def test_3Q_VAS_general():
"""3Q-VAS method test"""
mth = ThreeQ_VAS(channels=["87Rb"], spectral_dimensions=[{}, {}])
assert mth.name == "ThreeQ_VAS"
assert mth.description == "Simulate a 3Q variable-angle spinning spectrum."
assert mth.spectral_dimensions[0].events[0].transition_query == [
TransitionQuery(ch1={
"P": [-3],
"D": [0]
})
]
assert mth.spectral_dimensions[1].events[0].transition_query == [
TransitionQuery(ch1={
"P": [-1],
"D": [0]
})
]
assert ThreeQ_VAS.parse_dict_with_units(mth.json()) == mth
assert np.allclose(mth.affine_matrix, [0.5625, 0.4375, 0.0, 1.0])
serialize = mth.json()
_ = serialize.pop("affine_matrix")
assert serialize == {
"channels": ["87Rb"],
"description": "Simulate a 3Q variable-angle spinning spectrum.",
"name": "ThreeQ_VAS",
**sample_test_output(-3),
}
def test_3Q_VAS_general():
"""3Q-VAS method test"""
mth = ThreeQ_VAS(channels=["87Rb"], spectral_dimensions=[{}, {}])
assert mth.name == "ThreeQ_VAS"
assert mth.description == "Simulate a 3Q variable-angle spinning spectrum."
assert mth.spectral_dimensions[0].events[
0].transition_query == TransitionQuery(P={"channel-1": [[-3]]},
D={"channel-1": [[0]]})
assert mth.spectral_dimensions[1].events[
0].transition_query == TransitionQuery(P={"channel-1": [[-1]]},
D={"channel-1": [[0]]})
assert Method.parse_dict_with_units(mth.json()) == mth
def test_method_exp_sim():
spin_system = SpinSystem(sites=[
Site(
isotope="27Al",
isotropic_chemical_shift=64.5, # in ppm
quadrupolar={
"Cq": 3.22e6,
"eta": 0.66
}, # Cq is in Hz
)
])
data = cp.as_csdm(np.random.rand(1024, 512))
method = ThreeQ_VAS(
channels=["27Al"],
magnetic_flux_density=7,
spectral_dimensions=[
{
"count": 1024,
"spectral_width": 5000,
"reference_offset": -3e3
},
{
"count": 512,
"spectral_width": 10000,
"reference_offset": 4e3
},
],
experiment=data,
)
sim = Simulator()
sim.spin_systems = [spin_system]
sim.methods = [method]
sim.run()
def test_3QMAS():
"""3Q MAS correlation method declaration"""
mth = ThreeQ_VAS(
channels=["87Rb"],
magnetic_flux_density=9.4, # in T
spectral_dimensions=[
{
"count": 512,
"spectral_width": 5e6
},
{
"count": 128,
"spectral_width": 5e4
},
],
)
assert np.allclose(mth.affine_matrix, [0.5625, 0.4375, 0, 1])
assert ThreeQ_VAS.parse_dict_with_units(mth.json()) == mth
def setup_simulator():
site = Site(
isotope="23Na",
isotropic_chemical_shift=32,
shielding_symmetric={
"zeta": -120,
"eta": 0.1
},
quadrupolar={
"Cq": 1e5,
"eta": 0.31,
"beta": 5.12
},
)
sys = SpinSystem(sites=[site], abundance=0.123)
sim = Simulator()
sim.spin_systems.append(sys)
sim.methods.append(
BlochDecayCTSpectrum(channels=["2H"], rotor_frequency=1e3))
sim.methods.append(
BlochDecaySpectrum(channels=["2H"], rotor_frequency=12.5e3))
sim.methods.append(ThreeQ_VAS(channels=["27Al"]))
sim.methods.append(SSB2D(channels=["17O"], rotor_frequency=35500))
return sim
def test_MQMAS_spin_5halves():
spin_system = SpinSystem(sites=[
Site(
isotope="27Al",
isotropic_chemical_shift=64.5, # in ppm
quadrupolar={
"Cq": 3.22e6,
"eta": 0.66
}, # Cq is in Hz
)
])
method = ThreeQ_VAS(
channels=["27Al"],
magnetic_flux_density=7,
spectral_dimensions=[
{
"count": 1024,
"spectral_width": 5000,
"reference_offset": -3e3
},
{
"count": 512,
"spectral_width": 10000,
"reference_offset": 4e3
},
],
