| Next changeset 1:150301c057b0 (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_muairss_write commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 |
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added:
get_out_folder.py pm_muairss_write.xml test-data/Si.cell test-data/Si.cif test-data/Si.extxyz test-data/Si.param test-data/Si.xyz test-data/configcastep_t_no_out_folder_no_castep_param.yaml test-data/configcastep_t_with_out_folder_and_castep_param.yaml test-data/configdftb_t.yaml test-data/configuep_t.yaml test-data/tree_castep_t_no_outfolder_and_castep_param.txt test-data/tree_castep_t_with_out_folder_and_castep_param.txt test-data/tree_dftb.txt test-data/tree_uep.txt |
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| diff -r 000000000000 -r 0679aeb7cefc get_out_folder.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/get_out_folder.py Thu Aug 25 16:19:08 2022 +0000 |
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| @@ -0,0 +1,11 @@ +import sys + +import yaml + + +try: + with open('params.yaml') as f: + data = yaml.safe_load(f) + sys.stdout.write(data['out_folder']) +except KeyError: + sys.stdout.write('muon-airss-out') |
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| diff -r 000000000000 -r 0679aeb7cefc pm_muairss_write.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/pm_muairss_write.xml Thu Aug 25 16:19:08 2022 +0000 |
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| b'@@ -0,0 +1,246 @@\n+<tool id="pm_muairss_write" name="PyMuonSuite AIRSS Generate" version="@TOOL_VERSION@+galaxy@WRAPPER_VERSION@" python_template_version="3.5" profile="22.01">\n+ <description>generate muonated structures</description>\n+ <macros>\n+ <!-- version of underlying tool (PEP 440) -->\n+ <token name="@TOOL_VERSION@">0.2.1</token>\n+ <!-- version of this tool wrapper (integer) -->\n+ <token name="@WRAPPER_VERSION@">1</token>\n+ <!-- citation should be updated with every underlying tool version -->\n+ <!-- typical fields to update are version, month, year, and doi -->\n+ <token name="@TOOL_CITATION@">\n+ @software{pymuon-suite,\n+ author = {Sturniolo, Simone and Liborio, Leandro and Chadwick, Eli and Murgatroyd, Laura and Laverack, Adam and {Muon Spectroscopy Computational Project}},\n+ license = {GPL-3.0},\n+ title = {{pymuon-suite}},\n+ url = {https://github.com/muon-spectroscopy-computational-project/pymuon-suite},\n+ version = {v0.2.1},\n+ month = {2},\n+ year = {2022},\n+ doi = {}\n+ }\n+ </token>\n+ </macros>\n+ <creator>\n+ <person givenName="Eli" familyName="Chadwick" url="https://github.com/elichad" identifier="https://orcid.org/0000-0002-0035-6475"/>\n+ <person givenName="Jyothish" familyName="Thomas" identifier="https://orcid.org/0000-0003-4724-6924"/>\n+ <organization url="https://muon-spectroscopy-computational-project.github.io/index.html" name="The Muon Spectroscopy Computational Project"/>\n+ </creator>\n+ <requirements>\n+ <requirement type="package" version="@TOOL_VERSION@">pymuonsuite</requirement>\n+ <requirement type="package" version="3.0">zip</requirement>\n+ </requirements>\n+ <command detect_errors="exit_code"><![CDATA[\n+ structure_name_internal="input_structure.$structure.ext" &&\n+ ln -s $structure \\$structure_name_internal &&\n+ ln -s $params params.yaml &&\n+ #if str($iscastep.iscastep_sel)=="true":\n+ castep_param_name=\\$(sed \'s/ //g\' <<< "$castep_param.name") &&\n+ ln -s $castep_param \\$castep_param_name &&\n+ sed -i \'/^castep_param: /{h;s/:.