GEM-Selektor version 3

Default (Kernel) Thermodynamic Database

Contents  

1. GEMS default chemical thermodynamic database

1.1. PSI/Nagra TDB 12/07

1.1.1. Database structure

1.1.2 Data import

1.2. SUPCRT92 - slop98.dat

1.2.1 About data import from slop98.dat

1.3. Third-party databases

1.4. Write protection

2. List of files in default thermodynamic database

2.1. PSI/Nagra TDB 12/07 files

2.2. SUPCRT92 - slop98.dat files

2.3. Supporting database files

3. LES PSI Thermodynamics Group

4. References

1. GEMS Default Chemical Thermodynamic Database

For a broad applicability of the GEM-Selektor and GEMS3K codes, the GEM-Selektor v.3 package is distributed with a default chemical thermodynamic database that consists of three parts: (i) "PSI/Nagra TDB 12/07"; (ii) "SUPCRT92 - slop98.dat"; and (iii) "Third-party databases", selectable upon creation of modelling projects via the "Elements Wizard" dialog.

1.1. PSI/Nagra TDB 12/07

The PSI/Nagra Chemical Thermodynamic Database 12/07 (PSI/Nagra TDB 12/07) is an update of the Nagra/PSI Chemical Thermodynamic Data Base 01/01 (Nagra/PSI TDB 01/01), the latter of which was documented by HUMMEL et al. (2002) (http://les.web.psi.ch/TDBbook/index.htm). The selection of chemical elements, aqueous  species, and minerals and gases in the  PSI/Nagra TDB 12/07 reflect the (rather specific) main purpose of its compilation - the support of geochemical modelling related to nuclear waste disposal.

The present update is mainly based on the OECD NEA’s book series on “Chemical Thermodynamics”. The following volumes that appeared after publication of the Nagra/PSI TDB 01/01 have been considered in the present update:

In addition, thermodynamic data for silicon compounds and complexes have also been reviewed.

The report by THOENEN (2012a) lists all the selected data for U, Np, Pu, Am, Cm, Tc, Ni, Se, Zr, Th, Si, as well as updated or new auxiliary data. The update is documented in the following reports:

All other data contained in the Nagra/PSI TDB 01/01 have been adopted without any change.

1.1.1. Database structure

The PSI/Nagra TDB 12/07 distinguishes three types of data:

• Core Data
• Recommended Application Data
• Supplemental Data

Core data pertain to well characterized aqueous species, minerals and gases involved in almost any type of speciation calculation. These data have been carefully selected and are widely accepted in different fields of application. They basically comprise the CODATA key values (COX et al. 1989) and some other values of similar quality and almost worldwide acceptance.

Recommended application data pertain to well characterized aqueous species, minerals and gases of elements important in different fields of application. These fields of application are

• Modelling of groundwaters and surface waters
• Safety assessments of nuclear waste repositories
• Pollution dynamics of chemically toxic substances

The recommended application data are of high quality and are well established, but in contrast to the core data, which are not likely to be revised in the foreseeable future, the recommended application data originate from rather active fields in the environmental sciences and may be revised and improved over time.

Supplemental data pertain to aqueous species and minerals which are less well characterized than those with core or recommended application data. Supplemental data comprise uncertain data which did not meet the standards to be selected as recommended application data but are considered as suitable for scoping calculations and qualitative modelling. Their numerical values are either accompanied by large uncertainties or are considered as approximate or limiting. In several cases estimates are provided for important species where experimental data are missing or unreliable, particularly in cases where omission of such estimated data would lead to obviously unacceptable results. Such estimates are based on chemical analogies, linear free energy relationships or on other suitable estimation methods. Supplemental data were introduced with the update to the Nagra/PSI TDB 12/07.

The original Nagra/PSI TDB 01/01 was designed to be used with geochemical modeling codes that apply the law of mass action (LMA) algorithm. The essential thermodynamic data at 1 bar and 25 ̊C are equilibrium constants, logK(298), for the formation reactions of product species, which comprise aqueous species, solids, and gases. Each formation reaction involves a single product species which is related to at least one of the aqueous master species. Two types of such master species can be distinguished: The primary master species are the basic building blocks for setting up formation reactions, while the secondary master species themselves are related to primary master species by means of formation reactions (secondary master species are often chosen for convenience in formulating formation reactions). With this database structure (which has been retained for theNagra/PSI TDB 12/07), the minimal dataset required to calculate geochemical equilibria at 1 bar and 25 ̊C (0.1 MPa, 298.15 K), consists of a value for logK(298) for the formation reaction of each secondary master species and each product species, whereas no thermodynamic data are required for the primary master species.

