FreeGs Reports and Thermodynamic Calculator Help

• Reports and calculator functionality
• Database content
• Functionality
• System duplication
• FreeGs definitions
• Apparent Gibbs free energy
• Species
• Species Data Sets
• Standard State Definitions
• FreeGs search options
• General Search Notes
• Species Name
• Naming conventions
• Search by name
• Species Formula
• Formulae conventions
• Search by formula
• Species Type
• Species Model
• Preferred data set for a species
• Entered
• Updated
• FreeGs calculation functionality
• General comments
• TP area of calculations
• Setting TP areas for calculations
• Calculation of species properties
• Calculation of reaction properties
• My (custom) reactions
• Creating custom reactions
• Feedback
• Related links

Reports and calculator functionality

• Database content
• Functionality
• System duplication

Database content

FreeGs database contains thermodynamic data for

• Chemical Species (the primary focus of FreeGs)
• a limited number of reference chemical reactions

Additionally, using the FreeGs calculator, you can create a short list of your own custom reactions using species data held in the database.

[back to top]

Functionality

Using FreeGs Reports and Calculator pages, you can do the following:

Page	Description	Functionality
Reports	FreeGs Thermodynamic Data Reports	Interrogate the database to return a list of available species and the distinct data sets available for each species
Species Search & Properties	FreeGs Thermodynamic Calculator for database species	Interrogate the database to return a list of available species and the distinct data sets available for each species Calculate thermodynamic properties of the species selected from the list returned by your search Thermodynamic properties available in drop-down lists are calculated as functions of temperature and pressure
Stored Reactions	FreeGs Thermodynamic Calculator for the reactions stored in the database	Lists chemical reactions, composed of database species (or their specific data sets), stored in the FreeGs database Calculate thermodynamic properties of the reactions selected from the available list Thermodynamic properties available in drop-down lists are calculated as functions of temperature and pressure Note: Storing reactions is not the primary purpose of the database. The reaction list is currently only auxiliary. However, this option gives us the flexibility to add reactions in the future.
My Reactions	FreeGs Thermodynamic Calculator for your custom reactions	Maintain your own list of chemical reactions composed of database species (or their specific data sets) stored using a cookie Calculation functionality is the same as for Stored Reactions

[back to top]

System duplication

Currently, you can interrogate the database using the Reports or Species Search & Properties pages.

The reports from both pages are very similar, providing the same lists of species and links to their data sets. The Species Search & Properties page has the additional calculator functionality, while the reports pages lets you produce an Excel (XL) output for basic species data.

Though the current availability of two search pages may result in some confusion, we have chosen to preserve them until the calculator system is comprehensively tested.

[back to top]

FreeGs definitions

• Apparent Gibbs free energy
• Species
• Species Data Sets
• Standard State Definitions

Apparent Gibbs free energies

The standard molal Gibbs free energies of FreeGs species are represented as apparent standard molal Gibbs free energies (Δg(T,P)) of formation from the chemical elements at the given temperature and pressure. These apparent energies can be written as

Δg(T,P) = ΔGf + (G(T,P) - G(T_r,P_r)),

where ΔG_f denotes the standard molal Gibbs free energy of formation of the species from its elements in their stable phase at the reference temperature (T_r = 298.15 K) and pressure (P_r = 1 bar), and G(T,P) - G(T_r,P_r) refers to differences in the standard molal Gibbs free energy that arise from changes in temperature (T - T_r) and pressure (P - P_r).

[back to top]

Species

Species are entities that take part in chemical reactions.

FreeGs species include pure substances (gases and condensed substances including solids (minerals) and liquids) and aqueous species (ions and complexes).

Note: pure water (in its stable state) is considered to be an aqueous species rather than a pure substance.

Hypothetical end-members of solid solution series are classified as “condensed substances”.

Also see Species Types and Species Model.

[back to top]

Species Data Sets

An individual species may be characterised by a number of data sets (or species "versions"). The existence of multiple data sets for a single species is due to

• using different models to calculate thermodynamic properties and/or
• using different parameters for the same model

For each species there is usually a single preferred data set, which has been assessed by the system custodian to represent the most reasonable from a pmd*CRC modeller's point of view. Other users can make their own judgements on the appropriateness of the data by taking into account the estimate of the data quality in the Confidence Rating column and/or the more detailed metadata for individual data sets, which can be viewed by clicking on the HTML link in the Report page or the Details button in the Species Search & Properties page. See About FreeGs for a more detailed discussion.

