Elements in species have not been tabulated, SiO2

[kennedyantwi1]

Code: [Select]

Dear Dr. Parkhurst,
I'm attempting to model an H2-reservoir rock experimental study. I've included Quartz in my phases block and I'm getting the following error messages:
- Elements in species have not been tabulated, SiO2
- Reaction for species has not defined, SiO2

Please find below a portion of my code for your attention and guidance; Thanks in advance:

   [SOLUTION_MASTER_SPECIES
Tracer Tracer 0.0 1.0 1.0
Hydrogengas Hydrogengas 0.0 1.0 1.0

SOLUTION_SPECIES
Tracer = Tracer
-log_k 0.0
#-delta_h -4.184 kJ
#-analytic -9.3114 4.6473e-3 -49.335 1.4341 1.2815e5
#-T_c 33.2
#-P_c 12.80
#-Omega -0.2250   
-dw 1.0e-9
Hydrogengas = Hydrogengas
-log_k 0.0
-gamma 5.0 0.1650
-dw 0.793e-9
-millero -19.690 0.10580 -0.001256 1.617 -0.075 0.0008262 # density parameters
END

PHASES
Hydrogengas(g) # = H2(g) from phreeqc.dat
Hydrogengas = Hydrogengas
-log_k -3.1050
-delta_h -4.184 kJ
-analytic -9.3114 4.6473e-3 -49.335 1.4341 1.2815e5
-T_c 33.2
-P_c 12.80
-Omega -0.225

Pyrrhotite
FeS +1.0000 H+  =  + 1.0000 Fe++ + 1.0000 HS-
log_k -3.7193
-delta_H  -7.9496 kJ/mol # Calculated enthalpy of reaction Pyrrhotite
# Enthalpy of formation: -24 kcal/mol
-analytic -1.5785e+002 -5.2258e-002 3.9711e+003 6.3195e+001 6.2012e+001
# -Range:  0-300

Clinochlore-14A
Mg5Al2Si3O10(OH)8 +16.0000 H+  =  + 2.0000 Al+++ + 3.0000 SiO2 + 5.0000 Mg++ + 12.0000 H2O
log_k 67.2391
-delta_H -612.379 kJ/mol # Calculated enthalpy of reaction Clinochlore-14A
# Enthalpy of formation: -2116.96 kcal/mol
-analytic -2.0441e+002 -6.2268e-002 3.5388e+004 6.9239e+001 5.5225e+002
# -Range:  0-300

Daphnite-14A
Fe5AlAlSi3O10(OH)8 +16.0000 H+  =  + 2.0000 Al+++ + 3.0000 SiO2 + 5.0000 Fe++ + 12.0000 H2O
log_k 52.2821
-delta_H -517.561 kJ/mol # Calculated enthalpy of reaction Daphnite-14A
# Enthalpy of formation: -1693.04 kcal/mol
-analytic -1.5261e+002 -6.1392e-002 2.8283e+004 5.1788e+001 4.4137e+002
# -Range:  0-300

Quartz
SiO2 +2 H2O = H4SiO4
log_k -3.9993
-delta_H 32.949 kJ/mol # Calculated enthalpy of reaction Quartz
# Enthalpy of formation: -217.65 kcal/mol
-analytic 7.7698e-002 1.0612e-002 3.4651e+003 -4.3551e+000 -7.2138e+005
# -Range:  0-300
code]

[dlparkhurst]

You have used SiO2(aq) and H4SiO4(aq) in your definitions. You must use one or the other, depending on the database. SiO2 is used in llnl.dat type databases, and H4SiO4 is used in most others.

This will work with llnl.dat. Note that you do not need to redefine minerals if the definitions are the same as in the database.

For H4SiO4 databases, use the equation SiO2 + 2H2O = H4SiO4 (log_k 0) to convert all reactions in your input file that contain SiO2(aq).

Code: [Select]

SOLUTION_MASTER_SPECIES
Tracer Tracer 0.0 1.0 1.0
Hydrogengas Hydrogengas 0.0 1.0 1.0

SOLUTION_SPECIES
Tracer = Tracer
-log_k 0.0
#-delta_h -4.184 kJ
#-analytic -9.3114 4.6473e-3 -49.335 1.4341 1.2815e5
#-T_c 33.2
#-P_c 12.80
#-Omega -0.2250   
-dw 1.0e-9
Hydrogengas = Hydrogengas
-log_k 0.0
-gamma 5.0 0.1650
-dw 0.793e-9
-millero -19.690 0.10580 -0.001256 1.617 -0.075 0.0008262 # density parameters
END

PHASES
Hydrogengas(g) # = H2(g) from phreeqc.dat
Hydrogengas = Hydrogengas
-log_k -3.1050
-delta_h -4.184 kJ
-analytic -9.3114 4.6473e-3 -49.335 1.4341 1.2815e5
-T_c 33.2
-P_c 12.80
-Omega -0.225

