Soft Potato

Soft Potato is an open-source electrochemical simulation and analysis toolkit in Python.

Full documentation: https://softpotato.xyz/ | Try Live: Google Colab Starter | Roadmap: ROADMAP.md | Changelog: CHANGELOG.md

Installation

Zero-Install Browser Trial (Google Colab)

Run Soft Potato directly in your browser with no local Python setup required:

• Launch Soft Potato v3 Starter in Google Colab

Stable Release (v3.2.0)

Soft Potato v3.2.0 is available on PyPI and can be installed via pip:

pip install softpotato

Development Version (Milestone 3 in progress)

To install the latest development version directly from GitHub:

pip install git+https://github.com/oliverrdz/softpotato.git

Or clone the repository and install in development mode:

git clone https://github.com/oliverrdz/softpotato.git
cd softpotato
pip install -e ".[dev,docs]"

Quick Start: Solving 1D Diffusion with scipy_ivp

Soft Potato makes it straightforward to simulate chemical diffusion:

$$\frac{\partial c}{\partial t} = D \frac{\partial^2 c}{\partial x^2}$$

Here is a minimal example setting boundary conditions to $0$ at the left boundary ($x=0$) and $1.0$ at the right boundary ($x=1.0$):

import numpy as np
from softpotato.solver import DiffusionProblem, DirichletBC, get_solver

# 1. Define grid and diffusion problem (c = 0 at left, c = 1.0 at right)
grid = np.linspace(0.0, 1.0, 50)
problem = DiffusionProblem(
    grid=grid,
    diffusivity={"c": 1e-4},
    boundary_conditions={"c": (DirichletBC(0.0), DirichletBC(1.0))},
    initial_conditions={"c": 1.0},
)

# 2. Solve using SciPy's Method of Lines solver
solver = get_solver("scipy_ivp")
result = solver.solve(problem, t_span=(0.0, 1.0))

# 3. Save the concentration profile to a variable
c_profile = result["c"]  # 2D array of shape (N_times, N_points)
c_flux = result.fluxes["c"]  # The current can be calculated with i = n*F*A*c_flux

Non-Uniform Spatial Discretization (softpotato.grid)

Concentration gradients in electrochemical experiments are confined to a thin diffusion boundary layer ($\delta \approx 6\sqrt{D t_{\max}}$) adjacent to the working electrode. Soft Potato's grid module provides uniform, geometrically expanding, and exponential/hyperbolic coordinate meshes that cluster nodes near active interfaces while coarsening into the bulk solution:

from softpotato.grid import (
    create_diffusion_mesh,
    GeometricExpandingMesh,
    ExponentialMesh,
)
from softpotato.solver import DiffusionProblem, DirichletBC, get_solver

# Automatically size a geometrically expanding mesh to delta = 6 * sqrt(D * t_max)
mesh = create_diffusion_mesh(
    D=1e-9,
    t_max=1.0,
    kind="geometric",
    n_points=60,
    gamma=1.08,
)

problem = DiffusionProblem(
    grid=mesh,
    diffusivity={"Ox": 1e-9},
    boundary_conditions={"Ox": (DirichletBC(0.0), DirichletBC(1.0))},
    initial_conditions={"Ox": 1.0},
)
result = get_solver("scipy_ivp").solve(problem, t_span=(0.0, 1.0))

Electrode Coordinate Geometries (softpotato.geometry)

Soft Potato natively supports 1D Cartesian planar (PlanarGeometry), radial spherical/hemispherical (SphericalGeometry), and radial cylindrical (CylindricalGeometry) coordinate systems, with automatic Faradaic current integration ($I = n F A J$):

from softpotato.geometry import SphericalGeometry
from softpotato.grid import GeometricExpandingMesh
from softpotato.solver import DiffusionProblem, DirichletBC, get_solver

r0 = 10e-6  # 10 um spherical microelectrode radius
mesh = GeometricExpandingMesh(x_min=r0, x_max=r0 + 500e-6, n_points=80, gamma=1.06)

problem = DiffusionProblem(
    grid=mesh,
    diffusivity={"Ox": 1e-9},
    boundary_conditions={"Ox": (DirichletBC(0.0), DirichletBC(1.0))},
    initial_conditions={"Ox": 1.0},
    geometry=SphericalGeometry(r0=r0),
    n_electrons={"Ox": -1},
)
result = get_solver("scipy_ivp").solve(problem, t_span=(0.0, 2.0))
i_cathodic = result.currents["Ox"]  # Faradaic current in Amperes (IUPAC convention)

Analytical Equations & Benchmarking (softpotato.analytical)

Soft Potato provides exact closed-form analytical solutions and empirical models for benchmarking numerical solvers and rapid parameter estimation:

import numpy as np
import softpotato as sp

# 1. Planar Cottrell chronoamperometry current transient
t = np.linspace(0.1, 5.0, 50)
i_transient = sp.cottrell(t, n=1, D=1e-5, c_bulk=1e-3, area=1e-4)

# 2. Spherical electrode transient and steady-state limiting current
i_sphere = sp.cottrell_spherical(t, r=1e-5, n=1, D=1e-5, c_bulk=1e-3)

Interactive Tutorials & Examples

Step-by-step Jupyter notebook tutorials are located in examples/ and rendered in the online documentation:

Development Roadmap & Milestones

Soft Potato follows a staged milestone development roadmap for the 3.x series, maintaining strict backwards compatibility across releases:

For detailed architectural plans and deliverable specifications, see the full Roadmap.

Citation

If you use Soft Potato in your research or project, please cite the ChemRxiv preprint:

Rodríguez, O. (2022). Soft Potato: an open source electrochemical simulator and toolkit. ChemRxiv. doi:10.26434/chemrxiv-2022-4bs3w

@article{rodriguez2022softpotato,
  author    = {Rodr{\'i}guez, Oliver},
  title     = {Soft Potato: an open source electrochemical simulator and toolkit},
  journal   = {ChemRxiv},
  year      = {2022},
  doi       = {10.26434/chemrxiv-2022-4bs3w},
  url       = {https://chemrxiv.org/doi/full/10.26434/chemrxiv-2022-4bs3w}
}

License

This project is licensed under the BSD 3-Clause License - see the LICENSE file for details.