. Each tuple
            should be of the form (specie1, specie2, value), where value is the tolerance
            in Angstroms, and specie1 and specie2 can be strings, integers, Element objects,
            or pymatgen Specie objects. Custom values may also be set using set_tol
    """
    def __init__(self, *tuples, prototype="atomic", factor=1.0):
        f = factor
        self.prototype = prototype
        if prototype == "atomic":
            f *= 0.5
            attrindex = 5
            self.radius_type = "covalent"
        elif prototype == "molecular":
            attrindex = 5
            self.radius_type = "covalent"
            f *= 1.2
        elif prototype == "metallic":
            attrindex = 7
            self.radius_type = "metallic"
            f *= 0.5
        else:
            self.radius_type = "N/A"
        self.f = f
        H = Element('H')
        m = [[0.]*(len(H.elements_list)+1)]
        for i, tup1 in enumerate(H.elements_list):
            m.append([0.])
            for j, tup2 in enumerate(H.elements_list):
                #Get the appropriate atomic radii
                if tup1[attrindex] is None:
                    if tup1[5] is None:
                        val1 = None
                    else:
                        #Use the covalent radius
                        val1 = tup1[5]
                else:
                    val1 = tup1[attrindex]
                if tup2[attrindex] is None:
                    if tup2[5] is None:
                        val2 = None
                    else:
                        #Use the covalent radius
                        val2 = tup1[5]
                else:
                    val2 = tup2[attrindex]
                if val1 is not None and val2 is not None:
                    m[-1].append( f * (val1 + val2))
                else:
                    #If no radius is found for either atom, set tolerance to None
                    m[-1].append(None)
        self.matrix = np.array(m)
        """A symmetric numpy matrix storing the tolerance between specie pairs."""
        self.custom_values = []
        """A list of tuples storing which species pair tolerances have custom values."""

        try:
            for tup in tuples:
                self.set_tol(*tup)
        except:
            printx("Error: Could not set custom tolerance value(s).\n"
                +"All custom entries should be entered using the following form:\n"
                +"(specie1, specie2, value), where value is the tolerance in Angstroms.", priority=1)

        self.radius_list = []
        for i in range(len(self.matrix)):
            if i == 0: continue
            x = self.get_tol(i, i)
            self.radius_list.append(x)

    def get_tol(self, specie1, specie2):
        """
        Returns the tolerance between two species.
        
        Args:
            specie1, specie2: the atomic number (int or float), name (str), symbol (str),
                an Element object, or a pymatgen Specie object

        Returns:
            the tolerance between the provided pair of atomic species
        """
        if self.prototype == "single_value":
            return self.matrix[0][0]
        index1 = Element.number_from_specie(specie1)
        index2 = Element.number_from_specie(specie2)
        if index1 is not None and index2 is not None:
            return self.matrix[index1][index2]
        else:
            return None

    def set_tol(self, specie1, specie2, value):
        """
        Sets the distance tolerance between two species.
        
        Args:
            specie1, specie2: the atomic number (int or float), name (str), symbol (str),
                an Element object, or a pymatgen Specie object
            value:
                the tolerance (in Angstroms) to set to
        """
        index1 = Element.number_from_specie(specie1)
        index2 = Element.number_from_specie(specie2)
        if index1 is None or index2 is None:
            return
        self.matrix[index1][index2] = float(value)
        if index1 != index2:
            self.matrix[index2][index1] = float(value)
        if (index1, index2) not in self.custom_values and (index2, index1) not in self.custom_values:
            larger = max(index1, index2)
            smaller = min(index1, index2)
            self.custom_values.append((smaller, larger))

    @classmethod
    def from_matrix(self, matrix, prototype="atomic", factor=1.0, begin_with=0):
        """
        Given a tolerance matrix, returns a Tol_matrix object. Matrix indices correspond to
        the atomic number (with 0 pointing to Hydrogen by default). For atoms with atomic
        numbers not included in the matrix, the default value (specified by prototype) will be
        used, up to element 96. Note that if the matrix is asymmetric, only the value below the
        diagonal will be used.

        Args:
            matrix: a 2D matrix or list of tolerances between atomic species pairs. The
                indices correspond to atomic species (see begin_with variable description)
            prototype: a string representing the type of radii to use
                ("atomic", "molecular")
            factor: a float to scale the distances by. A smaller value means a smaller
                tolerance for distance checking
            begin_with: the index which points to Hydrogen within the matrix. Default 0

        Returns:
            a Tol_matrix object
        """
        m = np.array(matrix)
        tups = []
        for i, row in enumerate(matrix):
            for j, value in enumerate(row):
                if j > i: continue
                tups.append( (i+1-begin_with, j+1-begin_with, matrix[i][j]) )
        tm = Tol_matrix(prototype=prototype, factor=factor, *tups)
        return tm

    @classmethod
    def from_radii(self, radius_list, prototype="atomic", factor=1.0, begin_with=0):
        """
        Given a list of atomic radii, returns a Tol_matrix object. For atom-atom pairs, uses
        the average radii of the two species as the tolerance value. For atoms with atomic
        numbers not in the radius list, the default value (specified by prototype) will be
        used, up to element 96.

        Args:
            radius_list: a list of atomic radii (in Angstroms), beginning with Hydrogen
            prototype: a string representing the type of radii to use
                ("atomic", "molecular")
            factor: a float to scale the distances by. A smaller value means a smaller
                tolerance for distance checking
            begin_with: the index which points to Hydrogen within the list. Default 0

        Returns:
            a Tol_matrix object
        """
        tups = []
        f = factor * 0.5
        for i, r1 in enumerate(radius_list):
            for j, r2 in enumerate(radius_list):
                if j > i: continue
                tups.append( (i+1-begin_with, j+1-begin_with, f*(r1+r2)) )
        tm = Tol_matrix(prototype=prototype, factor=factor, *tups)
        return tm

    @classmethod
    def from_single_value(self, value):
        """
        Creates a Tol_matrix which only has a single tolerance value. Using get_tol will
        always return the same value.

        Args:
            value: the tolerance value to use

        Returns:
            a Tol_matrix object whose methods are overridden to use a single tolerance value
        """
        tm = Tol_matrix()
        tm.prototype = "single value"
        tm.matrix = np.array([[value]])
        tm.custom_values = [(1,1)]
        tm.radius_type = "N/A"
        return tm

    def __getitem__(self, index):
        new_index = Element.number_from_specie(index)
        return self.matrix[index]

    def print_all(self):
        print("--Tol_matrix class object--")
        print("  Prototype: "+str(self.prototype))
        print("  Atomic radius type: "+str(self.radius_type))
        print("  Radius scaling factor: "+str(self.f))
        if self.prototype == "single value":
            print("  Custom tolerance value: "+str(self.matrix([0][0])))
        else:
            if self.custom_values == []:
                print("  Custom tolerance values: None")
            else:
                print("  Custom tolerance values:")
                for tup in self.custom_values:
                    print("    "+str(Element(tup[0]).short_name)+", "+str(Element(tup[1]).short_name)+": "+str(self.get_tol(tup[0],tup[1])))

    def to_file(self, filename=None):
        """
        Creates a file with the given filename and file type to store the structure.
        By default, creates cif files for crystals and xyz files for clusters.
        By default, the filename is based on the stoichiometry.

        Args:
            fmt: the file type ('cif', 'xyz', etc.)
            filename: the file path

        Returns:
            Nothing. Creates a file at the specified path
        """
        if filename == None:
            given = False
        else:
            given = True
        if filename == None:
            filename = "custom_tol_matrix"
        #Check if filename already exists
        #If it does, add a new number to end of filename
        if os.path.exists(filename):
            i = 1
            while True:
                outdir = filename + "_" + str(i)
                if not os.path.exists(outdir):
                    break
                i += 1
                if i > 10000:
                    return "Could not create file: too many files already created."
        else:
            outdir = filename
        try:
            np.save(filename, [self])
            return "Output file to " + outdir + ".npy"
        except:
            return "Error: Could not save Tol_matrix to file."

    @classmethod
    def from_file(self, filename):
        try:
            tm = np.load(filename)[0]
            if type(tm) == Tol_matrix:
                return tm
            else:
                printx("Error: invalid file for Tol_matrix.", priority=0)
                return
        except:
            printx("Error: Could not load Tol_matrix from file.", priority=0)
            return

def gaussian(min, max, sigma=3.0):
    """
    Choose a random number from a Gaussian probability distribution centered
    between min and max. sigma is the number of standard deviations that min
    and max are away from the center. Thus, sigma is also the largest possible
    number of standard deviations corresponding to the returned value. sigma=2
    corresponds to a 95.45% probability of choosing a number between min and
    max.

    Args:
        min: the minimum acceptable value
        max: the maximum acceptable value
        sigma: the number of standard deviations between the center and min or max

    Returns:
        a value chosen randomly between min and max
    """
    center = (max+min)*0.5
    delta = math.fabs(max-min)*0.5
    ratio = delta/sigma
    while True:
        x = np.random.normal(scale=ratio, loc=center)
        if x > min and x < max:
            return x

def get_tol(specie):
    """
    Given an atomic specie name, return the covalent radius.
    
    Args:
        specie: a string for the atomic symbol

    Returns:
        the covalent radius in Angstroms
    """
    return Element(specie).covalent_radius

tols_from_species = np.vectorize(get_tol)
"""
Given a list of atomic species names, returns a list of
covalent radii

Args:
    species: a list of strings for atomic species names or symbols

Returns:
    A 1D numpy array of distances in Angstroms
"""

def check_distance(coord1, coord2, species1, species2, lattice, PBC=[1,1,1], tm=Tol_matrix(prototype="atomic"), d_factor=1.0):
    """
    Check the distances between two set of atoms. Distances between coordinates
    within the first set are not checked, and distances between coordinates within
    the second set are not checked. Only distances between points from different
    sets are checked.

    Args:
        coord1: a list of fractional coordinates e.g. [[.1,.6,.4]
            [.3,.8,.2]]
        coord2: a list of new fractional coordinates e.g. [[.7,.8,.9],
            [.4,.5,.6]]
        species1: a list of atomic species or numbers for coord1
        species2: a list of atomic species or numbers for coord2
        lattice: matrix describing the unit cell vectors
        PBC: A periodic boundary condition list, where 1 means periodic, 0 means not periodic.
            Ex: [1,1,1] -> full 3d periodicity, [0,0,1] -> periodicity along the z axis
        tm: a Tol_matrix object, or a string representing the type of Tol_matrix
            to use
        d_factor: the tolerance is multiplied by this amount. Larger values
            mean atoms must be farther apart

    Returns:
        a bool for whether or not the atoms are sufficiently far enough apart
    """
    #Check that there are points to compare
    if len(coord1) < 1 or len(coord2) < 1:
        return True

    #Create tolerance matrix from subset of tm
    tols = np.zeros((len(species1),len(species2)))
    for i1, specie1 in enumerate(species1):
        for i2, specie2 in enumerate(species2):
            tols[i1][i2] = tm.get_tol(specie1, specie2)

    #Calculate the distance between each i, j pair
    d = distance_matrix(coord1, coord2, lattice, PBC=PBC)

    if (np.array(d) < np.array(tols)).any():
        return False
    else:
        return True

def check_images(coords, species, lattice, PBC=[1,1,1], tm=Tol_matrix(prototype="atomic"), tol=None, d_factor=1.0):
    """
    Given a set of (unfiltered) fractional coordinates, checks if the periodic images are too close.
    
    Args:
        coords: a list of fractional coordinates
        species: the atomic species of each coordinate
        lattice: a 3x3 lattice matrix
        PBC: the periodic boundary conditions
        tm: a Tol_matrix object
        tol: a single override value for the distance tolerances
        d_factor: the tolerance is multiplied by this amount. Larger values
            mean atoms must be farther apart

    Returns:
        False if distances are too close. True if distances are not too close
    """
    #If no PBC, there are no images to check
    if PBC == [0,0,0]:
        return True
    #Create image coords from given coords and PBC
    coords = np.array(coords)
    m = create_matrix(PBC=PBC)
    new_coords = []
    new_species = []
    for v in m:
        #Omit the [0,0,0] vector
        if (v == [0,0,0]).all(): continue
        for v2 in coords+v:
            new_coords.append(v2)
    new_coords = np.array(new_coords)
    #Create a distance matrix
    dm = distance_matrix(coords, new_coords, lattice, PBC=[0,0,0])
    #Define tolerances
    if tol is None:
        tols = np.zeros((len(species), len(species)))
        for i, s1 in enumerate(species):
            for j, s2 in enumerate(species):
                if i <= j:
                    tols[i][j] = tm.get_tol(s1, s2)
                    tols[j][i] = tm.get_tol(s1, s2)
        tols2 = np.tile(tols, int(len(new_coords) / len(coords)))
        if (dm < tols2).any():
            return False
        else:
            return True
    elif tol is not None:
        if (dm < tol).any():
            return False
        else:
            return True
    return True

def get_center(xyzs, lattice, PBC=[1,1,1]):
    """
    Finds the geometric centers of the clusters under periodic boundary
    conditions.

    Args:
        xyzs: a list of fractional coordinates
        lattice: a matrix describing the unit cell
        PBC: A periodic boundary condition list, where 1 means periodic, 0 means not periodic.
            Ex: [1,1,1] -> full 3d periodicity, [0,0,1] -> periodicity along the z axis

    Returns:
        x,y,z coordinates for the center of the input coordinate list
    """
    matrix0 = create_matrix(PBC=PBC)
    xyzs -= np.round(xyzs)
    matrix_min = [0,0,0]
    for atom1 in range(1,len(xyzs)):
        dist_min = 10.0
        for atom2 in range(0, atom1):
            #shift atom1 to position close to atom2
            matrix = matrix0 + (xyzs[atom1] - xyzs[atom2])
            matrix = np.dot(matrix, lattice)
            dists = cdist(matrix, [[0,0,0]])
            if np.min(dists) < dist_min:
                dist_min = np.min(dists)
                matrix_min = matrix0[np.argmin(dists)]
        xyzs[atom1] += matrix_min
    center = xyzs.mean(0)
    return center

def para2matrix(cell_para, radians=True, format='lower'):
    """
    Given a set of lattic parameters, generates a matrix representing the
    lattice vectors

    Args:
        cell_para: a 1x6 list of lattice parameters [a, b, c, alpha, beta,
            gamma]. a, b, and c are the length of the lattice vectos, and
            alpha, beta, and gamma are the angles between these vectors. Can
            be generated by matrix2para
        radians: if True, lattice parameters should be in radians. If False,
            lattice angles should be in degrees
        format: a string ('lower', 'symmetric', or 'upper') for the type of
            matrix to be output

    Returns:
        a 3x3 matrix representing the unit cell. By default (format='lower'),
        the a vector is aligined along the x-axis, and the b vector is in the
        y-z plane
    """
    a = cell_para[0]
    b = cell_para[1]
    c = cell_para[2]
    alpha = cell_para[3]
    beta = cell_para[4]
    gamma = cell_para[5]
    if radians is not True:
        rad = pi/180.
        alpha *= rad
        beta *= rad
        gamma *= rad
    cos_alpha = math.cos(alpha)
    cos_beta = math.cos(beta)
    cos_gamma = math.cos(gamma)
    sin_gamma = math.sin(gamma)
    sin_alpha = math.sin(alpha)
    matrix = np.zeros([3,3])
    if format == 'lower':
        #Generate a lower-diagonal matrix
        c1 = c*cos_beta
        c2 = (c*(cos_alpha - (cos_beta * cos_gamma))) / sin_gamma
        matrix[0][0] = a
        matrix[1][0] = b * cos_gamma
        matrix[1][1] = b * sin_gamma
        matrix[2][0] = c1
        matrix[2][1] = c2
        matrix[2][2] = math.sqrt(c**2 - c1**2 - c2**2)
    elif format == 'symmetric':
        #TODO: allow generation of symmetric matrices
        pass
    elif format == 'upper':
        #Generate an upper-diagonal matrix
        a3 = a*cos_beta
        a2 = (a*(cos_gamma - (cos_beta * cos_alpha))) / sin_alpha
        matrix[2][2] = c
        matrix[1][2] = b * cos_alpha
        matrix[1][1] = b * sin_alpha
        matrix[0][2] = a3
        matrix[0][1] = a2
        matrix[0][0] = math.sqrt(a**2 - a3**2 - a2**2)
        pass
    return matrix

def Add_vacuum(lattice, coor, vacuum=10, PBC=[0,0,0]):
    """
    Adds space above and below a 2D or 1D crystal. This allows for treating the
    structure as a 3D crystal during energy optimization

    Args:
        lattice: the lattice matrix of the crystal
        coor: the relative coordinates of the crystal
        vacuum: the amount of space, in Angstroms, to add above and below
        PBC: A periodic boundary condition list, where 1 means periodic, 0 means not periodic.
            Ex: [1,1,1] -> full 3d periodicity, [0,0,1] -> periodicity along the z axis

    Returns:
        lattice, coor: The transformed lattice and coordinates after the
            vacuum space is added
    """
    absolute_coords = np.dot(coor, lattice)
    for i, a in enumerate(PBC):
        if not a:
            lattice[i] += (lattice[i]/np.linalg.norm(lattice[i])) * vacuum
    new_coor = np.dot(absolute_coords, np.linalg.inv(lattice))
    return lattice, new_coor

def matrix2para(matrix, radians=True):
    """
    Given a 3x3 matrix representing a unit cell, outputs a list of lattice
    parameters.

    Args:
        matrix: a 3x3 array or list, where the first, second, and third rows
            represent the a, b, and c vectors respectively
        radians: if True, outputs angles in radians. If False, outputs in
            degrees

    Returns:
        a 1x6 list of lattice parameters [a, b, c, alpha, beta, gamma]. a, b,
        and c are the length of the lattice vectos, and alpha, beta, and gamma
        are the angles between these vectors (in radians by default)
    """
    cell_para = np.zeros(6)
    #a
    cell_para[0] = np.linalg.norm(matrix[0])
    #b
    cell_para[1] = np.linalg.norm(matrix[1])
    #c
    cell_para[2] = np.linalg.norm(matrix[2])
    #alpha
    cell_para[3] = angle(matrix[1], matrix[2])
    #beta
    cell_para[4] = angle(matrix[0], matrix[2])
    #gamma
    cell_para[5] = angle(matrix[0], matrix[1])
    
    if not radians:
        #convert radians to degrees
        deg = 180./pi
        cell_para[3] *= deg
        cell_para[4] *= deg
        cell_para[5] *= deg
    return cell_para

def cellsize(group, dim=3):
    """
    Returns the number of duplicate atoms in the conventional lattice (in
    contrast to the primitive cell). Based on the type of cell centering (P,
    A, C, I, R, or F)

    Args:
        group: a Group object, or the space group number of the group
        dim: the dimension of the group (3 for space group, 2 for layer group,
            1 for Rod group, or 0 for 3D point group). If group is a Group
            object, dim will be overridden by group's value for dim
    
    Returns:
        an integer between 1 and 4, telling how many atoms are in the conventional cell
    """
    #Get the group dimension and number
    if type(group) == Group:
        num = group.number
        dim = group.dim
    elif type(int(group)) == int:
        num = group
    if dim == 0 or dim == 1:
        #Rod and point groups
        return 1
    elif dim == 2:
        #Layer groups
        if num in [10, 13, 18, 22, 26, 35, 36, 47, 48]:
            return 2
        else:
            return 1
    elif dim == 3:
        #space groups
        if num in [22, 42, 43, 69, 70, 196, 202, 203, 209, 210, 216, 219, 225, 226, 227, 228]:
            return 4 #F
        elif num in [146, 148, 155, 160, 161, 166, 167]:
            return 3 #R
        elif num in [5, 8, 9, 12, 15, 20, 21, 23, 24, 35, 36, 37,  38, 39, 40, 41,  44, 45, 46, 63, 64, 65, 66, 67, 68, 71, 72, 73, 74, 79, 80, 82, 87, 88, 97, 98, 107, 108, 109, 110, 119, 120, 121, 122, 139, 140, 141, 142, 197, 199, 204, 206, 211, 214, 217, 220, 229, 230]:
            return 2 #A, C, I
        else:
            return 1 #P

def find_short_dist(coor, lattice, tol, PBC=[1,1,1]):
    """
    Given a list of fractional coordinates, finds pairs which are closer
    together than tol, and builds the connectivity map

    Args:
        coor: a list of fractional 3-dimensional coordinates
        lattice: a matrix representing the crystal unit cell
        tol: the distance tolerance for pairing coordinates
        PBC: A periodic boundary condition list, where 1 means periodic, 0 means not periodic.
            Ex: [1,1,1] -> full 3d periodicity, [0,0,1] -> periodicity along the z axis
    
    Returns:
        pairs, graph: (pairs) is a list whose entries have the form [index1,
        index2, distance], where index1 and index2 correspond to the indices
        of a pair of points within the supplied list (coor). distance is the
        distance between the two points. (graph) is a connectivity map in the
        form of a list. Its first index represents a point within coor, and
        the second indices represent which point(s) it is connected to.
    """
    pairs=[]
    graph=[]
    for i in range(len(coor)):
        graph.append([])

    d = distance_matrix(coor, coor, lattice, PBC=PBC)
    ijs = np.where(d<= tol)
    for i in np.unique(ijs[0]):
        j = ijs[1][i]
        if j <= i: continue
        pairs.append([i, j, d[i][j]])

    pairs = np.array(pairs)
    if len(pairs) > 0:
        d_min = min(pairs[:,-1]) + 1e-3
        sequence = [pairs[:,-1] <= d_min]
        #Avoid Futurewarning
        #pairs1 = deepcopy(pairs)
        #pairs = pairs1[sequence]
        pairs = pairs[tuple(sequence)]
        for pair in pairs:
            pair0=int(pair[0])
            pair1=int(pair[1])
            graph[pair0].append(pair1)
            graph[pair1].append(pair0)

    return pairs, graph

def connected_components(graph):
    """
    Given an undirected graph (a 2d array of indices), return a set of
    connected components, each connected component being an (arbitrarily
    ordered) array of indices which are connected either directly or
    indirectly.

    Args:
        graph: a list reprenting the connections between points. The first index
            represents a point, and the 2nd indices represent the points to
            which the first point is connected. Can be generated by
            find_short_dist

    Returns:
        a list of connected components. The first index denotes a separate
        connected component. The second indices denote the points within the
        connected component which are connected to each other
    """
    def add_neighbors(el, seen=[]):
        """
        Find all elements which are connected to el. Return an array which
        includes these elements and el itself.
        """
        #seen stores already-visited indices
        if seen == []: seen = [el]
        #iterate through the neighbors (x) of el
        for x in graph[el]:
            if x not in seen:
                seen.append(x)
                #Recursively find neighbors of x
                add_neighbors(x, seen)
        return seen

    #Create a list of indices to iterate through
    unseen = list(range(len(graph)))
    sets = []
    i = 0
    while (unseen != []):
        #x is the index we are finding the connected component of
        x = unseen.pop()
        sets.append([])
        #Add neighbors of x to the current connected component
        for y in add_neighbors(x):
            sets[i].append(y)
            #Remove indices which have already been found
            if y in unseen: unseen.remove(y)
        i += 1
    return sets

def merge_coordinate(coor, lattice, group, tol):
    """
    Given a list of fractional coordinates, merges them within a given
    tolerance, and checks if the merged coordinates satisfy a Wyckoff
    position. Used for merging general Wyckoff positions into special Wyckoff
    positions within the random_crystal (and its derivative) classes.

    Args:
        coor: a list of fractional coordinates
        lattice: a 3x3 matrix representing the unit cell
        group: a pyxtal.symmetry.Group object
        tol: the cutoff distance for merging coordinates

    Returns:
        coor, index, point: (coor) is the new list of fractional coordinates after
        merging. index is a single index for the Wyckoff position within
        the sg. If no matching WP is found, returns False. point is a 3-vector;
        when plugged into the Wyckoff position, it will generate all the other
        points.
    """
    coor = np.array(coor)  
    #Get index of current Wyckoff position. If not one, return False
    index, point = check_wyckoff_position(coor, group)
    if index is False:
        return coor, False, None
    if point is None:
        printx("Error: Could not find generating point.", priority=1)
        printx("coordinates:")
        printx(str(coor))
        printx("Lattice: ")
        printx(str(lattice))
        printx("group: ")
        group.print_all()
        return coor, False, None
    PBC = group.PBC
    #Main loop for merging multiple times
    while True:
        #Check distances of current WP. If too small, merge
        dm = distance_matrix([coor[0]], coor, lattice, PBC=PBC)
        passed_distance_check = True
        x = np.argwhere(dm < tol)
        for y in x:
            #Ignore distance from atom to itself
            if y[0] == 0 and y[1] == 0:
                pass
            else:
                passed_distance_check = False
                break

        if passed_distance_check is False:
            mult1 = group[index].multiplicity
            #Find possible wp's to merge into
            possible = []
            for i, wp in enumerate(group):
                mult2 = wp.multiplicity
                #factor = mult2 / mult1
                if (mult2 < mult1) and (mult1 % mult2 == 0):
                    possible.append(i)
            if possible == []:
                return coor, False, None
            #Calculate minimum separation for each WP
            distances = []
            for i in possible:
                wp = group[i]
                projected_point = project_point(point, wp[0], lattice=lattice, PBC=PBC)
                new_coor = apply_ops(projected_point, wp)
                d = distance(point - projected_point, lattice, PBC=PBC)
                distances.append(np.min(d))
            #Choose wp with shortest translation for generating point
            tmpindex = np.argmin(distances)
            index = possible[tmpindex]
            newwp = group[index]
            projected_point = project_point(point, newwp[0], lattice=lattice, PBC=PBC)
            coor = apply_ops(projected_point, newwp)
            point = coor[0]
            index = newwp.index
        #Distances were not too small; return True
        else:
            return coor, index, point

def estimate_volume(numIons, species, factor=1.0):
    """
    Estimates the volume of a unit cell based on the number and types of ions.
    Assumes each atom takes up a sphere with radius equal to its covalent bond
    radius.

    Args:
        numIons: a list of the number of ions for each specie
        species: a corresponding list for the specie of each type of ion. Each
            element in the list should be a string for the atomic symbol
        factor: an optional factor to multiply the result by. Larger values
            allow more space between atoms
    
    Returns:
        a float value for the estimated volume
    """
    volume = 0
    for numIon, specie in zip(numIons, species):
        r = random.uniform(Element(specie).covalent_radius, Element(specie).vdw_radius)
        volume += numIon*4/3*pi*r**3
    return factor*volume

def generate_lattice(ltype, volume, minvec=tol_m, minangle=pi/6, max_ratio=10.0, maxattempts = 100, **kwargs):
    """
    Generates a lattice (3x3 matrix) according to the space group symmetry and
    number of atoms. If the spacegroup has centering, we will transform to
    conventional cell setting. If the generated lattice does not meet the
    minimum angle and vector requirements, we try to generate a new one, up to
    maxattempts times.

    Args:
        sg: International number of the space group
        volume: volume of the conventional unit cell
        minvec: minimum allowed lattice vector length (among a, b, and c)
        minangle: minimum allowed lattice angle (among alpha, beta, and gamma)
        max_ratio: largest allowed ratio of two lattice vector lengths
        maxattempts: the maximum number of attempts for generating a lattice
        kwargs: a dictionary of optional values. These include:
            'unique_axis': the axis ('a', 'b', or 'c') which is not symmetrically
                equivalent to the other two
            'min_l': the smallest allowed cell vector. The smallest vector must be larger
                than this.
            'mid_l': the second smallest allowed cell vector. The second smallest vector
                must be larger than this.
            'max_l': the third smallest allowed cell vector. The largest cell vector must
                be larger than this.

