Integration with AbstractSystem (#10)

Author: mfherbst

Project.toml

@@ -1,7 +1,7 @@
 name = "PseudoPotentialData"
 uuid = "5751a51d-ac76-4487-a056-413ecf6fbe19"
 authors = ["Michael F. Herbst <[email protected]> and contributors"]
-version = "0.2.2"
+version = "0.2.3"
 
 [deps]
 Artifacts = "56f22d72-fd6d-98f1-02f0-08ddc0907c33"
@@ -10,8 +10,15 @@ DocStringExtensions = "ffbed154-4ef7-542d-bbb7-c09d3a79fcae"
 LazyArtifacts = "4af54fe1-eca0-43a8-85a7-787d91b784e3"
 TOML = "fa267f1f-6049-4f14-aa54-33bafae1ed76"
 
+[weakdeps]
+AtomsBase = "a963bdd2-2df7-4f54-a1ee-49d51e6be12a"
+
+[extensions]
+PseudoPotentialDataAtomsBaseExt = "AtomsBase"
+
 [compat]
 Artifacts = "1"
+AtomsBase = "0.5"
 Compat = "4.16"
 DocStringExtensions = "0.9.3"
 LazyArtifacts = "1"
@@ -20,6 +27,8 @@ julia = "1.10"
 
 [extras]
 Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
+Unitful = "1986cc42-f94f-5a68-af5c-568840ba703d"
+AtomsBase = "a963bdd2-2df7-4f54-a1ee-49d51e6be12a"
 
 [targets]
-test = ["Test"]
+test = ["AtomsBase", "Unitful", "Test"]

docs/src/index.md

@@ -70,7 +70,18 @@ cutoffs of plane-wave bases. These can be also accessed more conveniently via
 ```@example index-example
 recommended_cutoff(family, :Si)
 ```
-Note, that the `Ecut` and `Ecut_density` values are in atomic Hartree units.
+The `Ecut` and `Ecut_density` values are provided in atomic Hartree units.
+Note, that if you are working with `AbstractSystem` objects from
+[AtomsBase.jl](https://github.com/JuliaMolSim/AtomsBase.jl) compatible packages
+you can also directly supply a system to `recommended_cutoff` in order to obtain
+the *maximal* recommended values over all elements contained in the respective
+system, e.g.
+```julia
+using AtomsBuilder
+system = bulk(:Si)
+recommended_cutoff(family, system)
+```
+
 
 ## Available pseudopotential families and naming convention
 A list of available pseudopotential families is available as

ext/PseudoPotentialDataAtomsBaseExt.jl

@@ -0,0 +1,24 @@
+module PseudoPotentialDataAtomsBaseExt
+using AtomsBase
+using PseudoPotentialData
+import PseudoPotentialData: recommended_cutoff
+
+"""
+    recommended_cutoff(family::PseudoFamily, system::AbstractSystem)
+
+Return the recommended kinetic energy cutoff, supersampling and density cutoff
+for this `system`. Values may be `missing` if the respective data cannot be determined.
+"""
+function recommended_cutoff(family::PseudoFamily, system::AbstractSystem)
+    function get_maximum(property)
+        maximum(system) do atom
+            getproperty(recommended_cutoff(family, element_symbol(atom)), property)
+        end
+    end
+
+    (; :Ecut          => get_maximum(:Ecut),
+       :supersampling => get_maximum(:supersampling),
+       :Ecut_density  => get_maximum(:Ecut_density))
+end
+
+end

src/pseudofamily.jl

@@ -61,6 +61,10 @@ function Base.show(io::IO, family::PseudoFamily)
 end
 Base.show(io::IO, ::MIME"text/plain", family::PseudoFamily) = show(io, family)
 
+function Base.:(==)(lhs::PseudoFamily, rhs::PseudoFamily)
+    lhs.identifier == rhs.identifier
+end
+
 """
 Get the full path to the file containing the pseudopotential information
 for a particular `element` (identified by an atomic symbol) and a particular

test/runtests.jl

@@ -1,5 +1,8 @@
+using AtomsBase
 using PseudoPotentialData
 using Test
+using Unitful
+
 
 @testset "PseudoPotentialData.jl" begin
     @testset "Test one family can be loaded" begin
@@ -59,6 +62,15 @@ using Test
         @test occursin("PseudoFamily", String(take!(io)))
     end
 
+    @testset "Comparison of family objects" begin
+        f1 = PseudoFamily("dojo.nc.sr.pbe.v0_4_1.stringent.upf")
+        f2 = PseudoFamily("dojo.nc.sr.lda.v0_4_1.stringent.upf")
+
+        @test f1 == f1
+        @test f2 == f2
+        @test f1 != f2
+    end
+
     @testset "Pseudometa on families" begin
         family = PseudoFamily("dojo.nc.sr.lda.v0_4_1.stringent.upf")
         meta = pseudometa(family)
@@ -114,4 +126,28 @@ using Test
             end
         end
     end
+
+    @testset "recommended_cutoff on systems" begin
+        family = PseudoFamily("dojo.nc.sr.lda.v0_4_1.standard.upf")
+        cutoffs_Si = recommended_cutoff(family, :Si)
+        cutoffs_Ga = recommended_cutoff(family, :Ga)
+        cutoffs_As = recommended_cutoff(family, :As)
+
+        ref_Ecut  = max(cutoffs_Ga.Ecut, cutoffs_As.Ecut, cutoffs_Si.Ecut)
+        ref_Edens = max(cutoffs_Ga.Ecut_density, cutoffs_As.Ecut_density,
+                        cutoffs_Si.Ecut_density)
+        ref_super = max(cutoffs_Ga.supersampling, cutoffs_As.supersampling,
+                        cutoffs_Si.supersampling)
+
+        box = [[10, 0.0, 0.0], [0.0, 5, 0.0], [0.0, 0.0, 7]]u"Å"
+        atoms = [:Si => [0.0, -0.125, 0.0],
+                 :Ga => [0.125, 0.0, 0.0],
+                 :As => [-0.125, 0.0, 0.0]]
+        system = periodic_system(atoms, box; fractional=true)
+
+        cutoffs = recommended_cutoff(family, system)
+        @test cutoffs.Ecut          == ref_Ecut
+        @test cutoffs.Ecut_density  == ref_Edens
+        @test cutoffs.supersampling == ref_super
+    end
 end