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planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_muairss_read commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507
author muon-spectroscopy-computational-project
date Fri, 03 Feb 2023 15:39:29 +0000
parents eb6382889b92
children 40071ff77285
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2:eb6382889b92 3:276a25ab05f2
1 <tool id="pm_muairss_read" name="PyMuonSuite AIRSS Cluster" version="@TOOL_VERSION@+galaxy@WRAPPER_VERSION@" python_template_version="3.5" profile="22.01"> 1 <tool id="pm_muairss_read" name="PyMuonSuite AIRSS Cluster" version="@TOOL_VERSION@+galaxy@WRAPPER_VERSION@" python_template_version="3.5" profile="22.05" license="MIT">
2 <description>run clustering for optimised structures</description> 2 <description>run clustering for optimised structures</description>
3 <macros> 3 <macros>
4 <!-- version of underlying tool (PEP 440) --> 4 <!-- version of underlying tool (PEP 440) -->
5 <token name="@TOOL_VERSION@">0.2.1</token> 5 <token name="@TOOL_VERSION@">0.2.3</token>
6 <!-- version of this tool wrapper (integer) --> 6 <!-- version of this tool wrapper (integer) -->
7 <token name="@WRAPPER_VERSION@">1</token> 7 <token name="@WRAPPER_VERSION@">0</token>
8 <!-- citation should be updated with every underlying tool version --> 8 <!-- citation should be updated with every underlying tool version -->
9 <!-- typical fields to update are version, month, year, and doi --> 9 <!-- typical fields to update are version, month, year, and doi -->
10 <token name="@TOOL_CITATION@"> 10 <token name="@TOOL_CITATION@">
11 @software{pymuon-suite, 11 @software{Sturniolo_pymuon-suite_2022,
12 author = {Sturniolo, Simone and Liborio, Leandro and Chadwick, Eli and Murgatroyd, Laura and Laverack, Adam and {Muon Spectroscopy Computational Project}}, 12 author = {Sturniolo, Simone and Liborio, Leandro and Chadwick, Eli and Murgatroyd, Laura and Laverack, Adam and Mudaraddi, Anish and {Muon Spectroscopy Computational Project}},
13 license = {GPL-3.0}, 13 license = {GPL-3.0},
14 month = {8},
14 title = {{pymuon-suite}}, 15 title = {{pymuon-suite}},
15 url = {https://github.com/muon-spectroscopy-computational-project/pymuon-suite}, 16 url = {https://github.com/muon-spectroscopy-computational-project/pymuon-suite},
16 version = {v0.2.1}, 17 version = {v0.2.3},
17 month = {2}, 18 doi = {10.5281/zenodo.7025644},
18 year = {2022}, 19 year = {2022}
19 doi = {}
20 } 20 }
21 </token> 21 </token>
22 </macros> 22 </macros>
23 <creator> 23 <creator>
24 <person givenName="Jyothish" familyName="Thomas" identifier="https://orcid.org/0000-0003-4724-6924"/> 24 <person givenName="Jyothish" familyName="Thomas" identifier="https://orcid.org/0000-0003-4724-6924"/>
30 </requirements> 30 </requirements>
31 <required_files> 31 <required_files>
32 <include type="literal" path="get_out_folder.py"/> 32 <include type="literal" path="get_out_folder.py"/>
33 </required_files> 33 </required_files>
34 <command detect_errors="exit_code"><![CDATA[ 34 <command detect_errors="exit_code"><![CDATA[
35 unzip "$optimisation_results" && 35 unzip '$optimisation_results' &&
36 if test -f "params.yaml"; then echo "params.yaml present"; else echo "params.yaml missing" && exit 64; fi 36 if test -f "params.yaml"; then echo "params.yaml present"; else echo "params.yaml missing" && exit 64; fi
37 && if ( test -f input_structure.* ) ; then echo "input structure present"; else echo "input structure missing" && exit 64; fi 37 && if ( test -f input_structure.* ) ; then echo "input structure present"; else echo "input structure missing" && exit 64; fi
38 && out_folder="`python ${__tool_directory__}/get_out_folder.py`" && 38 && out_folder="`python '${__tool_directory__}/get_out_folder.py'`" &&
39 pm-muairss -t r input_structure.* params.yaml 39 pm-muairss -t r input_structure.* params.yaml
40 ]]></command> 40 ]]></command>
41 <inputs> 41 <inputs>
42 <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."/> 42 <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."/>
43 </inputs> 43 </inputs>
44 <outputs> 44 <outputs>
45 <data label="Cluster report for $optimisation_results.name" name="cluster_report" format="txt" from_work_dir="$out_folder/*clusters.txt"/> 45 <data label="Cluster report for $optimisation_results.name" name="cluster_report" format="txt" from_work_dir="${out_folder}/*clusters.txt"/>
46 <data label="Cluster data for $optimisation_results.name" name="cluster_data" format="txt" from_work_dir="$out_folder/*clusters.dat"/> 46 <data label="Cluster data for $optimisation_results.name" name="cluster_data" format="txt" from_work_dir="${out_folder}/*clusters.dat"/>
47 </outputs> 47 </outputs>
48 <tests> 48 <tests>
49 <test expect_num_outputs="2"> 49 <test expect_num_outputs="2">
50 <param name="optimisation_results" value="uep-out.zip" ftype="zip"/> 50 <param name="optimisation_results" value="uep-out.zip" ftype="zip"/>
51 <output name="cluster_report" file="clustout-uep.txt" ftype="txt" lines_diff="2"/> 51 <output name="cluster_report" file="clustout-uep.txt" ftype="txt" lines_diff="2"/>
86 and ``params.yaml`` is the YAML parameter file used to configure the clustering (as well as any prior muonation and optimisation). 86 and ``params.yaml`` is the YAML parameter file used to configure the clustering (as well as any prior muonation and optimisation).
