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Refactor config parameters into UEP opt and read tools #128 #130

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merged 11 commits into from
Jul 18, 2023
Merged

Refactor config parameters into UEP opt and read tools #128 #130

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b02e099
Add cluster save options and refactor config #125
patrick-austin Feb 7, 2023
787120d
Add zip as a requirement for pm_muairss_read #125
patrick-austin Feb 7, 2023
0adf023
Refactor config parameters into UEP opt and read tools #128
patrick-austin Feb 24, 2023
5d3340b
Flake8 import order in config.py #128
patrick-austin Feb 24, 2023
302c582
Supercell refector and remove input save type #128
patrick-austin Apr 11, 2023
f2ef19a
Use input_structure as seedname for all files #128
patrick-austin Apr 12, 2023
0491802
Update tool versions and parallelise uep opt #128
patrick-austin Jun 12, 2023
54f418a
Merge branch 'dev' into patrick/128_stopping_site_changes
patrick-austin Jun 12, 2023
376efd0
Revert MSS 2.3.0, use doi for PMS 0.3.0 #128
patrick-austin Jun 13, 2023
29f18f6
Merge branch 'patrick/128_stopping_site_changes' of github.com:muon-s…
patrick-austin Jun 13, 2023
8b72755
Fix planemo lint delta and diff in pm_yaml
patrick-austin Jun 13, 2023
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2 changes: 1 addition & 1 deletion cif2cell/cif2cell.xml
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Expand Up @@ -9,7 +9,7 @@
<creator>
<person givenName="Anish" familyName="Mudaraddi" identifier="https://orcid.org/0000-0002-2135-2705"/>
<person givenName="Eli" familyName="Chadwick" url="https://github.com/elichad" identifier="https://orcid.org/0000-0002-0035-6475"/>
<person givenName="Patrick" familyName="Austin" url="https://github.com/patrick-austin"/>
<person givenName="Patrick" familyName="Austin" url="https://github.com/patrick-austin" identifier="https://orcid.org/0000-0002-6279-7823"/>
<organization url="https://muon-spectroscopy-computational-project.github.io/index.html" name="The Muon Spectroscopy Computational Project"/>
</creator>
<requirements>
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2 changes: 1 addition & 1 deletion muspinsim_plot/muspinsim_plot.xml
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Expand Up @@ -27,7 +27,7 @@
<creator>
<person givenName="Anish" familyName="Mudaraddi" identifier="https://orcid.org/0000-0002-2135-2705"/>
<person givenName="Eli" familyName="Chadwick" url="https://github.com/elichad" identifier="https://orcid.org/0000-0002-0035-6475"/>
<person givenName="Patrick" familyName="Austin" url="https://github.com/patrick-austin"/>
<person givenName="Patrick" familyName="Austin" url="https://github.com/patrick-austin" identifier="https://orcid.org/0000-0002-6279-7823"/>
<organization url="https://muon-spectroscopy-computational-project.github.io/index.html" name="The Muon Spectroscopy Computational Project"/>
</creator>
<requirements>
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20 changes: 3 additions & 17 deletions pm_asephonons/pm_asephonons.xml
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Expand Up @@ -2,23 +2,11 @@
<description>calculate phonons using ASE and DFTB+</description>
<macros>
<!-- version of underlying tool (PEP 440) -->
<token name="@TOOL_VERSION@">0.2.3</token>
<token name="@TOOL_VERSION@">0.3.0</token>
<!-- version of this tool wrapper (integer) -->
<token name="@WRAPPER_VERSION@">0</token>
<!-- citation should be updated with every underlying tool version -->
<!-- typical fields to update are version, month, year, and doi -->
<token name="@PYMUONSUITE_CITATION@">
@software{Sturniolo_pymuon-suite_2022,
author = {Sturniolo, Simone and Liborio, Leandro and Chadwick, Eli and Murgatroyd, Laura and Laverack, Adam and Mudaraddi, Anish and {Muon Spectroscopy Computational Project}},
license = {GPL-3.0},
month = {8},
title = {{pymuon-suite}},
url = {https://github.com/muon-spectroscopy-computational-project/pymuon-suite},
version = {v0.2.3},
doi = {10.5281/zenodo.7025644},
year = {2022}
}
</token>
<token name="@TOOL_CITATION@">10.5281/zenodo.8026711</token>
<import>muon_macros.xml</import>
</macros>
<creator>
Expand Down Expand Up @@ -188,9 +176,7 @@ force_clean: false</configfile>
|
]]></help>
<citations>
<citation type="bibtex">
@PYMUONSUITE_CITATION@
</citation>
<citation type="doi">@TOOL_CITATION@</citation>
