Merge branch 'main' into rpmd-docs-updates

Project.toml

@@ -1,7 +1,7 @@
 name = "NQCDynamics"
 uuid = "36248dfb-79eb-4f4d-ab9c-e29ea5f33e14"
 authors = ["James <james.gardner1421@gmail.com>"]
-version = "0.13.3"
+version = "0.13.4"
 
 [deps]
 AdvancedHMC = "0bf59076-c3b1-5ca4-86bd-e02cd72cde3d"
@@ -45,16 +45,16 @@ Unitful = "1986cc42-f94f-5a68-af5c-568840ba703d"
 UnitfulAtomic = "a7773ee8-282e-5fa2-be4e-bd808c38a91a"
 
 [compat]
-AdvancedHMC = "0.5"
-AdvancedMH = "0.6, 0.7"
-ComponentArrays = "0.11, 0.12, 0.13, 0.14"
+AdvancedHMC = "0.5, 0.6"
+AdvancedMH = "0.6, 0.7, 0.8"
+ComponentArrays = "0.11, 0.12, 0.13, 0.14, 0.15"
 DEDataArrays = "0.2"
 Dictionaries = "0.3"
 DiffEqBase = "6"
 Distributions = "0.25"
 FastBroadcast = "0.1, 0.2"
 FastLapackInterface = "1, 2"
-HDF5 = "0.15, 0.16"
+HDF5 = "0.15, 0.16, 0.17"
 Interpolations = "0.13, 0.14"
 MuladdMacro = "0.2"
 NQCBase = "0.2"
@@ -72,7 +72,7 @@ Reexport = "1"
 RingPolymerArrays = "0.1"
 Roots = "1, 2"
 Rotations = "1"
-SciMLBase = "1"
+SciMLBase = "1, 2"
 StaticArrays = "1"
 StatsBase = "0.33, 0.34"
 StochasticDiffEq = "6"
@@ -92,6 +92,7 @@ DiffEqNoiseProcess = "77a26b50-5914-5dd7-bc55-306e6241c503"
 FiniteDiff = "6a86dc24-6348-571c-b903-95158fe2bd41"
 JuLIP = "945c410c-986d-556a-acb1-167a618e0462"
 Logging = "56ddb016-857b-54e1-b83d-db4d58db5568"
+MKL = "33e6dc65-8f57-5167-99aa-e5a354878fb2"
 Plots = "91a5bcdd-55d7-5caf-9e0b-520d859cae80"
 PyCall = "438e738f-606a-5dbb-bf0a-cddfbfd45ab0"
 SafeTestsets = "1bc83da4-3b8d-516f-aca4-4fe02f6d838f"
@@ -100,4 +101,4 @@ Symbolics = "0c5d862f-8b57-4792-8d23-62f2024744c7"
 Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
 
 [targets]
-test = ["Test", "SafeTestsets", "CSV", "DataFrames", "DiffEqNoiseProcess", "FiniteDiff", "DiffEqDevTools", "Logging", "PyCall", "JuLIP", "Symbolics", "Statistics", "Plots"]
+test = ["Test", "SafeTestsets", "CSV", "DataFrames", "DiffEqNoiseProcess", "FiniteDiff", "DiffEqDevTools", "Logging", "MKL", "PyCall", "JuLIP", "Symbolics", "Statistics", "Plots"]

docs/Project.toml

@@ -26,5 +26,5 @@ Unitful = "1986cc42-f94f-5a68-af5c-568840ba703d"
 UnitfulAtomic = "a7773ee8-282e-5fa2-be4e-bd808c38a91a"
 
