def test_01():
system = SpinSystem(sites=[{"isotope": "13C"}, {"isotope": "1H"}])
tr = method1.get_transition_pathways(system)
expected = [
TransitionPathway([{"final": [-0.5, -0.5], "initial": [0.5, -0.5]}]),
TransitionPathway([{"final": [-0.5, 0.5], "initial": [0.5, 0.5]}]),
]
check_transition_set(tr, expected)
def get_transition_pathways(self, spin_system) -> List[TransitionPathway]:
"""Return a list of transition pathways from the given spin system that satisfy
the query selection criterion of the method.
Args:
SpinSystem spin_system: A SpinSystem object.
Returns:
A list of :ref:`transition_pathway_api` objects. Each TransitionPathway
object is an ordered collection of Transition objects.
Example:
>>> from mrsimulator import SpinSystem
>>> from mrsimulator.method.lib import ThreeQ_VAS
>>> sys = SpinSystem(sites=[{'isotope': '27Al'}, {'isotope': '29Si'}])
>>> method = ThreeQ_VAS(channels=['27Al'])
>>> pprint(method.get_transition_pathways(sys))
[|1.5, -0.5⟩⟨-1.5, -0.5| ⟶ |-0.5, -0.5⟩⟨0.5, -0.5|, weight=(1+0j),
|1.5, -0.5⟩⟨-1.5, -0.5| ⟶ |-0.5, 0.5⟩⟨0.5, 0.5|, weight=(1+0j),
|1.5, 0.5⟩⟨-1.5, 0.5| ⟶ |-0.5, -0.5⟩⟨0.5, -0.5|, weight=(1+0j),
|1.5, 0.5⟩⟨-1.5, 0.5| ⟶ |-0.5, 0.5⟩⟨0.5, 0.5|, weight=(1+0j)]
"""
segments, weights = self._get_transition_pathway_and_weights_np(spin_system)
return [
TransitionPathway(
[
Transition(initial=tr[0].tolist(), final=tr[1].tolist())
for tr in item
],
weight=w,
)
for item, w in zip(segments, weights)
if w != 0
]
def test_cosy():
system = SpinSystem(sites=[{"isotope": "1H"}, {"isotope": "1H"}])
cosy = Method2D(
channels=["1H"],
spectral_dimensions=[
{
"events": [
{"fraction": 1, "transition_query": {"P": [-1]}},
{"mixing_query": {"ch1": {"tip_angle": np.pi / 2, "phase": 0}}},
],
},
{
"events": [{"fraction": 1, "transition_query": {"P": [-1]}}],
},
],
)
tr = cosy.get_transition_pathways(system)
weights = np.asarray([1, -1, 1, 1, -1, 1, 1, 1, 1, 1, 1, -1, 1, 1, -1, 1]) * 0.25
transition_pathways = 0.5 * np.asarray(
[
[[[-1, 1], [-1, -1]], [[-1, 1], [-1, -1]]],
[[[-1, 1], [-1, -1]], [[1, -1], [-1, -1]]],
[[[-1, 1], [-1, -1]], [[1, 1], [-1, 1]]],
[[[-1, 1], [-1, -1]], [[1, 1], [1, -1]]],
#
[[[1, -1], [-1, -1]], [[-1, 1], [-1, -1]]],
[[[1, -1], [-1, -1]], [[1, -1], [-1, -1]]],
[[[1, -1], [-1, -1]], [[1, 1], [-1, 1]]],
[[[1, -1], [-1, -1]], [[1, 1], [1, -1]]],
#
[[[1, 1], [-1, 1]], [[-1, 1], [-1, -1]]],
[[[1, 1], [-1, 1]], [[1, -1], [-1, -1]]],
[[[1, 1], [-1, 1]], [[1, 1], [-1, 1]]],
[[[1, 1], [-1, 1]], [[1, 1], [1, -1]]],
#
[[[1, 1], [1, -1]], [[-1, 1], [-1, -1]]],
[[[1, 1], [1, -1]], [[1, -1], [-1, -1]]],
[[[1, 1], [1, -1]], [[1, 1], [-1, 1]]],
[[[1, 1], [1, -1]], [[1, 1], [1, -1]]],
]
)
expected = [
TransitionPathway(
pathway=[
{"initial": list(states[0]), "final": list(states[1])}
for states in transitions
],
weight=w,
)
for transitions, w in zip(transition_pathways, weights)
]
assert tr == expected
def add_site(doctest_namespace):
doctest_namespace["np"] = np
doctest_namespace["plt"] = plt
doctest_namespace["SpinSystem"] = SpinSystem
doctest_namespace["Simulator"] = Simulator
doctest_namespace["Site"] = Site
doctest_namespace["Coupling"] = Coupling
doctest_namespace["SymmetricTensor"] = SymmetricTensor
doctest_namespace["st"] = SymmetricTensor
doctest_namespace["pprint"] = pprint
doctest_namespace["Isotope"] = Isotope
doctest_namespace["sp"] = sp
doctest_namespace["Method2D"] = Method2D
site1 = Site(
isotope="13C",
isotropic_chemical_shift=20,
shielding_symmetric=SymmetricTensor(zeta=10, eta=0.5),
)
site2 = Site(
isotope="1H",
isotropic_chemical_shift=-4,
shielding_symmetric=SymmetricTensor(zeta=2.1, eta=0.1),
)
