adds module for straight chain alkanes

[ryanmrichard]

Is this pull request associated with an issue(s)?
No

Description
This adds a module which can generate arbitrary length straight chain alkanes.

TODOs
Get it to compile.

[ryanmrichard]

@jlheflin if you have time, see if you can finish this PR off. Otherwise I'll try to finish it on Monday. There's some bug causing an exception (run it under GDB and it'll show you exactly what line is causing the problem). The new module also needs a fleshed out description.

[jlheflin]

I tinkered at the issue all weekend, and it seems that there are multiple issues:

• Fixed up a string that was incorrect
• There's an issue with specifying 2 carbons to be generated when 'Bond-Based Fragmenter' even when set to 0 bonds

[2024-08-18 19:13:07.425] [Rank 0] [debug] The 8 atoms of the system were converted into 2 pseudoatoms.
[2024-08-18 19:13:07.425] [Rank 0] [debug] System has 7 bonds.
[2024-08-18 19:13:07.425] [Rank 0] [debug] Created a graph with 2 nodes and 1 edges.
[2024-08-18 19:13:07.425] [Rank 0] [debug] Created 2 fragments.
[2024-08-18 19:13:07.425] [Rank 0] [debug] Input fragment: 0,2,3,4
[2024-08-18 19:13:07.425] [Rank 0] [debug] Input fragment: 1,5,6,7
[2024-08-18 19:13:07.425] [Rank 0] [debug] Added 0 intersections.
[2024-08-18 19:13:07.425] [Rank 0] [debug] Input: 2 fragments and 7 bonds.
[2024-08-18 19:13:07.425] [Rank 0] [debug] Found 2 broken bonds.
[2024-08-18 19:13:07.425] [Rank 0] [debug] Added 2 caps.
ERROR:root:    Q: concern_mol-->returned_mol geometry matches ref_molFAILED
ERROR:root:     Q: concern_mol-->returned_mol geometry matches ref_mol: computed value (False) does not match (True) by difference ((n/a)).
Traceback (most recent call last):
  File "/home/jacob/Documents/Richard Group/GhostFragment/Hydrocarbon/Untitled.py", line 79, in <module>
    egy = mm.run_as(simde.TotalEnergy(), 'Fragment Based Method', chemist.ChemicalSystem(hc))
          ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/jacob/Applications/NWChemEx/install/friendzone/nwx2nwchem/__init__.py", line 36, in run_
    e = call_qcengine(pt, mol, 'nwchem', method=method, basis=basis)
        ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/jacob/Applications/NWChemEx/install/friendzone/nwx2qcengine/call_qcengine.py", line 69, in call_qcengine
    return results.return_result
           ^^^^^^^^^^^^^^^^^^^^^
AttributeError: 'FailedOperation' object has no attribute 'return_result'```

- As for the cxx test, I can not get gdb to tell me anything about the ctest information, it ends up just running.

[ryanmrichard]

Assuming this passes CI, it's r2g.

[jwaldrop107]

🚀 [bumpr] Bumped! New version:v1.1.0 Changes:v1.0.7...v1.1.0