| Next changeset 1:d8146a73b011 (2022-09-15) |
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Commit message:
planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_symmetry commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 |
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added:
pm_symmetry.xml pm_symmetry_test_report.html test-data/Si.cell test-data/Si.cif test-data/Si.extxyz test-data/Si.xyz test-data/test_out.txt |
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| diff -r 000000000000 -r 39d7644724dc pm_symmetry.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/pm_symmetry.xml Thu Aug 25 16:19:38 2022 +0000 |
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| @@ -0,0 +1,91 @@ +<tool id="pm_symmetry" name="PyMuonSuite Symmetry" version="@TOOL_VERSION@+galaxy@WRAPPER_VERSION@" python_template_version="3.5" profile="22.01"> + <description>generate Wyckoff points symmetry report</description> + <macros> + <!-- version of underlying tool (PEP 440) --> + <token name="@TOOL_VERSION@">0.2.1</token> + <!-- version of this tool wrapper (integer) --> + <token name="@WRAPPER_VERSION@">1</token> + <!-- citation should be updated with every underlying tool version --> + <!-- typical fields to update are version, month, year, and doi --> + <token name="@TOOL_CITATION@"> + @software{pymuon-suite, + author = {Sturniolo, Simone and Liborio, Leandro and Chadwick, Eli and Murgatroyd, Laura and Laverack, Adam and {Muon Spectroscopy Computational Project}}, + license = {GPL-3.0}, + title = {{pymuon-suite}}, + url = {https://github.com/muon-spectroscopy-computational-project/pymuon-suite}, + version = {v0.2.1}, + month = {2}, + year = {2022}, + doi = {} + } + </token> + </macros> + <creator> + <person givenName="Jyothish" familyName="Thomas" identifier="https://orcid.org/0000-0003-4724-6924"/> + <person givenName="Eli" familyName="Chadwick" url="https://github.com/elichad" identifier="https://orcid.org/0000-0002-0035-6475"/> + <organization url="https://muon-spectroscopy-computational-project.github.io/index.html" name="The Muon Spectroscopy Computational Project"/> + </creator> + <requirements> + <requirement type="package" version="@TOOL_VERSION@">pymuonsuite</requirement> + </requirements> + <command detect_errors="exit_code"><![CDATA[ + structure_name_internal=\$(sed 's/ /\_/g' <<< "$structure.name") && + ln -s $structure \$structure_name_internal && + pm-symmetry \$structure_name_internal > out.txt + ]]></command> + <inputs> + <param type="data" name="structure" label="Structure file" format="cell,cif,xyz,extxyz" help="The structure to calculate symmetries of. Accepted file types: cell."/> + </inputs> + <outputs> + <data label="symmetry of $structure.name" name="symmetry_report" format="txt" from_work_dir="out.txt"/> + </outputs> + <tests> + <test> + <param name="structure" value="Si.cell" ftype="cell"/> + <output name="symmetry_report" file="test_out.txt" ftype="txt" compare="re_match_multiline"/> + </test> + <test> + <param name="structure" value="Si.cif" ftype="cif"/> + <output name="symmetry_report" file="test_out.txt" ftype="txt" compare="re_match_multiline"/> + </test> + <test expect_failure="true"> + <param name="structure" value="Si.xyz" ftype="xyz"/> + <assert_stderr> + <has_text text="TypeError: 'NoneType' object is not subscriptable"/> + </assert_stderr> + </test> + <test> + <param name="structure" value="Si.extxyz" ftype="extxyz"/> + <output name="symmetry_report" file="test_out.txt" ftype="txt" compare="re_match_multiline"/> + </test> + </tests> + <help><![CDATA[ + usage: pm-symmetry structure + + Given an input structure, generates a Wyckoff points symmetry report for that structure. + ]]></help> + <citations> + <citation type="bibtex"> + @TOOL_CITATION@ + </citation> + <citation type="bibtex"> + @article{doi:10.1063/5.0012381, + author = {Sturniolo,Simone and Liborio,Leandro }, + title = {Computational prediction of muon stopping sites: A novel take on the unperturbed electrostatic potential method}, + journal = {The Journal of Chemical Physics}, + volume = {153}, + number = {4}, + pages = {044111}, + year = {2020}, + doi = {10.1063/5.0012381}, + URL = { + https://doi.org/10.1063/5.0012381 + }, + eprint = { + https://doi.org/10.1063/5.0012381 + }, + abstract = { Finding the stopping site of the muon in a muon-spin relaxation experiment is one of the main problems of muon spectroscopy, and computational techniques that make use of quantum chemistry simulations can be of great help when looking for this stopping site. The most thorough approach would require the use of simulations, such as Density Functional Theory (DFT), to test and optimise multiple possible sites, accounting for the effect that the added muon has on its surroundings. However, this can be computationally expensive and sometimes unnecessary. Hence, in this work, we present a software implementation of the Unperturbed Electrostatic Potential (UEP) Method: an approach used for finding the muon stopping site in crystalline materials. The UEP method requires only one DFT calculation, necessary to compute the electronic density. This, in turn, is used to calculate the minima of the crystalline material’s electrostatic potential and the estimates of the muon stopping site, relying on the approximation that the muon’s presence does not significantly affect its surroundings. One of the main UEP’s assumptions is that the muon stopping site will be one of the crystalline material’s electrostatic potential minima. In this regard, we also propose some symmetry-based considerations about the properties of this crystalline material’s electrostatic potential, in particular, which sites are more likely to be its minima and why the unperturbed approximation may be sufficiently robust for them. We introduce the Python software package pymuon-suite and the various utilities it provides to facilitate these calculations, and finally, we demonstrate the effectiveness of the method with some chosen example systems. } + } + </citation> + </citations> +</tool> |
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| diff -r 000000000000 -r 39d7644724dc pm_symmetry_test_report.html --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/pm_symmetry_test_report.html Thu Aug 25 16:19:38 2022 +0000 |
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</script>\n+ </body>\n+</html>\n\\ No newline at end of file\n" |
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| diff -r 000000000000 -r 39d7644724dc test-data/Si.cell --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/Si.cell Thu Aug 25 16:19:38 2022 +0000 |
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| @@ -0,0 +1,43 @@ +# CELL file written 11:14:42 (GMT-0.0) 17th February 2021 from run Si + +%BLOCK lattice_cart + ANG + 5.47538171155659 0.530767321973160E-35 -0.131324260787022E-34 + 0.530767321973160E-35 5.47538171155659 0.313104997179767E-35 + -0.131324260787022E-34 0.313104997179767E-35 5.47538171155659 +%ENDBLOCK lattice_cart + +%BLOCK cell_constraints + 1 1 1 + 0 0 0 +%ENDBLOCK cell_constraints + +%BLOCK positions_frac + Si 0.000000000000000 0.000000000000000 0.000000000000000 + Si 0.000000000000000 0.500000000000000 0.500000000000000 + Si 0.250000000000000 0.250000000000000 0.250000000000000 + Si 0.500000000000000 0.000000000000000 0.500000000000000 + Si 0.250000000000000 0.750000000000000 0.750000000000000 + Si 0.750000000000000 0.250000000000000 0.750000000000000 + Si 0.750000000000000 0.750000000000000 0.250000000000000 + Si 0.500000000000000 0.500000000000000 0.000000000000000 +%ENDBLOCK positions_frac + +FIX_COM : true + +%BLOCK species_pot + Si 3|1.8|5|6|7|30:31:32 +%ENDBLOCK species_pot + +SYMMETRY_TOL : 0.001000 + +%BLOCK symmetry_ops +# Symm. op. 1 E + 1.000000000000000 0.000000000000000 0.000000000000000 + 0.000000000000000 1.000000000000000 0.000000000000000 + 0.000000000000000 0.000000000000000 1.000000000000000 + 0.000000000000000 0.000000000000000 0.000000000000000 +%ENDBLOCK symmetry_ops + +kpoint_mp_grid : 2 2 2 + |
