def test_equality():
a = Coupling(site_index=[0, 1])
b = Coupling(site_index=[0, 1])
assert a == b
c = Coupling(site_index=[0, 1], isotropic_j=16)
assert a != c
def setup_partially_coupled_system():
"""Systems A-C-E, B, D, F"""
sites = setup_sites()
AC_couple = Coupling(site_index=[0, 2], isotropic_j=20)
CE_couple = Coupling(site_index=[2, 4], isotropic_j=40)
sys = SpinSystem(sites=sites,
couplings=[AC_couple, CE_couple],
abundance=50)
A, B, C, D, E, F = sites
simplified_sys = [
SpinSystem(sites=[B], abundance=50),
SpinSystem(sites=[D], abundance=50),
SpinSystem(sites=[F], abundance=50),
SpinSystem(
sites=[A, C, E],
couplings=[
Coupling(site_index=[0, 1], isotropic_j=20),
Coupling(site_index=[1, 2], isotropic_j=40),
],
abundance=50,
),
]
return sys, simplified_sys
def setup_somecoupled_system():
"""Systems A-C, B, D-E, F"""
sites = setup_sites()
AC_couple = Coupling(site_index=[0, 2], isotropic_j=20)
DE_couple = Coupling(site_index=[3, 4], isotropic_j=40)
sys = SpinSystem(sites=sites,
couplings=[AC_couple, DE_couple],
abundance=50)
A, B, C, D, E, F = sites
simplified_sys = [
SpinSystem(sites=[B], abundance=50),
SpinSystem(sites=[F], abundance=50),
SpinSystem(
sites=[A, C],
couplings=[Coupling(site_index=[0, 1], isotropic_j=20)],
abundance=50,
),
SpinSystem(
sites=[D, E],
couplings=[Coupling(site_index=[0, 1], isotropic_j=40)],
abundance=50,
),
]
return sys, simplified_sys
def setup_partially_coupled_system2():
"""Systems A-C-E-F, B-D"""
sites = setup_sites()
AC_couple = Coupling(site_index=[0, 2], isotropic_j=20)
BD_couple = Coupling(site_index=[1, 3], isotropic_j=120)
CE_couple = Coupling(site_index=[2, 4], isotropic_j=40)
EF_couple = Coupling(site_index=[4, 5], isotropic_j=10)
sys = SpinSystem(
sites=sites,
couplings=[AC_couple, BD_couple, CE_couple, EF_couple],
abundance=50,
)
A, B, C, D, E, F = sites
simplified_sys = [
SpinSystem(
sites=[A, C, E, F],
couplings=[
Coupling(site_index=[0, 1], isotropic_j=20),
Coupling(site_index=[1, 2], isotropic_j=40),
Coupling(site_index=[2, 3], isotropic_j=10),
],
abundance=50,
),
SpinSystem(
sites=[B, D],
couplings=[Coupling(site_index=[0, 1], isotropic_j=120)],
abundance=50,
),
]
return sys, simplified_sys
def coupled_spin_system(j_coup=0, dipole=0):
S1 = Site(
isotope="1H",
isotropic_chemical_shift=10, # in ppm
shielding_symmetric=SymmetricTensor(zeta=-80, eta=0.25), # zeta in ppm
)
S2 = Site(isotope="1H", isotropic_chemical_shift=-10)
S12 = Coupling(
site_index=[0, 1],
isotropic_j=j_coup,
dipolar=SymmetricTensor(D=dipole, eta=0),
)
return SpinSystem(sites=[S1, S2], couplings=[S12])
def setup_system_simplifiedSystem():
"""systems A-B-C, D-F, E"""
sites = setup_sites()
AB_couple = Coupling(site_index=[0, 1], isotropic_j=10, name="AB")
BC_couple = Coupling(site_index=[1, 2], isotropic_j=10, name="BC")
AC_couple = Coupling(site_index=[0, 2], isotropic_j=10, name="AC")
DF_couple = Coupling(site_index=[3, 5], isotropic_j=30, name="DF")
couplings = [AB_couple, BC_couple, AC_couple, DF_couple]
sys = SpinSystem(sites=sites, couplings=couplings, abundance=10)
A, B, C, D, E, F = sites
simplified_sys = [
SpinSystem(sites=[E], abundance=10),
SpinSystem(
sites=[D, F],
couplings=[Coupling(site_index=[0, 1], isotropic_j=30, name="DF")],
