Mercurial > repos > muon-spectroscopy-computational-project > pm_yaml_config
comparison pm_yaml_config.xml @ 2:2d9b2ffec9d5 draft
planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507
author | muon-spectroscopy-computational-project |
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date | Fri, 03 Feb 2023 15:40:12 +0000 |
parents | 6f271bc31aa8 |
children | 03f4f2aaa91c |
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1:6f271bc31aa8 | 2:2d9b2ffec9d5 |
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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"> | 1 <tool id="pm_yaml_config" name="PyMuonSuite AIRSS Configure" version="@TOOL_VERSION@+galaxy@WRAPPER_VERSION@" python_template_version="3.5" profile="22.05" license="MIT"> |
2 <description>define AIRSS parameters</description> | 2 <description>define AIRSS parameters</description> |
3 <macros> | 3 <macros> |
4 <!-- version of underlying tool (PEP 440) --> | 4 <!-- version of underlying tool (PEP 440) --> |
5 <!-- this wrapper doesn't have pymuonsuite as a dependency, but it will change according | 5 <!-- this wrapper doesn't have pymuonsuite as a dependency, but it will change according |
6 to the pymuonsuite interface, so follow the same versioning pattern --> | 6 to the pymuonsuite interface, so follow the same versioning pattern --> |
7 <token name="@TOOL_VERSION@">0.2.1</token> | 7 <token name="@TOOL_VERSION@">0.2.3</token> |
8 <!-- version of this tool wrapper (integer) --> | 8 <!-- version of this tool wrapper (integer) --> |
9 <token name="@WRAPPER_VERSION@">0</token> | 9 <token name="@WRAPPER_VERSION@">0</token> |
10 <!-- citation should be updated with every underlying tool version --> | 10 <!-- citation should be updated with every underlying tool version --> |
11 <!-- typical fields to update are version, month, year, and doi --> | 11 <!-- typical fields to update are version, month, year, and doi --> |
12 <token name="@TOOL_CITATION@"> | 12 <token name="@TOOL_CITATION@"> |
13 @software{pymuon-suite, | 13 @software{Sturniolo_pymuon-suite_2022, |
14 author = {Sturniolo, Simone and Liborio, Leandro and Chadwick, Eli and Murgatroyd, Laura and Laverack, Adam and {Muon Spectroscopy Computational Project}}, | 14 author = {Sturniolo, Simone and Liborio, Leandro and Chadwick, Eli and Murgatroyd, Laura and Laverack, Adam and Mudaraddi, Anish and {Muon Spectroscopy Computational Project}}, |
15 license = {GPL-3.0}, | 15 license = {GPL-3.0}, |
16 month = {8}, | |
16 title = {{pymuon-suite}}, | 17 title = {{pymuon-suite}}, |
17 url = {https://github.com/muon-spectroscopy-computational-project/pymuon-suite}, | 18 url = {https://github.com/muon-spectroscopy-computational-project/pymuon-suite}, |
18 version = {v0.2.1}, | 19 version = {v0.2.3}, |
19 month = {2}, | 20 doi = {10.5281/zenodo.7025644}, |
20 year = {2022}, | 21 year = {2022} |
21 doi = {} | |
22 } | 22 } |
23 </token> | 23 </token> |
24 <import>muon_macros.xml</import> | |
24 </macros> | 25 </macros> |
25 <creator> | 26 <creator> |
26 <person givenName="Jyothish" familyName="Thomas" identifier="https://orcid.org/0000-0003-4724-6924"/> | 27 <person givenName="Jyothish" familyName="Thomas" identifier="https://orcid.org/0000-0003-4724-6924"/> |
27 <person givenName="Eli" familyName="Chadwick" url="https://github.com/elichad" identifier="https://orcid.org/0000-0002-0035-6475"/> | 28 <person givenName="Eli" familyName="Chadwick" url="https://github.com/elichad" identifier="https://orcid.org/0000-0002-0035-6475"/> |
