From ea4d266afb14de2f9cf7cc885a7474c4a1002cb4 Mon Sep 17 00:00:00 2001
From: Chris Rackauckas <accounts@chrisrackauckas.com>
Date: Thu, 23 Jun 2022 15:09:54 -0400
Subject: [PATCH] format SciML Style
---
.JuliaFormatter.toml | 1 +
.github/workflows/FormatCheck.yml | 42 ++++++++++++++++++++++++++++++
docs/make.jl | 24 +++++++----------
docs/pages.jl | 4 +--
examples/liquid_argon.jl | 26 ++++++++++--------
examples/liquid_argon_omm_units.jl | 15 +++++------
examples/liquid_argon_reduced.jl | 12 ++++-----
examples/liquid_argon_sde.jl | 12 ++++-----
8 files changed, 87 insertions(+), 49 deletions(-)
create mode 100644 .JuliaFormatter.toml
create mode 100644 .github/workflows/FormatCheck.yml
diff --git a/.JuliaFormatter.toml b/.JuliaFormatter.toml
new file mode 100644
index 0000000..453925c
--- /dev/null
+++ b/.JuliaFormatter.toml
@@ -0,0 +1 @@
+style = "sciml"
\ No newline at end of file
diff --git a/.github/workflows/FormatCheck.yml b/.github/workflows/FormatCheck.yml
new file mode 100644
index 0000000..2a3517a
--- /dev/null
+++ b/.github/workflows/FormatCheck.yml
@@ -0,0 +1,42 @@
+name: format-check
+
+on:
+ push:
+ branches:
+ - 'master'
+ - 'release-'
+ tags: '*'
+ pull_request:
+
+jobs:
+ build:
+ runs-on: ${{ matrix.os }}
+ strategy:
+ matrix:
+ julia-version: [1]
+ julia-arch: [x86]
+ os: [ubuntu-latest]
+ steps:
+ - uses: julia-actions/setup-julia@latest
+ with:
+ version: ${{ matrix.julia-version }}
+
+ - uses: actions/checkout@v1
+ - name: Install JuliaFormatter and format
+ # This will use the latest version by default but you can set the version like so:
+ #
+ # julia -e 'using Pkg; Pkg.add(PackageSpec(name="JuliaFormatter", version="0.13.0"))'
+ run: |
+ julia -e 'using Pkg; Pkg.add(PackageSpec(name="JuliaFormatter"))'
+ julia -e 'using JuliaFormatter; format(".", verbose=true)'
+ - name: Format check
+ run: |
+ julia -e '
+ out = Cmd(`git diff --name-only`) |> read |> String
+ if out == ""
+ exit(0)
+ else
+ @error "Some files have not been formatted !!!"
+ write(stdout, out)
+ exit(1)
+ end'
diff --git a/docs/make.jl b/docs/make.jl
index 3cbe7d3..a899f75 100644
--- a/docs/make.jl
+++ b/docs/make.jl
@@ -2,18 +2,14 @@ using Documenter, NBodySimulator
include("pages.jl")
-makedocs(
- sitename="NbodySimulator.jl",
- authors="Chris Rackauckas",
- modules=[NBodySimulator],
- clean=true,doctest=false,
- format = Documenter.HTML(analytics = "UA-90474609-3",
- assets = ["assets/favicon.ico"],
- canonical="https://nbodysimulator.sciml.ai/stable/"),
- pages=pages
-)
+makedocs(sitename = "NbodySimulator.jl",
+ authors = "Chris Rackauckas",
+ modules = [NBodySimulator],
+ clean = true, doctest = false,
+ format = Documenter.HTML(analytics = "UA-90474609-3",
+ assets = ["assets/favicon.ico"],
+ canonical = "https://nbodysimulator.sciml.ai/stable/"),
+ pages = pages)
-deploydocs(
- repo = "github.com/SciML/NBodySimulator.jl.git";
- push_preview = true
-)
\ No newline at end of file
+deploydocs(repo = "github.com/SciML/NBodySimulator.jl.git";
+ push_preview = true)
diff --git a/docs/pages.jl b/docs/pages.jl
index 7b7d575..385c690 100644
--- a/docs/pages.jl
+++ b/docs/pages.jl
@@ -1,7 +1,7 @@
# Put in a separate page so it can be used by SciMLDocs.jl
-pages=[
+pages = [
"Home" => "index.md",
"examples.md",
- "nbodysimulator.md"
+ "nbodysimulator.md",
]
diff --git a/examples/liquid_argon.jl b/examples/liquid_argon.jl
index 50c4675..4164326 100644
--- a/examples/liquid_argon.jl
+++ b/examples/liquid_argon.jl
@@ -3,23 +3,27 @@ using NBodySimulator, StaticArrays
