Defining chemical systems
Contents
Defining chemical systems#
Written by Allan Leal (ETH Zurich) on Jan 4th, 2022
Attention
Always make sure you are using the latest version of Reaktoro. Otherwise, some new features documented on this website will not work on your machine and you may receive unintuitive errors. Follow these update instructions to get the latest version of Reaktoro!
Before performing chemical reaction calculations, such as chemical equilibrium and kinetics, we need to determine the phases that must be considered in the calculation and the chemical species that constitute these phases.
For example, to calculate the solubility of a mineral in water, two phases must be considered:
an aqueous phase representing water and dissolved species; and
a solid phase representing the mineral we want to dissolve in the aqueous solution.
Another example is the combustion of a solid substance. We must define a chemical system composed of:
a gaseous phase containing most of the gases relevant to the process; and
one or more solid/liquid substances (condensed phases) that may appear during the combustion process.
The concept of a chemical system is represented in Reaktoro using the ChemicalSystem class. You should expect to construct one object of this class for almost every chemical process you want to model.
In a ChemicalSystem object, you can find a list of Phase objects representing the phases. The Phase class is also an essential component of Reaktoro. It contains the list of chemical species composing the phase, as a list of Species objects. Additionally, each Phase object includes its activity model to account for its non-ideal thermodynamic behavior.
Note
We’ll learn more about activity models in a subsequent section and how to specify them for our phases.
Next, we will present how to construct a chemical system in Reaktoro for different applications.
Chemical system definition for a mineral solubility problem#
Let’s consider the chemical equilibrium problem associated with calculating the solubility of halite (NaCl) in water. The code block below demonstrates how a ChemicalSystem object is created with an aqueous and mineral phase.
from reaktoro import *
# Let's use one of PHREEQC's database
db = PhreeqcDatabase("phreeqc.dat")
# Define an aqueous solution with species that are pertinent to the problem
solution = AqueousPhase("H2O H+ OH- Na+ Cl-")
# Because we want to compute the solubility of halite, a mineral phase is needed
halite = MineralPhase("Halite")
# We can now create our ChemicalSystem object with the above phase specifications
system = ChemicalSystem(db, solution, halite)
That’s it! With the ChemicalSystem object created above, we can do some exciting things. For example, we can inspect the phases in the system and their composing chemical species:
for phase in system.phases():
print(phase.name())
for species in phase.species():
print(":: " + species.name())
AqueousPhase
:: H2O
:: H+
:: OH-
:: Na+
:: Cl-
Halite
:: Halite
Note
Reaktoro has default names for phases, such as AqueousPhase and GaseousPhase for aqueous and gaseous phases. For pure mineral phases, the phase name is the same as the name of the mineral species composing it. That’s is why the mineral phase above is named Halite, whose only composing species is called Halite. Note also that Reaktoro supports as many phases as you wish, each phase containing any number of species. We will demonstrate this in subsequent tutorials.
We can also inspect how the chemical species are ordered in the system:
for species in system.species():
print(species.name())
H2O
H+
OH-
Na+
Cl-
Halite
And inspect the chemical elements in the system:
for element in system.elements():
print(element.symbol())
H
O
Na
Cl
The ChemicalSystem class also contains the formula matrix \(A\) of the system, which is a matrix whose entry \(A_{j,i}\) contains the number of atoms of element with index \(j\) in species with index \(i\):
print(system.formulaMatrix())
[[ 2. 1. 1. 0. 0. 0.]
[ 1. 0. 1. 0. 0. 0.]
[ 0. 0. 0. 1. 0. 1.]
[ 0. 0. 0. 0. 1. 1.]
[ 0. 1. -1. 1. -1. 0.]]
The last row in the formula matrix contains the electric charge of each species.
Tip
Access the link ChemicalSystem to find out all methods available in class ChemicalSystem!
