Restart Concentration Field from ATS-PFLOTRAN Checkpoint File

[Xueyuan Kang]

Hello all,

I am trying to restart a reactive transport simulation in ATS–PFLOTRAN from a previously saved checkpoint file, but I am encountering an issue when loading the concentration fields.

When restarting the simulation, the log file reports the following error:

what(): No such variable "total_component_concentration.cell.0" in file "../RTM/checkpoint00575.h5"

 

However, upon inspecting the checkpoint file (checkpoint00575.h5), I found that the variables are stored with names such as: total_component_concentration.cell.Al+++, instead of indexed names like cell.0.

 

This makes me wonder:

• Does ATS expect component concentrations to be indexed numerically (e.g., cell.0, cell.1, etc.) during restart?
• If so, is there a required mapping between component names (e.g., Al+++) and indices for the checkpoint.h5 file?
• Or is there an additional configuration needed to ensure ATS correctly recognizes the named variables in the checkpoint file?

For initialization, I have specified the restart file for all PKs (canopy, snow, flow, overland flow, subsurface transport, surface transport, subsurface chemistry, and surface chemistry) as follows:

<ParameterList name="initial condition" type="ParameterList">
  <Parameter name="restart file" type="string" value="../RTM/checkpoint00575.h5"/>
</ParameterList>

 For the subsurface and surface chemistry PKs, I have also set the "initial conditions time" to match the checkpoint time.

Despite this, it seems that the solute concentrations (and potentially mineral-related fields such as volume fractions) are not being correctly read from the checkpoint.

I would greatly appreciate any suggestions. Thank you very much for your help!

Best regards,
Xueyuan

[Xueyuan Kang]

Forgot to mention that I am using the latest ATS master branch (installed a few days ago, on March 25).

[Afolabi Femi]

Hello, 

I am currently working on peatland response to storm. I would like to ask if anyone has thorough knowledge on how to go about it using amanzi and legacy dataset. 

--
You received this message because you are subscribed to the Google Groups "Amanzi-ATS Users" group.
To unsubscribe from this group and stop receiving emails from it, send an email to ats-users+...@googlegroups.com.
To view this discussion visit https://groups.google.com/d/msgid/ats-users/7fc5632f-f802-4500-a2b8-f70b90b539fdn%40googlegroups.com.

[Ethan Coon]

Was the checkpoint file generated with the same version of the code that the restart was done with?  If so, please submit a bug on the ATS github page and we will get this fixed.  I thought we had a regression test for this, but it’s possible that this slipped through the cracks.

Ethan

-------------------------------------------------------------------
Ethan Coon
917-969-6831
https://www.ornl.gov/staff-profile/ethan-t-coon
-------------------------------------------------------------------

To view this discussion visit https://groups.google.com/d/msgid/ats-users/CAAofpt0aRAUx0KuoGBYABVZ%2BkgK%3Dn6jOK73hmRfPd9Z%3Dko0jMg%40mail.gmail.com.

[Xueyuan Kang]

Hi Ethan,

Yes, the checkpoint file was generated using the same version of the code as the restart. I will go ahead and submit a bug report.

Best,
Xueyuan