CHANGES.md

---
layout: default
title: Change Log
nav_order: 4
---

# Changelog

## v2026.3.23

- PR #4595 Major reorganization of pymatgen repo. Now core functionality is in a separate pymatgen-core repo and released as a separate pypi package. All changes should be backwards compatible, i.e., pip install pymatgen still provides all the same functionality as before. (by @shyuep)
- PR #4592 Rewrite LOBSTER parsers with memory-efficient streaming architecture (by @tomdemeyere)
- PR #4589 Pass `process_entries` arguments to `solid_compat` in `MaterialsProjectAqueousCompatibility` (by @lkkmpn)
- PR #4584 Fix unstable sorting in phase diagram (by @DanielYang59)
- PR #4581 Add yaml for smoothPES correction (by @CompRhys)
- PR #4579 Allow for alchemical pseudoatoms in Abinit (by @GkAntonius)
- PR #4567 Symmetry no longer necessary to have first in geometry directive for NwChem (by @francescalb)
- PR #4565 Remove jupyter from dev dependency group (by @DanielYang59)
- PR #4555 Update MatPESStaticSet docstring: PBE_54 to PBE_64 (by @ThomasWarford)
- PR #4546 Speed/stability improvements to chemenv/coordination_environments (by @lutfia95)
- PR #4545 Chargemol fixes for VASP POTCAR 64 (by @esoteric-ephemera)
- PR #4542 Fix types for entry processing in phase diagram and compatibility (by @janosh)
- PR #4541 PatchedPhaseDiagram mimic PhaseDiagram Serialization (by @CompRhys)
- PR #4535 Minor fixes to typing for `io.vasp.outputs.Wavecar` and `io.wannier90.Unk` (by @mturiansky)
- PR #4531 Deprecate `CifParser` init support of `filename` as `StringIO` (by @DanielYang59)
- PR #4530 Fix icet kwargs (by @esoteric-ephemera)
- PR #4527 Replace assert with proper exceptions (by @DanielYang59)
- PR #4526 `VolumetricData.copy` preserve subclass type (by @DanielYang59)
- PR #4525 Minor type cleanup of `io.common` (by @DanielYang59)
- PR #4522 `Incar.proc_val` reuse `incar_parameters.json` to determine types (by @DanielYang59)
- PR #4521 Add ISEARCH parameter to incar_parameters.json (by @kavanase)
- PR #4520 Avoid dict mutation in VaspInputSet.structure setter (by @janosh)
- PR #4518 Enhance INCAR parsing: handle multi-line string and line continuation with backslash, fix handling of `!` as comment marker (by @DanielYang59)
- PR #4516 Python 3.14 support (by @DanielYang59)
- PR #4515 Update periodic table data: common oxidation states, critical temperature and electrical resistivity (by @DanielYang59)
- PR #4514 Fix `Ion.as_reduced_dict` doesn't reduce charge (by @DanielYang59)
- PR #4511 Fix PD Plotter to only show lowest energy for unstable composition (by @DanielYang59)
- PR #4507 Add references/source to periodic table data (by @DanielYang59)
- PR #4498 Allow for setting termination_ftol for film and substrate slabs separately (by @jinlhr542)
- PR #4482 Simplify and clean up LobsterNeighbors (by @naik-aakash)
- PR #4481 Fix icohpcollection & add missing keyword in Lobsterin (by @naik-aakash)
- PR #4414 Phase Diagram Serialization Improvement (by @felix-adams)
- PR #4148 Fix consideration of translation symmetry for some (extremely rare) edge cases in LobsterEnv (by @JaGeo)

## v2025.10.7

- PR #4503 Replace print statements with logging across library code and tests (by @DanielYang59)
- PR #4510 Suppress noisy RuntimeWarning messages from BoltzTraP2 during transport analysis (by @DanielYang59)
- PR #4512 Ensure source distribution (sdist) is published to PyPI alongside wheels (by @DanielYang59)
- PR #4494 Re-enable mypy “misc” rule and perform minor documentation, typing, and test cleanups (by @DanielYang59)
- PR #4491 Deprecate projected_magnetisation in favor of projected_magnetization (US spelling) (by @DanielYang59)
- PR #4493 Composition.get_wt_fraction now returns a float instead of FloatWithUnit (by @DanielYang59)
- PR #4496 Implement __rtruediv__ for FloatWithUnit and fix ArrayWithUnit losing unit_type on unpickling; add unit tests (by @DanielYang59)
- PR #4497 Improve pmg CLI tests; fix pmg diff header ordering and resolve pmg view color handling error (by @DanielYang59)
- PR #4490 Replace internal linear_assignment with scipy.optimize.linear_sum_assignment (by @DanielYang59)
- PR #4440 Add parsing/storage of vibrational modes and vibrational energy components to JDFTXOutfileSlice with tests (by @benrich37)
- PR #4487 Fix variable name collision in TranslateSitesTransformation.apply_transformation; strengthen test to catch issue (by @Rastow)
- PR #4463 Remove dev-only “ci” optional dependency group, migrate CI to uv, and update markdown docs (by @DanielYang59)
- PR #4447 Correct has_cobicar detection when NcICOBILIST is present in LOBSTER outputs (by @tomdemeyere)
- PR #4469 Loosen requests version pin and fix deprecations/new ruff issues (by @DanielYang59)
- PR #4479 Introduce JdftxInputSet (moved from atomate2), add base YAML preset and basic tests (by @cote3804)
- PR #4484 Make jdftx.outputs compatible with Python versions prior to 3.11 by removing starred-subscript usage (by @DanielYang59)
- PR #4473 Fix labels and values in NEBAnalysis plots, prefer exact glob matches, and deprecate spline_options in favor of zero_slope_saddle flag (by @DanielYang59)
- PR #4260 Move FHI-aims IO to external package (pyfhiaims) to reduce duplication and ease maintenance (by @tpurcell90)
- PR #4476 Patch ReDOS vulnerability in GaussianInput.from_string (by @lbluque)
- PR #4449 Address ruff PERF401 (manual list comprehension) for minor performance/cleanliness improvements (by @DanielYang59)
- PR #4448 Remove sensitivity to trailing newline in LOBSTER output parsers; improves robustness (by @DanielYang59)
- PR #4454 Correct documentation for Element density_of_solid and molar volume units (by @DanielYang59)
- PR #4455 Cache optional dependency installs in CI for macOS/Ubuntu; enable mcsqs and pyzeo tests; convert some skips to xfail (by @DanielYang59)
- PR #4461 Allow numpy arrays for selective dynamics in Structure and add tests; ensure JSON roundtrips (by @DanielYang59)
- PR #4464 Fix typo referencing site.species in SpacegroupAnalyzer.get_primitive_standard_structure (by @boyoungzheng)
- PR #4446 Improve performance of Species.__str__ by reducing redundant attribute lookups (by @kavanase)
- PR #4438 Add basic S3 object retrieval support to the pymatgen user agent for large MP datasets (by @esoteric-ephemera)

## v2025.6.14

- Treat LATTICE_CONSTRAINTS as is for INCARs.
- PR #4425 `JDFTXOutfileSlice.trajectory` revision by @benrich37
    Major changes:
    - feature 1: `JDFTXOutfileSlice.trajectory` is now initialized with `frame_properties` set
    -- `JOutStructure.properties` filled with relevant data for `frame_properties`
    -- More properties added to `JOutStructure.site_properties`
    ## Todos
    - Remove class attributes in `JOutStructure` now redundant to data stored in `JOutStructure.properties` and `JOutStructure.site_properties`
- PR #4431 Single source of truth for POTCAR directory structure by @esoteric-ephemera
    Modifies the pymatgen CLI to use the same POTCAR library directory structure as in `pymatgen.io.vasp.inputs` to close #4430. Possibly breaking from the CLI side (the directory structure will change)
    Pinging @mkhorton since #4424 was probably motivated by similar concerns?
- PR #4433 Speed up symmetry functions with faster `is_periodic_image` algorithm by @kavanase
    I noticed that in some of our `doped` testing workflows, `SpacegroupAnalyzer.get_primitive_standard_structure()` is one of the main bottlenecks (as to be expected). One of the dominant cost factors here is the usage of `is_periodic_image`, which can be expensive for large structures due to many `np.allclose()` calls.
    This PR implements a small change to instead use an equivalent (but faster) pure Python loop, which also breaks early if the tolerance is exceeded.
    In my test case, this reduced the time spent on `is_periodic_image` (and thus `SpacegroupAnalyzer.get_primitive_standard_structure()`) from 35s to 10s.
- PR #4432 Fingerprint sources by @JaGeo
    Add correct papers to tanimoto fingerprints
- PR #4061 Fix branch directory check in `io.vasp.outputs.get_band_structure_from_vasp_multiple_branches` by @DanielYang59
    ### Summary
    - Fix branch directory check in `io.vasp.outputs.get_band_structure_from_vasp_multiple_branches`, to fix #4060
    - [ ] Improve unit test (waiting for data, I don't have experience with "VASP multi-branch bandstructure calculation")
- PR #4409 Packmol constraints by @davidwaroquiers
    Added possibility to set individual constraints in packmol.
    Added some sanity checks.
    Added unit tests.
- PR #4428 Fixes a bug in `NanoscaleStability.plot_one_stability_map` and `plot_all_stability_map`. by @kmu
    Major changes:
    - Replaced incorrect `ax.xlabel()` and `ax.ylabel()` calls with correct `ax.set_xlabel()` and `ax.set_ylabel()`.
    - Added `ax.legend()` to `plot_all_stability_map` so that labels passed via `ax.plot(..., label=...)` are displayed.
    - Added `test_plot()` to `test_surface_analysis.py`.
- PR #4424 Add additional name mappings for new LDA v64 potcars by @mkhorton
    As title.
- PR #4426 Fix uncertainty as int for `EnergyAdjustment` by @DanielYang59
    - Avoid `==` or `!=` for possible float comparison
    - Fix uncertainty as int for `EnergyAdjustment` cannot generate repr:
    ```python
    from pymatgen.entries.computed_entries import EnergyAdjustment
    print(EnergyAdjustment(10, uncertainty=0))
    ```
    Gives:
    ```
    Traceback (most recent call last):
    File "/Users/yang/developer/pymatgen/test_json.py", line 25, in <module>
    print(EnergyAdjustment(10, uncertainty=0))
    File "/Users/yang/developer/pymatgen/src/pymatgen/entries/computed_entries.py", line 108, in __repr__
    return f"{type(self).__name__}({name=}, {value=:.3}, {uncertainty=:.3}, {description=}, {generated_by=})"
    ^^^^^^^^^^^^^^^^^
    ValueError: Precision not allowed in integer format specifier
    ```
- PR #4421 Cache `Lattice` property (`lengths/angles/volume`) for much faster `Structure.as_dict` by @DanielYang59
    ### Summary
    - `lengths/angles/volume` of `Lattice` would now be cached, related to #4385
    - `verbosity` in `as_dict` of `PeriodicSite/Lattice` now explicitly requires literal 0 or 1 to be consistent with docstring, instead of checking `if verbosity > 0` (currently in grace period, only warning issued) https://github.com/materialsproject/pymatgen/blob/34608d0b92166e5fc4a9dd52ed465ae7dccfa525/src/pymatgen/core/lattice.py#L904-L905
    ---
    ### Cache frequently used `Lattice` properties
    Currently `length/angles/volume` is not cached and is frequently used, for example accessing all lattice parameter related property would lead to `length/angles` being repeatedly calculated: https://github.com/materialsproject/pymatgen/blob/34608d0b92166e5fc4a9dd52ed465ae7dccfa525/src/pymatgen/core/lattice.py#L475-L524
    `structure.as_dict` now around 8x faster
    Before (1000 structure, each has 10-100 atoms):
    ```
    Total time: 3.29617 s
    File: create_dummp_json_structure.py
    Function: generate_and_save_structures at line 34
    Line #      Hits         Time  Per Hit   % Time  Line Contents
    ==============================================================
    34                                           @profile
    35                                           def generate_and_save_structures(n, output_dir):
    36         1         20.0     20.0      0.0      os.makedirs(output_dir, exist_ok=True)
    37
    38      1001        222.0      0.2      0.0      for i in range(n):
    39      1000     291789.0    291.8      8.9          structure = generate_dummy_structure()
    40      1000        583.0      0.6      0.0          filename = f"structure_{i:04d}.json.gz"
    41      1000       1942.0      1.9      0.1          filepath = os.path.join(output_dir, filename)
    42
    43      2000     224549.0    112.3      6.8          with gzip.open(filepath, "wb") as f:
    44      1000    2761900.0   2761.9     83.8              dct = structure.as_dict()
    45      1000      15163.0     15.2      0.5              f.write(orjson.dumps(dct))
    ```
    Now:
    ```
    Total time: 0.949622 s
    File: create_dummp_json_structure.py
    Function: generate_and_save_structures at line 34
    Line #      Hits         Time  Per Hit   % Time  Line Contents
    ==============================================================
    34                                           @profile
    35                                           def generate_and_save_structures(n, output_dir):
    36         1         37.0     37.0      0.0      os.makedirs(output_dir, exist_ok=True)
    37
    38      1001        195.0      0.2      0.0      for i in range(n):
    39      1000     286696.0    286.7     30.2          structure = generate_dummy_structure()
    40      1000        511.0      0.5      0.1          filename = f"structure_{i:04d}.json.gz"
    41      1000       1843.0      1.8      0.2          filepath = os.path.join(output_dir, filename)
    42
    43      2000     214130.0    107.1     22.5          with gzip.open(filepath, "wb") as f:
    44      1000     431677.0    431.7     45.5              dct = structure.as_dict()
    45      1000      14533.0     14.5      1.5              f.write(orjson.dumps(dct))
    ```
    ---
    Also note `lattice` (the performance bottleneck) is not used in the dict for site: https://github.com/materialsproject/pymatgen/blob/34608d0b92166e5fc4a9dd52ed465ae7dccfa525/src/pymatgen/core/structure.py#L2856-L2857
    So we could modify `as_dict` to control whether lattice would be generated at all
    This could reduce the runtime slightly so I guess it's not worth the effort:
    ```
    Total time: 0.867376 s
    ```
- PR #4391 Add custom as_dict/from_dict method for proper initialization of attributes of IcohpCollection by @naik-aakash
    Currently `IcohpCollection` instance is not serialized correctly, thus I added custom  from_dict  and as_dict methods here.

