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2-atomsbase-molly.jl
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2-atomsbase-molly.jl
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### A Pluto.jl notebook ###
# v0.19.26
using Markdown
using InteractiveUtils
# This Pluto notebook uses @bind for interactivity. When running this notebook outside of Pluto, the following 'mock version' of @bind gives bound variables a default value (instead of an error).
macro bind(def, element)
quote
local iv = try Base.loaded_modules[Base.PkgId(Base.UUID("6e696c72-6542-2067-7265-42206c756150"), "AbstractPlutoDingetjes")].Bonds.initial_value catch; b -> missing; end
local el = $(esc(element))
global $(esc(def)) = Core.applicable(Base.get, el) ? Base.get(el) : iv(el)
el
end
end
# ╔═╡ fce80334-c7ad-4208-836d-4e7f78b03663
begin
using ASEconvert
using AtomsIO
using AtomsIOPython
using AtomsView
using DFTK
using Molly
using PlutoUI
using GLMakie
using LinearAlgebra
using Unitful
using UnitfulAtomic
end
# ╔═╡ 9ae3be39-1b92-4239-8e94-acc752e81ce1
LocalResource("Logos.png")
# ╔═╡ 21c7ac3a-b94b-4aea-a137-9638de4cce21
md"# Atomistic modelling ecosystem (1/4)"
# ╔═╡ 2d512127-00b6-49a5-be34-b2e184802a30
md"""
## JuliaMolSim
The [**JuliaMolSim**](https://juliamolsim.github.io/) github organisation clusters a few activities related to atomistic modelling for molecules and solids. Currently about 20 researchers scattered around the world (Canada, France, US, UK, Switzerland, ...) are active in JuliaMolSim. Moreover pretty much all packages presented in these notebooks have a direct or indirect relation to JuliaMolSim.
In the past few JuliaCons members of JuliaMolSim have been directly involved in organising discussion sessions or minisymposia related to materials or atomistic modelling.
For more information about the organisation, including a link to a private Zulip chat, see the [JuliaMolSim website](https://juliamolsim.github.io/).
"""
# ╔═╡ 581bd874-6d17-43bf-bd9b-074e17a8d1e1
md"## AtomsBase"
# ╔═╡ 9fda9c06-7ca4-4046-8a20-5e7c935f0083
md"""
[**AtomsBase**](https://github.com/JuliaMolSim/AtomsBase.jl) is an interface package, which allows other Julia packages to share atomistic structures with each other.
For example we construct a silicon supercell using **ASE** (the atomistic simulation environment). Using [**ASEconvert**](https://github.com/mfherbst/ASEconvert.jl) we expose the resulting *ASE.Atoms* object to Julia.
$(@bind N PlutoUI.Slider(1:1:20; default=4, show_value=true))
"""
# ╔═╡ b4be035e-75df-43c6-ad44-d61f3b174e24
begin
silicon_ase = ase.build.bulk("Si", cubic=true) * pytuple((N, 1, 1))
silicon_supercell = pyconvert(AbstractSystem, silicon_ase)
end
# ╔═╡ 58d5cb8d-1e74-4b7c-bdcf-565512f27941
md"""
We already saw that [**DFTK**](https://dftk.org) can directly make use of AtomsBase structures. The visualisation you see now is done using [**AtomsView**](https://github.com/mfherbst/AtomsView.jl), which similarly is based on AtomsBase input.
