bug: fixed reading TSHS files

The ISC array offsets were read as C ordered arrays, but f2py returns
F ordered arrays.

Signed-off-by: Nick Papior <nickpapior@gmail.com>

Author: zerothi

NEWS

@@ -1,6 +1,9 @@
 0.8.X
 =====
 
+- Fix a bug when reading non-Gamma TSHS files, now the
+  supercell information is correct.
+
 - tbtncSileSiesta now distinguishes between:
     electronic_temperature [K]
   and

sisl/geometry.py

@@ -1779,24 +1779,36 @@ def osc2uc(self, orbs, uniq=False):
 
     def a2isc(self, a):
         """
-        Returns the super-cell index for a specific atom
+        Returns the super-cell index for a specific/list atom
 
-        Hence one can easily figure out the supercell
+        Returns a vector of 3 numbers with integers.
         """
         a = ensure_array(a)
         idx = np.where(a < self.na * np.arange(1, self.n_s + 1))[0][0]
         return self.sc.sc_off[idx, :]
 
+    def a2sc(self, a):
+        """
+        Returns the super-cell offset for a specific atom
+        """
+        return self.sc_offset(self.sc.sc_off[self.a2isc(a), :])
+
     def o2isc(self, o):
         """
         Returns the super-cell index for a specific orbital.
 
-        Hence one can easily figure out the supercell
+        Returns a vector of 3 numbers with integers.
         """
         o = ensure_array(o)
         idx = np.where(o < self.no * np.arange(1, self.n_s + 1))[0][0]
         return self.sc.sc_off[idx, :]
 
+    def o2sc(self, o):
+        """
+        Returns the super-cell offset for a specific orbital.
+        """
+        return self.sc_offset(self.sc.sc_off[self.o2isc(o), :])
+
     @classmethod
     def fromASE(cls, aseg):
         """ Returns geometry from an ASE object.

sisl/io/siesta/binaries.py

@@ -33,14 +33,14 @@ def read_sc(self):
 
         n_s = _siesta.read_tshs_sizes(self.file)[3]
         arr = _siesta.read_tshs_cell(self.file, n_s)
-        nsc = np.array(arr[0], np.int32)
-        cell = np.array(arr[1], np.float64)
+        nsc = np.array(arr[0].T, np.int32)
+        cell = np.array(arr[1].T, np.float64)
         cell.shape = (3, 3)
-        isc = np.array(arr[2], np.int32)
-        sc = np.array(arr[2], np.float64)
+        isc = np.array(arr[2].T, np.int32)
+        isc.shape = (-1, 3)
 
         SC = SuperCell(cell, nsc=nsc)
-        SC.sc_off = np.dot(sc.T, cell.T)
+        SC.sc_off = isc
         return SC
 
     def read_geom(self):
@@ -109,6 +109,7 @@ def read_es(self, **kwargs):
 
         H._data._D = np.empty([nnz, spin+1], np.float64)
         for i in range(spin):
+            # this is because of the F-ordering
             H._data._D[:, i] = dH[:, i]
         H._data._D[:, spin] = dS[:]
 

sisl/supercell.py

@@ -196,8 +196,7 @@ def rotate(self, angle, v, only='abc', radians=False):
         return self.__class__(cell, nsc=np.copy(self.nsc))
 
     def offset(self, isc=None):
-        """ Returns the supercell offset of the supercell index
-        """
+        """ Returns the supercell offset of the supercell index """
         if isc is None:
             return np.array([0, 0, 0], np.float64)
         return np.dot(isc, self.cell)