Mercurial > repos > muon-spectroscopy-computational-project > pm_muairss_read
annotate pm_muairss_read.xml @ 3:276a25ab05f2 draft
planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_muairss_read commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507
author | muon-spectroscopy-computational-project |
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date | Fri, 03 Feb 2023 15:39:29 +0000 |
parents | eb6382889b92 |
children | 40071ff77285 |
rev | line source |
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276a25ab05f2
planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_muairss_read commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507
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1 <tool id="pm_muairss_read" name="PyMuonSuite AIRSS Cluster" version="@TOOL_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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planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_muairss_read commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
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4 <!-- version of underlying tool (PEP 440) --> |
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planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_muairss_read commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507
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5 <token name="@TOOL_VERSION@">0.2.3</token> |
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planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_muairss_read commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
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6 <!-- version of this tool wrapper (integer) --> |
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planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_muairss_read commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507
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7 <token name="@WRAPPER_VERSION@">0</token> |
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planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_muairss_read commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
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8 <!-- citation should be updated with every underlying tool version --> |
49b6d76139da
planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_muairss_read commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
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9 <!-- typical fields to update are version, month, year, and doi --> |
49b6d76139da
planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_muairss_read commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
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10 <token name="@TOOL_CITATION@"> |
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planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_muairss_read commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507
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11 @software{Sturniolo_pymuon-suite_2022, |
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planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_muairss_read commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507
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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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planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_muairss_read commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
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13 license = {GPL-3.0}, |
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planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_muairss_read commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507
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14 month = {8}, |
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49b6d76139da
planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_muairss_read commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
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15 title = {{pymuon-suite}}, |
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planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_muairss_read commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
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16 url = {https://github.com/muon-spectroscopy-computational-project/pymuon-suite}, |
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planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_muairss_read commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507
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17 version = {v0.2.3}, |
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planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_muairss_read commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507
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18 doi = {10.5281/zenodo.7025644}, |
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planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_muairss_read commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507
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19 year = {2022} |
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planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_muairss_read commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
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20 } |
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planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_muairss_read commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
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21 </token> |
49b6d76139da
planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_muairss_read commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
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22 </macros> |
49b6d76139da
planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_muairss_read commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
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23 <creator> |
49b6d76139da
planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_muairss_read commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
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24 <person givenName="Jyothish" familyName="Thomas" identifier="https://orcid.org/0000-0003-4724-6924"/> |
49b6d76139da
planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_muairss_read commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
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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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planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_muairss_read 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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planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_muairss_read commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
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27 </creator> |
49b6d76139da
planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_muairss_read commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
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28 <requirements> |
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planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_muairss_read commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
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29 <requirement type="package" version="@TOOL_VERSION@">pymuonsuite</requirement> |
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30 </requirements> |
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31 <required_files> |
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32 <include type="literal" path="get_out_folder.py"/> |
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planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_muairss_read commit 1f0d5da860dd5cd0ffceac7a292773ed53617324
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33 </required_files> |
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planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_muairss_read commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
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34 <command detect_errors="exit_code"><![CDATA[ |
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35 unzip '$optimisation_results' && |
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36 if test -f "params.yaml"; then echo "params.yaml present"; else echo "params.yaml missing" && exit 64; fi |
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37 && if ( test -f input_structure.* ) ; then echo "input structure present"; else echo "input structure missing" && exit 64; fi |
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38 && out_folder="`python '${__tool_directory__}/get_out_folder.py'`" && |
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39 pm-muairss -t r input_structure.* params.yaml |
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40 ]]></command> |
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41 <inputs> |
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42 <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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43 </inputs> |
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44 <outputs> |
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45 <data label="Cluster report for $optimisation_results.name" name="cluster_report" format="txt" from_work_dir="${out_folder}/*clusters.txt"/> |
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46 <data label="Cluster data for $optimisation_results.name" name="cluster_data" format="txt" from_work_dir="${out_folder}/*clusters.dat"/> |
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47 </outputs> |
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48 <tests> |
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49 <test expect_num_outputs="2"> |
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50 <param name="optimisation_results" value="uep-out.zip" ftype="zip"/> |
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51 <output name="cluster_report" file="clustout-uep.txt" ftype="txt" lines_diff="2"/> |
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52 <output name="cluster_data" file="clustout-uep.dat" ftype="txt"/> |
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53 </test> |
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54 <test expect_num_outputs="2"> |
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55 <param name="optimisation_results" value="dftb-out.zip" ftype="zip"/> |
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56 <output name="cluster_report" file="clustout-dftb.txt" ftype="txt" lines_diff="2"/> |
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57 <output name="cluster_data" file="clustout-dftb.dat" ftype="txt"/> |
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58 </test> |
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59 </tests> |
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60 <help><![CDATA[ |
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61 Given a set of optimised muonated structures, clusters the structures based on similarity. |
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62 |
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63 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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64 If you are bringing files from elsewhere, make sure they fit the expected zip folder structure: |
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65 |
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66 .. code-block:: |
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67 |
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68 optimised-structures.zip/ |
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69 ├─ muon-airss-out/ |
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70 │ ├─ uep/ |
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71 │ │ ├─ struct_1/ |
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72 │ │ │ ├─ <files for optimised struct_1 go here> |
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73 │ │ ├─ struct_2/ |
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74 │ │ │ ├─ <files for optimised struct_2 go here> |
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75 │ │ ├─ struct_N/ |
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76 │ │ │ ├─ <files for optimised struct_N go here> |
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77 ├─ input.cell |
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78 ├─ params.yaml |
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79 |
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80 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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81 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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82 |
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83 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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84 |
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85 The files ``input.cell`` and ``params.yaml`` must have those exact names. ``input.cell`` should be your original structure file, |
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86 and ``params.yaml`` is the YAML parameter file used to configure the clustering (as well as any prior muonation and optimisation). |
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87 You should have created this YAML file using the 'Create YAML for pm-muairss' tool or written it yourself, then passed it into the |
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88 'Generate muon structures' tool or pm-muairss. |
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89 |
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90 Command-line usage: pm-muairss [-h] -t r structures parameter_file |
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91 |
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92 PyMuonSuite is distributed under the GPLv3 license. This tool wrapper is distributed under the MIT license. |
0
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93 ]]></help> |
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94 <citations> |
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95 <citation type="bibtex"> |
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96 @TOOL_CITATION@ |
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97 </citation> |
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98 <citation type="doi">10.1063/1.5024450</citation> |
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99 <citation type="doi">10.1063/1.5085197</citation> |
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100 <citation type="doi">10.1063/5.0012381</citation> |
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101 <citation type="bibtex"> |
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102 @article {castep, |
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103 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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104 title = {First principles methods using CASTEP}, |
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105 journal = {Zeitschrift fuer Kristallographie}, |
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106 volume = {220}, |
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107 pages = {567}, |
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108 year = {2005} |
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109 } |
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110 </citation> |
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111 </citations> |
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112 </tool> |