)
sim = Simulator()
sim.spin_systems = [spin_system]
sim.methods = [method]
sim.run()
data = sim.methods[0].simulation
dat = data.y[0].components[0]
index = np.where(dat == dat.max())[0]
# The isotropic coordinate of this peak is given by
# v_iso = -(17/31)*iso_shift + 8e6/93 * (vq/v0)^2 * (eta^2 / 3 + 1)
# ref: D. Massiot et al. / Solid State Nuclear Magnetic Resonance 6 (1996) 73-83
spin = method.channels[0].spin
v0 = method.channels[0].gyromagnetic_ratio * 7 * 1e6
vq = 3 * 3.22e6 / (2 * spin * (2 * spin - 1))
v_iso = -(17 / 31) * 64.5 - (8e6 / 93) * (vq / v0)**2 * ((0.66**2) / 3 + 1)
# the coordinate from spectrum along the iso dimension must be equal to v_iso
v_iso_spectrum = data.x[1].coordinates[index[0]].value
np.testing.assert_almost_equal(v_iso, v_iso_spectrum, decimal=2)
# The projection onto the MAS dimension should be the 1D block decay central
# transition spectrum
mas_slice = data.sum(axis=1).y[0].components[0]
# MAS spectrum
method = BlochDecayCTSpectrum(
channels=["27Al"],
magnetic_flux_density=7,
rotor_frequency=1e9,
spectral_dimensions=[{
"count": 512,
"spectral_width": 10000,
"reference_offset": 4e3
}],
)
sim = Simulator()
sim.spin_systems = [spin_system]
sim.methods = [method]
sim.config.integration_volume = "hemisphere"
sim.run()
data = sim.methods[0].simulation.y[0].components[0]
assert np.allclose(data / data.max(), mas_slice / mas_slice.max())
def test_ThreeQ_VAS_spin_3halves():
site = Site(
isotope="87Rb",
isotropic_chemical_shift=-9,
shielding_symmetric={
"zeta": 100,
"eta": 0
},
quadrupolar={
"Cq": 3.5e6,
"eta": 0.36,
"beta": 70 / 180 * np.pi
},
)
spin_system = SpinSystem(sites=[site])
method = ThreeQ_VAS(
channels=["87Rb"],
magnetic_flux_density=9.4,
spectral_dimensions=[
{
"count": 1024,
"spectral_width": 20000
},
{
"count": 512,
"spectral_width": 20000
},
],
)
sim = Simulator()
sim.spin_systems = [spin_system]
sim.methods = [method]
sim.config.integration_volume = "hemisphere"
sim.run()
data = sim.methods[0].simulation
dat = data.y[0].components[0]
index = np.where(dat == dat.max())[0]
# The isotropic coordinate of this peak is given by
# v_iso = (17/8)*iso_shift + 1e6/8 * (vq/v0)^2 * (eta^2 / 3 + 1)
# ref: D. Massiot et al. / Solid State Nuclear Magnetic Resonance 6 (1996) 73-83
spin = method.channels[0].spin
v0 = method.channels[0].gyromagnetic_ratio * 9.4 * 1e6
vq = (3 * 3.5e6) / (2 * spin * (2 * spin - 1))
v_iso = -9 * 17 / 8 + 1e6 / 8 * ((vq / v0)**2) * ((0.36**2) / 3 + 1)
# the coordinate from spectrum along the iso dimension must be equal to v_iso
v_iso_spectrum = data.x[1].coordinates[index[0]].value
np.testing.assert_almost_equal(v_iso, v_iso_spectrum, decimal=2)
# The projection onto the MAS dimension should be the 1D block decay central
# transition spectrum
mas_slice = data.sum(axis=1).y[0].components[0]
# MAS spectrum
method = BlochDecayCTSpectrum(
channels=["87Rb"],
magnetic_flux_density=9.4,
rotor_frequency=1e9,
spectral_dimensions=[{
"count": 512,
"spectral_width": 20000
}],
)
sim = Simulator()
sim.spin_systems = [spin_system]
sim.methods = [method]
sim.config.integration_volume = "hemisphere"
sim.run()
data = sim.methods[0].simulation.y[0].components[0]
assert np.allclose(data / data.max(), mas_slice / mas_slice.max())
sim = Simulator()