1.1.2. Data import

Data from the Nagra/PSI TDB 01/01 were imported by means of the PMATCHC code (http://les.web.psi.ch/Software/PMATCHC/index.htm), while the update to the Nagra/PSI TDB 12/07 was made entirely within the "Thermodynamic Database" Mode of GEMS.

In order to make the imported Nagra/PSI TDB 01/01 also usable at elevated temperatures and pressures, it was merged with a subset of the slop98.dat file (http://geopig.asu.edu), as follows (for more details, see THOENEN and KULIK 2003 ):

Primary master species were put into DComp records, with thermodynamic data (G0(298), H0(298), etc.) taken in most cases from SHOCK et al. (1997). Secondary  master species were also put into DComp records, with G0(298) calculated from the G0(298) values of the primary master species and from the logK(298) given by the Nagra/PSI TDB 01/01 for the corresponding formation reaction of the secondary master species. In this way, the logK(298) values of the secondary master species contained in the Nagra/PSI TDB 01/01 are perfectly reproducible with the G0(298) values contained in the respective DComp records. Most other aqueous species, solids, and gases were put into ReacDC records, with reaction data (logK(298), H0r(298), etc.) taken from the Nagra/PSI TDB 01/01. In order to take advantage of the HKF-parameters available for several aqueous species from the SUPCRT database, these species were put into DComp records, with G0(298) calculated from the corresponding logK(298) taken from the Nagra/PSI TDB 01/01 and from the G0(298) values of the primary or secondary master species taking part in the formation reaction. All other thermodynamic data including the HKF-parameters were then taken from the SUPCRT database.

The GEMS-version of the PSI/Nagra TDB 12/07 has inherited all these procedures. In cases where the PSI/Nagra TDB 12/07 lacks certain data, the following assumptions were made:

1. DComp records for aqueous species: If only G0(298) is known, then H0(298) is set equal to G0(298), all Cp = f(T) coefficients are set to 0, and their temperature applicability to 0 to 50 °C. If only Cp0(298) is known, but not S0(298), the temperature interval is also set to 0 to 50 °C. For records in HKF format, the default applicability intervals for the SUPCRT database apply (up to 1000 °C and 5000 bar).
2. ReacDC records: If only logK(298) is known, then H0r is set to 0, S0r is set to '---' (empty), and, after recalculation, the temperature interval is set to 0 to 50 °C. This procedure makes the equilibrium constant of the reaction independent of temperature.
3. ReacDC records: If V0r is unknown, then it is set to a fictive value, such that V0(298) = 0 for the species defined by the reaction. The pressure interval is then set to 0 to 100 bar. This procedure minimizes the error introduced into the total volume of the system by such species.
4. ReacDC records: If either logK(298) and H0r(298) or logK(298) and S0r(298) are known, then the temperature applicability interval is set to 0 to 150 °C.

This GEMS version of the PSI/Nagra TDB 12/07 can be used in some cases for the reliable calculation of aquatic equilibria up to 150 - 200 ̊C at saturated vapor pressures. In most cases, however, calculations should be restricted to a pressure of 1 bar and to a temperature of 25 ̊C.

The PSI/Nagra TDB 12/07 part of the GEMS default database can be used alone or in combination with the SUPCRT92 part of the GEMS default database.

1.2. SUPCRT92 - slop98.dat

The SUPCRT92 part of the GEMS default database can be used alone or in combination with the PSI/Nagra TDB 12/07 part of the GEMS default database

1.2.1. About data import from the slop98.dat file

The SUPCRT dataset was imported from the slop98.dat file (http://geopig.asu.edu) as follows:

The original slop98.dat file was first split into seven ASCII files in order to import separately (i) aqueous inorganic species; (ii) aqueous organic species; (iii) gases; (iv) minerals without phase transitions; (v) minerals with one phase transition; (vi) minerals with two phase transitions; and (vii) all remaining records.  Each file was imported into DComp records of appropriate configuration using a suitable import script (available in the GEMS import script library as SDref records in the /DB.default/sdref.support.template.scripts.ver3.0.pdb file):

"iscript-SUPCRT-aqs:0000:dcomp:"
"iscript-SUPCRT-gas:0000:dcomp:"
"iscript-SUPCRT-min1:0001:dcomp:"
"iscript-SUPCRT-min2:0002:dcomp:"
"iscript-SUPCRT-min3:0003:dcomp:"

During data import, some formatting errors were fixed in the source files (the scripts read the input file as a stream and not  in fixed field format as the SUPCRT92 code does). In a second step, all DComp record keys (generated by import scripts) were edited to bring them in accordance with the style and format of the GEMS default chemical thermodynamic database.