    Returns:
        a 3x3 matrix representing the lattice vectors of the unit cell. If
        generation fails, outputs a warning message and returns empty
    """
    maxangle = pi-minangle
    for n in range(maxattempts):
        #Triclinic
        #if sg <= 2:
        if ltype == "triclinic":
            #Derive lattice constants from a random matrix
            mat = random_shear_matrix(width=0.2)
            a, b, c, alpha, beta, gamma = matrix2para(mat)
            x = math.sqrt(1-math.cos(alpha)**2 - math.cos(beta)**2 - math.cos(gamma)**2 + 2*(math.cos(alpha)*math.cos(beta)*math.cos(gamma)))
            vec = random_vector()
            abc = volume/x
            xyz = vec[0]*vec[1]*vec[2]
            a = vec[0]*np.cbrt(abc)/np.cbrt(xyz)
            b = vec[1]*np.cbrt(abc)/np.cbrt(xyz)
            c = vec[2]*np.cbrt(abc)/np.cbrt(xyz)
        #Monoclinic
        #elif sg <= 15:
        elif ltype == "monoclinic":
            alpha, gamma  = pi/2, pi/2
            beta = gaussian(minangle, maxangle)
            x = math.sin(beta)
            vec = random_vector()
            xyz = vec[0]*vec[1]*vec[2]
            abc = volume/x
            a = vec[0]*np.cbrt(abc)/np.cbrt(xyz)
            b = vec[1]*np.cbrt(abc)/np.cbrt(xyz)
            c = vec[2]*np.cbrt(abc)/np.cbrt(xyz)
        #Orthorhombic
        #elif sg <= 74:
        elif ltype == "orthorhombic":
            alpha, beta, gamma = pi/2, pi/2, pi/2
            x = 1
            vec = random_vector()
            xyz = vec[0]*vec[1]*vec[2]
            abc = volume/x
            a = vec[0]*np.cbrt(abc)/np.cbrt(xyz)
            b = vec[1]*np.cbrt(abc)/np.cbrt(xyz)
            c = vec[2]*np.cbrt(abc)/np.cbrt(xyz)
        #Tetragonal
        #elif sg <= 142:
        elif ltype == "tetragonal":
            alpha, beta, gamma = pi/2, pi/2, pi/2
            x = 1
            vec = random_vector()
            c = vec[2]/(vec[0]*vec[1])*np.cbrt(volume/x)
            a = b = math.sqrt((volume/x)/c)
        #Trigonal/Rhombohedral/Hexagonal
        #elif sg <= 194:
        elif ltype in ["hexagonal", "trigonal", "rhombohedral"]:
            alpha, beta, gamma = pi/2, pi/2, pi/3*2
            x = math.sqrt(3.)/2.
            vec = random_vector()
            c = vec[2]/(vec[0]*vec[1])*np.cbrt(volume/x)
            a = b = math.sqrt((volume/x)/c)
        #Cubic
        #else:
        elif ltype == "cubic":
            alpha, beta, gamma = pi/2, pi/2, pi/2
            s = (volume) ** (1./3.)
            a, b, c = s, s, s
        #Check that lattice meets requirements
        maxvec = (a*b*c)/(minvec**2)

        #Define limits on cell dimensions
        if 'min_l' not in kwargs:
            min_l = minvec
        else:
            min_l = kwargs['min_l']
        if 'mid_l' not in kwargs:
            mid_l = min_l
        else:
            mid_l = kwargs['mid_l']
        if 'max_l' not in kwargs:
            max_l = mid_l
        else:
            max_l = kwargs['max_l']
        l_min = min(a, b, c)
        l_max = max(a, b, c)
        for x in (a, b, c):
            if x <= l_max and x >= l_min:
                l_mid = x
        if not (l_min >= min_l and l_mid >= mid_l and l_max >= max_l):
            continue

        if minvec < maxvec:
            #Check minimum Euclidean distances
            smallvec = min(a*math.cos(max(beta, gamma)), b*math.cos(max(alpha, gamma)), c*math.cos(max(alpha, beta)))
            if(a>minvec and b>minvec and c>minvec
            and a<maxvec and b<maxvec and c<maxvec
            and smallvec < minvec
            and alpha>minangle and beta>minangle and gamma>minangle
            and alpha<maxangle and beta<maxangle and gamma<maxangle
            and a/b<max_ratio and a/c<max_ratio and b/c<max_ratio
            and b/a<max_ratio and c/a<max_ratio and c/b<max_ratio):
                return np.array([a, b, c, alpha, beta, gamma])
    #If maxattempts tries have been made without success
    printx("Could not generate lattice after "+str(n+1)+" attempts for volume "+str(volume), priority=2)
    return

def generate_lattice_2D(ltype, volume, thickness=None, minvec=tol_m, minangle=pi/6, max_ratio=10.0, maxattempts = 100, **kwargs):
    """
    Generates a lattice (3x3 matrix) according to the spacegroup symmetry and
    number of atoms. If the layer group has centering, we will use the
    conventional cell setting. If the generated lattice does not meet the
    minimum angle and vector requirements, we try to generate a new one, up to
    maxattempts times.
    Note: The monoclinic layer groups have different unique axes. Groups 3-7
        have unique axis c, while 8-18 have unique axis a. We use non-periodic
        axis c for all layer groups.

    Args:
        num: International number of the space group
        volume: volume of the lattice
        thickness: 3rd-dimensional thickness of the unit cell. If set to None,
            a thickness is chosen automatically
        minvec: minimum allowed lattice vector length (among a, b, and c)
        minangle: minimum allowed lattice angle (among alpha, beta, and gamma)
        max_ratio: largest allowed ratio of two lattice vector lengths
        maxattempts: the maximum number of attempts for generating a lattice
        kwargs: a dictionary of optional values. These include:
            'unique_axis': the axis ('a', 'b', or 'c') which is not symmetrically
                equivalent to the other two
            'min_l': the smallest allowed cell vector. The smallest vector must be larger
                than this.
            'mid_l': the second smallest allowed cell vector. The second smallest vector
                must be larger than this.
            'max_l': the third smallest allowed cell vector. The largest cell vector must
                be larger than this.

    Returns:
        a 3x3 matrix representing the lattice vectors of the unit cell. If
        generation fails, outputs a warning message and returns empty
    """
    if 'unique_axis' not in kwargs:
        unique_axis = "c"
    else:
        unique_axis = kwargs['unique_axis']
    #Store the non-periodic axis
    NPA = 3
    #Set the unique axis for monoclinic cells
    #if num in range(3, 8): unique_axis = "c"
    #elif num in range(8, 19): unique_axis = "a"
    maxangle = pi-minangle
    for n in range(maxattempts):
        abc = np.ones([3])
        if thickness is None:
            v = random_vector()
            thickness1 = np.cbrt(volume)*(v[0]/(v[0]*v[1]*v[2]))
        else:
            thickness1 = thickness
        abc[NPA-1] = thickness1
        alpha, beta, gamma  = pi/2, pi/2, pi/2
        #Triclinic
        #if num <= 2:
        if ltype == "triclinic":
            mat = random_shear_matrix(width=0.2)
            a, b, c, alpha, beta, gamma = matrix2para(mat)
            x = math.sqrt(1-math.cos(alpha)**2 - math.cos(beta)**2 - math.cos(gamma)**2 + 2*(math.cos(alpha)*math.cos(beta)*math.cos(gamma)))
            abc[NPA-1] = abc[NPA-1]/x #scale thickness by outer product of vectors
            ab = volume/(abc[NPA-1]*x)
            ratio = a/b
            if NPA == 3:
                abc[0] = math.sqrt(ab*ratio)
                abc[1] = math.sqrt(ab/ratio)
            elif NPA == 2:
                abc[0] = math.sqrt(ab*ratio)
                abc[2] = math.sqrt(ab/ratio)
            elif NPA == 1:
                abc[1] = math.sqrt(ab*ratio)
                abc[2] = math.sqrt(ab/ratio)

        #Monoclinic
        #elif num <= 18:
        elif ltype == "monoclinic":
            a, b, c = random_vector()
            if unique_axis == "a":
                alpha = gaussian(minangle, maxangle)
                x = math.sin(alpha)
            elif unique_axis == "b":
                beta = gaussian(minangle, maxangle)
                x = math.sin(beta)
            elif unique_axis == "c":
                gamma = gaussian(minangle, maxangle)
                x = math.sin(gamma)
            ab = volume/(abc[NPA-1]*x)
            ratio = a/b
            if NPA == 3:
                abc[0] = math.sqrt(ab*ratio)
                abc[1] = math.sqrt(ab/ratio)
            elif NPA == 2:
                abc[0] = math.sqrt(ab*ratio)
                abc[2] = math.sqrt(ab/ratio)
            elif NPA == 1:
                abc[1] = math.sqrt(ab*ratio)
                abc[2] = math.sqrt(ab/ratio)

        #Orthorhombic
        #elif num <= 48:
        elif ltype == "orthorhombic":
            vec = random_vector()
            if NPA == 3:
                ratio = abs(vec[0]/vec[1]) #ratio a/b
                abc[1] = math.sqrt(volume/(thickness1*ratio))
                abc[0] = abc[1]* ratio
            elif NPA == 2:
                ratio = abs(vec[0]/vec[2]) #ratio a/b
                abc[2] = math.sqrt(volume/(thickness1*ratio))
                abc[0] = abc[2]* ratio
            elif NPA == 1:
                ratio = abs(vec[1]/vec[2]) #ratio a/b
                abc[2] = math.sqrt(volume/(thickness1*ratio))
                abc[1] = abc[2]* ratio

        #Tetragonal
        #elif num <= 64:
        elif ltype == "tetragonal":
            if NPA == 3:
                abc[0] = abc[1] = math.sqrt(volume/thickness1)
            elif NPA == 2:
                abc[0] = abc[1]
                abc[2] = volume/(abc[NPA-1]**2)
            elif NPA == 1:
                abc[1] = abc[0]
                abc[2] = volume/(abc[NPA-1]**2)

        #Trigonal/Hexagonal
        #elif num <= 80:
        elif ltype in ["hexagonal", "trigonal"]:
            gamma = pi/3*2
            x = math.sqrt(3.)/2.
            if NPA == 3:
                abc[0] = abc[1] = math.sqrt((volume/x)/abc[NPA-1])
            elif NPA == 2:
                abc[0] = abc[1]
                abc[2] = (volume/x)(thickness1**2)
            elif NPA == 1:
                abc[1] = abc[0]
                abc[2] = (volume/x)/(thickness1**2)

        para = np.array([abc[0], abc[1], abc[2], alpha, beta, gamma])

        a, b, c = abc[0], abc[1], abc[2]
        maxvec = (a*b*c)/(minvec**2)

        #Define limits on cell dimensions
        if 'min_l' not in kwargs:
            min_l = minvec
        else:
            min_l = kwargs['min_l']
        if 'mid_l' not in kwargs:
            mid_l = min_l
        else:
            mid_l = kwargs['mid_l']
        if 'max_l' not in kwargs:
            max_l = mid_l
        else:
            max_l = kwargs['max_l']
        l_min = min(a, b, c)
        l_max = max(a, b, c)
        for x in (a, b, c):
            if x <= l_max and x >= l_min:
                l_mid = x
        if not (l_min >= min_l and l_mid >= mid_l and l_max >= max_l):
            continue

        if minvec < maxvec:
            smallvec = min(a*math.cos(max(beta, gamma)), b*math.cos(max(alpha, gamma)), c*math.cos(max(alpha, beta)))
            if(a>minvec and b>minvec and c>minvec
            and a<maxvec and b<maxvec and c<maxvec
            and smallvec < minvec
            and alpha>minangle and beta>minangle and gamma>minangle
            and alpha<maxangle and beta<maxangle and gamma<maxangle
            and a/b<max_ratio and a/c<max_ratio and b/c<max_ratio
            and b/a<max_ratio and c/a<max_ratio and c/b<max_ratio):
                return para

    #If maxattempts tries have been made without success
    printx("Could not generate lattice after "+str(n+1)+" attempts for volume "+str(volume), priority=2)
    return

def generate_lattice_1D(ltype, volume, area=None, minvec=tol_m, minangle=pi/6, max_ratio=10.0, maxattempts = 100, **kwargs):
    """
    Generates a lattice (3x3 matrix) according to the spacegroup symmetry and
    number of atoms. If the spacegroup has centering, we will transform to
    conventional cell setting. If the generated lattice does not meet the
    minimum angle and vector requirements, we try to generate a new one, up to
    maxattempts times.
    Note: The monoclinic Rod groups have different unique axes. Groups 3-7
        have unique axis a, while 8-12 have unique axis c. We use periodic
        axis c for all Rod groups.

    Args:
        num: number of the Rod group
        volume: volume of the lattice
        area: cross-sectional area of the unit cell in Angstroms squared. If
            set to None, a value is chosen automatically
        minvec: minimum allowed lattice vector length (among a, b, and c)
        minangle: minimum allowed lattice angle (among alpha, beta, and gamma)
        max_ratio: largest allowed ratio of two lattice vector lengths
        maxattempts: the maximum number of attempts for generating a lattice
        kwargs: a dictionary of optional values. These include:
            'unique_axis': the axis ('a', 'b', or 'c') which is not symmetrically
                equivalent to the other two
            'min_l': the smallest allowed cell vector. The smallest vector must be larger
                than this.
            'mid_l': the second smallest allowed cell vector. The second smallest vector
                must be larger than this.
            'max_l': the third smallest allowed cell vector. The largest cell vector must
                be larger than this.

    Returns:
        a 3x3 matrix representing the lattice vectors of the unit cell. If
        generation fails, outputs a warning message and returns empty
    """
    try:
        unique_axis = kwargs['unique_axis']
    except:
        unique_axis = "a"
    #Store the periodic axis
    PA = 3
    #Set the unique axis for monoclinic cells
    #if num in range(3, 8): unique_axis = "a"
    #elif num in range(8, 13): unique_axis = "c"
    maxangle = pi-minangle
    for n in range(maxattempts):
        abc = np.ones([3])
        if area is None:
            v = random_vector()
            thickness1 = np.cbrt(volume)*(v[0]/(v[0]*v[1]*v[2]))
        else:
            thickness1 = volume/area
        abc[PA-1] = thickness1
        alpha, beta, gamma  = pi/2, pi/2, pi/2
        #Triclinic
        #if num <= 2:
        if ltype == "triclinic":
            mat = random_shear_matrix(width=0.2)
            a, b, c, alpha, beta, gamma = matrix2para(mat)
            x = math.sqrt(1-math.cos(alpha)**2 - math.cos(beta)**2 - math.cos(gamma)**2 + 2*(math.cos(alpha)*math.cos(beta)*math.cos(gamma)))
            abc[PA-1] = abc[PA-1]/x #scale thickness by outer product of vectors
            ab = volume/(abc[PA-1]*x)
            ratio = a/b
            if PA == 3:
                abc[0] = math.sqrt(ab*ratio)
                abc[1] = math.sqrt(ab/ratio)
            elif PA == 2:
                abc[0] = math.sqrt(ab*ratio)
                abc[2] = math.sqrt(ab/ratio)
            elif PA == 1:
                abc[1] = math.sqrt(ab*ratio)
                abc[2] = math.sqrt(ab/ratio)

        #Monoclinic
        #elif num <= 12:
        elif ltype == "monoclinic":
            a, b, c = random_vector()
            if unique_axis == "a":
                alhpa = gaussian(minangle, maxangle)
                x = math.sin(alpha)
            elif unique_axis == "b":
                beta = gaussian(minangle, maxangle)
                x = math.sin(beta)
            elif unique_axis == "c":
                gamma = gaussian(minangle, maxangle)
                x = math.sin(gamma)
            ab = volume/(abc[PA-1]*x)
            ratio = a/b
            if PA == 3:
                abc[0] = math.sqrt(ab*ratio)
                abc[1] = math.sqrt(ab/ratio)
            elif PA == 2:
                abc[0] = math.sqrt(ab*ratio)
                abc[2] = math.sqrt(ab/ratio)
            elif PA == 1:
                abc[1] = math.sqrt(ab*ratio)
                abc[2] = math.sqrt(ab/ratio)

        #Orthorhombic
        #lif num <= 22:
        elif ltype == "orthorhombic":
            vec = random_vector()
            if PA == 3:
                ratio = abs(vec[0]/vec[1]) #ratio a/b
                abc[1] = math.sqrt(volume/(thickness1*ratio))
                abc[0] = abc[1]* ratio
            elif PA == 2:
                ratio = abs(vec[0]/vec[2]) #ratio a/b
                abc[2] = math.sqrt(volume/(thickness1*ratio))
                abc[0] = abc[2]* ratio
            elif PA == 1:
                ratio = abs(vec[1]/vec[2]) #ratio a/b
                abc[2] = math.sqrt(volume/(thickness1*ratio))
                abc[1] = abc[2]* ratio

        #Tetragonal
        #elif num <= 41:
        elif ltype == "tetragonal":
            if PA == 3:
                abc[0] = abc[1] = math.sqrt(volume/thickness1)
            elif PA == 2:
                abc[0] = abc[1]
                abc[2] = volume/(abc[PA-1]**2)
            elif PA == 1:
                abc[1] = abc[0]
                abc[2] = volume/(abc[PA-1]**2)

        #Trigonal/Rhombohedral/Hexagonal
        #elif num <= 75:
        elif ltype in ["hexagonal", "trigonal"]:
            gamma = pi/3*2
            x = math.sqrt(3.)/2.
            if PA == 3:
                abc[0] = abc[1] = math.sqrt((volume/x)/abc[PA-1])
            elif PA == 2:
                abc[0] = abc[1]
                abc[2] = (volume/x)(thickness1**2)
            elif PA == 1:
                abc[1] = abc[0]
                abc[2] = (volume/x)/(thickness1**2)

        para = np.array([abc[0], abc[1], abc[2], alpha, beta, gamma])

        a, b, c = abc[0], abc[1], abc[2]
        maxvec = (a*b*c)/(minvec**2)

        #Define limits on cell dimensions
        if 'min_l' not in kwargs:
            min_l = minvec
        else:
            min_l = kwargs['min_l']
        if 'mid_l' not in kwargs:
            mid_l = min_l
        else:
            mid_l = kwargs['mid_l']
        if 'max_l' not in kwargs:
            max_l = mid_l
        else:
            max_l = kwargs['max_l']
        l_min = min(a, b, c)
        l_max = max(a, b, c)
        for x in (a, b, c):
            if x <= l_max and x >= l_min:
                l_mid = x
        if not (l_min >= min_l and l_mid >= mid_l and l_max >= max_l):
            continue

        if minvec < maxvec:
            smallvec = min(a*math.cos(max(beta, gamma)), b*math.cos(max(alpha, gamma)), c*math.cos(max(alpha, beta)))
            if(a>minvec and b>minvec and c>minvec
            and a<maxvec and b<maxvec and c<maxvec
            and smallvec < minvec
            and alpha>minangle and beta>minangle and gamma>minangle
            and alpha<maxangle and beta<maxangle and gamma<maxangle
            and a/b<max_ratio and a/c<max_ratio and b/c<max_ratio
            and b/a<max_ratio and c/a<max_ratio and c/b<max_ratio):
                return para

    #If maxattempts tries have been made without success
    printx("Could not generate lattice after "+str(n+1)+" attempts for volume "+str(volume), priority=2)
    return

def generate_lattice_0D(ltype, volume, area=None, minvec=tol_m, max_ratio=10.0, maxattempts = 100, **kwargs):
    """
    Generates a lattice (3x3 matrix) according to the spacegroup symmetry and
    number of atoms. If the spacegroup has centering, we will transform to
    conventional cell setting. If the generated lattice does not meet the
    minimum angle and vector requirements, we try to generate a new one, up to
    maxattempts times.
    Note: The monoclinic Rod groups have different unique axes. Groups 3-7
        have unique axis a, while 8-12 have unique axis c. We use periodic
        axis c for all Rod groups.

    Args:
        num: number of the Rod group
        volume: volume of the lattice
        area: cross-sectional area of the unit cell in Angstroms squared. If
            set to None, a value is chosen automatically
        minvec: minimum allowed lattice vector length (among a, b, and c)
        max_ratio: largest allowed ratio of two lattice vector lengths
        maxattempts: the maximum number of attempts for generating a lattice
        kwargs: a dictionary of optional values. Only used for ellipsoidal
            lattices, which pass the value to generate_lattice. Possible values include:
            'unique_axis': the axis ('a', 'b', or 'c') which is not symmetrically
                equivalent to the other two
            'min_l': the smallest allowed cell vector. The smallest vector must be larger
                than this.
            'mid_l': the second smallest allowed cell vector. The second smallest vector
                must be larger than this.
            'max_l': the third smallest allowed cell vector. The largest cell vector must
                be larger than this.

    Returns:
        a 3x3 matrix representing the lattice vectors of the unit cell. If
        generation fails, outputs a warning message and returns empty
    """
    if ltype == "spherical":
        #Use a cubic lattice with altered volume
        a = b = c = np.cbrt((3 * volume)/(4 * pi))
        alpha = beta = gamma = 0.5 * pi
        if a < minvec:
            printx("Could not generate spherical lattice; volume too small compared to minvec", priority=2)
            return
        return np.array([a, b, c, alpha, beta, gamma])
    if ltype == "ellipsoidal":
        #Use a matrix with only on-diagonal elements, with a = b
        alpha, beta, gamma = pi/2, pi/2, pi/2
        x = (4./3.)*pi
        for numattempts in range(maxattempts):
            vec = random_vector()
            c = vec[2]/(vec[0]*vec[1])*np.cbrt(volume/x)
            a = b = math.sqrt((volume/x)/c)
            if (a / c < 10.) and (c / a < 10.):
                return np.array([a, b, c, alpha, beta, gamma])
        return

def choose_wyckoff(group, number):
    """
    Choose a Wyckoff position to fill based on the current number of atoms
    needed to be placed within a unit cell
    Rules:
        1) The new position's multiplicity is equal/less than (number).
        2) We prefer positions with large multiplicity.

    Args:
        group: a pyxtal.symmetry.Group object
        number: the number of atoms still needed in the unit cell

    Returns:
        a single index for the Wyckoff position. If no position is found,
        returns False
    """
    wyckoffs_organized = group.wyckoffs_organized
    
    if random.uniform(0,1)>0.5: #choose from high to low
        for wyckoff in wyckoffs_organized:
            if len(wyckoff[0]) <= number:
                return random.choice(wyckoff)
        return False
    else:
        good_wyckoff = []
        for wyckoff in wyckoffs_organized:
            if len(wyckoff[0]) <= number:
                for w in wyckoff:
                    good_wyckoff.append(w)
        if len(good_wyckoff) > 0:
            return random.choice(good_wyckoff)
        else:
            return False

class Wyckoff_site():
    """
    Class for storing atomic Wyckoff positions with a single coordinate.
    
    Args:
        wp: a Wyckoff_position object
        coordinate: a fractional 3-vector for the generating atom's coordinate
        specie: an Element, element name or symbol, or atomic number of the atom
    """
    def __init__(self, wp, coordinate, specie):
        if type(wp) == Wyckoff_position:
            self.wp = wp
        else:
            printx("Error: wp must be a Wyckoff_position object.", priority=1)
            return
        self.position = np.array(coordinate)
        self.specie = Element(specie).short_name
        self.multiplicity = wp.multiplicity
        self.PBC = wp.PBC
        self.coords = apply_ops(self.position, self.wp)

    def __str__(self):
        return self.specie+": "+str(self.position)+" "+str(self.wp.multiplicity)+self.wp.letter+", site symmetry "+ss_string_from_ops(self.wp.symmetry_m[0], self.wp.number, dim=self.wp.dim)

    def __repr__(self):
        return str(self)

def check_wyckoff_sites(ws1, ws2, lattice, tm=Tol_matrix(prototype="atomic"), same_group=True):
    """
    Given two Wyckoff sites, checks the inter-atomic distances between them.

    Args:
        ws1: a Wyckoff_site object
        ws2: a different Wyckoff_site object (will always return False if
            two identical WS's are provided)
        lattice: a 3x3 cell matrix
        same_group: whether or not the two WS's are in the same structure.
            Default value True reduces the calculation cost

    Returns:
        True if all distances are greater than the allowed tolerances.
        False if any distance is smaller than the allowed tolerance
    """
    #Ensure the PBC values are valid
    if ws1.PBC != ws2.PBC:
        printx("Error: PBC values do not match between Wyckoff sites")
        return
    #Get tolerance
    tol = tm.get_tol(ws1.specie, ws2.specie)
    #Symmetry shortcut method: check only some atoms
    if same_group is True:
        #We can either check one atom in WS1 against all WS2, or vice-versa
        #Check which option is faster
        if ws1.multiplicity > ws2.multiplicity:
            coords1 = [ws1.coords[0]]
            coords2 = ws2.coords
        else:
            coords1 = [ws2.coords[0]]
            coords2 = ws1.coords
        #Calculate distances
        dm = distance_matrix(coords1, coords2, lattice, PBC=ws1.PBC)
        #Check if any distances are less than the tolerance
        if (dm < tol).any():
            return False
        else:
            return True
    #No symmetry method: check all atomic pairs
    else:
        dm = distance_matrix(ws1.coords, ws2.coords, lattice, PBC=ws1.PBC)
        #Check if any distances are less than the tolerance
        if (dm < tol).any():
            return False
        else:
            return True

def verify_distances(coordinates, species, lattice, factor=1.0, PBC=[1,1,1]):
    """
    Checks the inter-atomic distance between all pairs of atoms in a crystal.

    Args:
        coordinates: a 1x3 list of fractional coordinates
        species: a list of atomic symbols for each coordinate
        lattice: a 3x3 matrix representing the lattice vectors of the unit cell
        factor: a tolerance factor for checking distances. A larger value means
            atoms must be farther apart
        PBC: A periodic boundary condition list, where 1 means periodic, 0 means not periodic.
            Ex: [1,1,1] -> full 3d periodicity, [0,0,1] -> periodicity along the z axis
    
    Returns:
        True if no atoms are too close together, False if any pair is too close
    """
    for i, c1 in enumerate(coordinates):
        specie1 = species[i]
        for j, c2 in enumerate(coordinates):
            if j > i:
                specie2 = species[j]
                diff = np.array(c2) - np.array(c1)
                d_min = distance(diff, lattice, PBC=PBC)
                tol = factor*0.5*(Element(specie1).covalent_radius + Element(specie2).covalent_radius)
                if d_min < tol:
                    return False
    return True

class Lattice():
    """
    Class for storing and generating crystal lattices. Allows for specification
    of constraint values. Lattice types include triclinic, monoclinic, orthorhombic,
    tetragonal, trigonal, hexagonal, cubic, spherical, and ellipsoidal. The last
    two are used for generating point group structures, and do not actually represent
    a parallelepiped lattice.