function generate_bodies_in_line(n::Int, m::Real, v_dev::Real, L::Real)
dL = L / (ceil(n^(1 / 3)))
n_line = floor(Int, L / dL)
- rng = MersenneTwister(n);
+ rng = MersenneTwister(n)
velocities = v_dev * randn(rng, Float64, (3, n_line))
bodies = MassBody[]
x = y = L / 2
- for i = 1:n_line
+ for i in 1:n_line
r = SVector(x, y, i * dL)
- v = SVector{3}(velocities[:,i])
+ v = SVector{3}(velocities[:, i])
body = MassBody(r, v, m)
- push!(bodies, body)
+ push!(bodies, body)
end
return bodies
end
function generate_random_directions(n::Int)
- theta = acos.(1 - 2 * rand(n));
- phi = 2 * pi * rand(n);
- directions = [@SVector [sin(theta[i]) .* cos(phi[i]), sin(theta[i]) .* sin(phi[i]), cos(theta[i])] for i = 1:n]
+ theta = acos.(1 - 2 * rand(n))
+ phi = 2 * pi * rand(n)
+ directions = [@SVector [
+ sin(theta[i]) .* cos(phi[i]),
+ sin(theta[i]) .* sin(phi[i]),
+ cos(theta[i]),
+ ] for i in 1:n]
end
units = :real
@@ -33,8 +37,8 @@ const σ = 3.4e-10 # m
const ρ = 1374 # kg/m^3
const m = 39.95 * 1.6747 * 1e-27 # kg
const N = 216#floor(Int, ρ * L^3 / m)
-const L = (m*N/ρ)^(1/3)#10.229σ
-const R = 0.5*L
+const L = (m * N / ρ)^(1 / 3)#10.229σ
+const R = 0.5 * L
const v_dev = sqrt(kb * T / m)
const τ = 0.5e-15 # σ/v
const t1 = 0τ
@@ -48,7 +52,7 @@ pbc = CubicPeriodicBoundaryConditions(L)
lj_system = PotentialNBodySystem(bodies, Dict(:lennard_jones => jl_parameters));
simulation = NBodySimulation(lj_system, (t1, t2), pbc, kb);
#result = run_simulation(simulation, Tsit5())
-result = @time run_simulation(simulation, VelocityVerlet(), dt=τ)
+result = @time run_simulation(simulation, VelocityVerlet(), dt = τ)
#=
using Plots
@@ -95,4 +99,4 @@ write(file, "ts", ts)
write(file, "grf", grf)
write(file, "dr2", dr2)
close(file)
-=#
\ No newline at end of file
+=#
diff --git a/examples/liquid_argon_omm_units.jl b/examples/liquid_argon_omm_units.jl
index 88b291b..5e940da 100644
--- a/examples/liquid_argon_omm_units.jl
+++ b/examples/liquid_argon_omm_units.jl
@@ -6,11 +6,11 @@ const T0 = 90.0 # °K
const kb = 8.3144598e-3 # kJ/(K*mol)
const ϵ = T * kb
const σ = 0.34 # nm
-const ρ = 1374/1.6747# Da/nm^3
+const ρ = 1374 / 1.6747# Da/nm^3
const m = 39.95# Da
const N = 8
-const L = (m*N/ρ)^(1/3)#10.229σ
-const R = 0.5*L
+const L = (m * N / ρ)^(1 / 3)#10.229σ
+const R = 0.5 * L
const v_dev = sqrt(kb * T / m)
const bodies = generate_bodies_in_cell_nodes(N, m, v_dev, L)
@@ -28,15 +28,14 @@ const pbc = CubicPeriodicBoundaryConditions(L)
const simulation = NBodySimulation(lj_system, (t1, t2), pbc, thermostat, kb);
#result = @time run_simulation(simulation, VelocityVerlet(), dt=τ)
#result = @time run_simulation_sde(simulation, ISSEM(symplectic=true,theta=0.5))
-result = @time run_simulation(simulation, EM(), dt=τ)
+result = @time run_simulation(simulation, EM(), dt = τ)
#(rs, grf) = rdf(result)
#(ts, dr2) = msd(result)
-t = t1:τ:result.solution.t[end-1]
+t = t1:τ:result.solution.t[end - 1]
temper = @time temperature.(result, t)
-
#using Plots
#pl=plot(t, temper, ylim=[0,200], xlabel="t, ps", ylabel = "T, °K", label="Temperature, °K", linewidth=2)
#plot!(pl, t, T0*ones(length(t)), label = "90 °K", linewidth=2)
@@ -44,7 +43,6 @@ temper = @time temperature.(result, t)
#plot!(pl, title="Berendsen thermostat at tau=$(thermostat.τ) ps")
#plot!(pl, title="Nose-Hoover thermostat at tau=$(thermostat.τ) ps")
-
time_now = Dates.format(now(), "yyyy_mm_dd_HH_MM_SS")
Nactual = length(bodies)
timesteps = round(length(result.solution.t))
@@ -54,7 +52,6 @@ timesteps = round(length(result.solution.t))
#using JLD
