Drop deprecated features and a round of docs updating (#994)

.github/workflows/ci.yaml

@@ -38,7 +38,7 @@ jobs:
       - name: Setup Julia stable
         uses: julia-actions/setup-julia@v1
         with:
-          version: '1.9'
+          version: '1.10'
           arch: x64
         if: ${{ matrix.mode == 'stable' }}
       - name: Setup Julia nightly

Project.toml

@@ -49,6 +49,7 @@ UnitfulAtomic = "a7773ee8-282e-5fa2-be4e-bd808c38a91a"
 [weakdeps]
 CUDA = "052768ef-5323-5732-b1bb-66c8b64840ba"
 GenericLinearAlgebra = "14197337-ba66-59df-a3e3-ca00e7dcff7a"
+GeometryOptimization = "673bf261-a53d-43b9-876f-d3c1fc8329c2"
 IntervalArithmetic = "d1acc4aa-44c8-5952-acd4-ba5d80a2a253"
 JLD2 = "033835bb-8acc-5ee8-8aae-3f567f8a3819"
 JSON3 = "0f8b85d8-7281-11e9-16c2-39a750bddbf1"
@@ -60,6 +61,7 @@ wannier90_jll = "c5400fa0-8d08-52c2-913f-1e3f656c1ce9"
 [extensions]
 DFTKCUDAExt = "CUDA"
 DFTKGenericLinearAlgebraExt = "GenericLinearAlgebra"
+DFTKGeometryOptimizationExt = "GeometryOptimization"
 DFTKIntervalArithmeticExt = "IntervalArithmetic"
 DFTKJLD2Ext = "JLD2"
 DFTKJSON3Ext = "JSON3"
@@ -72,6 +74,7 @@ DFTKWriteVTKExt = "WriteVTK"
 AbstractFFTs = "1"
 Artifacts = "1"
 AtomsBase = "0.3.1"
+AtomsBuilder = "0.1"
 AtomsCalculators = "0.2"
 Brillouin = "0.5.14"
 CUDA = "5"
@@ -83,6 +86,7 @@ FFTW = "1.5"
 ForwardDiff = "0.10"
 GPUArraysCore = "0.1"
 GenericLinearAlgebra = "0.3"
+GeometryOptimization = "0.1"
 Interpolations = "0.14, 0.15"
 IntervalArithmetic = "0.20"
 IterTools = "1"
@@ -118,11 +122,12 @@ Unitful = "1"
 UnitfulAtomic = "1"
 Wannier = "0.3.2"
 WriteVTK = "1"
-julia = "1.9"
+julia = "1.10"
 wannier90_jll = "3.1"
 
 [extras]
 ASEconvert = "3da9722f-58c2-4165-81be-b4d7253e8fd2"
+AtomsBuilder = "f5cc8831-eeb7-4288-8d9f-d6c1ddb77004"
 Aqua = "4c88cf16-eb10-579e-8560-4a9242c79595"
 AtomsIO = "1692102d-eeb4-4df9-807b-c9517f998d44"
 AtomsIOPython = "9e4c859b-2281-48ef-8059-f50fe53c37b0"
@@ -148,4 +153,4 @@ WriteVTK = "64499a7a-5c06-52f2-abe2-ccb03c286192"
 wannier90_jll = "c5400fa0-8d08-52c2-913f-1e3f656c1ce9"
 
 [targets]
-test = ["Test", "TestItemRunner", "ASEconvert", "Aqua", "AtomsIO", "AtomsIOPython", "CUDA", "CUDA_Runtime_jll", "ComponentArrays", "DoubleFloats", "FiniteDiff", "FiniteDifferences", "GenericLinearAlgebra", "IntervalArithmetic", "JLD2", "JSON3", "Logging", "Plots", "QuadGK", "Random", "KrylovKit", "Wannier", "WriteVTK", "wannier90_jll"]
+test = ["Test", "TestItemRunner", "ASEconvert", "AtomsBuilder", "Aqua", "AtomsIO", "AtomsIOPython", "CUDA", "CUDA_Runtime_jll", "ComponentArrays", "DoubleFloats", "FiniteDiff", "FiniteDifferences", "GenericLinearAlgebra", "GeometryOptimization", "IntervalArithmetic", "JLD2", "JSON3", "Logging", "Plots", "QuadGK", "Random", "KrylovKit", "Wannier", "WriteVTK", "wannier90_jll"]