Of note, this implies that both packages immediately work with *any package* providing AtomsBase-compatible data, e.g. [**AtomsIO**](https://github.com/mfherbst/AtomsIO.jl), which supports parsing / writing a plethora of file formats:
"""
# ╔═╡ e6e48368-b000-4c61-ae43-cc7762089e52
silicon_loaded = load_system("Si.extxyz")
# ╔═╡ 497f36f5-c5fc-4baf-a6d8-4aacd51ca55c
HTML(AtomsView.visualize_structure(silicon_loaded, MIME("text/html")))
# ╔═╡ 33efd544-87ed-4eaf-af6d-6c59829085d3
md"""
!!! danger "todo above"
"""
# ╔═╡ 52e70d6b-d4c5-4b2a-9440-2d26f0f3d5e4
let
# Calculation with DFTK (Note: loaded already has pseudos attached)
model = model_PBE(silicon_loaded)
@show model.atoms
basis = PlaneWaveBasis(model; Ecut=15, kgrid=(4, 4, 4))
self_consistent_field(basis).energies.total
end
# ╔═╡ f49dde16-97aa-41e8-a776-1926ad39ae2d
md"""
For other things you can do with AtomsBase see the [list of packages implementing the AtomsBase interface](https://github.com/JuliaMolSim/AtomsBase.jl#packages-using-atomsbase). Unfortunately the ecosystem is still rapidly evolving and not all packages interoperate as flawlessly as desirable.
Note, that pretty much all of the packages we discuss in these notebooks are compatible with AtomsBase (e.g. [DFTK](https://dftk.org), [JuLIP](https://github.com/JuliaMolSim/JuLIP.jl/), [Molly](https://github.com/JuliaMolSim/Molly.jl)).
"""
# ╔═╡ 76596a49-f4e5-418a-84be-f261836f92fd
md"""## Molly
[**Molly**](https://github.com/JuliaMolSim/Molly.jl) is a molecular dynamics simulator written in Julia. Similar to DFTK the focus is to make use of features of the Julia programming language, e.g. to yield differentiable MD simulations or GPU support.
As an example we consider a simple LJ setup with $(@bind n_atoms PlutoUI.Slider(20:10:100; default=100, show_value=true)) atoms:
"""
# ╔═╡ ad254c47-4155-448a-b2b2-f68c8e737b94
begin
atom_mass = 10.0u"u"
atoms = [Molly.Atom(mass=atom_mass, σ=0.3u"nm", ϵ=0.2u"kJ * mol^-1") for i in 1:n_atoms]
boundary = CubicBoundary(2.0u"nm") # Periodic boundary; 2 nm cube
coords = place_atoms(n_atoms, boundary; min_dist=0.3u"nm") # Random placement
temp = 100.0u"K"
velocities = [random_velocity(atom_mass, temp) for i in 1:n_atoms]
pairwise_inters = (LennardJones(), ) # LJ interactions
# Log every 10 steps
loggers = (; temp=TemperatureLogger(10), coords=CoordinateLogger(10))
sys = System(; atoms, coords, boundary, velocities, pairwise_inters, loggers)
end;
# ╔═╡ 3c3c3f60-ebab-41df-9d93-76ec24adff35
simulator = VelocityVerlet(
dt = 0.002u"ps",
coupling = AndersenThermostat(temp, 1.0u"ps"),
);
# ╔═╡ 3ab03329-54be-421a-a7b7-4b1b2172f9c3
simulate!(sys, simulator, 1_000);
# ╔═╡ 50b9b95d-55d9-457f-83f6-9deae6f46def
begin
visualize(sys.loggers.coords, boundary, "sim_lj.mp4")
LocalResource("sim_lj.mp4")
end
# ╔═╡ 00000000-0000-0000-0000-000000000001
PLUTO_PROJECT_TOML_CONTENTS = """
[deps]
ASEconvert = "3da9722f-58c2-4165-81be-b4d7253e8fd2"
AtomsIO = "1692102d-eeb4-4df9-807b-c9517f998d44"
AtomsIOPython = "9e4c859b-2281-48ef-8059-f50fe53c37b0"
AtomsView = "ee286e10-dd2d-4ff2-afcb-0a3cd50c8041"
