Saravanan666/pypi-org huggingface dataset:
Package: aiida-grouppathx
aiida-grouppathxAiiDA plugin provides theGroupPathXclass.This plugin was kickstarted usingAiiDA plugin cutter,
intended to help developers get started with their AiiDA plugins.Features and usageThis package is provides a enhanced version ofGroupPath-GroupPathX.
The main feature is that it allows nodes stored under a group to benamedby an alias.
This way, one can address a specificNodeasGroupPath('mygroup/structure1').
In addition, ashow_treemethod is provided for visualising the content of a specificGroupPathX,
similiar to the command line tooltreethat works on the file system.
The goal is to provide a way for managing data with an interface what is similar to a file system based approach.tree aiida_grouppathx

aiida_grouppathx
├── __init__.py
├── pathx.py
└── __pycache__
   ├── __init__.cpython-38.pyc
   └── pathx.cpython-38.pycIn analogy:fromaiida_grouppathximportGroupPathXpath=GroupPathX('group1')path.get_or_create_group()path['group2'].get_or_create_group()path.add_node(Int(1).store(),'int1')path['group2'].add_node(Int(1).store(),'int2')path.show_tree()givesgroup1
├── group2
│   └── int2 *
└── int1 *where the*highlights that a leaf is aNoderather than a group.
This kind of mark up can be customised, for example, to show the status of workflow nodes.defdecorate_name(path):ifpath.is_node:return' '+str(path.get_node())path.show_tree(decorate_name)gives:group1
├── group2
│   └── int2  uuid: de79d244-d3bb-4f61-9d3a-b3f09e1afb72 (pk: 7060) value: 1
└── int1  uuid: e2f70643-0c25-4ae5-929a-a3e055969d10 (pk: 7059) value: 1Multiple decorators can be combinedfrom aiida_grouppathx import decorate_with_group_names, decorate_with_label decorate_with_uuid_first_n

path.show_tree(decorate_with_group_names, decorate_with_label, decorate_with_uuid_first_n())output:group1
├── group2
│   └── int2 group1/group2 |  | de79d244-d3b
└── int1 group1 |  | e2f70643-0c2The stored nodes can be access through:group1['group2/int2'].get_node()  # Gives node de89d2
group1.browse.group2.int2().get_node()  # Also gives node de89d2and alsopath.browse.<tab>
path.browse.int1()     # To access the `group1/int1` path
path.browse.int1().get_node()     # To access the `group1/int1` nodePlease see thepathx.pyfor the extended methods, and the official documentation for the concept ofGroupPath.The package does not change howGroupandNodeoperates in the AiiDA.
It is only built on top of the existing system as an alternative way to access the underlying data.Installationpipinstallaiida-grouppathx
verdiquicksetup# better to set up a new profileDevelopmentgitclonehttps://github.com/zhubonan/aiida-grouppathx.cdaiida-grouppathx
pipinstall--upgradepip
pipinstall-e.[pre-commit,testing]# install extra dependenciespre-commitinstall# install pre-commit hookspytest-v# discover and run all testsSee thedeveloper guidefor more information.LicenseMITContactzhubonan@outlook.com
Package: aiida-gudhi
aiida-gudhiAiiDA plugin for theGUDHIlibrary for topological data analysis.Installationgitclonehttps://github.com/ltalirz/aiida-gudhi.cdaiida-gudhi
pipinstall-e.# also installs aiida, if missing (but not postgres)#pip install -e .[precommit,testing] # install extras for more featuresverdiquicksetup# better to set up a new profileverdicalculationplugins# should now show your calclulation pluginsUsageHere goes a complete example of how to submit a test calculation using this plugin.LicenseMITContactleopold.talirz@gmail.com
Package: aiida-gulp
aiida-gulpAiiDA plugin for running theGULPcode.Documentation:https://readthedocs.org/projects/aiida-gulpInstallationTo install from Conda (recommended)::>>condainstall-cconda-forgeaiida-gulpaiida-core.servicesTo install from pypi::>>pipinstallaiida-gulpTo install the development version:>>gitclonehttps://github.com/chrisjsewell/aiida-gulp.
