pm_asephonons: pm_asephonons.xml annotate

annotate pm_asephonons.xml @ 3:fd28cbdb134e draft

planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_asephonons commit 70a4d37ecdf5d586703cfc509922311e95d3205c

author	muon-spectroscopy-computational-project
date	Tue, 18 Jul 2023 13:26:32 +0000
parents	dd3ca8457fcd
children	b47a2fd2b10f

rev	line source
3 fd28cbdb134e planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_asephonons commit 70a4d37ecdf5d586703cfc509922311e95d3205c muon-spectroscopy-computational-project parents: 2 diff changeset	1 <tool id="pm_asephonons" name="PyMuonSuite Phonons" version="@PYMUONSUITE_VERSION@+galaxy@WRAPPER_VERSION@" python_template_version="3.5" profile="22.05" license="MIT">
0 4bc5e66259ca planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_asephonons commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	2 <description>calculate phonons using ASE and DFTB+</description>
4bc5e66259ca planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_asephonons commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	3 <macros>
2 dd3ca8457fcd planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_asephonons commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: 1 diff changeset	4 <!-- version of this tool wrapper (integer) -->
dd3ca8457fcd planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_asephonons commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: 1 diff changeset	5 <token name="@WRAPPER_VERSION@">0</token>
dd3ca8457fcd planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_asephonons commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: 1 diff changeset	6 <import>muon_macros.xml</import>
0 4bc5e66259ca planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_asephonons commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	7 </macros>
4bc5e66259ca planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_asephonons commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	8 <creator>
4bc5e66259ca planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_asephonons commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	9 <person givenName="Jyothish" familyName="Thomas" identifier="https://orcid.org/0000-0003-4724-6924"/>
4bc5e66259ca planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_asephonons commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	10 <person givenName="Eli" familyName="Chadwick" url="https://github.com/elichad" identifier="https://orcid.org/0000-0002-0035-6475"/>
4bc5e66259ca planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_asephonons commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	11 <organization url="https://muon-spectroscopy-computational-project.github.io/index.html" name="The Muon Spectroscopy Computational Project"/>
4bc5e66259ca planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_asephonons commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	12 </creator>
4bc5e66259ca planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_asephonons commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	13 <requirements>
4bc5e66259ca planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_asephonons commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	14 <!-- note versioning is different due to multiple dependencies -->
3 fd28cbdb134e planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_asephonons commit 70a4d37ecdf5d586703cfc509922311e95d3205c muon-spectroscopy-computational-project parents: 2 diff changeset	15 <requirement type="package" version="@PYMUONSUITE_VERSION@">pymuonsuite</requirement>
0 4bc5e66259ca planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_asephonons commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	16 <requirement type="package" version="21.2">dftbplus</requirement>
4bc5e66259ca planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_asephonons commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	17 <requirement type="package" version="1.22.4">numpy</requirement> <!-- pinned due to numpy/ASE/DFTB+ incompatibility https://github.com/dftbplus/dftbplus/issues/1064 -->
4bc5e66259ca planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_asephonons commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	18 <requirement type="package" version="3.0">zip</requirement>
4bc5e66259ca planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_asephonons commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	19 </requirements>
4bc5e66259ca planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_asephonons commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	20 <command detect_errors="exit_code"><![CDATA[
2 dd3ca8457fcd planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_asephonons commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: 1 diff changeset	21 structure_name_internal='input_structure.$pbc.structure.ext' &&
dd3ca8457fcd planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_asephonons commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: 1 diff changeset	22 ln -s '$pho_params' pho_params.yaml &&
dd3ca8457fcd planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_asephonons commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: 1 diff changeset	23 ln -s '$pbc.structure' \$structure_name_internal &&
0 4bc5e66259ca planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_asephonons commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	24 cat pho_params.yaml &&
2 dd3ca8457fcd planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_asephonons commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: 1 diff changeset	25 err=0 &&
dd3ca8457fcd planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_asephonons commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: 1 diff changeset	26 pm-asephonons \$structure_name_internal pho_params.yaml \|\| err=\$? &&
0 4bc5e66259ca planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_asephonons commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	27 echo "Asephonons output:" &&
4bc5e66259ca planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_asephonons commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	28 cat asephonons.out &&
4bc5e66259ca planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_asephonons commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	29 if [ \$err != 0 ] ; then echo "errored" && exit 24 ; fi &&
