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Problem with runlog.out and flow.out files


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Good day,

 

I am working on a simulation on CO2 sequestration in ToughReact using PetraSim. I faced the problem with simulation files, especially runlog.out and flow.out. If I go to the Cell History Plot and 3D results, I can see some graphs and change of parameters in 3D as attached.

However, the simulation itself does not run and it shows the window with following: "Simulation halted prematurely. See: runlog.out and flow.out". 

When I click on the runlog.out file, it shows a warning in the notebook file. However when I click on the flow.out file, it does not open anything.

All the screenshots are attached below.

 

Hope for your help. Thank you.

 

Regards,

Aigerim

3d.png

error.png

cell history plot.png

runlog.png

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Aigerim,

 

Does the flow.out file exist in the file with the runlog.out file?  If it does, you should be able to open it outside of the PetraSim program.  If you continue to have problems, or if somehow the flow.out file is not being created, please send us your SIM File as we'll see if we can reproduce the problem.

 

Best Regards,

Alison

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Hi Aigerim,

 

I see that you are using TOUGHREACT v3.32, which is not quite as integrated with PetraSim as TOUGHREACT v1.2.

 

In order to get your model to run from a command line, I had to put the following DLL files in the same directory as the TOUGHREACT executable.

 

image.png

 

I then placed these same DLLS in the following directory, and the model ran through the PetraSim interface.

 

C:\Program Files\PetraSim 2020\tough64\treact_v3

 

The message about the simulation halting previously is inaccurate, as this model seems to run to completion (this is something we need to address as we add better support for TOUGHREACT v3.32).  I am able to access the flow.out and runlog.out using the links in the program.  Also, if I look in the directory with the SIM file, I see that the simulation has created TecPlot output files, but NOT CSV files.

 

The fact that you are able to view some results in the interface indicated that there are also CSV files in the model directory.  I am not sure why there are CSV files in the directory with your SIM File, but my guess is that these are left over from a previous TOUGHREACT v1.2 model run, or perhaps you used our online conversion tool to create them from the TecPlot output?

 

I would recommend that you delete ALL output files and rerun your model.  As a rule, each SIM file should be stored in its own directory to avoid confusion with overwriting output files.

 

 

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I believe I followed your recommendations accordingly. However even though I followed the procedure well, I could not get the runlog.out and flow.out files. The PetraSim file from drive C (C:\Program Files\PetraSim 2020\tough64\treact_v3\ccs_example) does not run saying that "Access is denied" and is not creating output files but only input files. Have not I understood you perfectly or still there is a problem with the simulation file?

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Aigerim,

 

You would not want to store your SIM file in the C:\Program Files\PetraSim 2020\tough64\treact_v3 directory.  You would only want to place the TOUGHREACT v3.32 executable and the required DLLs there.  Storing a SIM file and TOUGHREACT input files there would cause this Access Violation.

 

You should store the SIM file and related input files in a location such as the Documents folder on your computer.

 

The other option would be to place a copy of the TOUGHREACT executable and the required DLLs in the same directory as the input files, and run the simulation from a command line, rather than from the PetraSim interface.

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Dear Alison,

 

I am thankful and appreciate your help to solve the problem. I rebuilt the model using the Toughreact v.1.2. I got the output files, and there seems to be no error in the runlog and flow.out files, but the simulation still does not run. Could you please look at the file and check if there are results? I am attaching it below. 

 

Thank you.

 

Regards,

Aigerim

ccs_example_1_2.sim

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Aigerim,

 

There are a number of problems with your model.

 

I think the main problem is that you have not selected an aqueous species.  I tried switching to the "enable all" option, and got a message in the runlog.out file that there were too many derived aqueous species, so you will need to select some.

 

image.png

 

A few other things to note:

 

1.  In your initial water zone, you've assigned values of 0 for CGUESS and also values of 0 for CTOT for h2o and so4-2.  These should not be 0.

 

2.  Another problem that I noticed with your model is that you have not assigned any zones to the elements.  I would recommend that you do this by layer.  You can double click on a layer in the data tree on the left side of the window (for example, Caprock 1), and under chemical zones, set an initial water zone, mineral zone, etc.  My experience has been that you need to assign an initial water zone to all of the cells for a model to run.

 

image.png

 

I would recommend that you switch to a simpler model, maybe even just a single cell model, initially.  This would allow you to work out any problems with your water chemistry and minerals before moving on to a move complicated flow model.

 

You also might try creating the flow model without any chemistry initially, and then add the chemistry once your flow model is working.

 

 

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Oh my God, I forgot specifying zones! Thanks, Alison!

