Conceptual Models > Database selection and modification
Adding new species
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helenaig:
I am probably missing something really basic.
SOLUTION_MASTER_SPECIES
Pt Pt+2 0 198.084 195.084
Pt(4) Pt+4 0 198.084
Pd Pd+2 0 106.42 106.42
Pd(4) Pd+4 0 106.42
SOLUTION_SPECIES
Cl- + Pt+2 = PtCl+
log_k 4.97
2H+ + 0.5O2 + Pt = Pt+2 + H2O
log_k -0.21
2Cl- + Pt+2 = PtCl2
log_k 8.97
3Cl- + Pt+2 = PtCl3-
log_k 11.89
4Cl- + Pt+2 = Pt(Cl4)2-
log_k 13.99
-no_check
OH- + Pt+2 = Pt(OH)+
log_k 24.91
2OH- + Pt+2 = Pt(OH)2
log_k 28.81
3Cl- + H+ + H2O + Pd+2 = PdCl3(OH)-2
log_k 2.31
-no_check
H+ + H2O + Pd+2 = Pd(OH)+
log_k -1.86
-no_check
3H2O + Pd+2 = Pd(OH)3- + 3H+
log_k -15.93
4H2O + Pd+2 = Pd(OH)4-2 + 4H+
log_k -29.36
SOLUTION_SPREAD
-pH 2.09
Pt Pd Cl(-1) Na
mMol/kgw mMol/kgw mMol/kgw mMol/kgw
7.872850467 5.512294293 0.00001
and I get these errors:
ERROR: Elements in species have not been tabulated, Pd+4.
ERROR: Reaction for species has not been defined, Pd+4.
ERROR: Elements in species have not been tabulated, Pt.
ERROR: Reaction for species has not been defined, Pt.
ERROR: Elements in species have not been tabulated, Pt+4.
ERROR: Reaction for species has not been defined, Pt+4.
ERROR: Calculations terminating due to input errors.
How can I correct this? Many thanks
dlparkhurst:
You must also define Pt(2) and Pd(2) with secondary master species the same as the primary master species.
Try that and report any additional errors.
helenaig:
Thanks! I only now got back to my data analysis and tried it, and i get now these errors
SOLUTION_MASTER_SPECIES
Pt Pt+2 0 195.084 195.084
Pt(2) Pt+2 0 195.084
Pt(4) Pt+4 0 195.084
Pd Pd+2 0 106.42 106.42
Pd(2) Pd+2 0 106.42
Pd(4) Pd+4 0 106.42
SOLUTION_SPECIES
Cl- + Pt+2 = PtCl+
log_k 4.97
2H+ + 0.5O2 + Pt = Pt+2 + H2O
log_k -0.21
2Cl- + Pt+2 = PtCl2
log_k 8.97
3Cl- + Pt+2 = PtCl3-
log_k 11.89
4Cl- + Pt+2 = Pt(Cl4)2-
log_k 13.99
-no_check
OH- + Pt+2 = Pt(OH)+
log_k 24.91
2OH- + Pt+2 = Pt(OH)2
log_k 28.81
H2O + PdCl4 2- = PdCl3OH2- + Cl- + H+
log_k -8.98
-no_check
H+ + H2O + Pd+2 = Pd(OH)+
log_k -1.86
-no_check
3H2O + Pd+2 = Pd(OH)3- + 3H+
log_k -15.93
4H2O + Pd+2 = Pd(OH)4-2 + 4H+
log_k -29.36
SOLUTION_SPREAD
-pH 2
-units mg/l
Cl(-1) Pd Pt
mg/l mg/l mg/l
354.53 0.369801331 0.586618359
354.53 0.38058745 4.812944891
227.49 0.069265977 0.002002382
354.53 0.001717131 0.004538214
9100 0.048206 0.005173
ERROR: Elements in species have not been tabulated, Pd+4.
ERROR: Reaction for species has not been defined, Pd+4.
ERROR: Elements in species have not been tabulated, PdCl42-.
ERROR: Reaction for species has not been defined, PdCl42-.
ERROR: Elements in species have not been tabulated, Pt.
ERROR: Reaction for species has not been defined, Pt.
ERROR: Elements in species have not been tabulated, Pt+4.
ERROR: Reaction for species has not been defined, Pt+4.
ERROR: Calculations terminating due to input errors.
Any help would be much appreciated!
dlparkhurst:
The following will run, but you must carefully check the reactions and log Ks.
To model Pt(4) and Pd(4) you must define SOLUTION_SPECIES for reactions from Pt+2 to Pt+4 and Pd+2 to Pd+4, plus any other species associated with these valence states.
--- Code: ---SOLUTION_MASTER_SPECIES
Pt Pt+2 0 195.084 195.084
Pt(2) Pt+2 0 195.084
# Pt(4) Pt+4 0 195.084 #! no Pt+4 species defined
Pd Pd+2 0 106.42 106.42
Pd(2) Pd+2 0 106.42
# Pd(4) Pd+4 0 106.42 #! no Pd+4 species defined
SOLUTION_SPECIES
Pt+2 = Pt+2 #! need this reaction
log_k 0
Cl- + Pt+2 = PtCl+
log_k 4.97
#2H+ + 0.5O2 + Pt = Pt+2 + H2O #! don't think you want this reaction
# log_k -0.21
2Cl- + Pt+2 = PtCl2
log_k 8.97
3Cl- + Pt+2 = PtCl3-
log_k 11.89
4Cl- + Pt+2 = Pt(Cl4)-2 #! charge must be defined as -2, not 2-
log_k 13.99
# -no_check
OH- + Pt+2 = Pt(OH)+
log_k 24.91
2OH- + Pt+2 = Pt(OH)2
log_k 28.81
Pd+2 = Pd+2 #! need this reaction
log_k 0
Pd+2 + 4Cl- = PdCl4-2 #! need this reaction
log_k 0 #! need a log K
H2O + PdCl4-2 = PdCl3OH-2 + Cl- + H+ #! charge must be -2, not 2-
log_k -8.98
# -no_check
H2O + Pd+2 = Pd(OH)+ + H+ #! reaction balances with H+ on RHS
log_k -1.86
# -no_check
3H2O + Pd+2 = Pd(OH)3- + 3H+
log_k -15.93
4H2O + Pd+2 = Pd(OH)4-2 + 4H+
log_k -29.36
#! if you want +4 valence states, you must define species
#! Pt+2 = Pt+4 + 2e-
#! Pd+2 = Pd+4 + 2e-
SOLUTION
-units mg/L
Pd 1
Pt 1
Cl 1 charge
END
--- End code ---
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