Chemical system definition for a gas solubility problem#
We now consider a chemical system of interest for the computation of CO2 solubility in saline solutions. For this case, we will need an aqueous and gaseous phase:
from reaktoro import *
# Let's use the SUPCRTBL database this time (its complete version that includes organic species)
db = SupcrtDatabase("supcrtbl-organics")
# Define an aqueous solution with automatic species collection for given selected elements
solution = AqueousPhase(speciate("H O Na Cl Ca C"))
# Let Reaktoro automatically identify the gases by specifying an empty list of species below
gas = GaseousPhase()
# We can now create our ChemicalSystem object with the above phase specifications
system = ChemicalSystem(db, solution, gas)
Let’s print the species in the system, their names, formula, and molar mass:
print("{:<25}{:<25}{:<20}".format("Name", "Formula", "Molar Mass (kg/mol)"))
for species in system.species():
print("{:<25}{:<25}{:<20.6f}".format(species.name(), species.formula().str(), species.molarMass()))
Name Formula Molar Mass (kg/mol)
1-Butanol(aq) C4H9OH 0.074123
1-Butene(aq) C4H8 0.056108
1-Butyne(aq) C4H6 0.054092
1-Heptanol(aq) C7H15OH 0.116203
1-Heptene(aq) C7H14 0.098188
1-Heptyne(aq) C7H12 0.096172
1-Hexanol(aq) C6H13OH 0.102177
1-Hexene(aq) C6H12 0.084161
1-Hexyne(aq) C6H10 0.082145
1-Octanol(aq) C8H17OH 0.130230
1-Octene(aq) C8H16 0.112215
1-Octyne(aq) C8H14 0.110199
1-Pentanol(aq) C5H11OH 0.088150
1-Pentene(aq) C5H10 0.070134
1-Pentyne(aq) C5H8 0.068119
1-Propanol(aq) C3H7OH 0.060096
1-Propene(aq) C3H6 0.042081
1-Propyne(aq) C3H4 0.040065
2,3-DMP(aq) C6H3OHCH3CH3 0.122167
2,4-DMP(aq) C6H3OHCH3CH3 0.122167
2,5-DMP(aq) C6H3OHCH3CH3 0.122167
2,6-DMP(aq) C6H3OHCH3CH3 0.122167
2-Butanone(aq) C4H8O 0.072107
2-Heptanone(aq) C7H14O 0.114188
2-Hexanone(aq) C6H12O 0.100161
2-Hydroxybutanoate C4H7O3- 0.103098
2-Hydroxybutanoic(aq) C4H8O3 0.104106
2-Hydroxydecanoate C10H19O3- 0.187260
2-Hydroxydecanoic(aq) C10H20O3 0.188267
2-Hydroxyheptanoic C7H14O3 0.146186
2-Hydroxyhexanoate C6H11O3- 0.131152
2-Hydroxyhexanoic(aq) C6H12O3 0.132159
2-Hydroxynonanoate C9H17O3- 0.173233
2-Hydroxynonanoic(aq) C9H18O3 0.174240
2-Hydroxyoctanoate C8H15O3- 0.159206
2-Hydroxyoctanoic(aq) C8H16O3 0.160213
2-Hydroxypentanoic C5H10O3 0.118133
2-Octanone(aq) C8H16O 0.128214
2-Pentanone(aq) C5H10O 0.086134
3,4-DMP(aq) C6H3OHCH3CH3 0.122167
3,5-DMP(aq) C6H3OHCH3CH3 0.122167
Acetaldehyde(aq) CH3CHO 0.044053
Acetate- C2H3O2- 0.059045
Acetone(aq) C3H6O 0.058080
Adipate C6H8O4-2 0.144128
Adipic-Acid(aq) C6H10O4 0.146143
Azelaic-Acid(aq) C9H16O4 0.188224
Azelate C9H14O4-2 0.186209
Benzene(aq) C6H6 0.078114
Benzoate C7H5O2- 0.121116
Benzoic-Acid(aq) C7H6O2 0.122123
Butanal(aq) CH3(CH2)2CHO 0.072107
Butanoate C4H7O2- 0.087099
