Change log

v2020.12.3

Site insertion algorithm based on charge density (@jmmshn, #1997)
Allow calculation of Fermi level from occupancies in VASP calculation (@rkingsbury, #2000)
Improvement to legibility of 3D phase diagram plots (@bayesfactor, #1999)
Improvement to allow general input for exciting (@vorwerkc, #1975)
Improvements to code formatting (@mkhorton, #2008)
Bug fix for VASP run type detection (@rkingsbury, #1996)

v2020.11.11

Bug fix for PhononBandStructureSymmLine. (@gpetretto)
Improved robustness in ABINIT input generation. (@gpetretto)
Other minor bug fixes.

v2020.10.20

Cp2K support (@nwinner)
Better BSPlotter (@fraricci)
Better deprecation warnings.
Bug fix for Py3.9 support.
Bug fix for neutron diffraction get_plot.

v2020.10.9

Cube parsing and Cube integration to Bader (@nwinner, #1967)
Improvements to PhaseDiagram (@CompRhys, #1899)
Improvements to VASP sets to calculate NGX/Y/Z, NGX/Y/ZF (@jmmshn, #1959)
Changes to MPRelaxSet, default to low spin for Co (@shyuep, #1976)
Changes to MPScanSet (@rkingsbury, #1952)
Rename of Specie to Species, Specie will be retained for backwards compatibility (@shyuep, #1963)
Bug fix for VASP sets (@utf, #1979)
Bug fix for PDPlotter (@mattmcdermott, #1973)
Bug fix for EnergyAdjustment (@rkingsbury, #1960)

v2020.9.14

New Plotly backend for PhaseDiagram plotting (@mattmcdermott, #1936)
New reporting and logging of Materials Project database version in MPRester (@mkhorton, #1945)
Improvements and bug fixes with mcsqs integration (@rwoodsrobinson, #1942)
Improvements to PackmolRunner (@rkingsbury, #1947)
Improvements to ComputerEntry (@rkingsbury, #1948)
Improvements for MPScanSet (@rkingsbury, #1940)
Bug fix for Surface and Composition (@gpetretto, #1937)
Bug fix for EwaldSummation serialization (@lbluque, #1932)
Bug fix for SeeK k-path (@Ian496, #1930)
Fix for deprecation warning in MPRester (@rkingsbury, #1951)

v2020.8.13

New GibbsComputedStructureEntry (@mattmcdermott, #1921)
Changes to MPScanRelaxSet and new MPScanStaticSet (@rkingsbury, #1917)
Changes to LobsterSet (@JaGeo, #1928)
Bug fix and change for MPRelaxSet (@mkhorton, 9eb3ac2)
Bug fix for JMolNN (@utf, #1920)
Bug fix for Element valences (@rkurchin, #1926)
Bug fix for BabelMolAdaptor (@smheidrich, #1924)
Bug fix for Gaussion IO (@eimrek, #1918)

v2020.8.3

Change neighbor-finding algorithm extension to C instead of C++ for better cross-platform robustness (@chc273)
Add I/O for JARVIS Atoms (@knc6)

v2020.7.18

Add validation and extrapolation for stitching XAS (@yimingcheng)
Better error handling and possibly verbose warning to get_structure_by_material_id

v2020.7.16

Bug fix for boltztrap2 spin support. (@fraricci)

v2020.7.14

EwaldSummation is now MSONAble (@lbluque).
Fix for QChem freq parsing (@samblau)
Much improved linting and workflows.

v2020.7.10

Bug fix: serialization of slabs (@utf)
Bug fix: enumlib url (@wsyxbcl)
Bug fix: change in tolerance for Lattice comparison (@mbjumar)
Bug fix: k-path division by zero (@mfherbst)
New: support for openbabel 3.0 (@orioncohen)

v2020.7.3

Make Slabs properly serializable in as_dict. Fixes #1892.
Fixes for Critic2Caller (@yuuukuma)
Add cost data for He, H, Ar, Ne, Kr, Tc (@computron)
Parse scientific notation in OUTCAR (possibly without spaces in between)
Spin support for boltztrap2 (@fraricci)
New static method to generate basis functions Lobster (@JaGeo)
SLME and spillage analysis (@knc6)

v2020.6.8

New: Support for parsing WAVECARS with spin-orbit coupling (@mturiansky, #1861)
New: Support to convert WAVECAR to wannier90 UNK files (@mturiansky, #1861)
New: Site-weighted XAS spectrum (@yimingchen95, #1837)
Fixed: Elfcar serialization (@ayushgupta, #1859)
Fixed: Units in label for phonon plot (@ab5424, #1857)
Fixed: StructureMatcher serialization (@lbluque, #1850)
Fixed: Comment string in KPOINTS file (@arosen93, #1842)
Fixed: parsing of dielectric function in VASP output (@computron, #1836)

v2020.4.29

Improved SQS caller. (@rwoodsrobinson)
VolumetricData speedup (@mturiansk)
Misc bug fixes

v2020.4.2

New high-symmetry k-path algorithm (@munrojm, @kt-latimer)
New TEM diffraction calculator (@welltemperedpaprika, @thefrankwan, @shyamd)
New plotly plotting option for Wulff shapes (@richardtran415)
Improvements to SQS caller (@rwoodsrobinson)
Various bug fixes and improvements (@mfherbst, @chc273, @jacksund, @espottesmith, @hongyi-zhao, @montoyjh, @dongsenfo, @dynikon) including significant BrunnerNN, EconNN fixes (@utf), see individual pull requests for details.

v2020.3.13

Added angle_tolerance to CifWriter.
Change default float precision in CifWriter to 8. Adds float_prec kwarg to allow setting of arbitrary precision.
Rudimentary pymatgen.io.vasp.help.VaspDoc class for obtaining help from VASP wiki.
Massive documentation cleanup.
Reorganization of Entry, ComputedEntry (@ayushsgupta).
Bug fix for PourbaixDiagram (@montoyjh).
Read WAVECAR from gamma-point only VASP executable. (@bernstei)

v2020.3.2

New MonteCarloRattleTransformation and phonopy integration (@utf)
New structure connectivity features in Chemenv analysis (@davidwaroquiers)
Bug fixes (@richardtran415, @chc273, @JaGeo, @dskoda, @rkingsbury, @jmmshn, @espottesmith, @gVallverdu, @yimingchen95, @fraricci)

v2020.1.28

Plugin architecture for pymatgen.
Improvements to pymatgen.analysis.xas.spectrum.XAS class. (@yiming)
Fixes for ISYM uniform bug and auto-NEDSO (@fraricci)
Improvements to ReactionDiagram.
Chemenv improvements (@davidwaroquiers)
Misc bug fixes.

v2020.1.10

New connectivity analysis in Chemenv (@davidwaroquiers)
Improvements to DOSPlotter (@uthpalah)
Improvements to writing VASP input sets (@rkingsbury)
Bug fix for PhaseDiagram (@montoyjh)

v2019.12.22

Improvements to reaction calculator (@mattmcdermott)
VASP input set for SCAN from Materials Project, MPScanSet (@rkingsbury)
Bug fixes and documentation improvements (@LindaHung-TRI, @rkingsbury, @kwaters4, @rwoodsrobinson, @JaGeo, @nishiyamat, @smheidrich)

v2019.12.3

Respect KSPACING in INCAR.
Bug fixes.

