def test_fraction():
warning = ("The fraction attribute of each SpectralEvent in a "
"SpectralDimension should sum to 1. Sum is 1.5")
with pytest.warns(UserWarning, match=f".*{warning}.*"):
SpectralDimension(events=[
SpectralEvent(fraction=0.5),
SpectralEvent(fraction=0.5),
SpectralEvent(fraction=0.5),
])
def csa_1D_projection():
csa_only = Method(
channels=["87Rb"],
magnetic_flux_density=9.4, # in T
rotor_angle=70.12 * np.pi / 180, # in rads
rotor_frequency=np.inf,
spectral_dimensions=[
SpectralDimension(
count=512,
spectral_width=4e4,
reference_offset=-8e3,
events=[
SpectralEvent(
freq_contrib=[
"Quad2_0", "Shielding1_0", "Shielding1_2"
],
transition_queries=[{
"ch1": {
"P": [3],
"D": [0]
}
}],
),
],
)
],
)
return process_spectrum(csa_only)
def quad_1D_projection():
quad_only = Method(
channels=["87Rb"],
magnetic_flux_density=9.4, # in T
rotor_angle=70.12 * np.pi / 180, # in rads
rotor_frequency=np.inf,
spectral_dimensions=[
SpectralDimension(
count=512,
spectral_width=8e3,
reference_offset=-4e3,
events=[
SpectralEvent(
fraction=1 / 4,
freq_contrib=["Quad2_0"],
transition_queries=[{
"ch1": {
"P": [3],
"D": [0]
}
}],
),
MixingEvent(query={
"ch1": {
"angle": np.pi * 109.5 / 180,
"phase": 0
}
}),
SpectralEvent(
fraction=3 / 4,
freq_contrib=["Quad2_0", "Quad2_2"],
transition_queries=[{
"ch1": {
"P": [-1],
"D": [0]
}
}],
),
],
)
],
)
return process_spectrum(quad_only)
def coaster_simulation():
coaster = Method(
name="COASTER",
channels=["87Rb"],
magnetic_flux_density=9.4, # in T
rotor_angle=70.12 * np.pi / 180, # in rads
rotor_frequency=np.inf,
spectral_dimensions=[
SpectralDimension(
count=512,
spectral_width=4e4, # in Hz
reference_offset=-8e3, # in Hz
label="$\\omega_1$ (CSA)",
events=[
SpectralEvent(transition_queries=[{
"ch1": {
"P": [3],
"D": [0]
}
}]),
MixingEvent(query={"ch1": {
"angle": np.pi * 109.5 / 180
}}),
],
),
SpectralDimension(
count=512,
spectral_width=8e3, # in Hz
reference_offset=-4e3, # in Hz
label="$\\omega_2$ (Q)",
events=[
SpectralEvent(transition_queries=[{
"ch1": {
"P": [-1],
"D": [0]
}
}])
],
),
],
affine_matrix=[[1, 0], [1 / 4, 3 / 4]],
)
return process_spectrum(coaster)
def hahn_method():
return Method(
channels=["1H"],
magnetic_flux_density=9.4, # in T
rotor_angle=0, # in rads
spectral_dimensions=[
SpectralDimension(
count=512,
spectral_width=2e4, # in Hz
events=[
SpectralEvent(fraction=0.5,
transition_queries=positive_sq_tq),
MixingEvent(query={"ch1": {
"angle": np.pi,
"phase": 0
}}),
SpectralEvent(fraction=0.5,
transition_queries=negative_sq_tq),
],
)
],
)
def contrib_method(contrib):
return Method(
channels=["1H"],
magnetic_flux_density=9.4, # in T
spectral_dimensions=[
SpectralDimension(
count=512,
spectral_width=2e4,
events=[
SpectralEvent(freq_contrib=contrib,
transition_queries=negative_sq_tq)
],
)
],
)
method = Method(
name="Inner Satellite Spectrum",
channels=["27Al"],
magnetic_flux_density=21.14, # in T
rotor_frequency=np.inf, # in Hz
rotor_angle=54.7356 * np.pi / 180, # in rads
spectral_dimensions=[
SpectralDimension(
count=1024,
spectral_width=1e4, # in Hz
reference_offset=1e4, # in Hz
events=[
SpectralEvent(transition_queries=[
{
"ch1": {
"P": [-1],
"D": [2]
}
}, # inner satellite
])
],
)
],
)
