| Next changeset 1:904815426ba8 (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_uep_opt commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 |
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added:
get_out_folder.py pm_uep_opt.xml run.sh test-data/Si.castep test-data/Si.den_fmt test-data/Sifail.den_fmt test-data/muonated-default-folder.zip test-data/muonated.zip test-data/tree-default-folder.txt test-data/tree.txt |
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| diff -r 000000000000 -r e4097a3e3e75 get_out_folder.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/get_out_folder.py Thu Aug 25 16:20:08 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 e4097a3e3e75 pm_uep_opt.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/pm_uep_opt.xml Thu Aug 25 16:20:08 2022 +0000 |
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| b'@@ -0,0 +1,175 @@\n+<tool id="pm_uep_opt" name="PyMuonSuite AIRSS UEP Optimise" version="@TOOL_VERSION@+galaxy@WRAPPER_VERSION@" python_template_version="3.5" profile="22.01">\n+ <description>run UEP optimisation</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="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+ <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+ unzip "$muonated_structures" &&\n+ if test -f "params.yaml"; then echo "params.yaml present"; else echo "params.yaml missing" && exit 64; fi &&\n+ if ( test -f input_structure.* ) ; then echo "input structure present"; else echo "input structure missing" && exit 64; fi &&\n+ charge_density_name=\\$(sed \'s/ //g\' <<< "$charge_density.name") &&\n+ ln -s $charge_density \\$charge_density_name &&\n+ x="\\$charge_density_name" &&\n+ echo "calculated seed name \\$x" &&\n+ ln -s $castep_log "\\${x%%.*}.castep" &&\n+ out_folder="`python ${__tool_directory__}/get_out_folder.py`" &&\n+ find \\$out_folder -type f -name "*.yaml" | xargs sed -i "s#^chden_path: .*#chden_path: .\\/#g" &&\n+ find \\$out_folder -type f -name "*.yaml" | xargs sed -i "s#^chden_seed: .*#chden_seed: \\${x%%.*}#g" &&\n+ bash ${__tool_directory__}/run.sh \\$out_folder &&\n+ zip -r out_zip.zip \\$out_folder params.yaml input_structure.* &&\n+ find \\$out_folder > tree.txt\n+ ]]></command>\n+ <inputs>\n+ <param type="data" name="muonated_structures" label="Muonated structures (.zip)" format="zip" help="A zip folder containing muonated structures, as generated by the \'Generate muonated structures\' tool or pm-muairss."/>\n+ <param type="data" name="charge_density" label="Charge density file (.den_fmt)" format="txt" help="The charge density file created by CASTEP during your initial DFT simulation for the structure."/>\n+ <param type="data" name="castep_log" label="CASTEP log (.castep)" format="txt" help="The CASTEP log for your initial DFT simulation for the structure."