change AtomsBase constructor arguments

JuliaMolSim · Mar 18, 2024 · 94104ed · 94104ed
1 parent 49b79b4
commit 94104ed
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Showing 3 changed files with 12 additions and 7 deletions.
diff --git a/docs/src/examples.md b/docs/src/examples.md
@@ -740,7 +740,7 @@ AtomsCalculators.forces(ab_sys, calc)
 ```
 We can also convert the AtomsBase.jl system to a Molly [`System`](@ref):
 ```julia
-System(ab_sys, u"kJ", u"kJ/Å")
+System(ab_sys; force_units=u"kJ/Å", energy_units=u"kJ")
 ```
 ```
 System with 5 atoms, boundary CubicBoundary{Quantity{Float64, 𝐋, Unitful.FreeUnits{(Å,), 𝐋, nothing}}}(Quantity{Float64, 𝐋, Unitful.FreeUnits{(Å,), 𝐋, nothing}}[1.54732 Å, 1.4654985 Å, 1.792895 Å])

diff --git a/src/types.jl b/src/types.jl
@@ -1095,14 +1095,17 @@ end
 Base.show(io::IO, ::MIME"text/plain", s::Union{System, ReplicaSystem}) = show(io, s)
 
 """
-    System(abstract_system)
+    System(abstract_system; force_units=u"kJ * mol^-1 * nm^-1", energy_units=u"kJ * mol^-1")
 
 Convert an AtomsBase `AbstractSystem` to a Molly `System`.
 
+`force_units` and `energy_units` should be set as appropriate.
 To add properties not present in the AtomsBase interface (e.g. pair potentials) use the
 convenience constructor `System(sys::System)`.
 """
-function System(sys::AbstractSystem{D}, energy_units, force_units) where D
+function System(sys::AbstractSystem{D};
+                force_units=u"kJ * mol^-1 * nm^-1",
+                energy_units=u"kJ * mol^-1") where D
     # Convert BC to Molly types
     bb = bounding_box(sys)
     bcs = AtomsBase.boundary_conditions(sys)
@@ -1175,8 +1178,8 @@ function System(sys::AbstractSystem{D}, energy_units, force_units) where D
         boundary=molly_boundary,
         velocities=vels,
         atoms_data=atoms_data,
-        energy_units=energy_units,
         force_units=force_units,
+        energy_units=energy_units,
     )
 end
 
@@ -1251,7 +1254,8 @@ AtomsCalculators.@generate_interface function AtomsCalculators.forces(
         n_threads::Integer=Threads.nthreads(),
         kwargs...,
     )
-    sys_nointers = System(abstract_sys, calc.energy_units, calc.force_units)
+    sys_nointers = System(abstract_sys; force_units=calc.force_units,
+                          energy_units=calc.energy_units)
     sys = System(
         sys_nointers;
         pairwise_inters=calc.pairwise_inters,
@@ -1271,7 +1275,8 @@ AtomsCalculators.@generate_interface function AtomsCalculators.potential_energy(
         n_threads::Integer=Threads.nthreads(),
         kwargs...,
     )
-    sys_nointers = System(abstract_sys, calc.energy_units, calc.force_units)
+    sys_nointers = System(abstract_sys; force_units=calc.force_units,
+                          energy_units=calc.energy_units)
     sys = System(
         sys_nointers;
         pairwise_inters=calc.pairwise_inters,

diff --git a/test/basic.jl b/test/basic.jl
@@ -487,7 +487,7 @@ end
                         [0.0    , 1.4654985, 0.0      ],
                         [0.0    , 0.0      , 1.7928950]]u"Å",
     )
-    molly_sys = System(ab_sys_2, u"kJ", u"kJ/Å")
+    molly_sys = System(ab_sys_2; energy_units=u"kJ", force_units=u"kJ/Å")
     test_approx_eq(ab_sys_2, molly_sys; common_only=true)
 end