Skip to content

Chore/compat arianna v0.2 #68

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Open
romainljsimon wants to merge 5 commits into
base: main
Choose a base branch
from
Open

Chore/compat arianna v0.2 #68

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
5 commits
Select commit Hold shift + click to select a range
ad4d5c8
Add macro to callback functions
romainljsimon Feb 10, 2026
1311e86
Add new StoreCallbacks output to parse from toml files
romainljsimon Feb 10, 2026
3a80df3
Change all input/launch files to comply with new version
romainljsimon Feb 10, 2026
0cb40ac
New Arianna version
romainljsimon Feb 10, 2026
4dd7c5b
Specify systems of callbacks
romainljsimon Feb 10, 2026
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
2 changes: 1 addition & 1 deletion Project.toml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -18,7 +18,7 @@ Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"

[compat]
Aqua = "0.8"
Arianna = "0.1"
Arianna = "0.2"
Comonicon = "1.0"
ComponentArrays = "0.15"
ConcreteStructs = "0.2"
Expand Down
40 changes: 29 additions & 11 deletions examples/lj-mixture/run-validation.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -116,7 +116,12 @@ def create_params(parameters: dict, path_to_params: str) -> None:

[[simulation.output]]
algorithm = "StoreCallbacks"
callbacks = ["energy", "acceptance"]
callbacks = ["energy"]
scheduler_params = {{linear_interval = 100}}

[[simulation.output]]
algorithm = "StoreAcceptance"
dependencies = ["Metropolis"]
scheduler_params = {{linear_interval = 100}}

[[simulation.output]]
Expand All @@ -128,12 +133,12 @@ def create_params(parameters: dict, path_to_params: str) -> None:


def run_simulations(output_path: str) -> None:
df = pd.read_csv("reference-data.csv")
df_ref = pd.read_csv("reference-data.csv")

path_to_config = "config.exyz"
path_to_params = "params.toml"
data = []
for i, row in df.iterrows():
for i, row in df_ref.iterrows():
workdir = f"./tmp/{i}"
os.makedirs(workdir, exist_ok=True)

Expand Down Expand Up @@ -168,17 +173,31 @@ def run_simulations(output_path: str) -> None:
)

# Post-process the energies
energies = pd.read_csv(f"{workdir}/energy.dat", sep="\\s+", names=["i", "e"])[
energies = pd.read_csv(f"{workdir}/chains/1/energy.dat", sep="\\s+", names=["i", "e"])[
"e"
]
# Remove the first half as equilibration, just to be sure
energies = energies[int(len(energies) / 2) :]

moves = {
1: "displacement",
2: "swap",
}

df_acceptance_rates = pd.read_csv(
f"{workdir}/acceptance.dat", sep="\\s+", names=["i", "move", "swap"]
)
displacement_acceptance = float(df_acceptance_rates["move"].iloc[-1][1:-2])
swap_acceptance = float(df_acceptance_rates["swap"].iloc[-1][:-1])
dfs = []

for move_id, move_name in moves.items():
path = f"{workdir}/moves/{move_id}/acceptance.dat"
df = pd.read_csv(path, sep=r"\s+", names=["i", move_name])
dfs.append(df)

# Merge all on column "i"
df_acceptance_rates = dfs[0]
for df in dfs[1:]:
df_acceptance_rates = df_acceptance_rates.merge(df, on="i")

displacement_acceptance = float(df_acceptance_rates["displacement"].iloc[-1])
swap_acceptance = float(df_acceptance_rates["swap"].iloc[-1])

# Compute long-range corrections from the cutoff
# Formula from Gromacs https://manual.gromacs.org/current/reference-manual/functions/long-range-vdw.html
Expand Down Expand Up @@ -207,8 +226,7 @@ def run_simulations(output_path: str) -> None:
"acceptance_rate_swap": swap_acceptance,
}
)

df.merge(pd.DataFrame(data)).to_csv(output_path)
df_ref.merge(pd.DataFrame(data)).to_csv(output_path)


def plot_results(path_to_energies: str) -> None:
Expand Down
7 changes: 6 additions & 1 deletion examples/movie/params.toml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -20,7 +20,12 @@ parameters = {sigma = 0.05}

