Symmetry number estimations not always accurate

[nateharms]

Symmetry numbers calculated using RMG's symmetry package tend to result in incorrect estimations of symmetry numbers. Below is an example of ethane which should have a symmetry number of 6. This issue arose when creating PR #48. Some investigation into alternate packages may remedy this.

In [1]: from autotst.species import Conformer                                                                                

In [2]: conf = Conformer("CC")                                                                                               

In [3]: conf.calculate_symmetry_number()                                                                                     
symmetry.py:253 write_input_file INFO Symmetry input file written to ./CC.symm
symmetry.py:219 parse INFO Point group: C1
Out[3]: 1

[whgreen]

Nate, I suggest you discuss with Mark Goldman. Bill

Sent from my phone.

On Nov 19, 2019, at 2:48 PM, Nate Harms notifications@github.com wrote:



Symmetry numbers calculated using RMG's symmetry package tend to result in incorrect estimations of symmetry numbers. Below is an example of ethane which should have a symmetry number of 6https://webbook.nist.gov/cgi/cbook.cgi?ID=C74840&Mask=800. This issue arose when creating PR #48https://github.com/ReactionMechanismGenerator/AutoTST/pull/48. Some investigation into alternate packages may remedy this.

In [1]: from autotst.species import Conformer

In [2]: conf = Conformer("CC")

In [3]: conf.calculate_symmetry_number() symmetry.py:253 write_input_file INFO Symmetry input file written to ./CC.symm symmetry.py:219 parse INFO Point group: C1 Out[3]: 1

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[nateharms]

Thanks for the recommendation, I just reached out to him.

[goldmanm]

RMG's symmetry algorithm includes both internal (from sigma bond rotation) and external symmetry (from rotation the whole molecule). Since the C-C bond in ethane can rotate a methyl group, it has an internal rotational symmetry of 3. Combined with the external symmetry you cite, the symmetry number RMG's symmetry algorithm should return is 18.

Running the current RMG package leads to:

>>> from rmgpy.species import Species
>>> s = Species().from_smiles('CC')
>>> s.get_symmetry_number()
18.0

This seems to work in RMG. I am not sure why it isn't working in AutoTST.

[nateharms]

Thanks, I'll switch it to this. We are currently doing this at the moment as a method of autotst.species.Conformer:

    def calculate_symmetry_number(self):
        from rmgpy.qm.symmetry import PointGroupCalculator
        from rmgpy.qm.qmdata import QMData

        atom_numbers = self.ase_molecule.get_atomic_numbers()
        coordinates = self.ase_molecule.get_positions()

        qmdata = QMData(
            groundStateDegeneracy=1,  # Only needed to check if valid QMData
            numberOfAtoms=len(atom_numbers),
            atomicNumbers=atom_numbers,
            atomCoords=(coordinates, str('angstrom')),
            energy=(0.0, str('kcal/mol'))  # Only needed to avoid error
        )
        settings = type(str(''), (), dict(symmetryPath=str(
            'symmetry'), scratchDirectory="."))()  # Creates anonymous class
        pgc = PointGroupCalculator(settings, self.smiles, qmdata)
        pg = pgc.calculate()
        #os.remove("{}.symm".format(self.smiles))

        if pg is not None:
            symmetry_number = pg.symmetry_number
        else:
            symmetry_number = 1

        return symmetry_number

This aspect comes from what was done in the first version of AutoTST, but it's looking like it's time for a change.