CHANGELOG.md

Changelog

All notable changes to this project will be documented in this file.

This project adheres to Semantic Versioning.

Unreleased

0.37.0 - 2024-04-09

Added

• Add SphericalVector interpolation method using parallel transport (#163)
• Added arrayForEachDim method

Fixed

• Bugfix for regional grids with ny > nx
• Fix build for configuration setting ATLAS_BITS_LOCAL=64

Changed

• Use new LocalConfiguration baseclass functions in util::Config and util::Metadata instead of eckit::Value backdoor
• atlas_io is an adaptor library when eckit_codec is available (#181)

0.36.0 - 2023-12-11

Added

• Add TriangularMeshBuilder with Fortran API, so far for serial meshes only
• Add Fortran API for CellCollumns functionspace
• Add EqualAreaPartitioner which is geometry based rather than loadbalanced like EqualRegionsPartitioner

Fixed

• Compilation with Intel LLVM compiler
• Fix 180 degrees phase shift error in MDPI_gulfstream function

Changed

• Update install scripts
• Preparation for using eckit::codec as backend for atlas_io

0.35.1 - 2023-10-24

Added

• Don't output with output::Gmsh the triangle elements with wrong orientation when coordinates are "lonlat"
• Add control to skip Gmsh-output of triangles with too large edge length ratio
• Configurable geometry in KDTree
• Use configurable KDTree geometry in PointCloud
• atlas-grid-points executable to list grid points
• Allow constructor of atlas::io::ArrayShape with different integer types
• Support atlas_io with vectorstd::int64_t

Fixed

• Control FPE in StructuredColumns::checksum to avoid overflow and invalid in unimportant halo regions
• Fixes to MeshBuilder validate_mesh_vs_grid

Changed

• Use search radius in FiniteElement interpolation when mesh defines metadata to do so

0.35.0 - 2023-02-10

Added

• Add accessors for the GridBox class (MIR-632)
• Add FunctionSpace::partition() field
• Add configurable MPI communicator to data structures (#131)
• Add single precision support for fvm::Nabla
• Implement PointCloud parallel construction with halo_radius

Fixed

• Fix StructuredMeshGenerator for Gaussian grids that don't start at 0 degrees (ATLAS-375)
• Remove functionspace::Spectral via Trans initialisation (fixes #153)
• Enable MeshBuilder to set up the Grid (#152)
• Fix use of cmake option ATLAS_ENABLE_TRANS as in a bundle

Changed

• Cleanup long-standing temporary element types. API change but with deprecated old API
• Deprecated rename Mesh::nb_partitions -> Mesh::nb_parts
• Implement Delaunay triangulation using Qhull instead of CGAL but CGAL can still be enabled instead for now

0.34.0 - 2023-07-10

Added

• Fieldset::metadata (#126)
• Fieldset::adjointHaloExchange
• Field/Fieldset::clone method
• Functions to enable/disable FPE
• Add function to build mesh from imported connectivity data (#135)
• Implement field::for_each capabilities (#139)
• Introduce colon-separated environment variable ATLAS_PLUGIN_PATH to simplify plugin detection
• Introduce atlas::mdspan, contributed from github.com/kokkos/mdspan
• Add function Field::horizontal_dimension() -> std::vector<idx_t>
• Setup horizontal_dimensions() for BlockStructuredColumns fields
• Upgrade the halo exchange procedure for the function space 'PointCloud' (#120)

Fixed

• Enable latitude normalisation in KDTree coordinate transform (#140)
• Fix LocalView indexing bug for non-contiguous slices
• C++17 flag public propagation to downstream C++ CMake packages
• Fix cells().global_index() metadata for RegularLonLat grids in StructuredMeshGenerator
• BuildHalo: mark interior added cells as ghost

0.33.0 - 2023-04-03

Added

• Add support for StructuredPartitionPolygon with halo > 0
• Add information on atlas having PROJ support

Changed

• C++17 standard is now a requirement

Fixed

Fix StructuredInterpolation2D with retry for failed stencils

0.32.1 - 2023-02-09

Added

• Added (lon, lat) to (alpha, beta) transforms to cubed sphere projection

0.32.0 - 2023-01-23

Added

• Added BlockStructuredColumns FunctionSpace
• Added function SolidBodyRotation
• Added convenience Fortran constructors for ShiftedLonLat, SHiftedLon, ShiftedLat
• Support for more FunctionSpaces in various interpolation methods

Changed

• PolygonLocator now wraps around longitudes for non-matching domains
• StructuredMeshGenerator can generate meshes with partitions without elements
• SerialDistribution makes every MPI task have the entire mesh