Butanoic-Acid(aq) C4H8O2 0.088106
CH4(aq) CH4 0.016043
CO(aq) CO 0.028010
CO2(aq) CO2 0.044010
CO3-2 CO3-2 0.060010
Ca(Ac)+ CaCH3COO+ 0.099122
Ca(Ac)2(aq) Ca(CH3COO)2 0.158167
Ca(But)+ CaCH3(CH2)2CO2+ 0.127176
Ca(But)2(aq) Ca(CH3CH2CH2CO2)2 0.214275
Ca(For)+ CaCHO2+ 0.085095
Ca(For)2(aq) Ca(CHO2)2 0.130113
Ca(Glyc)+ CaCH3OCO2+ 0.115121
Ca(Glyc)2(aq) Ca(CH3OCO2)2 0.190166
Ca(HCO3)+ Ca(HCO3)+ 0.101095
Ca(Lac)+ CaCH3CH2OCO2+ 0.129148
Ca(Lac)2(aq) Ca(CH3CH2OCO2)2 0.218220
Ca(Pent)+ CaCH3(CH2)3CO2+ 0.141203
Ca(Pent)2(aq) Ca(CH3CH2CH2CH2CO2)2 0.242329
Ca(Prop)+ CaCH3CH2CO2+ 0.113149
Ca(Prop)2(aq) Ca(CH3CH2CO2)2 0.186221
Ca+2 Ca+2 0.040077
CaCO3(aq) CaCO3 0.100087
CaCl+ CaCl+ 0.075530
CaCl2(aq) CaCl2 0.110983
CaOH+ CaOH+ 0.057085
Cl- Cl- 0.035453
ClO- ClO- 0.051453
ClO2- ClO2- 0.067452
ClO3- ClO3- 0.083451
ClO4- ClO4- 0.099451
Decanal(aq) CH3(CH2)8CHO 0.156268
Decanoate C10H19O2- 0.171260
Decanoic-Acid(aq) C10H20O2 0.172268
Dodecanoate C12H23O2- 0.199314
Dodecanoic-Acid(aq) C12H24O2 0.200321
Ethane(aq) C2H6 0.030070
Ethanol(aq) C2H5OH 0.046069
Ethylacetate(aq) CH3COOCH2CH3 0.088106
Ethylbenzene(aq) C6H5C2H5 0.106167
Ethylene(aq) C2H4 0.028054
Ethyne(aq) C2H2 0.026038
Formaldehyde(aq) HCHO 0.030026
Formate HCO2- 0.045018
Formic-Acid(aq) H2CO2 0.046026
Glutarate C5H6O4-2 0.130101
Glutaric-Acid(aq) C5H8O4 0.132116
Glycolate C2H3O3- 0.075045
Glycolic-Acid(aq) C2H4O3 0.076052
H+ H+ 0.001007
H-Acetate(aq) C2H4O2 0.060053
H-Adipate C6H9O4- 0.145136
H-Azelate C9H15O4- 0.187216
H-Glutarate C5H7O4- 0.131109
H-Malonate C3H3O4- 0.103055
H-Oxalate C2HO4- 0.089028
H-Pimelate C7H11O4- 0.159162
H-Sebacate C10H17O4- 0.201243
H-Suberate C8H13O4- 0.173189
H-Succinate C4H5O4- 0.117082
H2(aq) H2 0.002016
H2O(aq) H2O 0.018015
H2O2(aq) H2O2 0.034015
HCO3- HCO3- 0.061018
HCl(aq) HCl 0.036461
HClO(aq) HClO 0.052460
HClO2(aq) HClO2 0.068459
HO2- HO2- 0.033007
Heptanal(aq) CH3(CH2)5CHO 0.114188
Heptanoate C7H13O2- 0.129180
Heptanoic-Acid(aq) C7H14O2 0.130187
Hexanal(aq) CH3(CH2)4CHO 0.100161
Hexanoate C6H11O2- 0.115153
Hexanoic-Acid(aq) C6H12O2 0.116160
Lactate C3H5O3- 0.089071
Lactic-Acid(aq) C3H6O3 0.090079
Malonate C3H2O4-2 0.102048
Malonic-Acid(aq) C3H4O4 0.104062
Methanol(aq) CH3OH 0.032042
Na(Ac)(aq) NaCH3COO 0.082034
Na(Ac)2- Na(CH3COO)2- 0.141080
Na(But)(aq) NaCH3(CH2)2CO2 0.110088
Na(But)2- Na(CH3CH2CH2CO2)2- 0.197187
Na(For)(aq) NaCHO2 0.068008
Na(For)2- Na(CHO2)2- 0.113026
Na(Glyc)(aq) Na(CH3OCO2) 0.098034
Na(Glyc)2- Na(CH3OCO2)2- 0.173078
Na(Lac)(aq) NaCH3CH2OCO2 0.112061
Na(Lac)2- Na(CH3CH2OCO2)2- 0.201132
Na(Pent)(aq) NaCH3(CH2)3CO2 0.124115
Na(Pent)2- Na(CH3CH2CH2CH2CO2)2- 0.225241
Na(Prop)(aq) NaCH3CH2CO2 0.096061
Na(Prop)2- Na(CH3CH2CO2)2- 0.169133
Na+ Na+ 0.022989
NaCl(aq) NaCl 0.058442
NaOH(aq) NaOH 0.039997
