Saravanan666/pypi-org huggingface dataset:
Package: aiida-cp2k
AiiDA CP2KAiiDAplugin forCP2K.InstallationIf you usepip, you can install it as:pip install aiida-cp2kTo install the plugin in an editable mode, run:git clone https://github.com/aiidateam/aiida-cp2k
cd aiida-cp2k
pip install -e .  # Also installs aiida, if missing (but not postgres/rabbitmq).LinksDocumentationfor the calculation examples and features of the plugin.Make an issuefor bug reports, questions and suggestions.AiiDAto learn about AiiDA.CP2Kto learn about CP2K.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 override the release tag.LicenseMITContactyakutovicha@gmail.comAcknowledgementsThis work is supported by:theMARVEL National Centre for Competency in Researchfunded by theSwiss National Science Foundation;theMaX European Centre of Excellencefunded by the Horizon 2020 EINFRA-5 program, Grant No. 676598;theswissuniversities P-5 project "Materials Cloud".
Package: aiida-cp2k-ng
AiiDA CP2KThe CP2K plugin for the AiiDA workflow and provenance engine.InstallationIf you usepip, you can install it as:pip install aiida-cp2kFeaturesFollowing the philosophy to''enable without getting in the way'', this plugin provides access to all of CP2K's capabilities through a small set of well-tested features:A fullCP2K inputhas to be provided as a nested Python dictionary (example):params = {'FORCE_EVAL': {'METHOD': 'Quickstep', 'DFT': { ... }}}
calc.use_parameters(ParameterData(dict=params))Section parameters are stored as key_in the dictionary:xc_section = {'XC_FUNCTIONAL': {'_': 'LDA'}}Repeated sections are stored as a list:kind_section = [{'_': 'H', 'BASIS_SET': 'DZVP-MOLOPT-GTH', 'POTENTIAL': 'GTH-LDA'},
                {'_': 'O', 'BASIS_SET': 'DZVP-MOLOPT-GTH', 'POTENTIAL': 'GTH-LDA'}]Most data files (basis sets, pseudo potentials, VdW, etc.) are auto-discovered from CP2K'sdata directory.dft_section = {'BASIS_SET_FILE_NAME': 'BASIS_MOLOPT', ...}Additional data files can be added as AiiDA SinglefileData (example):water_pot = SinglefileData(file="/tmp/water.pot")
calc.use_file(water_pot, linkname="water_pot")The start geometry can be provided as AiiDA StructureData (example):atoms = ase.build.molecule('H2O', vacuum=2.0)
calc.use_structure(StructureData(ase=atoms))Alternatively the start geometry can be contained in the CP2K input (example):coord_section = {' ': ['H    2.0   2.0   2.737166',
                       'H    2.0   2.0   2.000000']},For restarting a calculation a parent folder can be attached  (example):calc2.use_parent_folder(calc1.out.remote_folder)By default only the output and restart file (if present) are retrieved. Additional files are retrieved upon request (example):settings = {'additional_retrieve_list': ["*.cube"]}
calc.use_settings(ParameterData(dict=settings))The final geometry is extracted from the restart file (if present) and stored in AiiDA (example):print(calc.out.output_structure)From the CP2K output only the #warnings and final energy are parsed (example):print(calc.res.nwarnings, calc.res.energy, calc.res.energy_units)The calculation is considered failed if #warnings can not be found (example).The conversion of geometries between AiiDA and CP2K has a precision of at least 1e-10 Ångström (example).The Python code complies with theFlake8coding conventions.TestingEvery commit and pull request is automatically tested byTravisCI.To run the tests locally installDockerand execute the following commands:git clone https://github.com/cp2k/aiida-cp2k
docker build -t aiida_cp2k_test aiida-cp2k
docker run -it --init aiida_cp2k_test pytest -v
Package: aiida-crystal17
aiida-crystal17AiiDA plugin for running theCRYSTAL17code.
The code is principally tested against CRYSTAL17,
but the output parsing has also been tested against CRYSTAL14.Documentation:https://readthedocs.org/projects/aiida-crystal17InstallationTo install from Conda (recommended)::>>condainstall-cconda-forgeaiida-crystal17aiida-core.servicesTo install from pypi::>>pipinstallaiida-crystal17To install the development version:>>gitclonehttps://github.com/aiidaplugins/aiida-crystal17.