<citation type="doi">10.1063/1.5085197</citation>
<citation type="bibtex">
@article{larsen2017atomic,
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18 changes: 18 additions & 0 deletions pm_muairss_read/config.py
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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()
152 changes: 126 additions & 26 deletions pm_muairss_read/pm_muairss_read.xml
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<description>run clustering for optimised structures</description>
<macros>
<!-- version of underlying tool (PEP 440) -->
<token name="@TOOL_VERSION@">0.2.3</token>
<token name="@TOOL_VERSION@">0.3.0</token>
<!-- version of this tool wrapper (integer) -->
<token name="@WRAPPER_VERSION@">0</token>
<!-- citation should be updated with every underlying tool version -->
<!-- typical fields to update are version, month, year, and doi -->
<token name="@TOOL_CITATION@">
@software{Sturniolo_pymuon-suite_2022,
author = {Sturniolo, Simone and Liborio, Leandro and Chadwick, Eli and Murgatroyd, Laura and Laverack, Adam and Mudaraddi, Anish and {Muon Spectroscopy Computational Project}},
license = {GPL-3.0},
month = {8},
title = {{pymuon-suite}},
url = {https://github.com/muon-spectroscopy-computational-project/pymuon-suite},
version = {v0.2.3},
doi = {10.5281/zenodo.7025644},
year = {2022}
}
</token>
<token name="@TOOL_CITATION@">10.5281/zenodo.8026711</token>
<xml name="supercell">
<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.">
<validator type="regex" message="Input should only contain whitespace, '[', ']', ',' and digits.">^[\s\d,\[\]]+$</validator>
</param>
</xml>
</macros>
<creator>
<person givenName="Jyothish" familyName="Thomas" identifier="https://orcid.org/0000-0003-4724-6924"/>
<person givenName="Eli" familyName="Chadwick" url="https://github.com/elichad" identifier="https://orcid.org/0000-0002-0035-6475"/>
<person givenName="Patrick" familyName="Austin" url="https://github.com/patrick-austin" identifier="https://orcid.org/0000-0002-6279-7823"/>
<organization url="https://muon-spectroscopy-computational-project.github.io/index.html" name="The Muon Spectroscopy Computational Project"/>
</creator>
<requirements>
<requirement type="package" version="@TOOL_VERSION@">pymuonsuite</requirement>
<requirement type="package" version="3.0">zip</requirement>
</requirements>
<required_files>
<include type="literal" path="get_out_folder.py"/>
<include type="literal" path="config.py"/>
</required_files>
<command detect_errors="exit_code"><![CDATA[
unzip '$optimisation_results' &&
if test -f "params.yaml"; then echo "params.yaml present"; else echo "params.yaml missing" && exit 64; fi
&& if ( test -f input_structure.* ) ; then echo "input structure present"; else echo "input structure missing" && exit 64; fi
&& out_folder="`python '${__tool_directory__}/get_out_folder.py'`" &&
pm-muairss -t r input_structure.* params.yaml
&& out_folder="`python '${__tool_directory__}/get_out_folder.py'`"
&& python '${__tool_directory__}/config.py'
&& pm-muairss -t r input_structure.* params.yaml
#if $clustering_save.clustering_save_format != "none":
&& ln -s *_clusters/* minimal_clusters
#end if
]]></command>
<configfiles>
<configfile filename="incoming_params">clustering_method: $clustering.clustering_method
#if $clustering.clustering_method == "hier":
clustering_hier_t: $clustering.clustering_hier_t
#else if $clustering.clustering_method == "kmeans":
clustering_kmeans_k: $clustering.clustering_kmeans_k
#end if
#if $clustering_save.clustering_save_format != "none":
clustering_save_type: structures
clustering_save_format: $clustering_save.clustering_save_format
supercell: $clustering_save.supercell.replace('__ob__', '[').replace('__cb__', ']')
#if $clustering_save.clustering_save_format == "cell":
mu_symbol: $clustering_save.mu_symbol
#end if
#end if</configfile>
</configfiles>
<inputs>
<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."/>
<conditional name="clustering">
<param type="select" argument="clustering_method" display="radio" label="Clustering method" value="hier">
<option value="hier">hierarchical</option>
<option value="kmeans">k-means</option>
</param>
<when value="hier">
<param type="float" argument="clustering_hier_t" value="0.3" min="0.0" optional="true" label="t parameter for hierarchical clustering"/>
</when>
<when value="kmeans">
