Mercurial > repos > muon-spectroscopy-computational-project > larch_feff
annotate larch_feff.xml @ 3:8ee492af5586 draft default tip
planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_feff commit 4814f53888643f1d3667789050914675fffb7d59
| author | muon-spectroscopy-computational-project |
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| date | Fri, 23 Aug 2024 14:10:38 +0000 |
| parents | a6bd21767730 |
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| rev | line source |
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edf7f8ccf4af
planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_feff commit 5be486890442dedfb327289d597e1c8110240735
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1 <tool id="larch_feff" name="Larch FEFF" version="@TOOL_VERSION@+galaxy@WRAPPER_VERSION@" python_template_version="3.5" profile="22.05" license="MIT"> |
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edf7f8ccf4af
planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_feff commit 5be486890442dedfb327289d597e1c8110240735
muon-spectroscopy-computational-project
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2 <description>generate FEFF paths from XAFS data</description> |
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edf7f8ccf4af
planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_feff commit 5be486890442dedfb327289d597e1c8110240735
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3 <macros> |
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edf7f8ccf4af
planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_feff commit 5be486890442dedfb327289d597e1c8110240735
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4 <!-- version of underlying tool (PEP 440) --> |
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3
8ee492af5586
planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_feff commit 4814f53888643f1d3667789050914675fffb7d59
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5 <token name="@TOOL_VERSION@">0.9.80</token> |
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edf7f8ccf4af
planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_feff commit 5be486890442dedfb327289d597e1c8110240735
muon-spectroscopy-computational-project
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6 <!-- version of this tool wrapper (integer) --> |
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edf7f8ccf4af
planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_feff commit 5be486890442dedfb327289d597e1c8110240735
muon-spectroscopy-computational-project
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7 <token name="@WRAPPER_VERSION@">0</token> |
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edf7f8ccf4af
planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_feff commit 5be486890442dedfb327289d597e1c8110240735
muon-spectroscopy-computational-project
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8 <!-- citation should be updated with every underlying tool version --> |
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edf7f8ccf4af
planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_feff commit 5be486890442dedfb327289d597e1c8110240735
muon-spectroscopy-computational-project
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9 <!-- typical fields to update are version, month, year, and doi --> |
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edf7f8ccf4af
planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_feff commit 5be486890442dedfb327289d597e1c8110240735
muon-spectroscopy-computational-project
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10 <token name="@TOOL_CITATION@">10.1088/1742-6596/430/1/012007</token> |
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edf7f8ccf4af
planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_feff commit 5be486890442dedfb327289d597e1c8110240735
muon-spectroscopy-computational-project
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11 </macros> |
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edf7f8ccf4af
planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_feff commit 5be486890442dedfb327289d597e1c8110240735
muon-spectroscopy-computational-project
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12 <creator> |
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edf7f8ccf4af
planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_feff commit 5be486890442dedfb327289d597e1c8110240735
muon-spectroscopy-computational-project
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13 <person givenName="Patrick" familyName="Austin" url="https://github.com/patrick-austin" identifier="https://orcid.org/0000-0002-6279-7823"/> |
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edf7f8ccf4af
planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_feff commit 5be486890442dedfb327289d597e1c8110240735
muon-spectroscopy-computational-project
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14 </creator> |
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edf7f8ccf4af
planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_feff commit 5be486890442dedfb327289d597e1c8110240735
muon-spectroscopy-computational-project
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15 <requirements> |
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edf7f8ccf4af
planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_feff commit 5be486890442dedfb327289d597e1c8110240735
muon-spectroscopy-computational-project
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16 <requirement type="package" version="@TOOL_VERSION@">xraylarch</requirement> |
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edf7f8ccf4af
planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_feff commit 5be486890442dedfb327289d597e1c8110240735
muon-spectroscopy-computational-project
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17 <requirement type="package" version="3.5.2">matplotlib</requirement> |
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edf7f8ccf4af
planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_feff commit 5be486890442dedfb327289d597e1c8110240735
muon-spectroscopy-computational-project
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18 <requirement type="package" version="3.0">zip</requirement> |
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edf7f8ccf4af
planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_feff commit 5be486890442dedfb327289d597e1c8110240735
muon-spectroscopy-computational-project
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19 </requirements> |
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edf7f8ccf4af
planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_feff commit 5be486890442dedfb327289d597e1c8110240735
muon-spectroscopy-computational-project
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20 <required_files> |
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edf7f8ccf4af
planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_feff commit 5be486890442dedfb327289d597e1c8110240735
muon-spectroscopy-computational-project
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21 <include type="literal" path="larch_feff.py"/> |
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edf7f8ccf4af
planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_feff commit 5be486890442dedfb327289d597e1c8110240735
muon-spectroscopy-computational-project
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22 </required_files> |
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edf7f8ccf4af
planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_feff commit 5be486890442dedfb327289d597e1c8110240735