[[simulation.output]]
algorithm = "StoreCallbacks"
callbacks = ["energy", "acceptance"]
callbacks = ["energy"]
scheduler_params = {linear_interval = 500}

[[simulation.output]]
algorithm = "StoreAcceptance"
dependencies = ["Metropolis"]
scheduler_params = {linear_interval = 500}

[[simulation.output]]
Expand Down
7 changes: 6 additions & 1 deletion examples/ortho-terphenyl/2-equilibrate-at-different-temperatures/params-template.toml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -69,7 +69,12 @@ policy = "DoubleUniform"

[[simulation.output]]
algorithm = "StoreCallbacks"
callbacks = ["energy", "acceptance"]
callbacks = ["energy"]
scheduler_params = {linear_interval = 1000}

[[simulation.output]]
algorithm = "StoreAcceptance"
dependencies = ["Metropolis"]
scheduler_params = {linear_interval = 1000}

[[simulation.output]]
Expand Down
2 changes: 1 addition & 1 deletion examples/ortho-terphenyl/3-run-production/params-template.toml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -69,7 +69,7 @@ policy = "DoubleUniform"

[[simulation.output]]
algorithm = "StoreCallbacks"
callbacks = ["energy", "acceptance"]
callbacks = ["energy"]
scheduler_params = {linear_interval = 1000}

[[simulation.output]]
Expand Down
2 changes: 1 addition & 1 deletion examples/ortho-terphenyl/4-compute-correlation-functions/compute-observables.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -20,7 +20,7 @@ def compute_fskt() -> pd.DataFrame:
df_list = []
for T in temperatures:
print(f"T = {T}")
traj = Trajectory(f"../3-run-production/{T}/trajectories/1/trajectory.xyz")
traj = Trajectory(f"../3-run-production/{T}/chains/1/trajectory.xyz")

cf = pp.SelfIntermediateScatteringFast(
traj,
Expand Down
12 changes: 10 additions & 2 deletions src/ParticlesMC.jl
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -112,7 +112,7 @@ function compute_energy_particle(system::Particles, ids::AbstractVector)
end


export callback_energy
export energy
#export nearest_image_distance
export Model, GeneralKG, JBB, BHHP, SoftSpheres, KobAndersen, Trimer
export NeighbourList, LinkedList, CellList, EmptyList, VerletList
Expand Down Expand Up @@ -249,6 +249,7 @@ ParticlesMC implemented in Comonicon.
for output in sim["output"]
alg = output["algorithm"]
scheduler_params = output["scheduler_params"]
dependencies = get(output, "dependencies", nothing)
callbacks = get(output, "callbacks", [])
fmt = get(output, "fmt", "XYZ")
interval = scheduler_params["linear_interval"]
Expand All @@ -259,12 +260,19 @@ ParticlesMC implemented in Comonicon.
sched = build_schedule(steps, burn, interval)
end
if alg == "StoreCallbacks"
callbacks = map(c -> eval(Meta.parse("callback_$c")), callbacks)
callbacks = map(c -> eval(Meta.parse("$c")), callbacks)
algorithm = (
algorithm = eval(Meta.parse(alg)),
callbacks = callbacks,
scheduler = sched,
)
elseif alg == "StoreAcceptance"
dependencies = map(d -> eval(Meta.parse("$d")), dependencies)
algorithm = (
algorithm = eval(Meta.parse(alg)),
dependencies = dependencies,
scheduler = sched,
)
elseif alg == "StoreTrajectories" || alg == "StoreLastFrames"
algorithm = (
algorithm = eval(Meta.parse(alg)),
Expand Down
4 changes: 4 additions & 0 deletions src/molecules.jl
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -240,3 +240,7 @@ function compute_chain_correlation(system::Molecules)
end
return sum(correlation_array.^2)
end

