How to use the pyxtal.database.element.Element.number_from_specie function in pyxtal

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

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 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))

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))