# A graphical representation of the method object.
plt.figure(figsize=(4, 2.5))
method.plot()
plt.show()
# %%
# Create the Simulator object and add the method and the spin system object.
def test_2D():
site_Ni = Site(
isotope="2H",
isotropic_chemical_shift=-97, # in ppm
shielding_symmetric=dict(
zeta=-551,
eta=0.12,
alpha=62 * np.pi / 180,
beta=114 * np.pi / 180,
gamma=171 * np.pi / 180,
),
quadrupolar=dict(Cq=77.2e3, eta=0.9), # Cq in Hz
)
spin_system = SpinSystem(sites=[site_Ni])
data = []
for angle, n_gamma in zip([0, np.pi / 4], [1, 500]):
shifting_d = Method(
name="Shifting-d",
channels=["2H"],
magnetic_flux_density=9.395, # in T
rotor_frequency=0, # in Hz
rotor_angle=angle, # in Hz
spectral_dimensions=[
SpectralDimension(
count=512,
spectral_width=2.5e5, # in Hz
label="Quadrupolar frequency",
events=[
SpectralEvent(
transition_queries=[{
"ch1": {
"P": [-1]
}
}],
freq_contrib=["Quad1_2"],
),
MixingEvent(query="NoMixing"),
],
),
SpectralDimension(
count=256,
spectral_width=2e5, # in Hz
reference_offset=2e4, # in Hz
label="Paramagnetic shift",
events=[
SpectralEvent(
transition_queries=[{
"ch1": {
"P": [-1]
}
}],
freq_contrib=["Shielding1_0", "Shielding1_2"],
)
],
),
],
)
sim = Simulator(spin_systems=[spin_system], methods=[shifting_d])
sim.config.integration_volume = "hemisphere"
sim.config.number_of_gamma_angles = n_gamma
sim.run(auto_switch=False)
res = sim.methods[0].simulation.y[0].components[0]
data.append(res / res.max())
# _, ax = plt.subplots(1, 2)
# ax[0].imshow(data[0].real)
# ax[1].imshow(data[1].real)
# plt.show()
np.testing.assert_almost_equal(data[0], data[1], decimal=1.8)
# spinning speed spectrum.
coaster = Method2D(
name="COASTER",
channels=["87Rb"],
magnetic_flux_density=9.4, # in T
rotor_angle=70.12 * 3.14159 / 180, # in rads
spectral_dimensions=[
SpectralDimension(
count=256,
spectral_width=4e4, # in Hz
reference_offset=-8e3, # in Hz
label="3Q dimension",
events=[
SpectralEvent(transition_query=[{
"ch1": {
"P": [3],
"D": [0]
}
}])
],
),
# The last spectral dimension block is the direct-dimension
SpectralDimension(
count=256,
spectral_width=2e4, # in Hz
reference_offset=-3e3, # in Hz
label="70.12 dimension",
events=[
SpectralEvent(transition_query=[{
"ch1": {
"P": [-1],
"D": [0]
