Merge pull request #50 from cesmix-mit/IP_IBP

Merge InteratomicBasisPotentials.jl into InteratomicPotentials.jl + Updates from PotentialLearning.jl
cesmix-mit · Jan 4, 2024 · 973e0d5 · 973e0d5
2 parents 7ce2df9 + adc4b1a
commit 973e0d5
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diff --git a/.gitattributes b/.gitattributes
@@ -0,0 +1,2 @@
+# Auto detect text files and perform LF normalization
+* text=auto
diff --git a/.github/workflows/CI.yml b/.github/workflows/CI.yml
@@ -13,15 +13,18 @@ jobs:
       fail-fast: false
       matrix:
         version:
-          - "1.6"
-          - "nightly"
+          - "1.9"
         os:
           - ubuntu-latest
           - macOS-latest
           - windows-latest
         arch:
           - x64
     steps:
+      - name: Windows git setup
+        if: runner.os == 'Windows'
+        run:
+          git config --global core.autocrlf false
       - uses: actions/checkout@v2
       - uses: julia-actions/setup-julia@v1
         with:
@@ -43,6 +46,8 @@ jobs:
             using Pkg
             Pkg.Registry.add("General")
             Pkg.Registry.add(RegistrySpec(url = "https://github.com/cesmix-mit/CESMIX.git"))
+            Pkg.Registry.add(RegistrySpec(url = "https://github.com/JuliaMolSim/MolSim.git"))
+            Pkg.Registry.add(RegistrySpec(url = "https://github.com/ACEsuit/ACEregistry"))
           '
         shell: bash
       - uses: julia-actions/julia-buildpkg@v1

diff --git a/.github/workflows/Documentation.yml b/.github/workflows/Documentation.yml
@@ -21,6 +21,8 @@ jobs:
             using Pkg
             Pkg.Registry.add("General")
             Pkg.Registry.add(RegistrySpec(url = "https://github.com/cesmix-mit/CESMIX.git"))
+            Pkg.Registry.add(RegistrySpec(url = "https://github.com/JuliaMolSim/MolSim.git"))
+            Pkg.Registry.add(RegistrySpec(url = "https://github.com/ACEsuit/ACEregistry"))
           '
         shell: bash
       - name: instantiate docs
@@ -34,9 +36,7 @@ jobs:
         run: |
           julia --project=docs -e '
             using Documenter: DocMeta, doctest
-            using InteratomicPotentials
-            DocMeta.setdocmeta!(InteratomicPotentials, :DocTestSetup, :(using InteratomicPotentials); recursive=true)
-            doctest(InteratomicPotentials)
+            using DocumenterCitations
           '
       - name: generate docs
         run: DISPLAY=:0 xvfb-run -s '-screen 0 1024x768x24' julia --project=docs docs/make.jl

diff --git a/Project.toml b/Project.toml
@@ -1,22 +1,27 @@
 name = "InteratomicPotentials"
 uuid = "a9efe35a-c65d-452d-b8a8-82646cd5cb04"
 authors = ["Dallas Foster <fostdall@mit.edu>"]
-version = "0.2.6"
+version = "0.2.7"
 
 [deps]
+ACE1 = "e3f9bc04-086e-409a-ba78-e9769fe067bb"
 AtomsBase = "a963bdd2-2df7-4f54-a1ee-49d51e6be12a"
 Distances = "b4f34e82-e78d-54a5-968a-f98e89d6e8f7"
+Flux = "587475ba-b771-5e3f-ad9e-33799f191a9c"
+JuLIP = "945c410c-986d-556a-acb1-167a618e0462"
+LAMMPS = "ee2e13b9-eee9-4449-aafa-cfa6a2dbe14d"
 LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
 NearestNeighbors = "b8a86587-4115-5ab1-83bc-aa920d37bbce"
 StaticArrays = "90137ffa-7385-5640-81b9-e52037218182"
 Unitful = "1986cc42-f94f-5a68-af5c-568840ba703d"
 UnitfulAtomic = "a7773ee8-282e-5fa2-be4e-bd808c38a91a"
+Zygote = "e88e6eb3-aa80-5325-afca-941959d7151f"
 
