Adding new species

[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: [Select]

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