fixed last method renames to lattice

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

sisl/io/gulp/got.py

@@ -79,7 +79,7 @@ def read_lattice(self, key=None, **kwargs):
             raise ValueError(
                 'SileGULP tries to lookup the Lattice vectors '
                  'using key "' + self._keys['lattice'] + '". \n'
-                 'Use ".set_supercell_key(...)" to search for different name.\n'
+                 'Use ".set_lattice_key(...)" to search for different name.\n'
                  'This could not be found found in file: "' + self.file + '".')
 
         # skip 1 line
@@ -107,7 +107,7 @@ def read_geometry(self, **kwargs):
             if not f and ki == 0:
                 raise ValueError('SileGULP tries to lookup the Lattice vectors '
                                  'using key "' + self._keys['lattice'] + '". \n'
-                                 'Use ".set_supercell_key(...)" to search for different name.\n'
+                                 'Use ".set_lattice_key(...)" to search for different name.\n'
                                  'This could not be found found in file: "' + self.file + '".')
             elif f and ki == 0:
                 # supercell

sisl/io/openmx/omx.py

@@ -256,10 +256,10 @@ def read_basis(self, *args, **kwargs):
         Parameters
         ----------
         output: bool, optional
-            whether to read supercell from output files (default to read from
+            whether to read lattice from output files (default to read from
             the input file).
         order: {'dat', 'omx'}
-            the order of which to try and read the supercell.
+            the order of which to try and read the lattice
             If `order` is present `output` is disregarded.
         """
         order = kwargs.pop('order', ['dat', 'omx'])
@@ -339,31 +339,31 @@ def decompose_basis(l):
         return atom
 
     def read_lattice(self, output=False, *args, **kwargs):
-        """ Reads supercell
+        """ Reads lattice
 
         One can limit the tried files to only one file by passing
         only a single file ending.
 
         Parameters
         ----------
         output: bool, optional
-            whether to read supercell from output files (default to read from
+            whether to read lattice from output files (default to read from
             the input file).
         order: {'dat', 'omx'}
-            the order of which to try and read the supercell.
+            the order of which to try and read the lattice.
             If `order` is present `output` is disregarded.
         """
         if output:
             order = kwargs.pop('order', ['dat', 'omx'])
         else:
             order = kwargs.pop('order', ['dat', 'omx'])
         for f in order:
-            v = getattr(self, '_r_supercell_{}'.format(f.lower()))(*args, **kwargs)
+            v = getattr(self, '_r_lattice_{}'.format(f.lower()))(*args, **kwargs)
             if v is not None:
                 return v
         return None
 
-    def _r_supercell_omx(self, *args, **kwargs):
+    def _r_lattice_omx(self, *args, **kwargs):
         """ Returns `Lattice` object from the omx file """
         conv = self.get('Atoms.UnitVectors.Unit', default='Ang')
         if conv.upper() == 'AU':
@@ -384,7 +384,7 @@ def _r_supercell_omx(self, *args, **kwargs):
 
         return Lattice(cell)
 
-    _r_supercell_dat = _r_supercell_omx
+    _r_lattice_dat = _r_lattice_omx
 
     def read_geometry(self, output=False, *args, **kwargs):
         """ Returns Geometry object

sisl/io/siesta/fdf.py

@@ -644,24 +644,24 @@ def read_lattice_nsc(self, *args, **kwargs):
         """
         order = _listify_str(kwargs.pop("order", ["nc", "ORB_INDX"]))
         for f in order:
-            v = getattr(self, f"_r_supercell_nsc_{f.lower()}")(*args, **kwargs)
+            v = getattr(self, f"_r_lattice_nsc_{f.lower()}")(*args, **kwargs)
             if v is not None:
                 _track(self.read_lattice_nsc, f"found file {f}")
                 return v
         warn("number of supercells could not be read from output files. Assuming molecule cell "
              "(no supercell connections)")
         return _a.onesi(3)
 
