annotate pm_muairss_read.xml @ 5:17da9f67ed33 draft default tip

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author muon-spectroscopy-computational-project
date Fri, 26 Jul 2024 12:57:38 +0000
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1 <tool id="pm_muairss_read" name="PyMuonSuite AIRSS Cluster" version="@PYMUONSUITE_VERSION@+galaxy@WRAPPER_VERSION@" python_template_version="3.5" profile="22.05" license="MIT">
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2 <description>run clustering for optimised structures</description>
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3 <macros>
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4 <!-- version of this tool wrapper (integer) -->
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5 <token name="@WRAPPER_VERSION@">1</token>
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6 <import>muon_macros.xml</import>
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7 <xml name="supercell">
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8 <param type="text" argument="supercell" value="1" label="Supercell" help="Supercell size and shape to use when saving cluster structures. This can either be a single int, a list of three integers or a 3x3 matrix of integers. For a single number a diagonal matrix will be generated with the integer repeated on the diagonals. For a list of three numbers a diagonal matrix will be generated where the diagonal elements are set to the list. A matrix will be used directly as is. Default is a 3x3 identity matrix.">
40071ff77285 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_muairss_read commit 70a4d37ecdf5d586703cfc509922311e95d3205c
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9 <validator type="regex" message="Input should only contain whitespace, '[', ']', ',' and digits.">^[\s\d,\[\]]+$</validator>
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10 </param>
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11 </xml>
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12 </macros>
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13 <creator>
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14 <person givenName="Jyothish" familyName="Thomas" identifier="https://orcid.org/0000-0003-4724-6924"/>
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15 <person givenName="Eli" familyName="Chadwick" url="https://github.com/elichad" identifier="https://orcid.org/0000-0002-0035-6475"/>
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16 <person givenName="Patrick" familyName="Austin" url="https://github.com/patrick-austin" identifier="https://orcid.org/0000-0002-6279-7823"/>
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17 <organization url="https://muon-spectroscopy-computational-project.github.io/index.html" name="The Muon Spectroscopy Computational Project"/>
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18 </creator>
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19 <requirements>
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20 <requirement type="package" version="@PYMUONSUITE_VERSION@">pymuonsuite</requirement>
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21 <requirement type="package" version="3.0">zip</requirement>
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22 </requirements>
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23 <required_files>
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24 <include type="literal" path="get_out_folder.py"/>
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25 <include type="literal" path="config.py"/>
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26 </required_files>
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27 <command detect_errors="exit_code"><![CDATA[
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28 unzip '$optimisation_results' &&
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29 if test -f "params.yaml"; then echo "params.yaml present"; else echo "params.yaml missing" && exit 64; fi
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30 && if ( test -f input_structure.* ) ; then echo "input structure present"; else echo "input structure missing" && exit 64; fi
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31 && out_folder="`python '${__tool_directory__}/get_out_folder.py'`"
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32 && python '${__tool_directory__}/config.py'
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33 && pm-muairss -t r input_structure.* params.yaml
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34 #if $clustering_save.clustering_save_format != "none":
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35 && ln -s *_clusters/* minimal_clusters
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36 #end if
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37 ]]></command>
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38 <configfiles>
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39 <configfile filename="incoming_params">clustering_method: $clustering.clustering_method
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40 #if $clustering.clustering_method == "hier":
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41 clustering_hier_t: $clustering.clustering_hier_t
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42 #else if $clustering.clustering_method == "kmeans":
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43 clustering_kmeans_k: $clustering.clustering_kmeans_k
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44 #end if
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45 #if $clustering_save.clustering_save_format != "none":
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46 clustering_save_type: structures
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47 clustering_save_format: $clustering_save.clustering_save_format
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48 supercell: $clustering_save.supercell.replace('__ob__', '[').replace('__cb__', ']')
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49 #if $clustering_save.clustering_save_format == "cell":
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50 mu_symbol: $clustering_save.mu_symbol
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51 #end if
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52 #end if</configfile>
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53 </configfiles>
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54 <inputs>
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55 <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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56 <conditional name="clustering">
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57 <param type="select" argument="clustering_method" display="radio" label="Clustering method" value="hier">
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58 <option value="hier">hierarchical</option>
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59 <option value="kmeans">k-means</option>
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60 </param>
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61 <when value="hier">
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62 <param type="float" argument="clustering_hier_t" value="0.3" min="0.0" optional="true" label="t parameter for hierarchical clustering"/>