2 dd3ca8457fcd planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_asephonons commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: 1 diff changeset	30 ln -s '${name}_phonons.txt' phonon_report.txt &&
dd3ca8457fcd planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_asephonons commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: 1 diff changeset	31 zip -r out_zip.zip '$name' '${name}_phonons.txt' asephonons.out band.out pho_params.yaml
0 4bc5e66259ca planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_asephonons commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	32 ]]></command>
2 dd3ca8457fcd planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_asephonons commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: 1 diff changeset	33 <configfiles>
dd3ca8457fcd planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_asephonons commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: 1 diff changeset	34 <configfile name="pho_params">name: $name
dd3ca8457fcd planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_asephonons commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: 1 diff changeset	35 phonon_kpoint_grid: $phonon_kpoint_grid.replace('__ob__', '[').replace('__cb__', ']')
dd3ca8457fcd planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_asephonons commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: 1 diff changeset	36 kpoint_grid: $kpoint_grid.replace('__ob__', '[').replace('__cb__', ']')
dd3ca8457fcd planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_asephonons commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: 1 diff changeset	37 force_tol: $force_tol
dd3ca8457fcd planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_asephonons commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: 1 diff changeset	38 dftb_set: $dftb_set
dd3ca8457fcd planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_asephonons commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: 1 diff changeset	39 pbc: $pbc.pbc
dd3ca8457fcd planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_asephonons commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: 1 diff changeset	40 force_clean: false</configfile>
dd3ca8457fcd planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_asephonons commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: 1 diff changeset	41 </configfiles>
0 4bc5e66259ca planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_asephonons commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	42 <inputs>
2 dd3ca8457fcd planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_asephonons commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: 1 diff changeset	43 <param argument="name" type="text" value="struct" label="Structure name" help="Name of the structure."/>
dd3ca8457fcd planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_asephonons commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: 1 diff changeset	44 <param argument="phonon_kpoint_grid" type="text" value="[1, 1, 1]" label="Phonon k-points">
dd3ca8457fcd planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_asephonons commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: 1 diff changeset	45 <validator type="regex" message="Input should only contain whitespace, '[', ']', ',' and digits.">^[\s\d,\[\]]+$</validator>
dd3ca8457fcd planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_asephonons commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: 1 diff changeset	46 </param>
dd3ca8457fcd planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_asephonons commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: 1 diff changeset	47 <param argument="kpoint_grid" type="text" value="[1, 1, 1]" label="K-points used for DFTB+ calculation">
dd3ca8457fcd planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_asephonons commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: 1 diff changeset	48 <validator type="regex" message="Input should only contain whitespace, '[', ']', ',' and digits.">^[\s\d,\[\]]+$</validator>
0 4bc5e66259ca planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_asephonons commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	49 </param>
2 dd3ca8457fcd planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_asephonons commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: 1 diff changeset	50 <param argument="force_tol" type="float" min="0.0" value="0.01" label="Force tolerance for optimisation"/>
dd3ca8457fcd planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_asephonons commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: 1 diff changeset	51 <expand macro="dftb_set"/>
dd3ca8457fcd planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_asephonons commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: 1 diff changeset	52 <conditional name="pbc">
dd3ca8457fcd planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_asephonons commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: 1 diff changeset	53 <param argument="pbc" type="select" display="radio" multiple="false" label="Use periodic boundary conditions (PBC)" help="Whether to turn on PBC conditions in DFTB+. Note that XYZ files cannot be used with PBC.">
dd3ca8457fcd planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_asephonons commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: 1 diff changeset	54 <option selected="true" value="true">Yes</option>
dd3ca8457fcd planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_asephonons commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: 1 diff changeset	55 <option value="false">No</option>
dd3ca8457fcd planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_asephonons commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: 1 diff changeset	56 </param>
dd3ca8457fcd planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_asephonons commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: 1 diff changeset	57 <when value="true">
dd3ca8457fcd planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_asephonons commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: 1 diff changeset	58 <param name="structure" type="data" format="cell, cif, extxyz" label="Structure file" help="The structure to generate the phonon report from. Accepted file types: CELL, CIF, XYZ (extended ONLY)."/>