/>\n+ <param type="hidden" name="testing" label="Test mode" value="false"/>\n+ </inputs>\n+ <outputs>\n+ <data label="UEP results for $muonated_structures.name" name="uep_results" format="zip" from_work_dir="out_zip.zip"/>\n+ <data label="File tree (testing only)" name="file_tree" format="txt" from_work_dir="tree.txt" hidden="true">\n+ <filter>(testing == "true")</filter>\n+ </data>\n+ </outputs>\n+ <tests>\n'..b't={\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 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\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+ @article {castep,\n+ author = {Clark, S. J. and Segall, M. D. and Pickard, C. J. and Hasnip, P. J. and Probert, M. I. J. and Refson, K. and Payne, M. C.},\n+ title = {First principles methods using CASTEP},\n+ journal = {Zeitschrift fuer Kristallographie},\n+ volume = {220},\n+ pages = {567},\n+ year = {2005}\n+ }\n+ </citation>\n+ </citations>\n+</tool>\n' |
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| diff -r 000000000000 -r e4097a3e3e75 run.sh --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/run.sh Thu Aug 25 16:20:08 2022 +0000 |
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| @@ -0,0 +1,15 @@ +#! /bin/bash + +set -o errexit + +for x in $1/*/*/*.yaml +do + + if ! out=$(pm-uep-opt $x) + then + echo 1>&2 "$out"; exit 1 + else + echo "$out" + fi +done || exit +#pm-uep-opt \ No newline at end of file |
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| diff -r 000000000000 -r e4097a3e3e75 test-data/Si.castep --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/Si.castep Thu Aug 25 16:20:08 2022 +0000 |
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| b'@@ -0,0 +1,925 @@\n+ +-------------------------------------------------+\n+ | |\n+ | CCC AA SSS TTTTT EEEEE PPPP |\n+ | C A A S T E P P |\n+ | C AAAA SS T EEE PPPP |\n+ | C A A S T E P |\n+ | CCC A A SSS T EEEEE P |\n+ | |\n+ +-------------------------------------------------+\n+ | |\n+ | Welcome to Academic Release CASTEP version 18.1 | \n+ | Ab Initio Total Energy Program |\n+ | |\n+ | Authors: |\n+ | M. Segall, M. Probert, C. Pickard, P. Hasnip, |\n+ | S. Clark, K. Refson, J. R. Yates, M. Payne |\n+ | |\n+ | Contributors: |\n+ | P. Lindan, P. Haynes, J. White, V. Milman, |\n+ | N. Govind, M. Gibson, P. Tulip, V. Cocula, |\n+ | B. Montanari, D. Quigley, M. Glover, |\n+ | L. Bernasconi, A. Perlov, M. Plummer, |\n+ | E. McNellis, J. Meyer, J. Gale, D. Jochym |\n+ | J. Aarons, B. Walker, R. Gillen, D. Jones |\n+ | T. Green, I. J. Bush, C. J. Armstrong, |\n+ | E. J. Higgins, E. L. Brown, M. S. McFly, |\n+ | J. Wilkins, B-C. Shih, P. J. P. Byrne |\n+ | |\n+ | Copyright (c) 2000 - 2017 |\n+ | |\n+ | Distributed under the terms of an |\n+ | Agreement between the United Kingdom |\n+ | Car-Parrinello (UKCP) Consortium, |\n+ | Daresbury Laboratory and Accelrys, Inc. |\n+ | |\n+ | Please cite |\n+ | |\n+ | "First principles methods using CASTEP" |\n+ | |\n+ | Zeitschrift fuer Kristallographie |\n+ | 220(5-6) pp. 567-570 (2005) |\n+ | |\n+ | S. J. Clark, M. D. Segall, C. J. Pickard, |\n+ | P. J. Hasnip, M. J. Probert, K. Refson, |\n+ | M. C. Payne |\n+ | |\n+ | in all publications