enh: finalized TF suggestions and clarified intents

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

Author: zerothi

sisl/io/vasp/car.py

@@ -23,7 +23,7 @@ def _setup(self, *args, **kwargs):
         self._scale = 1.
 
     @sile_fh_open()
-    def write_geometry(self, geometry, dynamic=None, sort=False):
+    def write_geometry(self, geometry, dynamic=True, group_species=False):
         r""" Writes the geometry to the contained file
 
         Parameters
@@ -34,9 +34,9 @@ def write_geometry(self, geometry, dynamic=None, sort=False):
            define which atoms are dynamic in the VASP run (default is True,
            which means all atoms are dynamic).
            If None, the resulting file will not contain any dynamic flags
-        sort : bool, optional
+        group_species: bool, optional
            before writing `geometry` first re-order species to
-           have species in consecutive blocks (see `geometry_sort`)
+           have species in consecutive blocks (see `geometry_group`)
 
         Examples
         --------
@@ -48,13 +48,13 @@ def write_geometry(self, geometry, dynamic=None, sort=False):
 
         See Also
         --------
-        geometry_sort: method used to sort atoms in geometry
+        geometry_group: method used to group atoms together according to their species
         """
         # Check that we can write to the file
         sile_raise_write(self)
 
-        if sort:
-            geometry, idx = self.geometry_sort(geometry, ret_index=True)
+        if group_species:
+            geometry, idx = self.geometry_group(geometry, ret_index=True)
         else:
             # small hack to allow dynamic
             idx = _a.arangei(len(geometry))

sisl/io/vasp/sile.py

@@ -8,7 +8,7 @@
 __all__ = ['SileVASP', 'SileCDFVASP', 'SileBinVASP']
 
 
-def _geometry_sort(geometry, ret_index=False):
+def _geometry_group(geometry, ret_index=False):
     r""" Order atoms in geometry according to species such that all of one specie is consecutive
 
     When creating VASP input files (`poscarSileVASP` for instance) the equivalent
@@ -51,12 +51,12 @@ def _geometry_sort(geometry, ret_index=False):
 
 
 class SileVASP(Sile):
-    geometry_sort = staticmethod(_geometry_sort)
+    geometry_group = staticmethod(_geometry_group)
 
 
 class SileCDFVASP(SileCDF):
-    geometry_sort = staticmethod(_geometry_sort)
+    geometry_group = staticmethod(_geometry_group)
 
 
 class SileBinVASP(SileBin):
-    geometry_sort = staticmethod(_geometry_sort)
+    geometry_group = staticmethod(_geometry_group)

sisl/io/vasp/tests/test_car.py

@@ -27,7 +27,7 @@ def test_geometry_car_mixed(sisl_tmp):
     assert carSileVASP(f).read_geometry() == geom
 
 
-def test_geometry_car_sort(sisl_tmp):
+def test_geometry_car_group(sisl_tmp):
     f = sisl_tmp('test_sort.POSCAR', _dir)
 
     atoms = [Atom[1],
@@ -40,10 +40,10 @@ def test_geometry_car_sort(sisl_tmp):
     xyz = np.random.rand(len(atoms), 3)
     geom = Geometry(xyz, atoms, 100)
 
-    geom.write(carSileVASP(f, 'w'), sort=True)
+    geom.write(carSileVASP(f, 'w'), group_species=True)
 
     assert carSileVASP(f).read_geometry() != geom
-    geom = carSileVASP(f).geometry_sort(geom)
+    geom = carSileVASP(f).geometry_group(geom)
     assert carSileVASP(f).read_geometry() == geom
 
 
@@ -69,7 +69,7 @@ def test_geometry_car_dynamic(sisl_tmp):
     read = carSileVASP(f)
 
     # no dynamic (direct geometry)
-    geom.write(carSileVASP(f, 'w'))
+    geom.write(carSileVASP(f, 'w'), dynamic=None)
     g, dyn = read.read_geometry(ret_dynamic=True)
     assert dyn is None