def test_extend_array():
arr = rand(3,3)
nrep = 5
a0 = num.extend_array(arr, nrep, axis=0)
a1 = num.extend_array(arr, nrep, axis=1)
a2 = num.extend_array(arr, nrep, axis=2)
am1 = num.extend_array(arr, nrep, axis=-1)
assert a0.shape == (nrep,3,3)
assert a1.shape == (3,nrep,3)
assert a2.shape == (3,3,nrep)
assert am1.shape == (3,3,nrep)
equal(a2, am1)
for axis, aa in enumerate([a0, a1, a2]):
for ii in range(nrep):
# slicetake(a0, 3, 0) -> a0[3,:,:]
equal(arr, num.slicetake(aa, ii, axis=axis))
def test_cart2frac_traj():
nstep = 100
coords = rand(nstep,20,3)
coords_copy = coords.copy()
cell = rand(nstep,3,3)
c1 = np.array([np.dot(coords[ii,...], np.linalg.inv(cell[ii,...])) for ii in \
range(nstep)])
c2 = _flib.cart2frac_traj(coords, cell)
c3 = crys.coord_trans3d(coords, new=cell,
old=num.extend_array(np.identity(3),
nstep=nstep, axis=0))
assert (coords == coords_copy).all()
assert np.allclose(c1, c2)
assert np.allclose(c1, c3)
assert c2.flags.f_contiguous
def test_frac2cart_traj():
nstep = 100
coords_frac = rand(nstep,20,3)
coords_frac_copy = coords_frac.copy()
cell = rand(nstep,3,3)
c1 = np.array([np.dot(coords_frac[ii,...], cell[ii,...]) for ii in \
range(nstep)])
c2 = _flib.frac2cart_traj(coords_frac, cell)
c3 = crys.coord_trans3d(coords_frac, old=cell,
new=num.extend_array(np.identity(3),
nstep=nstep, axis=0))
assert (coords_frac == coords_frac_copy).all()
assert np.allclose(c1, c2)
assert np.allclose(c1, c3)
assert c2.flags.f_contiguous
def test_cart2frac_traj():
nstep = 100
coords = rand(nstep, 20, 3)
coords_copy = coords.copy()
cell = rand(nstep, 3, 3)
c1 = np.array([np.dot(coords[ii,...], np.linalg.inv(cell[ii,...])) for ii in \
range(nstep)])
c2 = _flib.cart2frac_traj(coords, cell)
c3 = crys.coord_trans3d(coords,
new=cell,
old=num.extend_array(np.identity(3),
nstep=nstep,
axis=0))
assert (coords == coords_copy).all()
assert np.allclose(c1, c2)
assert np.allclose(c1, c3)
assert c2.flags.f_contiguous
def test_frac2cart_traj():
nstep = 100
coords_frac = rand(nstep, 20, 3)
coords_frac_copy = coords_frac.copy()
cell = rand(nstep, 3, 3)
c1 = np.array([np.dot(coords_frac[ii,...], cell[ii,...]) for ii in \
range(nstep)])
c2 = _flib.frac2cart_traj(coords_frac, cell)
c3 = crys.coord_trans3d(coords_frac,
old=cell,
new=num.extend_array(np.identity(3),
nstep=nstep,
axis=0))
assert (coords_frac == coords_frac_copy).all()
assert np.allclose(c1, c2)
assert np.allclose(c1, c3)
assert c2.flags.f_contiguous
def test_dist_traj():
natoms = 10
nstep = 100
cell = rand(nstep, 3, 3)
stress = rand(nstep, 3, 3)
forces = rand(nstep, natoms, 3)
etot = rand(nstep)
cryst_const = crys.cell2cc3d(cell, axis=0)
coords_frac = np.random.rand(nstep, natoms, 3)
coords = crys.coord_trans3d(coords=coords_frac,
old=cell,
new=num.extend_array(np.identity(3),
nstep,
axis=0),
axis=1,
timeaxis=0)
assert cryst_const.shape == (nstep, 6)
assert coords.shape == (nstep, natoms, 3)
symbols = ['H'] * natoms
traj = Trajectory(
coords_frac=coords_frac,
cell=cell,
symbols=symbols,
forces=forces,
stress=stress,
etot=etot,
timestep=1,
)
for pbc in [True, False]:
# (nstep, natoms, natoms, 3)
distvecs_frac = traj.coords_frac[:,:,None,:] - \
traj.coords_frac[:,None,:,:]
assert distvecs_frac.shape == (nstep, natoms, natoms, 3)
if pbc:
distvecs_frac = crys.min_image_convention(distvecs_frac)
distvecs = np.empty((nstep, natoms, natoms, 3))
for ii in range(traj.nstep):
distvecs[ii, ...] = np.dot(distvecs_frac[ii, ...], traj.cell[ii,
...])
