| Next changeset 1:c5fba3c9f660 (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_read commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 |
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added:
get_out_folder.py pm_muairss_read.xml test-data/clusters.txt test-data/clusters_dat.dat test-data/clustout-dftb.dat test-data/clustout-dftb.txt test-data/clustout-uep.dat test-data/clustout-uep.txt test-data/dftb-out.zip test-data/uep-out.zip |
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| diff -r 000000000000 -r 49b6d76139da get_out_folder.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/get_out_folder.py Thu Aug 25 16:18:39 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 or FileNotFoundError: + sys.stdout.write('muon-airss-out') |
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| diff -r 000000000000 -r 49b6d76139da pm_muairss_read.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/pm_muairss_read.xml Thu Aug 25 16:18:39 2022 +0000 |
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| b'@@ -0,0 +1,158 @@\n+<tool id="pm_muairss_read" name="PyMuonSuite AIRSS Cluster" version="@TOOL_VERSION@+galaxy@WRAPPER_VERSION@" python_template_version="3.5" profile="22.01">\n+ <description>run clustering for optimised 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="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+ </requirements>\n+ <command detect_errors="exit_code"><![CDATA[\n+ unzip "$optimisation_results" &&\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+ && out_folder="`python ${__tool_directory__}/get_out_folder.py`" &&\n+ pm-muairss -t r input_structure.* params.yaml\n+ ]]></command>\n+ <inputs>\n+ <param type="data" name="optimisation_results" label="optimised muonated structures (.zip)" format="zip" help="A zip folder containing a set of optimised muonated structures, the original structure, and a YAML parameter file. See below for the expected folder structure."/>\n+ </inputs>\n+ <outputs>\n+ <data label="Cluster report for $optimisation_results.name" name="cluster_report" format="txt" from_work_dir="$out_folder/*clusters.txt"/>\n+ <data label="Cluster data for $optimisation_results.name" name="cluster_data" format="txt" from_work_dir="$out_folder/*clusters.dat"/>\n+ </outputs>\n+ <tests>\n+ <test>\n+ <param name="optimisation_results" value="uep-out.zip" ftype="zip"/>\n+ <output name="cluster_report" file="clustout-uep.txt" ftype="txt" lines_diff="2"/>\n+ <output name="cluster_data" file="clustout-uep.dat" ftype="txt"/>\n+ </test>\n+ <test>\n+ <param name="optimisation_results" value="dftb-out.zip" ftype="zip"/>\n+ <output name="cluster_report" file="clustout-dftb.txt" ftype="txt" lines_diff="2"/>\n+ <output name="cluster_data" file="clustout-dftb.dat" ftype="txt"/>\n+ </test>\n+ </tests>\n+ <help><![CDATA[\n+ Given a set of optimised muonated structures, clusters the structures based on similarity.\n+\n+ If you used the \'Run UEP optimisation\' tool for optimisation, the output from that tool can be used as the input to this one.\n+ If you are bringing files from elsewhere, make sure they fit the expected zip folder structure:\n+\n+ .. code-block::\n+\n+ optimised-structures.zip/\n+ \xe2\x94\x9c\xe2\x94\x80 muon-airss-o'..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 49b6d76139da test-data/clusters.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/clusters.txt Thu Aug 25 16:18:39 2022 +0000 |
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| @@ -0,0 +1,73 @@ + +**************************** +| | +| PYMUON-SUITE | +| MuAirss Clusters report | +| | +**************************** + +Name: si +Date: 2021-09-16 15:16:14.755024 +Structure file(s): input.cell +Parameter file: params.yaml + +Clustering method: Hierarchical + t = 0.2 + + +******************* + +Clusters for si: +CALCULATOR: uep + 2 clusters found + + + ----------- + Cluster 1 + ----------- + Structures: 40 + + Energy (eV): + Minimum Average StDev + -8.49 -8.49 0.00 + + Minimum energy structure: si_28 + + + Structure list: + si_1 si_3 si_4 si_5 + si_6 si_7 si_9 si_10 + si_11 si_12 si_13 si_14 + si_15 si_16 si_17 si_18 + si_19 si_20 si_21 si_22 + si_24 si_25 si_27 si_28 + si_29 si_30 si_31 si_32 + si_33 si_34 si_35 si_36 + si_37 si_38 si_39 si_40 + si_41 si_42 si_43 si_44 + + ----------- + Cluster 2 + ----------- + Structures: 4 + + Energy (eV): + Minimum Average StDev + -8.43 -8.43 0.00 + + Minimum energy structure: si_8 + + + Structure list: + si_2 si_8 si_23 si_26 + + ---------- + + Similarity (ranked): + 1 <--> 2 (distance = 0.200) + +-------------------------- + + +========================== + |
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| diff -r 000000000000 -r 49b6d76139da test-data/clusters_dat.dat --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/clusters_dat.dat Thu Aug 25 16:18:39 2022 +0000 |
