Update CI infrastructure (#14)

Author: mfherbst

.codecov.yml

@@ -0,0 +1 @@
+comment: false

.github/dependabot.yml

@@ -0,0 +1,7 @@
+# https://docs.github.com/github/administering-a-repository/configuration-options-for-dependency-updates
+version: 2
+updates:
+  - package-ecosystem: "github-actions"
+    directory: "/" # Location of package manifests
+    schedule:
+      interval: "weekly"

.github/workflows/CI.yml

@@ -26,26 +26,31 @@ jobs:
         arch:
           - x64
     steps:
-      - uses: actions/checkout@v3
-      - uses: julia-actions/setup-julia@v1
+      - uses: actions/checkout@v4
+      - uses: julia-actions/setup-julia@v2
         with:
           version: ${{ matrix.version }}
           arch: ${{ matrix.arch }}
-      - uses: julia-actions/cache@v1
+      - uses: julia-actions/cache@v2
       - uses: julia-actions/julia-buildpkg@v1
       - uses: julia-actions/julia-runtest@v1
+      - uses: julia-actions/julia-processcoverage@v1
+      - uses: codecov/codecov-action@v4
+        with:
+          files: lcov.info
+          token: ${{ secrets.CODECOV_TOKEN }}
   docs:
     name: Documentation
     runs-on: ubuntu-latest
     permissions:
       contents: write
       statuses: write
     steps:
-      - uses: actions/checkout@v3
-      - uses: julia-actions/setup-julia@v1
+      - uses: actions/checkout@v4
+      - uses: julia-actions/setup-julia@v2
         with:
           version: '1'
-      - name: Configure doc environment
+      - name: Install documentation dependencies
         run: |
           julia --project=docs/ -e '
             using Pkg

Project.toml

@@ -17,7 +17,7 @@ UnitfulAtomic = "a7773ee8-282e-5fa2-be4e-bd808c38a91a"
 
 [compat]
 AtomsBase = "0.3"
-AtomsBuilder = "=0.0.4"
+AtomsBuilder = "0.1"
 AtomsCalculators = "0.2"
 DocStringExtensions = "0.9"
 LineSearches = "7"

README.md

@@ -3,9 +3,44 @@
 [![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)
 
-A geometry optimization package for
+A package for optimising the structural parameters of an atomistic system,
+i.e. the step usually referred to as
+**geometry optimisation** or **structural relaxation**
+in electronic structure theory and atomistic modelling.
+
+The package is generic in the datastructures used to represent the geometry,
+the calculator used to evaluate energies and forces as well as the solver algorithm.
+Generally all
 [AtomsBase structures](https://github.com/JuliaMolSim/AtomsBase.jl)
-and [AtomsCalculator calculators](https://github.com/JuliaMolSim/AtomsCalculators.jl).
+and [AtomsCalculator calculators](https://github.com/JuliaMolSim/AtomsCalculators.jl)
+should work out of the box.
+
 See the [documentation](https://JuliaMolSim.github.io/GeometryOptimization.jl/stable/)
 for examples and further details.
+
+## Motivating example
+
+We consider the optimisation of the bondlength of a hydrogen
+molecule using a simple Lennard Jones potential:
+
+```julia
+using AtomsBase
+using EmpiricalPotentials
+using GeometryOptimization
+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"])
+calc = LennardJones(-1.17u"hartree", 0.743u"angstrom", 1, 1, 0.6u"nm")
+
+# Run the geometry optimisation
+results = minimize_energy!(system, calc)
+
+# Inspect the results
+optimised  = results.system
+bondlength = norm(position(optimised[1]) - position(optimised[2]))
+```

src/optimization.jl

@@ -131,7 +131,7 @@ function _minimize_energy!(system, calculator, solver;
 
         energy_converged = austrip(abs(geoopt_state.energy - Eold))    < austrip(tol_energy)
         force_converged  = austrip(maximum(norm, geoopt_state.forces)) < austrip(tol_force)
-        virial_converged = austrip(maximum(abs, geoopt_state.virial))  < austrip(tol_virial)
+        virial_converged = austrip(maximum(abs,  geoopt_state.virial)) < austrip(tol_virial)
 
         Eold = geoopt_state.energy
         converged = energy_converged && force_converged && virial_converged
@@ -140,8 +140,8 @@ function _minimize_energy!(system, calculator, solver;
 
     optimres = solve(problem, solver; maxiters, callback=inner_callback, kwargs...)
     (; system=update_not_clamped_positions(system, optimres.u * u"bohr"), converged,
-       energy=optimres.objective, state=geoopt_state.calc_state,
-       optimres.stats, optimres.alg, optimres)
+       energy=optimres.objective, geoopt_state.forces, geoopt_state.virial,
+       state=geoopt_state.calc_state, optimres.stats, optimres.alg, optimres)
 end
 
 # Default setup_solver function just passes things through