Remove mentions of bundled pseudopotentials from docs and tests (#1047)

JuliaMolSim · Jan 10, 2025 · a843649 · a843649
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diff --git a/Project.toml b/Project.toml
@@ -74,34 +74,43 @@ DFTKWriteVTKExt = "WriteVTK"
 
 [compat]
 AbstractFFTs = "1"
+Aqua = "0.8.5"
 Artifacts = "1"
+ASEconvert = "0.1"
 AtomsBase = "0.5"
 AtomsBuilder = "0.2"
 AtomsCalculators = "0.2.3"
+AtomsIO = "0.3"
+AtomsIOPython = "0.1"
 Brillouin = "0.5.14"
-CUDA = "5"
 ChainRulesCore = "1.15"
+ComponentArrays = "0.15"
+CUDA = "5"
 Dates = "1"
 DftFunctionals = "0.3"
 DiffResults = "1.1"
 DocStringExtensions = "0.9"
+DoubleFloats = "1"
 FFTW = "1.5"
+FiniteDiff = "2"
+FiniteDifferences = "0.12"
 ForwardDiff = "0.10"
-GPUArraysCore = "0.1"
 GenericLinearAlgebra = "0.3"
 GeometryOptimization = "0.1"
+GPUArraysCore = "0.1"
 Interpolations = "0.14, 0.15"
 IntervalArithmetic = "0.20"
 IterTools = "1"
 JLD2 = "0.4, 0.5"
 JSON3 = "1"
 KrylovKit = "0.8.3"
 Libxc = "0.3.17"
-LineSearches = "7"
 LinearAlgebra = "1"
 LinearMaps = "3"
-MPI = "0.20.22"
+LineSearches = "7"
+Logging = "1"
 Markdown = "1"
+MPI = "0.20.22"
 Optim = "1"
 PeriodicTable = "1"
 PkgVersion = "0.3"
@@ -113,13 +122,17 @@ Primes = "0.5"
 Printf = "1"
 PseudoPotentialData = "0.2.2"
 PseudoPotentialIO = "0.1"
+PythonCall = "0.9"
+QuadGK = "2"
 Random = "1"
 Roots = "2"
 SparseArrays = "1"
 SpecialFunctions = "2"
 Spglib = "0.9.4"
 StaticArrays = "1"
 Statistics = "1"
+Test = "1"
+TestItemRunner = "1"
 TimerOutputs = "0.5.12"
 Unitful = "1"
 UnitfulAtomic = "1"

diff --git a/README.release_notes b/README.release_notes
@@ -0,0 +1,7 @@
+@JuliaRegistrator register
+
+Release notes:
+
+Note that this release increases the minor version and contains a number of breaking changes:
+
+- The pseudopotential repository shipped with DFTK is now deprecated and slated for removal in a future version of DFTK. Please rely on the [PseudoPotentialData](https://github.com/JuliaMolSim/PseudoPotentialData.jl/) package for selecting pseudopotentials. Concretely this means that `list_psp` will be removed and `load_psp` will only be working with full paths to pseduopotential data files or e.g. combinations of `PseudoPotentialData.PseudoFamily` objects and an element symbol.
diff --git a/docs/logo/.gitignore b/docs/logo/.gitignore
@@ -0,0 +1,3 @@
+DFTK.png
+DFTK_100x50.png
+DFTK_150x50.png
diff --git a/docs/logo/DFTK_48.png b/docs/logo/DFTK_48.png
diff --git a/docs/logo/DFTK_48.svg b/docs/logo/DFTK_48.svg
diff --git a/docs/src/developer/data_structures.md b/docs/src/developer/data_structures.md
@@ -3,8 +3,9 @@
 ```@setup data_structures
 using DFTK
 using AtomsBuilder
-model  = model_DFT(bulk(:Si); functionals=LDA(),
-                           pseudopotentials=Dict(:Si => "hgh/lda/si-q4"))
+using PseudoPotentialData
+pseudopotentials = PseudoFamily("cp2k.nc.sr.lda.v0_1.semicore.gth")
+model  = model_DFT(bulk(:Si); functionals=LDA(), pseudopotentials)
 basis  = PlaneWaveBasis(model; Ecut=15, kgrid=[4, 4, 4])
 scfres = self_consistent_field(basis; tol=1e-4);
 ```