# (nstep, natoms, natoms)
dists = np.sqrt((distvecs**2.0).sum(axis=-1))
assert np.allclose(dists, crys.distances_traj(traj, pbc=pbc))
def test_coords_trans():
natoms = 10
nstep = 100
cell = rand(nstep, 3, 3)
cryst_const = crys.cell2cc3d(cell, axis=0)
coords_frac = rand(nstep, natoms, 3)
coords = crys.coord_trans3d(coords=coords_frac,
old=cell,
new=num.extend_array(np.identity(3),
nstep,
axis=0),
axis=1,
timeaxis=0)
traj = Trajectory(coords_frac=coords_frac, cell=cell)
assert np.allclose(cryst_const, traj.cryst_const)
assert np.allclose(coords, traj.coords)
traj = Trajectory(coords=coords, cell=cell)
assert np.allclose(coords_frac, traj.coords_frac)
def test_dist_traj():
natoms = 10
nstep = 100
cell = rand(nstep,3,3)
stress = rand(nstep,3,3)
forces = rand(nstep,natoms,3)
etot=rand(nstep)
cryst_const = crys.cell2cc3d(cell, axis=0)
coords_frac = np.random.rand(nstep,natoms,3)
coords = crys.coord_trans3d(coords=coords_frac,
old=cell,
new=num.extend_array(np.identity(3),
nstep,axis=0),
axis=1,
timeaxis=0)
assert cryst_const.shape == (nstep, 6)
assert coords.shape == (nstep,natoms,3)
symbols = ['H']*natoms
traj = Trajectory(coords_frac=coords_frac,
cell=cell,
symbols=symbols,
forces=forces,
stress=stress,
etot=etot,
timestep=1,
)
for pbc in [True, False]:
# (nstep, natoms, natoms, 3)
distvecs_frac = traj.coords_frac[:,:,None,:] - \
traj.coords_frac[:,None,:,:]
assert distvecs_frac.shape == (nstep, natoms, natoms, 3)
if pbc:
distvecs_frac = crys.min_image_convention(distvecs_frac)
distvecs = np.empty((nstep, natoms, natoms, 3))
for ii in range(traj.nstep):
distvecs[ii,...] = np.dot(distvecs_frac[ii,...], traj.cell[ii,...])
# (nstep, natoms, natoms)
dists = np.sqrt((distvecs**2.0).sum(axis=-1))
assert np.allclose(dists, crys.distances_traj(traj, pbc=pbc))
def test_coords_trans():
natoms = 10
nstep = 100
cell = rand(nstep,3,3)
cryst_const = crys.cell2cc3d(cell, axis=0)
coords_frac = rand(nstep,natoms,3)
coords = crys.coord_trans3d(coords=coords_frac,
old=cell,
new=num.extend_array(np.identity(3),
nstep,axis=0),
axis=1,
timeaxis=0)
traj = Trajectory(coords_frac=coords_frac,
cell=cell)
assert np.allclose(cryst_const, traj.cryst_const)
assert np.allclose(coords, traj.coords)
traj = Trajectory(coords=coords,
cell=cell)
assert np.allclose(coords_frac, traj.coords_frac)
def test_traj():
natoms = 10
nstep = 100
cell = rand(nstep,3,3)
stress = rand(nstep,3,3)
forces = rand(nstep,natoms,3)
etot = rand(nstep)
cryst_const = crys.cell2cc3d(cell, axis=0)
coords_frac = rand(nstep,natoms,3)
coords = crys.coord_trans3d(coords=coords_frac,
old=cell,
new=num.extend_array(np.identity(3),
nstep,axis=0),
axis=1,
timeaxis=0)
assert cryst_const.shape == (nstep, 6)
assert coords.shape == (nstep,natoms,3)
symbols = ['H']*natoms
# automatically calculated:
# coords
# cell
# pressure
# velocity (from coords)
# temperature (from ekin)
# ekin (from velocity)
traj = Trajectory(coords_frac=coords_frac,
cell=cell,
symbols=symbols,
forces=forces,
stress=stress,
etot=etot,
timestep=1,
)
