Example #1
0
def test_cell_tools():
    # test known values: simple cubic
    cell_a = 5.0
    cell = np.identity(3) * cell_a
    volume = cell_a**3.0
    cryst_const = np.array([cell_a] * 3 + [90.0] * 3)
    np.testing.assert_array_almost_equal(crys.cell2cc(cell), cryst_const)
    np.testing.assert_array_almost_equal(crys.cc2cell(cryst_const), cell)
    np.testing.assert_almost_equal(volume, crys.volume_cc(cryst_const))
    np.testing.assert_almost_equal(volume, crys.volume_cell(cell))
    np.testing.assert_array_almost_equal(crys.cc2cell(crys.cell2cc(cell)),
                                         cell)
    np.testing.assert_array_almost_equal(
        crys.cell2cc(crys.cc2cell(cryst_const)), cryst_const)

    # random
    #
    # volume : volume_cc() always returns positive values, whereas det() and
    #     volume_cell() may return the volume with negative sign but correct
    #     magnitude.
    # cell : A random cell does also have a random orientation in space. It
    #     does NOT conform the usual convention: a along x, b in x-y plane.
    #     However, the cryst_const and volume must be invariant.
    cell = np.random.rand(3, 3)
    cryst_const = crys.cell2cc(cell)
    volume = abs(np.linalg.det(cell))
    np.testing.assert_almost_equal(volume, crys.volume_cc(cryst_const))
    np.testing.assert_almost_equal(volume, abs(crys.volume_cell(cell)))
    # this must always fail for random cells
    try:
        np.testing.assert_array_almost_equal(crys.cc2cell(crys.cell2cc(cell)),
                                             cell)
    except AssertionError:
        pass
    # Here, we convert cryst_const to a *different* cell which conforms to the
    # orientation convention, and back to cryst_const.
    np.testing.assert_array_almost_equal(
        crys.cell2cc(crys.cc2cell(cryst_const)), cryst_const)

    # 3d
    cell = rand(100, 3, 3)
    cc = crys.cell2cc3d(cell, axis=0)
    vol_cell = np.abs(crys.volume_cell3d(cell, axis=0))
    vol_cc = crys.volume_cc3d(cc, axis=0)

    assert crys.cell2cc3d(cell, axis=0).shape == (100, 6)
    assert crys.cc2cell3d(cc, axis=0).shape == (100, 3, 3)

    assert vol_cc.shape == (100, )
    assert vol_cell.shape == (100, )
    aaae(vol_cell, vol_cc)
    aaae(crys.cell2cc3d(crys.cc2cell3d(cc)), cc)
Example #2
0
def test_cell_tools():
    # test known values: simple cubic
    cell_a = 5.0
    cell = np.identity(3)*cell_a
    volume = cell_a**3.0
    cryst_const = np.array([cell_a]*3 + [90.0]*3)
    np.testing.assert_array_almost_equal(crys.cell2cc(cell), cryst_const)
    np.testing.assert_array_almost_equal(crys.cc2cell(cryst_const), cell)
    np.testing.assert_almost_equal(volume, crys.volume_cc(cryst_const))
    np.testing.assert_almost_equal(volume, crys.volume_cell(cell))
    np.testing.assert_array_almost_equal(crys.cc2cell(crys.cell2cc(cell)), cell)
    np.testing.assert_array_almost_equal(crys.cell2cc(crys.cc2cell(cryst_const)),
                                         cryst_const)
                                         
    # random
    #
    # volume : volume_cc() always returns positive values, whereas det() and
    #     volume_cell() may return the volume with negative sign but correct
    #     magnitude.
    # cell : A random cell does also have a random orientation in space. It
    #     does NOT conform the usual convention: a along x, b in x-y plane.
    #     However, the cryst_const and volume must be invariant.
    cell = np.random.rand(3,3)
    cryst_const = crys.cell2cc(cell)
    volume = abs(np.linalg.det(cell))
    np.testing.assert_almost_equal(volume, crys.volume_cc(cryst_const))
    np.testing.assert_almost_equal(volume, abs(crys.volume_cell(cell)))
    # this must always fail for random cells
    try:
        np.testing.assert_array_almost_equal(crys.cc2cell(crys.cell2cc(cell)), cell)
    except AssertionError:
        pass
    # Here, we convert cryst_const to a *different* cell which conforms to the
    # orientation convention, and back to cryst_const.
    np.testing.assert_array_almost_equal(crys.cell2cc(crys.cc2cell(cryst_const)),
                                         cryst_const)

    # 3d
    cell = rand(100,3,3)
    cc = crys.cell2cc3d(cell, axis=0)
    vol_cell = np.abs(crys.volume_cell3d(cell, axis=0))
    vol_cc = crys.volume_cc3d(cc, axis=0)

    assert crys.cell2cc3d(cell, axis=0).shape == (100,6)
    assert crys.cc2cell3d(cc, axis=0).shape == (100,3,3)
    
    assert vol_cc.shape == (100,)
    assert vol_cell.shape == (100,)
    aaae(vol_cell, vol_cc)
    aaae(crys.cell2cc3d(crys.cc2cell3d(cc)), cc)
Example #3
0
    def get_random_cryst_const(self):
        """Create random cryst_const.

        Returns
        -------
        cryst_const : 1d array (6,)

        Raises
        ------
        RandomStructureFail
        """
        def _get():
            return np.concatenate(
                (uniform(self.length_range[0], self.length_range[1], 3),
                 uniform(self.angle_range[0], self.angle_range[1], 3)))

        cnt = 1
        while cnt <= self.cell_maxtry:
            cc = _get()
            vol = volume_cc(cc)
            if not self.vol_range[0] <= vol <= self.vol_range[1]:
                cc = _get()
                cnt += 1
            else:
                self.counters['cryst_const'] = cnt
                return cc
        raise RandomStructureFail("failed creating random cryst_const")
Example #4
0
    def get_random_cryst_const(self):
        """Create random cryst_const.

        Returns
        -------
        cryst_const : 1d array (6,)

        Raises
        ------
        RandomStructureFail
        """
        def _get():
            return np.concatenate((uniform(self.length_range[0], 
                                           self.length_range[1], 3),
                                   uniform(self.angle_range[0], 
                                           self.angle_range[1], 3)))
        cnt = 1
        while cnt <= self.cell_maxtry:
            cc = _get()
            vol = volume_cc(cc)
            if not self.vol_range[0] <= vol <= self.vol_range[1]:
                cc = _get()
                cnt += 1                                 
            else:
                self.counters['cryst_const'] = cnt
                return cc
        raise RandomStructureFail("failed creating random cryst_const")