<param type="integer" argument="clustering_kmeans_k" value="4" min="0" optional="true" label="Number of clusters for k-means clustering"/>
</when>
</conditional>
<conditional name="clustering_save">
<param argument="clustering_save_format" type="select" label="Clustering Save Format" help="If set, for each cluster a structural file with the specified format will be generated, corresponding to the structure in the cluster with minimal energy.">
<option value="none" selected="true">Do not generate</option>
<option value="cell">CELL</option>
<option value="cif">CIF</option>
<option value="xyz">XYZ</option>
</param>
<when value="none"/>
<when value="cell">
<expand macro="supercell"/>
<param argument="mu_symbol" type="text" value="H:mu" optional="true" label="Muon symbol" help="The symbol to use for the muon when writing out the CASTEP custom species. Should be a valid chemical symbol followed by `:`, then custom text."/>
</when>
<when value="cif">
<expand macro="supercell"/>
</when>
<when value="xyz">
<expand macro="supercell"/>
</when>
</conditional>
</inputs>
<outputs>
<data label="Cluster report for $optimisation_results.name" name="cluster_report" format="txt" from_work_dir="${out_folder}/*clusters.txt"/>
<data label="Cluster data for $optimisation_results.name" name="cluster_data" format="txt" from_work_dir="${out_folder}/*clusters.dat"/>
<collection name="saved_structures" type="list" label="Minimal energy structures" format="txt">
<filter>clustering_save["clustering_save_format"] != "none"</filter>
<discover_datasets pattern="__name_and_ext__" directory="minimal_clusters"/>
</collection>
</outputs>
<tests>
<test expect_num_outputs="2">
<param name="optimisation_results" value="uep-out.zip" ftype="zip"/>
<conditional name="clustering">
<param name="clustering_hier_t" value="0.2"/>
</conditional>
<output name="cluster_report" file="clustout-uep.txt" ftype="txt" lines_diff="2"/>
<output name="cluster_data" file="clustout-uep.dat" ftype="txt"/>
</test>
<test expect_num_outputs="3">
<param name="optimisation_results" value="uep-out.zip" ftype="zip"/>
<conditional name="clustering">
<param name="clustering_hier_t" value="0.2"/>
</conditional>
<conditional name="clustering_save">
<param name="clustering_save_format" value="cell"/>
</conditional>
<output name="cluster_report" file="clustout-uep.txt" ftype="txt" lines_diff="2"/>
<output name="cluster_data" file="clustout-uep.dat" ftype="txt"/>
<output_collection name="saved_structures" type="list" count="2"/>
</test>
<!-- Test optional save params -->
<test expect_num_outputs="3">
<param name="optimisation_results" value="uep-out.zip" ftype="zip"/>
<conditional name="clustering">
<param name="clustering_hier_t" value="0.2"/>
</conditional>
<conditional name="clustering_save">
<param name="clustering_save_format" value="cell"/>
<param name="supercell" value="2"/>
<param name="mu_symbol" value="H:nu"/>
</conditional>
<output name="cluster_report" file="clustout-uep.txt" ftype="txt" lines_diff="2"/>
<output name="cluster_data" file="clustout-uep.dat" ftype="txt"/>
<output_collection name="saved_structures" type="list" count="2">
<element name="Si_uep_min_cluster_1" file="Si_uep_min_cluster_1.cell"/>
<element name="Si_uep_min_cluster_2" file="Si_uep_min_cluster_2.cell"/>
</output_collection>
</test>
<test expect_num_outputs="2">
<param name="optimisation_results" value="dftb-out.zip" ftype="zip"/>
<conditional name="clustering">
<param name="clustering_hier_t" value="0.2"/>
</conditional>
<output name="cluster_report" file="clustout-dftb.txt" ftype="txt" lines_diff="2"/>
<output name="cluster_data" file="clustout-dftb.dat" ftype="txt"/>
</test>
<!-- Test overwrite of values in the existing params.yaml -->
<test expect_num_outputs="2">
<param name="optimisation_results" value="uep-out.zip" ftype="zip"/>
<conditional name="clustering">
<param name="clustering_method" value="kmeans"/>
<param name="clustering_kmeans_k" value="2"/>
</conditional>
<!-- kmeans gives predictable clusters, but orders them randomly -->
<!-- To prevent this from affecting tests, sort the lines -->
<!-- in the report and use regex matching for the dat file -->
<output name="cluster_report" file="clustout-uep-kmeans.txt" ftype="txt" lines_diff="2" sort="true"/>
<output name="cluster_data" file="clustout-uep-kmeans.dat" ftype="txt" compare="re_match"/>
</test>
</tests>
<help><![CDATA[
Given a set of optimised muonated structures, clusters the structures based on similarity.

