ChemicalComposition Action
This action is designed for use with the thermochemistry library Thermochimica Piro et al. (2013). Check out the corresponding submodule by running git submodule update --init --checkout modules/chemical_reactions/contrib/thermochimica.
Description
The ChemicalComposition action is used to initiate the framework for thermochemical calculations using the thermodynamics solver Thermochimica. The action creates variables needed for the analysis, reads the thermodynamic model for material system, and sets the units for temperature, pressure, and elemental amounts. It can optionally initiate the amounts of elements used in the model.
The ChemicalComposition action is also used to specify lists of chemical phases and chemical species for which concentrations should be output at each timestep. The phase and species names must match those in the data file specified. The ChemicalComposition action creates all AuxVariables needed for output of phase concentration data, chemical potentials, vapor pressures, etc. The list of phases is specified in the output_phases variable, and the list of species is specified in output_species. The species must be specified in the convention phase_name:species_name so that the desired species in the desired phase is uniquely identified. Alternatively, users can specify ALL to output all species present in the specified thermodynamic database. Other desired outputs such as element potentials, vapor pressures of species in gas phase and moles of elements in specified phases can be specified using output_element_potentials, output_vapor_pressures, and output_element_phases respectively. The ChemicalComposition action creates a UserObject derived from ThermochimicaNodalData or ThermochimicaElementData which runs Thermochimica at each node and stores the output in the created aux variables.
In this UserObject, the masses of elements included in the vector variable "elements" are input to the Fortran 90 module Thermochimica, along with the temperature and pressure. Optionally, the user may disable Thermochimica calculation re-initialization by setting "reinit_type" to none. This may reduce memory use in the calculation, but will likely greatly increase the length of each call to Thermochimica.
The ALL option circumvents the need for users to explicitly state each input element and the output variables. When used for specifying the input "elements", all the chemical elements present in the thermodynamic database are parsed and used to create the required MOOSE variables. The users must however be careful to specify the proper values of these elements either directly in the input file (for example, as done using ICs in MoRu.i) or using CSV inputs (such as in csv.i). When the ALL option is used to specify outputs, all phases / species / element potentials / etc. that are present in the thermodynamic database and which can exist with the given combination of input elements will be outputted. The users must be aware that, depending on the size of the thermodynamic database, this can lead to a large number of such variables being written to the output files leading to slowdown of both the simulations as well as higher memory use.
Variables for Chemical Elements
Chemical element variables to be used and initiated in the model using in ChemicalComposition action are specified using the block [GlobalParams], and vector elements as in Listing 1:
Listing 1: Chemical elements to be used in the model
[GlobalParams]
elements = 'Mo Ru'
[]The vector "elements" will be passed to the ChemicalComposition action and used to generate scalar variables, (e.g. Mo, and Ru) of the chemical elements contained in the vector.
The names of scalar variables listed in elements vector and created using ChemicalComposition action should not be used for other variables in the model, e.g. the model should not define variables Mo, or Ru in the [Variables] or [AuxVariables] blocks.
The element composition scalar variables can be initialized in ChemicalComposition action, or using [Functions] block combined with other MOOSE capabilities.
Variables for Chemical Phases, Species, and Element Chemical Potentials
Chemical phase and species variables, as well as chemical potentials of elements, to be used and initiated in the model using in ChemicalComposition action are specified using the block [GlobalParams], and vector "output_phases" as in Listing 2:
Listing 2: Chemical phases species to be used in the model, and list of desired output variables.
[GlobalParams<<<{"href": "../../syntax/GlobalParams/index.html"}>>>]
elements = 'Mo Ru'
output_phases = 'BCCN HCPN'
output_species = 'BCCN:Mo HCPN:Mo BCCN:Ru HCPN:Ru'
output_element_potentials = 'mu:Mo mu:Ru'
output_vapor_pressures = 'vp:gas_ideal:Mo'
output_element_phases = 'ep:BCCN:Mo'
[]The vectors "output_phases", "output_species", "output_element_potentials", "output_vapor_pressures", and "output_element_phases" will be passed to the ChemicalComposition action and used to generate scalar variables, (e.g. BCCN and BCCN:Mo) for the chemical phases and species contained in the vectors. The action will set up either a ThermochimicaNodalData or a ThermochimicaElementData userobject, depending on whether the "is_fv" parameter is set to false or true respectively.
The names of scalar variables listed in phases vector and created using ChemicalComposition action should not be used for other variables in the model, e.g. the model should not define variable BCCN in the [Variables] or [AuxVariables] blocks.
The format for entries in output_species must be phase_name:species_name or ALL, and both must match the specified thermodynamic database.
The format for entries in output_element_potentials must be mu:element_name or ALL.
The format for entries in output_vapor_pressures must be vp:gas_phase_name:species_name or ALL. The phase name must correspond to the gas phase in the thermodynamic database.
The format for entries in output_element_phases must be ep:phase_name:element_name or ALL.
The variables created by this action will be used by the UserObject ThermochimicaNodalData (or, more likely, a derived class specific to the application) to generate arrays in which to store the indices of the requested phases in Thermochimica calculation results, and to store the corresponding concentration values.
The elemental composition is used in Thermochimica calculations, e.g ThermochimicaNodalData or ThermochimicaElementData UserObject, that expect an elements vector.
This ChemicalComposition action syntax is shown on the ChemicalComposition action action system page.
References
- M.H.A. Piro, S. Simunovic, T.M. Besmann, B.J. Lewis, and W.T. Thompson.
The thermochemistry library thermochimica.
Computational Materials Science, 67:266–272, 2013.
URL: https://www.sciencedirect.com/science/article/pii/S0927025612005502, doi:https://doi.org/10.1016/j.commatsci.2012.09.011.[BibTeX]