TOC simulation

Fragmentation

When the overall degradation of an organic molecule should be simulated, one of the multi-species models must be used. Three different split models are available in pdom:

• incremental
• fragmentation
• excess bonds

To model the generalized split species, the size dependents of the desorption constant \(k_{\mathrm{ads}}\) must be described. You can either choose strong or weak dependents for your simulation. We chose a weak dependents in this example, due to the fewer needed parameters.

As before the config file example_toc_sim.ini can be generated with pdom.config. Lines with require user input are highlighted in yellow.

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

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: 3

How can you identify the initial molecule?
	1: chemID (https://pubchem.ncbi.nlm.nih.gov)
	2: name
Your choice: 1
Molecule: 4139
Found methylene blue cation (C16H18N3S+)

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: 0.4 L

How long should the simulation be?
  the allowed unis are: h, min, s
Value: 4 h

Which split model should be used?
	1: incremental
	2: fragmentation
	3: excess_bonds (slow)
Your choice: 2

Is the system in equilibrium (dark)?
	1: Yes
	2: No
Your choice: 1

Which model should be used
for the estimation of size dependent k_des?
	1: Strong
	2: Weak
Your choice: 2

What is the adsorption constant?
  the allowed unis are: m/s
Value: 2.1E-8 m/s

What is the desorption constant?
  the allowed unis are: 1/s
Value: 2.85E-2 1/s

What is the reaction constant?
  the allowed unis are: 1/s
Value: 2.85E-1 1/s

What is the value of beta_1?
  the allowed unis are: 1/s
Value: 0.2 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: 4 mg/L

With the generated config example_toc_sim.ini we can start the simulation with pdom.

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

In the folder <your_working_dir>/example_toc_sim, you find the raw data files with corresponding units and three plots. The first plot is an overview with TOC and the concentration of the initial molecule in solution. The other two show concentration developments of the segments in solution and on the surface.

Development of the concentration in solution and the total organic carbon (TOC) using fragmentation split model.

Development of the segments in solution when using the fragmentation split model.

Development of the segments on the surface when using the fragmentation split model.

Incremental

Because pdom is based on configuration files, you can simply make a copy of example_toc_sim.ini and change the settings quickly for a new simulation. You can alter the split_model key in the section MULTI to incremental for example:

...
[MULTI]
split_model = incremental
desorption_model = weak
...

This generates the following results:

Development of the concentration in solution and the total organic carbon (TOC) using the incremental split model.

Development of the segments in solution when using the incremental split model.

Development of the segments on the surface when using the incremental split model.