Fixed

• Remove assertion for checking of empty mesh in NodeColumns FunctionSpace
• Gaussian latitudes can now be computed for very high resolution, without running out of memory.
• Interpolation to functionspaces with empty partitions

0.31.1 - 2022-11-11

Fixed

• Fix bug introduced in StructuredMeshGenerator global numbering with release 0.31.0 in commit a63fc62a2
• Fix healpix global numbering for pentagon pole elements in parallel
• Fix validity check of atlas::HealpixGrid

0.31.0 - 2022-11-10

Added

• Extend PointCloud functionspace to do halo exchanges, including Fortran API
• Add FunctionSpace::gather and FunctionSpace::scatter abstraction

Changed

• Improve performance of MatchingMeshPartitionerLonLatPolygon using OpenMP
• Improve performance of BuildHalo using OpenMP and unordered_map
• Improve performance of StructuredMeshGenerator using OpenMP
• Improve performance of ATLAS_TRACE
• Reduce memory peak in GatherScatter setup
• Global element numbering of RegularLonLat grids is now following rows independent of partitioning

Fixed

• Running CI with Github Actions
• Fix output of atlas-grids y-range for shifted grids
• Fix building with ATLAS_BITS_LOCAL=64

0.30.0 - 2022-08-22

Added

• Fortran API for Interpolation::execute_adjoint()
• Fortran API for FieldSet::name()
• Fortran API for MeshGenerator::generate(grid,partitioner)
• Pentagon element type
• SphericalHarmonic function
• New interpolation method: ConservativeSphericalPolygonInterpolation
• Support 'variables' option in functionspace::PointCloud::createField

Changed

• Atlas-IO is now standalone project, still embedded but only depending on eckit
• Deprecate Trans naming of 'ifs' or 'trans' in favour of 'ectrans'
• Default StructuredMeshGenerator partitioner is equal_regions instead of trans/ectrans

Fixed

• Fix global numbering HEALPix grid to standard
• Fix NodeColumns remote_index for parallel orca grids
• Fix use of ATLAS_LINALG_DENSE_BACKEND environment variable

0.29.0 - 2022-04-21

Added

• MatchingMeshPartitioner "cubedsphere"
• Interpolator "cubedsphere-bilinear"
• Improvements to Interpolation::Cache
• Add support for rank 2 fields when a nonlinear action is added to the interpolator
• Create Array using ArraySpec only

Changed

• FieldSet::has(...) replaces FieldSet::has_field(...)
• Metadata return value to Interpolation::execute()
• Rename BilinearRemapping to UnstructuredBilinearLonLat

Fixed

• Compatibility with proj version >= 8
• Compatibility with eckit version <= 1.18.5
• Compatibility with GridTools backend and using 64bit idx_t
• Wrongly computed Jacobian::transpose() introduced in 0.28.0
• Fix bug where using ectrans was not enabling adjoint of invtrans
• Avoid segfault when OpenMP tasking is broken, as it is with AppleClang and LLVM libomp

0.28.1 - 2022-03-14

Fixed

• Fix compilation for GNU 7.3

0.28.0 - 2022-03-02

Added

• Assignment of ArrayView from ArrayView
• Grid "regional_variable_resolution" via a new VariableResolutionProjection
• CubedSphereDualMeshGenerator
• VortexRollup function as analytical field for initialising data
• ConvexSphericalPolygon utility class
• Improve Projection::Jacobian
• Initial implementation for bilinear interpolation for unstructured meshes

Changed

• Use new eckit (1.19.0) Sparse and Dense linear algebra API
• General robustness improvements to CubedSphere to using functionspaces with various halos

Fixed

• Workarounds to fix compilation with Fujitsu compiler
• Workarounds to avoid Cray compiler problems with certain flag combinations
• CellColumns::haloExchange for meshes with multiple element types
• Computation of HEALPix mesh remote indices.

0.27.0 - 2021-12-03

Added

• Adjoint interpolation with some restrictions
• Cubed sphere grid partitioner
• Cubed sphere parallel mesh generation
• Cubed sphere function spaces
• Fortran interfaces to Projection methods
• Support discovery of open-source ectrans
• Dense linear Algebra matrix_multiply abstraction

Changed

• Remove etc/atlas/config.yaml because defaults should be in code
• Naming of sparse_matrix_multiply backend 'omp' -> 'openmp'
• Applied clang-format 13.0.0 (all files touched)

0.26.0 - 2021-08-23

Added

• Support for cubed sphere grids and preliminary support for cubes sphere mesh generation.

