elasticipy 3.0.0__py3-none-any.whl → 4.0.0__py3-none-any.whl

Elasticipy/tensors/fourth_order.py

@@ -0,0 +1,591 @@
+import numpy as np
+from Elasticipy.tensors.second_order import SymmetricSecondOrderTensor, rotation_to_matrix, is_orix_rotation, \
+    SecondOrderTensor, ALPHABET
+from scipy.spatial.transform import Rotation
+from copy import deepcopy
+
+a = np.sqrt(2)
+KELVIN_MAPPING_MATRIX = np.array([[1, 1, 1, a, a, a],
+                                  [1, 1, 1, a, a, a],
+                                  [1, 1, 1, a, a, a],
+                                  [a, a, a, 2, 2, 2],
+                                  [a, a, a, 2, 2, 2],
+                                  [a, a, a, 2, 2, 2], ])
+
+
+def voigt_indices(i, j):
+    """
+    Translate the two-index notation to one-index notation
+
+    Parameters
+    ----------
+    i : int or np.ndarray
+        First index
+    j : int or np.ndarray
+        Second index
+
+    Returns
+    -------
+    Index in the vector of length 6
+    """
+    voigt_mat = np.array([[0, 5, 4],
+                          [5, 1, 3],
+                          [4, 3, 2]])
+    return voigt_mat[i, j]
+
+
+def unvoigt_index(i):
+    """
+    Translate the one-index notation to two-index notation
+
+    Parameters
+    ----------
+    i : int or np.ndarray
+        Index to translate
+    """
+    inverse_voigt_mat = np.array([[0, 0],
+                                  [1, 1],
+                                  [2, 2],
+                                  [1, 2],
+                                  [0, 2],
+                                  [0, 1]])
+    return inverse_voigt_mat[i]
+
+def rotate_tensor(full_tensor, r):
+    """
+    Rotate a (full) fourth-order tensor.
+
+    Parameters
+    ----------
+    full_tensor : numpy.ndarray
+        array of shape (3,3,3,3) or (...,3,3,3,3) containing all the components
+    r : scipy.spatial.Rotation or orix.quaternion.Rotation
+        Rotation, or set of rotations, to apply
+
+    Returns
+    -------
+    numpy.ndarray
+        Rotated tensor. If r is an array, the corresponding axes will be added as first axes in the result array.
+    """
+    rot_mat = rotation_to_matrix(r)
+    str_ein = '...im,...jn,...ko,...lp,...mnop->...ijkl'
+    return np.einsum(str_ein, rot_mat, rot_mat, rot_mat, rot_mat, full_tensor)
+
+class FourthOrderTensor:
+    """
+    Template class for manipulating symmetric fourth-order tensors.
+
+    Attributes
+    ----------
+    matrix : np.ndarray
+        (6,6) matrix gathering all the components of the tensor, using the Voigt notation.
+    """
+    tensor_name = '4th-order'
+
+    def __init__(self, M, mapping='Kelvin', check_minor_symmetry=True, force_minor_symmetry=False):
+        """
+        Construct of Fourth-order tensor with minor symmetry.
+
+        Parameters
+        ----------
+        M : np.ndarray
+            (6,6) matrix corresponding to the stiffness tensor, written using the Voigt notation, or array of shape
+            (3,3,3,3).
+        mapping : str or list of list, or numpy/ndarray, optional
+            Mapping convention to translate the (3,3,3,3) array to (6,6) matrix
+        check_minor_symmetry : bool, optional
+            If true (default), check that the input array have minor symmetries (see Notes). Only used if an array of
+            shape (...,3,3,3,3) is passed.
+        force_minor_symmetry :
+            Ensure that the tensor displays minor symmetry.
+
+        Notes
+        -----
+        The minor symmetry is defined so that:
+
+        .. math::
+
+            M_{ijkl}=M_{jikl}=M_{jilk}=M_{ijlk}
+
+        """
+        if isinstance(mapping, (list, tuple, np.ndarray)):
+            self.mapping_matrix = mapping
+            self.mapping_name = 'custom'
+        else:
+            mapping = mapping.capitalize()
+            self.mapping_name = mapping
+            if mapping == 'Kelvin':
+                self.mapping_matrix = KELVIN_MAPPING_MATRIX
+            elif mapping == 'Voigt':
+                self.mapping_matrix = np.ones((6,6))
+            else:
+                raise ValueError('The mapping to use can be either "Kelvin", "Voigt", or a (6,6) matrix.')