## v2025.5.28

- PR #4411 Add `orjson` as required dependency as default JSON handler when custom encoder/decoder is not needed by @DanielYang59
- PR #4417 adding radd dunder method to Volumetric data + test_outputs by @wladerer
- PR #4418 `JDFTXOutfileSlice` Durability Improvement by @benrich37
    Major changes:
    - feature 1: Improved durability of `JDFTXOutfileSlice._from_out_slice` method (less likely to error out on unexpected termination)
    -- So long as one step of electronic minimization has started on an out file slice, parsing shouldn't error out
    - fix 1: Allow partially dumped eigstats
    - fix 2: Added missing optical band gap dumped by eigstats
    - fix 3: Protect the final `JOutStructure` in initializing a `JOutStructures` with a try/except block
    - fix 4: Detect if positions were only partially dumped and revert to data from `init_structure` in `JOutStructure`
    - fix 5: Prevent partially dumped matrices from being used in initializing a `JOutStructure`
    ## Todos
    - feature 1: Ensure parse-ability as long as a `JDFTXOutfileSlice.infile` can be initialized
- PR #4419 Fix Molecule.get_boxed_structure when reorder=False by @gpetretto
- PR #4416 `JDFTXInfile` Comparison Methods by @benrich37
    Major changes:
    - feature 1: Convenience methods for comparing `JDFTXInfile` objects
    -- `JDFTXInfile.is_comparable_to`
    --- Returns True if at least one tag is found different
    --- Optional arguments `exclude_tags`, `exclude_tag_categories`, `ensure_include_tags` to ignore certain tags in the comparison
    ---- `exclude_tag_categories` defaults to `["export", "restart", "structure"]` as `"export"` and `"restart"` are very rarely pertinent  to comparability, `"structure"` as subtags of this category are generally the one thing being intentionally changed in comparisons (ie different local minima or a slab with/without an adsorbate)
    -- `JDFTXInfile.get_filtered_differing_tags`
    --- What is used in `JDFTXInfile.is_comparable_to` to get filtered differing tags between `JDFTXInfile` objects
    --- Convenient as a "verbose" alternative to `JDFTXInfile.is_comparable_to`
    -- `AbstractTag.is_equal_to` and `AbstractTag._is_equal_to`
    --- Used in tag comparison for finding differing tags
    --- `AbstractTag._is_equal_to` is an abstract method that must be implemented for each `AbstractTag` inheritor
    - feature 2: Default `JDFTXInfile` object `pymatgen.io.jdftx.inputs.ref_infile`
    -- Initialized from reading default JDFTx settings from `pymatgen.io.jdftx.jdftxinfile_default_inputs.default_inputs: dict`
    -- Used in `JDFTXInfile.get_differing_tags_from` for tags in `self` missing from `other` that are identical to the default setting
    - fix 1: Re-ordered contents of `JDFTXInfile` to follow the order: magic methods -> class methods / transformation methods -> validation methods -> properties -> private methods
    - fix 2: Checking for `'selective_dynamics'` in `site_properties` for a `Structure` passed in `JDFTXInfile.from_structure` (used if `selective_dynamics` argument left as `None`)
    ## Todos
    - feature 1: Add examples to documentation on how to properly use new comparison methods
    - feature 2: Improve the mapping of `TagContainer`s to their default values
    -- The current implementation of comparison for tags to default values only works if the tag as written exactly matches the full default value - at the very least the missing subtags of a partially filled `TagContainer` needs to be filled with the default values before comparing to the full default value
    -- Some subtags also change depending on the other subtags present for a particular tag (ie convergence threshold depending on algorithm specified for `'fluid-minimize'`, so an improved mapping for dynamic default values needs to be implemented
- PR #4413 `JDFTXOutputs.bandstructure: BandStructure` by @benrich37
    Major changes:
    - feature 1: Added 'kpts' storable variable to JDFTXOutputs
    -- Currently only able to obtain from the 'bandProjections' file
    - feature 2: Added `bandstructure` attribute to JDFTXOutputs
    -- Standard pymatgen `BandStrucure` object
    -- Request-able as a `store_var`, but functions slightly differently
    --- Ensures 'eigenvals' and 'kpts' are in `store_vars` and then is deleted
    -- Initialized if JDFTXOutputs has successfully stored at least 'kpts' and 'eigenvals'
    -- Fills `projections` field if also has stored 'bandProjections'
    - feature 3: Added `wk_list` to `JDFTXOutputs`
    -- List of weights for each k-point
    -- Currently doesn't have a use, but will be helpful for `ElecData` initializing in [`crawfish`](https://github.com/benrich37/crawfish)
    ## Todos
    - feature 1: Add reading 'kpts' from the standalone 'kPts' file dumped by JDFTx
    - feature 2: Outline how we might initialize `BandStructureSymmLine`(s) for calculations with explicitly defined 'kpoint' tags, as using 'kpoint's instead of `kpoint-folding` is most likely an indicator of a band-structure calculation
- PR #4415 speed-up Structure instantiation by @danielzuegner
    This PR speeds up the instantiation of `Structure` objects by preventing hash collisions in the `lru_cache` of `get_el_sp` and increasing its `maxsize`. The issue is that currently `Element` objects are hashed to the same value as the integer atomic numbers (e.g., `Element[H]` maps to the same hash as `int(1)`). This forces the `lru_hash` to perform an expensive `__eq__` comparison between the two, which reduces the performance of instantiating many `Structure` objects. Also here we increase the `maxsize` of `get_el_sp`'s `lru_cache` to 1024 for further performance improvements.
    This reduces time taken to instantiate 100,000 `Structure` objects from 31 seconds to 8.7s (avoid hash collisions) to 6.1s (also increase `maxsize` to 1024).
- PR #4410 JDFTx Inputs - boundary value checking by @benrich37
    Major changes:
    - feature 1: Revised boundary checking for input tags
    -- Added a `validate_value_bounds` method to `AbstractTag`, that by default always returns `True, ""`
    -- Added an alternate `AbstractNumericTag` that inherits `AbstractTag` to implement `validate_value_bounds` properly
    --- Changed boundary storing to the following fields
    ---- `ub` and `lb`
    ----- Can either be `None`, or some value to indicate an upper or lower bound
    ---- `ub_incl` and `lb_incl`
    ----- If True, applies `>=` instead of `>` in comparative checks on upper and lower bounds
    -- Switched inheritance of `FloatTag` and `IntTag` from `AbstractTag` to `AbstractNumericTag`
    -- Implemented `validate_value_bounds` for `TagContainer` to dispatch checking for contained subtags
    -- Added a method `validate_boundaries` to `JDFTXInfile` to run `validate_value_bounds` on all contained tags and values
    -- Added `validate_value_boundaries` argument for initialization methods of `JDFTXInfile`, which will run `validate_boundaries` after initializing `JDFTXInfile` but before returning when True
    --- Note that this is explicitly disabled when initializing a `JDFTXInfile` from the input summary in a `JDFTXOutfileSlice` - boundary values may exist internally in JDFTx for non-inclusive bounded tags as the default values, but cannot be passed in the input file. For this reason, errors on boundary checking must be an easily disabled feature for the construction and manipulation of a  `JDFTXInfile`, but out-of-bounds values must never be written when writing a file for passing to JDFTx.
    ## Todos
    - feature 1
    -- Implement some way boundary checking can run when adding tags to a pre-existing `JDFTXInfile` object
    --- boundary checking is currently only run when initializing from a pre-existing collection of input tags
    --- writing this into `JDFTXInfile.__setitem__` is too extreme as it would require adding an attribute to `JDFTXInfile` to allow disabling the check
    --- the better solution would be to implement a more obvious user-friendly method for reading in additional inputs so that the user doesn't need to learn how to properly write out the dictionary representation of complicated tag containers.
    -- Fill out reference tags for other unimplemented boundaries
- PR #4408 `to_jdftxinfile` method for JDFTXOutfile by @benrich37
    Major changes:
    - feature 1: Method `to_jdftxinfile` for JDFTXOutfile(Slice)
    -- Uses internal `JDFTXInfile` and `Structure` to create a new `JDFTXInfile` object that can be ran to restart a calculation
    - feature 2: Method `strip_structure_tags` for `JDFTXInfile`
    -- Strips all structural tags from a `JDFTXInfile` for creating equivalent `JDFTXInfile` objects with updated associated structures
    - fix 1: Changing 'nAlphaAdjustMax' shared tag from a `FloatTag` to an `IntTag`
    - fix 2: Adding an optional `minval` field for certain `FloatTag`s which prevent writing error-raising values
    -- Certain tag options in JDFTx can internally be the minimum value, but trying to pass the minimum value will raise an error
    ## Todos
    - feature 1: Testing for the `to_jdftxinfile`
    -- I know the function works from having used it, but I haven't written in an explicit test for it yet.
    - fix 2: Look through JDFTx source code and identify all the numeric tag value boundaries and add them to the FloatTag. This will likely require generalizing how boundaries are tested as a quick glance (see [here](https://github.com/shankar1729/jdftx/blob/master/jdftx/commands/fluid.cpp#L378)) shows there are tags that actually do use the `>=` operator
    - Unrelated: Reduce bloat in outputs module
    -- Remove references to deprecated fields
    -- Begin phasing out redundant fields
    --- i.e. `JDFTXOutfile.lattice` redundant to `JDFTXOutfile.structure.lattice.matrix`
    -- Generalize how optimization logs are stored in outputs module objects
    --- Fields like `grad_K` are part of a broad group of values that can be logged for an optimization step, and the fields present in each log varies a lot more than I previously thought when I initially wrote the JDFTx outputs module. Generalizing how these are stored into a dictionary of arbitrary keys should make the outputs module more robust, as well as helping reduce the bloat in the outputs module.
- PR #4407 JDFTXInfile addition (`__add__`) method tweak by @benrich37
    Changing addition method - now infiles with shared keys will either concatenate their inputs if the key is for a repeatable tag, or change to whatever value is in the second infile if it is not a repeatable tag. A bare minimum `if subval in params[key]` check is done to avoid adding duplicate values. This seems like something the `set` built-in could help with, but since the sub-values are dictionaries, using `set` is a little more difficult
    Major changes:
    - fix 1: Addition of two JDFTXInfiles (`jif1 = jif2 + jif3`) no longer requires each `jif2` and `jif3` to have a unique set of tags
    -- For a non-repeatable tag 'key', `jif1['key'] == jif3['key']`
    -- For a repeatable-tag 'key', `jif1['key'] = jif2['key'] + [val for val in jif3['key'] if not val in jif2['key']`
    -- implemented in `src/pymatgen/io/jdftx/inputs.py`
    -- tested in `tests/io/jdftx/test_jdftxinfile.py`
    --- error raising test for conflicting tag values removed
    ## Todos
    - fix 1: Add more robust checking for if two repeatable tag values represent the same information.
    -- This is likely fixed by implementing the pre-existing TODO - "Add default value filling like JDFTx does"
    - fix 2: Incorporate something to collapse repeated dump tags of the same frequency into a single value.
    -- The 'dump' tag currently can get bloated very quickly, as the newly implemented change for concatenating two repeatable tags will not detect that something like `{"End": {"State": True}}` is technically already in a list that contains something like `{"End": {"State": True, "Berry": True}}`
    -- A cleanup function that can convert `{'dump': [{"End": {"State": True, "BGW": True}}, {"End": {"State": True, "Berry": True}}]` into `{'dump': [{"End": {"State": True, "BGW": True, "Berry": True}}]` would fix this bloat risk
- PR #4404 Monoclinic Symmetry Handling Fix by @kavanase
    This issue is related to https://github.com/materialsproject/pymatgen/issues/1929 (for which a patch solution was added that fixed one case of this occurrence, but not in general).
    When handling monoclinic symmetry within `SpacegroupAnalyzer`, the standardisation attempts to reorder the lattice vectors depending on whether the alpha angle is >90 degrees or <90 degrees. If it is exactly 90 degrees, it defaults to the original lattice, however there was an issue with this implementation where it assumed that the beta and gamma angles were also 90 degrees (and so set the lattice matrix as `[[a, 0, 0], [0, b, 0], [0, 0, c]]`), which may not (and in most cases should not) be the case.
    This was causing weird behaviour for me where the volume of the primitive structures being returned by `SpacegroupAnalyzer` was different to `Structure.find_primitive()` (by a non-integer factor). I've added a test for this case, and also confirmed that the general implementation here works for the failure case noted in https://github.com/materialsproject/pymatgen/issues/1929
- PR #4406 `UFloat` update by @kavanase
    This is a minor addition to https://github.com/materialsproject/pymatgen/pull/4400.
    I found that there were some cases where an energy adjustment of `UFloat(0, 0)` were already present in `ComputedEntry.energy_adjustments`, avoiding the updated handling of setting `std_dev` to `np.nan` when it is 0 (and avoiding the `UFloat` warning about `std_dev` being 0).
- PR #4403 Ensure structure symmetrization in OrderDisorderedStructureTransformation by @esoteric-ephemera
    Close #4402 by ensuring that structures are always symmetrized when `symmetrized_structures = True` in `OrderDisorderedStructureTransformation`. Also allow for passing distance/angle precision kwargs to do on-the-fly symmetrization. Add tests
- PR #4401 JDFTXStructure - partial fix for special case lattice tags by @benrich37
    Major changes:
    - fix 1: `pymatgen.io.jdftx.inputs.JDFTXStructure`
    -- `JDFTXStructure.from_jdftxinfile` no longer assumes 'lattice' tag is provided in 3x3 matrix format
    -- Testing in `tests/io/jdftx/test_jdftxinfile.py` for `Structure <-> JDFTXStructure <-> JDFTXInfile` conversion for `JDFTXInfile` with newly implemented special case values for 'lattice' tag
    TODO:
    -  Implement `JDFTXStructure.from_jdftxinfile` for JDFTXInfile with special case tag 'lattice' value and non-identity value for 'latt-scale' tag
- PR #4400 Use `np.nan` instead of 0 for no uncertainty with `ufloat`, to avoid unnecessary warnings by @kavanase
    Closes #4386
- PR #4399 JDFTXOutfile `none_on_error` oversight fix by @benrich37
    - Fixing an error in `pymatgen/io/jdftx/outputs.py` that causes construction of a `JDFTXOutfile` to fail if none_on_error is turned on and the final `JDFTXOutfileSlice` in `slices` is None (ie a very common issue when parsing an interrupted job that hasn't restarted yet).
- PR #4397 JDFTx IO Module Overhaul by @benrich37
    - Revised typing for updated `mypy` criteria
    - Support for parsing JDFTx AIMD files
    - Expanded input tag support
- PR #4394 Updates to JDFTx inputs `generic_tags` helper module by @benrich37
    Major changes:
    - Phasing out use of redundant `TagContainer.multiline_tag` attribute
    -- (this change may cause problems without the corresponding changes in `jdftxinfile_master_format.py`, but all the tests still pass. Just in case, I will be prioritizing finishing merges for the JDFTx inputs module to avoid any untested consequences)
    - Fixing indentation on output of `TagContainer.write`
    - Removing the warning (and the test for this warning) on special constraints for "ion" tag
    -- Support for special constraints has been implemented on my fork and a PR for this support will soon be created
- PR #4392 Brute force order matcher speedup by @kavanase
    This is a small PR to add a `break_on_tol` option to `BruteForceOrderMatcher`, which allows one to massively speed up the molecule matching in cases where one just cares _if_ the molecules match within a given RMSD (rather than screening over _all_ possible permutations, to get the lowest possible RMSD).
    The speedup factor can be anywhere from 0% to several orders of magnitude, depending on the number of possible permutations and when a matching permutation is found.
    Also includes a small typo fix that for an error message that reference the original class name (in https://github.com/materialsproject/pymatgen/pull/1938) which was later renamed.
    I've also added some tests for this.
- PR #4393 Update JDFTx IO output utils private module by @benrich37
    Major changes:
    - function `get_colon_var_t1`
    -- Renaming to `get_colon_val`, but keeping an alias until renaming is updated outside this module
    -- Returning `np.nan` instead of `None` when "nan" is the value
    - updating `correct_geom_opt_type` for working with JDFTx AIMD out files
    - updating typing on array-construction functions
    - correcting ordering and syntax of orbital labels to exactly match JDFTx
- PR #4389 Adding missing reference options to JDFTx inputs submodule by @benrich37
    Beginning process of merging over stress-test updates, starting with missing options for JDFTx input files
    - Added missing DFT functional names
    - Added missing subtags for elec-minimize

## 2025.5.2

- Remove lxml since it is slower for many Vasprun parsing situations.

## v2025.5.1

- lxml is now used for faster Vasprun parsing.
- Minor bug fix for MPRester.get_entries summary_data for larger queries.
- New JSON for ptable with better value/unit handling (also slightly faster) (@DanielYang59)
- Handle missing trailing newline in ICOHPLIST.lobster (@alibh95)
- Updated MVLSlabSet with MPSurfaceSet parameters from atomate1 (@abhardwaj73)

## v2025.4.24

- Structure now has a calc_property method that enables one to get a wide range of elasticity, EOS, and phonon properties using matcalc. Requires matcalc to be
  installed.
- Bug fix and expansion of pymatgen.ext.matproj.MPRester. Now property_data is always consistent with the returned entry in get_entries. Summary data, which is not
  always consistent but is more comprehensive, can be obtained via a summary_data kwarg.
- PR #4378 Avoid merging if a structure has only one site by @kmu
    This PR fixes an error that occurs when calling `merge_sites` on a structure with only one site. For example:
- PR #4372 Reapply update to ptable vdw radii CSV source and JSON with CRC handbook by @DanielYang59
    - Update ptable vdw radii CSV source, to fix #4370
    - [x] Revert #4345 and apply changes to CSV
    vdw radii data source:
    > John R. Rumble, ed., CRC Handbook of Chemistry and Physics, 105th Edition (Internet Version 2024), CRC Press/Taylor & Francis, Boca Raton, FL.
    > If a specific table is cited, use the format: "Physical Constants of Organic Compounds," in CRC Handbook of Chemistry and Physics, 105th Edition (Internet Version 2024), John R. Rumble, ed., CRC Press/Taylor & Francis, Boca Raton, FL.

## v2025.4.20

- Updated `perturb` method to be in parity for Structure and Molecule.
- PR #4226 Fix file existence check in ChargemolAnalysis to verify directory instead. by @lllangWV
- PR #4324 GibbsComputedStructureEntry update to handle float temperature values by @slee-lab
- PR #4303 Fix mcl kpoints by @dgaines2
    Fixed errors in two of the k-points for the MCL reciprocal lattice (according to Table 16 in Setyawan-Curtarolo 2010)
    M2 and D1 aren't included in the recommended k-point path, but third-party software that plots k-point paths using pymatgen labelled M2 in the path instead of M1 due to it being the "same" k-point.
- PR #4344 Update "electron affinities" in `periodic_table.json` by @DanielYang59
- PR #4365 Python 3.13 support by @DanielYang59

## v2025.4.19

- MPRester.get_entries and get_entries_in_chemsys now supports property_data. inc_structure, conventional_only and
- PR #4367 fix perturb bug that displaced all atoms equally by @skasamatsu
- PR #4361 Replace `pybtex` with `bibtexparser` by @DanielYang59
- PR #4362 fix(MVLSlabSet): convert DIPOL vector to pure Python list before writing INCAR by @atulcthakur
- PR #4363 Ensure `actual_kpoints_weights` is `list[float]` and add test by @kavanase
- PR #4345 Fix inconsistent "Van der waals radius" and "Metallic radius" in `core.periodic_table.json` by @DanielYang59
- PR #4212 Deprecate `PymatgenTest`, migrate tests to `pytest` from `unittest` by @DanielYang59

## v2025.4.17

- Bug fix for list based searches in MPRester.

## v2025.4.16

- Major new feature and breaking change: Legacy MP API is no longer supported. Pymatgen also no longer support mp-api in the backend. Instead, Pymatgen's MPRester now
  has nearly 100% feature parity with mp-api's document searches. One major difference is that pymatgen's MPRester will follow the documented REST API end points exactly, i.e., users just need to refer to https://api.materialsproject.org/docs for the exact field names.
- PR #4360 Speed up `Vasprun` parsing by @kavanase
- PR #4343 Drop duplicate `iupac_ordering` entries in `core.periodic_table.json` by @DanielYang59
- PR #4348 Remove deprecated grain boundary analysis by @DanielYang59
- PR #4357 Fix circular import of `SymmOp` by @DanielYang59

## v2025.4.10

- Parity with MPRester.materials.summary.search in MPResterBasic.
- PR #4355 Fix round-trip constraints handling of `AseAtomsAdaptor` by @yantar92
    * src/pymatgen/io/ase.py (AseAtomsAdaptor.get_structure): When no explicit constraint is given for a site in ASE Atoms object, use "T T T" selective dynamics (no constraint).  The old code is plain wrong.
    * tests/io/test_ase.py (test_back_forth): Add new test case.
    Fixes #4354.
    Thanks to @yaoyi92 for reporting!
- PR #4352 Replace `to_dict` with `as_dict` by @DanielYang59
    - Deprecate `to_dict` with `as_dict`, to close #4351
    - Updated `contributing.md` to note preferred naming convention
    - [x] Regenerate `docs`
    The recent additional of JDFTx IOs have a relatively short grace period of 6 months, and others have one year
- PR #4342 Correct Mn "ionic radii" in `core.periodic_table.json` by @DanielYang59
    - Correct Mn "ionic radii" in `core.periodic_table.json`
    Our csv parser should copy the high spin ionic radii to the base entry:
    <img width="858" alt="image" src="https://github.com/user-attachments/assets/00f3ecff-3c78-4583-90b8-106ed362b78b" />
    https://github.com/materialsproject/pymatgen/blob/4c7892f5c9dcc51a1389b3ad2ada77632989a13e/dev_scripts/update_pt_data.py#L84-L87
- PR #4341 Remove "Electrical resistivity" for Se as "high" by @DanielYang59
    ### Summary
    - Remove "Electrical resistivity" for Se as "high", to fix #4312
    Current the data for Electrical resistivity of Se is "high" (with `10<sup>-8</sup> &Omega; m` as the unit), and our parser would interpret it to:
    ```python
    from pymatgen.core import Element
    print(Element.Se.electrical_resistivity)  # 1e-08 m ohm
    ```
    This is the only data as "high" in `periodic_table.json` AFAIK.
    After this, it would be None with a warning:
    ```
    /Users/yang/developer/pymatgen/debug/test_elements.py:3: UserWarning: No data available for electrical_resistivity for Se
    print(Element.Se.electrical_resistivity)
    None
    ```
- PR #4334 Updated Potentials Class in FEFF io to consider radius by @CharlesCardot
    Changed the Potentials class to consider the same radius that is used in
    the Atoms class. This is necessary to avoid a situation where the radius is small enough to only have a subset of the unique elements in a structure, but all the elements have potentials defined, which causes FEFF to fail when run.
    Major changes:
    - fix 1: **Previous behavior**: When creating a FEFFDictset using the feff.io tools, the potentials class defined a potential for every unique element in a structure, while the atoms class defined an atom coordinate for every atom in a radius around the absorbing atom. If the radius was defined to be small, only a subset of the unique atoms in the structure would be included in the atom class. **New behavior**: Updated the potentials class to only create potentials for atoms inside the radius specified when creating a FEFFDictset. Without this, a too small radius for a structure with unique elements outside of that radius would cause FEFF to fail, given that there was a Potential defined for an element that did not exist in the Atoms flag.
    ## Todos
    None, the work is complete
- PR #4068 Fix `monty` imports, enhance test for `Outcar` parser to cover uncompressed format by @DanielYang59
    ### Summary
    - Test `monty` fix for reverse readline, close #4033 and close #4237
    - Replace `reverse_readline` with faster `reverse_readfile`
    - Fix incorrect `monty` imports
    - [x] Enhance unit test for reported Outcar parser (need to test **unzipped format**)
- PR #4331 Optimized cube file parsing in from_cube for improved speed by @OliMarc
    # **Summary**
    ### **Major Changes:**
    This PR enhances the `from_cube` function in `io.common.VolumetricData` to significantly improve performance. When processing large `.cube` files, the original implementation took minutes to read and set Pymatgen objects. The optimized version incorporates several key improvements: file reading is now handled with `readlines()` instead of multiple `readline()` calls, reducing I/O operations. Voxel data parsing has been rewritten to use NumPy vectorized parsing instead of loops, making numerical processing faster. Atom site parsing has been improved by replacing the loop-based `readline()` approach with list comprehensions. Additionally, volumetric data parsing now leverages `np.fromstring()` instead of converting lists to NumPy arrays.
- PR #4329 Add protostructure and prototype functions from aviary by @CompRhys
    Adds functions to get protostructure labels from spglib, moyo and aflow-sym. This avoids users who wish to use this functionality from needing to download `aviary` [to use these functions](https://github.com/CompRhys/aviary/blob/main/aviary/wren/utils.py).
- PR #4321 [Breaking] `from_ase_atoms` constructor for `(I)Structure/(I)Molecule` returns the corresponding type by @DanielYang59
    ### Summary
    - Fix `from_ase_atoms` for `Molecule`, to close #4320
    - [x]  Add tests
- PR #4296 Make dict representation of `SymmetrizedStructure` MSONable by @DanielYang59
    ### Summary
    - Make dict representation of `SymmetrizedStructure` MSONable, to fix #3018
    - [x] Unit test
- PR #4323 Tweak POSCAR / XDATCAR to accommodate malformed files by @esoteric-ephemera
    Related to [this matsci.org issue](https://matsci.org/t/xdatcar-error-when-reading-xdatcar-could-not-convert-string-to-float/61831): sometimes the XDATCAR can be malformed because fortran uses fixed format floats when printing. In those cases, there's no space between coordinates:
    ```
    Direct configuration= 2
    -0.63265286-0.11227753 -0.15402785
    -0.12414874 -0.01213420 -0.28106824
    ...
    ```
    In some cases, this issue is reparable (a negative sign separates coordinates). This PR implements a fix when it is reparable and adds a few Trajectory-like convenience features to `Xdatcar`

## v2025.3.10

1. **PR #3680** - Add support for `vaspout.h5`, improvements to POTCAR handling by @esoteric-ephemera
   - Added support for parsing `vaspout.h5` and improvements in POTCAR handling.
   - Major additions include methods for processing `vaspout.h5` and ensuring compatibility with existing VASP I/O infrastructure.

2. **PR #4319** - Update `abitimer` in `io.abinit` by @gpetretto
   - Fixes parsing issues for newer versions of Abinit.
   - Updates compatibility with `pandas > 2` and includes test files for validation.

3. **PR #4315** - Patch to allow `pyzeo` integration by @daniel-sintef
   - Provides a patch to swap out `zeo++` with `pyzeo`, which is a more actively maintained version.

4. **PR #4281** - Add method to get the Pearson symbol to `SpaceGroupAnalyzer` by @CompRhys
   - Introduced a new method to retrieve the Pearson Symbol in `SpaceGroupAnalyzer`.

6. **PR #4295** - Pass `kwargs` to `IStructure.to` method in JSON format by @DanielYang59
   - Provides finer control over `json.dumps` behavior during format conversion.

7. **PR #4306** - `IStructure.to` defaults to JSON when `filename` is unspecified by @DanielYang59
   - Adjusts default file output behavior to JSON.

8. **PR #4297** - Bugfix for `Structure/ase.Atoms` interconversion by @wolearyc
   - Ensures deep copying to avoid shared memory issues between `Atoms.info` and `Structure.properties`.

9. **PR #4304** - `MagneticStructureEnumerator`: Expose `max_orderings` argument by @mkhorton
    - Makes `max_orderings` configurable via keyword argument.

10. **PR #4299** - Update inequality in `get_linear_interpolated_value` by @kavanase
    - Fixes interpolation logic to handle edge cases more robustly.

## v2025.2.18

1. **PR #4288**: `Dos.get_cbm_vbm` updates by @kavanase
   - Improvements for determining VBM/CBM eigenvalues from a DOS object to match expected values for `emmet-core` tests.

2. **PR #4278**: [Breaking] Fix valence electron configuration parsing by @DanielYang59
   - Addresses valence electron configuration parsing issue in `PotcarSingle.electron_configuration`, resolving #4269.

3. **PR #4275**: Fix default `transformation_kwargs` in `MagneticStructureEnumerator` by @DanielYang59
   - Corrects default `transformation_kwargs` to close #4184, with additional comment and type cleanup.

4. **PR #4274**: Move `occ_tol` to init in `OrderDisorderedStructureTransformation` by @Tinaatucsd
   - Resolved incompatibility with `StandardTransmuter` by moving `occ_tol` to class initialization.

5. **PR #4276**: Fix timeout in `EnumlibAdaptor` by @DanielYang59
   - Adjusts timeout handling to fix #4185 with associated unit test corrections.

6. **PR #4280**: Pre-commit autoupdate by @pre-commit-ci[bot]
   - Updates multiple pre-commit configurations, including ruff-pre-commit and markdownlint-cli.

7. **PR #4290**: Migrate type annotation tweaks from #4100 by @DanielYang59
   - Integrates type annotation improvements to aid review, addressing #4286.

