bioparticle

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a PFLOTRAN reaction sandbox for particle transport

View the Project on GitHub edsaac/bioparticle

Instructions

Available options in the reaction sandbox

How to compile?

Currently, the BIOPARTICLE sandbox is located on a fork of the PFLOTRAN project.

To use it, you can follow steps 1-3 in the installation instructions. For the fourth step, you will need to clone this fork, checkout the bioparticle branch and compile:

$ git clone https://edsaac@bitbucket.org/edsaac/pflotran.git 
$ cd $PFLOTRAN_DIR
$ git checkout bioparticle
$ mkdir bin
$ cd bin
$ make -j 8 -f ../src/pflotran/makefile SRC_DIR=../src/pflotran pflotran

How to use?

BIOPARTICLE

If all rates are set as CONSTANTS, the CHEMISTRY card should look something like this:

CHEMISTRY
  PRIMARY_SPECIES
    Vaq
  /
  
  IMMOBILE_SPECIES
    Vim
  /

  REACTION_SANDBOX
    BIOPARTICLE
      PARTICLE_NAME_AQ Vaq
      PARTICLE_NAME_IM Vim
      RATE_ATTACHMENT CONSTANT
        VALUE <katt> 1/h
      /
      RATE_DETACHMENT CONSTANT
        VALUE <kdet> 1/h
      /
      DECAY_AQUEOUS CONSTANT
        VALUE <decayAq> 1/h
      /
      DECAY_ADSORBED CONSTANT
        VALUE <decayIm> 1/h
      /
    /
  /
  LOG_FORMULATION
  TRUNCATE_CONCENTRATION 1.0E-35
  DATABASE rxn_database.dat
  OUTPUT
    TOTAL
    ALL
  /
END

If using temperature-based models for decay rates and colloid filtration theory for the attachment rate, the CHEMISTRY card should look something like this:

CHEMISTRY
  PRIMARY_SPECIES
    Vaq
  /
  
  IMMOBILE_SPECIES
    Vim
  /

  REACTION_SANDBOX
    BIOPARTICLE
      PARTICLE_NAME_AQ Vaq
      PARTICLE_NAME_IM Vim
      RATE_ATTACHMENT FILTRATION_MODEL
        DIAMETER_COLLECTOR <diamCollector>
        DIAMETER_PARTICLE <diamParticle>
        HAMAKER_CONSTANT <hamakerConstant>
        DENSITY_PARTICLE <rhoParticle>
      /
      RATE_DETACHMENT CONSTANT
        VALUE <kdet> 1/s
      /
      DECAY_AQUEOUS TEMPERATURE_MODEL
        TREF    4.0
        ZT      29.1
        N       2.0
        LOGDREF 2.3
      /
      DECAY_ADSORBED TEMPERATURE_MODEL
        TREF    4.0
        ZT      29.1
        N       2.0
        LOGDREF 2.3
      /
    /
  /
  LOG_FORMULATION
  TRUNCATE_CONCENTRATION 1.0E-50
  DATABASE ../MISCELLANEOUS/rxn_database.dat
  OUTPUT
    TOTAL
    ALL
  /
END

Installing the python API*

  1. Add the package to your python installation using pip. 
    $ cd ./src/jupypft/
$ pip install -e .

It worked when…

Using version Link
PFLOTRAN v3.0 PFLOTRAN
PETSc v3.13 PETSc
gfortran 7.5.0 gfortran
make 4.1 make
Ubuntu v20.04 ubuntu

More details about compiling a new PFLOTRAN’s reaction sandbox. » 🔗

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