+
+        M = np.asarray(M)
+        if M.shape[-2:] == (6, 6):
+            matrix = M
+        elif M.shape[-4:] == (3, 3, 3, 3):
+            Mijlk = np.swapaxes(M, -1, -2)
+            Mjikl = np.swapaxes(M, -3, -4)
+            Mjilk = np.swapaxes(Mjikl, -1, -2)
+            if force_minor_symmetry:
+                M = 0.25 * (M + Mijlk + Mjikl + Mjilk)
+            elif check_minor_symmetry:
+                symmetry = np.all(M == Mijlk) and np.all(M == Mjikl) and np.all(M == Mjilk)
+                if not symmetry:
+                    raise ValueError('The input array does not have minor symmetry')
+            matrix = self._full_to_matrix(M)
+        else:
+            raise ValueError('The input matrix must of shape (...,6,6) or (...,3,3,3,3)')
+        self.matrix = matrix
+        for i in range(0, 6):
+            for j in range(0, 6):
+                def getter(obj, I=i, J=j):
+                    return obj.matrix[...,I, J]
+
+                getter.__doc__ = f"Returns the ({i + 1},{j + 1}) component of the {self.tensor_name} matrix."
+                component_name = 'C{}{}'.format(i + 1, j + 1)
+                setattr(self.__class__, component_name, property(getter))  # Dynamically create the property
+
+    def __repr__(self):
+        if (self.ndim == 0) or ((self.ndim==1) and self.shape[0]<5):
+            msg = '{} tensor (in {} mapping):\n'.format(self.tensor_name, self.mapping_name)
+            msg += self.matrix.__str__()
+        else:
+            msg = '{} tensor array of shape {}'.format(self.tensor_name, self.shape)
+        return msg
+
+    @property
+    def shape(self):
+        """
+        Return the shape of the tensor array
+        Returns
+        -------
+        tuple
+            Shape of the tensor array
+        """
+        *shape, _, _ = self.matrix.shape
+        return tuple(shape)
+
+    def full_tensor(self):
+        """
+        Returns the full (unvoigted) tensor, as a [3, 3, 3, 3] array
+
+        Returns
+        -------
+        np.ndarray
+            Full tensor (4-index notation)
+        """
+        i, j, k, ell = np.indices((3, 3, 3, 3))
+        ij = voigt_indices(i, j)
+        kl = voigt_indices(k, ell)
+        m = self.matrix[..., ij, kl] / self.mapping_matrix[ij, kl]
+        return m
+
+    def flatten(self):
+        """
+        Flatten the tensor
+
+        If the tensor array is of shape (m,n,o...,r), the flattened array will be of shape (m*n*o*...*r,).
+
+        Returns
+        -------
+        SymmetricFourthOrderTensor
+            Flattened tensor
+        """
+        shape = self.shape
+        if shape:
+            t2 = deepcopy(self)
+            p = (np.prod(self.shape), 6, 6)
+            t2.matrix = self.matrix.reshape(p)
+            return t2
+        else:
+            return self
+
+    def _full_to_matrix(self, full_tensor):
+        kl, ij = np.indices((6, 6))
+        i, j = unvoigt_index(ij).T
+        k, ell = unvoigt_index(kl).T
+        return full_tensor[..., i, j, k, ell] * self.mapping_matrix[ij, kl]
+
+    def rotate(self, rotation):
+        """
+        Apply a single rotation to a tensor, and return its component into the rotated frame.