8. **PR #4291**: Remove deprecated memory units from `core` by @DanielYang59
   - Eliminates outdated memory units in `core` for clarity.

9. **PR #4292**: Fix for `plotly` `PDPlotter`/`ChemicalPotentialDiagram.get_plot()` by @kavanase
   - Resolves deprecated `titlefont` issue in plotly v6, updating dependency requirements.

10. **PR #4283**: `Composition` support formula strings with curly brackets by @janosh
    - Expands formula parsing to include curly brackets, with added tests for verification.

11. **PR #4279**: Fix P1 SymmOp string for `CifParser.get_symops` by @DanielYang59
    - Corrects SymmOp string to close #4230, supplemented by a unit test.

12. **PR #4265**: Clarify return type for `core.Composition.reduced_composition` by @DanielYang59
    - Refines return types and cleans up types in `core.Composition`.

13. **PR #4268**: Add `Structure.get_symmetry_dataset` method by @janosh
    - Introduces convenience method for `moyopy` symmetry analysis with a new optional dependency set.

14. **PR #4271**: Add missing parenthesis to `BoltztrapAnalyzer.get_extreme.is_isotropic` by @DanielYang59
    - Minor syntax fix and cleanup for the method, resolving #4165.

15. **PR #4270**: Add `seed: int = 0` parameter to `Structure.perturb()` by @janosh

16. New NEBSet and CINEBSet for NEB calculations. These replace the old MITNEBSet. @shyuep

## v2025.1.24

1. **PR #4159 by @DanielYang59**
   - Avoid using full equality `==` to compare float values to address issue #4158.
   - Recommend using `assert_allclose` over `assert_array_equal` for float arrays due to numerical imprecision.
   - Implement a ~3x speedup tweak to the `_proj` implementation.
   - Partially replace sequence of float comparison using `==` for list/tuple/dict as referenced [here](https://github.com/materialsproject/pymatgen/blob/bd9fba9ec62437b5b62fbd0b2c2c723216cc5a2c/tests/core/test_bonds.py#L56).
   - Introduce other type and comment tweaks.

2. **PR #4190 by @benrich37**
   - **Feature 0:** Hierarchical structure using class objects to represent data within a JDFTx out file.
     - Main hierarchy classes:
       - `JDFTXOutputs`
         - `JDFTXOutputs.outfile`
         - `JDFTXOutfile`
         - `JDFTXOutfile.slices[i]`
         - `JDFTXOutfileSlice`, etc.
   - **Feature 1:** `outputs.py` module with `JDFTXOutfile` for representing a JDFTx out file.
   - **Feature 2:** `jdftxoutfileslice.py` module with `JDFTXOutfileSlice` for file slices of a single JDFTx call.
   - **Feature 3:** `joutstructures.py` with `JOutStructures` for representing structures from an out file slice.
   - **Feature 4:** `joutstructure.py` with `JOutStructure` for each single structure within an out file.
   - **Feature 5:** `jelstep.py` with `JElStep` and `JElSteps` for SCF steps and convergences.
   - **Feature 6:** `jminsettings.py` with `JMinSettings` for minimization settings representations.

3. **PR #4189 by @benrich37**
   - **Feature 1:** `inputs.py` module containing `JDFTXInfile` for Pythonic representation of JDFTx calculation inputs.
   - **Feature 2:** `generic_tags.py` module with "Tag" objects (`AbstractTag` and its inheritors) for JDFTx input structure representation.
   - **Feature 3:** `jdftxinfile_master_format.py` for creating proper "Tag" objects for inputs.
   - **Feature 4:** `jdftxinfile_ref_options.py` for holding lists of acceptable strings for input tags.

## v2025.1.23

1. **PR #4255 by @peikai**: This PR resolves an inconsistency in the `run_type` for entries in a mixing scheme. The entry type was changed to 'r2SCAN', but the `MaterialsProjectDFTMixingScheme()` expected 'R2SCAN', causing errors and ignored entries in GGA(+U)/R2SCAN mixing scheme corrections.

2. **PR #4160 by @DanielYang59**: Enhancements and clarifications were made to the `io.vasp.outputs.Outcar` docstring/comment. This includes more specific type annotations for parsers and updating the default value in `getattr` to `False` for condition checks.

3. **PR #4257 by @njzjz**: This PR covers the intention to build Linux arm64 wheels, referencing the availability of free hosted runners for public repositories. However, specific features and fixes were not detailed.

4. **PR #4240 by @kavanase**: A minor fix in `FermiDos` improves the robustness of the `get_doping` method, addressing issues with handling rare cases with minimal energy increments between VBM and CBM indices.

5. **PR #4254 by @tpurcell90**: Adjustments regarding the use of libxc with FHI-aims to automatically add an override warning call, ensuring the process behaves as expected.

6. **PR #4256 by @kavanase**: Addresses a behavior issue with `Composition` for mixed species and element compositions, providing a fix that ensures compositions are interpreted correctly, avoiding incorrect results in representations and calculations.

7. **PR #4253 by @esoteric-ephemera**: This PR introduces the ability to convert between ASE and pymatgen trajectories, maintaining additional data such as energies, forces, and stresses, thus improving integration between the two programs and addressing related issues.

These updates range from bug fixes and enhancements to new features aimed at improving the functionality and reliability of the codebase.

## 2025.1.9
- Iterating Element no longer contains isotopes (D and T). (@DanielYang59)
- Remove is_rare_earth_metal from ElementBase (@jdewasseigeosium)
- Fix DOS parsing for SOC calculations (@kavanase)
- Added Pure Random Algo to OrderDisorderedStructureTransformation (@jmmshn)
- Fix ion formula check in ion_or_solid_comp_object of analysis.pourbaix_diagram (@DanielYang59)
- AseAtomsAdaptor: Support arbitrary selective dynamics constraints (@yantar92)
- Explicit UTF-8 encoding for zopen and open. (@DanielYang59)

## 2024.11.13

- CP2K fixes (@janosh)
- Fix borg.hive.SimpleVaspToComputedEntryDrone.assimilate ValueError when core file missing (@DanielYang59)
- Revert breaking analysis.local_env default_op_params/cn_opt_params rename (@DanielYang59)
- Added new Flag for AutoOxiStateDecorationTransformation (@jmmshn)
- Fixed execution of packmol in relative path. (@davidwaroquiers)
- Improve element mismatch handling with POTCAR for Poscar.from_file/str (@DanielYang59)
- Preprocess Structure Reduction Before Bulk Match (@lan496)
- Add min "thickness" check in CifParser to filter invalid structure which leads to infinite loop (@DanielYang59)

## 2024.10.29
- VaspDir has been renamed and moved to pymatgen.io.common.PMGDir for more general support of all IO classes. Note that
  this is a backwards incompatible change. It should not affect many users since VaspDir was introduced only in the last
  one week.
- Fixed execution of packmol in relative path. (@davidwaroquiers)
- VaspDoc.get_incar_tags: Use Mediawiki API (@yantar92)
- Fix comment pass in Kpoints constructors (@DanielYang59)

## v2024.10.27
- Bug fix for parsing of dielectric calculations from vasprun.xml.

## v2024.10.25
- VaspDir now supports nested directories. Also, supports returning strings where a parser is not defined.
- Bug fix for parsing of BSE vaspruns.xml.

## v2024.10.21
- New `pyamtgen.io.vasp.VaspDir` class for easy navigation of VASP directories as pymatgen objects.
- Fix gaussian input parser (@sio-salt)
- Fix: preserve site properties over cell transform (@Lattay)
- Make Incar keys case insensitive, fix init Incar from dict val processing for str/float/int (@DanielYang59)
- Fix: Preserve PBC info in AseAtomsAdaptor (@jsukpark)
- Migrate ext.COD from mysql to REST API (@DanielYang59)
- Fix: Parsing bugs in io.pwscf.PWInput (@jsukpark)
- Fix arg passing in inverse property of SymmOp (@DanielYang59)
- Add support for use_structure_charge keyword in FHI-aims input generator (@ansobolev)
- Fix: savefig in pmg.cli.plot (@DanielYang59)
- Fix: Volumetric data and XDATCAR parsing for monatomic structures (@esoteric-ephemera)
- Support to aims format from Structure instance (@ansobolev)
- Fix: Bugfix for Ion CO2(aq) reduced formula (@rkingsbury)
- Replace deprecated ExpCellFilter with FrechetCellFilter (@ab5424)

## v2024.10.3
- Enable parsing of "SCF energy" and "Total energy" from QCOutput for Q-chem 6.1.1+. (@Jaebeom-P)
- Fix dict equality check with numpy array (@DanielYang59)
- Fix usage of strict=True for zip in cp2k.outputs (@DanielYang59)
- Fix bug with species defaults (@tpurcell90)
- SLME Bug Fixes (@kavanase)


## v2024.9.17.1

- Emergency release No. 2 to fix yet another regression in chempot diagram. (Thanks @yang-ruoxi for fixing.)

## v2024.9.17

- Emergency release to fix broken phase diagram plotting due to completely unnecessary refactoring. (Thanks @yang-ruoxi for fixing.)

## v2024.9.10

💥 **Breaking**: NumPy/Cython integer type changed from `np.long`/`np.int_` to int64 on Windows to align with NumPy 2.x, [changing the default integer type to int64 on Windows 64-bit systems](https://numpy.org/doc/stable/release/2.0.0-notes.html) in favor of the platform-dependent `np.int_` type.
Recommendation: Please explicitly declare `dtype=np.int64` when initializing a NumPy array if it's passed to a Cythonized pymatgen function like `find_points_in_spheres`. You may also want to test downstream packages with [NumPy 1.x on Windows in CI pipelines](https://numpy.org/devdocs/dev/depending_on_numpy.html#build-time-dependency).

### 🛠 Enhancements

* Formatting customization for `PWInput` by @jsukpark in https://github.com/materialsproject/pymatgen/pull/4001
* DOS Fingerprints enhancements by @naik-aakash in https://github.com/materialsproject/pymatgen/pull/3946
* Add HSE-specific vdW parameters for dftd3 and dftd3-bj to MPHSERelaxSet. by @hongyi-zhao in https://github.com/materialsproject/pymatgen/pull/3955
* Add VASP setting for the dftd4 vdW functional and extend PBE_64 support. by @hongyi-zhao in https://github.com/materialsproject/pymatgen/pull/3967
* Add SOC & multiple `PROCAR` parsing functionalities by @kavanase in https://github.com/materialsproject/pymatgen/pull/3890
* Add modification to aims input to match atomate2 magnetic order script by @tpurcell90 in https://github.com/materialsproject/pymatgen/pull/3878

### 🐛 Bug Fixes

* Ion: fix CO2- and I3- parsing errors; enhance tests by @rkingsbury in https://github.com/materialsproject/pymatgen/pull/3991
* Fix ruff PD901 and prefer `sum` over `len`+`if` by @janosh in https://github.com/materialsproject/pymatgen/pull/4012
* Explicitly use `int64` in Numpy/cython code to avoid OS inconsistency by @DanielYang59 in https://github.com/materialsproject/pymatgen/pull/3992
* Update `FermiDos.get_doping()` to be more robust by @kavanase in https://github.com/materialsproject/pymatgen/pull/3879
* Fix missing `/src` in doc links to source code by @DanielYang59 in https://github.com/materialsproject/pymatgen/pull/4032
* Fix `LNONCOLLINEAR` match in `Outcar` parser by @DanielYang59 in https://github.com/materialsproject/pymatgen/pull/4034
* Fix in-place `VaspInput.incar` updates having no effect if `incar` is dict (not `Incar` instance) by @janosh in https://github.com/materialsproject/pymatgen/pull/4052
* Fix typo in `Cp2kOutput.parse_hirshfeld` `add_site_property("hirshf[i->'']eld")` by @janosh in https://github.com/materialsproject/pymatgen/pull/4055
* Fix `apply_operation(fractional=True)` by @kavanase in https://github.com/materialsproject/pymatgen/pull/4057

### 💥 Breaking Changes

* Pascal-case `PMG_VASP_PSP_DIR_Error` by @janosh in https://github.com/materialsproject/pymatgen/pull/4048

### 📖 Documentation

* Docstring tweaks for `io.vasp.inputs` and format tweaks for some other parts by @DanielYang59 in https://github.com/materialsproject/pymatgen/pull/3996
* Replace HTTP URLs with HTTPS, avoid `from pytest import raises/mark` by @DanielYang59 in https://github.com/materialsproject/pymatgen/pull/4021
* Fix incorrect attribute name in `Lobster.outputs.Cohpcar` docstring by @DanielYang59 in https://github.com/materialsproject/pymatgen/pull/4039

### 🧹 House-Keeping

* Use `strict=True` with `zip` to ensure length equality by @DanielYang59 in https://github.com/materialsproject/pymatgen/pull/4011

### 🚀 Performance

* add LRU cache to structure matcher by @kbuma in https://github.com/materialsproject/pymatgen/pull/4036

### 🚧 CI

* Install optional boltztrap, vampire and openbabel in CI by @DanielYang59 in https://github.com/materialsproject/pymatgen/pull/3985

### 💡 Refactoring

* Make AimsSpeciesFile a dataclass by @tpurcell90 in https://github.com/materialsproject/pymatgen/pull/4054

### 🧪 Tests

* Remove the `skip` mark for `test_delta_func` by @njzjz in https://github.com/materialsproject/pymatgen/pull/4014
* Recover commented out code in tests and mark with `pytest.mark.skip` instead by @DanielYang59 in https://github.com/materialsproject/pymatgen/pull/4027
* Add unit test for `io.vasp.help` by @DanielYang59 in https://github.com/materialsproject/pymatgen/pull/4020

### 🧹 Linting

* Fix failing ruff `PT001` on master by @DanielYang59 in https://github.com/materialsproject/pymatgen/pull/4003
* Fix fixable `ruff` rules by @DanielYang59 in https://github.com/materialsproject/pymatgen/pull/4015
* Fix `S101`, replace all `assert` in code base (except for tests) by @DanielYang59 in https://github.com/materialsproject/pymatgen/pull/4017
* Fix `ruff` PLC0206 and PLR6104 by @janosh in https://github.com/materialsproject/pymatgen/pull/4035

### 🏥 Package Health

* Drop Python 3.9 support by @DanielYang59 in https://github.com/materialsproject/pymatgen/pull/4009
* Avoid importing namespace package `pymatgen` directly  by @DanielYang59 in https://github.com/materialsproject/pymatgen/pull/4053

### 🏷️ Type Hints

* Set `kpoints` in `from_str` method as integer in auto Gamma and Monkhorst modes by @DanielYang59 in https://github.com/materialsproject/pymatgen/pull/3994
* Improve type annotations for `io.lobster.{lobsterenv/outputs}` by @DanielYang59 in https://github.com/materialsproject/pymatgen/pull/3887

### 🤷‍♂️ Other Changes

* VaspInputSet.write_input: Improve error message by @yantar92 in https://github.com/materialsproject/pymatgen/pull/3999

## New Contributors

* @yantar92 made their first contribution in https://github.com/materialsproject/pymatgen/pull/3999
* @kbuma made their first contribution in https://github.com/materialsproject/pymatgen/pull/4036

**Full Changelog**: https://github.com/materialsproject/pymatgen/compare/v2024.8.9...v2024.9.10

## v2024.8.9

* Revert bad split of sets.py, which broke downstream code.

### 🎉 New Features

* Add multiwfn QTAIM parsing capabilities by @espottesmith in https://github.com/materialsproject/pymatgen/pull/3926

### 🐛 Bug Fixes

* Fix chemical system method for different oxidation states by @danielzuegner in https://github.com/materialsproject/pymatgen/pull/3915
* Fix coordination number bug by @jmmshn in https://github.com/materialsproject/pymatgen/pull/3954
* Fix Ion formula parsing bug; add more special formulas by @rkingsbury in https://github.com/materialsproject/pymatgen/pull/3942
* Dedup `numpy`dependency in `pyproject` by @janosh in https://github.com/materialsproject/pymatgen/pull/3970
* test_graph: add filename only to pdf list by @drew-parsons in https://github.com/materialsproject/pymatgen/pull/3972
* Bugfix: `io.pwscf.PWInput.from_str()` by @jsukpark in https://github.com/materialsproject/pymatgen/pull/3931
* Fix d2k function by @tpurcell90 in https://github.com/materialsproject/pymatgen/pull/3932
* Assign frame properties to molecule/structure when indexing trajectory by @CompRhys in https://github.com/materialsproject/pymatgen/pull/3979

### 🛠 Enhancements

* `Element`/`Species`: order `full_electron_structure` by energy by @rkingsbury in https://github.com/materialsproject/pymatgen/pull/3944
* Extend `CubicSupercell` transformation to also be able to look for orthorhombic cells by @JaGeo in https://github.com/materialsproject/pymatgen/pull/3938
* Allow custom `.pmgrc.yaml` location via new `PMG_CONFIG_FILE` env var by @janosh in https://github.com/materialsproject/pymatgen/pull/3949
* Fix MPRester tests and access phonon properties from the new API without having `mp-api` installed. by @AntObi in https://github.com/materialsproject/pymatgen/pull/3950
* Adding Abinit magmoms from netCDF files to Structure.site_properties by @gbrunin in https://github.com/materialsproject/pymatgen/pull/3936
* Parallel Joblib Process Entries by @CompRhys in https://github.com/materialsproject/pymatgen/pull/3933
* Add OPTIMADE adapter by @ml-evs in https://github.com/materialsproject/pymatgen/pull/3876
* Check Inputs to Trajectory. by @CompRhys in https://github.com/materialsproject/pymatgen/pull/3978

### 📖 Documentation

* Replace expired BoltzTraP link by @DanielYang59 in https://github.com/materialsproject/pymatgen/pull/3929
* Correct method `get_projection_on_elements` docstring under `Procar` class by @DanielYang59 in https://github.com/materialsproject/pymatgen/pull/3945

### 🧹 House-Keeping

* Split VASP input sets into submodules by @janosh in https://github.com/materialsproject/pymatgen/pull/3865

### 🚧 CI

* Install some optional dependencies in CI by @DanielYang59 in https://github.com/materialsproject/pymatgen/pull/3786

### 💡 Refactoring

* Fix `Incar` `check_params` for `Union` type  by @DanielYang59 in https://github.com/materialsproject/pymatgen/pull/3958

### 🏥 Package Health

* build against NPY2 by @njzjz in https://github.com/materialsproject/pymatgen/pull/3894

### 🏷️ Type Hints

* Improve types for `electronic_structure.{bandstructure/cohp}` by @DanielYang59 in https://github.com/materialsproject/pymatgen/pull/3873
* Improve types for `electronic_structure.{core/dos}`  by @DanielYang59 in https://github.com/materialsproject/pymatgen/pull/3880

### 🤷‍♂️ Other Changes

* switch to attr access interface for transformation matrix by @tsmathis in https://github.com/materialsproject/pymatgen/pull/3964
* Fix import sorting by @janosh in https://github.com/materialsproject/pymatgen/pull/3968
* Don't run `issue-metrics` on forks by @ab5424 in https://github.com/materialsproject/pymatgen/pull/3962
* Enable Ruff rule family "N" and "S" by @DanielYang59 in https://github.com/materialsproject/pymatgen/pull/3892

## New Contributors

* @danielzuegner made their first contribution in https://github.com/materialsproject/pymatgen/pull/3915
* @tsmathis made their first contribution in https://github.com/materialsproject/pymatgen/pull/3964
* @jsukpark made their first contribution in https://github.com/materialsproject/pymatgen/pull/3931

**Full Changelog**: https://github.com/materialsproject/pymatgen/compare/v2024.7.18...v2024.8.8

## v2024.8.8

### 🎉 New Features

* Add multiwfn QTAIM parsing capabilities by @espottesmith in https://github.com/materialsproject/pymatgen/pull/3926

### 🐛 Bug Fixes

* Fix chemical system method for different oxidation states by @danielzuegner in https://github.com/materialsproject/pymatgen/pull/3915
* Fix coordination number bug by @jmmshn in https://github.com/materialsproject/pymatgen/pull/3954
* Fix Ion formula parsing bug; add more special formulas by @rkingsbury in https://github.com/materialsproject/pymatgen/pull/3942
* Dedup `numpy`dependency in `pyproject` by @janosh in https://github.com/materialsproject/pymatgen/pull/3970
* test_graph: add filename only to pdf list by @drew-parsons in https://github.com/materialsproject/pymatgen/pull/3972
* Bugfix: `io.pwscf.PWInput.from_str()` by @jsukpark in https://github.com/materialsproject/pymatgen/pull/3931
* Fix d2k function by @tpurcell90 in https://github.com/materialsproject/pymatgen/pull/3932
* Assign frame properties to molecule/structure when indexing trajectory by @CompRhys in https://github.com/materialsproject/pymatgen/pull/3979

### 🛠 Enhancements

* `Element`/`Species`: order `full_electron_structure` by energy by @rkingsbury in https://github.com/materialsproject/pymatgen/pull/3944
* Extend `CubicSupercell` transformation to also be able to look for orthorhombic cells by @JaGeo in https://github.com/materialsproject/pymatgen/pull/3938
* Allow custom `.pmgrc.yaml` location via new `PMG_CONFIG_FILE` env var by @janosh in https://github.com/materialsproject/pymatgen/pull/3949
* Fix MPRester tests and access phonon properties from the new API without having `mp-api` installed. by @AntObi in https://github.com/materialsproject/pymatgen/pull/3950
* Adding Abinit magmoms from netCDF files to Structure.site_properties by @gbrunin in https://github.com/materialsproject/pymatgen/pull/3936
* Parallel Joblib Process Entries by @CompRhys in https://github.com/materialsproject/pymatgen/pull/3933
* Add OPTIMADE adapter by @ml-evs in https://github.com/materialsproject/pymatgen/pull/3876
* Check Inputs to Trajectory. by @CompRhys in https://github.com/materialsproject/pymatgen/pull/3978

### 📖 Documentation

* Replace expired BoltzTraP link by @DanielYang59 in https://github.com/materialsproject/pymatgen/pull/3929
* Correct method `get_projection_on_elements` docstring under `Procar` class by @DanielYang59 in https://github.com/materialsproject/pymatgen/pull/3945

### 🧹 House-Keeping

* Split VASP input sets into submodules by @janosh in https://github.com/materialsproject/pymatgen/pull/3865

### 🚧 CI

* Install some optional dependencies in CI by @DanielYang59 in https://github.com/materialsproject/pymatgen/pull/3786

### 💡 Refactoring

* Fix `Incar` `check_params` for `Union` type  by @DanielYang59 in https://github.com/materialsproject/pymatgen/pull/3958

### 🏥 Package Health

* build against NPY2 by @njzjz in https://github.com/materialsproject/pymatgen/pull/3894

### 🏷️ Type Hints

* Improve types for `electronic_structure.{bandstructure/cohp}` by @DanielYang59 in https://github.com/materialsproject/pymatgen/pull/3873
* Improve types for `electronic_structure.{core/dos}`  by @DanielYang59 in https://github.com/materialsproject/pymatgen/pull/3880

### 🤷‍♂️ Other Changes

* switch to attr access interface for transformation matrix by @tsmathis in https://github.com/materialsproject/pymatgen/pull/3964
* Fix import sorting by @janosh in https://github.com/materialsproject/pymatgen/pull/3968
* Don't run `issue-metrics` on forks by @ab5424 in https://github.com/materialsproject/pymatgen/pull/3962
* Enable Ruff rule family "N" and "S" by @DanielYang59 in https://github.com/materialsproject/pymatgen/pull/3892

## New Contributors

* @danielzuegner made their first contribution in https://github.com/materialsproject/pymatgen/pull/3915
* @tsmathis made their first contribution in https://github.com/materialsproject/pymatgen/pull/3964
* @jsukpark made their first contribution in https://github.com/materialsproject/pymatgen/pull/3931

**Full Changelog**: https://github.com/materialsproject/pymatgen/compare/v2024.7.18...v2024.8.8

## v2024.7.18

* Fix `setuptools` for packaging (#3934)
* Improve Keep Redundant Spaces algorithm for PatchedPhaseDiagram (#3900)
* Add electronic structure methods for Species (#3902)
* Migrate `spglib` to new `SpglibDataset` format with version 2.5.0 (#3923)
* SpaceGroup changes (#3859)
* Add MD input set to FHI-aims (#3896)

## v2024.6.10

* Fix bug in `update_charge_from_potcar` (#3866)
* Fix bug in VASP parameter parsing (@mkhorton)
* Add `strict_anions` option to `MaterialsProject2020Compatibility` (@mkhorton)
* Slightly more robust `MSONAtoms` handling (@Andrew-S-Rosen)
* Bug fix: handle non-integer oxidation states in `Species` (@esoteric-ephemera)
* Revert change that removed test structure files from pymatgen source.