diff --git a/docs/src/developer/symmetries.md b/docs/src/developer/symmetries.md
@@ -87,11 +87,13 @@ reducible points, determines the weight of each irreducible ``k`` point.
 ## Example
 ```@setup symmetries
 using DFTK
+using PseudoPotentialData
 a = 10.26
 lattice = a / 2 * [[0 1 1.];
                    [1 0 1.];
                    [1 1 0.]]
-Si = ElementPsp(:Si, load_psp("hgh/lda/Si-q4"))
+pseudopotentials = PseudoFamily("cp2k.nc.sr.lda.v0_1.semicore.gth")
+Si = ElementPsp(:Si, pseudopotentials)
 atoms = [Si, Si]
 positions = [ones(3)/8, -ones(3)/8]
 ```

diff --git a/docs/src/ecosystem/atomsbase.jl b/docs/src/ecosystem/atomsbase.jl
@@ -27,19 +27,16 @@ system = bulk(:Si)
 using PseudoPotentialData  # defines PseudoFamily
 
 pd_lda_family = PseudoFamily("dojo.nc.sr.lda.v0_4_1.standard.upf")
-model = model_DFT(system;
-                  functionals=LDA(),
-                  temperature=1e-3,
+model = model_DFT(system; functionals=LDA(), temperature=1e-3,
                   pseudopotentials=pd_lda_family)
 
 # Alternatively the `pseudopotentials` object also accepts a `Dict{Symbol,String}`,
 # which provides for each element symbol the filename or identifier
 # of the pseudopotential to be employed, e.g.
 
-model = model_DFT(system;
-                  functionals=LDA(),
-                  temperature=1e-3,
-                  pseudopotentials=Dict(:Si => "hgh/lda/si-q4"))
+path_to_pspfile = PseudoFamily("cp2k.nc.sr.lda.v0_1.semicore.gth")[:Si]
+model = model_DFT(system; functionals=LDA(), temperature=1e-3,
+                  pseudopotentials=Dict(:Si => path_to_pspfile))
 
 # We can then discretise such a model and solve:
 basis  = PlaneWaveBasis(model; Ecut=15, kgrid=[4, 4, 4])
@@ -59,7 +56,7 @@ using AtomsIO
 system = load_system("Si.extxyz");
 
 # Run the LDA calculation:
-pseudopotentials = Dict(:Si => "hgh/lda/si-q4")
+pseudopotentials = PseudoFamily("cp2k.nc.sr.lda.v0_1.semicore.gth")
 model  = model_DFT(system; pseudopotentials, functionals=LDA(), temperature=1e-3)
 basis  = PlaneWaveBasis(model; Ecut=15, kgrid=[4, 4, 4])
 scfres = self_consistent_field(basis, tol=1e-8);
@@ -83,7 +80,7 @@ atoms  = [:Si => ones(3)/8, :Si => -ones(3)/8]
 system = periodic_system(atoms, lattice; fractional=true)
 
 ## Now run the LDA calculation:
-pseudopotentials = Dict(:Si => "hgh/lda/si-q4")
+pseudopotentials = PseudoFamily("cp2k.nc.sr.lda.v0_1.semicore.gth")
 model  = model_DFT(system; pseudopotentials, functionals=LDA(), temperature=1e-3)
 basis  = PlaneWaveBasis(model; Ecut=15, kgrid=[4, 4, 4])
 scfres = self_consistent_field(basis, tol=1e-4);
@@ -100,7 +97,7 @@ second_system = atomic_system(model)
 lattice = 5.431u"Å" / 2 * [[0 1 1.];
                            [1 0 1.];
                            [1 1 0.]];
-Si = ElementPsp(:Si, load_psp("hgh/lda/Si-q4"))
+Si = ElementPsp(:Si, pseudopotentials)
 atoms     = [Si, Si]
 positions = [ones(3)/8, -ones(3)/8]
 

diff --git a/docs/src/ecosystem/wannier.jl b/docs/src/ecosystem/wannier.jl
@@ -19,14 +19,15 @@ using DFTK
 using Plots
 using Unitful
 using UnitfulAtomic
+using PseudoPotentialData
 
 d = 10u"Å"
 a = 2.641u"Å"  # Graphene Lattice constant
 lattice = [a  -a/2    0;
            0  √3*a/2  0;
            0     0    d]
 
