annotate pm_uep_opt.xml @ 4:ec5f6b22417c draft

planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_uep_opt commit 70a4d37ecdf5d586703cfc509922311e95d3205c
author muon-spectroscopy-computational-project
date Tue, 18 Jul 2023 13:27:15 +0000
parents 523d44fcd03f
children eea73e1f65cb
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1 <tool id="pm_uep_opt" name="PyMuonSuite AIRSS UEP Optimise" version="@PYMUONSUITE_VERSION@+galaxy@WRAPPER_VERSION@" python_template_version="3.5" profile="22.05" license="MIT">
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2 <description>run UEP optimisation</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@">0</token>
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6 <import>muon_macros.xml</import>
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7 </macros>
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8 <creator>
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9 <person givenName="Jyothish" familyName="Thomas" identifier="https://orcid.org/0000-0003-4724-6924"/>
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10 <person givenName="Eli" familyName="Chadwick" url="https://github.com/elichad" identifier="https://orcid.org/0000-0002-0035-6475"/>
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11 <person givenName="Patrick" familyName="Austin" url="https://github.com/patrick-austin" identifier="https://orcid.org/0000-0002-6279-7823"/>
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12 <organization url="https://muon-spectroscopy-computational-project.github.io/index.html" name="The Muon Spectroscopy Computational Project"/>
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13 </creator>
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14 <requirements>
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15 <requirement type="package" version="@PYMUONSUITE_VERSION@">pymuonsuite</requirement>
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16 <requirement type="package" version="3.0">zip</requirement>
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17 </requirements>
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18 <required_files>
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19 <include type="literal" path="run.sh"/>
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20 <include type="literal" path="get_out_folder.py"/>
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21 </required_files>
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22 <command detect_errors="exit_code"><![CDATA[
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23 cat $params_yaml > params.yaml &&
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24 structure_name_internal='input_structure.$structure.ext' &&
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25 ln -s '$structure' \$structure_name_internal &&
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26 pm-muairss -t w \$structure_name_internal params.yaml &&
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27 #if $generation_params.allpos_ext != "none":
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28 mv allpos.$generation_params.allpos_ext $allpos_file &&
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29 #end if
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30 ln -s '$charge_density' input_structure.den_fmt &&
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31 ln -s '$castep_log' input_structure.castep &&
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32 out_folder="`python '${__tool_directory__}/get_out_folder.py'`" &&
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33 find \$out_folder -type f -name "*.yaml" | xargs sed -i "s#^chden_path: .*#chden_path: .\/#g" &&
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34 find \$out_folder -type f -name "*.yaml" | xargs sed -i "s#^chden_seed: .*#chden_seed: input_structure#g" &&
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35 bash '${__tool_directory__}/run.sh' \$out_folder &&
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36 zip -r out_zip.zip \$out_folder params.yaml \$structure_name_internal &&
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37 find \$out_folder > tree.txt
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38 ]]></command>
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39 <configfiles>
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40 <configfile name="params_yaml">poisson_r: $generation_params.poisson_r
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41 vdw_scale: $generation_params.vdw_scale
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42 #if $generation_params.random_seed:
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43 random_seed: $generation_params.random_seed
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44 #end if
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45 #if $generation_params.allpos_ext!="none":
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46 allpos_filename: allpos.$generation_params.allpos_ext
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47 #end if
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48 calculator: uep
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49 charged: true
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50 geom_steps: $optimisation_params.geom_steps
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51 geom_force_tol: $optimisation_params.geom_force_tol
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52 uep_gw_factor: $optimisation_params.uep_gw_factor</configfile>
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53 </configfiles>
0
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54 <inputs>
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55 <param type="data" name="structure" label="Structure file" format="cell, cif, extxyz" help="The structure to add muons to. The original file will be preserved. Accepted file types: CELL, CIF, XYZ (extended only)."/>
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56 <param type="data" name="charge_density" label="Charge density file (.den_fmt)" format="den_fmt" help="The charge density file created by CASTEP during your initial DFT simulation for the structure."/>
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57 <param type="data" name="castep_log" label="CASTEP log (.castep)" format="castep" help="The CASTEP log for your initial DFT simulation for the structure."/>
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58 <section name="generation_params" expanded="true" title="Generation Parameters">
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59 <param type="float" argument="poisson_r" value="0.8" min="0.0" label="Poisson radius" help=" Poisson sphere radius to use for random generation. No two starting muon positions will be closer than this distance. Smaller values make for bigger structure sets."/>