28 <organization url="https://muon-spectroscopy-computational-project.github.io/index.html" name="The Muon Spectroscopy Computational Project"/> | 29 <organization url="https://muon-spectroscopy-computational-project.github.io/index.html" name="The Muon Spectroscopy Computational Project"/> |
29 </creator> | 30 </creator> |
30 <requirements> | 31 <requirements> |
31 </requirements> | 32 </requirements> |
32 <command detect_errors="exit_code"><![CDATA[ | 33 <command detect_errors="exit_code"><![CDATA[ |
33 touch outputx.yaml && | 34 touch outputx.yaml && |
34 ([[ ! -z "$general_params.poisson_r" ]] && printf "poisson_r: $general_params.poisson_r\n">>outputx.yaml || ( >&2 echo "poisson_r empty" && exit 2)) && | 35 ([[ ! -z '$general_params.poisson_r' ]] && printf 'poisson_r: $general_params.poisson_r\n'>>outputx.yaml || ( >&2 echo "poisson_r empty" && exit 2)) && |
35 ([[ ! -z "$general_params.struct_name" ]] && printf "name: $general_params.struct_name\n">>outputx.yaml || ( >&2 echo "structure name is empty" && exit 2)) && | 36 ([[ ! -z '$general_params.name' ]] && printf 'name: $general_params.name\n'>>outputx.yaml || ( >&2 echo "structure name is empty" && exit 2)) && |
36 ([[ ! -z "$general_params.charged" ]] && printf "charged: $general_params.charged\n">>outputx.yaml || ( >&2 echo "charged muon empty" && exit 2)) && | 37 ([[ ! -z '$general_params.charged' ]] && printf 'charged: $general_params.charged\n'>>outputx.yaml || ( >&2 echo "charged muon empty" && exit 2)) && |
37 ([[ ! -z "$general_params.geom_steps" ]] && printf "geom_steps: $general_params.geom_steps\n">>outputx.yaml || ( >&2 echo "geom_steps empty" && exit 2)) && | 38 ([[ ! -z '$general_params.geom_steps' ]] && printf 'geom_steps: $general_params.geom_steps\n'>>outputx.yaml || ( >&2 echo "geom_steps empty" && exit 2)) && |
38 ([[ ! -z "$general_params.vdw_scale" ]] && printf "vdw_scale: $general_params.vdw_scale\n">>outputx.yaml || ( >&2 echo "vdw_scale empty" && exit 2)) && | 39 ([[ ! -z '$general_params.vdw_scale' ]] && printf 'vdw_scale: $general_params.vdw_scale\n'>>outputx.yaml || ( >&2 echo "vdw_scale empty" && exit 2)) && |
39 ([[ ! -z "$calculator_params.calculator_cond.calculator" ]] && printf "calculator: $calculator_params.calculator_cond.calculator\n">>outputx.yaml || ( >&2 echo "calculator unselected" && exit 2)) && | 40 ([[ ! -z '$calculator_params.calculator_cond.calculator' ]] && printf 'calculator: $calculator_params.calculator_cond.calculator\n'>>outputx.yaml || ( >&2 echo "calculator unselected" && exit 2)) && |
40 ([[ ! -z "$general_params.geom_force_tol" ]] && printf "geom_force_tol: $general_params.geom_force_tol\n">>outputx.yaml || ( >&2 echo "geom_force_tol empty" && exit 2)) && | 41 ([[ ! -z '$general_params.geom_force_tol' ]] && printf 'geom_force_tol: $general_params.geom_force_tol\n'>>outputx.yaml || ( >&2 echo "geom_force_tol empty" && exit 2)) && |
41 ([[ ! -z "$general_params.out_folder" ]] && printf "out_folder: $general_params.out_folder\n">>outputx.yaml || printf "out_folder: muon-airss-out\n">>outputx.yaml) && | 42 ([[ ! -z '$general_params.out_folder' ]] && printf 'out_folder: $general_params.out_folder\n'>>outputx.yaml || printf "out_folder: muon-airss-out\n">>outputx.yaml) && |
42 ([[ ! -z "$general_params.random_seed" ]] && printf "random_seed: $general_params.random_seed\n">>outputx.yaml || ( echo "random_seed empty")) && | 43 ([[ ! -z '$general_params.random_seed' ]] && printf 'random_seed: $general_params.random_seed\n'>>outputx.yaml || ( echo "random_seed empty")) && |
