Written by Allan Leal (ETH Zurich) on Jan 4th, 2022
{attention}
Always make sure you are using the [latest version of Reaktoro](https://anaconda.org/conda-forge/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](updating_reaktoro_via_conda) 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:
Another example is the combustion of a solid substance. We must define a chemical system composed of:
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.
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`!
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) H2O(aq) H2O 0.018015 CaOH+ CaOH+ 0.057085 CO(aq) CO 0.028010 CO2(aq) CO2 0.044010 CO3-2 CO3-2 0.060010 Ca(HCO3)+ Ca(HCO3)+ 0.101095 Ca+2 Ca+2 0.040077 CaCl+ CaCl+ 0.075530 CaCl2(aq) CaCl2 0.110983 Cl- Cl- 0.035453 HClO(aq) HClO 0.052460 ClO- ClO- 0.051453 ClO2- ClO2- 0.067452 ClO3- ClO3- 0.083451 ClO4- ClO4- 0.099451 H+ H+ 0.001007 H2(aq) H2 0.002016 HCO3- HCO3- 0.061018 HO2- HO2- 0.033007 Na+ Na+ 0.022989 NaCl(aq) NaCl 0.058442 NaOH(aq) NaOH 0.039997 O2(aq) O2 0.031999 OH- OH- 0.017008 H2O2(aq) H2O2 0.034015 HClO2(aq) HClO2 0.068459 HCl(aq) HCl 0.036461 CaCO3(aq) CaCO3 0.100087 CH4(aq) CH4 0.016043 H-Acetate(aq) C2H4O2 0.060053 Acetate- C2H3O2- 0.059045 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-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 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 o-Cresol(aq) C6H4OHCH3 0.108140 m-Cresol(aq) C6H4OHCH3 0.108140 p-Cresol(aq) C6H4OHCH3 0.108140 Decanoate C10H19O2- 0.171260 Decanoic-Acid(aq) C10H20O2 0.172268 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 3,4-DMP(aq) C6H3OHCH3CH3 0.122167 3,5-DMP(aq) C6H3OHCH3CH3 0.122167 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 Glutarate C5H6O4-2 0.130101 Glutaric-Acid(aq) C5H8O4 0.132116 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 Heptanoate C7H13O2- 0.129180 Heptanoic-Acid(aq) C7H14O2 0.130187 Hexanoate C6H11O2- 0.115153 Hexanoic-Acid(aq) C6H12O2 0.116160 m-Toluate C8H7O2- 0.135143 m-Toluic-Acid(aq) C8H8O2 0.136150 Malonate C3H2O4-2 0.102048 Malonic-Acid(aq) C3H4O4 0.104062 Methanol(aq) CH3OH 0.032042 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 Nonanoate C9H17O2- 0.157233 Nonanoic-Acid(aq) C9H18O2 0.158241 o-Toluate C8H7O2- 0.135143 o-Toluic-Acid(aq) C8H8O2 0.136150 Octanoate C8H15O2- 0.143206 Octanoic-Acid(aq) C8H16O2 0.144214 Oxalate C2O4-2 0.088021 Oxalic-Acid(aq) C2H2O4 0.090035 p-Toluate C8H7O2- 0.135143 p-Toluic-Acid(aq) C8H8O2 0.136150 Phenol(aq) C6H5OH 0.094113 Pimelate C7H10O4-2 0.158155 Pimelic-Acid(aq) C7H12O4 0.160170 Propane(aq) C3H8 0.044097 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 Acetaldehyde(aq) CH3CHO 0.044053 Butanal(aq) CH3(CH2)2CHO 0.072107 Decanal(aq) CH3(CH2)8CHO 0.156268 