rattle rename (#10)

Author: tjjarvinen

docs/src/utilities.md

@@ -20,8 +20,8 @@ rotate_system!(sys, rot)
 rotate_system(sys, rot)
 
 # rattle positions
-rattle_system(sys, 0.1)
-rattle_system!(sys, 0.1u"Å")
+rattle_positions(sys, 0.1)
+rattle_positions!(sys, 0.1u"Å")
 ```
 
 **Add system together or repeat them**

src/AtomsSystems.jl

@@ -37,8 +37,8 @@ export fractional_coordinates_as_matrix
 export generic_system
 export inv_cell
 export position_as_matrix
-export rattle_system
-export rattle_system!
+export rattle_positions
+export rattle_positions!
 export rotate_system
 export rotate_system!
 export system_view

src/utils.jl

@@ -481,15 +481,15 @@ Base.repeat(sys::CellSystem{3}, n::Integer) = Base.repeat(sys, (n,n,n))
 ##
 
 """ 
-    rattle_system(sys, q)
-    rattle_system!(sys, q)
+    rattle_positions(sys, q)
+    rattle_positions!(sys, q)
 
 Rattle the positions of atoms in the system `sys` by a random vector of length `q`.
 The random vector is in random uniform direction and uniform length in the range `0 <= r < q`.
 
 If `q` is not a `Unitful.Length`, it is assumed to be in the unit of the positions in the system.
 """
-function rattle_system!(sys::AbstractSystem{D}, q) where{D}
+function rattle_positions!(sys::AbstractSystem{D}, q) where{D}
     r0 = position(sys, 1)
     r0 = r0 ./ ustrip( norm(r0) )
     r0 *= isa(q, Unitful.Length) ? ustrip(unit(r0[1]), q) : q
@@ -500,10 +500,10 @@ function rattle_system!(sys::AbstractSystem{D}, q) where{D}
     end
 end
 
-function rattle_system(sys::AbstractSystem, q)
+function rattle_positions(sys::AbstractSystem, q)
     tmp = deepcopy(sys)
-    rattle_system!(tmp, q)
+    rattle_positions!(tmp, q)
     return tmp  
 end
 
-@doc (@doc rattle_system!) rattle_system
+@doc (@doc rattle_positions!) rattle_positions

test/runtests.jl

@@ -439,7 +439,7 @@ include("Aqua.jl")
 
         # rattle
         sys = generic_system(ref.system)
-        sys2 = rattle_system(sys, 0.1u"Å")
+        sys2 = rattle_positions(sys, 0.1u"Å")
         @test all( diag( distance(sys, sys2) ) ) do x 
            0.0u"Å" < x < 0.1u"Å"
         end