Crystallography
Documentation for Crystallography.
See the Index for the complete list of documented functions and types.
The code, which is hosted on GitHub, is tested using various continuous integration services for its validity.
This repository is created and maintained by @singularitti, and contributions are highly welcome.
Package features
Installation
The package can be installed with the Julia package manager. From the Julia REPL, type ]
to enter the Pkg mode and run:
pkg> add Crystallography
Or, equivalently, via Pkg.jl
:
julia> import Pkg; Pkg.add("Crystallography")
Resolving package versions... Installed EnumX ─────────────── v1.0.4 Installed Crystallography ───── v0.6.0 Installed Functors ──────────── v0.4.5 Installed CrystallographyBase ─ v0.10.1 Updating `~/work/Crystallography.jl/Crystallography.jl/docs/Project.toml` [3bff3928] ~ Crystallography v0.6.0 `~/.julia/dev/Crystallography` ⇒ v0.6.0 ⌅ [93b1d1cd] ↓ CrystallographyBase v0.11.0 ⇒ v0.10.1 Updating `~/work/Crystallography.jl/Crystallography.jl/docs/Manifest.toml` [1b8a1bdb] - AnonymousEnums v0.1.1 [a8cc5b0e] - Crayons v4.1.1 [6007d9b0] - CrystalInfoFramework v0.6.0 [3bff3928] ~ Crystallography v0.6.0 `~/.julia/dev/Crystallography` ⇒ v0.6.0 ⌅ [93b1d1cd] ↓ CrystallographyBase v0.11.0 ⇒ v0.10.1 [9a962f9c] - DataAPI v1.15.0 [a93c6f00] - DataFrames v1.6.1 [864edb3b] - DataStructures v0.18.15 [e2d170a0] - DataValueInterfaces v1.0.0 [4e289a0a] + EnumX v1.0.4 [8fc22ac5] - FilePaths v0.8.3 [48062228] - FilePathsBase v0.9.20 [d9f16b24] + Functors v0.4.5 [842dd82b] - InlineStrings v1.4.0 [41ab1584] - InvertedIndices v1.3.0 [82899510] - IteratorInterfaceExtensions v1.0.0 [692b3bcd] - JLLWrappers v1.5.0 [b964fa9f] - LaTeXStrings v1.3.0 [d42ef402] - Lerche v0.5.4 [1914dd2f] - MacroTools v0.5.10 [e1d29d7a] - Missings v1.1.0 [bac558e1] - OrderedCollections v1.6.2 [2dfb63ee] - PooledArrays v1.4.2 [08abe8d2] - PrettyTables v2.2.7 [189a3867] - Reexport v1.2.2 [ae029012] - Requires v1.3.0 [91c51154] - SentinelArrays v1.4.0 [a2af1166] - SortingAlgorithms v1.1.1 [f761d5c5] - Spglib v0.8.0 [892a3eda] - StringManipulation v0.3.0 [3783bdb8] - TableTraits v1.0.1 [bd369af6] - Tables v1.10.1 [30578b45] - URIParser v0.4.1 [a51ab1cf] - ICU_jll v69.1.0+0 [1d63c593] - LLVMOpenMP_jll v15.0.4+0 [76ed43ae] - SQLite_jll v3.42.0+0 [6fcef0ae] - cif_api_jll v0.4.2+0 [ac4a9f1e] - spglib_jll v2.0.2+0 [0dad84c5] - ArgTools v1.1.1 [f43a241f] - Downloads v1.6.0 [7b1f6079] - FileWatching [9fa8497b] - Future [b27032c2] - LibCURL v0.6.3 [44cfe95a] - Pkg v1.9.2 [2f01184e] - SparseArrays [10745b16] - Statistics v1.9.0 [a4e569a6] - Tar v1.10.0 [deac9b47] - LibCURL_jll v7.84.0+0 [29816b5a] - LibSSH2_jll v1.10.2+0 [c8ffd9c3] - MbedTLS_jll v2.28.2+0 [14a3606d] - MozillaCACerts_jll v2022.10.11 [bea87d4a] - SuiteSparse_jll v5.10.1+6 [83775a58] - Zlib_jll v1.2.13+0 [8e850ede] - nghttp2_jll v1.48.0+0 [3f19e933] - p7zip_jll v17.4.0+0 Info Packages marked with ⌅ have new versions available but compatibility constraints restrict them from upgrading. To see why use `status --outdated -m` Precompiling project... ✓ EnumX ✓ Functors ✓ CrystallographyBase ✓ Crystallography 4 dependencies successfully precompiled in 6 seconds. 19 already precompiled. 2 dependencies precompiled but different versions are currently loaded. Restart julia to access the new versions
Documentation
- STABLE — documentation of the most recently tagged version.
- DEV — documentation of the in-development version.
Project status
The package is developed for and tested against Julia v1.6
and above on Linux, macOS, and Windows.
Questions and contributions
You can post usage questions on our discussion page.
We welcome contributions, feature requests, and suggestions. If you encounter any problems, please open an issue. The Contributing page has a few guidelines that should be followed when opening pull requests and contributing code.
Manual outline
- Installation Guide
- Troubleshooting
- Contributing
- Style Guide
- Design Principles
- Consistency vs adherence
- Community contribution guidelines
- Open source contributions are allowed to start small and grow over time
- Generic code is preferred unless code is known to be specific
- Internal types should match the types used by users when possible
- Trait definition and adherence to generic interface is preferred when possible
- Macros should be limited and only be used for syntactic sugar
- Errors should be caught as early as possible, and error messages should be made contextually clear for newcomers
- Subpackaging and interface packages is preferred over conditional modules via Requires.jl
- Functions should either attempt to be non-allocating and reuse caches, or treat inputs as immutable
- Out-of-place and immutability is preferred when sufficient performant
- Tests should attempt to cover a wide gamut of input types
- When in doubt, a submodule should become a subpackage or separate package
- Globals should be avoided whenever possible
- Type-stable and type-grounded code is preferred wherever possible
- Closures should be avoided whenever possible
- Numerical functionality should use the appropriate generic numerical interfaces
- Functions should capture one underlying principle
- Internal choices should be exposed as options whenever possible
- Prefer code reuse over rewrites whenever possible
- Prefer to not shadow functions
Library outline
Index
Crystallography.SeitzOperator
CrystallographyBase.CartesianFromFractional
CrystallographyBase.FractionalFromCartesian
CrystallographyBase.Lattice
CrystallographyBase.MetricTensor
CrystallographyBase.PrimitiveFromStandardized
CrystallographyBase.ReciprocalLattice
CrystallographyBase.ReciprocalPoint
CrystallographyBase.StandardizedFromPrimitive
CrystallographyBase.cellvolume
CrystallographyBase.coordinates
CrystallographyBase.distance
CrystallographyBase.supercell
CrystallographyBase.weights