v2019.11.11

Extend grosspop class (@Jageo)
Add option to VaspInputSet to write output with POTCAR.spec
Add sort_structure option to Poscar.
Added ability to make gaussian input file without a geometry (@WardLT)
Misc big fixes.

v2019.10.16

Major refactoring of ABINIT IO to remove workflow-based packages (@gmatteo)
Use caching in MinimumVIRENN class. (Alex Ganose)
Changes to Lobster module and lobsterset (@jageo)
Eigenval object for EIGENVAL output file (@mturiansky)

v2019.10.4

Fix compile args.

v2019.10.3

Faster get_all_neighbors based on @chc273's improvements. get_all_neighbors now returns a Site-like object with nn_distance, image and index attrbutes. Much easier to use.
Bug fix for XCrySDen parser (@stevetorr)
Added optional mid_struct to direct interpolation (@jmmshn)

v2019.10.2

IRSpectra class (@henriquemiranda)
Much faster get_neighbors written in Cython (@chc273).
VolumetricData allows for sum or substraction of data with different structures, with warnings.

v2019.9.16

Updates to annotation, docstrings, etc. Linting service now provided on Github Actions as well as CircleCI.

v2019.9.12

Massive updates to type annotations, especially for core classes.
pycodestyle, pydocstyle and mypy will henchforth be enforced for all new PRs.

v2019.9.8

Supplemental release to address missing incar_parameters.json

v2019.9.7

New fast Pourbaix algorithm (@montoyjh)
VASP Incar parameter checking (@richardtran415)
New VASP input set for Lobster, read support for GROSSPOP file (@JaGeo)
New CombinedData class for LAMMPS (@htz1992213)
Improvements to molecule fragmenter (@samblau)
Various bug fixes and improvements (@dongsenfo, @shyuep, @ardunn, @nathan-diodan, @rkingsbury, @kmu)

v2019.8.23

pycodestyle now enforced, except on tests. Developers should install pycodestyle and the pre-commit hook (copy pre-commit to .git/hooks) provided in the repo to check before commits. CI now checks for code style and PRs must pass pycodestyle.
chemsys str input now allowed in get_entries_in_chemsys (@rkingsbury)
ComputedEntry and subclasses now support a normalize().
Speed improvements in fragmeter using igraph. (@samblau)

v2019.8.14

Update DOSCAR from lobster (@JaGEO)
PerturbStructureTransformation (@rees-c)
Misc bug fixes.

v2019.7.30

Bug fixes (@shyuep, @mfherbst)
More type hint annotations (@shyuep)
Improvements to BabelMolAdaptor (@smheidrich)
Convenience Transformations for AdsorbateSiteFinder (@mkhorton)

v2019.7.21

Add CubicSupercellTransformation and PerturbedSupercellsTransformation (@rees-c, @utf)
Add interface for ShengBTE (@rees-c, @utf)
Add interface for Vampire (@ncfrey)
Improved Lobster interface (@JaGeo)
Bug fixes (@sthartman, @dwinston, @utf)
New functionality for calculation of Heisenberg exchange parameters (@ncfrey)
Improvements to Miller indices handling and Lattice (@richardtran415)

v2019.7.2

Improvements to grain boundary transformations and Rester (@Tinaatucsd)
Improvements to AdsorbateSiteFinder (@oxana-a)
Improvements to Waveder support (@JRSuckert)
Improvements to run type detection (@darnoceloc)
Add XAS data to Rester (@yimingchen95)
Fix to ATAT input/output (@dongsenfo)
Initial support for Prismatic input (@mkhorton)

v2019.6.20

New interface class (@sivonxay, @kylebystrom, @shyamd)
Updates to SlabGenerator (@richardtran415)
Updates to PiezoTensor (@dongsenfo)
Add support for parsing on-site density matrix to Outcar (@mkhorton, @mhsiron, @clegaspi)
Fixes for magnetic space groups (@simonward86)
Fixes for Lobster class (@JaGeo)
Fix for FEFF (@stevetorr)
Fix for Waveder (@JRSuckert)

v2019.6.5

Linear scaling get_all_neighbors. Tested to be faster for > 100 atoms (@chc273).
Lobsterin class to handle input for Lobster (@JaGeo).
Strict options for composition parsing (@mkhorton).
Bug fix for CovalentBondNN.get_bonded_structure (@lan496).

v2019.5.28

New VASP Input Set "from previous" interface (@utf)
ELFCAR support (@mkhorton)
Improvements to plotting of band structures and densities of states (@ShuaishuaiYuan)
Convenience functions added to Composition including chemical system convention (@mkhorton)
Various bug fixes (@mkhorton, @utf)
Improvements to MEGNET API (@shyuep)
Improvements to Structure interpolation (@mturiansky)

v2019.5.8

Numerous updates and improvements to defect classes (@dbroberg)
New API for MEGNET models, see http://megnet.crystals.ai (@shyuep)
Update to NMR symmeterization (@dongsenfo)
Change CIF indexing (@kmu)
Add BoltzTraP mode to NonSCF input sets (@utf)

v2019.5.1

Small speeds to Structure.get_all_neighbors.
Big fixes for gulp_caller. (@kmu)
Plot fatbands from Lobster. (@jageo)
Speed up get_ir_mesh (@utf)
Parsing of plasma frequencies from Outcar.
Miscellaneous bug fixes.

v2019.4.11

Improvements to MimimumDistanceNN (@jmmshn)
Improvements to Lobster. (@JaGeo)
Implement a metal warning for ISMEAR < 1 and NSW > 0.
Misc bug fixes to input sets, including detection of metal systems and checking for standardization.

v2019.3.27

Bug fixes for OrderDisorderComparator (@utf), custom k-points

in MPNonSCFSet (@dyllamt), battery app (@jmmshn), MPSOCSet (@mkhorton), more * Improvements to COHP (@JaGeo) * Support to read WAVEDER files (@knc6) * Addition of van Arkel-Ketelaar triangle plots (@richardtran415) * Addition of optional user agent to MPRester API calls, see documentation for more information (@dwinston)

v2019.3.13

Streamlined Site, PeriodicSite, Molecule and Structure code by abandoning immutability for Site and PeriodicSite.
VaspInput class now supports a run_vasp method, which can be used to code runnable python scripts for running simple calculations (custodian still recommended for more complex calculations.). For example, the following is a kpoint convergence script that can be submitted in a queue

from pymatgen import MPRester
from pymatgen.io.vasp.sets import MPRelaxSet


VASP_CMD = ["mpirun", "-machinefile", "$PBS_NODEFILE", "-np", "16", "vasp"]


def main():
    mpr = MPRester()
    structure = mpr.get_structures("Li2O")[0]
    for k_dens in [100, 200, 400, 800]:
        vis = MPRelaxSet(structure,
            user_kpoints_settings={"reciprocal_density": k_dens})
        vi = vis.get_vasp_input()
        kpoints = vi["KPOINTS"].kpts[0][0]
        d = "Li2O_kpoints_%d" % kpoints

