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 test_mixing_query_connect_map():
MX1 = MixingEvent(mixing_query={"ch1": {"tip_angle": 0.12}})
MX2 = MixingEvent(mixing_query={"ch2": {"tip_angle": 1.12}})
spectral_dimmensions = [
SpectralDimension(events=[
{
"fraction": 0.5
}, # 0
MX1,
{
"duration": 0.5
}, # 1
{
"fraction": 0.5
}, # 2
MX2,
{
"duration": 0.5
}, # 3
]),
SpectralDimension(events=[
MX1,
MX2,
{
"duration": 0.5
}, # 4
MX2,
{
"duration": 0.5
}, # 5
{
"fraction": 1
}, # 2
]),
]
res = mixing_query_connect_map(spectral_dimmensions)
assert res == [
{
"mixing_query": MX1.mixing_query,
"near_index": [0, 1]
},
{
"mixing_query": MX2.mixing_query,
"near_index": [2, 3]
},
{
"mixing_query": MX1.mixing_query,
"near_index": [3, 4]
},
{
"mixing_query": MX2.mixing_query,
"near_index": [3, 4]
},
{
"mixing_query": MX2.mixing_query,
"near_index": [4, 5]
},
]
error = "SpectralDimension requires at least one SpectralEvent"
with pytest.raises(MissingSpectralEventError, match=f".*{error}.*"):
SpectralDimension(
events=[MX1, MX2, {
"duration": 0.5
}, MX2, {
"duration": 0.5
}])
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)
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]
}
}]),
],
)
],
)
# %%
# You may also visualize the method using the `plot` function.
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]
}
}],
),
MixingEvent(query="NoMixing"),
],
),
# The last spectral dimension block is the direct-dimension
SpectralDimension(
def test_mixing_query_connect_map():
MX1 = MixingEvent(query={"ch1": {"angle": 0.12}})
MX2 = MixingEvent(query={"ch2": {"angle": 1.12}})
TOTAL_MX = MixingEvent(query="TotalMixing")
# Use MixingEvents with non-enum queries
spectral_dimensions = [
SpectralDimension(events=[
{
"fraction": 0.5
}, # 0
MX1,
{
"duration": 0.5
}, # 1
{
"fraction": 0.5
}, # 2
MX2,
{
"duration": 0.5
}, # 3
]),
SpectralDimension(events=[
MX1,
MX2,
{
"duration": 0.5
}, # 4
MX2,
{
"duration": 0.5
}, # 5
{
"fraction": 1
}, # 6
]),
]
res = mixing_query_connect_map(spectral_dimensions)
assert res == [
{
"mixing_query_list": [MX1.query],
"near_index": [0, 1]
},
{
"mixing_query_list": [MX2.query],
"near_index": [2, 3]
},
{
"mixing_query_list": [MX1.query, MX2.query],
"near_index": [3, 4]
},
{
"mixing_query_list": [MX2.query],
"near_index": [4, 5]
},
]
# Combination of MixingEvents with dict queries and enum queries (total mixing)
spectral_dimensions = [
SpectralDimension(events=[
# Connect all, should return no list
{
"fraction": 0.5
}, # 0
TOTAL_MX,
{
"duration": 0.5
}, # 1
# Just MX1
{
"fraction": 0.5
}, # 2
TOTAL_MX,
MX1,
{
"duration": 0.5
}, # 3
]),
SpectralDimension(events=[
# MX1 and MX2
{
"fraction": 0.5
}, # 4
MX1,
TOTAL_MX,
MX2,
{
"duration": 0.5
}, # 5
# MX1, MX2, MX1
{
"fraction": 0.5
}, # 6
MX1,
TOTAL_MX,
MX2,
MX1,
TOTAL_MX,
{
"duration": 0.5
}, # 7
]),
]
res = mixing_query_connect_map(spectral_dimensions)
assert res == [
{
"mixing_query_list": [MX1.query],
"near_index": [2, 3]
},
{
"mixing_query_list": [MX1.query, MX2.query],
"near_index": [4, 5]
},
{
"mixing_query_list": [MX1.query, MX2.query, MX1.query],
"near_index": [6, 7]
},
]
error = "SpectralDimension requires at least one SpectralEvent"
with pytest.raises(MissingSpectralEventError, match=f".*{error}.*"):
SpectralDimension(
events=[MX1, MX2, {
"duration": 0.5
}, MX2, {
"duration": 0.5
}])
magnetic_flux_density=9.4, # in T
rotor_angle=0, # in rads
rotor_frequency=0, # in Hz
spectral_dimensions=[
SpectralDimension(
count=512,
spectral_width=2e4, # in Hz
events=[
SpectralEvent(fraction=0.5,
transition_queries=[{
"ch1": {
"P": [1]
}
}]),
MixingEvent(query={"ch1": {
"angle": np.pi,
"phase": 0
}}),
SpectralEvent(fraction=0.5,
transition_queries=[{
"ch1": {
"P": [-1]
}
}]),
],
)
],
)
# %%
# In the above code, we define the two SpectralEvent objects with fraction 0.5 and
# the transition_queries on channel-1 of P=[1] and P=[-1], respectively. Notice, the
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,
"phase": 0
}}),
],
),
# The last spectral dimension block is the direct-dimension
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]