## v2024.6.4

### 🐛 Bug Fixes

* Run CI with two different `uv` resolution strategies: `highest` and `lowest-direct` by @janosh in https://github.com/materialsproject/pymatgen/pull/3852
* Fix filter condition for warn msg of unphysical site occupancy in `io.cif` by @DanielYang59 in https://github.com/materialsproject/pymatgen/pull/3853

### 🛠 Enhancements

* Add new `.pmgrc.yaml` setting `PMG_VASP_PSP_SUB_DIRS: dict[str, str]` by @janosh in https://github.com/materialsproject/pymatgen/pull/3858

### 📖 Documentation

* Clarify argument `shift` for `SlabGenerator.get_slab` by @DanielYang59 in https://github.com/materialsproject/pymatgen/pull/3748

### 🚧 CI

* Add CI run without `'optional'` deps installed by @janosh in https://github.com/materialsproject/pymatgen/pull/3857

**Full Changelog**: https://github.com/materialsproject/pymatgen/compare/v2024.5.31...v2024.6.4

## 2024.5.31

### 🐛 Bug Fixes

* Make `Beautifulsoup` optional by @ab5424 in https://github.com/materialsproject/pymatgen/pull/3774
* Fix overlayed subplots in `BSPlotterProjected.get_projected_plots_dots()` by @janosh in https://github.com/materialsproject/pymatgen/pull/3798
* Fix `_get_dipole_info` for DDEC6 `ChargemolAnalysis` and add test case by @JonathanSchmidt1 in https://github.com/materialsproject/pymatgen/pull/3801
* `Cp2kOutput.parse_initial_structure()` use regex for line matching to allow arbitrary white space between Atom/Kind/Element/... by @janosh in https://github.com/materialsproject/pymatgen/pull/3810
* Fix the minor document error in `POTCAR Setup`. by @hongyi-zhao in https://github.com/materialsproject/pymatgen/pull/3834
* Use `isclose` over `==` for overlap position check in `SlabGenerator.get_slabs` by @DanielYang59 in https://github.com/materialsproject/pymatgen/pull/3825
* [Deprecation] Replace `Element` property `is_rare_earth_metal` with `is_rare_earth` to include Y and Sc  by @DanielYang59 in https://github.com/materialsproject/pymatgen/pull/3817

### 🛠 Enhancements

* Add `is_radioactive` property to Element class by @AntObi in https://github.com/materialsproject/pymatgen/pull/3804
* Add a `from_ase_atoms()` method to `Structure` by @Andrew-S-Rosen in https://github.com/materialsproject/pymatgen/pull/3812
* Adapt to the latest version of PWmat output file by @lhycms in https://github.com/materialsproject/pymatgen/pull/3823
* Update VASP sets to transition atomate2 to use pymatgen input sets exclusively by @esoteric-ephemera in https://github.com/materialsproject/pymatgen/pull/3835 (slightly breaking, see [#3860](https://github.com/materialsproject/pymatgen/issues/3860) for details)

### 📖 Documentation

* Imperative `get_...` method and `@property` doc strings by @janosh in https://github.com/materialsproject/pymatgen/pull/3802
* Doc string standardization by @janosh in https://github.com/materialsproject/pymatgen/pull/3805

### 🧹 House-Keeping

* Add types for `core.(molecular_orbitals|operations|sites|spectrum|tensor|xcfunc)` by @DanielYang59 in https://github.com/materialsproject/pymatgen/pull/3829
* Move test structures out of `util` directory by @DanielYang59 in https://github.com/materialsproject/pymatgen/pull/3831

### 🧪 Tests

* Improve type annotations for `core.(trajectory/units)` by @DanielYang59 in https://github.com/materialsproject/pymatgen/pull/3832

### 🏷️ Type Hints

* More type annotations by @janosh in https://github.com/materialsproject/pymatgen/pull/3800
* Add types for `core.periodic_table/bonds/composition/ion/lattice/libxcfunc`, new type `MillerIndex` and fix Lattice hash by @DanielYang59 in https://github.com/materialsproject/pymatgen/pull/3814
* Guard `TYPE_CHECKING` only imports by @DanielYang59 in https://github.com/materialsproject/pymatgen/pull/3827
* Improve type annotations and comments for `io.cif` by @DanielYang59 in https://github.com/materialsproject/pymatgen/pull/3820
* Improve type annotations for `core.structure` by @DanielYang59 in https://github.com/materialsproject/pymatgen/pull/3837

### 🤷‍♂️ Other Changes

* mixing scheme: change default for verbose by @tschaume in https://github.com/materialsproject/pymatgen/pull/3806
* `ruff` 0.4.3 auto-fixes by @janosh in https://github.com/materialsproject/pymatgen/pull/3808
* Re-enable some useful `ruff` rules by @DanielYang59 in https://github.com/materialsproject/pymatgen/pull/3813
* `pandas.read_csv`: replace deprecated `delim_whitespace=True` with `sep="\s+"` by @ab5424 in https://github.com/materialsproject/pymatgen/pull/3846
* Improve unphysical (greater than 1) occupancy handling in `CifParser` and add missing site label `if not check_occu` by @DanielYang59 in https://github.com/materialsproject/pymatgen/pull/3819

**Full Changelog**: https://github.com/materialsproject/pymatgen/compare/v2024.5.1...v2024.5.31

## v2024.5.1

### 🐛 Bug Fixes

* Fix OPTIMADE rester URL contruction and improve testing by @ml-evs in https://github.com/materialsproject/pymatgen/pull/3756
* Add fix for SFAC writer by @stefsmeets in https://github.com/materialsproject/pymatgen/pull/3779
* Fix LobsterSet by @naik-aakash in https://github.com/materialsproject/pymatgen/pull/3771
* Update `vasprun.converged_ionic` logic when `EDIFFG=0`, REDO of PR #3765 by @matthewkuner in https://github.com/materialsproject/pymatgen/pull/3783
* Fix for incorrect file path in `tests/io/test_zeopp.py` by @AntObi in https://github.com/materialsproject/pymatgen/pull/3784
* Fix for writing non-unique site labels in `CifWriter` by @stefsmeets in https://github.com/materialsproject/pymatgen/pull/3767
* Homogenize return type of `Lattice.get_points_in_sphere` to always be `np.array`(s) by @janosh in https://github.com/materialsproject/pymatgen/pull/3797

### 📖 Documentation

* Add note to documentation for usage of CrystalNN by @JaGeo in https://github.com/materialsproject/pymatgen/pull/3764
* Update to average Grüneisen documentation by @JaGeo in https://github.com/materialsproject/pymatgen/pull/3773
* Format doc strings by @janosh in https://github.com/materialsproject/pymatgen/pull/3790
* Imperative doc strings by @janosh in https://github.com/materialsproject/pymatgen/pull/3792

### 🧹 House-Keeping

* `pyright` fixes for `ext/io/phonon/symmetry/transformations/util/vis/dev_scripts` and improve `io.lobster` by @DanielYang59 in https://github.com/materialsproject/pymatgen/pull/3757
* Separate test files by modules and collect test files `csv/cif` into folders  by @DanielYang59 in https://github.com/materialsproject/pymatgen/pull/3746

### 🚧 CI

* Officially support Python 3.12 and test in CI by @janosh in https://github.com/materialsproject/pymatgen/pull/3685

### 🏥 Package Health

* Remove `gulp` from package data, code base and CI tests by @DanielYang59 in https://github.com/materialsproject/pymatgen/pull/3789

### 🏷️ Type Hints

* Add type annotations for `io.vasp.inputs/optics` by @DanielYang59 in https://github.com/materialsproject/pymatgen/pull/3740
* `pyright` fixes by @DanielYang59 in https://github.com/materialsproject/pymatgen/pull/3777
* Convert `kpts` in `Kpoints` to `Sequence[tuple]` and set it as `property` by @DanielYang59 in https://github.com/materialsproject/pymatgen/pull/3758

### 🤷‍♂️ Other Changes

* add `get_string->get_str` alias for `Poscar` by @timurbazhirov in https://github.com/materialsproject/pymatgen/pull/3763
* Fix `ruff` FURB192 by @janosh in https://github.com/materialsproject/pymatgen/pull/3785

## New Contributors

* @timurbazhirov made their first contribution in https://github.com/materialsproject/pymatgen/pull/3763
* @AntObi made their first contribution in https://github.com/materialsproject/pymatgen/pull/3784

**Full Changelog**: https://github.com/materialsproject/pymatgen/compare/v2024.4.13...2024.5.1

## v2024.4.13

Hot fix release for [v2024.4.12](#v2024412) to be yanked on PyPI due to https://github.com/materialsproject/pymatgen/issues/3751.

### 🐛 Bug Fixes

* Revert mistaken `Cohp.has_antibnd_states_below_efermi` rename by @JaGeo in https://github.com/materialsproject/pymatgen/pull/3750
* Fix `typing_extension` `ImportError` in downstream packages by @janosh in https://github.com/materialsproject/pymatgen/pull/3752
* Update some of the OPTIMADE aliases by @ml-evs in https://github.com/materialsproject/pymatgen/pull/3754

### 🧹 House-Keeping

* Remove duplicate ruff rule in `pyproject.toml` by @Andrew-S-Rosen in https://github.com/materialsproject/pymatgen/pull/3755

**Full Changelog**: https://github.com/materialsproject/pymatgen/compare/v2024.4.12...v2024.4.13

## v2024.4.12

### 🎉 New Features

* Add `pymatgen.io.openff` module by @orionarcher in https://github.com/materialsproject/pymatgen/pull/3729

### 🐛 Bug Fixes

* Fix blank line bug in `io.res.ResWriter` by @stefsmeets in https://github.com/materialsproject/pymatgen/pull/3671
* Reset label for sites changed by `Structure.replace_species()` by @stefsmeets in https://github.com/materialsproject/pymatgen/pull/3672
* Fix `phonopy.get_pmg_structure` `site_properties` key for magmoms by @JonathanSchmidt1 in https://github.com/materialsproject/pymatgen/pull/3679
* Improve Bandoverlaps parser by @naik-aakash in https://github.com/materialsproject/pymatgen/pull/3689
* Convert some `staticmethod` to `classmethod` by @DanielYang59 in https://github.com/materialsproject/pymatgen/pull/3710
* Correct units of Element.atomic_orbitals by @esoteric-ephemera in https://github.com/materialsproject/pymatgen/pull/3714
* Add a fix for if a parameter is None in AimsControlIn by @tpurcell90 in https://github.com/materialsproject/pymatgen/pull/3727
* Replace general `raise Exception` and add missing `raise` keyword by @DanielYang59 in https://github.com/materialsproject/pymatgen/pull/3728
* Fix `ChemicalPotentialDiagram` 2D plot not respecting `formal_chempots` setting by @uliaschauer in https://github.com/materialsproject/pymatgen/pull/3734
* Update ENCUT type to float in  incar_parameters.json by @yuuukuma in https://github.com/materialsproject/pymatgen/pull/3741
* Clean up `core.surface` comments and docstrings by @DanielYang59 in https://github.com/materialsproject/pymatgen/pull/3691
* Fix `io.cp2k.input.DataFile` by @DanielYang59 in https://github.com/materialsproject/pymatgen/pull/3745

### 🛠 Enhancements

* Ensure `MSONAtoms` is indeed `MSONable` when `Atoms.info` is loaded with goodies by @Andrew-S-Rosen in https://github.com/materialsproject/pymatgen/pull/3670
* Generalize fatband plots from Lobster by @JaGeo in https://github.com/materialsproject/pymatgen/pull/3688
* Plotting of Multicenter COBIs by @JaGeo in https://github.com/materialsproject/pymatgen/pull/2926
* Support appending vectors to positions in XSF format by @mturiansky in https://github.com/materialsproject/pymatgen/pull/3704
* Define `needs_u_correction(comp: CompositionLike) -> set[str]` utility function by @janosh in https://github.com/materialsproject/pymatgen/pull/3703
* Add more flexibility to `PhononDOSPlotter` and `PhononBSPlotter` by @ab5424 in https://github.com/materialsproject/pymatgen/pull/3700
* Define `ElementType` enum in `core/periodic_table.py` by @janosh in https://github.com/materialsproject/pymatgen/pull/3726

### 🚧 CI

* Migrate CI dependency installation from `pip` to `uv` by @janosh in https://github.com/materialsproject/pymatgen/pull/3675
* Prevent GitHub Actions from running docs-related CI on forks by @lan496 in https://github.com/materialsproject/pymatgen/pull/3697

### 📖 Documentation

* Reformat docstrings to Google style and add type annotations by @DanielYang59 in https://github.com/materialsproject/pymatgen/pull/3694
* Breaking: all plot methods return `plt.Axes` by @janosh in https://github.com/materialsproject/pymatgen/pull/3749

### 🧹 House-Keeping

* Clean up test files: VASP outputs by @DanielYang59 in https://github.com/materialsproject/pymatgen/pull/3653
* Clean up test files: VASP inputs by @DanielYang59 in https://github.com/materialsproject/pymatgen/pull/3674
* Clean up test files: dedicated VASP directories, `xyz`, `mcif`, `cssr`, `exciting`, `wannier90` by @DanielYang59 in https://github.com/materialsproject/pymatgen/pull/3681
* Remove exception printing when importing phonopy by @lan496 in https://github.com/materialsproject/pymatgen/pull/3696
* Standardize test names: e.g. `LatticeTestCase` -> `TestLattice` by @janosh in https://github.com/materialsproject/pymatgen/pull/3693
* Clean up tests by @janosh in https://github.com/materialsproject/pymatgen/pull/3713
* Fix import order for `if TYPE_CHECKING:` block by @DanielYang59 in https://github.com/materialsproject/pymatgen/pull/3711
* Use `Self` type in Method Signatures by @DanielYang59 in https://github.com/materialsproject/pymatgen/pull/3705
* Remove deprecated `analysis.interface`, rename classes to PascalCase and rename `with_*` to `from_*` by @DanielYang59 in https://github.com/materialsproject/pymatgen/pull/3725
* Test `EntrySet.ground_states` and CIF writing in `NEBSet.write_input` by @janosh in https://github.com/materialsproject/pymatgen/pull/3732

### 🚀 Performance

* Dynamic `__hash__` for `BalancedReaction` by @DanielYang59 in https://github.com/materialsproject/pymatgen/pull/3676

### 🧪 Tests

* Clean up tests 2 by @janosh in https://github.com/materialsproject/pymatgen/pull/3716
* Remove unnecessary `unittest.TestCase` subclassing by @janosh in https://github.com/materialsproject/pymatgen/pull/3718

### 🔒 Security Fixes

* Avoid using `exec` in code by @DanielYang59 in https://github.com/materialsproject/pymatgen/pull/3736
* Avoid using `eval`, replace manual offset in `enumerate` and rename single letter variables by @DanielYang59 in https://github.com/materialsproject/pymatgen/pull/3739

### 🏷️ Type Hints

* `Self` return type on `from_dict` methods by @janosh in https://github.com/materialsproject/pymatgen/pull/3702
* Return `self` from `Structure` methods `replace`, `substitute`, `remove_species`, `remove_sites` by @janosh in https://github.com/materialsproject/pymatgen/pull/3706
* `Self` return type on `Lattice` methods by @janosh in https://github.com/materialsproject/pymatgen/pull/3707

### 🤷‍♂️ Other Changes

* `os.path.(exists->isfile)` by @janosh in https://github.com/materialsproject/pymatgen/pull/3690

## New Contributors

* @JonathanSchmidt1 made their first contribution in https://github.com/materialsproject/pymatgen/pull/3679
* @uliaschauer made their first contribution in https://github.com/materialsproject/pymatgen/pull/3734

**Full Changelog**: https://github.com/materialsproject/pymatgen/compare/v2024.3.1...v2024.4.12

## v2024.3.1

## What's Changed

### 🐛 Bug Fixes

* Fix `BSPlotterProjected.get_projected_plots_dots_patom_pmorb` fix set & list intersect by @janosh in https://github.com/materialsproject/pymatgen/pull/3651
* Remove rounding during FEFF writing by @matthewcarbone in https://github.com/materialsproject/pymatgen/pull/3345
* Fix `get_niggli_reduced_lattice` if entering A1 case by @packer-jp in https://github.com/materialsproject/pymatgen/pull/3657
* Remove BadPoscarWarning when POSCAR elements set by POTCAR by @esoteric-ephemera in https://github.com/materialsproject/pymatgen/pull/3662
* Fix RuntimeError triggered in CI of downstream packages by @janosh in https://github.com/materialsproject/pymatgen/pull/3664

### 🛠 Enhancements

* `Kpoint.__eq__` and `PhononBandStructureSymmLine.__eq__` methods + tests by @janosh in https://github.com/materialsproject/pymatgen/pull/3650
* LOBSTER IO improvements by @naik-aakash in https://github.com/materialsproject/pymatgen/pull/3649

### 📖 Documentation

* Lobsterout update doc-string to match renamed class variable by @naik-aakash in https://github.com/materialsproject/pymatgen/pull/3655
* Fix installation.md formatting by @Andrew-S-Rosen in https://github.com/materialsproject/pymatgen/pull/3661

### 🧹 House-Keeping

* Use `np.eye(3)` instead of `[[1, 0, 0], [0, 1, 0], [0, 0, 1]]` for identies by @janosh in https://github.com/materialsproject/pymatgen/pull/3659

### 🧪 Tests

* Deprecate `_parse_atomic_densities` in `BaderAnalysis` and fix `Bader` test setup by @DanielYang59 in https://github.com/materialsproject/pymatgen/pull/3656

### 🏷️ Type Hints

* Improve INCAR tag check by @DanielYang59 in https://github.com/materialsproject/pymatgen/pull/3621

### 🤷‍♂️ Other Changes

* Avoid `bader_caller` from altering compressed file in place by @DanielYang59 in https://github.com/materialsproject/pymatgen/pull/3660

## New Contributors

* @matthewcarbone made their first contribution in https://github.com/materialsproject/pymatgen/pull/3345
* @packer-jp made their first contribution in https://github.com/materialsproject/pymatgen/pull/3657

**Full Changelog**: https://github.com/materialsproject/pymatgen/compare/v2024.2.23...v2024.3.1

## v2024.2.23

### 🐛 Bug Fixes

* Remove properties from abivars dict as this breaks the interface with… by @gmatteo in https://github.com/materialsproject/pymatgen/pull/3642

### 🛠 Enhancements

* Modified CifParser.check() as one possible solution for issue #3626 by @kaueltzen in https://github.com/materialsproject/pymatgen/pull/3628
* Add capability for Vasprun to read KPOINTS_OPT data by @bfield1 in https://github.com/materialsproject/pymatgen/pull/3509

### 🧪 Tests

* Compress test vasprun.xml files by @DanielYang59 in https://github.com/materialsproject/pymatgen/pull/3648

### 🤷‍♂️ Other Changes

* Modify `BadInputSetWarning` logic for relaxations of a likely metal by @Andrew-S-Rosen in https://github.com/materialsproject/pymatgen/pull/3634
* Fix Lobsterenv Bug by @naik-aakash in https://github.com/materialsproject/pymatgen/pull/3637
* [BugFix] Subclass Construction Locpot<:VolumetricData  by @jmmshn in https://github.com/materialsproject/pymatgen/pull/3639
* Add interface to icet SQS tools through SQSTransformation by @esoteric-ephemera in https://github.com/materialsproject/pymatgen/pull/3593
* Guard `MSONAtoms` definition behind ASE package availability by @ml-evs in https://github.com/materialsproject/pymatgen/pull/3645
* Alias `VaspInputSet` to `VaspInputGenerator`  by @janosh in https://github.com/materialsproject/pymatgen/pull/3566

## New Contributors

* @bfield1 made their first contribution in https://github.com/materialsproject/pymatgen/pull/3509

**Full Changelog**: https://github.com/materialsproject/pymatgen/compare/v2024.2.20...v2024.2.23

## v2024.2.20

This release addresses an important security issue that might affect some users of pymatgen who are parsing untrusted user input, for example a server using pymatgen to parse a user-uploaded CIF file. More information is available in the associated [CVE](https://github.com/materialsproject/pymatgen/security/advisories/GHSA-vgv8-5cpj-qj2f). Thank you to [William Khem-Marquez (@SteakEnthusiast)](https://github.com/SteakEnthusiast) for the discovery and responsible disclosure of this issue.

