Mercurial > repos > muon-spectroscopy-computational-project > pm_yaml_config
annotate pm_yaml_config.xml @ 1:6f271bc31aa8 draft
planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit 6a07c4caed5ef35f35198d54ebafd7d1d6d60edb
| author | muon-spectroscopy-computational-project |
|---|---|
| date | Thu, 15 Sep 2022 10:26:07 +0000 |
| parents | ed74ddbf1e80 |
| children | 2d9b2ffec9d5 |
| rev | line source |
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ed74ddbf1e80
planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
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1 <tool id="pm_yaml_config" name="PyMuonSuite AIRSS Configure" version="@TOOL_VERSION@+galaxy@WRAPPER_VERSION@" python_template_version="3.5" profile="22.01"> |
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ed74ddbf1e80
planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
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2 <description>define AIRSS parameters</description> |
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ed74ddbf1e80
planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
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3 <macros> |
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ed74ddbf1e80
planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
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4 <!-- version of underlying tool (PEP 440) --> |
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ed74ddbf1e80
planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
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5 <!-- this wrapper doesn't have pymuonsuite as a dependency, but it will change according |
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ed74ddbf1e80
planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
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6 to the pymuonsuite interface, so follow the same versioning pattern --> |
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ed74ddbf1e80
planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
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7 <token name="@TOOL_VERSION@">0.2.1</token> |
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ed74ddbf1e80
planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
muon-spectroscopy-computational-project
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8 <!-- version of this tool wrapper (integer) --> |
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ed74ddbf1e80
planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
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9 <token name="@WRAPPER_VERSION@">0</token> |
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ed74ddbf1e80
planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
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10 <!-- citation should be updated with every underlying tool version --> |
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ed74ddbf1e80
planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
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11 <!-- typical fields to update are version, month, year, and doi --> |
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ed74ddbf1e80
planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
muon-spectroscopy-computational-project
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12 <token name="@TOOL_CITATION@"> |
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ed74ddbf1e80
planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
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13 @software{pymuon-suite, |
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ed74ddbf1e80
planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
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14 author = {Sturniolo, Simone and Liborio, Leandro and Chadwick, Eli and Murgatroyd, Laura and Laverack, Adam and {Muon Spectroscopy Computational Project}}, |
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ed74ddbf1e80
planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
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15 license = {GPL-3.0}, |
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ed74ddbf1e80
planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
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16 title = {{pymuon-suite}}, |
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ed74ddbf1e80
planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
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17 url = {https://github.com/muon-spectroscopy-computational-project/pymuon-suite}, |
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ed74ddbf1e80
planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
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18 version = {v0.2.1}, |
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ed74ddbf1e80
planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
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19 month = {2}, |
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ed74ddbf1e80
planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
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20 year = {2022}, |
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ed74ddbf1e80
planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
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21 doi = {} |
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ed74ddbf1e80
planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
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22 } |
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ed74ddbf1e80
planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
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23 </token> |
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ed74ddbf1e80
planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
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24 </macros> |
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ed74ddbf1e80
planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
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25 <creator> |
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ed74ddbf1e80
planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
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26 <person givenName="Jyothish" familyName="Thomas" identifier="https://orcid.org/0000-0003-4724-6924"/> |
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ed74ddbf1e80
planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
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27 <person givenName="Eli" familyName="Chadwick" url="https://github.com/elichad" identifier="https://orcid.org/0000-0002-0035-6475"/> |
