Molly integration tests #2728
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Molly integration tests #2728
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Your PR requires formatting changes to meet the project's style guidelines. Click here to view the suggested changes.diff --git a/test/integration/Molly/runtests.jl b/test/integration/Molly/runtests.jl
index 6eb926bd..fb9ebf48 100644
--- a/test/integration/Molly/runtests.jl
+++ b/test/integration/Molly/runtests.jl
@@ -14,7 +14,7 @@ const run_parallel_tests = (Threads.nthreads() > 1)
@testset "Gradients" begin
inter = LennardJones()
boundary = CubicBoundary(5.0)
- a1, a2 = Atom(σ=0.3, ϵ=0.5), Atom(σ=0.3, ϵ=0.5)
+ a1, a2 = Atom(σ = 0.3, ϵ = 0.5), Atom(σ = 0.3, ϵ = 0.5)
function force_direct(dist)
c1 = SVector(1.0, 1.0, 1.0)
@@ -53,15 +53,15 @@ end
ff = MolecularForceField(
T,
joinpath.(ff_dir, ["ff99SBildn.xml", "tip3p_standard.xml", "his.xml"])...,
- units=false,
+ units = false,
)
sys = System(
joinpath(data_dir, "6mrr_equil.pdb"),
ff;
- units=false,
- array_type=AT,
- nonbonded_method=:pme,
- grad_safe=true,
+ units = false,
+ array_type = AT,
+ nonbonded_method = :pme,
+ grad_safe = true,
)
pme = sys.general_inters[1]
@@ -83,52 +83,52 @@ end
Const(Val(false)),
)[2]
- @test pe_ad ≈ pe atol=1e-7
- @test Fs_ad ≈ Fs atol=1e-10
- @test -d_sys.coords ≈ Fs atol=1e-10
+ @test pe_ad ≈ pe atol = 1.0e-7
+ @test Fs_ad ≈ Fs atol = 1.0e-10
+ @test -d_sys.coords ≈ Fs atol = 1.0e-10
function coord_fdm(c)
coords_mod = copy(sys.coords)
coords_mod[1] = SVector(c, coords_mod[1][2], coords_mod[1][3])
- sys_mod = System(deepcopy(sys); coords=coords_mod)
+ sys_mod = System(deepcopy(sys); coords = coords_mod)
return Molly.ewald_pe_forces!(Fs, nothing, sys_mod, pme, Val(false))
end
c = sys.coords[1][1]
coord_fdm(c)
coord_grad = central_fdm(5, 1)(coord_fdm, c)
- @test d_sys.coords[1][1] ≈ coord_grad atol=1e-6
+ @test d_sys.coords[1][1] ≈ coord_grad atol = 1.0e-6
function charge_fdm(ch)
atoms_mod = copy(sys.atoms)
at = sys.atoms[1]
- atoms_mod[1] = Atom(mass=at.mass, charge=ch, σ=at.σ, ϵ=at.σ)
- sys_mod = System(deepcopy(sys); atoms=atoms_mod)
+ atoms_mod[1] = Atom(mass = at.mass, charge = ch, σ = at.σ, ϵ = at.σ)
+ sys_mod = System(deepcopy(sys); atoms = atoms_mod)
return Molly.ewald_pe_forces!(Fs, nothing, sys_mod, pme, Val(false))
end
at = sys.atoms[1]
charge_fdm(charge(at))
charge_grad = central_fdm(5, 1)(charge_fdm, charge(at))
- @test charge(d_sys.atoms[1]) ≈ charge_grad atol=1e-6
+ @test charge(d_sys.atoms[1]) ≈ charge_grad atol = 1.0e-6
end
@testset "Differentiable simulation" begin
runs = [ # gpu par fwd f32 obc2 gbn2 tol_σ tol_r0
- ("CPU" , Array, false, false, false, false, false, 1e-4, 1e-4),