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63 </when>
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64 <when value="kmeans">
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65 <param type="integer" argument="clustering_kmeans_k" value="4" min="0" optional="true" label="Number of clusters for k-means clustering"/>
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66 </when>
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67 </conditional>
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68 <conditional name="clustering_save">
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69 <param argument="clustering_save_format" type="select" label="Clustering Save Format" help="If set, for each cluster a structural file with the specified format will be generated, corresponding to the structure in the cluster with minimal energy.">
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70 <option value="none" selected="true">Do not generate</option>
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71 <option value="cell">CELL</option>
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72 <option value="cif">CIF</option>
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73 <option value="xyz">XYZ</option>
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74 </param>
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75 <when value="none"/>
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76 <when value="cell">
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77 <expand macro="supercell"/>
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78 <param argument="mu_symbol" type="text" value="H:mu" optional="true" label="Muon symbol" help="The symbol to use for the muon when writing out the CASTEP custom species. Should be a valid chemical symbol followed by `:`, then custom text."/>
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79 </when>
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80 <when value="cif">
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81 <expand macro="supercell"/>
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82 </when>
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83 <when value="xyz">
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84 <expand macro="supercell"/>
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85 </when>
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86 </conditional>
0
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87 </inputs>
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88 <outputs>
5
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89 <data label="Cluster report on ${on_string}" name="cluster_report" format="txt" from_work_dir="${out_folder}/*clusters.txt"/>
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90 <data label="Cluster data on ${on_string}" name="cluster_data" format="txt" from_work_dir="${out_folder}/*clusters.dat"/>
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91 <collection name="saved_structures" type="list" label="Minimal energy structures on ${on_string}" format="txt">
4
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92 <filter>clustering_save["clustering_save_format"] != "none"</filter>
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93 <discover_datasets pattern="__name_and_ext__" directory="minimal_clusters"/>
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94 </collection>
0
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95 </outputs>
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96 <tests>
2
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97 <test expect_num_outputs="2">
0
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98 <param name="optimisation_results" value="uep-out.zip" ftype="zip"/>
4
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99 <conditional name="clustering">
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100 <param name="clustering_hier_t" value="0.2"/>
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101 </conditional>
0
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102 <output name="cluster_report" file="clustout-uep.txt" ftype="txt" lines_diff="2"/>
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103 <output name="cluster_data" file="clustout-uep.dat" ftype="txt"/>
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104 </test>
4
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105 <test expect_num_outputs="3">
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106 <param name="optimisation_results" value="uep-out.zip" ftype="zip"/>
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107 <conditional name="clustering">
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108 <param name="clustering_hier_t" value="0.2"/>
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109 </conditional>
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110 <conditional name="clustering_save">
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111 <param name="clustering_save_format" value="cell"/>
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112 </conditional>
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113 <output name="cluster_report" file="clustout-uep.txt" ftype="txt" lines_diff="2"/>
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114 <output name="cluster_data" file="clustout-uep.dat" ftype="txt"/>
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115 <output_collection name="saved_structures" type="list" count="2"/>
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116 </test>
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117 <!-- Test optional save params -->
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118 <test expect_num_outputs="3">
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119 <param name="optimisation_results" value="uep-out.zip" ftype="zip"/>
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120 <conditional name="clustering">
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121 <param name="clustering_hier_t" value="0.2"/>
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122 </conditional>
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123 <conditional name="clustering_save">
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124 <param name="clustering_save_format" value="cell"/>
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125 <param name="supercell" value="2"/>
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126 <param name="mu_symbol" value="H:nu"/>
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127 </conditional>
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128 <output name="cluster_report" file="clustout-uep.txt" ftype="txt" lines_diff="2"/>
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129 <output name="cluster_data" file="clustout-uep.dat" ftype="txt"/>
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130 <output_collection name="saved_structures" type="list" count="2">
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131 <element name="Si_uep_min_cluster_1" file="Si_uep_min_cluster_1.cell"/>
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132 <element name="Si_uep_min_cluster_2" file="Si_uep_min_cluster_2.cell"/>
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133 </output_collection>
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134 </test>
2