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ed74ddbf1e80
planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
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28 <organization url="https://muon-spectroscopy-computational-project.github.io/index.html" name="The Muon Spectroscopy Computational Project"/> |
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ed74ddbf1e80
planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
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29 </creator> |
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ed74ddbf1e80
planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
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30 <requirements> |
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ed74ddbf1e80
planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
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31 </requirements> |
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ed74ddbf1e80
planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
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32 <command detect_errors="exit_code"><![CDATA[ |
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ed74ddbf1e80
planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
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33 touch outputx.yaml && |
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ed74ddbf1e80
planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
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34 ([[ ! -z "$general_params.poisson_r" ]] && printf "poisson_r: $general_params.poisson_r\n">>outputx.yaml || ( >&2 echo "poisson_r empty" && exit 2)) && |
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ed74ddbf1e80
planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
muon-spectroscopy-computational-project
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35 ([[ ! -z "$general_params.struct_name" ]] && printf "name: $general_params.struct_name\n">>outputx.yaml || ( >&2 echo "structure name is empty" && exit 2)) && |
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ed74ddbf1e80
planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
muon-spectroscopy-computational-project
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36 ([[ ! -z "$general_params.charged" ]] && printf "charged: $general_params.charged\n">>outputx.yaml || ( >&2 echo "charged muon empty" && exit 2)) && |
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ed74ddbf1e80
planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
muon-spectroscopy-computational-project
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37 ([[ ! -z "$general_params.geom_steps" ]] && printf "geom_steps: $general_params.geom_steps\n">>outputx.yaml || ( >&2 echo "geom_steps empty" && exit 2)) && |
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ed74ddbf1e80
planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
muon-spectroscopy-computational-project
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38 ([[ ! -z "$general_params.vdw_scale" ]] && printf "vdw_scale: $general_params.vdw_scale\n">>outputx.yaml || ( >&2 echo "vdw_scale empty" && exit 2)) && |
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ed74ddbf1e80
planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
muon-spectroscopy-computational-project
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39 ([[ ! -z "$calculator_params.calculator_cond.calculator" ]] && printf "calculator: $calculator_params.calculator_cond.calculator\n">>outputx.yaml || ( >&2 echo "calculator unselected" && exit 2)) && |
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ed74ddbf1e80
planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
muon-spectroscopy-computational-project
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40 ([[ ! -z "$general_params.geom_force_tol" ]] && printf "geom_force_tol: $general_params.geom_force_tol\n">>outputx.yaml || ( >&2 echo "geom_force_tol empty" && exit 2)) && |
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ed74ddbf1e80
planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
muon-spectroscopy-computational-project
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41 ([[ ! -z "$general_params.out_folder" ]] && printf "out_folder: $general_params.out_folder\n">>outputx.yaml || printf "out_folder: muon-airss-out\n">>outputx.yaml) && |
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ed74ddbf1e80
planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
muon-spectroscopy-computational-project
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42 ([[ ! -z "$general_params.random_seed" ]] && printf "random_seed: $general_params.random_seed\n">>outputx.yaml || ( echo "random_seed empty")) && |
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ed74ddbf1e80
planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
muon-spectroscopy-computational-project
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43 ([[ ! -z "$clustering_params.supercell" ]] && (printf "supercell: $clustering_params.supercell\n" | sed "s/__ob__/[/g" | sed "s/__cb__/]/g" )>>outputx.yaml || ( >&2 echo "supercell empty" && exit 2)) && |
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ed74ddbf1e80
planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
muon-spectroscopy-computational-project
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44 ([[ ! -z "$clustering_params.k_points_grid" ]] && (printf "k_points_grid: $clustering_params.k_points_grid\n" | sed "s/__ob__/[/g" | sed "s/__cb__/]/g" ) >>outputx.yaml || ( >&2 echo "k_points_grid empty" && exit 2)) && |
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ed74ddbf1e80
planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
muon-spectroscopy-computational-project
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45 ([[ ! -z "$clustering_params.max_scc_steps" ]] && printf "max_scc_steps: $clustering_params.max_scc_steps\n">>outputx.yaml || ( >&2 echo "max_scc_steps empty")) && |
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ed74ddbf1e80
planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
muon-spectroscopy-computational-project
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46 #if str($calculator_params.calculator_cond.calculator)=="uep": |
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ed74ddbf1e80
planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
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47 ([[ ! -z "$calculator_params.calculator_cond.uep_gw_factor" ]] && printf "uep_gw_factor: $calculator_params.calculator_cond.uep_gw_factor\n">>outputx.yaml || ( >&2 echo "uep gaussian width unset" && exit 2)) && |