### 🐛 Bug Fixes

* Revert back `TransformedStructure.__getattr__` by @mjwen in https://github.com/materialsproject/pymatgen/pull/3617
* Fixed Incar object to allow for ML_MODE vasp tag by @davidwaroquiers in https://github.com/materialsproject/pymatgen/pull/3625
* Add missing `MPSCANRelaxSet.yaml` parameters and alphabetize by @Andrew-S-Rosen in https://github.com/materialsproject/pymatgen/pull/3615
* Fix `bader_analysis_from_path` using warning as file path and reinstate test by @janosh in https://github.com/materialsproject/pymatgen/pull/3632

### 🛠 Enhancements

* Breaking: fix SubstrateAnalyzer film + substrate vectors not using original crystal coordinates by @jinlhr542 in https://github.com/materialsproject/pymatgen/pull/3572
* Handle invalid selective dynamics info in POSCAR by @DanielYang59 in https://github.com/materialsproject/pymatgen/pull/3539
* Return `self` from all `SiteCollection/Structure/Molecule` in-place modification methods by @janosh in https://github.com/materialsproject/pymatgen/pull/3623
* Make the POTCAR setup instructions clearer by @Andrew-S-Rosen in https://github.com/materialsproject/pymatgen/pull/3630

### 🧹 House-Keeping

* Refactors + types + fix doc string returns to use Google format by @janosh in https://github.com/materialsproject/pymatgen/pull/3620

### 🚀 Performance

* Speeding up `get_nn_info` in local_env.py by @ftherrien in https://github.com/materialsproject/pymatgen/pull/3635

### 💥 Breaking Changes

* Lobsterenv improvements by @naik-aakash in https://github.com/materialsproject/pymatgen/pull/3624

### 🤷‍♂️ Other Changes

* Fix URL joining in OptimadeRester by @rdamaral in https://github.com/materialsproject/pymatgen/pull/3613
* Create a `CODEOWNERS` by @Andrew-S-Rosen in https://github.com/materialsproject/pymatgen/pull/3616
* Adds support for an `MSONAtoms` class that's an `MSONable` form of an ASE `Atoms` object by @Andrew-S-Rosen in https://github.com/materialsproject/pymatgen/pull/3619
* Lobster io improvements by @naik-aakash in https://github.com/materialsproject/pymatgen/pull/3627

## New Contributors

* @jinlhr542 made their first contribution in https://github.com/materialsproject/pymatgen/pull/3572
* @rdamaral made their first contribution in https://github.com/materialsproject/pymatgen/pull/3613
* @ftherrien made their first contribution in https://github.com/materialsproject/pymatgen/pull/3635

**Full Changelog**: https://github.com/materialsproject/pymatgen/compare/v2024.2.8...v2024.2.20

## v2024.2.8

### 🐛 Bug Fixes

* Fix `Vasprun.get_potcars` search method; tweak fake POTCARs by @esoteric-ephemera in https://github.com/materialsproject/pymatgen/pull/3587

### 🛠 Enhancements

* Aims input sets by @tpurcell90 in https://github.com/materialsproject/pymatgen/pull/3482
* Add `SiteCollection.reduced_formula` property by @janosh in https://github.com/materialsproject/pymatgen/pull/3610
* Add `Entry.(formula|reduced_formula)` by @janosh in https://github.com/materialsproject/pymatgen/pull/3611
* VASP IO `copy()` methods by @janosh in https://github.com/materialsproject/pymatgen/pull/3602

### 📖 Documentation

* Adding FHI-aims inputs developers by @tpurcell90 in https://github.com/materialsproject/pymatgen/pull/3592

### 🧹 House-Keeping

* chore: fix a typo by @VsevolodX in https://github.com/materialsproject/pymatgen/pull/3609

### 🧪 Tests

* Add tests for the New Vasp input sets by @Zhuoying in https://github.com/materialsproject/pymatgen/pull/3576

### 🏥 Package Health

* Switch macOS wheel building to new M1 runners by @janosh in https://github.com/materialsproject/pymatgen/pull/3596

### 🤷‍♂️ Other Changes

* Fix text formatting in `bug_report.yaml` by @Andrew-S-Rosen in https://github.com/materialsproject/pymatgen/pull/3589
* Minor update to avoid deprecation warning by @kavanase in https://github.com/materialsproject/pymatgen/pull/3601

## New Contributors

* @VsevolodX made their first contribution in https://github.com/materialsproject/pymatgen/pull/3609

**Full Changelog**: https://github.com/materialsproject/pymatgen/compare/v2024.1.27...v2024.2.8

## v2024.1.26

### 🐛 Bug Fixes

* Fix label propagation in `Symmetry.from_spacegroup` by @stefsmeets in https://github.com/materialsproject/pymatgen/pull/3527
* Bug fix: SpectrumPlotter.add_spectra by @minhsueh in https://github.com/materialsproject/pymatgen/pull/3529
* Fix bug in SQSTransformation by @esoteric-ephemera in https://github.com/materialsproject/pymatgen/pull/3541
* Fix failing CI due to broken BoltzTraP2 install by @janosh in https://github.com/materialsproject/pymatgen/pull/3543
* Enforce `zval` to be an integer to avoid improper syntax in `.cri` file by @wladerer in https://github.com/materialsproject/pymatgen/pull/3502
* Fix MaterialsProjectCompatibility run type handling for GGA+U by @rkingsbury in https://github.com/materialsproject/pymatgen/pull/3540
* Accept `Path` objects as `filename` in `IStructure.to()` by @janosh in https://github.com/materialsproject/pymatgen/pull/3553
* Retain `Structure.properties` in `structure_from_abivars()`/`structure_to_abivars()` round trip by @janosh in https://github.com/materialsproject/pymatgen/pull/3552
* Support `magmoms` in `get_phonopy_structure()` by @tomdemeyere in https://github.com/materialsproject/pymatgen/pull/3555
* Fix `ValueError: Invalid fmt` with `Structure.to(fmt='yml')` by @janosh in https://github.com/materialsproject/pymatgen/pull/3557
* Improve CIF checking, support for isotopes, and correct handling of new VASP 6.4.2 POSCAR format incl. slashes in header by @esoteric-ephemera in https://github.com/materialsproject/pymatgen/pull/3542
* Deprecate `Structure.ntypesp` replaced by `Structure.n_elems` by @janosh in https://github.com/materialsproject/pymatgen/pull/3562
* Ruff fixes by @janosh in https://github.com/materialsproject/pymatgen/pull/3564
* Fix highly-nested parens when formula parsing in `Composition` by @janosh in https://github.com/materialsproject/pymatgen/pull/3569
* Fix floating point imprecision error in ordering property of CollinearMagneticStructureAnalyzer by @kaueltzen in https://github.com/materialsproject/pymatgen/pull/3574
* Support parsing of "final_energy" in Q-Chem 6.1.1 by @Andrew-S-Rosen in https://github.com/materialsproject/pymatgen/pull/3580

### 🛠 Enhancements

* Add GitHub Issue Templates by @DanielYang59 in https://github.com/materialsproject/pymatgen/pull/3528
* Improve `PhononBandStructure.has_imaginary_gamma_freq()` by checking for negative freqs at all q-points close to Gamma by @janosh in https://github.com/materialsproject/pymatgen/pull/3530
* Add default issue template labels  by @DanielYang59 in https://github.com/materialsproject/pymatgen/pull/3531
* Add functionality to read ASE *.traj file in Trajectory class method from_file() by @exenGT in https://github.com/materialsproject/pymatgen/pull/3422
* Add `PhononDos.r2_score` method by @janosh in https://github.com/materialsproject/pymatgen/pull/3535
* Add codespace container for reproducing issues by @DanielYang59 in https://github.com/materialsproject/pymatgen/pull/3537
* Phonon convenience imports by @janosh in https://github.com/materialsproject/pymatgen/pull/3544
* Add diffusive thermal conductivity model proposed by Agne et al. by @naik-aakash in https://github.com/materialsproject/pymatgen/pull/3546
* Add flag `write_site_properties = False` in `CifWriter` for writing `Structure.site_properties` as `_atom_site_{prop}`  by @Andrew-S-Rosen in https://github.com/materialsproject/pymatgen/pull/3550
* Add `pymatgen.io.pwmat` module by @lhycms in https://github.com/materialsproject/pymatgen/pull/3512
* Lazy import `pandas` in `Structure.as_dataframe()` to improve startup speed by @janosh in https://github.com/materialsproject/pymatgen/pull/3568
* Return `self` in `SiteCollection` spin/oxi state add/remove methods by @janosh in https://github.com/materialsproject/pymatgen/pull/3573
* Added threshold_ordering parameter to CollinearMagneticStructureAnalyzer in addition to PR #3574 by @kaueltzen in https://github.com/materialsproject/pymatgen/pull/3577

### 🧹 House-Keeping

* Pass file IO modes as kwarg by @janosh in https://github.com/materialsproject/pymatgen/pull/3560
* Remove deprecated `(to|from|as|get)_string` methods by @janosh in https://github.com/materialsproject/pymatgen/pull/3561

### 🧪 Tests

* Improve handling of Vasprun POTCAR search, expanded fake POTCAR library for VASP I/O tests by @esoteric-ephemera in https://github.com/materialsproject/pymatgen/pull/3491
* Add test for `NEBAnalysis.get_plot()` by @janosh in https://github.com/materialsproject/pymatgen/pull/3570
* `tests/io/aims` use `numpy.testing.assert_allclose` and `pytest.MonkeyPatch` by @janosh in https://github.com/materialsproject/pymatgen/pull/3575

### 💥 Breaking Changes

* Breaking: remove single-use `PolarizationLattice` which inherited from `Structure` (antipattern) by @janosh in https://github.com/materialsproject/pymatgen/pull/3585

### 🤷‍♂️ Other Changes

* Standardise and update VASP input sets by @utf in https://github.com/materialsproject/pymatgen/pull/3484

## New Contributors

* @DanielYang59 made their first contribution in https://github.com/materialsproject/pymatgen/pull/3528
* @minhsueh made their first contribution in https://github.com/materialsproject/pymatgen/pull/3529
* @exenGT made their first contribution in https://github.com/materialsproject/pymatgen/pull/3422
* @wladerer made their first contribution in https://github.com/materialsproject/pymatgen/pull/3502
* @tomdemeyere made their first contribution in https://github.com/materialsproject/pymatgen/pull/3555
* @lhycms made their first contribution in https://github.com/materialsproject/pymatgen/pull/3512

**Full Changelog**: https://github.com/materialsproject/pymatgen/compare/v2023.12.18...v2024.1.26

## v2023.12.18

### 🐛 Bug Fixes

* Improve doc strings substitution_probability.py by @JaGeo in https://github.com/materialsproject/pymatgen/pull/3477
* Convert all FHI-aims stresses to be 3x3 instead of Voigt notation by @tpurcell90 in https://github.com/materialsproject/pymatgen/pull/3476
* Revert `pymatgen/symmetry/groups.py` module-scoped `SymmOp` import causing circular import by @janosh in https://github.com/materialsproject/pymatgen/pull/3486
* fix reciprocal_density in MPHSEBSSet and tests by @fraricci in https://github.com/materialsproject/pymatgen/pull/3499
* fix TypeError when attr force_field not exists by @xjf729 in https://github.com/materialsproject/pymatgen/pull/3495
* Fix pdplotter.show with matplotlib backend by @lbluque in https://github.com/materialsproject/pymatgen/pull/3493
* Fix legend label order in `PhononBSPlotter.plot_compare()` by @janosh in https://github.com/materialsproject/pymatgen/pull/3510

### 🛠 Enhancements

* Define `PBE64Base.yaml` for new VASP PBE_64 POTCARs by @janosh in https://github.com/materialsproject/pymatgen/pull/3470
* `(Structure|Molecule).alphabetical_formula` by @janosh in https://github.com/materialsproject/pymatgen/pull/3478
* Improvements to `PhononDosPlotter` and `PhononBSPlotter` by @janosh in https://github.com/materialsproject/pymatgen/pull/3479
* `PhononDosPlotter.plot_dos()` add support for existing `plt.Axes` by @janosh in https://github.com/materialsproject/pymatgen/pull/3487
* Allow Structure.interpolate to extrapolate by @kyledmiller in https://github.com/materialsproject/pymatgen/pull/3467
* Updates for Vasprun with MD simulations by @gpetretto in https://github.com/materialsproject/pymatgen/pull/3489
* Add gradient, Hessian, and orbital coeffs scratch file parsers to `pymatgen.io.qchem.outputs` by @Andrew-S-Rosen in https://github.com/materialsproject/pymatgen/pull/3483
* Add multipole parsing for Q-Chem IO by @espottesmith in https://github.com/materialsproject/pymatgen/pull/3490
* `CifParser` only warn about `primitive` default value change to `False` if not passed to `parse_structures` explicitly by @janosh in https://github.com/materialsproject/pymatgen/pull/3505
* `PhononBSPlotter.plot_compare()` add legend labels by @janosh in https://github.com/materialsproject/pymatgen/pull/3507
* Define arithmetic ops `__add__` `__sub__` `__mul__` `__neg__` `__eq__` for `PhononDos` with tests by @janosh in https://github.com/materialsproject/pymatgen/pull/3511
* Equalize `Phonon(Dos|BS)Plotter` colors, allow custom plot settings per-DOS by @janosh in https://github.com/materialsproject/pymatgen/pull/3514
* Add bold flag to `latexify` by @janosh in https://github.com/materialsproject/pymatgen/pull/3516
* `Composition` raise `ValueError` if `formula` string is only numbers and spaces by @janosh in https://github.com/materialsproject/pymatgen/pull/3517
* Raise `ValueError` for `float('NaN')` in `Composition` by @janosh in https://github.com/materialsproject/pymatgen/pull/3519
* Add `PhononDos.mae()` and `PhononBandStructure.has_imaginary_gamma_freq()` methods by @janosh in https://github.com/materialsproject/pymatgen/pull/3520
* `PhononDos.get_smeared_densities` return unchanged for `sigma=0` by @janosh in https://github.com/materialsproject/pymatgen/pull/3524
* Add `PhononDos.get_last_peak()` by @janosh in https://github.com/materialsproject/pymatgen/pull/3525

### 📖 Documentation

* QCInput: add docstrings for svp and pcm_nonels by @rkingsbury in https://github.com/materialsproject/pymatgen/pull/3522

### 🚀 Performance

* Avoid redirects in `MPRester` requests by @tschaume in https://github.com/materialsproject/pymatgen/pull/3496

### 🧪 Tests

* Fix weak `__str__` tests across pymatgen by @janosh in https://github.com/materialsproject/pymatgen/pull/3472
* Test improvements by @janosh in https://github.com/materialsproject/pymatgen/pull/3497

### 🏷️ Type Hints

* `ruff` automatic type annotations by @janosh in https://github.com/materialsproject/pymatgen/pull/3498

## New Contributors

* @kyledmiller made their first contribution in https://github.com/materialsproject/pymatgen/pull/3467

**Full Changelog**: https://github.com/materialsproject/pymatgen/compare/v2023.11.12...v2023.12.18

## v2023.11.12

### 🐛 Bug Fixes

* Hot fix: `pymatgen` package missing `potcar-summary-stats.json.bz2` by @janosh in https://github.com/materialsproject/pymatgen/pull/3468

### 🛠 Enhancements

* Add `Composition.charge` and `charge_balanced` properties by @janosh in https://github.com/materialsproject/pymatgen/pull/3471

## v2023.11.10

### 🐛 Bug Fixes

* Fix `LobsterMatrices` calculated incorrectly by @naik-aakash in https://github.com/materialsproject/pymatgen/pull/3407
* Fix `test_relax_chgnet` by @janosh in https://github.com/materialsproject/pymatgen/pull/3417
* Breaking: return sum of `Species` with matching `Element` in `Composition.__getitem__` by @janosh in https://github.com/materialsproject/pymatgen/pull/3427
* Update inputs.py by @RedStar-Iron in https://github.com/materialsproject/pymatgen/pull/3430
* Fix lattice velocities formatting by @gpetretto in https://github.com/materialsproject/pymatgen/pull/3433
* Fix lobsterin dict inheritance and treat \t in lobsterins correctly by @JaGeo in https://github.com/materialsproject/pymatgen/pull/3439
* Fix `BSPlotterProjected.get_elt_projected_plots`  by @janosh in https://github.com/materialsproject/pymatgen/pull/3451
* Fix `Atoms.cluster_from_file()` in  `io.feff.inputs` giving wrong number of atoms by @kaifengZheng in https://github.com/materialsproject/pymatgen/pull/3426
* Write test-created files to temporary directory, don't pollute test dir by @janosh in https://github.com/materialsproject/pymatgen/pull/3454
* Issue stronger warning if `bader` is run without the `AECCAR`s by @janosh in https://github.com/materialsproject/pymatgen/pull/3458
* Fix Vasprun not interpreting float overflow as nan by @tawe141 in https://github.com/materialsproject/pymatgen/pull/3452
* Aims bug fixes by @tpurcell90 in https://github.com/materialsproject/pymatgen/pull/3466

### 🛠 Enhancements

* Add `LobsterMatrices` parser to `lobster.io.outputs` by @naik-aakash in https://github.com/materialsproject/pymatgen/pull/3361
* Propagate site labels in `SymmetrizedStructure()` by @stefsmeets in https://github.com/materialsproject/pymatgen/pull/3423
* Add lattice velocities to Poscar by @gpetretto in https://github.com/materialsproject/pymatgen/pull/3428
* Add `summary_stats` key to `Vasprun.potcar_spec` by @esoteric-ephemera in https://github.com/materialsproject/pymatgen/pull/3434
* Deprecate `CifParser.get_structures()` in favor of new `parse_structures` in which `primitive`  defaults to `False` by @janosh in https://github.com/materialsproject/pymatgen/pull/3419
* FHI-aims IO Parsers by @tpurcell90 in https://github.com/materialsproject/pymatgen/pull/3435

### 🧹 House-Keeping

* Rename `Poscar.from_file()` `check_for_POTCAR` to `check_for_potcar` by @janosh in https://github.com/materialsproject/pymatgen/pull/3406
* Remove warning in cohp module by @JaGeo in https://github.com/materialsproject/pymatgen/pull/3418
* Drop `black` for `ruff format` by @janosh in https://github.com/materialsproject/pymatgen/pull/3420
* Refresh OPTIMADE aliases and update docstrings by @ml-evs in https://github.com/materialsproject/pymatgen/pull/3447
* Use convenience exports from `pymatgen/core/__init__.py` where no risk of circular imports by @janosh in https://github.com/materialsproject/pymatgen/pull/3461
* Move needlessly function-scoped imports to module scope by @janosh in https://github.com/materialsproject/pymatgen/pull/3462
* Module-scoped imports by @janosh in https://github.com/materialsproject/pymatgen/pull/3464

### 🤷‍♂️ Other Changes

* Create jekyll-gh-pages.yml by @shyuep in https://github.com/materialsproject/pymatgen/pull/3410
* Make `from_(str|file)` `(static->class)methods` by @janosh in https://github.com/materialsproject/pymatgen/pull/3429

### New Contributors

* @RedStar-Iron made their first contribution in https://github.com/materialsproject/pymatgen/pull/3430
* @tawe141 made their first contribution in https://github.com/materialsproject/pymatgen/pull/3452
* @tpurcell90 made their first contribution in https://github.com/materialsproject/pymatgen/pull/3435

**Full Changelog**: https://github.com/materialsproject/pymatgen/compare/v2023.10.11...v2023.11.10

## v2023.10.11

### 🐛 Bug Fixes

* Fix outdated `setup.py` `find_namespace_packages` and add `test_egg_sources_txt_is_complete` by @janosh in <https://github.com/materialsproject/pymatgen/pull/3374>
* `release.yml` add option to publish to TestPyPI by @janosh in <https://github.com/materialsproject/pymatgen/pull/3375>
* Fix wrong unit=eV in `get_band_(skewness|kurtosis)` doc string by @janosh in <https://github.com/materialsproject/pymatgen/pull/3383>
* Further updating POTCAR validation / identification by @esoteric-ephemera in <https://github.com/materialsproject/pymatgen/pull/3392>
* `MatPESStaticSet.yaml` set `LMAXMIX: 6` by @janosh in <https://github.com/materialsproject/pymatgen/pull/3400>
* Fix type annotations in phonon/ and lammps/ by @ab5424 in <https://github.com/materialsproject/pymatgen/pull/3401>
* Fix `OBAlign(includeH=False, symmetry=False)` can't take keywords by @janosh in <https://github.com/materialsproject/pymatgen/pull/3403>