[back to top]

Standard state definitions

Species type	Standard state convention
Aqueous species (other than H2O)	Unit activity of the species in a hypothetical 1 molal solution referenced to infinite dilution at any temperature and pressure
Pure water	Unit activity of the pure component at all temperatures and pressures
Condensed substances (solids and/or liquids)	Unit activity of the pure component at all temperatures and pressures
Gases	(a) The hypothetical state of unit fugacity (1 bar) at any temperature (default). (b) Unit activity of the pure component at all temperatures and pressures (optional)

[back to top]

FreeGs search options

• General Search Notes
• Species Name
• Naming conventions
• Search by name
• Species Formula
• Formulae conventions
• Search by formula
• Species Type
• Species Model
• Preferred data set for a species
• Entered
• Updated

General Search Notes

The values in the search boxes and drop-down list are combined using logical “AND”s to limit your search.

[back to top]

Species Name

Naming conventions
Species type	FreeGs naming convention
Aqueous species including water	Common chemical formula. (eg, Na+, Fe++, AgCl4---) plus an optional identifier. Note that species charge is identified by an appropriate number of pluses and minuses for positively and negatively charged species, respectively. The neutral aqueous species will normally contain an additional identifier preceded by a space: (aq) (eg, H2 (aq)).
Condensed substances (solids and/or liquids)	Common substance name (eg, Albite)
Gases	Common substance name (eg, Hydrogen). Alternatively, a chemical formula of the gas followed by the “,gas” identifier (eg, SO2,gas)

[back to top]

Search by name

Use this input box to search for a species by its name, or by a part of its name. For example, type in Albite, albite, or bit to look for albite. Note that this search is case-insensitive. You can use the percent sign (%) as a wild-card character (eg, a%e).

Note: Use the chemical formula to search for water.

[back to top]

Species Formula

Formulae conventions
Species type	FreeGs naming convention
Aqueous species including water	Common chemical formula. (eg, Na+, Fe++, AgCl4---). Note that species charge is identified by an appropriate number of pluses and minuses for positively and negatively charged species, respectively. There is NO charge identifier for the neutral aqueous species (eg, H2).
Condensed substances (solids and/or liquids)	Common structural formula (eg, NaAlSi3O8).
Gases	Common chemical formula. (eg, H2, or CH4)

[back to top]

Search by formula

Use this input box to pick up all the species containing a particular chemical element. For example, type in Na to look for all the species containing sodium, or F for the species containing fluorine.

Note: In contrast with the Name search box, the search will be case-sensitive!

Note: The exact results of your search by element will depend on the values set in the other search boxes. For example, you can limit your search for aqueous species containing your element of interest.

Warning: No logical operators allowing search by combination of elements are implemented at this stage. You can use the Formula search box in the same manner as the text box (eg, looking for all formulas containing the string Na%Al will only return results where Na occurs to the left of Al in the species formula; that is for any formula where Na precedes Al, but none for formulas where Al only precedes Na).

[back to top]

Species Type

The FreeGs species are grouped as follows:

Species Type	Abbreviation	Explanation
Aqueous species	(aq)	ions and complexes plus water in its stable state
Condensed substances	(c)	solids(minerals) and/or non-aqueous liquids
Gases	(gas)

Species types are not part of the chemical formulae stored in the database.

[back to top]

Species Model

The model identifies an equation of state (or another algorithm) used to calculate thermodynamic properties for a particular species dataset. In the general case, the same species can be characterised by a number of data sets that would be different either by parameters used for the same model, or by a model itself.