+
+        Parameters
+        ----------
+        rotation : Rotation or orix.quaternion.rotation.Rotation
+            Rotation to apply
+
+        Returns
+        -------
+        SymmetricFourthOrderTensor
+            Rotated tensor
+        """
+        t2 = deepcopy(self)
+        rotated_tensor = rotate_tensor(self.full_tensor(), rotation)
+        t2.matrix = self._full_to_matrix(rotated_tensor)
+        return t2
+
+    @property
+    def ndim(self):
+        """
+        Returns the dimensionality of the tensor (number of dimensions in the orientation array)
+
+        Returns
+        -------
+        int
+            Number of dimensions
+        """
+        shape = self.shape
+        if shape:
+            return len(shape)
+        else:
+            return 0
+
+    def mean(self, axis=None):
+        """
+        Compute the mean value of the tensor T
+
+        Parameters
+        ----------
+        axis : int or list of int or tuple of int, optional
+            axis along which to compute the mean. If None, the mean is computed on the flattened tensor
+
+        Returns
+        -------
+        numpy.ndarray
+            If no axis is given, the result will be of shape (3,3,3,3).
+            Otherwise, if T.ndim=m, and len(axis)=n, the returned value will be of shape (...,3,3,3,3), with ndim=m-n+4
+        """
+        t2 = deepcopy(self)
+        if axis is None:
+            axis = tuple([i for i in range(0,self.ndim)])
+        t2.matrix = np.mean(self.matrix, axis=axis)
+        return t2
+
+    def __add__(self, other):
+        if isinstance(other, np.ndarray):
+            if other.shape == (6, 6):
+                mat = self.matrix + other
+            elif other.shape == (3, 3, 3, 3):
+                mat = self._full_to_matrix(self.full_tensor() + other)
+            else:
+                raise ValueError('The input argument must be either a 6x6 matrix or a (3,3,3,3) array.')
+        elif isinstance(other, FourthOrderTensor):
+            if type(other) == type(self):
+                mat = self.full_tensor() + other.full_tensor()
+            else:
+                raise ValueError('The two tensors to add must be of the same class.')
+        else:
+            raise ValueError('I don''t know how to add {} with {}.'.format(type(self), type(other)))
+        return self.__class__(mat, mapping=self.mapping_matrix)
+
+    def __sub__(self, other):
+        if isinstance(other, FourthOrderTensor):
+            return self.__add__(-other.matrix)
+        else:
+            return self.__add__(-other)
+
+    def __neg__(self):
+        t = deepcopy(self)
+        t.matrix = -t.matrix
+        return t
+
+    def ddot(self, other, mode='pair'):
+        """
+        Perform tensor product contracted twice (":") between two fourth-order tensors
+
+        Parameters
+        ----------
+        other : FourthOrderTensor or SecondOrderTensor
+            Right-hand side of ":" symbol
+        mode : str, optional
+            If mode=="pair", the tensors must be broadcastable, and the tensor product are performed on the last axes.
+            If mode=="cross", all cross-combinations are considered.
+
+        Returns
+        -------
+        FourthOrderTensor or numpy.ndarray
+         If both the tensors are 0D (no orientation), the return value will be of type SymmetricTensor
+         Otherwise, the return value will be the full tensor, of shape (...,3,3,3,3).
+        """
+        if isinstance(other, FourthOrderTensor):
+            if self.ndim == 0 and other.ndim == 0:
+                return FourthOrderTensor(np.einsum('ijmn,nmkl->ijkl', self.full_tensor(), other.full_tensor()))
+            else:
+                if mode == 'pair':
+                    ein_str = '...ijmn,...nmkl->...ijkl'
+                else:
+                    ndim_0 = self.ndim
+                    ndim_1 = other.ndim
+                    indices_0 = ALPHABET[:ndim_0]
+                    indices_1 = ALPHABET[:ndim_1].upper()
+                    indices_2 = indices_0 + indices_1
+                    ein_str = indices_0 + 'wxXY,' + indices_1 + 'YXyz->' + indices_2 + 'wxyz'
+                matrix = np.einsum(ein_str, self.full_tensor(), other.full_tensor())
+                return FourthOrderTensor(matrix)
+        elif isinstance(other, SecondOrderTensor):
+            if self.ndim == 0 and other.ndim == 0:
+                return SymmetricSecondOrderTensor(np.einsum('ijkl,kl->ij', self.full_tensor(), other.matrix))