Yes, I actually need SO2 (aq) and Fe+3 for pyrite's additional mechanism. But when I found and selected from aqueous complexes, the runlog file said that these compounds are not found in the database even though they are there.

image.png.ffdfa903fe0f75bb24cd3521636fa544.png

image.png.59988e3d8ded643cd958331fbe6d4458.png

 

That is why I deleted them from aqueous complexes, but according to you, we cannot ignore them and need to specify. Why is it so? I am using thermodb.txt thermodynamic database.

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The main reason your model will not run is that you have not assigned an Initial Water zone to all of the elements in the model.  I did this, and the model does run for a little while.  However, if you look at the runlog.out file, you'll see lots of errors about convergence problems, so it seems that you have more work to do on your initial water chemistry and minerals.

 

Have you put together a static geochemical model using a program such as PHREEQC or GWB?  If not, you should really do that before trying to add the chemistry to TOUGHREACT.  Ideally, you will want your minerals and water to be in equilibrium.  As I had mentioned, it might help for you to put together some single cell models testing your initial water and chemistry before trying to run a more complex model.

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Hello, Alison,

Thank you for your previous reply.

We have created a PHREEQC program where we equilibrated minerals and initial water composition and got the results. Now we have two questions:

1) In the output file, water is obtained with the following molality. Since the species' amounts should be in mol/kg of water, we have seen that water amount in Toughreact simulation should be 1.0 mol in "Water zone" input data. Is it really so? So should we divide the molalities here by 5.553e+01? For example, would the amount of Al in "Water zone" be 1.153e-08/5.553e+01 or should we take them as they are?

image.png.a96c1322d8b77bf0f94d7d9fb5e635b9.png

 

2) Are we right thinking that CGUESS value of Al+3 (ions), for example, here 1.329e-12, but CTOT value is 1.153e-08? (Or based on the 1st question, divided by water amount)?

Then what CGUESS and CTOT values will be for H+ species given only the output data shown above and the following one:

image.png.3d9de75659c7a3d05a2b5c2a5efea007.png

 

Thank you. 

 

Regards,

Aigerim

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Aigerim,

 

These all would be a better question for the LBL forum and I ask that you repost these questions there.

 

1. For CTOT, I THINK that you would use all of these molality values as they are listed, but use 1 for h2o.  If you determine that this is incorrect, please come back and share that information here.

 

2. Regarding CGUESS, I believe that normally, you can use the same value as CTOT, or one order of magnitude lower.  Here is a link to a discussion about "guess" and "tot" on the LBL forum:  https://tough.forumbee.com/t/36a3b9/setting-up-initial-water-chemistry

 

3.  Regarding h+, take a look at the TOUGHREACT manual for ICON =3 (known activity).  This is often used to define a known pH "For example, to
input a known pH value, use this option and set CTOT = 10-pH for H+ activity."

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  • 2 weeks later...

Dear Alison,

 

I am back here with other questions :) Thank you for your previous reply, I understood regarding chemical compositions and now would like to ask about time steps. When I run a simulation for monitoring for 1000 years (with no co2 injection), the following message is shown, not allowing to finish the simulation: 

 

image.png.ebcc0f387b10a17385457386ac5b83eb.png

 

What does this mean? I tried to give lower time steps, but the simulation still does not go till the end. How can the time step and max time steps be adjusted? Due to the limit of files being attached, the simulation file cannot be attached here. I will send it in the next reply.

Thank you.

 

Regards,

 

Aigerim

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2 minutes ago, Aigerim said:

Dear Alison,

 

I am back here with other questions :) Thank you for your previous reply, I understood regarding chemical compositions and now would like to ask about time steps. When I run a simulation for monitoring for 1000 years (with no co2 injection), the following message is shown, not allowing to finish the simulation: 

 

image.png.ebcc0f387b10a17385457386ac5b83eb.png

 

What does this mean? I tried to give lower time steps, but the simulation still does not go till the end. How can the time step and max time steps be adjusted? Due to the limit of files being attached, the simulation file cannot be attached here. I will send it in the next reply.

Thank you.

 

Regards,

 

Aigerim

Seems like I cannot attach it...

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Please go ahead and email your SIM file to tech@rockware.com and we will take a look.  If you have not tried running your model without the chemistry, please do this first.  This should hopefully help you determine if the problem is with the flow portion of the model, or the chemistry.

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You can disable the chemistry portion of the model by unchecking Enable Reactive Transport.  This is an option under the Properties|Global Properties menu in PetraSim.

 

I think this changes MOPR(1) to 2, but you should check this to confirm the setting.  Please see the TOUGHREACT v3.32 "QuickRef" PDF for a description of this.

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