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CHANGELOG.md

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Changelog

All notable changes to libcasm-configuration will be documented in this file.

The format is based on Keep a Changelog, and this project adheres to Semantic Versioning.

[2.0a7] - 2024-12-12

Fixed

  • Fixed tests in test_config_space_analysis.py which were overly strict and failed unnecessarily.

[2.0a6] - 2024-12-10

Added

  • Added libcasm.clusterography.make_custom_cluster_specs, which takes a custom site filter function to generate a ClusterSpecs with custom_generators generated with the custom site filter. This approach allows creating a ClusterSpecs that is customized, as with a custom site filter, but still works to save/load without to_dict/from_dict needing the custom filter.
  • Added make_canonical_local_configuration, make_distinct_local_cluster_sites, and make_distinct_local_perturbations to libcasm.enumerate.
  • Added local_symgroup_rep to libcasm.configuration.Supercell.
  • Added distances and phenomenal_distances to libcasm.clusterography.Cluster
  • Added libcasm.local_configuration for local configuration enumeration and comparison.
  • Added libcasm.enumerate.ConfigEnumLocalOccupations for local configuration enumeration.
  • Added make_supercells_for_point_defects, find_optimal_point_defect_supercells, make_required_sites, plot_point_defect_supercell_scores, and print_point_defect_supercell_info to libcasm.enumerate to help find optimal supercells for calculations.

Changed

  • Changed libcasm.clusterography.make_cluster_group documentation to state how the head group of the cluster group is set.
  • Changed libcasm.occ_events.make_occevent_group to set the head group of the occ_event group to the head group of the group used to generate the occ_event group. In typical use this means the head group of the occ_event group is the prim factor group rather than a subgroup, even if a subgroup was used to generate the occ_event group.
  • Changed the sorting order of libcasm.occ_events.OccEvent to sort by (cluster size, site distances, reverse molecule count), instead of by (cluster size, molecule count, site distances).

Fixed

  • Fixed libcasm.occ_events.OccEvent.copy_reverse, which was doing copy_sort instead.

[2.0a5] - 2024-08-13

Fixed

  • Fixed libcasm.clusterography.equivalents_info_from_dict, which was trying to read clusters from the wrong position. This method was not used to read equivalents_info.json for KMC simulations.
  • Fixed libcasm.occ_events.get_occevent_coordinate, which was using the reverse of the appropriate translation to get the unitcell_index.
  • Fixed to_json(to_json(config::Configuration) and read_dof_values to properly support writing and reading DoF values in both the prim and standard basis.

Changed

  • Changed the by_supercell and by_supercell_list methods of libcasm.enumerate.ConfigEnumAllOccupations to only do default continuous DoF.
  • Changed the skip_non_canonical parameter of the by_linear_site_indices, by_integral_site_coordinate, by_sublattice, by_cluster, and by_cluster_list methods of libcasm.enumerate.ConfigEnumAllOccupations to skip_equivalents.
  • Changed ConfigEnumAllOccupations methods that take a background configuration to maintain the orientation of continuous DoF.
  • Changed ClusterSpecs.from_dict to allow reading CASM v1 cluster specs JSON by checking for a "params" attribute and parsing that if it exists.
  • Changed ClusterSpecs.from_dict to warn if the prim has local DoF but no "orbit_branch_specs" attribute is present.
  • Changed occ_events to_json methods for occ_events::OccPosition, occ_events::OccTrajectory, and occ_events::OccEvent to optionally accept occ_events::OccSystem.

Added

  • Added option to include phenomenal site to local-cluster site distances by passing the phenomenal cluster to libcasm.clusterography.Cluster.to_dict.
  • Added libcasm.configuration.Supercell.symgroup_rep.
  • Added copy methods for libcasm.configuration.SupercellSymOp.
  • Added Configuration.copy, ConfigurationWithProperties.copy, SupercellRecord.copy, ConfigurationRecord.copy, Cluster.copy, and OccEvent.copy methods.
  • Added libcasm.configuration.copy_local_dof_values and libcasm.configuration.copy_global_dof_values
  • Added which_dofs parameter to libcasm.configuration.make_invariant_subgroup
  • Added libcasm.enumerate.SuperConfigEnum
  • Added libcasm.ConfigEnumAllOccupations.by_supercell_with_continuous_dof
  • Added __repr__ for Cluster, ClusterOrbitGenerator, and ClusterSpecs.
  • Added to_json methods for config::ConfigSpaceAnalysisResults and config::DoFSpaceAnalysisResults.
  • Added Prim.__repr__, Supercell.__repr__, SupercellRecord.__repr__, Configuration.__repr__, ConfigurationRecord.__repr__, ConfigurationWithProperties.__repr__, DoFSpaceAnalysisResults.__repr__.
  • Added ConfigSpaceAnalysisResults.to_dict and DoFSpaceAnalysisResults.to_dict methods.
  • Added OccSystem.__repr__, OccPosition.copy, OccPosition.__copy__, OccPosition.__deepcopy__, OccPosition.__repr__, OccEventRep.__repr__, OccEventRep.copy, OccEventRep.__copy__, OccEventRep.__deepcopy__, OccEvent.__repr__.