abundance=10,
),
SpinSystem(
sites=[A, B, C], couplings=[AB_couple, AC_couple, BC_couple], abundance=10
),
]
return sys, simplified_sys
def test_simulator_2():
sim = Simulator()
sim.spin_systems = [
SpinSystem(
sites=[Site(isotope="1H"),
Site(isotope="23Na")],
couplings=[Coupling(site_index=[0, 1], isotropic_j=15)],
)
]
sim.methods = [
BlochDecaySpectrum(
channels=["1H"],
spectral_dimensions=[{
"count": 10
}],
experiment=cp.as_csdm(np.arange(10)),
)
]
sim.name = "test"
sim.label = "test0"
sim.description = "testing-testing 1.2.3"
sim.run()
# save
sim.save("test_sim_save.temp")
sim_load = Simulator.load("test_sim_save.temp")
sim_load_data = sim_load.methods[0].simulation
sim_data = sim.methods[0].simulation
sim_load_data._timestamp = ""
assert sim_load_data.dict() == sim_data.dict()
sim_load.methods[0].simulation = None
sim.methods[0].simulation = None
assert sim_load.spin_systems == sim.spin_systems
assert sim_load.methods == sim.methods
assert sim_load.name == sim.name
assert sim_load.description == sim.description
os.remove("test_sim_save.temp")
def test_direct_init_coupling1():
# test 1 --------------------------------------------------------------------------
the_coupling = Coupling(site_index=[0, 1], isotropic_j=10)
assert the_coupling.site_index == [0, 1]
assert the_coupling.isotropic_j == 10
assert the_coupling.property_units["isotropic_j"] == "Hz"
assert the_coupling.j_symmetric is None
assert the_coupling.j_antisymmetric is None
assert the_coupling.dipolar is None
# test 2 --------------------------------------------------------------------------
the_coupling = Coupling(site_index=[0, 1],
isotropic_j=10,
j_symmetric=None)
assert the_coupling.j_symmetric is None
assert the_coupling.j_antisymmetric is None
assert the_coupling.dipolar is None
# test 3 --------------------------------------------------------------------------
the_coupling = Coupling(
site_index=[2, 3],
isotropic_j=10,
j_symmetric={
"zeta": 12.1,
"eta": 0.1
},
)
assert the_coupling.site_index == [2, 3]
assert the_coupling.isotropic_j == 10
assert the_coupling.property_units["isotropic_j"] == "Hz"
assert the_coupling.j_antisymmetric is None
assert the_coupling.dipolar is None
assert the_coupling.j_symmetric.zeta == 12.1
assert the_coupling.j_symmetric.property_units["zeta"] == "Hz"
assert the_coupling.j_symmetric.eta == 0.1
# test 4 --------------------------------------------------------------------------
error = "ensure this value is less than or equal to 1"
with pytest.raises(ValidationError, match=f".*{error}.*"):
Coupling(
site_index=[3, 1],
isotropic_j=10,
j_symmetric={
"zeta": 12.1,
"eta": 1.5
},
)
error = [
"Site index must a list of two integers",
"The two site indexes must be unique integers",
]
with pytest.raises(ValidationError, match=".*{}.*".format(*error)):
Coupling(site_index=[])
with pytest.raises(ValidationError, match=".*{}.*".format(*error)):
Coupling(site_index=[2, 3, 4])
with pytest.raises(ValidationError, match=".*{}.*".format(*error)):
Coupling(site_index=[2])
with pytest.raises(ValidationError, match=".*{1}.*".format(*error)):
Coupling(site_index=[1, 1])
ax = Coupling.parse_dict_with_units({
"site_index": [0, 1],
"isotropic_j": "5 cHz"
})