Finally, in every record, the chemical formula (DCform field) was edited to bring it into conformance with the syntax of GEMS chemical formulae. In some cases, the explicit valence of redox-sensitive elements was entered to make sure that the correct formula charge is calculated. Note that the explicit valences in chemical formulae have been entered solely to balance the formula charge and, hence, these numbers neither correspond to actual ionic charges nor reflect any crystallochemical properties of ionic, covalent, hydrogen or other chemical bonds.

After that, each DComp record was re-calculated to check the internal consistency of the G0d, H0d, and S0d values. In rare cases, where the H0d value was found to be inconsistent, it was replaced by a consistent one (computed from G0d and S0d values), and a remark about this correction was placed in the dsDval field.

Data for minerals were imported assuming a constant molar volume (independent of T, P). For many minerals with one or two phase transitions, the slop98.dat file contains a "NULL" value (999999) for some or all parameters of the phase transition; such values would result in errors when thermodynamic properties were calculated in GEMS at temperatures above the phase transition. Hence, those "NULL" values were provisionally replaced by zeros in the default database file of GEM-Selektor (will be available in the next released version);  please, keep in mind that these data may still be incomplete and require separate checking before using them in calculations of chemical equilibria.

For a considerable number of minerals (e.g. zeolites), "NULL" values (999999 cal/mol) are given for standard molar Gibbs energy and enthalpy in the source slop98.dat file, indicating that these values are unknown. After import, these data in GEMS default database have been replaced by 7777777 J/mol in G0d[0] and H0d[0] cells. All such minerals were not referenced in Phase records to prevent taking them into calculations of chemical equilibria.

The calculation of the DComp record for NESQEHONITE resulted in Cp0(298) = -3689.18 J/K/mol, indicating an error in the Maier-Kelley coefficients for this mineral as given in the slop98.dat file. For Pd-Oxyannite, the chemical formula seems to be wrong as it produces a charge imbalance.

1.3. Third-party databases

1.4. Write protection

Note that all files of the default GEMS database (located in the /Resources/DB.default/ folder) are  write-protected, so that only developers can modify any data records. This is done to ensure a backward compatibility between different modelling projects. A modelling application produced using GEMS is actually a directory of database files, which, taken together, comprise a "modelling project".  All changes, input data, and results of modelling calculations will be stored in the project database files, which can be modified by the user who created it. A project directory can be packed and shared with other users or contributed to this site as a test example.

The user can create any number of projects, but typically, each project is created for a separate geochemical modelling study in a system of known elemental stoichiometry.  Only part of the default database (i.e. species and phases defined by a selection of stoichiometry units) will be copied into the project database. The latter can be extended or modified any time at the user's discretion, but none of these changes will  affect the default GEMS database (unless the user will find and report a bug in a record from the default database).  

2. List of files in the default thermodynamic database

<gems3-app>/Resources/DB.default/

The exact form of <gems3-app> depends on the PC platform, e.g.

Each file in GEMS database format, e.g. phase.supcrt.inorg.ver1998.pdb, comes with an (automatically created) index part, e.g. phase.supcrt.inorg.ver1998.ndx. This index file is used by the program to speed-up reading of database files and linking them into the database chains. For brevity, the *.ndx files are not shown in the lists below.

2.1. PSI/Nagra part of GEMS default database is located in files:

In the GEMS-version of the PSI/Nagra TDB 12/07 core data and recommended application data are taken together (they are referred to as recommended data) and are separated from the supplemental data in such a way that calculations can be made with recommended data only, or with a combination of recommended and supplemental data. There is no use in calculations with supplemental data only. The following database files concerning the PSI/Nagra TDB 12/07 are contained in DB.default:

2.2. SUPCRT92 part of the default database (imported) is located in files:

2.3. Supporting database files

This default script library consits of a collection of SDref records that contain print/export, import, and template math scripts that should help users to perform data import/export operations and to write math scripts. This default script library is located in the sdref.template.scripts.*  files in the /program/DB.default directory. The files are automatically linked to every user-created modelling project to make the script libraries accessible. 

3. LES PSI Thermodynamics Group

The LES PSI Thermodynamics Group (see http://les.web.psi.ch/groups) maintains the PSI/Nagra database which is provided as the default dataset with the GEM-Selektor code and which is oriented mainly to nuclear waste management applications at low temperatures and pressures.

