RE: ERROR(0): Uninitialized material id in patch at cell 1

[Kumar, Girish]

Hello,

I'm trying to simulate a simple 1D diffusion-sorption problem in PFLOTRAN. From the outset, I have checked and rechecked to see that I'm following all the appropriate rules to creating the input file for my problem, and yet I see an error related to initializing material at cell 1. 

Attached is the input and output file with the log at the point where PFLOTRAN throws an error.  I'm using the Development Version. Could you please help me identify what's the issue is at your earliest convenience? I'd greatly appreciate it.

Thanks,

Girish

Girish Kumar, PhD

Research Associate

Maseeh Department of Civil, Architectural and Environmental Engineering

Cockrell School of Engineering  

The University of Texas at Austin

Work Email: girish...@austin.utexas.edu

Personal Email: girish...@gmail.com

Mobile: 312-721-7864

[Hammond, Glenn E]

Girish,

 

Nice to hear from you. You need to use separate STRATA block for each REGION/MATERIAL pair.

 

STRATA

  REGION clay_top

  MATERIAL clay

END 

 

STRATA

  REGION sand_gac_layer

  MATERIAL sand_gac

END

 

STRATA

  REGION clay_bottom

  MATERIAL clay

END

 

When I fix that, there is a species GAC is not recognized (not found in database):

 

Mineral "GAC" not found in database.

 

ERROR: Species not found in database.

Glenn

 

From: pflotra...@googlegroups.com <pflotra...@googlegroups.com> on behalf of Kumar, Girish <girish...@austin.utexas.edu>
Date: Thursday, June 26, 2025 at 12:18 PM
To: pflotra...@googlegroups.com <pflotra...@googlegroups.com>
Subject: [pflotran-users: 8462] RE: ERROR(0): Uninitialized material id in patch at cell 1

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[Girish Kumar]

Thanks, Glenn! That worked just fine. Should have asked sooner. I've defined the species in the database. 

Although, despite the fix for the STRATA block, I did run into error where the simulation stopped for not initializing ROCK_DENSITY in MATERIAL_PROPERTY. I thought that was an optional card but I couldn't run without defining it. Curious to know if the code internally recalculates this property based on the mineral volume fractions, molar mass and molar volume for the region and then overrides the specified value?

Regards,

Girish 

--

[Hammond, Glenn E]

Girish,

Your input deck MATERIAL_PROPERTY blocks require a ROCK_DENSITY due to your SORPTION DISTRIBUTION_COEFFICIENTs having units of "L/kg". The "kg" is kg rock, and there is no way to calculate the number of kilograms of rock without a rock density.

Glenn

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[Girish Kumar]

Ahh...makes sense! Thanks for clarifying, Glenn. 

Regards,

Girish

[Girish Kumar]

Hello Glenn,

Is it possible to print time series of aqueous species at an observation point (say a grid point) in the domain when simulating only diffusive transport? Below is the output block I have in my input file and I see an error pertaining to variables block in the OBSERVATION_FILE card when I use it.

OUTPUT
  PERIODIC_OBSERVATION TIME 0.1 day
  SNAPSHOT_FILE
    TIMES d 1 2 5 10 15 30
    FORMAT TECPLOT POINT
    VARIABLES
     POROSITY
    /
  /
  MASS_BALANCE_FILE
    PERIODIC TIMESTEP 1
  END
  OBSERVATION_FILE
    PERIODIC TIME 10.0 s
    VARIABLES
     TCE(aq)
    /
    OBSERVATION
     REGION point1
    /
  /
END

I understand that specifying the primary species as variables is not allowed, but can you please advise about the right way to go about it? I was unable to attach the full input file and the dbs file here. Please let me know if you'd like me to send it to you separately. 

Thanks so much,
Girish

[Hammond, Glenn E]

Girish,

Output of individual chemical species is specified in the CHEMISTRY OUTPUT block. Take a look at https://bitbucket.org/pflotran/pflotran/src/master/shortcourse/exercises/regional_doublet/regional_doublet.in where output at observation points is demonstrated. I tend to output the TOTAL concentration of ALL species, but you can specify them individually.

Glenn

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