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

annotate pm_asephonons.xml @ 4:b47a2fd2b10f draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_asephonons commit 389608650050596b28bc0c055de9f98c513a6f65
author muon-spectroscopy-computational-project
date Thu, 18 Jul 2024 09:07:17 +0000
parents fd28cbdb134e
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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) -->
4
b47a2fd2b10f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_asephonons commit 389608650050596b28bc0c055de9f98c513a6f65
muon-spectroscopy-computational-project
parents: 3
diff changeset
5 <token name="@WRAPPER_VERSION@">1</token>
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
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>
4
b47a2fd2b10f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_asephonons commit 389608650050596b28bc0c055de9f98c513a6f65
muon-spectroscopy-computational-project
parents: 3
diff changeset
66 <data label="phonons outputs on ${on_string}" name="phonon_outputs" format="zip" from_work_dir="out_zip.zip"/>
b47a2fd2b10f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_asephonons commit 389608650050596b28bc0c055de9f98c513a6f65
muon-spectroscopy-computational-project
parents: 3
diff changeset
67 <data label="phonon report on ${on_string}" 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>