Formaldehyde(aq) HCHO 0.030026 Heptanal(aq) CH3(CH2)5CHO 0.114188 Hexanal(aq) CH3(CH2)4CHO 0.100161 Nonanal(aq) CH3(CH2)7CHO 0.142241 Octanal(aq) CH3(CH2)6CHO 0.128214 Pentanal(aq) CH3(CH2)3CHO 0.086134 Propanal(aq) CH3CH2CHO 0.058080 Na(Ac)(aq) NaCH3COO 0.082034 Na(Ac)2- Na(CH3COO)2- 0.141080 Ca(Ac)+ CaCH3COO+ 0.099122 Ca(Ac)2(aq) Ca(CH3COO)2 0.158167 Lactate C3H5O3- 0.089071 Lactic-Acid(aq) C3H6O3 0.090079 Ca(Lac)+ CaCH3CH2OCO2+ 0.129148 Ca(Lac)2(aq) Ca(CH3CH2OCO2)2 0.218220 Na(Lac)(aq) NaCH3CH2OCO2 0.112061 Na(Lac)2- Na(CH3CH2OCO2)2- 0.201132 Glycolic-Acid(aq) C2H4O3 0.076052 Glycolate C2H3O3- 0.075045 Ca(Glyc)+ CaCH3OCO2+ 0.115121 Ca(Glyc)2(aq) Ca(CH3OCO2)2 0.190166 Na(Glyc)(aq) Na(CH3OCO2) 0.098034 Na(Glyc)2- Na(CH3OCO2)2- 0.173078 Formic-Acid(aq) H2CO2 0.046026 Formate HCO2- 0.045018 Ca(For)+ CaCHO2+ 0.085095 Ca(For)2(aq) Ca(CHO2)2 0.130113 Na(For)(aq) NaCHO2 0.068008 Na(For)2- Na(CHO2)2- 0.113026 Propanoic-Acid(aq) C3H6O2 0.074079 Propanoate C3H5O2- 0.073072 Ca(Prop)+ CaCH3CH2CO2+ 0.113149 Ca(Prop)2(aq) Ca(CH3CH2CO2)2 0.186221 Na(Prop)(aq) NaCH3CH2CO2 0.096061 Na(Prop)2- Na(CH3CH2CO2)2- 0.169133 Butanoic-Acid(aq) C4H8O2 0.088106 Butanoate C4H7O2- 0.087099 Ca(But)+ CaCH3(CH2)2CO2+ 0.127176 Ca(But)2(aq) Ca(CH3CH2CH2CO2)2 0.214275 Na(But)(aq) NaCH3(CH2)2CO2 0.110088 Na(But)2- Na(CH3CH2CH2CO2)2- 0.197187 Pentanoic-Acid(aq) C5H10O2 0.102133 Pentanoate C5H9O2- 0.101126 Ca(Pent)+ CaCH3(CH2)3CO2+ 0.141203 Ca(Pent)2(aq) Ca(CH3CH2CH2CH2CO2)2 0.242329 Na(Pent)(aq) NaCH3(CH2)3CO2 0.124115 Na(Pent)2- Na(CH3CH2CH2CH2CO2)2- 0.225241 CH4(g) CH4 0.016043 CO(g) CO 0.028010 CO2(g) CO2 0.044010 H2(g) H2 0.002016 O2(g) O2 0.031999 H2O(g) H2O 0.018015 Phenol(g) C6H5OH 0.094113 o-Cresol(g) CH3C6H4(OH) 0.108140 m-Cresol(g) CH3C6H4(OH) 0.108140 p-Cresol(g) CH3C6H4(OH) 0.108140 Ethylene(g) C2H4 0.028054
This chemical system contains many species. The SUPCRTBL database contains many organic species that should play an insignificant role in accurately computing CO{{_2}} 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())
H2O(aq) CaOH+ CO(aq) CO2(aq) CO3-2 Ca(HCO3)+ Ca+2 CaCl+ CaCl2(aq) Cl- HClO(aq) ClO- ClO2- ClO3- ClO4- H+ H2(aq) HCO3- HO2- Na+ NaCl(aq) NaOH(aq) O2(aq) OH- H2O2(aq) HClO2(aq) HCl(aq) CaCO3(aq) 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)
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 :: SO2@ :: 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 Corundum :: Corundum 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 Fe2O3 :: Fe2O3 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 Periclase :: Periclase 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
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, K{{_2}}S(cd), K{{_2}}SO{{_4}}(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!