87 You should have created this YAML file using the 'Create YAML for pm-muairss' tool or written it yourself, then passed it into the 87 You should have created this YAML file using the 'Create YAML for pm-muairss' tool or written it yourself, then passed it into the
88 'Generate muon structures' tool or pm-muairss. 88 'Generate muon structures' tool or pm-muairss.
89 89
90 Command-line usage: pm-muairss [-h] -t r structures parameter_file 90 Command-line usage: pm-muairss [-h] -t r structures parameter_file
91
92 PyMuonSuite is distributed under the GPLv3 license. This tool wrapper is distributed under the MIT license.
91 ]]></help> 93 ]]></help>
92 <citations> 94 <citations>
93 <citation type="bibtex"> 95 <citation type="bibtex">
94 @TOOL_CITATION@ 96 @TOOL_CITATION@
95 </citation> 97 </citation>
96 <citation type="bibtex"> 98 <citation type="doi">10.1063/1.5024450</citation>
97 @article{airss, 99 <citation type="doi">10.1063/1.5085197</citation>
98 author = {Liborio, L. and Sturniolo, S. and Jochym, D.}, 100 <citation type="doi">10.1063/5.0012381</citation>
99 title = {Computational prediction of muon stopping sites using ab initio random structure searching (AIRSS)},
100 journal = {The Journal of Chemical Physics},
101 volume = {148},
102 pages = {134114},
103 year = {2018},
104 doi={10.1063/1.5024450},
105 URL={
106 https://doi.org/10.1063/1.5024450
107 },
108 eprint={
109 https://doi.org/10.1063/1.5024450
110 }
111 }
112 </citation>
113 <citation type="bibtex">
114 @article{doi:10.1063/1.5085197,
115 author = {Sturniolo,Simone and Liborio,Leandro and Jackson,Samuel },
116 title = {Comparison between density functional theory and density functional tight binding approaches for finding the muon stopping site in organic molecular crystals},
117 journal = {The Journal of Chemical Physics},
118 volume = {150},
119 number = {15},
120 pages = {154301},
121 year = {2019},
122 doi = {10.1063/1.5085197},
123 URL = {
124 https://doi.org/10.1063/1.5085197
125 },
126 eprint = {
127 https://doi.org/10.1063/1.5085197
128 }
129 }
130 </citation>
131 <citation type="bibtex">
132 @article{doi:10.1063/5.0012381,
133 author = {Sturniolo,Simone and Liborio,Leandro },
134 title = {Computational prediction of muon stopping sites: A novel take on the unperturbed electrostatic potential method},
135 journal = {The Journal of Chemical Physics},
136 volume = {153},
137 number = {4},
138 pages = {044111},
139 year = {2020},
140 doi = {10.1063/5.0012381},
141 URL = {
142 https://doi.org/10.1063/5.0012381
143 },
144 eprint = {
145 https://doi.org/10.1063/5.0012381
146 },
147 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. }
148 }
149 </citation>
150 <citation type="bibtex"> 101 <citation type="bibtex">
151 @article {castep, 102 @article {castep,
152 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.}, 103 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.},
153 title = {First principles methods using CASTEP}, 104 title = {First principles methods using CASTEP},
154 journal = {Zeitschrift fuer Kristallographie}, 105 journal = {Zeitschrift fuer Kristallographie},