Arianna.@callback function chain_correlation(system::Molecules)
return compute_chain_correlation(system)
end
8 changes: 2 additions & 6 deletions src/utils.jl
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -48,12 +48,8 @@ function SpeciesList(species)
return SpeciesList(ids, heads)
end

function callback_energy(simulation)
return mean(system.energy[1] / length(system) for system in simulation.chains)
end

function callback_chain_correlation(simulation)
return mean(compute_chain_correlation(system) for system in simulation.chains)
Arianna.@callback function energy(system::Particles)
return system.energy[1]
Copy link
Contributor

@V-Francois V-Francois Feb 13, 2026

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Is this the total energy, or the energy per particle? The previous callback was per particle.

Ideally, there should be a comment to say explicitly which one it is.

Copy link
Contributor

@V-Francois V-Francois Feb 13, 2026

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

I just ran a test, and it looks like now the energy is the total energy, instead of the energy/particles.
Is this intended?

end

function volume_sphere(r, d::Int)
Expand Down
10 changes: 6 additions & 4 deletions test/gerhard_energy_distribution.jl
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -29,7 +29,6 @@ steps = 1000
burn = 0
block = [0, 10]
sampletimes = build_schedule(steps, burn, block)
callbacks = (callback_energy, callback_acceptance)

# NO SWAPS
pswap = 0.0
Expand All @@ -41,7 +40,8 @@ pool = (

algorithm_list = (
(algorithm=Metropolis, pool=pool, seed=seed, parallel=false, sweepstep=system.N),
(algorithm=StoreCallbacks, callbacks=(callback_energy, callback_acceptance), scheduler=sampletimes),
(algorithm=StoreCallbacks, callbacks=(energy,), scheduler=sampletimes),
(algorithm=StoreAcceptance, dependencies=(Metropolis,), scheduler=sampletimes),
(algorithm=StoreTrajectories, scheduler=sampletimes, fmt=EXYZ()),
(algorithm=StoreLastFrames, scheduler=[steps], fmt=EXYZ()),
(algorithm=PrintTimeSteps, scheduler=build_schedule(steps, burn, steps ÷ 10)),
Expand Down Expand Up @@ -72,7 +72,8 @@ pool = (
)
algorithm_list = (
(algorithm=Metropolis, pool=pool, seed=seed, parallel=false, sweepstep=system.N),
(algorithm=StoreCallbacks, callbacks=(callback_energy, callback_acceptance), scheduler=sampletimes),
(algorithm=StoreCallbacks, callbacks=(energy,), scheduler=sampletimes),
(algorithm=StoreAcceptance, dependencies=(Metropolis,), scheduler=sampletimes),
(algorithm=StoreTrajectories, scheduler=sampletimes, fmt=LAMMPS()),
(algorithm=StoreLastFrames, scheduler=[steps], fmt=EXYZ()),
(algorithm=PrintTimeSteps, scheduler=build_schedule(steps, burn, steps ÷ 10)),
Expand Down Expand Up @@ -105,7 +106,8 @@ pool = (
)
algorithm_list = (
(algorithm=Metropolis, pool=pool, seed=seed, parallel=false, sweepstep=system.N),
(algorithm=StoreCallbacks, callbacks=(callback_energy, callback_acceptance), scheduler=sampletimes),
(algorithm=StoreCallbacks, callbacks=(energy,), scheduler=sampletimes),
(algorithm=StoreAcceptance, dependencies=(Metropolis,), scheduler=sampletimes),
(algorithm=StoreTrajectories, scheduler=sampletimes, fmt=LAMMPS()),
(algorithm=StoreLastFrames, scheduler=[steps], fmt=LAMMPS()),
(algorithm=PrintTimeSteps, scheduler=build_schedule(steps, burn, steps ÷ 10)),
Expand Down
4 changes: 2 additions & 2 deletions test/molecules_test.jl
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -43,8 +43,8 @@ callbacks = (callback_energy, callback_acceptance)
path = "data/test/particles/Molecules/T$temperature/N$N/M$M/seed$seed"
algorithm_list = (
(algorithm=Metropolis, pool=pool, seed=seed, parallel=false, sweepstep=N),
(algorithm=StoreCallbacks, callbacks=(callback_energy, callback_acceptance), scheduler=sampletimes),
(algorithm=StoreTrajectories, scheduler=sampletimes, fmt=XYZ()),
(algorithm=StoreCallbacks, callbacks=(energy,), scheduler=sampletimes),
(algorithm=StoreAcceptance, dependencies=(Metropolis,), scheduler=sampletimes), (algorithm=StoreTrajectories, scheduler=sampletimes, fmt=XYZ()),
(algorithm=StoreLastFrames, scheduler=[steps], fmt=XYZ()),
(algorithm=PrintTimeSteps, scheduler=build_schedule(steps, burn, steps ÷ 10), fmt=XYZ())
)
Expand Down
7 changes: 6 additions & 1 deletion test/params.toml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -20,9 +20,14 @@ parameters = {sigma = 0.05}