README.md

@@ -2,9 +2,9 @@
 
 # Density-functional toolkit
 
-| **Documentation**                                                                 | **Build Status**                                |  **License**                     |
-|:--------------------------------------------------------------------------------- |:----------------------------------------------- |:-------------------------------- |
-| [![][docs-img]][docs-url] [![][ddocs-img]][ddocs-url] [![][chat-img]][chat-url] | [![][ci-img]][ci-url] [![][cigpu-img]][cigpu-url] [![][ccov-img]][ccov-url] | [![][license-img]][license-url]  |
+| **Documentation**                                                               | **Build Status**                                |  **License**                     |
+|:------------------------------------------------------------------------------- |:----------------------------------------------- |:-------------------------------- |
+| [![][docs-img]][docs-url] [![][ddocs-img]][ddocs-url] [![][chat-img]][chat-url] | [![][ci-img]][ci-url] [![][ccov-img]][ccov-url] | [![][license-img]][license-url]  |
 
 [ddocs-img]: https://img.shields.io/badge/docs-dev-blue.svg
 [ddocs-url]: https://docs.dftk.org/dev
@@ -18,9 +18,6 @@
 [ci-img]: https://github.com/JuliaMolSim/DFTK.jl/workflows/CI/badge.svg?branch=master&event=push
 [ci-url]: https://github.com/JuliaMolSim/DFTK.jl/actions
 
-[cigpu-img]: https://git.uni-paderborn.de/herbstm/DFTK.jl/badges/master/pipeline.svg?key_text=GPU%20CI
-[cigpu-url]: https://git.uni-paderborn.de/herbstm/DFTK.jl/-/pipelines
-
 [ccov-img]: https://codecov.io/gh/JuliaMolSim/DFTK.jl/branch/master/graph/badge.svg?token=A23M0VZ8PQ
 [ccov-url]: https://codecov.io/gh/JuliaMolSim/DFTK.jl
 
@@ -46,7 +43,7 @@ For getting started with DFTK, see [our documentation](https://docs.dftk.org):
 - [Tutorial](https://docs.dftk.org/stable/guide/tutorial/)
 - [Basic DFT examples](https://docs.dftk.org/stable/examples/metallic_systems/)
 
-Note that at least **Julia 1.9** is required.
+Note that at least **Julia 1.10** is required.
 
 ## Support and citation
 DFTK is mostly developed as part of academic research.

docs/.gitignore

@@ -1,16 +1,24 @@
 build/
 site/
 src/examples/
-src/guide/tutorial.md
-src/guide/tutorial.ipynb
-src/guide/periodic_problems.ipynb
-src/guide/periodic_problems.md
+src/ecosystem/atomsbase.ipynb
+src/ecosystem/atomsbase.md
+src/ecosystem/atomscalculators.ipynb
+src/ecosystem/atomscalculators.md
+src/ecosystem/input_output.ipynb
+src/ecosystem/input_output.md
+src/ecosystem/wannier.ipynb
+src/ecosystem/wannier.md
 src/guide/atomic_chains.ipynb
 src/guide/atomic_chains.md
-src/guide/self_consistent_field.ipynb
-src/guide/self_consistent_field.md
 src/guide/discretisation.ipynb
 src/guide/discretisation.md
+src/guide/periodic_problems.ipynb
+src/guide/periodic_problems.md
+src/guide/self_consistent_field.ipynb
+src/guide/self_consistent_field.md
+src/guide/tutorial.ipynb
+src/guide/tutorial.md
 src/tricks/scf_checkpoints.ipynb
 src/tricks/scf_checkpoints.md
 /Artifacts.toml

docs/Project.toml

@@ -2,12 +2,15 @@
 ASEconvert = "3da9722f-58c2-4165-81be-b4d7253e8fd2"
 Artifacts = "56f22d72-fd6d-98f1-02f0-08ddc0907c33"
 AtomsBase = "a963bdd2-2df7-4f54-a1ee-49d51e6be12a"
+AtomsCalculators = "a3e0e189-c65a-42c1-833c-339540406eb1"
+AtomsBuilder = "f5cc8831-eeb7-4288-8d9f-d6c1ddb77004"
 AtomsIO = "1692102d-eeb4-4df9-807b-c9517f998d44"
 AtomsIOPython = "9e4c859b-2281-48ef-8059-f50fe53c37b0"
 Brillouin = "23470ee3-d0df-4052-8b1a-8cbd6363e7f0"
 DFTK = "acf6eb54-70d9-11e9-0013-234b7a5f5337"
 Documenter = "e30172f5-a6a5-5a46-863b-614d45cd2de4"
 ForwardDiff = "f6369f11-7733-5829-9624-2563aa707210"
+GeometryOptimization = "673bf261-a53d-43b9-876f-d3c1fc8329c2"
 IterativeSolvers = "42fd0dbc-a981-5370-80f2-aaf504508153"
 JLD2 = "033835bb-8acc-5ee8-8aae-3f567f8a3819"
 JSON3 = "0f8b85d8-7281-11e9-16c2-39a750bddbf1"
@@ -19,7 +22,6 @@ Literate = "98b081ad-f1c9-55d3-8b20-4c87d4299306"
 Optim = "429524aa-4258-5aef-a3af-852621145aeb"
 Pkg = "44cfe95a-1eb2-52ea-b672-e2afdf69b78f"
 Plots = "91a5bcdd-55d7-5caf-9e0b-520d859cae80"
-PyCall = "438e738f-606a-5dbb-bf0a-cddfbfd45ab0"
 StaticArrays = "90137ffa-7385-5640-81b9-e52037218182"
 TimerOutputs = "a759f4b9-e2f1-59dc-863e-4aeb61b1ea8f"
 Unitful = "1986cc42-f94f-5a68-af5c-568840ba703d"
@@ -30,3 +32,6 @@ wannier90_jll = "c5400fa0-8d08-52c2-913f-1e3f656c1ce9"
 