dd3ca8457fcd planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_asephonons commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: 1 diff changeset	59 </when>
dd3ca8457fcd planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_asephonons commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: 1 diff changeset	60 <when value="false">
dd3ca8457fcd planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_asephonons commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: 1 diff changeset	61 <param name="structure" type="data" format="cell, cif, extxyz, xyz" label="Structure file" help="The structure to generate the phonon report from. Accepted file types: CELL, CIF, XYZ (standard or extended)."/>
dd3ca8457fcd planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_asephonons commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: 1 diff changeset	62 </when>
dd3ca8457fcd planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_asephonons commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: 1 diff changeset	63 </conditional>
0 4bc5e66259ca planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_asephonons commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	64 </inputs>
4bc5e66259ca planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_asephonons commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	65 <outputs>
2 dd3ca8457fcd planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_asephonons commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: 1 diff changeset	66 <data label="phonons outputs of $pbc.structure.name" name="phonon_outputs" format="zip" from_work_dir="out_zip.zip"/>
dd3ca8457fcd planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_asephonons commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: 1 diff changeset	67 <data label="phonon report for $pbc.structure.name" name="phonon_report" format="txt" from_work_dir="phonon_report.txt"/>
0 4bc5e66259ca planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_asephonons commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	68 </outputs>
4bc5e66259ca planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_asephonons commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	69 <tests>
1 641fda3dfb62 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_asephonons commit 6a07c4caed5ef35f35198d54ebafd7d1d6d60edb muon-spectroscopy-computational-project parents: 0 diff changeset	70 <test expect_num_outputs="2">
2 dd3ca8457fcd planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_asephonons commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: 1 diff changeset	71 <param name="name" value="Si"/>
dd3ca8457fcd planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_asephonons commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: 1 diff changeset	72 <param name="dftb_set" value="pbc-0-3"/>
dd3ca8457fcd planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_asephonons commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: 1 diff changeset	73 <conditional name="pbc">
dd3ca8457fcd planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_asephonons commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: 1 diff changeset	74 <param name="structure" value="Si.cell" ftype="cell"/>
dd3ca8457fcd planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_asephonons commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: 1 diff changeset	75 </conditional>
dd3ca8457fcd planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_asephonons commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: 1 diff changeset	76 <output name="phonon_report" file="test_out.txt" ftype="txt" compare="re_match">
dd3ca8457fcd planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_asephonons commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: 1 diff changeset	77 <assert_contents>
dd3ca8457fcd planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_asephonons commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: 1 diff changeset	78 <has_size value="8255" delta="20"/>
dd3ca8457fcd planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_asephonons commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: 1 diff changeset	79 </assert_contents>
dd3ca8457fcd planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_asephonons commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: 1 diff changeset	80 </output>
dd3ca8457fcd planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_asephonons commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: 1 diff changeset	81 </test>
dd3ca8457fcd planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_asephonons commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: 1 diff changeset	82 <test expect_num_outputs="2">
0 4bc5e66259ca planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_asephonons commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	83 <param name="name" value="Si"/>
4bc5e66259ca planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_asephonons commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	84 <param name="dftb_set" value="pbc-0-3"/>
2 dd3ca8457fcd planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_asephonons commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: 1 diff changeset	85 <conditional name="pbc">
dd3ca8457fcd planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_asephonons commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: 1 diff changeset	86 <param name="structure" value="Si.cif" ftype="cif"/>
dd3ca8457fcd planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_asephonons commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: 1 diff changeset	87 </conditional>
dd3ca8457fcd planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_asephonons commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: 1 diff changeset	88 <output name="phonon_report" file="test_out.txt" ftype="txt" compare="re_match">
dd3ca8457fcd planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_asephonons commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: 1 diff changeset	89 <assert_contents>
dd3ca8457fcd planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_asephonons commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: 1 diff changeset	90 <has_size value="8255" delta="20"/>