# method parameters, as shown below. Note, the Method2D method simulates an infinite
# spinning speed spectrum.
das = Method2D(
name="Dynamic Angle Spinning",
channels=["17O"],
magnetic_flux_density=11.74, # in T
spectral_dimensions=[
SpectralDimension(
count=256,
spectral_width=5e3, # in Hz
reference_offset=0, # in Hz
label="DAS isotropic dimension",
events=[
SpectralEvent(
fraction=0.5,
rotor_angle=37.38 * 3.14159 / 180,
transition_query=[{"ch1": {"P": [-1], "D": [0]}}],
),
SpectralEvent(
fraction=0.5,
rotor_angle=79.19 * 3.14159 / 180,
transition_query=[{"ch1": {"P": [-1], "D": [0]}}],
),
],
),
# The last spectral dimension block is the direct-dimension
SpectralDimension(
count=256,
spectral_width=2e4, # in Hz
reference_offset=0, # in Hz
label="MAS dimension",
# the two SpectralEvent. A MixingEvent does not directly contribute to the frequencies.
# As the name suggests, a mixing event is used for the mixing of transitions in a
# multi-event method such as HahnEcho. In the following code, we define a mixing query
# on channel-1 by setting the attributes ``tip_angle`` and ``phase`` to :math:`\pi` and
# 0, respectively. There two parameters are analogous to the pulse angle and phase.
hahn_echo = Method1D(
channels=["1H"],
magnetic_flux_density=9.4, # in T
spectral_dimensions=[
SpectralDimension(
count=512,
spectral_width=2e4, # in Hz
events=[
SpectralEvent(fraction=0.5,
transition_query=[{
"ch1": {
"P": [1]
}
}]),
MixingEvent(
mixing_query={"ch1": {
"tip_angle": np.pi,
"phase": 0
}}),
SpectralEvent(fraction=0.5,
transition_query=[{
"ch1": {
"P": [-1]
}
}]),
],
)
# Get the spectral dimension parameters from the experiment.
spectral_dims = get_spectral_dimensions(experiment)
DAS = Method(
channels=["17O"],
magnetic_flux_density=11.744, # in T
rotor_frequency=np.inf,
spectral_dimensions=[
SpectralDimension(
**spectral_dims[0],
events=[
SpectralEvent(
fraction=0.5,
rotor_angle=37.38 * np.pi / 180, # in rads
transition_queries=[{
"ch1": {
"P": [-1],
"D": [0]
}
}],
),
MixingEvent(query="NoMixing"),
SpectralEvent(
fraction=0.5,
rotor_angle=79.19 * np.pi / 180, # in rads
transition_queries=[{
"ch1": {
"P": [-1],
"D": [0]
}
}],
),
# method simulates an infinite spinning speed spectrum.
maf = Method2D(
name="Magic Angle Flipping",
channels=["29Si"],
magnetic_flux_density=14.1, # in T
spectral_dimensions=[
SpectralDimension(
count=128,
spectral_width=2e4, # in Hz
label="Anisotropic dimension",
events=[
SpectralEvent(
rotor_angle=90 * 3.14159 / 180,
transition_query=[{
"ch1": {
"P": [-1],
"D": [0]
}
}],
)
],
),
SpectralDimension(
count=128,
spectral_width=3e3, # in Hz
reference_offset=-1.05e4, # in Hz
label="Isotropic dimension",
events=[
SpectralEvent(
rotor_angle=54.735 * 3.14159 / 180,
transition_query=[{
# channel has a zero phase and angle. Since all spin systems in this example have a
# single site, defining no mixing between the two spectral events is superfluous.
# We include it such that the method is applicable with multi-site spin systems.
maf = Method(
name="Magic Angle Flipping",
channels=["29Si"],
magnetic_flux_density=14.1, # in T
rotor_frequency=np.inf,
spectral_dimensions=[
SpectralDimension(
count=128,
spectral_width=2e4, # in Hz
label="Anisotropic dimension",
events=[
SpectralEvent(
rotor_angle=90 * np.pi / 180, # in rads
transition_queries=[{"ch1": {"P": [-1], "D": [0]}}],
),
MixingEvent(query="NoMixing"),
],
),
SpectralDimension(
count=128,
spectral_width=3e3, # in Hz
reference_offset=-1.05e4, # in Hz
label="Isotropic dimension",
events=[
SpectralEvent(
rotor_angle=54.735 * np.pi / 180, # in rads
transition_queries=[{"ch1": {"P": [-1], "D": [0]}}],
)
],
sas = Method(
channels=["87Rb"],
magnetic_flux_density=4.2, # in T
rotor_frequency=np.inf,
spectral_dimensions=[
SpectralDimension(
count=256,
spectral_width=1.5e4, # in Hz
reference_offset=-5e3, # in Hz
label="70.12 dimension",
events=[
SpectralEvent(
rotor_angle=70.12 * np.pi / 180, # in radians
transition_queries=[{
"ch1": {
"P": [-1],
"D": [0]
}
}],
)
],
),
SpectralDimension(
count=512,
spectral_width=15e3, # in Hz
reference_offset=-7e3, # in Hz
label="MAS dimension",
events=[
SpectralEvent(
rotor_angle=54.74 * np.pi / 180, # in radians
transition_queries=[{
method = Method(
name="Arbitrary Transition Method",
channels=["27Al"],
magnetic_flux_density=21.14, # in T
rotor_frequency=np.inf, # in Hz
rotor_angle=54.7356 * np.pi / 180, # in rads
spectral_dimensions=[
SpectralDimension(
count=1024,
spectral_width=5e3, # in Hz
reference_offset=2.5e4, # in Hz
events=[
SpectralEvent(
# symmetric triple quantum transitions
transition_queries=[{
"ch1": {
"P": [-3],
"D": [0]
}
}]),
],
)
],
)