- ("CPU forward" , Array, false, true , false, false, false, 0.5 , 0.1 ),
- ("CPU f32" , Array, false, false, true , false, false, 0.01, 5e-4),
- ("CPU obc2" , Array, false, false, false, true , false, 1e-4, 1e-4),
- ("CPU gbn2" , Array, false, false, false, false, true , 1e-4, 1e-4),
- ("CPU gbn2 forward", Array, false, true , false, false, true , 0.5 , 0.1 ),
+ ("CPU", Array, false, false, false, false, false, 1.0e-4, 1.0e-4),
+ ("CPU forward", Array, false, true, false, false, false, 0.5, 0.1),
+ ("CPU f32", Array, false, false, true, false, false, 0.01, 5.0e-4),
+ ("CPU obc2", Array, false, false, false, true, false, 1.0e-4, 1.0e-4),
+ ("CPU gbn2", Array, false, false, false, false, true, 1.0e-4, 1.0e-4),
+ ("CPU gbn2 forward", Array, false, true, false, false, true, 0.5, 0.1),
]
if run_parallel_tests # gpu par fwd f32 obc2 gbn2 tol_σ tol_r0
- push!(runs, ("CPU parallel" , Array, true , false, false, false, false, 1e-4, 1e-4))
- push!(runs, ("CPU parallel forward", Array, true , true , false, false, false, 0.5 , 0.1 ))
- push!(runs, ("CPU parallel f32" , Array, true , false, true , false, false, 0.01, 5e-4))
+ push!(runs, ("CPU parallel", Array, true, false, false, false, false, 1.0e-4, 1.0e-4))
+ push!(runs, ("CPU parallel forward", Array, true, true, false, false, false, 0.5, 0.1))
+ push!(runs, ("CPU parallel f32", Array, true, false, true, false, false, 0.01, 5.0e-4))
end
- function mean_min_separation(coords, boundary, ::Val{T}) where T
+ function mean_min_separation(coords, boundary, ::Val{T}) where {T}
min_seps = T[]
for i in eachindex(coords)
min_sq_sep = T(100.0)
@@ -143,9 +143,11 @@ end
return mean(min_seps)
end
- function loss(σ, r0, coords, velocities, boundary, pairwise_inters, general_inters,
- neighbor_finder, simulator, n_steps, n_threads, n_atoms, atom_mass, bond_dists,
- bond_is, bond_js, angles, torsions, rng, ::Val{T}, ::Val{AT}) where {T, AT}
+ function loss(
+ σ, r0, coords, velocities, boundary, pairwise_inters, general_inters,
+ neighbor_finder, simulator, n_steps, n_threads, n_atoms, atom_mass, bond_dists,
+ bond_is, bond_js, angles, torsions, rng, ::Val{T}, ::Val{AT}
+ ) where {T, AT}
atoms = [Atom(i, 1, atom_mass, (i % 2 == 0 ? T(-0.02) : T(0.02)), σ, T(0.2)) for i in 1:n_atoms]
bonds_inner = HarmonicBond{T, T}[]
for i in 1:(n_atoms ÷ 2)
@@ -158,26 +160,26 @@ end
)
sys = System(
- atoms=to_device(atoms, AT),
- coords=to_device(coords, AT),
- boundary=boundary,
- velocities=to_device(velocities, AT),
- pairwise_inters=pairwise_inters,
- specific_inter_lists=(bonds, angles, torsions),
- general_inters=general_inters,
- neighbor_finder=neighbor_finder,
- force_units=NoUnits,
- energy_units=NoUnits,
+ atoms = to_device(atoms, AT),
+ coords = to_device(coords, AT),
+ boundary = boundary,