 [compat]
-AtomsBase = "0.2, 0.3"
+AtomsBase = "0.3"
 Distances = "0.10"
 NearestNeighbors = "0.4.9"
 StaticArrays = "1"
 Unitful = "1"
 UnitfulAtomic = "1"
-julia = "1.6"
+julia = "1.9"
diff --git a/README.md b/README.md
@@ -6,9 +6,9 @@
 [![Docs](https://img.shields.io/badge/docs-stable-blue.svg)](https://cesmix-mit.github.io/InteratomicPotentials.jl/stable)
 [![Docs](https://img.shields.io/badge/docs-dev-blue.svg)](https://cesmix-mit.github.io/InteratomicPotentials.jl/dev)
 
-This repository implements some basic language and syntax for manipulating interatomic potentials in Julia. The primary purpose of this package is to design a flexible package for use with data-driven and parameter-fitted interatomic potentials. This package is also being designed in order to allow users to define custom potentials and forces for use in molecular dynamics.
+This repository implements some basic language and syntax for manipulating interatomic potentials in Julia. The primary purpose of this package is to design a flexible package for use with data-driven and parameter-fitted interatomic potentials. This package is also being designed in order to allow users to define custom potentials and forces for use in molecular dynamics. This package also supports the Spectral Neighbor Analysis Potential (SNAP) potential of Thompson et al. 2015 (see documentation for bibliography) and a naive hacking of the Atomic Cluster Expansion of Drautz 2019 through the [ACE1.jl](https://github.com/ACEsuit/ACE1.jl/) julia package. We are working toward more complete implementation of these machine learning or data-driven potentials in the context of the CESMIX julia suite that seeks to fit and run these potentials for molecular dynamics. For additional details, see the [CESMIX](https://github.com/cesmix-mit) ecosystem.
 
-This package is part of the CESMIX molecular modeling suite. This package is also intended to be used with Atomistic.jl (for molecular dynamics, with Molly.jl), InteratomicBasisPotentials.jl (for machine learning potentials like SNAP and ACE), and  PotentialLearning.jl (for fitting potentials from data).
+This package is part of the CESMIX molecular modeling suite. This package is also intended to be used with Atomistic.jl (for molecular dynamics, with Molly.jl), and  PotentialLearning.jl (for fitting potentials from data).
 
 This package is a work in progress. 
 
@@ -68,7 +68,7 @@ set_parameters(lj, (ϵ = 2.0 * 1u"eV", σ = 1.0 * 1u"Å")) # Set parameters (re
 
 ## Potential Types
 
-All interatomic potentials listed in this project are subtypes of `ArbitraryPotential`. At this point, as of v2.0, there are two branches of potentials: `EmpiricalPotential` and `MixedPotentials`. A sister package, ```julia InteratomicBasisPotentials.jl``` defines a potential called `BasisPotential`, see that package for additional details.
+All interatomic potentials listed in this project are subtypes of `ArbitraryPotential`. There are three types of potentials currently implemented: `EmpiricalPotential`, `BasisPotential`, and combination potentials via `MixedPotentials`.
 