43 ([[ ! -z "$clustering_params.supercell" ]] && (printf "supercell: $clustering_params.supercell\n" | sed "s/__ob__/[/g" | sed "s/__cb__/]/g" )>>outputx.yaml || ( >&2 echo "supercell empty" && exit 2)) && | 44 ([[ ! -z '$clustering_params.supercell' ]] && (printf 'supercell: $clustering_params.supercell\n' | sed "s/__ob__/[/g" | sed "s/__cb__/]/g" )>>outputx.yaml || ( >&2 echo "supercell empty" && exit 2)) && |
44 ([[ ! -z "$clustering_params.k_points_grid" ]] && (printf "k_points_grid: $clustering_params.k_points_grid\n" | sed "s/__ob__/[/g" | sed "s/__cb__/]/g" ) >>outputx.yaml || ( >&2 echo "k_points_grid empty" && exit 2)) && | 45 ([[ ! -z '$clustering_params.k_points_grid' ]] && (printf 'k_points_grid: $clustering_params.k_points_grid\n' | sed "s/__ob__/[/g" | sed "s/__cb__/]/g" ) >>outputx.yaml || ( >&2 echo "k_points_grid empty" && exit 2)) && |
45 ([[ ! -z "$clustering_params.max_scc_steps" ]] && printf "max_scc_steps: $clustering_params.max_scc_steps\n">>outputx.yaml || ( >&2 echo "max_scc_steps empty")) && | 46 ([[ ! -z '$clustering_params.max_scc_steps' ]] && printf 'max_scc_steps: $clustering_params.max_scc_steps\n'>>outputx.yaml || ( >&2 echo "max_scc_steps empty")) && |
46 #if str($calculator_params.calculator_cond.calculator)=="uep": | 47 #if str($calculator_params.calculator_cond.calculator)=="uep": |
47 ([[ ! -z "$calculator_params.calculator_cond.uep_gw_factor" ]] && printf "uep_gw_factor: $calculator_params.calculator_cond.uep_gw_factor\n">>outputx.yaml || ( >&2 echo "uep gaussian width unset" && exit 2)) && | 48 ([[ ! -z '$calculator_params.calculator_cond.uep_gw_factor' ]] && printf 'uep_gw_factor: $calculator_params.calculator_cond.uep_gw_factor\n'>>outputx.yaml || ( >&2 echo "uep gaussian width unset" && exit 2)) && |
48 ([[ ! -z "$calculator_params.calculator_cond.uep_chden" ]] && printf "uep_chden: $calculator_params.calculator_cond.uep_chden.value\n">>outputx.yaml || echo "den_fmt path unset") && | 49 ([[ ! -z '$calculator_params.calculator_cond.uep_chden' ]] && printf 'uep_chden: $calculator_params.calculator_cond.uep_chden.value\n'>>outputx.yaml || echo "den_fmt path unset") && |
49 #else if str($calculator_params.calculator_cond.calculator)=="CASTEP": | 50 #else if str($calculator_params.calculator_cond.calculator)=="CASTEP": |
50 ([[ ! -z "$calculator_params.calculator_cond.castep_command" ]] && printf "castep_command: $calculator_params.calculator_cond.castep_command\n">>outputx.yaml || echo "CASTEP command unset") && | 51 ([[ ! -z '$calculator_params.calculator_cond.castep_command' ]] && printf 'castep_command: $calculator_params.calculator_cond.castep_command\n'>>outputx.yaml || echo "CASTEP command unset") && |
51 ([[ ! -z "$calculator_params.calculator_cond.castep_param" ]] && printf "castep_param: $calculator_params.calculator_cond.castep_param\n">>outputx.yaml || echo "CASTEP param unset") && | 52 ([[ ! -z '$calculator_params.calculator_cond.castep_param' ]] && printf 'castep_param: $calculator_params.calculator_cond.castep_param\n'>>outputx.yaml || echo "CASTEP param unset") && |
52 ([[ ! -z "$calculator_params.calculator_cond.mu_symbol" ]] && printf "mu_symbol: $calculator_params.calculator_cond.mu_symbol\n">>outputx.yaml || echo "mu symbol unset") && | 53 ([[ ! -z '$calculator_params.calculator_cond.mu_symbol' ]] && printf 'mu_symbol: $calculator_params.calculator_cond.mu_symbol\n'>>outputx.yaml || echo "mu symbol unset") && |
53 #else if str($calculator_params.calculator_cond.calculator)=="dftb+": | 54 #else if str($calculator_params.calculator_cond.calculator)=="dftb+": |