For example, thermodynamic properties of the same aqueous complex Au(HS)2- can be defined either via the Modified Ryzhenko-Bryzgalin model, or via the Revised Helgeson-Kirkham-Flowers model. In turn, its parameters for the Revised Helgeson-Kirkham-Flowers model can come from different sources:

Example results table
Name, Formula and Type	Summary	Instances	Model	Preferred	Confidence Rating	View Data As
Au(HS)2- Au(HS)2- Aqueous species	html xl	1	MHKF	Y	4	html    xl
		2	MHKF	N	3	html    xl
		3	MHKF	N	3	html    xl
		4	MRB	N	3	html    xl

Currently, the following models are implemented:

• Haar-Gallagher-Kell model for pure water (HGK)
• pK(H₂O) from Marshall and Franck (1981) for OH- (MF)
• Revised Helgeson-Kirkham-Flowers model for aqueous species (ions and complexes) (MHKF)
• Modified Ryzhenko-Bryzgalin model for aqueous complexes (MRB)
• Akinfiev-Diamond model for aqueous nonelectrolytes (AD)
• Peng-Robinson Stryjek-Vera (1986) for gases (PRSV)
• Generic model for pure substances (GMPS)
• "Incomplete" data sets keep arbitrary parameters that are not supported by calculation algorithms (IDS)

[back to top]

Preferred data set for a species

For each chemical species there is a preferred data set. The preferred data sets for species are subjectively reasonable from a modeller’s point of view (i.e., they reproduce the natural or experimental equilibria to the satisfaction of the FreeGs maintenance team).

Alternatively, a dataset might be "preferred" even if the data are of a provisional quality - but currently there are no alternatives.

If you are an external user, we leave the choice of the selected data sets and responsibility for this choice entirely to you. See FreeGs thermodynamic database project for more details.

When searching we recommend the Yes (i.e. preferred) values for the pmd*CRC community.

[back to top]

Entered

Use this list box to check what species/data sets have been added since your last visit.

Updated

Use this list box to check what species/data have been modified since your last visit.

[back to top]

FreeGs calculation functionality

• General comments
• TP area of calculations
• Setting TP areas for calculations
• Calculation of species properties
• Calculation of reaction properties
• My (custom) reactions
• Creating custom reactions

General comments

The main purpose of the FreeGs database and calculator is to provide parameters to enable calculation of chemical equilibria via Gibbs free energy minimisation or log K-based techniques; thus the selection of the available thermodynamic functions is specifically tailored for this purpose.

[back to top]

TP area of calculations

Currently the user is forced to stay within the temperature-pressure range of the revised Helgeson-Kirkham-Flowers model for aqueous species (temperatures to 1000°C and pressures up to 5 kbar).

The default TP grid for calculations follows the format

t(°C) = 25, 50 to 500 by 50
P(bar) = 0, 500, 1000, 2000, 5000

Note: Zero (0) value for pressure designates the vapour saturation pressure of pure water (PSAT).

This default grid can be changed to a customised even grid using the Set PT Table function.

[back to top]

Setting TP areas for calculations

Using this function, you can modify the temperature-pressure (TP) grid and the gas standard state for calculation of the requested properties. The applied changes will take effect simultaneously for all the FreeGs calculator pages - Species Search & Properties, Stored Reactions, My Reactions - and so will affect both species and reaction calculations.

The TP grid and the gas standard state are changed independently (use the "Apply" and "Set" buttons, respectively).

You can simultaneously restore the default TP grid and the gas standard state (1 bar) by clicking the "Revert to Default" button.

[back to top]

Calculation of species properties

To calculate the property of interest for a species data set complete the following steps:

1. Search for the desired species
2. Select a species data set from the results list (by ticking the appropriate check box). If required, you can select a number of species simultaneously
3. Select the property of interest from the drop-down list
4. Press the "Calculate" button

Currently, you can calculate the following thermodynamic properties (T,P) of the database species:

Property	Species
Apparent Gibbs free energy	All
Density of pure water	Pure water according to the Haar-Gallagher-Kell model
Dielectric constant of pure water	Pure water
Fugacity	Water and gases
Fugacity coefficient	Water and gases

The standard states are defined above.

Note:

• The calculated values of the apparent Gibbs free energy for gaseous species will depend on the set standard state for the gaseous species (1 bar by default)
• Fugacity and fugacity coefficients of water and gases in any stable state (liquid or gaseous) are always calculated by FreeGs according to the default gas standard state (1 bar)

The requested property will be tabulated in a new browser window(s).