        # Directly run vasp.
        vi.run_vasp(d, vasp_cmd=VASP_CMD)
        # Use the final structure as the new initial structure to speed up calculations.
        structure = Vasprun("%s/vasprun.xml" % d).final_structure


if __name__ == "__main__":
    main()

Many pymatgen from_file methods now support pathlib.Path as well as strings.
Misc bug fixes.

v2019.2.28

Type hints now available for core classes.
New pymatgen.util.typing module for useful types.
Misc bug fixes.

v2019.2.24

New EntrySet class for easy manipulation of entries to grab subsets, remove non-ground-states, etc. Makes it easier to grab a large set of entries and work with sub chemical systems. Also MSONable for caching.
Performance improvements in core classes and Poscar (@ExpHP).
New/changed methods for IcohpCollection and Completecohp

v2019.2.4

New Trajectory class for MD simulations (@sivonxay)
Lattice.get_vector_along_lattice_directions (@blondgeek)
Misc bug fixes.

v2019.1.24

Python 3 only!
Improvements to local environment code including VESTA bond emulation (@utf)
Update Cohp analysis (@JaGEO)
Updates to Boltztrap2 (@fraricci)

v2019.1.13

Pymatgen is now Py3 ONLY. If you need Py27 support, please use versions < 2019.1.1.
PARCHG parsing from WAVECAR (@mturiansky)
Improvements to defect generation algorithms (@dbroberg)
Simplifications to COHP plotting (@JaGeo)

v2018.12.12

Support for IUPAC ordering of elements in Composition formulae (@utf)
Various bug fixes including returning integer miller indices, catching negative values in Composition and fixes to graph analysis (@utf), fix to Composition serialization (@jmmshen), defect analysis (@HanmeiTang), removing sites in surfaces (@yiming-xu), and fix to support the new PROCAR format in VASP (@dkorotin)
PMG_MAPI_ENDPOINT environment variable added to support different endpoints for the Materials Project REST interface (@mkhorton)

v2018.11.30

MPRester.query now supports bulk queries for large scale requests. (@dwinston)
MVLRelax52Set which uses VASP 52 pseudopotentials. (@HanmeiTang)
EPH calculations in ABINIT (@gmatteo)
New ScaleToRelaxedTransformation (@richardtran415)
New dimensionality finder, and consolidation of existing algorithms (@utf)
New dopant predictor built on structure predictor (@utf)
Misc bug fixes (@HanmeiTang, @utf, @tamuhey, @mkhorton, @yiming-xu, @richardtran415)

v2018.11.6

Ionic radius based CrystalNN (@computron)
InterfacialReactivity (@dbroberg)
Misc bug fixes

v2018.10.18

New bond fragmenter and bond dissociation analysis modules (@samblau)
Improvements to MoleculeGraph (@espottesmith)
Fix: bug in triclinic tensor conversion to IEEE standard (@montoyjh)
Fix: insertion battery summary dictionary format (@jmmshn)
Speed improvements to certain tests (@shyuep, @samblau)

v2018.9.30

Fix: increased cut-off to VoronoiNN to avoid scipy crash (@utf)
Fix: Outcar parsing issues with certain values of electrostatic potential (@sivonxay)
Fix: bug in EnumlibAdaptor/EnumerateStructureTransformation involving incorrect stoichiometries in some instances (#1286) (@shyuep)
Fix: fractional co-ordinate finite precision errors in CifParser, now also includes additional warnings for implicit hydrogens (@mkhorton)
New features and improvements to GBGenerator (@ucsdlxg, @shyuep)
New analysis options in StructureGraph, speed up tests (@mkhorton)
New utility function to pretty print disordered formulae, along with a ordered-to-disordered structure transformation (@mkhorton)
Ability to use pymatgen's StructureMatcher against AFLOW's library of crystallographic prototypes (@mkhorton)
Make Chgcar serializable to/from dict for database insertion (@jmmshn)

v2018.9.19

Fix to composition handling in MolecularOrbitals (@dyllamt)
Fix to allow mixed compressed/uncompressed loading of VASP band structures (@ajjackson)
New features and fixes to chemenv analysis module (@davidwaroquiers)
Fix to include structure predictor data with pip/conda-installed pymatgen (@shyamd)
Fixes to Defect objects, icluding allowing rotational supercell transformations (@dbroberg)
Fix to BSDOSPlotter to correctly fill in parts of DOS (@fraricci)
Added '@' notation parsing in Composition (@tamuhey)
BibTex reference extraction updated in CifParser to support ICSD CIFs (@shyamd)
Various updates to speed up and fix test suite (@shyuep, @fraricci)
Improvements to BoltzTraP 2 support (@shyuep, @fraricci)

v2018.9.12

Use boltztrap2 (@fraricci)
Refactoring of tensor code to core (@montoyjh)
Support for new Lobster version (@JaGeo)
Misc bug fixes

v2018.8.10

Bug fix for pymatgen.analysis.gb and pymatgen.io.lammps.

v2018.8.7

Massive refactoring of LAMMPS support. (@adengz)
Allow kwargs passthrough for Structure.to.
Updates to ABINIT support (@gmatteo)
GrainBoundaryTransformation class. (@Tinaatucsd)

v2018.7.15

Grain boundary generator (Xiangguo Li @ucsdlxg)
Massive updates to defect code and new DefectTransformation (@shyamd)
Bug fix for OUTCAR parsing with more than one space in electrostatic potential.
get_fermi_interextrapolated to support wider range of input doping (@albalu)
Update to cython compile to support Py3.7.
Update VoronoiNN cutoff dynamically (@computron)

v2018.6.27

Improved local_env and MoleculeGraph (@WardLT, @espottesmith)
Improve BabelMolAdaptor with conformer search and other functions (@Qi-Max)
Improved surface analysis (@richardtran415)

v2018.6.11

Updates to ABINIT support for 8.1.3
Updates to Interface analyzer.
Fix bug in deserialization of ComputedStructureEntry.
Misc bug fixes.

v2018.5.22

Misc bug fixes.

v2018.5.21

Bug-fix for missing HHI data file.
Misc bug fixes.

v2018.5.14

Dash docs now avaiable for pymatgen. See pymatgen.org "Offline docs" section for details.
Better CrystalNN. (Anubhav Jain)
Fixes for elastic module. (Joseph Montoya)

v2018.5.3

Improvements to qchem (@samblau).
Improvements to nwchem to support tddft input and parsing (@shyuep).
Improvements to CrystalNN (@computron).
Add methods for getting phonon BS, DOS, and DDB output (@dwinston).