+ velocities = to_device(velocities, AT),
+ pairwise_inters = pairwise_inters,
+ specific_inter_lists = (bonds, angles, torsions),
+ general_inters = general_inters,
+ neighbor_finder = neighbor_finder,
+ force_units = NoUnits,
+ energy_units = NoUnits,
)
- simulate!(sys, simulator, n_steps; n_threads=n_threads, rng=rng)
+ simulate!(sys, simulator, n_steps; n_threads = n_threads, rng = rng)
return mean_min_separation(sys.coords, boundary, Val(T))
end
for (name, AT, parallel, forward, f32, obc2, gbn2, tol_σ, tol_r0) in runs
T = (f32 ? Float32 : Float64)
- σ = T(0.4)
+ σ = T(0.4)
r0 = T(1.0)
n_atoms = 50
n_steps = 100
@@ -185,70 +187,74 @@ end
boundary = CubicBoundary(T(3.0))
temp = T(1.0)
simulator = VelocityVerlet(
- dt=T(0.001),
- coupling=(ImmediateThermostat(temp),),
+ dt = T(0.001),
+ coupling = (ImmediateThermostat(temp),),
)
rng = Xoshiro(1000) # Same system every time, not required but increases stability
- coords = place_atoms(n_atoms, boundary; min_dist=T(0.6), max_attempts=500, rng=rng)
- velocities = [random_velocity(atom_mass, temp; rng=rng) for i in 1:n_atoms]
+ coords = place_atoms(n_atoms, boundary; min_dist = T(0.6), max_attempts = 500, rng = rng)
+ velocities = [random_velocity(atom_mass, temp; rng = rng) for i in 1:n_atoms]
nb_cutoff = T(1.2)
- lj = LennardJones(cutoff=DistanceCutoff(nb_cutoff), use_neighbors=true)
+ lj = LennardJones(cutoff = DistanceCutoff(nb_cutoff), use_neighbors = true)
crf = CoulombReactionField(
- dist_cutoff=nb_cutoff,
- solvent_dielectric=T(Molly.crf_solvent_dielectric),
- use_neighbors=true,
- coulomb_const=T(ustrip(Molly.coulomb_const)),
+ dist_cutoff = nb_cutoff,
+ solvent_dielectric = T(Molly.crf_solvent_dielectric),
+ use_neighbors = true,
+ coulomb_const = T(ustrip(Molly.coulomb_const)),
)
pairwise_inters = (lj, crf)
bond_is = to_device(Int32.(collect(1:(n_atoms ÷ 2))), AT)
bond_js = to_device(Int32.(collect((1 + n_atoms ÷ 2):n_atoms)), AT)
- bond_dists = [norm(vector(coords[i], coords[i + n_atoms ÷ 2], boundary))
- for i in 1:(n_atoms ÷ 2)]
- angles_inner = [HarmonicAngle(k=T(10.0), θ0=T(2.0)) for i in 1:15]
+ bond_dists = [
+ norm(vector(coords[i], coords[i + n_atoms ÷ 2], boundary))
+ for i in 1:(n_atoms ÷ 2)
+ ]
+ angles_inner = [HarmonicAngle(k = T(10.0), θ0 = T(2.0)) for i in 1:15]
angles = InteractionList3Atoms(
- to_device(Int32.(collect( 1:15)), AT),
+ to_device(Int32.(collect(1:15)), AT),
to_device(Int32.(collect(16:30)), AT),
to_device(Int32.(collect(31:45)), AT),
to_device(angles_inner, AT),
)
- torsions_inner = [PeriodicTorsion(
- periodicities=[1, 2, 3],
- phases=T[1.0, 0.0, -1.0],
- ks=T[10.0, 5.0, 8.0],
- n_terms=6,
- ) for i in 1:10]
+ torsions_inner = [
+ PeriodicTorsion(
+ periodicities = [1, 2, 3],