 [compat]
 Documenter = "~1.5"
+AtomsBuilder = "0.1"
+AtomsCalculators = "0.2"
+GeometryOptimization = "0.1"

docs/make.jl

@@ -50,9 +50,11 @@ PAGES = [
     "Ecosystem integration" => [
         # This concerns the discussion of interfaces, IO and integration
         # options we have
-        "examples/atomsbase.jl",
-        "examples/input_output.jl",
-        "examples/wannier.jl",
+        "ecosystem/atomsbase.jl",
+        "ecosystem/atomscalculators.jl",
+        "ecosystem/input_output.jl",
+        "ecosystem/atomistic_simulation_environment.md",
+        "ecosystem/wannier.jl",
     ],
     "Tips and tricks" => [
         # Resolving convergence issues, what solver to use, improving performance or
@@ -80,6 +82,7 @@ PAGES = [
     ],
     "Developer resources" => [
         "developer/setup.md",
+        "developer/testsystem.md",
         "developer/conventions.md",
         "developer/style_guide.md",
         "developer/data_structures.md",
@@ -93,7 +96,7 @@ PAGES = [
 
 # Files from the /examples folder that need to be copied over to the docs
 # (typically images, input or data files etc.)
-EXAMPLE_ASSETS = ["examples/Fe_afm.pwi", "examples/Si.extxyz"]
+EXAMPLE_ASSETS = []  # Specify e.g. as "examples/Fe_afm.pwi"
 
 #
 # Configuration and setup

docs/src/assets/0_pregenerate.jl

@@ -28,7 +28,7 @@ let
         atoms     = [ElementPsp(:Si; psp)]
         positions = [zeros(3)]
 
-        model = model_LDA(lattice, atoms, positions; temperature=1e-2)
+        model = model_DFT(lattice, atoms, positions; functionals=LDA(), temperature=1e-2)
         basis = PlaneWaveBasis(model; Ecut, kgrid=[8, 8, 8])
         self_consistent_field(basis; tol=1e-8)
     end

docs/src/developer/data_structures.md

@@ -2,18 +2,10 @@
 
 ```@setup data_structures
 using DFTK
-a = 10.26  # Silicon lattice constant in Bohr
-lattice = a / 2 * [[0 1 1.];
-                   [1 0 1.];
-                   [1 1 0.]]
-Si = ElementPsp(:Si; psp=load_psp("hgh/lda/Si-q4"))
-atoms = [Si, Si]
-positions = [ones(3)/8, -ones(3)/8]
-
-model = model_LDA(lattice, atoms, positions)
-kgrid = [4, 4, 4]
-Ecut = 15
-basis = PlaneWaveBasis(model; Ecut, kgrid)
+using AtomsBuilder
+system = attach_psp(bulk(:Si); Si="hgh/lda/si-q4")
+model  = model_DFT(system; functionals=LDA())
+basis  = PlaneWaveBasis(model; Ecut=15, kgrid=[4, 4, 4])
 scfres = self_consistent_field(basis; tol=1e-4);
 ```
 
@@ -64,20 +56,19 @@ the definition of the above terms in the
 By mixing and matching these terms, the user can create custom models
 not limited to DFT. Convenience constructors are provided for common cases:
 
