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 all_transitions(self) -> TransitionList:
"""Returns a list of all possible spin transitions in the given spin system.
Example
-------
>>> spin_system_1H_13C.get_isotopes() # two site (spin-1/2) spin system
['13C', '1H']
>>> spin_system_1H_13C.all_transitions() # 16 two energy level transitions
[|-0.5, -0.5⟩⟨-0.5, -0.5|,
|-0.5, 0.5⟩⟨-0.5, -0.5|,
|0.5, -0.5⟩⟨-0.5, -0.5|,
|0.5, 0.5⟩⟨-0.5, -0.5|,
|-0.5, -0.5⟩⟨-0.5, 0.5|,
|-0.5, 0.5⟩⟨-0.5, 0.5|,
|0.5, -0.5⟩⟨-0.5, 0.5|,
|0.5, 0.5⟩⟨-0.5, 0.5|,
|-0.5, -0.5⟩⟨0.5, -0.5|,
|-0.5, 0.5⟩⟨0.5, -0.5|,
|0.5, -0.5⟩⟨0.5, -0.5|,
|0.5, 0.5⟩⟨0.5, -0.5|,
|-0.5, -0.5⟩⟨0.5, 0.5|,
|-0.5, 0.5⟩⟨0.5, 0.5|,
|0.5, -0.5⟩⟨0.5, 0.5|,
|0.5, 0.5⟩⟨0.5, 0.5|]
"""
transitions = self._all_transitions()
return TransitionList([
Transition(initial=item[0].tolist(), final=item[1].tolist())
for item in transitions
])
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 all_transitions(self) -> TransitionList:
"""Returns a list of all possible spin :ref:`transition_api` objects in the
given spin system.
Example
-------
>>> spin_system_1H_13C.all_transitions() # 16 two energy level transitions
[|-0.5, -0.5⟩⟨-0.5, -0.5|,
|-0.5, 0.5⟩⟨-0.5, -0.5|,
|0.5, -0.5⟩⟨-0.5, -0.5|,
|0.5, 0.5⟩⟨-0.5, -0.5|,
|-0.5, -0.5⟩⟨-0.5, 0.5|,
|-0.5, 0.5⟩⟨-0.5, 0.5|,
|0.5, -0.5⟩⟨-0.5, 0.5|,
|0.5, 0.5⟩⟨-0.5, 0.5|,
|-0.5, -0.5⟩⟨0.5, -0.5|,
|-0.5, 0.5⟩⟨0.5, -0.5|,
|0.5, -0.5⟩⟨0.5, -0.5|,
|0.5, 0.5⟩⟨0.5, -0.5|,
|-0.5, -0.5⟩⟨0.5, 0.5|,
|-0.5, 0.5⟩⟨0.5, 0.5|,
|0.5, -0.5⟩⟨0.5, 0.5|,
|0.5, 0.5⟩⟨0.5, 0.5|]
Returns
A list of :ref:`transition_api` objects.
"""
transitions = self._all_transitions()
return TransitionList(
[
Transition(initial=item[0].tolist(), final=item[1].tolist())
for item in transitions
]
)
def test_transition_1():
# set up
a = {"initial": [0.5, 1.5], "final": [-0.5, 1.5]}
tran = Transition(**a)
assert tran.initial == [0.5, 1.5]
assert tran.final == [-0.5, 1.5]
# to dict with unit
assert tran.json() == a
assert tran.tolist() == [0.5, 1.5, -0.5, 1.5]
assert tran.json() == a
# p and Δm
assert tran.p == -1
assert tran.delta_m == -1
def get_transition_pathways(self, spin_system) -> list:
"""
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:
An array of TransitionPathway objects. Each TransitionPathway object is an
ordered collection of Transition objects.
"""
segments = self._get_transition_pathways_np(spin_system)
return [
TransitionPathway([
Transition(initial=tr[0].tolist(), final=tr[1].tolist())
for tr in item
]) for item in segments
]
def test_transition_list_1():
# create a list.
tran_list = TransitionList()
# append to a list.
a = {"initial": [0.5, 1.5], "final": [-0.5, 1.5]}
tran_list.append(a)
assert tran_list[0] == Transition(**a)
b = Transition(**{"initial": [-0.5, -1.5], "final": [-1.5, -1.5]})
tran_list.append(b)
assert tran_list[1] == b
error = (
"Expecting a Transition object or an equivalent python dict object, instead "
"found str."
)
with pytest.raises(ValueError, match=f".*{error}.*"):
tran_list.append("test")
# assign an item at a list index.
c = {"initial": [-1.5, -1.5], "final": [1.5, -1.5]}
tran_list[1] = c
assert tran_list[1] == Transition(**c)
with pytest.raises(ValueError, match=f".*{error}.*"):
tran_list[1] = "test"
# inset an item to a list.
tran_list.insert(1, b)
assert tran_list[1] == b
assert tran_list[2] == Transition(**c)
# length of the list.
assert len(tran_list) == 3
# delete an item from the list.
del tran_list[1]
assert len(tran_list) == 2
assert tran_list[0] == Transition(**a)
assert tran_list[1] == Transition(**c)
# equality test
assert tran_list != "a"
assert tran_list != TransitionList([a])
assert tran_list != TransitionList([a, b])
assert tran_list == TransitionList([a, c])
# appending b for further filter tests.
tran_list.insert(1, b)
assert tran_list == TransitionList([a, b, c])
# filter
tran_filter_1 = tran_list.filter()
assert tran_filter_1 == tran_list
# test for P
tran_filter_1 = tran_list.filter(P=[-1, 0])
assert tran_filter_1 == TransitionList([a, b])
tran_filter_1 = tran_list.filter(P=[-1, -1])
assert tran_filter_1 == TransitionList([])
# test for D
tran_filter_1 = tran_list.filter(D=[0, 0])
assert tran_filter_1 == TransitionList([a, c])
# test for P and D
tran_filter_1 = tran_list.filter(P=[3, 0], D=[0, 0])
assert tran_filter_1 == TransitionList([c])
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