Activity log
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Welcome to the Hercules 2022 Oasys tutorial written by Manuel Sanchez del Rio and Juan Reyes Herrera.
The aim of this course is to learn the following:
- Calculate main characteristics of synchrotron source (Bending magnets and Insertion devices).
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Calculate the heat-load on different beamline components.
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Simulating beamline optics by ray-tracing to obtain main parameters of the beam, e. g., size and divergence, energy resolution, intensity/flux.
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Understand basic principles of X-ray optics: Mirrors and Crystals.
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Basic concepts about coherence.
And it is split into four sections:
1. Introduction
2. Power Transport
3. Photon Transport
4. Coherence Transport
Before going to the content, it is important to explain that you can use OASYS in two ways:
1. Install Oasys on your own laptop. Follow the instructions in the following links:
[Mac OS](https://github.com/oasys-kit/oasys-installation-scripts/wiki/Install-Oasys-in-MacOS) ** ** [Windows OS](https://github.com/oasys-kit/oasys-installation-scripts/wiki/Install-Oasys-in-Windows-10) ** ** [Linux OS](https://github.com/oasys-kit/oasys-installation-scripts/wiki/Install-Oasys-in-Linux) ** ** [Docker
](https://github.com/oasys-kit/oasys-installation-scripts/wiki/Use-Docker-Oasys-container)
This course needs the installation of the ESRF add-on in OASYS. Open OASYS and follow the "install as user" instructions[](https://github.com/oasys-kit/oasys-installation-scripts/wiki/Use-Docker-Oasys-container)[here](https://github.com/oasys-esrf-kit/OASYS1-ESRF-Extensions/blob/master/README.md).
2. Login and get an account in: [https://vuo.elettra.eu](https://vuo.elettra.eu)
Once logged in (please use Chrome), you have to go to **Virtual Laboratory** and click on **My applications** , then click on [Start] of _ **SCITOOLBOX** _ application, and then click [next] and wait a few minutes (only the first time).
When your session is open, open OASYS as shown below:
**It is very important** to let us know if you want to use this second option in order to give you the necessary permissions to use the app.
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to: ["fr/computing/scientific/crispy/github page"]
Someone
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to: Crispy is a modern interface for calculating core-level spectra.
It uses [Quanty](http://quanty.org/) for calculations and is written in python.
Its primary use is as a sleek GUI that runs on your computer.
However it can also be used like a python module within a Jupyter notebook.
Here you can have a go at using Crispy without local installation:
1. Launch **JupyterHub**
2. Click **Start my server**
3. Select **0-first\_calculation.ipynb**
Crispy Documentation: [https://www.esrf.fr/computing/scientific/crispy/](https://www.esrf.fr/computing/scientific/crispy/)
GitHub Page: [https://github.com/mretegan/crispy](https://github.com/mretegan/crispy)
pan-training
pan-training
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Introduction to Neutron Reflectometry Fitting at 2025-02-01 11:31:06 UTC.
Someone
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Someone
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to: This course was originally developed by **[Andrew McCluskey](mailto:andrew.mccluskey@ess.eu)** from the **[European Spallation Source](https://europeanspallationsource.se/)** for the ISIS Virtual Reflectometry Training Course.
The full course can be read as a online book at: [**https://www.reflectometry.org/isis\_school/intro.html**](https://www.reflectometry.org/isis_school/intro.html)
The files can found on GitHub at [**https://github.com/reflectivity/isis\_school**](https://github.com/reflectivity/isis_school)
To run the course as interactive Jupyter notebooks here, click on the **JupyterHub ** link and then **Start My Server
If you have self enrolled onto the course please wait 5 minutes before launching the JupyterHub.**
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to: [" data analysis library pandas", "-ikon/tree/master/notebooks"]
Someone
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to: **If you have self enrolled onto the course please wait 5 minutes before launching the JupyterHub**
Access the course by clicking on the **JupyterHub** link.
Click **Start My Server** \> **Start** and your container will launch.
In the folder called **Notebooks** you will find the following:
1. **Jupyter basics: ** Jupyter notebook introduction.
2. **Python basics: ** Basic language principles, Sequence data types, Control structures, Working with functions, Using modules, Input and output, Python 2 vs 3, Python classes.
3. **Using external Libraries: ** Scientific libraries numpy, Plotting with matplotlib, Ipywidgets, Fitting scipy, Data analysis library pandas, Testing.
4. **Molecular visualization: ** Visualization tutorial, Atomistic simulation environment.
5. **McStas script**
6. **SCIPP**
You can find a copy of the notebooks at [https://github.com/ess-dmsc-dram/python-course-ikon/tree/master/notebooks](https://github.com/ess-dmsc-dram/python-course-ikon/tree/master/notebooks)
_This course was created by the Data Reduction, Analysis and Modelling group of the ESS.
This version of the course was specifically created for IKON21 in September 2021._
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to: ["Moodle course", "e-learning"]
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to: ["extract key length scales"]
Someone
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to: Course image taken by Andrew Brookes.
