Add numpydoc References sections to model docstrings

docs/docs/tutorials/diffusion_model.ipynb

@@ -29,7 +29,11 @@
    "id": "2",
    "metadata": {},
    "source": [
-    "## Brownian Translational Diffusion"
+    "## Brownian Translational Diffusion\n",
+    "In Brownian Translational Diffusion the scattering is a Lorentzian whose width grows as $Q^2$, following\n",
+    "\n",
+    "> G. H. Vineyard, *Scattering of Slow Neutrons by a Liquid*, Phys. Rev. **110**, 999 (1958),\n",
+    "> [doi:10.1103/PhysRev.110.999](https://doi.org/10.1103/PhysRev.110.999)."
    ]
   },
   {
@@ -112,7 +116,13 @@
    "metadata": {},
    "source": [
     "## Jump Translational Diffusion\n",
-    "In Jump Translational Diffusion, the particle waits for a relaxation time $t$ between jumps. At low $Q$ the width follows the Brownian result, $\\Gamma \\approx \\hbar D Q^2$, but at high $Q$ it levels off:\n",
+    "In Jump Translational Diffusion, the particle waits for a relaxation time $t$ between jumps, as in the model of\n",
+    "\n",
+    "> K. S. Singwi and A. Sjölander, *Diffusive Motions in Water and Cold Neutron Scattering*,\n",
+    "> Phys. Rev. **119**, 863 (1960),\n",
+    "> [doi:10.1103/PhysRev.119.863](https://doi.org/10.1103/PhysRev.119.863).\n",
+    "\n",
+    "At low $Q$ the width follows the Brownian result, $\\Gamma \\approx \\hbar D Q^2$, but at high $Q$ it levels off:\n",
     "\n",
     "$$\\Gamma(Q) = \\frac{\\hbar D Q^2}{1 + D t Q^2},$$\n",
     "\n",

src/easydynamics/sample_model/components/damped_harmonic_oscillator.py

@@ -26,6 +26,17 @@ class DampedHarmonicOscillator(CreateParametersMixin, ModelComponent):
     width at half max (``width``). area has unit = x_unit * y_unit; center and width have unit =
     x_unit.
 
+    References
+    ----------
+    1. W. Cochran, *Crystal stability and the theory of ferroelectricity*, Adv. Phys. **9**, 387
+       (1960), [doi:10.1080/00018736000101229](https://doi.org/10.1080/00018736000101229).
+    2. R. A. Cowley, *The lattice dynamics of an anharmonic crystal*, Adv. Phys. **12**, 421
+       (1963), [doi:10.1080/00018736300101333](https://doi.org/10.1080/00018736300101333).
+    3. R. A. Cowley, *Anharmonic crystals*, Rep. Prog. Phys. **31**, 123 (1968),
+       [doi:10.1088/0034-4885/31/1/303](https://doi.org/10.1088/0034-4885/31/1/303).
+    4. S. W. Lovesey, *Theory of Neutron Scattering from Condensed Matter*, Clarendon Press, Oxford
+       (1984).
+
     Examples
     --------
     **Creating a Damped Harmonic Oscillator**

src/easydynamics/sample_model/components/diffusion_damped_mittag_leffler.py

@@ -20,12 +20,7 @@ class DiffusionDampedMittagLeffler(CreateParametersMixin, ModelComponent):
     Model of the diffusion-damped Mittag-Leffler relaxation spectrum, Eq. (42) of Hassani et al.
 
     This is the spectral (energy-domain) form of the multiscale relaxation model used for
-    intrinsically disordered proteins in
-
-    A. N. Hassani, L. Haris, M. Appel, T. Seydel, A. M. Stadler and G. R. Kneller, *Multiscale
-    relaxation dynamics and diffusion of myelin basic protein in solution studied by quasielastic
-    neutron scattering*, J. Chem. Phys. **156**, 025102 (2022),
-    [doi:10.1063/5.0077100](https://doi.org/10.1063/5.0077100).
+    intrinsically disordered proteins by Hassani et al. (see References).
 
