Update Spglib interface

zhubonan · Dec 13, 2022 · 2e4071d · 2e4071d
1 parent 3e05108
commit 2e4071d
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Showing 3 changed files with 24 additions and 6 deletions.
diff --git a/src/spg.jl b/src/spg.jl
@@ -1,7 +1,7 @@
 import Base
 import Spglib
 import Spglib: get_symmetry, get_international, get_dataset
-import Spglib: standardize_cell, find_primitive, refine_cell, SpglibError
+import Spglib: standardize_cell, find_primitive, refine_cell, niggli_reduce, SpglibError
 
 struct SpglibConversionError <: Exception
     var::String
@@ -101,20 +101,30 @@ end
 @extend_scell_roundtrip standardize_cell
 @extend_scell_roundtrip find_primitive
 @extend_scell_roundtrip refine_cell
-@extend_scell_roundtrip niggli_reduce
+#@extend_scell_roundtrip niggli_reduce
 @extend_scell_roundtrip delaunay_reduce
 
 """
     niggli_reduce_cell(cell::Cell; wrap_pos=true)
 
 Apply niggli reduction to the lattice using Spglib 
 """
-function niggli_reduce_cell(cell::Cell; wrap_pos=true)
-    reduced_cellmat = Spglib.niggli_reduce(cellmat(cell))
+function niggli_reduce_cell(cell::Cell, symprec=1e-5; wrap_pos=true)
+    reduced_cellmat = Spglib.niggli_reduce(cellmat(cell), symprec)
     outcell = deepcopy(cell)
     set_cellmat!(outcell, reduced_cellmat, scale_positions=false)
     wrap_pos && wrap!(outcell)
     outcell
 end
 
-export get_symmetry, get_dataset, get_international, refine_cell, standardize_cell, find_primitive, niggli_reduce_cell
+"""
+    niggli_reduce(cell::Cell, symprec=1e-5;)
+
+Apply niggli reduction to the lattice using Spglib. 
+The positions are not wrapped.
+"""
+function Spglib.niggli_reduce(cell::Cell, symprec=1e-5)
+    niggli_reduce_cell(cell, symprec;wrap_pos=false)
+end
+
+export get_symmetry, get_dataset, get_international, refine_cell, standardize_cell, find_primitive, niggli_reduce_cell, niggli_reduce
diff --git a/test/test_cell.jl b/test/test_cell.jl
@@ -183,6 +183,14 @@ end
         @test all(get_scaled_positions(reduced_cell) .== get_scaled_positions(reduced_cell2))
     end
 
+    @testset "niggli_reduce" begin
+        testcell = Cell(Lattice(5.,5.,5.,30.,30.,30.), [1,2,3,3,3], pos)
+        testtmp = testcell
+        reduced_cell = niggli_reduce(testcell)
+        reduced_cell2 = niggli_reduce_cell(testcell;wrap_pos=false)
+        @test all(isapprox.(get_scaled_positions(reduced_cell), get_scaled_positions(reduced_cell2), atol=1e-7))
+    end
+
     @testset "roundtrip functions" begin
         testcell = Cell(Lattice(5.,5.,5.,30.,30.,30.), [1,2,3,3,3], pos)
         @test isa(standardize_cell(testcell), Cell)

diff --git a/test/test_composition.jl b/test/test_composition.jl
@@ -35,7 +35,7 @@ using CellBase: Composition, Cell, Lattice, formula
 
     c1 = Composition("C3O4")
     @test formula(c1) == :C3O4
-    show(c1)
+    show(devnull, c1)
 
     # Equality test
     @test Composition(formula(c1)) == c1