Mercurial > repos > muon-spectroscopy-computational-project > pm_muairss_read
annotate pm_muairss_read.xml @ 0:49b6d76139da draft
planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_muairss_read commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
| author | muon-spectroscopy-computational-project |
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| date | Thu, 25 Aug 2022 16:18:39 +0000 |
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| children | c5fba3c9f660 |
| rev | line source |
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49b6d76139da
planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_muairss_read commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
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1 <tool id="pm_muairss_read" name="PyMuonSuite AIRSS Cluster" version="@TOOL_VERSION@+galaxy@WRAPPER_VERSION@" python_template_version="3.5" profile="22.01"> |
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49b6d76139da
planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_muairss_read commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
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2 <description>run clustering for optimised structures</description> |
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49b6d76139da
planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_muairss_read commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
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3 <macros> |
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49b6d76139da
planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_muairss_read commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
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4 <!-- version of underlying tool (PEP 440) --> |
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49b6d76139da
planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_muairss_read commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
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5 <token name="@TOOL_VERSION@">0.2.1</token> |
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49b6d76139da
planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_muairss_read commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
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6 <!-- version of this tool wrapper (integer) --> |
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49b6d76139da
planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_muairss_read commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
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7 <token name="@WRAPPER_VERSION@">1</token> |
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49b6d76139da
planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_muairss_read commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
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8 <!-- citation should be updated with every underlying tool version --> |
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49b6d76139da
planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_muairss_read commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
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9 <!-- typical fields to update are version, month, year, and doi --> |
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49b6d76139da
planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_muairss_read commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
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10 <token name="@TOOL_CITATION@"> |
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49b6d76139da
planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_muairss_read commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
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11 @software{pymuon-suite, |
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49b6d76139da
planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_muairss_read commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
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12 author = {Sturniolo, Simone and Liborio, Leandro and Chadwick, Eli and Murgatroyd, Laura and Laverack, Adam and {Muon Spectroscopy Computational Project}}, |
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49b6d76139da
planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_muairss_read commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
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13 license = {GPL-3.0}, |
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49b6d76139da
planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_muairss_read commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
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14 title = {{pymuon-suite}}, |
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49b6d76139da
planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_muairss_read commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
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15 url = {https://github.com/muon-spectroscopy-computational-project/pymuon-suite}, |
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49b6d76139da
planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_muairss_read commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
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16 version = {v0.2.1}, |
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49b6d76139da
planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_muairss_read commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
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17 month = {2}, |
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49b6d76139da
planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_muairss_read commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
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18 year = {2022}, |
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49b6d76139da
planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_muairss_read commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
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19 doi = {} |
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49b6d76139da
planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_muairss_read commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
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20 } |
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49b6d76139da
planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_muairss_read commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
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21 </token> |
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49b6d76139da
planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_muairss_read commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
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22 </macros> |
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49b6d76139da
planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_muairss_read commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
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23 <creator> |
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49b6d76139da
planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_muairss_read commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
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24 <person givenName="Jyothish" familyName="Thomas" identifier="https://orcid.org/0000-0003-4724-6924"/> |
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49b6d76139da
planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_muairss_read commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
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25 <person givenName="Eli" familyName="Chadwick" url="https://github.com/elichad" identifier="https://orcid.org/0000-0002-0035-6475"/> |
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49b6d76139da
planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_muairss_read commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
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26 <organization url="https://muon-spectroscopy-computational-project.github.io/index.html" name="The Muon Spectroscopy Computational Project"/> |
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49b6d76139da
planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_muairss_read commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
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27 </creator> |
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49b6d76139da
planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_muairss_read commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
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28 <requirements> |
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49b6d76139da
planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_muairss_read commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
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29 <requirement type="package" version="@TOOL_VERSION@">pymuonsuite</requirement> |
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49b6d76139da
planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_muairss_read commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
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30 </requirements> |
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49b6d76139da
planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_muairss_read commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
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31 <command detect_errors="exit_code"><![CDATA[ |
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49b6d76139da
planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_muairss_read commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
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32 unzip "$optimisation_results" && |
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49b6d76139da
planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_muairss_read commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
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33 if test -f "params.yaml"; then echo "params.yaml present"; else echo "params.yaml missing" && exit 64; fi |
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49b6d76139da
planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_muairss_read commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
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34 && if ( test -f input_structure.* ) ; then echo "input structure present"; else echo "input structure missing" && exit 64; fi |
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49b6d76139da
planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_muairss_read commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
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35 && out_folder="`python ${__tool_directory__}/get_out_folder.py`" && |
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49b6d76139da
planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_muairss_read commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
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36 pm-muairss -t r input_structure.* params.yaml |
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49b6d76139da
planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_muairss_read commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
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37 ]]></command> |
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49b6d76139da
planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_muairss_read commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
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38 <inputs> |
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planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_muairss_read commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