Pyrrhotite
FeS +1.0000 H+  =  + 1.0000 Fe++ + 1.0000 HS-
log_k -3.7193
-delta_H  -7.9496 kJ/mol # Calculated enthalpy of reaction Pyrrhotite
# Enthalpy of formation: -24 kcal/mol
-analytic -1.5785e+002 -5.2258e-002 3.9711e+003 6.3195e+001 6.2012e+001
# -Range:  0-300

Clinochlore-14A
Mg5Al2Si3O10(OH)8 +16.0000 H+  =  + 2.0000 Al+++ + 3.0000 SiO2 + 5.0000 Mg++ + 12.0000 H2O
log_k 67.2391
-delta_H -612.379 kJ/mol # Calculated enthalpy of reaction Clinochlore-14A
# Enthalpy of formation: -2116.96 kcal/mol
-analytic -2.0441e+002 -6.2268e-002 3.5388e+004 6.9239e+001 5.5225e+002
# -Range:  0-300

Daphnite-14A
Fe5AlAlSi3O10(OH)8 +16.0000 H+  =  + 2.0000 Al+++ + 3.0000 SiO2 + 5.0000 Fe++ + 12.0000 H2O
log_k 52.2821
-delta_H -517.561 kJ/mol # Calculated enthalpy of reaction Daphnite-14A
# Enthalpy of formation: -1693.04 kcal/mol
-analytic -1.5261e+002 -6.1392e-002 2.8283e+004 5.1788e+001 4.4137e+002
# -Range:  0-300

Quartz
        SiO2 = SiO2
        log_k -3.9993
-delta_H 32.949 kJ/mol # Calculated enthalpy of reaction Quartz
# Enthalpy of formation: -217.65 kcal/mol
        -analytic 7.7698e-2 1.0612e-2 3.4651e+3 -4.3551e+0 -7.2138e+5
#       -Range:  0-300


[kennedyantwi1]

Code: [Select]

Thanks for your swift response Dr. Parkhurst; i'm however getting the same error messages using the Phreeqc.dat. The input file is again copied here for your guidance, thanks.

 [SOLUTION_MASTER_SPECIES
Tracer Tracer 0.0 1.0 1.0
Hydrogengas Hydrogengas 0.0 1.0 1.0

SOLUTION_SPECIES
Tracer = Tracer
-log_k 0.0
#-delta_h -4.184 kJ
#-analytic -9.3114 4.6473e-3 -49.335 1.4341 1.2815e5
#-T_c 33.2
#-P_c 12.80
#-Omega -0.2250   
-dw 1.0e-9
Hydrogengas = Hydrogengas
-log_k 0.0
-gamma 5.0 0.1650
-dw 0.793e-9
-millero -19.690 0.10580 -0.001256 1.617 -0.075 0.0008262 # density parameters
END

PHASES
Hydrogengas(g) # = H2(g) from phreeqc.dat
Hydrogengas = Hydrogengas
-log_k -3.1050
-delta_h -4.184 kJ
-analytic -9.3114 4.6473e-3 -49.335 1.4341 1.2815e5
-T_c 33.2
-P_c 12.80
-Omega -0.225

Pyrrhotite
FeS +1.0000 H+  =  + 1.0000 Fe++ + 1.0000 HS-
log_k -3.7193
-delta_H  -7.9496 kJ/mol # Calculated enthalpy of reaction Pyrrhotite
# Enthalpy of formation: -24 kcal/mol
-analytic -1.5785e+002 -5.2258e-002 3.9711e+003 6.3195e+001 6.2012e+001
# -Range:  0-300

Clinochlore-14A
Mg5Al2Si3O10(OH)8 +16.0000 H+  =  + 2.0000 Al+++ + 3.0000 SiO2 + 5.0000 Mg++ + 12.0000 H2O
log_k 67.2391
-delta_H -612.379 kJ/mol # Calculated enthalpy of reaction Clinochlore-14A
# Enthalpy of formation: -2116.96 kcal/mol
-analytic -2.0441e+002 -6.2268e-002 3.5388e+004 6.9239e+001 5.5225e+002
# -Range:  0-300

Daphnite-14A
Fe5AlAlSi3O10(OH)8 +16.0000 H+  =  + 2.0000 Al+++ + 3.0000 SiO2 + 5.0000 Fe++ + 12.0000 H2O
log_k 52.2821
-delta_H -517.561 kJ/mol # Calculated enthalpy of reaction Daphnite-14A
# Enthalpy of formation: -1693.04 kcal/mol
-analytic -1.5261e+002 -6.1392e-002 2.8283e+004 5.1788e+001 4.4137e+002
# -Range:  0-300

Quartz
SiO2 = SiO2
log_k -3.9993
-delta_H 32.949 kJ/mol # Calculated enthalpy of reaction Quartz
# Enthalpy of formation: -217.65 kcal/mol
-analytic 7.7698e-2 1.0612e-2 3.4651e+3 -4.3551e+0 -7.2138e+5
# -Range:  0-300
END

code]

[dlparkhurst]

Let me repeat, you cannot use SiO2(aq) with phreeqc.dat.