    Args:
        ltype: a string representing the type of lattice (from the above list)
        volume: the volume, in Angstroms cubed, of the lattice
        PBC: A periodic boundary condition list, where 1 means periodic, 0 means not periodic.
            Ex: [1,1,1] -> full 3d periodicity, [0,0,1] -> periodicity along the z axis
        kwargs: various values which may be defined. If none are defined, random ones
            will be generated. Values will be passed to generate_lattice. Options include:
            area: The cross-sectional area (in Angstroms squared). Only used to generate 1D
                crystals
            thickness: The unit cell's non-periodic thickness (in Angstroms). Only used to
                generate 2D crystals
            unique_axis: The unique axis for certain symmetry (and especially layer) groups.
                Because the symmetry operations are not also transformed, you should use the
                default values for random crystal generation
            random: If False, keeps the stored values for the lattice geometry even upon applying
                reset_matrix. To alter the matrix, use set_matrix() or set_para
            'unique_axis': the axis ('a', 'b', or 'c') which is not symmetrically
                equivalent to the other two
            'min_l': the smallest allowed cell vector. The smallest vector must be larger
                than this.
            'mid_l': the second smallest allowed cell vector. The second smallest vector
                must be larger than this.
            'max_l': the third smallest allowed cell vector. The largest cell vector must
                be larger than this.
            'allow_volume_reset': a bool stating whether or not the volume should be reset during
                each crystal generation attempt
    """
    def __init__(self, ltype, volume, PBC=[1,1,1], **kwargs):
        #Set required parameters
        if ltype in ["triclinic", "monoclinic", "orthorhombic", "tetragonal",
                "trigonal", "hexagonal", "cubic", "spherical", "ellipsoidal"]:
            self.ltype = ltype
        elif ltype == None:
            self.ltype = "triclinic"
        else:
            printx("Error: Invalid lattice type.", priority=1)
            return
        self.volume = float(volume)
        self.PBC = PBC
        self.dim = sum(PBC)
        self.kwargs = {}
        self.random = True
        #Set optional values
        self.allow_volume_reset = True
        for key, value in kwargs.items():
            if key in ["area", "thickness", "unique_axis", "random", "min_l", "mid_l", "max_l"]:
                setattr(self, key, value)
                self.kwargs[key] = value
                if key == "allow_volume_reset":
                    if value == False:
                        self.allow_volume_reset = False
        try:
            self.unique_axis
        except:
            self.unique_axis = "c"
        #Set stress normalization info
        if self.ltype == "triclinic":
            self.stress_normalization_matrix = np.array([[1,1,1],[1,1,1],[1,1,1]])
        elif self.ltype == "monoclinic":
            if self.PBC == [1,1,1]:
                self.stress_normalization_matrix = np.array([[1,0,0],[0,1,0],[1,0,1]])
            else:
                if self.unique_axis == "a":
                    self.stress_normalization_matrix = np.array([[1,0,0],[0,1,0],[0,1,1]])
                elif self.unique_axis == "b":
                    self.stress_normalization_matrix = np.array([[1,0,0],[0,1,0],[1,0,1]])
                elif self.unique_axis == "c":
                    self.stress_normalization_matrix = np.array([[1,0,0],[1,1,0],[0,0,1]])
        elif self.ltype in ["orthorhombic", "tetragonal", "trigonal", "hexagonal", "cubic"]:
            self.stress_normalization_matrix = np.array([[1,0,0],[0,1,0],[0,0,1]])
        elif self.ltype in ["spherical", "ellipsoidal"]:
            self.stress_normalization_matrix = np.array([[0,0,0],[0,0,0],[0,0,0]])
        #Set info for on-diagonal stress symmetrization
        if self.ltype in ["tetragonal", "trigonal", "hexagonal", "rhombohedral"]:
            self.stress_indices = [(0,0),(1,1)]
        elif self.ltype == "cubic":
            self.stress_indices = [(0,0),(1,1),(2,2)]
        else:
            self.stress_indices = []
        #Set values for the matrix
        self.reset_matrix()

    def generate_para(self):
        if self.dim == 3:
            return generate_lattice(self.ltype, self.volume, **self.kwargs)
        elif self.dim == 2:
            return generate_lattice_2D(self.ltype, self.volume, **self.kwargs)
        elif self.dim == 1:
            return generate_lattice_1D(self.ltype, self.volume, **self.kwargs)
        elif self.dim == 0:
            return generate_lattice_0D(self.ltype, self.volume, **self.kwargs)

    def generate_matrix(self):
        """
        Generates a 3x3 matrix for the lattice based on the lattice type and volume
        """
        #Try multiple times in case of failure
        for i in range(10):
            para = self.generate_para()
            if para is not None:
                return para2matrix(para)
        printx("Error: Could not generate lattice matrix.", priority=1)
        return

    def get_matrix(self):
        """
        Returns a 3x3 numpy array representing the lattice vectors.
        """
        try:
            return self.matrix
        except:
            printx("Error: Lattice matrix undefined.", priority=1)
            return

    def get_para(self):
        """
        Returns a tuple of lattice parameters.
        """
        return (self.a, self.b, self.c, self.alpha, self.beta, self.gamma)

    def set_matrix(self, matrix=None):
        if matrix != None:
            m = np.array(matrix)
            if np.shape(m) == (3,3):
                self.matrix = m
            else:
                printx("Error: matrix must be a 3x3 numpy array or list", priority=1)
        elif matrix == None:
            self.reset_matrix()
        para = matrix2para(self.matrix)
        self.a, self.b, self.c, self.alpha, self.beta, self.gamma = para

    def set_para(self, para=None, radians=False):
        if para is not None:
            if radians is False:
                para[3] *= rad
                para[4] *= rad
                para[5] *= rad
            self.set_matrix(para2matrix(para))
        else:
            self.set_matrix()

    def reset_matrix(self):
        if self.random is True:
            for i in range(3):
                m = self.generate_matrix()
                if m is not None:
                    self.matrix = m
                    [a, b, c, alpha, beta, gamma] = matrix2para(self.matrix)
                    self.a = a
                    self.b = b
                    self.c = c
                    self.alpha = alpha
                    self.beta = beta
                    self.gamma = gamma
                    break

    def set_volume(self, volume):
        if self.allow_volume_reset is True:
            self.volume = volume

    def generate_point(self):
        point = np.random.random(3)
        if self.ltype in ["spherical", "ellipsoidal"]:
            #Choose a point within an octant of the unit sphere
            while dsquared(point) > 1:
                point = np.random.random(3)
            #Randomly flip some coordinates
            for index, x in enumerate(point):
                #Scale the point by the max radius
                if random.uniform(0,1) < 0.5:
                    point[index] *= -1
        else:
            for i, a in enumerate(self.PBC):
                if not a:
                    if self.ltype in ["hexagonal", "trigonal", "rhombohedral"]:
                        point[i] *= 1./math.sqrt(3.)
                    else:
                        point[i] -= 0.5
        return point

    @classmethod
    def from_para(self, a, b, c, alpha, beta, gamma, ltype="triclinic", radians=False, PBC=[1,1,1], **kwargs):
        """
        Creates a Lattice object from 6 lattice parameters. Additional keyword arguments
        are available. Unless specified by the keyword random=True, does not create a
        new matrix upon calling reset_matrix. This allows for generation of random
        crystals with a specific choice of unit cell.

        Args:
            a, b, c: The length (in Angstroms) of the unit cell vectors
            alpha: the angle (in degrees) between the b and c vectors
            beta: the angle (in degrees) between the a and c vectors
            gamma: the angle (in degrees) between the a and b vectors
            ltype: the lattice type ("cubic, tetragonal, etc."). Also available are "spherical",
                which confines generated points to lie within a sphere, and "ellipsoidal", which
                confines generated points to lie within an ellipse (oriented about the z axis)
            radians: whether or not to use radians (instead of degrees) for the lattice angles
            PBC: A periodic boundary condition list, where 1 means periodic, 0 means not periodic.
                Ex: [1,1,1] -> full 3d periodicity, [0,0,1] -> periodicity along the z axis
            kwargs: various values which may be defined. If none are defined, random ones
                will be generated. Values will be passed to generate_lattice. Options include:
                area: The cross-sectional area (in Angstroms squared). Only used to generate 1D
                    crystals
                thickness: The unit cell's non-periodic thickness (in Angstroms). Only used to
                    generate 2D crystals
                unique_axis: The unique axis for certain symmetry (and especially layer) groups.
                    Because the symmetry operations are not also transformed, you should use the
                    default values for random crystal generation
                random: If False, keeps the stored values for the lattice geometry even upon applying
                    reset_matrix. To alter the matrix, use set_matrix() or set_para
                'unique_axis': the axis ('a', 'b', or 'c') which is not symmetrically
                    equivalent to the other two
                'min_l': the smallest allowed cell vector. The smallest vector must be larger
                    than this.
                'mid_l': the second smallest allowed cell vector. The second smallest vector
                    must be larger than this.
                'max_l': the third smallest allowed cell vector. The largest cell vector must
                    be larger than this.

        Returns:
            a Lattice object with the specified parameters
        """
        try:
            cell_matrix = para2matrix((a,b,c,alpha,beta,gamma), radians=radians)
        except:
            printx("Error: invalid cell parameters for lattice.", priority=1)
            return
        volume = np.linalg.det(cell_matrix)
        #Initialize a Lattice instance
        l = Lattice(ltype, volume, PBC=PBC, **kwargs)
        l.a = a
        l.b = b
        l.c = c
        l.alpha = alpha*rad
        l.beta = beta*rad
        l.gamma = gamma*rad
        l.matrix = cell_matrix
        l.ltype = ltype
        l.volume = volume
        l.random = False
        l.allow_volume_reset = False
        return l

    @classmethod
    def from_matrix(self, matrix, ltype="triclinic", PBC=[1,1,1], **kwargs):
        """
        Creates a Lattice object from a 3x3 cell matrix. Additional keyword arguments
        are available. Unless specified by the keyword random=True, does not create a
        new matrix upon calling reset_matrix. This allows for generation of random
        crystals with a specific choice of unit cell.

        Args:
            matrix: a 3x3 real matrix (numpy array or nested list) describing the cell vectors
            ltype: the lattice type ("cubic, tetragonal, etc."). Also available are "spherical",
                which confines generated points to lie within a sphere, and "ellipsoidal", which
                confines generated points to lie within an ellipsoid (oriented about the z axis)
            PBC: A periodic boundary condition list, where 1 means periodic, 0 means not periodic.
                Ex: [1,1,1] -> full 3d periodicity, [0,0,1] -> periodicity along the z axis
            kwargs: various values which may be defined. If none are defined, random ones
                will be generated. Values will be passed to generate_lattice. Options include:
                area: The cross-sectional area (in Angstroms squared). Only used to generate 1D
                    crystals
                thickness: The unit cell's non-periodic thickness (in Angstroms). Only used to
                    generate 2D crystals
                unique_axis: The unique axis for certain symmetry (and especially layer) groups.
                    Because the symmetry operations are not also transformed, you should use the
                    default values for random crystal generation
                random: If False, keeps the stored values for the lattice geometry even upon applying
                    reset_matrix. To alter the matrix, use set_matrix() or set_para
                'unique_axis': the axis ('a', 'b', or 'c') which is not symmetrically
                    equivalent to the other two
                'min_l': the smallest allowed cell vector. The smallest vector must be larger
                    than this.
                'mid_l': the second smallest allowed cell vector. The second smallest vector
                    must be larger than this.
                'max_l': the third smallest allowed cell vector. The largest cell vector must
                    be larger than this.

        Returns:
            a Lattice object with the specified parameters
        """
        m = np.array(matrix)
        if np.shape(m) != (3,3):
            printx("Error: Lattice matrix must be 3x3", priority=1)
            return
        [a, b, c, alpha, beta, gamma] = matrix2para(m)
        volume = np.linalg.det(m)
        #Initialize a Lattice instance
        l = Lattice(ltype, volume, PBC=PBC, **kwargs)
        l.a = a
        l.b = b
        l.c = c
        l.alpha = alpha
        l.beta = beta
        l.gamma = gamma
        l.matrix = m
        l.ltype = ltype
        l.volume = volume
        l.random = False
        l.allow_volume_reset = False
        return l

    def __str__(self):
        s = str(self.ltype)+" lattice:"
        s += "\na: "+str(self.a)
        s += "\nb: "+str(self.b)
        s += "\nc: "+str(self.c)
        s += "\nalpha: "+str(self.alpha*deg)
        s += "\nbeta: "+str(self.beta*deg)
        s += "\ngamma: "+str(self.gamma*deg)
        return s

    def __repr__(self):
        return str(self)

class random_crystal():
    """
    Class for storing and generating atomic crystals based on symmetry
    constraints. Given a spacegroup, list of atomic symbols, the stoichiometry,
    and a volume factor, generates a random crystal consistent with the
    spacegroup's symmetry. This crystal is stored as a pymatgen struct via
    self.struct
    
    Args:
        group: the international spacegroup number, or a Group object
        species: a list of atomic symbols for each ion type
        numIons: a list of the number of each type of atom within the
            primitive cell (NOT the conventional cell)
        tm: the Tol_matrix object used to generate the crystal
        factor: a volume factor used to generate a larger or smaller
            unit cell. Increasing this gives extra space between atoms
        lattice: an optional Lattice object to use for the unit cell
    """
    def init_common(self, species, numIons, factor, group, lattice, tm):
        """
        Common init functionality for 0D-3D cases of random_crystal.
        """
        self.valid = False
        #Check that numIons are integers greater than 0
        for num in numIons:
            if int(num) != num or num < 1:
                printx("Error: stoichiometry must consist of integers greater than 0.", priority=1)
                return False
        if type(group) == Group:
            self.group = group
            """A pyxtal.symmetry.Group object storing information about the space/layer
            /Rod/point group, and its Wyckoff positions."""
        else:
            self.group = Group(group, dim=self.dim)
        self.number = self.group.number
        """The international group number of the crystal:
        1-230 for 3D space groups
        1-80 for 2D layer groups
        1-75 for 1D Rod groups
        1-32 for crystallographic point groups
        None otherwise
        """
        self.numattempts = 0
        """The number of attempts needed to generate the crystal. Has a maximum
        value of max1*max2*max3."""
        numIons = np.array(numIons) #must convert it to np.array
        self.factor = factor
        """The supplied volume factor for the unit cell."""
        self.numIons0 = numIons
        """The number of each type of atom in the PRIMITIVE cell."""
        self.numIons = self.numIons0 * cellsize(self.group)
        """The number of each type of atom in the CONVENTIONAL cell."""
        self.species = species
        """A list of atomic symbols for the types of atoms in the crystal."""
        self.Msgs()
        """A list of warning messages to use during generation."""
        if lattice is not None:
            #Use the provided lattice
            self.lattice = lattice
            self.volume = lattice.volume
            #Make sure the custom lattice PBC axes are correct.
            if lattice.PBC != self.PBC:
                self.lattice.PBC = self.PBC
                printx("\n  Warning: converting custom lattice PBC to "+str(self.PBC))
        elif lattice == None:
            #Determine the unique axis
            if self.dim == 2:
                if self.number in range(3, 8):
                    unique_axis = "c"
                else:
                    unique_axis = "a"
            elif self.dim == 1:
                if self.number in range(3, 8):
                    unique_axis = "a"
                else:
                    unique_axis = "c"
            else:
                unique_axis = "c"
            #Generate a Lattice instance
            self.volume = estimate_volume(self.numIons, self.species, self.factor)
            """The volume of the generated unit cell."""
            if self.dim == 3 or self.dim == 0:
                self.lattice = Lattice(self.group.lattice_type, self.volume, PBC=self.PBC, unique_axis=unique_axis)
            elif self.dim == 2:
                self.lattice = Lattice(self.group.lattice_type, self.volume, PBC=self.PBC, unique_axis=unique_axis, thickness=self.thickness)
            elif self.dim == 1:
                self.lattice = Lattice(self.group.lattice_type, self.volume, PBC=self.PBC, unique_axis=unique_axis, area=self.area)
        #Set the tolerance matrix
        if type(tm) == Tol_matrix:
            self.tol_matrix = tm
            """The Tol_matrix object used for checking inter-atomic distances within the structure."""
        else:
            try:
                self.tol_matrix = Tol_matrix(prototype=tm)
            except:
                printx("Error: tm must either be a Tol_matrix object or a prototype string for initializing one.", priority=1)
                self.valid = False
                self.struct = None
                return
        #Generate the crystal
        self.generate_crystal()

    def __init__(self, group, species, numIons, factor, lattice=None, tm=Tol_matrix(prototype="atomic")):
        self.dim = 3
        """The number of periodic dimensions of the crystal"""
        if type(group) != Group:
            group = Group(group, self.dim)
        self.sg = group.number
        """The international spacegroup number of the crystal."""
        self.PBC = [1,1,1]
        """The periodic boundary axes of the crystal"""
        self.init_common(species, numIons, factor, group, lattice, tm)

    def Msgs(self):
        """
        Define a set of error and warning message if generation fails.

        Returns:
            nothing
        """
        self.Msg1 = 'Error: the stoichiometry is incompatible with the wyckoff sites choice'
        self.Msg2 = 'Error: failed in the cycle of generating structures'
        self.Msg3 = 'Warning: failed in the cycle of adding species'
        self.Msg4 = 'Warning: failed in the cycle of choosing wyckoff sites'
        self.Msg5 = 'Finishing: added the specie'
        self.Msg6 = 'Finishing: added the whole structure'
        self.Msg7 = 'Error: invalid paramaters for initialization'

    def check_compatible(group, numIons):
        """
        Checks if the number of atoms is compatible with the Wyckoff
        positions. Considers the number of degrees of freedom for each Wyckoff
        position, and makes sure at least one valid combination of WP's exists.
        """
        #Store whether or not at least one degree of freedom exists
        has_freedom = False
        #Store the wp's already used that don't have any freedom
        used_indices = []
        #Loop over species
        for numIon in numIons:
            #Get lists of multiplicity, maxn and freedom
            l_mult0 = []
            l_maxn0 = []
            l_free0 = []
            indices0 = []
            for i_wp, wp in enumerate(group):
                indices0.append(i_wp)
                l_mult0.append(len(wp))
                l_maxn0.append(numIon // len(wp))
                if np.allclose(wp[0].rotation_matrix, np.zeros([3,3])):
                    l_free0.append(False)
                else:
                    l_free0.append(True)
            #Remove redundant multiplicities:
            l_mult = []
            l_maxn = []
            l_free = []
            indices = []
            for mult, maxn, free, i_wp in zip(l_mult0, l_maxn0, l_free0, indices0):
                if free is True:
                    if mult not in l_mult:
                        l_mult.append(mult)
                        l_maxn.append(maxn)
                        l_free.append(True)
                        indices.append(i_wp)
                elif free is False and i_wp not in used_indices:
                    l_mult.append(mult)
                    indices.append(i_wp)
                    if mult <= numIon:
                        l_maxn.append(1)
                    elif mult > numIon:
                        l_maxn.append(0)
                    l_free.append(False)
            #Loop over possible combinations
            #Create pointer variable to move through lists
            p = 0
            #Store the number of each WP, used across possible WP combinations
            n0 = [0]*len(l_mult)
            n = deepcopy(n0)
            for i, mult in enumerate(l_mult):
                if l_maxn[i] != 0:
                    p = i
                    n[i] = l_maxn[i]
                    break
            p2 = p
            if n == n0:
                return False
            while True:
                num = np.dot(n, l_mult)
                dobackwards = False
                #The combination works: move to next species
                if num == numIon:
                    #Check if at least one degree of freedom exists
                    for val, free, i_wp in zip(n, l_free, indices):
                        if val > 0:
                            if free is True:
                                has_freedom = True
                            elif free is False:
                                used_indices.append(i_wp)
                    break
                #All combinations failed: return False
                if n == n0 and p >= len(l_mult) - 1:
                    return False
                #Too few atoms
                if num < numIon:
                    #Forwards routine
                    #Move p to the right and max out
                    if p < len(l_mult) - 1:
                        p += 1
                        n[p] = min((numIon - num) // l_mult[p], l_maxn[p])
                    elif p == len(l_mult) - 1:
                        #p is already at last position: trigger backwards routine
                        dobackwards = True
                #Too many atoms
                if num > numIon or dobackwards is True:
                    #Backwards routine
                    #Set n[p] to 0, move p backwards to non-zero, and decrease by 1
                    n[p] = 0
                    while p > 0 and p > p2:
                        p -= 1
                        if n[p] != 0:
                            n[p] -= 1
                            if n[p] == 0 and p == p2:
                                p2 = p + 1
                            break
        #All species passed: return True
        if has_freedom is True:
            return True
        #All species passed, but no degrees of freedom: return 0
        elif has_freedom is False:
            return 0

    def to_file(self, fmt="cif", filename=None):
        """
        Creates a file with the given filename and file type to store the structure.
        By default, creates cif files for crystals and xyz files for clusters.
        By default, the filename is based on the stoichiometry.

        Args:
            fmt: the file type ('cif', 'xyz', etc.)
            filename: the file path

        Returns:
            Nothing. Creates a file at the specified path
        """
        if filename == None:
            given = False
        else:
            given = True
        if self.valid:
            if self.dim == 0:
                if filename == None:
                    filename = str(self.molecule.formula).replace(" ","") + "." + fmt
            if self.dim != 0:
                if filename == None:
                    filename = str(self.struct.formula).replace(" ","") + "." + fmt
            #Check if filename already exists
            #If it does, add a new number to end of filename
            if os.path.exists(filename):
                if given is False:
                    filename = filename[:(-len(fmt)-1)]
                i = 1
                while True:
                    outdir = filename + "_" + str(i)
                    if given is False:
                        outdir += "." + fmt
                    if not os.path.exists(outdir):
                        break
                    i += 1
                    if i > 10000:
                        return "Could not create file: too many files already created."
            else:
                outdir = filename
            if self.dim == 0 and fmt == "xyz":
                self.molecule.to(fmt=fmt, filename=outdir)
            else:
                self.struct.to(fmt=fmt, filename=outdir)
            return "Output file to " + outdir
        elif self.valid is False:
            printx("Cannot create file: structure did not generate.", priority=1)

    def print_all(self):
        """
        Prints useful information about the generated crystal.
        """
        print("--Random Crystal--")
        print("Dimension: "+str(self.dim))
        print("Group: "+self.group.symbol)
        print("Volume factor: "+str(self.factor))
        if self.valid is True:
            print("Wyckoff sites:")
            for x in self.wyckoff_sites:
                print("  "+str(x))
            print("Pymatgen Structure:")
            print(self.struct)
        elif self.valid is False:
            print("Structure not generated.")

    def generate_crystal(self, max1=max1, max2=max2, max3=max3):
        """
        The main code to generate a random atomic crystal. If successful,
        stores a pymatgen.core.structure object in self.struct and sets
        self.valid to True. If unsuccessful, sets self.valid to False and
        outputs an error message.

        Args:
            max1: the number of attempts for generating a lattice
            max2: the number of attempts for a given lattice
            max3: the number of attempts for a given Wyckoff position
        """
        #Check the minimum number of degrees of freedom within the Wyckoff positions
        self.numattempts = 1
        degrees = random_crystal.check_compatible(self.group, self.numIons)
        if degrees is False:
            printx(self.Msg1, priority=1)
            self.struct = None
            self.valid = False
            return
        else:
            if degrees is 0:
                max1 = 5
                max2 = 5
                max3 = 5
            #Calculate a minimum vector length for generating a lattice
            minvector = max(max(1.0*self.tol_matrix.get_tol(specie,specie) for specie in self.species), tol_m)
            for cycle1 in range(max1):
                self.cycle1 = cycle1
                #1, Generate a lattice
                if self.lattice.allow_volume_reset is True:
                    self.volume = estimate_volume(self.numIons, self.species, self.factor)
                    self.lattice.volume = self.volume
                self.lattice.reset_matrix()
                try:
                    cell_matrix = self.lattice.get_matrix()
                    if cell_matrix is None:
                        continue
                except:
                    continue
                #Check that the correct volume was generated
                if self.lattice.random is True:
                    if self.dim != 0 and abs(self.volume - np.linalg.det(cell_matrix)) > 1.0: 
                        printx("Error, volume is not equal to the estimated value: "+str(self.volume)
                            +" -> "+str(np.linalg.det(cell_matrix))
                            +"cell_para:  "+str(matrix2para(cell_matrix)), priority=0)
                        self.valid = False
                        self.struct = None
                        return


                good_structure = False
                
                # to try to generate atomic coordinates
                for cycle2 in range(max2):

                    coordinates_total = [] #to store the added coordinates
                    sites_total = []      #to store the corresponding specie
                    wyckoff_sites_total = []
                    self.cycle2 = cycle2
                    coordinates_tmp = deepcopy(coordinates_total)
                    sites_tmp = deepcopy(sites_total)
                    wyckoff_sites_tmp = deepcopy(wyckoff_sites_total)
                    
                    #Add specie by specie
                    for numIon, specie in zip(self.numIons, self.species):
                        numIon_added = 0
                        tol = self.tol_matrix.get_tol(specie,specie)

                        #Now we start to add the specie to the wyckoff position
                        cycle3 = 0
                        while cycle3 < max3:
                            self.cycle3 = cycle3
                            #Choose a random Wyckoff position for given multiplicity: 2a, 2b, 2c
                            ops = choose_wyckoff(self.group, numIon-numIon_added) 
                            if ops is not False:
                            #Generate a list of coords from ops
                                point = self.lattice.generate_point()
                                projected_point = project_point(point, ops[0], lattice=cell_matrix, PBC=self.PBC)
                                coords = apply_ops(projected_point, ops)
                                #Merge coordinates if the atoms are close
                                coords_toadd, wp_index, point = merge_coordinate(coords, cell_matrix, self.group, tol)

                                if wp_index is not False:
                                    #Use a Wyckoff_site object for the current site
                                    current_site = Wyckoff_site(self.group[wp_index], point, specie)

                                    #Check current WP against existing WP's
                                    passed_wp_check = True
                                    for ws in wyckoff_sites_tmp:
                                        if check_wyckoff_sites(current_site, ws, cell_matrix, tm=self.tol_matrix) is False:
                                            passed_wp_check = False

                                    if passed_wp_check is True:
                                        #The current Wyckoff site passed; store it
                                        if coordinates_tmp == []:
                                            coordinates_tmp = current_site.coords
                                        else:
                                            coordinates_tmp = np.vstack([coordinates_tmp, current_site.coords])
                                        sites_tmp += [specie]*len(coords_toadd)
                                        wyckoff_sites_tmp.append(current_site)
                                        numIon_added += len(coords_toadd)
                                        #Check if enough atoms have been added
                                        if numIon_added == numIon:
                                            coordinates_total = deepcopy(coordinates_tmp)
                                            sites_total = deepcopy(sites_tmp)
                                            wyckoff_sites_total = deepcopy(wyckoff_sites_tmp)
                                            break
                                    else:
                                        cycle3 += 1
                                        self.numattempts += 1
                                else:
                                    cycle3 += 1
                                    self.numattempts += 1
                            else:
                                cycle3 += 1
                                self.numattempts += 1

                        if numIon_added != numIon:
                            coordinates_total = []
                            sites_total = []
                            wyckoff_sites_total = []
                            break  #need to repeat from the 1st species

                    if numIon_added == numIon:
                        good_structure = True
                        break
                    else: #reset the coordinates and sites
                        coordinates_total = []
                        sites_total = []

                if good_structure:
                    final_coor = []
                    final_site = []
                    final_number = []
                    final_lattice = cell_matrix
                    for coor, ele in zip(coordinates_total, sites_total):
                        final_coor.append(coor)
                        final_site.append(ele)
                        final_number.append(Element(ele).z)
                    final_coor = np.array(final_coor)

                    if self.dim != 0:
                        final_lattice, final_coor = Add_vacuum(final_lattice, final_coor, PBC=self.PBC)
                        self.lattice_matrix = final_lattice   
                        """A 3x3 matrix representing the lattice of the unit
                        cell."""
                        self.frac_coords = np.array(final_coor)
                        """The fractional coordinates for each atom in the
                        final structure"""
                        self.cart_coords = np.dot(final_coor, final_lattice)
                        """The absolute coordinates for each atom in the
                        final structure"""
                        self.sites = final_site
                        """A list of atomic symbols corresponding to the type
                        of atom for each site in self.coordinates"""
                        self.struct = Structure(final_lattice, final_site, np.array(final_coor))
                        """A pymatgen.core.structure.Structure object for the
                        final generated crystal."""
                        self.spg_struct = (final_lattice, np.array(final_coor), final_number)
                        """A list of information describing the generated
                        crystal, which may be used by spglib for symmetry
                        analysis."""
                        self.wyckoff_sites = wyckoff_sites_total
                        """A list of Wyckoff_site objects describing the Wyckoff positions in
                        the structure."""
                        self.valid = True
                        return
                    elif self.dim == 0:
                        self.lattice_matrix = final_lattice   
                        """A 3x3 matrix representing the lattice of the unit
                        cell."""
                        self.frac_coords = np.array(final_coor)
                        """The relative coordinates for each atom in the
                        final structure""" 
                        self.cart_coords = np.dot(final_coor, final_lattice)
                        """The absolute coordinates for each atom in the
                        final structure"""                  
                        self.sites = final_site
                        """A list of atomic symbols corresponding to the type
                        of atom for each site in self.coordinates"""
                        self.species = final_site
                        """A list of atomic symbols corresponding to the type
                        of atom for each site in self.coordinates"""
                        self.molecule = Molecule(self.species, self.cart_coords)
                        """A pymatgen.core.structure.Molecule object for the
                        final generated cluster."""
                        #Calculate binding box
                        maxx = max(self.cart_coords[:,0])
                        minx = min(self.cart_coords[:,0])
                        maxy = max(self.cart_coords[:,1])
                        miny = min(self.cart_coords[:,1])
                        maxz = max(self.cart_coords[:,2])
                        minz = min(self.cart_coords[:,2])
                        self.struct = self.molecule.get_boxed_structure(maxx-minx+10, maxy-miny+10, maxz-minz+10)
                        """A pymatgen.core.structure.Structure object for the
                        final generated object."""
                        self.wyckoff_sites = wyckoff_sites_total
                        """A list of Wyckoff_site objects describing the Wyckoff positions in
                        the structure."""
                        self.valid = True
                        """Whether or not a valid crystal was generated."""
                        return
        if degrees == 0: printx("Wyckoff positions have no degrees of freedom.", priority=2)
        self.struct = None
        self.valid = False
        return

class random_crystal_2D(random_crystal):
    """
    A 2d counterpart to random_crystal. Generates a random atomic crystal based
    on a 2d layer group instead of a 3d spacegroup. Note that each layer group
    is equal to a corresponding 3d spacegroup, but without periodicity in one
    direction. The generated pymatgen structure can be accessed via self.struct

