Explicitly specify water potential

[sudarsan-surendralal]

Could possible fix the failing integration notebooks!

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Pull Request Test Coverage Report for Build 1213865548

• 0 of 0 changed or added relevant lines in 0 files are covered.
• 2 unchanged lines in 1 file lost coverage.
• Overall coverage decreased (-0.01%) to 68.281%

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Files with Coverage Reduction	New Missed Lines	%
pyiron_atomistics/atomistics/master/murnaghan.py	2	71.77%

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Change from base Build 1212254905:	-0.01%
Covered Lines:	11082
Relevant Lines:	16230

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[sudarsan-surendralal]

It turns out that the integration tests fail because the TIP3P water potential, which is now explicitly specified in the notebook, is not available:

~/work/pyiron_atomistics/pyiron_atomistics/pyiron_atomistics/atomistics/job/potentials.py in find_by_name(self, potential_name)
     74         mask = (self._potential_df["Name"] == potential_name)
     75         if not mask.any():
---> 76             raise ValueError("Potential '{}' not found in database.".format(
     77                              potential_name))
     78         return self._potential_df[mask]
ValueError: Potential 'H2O_tip3p' not found in database.

I think the reason is that these potentials are not included in pyiron-resources. @jan-janssen, this also explains #349. When the water potentials are not found, pyiron tries to search for alternate potentials with H and O which are some of the REAXFF potentials which are developed for oxides and adsorbates that happend to have hydrogen and oxygen but not for water molecules. But to even use these potentials, explicit charge has to be specified for each of the atoms. Which means we need to reevaluate how we automatically assign potentials in pyiron!

[jan-janssen]

@sudarsan-surendralal Can not you define the water potential, just like you did in https://github.com/pyiron/pyiron_atomistics/blob/master/notebooks/water_MD.ipynb ?

[sudarsan-surendralal]

Thanks this should work now!