Merge pull request #6 from ajjackson/test

Add a test for get_spacegroup, update for modern spglib

mctools/generic/get_spacegroup.py

@@ -1,41 +1,43 @@
 # -*- coding: utf-8 -*-
 
 import argparse
-import os
+from pathlib import Path
+from typing import Optional
 
 import ase.io
 import spglib
 
 
-def get_spacegroup(filename=False, format=False):
+def get_default_file() -> Path:
+    for candidate in ("geometry.in", "POSCAR", "castep.cell"):
+        if (structure_file := Path.cwd() / candidate).is_file():
+            return structure_file
 
-    if filename:
-        pass
-    elif os.path.isfile('geometry.in'):
-        filename = 'geometry.in'
-    elif os.path.isfile('POSCAR'):
-        filename = 'POSCAR'
-    else:
-        raise Exception('No input file!')
+    raise ValueError("Input file not specified, no default found.")
 
-    if format:
-        atoms = ase.io.read(filename, format=format)
-    else:
-        atoms = ase.io.read(filename)
+
+def get_spacegroup(filename: Optional[Path] = None,
+                   filetype: Optional[str] = None):
+
+    if filename is None:
+        filename = get_default_file()
+
+    atoms = ase.io.read(str(filename), format=filetype)
+    cell = (atoms.cell.array, atoms.get_scaled_positions(), atoms.numbers)
 
     print("| Threshold / Å |    Space group    |")
     print("|---------------|-------------------|")
 
     for threshold in (1e-5, 1e-4, 5e-4, 1e-3, 5e-3, 1e-2, 5e-2, 1e-1):
         print("|    {0:0.5f}    |  {1: <16} |".format(
-            threshold, spglib.get_spacegroup(atoms, symprec=threshold)))
+            threshold, spglib.get_spacegroup(cell, symprec=threshold)))
 
 
 def main():
     parser = argparse.ArgumentParser()
-    parser.add_argument('filename', action='store', default=False,
+    parser.add_argument("filename", type=Path, default=None, nargs="?",
                         help="Input structure file")
-    parser.add_argument('-f', '--format', action='store', default=False,
+    parser.add_argument("-f", "--filetype", type=str, default=None,
                         help="File format for ASE importer")
     args = parser.parse_args()
-    get_spacegroup(filename=args.filename, format=args.format)
+    get_spacegroup(filename=args.filename, filetype=args.filetype)

tests/test_get_spacegroup.py

@@ -0,0 +1,51 @@
+import textwrap
+
+import ase.build
+from numpy import logical_not
+from numpy.random import RandomState
+import pytest
+
+from mctools.generic.get_spacegroup import get_spacegroup
+
+
+FILENAME = "cu_rattled.extxyz"
+
+REF_TEXT = textwrap.dedent(
+    """\
+    | Threshold / Å |    Space group    |
+    |---------------|-------------------|
+    |    0.00001    |  P1 (1)           |
+    |    0.00010    |  P1 (1)           |
+    |    0.00050    |  Pm (6)           |
+    |    0.00100    |  Pm (6)           |
+    |    0.00500    |  Pmc2_1 (26)      |
+    |    0.01000    |  Fm-3m (225)      |
+    |    0.05000    |  Fm-3m (225)      |
+    |    0.10000    |  Fm-3m (225)      |
+    """
+)
+
+
+@pytest.fixture
+def symmetry_broken_cu() -> ase.Atoms:
+    atoms = ase.build.bulk("Cu", cubic=True) * (2, 2, 2)
+
+    rng = RandomState(seed=1)
+
+    # Break symmetry by up to 0.01 on a mirror plane
+    xy_plane = atoms.positions[:, 2] == 0.0
+    atoms.positions[xy_plane, :2] += 5e-3 - 1e-2 * rng.rand(xy_plane.sum(), 2)
+
+    # Break symmetry by up to 0.0001 elsewhere
+    off_plane = logical_not(xy_plane)
+    atoms.positions[off_plane] += 5e-5 - 1e-4 * rng.rand(off_plane.sum(), 3)
+
+    return atoms
+
+
+def test_get_spacegroup(symmetry_broken_cu, tmp_path, capsys) -> None:
+    symmetry_broken_cu.write(tmp_path / FILENAME)
+    get_spacegroup(filename=str(tmp_path / FILENAME))
+    captured = capsys.readouterr()
+
+    assert captured.out == REF_TEXT