>>cdaiida-gulp
>>pipinstall-e.# also installs aiida, if missing (but not postgres)>>#pip install -e .[pre-commit,testing] # install extras for more features>>verdiquicksetup# set up a new profile>>verdicalculationplugins# should now show the calculation plugins (with prefix gulp.)DevelopmentTesting against mock GULP executablesBecause GULP is a licensed software, it is not possible to source a copy of the executable on Travis CI.
Therefore, a mock executable (gulp_mock) has been created for testing purposes (which also speeds up test runs).This executable computes the md5 hash of the supplied input file and tries to match it against a dictionary of
precomputed hashes. If found, the executable will write the matching output (fromtest/output_files) to stdout.The following will discover and run all unit test:>>pipinstall-e.[testing]>>reentryscan-raiida
>>pytest-vTo omit tests which call external executables (likegulp):>>pytest--gulp-skip-execTo call the actual executable (e.g.gulpinstead ofgulp_mock):>>pytest--gulp-no-mockTo output the results of calcjob executions to a specific directory:>>pytest--gulp-workdir"test_workdir"Coding Style RequirementsThe code style is tested usingflake8,
with the configuration set in.flake8, and code should be formatted withblack.Installing withaiida-gulp[code_style]makes thepre-commitpackage available, which will ensure these tests are passed by reformatting the code
and testing for lint errors before submitting a commit.
It can be setup by:>>cdaiida-gulp
>>pre-commitinstallOptionally you can runblackandflake8separately:>>black.# recursively find and format files in-place>>flake8Editors like VS Code also have automatic code reformat utilities, which can adhere to this standard.LicenseSeeLICENSEfileContactchrisj_sewell@hotmail.com
Package: aiida-hyperqueue
AiiDA HyperQueue pluginAiiDA plugin for theHyperQueuemetascheduler.❗️ This package is still in the early stages of development and we will most likely break the API regularly in new 0.X versions. Be sure to pin the version when installing this package in scripts.FeaturesAllows task farming on Slurm machines through the submission of AiiDA calculations to theHyperQueuemetascheduler.
See theDocumentationfor more information on how to install and use the plugin.
Package: aiida-kkr
aiida-kkrAiiDAplugin for theJülich KKR codesplus workflows and utility.FeaturesKKR calculations for bulk and interfacestreatment of alloys using VCA or CPAself-consistency, DOS and bandstructure calculationsextraction of magnetic exchange coupling parameters (J_ij,D_ij)impurity embedding solving the Dyson equationHow to citeIf you use this plugin please cite:Rüßmann, P., Bertoldo, F. & Blügel, S. The AiiDA-KKR plugin and its application to high-throughput impurity embedding into a topological insulator.npj Comput Mater7, 13 (2021). https://doi.org/10.1038/s41524-020-00482-5The ArXiv preprint can be found here:Philipp Rüßmann, Fabian Bertoldo and Stefan Blügel,The AiiDA-KKR plugin and its application to high-throughput impurity embedding into a topological insulator, arXiv:2003.08315 [cond-mat.mtrl-sci] (2020)Installation$pipinstallaiida-kkr# install latest version of aiida-kkr (published on pypi.org)$reentryscan-raiida# update entry points, needed in order to find kkr.* entrypoints in aiida# setupt aiida if this was not done already:$verdiquicksetup# better to set up a new profile$verdicalculationplugins# should now show kkr.* entrypointsTo install the developer version download the repository and install the downloaded version (seesetup.jsonfor a list of optional packages that are installed with the extras given in[])$gitclonehttps://github.com/JuDFTteam/aiida-kkr.git
$pipinstall-eaiida-kkr[testing,devtools,docs]$reentryscan-raiidaRemarks about dependencies and extrasTheaiida-kkrplugin uses theaseandpymatgenpackages for structure conversions.Foraiida-core>=1.5,<1.6make sure to use the requirements specified inrequirements_aiida-core_1.5.txt(usepip install -r requirements_aiida-core_1.5.txt aiida-kkrfor the installation to overwrite the aiida-core dependency).Other extras that can be optionally installed withaiida-kkrarepre-commitwhich installes the pre-commit hooks that allow style (yapf) and static code checking (pylint)testingwhich installspytestand all extension used in the testsdocswhich installsSphinxto build the documentationdevtoolswhich installs tools that might be helpful during developmentUsage and Documentationseehttp://aiida-kkr.readthedocs.iofor user's guide and API reference.check outhttp://judft.deandhttps://jukkr.fz-juelich.defor information of the KKR codes used by the pluginContributingThank you for your interest in contributing to aiida-kkr.