dd3ca8457fcd planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_asephonons commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: 1 diff changeset	91 </assert_contents>
dd3ca8457fcd planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_asephonons commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: 1 diff changeset	92 </output>
dd3ca8457fcd planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_asephonons commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: 1 diff changeset	93 </test>
dd3ca8457fcd planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_asephonons commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: 1 diff changeset	94 <test expect_num_outputs="2">
dd3ca8457fcd planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_asephonons commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: 1 diff changeset	95 <param name="name" value="Si"/>
dd3ca8457fcd planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_asephonons commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: 1 diff changeset	96 <param name="dftb_set" value="pbc-0-3"/>
dd3ca8457fcd planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_asephonons commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: 1 diff changeset	97 <conditional name="pbc">
dd3ca8457fcd planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_asephonons commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: 1 diff changeset	98 <param name="pbc" value="false"/>
dd3ca8457fcd planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_asephonons commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: 1 diff changeset	99 <param name="structure" value="Si.xyz" ftype="xyz"/>
dd3ca8457fcd planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_asephonons commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: 1 diff changeset	100 </conditional>
0 4bc5e66259ca planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_asephonons commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	101 <output name="phonon_report" file="test_out.txt" ftype="txt" compare="re_match">
4bc5e66259ca planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_asephonons commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	102 <assert_contents>
4bc5e66259ca planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_asephonons commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	103 <has_size value="8155" delta="20"/>
4bc5e66259ca planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_asephonons commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	104 </assert_contents>
4bc5e66259ca planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_asephonons commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	105 </output>
4bc5e66259ca planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_asephonons commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	106 </test>
1 641fda3dfb62 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_asephonons commit 6a07c4caed5ef35f35198d54ebafd7d1d6d60edb muon-spectroscopy-computational-project parents: 0 diff changeset	107 <test expect_num_outputs="2">
0 4bc5e66259ca planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_asephonons commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	108 <param name="name" value="Si"/>
4bc5e66259ca planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_asephonons commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	109 <param name="dftb_set" value="pbc-0-3"/>
2 dd3ca8457fcd planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_asephonons commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: 1 diff changeset	110 <conditional name="pbc">
dd3ca8457fcd planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_asephonons commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: 1 diff changeset	111 <param name="structure" value="Si.extxyz" ftype="extxyz"/>
dd3ca8457fcd planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_asephonons commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: 1 diff changeset	112 </conditional>
0 4bc5e66259ca planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_asephonons commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	113 <output name="phonon_report" file="test_out.txt" ftype="txt" compare="re_match">
4bc5e66259ca planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_asephonons commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	114 <assert_contents>
2 dd3ca8457fcd planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_asephonons commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: 1 diff changeset	115 <has_size value="8255" delta="20"/>
0 4bc5e66259ca planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_asephonons commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	116 </assert_contents>
4bc5e66259ca planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_asephonons commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	117 </output>
4bc5e66259ca planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_asephonons commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	118 </test>
4bc5e66259ca planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_asephonons commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	119 </tests>
4bc5e66259ca planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_asephonons commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	120 <help><![CDATA[
4bc5e66259ca planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_asephonons commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	121 usage: pm-asephonons structure params
4bc5e66259ca planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_asephonons commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	122
4bc5e66259ca planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_asephonons commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	123 Given an input structure, this tool generates a phonon report for that structure using the parameters provided.
4bc5e66259ca planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_asephonons commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	124
2 dd3ca8457fcd planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_asephonons commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: 1 diff changeset	125 PyMuonSuite is distributed under the GPLv3 license. This tool wrapper is distributed under the MIT license.