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39 <param type="data" name="optimisation_results" label="optimised muonated structures (.zip)" format="zip" help="A zip folder containing a set of optimised muonated structures, the original structure, and a YAML parameter file. See below for the expected folder structure."/> |
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49b6d76139da
planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_muairss_read commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
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40 </inputs> |
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49b6d76139da
planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_muairss_read commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
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41 <outputs> |
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planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_muairss_read commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
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42 <data label="Cluster report for $optimisation_results.name" name="cluster_report" format="txt" from_work_dir="$out_folder/*clusters.txt"/> |
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planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_muairss_read commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
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43 <data label="Cluster data for $optimisation_results.name" name="cluster_data" format="txt" from_work_dir="$out_folder/*clusters.dat"/> |
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planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_muairss_read commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
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44 </outputs> |
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planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_muairss_read commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
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45 <tests> |
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planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_muairss_read commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
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46 <test> |
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49b6d76139da
planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_muairss_read commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
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47 <param name="optimisation_results" value="uep-out.zip" ftype="zip"/> |
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49b6d76139da
planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_muairss_read commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
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48 <output name="cluster_report" file="clustout-uep.txt" ftype="txt" lines_diff="2"/> |
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49b6d76139da
planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_muairss_read commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
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49 <output name="cluster_data" file="clustout-uep.dat" ftype="txt"/> |
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planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_muairss_read commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
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50 </test> |
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planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_muairss_read commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
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51 <test> |
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planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_muairss_read commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
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52 <param name="optimisation_results" value="dftb-out.zip" ftype="zip"/> |
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49b6d76139da
planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_muairss_read commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
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53 <output name="cluster_report" file="clustout-dftb.txt" ftype="txt" lines_diff="2"/> |
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49b6d76139da
planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_muairss_read commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
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54 <output name="cluster_data" file="clustout-dftb.dat" ftype="txt"/> |
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49b6d76139da
planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_muairss_read commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
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55 </test> |
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planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_muairss_read commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
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56 </tests> |
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planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_muairss_read commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
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57 <help><![CDATA[ |
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58 Given a set of optimised muonated structures, clusters the structures based on similarity. |
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planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_muairss_read commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
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59 |
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49b6d76139da
planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_muairss_read commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
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60 If you used the 'Run UEP optimisation' tool for optimisation, the output from that tool can be used as the input to this one. |
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49b6d76139da
planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_muairss_read commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
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61 If you are bringing files from elsewhere, make sure they fit the expected zip folder structure: |
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49b6d76139da
planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_muairss_read commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
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62 |
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49b6d76139da
planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_muairss_read commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
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63 .. code-block:: |
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49b6d76139da
planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_muairss_read commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
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64 |
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planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_muairss_read commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
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65 optimised-structures.zip/ |
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planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_muairss_read commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
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66 ├─ muon-airss-out/ |
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planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_muairss_read commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
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67 │ ├─ uep/ |
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planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_muairss_read commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
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68 │ │ ├─ struct_1/ |
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planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_muairss_read commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
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69 │ │ │ ├─ <files for optimised struct_1 go here> |
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planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_muairss_read commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
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70 │ │ ├─ struct_2/ |
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planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_muairss_read commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
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71 │ │ │ ├─ <files for optimised struct_2 go here> |
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planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_muairss_read commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
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72 │ │ ├─ struct_N/ |
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planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_muairss_read commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
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73 │ │ │ ├─ <files for optimised struct_N go here> |
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planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_muairss_read commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
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74 ├─ input.cell |
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planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_muairss_read commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
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75 ├─ params.yaml |
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planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_muairss_read commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
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76 |
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77 This folder represents a run with the output folder name ``muon-airss-out``, the structure name ``struct``, and the UEP calculator. |
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78 If you use different parameters, these names should match your own settings. (``dftb+`` and ``castep`` are used as folder names for the respective calculators) |
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79 |
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planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_muairss_read commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
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80 The zip folder itself has been named ``optimised-structures.zip`` in this example, but it doesn't matter what you call it. |
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81 |
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82 The files ``input.cell`` and ``params.yaml`` must have those exact names. ``input.cell`` should be your original structure file, |
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83 and ``params.yaml`` is the YAML parameter file used to configure the clustering (as well as any prior muonation and optimisation). |
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planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_muairss_read commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
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84 You should have created this YAML file using the 'Create YAML for pm-muairss' tool or written it yourself, then passed it into the |
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planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_muairss_read commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
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85 'Generate muon structures' tool or pm-muairss. |
