annotate pm_dftb_opt.xml @ 3:996f777bec11 draft default tip

planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_dftb_opt commit 389608650050596b28bc0c055de9f98c513a6f65
author muon-spectroscopy-computational-project
date Fri, 26 Jul 2024 12:57:29 +0000
parents 6a99165bb7ca
children
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1 <tool id="pm_dftb_opt" name="PyMuonSuite AIRSS DFTB+ Optimise" version="@TOOL_VERSION@+galaxy@WRAPPER_VERSION@" python_template_version="3.5" profile="22.05" license="MIT">
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2 <description>run DFTB+ optimisation</description>
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3 <macros>
2
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4 <!-- version of underlying tool (PEP 440) -->
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5 <token name="@TOOL_VERSION@">0.2.3</token>
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6 <!-- version of this tool wrapper (integer) -->
3
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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 -->
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9 <!-- typical fields to update are version, month, year, and doi -->
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10 <token name="@PYMUONSUITE_CITATION@">
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11 @software{Sturniolo_pymuon-suite_2022,
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12 author = {Sturniolo, Simone and Liborio, Leandro and Chadwick, Eli and Murgatroyd, Laura and Laverack, Adam and Mudaraddi, Anish and {Muon Spectroscopy Computational Project}},
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13 license = {GPL-3.0},
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14 month = {8},
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15 title = {{pymuon-suite}},
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16 url = {https://github.com/muon-spectroscopy-computational-project/pymuon-suite},
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17 version = {v0.2.3},
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18 doi = {10.5281/zenodo.7025644},
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19 year = {2022}
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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"/>
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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>
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28 <requirements>
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29 <!-- note versioning is different due to multiple dependencies -->
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30 <requirement type="package" version="21.2">dftbplus</requirement>
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31 <requirement type="package" version="@TOOL_VERSION@">pymuonsuite</requirement>
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32 <requirement type="package" version="3.0">zip</requirement>
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33 </requirements>
1
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34 <required_files>
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35 <include type="literal" path="get_out_folder.py"/>
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36 <include type="literal" path="run.sh"/>
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37 <include type="prefix" path="README-"/>
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38 </required_files>
0
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39 <command detect_errors="exit_code"><![CDATA[
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40 unzip '$muonated_structures' &&
0
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41 if test -f "params.yaml"; then echo "params.yaml present"; else echo "params.yaml missing" && exit 64; fi
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42 && if ( test -f input_structure.* ) ; then echo "input structure present"; else echo "input structure missing" && exit 64; fi
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43 && out_folder="`python '${__tool_directory__}/get_out_folder.py'`" ;
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44 bash '${__tool_directory__}/run.sh' \$out_folder ;
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45 passed=$? &&
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46 echo \$passed &&
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47 if [ \$passed == 2 ]; then echo "input file structure is not dftb" && exit 25; elif [ \$passed == 3 ]; then echo "error in parsing dftb file. check log for details" && exit 26; else echo "parse ok"; fi &&
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48 if grep -q 'pbc-0-3' params.yaml; then cp '${__tool_directory__}/README-pbc' \$out_folder/README; elif grep -q '3ob-3-1' params.yaml; then cp '${__tool_directory__}/README-3ob' \$out_folder README; else ( cp '${__tool_directory__}/README-3ob' \$out_folder README-3ob && cp '${__tool_directory__}/README-pbc' \$out_folder/README-pbc ); fi;
0
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49 zip -r dftb_results.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="hidden" name="testing" label="Test mode" value="false"/>
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55 </inputs>
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56 <outputs>
3
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57 <data label="DFTB results on ${on_string}" name="dftb_results" format="zip" from_work_dir="dftb_results.zip"/>
0
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58 <data label="File tree (testing only)" name="file_tree" format="txt" from_work_dir="tree.txt" hidden="true">
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59 <filter>(testing == "true")</filter>
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60 </data>
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61 </outputs>
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62 <tests>
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63 <test expect_num_outputs="2">
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64 <param name="testing" value="true"/>
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65 <param name="muonated_structures" value="muonated-dftb.zip" ftype="zip"/>
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66 <output name="file_tree" file="tree.txt" ftype="txt" sort="true"/>
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67 </test>
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68 <!-- check that file_tree filter works -->
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69 <test expect_num_outputs="1">
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70 <param name="testing" value="false"/>
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71 <param name="muonated_structures" value="muonated-dftb.zip" ftype="zip"/>
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72 </test>
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73 </tests>
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74 <help><![CDATA[
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75 usage: dftb+
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76 Given some input muonated structures (structures containing a muon), applies DFTB+ optimization to refine them.