Fixed

• Compilation with altas_bits_local=64
• Too aggressive optimisation with gnu 11
• Compatibility with cmake 3.20 and nvhpc compilers

0.25.0 - 2021-05-18

Added

• New concept Redistribution to redistribute field on same grid but with different partitioner
• Support for Trans::invtrans_adj() and related methods
• Introduce ~atlas/etc/atlas/config.yaml
• atlas-io with support for encoding/decoding std::array
• atlas-io print support for tiny arrays

Changed

• atlas-io version 0.2
• Move util::SpecRegistry to non-templated grid::SpecRegistry

Fixed

• minor bug fixes

0.24.1 - 2021-04-06

Fixed

• Periodic halo for HEALPix mesh
• General warnings and suggestions by DeepCode bot
• Compilation problems with clang 3.8

0.24.0 - 2021-03-19

Fixed

• Fixed hang in band distribution for L160000x8000 grid
• Fixes to Spectral functionspace and TransIFS regarding vertical levels

Changed

• Requires eckit 1.16

Added

• atlas-io first version, not for operational use
• Spec registry for grids

0.23.0 - 2021-01-19

Fixed

• Structured interpolation method interpolating to area straddling Greenwich.
• Fixes when compiling with ATLAS_BITS_LOCAL=64

Changed

• Possibility to link to alternative open-source version of IFS trans library.

Added

• Caching mechanism for interpolation

0.22.1 - 2020-10-22

Fixed

• Installation of PGI compilers via tools/install-pgi.sh
• Allow dependency on older Eigen 3.2 which does not use CMake targets

0.22.0 - 2020-10-14

Fixed

• Feature INIT_SNAN was not working
• Support KNearestNeighbour interpolation for functionspace with smaller halo than the mesh contains
• Support array size up to size_t limit

Changed

• Migration to use ecbuild 3.4
• ATLAS_BITS_LOCAL can be configured to 32 or 64

Added

• Fields can be created with given alignment, which adds padding in innermost dimension
• Added conservative interpolation with "grid-box average" and "grid-box maximum"
• Missing value definition for fields
• Add support for missing values in matrix-based interpolation methods
• Floating point trapping and signal handling mechanism
• Fortran: GridDistribution constructors
• Fortran: Domain access
• Fortran: Get lonlat_bounding_box via domain
• Possibility to access Jacobian of projections (with only some projections implemented)

0.21.0 - 2020-06-23

Fixed

• Fixed Rotation order of applying the rotation angle
• Fix nabla computation of surface vector fields
• Fix registration and destruction issues of halo-exchange caches
• Workaround Clang compiler problem with OpenMP tasking, using introspection
• Fix bug in conversion of negative degrees to microdegrees
• Fix problem in distribution of work amongst OpenMP threads in StructuredColumns::setup
• Fix problem with StructuredColumns creation for grids defined with domains with negative West
• Fix computation of Grid::lonlatBoundingBox for arbitrary projections crossing the dateline.

Changed

• Snap LinearSpacing values to start and endpoint to allow exact comparisons
• Improved performance and memory requirement of cropping of large StructuredGrids
• Regional grids by default now have a positive y-numbering (previously negative).

Added

• PolygonLocator based on functionspace partition polygons.
• KDTree class which abstracts eckit concrete implementations, including Fortran interface
• Geometry class with factory mechanism to configure which spheroid to use, including Fortran interface
• StrcutredGrid function for i,j to index and inverse
• Fortran interface to create StructuredColumns with custom distribution
• Fortran interface to grid spec
• Fortran interface to Projection
• Adjoint of HaloExchange
• Plugin mechanism to load plugins at runtime.
• Fortran constructors for atlas_RegionalGrid
• Fortran constructors for projected reduced Gaussian grids
• Add copy constructor and assignment operator for atlas::vector
• Mercator projection support for scaling, and operation on ellipsoid.
• Grid Distribution can now also be created as a function, e.g. for Serial or Bands

0.20.2 - 2020-04-27

Fixed

• Avoid 100ds of compilation warnings introduced in version 0.20.0

0.20.1 - 2020-04-08

Fixed

• Make feature BOUNDSCHECKING work again. It was not turned on for DEBUG builds
• Workaround clang OpenMP bug
• Fix Segfault due to unexpected order of destruction of singleton objects

Added

• atlas-grids tool can now be used to compute approximate North-South grid resolution

0.20.0 - 2020-03-06

Fixed

• Pole edges hould not be created for global regular grids with points at poles
• Update compatibility with more recent GridTools
• HaloExchange with CUDA
• Self registration from external library

Added

• Proj-based projections
• OpenMP functions for sorting, filling, copying
• Parallel structured grid interpolation

Changed

• Grid iterators can have random access
• Speed improvements for StructuredColumns constructor
• Speed improvements for LonLatPolygon::contains()
• Port to ecbuild 3 (also minimum required version)
• Tidying up of atlas tools