[[simulation.output]]
algorithm = "StoreCallbacks"
callbacks = ["energy", "acceptance"]
callbacks = ["energy"]
scheduler_params = {linear_interval = 100}

[[simulation.output]]
algorithm = "StoreAcceptance"
dependencies = ["Metropolis"]
scheduler_params = {linear_interval = 500}

[[simulation.output]]
algorithm = "StoreTrajectories"
scheduler_params = {linear_interval = 100}
Expand Down
25 changes: 13 additions & 12 deletions test/runtests.jl
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -46,7 +46,6 @@ end
burn = 0
block = [0, 1, 2, 4, 8]
sampletimes = build_schedule(steps, burn, block)
callbacks = (callback_energy, callback_acceptance)

# NO SWAPS
pswap = 0.0
Expand All @@ -57,7 +56,8 @@ end
)
algorithm_list = (
(algorithm=Metropolis, pool=pool, seed=seed, parallel=false, sweepstep=system_el.N),
(algorithm=StoreCallbacks, callbacks=(callback_energy, callback_acceptance), scheduler=sampletimes),
(algorithm=StoreCallbacks, callbacks=(energy,), scheduler=sampletimes),
(algorithm=StoreAcceptance, dependencies=(Metropolis,), scheduler=sampletimes),
(algorithm=StoreTrajectories, scheduler=sampletimes, fmt=EXYZ()),
(algorithm=StoreLastFrames, scheduler=[steps], fmt=LAMMPS()),
(algorithm=PrintTimeSteps, scheduler=build_schedule(steps, burn, steps ÷ 10)),
Expand All @@ -81,9 +81,9 @@ end
run!(simulation)

## Read energy data and compare
path_energy_el = joinpath(path_el, "energy.dat")
path_energy_ll = joinpath(path_ll, "energy.dat")
path_energy_vl = joinpath(path_vl, "energy.dat")
path_energy_el = joinpath(path_el, "chains/1/energy.dat")
path_energy_ll = joinpath(path_ll, "chains/1/energy.dat")
path_energy_vl = joinpath(path_vl, "chains/1/energy.dat")
energy_el= readdlm(path_energy_el)[:, 2]
energy_ll = readdlm(path_energy_ll)[:, 2]
energy_vl = readdlm(path_energy_vl)[:, 2]
Expand All @@ -103,7 +103,8 @@ end
)
algorithm_list = (
(algorithm=Metropolis, pool=pool, seed=seed, parallel=false, sweepstep=system_el.N),
(algorithm=StoreCallbacks, callbacks=(callback_energy, callback_acceptance), scheduler=sampletimes, fmt=XYZ()),
(algorithm=StoreCallbacks, callbacks=(energy,), scheduler=sampletimes),
(algorithm=StoreAcceptance, dependencies=(Metropolis,), scheduler=sampletimes),
(algorithm=StoreTrajectories, scheduler=sampletimes, fmt=XYZ()),
(algorithm=StoreLastFrames, scheduler=[steps], fmt=XYZ()),
(algorithm=PrintTimeSteps, scheduler=build_schedule(steps, burn, steps ÷ 10), fmt=XYZ()),
Expand All @@ -121,8 +122,8 @@ end
run!(simulation)