    Args:
        group: the layer group number between 1 and 80. NOT equal to the
            international space group number, which is between 1 and 230
            OR, a pyxtal.symmetry.Group object
        species: a list of atomic symbols for each ion type
        numIons: a list of the number of each type of atom within the
            primitive cell (NOT the conventional cell)
        thickness: the thickness, in Angstroms, of the unit cell in the 3rd
            dimension (the direction which is not repeated periodically)
        factor: a volume factor used to generate a larger or smaller
            unit cell. Increasing this gives extra space between atoms
        lattice: an optional Lattice object to use for the unit cell
        tm: the Tol_matrix object used to generate the crystal
    """
    def __init__(self, group, species, numIons, factor, thickness=None, lattice=None, tm=Tol_matrix(prototype="atomic")):
        self.dim = 2
        """The number of periodic dimensions of the crystal"""
        self.PBC = [1,1,0]
        """The periodic boundary axes of the crystal"""
        if type(group) != Group:
            group = Group(group, self.dim)
        number = group.number
        """The layer group number of the crystal."""
        self.thickness = thickness
        """the thickness, in Angstroms, of the unit cell in the 3rd
        dimension."""
        self.init_common(species, numIons, factor, number, lattice, tm)

class random_crystal_1D(random_crystal):
    """
    A 1d counterpart to random_crystal. Generates a random atomic crystal based
    on a 1d Rod group instead of a 3d spacegroup. The generated pymatgen
    structure can be accessed via self.struct

    Args:
        group: the Rod group number between 1 and 75. NOT equal to the
            international space group number, which is between 1 and 230
            OR, a pyxtal.symmetry.Group object
        species: a list of atomic symbols for each ion type
        numIons: a list of the number of each type of atom within the
            primitive cell (NOT the conventional cell)
        area: the effective cross-sectional area, in Angstroms squared, of the
            unit cell
        factor: a volume factor used to generate a larger or smaller
            unit cell. Increasing this gives extra space between atoms
        lattice: an optional Lattice object to use for the unit cell
        tm: the Tol_matrix object used to generate the crystal
    """
    def __init__(self, group, species, numIons, factor, area=None, lattice=None, tm=Tol_matrix(prototype="atomic")):
        self.dim = 1
        """The number of periodic dimensions of the crystal"""
        self.PBC = [0,0,1]
        """The periodic axis of the crystal."""
        self.sg = None
        """The international space group number (there is not a 1-1 correspondence
        with Rod groups)."""
        self.area = area
        """the effective cross-sectional area, in Angstroms squared, of the
        unit cell."""
        self.init_common(species, numIons, factor, group, lattice, tm)

class random_cluster(random_crystal):
    """
    A 0d counterpart to random_crystal. Generates a random atomic cluster based
    on a 0d Point group instead of a 3d spacegroup. The generated pymatgen
    structure can be accessed via self.struct

    Args:
        group: the Schoenflies symbol for the point group (ex: "Oh", "C5v", "D3")
            OR the number between 1-32 for a crystallographic point group,
            OR, a pyxtal.symmetry.Group object
            See:
            https://en.wikipedia.org/wiki/Schoenflies_notation#Point_groups
            for more information
        species: a list of atomic symbols for each ion type
        numIons: a list of the number of each type of atom within the
            primitive cell (NOT the conventional cell)
        factor: a volume factor used to generate a larger or smaller
            unit cell. Increasing this gives extra space between atoms
        lattice: an optional Lattice object to use for the unit cell
        tm: the Tol_matrix object used to generate the crystal
    """
    def __init__(self, group, species, numIons, factor, lattice=None, tm=Tol_matrix(prototype="atomic", factor=0.7)):
        tol_m = 0.1
        self.dim = 0
        """The number of periodic dimensions of the crystal"""
        self.PBC = [0,0,0]
        """The periodic axis of the crystal."""
        self.sg = None
        """The international space group number (there is not a 1-1 correspondence
        with Point groups)."""
        self.init_common(species, numIons, factor, group, lattice, tm)


if __name__ == "__main__":
    #-------------------------------- Options -------------------------
    import os
    from time import time
    from optparse import OptionParser
    from spglib import get_symmetry_dataset

    parser = OptionParser()
    parser.add_option("-s", "--spacegroup", dest="sg", metavar='sg', default=36, type=int,
            help="desired space group number (1-230) or layer group number (1-80), e.g., 36")
    parser.add_option("-e", "--element", dest="element", default='Li', 
            help="desired elements: e.g., Li", metavar="element")
    parser.add_option("-n", "--numIons", dest="numIons", default=16, 
            help="desired numbers of atoms: 16", metavar="numIons")
    parser.add_option("-f", "--factor", dest="factor", default=1.0, type=float, 
            help="volume factor: default 1.0", metavar="factor")
    parser.add_option("-v", "--verbosity", dest="verbosity", default=0, type=int, 
            help="verbosity: default 0; higher values print more information", metavar="verbosity")
    parser.add_option("-a", "--attempts", dest="attempts", default=1, type=int, 
            help="number of crystals to generate: default 1", metavar="attempts")
    parser.add_option("-o", "--outdir", dest="outdir", default="out", type=str, 
            help="Directory for storing output cif files: default 'out'", metavar="outdir")
    parser.add_option("-d", "--dimension", dest="dimension", metavar='dimension', default=3, type=int,
            help="desired dimension: (3, 2, or 1 for 3d, 2d, or 1D respectively): default 3")
    parser.add_option("-t", "--thickness", dest="thickness", metavar='thickness', default=None, type=float,
            help="Thickness, in Angstroms, of a 2D crystal, or area of a 1D crystal, None generates a value automatically: default None")

    (options, args) = parser.parse_args()
    sg = options.sg
    dimension = options.dimension
    if dimension == 3:
        if sg < 1 or sg > 230:
            print("Invalid space group number. Must be between 1 and 230.")
            sys.exit(0)
    elif dimension == 2:
        if sg < 1 or sg > 80:
            print("Invalid layer group number. Must be between 1 and 80.")
            sys.exit(0)
    elif dimension == 1:
        if sg < 1 or sg > 75:
            print("Invalid Rod group number. Must be between 1 and 75.")
            sys.exit(0)
    else:
        print("Invalid dimension. Use dimension 0, 1, 2, or 3.")
        sys.exit(0)

    element = options.element
    number = options.numIons
    numIons = []
    if element.find(',') > 0:
        system = element.split(',')
        for x in number.split(','):
            numIons.append(int(x))
    else:
        system = [element]
        numIons = [int(number)]

    factor = options.factor
    if factor < 0:
        print("Error: Volume factor must be greater than 0.")
        sys.exit(0)

    verbosity = options.verbosity
    attempts = options.attempts
    outdir = options.outdir
    dimension = options.dimension
    thickness = options.thickness

    try:
        os.mkdir(outdir)
    except: pass

    filecount = 1 #To check whether a file already exists
    for i in range(attempts):
        numIons0 = np.array(numIons)
        sg = options.sg
        start = time()
        if dimension == 3:
            rand_crystal = random_crystal(options.sg, system, numIons0, factor)
            sg1 = sg
        elif dimension == 2:
            rand_crystal = random_crystal_2D(options.sg, system, numIons0, thickness, factor)
            sg1 = rand_crystal.sg
        elif dimension == 1:
            rand_crystal = random_crystal_1D(options.sg, system, numIons0, thickness, factor)
            sg1 = "?"
        if dimension == 0:
            rand_crystal = random_cluster(options.sg, system, numIons0, factor)
            sg1 = sg
        end = time()
        timespent = np.around((end - start), decimals=2)

        if rand_crystal.valid:
            #Output a cif file
            written = False
            try:
                comp = str(rand_crystal.struct.composition)
                comp = comp.replace(" ", "")
                cifpath = outdir + '/' + comp + "_" + str(filecount) + '.cif'
                while os.path.isfile(cifpath):
                    filecount += 1
                    cifpath = outdir + '/' + comp + "_" + str(filecount) + '.cif'
                CifWriter(rand_crystal.struct, symprec=0.1).write_file(filename = cifpath)
                written = True
            except: pass
            #POSCAR output
            #rand_crystal.struct.to(fmt="poscar", filename = '1.vasp')

            #spglib style structure called cell
            ans = get_symmetry_dataset(rand_crystal.spg_struct, symprec=1e-1)['number']
            print('Space group  requested:', sg1, ' generated:', ans)
            if written is True:
                print("    Output to "+cifpath)
            else:
                print("    Could not write cif file.")

            #Print additional information about the structure
            if verbosity > 0:
                print("Time required for generation: " + str(timespent) + "s")
                print(rand_crystal.struct)


        #If generation fails
        else: 
            print('something is wrong')
            print('Time spent during generation attempt: ' + str(timespent) + "s")


<filename>pyxtal/crystal.py
#Standard Libraries
import sys
import os
import random

#External Libraries
from pymatgen.core.structure import Structure
from pymatgen.core.structure import Molecule
from pymatgen.io.cif import CifWriter

#PyXtal imports
from pyxtal.symmetry import *
from pyxtal.database.element import Element
import pyxtal.database.hall as hall

#Constants
#------------------------------
tol_m = 0.3 #seperation tolerance in Angstroms
max1 = 40 #Attempts for generating lattices
max2 = 10 #Attempts for a given lattice
max3 = 20 #Attempts for a given Wyckoff position
minvec = 1.0 #minimum vector length

#Define functions
#------------------------------
class Tol_matrix():
    """
    Class for variable distance tolerance checking. Used within random_crystal and
    molecular_crystal to verify whether atoms are too close. Stores a matrix of atom-
    atom pair tolerances. Note that the matrix's indices correspond to atomic numbers,
    with the 0th entries being 0 (there is no atomic number 0).

    Args:
        prototype: a string representing the type of radii to use
            ("atomic", "molecular", or "metallic")
        factor: a float to scale the distances by. A smaller value means a smaller
            tolerance for distance checking
        tuples: a list or tuple of tuples, which define custom tolerance values. Each tuple
            should be of the form (specie1, specie2, value), where value is the tolerance
            in Angstroms, and specie1 and specie2 can be strings, integers, Element objects,
            or pymatgen Specie objects. Custom values may also be set using set_tol
    """
    def __init__(self, *tuples, prototype="atomic", factor=1.0):
        f = factor
        self.prototype = prototype
        if prototype == "atomic":
            f *= 0.5
            attrindex = 5
            self.radius_type = "covalent"
        elif prototype == "molecular":
            attrindex = 5
            self.radius_type = "covalent"
            f *= 1.2
        elif prototype == "metallic":
            attrindex = 7
            self.radius_type = "metallic"
            f *= 0.5
        else:
            self.radius_type = "N/A"
        self.f = f
        H = Element('H')
        m = [[0.]*(len(H.elements_list)+1)]
        for i, tup1 in enumerate(H.elements_list):
            m.append([0.])
            for j, tup2 in enumerate(H.elements_list):
                #Get the appropriate atomic radii
                if tup1[attrindex] is None:
                    if tup1[5] is None:
                        val1 = None
                    else:
                        #Use the covalent radius
                        val1 = tup1[5]
                else:
                    val1 = tup1[attrindex]
                if tup2[attrindex] is None:
                    if tup2[5] is None:
                        val2 = None
                    else:
                        #Use the covalent radius
                        val2 = tup1[5]
                else:
                    val2 = tup2[attrindex]
                if val1 is not None and val2 is not None:
                    m[-1].append( f * (val1 + val2))
                else:
                    #If no radius is found for either atom, set tolerance to None
                    m[-1].append(None)
        self.matrix = np.array(m)
        """A symmetric numpy matrix storing the tolerance between specie pairs."""
        self.custom_values = []
        """A list of tuples storing which species pair tolerances have custom values."""

        try:
            for tup in tuples:
                self.set_tol(*tup)
        except:
            printx("Error: Could not set custom tolerance value(s).\n"
                +"All custom entries should be entered using the following form:\n"
                +"(specie1, specie2, value), where value is the tolerance in Angstroms.", priority=1)

        self.radius_list = []
        for i in range(len(self.matrix)):
            if i == 0: continue
            x = self.get_tol(i, i)
            self.radius_list.append(x)

    def get_tol(self, specie1, specie2):
        """
        Returns the tolerance between two species.
        
        Args:
            specie1, specie2: the atomic number (int or float), name (str), symbol (str),
                an Element object, or a pymatgen Specie object

        Returns:
            the tolerance between the provided pair of atomic species
        """
        if self.prototype == "single_value":
            return self.matrix[0][0]
        index1 = Element.number_from_specie(specie1)
        index2 = Element.number_from_specie(specie2)
        if index1 is not None and index2 is not None:
            return self.matrix[index1][index2]
        else:
            return None

    def set_tol(self, specie1, specie2, value):
        """
        Sets the distance tolerance between two species.
        
        Args:
            specie1, specie2: the atomic number (int or float), name (str), symbol (str),
                an Element object, or a pymatgen Specie object
            value:
                the tolerance (in Angstroms) to set to
        """
        index1 = Element.number_from_specie(specie1)
        index2 = Element.number_from_specie(specie2)
        if index1 is None or index2 is None:
            return
        self.matrix[index1][index2] = float(value)
        if index1 != index2:
            self.matrix[index2][index1] = float(value)
        if (index1, index2) not in self.custom_values and (index2, index1) not in self.custom_values:
            larger = max(index1, index2)
            smaller = min(index1, index2)
            self.custom_values.append((smaller, larger))

    @classmethod
    def from_matrix(self, matrix, prototype="atomic", factor=1.0, begin_with=0):
        """
        Given a tolerance matrix, returns a Tol_matrix object. Matrix indices correspond to
        the atomic number (with 0 pointing to Hydrogen by default). For atoms with atomic
        numbers not included in the matrix, the default value (specified by prototype) will be
        used, up to element 96. Note that if the matrix is asymmetric, only the value below the
        diagonal will be used.

        Args:
            matrix: a 2D matrix or list of tolerances between atomic species pairs. The
                indices correspond to atomic species (see begin_with variable description)
            prototype: a string representing the type of radii to use
                ("atomic", "molecular")
            factor: a float to scale the distances by. A smaller value means a smaller
                tolerance for distance checking
            begin_with: the index which points to Hydrogen within the matrix. Default 0

        Returns:
            a Tol_matrix object
        """
        m = np.array(matrix)
        tups = []
        for i, row in enumerate(matrix):
            for j, value in enumerate(row):
                if j > i: continue
                tups.append( (i+1-begin_with, j+1-begin_with, matrix[i][j]) )
        tm = Tol_matrix(prototype=prototype, factor=factor, *tups)
        return tm

    @classmethod
    def from_radii(self, radius_list, prototype="atomic", factor=1.0, begin_with=0):
        """
        Given a list of atomic radii, returns a Tol_matrix object. For atom-atom pairs, uses
        the average radii of the two species as the tolerance value. For atoms with atomic
        numbers not in the radius list, the default value (specified by prototype) will be
        used, up to element 96.

        Args:
            radius_list: a list of atomic radii (in Angstroms), beginning with Hydrogen
            prototype: a string representing the type of radii to use
                ("atomic", "molecular")
            factor: a float to scale the distances by. A smaller value means a smaller
                tolerance for distance checking
            begin_with: the index which points to Hydrogen within the list. Default 0

        Returns:
            a Tol_matrix object
        """
        tups = []
        f = factor * 0.5
        for i, r1 in enumerate(radius_list):
            for j, r2 in enumerate(radius_list):
                if j > i: continue
                tups.append( (i+1-begin_with, j+1-begin_with, f*(r1+r2)) )
        tm = Tol_matrix(prototype=prototype, factor=factor, *tups)
        return tm

    @classmethod
    def from_single_value(self, value):
        """
        Creates a Tol_matrix which only has a single tolerance value. Using get_tol will
        always return the same value.

        Args:
            value: the tolerance value to use

        Returns:
            a Tol_matrix object whose methods are overridden to use a single tolerance value
        """
        tm = Tol_matrix()
        tm.prototype = "single value"
        tm.matrix = np.array([[value]])
        tm.custom_values = [(1,1)]
        tm.radius_type = "N/A"
        return tm

    def __getitem__(self, index):
        new_index = Element.number_from_specie(index)
        return self.matrix[index]

    def print_all(self):
        print("--Tol_matrix class object--")
        print("  Prototype: "+str(self.prototype))
        print("  Atomic radius type: "+str(self.radius_type))
        print("  Radius scaling factor: "+str(self.f))
        if self.prototype == "single value":
            print("  Custom tolerance value: "+str(self.matrix([0][0])))
        else:
            if self.custom_values == []:
                print("  Custom tolerance values: None")
            else:
                print("  Custom tolerance values:")
                for tup in self.custom_values:
                    print("    "+str(Element(tup[0]).short_name)+", "+str(Element(tup[1]).short_name)+": "+str(self.get_tol(tup[0],tup[1])))

    def to_file(self, filename=None):
        """
        Creates a file with the given filename and file type to store the structure.
        By default, creates cif files for crystals and xyz files for clusters.
        By default, the filename is based on the stoichiometry.

        Args:
            fmt: the file type ('cif', 'xyz', etc.)
            filename: the file path

        Returns:
            Nothing. Creates a file at the specified path
        """
        if filename == None:
            given = False
        else:
            given = True
        if filename == None:
            filename = "custom_tol_matrix"
        #Check if filename already exists
        #If it does, add a new number to end of filename
        if os.path.exists(filename):
            i = 1
            while True:
                outdir = filename + "_" + str(i)
                if not os.path.exists(outdir):
                    break
                i += 1
                if i > 10000:
                    return "Could not create file: too many files already created."
        else:
            outdir = filename
        try:
            np.save(filename, [self])
            return "Output file to " + outdir + ".npy"
        except:
            return "Error: Could not save Tol_matrix to file."

    @classmethod
    def from_file(self, filename):
        try:
            tm = np.load(filename)[0]
            if type(tm) == Tol_matrix:
                return tm
            else:
                printx("Error: invalid file for Tol_matrix.", priority=0)
                return
        except:
            printx("Error: Could not load Tol_matrix from file.", priority=0)
            return

def gaussian(min, max, sigma=3.0):
    """
    Choose a random number from a Gaussian probability distribution centered
    between min and max. sigma is the number of standard deviations that min
    and max are away from the center. Thus, sigma is also the largest possible
    number of standard deviations corresponding to the returned value. sigma=2
    corresponds to a 95.45% probability of choosing a number between min and
    max.

    Args:
        min: the minimum acceptable value
        max: the maximum acceptable value
        sigma: the number of standard deviations between the center and min or max

    Returns:
        a value chosen randomly between min and max
    """
    center = (max+min)*0.5
    delta = math.fabs(max-min)*0.5
    ratio = delta/sigma
    while True:
        x = np.random.normal(scale=ratio, loc=center)
        if x > min and x < max:
            return x

def get_tol(specie):
    """
    Given an atomic specie name, return the covalent radius.
    
    Args:
        specie: a string for the atomic symbol

    Returns:
        the covalent radius in Angstroms
    """
    return Element(specie).covalent_radius

tols_from_species = np.vectorize(get_tol)
"""
Given a list of atomic species names, returns a list of
covalent radii

Args:
    species: a list of strings for atomic species names or symbols

Returns:
    A 1D numpy array of distances in Angstroms
"""

def check_distance(coord1, coord2, species1, species2, lattice, PBC=[1,1,1], tm=Tol_matrix(prototype="atomic"), d_factor=1.0):
    """
    Check the distances between two set of atoms. Distances between coordinates
    within the first set are not checked, and distances between coordinates within
    the second set are not checked. Only distances between points from different
    sets are checked.

    Args:
        coord1: a list of fractional coordinates e.g. [[.1,.6,.4]
            [.3,.8,.2]]
        coord2: a list of new fractional coordinates e.g. [[.7,.8,.9],
            [.4,.5,.6]]
        species1: a list of atomic species or numbers for coord1
        species2: a list of atomic species or numbers for coord2
        lattice: matrix describing the unit cell vectors
        PBC: A periodic boundary condition list, where 1 means periodic, 0 means not periodic.
            Ex: [1,1,1] -> full 3d periodicity, [0,0,1] -> periodicity along the z axis
        tm: a Tol_matrix object, or a string representing the type of Tol_matrix
            to use
        d_factor: the tolerance is multiplied by this amount. Larger values
            mean atoms must be farther apart

    Returns:
        a bool for whether or not the atoms are sufficiently far enough apart
    """
    #Check that there are points to compare
    if len(coord1) < 1 or len(coord2) < 1:
        return True

    #Create tolerance matrix from subset of tm
    tols = np.zeros((len(species1),len(species2)))
    for i1, specie1 in enumerate(species1):
        for i2, specie2 in enumerate(species2):
            tols[i1][i2] = tm.get_tol(specie1, specie2)

    #Calculate the distance between each i, j pair
    d = distance_matrix(coord1, coord2, lattice, PBC=PBC)

    if (np.array(d) < np.array(tols)).any():
        return False
    else:
        return True

def check_images(coords, species, lattice, PBC=[1,1,1], tm=Tol_matrix(prototype="atomic"), tol=None, d_factor=1.0):
    """
    Given a set of (unfiltered) fractional coordinates, checks if the periodic images are too close.
    
    Args:
        coords: a list of fractional coordinates
        species: the atomic species of each coordinate
        lattice: a 3x3 lattice matrix
        PBC: the periodic boundary conditions
        tm: a Tol_matrix object
        tol: a single override value for the distance tolerances
        d_factor: the tolerance is multiplied by this amount. Larger values
            mean atoms must be farther apart

    Returns:
        False if distances are too close. True if distances are not too close
    """
    #If no PBC, there are no images to check
    if PBC == [0,0,0]:
        return True
    #Create image coords from given coords and PBC
    coords = np.array(coords)
    m = create_matrix(PBC=PBC)
    new_coords = []
    new_species = []
    for v in m:
        #Omit the [0,0,0] vector
        if (v == [0,0,0]).all(): continue
        for v2 in coords+v:
            new_coords.append(v2)
    new_coords = np.array(new_coords)
    #Create a distance matrix
    dm = distance_matrix(coords, new_coords, lattice, PBC=[0,0,0])
    #Define tolerances
    if tol is None:
        tols = np.zeros((len(species), len(species)))
        for i, s1 in enumerate(species):
            for j, s2 in enumerate(species):
                if i <= j:
                    tols[i][j] = tm.get_tol(s1, s2)
                    tols[j][i] = tm.get_tol(s1, s2)
        tols2 = np.tile(tols, int(len(new_coords) / len(coords)))
        if (dm < tols2).any():
            return False
        else:
            return True
    elif tol is not None:
        if (dm < tol).any():
            return False
        else:
            return True
    return True

def get_center(xyzs, lattice, PBC=[1,1,1]):
    """
    Finds the geometric centers of the clusters under periodic boundary
    conditions.

    Args:
        xyzs: a list of fractional coordinates
        lattice: a matrix describing the unit cell
        PBC: A periodic boundary condition list, where 1 means periodic, 0 means not periodic.
            Ex: [1,1,1] -> full 3d periodicity, [0,0,1] -> periodicity along the z axis

    Returns:
        x,y,z coordinates for the center of the input coordinate list
    """
    matrix0 = create_matrix(PBC=PBC)
    xyzs -= np.round(xyzs)
    matrix_min = [0,0,0]
    for atom1 in range(1,len(xyzs)):
        dist_min = 10.0
        for atom2 in range(0, atom1):
            #shift atom1 to position close to atom2
            matrix = matrix0 + (xyzs[atom1] - xyzs[atom2])
            matrix = np.dot(matrix, lattice)
            dists = cdist(matrix, [[0,0,0]])
            if np.min(dists) < dist_min:
                dist_min = np.min(dists)
                matrix_min = matrix0[np.argmin(dists)]
        xyzs[atom1] += matrix_min
    center = xyzs.mean(0)
    return center

def para2matrix(cell_para, radians=True, format='lower'):
    """
    Given a set of lattic parameters, generates a matrix representing the
    lattice vectors

    Args:
        cell_para: a 1x6 list of lattice parameters [a, b, c, alpha, beta,
            gamma]. a, b, and c are the length of the lattice vectos, and
            alpha, beta, and gamma are the angles between these vectors. Can
            be generated by matrix2para
        radians: if True, lattice parameters should be in radians. If False,
            lattice angles should be in degrees
        format: a string ('lower', 'symmetric', or 'upper') for the type of
            matrix to be output

    Returns:
        a 3x3 matrix representing the unit cell. By default (format='lower'),
        the a vector is aligined along the x-axis, and the b vector is in the
        y-z plane
    """
    a = cell_para[0]
    b = cell_para[1]
    c = cell_para[2]
    alpha = cell_para[3]
    beta = cell_para[4]
    gamma = cell_para[5]
    if radians is not True:
        rad = pi/180.
        alpha *= rad
        beta *= rad
        gamma *= rad
    cos_alpha = math.cos(alpha)
    cos_beta = math.cos(beta)
    cos_gamma = math.cos(gamma)
    sin_gamma = math.sin(gamma)
    sin_alpha = math.sin(alpha)
    matrix = np.zeros([3,3])
    if format == 'lower':
        #Generate a lower-diagonal matrix
        c1 = c*cos_beta
        c2 = (c*(cos_alpha - (cos_beta * cos_gamma))) / sin_gamma
        matrix[0][0] = a
        matrix[1][0] = b * cos_gamma
        matrix[1][1] = b * sin_gamma
        matrix[2][0] = c1
        matrix[2][1] = c2
        matrix[2][2] = math.sqrt(c**2 - c1**2 - c2**2)
    elif format == 'symmetric':
        #TODO: allow generation of symmetric matrices
        pass
    elif format == 'upper':
        #Generate an upper-diagonal matrix
        a3 = a*cos_beta
        a2 = (a*(cos_gamma - (cos_beta * cos_alpha))) / sin_alpha
        matrix[2][2] = c
        matrix[1][2] = b * cos_alpha
        matrix[1][1] = b * sin_alpha
        matrix[0][2] = a3
        matrix[0][1] = a2
        matrix[0][0] = math.sqrt(a**2 - a3**2 - a2**2)
        pass
    return matrix

def Add_vacuum(lattice, coor, vacuum=10, PBC=[0,0,0]):
    """
    Adds space above and below a 2D or 1D crystal. This allows for treating the
    structure as a 3D crystal during energy optimization

    Args:
        lattice: the lattice matrix of the crystal
        coor: the relative coordinates of the crystal
        vacuum: the amount of space, in Angstroms, to add above and below
        PBC: A periodic boundary condition list, where 1 means periodic, 0 means not periodic.
            Ex: [1,1,1] -> full 3d periodicity, [0,0,1] -> periodicity along the z axis

    Returns:
        lattice, coor: The transformed lattice and coordinates after the
            vacuum space is added
    """
    absolute_coords = np.dot(coor, lattice)
    for i, a in enumerate(PBC):
        if not a:
            lattice[i] += (lattice[i]/np.linalg.norm(lattice[i])) * vacuum
    new_coor = np.dot(absolute_coords, np.linalg.inv(lattice))
    return lattice, new_coor

def matrix2para(matrix, radians=True):
    """
    Given a 3x3 matrix representing a unit cell, outputs a list of lattice
    parameters.