### 🛠 Enhancements

* New class to handle `NcICOBILIST.lobster` files by @QuantumChemist in <https://github.com/materialsproject/pymatgen/pull/2878>
* Add `inplace: bool=True` arg to `Structure.apply_strain()` by @janosh in <https://github.com/materialsproject/pymatgen/pull/3376>
* Add `Structure.to_(conventional|primitive|cell)` methods by @janosh in <https://github.com/materialsproject/pymatgen/pull/3384>
* Add `SiteCollection.to_ase_atoms()` by @janosh in <https://github.com/materialsproject/pymatgen/pull/3389>
* Add `mode: Literal["w", "a", "wt", "at"] = "w"` keyword to `CifWriter.write_file()` by @janosh in <https://github.com/materialsproject/pymatgen/pull/3399>

### 📖 Documentation

* Add `docs/fetch_pmg_contributors.py` script by @janosh in <https://github.com/materialsproject/pymatgen/pull/3387>

### 🧹 House-Keeping

* Fix ruff `FURB` violations by @janosh in <https://github.com/materialsproject/pymatgen/pull/3382>
* Remove deprecated module `pymatgen/util/convergence.py` by @janosh in <https://github.com/materialsproject/pymatgen/pull/3388>
* Remove `pylint: disable` comments by @janosh in <https://github.com/materialsproject/pymatgen/pull/3390>
* Fix `ruff` `N806` by @janosh in <https://github.com/materialsproject/pymatgen/pull/3394>

### 🧪 Tests

* Update `incar_parameters.json` to allow `ISIF=8` by @matthewkuner in <https://github.com/materialsproject/pymatgen/pull/3381>
* Add `test_potcar_summary_stats()` by @janosh in <https://github.com/materialsproject/pymatgen/pull/3395>
* Mirror atomate2 fix and improve `MPScanRelaxSet.test_kspacing` edge case coverage by @janosh in <https://github.com/materialsproject/pymatgen/pull/3396>

### 💥 Breaking Changes

* Breaking: snake_case `FiestaInput` keywords and class attributes by @janosh in <https://github.com/materialsproject/pymatgen/pull/3386>
* Ion: default hydrates=False in reduced_formula by @rkingsbury in <https://github.com/materialsproject/pymatgen/pull/3350>

### 🏷️ Type Hints

* Add type annotations to io/lammps by @ab5424 in <https://github.com/materialsproject/pymatgen/pull/3379>
* Add type annotations to phonon by @ab5424 in <https://github.com/materialsproject/pymatgen/pull/3393>

**Full Changelog**: <https://github.com/materialsproject/pymatgen/compare/v2023.10.4...v2023.10.11>

## v2023.10.4

### 🐛 Bug Fixes

* Fix missing `potcar_summary_stats.json.gz` in `setup.package_data` by @janosh in <https://github.com/materialsproject/pymatgen/pull/3372>
* Bug fixes for MPRester and packaged data by @shyuep

**Full Changelog**: <https://github.com/materialsproject/pymatgen/compare/v2023.10.3...v2023.10.4>

## v2023.10.3

### 🐛 Bug Fixes

* Revert `openbabel.OBAlign()` in `molecule_matcher.py` to use positional args for `includeH`, `symmetry` by @janosh in <https://github.com/materialsproject/pymatgen/pull/3353>
* Fix MPMD set bug by @MichaelWolloch in <https://github.com/materialsproject/pymatgen/pull/3355>
* Fix `TestMPResterNewBasic` + `AseAtomsAdaptor` test errors and `TransformedStructure.from_snl` overwriting `hist` variable by @janosh in <https://github.com/materialsproject/pymatgen/pull/3362>
* Fix `TypeError`: can only join an iterable with AECCAR in `VolumetricData.write_file` by @chiang-yuan in <https://github.com/materialsproject/pymatgen/pull/3343>

### 🛠 Enhancements

* Don't rely on `jsanitize` in `Atoms` <--> `Structure` object interconversion  by @Andrew-S-Rosen in <https://github.com/materialsproject/pymatgen/pull/3359>
* Breaking: New method of POTCAR validation by @esoteric-ephemera in <https://github.com/materialsproject/pymatgen/pull/3351>
* Add alias `.to_file()` for `.to()` method of structures and molecules by @QuantumChemist in <https://github.com/materialsproject/pymatgen/pull/3356>

### 🧹 House-Keeping

* Chargemol minor refactor by @janosh in <https://github.com/materialsproject/pymatgen/pull/3357>
* Breaking typo fix: `Targe(tt->t)edPenaltiedAbundanceChemenvStrategy` by @janosh in <https://github.com/materialsproject/pymatgen/pull/3360>
* Fix undiscovered tests by @janosh in <https://github.com/materialsproject/pymatgen/pull/3369>

### 🏥 Package Health

* Bump min `numpy` to v1.25.0 by @janosh in <https://github.com/materialsproject/pymatgen/pull/3352>

## New Contributors

* @esoteric-ephemera made their first contribution in <https://github.com/materialsproject/pymatgen/pull/3351>
* @QuantumChemist made their first contribution in <https://github.com/materialsproject/pymatgen/pull/3356>

**Full Changelog**: <https://github.com/materialsproject/pymatgen/compare/v2023.9.25...v2023.10.3>

## v2023.9.25

* New basic MPRester implemented that supports the most common use cases without having to install mp-api. mp-api is no longer a dependency of pymatgen.
* Breaking: rename get_ax3d_fig_plt->get_ax3d_fig and get_ax_fig_plt->get_ax_fig plus no longer return plt
* Misc bug fixes.

## v2023.9.10

### 🐛 Bug Fixes

* Fix code comment in ASE adapter by @Andrew-S-Rosen in <https://github.com/materialsproject/pymatgen/pull/3298>
* Fix IndexError when parsing Hessian from Gaussian frequency job by @janosh in <https://github.com/materialsproject/pymatgen/pull/3308>

### 🛠 Enhancements

* Add an input arg check for `Kpoints.automatic_density_by_lengths` by @Andrew-S-Rosen in <https://github.com/materialsproject/pymatgen/pull/3299>

### 🏥 Package Health

* Remove pydantic < 2 from `setup.py` and bump monty in `requirements.txt` by @Andrew-S-Rosen in <https://github.com/materialsproject/pymatgen/pull/3303>
* Move `py.typed` to package root by @Andrew-S-Rosen in <https://github.com/materialsproject/pymatgen/pull/3307>
* Consistent casing `setup->setUp` across test classes by @janosh in <https://github.com/materialsproject/pymatgen/pull/3305>

**Full Changelog**: <https://github.com/materialsproject/pymatgen/compare/v2023.9.2...v2023.9.10>

### 🛠 Enhancements

* Add an input arg check for `Kpoints.automatic_density_by_lengths` by @Andrew-S-Rosen in <https://github.com/materialsproject/pymatgen/pull/3299>

### 🏥 Package Health

* Remove pydantic < 2 from `setup.py` and bump monty in `requirements.txt` by @Andrew-S-Rosen in <https://github.com/materialsproject/pymatgen/pull/3303>
* Move `py.typed` to package root by @Andrew-S-Rosen in <https://github.com/materialsproject/pymatgen/pull/3307>
* Consistent casing `setup->setUp` across test classes by @janosh in <https://github.com/materialsproject/pymatgen/pull/3305>

**Full Changelog**: <https://github.com/materialsproject/pymatgen/compare/v2023.9.2...v2023.9.10>

## v2023.9.2

* Add `Lattice` property `params_dict` by @janosh in <https://github.com/materialsproject/pymatgen/pull/3239>
* Generate SupercellTransformation from minimum boundary distance by @JiQi535 in <https://github.com/materialsproject/pymatgen/pull/3238>
* More concise `test_from_boundary_distance`  by @janosh in <https://github.com/materialsproject/pymatgen/pull/3242>
* Breaking: remove deprecated keyword `properties` from `Species`  by @janosh in <https://github.com/materialsproject/pymatgen/pull/3243>
* Typo in Docs for PeriodicsSite by @jmmshn in <https://github.com/materialsproject/pymatgen/pull/3249>
* Fix `Vasprun.converged_electronic` check if `ALGO=CHI` in `INCAR` by @janosh in <https://github.com/materialsproject/pymatgen/pull/3250>
* Breaking: Have plot methods return `plt.Axes` object, not `matplotlib` module by @janosh in <https://github.com/materialsproject/pymatgen/pull/3237>
* Fix `ruff` D212 by @janosh in <https://github.com/materialsproject/pymatgen/pull/3251>
* Fix some Kpoints generated using wrong mesh types by @matthewkuner in <https://github.com/materialsproject/pymatgen/pull/3245>
* read `mag` from OSZICAR by @chiang-yuan in <https://github.com/materialsproject/pymatgen/pull/3146>
* Use `numpy.testing.assert_allclose` over `assert np.allclose` by @janosh in <https://github.com/materialsproject/pymatgen/pull/3253>
* Don't let tests pollute the `pymatgen` repo by @janosh in <https://github.com/materialsproject/pymatgen/pull/3255>
* Update `compatibility.md` by @mbercx in <https://github.com/materialsproject/pymatgen/pull/3260>
* Google-style doc string return types by @janosh in <https://github.com/materialsproject/pymatgen/pull/3258>
* Quasi-RRHO Thermochemistry Analysis Module by @arepstein in <https://github.com/materialsproject/pymatgen/pull/2028>
* Add keyword `check_occu: bool = True` to `CifParser.get_structures()` by @jonathanjdenney in <https://github.com/materialsproject/pymatgen/pull/2836>
* Fix bug in feff inputs.py by @kaifengZheng in <https://github.com/materialsproject/pymatgen/pull/3256>
* Cancel concurrent CI runs to save budget by @janosh in <https://github.com/materialsproject/pymatgen/pull/3263>
* Fix `Procar.get_projection_on_elements` for structures with multiple same-element ionic sites by @Na-Kawa in <https://github.com/materialsproject/pymatgen/pull/3261>
* Fix `TestMPScanStaticSet.test_as_from_dict()` by @janosh in <https://github.com/materialsproject/pymatgen/pull/3266>
* Bump activesupport from 7.0.6 to 7.0.7.2 in /docs by @dependabot in <https://github.com/materialsproject/pymatgen/pull/3267>
* Fix `TestMPStaticSet` using `MPRelaxSet` in `test_user_incar_kspacing` and `test_kspacing_override`  by @janosh in <https://github.com/materialsproject/pymatgen/pull/3268>
* Fix `nelectrons` not updating when replacing species in `Molecule` by @janosh in <https://github.com/materialsproject/pymatgen/pull/3269>
* Add `properties` to Structure and Molecule by @gpetretto in <https://github.com/materialsproject/pymatgen/pull/3264>
* Fix `CifParser.get_structures(check_occu=False)` by @janosh in <https://github.com/materialsproject/pymatgen/pull/3272>
* Add `PotcarSingle.__repr__` by @janosh in <https://github.com/materialsproject/pymatgen/pull/3273>
* `__str__` to `__repr__` by @janosh in <https://github.com/materialsproject/pymatgen/pull/3274>
* Ion: handle dissolved gas formulas by @rkingsbury in <https://github.com/materialsproject/pymatgen/pull/3275>
* Add VASP input set `MatPESStaticSet` by @SophiaRuan in <https://github.com/materialsproject/pymatgen/pull/3254>
* Fix `test_valid_magmom_struct()` error message regex by @janosh in <https://github.com/materialsproject/pymatgen/pull/3276>
* fix tests of MatPESStaticSet  by @SophiaRuan in <https://github.com/materialsproject/pymatgen/pull/3281>
* Breaking: bump minimum Python version to 3.9 by @janosh in <https://github.com/materialsproject/pymatgen/pull/3283>
* Breaking: Update `AseAtomsAdaptor` to handle `Structure.properties`/`Molecule.properties` by @Andrew-S-Rosen in <https://github.com/materialsproject/pymatgen/pull/3270>
* Slightly relax the constraint satisfy condition of get_primitive_structure() by @fyalcin in <https://github.com/materialsproject/pymatgen/pull/3285>
* [WIP] add custodian modified incar settings to incar and modify tests by @SophiaRuan in <https://github.com/materialsproject/pymatgen/pull/3284>
* Add keyword `bandgap_tol: float = 1e-4` to `MPScanRelaxSet` by @janosh in <https://github.com/materialsproject/pymatgen/pull/3287>
* `np.(arange->linspace)` in `io/vasp/optics.py` `get_delta`, `get_setp` and `epsilon_imag` by @LucasGVerga in <https://github.com/materialsproject/pymatgen/pull/3286>
* MatPESStaticSet restore GGA tag removal if xc_functional.upper() == "R2SCAN" by @janosh in <https://github.com/materialsproject/pymatgen/pull/3288>
* Bump pypa/cibuildwheel from 2.14.1 to 2.15.0 by @dependabot in <https://github.com/materialsproject/pymatgen/pull/3294>
* Bump cython from 3.0.0 to 3.0.2 by @dependabot in <https://github.com/materialsproject/pymatgen/pull/3292>
* Bump scipy from 1.11.1 to 1.11.2 by @dependabot in <https://github.com/materialsproject/pymatgen/pull/3291>
* Bump plotly from 5.11.0 to 5.16.1 by @dependabot in <https://github.com/materialsproject/pymatgen/pull/3289>
* Bump joblib from 1.3.1 to 1.3.2 by @dependabot in <https://github.com/materialsproject/pymatgen/pull/3290>
* Bump mp-api from 0.33.3 to 0.35.1 by @dependabot in <https://github.com/materialsproject/pymatgen/pull/3293>
* xyz.**iter**() -> iter(xyz) by @janosh in <https://github.com/materialsproject/pymatgen/pull/3228>
* Deprecate overlooked `from/as_..._string` methods by @janosh in <https://github.com/materialsproject/pymatgen/pull/3295>

## v2023.8.10

* fix `estimate_nbands` function by @matthewkuner in <https://github.com/materialsproject/pymatgen/pull/3149>
* Add `CifParser.get_structures(on_error='warn')` by @janosh in <https://github.com/materialsproject/pymatgen/pull/3175>
* `ruff . --fix` by @janosh in <https://github.com/materialsproject/pymatgen/pull/3176>
* `AseAtomsAdaptor`: Retain `tags` property when interconverting `Atoms` and `Structure`/`Molecule` by @Andrew-S-Rosen in <https://github.com/materialsproject/pymatgen/pull/3151>
* Fix a bug in pwscf.py. The proc_val function modifies string values. by @pablogalaviz in <https://github.com/materialsproject/pymatgen/pull/3172>
* Delete commented out print statements by @janosh in <https://github.com/materialsproject/pymatgen/pull/3178>
* lots of `from_string` should be `classmethod` by @njzjz in <https://github.com/materialsproject/pymatgen/pull/3177>
* Extend lobsterenv for coop/cobi by @naik-aakash in <https://github.com/materialsproject/pymatgen/pull/3050>
* BUG: fix setting zero magmoms by @lbluque in <https://github.com/materialsproject/pymatgen/pull/3179>
* Prefer `pymatviz` interactive plotly version of periodic table heatmap if available by @janosh in <https://github.com/materialsproject/pymatgen/pull/3180>
* Better Composition `repr` by @janosh in <https://github.com/materialsproject/pymatgen/pull/3182>
* Breaking: Return True for `Element in Composition` if `Species.symbol` matches `Element` by @janosh in <https://github.com/materialsproject/pymatgen/pull/3184>
* Revert `LMAXMIX` "fix" added in #3041 by @janosh in <https://github.com/materialsproject/pymatgen/pull/3189>
* Add `bader_exe_path` keyword to `BaderAnalysis` and run `bader` tests in CI by @janosh in <https://github.com/materialsproject/pymatgen/pull/3191>
* Unskip and fix `packmol` tests by @janosh in <https://github.com/materialsproject/pymatgen/pull/3195>
* Propagate labels through various Structure operations by @stefsmeets in <https://github.com/materialsproject/pymatgen/pull/3183>
* Delete variable self assignments by @janosh in <https://github.com/materialsproject/pymatgen/pull/3196>
* Improve `Structure` tests by @janosh in <https://github.com/materialsproject/pymatgen/pull/3197>
* Test `class XYZ` edge cases by @janosh in <https://github.com/materialsproject/pymatgen/pull/3206>
* Fix `EnergyAdjustment.__repr__` by @janosh in <https://github.com/materialsproject/pymatgen/pull/3207>
* Markdownlint by @janosh in <https://github.com/materialsproject/pymatgen/pull/3209>
* Fix codecov by @janosh in <https://github.com/materialsproject/pymatgen/pull/3210>
* Update `pytest-split` durations by @janosh in <https://github.com/materialsproject/pymatgen/pull/3211>
* Fix GitHub language statistics after test files migration by @janosh in <https://github.com/materialsproject/pymatgen/pull/3214>
* Fix `automatic_density_by_lengths` and add tests for it by @janosh in <https://github.com/materialsproject/pymatgen/pull/3218>
* Prefer `len(structure)` over `structure.num_sites` by @janosh in <https://github.com/materialsproject/pymatgen/pull/3219>
* Add `PhaseDiagram` method `get_reference_energy` by @janosh in <https://github.com/materialsproject/pymatgen/pull/3222>
* Fix isomorphic for molecular graphs by @rohithsrinivaas in <https://github.com/materialsproject/pymatgen/pull/3221>
* Add `Structure.elements` property by @janosh in <https://github.com/materialsproject/pymatgen/pull/3223>
* Add keyword `in_place: bool = True` to `SiteCollection.replace_species` by @janosh in <https://github.com/materialsproject/pymatgen/pull/3224>
* list offending elements in `BVAnalyzer.get_valences` error message by @janosh in <https://github.com/materialsproject/pymatgen/pull/3225>
* Add `Entry.elements` property by @janosh in <https://github.com/materialsproject/pymatgen/pull/3226>
* Move `PymatgenTest.TEST_FILES_DIR` attribute into module scope by @janosh in <https://github.com/materialsproject/pymatgen/pull/3227>
* f-string path construction everywhere, no need for `os.path.join(...)` by @janosh in <https://github.com/materialsproject/pymatgen/pull/3229>
* speed up `bader_caller` and `chargemol_caller` by @chiang-yuan in <https://github.com/materialsproject/pymatgen/pull/3192>
* Fix `ruff` PYI041 and ignore PYI024 by @janosh in <https://github.com/materialsproject/pymatgen/pull/3232>
* Deprecate `get_string()` methods in favor of `get_str()` by @janosh in <https://github.com/materialsproject/pymatgen/pull/3231>
* `Structure/Molecule.to()` now always return same string written to file by @janosh in <https://github.com/materialsproject/pymatgen/pull/3236>

### New Contributors

* @matthewkuner made their first contribution in <https://github.com/materialsproject/pymatgen/pull/3149>
* @pablogalaviz made their first contribution in <https://github.com/materialsproject/pymatgen/pull/3172>
* @rohithsrinivaas made their first contribution in <https://github.com/materialsproject/pymatgen/pull/3221>

**Full Changelog**: <https://github.com/materialsproject/pymatgen/compare/v2023.7.20...v2023.08.10>

## v2023.7.20

* Unreadable string concat ops to f-string by @janosh in <https://github.com/materialsproject/pymatgen/pull/3162>
* Revert `mp-api<0.34.0` pin by @janosh in <https://github.com/materialsproject/pymatgen/pull/3165>
* Fix CI error `"pdentries_test.csv"` not found by @janosh in <https://github.com/materialsproject/pymatgen/pull/3168>
* Fix issues with labels by @stefsmeets in <https://github.com/materialsproject/pymatgen/pull/3169>

## v2023.7.17

* Cython 3.0 support.
* PR #3157 from @mattmcdermott magnetic-analyzer-fix. Fixes bug briefly mentioned in #3070, where recent
  spin property changes resulted in the `MagneticStructureEnumerator` failing. This is apparently due to
  creating structures where only some `Species.spin` properties are defined, causing
  CollinearMagneticStructureEnumerator` to fail.
* PR #3070 from @mattmcdermott magnetic-enumerator-fix. To summarize: changes to default magnetic moments
  introduced in #2727 now mean that structures with only partially defined magnetic moments (e.g., on
  half the sites) cannot be successfully analyzed by `SpaceGroupAnalyzer`. This was encountered when
  performing magnetic ordering enumeration, as the previous default behavior for `
MagOrderingTransformation` does not implicitly yield spins of 0 on the nonmagnetic sites. This has now
  been fixed.

## v2023.7.14

* Emergency bug fix release to remove use of sys.path in pymatgen.io.ase package.
* Fix "Incompatible POTCAR" error on ComputedEntries with oxidation states.
* New global config variable `PMG_POTCAR_CHECKS` provides means to disable all POTCAR checking.

## v2023.7.11

* Use joblib to speed up expensive enumeration energy computations.
* Minor cleanups.

## v2023.6.28

* Use lru_cache to speed up get_el_sp by 400x (@v1kko).
* Related to lru_cache of get_el_sp, Species.properties is now deprecated in favor of setting Species(spin=5). The rationale is
  that spin is the only supported property for Species anyway. Species and DummySpecies is now mostly immutable, i.e., setting specie.spin = 5 have no effect. This is as intended since the first version of pymatgen.
* PR #3111 from @xjf729 fix-MoleculeGraph-draw_graph
* PR #3030 from @lbluque Remove superfluous structure argument docstring from `SQSTransformation` init
* PR #3031 from @kavanase Quick fix to allow direct initialisation of the `DictSet` class.
* PR #3015 from @lbluque Optimized cython code in `find_points_in_spheres`, getting ~5x faster runtime.