muon-spectroscopy-computational-project
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23 <command detect_errors="exit_code"><![CDATA[ |
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edf7f8ccf4af
planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_feff commit 5be486890442dedfb327289d597e1c8110240735
muon-spectroscopy-computational-project
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24 python '${__tool_directory__}/larch_feff.py' '$format.structure_file' '$inputs' |
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edf7f8ccf4af
planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_feff commit 5be486890442dedfb327289d597e1c8110240735
muon-spectroscopy-computational-project
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25 && zip -r out.zip feff |
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edf7f8ccf4af
planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_feff commit 5be486890442dedfb327289d597e1c8110240735
muon-spectroscopy-computational-project
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26 ]]></command> |
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edf7f8ccf4af
planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_feff commit 5be486890442dedfb327289d597e1c8110240735
muon-spectroscopy-computational-project
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27 <configfiles> |
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edf7f8ccf4af
planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_feff commit 5be486890442dedfb327289d597e1c8110240735
muon-spectroscopy-computational-project
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28 <inputs name="inputs"/> |
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edf7f8ccf4af
planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_feff commit 5be486890442dedfb327289d597e1c8110240735
muon-spectroscopy-computational-project
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29 </configfiles> |
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edf7f8ccf4af
planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_feff commit 5be486890442dedfb327289d597e1c8110240735
muon-spectroscopy-computational-project
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30 <inputs> |
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edf7f8ccf4af
planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_feff commit 5be486890442dedfb327289d597e1c8110240735
muon-spectroscopy-computational-project
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31 <conditional name="format"> |
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edf7f8ccf4af
planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_feff commit 5be486890442dedfb327289d597e1c8110240735
muon-spectroscopy-computational-project
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32 <param name="format" type="select" display="radio" label="Structure file format"> |
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edf7f8ccf4af
planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_feff commit 5be486890442dedfb327289d597e1c8110240735
muon-spectroscopy-computational-project
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33 <option value="feff" selected="true">FEFF input</option> |
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edf7f8ccf4af
planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_feff commit 5be486890442dedfb327289d597e1c8110240735
muon-spectroscopy-computational-project
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34 <option value="cif">CIF</option> |
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edf7f8ccf4af
planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_feff commit 5be486890442dedfb327289d597e1c8110240735
muon-spectroscopy-computational-project
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35 </param> |
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edf7f8ccf4af
planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_feff commit 5be486890442dedfb327289d597e1c8110240735
muon-spectroscopy-computational-project
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36 <when value="feff"> |
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edf7f8ccf4af
planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_feff commit 5be486890442dedfb327289d597e1c8110240735
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37 <param name="structure_file" type="data" format="inp" label="Crystal structure file" help="Crystal structure file to be used for fitting, already in FEFF .inp format."/> |
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edf7f8ccf4af
planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_feff commit 5be486890442dedfb327289d597e1c8110240735
muon-spectroscopy-computational-project
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38 </when> |
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edf7f8ccf4af
planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_feff commit 5be486890442dedfb327289d597e1c8110240735
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39 <when value="cif"> |
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edf7f8ccf4af
planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_feff commit 5be486890442dedfb327289d597e1c8110240735
muon-spectroscopy-computational-project
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40 <param name="structure_file" type="data" format="cif" label="Crystal structure file" help="Crystal structure file to be used for fitting, in CIF format."/> |
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edf7f8ccf4af
planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_feff commit 5be486890442dedfb327289d597e1c8110240735
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41 <param name="absorbing_atom" type="text" value="0" label="Absorbing atom" help="Either the chemical symbol or index of the absorbing atom within the structure."/> |
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edf7f8ccf4af
planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_feff commit 5be486890442dedfb327289d597e1c8110240735
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42 <param name="radius" type="float" value="4.0" label="Radius" help="Atoms within this distance of the absorbing atom will be included in the FEFF calculation. Note that this must include at least one atom for each unique potential identified in the strucutre. Larger radii will lead to more potential scattering paths."/> |
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edf7f8ccf4af
planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_feff commit 5be486890442dedfb327289d597e1c8110240735
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43 </when> |
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edf7f8ccf4af
planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_feff commit 5be486890442dedfb327289d597e1c8110240735
muon-spectroscopy-computational-project
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44 </conditional> |
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planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_feff commit 5be486890442dedfb327289d597e1c8110240735
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45 </inputs> |
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planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_feff commit 5be486890442dedfb327289d597e1c8110240735
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46 <outputs> |
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planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_feff commit 5be486890442dedfb327289d597e1c8110240735