# A graphical representation of the method object.
plt.figure(figsize=(4, 2.5))
method.plot()
plt.show()
# %%
# Create the Simulator object and add the method and the spin system object.
# Get the spectral dimension parameters from the experiment.
spectral_dims = get_spectral_dimensions(experiment)
shifting_d = Method2D(
channels=["2H"],
magnetic_flux_density=9.395, # in T
spectral_dimensions=[
SpectralDimension(
**spectral_dims[0],
label="Quadrupolar frequency",
events=[
SpectralEvent(
rotor_frequency=0,
transition_query=[{
"ch1": {
"P": [-1]
}
}],
freq_contrib=["Quad1_2"],
)
],
),
SpectralDimension(
**spectral_dims[1],
label="Paramagnetic shift",
events=[
SpectralEvent(
rotor_frequency=0,
transition_query=[{
"ch1": {
"P": [-1]
spectral_dims = get_spectral_dimensions(experiment)
shifting_d = Method(
channels=["2H"],
magnetic_flux_density=9.395, # in T
rotor_frequency=0, # in Hz
rotor_angle=0, # in rads
spectral_dimensions=[
SpectralDimension(
**spectral_dims[0],
label="Quadrupolar frequency",
events=[
SpectralEvent(
transition_queries=[{
"ch1": {
"P": [-1]
}
}],
freq_contrib=["Quad1_2"],
),
MixingEvent(query="NoMixing"),
],
),
SpectralDimension(
**spectral_dims[1],
label="Paramagnetic shift",
events=[
SpectralEvent(
transition_queries=[{
"ch1": {
"P": [-1]
}
def test_spectral_dimension():
# test-1 single event spectral dimensions
# parse dict with units
event_dictionary = {
"fraction": 1,
"freq_contrib": freq_default,
"magnetic_flux_density": "9.6 T",
"rotor_frequency": "1 kHz",
"rotor_angle": "54.735 deg",
}
dimension_dictionary = {
"count": 1024,
"spectral_width": "100 Hz",
"reference_offset": "0 GHz",
"events": [event_dictionary],
}
the_dimension = SpectralDimension.parse_dict_with_units(
dimension_dictionary)
basic_spectral_dimension_tests(the_dimension)
# direct initialization
the_dimension = SpectralDimension(
count=1024,
spectral_width=100,
events=[SpectralEvent.parse_dict_with_units(event_dictionary)],
)
basic_spectral_dimension_tests(the_dimension)
# test-2: two event spectral dimension
# parse dict with units
event_dictionary = {
"fraction": 0.5,
"freq_contrib": freq_default,
"magnetic_flux_density": "9.6 T",
"rotor_frequency": "1 kHz",
"rotor_angle": "54.735 deg",
}
dimension_dictionary = {
"count": 1024,
"spectral_width": "100 Hz",
"reference_offset": "0 GHz",
"events": [event_dictionary, event_dictionary],
}
the_dimension = SpectralDimension.parse_dict_with_units(
dimension_dictionary)
# direct initialization
the_dimension2 = SpectralDimension(
count=1024,
spectral_width=100,
events=[
SpectralEvent.parse_dict_with_units(event_dictionary)
for _ in range(2)
],
)
# json()
should_be = dict(
count=1024,
spectral_width="100.0 Hz",
events=[
{
"fraction": 0.5,
"magnetic_flux_density": "9.6 T",
"rotor_angle": "0.9553059660790962 rad",
"rotor_frequency": "1000.0 Hz",