## v2023.6.23

* PR #3062 from @Andrew-S-Rosen asefix
  Closes #3061. @JaGeo
* PR #3030 from @lbluque master
  Remove superfluous structure argument docstring from `SQSTransformation` init
* PR #3031 from @kavanase master
  This is a quick fix to allow direct initialisation of the `DictSet` class, which was possible before but broke in <https://github.com/materialsproject/pymatgen/pull/2972> due to the `Yb_2` check querying `self.CONFIG`, which is only defined if `DictSet` was being initialised from a subclass and not directly.
* PR #3015 from @lbluque neighbors
  Optimized cython code in `find_points_in_spheres`, getting ~5x faster runtime.

## v2023.5.31

* Breaking: Default user_potcar_settings to {"W": "W_sv"} in all input sets if user_potcar_functional == "PBE_54" [#3022](https://github.com/materialsproject/pymatgen/pull/3022)
* Unignore ruff PD011 [#3020](https://github.com/materialsproject/pymatgen/pull/3020)
* Tweak variable names [#3019](https://github.com/materialsproject/pymatgen/pull/3019)
* MaterialsProjectCompatibility issue silencable deprecation warning [#3017](https://github.com/materialsproject/pymatgen/pull/3017)
* Optimize cython find_points_in \_spheres [#3015](https://github.com/materialsproject/pymatgen/pull/3015)
* Cp2k 2.0 [#2672](https://github.com/materialsproject/pymatgen/pull/2672)
* Added methods to compute and compare DOS fingerprints [#2772](https://github.com/materialsproject/pymatgen/pull/2772)
* Breaking: Overhaul class PymatgenTest [#3014](https://github.com/materialsproject/pymatgen/pull/3014)
* Fix ValueError when structure.selective_dynamics has type np.array [#3012](https://github.com/materialsproject/pymatgen/pull/3012)
* Clean up [#3010](https://github.com/materialsproject/pymatgen/pull/3010)
* Update .pytest-split-durations [#3005](https://github.com/materialsproject/pymatgen/pull/3005)
* Lookup MPRester API key in settings if None provided as arg [#3004](https://github.com/materialsproject/pymatgen/pull/3004)
* Support writing structures to compressed JSON (.json.gz .json.bz2 .json.xz .json.lzma) [#3003](https://github.com/materialsproject/pymatgen/pull/3003)
* Add LightStructureEnvironments.from_structure_environments() fallback value if ce_and_neighbors is None [#3002](https://github.com/materialsproject/pymatgen/pull/3002)
* Species parse oxi state from symbol str [#2998](https://github.com/materialsproject/pymatgen/pull/2998)
* Re-export SiteCollection + DummySpecies from pymatgen.core [#2995](https://github.com/materialsproject/pymatgen/pull/2995)
* Orbital-resolved icohplist [#2993](https://github.com/materialsproject/pymatgen/pull/2993)
* Hide all type-hint-only imports behind if TYPE_CHECKING [#2992](https://github.com/materialsproject/pymatgen/pull/2992)
* Add type hints for pymatgen.io.ase module [#2991](https://github.com/materialsproject/pymatgen/pull/2991)
* Enable ruff doc rules in CI [#2990](https://github.com/materialsproject/pymatgen/pull/2990)
* Suspected Typo Fix in pymatgen.io.vasp.optics [#2989](https://github.com/materialsproject/pymatgen/pull/2989)
* Doc strings [#2987](https://github.com/materialsproject/pymatgen/pull/2987)
* Fix average error [#2986](https://github.com/materialsproject/pymatgen/pull/2986)
* Drop deprecated SubstrateAnalyzer + ZSLGenerator reexports [#2981](https://github.com/materialsproject/pymatgen/pull/2981)
* Breaking: Default user_potcar_settings to {"W": "W_sv"} in all input sets if user_potcar_functional == "PBE_54" (#3022) [#3022](https://github.com/materialsproject/pymatgen/pull/3022)
* fix unwanted x margins in get_elt_projected_plots_color (closes #562) [#562](https://github.com/materialsproject/pymatgen/issues/562)
* Add LightStructureEnvironments.from_structure_environments() fallback value if ce_and_neighbors is None (#3002) [#2756](https://github.com/materialsproject/pymatgen/issues/2756)
* add doc str explaining need for class ElementBase (closes #2999) [#2999](https://github.com/materialsproject/pymatgen/issues/2999)
* Update docs. `3e3c31c <https://github.com/materialsproject/pymatgen/commit/3e3c31c8d342c84f2c6bbb961c321e458b9accb9>`\_
* ruff set isort.split-on-trailing-comma = false `c0ec534 <https://github.com/materialsproject/pymatgen/commit/c0ec53452c3dc87c6cca5edc1c6b2b6218f15569>`\_

## v2023.5.10

* Fix mem leak in pbc_shortest_vector cython code. (@stichri)
* Set all cython code to language level 3.

## v2023.5.8

❗ The Yb_2 deprecation release ❗

This release changes the Ytterbium (Yb) pseudo-potential (PSP) from Yb_2 to Yb_3 for all PBE_54 VASP input sets.

Background: The `A-lab <https://newscenter.lbl.gov/2023/04/17/meet-the-autonomous-lab-of-the-future>` revealed that as a result of using Yb_2 the energy on Yb compounds is off by a lot, resulting in supposedly stable things being unsynthesizable. While an unfortunate mistake, it's also great to see how experiment can help surface simulation errors.

On pre-PBE_54 input sets, we now issue a warning that Yb_2 will give bad results for most systems since Yb is most often in oxidation state Yb3+.

Reason: The better fix Yb_3 only became available in the PBE_54 PSP set. Requiring it on pre-PBE_54 input sets would mean you can't run Yb compounds.

For more details see [#2968](https://github.com/materialsproject/pymatgen/pull/2968)and [#2969](https://github.com/materialsproject/pymatgen/pull/2969).

What's Changed

* Fix TypeError: a bytes-like object is required, not 'list' when passing triplet of bools to find_points_in_spheres() pbc kwarg by @janosh in [#2907](https://github.com/materialsproject/pymatgen/pull/2907)
* Fix ValueError: not enough values to unpack in PDPlotter if no unstable entries in PD by @janosh in [#2908](https://github.com/materialsproject/pymatgen/pull/2908)
* Fix VolumetricData.to_cube() not preserving structure dimensions by @janosh in [#2909](https://github.com/materialsproject/pymatgen/pull/2909)
* Update team.rst by @jmmshn in [#2912](https://github.com/materialsproject/pymatgen/pull/2912)
* Faff by @janosh in [#2915](https://github.com/materialsproject/pymatgen/pull/2915)
* Add formal_chempots option to ChemicalPotentialDiagram to plot the formal chemical potentials rather than the DFT energies by @kavanase in [#2916](https://github.com/materialsproject/pymatgen/pull/2916)
* Modified dosplotter by @kaueltzen in [#2844](https://github.com/materialsproject/pymatgen/pull/2844)
* auto version by @jmmshn in [#2925](https://github.com/materialsproject/pymatgen/pull/2925)
* bug fix for potcar parsing by @jmmshn in [#2910](https://github.com/materialsproject/pymatgen/pull/2910)
* Fix breaking changes from pandas v2 by @janosh in [#2935](https://github.com/materialsproject/pymatgen/pull/2935)
* add kwarg to MoleculeGraph method and fix PackmolSet bug by @orionarcher in [#2927](https://github.com/materialsproject/pymatgen/pull/2927)
* fix on reading multiple route in Gaussian input file by @Ameyanagi in [#2939](https://github.com/materialsproject/pymatgen/pull/2939)
* Fix CI errors by @janosh in [#2940](https://github.com/materialsproject/pymatgen/pull/2940)
* Add ResParser support for reading files with spin values by @ScottNotFound in [#2941](https://github.com/materialsproject/pymatgen/pull/2941)
* Ignore bad unicode characters in Structure.from_file() by @janosh in [#2948](https://github.com/materialsproject/pymatgen/pull/2948)
* Minor modification for symmetrically distinct Miller index generation by @fyalcin in [#2949](https://github.com/materialsproject/pymatgen/pull/2949)
* Fixed Wulff shape for new versions of matplotlib by @CifLord in [#2950](https://github.com/materialsproject/pymatgen/pull/2950)
* Test figure returned by WulffShape.get_plot() contains single Axes3D by @janosh in [#2953](https://github.com/materialsproject/pymatgen/pull/2953)
* Fix Cp2kOutput.spin_polarized() likely not doing what author intended by @janosh in [#2954](https://github.com/materialsproject/pymatgen/pull/2954)
* For MPcules: Molecule Trajectory and graph hashes by @espottesmith in [#2945](https://github.com/materialsproject/pymatgen/pull/2945)
* self.assertArrayEqual->assert by @janosh in [#2955](https://github.com/materialsproject/pymatgen/pull/2955)
* fix GaussianOutput bug with multiple route lines by @xjf729 in [#2937](https://github.com/materialsproject/pymatgen/pull/2937)
* Fix ValueError when passing selective_dynamics to Poscar by @chiang-yuan in [#2951](https://github.com/materialsproject/pymatgen/pull/2951)
* Link /addons from new subsection on /contributing page by @janosh in [#2967](https://github.com/materialsproject/pymatgen/pull/2967)
* Breaking: change Yb pseudo-potential on all VASP input sets from Yb_2 to Yb_3 by @janosh in [#2969](https://github.com/materialsproject/pymatgen/pull/2969)
* fix recursion error by adding copy and deepcopy dunder methods by @orionarcher in [#2973](https://github.com/materialsproject/pymatgen/pull/2973)
* Revert to Yb_2 on pre-PBE_54 input sets by @janosh in [#2972](https://github.com/materialsproject/pymatgen/pull/2972)

## v2023.3.23

* Misc bug fixes.
* Enable Structure relaxations with TrajectoryObserver (@janosh)
* Breaking: Rename `gen_sl_transform_matrices->gen_sl_transform_matrices` (#2894)

## v2023.3.10

* PR #2882 substrate-optimizations for speed up (@mkhorton)
* Fix very fragile POTCAR parsing.

## v2023.2.28

* 69a548e210 revert adding ubuntu-latest to release job matrix
* e63cab3620 add 3.11 to release job python-versions
* c03dacb94d use `cibuildwheel` to build linux wheels (#2800)
* fe2597d92e Merge setup.cfg into pyproject.toml (#2858)
* 40cbf1d7c4 del class AtomicFile, \_maketemp(), ask_yesno() from pymatgen/util/io_utils.py (#2860)
* 0b16987f2c fix reduced formula in Ion (#2864)

## v2023.2.22

* PR #2848 from @ml-evs ml-evs/update_optimade_aliases
  Currently `OptimadeRester` defaults to an outdated list of OPTIMADE database URLs (several of which fail) and the design of the class is such that refreshing these aliases can only be done post-init which means they will not be used if the user provides their own filtered list of aliases, without doing some extra work.
  This PR refreshes the vendored list of aliases (which should be much more stable now since their initial addition 2 years ago), and also adds the option to refresh the aliases on initialization of the class.
  This currently affects the pymatgen OPTIMADE tutorials at <https://github.com/Materials-Consortia/optimade-tutorial-exercises>.

## v2023.1.30

* PR #2806 from @samblau qchem
  * Major changes to Q-Chem IO (inputs.py and outputs.py) to accommodate differences and new features in version 6+
  * Additional parsing capabilities for HOMO/LUMO, dipoles, NBO info (hyperbonds and 3C bonds) in outputs.py
  * Utility for processing a parsed binary Hessian scratch file
  * Overdue updates to default values in sets.py and new defaults associated with differences and new features in Q-Chem 6+
* PR #2814 from @jmmshn patch_dos

## Added Convenience to obtain the normalized CompleteDos object

    Added tests to make sure calling it multiple time still only gives one result.

## v2023.1.20

* Passthrough kwargs support for Structure.from_file and Structure.from_str
* Allow the `frac_tolerance` to be specified for rounding coordinates in CifParser.
* PR #2803 from @amkrajewski add_weightbasedfunctions
  When working with metallic alloys, weight-fraction-based notations such as Ti64 / Ti-6V-4Al or NiTiNOL60 / Ni-40Ti are commonly employed in both industrial specifications and scientific literature. Regardless of the numerous downsides of this situation, including errors in scientific experiments or NLP-parsing when they are mistaken for atomic fractions or chemical formulas, being able to create a Composition object from them (under correct interpretation) would be a useful pymatgen feature.
  * Composition class method to initialize it from a dictionary of weight fractions
  * Composition property giving a dictionary of weight fractions
  * concise tests for the two above were added
    QChem: translate DMSO name in smd_solvent

## v2023.1.9

* PR #2792 from @JaGeo bug_fix
* PR #2773 from @ab5424 cbar
* PR #2776 from @MichaelWolloch master
* PR #2762 from @MichaelWolloch master
* PR #2774 from @dgaines2 fix-poscar
* PR #2667 from @nwinner volumetric-data-patch
* PR #2764 from @naik-aakash lobster_lsodos
* PR #2215 from @rkingsbury cmirs
* PR #2742 from @materialsproject pip-dependabot
* PR #2741 from @materialsproject resurrect-req-txt
* PR #2735 from @njzjz patch-1

## v2022.11.7

* PR #2724 from @janosh: raise ValueError in SpacegroupAnalyzer.get_symmetrized_structure() if spglib returns no symmetries
* PR #2720 by @utf: Fix tensor mapping
* PR #2562 from @sudarshanv01: In case the Fock-matrix and eigenvalues are requested by the user (though the flags `scf_final_print` or `scf_print`), outputs.py now allows parsing both these quantities.

## v2022.11.1

* Order of kwargs `fmt` and `filename` in `Structure.to()` swapped for ease of use (note: this can break codes that do not use these options as kwargs).
* @yuzie007 Parse "Atomic configuration" in POTCAR (52 and 54). Useful for estimating a reasonable NBANDS value.
* EnumerateStructureTransformation now supports `m3gnet_relax` or `m3gnet_static` options.

## v2022.10.22

* Allow env settings to override .pmgrc.yaml (@janosh)
* Add EntryLike type (@janosh)
* Update spglib to 2.0+.
* @cnncnnzh Method to plot the atom-resolved phonon band structures.
* @jmmshn More Flexible reproduction of VASP's optical code
* @Ameyanagi Fix the sorting of the FEFF IO module to create ATOMS input.
* @JaGeo Extend the ThermalDisplacementMatrices class to read cif files in P1 format.
* @rkingsbury Changes to FEFF I/O to support the use of non-periodic input structures.
* @jmmshn Merge Waverder and Wavederf
* @jmmshn Set the structure_charge while parsing Potcar

## v2022.9.21

* @chunweizhu fix the bugs when running `TEMCalculator`
* @munrojm Support for new MPRester.

## v2022.9.8

* @janosh Add AirssProvider.as_dict
* @gpetretto Outcar parsing optimization.
* @ScottNotFound Adds res file io to handle results from airss searches
* @janosh Fixes the `AttributeError` currently raised when passing disordered structures to methods like `get_cn()` and `get_bonded_structure()` of `CrystalNN` and other `NearNeighbors` subclasses.
* @naik-aakash Added new option `standard_with_comp_range` for generating lobsterin files using vasp

## v2022.8.23

* Structure Graphs from Lobster Data (@JaGeo)
* Added 'get_orbit_and_generators'-method to SpaceGroup class (@nheinsdorf)
* Class to handle Thermal displacements matrices (@JaGeo)
* Change default number of significant digits to write VASP POSCAR (@henriquemiranda)
* Misc bug fixes.

## v2022.7.25

* Implemented sufficient methods for new MPRester to cover about 70-80% of common use cases.

## v2022.7.24.1

* Implementation changed to allow seamless use of MPRester regardless of whether new or old API key is used.

## v2022.7.24

* Initial implementation of MPRester2 with new API support. Basic functionality for now.

## v2022.7.19

This will be the final release with the pymatgen.analysis.defects
module included in the standard pymatgen package. This release will
include the older defects code by default, but can also be replaced with
the newer defects code through installation of pymatgen-analysis-defects.

Subsequent versions of pymatgen will require
the additional installation of `pymatgen-analysis-defects <https://github.com/materialsproject/pymatgen-analysis-defects>`\_ for all defect-related
functionality via pip install pymatgen-analysis-defects.

Relevant imports will still be from the pymatgen.analysis.defects namespace but the code will now be maintained and developed in this separate repository.

There will be significant changes to the defects code to support new functionality.Existing PyCDT users should use this version of pymatgen or older. Any questions
about this change should be directed to Jimmy-Xuan Shen, @jmmshn.

For more information about other pymatgen "add-on" packages, please see
`this page in our documentation <https://pymatgen.org/addons.html>`\_.

* Preparation for the removal of the defects module, PR #2582 by @jmmshn

## v2022.7.8

Welcome to new contributors @naveensrinivasan, @xivh, @dgaines2, @yang-ruoxi, @cajfisher and @mjwen!

* New: Partial periodic boundary conditions, PR #2429 by @gpetretto
* New: Element.from_name(), PR #2567 by @rkingsbury
* New: Materials Project input set for absorption calculations, PR #2320 by @yang-ruoxi
* Enhancement: compressed LAMMPS and XYZ files in pymatgen.io.lammps, PR #2538 by @ab5424
* Enhancement: remove vertical lines from VoltageProfilePlotter.get_plotly_figure(), PR #2552 by @acrutt
* Enhancement: chemical potential plot background color changed, PR #2559 @jmmshn
* Enhancement: ability to change voronoi_distance_cutoff in ChemEnv, PR #2568 by @JaGeo
* Enhancement: Ion.oxi_state_guesses will use correct charge by default, PR #2566 by @rkingsbury
* Enhancement: Remove not converged warning for VASP AIMD runs, PR #2571 by @mjwen
* Fix: generation of continuous line-mode band structures, PR #2533 by @munrojm
* Fix: duplicate site properties for magnetic moments hwen using `AseAtomsAdaptor`, PR #2545 by @Andrew-S-Rosen
* Fix: bug in Grüneisen parameter calculation, PR #2543 by @ab5424
* Fix: allow a comment on final line of KPOINTS file, PR #2549 by @xivh
* Fix: for `Composition.replace` with complex mappings, PR #2555 by @jacksund
* Fix: Implement equality method and fix **iter** for InputSet, PR #2575 by @rkingsbury
* Fix: use negative charge convention for electron in "update_charge_from_potcar", PR #2577 by @jmmshn
* Fix: ensure charge is applied to initial and final structures parsed from vasprun.xml, PR #2579 by @jmmshn
* Chore: Set permissions for GitHub actions, PR #2547 by @naveensrinivasan
* Chore: Included GitHub actions in the Dependabot config, PR #2548 by @naveensrinivasan
* Documentation: fix typos in pymatgen.symmetry.analyzer docstrings, PR #2561 by @dgaines2
* Documentation: clarification about usage of InputFile, PR #2570 by @orionarcher
* Documentation: Improve messages and warnings, PR #2572 and PR #2573 by @cajfisher
* Documentation: fix typo, PR #2580 by @janosh

Notice: functionality from pymatgen.analysis.defects will be incorporated into a separate add-on package in the future,
see deprecation notice.

## v2022.5.26

* Q-Chem updates to NBO and new geometry optimizer, PR #2521 by @samblau
* Bug fix for VolumetricData, PR #2525 by @jmmshn
* Bug fix for MPRester, PR #2531 by @janosh

## v2022.5.19

* Added option for additional criteria to be passed to MPRester.get_entries_in_chemsys (@shyuep).

## v2022.5.18.1

* Initial support for parsing ML MD runs from vasprun.xml (@shyuep).

## v2022.5.18

* Bug fix for sulfide_type. Sometimes symmetry analysis fails because of tolerance issues. A fallback to analyze all sites.

## v2022.5.17

* PR #2518 from @JaGeo. Fixed wrong line in ICOHPLIST.lobster being read to assess whether orbitalwise interactions are included in these files.
* PR #2520 from @Andrew-S-Rosen. Adds a new property to the `PointGroupAnalyzer`: the rotational symmetry number.
* PR #2522 from @jmmshn. Fixes PD JSON serialization.
* PR #2514 from @qianchenqc. Replaced the IALGO tag with ALGO as recommended in the vasp documentation <https://www.vasp.at/wiki/index.php/IALGO>.
* PR #2404 from @nheinsdorf. Added a method that gets all the neighbors up a maximum distance for a Structure, and groups these 'bonds' according to their symmetry.
* PR #2509 from @jacksund Fix NMR Set.

## v2022.4.26

* Fix dipole units in recent vasp versions (at least 6.3, maybe even before) (@fraricci)
* Removed complex numbers from the definition of WSWQ (@jmmshn)
* MP database version logging is now no longer logged in the .pmgrc.yaml but rather in the .mprester.log.yaml.
  This avoids the MPRester constantly rewriting a config file and causing users' pymatgen to completely fail.

## v2022.4.19

* Fix for discharged and charged entries in conversion battery. (@peikai)`pylint` in `.pre-commit-config.yaml`.
* Allow skipping of structure reduction in StructureMatcher.group_structures (@lan496)
* Return NotImplemented for composition comparison methods. (@janosh)
* BSPlotter bug fixes (@fraricci)
* Misc bug fixes and deprecation fixes.

