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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 70a4d37ecdf5d586703cfc509922311e95d3205c |
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modified:
pm_muairss_read.xml |
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added:
config.py muon_macros.xml test-data/Si_uep_min_cluster_1.cell test-data/Si_uep_min_cluster_2.cell test-data/clustout-uep-kmeans.dat test-data/clustout-uep-kmeans.txt |
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| diff -r 276a25ab05f2 -r 40071ff77285 config.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/config.py Tue Jul 18 13:26:40 2023 +0000 |
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| @@ -0,0 +1,18 @@ +import yaml + + +def main(): + with open("params.yaml") as f: + existing_params = yaml.safe_load(f) + + with open("incoming_params") as f: + incoming_params = yaml.safe_load(f) + + merged_params = {**existing_params, **incoming_params} + + with open("params.yaml", "w") as f: + yaml.safe_dump(merged_params, f) + + +if __name__ == "__main__": + main() |
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| diff -r 276a25ab05f2 -r 40071ff77285 muon_macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/muon_macros.xml Tue Jul 18 13:26:40 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 |
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| diff -r 276a25ab05f2 -r 40071ff77285 pm_muairss_read.xml --- a/pm_muairss_read.xml Fri Feb 03 15:39:29 2023 +0000 +++ b/pm_muairss_read.xml Tue Jul 18 13:26:40 2023 +0000 |
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| b'@@ -1,67 +1,165 @@\n-<tool id="pm_muairss_read" name="PyMuonSuite AIRSS Cluster" version="@TOOL_VERSION@+galaxy@WRAPPER_VERSION@" python_template_version="3.5" profile="22.05" license="MIT">\n+<tool id="pm_muairss_read" name="PyMuonSuite AIRSS Cluster" version="@PYMUONSUITE_VERSION@+galaxy@WRAPPER_VERSION@" python_template_version="3.5" profile="22.05" license="MIT">\n <description>run clustering for optimised structures</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+ <xml name="supercell">\n+ <param type="text" argument="supercell" value="1" label="Supercell" help="Supercell size and shape to use when saving cluster structures. This can either be a single int, a list of three integers or a 3x3 matrix of integers. For a single number a diagonal matrix will be generated with the integer repeated on the diagonals. For a list of three numbers a diagonal matrix will be generated where the diagonal elements are set to the list. A matrix will be used directly as is. Default is a 3x3 identity matrix.">\n+ <validator type="regex" message="Input should only contain whitespace, \'[\', \']\', \',\' and digits.">^[\\s\\d,\\[\\]]+$</validator>\n+ </param>\n+ </xml>\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 <include type="literal" path="get_out_folder.py"/>\n+ <include type="literal" path="config.py"/>\n </required_files>\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+ && out_folder="`python \'${__tool_directory__}/get_out_folder.py\'`"\n+ && python \'${__tool_directory__}/config.py\' \n+ && pm-muairss -t r input_structure.* params.yaml\n+ #if $clustering_save.cluste'..b'tout-dftb.txt" ftype="txt" lines_diff="2"/>\n <output name="cluster_data" file="clustout-dftb.dat" ftype="txt"/>\n </test>\n+ <!