    Args:
        matrix: a 3x3 array or list, where the first, second, and third rows
            represent the a, b, and c vectors respectively
        radians: if True, outputs angles in radians. If False, outputs in
            degrees

    Returns:
        a 1x6 list of lattice parameters [a, b, c, alpha, beta, gamma]. a, b,
        and c are the length of the lattice vectos, and alpha, beta, and gamma
        are the angles between these vectors (in radians by default)
    """
    cell_para = np.zeros(6)
    #a
    cell_para[0] = np.linalg.norm(matrix[0])
    #b
    cell_para[1] = np.linalg.norm(matrix[1])
    #c
    cell_para[2] = np.linalg.norm(matrix[2])
    #alpha
    cell_para[3] = angle(matrix[1], matrix[2])
    #beta
    cell_para[4] = angle(matrix[0], matrix[2])
    #gamma
    cell_para[5] = angle(matrix[0], matrix[1])
    
    if not radians:
        #convert radians to degrees
        deg = 180./pi
        cell_para[3] *= deg
        cell_para[4] *= deg
        cell_para[5] *= deg
    return cell_para

def cellsize(group, dim=3):
    """
    Returns the number of duplicate atoms in the conventional lattice (in
    contrast to the primitive cell). Based on the type of cell centering (P,
    A, C, I, R, or F)

    Args:
        group: a Group object, or the space group number of the group
        dim: the dimension of the group (3 for space group, 2 for layer group,
            1 for Rod group, or 0 for 3D point group). If group is a Group
            object, dim will be overridden by group's value for dim
    
    Returns:
        an integer between 1 and 4, telling how many atoms are in the conventional cell
    """
    #Get the group dimension and number
    if type(group) == Group:
        num = group.number
        dim = group.dim
    elif type(int(group)) == int:
        num = group
    if dim == 0 or dim == 1:
        #Rod and point groups
        return 1
    elif dim == 2:
        #Layer groups
        if num in [10, 13, 18, 22, 26, 35, 36, 47, 48]:
            return 2
        else:
            return 1
    elif dim == 3:
        #space groups
        if num in [22, 42, 43, 69, 70, 196, 202, 203, 209, 210, 216, 219, 225, 226, 227, 228]:
            return 4 #F
        elif num in [146, 148, 155, 160, 161, 166, 167]:
            return 3 #R
        elif num in [5, 8, 9, 12, 15, 20, 21, 23, 24, 35, 36, 37,  38, 39, 40, 41,  44, 45, 46, 63, 64, 65, 66, 67, 68, 71, 72, 73, 74, 79, 80, 82, 87, 88, 97, 98, 107, 108, 109, 110, 119, 120, 121, 122, 139, 140, 141, 142, 197, 199, 204, 206, 211, 214, 217, 220, 229, 230]:
            return 2 #A, C, I
        else:
            return 1 #P

def find_short_dist(coor, lattice, tol, PBC=[1,1,1]):
    """
    Given a list of fractional coordinates, finds pairs which are closer
    together than tol, and builds the connectivity map

    Args:
        coor: a list of fractional 3-dimensional coordinates
        lattice: a matrix representing the crystal unit cell
        tol: the distance tolerance for pairing coordinates
        PBC: A periodic boundary condition list, where 1 means periodic, 0 means not periodic.
            Ex: [1,1,1] -> full 3d periodicity, [0,0,1] -> periodicity along the z axis
    
    Returns:
        pairs, graph: (pairs) is a list whose entries have the form [index1,
        index2, distance], where index1 and index2 correspond to the indices
        of a pair of points within the supplied list (coor). distance is the
        distance between the two points. (graph) is a connectivity map in the
        form of a list. Its first index represents a point within coor, and
        the second indices represent which point(s) it is connected to.
    """
    pairs=[]
    graph=[]
    for i in range(len(coor)):
        graph.append([])

    d = distance_matrix(coor, coor, lattice, PBC=PBC)
    ijs = np.where(d<= tol)
    for i in np.unique(ijs[0]):
        j = ijs[1][i]
        if j <= i: continue
        pairs.append([i, j, d[i][j]])

    pairs = np.array(pairs)
    if len(pairs) > 0:
        d_min = min(pairs[:,-1]) + 1e-3
        sequence = [pairs[:,-1] <= d_min]
        #Avoid Futurewarning
        #pairs1 = deepcopy(pairs)
        #pairs = pairs1[sequence]
        pairs = pairs[tuple(sequence)]
        for pair in pairs:
            pair0=int(pair[0])
            pair1=int(pair[1])
            graph[pair0].append(pair1)
            graph[pair1].append(pair0)

    return pairs, graph

def connected_components(graph):
    """
    Given an undirected graph (a 2d array of indices), return a set of
    connected components, each connected component being an (arbitrarily
    ordered) array of indices which are connected either directly or
    indirectly.

    Args:
        graph: a list reprenting the connections between points. The first index
            represents a point, and the 2nd indices represent the points to
            which the first point is connected. Can be generated by
            find_short_dist

    Returns:
        a list of connected components. The first index denotes a separate
        connected component. The second indices denote the points within the
        connected component which are connected to each other
    """
    def add_neighbors(el, seen=[]):
        """
        Find all elements which are connected to el. Return an array which
        includes these elements and el itself.
        """
        #seen stores already-visited indices
        if seen == []: seen = [el]
        #iterate through the neighbors (x) of el
        for x in graph[el]:
            if x not in seen:
                seen.append(x)
                #Recursively find neighbors of x
                add_neighbors(x, seen)
        return seen

    #Create a list of indices to iterate through
    unseen = list(range(len(graph)))
    sets = []
    i = 0
    while (unseen != []):
        #x is the index we are finding the connected component of
        x = unseen.pop()
        sets.append([])
        #Add neighbors of x to the current connected component
        for y in add_neighbors(x):
            sets[i].append(y)
            #Remove indices which have already been found
            if y in unseen: unseen.remove(y)
        i += 1
    return sets

def merge_coordinate(coor, lattice, group, tol):
    """
    Given a list of fractional coordinates, merges them within a given
    tolerance, and checks if the merged coordinates satisfy a Wyckoff
    position. Used for merging general Wyckoff positions into special Wyckoff
    positions within the random_crystal (and its derivative) classes.

    Args:
        coor: a list of fractional coordinates
        lattice: a 3x3 matrix representing the unit cell
        group: a pyxtal.symmetry.Group object
        tol: the cutoff distance for merging coordinates

    Returns:
        coor, index, point: (coor) is the new list of fractional coordinates after
        merging. index is a single index for the Wyckoff position within
        the sg. If no matching WP is found, returns False. point is a 3-vector;
        when plugged into the Wyckoff position, it will generate all the other
        points.
    """
    coor = np.array(coor)  
    #Get index of current Wyckoff position. If not one, return False
    index, point = check_wyckoff_position(coor, group)
    if index is False:
        return coor, False, None
    if point is None:
        printx("Error: Could not find generating point.", priority=1)
        printx("coordinates:")
        printx(str(coor))
        printx("Lattice: ")
        printx(str(lattice))
        printx("group: ")
        group.print_all()
        return coor, False, None
    PBC = group.PBC
    #Main loop for merging multiple times
    while True:
        #Check distances of current WP. If too small, merge
        dm = distance_matrix([coor[0]], coor, lattice, PBC=PBC)
        passed_distance_check = True
        x = np.argwhere(dm < tol)
        for y in x:
            #Ignore distance from atom to itself
            if y[0] == 0 and y[1] == 0:
                pass
            else:
                passed_distance_check = False
                break

        if passed_distance_check is False:
            mult1 = group[index].multiplicity
            #Find possible wp's to merge into
            possible = []
            for i, wp in enumerate(group):
                mult2 = wp.multiplicity
                #factor = mult2 / mult1
                if (mult2 < mult1) and (mult1 % mult2 == 0):
                    possible.append(i)
            if possible == []:
                return coor, False, None
            #Calculate minimum separation for each WP
            distances = []
            for i in possible:
                wp = group[i]
                projected_point = project_point(point, wp[0], lattice=lattice, PBC=PBC)
                new_coor = apply_ops(projected_point, wp)
                d = distance(point - projected_point, lattice, PBC=PBC)
                distances.append(np.min(d))
            #Choose wp with shortest translation for generating point
            tmpindex = np.argmin(distances)
            index = possible[tmpindex]
            newwp = group[index]
            projected_point = project_point(point, newwp[0], lattice=lattice, PBC=PBC)
            coor = apply_ops(projected_point, newwp)
            point = coor[0]
            index = newwp.index
        #Distances were not too small; return True
        else:
            return coor, index, point

def estimate_volume(numIons, species, factor=1.0):
    """
    Estimates the volume of a unit cell based on the number and types of ions.
    Assumes each atom takes up a sphere with radius equal to its covalent bond
    radius.

    Args:
        numIons: a list of the number of ions for each specie
        species: a corresponding list for the specie of each type of ion. Each
            element in the list should be a string for the atomic symbol
        factor: an optional factor to multiply the result by. Larger values
            allow more space between atoms
    
    Returns:
        a float value for the estimated volume
    """
    volume = 0
    for numIon, specie in zip(numIons, species):
        r = random.uniform(Element(specie).covalent_radius, Element(specie).vdw_radius)
        volume += numIon*4/3*pi*r**3
    return factor*volume

def generate_lattice(ltype, volume, minvec=tol_m, minangle=pi/6, max_ratio=10.0, maxattempts = 100, **kwargs):
    """
    Generates a lattice (3x3 matrix) according to the space group symmetry and
    number of atoms. If the spacegroup has centering, we will transform to
    conventional cell setting. If the generated lattice does not meet the
    minimum angle and vector requirements, we try to generate a new one, up to
    maxattempts times.

    Args:
        sg: International number of the space group
        volume: volume of the conventional unit cell
        minvec: minimum allowed lattice vector length (among a, b, and c)
        minangle: minimum allowed lattice angle (among alpha, beta, and gamma)
        max_ratio: largest allowed ratio of two lattice vector lengths
        maxattempts: the maximum number of attempts for generating a lattice
        kwargs: a dictionary of optional values. These include:
            'unique_axis': the axis ('a', 'b', or 'c') which is not symmetrically
                equivalent to the other two
            'min_l': the smallest allowed cell vector. The smallest vector must be larger
                than this.
            'mid_l': the second smallest allowed cell vector. The second smallest vector
                must be larger than this.
            'max_l': the third smallest allowed cell vector. The largest cell vector must
                be larger than this.

    Returns:
        a 3x3 matrix representing the lattice vectors of the unit cell. If
        generation fails, outputs a warning message and returns empty
    """
    maxangle = pi-minangle
    for n in range(maxattempts):
        #Triclinic
        #if sg <= 2:
        if ltype == "triclinic":
            #Derive lattice constants from a random matrix
            mat = random_shear_matrix(width=0.2)
            a, b, c, alpha, beta, gamma = matrix2para(mat)
            x = math.sqrt(1-math.cos(alpha)**2 - math.cos(beta)**2 - math.cos(gamma)**2 + 2*(math.cos(alpha)*math.cos(beta)*math.cos(gamma)))
            vec = random_vector()
            abc = volume/x
            xyz = vec[0]*vec[1]*vec[2]
            a = vec[0]*np.cbrt(abc)/np.cbrt(xyz)
            b = vec[1]*np.cbrt(abc)/np.cbrt(xyz)
            c = vec[2]*np.cbrt(abc)/np.cbrt(xyz)
        #Monoclinic
        #elif sg <= 15:
        elif ltype == "monoclinic":
            alpha, gamma  = pi/2, pi/2
            beta = gaussian(minangle, maxangle)
            x = math.sin(beta)
            vec = random_vector()
            xyz = vec[0]*vec[1]*vec[2]
            abc = volume/x
            a = vec[0]*np.cbrt(abc)/np.cbrt(xyz)
            b = vec[1]*np.cbrt(abc)/np.cbrt(xyz)
            c = vec[2]*np.cbrt(abc)/np.cbrt(xyz)
        #Orthorhombic
        #elif sg <= 74:
        elif ltype == "orthorhombic":
            alpha, beta, gamma = pi/2, pi/2, pi/2
            x = 1
            vec = random_vector()
            xyz = vec[0]*vec[1]*vec[2]
            abc = volume/x
            a = vec[0]*np.cbrt(abc)/np.cbrt(xyz)
            b = vec[1]*np.cbrt(abc)/np.cbrt(xyz)
            c = vec[2]*np.cbrt(abc)/np.cbrt(xyz)
        #Tetragonal
        #elif sg <= 142:
        elif ltype == "tetragonal":
            alpha, beta, gamma = pi/2, pi/2, pi/2
            x = 1
            vec = random_vector()
            c = vec[2]/(vec[0]*vec[1])*np.cbrt(volume/x)
            a = b = math.sqrt((volume/x)/c)
        #Trigonal/Rhombohedral/Hexagonal
        #elif sg <= 194:
        elif ltype in ["hexagonal", "trigonal", "rhombohedral"]:
            alpha, beta, gamma = pi/2, pi/2, pi/3*2
            x = math.sqrt(3.)/2.
            vec = random_vector()
            c = vec[2]/(vec[0]*vec[1])*np.cbrt(volume/x)
            a = b = math.sqrt((volume/x)/c)
        #Cubic
        #else:
        elif ltype == "cubic":
            alpha, beta, gamma = pi/2, pi/2, pi/2
            s = (volume) ** (1./3.)
            a, b, c = s, s, s
        #Check that lattice meets requirements
        maxvec = (a*b*c)/(minvec**2)

        #Define limits on cell dimensions
        if 'min_l' not in kwargs:
            min_l = minvec
        else:
            min_l = kwargs['min_l']
        if 'mid_l' not in kwargs:
            mid_l = min_l
        else:
            mid_l = kwargs['mid_l']
        if 'max_l' not in kwargs:
            max_l = mid_l
        else:
            max_l = kwargs['max_l']
        l_min = min(a, b, c)
        l_max = max(a, b, c)
        for x in (a, b, c):
            if x <= l_max and x >= l_min:
                l_mid = x
        if not (l_min >= min_l and l_mid >= mid_l and l_max >= max_l):
            continue

        if minvec < maxvec:
            #Check minimum Euclidean distances
            smallvec = min(a*math.cos(max(beta, gamma)), b*math.cos(max(alpha, gamma)), c*math.cos(max(alpha, beta)))
            if(a>minvec and b>minvec and c>minvec
            and a<maxvec and b<maxvec and c<maxvec
            and smallvec < minvec
            and alpha>minangle and beta>minangle and gamma>minangle
            and alpha<maxangle and beta<maxangle and gamma<maxangle
            and a/b<max_ratio and a/c<max_ratio and b/c<max_ratio
            and b/a<max_ratio and c/a<max_ratio and c/b<max_ratio):
                return np.array([a, b, c, alpha, beta, gamma])
    #If maxattempts tries have been made without success
    printx("Could not generate lattice after "+str(n+1)+" attempts for volume "+str(volume), priority=2)
    return

def generate_lattice_2D(ltype, volume, thickness=None, minvec=tol_m, minangle=pi/6, max_ratio=10.0, maxattempts = 100, **kwargs):
    """
    Generates a lattice (3x3 matrix) according to the spacegroup symmetry and
    number of atoms. If the layer group has centering, we will use the
    conventional cell setting. If the generated lattice does not meet the
    minimum angle and vector requirements, we try to generate a new one, up to
    maxattempts times.
    Note: The monoclinic layer groups have different unique axes. Groups 3-7
        have unique axis c, while 8-18 have unique axis a. We use non-periodic
        axis c for all layer groups.

    Args:
        num: International number of the space group
        volume: volume of the lattice
        thickness: 3rd-dimensional thickness of the unit cell. If set to None,
            a thickness is chosen automatically
        minvec: minimum allowed lattice vector length (among a, b, and c)
        minangle: minimum allowed lattice angle (among alpha, beta, and gamma)
        max_ratio: largest allowed ratio of two lattice vector lengths
        maxattempts: the maximum number of attempts for generating a lattice
        kwargs: a dictionary of optional values. These include:
            'unique_axis': the axis ('a', 'b', or 'c') which is not symmetrically
                equivalent to the other two
            'min_l': the smallest allowed cell vector. The smallest vector must be larger
                than this.
            'mid_l': the second smallest allowed cell vector. The second smallest vector
                must be larger than this.
            'max_l': the third smallest allowed cell vector. The largest cell vector must
                be larger than this.

    Returns:
        a 3x3 matrix representing the lattice vectors of the unit cell. If
        generation fails, outputs a warning message and returns empty
    """
    if 'unique_axis' not in kwargs:
        unique_axis = "c"
    else:
        unique_axis = kwargs['unique_axis']
    #Store the non-periodic axis
    NPA = 3
    #Set the unique axis for monoclinic cells
    #if num in range(3, 8): unique_axis = "c"
    #elif num in range(8, 19): unique_axis = "a"
    maxangle = pi-minangle
    for n in range(maxattempts):
        abc = np.ones([3])
        if thickness is None:
            v = random_vector()
            thickness1 = np.cbrt(volume)*(v[0]/(v[0]*v[1]*v[2]))
        else:
            thickness1 = thickness
        abc[NPA-1] = thickness1
        alpha, beta, gamma  = pi/2, pi/2, pi/2
        #Triclinic
        #if num <= 2:
        if ltype == "triclinic":
            mat = random_shear_matrix(width=0.2)
            a, b, c, alpha, beta, gamma = matrix2para(mat)
            x = math.sqrt(1-math.cos(alpha)**2 - math.cos(beta)**2 - math.cos(gamma)**2 + 2*(math.cos(alpha)*math.cos(beta)*math.cos(gamma)))
            abc[NPA-1] = abc[NPA-1]/x #scale thickness by outer product of vectors
            ab = volume/(abc[NPA-1]*x)
            ratio = a/b
            if NPA == 3:
                abc[0] = math.sqrt(ab*ratio)
                abc[1] = math.sqrt(ab/ratio)
            elif NPA == 2:
                abc[0] = math.sqrt(ab*ratio)
                abc[2] = math.sqrt(ab/ratio)
            elif NPA == 1:
                abc[1] = math.sqrt(ab*ratio)
                abc[2] = math.sqrt(ab/ratio)

        #Monoclinic
        #elif num <= 18:
        elif ltype == "monoclinic":
            a, b, c = random_vector()
            if unique_axis == "a":
                alpha = gaussian(minangle, maxangle)
                x = math.sin(alpha)
            elif unique_axis == "b":
                beta = gaussian(minangle, maxangle)
                x = math.sin(beta)
            elif unique_axis == "c":
                gamma = gaussian(minangle, maxangle)
                x = math.sin(gamma)
            ab = volume/(abc[NPA-1]*x)
            ratio = a/b
            if NPA == 3:
                abc[0] = math.sqrt(ab*ratio)
                abc[1] = math.sqrt(ab/ratio)
            elif NPA == 2:
                abc[0] = math.sqrt(ab*ratio)
                abc[2] = math.sqrt(ab/ratio)
            elif NPA == 1:
                abc[1] = math.sqrt(ab*ratio)
                abc[2] = math.sqrt(ab/ratio)

        #Orthorhombic
        #elif num <= 48:
        elif ltype == "orthorhombic":
            vec = random_vector()
            if NPA == 3:
                ratio = abs(vec[0]/vec[1]) #ratio a/b
                abc[1] = math.sqrt(volume/(thickness1*ratio))
                abc[0] = abc[1]* ratio
            elif NPA == 2:
                ratio = abs(vec[0]/vec[2]) #ratio a/b
                abc[2] = math.sqrt(volume/(thickness1*ratio))
                abc[0] = abc[2]* ratio
            elif NPA == 1:
                ratio = abs(vec[1]/vec[2]) #ratio a/b
                abc[2] = math.sqrt(volume/(thickness1*ratio))
                abc[1] = abc[2]* ratio

        #Tetragonal
        #elif num <= 64:
        elif ltype == "tetragonal":
            if NPA == 3:
                abc[0] = abc[1] = math.sqrt(volume/thickness1)
            elif NPA == 2:
                abc[0] = abc[1]
                abc[2] = volume/(abc[NPA-1]**2)
            elif NPA == 1:
                abc[1] = abc[0]
                abc[2] = volume/(abc[NPA-1]**2)

        #Trigonal/Hexagonal
        #elif num <= 80:
        elif ltype in ["hexagonal", "trigonal"]:
            gamma = pi/3*2
            x = math.sqrt(3.)/2.
            if NPA == 3:
                abc[0] = abc[1] = math.sqrt((volume/x)/abc[NPA-1])
            elif NPA == 2:
                abc[0] = abc[1]
                abc[2] = (volume/x)(thickness1**2)
            elif NPA == 1:
                abc[1] = abc[0]
                abc[2] = (volume/x)/(thickness1**2)

        para = np.array([abc[0], abc[1], abc[2], alpha, beta, gamma])

        a, b, c = abc[0], abc[1], abc[2]
        maxvec = (a*b*c)/(minvec**2)

        #Define limits on cell dimensions
        if 'min_l' not in kwargs:
            min_l = minvec
        else:
            min_l = kwargs['min_l']
        if 'mid_l' not in kwargs:
            mid_l = min_l
        else:
            mid_l = kwargs['mid_l']
        if 'max_l' not in kwargs:
            max_l = mid_l
        else:
            max_l = kwargs['max_l']
        l_min = min(a, b, c)
        l_max = max(a, b, c)
        for x in (a, b, c):
            if x <= l_max and x >= l_min:
                l_mid = x
        if not (l_min >= min_l and l_mid >= mid_l and l_max >= max_l):
            continue

        if minvec < maxvec:
            smallvec = min(a*math.cos(max(beta, gamma)), b*math.cos(max(alpha, gamma)), c*math.cos(max(alpha, beta)))
            if(a>minvec and b>minvec and c>minvec
            and a<maxvec and b<maxvec and c<maxvec
            and smallvec < minvec
            and alpha>minangle and beta>minangle and gamma>minangle
            and alpha<maxangle and beta<maxangle and gamma<maxangle
            and a/b<max_ratio and a/c<max_ratio and b/c<max_ratio
            and b/a<max_ratio and c/a<max_ratio and c/b<max_ratio):
                return para

    #If maxattempts tries have been made without success
    printx("Could not generate lattice after "+str(n+1)+" attempts for volume "+str(volume), priority=2)
    return

def generate_lattice_1D(ltype, volume, area=None, minvec=tol_m, minangle=pi/6, max_ratio=10.0, maxattempts = 100, **kwargs):
    """
    Generates a lattice (3x3 matrix) according to the spacegroup symmetry and
    number of atoms. If the spacegroup has centering, we will transform to
    conventional cell setting. If the generated lattice does not meet the
    minimum angle and vector requirements, we try to generate a new one, up to
    maxattempts times.
    Note: The monoclinic Rod groups have different unique axes. Groups 3-7
        have unique axis a, while 8-12 have unique axis c. We use periodic
        axis c for all Rod groups.

    Args:
        num: number of the Rod group
        volume: volume of the lattice
        area: cross-sectional area of the unit cell in Angstroms squared. If
            set to None, a value is chosen automatically
        minvec: minimum allowed lattice vector length (among a, b, and c)
        minangle: minimum allowed lattice angle (among alpha, beta, and gamma)
        max_ratio: largest allowed ratio of two lattice vector lengths
        maxattempts: the maximum number of attempts for generating a lattice
        kwargs: a dictionary of optional values. These include:
            'unique_axis': the axis ('a', 'b', or 'c') which is not symmetrically
                equivalent to the other two
            'min_l': the smallest allowed cell vector. The smallest vector must be larger
                than this.
            'mid_l': the second smallest allowed cell vector. The second smallest vector
                must be larger than this.
            'max_l': the third smallest allowed cell vector. The largest cell vector must
                be larger than this.

