| Previous changeset 3:523d44fcd03f (2023-02-03) Next changeset 5:eea73e1f65cb (2023-07-26) |
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Commit message:
planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_uep_opt commit 70a4d37ecdf5d586703cfc509922311e95d3205c |
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modified:
pm_uep_opt.xml run.sh test-data/tree.txt |
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added:
muon_macros.xml test-data/Si.cell test-data/Si.cif test-data/Si.extxyz test-data/Si.xyz test-data/allpos.cell test-data/allpos.cif test-data/allpos.xyz |
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removed:
test-data/muonated-default-folder.zip test-data/muonated.zip |
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| diff -r 523d44fcd03f -r ec5f6b22417c muon_macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/muon_macros.xml Tue Jul 18 13:27:15 2023 +0000 |
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| @@ -0,0 +1,29 @@ +<macros> + <xml name="dftb_set"> + <param type="select" name="dftb_set" value="3ob-3-1" display="radio" label="DFTB parameter set" help="The parameter set to use for DFTB+. Currently supported are: 3ob-3-1 and pbc-0-3. See help section at the bottom of the page for details."> + <option value="3ob-3-1">3ob-3-1</option> + <option value="pbc-0-3">pbc-0-3</option> + </param> + </xml> + <xml name="dftb+"> + <expand macro="dftb_set"/> + <param type="boolean" name="dftb_pbc" label="Use periodic boundary conditions" help="Whether to turn on periodic boundary conditions in DFTB+." checked="true"/> + </xml> + <xml name="dftb_optionals"> + <param type="text" argument="dftb_optionals" value="[]" optional="true" label="DFTB optional files" help="Additional optional json files to activate for DFTBArgs (for example, dftd3.json will use DFTD3 dispersion forces for 3ob-3-1 if DFTB+ has been compiled to support them)."/> + </xml> + <xml name="k_points_grid"> + <param type="text" argument="k_points_grid" value="[1,1,1]" label="K-points grid" help="List of three integer k-points. Default is [1,1,1]."> + <validator type="regex" message="Input should only contain whitespace, '[', ']', ',' and digits.">^[\s\d,\[\]]+$</validator> + </param> + </xml> + <!-- version of underlying tool (PEP 440) --> + <!-- citation should be updated with every underlying tool version --> + <!-- concept is not updated, and should only be used for referencing the idea of the software --> + <token name="@MUSPINSIM_VERSION@">2.2.1</token> + <token name="@MUSPINSIM_CITATION@">10.5281/zenodo.7733979</token> + <token name="@MUSPINSIM_CONCEPT@">10.5281/zenodo.6517626</token> + <token name="@PYMUONSUITE_VERSION@">0.3.0</token> + <token name="@PYMUONSUITE_CITATION@">10.5281/zenodo.8026711</token> + <token name="@PYMUONSUITE_CONCEPT@">10.5281/zenodo.7025643</token> +</macros> \ No newline at end of file |
| b |
| diff -r 523d44fcd03f -r ec5f6b22417c pm_uep_opt.xml --- a/pm_uep_opt.xml Fri Feb 03 15:40:08 2023 +0000 +++ b/pm_uep_opt.xml Tue Jul 18 13:27:15 2023 +0000 |
| [ |
