# HG changeset patch
# User muon-spectroscopy-computational-project
# Date 1675438757 0
# Node ID dd3ca8457fcd176bcd70e2d30da5f302e1dfac64
# Parent 641fda3dfb625e0fd5ef34173927241d2eefde0f
planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_asephonons commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507
diff -r 641fda3dfb62 -r dd3ca8457fcd muon_macros.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/muon_macros.xml Fri Feb 03 15:39:17 2023 +0000
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diff -r 641fda3dfb62 -r dd3ca8457fcd pm_asephonons.xml
--- a/pm_asephonons.xml Thu Sep 15 10:24:36 2022 +0000
+++ b/pm_asephonons.xml Fri Feb 03 15:39:17 2023 +0000
@@ -1,20 +1,25 @@
-
+
calculate phonons using ASE and DFTB+
+
+ 0.2.3
+
+ 0
- @software{pymuon-suite,
- author = {Sturniolo, Simone and Liborio, Leandro and Chadwick, Eli and Murgatroyd, Laura and Laverack, Adam and {Muon Spectroscopy Computational Project}},
+ @software{Sturniolo_pymuon-suite_2022,
+ author = {Sturniolo, Simone and Liborio, Leandro and Chadwick, Eli and Murgatroyd, Laura and Laverack, Adam and Mudaraddi, Anish and {Muon Spectroscopy Computational Project}},
license = {GPL-3.0},
+ month = {8},
title = {{pymuon-suite}},
url = {https://github.com/muon-spectroscopy-computational-project/pymuon-suite},
- version = {v0.2.1},
- month = {2},
- year = {2022},
- doi = {}
+ version = {v0.2.3},
+ doi = {10.5281/zenodo.7025644},
+ year = {2022}
}
+ muon_macros.xml
@@ -23,51 +28,92 @@
- pymuonsuite
+ pymuonsuite
dftbplus
numpy
zip
>pho_params.yaml || ( >&2 echo "name empty" && exit 2)) &&
- ([[ ! -z "$phonon_kpoint_grid" ]] && ( printf "phonon_kpoint_grid: $phonon_kpoint_grid \n" | sed "s/__ob__/[/g" | sed "s/__cb__/]/g" )>>pho_params.yaml || ( >&2 echo "phonon_kpoint_grid empty" && exit 2)) &&
- ([[ ! -z "$kpoint_grid" ]] && ( printf "kpoint_grid: $kpoint_grid \n" | sed "s/__ob__/[/g" | sed "s/__cb__/]/g" )>>pho_params.yaml || ( >&2 echo "kpoint_grid empty" && exit 2)) &&
- ([[ ! -z "$force_tol" ]] && printf "force_tol: $force_tol \n">>pho_params.yaml || ( >&2 echo "force_tol empty" && exit 2)) &&
- ([[ ! -z "$dftb_set" ]] && printf "dftb_set: $dftb_set \n">>pho_params.yaml || ( >&2 echo "dftb_set empty" && exit 2)) &&
- ([[ ! -z "$pbc" ]] && printf "pbc: $pbc \n">>pho_params.yaml || ( >&2 echo "pbc empty" && exit 2)) &&
- printf "force_clean: false \n">>pho_params.yaml &&
- ln -s $structure \$structure_name_internal &&
+ structure_name_internal='input_structure.$pbc.structure.ext' &&
+ ln -s '$pho_params' pho_params.yaml &&
+ ln -s '$pbc.structure' \$structure_name_internal &&
cat pho_params.yaml &&
- pm-asephonons \$structure_name_internal pho_params.yaml ; err=\$? &&
+ err=0 &&
+ pm-asephonons \$structure_name_internal pho_params.yaml || err=\$? &&
echo "Asephonons output:" &&
cat asephonons.out &&
if [ \$err != 0 ] ; then echo "errored" && exit 24 ; fi &&
- ln -s "${name}_phonons.txt" phonon_report.txt &&
- zip -r out_zip.zip $name "${name}_phonons.txt" asephonons.out band.out pho_params.yaml
+ ln -s '${name}_phonons.txt' phonon_report.txt &&
+ zip -r out_zip.zip '$name' '${name}_phonons.txt' asephonons.out band.out pho_params.yaml
]]>
+
+ name: $name
+phonon_kpoint_grid: $phonon_kpoint_grid.replace('__ob__', '[').replace('__cb__', ']')
+kpoint_grid: $kpoint_grid.replace('__ob__', '[').replace('__cb__', ']')
+force_tol: $force_tol
+dftb_set: $dftb_set
+pbc: $pbc.pbc
+force_clean: false
+
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@@ -110,29 +138,60 @@
Given an input structure, this tool generates a phonon report for that structure using the parameters provided.