>>cdaiida-crystal17
>>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 calclulation plugins (with prefix crystal17.)DevelopmentTesting against mock CRYSTAL17 executablesBecause CRYSTAL17 is a licensed software, it is not possible to source a copy of the executable on Travis CI.
Therefore, a mock executable (mock_runcry17) 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 (likecrystal17):>>pytest--cry17-skip-execTo call the actual executables (e.g.crystal17instead ofmock_crystal17):>>pytest--cry17-no-mockTo output the results of calcjob executions to a specific directory:>>pytest--cry17-workdir"test_workdir"Coding Style RequirementsThe code style is tested usingflake8,
with the configuration set in.flake8, and code should be formatted withyapf(configuration set in.style.yapf).Installing withaiida-crystal17[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-crystal17
>>pre-commitinstallOptionally you can runyapfandflake8separately:>>yapf-r-i.# recrusively find and format files in-place>>flake8Editors like VS Code also have automatic code reformat utilities, which can adhere to this standard.Setting up CRYSTAL17 locallyTo set up local version of CRYSTAL17 on a mac (after downloading a copy from the distributor), I had to:Remove the quarantine from the executable permissions:xattr-ccrystal
xattr-cpropertiesCreate versions of the lapack/blas libraries in the expected folders:sudoportinstalllapack
sudocp/opt/local/lib/lapack/liblapack.3.dylib/usr/local/opt/lapack/lib/liblapack.3.dylib
sudocp/opt/local/lib/lapack/libblas.3.dylib/usr/local/opt/lapack/lib/libblas.3.dylibDefine environmental variables in~/.bashrc, as detailed incry17_scripts/cry17.bashrcCopy or symlink thecry17_scripts/runcry17script into/usr/local/bin/LicenseSeeLICENSEfileContactchrisj_sewell@hotmail.com
Package: aiida-crystal-dft
aiida-crystal-dftThis is an AiiDA plugin for running theCRYSTALcode, spin-off from theaiida-crystal17plugin by Chris Sewell.InstallationAs of now, the development version can be installed:>>gitcloneaiida-crystal-dft
>>pipinstall-eaiida-crystal-dftUsageThe plugin can be used as any other AiiDA plugin.
Package: aiida-cusp
aiida-cusp - a Custodian based VASP Plugin for AiiDACustodianplugin for VASP enabling automated error correction forAiiDAmanaged VASP calculationsHighlightsAutomated error corrections for VASP calculations on the calculation's runtime level (rather than on the workflow level)Full compatability withpymatgenand easy access to set of therein implemented tools for pre- and postprocessing of VASP calculations directly from the implemented datatypesIt's still VASP, but better!InstallationPlease refer to aiida-cusp'sdocumentationfor further information.ContributingSuggestions for useful improvements, feature requests, bug reports and the like are highly welcome and appreciated.
Especially the contribution of new workflows that were developed based on this plugin is highly encouraged to transform this plugin into a powerful tool for the scientific community.Bug ReportsIf you think you found a bug feel free to open an issue on the plugin'sGitHub repository.Adding new Features and ChangesFor changes you would like to add to the plugin please refer to theCONTRIBUTING.mdfile located in the repository root.LicenseTheaiida-cuspplugin for AiiDA is distributed as free and open-source software (FOSS) licensed under the MIT open-source license (seeLICENSE).
