From 139001029bf43deaff9b60250fdecea0ee546003 Mon Sep 17 00:00:00 2001 From: Sylvain Tricot Date: Tue, 22 Jul 2025 18:30:57 +0200 Subject: [PATCH] Update html --- .../_build/html/Activity01/Activity01.html | 11 +- .../html/Activity01/Activity01_light.html | 1148 +++++++++++++ .../_build/html/Activity02/Activity02.html | 7 +- .../html/Activity02/Activity02_light.html | 1521 +++++++++++++++++ .../_build/html/Activity03/Activity03.html | 10 +- .../html/Activity03/Activity03_light.html | 654 +++++++ .../_build/html/Activity04/Activity04.html | 36 +- .../html/Activity04/Activity04_light.html | 519 ++++++ .../_build/html/Activity05/Activity05.html | 80 +- .../html/Activity05/Activity05_light.html | 1125 ++++++++++++ .../_build/html/Activity06/Activity06.html | 11 +- .../html/Activity06/Activity06_light.html | 640 +++++++ .../_build/html/Activity07/Activity07.html | 14 +- .../html/Activity07/Activity07_light.html | 588 +++++++ .../_build/html/Activity08/Activity08.html | 24 +- .../html/Activity08/Activity08_light.html | 506 ++++++ .../_build/html/Activity09/Activity09.html | 13 +- .../html/Activity09/Activity09_light.html | 531 ++++++ .../_build/html/Activity10/Activity10.html | 21 +- .../html/Activity10/Activity10_light.html | 517 ++++++ .../_build/html/Activity11/Activity11.html | 2 +- .../1294d44b079d2ab82b330376a2530741/SbAg.py | 55 + .../Cu_temperature.py | 126 ++ .../copper.cif | 51 + .../RhO_tofill.py | 23 + .../TiSe2_1_tofill.py | 40 + .../a4639febc8162e65b41b0e03dfeeaa17/cu.py | 24 + .../aa51bfc01de3fe879c2507956d0a2b8c/data.txt | 121 ++ .../b820873b74a9711a6b5f02470505cc1a/Si001.py | 56 + msspecbook/_build/html/_images/Ni_SSCvsMI.png | Bin 718517 -> 0 bytes msspecbook/_build/html/_images/Ni_fig1.png | Bin 126575 -> 0 bytes .../html/_sources/Activity01/Activity01.ipynb | 32 +- .../Activity01/Activity01_light.ipynb | 926 ++++++++++ .../html/_sources/Activity02/Activity02.ipynb | 8 +- .../Activity02/Activity02_light.ipynb | 1178 +++++++++++++ .../html/_sources/Activity03/Activity03.ipynb | 10 +- .../Activity03/Activity03_light.ipynb | 346 ++++ .../html/_sources/Activity04/Activity04.ipynb | 20 +- .../Activity04/Activity04_light.ipynb | 147 ++ .../html/_sources/Activity05/Activity05.ipynb | 88 +- .../Activity05/Activity05_light.ipynb | 842 +++++++++ .../html/_sources/Activity06/Activity06.ipynb | 16 +- .../Activity06/Activity06_light.ipynb | 118 ++ .../html/_sources/Activity07/Activity07.ipynb | 57 +- .../Activity07/Activity07_light.ipynb | 171 ++ .../html/_sources/Activity08/Activity08.ipynb | 34 +- .../Activity08/Activity08_light.ipynb | 147 ++ .../html/_sources/Activity09/Activity09.ipynb | 54 +- .../Activity09/Activity09_light.ipynb | 150 ++ .../html/_sources/Activity10/Activity10.ipynb | 47 +- .../Activity10/Activity10_light.ipynb | 102 ++ msspecbook/_build/html/backmatter.html | 2 +- msspecbook/_build/html/genindex.html | 2 +- msspecbook/_build/html/intro.html | 2 +- msspecbook/_build/html/objects.inv | Bin 2477 -> 2595 bytes .../reports/Activity04/Activity04.err.log | 43 - msspecbook/_build/html/search.html | 2 +- msspecbook/_build/html/searchindex.js | 2 +- 58 files changed, 12742 insertions(+), 278 deletions(-) create mode 100644 msspecbook/_build/html/Activity01/Activity01_light.html create mode 100644 msspecbook/_build/html/Activity02/Activity02_light.html create mode 100644 msspecbook/_build/html/Activity03/Activity03_light.html create mode 100644 msspecbook/_build/html/Activity04/Activity04_light.html create mode 100644 msspecbook/_build/html/Activity05/Activity05_light.html create mode 100644 msspecbook/_build/html/Activity06/Activity06_light.html create mode 100644 msspecbook/_build/html/Activity07/Activity07_light.html create mode 100644 msspecbook/_build/html/Activity08/Activity08_light.html create mode 100644 msspecbook/_build/html/Activity09/Activity09_light.html create mode 100644 msspecbook/_build/html/Activity10/Activity10_light.html create mode 100644 msspecbook/_build/html/_downloads/1294d44b079d2ab82b330376a2530741/SbAg.py create mode 100644 msspecbook/_build/html/_downloads/3fdd553b457dd9aab1086c697e8ad08e/Cu_temperature.py create mode 100644 msspecbook/_build/html/_downloads/54a8452b27a8c6284cf1a8a05665f3a4/copper.cif create mode 100644 msspecbook/_build/html/_downloads/79fef44b9d7fb8ae298952070d9ba3ce/RhO_tofill.py create mode 100644 msspecbook/_build/html/_downloads/7cc7f59f1ea682f79421b71b98d87b23/TiSe2_1_tofill.py create mode 100644 msspecbook/_build/html/_downloads/a4639febc8162e65b41b0e03dfeeaa17/cu.py create mode 100644 msspecbook/_build/html/_downloads/aa51bfc01de3fe879c2507956d0a2b8c/data.txt create mode 100644 msspecbook/_build/html/_downloads/b820873b74a9711a6b5f02470505cc1a/Si001.py delete mode 100644 msspecbook/_build/html/_images/Ni_SSCvsMI.png delete mode 100644 msspecbook/_build/html/_images/Ni_fig1.png create mode 100644 msspecbook/_build/html/_sources/Activity01/Activity01_light.ipynb create mode 100644 msspecbook/_build/html/_sources/Activity02/Activity02_light.ipynb create mode 100644 msspecbook/_build/html/_sources/Activity03/Activity03_light.ipynb create mode 100644 msspecbook/_build/html/_sources/Activity04/Activity04_light.ipynb create mode 100644 msspecbook/_build/html/_sources/Activity05/Activity05_light.ipynb create mode 100644 msspecbook/_build/html/_sources/Activity06/Activity06_light.ipynb create mode 100644 msspecbook/_build/html/_sources/Activity07/Activity07_light.ipynb create mode 100644 msspecbook/_build/html/_sources/Activity08/Activity08_light.ipynb create mode 100644 msspecbook/_build/html/_sources/Activity09/Activity09_light.ipynb create mode 100644 msspecbook/_build/html/_sources/Activity10/Activity10_light.ipynb delete mode 100644 msspecbook/_build/html/reports/Activity04/Activity04.err.log diff --git a/msspecbook/_build/html/Activity01/Activity01.html b/msspecbook/_build/html/Activity01/Activity01.html index 14e2aac..a7200b8 100644 --- a/msspecbook/_build/html/Activity01/Activity01.html +++ b/msspecbook/_build/html/Activity01/Activity01.html @@ -32,7 +32,7 @@ - + @@ -489,6 +489,11 @@ Building atomic systems, structures… is pretty straightforward:

