Configuration¶

Simulation¶

To run the simulation pdom needs a couple of information from the user. For pdom, this data is saved in an .ini file. This ensures that the results of a simulation can always be accompanied by the parameters that created them.

A simple config for pdom looks like this:

simple.ini¶

[SIMULATION]
id = simple_degradation_methylene_blue
multi = False
fit = False
duration = 5 h

[SYSTEM]
concentration_solution = 0.08 mmol/L
k_ads = 9.0E-10 m/s
k_des = 1.0E-3 1/s
k_reac = 1.1E-2 1/s

[CATALYST]
concentration = 2.0 g/L
surface = 50 m^2/g
volume = 1e-3 m^3

[MOLECULE]
name = methylene blue
composition = C16H18S1N3
molar_volume = 226.6 Ang^3/molecule
molar_surface = 99.7 Ang^2/molecule
diffusion_model = s

The parameters are arranged in different sections. Not all sections need to exist for each simulation.

To create a new .ini file you can use the configuration tool of pdom.

$ pdom.config --out 'my_new.ini'

It will guide you through the process by collecting all relevant information. For the parameters of the initial molecule, it is helpful to look up its chemID in PubChem before you start the process. This enables the automatic gathering of the molecule parameters from this database.

Most of the time, the automatic process should suffice. But if you want to build your .ini file from scratch, take a look into the available Configuration settings.

Experimental data¶

To extract parameters, we need to compare experimental data to the simulation. This data needs to be provided in a structured way. For pdom we use a .json file. Depending on the type of fit you want to carry out, the available features differ slightly.

Adsorption-Desorption experiments¶

Adsorption-Desorption experiments in the dark are analyzed with the single-species model. As it is common to have multiple repetitions that are based on the same setup. pdom supports multiple time series in its fits. The initial concentration and time steps can be different between the series. Below are examples of such a data file.

ads_des_multi.json¶

{
  "time_series": [
    [
      [0, 10, 15, 30, 60, 120, 240], [0.000, 0.076, 0.143, 0.175, 0.199, 0.207, 0.209]
    ], [
      [0, 10, 15, 30, 60, 120, 240], [0.000, 0.251, 0.452, 0.570, 0.609, 0.637, 0.633]
    ], [
      [0, 10, 15, 30, 60, 120, 240], [0.000, 0.598, 0.750, 0.898, 0.998, 1.021, 1.020]
    ], [
      [0, 10, 15, 30, 60, 120, 240], [0.000, 0.700, 0.996, 1.248, 1.396, 1.415, 1.415]
    ]
  ],
  "time_series_meta": [
    {
      "unit": "min",
      "type": "t"
    },
    {
      "unit": "mo/mc",
      "factor": 1E-3,
      "type": "surface"
    }
  ],
  "initial_concentration": [5.0, 15.0, 25.0, 35.0],
  "initial_concentration_meta": {
    "unit": "mg/L",
    "type": "solution"
  }
}

Degradation experiments¶

For degradation experiments all time series have to start with the same initial concentration set in the .ini file. This is the data file from the example Degradation fit.

fit_reac_mutli.json¶

{
  "time_series": [
    [
      [0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 12, 14, 16, 20, 25],
      [3.442, 2.847, 2.428, 2.229, 1.949, 1.801, 1.705, 1.535,
        1.315, 1.021, 0.9690, 0.8238, 0.5114, 0.2839, 0.1353]
    ], [
      [0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 12, 14, 16, 20, 25],
      [3.505, 2.876, 2.586, 2.323, 2.242, 2.097, 1.781, 1.681,
        1.461, 1.249, 0.9543, 1.0852, 0.7665, 0.4324, 0.2368]
    ]
  ],
  "time_series_meta": [
    {
      "unit": "min",
      "type": "t"
    }, {
      "unit": "mg/L",
      "type": "solution"
    }
  ]
}

Multi species model¶

To compare multi-species model simulations to experiments, TOC (or NPOC) can be used. In general, the fit to TOC data is the last step in the experiment analytics. This fit is limited to a single TOC curve, due to the usually demanding experimental process. If multiple TOC experiments are available, the results should be average before simulation. As just one initial concentration is needed, it is taken from the .ini file.