Check out ourcontributing guidefor some information.
Package: aiidalab
AiiDAlab packageTheaiidalabpackage sets up the python environment found on theAiiDAlab.InstallationInstall latest version from pypi:pip install aiidalabor from theconda-forgeconda channel:conda install -c conda-forge aiidalabDocumentationThe documentation can be found on thefollowing web page.For maintainersTo create a new release, clone the repository, install development dependencies withpip install -e '.[dev]', and then executebumpver update.
This will:Create a tagged release with bumped version and push it to the repository.Trigger a GitHub actions workflow that creates a GitHub release.Additional notes:Use the--dryoption to preview the release change.The release tag (e.g. a/b/rc) is determined from the last release.
Use the--tagoption to switch the release tag.LicenseMITCitationUsers of AiiDAlab are kindly asked to cite the following publication in their own work:A. V. Yakutovich et al., Comp. Mat. Sci. 188, 110165 (2021).DOI:10.1016/j.commatsci.2020.110165Contactaiidalab@materialscloud.orgAcknowledgementsThis work is supported by theMARVEL National Centre for Competency in Researchfunded by theSwiss National Science Foundation, as well as by theMaX
European Centre of Excellencefunded by the Horizon 2020 EINFRA-5 program,
Grant No. 676598.
Package: aiidalab-eln
AiiDAlab-ELNIntegrate AiiDAlab with Electronic Laboratory Notebooks (ELN). This repository implements a general API for interfacing AiiDAlab with some ELN and a concrete implementation for the integration with thecheminfo ELN.AiiDAlab-Cheminfo ELN implementationAs a first prototype we implemented an integration with the open-sourcecheminfo ELN.
The ELN and integration can be tested via thepublic deployment of the ELN. Documentation on how to use the frontend can be foundhere.APIeln_instancerefers to the URL of the ELN API.eln_typereferst to the type of ELN, e.g. "cheminfo", "openbis".data_type"subfolder" in the cheminfo data schema of characterization techniques, e.g., "xray", "isotherm"spectrum_typewill be renamed to thissample_uuidrefers to the sample unique identifier in the ELN databasefile_namerefers to the name of the file attached to the sample and containing information of the specifieddata_type.file_contentrefers to the content of the file attached to the sample.noderefers to the AiiDA database node.tokenrefers to the token that gives access to the ELN database.export_data()sends the AiiDA node (stored in thenodeattribute) to the ELN.import_data()import ELN data into an AiiDA node.sampleobject that refers to an ELN sample, previously known assample_manager.sample.put_data()- put data into the ELN sample.sample.get_data()- get data from the ELN sample.For maintainersTo create a new release, clone the repository, install development dependencies withpip install '.[dev]', and then executebumpver update --major/--minor/--patch.
This will:Create a tagged release with bumped version and push it to the repository.Trigger a GitHub actions workflow that creates a GitHub release.Additional notes:Use the--dryoption to preview the release change.The release tag (e.g. a/b/rc) is determined from the last release.
Use the--tagoption to switch the release tag.AcknowledgementsThis work is supported by theMARVEL National Centre for Competency in Researchfunded by theSwiss National Science Foundation, as well as by theMaX
European Centre of Excellencefunded by the Horizon 2020 EINFRA-5 program,
Grant No. 676598 and an European Research Council (ERC) Advanced Grant (Grant Agreement No. 666983, MaGic).
