Mercurial > repos > muon-spectroscopy-computational-project > pm_asephonons
diff pm_asephonons.xml @ 0:4bc5e66259ca draft
planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_asephonons commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
| author | muon-spectroscopy-computational-project |
|---|---|
| date | Thu, 25 Aug 2022 16:17:41 +0000 |
| parents | |
| children | 641fda3dfb62 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/pm_asephonons.xml Thu Aug 25 16:17:41 2022 +0000 @@ -0,0 +1,149 @@ +<tool id="pm_asephonons" name="PyMuonSuite Phonons" version="0.1.1" python_template_version="3.5" profile="22.01"> + <description>calculate phonons using ASE and DFTB+</description> + <macros> + <!-- citation should be updated with every underlying tool version --> + <!-- typical fields to update are version, month, year, and doi --> + <token name="@PYMUONSUITE_CITATION@"> + @software{pymuon-suite, + author = {Sturniolo, Simone and Liborio, Leandro and Chadwick, Eli and Murgatroyd, Laura and Laverack, Adam and {Muon Spectroscopy Computational Project}}, + license = {GPL-3.0}, + title = {{pymuon-suite}}, + url = {https://github.com/muon-spectroscopy-computational-project/pymuon-suite}, + version = {v0.2.1}, + month = {2}, + year = {2022}, + doi = {} + } + </token> + </macros> + <creator> + <person givenName="Jyothish" familyName="Thomas" identifier="https://orcid.org/0000-0003-4724-6924"/> + <person givenName="Eli" familyName="Chadwick" url="https://github.com/elichad" identifier="https://orcid.org/0000-0002-0035-6475"/> + <organization url="https://muon-spectroscopy-computational-project.github.io/index.html" name="The Muon Spectroscopy Computational Project"/> + </creator> + <requirements> + <!-- note versioning is different due to multiple dependencies --> + <requirement type="package" version="0.2.1">pymuonsuite</requirement> + <requirement type="package" version="21.2">dftbplus</requirement> + <requirement type="package" version="1.22.4">numpy</requirement> <!-- pinned due to numpy/ASE/DFTB+ incompatibility https://github.com/dftbplus/dftbplus/issues/1064 --> + <requirement type="package" version="3.0">zip</requirement> + </requirements> + <command detect_errors="exit_code"><![CDATA[ + structure_name_internal="input_structure.$structure.ext" && + touch pho_params.yaml && + ([[ ! -z "$name" ]] && printf "name: $name \n">>pho_params.yaml || ( >&2 echo "name empty" && exit 2)) && + ([[ ! -z "$phonon_kpoint_grid" ]] && ( printf "phonon_kpoint_grid: $phonon_kpoint_grid \n" | sed "s/__ob__/[/g" | sed "s/__cb__/]/g" )>>pho_params.yaml || ( >&2 echo "phonon_kpoint_grid empty" && exit 2)) && + ([[ ! -z "$kpoint_grid" ]] && ( printf "kpoint_grid: $kpoint_grid \n" | sed "s/__ob__/[/g" | sed "s/__cb__/]/g" )>>pho_params.yaml || ( >&2 echo "kpoint_grid empty" && exit 2)) && + ([[ ! -z "$force_tol" ]] && printf "force_tol: $force_tol \n">>pho_params.yaml || ( >&2 echo "force_tol empty" && exit 2)) && + ([[ ! -z "$dftb_set" ]] && printf "dftb_set: $dftb_set \n">>pho_params.yaml || ( >&2 echo "dftb_set empty" && exit 2)) && + ([[ ! -z "$pbc" ]] && printf "pbc: $pbc \n">>pho_params.yaml || ( >&2 echo "pbc empty" && exit 2)) && + printf "force_clean: false \n">>pho_params.yaml && + ln -s $structure \$structure_name_internal && + cat pho_params.yaml && + pm-asephonons \$structure_name_internal pho_params.yaml ; err=\$? && + echo "Asephonons output:" && + cat asephonons.out && + if [ \$err != 0 ] ; then echo "errored" && exit 24 ; fi && + ln -s "${name}_phonons.txt" phonon_report.txt && + zip -r out_zip.zip $name "${name}_phonons.txt" asephonons.out band.out pho_params.yaml + ]]></command> + <inputs> + <param type="data" name="structure" label="Structure file" format="cell" help="The structure to generate the phonon report from. Accepted file types: cell."