-C = ElementPsp(:C, load_psp("hgh/pbe/c-q4"))
+C = ElementPsp(:C, PseudoFamily("cp2k.nc.sr.pbe.v0_1.semicore.gth"))
 atoms     = [C, C]
 positions = [[0.0, 0.0, 0.0], [1//3, 2//3, 0.0]]
 model = model_DFT(lattice, atoms, positions; functionals=PBE())

diff --git a/docs/src/tricks/achieving_convergence.md b/docs/src/tricks/achieving_convergence.md
@@ -7,8 +7,9 @@ of inspiration for what you can try. Your mileage may vary.
 ```@setup convergence
 using DFTK
 using AtomsBuilder
-model = model_DFT(bulk(:Si); functionals=LDA(),
-                  pseudopotentials=Dict(:Si => "hgh/lda/si-q4"))
+using PseudoPotentialData
+pseudopotentials = PseudoFamily("cp2k.nc.sr.lda.v0_1.semicore.gth")
+model = model_DFT(bulk(:Si); functionals=LDA(), pseudopotentials)
 basis = PlaneWaveBasis(model; Ecut=15, kgrid=(3, 3, 3))
 ```
 

diff --git a/docs/src/tricks/parallelization.md b/docs/src/tricks/parallelization.md
@@ -5,11 +5,13 @@ to monitor and influence performance of the code.
 
 ```@setup parallelization
 using DFTK
+using PseudoPotentialData
 a = 10.26  # Silicon lattice constant in Bohr
 lattice = a / 2 * [[0 1 1.];
                    [1 0 1.];
                    [1 1 0.]]
-Si = ElementPsp(:Si, load_psp("hgh/lda/Si-q4"))
+pseudopotentials = PseudoFamily("cp2k.nc.sr.lda.v0_1.semicore.gth")
+Si = ElementPsp(:Si, pseudopotentials)
 atoms = [Si, Si]
 positions = [ones(3)/8, -ones(3)/8]
 

diff --git a/docs/src/tricks/scf_checkpoints.jl b/docs/src/tricks/scf_checkpoints.jl
@@ -25,11 +25,13 @@
 using DFTK
 using LinearAlgebra
 using JLD2
+using PseudoPotentialData
 
 d = 2.079  # oxygen-oxygen bondlength
 a = 9.0    # size of the simulation box
 lattice = a * I(3)
-O = ElementPsp(:O, load_psp("hgh/pbe/O-q6.hgh"))
+pseudopotentials = PseudoFamily("cp2k.nc.sr.pbe.v0_1.semicore.gth")
+O = ElementPsp(:O, pseudopotentials)
 atoms     = [O, O]
 positions = d / 2a * [[0, 0, 1], [0, 0, -1]]
 magnetic_moments = [1., 1.]

diff --git a/examples/arbitrary_floattype.jl b/examples/arbitrary_floattype.jl
@@ -25,16 +25,12 @@
 #     [ArXiv 2004.13549](https://arxiv.org/abs/2004.13549)
 
 using DFTK
+using PseudoPotentialData
+using AtomsBuilder
 
-## Setup silicon lattice
-a = 10.263141334305942  # lattice constant in Bohr
-lattice = a / 2 .* [[0 1 1.]; [1 0 1.]; [1 1 0.]]
-Si = ElementPsp(:Si, load_psp("hgh/lda/Si-q4"))
-atoms = [Si, Si]
-positions = [ones(3)/8, -ones(3)/8]
-
-## Cast to Float32, setup model and basis
-model = model_DFT(lattice, atoms, positions; functionals=LDA())
+## Use AtomsBuilder to setup silicon lattice and cast model to Float32
+pseudopotentials = PseudoFamily("cp2k.nc.sr.lda.v0_1.largecore.gth")
+model = model_DFT(bulk(:Si); functionals=LDA(), pseudopotentials)
 basis = PlaneWaveBasis(convert(Model{Float32}, model), Ecut=7, kgrid=[4, 4, 4])
 
 ## Run the SCF