+ PyMuonSuite is distributed under the GPLv3 license. This tool wrapper is distributed under the MIT license.
+
+ All data is licensed under the Creative Commons Attribution-ShareAlike 4.0
+ International License. The full text of the license can be found at:
+
+ https://creativecommons.org/licenses/by-sa/4.0/legalcode
+
+ For specific data sets remember to cite the following papers, by element :
+
+ | **3-ob-1**
+
+ +--------------+------------------------------------------------+-----------------------------------+------------------------------------+
+ | [JCTC2013] | \ J. Chem. Theory Comput., 2013, 9, 338-354. | (O, N, C, H) | https://doi.org/10.1021/ct300849w |
+ +--------------+------------------------------------------------+-----------------------------------+------------------------------------+
+ | [JCTC2014] | \ J. Chem. Theory Comput., 2014, 10, 1518-1537.| (P,S-\*) | https://doi.org/10.1021/ct401002w |
+ +--------------+------------------------------------------------+-----------------------------------+------------------------------------+
+ | [JCTC2015-1] | \ J. Phys. Chem. B, 2015, 119, 1062-1082. | (Mg,Zn-\*) | https://doi.org/10.1021/jp506557r |
+ +--------------+------------------------------------------------+-----------------------------------+------------------------------------+
+ | [JCTC2015-2] | \ J. Chem. Theory Comput., 2015, 11, 332-342. | (Na,F,K,Ca,Cl,Br,I-\*) | https://doi.org/10.1021/ct5009137 |
+ +--------------+------------------------------------------------+-----------------------------------+------------------------------------+
+
+ |
+ | **pbc-0-3**
+
+ +------------+--------------------------------------------------------------------------------------------+---------+------------------------------------------------+
+ | [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 |
+ +------------+--------------------------------------------------------------------------------------------+---------+------------------------------------------------+
+ | [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 |
+ +------------+--------------------------------------------------------------------------------------------+---------+------------------------------------------------+
+ | [Silicon] | \ A. Sieck, Th. Frauenheim, and K. A. Jackson, phys. stat. sol. (b) 240, 537 (2003). | (Si) | https://doi.org/10.1002/pssb.200301886 |
+ +------------+--------------------------------------------------------------------------------------------+---------+------------------------------------------------+
+ | [Fluorine] | \ C. Koehler and Th. Frauenheim, Surf. Sci. 600, 453 (2006). | \ (F) | https://doi.org/10.1016/j.susc.2005.10.044 |
+ +------------+--------------------------------------------------------------------------------------------+---------+------------------------------------------------+
+ | [Iron] | \ C. Koehler, G. Seifert and Th. Frauenheim, Chem. Phys. 309, 23 (2005). | (Fe) | https://doi.org/10.1016/j.chemphys.2004.03.034 |
+ +------------+--------------------------------------------------------------------------------------------+---------+------------------------------------------------+
+ | [SiSi] | \ A. Sieck, PhD. Thesis, University of Paderborn, 2000. | (Si-Si) | https://www.osti.gov/etdeweb/biblio/20249635 |
+ +------------+--------------------------------------------------------------------------------------------+---------+------------------------------------------------+
+
+ |
+ | The full sets and all other data can be found at the following URLs:
+
+ +----------+------------------------------------------------------------+
+ | 3-ob-1 | https://www.dftb.org/parameters/download/3ob/3ob-3-1-cc/ |
+ +----------+------------------------------------------------------------+
+ | pbc-0-3 | https://www.dftb.org/parameters/download/pbc/pbc-0-3-cc/ |
+ +----------+------------------------------------------------------------+
+
+ |
]]>
@PYMUONSUITE_CITATION@
-
- @article{doi:10.1063/1.5085197,
- author = {Sturniolo,Simone and Liborio,Leandro and Jackson,Samuel },
- title = {Comparison between density functional theory and density functional tight binding approaches for finding the muon stopping site in organic molecular crystals},
- journal = {The Journal of Chemical Physics},
- volume = {150},
- number = {15},
- pages = {154301},
- year = {2019},
- doi = {10.1063/1.5085197},
- URL = {
- https://doi.org/10.1063/1.5085197
- },
- eprint = {
- https://doi.org/10.1063/1.5085197
- }
- }
-
+ 10.1063/1.5085197
@article{larsen2017atomic,
title={The atomic simulation environment—a Python library for working with atoms},