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60 <param type="float" argument="vdw_scale" value="0.5" min="0.0" label="Van der Waals scale" help="Van der Waals scaling factor to use when generating muon sites to avoid existing atoms. Smaller values will allow muons to get closer to the other ions."/>
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61 <param type="integer" argument="random_seed" label="Random Seed" optional="true" help="Seed used to randomise the positions of the muons in the generated structures."/>
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62 <param type="select" name="allpos_ext" value="none" label="Format for file containing all muon positions (optional)" help="If set, generates an extra output file containing all the muon positions using the specified file type.">
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63 <option value="none">Do not generate</option>
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64 <option value="cell">CELL</option>
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65 <option value="cif">CIF</option>
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66 <option value="xyz">XYZ</option>
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67 </param>
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68 </section>
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69 <section name="optimisation_params" expanded="true" title="Optimisation Parameters">
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70 <param type="integer" argument="geom_steps" value="30" min="0" label="Geometry optimization steps" help="Maximum number of geometry optimisation steps."/>
ec5f6b22417c planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_uep_opt commit 70a4d37ecdf5d586703cfc509922311e95d3205c
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71 <param type="float" argument="geom_force_tol" value="0.05" min="0.0" label="Geometry optimization tolerance" help="Tolerance on geometry optimisation in units of eV/Ã…."/>
ec5f6b22417c planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_uep_opt commit 70a4d37ecdf5d586703cfc509922311e95d3205c
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72 <param type="float" argument="uep_gw_factor" optional="true" value="5.0" min="0.0" label="Gaussian width factor" help="Gaussian width factor for UEP calculation. Higher values will make the potential of atomic nuclei closer to the point-like approximation but may introduce artifacts."/>
ec5f6b22417c planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_uep_opt commit 70a4d37ecdf5d586703cfc509922311e95d3205c
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73 </section>
0
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74 <param type="hidden" name="testing" label="Test mode" value="false"/>
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75 </inputs>
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76 <outputs>
4
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77 <data name="uep_results" format="zip" from_work_dir="out_zip.zip"/>
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78 <data label="File containing the positions of all muon sites" name="allpos_file" auto_format="true">
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79 <filter>(generation_params["allpos_ext"] != "none")</filter>
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80 </data>
0
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81 <data label="File tree (testing only)" name="file_tree" format="txt" from_work_dir="tree.txt" hidden="true">
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82 <filter>(testing == "true")</filter>
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83 </data>
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84 </outputs>
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85 <tests>
4
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86 <!-- UEP with CELL -->
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87 <test expect_num_outputs="3">
0
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88 <param name="testing" value="true"/>
4
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89 <param name="structure" value="Si.cell" ftype="cell"/>
3
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90 <param name="charge_density" value="Si.den_fmt" ftype="den_fmt"/>
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91 <param name="castep_log" value="Si.castep" ftype="castep"/>
4
ec5f6b22417c planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_uep_opt commit 70a4d37ecdf5d586703cfc509922311e95d3205c
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92 <section name="generation_params">
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93 <param name="poisson_r" value="1.18"/>
ec5f6b22417c planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_uep_opt commit 70a4d37ecdf5d586703cfc509922311e95d3205c
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94 <param name="vdw_scale" value="0.25"/>
ec5f6b22417c planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_uep_opt commit 70a4d37ecdf5d586703cfc509922311e95d3205c
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95 <param name="random_seed" value="7357"/>
ec5f6b22417c planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_uep_opt commit 70a4d37ecdf5d586703cfc509922311e95d3205c
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96 <param name="allpos_ext" value="cell"/>
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97 </section>
ec5f6b22417c planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_uep_opt commit 70a4d37ecdf5d586703cfc509922311e95d3205c
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98 <section name="optimisation_params">
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99 <param name="geom_steps" value="300"/>
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100 <param name="uep_gw_factor" value="4.0"/>
ec5f6b22417c planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_uep_opt commit 70a4d37ecdf5d586703cfc509922311e95d3205c
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101 </section>
ec5f6b22417c planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_uep_opt commit 70a4d37ecdf5d586703cfc509922311e95d3205c
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102 <output name="allpos_file" file="allpos.cell"/>
0
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103 <output name="file_tree" file="tree.txt" ftype="txt" sort="true">
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104 <assert_contents>
4
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105 <has_size value="3280"/>
0
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106 </assert_contents>
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107 </output>
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108 </test>
4
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109 <!-- UEP with XYZ -->
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110 <test expect_failure="true">
0
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111 <param name="testing" value="true"/>
4