assert ax.json() == {
"site_index": [0, 1],
"isotropic_j": "0.05 Hz",
}
# **Isotopomer 1**
#
# Now, let's define the couplings and build the spin system for the most abundant
# isotopomer (pictured below).
#
# .. figure:: ../../_static/iso1.*
# :width: 200
# :alt: figure
# :align: center
#
# An isotopomer of ethanol containing all :math:`^{1}\text{H}` and all
# :math:`^{12}\text{C}` isotopes.
#
iso1_sites = [H_CH3, H_CH3, H_CH3, H_CH2, H_CH2, H_OH]
HH_coupling_1 = Coupling(site_index=[0, 3], isotropic_j=7)
HH_coupling_2 = Coupling(site_index=[0, 4], isotropic_j=7)
HH_coupling_3 = Coupling(site_index=[1, 3], isotropic_j=7)
HH_coupling_4 = Coupling(site_index=[1, 4], isotropic_j=7)
HH_coupling_5 = Coupling(site_index=[2, 3], isotropic_j=7)
HH_coupling_6 = Coupling(site_index=[2, 4], isotropic_j=7)
iso1_couplings = [
HH_coupling_1,
HH_coupling_2,
HH_coupling_3,
HH_coupling_4,
HH_coupling_5,
HH_coupling_6,
]
def setup_partially_coupled_system3():
"""Systems A-B-C-D-E-F"""
sys, _ = setup_partially_coupled_system2()
sys.couplings.insert(0, Coupling(site_index=[0, 1], isotropic_j=1020))
return sys, [sys]
from mrsimulator.spin_system.tensors import SymmetricTensor
# sphinx_gallery_thumbnail_number = 2
# %%
# For demonstration, we will create two spin systems, one with a single site and other
# with two spin 1/2 sites.
S1 = Site(
isotope="1H",
isotropic_chemical_shift=10, # in ppm
shielding_symmetric=SymmetricTensor(zeta=-80, eta=0.25), # zeta in ppm
)
S2 = Site(isotope="1H", isotropic_chemical_shift=-10)
S12 = Coupling(site_index=[0, 1],
isotropic_j=100,
dipolar=SymmetricTensor(D=2000, eta=0, alpha=0))
spin_system_1 = SpinSystem(sites=[S1], label="Uncoupled system")
spin_system_2 = SpinSystem(sites=[S1, S2],
couplings=[S12],
label="Coupled system")
# %%
# **Create a custom method**
#
# Writing a custom method is simply specifying an appropriate list of event objects per
# spectral dimension. In this example, we are interested in a one-dimensional Hahnecho
# method, and we use the generic `Method1D` class as a template. For a Hahnecho, we will
# use two types of Event objects---SpectralEvent and MixingEvent.
#
def test_direct_init_spin_system():
# test-1 # empty spin system
the_spin_system = SpinSystem(sites=[],
abundance=10,
transition_pathways=None)
assert the_spin_system.sites == []
assert the_spin_system.abundance == 10.0
assert the_spin_system.transition_pathways is None
assert the_spin_system.json() == {"abundance": "10.0 %"}
assert the_spin_system.json(units=False) == {
"abundance": 10.0,
}
# test-2 # site
test_site = Site(isotope="29Si", isotropic_chemical_shift=10)
assert test_site.isotope.symbol == "29Si"
assert test_site.isotropic_chemical_shift == 10.0
assert test_site.property_units["isotropic_chemical_shift"] == "ppm"
assert test_site.json() == {
"isotope": "29Si",
"isotropic_chemical_shift": "10.0 ppm",
}
assert test_site.json(units=False) == {
"isotope": "29Si",
"isotropic_chemical_shift": 10.0,
}
# test-3 # one site spin system
the_spin_system = SpinSystem(sites=[test_site], abundance=10)
assert isinstance(the_spin_system.sites[0], Site)
assert the_spin_system.abundance == 10.0
assert the_spin_system.json() == {
"sites": [{
"isotope": "29Si",
"isotropic_chemical_shift": "10.0 ppm"
}],
"abundance": "10.0 %",
}
assert the_spin_system.json(units=False) == {
"sites": [{