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ed74ddbf1e80
planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
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48 ([[ ! -z "$calculator_params.calculator_cond.uep_chden" ]] && printf "uep_chden: $calculator_params.calculator_cond.uep_chden.value\n">>outputx.yaml || echo "den_fmt path unset") && |
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ed74ddbf1e80
planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
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49 #else if str($calculator_params.calculator_cond.calculator)=="CASTEP": |
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ed74ddbf1e80
planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
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50 ([[ ! -z "$calculator_params.calculator_cond.castep_command" ]] && printf "castep_command: $calculator_params.calculator_cond.castep_command\n">>outputx.yaml || echo "CASTEP command unset") && |
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ed74ddbf1e80
planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
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51 ([[ ! -z "$calculator_params.calculator_cond.castep_param" ]] && printf "castep_param: $calculator_params.calculator_cond.castep_param\n">>outputx.yaml || echo "CASTEP param unset") && |
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ed74ddbf1e80
planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
muon-spectroscopy-computational-project
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52 ([[ ! -z "$calculator_params.calculator_cond.mu_symbol" ]] && printf "mu_symbol: $calculator_params.calculator_cond.mu_symbol\n">>outputx.yaml || echo "mu symbol unset") && |
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ed74ddbf1e80
planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
muon-spectroscopy-computational-project
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53 #else if str($calculator_params.calculator_cond.calculator)=="dftb+": |
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ed74ddbf1e80
planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
muon-spectroscopy-computational-project
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54 ([[ ! -z "$calculator_params.calculator_cond.dftb_set" ]] && printf "dftb_set: $calculator_params.calculator_cond.dftb_set\n">>outputx.yaml || ( >&2 echo "dftb parameter set unselected" && exit 2)) && |
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ed74ddbf1e80
planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
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55 ([[ ! -z "$calculator_params.calculator_cond.dftb_pbc" ]] && printf "dftb_pbc: $calculator_params.calculator_cond.dftb_pbc\n">>outputx.yaml || echo "dftb periodic boundary condition unselected") && |
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ed74ddbf1e80
planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
muon-spectroscopy-computational-project
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56 #else if str($calculator_params.calculator_cond.calculator)=="all": |
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ed74ddbf1e80
planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
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57 ([[ ! -z "$calculator_params.calculator_cond.uep_gw_factor" ]] && printf "uep_gw_factor: $calculator_params.calculator_cond.uep_gw_factor\n">>outputx.yaml || echo "uep gaussian width unset") && |
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58 ([[ ! -z "$calculator_params.calculator_cond.uep_chden" ]] && printf "uep_chden: $calculator_params.calculator_cond.uep_chden\n">>outputx.yaml || echo "den_fmt path unset") && |
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planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
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59 ([[ ! -z "$calculator_params.calculator_cond.castep_command" ]] && printf "castep_command: $calculator_params.calculator_cond.castep_command\n">>outputx.yaml || echo "CASTEP command unset") && |
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planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
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60 ([[ ! -z "$calculator_params.calculator_cond.castep_param" ]] && printf "castep_param: $calculator_params.calculator_cond.castep_param\n">>outputx.yaml || echo "CASTEP param unset") && |
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planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
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61 ([[ ! -z "$calculator_params.calculator_cond.mu_symbol" ]] && printf "mu_symbol: $calculator_params.calculator_cond.mu_symbol\n">>outputx.yaml || echo "mu symbol unset") && |
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planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
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62 ([[ ! -z "$calculator_params.calculator_cond.mu_symbol" ]] && printf "dftb_set: $calculator_params.calculator_cond.dftb_set\n">>outputx.yaml || echo "dftb parameter set unselected") && |
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planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
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63 ([[ ! -z "$calculator_params.calculator_cond.dftb_pbc" ]] && printf "dftb_pbc: $calculator_params.calculator_cond.dftb_pbc\n">>outputx.yaml || echo "dftb periodic boundary condition unselected") && |
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planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
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64 #end if |
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65 ([[ ! -z "$clustering_params.clustering.clustering_method " ]] && printf "clustering_method: $clustering_params.clustering.clustering_method\n">>outputx.yaml || ( echo "clustering method unselected" && exit 2)) && |
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planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
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66 #if str($clustering_params.clustering.clustering_method)=="hier": |
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67 ([[ ! -z "$clustering_params.clustering.clustering_hier_t" ]] && printf "clustering_hier_t: $clustering_params.clustering.clustering_hier_t\n">>outputx.yaml || echo "clustering_hier_t unset") && |
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planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
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68 #else if str($clustering_params.clustering.clustering_method)=="kmeans": |