*/: $castep_param.name/};\\${x;/^$/{s//castep_param: $castep_param.name/;H};x}\' params.yaml &&\n+ #end if\n+ pm-muairss -t w \\$structure_name_internal params.yaml &&\n+ out_folder="`python ${__tool_directory__}/get_out_folder.py`" &&\n+ #if str($iscastep.iscastep_sel)=="true":\n+ zip -r out_zip.zip \\$out_folder params.yaml \\$structure_name_internal \\$castep_param_name &&\n+ #else if str($iscastep.iscastep_sel)=="false":\n+ zip -r out_zip.zip \\$out_folder params.yaml \\$structure_name_internal &&\n+ #end if\n+ #if $testing=="true" and str($iscastep.iscastep_sel)=="true":\n+ grep "castep_param" params.yaml > tree.txt &&\n+ #end if\n+ find \\$out_folder >> tree.txt\n+\n+ ]]></command>\n+ <inputs>\n+ <param type="data" name="structure" label="Structure file" format="cell, cif, xyz, extxyz" help="The structure to add muons to. The original file will be preserved. Accepted file types: CELL, CIF, XYZ (standard or extended)."/>\n+ <param type="data" name="params" label="YAML parameter file" format="yaml" help="YAML parameters for this and subsequent tools. You can create this file using the [YAML config generator] tool."/>\n+ <conditional name="iscastep">\n+ <param type="boolean" value="false" name="iscastep_sel" label="Does your configuration use the CASTEP calculator?" help="Select \'Yes\' if the \'calculator\' parameter is set to \'castep\' in your chosen YAML file (not case sensitive).">\n+ <option value="false">no</option>\n+ <option value="true">yes</option>\n+ </param>\n+ <when value="true">\n+ <param type="da'..b'n stopping sites using ab initio random structure searching (AIRSS)},\n+ journal = {The Journal of Chemical Physics},\n+ volume = {148},\n+ pages = {134114},\n+ year = {2018},\n+ doi={10.1063/1.5024450},\n+ URL={\n+ https://doi.org/10.1063/1.5024450\n+ },\n+ eprint={\n+ https://doi.org/10.1063/1.5024450\n+ }\n+ }\n+ </citation>\n+ <citation type="bibtex">\n+ @article{doi:10.1063/1.5085197,\n+ author = {Sturniolo,Simone and Liborio,Leandro and Jackson,Samuel },\n+ title = {Comparison between density functional theory and density functional tight binding approaches for finding the muon stopping site in organic molecular crystals},\n+ journal = {The Journal of Chemical Physics},\n+ volume = {150},\n+ number = {15},\n+ pages = {154301},\n+ year = {2019},\n+ doi = {10.1063/1.5085197},\n+ URL = {\n+ https://doi.org/10.1063/1.5085197\n+ },\n+ eprint = {\n+ https://doi.org/10.1063/1.5085197\n+ }\n+ }\n+ </citation>\n+ <citation type="bibtex">\n+ @article{doi:10.1063/5.0012381,\n+ author = {Sturniolo,Simone and Liborio,Leandro },\n+ title = {Computational prediction of muon stopping sites: A novel take on the unperturbed electrostatic potential method},\n+ journal = {The Journal of Chemical Physics},\n+ volume = {153},\n+ number = {4},\n+ pages = {044111},\n+ year = {2020},\n+ doi = {10.1063/5.0012381},\n+ URL = {\n+ https://doi.org/10.1063/5.0012381\n+ },\n+ eprint = {\n+ https://doi.org/10.1063/5.0012381\n+ },\n+ 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 optimize 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\xe2\x80\x99s electrostatic potential and the estimates of the muon stopping site, relying on the approximation that the muon\xe2\x80\x99s presence does not significantly affect its surroundings. One of the main UEP\xe2\x80\x99s assumptions is that the muon stopping site will be one of the crystalline material\xe2\x80\x99s electrostatic potential minima. In this regard, we also propose some symmetry-based considerations about the properties of this crystalline material\xe2\x80\x99s 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. }\n+ }\n+ </citation>\n+ <citation type="bibtex">\n+ @TOOL_CITATION@\n+ </citation>\n+ </citations>\n+</tool>\n' |