"isotope": "29Si",
"isotropic_chemical_shift": 10.0
}],
"abundance": 10,
}
# test-4 # two sites spin system
the_spin_system = SpinSystem(sites=[test_site, test_site], abundance=10)
assert isinstance(the_spin_system.sites[0], Site)
assert isinstance(the_spin_system.sites[1], Site)
assert id(the_spin_system.sites[0]) != id(the_spin_system.sites[1])
assert the_spin_system.abundance == 10.0
assert the_spin_system.json() == {
"sites": [
{
"isotope": "29Si",
"isotropic_chemical_shift": "10.0 ppm"
},
{
"isotope": "29Si",
"isotropic_chemical_shift": "10.0 ppm"
},
],
"abundance":
"10.0 %",
}
assert the_spin_system.json(units=False) == {
"sites": [
{
"isotope": "29Si",
"isotropic_chemical_shift": 10.0
},
{
"isotope": "29Si",
"isotropic_chemical_shift": 10.0
},
],
"abundance":
10,
}
# test-5 # coupling
test_coupling = Coupling(site_index=[0, 1],
isotropic_j=10,
dipolar={"D": 100})
assert test_coupling.site_index == [0, 1]
assert test_coupling.isotropic_j == 10.0
assert test_coupling.property_units["isotropic_j"] == "Hz"
assert test_coupling.dipolar.D == 100.0
assert test_coupling.dipolar.property_units["D"] == "Hz"
assert test_coupling.json() == {
"site_index": [0, 1],
"isotropic_j": "10.0 Hz",
"dipolar": {
"D": "100.0 Hz"
},
}
assert test_coupling.json(units=False) == {
"site_index": [0, 1],
"isotropic_j": 10.0,
"dipolar": {
"D": 100.0
},
}
# test-6 # two sites and one coupling spin system
the_spin_system = SpinSystem(sites=[test_site, test_site],
couplings=[test_coupling],
abundance=10)
assert isinstance(the_spin_system.sites[0], Site)
assert isinstance(the_spin_system.sites[1], Site)
assert isinstance(the_spin_system.couplings[0], Coupling)
assert id(the_spin_system.sites[0]) != id(the_spin_system.sites[1])
assert the_spin_system.abundance == 10.0
assert the_spin_system.json() == {
"sites": [
{
"isotope": "29Si",
"isotropic_chemical_shift": "10.0 ppm"
},
{
"isotope": "29Si",
"isotropic_chemical_shift": "10.0 ppm"
},
],
"couplings": [{
"site_index": [0, 1],
"isotropic_j": "10.0 Hz",
"dipolar": {
"D": "100.0 Hz"
},
}],
"abundance":
"10.0 %",
}
assert the_spin_system.json(units=False) == {
"sites": [
{
"isotope": "29Si",
"isotropic_chemical_shift": 10.0
},
{
"isotope": "29Si",
"isotropic_chemical_shift": 10.0
},
],
"couplings": [{
"site_index": [0, 1],
"isotropic_j": 10.0,
"dipolar": {
"D": 100.0
}
}],
"abundance":
10,
}
# test-5
the_spin_system = SpinSystem(
name="Just a test",
description="The same",
sites=[
{
"isotope": "1H",
"isotropic_chemical_shift": 0
},
{
"isotope": "17O",
"isotropic_chemical_shift": -10,
"quadrupolar": {
"Cq": 5.1e6,
"eta": 0.5
},
},
],
couplings=[{
"site_index": [0, 1],
"isotropic_j": 34
}],
abundance=4.23,
)
assert the_spin_system.name == "Just a test"
assert the_spin_system.description == "The same"
assert the_spin_system.sites[0].isotope.symbol == "1H"
assert the_spin_system.sites[0].isotropic_chemical_shift == 0
assert the_spin_system.sites[1].isotope.symbol == "17O"
assert the_spin_system.sites[1].isotropic_chemical_shift == -10
assert the_spin_system.sites[1].quadrupolar.Cq == 5.1e6
assert the_spin_system.sites[1].quadrupolar.eta == 0.5
assert the_spin_system.couplings[0].site_index == [0, 1]
assert the_spin_system.couplings[0].isotropic_j == 34.0
assert the_spin_system.abundance == 4.23
serialize = the_spin_system.json()
assert serialize == {
"name":
"Just a test",