| b'@@ -1,32 +1,18 @@\n-<tool id="pm_uep_opt" name="PyMuonSuite AIRSS UEP Optimise" version="@TOOL_VERSION@+galaxy@WRAPPER_VERSION@" python_template_version="3.5" profile="22.05" license="MIT">\n+<tool id="pm_uep_opt" name="PyMuonSuite AIRSS UEP Optimise" version="@PYMUONSUITE_VERSION@+galaxy@WRAPPER_VERSION@" python_template_version="3.5" profile="22.05" license="MIT">\n <description>run UEP optimisation</description>\n <macros>\n- <!-- version of underlying tool (PEP 440) -->\n- <token name="@TOOL_VERSION@">0.2.3</token>\n <!-- version of this tool wrapper (integer) -->\n <token name="@WRAPPER_VERSION@">0</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{Sturniolo_pymuon-suite_2022,\n- author = {Sturniolo, Simone and Liborio, Leandro and Chadwick, Eli and Murgatroyd, Laura and Laverack, Adam and Mudaraddi, Anish and {Muon Spectroscopy Computational Project}},\n- license = {GPL-3.0},\n- month = {8},\n- title = {{pymuon-suite}},\n- url = {https://github.com/muon-spectroscopy-computational-project/pymuon-suite},\n- version = {v0.2.3},\n- doi = {10.5281/zenodo.7025644},\n- year = {2022}\n- }\n- </token>\n+ <import>muon_macros.xml</import>\n </macros>\n <creator>\n <person givenName="Jyothish" familyName="Thomas" identifier="https://orcid.org/0000-0003-4724-6924"/>\n <person givenName="Eli" familyName="Chadwick" url="https://github.com/elichad" identifier="https://orcid.org/0000-0002-0035-6475"/>\n+ <person givenName="Patrick" familyName="Austin" url="https://github.com/patrick-austin" identifier="https://orcid.org/0000-0002-6279-7823"/>\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="@PYMUONSUITE_VERSION@">pymuonsuite</requirement>\n <requirement type="package" version="3.0">zip</requirement>\n </requirements>\n <required_files>\n@@ -34,101 +20,230 @@\n <include type="literal" path="get_out_folder.py"/>\n </required_files>\n <command detect_errors="exit_code"><![CDATA[\n- unzip \'$muonated_structures\' &&\n- if test -f "params.yaml"; then echo "params.yaml present"; else echo "params.yaml missing" && exit 64; fi &&\n- if ( test -f input_structure.* ) ; then echo "input structure present"; else echo "input structure missing" && exit 64; fi &&\n- ## PyMuonSuite will attempt to load \'<chden_seed>.den_fmt\' and\n- ## \'<chden_seed>.castep\', but $charge_density.name may or may not end\n- ## with \'.den_fmt\' so strip any extension and manually include \'den_fmt\'\n- ## and \'.castep\' in the linked file names\n- charge_density_name=\\$(sed \'s/ //g\' <<< \'$charge_density.name\') &&\n- charge_density_seed=\\${charge_density_name%%.*} &&\n- echo "Calculated seed name \\$charge_density_seed" &&\n- ln -s \'$charge_density\' \\$charge_density_seed.den_fmt && \n- ln -s \'$castep_log\' \\$charge_density_seed.castep &&\n+ cat $params_yaml > params.yaml &&\n+ structure_name_internal=\'input_structure.$structure.ext\' &&\n+ ln -s \'$structure\' \\$structure_name_internal &&\n+ pm-muairss -t w \\$structure_name_internal params.yaml &&\n+ #if $generation_params.allpos_ext != "none":\n+ mv allpos.