mnt: ensured delta files need not have diagonal components

Should make delta files smaller and just needs
a small test in tbtrans.

CHANGELOG.md

@@ -18,6 +18,11 @@ we hit release version 1.0.0.
  as the only argument.
 
 ### Fixed
+- delta-files (netCDF) would always have diagonal components,
+ this has now been removed since it only needs the elements with
+ values
+- Siesta sparse matrices could in some cases set wrong diagonal
+ components
 - orbital quantum numbers from HSX file was wrong in v1, #462
 - RealSpaceSI for right semi-infinite directions, #475
 - tbtrans files now have a separate entry in the documentation

sisl/io/siesta/_help.py

@@ -45,9 +45,17 @@ def _csr_from_siesta(geom, csr):
  _csr_from_sc_off(geom, _siesta.siesta_sc_off(*geom.nsc).T, csr)
 
 
-def _csr_to_siesta(geom, csr):
- """ Internal routine to convert *any* SparseCSR matrix from sisl nsc to siesta nsc """
- _ensure_diagonal(csr)
+def _csr_to_siesta(geom, csr, diag=True):
+ """ Internal routine to convert *any* SparseCSR matrix from sisl nsc to siesta nsc
+
+ Parameters
+ ----------
+ ...
+ diag: bool, optional
+ whether the csr matrix will be ensured diagonal as well
+ """
+ if diag:
+ _ensure_diagonal(csr)
  _csr_to_sc_off(geom, _siesta.siesta_sc_off(*geom.nsc).T, csr)
 
 

sisl/io/tbtrans/delta.py

@@ -280,7 +280,7 @@ def write_delta(self, delta, **kwargs):
  raise SileError(f"{self!s}.write_overlap cannot write a zero element sparse matrix!")
 
  # convert to siesta thing and store
- _csr_to_siesta(delta.geometry, csr)
+ _csr_to_siesta(delta.geometry, csr, diag=False)
  # delta should always write sorted matrices
  csr.finalize(sort=True)
  _mat_spin_convert(csr, delta.spin)