## v2022.3.29

* Major update to CP2K module, PR #2475 from @nwinner
* Bug fix to remove problematic import, PR #2477 from @mkhorton

## v2022.3.24

* Emergency bugfix release to fix circular import (@janosh)

## v2022.3.22

* Support kwargs for ASE adaptor. (@Andrew-S-Rosen)
* Fix for cation error in Lobster analysis. (@JaGeo)
* Major revampt of Abstract interface for Input classes in IO. (@rkingsbury)
* Orbital-projected band center, band filling, band center, skewness, kurtosis, etc. (@Andrew-S-Rosen)
* Misc cleanups. (@janosh)

## v2022.3.7

* Add VASP WSWQ file parsing, PR #2439 from @jmmshn
* Improve chemical potential diagram plotting, PR #2447 from @mattmcdermott
* Update to Lobster calculation settings, PR #2434 from @JaGeo master
* Allow non-integer G-vector cut-off values when parsing WAVECAR, PR #2410 from @Andrew-S-Rosen
* Fix for Structure.from_file when file is in YAML format from @janosh fix-structure-from-yml
* Update of linter configuration, PR #2440 from @janosh
* Update to ChemEnv citation, PR #2448 from @JaGeo
* Type annotation fix, PR #2432 from @janosh
* Documentation fix for Structure.apply_operation, PR #2433 from @janosh
* Add caching to compatibility classes as speed optimization, PR #2450 from @munrojm

This release was previously intended for v2022.2.25.

Important note: an update to a library that pymatgen depends upon has led to the
~/.pmgrc.yml configuration file being corrupted for many users. If you are affected,
you may need to re-generate this file. This issue should now be fixed and not re-occur.

## v2022.2.10

* Require Cython during setup. (@jonringer)

## v2022.2.7

* Critical bug fix for pmgrc.yaml being overwritten in MPRester in a non-standard way.
* Change in config file for Lobster basis. Removed the 2p orbitals for Be as they led to problems in our computations and probably should be optional during the projection. (@JaGeo)
* Return None for ISPIN=1 for `Vasprun('vasprun.xml').complete_dos.spin_polarization`.

## v2022.2.1

* Chargemol caller for partial atomic charge analysis (@Andrew-S-Rosen)
* ASEAtomAdaptor: (1) Updates to magmom support, (2) Oxidation states support, (3) Charges are now passed (@Andrew-S-Rosen)
* Cleanup of deprecated methods. (@janosh)
* Bigfix for gzipped DOSCAR (@JaGeo)
* Updates for QChem Support (@samblau)
* QuantumEspresso k-grid fix input fix. (@vorwerkc)
* `Entry.__repr__()` now outputs name where available. (@janosh)
* Fixes to Vasprun.final_energy to report `e_0_energy` (the desired energy quantity) for VASP 6+. (@Andrew-S-Rosen)
* `Outcar().final_energy` now prints out `e_0_energy` (also called "energy(sigma->0)" in the OUTCAR) rather than `energy_fr_energy` (also called "free energy TOTEN" in the OUTCAR). This is to be consistent with `Vasprun().final_energy` and because it is generally the desired quantity. `Outcar` now has two new attributes: `.final_energy_wo_entrp` and `final_fr_energy`, which correspond to `e_wo_entrp` and `e_fr_energy`, respectively. (@Andrew-S-Rosen)
* Improved parsing of coupled cluster calculations in QChem (@espottesmith).

## v2022.1.24

* Misc bug fixes, e.g., handling of yaml files and type check for MAGMOM flag.

## v2022.1.20

* Unicode fixes (@janosh)
* YAML deprecation fixes. (@janosh)
* ASE adaptor support for charge, spin multiiciplity and site properties of molecules. (@Andrew-S-Rosen).
* New keyword option (`keep_site_properties`) in various `structure.symmetry.analyzer` functions to keep the site properties on the sites after a transformation. (@Andrew-S-Rosen)
* Bug fixes for Lobster module (@JaGeo).
* SCAN / GGA(+U) mixing scheme (@rkingsbury). Mixing scheme code lives in the new file `mixing_scheme.py` and is implemented as a `Compatibility` class.
* Fix for parsing of QuantumExpresso files due to new format (@vorwerkc)

## v2022.1.9

* Formal support for Python 3.10.
* Misc refactoring and bug fixes. No new functionality.

## v2022.1.8

* First proper new release of 2022 formalizes the switch back to date-based versioning introduced as a temporary measure last year.
* Numpy version pinned to 1.22.0. This is necessary to avoid binary incompatibility.
* With the numpy version, py37 support is dropped.
* ASE io improvements (e.g., magnetic moments and selective dynamics transfer). @Andrew-S-Rosen
* New automatic k-point generation scheme, `automatic_density_by_lengths`, which allows the user to specify a density of k-points in each dimension (rather than just for the entire volume). @Andrew-S-Rosen
* Build improvements to dynamically generate C code by running Cython on pyx files rather than having hard-generated .c files.

## v2022.0.17

Welcome to new contributor @e-kwsm!

* More robust smart fermi method by @utf in <https://github.com/materialsproject/pymatgen/pull/2303>
* Replace-species by @janosh in <https://github.com/materialsproject/pymatgen/pull/2291>
* Add warning if improper ALGO is used for hybrid calculations by @Andrew-S-Rosen in <https://github.com/materialsproject/pymatgen/pull/2298>
* Wrap supercell to unit cell when performing change of setting by @jmmshn in <https://github.com/materialsproject/pymatgen/pull/2300>
* Clearer handling of the MAGMOM flag in pymatgen.io.vasp.sets by @Andrew-S-Rosen in <https://github.com/materialsproject/pymatgen/pull/2301>
* Add warning if LASPH != True for meta-GGA/hybrid/vdW/+U by @Andrew-S-Rosen in <https://github.com/materialsproject/pymatgen/pull/2297>
* Add ability to request additional OPTIMADE fields by @ml-evs in <https://github.com/materialsproject/pymatgen/pull/2315>
* Add missing elements to MPScanRelaxSet PBE .54 potentials by @Andrew-S-Rosen in <https://github.com/materialsproject/pymatgen/pull/2316>

* Fix write Trajectory XDATACAR with variable lattice by @gpetretto in <https://github.com/materialsproject/pymatgen/pull/2310>
* Fix small cutoff neighbor by @chc273 in <https://github.com/materialsproject/pymatgen/pull/2277>
* Add Composition.replace() by @janosh in <https://github.com/materialsproject/pymatgen/pull/2284>
* Ion bugfixes and enhancements by @rkingsbury in <https://github.com/materialsproject/pymatgen/pull/2287>
* Fix oddly split strings and a few typos by @janosh in <https://github.com/materialsproject/pymatgen/pull/2285>
* InsertionElectrode bug fix and documentation update by @acrutt in <https://github.com/materialsproject/pymatgen/pull/2257>
* Remove accidentally tracked files and unset executable flag by @e-kwsm in <https://github.com/materialsproject/pymatgen/pull/2296>

* Update DOI URLs by @e-kwsm in <https://github.com/materialsproject/pymatgen/pull/2295>
* Documentation update: Fix missing Outcar attributes and update elemental_dos_dos string by @Andrew-S-Rosen in <https://github.com/materialsproject/pymatgen/pull/2293>
* Documentation update for CutOffDictNN by @ltalirz in <https://github.com/materialsproject/pymatgen/pull/2278>

## v2022.0.16

* Fix to allow PhaseDiagram to be JSON-serializable with computed data cached (@mkhorton, #2276)
* Temporarily revert #2239 pending investigation into slow-down in some nearest neighbor finding routines. This does not affect the behavior of any of these classes.

## v2022.0.15

Welcome to new contributors @blokhin, @pzarabadip, @ml-evs, @wuxiaohua1011, @janssenhenning and @penicillin0. A reminder to all new contributors to
ensure your information is accurate at <https://pymatgen.org/team.html> so that
you are acknowledged appropriately by filling out the linked form.

* Breaking change in PhaseDiagram serialization which will affect any users of BasePhaseDiagram which has now been removed (@shyuep, 2b9911d)

* Speed up nearest-neighbor routines & structure graph generation (@ltalirz, #2239)
* Add two more pre-defined OPTIMADE aliases (@blokhin, #2242)
* Refactor `interface_reactions` module, adding support for Plotly (@mattmcdermott, #2233)

* Update NOMAD access in MPRester (@wuxiaohua1011, #1958)
* General improvements to Phase Diagram code (@CompyRhys, #2263, #2264, #2268)
* Improve appearance of periodic table heatmap (@penicillin0, #2272)
* Small improvements to battery classes (@jmmshn, #2262)
* Fix for Composition.chemical_system to match expected behavior for compositions with oxidation states (@CompRhys, #2249)
* Fix for bad param in OPTIMADE response fields (@ml-evs, #2244)
* Fix for issue in parsing `bandOverlaps.lobster` file (@pzarabadip, #2237)
* Fix for Moladaptor (@orioncohen, #2269)
* Fix for incorrect Potcar hash warnings (@mkhorton, #2273)

* Type hint and correct documentation of Structure.remove_site_properties (@kmu, #2256)
* Type hint improvements across pymatgen (@janosh, #2241, #2247, #2261)
* Add `pymatgen-io-fleur` addon to addons page (@janssenhenning, #2232)

## v2022.0.14

* Update OPTIMADE interface to allow querying multiple providers, this changes the
  method signature of OptimadeRester and so is considered a backwards incompatible change (@mkhorton, #2238)

## v2022.0.13

* New feature to plot chemical potential diagrams (@mattmcdermott, #2218), see ArXiv:2104.05986 for example
* Numerous updates to LOBSTER support for new version and including handling COBICAR, SitePotentials and MadelungEnergies (@JaGeo, #2228)
* Updates and fixes for LAMMPS CombinedData (@htz1992213, #2191)
* Bug fix for Bader caller (@nwinner, #2230)
* Documentation fix for Composition (@CompRhys, #2231)

## v2022.0.12

* @chc273 Major bugfix for cython handling of fractional coordinates wrapping.
* @mattmcdermott Bug fix for entry_ID phase diagram plotting bug described in this Issue: #2219
* @FCMeng Fix for PWSCF to distinguish same element with different oxidation state, which might have different pseudopotentials.
* @gmatteo fix minor bug when reading Structure from a netcdf4 file with hdf5 groups

## v2022.0.11

* New features to handle Grüneisen parameters (@JaGeo, @ab5424, @gpetretto, #2190)
* New option to return SymmetrizedStructure in CifParser (@mkhorton, 0d9a455)
* Fix for SubstrateAnalyzer (@shyamd, #2198)
* Fix for BandFillingCorrection (@kavanase, #2193)

## v2022.0.10

* Add spin-dependent eigenvalue band properties (@Andrew-S-Rosen, #2187)
* Bug fix for settings loading (@ardunn, #2186)

## v2022.0.9

* Significant new functionality for handling interfaces between structures (@shyamd, #2149)
* Add input/output for CREST (@arepstein, #2020)
* Add RadialSiteDistortionTransformation (@nwinner, #2108)
* Add Q-Chem NBO functionality (@samblau, #2174)
* Change hkl annotation format in diffraction plots (@flaviu-gostin, #2143)
* Add space group to print output of `SymmetrizedStructure` (@CompRhys, #2139)
* Better error handling in QCOutput (@rkingsbury, #2147, #2165, #2135)
* Add progress bar for applying compatibility scheme (@CompRhys, #2136)
* Allow combining data with multiple molecule IDs in LAMMPS (@htz1992213, #2157)
* Update EDIFF in DFPT input set to be consistent with atomate (@utf, #2172)

* Change names of high-symmetry paths (@munrojm, #2144)
* Change default for filter_solids argument of PourbaixDiagram (@rkingsbury, #2177)

* Fix to improve precision in `FermiDos`, NOTE: this can result in significant changes in some instances (@nwinner, #2109)
* Fix for handling of Exceptions (@kmu, #2150)
* Fix for PourbaixEntry (@JosephMontoya-TRI, #2148)
* Fix for loading of settings from file when environment variables also set (@ardunn, #2164)
* Fix equation for calculation of k-spacing in SCAN sets, NOTE: this now results in a lower k-point density (@ab5424, #2163)
* Fix for parsing of VASP vasprun.xml when ALGO=CHI (@KazMorita, #2171)

* Documentation update for MP2020 corrections scheme (@rkingsbury, #2141)
* Documentation update for SCAN sets (@janosh, #2140)
* Documentation update for using CifWriter (@755452800, #2156)

## v2022.0.8

* PR #2130 @rkingsbury ensures that energy corrections applied to each anion
  have unique names (e.g., N vs. Cl vs. Br).
* PR #2133 @rkingsbury adds support for custom vdW radii to `QCInput` and
  `QChemDictSet`. These radii are used in the construction of PCM cavities and
  when calculating charges.
* PR #2123 from @gpetretto fixes bug in `get_conventional_standard_structure`
  method of the `SpacegroupAnalyzer` for triclinic crystals.
* PR #2134 from @ab5424 supports zopen in parsing lammps logs
* PR #2132 from @htz1992213 speeds up LammpsData.as_string for
  non-hybrid data with large coeff sections and adds as_lammpsdata method to
  CombinedData
* PR #2129 from @CifLord improves analysis of surface symmetry of slabs.
* PR #2117 from @nwinner contains bug fixes for bader caller.

## v2022.0.7

* Improved Gaussian Cube I/O (@nwinner, #2121)
* Updated van der Waals radii (@rkingsbury, #2122)
* Update `MaterialsProject2020Compatibility` for multi-anion systems (@rkingsbury, #2128)
* Fixes and improvements to Q-Chem parsing (@samblau, #2125)
* Bug fix for isseus with hard-coded path in `MaterialsProject2020Compatibility` (@CompRhys, #2124)
* Bug fix for DOS serialization (@zooks97, #2119)
* Bug fix for XDATCAR lattice parsing (@nkeilbart, #2115)
* Documentation link fix (@adam-kerrigan, #2127)

## v2022.0.6

* Feature to calculate Selling vectors and distances between Lattices (@bwjustus, #1888)
* XPS Spectrum class added (@shyuep, #2110, see `galore <https://github.com/SMTG-UCL/galore>`\_)
* Updated `MaterialsProject2020Compatibility` for formation energy correction (@rkingsbury, #2106)
* Bug fix for detecting broken bonds in slab generation (@fyalcin, #2015)
* Bug fix for electrodes (@jmmshn, #2101)
* Documentation improvement for get_conventional_standard_structure (@tom-wood, #2100)

## v2022.0.5

* Bug fix to remove possibility of duplicate edges in `StructureGraph` (@mkhorton, #2095)

## v2022.0.4 / v2021.3.9

* Element now has `ionization_energies`, `ionization_energy` and
  `electron_affinity` properties.
* Extensive documentation has been added on pymatgen compatibility and the
  new namespace architecture! We have also released a
  `template repo <https://github.com/materialsproject/pymatgen-addon-template>`\_
  to help new developers write add-ons for pymatgen! Check out our
  :doc:`contributing page</contributing>` for details.

## v2022.0.3

* Another bug fix release! Now SETTINGS have been moved to pymatgen.core.

## v2022.0.2 (Yanked)

* Bug fix release for missing package data files in v2022.0.1

## v2022.0.1 (Yanked)

* `pymatgen`, `pymatgen.ext`, `pymatgen.io` and `pymatgen.analysis` are now
  namespace packages. Note that this does not affect normal usage of pymatgen
  from v2022.0.0. All imports remain the same. However, it does allow developers
  to write "add-ons" to these subpackages. A full documentation with examples
  and templates is in the works to guide developers on how to write these
  packages.

## v2022.0.0 (Yanked)

* This is the new version of pymatgen going forward. Root-level imports have been removed. Please see
  <https://pymatgen.org/compatibility.html> on how to update your code for compatibility with v2022.

## v2021.3.5

* Backwards incompatible changes in v2021.3.4 have been removed. Instead another semantic version v2022.0.0 has been
  released. Future critical bug fixes will be backported to v2021.x.x, but the main line of development will occur on
  v2022.0.0 onwards.

## v2021.3.4 (Yanked)

* **Backwards incompatible**: Pymatgen root imports have been removed from
  v2021.3.4 in preparation for a change to a more modular, extensible
  architecture that will allow more developers to contribute.

  If your existing code uses `from pymatgen import <something>`, you will need to make
  modifications. The easiest way is to use an IDE to run a Search and Replace.
  First, replace any `from pymatgen import MPRester` with
  `from pymatgen.ext.matproj import MPRester`. Then, replace
  `from pymatgen import` with `from pymatgen.core import`. Alternatively, if you
  are using a Mac command line, you can do::

  find . -name '_.py' | xargs sed -i "" 's/from pymatgen import MPRester/from pymatgen.ext.matproj import MPRester/g'
  find . -name '_.py' | xargs sed -i "" 's/from pymatgen import/from pymatgen.core import/g'

  From a Linux command line, you can do::

  find . -name '_.py' | xargs sed -i 's/from pymatgen import MPRester/from pymatgen.ext.matproj import MPRester/g'
  find . -name '_.py' | xargs sed -i 's/from pymatgen import/from pymatgen.core import/g'

  This should resolve most import errors and only a few more modifications may
  need to be done by hand.

  Specifically, the following "convenience imports" have been removed in favor of
  their canonical import::

  from pymatgen import Composition # now "from pymatgen.core.composition import Composition"
  from pymatgen import Lattice # now "from pymatgen.core.lattice import Lattice"
  from pymatgen import SymmOp # now "from pymatgen.core.operations import SymmOp"
  from pymatgen import DummySpecie, DummySpecies, Element, Specie, Species # now "from pymatgen.core.periodic_table ..."
  from pymatgen import PeriodicSite, Site # now "from pymatgen.core.sites ..."
  from pymatgen import IMolecule, IStructure, Molecule, Structure # now "from pymatgen.core.structure ..."
  from pymatgen import ArrayWithUnit, FloatWithUnit, Unit # now "from pymatgen.core.units ..."
  from pymatgen import Orbital, Spin # now "from pymatgen.electronic_structure.core ..."
  from pymatgen import MPRester # now "from pymatgen.ext.matproj ..."

## v2021.3.3

* **Backwards incompatible**: pymatgen.SETTINGS have been moved to
  pymatgen.settings.SETTINGS. In general, this should not lead to many breakages
  since most of these settings are used within pymatgen itself.
* **Backwards incompatible**: pymatgen.loadfn and get_structure_from_mp have been
  removed since no one was using them.
* critic2_caller has been refactored. (@samblau)
* Improved hash for Composition (@CompRhys)
* Fixes Outcar parsing for VASP 6.2.0. (@MichaelWolloch)
* Allow None for Gaussian functional, bset, charge and multiplicity (@eimrek)

## v2021.2.16

* Add a new interface to OPTIMADE-compliant APIs in pymatgen.ext.optimade (@mkhorton, #2066)
* Addresses missing text file, all_cg.txt, in package
* Note that a previous released increased the suggested minimum numpy version and suggested minimum Python version
* Previous release also dropped support for aconvasp since this the interface has not been maintained

## v2021.2.14

* Misc bug fixes.

## v2021.2.12

* Misc bug fixes.

## v2021.2.8.1

* Patch release to restore `CompositionError` to preserve backwards compatibility.

## v2021.2.8

* Addition of new job types to Q-Chem IO (@espottesmith, #2055),
  note `metal_edge_extender` has been moved into `local_env` for this change
* Improvements to string utils, new Stringify mixin with
  to_pretty_string(), to_latex_string(), to_unicode_string(), to_html_string() (@shyuep)
* Improvements to build system (@shyuep, @ltalirz, see #2046)
* Entry is now immutable, removing "in_place" option for normalize (@mkhorton, @mattmcdermott, #2060)
* Bug fix for co-ordination geometry finder (@davidwaroquiers, #2035)
* Bug fix for GibbsComputedStructureEntry (@mattmcdermott)

## v2021.1.28

* Ability to read Lobster wavefunctions (@JaGeo, #2034)
* Method to estimate number of bands for VASP calculation (@rwoodsrobinson, #2044)
* Q-Chem cube file plotting and improvements to output parsring (@samblau, #2032)
* Improvements to PhaseDiagram hashing and equality checking (@CompRhys, #2014)
* Improvements to pymatgen import speed (@mkhorton, #2031)
* Bug fix for k-path generation (@munrojm, #2037)
* Bug fix for parsing of core potentials from VASP (@utf, #2033)

## v2020.12.31

* End of 2020 release with minor bug fixes for cli scripts.

## v2020.12.18

* New IsayevNN nearest-neighbor algorithm (@utf, #2011)
* Improvements to electrode objects (@jmmshn, #2016)
* Improvements to Element and PhaseDiagram (@jmmshn, #2005)
* Bug fix to increase minimum version of setuptools which was causing incompatible versions of numpy to be installed for some users (@shyuep, see issue #2010)
* Bug fix to VASP run type detection (@rkingsbury, #2007)

## 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

1. Cp2K support (@nwinner)
2. Better BSPlotter (@fraricci)
3. Better deprecation warnings.
4. Bug fix for Py3.9 support.
5. 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 (@Andrew-S-Rosen, #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 (@CifLord)
* 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 (@CifLord, @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

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

## v2019.10.4

1. 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 attributes.
  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 subtraction 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 (@CifLord)
* 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 (@CifLord)

## 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 (@CifLord)
* 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 (@CifLord)
* 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

.. code-block:: pycon

    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 = f"Li2O_kpoints_{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(f"{d}/vasprun.xml").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 (@CifLord)
* 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, @CifLord)

## 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 coordinate 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, including 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 (@CifLord)

## 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 available 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)
* Optional 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.
* Switch 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 significant 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 NDarray 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 analyzer. Invert sq_disp_ions for more intuitive handling.

## v3.0.2

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.

## 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 <https://pypi.python.org/pypi/monty>`\_, 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
  structures (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.