# Test if all getters work.
for name in traj.attr_lst:
print "test if getters work:", name
traj.try_set_attr(name)
assert getattr(traj, name) is not None, "attr None: %s" %name
assert eval('traj.get_%s()'%name) is not None, "getter returns None: %s" %name
print "test if getters work:", name, "... ok"
aaae(coords_frac, traj.coords_frac)
aaae(coords, traj.coords)
aaae(cryst_const, traj.cryst_const)
aaae(np.trace(stress, axis1=1, axis2=2)/3.0, traj.pressure)
assert traj.coords.shape == (nstep,natoms,3)
assert traj.cell.shape == (nstep,3,3)
assert traj.velocity.shape == (nstep, natoms, 3)
assert traj.temperature.shape == (nstep,)
assert traj.ekin.shape == (nstep,)
assert traj.nstep == nstep
assert traj.natoms == natoms
traj = Trajectory(coords_frac=coords_frac,
symbols=symbols,
cell=cell)
aaae(coords, traj.coords)
# Cell calculated from cryst_const has defined orientation in space which may be
# different from the original `cell`, but the volume and underlying cryst_const
# must be the same.
traj = Trajectory(coords_frac=coords_frac,
symbols=symbols,
cryst_const=cryst_const)
np.testing.assert_almost_equal(crys.volume_cell3d(cell),
crys.volume_cell3d(traj.cell))
aaae(cryst_const, crys.cell2cc3d(traj.cell))
# extend arrays
cell2d = rand(3,3)
cc2d = crys.cell2cc(cell2d)
traj = Trajectory(coords_frac=coords_frac,
cell=cell2d,
symbols=symbols)
assert traj.cell.shape == (nstep,3,3)
assert traj.cryst_const.shape == (nstep,6)
for ii in range(traj.nstep):
assert (traj.cell[ii,...] == cell2d).all()
assert (traj.cryst_const[ii,:] == cc2d).all()
traj = Trajectory(coords_frac=coords_frac,
cryst_const=cc2d,
symbols=symbols)
assert traj.cell.shape == (nstep,3,3)
assert traj.cryst_const.shape == (nstep,6)
for ii in range(traj.nstep):
assert (traj.cryst_const[ii,:] == cc2d).all()
# units
traj = Trajectory(coords_frac=coords_frac,
cell=cell,
symbols=symbols,
stress=stress,
forces=forces,
units={'length': 2, 'forces': 3, 'stress': 4})
aaae(2*coords, traj.coords)
aaae(3*forces, traj.forces)
aaae(4*stress, traj.stress)
# iterate, check if Structures are complete
traj = Trajectory(coords=coords,
symbols=symbols,
cell=cell,
forces=forces,
stress=stress,
etot=etot,
timestep=1.0)
for struct in traj:
assert struct.is_struct, "st is not Structure"
assert not struct.is_traj, "st is Trajectory"
assert_attrs_not_none(struct)
struct = traj[0]
for attr_name in traj.attr_lst:
if attr_name in struct.attrs_only_traj:
msg = "tr[0] %s is not None" %attr_name
assert getattr(struct,attr_name) is None, msg
else:
msg = "tr[0] %s is None" %attr_name
assert getattr(struct,attr_name) is not None, msg
# slices, return traj
keys = traj.attr_lst[:]
tsl = traj[10:80:2]
assert tsl.nstep == traj.nstep / 2 - 15
