[Pourbaix diagram] Reference of the ion energies

Materials Project
1

Hello,

I have a question on the Pourbaix diagram app. When I load a specific Pourbaix diagram, and try to look at the reference of each ion energies by clicking on the book icon, it just shows “citation ion-0”. Is there a way to find the reference information of each of the ion energies that were used for building the Pourbaix diagrams in MP?

Many Thanks,

KyuJung

2

Hi @KyuJung_Jun, thanks for pointing out this glitch. We are in the process of developing an updated site and will make sure the new Pourbaix app shows references correctly.

We have recently migrated all the ion reference data to portal.mpcontribs.org. If you go to that site, click “Browse” and then log in (you may have to make a new account), you can open the “Aqueous Ion Reference Data” project to see all the data in tabular form, with links to the associated references.

The majority of the ion reference energies are taken from the NIST NBS Tables, .pdfs of which are available via the links on the MPContribs project or by googling.

I hope that helps!

3

Hi @rkingsbury

I used to query ion data through old pymatgen MPRester using the method mentioned in this thread: Aqueous ion reference data for Pourbaix diagrams

Is new ion reference data different from new one? If so, how should I query them?

Thank you,

Zhuohan

4

Hi Zhuohan,

The aqueous ion reference data (MPContribs landing page) can be retrieved programmatically using the mpcontribs-client library. I recommend using an appropriate query to reduce the number of results and also restrict the returned fields. The list of filters is available here. Below some example code.

from mpcontribs.client import Client

client = Client(project="ion_ref_data")

# example queries - filters can be combined in same `query`
query = {"formula__in": ["Li[+]", "N2(aq)"]}  # filter by formula
query = {"data__RefSolid__contains": "B2O3"} # filter RefSolid by substring
query = {"data__ΔGᶠ__gt": 100} # filter by Gibbs Free Energy of Formation
fields = ["id", "formula", "data.ΔGᶠ"]  # fields to return

client.query_contributions(query=query, fields=fields, paginate=True)

HTH,
Patrick

5

As an alternative, if you have the new API client installed you can use the get_ion_reference_data() to download the entire data set (it’s the same data you get via the method in @tschaume post above).

make sure you have installed and updated mp-api and mpcontribs-client, and then:

from mp_api.client import MPRester

mpr = MPRester("<your api key>")
ion_data = mpr.get_ion_reference_data()

You can also use mpr.get_ion_reference_data_for_chemsys() to get data for a specific chemical system.

2 Likes
6

Dear sir,

I was trying to make the local copy of all ion reference data in my computer, and I have tried your code. However, it turns error

File /opt/conda/lib/python3.11/site-packages/mp_api/client/mprester.py:903, in MPRester.get_ion_reference_data(self)
874 @lru_cache
875 def get_ion_reference_data(self) → list[dict]:
876 “”“Download aqueous ion reference data used in the construction of Pourbaix diagrams.
877
878 Use this method to examine the ion reference data and to add additional
(…)
901 compounds and aqueous species, Wiley, New York (1978)'}}
902 “””
→ 903 return self.contribs.query_contributions(
904 query={“project”: “ion_ref_data”},
905 fields=[“identifier”, “formula”, “data”],
906 paginate=True,
907 ).get(“data”)

AttributeError: ‘NoneType’ object has no attribute ‘query_contributions’

What can I do to solve it?

Any help will be appreciated.

7

Please install the python client for the MPContribs API:

pip install mpcontribs-client

8

Dear Sir,

Much thanks for your help. I have successfully download all the ion data. However, I found a little problem,. The delta G of LiOH(aq) in the ion database I download is about -451.85 kJ/molkJ/mol, equal to the-4.683eV.However, when I tried to plot the pourbaix, by mpr.get_pourbaix_entries, I got PourbaixEntry(Li1 O1 H1 with energy=-2.6052, npH=-1.0, nPhi=-1.0, nH2O=1.0, entry_id=‘ion-1’), Such energy can’t be consistent, such things also happened in the Li+, the energy of the ion database is shown to be -293.71Kj/mol, equal to -3.04 eV, I got PourbaixEntry(Li1 O1 H1 with energy=-2.6052, npH=-1.0, nPhi=-1.0, nH2O=1.0, entry_id=‘ion-1’). Is there any detail I ignores?

Any help will be appreciated!!

9

tagging @rkingsbury here - he might be able to help.

10

Dear Sir,

Much thanks for your help, @rkingsbury,can you help me with this problem?

Any help will be appreciated.

11

Hi @Chengyi_Zhang , you should not expect those energies to match. The ion data contains three things:

  1. The experimental free energy of formation of the aqueous species, e.g. (LiOH(aq))
  2. The identity of the referencee solid for that aqueous species (e.g. Li2O)
  3. The experimental free energy of formation of the reference solid

The Pourbaix Diagram does not show you formation free energies, but rather the aqueous phase free energies of different reactions / reaction products.

12

Dear Sir,

Much thanks for your reply. It should be the problem of the convex hull.

Thank you so much for helping.