The different panels in the Input Workspace present different steps in implementing the geochemical models. This information is assembled in the phreeqc.in file for the simulation. Hereafter, some general guidelines are given; however the user has some flexibility in deciding which input is given in the individual tabs. The flexibility increases when the user understands the structure of the phreeqc.in file.


Database Panel

The Database panel allows to select the thermodynamic database:

  • In many cases, a default database is already filled in (see Databases).
  • An alternative database can be selected via the Database Manager.
  • In a Managed Project, a drop-down list is available with thermodynamic databases already included in the project


In hpgeochemistry, the relevant components for the simulation can be selected. This does not mean other components cannot be used in this particular simulation. The selection just serves for the input towards the Help Trees and autocompletion in the Input Text Editors.


The last action in this panel is adding new thermodynamic or kinetic information. When information is added via the Database panel, then:

  • the information is dynamically included in the other panels of the Input Workspace,
  • the information can be exported to be imported in other simulations.


Reactive Transport Panel

In the Reactive Transport Panel (only in HYDRUS), the user selects the components to be transported and activates some options specifically for reactive transport calculations.


For reactive transport simulations, definition of the components is obliged. In Selection of Components, the user selects the different components by:


Other options are related to the model (e.g. evolving transport properties) and parallel computing.


Global Definitions Panel

The Global Definition Panel allows for some advanced features that are implemented in HPGeochemistry and HYDRUS. This panel is optionally and its use depends on the complexity of the problem and the expertise of the user.


       

Global Variables

A GUI for defining inline variables which will be dynamically included  in the other panels. The information is inserted in the phreeqc.in file via the command GLOBAL_VARIABLE.

DataBlock

A GUI for defining data blocks which is a vector or matrix implementation for defining inline variables. Information will be dynamically included in the other panels. The information is inserted in the phreeqc.in file via the command DATABLOCK.

Transformation

A GUI to define scripts for pre-processing input definitions and variables. The  information is inserted in the phreeqc.in file via the command GLOBAL_VARIABLE or calculated_values (-state definition). 

Counter

A GUI to define the special inline variable COUNTER (value of the inline variable changes when it is used). This can be used for automatic numbering of entities, or for reaction path modelling. The  information is inserted in the phreeqc.in file via the command COUNTER and COUNTERINCR. 

Include Files

A GUI to define input files that should be included in the file phreeqc.in via the command INCLUDE$. The user can specify where to include the specific file.


Default Input Text Editors

The Input Workspace has two or four (in respectively, hpgeochemistry and hydrus) input text editors to define the geochemical model using the PHREEQC input format. The content of these text editors are included in phreeqc.in the at specific locations. Following the guidelines hereafter will produce logic input files for either hpgeochemistry or hydrus.


 

Additions to the database

The original aim of this panel was to add additional information such are thermodynamic data or some general definitions. In the current GUI, much of that information can be defined via the graphical forms mentioned above. Nevertheless, as the content of this panel is put before the content of the other panels in phreeqc.in, it still can be used to add general definitions.

Solution Definitions

(only in hydrus). This panel is used to define the geochemical compositions of initial and boundary solutions (Phreeqc command solution). The solution numbers are linked to the numbers that are defined in the HYDRUS GUI for defining the initial and boundary conditions. 

In case diffusion in the gas phase, the composition of the gas phase of a boundary condition is defined here as well with the phreeqc command gas_phase (see example Gas Diffusion).

IMPORTANT: it is good practice to avoid that solution numbers are less than the number of computational nodes in the geometrical domain in HYDRUS. If they are smaller, one could have strange and unexpected initial conditions and/or simulation results. 

Geochemistry

In HPGeochemistry, this panel is used to input the geochemical simulation and commands related to output.

In HYDRUS, the panel typically contains the nodal information about the geochemical entities EXCHANGE, equilibrium_phases, kinetics, solid_solution and surface. In case of diffusion in the gas phase, also the gas phase composition is defined (gas_phase). Linkage to the geometrical domain is done by:

  • Set the entity number equal to the node number, or
  • Link the entity to a material type using -material identifier. IMPORTANT: it is good practice to avoid that entity numbers are less than the number of computational nodes in the geometrical domain in HYDRUS. If they are smaller, one could have strange and unexpected initial conditions and/or simulation results. 

Output

The user defines here which variables must be written to the output files using selected_output and user_punch.

In the HYDRUS GUI, only the spatial distribution plots for 2D simulations can be viewed. Other output needs to be visualized in HPOUTPUT (see Checking the Simulation Results).

By default, spatial distributions at selected print times (defined in the HYDRUS GUI Output Information dialogue window) and time series at selected observation nodes (defined in the HYDRUS GUI  Domain Properties -> Observation nodes menu) are saved. For 2D, also geochemical information over mesh-lines (defined in the HYDRUS GUI Auxiliary Objects - Mesh-Lines menu) are saved.

Additional type of output information can be requested, such as integrated (summed) variable over a domain (-horizon, -layer, -node, -depth), cross-sections (2D, -crosssection), and 2D domains (-contour). With selected_graph, figures with combination of different variables can be defined.



Additional input files

Additional input files can be made by opening input text editors with the toolstrip Adding, Saving and Closing Input Tabs.

Important: Open additional input files are not automatically included in the input file. The user needs to have the phreeqc INCLUDE$ command in one of two (hpgeochemistry) or four (hydrus) default input text editors defined above. Reversely, files hat will be included via the phreeqc INCLUDE$ command does not have to be opened in an additional input text editor.