assert_attrs_not_none(tsl, attr_lst=keys)
tsl = traj[slice(10,80,2)]
assert tsl.nstep == traj.nstep / 2 - 15
assert_attrs_not_none(tsl, attr_lst=keys)
tsl = traj[np.s_[10:80:2]]
assert tsl.nstep == traj.nstep / 2 - 15
assert_attrs_not_none(tsl, attr_lst=keys)
assert tsl.is_traj
# iteration over sliced traj
tsl = traj[10:80:2]
for x in tsl:
pass
for x in tsl.copy():
pass
# repeat iter
for i in range(2):
cnt = 0
for st in traj:
cnt += 1
assert cnt == nstep, "%i, %i" %(cnt, nstep)
# copy
traj2 = traj.copy()
for name in traj.attr_lst:
val = getattr(traj,name)
if val is not None and not (isinstance(val, types.IntType) or \
isinstance(val, types.FloatType)):
val2 = getattr(traj2,name)
print "test copy:", name, type(val), type(val2)
assert id(val2) != id(val)
assert_all_types_equal(val2, val)
assert_dict_with_all_types_equal(traj.__dict__, traj2.__dict__,
keys=traj.attr_lst)
def test_scell():
cell = np.identity(3)
coords_frac = np.array([[0.5, 0.5, 0.5],
[1,1,1]])
symbols = ['Al', 'N']
sc = crys.scell(Structure(coords_frac=coords_frac,
cell=cell,
symbols=symbols), (2,2,2))
sc_coords_frac = \
np.array([[ 0.25, 0.25, 0.25],
[ 0.25, 0.25, 0.75],
[ 0.25, 0.75, 0.25],
[ 0.25, 0.75, 0.75],
[ 0.75, 0.25, 0.25],
[ 0.75, 0.25, 0.75],
[ 0.75, 0.75, 0.25],
[ 0.75, 0.75, 0.75],
[ 0.5 , 0.5 , 0.5 ],
[ 0.5 , 0.5 , 1. ],
[ 0.5 , 1. , 0.5 ],
[ 0.5 , 1. , 1. ],
[ 1. , 0.5 , 0.5 ],
[ 1. , 0.5 , 1. ],
[ 1. , 1. , 0.5 ],
[ 1. , 1. , 1. ]])
sc_symbols = ['Al']*8 + ['N']*8
sc_cell = \
np.array([[ 2., 0., 0.],
[ 0., 2., 0.],
[ 0., 0., 2.]])
assert sc.symbols == sc_symbols
np.testing.assert_array_almost_equal(sc.coords_frac, sc_coords_frac)
np.testing.assert_array_almost_equal(sc.cell, sc_cell)
# non-orthorhombic cell
cell = \
np.array([[ 1., 0.5, 0.5],
[ 0.25, 1., 0.2],
[ 0.2, 0.5, 1.]])
sc = crys.scell(Structure(coords_frac=coords_frac,
cell=cell,
symbols=symbols), (2,2,2))
sc_cell = \
np.array([[ 2. , 1. , 1. ],
[ 0.5, 2. , 0.4],
[ 0.4, 1. , 2. ]])
np.testing.assert_array_almost_equal(sc.cell, sc_cell)
# crystal coords are cell-independent
np.testing.assert_array_almost_equal(sc.coords_frac, sc_coords_frac)
# slab
#
# Test if old and new implementation behave for a tricky case: natoms == 2
# mask.shape[0], i.e. if reshape() behaves correctly.
# Reference generated with old implementation. Default is new.
cell = np.identity(3)
coords_frac = np.array([[0.5, 0.5, 0.5],
[1,1,1]])
symbols = ['Al', 'N']
sc = crys.scell(Structure(coords_frac=coords_frac,
cell=cell,
symbols=symbols), (1,1,2))
sc_coords_frac = \
np.array([[ 0.5 , 0.5 , 0.25],
[ 0.5 , 0.5 , 0.75],
[ 1. , 1. , 0.5 ],
[ 1. , 1. , 1. ]])
sc_cell = \
np.array([[ 1., 0., 0.],
[ 0., 1., 0.],
[ 0., 0., 2.]])
