Example #1
0
def test_geometry_car_allsame(sisl_tmp):
    f = sisl_tmp('test_read_write.POSCAR', _dir)

    atoms = Atom[1]
    xyz = np.random.rand(10, 3)
    geom = Geometry(xyz, atoms, 100)

    geom.write(carSileVASP(f, 'w'))

    assert carSileVASP(f).read_geometry() == geom
Example #2
0
def test_geometry_car_mixed(sisl_tmp):
    f = sisl_tmp('test_read_write.POSCAR', _dir)

    atoms = [Atom[1], Atom[2], Atom[2], Atom[1], Atom[1], Atom[2], Atom[3]]
    xyz = np.random.rand(len(atoms), 3)
    geom = Geometry(xyz, atoms, 100)

    geom.write(carSileVASP(f, 'w'))

    assert carSileVASP(f).read_geometry() == geom
Example #3
0
def test_geometry_car_group(sisl_tmp):
    f = sisl_tmp('test_sort.POSCAR', _dir)

    atoms = [Atom[1], Atom[2], Atom[2], Atom[1], Atom[1], Atom[2], Atom[3]]
    xyz = np.random.rand(len(atoms), 3)
    geom = Geometry(xyz, atoms, 100)

    geom.write(carSileVASP(f, 'w'), group_species=True)

    assert carSileVASP(f).read_geometry() != geom
    geom = carSileVASP(f).geometry_group(geom)
    assert carSileVASP(f).read_geometry() == geom
Example #4
0
def test_geometry_car_dynamic(sisl_tmp):
    f = sisl_tmp('test_dynamic.POSCAR', _dir)

    atoms = Atom[1]
    xyz = np.random.rand(10, 3)
    geom = Geometry(xyz, atoms, 100)

    read = carSileVASP(f)

    # no dynamic (direct geometry)
    geom.write(carSileVASP(f, 'w'), dynamic=None)
    g, dyn = read.read_geometry(ret_dynamic=True)
    assert dyn is None

    geom.write(carSileVASP(f, 'w'), dynamic=False)
    g, dyn = read.read_geometry(ret_dynamic=True)
    assert not np.any(dyn)

    geom.write(carSileVASP(f, 'w'), dynamic=True)
    g, dyn = read.read_geometry(ret_dynamic=True)
    assert np.all(dyn)

    dynamic = [False] * len(geom)
    dynamic[0] = [True, False, True]
    geom.write(carSileVASP(f, 'w'), dynamic=dynamic)
    g, dyn = read.read_geometry(ret_dynamic=True)
    assert np.array_equal(dynamic[0], dyn[0])
    assert not np.any(dyn[1:])
Example #5
0
def test_nc_ghost(sisl_tmp):
    f = sisl_tmp('ghost.nc', _dir)
    a1 = Atom(1)
    am1 = Atom(-1)
    g = Geometry([[0., 0., i] for i in range(2)], [a1, am1], 2.)
    g.write(ncSileSiesta(f, 'w'))

    g2 = ncSileSiesta(f).read_geometry()
    assert np.allclose(g.cell, g2.cell)
    assert np.allclose(g.xyz, g2.xyz)
    assert np.allclose(g.atoms.Z, g2.atoms.Z)
    assert g.atoms[0].__class__ is g2.atoms[0].__class__
    assert g.atoms[1].__class__ is g2.atoms[1].__class__
    assert g.atoms[0].__class__ is not g2.atoms[1].__class__