 `EmpiricalPotential`s include two-body potentials like `BornMayer`, `LennardJones`. `MixedPotential` is a convenience type for allowing the linear combination of potentials. An example would be:
 ```julia
@@ -87,7 +87,6 @@ ZBL         <: EmpiricalPotential
 
 LinearCombinationPotential <: MixedPotential
 
-# See InteratomicBasisPotentials.jl
 BasisPotential <: AbstractPotential
 SNAP           <: BasisPotential
 ACE            <: BasisPotential

diff --git a/benchmarks/Project.toml b/benchmarks/Project.toml
@@ -0,0 +1,19 @@
+[deps]
+ACE1 = "e3f9bc04-086e-409a-ba78-e9769fe067bb"
+AtomsBase = "a963bdd2-2df7-4f54-a1ee-49d51e6be12a"
+BenchmarkTools = "6e4b80f9-dd63-53aa-95a3-0cdb28fa8baf"
+Distances = "b4f34e82-e78d-54a5-968a-f98e89d6e8f7"
+Flux = "587475ba-b771-5e3f-ad9e-33799f191a9c"
+GR = "28b8d3ca-fb5f-59d9-8090-bfdbd6d07a71"
+JuLIP = "945c410c-986d-556a-acb1-167a618e0462"
+LAMMPS = "ee2e13b9-eee9-4449-aafa-cfa6a2dbe14d"
+LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
+NearestNeighbors = "b8a86587-4115-5ab1-83bc-aa920d37bbce"
+PProf = "e4faabce-9ead-11e9-39d9-4379958e3056"
+StaticArrays = "90137ffa-7385-5640-81b9-e52037218182"
+Unitful = "1986cc42-f94f-5a68-af5c-568840ba703d"
+UnitfulAtomic = "a7773ee8-282e-5fa2-be4e-bd808c38a91a"
+Zygote = "e88e6eb3-aa80-5325-afca-941959d7151f"
+
+[compat]
+julia = "1.9"
diff --git a/benchmarks/lj_1000.jl b/benchmarks/lj_1000.jl
@@ -1,11 +1,20 @@
-include("helpers.jl")
+push!(Base.LOAD_PATH, "../../")
 
+using AtomsBase
+using InteratomicPotentials
+using LinearAlgebra
+using Unitful
+using UnitfulAtomic
 using BenchmarkTools
+using Plots
+using BenchmarkTools
+
+include("utils.jl")
 
-T, = parse.(Int, ARGS)
+T = parse.(Int, ARGS) # E.g. 10
 
 potential = LennardJones(1.0u"eV", 1.0u"Å", 100.0u"Å", [:Ar])
 
-system = load_configuration("benchmarks/data/lj_clusters/1000.xyz")
+system = load_configuration("data/lj_clusters/1000.xyz")
 
 display(@benchmark energy_and_force($system, $potential) seconds = T)
diff --git a/benchmarks/profile.jl b/benchmarks/profile.jl
@@ -1,9 +1,16 @@
-include("helpers.jl")
+push!(Base.LOAD_PATH, "../../")
 
+using AtomsBase
+using InteratomicPotentials
+using LinearAlgebra
+using Unitful
+using UnitfulAtomic
 using BenchmarkTools
 using PProf
 
-@show N, NUM_ITER = parse.(Int, ARGS)
+include("utils.jl")
+
+@show N, NUM_ITER = parse.(Int, ARGS) # E.g. 100, 100
 
 potential = LennardJones(1.0u"eV", 1.0u"Å", 100.0u"Å", [:Ar])
 

diff --git a/benchmarks/scalability.jl b/benchmarks/scalability.jl
@@ -1,11 +1,18 @@
-include("helpers.jl")
+push!(Base.LOAD_PATH, "../../")
 
+using AtomsBase
+using InteratomicPotentials
+using LinearAlgebra
+using Unitful
+using UnitfulAtomic
 using BenchmarkTools
 using Plots
 
+include("utils.jl")
+
 potential = LennardJones(1.0u"eV", 1.0u"Å", 100.0u"Å", [:Ar])
 
-ns = 250:250:10000
+ns = 250:250:1000
 @time times = map(ns) do N
     system = generate_lj_cluster(N)
     time = @belapsed energy_and_force($system, $potential)
@@ -15,6 +22,9 @@ end
 
 @show times
 
-p = plot(title="Scaling of energy_and_force on LJ Clusters", xlabel="Number of Atoms", ylabel="Median Time Elapsed (s)", legend=false)
+p = plot(title="Scaling of energy_and_force on LJ Clusters",
+         xlabel="Number of Atoms",
+         ylabel="Median Time Elapsed (s)",
+         legend=false)
 plot!(p, ns, times, markershape=:circle)
 savefig(p, "scaling.svg")
diff --git a/benchmarks/helpers.jl → benchmarks/utils.jl b/benchmarks/helpers.jl → benchmarks/utils.jl
@@ -1,9 +1,3 @@
-using AtomsBase
-using InteratomicPotentials
-using LinearAlgebra
-using Unitful
-using UnitfulAtomic
-
 function load_configuration(filename::String)
     box = [[8.0, 0.0, 0.0], [0.0, 8.0, 0.0], [0.0, 0.0, 8.0]] * 1u"Å"
     bcs = [DirichletZero(), DirichletZero(), DirichletZero()]

diff --git a/docs/citation.bib b/docs/citation.bib
@@ -0,0 +1,25 @@
+@article{Drautz2019,
+  title = {Atomic cluster expansion for accurate and transferable interatomic potentials},
+  author = {Drautz, Ralf},
+  journal = {Phys. Rev. B},
+  volume = {99},
+  issue = {1},
+  pages = {014104},
+  numpages = {15},
+  year = {2019},
+  month = {Jan},