dd3ca8457fcd planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_asephonons commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: 1 diff changeset	126
dd3ca8457fcd planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_asephonons commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: 1 diff changeset	127 All data is licensed under the Creative Commons Attribution-ShareAlike 4.0
dd3ca8457fcd planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_asephonons commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: 1 diff changeset	128 International License. The full text of the license can be found at:
dd3ca8457fcd planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_asephonons commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: 1 diff changeset	129
dd3ca8457fcd planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_asephonons commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: 1 diff changeset	130 https://creativecommons.org/licenses/by-sa/4.0/legalcode
dd3ca8457fcd planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_asephonons commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: 1 diff changeset	131
dd3ca8457fcd planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_asephonons commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: 1 diff changeset	132 For specific data sets remember to cite the following papers, by element :
dd3ca8457fcd planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_asephonons commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: 1 diff changeset	133
dd3ca8457fcd planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_asephonons commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: 1 diff changeset	134 \| 3-ob-1
dd3ca8457fcd planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_asephonons commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: 1 diff changeset	135
dd3ca8457fcd planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_asephonons commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: 1 diff changeset	136 +--------------+------------------------------------------------+-----------------------------------+------------------------------------+
dd3ca8457fcd planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_asephonons commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: 1 diff changeset	137 \| [JCTC2013] \| \ J. Chem. Theory Comput., 2013, 9, 338-354. \| (O, N, C, H) \| https://doi.org/10.1021/ct300849w \|
dd3ca8457fcd planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_asephonons commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: 1 diff changeset	138 +--------------+------------------------------------------------+-----------------------------------+------------------------------------+
dd3ca8457fcd planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_asephonons commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: 1 diff changeset	139 \| [JCTC2014] \| \ J. Chem. Theory Comput., 2014, 10, 1518-1537.\| (P,S-\*) \| https://doi.org/10.1021/ct401002w \|
dd3ca8457fcd planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_asephonons commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: 1 diff changeset	140 +--------------+------------------------------------------------+-----------------------------------+------------------------------------+
dd3ca8457fcd planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_asephonons commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: 1 diff changeset	141 \| [JCTC2015-1] \| \ J. Phys. Chem. B, 2015, 119, 1062-1082. \| (Mg,Zn-\*) \| https://doi.org/10.1021/jp506557r \|
dd3ca8457fcd planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_asephonons commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: 1 diff changeset	142 +--------------+------------------------------------------------+-----------------------------------+------------------------------------+
dd3ca8457fcd planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_asephonons commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: 1 diff changeset	143 \| [JCTC2015-2] \| \ J. Chem. Theory Comput., 2015, 11, 332-342. \| (Na,F,K,Ca,Cl,Br,I-\*) \| https://doi.org/10.1021/ct5009137 \|
dd3ca8457fcd planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_asephonons commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: 1 diff changeset	144 +--------------+------------------------------------------------+-----------------------------------+------------------------------------+
dd3ca8457fcd planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_asephonons commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: 1 diff changeset	145
dd3ca8457fcd planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_asephonons commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: 1 diff changeset	146 \|
dd3ca8457fcd planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_asephonons commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: 1 diff changeset	147 \| pbc-0-3
dd3ca8457fcd planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_asephonons commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: 1 diff changeset	148
dd3ca8457fcd planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_asephonons commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: 1 diff changeset	149 +------------+--------------------------------------------------------------------------------------------+---------+------------------------------------------------+
dd3ca8457fcd planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_asephonons commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: 1 diff changeset	150 \| [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 \|
dd3ca8457fcd planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_asephonons commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: 1 diff changeset	151 +------------+--------------------------------------------------------------------------------------------+---------+------------------------------------------------+
dd3ca8457fcd planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_asephonons commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: 1 diff changeset	152 \| [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 \|
dd3ca8457fcd planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_asephonons commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: 1 diff changeset	153 +------------+--------------------------------------------------------------------------------------------+---------+------------------------------------------------+
dd3ca8457fcd planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_asephonons commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: 1 diff changeset	154 \| [Silicon] \| \ A. Sieck, Th. Frauenheim, and K. A. Jackson, phys. stat. sol. (b) 240, 537 (2003). \| (Si) \| https://doi.org/10.1002/pssb.200301886 \|
dd3ca8457fcd planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_asephonons commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: 1 diff changeset	155 +------------+--------------------------------------------------------------------------------------------+---------+------------------------------------------------+