    Returns:
        a 3x3 matrix representing the lattice vectors of the unit cell. If
        generation fails, outputs a warning message and returns empty
    """
    try:
        unique_axis = kwargs['unique_axis']
    except:
        unique_axis = "a"
    #Store the periodic axis
    PA = 3
    #Set the unique axis for monoclinic cells
    #if num in range(3, 8): unique_axis = "a"
    #elif num in range(8, 13): unique_axis = "c"
    maxangle = pi-minangle
    for n in range(maxattempts):
        abc = np.ones([3])
        if area is None:
            v = random_vector()
            thickness1 = np.cbrt(volume)*(v[0]/(v[0]*v[1]*v[2]))
        else:
            thickness1 = volume/area
        abc[PA-1] = thickness1
        alpha, beta, gamma  = pi/2, pi/2, pi/2
        #Triclinic
        #if num <= 2:
        if ltype == "triclinic":
            mat = random_shear_matrix(width=0.2)
            a, b, c, alpha, beta, gamma = matrix2para(mat)
            x = math.sqrt(1-math.cos(alpha)**2 - math.cos(beta)**2 - math.cos(gamma)**2 + 2*(math.cos(alpha)*math.cos(beta)*math.cos(gamma)))
            abc[PA-1] = abc[PA-1]/x #scale thickness by outer product of vectors
            ab = volume/(abc[PA-1]*x)
            ratio = a/b
            if PA == 3:
                abc[0] = math.sqrt(ab*ratio)
                abc[1] = math.sqrt(ab/ratio)
            elif PA == 2:
                abc[0] = math.sqrt(ab*ratio)
                abc[2] = math.sqrt(ab/ratio)
            elif PA == 1:
                abc[1] = math.sqrt(ab*ratio)
                abc[2] = math.sqrt(ab/ratio)

        #Monoclinic
        #elif num <= 12:
        elif ltype == "monoclinic":
            a, b, c = random_vector()
            if unique_axis == "a":
                alhpa = gaussian(minangle, maxangle)
                x = math.sin(alpha)
            elif unique_axis == "b":
                beta = gaussian(minangle, maxangle)
                x = math.sin(beta)
            elif unique_axis == "c":
                gamma = gaussian(minangle, maxangle)
                x = math.sin(gamma)
            ab = volume/(abc[PA-1]*x)
            ratio = a/b
            if PA == 3:
                abc[0] = math.sqrt(ab*ratio)
                abc[1] = math.sqrt(ab/ratio)
            elif PA == 2:
                abc[0] = math.sqrt(ab*ratio)
                abc[2] = math.sqrt(ab/ratio)
            elif PA == 1:
                abc[1] = math.sqrt(ab*ratio)
                abc[2] = math.sqrt(ab/ratio)

        #Orthorhombic
        #lif num <= 22:
        elif ltype == "orthorhombic":
            vec = random_vector()
            if PA == 3:
                ratio = abs(vec[0]/vec[1]) #ratio a/b
                abc[1] = math.sqrt(volume/(thickness1*ratio))
                abc[0] = abc[1]* ratio
            elif PA == 2:
                ratio = abs(vec[0]/vec[2]) #ratio a/b
                abc[2] = math.sqrt(volume/(thickness1*ratio))
                abc[0] = abc[2]* ratio
            elif PA == 1:
                ratio = abs(vec[1]/vec[2]) #ratio a/b
                abc[2] = math.sqrt(volume/(thickness1*ratio))
                abc[1] = abc[2]* ratio

        #Tetragonal
        #elif num <= 41:
        elif ltype == "tetragonal":
            if PA == 3:
                abc[0] = abc[1] = math.sqrt(volume/thickness1)
            elif PA == 2:
                abc[0] = abc[1]
                abc[2] = volume/(abc[PA-1]**2)
            elif PA == 1:
                abc[1] = abc[0]
                abc[2] = volume/(abc[PA-1]**2)

        #Trigonal/Rhombohedral/Hexagonal
        #elif num <= 75:
        elif ltype in ["hexagonal", "trigonal"]:
            gamma = pi/3*2
            x = math.sqrt(3.)/2.
            if PA == 3:
                abc[0] = abc[1] = math.sqrt((volume/x)/abc[PA-1])
            elif PA == 2:
                abc[0] = abc[1]
                abc[2] = (volume/x)(thickness1**2)
            elif PA == 1:
                abc[1] = abc[0]
                abc[2] = (volume/x)/(thickness1**2)

        para = np.array([abc[0], abc[1], abc[2], alpha, beta, gamma])

        a, b, c = abc[0], abc[1], abc[2]
        maxvec = (a*b*c)/(minvec**2)

        #Define limits on cell dimensions
        if 'min_l' not in kwargs:
            min_l = minvec
        else:
            min_l = kwargs['min_l']
        if 'mid_l' not in kwargs:
            mid_l = min_l
        else:
            mid_l = kwargs['mid_l']
        if 'max_l' not in kwargs:
            max_l = mid_l
        else:
            max_l = kwargs['max_l']
        l_min = min(a, b, c)
        l_max = max(a, b, c)
        for x in (a, b, c):
            if x <= l_max and x >= l_min:
                l_mid = x
        if not (l_min >= min_l and l_mid >= mid_l and l_max >= max_l):
            continue

        if minvec < maxvec:
            smallvec = min(a*math.cos(max(beta, gamma)), b*math.cos(max(alpha, gamma)), c*math.cos(max(alpha, beta)))
            if(a>minvec and b>minvec and c>minvec
            and a<maxvec and b<maxvec and c<maxvec
            and smallvec < minvec
            and alpha>minangle and beta>minangle and gamma>minangle
            and alpha<maxangle and beta<maxangle and gamma<maxangle
            and a/b<max_ratio and a/c<max_ratio and b/c<max_ratio
            and b/a<max_ratio and c/a<max_ratio and c/b<max_ratio):
                return para

    #If maxattempts tries have been made without success
    printx("Could not generate lattice after "+str(n+1)+" attempts for volume "+str(volume), priority=2)
    return

def generate_lattice_0D(ltype, volume, area=None, minvec=tol_m, max_ratio=10.0, maxattempts = 100, **kwargs):
    """
    Generates a lattice (3x3 matrix) according to the spacegroup symmetry and
    number of atoms. If the spacegroup has centering, we will transform to
    conventional cell setting. If the generated lattice does not meet the
    minimum angle and vector requirements, we try to generate a new one, up to
    maxattempts times.
    Note: The monoclinic Rod groups have different unique axes. Groups 3-7
        have unique axis a, while 8-12 have unique axis c. We use periodic
        axis c for all Rod groups.

    Args:
        num: number of the Rod group
        volume: volume of the lattice
        area: cross-sectional area of the unit cell in Angstroms squared. If
            set to None, a value is chosen automatically
        minvec: minimum allowed lattice vector length (among a, b, and c)
        max_ratio: largest allowed ratio of two lattice vector lengths
        maxattempts: the maximum number of attempts for generating a lattice
        kwargs: a dictionary of optional values. Only used for ellipsoidal
            lattices, which pass the value to generate_lattice. Possible values include:
            'unique_axis': the axis ('a', 'b', or 'c') which is not symmetrically
                equivalent to the other two
            'min_l': the smallest allowed cell vector. The smallest vector must be larger
                than this.
            'mid_l': the second smallest allowed cell vector. The second smallest vector
                must be larger than this.
            'max_l': the third smallest allowed cell vector. The largest cell vector must
                be larger than this.

    Returns:
        a 3x3 matrix representing the lattice vectors of the unit cell. If
        generation fails, outputs a warning message and returns empty
    """
    if ltype == "spherical":
        #Use a cubic lattice with altered volume
        a = b = c = np.cbrt((3 * volume)/(4 * pi))
        alpha = beta = gamma = 0.5 * pi
        if a < minvec:
            printx("Could not generate spherical lattice; volume too small compared to minvec", priority=2)
            return
        return np.array([a, b, c, alpha, beta, gamma])
    if ltype == "ellipsoidal":
        #Use a matrix with only on-diagonal elements, with a = b
        alpha, beta, gamma = pi/2, pi/2, pi/2
        x = (4./3.)*pi
        for numattempts in range(maxattempts):
            vec = random_vector()
            c = vec[2]/(vec[0]*vec[1])*np.cbrt(volume/x)
            a = b = math.sqrt((volume/x)/c)
            if (a / c < 10.) and (c / a < 10.):
                return np.array([a, b, c, alpha, beta, gamma])
        return

def choose_wyckoff(group, number):
    """
    Choose a Wyckoff position to fill based on the current number of atoms
    needed to be placed within a unit cell
    Rules:
        1) The new position's multiplicity is equal/less than (number).
        2) We prefer positions with large multiplicity.

    Args:
        group: a pyxtal.symmetry.Group object
        number: the number of atoms still needed in the unit cell

    Returns:
        a single index for the Wyckoff position. If no position is found,
        returns False
    """
    wyckoffs_organized = group.wyckoffs_organized
    
    if random.uniform(0,1)>0.5: #choose from high to low
        for wyckoff in wyckoffs_organized:
            if len(wyckoff[0]) <= number:
                return random.choice(wyckoff)
        return False
    else:
        good_wyckoff = []
        for wyckoff in wyckoffs_organized:
            if len(wyckoff[0]) <= number:
                for w in wyckoff:
                    good_wyckoff.append(w)
        if len(good_wyckoff) > 0:
            return random.choice(good_wyckoff)
        else:
            return False

class Wyckoff_site():
    """
    Class for storing atomic Wyckoff positions with a single coordinate.
    
    Args:
        wp: a Wyckoff_position object
        coordinate: a fractional 3-vector for the generating atom's coordinate
        specie: an Element, element name or symbol, or atomic number of the atom
    """
    def __init__(self, wp, coordinate, specie):
        if type(wp) == Wyckoff_position:
            self.wp = wp
        else:
            printx("Error: wp must be a Wyckoff_position object.", priority=1)
            return
        self.position = np.array(coordinate)
        self.specie = Element(specie).short_name
        self.multiplicity = wp.multiplicity
        self.PBC = wp.PBC
        self.coords = apply_ops(self.position, self.wp)

    def __str__(self):
        return self.specie+": "+str(self.position)+" "+str(self.wp.multiplicity)+self.wp.letter+", site symmetry "+ss_string_from_ops(self.wp.symmetry_m[0], self.wp.number, dim=self.wp.dim)

    def __repr__(self):
        return str(self)

def check_wyckoff_sites(ws1, ws2, lattice, tm=Tol_matrix(prototype="atomic"), same_group=True):
    """
    Given two Wyckoff sites, checks the inter-atomic distances between them.

    Args:
        ws1: a Wyckoff_site object
        ws2: a different Wyckoff_site object (will always return False if
            two identical WS's are provided)
        lattice: a 3x3 cell matrix
        same_group: whether or not the two WS's are in the same structure.
            Default value True reduces the calculation cost

    Returns:
        True if all distances are greater than the allowed tolerances.
        False if any distance is smaller than the allowed tolerance
    """
    #Ensure the PBC values are valid
    if ws1.PBC != ws2.PBC:
        printx("Error: PBC values do not match between Wyckoff sites")
        return
    #Get tolerance
    tol = tm.get_tol(ws1.specie, ws2.specie)
    #Symmetry shortcut method: check only some atoms
    if same_group is True:
        #We can either check one atom in WS1 against all WS2, or vice-versa
        #Check which option is faster
        if ws1.multiplicity > ws2.multiplicity:
            coords1 = [ws1.coords[0]]
            coords2 = ws2.coords
        else:
            coords1 = [ws2.coords[0]]
            coords2 = ws1.coords
        #Calculate distances
        dm = distance_matrix(coords1, coords2, lattice, PBC=ws1.PBC)
        #Check if any distances are less than the tolerance
        if (dm < tol).any():
            return False
        else:
            return True
    #No symmetry method: check all atomic pairs
    else:
        dm = distance_matrix(ws1.coords, ws2.coords, lattice, PBC=ws1.PBC)
        #Check if any distances are less than the tolerance
        if (dm < tol).any():
            return False
        else:
            return True

def verify_distances(coordinates, species, lattice, factor=1.0, PBC=[1,1,1]):
    """
    Checks the inter-atomic distance between all pairs of atoms in a crystal.

    Args:
        coordinates: a 1x3 list of fractional coordinates
        species: a list of atomic symbols for each coordinate
        lattice: a 3x3 matrix representing the lattice vectors of the unit cell
        factor: a tolerance factor for checking distances. A larger value means
            atoms must be farther apart
        PBC: A periodic boundary condition list, where 1 means periodic, 0 means not periodic.
            Ex: [1,1,1] -> full 3d periodicity, [0,0,1] -> periodicity along the z axis
    
    Returns:
        True if no atoms are too close together, False if any pair is too close
    """
    for i, c1 in enumerate(coordinates):
        specie1 = species[i]
        for j, c2 in enumerate(coordinates):
            if j > i:
                specie2 = species[j]
                diff = np.array(c2) - np.array(c1)
                d_min = distance(diff, lattice, PBC=PBC)
                tol = factor*0.5*(Element(specie1).covalent_radius + Element(specie2).covalent_radius)
                if d_min < tol:
                    return False
    return True

class Lattice():
    """
    Class for storing and generating crystal lattices. Allows for specification
    of constraint values. Lattice types include triclinic, monoclinic, orthorhombic,
    tetragonal, trigonal, hexagonal, cubic, spherical, and ellipsoidal. The last
    two are used for generating point group structures, and do not actually represent
    a parallelepiped lattice.

    Args:
        ltype: a string representing the type of lattice (from the above list)
        volume: the volume, in Angstroms cubed, of the lattice
        PBC: A periodic boundary condition list, where 1 means periodic, 0 means not periodic.
            Ex: [1,1,1] -> full 3d periodicity, [0,0,1] -> periodicity along the z axis
        kwargs: various values which may be defined. If none are defined, random ones
            will be generated. Values will be passed to generate_lattice. Options include:
            area: The cross-sectional area (in Angstroms squared). Only used to generate 1D
                crystals
            thickness: The unit cell's non-periodic thickness (in Angstroms). Only used to
                generate 2D crystals
            unique_axis: The unique axis for certain symmetry (and especially layer) groups.
                Because the symmetry operations are not also transformed, you should use the
                default values for random crystal generation
            random: If False, keeps the stored values for the lattice geometry even upon applying
                reset_matrix. To alter the matrix, use set_matrix() or set_para
            'unique_axis': the axis ('a', 'b', or 'c') which is not symmetrically
                equivalent to the other two
            'min_l': the smallest allowed cell vector. The smallest vector must be larger
                than this.
            'mid_l': the second smallest allowed cell vector. The second smallest vector
                must be larger than this.
            'max_l': the third smallest allowed cell vector. The largest cell vector must
                be larger than this.
            'allow_volume_reset': a bool stating whether or not the volume should be reset during
                each crystal generation attempt
    """
    def __init__(self, ltype, volume, PBC=[1,1,1], **kwargs):
        #Set required parameters
        if ltype in ["triclinic", "monoclinic", "orthorhombic", "tetragonal",
                "trigonal", "hexagonal", "cubic", "spherical", "ellipsoidal"]:
            self.ltype = ltype
        elif ltype == None:
            self.ltype = "triclinic"
        else:
            printx("Error: Invalid lattice type.", priority=1)
            return
        self.volume = float(volume)
        self.PBC = PBC
        self.dim = sum(PBC)
        self.kwargs = {}
        self.random = True
        #Set optional values
        self.allow_volume_reset = True
        for key, value in kwargs.items():
            if key in ["area", "thickness", "unique_axis", "random", "min_l", "mid_l", "max_l"]:
                setattr(self, key, value)
                self.kwargs[key] = value
                if key == "allow_volume_reset":
                    if value == False:
                        self.allow_volume_reset = False
        try:
            self.unique_axis
        except:
            self.unique_axis = "c"
        #Set stress normalization info
        if self.ltype == "triclinic":
            self.stress_normalization_matrix = np.array([[1,1,1],[1,1,1],[1,1,1]])
        elif self.ltype == "monoclinic":
            if self.PBC == [1,1,1]:
                self.stress_normalization_matrix = np.array([[1,0,0],[0,1,0],[1,0,1]])
            else:
                if self.unique_axis == "a":
                    self.stress_normalization_matrix = np.array([[1,0,0],[0,1,0],[0,1,1]])
                elif self.unique_axis == "b":
                    self.stress_normalization_matrix = np.array([[1,0,0],[0,1,0],[1,0,1]])
                elif self.unique_axis == "c":
                    self.stress_normalization_matrix = np.array([[1,0,0],[1,1,0],[0,0,1]])
        elif self.ltype in ["orthorhombic", "tetragonal", "trigonal", "hexagonal", "cubic"]:
            self.stress_normalization_matrix = np.array([[1,0,0],[0,1,0],[0,0,1]])
        elif self.ltype in ["spherical", "ellipsoidal"]:
            self.stress_normalization_matrix = np.array([[0,0,0],[0,0,0],[0,0,0]])
        #Set info for on-diagonal stress symmetrization
        if self.ltype in ["tetragonal", "trigonal", "hexagonal", "rhombohedral"]:
            self.stress_indices = [(0,0),(1,1)]
        elif self.ltype == "cubic":
            self.stress_indices = [(0,0),(1,1),(2,2)]
        else:
            self.stress_indices = []
        #Set values for the matrix
        self.reset_matrix()

    def generate_para(self):
        if self.dim == 3:
            return generate_lattice(self.ltype, self.volume, **self.kwargs)
        elif self.dim == 2:
            return generate_lattice_2D(self.ltype, self.volume, **self.kwargs)
        elif self.dim == 1:
            return generate_lattice_1D(self.ltype, self.volume, **self.kwargs)
        elif self.dim == 0:
            return generate_lattice_0D(self.ltype, self.volume, **self.kwargs)

    def generate_matrix(self):
        """
        Generates a 3x3 matrix for the lattice based on the lattice type and volume
        """
        #Try multiple times in case of failure
        for i in range(10):
            para = self.generate_para()
            if para is not None:
                return para2matrix(para)
        printx("Error: Could not generate lattice matrix.", priority=1)
        return

    def get_matrix(self):
        """
        Returns a 3x3 numpy array representing the lattice vectors.
        """
        try:
            return self.matrix
        except:
            printx("Error: Lattice matrix undefined.", priority=1)
            return

    def get_para(self):
        """
        Returns a tuple of lattice parameters.
        """
        return (self.a, self.b, self.c, self.alpha, self.beta, self.gamma)

    def set_matrix(self, matrix=None):
        if matrix != None:
            m = np.array(matrix)
            if np.shape(m) == (3,3):
                self.matrix = m
            else:
                printx("Error: matrix must be a 3x3 numpy array or list", priority=1)
        elif matrix == None:
            self.reset_matrix()
        para = matrix2para(self.matrix)
        self.a, self.b, self.c, self.alpha, self.beta, self.gamma = para

    def set_para(self, para=None, radians=False):
        if para is not None:
            if radians is False:
                para[3] *= rad
                para[4] *= rad
                para[5] *= rad
            self.set_matrix(para2matrix(para))
        else:
            self.set_matrix()

    def reset_matrix(self):
        if self.random is True:
            for i in range(3):
                m = self.generate_matrix()
                if m is not None:
                    self.matrix = m
                    [a, b, c, alpha, beta, gamma] = matrix2para(self.matrix)
                    self.a = a
                    self.b = b
                    self.c = c
                    self.alpha = alpha
                    self.beta = beta
                    self.gamma = gamma
                    break

    def set_volume(self, volume):
        if self.allow_volume_reset is True:
            self.volume = volume

    def generate_point(self):
        point = np.random.random(3)
        if self.ltype in ["spherical", "ellipsoidal"]:
            #Choose a point within an octant of the unit sphere
            while dsquared(point) > 1:
                point = np.random.random(3)
            #Randomly flip some coordinates
            for index, x in enumerate(point):
                #Scale the point by the max radius
                if random.uniform(0,1) < 0.5:
                    point[index] *= -1
        else:
            for i, a in enumerate(self.PBC):
                if not a:
                    if self.ltype in ["hexagonal", "trigonal", "rhombohedral"]:
                        point[i] *= 1./math.sqrt(3.)
                    else:
                        point[i] -= 0.5
        return point

    @classmethod
    def from_para(self, a, b, c, alpha, beta, gamma, ltype="triclinic", radians=False, PBC=[1,1,1], **kwargs):
        """
        Creates a Lattice object from 6 lattice parameters. Additional keyword arguments
        are available. Unless specified by the keyword random=True, does not create a
        new matrix upon calling reset_matrix. This allows for generation of random
        crystals with a specific choice of unit cell.

        Args:
            a, b, c: The length (in Angstroms) of the unit cell vectors
            alpha: the angle (in degrees) between the b and c vectors
            beta: the angle (in degrees) between the a and c vectors
            gamma: the angle (in degrees) between the a and b vectors
            ltype: the lattice type ("cubic, tetragonal, etc."). Also available are "spherical",
                which confines generated points to lie within a sphere, and "ellipsoidal", which
                confines generated points to lie within an ellipse (oriented about the z axis)
            radians: whether or not to use radians (instead of degrees) for the lattice angles
            PBC: A periodic boundary condition list, where 1 means periodic, 0 means not periodic.
                Ex: [1,1,1] -> full 3d periodicity, [0,0,1] -> periodicity along the z axis
            kwargs: various values which may be defined. If none are defined, random ones
                will be generated. Values will be passed to generate_lattice. Options include:
                area: The cross-sectional area (in Angstroms squared). Only used to generate 1D
                    crystals
                thickness: The unit cell's non-periodic thickness (in Angstroms). Only used to
                    generate 2D crystals
                unique_axis: The unique axis for certain symmetry (and especially layer) groups.
                    Because the symmetry operations are not also transformed, you should use the
                    default values for random crystal generation
                random: If False, keeps the stored values for the lattice geometry even upon applying
                    reset_matrix. To alter the matrix, use set_matrix() or set_para
                'unique_axis': the axis ('a', 'b', or 'c') which is not symmetrically
                    equivalent to the other two
                'min_l': the smallest allowed cell vector. The smallest vector must be larger
                    than this.
                'mid_l': the second smallest allowed cell vector. The second smallest vector
                    must be larger than this.
                'max_l': the third smallest allowed cell vector. The largest cell vector must
                    be larger than this.

        Returns:
            a Lattice object with the specified parameters
        """
        try:
            cell_matrix = para2matrix((a,b,c,alpha,beta,gamma), radians=radians)
        except:
            printx("Error: invalid cell parameters for lattice.", priority=1)
            return
        volume = np.linalg.det(cell_matrix)
        #Initialize a Lattice instance
        l = Lattice(ltype, volume, PBC=PBC, **kwargs)
        l.a = a
        l.b = b
        l.c = c
        l.alpha = alpha*rad
        l.beta = beta*rad
        l.gamma = gamma*rad
        l.matrix = cell_matrix
        l.ltype = ltype
        l.volume = volume
        l.random = False
        l.allow_volume_reset = False
        return l

    @classmethod
    def from_matrix(self, matrix, ltype="triclinic", PBC=[1,1,1], **kwargs):
        """
        Creates a Lattice object from a 3x3 cell matrix. Additional keyword arguments
        are available. Unless specified by the keyword random=True, does not create a
        new matrix upon calling reset_matrix. This allows for generation of random
        crystals with a specific choice of unit cell.

        Args:
            matrix: a 3x3 real matrix (numpy array or nested list) describing the cell vectors
            ltype: the lattice type ("cubic, tetragonal, etc."). Also available are "spherical",
                which confines generated points to lie within a sphere, and "ellipsoidal", which
                confines generated points to lie within an ellipsoid (oriented about the z axis)
            PBC: A periodic boundary condition list, where 1 means periodic, 0 means not periodic.
                Ex: [1,1,1] -> full 3d periodicity, [0,0,1] -> periodicity along the z axis
            kwargs: various values which may be defined. If none are defined, random ones
                will be generated. Values will be passed to generate_lattice. Options include:
                area: The cross-sectional area (in Angstroms squared). Only used to generate 1D
                    crystals
                thickness: The unit cell's non-periodic thickness (in Angstroms). Only used to
                    generate 2D crystals
                unique_axis: The unique axis for certain symmetry (and especially layer) groups.
                    Because the symmetry operations are not also transformed, you should use the
                    default values for random crystal generation
                random: If False, keeps the stored values for the lattice geometry even upon applying
                    reset_matrix. To alter the matrix, use set_matrix() or set_para
                'unique_axis': the axis ('a', 'b', or 'c') which is not symmetrically
                    equivalent to the other two
                'min_l': the smallest allowed cell vector. The smallest vector must be larger
                    than this.
                'mid_l': the second smallest allowed cell vector. The second smallest vector
                    must be larger than this.
                'max_l': the third smallest allowed cell vector. The largest cell vector must
                    be larger than this.

        Returns:
            a Lattice object with the specified parameters
        """
        m = np.array(matrix)
        if np.shape(m) != (3,3):
            printx("Error: Lattice matrix must be 3x3", priority=1)
            return
        [a, b, c, alpha, beta, gamma] = matrix2para(m)
        volume = np.linalg.det(m)
        #Initialize a Lattice instance
        l = Lattice(ltype, volume, PBC=PBC, **kwargs)
        l.a = a
        l.b = b
        l.c = c
        l.alpha = alpha
        l.beta = beta
        l.gamma = gamma
        l.matrix = m
        l.ltype = ltype
        l.volume = volume
        l.random = False
        l.allow_volume_reset = False
        return l

    def __str__(self):
        s = str(self.ltype)+" lattice:"
        s += "\na: "+str(self.a)
        s += "\nb: "+str(self.b)
        s += "\nc: "+str(self.c)
        s += "\nalpha: "+str(self.alpha*deg)
        s += "\nbeta: "+str(self.beta*deg)
        s += "\ngamma: "+str(self.gamma*deg)
        return s

    def __repr__(self):
        return str(self)

class random_crystal():
    """
    Class for storing and generating atomic crystals based on symmetry
    constraints. Given a spacegroup, list of atomic symbols, the stoichiometry,
    and a volume factor, generates a random crystal consistent with the
    spacegroup's symmetry. This crystal is stored as a pymatgen struct via
    self.struct
    
    Args:
        group: the international spacegroup number, or a Group object
        species: a list of atomic symbols for each ion type
        numIons: a list of the number of each type of atom within the
            primitive cell (NOT the conventional cell)
        tm: the Tol_matrix object used to generate the crystal
        factor: a volume factor used to generate a larger or smaller
            unit cell. Increasing this gives extra space between atoms
        lattice: an optional Lattice object to use for the unit cell
    """
    def init_common(self, species, numIons, factor, group, lattice, tm):
        """
        Common init functionality for 0D-3D cases of random_crystal.
        """
        self.valid = False
        #Check that numIons are integers greater than 0
        for num in numIons:
            if int(num) != num or num < 1:
                printx("Error: stoichiometry must consist of integers greater than 0.", priority=1)
                return False
        if type(group) == Group:
            self.group = group
            """A pyxtal.symmetry.Group object storing information about the space/layer
            /Rod/point group, and its Wyckoff positions."""
        else:
            self.group = Group(group, dim=self.dim)
        self.number = self.group.number
        """The international group number of the crystal:
        1-230 for 3D space groups
        1-80 for 2D layer groups
        1-75 for 1D Rod groups
        1-32 for crystallographic point groups
        None otherwise
        """
        self.numattempts = 0
        """The number of attempts needed to generate the crystal. Has a maximum
        value of max1*max2*max3."""
        numIons = np.array(numIons) #must convert it to np.array
        self.factor = factor
        """The supplied volume factor for the unit cell."""
        self.numIons0 = numIons
        """The number of each type of atom in the PRIMITIVE cell."""
        self.numIons = self.numIons0 * cellsize(self.group)
        """The number of each type of atom in the CONVENTIONAL cell."""
        self.species = species
        """A list of atomic symbols for the types of atoms in the crystal."""
        self.Msgs()
        """A list of warning messages to use during generation."""
        if lattice is not None:
            #Use the provided lattice
            self.lattice = lattice
            self.volume = lattice.volume
            #Make sure the custom lattice PBC axes are correct.
            if lattice.PBC != self.PBC:
                self.lattice.PBC = self.PBC
                printx("\n  Warning: converting custom lattice PBC to "+str(self.PBC))
        elif lattice == None:
            #Determine the unique axis
            if self.dim == 2:
                if self.number in range(3, 8):
                    unique_axis = "c"
                else:
                    unique_axis = "a"
            elif self.dim == 1:
                if self.number in range(3, 8):
                    unique_axis = "a"
                else:
                    unique_axis = "c"
            else:
                unique_axis = "c"
            #Generate a Lattice instance
            self.volume = estimate_volume(self.numIons, self.species, self.factor)
            """The volume of the generated unit cell."""
            if self.dim == 3 or self.dim == 0:
                self.lattice = Lattice(self.group.lattice_type, self.volume, PBC=self.PBC, unique_axis=unique_axis)
            elif self.dim == 2:
                self.lattice = Lattice(self.group.lattice_type, self.volume, PBC=self.PBC, unique_axis=unique_axis, thickness=self.thickness)
            elif self.dim == 1:
                self.lattice = Lattice(self.group.lattice_type, self.volume, PBC=self.PBC, unique_axis=unique_axis, area=self.area)
        #Set the tolerance matrix
        if type(tm) == Tol_matrix:
            self.tol_matrix = tm
            """The Tol_matrix object used for checking inter-atomic distances within the structure."""
        else:
            try:
                self.tol_matrix = Tol_matrix(prototype=tm)
            except:
                printx("Error: tm must either be a Tol_matrix object or a prototype string for initializing one.", priority=1)
                self.valid = False
                self.struct = None
                return
        #Generate the crystal
        self.generate_crystal()

    def __init__(self, group, species, numIons, factor, lattice=None, tm=Tol_matrix(prototype="atomic")):
        self.dim = 3
        """The number of periodic dimensions of the crystal"""
        if type(group) != Group:
            group = Group(group, self.dim)
        self.sg = group.number
        """The international spacegroup number of the crystal."""
        self.PBC = [1,1,1]
        """The periodic boundary axes of the crystal"""
        self.init_common(species, numIons, factor, group, lattice, tm)

    def Msgs(self):
        """
        Define a set of error and warning message if generation fails.

