Follow their official user manual. I think they need to provide some more detailed examples in their manual. I use this cheat sheet for my own use a lot. Review, update and share any comments.
1.0_RXN-activity inputs
Commands that works
ACTIVITY
To assign activity, use “activity” or “a” followed by constituent name.
- Rxn> activity Ca++ = .3
- Rxn> a H2O = .9
- Rxn> log a H+ = -5
- Rxn> a U++++=?
- Rxn>
Common Errors:
Rxn> activity Ca+2 = .3
— Error: Don’t know species Ca+2
Can’t set activity of Ca+2
Rxn> actibity Ca++ = .3
— Error: Unknown command: actibity
FUGACITY:
“fugacity” command (“f”) is used to set gas fugacities (on an atm scale) for the calculation.
- fugacity O2(g) = .2
- f CO2(g) = 0.0003
- log f S2(g) = 30
Rxn> f CO2 = 10
— Error: Don’t know species CO2
Can’t set fugacity of CO2
Rxn> f CO2(g) = .004
— Error: Gas CO2(g) needs to be swapped into the basis
Can’t set fugacity of CO2(g)
ADD
Adds species to the reaction model
- add Na+
- add HCO3-
REMOVE:
This command removes species from the reaction model. You must have the basis species in the model already:
Rxn> remove Quartz Calcite
— Error: Species Quartz not in basis
— Error: Species Calcite not in basis
Rxn> add Quartz
— Error: Don’t know basis species Quartz
Rxn> add Na+
Rxn> add Calcite
— Error: Don’t know basis species Calcite
Rxn> remove Na+
Rxn> add K+
Rxn>
ALTER
“alter” command is used to change values of the equilibrium constant for the reaction of
a species, mineral, or gas.
Equilibrium constants are given as log(10) K’s at 0°C, 25°C,60°C, 100°C, 150°C, 200°C, 250°C, 300°C; values of “500” represent a lack of data at the corresponding temperature.
CLEAR
Clean the command panel.
Pwd:
returns the name of the current working directory
Rxn> pwd
Working directory: c:\users\ankan.basu
Quit:
- does what it says, quits the program.
CLIPBOARD:
- Great command. It copies your reaction to the clipboard. You can then easily paste it to word.
- Example paste from clipboard: Akermanite + 6 H+ = 2 Ca++ + 3 H2O + Mg++ + 2 SiO2(aq)
EXPLAIN
Rxn> explain Analcime
Analcime: NaAlSi2O6:H2O zeolite
mole weight = 220.154 g/mol
molar volume = 97.100 cm3/mol, density = 2.267 g/cm3
Rxn> explanin Calcium Carbonate
— Error: Unknown command: explanin
Rxn> explain Calcium Carbonate
Calcium: element
mole weight = 40.080 g/mol
— Carbonate is not a known species, mineral, or gas
Rxn> explain CaCO3
CaCO3: aqueous species
mole weight = 100.089 g/mol
FACTOR:
“factor” is another cool command that I use periodically. Extremely useful to:
- Reverse a reaction ( Negative values reverse the reaction)
- multiply reaction coefficients by a numeric value
- factor -1
- factor 2
- factor 5/2
- With factor 1: AgCl4— = Ag+ + 4 Cl-
- With factor -1: Ag+ + 4 Cl- = AgCl4—
- With factor 5/2: 2.5 Ag+ + 10 Cl- = 2.5 AgCl4—
HISTORY:
It does what it means.
Rxn> history
- 156: go
- 157: factor 1
- 158: go
- 159: factr -1
- 160: factor -1
- 161: go
- 162: factor 5/2
- 163: clipboard
- 164: clipboard newpane
- 165: go
- 166: clipboard docopy
- 167: clipboard oldpane
- 168: f CO2 = 10
- 169: f CO2(g) = .004
- 170: add Ni++
- 171: remove Ni++
- 172: add HCO3-
- 173: swap CO2(g) HCO3-
- 174: go
- 175: f CO2(g) = .004
- 176: go
- 177: go
IONIC_STRENGTH
- Use: ionic_strength=.5; or I=.5; or IS=.5 to set the ionic strength of the solution.