DFTK = "acf6eb54-70d9-11e9-0013-234b7a5f5337"
GLMakie = "e9467ef8-e4e7-5192-8a1a-b1aee30e663a"
LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
Molly = "aa0f7f06-fcc0-5ec4-a7f3-a573f33f9c4c"
PlutoUI = "7f904dfe-b85e-4ff6-b463-dae2292396a8"
Unitful = "1986cc42-f94f-5a68-af5c-568840ba703d"
UnitfulAtomic = "a7773ee8-282e-5fa2-be4e-bd808c38a91a"
[compat]
ASEconvert = "~0.1.5"
AtomsIO = "~0.2.1"
AtomsIOPython = "~0.1.0"
AtomsView = "~0.1.1"
DFTK = "~0.6.8"
GLMakie = "~0.8.5"
Molly = "~0.16.0"
PlutoUI = "~0.7.51"
Unitful = "~1.14.0"
UnitfulAtomic = "~1.0.0"
"""
# ╔═╡ 00000000-0000-0000-0000-000000000002
PLUTO_MANIFEST_TOML_CONTENTS = """
# This file is machine-generated - editing it directly is not advised
julia_version = "1.9.0"
manifest_format = "2.0"
project_hash = "5a0268af66c6c8c79e9b455ef265ddf3511dcab7"
[[deps.ASEconvert]]
deps = ["AtomsBase", "CondaPkg", "PeriodicTable", "PythonCall", "Unitful", "UnitfulAtomic"]
git-tree-sha1 = "2590f99b4970b99036897ed423895fba751d8633"
uuid = "3da9722f-58c2-4165-81be-b4d7253e8fd2"
version = "0.1.5"
[[deps.AbstractFFTs]]
deps = ["LinearAlgebra"]
git-tree-sha1 = "16b6dbc4cf7caee4e1e75c49485ec67b667098a0"
uuid = "621f4979-c628-5d54-868e-fcf4e3e8185c"
version = "1.3.1"
weakdeps = ["ChainRulesCore"]
[deps.AbstractFFTs.extensions]
AbstractFFTsChainRulesCoreExt = "ChainRulesCore"
[[deps.AbstractPlutoDingetjes]]
deps = ["Pkg"]
git-tree-sha1 = "8eaf9f1b4921132a4cff3f36a1d9ba923b14a481"
uuid = "6e696c72-6542-2067-7265-42206c756150"
version = "1.1.4"
[[deps.AbstractTrees]]
git-tree-sha1 = "faa260e4cb5aba097a73fab382dd4b5819d8ec8c"
uuid = "1520ce14-60c1-5f80-bbc7-55ef81b5835c"
version = "0.4.4"
[[deps.Adapt]]
deps = ["LinearAlgebra", "Requires"]
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uuid = "79e6a3ab-5dfb-504d-930d-738a2a938a0e"
version = "3.6.2"
weakdeps = ["StaticArrays"]
[deps.Adapt.extensions]
AdaptStaticArraysExt = "StaticArrays"
[[deps.Animations]]
deps = ["Colors"]
git-tree-sha1 = "e81c509d2c8e49592413bfb0bb3b08150056c79d"
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[[deps.ArgCheck]]
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[[deps.ArgTools]]
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[deps.ArrayInterface.extensions]
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ArrayInterfaceBlockBandedMatricesExt = "BlockBandedMatrices"
ArrayInterfaceCUDAExt = "CUDA"
ArrayInterfaceGPUArraysCoreExt = "GPUArraysCore"
ArrayInterfaceStaticArraysCoreExt = "StaticArraysCore"
ArrayInterfaceTrackerExt = "Tracker"
[deps.ArrayInterface.weakdeps]
BandedMatrices = "aae01518-5342-5314-be14-df237901396f"
BlockBandedMatrices = "ffab5731-97b5-5995-9138-79e8c1846df0"
CUDA = "052768ef-5323-5732-b1bb-66c8b64840ba"
GPUArraysCore = "46192b85-c4d5-4398-a991-12ede77f4527"
StaticArraysCore = "1e83bf80-4336-4d27-bf5d-d5a4f845583c"
Tracker = "9f7883ad-71c0-57eb-9f7f-b5c9e6d3789c"
[[deps.Artifacts]]
uuid = "56f22d72-fd6d-98f1-02f0-08ddc0907c33"
[[deps.Atomix]]
deps = ["UnsafeAtomics"]
git-tree-sha1 = "c06a868224ecba914baa6942988e2f2aade419be"
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