#save("d:/nosehoover thermostat for water liquid argon $T0 and $(thermostat.τ) _$time_now.jld", "t",t, "temper", temper, "T0", T0, "τ", thermostat.τ)
-
#=
using MAT
@@ -74,4 +71,4 @@ end
#write(file, "grf", grf)
#write(file, "dr2", dr2)
close(file)
-=#
\ No newline at end of file
+=#
diff --git a/examples/liquid_argon_reduced.jl b/examples/liquid_argon_reduced.jl
index 561b5ec..506c4a4 100644
--- a/examples/liquid_argon_reduced.jl
+++ b/examples/liquid_argon_reduced.jl
@@ -7,8 +7,8 @@ const σ = 3.4e-10 # m
const ρ = 1374 # kg/m^3
const m = 39.95 * 1.6747 * 1e-27 # kg
const N = 216#floor(Int, ρ * L^3 / m)
-const L = (m*N/ρ)^(1/3)#10.229σ
-const R = 2.25σ
+const L = (m * N / ρ)^(1 / 3)#10.229σ
+const R = 2.25σ
const v_dev = sqrt(kb * T / m)
const τ = 0.5e-15 # σ/v, fs
const t1 = 0.0
@@ -26,9 +26,10 @@ const _t2 = t2 * sqrt(ϵ / m) / σ
bodies = generate_bodies_in_cell_nodes(N, _m, _v, _L)
parameters = LennardJonesParameters(_ϵ, _σ, _R)
lj_system = PotentialNBodySystem(bodies, Dict(:lennard_jones => parameters));
-simulation = NBodySimulation(lj_system, (_t1, _t2), CubicPeriodicBoundaryConditions(_L), _ϵ/T);
+simulation = NBodySimulation(lj_system, (_t1, _t2), CubicPeriodicBoundaryConditions(_L),
+ _ϵ / T);
#result = run_simulation(simulation, Tsit5())
-result = @time run_simulation(simulation, VelocityVerlet(), dt=_τ)
+result = @time run_simulation(simulation, VelocityVerlet(), dt = _τ)
#(rs, grf) = rdf(result)
#(ts, dr2) = msd(result)
@@ -37,9 +38,8 @@ result = @time run_simulation(simulation, VelocityVerlet(), dt=_τ)
#plot(rs, grf, xlim=[0, 0.4999_L], label=["Radial distribution function"],ylabel="g(r)", xlabel="r")
#plot(rs/_σ, grf, xlim=[0, 0.4999_L/_σ], label=["Radial distribution function"],ylabel="g(r)", xlabel="r/sigma")
-
#time_now = Dates.format(now(), "yyyy_mm_dd_HH_MM_SS")
#Nactual = length(bodies)
#timesteps = round(length(result.solution.t))
-#@time save_to_pdb(result, "D:/liquid argon simulation $Nactual molecules and $timesteps steps $time_now.pdb" )
\ No newline at end of file
+#@time save_to_pdb(result, "D:/liquid argon simulation $Nactual molecules and $timesteps steps $time_now.pdb" )
diff --git a/examples/liquid_argon_sde.jl b/examples/liquid_argon_sde.jl
index f53352f..59a3203 100644
--- a/examples/liquid_argon_sde.jl
+++ b/examples/liquid_argon_sde.jl
@@ -6,11 +6,11 @@ T0 = 90
kb = 8.3144598e-3 # kJ/(K*mol)
ϵ = T * kb
σ = 0.34 # nm
-ρ = 1374/1.6747# Da/nm^3
+ρ = 1374 / 1.6747# Da/nm^3
m = 39.95# Da
N = 216
-L = (m*N/ρ)^(1/3)#10.229σ
-R = 0.5*L
+L = (m * N / ρ)^(1 / 3)#10.229σ
+R = 0.5 * L
v_dev = sqrt(kb * T / m)
bodies = generate_bodies_in_cell_nodes(N, m, v_dev, L)
@@ -26,14 +26,13 @@ thermostat = LangevinThermostat(T0, 10.0)
pbc = CubicPeriodicBoundaryConditions(L)
simulation = NBodySimulation(lj_system, (t1, t2), pbc, thermostat, kb);
#result = @time run_simulation(simulation, VelocityVerlet(), dt=τ)
-result = @time run_simulation_sde(simulation, EM(), dt=τ)
+result = @time run_simulation_sde(simulation, EM(), dt = τ)
#=
time_now = Dates.format(now(), "yyyy_mm_dd_HH_MM_SS")
Nactual = length(bodies)
timesteps = round(length(result.solution.t))
-
using Plots
t = t1:τ:result.solution.t[end-1]
temper = temperature.(result, t)
@@ -41,7 +40,6 @@ pl=plot(t, temper, ylim=[0,500], xlabel="t, ps", ylabel = "T, °K", label="Tempe
plot!(pl, t, T0*ones(length(t)), label = "$T0 °K", linewidth=2)
plot!(pl, title="Langevin thermostat at gamma=$(thermostat.γ) 1/ps")
-
using JLD
save("d:/$(typeof(thermostat)) thermostat for water $T0 _$time_now.jld", "t",t, "temper", temper, "T0", T0, "thermostat", thermostat)
-=#
\ No newline at end of file
+=#