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135 <test expect_num_outputs="2">
0
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136 <param name="optimisation_results" value="dftb-out.zip" ftype="zip"/>
4
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137 <conditional name="clustering">
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138 <param name="clustering_hier_t" value="0.2"/>
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139 </conditional>
0
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140 <output name="cluster_report" file="clustout-dftb.txt" ftype="txt" lines_diff="2"/>
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141 <output name="cluster_data" file="clustout-dftb.dat" ftype="txt"/>
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142 </test>
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143 <!-- Test overwrite of values in the existing params.yaml -->
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144 <test expect_num_outputs="2">
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145 <param name="optimisation_results" value="uep-out.zip" ftype="zip"/>
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146 <conditional name="clustering">
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147 <param name="clustering_method" value="kmeans"/>
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148 <param name="clustering_kmeans_k" value="2"/>
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149 </conditional>
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150 <!-- kmeans gives predictable clusters, but orders them randomly -->
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151 <!-- To prevent this from affecting tests, sort the lines -->
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152 <!-- in the report and use regex matching for the dat file -->
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153 <output name="cluster_report" file="clustout-uep-kmeans.txt" ftype="txt" lines_diff="2" sort="true"/>
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154 <output name="cluster_data" file="clustout-uep-kmeans.dat" ftype="txt" compare="re_match"/>
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155 </test>
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156 </tests>
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157 <help><![CDATA[
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158 Given a set of optimised muonated structures, clusters the structures based on similarity.
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159
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160 This is intended to be used with the output from '`PyMuonSuite AIRSS UEP Optimise`_'.
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161 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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162 If you are bringing files from elsewhere (such as running PyMuonSuite from the command line, or with a different optimisation calculator), make sure they fit the expected zip folder structure:
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163
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164 .. code-block::
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165
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166 optimised-structures.zip/
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167 ├─ muon-airss-out/
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168 │ ├─ uep/
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169 │ │ ├─ struct_1/
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170 │ │ │ ├─ <files for optimised struct_1 go here>
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171 │ │ ├─ struct_2/
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172 │ │ │ ├─ <files for optimised struct_2 go here>
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173 │ │ ├─ struct_N/
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174 │ │ │ ├─ <files for optimised struct_N go here>
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175 ├─ input.cell
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176 ├─ params.yaml
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177
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178 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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179 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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180 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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181
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182 The files ``input.cell`` and ``params.yaml`` must have those exact names. ``input.cell`` should be your original structure file,
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183 and ``params.yaml`` is the YAML parameter file used to configure the muonation and optimisation.
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184 This file is created automatically when using '`PyMuonSuite AIRSS UEP Optimise`_'.
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185 Any parameters relating to the clustering process present in the original file will be overwritten with the values selected here.
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186
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187 Command-line usage: pm-muairss [-h] -t r structures parameter_file
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188
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189 .. _PyMuonSuite AIRSS UEP Optimise: /tool_runner?tool_id=pm_uep_opt
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190
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191 PyMuonSuite is distributed under the GPLv3 license. This tool wrapper is distributed under the MIT license.
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192 ]]></help>
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193 <citations>
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194 <citation type="doi">@PYMUONSUITE_CITATION@</citation>
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195 <citation type="doi">10.1063/1.5024450</citation>
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196 <citation type="doi">10.1063/1.5085197</citation>
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197 <citation type="doi">10.1063/5.0012381</citation>
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198 <citation type="bibtex">
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199 @article {castep,
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200 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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201 title = {First principles methods using CASTEP},
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202 journal = {Zeitschrift fuer Kristallographie},
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203 volume = {220},
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204 pages = {567},
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205 year = {2005}
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206 }
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207 </citation>
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208 </citations>
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209 </tool>