v2018.4.20

Neutron diffraciton calculator (Yuta)
Non-existent electronegativity (e.g., He and Ne) are now returned as NaN instead of infinity.
CifParser now handles Elements that are in all caps, which is found in some databases. (Gpretto)
Improvements to local_env (Anubhav Jain)
Improvements to Qchem ()
Inputs sets for NMR (Shyam)
New ChargeDensityAnalyzer class to find interstitial sites from charge density (Hanmei)

v2018.4.6

Updated debye temperature formulation (Joey Montoya)
Add bandgap option for FermiDos for scissoring (Alireza Faghaninia)
Improved Pourbaix code (Joey Montoya)
Local env code improvements (Nils)

v2018.3.22

Bug fixes to structure, phase diagram module, enumlib adaptor, local env analysis.

v2018.3.14

ReactionDiagram for calculating possible reactions between two compositions.
Misc bug fixes for EnumlibAdaptor and MagOrderingTransformation

v2018.3.13

Support for VESTA lattice vector definitions.
GaussianOutput read now bond_orders of a NBO calculations (@gVallverdu)
Bug fixes to phonons, abinit support.

v2018.3.2

Various algorithms for nearest neighbor analysis (Hillary Pan)
Cleanup of local_env modules (Nils)
Enhancements to surface packages (Richard)
Misc bud fixes

v2018.2.13

Improved chemenv parameters and bug fixes (David Waroquiers).
Improved Qchem IO (Shyam).
Improved interfacial reactions.
local_env update (Nils).
Improved ABINIT support (@gmatteo).
Misc bug fixes.

v2018.1.29

Improvements to local_env (Nils)
Term symbols for Element (Weike Ye).
Timeout for enumlib (Horton).

v2018.1.19

Phonon plotting and analysis improvements (Guido Petretto).
Voronoi site finder (Hanmei Tang)
Some bug fixes for Gaussian (Marco Esters)
Misc improvements.

v2017.12.30

Added detailed Shannon radii information and method.
Magoms for lanthanides (Weike Ye)
Chemenv improvements (David Waroquiers)
Ewald summation improvements (Logan Ward)
Update to ABINIT support (G Matteo)

v2017.12.16

Add optical absorption coefficient method
Improve plot_element_profile

v2017.12.15

Deprecated methods cleanup for 2018. Note that this may break some legacy code. Please make sure you update your code!
Better dielectric parsing for VASP 5.4.4 to include both density-density and velocity-velocity functions.
Orbital-resolved COHPs support (Macro Esters)
Convenient plot_element_profile method in PDPlotter.
Input set for SCAN functional calculations.
Misc bug fixes and code improvements.

v2017.12.8

Pymatgen no longer depends on pyhull.
MPRester method to get interface reaction kinks between two reactants.
Misc improvements.

v2017.12.6

Support for HDF5 output for VolumetricData (CHGCAR, LOCPOT, etc.).
Support for Crystal Orbital Hamilton Populations (COHPs) (@marcoesters)
REST interface for Pourbaix data
Support for optical property parsing in Vasprun.
Improvements to LammpsData
Misc bug fixes.

v2017.11.30

Fix for severe enumlib_caller bug. This causes enumerations not to be carried out properly due to bad accounting of symmetry of ordered sites. It results in too few orderings.
New method to extract clusters of atoms from a Molecule based on bonds.

v2017.11.27

Improvements to FEFF
MPRester now supports surface data.
Improvement to DiscretizeOccupanciesTransformation.

v2017.11.9

Massive rewrite of LAMMPSData to support more functionality (Zhi Deng)
Misc bug fixes.

v2017.11.6

Better exception handling in EnumlibAdaptor and EnumerateStructureTransformation.
Allow bypassing of ewald calculation in EnumerateStructureTransformation.
get_symmetry_operations API convenience method for PointGroupAnalyzer.
New DiscretizeOccupanciesTransformation to help automate ordering of disordered structures.
Fix POTCAR check for POSCAR.
Minor updates to periodic table data.
Misc bug fixes.

v2017.10.16

Added many more OPs and made normalization procedure more robust (Nils Zimmermann)
Molecular orbitals functionality in Element (Maxwell Dylla)
Improvements in chemenv (David Waroquiers)
Add I/O for ATAT’s mcsqs lattice format (Matthew Horton)

v2017.9.29

critic2 command line caller for topological analysis (M. Horton)
Refactor coord_util -> coord.

v2017.9.23

Gibbs free energy of a material with respect to Pourbaix stable domains.
Phonopy io now supports structure conversions.
EnumerateStructureTransformation now implements a useful occupancy rounding.
MVLNPTMDSet
Improved PDPlotter options.
Misc bug fixes.

v2017.9.3

VDW support (Marco Esters)
Bug fix release.

v2017.9.1

Massive refactoring of PhaseDiagram. Now, PDAnalyzer is completely defunct and all analysis is carried out within PhaseDiagram itself, e.g., pd.get_e_above_hull as opposed to PDAnalyzer(pd).get_e_above_hull.
Refactoring of structure prediction. Now in pymatgen.analysis.structure_prediction.
New core Spectrum object and associated pymatgen.vis.plotters.SpectrumPlotter.
Parsing energies from gen_scfman module in Qchem 5 (Brandon Wood)
Improvements to LAMMPSData, vasp IO.

v2017.8.21

Minor bug fixes.

v2017.8.20

Input sets for GW and BSE calculations (Zhenbin Wang) and grain boundary calculations (Hui Zheng). Input sets now support overriding of POTCAR settings.
Haven ratio calculation (Iek-Heng Chu).
LAMMPS io updates (Kiran Matthews).
Oxidation state guessing algorithms based on ICSD data (Anubhav Jain).
New local_env module for local environment analysis. (Nils Zimmerman).
pymatgen.util.plotting.periodic_table_heatmap (Iek-Heng Chu).
Improvements to surface code for tasker 3 to 2 reconstructions.
pymatgen.analysis.interface_reactions.py for analyzing interfacial reactions (Yihan Xiao).

v2017.8.16

PointGroupAnalyzer now allows for symmetrization of molecules. (@mcocdawc)
QuasiharmonicDebyeApprox with anharmonic contribution. (Brandon)
Improvements to LAMMPS io. (Kiran)
Misc bug fixes.

v2017.8.14

Fixes and minor improvements to elastic, bader and defect analyses.

v2017.8.4

Major refactoring and improvements to lammps io. (Kiran)
Major improvements to BaderAnalysis. (Joey and Zhi)
Major improvements to Magmom support in cifs, SOC calculations, etc. (Matthew Horton)
Add remove_site_property function. Add magmom for Eu3+ and Eu2+.
BoltztrapAnalyzer/Plotter support for seebeck effective mass and complexity factor (fraricci)

v2017.7.21

Misc bug fixes to elastic (J. Montaya),
Decrease default symprec in SpacegroupAnalyzer to 0.01, which should be sufficiently flexible for a lot of non-DFT applications.

v2017.7.4

Bug fixes for oxide corrections for MP queried entries, and pickling of Potcars.
Default to LPEAD=T for LEPSILON=T.

v2017.6.24

New package pymatgen.ext supporting external interfaces. Materials Project REST interface has been moved to pymatgen.ext.matproj. Backwards compatibility will be maintained until 2018.
Two new interfaces have been added: i) Support for John Hopkin's Mueller group's efficient k-point servelet (J Montaya). ii) Support for Crystallography Open Database structure queries and downloads. (S. P. Ong). See the examples page for usage in getting structures from online sources.