$generation_params.allpos_ext $allpos_file &&\n+ #end if\n+ ln -s \'$charge_density\' input_structure.den_fmt && \n+ ln -s \'$castep_log\' input_structure.castep &&\n out_folder="`python \'${__tool_dir'..b'ype="cell"/>\n <param name="charge_density" value="Si.den_fmt" ftype="den_fmt"/>\n <param name="castep_log" value="Si.castep" ftype="castep"/>\n+ <section name="generation_params">\n+ <param name="poisson_r" value="1.18"/>\n+ <param name="vdw_scale" value="0.25"/>\n+ <param name="random_seed" value="7357"/>\n+ </section>\n+ <section name="optimisation_params">\n+ <param name="geom_steps" value="300"/>\n+ <param name="uep_gw_factor" value="4.0"/>\n+ </section>\n </test>\n <!-- Check that the chden parameters are set correctly when $charge_density.name does not have the .den_fmt extension -->\n <test expect_num_outputs="2">\n <param name="testing" value="true"/>\n- <param name="muonated_structures" value="muonated.zip" ftype="zip"/>\n+ <param name="structure" value="Si.cell" ftype="cell"/>\n <param name="charge_density" value="Si_den_fmt" ftype="den_fmt"/>\n <param name="castep_log" value="Si.castep" ftype="castep"/>\n+ <section name="generation_params">\n+ <param name="poisson_r" value="1.18"/>\n+ <param name="vdw_scale" value="0.25"/>\n+ <param name="random_seed" value="7357"/>\n+ </section>\n+ <section name="optimisation_params">\n+ <param name="geom_steps" value="300"/>\n+ <param name="uep_gw_factor" value="4.0"/>\n+ </section>\n <output name="file_tree" file="tree.txt" ftype="txt" sort="true">\n <assert_contents>\n- <has_size value="1780"/>\n+ <has_size value="3280"/>\n </assert_contents>\n </output>\n </test>\n </tests>\n <help><![CDATA[\n- Given a set of input muonated structures (structures containing a muon), applies UEP optimisation to refine them.\n+ Given an input structure, this tool generates a set of duplicate structures,\n+ each with a single muon added in a random location.\n+ These are known as "muonated" structures.\n+ Following this, UEP optimisation is used to refine the positions of the muons.\n \n- This tool requires CASTEP inputs for the UEP method, meaning your initial DFT simulation must have been done with CASTEP.\n- The structure you used as input to the \'`Generate muonated structures`_\' tool or pm-muairss beforehand should come from the same simulation run.\n+ This tool requires CASTEP inputs in order to perform the UEP method,\n+ meaning your initial DFT simulation must have been done with CASTEP.\n+ This simulation should have used the same structure as is used here.\n \n- Command-line usage: pm-uep-opt [-h] [-t {r,w}] structures parameter_file\n+ Following this, the individual refined positions can be clustered to\n+ represent potential stopping sites by using \'`PyMuonSuite AIRSS Cluster`_\'.\n \n- .. _Generate muonated structures: /tool_runner?tool_id=pm_muairss_write\n+ Command-line usage (generation): pm-muairss [-h] -t w structures parameter_file\n+ \n+ Command-line usage (optimisation): pm-uep-opt [-h] parameter_file\n \n- PyMuonSuite is distributed under the GPLv3 license. This tool wrapper is distributed under the MIT license.\n+ .. _PyMuonSuite AIRSS Cluster: /tool_runner?tool_id=pm_muairss_read\n+\n+ PyMuonSuite is distributed under the GPLv3 license.\n+ This tool wrapper is distributed under the MIT license.\n ]]></help>\n <citations>\n- <citation type="bibtex">\n- @TOOL_CITATION@\n- </citation>\n+ <citation type="doi">@PYMUONSUITE_CITATION@</citation>\n <citation type="doi">10.1063/1.5024450</citation>\n <citation type="doi">10.1063/1.5085197</citation>\n <citation type="doi">10.1063/5.0012381</citation>\n' |
