Surface complexciation

[Anvj0705]

I  am attempting to model the adsorption of DFOB on a pyrite surface, but I am encountering the following error...
Although Sid-3 is already included in the species section, I am still encountering the following error. Could you please help me resolve it?
Thank you!"

ERROR: Elements in species have not been tabulated, Sid-3.
ERROR: Reaction for species has not been defined, Sid-3.
ERROR: Calculations terminating due to input errors.

Code: [Select]

TITLE Sorption of DFOB on Pyrite.

SURFACE_MASTER_SPECIES
Surf_s Surf_sSH
#Surf_w Surf_wOH

EQUILIBRIUM_PHASES 1
Pyrite 0 4.167E-3

SURFACE_SPECIES
Surf_sSH = Surf_sSH
log_k 0.0
Surf_sSH = Surf_sS- + H+
log_k -6.45
#Surf_sOH = Surf_sOH
log_k 0.0
#Surf_sOH = Surf_sO- + H+
log_k -3.12
Surf_sSH + Sid-3 + 4H+ = Surf_sSH4Sid + H+
log_k 5
Surf_sSH + Sid-3 + H+ + Fe+3 = Surf_sSFeHSid + H+
log_k 7
Surf_sSH + Sid-3 + 2H+ + Fe+3 = Surf_sSFeH2Sid+ + H+
log_k 10



PHASES
Fix_H+
H+ = H+
log_k 0.0
END

SOLUTION_SPECIES
1.000Sid-3 = 1.000Sid-3
     log_k     0.000     

1.000Sid-3 + 1.000H+     = 1.000HSid-2
log_k 11.45

1.000Sid-3 + 2.000H+     = 1.000H2Sid-
log_k 21.44

1.000Sid-3 + 3.000H+     = 1.000H3Sid
log_k 30.62

1.000Sid-3 + 4.000H+     = 1.000H4Sid+
log_k 38.94

1.000Sid-3 + 3.000H+ + 1.000Fe+2  = 1.000FeH3Sid+2
log_k 33.53

1.000Sid-3 + 2.000H+ + 1.000Fe+2  = 1.000FeH2Sid+
log_k 27.90

1.000Sid-3 + 1.000Fe+3 = 1.000FeSid
log_k 30.10

1.000Sid-3 + 1.000H+ + 1.000Fe+3 = FeHSid+
log_k 41.36

1.000Sid-3 + 2.000H+ + 1.000Fe+3 = FeH2Sid+2
log_k 42.33

SOLUTION_MASTER_SPECIES
#element      species       alk           gfw_formula   element_gfw
Sid          Sid-3        2             Sid-3          656.8

END



SOLUTION 1
temp 25
units mol/kgw
O(0) 1 O2(g) -0.7 #O(0):dissolved Oxygen: 1ppm; O2(g):concentration will be adjusted until a log partial pressure of oxygen gas of -0.7 is achieved.
#Fe(3) 0.497e-4
-water 1 #kg
END


USE solution 1
SURFACE 1
-equilibrate with solution 1
Surf_sSH 5.575E-9 0.0671 2.0
#Surf_wOH
-donnan 1e-9

END

SELECTED_OUTPUT
        -file surface_complex.sel
  -reset false
        -molalities tot_Fe Sid Surf_sSH Surf_sS- Surf_sSH4Sid Surf_sSFeHSid Surf_sSFeH2Sid+
 

USE solution 1
REACTION
Sid 5E-4
USE SURFACE 1
EQUILIBRIUM_PHASES 1
Fix_H+ -2.0 HCl 10
Pyrite 0 4.167E-3
Goethite 0 0
Hematite 0 0
Magnetite 0 0
Ferryhydrite 0 0
 
END

USE solution 1
REACTION
Sid 5E-4
USE SURFACE 1
EQUILIBRIUM_PHASES 1
Fix_H+ -2.5 HCl 10
Pyrite 0 4.167E-3
Goethite 0 0
Hematite 0 0
Magnetite 0 0
Ferryhydrite 0 0
 