 [compat]
-Documenter = "0.27"
+Documenter = "1"
 DocumenterCitations = "1"

docs/add_profiling_info.jl

@@ -0,0 +1,37 @@
+
+function add_text_blocks(file)
+    preamble = """
+    ```@setup logging
+    @info "Expanding $file..."
+    start_time = time()
+    ```
+    """
+
+    postamble = """
+    ```@setup logging
+    runtime = round(time() - start_time; digits=2)
+    @info "...done after \$runtime s."
+    ```
+    """
+
+    (tmppath, tmpio) = mktemp()
+    open(file) do io
+        write(tmpio, preamble)
+        for line in eachline(io, keep=true) # keep so the new line isn't chomped
+            write(tmpio, line)
+        end
+        write(tmpio, postamble)
+    end
+    close(tmpio)
+    mv(tmppath, file, force=true)
+end
+
+
+for (root, dirs, files) in walkdir("src")
+    for file in files
+        if splitext(file)[2] == ".md"
+            filepath = joinpath(root, file)
+            add_text_blocks(filepath)
+        end
+    end
+end

docs/make.jl

@@ -3,10 +3,6 @@ using DocumenterCitations
 using NQCBase, NQCModels, NQCDistributions, NQCDynamics
 using CubeLDFAModel, NNInterfaces
 
-DocMeta.setdocmeta!(NQCDynamics, :DocTestSetup, :(using NQCDynamics); recursive=true)
-DocMeta.setdocmeta!(NQCModels, :DocTestSetup, :(using NQCModels, Symbolics); recursive=true)
-DocMeta.setdocmeta!(NQCBase, :DocTestSetup, :(using NQCBase); recursive=true)
-
 bib = CitationBibliography(joinpath(@__DIR__, "references.bib"))
 
 function find_all_files(directory)
@@ -16,16 +12,15 @@ function find_all_files(directory)
     )
 end
 
-@time makedocs(
-    bib,
+@time makedocs(;
+    plugins=[bib],
     sitename="NQCDynamics.jl",
     modules=[NQCDynamics, NQCDistributions, NQCModels, NQCBase, CubeLDFAModel],
-    strict=true,
+    doctest=false,
     format=Documenter.HTML(
         prettyurls=get(ENV, "CI", nothing) == "true",
         canonical="https://nqcd.github.io/NQCDynamics.jl/stable/",
         assets=["assets/favicon.ico", "assets/citations.css"],
-        ansicolor=true,
     ),
     authors="James Gardner and contributors.",
     pages=[

docs/src/NQCDistributions/overview.md

@@ -1,3 +1,7 @@
+```@setup logging
+@info "Expanding src/NQCDistributions/overview.md..."
+start_time = time()
+```
 # NQCDistributions.jl
 
 # Storing and sampling distributions
@@ -67,7 +71,7 @@ read on to the next sections about the included sampling methods.
 ### VelocityBoltzmann
 
 When performing equilibrium simulations it is often desirable to initialise trajectories
-when thermal velocities, e.g. in combination with positions obtained from Monte Carlo sampling.
+with thermal velocities, e.g. in combination with positions obtained from Monte Carlo sampling.
 These can be obtained for each atom from a gaussian distribution of the appropriate
 width, or alternatively, using the [`VelocityBoltzmann`](@ref) distribution which simplifies
 the process.
@@ -155,3 +159,8 @@ total_dist.electronic.state # Returns the chosen electronic state.
 
 ```
 
+
+```@setup logging
+runtime = round(time() - start_time; digits=2)
+@info "...done after $runtime s."
+```

docs/src/NQCModels/analyticmodels.md

@@ -1,3 +1,7 @@
+```@setup logging
+@info "Expanding src/NQCModels/analyticmodels.md..."
+start_time = time()
+```
 # Analytic model library
 
 This page plots many of the analytic models included in `NQCDynamics`.
@@ -93,3 +97,7 @@ z = range(-0.5, 4.0, length=200)
 contour(x, z, v1, color=:blue, levels=0:0.01:0.1, label="V11", colorbar=false)
 contour!(x, z, v2, color=:red, levels=0:0.01:0.1, label="V22")
 ```
+```@setup logging
+runtime = round(time() - start_time; digits=2)
+@info "...done after $runtime s."
+```

docs/src/NQCModels/ase.md

@@ -1,3 +1,7 @@
+```@setup logging
+@info "Expanding src/NQCModels/ase.md..."
+start_time = time()
+```
 # ASE interface
 
