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README.md
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SpecMiCP / ReactMiCP
====================
Overview
--------
SpecMiCP is a speciation solver to find the equilibrium state of a chemical
system. The system is based on a mixed complementarity formulation of the
equilibrium condition for minerals.
For a mineral with volume fraction Sm, the equilibrium condition is :
Sm >= 0, -log(IAPm/K) >= 0, -Sm*log(IAPm/K) = 0
where IAPm is the ion activity product and K the equilibrium constant.
This condition is reformulated using the penalized Fischer-Burmeister C-function and the system is solved
using a semismooth method.
ReactMiCP is a reactive transport solver built on top of specmicp.
It uses the operator splitting approach to couple transport and chemistry.
Modules
-------
SpecMiCP is not (yet) a program but a set of libraries that can be used to solve
specific problems.
The following modules are already available :
- **specmicp** : *core* of the library, set the system, and solve it
- **reactmicp** : the reactive transport solver
- **database** : manage the database, parse it from a file, swap the basis,
select the correct species, ...
- **micpsolver** : Solve a Mixed Complementarity problem
- **odeint** : integration methods for solving ordinary differential
equations (for problem involving kinetics for example)
- **dfpm** : a finite element module
The **micpsolver** and **odeint** modules can be use independantly.
Examples of use are provided in the examples directory.
Using SpecMiCP
==============
Examples
--------
To build and install SpecMiCP/ReactMiCP see the INSTALL file.
To learn how to use the API the best is to look at the examples.
The starting point should be the leaching in CO2-saturated examples :
examples/reactmicp/saturated_react/carbonation.cpp.
This file is heavily commented.
Example of use of the Python interface can be found in the tests/cython directory.
Use in your own project
-----------------------
A cmake module can be used to find SpecMiCP in your own project. It will be installed at
<prefix>/share/specmicp/cmake/FindSpecMiCP.cmake
The python module can be used directly if it is in your python path.
Documentation
-------------
The API is documented with Doxygen and the documentation can be generated with the command :
make doc
A (maybe outdated) version of the doc can be found [here][3].
Warning
-------
The code is in development and the API is not considered stable yet.
Python binding
--------------
A python binding is available at the following address :
https://bitbucket.org/specmicp/specmicppy
About
=====
SpecMiCP is developped by F. Georget (fabieng aT princeton DoT edu). It is part
of my Ph.D. work. The purpose of the PhD is to develop a reactive transport model
to model the coupling between hydration, drying and carbonation in cement paste.
This Ph.D. is funded by [Princeton university][6], [Lafarge][4] and the [CSTB][5].
References :
- F. Georget, J. H. Prévost, and R. J. Vanderbei. A speciation solver for cement paste modeling and the semismooth Newton method . Cement and Concrete Research, 68(0):139--147, 2015.
- F. Georget, J. H. Prévost and B. Huet Validation of a reactive transport solver based on a semismooth speciation solver (submitted to Computational Geosciences)
A list of the references used in the code can be found in the [documentation][7].
[2]: http://www.empa.ch/plugin/template/empa/*/62204/---/l=1
[3]: http://www.princeton.edu/~fabieng/specmicpdoc/index.html
[4]: http://www.lafarge.com/en
[5]: http://www.cstb.fr/
[6]: http://princeton.edu
[7]: http://www.princeton.edu/~fabieng/specmicpdoc/citelist.html

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