PED polar scan for Cu(001)#

+

download the cu.py python script and the copper.cif file. Put those files in the same folder. You can run your first MsSpec calculation by typing in a terminal:

+
$ python cu.py
+
+
+

Here is the content of the script file:

1from ase.io import read
 2from msspec.calculator import MSSPEC
 3
@@ -816,12 +821,14 @@ Building atomic systems, structures… is pretty straightforward:

Based on the previous *.cif file, create a new cluster without the deepest plane and run the same calculation for the same emitter

Note

+

Use the cluster.edit() method to interactively remove atoms…

As the cluster will contain fewer atoms, the emitter index will be different

What do you conclude ?

-
+

Building the cluster#

-

Let’s start by building the cluster

+

Let’s start by building the cluster. You can copy/paste directly the code from this page to your text editor or you can download the script SbAg.py. You will also need the data.txt file.

 1from ase.build import bulk
  2from ase.visualize import view
  3
@@ -1409,7 +1409,8 @@ The idea is to use low energy photoelectron diffraction to see the substitution
 
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diff --git a/msspecbook/_build/html/Activity04/Activity04_light.html b/msspecbook/_build/html/Activity04/Activity04_light.html new file mode 100644 index 0000000..9fc0a5d --- /dev/null +++ b/msspecbook/_build/html/Activity04/Activity04_light.html @@ -0,0 +1,519 @@ + + + + + + + + + + + Activity 4: From single scattering to multiple scattering — MsSpec Tour + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
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Activity 4: From single scattering to multiple scattering

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Activity 4: From single scattering to multiple scattering#

+

In the previous activity, we saw that simple single scattering calculations (SSC) can be used to simulate photodiffraction diagrams with good accuracy. The approximation works fine when the emitting atom is very close to the surface. +However, the SSC approach is no longer suitable for deeper emitter atoms, where multiple scattering effects come into play. In this activity, we will focus on a major consequence of multiple scattering: the defocusing effect.