END

USE solution 1
REACTION
Sid 5E-4
USE SURFACE 1
EQUILIBRIUM_PHASES 1
Fix_H+ -3.0 HCl 10
Pyrite 0 4.167E-3
Goethite 0 0
Hematite 0 0
Magnetite 0 0
Ferryhydrite 0 0
 
END

USE solution 1
REACTION
Sid 5E-4
USE SURFACE 1
EQUILIBRIUM_PHASES 1
Fix_H+ -3.5 HCl 10
Pyrite 0 4.167E-3
Goethite 0 0
Hematite 0 0
Magnetite 0 0
Ferryhydrite 0 0
 
END

USE solution 1
REACTION
Sid 5E-4
USE SURFACE 1
EQUILIBRIUM_PHASES 1
Fix_H+ -4.0 HCl 10
Pyrite 0 4.167E-3
Goethite 0 0
Hematite 0 0
Magnetite 0 0
Ferryhydrite 0 0
 
END

USE solution 1
REACTION
Sid 5E-4
USE SURFACE 1
EQUILIBRIUM_PHASES 1
Fix_H+ -4.5 NaOH 10
Pyrite 0 4.167E-3
Goethite 0 0
Hematite 0 0
Magnetite 0 0
Ferryhydrite 0 0
 
END

USE solution 1
REACTION
Sid 5E-4
USE SURFACE 1
EQUILIBRIUM_PHASES 1
Fix_H+ -5.1 NaOH 10
Pyrite 0 4.167E-3
Goethite 0 0
Hematite 0 0
Magnetite 0 0
Ferryhydrite 0 0
 
END

USE solution 1
REACTION
Sid 5E-4
USE SURFACE 1
EQUILIBRIUM_PHASES 1
Fix_H+ -5.8 NaOH 10
Pyrite 0 4.167E-3
Goethite 0 0
Hematite 0 0
Magnetite 0 0
Ferryhydrite 0 0
 
END

USE solution 1
REACTION
Sid 5E-4
USE SURFACE 1
EQUILIBRIUM_PHASES 1
Fix_H+ -6.0 NaOH 10
Pyrite 0 4.167E-3
Goethite 0 0
Hematite 0 0
Magnetite 0 0
Ferryhydrite 0 0
 
END

USE solution 1
REACTION
Sid 5E-4
USE SURFACE 1
EQUILIBRIUM_PHASES 1
Fix_H+ -6.6 NaOH 10
Pyrite 0 4.167E-3
Goethite 0 0
Hematite 0 0
Magnetite 0 0
Ferryhydrite 0 0
 
END

USE solution 1
REACTION
Sid 5E-4
USE SURFACE 1
EQUILIBRIUM_PHASES 1
Fix_H+ -7.0 NaOH 10
Pyrite 0 4.167E-3
Goethite 0 0
Hematite 0 0
Magnetite 0 0
Ferryhydrite 0 0
 
END

USE solution 1
REACTION
Sid 5E-4
USE SURFACE 1
EQUILIBRIUM_PHASES 1
Fix_H+ -7.5 NaOH 10
Pyrite 0 4.167E-3
Goethite 0 0
Hematite 0 0
Magnetite 0 0
Ferryhydrite 0 0
 
END

USE solution 1
REACTION
Sid 5E-4
USE SURFACE 1
EQUILIBRIUM_PHASES 1
Fix_H+ -8.0 NaOH 10
Pyrite 0 4.167E-3
Goethite 0 0
Hematite 0 0
Magnetite 0 0
Ferryhydrite 0 0
 
END

USE solution 1
REACTION
Sid 5E-4
USE SURFACE 1
EQUILIBRIUM_PHASES 1
Fix_H+ -8.5 NaOH 10
Pyrite 0 4.167E-3
Goethite 0 0
Hematite 0 0
Magnetite 0 0
Ferryhydrite 0 0
 
END

USE solution 1
REACTION
Sid 5E-4
USE SURFACE 1
EQUILIBRIUM_PHASES 1
Fix_H+ -9.0 NaOH 10
Pyrite 0 4.167E-3
Goethite 0 0
Hematite 0 0
Magnetite 0 0
Ferryhydrite 0 0
 
