modify solute concentration in the checkpoint file

[Kewei Chen]

Dear all,

I am trying to modify the solute concentration in the checkpoint file by multiplying the concentration of a specific species by a scale factor. The HDF5 file structure is /PMCSubsurfaceTransport/transport/Primary_Variable, which contains a 1-D array of length 67,200. This value reflects the product of 1,920 grid cells and 35 species (17 primary species + 18 immobile species defined in the sandbox). 

I would like to apply a scaling factor to several immobile species, but I am unsure how the 67,200 entries are organized. Are they arranged by grid or by species? In other words, does the file store the first 35 elements as all species in the first grid cell (followed by the next 35 elements for the second grid cell), or does it store the first 1,920 elements as the first species across all grid cells (followed by the next 1,920 elements for the second species)? Any insights would be greatly appreciated.

Best,

Kewei 

[Hammond, Glenn E]

Kewei,

That 1D array is organized identical to the solution vector field%tran_xx

https://bitbucket.org/pflotran/pflotran/src/6a73cd67ba492f6b77ac9442b2d49f3188703727/src/pflotran/pm_rt.F90#lines-2248

The first 35 entries are the aqueous and immobile concentrations for grid cell #1 followed by the 35 for grid cell #2.

Glenn

From: pflotra...@googlegroups.com <pflotra...@googlegroups.com> on behalf of Kewei Chen <chenke...@gmail.com>
Date: Thursday, September 25, 2025 at 1:22 PM
To: pflotran-users <pflotra...@googlegroups.com>
Subject: [pflotran-users: 8572] modify solute concentration in the checkpoint file

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[Kewei Chen]

Thanks, Glenn! I will check it.

Best,

Kewei