Your input file has the following:

Code: [Select]

Clinochlore-14A
Mg5Al2Si3O10(OH)8 +16.0000 H+  =  + 2.0000 Al+++ + 3.0000 SiO2 + 5.0000 Mg++ + 12.0000 H2O

That reaction must be converted from SiO2 on the right-hand-side to H4SiO4.

[kennedyantwi1]

Code: [Select]

Dear Dr. Parkhurst, I managed to convert SiO2 to H4SiO4 on the rhs of both reactions. The Error messages i'm getting this time relates to H2O as follows:
 - Elements in species have not  been tabulated, H2O
 - Reaction for the species has not been defined, H2O
I proceeded to fetch the reaction equation and thermodynamic data for H2O from the llnl database in case i'd need to include them in the input file:
2H2O =  O2 + 4H+ + 4e- 
-log_k -85.9951
-delta_H 559.543 kJ/mol # Calculated enthalpy of reaction O2
# Enthalpy of formation: -2.9 kcal/mol
-analytic   38.0229    7.99407E-03   -2.7655e+004  -1.4506e+001  199838.45
# Range:  0-300


Please, the code is attached here for your appreciated guidance.
Thanks.

[SOLUTION_MASTER_SPECIES
Tracer Tracer 0.0 1.0 1.0
Hydrogengas Hydrogengas 0.0 1.0 1.0

SOLUTION_SPECIES
Tracer = Tracer
-log_k 0.0
#-delta_h -4.184 kJ
#-analytic -9.3114 4.6473e-3 -49.335 1.4341 1.2815e5
#-T_c 33.2
#-P_c 12.80
#-Omega -0.2250   
-dw 1.0e-9
Hydrogengas = Hydrogengas
log_k 0.0
-gamma 5.0 0.1650
-dw 0.793e-9
-millero -19.690 0.10580 -0.001256 1.617 -0.075 0.0008262 # density parameters

PHASES
Hydrogengas(g) # = H2(g) from phreeqc.dat
Hydrogengas = Hydrogengas
log_k -3.1050
-delta_h -4.184 kJ
-analytic -9.3114 4.6473e-3 -49.335 1.4341 1.2815e5
-T_c 33.2
-P_c 12.80
-Omega -0.225

Pyrrhotite
FeS +1.0000 H+  =  + 1.0000 Fe++ + 1.0000 HS-
log_k -3.7193
-delta_H  -7.9496 kJ/mol # Calculated enthalpy of reaction Pyrrhotite
# Enthalpy of formation: -24 kcal/mol
-analytic -1.5785e+002 -5.2258e-002 3.9711e+003 6.3195e+001 6.2012e+001
# -Range:  0-300

Clinochlore-14A
Mg5Al2Si3O10(OH)8 + 16.0000 H+ = 2.0000 Al+++ + 3.0000 H4SiO4 + 5.0000 Mg++ + 6.0000 H20 
log_k 67.2391
-delta_H -612.379 kJ/mol # Calculated enthalpy of reaction Clinochlore-14A
# Enthalpy of formation: -2116.96 kcal/mol
-analytic -2.0441e+002 -6.2268e-002 3.5388e+004 6.9239e+001 5.5225e+002
# -Range:  0-300

Daphnite-14A
Fe5AlAlSi3O10(OH)8 +16.0000 H+  =  + 2.0000 Al+++ + 3.0000 H4SiO4 + 5.0000 Fe++ + 6.0000 H2O
log_k 52.2821
-delta_H -517.561 kJ/mol # Calculated enthalpy of reaction Daphnite-14A
# Enthalpy of formation: -1693.04 kcal/mol
-analytic -1.5261e+002 -6.1392e-002 2.8283e+004 5.1788e+001 4.4137e+002
# -Range:  0-300

END
code]

[dlparkhurst]

I don't see a question. I don't "check" code.

[kennedyantwi1]

 Please Dr. Parkhurst, the issue is how to solve the H2O error as stated below, thanks:
 - Elements in species have not  been tabulated, H2O
 - Reaction for the species has not been defined, H2O

[dlparkhurst]

Debug your input file.

Remove each mineral sequentially until you isolate the error.

[dlparkhurst]

You have added more minerals, and I don't know what database you are using.

Remove items until you have a file that runs, and then add items back in to isolate the problem. I'm done with this thread.

[kennedyantwi1]

I will do as you have suggested.
Thanks for your appreciated time.