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| diff -r 523d44fcd03f -r ec5f6b22417c run.sh --- a/run.sh Fri Feb 03 15:40:08 2023 +0000 +++ b/run.sh Tue Jul 18 13:27:15 2023 +0000 |
| [ |
| @@ -2,14 +2,33 @@ set -o errexit -for x in $1/*/*/*.yaml -do - - if ! out=$(pm-uep-opt $x) - then - echo 1>&2 "$out"; exit 1 +run(){ + if ! out=$(pm-uep-opt $1); then + echo 1>&2 "$out"; exit 1 else - echo "$out" + echo "$out" fi -done || exit -#pm-uep-opt \ No newline at end of file +} + +pids=() +for x in $1/*/*/*.yaml; do + run $x & pids+=($!) +done + +declare -i failed=0 +for pid in ${pids[@]}; do + if ! wait $pid; then + failed+=1 + fi +done + +if [ $failed -eq ${#pids[@]} ]; then + >&2 echo "ERROR: All optimisations failed" + exit 1 +elif [ $failed -eq 0 ]; then + echo "All optimisations succeeded" + exit 0 +else + echo "WARNING: $failed optimisation(s) failed" + exit 0 +fi |
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| diff -r 523d44fcd03f -r ec5f6b22417c test-data/Si.cell --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/Si.cell Tue Jul 18 13:27:15 2023 +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 523d44fcd03f -r ec5f6b22417c test-data/Si.cif --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/Si.cif Tue Jul 18 13:27:15 2023 +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 523d44fcd03f -r ec5f6b22417c test-data/Si.extxyz --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/Si.extxyz Tue Jul 18 13:27:15 2023 +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 523d44fcd03f -r ec5f6b22417c test-data/Si.xyz --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/Si.xyz Tue Jul 18 13:27:15 2023 +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 523d44fcd03f -r ec5f6b22417c test-data/allpos.cell --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/allpos.cell Tue Jul 18 13:27:15 2023 +0000 |
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| @@ -0,0 +1,38 @@ +####################################################### +#CASTEP cell file: allpos.cell +#Created using the Atomic Simulation Environment (ASE)# +####################################################### + +%BLOCK LATTICE_CART + 5.475382 0.000000 -0.000000 + 0.000000 5.475382 0.000000 +-0.000000 0.000000 5.475382 +%ENDBLOCK LATTICE_CART + +%BLOCK POSITIONS_ABS +Si 0.000000 0.000000 0.000000 +Si -0.000000 2.737691 2.737691 +Si 1.368845 1.368845 1.368845 +Si 2.737691 0.000000 2.737691 +Si 1.368845 4.106536 4.106536 +Si 4.106536 1.368845 4.106536 +Si 4.106536 4.106536 1.368845 +Si 2.737691 2.737691 -0.000000 +H:mu 3.125152 3.041799 2.994236 +H:mu 4.170048 2.685234 3.919204 +H:mu 2.896190 3.055878 1.069474 +H:mu 2.499357 2.738732 5.011782 +H:mu 1.856384 1.305645 0.684300 +H:mu 0.710100 1.663543 1.366143 +H:mu 2.926805 4.554958 3.173796 +H:mu 4.041556 2.285971 2.357787 +H:mu 2.153772 1.685845 2.712357 +H:mu 3.369247 0.881320 2.641127 +H:mu 4.631185 3.830276 4.640470 +H:mu 2.828731 1.963913 1.697286 +H:mu 2.176625 2.144297 3.912156 +H:mu 1.805850 2.882961 2.746759 +H:mu 1.403305 0.559980 1.522521 +H:mu 3.251047 3.565876 4.157223 +%ENDBLOCK POSITIONS_ABS + |
