scottsoren/pycoox_public

Data, analysis, and plotting scripts for articles

pyCOox_public

Data, analysis, and plotting scripts for articles

This repository is made for the curious reader of the two articles

• Soren B. Scott, Jakob Kinsgaard, Peter C. K. Vesborg, and Ib Chorkendorff. Tracking oxygen atoms in electrochemical CO oxidation – Part I: Oxygen exchange via CO2 hydration. Electrochimica Acta, 2021.
• Soren B. Scott, Jakob Kinsgaard, Peter C. K. Vesborg, and Ib Chorkendorff. Tracking oxygen atoms in electrochemical CO oxidation - Part II: Lattice oxygen reactivity in oxides of Pt and Ir. Electrochimica Acta, 2021.

It has all of the data analysis and plotting scripts. These scripts can serve as examples of electrochemistry - mass spectrometry (EC-MS) data analysis, especially for isotope-labeling experiments.

Setup

This version of the repository works with ixdat v0.2.5 (updated June 21, 2023).

For a version compatible with ixdat v0.1.x, see the ixdat_v0p1 branch

To run the scripts:

1. Make sure you have python 3.6+ installed with the numpy, scipy, and matplotlib packages as a minimum. I recommend Anaconda python.
2. Install the latest version of ixdat by typing in your terminal or Anaconda prompt:

$ pip install --upgrade ixdat

3. Clone or download this repository using git or github.
4. Copy all of the .pkl files from here into the folder called data.

5. Run the scripts with your favorite pythin IDE. I recommend spyder for quick plotting/analysis or PyCharm for development. A few are also available as .ipynb for use as tutorials with Jupyter Notebooks

The Scripts

The following folders contain a script and some files it produces. They are listed in an order logical for data flow. Scripts may depend on files produced by other scripts above them in this list (if so this will be clear in the comments of the script.)

paper_I_fig_S1

Supplementary Figure S1 of Tracking oxygen atoms in electrochemical CO oxidation – Part I: Oxygen exchange via CO2 hydration (Paper I) shows the derivation of the mass spec calibration (sensitivity factors), RHE calibration, and working distance calibration used throughout the articles.

The script paper_I_fig_S1.py works produces the three subfigures and functions as a tutorial on chip EC-MS calibration. The folder also contains the calibration file (produced by the script) that other scripts in this repository read.

paper_I_fig_2

Figure 2 of Paper I is a repeat of the classic Figure 3 of Trimarco et al, 2018 but in 18-O labeled electrolyte. Two experiments are ploted: cyclic voltammatry in He-saturated and CO-saturated electrolyte (a and b), and a CO stripping experiment (c and d).

The script makes the EC-MS plots of calibrated molecular fluxes together with electrohemical data both vs time (a and c) and vs potential (b and d). It shows that manipulation of these EC-MS data sets becomes easy and (dare I admit it) fun with ixdat.

paper_I_fig_3

Figure 3 of Paper I

See old/20G07_hydration_model/Pt_25C_CO_strip.py

paper_I_fig_4

Figure 4 of Paper I

See old/20G07_hydration_model/Pt_25C_CO_strip.py

paper_I_fig_S2

Supplementary Figure S2 of Paper I

See old/20G07_hydration_model/Pt_35C_CO_burst.py

paper_II_fig_S1

Figure S1 of Tracking oxygen atoms in electrochemical CO oxidation - Part II: Lattice oxygen reactivity in oxides of Pt and Ir.. (Paper II) is for iridium what Figure 2 of Paper I (itself a repeat of the classic Figure 3 of Trimarco et al, 2018) is for platinum: Cyclic voltammatry in He-saturated and CO-saturated 1.0 M HClO4 electrolyte, and a CO stripping experiment.

The script makes the EC-MS plots of calibrated molecular fluxes together with electrohemical data both vs time and vs potential. It shows that manipulation of these EC-MS data sets becomes easy and (dare I admit it) fun with ixdat.

Interesting, Ir behaves very similar to Pt with respect to hydrogen and carbon (HER and CO oxidation), but as the rest of the paper makes clear, very differently when it comes to oxygen (OER).

paper_II_fig_S2

Supplementary Figure S2 of Paper II shows the formation of PtOx and IrOx during constant anodic current on Pt and Ir, respectively, and their subsequent reduction to determine the thickness of the oxide layer.

It shows how to calculated the difference in charge passed in corresponding parts of two cyclic voltammograms using ixdat.

paper_II_fig_1

Figure 1 of Paper II shows the reaction of the electrochemical oxide layer in Pt(18)Ox with CO.

First, Figure 1a plots the raw data. Then, the data is calibrated and plottet again on two axes to highlight the isotopic effect. The amount of excess 18-O incorporated first in the O2 evolved during OER, and then in the CO2 evolved during CO oxidation as the surface is slowly reduced, is calculated.

This analysis is done semi-manually, but in the future will also be done with a special OERIsotopeExperiment class in ixdat.

paper_II_fig_S3

Supplementary Figure S3 of Paper II

See old/20E16_Pt/fig_Pt_extraction.py

paper_II_fig_S4

Supplementary Figure S4 of Paper II

See old/20E16_Pt/fig_Pt_extraction.py

paper_II_fig_S5

Supplementary Figure S5 of Paper II

See old/20E23_Ir/fig_Ir_extraction_sputtered_IrO2.py

paper_II_fig_S6

Supplementary Figure S6 of Paper II

See old/20E23_Ir/fig_Ir_extraction_sputtered_IrO2.py

paper_II_fig_3

Figure 3 of Paper II

See old/20E23_Ir/fig_Ir_extraction_sputtered_IrO2.py

paper_II_fig_S7

Supplementary Figure S7 of Paper II

See old/20E23_Ir/fig_Ir_extraction_1.py

paper_II_fig_S8

Supplementary Figure S8 of Paper II

See old/20E23_Ir/fig_Ir_extraction_butterfly_Ir.py

paper_I_fig_5

Supplementary Figure 5 of Paper I

See old/20G24_comparison/comparison_bar_plot.py

We're still working on it!

At present, not all of the scripts are reworked for use with ixdat, and instead still require the legacy EC_MS package. Analysis and plotting which has not been converted is in the folder old, in the location indicated above. The scripts in this folder are unfortunately not very well organized and readable. Please contact me if you need the script working for one of the figures before it is ready.

End

Enjoy, and if you find this useful, help us make ixdat even more useful for everyone: https://ixdat.readthedocs.io/en/latest/introduction.html

pycoox_public's Issues

Error related to "raw potential" series

Dear Scott

I received the following error report from a customer that attempted to re-run one of the publication scripts in this repository. As discussed on Slack, whether to fix this or not is basically up to a policy about whether to keep publication repositories up to date with new ixdat version or not.

The error is detailed in the attached document.

error tutorial script.docx

I seem to remember that there was some work done, which changed somehow the names of some of the series, so it might just be that. If you don't have the bandwidth, but can point me in the right direction I so a PR for it.