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| diff -r 000000000000 -r 0679aeb7cefc test-data/Si.cell --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/Si.cell Thu Aug 25 16:19:08 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 0679aeb7cefc test-data/Si.cif --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/Si.cif Thu Aug 25 16:19:08 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 0679aeb7cefc test-data/Si.extxyz --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/Si.extxyz Thu Aug 25 16:19:08 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 |
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| diff -r 000000000000 -r 0679aeb7cefc test-data/Si.param --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/Si.param Thu Aug 25 16:19:08 2022 +0000 |
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| @@ -0,0 +1,13 @@ +task : geometryoptimisation +opt_strategy : speed +num_dump_cycles : 0 +cutoff_energy : 450 eV +elec_energy_tol : 1.0e-9 eV +write_cell_structure : true +max_scf_cycles : 100 +xc_functional : pbe +geom_max_iter : 100 +geom_force_tol : 0.05 +backup_interval : 3600 +continuation : default +write_formatted_density : true |
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| diff -r 000000000000 -r 0679aeb7cefc test-data/Si.xyz --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/Si.xyz Thu Aug 25 16:19:08 2022 +0000 |
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| @@ -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 0679aeb7cefc test-data/configcastep_t_no_out_folder_no_castep_param.yaml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/configcastep_t_no_out_folder_no_castep_param.yaml Thu Aug 25 16:19:08 2022 +0000 |
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| @@ -0,0 +1,12 @@ +poisson_r: 1.18 +name: Si +charged: true +geom_steps: 300 +vdw_scale: 0.25 +calculator: castep +geom_force_tol: 0.05 +clustering_method: hier +clustering_hier_t: 0.2 +castep_command: castep.serial +mu_symbol: H:mu +random_seed: 7357 |
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| diff -r 000000000000 -r 0679aeb7cefc test-data/configcastep_t_with_out_folder_and_castep_param.yaml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/configcastep_t_with_out_folder_and_castep_param.yaml Thu Aug 25 16:19:08 2022 +0000 |
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| @@ -0,0 +1,14 @@ +poisson_r: 1.18 +name: Si +charged: true +geom_steps: 300 +vdw_scale: 0.25 +calculator: castep +geom_force_tol: 0.05 +clustering_method: hier +clustering_hier_t: 0.2 +out_folder: Si-out +castep_command: castep.serial +castep_param: test.param +mu_symbol: H:mu +random_seed: 7357 \ No newline at end of file |
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| diff -r 000000000000 -r 0679aeb7cefc test-data/configdftb_t.yaml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/configdftb_t.yaml Thu Aug 25 16:19:08 2022 +0000 |
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| @@ -0,0 +1,13 @@ +poisson_r: 1.18 +name: Si +charged: true +geom_steps: 300 +vdw_scale: 0.25 +calculator: dftb+ +geom_force_tol: 0.05 +clustering_method: hier +clustering_hier_t: 0.2 +out_folder: Si-out +dftb_set: 3ob-3-1 +dftb_pbc: true +random_seed: 7357 |
