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planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_asephonons commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507
author muon-spectroscopy-computational-project
date Fri, 03 Feb 2023 15:39:17 +0000
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children fd28cbdb134e
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dd3ca8457fcd planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_asephonons commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507
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1 <tool id="pm_asephonons" name="PyMuonSuite Phonons" version="@TOOL_VERSION@+galaxy@WRAPPER_VERSION@" python_template_version="3.5" profile="22.05" license="MIT">
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2 <description>calculate phonons using ASE and DFTB+</description>
4bc5e66259ca planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_asephonons commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
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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) -->
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7 <token name="@WRAPPER_VERSION@">0</token>
0
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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},
0
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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}
0
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20 }
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21 </token>
2
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22 <import>muon_macros.xml</import>
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23 </macros>
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24 <creator>
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25 <person givenName="Jyothish" familyName="Thomas" identifier="https://orcid.org/0000-0003-4724-6924"/>
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26 <person givenName="Eli" familyName="Chadwick" url="https://github.com/elichad" identifier="https://orcid.org/0000-0002-0035-6475"/>
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27 <organization url="https://muon-spectroscopy-computational-project.github.io/index.html" name="The Muon Spectroscopy Computational Project"/>
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28 </creator>
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29 <requirements>
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30 <!-- note versioning is different due to multiple dependencies -->
2
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31 <requirement type="package" version="@TOOL_VERSION@">pymuonsuite</requirement>
0
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32 <requirement type="package" version="21.2">dftbplus</requirement>
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33 <requirement type="package" version="1.22.4">numpy</requirement> <!-- pinned due to numpy/ASE/DFTB+ incompatibility https://github.com/dftbplus/dftbplus/issues/1064 -->
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34 <requirement type="package" version="3.0">zip</requirement>
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35 </requirements>
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36 <command detect_errors="exit_code"><![CDATA[
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37 structure_name_internal='input_structure.$pbc.structure.ext' &&
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38 ln -s '$pho_params' pho_params.yaml &&
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39 ln -s '$pbc.structure' \$structure_name_internal &&
0
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40 cat pho_params.yaml &&
2
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41 err=0 &&
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42 pm-asephonons \$structure_name_internal pho_params.yaml || err=\$? &&
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43 echo "Asephonons output:" &&
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44 cat asephonons.out &&
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45 if [ \$err != 0 ] ; then echo "errored" && exit 24 ; fi &&
2
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46 ln -s '${name}_phonons.txt' phonon_report.txt &&
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47 zip -r out_zip.zip '$name' '${name}_phonons.txt' asephonons.out band.out pho_params.yaml
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48 ]]></command>
2
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49 <configfiles>
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50 <configfile name="pho_params">name: $name
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51 phonon_kpoint_grid: $phonon_kpoint_grid.replace('__ob__', '[').replace('__cb__', ']')
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52 kpoint_grid: $kpoint_grid.replace('__ob__', '[').replace('__cb__', ']')
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53 force_tol: $force_tol
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54 dftb_set: $dftb_set
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55 pbc: $pbc.pbc
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56 force_clean: false</configfile>
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57 </configfiles>
0
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58 <inputs>
2
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59 <param argument="name" type="text" value="struct" label="Structure name" help="Name of the structure."/>
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60 <param argument="phonon_kpoint_grid" type="text" value="[1, 1, 1]" label="Phonon k-points">
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61 <validator type="regex" message="Input should only contain whitespace, '[', ']', ',' and digits.">^[\s\d,\[\]]+$</validator>
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62 </param>
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63 <param argument="kpoint_grid" type="text" value="[1, 1, 1]" label="K-points used for DFTB+ calculation">
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64 <validator type="regex" message="Input should only contain whitespace, '[', ']', ',' and digits.">^[\s\d,\[\]]+$</validator>
0
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65 </param>
2
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66 <param argument="force_tol" type="float" min="0.0" value="0.01" label="Force tolerance for optimisation"/>
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67 <expand macro="dftb_set"/>
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68 <conditional name="pbc">
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69 <param argument="pbc" type="select" display="radio" multiple="false" label="Use periodic boundary conditions (PBC)" help="Whether to turn on PBC conditions in DFTB+. Note that XYZ files cannot be used with PBC.">
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70 <option selected="true" value="true">Yes</option>
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71 <option value="false">No</option>
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72 </param>
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73 <when value="true">
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74 <param name="structure" type="data" format="cell, cif, extxyz" label="Structure file" help="The structure to generate the phonon report from. Accepted file types: CELL, CIF, XYZ (extended ONLY)."/>
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75 </when>
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76 <when value="false">
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77 <param name="structure" type="data" format="cell, cif, extxyz, xyz" label="Structure file" help="The structure to generate the phonon report from. Accepted file types: CELL, CIF, XYZ (standard or extended)."/>
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78 </when>
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79 </conditional>
0
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80 </inputs>
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81 <outputs>
2
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82 <data label="phonons outputs of $pbc.structure.name" name="phonon_outputs" format="zip" from_work_dir="out_zip.zip"/>
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83 <data label="phonon report for $pbc.structure.name" name="phonon_report" format="txt" from_work_dir="phonon_report.txt"/>
0
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84 </outputs>
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85 <tests>
1
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86 <test expect_num_outputs="2">
2
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87 <param name="name" value="Si"/>
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88 <param name="dftb_set" value="pbc-0-3"/>
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89 <conditional name="pbc">
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90 <param name="structure" value="Si.cell" ftype="cell"/>
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91 </conditional>
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92 <output name="phonon_report" file="test_out.txt" ftype="txt" compare="re_match">
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93 <assert_contents>
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94 <has_size value="8255" delta="20"/>
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95 </assert_contents>
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96 </output>
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97 </test>
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98 <test expect_num_outputs="2">
0
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99 <param name="name" value="Si"/>
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100 <param name="dftb_set" value="pbc-0-3"/>
2
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101 <conditional name="pbc">
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102 <param name="structure" value="Si.cif" ftype="cif"/>
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103 </conditional>
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104 <output name="phonon_report" file="test_out.txt" ftype="txt" compare="re_match">
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105 <assert_contents>
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106 <has_size value="8255" delta="20"/>
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107 </assert_contents>
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108 </output>