# load the spin systems from url.
filename = "https://sandbox.zenodo.org/record/687656/files/coesite.mrsys"
sim.load_spin_systems(filename)
method = ThreeQ_VAS(
channels=["17O"],
magnetic_flux_density=11.7, # in T
spectral_dimensions=[
{
"count": 256,
"spectral_width": 5e3, # in Hz
"reference_offset": -2.5e3, # in Hz
"label": "Isotropic dimension",
},
# The last spectral dimension block is the direct-dimension
{
"count": 256,
"spectral_width": 2e4, # in Hz
"reference_offset": 0, # in Hz
"label": "MAS dimension",
},
],
)
sim.methods = [method] # add the method.
sim.run() # Run the simulation
# %%
# The plot of the simulation.
data = sim.methods[0].simulation
abundance=pdf,
)
len(spin_systems)
# %%
# Simulate a :math:`^{27}\text{Al}` 3Q-MAS spectrum by using the `ThreeQ_MAS` method.
method = ThreeQ_VAS(
channels=["87Rb"],
magnetic_flux_density=9.4, # in T
rotor_angle=54.735 * np.pi / 180,
spectral_dimensions=[
dict(
count=96,
spectral_width=7e3, # in Hz
reference_offset=-7e3, # in Hz
label="Isotropic dimension",
),
dict(
count=256,
spectral_width=1e4, # in Hz
reference_offset=-4e3, # in Hz
label="MAS dimension",
),
],
)
# %%
# Create the simulator object, add the spin systems and method, and run the simulation.
sim = Simulator()
sim.spin_systems = spin_systems # add the spin systems
sim.methods = [method] # add the method
sites = [Rb87_1, Rb87_2, Rb87_3] # all sites
spin_systems = [SpinSystem(sites=[s]) for s in sites]
# %%
# Select a Triple Quantum variable-angle spinning method. You may optionally
# provide a `rotor_angle` to the method. The default `rotor_angle` is the magic-angle.
method = ThreeQ_VAS(
channels=["87Rb"],
magnetic_flux_density=9.4, # in T
spectral_dimensions=[
{
"count": 128,
"spectral_width": 7e3, # in Hz
"reference_offset": -7e3, # in Hz
"label": "Isotropic dimension",
},
{
"count": 256,
"spectral_width": 1e4, # in Hz
"reference_offset": -4e3, # in Hz
"label": "MAS dimension",
},
],
)
# %%
# Create the Simulator object, add the method and spin system objects, and
# run the simulation.
sim = Simulator()
sim.spin_systems = spin_systems # add the spin systems
sim.methods = [method] # add the method.
)
spin_systems = [SpinSystem(sites=[site])]
# %%
# Select a Triple Quantum variable-angle spinning method. You may optionally
# provide a `rotor_angle` to the method. The default `rotor_angle` is the magic-angle.
method = ThreeQ_VAS(
channels=["27Al"],
magnetic_flux_density=7, # in T
spectral_dimensions=[
dict(
count=256,
spectral_width=1e4, # in Hz
reference_offset=-3e3, # in Hz
label="Isotropic dimension",
),
dict(
count=512,
spectral_width=1e4, # in Hz
reference_offset=4e3, # in Hz
label="MAS dimension",
),
],
)
# %%
# Create the Simulator object, add the method and spin system objects, and
# run the simulation.
sim = Simulator()
sim.spin_systems = spin_systems # add the spin systems
sim.methods = [method] # add the method.
sim = Simulator()
# load the spin systems from url.
filename = "https://sandbox.zenodo.org/record/835664/files/coesite.mrsys"
sim.load_spin_systems(filename)
method = ThreeQ_VAS(
channels=["17O"],
magnetic_flux_density=11.74, # in T
spectral_dimensions=[
dict(
count=256,
spectral_width=5e3, # in Hz
reference_offset=-2.5e3, # in Hz
label="Isotropic dimension",
),
# The last spectral dimension block is the direct-dimension
dict(
count=256,
spectral_width=2e4, # in Hz
reference_offset=0, # in Hz
label="MAS dimension",
),
],
)
sim.methods = [method] # add the method.