54 ([[ ! -z "$calculator_params.calculator_cond.dftb_set" ]] && printf "dftb_set: $calculator_params.calculator_cond.dftb_set\n">>outputx.yaml || ( >&2 echo "dftb parameter set unselected" && exit 2)) && | 55 ([[ ! -z '$calculator_params.calculator_cond.dftb_set' ]] && printf 'dftb_set: $calculator_params.calculator_cond.dftb_set\n'>>outputx.yaml || ( >&2 echo "dftb parameter set unselected" && exit 2)) && |
55 ([[ ! -z "$calculator_params.calculator_cond.dftb_pbc" ]] && printf "dftb_pbc: $calculator_params.calculator_cond.dftb_pbc\n">>outputx.yaml || echo "dftb periodic boundary condition unselected") && | 56 ([[ ! -z '$calculator_params.calculator_cond.dftb_optionals' ]] && (printf 'dftb_optionals: $calculator_params.calculator_cond.dftb_optionals\n' | sed "s/__ob__/[/g" | sed "s/__cb__/]/g" ) >>outputx.yaml || echo "dftb optional json files unset") && |
57 ([[ ! -z '$calculator_params.calculator_cond.dftb_pbc' ]] && printf 'dftb_pbc: $calculator_params.calculator_cond.dftb_pbc\n'>>outputx.yaml || echo "dftb periodic boundary condition unselected") && | |
56 #else if str($calculator_params.calculator_cond.calculator)=="all": | 58 #else if str($calculator_params.calculator_cond.calculator)=="all": |
57 ([[ ! -z "$calculator_params.calculator_cond.uep_gw_factor" ]] && printf "uep_gw_factor: $calculator_params.calculator_cond.uep_gw_factor\n">>outputx.yaml || echo "uep gaussian width unset") && | 59 ([[ ! -z '$calculator_params.calculator_cond.uep_gw_factor' ]] && printf 'uep_gw_factor: $calculator_params.calculator_cond.uep_gw_factor\n'>>outputx.yaml || echo "uep gaussian width unset") && |
58 ([[ ! -z "$calculator_params.calculator_cond.uep_chden" ]] && printf "uep_chden: $calculator_params.calculator_cond.uep_chden\n">>outputx.yaml || echo "den_fmt path unset") && | 60 ([[ ! -z '$calculator_params.calculator_cond.uep_chden' ]] && printf 'uep_chden: $calculator_params.calculator_cond.uep_chden\n'>>outputx.yaml || echo "den_fmt path unset") && |
59 ([[ ! -z "$calculator_params.calculator_cond.castep_command" ]] && printf "castep_command: $calculator_params.calculator_cond.castep_command\n">>outputx.yaml || echo "CASTEP command unset") && | 61 ([[ ! -z '$calculator_params.calculator_cond.castep_command' ]] && printf 'castep_command: $calculator_params.calculator_cond.castep_command\n'>>outputx.yaml || echo "CASTEP command unset") && |
60 ([[ ! -z "$calculator_params.calculator_cond.castep_param" ]] && printf "castep_param: $calculator_params.calculator_cond.castep_param\n">>outputx.yaml || echo "CASTEP param unset") && | 62 ([[ ! -z '$calculator_params.calculator_cond.castep_param' ]] && printf 'castep_param: $calculator_params.calculator_cond.castep_param\n'>>outputx.yaml || echo "CASTEP param unset") && |
61 ([[ ! -z "$calculator_params.calculator_cond.mu_symbol" ]] && printf "mu_symbol: $calculator_params.calculator_cond.mu_symbol\n">>outputx.yaml || echo "mu symbol unset") && | 63 ([[ ! -z '$calculator_params.calculator_cond.mu_symbol' ]] && printf 'mu_symbol: $calculator_params.calculator_cond.mu_symbol\n'>>outputx.yaml || echo "mu symbol unset") && |
62 ([[ ! -z "$calculator_params.calculator_cond.mu_symbol" ]] && printf "dftb_set: $calculator_params.calculator_cond.dftb_set\n">>outputx.yaml || echo "dftb parameter set unselected") && | 64 ([[ ! -z '$calculator_params.calculator_cond.dftb_set' ]] && printf 'dftb_set: $calculator_params.calculator_cond.dftb_set\n'>>outputx.yaml || echo "dftb parameter set unselected") && |
63 ([[ ! -z "$calculator_params.calculator_cond.dftb_pbc" ]] && printf "dftb_pbc: $calculator_params.calculator_cond.dftb_pbc\n">>outputx.yaml || echo "dftb periodic boundary condition unselected") && | 65 ([[ ! -z '$calculator_params.calculator_cond.dftb_optionals' ]] && (printf 'dftb_optionals: $calculator_params.calculator_cond.dftb_optionals\n' | sed "s/__ob__/[/g" | sed "s/__cb__/]/g" ) >>outputx.yaml || echo "dftb optional json files unset") && |
