Frank Bok
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Posts posted by Frank Bok
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Dear Jia,
I did as recommended in the GWB-Pyhton support page and re-run the installer. I also checked the system environment variables, the settings there are ok. But the problem remains, somethin is wrong with the loading of the GWBplugin:
QuoteTraceback (most recent call last):
File "c:\users\fb5950\desktop\python\gwb-test.py", line 13, in <module>
from GWBplugin import *
File "C:\Program Files\Gwb\src\GWBplugin.py", line 14, in <module>
gwbdll = cdll.LoadLibrary(bin_path + 'gwbplugin')
File "C:\Users\fb5950\AppData\Local\Programs\MUEDIT~1\Python\lib\ctypes\__init__.py", line 451, in LoadLibrary
return self._dlltype(name)
File "C:\Users\fb5950\AppData\Local\Programs\MUEDIT~1\Python\lib\ctypes\__init__.py", line 373, in __init__
self._handle = _dlopen(self._name, mode)
FileNotFoundError: Could not find module 'gwbplugin' (or one of its dependencies). Try using the full path with constructor syntax.
>>>
---------- FINISHED ----------
exit code: 2 status: 0
I also tried to give Python the path directly via:
sys.path.append("c:/program files/gwb/src")
Same effect.
I will try it on my second device this afternoon.
Thanks and best regards,
Frank -
Dear Jia,
many thanks for these hints, I will try them and hopefully can bring my scripts back to life.
Thanks and best regards,
Frank -
Dear GWB team,
In the past I have used the GWBplugin in Python using this synthax in my Python scripts:
import GWBplugin # class from GWBplugin import * # Call GWB myGWB = GWBplugin() print ("Hello")
This now (even in my old unchanged examples) brings the error message:
Quote"FileNotFoundError: Could not find module 'gwbplugin' (or one of its dependencies). Try using the full path with constructor syntax."
Adding the full path does not work and brings:
Quote" import c:\Program Files/gwb/src\GWBplugin # class
^
SyntaxError: invalid syntax"What can I do here (I am far away from beeing an Python expert), so any help is highly appreciated!
Many thanks in advance and best regards,
Frank -
Dear Jia,
Thank you for explaining this phenomenon, which was unusual to me!
Best wishes,
Frank -
Hello Jia,
thanks for explaining me where I am wrong! I am looking forward for the Kinetic workshop.
I have reduced my calculation by precalculating the rate constant in Excel and directly adding the rate constant for Fe(OH)3(ppd) in the input file. Even then, at lower temperatures and lower rate constants (K = 2.0875E-8 mol/cm s @ T = 20 °C vs. K = 8.4319E-9 mol/cm s @ T = 10 °C) the reaction is calculated to be faster at lower temperatures. This should not be the case?!
Many thanks,
Frank
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Dear Jia,
many thanks for the helpful information. I managed to include the rate law via a .bas file. So I am even more curios on the kinetic woekshop in June!
Many thanks and best regards,
Frank -
Dear Jia, dear Brian,
my knowledge in kinetic modelling is still limited. So maybe this is a trivial question but I cannot solve it on my own:
I want to model the (calcite buffered) pyrite oxidation with ferrihydrite precipitation including the dissolution kinetics of ferrihydrite and the following formation of goethite. My colleaques have come up with the function for the kinetic rate constant of the form
log10(k) = a·T + b·pH² + c·pH + d
with T is the temperature in °C.
Can you help me setting up this equation in React?!
Attached is my current status of the calculation, the kinetics data inside are only dummy data to make the script executable so far.
Many thanks in advance and best regards,
Frank -
Hello Jia,
thank you for the information. Actually, yesterday afternoon my copy of GWB allready did its update.
Many thanks and best regards,
Frank
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Hello Jia,
thanks for the update! Your installer works fine on my PC, no issues here. Concerning TEdit, I tried the PHREEQC file from the initial post again. The importer now includes all triple interactions.
Thank you very much and best regards,
Frank -
Hello Jia,
many thanks, please keep me up to date. I need eta and mu interactions in my dataset.
Best regards,
Frank -
Dear GWB team,
I tried TEdit zu transform a PHREEQC database into GWB format (both attached). From the PITZER block in the PHREEQC, the ETA (NCC / NAA combinations) as well as from the MU (NN'C / NN'A) interaction parameter have not been imported. Specifically, I am referring to these entries from the PHREEQC file:
-ETA
O2 Cl- SO4-2 -0.01709 0 0 0 0 0
O2 Na+ Mg+2 -0.01445 0 0 0 0 0
-MU
O2 H+ H3PO4 -0.1637 0 0 0 0 0
Does GWB not handle these kind of (rare) interactions? Or did I something wrong?Many thanks and best wishes,
Frank
P.S.: Sorry for the incomlete translation!
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Dear Jia,
many thanks for this helpful tip!
Best regards,
Frank -
Hello Jia,
thanks for your answer. Actually I want to model the retardation of ions in a natural soil sample where I know the mineral composition: Quartz (76.0%), Albite (5,7%), Orthoclase (3,4%), Microcline (6,6%), Illite (2,6%), Kaolinite (2,6%), Montmorillonite (3,1%). With your help I managed to include them all into a calculation at the same time using kinetics. I also created an surface complexation modelling dataset using an bottom-up approach. But wand to include ion-exchange for several minerals - at least Montmorillonite, Illite and Kaolinite - because Ion-Exchange is a major contribution process on retadration. So my problem is to include mineral specific Ion-exchange data and I am looking for a way to simultaniously include Ion-exchange data for Montmorillonite, Illite and Kaolinite. Is this somehow possible?