+            else:
+                if mode == 'pair':
+                    ein_str = '...ijkl,...kl->...ij'
+                else:
+                    ndim_0 = self.ndim
+                    ndim_1 = other.ndim
+                    indices_0 = ALPHABET[:ndim_0]
+                    indices_1 = ALPHABET[:ndim_1].upper()
+                    indices_2 = indices_0 + indices_1
+                    ein_str = indices_0 + 'wxXY,' + indices_1 + 'XY->' + indices_2 + 'wx'
+                matrix = np.einsum(ein_str, self.full_tensor(), other.matrix)
+                return SecondOrderTensor(matrix)
+
+
+    def __mul__(self, other):
+        if isinstance(other, (FourthOrderTensor, SecondOrderTensor)):
+            return self.ddot(other)
+        elif isinstance(other, np.ndarray):
+            shape = other.shape
+            if other.shape == self.shape[-len(shape):]:
+                matrix = self.matrix * other[...,np.newaxis, np.newaxis]
+                return self.__class__(matrix)
+            else:
+                raise ValueError('The arrays to multiply could not be broadcasted with shapes {} and {}'.format(self.shape, other.shape[:-2]))
+        elif isinstance(other, Rotation) or is_orix_rotation(other):
+            return self.rotate(other)
+        else:
+            return self.__class__(self.matrix * other)
+
+    def __truediv__(self, other):
+        if isinstance(other, (SecondOrderTensor, FourthOrderTensor)):
+            return self * other.inv()
+        else:
+            return self * (1 / other)
+
+
+    def transpose_array(self):
+        """
+        Transpose the orientations of the tensor array
+
+        Returns
+        -------
+        FourthOrderTensor
+            The same tensor, but with transposed axes
+        """
+        ndim = self.ndim
+        if ndim==0 or ndim==1:
+            return self
+        else:
+            new_axes = tuple(range(ndim))[::-1] + (ndim, ndim + 1)
+            transposed_matrix = self.matrix.transpose(new_axes)
+            return self.__class__(transposed_matrix)
+
+    def __rmul__(self, other):
+        if isinstance(other, (Rotation, float, int, np.number)) or is_orix_rotation(other):
+            return self * other
+        else:
+            raise NotImplementedError('A fourth order tensor can be left-multiplied by rotations or scalar only.')
+
+    def __eq__(self, other):
+        if isinstance(other, FourthOrderTensor):
+            return np.all(self.matrix == other.matrix, axis=(-1,-2))
+        elif isinstance(other, (float, int)) or (isinstance(other, np.ndarray) and other.shape[-2:] == (6, 6)):
+            return np.all(self.matrix == other, axis=(-1,-2))
+        else:
+            raise NotImplementedError('The element to compare with must be a fourth-order tensor '
+                                      'or an array of shape (6,6).')
+
+    def __getitem__(self, item):
+        if self.ndim:
+            sub_mat= self.matrix[item]
+            if sub_mat.shape[-2:] != (6,6):
+                raise IndexError('Too many indices for tensor array: array is {}-dimensional, but {} were provided'.format(self.ndim, len(item)))
+            else:
+                return self.__class__(sub_mat)
+        else:
+            raise IndexError('A single tensor cannot be subindexed')
+
+    def __setitem__(self, index, value):
+        if isinstance(value, np.ndarray):
+            if value.shape[-2:] == (6,6):
+                self.matrix[index] = value
+            elif value.shape[-4:] == (3,3,3,3):
+                submatrix = self._full_to_matrix(value)
+                self.matrix[index] = submatrix
+            else:
+                return ValueError('The R.h.s must be either of shape (...,6,6) or (...,3,3,3,3)')
+        elif isinstance(value, FourthOrderTensor):
+            self.matrix[index] = value.matrix / value.mapping_matrix * self.mapping_matrix
+        else:
+            raise NotImplementedError('The r.h.s must be either an ndarray or an object of class {}'.format(self.__class__))
+
+    @classmethod
+    def identity(cls, shape=(), return_full_tensor=False, mapping='Kelvin'):
+        """
+        Create a 4th-order identity tensor
+
+        Parameters
+        ----------
+        shape : int or tuple, optional
+            Shape of the tensor to create
+        return_full_tensor : bool, optional
+            If True, return the full tensor as a (3,3,3,3) or a (...,3,3,3,3) array. Otherwise, the tensor is returned
+            as a SymmetricTensor object.