-    def _r_supercell_nsc_nc(self, *args, **kwargs):
+    def _r_lattice_nsc_nc(self, *args, **kwargs):
         f = self.dir_file(self.get("SystemLabel", default="siesta") + ".nc")
-        _track_file(self._r_supercell_nsc_nc, f)
+        _track_file(self._r_lattice_nsc_nc, f)
         if f.is_file():
             return ncSileSiesta(f).read_lattice_nsc()
         return None
 
-    def _r_supercell_nsc_orb_indx(self, *args, **kwargs):
+    def _r_lattice_nsc_orb_indx(self, *args, **kwargs):
         f = self.dir_file(self.get("SystemLabel", default="siesta") + ".ORB_INDX")
-        _track_file(self._r_supercell_nsc_orb_indx, f)
+        _track_file(self._r_lattice_nsc_orb_indx, f)
         if f.is_file():
             return orbindxSileSiesta(f).read_lattice_nsc()
         return None
@@ -695,13 +695,13 @@ def read_lattice(self, output=False, *args, **kwargs):
         else:
             order = _listify_str(kwargs.pop("order", ["fdf"]))
         for f in order:
-            v = getattr(self, f"_r_supercell_{f.lower()}")(*args, **kwargs)
+            v = getattr(self, f"_r_lattice_{f.lower()}")(*args, **kwargs)
             if v is not None:
                 _track(self.read_lattice, f"found file {f}")
                 return v
         return None
 
-    def _r_supercell_fdf(self, *args, **kwargs):
+    def _r_lattice_fdf(self, *args, **kwargs):
         """ Returns `Lattice` object from the FDF file """
         s = self.get("LatticeConstant", unit="Ang")
         if s is None:
@@ -731,47 +731,47 @@ def _r_supercell_fdf(self, *args, **kwargs):
 
         return Lattice(cell, nsc=nsc)
 
-    def _r_supercell_nc(self):
+    def _r_lattice_nc(self):
         # Read supercell from <>.nc file
         f = self.dir_file(self.get("SystemLabel", default="siesta") + ".nc")
-        _track_file(self._r_supercell_nc, f)
+        _track_file(self._r_lattice_nc, f)
         if f.is_file():
             return ncSileSiesta(f).read_lattice()
         return None
 
-    def _r_supercell_xv(self, *args, **kwargs):
+    def _r_lattice_xv(self, *args, **kwargs):
         """ Returns `Lattice` object from the XV file """
         f = self.dir_file(self.get("SystemLabel", default="siesta") + ".XV")
-        _track_file(self._r_supercell_xv, f)
+        _track_file(self._r_lattice_xv, f)
         if f.is_file():
             nsc = self.read_lattice_nsc()
             lattice = xvSileSiesta(f).read_lattice()
             lattice.set_nsc(nsc)
             return lattice
         return None
 
-    def _r_supercell_struct(self, *args, **kwargs):
+    def _r_lattice_struct(self, *args, **kwargs):
         """ Returns `Lattice` object from the STRUCT files """
         for end in ["STRUCT_NEXT_ITER", "STRUCT_OUT", "STRUCT_IN"]:
             f = self.dir_file(self.get("SystemLabel", default="siesta") + f".{end}")
-            _track_file(self._r_supercell_struct, f)
+            _track_file(self._r_lattice_struct, f)
             if f.is_file():
                 nsc = self.read_lattice_nsc()
                 lattice = structSileSiesta(f).read_lattice()
                 lattice.set_nsc(nsc)
                 return lattice
         return None
 
-    def _r_supercell_tshs(self, *args, **kwargs):
+    def _r_lattice_tshs(self, *args, **kwargs):
         f = self.dir_file(self.get("SystemLabel", default="siesta") + ".TSHS")
-        _track_file(self._r_supercell_tshs, f)
+        _track_file(self._r_lattice_tshs, f)
         if f.is_file():
             return tshsSileSiesta(f).read_lattice()
         return None
 