 The easiest way to obtain potentials and forces from established codes is to
@@ -23,12 +27,12 @@ associated calculator to implement the required [`potential`](@ref) and
 First, it is necessary to import `ase` and create the `ase.Atoms` object and attach
 the desired calculator. This works exactly as in Python:
 ```@example ase
-using PyCall
+using PythonCall: pyimport, pylist
+using ASEconvert
 
-ase = pyimport("ase")
 emt = pyimport("ase.calculators.emt")
 
-h2 = ase.Atoms("H2", [(0, 0, 0), (0, 0, 0.74)])
+h2 = ase.Atoms("H2", pylist([(0, 0, 0), (0, 0, 0.74)]))
 h2.calc = emt.EMT()
 nothing # hide
 ```
@@ -53,3 +57,7 @@ derivative(model, rand(3, 2))
     [SchNetPack (SPK)](https://github.com/atomistic-machine-learning/schnetpack) by
     passing their ASE calculator to the `AdiabaticASEModel`.
     Take a look at [Neural network models](@ref) to learn more.
+```@setup logging
+runtime = round(time() - start_time; digits=2)
+@info "...done after $runtime s."
+```

docs/src/NQCModels/frictionmodels.md

@@ -1,3 +1,7 @@
+```@setup logging
+@info "Expanding src/NQCModels/frictionmodels.md..."
+start_time = time()
+```
 # [Electronic friction models](@id models-friction)
 
 To perform [molecular dynamics with electronic friction (MDEF)](@ref mdef-dynamics)
@@ -69,3 +73,7 @@ to obtain the time-dependent perturbation theory friction from the atomic positi
 As with LDFA, one of these models is used in the
 [reactive scattering example](@ref example-h2scattering).
 
+```@setup logging
+runtime = round(time() - start_time; digits=2)
+@info "...done after $runtime s."
+```

docs/src/NQCModels/neuralnetworkmodels.md

@@ -1,3 +1,7 @@
+```@setup logging
+@info "Expanding src/NQCModels/neuralnetworkmodels.md..."
+start_time = time()
+```
 # Neural network models
 
 Using the [ASE interface](@ref) we can directly use models trained using
@@ -59,3 +63,7 @@ r = [0 0; 0 0; 0 ustrip(auconvert(0.74u"Å"))]
 potential(model, r)
 derivative(model, r)
 ```
+```@setup logging
+runtime = round(time() - start_time; digits=2)
+@info "...done after $runtime s."
+```

docs/src/NQCModels/overview.md

@@ -1,3 +1,7 @@
+```@setup logging
+@info "Expanding src/NQCModels/overview.md..."
+start_time = time()
+```
 # NQCModels.jl
 
 To perform nonadiabatic molecular dynamics simulations, it is necessary to define
@@ -102,3 +106,7 @@ AbstractTrees.print_tree(Model) # hide
 
     To learn more about NQCModels.jl and learn how to implement new models,
     visit the [developer documentation](@ref devdocs-model).
+```@setup logging
+runtime = round(time() - start_time; digits=2)
+@info "...done after $runtime s."
+```

docs/src/api/NQCBase/nqcbase.md

@@ -1,6 +1,14 @@
+```@setup logging
+@info "Expanding src/api/NQCBase/nqcbase.md..."
+start_time = time()
+```
 
 # NQCBase
 
 ```@autodocs
 Modules=[NQCBase]
 ```
+```@setup logging
+runtime = round(time() - start_time; digits=2)
+@info "...done after $runtime s."
+```

docs/src/api/NQCDistributions/nqcdistributions.md

@@ -1,6 +1,14 @@
+```@setup logging
+@info "Expanding src/api/NQCDistributions/nqcdistributions.md..."
+start_time = time()
+```
 
 # NQCDistributions
 