+  publisher = {American Physical Society},
+  doi = {10.1103/PhysRevB.99.014104},
+  url = {https://link.aps.org/doi/10.1103/PhysRevB.99.014104}
+}
+@article{Thompson2015,
+    title = {Spectral neighbor analysis method for automated generation of quantum-accurate interatomic potentials},
+    journal = {Journal of Computational Physics},
+    volume = {285},
+    pages = {316-330},
+    year = {2015},
+    issn = {0021-9991},
+    doi = {https://doi.org/10.1016/j.jcp.2014.12.018},
+    url = {https://www.sciencedirect.com/science/article/pii/S0021999114008353},
+    author = {A.P. Thompson and L.P. Swiler and C.R. Trott and S.M. Foiles and G.J. Tucker},
+}
diff --git a/docs/make.jl b/docs/make.jl
@@ -5,47 +5,65 @@ using Documenter
 using DocumenterCitations
 using Literate
 
-DocMeta.setdocmeta!(InteratomicPotentials, :DocTestSetup, :(using InteratomicPotentials); recursive = true)
+DocMeta.setdocmeta!(
+    InteratomicPotentials,
+    :DocTestSetup,
+    :(using InteratomicPotentials);
+    recursive = true,
+)
 
-bib = CitationBibliography(joinpath(@__DIR__, "citations.bib"))
+bib = CitationBibliography(joinpath(@__DIR__, "citation.bib"))
 
 # Generate examples
 
 const EXAMPLES_DIR = joinpath(@__DIR__, "..", "examples")
 const OUTPUT_DIR = joinpath(@__DIR__, "src/generated")
 
-examples = Pair{String,String}[]
+examples = [
+    "Lennard Jones Cluster" => "LJCluster/feature_exploration.jl"
+]
 
-for (_, name) in examples
-    example_filepath = joinpath(EXAMPLES_DIR, string(name, ".jl"))
-    Literate.markdown(example_filepath, OUTPUT_DIR, documenter = true)
+for (_, example_path) in examples
+    s = split(example_path, "/")
+    sub_path, file_name = string(s[1:end-1]...), s[end]
+    example_filepath = joinpath(EXAMPLES_DIR, example_path)
+    Literate.markdown(example_filepath,
+                      joinpath(OUTPUT_DIR, sub_path),
+                      documenter = true)
 end
 
-examples = [title => joinpath("generated", string(name, ".md")) for (title, name) in examples]
+examples = [title => joinpath("generated", replace(example_path, ".jl" => ".md"))
+            for (title, example_path) in examples]
 
-makedocs(bib;
-    modules = [InteratomicPotentials],
-    authors = "CESMIX-MIT",
-    repo = "https://github.com/cesmix-mit/InteratomicPotentials.jl/blob/{commit}{path}#{line}",
-    sitename = "InteratomicPotentials.jl",
-    format = Documenter.HTML(;
-        prettyurls = get(ENV, "CI", "false") == "true",
-        canonical = "https://cesmix-mit.github.io/InteratomicPotentials.jl",
-        assets = String[],
-    ),
-    pages = [
+makedocs(
+      root    =  joinpath(dirname(pathof(InteratomicPotentials)), "..", "docs"),
+      source  = "src",
+      build   = "build",
+      clean   = true,
+      doctest = true,
+      modules = [InteratomicPotentials],
+      repo    = "https://github.com/cesmix-mit/InteratomicPotentials.jl/blob/{commit}{path}#{line}",
+      highlightsig = true,
+      sitename = "InteratomicPotentials.jl",
+      expandfirst = [],
+      draft = false,
+      pages = [
         "Home" => "index.md",
         "InteratomicPotentials Interface" => "interface.md",
         "Examples" => examples,
         "API Reference" => "api.md",
-    ],
-    doctest = true,
-    linkcheck = true,
-    strict = true
+        "References" => "bibliography.md"
+      ],
+      format = Documenter.HTML(;
+        prettyurls = get(ENV, "CI", "false") == "true",
+        canonical = "https://cesmix-mit.github.io/InteratomicPotentials.jl",
+        assets = String[],
+      ),
+      plugins=[bib]
 )
 
 deploydocs(;
     repo = "github.com/cesmix-mit/InteratomicPotentials.jl",
     devbranch = "main",
     push_preview = true
-)
+)
diff --git a/docs/src/bibliography.md b/docs/src/bibliography.md
@@ -0,0 +1,2 @@
+```@bibliography
+```
diff --git a/docs/src/index.md b/docs/src/index.md
@@ -1,6 +1,6 @@
 # InteratomicPotentials
 
-Package that provides a flexible suite for working with interatomic potentials. Defines an API for abstract interatomic potentials (currently supporting 2-body interactions) and the atomic configuration interface defined by AtomsBase.jl.