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47 <data name="out_csv" format="feff" from_work_dir="out.csv" label="CSV summary of ${format.structure_file.name}"/> |
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planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_feff commit 5be486890442dedfb327289d597e1c8110240735
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48 <data name="out_dir" format="zip" from_work_dir="out.zip" label="FEFF paths of ${format.structure_file.name}"/> |
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planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_feff commit 5be486890442dedfb327289d597e1c8110240735
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49 <data name="feff_inp" format="inp" from_work_dir="feff/feff.inp" label="FEFF input of ${format.structure_file.name}"> |
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planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_feff commit 5be486890442dedfb327289d597e1c8110240735
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50 <filter>format["format"]=="cif"</filter> |
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planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_feff commit 5be486890442dedfb327289d597e1c8110240735
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51 </data> |
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planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_feff commit 5be486890442dedfb327289d597e1c8110240735
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52 </outputs> |
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planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_feff commit 5be486890442dedfb327289d597e1c8110240735
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53 <tests> |
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planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_feff commit 0f66842e802430e887d1c6cb7be1cc5436408fd2
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54 <!-- 1: Test FEFF input --> |
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55 <test expect_num_outputs="2"> |
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planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_feff commit 5be486890442dedfb327289d597e1c8110240735
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56 <conditional name="format"> |
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planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_feff commit 5be486890442dedfb327289d597e1c8110240735
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57 <param name="format" value="feff"/> |
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planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_feff commit 5be486890442dedfb327289d597e1c8110240735
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58 <param name="structure_file" value="test.inp"/> |
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planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_feff commit 5be486890442dedfb327289d597e1c8110240735
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59 </conditional> |
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planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_feff commit 5be486890442dedfb327289d597e1c8110240735
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60 <output name="out_csv" file="[CSV_summary_of_test.inp].csv"/> |
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planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_feff commit 5be486890442dedfb327289d597e1c8110240735
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61 <output name="out_dir"> |
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planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_feff commit 5be486890442dedfb327289d597e1c8110240735
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62 <assert_contents> |
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planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_feff commit 5be486890442dedfb327289d597e1c8110240735
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63 <has_size value="276800" delta="100"/> |
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planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_feff commit 5be486890442dedfb327289d597e1c8110240735
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64 </assert_contents> |
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planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_feff commit 5be486890442dedfb327289d597e1c8110240735
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65 </output> |
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planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_feff commit 5be486890442dedfb327289d597e1c8110240735
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66 </test> |
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1
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planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_feff commit 0f66842e802430e887d1c6cb7be1cc5436408fd2
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67 <!-- 2: Test CIF input FeS2 --> |
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planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_feff commit 5be486890442dedfb327289d597e1c8110240735
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68 <test expect_num_outputs="3"> |
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planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_feff commit 5be486890442dedfb327289d597e1c8110240735
muon-spectroscopy-computational-project
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69 <conditional name="format"> |
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edf7f8ccf4af
planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_feff commit 5be486890442dedfb327289d597e1c8110240735
muon-spectroscopy-computational-project
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70 <param name="format" value="cif"/> |
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edf7f8ccf4af
planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_feff commit 5be486890442dedfb327289d597e1c8110240735
muon-spectroscopy-computational-project
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71 <param name="structure_file" value="1564889.cif"/> |
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edf7f8ccf4af
planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_feff commit 5be486890442dedfb327289d597e1c8110240735
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72 </conditional> |
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73 <output name="feff_inp" file="[FEFF_input_of_1564889.cif].txt"/> |
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74 <output name="out_csv" file="[CSV_summary_of_1564889.cif].csv"/> |
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75 <output name="out_dir"> |
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76 <assert_contents> |
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1
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77 <has_size value="88900" delta="100"/> |
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78 </assert_contents> |
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79 </output> |
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80 </test> |
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81 <!-- 3: Test CIF input FeS2 string species --> |
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82 <test expect_num_outputs="3"> |