"description":
"The same",
"sites": [
{
"isotope": "1H",
"isotropic_chemical_shift": "0.0 ppm"
},
{
"isotope": "17O",
"isotropic_chemical_shift": "-10.0 ppm",
"quadrupolar": {
"Cq": "5100000.0 Hz",
"eta": 0.5
},
},
],
"couplings": [{
"site_index": [0, 1],
"isotropic_j": "34.0 Hz"
}],
"abundance":
"4.23 %",
}
assert the_spin_system == SpinSystem.parse_dict_with_units(serialize)
json_no_unit = the_spin_system.json(units=False)
assert json_no_unit == {
"name":
"Just a test",
"description":
"The same",
"sites": [
{
"isotope": "1H",
"isotropic_chemical_shift": 0
},
{
"isotope": "17O",
"isotropic_chemical_shift": -10.0,
"quadrupolar": {
"Cq": 5100000,
"eta": 0.5
},
},
],
"couplings": [{
"site_index": [0, 1],
"isotropic_j": 34.0
}],
"abundance":
4.23,
}
assert the_spin_system == SpinSystem(**json_no_unit)
from mrsimulator.methods import BlochDecaySpectrum
from mrsimulator import signal_processing as sp
from mrsimulator.spin_system.tensors import SymmetricTensor
# sphinx_gallery_thumbnail_number = 1
# %%
# **Spin Systems**
#
# Create a 13C-1H coupled spin system.
spin_system = SpinSystem(
sites=[
Site(isotope="13C", isotropic_chemical_shift=0.0),
Site(isotope="1H", isotropic_chemical_shift=0.0),
],
couplings=[Coupling(site_index=[0, 1], dipolar=SymmetricTensor(D=-2e4))],
)
# %%
# **Methods**
#
# Create a BlochDecaySpectrum method.
method = BlochDecaySpectrum(
channels=["13C"],
magnetic_flux_density=9.4, # in T
spectral_dimensions=[dict(count=2048, spectral_width=8.0e4)],
)
# %%
# **Simulator**
#
# Create the Simulator object and add the method and the spin system object.
def test_parse_json_site():
# test 1 --------------------------------------------------------------------------
good_json_coupling = {
"site_index": [0, 1],
"isotropic_j": "5 Hz",
"j_symmetric": {
"zeta": "13.89 Hz",
"eta": 0.25
},
}
# testing method parse_dict_with_units()
the_coupling = Coupling.parse_dict_with_units(good_json_coupling)
assert the_coupling.site_index == [0, 1]
assert the_coupling.isotropic_j == 5
assert the_coupling.property_units["isotropic_j"] == "Hz"
assert the_coupling.j_antisymmetric is None
assert the_coupling.dipolar is None
assert the_coupling.j_symmetric.zeta == 13.89
assert the_coupling.j_symmetric.property_units["zeta"] == "Hz"
assert the_coupling.j_symmetric.eta == 0.25
assert the_coupling.j_symmetric.alpha is None
assert the_coupling.j_symmetric.beta is None
assert the_coupling.j_symmetric.gamma is None
# test 2 --------------------------------------------------------------------------
good_json_2 = {
"site_index": [5, 3],
"isotropic_j": "-10 Hz",
"dipolar": {
"D": "5.12 kHz",
"eta": 0.5
},
}
the_coupling = Coupling.parse_dict_with_units(good_json_2)
assert the_coupling.site_index == [5, 3]
assert the_coupling.isotropic_j == -10.0
assert the_coupling.property_units["isotropic_j"] == "Hz"
assert the_coupling.j_antisymmetric is None
assert the_coupling.j_symmetric is None
assert the_coupling.dipolar.D == 5120.0
assert the_coupling.dipolar.eta == 0.5
# test 3 bad input ----------------------------------------------------------------
bad_json = {"zite_index": [0, 1], "isotropic_j": "5 ppm"}
error = "Error enforcing units for isotropic_j: 5 ppm"
with pytest.raises(Exception, match=f".*{error}.*"):
Coupling.parse_dict_with_units(bad_json)
error = "Error enforcing units for j_symmetric.zeta: ppm."