Package: aiidalab-widgets-base
AiiDAlab WidgetsAiiDAlabapplications typically involve some of following steps:Prepare the input for a calculation (e.g. an atomic structure).Select computational resources and submit a calculation to AiiDA.Monitor a running calculation.Find and analyze the results of a calculation.The AiiDAlab widgets help with these common tasks.DocumentationHosted onaiidalab-widgets-base.readthedocs.io.For maintainersTo create a new release, clone the repository, install development dependencies withpip install -e '.[dev]', and then executebumpver update [--major|--minor|--patch] [--tag-num --tag [alpha|beta|rc]].
This will:Create a tagged release with bumped version and push it to the repository.Trigger a GitHub actions workflow that creates a GitHub release and publishes it on PyPI.Additional notes:Use the--dryoption to preview the release change.The release tag (e.g. a/b/rc) is determined from the last release.
Use the--tagoption to switch the release tag.This package followssemantic versioning.LicenseMITCitationUsers of AiiDAlab are kindly asked to cite the following publication in their own work:A. V. Yakutovich et al., Comp. Mat. Sci. 188, 110165 (2021).DOI:10.1016/j.commatsci.2020.110165Contactaiidalab@materialscloud.orgAcknowledgementsThis work is supported by theMARVEL National Centre for Competency in Researchfunded by theSwiss National Science Foundation, as well as by theMaX
European Centre of Excellencefunded by the Horizon 2020 EINFRA-5 program,
Grant No. 676598.
Package: aiida-lammps
AiiDA LAMMPS pluginAnAiiDAplugin for the classical molecular dynamics codeLAMMPS.This plugin contains 2 types of calculations:lammps.base: Calculation making use of parameter based input generation for single stage LAMMPS calculations.lammps.raw: Calculation making use of a pre-made LAMMPS input file.Thelammps.baseis also used to handle three workflows:lammps.base: A workflow that can be used to submit any single stage LAMMPS calculation.lammps.relax: A workflow to submit a structural relaxation using LAMMPS.lammps.md: A workflow to submit a molecular dynamics calculation using LAMMPS.AiiDA LAMMPS pluginInstallationBuilt-in Potential SupportExamplesCode SetupStructure SetupPotential SetupForce CalculationOptimisation CalculationMD CalculationDevelopmentCoding Style RequirementsTestingInstallationTo install a stable version from pypi:pipinstallaiida-lammpsTo install from source:gitclonehttps://github.com/aiidaplugins/aiida-lammps.git
pipinstall-eaiida-lammpsBuilt-in Potential SupportThelammps.basecalculation and associated workflows make use of theLammpsPotentialDatadata structure which is created by passing a potential file, plus some labelling parameters to it.This data structure can be used to handle the following potential types:Single file potentials: Any potential that can be stored in a single file, e.g.EAM,MEAM,TersoffandReaxFF.Directly parametrized potentials: Potentials whose parameters are directly given viapair_coeffin the input file, e.gBorn,Lennard-JonesandYukawa. These parameters should be written into a file that is then stored into aLammpsPotentialDatanode.ExamplesMore example calculations are found in the folder/examplesas well as in the documentation. The examples touch some common cases for the usage of LAMMPS for a single stage calculation.DevelopmentRunning testsThe test suite can be run in an isolated, virtual environment usingtox(seetox.iniin the repo):pipinstalltox
tox-e3.9-aiida_lammps--tests/or directly:pipinstall.[testing]pytest-vThe tests require that both PostgreSQL and RabbitMQ are running.
