[Bug]: Seemingly unnecessary upper triangular transformation in `NVT` MD

[Andrew-S-Rosen]

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Version

main

Which OS(es) are you using?

• MacOS
• Windows
• Linux

What happened?

matcalc/src/matcalc/_md.py

Lines 199 to 208 in aea727d

	if ensemble in ("nvt", "nvt_nose_hoover"):
	self._upper_triangular_cell(atoms)
	return NoseHooverChainNVT(
	atoms,
	timestep_fs,
	tdamp=taut,
	temperature_K=self.temperature,
	logfile=self.logfile,
	loginterval=self.loginterval,
	)

When calling NoseHooverChainNVT, an upper triangular cell is made. But I do not see anything in the ASE documentation requiring this. Indeed, the matcalc documentation itself acknowledges this is for the NPT implementation.

matcalc/src/matcalc/_md.py

Lines 320 to 327 in aea727d

	def _upper_triangular_cell(self, atoms: Atoms) -> None:
	"""
	Transforms the cell of the given atoms object to an upper triangular form if it is not already,
	as required by the Nose-Hoover NPT implementation.
	Parameters:
	atoms (Atoms): ASE atoms object.
	"""

I believe this should be modified.

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