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112 <param name="structure" value="Si.xyz" ftype="xyz"/>
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113 <param name="charge_density" value="Si.den_fmt" ftype="den_fmt"/>
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114 <param name="castep_log" value="Si.castep" ftype="castep"/>
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115 <section name="generation_params">
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116 <param name="poisson_r" value="1.18"/>
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117 <param name="vdw_scale" value="0.25"/>
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118 <param name="random_seed" value="7357"/>
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119 </section>
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120 <section name="optimisation_params">
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121 <param name="geom_steps" value="300"/>
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122 <param name="uep_gw_factor" value="4.0"/>
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123 </section>
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124 <assert_stderr>
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125 <has_text text="TypeError: cannot unpack non-iterable NoneType object"/>
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126 </assert_stderr>
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127 </test>
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128 <!-- UEP with extended XYZ -->
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129 <test expect_num_outputs="3">
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130 <param name="testing" value="true"/>
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131 <param name="structure" value="Si.extxyz" ftype="extxyz"/>
3
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132 <param name="charge_density" value="Si.den_fmt" ftype="den_fmt"/>
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133 <param name="castep_log" value="Si.castep" ftype="castep"/>
4
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134 <section name="generation_params">
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135 <param name="poisson_r" value="1.18"/>
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136 <param name="vdw_scale" value="0.25"/>
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137 <param name="random_seed" value="7357"/>
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138 <param name="allpos_ext" value="xyz"/>
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139 </section>
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140 <section name="optimisation_params">
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141 <param name="geom_steps" value="300"/>
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142 <param name="uep_gw_factor" value="4.0"/>
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143 </section>
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144 <output name="allpos_file" file="allpos.xyz"/>
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145 <output name="file_tree" file="tree.txt" ftype="txt" sort="true">
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146 <assert_contents>
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147 <has_size value="3280"/>
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148 </assert_contents>
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149 </output>
0
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150 </test>
4
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151 <!-- UEP with CIF -->
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152 <test expect_num_outputs="3">
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153 <param name="testing" value="true"/>
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154 <param name="structure" value="Si.cif" ftype="cif"/>
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155 <param name="charge_density" value="Si.den_fmt" ftype="den_fmt"/>
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156 <param name="castep_log" value="Si.castep" ftype="castep"/>
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157 <section name="generation_params">
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158 <param name="poisson_r" value="1.18"/>
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159 <param name="vdw_scale" value="0.25"/>
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160 <param name="random_seed" value="7357"/>
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161 <param name="allpos_ext" value="cif"/>
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162 </section>
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163 <section name="optimisation_params">
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164 <param name="geom_steps" value="300"/>
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165 <param name="uep_gw_factor" value="4.0"/>
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166 </section>
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167 <output name="allpos_file" file="allpos.cif"/>
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168 <output name="file_tree" file="tree.txt" ftype="txt" sort="true">
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169 <assert_contents>
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170 <has_size value="3280"/>
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171 </assert_contents>
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172 </output>
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173 </test>
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174 <!-- Expect total failure for badly formatted den_fmt -->
0
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175 <test expect_failure="true">
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176 <param name="testing" value="true"/>
4
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177 <param name="structure" value="Si.cell" ftype="cell"/>
3
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178 <param name="castep_log" value="Si.castep" ftype="castep"/>
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179 <param name="charge_density" value="Sifail.den_fmt" ftype="den_fmt"/>
0
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180 <assert_stderr>
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181 <has_text text="Error: FMT file has no header"/>
4
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182 <has_text text="ERROR: All optimisations failed"/>
0
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183 </assert_stderr>
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184 </test>
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185 <!-- check that file_tree filter works -->
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186 <test expect_num_outputs="1">
