| Previous changeset 1:6f271bc31aa8 (2022-09-15) Next changeset 3:03f4f2aaa91c (2023-07-18) |
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Commit message:
planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 |
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modified:
pm_yaml_config.xml |
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added:
muon_macros.xml test-data/config-all.yaml test-data/config-dftb.yaml |
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| diff -r 6f271bc31aa8 -r 2d9b2ffec9d5 muon_macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/muon_macros.xml Fri Feb 03 15:40:12 2023 +0000 |
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| @@ -0,0 +1,20 @@ +<macros> + <xml name="dftb_set"> + <param type="select" name="dftb_set" value="3ob-3-1" display="radio" 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."> + <option value="3ob-3-1">3ob-3-1</option> + <option value="pbc-0-3">pbc-0-3</option> + </param> + </xml> + <xml name="dftb+"> + <expand macro="dftb_set"/> + <param type="boolean" name="dftb_pbc" label="Use periodic boundary conditions" help="Whether to turn on periodic boundary conditions in DFTB+." checked="true"/> + </xml> + <xml name="dftb_optionals"> + <param type="text" argument="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)."/> + </xml> + <xml name="k_points_grid"> + <param type="text" argument="k_points_grid" value="[1,1,1]" label="K-points grid" help="List of three integer k-points. Default is [1,1,1]."> + <validator type="regex" message="Input should only contain whitespace, '[', ']', ',' and digits.">^[\s\d,\[\]]+$</validator> + </param> + </xml> +</macros> \ No newline at end of file |
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| diff -r 6f271bc31aa8 -r 2d9b2ffec9d5 pm_yaml_config.xml --- a/pm_yaml_config.xml Thu Sep 15 10:26:07 2022 +0000 +++ b/pm_yaml_config.xml Fri Feb 03 15:40:12 2023 +0000 |
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| b'@@ -1,26 +1,27 @@\n-<tool id="pm_yaml_config" name="PyMuonSuite AIRSS Configure" version="@TOOL_VERSION@+galaxy@WRAPPER_VERSION@" python_template_version="3.5" profile="22.01">\n+<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">\n <description>define AIRSS parameters</description>\n <macros>\n <!-- version of underlying tool (PEP 440) -->\n <!-- this wrapper doesn\'t have pymuonsuite as a dependency, but it will change according\n to the pymuonsuite interface, so follow the same versioning pattern -->\n- <token name="@TOOL_VERSION@">0.2.1</token>\n+ <token name="@TOOL_VERSION@">0.2.3</token>\n <!-- version of this tool wrapper (integer) -->\n <token name="@WRAPPER_VERSION@">0</token>\n <!-- citation should be updated with every underlying tool version -->\n <!-- typical fields to update are version, month, year, and doi -->\n <token name="@TOOL_CITATION@">\n- @software{pymuon-suite,\n- author = {Sturniolo, Simone and Liborio, Leandro and Chadwick, Eli and Murgatroyd, Laura and Laverack, Adam and {Muon Spectroscopy Computational Project}},\n+ @software{Sturniolo_pymuon-suite_2022,\n+ author = {Sturniolo, Simone and Liborio, Leandro and Chadwick, Eli and Murgatroyd, Laura and Laverack, Adam and Mudaraddi, Anish and {Muon Spectroscopy Computational Project}},\n license = {GPL-3.0},\n+ month = {8},\n title = {{pymuon-suite}},\n url = {https://github.com/muon-spectroscopy-computational-project/pymuon-suite},\n- version = {v0.2.1},\n- month = {2},\n- year = {2022},\n- doi = {}\n+ version = {v0.2.3},\n+ doi = {10.5281/zenodo.7025644},\n+ year = {2022}\n }\n </token>\n+ <import>muon_macros.xml</import>\n </macros>\n <creator>\n <person givenName="Jyothish" familyName="Thomas" identifier="https://orcid.org/0000-0003-4724-6924"/>\n@@ -31,131 +32,118 @@\n </requirements>\n <command detect_errors="exit_code"><![CDATA[\n touch outputx.yaml &&\n- ([[ ! -z "$general_params.poisson_r" ]] && printf "poisson_r: $general_params.poisson_r\\n">>outputx.yaml || ( >&2 echo "poisson_r empty" && exit 2)) &&\n- ([[ ! -z "$general_params.struct_name" ]] && printf "name: $general_params.struct_name\\n">>outputx.yaml || ( >&2 echo "structure name is empty" && exit 2)) &&\n- ([[ ! -z "$general_params.charged" ]] && printf "charged: $general_params.charged\\n">>outputx.yaml || ( >&2 echo "charged muon empty" && exit 2)) &&\n- ([[ ! -z "$general_params.geom_steps" ]] && printf "geom_steps: $general_params.geom_steps\\n">>outputx.yaml || ( >&2 echo "geom_steps empty" && exit 2)) &&\n- ([[ ! -z "$general_params.vdw_scale" ]] && printf "vdw_scale: $general_params.vdw_scale\\n">>outputx.yaml || ( >&2 echo "vdw_scale empty" && exit 2)) &&\n- ([[ ! -z "$calculator_params.calculator_cond.calculator" ]] && printf "calculator: $calculator_params.calculator_cond.calculator\\n">>outputx.yaml || ( >&2 echo "calculator unselected" && exit 2)) &&\n- ([[ ! -z "$general_params.geom_force_tol" ]] && printf "geom_force_tol: $general_params.geom_force_tol\\n">>outputx.yaml || ( >&2 echo "geom_force_tol empty" && exit 2)) &&\n- ([[ ! -z "$general_params.out_folder" ]] && printf "out_folder: $general_params.out_folder\\n">>outputx.yaml || printf "out_folder: muon-airss-out\\n">>outputx.yaml) &&\n- ([[ ! -z "$general_params.random_seed" ]] && printf "random_seed: $general_params.random_seed\\n">>outputx.yaml || ( echo "random_seed empty")) &&\n- ([[ ! -z "$clustering_params.supercell" ]] && (printf "supercell: $clustering_params.supercell\\n" | sed "s/__ob__/[/g" | sed "s/__cb__/]/g" )>>o'..b'bel="Max SCC steps" help="If applicable, max number of SCC steps to perform before giving up. Default is 200 for DFTB+ and 30 for CASTEP."