Package: aiida-dataframe
aiida-dataframeAiiDA data plugin for pandas DataFrame objectsFeaturesStorepandas.DataFrameobjects in the Database:importpandasaspdPandasFrameData=DataFactory('dataframe.frame')df=pd.DataFrame({"A":1.0,"B":pd.Timestamp("20130102"),"C":pd.Series(1,index=list(range(4)),dtype="float32"),"D":np.array([3]*4,dtype="int32"),"E":pd.Categorical(["test","train","test","train"]),"F":"foo",})df_node=PandasFrameData(df)df_node.store()Retrieving thepandas.DataFramefrom the Database :fromaiida.ormimportQueryBuilderdf_node=QueryBuilder().append(PandasFrameData).first()[0]df=df_node.df#The df property reconstructs the pandas DataFrameprint(df.head())Installationpipinstallaiida-dataframe
verdiquicksetup# better to set up a new profileverdipluginlistaiida.data# should now show your data pluginsUsageThe plugin also includes verdi commands to inspect its data types:verdidatadataframelist
verdidatadataframeexport<PK>
verdidatadataframeshow<PK>Developmentgitclonehttps://github.com/janssenhenning/aiida-dataframe.cdaiida-dataframe
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.LicenseMITContacthenning.janssen@gmx.net
Package: aiida-ddec
PluginAiiDAPython2.0.01.1.0aiida-ddecpluginADDECplugin for AiiDA.Installationpipinstallaiida-ddecUsageExamples in theexamplesfolder:test_cp2k_ddec_h2o.py: Run an ENERGY calculation, printing the
electron density cube file, and compute the DDEC charges from thatRun testsgitclonehttps://github.com/lsmo-epfl/aiida-ddeccdaiida-ddec
pipinstall-e.['pre-commit','testing']pytestIf you are changing the inputs of existing tests or need to regenerate test data, place an.aiida-testing-config.ymlfile in your repository that points to the required simulation codes:---mock_code:# code-label: absolute pathcp2k-7.1:/path/to/cp2k.soptchargemol-09_26_2017:/path/to/Chargemol_09_02_2017_linux_serialLicenseMITContactaliaksandr.yakutovich@epfl.ch
Package: aiida-defects
Welcome to AiiDA-DefectsAiiDA-Defects is a plugin for theAiiDAcomputational materials science framework, and provides tools and automated workflows for the study of defects in materials.The package is available for download fromGitHub.If you use AiiDA-Defects in your work, please cite:AiiDA-defects: An automated and fully reproducible workflow for the complete characterization of defect chemistry in functional materialsdoi.org/10.48550/arXiv.2303.12465 (preprint)Please also remember to cite theAiiDA paper.Quick SetupInstall the latest release of this package by running the following in your shell:$ pip install aiida-defectsThis will install all of the prerequisites automatically (including for the optional docs)
in your environment, including AiiDA core, if it not already installed.Getting StartedExpample usage of the workchains is documented in the collection of Jupyter notebooks in theexamplesdirectory.AcknowledgementsThis work is supported by the MARVEL National Centre of Competence in Research (NCCR) funded by the Swiss National Science Foundation (grant agreement ID 51NF40-182892) and by the European Union’s Horizon 2020 research and innovation program under Grant Agreement No. 824143 (European MaX Centre of Excellence “Materials design at the Exascale”) and Grant Agreement No. 814487 (INTERSECT project). We thank Chiara Ricca and Ulrich Aschauer for discussions and prototype implementation ideas. The authors also would like to thank the Swiss National Supercomputing Centre CSCS (project s1073) for providing the computational ressources and Solvay for funding this project. We thank Arsalan Akhtar, Lorenzo Bastonero, Luca Bursi, Francesco Libbi, Riccardo De Gennaro and Daniele Tomerini for useful discussions and feedback.
Package: aiida-environ
aiida-environThis plugin builds on top ofaiida-quantumespresso.CompatibilityCurrently tested with aiida-core1.6 and aiida-quantumespresso3.5InstallationTo install from PyPI,pip install aiida-environTo install from sourcegit clone https://github.com/environ-developers/aiida-environ
pip install aiida-environLicenseSee theLICENSE.txtfile for more details.
Package: aiida-fenics
Enabling usage of the FEniCS computing platform with AiiDAThis software contains a plugins that enables the usage of the FENiCS computing platform with theAiiDA framework. It includes special plugins for software building on FENiCs like the Phasefield dislocation interaction program Pdfdisloc. The enables provenance tracking for such simulations and workflows, which is need for research datamanagement, reproducibility and FAIR data.DocumentationHosted athttp://aiida-fenics.readthedocs.io/en/develop/index.html.
For other information see the AiiDA-core docs, or the FeniCs project.License:MIT license.
