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SebFuchs

Cannot open thermo data file / corrupt file?

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Hi,

 

I was working on my thermo.dat this morning and added some new aqueous and mineral species.

After saving the file and closing TEdit programm, I am not able to open thermo.dat file anymore.

The program closes with the message: "TEdit is not working". I tried to restart the computer and open the file using ACT but nothing is working.

I was only able to open an older backup of the file that made weeks ago.

 

So I guess something went wrong when saved the file.

 

Can you please help me to solve the problem?

 

The file is too large to attach (600KB) but I can email it.

 

Many thanks in advance.

 

Sebastian

 

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Hi Sebastian,

 

Can you please let me know what GWB release you're using? If you send the thermo dataset to support@gwb.com I'll take a look.

 

Regards,

 

Brian Farrell

Aqueous Solutions LLC

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Hi Brian,

 

I am using GWB 11.

 

I sent you my database file right now by email.

 

Cheers,

Sebastian

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Hi Sebastian,

 

If there's a problem with your dataset and it can't be read into TEdit or any of the GWB programs, you can still use Notepad or another text editor to view it. When I did this, I noticed an entry "New Mineral" in the minerals section. The blank entry seems to be what's causing your problem. Just remove it from the dataset in Notepad and save your file to fix the problem.

 

I also noticed that a few reactions are duplicated within the thermo dataset. The reactions for U+++ and U++++, for example, appear in both the redox couples and aqueous species sections. And there is an H2(aq) in the redox couples section and an H2(aq)(aq) in the aqueous species section (TEdit tries to add suffixes where species in different parts of the dataset have the same name). I would delete the entries from the aqueous species section so that you have more flexibility over redox chemistry in your models.

 

Hope this helps,

Brian

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Hi Brian,

 

many thanks for your help. I removed the entry "new mineral" and all the duplicates and it solved the problem.

I have 2 more questions to you, regarding the database and SpecE8 / GSS. I want to calculate the metal speciations and mineral saturation states (esp. for gold).

 

1) Both SpecE8 and GSS calculate at the fixed pressures defined in the database. In the thermo.tdat file the pressure for 250 °C is 39.776 bars .

Is it possible to do the calculation at a specific pressure, e.g., 50 bars at 250°C, without modifying the whole database?

 

2) I have 2 sulphur species SO4 and H2S as input values. In GSS I used SO4-- as basis species and change it SO4, and HS- to H2S(aq).

When I used SpecE8 I was only able to add 1 sulphur species (e.g., SO4-- as H2S(aq)).

 

When I did the calculations with GSS, the program did not calculate the saturation state for gold.

In SpecE8 (using only H2S(aq)), however it calculated the saturation state for gold.

In the database gold is defined as: Gold + H(+) + 0.25 O2 = Au(+) + 0.5 H2O

 

Do you know why it is not possible to calculate the saturation state of gold using 2 sulphur species in GSS (it is also not possible when I am transferring the data to SpecE8)?

 

Many thanks,

Sebastian

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Hi Sebastian,

 

You can use a thermo dataset compiled at the pressure of interest, but you can’t specify a confining pressure within your model that deviates from what’s in the database. It’s common to assume the effects of confining pressure are small compared to the uncertainty in determining log Ks and activity coefficients. Note, however, that gas partial pressures are almost invariably significant. You account for the partial pressure of a coexisting gas by setting its fugacity.

 

I’m not exactly sure what you’re doing, but I’d like to clarify that the “as” options within GSS, SpecE8, and the other apps refer to how you’d like to constrain the amount of some component. The mole weights of HS-, H2S, and S are all different, so 1 mg of HS- is not the same as 1 mg of H2S or S. Your analytical instrument could report a concentration in terms of either of the species or in terms of the amount of the element itself, so you use the “as” option to set up your input correctly. Please see section 3.1, Your first data sheet, and 7.1, Example calculation, in the GWB Essentials Guide for more info.

 

You need to disable redox coupling reactions to treat separate oxidation states as independent components within your model. By adding both a basis species (SO4--) and a redox species (HS-) to your spreadsheet in GSS, the HS-/ SO4—redox pair is automatically disabled (check the Data – Redox Couples dialog to confirm). SpecE8 behaves slightly differently in that you need to decouple the pair (Config – Redox couples) before you add the redox species (HS-) to your basis. Please see section 2.4, Redox couples, and 7.3, Redox disequilibrium, in the GWB Essentials Guide for more info.

 

As for the gold, you should check to ensure whether redox coupling is set up the same way in GSS and SpecE8, and whether you have the same set of constraints in each. Do you have O2(aq) in SpecE8 but not in GSS?

 

Regards,

Brian

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Hi Brian,

 

many thanks for your help. To disable redox coupling helped to set two set both initial values for SO4 and H2S.

My analytical instrument provides elemental concentrations - that's why I used the "as" function.

 

I still did not find a solution why gold is not the list of minerals (for mineral saturation) in GSS, as it is in SpecE8 and REACT.

The reason is O2. In SpecE8 I use H2(aq) swapped for initial O2, in GSS it is only possible to add H2(aq) as basis species.

Only if I add O2 to the system in GSS then I will have gold in the list.

 

I am wondering, if there is a workaround in GSS, that I do not to provide values for O2.

 

Cheers,

Sebastian

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Hi Sebastian,

 

If your instrument provides elemental concentrations, then you would want to add SO4-- as S, and HS- as S.

 

GSS uses SpecE8 to perform its calculations, so you can give GSS any command that SpecE8 would accept as a "trailer command". The GWB Reference Manual includes all of the commands that all the GWB programs, including SpecE8, accept. You can also go to the Run - History dialog in SpecE8 to see the command that is equivalent to every click that you make on the GUI. In your case, you'll want to swap H2(aq) for O2(aq), like you do in SpecE8, then set its concentration. Just go to Data - Constraints to add the trailer command. For more info, please see 3.2.5, Calculating analytes, and 3.5, Launching SpecE8 and React, in the GWB Essentials Modeling Guide.

 

Hope this helps,

Brian

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