## Read energy data and compare
path_energy_el = joinpath(path_el, "energy.dat")
path_energy_ll = joinpath(path_ll, "energy.dat")
path_energy_el = joinpath(path_el, "chains/1/energy.dat")
path_energy_ll = joinpath(path_ll, "chains/1/energy.dat")
energy_el= readdlm(path_energy_el)[:, 2]
energy_ll = readdlm(path_energy_ll)[:, 2]
@test isapprox(energy_el, energy_ll, atol=1e-6)
Expand Down Expand Up @@ -154,7 +155,6 @@ end
burn = 0
block = [0, 1, 2, 4, 8]
sampletimes = build_schedule(steps, burn, block)
callbacks = (callback_energy, callback_acceptance)

# NO SWAPS
pswap = 0.0
Expand All @@ -165,7 +165,8 @@ end
)
algorithm_list = (
(algorithm=Metropolis, pool=pool, seed=seed, parallel=false, sweepstep=system_el.N),
(algorithm=StoreCallbacks, callbacks=(callback_energy, callback_acceptance), scheduler=sampletimes),
(algorithm=StoreCallbacks, callbacks=(energy,), scheduler=sampletimes),
(algorithm=StoreAcceptance, dependencies=(Metropolis,), scheduler=sampletimes),
(algorithm=StoreTrajectories, scheduler=sampletimes, fmt=EXYZ()),
(algorithm=StoreLastFrames, scheduler=[steps], fmt=EXYZ()),
(algorithm=PrintTimeSteps, scheduler=build_schedule(steps, burn, steps ÷ 10)),
Expand All @@ -183,8 +184,8 @@ end
run!(simulation)

## Read energy data and compare
path_energy_el = joinpath(path_el, "energy.dat")
path_energy_ll = joinpath(path_ll, "energy.dat")
path_energy_el = joinpath(path_el, "chains/1/energy.dat")
path_energy_ll = joinpath(path_ll, "chains/1/energy.dat")
energy_el= readdlm(path_energy_el)[:, 2]
energy_ll = readdlm(path_energy_ll)[:, 2]
@test isapprox(energy_el, energy_ll, atol=1e-6)
Expand Down
4 changes: 2 additions & 2 deletions test/simple_test.jl
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -49,8 +49,8 @@ callbacks = (callback_energy, callback_acceptance)

algorithm_list = (
(algorithm=Metropolis, pool=pool, seed=seed, parallel=false, sweepstep=length(system_ll)),
(algorithm=StoreCallbacks, callbacks=(callback_energy, callback_acceptance), scheduler=sampletimes),
(algorithm=StoreTrajectories, scheduler=sampletimes, fmt=XYZ()),
(algorithm=StoreCallbacks, callbacks=(energy,), scheduler=sampletimes),
(algorithm=StoreAcceptance, dependencies=(Metropolis,), scheduler=sampletimes), (algorithm=StoreTrajectories, scheduler=sampletimes, fmt=XYZ()),
(algorithm=StoreLastFrames, scheduler=[steps], fmt=XYZ()),
(algorithm=PrintTimeSteps, scheduler=build_schedule(steps, burn, steps ÷ 10)),
)
Expand Down