Nonanal(aq) CH3(CH2)7CHO 0.142241
Nonanoate C9H17O2- 0.157233
Nonanoic-Acid(aq) C9H18O2 0.158241
O2(aq) O2 0.031999
OH- OH- 0.017008
Octanal(aq) CH3(CH2)6CHO 0.128214
Octanoate C8H15O2- 0.143206
Octanoic-Acid(aq) C8H16O2 0.144214
Oxalate C2O4-2 0.088021
Oxalic-Acid(aq) C2H2O4 0.090035
Pentanal(aq) CH3(CH2)3CHO 0.086134
Pentanoate C5H9O2- 0.101126
Pentanoic-Acid(aq) C5H10O2 0.102133
Phenol(aq) C6H5OH 0.094113
Pimelate C7H10O4-2 0.158155
Pimelic-Acid(aq) C7H12O4 0.160170
Propanal(aq) CH3CH2CHO 0.058080
Propane(aq) C3H8 0.044097
Propanoate C3H5O2- 0.073072
Propanoic-Acid(aq) C3H6O2 0.074079
Sebacate C10H16O4-2 0.200236
Sebacic-Acid(aq) C10H18O4 0.202251
Suberate C8H12O4-2 0.172182
Suberic-Acid(aq) C8H14O4 0.174197
Succinate C4H4O4-2 0.116074
Succinic-Acid(aq) C4H6O4 0.118089
Toluene(aq) C6H5CH3 0.092141
Undecanoate C11H21O2- 0.185287
Undecanoic-Acid(aq) C11H22O2 0.186294
m-Cresol(aq) C6H4OHCH3 0.108140
m-Toluate C8H7O2- 0.135143
m-Toluic-Acid(aq) C8H8O2 0.136150
n-Butane(aq) C4H10 0.058123
n-Butylbenzene(aq) C6H5C4H9 0.134221
n-Heptane(aq) C7H16 0.100204
n-Heptylbenzene(aq) C6H5C7H15 0.176302
n-Hexane(aq) C6H14 0.086177
n-Hexylbenzene(aq) C6H5C6H13 0.162275
n-Octane(aq) C8H18 0.114231
n-Octylbenzene(aq) C6H5C8H17 0.190329
n-Pentane(aq) C5H12 0.072150
n-Pentylbenzene(aq) C6H5C5H1 0.148248
n-Propylbenzene(aq) C6H5C3H7 0.120194
o-Cresol(aq) C6H4OHCH3 0.108140
o-Toluate C8H7O2- 0.135143
o-Toluic-Acid(aq) C8H8O2 0.136150
p-Cresol(aq) C6H4OHCH3 0.108140
p-Toluate C8H7O2- 0.135143
p-Toluic-Acid(aq) C8H8O2 0.136150
CH4(g) CH4 0.016043
CO(g) CO 0.028010
CO2(g) CO2 0.044010
Ethylene(g) C2H4 0.028054
H2(g) H2 0.002016
H2O(g) H2O 0.018015
O2(g) O2 0.031999
Phenol(g) C6H5OH 0.094113
m-Cresol(g) CH3C6H4(OH) 0.108140
o-Cresol(g) CH3C6H4(OH) 0.108140
p-Cresol(g) CH3C6H4(OH) 0.108140
This chemical system contains many species. The SUPCRTBL database contains many organic species that should play an insignificant role in accurately computing CO2 solubility. All organic species in SUPCRT and SUPCRTBL databases in Reaktoro’s YAML format have an organic tag which we can use to filter out them.
Let’s then redefine our ChemicalSystem object system by excluding those
organic aqueous species and specifying exactly the gases we want:
solution = AqueousPhase(speciate("H O Na Cl Ca C"), exclude("organic"))
gas = GaseousPhase("CO2(g)")
system = ChemicalSystem(db, solution, gas)
Warning
Make sure you specify species names exactly how they exist in the Database
object you have created, such as in GaseousPhase("CO2(g)") above. Otherwise
you will get a runtime exception!
Note
You can use SupcrtDatabase("supcrtbl") if you want the SUPCRTBL database version without organic species. In this case, the exclude("organic") filter is not needed and has no effect.