        Returns:
            nothing
        """
        self.Msg1 = 'Error: the stoichiometry is incompatible with the wyckoff sites choice'
        self.Msg2 = 'Error: failed in the cycle of generating structures'
        self.Msg3 = 'Warning: failed in the cycle of adding species'
        self.Msg4 = 'Warning: failed in the cycle of choosing wyckoff sites'
        self.Msg5 = 'Finishing: added the specie'
        self.Msg6 = 'Finishing: added the whole structure'
        self.Msg7 = 'Error: invalid paramaters for initialization'

    def check_compatible(group, numIons):
        """
        Checks if the number of atoms is compatible with the Wyckoff
        positions. Considers the number of degrees of freedom for each Wyckoff
        position, and makes sure at least one valid combination of WP's exists.
        """
        #Store whether or not at least one degree of freedom exists
        has_freedom = False
        #Store the wp's already used that don't have any freedom
        used_indices = []
        #Loop over species
        for numIon in numIons:
            #Get lists of multiplicity, maxn and freedom
            l_mult0 = []
            l_maxn0 = []
            l_free0 = []
            indices0 = []
            for i_wp, wp in enumerate(group):
                indices0.append(i_wp)
                l_mult0.append(len(wp))
                l_maxn0.append(numIon // len(wp))
                if np.allclose(wp[0].rotation_matrix, np.zeros([3,3])):
                    l_free0.append(False)
                else:
                    l_free0.append(True)
            #Remove redundant multiplicities:
            l_mult = []
            l_maxn = []
            l_free = []
            indices = []
            for mult, maxn, free, i_wp in zip(l_mult0, l_maxn0, l_free0, indices0):
                if free is True:
                    if mult not in l_mult:
                        l_mult.append(mult)
                        l_maxn.append(maxn)
                        l_free.append(True)
                        indices.append(i_wp)
                elif free is False and i_wp not in used_indices:
                    l_mult.append(mult)
                    indices.append(i_wp)
                    if mult <= numIon:
                        l_maxn.append(1)
                    elif mult > numIon:
                        l_maxn.append(0)
                    l_free.append(False)
            #Loop over possible combinations
            #Create pointer variable to move through lists
            p = 0
            #Store the number of each WP, used across possible WP combinations
            n0 = [0]*len(l_mult)
            n = deepcopy(n0)
            for i, mult in enumerate(l_mult):
                if l_maxn[i] != 0:
                    p = i
                    n[i] = l_maxn[i]
                    break
            p2 = p
            if n == n0:
                return False
            while True:
                num = np.dot(n, l_mult)
                dobackwards = False
                #The combination works: move to next species
                if num == numIon:
                    #Check if at least one degree of freedom exists
                    for val, free, i_wp in zip(n, l_free, indices):
                        if val > 0:
                            if free is True:
                                has_freedom = True
                            elif free is False:
                                used_indices.append(i_wp)
                    break
                #All combinations failed: return False
                if n == n0 and p >= len(l_mult) - 1:
                    return False
                #Too few atoms
                if num < numIon:
                    #Forwards routine
                    #Move p to the right and max out
                    if p < len(l_mult) - 1:
                        p += 1
                        n[p] = min((numIon - num) // l_mult[p], l_maxn[p])
                    elif p == len(l_mult) - 1:
                        #p is already at last position: trigger backwards routine
                        dobackwards = True
                #Too many atoms
                if num > numIon or dobackwards is True:
                    #Backwards routine
                    #Set n[p] to 0, move p backwards to non-zero, and decrease by 1
                    n[p] = 0
                    while p > 0 and p > p2:
                        p -= 1
                        if n[p] != 0:
                            n[p] -= 1
                            if n[p] == 0 and p == p2:
                                p2 = p + 1
                            break
        #All species passed: return True
        if has_freedom is True:
            return True
        #All species passed, but no degrees of freedom: return 0
        elif has_freedom is False:
            return 0

    def to_file(self, fmt="cif", filename=None):
        """
        Creates a file with the given filename and file type to store the structure.
        By default, creates cif files for crystals and xyz files for clusters.
        By default, the filename is based on the stoichiometry.

        Args:
            fmt: the file type ('cif', 'xyz', etc.)
            filename: the file path

        Returns:
            Nothing. Creates a file at the specified path
        """
        if filename == None:
            given = False
        else:
            given = True
        if self.valid:
            if self.dim == 0:
                if filename == None:
                    filename = str(self.molecule.formula).replace(" ","") + "." + fmt
            if self.dim != 0:
                if filename == None:
                    filename = str(self.struct.formula).replace(" ","") + "." + fmt
            #Check if filename already exists
            #If it does, add a new number to end of filename
            if os.path.exists(filename):
                if given is False:
                    filename = filename[:(-len(fmt)-1)]
                i = 1
                while True:
                    outdir = filename + "_" + str(i)
                    if given is False:
                        outdir += "." + fmt
                    if not os.path.exists(outdir):
                        break
                    i += 1
                    if i > 10000:
                        return "Could not create file: too many files already created."
            else:
                outdir = filename
            if self.dim == 0 and fmt == "xyz":
                self.molecule.to(fmt=fmt, filename=outdir)
            else:
                self.struct.to(fmt=fmt, filename=outdir)
            return "Output file to " + outdir
        elif self.valid is False:
            printx("Cannot create file: structure did not generate.", priority=1)

    def print_all(self):
        """
        Prints useful information about the generated crystal.
        """
        print("--Random Crystal--")
        print("Dimension: "+str(self.dim))
        print("Group: "+self.group.symbol)
        print("Volume factor: "+str(self.factor))
        if self.valid is True:
            print("Wyckoff sites:")
            for x in self.wyckoff_sites:
                print("  "+str(x))
            print("Pymatgen Structure:")
            print(self.struct)
        elif self.valid is False:
            print("Structure not generated.")

    def generate_crystal(self, max1=max1, max2=max2, max3=max3):
        """
        The main code to generate a random atomic crystal. If successful,
        stores a pymatgen.core.structure object in self.struct and sets
        self.valid to True. If unsuccessful, sets self.valid to False and
        outputs an error message.

        Args:
            max1: the number of attempts for generating a lattice
            max2: the number of attempts for a given lattice
            max3: the number of attempts for a given Wyckoff position
        """
        #Check the minimum number of degrees of freedom within the Wyckoff positions
        self.numattempts = 1
        degrees = random_crystal.check_compatible(self.group, self.numIons)
        if degrees is False:
            printx(self.Msg1, priority=1)
            self.struct = None
            self.valid = False
            return
        else:
            if degrees is 0:
                max1 = 5
                max2 = 5
                max3 = 5
            #Calculate a minimum vector length for generating a lattice
            minvector = max(max(1.0*self.tol_matrix.get_tol(specie,specie) for specie in self.species), tol_m)
            for cycle1 in range(max1):
                self.cycle1 = cycle1
                #1, Generate a lattice
                if self.lattice.allow_volume_reset is True:
                    self.volume = estimate_volume(self.numIons, self.species, self.factor)
                    self.lattice.volume = self.volume
                self.lattice.reset_matrix()
                try:
                    cell_matrix = self.lattice.get_matrix()
                    if cell_matrix is None:
                        continue
                except:
                    continue
                #Check that the correct volume was generated
                if self.lattice.random is True:
                    if self.dim != 0 and abs(self.volume - np.linalg.det(cell_matrix)) > 1.0: 
                        printx("Error, volume is not equal to the estimated value: "+str(self.volume)
                            +" -> "+str(np.linalg.det(cell_matrix))
                            +"cell_para:  "+str(matrix2para(cell_matrix)), priority=0)
                        self.valid = False
                        self.struct = None
                        return


                good_structure = False
                
                # to try to generate atomic coordinates
                for cycle2 in range(max2):

                    coordinates_total = [] #to store the added coordinates
                    sites_total = []      #to store the corresponding specie
                    wyckoff_sites_total = []
                    self.cycle2 = cycle2
                    coordinates_tmp = deepcopy(coordinates_total)
                    sites_tmp = deepcopy(sites_total)
                    wyckoff_sites_tmp = deepcopy(wyckoff_sites_total)
                    
                    #Add specie by specie
                    for numIon, specie in zip(self.numIons, self.species):
                        numIon_added = 0
                        tol = self.tol_matrix.get_tol(specie,specie)

                        #Now we start to add the specie to the wyckoff position
                        cycle3 = 0
                        while cycle3 < max3:
                            self.cycle3 = cycle3
                            #Choose a random Wyckoff position for given multiplicity: 2a, 2b, 2c
                            ops = choose_wyckoff(self.group, numIon-numIon_added) 
                            if ops is not False:
                            #Generate a list of coords from ops
                                point = self.lattice.generate_point()
                                projected_point = project_point(point, ops[0], lattice=cell_matrix, PBC=self.PBC)
                                coords = apply_ops(projected_point, ops)
                                #Merge coordinates if the atoms are close
                                coords_toadd, wp_index, point = merge_coordinate(coords, cell_matrix, self.group, tol)

                                if wp_index is not False:
                                    #Use a Wyckoff_site object for the current site
                                    current_site = Wyckoff_site(self.group[wp_index], point, specie)

                                    #Check current WP against existing WP's
                                    passed_wp_check = True
                                    for ws in wyckoff_sites_tmp:
                                        if check_wyckoff_sites(current_site, ws, cell_matrix, tm=self.tol_matrix) is False:
                                            passed_wp_check = False

                                    if passed_wp_check is True:
                                        #The current Wyckoff site passed; store it
                                        if coordinates_tmp == []:
                                            coordinates_tmp = current_site.coords
                                        else:
                                            coordinates_tmp = np.vstack([coordinates_tmp, current_site.coords])
                                        sites_tmp += [specie]*len(coords_toadd)
                                        wyckoff_sites_tmp.append(current_site)
                                        numIon_added += len(coords_toadd)
                                        #Check if enough atoms have been added
                                        if numIon_added == numIon:
                                            coordinates_total = deepcopy(coordinates_tmp)
                                            sites_total = deepcopy(sites_tmp)
                                            wyckoff_sites_total = deepcopy(wyckoff_sites_tmp)
                                            break
                                    else:
                                        cycle3 += 1
                                        self.numattempts += 1
                                else:
                                    cycle3 += 1
                                    self.numattempts += 1
                            else:
                                cycle3 += 1
                                self.numattempts += 1

                        if numIon_added != numIon:
                            coordinates_total = []
                            sites_total = []
                            wyckoff_sites_total = []
                            break  #need to repeat from the 1st species

                    if numIon_added == numIon:
                        good_structure = True
                        break
                    else: #reset the coordinates and sites
                        coordinates_total = []
                        sites_total = []

                if good_structure:
                    final_coor = []
                    final_site = []
                    final_number = []
                    final_lattice = cell_matrix
                    for coor, ele in zip(coordinates_total, sites_total):
                        final_coor.append(coor)
                        final_site.append(ele)
                        final_number.append(Element(ele).z)
                    final_coor = np.array(final_coor)

                    if self.dim != 0:
                        final_lattice, final_coor = Add_vacuum(final_lattice, final_coor, PBC=self.PBC)
                        self.lattice_matrix = final_lattice   
                        """A 3x3 matrix representing the lattice of the unit
                        cell."""
                        self.frac_coords = np.array(final_coor)
                        """The fractional coordinates for each atom in the
                        final structure"""
                        self.cart_coords = np.dot(final_coor, final_lattice)
                        """The absolute coordinates for each atom in the
                        final structure"""
                        self.sites = final_site
                        """A list of atomic symbols corresponding to the type
                        of atom for each site in self.coordinates"""
                        self.struct = Structure(final_lattice, final_site, np.array(final_coor))
                        """A pymatgen.core.structure.Structure object for the
                        final generated crystal."""
                        self.spg_struct = (final_lattice, np.array(final_coor), final_number)
                        """A list of information describing the generated
                        crystal, which may be used by spglib for symmetry
                        analysis."""
                        self.wyckoff_sites = wyckoff_sites_total
                        """A list of Wyckoff_site objects describing the Wyckoff positions in
                        the structure."""
                        self.valid = True
                        return
                    elif self.dim == 0:
                        self.lattice_matrix = final_lattice   
                        """A 3x3 matrix representing the lattice of the unit
                        cell."""
                        self.frac_coords = np.array(final_coor)
                        """The relative coordinates for each atom in the
                        final structure""" 
                        self.cart_coords = np.dot(final_coor, final_lattice)
                        """The absolute coordinates for each atom in the
                        final structure"""                  
                        self.sites = final_site
                        """A list of atomic symbols corresponding to the type
                        of atom for each site in self.coordinates"""
                        self.species = final_site
                        """A list of atomic symbols corresponding to the type
                        of atom for each site in self.coordinates"""
                        self.molecule = Molecule(self.species, self.cart_coords)
                        """A pymatgen.core.structure.Molecule object for the
                        final generated cluster."""
                        #Calculate binding box
                        maxx = max(self.cart_coords[:,0])
                        minx = min(self.cart_coords[:,0])
                        maxy = max(self.cart_coords[:,1])
                        miny = min(self.cart_coords[:,1])
                        maxz = max(self.cart_coords[:,2])
                        minz = min(self.cart_coords[:,2])
                        self.struct = self.molecule.get_boxed_structure(maxx-minx+10, maxy-miny+10, maxz-minz+10)
                        """A pymatgen.core.structure.Structure object for the
                        final generated object."""
                        self.wyckoff_sites = wyckoff_sites_total
                        """A list of Wyckoff_site objects describing the Wyckoff positions in
                        the structure."""
                        self.valid = True
                        """Whether or not a valid crystal was generated."""
                        return
        if degrees == 0: printx("Wyckoff positions have no degrees of freedom.", priority=2)
        self.struct = None
        self.valid = False
        return

class random_crystal_2D(random_crystal):
    """
    A 2d counterpart to random_crystal. Generates a random atomic crystal based
    on a 2d layer group instead of a 3d spacegroup. Note that each layer group
    is equal to a corresponding 3d spacegroup, but without periodicity in one
    direction. The generated pymatgen structure can be accessed via self.struct

    Args:
        group: the layer group number between 1 and 80. NOT equal to the
            international space group number, which is between 1 and 230
            OR, a pyxtal.symmetry.Group object
        species: a list of atomic symbols for each ion type
        numIons: a list of the number of each type of atom within the
            primitive cell (NOT the conventional cell)
        thickness: the thickness, in Angstroms, of the unit cell in the 3rd
            dimension (the direction which is not repeated periodically)
        factor: a volume factor used to generate a larger or smaller
            unit cell. Increasing this gives extra space between atoms
        lattice: an optional Lattice object to use for the unit cell
        tm: the Tol_matrix object used to generate the crystal
    """
    def __init__(self, group, species, numIons, factor, thickness=None, lattice=None, tm=Tol_matrix(prototype="atomic")):
        self.dim = 2
        """The number of periodic dimensions of the crystal"""
        self.PBC = [1,1,0]
        """The periodic boundary axes of the crystal"""
        if type(group) != Group:
            group = Group(group, self.dim)
        number = group.number
        """The layer group number of the crystal."""
        self.thickness = thickness
        """the thickness, in Angstroms, of the unit cell in the 3rd
        dimension."""
        self.init_common(species, numIons, factor, number, lattice, tm)

class random_crystal_1D(random_crystal):
    """
    A 1d counterpart to random_crystal. Generates a random atomic crystal based
    on a 1d Rod group instead of a 3d spacegroup. The generated pymatgen
    structure can be accessed via self.struct

    Args:
        group: the Rod group number between 1 and 75. NOT equal to the
            international space group number, which is between 1 and 230
            OR, a pyxtal.symmetry.Group object
        species: a list of atomic symbols for each ion type
        numIons: a list of the number of each type of atom within the
            primitive cell (NOT the conventional cell)
        area: the effective cross-sectional area, in Angstroms squared, of the
            unit cell
        factor: a volume factor used to generate a larger or smaller
            unit cell. Increasing this gives extra space between atoms
        lattice: an optional Lattice object to use for the unit cell
        tm: the Tol_matrix object used to generate the crystal
    """
    def __init__(self, group, species, numIons, factor, area=None, lattice=None, tm=Tol_matrix(prototype="atomic")):
        self.dim = 1
        """The number of periodic dimensions of the crystal"""
        self.PBC = [0,0,1]
        """The periodic axis of the crystal."""
        self.sg = None
        """The international space group number (there is not a 1-1 correspondence
        with Rod groups)."""
        self.area = area
        """the effective cross-sectional area, in Angstroms squared, of the
        unit cell."""
        self.init_common(species, numIons, factor, group, lattice, tm)

class random_cluster(random_crystal):
    """
    A 0d counterpart to random_crystal. Generates a random atomic cluster based
    on a 0d Point group instead of a 3d spacegroup. The generated pymatgen
    structure can be accessed via self.struct

    Args:
        group: the Schoenflies symbol for the point group (ex: "Oh", "C5v", "D3")
            OR the number between 1-32 for a crystallographic point group,
            OR, a pyxtal.symmetry.Group object
            See:
            https://en.wikipedia.org/wiki/Schoenflies_notation#Point_groups
            for more information
        species: a list of atomic symbols for each ion type
        numIons: a list of the number of each type of atom within the
            primitive cell (NOT the conventional cell)
        factor: a volume factor used to generate a larger or smaller
            unit cell. Increasing this gives extra space between atoms
        lattice: an optional Lattice object to use for the unit cell
        tm: the Tol_matrix object used to generate the crystal
    """
    def __init__(self, group, species, numIons, factor, lattice=None, tm=Tol_matrix(prototype="atomic", factor=0.7)):
        tol_m = 0.1
        self.dim = 0
        """The number of periodic dimensions of the crystal"""
        self.PBC = [0,0,0]
        """The periodic axis of the crystal."""
        self.sg = None
        """The international space group number (there is not a 1-1 correspondence
        with Point groups)."""
        self.init_common(species, numIons, factor, group, lattice, tm)


if __name__ == "__main__":
    #-------------------------------- Options -------------------------
    import os
    from time import time
    from optparse import OptionParser
    from spglib import get_symmetry_dataset

    parser = OptionParser()
    parser.add_option("-s", "--spacegroup", dest="sg", metavar='sg', default=36, type=int,
            help="desired space group number (1-230) or layer group number (1-80), e.g., 36")
    parser.add_option("-e", "--element", dest="element", default='Li', 
            help="desired elements: e.g., Li", metavar="element")
    parser.add_option("-n", "--numIons", dest="numIons", default=16, 
            help="desired numbers of atoms: 16", metavar="numIons")
    parser.add_option("-f", "--factor", dest="factor", default=1.0, type=float, 
            help="volume factor: default 1.0", metavar="factor")
    parser.add_option("-v", "--verbosity", dest="verbosity", default=0, type=int, 
            help="verbosity: default 0; higher values print more information", metavar="verbosity")
    parser.add_option("-a", "--attempts", dest="attempts", default=1, type=int, 
            help="number of crystals to generate: default 1", metavar="attempts")
    parser.add_option("-o", "--outdir", dest="outdir", default="out", type=str, 
            help="Directory for storing output cif files: default 'out'", metavar="outdir")
    parser.add_option("-d", "--dimension", dest="dimension", metavar='dimension', default=3, type=int,
            help="desired dimension: (3, 2, or 1 for 3d, 2d, or 1D respectively): default 3")
    parser.add_option("-t", "--thickness", dest="thickness", metavar='thickness', default=None, type=float,
            help="Thickness, in Angstroms, of a 2D crystal, or area of a 1D crystal, None generates a value automatically: default None")

    (options, args) = parser.parse_args()
    sg = options.sg
    dimension = options.dimension
    if dimension == 3:
        if sg < 1 or sg > 230:
            print("Invalid space group number. Must be between 1 and 230.")
            sys.exit(0)
    elif dimension == 2:
        if sg < 1 or sg > 80:
            print("Invalid layer group number. Must be between 1 and 80.")
            sys.exit(0)
    elif dimension == 1:
        if sg < 1 or sg > 75:
            print("Invalid Rod group number. Must be between 1 and 75.")
            sys.exit(0)
    else:
        print("Invalid dimension. Use dimension 0, 1, 2, or 3.")
        sys.exit(0)

    element = options.element
    number = options.numIons
    numIons = []
    if element.find(',') > 0:
        system = element.split(',')
        for x in number.split(','):
            numIons.append(int(x))
    else:
        system = [element]
        numIons = [int(number)]

    factor = options.factor
    if factor < 0:
        print("Error: Volume factor must be greater than 0.")
        sys.exit(0)

    verbosity = options.verbosity
    attempts = options.attempts
    outdir = options.outdir
    dimension = options.dimension
    thickness = options.thickness

    try:
        os.mkdir(outdir)
    except: pass

    filecount = 1 #To check whether a file already exists
    for i in range(attempts):
        numIons0 = np.array(numIons)
        sg = options.sg
        start = time()
        if dimension == 3:
            rand_crystal = random_crystal(options.sg, system, numIons0, factor)
            sg1 = sg
        elif dimension == 2:
            rand_crystal = random_crystal_2D(options.sg, system, numIons0, thickness, factor)
            sg1 = rand_crystal.sg
        elif dimension == 1:
            rand_crystal = random_crystal_1D(options.sg, system, numIons0, thickness, factor)
            sg1 = "?"
        if dimension == 0:
            rand_crystal = random_cluster(options.sg, system, numIons0, factor)
            sg1 = sg
        end = time()
        timespent = np.around((end - start), decimals=2)

        if rand_crystal.valid:
            #Output a cif file
            written = False
            try:
                comp = str(rand_crystal.struct.composition)
                comp = comp.replace(" ", "")
                cifpath = outdir + '/' + comp + "_" + str(filecount) + '.cif'
                while os.path.isfile(cifpath):
                    filecount += 1
                    cifpath = outdir + '/' + comp + "_" + str(filecount) + '.cif'
                CifWriter(rand_crystal.struct, symprec=0.1).write_file(filename = cifpath)
                written = True
            except: pass
            #POSCAR output
            #rand_crystal.struct.to(fmt="poscar", filename = '1.vasp')

            #spglib style structure called cell
            ans = get_symmetry_dataset(rand_crystal.spg_struct, symprec=1e-1)['number']
            print('Space group  requested:', sg1, ' generated:', ans)
            if written is True:
                print("    Output to "+cifpath)
            else:
                print("    Could not write cif file.")

            #Print additional information about the structure
            if verbosity > 0:
                print("Time required for generation: " + str(timespent) + "s")
                print(rand_crystal.struct)


        #If generation fails
        else: 
            print('something is wrong')
            print('Time spent during generation attempt: ' + str(timespent) + "s")