See the license file.How to cite:If you use this package please consider citing:Comments/Disclaimer:ContentsIntroductionInstallation InstructionsCode DependenciesFurther InformationIntroductionThis is a python package (AiiDA plugin and utility)
allowing to use the pdfdisloc code in the AiiDA Framework.
The Pdfdisloc program contains workflows based on Fenics a finite element solver,
that is widely applied in the material science and physics community.The plugin :The plugin consists of:1. A data-structure representing Meshes.
2. pdfdisloc calculationInstallation InstructionsFrom the aiida-fenics folder (after downloading the code, recommended) use:$ pip install .
# or which is very useful to keep track of the changes (developers)
$ pip install -e .To uninstall use:$ pip uninstall aiida-fenicsOr install latest release version from pypi:$ pip install aiida-fenicsTest InstallationTo test rather the installation was successful use:$verdipluginslistaiida.calculations# example output:## Pass as a further parameter one (or more) plugin names## to get more details on a given plugin....*fenics.dfdislocYou should see 'fenics.*' in the listThe other entry points can be checked with the AiiDA Factories (Data, Workflow, Calculation, Parser).
(this is done in test_entry_points.py)We suggest to run all the (unit)tests in the aiida-fleur/aiida_fleur/tests/ folder.$ bash run_all_cov.shCode DependenciesRequirements are listed in setup.json.most important are:aiida_core >= 1.3.0Mainly AiiDA:Download fromwww.aiida.net -> Downloadinstall and setup ->aiida's documentationFurther InformationUsage examples are shown in 'examples'.AcknowledgementsBesides the Forschungszentrum Juelich GmbH (FZJ), this project was supported within the hub Information at the FZJ by the Helmholtz Metadata Collaboration (HMC), an incubator-platform of the Helmholtz Association within the framework of the Information and Data Science strategic initiative.
Package: aiida_firecrest
aiida-firecrest [IN-DEVELOPMENT]AiiDA Transport/Scheduler plugins for interfacing withFirecRESTInstallation(pip not yet available)pipinstallaiida-firecrestOr for development:gitclonecdaiida-firecrest
pipinstall-e.CLI Usage$aiida-firecrest-cli--helpUsage: aiida-firecrest-cli [OPTIONS] COMMAND [ARGS]...FireCrest CLI.Options:--config PATH  Path to the connection file (default: .firecrest-config.json).--help         Show this message and exit.Commands:fs      File system operations.slurm   Slurm operations.stat    Status operations.The configuration file should look like this:{"url":"https://firecrest.cscs.ch","token_uri":"https://auth.cscs.ch/auth/realms/cscs/protocol/openid-connect/token","client_id":"username-client","client_secret":"xyz","machine":"daint","scratch_path":"/scratch/snx3000/username"}scratch_pathis optional.
If specified, all operations will be relative to this path.$aiida-firecrest-clistatUsage: aiida-firecrest-cli stat [OPTIONS] COMMAND [ARGS]...Status operations.Options:--help  Show this message and exit.Commands:parameters  Get parameters that can be configured in environment files.service     Information about a service.services    List available services.system      Information about a system.systems     List available systems.$aiida-firecrest-clifsUsage: aiida-firecrest-cli fs [OPTIONS] COMMAND [ARGS]...File system operations.Options:--help  Show this message and exit.Commands:cat      Get the contents of a file.chmod    Change the mode of a file.cwd      Get the current working directory.ls       List files in a path.putfile  Upload file to the remote.stat     Get information about a file.$aiida-firecrest-clislurmUsage: aiida-firecrest-cli slurm [OPTIONS] COMMAND [ARGS]...Slurm operations.Options:--help  Show this message and exit.Commands:sacct   Retrieve information for all jobs.squeue  Retrieves information for queued jobs.submit  Submit a job script.Code StyleTo format the code and lint it, runpre-commit:pre-commitrun--all-filesTestingIt is recommended to run the tests viatox.toxBy default, the tests are run using a mock FirecREST server (in a temporary folder).