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83 <conditional name="format"> |
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84 <param name="format" value="cif"/> |
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85 <param name="structure_file" value="1564889.cif"/> |
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86 <param name="absorbing_atom" value="Fe"/> |
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87 </conditional> |
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88 <output name="feff_inp" file="[FEFF_input_of_1564889.cif].txt"/> |
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89 <output name="out_csv" file="[CSV_summary_of_1564889.cif].csv"/> |
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90 <output name="out_dir"> |
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91 <assert_contents> |
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92 <has_size value="88900" delta="100"/> |
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93 </assert_contents> |
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94 </output> |
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95 </test> |
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96 <!-- 4: Test CIF input Pd --> |
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97 <test expect_num_outputs="3"> |
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98 <conditional name="format"> |
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99 <param name="format" value="cif"/> |
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100 <param name="structure_file" value="1627088.cif"/> |
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101 <param name="radius" value="5.0"/> |
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102 </conditional> |
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103 <output name="feff_inp" file="[FEFF_input_of_1627088.cif].txt"/> |
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104 <output name="out_csv" file="[CSV_summary_of_1627088.cif].csv"/> |
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105 <output name="out_dir"> |
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106 <assert_contents> |
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107 <has_size value="62500" delta="100"/> |
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108 </assert_contents> |
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109 </output> |
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110 </test> |
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111 <!-- 5: Test CIF input Pd string species --> |
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112 <test expect_num_outputs="3"> |
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113 <conditional name="format"> |
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114 <param name="format" value="cif"/> |
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115 <param name="structure_file" value="1627088.cif"/> |
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116 <param name="absorbing_atom" value="Pd"/> |
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117 <param name="radius" value="5.0"/> |
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118 </conditional> |
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119 <output name="feff_inp" file="[FEFF_input_of_1627088.cif].txt"/> |
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120 <output name="out_csv" file="[CSV_summary_of_1627088.cif].csv"/> |
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121 <output name="out_dir"> |
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122 <assert_contents> |
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123 <has_size value="62500" delta="100"/> |
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124 </assert_contents> |
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125 </output> |
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126 </test> |
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127 <!-- 6: Test CIF input Pd modified --> |
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128 <test expect_num_outputs="3"> |
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129 <conditional name="format"> |
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130 <param name="format" value="cif"/> |
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131 <param name="structure_file" value="1627088_modified.cif"/> |
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132 <param name="radius" value="5.0"/> |
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133 </conditional> |
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134 <output name="feff_inp" file="[FEFF_input_of_1627088_modified.cif].txt"/> |
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135 <output name="out_csv" file="[CSV_summary_of_1627088.cif].csv"/> |
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136 <output name="out_dir"> |
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137 <assert_contents> |
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138 <has_size value="62500" delta="100"/> |
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0
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139 </assert_contents> |
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140 </output> |
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141 </test> |
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1
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142 <!-- 7: Test CIF input Pd modified string species --> |
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143 <test expect_num_outputs="3"> |
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144 <conditional name="format"> |
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145 <param name="format" value="cif"/> |
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146 <param name="structure_file" value="1627088_modified.cif"/> |
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147 <param name="absorbing_atom" value="Pd"/> |
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148 <param name="radius" value="5.0"/> |
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149 </conditional> |
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150 <output name="feff_inp" file="[FEFF_input_of_1627088_modified.cif].txt"/> |
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151 <output name="out_csv" file="[CSV_summary_of_1627088.cif].csv"/> |
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152 <output name="out_dir"> |
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153 <assert_contents> |
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154 <has_size value="62500" delta="100"/> |
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155 </assert_contents> |
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156 </output> |
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157 </test> |
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158 <!-- 8: Test CIF input LaMnO3 --> |
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159 <test expect_num_outputs="3"> |
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160 <conditional name="format"> |
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161 <param name="format" value="cif"/> |
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162 <param name="structure_file" value="1667441.cif"/> |
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163 <param name="absorbing_atom" value="1"/> |
