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
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
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
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:])
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__