-- Test overwrite of values in the existing params.yaml -->\n+ <test expect_num_outputs="2">\n+ <param name="optimisation_results" value="uep-out.zip" ftype="zip"/>\n+ <conditional name="clustering">\n+ <param name="clustering_method" value="kmeans"/>\n+ <param name="clustering_kmeans_k" value="2"/>\n+ </conditional>\n+ <!-- kmeans gives predictable clusters, but orders them randomly -->\n+ <!-- To prevent this from affecting tests, sort the lines -->\n+ <!-- in the report and use regex matching for the dat file -->\n+ <output name="cluster_report" file="clustout-uep-kmeans.txt" ftype="txt" lines_diff="2" sort="true"/>\n+ <output name="cluster_data" file="clustout-uep-kmeans.dat" ftype="txt" compare="re_match"/>\n+ </test>\n </tests>\n <help><![CDATA[\n Given a set of optimised muonated structures, clusters the structures based on similarity.\n \n+ This is intended to be used with the output from \'`PyMuonSuite AIRSS UEP Optimise`_\'.\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+ If you are bringing files from elsewhere (such as running PyMuonSuite from the command line, or with a different optimisation calculator), make sure they fit the expected zip folder structure:\n \n .. code-block::\n \n@@ -77,24 +175,23 @@\n \xe2\x94\x9c\xe2\x94\x80 input.cell\n \xe2\x94\x9c\xe2\x94\x80 params.yaml\n \n- This folder represents a run with the output folder name ``muon-airss-out``, the structure name ``struct``, and the UEP calculator.\n- If you use different parameters, these names should match your own settings. (``dftb+`` and ``castep`` are used as folder names for the respective calculators)\n-\n+ This folder represents a run with the output folder name ``muon-airss-out``, the structure name ``struct``, and the ``uep`` calculator.\n+ If you use different parameters, these names should match your own settings (``dftb+`` and ``castep`` are used as folder names for the respective calculators).\n The zip folder itself has been named ``optimised-structures.zip`` in this example, but it doesn\'t matter what you call it.\n \n The files ``input.cell`` and ``params.yaml`` must have those exact names. ``input.cell`` should be your original structure file,\n- and ``params.yaml`` is the YAML parameter file used to configure the clustering (as well as any prior muonation and optimisation).\n- You should have created this YAML file using the \'Create YAML for pm-muairss\' tool or written it yourself, then passed it into the\n- \'Generate muon structures\' tool or pm-muairss.\n+ and ``params.yaml`` is the YAML parameter file used to configure the muonation and optimisation.\n+ This file is created automatically when using \'`PyMuonSuite AIRSS UEP Optimise`_\'.\n+ Any parameters relating to the clustering process present in the original file will be overwritten with the values selected here.\n \n Command-line usage: pm-muairss [-h] -t r structures parameter_file\n \n+ .. _PyMuonSuite AIRSS UEP Optimise: /tool_runner?tool_id=pm_uep_opt\n+\n PyMuonSuite is distributed under the GPLv3 license. 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 276a25ab05f2 -r 40071ff77285 test-data/Si_uep_min_cluster_1.cell --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/Si_uep_min_cluster_1.cell Tue Jul 18 13:26:40 2023 +0000 |