#Standard Libraries #External Libraries #PyXtal imports #Constants #------------------------------ #seperation tolerance in Angstroms #Attempts for generating lattices #Attempts for a given lattice #Attempts for a given Wyckoff position #minimum vector length #Define functions #------------------------------ Class for variable distance tolerance checking. Used within random_crystal and     molecular_crystal to verify whether atoms are too close. Stores a matrix of atom-     atom pair tolerances. Note that the matrix's indices correspond to atomic numbers,     with the 0th entries being 0 (there is no atomic number 0).      Args:         prototype: a string representing the type of radii to use             ("atomic", "molecular", or "metallic")         factor: a float to scale the distances by. A smaller value means a smaller             tolerance for distance checking         tuples: a list or tuple of tuples, which define custom tolerance values. Each tuple             should be of the form (specie1, specie2, value), where value is the tolerance             in Angstroms, and specie1 and specie2 can be strings, integers, Element objects,             or pymatgen Specie objects. Custom values may also be set using set_tol #Get the appropriate atomic radii #Use the covalent radius #Use the covalent radius #If no radius is found for either atom, set tolerance to None A symmetric numpy matrix storing the tolerance between specie pairs. A list of tuples storing which species pair tolerances have custom values. Returns the tolerance between two species.                  Args:             specie1, specie2: the atomic number (int or float), name (str), symbol (str),                 an Element object, or a pymatgen Specie object          Returns:             the tolerance between the provided pair of atomic species Sets the distance tolerance between two species.                  Args:             specie1, specie2: the atomic number (int or float), name (str), symbol (str),                 an Element object, or a pymatgen Specie object             value:                 the tolerance (in Angstroms) to set to Given a tolerance matrix, returns a Tol_matrix object. Matrix indices correspond to         the atomic number (with 0 pointing to Hydrogen by default). For atoms with atomic         numbers not included in the matrix, the default value (specified by prototype) will be         used, up to element 96. Note that if the matrix is asymmetric, only the value below the         diagonal will be used.          Args:             matrix: a 2D matrix or list of tolerances between atomic species pairs. The                 indices correspond to atomic species (see begin_with variable description)             prototype: a string representing the type of radii to use                 ("atomic", "molecular")             factor: a float to scale the distances by. A smaller value means a smaller                 tolerance for distance checking             begin_with: the index which points to Hydrogen within the matrix. Default 0          Returns:             a Tol_matrix object Given a list of atomic radii, returns a Tol_matrix object. For atom-atom pairs, uses         the average radii of the two species as the tolerance value. For atoms with atomic         numbers not in the radius list, the default value (specified by prototype) will be         used, up to element 96.          Args:             radius_list: a list of atomic radii (in Angstroms), beginning with Hydrogen             prototype: a string representing the type of radii to use                 ("atomic", "molecular")             factor: a float to scale the distances by. A smaller value means a smaller                 tolerance for distance checking             begin_with: the index which points to Hydrogen within the list. Default 0          Returns:             a Tol_matrix object Creates a Tol_matrix which only has a single tolerance value. Using get_tol will         always return the same value.          Args:             value: the tolerance value to use          Returns:             a Tol_matrix object whose methods are overridden to use a single tolerance value Creates a file with the given filename and file type to store the structure.         By default, creates cif files for crystals and xyz files for clusters.         By default, the filename is based on the stoichiometry.          Args:             fmt: the file type ('cif', 'xyz', etc.)             filename: the file path          Returns:             Nothing. Creates a file at the specified path #Check if filename already exists #If it does, add a new number to end of filename Choose a random number from a Gaussian probability distribution centered     between min and max. sigma is the number of standard deviations that min     and max are away from the center. Thus, sigma is also the largest possible     number of standard deviations corresponding to the returned value. sigma=2     corresponds to a 95.45% probability of choosing a number between min and     max.      Args:         min: the minimum acceptable value         max: the maximum acceptable value         sigma: the number of standard deviations between the center and min or max      Returns:         a value chosen randomly between min and max Given an atomic specie name, return the covalent radius.          Args:         specie: a string for the atomic symbol      Returns:         the covalent radius in Angstroms Given a list of atomic species names, returns a list of covalent radii  Args:     species: a list of strings for atomic species names or symbols  Returns:     A 1D numpy array of distances in Angstroms Check the distances between two set of atoms. Distances between coordinates     within the first set are not checked, and distances between coordinates within     the second set are not checked. Only distances between points from different     sets are checked.      Args:         coord1: a list of fractional coordinates e.g. [[.1,.6,.4]             [.3,.8,.2]]         coord2: a list of new fractional coordinates e.g. [[.7,.8,.9],             [.4,.5,.6]]         species1: a list of atomic species or numbers for coord1         species2: a list of atomic species or numbers for coord2         lattice: matrix describing the unit cell vectors         PBC: A periodic boundary condition list, where 1 means periodic, 0 means not periodic.             Ex: [1,1,1] -> full 3d periodicity, [0,0,1] -> periodicity along the z axis         tm: a Tol_matrix object, or a string representing the type of Tol_matrix             to use         d_factor: the tolerance is multiplied by this amount. Larger values             mean atoms must be farther apart      Returns:         a bool for whether or not the atoms are sufficiently far enough apart #Check that there are points to compare #Create tolerance matrix from subset of tm #Calculate the distance between each i, j pair Given a set of (unfiltered) fractional coordinates, checks if the periodic images are too close.          Args:         coords: a list of fractional coordinates         species: the atomic species of each coordinate         lattice: a 3x3 lattice matrix         PBC: the periodic boundary conditions         tm: a Tol_matrix object         tol: a single override value for the distance tolerances         d_factor: the tolerance is multiplied by this amount. Larger values             mean atoms must be farther apart      Returns:         False if distances are too close. True if distances are not too close #If no PBC, there are no images to check #Create image coords from given coords and PBC #Omit the [0,0,0] vector #Create a distance matrix #Define tolerances Finds the geometric centers of the clusters under periodic boundary     conditions.      Args:         xyzs: a list of fractional coordinates         lattice: a matrix describing the unit cell         PBC: A periodic boundary condition list, where 1 means periodic, 0 means not periodic.             Ex: [1,1,1] -> full 3d periodicity, [0,0,1] -> periodicity along the z axis      Returns:         x,y,z coordinates for the center of the input coordinate list #shift atom1 to position close to atom2 Given a set of lattic parameters, generates a matrix representing the     lattice vectors      Args:         cell_para: a 1x6 list of lattice parameters [a, b, c, alpha, beta,             gamma]. a, b, and c are the length of the lattice vectos, and             alpha, beta, and gamma are the angles between these vectors. Can             be generated by matrix2para         radians: if True, lattice parameters should be in radians. If False,             lattice angles should be in degrees         format: a string ('lower', 'symmetric', or 'upper') for the type of             matrix to be output      Returns:         a 3x3 matrix representing the unit cell. By default (format='lower'),         the a vector is aligined along the x-axis, and the b vector is in the         y-z plane #Generate a lower-diagonal matrix #TODO: allow generation of symmetric matrices #Generate an upper-diagonal matrix Adds space above and below a 2D or 1D crystal. This allows for treating the     structure as a 3D crystal during energy optimization      Args:         lattice: the lattice matrix of the crystal         coor: the relative coordinates of the crystal         vacuum: the amount of space, in Angstroms, to add above and below         PBC: A periodic boundary condition list, where 1 means periodic, 0 means not periodic.             Ex: [1,1,1] -> full 3d periodicity, [0,0,1] -> periodicity along the z axis      Returns:         lattice, coor: The transformed lattice and coordinates after the             vacuum space is added Given a 3x3 matrix representing a unit cell, outputs a list of lattice     parameters.      Args:         matrix: a 3x3 array or list, where the first, second, and third rows             represent the a, b, and c vectors respectively         radians: if True, outputs angles in radians. If False, outputs in             degrees      Returns:         a 1x6 list of lattice parameters [a, b, c, alpha, beta, gamma]. a, b,         and c are the length of the lattice vectos, and alpha, beta, and gamma         are the angles between these vectors (in radians by default) #a #b #c #alpha #beta #gamma #convert radians to degrees Returns the number of duplicate atoms in the conventional lattice (in     contrast to the primitive cell). Based on the type of cell centering (P,     A, C, I, R, or F)      Args:         group: a Group object, or the space group number of the group         dim: the dimension of the group (3 for space group, 2 for layer group,             1 for Rod group, or 0 for 3D point group). If group is a Group             object, dim will be overridden by group's value for dim          Returns:         an integer between 1 and 4, telling how many atoms are in the conventional cell #Get the group dimension and number #Rod and point groups #Layer groups #space groups #F #R #A, C, I #P Given a list of fractional coordinates, finds pairs which are closer     together than tol, and builds the connectivity map      Args:         coor: a list of fractional 3-dimensional coordinates         lattice: a matrix representing the crystal unit cell         tol: the distance tolerance for pairing coordinates         PBC: A periodic boundary condition list, where 1 means periodic, 0 means not periodic.             Ex: [1,1,1] -> full 3d periodicity, [0,0,1] -> periodicity along the z axis          Returns:         pairs, graph: (pairs) is a list whose entries have the form [index1,         index2, distance], where index1 and index2 correspond to the indices         of a pair of points within the supplied list (coor). distance is the         distance between the two points. (graph) is a connectivity map in the         form of a list. Its first index represents a point within coor, and         the second indices represent which point(s) it is connected to. #Avoid Futurewarning #pairs1 = deepcopy(pairs) #pairs = pairs1[sequence] Given an undirected graph (a 2d array of indices), return a set of     connected components, each connected component being an (arbitrarily     ordered) array of indices which are connected either directly or     indirectly.      Args:         graph: a list reprenting the connections between points. The first index             represents a point, and the 2nd indices represent the points to             which the first point is connected. Can be generated by             find_short_dist      Returns:         a list of connected components. The first index denotes a separate         connected component. The second indices denote the points within the         connected component which are connected to each other Find all elements which are connected to el. Return an array which         includes these elements and el itself. #seen stores already-visited indices #iterate through the neighbors (x) of el #Recursively find neighbors of x #Create a list of indices to iterate through #x is the index we are finding the connected component of #Add neighbors of x to the current connected component #Remove indices which have already been found Given a list of fractional coordinates, merges them within a given     tolerance, and checks if the merged coordinates satisfy a Wyckoff     position. Used for merging general Wyckoff positions into special Wyckoff     positions within the random_crystal (and its derivative) classes.      Args:         coor: a list of fractional coordinates         lattice: a 3x3 matrix representing the unit cell         group: a pyxtal.symmetry.Group object         tol: the cutoff distance for merging coordinates      Returns:         coor, index, point: (coor) is the new list of fractional coordinates after         merging. index is a single index for the Wyckoff position within         the sg. If no matching WP is found, returns False. point is a 3-vector;         when plugged into the Wyckoff position, it will generate all the other         points. #Get index of current Wyckoff position. If not one, return False #Main loop for merging multiple times #Check distances of current WP. If too small, merge #Ignore distance from atom to itself #Find possible wp's to merge into #factor = mult2 / mult1 #Calculate minimum separation for each WP #Choose wp with shortest translation for generating point #Distances were not too small; return True Estimates the volume of a unit cell based on the number and types of ions.     Assumes each atom takes up a sphere with radius equal to its covalent bond     radius.      Args:         numIons: a list of the number of ions for each specie         species: a corresponding list for the specie of each type of ion. Each             element in the list should be a string for the atomic symbol         factor: an optional factor to multiply the result by. Larger values             allow more space between atoms          Returns:         a float value for the estimated volume Generates a lattice (3x3 matrix) according to the space group symmetry and     number of atoms. If the spacegroup has centering, we will transform to     conventional cell setting. If the generated lattice does not meet the     minimum angle and vector requirements, we try to generate a new one, up to     maxattempts times.      Args:         sg: International number of the space group         volume: volume of the conventional unit cell         minvec: minimum allowed lattice vector length (among a, b, and c)         minangle: minimum allowed lattice angle (among alpha, beta, and gamma)         max_ratio: largest allowed ratio of two lattice vector lengths         maxattempts: the maximum number of attempts for generating a lattice         kwargs: a dictionary of optional values. These include:             'unique_axis': the axis ('a', 'b', or 'c') which is not symmetrically                 equivalent to the other two             'min_l': the smallest allowed cell vector. The smallest vector must be larger                 than this.             'mid_l': the second smallest allowed cell vector. The second smallest vector                 must be larger than this.             'max_l': the third smallest allowed cell vector. The largest cell vector must                 be larger than this.      Returns:         a 3x3 matrix representing the lattice vectors of the unit cell. If         generation fails, outputs a warning message and returns empty #Triclinic #if sg <= 2: #Derive lattice constants from a random matrix #Monoclinic #elif sg <= 15: #Orthorhombic #elif sg <= 74: #Tetragonal #elif sg <= 142: #Trigonal/Rhombohedral/Hexagonal #elif sg <= 194: #Cubic #else: #Check that lattice meets requirements #Define limits on cell dimensions #Check minimum Euclidean distances #If maxattempts tries have been made without success Generates a lattice (3x3 matrix) according to the spacegroup symmetry and     number of atoms. If the layer group has centering, we will use the     conventional cell setting. If the generated lattice does not meet the     minimum angle and vector requirements, we try to generate a new one, up to     maxattempts times.     Note: The monoclinic layer groups have different unique axes. Groups 3-7         have unique axis c, while 8-18 have unique axis a. We use non-periodic         axis c for all layer groups.      Args:         num: International number of the space group         volume: volume of the lattice         thickness: 3rd-dimensional thickness of the unit cell. If set to None,             a thickness is chosen automatically         minvec: minimum allowed lattice vector length (among a, b, and c)         minangle: minimum allowed lattice angle (among alpha, beta, and gamma)         max_ratio: largest allowed ratio of two lattice vector lengths         maxattempts: the maximum number of attempts for generating a lattice         kwargs: a dictionary of optional values. These include:             'unique_axis': the axis ('a', 'b', or 'c') which is not symmetrically                 equivalent to the other two             'min_l': the smallest allowed cell vector. The smallest vector must be larger                 than this.             'mid_l': the second smallest allowed cell vector. The second smallest vector                 must be larger than this.             'max_l': the third smallest allowed cell vector. The largest cell vector must                 be larger than this.      Returns:         a 3x3 matrix representing the lattice vectors of the unit cell. If         generation fails, outputs a warning message and returns empty #Store the non-periodic axis #Set the unique axis for monoclinic cells #if num in range(3, 8): unique_axis = "c" #elif num in range(8, 19): unique_axis = "a" #Triclinic #if num <= 2: #scale thickness by outer product of vectors #Monoclinic #elif num <= 18: #Orthorhombic #elif num <= 48: #ratio a/b #ratio a/b #ratio a/b #Tetragonal #elif num <= 64: #Trigonal/Hexagonal #elif num <= 80: #Define limits on cell dimensions #If maxattempts tries have been made without success Generates a lattice (3x3 matrix) according to the spacegroup symmetry and     number of atoms. If the spacegroup has centering, we will transform to     conventional cell setting. If the generated lattice does not meet the     minimum angle and vector requirements, we try to generate a new one, up to     maxattempts times.     Note: The monoclinic Rod groups have different unique axes. Groups 3-7         have unique axis a, while 8-12 have unique axis c. We use periodic         axis c for all Rod groups.      Args:         num: number of the Rod group         volume: volume of the lattice         area: cross-sectional area of the unit cell in Angstroms squared. If             set to None, a value is chosen automatically         minvec: minimum allowed lattice vector length (among a, b, and c)         minangle: minimum allowed lattice angle (among alpha, beta, and gamma)         max_ratio: largest allowed ratio of two lattice vector lengths         maxattempts: the maximum number of attempts for generating a lattice         kwargs: a dictionary of optional values. These include:             'unique_axis': the axis ('a', 'b', or 'c') which is not symmetrically                 equivalent to the other two             'min_l': the smallest allowed cell vector. The smallest vector must be larger                 than this.             'mid_l': the second smallest allowed cell vector. The second smallest vector                 must be larger than this.             'max_l': the third smallest allowed cell vector. The largest cell vector must                 be larger than this.      Returns:         a 3x3 matrix representing the lattice vectors of the unit cell. If         generation fails, outputs a warning message and returns empty #Store the periodic axis #Set the unique axis for monoclinic cells #if num in range(3, 8): unique_axis = "a" #elif num in range(8, 13): unique_axis = "c" #Triclinic #if num <= 2: #scale thickness by outer product of vectors #Monoclinic #elif num <= 12: #Orthorhombic #lif num <= 22: #ratio a/b #ratio a/b #ratio a/b #Tetragonal #elif num <= 41: #Trigonal/Rhombohedral/Hexagonal #elif num <= 75: #Define limits on cell dimensions #If maxattempts tries have been made without success Generates a lattice (3x3 matrix) according to the spacegroup symmetry and     number of atoms. If the spacegroup has centering, we will transform to     conventional cell setting. If the generated lattice does not meet the     minimum angle and vector requirements, we try to generate a new one, up to     maxattempts times.     Note: The monoclinic Rod groups have different unique axes. Groups 3-7         have unique axis a, while 8-12 have unique axis c. We use periodic         axis c for all Rod groups.      Args:         num: number of the Rod group         volume: volume of the lattice         area: cross-sectional area of the unit cell in Angstroms squared. If             set to None, a value is chosen automatically         minvec: minimum allowed lattice vector length (among a, b, and c)         max_ratio: largest allowed ratio of two lattice vector lengths         maxattempts: the maximum number of attempts for generating a lattice         kwargs: a dictionary of optional values. Only used for ellipsoidal             lattices, which pass the value to generate_lattice. Possible values include:             'unique_axis': the axis ('a', 'b', or 'c') which is not symmetrically                 equivalent to the other two             'min_l': the smallest allowed cell vector. The smallest vector must be larger                 than this.             'mid_l': the second smallest allowed cell vector. The second smallest vector                 must be larger than this.             'max_l': the third smallest allowed cell vector. The largest cell vector must                 be larger than this.      Returns:         a 3x3 matrix representing the lattice vectors of the unit cell. If         generation fails, outputs a warning message and returns empty #Use a cubic lattice with altered volume #Use a matrix with only on-diagonal elements, with a = b Choose a Wyckoff position to fill based on the current number of atoms     needed to be placed within a unit cell     Rules:         1) The new position's multiplicity is equal/less than (number).         2) We prefer positions with large multiplicity.      Args:         group: a pyxtal.symmetry.Group object         number: the number of atoms still needed in the unit cell      Returns:         a single index for the Wyckoff position. If no position is found,         returns False #choose from high to low Class for storing atomic Wyckoff positions with a single coordinate.          Args:         wp: a Wyckoff_position object         coordinate: a fractional 3-vector for the generating atom's coordinate         specie: an Element, element name or symbol, or atomic number of the atom Given two Wyckoff sites, checks the inter-atomic distances between them.      Args:         ws1: a Wyckoff_site object         ws2: a different Wyckoff_site object (will always return False if             two identical WS's are provided)         lattice: a 3x3 cell matrix         same_group: whether or not the two WS's are in the same structure.             Default value True reduces the calculation cost      Returns:         True if all distances are greater than the allowed tolerances.         False if any distance is smaller than the allowed tolerance #Ensure the PBC values are valid #Get tolerance #Symmetry shortcut method: check only some atoms #We can either check one atom in WS1 against all WS2, or vice-versa #Check which option is faster #Calculate distances #Check if any distances are less than the tolerance #No symmetry method: check all atomic pairs #Check if any distances are less than the tolerance Checks the inter-atomic distance between all pairs of atoms in a crystal.      Args:         coordinates: a 1x3 list of fractional coordinates         species: a list of atomic symbols for each coordinate         lattice: a 3x3 matrix representing the lattice vectors of the unit cell         factor: a tolerance factor for checking distances. A larger value means             atoms must be farther apart         PBC: A periodic boundary condition list, where 1 means periodic, 0 means not periodic.             Ex: [1,1,1] -> full 3d periodicity, [0,0,1] -> periodicity along the z axis          Returns:         True if no atoms are too close together, False if any pair is too close Class for storing and generating crystal lattices. Allows for specification     of constraint values. Lattice types include triclinic, monoclinic, orthorhombic,     tetragonal, trigonal, hexagonal, cubic, spherical, and ellipsoidal. The last     two are used for generating point group structures, and do not actually represent     a parallelepiped lattice.      Args:         ltype: a string representing the type of lattice (from the above list)         volume: the volume, in Angstroms cubed, of the lattice         PBC: A periodic boundary condition list, where 1 means periodic, 0 means not periodic.             Ex: [1,1,1] -> full 3d periodicity, [0,0,1] -> periodicity along the z axis         kwargs: various values which may be defined. If none are defined, random ones             will be generated. Values will be passed to generate_lattice. Options include:             area: The cross-sectional area (in Angstroms squared). Only used to generate 1D                 crystals             thickness: The unit cell's non-periodic thickness (in Angstroms). Only used to                 generate 2D crystals             unique_axis: The unique axis for certain symmetry (and especially layer) groups.                 Because the symmetry operations are not also transformed, you should use the                 default values for random crystal generation             random: If False, keeps the stored values for the lattice geometry even upon applying                 reset_matrix. To alter the matrix, use set_matrix() or set_para             'unique_axis': the axis ('a', 'b', or 'c') which is not symmetrically                 equivalent to the other two             'min_l': the smallest allowed cell vector. The smallest vector must be larger                 than this.             'mid_l': the second smallest allowed cell vector. The second smallest vector                 must be larger than this.             'max_l': the third smallest allowed cell vector. The largest cell vector must                 be larger than this.             'allow_volume_reset': a bool stating whether or not the volume should be reset during                 each crystal generation attempt #Set required parameters #Set optional values #Set stress normalization info #Set info for on-diagonal stress symmetrization #Set values for the matrix Generates a 3x3 matrix for the lattice based on the lattice type and volume #Try multiple times in case of failure Returns a 3x3 numpy array representing the lattice vectors. Returns a tuple of lattice parameters. #Choose a point within an octant of the unit sphere #Randomly flip some coordinates #Scale the point by the max radius Creates a Lattice object from 6 lattice parameters. Additional keyword arguments         are available. Unless specified by the keyword random=True, does not create a         new matrix upon calling reset_matrix. This allows for generation of random         crystals with a specific choice of unit cell.          Args:             a, b, c: The length (in Angstroms) of the unit cell vectors             alpha: the angle (in degrees) between the b and c vectors             beta: the angle (in degrees) between the a and c vectors             gamma: the angle (in degrees) between the a and b vectors             ltype: the lattice type ("cubic, tetragonal, etc."). Also available are "spherical",                 which confines generated points to lie within a sphere, and "ellipsoidal", which                 confines generated points to lie within an ellipse (oriented about the z axis)             radians: whether or not to use radians (instead of degrees) for the lattice angles             PBC: A periodic boundary condition list, where 1 means periodic, 0 means not periodic.                 Ex: [1,1,1] -> full 3d periodicity, [0,0,1] -> periodicity along the z axis             kwargs: various values which may be defined. If none are defined, random ones                 will be generated. Values will be passed to generate_lattice. Options include:                 area: The cross-sectional area (in Angstroms squared). Only used to generate 1D                     crystals                 thickness: The unit cell's non-periodic thickness (in Angstroms). Only used to                     generate 2D crystals                 unique_axis: The unique axis for certain symmetry (and especially layer) groups.                     Because the symmetry operations are not also transformed, you should use the                     default values for random crystal generation                 random: If False, keeps the stored values for the lattice geometry even upon applying                     reset_matrix. To alter the matrix, use set_matrix() or set_para                 'unique_axis': the axis ('a', 'b', or 'c') which is not symmetrically                     equivalent to the other two                 'min_l': the smallest allowed cell vector. The smallest vector must be larger                     than this.                 'mid_l': the second smallest allowed cell vector. The second smallest vector                     must be larger than this.                 'max_l': the third smallest allowed cell vector. The largest cell vector must                     be larger than this.          Returns:             a Lattice object with the specified parameters #Initialize a Lattice instance Creates a Lattice object from a 3x3 cell matrix. Additional keyword arguments         are available. Unless specified by the keyword random=True, does not create a         new matrix upon calling reset_matrix. This allows for generation of random         crystals with a specific choice of unit cell.          Args:             matrix: a 3x3 real matrix (numpy array or nested list) describing the cell vectors             ltype: the lattice type ("cubic, tetragonal, etc."). Also available are "spherical",                 which confines generated points to lie within a sphere, and "ellipsoidal", which                 confines generated points to lie within an ellipsoid (oriented about the z axis)             PBC: A periodic boundary condition list, where 1 means periodic, 0 means not periodic.                 Ex: [1,1,1] -> full 3d periodicity, [0,0,1] -> periodicity along the z axis             kwargs: various values which may be defined. If none are defined, random ones                 will be generated. Values will be passed to generate_lattice. Options include:                 area: The cross-sectional area (in Angstroms squared). Only used to generate 1D                     crystals                 thickness: The unit cell's non-periodic thickness (in Angstroms). Only used to                     generate 2D crystals                 unique_axis: The unique axis for certain symmetry (and especially layer) groups.                     Because the symmetry operations are not also transformed, you should use the                     default values for random crystal generation                 random: If False, keeps the stored values for the lattice geometry even upon applying                     reset_matrix. To alter the matrix, use set_matrix() or set_para                 'unique_axis': the axis ('a', 'b', or 'c') which is not symmetrically                     equivalent to the other two                 'min_l': the smallest allowed cell vector. The smallest vector must be larger                     than this.                 'mid_l': the second smallest allowed cell vector. The second smallest vector                     must be larger than this.                 'max_l': the third smallest allowed cell vector. The largest cell vector must                     be larger than this.          Returns:             a Lattice object with the specified parameters #Initialize a Lattice instance Class for storing and generating atomic crystals based on symmetry     constraints. Given a spacegroup, list of atomic symbols, the stoichiometry,     and a volume factor, generates a random crystal consistent with the     spacegroup's symmetry. This crystal is stored as a pymatgen struct via     self.struct          Args:         group: the international spacegroup number, or a Group object         species: a list of atomic symbols for each ion type         numIons: a list of the number of each type of atom within the             primitive cell (NOT the conventional cell)         tm: the Tol_matrix object used to generate the crystal         factor: a volume factor used to generate a larger or smaller             unit cell. Increasing this gives extra space between atoms         lattice: an optional Lattice object to use for the unit cell Common init functionality for 0D-3D cases of random_crystal. #Check that numIons are integers greater than 0 A pyxtal.symmetry.Group object storing information about the space/layer             /Rod/point group, and its Wyckoff positions. The international group number of the crystal:         1-230 for 3D space groups         1-80 for 2D layer groups         1-75 for 1D Rod groups         1-32 for crystallographic point groups         None otherwise The number of attempts needed to generate the crystal. Has a maximum         value of max1*max2*max3. #must convert it to np.array The supplied volume factor for the unit cell. The number of each type of atom in the PRIMITIVE cell. The number of each type of atom in the CONVENTIONAL cell. A list of atomic symbols for the types of atoms in the crystal. A list of warning messages to use during generation. #Use the provided lattice #Make sure the custom lattice PBC axes are correct. #Determine the unique axis #Generate a Lattice instance The volume of the generated unit cell. #Set the tolerance matrix The Tol_matrix object used for checking inter-atomic distances within the structure. #Generate the crystal The number of periodic dimensions of the crystal The international spacegroup number of the crystal. The periodic boundary axes of the crystal Define a set of error and warning message if generation fails.          Returns:             nothing Checks if the number of atoms is compatible with the Wyckoff         positions. Considers the number of degrees of freedom for each Wyckoff         position, and makes sure at least one valid combination of WP's exists. #Store whether or not at least one degree of freedom exists #Store the wp's already used that don't have any freedom #Loop over species #Get lists of multiplicity, maxn and freedom #Remove redundant multiplicities: #Loop over possible combinations #Create pointer variable to move through lists #Store the number of each WP, used across possible WP combinations #The combination works: move to next species #Check if at least one degree of freedom exists #All combinations failed: return False #Too few atoms #Forwards routine #Move p to the right and max out #p is already at last position: trigger backwards routine #Too many atoms #Backwards routine #Set n[p] to 0, move p backwards to non-zero, and decrease by 1 #All species passed: return True #All species passed, but no degrees of freedom: return 0 Creates a file with the given filename and file type to store the structure.         By default, creates cif files for crystals and xyz files for clusters.         By default, the filename is based on the stoichiometry.          Args:             fmt: the file type ('cif', 'xyz', etc.)             filename: the file path          Returns:             Nothing. Creates a file at the specified path #Check if filename already exists #If it does, add a new number to end of filename Prints useful information about the generated crystal. The main code to generate a random atomic crystal. If successful,         stores a pymatgen.core.structure object in self.struct and sets         self.valid to True. If unsuccessful, sets self.valid to False and         outputs an error message.          Args:             max1: the number of attempts for generating a lattice             max2: the number of attempts for a given lattice             max3: the number of attempts for a given Wyckoff position #Check the minimum number of degrees of freedom within the Wyckoff positions #Calculate a minimum vector length for generating a lattice #1, Generate a lattice #Check that the correct volume was generated # to try to generate atomic coordinates #to store the added coordinates #to store the corresponding specie #Add specie by specie #Now we start to add the specie to the wyckoff position #Choose a random Wyckoff position for given multiplicity: 2a, 2b, 2c #Generate a list of coords from ops #Merge coordinates if the atoms are close #Use a Wyckoff_site object for the current site #Check current WP against existing WP's #The current Wyckoff site passed; store it #Check if enough atoms have been added #need to repeat from the 1st species #reset the coordinates and sites A 3x3 matrix representing the lattice of the unit                         cell. The fractional coordinates for each atom in the                         final structure The absolute coordinates for each atom in the                         final structure A list of atomic symbols corresponding to the type                         of atom for each site in self.coordinates A pymatgen.core.structure.Structure object for the                         final generated crystal. A list of information describing the generated                         crystal, which may be used by spglib for symmetry                         analysis. A list of Wyckoff_site objects describing the Wyckoff positions in                         the structure. A 3x3 matrix representing the lattice of the unit                         cell. The relative coordinates for each atom in the                         final structure The absolute coordinates for each atom in the                         final structure A list of atomic symbols corresponding to the type                         of atom for each site in self.coordinates A list of atomic symbols corresponding to the type                         of atom for each site in self.coordinates A pymatgen.core.structure.Molecule object for the                         final generated cluster. #Calculate binding box A pymatgen.core.structure.Structure object for the                         final generated object. A list of Wyckoff_site objects describing the Wyckoff positions in                         the structure. Whether or not a valid crystal was generated. A 2d counterpart to random_crystal. Generates a random atomic crystal based     on a 2d layer group instead of a 3d spacegroup. Note that each layer group     is equal to a corresponding 3d spacegroup, but without periodicity in one     direction. The generated pymatgen structure can be accessed via self.struct      Args:         group: the layer group number between 1 and 80. NOT equal to the             international space group number, which is between 1 and 230             OR, a pyxtal.symmetry.Group object         species: a list of atomic symbols for each ion type         numIons: a list of the number of each type of atom within the             primitive cell (NOT the conventional cell)         thickness: the thickness, in Angstroms, of the unit cell in the 3rd             dimension (the direction which is not repeated periodically)         factor: a volume factor used to generate a larger or smaller             unit cell. Increasing this gives extra space between atoms         lattice: an optional Lattice object to use for the unit cell         tm: the Tol_matrix object used to generate the crystal The number of periodic dimensions of the crystal The periodic boundary axes of the crystal The layer group number of the crystal. the thickness, in Angstroms, of the unit cell in the 3rd         dimension. A 1d counterpart to random_crystal. Generates a random atomic crystal based     on a 1d Rod group instead of a 3d spacegroup. The generated pymatgen     structure can be accessed via self.struct      Args:         group: the Rod group number between 1 and 75. NOT equal to the             international space group number, which is between 1 and 230             OR, a pyxtal.symmetry.Group object         species: a list of atomic symbols for each ion type         numIons: a list of the number of each type of atom within the             primitive cell (NOT the conventional cell)         area: the effective cross-sectional area, in Angstroms squared, of the             unit cell         factor: a volume factor used to generate a larger or smaller             unit cell. Increasing this gives extra space between atoms         lattice: an optional Lattice object to use for the unit cell         tm: the Tol_matrix object used to generate the crystal The number of periodic dimensions of the crystal The periodic axis of the crystal. The international space group number (there is not a 1-1 correspondence         with Rod groups). the effective cross-sectional area, in Angstroms squared, of the         unit cell. A 0d counterpart to random_crystal. Generates a random atomic cluster based     on a 0d Point group instead of a 3d spacegroup. The generated pymatgen     structure can be accessed via self.struct      Args:         group: the Schoenflies symbol for the point group (ex: "Oh", "C5v", "D3")             OR the number between 1-32 for a crystallographic point group,             OR, a pyxtal.symmetry.Group object             See:             https://en.wikipedia.org/wiki/Schoenflies_notation#Point_groups             for more information         species: a list of atomic symbols for each ion type         numIons: a list of the number of each type of atom within the             primitive cell (NOT the conventional cell)         factor: a volume factor used to generate a larger or smaller             unit cell. Increasing this gives extra space between atoms         lattice: an optional Lattice object to use for the unit cell         tm: the Tol_matrix object used to generate the crystal The number of periodic dimensions of the crystal The periodic axis of the crystal. The international space group number (there is not a 1-1 correspondence         with Point groups). #-------------------------------- Options ------------------------- #To check whether a file already exists #Output a cif file #POSCAR output #rand_crystal.struct.to(fmt="poscar", filename = '1.vasp') #spglib style structure called cell #Print additional information about the structure #If generation fails