2
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77
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78 PyMuonSuite is distributed under the GPLv3 license. This tool wrapper is distributed under the MIT license.
0
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79
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80 **LICENSE**
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81
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82 All data is licensed under the Creative Commons Attribution-ShareAlike 4.0
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83 International License. The full text of the license can be found at:
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84
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85 https://creativecommons.org/licenses/by-sa/4.0/legalcode
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86
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87 For specific data sets remember to cite the following papers, by element :
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88
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89 | **3-ob-1**
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90
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91
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92 +--------------+------------------------------------------------+-----------------------------------+------------------------------------+
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93 | [JCTC2013] | \ J. Chem. Theory Comput., 2013, 9, 338-354. | (O, N, C, H) | https://doi.org/10.1021/ct300849w |
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94 +--------------+------------------------------------------------+-----------------------------------+------------------------------------+
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95 | [JCTC2014] | \ J. Chem. Theory Comput., 2014, 10, 1518-1537.| (P,S-\*) | https://doi.org/10.1021/ct401002w |
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96 +--------------+------------------------------------------------+-----------------------------------+------------------------------------+
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97 | [JCTC2015-1] | \ J. Phys. Chem. B, 2015, 119, 1062-1082. | (Mg,Zn-\*) | https://doi.org/10.1021/jp506557r |
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98 +--------------+------------------------------------------------+-----------------------------------+------------------------------------+
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99 | [JCTC2015-2] | \ J. Chem. Theory Comput., 2015, 11, 332-342. | (Na,F,K,Ca,Cl,Br,I-\*) | https://doi.org/10.1021/ct5009137 |
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100 +--------------+------------------------------------------------+-----------------------------------+------------------------------------+
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101
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102 |
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103 | **pbc-0-3**
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104
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105 +------------+--------------------------------------------------------------------------------------------+---------+------------------------------------------------+
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106 | [SiC] | \ E. Rauls, R. Gutierrez, J. Elsner, and Th. Frauenheim, Sol. State Comm. 111, 459 (1999) | (Si-C) | https://doi.org/10.1016/S0038-1098(99)00137-4 |
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107 +------------+--------------------------------------------------------------------------------------------+---------+------------------------------------------------+
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108 | [SiO] | \ C. Koehler, Z. Hajnal, P. Deak, Th. Frauenheim, S. Suhai, Phys. Rev. B 64, 085333 (2001) | (Si-O) | https://doi.org/10.1103/PhysRevB.64.085333 |
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109 +------------+--------------------------------------------------------------------------------------------+---------+------------------------------------------------+
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110 | [Silicon] | \ A. Sieck, Th. Frauenheim, and K. A. Jackson, phys. stat. sol. (b) 240, 537 (2003). | (Si) | https://doi.org/10.1002/pssb.200301886 |
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111 +------------+--------------------------------------------------------------------------------------------+---------+------------------------------------------------+
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112 | [Fluorine] | \ C. Koehler and Th. Frauenheim, Surf. Sci. 600, 453 (2006). | \ (F) | https://doi.org/10.1016/j.susc.2005.10.044 |
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113 +------------+--------------------------------------------------------------------------------------------+---------+------------------------------------------------+
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114 | [Iron] | \ C. Koehler, G. Seifert and Th. Frauenheim, Chem. Phys. 309, 23 (2005). | (Fe) | https://doi.org/10.1016/j.chemphys.2004.03.034 |
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115 +------------+--------------------------------------------------------------------------------------------+---------+------------------------------------------------+
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116 | [SiSi] | \ A. Sieck, PhD. Thesis, University of Paderborn, 2000. | (Si-Si) | https://www.osti.gov/etdeweb/biblio/20249635 |
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117 +------------+--------------------------------------------------------------------------------------------+---------+------------------------------------------------+
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118
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119 |
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120 | The full sets and all other data can be found at the following URLs:
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121
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122 +----------+------------------------------------------------------------+
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123 | 3-ob-1 | https://www.dftb.org/parameters/download/3ob/3ob-3-1-cc/ |
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124 +----------+------------------------------------------------------------+
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125 | pbc-0-3 | https://www.dftb.org/parameters/download/pbc/pbc-0-3-cc/ |
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126 +----------+------------------------------------------------------------+
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127 ]]></help>
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128 <citations>
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129 <citation type="bibtex">
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130 @PYMUONSUITE_CITATION@
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131 </citation>
2
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132 <citation type="doi">10.1063/1.5143190</citation>
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133 </citations>
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134 </tool>