[2.0a4] - 2024-07-16

Added

  • Added libcasm.sym_info.make_lattice_point_group
  • Added libcasm.configuration.Prim.lattice_point_group
  • Added libcasm.configuration.io.tools to get properties from CASM objects
  • Added libcasm.configuration.io.spglib to interface with spglib
  • Added libcasm.io.symgroup_to_dict_with_group_classification to add group classification from spglib to SymGroup.to_dict data.
  • Added libcasm.clusterography.make_local_cluster_group

Changed

  • Changed libcasm.clusterography.make_cluster_group, CASM::clust::make_cluster_group, and CASM::clust::make_cluster_groups so that the head group of the cluster group is set to the head group of the group used to generate the cluster group. In typical use this means the head group of the cluster group is the prim factor group rather than a subgroup, even if a subgroup was used to generate the cluster group.
  • Fixed spelling of reservoir (#16)
  • Wheels compiled with numpy>=2.0.0

Fixed

  • Fixed occ_symgroup_rep and atom_position_symgroup_rep in CASM::config::PrimSymInfo and libcasm.configuration.Prim, which were giving the inverse of the documented permutation.

[2.0a3] - 2024-03-15

Fixed

  • Fixed CASM::config::make_distinct_cluster_sites
  • Fixed CASM::config::dof_space_analysis for global DoF with non-primitive unit cell configuration
  • Fixed bug in Configuration.from_structure that caused error in resulting occupation

Changed

  • Changed libcasm.configuration.Prim.is_atomic, which was returning has_anisotropic_occupants
  • Changed libcasm.configuration.is_canonical_configuration arguments for providing a subgroup
  • Changed most methods with no arguments that return a value without doing additional work to readonly attributes

Added

  • Added prototype and include_subclusters attributes to libcasm.clusterography.IntegralClusterOrbitGenerator
  • Added ConfigEnumAllOccupations, ConfigEnumInfo, ConfigEnumMeshGrid, ScelEnum, make_all_distinct_periodic_perturbations, and make_distinct_cluster_sites to libcasm.enumerate
  • Added make_all_super_configurations_by_subsets and make_distinct_super_configurations to libcasm.configuration
  • Added excluded_species option to Configuration.to_structure and ConfigurationWithProperties.to_structure
  • Added with_prim_basis option to Configuration.to_dict and ConfigurationSet.to_dict to allow output of DoF values in the prim basis, along with "basis" tag which is respected on reading from JSON/dict.
  • Added set_order_parameters, make_dof_space, order_parameters, order_parameters_contribution, dof_values_vector, and dof_values_vector_contribution methods to libcasm.configuration.Configuration
  • Added CASM::config::cluster_from_index_vector and CASM::config::cluster_from_index_set
  • Added libcasm.irreps.IrrepDecomposition and libcasm.irreps.MatrixRepGroup for generic irreducible space decompositions

Removed

  • Removed to_canonical_supercell and from_canonical_supercell which can be too easily misinterpreted.

[2.0a2] - 2023-12-11

Fixed

  • Fix bug in irrep decomposition
  • Fix comparison of Configuration with equivalent but distinct supercell

Added

  • Added more irrep decomposition, DoF space analysis, and config space analysis tests
  • Added options to config_space_analysis and dof_space_analysis methods to specify default occupation mode on a site or sublattice basis
  • Added CASM::config::make_dof_space_rep and libcasm.configuration.make_dof_space_rep
  • Added libcasm.configuration.ConfigurationWithProperties, and methods for libcasm.configuration.SupercellSymOp to act on ConfigurationWithProperties
  • Added site_index_converter and unitcell_index_converter accessors to libcasm.Supercell.
  • Added to_structure and from_structure to libcasm.configuration.Configuration and libcasm.configuration.ConfigurationWithProperties for conversions between atomic structures and configuration
  • Added more access to matrix reps from PrimSymInfo in libcasm.configuration.Prim
  • Added to_index_list, to_index_set, sort, sorted, is_sorted, rmul to libcasm.clusterography.Cluster
  • Added make_periodic_equivalence_map, make_periodic_equivalence_map_indices, make_local_equivalence_map, and make_local_equivalence_map_indices to libcasm.clusterography
  • Added to_dict and from_dict methods to libcasm.configuration.Prim

Changed

  • Changed libcasm.clusterography.make_prim_periodic_orbits to make_periodic_orbits

Deprecated

  • Deprecated to_json and from_json methods of libcasm.configuration.Prim

[2.0a1] - 2023-08-21

This release creates the libcasm-configuration comparison and enumeration module. It includes:

  • Classes for representing supercells, configurations, clusters, and occupation events
  • Methods for comparing and enumerating unique configurations, clusters, occupation events, and local environments
  • Methods for generating orbits of symmetrically equivalent configurations, clusters, and occupation events
  • Methods for copying configurations to make sub- or super-configurations
  • Methods for generating symmetry groups, and constructing and applying symmetry representations
  • Methods for performing irreducible space decompositions and finding symmetry adapted order parameters

This distribution package libcasm-configuration contains several Python packages of use for configuration comparison and enumeration:

  • libcasm.sym_info
  • libcasm.irreps
  • libcasm.clusterography
  • libcasm.configuration
  • libcasm.occ_events
  • libcasm.enumerate

This package may be installed via pip install, using scikit-build, CMake, and pybind11. This release also includes usage examples and API documentation, built using Sphinx.