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| diff -r 000000000000 -r 39d7644724dc test-data/Si.cif --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/Si.cif Thu Aug 25 16:19:38 2022 +0000 |
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| @@ -0,0 +1,33 @@ +data_image0 +_chemical_formula_structural Si8 +_chemical_formula_sum "Si8" +_cell_length_a 5.47545 +_cell_length_b 5.47545 +_cell_length_c 5.47545 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_space_group_name_H-M_alt "P 1" +_space_group_IT_number 1 + +loop_ + _space_group_symop_operation_xyz + 'x, y, z' + +loop_ + _atom_site_type_symbol + _atom_site_label + _atom_site_symmetry_multiplicity + _atom_site_fract_x + _atom_site_fract_y + _atom_site_fract_z + _atom_site_occupancy + Si Si1 1.0 0.00000 0.00000 0.00000 1.0000 + Si Si2 1.0 0.75000 0.75000 0.25000 1.0000 + Si Si3 1.0 0.50000 0.00000 0.50000 1.0000 + Si Si4 1.0 0.75000 0.25000 0.75000 1.0000 + Si Si5 1.0 0.00000 0.50000 0.50000 1.0000 + Si Si6 1.0 0.25000 0.25000 0.25000 1.0000 + Si Si7 1.0 0.25000 0.75000 0.75000 1.0000 + Si Si8 1.0 0.50000 0.50000 0.00000 1.0000 |
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| diff -r 000000000000 -r 39d7644724dc test-data/Si.extxyz --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/Si.extxyz Thu Aug 25 16:19:38 2022 +0000 |
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| @@ -0,0 +1,10 @@ +8 +Lattice="5.47545112629462 4.96819156878786e-36 1.10608096941637e-36 4.96819156878786e-36 5.47545112629462 -3.12695835139248e-36 1.10608096941637e-36 -3.12695835139248e-36 5.47545112629462" Properties=species:S:1:pos:R:3:initial_magmoms:R:1:castep_labels:S:1 pbc="T T T" +Si 0.00000000 0.00000000 0.00000000 0.00000000 NULL +Si 4.10658834 4.10658834 1.36886278 0.00000000 NULL +Si 2.73772556 0.00000000 2.73772556 0.00000000 NULL +Si 4.10658834 1.36886278 4.10658834 0.00000000 NULL +Si 0.00000000 2.73772556 2.73772556 0.00000000 NULL +Si 1.36886278 1.36886278 1.36886278 0.00000000 NULL +Si 1.36886278 4.10658834 4.10658834 0.00000000 NULL +Si 2.73772556 2.73772556 -0.00000000 0.00000000 NULL |
| b |
| diff -r 000000000000 -r 39d7644724dc test-data/Si.xyz --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/Si.xyz Thu Aug 25 16:19:38 2022 +0000 |
| b |
| @@ -0,0 +1,10 @@ +8 +Generated by cif2cell 2.0.0. : Kitano, A. et al., Physical Review, Serie 3. B - Condensed Matter (18,1978-) 64, 0452061-0452069 (2001). +Si 0.000000000000000 0.000000000000000 0.000000000000000 +Si 4.035750000000000 4.035750000000000 1.345250000000000 +Si 2.690500000000000 0.000000000000000 2.690500000000000 +Si 4.035750000000000 1.345250000000000 4.035750000000000 +Si 0.000000000000000 2.690500000000000 2.690500000000000 +Si 1.345250000000000 1.345250000000000 1.345250000000000 +Si 1.345250000000000 4.035750000000000 4.035750000000000 +Si 2.690500000000000 2.690500000000000 0.000000000000000 |
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| diff -r 000000000000 -r 39d7644724dc test-data/test_out.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_out.txt Thu Aug 25 16:19:38 2022 +0000 |
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| @@ -0,0 +1,5 @@ +Wyckoff points symmetry report for Si\.(cell|cif|xyz|extxyz) +Space Group International Symbol: Fd-3m +Space Group Hall Number: 525 +Absolute\t\tFractional\t\tHessian constraints\tOccupied +((\[(-?\d+\.\d+ ?){3}\]\t){2}(none|isotropic)\t\t\tX?\n){48} \ No newline at end of file |