update CellListMap usage

m3g · May 2, 2024 · 65657c7 · 65657c7
1 parent c6f3f34
commit 65657c7
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Showing 3 changed files with 10 additions and 10 deletions.
diff --git a/src/Packmol.jl b/src/Packmol.jl
@@ -4,7 +4,7 @@ using TestItems
 using Parameters
 using StaticArrays
 import CellListMap
-using CellListMap.PeriodicSystems
+using CellListMap
 using SPGBox
 import LinearAlgebra: norm
 import Statistics: mean

diff --git a/src/mono_atomic.jl b/src/mono_atomic.jl
@@ -1,4 +1,4 @@
-using CellListMap.PeriodicSystems
+using CellListMap
 using StaticArrays
 using SPGBox
 
@@ -11,7 +11,7 @@ mutable struct MonoAtomicFG{N,T}
 end
 
 # Custom copy, reset and reducer functions
-import CellListMap.PeriodicSystems: copy_output, reset_output!, reducer
+import CellListMap: copy_output, reset_output!, reducer
 copy_output(x::MonoAtomicFG) = MonoAtomicFG(x.f, copy(x.g), x.dmin)
 function reset_output!(output::MonoAtomicFG{N,T}) where {N,T}
     output.f = zero(T)
@@ -127,7 +127,7 @@ function pack_monoatomic!(
     cutoff = (volume / ncells)^(1/N)
     println("Using cell list cutoff: ", cutoff)
     println("Using packing tolerance: ", packing_tol)
-    system = PeriodicSystem(
+    system = ParticleSystem(
         xpositions=positions,
         unitcell=unitcell,
         cutoff=cutoff,
@@ -160,14 +160,14 @@ end
 @testitem "gradient" begin
     using StaticArrays
     using FiniteDifferences
-    using CellListMap.PeriodicSystems
+    using CellListMap
     import Packmol: MonoAtomicFG, fg!
 
     # Testing function that computes the function value with the definition 
     # of fg! above, to use finite-differences to check the gradient
     function f(x; dimension=2, unitcell=[1, 1], tol=0.1, parallel=false, return_grad=false)
         positions = [SVector{dimension}(x[i:i+dimension-1]) for i in 1:dimension:length(x)]
-        system = PeriodicSystem(
+        system = ParticleSystem(
             xpositions=positions,
             unitcell=unitcell,
             cutoff=tol,

diff --git a/src/rigid_body.jl b/src/rigid_body.jl
@@ -108,7 +108,7 @@ function random_move!(
     scale = 100.0
 
     # Generate random coordinates for the center of mass
-    cmin, cmax = PeriodicSystems.get_computing_box(system)
+    cmin, cmax = CellListMap.get_computing_box(system)
     newcm = SVector{3}(scale * (cmin[i] + rand(RNG, Float64) * (cmax[i] - cmin[i])) for i in 1:3)
 
     # Generate random rotation angles 
@@ -132,7 +132,7 @@ end
     using Packmol
     using StaticArrays
     using LinearAlgebra: norm
-    using CellListMap.PeriodicSystems
+    using CellListMap
     import Random
 
     function check_internal_distances(x, y)
@@ -151,7 +151,7 @@ end
     RNG = Random.Xoshiro()
     # Orthorhombic cell
     x = [-1.0 .+ 2 * rand(SVector{3,Float64}) for _ = 1:5]
-    system = PeriodicSystem(positions=x, cutoff=0.1, unitcell=SVector(10.0, 10.0, 10.0), output=0.0)
+    system = ParticleSystem(positions=x, cutoff=0.1, unitcell=SVector(10.0, 10.0, 10.0), output=0.0)
     @test check_internal_distances(x, Packmol.random_move!(copy(x), 1, system, RNG))
     system.xpositions .= [-9.0 .+ 2 * rand(SVector{3,Float64}) for _ = 1:5]
     @test check_internal_distances(x, Packmol.random_move!(copy(x), 1, system, RNG))
@@ -160,7 +160,7 @@ end
 
     # Triclinic cell
     x = [-1.0 .+ 2 * rand(SVector{3,Float64}) for _ = 1:5]
-    system = PeriodicSystem(positions=x, cutoff=0.1, unitcell=@SMatrix[10.0 5.0 0.0; 0.0 10.0 0.0; 0.0 0.0 10.0], output=0.0)
+    system = ParticleSystem(positions=x, cutoff=0.1, unitcell=@SMatrix[10.0 5.0 0.0; 0.0 10.0 0.0; 0.0 0.0 10.0], output=0.0)
     @test check_internal_distances(x, Packmol.random_move!(copy(x), 1, system, RNG))
     system.xpositions .= [-9.0 .+ 2 * rand(SVector{3,Float64}) for _ = 1:5]
     @test check_internal_distances(x, Packmol.random_move!(copy(x), 1, system, RNG))