/>\n+ <param type="text" argument="supercell" value="1" label="Supercell" help="Supercell size and shape to use. This can either be a single int, a list of three integers or a 3x3 matrix of integers. For a single number a diagonal matrix will be generated with the integer repeated on the diagonals. For a list of three numbers a diagonal matrix will be generated where the diagonal elements are set to the list. A matrix will be used directly as is. Default is a 3x3 identity matrix.">\n+ <validator type="regex" message="Input should only contain whitespace, \'[\', \']\', \',\' and digits.">^[\\s\\d,\\[\\]]+$</validator>\n+ </param>\n+ <expand macro="k_points_grid"/>\n+ <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."/>\n </section>\n </inputs>\n <outputs>\n- <data label="Configuration for $general_params.struct_name" name="out_yaml" format="yaml" from_work_dir="output.yaml"/>\n+ <data label="Configuration for $general_params.name" name="out_yaml" format="yaml" from_work_dir="output.yaml"/>\n </outputs>\n <tests>\n <test expect_num_outputs="1">\n <section name="general_params">\n <param name="poisson_r" value="0.8"/>\n- <param name="struct_name" value="Si"/>\n+ <param name="name" value="Si"/>\n <param name="charged" value="true"/>\n <param name="geom_steps" value="300"/>\n <param name="vwd_scale" value="0.25"/>\n@@ -189,10 +177,54 @@\n </section>\n <output name="out_yaml" file="config-default.yaml" ftype="yaml" delta="100"/>\n </test>\n+ <test expect_num_outputs="1">\n+ <section name="general_params">\n+ </section>\n+ <section name="calculator_params">\n+ <conditional name="calculator_cond">\n+ <param name="calculator" value="dftb+"/>\n+ </conditional>\n+ </section>\n+ <section name="clustering_params">\n+ </section>\n+ <output name="out_yaml" file="config-dftb.yaml" ftype="yaml" delta="100"/>\n+ </test>\n+ <test expect_num_outputs="1">\n+ <section name="general_params">\n+ </section>\n+ <section name="calculator_params">\n+ <conditional name="calculator_cond">\n+ <param name="calculator" value="all"/>\n+ </conditional>\n+ </section>\n+ <section name="clustering_params">\n+ </section>\n+ <output name="out_yaml" file="config-all.yaml" ftype="yaml" delta="100"/>\n+ </test>\n+ <test expect_failure="true">\n+ <section name="general_params">\n+ </section>\n+ <section name="calculator_params">\n+ </section>\n+ <section name="clustering_params">\n+ <param name="supercell" value="bad format"/>\n+ </section>\n+ </test>\n+ <test expect_failure="true">\n+ <section name="general_params">\n+ </section>\n+ <section name="calculator_params">\n+ </section>\n+ <section name="clustering_params">\n+ <param name="k_points_grid" value="bad format"/>\n+ </section>\n+ </test>\n </tests>\n <help><![CDATA[\n Creates a YAML configuration file from input parameters.\n \n+ PyMuonSuite is distributed under the GPLv3 license. This tool wrapper is distributed under the MIT license.\n+\n **DFTB+ parameter sets:**\n \n +------------+-------------------------------------+-----------------------------------+\n' |
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| diff -r 6f271bc31aa8 -r 2d9b2ffec9d5 test-data/config-all.yaml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/config-all.yaml Fri Feb 03 15:40:12 2023 +0000 |
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| @@ -0,0 +1,19 @@ +poisson_r: 0.8 +name: struct +charged: true +geom_steps: 30 +vdw_scale: 0.5 +calculator: all +geom_force_tol: 0.05 +out_folder: muon-airss-out +supercell: 1 +k_points_grid: [1,1,1] +max_scc_steps: 200 +uep_gw_factor: 5.0 +castep_command: castep.serial +mu_symbol: H:mu +dftb_set: 3ob-3-1 +dftb_optionals: [] +dftb_pbc: true +clustering_method: hier +clustering_hier_t: 0.3 |
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| diff -r 6f271bc31aa8 -r 2d9b2ffec9d5 test-data/config-dftb.yaml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/config-dftb.yaml Fri Feb 03 15:40:12 2023 +0000 |
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| @@ -0,0 +1,16 @@ +poisson_r: 0.8 +name: struct +charged: true +geom_steps: 30 +vdw_scale: 0.5 +calculator: dftb+ +geom_force_tol: 0.05 +out_folder: muon-airss-out +supercell: 1 +k_points_grid: [1,1,1] +max_scc_steps: 200 +dftb_set: 3ob-3-1 +dftb_optionals: [] +dftb_pbc: true +clustering_method: hier +clustering_hier_t: 0.3 |