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planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
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69 ([[ ! -z "$clustering_params.clustering.clustering_kmeans_k" ]] && printf "clustering_kmeans_k: $clustering_params.clustering.clustering_kmeans_k\n">>outputx.yaml || echo "clustering_kmeans_k unset") && |
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planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
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70 #end if |
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71 ln -s outputx.yaml output.yaml |
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72 ]]></command> |
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73 <inputs> |
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74 <section name="general_params" expanded="true" title="General Parameters"> |
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75 <param type="float" name="poisson_r" argument="poisson_r" value="0.8" label="Poisson radius" help=" Poisson sphere radius to use for random generation. No two starting muon positions will be closer than this distance. Smaller values make for bigger structure sets."/> |
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76 <param type="text" argument="struct_name" name="struct_name" value="struct" label="Name" help="Name of the structure. This name will be postfixed with a unique number, e.g. struct_001 for each generated structure."/> |
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planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
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77 <param type="select" argument="charged" name="charged" label="Charged muon" value="true" help="If true, the muon will be considered charged instead of a muonium with an accompanying electron. Must be true for UEP calculations."> |
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ed74ddbf1e80
planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
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78 <option value="true">true</option> |
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planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
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79 <option value="false">false</option> |
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80 </param> |
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81 <param type="integer" argument="geom_steps" name="geom_steps" value="30" label="Geometry optimization steps" help="Maximum number of geometry optimisation steps."/> |
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82 <param type="float" argument="vdw_scale" name="vdw_scale" value="0.5" label="Van der Waals scale" help="Van der Waals scaling factor to use when generating muon sites to avoid existing atoms. Smaller values will allow muons to get closer to the other ions."/> |
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planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
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83 <param type="text" argument="out_folder" optional="true" name="out_folder" value="muon-airss-out" label="Output folder name" help="Name to call the output folder used to store the files that the script generates."/> |
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84 <param type="float" argument="geom_force_tol" name="geom_force_tol" value="0.05" label="Geometry optimization tolerance" help="Tolerance on geometry optimisation in units of eV/Å."/> |
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85 <param type="integer" argument="random_seed" name="random_seed" label="Random Seed" optional="true" help="Random seed for pymuonsuite."/> |
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86 </section> |
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87 <section name="calculator_params" expanded="true" title="Calculator parameters"> |
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88 <conditional name="calculator_cond"> |
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89 <param type="select" display="radio" label="Optimization calculator" argument="calculator" name="calculator" value="uep" help="Calculator to generate structure files for. Must be a single word or a comma seperated list of values. Currently supported calculators are CASTEP, DFTB+ and UEP. Can also select 'all' to generate files for all calculators."> |
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planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
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90 <option value="uep">UEP</option> |
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91 <option value="castep">CASTEP</option> |
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92 <option value="dftb+">DFTB+</option> |
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93 <option value="all">all</option> |
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94 </param> |
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95 <when value="uep"> |
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96 <param type="float" argument="uep_gw_factor" name="uep_gw_factor" optional="true" value="5.0" label="Gaussian width factor" help="Gaussian width factor for UEP calculation. Higher values will make the potential of atomic nuclei closer to the point-like approximation but may introduce artifacts."/> |
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planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
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97 <param type="text" argument="uep_chden" name="uep_chden" optional="true" label="Path to .den_fmt and .castep files" help="Name of the .den_fmt file containing the electronic density for an Unperturbed Electrostatic Potential optimisation. The corresponding .castep file must be with the same seedname. Only required for use outside Muon Galaxy"/> |
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98 </when> |
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99 <when value="castep"> |
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100 <param type="text" argument="castep_command" name="castep_command" optional="true" value="castep.serial" label="CASTEP command" help="Command to use to run CASTEP."/> |
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101 <param type="text" argument="castep_param" name="castep_param" optional="true" label="PARAM path" help="File path to the CASTEP parameter file."/> |
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102 <param type="text" argument="mu_symbol" name="mu_symbol" optional="true" label="Muon symbol" value="H:mu" help="The symbol to use for the muon when writing out the CASTEP custom species."/> |