+

The defocusing effect is presented in the figure below for a chain of nickel atoms. Although purely illustrative, understanding multiple scattering in atomic chains is fundamental because they are found in many situations, such as in particular directions of a crystal or in molecules of various lengths.

+
+defocusing effect + +
+

The defocusing effect dur to multiple scattering in an atomic chain of Ni atoms.#

+
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+

In 1989, M.-L Xu, J.J. Barton and M.A. Van Hove studied these multiple scattering effects on atomic chains (see their paper below). +In the spirit of figure 3 of their paper, we will create 3 atomic chains of Ni atoms (2, 3 and 5 atoms) tilted by 45° and we will compare the intensity of the forward scattering peak for single scattering and for full multiple scattering.

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See also

+

based on this paper from M.-L. Xu et al. +Phys. Rev. B 39 p8275 (1989)

+
+
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Polar scans of Ni atomic chains#

+
+

Building a chain of atoms#

+

Start by creating a simple chain of 2 Ni atoms: an emitter and a scatterer in the [101] direction.

+
+

Tip

+

Nickel is fcc with lattice parameter \(a\)=3.499 Å. Use the Atoms class of ase like in the previous activity

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Create an MSSPEC calculator with expansion algortithm and set the scattering_order=1 to compute a polar scan of the Ni(3s) in single scattering. How is varying the height of the peak at 45° (along the chain) if you increase the number of atoms in the chain ?

+

Repeat the same experiment with inversion algorithm for having the full multiple scattering result. What do you observe ?

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+ + + + + + + + \ No newline at end of file diff --git a/msspecbook/_build/html/Activity05/Activity05.html b/msspecbook/_build/html/Activity05/Activity05.html index 48aa649..135c185 100644 --- a/msspecbook/_build/html/Activity05/Activity05.html +++ b/msspecbook/_build/html/Activity05/Activity05.html @@ -32,7 +32,7 @@ - + @@ -427,23 +427,23 @@ document.write(`
-

Complete the code snipet provided below to create a small TiSe2 cluster with Ti emitter in the 2nd plane:

+

Complete the code snipet provided below (or here) to create a small TiSe2 cluster with Ti emitter in the 2nd plane:

 1from ase.build import mx2
  2from ase.visualize import view
  3from msspec.calculator import MSSPEC
  4from msspec.utils import hemispherical_cluster, get_atom_index
  5
  6# Some usefull constants (a, c, d, D) for defining the structure
- 7a=...
- 8
+ 7a=...
+ 8
  9# Create the TiSe2 trilayer
 10# use ase help for this function
-11TiSe2 = mx2(formula=...)
-12
+11TiSe2 = mx2(formula=...)
+12
 13# The preious cell is 2D, let's define the c-axis to take into account 
 14# the Van der Waals gap between trilayers
-15TiSe2.cell[2] = [0, 0, ...]
-16
+15TiSe2.cell[2] = [0, 0, ...]
+16
 17# To be aligned like in the paper
 18TiSe2.rotate(60, 'z', rotate_cell=True)
 19
@@ -453,54 +453,37 @@ document.write(`
 23for i in range(3): 
 24    TiSe2[i].tag = i
 25
-26cluster = hemispherical_cluster(TiSe2, emitter_tag=..., emitter_plane=..., planes=5)
-27cluster.emitter = get_atom_index(cluster, 0, 0, 0)
+26cluster = hemispherical_cluster(TiSe2, emitter_tag=..., emitter_plane=..., planes=5)
+27cluster.emitter = get_atom_index(cluster, 0, 0, 0)
 28
 29view(cluster)
-30
 
-
-
- - -Hide code cell content - -
-
from ase.build import mx2
-from ase.visualize import view
-from msspec.calculator import MSSPEC
-from msspec.utils import hemispherical_cluster, get_atom_index
-
-# Some usefull constants (a, c, d, D) for defining the structure
-a=3.535;c=6.004;d=3.450;D=2.554
-
-# Create the TiSe2 trilayer
-# use ase help for this function
-TiSe2 = mx2(formula='TiSe2', kind='1T', a=a, thickness=d, size=(1, 1, 1), vacuum=None)
-
-# The preious cell is 2D, let's define the c-axis to take into account 
-# the Van der Waals gap between trilayers
-TiSe2.cell[2] = [0, 0, c]
-
-# To be aligned like in the paper
-TiSe2.rotate(60, 'z', rotate_cell=True)
-
-# Since the material is multi-elements, "tag" each inequivalent atom 
-# of the unit cell with a number. The "Ti" atom is tagged 0 and "Se" 
-# atoms are 1 and 2.
-for i in range(3): 
-    TiSe2[i].tag = i
-
-cluster = hemispherical_cluster(TiSe2, emitter_tag=0, emitter_plane=1, planes=5)
-cluster.emitter = get_atom_index(cluster, 0, 0, 0)
+
-
-
@@ -1053,7 +1036,8 @@ What do you conclude about the value of the +