v2017.6.22

Speed up pmg load times.
Selective dynamics parsing for Vasprun (Joseph Montaya)
Allow element radius updates in get_dimensionality (Viet-Anh Ha).
Dielectric function parse for vasp 5.4.4 (Zhenbin Wang).
Parsing for CIF implicit hydrogens (Xiaohui Qu).

v2017.6.8

Switch to date-based version for pymatgen.
Electronegativities now available for all elements except for He, Ne and Ar, which are set to infinity with a warning.
Bond lengths are now set to sum of atomic radii with warning if not available.
Bug fixes to boltztrap, symmetry for trigonal-hex systems, etc.

v4.7.7

Magnetic symmetry and CIF support. (Horton)
Improved PWSCF Input file generation.
Misc bug fixes.

v4.7.6

Fix serious bug in PointGroupAnalyzer that resulted in wrong point groups assigned to non-centered molecules.
Useful get_structure_from_mp at the root level for quick retrieval of common structures for analysis.
More efficient kpoint grids.
Misc bug fixes.

v4.7.5

MultiXYZ support (Xiaohui Xu)
Misc bug fixes and cleanup.

v4.7.4

New ferroelectric analysis module (Tess).
Magmom support and MagSymmOp (Matthew Horton).
Improved CIF Parsing.

v4.7.3

Sympy now a dependency.
Massive improvements to elastic package. (Joseph Montoya)
Symmetrized structures now contain Wyckoff symbols.
More robust CIF parsing and MITRelaxSet parameters (Will).

v4.7.2

Support for Abinit 8.2.2, including support for DFPT calculations. (Matteo)

v4.7.1

Pathfinder speedup
Minor bug fix for plots.

v4.7.0

Improvements to BSDOSPlotter.
Enhancements to Phase diagram analysis and reaction calculator.
Enhancements to surface slab and adsorption. (Richard and Joey)
Support NpT ensemble in diffusion analysis.

v4.6.2

Improve Spacegroup class support for alternative settings. Add a get_settings class method.
Improvements to FEFF support.
Improvements to EOS class.

v4.6.1

Phonon bandstructure plotting and analysis. (Guido Petretto)
New capabilities for performing adsorption on slabs. (Joey Montoya)
Remove pathlib dependency.

v4.6.0

Improve support for alternative settings in SpaceGroup.
Fix respect for user_incar_settings in MPNonSCFSet and MPSOCSet
Support for argcomplete in pmg script.
Speed ups to Ewald summation.
Add functionality to parse frequency dependent dielectric function.
Improvements to Bolztrap support.

v4.5.7

PMG settings are now prefixed with PMG_ to ensure proper namespacing.
Improve error output in command line bader caller.
Add Py3.6 classifier.
Misc bug fixes.

v4.5.6

Minor bug fix.
Fixed elastic energy density

v4.5.5

Fix bad reading of pmgrc.
Gaussian opt section added allowing for torsion constraints
Update spglib.

v4.5.4

BSDOSPlotter (Anubhav Jain)
Fixes to defect analysis (Bharat)
intrans as an input to BoltztrapAnalyzer. Allows for scissor operation.
Pmg is now continuously tested on win-64/py35 using Appveyor!

v4.5.3

Added an alternative interstitial finder that works with a grid-based structure-motif search. (Nils Zimmermann)
Optionnal possibility to specify that the saddle_point in the NEB should have a zero slope. (David Waroquiers)
Read intensity and normal modes for Gaussian. (Germain Salvato Vallverdu)
Minor bug fixes.

v4.5.2

Minor bug fix for POTCAR settings.

v4.5.1

You can now specify a different default functional choice for pymatgen by setting PMG_DEFAULT_FUNCTIONAL in .pmgrc.yaml. For use with newer functional sets, you need to specify PBE_52 or PBE_54 for example.
Swtich to ISYM 3 by default for HSE.
Updates to FEFF>
Misc bug fixes and startup speed improvements.

v4.5.0

Major speed up of initial load.
Collection of misc changes.

v4.4.12

Fix for dynamic numpy import.

v4.4.11

Update to new version of spglib.

v4.4.10

Minor fixes for proper gzipped structure file support and MVLSlabSet.

v4.4.9

Dependency cleanup. Now, basic pymatgen requires on much fewer packages.
Fixed reading of POSCAR files when more than 20 types of atoms.
Misc bug fixes.

v4.4.8

Cleanup of entry points and dependencies.

v4.4.7

Update to spglib 1.9.7.1
Proper use of dependency markers for enum34.

v4.4.6

Update to spglib 1.9.6, which fixes some bugs and is Windows compatible.

v4.4.5

Bug fix for SubstitutionProb.

v4.4.4

Bug fix for electronic structure plotter.

v4.4.3

Bug fix for Diffusion Analyzer.

v4.4.2

Bug fix for BS serialization.
Cleanup dependencies.

v4.4.1

Massive updates to FEFF support (Kiran Mathews).
Bug fixes in band structure plotting.

v4.4.0

Much more Pythonic API for modifying Structure/Molecule species. Now, strings, slices, and sequences should magically work, in addition to the previous API of simple int indices. Examples:

s[0] = "Fe"
s[0] = "Fe", [0.5, 0.5, 0.5]  # Replaces site and fractional coordinates.
s[0] = "Fe", [0.5, 0.5, 0.5], {"spin": 2}  # Replaces site and fractional coordinates and properties.
s[(0, 2, 3)] = "Fe"  # Replaces sites 0, 2 and 3 with Fe.
s[0::2] = "Fe"  # Replaces all even index sites with Fe.
s["Mn"] = "Fe"  # Replaces all Mn in the structure with Fe.
s["Mn"] = "Fe0.5Co0.5"  # Replaces all Mn in the structure with Fe: 0.5, Co: 0.5, i.e.,creates a disordered structure!

Massive update to internal representation of Bandstructure objects for memory and computational efficiency.
Bug fixes to CIF parsing in some edge cases. (Will Richards).

v4.3.2

Massive speedup of Bandstructure, especially projected band structures, parsing.
Massive update to pmg cli script, with new query functions as well as a more rational command structure.
Updates to ChemEnv.
Misc bug fixes.

v4.3.1

Upgrade monty and spglib requirements for bug fixes.
Updates to feff support (Kiran).

v4.3.0

Massive update to elastic module. (Joey Montaya)
Pathfinder algorithm for NEB calculations. (Ziqing Rong)
Wheels for Windows and Mac Py27 and Py35.

v4.2.5

Bug fix for BSPlotter.

v4.2.4

Bug fix for kpoint weight calculation for Monkhorst meshes.

v4.2.3

Minor cleanup.
Simplified installation. enumlib and bader can now be installed using pmg setup --install.

v4.2.2

Global configuration variables such as VASP_PSP_DIR and MAPI_KEY are now stored in "~/.pmgrc.yaml". If you are setting these as environmental variables right now, you can easily transition to the new system using:
```
pmg config --add VASP_PSP_DIR $VASP_PSP_DIR MAPI_KEY $MAPI_KEY
```
This new scheme will provide greater flexibility for user-defined global behavior in pymatgen, e.g., tolerances, default input sets for transmuters, etc., in future.
Beta of k-point weight calculator.
Use default MSONable as and from_dict for all transformations.