This is the data file from the example TOC fit.

fit_toc.json¶

{
  "time_series": [
    [0, 60, 120, 180, 360],
    [12.6, 8.8, 6.78, 4.1, 2.77]
  ],
  "time_series_meta": [
    {
      "unit": "min",
      "type": "t"
    }, {
      "unit": "mg/L",
      "type": "toc"
    }
  ]
}

Configuration settings¶

SIMULATION

id → str

default: example_mb

multi → bool

default: True

note: MULTI section needed if True

fit → bool

default: False

note: FIT section needed if True

duration → float

default: 5 h

units: h, min, s

SOLVER

Relative and absolute tolerances for the LSODA solver

rtol → float

default: 1e-9
atol → float

default: 1e-5

ENVIRONMENT

temperature → float

default: 20 C

units: K, C

CATALYST

concentration → float

default: 2.5 g/L

units: g/m^3, g/L, mg/L

surface → float

default: 56e3 m^2/g

units: m^2/g, cm^2/g

volume → float

default: 1e-3 m^3

units: m^3, L, cm^3, mL

MOLECULE

name → str

default: methylene blue

composition → chem_formula

default: C16H18S1N3

excess_bonds → int

default: 14

molar_volume → float

default: 226.6 Ang^3/molecule

units: Ang^3/molecule, nm^3/molecule, cm^3/mol

molar_surface → float

default: 99.7 Ang^2/molecule

units: Ang^2/molecule, nm^2/molecule, m^2/molecule

diffusion_model → str

default: s

note: s: Stokes (default), wc: Wilke-Chang, hm: Hayduk-Minhas

SYSTEM

concentration_solution → float

default: 10 mg/L

units: molecule/m^3, molecule/L, mol/m^3, mmol/L, M, mol/L, mo/mc, g/L, mg/L, g/m^3

concentration_surface → float

default: 0

units: molecule/m^2, mol/m^2, g/m^2, mg/m^2

note: if concentration_surface is not set system is considered in equilibrium (dark)

k_ads → float

default: 1E-9 m/s

unit: m/s

k_des → float

default: 1E-3 1/s

unit: 1/s

k_reac → float

default: 1E-2 1/s

unit: 1/s

FIT

This section is just active if fit is True

type → str

default: dark

note: dark, reaction or toc
search → str

default: relative

note: minima search absolute, relative or relative_square

note: does not apply to fit type toc
max_step → int

default: 100

note: does not apply to fit type toc

MULTI

This section is just active if multi is True

split_model → str

default: fragmentation

note: incremental, fragmentation or excess_bonds
desorption_model → str

default: weak

note: weak or strong
TOC_estimation → str

default: all

note: all or volume
segment_export → str

default: mass

note: mass or molecule_count

MULTI_WEAK

This section is just active if desorption_model is set to weak. Just one value needed if k_des is set.

beta_0 → float

default: -0.029 1/s

unit: 1/s
beta_1 → float

default: 0.8 1/s

unit: 1/s

MULTI_STRONG

This section is just active if desorption_model is set to strong

E_0 → float

default: 44.0 kJ/mol

unit: kJ/mol
E_1 → float

default: 3.0 kJ/mol

unit: kJ/mol
alpha_0 → float

default: 1.51e8 1/s

unit: 1/s
alpha_1 → float

default: 0.412

default:	`dark`
note:	dark, reaction or toc

default:	`relative`
note:	minima search absolute, relative or relative_square
note:	does not apply to fit type toc

default:	`fragmentation`
note:	incremental, fragmentation or excess_bonds

default:	`mass`
note:	mass or molecule_count