66 ([[ ! -z '$calculator_params.calculator_cond.dftb_pbc' ]] && printf 'dftb_pbc: $calculator_params.calculator_cond.dftb_pbc\n'>>outputx.yaml || echo "dftb periodic boundary condition unselected") && | |
64 #end if | 67 #end if |
65 ([[ ! -z "$clustering_params.clustering.clustering_method " ]] && printf "clustering_method: $clustering_params.clustering.clustering_method\n">>outputx.yaml || ( echo "clustering method unselected" && exit 2)) && | 68 ([[ ! -z '$clustering_params.clustering.clustering_method' ]] && printf 'clustering_method: $clustering_params.clustering.clustering_method\n'>>outputx.yaml || ( echo "clustering method unselected" && exit 2)) && |
66 #if str($clustering_params.clustering.clustering_method)=="hier": | 69 #if str($clustering_params.clustering.clustering_method)=="hier": |
67 ([[ ! -z "$clustering_params.clustering.clustering_hier_t" ]] && printf "clustering_hier_t: $clustering_params.clustering.clustering_hier_t\n">>outputx.yaml || echo "clustering_hier_t unset") && | 70 ([[ ! -z '$clustering_params.clustering.clustering_hier_t' ]] && printf 'clustering_hier_t: $clustering_params.clustering.clustering_hier_t\n'>>outputx.yaml || echo "clustering_hier_t unset") && |
68 #else if str($clustering_params.clustering.clustering_method)=="kmeans": | 71 #else if str($clustering_params.clustering.clustering_method)=="kmeans": |
69 ([[ ! -z "$clustering_params.clustering.clustering_kmeans_k" ]] && printf "clustering_kmeans_k: $clustering_params.clustering.clustering_kmeans_k\n">>outputx.yaml || echo "clustering_kmeans_k unset") && | 72 ([[ ! -z '$clustering_params.clustering.clustering_kmeans_k' ]] && printf 'clustering_kmeans_k: $clustering_params.clustering.clustering_kmeans_k\n'>>outputx.yaml || echo "clustering_kmeans_k unset") && |
70 #end if | 73 #end if |
71 ln -s outputx.yaml output.yaml | 74 ln -s outputx.yaml output.yaml |
72 ]]></command> | 75 ]]></command> |
73 <inputs> | 76 <inputs> |
74 <section name="general_params" expanded="true" title="General Parameters"> | 77 <section name="general_params" expanded="true" title="General Parameters"> |
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."/> | 78 <param type="float" argument="poisson_r" value="0.8" min="0.0" 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."/> |
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."/> | 79 <param type="text" argument="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."/> |
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."> | 80 <param argument="charged" type="boolean" checked="true" label="Charged muon" help="If true, the muon will be charged. Otherwise, will be muonium (with an accompanying electron). Must be true for UEP calculations."/> |
78 <option value="true">true</option> | 81 <param type="integer" argument="geom_steps" value="30" min="0" label="Geometry optimization steps" help="Maximum number of geometry optimisation steps."/> |
79 <option value="false">false</option> | 82 <param type="float" argument="vdw_scale" value="0.5" min="0.0" 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."/> |
80 </param> | 83 <param type="text" argument="out_folder" optional="true" value="muon-airss-out" label="Output folder name" help="Name to call the output folder used to store the files that the script generates."/> |