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| diff -r 523d44fcd03f -r ec5f6b22417c test-data/allpos.cif --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/allpos.cif Tue Jul 18 13:27:15 2023 +0000 |
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| @@ -0,0 +1,49 @@ +data_image0 +_chemical_formula_structural Si8H16 +_chemical_formula_sum "Si8 H16" +_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 + H H1 1.0 0.57076 0.55554 0.54685 1.0000 + H H2 1.0 0.76160 0.49042 0.71579 1.0000 + H H3 1.0 0.52895 0.55811 0.19532 1.0000 + H H4 1.0 0.45647 0.50019 0.91533 1.0000 + H H5 1.0 0.33904 0.23846 0.12498 1.0000 + H H6 1.0 0.12969 0.30382 0.24951 1.0000 + H H7 1.0 0.53454 0.83190 0.57965 1.0000 + H H8 1.0 0.73813 0.41750 0.43062 1.0000 + H H9 1.0 0.39336 0.30790 0.49537 1.0000 + H H10 1.0 0.61534 0.16096 0.48236 1.0000 + H H11 1.0 0.84582 0.69955 0.84752 1.0000 + H H12 1.0 0.51663 0.35868 0.30999 1.0000 + H H13 1.0 0.39753 0.39163 0.71450 1.0000 + H H14 1.0 0.32981 0.52653 0.50166 1.0000 + H H15 1.0 0.25629 0.10227 0.27807 1.0000 + H H16 1.0 0.59376 0.65126 0.75926 1.0000 |
| b |
| diff -r 523d44fcd03f -r ec5f6b22417c test-data/allpos.xyz --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/allpos.xyz Tue Jul 18 13:27:15 2023 +0000 |
| b |
| @@ -0,0 +1,26 @@ +24 +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:masses:R:1:castep_custom_species:S:1 pbc="T T T" +Si 0.00000000 0.00000000 0.00000000 0.00000000 NULL 28.08500000 Si +Si 4.10658834 4.10658834 1.36886278 0.00000000 NULL 28.08500000 Si +Si 2.73772556 0.00000000 2.73772556 0.00000000 NULL 28.08500000 Si +Si 4.10658834 1.36886278 4.10658834 0.00000000 NULL 28.08500000 Si +Si 0.00000000 2.73772556 2.73772556 0.00000000 NULL 28.08500000 Si +Si 1.36886278 1.36886278 1.36886278 0.00000000 NULL 28.08500000 Si +Si 1.36886278 4.10658834 4.10658834 0.00000000 NULL 28.08500000 Si +Si 2.73772556 2.73772556 -0.00000000 0.00000000 NULL 28.08500000 Si +H 3.12519205 3.04183727 2.99427396 0.00000000 0 0.11342893 H:mu +H 4.17010122 2.68526782 3.91925381 0.00000000 0 0.11342893 H:mu +H 2.89622675 3.05591660 1.06948758 0.00000000 0 0.11342893 H:mu +H 2.49938846 2.73876636 5.01184564 0.00000000 0 0.11342893 H:mu +H 1.85640768 1.30566198 0.68430879 0.00000000 0 0.11342893 H:mu +H 0.71010928 1.66356372 1.36616075 0.00000000 0 0.11342893 H:mu +H 2.92684216 4.55501571 3.17383586 0.00000000 0 0.11342893 H:mu +H 4.04160737 2.28599955 2.35781702 0.00000000 0 0.11342893 H:mu +H 2.15379948 1.68586666 2.71239184 0.00000000 0 0.11342893 H:mu +H 3.36928999 0.88133137 2.64116057 0.00000000 0 0.11342893 H:mu +H 4.63124403 3.83032454 4.64052920 0.00000000 0 0.11342893 H:mu +H 2.82876687 1.96393752 1.69730779 0.00000000 0 0.11342893 H:mu +H 2.17665215 2.14432399 3.91220567 0.00000000 0 0.11342893 H:mu +H 1.80587242 2.88299761 2.74679403 0.00000000 0 0.11342893 H:mu +H 1.40332274 0.55998727 1.52254060 0.00000000 0 0.11342893 H:mu +H 3.25108839 3.56592083 4.15727584 0.00000000 0 0.11342893 H:mu |