This is intended to be used with the output from '`PyMuonSuite AIRSS UEP Optimise`_'.
If you used the 'Run UEP optimisation' tool for optimisation, the output from that tool can be used as the input to this one.
If you are bringing files from elsewhere, make sure they fit the expected zip folder structure:
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:

.. code-block::

Expand All @@ -77,24 +178,23 @@
├─ input.cell
├─ params.yaml

This folder represents a run with the output folder name ``muon-airss-out``, the structure name ``struct``, and the UEP calculator.
If you use different parameters, these names should match your own settings. (``dftb+`` and ``castep`` are used as folder names for the respective calculators)

This folder represents a run with the output folder name ``muon-airss-out``, the structure name ``struct``, and the ``uep`` calculator.
If you use different parameters, these names should match your own settings (``dftb+`` and ``castep`` are used as folder names for the respective calculators).
The zip folder itself has been named ``optimised-structures.zip`` in this example, but it doesn't matter what you call it.

The files ``input.cell`` and ``params.yaml`` must have those exact names. ``input.cell`` should be your original structure file,
and ``params.yaml`` is the YAML parameter file used to configure the clustering (as well as any prior muonation and optimisation).
You should have created this YAML file using the 'Create YAML for pm-muairss' tool or written it yourself, then passed it into the
'Generate muon structures' tool or pm-muairss.
and ``params.yaml`` is the YAML parameter file used to configure the muonation and optimisation.
This file is created automatically when using '`PyMuonSuite AIRSS UEP Optimise`_'.
Any parameters relating to the clustering process present in the original file will be overwritten with the values selected here.

Command-line usage: pm-muairss [-h] -t r structures parameter_file

.. _PyMuonSuite AIRSS UEP Optimise: /tool_runner?tool_id=pm_uep_opt

PyMuonSuite is distributed under the GPLv3 license. This tool wrapper is distributed under the MIT license.
]]></help>
<citations>
<citation type="bibtex">
@TOOL_CITATION@
</citation>
<citation type="doi">@TOOL_CITATION@</citation>
<citation type="doi">10.1063/1.5024450</citation>
<citation type="doi">10.1063/1.5085197</citation>
<citation type="doi">10.1063/5.0012381</citation>
Expand Down
91 changes: 91 additions & 0 deletions pm_muairss_read/test-data/Si_uep_min_cluster_1.cell
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#######################################################
#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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