v2025.10.7

• PR #4502 Fix: indexing error in Procar._read() by @finnrk
  Major changes:
  • Fixes a bug related to indices when skipping repeated k-points while reading PROCAR (for example, the double-counting of symmetry points when using a k-path for plotting bandstructure).
    Previously, projections, eigenvalues, occupations and weights would be attributed to the wrong k-points. Also, the k-point following the skipped k-point would have complex projections of NaN, as well as an occupation, weight, eigenvalue and squared projections of 0.
• PR #4503 Replace print with logging by @DanielYang59
  • replace print with logging, I assume pymatgen as a lib code shouldn't use print...
  • remove some print from tests
• PR #4510 suppress runtime warning from boltztrap2 by @DanielYang59
  close #2317
• PR #4512 Fix missing sdist from PyPI by @DanielYang59
  fix #4509
  tested in my fork: https://github.com/DanielYang59/pymatgen/actions/runs/18279908313/job/52040659228
• PR #4491 Deprecate projected_magnetisation with projected_magnetization (US spelling) by @DanielYang59
  fix #4382
• PR #4493 Composition.get_wt_fraction return float instead of FloatWithUnit by @DanielYang59
  fix #4492
• PR #4496 Overwrite __rtruediv__ for FloatWithUnit, fix ArrayWithUnit loses unit_type when unpickled by @DanielYang59
  • fix #4495
  • Check ArrayWithUnit behaviour
  • Fix unpickle ArrayWithUnit loses unit_type
  • Add some tests for core.units, https://app.codecov.io/gh/materialsproject/pymatgen/blob/master/pymatgen%2Fcore%2Funits.py
• PR #4490 Replace linear_assignment with scipy linear_sum_assignment by @DanielYang59
  • Replace linear_assignment with scipy linear_sum_assignment
  • Speed benchmark

  Benchmark

  WSL2 Ubuntu 24.04 (AMD64)
  Master branch:

  n | avg_time (s) |  std_dev (s)
  ------------------------------------
  100 |     0.000104 |     0.000018
  500 |     0.004302 |     0.002333
  1000 |     0.018374 |     0.006702
  5000 |     1.049615 |     0.327349
  

  Current branch:

  n | avg_time (s) |  std_dev (s)
  ------------------------------------
  100 |     0.000121 |     0.000030
  500 |     0.005082 |     0.002957
  1000 |     0.018487 |     0.006484
  5000 |     1.062805 |     0.332552
  

• PR #4440 JDFTXOutfileSlice.vibrational_modes and JDFTXOutfileSlice.vibrational_energy_components by @benrich37
  Major changes:
  • feature 1: Parsing and storage of vibrational modes within a JDFTXOutfileSlice
    -- Stored as a list[dict], where each dict contains
    --- "Type": str
    ---- either "Imaginary", "Zero", or "Real"
    --- "Type index": int
    ---- (Base 1) index of the mode among other modes of the same frequency type
    --- "Degeneracy": int
    ---- Degeneracy of the mode (ie if mode["Degeneracy"] == 2, than there is one other mode in the list with the same frequency)
    --- "Frequency": float | complex
    ---- Frequency of the vibration in eV
    --- "IR intensity": float
    ---- IR intensity of the vibrational mode in e^2/amu as derived from dipole of the vibration
    --- "Displacements": NDArray[float]
    ---- Displacement vector representing the vibrational mode (converted from Bohr to Angstrom as magnitude of vector is a input variable for vibrational analysis in JDFTx)
    -- Testing for vibrational mode parsing
  • feature 2: Parsing and storage of vibration energy components within a JDFTXOutfileSlice
    -- Stored as a dict[str, float], containing
    --- "T" : Temperature at which free energy was evaluated (in K)
    --- Dumped free energy components in eV
    -- Testing for vibrational energy components parsing
• PR #4487 Fix TranslateSitesTransformation by @Rastow
  There was a bug in the TranslateSitesTransformation class. Both index variables in apply_transformation are named identically. The test case did not capture this error. I changed the existing test case to fail when run with the old code and renamed the variables.
• PR #4447 Fix has_cobicar when NcICOBILIST is present by @tomdemeyere
  When icobiBetween is activated lobster prints out the NcICOBILIST.lobster file. In the lobster output we find "Writing COBICAR.lobster, ICOBILIST.lobster and NcICOBILIST.lobster..." instead of the regular line. The current parser then returns False even if the COBICAR.lobster is present.
  Also, it seems that has_cohpcar and has_coopcar are flipped?
  Switching to a regex approach on the whole files (not \n split) would allow much greater flexbility, performance and robustness.
  @JaGeo @naik-aakash
  • Google format doc strings added. Check with ruff.
  • Type annotations included. Check with mypy.
  • Tests added for new features/fixes.
  • If applicable, new classes/functions/modules have duecredit @due.dcite decorators to reference relevant papers by DOI (example)
    Tip: Install pre-commit hooks to auto-check types and linting before every commit:

  pip install -U pre-commit
  pre-commit install

• PR #4469 Loosen requests lower pin, fix pre-commit errors by @DanielYang59

  Summary

  • Loosen requests upper pin, current pin seems too strict and might cause unresolvable dependency
  • Fix a few deprecation warnings
  • Fix some new ruff errors from pre-commit
• PR #4479 Move JDFTx sets from atomate2 to pymatgen by @cote3804
  Following a request by @utf in an atomate2 PR, I am moving our input set from atomate2 to pymatgen.
  This PR adds a sets.py file with one new class, JdftxInputSet, which does little more than wrap the other JDFTx I/o classes. The only minor change to the original atomate2 code is that the __init__ method now accepts a pymatgen Structure instead of a JDFTXStructure.
  A yaml defining the base input set, BaseJdftxSet.yaml was also moved from atomate2.
  I added two basic tests to check that both loading from an input file and from a JdftxInfile are working and that the file written by the input set yields the expected JdftxInfile.
• PR #4484 Fix jdftx.outputs usage of 3.11+ only syntax by @DanielYang59
  Fix the following 3.11+ only syntax:
• PR #4473 Fix label in NEBAnalysis by @DanielYang59
  To close #4465
  • Incorrect label (and value)
  • glob now would use exact match first (['path_1_Li_sv2004_test/00/POSCAR.xyz', 'path_1_Li_sv2004_test/00/POSCAR', 'path_1_Li_sv2004_test/00/POSCAR.vasp'])https://github.com/materialsproject/pymatgen/blob/f01009c390a3df02d4d45b8f0225cf59305ee7bf/src/pymatgen/analysis/transition_state.py#L261
  • Deprecate spline_options dict with boolean flag zero_slope_saddle as there's only one boolean config available: https://github.com/materialsproject/pymatgen/blob/f01009c390a3df02d4d45b8f0225cf59305ee7bf/src/pymatgen/analysis/transition_state.py#L70
• PR #4260 Use external Package for FHI-aims IO interface by @tpurcell90
  Major changes:
  • moved FHI-aims specific content into a separate package (pyfhiaims) for ease of maintenance (stop multiple libraries from implementing the same basic interface)

  Todos

  If this is work in progress, what else needs to be done?
  • Workout how to best test the aims io interface/dependency tracker
  • check with community this does not break their setups
• PR #4476 patch ReDOS vulnerability in GaussianInput.from_string by @lbluque
  Major changes:
  • Patches ReDOS vulnerability mentioned in #2755
• PR #4448 Remove LOBSTER output file trailing line sensitivity by @DanielYang59
  • Remove LOBSTER output file trailing line sensitivity, fix #4215
    str.splitlines(keepends=False):

  Unlike split() when a delimiter string sep is given, this method returns an empty list for the empty string, and a terminal line break does not result in an extra line:
  cc @JaGeo @naik-aakash

• PR #4454 Fix unit for Element properties: density_of_solid and Molar volume by @DanielYang59

  Summary

  • Remove unit in docstring for Element properties, to close #4453
  • Check other units in docstring
• PR #4461 Handle numpy array for selective dynamics in Structure by @DanielYang59

  Summary

  • Handle numpy array for selective dynamics in Structure, to fix #4460
  • Double check consistent behaviour from json and orjson, also check round trip?
  • Unit test
• PR #4464 Update analyzer.py by @boyoungzheng
  Missing a letter "s" for site.species in pymatgen.symmetry.analyser.SpacegroupAnalyzer.get_primitive_standard_structure()
  Major changes:
  • feature 0:
  • fix 1: Missing a letter "s" for site.species in pymatgen.symmetry.analyser.SpacegroupAnalyzer.get_primitive_standard_structure()
• PR #4446 Efficiency updates for __str__() methods by @kavanase
  Small change to improve the efficiency of Species.__str__, which can become a bottleneck in some workflows which e.g. subselect sites in a structure based on the species, before doing further processing (e.g. defect site matching in doped).
  Improves efficiency by reducing redundant getattr calls.
• PR #4438 Add basic S3 object retrieval to the pymatgen user agent by @esoteric-ephemera
  The MP API has changed to accommodate incre...

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:

  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 TagContainers 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

  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 FloatTags 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) 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...

v2025.5.2

• 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
  • 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