pymatgen

• Fix missing yaml files that have been moved.

• Major refactoring of pymatgen.io. Now, the io suffix is dropped from all io classes. i.e., it is just pymatgen.io.vasp, not pymatgen.io.vaspio. Also, all input sets have been moved within the relevant package, e.g., pymatgen.io.vasp.sets. All changes are backwards compatible for now. But deprecation messages have been included which states that the stubs will be removed in pymatgen 4.0. Pls migrate code when you see the deprecation messages.
• Make Composition.anonymized_formula truly chemistry independent (No A2B2 for peroxides or A2 for diatomic gasses)
• Allowing CIF data_* header to be prefixed with spaces and tabulations.

• HHI Resource Analysis (by Anubhav Jain).
• Bug fixes for surfaces normalizatino.
• Bug fix for Vasprun parsing of response function keys.
• Dockerfile for generation of an image for pymatgen.
• Updated requirements.txt for latest requests, scipy, numpy.

• Bug fixes for SpacegroupAnalyzer and SlabGenerator.
• Much faster normal vec search.

• Much improved surface generation algorithm that provides for orthogonality constraints.
• Transition state analysis tools! (beta)
• Massive improvements in Outcar parsing which provides a powerful grepping syntax.
• PWSCFInput generation (beta).
• Reduce default SIGMA to 0.05 for MP input sets.
• Update spglib to 1.7.3 as per recommendation of Togo.
• Many bug fixes and efficiency improvements.

• Bug fix for parsing certain types of CIFs.
• MPRester now has get_materials_id_references helper method.
• Minor fix for Vasprun.final_energy.
• Added mp_decode option to MPRester.query to allow option to not decode into pymatgen objects.
• New POTCAR hash scheme to more robustly identify unique POTCARs.
• Link to http://bit.ly/materialsapi for information on Materials API document schema for use with MPRester.query method.

v3.0.11

• Lots of abinitio improvements (Matteo).
• Added mp_decode option to MPRester.query to allow option to not decode into pymatgen objects.

• Fix cartesian coord parsing in Poscar class.
• Vasprun now works with non

• Major bug fixes for CIF parsing (Will Richards).
• Support for {Li,Na} syntax in parse_criteria for MPRester.
• Additional example notebook for ordering and enumeration.
• More robust checking for oxidation states in EnumerateStructureTRansformation.
• Improvements to Slab polarity checking.

v3.0.8

• Massive update to abinitio (Matteo).
• Improvements to OUTCAR parsing (Ioannis Petousis).

v3.0.7

• Powerful Slab generation algorithms (beta!).
• Improvements to DiffusionAnalyzer with constant smoothing option.
• Significantly improve look of DOS plots using prettyplotlib.

• Cost analysis module (Anubhav Jain)
• More Py3k fixes.
• Extensive abinitio updates (Matteo).

v3.0.5

• Completely revamped symmetry package. The finder.SymmetryFinder and pointgroup and spacegroup modules are now deprecated. Instead, all symmetry analysis is in the :module:pymatgen.symmetry.analyzer_ module. There is also a completely rewritten support for symmetry groups in :module:pymatgen.symmetry.groups_. Structure now supports a static constructor to generate a structure from a spacegroup (see examples).
• BatteryAnalyzer class (Anubhav Jain) to provide for some common analysis of intercalation electrodes.
• Minor bug fixes for structure_matcher, lattice, abinitio.
• MOAB qadapter for abinit. (Liam Damewood)

v3.0.4

• Fix missing structures json data.