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| diff -r 523d44fcd03f -r ec5f6b22417c test-data/muonated-default-folder.zip |
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| Binary file test-data/muonated-default-folder.zip has changed |
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| diff -r 523d44fcd03f -r ec5f6b22417c test-data/muonated.zip |
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| Binary file test-data/muonated.zip has changed |
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| diff -r 523d44fcd03f -r ec5f6b22417c test-data/tree.txt --- a/test-data/tree.txt Fri Feb 03 15:40:08 2023 +0000 +++ b/test-data/tree.txt Tue Jul 18 13:27:15 2023 +0000 |
| b |
| @@ -1,73 +1,83 @@ -Si-out -Si-out/uep -Si-out/uep/Si_1 -Si-out/uep/Si_1/Si_1.yaml -Si-out/uep/Si_1/Si_1.uep -Si-out/uep/Si_1/Si_1.uep.pkl -Si-out/uep/Si_1/Si_1.xyz -Si-out/uep/Si_2 -Si-out/uep/Si_2/Si_2.yaml -Si-out/uep/Si_2/Si_2.uep -Si-out/uep/Si_2/Si_2.uep.pkl -Si-out/uep/Si_2/Si_2.xyz -Si-out/uep/Si_3 -Si-out/uep/Si_3/Si_3.yaml -Si-out/uep/Si_3/Si_3.uep -Si-out/uep/Si_3/Si_3.uep.pkl -Si-out/uep/Si_3/Si_3.xyz -Si-out/uep/Si_4 -Si-out/uep/Si_4/Si_4.yaml -Si-out/uep/Si_4/Si_4.uep -Si-out/uep/Si_4/Si_4.uep.pkl -Si-out/uep/Si_4/Si_4.xyz -Si-out/uep/Si_5 -Si-out/uep/Si_5/Si_5.yaml -Si-out/uep/Si_5/Si_5.uep -Si-out/uep/Si_5/Si_5.uep.pkl -Si-out/uep/Si_5/Si_5.xyz -Si-out/uep/Si_6 -Si-out/uep/Si_6/Si_6.yaml -Si-out/uep/Si_6/Si_6.uep -Si-out/uep/Si_6/Si_6.uep.pkl -Si-out/uep/Si_6/Si_6.xyz -Si-out/uep/Si_7 -Si-out/uep/Si_7/Si_7.yaml -Si-out/uep/Si_7/Si_7.uep -Si-out/uep/Si_7/Si_7.uep.pkl -Si-out/uep/Si_7/Si_7.xyz -Si-out/uep/Si_8 -Si-out/uep/Si_8/Si_8.yaml -Si-out/uep/Si_8/Si_8.uep -Si-out/uep/Si_8/Si_8.uep.pkl -Si-out/uep/Si_8/Si_8.xyz -Si-out/uep/Si_9 -Si-out/uep/Si_9/Si_9.yaml -Si-out/uep/Si_9/Si_9.uep -Si-out/uep/Si_9/Si_9.uep.pkl -Si-out/uep/Si_9/Si_9.xyz -Si-out/uep/Si_10 -Si-out/uep/Si_10/Si_10.yaml -Si-out/uep/Si_10/Si_10.uep -Si-out/uep/Si_10/Si_10.uep.pkl -Si-out/uep/Si_10/Si_10.xyz -Si-out/uep/Si_11 -Si-out/uep/Si_11/Si_11.yaml -Si-out/uep/Si_11/Si_11.uep -Si-out/uep/Si_11/Si_11.uep.pkl -Si-out/uep/Si_11/Si_11.xyz -Si-out/uep/Si_12 -Si-out/uep/Si_12/Si_12.yaml -Si-out/uep/Si_12/Si_12.uep -Si-out/uep/Si_12/Si_12.uep.pkl -Si-out/uep/Si_12/Si_12.xyz -Si-out/uep/Si_13 -Si-out/uep/Si_13/Si_13.yaml -Si-out/uep/Si_13/Si_13.uep -Si-out/uep/Si_13/Si_13.uep.pkl -Si-out/uep/Si_13/Si_13.xyz -Si-out/uep/Si_14 -Si-out/uep/Si_14/Si_14.yaml -Si-out/uep/Si_14/Si_14.uep -Si-out/uep/Si_14/Si_14.uep.pkl -Si-out/uep/Si_14/Si_14.xyz -Si-out/uep/.collection +muon-airss-out +muon-airss-out/uep +muon-airss-out/uep/struct_1 +muon-airss-out/uep/struct_1/struct_1.yaml +muon-airss-out/uep/struct_1/struct_1.uep +muon-airss-out/uep/struct_1/struct_1.uep.pkl +muon-airss-out/uep/struct_1/struct_1.xyz +muon-airss-out/uep/struct_2 +muon-airss-out/uep/struct_2/struct_2.yaml +muon-airss-out/uep/struct_2/struct_2.uep +muon-airss-out/uep/struct_2/struct_2.uep.pkl +muon-airss-out/uep/struct_2/struct_2.xyz +muon-airss-out/uep/struct_3 +muon-airss-out/uep/struct_3/struct_3.yaml +muon-airss-out/uep/struct_3/struct_3.uep +muon-airss-out/uep/struct_3/struct_3.uep.pkl +muon-airss-out/uep/struct_3/struct_3.xyz +muon-airss-out/uep/struct_4 +muon-airss-out/uep/struct_4/struct_4.yaml +muon-airss-out/uep/struct_4/struct_4.uep +muon-airss-out/uep/struct_4/struct_4.uep.pkl +muon-airss-out/uep/struct_4/struct_4.xyz +muon-airss-out/uep/struct_5 +muon-airss-out/uep/struct_5/struct_5.yaml +muon-airss-out/uep/struct_5/struct_5.uep +muon-airss-out/uep/struct_5/struct_5.uep.pkl +muon-airss-out/uep/struct_5/struct_5.xyz +muon-airss-out/uep/struct_6 +muon-airss-out/uep/struct_6/struct_6.yaml +muon-airss-out/uep/struct_6/struct_6.uep +muon-airss-out/uep/struct_6/struct_6.uep.pkl +muon-airss-out/uep/struct_6/struct_6.xyz +muon-airss-out/uep/struct_7 +muon-airss-out/uep/struct_7/struct_7.yaml +muon-airss-out/uep/struct_7/struct_7.uep +muon-airss-out/uep/struct_7/struct_7.uep.pkl +muon-airss-out/uep/struct_7/struct_7.xyz +muon-airss-out/uep/struct_8 +muon-airss-out/uep/struct_8/struct_8.yaml +muon-airss-out/uep/struct_8/struct_8.uep +muon-airss-out/uep/struct_8/struct_8.uep.pkl +muon-airss-out/uep/struct_8/struct_8.xyz +muon-airss-out/uep/struct_9 +muon-airss-out/uep/struct_9/struct_9.yaml +muon-airss-out/uep/struct_9/struct_9.uep +muon-airss-out/uep/struct_9/struct_9.uep.pkl +muon-airss-out/uep/struct_9/struct_9.xyz +muon-airss-out/uep/struct_10 +muon-airss-out/uep/struct_10/struct_10.yaml +muon-airss-out/uep/struct_10/struct_10.uep +muon-airss-out/uep/struct_10/struct_10.uep.pkl +muon-airss-out/uep/struct_10/struct_10.xyz +muon-airss-out/uep/struct_11 +muon-airss-out/uep/struct_11/struct_11.yaml +muon-airss-out/uep/struct_11/struct_11.uep +muon-airss-out/uep/struct_11/struct_11.uep.pkl +muon-airss-out/uep/struct_11/struct_11.xyz +muon-airss-out/uep/struct_12 +muon-airss-out/uep/struct_12/struct_12.yaml +muon-airss-out/uep/struct_12/struct_12.uep +muon-airss-out/uep/struct_12/struct_12.uep.pkl +muon-airss-out/uep/struct_12/struct_12.xyz +muon-airss-out/uep/struct_13 +muon-airss-out/uep/struct_13/struct_13.yaml +muon-airss-out/uep/struct_13/struct_13.uep +muon-airss-out/uep/struct_13/struct_13.uep.pkl +muon-airss-out/uep/struct_13/struct_13.xyz +muon-airss-out/uep/struct_14 +muon-airss-out/uep/struct_14/struct_14.yaml +muon-airss-out/uep/struct_14/struct_14.uep +muon-airss-out/uep/struct_14/struct_14.uep.pkl +muon-airss-out/uep/struct_14/struct_14.xyz +muon-airss-out/uep/struct_15 +muon-airss-out/uep/struct_15/struct_15.yaml +muon-airss-out/uep/struct_15/struct_15.uep +muon-airss-out/uep/struct_15/struct_15.uep.pkl +muon-airss-out/uep/struct_15/struct_15.xyz +muon-airss-out/uep/struct_16 +muon-airss-out/uep/struct_16/struct_16.yaml +muon-airss-out/uep/struct_16/struct_16.uep +muon-airss-out/uep/struct_16/struct_16.uep.pkl +muon-airss-out/uep/struct_16/struct_16.xyz +muon-airss-out/uep/.collection |