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109 </test>
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110 <test expect_num_outputs="2">
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111 <param name="name" value="Si"/>
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112 <param name="dftb_set" value="pbc-0-3"/>
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113 <conditional name="pbc">
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114 <param name="pbc" value="false"/>
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115 <param name="structure" value="Si.xyz" ftype="xyz"/>
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116 </conditional>
0
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117 <output name="phonon_report" file="test_out.txt" ftype="txt" compare="re_match">
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118 <assert_contents>
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119 <has_size value="8155" delta="20"/>
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120 </assert_contents>
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121 </output>
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122 </test>
1
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123 <test expect_num_outputs="2">
0
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124 <param name="name" value="Si"/>
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125 <param name="dftb_set" value="pbc-0-3"/>
2
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126 <conditional name="pbc">
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127 <param name="structure" value="Si.extxyz" ftype="extxyz"/>
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128 </conditional>
0
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129 <output name="phonon_report" file="test_out.txt" ftype="txt" compare="re_match">
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130 <assert_contents>
2
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131 <has_size value="8255" delta="20"/>
0
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132 </assert_contents>
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133 </output>
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134 </test>
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135 </tests>
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136 <help><![CDATA[
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137 usage: pm-asephonons structure params
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138
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139 Given an input structure, this tool generates a phonon report for that structure using the parameters provided.
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140
2
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141 PyMuonSuite is distributed under the GPLv3 license. This tool wrapper is distributed under the MIT license.
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142
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143 All data is licensed under the Creative Commons Attribution-ShareAlike 4.0
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144 International License. The full text of the license can be found at:
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145
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146 https://creativecommons.org/licenses/by-sa/4.0/legalcode
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147
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148 For specific data sets remember to cite the following papers, by element :
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149
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150 | **3-ob-1**
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151
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152 +--------------+------------------------------------------------+-----------------------------------+------------------------------------+
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153 | [JCTC2013] | \ J. Chem. Theory Comput., 2013, 9, 338-354. | (O, N, C, H) | https://doi.org/10.1021/ct300849w |
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154 +--------------+------------------------------------------------+-----------------------------------+------------------------------------+
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155 | [JCTC2014] | \ J. Chem. Theory Comput., 2014, 10, 1518-1537.| (P,S-\*) | https://doi.org/10.1021/ct401002w |
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156 +--------------+------------------------------------------------+-----------------------------------+------------------------------------+
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157 | [JCTC2015-1] | \ J. Phys. Chem. B, 2015, 119, 1062-1082. | (Mg,Zn-\*) | https://doi.org/10.1021/jp506557r |
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158 +--------------+------------------------------------------------+-----------------------------------+------------------------------------+
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159 | [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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160 +--------------+------------------------------------------------+-----------------------------------+------------------------------------+
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161
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162 |
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163 | **pbc-0-3**
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164
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165 +------------+--------------------------------------------------------------------------------------------+---------+------------------------------------------------+
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166 | [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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167 +------------+--------------------------------------------------------------------------------------------+---------+------------------------------------------------+
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168 | [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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169 +------------+--------------------------------------------------------------------------------------------+---------+------------------------------------------------+
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170 | [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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171 +------------+--------------------------------------------------------------------------------------------+---------+------------------------------------------------+
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172 | [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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173 +------------+--------------------------------------------------------------------------------------------+---------+------------------------------------------------+
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174 | [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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175 +------------+--------------------------------------------------------------------------------------------+---------+------------------------------------------------+
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176 | [SiSi] | \ A. Sieck, PhD. Thesis, University of Paderborn, 2000. | (Si-Si) | https://www.osti.gov/etdeweb/biblio/20249635 |
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177 +------------+--------------------------------------------------------------------------------------------+---------+------------------------------------------------+
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178
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179 |
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180 | The full sets and all other data can be found at the following URLs:
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181
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182 +----------+------------------------------------------------------------+
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183 | 3-ob-1 | https://www.dftb.org/parameters/download/3ob/3ob-3-1-cc/ |
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184 +----------+------------------------------------------------------------+
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185 | pbc-0-3 | https://www.dftb.org/parameters/download/pbc/pbc-0-3-cc/ |
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186 +----------+------------------------------------------------------------+
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187
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188 |
0
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189 ]]></help>
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190 <citations>
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191 <citation type="bibtex">
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192 @PYMUONSUITE_CITATION@
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193 </citation>
2
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194 <citation type="doi">10.1063/1.5085197</citation>
0
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195 <citation type="bibtex">
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196 @article{larsen2017atomic,
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197 title={The atomic simulation environment—a Python library for working with atoms},
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198 author={Larsen, Ask Hjorth and Mortensen, Jens J{\o}rgen and Blomqvist, Jakob and Castelli, Ivano E and Christensen, Rune and Du{\l}ak, Marcin and Friis, Jesper and Groves, Michael N and Hammer, Bj{\o}rk and Hargus, Cory and others},
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199 journal={Journal of Physics: Condensed Matter},
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200 volume={29},
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201 number={27},
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202 pages={273002},
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203 year={2017},
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204 publisher={IOP Publishing}
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205 }
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206 </citation>
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207 </citations>
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208 </tool>