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| @@ -0,0 +1,91 @@ +####################################################### +#CASTEP cell file: Si_clusters/uep/Si_uep_min_cluster_1.cell +#Created using the Atomic Simulation Environment (ASE)# +####################################################### + +%BLOCK LATTICE_CART +10.950902 0.000000 0.000000 + 0.000000 10.950902 -0.000000 + 0.000000 -0.000000 10.950902 +%ENDBLOCK LATTICE_CART + +%BLOCK POSITIONS_ABS +Si 0.000000 0.000000 0.000000 +Si 4.106588 4.106588 1.368863 +Si 2.737726 0.000000 2.737726 +Si 4.106588 1.368863 4.106588 +Si 0.000000 2.737726 2.737726 +Si 1.368863 1.368863 1.368863 +Si 1.368863 4.106588 4.106588 +Si 2.737726 2.737726 0.000000 +Si 0.000000 0.000000 5.475451 +Si 4.106588 4.106588 6.844314 +Si 2.737726 0.000000 8.213177 +Si 4.106588 1.368863 9.582039 +Si 0.000000 2.737726 8.213177 +Si 1.368863 1.368863 6.844314 +Si 1.368863 4.106588 9.582039 +Si 2.737726 2.737726 5.475451 +Si 0.000000 5.475451 0.000000 +Si 4.106588 9.582039 1.368863 +Si 2.737726 5.475451 2.737726 +Si 4.106588 6.844314 4.106588 +Si 0.000000 8.213177 2.737726 +Si 1.368863 6.844314 1.368863 +Si 1.368863 9.582039 4.106588 +Si 2.737726 8.213177 0.000000 +Si 0.000000 5.475451 5.475451 +Si 4.106588 9.582039 6.844314 +Si 2.737726 5.475451 8.213177 +Si 4.106588 6.844314 9.582039 +Si 0.000000 8.213177 8.213177 +Si 1.368863 6.844314 6.844314 +Si 1.368863 9.582039 9.582039 +Si 2.737726 8.213177 5.475451 +Si 5.475451 0.000000 0.000000 +Si 9.582039 4.106588 1.368863 +Si 8.213177 0.000000 2.737726 +Si 9.582039 1.368863 4.106588 +Si 5.475451 2.737726 2.737726 +Si 6.844314 1.368863 1.368863 +Si 6.844314 4.106588 4.106588 +Si 8.213177 2.737726 0.000000 +Si 5.475451 0.000000 5.475451 +Si 9.582039 4.106588 6.844314 +Si 8.213177 0.000000 8.213177 +Si 9.582039 1.368863 9.582039 +Si 5.475451 2.737726 8.213177 +Si 6.844314 1.368863 6.844314 +Si 6.844314 4.106588 9.582039 +Si 8.213177 2.737726 5.475451 +Si 5.475451 5.475451 0.000000 +Si 9.582039 9.582039 1.368863 +Si 8.213177 5.475451 2.737726 +Si 9.582039 6.844314 4.106588 +Si 5.475451 8.213177 2.737726 +Si 6.844314 6.844314 1.368863 +Si 6.844314 9.582039 4.106588 +Si 8.213177 8.213177 0.000000 +Si 5.475451 5.475451 5.475451 +Si 9.582039 9.582039 6.844314 +Si 8.213177 5.475451 8.213177 +Si 9.582039 6.844314 9.582039 +Si 5.475451 8.213177 8.213177 +Si 6.844314 6.844314 6.844314 +Si 6.844314 9.582039 9.582039 +Si 8.213177 8.213177 5.475451 +H:nu 2.737259 2.736006 2.738945 +%ENDBLOCK POSITIONS_ABS + +%BLOCK SPECIES_GAMMA +radsectesla +H:nu 851615456.5978916 +%ENDBLOCK SPECIES_GAMMA + +%BLOCK SPECIES_MASS +AMU +H:nu 0.1134289259 +%ENDBLOCK SPECIES_MASS + +KPOINT_MP_GRID: 1 1 1 +FIX_ALL_CELL: True |
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| diff -r 276a25ab05f2 -r 40071ff77285 test-data/Si_uep_min_cluster_2.cell --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/Si_uep_min_cluster_2.cell Tue Jul 18 13:26:40 2023 +0000 |