If you wish to run an isolated RabbitMQ instance, see thedocker-compose.ymlfile in the repo.Some tests require that alammpsexecutable be present.The easiest way to achieve this is to use Conda:condainstalllammps==2019.06.05# this will install lmp_serial and lmp_mpiYou can specify a different executable name for LAMMPS with:tox-e3.9-aiida_lammps----lammps-execlmp_execTo output the results of calcjob executions to a specific directory:pytest--lammps-workdir"test_workdir"Pre-commitThe code is formatted and linted usingpre-commit, so that the code conform to the standard:cdaiida-lammps
pre-commitrun--allor to automate runs, triggered before each commit:pre-commitinstallLicenseTheaiida-lammpsplugin package is released under the MIT license. See theLICENSEfile for more details.
Package: aiida-nanotech-empa
aiida-nanotech-empaAiiDA library containing plugins/workflows developed at nanotech@surfaces group from Empa.Contents:nanotech_empa.nanoribbon: work chain to characterize 1D periodic systems based on Quantum Espresso.nanotech_empa.gaussian.spin: Work chain to characterize spin properties of molecular systems with Gaussian. Calls multiple child work chains. Steps:Wavefunction stability is tested for each spin multiplicityGeometry is relaxed for the different spin states and ground state is foundProperty calcuation on the ground state: ionization potential and electron affinity with Δ-SCF, natural orbital analysis in case of open-shell singletVertical excitation energies for non-ground state multiplicitiesOrbitals and densities are rendered with PyMOL (needs to be installed separately as a python library, e.g. frompymol-open-source)Installationpipinstallaiida-nanotech-empaFor maintainersTo create a new release, clone the repository, install development dependencies withpip install '.[dev]', and then executebumpver update --major/--minor/--patch.
This will:Create a tagged release with bumped version and push it to the repository.Trigger a GitHub actions workflow that creates a GitHub release.Additional notes:Use the--dryoption to preview the release change.The release tag (e.g. a/b/rc) is determined from the last release.
Use the--tagoption to switch the release tag.
Package: aiida-nwchem
aiida-nwchemAiiDA-NWChem is the AiiDA plugin for the NWChem code.The plugin provides support for the following calculation tasks:energyoptimizefreq...using these theory types:scfdftNWPW BandNWPW PSPWTCECompatibility matrixThe matrix below shows the versions ofaiida-coreand Python with which the plugin is compatible for various plugin version ranges:PluginAiiDAPythonv3.0 < v4.0v2.0 < v3.0DocumentationThe documentation for this package can be found on Read the Docs athttp://aiida-nwchem.readthedocs.io/en/latest/AcknowledgementsThis work is supported by theMARVEL National Centre for Competency in Researchfunded by theSwiss National Science Foundation.
Package: aiida_orca
aiida-orcaAiiDAplugin fororcapackageDISCLAIMER: Under heavy development!Compatible with:InstallationThe latest release can be installed fromPyPIpip install aiida-orcaThe current development version can be installed viagit clone https://github.com/pzarabadip/aiida-orca.gitcd aiida-orcapip install .aiida-common-workflowsTheaiida-orcapackage is available in theaiida-common-workflowpackage.
You may try it to have a quick setup and exploration ofaiida-orcaand many more packages.
For further details, please checkour paperonaiida-common-worlflows.Contribution guideWe welcome contribution to the code either it is a new feature implementation or bug fix.
Please check theDeveloper Guidein documentation for the instructions.Issue reportingPlease feel free to open an issue to report bugs or requesting new features.AcknowledgmentI would like to thank the funding received from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Actions and cofinancing by the South Moravian Region under agreement 665860. This software reflects only the authors’ view and the EU is not responsible for any use that may be made of the information it contains.
Package: aiida-phonopy
aiida-phonopyThis is the official AiiDA plugin forPhonopy.CompatibilityFromv0.7.0this plugin does not support retro-compatibility with previous versions,
due to a restructure of the package.PluginAiiDAPhonopy>=v1.0.0< v2.0.0>=v2.0.0<v3.0.0>=v2.14.0<v3.0.0>=v0.7.0< v1.0.0>=v1.6.0<v2.0.0>=v2.14.0<v3.0.0InstallationTo install from PyPI, simply execute:pip install aiida-phonopyor when installing from source:git clone https://github.com/aiida-phonopy/aiida-phonopy
pip install .LicenseTheaiida-phonopyplugin package is released under the MIT license.
