Run index example automatically (#25)

Author: mfherbst

Project.toml

@@ -38,9 +38,10 @@ julia = "1.10"
 [extras]
 ASEconvert = "3da9722f-58c2-4165-81be-b4d7253e8fd2"
 AtomsBuilder = "f5cc8831-eeb7-4288-8d9f-d6c1ddb77004"
+EmpiricalPotentials = "38527215-9240-4c91-a638-d4250620c9e2"
 PythonCall = "6099a3de-0909-46bc-b1f4-468b9a2dfc0d"
 Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
 TestItemRunner = "f8b46487-2199-4994-9208-9a1283c18c0a"
 
 [targets]
-test = ["ASEconvert", "AtomsBuilder", "PythonCall", "Test", "TestItemRunner"]
+test = ["ASEconvert", "AtomsBuilder", "EmpiricalPotentials", "PythonCall", "Test", "TestItemRunner"]

README.md

@@ -3,7 +3,7 @@
 [![Stable](https://img.shields.io/badge/docs-stable-blue.svg)](https://JuliaMolSim.github.io/GeometryOptimization.jl/stable/)
 [![Dev](https://img.shields.io/badge/docs-dev-blue.svg)](https://JuliaMolSim.github.io/GeometryOptimization.jl/dev/)
 [![Build Status](https://github.com/JuliaMolSim/GeometryOptimization.jl/actions/workflows/CI.yml/badge.svg?branch=main)](https://github.com/JuliaMolSim/GeometryOptimization.jl/actions/workflows/CI.yml?query=branch%3Amain)
-[![Coverage](https://codecov.io/gh/JuliaMolSim/GeometryOptimization.jl/branch/master/graph/badge.svg)](https://codecov.io/gh/JuliaMolSim/GeometryOptimization.jl)
+[![Coverage](https://codecov.io/gh/JuliaMolSim/GeometryOptimization.jl/branch/main/graph/badge.svg)](https://codecov.io/gh/JuliaMolSim/GeometryOptimization.jl)
 
 A package for optimising the structural parameters of an atomistic system,
 i.e. the step usually referred to as
@@ -29,22 +29,24 @@ molecule using a simple Lennard Jones potential:
 using AtomsBase
 using EmpiricalPotentials
 using GeometryOptimization
+using LinearAlgebra
 using Unitful
 using UnitfulAtomic
 
 # Setup system and calculator
-system = isolated_system([:H => [0, 0, 0.0]u"bohr",
-                          :H => [0, 0, 1.9]u"bohr"])
-
+cell_vectors = ([10.0, 0.0, 0.0]u"Å", [0.0, 10.0, 0.0]u"Å", [0.0, 0.0, 10.0]u"Å")
+system = periodic_system([:H => [0, 0, 0.0]u"bohr",
+                          :H => [0, 0, 1.9]u"bohr"],
+                         cell_vectors)
 zH = 1
 emins = Dict((zH, zH) => -1.17u"hartree", )
-rmins = Dict((zH, zH) => 0.743u"Å", )
+rmins = Dict((zH, zH) =>  0.743u"Å",      )
 calc = LennardJones(emins, rmins, 5.0u"Å")
 
 # Run the geometry optimisation
 results = minimize_energy!(system, calc)
 
 # Inspect the results
-optimised  = results.system
-bondlength = norm(position(optimised[1]) - position(optimised[2]))
+optsystem = results.system
+optimised_bondlength = norm(position(optsystem[1]) - position(optsystem[2]))
 ```

docs/src/examples/tial_lj.md

@@ -8,7 +8,7 @@ using AtomsIO
 using EmpiricalPotentials
 
 system = load_system(joinpath(pkgdir(EmpiricalPotentials), "data/TiAl-1024.xyz"))
-nothing
+nothing  # hide
 ```
 
 Setup calculator:
@@ -28,7 +28,7 @@ rmins = Dict( (zAl, zAl) => 2.7u"Å",
               (zAl, zTi) => 3.2u"Å",
               (zTi, zTi) => 3.0u"Å" )
 calc = LennardJones(emins, rmins, rcut)
-nothing
+nothing  # hide
 ```
 
 Minimise energy:
@@ -37,7 +37,7 @@ using GeometryOptimization
 GO = GeometryOptimization
 
 results = minimize_energy!(system, calc, GO.OptimCG(); maxiters=10, verbosity=1)
-results.energy
+nothing  # hide
 ```
 
 Final structure:

docs/src/index.md

@@ -14,28 +14,31 @@ The source code can be found [on github](https://github.com/JuliaMolSim/Geometry
 We consider the optimisation of the bondlength of a hydrogen
 molecule using a simple Lennard Jones potential:
 
-```julia
-## TODO: Should run as @example once EmpiricalPotentials is compatible
+```@example
 using AtomsBase
 using EmpiricalPotentials
 using GeometryOptimization
+using LinearAlgebra
 using Unitful
 using UnitfulAtomic
 
 # Setup system and calculator
-system = isolated_system([:H => [0, 0, 0.0]u"bohr",
-                          :H => [0, 0, 1.9]u"bohr"])
+cell_vectors = ([10.0, 0.0, 0.0]u"Å", [0.0, 10.0, 0.0]u"Å", [0.0, 0.0, 10.0]u"Å")
+system = periodic_system([:H => [0, 0, 0.0]u"bohr",
+                          :H => [0, 0, 1.9]u"bohr"],
+                         cell_vectors)
 zH = 1
 emins = Dict((zH, zH) => -1.17u"hartree", )
-rmins = Dict((zH, zH) => 0.743u"Å", )
+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)
 
 # Inspect the results
-optimised_system = results.system
+optsystem = results.system
 optimised_bondlength = norm(position(optsystem[1]) - position(optsystem[2]))
+nothing  # hide
 ```
 
 The idea is that