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Zeolite20 (ZEO20)Database


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The zeolite20 database (attached) is free on the EMPA website.  It says it is in Phreeqc format but it is Phreeqc for the EMPA software known as GEMS.  The coefficients for each zeolite are the coefficients for the equation log K = a + b*(Tk-Tr) + c*(Tk^2-Tr^2)*   + d*(1/Tk - 1/Tr) + e*(1/Tk^2 - 1/Tr^2) + f*ln(Tk/Tr).  I noted that CEMDATA from the EMPA website was converted to GWB format using TEdit  in GWB Release 15.  I tried using TEdit and since this is a notepad text version of the database, TEdit does not recognize it as an acceptable database.  And, I am at a loss as to how to convert the above equation into the GWB Log K polynomial temperature coefficients even though there is a tutorial in the comments in the CEMDATA GWB database. 

Since, this ZEO20 database would be useful for the entire geochemical community, can Aqueous Solutions convert this database and post it on your website.  It only contains 20-25 zeolites, so it is not a large database

However, for your consideration, there is a new ZEO19 database (I attach the reference) that is quite extensive.  I have not found any electronic files associated with it and I was told by one of the co-authors that it runs only on the GEMS software.

Zeolite-Na-Ca-Phreeqc version.txt 2020_Zhen-Wu et al_Nature_MatDegradation.pdf

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Hello Carol,

Thank you for alerting us and the community to these new databases. You can most certainly use TEdit to convert a PhreeqC dataset to GWB format. However, the text file you attached only contains mineral reactions formatted with compatibility to be read in by PhreeqC. If you open a PhreeqC dataset, you will see that there are additional sections defining elements and aqueous species that are missing in your text file to make this a complete dataset that can be used for geochemical calculations. TEdit uses this information as part of the conversion. 

According to EMPA's website, the zeolite20 database shares the same SOLUTION_MASTER_SPECIES and SOLUTION_SPECIES sections as the Cemdata database. An easy approach to building a valid dataset that contains the reactions from zeolite20 is to take the two sections mentioned above from Cemdata (formatted for PhreeqC) and adding it to your text file to create a valid PhreeqC dataset. You can download a PhreeqC formatted Cemdata dataset from EMPA's website. You would also need to add a line "PHASES" above your mineral reactions as it is done in PhreeqC datasets to signal the beginning of mineral and gas reactions. If you wish to include mineral reactions from the original Cemdata dataset, you can simply copy and paste them into your text file under the PHASES section too. The website notes that certain zeolites in Cemdata18 overlap with data in zeolite20, so you should avoid duplicating reactions in your dataset. When your dataset is ready, you can convert it to GWB format by dragging and dropping the text file in TEdit. You can refer to section 9.3 Importing PhreeqC datasets in the GWB Essentials User Guide for more details regarding the converter. If you have issues converting a PhreeqC dataset after you have added the sections mentioned above, please attach your file so we can take a closer look.

Please note that the GWB uses the polynomial log K = a + b*(Tk-Tr) + c*(Tk^2-Tr^2)*   + d*(1/Tk - 1/Tr) + e*(1/Tk^2 - 1/Tr^2) + f*ln(Tk/Tr) for temperature expansions. I believe PhreeqC uses a different polynomial for Log K temperature dependence. You can find this equation in PhreeqC's user guide. The header section of thermo_CEMDATA.tdat shows the equations used to converted from coefficients A1-A6 (from PhreeqC's polynomial) to coefficients a-f used in GWB. For more information on how GWB datasets are formatted, please refer to section 3. Thermo datasets in the GWB Reference Manual.

Hope this helps,
Jia Wang
Aqueous Solutions LLC

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This section in quotes is the part that I am having problems understanding...

"The header section of thermo_CEMDATA.tdat shows the equations used to converted from coefficients A1-A6 (from PhreeqC's polynomial) to coefficients a-f used in GWB. For more information on how GWB datasets are formatted, please refer to section 3. Thermo datasets in the GWB Reference Manual."  Sorry, I am trying to figure this out this AM.

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 And do you know what this extra c= is under HEU(Ca)-1 ?  I am presuming it is the chemical equation and they are just using c to represent HEU(Ca)????

HEU(Ca)-1                        
ç = 2.14AlO2- + 1.07Ca+2 + 6.86SiO2 + 4.4H2O                        
-Vm    317.88

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Hello Carol,

PhreeqC uses a different polynomial expansion to account for Log K temperature dependence than that of GWB. The expansion is: 

phreeqc3-30.png and you can find this in PhreeqC's user manual here. GWB polynomial coefficients were converted from coefficients A1-A6 in PhreeqC's analytic expression as follows:

 a= log10 K(298.15 K) = A1 + A2*Tr + A3/Tr + A4*log10(Tr) + A5/Tr^2 + A6*Tr^2
  b= A2
  c= A6
  d= A3
  e= A5
  f= A4/ln(10)

where Tr is 298.15 Kelvins. You can refer to section 9.3 Importing PhreeqC datasets in the GWB Essentials User Guide for more details. You can plug conversion into the GWB polynomial to check that you attain the same polynomial as the PhreeqC expansion. 

3 hours ago, Carol M. Jantzen said:

 And do you know what this extra c= is under HEU(Ca)-1 ?  I am presuming it is the chemical equation and they are just using c to represent HEU(Ca)????

