Function (& its test) that calculates electrochemical stability, updated version.

[apalizha]

Add a function that calculates electrochemical stability of bulk composition under reaction conditions. It is created as a stand-alone function because each chemical reaction has its own reaction condition, so it's better to have this function as a helper function.

[ktran9891]

Just found this again. I remember @samueldy having some suggestions. What's the status on this PR?

[apalizha]

Made changes with all suggestions and this was the updated PR. Was waiting on it to be merged.

On Thu, Jun 11, 2020, 3:25 PM Kevin Tran notifications@github.com wrote:

Just found this again. I remember @samueldy https://github.com/samueldy having some suggestions. What's the status on this PR?

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[apalizha]

@ktran9891 Think you could merge this when you get a chance? Thanks!

[ktran9891]

Half of the unit tests across the board are failing now for various reasons. Might have something to do with pymatgen version control issues, test caching issues, and/or something else entirely. You said that all your tests are passing? Can you confirm that the test caches are updated and also confirm what image you are using when testing?

[ktran9891]

Failing a test on my end:

gasdb_test.py::test_get_electrochemical_stability FAILED                                                                           [100%]
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> traceback >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>

    def test_get_electrochemical_stability():
        # at pH=0, V=0.9
        expected_stabilities = {'mp-126': 0.884,  # Pt
                                'mp-81': 0.0}    # Au
        for mpid, expected_stability in expected_stabilities.items():
            stability = get_electrochemical_stability(mpid, 0, 0.9)
>           assert math.isclose(stability, expected_stability, rel_tol=1e-6)
E           assert False
E            +  where False = <built-in function isclose>(0.861, 0.884, rel_tol=1e-06)
E            +    where <built-in function isclose> = math.isclose

gasdb_test.py:518: AssertionError
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> entering PDB >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>

>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> PDB post_mortem (IO-capturing turned off) >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
> /home/GASpy/gaspy/tests/gasdb_test.py(518)test_get_electrochemical_stability()
-> assert math.isclose(stability, expected_stability, rel_tol=1e-6)
(Pdb) l
513         # at pH=0, V=0.9
514         expected_stabilities = {'mp-126': 0.884,  # Pt
515                                 'mp-81': 0.0}    # Au
516         for mpid, expected_stability in expected_stabilities.items():
517             stability = get_electrochemical_stability(mpid, 0, 0.9)
518  ->         assert math.isclose(stability, expected_stability, rel_tol=1e-6)
[EOF]
(Pdb) stability
0.861
(Pdb) expected_stability
0.884

[apalizha]

Yeah saw that too. Might be related to atoms_operator_test -->pmg stuff. Nothing was failing when I tested it. I'll look at it again this weekend altogether.

On Thu, Jun 25, 2020, 3:23 PM Kevin Tran notifications@github.com wrote:

Failing a test on my end:

gasdb_test.py::test_get_electrochemical_stability FAILED [100%]

traceback >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>

def test_get_electrochemical_stability():
    # at pH=0, V=0.9
    expected_stabilities = {'mp-126': 0.884,  # Pt
                            'mp-81': 0.0}    # Au
    for mpid, expected_stability in expected_stabilities.items():
        stability = get_electrochemical_stability(mpid, 0, 0.9)

      assert math.isclose(stability, expected_stability, rel_tol=1e-6)

E assert False E + where False = (0.861, 0.884, rel_tol=1e-06) E + where = math.isclose

gasdb_test.py:518: AssertionError

entering PDB >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>

PDB post_mortem (IO-capturing turned off) >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /home/GASpy/gaspy/tests/gasdb_test.py(518)test_get_electrochemical_stability() -> assert math.isclose(stability, expected_stability, rel_tol=1e-6) (Pdb) l 513 # at pH=0, V=0.9 514 expected_stabilities = {'mp-126': 0.884, # Pt 515 'mp-81': 0.0} # Au 516 for mpid, expected_stability in expected_stabilities.items(): 517 stability = get_electrochemical_stability(mpid, 0, 0.9) 518 -> assert math.isclose(stability, expected_stability, rel_tol=1e-6) [EOF] (Pdb) stability 0.861 (Pdb) expected_stability 0.884

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[apalizha]

ehh... messed up couple things, had to discard some stuff, will open another PR.