-    def _r_supercell_onlys(self, *args, **kwargs):
+    def _r_lattice_onlys(self, *args, **kwargs):
         f = self.dir_file(self.get("SystemLabel", default="siesta") + ".onlyS")
-        _track_file(self._r_supercell_onlys, f)
+        _track_file(self._r_lattice_onlys, f)
         if f.is_file():
             return onlysSileSiesta(f).read_lattice()
         return None

sisl/io/siesta/out.py

@@ -116,13 +116,13 @@ def read_basis(self):
 
         return [Atom(**atoms[tag]) for tag in order]
 
-    def _r_supercell_outcell(self):
+    def _r_lattice_outcell(self):
         """ Wrapper for reading the unit-cell from the outcoor block """
 
         # Read until outcell is found
         found, line = self.step_to("outcell: Unit cell vectors")
         if not found:
-            raise ValueError(f"{self.__class__.__name__}._r_supercell_outcell did not find outcell key")
+            raise ValueError(f"{self.__class__.__name__}._r_lattice_outcell did not find outcell key")
 
         Ang = 'Ang' in line
 
@@ -168,7 +168,7 @@ def _r_geometry_outcoor(self, line, atoms=None):
         # Retrieve the unit-cell (but do not skip file-descriptor position)
         # This is because the current unit-cell is not always written.
         pos = self.fh.tell()
-        cell = self._r_supercell_outcell()
+        cell = self._r_lattice_outcell()
         if is_final and self.fh.tell() < pos:
             # we have wrapped around the file
             self.fh.seek(pos, os.SEEK_SET)
@@ -207,7 +207,7 @@ def _r_geometry_atomic(self, line, atoms=None):
         # Retrieve the unit-cell (but do not skip file-descriptor position)
         # This is because the current unit-cell is not always written.
         pos = self.fh.tell()
-        cell = self._r_supercell_outcell()
+        cell = self._r_lattice_outcell()
         self.fh.seek(pos, os.SEEK_SET)
 
         # Convert xyz

sisl/lattice.py

@@ -22,7 +22,7 @@
 from .shape.prism4 import Cuboid
 from .quaternion import Quaternion
 from ._math_small import cross3, dot3
-from ._supercell import cell_invert, cell_reciprocal
+from ._lattice import cell_invert, cell_reciprocal
 
 
 __all__ = ["Lattice", "SuperCell", "LatticeChild"]
@@ -1042,7 +1042,7 @@ def angle(self, i, j, rad=False):
 
     @staticmethod
     def read(sile, *args, **kwargs):
-        """ Reads the supercell from the `Sile` using ``Sile.read_supercell``
+        """ Reads the supercell from the `Sile` using ``Sile.read_lattice``
 
         Parameters
         ----------
@@ -1054,7 +1054,7 @@ def read(sile, *args, **kwargs):
         # have been imported previously
         from sisl.io import get_sile, BaseSile
         if isinstance(sile, BaseSile):
-            return sile.read_supercell(*args, **kwargs)
+            return sile.read_lattice(*args, **kwargs)
         else:
             with get_sile(sile, mode='r') as fh:
                 return fh.read_lattice(*args, **kwargs)

sisl/viz/plots/geometry.py

@@ -20,7 +20,7 @@
 )
 from ..plotutils import values_to_colors
 from sisl._dispatcher import AbstractDispatch
-from sisl._supercell import cell_invert
+from sisl._lattice import cell_invert
 
 
 class BoundGeometry(AbstractDispatch):

sisl/viz/plots/grid.py

@@ -8,7 +8,7 @@
 
 import sisl
 from sisl.messages import warn
-from sisl._supercell import cell_invert
+from sisl._lattice import cell_invert
 from sisl import _array as _a
 from ..plot import Plot, entry_point
 from ..input_fields import (