     In the time domain the internal dynamics is described by the Mittag-Leffler (ML) relaxation
     function $\phi_{ML}(t) = E_\alpha(-(|t|/\tau_R)^\alpha)$ (their Eq. 28), damped by global
@@ -65,6 +60,13 @@ class DiffusionDampedMittagLeffler(CreateParametersMixin, ModelComponent):
     positive ``damping`` is enforced, the profile stays regular at $x = 0$, where the undamped ML
     spectrum would diverge as $|\omega|^{\alpha - 1}$.
 
+    References
+    ----------
+    A. N. Hassani, L. Haris, M. Appel, T. Seydel, A. M. Stadler and G. R. Kneller, *Multiscale
+    relaxation dynamics and diffusion of myelin basic protein in solution studied by quasielastic
+    neutron scattering*, J. Chem. Phys. **156**, 025102 (2022),
+    [doi:10.1063/5.0077100](https://doi.org/10.1063/5.0077100).
+
     Examples
     --------
     **Creating a diffusion-damped Mittag-Leffler component**

src/easydynamics/sample_model/components/stretched_exponential.py

@@ -471,6 +471,15 @@ class StretchedExponential(CreateParametersMixin, ModelComponent):
     Note that the x-axis has to be an energy, since the relaxation time is turned into an energy
     scale through $\hbar$.
 
+    References
+    ----------
+    1. R. Kohlrausch, *Theorie des elektrischen Rückstandes in der Leidener Flasche*, Ann. Phys.
+       **167**, 179 (1854),
+       [doi:10.1002/andp.18541670203](https://doi.org/10.1002/andp.18541670203).
+    2. G. Williams and D. C. Watts, *Non-symmetrical dielectric relaxation behaviour arising from a
+       simple empirical decay function*, Trans. Faraday Soc. **66**, 80 (1970),
+       [doi:10.1039/TF9706600080](https://doi.org/10.1039/TF9706600080).
+
     Examples
     --------
     **Creating a stretched exponential**

src/easydynamics/sample_model/diffusion_model/brownian_translational_diffusion.py

@@ -25,6 +25,11 @@ class BrownianTranslationalDiffusion(DiffusionModelBase):
     have units of 1/angstrom. Creates ComponentCollections with Lorentzian components for given
     Q-values.
 
+    References
+    ----------
+    G. H. Vineyard, *Scattering of Slow Neutrons by a Liquid*, Phys. Rev. **110**, 999 (1958),
+    [doi:10.1103/PhysRev.110.999](https://doi.org/10.1103/PhysRev.110.999).
+
     Examples
     --------
     **Creating a BrownianTranslationalDiffusion model**

src/easydynamics/sample_model/diffusion_model/delta_lorentz.py

@@ -35,6 +35,20 @@ class DeltaLorentz(DiffusionModelBase):
     the same at all $Q$ or be allowed to vary with $Q$.
 
 
+    References
+    ----------
+    1. M. Bée, *Quasielastic Neutron Scattering: Principles and Applications in Solid State
+       Chemistry, Biology and Materials Science*, Adam Hilger, Bristol (1988).
+    2. R. Weinstock, *Inelastic Scattering of Slow Neutrons*, Phys. Rev. **65**, 1 (1944),
+       [doi:10.1103/PhysRev.65.1](https://doi.org/10.1103/PhysRev.65.1).
+    3. A. J. Dianoux, F. Volino and H. Hervet, *Incoherent scattering law for neutron quasi-elastic
+       scattering in liquid crystals*, Mol. Phys. **30**, 1181 (1975),
+       [doi:10.1080/00268977500102721](https://doi.org/10.1080/00268977500102721).
+    4. F. Volino and A. J. Dianoux, *Neutron incoherent scattering law for diffusion in a potential
+       of spherical symmetry: general formalism and application to diffusion inside a sphere*,
+       Mol. Phys. **41**, 271 (1980),
+       [doi:10.1080/00268978000102761](https://doi.org/10.1080/00268978000102761).
+
     Examples
     --------
     **Creating a DeltaLorentz model with Q-dependent parameters**

src/easydynamics/sample_model/diffusion_model/jump_translational_diffusion.py

@@ -28,6 +28,12 @@ class JumpTranslationalDiffusion(DiffusionModelBase):
     units of 1/angstrom. Creates ComponentCollections with Lorentzian components for given
     Q-values.
 