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| @@ -0,0 +1,2 @@ +1 40 -8.489815283944159 -8.48953725056192 0.00024952657863316923 2.738346970780946 2.7349964592271503 2.738350577627245 +2 4 -8.434721984298898 -8.43336958648337 0.0010603634471999137 4.789371896620391 3.4238847570583855 4.7892691550320245 |
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| diff -r 000000000000 -r 49b6d76139da test-data/clustout-dftb.dat --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/clustout-dftb.dat Thu Aug 25 16:18:39 2022 +0000 |
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| @@ -0,0 +1,3 @@ +1 27 -280.6035855579993 -280.60202336915836 0.0014309752898857598 3.3226068 0.7423389456 3.311549515 +2 3 -284.5412648607569 -284.54031723784425 0.0008843908674425659 2.349332209 2.364682032 2.966647288 +3 14 -282.62616915666706 -282.62574079969306 0.00029348507875924686 2.648214456 2.64892216 2.79616573 |
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| diff -r 000000000000 -r 49b6d76139da test-data/clustout-dftb.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/clustout-dftb.txt Thu Aug 25 16:18:39 2022 +0000 |
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| @@ -0,0 +1,90 @@ + +**************************** +| | +| PYMUON-SUITE | +| MuAirss Clusters report | +| | +**************************** + +Name: Si +Date: 2022-06-21 09:31:14.069470 +Structure file(s): input_structure.cell +Parameter file: params.yaml + +Clustering method: Hierarchical + t = 0.2 + + +******************* + +Clusters for Si: +CALCULATOR: dftb+ + 3 clusters found + + + ----------- + Cluster 1 + ----------- + Structures: 27 + + Energy (eV): + Minimum Average StDev + -280.60 -280.60 0.00 + + Minimum energy structure: Si_2 + + + Structure list: + Si_1 Si_2 Si_5 Si_7 + Si_8 Si_10 Si_12 Si_15 + Si_17 Si_19 Si_20 Si_21 + Si_22 Si_23 Si_27 Si_28 + Si_29 Si_30 Si_31 Si_32 + Si_33 Si_34 Si_35 Si_37 + Si_40 Si_41 Si_43 + + ----------- + Cluster 2 + ----------- + Structures: 3 + + Energy (eV): + Minimum Average StDev + -284.54 -284.54 0.00 + + Minimum energy structure: Si_9 + + + Structure list: + Si_9 Si_25 Si_38 + + ----------- + Cluster 3 + ----------- + Structures: 14 + + Energy (eV): + Minimum Average StDev + -282.63 -282.63 0.00 + + Minimum energy structure: Si_42 + + + Structure list: + Si_3 Si_4 Si_6 Si_11 + Si_13 Si_14 Si_16 Si_18 + Si_24 Si_26 Si_36 Si_39 + Si_42 Si_44 + + ---------- + + Similarity (ranked): + 2 <--> 3 (distance = 1.917) + 1 <--> 3 (distance = 2.056) + 1 <--> 2 (distance = 3.951) + +-------------------------- + + +========================== + |
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| diff -r 000000000000 -r 49b6d76139da test-data/clustout-uep.dat --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/clustout-uep.dat Thu Aug 25 16:18:39 2022 +0000 |
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| @@ -0,0 +1,2 @@ +1 12 -8.48981735648929 -8.489653583517093 0.00024027756008448932 2.737258848758643 2.7360057598043412 2.7389450032513163 +2 2 -8.434721105141751 -8.4346637258869 5.737925485060913e-05 4.793737331680057 3.4196257709744113 4.79365085189437 |
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| diff -r 000000000000 -r 49b6d76139da test-data/clustout-uep.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/clustout-uep.txt Thu Aug 25 16:18:39 2022 +0000 |
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| @@ -0,0 +1,66 @@ + +**************************** +| | +| PYMUON-SUITE | +| MuAirss Clusters report | +| | +**************************** + +Name: Si +Date: 2022-06-21 09:32:03.839222 +Structure file(s): input_structure.cell +Parameter file: params.yaml + +Clustering method: Hierarchical + t = 0.2 + + +******************* + +Clusters for Si: +CALCULATOR: uep + 2 clusters found + + + ----------- + Cluster 1 + ----------- + Structures: 12 + + Energy (eV): + Minimum Average StDev + -8.49 -8.49 0.00 + + Minimum energy structure: Si_1 + + + Structure list: + Si_1 Si_2 Si_5 Si_6 + Si_7 Si_8 Si_9 Si_10 + Si_11 Si_12 Si_13 Si_14 + + ----------- + Cluster 2 + ----------- + Structures: 2 + + Energy (eV): + Minimum Average StDev + -8.43 -8.43 0.00 + + Minimum energy structure: Si_3 + + + Structure list: + Si_3 Si_4 + + ---------- + + Similarity (ranked): + 1 <--> 2 (distance = 0.218) + +-------------------------- + + +========================== + |
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| diff -r 000000000000 -r 49b6d76139da test-data/dftb-out.zip |
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| Binary file test-data/dftb-out.zip has changed |
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| diff -r 000000000000 -r 49b6d76139da test-data/uep-out.zip |
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| Binary file test-data/uep-out.zip has changed |