with pytest.raises(ValueError, match=f".*{error}.*"):
Coupling.parse_dict_with_units({
"site_index": [0, 1],
"isotropic_j": "10 kHz",
"j_symmetric": {
"zeta": "12.1 ppm",
"eta": 0.5
},
})
def test_site_dipolar_set_to_None():
a = Coupling(site_index=[0, 1], dipolar=None)
assert a.site_index == [0, 1]
assert a.isotropic_j == 0
assert a.dipolar is None
def test_site_object_methods():
good_json_2 = {"site_index": [0, 1], "isotropic_j": "-10 Hz"}
the_coupling = Coupling.parse_dict_with_units(good_json_2)
# testing method dict()
result = {
"site_index": [0, 1],
"isotropic_j": -10.0,
"property_units": {
"isotropic_j": "Hz"
},
"name": None,
"label": None,
"description": None,
"dipolar": None,
"j_symmetric": None,
"j_antisymmetric": None,
}
assert the_coupling.dict() == result, "Failed Coupling.dict()"
# testing method json()
result = {"site_index": [0, 1], "isotropic_j": "-10.0 Hz"}
assert the_coupling.json() == result, "Failed Coupling.json()"
result = {
"site_index": [1, 2],
"isotropic_j": "10.0 Hz",
"j_symmetric": {
"zeta": "12.1 Hz",
"eta": 0.1,
"alpha": "2.1 rad"
},
"j_antisymmetric": {
"zeta": "-1.1 Hz",
"alpha": "0.1 rad",
"beta": "2.5 rad",
},
"dipolar": {
"D": "10000.0 Hz",
"eta": 0.6
},
}
the_coupling = Coupling(
site_index=[1, 2],
isotropic_j=10,
j_symmetric={
"zeta": 12.1,
"eta": 0.1,
"alpha": 2.1
},
j_antisymmetric={
"zeta": -1.1,
"alpha": 0.1,
"beta": 2.5
},
dipolar={
"D": 10e3,
"eta": 0.6
},
)
assert the_coupling.json() == result, "Failed Coupling.json()"
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
# - 1) an uncoupled :math:`^{119}\text{Sn}` and
# - 2) a coupled :math:`^{119}\text{Sn}`-:math:`^{117}\text{Sn}` spin systems.
sn119 = Site(
isotope="119Sn",
isotropic_chemical_shift=-210,
shielding_symmetric={
"zeta": 700,
"eta": 0.1
},
)
sn117 = Site(
isotope="117Sn",
isotropic_chemical_shift=0,
)
j_sn = Coupling(
site_index=[0, 1],
isotropic_j=8150.0,
)
sn117_abundance = 7.68 # in %
spin_systems = [
# uncoupled spin system
SpinSystem(sites=[sn119], abundance=100 - sn117_abundance),
# coupled spin systems
SpinSystem(sites=[sn119, sn117],
couplings=[j_sn],
abundance=sn117_abundance),
]
# %%
# **Method**
isotope="13C",
isotropic_chemical_shift=0.0, # in ppm
shielding_symmetric=SymmetricTensor(
zeta=18.87562, # in ppm
eta=0.4,
beta=beta,
),
),
Site(
isotope="1H",
isotropic_chemical_shift=0.0, # in ppm
),
],
couplings=[
Coupling(
site_index=[0, 1], isotropic_j=200.0, dipolar=SymmetricTensor(D=-2.1e4)
)
],
)
for beta in beta_orientation
]
# %%
# Next, we create methods to simulate the sideband manifolds for the above spin
# systems at four spinning rates: 3 kHz, 5 kHz, 8 kHz, 12 kHz.
spin_rates = [3e3, 5e3, 8e3, 12e3] # in Hz
# The variable `methods` is a list of four BlochDecaySpectrum methods.
methods = [
BlochDecaySpectrum(
channels=["13C"],