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164 <param name="radius" value="5.0"/> |
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165 </conditional> |
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166 <output name="feff_inp" file="[FEFF_input_of_1667441.cif].txt"/> |
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167 <output name="out_csv" file="[CSV_summary_of_1667441.cif].csv"/> |
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168 <output name="out_dir"> |
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169 <assert_contents> |
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170 <has_size value="142700" delta="100"/> |
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171 </assert_contents> |
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172 </output> |
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173 </test> |
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174 <!-- 9: Test CIF input LaMnO3 string species --> |
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175 <test expect_num_outputs="3"> |
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176 <conditional name="format"> |
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177 <param name="format" value="cif"/> |
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178 <param name="structure_file" value="1667441.cif"/> |
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179 <param name="absorbing_atom" value="Mn"/> |
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180 <param name="radius" value="5.0"/> |
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181 </conditional> |
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182 <output name="feff_inp" file="[FEFF_input_of_1667441.cif].txt"/> |
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183 <output name="out_csv" file="[CSV_summary_of_1667441.cif].csv"/> |
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184 <output name="out_dir"> |
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185 <assert_contents> |
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186 <has_size value="142700" delta="100"/> |
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187 </assert_contents> |
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188 </output> |
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189 </test> |
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190 <!-- 10: Test CIF input Cu --> |
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191 <test expect_num_outputs="3"> |
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192 <conditional name="format"> |
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193 <param name="format" value="cif"/> |
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194 <param name="structure_file" value="AMS_Cu.cif"/> |
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195 <param name="radius" value="5.0"/> |
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196 </conditional> |
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197 <output name="feff_inp" file="[FEFF_input_of_AMS_Cu.cif].txt"/> |
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198 <output name="out_csv" file="[CSV_summary_of_AMS_Cu.cif].csv"/> |
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199 <output name="out_dir"> |
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200 <assert_contents> |
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201 <has_size value="64300" delta="100"/> |
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202 </assert_contents> |
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203 </output> |
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204 </test> |
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205 <!-- 11: Test CIF input Cu string species --> |
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206 <test expect_num_outputs="3"> |
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207 <conditional name="format"> |
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208 <param name="format" value="cif"/> |
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209 <param name="structure_file" value="AMS_Cu.cif"/> |
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210 <param name="absorbing_atom" value="Cu"/> |
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211 <param name="radius" value="5.0"/> |
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212 </conditional> |
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213 <output name="feff_inp" file="[FEFF_input_of_AMS_Cu.cif].txt"/> |
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214 <output name="out_csv" file="[CSV_summary_of_AMS_Cu.cif].csv"/> |
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215 <output name="out_dir"> |
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216 <assert_contents> |
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217 <has_size value="64300" delta="100"/> |
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218 </assert_contents> |
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219 </output> |
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220 </test> |
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221 <!-- 12: Test CIF input failure with low radius --> |
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222 <test expect_failure="true"> |
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223 <conditional name="format"> |
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224 <param name="format" value="cif"/> |
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225 <param name="structure_file" value="1564889.cif"/> |
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226 <param name="absorbing_atom" value="S"/> |
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227 <param name="radius" value="0.1"/> |
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228 </conditional> |
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229 </test> |
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230 </tests> |
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231 <help><![CDATA[ |
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232 Runs a FEFF6 calculation to find potential scattering paths in the provided structure. |
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233 |
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234 If a ``cif`` file is used, the formatted FEFF ``inp`` file will be produced as an output that can be used again in the future. |
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235 Be aware that the choice of Absorbing atom and Radius will affect the success of the calculation, as all unique potentials must be represented in the final structure. |
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236 It is also possible that the ``cif`` file itself is not suitable, for example chemical symbols denoting ions (e.g. ``Fe2+``) are not supported. |
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237 ]]></help> |
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238 <citations> |
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239 <citation type="doi">@TOOL_CITATION@</citation> |
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240 <citation type="doi">10.1107/S0909049505012719</citation> |
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241 <citation type="doi">10.1016/j.commatsci.2012.10.028</citation> |
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242 </citations> |
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243 </tool> |