-- `model_LDA`: LDA model using the
-  [Teter parametrisation](https://doi.org/10.1103/PhysRevB.54.1703)
-- `model_DFT`: Assemble a DFT model using
-   any of the LDA or GGA functionals of the
-   [libxc](https://tddft.org/programs/libxc/functionals/) library,
-   for example:
+- `model_DFT`: Assemble a DFT model using any of the LDA or GGA functionals of the
+   [libxc](https://libxc.gitlab.io/functionals/) library, for example:
    ```
-   model_DFT(lattice, atoms, positions, [:gga_x_pbe, :gga_c_pbe])
-   model_DFT(lattice, atoms, positions, :lda_xc_teter93)
+   model_DFT(lattice, atoms, positions; functionals=LDA())
+   model_DFT(lattice, atoms, positions; functionals=[:lda_x, :lda_c_pw])
+   model_DFT(lattice, atoms, positions; functionals=[:gga_x_pbe, :gga_c_pbe])
    ```
-   where the latter is equivalent to `model_LDA`.
-   Specifying no functional is the reduced Hartree-Fock model:
+   For common functional combinations DFTK additionally offers shorthands.
+   E.g. in the above example specifying [`LDA`](@ref) expands to
+   `[:lda_x, :lda_c_pw]`, such that the first two examples are identical.
+   Note, that specifying no functional is the reduced Hartree-Fock model:
    ```
-   model_DFT(lattice, atoms, positions, [])
+   model_DFT(lattice, atoms, positions; functionals=[])
    ```
 - `model_atomic`: A linear model, which contains no electron-electron interaction
   (neither Hartree nor XC term).
@@ -95,7 +86,7 @@ of `PlaneWaveBasis`, the latter is controlled by the
 cutoff energy parameter `Ecut`:
 
 ```@example data_structures
-PlaneWaveBasis(model; Ecut, kgrid)
+PlaneWaveBasis(model; Ecut=15, kgrid=[4, 4, 4])
 ```
 
 The `PlaneWaveBasis` by default uses symmetry to reduce the number of

docs/src/developer/setup.md

@@ -58,37 +58,3 @@ At the time of writing dropping a file `LocalPreferences.toml` in DFTK's root fo
 [DFTK]
 precompile_workload = false
 ```
-
-## Running the tests
-
-We use [TestItemRunner](https://github.com/julia-vscode/TestItemRunner.jl) to manage the
-tests. It reduces the risk to have undefined behavior by preventing tests from being run in
-global scope.
-
-Moreover, it allows for greater flexibility by providing ways to launch a specific subset of
-the tests.
-For instance, to launch core functionality tests, one can use
-```julia
-using TestEnv       # Optional: automatically installs required packages
-TestEnv.activate()  # for tests in a temporary environment.
-using TestItemRunner
-cd("test")          # By default, the following macro runs everything from the parent folder.
-@run_package_tests filter = ti -> :core ∈ ti.tags
-```
-Or to only run the tests of a particular file `serialisation.jl` use
-```julia
-@run_package_tests filter = ti -> occursin("serialisation.jl", ti.filename)
-```
-
-If you need to write tests, note that you can create modules with `@testsetup`. To use
-a function `my_function` of a module `MySetup` in a `@testitem`, you can import it with
-```julia
-using .MySetup: my_function
-```
-It is also possible to use functions from another module within a module. But for this the
-order of the modules in the `setup` keyword of `@testitem` is important: you have to add the
-module that will be used before the module using it. From the latter, you can then use it
-with
-```julia
-using ..MySetup: my_function
-```

docs/src/developer/symmetries.md

@@ -94,24 +94,22 @@ lattice = a / 2 * [[0 1 1.];
 Si = ElementPsp(:Si; psp=load_psp("hgh/lda/Si-q4"))
 atoms = [Si, Si]
 positions = [ones(3)/8, -ones(3)/8]
-Ecut = 5
-kgrid = [4, 4, 4]
 ```
 Let us demonstrate this in practice.
 We consider silicon, setup appropriately in the `lattice`, `atoms` and `positions`
 objects as in [Tutorial](@ref) and to reach a fast execution, we take a small `Ecut` of `5`
 and a `[4, 4, 4]` Monkhorst-Pack grid.
 First we perform the DFT calculation disabling symmetry handling
 ```@example symmetries
-model_nosym = model_LDA(lattice, atoms, positions; symmetries=false)
-basis_nosym = PlaneWaveBasis(model_nosym; Ecut, kgrid)
+model_nosym = model_DFT(lattice, atoms, positions; functionals=LDA(), symmetries=false)
+basis_nosym = PlaneWaveBasis(model_nosym; Ecut=5, kgrid=[4, 4, 4])
 scfres_nosym = @time self_consistent_field(basis_nosym, tol=1e-6)
 nothing  # hide
 ```
 and then redo it using symmetry (the default):
 ```@example symmetries
-model_sym = model_LDA(lattice, atoms, positions)
-basis_sym = PlaneWaveBasis(model_sym; Ecut, kgrid)
+model_sym = model_DFT(lattice, atoms, positions; functionals=LDA())
+basis_sym = PlaneWaveBasis(model_sym; Ecut=5, kgrid=[4, 4, 4])
 scfres_sym = @time self_consistent_field(basis_sym, tol=1e-6)
 nothing  # hide
 ```