LONG:
- Use long to get a more detailed output
pe and pH:
- Set the pe and pH of the reaction
Rxn> pe = 10
— Error: Species e- needs to be swapped into the basis
Can’t set pe of e-
Remember to swap e- for O2(aq)
Rxn> pe = 10
Rxn> pH=5
Rxn>
POLYMORPH:
polymorph Two compounds that have the same composition, but different crystal structures are said to be polymorphs. Examples: calcite/aragonite, quartz/coesite, forsterite/wadsleyite, sillimanite/andalusite/kyanite.
This command is useful tool to check for polymorphs of various minerals. Example:
Rxn> polymorphs Quartz
Polymorphs of Quartz: Amrph^silica Chalcedony Cristobalite Tridymite
Rxn>
RATIO:
“ratio” command is used to set activity or fugacity ratios for the calculation.
swap Ca++/Na+^2 for Ca++
ratio Ca++/Na+^2 = 0.3
REACT
Use this to run a reaction.
Rxn> react CH4(g) log fugacity = 1
Rxn> factor -1
Rxn> factor 1/2.5
The command above produces:
CH4(g) + 2 O2(aq) = H2O + H+ + HCO3-
Log K’s:
0 °C: 155.2433 150 °C: 94.7897
25 °C: 141.2878 200 °C: 82.5627
60 °C: 125.0031 250 °C: 72.2857
100 °C: 109.9354 300 °C: 63.4931
Polynomial fit:
log K = 155.2 – .599 × T + .001812 × T^2 – 3.93e-6 × T^3 + 3.832e-9 × T^4
Assumptions implicit in equilibrium equation:
fugacity of CH4(g) = 10^1
Equilibrium equation:
log K = -1 + log a[H2O] + log a[H+] + log a[HCO3-]
– 2 × log a[O2(aq)]
REPORT:
This command can be used to look for various values within the model.
Rxn> report
error no keyword to report
Rxn> report options
equil_eqn equil_temp equil_favors
logk logks nlogks
polyfit reaction temps
Rxn> report logk
error Temp_c is null
Rxn> report polyfir
error keyword not recognized
Rxn> report polyfit
155.225053542 -0.599041625361 0.00181192384091 -3.93044855342e-0063.83157076295e-009
Rxn> report equil_favors
none
Rxn>
REVERSE:
This command does the same thing as factor -1.
SAVE:
This command will save a concise database.
Rxn> save
Save current system to what file? : test
Display saved file? (y/n): y
# Rxn script, saved Wed Dec 04 2013 by Ankan.Basu
data = “C:\Program Files (x86)\Gwb\Gtdata\thermo.dat” verify
ionic_strength = .9
react CH4(g)
log fugacity CH4(g) = 1
activity H2O = ?
activity H+ = ?
activity HCO3- = ?
activity O2(aq) = ?
activity K+ = ?
long
Rxn>
SHOW:
Use it to debug.
Rxn> show
Balancing reaction for:
(UO2)2(CO3)(OH)3- Activity = 10^1
In terms of the basis:
H2O Activity = 10^???
H+ Activity = 10^???
HCO3- Activity = 10^???
O2(aq) Activity = 10^???
U++++ Activity = 10^???
Ionic strength (molal) = .9 (true), ??? (stoichiometric)
Thermo dataset: C:\Program Files (x86)\Gwb\Gtdata\thermo.dat
Working directory: c:\users\ankan.basu
Other “show” options: type “show show”
Rxn>
SWAP:
This is a very powerful command as it can be used to change the set of basis entries.
- swap CO3for
- HCO3swap
- Quartz for SiO2(aq)
- swap CO2(g) for H+
- swap O2(g) for O2(aq)
swap Ca++/Na+^2 for Ca++
TEMPERATURE:
Use this command to set the temperature.
- temperature 29 C
- temperature 310 F
- T = 298 K
What I don’t know:
- How to use the BLOCK command in RXN. Send me any info that you may have.
- Not sure how to set up the redox-coupling properly.
- How to use “read” command