annotate pm_uep_opt.xml @ 1:904815426ba8 draft

planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_uep_opt commit 1f0d5da860dd5cd0ffceac7a292773ed53617324
author muon-spectroscopy-computational-project
date Thu, 15 Sep 2022 10:20:50 +0000
parents e4097a3e3e75
children 8f41a71fc710
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e4097a3e3e75 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_uep_opt commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
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1 <tool id="pm_uep_opt" name="PyMuonSuite AIRSS UEP Optimise" version="@TOOL_VERSION@+galaxy@WRAPPER_VERSION@" python_template_version="3.5" profile="22.01">
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2 <description>run UEP optimisation</description>
e4097a3e3e75 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_uep_opt commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
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3 <macros>
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4 <!-- version of underlying tool (PEP 440) -->
e4097a3e3e75 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_uep_opt commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
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5 <token name="@TOOL_VERSION@">0.2.1</token>
e4097a3e3e75 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_uep_opt commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
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6 <!-- version of this tool wrapper (integer) -->
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7 <token name="@WRAPPER_VERSION@">1</token>
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8 <!-- citation should be updated with every underlying tool version -->
e4097a3e3e75 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_uep_opt commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
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9 <!-- typical fields to update are version, month, year, and doi -->
e4097a3e3e75 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_uep_opt commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
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10 <token name="@TOOL_CITATION@">
e4097a3e3e75 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_uep_opt commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
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11 @software{pymuon-suite,
e4097a3e3e75 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_uep_opt 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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13 license = {GPL-3.0},
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14 title = {{pymuon-suite}},
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15 url = {https://github.com/muon-spectroscopy-computational-project/pymuon-suite},
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16 version = {v0.2.1},
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17 month = {2},
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18 year = {2022},
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19 doi = {}
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20 }
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21 </token>
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22 </macros>
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23 <creator>
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24 <person givenName="Jyothish" familyName="Thomas" identifier="https://orcid.org/0000-0003-4724-6924"/>
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25 <person givenName="Eli" familyName="Chadwick" url="https://github.com/elichad" identifier="https://orcid.org/0000-0002-0035-6475"/>
e4097a3e3e75 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_uep_opt 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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27 </creator>
e4097a3e3e75 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_uep_opt commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
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28 <requirements>
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29 <requirement type="package" version="@TOOL_VERSION@">pymuonsuite</requirement>
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30 <requirement type="package" version="3.0">zip</requirement>
e4097a3e3e75 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_uep_opt commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
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31 </requirements>
1
904815426ba8 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_uep_opt commit 1f0d5da860dd5cd0ffceac7a292773ed53617324
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32 <required_files>
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33 <include type="literal" path="run.sh"/>
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34 <include type="literal" path="get_out_folder.py"/>
904815426ba8 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_uep_opt commit 1f0d5da860dd5cd0ffceac7a292773ed53617324
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35 </required_files>
0
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36 <command detect_errors="exit_code"><![CDATA[
e4097a3e3e75 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_uep_opt commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
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37 unzip "$muonated_structures" &&
e4097a3e3e75 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_uep_opt commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
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38 if test -f "params.yaml"; then echo "params.yaml present"; else echo "params.yaml missing" && exit 64; fi &&
e4097a3e3e75 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_uep_opt commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
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39 if ( test -f input_structure.* ) ; then echo "input structure present"; else echo "input structure missing" && exit 64; fi &&
e4097a3e3e75 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_uep_opt commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
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40 charge_density_name=\$(sed 's/ //g' <<< "$charge_density.name") &&
e4097a3e3e75 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_uep_opt commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
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41 ln -s $charge_density \$charge_density_name &&
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42 x="\$charge_density_name" &&
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43 echo "calculated seed name \$x" &&
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44 ln -s $castep_log "\${x%%.*}.castep" &&
e4097a3e3e75 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_uep_opt commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
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45 out_folder="`python ${__tool_directory__}/get_out_folder.py`" &&
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46 find \$out_folder -type f -name "*.yaml" | xargs sed -i "s#^chden_path: .*#chden_path: .\/#g" &&
e4097a3e3e75 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_uep_opt commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
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47 find \$out_folder -type f -name "*.yaml" | xargs sed -i "s#^chden_seed: .*#chden_seed: \${x%%.*}#g" &&
e4097a3e3e75 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_uep_opt commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
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48 bash ${__tool_directory__}/run.sh \$out_folder &&
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49 zip -r out_zip.zip \$out_folder params.yaml input_structure.* &&
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50 find \$out_folder > tree.txt
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51 ]]></command>
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52 <inputs>
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53 <param type="data" name="muonated_structures" label="Muonated structures (.zip)" format="zip" help="A zip folder containing muonated structures, as generated by the 'Generate muonated structures' tool or pm-muairss."/>
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54 <param type="data" name="charge_density" label="Charge density file (.den_fmt)" format="txt" help="The charge density file created by CASTEP during your initial DFT simulation for the structure."/>
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55 <param type="data" name="castep_log" label="CASTEP log (.castep)" format="txt" help="The CASTEP log for your initial DFT simulation for the structure."/>
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56 <param type="hidden" name="testing" label="Test mode" value="false"/>
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57 </inputs>
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58 <outputs>
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59 <data label="UEP results for $muonated_structures.name" name="uep_results" format="zip" from_work_dir="out_zip.zip"/>
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60 <data label="File tree (testing only)" name="file_tree" format="txt" from_work_dir="tree.txt" hidden="true">
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61 <filter>(testing == "true")</filter>
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62 </data>
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63 </outputs>
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64 <tests>
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65 <test>
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66 <param name="testing" value="true"/>