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planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_muairss_read commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
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86 |
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87 Command-line usage: pm-muairss [-h] -t r structures parameter_file |
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88 ]]></help> |
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89 <citations> |
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planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_muairss_read commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
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90 <citation type="bibtex"> |
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planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_muairss_read commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
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91 @TOOL_CITATION@ |
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planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_muairss_read commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
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92 </citation> |
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planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_muairss_read commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
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93 <citation type="bibtex"> |
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planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_muairss_read commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
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94 @article{airss, |
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planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_muairss_read commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
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95 author = {Liborio, L. and Sturniolo, S. and Jochym, D.}, |
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planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_muairss_read commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
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96 title = {Computational prediction of muon stopping sites using ab initio random structure searching (AIRSS)}, |
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planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_muairss_read commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
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97 journal = {The Journal of Chemical Physics}, |
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planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_muairss_read commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
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98 volume = {148}, |
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planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_muairss_read commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
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99 pages = {134114}, |
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planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_muairss_read commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
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100 year = {2018}, |
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planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_muairss_read commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
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101 doi={10.1063/1.5024450}, |
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planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_muairss_read commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
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102 URL={ |
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103 https://doi.org/10.1063/1.5024450 |
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planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_muairss_read commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
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104 }, |
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105 eprint={ |
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106 https://doi.org/10.1063/1.5024450 |
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planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_muairss_read commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
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107 } |
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108 } |
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109 </citation> |
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110 <citation type="bibtex"> |
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111 @article{doi:10.1063/1.5085197, |
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planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_muairss_read commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
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112 author = {Sturniolo,Simone and Liborio,Leandro and Jackson,Samuel }, |
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113 title = {Comparison between density functional theory and density functional tight binding approaches for finding the muon stopping site in organic molecular crystals}, |
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planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_muairss_read commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
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114 journal = {The Journal of Chemical Physics}, |
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planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_muairss_read commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
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115 volume = {150}, |
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planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_muairss_read commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
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116 number = {15}, |
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planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_muairss_read commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
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117 pages = {154301}, |
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planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_muairss_read commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
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118 year = {2019}, |
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planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_muairss_read commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
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119 doi = {10.1063/1.5085197}, |
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planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_muairss_read commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
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120 URL = { |
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121 https://doi.org/10.1063/1.5085197 |
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122 }, |
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123 eprint = { |
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124 https://doi.org/10.1063/1.5085197 |
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125 } |
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126 } |
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127 </citation> |
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128 <citation type="bibtex"> |
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129 @article{doi:10.1063/5.0012381, |
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130 author = {Sturniolo,Simone and Liborio,Leandro }, |
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131 title = {Computational prediction of muon stopping sites: A novel take on the unperturbed electrostatic potential method}, |
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132 journal = {The Journal of Chemical Physics}, |
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133 volume = {153}, |
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134 number = {4}, |
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135 pages = {044111}, |
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136 year = {2020}, |
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137 doi = {10.1063/5.0012381}, |
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138 URL = { |
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139 https://doi.org/10.1063/5.0012381 |
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140 }, |
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141 eprint = { |
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142 https://doi.org/10.1063/5.0012381 |
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143 }, |
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144 abstract = { Finding the stopping site of the muon in a muon-spin relaxation experiment is one of the main problems of muon spectroscopy, and computational techniques that make use of quantum chemistry simulations can be of great help when looking for this stopping site. The most thorough approach would require the use of simulations, such as Density Functional Theory (DFT), to test and optimise multiple possible sites, accounting for the effect that the added muon has on its surroundings. However, this can be computationally expensive and sometimes unnecessary. Hence, in this work, we present a software implementation of the Unperturbed Electrostatic Potential (UEP) Method: an approach used for finding the muon stopping site in crystalline materials. The UEP method requires only one DFT calculation, necessary to compute the electronic density. This, in turn, is used to calculate the minima of the crystalline material’s electrostatic potential and the estimates of the muon stopping site, relying on the approximation that the muon’s presence does not significantly affect its surroundings. One of the main UEP’s assumptions is that the muon stopping site will be one of the crystalline material’s electrostatic potential minima. In this regard, we also propose some symmetry-based considerations about the properties of this crystalline material’s electrostatic potential, in particular, which sites are more likely to be its minima and why the unperturbed approximation may be sufficiently robust for them. We introduce the Python software package pymuon-suite and the various utilities it provides to facilitate these calculations, and finally, we demonstrate the effectiveness of the method with some chosen example systems. } |
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145 } |
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146 </citation> |
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147 <citation type="bibtex"> |
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148 @article {castep, |
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149 author = {Clark, S. J. and Segall, M. D. and Pickard, C. J. and Hasnip, P. J. and Probert, M. I. J. and Refson, K. and Payne, M. C.}, |
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150 title = {First principles methods using CASTEP}, |
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151 journal = {Zeitschrift fuer Kristallographie}, |
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152 volume = {220}, |
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153 pages = {567}, |
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154 year = {2005} |
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155 } |
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156 </citation> |
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157 </citations> |
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158 </tool> |