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Dimitri

updated thermo.dat database?

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Is there an updated version of thermo.dat available based on a more recent version of the SUPCRT database (e.g. slop07.dat)? This would include data for many more organic species than the default.

 

Thanks in advance,

Dimitri Vlassopoulos

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Hi Dimitri,

 

We try to limit changes to the datasets that we distribute with GWB, especially the default thermo.dat, so as not to affect our users' model outputs. The thermo.com.V8.R6+.dat dataset (distributed with GWB) is based on a later release of the LLNL dataset and includes many organic species. Perhaps other users on the forum will have more knowledge of databases with organic species.

 

Regards,

 

Brian Farrell

Aqueous Solutions LLC

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A version of thermo.dat based on slop07.dat (maintained by the Geopig group at Arizona State U) and generated using SUPCRT would be very useful, because thermo.dat is woefully outdated, while thermo.com.V8.R6+.dat is internally inconsistent and in other respects buggy.

 

Consistency in using the same old thermo.com is nice, but better quality, internally consistent data should trump we've-been-doing-it-this-way-since-GWB-1.0.

 

slop07.dat represents properties of individual species rather than reactions. Thus, a dataset generated using slop07.dat + SUPCRT would be internally consistent and, of course, Geopig is a highly reliable source.

 

Yes, I know that I could license DBCreate and do it myself, but a thousand bucks for a program that I would use once or twice seems a bit pricey.

 

If Aqueous Solutions were to license DBCreate and generate a data base from slop07.dat, I would happily pay $100 for a copy and I am sure many other GWB users would as well.

 

Meanwhile, recommended links on the support page to database projects in Japan and France no longer work.

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All of the source code and executables for DBCreate can be downloaded from the journal in which the article was published, Computers & Geosciences as an "Application" file.

 

Kong, X. Z., Tutolo, B. M., & Saar, M. O. (2013). DBCreate: A SUPCRT92-based Program for Producing EQ3/6, TOUGHREACT, and GWB Thermodynamic Databases at user-defined T and P. Computers & Geosciences 51: 415–417.

http://www.sciencedirect.com/science/article/pii/S0098300412002828

 

If there are any problems, we can work with you to produce a new GWB-formatted data set. Please be sure to cite DBCreate whenever you utilize it.

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Hello Benjamin,

 

I contacted your co-author XZ Kong, and he was kind enough to send me the MacIntosh version of DBCreate. With some considerable effort (including buying an old Mac on eBay and translating the bulk of slop07.dat to use GWB naming and orthographic conventions) I got DBCreate to work -- sort of. It runs and generates a new GWB data base, but the new base is identical to the one input. Using a different .con file makes no difference.

There is another post on the Forum from someone saying that you were kind enough to provide a version of DBCreate which works correctly.

Would you be so kind to provide me a copy ? Most of my computers run Windows 7 Pro, 64 bit, but I also have a Mac (bought for this very purpose). So, a 64 bit Windows version ideal, or a Mac version acceptable.

Thank you in advance,

Oleh Weres

Reno

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Hi Oleh,

Were you able to get DBCreate to work for you, and did you make a GWB formatted database using data from SUPCRT92 and slop07.dat?

Thanks,

Shanna

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I also ran into some problems with the source code I received from the authors (though I should mention they were pretty responsive and did seem to want to get me up and running). I had to make a couple of specific changes to make the code work for me, and then I was able to generate new databases, but as Oleh points out, the formatting differences between the slop07.dat and the originating database packaged with DBCreate (thermo.com.dat) prevent using the slop07.dat thermodynamic file, so I was still restricted to using speq06.dat. In any case, here is what worked for me:

Source Code Changes:

I had to make 2 changes to the maker.f source file (Note that I started with a newer version of the code than what accompanied the article online back in 2012. Can't remember if I got it off UMN's website or if the authors sent it directly):

1. On line 24 (approximate line number depending on version of source code: PARAMETER (MAXSPX=30) --> Had to change 10 to 30

As I did this a while ago, I don't remember the exact reason, but I was hitting some kind of limit

2. On line 25: PARAMETER (idafile=77, irxnspx=11,ireacf=41,iNotFound=27) --> Added the unit number assignment for idafile (should be between 1-99) which the original code does not have.