 ```@autodocs
 Modules=[NQCDistributions]
 ```
+```@setup logging
+runtime = round(time() - start_time; digits=2)
+@info "...done after $runtime s."
+```

docs/src/api/NQCDynamics/calculators.md

@@ -1,5 +1,13 @@
+```@setup logging
+@info "Expanding src/api/NQCDynamics/calculators.md..."
+start_time = time()
+```
 # Calculators
 
 ```@autodocs
 Modules=[NQCDynamics.Calculators]
 ```
+```@setup logging
+runtime = round(time() - start_time; digits=2)
+@info "...done after $runtime s."
+```

docs/src/api/NQCDynamics/dynamicsmethods.md

@@ -1,3 +1,7 @@
+```@setup logging
+@info "Expanding src/api/NQCDynamics/dynamicsmethods.md..."
+start_time = time()
+```
 
 # DynamicsMethods
 
@@ -34,3 +38,7 @@ Modules=[NQCDynamics.DynamicsMethods.EhrenfestMethods]
 ```@autodocs
 Modules=[NQCDynamics.DynamicsMethods.IntegrationAlgorithms]
 ```
+```@setup logging
+runtime = round(time() - start_time; digits=2)
+@info "...done after $runtime s."
+```

docs/src/api/NQCDynamics/dynamicsoutputs.md

@@ -1,3 +1,7 @@
+```@setup logging
+@info "Expanding src/api/NQCDynamics/dynamicsoutputs.md..."
+start_time = time()
+```
 
 # DynamicsOutputs
 
@@ -15,3 +19,7 @@ Private=false
 Modules=[NQCDynamics.DynamicsOutputs]
 Public=false
 ```
+```@setup logging
+runtime = round(time() - start_time; digits=2)
+@info "...done after $runtime s."
+```

docs/src/api/NQCDynamics/dynamicsutils.md

@@ -1,6 +1,14 @@
+```@setup logging
+@info "Expanding src/api/NQCDynamics/dynamicsutils.md..."
+start_time = time()
+```
 
 # DynamicsUtils
 
 ```@autodocs
 Modules=[NQCDynamics.DynamicsUtils]
 ```
+```@setup logging
+runtime = round(time() - start_time; digits=2)
+@info "...done after $runtime s."
+```

docs/src/api/NQCDynamics/ensembles.md

@@ -1,6 +1,14 @@
+```@setup logging
+@info "Expanding src/api/NQCDynamics/ensembles.md..."
+start_time = time()
+```
 
 # Ensembles
 
 ```@autodocs
 Modules=[NQCDynamics.Ensembles]
 ```
+```@setup logging
+runtime = round(time() - start_time; digits=2)
+@info "...done after $runtime s."
+```

docs/src/api/NQCDynamics/estimators.md

@@ -1,6 +1,14 @@
+```@setup logging
+@info "Expanding src/api/NQCDynamics/estimators.md..."
+start_time = time()
+```
 
 # Estimators
 
 ```@autodocs
 Modules=[NQCDynamics.Estimators]
 ```
+```@setup logging
+runtime = round(time() - start_time; digits=2)
+@info "...done after $runtime s."
+```

docs/src/api/NQCDynamics/initialconditions.md

@@ -1,3 +1,7 @@
+```@setup logging
+@info "Expanding src/api/NQCDynamics/initialconditions.md..."
+start_time = time()
+```
 
 # InitialConditions
 
@@ -22,3 +26,7 @@ Modules=[NQCDynamics.InitialConditions.QuantisedDiatomic]
 ```@autodocs
 Modules=[NQCDynamics.InitialConditions.MetropolisHastings]
 ```
+```@setup logging
+runtime = round(time() - start_time; digits=2)
+@info "...done after $runtime s."
+```