+
+        Returns
+        -------
+        numpy.ndarray or SymmetricTensor
+            Identity tensor
+        """
+        eye = np.eye(3)
+        if isinstance(shape, int):
+            shape = (shape,)
+        if len(shape):
+            for n in np.flip(shape):
+                eye = np.repeat(eye[np.newaxis,...], n, axis=0)
+        a = np.einsum('...ik,...jl->...ijkl', eye, eye)
+        b = np.einsum('...il,...jk->...ijkl', eye, eye)
+        full = 0.5*(a + b)
+        if return_full_tensor:
+            return full
+        else:
+            return cls(full, mapping=mapping)
+
+    def inv(self):
+        """
+        Invert the tensor. The inverted tensors inherits the properties (if any)
+
+        Returns
+        -------
+        FourthOrderTensor
+            Inverse tensor
+        """
+        t2 = deepcopy(self)
+        new_matrix = np.linalg.inv(self.matrix)
+        t2.matrix = new_matrix
+        return t2
+
+    @classmethod
+    def zeros(cls, shape=()):
+        """
+        Create a fourth-order tensor populated with zeros
+
+        Parameters
+        ----------
+        shape : int or tuple, optional
+            Shape of the tensor to create
+        Returns
+        -------
+        FourthOrderTensor
+        """
+        if isinstance(shape, int):
+            shape = (shape, 6, 6)
+        else:
+            shape = shape + (6,6)
+        zeros = np.zeros(shape)
+        return cls(zeros)
+
+class SymmetricFourthOrderTensor(FourthOrderTensor):
+    tensor_name = 'Symmetric 4th-order'
+
+    def __init__(self, M, check_symmetries=True, force_symmetries=False, **kwargs):
+        """
+        Construct a fully symmetric fourth-order tensor from a (...,6,6) or a (3,3,3,3) array.
+
+        The input matrix must be symmetric, otherwise an error is thrown (except if check_symmetry==False, see below)
+
+        Parameters
+        ----------
+        M : np.ndarray
+            (6,6) matrix corresponding to the stiffness tensor, written using the Voigt notation, or array of shape
+            (3,3,3,3).
+        check_symmetries : bool, optional
+            Whether to check or not that the tensor to built displays both major and minor symmetries (see Notes).
+        force_symmetries : bool, optional
+            If true, ensure that the tensor displays both minor and major symmetries.
+
+        Notes
+        -----
+        The major symmetry is defined so that:
+
+        .. math::
+
+            M_{ijkl}=M_{klij}
+
+        whereas the minor symmetry is:
+
+        .. math::
+
+            M_{ijkl}=M_{jikl}=M_{jilk}=M_{ijlk}
+        """
+        super().__init__(M, check_minor_symmetry=check_symmetries, force_minor_symmetry=force_symmetries, **kwargs)
+        if force_symmetries:
+            self.matrix = 0.5*(self.matrix + self.matrix.swapaxes(-1,-2))
+        elif check_symmetries and not np.all(np.isclose(self.matrix, self.matrix.swapaxes(-1, -2))):
+            raise ValueError('The input matrix must be symmetric')
+
+    def invariants(self, order='all'):
+        """
+        Compute the invariants of the tensor.