v4.2.1

New DopingTransformation that implements an automated doping strategy.
Updated MIC algorithm that is a lot more robust (Will Richards).
Major update to chemenv package (David Waroquiers)

v4.2.0

Fix important bug in minimum image distance computation for very skewed cells.
Major refactoring of WulffShape code.
Misc bug fixes for elastic tensor and other codes.

v4.1.1

Major refactoring of WulffShape and lammps support.

v4.1.0

Wulff shape generator and analysis.
Minor bug fixes.

v4.0.2

Fix kpoint reciprocal density.

v4.0.1

Minor bug fix release.

v4.0.0

Massive update with many deprecated methods removed. Note that this may break backwards incompatibility!
Support for ABINIT 8.
Improved sulfide compatibility.

v3.7.1

Fix deprecation bug.

v3.7.0

Last version before pymatgen 4.0, where deprecated modules will be removed!
Massive update to LAMMPS (Kiran Matthews).
New input sets with a different interface that replaces old input sets.
Massive update to elastic properties.

v3.6.1

Massive cleanup to Boltztrap interface (Anubhav Jain)
Refactor of piezoelectric analysis to use tensor base class (Joey)
More robust CIF parsing.

v3.6.0

Pymatgen now uses spglib directly from Togo's website. Spglib is no longer bundled as a dependency.
Improved support for velocities in Poscar (Germaine Vallverdu)
Backwards incompatible change in Born charge format in Outcar.
Fixes for Lammps input serialization

v3.5.3

Misc refactorings and bug fixes, especially for Outcar and Boltztrap classes.

v3.5.2

Minor update to DerivedInputSet interface.

v3.5.1

New derived input sets for generating inputs that depende on previuos calculations. Old input sets deprecated.

v3.5.0

Chemical environment analysis package (David Waroquiers).
Piezoelectric property analysis (Shayam).
Cythonize certain expensive core functions. 5-10x speedup in large structure matching (Will Richards).
New NMR parsing functionality for Outcar (Xiaohui Qu).
Improved io.lammps (Kiran Mathews).
Update to spglib 1.9.2.
Element properties now return unitized float where possible.
Bug fix for get_primitive_standard affecting rhombohedral cells (important for band structures).
Vasprun.final_energy now returns corrected energy with warning if it is different from final electronic step.

v3.4.0

10-100x speed up to Structure copying and Site init, which means many functionality has seen signifcant speed improvement (e.g., structure matching).
Convenience method Structure.matches now perform similarity matching for Structures.
Bugfix for band gap determination.

v3.3.6

Update to use enum.x instead of multienum.x.
Minor robustness fixes to VaspInputSet serialization.
Add a reciprocal density parameter to vasp sets.
Minor bug fixes to Vasprun parsing.

v3.3.5

StructureMatcher can now work with ignored species.
Added interpolation failure warnings and smooth tolerance for scipy.interpolate.splrep in bandstructures (Tess).
Added DiffusionAnalyzer.get_framework_rms_plot.
Complete rewrite of Procar class to use ND array access and zero-based indexing.
OrderParameters class for analysis of local structural features (Nils Zimmermann).
Bug fixes for Procar, MPRester and SpaceGroup 64.
Added Github templates for contributing to pymatgen.

v3.3.4

Procar now supports parsing of phase factors.
Miscellaneous bug fixes.

v3.3.3

Bug fixes for Poscar.
Fix Kpoints pickling.

v3.3.2

Bug fixes for pymatgen.io.abinit
Other minor big fixes.

v3.3.1

Minor bug fix release for pickle and elastic constants.

v3.3.0

Updated and checked for Python 3.5.* compatibility.
Element, Spin, Orbital and various other Enum-like classes are now actually implemented using Enum (with enum34 dependency for Python < 3.4).
Speed up Site creation by 20% for ordered sites, with cost in terms of slightly slower non-ordered Sites. Since ordered Sites is the far more common case, this gives significant boost for large scale manipulations of structures.
Alternative, more pythonic syntax for creating supercells via simply Structure * 3 or Structure * (3, 1, 1).
zeo++ fixes.
More stable incar settings for MITMDVaspInputSet.

v3.2.10

Fix missing scripts
Improvements to units module.
Speed up EwaldSummation.

v3.2.9

Major PD stability improvements, especially for very high dim hulls with lots of entries.
Improvements to Ewald summation to be close to GULP implementation.
Deprecate physical constants module in favor of scipy's version.
Remove many pyhull references to use scipy's ConvexHull implementation.
Bug fix for sulfide correction.

v3.2.8

Make pyhull optional.
Sulfur correction added to MaterialsProjectCompatibility for more accurate sulfide formation energies.
ADF io support. (Xin Chen)
Bug fixes for spacegroup subgroup testing.

v3.2.7

Add warning for limited subgroup testing functionality in Spacegroup.

v3.2.6

Extensive support for elasticity tensor analysis (Joseph Montoya).
Misc bug fixes and performance improvements.
Add support for QChem4.3 new format of Batch jobs

v3.2.5

Improved potcar setup via "pmg setup", with MAPI setup.
Support for new POTCARs issued by VASP.
Improvements to ABINIT support.
Improvement to Boltztrap support, e.g., scissor band gap, etc.
Vasprun now issues warning when unconverged run is detected.

v3.2.4

GaussianOutput can now parse frequencies, normal modes and cartesian forces (Xin Chen).
Support for Aiida<->pymatgen conversion by the Aiida development team (Andrius Merkys).
Specialized BSVasprun parser that is ~2-3x faster than Vasprun.
Refactor the boltztrap package (merge a few methods together) and add several new methods (power factor, seebeck...)
Support of the new PCM format in QChem 4.3
Local environment analysis to pmg script.
Deprecate prettytable in favor of tabulate package.
Improvements to MITNEBVaspInputSet.
Misc bug fixes.

v3.2.3

Massive update to abinit support. Note that pymatgen.io.abinitio has been refactored to pymatgen.io.abinit. (Matteo, Setten)
NwOutput now supports parsing of Hessian matrices (contributed by Xin Chen)
Gaussian support now has the ability to read potential energy surface and electronic transitions computed with TD-DFT (Germain Salvato Vallverdu)
Bug fixes for CifWriter with symmetry.
Bug fixes for surface generation and reactions.
Monty requirement increased.

v3.2.1

Fix wrong U value for Ce and Eu.
Properly handle empty multiline strings in Cif
Add ability to get specific data in MPRester.get_entries. Make all get_entry methods consistent in kwargs.

v3.2.0

Force conversion to an actual list in selective dynamics and velocities in Poscar.
fix small bug in BSPlotter (wrong ylim)
Elastic tensor parsing in Outcar

v3.1.9

Fix scripts.

v3.1.7

Bug fixes for MPRester.
Ensure correct monty version requirement in setup.py.