81 <param type="integer" argument="geom_steps" name="geom_steps" value="30" label="Geometry optimization steps" help="Maximum number of geometry optimisation steps."/> | 84 <param type="float" argument="geom_force_tol" value="0.05" min="0.0" label="Geometry optimization tolerance" help="Tolerance on geometry optimisation in units of eV/Å."/> |
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."/> | 85 <param type="integer" argument="random_seed" label="Random Seed" optional="true" help="Random seed for pymuonsuite."/> |
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."/> | |
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."/> | |
85 <param type="integer" argument="random_seed" name="random_seed" label="Random Seed" optional="true" help="Random seed for pymuonsuite."/> | |
86 </section> | 86 </section> |
87 <section name="calculator_params" expanded="true" title="Calculator parameters"> | 87 <section name="calculator_params" expanded="true" title="Calculator parameters"> |
88 <conditional name="calculator_cond"> | 88 <conditional name="calculator_cond"> |
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."> | 89 <param type="select" display="radio" label="Optimization calculator" argument="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."> |
90 <option value="uep">UEP</option> | 90 <option value="uep">UEP</option> |
91 <option value="castep">CASTEP</option> | 91 <option value="castep">CASTEP</option> |
92 <option value="dftb+">DFTB+</option> | 92 <option value="dftb+">DFTB+</option> |
93 <option value="all">all</option> | 93 <option value="all">all</option> |
94 </param> | 94 </param> |
95 <when value="uep"> | 95 <when value="uep"> |
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."/> | 96 <param type="float" argument="uep_gw_factor" optional="true" value="5.0" min="0.0" 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."/> |
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"/> | 97 <param type="text" argument="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"/> |
98 </when> | 98 </when> |
99 <when value="castep"> | 99 <when value="castep"> |
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."/> | 100 <param type="text" argument="castep_command" optional="true" value="castep.serial" label="CASTEP command" help="Command to use to run CASTEP."/> |
101 <param type="text" argument="castep_param" name="castep_param" optional="true" label="PARAM path" help="File path to the CASTEP parameter file."/> | 101 <param type="text" argument="castep_param" optional="true" label="PARAM path" help="File path to the CASTEP parameter file."/> |
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."/> | 102 <param type="text" argument="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."/> |
103 </when> | 103 </when> |
104 <when value="dftb+"> | 104 <when value="dftb+"> |
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."> | 105 <expand macro="dftb+"/> |
106 <option value="3ob-3-1" selected="true">3ob-3-1</option> | 106 <expand macro="dftb_optionals"/> |
107 <option value="pbc-0-3">pbc-0-3</option> | |
108 </param> | |
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)."/> | |
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+."> | |
111 <option value="true" selected="true">true</option> | |
112 <option value="false">false</option> | |
113 </param> | |
114 </when> | 107 </when> |
115 <when value="all"> | 108 <when value="all"> |
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."/> | 109 <param type="float" argument="uep_gw_factor" optional="true" value="5.0" min="0.0" 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."/> |