HEU(Ca)-1                        
ç = 2.14AlO2- + 1.07Ca+2 + 6.86SiO2 + 4.4H2O                        
-Vm    317.88

When I open the txt file from your original post, I see:

HEU(Ca)-1                        
Ca1.07(Al2.14Si6.86)O18(H2O)4.4 = 2.14AlO2- + 1.07Ca+2 + 6.86SiO2 + 4.4H2O                        
-Vm    317.88                        
-analytical_expression    35.4187    0    -12625.9    -13.52071059    0    0    0
-log_K    -40.392857            

Maybe your file was altered accidentally? On the same webpage of the PhreeqC manual states: "The chemical formula for the defined phase must be the first chemical formula on the left-hand side of the equation." You can down the attached file again to see the original text. I opened the file in Notepad. 

Hope this helps,
Jia 
            

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Yes, that helped a lot.  

In the meantime, I did a comparison of the zeolites contained in Thermo.dat, CEMDATA.dat, YMP.dat against the zeolites in ZEO20.  Most of the same zeolites are contained in CEMDATA and YMP that are in ZEO20.  There are 22 zeolites in ZEO20 and 4 overlap with the zeolite data in CEMDATA.  Is there a way that I can import the "extra" 18 zeolites into CEMDATA or do I have to do the conversion that you suggest above in TEdit and then merge CEMDATA and ZEO20.  Just looking for ways to have all the zeolite data in one place instead of having to run different databases.

Thanks for all your help.

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OK - I did as you suggested.  I took the Phreeqc version of CEMDATA18 on the EMPA website and merged it with the ZEO20 Phreeqc version of the zeolite database on the EMPA website and removed one of the 4 zeolite entries that overlapped in those 2 databases.  Then I ported the file which I called JANT-ZEO-CEM.dat into TEdit and it converted it to a GWB file.  

I did not convert each polynomial for the log K expression manually as I "assumed" that TEdit would do that. Perhaps I am wrong and you need to tell me if I have to manually convert each expression and retype it in the polynomial expression coefficients.  I attach the JANT-ZEO-CEM.dat file that I created for your scrutiny to tell me what I may have done wrong.

TEdit converted JANT-ZEO-CEM.dat to a GWB format successfully.  But when I ran a solution that I had run previously in REACT using the CEMDATA18 for GWB that is available on your website, I got a much different answer.  The 2 most saturated phases were the same but the rest were not.

I am assuming that I have done something wrong but the conversion from TEdit appears to work..the phases produced with JANT-ZEO-CEM.dat are actually phases that may form.  Please advise...I have tried and I am a newbie at this modeling although a 50+ year geochemist.

JANT-ZEO-CEMDATA-Phreeqc.txt

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Hi, it's Carol again...

This morning I reran my solution that I had run previously in REACT, I will call it CF for now, with my newly converted JANT-ZEO-CEMDATA that is now in GWB format.  AND I ran the exact same CF solution using Aqueous Solutions version of CEMDATA18.  And I got the same answers (not different answers as I said in the last post).  I must have done something wrong late yesterday afternoon.

None-the-less, could you check my txt datafile that I posted yesterday.

Thanks.

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Hello Carol,

It looks like you are successful with the dataset conversion. With regards to the polynomial conversion, the PhreeqC importer in Tedit will convert the polynomial coefficients for you. There's no need to manually perform the conversion. You can always check the conversion by hand to confirm that the coefficients are correct if you like though. 

I took a quick glance at the input you attached and didn't spot any issues with the formatting of the dataset. I think chabazite overlaps between Cemdata and Zeolite20, so you might consider deleting or commenting out (using # in front of each line) one of the reactions as EMPA's website suggested. 

Just a couple more notes regarding the dataset that might be helpful. If you would like to include the reference information regarding the dataset (i.e. the text before the Solution_master_species section in your PhreeqC file) you can add that in the Headers pane in the Preamble section in the new GWB tdat file. That information will not be preserved when the dataset is converted. I would also point out that thermo_cemdata.tdat on the GWB thermo page includes the mineral type labels as well as factors for evaluating gas coefficients in the GWB for some gasses, added in after the conversion from PhreeqC. If want to add this information in your thermodynamic dataset, you can copy the new zeolite reactions JANT-ZEO-CEMDATA.tdat to thermo_cemdata.tdat or alternatively, manually edit the entries in your newly converted dataset. If you are choosing the first, you would need to delete the duplicated zeolite mineral reactions in thermo_cemdata.tdat. 

Hope this helps,
Jia 

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Hi Jia -

Thanks for all your help.  I saw that overlap with chabazite but I checked and the thermodynamic coefficients were different. May be a slightly different composition.  So I left that overlap in the merged dataset.  As you know there are Ca and Na rich chabazites and anything in-between.  I have been using the merged dataset and it is great.  Just what I needed !!

Carol

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  • 8 months later...

Hi Carol,

I'm writing to let you know that with the GWB 2022 release, the Cemdata 18 database is now installed with the GWB software as "thermo_cemdata.tdat". Furthermore, the database was extended to include phosphate and zeolite minerals from Empa. The zeolite data is from Empa's "zeolite21" database, an update to their "zeolite20" compilation to include K zeolites. The GWB-format dataset is annotated with additional information that may be of use.

The GWB 2022 release additionally features a binary solid solution model. Solid solutions defined in the original Cemdata 18 reference have been included in thermo_cemdata.tdat. Additional solid solutions can be added to the database, or configured by the user at run time. For more information, please see section 2.5, Solid solutions, in the GWB Essentials Guide, as well as section 3.4.7, Solid solutions, in the GWB Reference Manual.

Regards,

Brian Farrell
Aqueous Solutions

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