Course created by **Amanda Martinez Rodriguez**
We will learn with Pabitra Biswas what a [superconductor](https://en.wikipedia.org/wiki/Superconductivity) is, how we measure [magnetic fields](https://en.wikipedia.org/wiki/London_penetration_depth), extract key length scales ([vortex lattice](http://hyperphysics.phy-astr.gsu.edu/hbase/Solids/lattice.html)), see how the measurement works, what kind of data you get, and gain an overview of how to understand the new physics.
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to: [" analyse sas test data", " - polydispersity - resolution - interparticle interaction"]
Someone
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to: Teacher: **Wojciech Potrzebowski**
This course will demonstrate how to approach small-angle scattering (SAS) data analysis.
In **Section 1** you will familiarise yourself with the basic use of SasView.
In **Section 2** , you will **analyse SAS test data** with SasView software and see the effects of:
- Polydispersity
- Resolution
- Interparticle interaction.
**Section 3 and 4** are optional and will lead you through simultaneous fitting and \[P(r) \] analysis.
Software for this session: **SasView 5.0.5.**
General introduction to SasView: [https://youtu.be/Sbzf\_wdlPnQ](https://youtu.be/Sbzf_wdlPnQ)
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to: ["sans\r\ncase study", "sans wiki simulation project", "mcstas simulation tool"]
Someone
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to: This course is split into two sections:
- Theoretical background to SANS
- Case study of nanodisks using the LOKI instrument
**Useful links:**
[SasView course](https://pan-learning.org/moodle/course/view.php?id=19)
[Wiki page on SANS
](https://pan-learning.org/wiki/index.php/Small_angle_neutron_scattering,_SANS)[Wiki problems (exercises with solutions) on SANS](https://pan-learning.org/wiki/index.php/Page_of_all_exercises#Exercises_in_Small_angle_neutron_scattering)
[Wiki simulation project (based on SANS-2 at PSI)
](https://pan-learning.org/wiki/index.php/Simulation_project_SANS-2:_A_small_angle_neutron_scattering_instrument)[McStas Simulation Tool:](https://sim.e-neutrons.esss.dk/instrument-menu/intro-ns) Use the same login details as for pan-learning.org. There are currently two instruments: SANSsimple and SANSsimpleSpheres
Course photo courtesy of CERIC-EIRC
pan-training
pan-training
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Introduction to small angle scattering at 2025-02-01 11:30:59 UTC.
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to: ["id=19\r\nsans simulation tool", "sanssimplespheres\r\npan-learning wiki pagehttps", "_a_small_angle_neutron_scattering_instrument\r\nill youtube videowww", "uwe keiderling - berlin neutron scattering schoolmartin müller - hercules 2016frank gabel - hercules 2016marianne liebi - hercules 2016", "paolo mariani - sisn 2015francesco spinozzi - sisn 2015leonardo chiappisi - bilbao neutron scattering school 2019adel len - cets 2019g", "pépy - cets 2019wim bouwman - erice 2017", "markus strobl - erice 2017"]
Someone
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to: **Link to SasView moodle course on PaN-learning.org**
[https://pan-learning.org/moodle/course/view.php?id=19](https://pan-learning.org/moodle/course/view.php?id=19)
**SANS simulation tool with McStas**
[https://sim.e-neutrons.esss.dk/instrument-menu/intro-ns
](https://sim.e-neutrons.esss.dk/instrument-menu/intro-ns)Use the same login details as for pan-learning.org. [
](https://sim.e-neutrons.esss.dk/instrument-menu/intro-ns)There are currently two instruments: SANSsimple and SANSsimpleSpheres
**PaN-learning wiki page**
[https://pan-learning.org/wiki/index.php/Small\_angle\_neutron\_scattering,\_SANS
](https://pan-learning.org/wiki/index.php/Small_angle_neutron_scattering,_SANS)[https://pan-learning.org/wiki/index.php/Page\_of\_all\_exercises#Exercises\_in\_Small\_angle\_neutron\_scattering](https://pan-learning.org/wiki/index.php/Page_of_all_exercises#Exercises_in_Small_angle_neutron_scattering)
[https://pan-learning.org/wiki/index.php/Simulation\_project\_SANS-2:\_A\_small\_angle\_neutron\_scattering\_instrument](https://pan-learning.org/wiki/index.php/Simulation_project_SANS-2:_A_small_angle_neutron_scattering_instrument)
**ILL youtube video**
[www.youtube.com/watch?v=doovK7DBuEM](https://pan-learning.org/moodle/www.youtube.com/watch?v=doovK7DBuEM)
There are also a set of animations for part of a SANS instrument, one of which is
[www.youtube.com/watch?v=xxYj9VLlBKI](https://pan-learning.org/moodle/www.youtube.com/watch?v=xxYj9VLlBKI)
**Slides from lectures by:**
Uwe Keiderling - Berlin neutron scattering school
Martin Müller - Hercules 2016
Frank Gabel - Hercules 2016
Marianne Liebi - Hercules 2016 (SAXS)
Paolo Mariani - SISN 2015
Francesco Spinozzi - SISN 2015
Leonardo Chiappisi - Bilbao neutron scattering school 2019
Adel Len - CETS 2019
G. Pépy - CETS 2019
Wim Bouwman - Erice 2017 (SESANS)
Markus Strobl - Erice 2017 (SEMSANS)
The following sections were pulled from existing courses on PaN-learning.org
pan-training
pan-training
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Including Jupyter Notebooks in your Course at 2025-02-01 11:30:59 UTC.