The tabulation will be completed according to the predefined default temperature-pressure grid. You can modify it at any time using the Set PT Table function.

Note:

• Calculation of "unique" properties such as Density of pure water and Dielectric constant of pure water can be completed at any time without any selection
• If you select an inappropriate property for a species model (eg if you try to calculate Fugacity for an aqueous species), the output browser window will return an error message. See the table of species properties for details
• If you attempt to calculate properties for a species or one of its data sets defined by a thermodynamic model that is not supported by calculation routines, the output table will return Null values
• For aqueous species defined according to the Revised Helgeson-Kirkham-Flowers and Modified Ryzhenko-Bryzgalin models, for the TP point with the water density < 0.35 g cm-3, the output table will return gas values

[back to top]

Calculation of reaction properties

The calculation functionality of the Stored Reactions and My Reactions pages is similar. You can calculate the following thermodynamic properties (T,P) of the stored chemical reactions:

• Gibbs free energy change of reaction
• log K value of reaction (the default values of the drop-down property list)
• ln K (natural logarithm) value of reaction
• pK value of reaction (= - log K)

Both the Stored Reactions and My Reactions pages contain reaction lists detailing reaction names and reaction equations. The reaction equations are made up of the species formulae and their associated type (eg aq, g or c). Note that species types are NOT stored as part of individual chemical formulae in the database.

To calculate the property of interest for a reaction, complete the following steps:

1. Select (tick the check box for) a reaction from the list. If required, you can choose a number of reactions simultaneously
2. Select the property of interest from the drop-down list
3. Press the "Calculate" button

The requested property will be tabulated in a new browser window(s).

The tabulation will be completed according to the predefined default temperature-pressure grid. You can modify it at any time using the Set PT Table function.

Note: The calculated values for reactions involving gaseous species will depend on the set standard state for the gaseous species (1 bar by default).

[back to top]

My (custom) reactions

Using this page, you can create a short list of your own custom reactions built from the database species or their particular versions. Those are stored in a cookie file on your hard disk. To take advantage of this feature, you must enable cookies in your browser.

The first time you visit this page (or after deleting cookies from your computer) your reaction list is empty.

To create a new reaction, press the "New reaction" button.

Note: The maximum number of reactions on your page will be limited by the maximum size of the cookie (4KB). Individual reactions will use different amounts of space in your cookie - the more species in your reaction, the more space will be taken up.

[back to top]

Creating custom reactions

To add a new reaction, you should complete the following steps:

1. Initialise the Reactants drop-down lists. By default, they are empty at the start to speed up the loading of this web form.

   To simplify selection of the reactants at Step 3, we recommend that you limit the reactants lists. To do this, before the initialisation, you can optionally

   • Specify a number of chemical elements separated by commas. The comma plays a role of the logical OR (eg, specifying Fe, S, O will return lists of all database species containing Fe or S or O)
   • Choose to query the database for preferred species data sets only

2. Add an arbitrary reaction name.
3. Add at least two reactants from the drop-down lists with appropriate stoichiometric coefficients - negative for reactants (eg -1), positive for products (eg 1) (may be non-integers).
   • The reactants in the drop-down list show species (and their types) and all their available data sets. The reactants are ordered by chemical formulae and the (arbitrary) position of the data set relative to other data sets of the same species. Press the "Details" button next to the selected item to look up the detailed data set information
   • The reactants in a drop-down list are in alphabetical order
   • The reaction balance is not checked by the current program version!
4. Click the "Save" button. The reaction will be saved on your My Reactions page.

[back to top]

Feedback

If you have any problems with the calculator pages, suggestions or other issues please contact Evgeniy Bastrakov (evgeniy.bastrakov@ga.gov.au) at Geoscience Australia.

We have made extensive use of Javascript in the FreeGs Calculator pages to make the functionality user friendly - if you do not wish to use Javascript you can still use the FreeGs Report pages to access the basic thermodynamic data.

[back to top]

Related links

• Virtual centre for geofluids and thermodynamic data
• Fluids inclusion database project
• FreeGs project
• FreeGs thermodynamic calculator
• HCh package for geochemical modelling