update examples

examples/notebooks/builtin_omps_uq.ipynb

@@ -7,7 +7,7 @@
    "source": [
     "# Compare built-in uncertainty-quantified optical potentials\n",
     "\n",
-    "This notebook compares several uncertainty-quantified optical potentials on the same elastic-scattering observable. It is a good companion to the KDUQ-specific tutorial when you want to understand how the built-in UQ-ready models differ in practice.\n"
+    "This notebook compares several uncertainty-quantified optical potentials on the same elastic-scattering observable. "
    ]
   },
   {

examples/notebooks/example_jlm.ipynb

@@ -4,7 +4,9 @@
    "cell_type": "markdown",
    "id": "md-001",
    "metadata": {},
-   "source": "# JLM and JLMB semi-microscopic optical potentials\n"
+   "source": [
+    "# JLM and JLMB semi-microscopic optical potentials\n"
+   ]
   },
   {
    "cell_type": "code",
@@ -35,15 +37,15 @@
    "id": "df297f43-6c36-4cf7-a4b4-54911b89672a",
    "metadata": {},
    "source": [
-    "# Optical potential from nuclear matter\n",
+    "## Optical potential from nuclear matter\n",
     "\n",
     "The JLM (for J. P. Jeukenne, A. Lejeune, and C. Mahaux) model for the nuclear matter self-energy is included in jitr, as defined in the seminal works [JLM, 1974](https://journals.aps.org/prc/abstract/10.1103/PhysRevC.10.1391), [JLM, 1977a](https://journals.aps.org/prc/abstract/10.1103/PhysRevC.16.80), and [JLM, 1977b](https://journals.aps.org/prc/abstract/10.1103/PhysRevC.15.10).\n",
     "\n",
-    "The goal was to try to model an effective interactions (optical potentials) for nucleons scattering on nuclei by treating the many-body dynamics as if that nucleon where interacting with a system of *homogenous nuclear matter*. This work takes multiple steps:\n",
+    "The goal was to try to model the effective interactions (optical potential) nucleons feel in when scattering on a nucleus by treating the many-body dynamics as if that nucleon where interacting with a system of *homogenous nuclear matter*, at the local *local density* of its position withion the medium of the finite nucleus. This work takes multiple steps:\n",
     "\n",
-    "1. Brueckner-Hartree Fock calculations of the self-energy in symmetric nuclear matter and nuclear matter with neutron excess, using Reid's hard core interaction, at various matter densities (Fermi momenta) and a range of positive energies from 10 to 160 MeV, producing isoscalar and isovector potentials that are functions of matter density $\\rho$ and projectile energy $E$: $\\Sigma(\\rho,E)$.\n",
-    "2. determine a model for the density distribution of a finite nucleus $\\rho(r)$\n",
-    "3. Evaluate the optical potential for the finite nucleus in the *local density approximation*: $\\Sigma(r,E) = \\Sigma(\\rho(r),E)$\n",
+    "1. Calculate the nuclear matter self energy at various matter densities $\\rho$ and nucleon energies $E$: $\\Sigma(\\rho,E)$ \n",
+    "3. determine a model for the density distribution of a finite nucleus $\\rho(r)$\n",
+    "4. Evaluate the optical potential for the finite nucleus in the *local density approximation*: $\\Sigma(r,E) = \\Sigma(\\rho(r),E)$\n",
     "\n",
     "Later, E. Bauge, J. P. Delaroche, and M. Girod updated this JLM microscopic optical potential in various ways, including adjusting the energy dependence to fit to scattering data (See [BDG 1998](https://journals.aps.org/prc/abstract/10.1103/PhysRevC.58.1118) and [BDG, 2001](https://journals.aps.org/prc/abstract/10.1103/PhysRevC.63.024607)). This is known as the JLMB semi-microscopic optical potential, and it is included in the reaction code [TALYS](https://github.com/arjankoning1/talys/), which is used for nuclear data evaluation.\n",
     "\n",
@@ -57,14 +59,14 @@
    "source": [
     "### The nuclear matter self energy\n",
     "\n",
-    "\n",
-    "The first step is to determine the isoscalar and isovector nuclear matter self-energies:\n",
+    "The nuclear matter self energy is determined from Brueckner-Hartree Fock (BHF) calculations of the $g$-matrix in symmetric nuclear matter and nuclear matter with neutron excess, using Reid's hard core interaction, at various matter densities (Fermi momenta) and a range of positive energies from 10 to 160 MeV, producing isoscalar and isovector effective 2-body interactions. By contracting these two-body interactions over the occupied states in nuclear matter, one determines the nuclear matter self-energy felt by a single nucleon.\n",
+    "This self energy can be decomposed into isoscalar and isovector terms:\n",
     "\n",
     "\\begin{equation}\n",
     "U(\\rho,E) = V_0(\\rho,E) + i W(\\rho,E) \\pm \\alpha \\left( V_0(\\rho,E) + i W(\\rho,E) \\right),\n",
     "\\end{equation}\n",
     "\n",
-    "with $\\alpha = (\\rho_n - \\rho_p) / (\\rho_n + \\rho_p)$, and the $+(-)$ sign is for neutrons(protons).\n",
+    "with $\\alpha = (\\rho_n - \\rho_p) / (\\rho_n + \\rho_p)$, and the $+(-)$ sign for neutrons(protons).\n",
     "\n",
     "The isoscalar real self energy, $V_0(\\rho,E)$ was parameterized as a polynomial fit to the BHF results:\n",
     "\n",
@@ -161,6 +163,14 @@
     "jlm.fermi_energy_MeV(rho_sat_fm3)"
    ]
   },
+  {
+   "cell_type": "markdown",
+   "id": "37d46f66-b4a5-4dd3-b208-65b4067dc571",
+   "metadata": {},
+   "source": [
+    "Note that the BHF calculation using Reid's hard core interaction do not preduce the empirical saturation in nuclear matter. "
+   ]
+  },
   {
    "cell_type": "code",
    "execution_count": 5,
@@ -1259,6 +1269,14 @@
     "plt.tight_layout()"
    ]
   },
+  {
+   "cell_type": "markdown",
+   "id": "ac9056d0-550b-4b16-a698-d2233cf53657",
+   "metadata": {},
+   "source": [
+    "Let's try tweaking some 2pF densities by hand, and seeing what effect it has."
+   ]
+  },
   {
    "cell_type": "code",
    "execution_count": 30,
@@ -1361,14 +1379,6 @@
     "plt.legend(ncol=2, framealpha=0)\n",
     "plt.tight_layout()"
    ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "ff503abe-f446-4160-89d0-06a0d6781123",
-   "metadata": {},
-   "outputs": [],
-   "source": []
   }
  ],
  "metadata": {
@@ -1392,4 +1402,4 @@
  },
  "nbformat": 4,
  "nbformat_minor": 5
-}
+}