This was required for me b/c the openf command on line 47 was not otherwise finding the direct access file (dpeq06.dat in my case), and though my memory is fuzzy on this point, this error may have resulted in an output database that was the same as the input, similar to what Oleh describes, though it seems like an error should be thrown in this case.

Once I made these changes and recompiled the code, I got results for the new PT conditions contained in my con file. 

Modifications to included thermodynamic file: speq06.dat

Regarding the use of slop07.dat, One other suggestion I would make is that instead of trying to make slop07.dat work, you might consider adding what you need to the sequantial access database that comes with DBCreate (speq06.dat), then using cprons92 to regenerate the direct access file from this (e.g., dpeq06.dat), then re-running DBCreate to create your GWB-ready database. This way, you only have to make sure the new stuff has the right format, rather than trying to reformat an entirely different sequential access database. I did this with some UO2++ species, and was then able to load the new database into GWB and model these species. 

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I ended  up doing exactly what "superflyben" recommended:  Start with speq06.dat and add whatever else you may need to it.  speq06.dat is basically slop98.dat translated into LLNL naming conventions (to make it compatible with the data files provided with GWB) plus a few things added.  The later slop editions mostly added organic species and complexes, which you could copy and add to speq06.dat.  You would also need to add them to your source GWB data base.

Benjamin Tutolo was kind enough to send me a copy of DBCreate and the necessary batch file in versions modified to run under Windows.  It is a tricky program very sensitive to PRECISE format of the input files, but I did manage to get it to run more-or-less reliably without digging into the source code (which I do not even have).

Hope this helps.  -- Oleh

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Thank you superflyben and Oleh! Your comments are very helpful!

I don't actually have access to DBCreate at the moment. It sounds like the best way to obtain DBCreate is by kindly asking Benjamin Tutolo?

Can DBCreate by any chance convert a data0 file for EQ3/6 directly to the format for a GWB database? 

I was taught how to model geochemistry by a professor who has worked with GEOPIG, and she didn't teach GWB due to the lack of a readily available, up to date, internally consistent database for GWB. As such, I learned how to model by using EQ3/6 with a data0 file maintained by GEOPIG. I am just now making the shift to GWB for a job I recently started, and I found this post in an attempt to learn if anyone else has considered a GWB database based on SUPCRT92 and the updated slop files. I'm delighted to find that people have also thought about this and have made progress!! Like Oleh mentioned in an earlier comment, I'm sure many other GWB users would be/are interested in this. Have either of you considered or are either of you willing to share your GWB databases produced with DBCreate with the GWB community or even with GEOPIG directly?

Thank you in advance for any more advice! 

Shanna

 

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Shanna,

Not sure I can be much help with how DBC interacts with EQ3/6 as I've only ever dealt with the GWB side of things, but based on my reading of the command options (accessed on mac with ./DBCreate -h), it would seem that you can start with data0 and go straight to a GWB formatted database.

I think you make an excellent point that there should be more sharing in general of database files to avoid duplicating work, so I've gone ahead and posted the database I work with here, but I suspect it will be of limited utility b/c mine is targeted at working in deep-sea hydrothermal systems and doesn't include much in the way of organics. For that reason, it's probably worth figuring out how to generate a database as there will always be the need for additional modifications. So, yes, I would suggest contacting the authors to ask for code/executables as they seem to be willing to help. 

Regarding Geopig, the geopig.asu.edu link appears to be broken and a cursory Google Search has not turned up a new location. Do you know if these resources are still available? 

- Ben Larson

thermo.500.dat

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Hi Ben, 

Thank you again for your advice, and thank you for sharing some of your hard work! I agree that it will still be helpful to me to be able to build my own database with DBCreate, and I also agree that it is helpful to avoid duplicating work!

I didn't realize the GEOPIG link is broken, but it definitely is! I'm not sure why that is, but I do know that slop07.dat can be accessed interactively at this URL (which seems to still be working):

http://geopig3.la.asu.edu:8080/GEOPIG/pigopt1.html

Thanks,

Shanna

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