sc_symbols = ['Al', 'Al', 'N', 'N']
assert sc.symbols == sc_symbols
np.testing.assert_array_almost_equal(sc.cell, sc_cell)
np.testing.assert_array_almost_equal(sc.coords_frac, sc_coords_frac)
sc = crys.scell(Structure(coords_frac=coords_frac,
cell=cell,
symbols=symbols), (1,2,1))
sc_coords_frac = \
np.array([[ 0.5 , 0.25, 0.5 ],
[ 0.5 , 0.75, 0.5 ],
[ 1. , 0.5 , 1. ],
[ 1. , 1. , 1. ]])
sc_cell = \
np.array([[ 1., 0., 0.],
[ 0., 2., 0.],
[ 0., 0., 1.]])
assert sc.symbols == sc_symbols
np.testing.assert_array_almost_equal(sc.cell, sc_cell)
np.testing.assert_array_almost_equal(sc.coords_frac, sc_coords_frac)
sc = crys.scell(Structure(coords_frac=coords_frac,
cell=cell,
symbols=symbols), (2,1,1))
sc_coords_frac = \
np.array([[ 0.25, 0.5 , 0.5 ],
[ 0.75, 0.5 , 0.5 ],
[ 0.5 , 1. , 1. ],
[ 1. , 1. , 1. ]])
sc_cell = \
np.array([[ 2., 0., 0.],
[ 0., 1., 0.],
[ 0., 0., 1.]])
assert sc.symbols == sc_symbols
np.testing.assert_array_almost_equal(sc.cell, sc_cell)
np.testing.assert_array_almost_equal(sc.coords_frac, sc_coords_frac)
# symbols = None
sc = crys.scell(Structure(coords_frac=coords_frac,
cell=cell,
symbols=None), (2,2,2))
assert sc.symbols is None
# Trajectory
natoms = 4
nstep = 100
symbols = [syms.next() for ii in range(natoms)]
# cell 2d
coords_frac = rand(nstep,natoms,3)
cell = rand(3,3)
dims = (2,3,4)
nmask = np.prod(dims)
sc = crys.scell(Trajectory(coords_frac=coords_frac,
cell=cell,
symbols=symbols),
dims=dims)
assert sc.coords_frac.shape == (nstep, nmask*natoms, 3)
assert sc.symbols == common.flatten([[sym]*nmask for sym in symbols])
assert sc.cell.shape == (nstep,3,3)
np.testing.assert_array_almost_equal(sc.cell,
num.extend_array(cell * np.asarray(dims)[:,None],
sc.nstep,
axis=0))
# cell 3d
cell = rand(nstep,3,3)
sc = crys.scell(Trajectory(coords_frac=coords_frac,
cell=cell,
symbols=symbols),
dims=dims)
assert sc.coords_frac.shape == (nstep, nmask*natoms, 3)
coords_frac2 = np.array([crys.scell(Structure(coords_frac=coords_frac[ii,...,],
cell=cell[ii,...],
symbols=symbols), dims=dims).coords_frac \
for ii in range(nstep)])
np.testing.assert_array_almost_equal(sc.coords_frac, coords_frac2)
assert sc.symbols == common.flatten([[sym]*nmask for sym in symbols])
assert sc.cell.shape == (nstep,3,3)
np.testing.assert_array_almost_equal(sc.cell,
cell * np.asarray(dims)[None,:,None])
# methods
natoms = 20
coords_frac = rand(natoms,3)
cell = rand(3,3)
dims = (2,3,4)
symbols = [syms.next() for ii in range(natoms)]
struct = Structure(coords_frac=coords_frac,
cell=cell,
symbols=symbols)
sc1 = crys.scell(struct, dims=dims, method=1)
sc2 = crys.scell(struct, dims=dims, method=2)
d1 = dict([(key, getattr(sc1, key)) for key in sc1.attr_lst])
d2 = dict([(key, getattr(sc2, key)) for key in sc2.attr_lst])
tools.assert_dict_with_all_types_almost_equal(d1, d2)
def test_traj():
natoms = 10
nstep = 100
cell = rand(nstep, 3, 3)
stress = rand(nstep, 3, 3)
forces = rand(nstep, natoms, 3)
etot = rand(nstep)
cryst_const = crys.cell2cc3d(cell, axis=0)
coords_frac = rand(nstep, natoms, 3)
coords = crys.coord_trans3d(coords=coords_frac,
old=cell,
new=num.extend_array(np.identity(3),
nstep,
axis=0),
axis=1,
timeaxis=0)
assert cryst_const.shape == (nstep, 6)
assert coords.shape == (nstep, natoms, 3)
symbols = ['H'] * natoms
# automatically calculated:
# coords
# cell
# pressure
# velocity (from coords)
# temperature (from ekin)
# ekin (from velocity)
traj = Trajectory(
coords_frac=coords_frac,
cell=cell,
symbols=symbols,
forces=forces,
stress=stress,
etot=etot,
timestep=1,
)