arising from |\n+ | your use of CASTEP |\n+ | |\n+ +-------------------------------------------------+\n+ \n+ \n+ Compiled for linux_x86_64_ifort17 on Wed, 28 Feb 2018 17:00:19 +0000\n+ from code version baee3ec33e17+ Mon, 11 Dec 2017 11:05:17 +0000\n+ Compiler: Intel Fortran 17.0.2.174; Optimisation: fast\n+ MATHLIBS: Intel MKL(2017.0.2) (LAPACK version 3.7.0)\n+ FFT Lib : mkl\n+ Fundamental constants values: CODATA 2014\n+ \n+ Run started: Mon, 06 Sep 2021 11:25:23 +0100\n+ \n+ Atomic calculation performed for Si: 1s2 2s2 2p6 3s2 3p2\n+ \n+ Converged in 54 iterations to an ae energy of -7886.857 eV\n+ \n+ ============================================================ \n+ | Pseudopotential Report - Date of generation 6-09-2021 | \n+ ------------------------------------------------------------ \n+ | Element: Si Ionic charge: 4.00 Level of theory: PBE | \n+ | Atomic Solver: Koelling-Harmon | \n+ | | \n+ | Reference Electronic Structure | \n+ | Orbital Occupation Energy | \n+ | 3s 2.000 -0.397 | \n+ | 3p 2.000 '..b' 0.879\n+ Si 1 Py 0.879\n+ Si 1 Pz 0.879\n+ Si 2 S 1.363\n+ Si 2 Px 0.879\n+ Si 2 Py 0.879\n+ Si 2 Pz 0.879\n+ Si 3 S 1.363\n+ Si 3 Px 0.879\n+ Si 3 Py 0.879\n+ Si 3 Pz 0.879\n+ Si 4 S 1.363\n+ Si 4 Px 0.879\n+ Si 4 Py 0.879\n+ Si 4 Pz 0.879\n+ Si 5 S 1.362\n+ Si 5 Px 0.879\n+ Si 5 Py 0.879\n+ Si 5 Pz 0.879\n+ Si 6 S 1.363\n+ Si 6 Px 0.879\n+ Si 6 Py 0.879\n+ Si 6 Pz 0.879\n+ Si 7 S 1.363\n+ Si 7 Px 0.879\n+ Si 7 Py 0.879\n+ Si 7 Pz 0.879\n+ Si 8 S 1.362\n+ Si 8 Px 0.879\n+ Si 8 Py 0.879\n+ Si 8 Pz 0.879\n+ -------------------------------------------\n+ Total: 32.000\n+ -------------------------------------------\n+ \n+ Atomic Populations (Mulliken)\n+ -----------------------------\n+Species Ion s p d f Total Charge (e)\n+=====================================================================\n+ Si 1 1.36 2.64 0.00 0.00 4.00 0.00\n+ Si 2 1.36 2.64 0.00 0.00 4.00 0.00\n+ Si 3 1.36 2.64 0.00 0.00 4.00 0.00\n+ Si 4 1.36 2.64 0.00 0.00 4.00 0.00\n+ Si 5 1.36 2.64 0.00 0.00 4.00 0.00\n+ Si 6 1.36 2.64 0.00 0.00 4.00 0.00\n+ Si 7 1.36 2.64 0.00 0.00 4.00 0.00\n+ Si 8 1.36 2.64 0.00 0.00 4.00 0.00\n+=====================================================================\n+ \n+ Bond Population Length (A)\n+======================================================================\n+ Si 7 -- Si 8 0.74 2.37094\n+ Si 6 -- Si 8 0.74 2.37094\n+ Si 5 -- Si 7 0.74 2.37094\n+ Si 5 -- Si 6 0.74 2.37094\n+ Si 4 -- Si 8 0.74 2.37094\n+ Si 4 -- Si 5 0.74 2.37094\n+ Si 3 -- Si 7 0.74 2.37094\n+ Si 3 -- Si 6 0.74 2.37094\n+ Si 3 -- Si 4 0.74 2.37094\n+ Si 2 -- Si 8 0.74 2.37094\n+ Si 2 -- Si 5 0.74 2.37094\n+ Si 2 -- Si 3 0.74 2.37094\n+ Si 1 -- Si 7 0.74 2.37094\n+ Si 1 -- Si 6 0.74 2.37094\n+ Si 1 -- Si 4 0.74 2.37094\n+ Si 1 -- Si 2 0.74 2.37094\n+======================================================================\n+ \n+\n+Writing analysis data to Si.castep_bin\n+\n+Writing model to Si.check\n+ \n+ A BibTeX formatted list of references used in this run has been written to \n+ Si.bib\n+ \n+Initialisation time = 3.71 s\n+Calculation time = 28.61 s\n+Finalisation time = 0.61 s\n+Total time = 32.92 s\n+Peak Memory Use = 416432 kB\n' |