v3.0.3

• Updates to DiffusionAnalyzer for more fine

1. Consistent use of unicode throughout pymatgen.
2. Minor bug fixes.

v3.0.1

1. Minor bug fixes for cifio.
2. Py3k updates for abinitio.

• Pymatgen is now completely Python 2.7 and Python 3.x compatible!
• Spglib and pyhull have been updated to support Python 3.x.
• Completely rewritten pure python cifio module (courtesy of William Davidson Richards) removed dependency on PyCIFRW, which has been causing many issues with installation.
• Structure and Molecule now supports a very convenient to() and from_str and from_file functionality. Instead of trying to load the appropriate parser, you can output and read from the appropriate formats directly. See example usage.
• ~50% speedup to LinearAssignment code.
• Continuous integration and contribution guidelines now include Python 3.
• Backwards incompatible changes
• matgenie.py has now been renamed simply "pmg" for brevity.
• All deprecated methods in pymatgen 2.x have been removed. E.g., pymatgen.core.structure_modifier is no longer available.
• Pymatgen classes now uses the as_dict() method protocol implemented in the Monty package. The to_dict property is now deprecated and will be removed in pymatgen v3.1.
• Update main docs page examples with the new Structure to, from formats.

• Bug fix for np1.9 incompatibility. Now works.
• Use wheel for pymatgen deployments.
• matgenie.py is now renamed to pmg for faster CLI usage.
• Improvements to KPOINTS automatic generation.
• Simpler and faster Structure.get_all_neighbors

• DiffusionAnalyzer now has non-smoothed option.
• Kpoints generation algorithm now guarantees minimum # of points.
• Compatibility now has a proper explanation dict.
• Vaspruns with NSW == 1 now checked properly for electronic conv.
• make_movie now supports kwargs.

• MPRester.query now supports a simple but powerful string criteria syntax with support for wild cards.
• Improvements to Composition - support for negative compositions, sorting etc.
• Speed ups to StructureMatcher.

• Bug fix for Projected DOS parsing in new Vasprun.
• Compatibility now has a explain method which provides a detailed outline of the changes that a Compatibility makes to an Entry.

• Minor fix for monty requirements in setup.py.

• Major update: MPRester now uses Materials API v2! Also major refactoring of MPRester.
• Vastly improved Vasprun parser using cElementTree. Twice as fast, half as much code and easier to maintain.
• Vast improvements to Qchem functionality (Xiaohui Qu).
• Improved handling of Structure manipulations for extremely large structures (particularly in terms of memory consumption).
• Bug fix for XYZ parsing for scientific notation.
• Improve monty.serialization for transparent handling of JSON vs YAML. Requirements updated to monty>=0.3.3.
• Update numpy requirements to 1.8+. Fixes memory leak.
• Other minor bug fixes.

• Implements Structure.sort method. Both Structure.sort and the get_sorted_structure methods now supports all arguments supported by list .sort().
• VaspInputSets configs, as well as several other configs now uses yaml. Note the new dependency on pyyaml. It is highly recommended that you install pyyaml with the libyaml C bindings.
• Fix missing spglib dependency.
• Use monty.serialization for transparent handling of JSON vs YAML. Requirements updated to monty>=0.3.1.

• Urgent bug fix for missing compatibility yamls.

• Defect transformations (Bharat).
• Support for optical properties (Geoffroy Hautier and David Waroquiers).
• Improved support for some VASP output files (XDATCAR and OSZICAR).
• Refactored compatibilities now uses YAML for ease of reading.

• Bug fix for get_xrd_plot.
• Speed up XRD calculator by allowing specification of two theta ranges.
• Minor improvements to Gulp caller.

• Bug fix for unequal coefficients sizes in XRD.
• Support for Ag radiation in XRD calculator.
• Improved Procar class for extraction of information. (Germain Salvato Vallverdu)
• Bug fix for extraction of GGA data from Materials API.

• XRDCalculator now supports disordered structures.
• Minor speed ups and improvements.

• Initial beta version of XRD pattern calculator.
• Pymatgen now uses spglib 1.6.0.
• Update to Vasprun to compute static deilectric constants with DFPT in VASP. (Geoffroy Hautier)

• Quick bug-fix release that provides a better solution to Structure handling of properties instead of sanitizing MPRester structures.

