strip down visualization code

Author: jrdegreeff

Project.toml

@@ -1,25 +1,8 @@
-authors = ["Jeremiah DeGreeff <[email protected]>"]
 name = "Atomistic"
 uuid = "3e762ff9-b8d8-45cf-a902-edcbc7124e71"
+authors = ["Jeremiah DeGreeff <[email protected]>"]
 version = "0.3.4"
 
-[compat]
-AtomsBase = "0.2"
-DFTK = "0.4"
-Distances = "0.10"
-InteratomicPotentials = "0.1"
-Molly = "0.9"
-NBodySimulator = "1"
-PeriodicTable = "1"
-Plots = "1"
-PyCall = "1"
-Reexport = "1"
-StaticArrays = "1"
-Unitful = "1"
-UnitfulAtomic = "1"
-UnitfulRecipes = "1"
-julia = "1.7"
-
 [deps]
 AtomsBase = "a963bdd2-2df7-4f54-a1ee-49d51e6be12a"
 DFTK = "acf6eb54-70d9-11e9-0013-234b7a5f5337"
@@ -30,12 +13,27 @@ Molly = "aa0f7f06-fcc0-5ec4-a7f3-a573f33f9c4c"
 NBodySimulator = "0e6f8da7-a7fc-5c8b-a220-74e902c310f9"
 PeriodicTable = "7b2266bf-644c-5ea3-82d8-af4bbd25a884"
 Plots = "91a5bcdd-55d7-5caf-9e0b-520d859cae80"
-PyCall = "438e738f-606a-5dbb-bf0a-cddfbfd45ab0"
 Reexport = "189a3867-3050-52da-a836-e630ba90ab69"
 StaticArrays = "90137ffa-7385-5640-81b9-e52037218182"
 Unitful = "1986cc42-f94f-5a68-af5c-568840ba703d"
 UnitfulAtomic = "a7773ee8-282e-5fa2-be4e-bd808c38a91a"
 UnitfulRecipes = "42071c24-d89e-48dd-8a24-8a12d9b8861f"
 
+[compat]
+AtomsBase = "0.2"
+DFTK = "0.4"
+Distances = "0.10"
+InteratomicPotentials = "0.1"
+Molly = "0.9"
+NBodySimulator = "1"
+PeriodicTable = "1"
+Plots = "1"
+Reexport = "1"
+StaticArrays = "1"
+Unitful = "1"
+UnitfulAtomic = "1"
+UnitfulRecipes = "1"
+julia = "1.7"
+
 [extras]
 CPUSummary = "2a0fbf3d-bb9c-48f3-b0a9-814d99fd7ab9"

examples/argon/molly_dftk_ab_initio_simulation.jl

@@ -45,7 +45,6 @@ display(@time plot_temperature(ab_initio_result, 1))
 display(@time plot_energy(ab_initio_result, 1))
 display(@time plot_rdf(ab_initio_result, potential.σ))
 
-write_molly_visualization(ab_initio_result, "artifacts/argon_ab_initio_molly.mp4")
-write_ase_trajectory(ab_initio_result, "artifacts/argon_ab_initio_molly.traj")
+visualize(ab_initio_result, "artifacts/argon_ab_initio_molly.mp4")
 
 ;

examples/argon/nbs_dftk_ab_initio_simulation.jl

@@ -44,7 +44,6 @@ display(@time plot_temperature(ab_initio_result, 1))
 display(@time plot_energy(ab_initio_result, 1))
 display(@time plot_rdf(ab_initio_result, potential.σ))
 
-write_nbs_animation(ab_initio_result, "artifacts/argon_ab_initio_nbs.gif")
-write_ase_trajectory(ab_initio_result, "artifacts/argon_ab_initio_nbs.traj")
+animate(ab_initio_result, "artifacts/argon_ab_initio_nbs.gif")
 
 ;

src/Atomistic.jl

@@ -9,17 +9,14 @@ using Distances
 using LinearAlgebra
 using StaticArrays
 using Base.Threads
-@reexport using Unitful
-@reexport using UnitfulAtomic
+@reexport using Unitful, UnitfulAtomic
 
 using DFTK
 using Molly
 using NBodySimulator
 
 using PeriodicTable
-using Plots
-using PyCall
-using UnitfulRecipes
+using Plots, UnitfulRecipes
 
 import Base: @kwdef
 import DFTK: Mixing
@@ -52,8 +49,6 @@ include("integrations/initialization.jl")
 # Analysis
 export plot_temperature, plot_temperature!, plot_energy, plot_energy!, plot_rdf
 include("analysis/plotting.jl")
-export write_nbs_animation, write_molly_visualization, write_ase_trajectory
-include("analysis/visualization.jl")
 
 # DFTK Integrations
 export DFTKPotential

src/analysis/visualization.jl

@@ -42,4 +42,14 @@ get_particles(result::MollyResult, t::Integer) = AtomsBase.Atom.(result.system.a
 
 temperature(result::MollyResult, t::Integer) = result.system.loggers["t"].temperatures[t]
 kinetic_energy(result::MollyResult, t::Integer) = result.system.loggers["k"].energies[t]
-potential_energy(result::MollyResult, t::Integer) = result.system.loggers["p"].energies[t]
+potential_energy(result::MollyResult, t::Integer) = result.system.loggers["p"].energies[t]
+
+"""
+    visualize(result::MollyResult, filename::String; kwargs...)
+
+Animate a `MollyResult` using Molly's `visualize` function and store the result in a file.
+Any kwargs will be passed directly to the `visualize` function.
+
+This function is only available when GLMakie is imported.
+"""
+Molly.visualize(result::MollyResult, filename::String; kwargs...) = visualize(result.system.loggers["c"], result.system.box_size, filename; kwargs...)

src/implementations/molly/molly_result.jl

@@ -38,3 +38,10 @@ get_particles(result::NBSResult, t::Integer) = AtomsBase.Atom.(result.result.sim
 temperature(result::NBSResult, t::Integer) = NBodySimulator.temperature(result.result, result.result.solution.t[t]) * TEMPERATURE_UNIT
 kinetic_energy(result::NBSResult, t::Integer) = NBodySimulator.kinetic_energy(result.result, result.result.solution.t[t]) * ENERGY_UNIT
 potential_energy(result::NBSResult, t::Integer) = result.energy_cache[t] * ENERGY_UNIT
+
+"""
+    animate(result::NBSResult, filename::String; kwargs...)
+
+Animate an `NBSResult` using the interface provided by NBodySimulator.jl and store the result in a file.
+"""
+Plots.animate(result::NBSResult, filename::String; kwargs...) = animate(result.result, filename; kwargs...)

src/implementations/nbodysimulator/nbodysimulator_result.jl

@@ -40,6 +40,5 @@ Base.:(==)(a1::Atomistic.AugmentedAtomData, a2::Atomistic.AugmentedAtomData) = p
     end
     @testset "Analysis Unit Tests" begin
         include("analysis/plotting.jl")
-        include("analysis/visualization.jl")
     end
 end