And here is the updated list of species (only their names this time):
for species in system.species():
print(species.name())
CO(aq)
CO2(aq)
CO3-2
Ca(HCO3)+
Ca+2
CaCO3(aq)
CaCl+
CaCl2(aq)
CaOH+
Cl-
ClO-
ClO2-
ClO3-
ClO4-
H+
H2(aq)
H2O(aq)
H2O2(aq)
HCO3-
HCl(aq)
HClO(aq)
HClO2(aq)
HO2-
Na+
NaCl(aq)
NaOH(aq)
O2(aq)
OH-
CO2(g)
You may still be discontent with so many aqueous species for the sake of CO2 solubility calculation. We demonstrate with the code block below how to specify the exact aqueous species to be considered in the phase using a list of species names.
aqueous_species = [
"H2O(aq)",
"CaOH+",
"CO2(aq)",
"CO3-2",
"Ca(HCO3)+",
"Ca+2",
"CaCl+",
"Cl-",
"H+",
"HCO3-",
"HO2-",
"Na+",
"OH-"
]
solution = AqueousPhase(aqueous_species)
system = ChemicalSystem(db, solution, gas)
for species in system.species():
print(species.name())
H2O(aq)
CaOH+
CO2(aq)
CO3-2
Ca(HCO3)+
Ca+2
CaCl+
Cl-
H+
HCO3-
HO2-
Na+
OH-
CO2(g)
Chemical system definition with many phases#
Now, let’s overcomplicate and define a chemical system with many phases and species. We have an aqueous solution for which we know the chemical elements of interest. We want Reaktoro to automatically include in our chemical system all minerals that could potentially be important (e.g., minerals that could precipitate as the solution temperature is changed). These are minerals in the database whose constituting elements are found in the aqueous solution. We also want to show how a mineral phase can be defined as a solid solution (containing more than one mineral end-member).
We demonstrate the above requirements for creating a chemical system in the
code block below. Note the use of the cemdata18 database provided by
ThermoFun, which is suitable for modeling cement chemistry.
db = ThermoFunDatabase("cemdata18")
solution = AqueousPhase(speciate("H O Na Cl Ca Mg C Si Fe Al K S"))
gas = GaseousPhase()
pureminerals = MineralPhases()
solidsolution = MineralPhase("ettringite Fe-ettringite")
system = ChemicalSystem(db, solution, gas, pureminerals, solidsolution)
Let’s now print the phase names and their composing species:
for phase in system.phases():
print(phase.name())
for species in phase.species():
print(":: " + species.name())
AqueousPhase
:: Al(SO4)+
:: Al(SO4)2-
:: Al+3
:: AlO+
:: AlO2-
:: AlO2H@
:: AlOH+2
:: AlSiO5-3
:: CH4@
:: CO2@
:: CO3-2
:: Ca(CO3)@
:: Ca(HCO3)+
:: Ca(HSiO3)+
:: Ca(SO4)@
:: Ca+2
:: CaOH+
:: CaSiO3@
:: Cl-
:: ClO4-
:: Fe(CO3)@
:: Fe(HCO3)+
:: Fe(HSO4)+
:: Fe(HSO4)+2
:: Fe(SO4)+
:: Fe(SO4)2-
:: Fe(SO4)@
:: Fe+2
:: Fe+3
:: FeCl+
:: FeCl+2
:: FeCl2+
:: FeCl3@
:: FeO+
:: FeO2-
:: FeO2H@
:: FeOH+
:: FeOH+2
:: H+
:: H2@
:: H2O@
:: H2S@
:: HCO3-
:: HS-
:: HSO3-
:: HSO4-
:: HSiO3-
:: K(SO4)-
:: K+
:: KOH@
:: Mg(CO3)@
:: Mg(HCO3)+
:: Mg(HSiO3)+
:: Mg+2
:: MgOH+
:: MgSO4@
:: Na(CO3)-
:: Na(HCO3)@
:: Na(SO4)-
:: Na+
:: NaOH@
:: O2@
:: OH-
:: S2O3-2
:: SO3-2
:: SO4-2
:: Si4O10-4
:: SiO2@
:: SiO3-2
GaseousPhase
:: CH4
:: CO2
:: H2
:: H2O
:: H2S
:: O2
ettringite
:: ettringite
:: Fe-ettringite
5CA
:: 5CA
5CNA
:: 5CNA
AlOHam
:: AlOHam
AlOHmic
:: AlOHmic
Amor-Sl
:: Amor-Sl
Anh
:: Anh
Arg
:: Arg
Brc
:: Brc
C12A7
:: C12A7
C2AClH5
:: C2AClH5
C2AH65
:: C2AH65
C2AH7.5
:: C2AH7.5
C2S
:: C2S
C3A
:: C3A
C3AFS0.84H4.32
:: C3AFS0.84H4.32