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| diff -r 000000000000 -r 0679aeb7cefc test-data/configuep_t.yaml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/configuep_t.yaml Thu Aug 25 16:19:08 2022 +0000 |
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| @@ -0,0 +1,13 @@ +poisson_r: 1.18 +name: Si +charged: true +geom_steps: 300 +vdw_scale: 0.25 +calculator: uep +geom_force_tol: 0.05 +clustering_method: hier +clustering_hier_t: 0.2 +out_folder: Si-out +uep_gw_factor: 4.0 +uep_chden: Si.den_fmt +random_seed: 7357 \ No newline at end of file |
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| diff -r 000000000000 -r 0679aeb7cefc test-data/tree_castep_t_no_outfolder_and_castep_param.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/tree_castep_t_no_outfolder_and_castep_param.txt Thu Aug 25 16:19:08 2022 +0000 |
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| @@ -0,0 +1,52 @@ +castep_param: Si.param +muon-airss-out +muon-airss-out/castep +muon-airss-out/castep/Si_1 +muon-airss-out/castep/Si_1/Si_1.cell +muon-airss-out/castep/Si_1/Si_1.param +muon-airss-out/castep/Si_2 +muon-airss-out/castep/Si_2/Si_2.cell +muon-airss-out/castep/Si_2/Si_2.param +muon-airss-out/castep/Si_3 +muon-airss-out/castep/Si_3/Si_3.cell +muon-airss-out/castep/Si_3/Si_3.param +muon-airss-out/castep/Si_4 +muon-airss-out/castep/Si_4/Si_4.cell +muon-airss-out/castep/Si_4/Si_4.param +muon-airss-out/castep/Si_5 +muon-airss-out/castep/Si_5/Si_5.cell +muon-airss-out/castep/Si_5/Si_5.param +muon-airss-out/castep/Si_6 +muon-airss-out/castep/Si_6/Si_6.cell +muon-airss-out/castep/Si_6/Si_6.param +muon-airss-out/castep/Si_7 +muon-airss-out/castep/Si_7/Si_7.cell +muon-airss-out/castep/Si_7/Si_7.param +muon-airss-out/castep/Si_8 +muon-airss-out/castep/Si_8/Si_8.cell +muon-airss-out/castep/Si_8/Si_8.param +muon-airss-out/castep/Si_9 +muon-airss-out/castep/Si_9/Si_9.cell +muon-airss-out/castep/Si_9/Si_9.param +muon-airss-out/castep/Si_10 +muon-airss-out/castep/Si_10/Si_10.cell +muon-airss-out/castep/Si_10/Si_10.param +muon-airss-out/castep/Si_11 +muon-airss-out/castep/Si_11/Si_11.cell +muon-airss-out/castep/Si_11/Si_11.param +muon-airss-out/castep/Si_12 +muon-airss-out/castep/Si_12/Si_12.cell +muon-airss-out/castep/Si_12/Si_12.param +muon-airss-out/castep/Si_13 +muon-airss-out/castep/Si_13/Si_13.cell +muon-airss-out/castep/Si_13/Si_13.param +muon-airss-out/castep/Si_14 +muon-airss-out/castep/Si_14/Si_14.cell +muon-airss-out/castep/Si_14/Si_14.param +muon-airss-out/castep/Si_15 +muon-airss-out/castep/Si_15/Si_15.cell +muon-airss-out/castep/Si_15/Si_15.param +muon-airss-out/castep/Si_16 +muon-airss-out/castep/Si_16/Si_16.cell +muon-airss-out/castep/Si_16/Si_16.param +muon-airss-out/castep/.collection |
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| diff -r 000000000000 -r 0679aeb7cefc test-data/tree_castep_t_with_out_folder_and_castep_param.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/tree_castep_t_with_out_folder_and_castep_param.txt Thu Aug 25 16:19:08 2022 +0000 |
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| @@ -0,0 +1,52 @@ +castep_param: Si.param +Si-out +Si-out/castep +Si-out/castep/Si_1 +Si-out/castep/Si_1/Si_1.cell +Si-out/castep/Si_1/Si_1.param +Si-out/castep/Si_2 +Si-out/castep/Si_2/Si_2.cell +Si-out/castep/Si_2/Si_2.param +Si-out/castep/Si_3 +Si-out/castep/Si_3/Si_3.cell +Si-out/castep/Si_3/Si_3.param +Si-out/castep/Si_4 +Si-out/castep/Si_4/Si_4.cell +Si-out/castep/Si_4/Si_4.param +Si-out/castep/Si_5 +Si-out/castep/Si_5/Si_5.cell +Si-out/castep/Si_5/Si_5.param +Si-out/castep/Si_6 +Si-out/castep/Si_6/Si_6.cell +Si-out/castep/Si_6/Si_6.param +Si-out/castep/Si_7 +Si-out/castep/Si_7/Si_7.cell +Si-out/castep/Si_7/Si_7.param +Si-out/castep/Si_8 +Si-out/castep/Si_8/Si_8.cell +Si-out/castep/Si_8/Si_8.param +Si-out/castep/Si_9 +Si-out/castep/Si_9/Si_9.cell +Si-out/castep/Si_9/Si_9.param +Si-out/castep/Si_10 +Si-out/castep/Si_10/Si_10.cell +Si-out/castep/Si_10/Si_10.param +Si-out/castep/Si_11 +Si-out/castep/Si_11/Si_11.cell +Si-out/castep/Si_11/Si_11.param +Si-out/castep/Si_12 +Si-out/castep/Si_12/Si_12.cell +Si-out/castep/Si_12/Si_12.param +Si-out/castep/Si_13 +Si-out/castep/Si_13/Si_13.cell +Si-out/castep/Si_13/Si_13.param +Si-out/castep/Si_14 +Si-out/castep/Si_14/Si_14.cell +Si-out/castep/Si_14/Si_14.param +Si-out/castep/Si_15 +Si-out/castep/Si_15/Si_15.cell +Si-out/castep/Si_15/Si_15.param +Si-out/castep/Si_16 +Si-out/castep/Si_16/Si_16.cell +Si-out/castep/Si_16/Si_16.param +Si-out/castep/.collection |
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| diff -r 000000000000 -r 0679aeb7cefc test-data/tree_dftb.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/tree_dftb.txt Thu Aug 25 16:19:08 2022 +0000 |
| b |
| @@ -0,0 +1,52 @@ +Si-out +Si-out/dftb.LICENSE +Si-out/dftb+ +Si-out/dftb+/Si_1 +Si-out/dftb+/Si_1/dftb_in.hsd +Si-out/dftb+/Si_1/geo_end.gen +Si-out/dftb+/Si_2 +Si-out/dftb+/Si_2/dftb_in.hsd +Si-out/dftb+/Si_2/geo_end.gen +Si-out/dftb+/Si_3 +Si-out/dftb+/Si_3/dftb_in.hsd +Si-out/dftb+/Si_3/geo_end.gen +Si-out/dftb+/Si_4 +Si-out/dftb+/Si_4/dftb_in.hsd +Si-out/dftb+/Si_4/geo_end.gen +Si-out/dftb+/Si_5 +Si-out/dftb+/Si_5/dftb_in.hsd +Si-out/dftb+/Si_5/geo_end.gen +Si-out/dftb+/Si_6 +Si-out/dftb+/Si_6/dftb_in.hsd +Si-out/dftb+/Si_6/geo_end.gen +Si-out/dftb+/Si_7 +Si-out/dftb+/Si_7/dftb_in.hsd +Si-out/dftb+/Si_7/geo_end.gen +Si-out/dftb+/Si_8 +Si-out/dftb+/Si_8/dftb_in.hsd +Si-out/dftb+/Si_8/geo_end.gen +Si-out/dftb+/Si_9 +Si-out/dftb+/Si_9/dftb_in.hsd +Si-out/dftb+/Si_9/geo_end.gen +Si-out/dftb+/Si_10 +Si-out/dftb+/Si_10/dftb_in.hsd +Si-out/dftb+/Si_10/geo_end.gen +Si-out/dftb+/Si_11 +Si-out/dftb+/Si_11/dftb_in.hsd +Si-out/dftb+/Si_11/geo_end.gen +Si-out/dftb+/Si_12 +Si-out/dftb+/Si_12/dftb_in.hsd +Si-out/dftb+/Si_12/geo_end.gen +Si-out/dftb+/Si_13 +Si-out/dftb+/Si_13/dftb_in.hsd +Si-out/dftb+/Si_13/geo_end.gen +Si-out/dftb+/Si_14 +Si-out/dftb+/Si_14/dftb_in.hsd +Si-out/dftb+/Si_14/geo_end.gen +Si-out/dftb+/Si_15 +Si-out/dftb+/Si_15/dftb_in.hsd +Si-out/dftb+/Si_15/geo_end.gen +Si-out/dftb+/Si_16 +Si-out/dftb+/Si_16/dftb_in.hsd +Si-out/dftb+/Si_16/geo_end.gen +Si-out/dftb+/.collection |
| b |
| diff -r 000000000000 -r 0679aeb7cefc test-data/tree_uep.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/tree_uep.txt Thu Aug 25 16:19:08 2022 +0000 |
| b |
| @@ -0,0 +1,35 @@ +Si-out +Si-out/uep +Si-out/uep/Si_1 +Si-out/uep/Si_1/Si_1.yaml +Si-out/uep/Si_2 +Si-out/uep/Si_2/Si_2.yaml +Si-out/uep/Si_3 +Si-out/uep/Si_3/Si_3.yaml +Si-out/uep/Si_4 +Si-out/uep/Si_4/Si_4.yaml +Si-out/uep/Si_5 +Si-out/uep/Si_5/Si_5.yaml +Si-out/uep/Si_6 +Si-out/uep/Si_6/Si_6.yaml +Si-out/uep/Si_7 +Si-out/uep/Si_7/Si_7.yaml +Si-out/uep/Si_8 +Si-out/uep/Si_8/Si_8.yaml +Si-out/uep/Si_9 +Si-out/uep/Si_9/Si_9.yaml +Si-out/uep/Si_10 +Si-out/uep/Si_10/Si_10.yaml +Si-out/uep/Si_11 +Si-out/uep/Si_11/Si_11.yaml +Si-out/uep/Si_12 +Si-out/uep/Si_12/Si_12.yaml +Si-out/uep/Si_13 +Si-out/uep/Si_13/Si_13.yaml +Si-out/uep/Si_14 +Si-out/uep/Si_14/Si_14.yaml +Si-out/uep/Si_15 +Si-out/uep/Si_15/Si_15.yaml +Si-out/uep/Si_16 +Si-out/uep/Si_16/Si_16.yaml +Si-out/uep/.collection |