Enable empirical potentials (#23)

Author: mfherbst

README.md

@@ -35,7 +35,11 @@ using UnitfulAtomic
 # Setup system and calculator
 system = isolated_system([:H => [0, 0, 0.0]u"bohr",
                           :H => [0, 0, 1.9]u"bohr"])
-calc = LennardJones(-1.17u"hartree", 0.743u"angstrom", 1, 1, 0.6u"nm")
+
+zH = 1
+emins = Dict((zH, zH) => -1.17u"hartree", )
+rmins = Dict((zH, zH) => 0.743u"Å", )
+calc = LennardJones(emins, rmins, 5.0u"Å")
 
 # Run the geometry optimisation
 results = minimize_energy!(system, calc)

docs/Project.toml

@@ -6,6 +6,7 @@ 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"

docs/src/examples/tial_lj.md

@@ -3,8 +3,7 @@
 TODO Write some text motivating this example
 
 Setup system:
-```julia
-## TODO: Should run as @example once EmpiricalPotentials is compatible with AB 0.5
+```@example tial
 using AtomsIO
 using EmpiricalPotentials
 
@@ -13,18 +12,27 @@ nothing
 ```
 
 Setup calculator:
-```julia
-## TODO: Should run as @example once EmpiricalPotentials is compatible with AB 0.5
+```@example tial
 using Unitful
 using UnitfulAtomic
 
-calc = LennardJones(-1.0u"meV", 3.1u"Å", 13, 13, 6.0u"Å")
+# Note: These are completely made up parameters,
+#       please do not use in production
+rcut = 5.0u"Å"
+zAl = atomic_number(ChemicalSpecies(:Al))
+zTi = atomic_number(ChemicalSpecies(:Ti))
+emins = Dict( (zAl, zAl) => -1.0u"eV",
+              (zAl, zTi) => -1.234u"eV",
+              (zTi, zTi) => -0.345u"eV" )
+rmins = Dict( (zAl, zAl) => 2.7u"Å",
+              (zAl, zTi) => 3.2u"Å",
+              (zTi, zTi) => 3.0u"Å" )
+calc = LennardJones(emins, rmins, rcut)
 nothing
 ```
 
 Minimise energy:
-```julia
-## TODO: Should run as @example once EmpiricalPotentials is compatible with AB 0.5
+```@example tial
 using GeometryOptimization
 GO = GeometryOptimization
 
@@ -33,8 +41,6 @@ results.energy
 ```
 
 Final structure:
-```julia
-## TODO: Should run as @example once EmpiricalPotentials is compatible with AB 0.5
-
+```@example tial
 results.system
 ```

docs/src/index.md

@@ -25,7 +25,10 @@ using UnitfulAtomic
 # Setup system and calculator
 system = isolated_system([:H => [0, 0, 0.0]u"bohr",
                           :H => [0, 0, 1.9]u"bohr"])
-calc = LennardJones(-1.17u"hartree", 0.743u"angstrom", 1, 1, 0.6u"nm")
+zH = 1
+emins = Dict((zH, zH) => -1.17u"hartree", )
+rmins = Dict((zH, zH) => 0.743u"Å", )
+calc = LennardJones(emins, rmins, 5.0u"Å")
 
 # Run the geometry optimisation (using verbosity=1 to print the progress)
 results = minimize_energy!(system, calc; verbosity=1)