GEMSFITS

Code and Graphical Shell for GEM Input Parameter Optimization and Inverse Modelling Linux, OSX, Windows

What GEMSFITS can do?

• Can fit internally consistent input parameters of chemical thermodynamic models against the experimental data
• Is coupled with the GEMS3K code for Gibbs Energy Minimization calculation of equilibrium states
• Allows for bound, (non-)linear (in-)equality constrained minimization of weighted squared residuals
• Written in C/C++, available with source code, completely parallelizable on HPC architectures
• Provides tools for statistical analysis with thorough evaluation of the fitted parameters uncertainty
• Results of fitting and statistics can be visualized and printed in various graphical formats using the graphical shell
• Can import, manage and query extensive sets of the experimental data accumulated in NoSQL database files

Learn more and contact us on GEMSFITS web page.

If you find GEMSFITS useful for your research applications, please cite the following papers:

• Miron G.D., Kulik D.A., Dmytrieva S.V., Wagner T. (2015): GEMSFITS: Code package for optimization of geochemical model parameters and inverse modeling. Applied Geochemistry 55, 28-45, doi.
• Kulik D.A., Wagner T., Dmytrieva S.V., Kosakowski G., Hingerl F.F., Chudnenko K.V., Berner U. (2013): GEM-Selektor geochemical modeling package: revised algorithm and GEMS3K numerical kernel for coupled simulation codes. Computational Geosciences 17, 1-24, doi.
• Wagner T., Kulik D.A., Hingerl F.F., Dmytrieva S.V. (2012): GEM-Selektor geochemical modeling package: TSolMod library and data interface for multicomponent phase models. Canadian Mineralogist 50, 1173-1195, doi.

How to clone (download) the GEMSFITS source code?

• Download gemsfits source code using git clone command:

git clone --recurse-submodules https://bitbucket.org/gems4/gemsfits.git

How to build GEMSFITS Ubuntu Linux and MacOS?

• Make sure you have g++, CMake and Qt6 installed. If not, install them:

sudo apt-get install g++ cmake git

For MacOS, make sure that Homebrew is installed (see Homebrew web site )

• Install Dependencies

In order to build the gemsfits library on Ubuntu Linux or MacOS, first execute the following (may ask your sudo password):

cd ~/gemsfits
./gemsfits-install-dependencies.sh  [ OLD_EJDB ]

• Build gemsfits applications

To build gemsfits and install it in your home directory or in the system directory (as in the example below), a typical sequence of commands can be executed in the terminal:

cd ~/gemsfits
mkdir build
cd build
cmake .. -DCMAKE_BUILD_TYPE=Release -DCMAKE_PREFIX_PATH=/home/<you>/Qt/6.5.0/gcc_64  [ -DUSE_OLD_EJDB=ON ]
make -j 4

If you are using Qt installed in your home folder you will probably encounter an error about missing gl.h when building with QT. To avoid this do:

sudo apt-get install build-essential libgl1-mesa-dev libxcb-xinerama0 libxcb-cursor0

Compiling gemsfits applications in Qt Creator

• In Qt Creator open ~/gemsfits/gemsfit2/gemsfit2.pro
• Set the build folder to ~/gemsfits/gemsfit2-build
• In Qt Creator open ~/gemsfits/gfshell2/gemsfit2-gui.pro
• Set the build folder to ~/gemsfits/gfshell2-build
• After the successful compilation try to run gemsfit2-gui GUI from Qt Creator.

How to build gemsfits applications (on conda-devenv)

Before building gemsfits, make sure you have the conda-devenv tool installed. Otherwise, run the following command in a terminal (assuming here that conda is already installed!):

conda install conda-devenv

We will use this tool now to create the gemsfits conda environment which contains all the dependencies for building gemsfits code. In the terminal, do:

cd path/to/gemsfits
conda devenv

Once this step is successfully completed, you can activate the gemsfits conda environment as follows:

conda activate gemsfits

In order to build the 'gemsfits' library on Linux or MacOS, first execute the following:

./conda-install-dependencies.sh  [ OLD_EJDB ]

Now it's time to use cmake to configure and build the C++ applications:

cmake -S . -B build   [ -DUSE_OLD_EJDB=ON ]
cmake --build build --parallel

This step will produce (inside the created directory gemsfits/build):

How to run gemsfits applications

• gemsfit3

To start the application, open a terminal window and execute:

cd ~/gemsfits/build/bin
./gemsfit3 ...

• To run Qt GUI launcher, execute the following (or use gemsfits/gfshell2/gemsfit-gui.pro with QtCreator):

cd ~/gemsfits/build/bin
./shellfit3

License

GEMSFITS is free software: you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.

GEMSFITS is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more details.

You should have received a copy of the GNU Lesser General Public License along with the source code. If not, see http://www.gnu.org/licenses/.

Contribution guidelines

• Writing tests
• Code review
• Other guidelines

Who do I talk to?

• Repo owner or admin
• Other community or team contact