0.19.2 - 2020-01-28

Changed

• Compatibility with eckit 1.7 due to API change in eckit::LocalConfiguration

0.19.1 - 2019-12-19

Fixed

• Keep Gaussian identity of a Gaussian grid if a given domain does not crop any latitudes
• Fix naming for LegendreCache, to be more specific, and platform independent

0.19.0 - 2019-10-01

Fixed

• Lambert ( conformal conic ) projection xy coordinates are now corrected

Changed

• LambertProjection renamed to LambertConformalConic

Added

• Reordering of nodes strategies (Hilbert curve, ReverseCuthillMckee)
• Preliminary CellColumns functionspace with Gmsh IO; halos are not yet fully supported

0.18.1 - 2019-08-10

Fixed

• Match vertical structured interpolation to IFS
• Fix in creating vertical dimension in StructuredColumns using interval
• Fix in caching StructuredColumnsHaloExchange

0.18.0 - 2019-07-15

Changed

• Make grid hashes crossplatform

Added

• Fortran: Can now use TransLocal
• Fortran: Can now create unstructured grids
• LonLat Bounding box computations for grids using its projection
• Serialisation of Mesh Connectivity tables to/from eckit::Stream

Fixed

• Structured interpolation bugs
• StructuredColumns bug with iSend
• Memory corruption in Spectral functionspace with GT CUDA backend

0.17.2 - 2019-06-04

Fixed

• Compilation with PGI 19.4
• Structured Grid creation for periodic domains that do not start at 0 degrees longitude (Greenwich)

0.17.1 - 2019-04-22

Added

• Option to declaration of field type (vector/scalar) when creating field in FunctionSpace
• New projection: Lambert Azimuthal Equal Area
• StructuredInterpolation2D to target FunctionSpace StructuredColumns

Fixed

• Compilation with IBM XL 19
• Compilation with Intel 19

0.17.0 - 2019-04-02

Changed

• OpenMP is now private dependency
• Dependencies are now added in a modern CMake3 way
• Fortran modules are installed in /module/atlas

Added

• Spectral functionspace better used in distributed context
• Nabla now holds shared_ptr to Method
• Fortran access to vertical coordinates from StructuredColumns

Fixed

• Compilation with PGI/19.1 (regression)
• Add missing halo_exchange for Fortran rank-4 arrays
• Memory leaks with StructuredColumns

0.16.0 - 2019-02-14

Changed

• Interpolation makes use of OpenMP
• Cleanup of header includes
• fypp Fortran preprocessor is ported to fckit 0.6

Added

• Parallel structured interpolation methods (2D,3D): linear, cubic, quasicubic
• Interpolation for multi-level and multi-variable fields
• atlas_Trace: Fortran API and use within OpenMP parallel regions
• StructuredColumns halo-exchange for vector fields
• Field::halo_exchange() function

Fixed

• Fortran compilation with PGI 18.10
• Access to Field view within OpenMP parallel region
• FunctionSpaces use only required halo, even if larger halo is available in mesh
• Fixed faulty name of a Field when created through Fortran API, wrapping existing memory
• Fix NodeColumns functionspace when mesh is created from projected grid.
• Parallel interpolation from regular lonlat grid.
• Spectral spherical harmonics transforms for large cases

0.15.2 - 2018-08-31

Changed

• Initialisation of Fields to signalling NaN in debug builds, uninitialised in non-debug builds (used to be initialised to zero as part of std::vector construction)

Added

• Implementation of cropped unstructured grids so that spectral transforms to unstructured grids are allowed

Fixed

• Spectral transforms to grids including pole and equator
• Build with gridtools CUDA backend

0.15.1 - 2018-07-17

Fixed

• Compilation for Intel 18 debug
• Memory bug for spherical harmonics
• Compatibility with fckit 0.5.1

0.15.0 - 2018-06-19

Changed

• Native Array data storage uses now a raw C pointer instead of std::vector
• Significant performance improvements to Spherical harmonics transforms

Fixed

• Various bugs related to parallel halos
• Bit reproducibility for parallel interpolation

0.14.0 - 2018-03-22

Added

• Spherical Harmonics transforms can receive a cache memory handle

Changed

• Earth interface (C++)
• Requires eckit 0.20.0, fckit 0.5.0

0.13.2 - 2018-03-20

Fixed

• C++ compilation using PGI 17, 18 and GCC 7
• Support Python 3 to generate Fortran bindings
• Travis CI linked with github repository
• Problem with CUDA allocated memory

0.13.1 - 2018-03-01

Fixed

• Fortran compilation using Intel 18
• GridTools compatibility

0.13.0 - 2018-02-16