Adsorption - Desorption equilibriumΒΆ

In this first example, the goal is to simulate a system reaching equilibrium in the dark. To run the simulation, we are going to create a configuration file for pdom first. After calling pdom.config we need to answer a few questions. The parts which require user input are highlighted in yellow.

$ pdom.config
ID of the system (avoid spaces): example_ads_des

Should data be fitted to the simulation?
    1: fit
    2: just simulation
Your choice: 2

What kind of simulation?
    1: Adsorption-Desorption
    2: Degradation
    3: TOC
Your choice: 1

How can you identify the initial molecule?
    1: chemID (https://pubchem.ncbi.nlm.nih.gov)
    2: name
Your choice: 1
Molecule: 2764
Found ciprofloxacin (C17H18FN3O3)

What is the catalyst concentration?
  the allowed unis are: g/m^3, g/L, mg/L
Value: 1 g/L

What is the catalyst surface area?
  the allowed unis are: m^2/g, cm^2/g
Value: 56 m^2/g

What is the overall volume?
  the allowed unis are: m^3, L, cm^3, mL
Value: 0.3 L

How long should the simulation be?
  the allowed unis are: h, min, s
Value: 15 min

What is the adsorption constant?
  the allowed unis are: m/s
Value: 3.7E-8 m/s

What is the desorption constant?
  the allowed unis are: 1/s
Value: 2.0E-2 1/s

What is concentration in the solution?
  the allowed unis are: molecule/m^3, molecule/L, mol/m^3, mmol/L, M, mol/L, mo/mc, g/L, mg/L, g/m^3
Value: 0.1 mmol/L

What is concentration on the surface?
  the allowed unis are: molecule/m^2, mol/m^2, g/m^2, mg/m^2
Value: 0 mol/m^2

The resulting file example_ads_des.ini is now in your working directory. To start the simulation simply call pdom:

$ pdom example_ads_des.ini
Start calculating single species model
Calculation finished!
Results saved in <your_working_dir>/example_ads_des

In the newly created folder <your_working_dir>/example_ads_des, you find the raw data files with corresponding units and a plot of the concentration development over time.

example_ads_des plot