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Re: Aqueous species oscillations within transport calculation




Sorry to take so long to get back to you. I apologize, but there were some
fairly serious bugs in the previous version. I have been working as time
permits on some of the problems and testing a little more systematically.
Here is a revised version that I hope is more robust.

The stiff solver (cvode) is not always faster than the Runge-Kutta method
in the standard PHREEQC release, so you probably need to experiment to see
which solver suits each problem. I think cvode works best with smooth rate
functions that don't have a lot of "if" statements that cause
discontinuities in the rates or their derivatives, whereas RK works better
if the rates are not smooth. Cvode handles rates that are fast relative to
the time step much better than RK.

When you include pyrite, it will help if you include the following species
definition.

SOLUTION_SPECIES
      H2O + 0.01e- = H2O-0.01
      log_k -9

This is a fictitious species that has a concentration of about 1e-9 under
all conditions. However, it helps with redox problems where there is
virtually no redox buffering. For the redox equation, PHREEQC needs an
element that exists in the solution in at least two redox states at
concentrations greater than 1e-14, which this species satisfies.

Good luck. Please send any input files that crash (segmentation fault or
similar error) or if you have other problems getting the ODE solvers to
work. Working with rates can be a bit of an art.

David

(See attached file: phreeqc_cvode.exe)

David Parkhurst (dlpark@xxxxxxxx)
U.S. Geological Survey
Box 25046, MS 413
Denver Federal Center
Denver, CO 80225

Project web page: http://wwwbrr.cr.usgs.gov/projects/GWC_coupled



                                                                                                               
                      "Fiona Hunter"                                                                           
                      <Fiona.Hunter@xxxxxxxx        To:       "<"                                              
                      urance.com>                   cc:                                                        
                                                    Subject:  Re: Aqueous species oscillations within          
                      06/26/03 09:53 AM              transport calculation                                     
                                                                                                               
                                                                                                               




Dear David
I've been running your beta test Phreeqc code as you suggested.  This
works much better...  I've attached an input file, a section of the
output file and a selected output file (k21, k21.out and k21.sel), for
advection of alkaline solution through the Boom Clay column.  I've
removed Pyrite  and Fe from the calculation to remove any redox changes
for Fe, increased the water mass to 1kg and increased the mineral
proportions accordingly.  For each kinetic phase, I've increased the
tolerance to 1e-5.  I've used the Llnl.dat database again.

However, my main concern is the selected output file.  I want to
monitor cell 32,  (i.e. the effluent coming out of the end of the
colum), this should initially be at around pH 8, increasing slowly as
the alkaline fluid advects through.  However, you can see from the
selected output file that the pH is initially recorded at pH 8.8, but
then drops to zero for several time steps, before returning to the
correct value of around pH 9, then drops to zero and so on. For example,
during transport step 9, cells 1-9 are at pH~13, but cells 10-32 at
pH=0; the pE also oscillates quite a lot over this interval.

I assume this is a problem with the new version of phreeqc, or is can
you see anything in my input file?

Thanks again for your comprehensive reply this morning.  That has been
really useful!

Best regards
Fiona Hunter

~~~~~~~~~~~~~~~~~~~~~~~~~~
Dr Fiona Hunter    MRSC
Serco Assurance
Building 150
Harwell International Business Centre, Didcot
Oxfordshire OX11 0QJ
Telephone: +44 (0)1635 280418
Facsimile: +44 (0)1635 280305
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<<<<GWIASIG 0.07>>>>(See attached file: k21.sel)(See attached file: k21)
(See attached file: k21.out)

Attachment: phreeqc_cvode.exe
Description: Binary data

Attachment: k21.sel
Description: Binary data

Attachment: k21
Description: Binary data

Attachment: k21.out
Description: Binary data



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