Fixes for native hamiltonian format

[tfrederiksen]

Closes #887

This PR produces the following test1.ham that looks complete and correct:

begin cell
  2.13000000 -1.22975607 0.00000000
  2.13000000 1.22975607 0.00000000
  0.00000000 0.00000000 20.00000000
end cell

supercell 3 3 1

begin atoms
  6 0.00000000 0.00000000 0.00000000
  6 1.42000000 0.00000000 0.00000000
end atoms

begin matrix 0 0 0
 0 1 -2.7
end matrix 0 0 0

begin matrix 1 0 0
 0 0 -0.2
 1 0 -2.7
 1 1 -0.2
end matrix 1 0 0

begin matrix -1 1 0
 0 0 -0.2
 0 1 -0.18
 1 1 -0.2
 1 0 -0.18
end matrix -1 1 0

begin matrix 0 1 0
 0 0 -0.2
 1 0 -2.7
 1 1 -0.2
end matrix 0 1 0

begin matrix 1 1 0
 1 0 -0.18
end matrix 1 1 0

[tfrederiksen]

One should perhaps take this opportunity to also include some tests....

[zerothi]

Thanks for this, I can see why this fixes the issue, I will have to amend this to ensure it works for all sc_off cases (in fact, users can specify their own ordering of supercells, so I'll have to check that (shouldn't be difficult!

[tfrederiksen]

Thanks for this, I can see why this fixes the issue, I will have to amend this to ensure it works for all sc_off cases (in fact, users can specify their own ordering of supercells, so I'll have to check that (shouldn't be difficult!

Yes, indeed this algorithm assumes a specific ordering.

[codecov]

Codecov Report

Attention: Patch coverage is 84.61538% with 14 lines in your changes missing coverage. Please review.

Project coverage is 86.82%. Comparing base (39aab90) to head (989830e).
Report is 4 commits behind head on main.

Files with missing lines	Patch %	Lines
src/sisl/io/ham.py	81.57%	14 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #888      +/-   ##
==========================================
- Coverage   86.87%   86.82%   -0.06%     
==========================================
  Files         405      405              
  Lines       53231    53294      +63     
==========================================
+ Hits        46247    46272      +25     
- Misses       6984     7022      +38     

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[zerothi]

@tfrederiksen I have fixed lots of small problems. With added tests.
Please have a look, once the tests pass, I'll merge!

Thanks for the fixes and report!

[zerothi]

Thanks!