+ phases = T[1.0, 0.0, -1.0],
+ ks = T[10.0, 5.0, 8.0],
+ n_terms = 6,
+ ) for i in 1:10
+ ]
torsions = InteractionList4Atoms(
- to_device(Int32.(collect( 1:10)), AT),
+ to_device(Int32.(collect(1:10)), AT),
to_device(Int32.(collect(11:20)), AT),
to_device(Int32.(collect(21:30)), AT),
to_device(Int32.(collect(31:40)), AT),
to_device(torsions_inner, AT),
)
- atoms_setup = [Atom(charge=zero(T), σ=zero(T)) for i in 1:n_atoms]
+ atoms_setup = [Atom(charge = zero(T), σ = zero(T)) for i in 1:n_atoms]
if obc2
imp_obc2 = ImplicitSolventOBC(
to_device(atoms_setup, AT),
- [AtomData(element="O") for i in 1:n_atoms],
+ [AtomData(element = "O") for i in 1:n_atoms],
InteractionList2Atoms(bond_is, bond_js, nothing);
- kappa=T(0.7),
- use_OBC2=true,
+ kappa = T(0.7),
+ use_OBC2 = true,
)
general_inters = (imp_obc2,)
elseif gbn2
imp_gbn2 = ImplicitSolventGBN2(
to_device(atoms_setup, AT),
- [AtomData(element="O") for i in 1:n_atoms],
+ [AtomData(element = "O") for i in 1:n_atoms],
InteractionList2Atoms(bond_is, bond_js, nothing);
- kappa=T(0.7),
+ kappa = T(0.7),
)
general_inters = (imp_gbn2,)
else
general_inters = ()
end
neighbor_finder = DistanceNeighborFinder(
- eligible=to_device(trues(n_atoms, n_atoms), AT),
- n_steps=10,
- dist_cutoff=T(1.5),
+ eligible = to_device(trues(n_atoms, n_atoms), AT),
+ n_steps = 10,
+ dist_cutoff = T(1.5),
)
n_threads = (parallel ? Threads.nthreads() : 1)
@@ -299,9 +305,9 @@ end
),
)
for (prefix, genz, gfd, tol) in zip(("σ", "r0"), grad_enzyme, grad_fd, (tol_σ, tol_r0))
- if abs(gfd) < 1e-13
+ if abs(gfd) < 1.0e-13
@info "$(rpad(name, 20)) - $(rpad(prefix, 2)) - FD $gfd, Enzyme $genz"
- ztol = (contains(name, "f32") ? 1e-8 : 1e-10)
+ ztol = (contains(name, "f32") ? 1.0e-8 : 1.0e-10)
@test isnothing(genz) || abs(genz) < ztol
elseif isnothing(genz)
@info "$(rpad(name, 20)) - $(rpad(prefix, 2)) - FD $gfd, Enzyme $genz"
@@ -317,15 +323,15 @@ end
@testset "Differentiable protein" begin
function create_sys(AT)
- ff = MolecularForceField(joinpath.(ff_dir, ["ff99SBildn.xml", "his.xml"])...; units=false)
+ ff = MolecularForceField(joinpath.(ff_dir, ["ff99SBildn.xml", "his.xml"])...; units = false)
return System(
joinpath(data_dir, "6mrr_nowater.pdb"),
ff;
- units=false,
- array_type=AT,
- nonbonded_method=:cutoff,
- implicit_solvent=:gbn2,
- kappa=0.7,
+ units = false,
+ array_type = AT,
+ nonbonded_method = :cutoff,
+ implicit_solvent = :gbn2,
+ kappa = 0.7,
)
end
@@ -335,119 +341,119 @@ end
atoms, pis, sis, gis = Molly.inject_gradients(sys_ref, params_dic)
sys = System(
- atoms=atoms,
- coords=coords,
- boundary=sys_ref.boundary,
- pairwise_inters=pis,
- specific_inter_lists=sis,
- general_inters=gis,
- neighbor_finder=neighbor_finder,
- force_units=NoUnits,
- energy_units=NoUnits,