You can also provide connections details to a real FirecREST server:tox----firecrest-config=".firecrest-config.json"The format of the.firecrest-config.jsonfile is:{"url":"https://firecrest.cscs.ch","token_uri":"https://auth.cscs.ch/auth/realms/cscs/protocol/openid-connect/token","client_id":"username-client","client_secret":"xyz","machine":"daint","scratch_path":"/scratch/snx3000/username"}
Package: aiida-gaussian
aiida-gaussianAiiDA plugin for the Gaussian quantum chemistry softwareFeaturesGaussian input can be provided as a python dictionary following the convention defined bypymatgenparameters={'functional':'PBE1PBE','basis_set':'6-31g','charge':0,'multiplicity':1,'link0_parameters':{'%chk':'aiida.chk','%mem':"1024MB",'%nprocshared':4,},'route_parameters':{'scf':{'maxcycle':128,'cdiis':None,},'nosymm':None,'output':'wfx','opt':'tight',},'input_parameters':{# appended at the end of the input'output.wfx':None},}Inroute_parameters, specifyingkey: Noneadds onlykeywithout the equals sign to the input script.Parsing of the results is performed with theccliblibrary and by default all of its output is stored in theoutput_parametersnode.Additionally, simple plugins to submit the Gaussian utilitiesformchkandcubegenare provided.Installationpipinstallaiida-gaussianThis installs the plugins to the AiiDA instance (to double-check, one can list all installed plugins byverdi plugin list aiida.calculations). After this, the Gaussian codes should be set up using the plugins (https://aiida.readthedocs.io/projects/aiida-core/en/latest/).UsageA quick demo of how to submit a calculation:verdidaemonstart# make sure the daemon is runningcdexamples# Submit test calculation (argument is the label of gaussian code)verdirunexample_01_opt.pygaussian09For 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-graphql
aiida-graphqlStrawberry-based GraphQL Server for AiiDAWhy GraphQL when there is already the REST API? Seehttps://www.howtographql.com/basics/1-graphql-is-the-better-rest/... a lot of possible optimizations and fits the graph-based structure of the AiiDA DB a lot better than a REST API.RequirementsPython 3.7+https://pypi.org/project/strawberry-graphql/0.16.7+https://pypi.org/project/aiida-core/1.0.0b6+For development:https://poetry.eustace.io/Why Strawberry for GraphQL? It uses graphql-core v3 (while graphene is still stuck with v2), uses typings and dataclasses for both validation and schema generation. And it uses modern Python to write the schema, in comparison to theschema-first approach.Why Python 3.7+? It's the future, and for Strawberry. In fact, were it not for a bug inuvloopthis would be Python 3.8+ (for the walrus operator). And given the timeline these projects are running for, we'll probably see Python 3.9 until people effectively start using it.Why Poetry? I wanted to get away fromsetuptoolsand used Poetry already in adifferent projectand liked the virtualenv integration.UsageDevelopmentInstalling the dependencies:gitclonehttps://github.com/dev-zero/aiida-graphql.gitcdaiida-graphql# for poetry installation use the official documentationpoetryinstallTo run the development server:$poetryrunstrawberryserveraiida_graphql.schemathen visithttp://localhost:8000/graphqlwith your browser.Example query:{computers{uuidnamedescriptionschedulerTypetransportType}}Available fieldsnodecalculationcomputerusersinglefilegaussian_basissets (only if theaiida-gaussian-datatypesis installed)Documentation and schema are embedded in the development server.
Package: aiida-gromacs
aiida-gromacsThe GROMACS plugin for AiiDA aims to enable the capture and sharing of the full
provenance of data when parameterising and running molecular dynamics
simulations. This plugin is being developed as part of the Physical Sciences
Data Infrastructure programme to improve the practices around data within the
Physical Sciences remit area within the UK.This package is currently a work in progress and we will be adding much more
complete functionality to this plugin in the coming months.The design pattern we are aiming for is to simply allow researchers to capture
the full data provenance for their simulations by only switching on an AiiDA
conda environment, along with modifying your command lines very slightly.This means that you should gain access to powerful FAIR data practices without
wholesale cultural or usage pattern shifts in your daily work.DocumentationSeeherefor documentation for users and developers.LicenseMITContactjames.gebbie@stfc.ac.ukjas.kalayan@stfc.ac.uk