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Changeset 3:523d44fcd03f (2023-02-03)

Previous changeset 2:8f41a71fc710 (2022-09-15) Next changeset 4:ec5f6b22417c (2023-07-18)

Commit message:
planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_uep_opt commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507

modified:
pm_uep_opt.xml

added:
test-data/Si_den_fmt

diff -r 8f41a71fc710 -r 523d44fcd03f pm_uep_opt.xml
--- a/pm_uep_opt.xml Thu Sep 15 10:25:47 2022 +0000
+++ b/pm_uep_opt.xml Fri Feb 03 15:40:08 2023 +0000

[

b'@@ -1,22 +1,22 @@\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+<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 <description>run UEP optimisation</description>\n <macros>\n \n- <token name="@TOOL_VERSION@">0.2.1</token>\n+ <token name="@TOOL_VERSION@">0.2.3</token>\n \n- <token name="@WRAPPER_VERSION@">1</token>\n+ <token name="@WRAPPER_VERSION@">0</token>\n \n \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+ @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 = {v0.2.1},\n- month = {2},\n- year = {2022},\n- doi = {}\n+ version = {v0.2.3},\n+ doi = {10.5281/zenodo.7025644},\n+ year = {2022}\n }\n </token>\n </macros>\n@@ -34,25 +34,29 @@\n <include type="literal" path="get_out_folder.py"/>\n </required_files>\n <command detect_errors="exit_code"><![CDATA[\n- unzip "$muonated_structures" &&\n+ unzip \'$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+ ## 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+ 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+ find \\$out_folder -type f -name "*.yaml" | xargs sed -i "s#^chden_seed: .*#chden_seed: \\$charge_density_seed#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'..b' 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 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="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 <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'

diff -r 8f41a71fc710 -r 523d44fcd03f test-data/Si_den_fmt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/Si_den_fmt Fri Feb 03 15:40:08 2023 +0000

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'