dd3ca8457fcd planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_asephonons commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: 1 diff changeset	156 \| [Fluorine] \| \ C. Koehler and Th. Frauenheim, Surf. Sci. 600, 453 (2006). \| \ (F) \| https://doi.org/10.1016/j.susc.2005.10.044 \|
dd3ca8457fcd planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_asephonons commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: 1 diff changeset	157 +------------+--------------------------------------------------------------------------------------------+---------+------------------------------------------------+
dd3ca8457fcd planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_asephonons commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: 1 diff changeset	158 \| [Iron] \| \ C. Koehler, G. Seifert and Th. Frauenheim, Chem. Phys. 309, 23 (2005). \| (Fe) \| https://doi.org/10.1016/j.chemphys.2004.03.034 \|
dd3ca8457fcd planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_asephonons commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: 1 diff changeset	159 +------------+--------------------------------------------------------------------------------------------+---------+------------------------------------------------+
dd3ca8457fcd planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_asephonons commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: 1 diff changeset	160 \| [SiSi] \| \ A. Sieck, PhD. Thesis, University of Paderborn, 2000. \| (Si-Si) \| https://www.osti.gov/etdeweb/biblio/20249635 \|
dd3ca8457fcd planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_asephonons commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: 1 diff changeset	161 +------------+--------------------------------------------------------------------------------------------+---------+------------------------------------------------+
dd3ca8457fcd planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_asephonons commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: 1 diff changeset	162
dd3ca8457fcd planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_asephonons commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: 1 diff changeset	163 \|
dd3ca8457fcd planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_asephonons commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: 1 diff changeset	164 \| The full sets and all other data can be found at the following URLs:
dd3ca8457fcd planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_asephonons commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: 1 diff changeset	165
dd3ca8457fcd planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_asephonons commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: 1 diff changeset	166 +----------+------------------------------------------------------------+
dd3ca8457fcd planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_asephonons commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: 1 diff changeset	167 \| 3-ob-1 \| https://www.dftb.org/parameters/download/3ob/3ob-3-1-cc/ \|
dd3ca8457fcd planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_asephonons commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: 1 diff changeset	168 +----------+------------------------------------------------------------+
dd3ca8457fcd planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_asephonons commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: 1 diff changeset	169 \| pbc-0-3 \| https://www.dftb.org/parameters/download/pbc/pbc-0-3-cc/ \|
dd3ca8457fcd planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_asephonons commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: 1 diff changeset	170 +----------+------------------------------------------------------------+
dd3ca8457fcd planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_asephonons commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: 1 diff changeset	171
dd3ca8457fcd planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_asephonons commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: 1 diff changeset	172 \|
0 4bc5e66259ca planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_asephonons commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	173 ]]></help>
4bc5e66259ca planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_asephonons commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	174 <citations>
3 fd28cbdb134e planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_asephonons commit 70a4d37ecdf5d586703cfc509922311e95d3205c muon-spectroscopy-computational-project parents: 2 diff changeset	175 <citation type="doi">@PYMUONSUITE_CITATION@</citation>
2 dd3ca8457fcd planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_asephonons commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: 1 diff changeset	176 <citation type="doi">10.1063/1.5085197</citation>
0 4bc5e66259ca planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_asephonons commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	177 <citation type="bibtex">
4bc5e66259ca planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_asephonons commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	178 @article{larsen2017atomic,
4bc5e66259ca planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_asephonons commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	179 title={The atomic simulation environment—a Python library for working with atoms},
4bc5e66259ca planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_asephonons commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	180 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},
4bc5e66259ca planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_asephonons commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	181 journal={Journal of Physics: Condensed Matter},
4bc5e66259ca planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_asephonons commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	182 volume={29},
4bc5e66259ca planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_asephonons commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	183 number={27},
4bc5e66259ca planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_asephonons commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	184 pages={273002},
4bc5e66259ca planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_asephonons commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	185 year={2017},
4bc5e66259ca planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_asephonons commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	186 publisher={IOP Publishing}
4bc5e66259ca planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_asephonons commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	187 }
4bc5e66259ca planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_asephonons commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	188 </citation>
4bc5e66259ca planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_asephonons commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	189 </citations>
4bc5e66259ca planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_asephonons commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	190 </tool>

Mercurial > repos > muon-spectroscopy-computational-project > pm_asephonons

annotate pm_asephonons.xml @ 3:fd28cbdb134e draft