Finding the Muon Stopping Site: pymuon-suite in Galaxy 1.0
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This workflows is part of the tutorial Finding the muon stopping site with pymuon-suite in Galaxy, available in the GTN
Features
- Includes Galaxy Workflow Tests
Thanks to...
Workflow Author(s): Muon Spectroscopy Computational Project
Tutorial Author(s): Leandro Liborio, Eli Chadwick, Patrick Austin
Tutorial Contributor(s): Leandro Liborio, Helena Rasche, Patrick Austin, Björn Grüning
Grants(s): EuroScienceGateway
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
1.0
Creators and Submitter
Views: 1196 Downloads: 200 Runs: 0
Created: 2nd Jun 2025 at 10:59
Last updated: 28th Jul 2025 at 10:51
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Teams: EuroScienceGateway
Organizations: Science and Technology Facilities Council
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Teams: Galaxy Training Network
Organizations: Galaxy
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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
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
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