Common RXN commands for the Geochemist’s Workbench software

1.0_RXN-activity inputs

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

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

 

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