/> + <param type="text" name="name" label="Structure name" help="Name of the structure." value="struct"/> + <param type="text" name="phonon_kpoint_grid" label="Phonon k-points" value="[1, 1, 1]"/> + <param type="text" name="kpoint_grid" label="K-points used for DFTB+ calculation" value="[1, 1, 1]"/> + <param type="float" name="force_tol" label="Force tolerance for optimisation" value="0.01"/> + <param type="select" name="dftb_set" label="DFTB set to use" value="3ob-3-1"> + <option value="3ob-3-1">3ob-3-1</option> + <option value="pbc-0-3">pbc-0-3</option> + </param> + <param type="boolean" name="pbc" label="Use periodic boundary conditions" help="Whether to turn on periodic boundary conditions in DFTB+." value="true"/> + </inputs> + <outputs> + <data label="phonons outputs of $structure.name" name="phonon_outputs" format="zip" from_work_dir="out_zip.zip"/> + <data label="phonon report for $structure.name" name="phonon_report" format="txt" from_work_dir="phonon_report.txt"/> + </outputs> + <tests> + <test> + <param name="structure" value="Si.cell" ftype="cell"/> + <param name="name" value="Si"/> + <param name="dftb_set" value="pbc-0-3"/> + <output name="phonon_report" file="test_out.txt" ftype="txt" compare="re_match"> + <assert_contents> + <has_size value="8155" delta="20"/> + </assert_contents> + </output> + </test> + <test> + <param name="structure" value="Si.cif" ftype="cif"/> + <param name="name" value="Si"/> + <param name="dftb_set" value="pbc-0-3"/> + <output name="phonon_report" file="test_out.txt" ftype="txt" compare="re_match"> + <assert_contents> + <has_size value="8155" delta="20"/> + </assert_contents> + </output> + </test> + <test> + <param name="structure" value="Si.xyz" ftype="xyz"/> + <param name="name" value="Si"/> + <param name="dftb_set" value="pbc-0-3"/> + <output name="phonon_report" file="test_out.txt" ftype="txt" compare="re_match"> + <assert_contents> + <has_size value="8155" delta="20"/> + </assert_contents> + </output> + </test> + <test> + <param name="structure" value="Si.extxyz" ftype="extxyz"/> + <param name="name" value="Si"/> + <param name="dftb_set" value="pbc-0-3"/> + <output name="phonon_report" file="test_out.txt" ftype="txt" compare="re_match"> + <assert_contents> + <has_size value="8155" delta="20"/> + </assert_contents> + </output> + </test> + </tests> + <help><![CDATA[ + usage: pm-asephonons structure params + + Given an input structure, this tool generates a phonon report for that structure using the parameters provided. + + ]]></help> + <citations> + <citation type="bibtex"> + @PYMUONSUITE_CITATION@ + </citation> + <citation type="bibtex"> + @article{doi:10.1063/1.5085197, + author = {Sturniolo,Simone and Liborio,Leandro and Jackson,Samuel }, + title = {Comparison between density functional theory and density functional tight binding approaches for finding the muon stopping site in organic molecular crystals}, + journal = {The Journal of Chemical Physics}, + volume = {150}, + number = {15}, + pages = {154301}, + year = {2019}, + doi = {10.1063/1.5085197}, + URL = { + https://doi.org/10.1063/1.5085197 + }, + eprint = { + https://doi.org/10.1063/1.5085197 + } + } + </citation> + <citation type="bibtex"> + @article{larsen2017atomic, + title={The atomic simulation environment—a Python library for working with atoms}, + author={Larsen, Ask Hjorth and Mortensen, Jens J{\o}rgen and Blomqvist, Jakob and Castelli, Ivano E and Christensen, Rune and Du{\l}ak, Marcin and Friis, Jesper and Groves, Michael N and Hammer, Bj{\o}rk and Hargus, Cory and others}, + journal={Journal of Physics: Condensed Matter}, + volume={29}, + number={27}, + pages={273002}, + year={2017}, + publisher={IOP Publishing} + } + </citation> + </citations> +</tool>