Reorganisation/cleanup possibilities

[vatai]

• zeeman_hamiltonian() should be substituted with explicit 1d/3d versions. The only "magic" is happening in total_hamiltonian when use for anisotropy.
• unify zeeman 1d/3d.
• add B_axis parameter to mary().
• remove total_hamiltonian().

[vatai]

Code experimenting with zeeman 3d (to include with 1d):

import numpy as np

import radicalpy as rp
from radicalpy.data import Molecule

molecules = [
    Molecule.fromdb("flavin_anion", ["N5"]),
    Molecule.fromdb("tryptophan_cation", ["Hbeta1", "H1"]),
]
sim = rp.simulation.HilbertSimulation(molecules)

print(f"{rp.utils.spherical_to_cartesian(0, 0)=}")
print(f"{rp.utils.spherical_to_cartesian(np.pi/2, 0)=}")
print(f"{rp.utils.spherical_to_cartesian(np.pi/2, np.pi/2)=}")

zeeman = sim.zeeman_hamiltonian_3d(1, 0, 0)
s = sim.spin_operator(0, "x")
print(f"{s.shape=}")
print(f"{zeeman.shape=}")

a = np.random.uniform(size=(3, 4))
b = np.random.uniform(size=3)
print(f"{a.shape=}")
print(f"{b.shape=}")
print(f"{b.dot(a).shape=}")

print("Hello")

Output:

rp.utils.spherical_to_cartesian(0, 0)=array([0., 0., 1.])
rp.utils.spherical_to_cartesian(np.pi/2, 0)=array([1.000000e+00, 0.000000e+00, 6.123234e-17])
rp.utils.spherical_to_cartesian(np.pi/2, np.pi/2)=array([6.123234e-17, 1.000000e+00, 6.123234e-17])
s.shape=(48, 48)
zeeman.shape=(48, 48)
a.shape=(3, 4)
b.shape=(3,)
b.dot(a).shape=(4,)
Hello