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| diff -r 000000000000 -r e4097a3e3e75 test-data/Si.den_fmt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/Si.den_fmt Thu Aug 25 16:20:08 2022 +0000 |
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| b'@@ -0,0 +1,46668 @@\n+ BEGIN header\n+ \n+ Real Lattice(A) Lattice parameters(A) Cell Angles\n+ 5.4754511 0.0000000 0.0000000 a = 5.475451 alpha = 90.000000\n+ 0.0000000 5.4754511 -0.0000000 b = 5.475451 beta = 90.000000\n+ 0.0000000 -0.0000000 5.4754511 c = 5.475451 gamma = 90.000000\n+ \n+ 1 ! nspins\n+ 36 36 36 ! fine FFT grid along <a,b,c>\n+ END header: data is "<a b c> charge" in units of electrons/grid_point * number \n+ of grid_points\n+ \n+ 1 1 1 220.238914\n+ 2 1 1 152.967159\n+ 3 1 1 48.785103\n+ 4 1 1 23.970215\n+ 5 1 1 48.333596\n+ 6 1 1 61.430956\n+ 7 1 1 57.371882\n+ 8 1 1 46.908062\n+ 9 1 1 35.904445\n+ 10 1 1 26.543912\n+ 11 1 1 19.362941\n+ 12 1 1 14.008228\n+ 13 1 1 10.188971\n+ 14 1 1 7.473550\n+ 15 1 1 5.648426\n+ 16 1 1 4.414626\n+ 17 1 1 3.665323\n+ 18 1 1 3.237108\n+ 19 1 1 3.147344\n+ 20 1 1 3.237108\n+ 21 1 1 3.665323\n+ 22 1 1 4.414626\n+ 23 1 1 5.648426\n+ 24 1 1 7.473550\n+ 25 1 1 10.188971\n+ 26 1 1 14.008228\n+ 27 1 1 19.362941\n+ 28 1 1 26.543912\n+ 29 1 1 35.904445\n+ 30 1 1 46.908062\n+ 31 1 1 57.371882\n+ 32 1 1 61.430956\n+ 33 1 1 48.333596\n+ 34 1 1 23.970215\n+ 35 1 1 48.785103\n+ 36 1 1 152.967159\n+ 1 2 1 152.967159\n+ 2 2 1 104.809941\n+ 3 2 1 35.120633\n+ 4 2 1 27.319186\n+ 5 2 1 51.804181\n+ 6 2 1 62.357129\n+ 7 2 1 57.359611\n+ 8 2 1 46.802978\n+ 9 2 1 35.862105\n+ 10 2 1 26.625557\n+ 11 2 1 19.485963\n+ 12 2 1 14.178751\n+ 13 2 1 10.343865\n+ 14 2 1 7.645945\n+ 15 2 1 5.794906\n+ 16 2 1 4.563292\n+ 17 2 1 3.799243\n+ 18 2 1 3.369862\n+ 19 2 1 3.237108\n+ 20 2 1 3.369862\n+ 21 2 1 3.799243\n+ 22 2 1 4.563292\n+ 23 2 1 5.794906\n+ 24 2 1 7.645945\n+ 25 2 1 10.343865\n+ 26 2 1 14.178751\n+ 27 2 1 19.485963\n+ 28 2 1 26.625557\n+ 29 2 1 35.862105\n+ 30 2 1 46.802978\n+ 31 2 1 57.359611\n+ 32 2 1 62.357129\n+ 33 2 1 51.804181\n+ 34 2 1 27.319186\n+ 35 2 1 35.120633\n+ 36 2 1 104.809941\n+ 1 3 1 48.785103\n+ 2 3 1 35.120633\n+ 3 3 1 23.753120\n+ 4 3 1 39.842780\n+ 5 3 1 59.715872\n+ 6 3 1 63.921771\n+ 7 3 1 57.010179\n+ 8 3 1 46.312864\n+ 9 3 1 35.709647\n+ 10 3 1 26.803073\n+ 11 3 1 19.858724\n+ 12 3 1 14.646952\n+ 13 3 1 10.842104\n+ 14 3 '..b' 9 34 36 41.163766\n+ 10 34 36 31.848568\n+ 11 34 36 24.335626\n+ 12 34 36 18.485579\n+ 13 34 36 14.082301\n+ 14 34 36 10.833364\n+ 15 34 36 8.495529\n+ 16 34 36 6.825657\n+ 17 34 36 5.692178\n+ 18 34 36 4.959410\n+ 19 34 36 4.563292\n+ 20 34 36 4.471475\n+ 21 34 36 4.681128\n+ 22 34 36 5.219047\n+ 23 34 36 6.189704\n+ 24 34 36 7.672657\n+ 25 34 36 9.868347\n+ 26 34 36 12.957742\n+ 27 34 36 17.211215\n+ 28 34 36 22.834539\n+ 29 