+
+        Compute the linear or/and quadratic invariant of the fourth-order tensor (see notes)
+
+        Parameters
+        ----------
+        order : str, optional
+            If 'linear', only A1 and A2 are returned
+            If 'quadratic', A1², A2², B1, B2, B3, B4 and B5 are returned
+            If 'all' (default), A1, A2, A1², A2², B1, B2, B3, B4 and B5 are returned
+
+        Returns
+        -------
+        tuple
+            invariants of the given order (see above)
+
+        Notes
+        -----
+        The nomenclature of the invariants follows that of [4]_. The linear invariants are:
+
+        .. math::
+
+            A_1=C_{ijij}
+
+            A_2=C_{iijj}
+
+        whereas the quadratic invariants are:
+
+        .. math::
+
+            B_1 = C_{ijkl}C_{ijkl}
+
+            B_2 = C_{iikl}C_{jjkl}
+
+            B_3 = C_{iikl}C_{jkjl}
+
+            B_4 = C_{kiil}C_{kjjl}
+
+            B_5 = C_{ijkl}C_{ikjl}
+
+        References
+        ----------
+        .. [4] Norris, A. N. (22 May 2007). "Quadratic invariants of elastic moduli". The Quarterly Journal of Mechanics
+         and Applied Mathematics. 60 (3): 367–389. doi:10.1093/qjmam/hbm007
+        """
+        t = self.full_tensor()
+        order = order.lower()
+        A1 = np.einsum('...ijij->...',t)
+        A2 = np.einsum('...iijj->...',t)
+        lin_inv = (A1, A2)
+        if order == 'linear':
+            return lin_inv
+        B1 = np.einsum('...ijkl,...ijkl->...',t, t)
+        B2 = np.einsum('...iikl,...jjkl->...', t, t)
+        B3 = np.einsum('...iikl,...jkjl->...', t, t)
+        B4 = np.einsum('...kiil,...kjjl->...', t, t)
+        B5 = np.einsum('...ijkl,...ikjl->...', t, t)
+        quad_inv = (A1**2, A2**2, A1*A2, B1, B2, B3, B4, B5)
+        if order == 'quadratic':
+            return quad_inv
+        else:
+            return lin_inv + quad_inv

Elasticipy/{SecondOrderTensor.py → tensors/second_order.py}

@@ -552,7 +552,7 @@ class SecondOrderTensor:
 
         Examples
         --------
-        >>> from Elasticipy.SecondOrderTensor import SecondOrderTensor
+        >>> from Elasticipy.tensors.second_order import SecondOrderTensor
         >>> A=SecondOrderTensor.rand(10)
         >>> B=SecondOrderTensor.rand(10)
         >>> AB_pair = A.dot(B)
@@ -1078,7 +1078,7 @@ class SecondOrderTensor:
         --------
         Generate a single random tensor:
 
-        >>> from Elasticipy.SecondOrderTensor import SecondOrderTensor as tensor
+        >>> from Elasticipy.tensors.second_order import SecondOrderTensor as tensor
         >>> tensor.rand(seed=123)
         Second-order tensor
         [[0.68235186 0.05382102 0.22035987]
@@ -1364,7 +1364,7 @@ class SecondOrderTensor:
         flatten : Converts a tensor array to 1D tensor array
         """
         try:
-            from Elasticipy.StressStrainTensors import StrainTensor, StressTensor
+            from Elasticipy.tensors.stress_strain import StrainTensor, StressTensor
             if isinstance(self, StrainTensor):
                 from pymatgen.analysis.elasticity import Strain as Constructor
             elif isinstance(self, StressTensor):
@@ -1403,7 +1403,7 @@ class SymmetricSecondOrderTensor(SecondOrderTensor):
         --------
         We can create a symmetric tensor by privoding the full matrix, as long it is symmetric:
 
-        >>> from Elasticipy.SecondOrderTensor import SymmetricSecondOrderTensor
+        >>> from Elasticipy.tensors.second_order import SymmetricSecondOrderTensor
         >>> a = SymmetricSecondOrderTensor([[11, 12, 13],[12, 22, 23],[13, 23, 33]])
         >>> print(a)
         Symmetric second-order tensor
@@ -1462,7 +1462,7 @@ class SymmetricSecondOrderTensor(SecondOrderTensor):
 
         Examples
         --------
-        >>> from Elasticipy.SecondOrderTensor import SymmetricSecondOrderTensor
+        >>> from Elasticipy.tensors.second_order import SymmetricSecondOrderTensor
         >>> SymmetricSecondOrderTensor.from_Voigt([11, 22, 33, 23, 13, 12])
         Symmetric second-order tensor
         [[11. 12. 13.]
@@ -1573,7 +1573,7 @@ class SkewSymmetricSecondOrderTensor(SecondOrderTensor):
         --------
         One can construct a skew-symmetric tensor by providing the full skew-symmetric matrix:
 
-        >>> from Elasticipy.SecondOrderTensor import SkewSymmetricSecondOrderTensor
+        >>> from Elasticipy.tensors.second_order import SkewSymmetricSecondOrderTensor
         >>> a = SkewSymmetricSecondOrderTensor([[0, 12, 13],[-12, 0, 23],[-13, -23, 0]])
         >>> print(a)
         Skew-symmetric second-order tensor