site3 = Site(
isotope="27Al",
isotropic_chemical_shift=120,
shielding_symmetric=SymmetricTensor(zeta=2.1, eta=0.1),
quadrupolar=SymmetricTensor(Cq=5.1e6, eta=0.5),
)
doctest_namespace["spin_system_1H_13C"] = SpinSystem(sites=[site1, site2])
doctest_namespace["spin_systems"] = SpinSystem(sites=[site1, site2, site3])
spin_systems = [SpinSystem(sites=[site]) for site in [site1, site2, site3]]
sim = Simulator()
sim.spin_systems += spin_systems
doctest_namespace["sim"] = sim
# Transitions
t1 = Transition(initial=[0.5, 0.5], final=[0.5, -0.5])
doctest_namespace["t1"] = t1
t2 = Transition(initial=[0.5, 0.5], final=[-0.5, 0.5])
doctest_namespace["t2"] = t2
path = TransitionPathway([t1, t2])
doctest_namespace["path"] = path
def add_site(doctest_namespace):
doctest_namespace["np"] = np
doctest_namespace["plt"] = plt
doctest_namespace["SpinSystem"] = SpinSystem
doctest_namespace["Simulator"] = Simulator
doctest_namespace["Site"] = Site
doctest_namespace["Coupling"] = Coupling
doctest_namespace["SymmetricTensor"] = SymmetricTensor
doctest_namespace["st"] = SymmetricTensor
doctest_namespace["pprint"] = pprint
doctest_namespace["Isotope"] = Isotope
doctest_namespace["sp"] = sp
doctest_namespace["Method2D"] = Method2D
site1 = Site(
isotope="13C",
isotropic_chemical_shift=20,
shielding_symmetric=SymmetricTensor(zeta=10, eta=0.5),
)
doctest_namespace["site1"] = site1
coupling1 = Coupling(
site_index=[0, 1],
isotropic_j=20,
j_symmetric=SymmetricTensor(zeta=10, eta=0.5),
)
doctest_namespace["coupling1"] = coupling1
site2 = Site(
isotope="1H",
isotropic_chemical_shift=-4,
shielding_symmetric=SymmetricTensor(zeta=2.1, eta=0.1),
)
doctest_namespace["site2"] = site2
site3 = Site(
isotope="27Al",
isotropic_chemical_shift=120,
shielding_symmetric=SymmetricTensor(zeta=2.1, eta=0.1),
quadrupole=SymmetricTensor(Cq=5.1e6, eta=0.5),
)
doctest_namespace["site3"] = site3
spin_system_1H_13C = SpinSystem(sites=[site1, site2])
doctest_namespace["spin_system_1H_13C"] = spin_system_1H_13C
spin_system_1 = SpinSystem(sites=[site1])
doctest_namespace["spin_system_1"] = spin_system_1
doctest_namespace["spin_systems"] = SpinSystem(sites=[site1, site2, site3])
spin_systems = [SpinSystem(sites=[site]) for site in [site1, site2, site3]]
sim = Simulator()
sim.spin_systems += spin_systems
doctest_namespace["sim"] = sim
# coesite
O17_1 = Site(
isotope="17O",
isotropic_chemical_shift=29,
quadrupolar=SymmetricTensor(Cq=6.05e6, eta=0.000),
)
O17_2 = Site(
isotope="17O",
isotropic_chemical_shift=41,
quadrupolar=SymmetricTensor(Cq=5.43e6, eta=0.166),
)
O17_3 = Site(
isotope="17O",
isotropic_chemical_shift=57,
quadrupolar=SymmetricTensor(Cq=5.45e6, eta=0.168),
)
O17_4 = Site(
isotope="17O",
isotropic_chemical_shift=53,
quadrupolar=SymmetricTensor(Cq=5.52e6, eta=0.169),
)
O17_5 = Site(
isotope="17O",
isotropic_chemical_shift=58,
quadrupolar=SymmetricTensor(Cq=5.16e6, eta=0.292),
)
sites = [O17_1, O17_2, O17_3, O17_4, O17_5]
abundance = [0.83, 1.05, 2.16, 2.05, 1.90] # abundance of each spin system
spin_systems = [
SpinSystem(sites=[s], abundance=a) for s, a in zip(sites, abundance)
]
method = BlochDecayCTSpectrum(
channels=["17O"],
rotor_frequency=14000,
spectral_dimensions=[{
"count": 2048,
"spectral_width": 50000
}],
)
sim_coesite = Simulator()
sim_coesite.spin_systems += spin_systems
sim_coesite.methods += [method]
doctest_namespace["sim_coesite"] = sim_coesite
# Transitions
t1 = Transition(initial=[0.5, 0.5], final=[0.5, -0.5])
doctest_namespace["t1"] = t1
t2 = Transition(initial=[0.5, 0.5], final=[-0.5, 0.5])
doctest_namespace["t2"] = t2
path = TransitionPathway([t1, t2])
doctest_namespace["path"] = path