C3AH6
:: C3AH6
C3AS0.41H5.18
:: C3AS0.41H5.18
C3AS0.84H4.32
:: C3AS0.84H4.32
C3FH6
:: C3FH6
C3FS0.84H4.32
:: C3FS0.84H4.32
C3FS1.34H3.32
:: C3FS1.34H3.32
C3S
:: C3S
C4AClH10
:: C4AClH10
C4AF
:: C4AF
C4AH11
:: C4AH11
C4AH13
:: C4AH13
C4AH19
:: C4AH19
C4AsClH12
:: C4AsClH12
C4FH13
:: C4FH13
CA
:: CA
CA2
:: CA2
CAH10
:: CAH10
CSH3T-T2C
:: CSH3T-T2C
CSH3T-T5C
:: CSH3T-T5C
CSH3T-TobH
:: CSH3T-TobH
CSHQ-JenD
:: CSHQ-JenD
CSHQ-JenH
:: CSHQ-JenH
CSHQ-TobD
:: CSHQ-TobD
CSHQ-TobH
:: CSHQ-TobH
Cal
:: Cal
Dis-Dol
:: Dis-Dol
ECSH1-KSH
:: ECSH1-KSH
ECSH1-NaSH
:: ECSH1-NaSH
ECSH1-SH
:: ECSH1-SH
ECSH1-TobCa
:: ECSH1-TobCa
ECSH2-JenCa
:: ECSH2-JenCa
ECSH2-KSH
:: ECSH2-KSH
ECSH2-NaSH
:: ECSH2-NaSH
ECSH2-TobCa
:: ECSH2-TobCa
Ettringite13_des
:: Ettringite13_des
Ettringite9_des
:: Ettringite9_des
Fe
:: Fe
Fe-ettringite
:: Fe-ettringite
Fe-ettringite05
:: Fe-ettringite05
Fe-hemicarbonate
:: Fe-hemicarbonate
Fe-monosulph05
:: Fe-monosulph05
Fe-monosulphate
:: Fe-monosulphate
FeOOHmic
:: FeOOHmic
Femonocarbonate
:: Femonocarbonate
Gbs
:: Gbs
Gp
:: Gp
Gr
:: Gr
Gt
:: Gt
Hem
:: Hem
INFCA
:: INFCA
INFCN
:: INFCN
INFCNA
:: INFCNA
Jennite
:: Jennite
K2O
:: K2O
K2SO4
:: K2SO4
KSiOH
:: KSiOH
Kln
:: Kln
Lim
:: Lim
M075SH
:: M075SH
M15SH
:: M15SH
M4A-OH-LDH
:: M4A-OH-LDH
M6A-OH-LDH
:: M6A-OH-LDH
M8A-OH-LDH
:: M8A-OH-LDH
Mag
:: Mag
Melanterite
:: Melanterite
Mg2AlC0.5OH
:: Mg2AlC0.5OH
Mg2FeC0.5OH
:: Mg2FeC0.5OH
Mg3AlC0.5OH
:: Mg3AlC0.5OH
Mg3FeC0.5OH
:: Mg3FeC0.5OH
Mgs
:: Mgs
Na2O
:: Na2O
Na2SO4
:: Na2SO4
NaSiOH
:: NaSiOH
Ord-Dol
:: Ord-Dol
Portlandite
:: Portlandite
Py
:: Py
Qtz
:: Qtz
Sd
:: Sd
Sulfur
:: Sulfur
T2C-CNASHss
:: T2C-CNASHss
T5C-CNASHss
:: T5C-CNASHss
Tob-I
:: Tob-I
Tob-II
:: Tob-II
TobH-CNASHss
:: TobH-CNASHss
Tro
:: Tro
chabazite
:: chabazite
ettringite!
:: ettringite
ettringite03_ss
:: ettringite03_ss
ettringite05
:: ettringite05
ettringite13
:: ettringite13
ettringite30
:: ettringite30
ettringite9
:: ettringite9
ettringite_ss
:: ettringite_ss
hemicarbonat10.5
:: hemicarbonat10.5
hemicarbonate
:: hemicarbonate
hemicarbonate9
:: hemicarbonate9
hemihydrate
:: hemihydrate
hydrotalcite
:: hydrotalcite
monocarbonate
:: monocarbonate
monocarbonate05
:: monocarbonate05
monocarbonate9
:: monocarbonate9
monosulphate10.5
:: monosulphate10.5
monosulphate12
:: monosulphate12
monosulphate1205
:: monosulphate1205
monosulphate14
:: monosulphate14
monosulphate16
:: monosulphate16
monosulphate9
:: monosulphate9
natrolite
:: natrolite
straetlingite
:: straetlingite
straetlingite5.5
:: straetlingite5.5
straetlingite7
:: straetlingite7
syngenite
:: syngenite
thaumasite
:: thaumasite
tricarboalu
:: tricarboalu
tricarboalu03
:: tricarboalu03
zeoliteP_Ca
:: zeoliteP_Ca
zeoliteX
:: zeoliteX
zeoliteY
:: zeoliteY
Tip
If efficient calculations are required in your application, you may want to be more selective in the phases and species that populate your chemical system! Unfortunately, it is not always possible to know in advance the species that do not make sense for our model. So do it carefully. Ensure that for all thermodynamic/chemical conditions of interest (e.g. for temperature, pressure ranges of interest) the species you want to exclude from the system are negligible (i.e. exist with numerically zero or tiny amounts).