34 36 30.033397\n+ 30 34 36 38.676559\n+ 31 34 36 47.870869\n+ 32 34 36 55.423357\n+ 33 34 36 57.792796\n+ 34 34 36 51.108406\n+ 35 34 36 37.795738\n+ 36 34 36 28.258108\n+ 1 35 36 35.120633\n+ 2 35 36 28.294727\n+ 3 35 36 29.348648\n+ 4 35 36 50.670273\n+ 5 35 36 68.998348\n+ 6 35 36 71.053476\n+ 7 35 36 62.837984\n+ 8 35 36 51.159075\n+ 9 35 36 39.754665\n+ 10 35 36 30.107957\n+ 11 35 36 22.516717\n+ 12 35 36 16.726191\n+ 13 35 36 12.455185\n+ 14 35 36 9.369886\n+ 15 35 36 7.193850\n+ 16 35 36 5.692178\n+ 17 35 36 4.692866\n+ 18 35 36 4.078143\n+ 19 35 36 3.799243\n+ 20 35 36 3.775884\n+ 21 35 36 4.061763\n+ 22 35 36 4.681128\n+ 23 35 36 5.719611\n+ 24 35 36 7.321028\n+ 25 35 36 9.677911\n+ 26 35 36 13.030536\n+ 27 35 36 17.674884\n+ 28 35 36 23.885239\n+ 29 35 36 31.914543\n+ 30 35 36 41.506422\n+ 31 35 36 51.264344\n+ 32 35 36 57.751820\n+ 33 35 36 54.731227\n+ 34 35 36 37.795738\n+ 35 35 36 22.072715\n+ 36 35 36 26.935435\n+ 1 36 36 104.809941\n+ 2 36 36 70.374934\n+ 3 36 36 28.294727\n+ 4 36 36 34.493369\n+ 5 36 36 58.835146\n+ 6 36 36 66.740292\n+ 7 36 36 60.451590\n+ 8 36 36 49.255424\n+ 9 36 36 37.891351\n+ 10 36 36 28.322307\n+ 11 36 36 20.860572\n+ 12 36 36 15.286005\n+ 13 36 36 11.209371\n+ 14 36 36 8.326384\n+ 15 36 36 6.313359\n+ 16 36 36 4.959410\n+ 17 36 36 4.078143\n+ 18 36 36 3.601229\n+ 19 36 36 3.369862\n+ 20 36 36 3.457702\n+ 21 36 36 3.775884\n+ 22 36 36 4.471475\n+ 23 36 36 5.595396\n+ 24 36 36 7.320087\n+ 25 36 36 9.830488\n+ 26 36 36 13.436412\n+ 27 36 36 18.411884\n+ 28 36 36 25.146139\n+ 29 36 36 33.835468\n+ 30 36 36 44.192753\n+ 31 36 36 54.272174\n+ 32 36 36 59.527359\n+ 33 36 36 51.042639\n+ 34 36 36 28.258108\n+ 35 36 36 26.935435\n+ 36 36 36 72.644041\n' |
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| diff -r 000000000000 -r e4097a3e3e75 test-data/Sifail.den_fmt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/Sifail.den_fmt Thu Aug 25 16:20:08 2022 +0000 |
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| @@ -0,0 +1,1 @@ +This should fail \ No newline at end of file |
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| diff -r 000000000000 -r e4097a3e3e75 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 000000000000 -r e4097a3e3e75 test-data/muonated.zip |
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| Binary file test-data/muonated.zip has changed |
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| diff -r 000000000000 -r e4097a3e3e75 test-data/tree-default-folder.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/tree-default-folder.txt Thu Aug 25 16:20:08 2022 +0000 |
| b |
