grad test tolerances

README.md

@@ -49,7 +49,7 @@ Enter the package mode by pressing `]` and run `add Molly`.
 
 Some examples are given here, see [the documentation](https://juliamolsim.github.io/Molly.jl/stable/docs) for more on how to use the package.
 
-Simulation of a Lennard-Jones gas:
+Simulation of a Lennard-Jones fluid:
 ```julia
 using Molly
 

docs/src/differentiable.md

@@ -15,7 +15,7 @@ Differentiable simulation does not currently work with units, user-defined types
 
 ## General interactions
 
-First, we show how taking gradients through a simulation can be used to optimise an atom property in a [Lennard-Jones](https://en.wikipedia.org/wiki/Lennard-Jones_potential) gas.
+First, we show how taking gradients through a simulation can be used to optimise an atom property in a [Lennard-Jones](https://en.wikipedia.org/wiki/Lennard-Jones_potential) fluid.
 In this type of simulation each atom has a σ value that determines how close it likes to get to other atoms.
 We are going to find the σ value that results in a desired distance of each atom to its closest neighbor.
 First we need a function to obtain the mean distance of each atom to its closest neighbor:

docs/src/docs.md

@@ -10,9 +10,9 @@ To run a simulation you create a [`System`](@ref) object and call [`simulate!`](
 The different components of the system and simulation can be used as defined by the package, or you can define your own versions.
 An important principle of the package is that your custom components, particularly force functions, should be easy to define and just as performant as the built-in versions.
 
-## Simulating a gas
+## Simulation basics
 
-Let's look at the simulation of a gas acting under the [Lennard-Jones](https://en.wikipedia.org/wiki/Lennard-Jones_potential) potential to start with.
+Let's look at the simulation of a fluid acting under the [Lennard-Jones](https://en.wikipedia.org/wiki/Lennard-Jones_potential) potential to start with.
 First, we'll need some atoms with the relevant parameters defined.
 ```julia
 using Molly

test/energy_conservation.jl

@@ -4,7 +4,7 @@ using Base.Threads
 using Statistics
 using Test
 
-@testset "Lennard-Jones gas energy conservation" begin
+@testset "Lennard-Jones energy conservation" begin
     temp = 1.0u"K"
     n_steps = 10_000
     box_size = SVector(50.0, 50.0, 50.0)u"nm"

test/runtests.jl

@@ -17,15 +17,17 @@ using Test
 
 # Allow testing of particular components
 const GROUP = get(ENV, "GROUP", "All")
+if GROUP == "Zygote"
+    @warn "Only running Zygote tests as GROUP is set to Zygote"
+end
 
 # GLMakie doesn't work on CI
 run_visualize_tests = !haskey(ENV, "CI")
-
 if run_visualize_tests
     using GLMakie
-    @info "The visualization tests will be run as run_visualize_tests is set to true"
+    @info "The visualization tests will be run as this is not CI"
 else
-    @warn "The visualization tests will not be run as run_visualize_tests is set to false"
+    @warn "The visualization tests will not be run as this is CI"
 end
 
 run_parallel_tests = nthreads() > 1
@@ -49,7 +51,7 @@ data_dir = normpath(@__DIR__, "..", "data")
 temp_fp_pdb = tempname(cleanup=true) * ".pdb"
 temp_fp_viz = tempname(cleanup=true) * ".mp4"
 
-if GROUP == "All" || GROUP == "Basic"
+if GROUP == "All"
     # Some failures due to dependencies but there is an unbound args error
     Aqua.test_all(
         Molly;
@@ -59,9 +61,6 @@ if GROUP == "All" || GROUP == "Basic"
     )
 
     include("basic.jl")
-end
-
-if GROUP == "All"
     include("simulation.jl")
     include("protein.jl")
     include("agent.jl")

test/simulation.jl

@@ -1,4 +1,4 @@
-@testset "Lennard-Jones gas 2D" begin
+@testset "Lennard-Jones 2D" begin
     n_atoms = 10
     n_steps = 20_000
     temp = 298.0u"K"
@@ -30,7 +30,7 @@
     run_visualize_tests && visualize(s.loggers["coords"], box_size, temp_fp_viz)
 end
 
-@testset "Lennard-Jones gas" begin
+@testset "Lennard-Jones" begin
     n_atoms = 100
     n_steps = 20_000
     temp = 298.0u"K"
@@ -77,7 +77,7 @@ end
     end
 end
 
-@testset "Lennard-Jones gas Störmer-Verlet" begin
+@testset "Lennard-Jones Störmer-Verlet" begin
     n_atoms = 100
     n_steps = 20_000
     box_size = SVector(2.0, 2.0, 2.0)u"nm"

test/zygote.jl

@@ -123,17 +123,17 @@
     end
 
     runs = [
-        ("cpu"           , [false, false, false, true , true ], 0.1 , 0.2 ),
+        ("cpu"           , [false, false, false, true , true ], 0.1 , 0.25),
         ("cpu forward"   , [false, true , false, true , true ], 0.01, 0.01),
         ("cpu f32"       , [false, false, true , true , true ], 0.2 , 5.0 ),
         ("cpu nospecific", [false, false, false, true , false], 0.1 , 0.0 ),
-        ("cpu nogeneral" , [false, false, false, false, true ], 0.0 , 0.2 ),
+        ("cpu nogeneral" , [false, false, false, false, true ], 0.0 , 0.25),
     ]
     if run_gpu_tests
-        push!(runs, ("gpu"           , [true , false, false, true , true ], 0.2 , 5.0 ))
+        push!(runs, ("gpu"           , [true , false, false, true , true ], 0.25, 5.0 ))
         push!(runs, ("gpu forward"   , [true , true , false, true , true ], 0.01, 0.01))
-        push!(runs, ("gpu f32"       , [true , false, true , true , true ], 0.5 , 10.0))
-        push!(runs, ("gpu nospecific", [true , false, false, true , false], 0.2 , 0.0 ))
+        push!(runs, ("gpu f32"       , [true , false, true , true , true ], 0.5 , 50.0))
+        push!(runs, ("gpu nospecific", [true , false, false, true , false], 0.25, 0.0 ))
         push!(runs, ("gpu nogeneral" , [true , false, false, false, true ], 0.0 , 10.0))
     end