Update distance_matrix interface

src/cell.jl

@@ -404,21 +404,52 @@ end
 Base.length(cell::Cell) = natoms(cell)
 Base.getindex(cell::Cell, i::Int) = Site(@view(cell.positions[:, i]), i, cell.symbols[i])
 
+
+function distance_matrix(cell::Cell;mic=true)
+    if mic == true
+        _distance_matrix_mic(cell)
+    else
+        _distance_matrix_no_mic(cell)
+    end
+end
+
+
+"""
+    _distance_matrix_no_mic(structure::Cell)
+
+Compute the distnace matrix without minimum image convention, e.g. the PBC is not respected.
+"""
+function _distance_matrix_no_mic(cell::Cell)
+    # Compute the naive pair-wise vectors
+    nn = nions(cell)
+    pos = sposarray(cell)
+    dmat = zeros(nn, nn)
+    for i in 1:nn
+        for j in i+1:nn
+            d = norm(pos[j] - pos[i])
+            dmat[i, j] = d
+            dmat[j, i] = d
+        end
+    end
+    dmat
+end
+
+
 """
-    distance_matrix(structure::Cell; mic=true)
+    _distance_matrix_mic(cell::Cell)
 
 Compute the distance matrix for the given structure, using the minimum image convention (or not).
 
 Note the returned matrix does not expand the cell. The distance matrix cannot be safety used for obtaining the minimum separations.
 For example, a structure with a single atom would be a distance matrix containing only zero.
 
 """
-function distance_matrix(structure::Cell)
+function _distance_matrix_mic(cell::Cell)
 
     # Compute the naive pair-wise vectors
-    nn = nions(structure)
+    nn = nions(cell)
     vecs = zeros(3, nn*nn)
-    pos = sposarray(structure)
+    pos = sposarray(cell)
     dmat = zeros(nn, nn)
     ivec = 0
     for i in 1:nn
@@ -428,7 +459,7 @@ function distance_matrix(structure::Cell)
         end
     end
     # Apply minimum image conventions
-    _, dmic = mic(lattice(structure), @view(vecs[:, 1:ivec]))
+    _, dmic = mic(lattice(cell), @view(vecs[:, 1:ivec]))
     # Unpack computed distances
     ivec = 0
     for i in 1:nn