added --remove to sgeom

Signed-off-by: Nick Papior <[email protected]>

Author: zerothi

CHANGELOG.md

@@ -8,6 +8,7 @@ we hit release version 1.0.0.
 ## [0.14.0] - YYYY-MM-DD
 
 ### Added
+- added --remove to sgeom for removing single atoms
 - added a EllipticalCylinder as a new shape
 - added basis-enthalpy to the stdoutSiestaSile.read_energy routine
 - added `read_trajectory` to read cell vectors, atomic positions, and forces from VASP OUTCAR

src/sisl/geometry.py

@@ -4758,8 +4758,17 @@ def __call__(self, parser, ns, value, option_string=None):
                 # Get atomic indices
                 rng = lstranges(strmap(int, value))
                 ns._geometry = ns._geometry.sub(rng)
-        p.add_argument(*opts('--sub', '-s'), metavar='RNG',
+        p.add_argument('--sub', metavar='RNG',
                        action=ReduceSub,
+                       help='Retains specified atoms, can be complex ranges.')
+
+        class ReduceRemove(argparse.Action):
+            def __call__(self, parser, ns, value, option_string=None):
+                # Get atomic indices
+                rng = lstranges(strmap(int, value))
+                ns._geometry = ns._geometry.remove(rng)
+        p.add_argument('--remove', metavar='RNG',
+                       action=ReduceRemove,
                        help='Removes specified atoms, can be complex ranges.')
 
         # Swaps atoms

src/sisl/tests/test_sgeom.py

@@ -112,11 +112,18 @@ def test_repeat2(self, setup):
                     t = setup.sg_g(argv=argv)
                     assert np.allclose(cell, t.lattice.cell)
 
-    def test_sub1(self, setup):
+    def test_sub(self, setup):
         for a, l in [('0', 1), ('0,1', 2), ('0-1', 2)]:
             g = setup.sg_g(argv=['--sub', a])
             assert len(g) == l
 
+    def test_remove(self, setup):
+        geom = setup.g.tile(2, 0).tile(2, 1)
+        N = len(geom)
+        for a, l in [('0', 1), ('0,1', 2), ('0-1', 2)]:
+            g = setup.sg_g(geometry=geom.copy(), argv=['--remove', a])
+            assert len(g) == N - l
+
     def test_rotation1(self, setup):
         print(setup.g.cell)
         rot = setup.sg_g(argv='--rotate 180 z'.split())