The chemical database
Notation and definitions are described in Nomenclature.
This page describes the GWB format, using a database file downloaded from the geochemist workbench site. See the "Thermo Datasets" chapter of Bethke et al. (2020) and https://academy.gwb.com
A database in GWB format can be converted to a MOOSE-formatted database using the supplied python utility
geochemistry/python/database_converter.py -i gwb_database --format gwb -o moose_database.json
The following details the GWB database section-by-section.
Descriptive header
The database file begins with a descriptive header:
dataset of thermodynamic data for gwb programs
dataset format: jan19
activity model: debye-huckel
fugacity model: tsonopoulos
Only the Debye-Huckel activity model model is currently supported. Only the Spycher-Reed fugacity model model is currently supported.
Temperature definition
All equilibrium coefficients, activity coefficients, etc, are evaluated at a set of temperatures. These are assumed to be in C, and defined by the line(s)
* temperatures
0.0000 25.0000 60.0000 100.0000
150.0000 200.0000 250.0000 300.0000
If a numerical simulation is performed at a temperature that is not one of these 8 values, a fourth-order polynomial fit to the data is used.
Steam saturation curve
The pressures — in bars (1 bar Pa) — along the steam saturation curve, at the temperatures defined above are given in the form
* pressures
1.0134 1.0134 1.0134 1.0134
4.7600 15.5490 39.7760 85.9270
Debye-Huckel coefficients
The Debye-Huckel coefficients are given next. These are evaluated at the temperatures defined above
* debye huckel a (adh)
.4913 .5092 .5450 .5998
.6898 .8099 .9785 1.2555
* debye huckel b (bdh)
.3247 .3283 .3343 .3422
.3533 .3655 .3792 .3965
* bdot
.0174 .0410 .0440 .0460
.0470 .0470 .0340 0.0000
The units are
has units mol.kg;
has units mol.kg.;
has units mol.kg.
So, for instance, at 25C
mol.kg,
mol.kg. and
mol.kg.
Neutral species activity coefficients
The temperature dependence of the parameters , , and that define the activity coefficients for the neutral species:
* c co2 1
.1224 .1127 .09341 .08018
.08427 .09892 .1371 .1967
* c co2 2
-.004679 -.01049 -.0036 -.001503
-.01184 -.0104 -.007086 -.01809
* c co2 3
-.0004114 .001545 9.609e-5 .0005009
.003118 .001386 -.002887 -.002497
* c co2 4
0.0000 0.0000 0.0000 0.0000
0.0000 0.0000 0.0000 0.0000
The formulae for neutral species is given in the activity coefficients page, and the special keyword acts as a flag to the solver to use this instead of the Debye-Huckel formula (for instance, see the basis species B(OH)3, below). See Section 3.1.4 of Bethke et al. (2020).
Water activity
The activity of water is defined by four coefficients, , , and , whose temperature dependence is given by
* c h2o 1
500.0000 1.45397 500.0000 1.5551
1.6225 500.0000 500.0000 500.0000
* c h2o 2
500.0000 .022357 500.0000 .036478
.045891 500.0000 500.0000 500.0000
* c h2o 3
500.0000 .0093804 500.0000 .0064366
.0045221 500.0000 500.0000 500.0000
* c h2o 4
500.0000 -.0005362 500.0000 -.0007132
-.0008312 500.0000 500.0000 500.0000
Note that only their values at 25C, 100C and 200C are given: the values of 500.0000 indicates "no value".
Element definitions
The names, chemical abbreviations and mole weights are provided by the following lines:
46 elements
Silver (Ag) mole wt.= 107.8680 g
Aluminum (Al) mole wt.= 26.9815 g
Americium (Am) mole wt.= 241.0600 g
...
-end-
Basis species
A list of the basis species and their properties are given by:
47 basis species
H2O
charge= 0 ion size= 0.0 A mole wt.= 18.0152 g
2 elements in species
2.000 H 1.000 O
Ag+
charge= 1 ion size= 2.5 A mole wt.= 107.8680 g
1 elements in species
1.000 Ag
...
B(OH)3
charge= 0 ion size= -.5 A mole wt.= 61.8329 g
3 elements in species
1.000 B 3.000 H 3.000 O
...
-end-
In these entries:
The first line defines the name (H2O, Ag+, etc)
The second line provides the charge, , and ion size, (both used in computing the activity) and the molecular weight. For neutral species, the activity is calculated (see Section 3.1.4 of Bethke et al. (2020)):
If
ion size=0and the species isH2O, the formula for the activity of water is usedIf
ion size=0and the species is notH2O, the activity is set to 1.If
ion size=-0.5Athe activity is calculated using the CO2 coefficientsIf
ion size<=-1Athe formula is used.
The remaining data provides the elemental decomposition.