4. References

BROWN, P.L., CURTI, E., GRAMBOW, B. (2005): Chemical Thermodynamics of Zirconium. Elsevier, Amsterdam, 512p.

COX, J.D., WAGMAN, D.D., MEDVEDEV, V.A. (1989): CODATA Key Values for Thermodynamics. Hemisphere, New York, 271p.

GAMSJÄGER, H., BUGAJSKI, J., GAJDA, T., LEMIRE, R.J., PREIS,W. (2005): Chemical Thermodynamics of Nickel. Elsevier, Amsterdam, 617p.

GUILLAUMONT, R., FANGHÄNEL, T., FUGER, J., GRENTHE, I., NECK, V., PALMER, D.A., RAND, M.A. (2003): Update on the Chemical Thermodynamics of Uranium, Neptunium, Plutonium, Americium and Technetium. Elsevier, Amsterdam, 763p.

HELGESON, H.C., KIRKHAM, D.H., FLOWERS, G.C. (1981): Theroretical prediction of the thermodynamic behavior of aqueous electrolytes at high pressures and temperatures: IV. Calculation of activity coefficients, osmotic coefficients, and apparent molal and standard and relative partial molal properties to 600˚C and 5 kb. American Journal of Science, 281, 1249-1516.

HUMMEL, W., BERNER, U., CURTI, E., PEARSON, F.J., THOENEN, T. (2002): Nagra/PSI Chemical Thermodynamic Data Base 01/01. Nagra NTB 02-16, Nagra, Wettingen, Switzerland. Also published by Universal Publishers/upublish.com, Parkland, USA. The Nagra NTB 02-16 can be downloaded free of charge from http://www.nagra.ch/g3.cms/s_page/77900/s_name/shopengl/S_NAME/shopde/lang/EN.

HUMMEL, W. (2012): The PSI/Nagra Chemical Thermodynamic Database 12/07 (Update of the Nagra/PSI TDB 01/01): Data Selection for Silicon. PSI Internal Report, TM-44-12-05, Paul Scherrer Institut, Villigen, Switzerland.

HUMMEL, W. (in prep.): The PSI/Nagra Chemical Thermodynamic Database 12/07 (Update of the Nagra/PSI TDB 01/01): Data Selection for Nickel. PSI Internal Report, TM-44-xx-xx, Paul Scherrer Institut, Villigen, Switzerland.

HUMMEL, W., revised by THOENEN, T. (2012): The PSI/Nagra Chemical Thermodynamic Database 12/07 (Update of the Nagra/PSI TDB 01/01): Data Selection for Technetium. PSI Internal Report, TM-44-12-02, Paul Scherrer Institut, Villigen, Switzerland.

HUMMEL, W., revised by THOENEN, T. (in prep.): The PSI/Nagra Chemical Thermodynamic Database 12/07 (Update of the Nagra/PSI TDB 01/01): Data Selection for Uranium. PSI Internal Report, TM-44-xx-xx, Paul Scherrer Institut, Villigen, Switzerland.

JOHNSON, J.W., OELKERS, E.H., HELGESON, H.C. (1992): SUPCRT92: A software package for calculating the standard molal thermodynamic properties of minerals, gases, aqueous species, and reactions from 1 to 5000 bar and 0 to 1000°C. Computers & Geosciences, 18, 899-947.

OLIN, Å, NOLÄNG, G., OSADCHII, E., ÖHMAN, L.-O., ROSÉN, E. (2005): Chemical Thermodynamics of Selenium. Elsevier, Amsterdam, 851p.

RAND, M., FUGER, J., GRENTHE, I., NECK, V., RAI, D. (2009): Chemical Thermodynamics of Thorium. OECD NEA, Issy-les-Moulineaux, France, 900p.

SHOCK, E.L., SASSANI, D.C., WILLIS, M. & SVERJENSKY, D.A. (1997): Inorganic species in geologic fluids: Correlations among standard molal thermodynamic properties of aqueous ions and hydroxide complexes. Geochimica et Cosmochimica Acta, 61, 907-950 (and references therein).

THOENEN, T., KULIK, D. (2003): Nagra/PSI Chemical Thermodynamic Data Base 01/01 for the GEM-Selektor (V.2-PSI) Geochemical Modeling Code: Release 28-02-03. PSI Internal Report, TM-44-03-04, Paul Scherrer Institut, Villigen, Switzerland. (http://les.web.psi.ch/Software/GEMS-PSI/doc/pdf/TM-44-03-04-web.pdf)

Last change: 30.04.2013 TT, DK

Copyright (c) 2003-2013  GEMS Development Team.