# Test if all getters work.
for name in traj.attr_lst:
print("test if getters work:", name)
traj.try_set_attr(name)
assert getattr(traj, name) is not None, "attr None: %s" % name
assert eval('traj.get_%s()' %
name) is not None, "getter returns None: %s" % name
print("test if getters work:", name, "... ok")
aaae(coords_frac, traj.coords_frac)
aaae(coords, traj.coords)
aaae(cryst_const, traj.cryst_const)
aaae(np.trace(stress, axis1=1, axis2=2) / 3.0, traj.pressure)
assert traj.coords.shape == (nstep, natoms, 3)
assert traj.cell.shape == (nstep, 3, 3)
assert traj.velocity.shape == (nstep, natoms, 3)
assert traj.temperature.shape == (nstep, )
assert traj.ekin.shape == (nstep, )
assert traj.nstep == nstep
assert traj.natoms == natoms
traj = Trajectory(coords_frac=coords_frac, symbols=symbols, cell=cell)
aaae(coords, traj.coords)
# Cell calculated from cryst_const has defined orientation in space which may be
# different from the original `cell`, but the volume and underlying cryst_const
# must be the same.
traj = Trajectory(coords_frac=coords_frac,
symbols=symbols,
cryst_const=cryst_const)
np.testing.assert_almost_equal(crys.volume_cell3d(cell),
crys.volume_cell3d(traj.cell))
aaae(cryst_const, crys.cell2cc3d(traj.cell))
# extend arrays
cell2d = rand(3, 3)
cc2d = crys.cell2cc(cell2d)
traj = Trajectory(coords_frac=coords_frac, cell=cell2d, symbols=symbols)
assert traj.cell.shape == (nstep, 3, 3)
assert traj.cryst_const.shape == (nstep, 6)
for ii in range(traj.nstep):
assert (traj.cell[ii, ...] == cell2d).all()
assert (traj.cryst_const[ii, :] == cc2d).all()
traj = Trajectory(coords_frac=coords_frac,
cryst_const=cc2d,
symbols=symbols)
assert traj.cell.shape == (nstep, 3, 3)
assert traj.cryst_const.shape == (nstep, 6)
for ii in range(traj.nstep):
assert (traj.cryst_const[ii, :] == cc2d).all()
# units
traj = Trajectory(coords_frac=coords_frac,
cell=cell,
symbols=symbols,
stress=stress,
forces=forces,
units={
'length': 2,
'forces': 3,
'stress': 4
})
aaae(2 * coords, traj.coords)
aaae(3 * forces, traj.forces)
aaae(4 * stress, traj.stress)
# iterate, check if Structures are complete
traj = Trajectory(coords=coords,
symbols=symbols,
cell=cell,
forces=forces,
stress=stress,
etot=etot,
timestep=1.0)
for struct in traj:
assert struct.is_struct, "st is not Structure"
assert not struct.is_traj, "st is Trajectory"
assert_attrs_not_none(struct)
struct = traj[0]
for attr_name in traj.attr_lst:
if attr_name in struct.attrs_only_traj:
msg = "tr[0] %s is not None" % attr_name
assert getattr(struct, attr_name) is None, msg
else:
msg = "tr[0] %s is None" % attr_name
assert getattr(struct, attr_name) is not None, msg
# slices, return traj
keys = traj.attr_lst[:]
tsl = traj[10:80:2]