• Patch to allow 1D phase diagrams (essentially finding the lowest energy phase).
• Better error checking for Bandstructure KPOINTs.
• Patch to sanitize structures obtained from MPRester.

• Bug fix for linear assignment, which may sometimes affect Structure Matcher results.
• Minor improvement to the way grand canonical PDs work.

• Bug fix for Pourbaix Maker (Sai).
• Streamline use of scratch directories for various calls. Require monty >= 0.1.2.
• High accuracy mode for Zeo++ (Bharat Medasani).

• Bug fix release for printing TransformedStructures from Substitutor (Will Richards).
• Misc improvements in BVAnalyzer, coord_utils and defects (Will Richards, David Waroquiers and Bharat Medasani).

• Bug fix release for DummySpecie, which failed when deserializing from json and had bad hash function.

• Structure/Molecule now supports Pythonic list-like API for replacing and removing sites. See quick_start for examples.

• Updates to support ABINIT 7.6.1 (by Matteo Giantomassi).
• Vastly improved docs.
• Refactoring to move commonly used Python utility functions to Monty package <https://pypi.python.org/pypi/monty>_, which is now a dependency for pymatgen.
• Minor fixes and improvements to DiffusionAnalyzer.
• Many bug fixes and improvements.

• Refactoring of qchemio module (by Xiaohui Qu).

• qchemio module (by Xiaohui Qu).

• Minor bug fix release for Structure species substitution methods.

• Massive update to pymatgen.io.abinitio package (by Matteo Giantomassi).
• Bug fixes for StructureMatcher's group_structure.
• Misc bug fixes and cleanup.

• Bug fix for VASP io set introduced by the default to sorting of structure sites when generating VASP input.

• Big fix release for json dumping for unitized floats.

• Bug fix release to improve CIF parsing for more non-standard CIF files. In particular, non-ascii characters are removed and _cgraph* fields are removed prior to parsing for better support in PyCiFRW.

• Bug fix release. Incorrect units assigned for ionic radii.
• Improved nwchemio supports COSMO and ESP calculations (Nav Rajput).

• Units. Pymatgen now has a new system of managing units, defined in pymatgen.core.units. Typical energy, length, time, temperature and charge units are supported. Units subclass float, which makes the usage transparent in all functions. The value that they being are in terms of conversions between different units and addition and subtraction of different units of the same type. Some basic quantities like ionic radii and atomic masses are now returned in unitized forms for easy conversion. Please see pymatgen.core.units and the examples for a demonstration of house to use units in pymatgen.

• Minor backwards-incompatible change. Structures are now sorted by default when generating VASP input files using vaspio_set. Old behavior can be obtained by setting sort_structure=False in the constructor. This is typically the desired behavior and prevents the generation of large POTCARs when atomic species are not grouped together.

• Bug fix for Molecule.substitute. Earlier algorithm was not detecting terminal atoms properly.

• Additional conversion tools for ABINIT (by Matteo Giantomassi).

• Minor bug fix release to fix pyhull dependencies to be more friendly.
• Improved structure matcher that allows for more flexible matching. New matching between ordered and disordered comparator.

• Beta new Gulp Caller and Zeo++ interface classes (Bharat . Zeo++ is an open source software for performing high-throughput geometry-based analysis of porous materials and their voids. Please see http://www.maciejharanczyk.info/Zeopp/about.html.
• Specify version of distribute to 0.6.34 for better compatibility.

• Support for VTK 6.x in structure visualization.
• Updated install instructions for openbabel.
• Preliminary pourbaix analysis (Sai Jayaratnam).

• Vastly improved Nwchem IO (by Shyue Ping Ong).
• Much improved ABINIT support (by Matteo Giantomassi).

• Added basic Nwchem (http://www.nwchem-sw.org/) IO support. (by: Shyue Ping Ong).
• New MoleculeMatcher class for comparing molecules by RMS. Requires openbabel with python bindings. (by: Xiaohui Qu)
• New functional group substitution capability for molecules (by: Lei Cheng and Shyue Ping Ong).