"transition_queries": [{
"ch1": {
"P": [0]
}
}],
},
{
"fraction": 0.5,
"magnetic_flux_density": "9.6 T",
"rotor_angle": "0.9553059660790962 rad",
"rotor_frequency": "1000.0 Hz",
"transition_queries": [{
"ch1": {
"P": [0]
}
}],
},
],
)
assert the_dimension.json() == should_be
assert the_dimension2.json() == should_be
# json(units=False)
json_no_unit = dict(
count=1024,
spectral_width=100.0,
events=[
{
"fraction": 0.5,
# "freq_contrib": freq_default,
"magnetic_flux_density": 9.6,
"rotor_angle": 0.9553059660790962,
"rotor_frequency": 1000.0,
"transition_queries": [{
"ch1": {
"P": [0]
}
}],
},
{
"fraction": 0.5,
# "freq_contrib": freq_default,
"magnetic_flux_density": 9.6,
"rotor_angle": 0.9553059660790962,
"rotor_frequency": 1000.0,
"transition_queries": [{
"ch1": {
"P": [0]
}
}],
},
],
)
assert the_dimension.json(units=False) == json_no_unit
assert the_dimension2.json(units=False) == json_no_unit
def test_rotor_frequency():
"""Ensures only 1 non-zero finite spinning speed in method"""
# Good method, should not throw error
Method(
channels=["1H"],
spectral_dimensions=[
SpectralDimension(events=[
SpectralEvent(fraction=0.5, rotor_frequency=123),
SpectralEvent(fraction=0.5, rotor_frequency=0),
]),
SpectralDimension(events=[SpectralEvent(rotor_frequency=np.inf)]),
],
)
# Bad method, should throw error for multiple finite speeds
for cls in [Method, Method1D]:
with pytest.raises(NotImplementedError):
cls(
channels=["1H"],
spectral_dimensions=[
SpectralDimension(events=[
SpectralEvent(fraction=0.5, rotor_frequency=123),
SpectralEvent(fraction=0.5, rotor_frequency=456),
])
],
)
with pytest.raises(NotImplementedError):
Method2D(
channels=["1H"],
spectral_dimensions=[
SpectralDimension(events=[
SpectralEvent(fraction=0.5, rotor_frequency=123),
SpectralEvent(fraction=0.5, rotor_frequency=np.inf),
]),
SpectralDimension(events=[
SpectralEvent(fraction=0.5, rotor_frequency=0),
SpectralEvent(fraction=0.5, rotor_frequency=456),
]),
],
)
with pytest.raises(NotImplementedError):
Method(
channels=["27Al"],
rotor_frequency=np.inf,
spectral_dimensions=[
SpectralDimension(events=[
SpectralEvent(fraction=0.5, rotor_frequency=0.1),
SpectralEvent(fraction=0.5, rotor_frequency=456),
])
],
)
# satellite transition.
method = Method1D(
name="Inner Satellite Spectrum",
channels=["27Al"],
magnetic_flux_density=21.14, # in T
rotor_frequency=1e9, # in Hz
spectral_dimensions=[
SpectralDimension(
count=1024,
spectral_width=1e4, # in Hz
reference_offset=1e4, # in Hz
events=[
SpectralEvent(
# Selecting the inner satellite transitions
transition_query=[{
"ch1": {
"P": [-1],
"D": [2]
}
}], )
],
)
],
)
# A graphical representation of the method object.
plt.figure(figsize=(5, 3))
method.plot()
plt.show()
# %%
# Create the Simulator object and add the method and the spin system object.