New scheduler building logic ; Arianna.jl dependency to v0.2.1 (#79)

This PR is using `Arianna.jl` new dependency which introduces a new way
to schedule outputs in simulation.

Created the `build_sched(scheduler_params, steps, burn)` helper function
to eliminate duplicated [if/else](url) structures block for observables
and outputs.
The new scheduler is called in TOML by the keyword : `multi_origins`. 
e.g : `scheduler_params = {multi_origins = {tmax = x , tw = y , N = z}}`

Author: cyfraysse

src/ParticlesMC.jl

@@ -112,6 +112,24 @@ function compute_energy_particle(system::Particles, ids::AbstractVector)
     return map(i -> compute_energy_particle(system, i), ids)
 end
 
+"""
+    Helper for building scheduler based on TOML schedul parameters
+"""
+
+function parse_schedule(scheduler_params, steps, burn)
+    if haskey(scheduler_params, "multi_origins")
+        tw   = scheduler_params["multi_origins"]["tw"]
+        N    = scheduler_params["multi_origins"]["N"]
+        return build_schedule(steps, MultiOrigins(tw, N), burn=burn)
+    elseif haskey(scheduler_params, "log_base")
+        interval = get(scheduler_params, "linear_interval", 1)
+        block    = build_schedule(interval, 0, 2.0)
+        return build_schedule(steps, burn, block)
+    else
+        interval = get(scheduler_params, "linear_interval", 1)
+        return build_schedule(steps, burn, interval)
+    end
+end
 
 export energy
 #export nearest_image_distance
@@ -256,13 +274,7 @@ ParticlesMC implemented in Comonicon.
     for observable in get(sim, "observable", [])
         alg = observable["algorithm"]
         scheduler_params = observable["scheduler_params"]
-        interval = get(scheduler_params, "linear_interval", 1)
-        if "log_base" in keys(scheduler_params)
-            block = build_schedule(interval, 0, 2.0)
-            sched = build_schedule(steps, burn, block)
-        else
-            sched = build_schedule(steps, burn, interval)
-        end
+        sched = parse_schedule(scheduler_params, steps, burn)
         if alg == "ComputeRotation"
             parameters = get(observable, "parameters", Dict())
             theta_T    = Float64.(get(parameters, "theta_T", [π/4]))
@@ -284,13 +296,7 @@ ParticlesMC implemented in Comonicon.
         dependencies = get(output, "dependencies", nothing)
         callbacks = get(output, "callbacks", [])
         fmt = get(output, "fmt", "XYZ")
-        interval = scheduler_params["linear_interval"]
-        if "log_base" in keys(scheduler_params)
-            block = build_schedule(interval, 0, 2.0)
-            sched = build_schedule(steps, burn, block)
-        else
-            sched = build_schedule(steps, burn, interval)
-        end
+        sched = parse_schedule(scheduler_params, steps, burn)
         if alg == "StoreCallbacks"
             callbacks = map(c -> eval(Meta.parse("$c")), callbacks)
             algorithm = (

src/rotation.jl

@@ -3,7 +3,7 @@
 # Compute on-the-fly rotation tracker.
 # Two algorithms :
 # 1. ComputeRotation : updates system.Φ (simulation.observable)
-# 2. StoreΦTrajectory : writes system.Φ to disk
+# 2. StorePhiTrajectory : writes system.Φ to disk
 # system.Φ[k][m] = rotation vector for molecule m under theta_T[k]
 
 using LinearAlgebra
@@ -126,7 +126,7 @@ end
 
 function Arianna.make_step!(simulation::Simulation, algorithm::ComputeRotation)
 
-    collect(eachindex(simulation.chains) |> Transducers.Map(c -> begin
+    tcollect(eachindex(simulation.chains) |> Transducers.Map(c -> begin
         system = simulation.chains[c]
         state  = algorithm.states[c]
         N_mol  = system.Nmol