Definition of chemical species

A new chemical species can be included into the model using the materials list of CrysMAS. For each indented species the corresponding material should be defined. The material for species is the same as each material used for materials distribution over the model geometry. The only specialty of such material is that it serves as the data holder for the chemical species. The materials used in the materials distribution over the computational domain may be used for definition of the chemical species too. Nevertheless is advised to create new materials which will be used exclusively in the chemical model. For creation of new materials see section Adding, Replacing and Deleting Materials.

The physical properties of the material used in the chemical model are

If the checkbox effect on gas convection is checked, then additional material properties of the chemical species are utilized for computation of the effective properties of the gas mixture, provided the transport medium is an ideal gas.

Density and effective diffusion coefficient are then recalculated with account of the actual species composition too. Effective transport coefficients are computed using the actual distribution of the species concentration and their material data according to Wilke approximation, see Kleijn in Bibliography .

After all required materials for chemical species are created, one starts with definition of chemical species for the chemical model.

In Simulation mode open the dialog window Settings->Species.

Species dialog at the beginning of the chemical model definition. 

Figure 104. Species dialog at the beginning of the chemical model definition.

The meaning and functions of the dialog items are explained in detail in section Setting of chemical species .

If still no species were defined, then only single default entry "reagentA" is available in the species list in the dialog box choose chemical list from the list".

One starts with the selection of material from the materials list "material for species/transport medium", see figure above. The selected material is used then for definition of a new chemical species or its attributes or changes on the defined species.

After the material name is selected, click on the button chemical species changes the identificator name on this button. It will be set equal to the material name selected in the dialog list choose chemical list from the list".

The same procedure is done for the transport medium of the defined species. The corresponding material should be preselected again before the transport medium for species is defined. The material of the transport medium is considered not as a species but as the material available in the regions of the computational domain. The definition of the transport medium for the species restricts the existence of the chemical species to the regions filled with defined material and meshed structurally. The transport medium has a meaning only for liquid species. Solid species are not attached to any medium but to the interfaces. Therefore the transport medium for solid species may be arbitrary.

Changes in the dialog window after settings of the species and transport medium names should be confirmed by the button press account change. If the species list was empty and the first species was edited, then this can be done also by the add new species button press. The accounted species occur in the species list of the considered dialog window. It will appear also in all dynamically allocated species lists of the other dialog tabs of the Species dialog. The data of the species is then still not stored into the computational chemical model. The data storage on the computational level takes place after the button Apply or OK is pressed. Then the whole mnemonic description of the chemical model will be generated and checked for consistency.

If no problem occurs, will be stored outside of the GUI data of the chemical model. Also the variables list of the chemical model in the main CrysMAS window will be adjusted and all defined species will be included as the computed variables of the chemistry variables group,

Otherwise the conflicts in the definitions will be reported.

It is recommended to do it only after at least all species are defined.

For expansion of the species list press the button add new species. The species list will be expanded with the default species name. Set proper species and transport medium identifiers and account it with the account change button press. Then you can continue with entering of new species.


You should define all necessary chemical species in the Species tab of the Species dialog window and only then proceed with definition of the chemical reactions. Otherwise, if chemical reactions are defined and the list of chemical species will be changed, the chemical reactions data may be corrupted and should be corrected.

Related Procedures

Setting of chemical species