Imagine, however, you are dealing with two minerals and water and you don’t want to specify the chemical elements in the definition of the aqueous phase. This is what you can do:
db = PhreeqcDatabase("phreeqc.dat")
solution = AqueousPhase()
albite = MineralPhase("Albite")
kaolinite = MineralPhase("Kaolinite")
system = ChemicalSystem(db, albite, kaolinite, solution)
Let’s now find out which aqueous species were selected automatically for our aqueous phase:
aqueousphase = system.phases().get("AqueousPhase")
for species in aqueousphase.species():
print(species.name())
H+
H2O
Al+3
Al(OH)2+
Al(OH)3
Al(OH)4-
AlOH+2
H2
H4SiO4
H2SiO4-2
H3SiO4-
Na+
OH-
NaOH
O2
Chemical system definition for a combustion problem#
Forget about water now and let’s construct a chemical system suitable for modeling the combustion of black powder. Black powder is composed of potassium nitrate (KNO3), charcoal (C10Ca0.026H4.774N0.039O1.234), and sulfur (S8).
In the code block below we construct a chemical system using the chemical elements above.
# Let's use the NASA-CEA database for this example
db = NasaDatabase("nasa-cea")
# Consider all possible condensed phases (solid or liquid substances) with given elements
condensed = CondensedPhases(speciate("K N O C Ca H S"))
# Automatically select the gases based on the elements above
gases = GaseousPhase()
# Create a chemical system suitable for modeling combustion of black powder!
system = ChemicalSystem(db, gases, condensed)
We print below the gases and condensed phases constituting our chemical system:
print("Gases")
for species in system.species():
if species.aggregateState() == AggregateState.Gas:
print(":: " + species.name())
print("Condensed Phases")
for species in system.species():
if species.aggregateState() == AggregateState.CondensedPhase:
print(":: " + species.name())
Gases
:: e-
:: C
:: C+
:: C-
:: CH
:: CH+
:: CH2
:: CH3
:: CH2OH
:: CH2OH+
:: CH3O
:: CH4
:: CH3OH
:: CH3OOH
:: CN
:: CN+
:: CN-
:: CNN
:: CO
:: CO+
:: COS
:: CO2
:: CO2+
:: COOH
:: CS
:: CS2
:: C2
:: C2+
:: C2-
:: C2H
:: C2H2,acetylene
:: C2H2,vinylidene
:: CH2CO,ketene
:: O(CH)2O
:: HO(CO)2OH
:: C2H3,vinyl
:: CH3CN
:: CH3CO,acetyl
:: C2H4
:: C2H4O,ethylen-o
:: CH3CHO,ethanal
:: CH3COOH
:: OHCH2COOH
:: C2H5
:: C2H6
:: CH3N2CH3
:: C2H5OH
:: CH3OCH3
:: CH3O2CH3
:: CCN
:: CNC
:: OCCN
:: C2N2
:: C2O
:: C2S2
:: C3
:: C3H3,1-propynl
:: C3H3,2-propynl
:: C3H4,allene
:: C3H4,propyne
:: C3H4,cyclo-
:: C3H5,allyl
:: C3H6,propylene
:: C3H6,cyclo-
:: C3H6O,propylox
:: C3H6O,acetone
:: C3H6O,propanal
:: C3H7,n-propyl
:: C3H7,i-propyl
:: C3H8
:: C3H8O,1propanol
:: C3H8O,2propanol
:: CNCOCN
:: C3OS
:: C3O2
:: C3S2
:: C4
:: C4H2,butadiyne
:: C4H4,1,3-cyclo-
:: C4H6,butadiene
:: C4H6,1butyne
:: C4H6,2butyne
:: C4H6,cyclo-
:: C4H8,1-butene
:: C4H8,cis2-buten
:: C4H8,tr2-butene
:: C4H8,isobutene