+ atoms = atoms,
+ coords = coords,
+ boundary = sys_ref.boundary,
+ pairwise_inters = pis,
+ specific_inter_lists = sis,
+ general_inters = gis,
+ neighbor_finder = neighbor_finder,
+ force_units = NoUnits,
+ energy_units = NoUnits,
)
- return potential_energy(sys; n_threads=n_threads)
+ return potential_energy(sys; n_threads = n_threads)
end
function test_forces_grad(params_dic, sys_ref, coords, neighbor_finder, n_threads)
atoms, pis, sis, gis = Molly.inject_gradients(sys_ref, params_dic)
sys = System(
- atoms=atoms,
- coords=coords,
- boundary=sys_ref.boundary,
- pairwise_inters=pis,
- specific_inter_lists=sis,
- general_inters=gis,
- neighbor_finder=neighbor_finder,
- force_units=NoUnits,
- energy_units=NoUnits,
+ atoms = atoms,
+ coords = coords,
+ boundary = sys_ref.boundary,
+ pairwise_inters = pis,
+ specific_inter_lists = sis,
+ general_inters = gis,
+ neighbor_finder = neighbor_finder,
+ force_units = NoUnits,
+ energy_units = NoUnits,
)
- fs = forces(sys; n_threads=n_threads)
+ fs = forces(sys; n_threads = n_threads)
return sum(sum.(abs, fs))
end
params_dic = Dict(
- "atom_C8_σ" => 0.33996695084235345,
- "atom_C8_ϵ" => 0.4577296,
- "atom_C9_σ" => 0.33996695084235345,
- "atom_C9_ϵ" => 0.4577296,
- "atom_CA_σ" => 0.33996695084235345,
- "atom_CA_ϵ" => 0.359824,
- "atom_CT_σ" => 0.33996695084235345,
- "atom_CT_ϵ" => 0.4577296,
- "atom_C_σ" => 0.33996695084235345,
- "atom_C_ϵ" => 0.359824,
- "atom_N3_σ" => 0.32499985237759577,
- "atom_N3_ϵ" => 0.71128,
- "atom_N_σ" => 0.32499985237759577,
- "atom_N_ϵ" => 0.71128,
- "atom_O2_σ" => 0.2959921901149463,
- "atom_O2_ϵ" => 0.87864,
- "atom_OH_σ" => 0.30664733878390477,
- "atom_OH_ϵ" => 0.8803136,
- "atom_O_σ" => 0.2959921901149463,
- "atom_O_ϵ" => 0.87864,
- "inter_CO_weight_14" => 0.8333,
- "inter_GB_neck_cut" => 0.68,
- "inter_GB_neck_scale" => 0.826836,
- "inter_GB_offset" => 0.0195141,
- "inter_GB_params_C_α" => 0.733756,
- "inter_GB_params_C_β" => 0.506378,
- "inter_GB_params_C_γ" => 0.205844,
- "inter_GB_params_N_α" => 0.503364,
- "inter_GB_params_N_β" => 0.316828,
- "inter_GB_params_N_γ" => 0.192915,
- "inter_GB_params_O_α" => 0.867814,
- "inter_GB_params_O_β" => 0.876635,
- "inter_GB_params_O_γ" => 0.387882,
- "inter_GB_probe_radius" => 0.14,
- "inter_GB_radius_C" => 0.17,
- "inter_GB_radius_N" => 0.155,
- "inter_GB_radius_O" => 0.15,
- "inter_GB_radius_O_CAR" => 0.14,
- "inter_GB_sa_factor" => 28.3919551,
- "inter_GB_screen_C" => 1.058554,
- "inter_GB_screen_N" => 0.733599,
- "inter_GB_screen_O" => 1.061039,
- "inter_LJ_weight_14" => 0.5,
- "inter_PT_-/C/CT/-_k_1" => 0.0,
- "inter_PT_-/C/N/-_k_1" => -10.46,
- "inter_PT_-/CA/CA/-_k_1" => -15.167,
- "inter_PT_-/CA/CT/-_k_1" => 0.0,
- "inter_PT_-/CT/C8/-_k_1" => 0.64852,
