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        "author": "Dallas R. Trinkle",
        "author_email": "dtrinkle@illinois.edu",
        "bugtrack_url": null,
        "classifiers": [
            "Development Status :: 4 - Beta",
            "Intended Audience :: Science/Research",
            "License :: OSI Approved :: MIT License",
            "Programming Language :: Python :: 3",
            "Programming Language :: Python :: 3.3",
            "Programming Language :: Python :: 3.4",
            "Programming Language :: Python :: 3.5",
            "Programming Language :: Python :: 3.6",
            "Topic :: Scientific/Engineering :: Physics"
        ],
        "description": "Onsager\n=======\n\n[![PyPI version](https://img.shields.io/pypi/v/onsager.svg)](http://pypi.python.org/pypi/onsager)\n\nDocumentation now available at the [Onsager github page](http://dallastrinkle.github.io/Onsager/). Please cite as [![DOI](https://zenodo.org/badge/14172/DallasTrinkle/Onsager.svg)](https://zenodo.org/badge/latestdoi/14172/DallasTrinkle/Onsager) or see `Onsager github <https://github.com/DallasTrinkle/Onsager>`_ for current version doi information.\n\nThe Onsager package provides routines for the general calculation of transport coefficients in vacancy-mediated diffusion and interstitial diffusion. It does this using a Green function approach, combined with point group symmetry reduction for maximum efficiency.\n\nTypical usage can be seen in the ipython notebooks in `examples`; the usual import will be::\n\n    #!/usr/bin/env python\n\n\tfrom onsager import crystal\n\tfrom onsager import OnsagerCalc\n\n    ...\n\nMany of the subpackages within Onsager are support for the main attraction, which is in OnsagerCalc. Interstitial calculation examples are available in `bin`, including three YAML input files, as well as a interstitial diffuser. An example of vacancy-mediated diffusion is shown in `bin/fivefreq.py`, which computes the well-known five-frequency model for substitutional solute transport in an FCC lattice. The script `CLdiffuser` is a command-line diffuser calculator that is designed to read in an HDF5 file of a diffuser, along with a JSON file that includes the thermal/kinetic data, and computes diffusivity components for different temperatures.\n\nThe tests for the package are include in `test`; `tests.py` will run all of the tests in the directory with verbosity level 2. This can be time-consuming (on the order of several of minutes) to run all tests; coverage is currently >90%.\n\nThe code uses YAML format for input/output of crystal structures, and diffusion data for the interstitial calculator. The vacancy-mediated calculator requires much more data, and uses HDF5 format to save/reload as needed. The vacancy-mediated calculator uses tags (unique human-readable-ish strings) to identify all (symmetry-unique) vacancy, solute, and complex states, and transitions between them.\nThe vacancy-mediated diffuser can be stored as an HDF5 file (which internally stores the crystal structure in YAML format). The thermal/kinetic data is most easily serialized as JSON, but any dictionary-compatible format will do, by making use of tags.\n\n\nReleases\n--------\n\n* 0.9. Full release of Interstitial calculator, along with theory paper (see References below).\n* 0.9.1. Added spin degrees of freedom to `crystal` for symmetry purposes; added `supercell` class to aid in automated setup of calculation.\n* 1.0 Now including automator for supercell calculations.\n* 1.1 Automator update with Makefile; corrections for possible overflow error when omega2 gets very large.\n* 1.2 Combined \"large omega2\" and \"non-zero bias\" algorithms; notebook for Fe-C added to documentation; cleanup of code and improved testing.\n* 1.2.1 Additional notebooks added for vacancy-mediated diffuser.\n* 1.2.2 New internal friction calculator for interstitial diffuser; improvement in `Crystal` class symmetry to handle larger error in unit cell.\n* 1.3 Two-dimensional lattice support added; new notebooks for variational calculations.\n* 1.3.1 Bug fix in `crystal.Crystal.jumpnetwork` for search range.\n* 1.3.2 Bug fix in `OnsagerCalc.VacancyMediated` for cases with non-zero bias vector (caused unusual occasional test failures).\n\n\nReferences\n----------\n\n* Dallas R. Trinkle, \"Diffusivity and derivatives for interstitial solutes: Activation energy, volume, and elastodiffusion tensors.\" Philos. Mag. (2016) [doi:10.1080/14786435.2016.1212175](http://dx.doi.org/10.1080/14786435.2016.1212175); [arXiv:1605.03623](http://arxiv.org/abs/1605.03623)\n* Dallas R. Trinkle, \"Automatic numerical evaluation of vacancy-mediated transport for arbitrary crystals: Onsager coefficients in the dilute limit using a Green function approach.\" Philos. Mag. (2017) [doi:10.1080/14786435.2017.1340685](http://dx.doi.org/10.1080/14786435.2017.1340685); [arXiv:1608.01252](http://arxiv.org/abs/1608.01252)\n* Dallas R. Trinkle, \"A variational principle for mass transport.\" *submitted* (2018); [arXiv:1805.11618](http://arxiv.org/abs/1805.11618)\n\n\nContributors\n------------\n\n* Dallas R. Trinkle, initial design, derivation, and implementation.\n* Ravi Agarwal, testing of HCP interstitial calculations; testing of HCP vacancy-mediated diffusion calculations\n* Abhinav Jain, testing of HCP vacancy-mediated diffusion calculations.\n\nThanks to discussions with Maylise Nastar (CEA, Saclay), Thomas Garnier (CEA, Saclay and UIUC), Thomas Schuler (CEA, Saclay), and Pascal Bellon (UIUC).\n\nSupport\n-------\n\nThis work has been supported in part by\n\n* DOE/BES grant DE-FG02-05ER46217,\n* ONR grant N000141210752,\n* NSF/CDSE grant 1411106.\n* Dallas R. Trinkle began the theoretical work for this code during the long program on Material Defects at the [Institute for Pure and Applied Mathematics](https://www.ipam.ucla.edu/) at UCLA, Fall 2012, and again during the long program on Complex Energy Landscapes, Fall 2017. IPAM is supported by the National Science Foundation.",
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        "keywords": "diffusion,elastodiffusion,mass transport,Onsager coefficients,transport coefficieints",
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