v3.1.6

Rudimentary PWSCF output reading.
Fix ASE support.
Support for WAVEDERF and reading multiple dielectricfunctions in vasprun.xml. (Miguel Dias Costa)

v3.1.5

Move vasp.vasp*put to vasp.*puts. Also, maintain backwards compatibility with vaspio.vasp_*put

v3.1.4

Fix missing yaml files that have been moved.

v3.1.3

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.

v3.1.2

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.

v3.1.1

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

v3.1.0

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.

v3.0.13

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.

v3.0.10

Fix cartesian coord parsing in Poscar class.
Vasprun now works with non-GGA PBE runs
Misc bug fixes

v3.0.9

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.

v3.0.6

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-grained statistics.
Bug fixes and tweaks to linear assignment
Improved PymatgenTest class which provides a suite of test structures.
Speedups to Phase Diagram
Lots of improvements to Gaussian support (Nicolas Dardenne) and Abinit IO (Matteo).
Lots of Py3k minor updates.
Updated doc for Diffusion anaylzer. Invert sq_disp_ions for more intuitive handling.

v3.0.2

Consistent use of unicode throughout pymatgen.
Minor bug fixes.

v3.0.1

Minor bug fixes for cifio.
Py3k updates for abinitio.

v3.0.0

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.

v2.10.6

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

v2.10.5

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.

v2.10.3

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.

v2.10.2

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.

v2.10.1

Minor fix for monty requirements in setup.py.

v2.10.0

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.

v2.9.14

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.

v2.9.13

Urgent bug fix for missing compatibility yamls.

v2.9.12

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.

v2.9.11

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

v2.9.10

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.

v2.9.9

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

v2.9.8

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)

v2.9.7

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

v2.9.6

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.

v2.9.5

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

v2.9.4

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).

v2.9.3

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).

v2.9.2

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

v2.9.1

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

v2.9.0

Updates to support ABINIT 7.6.1 (by Matteo Giantomassi).
Vastly improved docs.
Refactoring to move commonly used Python utility functions to Monty package, which is now a dependency for pymatgen.
Minor fixes and improvements to DiffusionAnalyzer.
Many bug fixes and improvements.

v2.8.10

Refactoring of qchemio module (by Xiaohui Qu).

v2.8.9

qchemio module (by Xiaohui Qu).

v2.8.8

Minor bug fix release for Structure species substitution methods.

v2.8.7

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

v2.8.6

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

v2.8.4

Completely revamped Compatibility/Correction system which improves readability (Shyue Ping Ong/Anubhav Jain/Sai Jayaraman). This change is backwards compatible for the most part.

v2.8.3

Big fix release for json dumping for unitized floats.

v2.8.2

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.

v2.8.1

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

v2.8.0

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 :mod:`pymatgen.core.units` and the :doc:`examples </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).

v2.7.9

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.

v2.7.7

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.

v2.7.6

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

v2.7.5

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

v2.7.4

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).

v2.7.2

Minor bug fix release to fix some rare errors in very high dimensional phase diagrams. Requires new pyhull version (1.3.8).

v2.7.1

Major backwards-incompatible change. With effect from v2.7.1, the default Structure and Molecule classes are now mutable objects. All functionality in the :mod:`pymatgen.core.structure_modifier` has been ported over to the new mutable classes. This change was implemented because the immutability of Structure and Molecule has resulted in very awkward code to make changes to them. The main cost of this change is that Structure and Molecule can no longer be used as dict keys (__hash__ has been set to None). However, we believe this is a minor cost given that we have rarely seen the use of Structure or Molecule as dict keys in any case. For the rare instances where such functionality is needed, we have provided the IStructure and IMolecule classes (where I indicates immutability) which will perform exactly the same way as the previous classes. With this change, the :mod:`pymatgen.core.structure_modifier` module is now deprecated and will be removed in a future version.
read_structure and write_structure now supports pymatgen's json serialized structures.
read_mol and write_mol functions now available (analogues of read_structure and write_structure for molecules)

v2.7.0

Beta support for ABINIT input and output via pymatgen.io.abinitio (courtesy of the excellent work of Matteo Giantomassi).
Properties are now checked when comparing two Species for equality.
MaterialsProjectVaspInputSet is now renamed to MPVaspInputSet for easier typing. The old input sets have been deprecated.
New VaspInputSets for MPStatic, MPNonSCF, MITMD which supports uniform grid, bandstructure and molecular dynamics calculations. The MD input set uses MIT parameters for speed.
A beta DiffusionAnalysis class in the apps package.
A revised KPOINT grid algorithm that generates more reasonable meshes.
A guided install script is now provided for Mac and Linux users.

v2.6.6

Updates to feffio (credit: Alan Dozier)
Added detailed installation instructions for various platforms.
Support for charge and spin multiplicity in Molecule. Expanded methods available in Molecule.
Added supercell matching capabilities to StructureMatcher.
More robust creation of PhaseDiagrams to take into account potential qhull precision errors.

v2.6.5

Added a command_line caller to do Bader charge analysis using Henkelmann et al.'s algorithm.
Bug fix for POSCAR parsing when title line is an empty string.
Added __rmul__ operator for Composition.
Vastly expanded available aliases.

v2.6.4

Bug fixes for selective dynamics in Poscar.
Improved Procar parsing to support both simple and detailed PROCARs.

v2.6.3

Added new MaterialsProject REST interfaces for submit/query/delete_snl (currently open in beta for collaborators only).
Added support for new MaterialsProject REST method get_stability.
Added aliases for PhaseDiagram, GrandPotentialPhaseDiagram, PDAnalyzer and PDPlotter in pymatgen.phasediagrams.
Improvements to StructureMatcher: stol (site - tolerance) redefined as a fraction of the average length per atom. Structures matched in fractional space are now also matched in cartesian space and a rms displacement normalized by length per atom can be returned using the rms_dist method.

v2.6.2

Site and PeriodicSite now uses a Composition mapping type to represent the species and occupancy, instead of a standard dict.
Bug fix for reading and re-writing out of Potcars.
VaspInputSet now supports MSONable framework.
Strain cell option in StructureEditor.
Miscellaneous bug fixes and speedups.

v2.6.1

Use requests.Session in MPRester for connection pooling and code simplicity.
Support for "with" context manager in MPRester.
Updated periodic table data to correct errors in Ru, Tc and other elements.
New methods in Lattice to obtain Wigner-Seitz cell and Brillouin Zone.
Miscellaneous bug fixes and speedups.

v2.5.5

Bug fix release for cifio for rhombohedral structures.
Miscellaneous bug fixes and speedups.

v2.5.4

Vastly improved Gaussian input file parsing that supports more varieties of input specifications.
StructureNL now supports molecules as well as structures.
Updated atomic and vdw radius for Elements.
Miscellaneous bug fixes and speedups.

v2.5.3

Bug fix for StructureNotationalLanguage.
Support for LDA US potential. matgenie.py script option to generate POTCARs.
Beta version of StructureNotationLanguage, a markup format for Structure data with metadata such as authors and references. (Anubhav Jain)
Vasprun parsing now parses dielectric constant where available. (Geoffroy Hautier)
New custom ipython shell script for pymatgen.
Miscellaneous bug fixes and speedups.

