Tutorial

The edumud package can be used to build up a colloidal system with an (ionic) electrolyte and particles. The characteristics of the colloid are read from a configuration file in *.yaml format.

Using edumud always starts with the import of the necessary physical constants and Python objects. The main objects are Elektrolyte, Particle and Colloid. Also, the load_config function is imported.

from edumud.constants import *
from edumud.electrolytes import Electrolyte
from edumud.particles import Particle
from edumud import Colloid
from edumud.file_utils import load_config

Next, a configuration can be read from file. As an example load the file ‘cegm.yaml’.

from pathlib import Path

DATADIR = Path(__file__).parent
CONFIG = "cegm.yaml"

el = Electrolyte(str(DATADIR / CONFIG))
el.calc_kappa()

param = load_config(str(DATADIR / CONFIG))
part = Particle.from_dict(param["particles"][0])

The structure of the configuration file closely follows the structure of the Elektrolyte object:

Elektrolyte

  • concentration in mM

  • ions

    • chemical name e.g. “K”, “Cl”, “PO4”

    • diffusion constant D

    • ionic charge z (with sign)

    • stoechiometry

As an example the configuration for a 5 mM KCl solution is given:

electrolyte:
  -
    conc: 5.0
    ions:
      -
        name: K
        D: 2.0e-9
        z: 1
        nu: 1
      -
        name: Cl
        D: 3.0e-9
        z: -1
        nu: 1

The Elektrolyte object contains a list of {concentration, ions} dictionaries for each dissolved salt. Usually there will be one salt in the Elektrolyte but the *.yaml format allows for an extension with multiple dissolved salts.

In a similar way, particle species can be added to the colloid. The configuration yields a list of Particle objects. consisting of:

  • radius

  • relative zeta potential in units of .. math:: /kT

  • relative electrical permittivity epsilon

  • Hamaker constant from DLVO theory

  • phi zero

  • mass fraction

particles:
  -
    radius: 250.0e-9
    rel_zeta: 4.0
    eps: 2.0
    Hamaker: 5.0e-21
    phi_zero: 1
    fraction: 0.01

Once the elektrolyte and particles are configured, they can be merged into a Colloid system.

zeta_zero = BOLTZ_T / (el.z_plus * E_CHARGE)
print(f"zeta_zero: {1000 * zeta_zero} mV")
psi_zero = 0.5 * zeta_zero