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187 <param name="testing" value="false"/>
4
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188 <param name="structure" value="Si.cell" ftype="cell"/>
3
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189 <param name="charge_density" value="Si.den_fmt" ftype="den_fmt"/>
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190 <param name="castep_log" value="Si.castep" ftype="castep"/>
4
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191 <section name="generation_params">
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192 <param name="poisson_r" value="1.18"/>
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193 <param name="vdw_scale" value="0.25"/>
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194 <param name="random_seed" value="7357"/>
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195 </section>
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196 <section name="optimisation_params">
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197 <param name="geom_steps" value="300"/>
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198 <param name="uep_gw_factor" value="4.0"/>
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199 </section>
3
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200 </test>
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201 <!-- Check that the chden parameters are set correctly when $charge_density.name does not have the .den_fmt extension -->
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202 <test expect_num_outputs="2">
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203 <param name="testing" value="true"/>
4
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204 <param name="structure" value="Si.cell" ftype="cell"/>
3
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205 <param name="charge_density" value="Si_den_fmt" ftype="den_fmt"/>
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206 <param name="castep_log" value="Si.castep" ftype="castep"/>
4
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207 <section name="generation_params">
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208 <param name="poisson_r" value="1.18"/>
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209 <param name="vdw_scale" value="0.25"/>
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210 <param name="random_seed" value="7357"/>
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211 </section>
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212 <section name="optimisation_params">
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213 <param name="geom_steps" value="300"/>
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214 <param name="uep_gw_factor" value="4.0"/>
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215 </section>
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216 <output name="file_tree" file="tree.txt" ftype="txt" sort="true">
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217 <assert_contents>
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218 <has_size value="3280"/>
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219 </assert_contents>
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220 </output>
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221 </test>
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222 </tests>
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223 <help><![CDATA[
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224 Given an input structure, this tool generates a set of duplicate structures,
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225 each with a single muon added in a random location.
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226 These are known as "muonated" structures.
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227 Following this, UEP optimisation is used to refine the positions of the muons.
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228
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229 This tool requires CASTEP inputs in order to perform the UEP method,
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230 meaning your initial DFT simulation must have been done with CASTEP.
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231 This simulation should have used the same structure as is used here.
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232
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233 Following this, the individual refined positions can be clustered to
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234 represent potential stopping sites by using '`PyMuonSuite AIRSS Cluster`_'.
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235
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236 Command-line usage (generation): pm-muairss [-h] -t w structures parameter_file
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237
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238 Command-line usage (optimisation): pm-uep-opt [-h] parameter_file
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239
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240 .. _PyMuonSuite AIRSS Cluster: /tool_runner?tool_id=pm_muairss_read
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241
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242 PyMuonSuite is distributed under the GPLv3 license.
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243 This tool wrapper is distributed under the MIT license.
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244 ]]></help>
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245 <citations>
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246 <citation type="doi">@PYMUONSUITE_CITATION@</citation>
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247 <citation type="doi">10.1063/1.5024450</citation>
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248 <citation type="doi">10.1063/1.5085197</citation>
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249 <citation type="doi">10.1063/5.0012381</citation>
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250 <citation type="bibtex">
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251 @article {castep,
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252 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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253 title = {First principles methods using CASTEP},
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254 journal = {Zeitschrift fuer Kristallographie},
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255 volume = {220},
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256 pages = {567},
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257 year = {2005}
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258 }
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259 </citation>
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260 </citations>
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261 </tool>