IMPORTANT: THIS REPOSITORY IS EXCLUSIVELY FOR THE BIOCRUNCH AND CHOMBO-CRUNCH VERSIONS OF CRUNCHFLOW. FOR ANY OHER USE, REFER TO THE CURRENT VERSION OF CRUNCHFLOW/CRUNCHTOPE AVAiLABLE AT https://github.com/cisteefel/crunchtope

BioCrunch

BioCrunch was developed from CrunchFlow to explicitly represent microbes using ‘omics-derived information. It applies a dual-Monod type approach to simulate redox thermodynamics to predict the energy available for cellular maintenance, respiration, biomass development, and enzyme production. Reaction rates are further constrained based on thermodynamics formulations of either Jin and Bethke, 2003 or Larowe et al., 2012. These relationships define how microbial physiological traits impact fitness, how biogeochemical processes are impacted by changing microbial composition, and how biogeochemistry affects microbial fitness and community assembly. These feedback mechanisms are enabled through dynamic calculations of these key redox/energetic parameters at each time step. Supporting scripts allow for a multitude of genomes to be reduced to genome clusters/guilds with similar functional trait distributions based on derived matrices of functional traits. Further steps allow for ‘representative organisms’ to be created to statistically represent the distribution of traits within guilds and enable information loss to be quantified as all genomes are condensed to these ‘representative organisms’. This reduction of genome complexity can account for any needed computational tradeoffs between selecting the numbers of organisms (these catalysts are represented as unique biomass terms in BioCrunch) and numbers of chemical reactions calculated per time step.

BioCrunch is available by cloning the BioCrunch branch of the repository

$ git clone --branch BioCrunch https://bitbucket.org/crunchflow/crunchtope-dev.git

Chombo-Crunch

Chombo-Crunch is a code for the simulation of reactive transport processes at the pore scale as well as in multiscale (pore and continuum) scale systems. Chombo-Crunch uses CrunchFlow as geochemical solver via a custom interface. This repository contains the version of CrunchFlow developed for use with Chombo-Crunch, which is managed in a separated repository.

Contact

This repository is currently managed by Sergi Molins only for BioCrunch and Chombo-Crunch related development.

If you are looking to use CrunchFlow/CrunchTope, it is made available on github by Carl Steefel.

CrunchFlow/CrunchTope

CrunchFlow/CrunchTope is a powerful software package for simulating reactive transport developed by Carl Steefel and co-workers and applied since 1988 to a variety of problems in the earth and environmental sciences. The code is based on a finite volume discretization of the governing coupled partial differential equations that link flow, solute transport, and multi-component equilibrium and kinetic reactions in porous and/or fluid media. CrunchFlow/CrunchTope is the recipient of an R&D 100 Award for Cutting-Edge Technologies in 2017.

Copyright notice

CrunchFlow, Copyright (c) 2016, The Regents of the University of California, through Lawrence Berkeley National Laboratory (subject to receipt of any required approvals from the U.S. Dept. of Energy). All rights reserved.

If you have questions about your rights to use or distribute this software, please contact Berkeley Lab's Innovation & Partnerships Office at IPO@lbl.gov.

NOTICE. This Software was developed under funding from the U.S. Department of Energy and the U.S. Government consequently retains certain rights. As such, the U.S. Government has been granted for itself and others acting on its behalf a paid-up, nonexclusive, irrevocable, worldwide license in the Software to reproduce, distribute copies to the public, prepare derivative works, and perform publicly and display publicly, and to permit other to do so.

License Agreement

CrunchFlow, Copyright (c) 2016, The Regents of the University of California, through Lawrence Berkeley National Laboratory (subject to receipt of any required approvals from the U.S. Dept. of Energy). All rights reserved."

Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met:

(1) Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.

(2) Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution.

(3) Neither the name of the University of California, Lawrence Berkeley National Laboratory, U.S. Dept. of Energy nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission.

THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

You are under no obligation whatsoever to provide any bug fixes, patches, or upgrades to the features, functionality or performance of the source code ("Enhancements") to anyone; however, if you choose to make your Enhancements available either publicly, or directly to Lawrence Berkeley National Laboratory, without imposing a separate written license agreement for such Enhancements, then you hereby grant the following license: a non-exclusive, royalty-free perpetual license to install, use, modify, prepare derivative works, incorporate into other computer software, distribute, and sublicense such enhancements or derivative works thereof, in binary and source code form.