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)
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)
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_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)