assert tsl.nstep == traj.nstep / 2 - 15
assert_attrs_not_none(tsl, attr_lst=keys)
tsl = traj[slice(10, 80, 2)]
assert tsl.nstep == traj.nstep / 2 - 15
assert_attrs_not_none(tsl, attr_lst=keys)
tsl = traj[np.s_[10:80:2]]
assert tsl.nstep == traj.nstep / 2 - 15
assert_attrs_not_none(tsl, attr_lst=keys)
assert tsl.is_traj
# iteration over sliced traj
tsl = traj[10:80:2]
for x in tsl:
pass
for x in tsl.copy():
pass
# repeat iter
for i in range(2):
cnt = 0
for st in traj:
cnt += 1
assert cnt == nstep, "%i, %i" % (cnt, nstep)
# copy
traj2 = traj.copy()
for name in traj.attr_lst:
val = getattr(traj, name)
if val is not None and not (isinstance(val, int) or \
isinstance(val, float)):
val2 = getattr(traj2, name)
print("test copy:", name, type(val), type(val2))
assert id(val2) != id(val)
assert_all_types_equal(val2, val)
assert_dict_with_all_types_equal(traj.__dict__,
traj2.__dict__,
keys=traj.attr_lst)
def test_scell():
cell = np.identity(3)
coords_frac = np.array([[0.5, 0.5, 0.5], [1, 1, 1]])
symbols = ['Al', 'N']
sc = crys.scell(
Structure(coords_frac=coords_frac, cell=cell, symbols=symbols),
(2, 2, 2))
sc_coords_frac = \
np.array([[ 0.25, 0.25, 0.25],
[ 0.25, 0.25, 0.75],
[ 0.25, 0.75, 0.25],
[ 0.25, 0.75, 0.75],
[ 0.75, 0.25, 0.25],
[ 0.75, 0.25, 0.75],
[ 0.75, 0.75, 0.25],
[ 0.75, 0.75, 0.75],
[ 0.5 , 0.5 , 0.5 ],
[ 0.5 , 0.5 , 1. ],
[ 0.5 , 1. , 0.5 ],
[ 0.5 , 1. , 1. ],
[ 1. , 0.5 , 0.5 ],
[ 1. , 0.5 , 1. ],
[ 1. , 1. , 0.5 ],
[ 1. , 1. , 1. ]])
sc_symbols = ['Al'] * 8 + ['N'] * 8
sc_cell = \
np.array([[ 2., 0., 0.],
[ 0., 2., 0.],
[ 0., 0., 2.]])
assert sc.symbols == sc_symbols
np.testing.assert_array_almost_equal(sc.coords_frac, sc_coords_frac)
np.testing.assert_array_almost_equal(sc.cell, sc_cell)
# non-orthorhombic cell
cell = \
np.array([[ 1., 0.5, 0.5],
[ 0.25, 1., 0.2],
[ 0.2, 0.5, 1.]])
sc = crys.scell(
Structure(coords_frac=coords_frac, cell=cell, symbols=symbols),
(2, 2, 2))
sc_cell = \
np.array([[ 2. , 1. , 1. ],
[ 0.5, 2. , 0.4],
[ 0.4, 1. , 2. ]])
np.testing.assert_array_almost_equal(sc.cell, sc_cell)
# crystal coords are cell-independent
np.testing.assert_array_almost_equal(sc.coords_frac, sc_coords_frac)
# slab
#
# Test if old and new implementation behave for a tricky case: natoms == 2
# mask.shape[0], i.e. if reshape() behaves correctly.
# Reference generated with old implementation. Default is new.
cell = np.identity(3)
coords_frac = np.array([[0.5, 0.5, 0.5], [1, 1, 1]])
symbols = ['Al', 'N']
sc = crys.scell(
Structure(coords_frac=coords_frac, cell=cell, symbols=symbols),
(1, 1, 2))
sc_coords_frac = \
np.array([[ 0.5 , 0.5 , 0.25],
[ 0.5 , 0.5 , 0.75],
[ 1. , 1. , 0.5 ],
[ 1. , 1. , 1. ]])
sc_cell = \
np.array([[ 1., 0., 0.],
[ 0., 1., 0.],
[ 0., 0., 2.]])