- "inter_PT_-/CT/C9/-_k_1" => 0.64852,
- "inter_PT_-/CT/CT/-_k_1" => 0.6508444444444447,
- "inter_PT_-/CT/N/-_k_1" => 0.0,
- "inter_PT_-/CT/N3/-_k_1" => 0.6508444444444447,
- "inter_PT_C/N/CT/C_k_1" => -0.142256,
- "inter_PT_C/N/CT/C_k_2" => 1.40164,
- "inter_PT_C/N/CT/C_k_3" => 2.276096,
- "inter_PT_C/N/CT/C_k_4" => 0.33472,
- "inter_PT_C/N/CT/C_k_5" => 1.6736,
- "inter_PT_CT/CT/C/N_k_1" => 0.8368,
- "inter_PT_CT/CT/C/N_k_2" => 0.8368,
- "inter_PT_CT/CT/C/N_k_3" => 1.6736,
- "inter_PT_CT/CT/N/C_k_1" => 8.368,
- "inter_PT_CT/CT/N/C_k_2" => 8.368,
- "inter_PT_CT/CT/N/C_k_3" => 1.6736,
- "inter_PT_H/N/C/O_k_1" => 8.368,
- "inter_PT_H/N/C/O_k_2" => -10.46,
- "inter_PT_H1/CT/C/O_k_1" => 3.3472,
- "inter_PT_H1/CT/C/O_k_2" => -0.33472,
+ "atom_C8_σ" => 0.33996695084235345,
+ "atom_C8_ϵ" => 0.4577296,
+ "atom_C9_σ" => 0.33996695084235345,
+ "atom_C9_ϵ" => 0.4577296,
+ "atom_CA_σ" => 0.33996695084235345,
+ "atom_CA_ϵ" => 0.359824,
+ "atom_CT_σ" => 0.33996695084235345,
+ "atom_CT_ϵ" => 0.4577296,
+ "atom_C_σ" => 0.33996695084235345,
+ "atom_C_ϵ" => 0.359824,
+ "atom_N3_σ" => 0.32499985237759577,
+ "atom_N3_ϵ" => 0.71128,
+ "atom_N_σ" => 0.32499985237759577,
+ "atom_N_ϵ" => 0.71128,
+ "atom_O2_σ" => 0.2959921901149463,
+ "atom_O2_ϵ" => 0.87864,
+ "atom_OH_σ" => 0.30664733878390477,
+ "atom_OH_ϵ" => 0.8803136,
+ "atom_O_σ" => 0.2959921901149463,
+ "atom_O_ϵ" => 0.87864,
+ "inter_CO_weight_14" => 0.8333,
+ "inter_GB_neck_cut" => 0.68,
+ "inter_GB_neck_scale" => 0.826836,
+ "inter_GB_offset" => 0.0195141,
+ "inter_GB_params_C_α" => 0.733756,
+ "inter_GB_params_C_β" => 0.506378,
+ "inter_GB_params_C_γ" => 0.205844,
+ "inter_GB_params_N_α" => 0.503364,
+ "inter_GB_params_N_β" => 0.316828,
+ "inter_GB_params_N_γ" => 0.192915,
+ "inter_GB_params_O_α" => 0.867814,
+ "inter_GB_params_O_β" => 0.876635,
+ "inter_GB_params_O_γ" => 0.387882,
+ "inter_GB_probe_radius" => 0.14,
+ "inter_GB_radius_C" => 0.17,
+ "inter_GB_radius_N" => 0.155,
+ "inter_GB_radius_O" => 0.15,
+ "inter_GB_radius_O_CAR" => 0.14,
+ "inter_GB_sa_factor" => 28.3919551,
+ "inter_GB_screen_C" => 1.058554,
+ "inter_GB_screen_N" => 0.733599,
+ "inter_GB_screen_O" => 1.061039,
+ "inter_LJ_weight_14" => 0.5,
+ "inter_PT_-/C/CT/-_k_1" => 0.0,
+ "inter_PT_-/C/N/-_k_1" => -10.46,
+ "inter_PT_-/CA/CA/-_k_1" => -15.167,
+ "inter_PT_-/CA/CT/-_k_1" => 0.0,
+ "inter_PT_-/CT/C8/-_k_1" => 0.64852,
+ "inter_PT_-/CT/C9/-_k_1" => 0.64852,
+ "inter_PT_-/CT/CT/-_k_1" => 0.6508444444444447,
+ "inter_PT_-/CT/N/-_k_1" => 0.0,
+ "inter_PT_-/CT/N3/-_k_1" => 0.6508444444444447,
+ "inter_PT_C/N/CT/C_k_1" => -0.142256,
+ "inter_PT_C/N/CT/C_k_2" => 1.40164,
+ "inter_PT_C/N/CT/C_k_3" => 2.276096,
+ "inter_PT_C/N/CT/C_k_4" => 0.33472,
+ "inter_PT_C/N/CT/C_k_5" => 1.6736,
