JuliaMolSim · kellertuer · May 26, 2025 · May 26, 2025 · May 26, 2025 · May 26, 2025
diff --git a/Project.toml b/Project.toml
@@ -20,12 +20,10 @@ Interpolations = "a98d9a8b-a2ab-59e6-89dd-64a1c18fca59"
 IterTools = "c8e1da08-722c-5040-9ed9-7db0dc04731e"
 KrylovKit = "0b1a1467-8014-51b9-945f-bf0ae24f4b77"
 Libxc = "66e17ffc-8502-11e9-23b5-c9248d0eb96d"
-LineSearches = "d3d80556-e9d4-5f37-9878-2ab0fcc64255"
 LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
 LinearMaps = "7a12625a-238d-50fd-b39a-03d52299707e"
 MPI = "da04e1cc-30fd-572f-bb4f-1f8673147195"
 Markdown = "d6f4376e-aef5-505a-96c1-9c027394607a"
-Optim = "429524aa-4258-5aef-a3af-852621145aeb"
 PeriodicTable = "7b2266bf-644c-5ea3-82d8-af4bbd25a884"
 PkgVersion = "eebad327-c553-4316-9ea0-9fa01ccd7688"
 Polynomials = "f27b6e38-b328-58d1-80ce-0feddd5e7a45"
@@ -53,7 +51,10 @@ GeometryOptimization = "673bf261-a53d-43b9-876f-d3c1fc8329c2"
 IntervalArithmetic = "d1acc4aa-44c8-5952-acd4-ba5d80a2a253"
 JLD2 = "033835bb-8acc-5ee8-8aae-3f567f8a3819"
 JSON3 = "0f8b85d8-7281-11e9-16c2-39a750bddbf1"
+Manifolds = "1cead3c2-87b3-11e9-0ccd-23c62b72b94e"
+Manopt = "0fc0a36d-df90-57f3-8f93-d78a9fc72bb5"
 Plots = "91a5bcdd-55d7-5caf-9e0b-520d859cae80"
+RecursiveArrayTools = "731186ca-8d62-57ce-b412-fbd966d074cd"
 Wannier = "2b19380a-1f7e-4d7d-b1b8-8aa60b3321c9"
 WriteVTK = "64499a7a-5c06-52f2-abe2-ccb03c286192"
 wannier90_jll = "c5400fa0-8d08-52c2-913f-1e3f656c1ce9"
@@ -66,6 +67,7 @@ DFTKGeometryOptimizationExt = "GeometryOptimization"
 DFTKIntervalArithmeticExt = "IntervalArithmetic"
 DFTKJLD2Ext = "JLD2"
 DFTKJSON3Ext = "JSON3"
+DFTKManifoldsManoptRATExt = ["Manifolds", "Manopt", "RecursiveArrayTools"]
 DFTKPlotsExt = "Plots"
 DFTKWannier90Ext = "wannier90_jll"
 DFTKWannierExt = "Wannier"
@@ -104,13 +106,13 @@ JLD2 = "0.4, 0.5, 0.6"
 JSON3 = "1"
 KrylovKit = "0.8.3, 0.9, 0.10"
 Libxc = "0.3.17"
-LineSearches = "7"
 LinearAlgebra = "1"
 LinearMaps = "3"
 Logging = "1"
 MPI = "0.20.22"
+Manifolds = "0.10.17"
+Manopt = "0.5.23"
 Markdown = "1"
-Optim = "1"
 PeriodicTable = "1"
 PkgVersion = "0.3"
 Plots = "1"
@@ -123,6 +125,7 @@ PseudoPotentialIO = "0.1"
 PythonCall = "0.9"
 QuadGK = "2"
 Random = "1"
+RecursiveArrayTools = "3.33.0"
 Roots = "2"
 SparseArrays = "1"
 SpecialFunctions = "2"
@@ -158,15 +161,18 @@ JLD2 = "033835bb-8acc-5ee8-8aae-3f567f8a3819"
 JSON3 = "0f8b85d8-7281-11e9-16c2-39a750bddbf1"
 KrylovKit = "0b1a1467-8014-51b9-945f-bf0ae24f4b77"
 Logging = "56ddb016-857b-54e1-b83d-db4d58db5568"
+Manifolds = "1cead3c2-87b3-11e9-0ccd-23c62b72b94e"
+Manopt = "0fc0a36d-df90-57f3-8f93-d78a9fc72bb5"
 Plots = "91a5bcdd-55d7-5caf-9e0b-520d859cae80"
 PythonCall = "6099a3de-0909-46bc-b1f4-468b9a2dfc0d"
 QuadGK = "1fd47b50-473d-5c70-9696-f719f8f3bcdc"
 Random = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c"
+RecursiveArrayTools = "731186ca-8d62-57ce-b412-fbd966d074cd"
 Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
 TestItemRunner = "f8b46487-2199-4994-9208-9a1283c18c0a"
 Wannier = "2b19380a-1f7e-4d7d-b1b8-8aa60b3321c9"
 WriteVTK = "64499a7a-5c06-52f2-abe2-ccb03c286192"
 wannier90_jll = "c5400fa0-8d08-52c2-913f-1e3f656c1ce9"
 
