Form of KINETIC_MODIFY for more than one component

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Ivan M

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May 17, 2013, 10:33:45 PM5/17/13
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Hi David,

Still related to my previous question - the zeros in time -99 for kinetic reactants - what is the proper form of the KINETIC_MODIFY block? I'm using

      ierr = AccumulateLine(id, '80  PUNCH KIN("Biomass_O2")')
      ierr = AccumulateLine(id, '90  PUNCH KIN("Biomass_SO4")')

In the SELECTED_OUTPUT section, and

      ierr = AccumulateLine(id, "KINETICS_MODIFY 1")
      write( cvalue, '( e30.15 )' )  um(1)
      ierr = AccumulateLine(id, "-component Biomass_O2 -m  " // cvalue)
      write( cvalue, '( e30.15 )' )  um(2)
      ierr = AccumulateLine(id, "Biomass_SO4 -m  " // cvalue)

for the KINETICS_MODIFY, what would be 

KINETICS_MODIFY 1
-component Biomass_O2 -m 3.0e-5
Biomass_SO4 -m 3.0e-5

Is this correct? I'm still getting only zeros.

Cheers
_________________________________________
Ivan S.P. Marin, PhD
 
Postdoctoral Associate
Département de géologie et de génie géologique
Pavillon Adrien-Pouliot, local 3744
1065. ave de la Médecine
Université Laval
Québec (Québec) Canada
G1V 0A6
418-656-2131 poste 7246

Parkhurst, David

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May 17, 2013, 11:28:44 PM5/17/13
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If you are talking about state = i_soln, there will never be results for kinetics. The initial solution calculation only has a solution and no other reactants. If you don't want it in the selected output file use PRINT; -selected_output false and PRINT; -selected_output true to turn printing off and on.

The form for KINETICS_MODIFY is given in the appendix of the manual. You can also use DUMP to dump the entire KINETICS_RAW format. You can include any parts of the KINETICS_RAW format for KINETICS_MODIFY. Indentation indicates  fields required to define the fields with greater indentation.


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Ivan M

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May 18, 2013, 7:30:06 PM5/18/13
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Sorry, I didn't understand the identation part for the KINETICS_MODIFY. The block

KINETICS_MODIFY 1
 -component Biomass_O2  -m 0.2
 -component Biomass_SO4 -m 0.3

doesn't work. The block
KINETICS_MODIFY 1
 -component 
       Biomass_O2  
            -m 0.2
       Biomass_SO4 
            -m 0.3
Also doesn't work, even following the manual's identation.

 The block
KINETICS_MODIFY 1
 -component Biomass_O2  -m 0.2

works, though. 

Thanks again

_________________________________________
Ivan S.P. Marin, PhD
 
Postdoctoral Associate
Département de géologie et de génie géologique
Pavillon Adrien-Pouliot, local 3744
1065. ave de la Médecine
Université Laval
Québec (Québec) Canada
G1V 0A6
418-656-2131 poste 7246


2013/5/17 Parkhurst, David <dlp...@usgs.gov>

Parkhurst, David

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May 18, 2013, 7:45:03 PM5/18/13
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I don't think any of them are correct.
Should be

KINETICS_MODIFY 1
 -component     Biomass_O2  
            -m 0.2
-component      Biomass_SO4 
            -m 0.3

Should not be a limit on the length of a string submitted to AccumulateLine, but I can check next week. Are you saying you had more than 91 characters in the string for AccumulateLine, or more than 91 fields defined for SELECTED_OUTPUT? Please send a snippet of what failed (and the error message).

Ivan M

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May 18, 2013, 9:41:59 PM5/18/13
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I'm trying this form, but wihtout any error message the computation does not calculate anything. I'll check my code again for the kinetics_modify part, but it seems that if I try to put the second kinetic reactant none of them are found. 

An example:

ierr = AccumulateLine(id, "100 react1 = - kB_max   *   BSO4   *   (SubsA   /   (kB_half   +    SubsA ))  *  (EA2  /  (  EA2  +  kEAS_half)   )" )

and a subsequent run_cells would not output an error message, but GetSelectedOutputColumnCount(id) would return zero, while if the exact same line is shorter than 91 characters the program works and GetSelectedOutputColumnCount(id) returns the correct number of columns. 

I'll try to come up with a very simple fortran code to exemplify this behavior.

Cheers

_________________________________________
Ivan S.P. Marin, PhD
 
Postdoctoral Associate
Département de géologie et de génie géologique
Pavillon Adrien-Pouliot, local 3744
1065. ave de la Médecine
Université Laval
Québec (Québec) Canada
G1V 0A6
418-656-2131 poste 7246


2013/5/18 Parkhurst, David <dlp...@usgs.gov>

Parkhurst, David

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May 18, 2013, 10:41:29 PM5/18/13
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On Sat, May 18, 2013 at 7:41 PM, Ivan M <ispm...@gmail.com> wrote:
I'm trying this form, but wihtout any error message the computation does not calculate anything. I'll check my code again for the kinetics_modify part, but it seems that if I try to put the second kinetic reactant none of them are found. 
RATES
Constant1
-start
10 SAVE 1e-6
-end
Constant2
-start
10 SAVE 2e-6
-end
END
KINETICS 1
Constant1
-formula NaCl
-m  1.
END
DUMP
-file test_dump
    -kinetics             1
END
KINETICS_MODIFY 1
-component Constant1
-m 0.1
-component Constant2
-NameCoef
KBr 1
-m 0.2
END
DUMP
-append true
    -kinetics             1
END
SOLUTION 1
END
USE solution 1
USE kinetics 1
END

Parkhurst, David

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May 20, 2013, 6:13:45 PM5/20/13
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Here is his example.

Parkhurst, David

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May 20, 2013, 6:14:24 PM5/20/13
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Sorry, did not mean to post the previous.
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