sim.run() # Run the simulation
# %%
# The plot of the simulation.
data = sim.methods[0].simulation
)
spin_systems = [SpinSystem(sites=[site])]
# %%
# Select a Triple Quantum variable-angle spinning method. You may optionally
# provide a `rotor_angle` to the method. The default `rotor_angle` is the magic-angle.
method = ThreeQ_VAS(
channels=["27Al"],
magnetic_flux_density=7, # in T
spectral_dimensions=[
{
"count": 256,
"spectral_width": 1e4, # in Hz
"reference_offset": -3e3, # in Hz
"label": "Isotropic dimension",
},
{
"count": 512,
"spectral_width": 1e4, # in Hz
"reference_offset": 4e3, # in Hz
"label": "MAS dimension",
},
],
)
# %%
# Create the Simulator object, add the method and spin system objects, and
# run the simulation.
sim = Simulator()
sim.spin_systems = spin_systems # add the spin systems
sim.methods = [method] # add the method.
"eta": eta
},
abundance=abundance,
)
# %%
# **Method**
#
# Create the 3QMAS method.
# Get the spectral dimension parameters from the experiment.
spectral_dims = get_spectral_dimensions(experiment)
MQMAS = ThreeQ_VAS(
channels=["87Rb"],
magnetic_flux_density=9.395, # in T
spectral_dimensions=spectral_dims,
experiment=experiment, # add the measurement to the method.
)
# Optimize the script by pre-setting the transition pathways for each spin system from
# the das method.
for sys in spin_systems:
sys.transition_pathways = MQMAS.get_transition_pathways(sys)
# %%
# **Guess Spectrum**
# Simulation
# ----------
sim = Simulator(spin_systems=spin_systems, methods=[MQMAS])
sim.config.number_of_sidebands = 1
quadrupolar={"Cq": Cq * 1e6, "eta": eta}, # Cq in Hz
abundance=pdf,
)
len(spin_systems)
# %%
# Simulate a :math:`^{27}\text{Al}` 3Q-MAS spectrum by using the `ThreeQ_MAS` method.
mqvas = ThreeQ_VAS(
channels=["27Al"],
spectral_dimensions=[
dict(
count=512,
spectral_width=26718.475776, # in Hz
reference_offset=-4174.76184, # in Hz
label="Isotropic dimension",
),
dict(
count=512,
spectral_width=2e4, # in Hz
reference_offset=2e3, # in Hz
label="MAS dimension",
),
],
)
# %%
# Create the simulator object, add the spin systems and method, and run the simulation.
sim = Simulator()
sim.spin_systems = spin_systems # add the spin systems
sim.methods = [mqvas] # add the method
sim.config.number_of_sidebands = 1
}, # Cq in Hz
abundance=pdf,
)
len(spin_systems)
# %%
# Simulate a :math:`^{27}\text{Al}` 3Q-MAS spectrum by using the `ThreeQ_MAS` method.
mqvas = ThreeQ_VAS(
channels=["27Al"],
spectral_dimensions=[
{
"count": 512,
"spectral_width": 26718.475776, # in Hz
"reference_offset": -4174.76184, # in Hz
"label": "Isotropic dimension",
},
{
"count": 512,
"spectral_width": 2e4, # in Hz
"reference_offset": 2e3, # in Hz
"label": "MAS dimension",
},
],
)
# %%
# Create the simulator object, add the spin systems and method, and run the simulation.
sim = Simulator()
sim.spin_systems = spin_systems # add the spin systems
sim.methods = [mqvas] # add the method
sim.config.number_of_sidebands = 1
sites = [Rb87_1, Rb87_2, Rb87_3] # all sites
spin_systems = [SpinSystem(sites=[s]) for s in sites]
# %%
# Select a Triple Quantum variable-angle spinning method. You may optionally
# provide a `rotor_angle` to the method. The default `rotor_angle` is the magic-angle.
method = ThreeQ_VAS(
channels=["87Rb"],
magnetic_flux_density=9.4, # in T
spectral_dimensions=[
dict(
count=128,
spectral_width=7e3, # in Hz
reference_offset=-7e3, # in Hz
label="Isotropic dimension",
),
dict(
count=256,
spectral_width=1e4, # in Hz
reference_offset=-4e3, # in Hz
label="MAS dimension",
),
],
)
# A graphical representation of the method object.
plt.figure(figsize=(5, 3.5))
method.plot()
plt.show()
# %%