 [targets]
-test = ["Test", "TestItemRunner", "AMDGPU", "ASEconvert", "AtomsBuilder", "Aqua", "AtomsIO", "AtomsIOPython", "CUDA", "CUDA_Runtime_jll", "ComponentArrays", "DoubleFloats", "FiniteDiff", "FiniteDifferences", "GenericLinearAlgebra", "GeometryOptimization", "IntervalArithmetic", "JLD2", "JSON3", "Logging", "Plots", "PythonCall", "QuadGK", "Random", "KrylovKit", "Wannier", "WriteVTK", "wannier90_jll"]
+test = ["Test", "TestItemRunner", "AMDGPU", "ASEconvert", "AtomsBuilder", "Aqua", "AtomsIO", "AtomsIOPython", "CUDA", "CUDA_Runtime_jll", "ComponentArrays", "DoubleFloats", "FiniteDiff", "FiniteDifferences", "GenericLinearAlgebra", "GeometryOptimization", "IntervalArithmetic", "JLD2", "JSON3", "Logging", "Manifolds", "Manopt", "Plots", "PythonCall", "QuadGK", "Random", "RecursiveArrayTools", "KrylovKit", "Wannier", "WriteVTK", "wannier90_jll"]
diff --git a/docs/Project.toml b/docs/Project.toml
@@ -11,6 +11,8 @@ Brillouin = "23470ee3-d0df-4052-8b1a-8cbd6363e7f0"
 CUDA = "052768ef-5323-5732-b1bb-66c8b64840ba"
 DFTK = "acf6eb54-70d9-11e9-0013-234b7a5f5337"
 Documenter = "e30172f5-a6a5-5a46-863b-614d45cd2de4"
+DocumenterCitations = "daee34ce-89f3-4625-b898-19384cb65244"
+DocumenterInterLinks = "d12716ef-a0f6-4df4-a9f1-a5a34e75c656"
 ForwardDiff = "f6369f11-7733-5829-9624-2563aa707210"
 GeometryOptimization = "673bf261-a53d-43b9-876f-d3c1fc8329c2"
 IterativeSolvers = "42fd0dbc-a981-5370-80f2-aaf504508153"
@@ -21,12 +23,15 @@ LazyArtifacts = "4af54fe1-eca0-43a8-85a7-787d91b784e3"
 LibGit2 = "76f85450-5226-5b5a-8eaa-529ad045b433"
 LinearMaps = "7a12625a-238d-50fd-b39a-03d52299707e"
 Literate = "98b081ad-f1c9-55d3-8b20-4c87d4299306"
+Manifolds = "1cead3c2-87b3-11e9-0ccd-23c62b72b94e"
+Manopt = "0fc0a36d-df90-57f3-8f93-d78a9fc72bb5"
 Optim = "429524aa-4258-5aef-a3af-852621145aeb"
 Pkg = "44cfe95a-1eb2-52ea-b672-e2afdf69b78f"
 Plots = "91a5bcdd-55d7-5caf-9e0b-520d859cae80"
 Printf = "de0858da-6303-5e67-8744-51eddeeeb8d7"
 PseudoPotentialData = "5751a51d-ac76-4487-a056-413ecf6fbe19"
 PythonCall = "6099a3de-0909-46bc-b1f4-468b9a2dfc0d"
+RecursiveArrayTools = "731186ca-8d62-57ce-b412-fbd966d074cd"
 StaticArrays = "90137ffa-7385-5640-81b9-e52037218182"
 TimerOutputs = "a759f4b9-e2f1-59dc-863e-4aeb61b1ea8f"
 Unitful = "1986cc42-f94f-5a68-af5c-568840ba703d"
@@ -35,9 +40,15 @@ Wannier = "2b19380a-1f7e-4d7d-b1b8-8aa60b3321c9"
 WriteVTK = "64499a7a-5c06-52f2-abe2-ccb03c286192"
 wannier90_jll = "c5400fa0-8d08-52c2-913f-1e3f656c1ce9"
 
+[sources]
+DFTK = {path = ".."}
+
 [compat]
 AtomsBuilder = "0.2"
 AtomsCalculators = "0.2.3"
 Documenter = "~1.8"
 GeometryOptimization = "0.1"
 PseudoPotentialData = "0.2.0"
+
+[extras]
+CUDA_Runtime_jll = "76a88914-d11a-5bdc-97e0-2f5a05c973a2"
diff --git a/docs/make.jl b/docs/make.jl
@@ -93,6 +93,7 @@ PAGES = [
         "developer/symmetries.md",
         "developer/gpu_computations.md",
     ],
+    "Extensions" => "extensions/index.md",
     "api.md",
     "publications.md",
 ]
@@ -121,7 +122,6 @@ DFTKREPO   = DFTKGH * ".git"
 # Setup julia dependencies for docs generation if not yet done
 Pkg.activate(@__DIR__)
 if !isfile(joinpath(@__DIR__, "Manifest.toml"))
-    Pkg.develop(Pkg.PackageSpec(; path=ROOTPATH))
     Pkg.instantiate()
 end
 