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67 <param name="muonated_structures" value="muonated.zip" ftype="zip"/>
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68 <param name="charge_density" value="Si.den_fmt" ftype="txt"/>
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69 <param name="castep_log" value="Si.castep" ftype="txt"/>
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70 <output name="file_tree" file="tree.txt" ftype="txt" sort="true">
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71 <assert_contents>
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72 <has_size value="1780"/>
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73 </assert_contents>
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74 </output>
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75 </test>
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76 <test expect_num_outputs="2">
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77 <param name="testing" value="true"/>
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78 <param name="muonated_structures" value="muonated-default-folder.zip" ftype="zip"/>
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79 <param name="charge_density" value="Si.den_fmt" ftype="txt"/>
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80 <param name="castep_log" value="Si.castep" ftype="txt"/>
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81 <output name="file_tree" file="tree-default-folder.txt" sort="true"/>
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82 </test>
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83 <test expect_failure="true">
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84 <param name="testing" value="true"/>
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85 <param name="muonated_structures" value="muonated-default-folder.zip" ftype="zip"/>
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86 <param name="castep_log" value="Si.castep" ftype="txt"/>
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87 <param name="charge_density" value="Sifail.den_fmt" ftype="txt"/>
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88 <assert_stderr>
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89 <has_text text="Error: FMT file has no header"/>
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90 </assert_stderr>
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91 </test>
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92 <!-- check that file_tree filter works -->
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93 <test expect_num_outputs="1">
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94 <param name="testing" value="false"/>
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95 <param name="muonated_structures" value="muonated.zip" ftype="zip"/>
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96 <param name="charge_density" value="Si.den_fmt" ftype="txt"/>
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97 <param name="castep_log" value="Si.castep" ftype="txt"/>
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98 </test>
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99 </tests>
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100 <help><![CDATA[
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101 Given a set of input muonated structures (structures containing a muon), applies UEP optimisation to refine them.
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102
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103 This tool requires CASTEP inputs for the UEP method, meaning your initial DFT simulation must have been done with CASTEP.
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104 The structure you used as input to the '`Generate muonated structures`_' tool or pm-muairss beforehand should come from the same simulation run.
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105
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106 Command-line usage: pm-uep-opt [-h] [-t {r,w}] structures parameter_file
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107
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108 .. _Generate muonated structures: /tool_runner?tool_id=pm_muairss_write
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109 ]]></help>
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110 <citations>
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111 <citation type="bibtex">
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112 @TOOL_CITATION@
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113 </citation>
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114 <citation type="bibtex">
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115 @article{airss,
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116 author = {Liborio, L. and Sturniolo, S. and Jochym, D.},
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117 title = {Computational prediction of muon stopping sites using ab initio random structure searching (AIRSS)},
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118 journal = {The Journal of Chemical Physics},
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119 volume = {148},
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120 pages = {134114},
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121 year = {2018},
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122 doi={10.1063/1.5024450},
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123 URL={
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124 https://doi.org/10.1063/1.5024450
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125 },
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126 eprint={
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127 https://doi.org/10.1063/1.5024450
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128 }
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129 }
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130 </citation>
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131 <citation type="bibtex">
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132 @article{doi:10.1063/1.5085197,
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133 author = {Sturniolo,Simone and Liborio,Leandro and Jackson,Samuel },
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134 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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135 journal = {The Journal of Chemical Physics},
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136 volume = {150},
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137 number = {15},
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138 pages = {154301},
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139 year = {2019},
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140 doi = {10.1063/1.5085197},
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141 URL = {
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142 https://doi.org/10.1063/1.5085197
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143 },
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144 eprint = {
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145 https://doi.org/10.1063/1.5085197
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146 }
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147 }
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148 </citation>
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149 <citation type="bibtex">
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150 @article{doi:10.1063/5.0012381,
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151 author = {Sturniolo,Simone and Liborio,Leandro },
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152 title = {Computational prediction of muon stopping sites: A novel take on the unperturbed electrostatic potential method},
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153 journal = {The Journal of Chemical Physics},
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154 volume = {153},
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155 number = {4},
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156 pages = {044111},
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157 year = {2020},
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158 doi = {10.1063/5.0012381},
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159 URL = {
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160 https://doi.org/10.1063/5.0012381
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161 },
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162 eprint = {
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163 https://doi.org/10.1063/5.0012381
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164 },
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165 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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166 }
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167 </citation>
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168 <citation type="bibtex">
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169 @article {castep,
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170 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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171 title = {First principles methods using CASTEP},
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172 journal = {Zeitschrift fuer Kristallographie},
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173 volume = {220},
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174 pages = {567},
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175 year = {2005}
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176 }
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177 </citation>
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178 </citations>
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179 </tool>