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"/> | 110 <param type="text" argument="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"/> |
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."/> | 111 <param type="text" argument="castep_command" optional="true" value="castep.serial" label="CASTEP command" help="Command to use to run CASTEP."/> |
119 <param type="text" argument="castep_param" name="castep_param" optional="true" label="PARAM path" help="File path to the CASTEP parameter file."/> | 112 <param type="text" argument="castep_param" optional="true" label="PARAM path" help="File path to the CASTEP parameter file."/> |
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."/> | 113 <param type="text" argument="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."/> |
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."> | 114 <expand macro="dftb+"/> |
122 <option value="3ob-3-1" selected="true">3ob-3-1</option> | 115 <expand macro="dftb_optionals"/> |
123 <option value="pbc-0-3">pbc-0-3</option> | |
124 </param> | |
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)."/> | |
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+."> | |
127 <option value="true" selected="true">true</option> | |
128 <option value="false">false</option> | |
129 </param> | |
130 </when> | 116 </when> |
131 </conditional> | 117 </conditional> |
132 </section> | 118 </section> |
133 <section name="clustering_params" expanded="true" title="Clustering Parameters"> | 119 <section name="clustering_params" expanded="true" title="Clustering Parameters"> |
134 <conditional name="clustering"> | 120 <conditional name="clustering"> |
135 <param type="select" argument="clustering_method" name="clustering_method" label="Clustering method" value="hier"> | 121 <param type="select" argument="clustering_method" display="radio" label="Clustering method" value="hier"> |
136 <option value="hier">hierarchical</option> | 122 <option value="hier">hierarchical</option> |
137 <option value="kmeans">k-means</option> | 123 <option value="kmeans">k-means</option> |
138 </param> | 124 </param> |
139 <when value="hier"> | 125 <when value="hier"> |
140 <param type="float" argument="clustering_hier_t" name="clustering_hier_t" value="0.3" optional="true" label="t parameter for hierarchical clustering"/> | 126 <param type="float" argument="clustering_hier_t" value="0.3" min="0.0" optional="true" label="t parameter for hierarchical clustering"/> |
141 </when> | 127 </when> |
142 <when value="kmeans"> | 128 <when value="kmeans"> |
143 <param type="integer" argument="clustering_kmeans_k" name="clustering_kmeans_k" value="4" optional="true" label="Number of clusters for k-means clustering"/> | 129 <param type="integer" argument="clustering_kmeans_k" value="4" min="0" optional="true" label="Number of clusters for k-means clustering"/> |
144 </when> | 130 </when> |
145 </conditional> | 131 </conditional> |
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."/> | 132 <param type="text" argument="supercell" value="1" label="Supercell" 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."> |
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]."/> | 133 <validator type="regex" message="Input should only contain whitespace, '[', ']', ',' and digits.">^[\s\d,\[\]]+$</validator> |
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."/> | 134 </param> |
135 <expand macro="k_points_grid"/> | |
136 <param type="integer" argument="max_scc_steps" value="200" min="0" 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."/> | |
149 </section> | 137 </section> |
150 </inputs> | 138 </inputs> |