@@ -133,8 +133,10 @@ ENV["PLOTS_TEST"] = "true"
 # Import packages for docs generation
 using DFTK
 using Documenter
+using DocumenterCitations, DocumenterInterLinks
 using Literate
-
+# For documentation in extensions:
+using Manifolds, Manopt, RecursiveArrayTools
 #
 # Generate the docs
 #
@@ -187,7 +189,7 @@ for file in literate_files
         badges = [
             "[![](https://mybinder.org/badge_logo.svg)]" *
                 "(@__BINDER_ROOT_URL__/$subfolder/@__NAME__.ipynb)",
-            "[![](https://img.shields.io/badge/show-nbviewer-579ACA.svg)]" * 
+            "[![](https://img.shields.io/badge/show-nbviewer-579ACA.svg)]" *
                 "(@__NBVIEWER_ROOT_URL__/$subfolder/@__NAME__.ipynb)",
         ]
     else
@@ -216,8 +218,18 @@ mathengine  = Documenter.MathJax3(Dict(
     ),
 ))
 
+#Setup Citations and InterLinks
+links = InterLinks(
+    "Manopt" => ("https://manoptjl.org/stable/"),
+    "ManifoldsBase" => ("https://juliamanifolds.github.io/ManifoldsBase.jl/stable/"),
+    "Manifolds" => ("https://juliamanifolds.github.io/Manifolds.jl/stable/"),
+)
+bib = CitationBibliography(joinpath(@__DIR__, "src", "references.bib"); style=:alpha)
 makedocs(;
-    modules=[DFTK],
+    modules=[
+        DFTK,
+        Base.get_extension(DFTK, :DFTKManifoldsManoptRATExt),
+    ],
     format=Documenter.HTML(;
         # Use clean URLs, unless built as a "local" build
         prettyurls=CONTINUOUS_INTEGRATION,
@@ -231,6 +243,7 @@ makedocs(;
     authors = "Michael F. Herbst, Antoine Levitt and contributors.",
     pages=transform_to_md(PAGES),
     checkdocs=:exports,
+    plugins=[bib, links],
     warnonly=DEBUG,
     remote_args...,
 )

diff --git a/docs/src/extensions/index.md b/docs/src/extensions/index.md
@@ -0,0 +1,6 @@
+# Extensions
+
+## Manopt.jl
+
+```@docs
+```
diff --git a/docs/src/references.bib b/docs/src/references.bib
diff --git a/examples/anyons.jl b/examples/anyons.jl
@@ -5,6 +5,7 @@
 using DFTK
 using StaticArrays
 using Plots
+using Manifolds, Manopt, RecursiveArrayTools
 
 ## Unit cell. Having one of the lattice vectors as zero means a 2D system
 a = 14

diff --git a/examples/compare_solvers.jl b/examples/compare_solvers.jl
@@ -8,6 +8,7 @@ using AtomsBuilder
 using DFTK
 using LinearAlgebra
 using PseudoPotentialData
+using Manopt, Manifolds, RecursiveArrayTools
 
 pseudopotentials = PseudoFamily("dojo.nc.sr.pbesol.v0_4_1.standard.upf")
 model = model_DFT(bulk(:Si); functionals=PBEsol(), pseudopotentials)

diff --git a/examples/gross_pitaevskii.jl b/examples/gross_pitaevskii.jl
@@ -24,7 +24,7 @@ lattice = a .* [[1 0 0.]; [0 0 0]; [0 0 0]];
 # which is special cased in DFTK to support 1D models.
 #
 # For the potential term `V` we pick a harmonic
-# potential. We use the function `ExternalFromReal` which uses 
+# potential. We use the function `ExternalFromReal` which uses
 # Cartesian coordinates ( see [Lattices and lattice vectors](@ref conventions-lattice)).
 pot(x) = (x - a/2)^2;
 
@@ -39,6 +39,7 @@ C = 1.0
 # … and with this build the model
 using DFTK
 using LinearAlgebra
+using Manopt, Manifolds, RecursiveArrayTools
 
 n_electrons = 1  # Increase this for fun
 terms = [Kinetic(),

diff --git a/examples/gross_pitaevskii_2D.jl b/examples/gross_pitaevskii_2D.jl
@@ -9,6 +9,7 @@
 using DFTK
 using StaticArrays
 using Plots
+using Manifolds, Manopt, RecursiveArrayTools
 
 ## Unit cell. Having one of the lattice vectors as zero means a 2D system
 a = 15