I just wonder if this could be realized by having different exchange-sites (>X:Na, >Y:Na, >Z:Na)? But then the exchange capacity is not mineral-specific.
Many thanks and best regards,
Frank
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Hello,
I would like to model a scenarion involving several minerals that are capable of cation exchange (Montmorillonite, Illite, Smectite, ...). I also collected some mineral-specific exchange parameters and want to set up a Ion-Exchange surface file (*.sdat). Is there a way to connect the different exchange reactions and their coefficients to the corresponding minerals? For surface complexation modelling data, this can be done quit nicely in one single file by defining different minerals with their surface groups. But for Ion-Exchange reactions I haven't found a solution. Any help is highly appiciated!
Many thanks in advance and all the best!
Frank
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Hello Jia,
many thanks for these large amount of really useful information! I actually use the Python GWB plugin. Works great!
Many thanks and best regards,
Frank
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Dear Jia,
I have successfully implemented this solution - thank you again! Since I want to run a large number of individual calculations here (>>100,000) automatized:
Is there also a solution for SpecE8 or does including a larger number of minerals only work with React? As this would reduce computing time...Many thanks and best regards,
Frank
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Dear Jia,
many thanks for the quick answer, I will try it. My other concerns are on data consistency for the sorption data. Not only the available SCM data is far from beeing complete (here I have to finde a way using chemical analogues) but it is also scattered over several surface complexation models (most double layer and triple model). Here I have to check in the consequences of mixin different models in a sumilation. But that's just part of my work.
Many thanks and best regards,
Frank
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Hello,
I would like to set up a calculation of a natural scenario that includes sorption (SCM) onto several natural occuring mineral phases (Quartz, Albite, Orthoclase, Microcline, Illite, Kaolinite, Montmorillonite). Including so many minerals using swap 'mineralname' for SiO2(aq), Al+++ etc. does not work. There are simply not enough elements to swap all in.
Can you give me a hint how to do this?
Many thanks in advance and best regards,
Frank -
Hi!
I would like to model a 2D transport calculation with two spatially separated mineral phases. Is this possible to set up a model with different minerals in different blocks?
And, due to the effects of grain boundaries and surface roughness, is it somehow possible to have different surface areas for the minerals in different blocks?
Thanks in advance and best regards,
Frank
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Hi Brian,
thank you very much for your comment! ?
Best regards,
Frank
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Dear Forum members,
recently I tried to model a seawater evaporation and I ended up with different results (using the same Pitzer database) with the identical .rea-files input just with different order of entries n(concerning the species in Basis) in the two files. One file I had created in my own in React (Working_example.rea), the other one (Aborting_example.rea) was created by launching React from GSS. The chemical composition is the same in both files but the one from the GSS-launched React instance stops much earlier.
I would like to understand the different behavior, in principle, it shouldn't do that.
Thank you in advance and best regards,
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Hi Brian,
thank you for the information. Acutally I wanted to use the activity model "phreeqc" so this is one of the reasons I got in this trouble. I should more often remember to "RTFM"... ;-)
Thank you and best wishes!
Frank
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Hello,
I have prepared a database (attached) and both TEdit and React are loading the file without any warning. But even the simplest calculations fail and give an error message like this:
QuoteSolving for initial system.
Loaded: 5 aqueous species,
0 minerals,
0 gases,
0 surface species,
4 elements,
0 oxides.Newton-Raphson did not converge after 999 iterations, maximum residual = 1, Xi = 0.0000
Largest residual(s):
Resid Resid/Totmol Cbasis
---------------------------------------------------------
Cl- 1.007e+200 1 3.406e-109
Na+ 2.007e+200 1 6.813e-109
---------------------------------------------------------Is there a way to locate the error to make it work?
Thank you in advance and best regards,
Frank -
Hi Brian et al.
I would like to learn using the new Phase2 program and to do so, I started with something simple: the Eh-pH diagram of Uranium using thermo.tdat. With Act2 this works over the whole range (pH = 0 to 14, Eh = -0.9 to 1.25 V). Trying to do the same with Phase2, I run into several problems:
If I try the whole pH range (starting at pH = 0), the initial system cannot be solved:
Newton-Raphson did not converge after 999 iterations, maximum residual = 5.42e-15, Xi = 0.0000
Largest residual(s):
Resid Resid/Totmol Cbasis
---------------------------------------------------------
Na+ 3.338e-05 5.422e-15 7.396e+05
---------------------------------------------------------Reducing the pH range to 4-10 and deactivating charge balancing, the diagram can be calculated. But: The resulting diagrams of Act2 and Phase2 does not match.
If I try to go higher, either GWB runs with full CPU workload and does not respond (Windows then kills the program if I try to close it) or produces an incorrect *.p2p file.
Can you give me a hint how to correctly use Phase2?!
Thank you in advance and best regards,
Frank
Import GWBplugin in Python
in The Geochemist's Workbench
Posted
Dear Jia,
thanks for your help! The problem was within the environment variables. Since my companies computers are not maintained by the user but by the administration team, the environment variables were set to the admin account (and were labeled GWB instead of GWB_BIN_PATH). After setting this into the systemwide environment variables, it now works again.
Many many thanks and best regards,
Frank