151 <outputs> | 139 <outputs> |
152 <data label="Configuration for $general_params.struct_name" name="out_yaml" format="yaml" from_work_dir="output.yaml"/> | 140 <data label="Configuration for $general_params.name" name="out_yaml" format="yaml" from_work_dir="output.yaml"/> |
153 </outputs> | 141 </outputs> |
154 <tests> | 142 <tests> |
155 <test expect_num_outputs="1"> | 143 <test expect_num_outputs="1"> |
156 <section name="general_params"> | 144 <section name="general_params"> |
157 <param name="poisson_r" value="0.8"/> | 145 <param name="poisson_r" value="0.8"/> |
158 <param name="struct_name" value="Si"/> | 146 <param name="name" value="Si"/> |
159 <param name="charged" value="true"/> | 147 <param name="charged" value="true"/> |
160 <param name="geom_steps" value="300"/> | 148 <param name="geom_steps" value="300"/> |
161 <param name="vwd_scale" value="0.25"/> | 149 <param name="vwd_scale" value="0.25"/> |
162 <param name="out_folder" value="Si-out"/> | 150 <param name="out_folder" value="Si-out"/> |
163 <param name="geom_force_tol" value="0.05"/> | 151 <param name="geom_force_tol" value="0.05"/> |
187 </section> | 175 </section> |
188 <section name="clustering_params"> | 176 <section name="clustering_params"> |
189 </section> | 177 </section> |
190 <output name="out_yaml" file="config-default.yaml" ftype="yaml" delta="100"/> | 178 <output name="out_yaml" file="config-default.yaml" ftype="yaml" delta="100"/> |
191 </test> | 179 </test> |
180 <test expect_num_outputs="1"> | |
181 <section name="general_params"> | |
182 </section> | |
183 <section name="calculator_params"> | |
184 <conditional name="calculator_cond"> | |
185 <param name="calculator" value="dftb+"/> | |
186 </conditional> | |
187 </section> | |
188 <section name="clustering_params"> | |
189 </section> | |
190 <output name="out_yaml" file="config-dftb.yaml" ftype="yaml" delta="100"/> | |
191 </test> | |
192 <test expect_num_outputs="1"> | |
193 <section name="general_params"> | |
194 </section> | |
195 <section name="calculator_params"> | |
196 <conditional name="calculator_cond"> | |
197 <param name="calculator" value="all"/> | |
198 </conditional> | |
199 </section> | |
200 <section name="clustering_params"> | |
201 </section> | |
202 <output name="out_yaml" file="config-all.yaml" ftype="yaml" delta="100"/> | |
203 </test> | |
204 <test expect_failure="true"> | |
205 <section name="general_params"> | |
206 </section> | |
207 <section name="calculator_params"> | |
208 </section> | |
209 <section name="clustering_params"> | |
210 <param name="supercell" value="bad format"/> | |
211 </section> | |
212 </test> | |
213 <test expect_failure="true"> | |
214 <section name="general_params"> | |
215 </section> | |
216 <section name="calculator_params"> | |
217 </section> | |
218 <section name="clustering_params"> | |
219 <param name="k_points_grid" value="bad format"/> | |
220 </section> | |
221 </test> | |
192 </tests> | 222 </tests> |
193 <help><![CDATA[ | 223 <help><![CDATA[ |
194 Creates a YAML configuration file from input parameters. | 224 Creates a YAML configuration file from input parameters. |
225 | |
226 PyMuonSuite is distributed under the GPLv3 license. This tool wrapper is distributed under the MIT license. | |
195 | 227 |
196 **DFTB+ parameter sets:** | 228 **DFTB+ parameter sets:** |
197 | 229 |
198 +------------+-------------------------------------+-----------------------------------+ | 230 +------------+-------------------------------------+-----------------------------------+ |
199 | set | elements | context | | 231 | set | elements | context | |