From 0abb2d38ac4929df39c5726fba84d105f6390a9a Mon Sep 17 00:00:00 2001
From: Sylvain Tricot <sylvain.tricot@univ-rennes1.fr>
Date: Mon, 7 Jul 2025 17:52:33 +0200
Subject: [PATCH] Update Activity06

---
 msspecbook/Activity06/Activity06.ipynb | 41 +++++++++++++++++++++++++-
 1 file changed, 40 insertions(+), 1 deletion(-)

diff --git a/msspecbook/Activity06/Activity06.ipynb b/msspecbook/Activity06/Activity06.ipynb
index b4aa3ad..382ee46 100644
--- a/msspecbook/Activity06/Activity06.ipynb
+++ b/msspecbook/Activity06/Activity06.ipynb
@@ -5,8 +5,47 @@
    "id": "c0a860db-0f72-4785-81f4-831e48b3a49f",
    "metadata": {},
    "source": [
-    "# Activity 6: Effect of the temperature"
+    "# Activity 6: Effect of the temperature\n",
+    "\n",
+    "\n",
+    "\n",
+    "\n",
+    "\n",
+    "## Surface and bulk effects of the temperature\n",
+    "\n",
+    "In this example, we will look at the effects of the temperature on the X-Ray photoelectron diffraction from a copper substrate. We will base our python script on a paper published in 1986 by R. Trehan and S. Fadley. In their work, they performed azimutal scans of a copper(001) surface at 2 different polar angles: one at grazing incidence and one at 45° for incresing temperatures from 298K to roughly 1000K.\n",
+    "\n",
+    "For each azimutal scan, they looked at the anisotropy of the signal, that is:\n",
+    "\n",
+    "$\\frac{\\Delta I}{I_{max}}$\n",
+    "\n",
+    "This value is representative of how clear are the *modulations* of the signal. As it was shown by their experiments, this anisotropy decreases when the temperature is increased due to the increased disorder in the structure coming from thermal agitation. They also showed that this variation in anisotropy is more pronounced for grazing incidence angles. This is related to the fact that surface atoms are expected to vibrate more than bulk ones. They also proposed single scattering calculations that reproduced well these results.\n",
+    "\n",
+    "We propose here to reproduce this kind of calculation to introduce the parameters that control the vibrational damping.\n",
+    "\n",
+    ":::{seealso}\n",
+    "based on this paper from R. Trehan and C.S. Fadley\n",
+    "[Phys. Rev. B **34** p6784–98 (2012)](https://doi.org/10.1103/PhysRevB.34.6784)\n",
+    ":::\n",
+    "\n",
+    "### The script\n",
+    "\n",
+    "Let's start by downloading this [python script ](./Cu_temperature.py). \n",
+    "\n",
+    "Since we want to distinguish between bulk (low polar angles) and surface effects (large polar angles), we need to compute scans for different emitters and different depths in the cluster.\n",
+    "\n",
+    "The script contains 3 functions:\n",
+    "1. The `create_clusters` function will build 3 cluster: one with the emitter on the surface, one in the subsurface and one n the 3{sup}`rd` plane.\n",
+    "2. The function `compute` will compute the azimuthal scan"
    ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "b8de98a0-12f6-49f4-99d9-db561e6738bf",
+   "metadata": {},
+   "outputs": [],
+   "source": []
   }
  ],
  "metadata": {