Redox pairs
The database also contains redox pair information in the form:
48 redox couples
(O-phth)--
charge= -2 ion size= 4.0 A mole wt.= 164.1172 g
4 species in reaction
-5.000 H2O 8.000 HCO3- 6.000 H+
-7.500 O2(aq)
594.3211 542.8292 482.3612 425.9738
368.7004 321.8658 281.8216 246.4849
Am++++
charge= 4 ion size= 11.0 A mole wt.= 241.0600 g
4 species in reaction
-.500 H2O 1.000 H+ 1.000 Am+++
.250 O2(aq)
18.7967 18.0815 17.2698 16.5278
15.8024 15.2312 14.7898 14.4250
...
-end-
In these entries:
The first line defines the name ((O-phth)–, Am++++, etc)
The second line provides the charge, , and ion size, and the molecular weight. The former two are used to compute the activity for "decoupled" redox pairs.
The remaining data provides the equilibrium reaction (in terms of the basis species, or any redox species that have been defined so far), along with its temperature-dependent equilibrium constant, which are used when the redox pair is "coupled", for two purposes: (a) to eliminate the alternative oxidataion state ((O-phth)–, Am++++, etc) from all reactions in favour of the basis species; (b) to form another secondary-species reaction.
Aqueous species
Much of the database concerns equilibrium reactions to produce secondary species:
551 aqueous species
(NpO2)2(OH)2++
charge= 2 ion size= 5.0 A mole wt.= 572.1086 g
3 species in reaction
-2.000 H+ 2.000 H2O 2.000 NpO2++
7.0580 6.2979 5.5317 4.9568
4.5346 4.3362 4.2830 4.3258
(NpO2)3(OH)5+
charge= 1 ion size= 4.0 A mole wt.= 892.1775 g
3 species in reaction
-5.000 H+ 5.000 H2O 3.000 NpO2++
19.2691 17.3865 15.4529 13.9264
12.6876 11.9568 11.5491 11.3537
...
-end-
In these entries:
The first line defines the name ((NpO2)2(OH)2, etc)
The second line provides the charge, , and ion size, and the molecular weight. The first two are used to compute the activity coefficient for the species.
The remaining data provides the equilibrium reaction (in terms of basis species and redox couples) along with its temperature-dependent equilibrium constant.
Free electron
The data base contains:
1 free electron
e-
charge= -1 ion size= 0.0 A mole wt.= 0.0000 g
3 species in reaction
.500 H2O -.250 O2(g) -1.000 H+
22.76135 20.7757 18.513025 16.4658
14.473225 12.92125 11.68165 10.67105
-end-
Minerals
Mineralisation reactions are defined in ths following block:
624 minerals
(BaO)2^(SiO2)3(c) type=
formula=
mole vol.= 122.8000 cc mole wt.= 486.9117 g
4 species in reaction
-4.000 H+ 2.000 Ba++ 3.000 SiO2(aq)
2.000 H2O
24.8965 23.3104 21.2301 19.2286
17.2446 15.6907 14.3849 13.0572
...
Acanthite type= sulfide
formula= Ag2S
mole vol.= 34.2000 cc mole wt.= 247.7960 g
3 species in reaction
2.000 Ag+ -1.000 H+ 1.000 HS-
-39.7042 -36.0478 -31.9375 -28.2491
-24.6984 -22.0245 -20.0510 -18.7392
...
-end-
In these entries:
The first line defines the name ((BaO)2^(SiO2)3(c), Acanthite, etc)
The "type" and "formula" are optional, and are not used in the
geochemistrymoduleThe mole volume and mole weight are quantified (the activity for each mineral is unity)
The remaining data provides the equilibrium reaction (in terms of basis species and redox couples) along with its temperature-dependent equilibrium constant.
Gases
The thermodynamics of gases and reactions involving them are included in the database as:
10 gases
CH4(g)
mole wt.= 16.0426 g
chi= -537.779 1.54946 -.000927827 1.20861 -.00370814 3.33804e-6
Pcrit= 46.0 bar Tcrit= 190.4 K omega= .011
1 species in reaction
1.000 CH4(aq)
-2.6487 -2.8202 -2.9329 -2.9446
-2.9163 -2.7253 -2.4643 -2.1569
...
-end-
In these blocks:
The first line defines the name (CH4(g), etc)
The "chi" line defines the Spycher-Reed coefficients
The "Pcrit" line is used to evaluate Tsonopoulos and Peng-Robinson pressure models, and are not used in the
geochemistrymoduleThe remaining data define the equilibrium reaction and its constant.
References
- C. M Bethke, B. Farrell, and S. Yeakel.
The Geochemists's Workbench, Release 14: GWB Reference Manual.
Aqueous Solutions LLC, Champaign, UL, USA, 2020.
URL: https://www.gwb.com/pdf/GWB12/GWBreference.pdf.[BibTeX]