(theory)=
# Theory

Omnisoot consists of six sub-models:
* {ref}`sec:reactors` provide zero-dimensional approximate representations of complex reactive flows in the form of ODEs that track changes in the mass and energy of the gas phase, mass fractions of individual gaseous species, elemental (carbon and hydrogen) mass of solid particles, and number densities of agglomerates and primary particles.

* {ref}`sec:particledynamics` describe the morphological features of solid particles in terms of characteristic agglomerate diameters and calculate particle collision rates. Particle dynamics models determine the contributions of inception, surface growth, oxidation, and coagulation to the source terms in the equations that track particle properties.

* {ref}`sec:pahgrowmodel` calculate the rates of particle inception and surface growth through the adsorption of aromatic precursors.

* {ref}`sec:surfreacmodel` compute the rate of surface growth by $\mathrm{C}_2\mathrm{H}_2$ and oxidation by $\mathrm{O_2}$ and $\mathrm{OH}$ using hydrogen-abstraction-acetylene($\mathrm{C}_2\mathrm{H}_2$)-addition {cite:p}`appel2000kinetic`.

* {ref}`surface-sites` define approaches for estimating the number of reactive sites on the particle surface used to calculate surface growth and oxidation rates in surface reaction models.

* {ref}`carbonization` describes the decrease in the hydrogen content of particles due to particle maturation, i.e., the evolution of their internal structure toward graphitic layers. 

```{figure} ../assets/images/structure.png
:width: 90%
:align: center
:name: fig-structure

The structure of Omnisoot package and sub-models.
```

Read {ref}`general` to get familiar with the assumptions, conventions, and terminology used in developing the theory of Omnisoot.

```{toctree}
:maxdepth: 3
:caption: Contents

general/index
reactors/index
particle-dynamics/index
PAH-growth-models/index
surface-reactions/index
surface-sites/index
carbonization/index
bibliography/index
```

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