+Package that provides a flexible suite for working with interatomic potentials. Defines an API for abstract interatomic potentials (currently supporting 2-body interactions) and the atomic configuration interface defined by AtomsBase.jl. This package also provides interatomic potentials that are defined using basis functions, in particular we support the Spectral Neighbor Analysis Potential (SNAP) (Thompson, 2015) and the Atomic Cluster Expansion (ACE) (Drautz, 2019). Defines an API for abstract interatomic potentials (currently supporting 2-body interactions) and the atomic configuration interface defined by AtomsBase.jl.
 
 Developed as part of the CESMIX Julia package suite. See also ComposableWorkflows, InteratomicPotentials.jl, and PotentialLearning.jl.
 
@@ -15,3 +15,7 @@ The unit convention throughout the package and other packages in the CESMIX Juli
 If you would like to use InteratomicPotentials in a molecular dynamics simulator, see [Atomistic.jl](https://github.com/cesmix-mit/Atomistic.jl). There, you will learn more about how the abstract classes provided in the present package can be used in conjuction with the Atomistic API and a variety of MD simulators. 
 
 If you would like to fit your potential parameters to data, see our project at [PotentialLearning.jl](https://github.com/cesmix-mit/PotentialLearning.jl), a work in progress, that aims to provide support for a variety of learning and inference tasks.
+
+## References
+Thompson, A.P., et al.: Spectral neighbor analysis method for automated generation of quantum-accurate interatomic potentials, Journal of Computational Physics, 285, 2015.
+Drautz, R.: Atomic cluster expansion for accurate and transferable interatomic potentials. Phys. Rev. B Condens. Matter. 99, 014104 (2019).
diff --git a/docs/src/interface.md b/docs/src/interface.md
@@ -1,7 +1,7 @@
 # InteratomicPotentials Interface
 
 # Instantiating a Built-In Interatomic Potentials
-There are a number of built-in interatomic potentials that are available for users: Born-Mayer-Huggins, Lennard-Jones, Coulomb's Law, and Morse. These potentials are subtypes of `EmpiricalPotential`. There are additional basis potentials, the Spectral Neighbor Analysis Potential and Atomic Cluster Expansion, available in the related package `InteratomicBasisPotentials.jl`. In order to instantiate a potential, you need to provide the necessary potential parameters (see API documentation), radial cutoff, and species (i.e. elements) for which the potential is defined for.
+There are a number of built-in interatomic potentials that are available for users: Born-Mayer-Huggins, Lennard-Jones, Coulomb's Law, and Morse. These potentials are subtypes of `EmpiricalPotential`. There are additional basis potentials, the Spectral Neighbor Analysis Potential and Atomic Cluster Expansion. In order to instantiate a potential, you need to provide the necessary potential parameters (see API documentation), radial cutoff, and species (i.e. elements) for which the potential is defined for.
 
 Below is an example for the Lennard-Jones potential:
 ```julia
@@ -18,6 +18,18 @@ CustomPotential{T<:AbstractFloat} <: EmpiricalPotential{NamedTuple{(:a, :b, ...,
 # where parameters are :a, :b, ..., :e
 ```
 
+Below is an example for building an Atomic Cluster Expansion (ACE) potential:
+```julia
+body_order = 2 
+polynomial_degree = 8
+r_inner_cutoff = 0.5 * u"Å"
+r_cutoff = 4.0 * u"Å"
+species = [:Ar, ]
+wL      = 1.0 
+csp     = 1.0
+ace_params = RPIParams(species, body_order, polynomial_degree, wL, csp, r_inner_cutoff, r_cutoff)
+```
+
 # Evaluating Interatomic Potentials
 There are a number of signatures for evaluating the potential energy, force, and virial stress for the interatomic potentials. For most users it will be most convenient in order to define a configuration in terms of an `AtomsBase.jl` system (i.e., using a `FlexibleSystem`), which requires a list of atoms, boundary conditions, and box information. With such a system, evaluating the potential energy and force are straightforward:
 

diff --git a/examples/LJCluster/Project.toml b/examples/LJCluster/Project.toml