v2.5.1

Bug fixes for primitive cell finder.
Remove deprecated use_external_qhull option in PhaseDiagram classes.
Miscellaneous bug fixes and speedups.

v2.5.0

Added optimization package with linear assignment class.
Improved robustness of StructureMatcher using linear assignment.
Improved primitive cell search (faster and more robust).
Cleanup of deprecated methods, including pymatgen.alchemy.materials.TransformedMaterial.undo/redo_last_transformation, pymatgen.core.site.Site.distance_and_image_old, Poscar.struct, StructureFitter and tests.
Miscellaneous bug fixes and speedups.

v2.4.3

Bug fix for StructureMatcher.
Miscellaneous speedups.

v2.4.0

New StructureMatcher that effectively replaces StructureFitter. Orders of magnitude faster and more robust. StructureFitter is now deprecated.
Vastly improved PrimitiveCellTransformation.
A lot of core methods have been rewritten to take advantage of vectorization in numpy, resulting in orders of magnitude improvement in speed.
Miscellaneous bug fixes and speedups.

v2.3.2

More utilities for working with Periodic Boundary Conditions.
Improved MPRester that supports more data and a new method of specifying the API key for heavy users via a MAPI_KEY environment variable. Please refer to the :doc:`usage pages </usage>` for more information.
Vastly improved POTCAR setup script in scripts directly that is now installed as part of a default pymatgen installation.
Miscellaneous bug fixes and speedups.

v2.3.1

Significant improvements to the high-level interface to the Materials API. New interface provides more options to make it easier to get structures and entries, better warnings and error handling. It uses the requests library for a cleaner API.
Bug fix for VolumetricData parsing and methods such as CHGCAR and LOCPOT. Previously, the parsing was done incorrectly because VASP actually provides data by running through the x-axis first, followed by y, then z.
Bug fix for reverse_readline so that it works for gzipped and bzipped strucutures (courtesy of Anubhav Jain).
Fix "lossy" composition to_dict method. Now composition.to_dict properly returns a correct species string as a key for compositions using species, instead of just the element symbols.
Miscellaneous bug fixes.

v2.3.0

Remove usage of scipy and external qhull callers. Now uses pyhull package. Please note that this change implies that the pyhull package is now a required dependency. If you install pymatgen through the usual easy_install or pip install methods, this should be taken care of automatically for you. Otherwise, please look for the pyhull package on PyPI to download and install it.
Miscellaneous bug fixes.

v2.2.6

Brand new beta bond valence analyzer based on a Maximum A Posteriori algo using data-mined ICSD data.
Speed up and improvements to core classes.
Improved structure fitter (credits to Geoffroy Hautier).
Brand new entry_tools module (pymatgen.entries.entry_tools).
Vastly improved Outcar parser based on reverse parsing that speeds up reading of OUTCAR files by orders of magnitude.
Miscellaneous bug fixes.

v2.2.4

Fixed bug in hexagonal cell KPOINTS file generation.
New RelaxationAnalyzer to compare structures.
New beta bond valence analyzer.
Miscellaneous bug fixes.

v2.2.3

New filter framework for filtering structures in pymatgen.alchemy.
Updated feff io classes to support FEFF 9.6 and other code improvements.
Miscellaneous bug fixes.

v2.2.2

Bug fix release for REST interface.
Improvements to unittests.

v2.2.1

Improvements to feffio.
Master matgenie.py script which replaces many analysis scripts.
More memory efficient parsing of VolumetricData.
Beta version of structure prediction classes.
Changes to MPRester to work with v1 release of the Materials API.
Miscellaneous bug fixes and speed improvements.

v2.2.0

Beta modules (pymatgen.io.feffio) for io for FEFF, courtesy of Alan Dozier.
New smartio module that intelligently reads structure input files based on file extension.
Spglib_adaptor module has been renamed to finder for brevity.
Upgraded spglib to version 1.2.2. Improved handling of spglib install on Mac OS X and Solaris.
Major cleanup of code for PEP8 compliance.
Cssr module now supports reading of input files.
Miscellaneous bug fixes and speed improvements.

v2.1.2

Brand new CompoundPD class that allows the plotting of phase diagrams that do not have elements as their terminal points.
Spglib is now completely integrated as part of the setup.py installation.
Major (but completely backwards compatible) refactoring of sites and vaspio.
Added a EnumerateStructureTransformation with optional dependency on the enum library by Gus Hart. This provides a robust way to enumerate derivative structures,
Implemented LLL lattice reduction algorithm. Also added option to sanitize a Structure on copy.
Bug fix for missing Compatibility file in release distribution.
Vastly improved StructureFitter which performs cell reduction where necessary to speed up fitting.
Miscellaneous bug fixes and speed improvements.

v2.0.0

Brand new module (pymatgen.matproj.rest) for interfacing with the MaterialsProject REST interface.

Useful aliases for commonly used Objects, similar in style to numpy. Supported objects include Element, Composition, Structure, Molecule, Spin and Orbital. For example, the following will now work:

import pymatgen as mg
# Elemental Si
fe = mg.Element("Si")
# Composition of Fe2O3
comp = mg.Composition("Fe2O3")
# CsCl structure
structure = mg.Structure(mg.Lattice.cubic(4.2), ["Cs", "Cl"],
                         [[0, 0, 0], [0.5, 0.5, 0.5]])

New PDAnalyzer method to generate chemical potential maps.
Enhanced POSCAR class to support parsing of velocities and more formatting options.
Reorganization of Bandstructure module. Beta support for projected bandstructure and eigenvalues in vaspio and electronic_structure.
Miscellaneous bug fixes and speed improvements.

v1.9.0

Completely new json encoder and decoder that support serialization of almost all pymatgen objects.
Simplification to Borg API utilizing the new json API.
Bandstructure classes now support spin-polarized runs.
Beta classes for battery (insertion and conversion) analysis.

v1.8.3

spglib_adaptor now supports disordered structures.
Update to support new spglib with angle_tolerance.
Changes to Borg API to support both file and directory style paths.
Speed up for COMPLETE_ORDERING algo for PartialRemoveSpecieTransformation.

v1.8.1

Revamped transmuter classes for better readability and long term support.
Much improved speed for PartialRemoveSpecieTransformations.
Misc bug fixes.

v1.8.0

Support for additional properties on Specie (Spin) and Site (magmom, charge).
Molecule class to support molecules without periodicity.
Beta io class for XYZ and GaussianInput.

v1.7.2

Bug fixes for vaspio_set and compatibility classes.

v1.7.0

Complete reorganization of modules for electronic structure.
Beta of band structure classes.
Misc improvements to vaspio classes.
Bug fixes.

v1.6.0

Beta of pymatgen.borg package implemented for high-throughput data assimilation.
Added ComputedEntry classes for handling calculated data.
New method of specifying VASP pseudopotential location using a VASP_PSP_DIR environment variable.
Bug fix for pymatgen.symmetry
Ewald sum speed up by factor of 2 or more.

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