END

USE solution 1
REACTION
Sid 5E-4
USE SURFACE 1
EQUILIBRIUM_PHASES 1
Fix_H+ -9.5 NaOH 10
Pyrite 0 4.167E-3
Goethite 0 0
Hematite 0 0
Magnetite 0 0
Ferryhydrite 0 0
 
END

USE solution 1
REACTION
Sid 5E-4
USE SURFACE 1
EQUILIBRIUM_PHASES 1
Fix_H+ -10.0 NaOH 10
Pyrite 0 4.167E-3
#Goethite 0 0
#Hematite 0 0
#Magnetite 0 0
#Ferryhydrite 0 0
 
END

USE solution 1
REACTION
Sid 5E-4
USE SURFACE 1
EQUILIBRIUM_PHASES 1
Fix_H+ -10.5 NaOH 15
-force_equality
Pyrite 0 4.167E-3
Goethite 0 0
Hematite 0 0
Magnetite 0 0
Ferryhydrite 0 0
 
END

USE solution 1
REACTION
Sid 5E-4
USE SURFACE 1
EQUILIBRIUM_PHASES 1
Fix_H+ -11.0 NaOH 15
-force_equality
Pyrite 0 4.167E-3
Goethite 0 0
Hematite 0 0
Magnetite 0 0
Ferryhydrite 0 0
 
END

USE solution 1
REACTION
Sid 5E-4
USE SURFACE 1
EQUILIBRIUM_PHASES 1
Fix_H+ -11.1 NaOH 15
-force_equality
Pyrite 0 4.167E-3
Goethite 0 0
Hematite 0 0
Magnetite 0 0
Ferryhydrite 0 0
 
END

USE solution 1
REACTION
Sid 5E-4
USE SURFACE 1
EQUILIBRIUM_PHASES 1
Fix_H+ -11.2 NaOH 15
-force_equality
Pyrite 0 4.167E-3
Goethite 0 0
Hematite 0 0
Magnetite 0 0
Ferryhydrite 0 0
 
END

USE solution 1
REACTION
Sid 5E-4
USE SURFACE 1
EQUILIBRIUM_PHASES 1
Fix_H+ -11.3 NaOH 15
-force_equality
Pyrite 0 4.167E-3
Goethite 0 0
Hematite 0 0
Magnetite 0 0
Ferryhydrite 0 0
 
END

USE solution 1
REACTION
Sid 5E-4
USE SURFACE 1
EQUILIBRIUM_PHASES 1
Fix_H+ -11.4 NaOH 15
-force_equality
Pyrite 0 4.167E-3
Goethite 0 0
Hematite 0 0
Magnetite 0 0
Ferryhydrite 0 0
 
END

USE solution 1
REACTION
Sid 5E-4
USE SURFACE 1
EQUILIBRIUM_PHASES 1
Fix_H+ -11.5 NaOH 15
-force_equality
Pyrite 0 4.167E-3
Goethite 0 0
Hematite 0 0
Magnetite 0 0
Ferryhydrite 0 0
 
END


[dlparkhurst]

You must define SOLUTION_MASTER_SPECIES and SOLUTION_SPECIES in the same data block (before the END) or in an earlier data bloc than the  use of Sid in the SURFACE_SPECIES definition.

You can remove the END statement indicated below. Logically, you should put the SOLUTION_MASTER_SPECIES and SOLUTION_SPECIES before their use in the SURFACE_SPECIES definitions, but anywhere before the END is acceptable.

As a rule, I like to put the block of database-modifying definitions--SOLUTION_MASTER_SPECIES, SOLUTION_SPECIES, SURFACE_MASTER_SPECIES, SURFACE_SPECIES, EXCHANGE_MASTER_SPECIES, EXCHANGE_SPECIES, PHASES, and RATES--at the beginning of the file followed by an END. That clearly sets all the definitions for the remainder of the run. In your case, I would move EQUILIBRIUM_PHASES, and in general all reactant definitions, to follow that block.

Code: [Select]

PHASES
Fix_H+
H+ = H+
log_k 0.0
#END