Finding the Muon Stopping Site using PyMuonSuite Version 1
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Run on GalaxyFinding potential muon stopping sites in crystalline copper
Inputs
| ID | Name | Description | Type |
|---|---|---|---|
| Copper-out.cell | Copper-out.cell | CASTEP structural file for the relaxed host material |
|
| Copper.castep | Copper.castep | main CASTEP output file |
|
| Copper.den_fmt | Copper.den_fmt | CASTEP charge density file |
|
Steps
| ID | Name | Description |
|---|---|---|
| 3 | PyMuonSuite AIRSS UEP Optimise | Galaxy tool used to: load the CASTEP files; complete the Generation parameters to set up the creation of randomly populated muonated structures; and complete the Optimisation parameters to set up the relaxation the electrostatic forces of the muon in each of the randomly populated muonated structures. toolshed.g2.bx.psu.edu/repos/muon-spectroscopy-computational-project/pm_uep_opt/pm_uep_opt/0.3.0+galaxy1 |
| 4 | PyMuonSuite AIRSS Cluster | toolshed.g2.bx.psu.edu/repos/muon-spectroscopy-computational-project/pm_muairss_read/pm_muairss_read/0.3.0+galaxy0 |
Outputs
| ID | Name | Description | Type |
|---|---|---|---|
| All muons in host material | All muons in host material | n/a |
|
Version History
Version 1 (earliest) Created 15th Feb 2024 at 11:52 by Paul De Geest
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Created: 15th Feb 2024 at 11:52
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Teams: EuroScienceGateway, ELIXIR Belgium
Organizations: ELIXIR Belgium
https://orcid.org/0000-0002-8940-4946
ELIXIR is an intergovernmental organisation that brings together life science resources from across Europe. These resources include databases, software tools, training materials, cloud storage and supercomputers.
The goal of ELIXIR is to coordinate these resources so that they form a single infrastructure. This infrastructure makes it easier for scientists to find and share data, exchange expertise, and agree on best practices. Ultimately, it will help them gain new insights into how living ...
Teams: ELIXIR Training, FAIR Computational Workflows, EuroScienceGateway, BY-COVID (general), ELIXIR Tools platform, ELIXIR Metabolomics
Web page: https://elixir-europe.org/
EuroScienceGateway will leverage a distributed computing network across 13 European countries, accessible via 6 national, user-friendly web portals, facilitating access to compute and storage infrastructures across Europe as well as to data, tools, workflows and services that can be customized to suit researchers’ needs.EuroScienceGateway will deliver a robust, scalable, seamlessly integrated open infrastructure for data-driven research, contributing an innovative and customizable service for ...
Space: ELIXIR
Public web page: https://eurosciencegateway.eu/
Start date: 1st Oct 2022
End date: 31st Aug 2025
This is a training dataset for use in Galaxy materials science tutorials. These files can be used to demonstrate the AIRSS (Ab-Initio Random Structure Searching) method for finding muon stopping sites, using the UEP (Unperturbed Electrostatic Potential) technique for the optimisation stage of that method.
The files included are:
Si.cell: structure file containing atom locations Si.den_fmt: electron density data, generated with CASTEP Si.castep: CASTEP log file for the electron density calculation ...
Creators: Eli Chadwick, Muon Spectroscopy Computational Project
Submitter: Stian Soiland-Reyes
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Abstract (Expand)
Authors: Stian Soiland-Reyes, Björn Grüning, Paul De Geest
Date Published: 29th Feb 2024
Publication Type: Tech report
Collection of workflows used or developed by the EuroScienceGateway project.
Maintainers: Stian Soiland-Reyes, Paul De Geest, Eli Chadwick, Armin Dadras
Number of items: 48
Tags: Not specified
