USER_PUNCH/USER_GRAPH > SELECTED_OUTPUT

Selected Output for Reactions Only

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sestes:
Hello All,

I am attempting to couple PHREEQC with PEST for the purposes of simultaneously optimizing log K and enthalpy values for various reactions using experimental isothermal titration calorimetry data. To do this, I need PHREEQC to calculate and print (selected output) the calculated cumulative heat for each step of a reaction. I can do this with USER_PUNCH and the new BASIC command DELTA_H_SPECIES("x"), see example code. However, for systems with exchange or surface complexation reactions, the selected output also prints the initial solution conditions and the initial exchange conditions, which makes it difficult to directly use the selected output from PHREEQC as the model input for PEST. Does anyone know how to omit these initial conditions from the selected output? I've put a working PHREEQC example and the selected output from that example in the code boxes below. Basically, I need to remove the first two rows of output (i.e., "i_soln" and "i_exch" rows). Thanks for your help!

PHREEQC Example:

--- Code: ---#Cation Exchange Example

EXCHANGE_SPECIES
        X- = X-
        log_k           0.0

        Na+ + X- = NaX
        log_k   0.0
        -llnl_gamma  4.0
        delta_h  0.0     

        K+ + X- = KX
        log_k   1.0
        -llnl_gamma  3.0
        delta_h  -1.24   # Jardine & Sparks, 1984

SOLUTION 1
    temp      25
    pH        7 charge
    pe        4
    redox     pe
    units     mol/kgw
    Cl        0.1
    Na        0.1
    -water    6.0E-04 # kg

EXCHANGE 1
NaX 0.00000764
KX 0
-equilibrate with solution 1

REACTION 1
KCl 1
H2O 555
40 micromoles in 16 steps

CALCULATE_VALUES
mol_NaX(i)
-start
10 PUT(MOL("NaX")*TOT("water") , (STEP_NO))
-end

SELECTED_OUTPUT
    -file                 Na-K_Exchange w Dilution.sel
    -reset   false
    -step   true
    -state   true
    -user_punch   true
    #-totals               K  Na  Cl  X
    #-molalities           Na+ NaCl K+ KCl  KX  NaX

USER_PUNCH
    -start
    -headings cumulative_heat
    10 PUNCH ((((MOL("NaX")*TOT("water"))- 7.640e-06)* DELTA_H_SPECIES("NaX") * -1000)+(((MOL("KX")*TOT("water"))- 0)* DELTA_H_SPECIES("KX")))
    -end

END

--- End code ---

Selected Output Example:

--- Code: ---       state         step cumulative_heat
      i_soln          -99 -7.4401e-103
      i_exch          -99 -7.4401e-103
       react            1 -1.5854e-06
       react            2 -2.8699e-06
       react            3 -3.8903e-06
       react            4 -4.6946e-06
       react            5 -5.3299e-06
       react            6 -5.8358e-06
       react            7 -6.2433e-06
       react            8 -6.5760e-06
       react            9 -6.8511e-06
       react           10 -7.0814e-06
       react           11 -7.2764e-06
       react           12 -7.4434e-06
       react           13 -7.5877e-06
       react           14 -7.7136e-06
       react           15 -7.8241e-06
       react           16 -7.9220e-06
--- End code ---

dlparkhurst:
I think the best way would be to add END statements after each data block. And then add the following to the end of the script.


--- Code: ---RUN_CELLS
-cell 1

--- End code ---

Adding ENDs eliminates all the default reaction calculations, which bring together a SOLUTION (or USE solution or MIX) and all other reactants defined from one END to the next END. With your current script, all keyword data blocks are defined within the same "simulation", because there is only one END. Thus SELECTED_OUTPUT and USER_PUNCH are defined at the point that the initial SOLUTION and initial EXCHANGE calculations are performed, and so, they are written to the selected output file. By adding ENDs, SELECTED_OUTPUT and USER_PUNCH are not defined until after the initial solution and initial exchange calculations have already been performed.

RUN_CELLS; -cell 1 will bring together all the reaction entities defined with user number 1--SOLUTION 1, EXCHANGE 1, and REACTION 1--and perform the reaction calculation. In your case, RUN_CELLS is equivalent to


--- Code: ---USE solution 1
USE exchange 1
USE reaction 1
SAVE solution 1
SAVE exchange 1

--- End code ---

Once you split up calculations with ENDs, you can also turn SELECTED_OUTPUT/USER_PUNCH off/on with


--- Code: ---SELECTED_OUTPUT 1
-active false/true

--- End code ---

sestes:
Thank you, thank you, Dr. Parkhurst! I really appreciate your rapid responses in this forum. I'm still a PHREEQC newbie, but I'm very quickly becoming appreciative of the power and versatility of this software.

Your simple solution exactly did the trick. Onwards to optimizing enthalpy values! Woo!

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