:: C4H8,cyclo-
:: (CH3COOH)2
:: C4H9,n-butyl
:: C4H9,i-butyl
:: C4H9,s-butyl
:: C4H9,t-butyl
:: C4H10,n-butane
:: C4H10,isobutane
:: C4N2
:: C5
:: C5H6,1,3cyclo-
:: C5H8,cyclo-
:: C5H10,1-pentene
:: C5H10,cyclo-
:: C5H11,pentyl
:: C5H11,t-pentyl
:: C5H12,n-pentane
:: C5H12,i-pentane
:: CH3C(CH3)2CH3
:: C6H2
:: C6H5,phenyl
:: C6H5O,phenoxy
:: C6H6
:: C6H5OH,phenol
:: C6H10,cyclo-
:: C6H12,1-hexene
:: C6H12,cyclo-
:: C6H13,n-hexyl
:: C6H14,n-hexane
:: C7H7,benzyl
:: C7H8
:: C7H8O,cresol-mx
:: C7H14,1-heptene
:: C7H15,n-heptyl
:: C7H16,n-heptane
:: C7H16,2-methylh
:: C8H8,styrene
:: C8H10,ethylbenz
:: C8H16,1-octene
:: C8H17,n-octyl
:: C8H18,n-octane
:: C8H18,isooctane
:: C9H19,n-nonyl
:: C10H8,naphthale
:: C10H21,n-decyl
:: C12H9,o-bipheny
:: C12H10,biphenyl
:: Ca
:: Ca+
:: CaH
:: CaO
:: CaO+
:: CaOH
:: CaOH+
:: Ca(OH)2
:: CaS
:: Ca2
:: H
:: H+
:: H-
:: HCN
:: HCO
:: HCO+
:: HCCN
:: HCCO
:: HNC
:: HNCO
:: HNO
:: HNO2
:: HNO3
:: HO2
:: HO2-
:: H2
:: H2+
:: H2-
:: HCHO,formaldehy
:: HCOOH
:: H2O
:: H2O+
:: H2O2
:: H2S
:: H2SO4
:: H3O+
:: (HCOOH)2
:: K
:: K+
:: K-
:: KCN
:: KH
:: KNO2
:: KNO3
:: KO
:: KOH
:: K2
:: K2+
:: K2CO3
:: K2C2N2
:: K2O
:: K2O+
:: K2O2
:: K2O2H2
:: K2SO4
:: N
:: N+
:: N-
:: NCO
:: NH
:: NH+
:: NH2
:: NH3
:: NH2OH
:: NH4+
:: NO
:: NO+
:: NO2
:: NO2-
:: NO3
:: NO3-
:: N2
:: N2+
:: N2-
:: NCN
:: N2H2
:: NH2NO2
:: N2H4
:: N2O
:: N2O+
:: N2O3
:: N2O4
:: N2O5
:: N3
:: N3H
:: O
:: O+
:: O-
:: OH
:: OH+
:: OH-
:: O2
:: O2+
:: O2-
:: O3
:: S
:: S+
:: S-
:: SH
:: SH-
:: SN
:: SO
:: SO-
:: SO2
:: SO2-
:: SO3
:: S2
:: S2-
:: S2O
:: S3
:: S4
:: S5
:: S6
:: S7
:: S8
:: JP-10(g)
:: Jet-A(g)
Condensed Phases
:: Ca(cd)
:: CaCO3(cd)
:: CaH2(cd)
:: CaO(cd)
:: Ca(OH)2(cd)
:: CaS(cd)
:: CaSO4(cd)
:: K(cd)
:: KCN(cd)
:: KH(cd)
:: KNO2(cd)
:: KNO3(cd)
:: KOH(cd)
:: KO2(cd)
:: K2CO3(cd)
:: K2O(cd)
:: K2O2(cd)
:: K2S(cd)
:: K2SO4(cd)
:: S(cd)
:: NH4NO3(cd)
Let’s check how many phases and species were collected in our system:
print("Number of species in the system:", system.species().size())
print("Number of phases in the system:", system.phases().size())
Number of species in the system: 317
Number of phases in the system: 67
This is an impressive number of species and phases to be able to model the combustion of black powder!
Note
By including as many gases and condensed phases as possible, Reaktoro will be able to determine those that may appear after burning black powder. For example, K2S(cd), K2SO4(cd) and CaS(cd) are typically formed in the combustion process. By including them in the definition of the chemical system, the chemical equilibrium solver will be able to find positive amounts for them (i.e., the solver will identify these condensed phases as stable in equilibrium).
Keep reading to learn more about how the ChemicalSystem class plays an important role in Reaktoro!