| @@ -0,0 +1,93 @@ +muon-airss-out +muon-airss-out/uep +muon-airss-out/uep/.collection +muon-airss-out/uep/Si_1 +muon-airss-out/uep/Si_1/Si_1.uep +muon-airss-out/uep/Si_1/Si_1.uep.pkl +muon-airss-out/uep/Si_1/Si_1.xyz +muon-airss-out/uep/Si_1/Si_1.yaml +muon-airss-out/uep/Si_10 +muon-airss-out/uep/Si_10/Si_10.uep +muon-airss-out/uep/Si_10/Si_10.uep.pkl +muon-airss-out/uep/Si_10/Si_10.xyz +muon-airss-out/uep/Si_10/Si_10.yaml +muon-airss-out/uep/Si_11 +muon-airss-out/uep/Si_11/Si_11.uep +muon-airss-out/uep/Si_11/Si_11.uep.pkl +muon-airss-out/uep/Si_11/Si_11.xyz +muon-airss-out/uep/Si_11/Si_11.yaml +muon-airss-out/uep/Si_12 +muon-airss-out/uep/Si_12/Si_12.uep +muon-airss-out/uep/Si_12/Si_12.uep.pkl +muon-airss-out/uep/Si_12/Si_12.xyz +muon-airss-out/uep/Si_12/Si_12.yaml +muon-airss-out/uep/Si_13 +muon-airss-out/uep/Si_13/Si_13.uep +muon-airss-out/uep/Si_13/Si_13.uep.pkl +muon-airss-out/uep/Si_13/Si_13.xyz +muon-airss-out/uep/Si_13/Si_13.yaml +muon-airss-out/uep/Si_14 +muon-airss-out/uep/Si_14/Si_14.uep +muon-airss-out/uep/Si_14/Si_14.uep.pkl +muon-airss-out/uep/Si_14/Si_14.xyz +muon-airss-out/uep/Si_14/Si_14.yaml +muon-airss-out/uep/Si_15 +muon-airss-out/uep/Si_15/Si_15.uep +muon-airss-out/uep/Si_15/Si_15.uep.pkl +muon-airss-out/uep/Si_15/Si_15.xyz +muon-airss-out/uep/Si_15/Si_15.yaml +muon-airss-out/uep/Si_16 +muon-airss-out/uep/Si_16/Si_16.uep +muon-airss-out/uep/Si_16/Si_16.uep.pkl +muon-airss-out/uep/Si_16/Si_16.xyz +muon-airss-out/uep/Si_16/Si_16.yaml +muon-airss-out/uep/Si_17 +muon-airss-out/uep/Si_17/Si_17.uep +muon-airss-out/uep/Si_17/Si_17.uep.pkl +muon-airss-out/uep/Si_17/Si_17.xyz +muon-airss-out/uep/Si_17/Si_17.yaml +muon-airss-out/uep/Si_18 +muon-airss-out/uep/Si_18/Si_18.uep +muon-airss-out/uep/Si_18/Si_18.uep.pkl +muon-airss-out/uep/Si_18/Si_18.xyz +muon-airss-out/uep/Si_18/Si_18.yaml +muon-airss-out/uep/Si_2 +muon-airss-out/uep/Si_2/Si_2.uep +muon-airss-out/uep/Si_2/Si_2.uep.pkl +muon-airss-out/uep/Si_2/Si_2.xyz +muon-airss-out/uep/Si_2/Si_2.yaml +muon-airss-out/uep/Si_3 +muon-airss-out/uep/Si_3/Si_3.uep +muon-airss-out/uep/Si_3/Si_3.uep.pkl +muon-airss-out/uep/Si_3/Si_3.xyz +muon-airss-out/uep/Si_3/Si_3.yaml +muon-airss-out/uep/Si_4 +muon-airss-out/uep/Si_4/Si_4.uep +muon-airss-out/uep/Si_4/Si_4.uep.pkl +muon-airss-out/uep/Si_4/Si_4.xyz +muon-airss-out/uep/Si_4/Si_4.yaml +muon-airss-out/uep/Si_5 +muon-airss-out/uep/Si_5/Si_5.uep +muon-airss-out/uep/Si_5/Si_5.uep.pkl +muon-airss-out/uep/Si_5/Si_5.xyz +muon-airss-out/uep/Si_5/Si_5.yaml +muon-airss-out/uep/Si_6 +muon-airss-out/uep/Si_6/Si_6.uep +muon-airss-out/uep/Si_6/Si_6.uep.pkl +muon-airss-out/uep/Si_6/Si_6.xyz +muon-airss-out/uep/Si_6/Si_6.yaml +muon-airss-out/uep/Si_7 +muon-airss-out/uep/Si_7/Si_7.uep +muon-airss-out/uep/Si_7/Si_7.uep.pkl +muon-airss-out/uep/Si_7/Si_7.xyz +muon-airss-out/uep/Si_7/Si_7.yaml +muon-airss-out/uep/Si_8 +muon-airss-out/uep/Si_8/Si_8.uep +muon-airss-out/uep/Si_8/Si_8.uep.pkl +muon-airss-out/uep/Si_8/Si_8.xyz +muon-airss-out/uep/Si_8/Si_8.yaml +muon-airss-out/uep/Si_9 +muon-airss-out/uep/Si_9/Si_9.uep +muon-airss-out/uep/Si_9/Si_9.uep.pkl +muon-airss-out/uep/Si_9/Si_9.xyz +muon-airss-out/uep/Si_9/Si_9.yaml |
| b |
| diff -r 000000000000 -r e4097a3e3e75 test-data/tree.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/tree.txt Thu Aug 25 16:20:08 2022 +0000 |
| b |
| @@ -0,0 +1,73 @@ +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 |