def test_qm_spinsystem_peaklist():
# GIVEN v and J inputs
v, J = rioux()
# WHEN qm_spinsystem is called with v and J and all possible cache/sparse
spectrum_TT = qm_spinsystem(v, J, cache=True, sparse=True, normalize=True)
spectrum_FT = qm_spinsystem(v, J, cache=False, sparse=True, normalize=True)
spectrum_TF = qm_spinsystem(v, J, cache=True, sparse=False, normalize=True)
spectrum_FF = qm_spinsystem(v,
J,
cache=False,
sparse=False,
normalize=True)
# THEN they all match the expected result
for s in [spectrum_TT, spectrum_FT, spectrum_TF, spectrum_FF]:
assert np.allclose(s, SPECTRUM_RIOUX)
def abx_wrapper(va=110.0, vb=90.0, vx=200.0, Jax=5.0, Jbx=10.0, Jab=13.0):
# x = np.linspace(0, 235, 8000)
freqs = [va, vb, vx]
Js = np.array(
[[0.0, Jab, Jax],
[Jab, 0.0, Jbx],
[Jax, Jbx, 0]])
peaklist = qm_spinsystem(freqs, Js)
# y = add_lorentzians(x, peaklist, 0.5)
return peaklist
def peaklist(self):
"""Return a list of (frequency, intensity) signals.
Returns
-------
[(float, float)...]
Array of (frequency, intensity) signals.
"""
if self._second_order:
return qm_spinsystem(self._v, self._J)
else:
return first_order_spin_system(self._v, self._J)
def interactive_aaxx(va=110.0, vx=90.0,
Jaa=15.0, Jxx=15.0, Jax=7.0, Jax_prime=7.0):
datapoints = max(abs(int(va - vx)) * 100, 800)
# x = np.linspace(min_, max_, 8000)
freqs = [va, va, vx, vx]
Js = np.array(
[[0.0, Jaa, Jax, Jax_prime],
[Jaa, 0.0, Jax_prime, Jax],
[Jax, Jax_prime, 0, Jxx],
[Jax_prime, Jax, Jxx, 0]])
peaklist = qm_spinsystem(freqs, Js)
xy = lineshape_from_peaklist(peaklist, points=datapoints)
plot = hv.Curve(zip(*xy))
return plot.options(axiswise=True, invert_xaxis=True,
xlabel='𝜈',
height=300, responsive=True
).redim(y=hv.Dimension('intensity', range=(-0.4, 1.2)))
def AABB(Vab, Jaa, Jbb, Jab, Jab_prime, Vcentr, normalize=True, **kwargs):
"""
A wrapper for a second-order AA'BB' calculation, but using the
same arguments as WINDNMR.
Parameters
---------
Vab : float
the difference in frequency (Hz) between Ha and Hb in the absence of
coupling. A positive number indicates vb > va.
Jaa, Jbb, Jab, Jab_prime : float
Jaa is the JAA' coupling constant;
Jxx the JXX';
Jax the JAX; and
JAX_prime the JAX'.
Vcentr : float
the frequency for the center of the signal.
normalize: bool
whether the signal intensity should be normalized.
Returns
-------
[(float, float)...]
a list of (frequency, intensity) tuples.
"""
from nmrsim.qm import qm_spinsystem
va = Vcentr - Vab / 2
vb = Vcentr + Vab / 2
freqlist = [va, va, vb, vb]
J = np.zeros((4, 4))
J[0, 1] = Jaa
J[0, 2] = Jab
J[0, 3] = Jab_prime
J[1, 2] = Jab_prime
J[1, 3] = Jab
J[2, 3] = Jbb
J = J + J.T
result = qm_spinsystem(freqlist,
J,
normalize=normalize,
sparse=False,
**kwargs)
return result
def update_qm(self, *args):
peaklist = qm_spinsystem(*args)
return self.peaklist_to_xy(peaklist)