sc_symbols = ['Al', 'Al', 'N', 'N']
assert sc.symbols == sc_symbols
np.testing.assert_array_almost_equal(sc.cell, sc_cell)
np.testing.assert_array_almost_equal(sc.coords_frac, sc_coords_frac)
sc = crys.scell(
Structure(coords_frac=coords_frac, cell=cell, symbols=symbols),
(1, 2, 1))
sc_coords_frac = \
np.array([[ 0.5 , 0.25, 0.5 ],
[ 0.5 , 0.75, 0.5 ],
[ 1. , 0.5 , 1. ],
[ 1. , 1. , 1. ]])
sc_cell = \
np.array([[ 1., 0., 0.],
[ 0., 2., 0.],
[ 0., 0., 1.]])
assert sc.symbols == sc_symbols
np.testing.assert_array_almost_equal(sc.cell, sc_cell)
np.testing.assert_array_almost_equal(sc.coords_frac, sc_coords_frac)
sc = crys.scell(
Structure(coords_frac=coords_frac, cell=cell, symbols=symbols),
(2, 1, 1))
sc_coords_frac = \
np.array([[ 0.25, 0.5 , 0.5 ],
[ 0.75, 0.5 , 0.5 ],
[ 0.5 , 1. , 1. ],
[ 1. , 1. , 1. ]])
sc_cell = \
np.array([[ 2., 0., 0.],
[ 0., 1., 0.],
[ 0., 0., 1.]])
assert sc.symbols == sc_symbols
np.testing.assert_array_almost_equal(sc.cell, sc_cell)
np.testing.assert_array_almost_equal(sc.coords_frac, sc_coords_frac)
# symbols = None
sc = crys.scell(
Structure(coords_frac=coords_frac, cell=cell, symbols=None), (2, 2, 2))
assert sc.symbols is None
# Trajectory
natoms = 4
nstep = 100
symbols = [next(syms) for ii in range(natoms)]
# cell 2d
coords_frac = rand(nstep, natoms, 3)
cell = rand(3, 3)
dims = (2, 3, 4)
nmask = np.prod(dims)
sc = crys.scell(Trajectory(coords_frac=coords_frac,
cell=cell,
symbols=symbols),
dims=dims)
assert sc.coords_frac.shape == (nstep, nmask * natoms, 3)
assert sc.symbols == common.flatten([[sym] * nmask for sym in symbols])
assert sc.cell.shape == (nstep, 3, 3)
np.testing.assert_array_almost_equal(
sc.cell,
num.extend_array(cell * np.asarray(dims)[:, None], sc.nstep, axis=0))
# cell 3d
cell = rand(nstep, 3, 3)
sc = crys.scell(Trajectory(coords_frac=coords_frac,
cell=cell,
symbols=symbols),
dims=dims)
assert sc.coords_frac.shape == (nstep, nmask * natoms, 3)
coords_frac2 = np.array([crys.scell(Structure(coords_frac=coords_frac[ii,...,],
cell=cell[ii,...],
symbols=symbols), dims=dims).coords_frac \
for ii in range(nstep)])
np.testing.assert_array_almost_equal(sc.coords_frac, coords_frac2)
assert sc.symbols == common.flatten([[sym] * nmask for sym in symbols])
assert sc.cell.shape == (nstep, 3, 3)
np.testing.assert_array_almost_equal(
sc.cell,
cell * np.asarray(dims)[None, :, None])
# methods
natoms = 20
coords_frac = rand(natoms, 3)
cell = rand(3, 3)
dims = (2, 3, 4)
symbols = [next(syms) for ii in range(natoms)]
struct = Structure(coords_frac=coords_frac, cell=cell, symbols=symbols)
sc1 = crys.scell(struct, dims=dims, method=1)
sc2 = crys.scell(struct, dims=dims, method=2)
d1 = dict([(key, getattr(sc1, key)) for key in sc1.attr_lst])
d2 = dict([(key, getattr(sc2, key)) for key in sc2.attr_lst])
tools.assert_dict_with_all_types_almost_equal(d1, d2)