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103 </when> |
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104 <when value="dftb+"> |
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105 <param type="select" argument="dftb_set" name="dftb_set" optional="true" value="3ob-3-1" label="DFTB parameter set" help="The parameter set to use for DFTB+. Currently supported are: 3ob-3-1 and pbc-0-3. See help section at the bottom of the page for details."> |
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106 <option value="3ob-3-1" selected="true">3ob-3-1</option> |
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107 <option value="pbc-0-3">pbc-0-3</option> |
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108 </param> |
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109 <param type="text" argument="dftb_optionals" name="dftb_optionals" value="[]" optional="true" label="DFTB optional files" help="Additional optional json files to activate for DFTBArgs (for example, dftd3.json will use DFTD3 dispersion forces for 3ob-3-1 if DFTB+ has been compiled to support them)."/> |
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110 <param type="select" argument="dftb_pbc" name="dftb_pbc" optional="true" value="true" label="Use periodic boundary conditions" help="Whether to turn on periodic boundary conditions in DFTB+."> |
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111 <option value="true" selected="true">true</option> |
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112 <option value="false">false</option> |
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113 </param> |
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114 </when> |
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115 <when value="all"> |
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116 <param type="float" argument="uep_gw_factor" name="uep_gw_factor" optional="true" value="5.0" label="Gaussian width factor" help="Gaussian width factor for UEP calculation. Higher values will make the potential of atomic nuclei closer to the point-like approximation but may introduce artifacts."/> |
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117 <param type="text" argument="uep_chden" name="uep_chden" optional="true" label="Path to .den_fmt and CASTEP files" help="Name of the .den_fmt file containing the electronic density for an Unperturbed Electrostatic Potential optimisation. The corresponding .castep file must be with the same seedname. Only required for use outside Muon Galaxy"/> |
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118 <param type="text" argument="castep_command" name="castep_command" optional="true" value="castep.serial" label="CASTEP command" help="Command to use to run CASTEP."/> |
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119 <param type="text" argument="castep_param" name="castep_param" optional="true" label="PARAM path" help="File path to the CASTEP parameter file."/> |
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120 <param type="text" argument="mu_symbol" name="mu_symbol" optional="true" label="Muon symbol" value="H:mu" help="The symbol to use for the muon when writing out the CASTEP custom species."/> |
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121 <param type="select" argument="dftb_set" name="dftb_set" optional="true" value="3ob-3-1" label="DFTB parameter set" help="The parameter set to use for DFTB+. Currently supported are: 3ob-3-1 and pbc-0-3. See help section at the bottom of the page for details."> |
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122 <option value="3ob-3-1" selected="true">3ob-3-1</option> |
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123 <option value="pbc-0-3">pbc-0-3</option> |
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124 </param> |
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125 <param type="text" argument="dftb_optionals" name="dftb_optionals" value="[]" optional="true" label="DFTB optional files" help="Additional optional json files to activate for DFTBArgs (for example, dftd3.json will use DFTD3 dispersion forces for 3ob-3-1 if DFTB+ has been compiled to support them)."/> |
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126 <param type="select" argument="dftb_pbc" name="dftb_pbc" optional="true" value="true" label="Use periodic boundary conditions" help="Whether to turn on periodic boundary conditions in DFTB+."> |
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127 <option value="true" selected="true">true</option> |
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128 <option value="false">false</option> |
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129 </param> |
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130 </when> |
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131 </conditional> |
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132 </section> |
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133 <section name="clustering_params" expanded="true" title="Clustering Parameters"> |
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134 <conditional name="clustering"> |
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135 <param type="select" argument="clustering_method" name="clustering_method" label="Clustering method" value="hier"> |
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136 <option value="hier">hierarchical</option> |
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137 <option value="kmeans">k-means</option> |
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138 </param> |
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139 <when value="hier"> |
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140 <param type="float" argument="clustering_hier_t" name="clustering_hier_t" value="0.3" optional="true" label="t parameter for hierarchical clustering"/> |
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141 </when> |
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142 <when value="kmeans"> |
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143 <param type="integer" argument="clustering_kmeans_k" name="clustering_kmeans_k" value="4" optional="true" label="Number of clusters for k-means clustering"/> |
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144 </when> |
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145 </conditional> |
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146 <param type="integer" argument="supercell" name="supercell" value="1" label="Supercell" multiple="true" help="Supercell size and shape to use. This can either be a single int, a list of three integers or a 3x3 matrix of integers. For a single number a diagonal matrix will be generated with the integer repeated on the diagonals. For a list of three numbers a diagonal matrix will be generated where the diagonal elements are set to the list. A matrix will be used directly as is. Default is a 3x3 identity matrix."/> |