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to: ["analyse experimental data", "virtually explore large scale facility instruments", "- teach students data modelling", "include common scientific python modules"]
Someone
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to: Course image by [GustavoAckles](https://pixabay.com/users/gustavoackles-6863234/?utm_source=link-attribution&utm_medium=referral&utm_campaign=image&utm_content=4869815) from [Pixabay](https://pixabay.com/?utm_source=link-attribution&utm_medium=referral&utm_campaign=image&utm_content=4869815).
As a teacher, you can link a JupyterHub instance to your course that runs on our e-learning servers.
The JupyterHub instance runs as a docker container that is launched when a student clicks on the link.
The container will clone your chosen github repository where you can edit and store Jupyter notebooks.
Students will be able to open these Jupyter notebooks and execute them remotely.
Crucially students do not require Jupyter to be installed on their computers or have prior knowledge of python.
Examples where this might be useful:
- Show students how to **reduce** and **analyse** experimental data themselves using **python**.
- Introduce students to **python modules** or **software** used in data reduction and analysis.
- Allow students to **virtually explore** large scale facility instruments. For example by using **McStas** (neutron instrument simulator).
- Teach students **data modelling** and **simulation** techniques that use **python**.
**Requirements:**
What the student will interact with must be in the form of a **Jupyter notebook**.
Your notebooks must be on a public **github repository**.
Note that the **entire repository** you provide will be **cloned** not just selected notebooks. However it does not have to be the master branch.
Our containers already include common scientific python modules such as numpy, matplotlib and ipython.
In addition we have containers with the following software installed:
1. McStas, McXtrace, SCIPP, SasVIew
2. Crispy
3. SimEx
If you require a container with other software to be installed it is possible to have a custom container created.
Please email admin@pan-learning.org for help.
**Useful Links:**
- **[Jupyter notebooks](https://jupyter.org/)**
- [**What is a docker container**?](https://www.docker.com/resources/what-container)(and the **[wiki page](https://en.wikipedia.org/wiki/Docker_(software))**)
- [**Docker and Jupyterhub**](https://hub.docker.com/r/jupyterhub/jupyterhub/#help-and-resources)
If you wish to include a link to a Jupyterhub container for your course.
Please fill the form: Information to set up your container
Once you have filled in the form you will receive an email to let you know the JupyterHub link is being set up and any further instructions that are required.
Please note it may take a few days to be up and running.
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Someone
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to: We recommend Open Broadcasting Software (OBS) as a great way to record yourself giving a presentation or lecture.
It has more flexibility and results in a higher quality video than simply recording your screen on zoom/skype.
It is easy to install and much easier to use than any video editing software.
Use the following four resources to help you:
1. **Introduction to OBS** and how it can be used.
2. Tips for good **video layout** (this is useful regardless of whether you chose to use OBS).
3. Links to **OBS download instructions** for Mac, Windows & Linux.
4. How you could **include live annotations** or a blackboard style presentation with OBS
Photos by [Jeremy Yap](https://unsplash.com/@jeremyyappy) and [Science in HD](https://unsplash.com/@scienceinhd) on [Unsplash](https://unsplash.com/s/photos/blackboard?utm_source=unsplash&utm_medium=referral&utm_content=creditCopyText)
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pan-training
pan-training
updated
Introduction to X-ray Spectroscopy Calculations at 2025-02-01 11:30:56 UTC.
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pan-training
pan-training
updated
Introduction to X-ray fluorescence (XRF) at 2025-02-01 11:30:56 UTC.
Someone
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to: ["gain knowledge basic knowledge", "cultural heritage\r\nshort test", "real raw data\r\n\r\nkey resources"]
Someone
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to: Introduction to X-ray fluorescence (XRF) is a short introductory course intended for students of physics, chemistry and material science that want to get acquainted with basic principles of XRF and some of its use cases. It has been designed by [Alessandra Gianoncelli](http://www.elettra.eu/PEOPLE/index.php?n=AlessandraGianoncelli.HomePage) (Elettra Sincrotrone, Italy) and [Aljoša Hafner](https://www.ceric-eric.eu/about-us/staff#hafner-aljosa---computational-physicist) (CERIC-ERIC, Italy).
Course duration is approximately 45 min.
The main goal of the course is to gain knowledge basic knowledge of synchrotron XRF and its applications. The following topics are covered:
- Basic theoretical background and principles
- Instrumentation and experimental setup (source, samples, detection)
- Scientific examples from biomedical applications and cultural heritage
- Short test of knowledge gained on real RAW data
Key resources:
- [https://en.wikipedia.org/wiki/X-ray\_fluorescence](https://en.wikipedia.org/wiki/X-ray_fluorescence)
- [https://www.amptek.com/resources/xrf](https://www.amptek.com/resources/xrf)