Merge pull request #18 from JuliaMolSim/ab05

Author: mfherbst

Project.toml

@@ -1,7 +1,7 @@
 name = "GeometryOptimization"
 uuid = "673bf261-a53d-43b9-876f-d3c1fc8329c2"
 authors = ["JuliaMolSim community"]
-version = "0.1.0"
+version = "0.1.1"
 
 [deps]
 AtomsBase = "a963bdd2-2df7-4f54-a1ee-49d51e6be12a"
@@ -19,9 +19,10 @@ Unitful = "1986cc42-f94f-5a68-af5c-568840ba703d"
 UnitfulAtomic = "a7773ee8-282e-5fa2-be4e-bd808c38a91a"
 
 [compat]
-AtomsBase = "0.3"
-AtomsBuilder = "0.1"
-AtomsCalculators = "0.2"
+ASEconvert = "0.1.8"
+AtomsBase = "0.5"
+AtomsBuilder = "0.2.2"
+AtomsCalculators = "0.2.3"
 DocStringExtensions = "0.9"
 LineSearches = "7"
 Optimization = "3"

docs/Project.toml

@@ -6,15 +6,13 @@ AtomsCalculators = "a3e0e189-c65a-42c1-833c-339540406eb1"
 AtomsIO = "1692102d-eeb4-4df9-807b-c9517f998d44"
 DFTK = "acf6eb54-70d9-11e9-0013-234b7a5f5337"
 Documenter = "e30172f5-a6a5-5a46-863b-614d45cd2de4"
-EmpiricalPotentials = "38527215-9240-4c91-a638-d4250620c9e2"
 GeometryOptimization = "673bf261-a53d-43b9-876f-d3c1fc8329c2"
 LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
 OptimizationNLopt = "4e6fcdb7-1186-4e1f-a706-475e75c168bb"
 Unitful = "1986cc42-f94f-5a68-af5c-568840ba703d"
 UnitfulAtomic = "a7773ee8-282e-5fa2-be4e-bd808c38a91a"
 
 [compat]
-ASEconvert = "0.1"
-DFTK = "0.6"
-Documenter = "~1.5"
-EmpiricalPotentials = "0.1"
+ASEconvert = "0.1.8"
+DFTK = "0.7"
+Documenter = "~1.8"

docs/src/examples/aluminium_dftk.md

@@ -15,27 +15,22 @@ system = rattle!(bulk(:Al; cubic=true), 0.2u"Å")
 Next we create a calculator employing the
 [density-functional toolkit](https://dftk.org/)
 to compute energies and forces at using the LDA density functional.
+As pseudopotentials we use the [PseudoDojo](http://pseudo-dojo.org) as available
+in the [PseudoPotentialData](https://github.com/JuliaMolSim/PseudoPotentialData.jl/)
+package.
 ```@example dftk-aluminium
 using DFTK
+using PseudoPotentialData
 
-model_kwargs = (; functionals=[:lda_x, :lda_c_pw], temperature=1e-3)
+pseudopotentials = PseudoFamily("dojo.nc.sr.lda.v0_4_1.oncvpsp3.standard.upf")
+model_kwargs = (; functionals=LDA(), temperature=1e-3, pseudopotentials)
 basis_kwargs = (; kgrid=(3, 3, 3), Ecut=10.0)
 scf_kwargs   = (; mixing=KerkerMixing())
 calc = DFTKCalculator(; model_kwargs, basis_kwargs, scf_kwargs)
-nothing
-```
-
-We attach pseudopotentials to the aluminium system,
-i.e. we tell DFTK, that each aluminium atom should be modelled using
-a pseudopotential rather than the full Coulomb potential.
-
-```@example dftk-aluminium
-system = attach_psp(system; Al="hgh/lda/al-q3")
-nothing
 ```
 
 !!! info "Crude computational parameters"
-    Note, that these numerical parameters are chosen rather crudely in order
+    Note, that the numerical parameters above are chosen rather crudely in order
     to give a fast runtime on CI systems. For production calculations one would
     require larger computational parameters.
 

docs/src/examples/other_solvers.md

@@ -11,12 +11,12 @@ to compute energies and forces at using the LDA density functional.
 
 ```@example other-solvers
 using DFTK
+using PseudoPotentialData
 
-model_kwargs = (; functionals=[:lda_x, :lda_c_pw])
+pseudopotentials = PseudoFamily("dojo.nc.sr.lda.v0_4_1.oncvpsp3.standard.upf")
+model_kwargs = (; functionals=LDA(), pseudopotentials)
 basis_kwargs = (; kgrid=(1, 1, 1), Ecut=20.0)
-scf_kwargs   = (; tol=1e-6)
-calc = DFTKCalculator(; model_kwargs, basis_kwargs, scf_kwargs)
-nothing
+calc = DFTKCalculator(; model_kwargs, basis_kwargs)
 ```
 
 and we build the hydrogen molecular system,
@@ -31,7 +31,6 @@ bounding_box = [[10.0, 0.0, 0.0], [0.0, 10.0, 0.0], [0.0, 0.0, 10.0]]u"Å"
 system = periodic_system([:H => [0, 0, 1.]u"bohr",
                           :H => [0, 0, 3.]u"bohr"],
                          bounding_box)
-system = attach_psp(system; H="hgh/lda/h-q1")
 nothing
 ```
 

docs/src/examples/tial_lj.md

@@ -3,36 +3,38 @@
 TODO Write some text motivating this example
 
 Setup system:
-```@example tial
-using AtomsBase
+```julia
+## TODO: Should run as @example once EmpiricalPotentials is compatible with AB 0.5
 using AtomsIO
 using EmpiricalPotentials
-using GeometryOptimization
-GO = GeometryOptimization
 
 system = load_system(joinpath(pkgdir(EmpiricalPotentials), "data/TiAl-1024.xyz"))
 nothing
 ```
 
 Setup calculator:
-```@example tial
+```julia
+## TODO: Should run as @example once EmpiricalPotentials is compatible with AB 0.5
 using Unitful
 using UnitfulAtomic
+
 calc = LennardJones(-1.0u"meV", 3.1u"Å", 13, 13, 6.0u"Å")
 nothing
 ```
 
 Minimise energy:
 ```julia
-## TODO: Should run as @example once EmpiricalPotentials is compatible
+## TODO: Should run as @example once EmpiricalPotentials is compatible with AB 0.5
+using GeometryOptimization
+GO = GeometryOptimization
 
 results = minimize_energy!(system, calc, GO.OptimCG(); maxiters=10, verbosity=1)
 results.energy
 ```
 
 Final structure:
 ```julia
-## TODO: Should run as @example once EmpiricalPotentials is compatible
+## TODO: Should run as @example once EmpiricalPotentials is compatible with AB 0.5
 
 results.system
 ```

src/clamping_updating_positions.jl

@@ -31,7 +31,7 @@ updated to the ones provided (in the order in which they appear in the system).
 """
 function update_not_clamped_positions(system, positions::AbstractVector{<:Unitful.Length})
     mask = [!get(atom, :clamped, false) for atom in system]
-    new_positions = deepcopy(position(system))
+    new_positions = deepcopy(position(system, :))
     new_positions[mask] = reinterpret(reshape, SVector{3, eltype(positions)},
                                       reshape(positions, 3, :))
     update_positions(system, new_positions)