+    References
+    ----------
+    K. S. Singwi and A. Sjölander, *Diffusive Motions in Water and Cold Neutron Scattering*, Phys.
+    Rev. **119**, 863 (1960),
+    [doi:10.1103/PhysRev.119.863](https://doi.org/10.1103/PhysRev.119.863).
+
     Examples
     --------
     **Creating a JumpTranslationalDiffusion model**

src/easydynamics/sample_model/diffusion_model/mittag_leffler_diffusion.py

@@ -29,12 +29,7 @@
 class MittagLefflerDiffusion(DiffusionModelBase):
     r"""
     Multiscale relaxation model of Hassani et al.: Mittag-Leffler internal dynamics damped by
-    global translational diffusion.
-
-    A. N. Hassani, L. Haris, M. Appel, T. Seydel, A. M. Stadler and G. R. Kneller, *Multiscale
-    relaxation dynamics and diffusion of myelin basic protein in solution studied by quasielastic
-    neutron scattering*, J. Chem. Phys. **156**, 025102 (2022),
-    [doi:10.1063/5.0077100](https://doi.org/10.1063/5.0077100).
+    global translational diffusion (see References).
 
     The intermediate scattering function is written as an internal relaxation, described by a
     Mittag-Leffler function, times a global diffusion factor (their Eqs. 38-39),
@@ -65,6 +60,13 @@ class MittagLefflerDiffusion(DiffusionModelBase):
     Fig. 5); pass ``allow_Q_variation={'A_0': True, 'relaxation_rate': True, 'alpha': True}`` to
     reproduce that. Q is assumed to be in 1/angstrom and $D$ in m^2/s.
 
+    References
+    ----------
+    A. N. Hassani, L. Haris, M. Appel, T. Seydel, A. M. Stadler and G. R. Kneller, *Multiscale
+    relaxation dynamics and diffusion of myelin basic protein in solution studied by quasielastic
+    neutron scattering*, J. Chem. Phys. **156**, 025102 (2022),
+    [doi:10.1063/5.0077100](https://doi.org/10.1063/5.0077100).
+
     Examples
     --------
     **Creating a MittagLefflerDiffusion model with the paper's per-Q parameters**
@@ -619,6 +621,13 @@ def calculate_relaxation_rate_spectrum(self, rate: np.ndarray, Q: Q_type = None)
         ------
         ValueError
             If any requested rate is not strictly positive.
+
+        References
+        ----------
+        A. N. Hassani, L. Haris, M. Appel, T. Seydel, A. M. Stadler and G. R. Kneller, *Multiscale
+        relaxation dynamics and diffusion of myelin basic protein in solution studied by
+        quasielastic neutron scattering*, J. Chem. Phys. **156**, 025102 (2022),
+        [doi:10.1063/5.0077100](https://doi.org/10.1063/5.0077100).
         """
         rate = np.atleast_1d(np.asarray(rate, dtype=float))
         if np.any(rate <= 0):
@@ -662,6 +671,13 @@ def calculate_energy_barrier_distribution(
         -------
         np.ndarray
             Array of shape ``(len(Q), len(barrier_height))`` holding P(h) for each Q.
+
+        References
+        ----------
+        A. N. Hassani, L. Haris, M. Appel, T. Seydel, A. M. Stadler and G. R. Kneller, *Multiscale
+        relaxation dynamics and diffusion of myelin basic protein in solution studied by
+        quasielastic neutron scattering*, J. Chem. Phys. **156**, 025102 (2022),
+        [doi:10.1063/5.0077100](https://doi.org/10.1063/5.0077100).
         """
         barrier_height = np.atleast_1d(np.asarray(barrier_height, dtype=float))