+ "inter_PT_CT/CT/C/N_k_1" => 0.8368,
+ "inter_PT_CT/CT/C/N_k_2" => 0.8368,
+ "inter_PT_CT/CT/C/N_k_3" => 1.6736,
+ "inter_PT_CT/CT/N/C_k_1" => 8.368,
+ "inter_PT_CT/CT/N/C_k_2" => 8.368,
+ "inter_PT_CT/CT/N/C_k_3" => 1.6736,
+ "inter_PT_H/N/C/O_k_1" => 8.368,
+ "inter_PT_H/N/C/O_k_2" => -10.46,
+ "inter_PT_H1/CT/C/O_k_1" => 3.3472,
+ "inter_PT_H1/CT/C/O_k_2" => -0.33472,
"inter_PT_HC/CT/C4/CT_k_1" => 0.66944,
- "inter_PT_N/CT/C/N_k_1" => 2.7196,
- "inter_PT_N/CT/C/N_k_10" => 0.1046,
- "inter_PT_N/CT/C/N_k_11" => -0.046024,
- "inter_PT_N/CT/C/N_k_2" => -0.824248,
- "inter_PT_N/CT/C/N_k_3" => 6.04588,
- "inter_PT_N/CT/C/N_k_4" => 2.004136,
- "inter_PT_N/CT/C/N_k_5" => -0.0799144,
- "inter_PT_N/CT/C/N_k_6" => -0.016736,
- "inter_PT_N/CT/C/N_k_7" => -1.06692,
- "inter_PT_N/CT/C/N_k_8" => 0.3138,
- "inter_PT_N/CT/C/N_k_9" => 0.238488,
+ "inter_PT_N/CT/C/N_k_1" => 2.7196,
+ "inter_PT_N/CT/C/N_k_10" => 0.1046,
+ "inter_PT_N/CT/C/N_k_11" => -0.046024,
+ "inter_PT_N/CT/C/N_k_2" => -0.824248,
+ "inter_PT_N/CT/C/N_k_3" => 6.04588,
+ "inter_PT_N/CT/C/N_k_4" => 2.004136,
+ "inter_PT_N/CT/C/N_k_5" => -0.0799144,
+ "inter_PT_N/CT/C/N_k_6" => -0.016736,
+ "inter_PT_N/CT/C/N_k_7" => -1.06692,
+ "inter_PT_N/CT/C/N_k_8" => 0.3138,
+ "inter_PT_N/CT/C/N_k_9" => 0.238488,
)
platform_runs = [("CPU", Array, false)]
@@ -455,8 +461,8 @@ end
push!(platform_runs, ("CPU parallel", Array, true))
end
test_runs = [
- ("Energy", test_energy_grad, 1e-8),
- ("Force" , test_forces_grad, 1e-8),
+ ("Energy", test_energy_grad, 1.0e-8),
+ ("Force", test_forces_grad, 1.0e-8),
]
params_to_test = (
"atom_N_ϵ",
@@ -485,8 +491,8 @@ end
end
frac_diff = abs(genz - gfd) / abs(gfd)
@info "$(rpad(test_name, 6)) - $(rpad(platform, 12)) - $(rpad(param, 21)) - " *
- "FD $gfd, Enzyme $genz, fractional difference $frac_diff"
- tol = (test_name == "Force" && param == "atom_N_ϵ" ? 2e-3 : test_tol)
+ "FD $gfd, Enzyme $genz, fractional difference $frac_diff"
+ tol = (test_name == "Force" && param == "atom_N_ϵ" ? 2.0e-3 : test_tol)
@test frac_diff < tol
end
end |
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vchuravy
approved these changes
Nov 3, 2025
giordano
reviewed
Nov 4, 2025
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This took a while as Molly was in a state of flux, but with the release of v0.23.0 integration tests can be added as discussed in #2528.
These tests pass on Julia 1.11 but error on 1.10 with a forward mode error that I can minimise next week. 1.12 also fails but I think that is being dealt with elsewhere.
Some of the tests are not at all minimal, but I am happy to be tagged to create minimal examples if they break. Having complex examples is beneficial as I do find that they break regularly.