#!/usr/bin/env python
# -*- coding: utf-8 -*-
"""
Non-coincidental Quad and CSA, 17O (I=5/2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

17O (I=5/2) quadrupolar static spectrum simulation.
"""
# %%
# The following example illustrates the simulation of NMR spectra arising from
# non-coincidental quadrupolar and shielding tensors. The tensor parameter values for
# the simulation are obtained from Yamada `et. al.` [#f1]_, for the
# :math:`^{17}\text{O}` site in benzanilide.
#
# .. warning::
#     The Euler angles representation using by Yamada `et. al` is different from the
#     representation used in mrsimulator. The resulting simulation might not resemble
#     the published spectrum.
import matplotlib as mpl
import matplotlib.pyplot as plt
from mrsimulator import Simulator, SpinSystem, Site
from mrsimulator.methods import BlochDecayCentralTransitionSpectrum
import numpy as np

# global plot configuration
mpl.rcParams["figure.figsize"] = [4.5, 3.0]
# sphinx_gallery_thumbnail_number = 1

# %%
# **Step 1:** Create the spin system.
site = Site(
    isotope="17O",
    isotropic_chemical_shift=320,  # in ppm
    shielding_symmetric={"zeta": 376.667, "eta": 0.345},
    quadrupolar={
        "Cq": 8.97e6,  # in Hz
        "eta": 0.15,
        "alpha": 5 * np.pi / 180,
        "beta": np.pi / 2,
        "gamma": 70 * np.pi / 180,
    },
)
spin_system = SpinSystem(sites=[site])

# %%
# **Step 2:** Create a central transition selective Bloch decay spectrum method.
method = BlochDecayCentralTransitionSpectrum(
    channels=["17O"],
    magnetic_flux_density=11.74,  # in T
    rotor_frequency=0,  # in Hz
    spectral_dimensions=[
        {
            "count": 1024,
            "spectral_width": 1e5,  # in Hz
            "reference_offset": 22500,  # in Hz
            "label": r"$^{17}$O resonances",
        }
    ],
)

# %%
# **Step 3:** Create the Simulator object and add method and spin system objects.
sim = Simulator()
sim.spin_systems = [spin_system]  # add the spin system
sim.methods = [method]  # add the method

# Since the spin system have non-zero Euler angles, set the integration_volume to
# hemisphere.
sim.config.integration_volume = "hemisphere"

# %%
# **Step 4:** Simulate the spectrum.
sim.run()

# The plot of the simulation before signal processing.
ax = plt.subplot(projection="csdm")
ax.plot(sim.methods[0].simulation.real, color="black", linewidth=1)
ax.invert_xaxis()
plt.tight_layout()
plt.show()


# %%
# .. [#f1] Yamada, K., Dong, S., Wu, G., Solid-State 17O NMR Investigation of the
#       Carbonyl Oxygen Electric-Field-Gradient Tensor and Chemical Shielding Tensor in
#       Amides, J. Am. Chem. Soc. 2000, **122**, 11602-11609.
#       `DOI: 10.1021/ja0008315 <https://doi.org/10.1021/ja0008315>`_