Spectro-Electrochemistry

Spectro-Electrochemsitry (S-EC) can refer to (i) a broad range of in-situ techniques hyphenating electrochemistry to some kind of spectrometry (see e.g. Lozeman et al, 2020 ) or (ii) more specifically, the combination of electrochemistry and visible-light spectroscopy. In ixdat, we use the latter meaning.

S-EC data is organized in a SpectroECMeasurement, which inherits from ECMeasurement (see Electrochemistry) and uses a SpectrumSeries (see Spectra) for managing the 2-D data array formed by the sequential spectra (see Figure). To this, the class adds delta optical density (dOD) calculations. Methods such as calc_dOD, get_dOD_spectrum, and track_wavelength take as an optional argument a specification of the time/potential/spectrum index to use as the reference for optical density calculation. If not provided, the object’s reference_spectrum is used, which itself can be set by the set_reference_spectrum method.

The data structure is the same whether the experiment is done as a slow potential scan with adsorption vs potential in mind, or as a potential jump or release with time-resolved behavior in mind.

Plots of S-EC are made by the SECPlotter. These are either heat plots (plot_measurement and plot_vs_potential) or coplotted cross-sections (plot_waterfall and plot_wavelengths). Exporting SEC data results in a master file with the EC data and any tracked wavelengths and two auxiliary files with (i) the spectrum series and (ii) the reference spectrum.

A jupyter notebook tutorial for S-EC is available.

Fitting of spectroelectrochemistry data is not yet supported in ixdat.

The spectroelectrochemistry module

class ixdat.techniques.spectroelectrochemistry.SpectroECMeasurement(*args, **kwargs)

calc_dOD(V_ref=None, t_ref=None, index_ref=None)

Calculate the optical density with respect to a reference

Provide at most one of V_ref, t_ref, or index. If none are provided the default reference spectrum (self.reference_spectrum) will be used.

Parameters:

• V_ref (float) – The potential at which to get the reference spectrum
• t_ref (float) – The time at which to get the reference spectrum
• index_ref (int) – The index of the reference spectrum

Return Field: the delta optical density spanning time and wavelength

exporter

The default plotter for SpectroECMeasurement is SECExporter

get_dOD_spectrum(V=None, t=None, index=None, V_ref=None, t_ref=None, index_ref=None)

Return the delta optical density Spectrum given a point and reference point.

Provide exactly one of V, t, and index, and at most one of V_ref, t_ref, and index_ref. For V and V_ref to work, the potential in the measurement must be monotonically increasing.

Parameters:

• V (float) – The potential at which to get the spectrum.
• t (float) – The time at which to get the spectrum
• index (int) – The index of the spectrum
• V_ref (float) – The potential at which to get the reference spectrum
• t_ref (float) – The time at which to get the reference spectrum
• index_ref (int) – The index of the reference spectrum

Return Spectrum: The dOD spectrum. The data is (spectrum.x, spectrum.y)

get_spectrum(V=None, t=None, index=None, name=None)

Return the Spectrum at a given potential V, time t, or index

Exactly one of V, t, and index should be given. If V (t) is out of the range of self.v (self.t), then first or last spectrum will be returned.

Parameters:

• V (float) – The potential at which to get the spectrum. Measurement.v must be monotonically increasing for this to work.
• t (float) – The time at which to get the spectrum
• index (int) – The index of the spectrum
• name (str) – Optional. name to give the new spectrum if interpolated

Return Spectrum: The spectrum. The data is (spectrum.x, spectrum.y)

plotter

The default plotter for SpectroECMeasurement is SECPlotter

reference_spectrum

The spectrum which will by default be used to calculate dOD

set_reference_spectrum(spectrum=None, t_ref=None, V_ref=None)

Set the spectrum used as the reference when calculating dOD.

Parameters:

• spectrum (Spectrum or str) – If a Spectrum is given, it becomes the reference spectrum. The string “reference” can be given to make the reference spectrum become (via the reference_spectrum property) one that the measurement was loaded with (evt. for definition of wavelengths).
• t_ref (float) – The time (with respect to self.tstamp) to use as the reference spectrum
• V_ref (float) – The potential to use as the reference spectrum. This will only work if the potential is monotonically increasing.

spectra

The Field that is the spectra of the SEC Measurement

spectrum_series

The SpectrumSeries that is the spectra of the SEC Measurement

track_wavelength(wl, width=10, V_ref=None, t_ref=None, index_ref=None)

Return and cache a ValueSeries for the dOD for a specific wavelength.

The cacheing adds wl_str to the SECMeasurement’s data series, where

wl_str = “w” + int(wl) This is dOD. The raw is also added as wl_str + “_raw”.

So, to get the raw counts for a specific wavelength, call this function and

then use __getitem__, as in: sec_meas[wl_str + “_raw”]

If V_ref, t_ref, or index_ref are provided, they specify what to reference dOD

to. Otherwise, dOD is referenced to the SECMeasurement’s reference_spectrum.

Parameters:

• wl (float) – The wavelength to track in [nm]
• width (float) – The width around wl to average. For example, if wl=400 and width = 20, the spectra will be averaged between 390 and 410 nm to get the values. Defaults to 10. To interpolate at the exact wavelength rather than averaging, specify width=0.
• V_ref (float) – The potential at which to get the reference spectrum
• t_ref (float) – The time at which to get the reference spectrum
• index_ref (int) – The index of the reference spectrum

Returns ValueSeries: The dOD value of the spectrum at wl.

wavelength

A DataSeries with the wavelengths for the SEC spectra

wl

A numpy array with the wavelengths in [nm] for the SEC spectra