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147 <param type="text" argument="k_points_grid" name="k_points_grid" value="[1,1,1]" label="K-points grid" multiple="true" help="List of three integer k-points. Default is [1,1,1]."/> |
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148 <param type="integer" argument="max_scc_steps" name="max_scc_steps" value="200" optional="true" label="Max SCC steps" help="If applicable, max number of SCC steps to perform before giving up. Default is 200 for DFTB+ and 30 for CASTEP."/> |
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149 </section> |
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150 </inputs> |
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151 <outputs> |
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152 <data label="Configuration for $general_params.struct_name" name="out_yaml" format="yaml" from_work_dir="output.yaml"/> |
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153 </outputs> |
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154 <tests> |
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155 <test expect_num_outputs="1"> |
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156 <section name="general_params"> |
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157 <param name="poisson_r" value="0.8"/> |
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158 <param name="struct_name" value="Si"/> |
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159 <param name="charged" value="true"/> |
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160 <param name="geom_steps" value="300"/> |
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161 <param name="vwd_scale" value="0.25"/> |
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162 <param name="out_folder" value="Si-out"/> |
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163 <param name="geom_force_tol" value="0.05"/> |
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164 </section> |
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165 <section name="calculator_params"> |
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166 <conditional name="calculator_cond"> |
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167 <param name="calculator" value="uep"/> |
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168 <param name="uep_gw_factor" value="0.4"/> |
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169 <param name="uep_chden" value="test.den_fmt"/> |
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170 </conditional> |
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171 </section> |
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172 <section name="clustering_params"> |
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173 <conditional name="clustering"> |
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174 <param name="clustering_method" value="hier"/> |
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175 <param name="clustering_hier_t" value="0.2"/> |
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176 </conditional> |
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177 <param name="supercell" value="1"/> |
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178 <param name="k_points_grid" value="[1,1,1]"/> |
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179 <param name="max_scc_steps" value="200"/> |
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180 </section> |
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181 <output name="out_yaml" file="config.yaml" ftype="yaml" delta="100"/> |
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182 </test> |
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183 <test expect_num_outputs="1"> |
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184 <section name="general_params"> |
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185 </section> |
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186 <section name="calculator_params"> |
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187 </section> |
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188 <section name="clustering_params"> |
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189 </section> |
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190 <output name="out_yaml" file="config-default.yaml" ftype="yaml" delta="100"/> |
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191 </test> |
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192 </tests> |
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193 <help><![CDATA[ |
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194 Creates a YAML configuration file from input parameters. |
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195 |
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196 **DFTB+ parameter sets:** |
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197 |
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198 +------------+-------------------------------------+-----------------------------------+ |
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199 | set | elements | context | |
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200 +============+=====================================+===================================+ |
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201 | 3ob-3-1 | Br-C-Ca-Cl-F-H-I-K-Mg-N-Na-O-P-S-Zn | DFTB3 files for bio and organic | |
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202 | | | molecules | |
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203 +------------+-------------------------------------+-----------------------------------+ |
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204 | pbc-0-3 | Si - F - O - N - C - H / Fe | SCC files for solids and surfaces | |
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205 +------------+-------------------------------------+-----------------------------------+ |
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206 ]]></help> |
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207 <citations> |
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208 <citation type="bibtex"> |
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209 @TOOL_CITATION@ |
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210 </citation> |
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211 </citations> |
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212 </tool> |