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| @@ -0,0 +1,91 @@ +####################################################### +#CASTEP cell file: Si_clusters/uep/Si_uep_min_cluster_2.cell +#Created using the Atomic Simulation Environment (ASE)# +####################################################### + +%BLOCK LATTICE_CART +10.950902 0.000000 0.000000 + 0.000000 10.950902 -0.000000 + 0.000000 -0.000000 10.950902 +%ENDBLOCK LATTICE_CART + +%BLOCK POSITIONS_ABS +Si 0.000000 0.000000 0.000000 +Si 4.106588 4.106588 1.368863 +Si 2.737726 0.000000 2.737726 +Si 4.106588 1.368863 4.106588 +Si 0.000000 2.737726 2.737726 +Si 1.368863 1.368863 1.368863 +Si 1.368863 4.106588 4.106588 +Si 2.737726 2.737726 0.000000 +Si 0.000000 0.000000 5.475451 +Si 4.106588 4.106588 6.844314 +Si 2.737726 0.000000 8.213177 +Si 4.106588 1.368863 9.582039 +Si 0.000000 2.737726 8.213177 +Si 1.368863 1.368863 6.844314 +Si 1.368863 4.106588 9.582039 +Si 2.737726 2.737726 5.475451 +Si 0.000000 5.475451 0.000000 +Si 4.106588 9.582039 1.368863 +Si 2.737726 5.475451 2.737726 +Si 4.106588 6.844314 4.106588 +Si 0.000000 8.213177 2.737726 +Si 1.368863 6.844314 1.368863 +Si 1.368863 9.582039 4.106588 +Si 2.737726 8.213177 0.000000 +Si 0.000000 5.475451 5.475451 +Si 4.106588 9.582039 6.844314 +Si 2.737726 5.475451 8.213177 +Si 4.106588 6.844314 9.582039 +Si 0.000000 8.213177 8.213177 +Si 1.368863 6.844314 6.844314 +Si 1.368863 9.582039 9.582039 +Si 2.737726 8.213177 5.475451 +Si 5.475451 0.000000 0.000000 +Si 9.582039 4.106588 1.368863 +Si 8.213177 0.000000 2.737726 +Si 9.582039 1.368863 4.106588 +Si 5.475451 2.737726 2.737726 +Si 6.844314 1.368863 1.368863 +Si 6.844314 4.106588 4.106588 +Si 8.213177 2.737726 0.000000 +Si 5.475451 0.000000 5.475451 +Si 9.582039 4.106588 6.844314 +Si 8.213177 0.000000 8.213177 +Si 9.582039 1.368863 9.582039 +Si 5.475451 2.737726 8.213177 +Si 6.844314 1.368863 6.844314 +Si 6.844314 4.106588 9.582039 +Si 8.213177 2.737726 5.475451 +Si 5.475451 5.475451 0.000000 +Si 9.582039 9.582039 1.368863 +Si 8.213177 5.475451 2.737726 +Si 9.582039 6.844314 4.106588 +Si 5.475451 8.213177 2.737726 +Si 6.844314 6.844314 1.368863 +Si 6.844314 9.582039 4.106588 +Si 8.213177 8.213177 0.000000 +Si 5.475451 5.475451 5.475451 +Si 9.582039 9.582039 6.844314 +Si 8.213177 5.475451 8.213177 +Si 9.582039 6.844314 9.582039 +Si 5.475451 8.213177 8.213177 +Si 6.844314 6.844314 6.844314 +Si 6.844314 9.582039 9.582039 +Si 8.213177 8.213177 5.475451 +H:nu 4.793737 3.419626 4.793651 +%ENDBLOCK POSITIONS_ABS + +%BLOCK SPECIES_GAMMA +radsectesla +H:nu 851615456.5978916 +%ENDBLOCK SPECIES_GAMMA + +%BLOCK SPECIES_MASS +AMU +H:nu 0.1134289259 +%ENDBLOCK SPECIES_MASS + +KPOINT_MP_GRID: 1 1 1 +FIX_ALL_CELL: True |
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| diff -r 276a25ab05f2 -r 40071ff77285 test-data/clustout-uep-kmeans.dat --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/clustout-uep-kmeans.dat Tue Jul 18 13:26:40 2023 +0000 |
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| @@ -0,0 +1,2 @@ +1 1?2 -8\.4\d+ -8\.4\d+ \d\.\d+e?-?\d{0,2} \d\.\d+ \d\.\d+ \d\.\d+ +2 1?2 -8\.4\d+ -8\.4\d+ \d\.\d+e?-?\d{0,2} \d\.\d+ \d\.\d+ \d\.\d+ |
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| diff -r 276a25ab05f2 -r 40071ff77285 test-data/clustout-uep-kmeans.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/clustout-uep-kmeans.txt Tue Jul 18 13:26:40 2023 +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: k-Means + k = 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) + +-------------------------- + + +========================== + |