See theLICENSE.txtfile for more details.AcknowlegementsWe acknowledge support from:theU Bremen Excellence Chairsprogram funded within the scope of theExcellence Strategy of Germany’s federal and state governments;theMAPEXCenter for Materials and Processes.
Package: aiida-phtools
aiida-phtoolsAiiDA plugin for persistence homology tools, used to analyze nanoporous materials.Installationgitclonehttps://github.com/ltalirz/aiida-phtools.cdaiida-phtools
pipinstall-e.# also installs aiida, if missing (but not postgres)#pip install -e .[precommit,testing] # install extras for more featuresverdiquicksetup# better to set up a new profileverdicalculationplugins# should now show your calclulation pluginsUsageHere goes a complete example of how to submit a test calculation using this plugin.LicenseMITContactleopold.talirz@gmail.com
Package: aiida-plumed
aiida-plumedAiiDA plugin providing support for Plumed2This plugin is the default output of theAiiDA plugin cutter,
intended to help developers get started with their AiiDA plugins.FeaturesAdd input files usingSinglefileData:SinglefileData=DataFactory('singlefile')inputs['file1']=SinglefileData(file='/path/to/file1')inputs['file2']=SinglefileData(file='/path/to/file2')Specify command line options via a python dictionary andDiffParameters:d={'ignore-case':True}DiffParameters=DataFactory('plumed')inputs['parameters']=DiffParameters(dict=d)DiffParametersdictionaries are validated usingvoluptuous.
Find out about supported options:DiffParameters=DataFactory('plumed')print(DiffParameters.schema.schema)Installationpipinstallaiida-plumed
verdiquicksetup# better to set up a new profileverdipluginlistaiida.calculations# should now show your calclulation pluginsUsageHere goes a complete example of how to submit a test calculation using this plugin.A quick demo of how to submit a calculation:verdidaemonstart# make sure the daemon is runningcdexamples
verdirunsubmit.py# submit test calculationverdiprocesslist-a# check status of calculationThe plugin also includes verdi commands to inspect its data types:verdidataplumedlist
verdidataplumedexport<PK>Developmentgitclonehttps://github.com/ConradJohnston/aiida-plumed.cdaiida-plumed
pipinstall-e.[pre-commit,testing]# install extra dependenciespre-commitinstall# install pre-commit hookspytest-v# discover and run all testsSee thedeveloper guidefor more information.LicenseMITContactconrad.s.johnston@googlemail.com
Package: aiida-porousmaterials
aiida-porousmaterialsAiiDAplugin forPorousMaterialspackageInstallationgit clone https://github.com/pzarabadip/aiida-porousmaterialspip install -e .NOTECurrently, it is minimal plugin for an ongoing project. It will be updated to be able for doing wider ranger of calculations.LicenseMITContactpzarabadip@gmail.comAcknowledgmentI would like to thank the funding received from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Actions and cofinancing by the South Moravian Region under agreement 665860. This software reflects only the authors’ view and the EU is not responsible for any use that may be made of the information it contains.
Package: aiida-pseudo
aiida-pseudoAiiDA plugin that simplifies working with pseudopotentials.
For more information on how to install and use the package, please consultthe documentation.Compatibility matrixThe following table shows which versions ofaiida-pseudoare compatible with which versions of AiiDA and Python.PluginAiiDAPythonv1.5.0 < v2.0.0v0.8.0 < v1.5.0v0.7.0 < v0.8.0v0.1.0 < v0.7.0LicenseTheaiida-pseudoplugin package is released under the MIT license.
See theLICENSE.txtfile for more details.AcknowledgementsWe acknowledge support from:NCCR MARVELfunded by the Swiss National Science FoundationEU Centre of Excellence MaX(Horizon 2020 EINFRA-5, Grant No. 676598)swissuniversitiesP-5 project "Materials Cloud"