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Commit message:
planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_asephonons commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 |
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modified:
pm_asephonons.xml |
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added:
muon_macros.xml |
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| diff -r 641fda3dfb62 -r dd3ca8457fcd muon_macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/muon_macros.xml Fri Feb 03 15:39:17 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 641fda3dfb62 -r dd3ca8457fcd pm_asephonons.xml --- a/pm_asephonons.xml Thu Sep 15 10:24:36 2022 +0000 +++ b/pm_asephonons.xml Fri Feb 03 15:39:17 2023 +0000 |
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| b'@@ -1,20 +1,25 @@\n-<tool id="pm_asephonons" name="PyMuonSuite Phonons" version="0.1.1" python_template_version="3.5" profile="22.01">\n+<tool id="pm_asephonons" name="PyMuonSuite Phonons" version="@TOOL_VERSION@+galaxy@WRAPPER_VERSION@" python_template_version="3.5" profile="22.05" license="MIT">\n <description>calculate phonons using ASE and DFTB+</description>\n <macros>\n+ <!-- version of underlying tool (PEP 440) -->\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="@PYMUONSUITE_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@@ -23,51 +28,92 @@\n </creator>\n <requirements>\n <!-- note versioning is different due to multiple dependencies -->\n- <requirement type="package" version="0.2.1">pymuonsuite</requirement>\n+ <requirement type="package" version="@TOOL_VERSION@">pymuonsuite</requirement>\n <requirement type="package" version="21.2">dftbplus</requirement>\n <requirement type="package" version="1.22.4">numpy</requirement> <!-- pinned due to numpy/ASE/DFTB+ incompatibility https://github.com/dftbplus/dftbplus/issues/1064 -->\n <requirement type="package" version="3.0">zip</requirement>\n </requirements>\n <command detect_errors="exit_code"><![CDATA[\n- structure_name_internal="input_structure.$structure.ext" &&\n- touch pho_params.yaml &&\n- ([[ ! -z "$name" ]] && printf "name: $name \\n">>pho_params.yaml || ( >&2 echo "name empty" && exit 2)) &&\n- ([[ ! -z "$phonon_kpoint_grid" ]] && ( printf "phonon_kpoint_grid: $phonon_kpoint_grid \\n" | sed "s/__ob__/[/g" | sed "s/__cb__/]/g" )>>pho_params.yaml || ( >&2 echo "phonon_kpoint_grid empty" && exit 2)) &&\n- ([[ ! -z "$kpoint_grid" ]] && ( printf "kpoint_grid: $kpoint_grid \\n" | sed "s/__ob__/[/g" | sed "s/__cb__/]/g" )>>pho_params.yaml || ( >&2 echo "kpoint_grid empty" && exit 2)) &&\n- ([[ ! -z "$force_tol" ]] && printf "force_tol: $force_tol \\n">>pho_params.yaml || ( >&2 echo "force_tol empty" && exit 2)) &&\n- ([[ ! -z "$dftb_set" ]] && printf "dftb_set: $dftb_set \\n">>pho_params.yaml || ( >&2 echo "dftb_set empty" && exit 2)) &&\n- ([[ ! -z "$pbc" ]] && printf "pbc: $pbc \\n">>pho_params.yaml || ( >&2 echo "pbc empty" && exit 2)) &&\n- printf "force_clean: false \\n">>pho_params.yaml &&\n- ln -s $structure \\$structure_name_internal &&\n+ structure_name_internal=\'input_structure.$pbc.structure.ext\' &&\n+ ln -s \'$pho_params\' pho_params.yaml &&\n+ ln -s \'$pbc.structure\' \\$structure_name_internal &&\n cat pho_params.yaml &&\n- pm-asephonons \\$structure_name_internal pho_p'..b' +------------+--------------------------------------------------------------------------------------------+---------+------------------------------------------------+\n+ | [SiC] | \\ E. Rauls, R. Gutierrez, J. Elsner, and Th. Frauenheim, Sol. State Comm. 111, 459 (1999) | (Si-C) | https://doi.org/10.1016/S0038-1098(99)00137-4 |\n+ +------------+--------------------------------------------------------------------------------------------+---------+------------------------------------------------+\n+ | [SiO] | \\ C. Koehler, Z. Hajnal, P. Deak, Th. Frauenheim, S. Suhai, Phys. Rev. B 64, 085333 (2001) | (Si-O) | https://doi.org/10.1103/PhysRevB.64.085333 |\n+ +------------+--------------------------------------------------------------------------------------------+---------+------------------------------------------------+\n+ | [Silicon] | \\ A. Sieck, Th. Frauenheim, and K. A. Jackson, phys. stat. sol. (b) 240, 537 (2003). | (Si) | https://doi.org/10.1002/pssb.200301886 |\n+ +------------+--------------------------------------------------------------------------------------------+---------+------------------------------------------------+\n+ | [Fluorine] | \\ C. Koehler and Th. Frauenheim, Surf. Sci. 600, 453 (2006). | \\ (F) | https://doi.org/10.1016/j.susc.2005.10.044 |\n+ +------------+--------------------------------------------------------------------------------------------+---------+------------------------------------------------+\n+ | [Iron] | \\ C. Koehler, G. Seifert and Th. Frauenheim, Chem. Phys. 309, 23 (2005). | (Fe) | https://doi.org/10.1016/j.chemphys.2004.03.034 |\n+ +------------+--------------------------------------------------------------------------------------------+---------+------------------------------------------------+\n+ | [SiSi] | \\ A. Sieck, PhD. Thesis, University of Paderborn, 2000. | (Si-Si) | https://www.osti.gov/etdeweb/biblio/20249635 |\n+ +------------+--------------------------------------------------------------------------------------------+---------+------------------------------------------------+\n+\n+ |\n+ | The full sets and all other data can be found at the following URLs:\n+\n+ +----------+------------------------------------------------------------+\n+ | 3-ob-1 | https://www.dftb.org/parameters/download/3ob/3ob-3-1-cc/ |\n+ +----------+------------------------------------------------------------+\n+ | pbc-0-3 | https://www.dftb.org/parameters/download/pbc/pbc-0-3-cc/ |\n+ +----------+------------------------------------------------------------+\n+\n+ |\n ]]></help>\n <citations>\n <citation type="bibtex">\n @PYMUONSUITE_CITATION@\n </citation>\n- <citation type="bibtex">\n- @article{doi:10.1063/1.5085197,\n- author = {Sturniolo,Simone and Liborio,Leandro and Jackson,Samuel },\n- title = {Comparison between density functional theory and density functional tight binding approaches for finding the muon stopping site in organic molecular crystals},\n- journal = {The Journal of Chemical Physics},\n- volume = {150},\n- number = {15},\n- pages = {154301},\n- year = {2019},\n- doi = {10.1063/1.5085197},\n- URL = {\n- https://doi.org/10.1063/1.5085197\n- },\n- eprint = {\n- https://doi.org/10.1063/1.5085197\n- }\n- }\n- </citation>\n+ <citation type="doi">10.1063/1.5085197</citation>\n <citation type="bibtex">\n @article{larsen2017atomic,\n title={The atomic simulation environment\xe2\x80\x94a Python library for working with atoms},\n' |