      ___________________   _____    _________
     /  _____/\_   _____/  /     \  /   _____/
    /   \  ___ |    __)_  /  \ /  \ \_____  \ 
    \    \_\  \|        \/    Y    \/        \
     \______  /_______  /\____|__  /_______  /
            \/        \/         \/        \/ 
         is an Extensible Molecular Simulator

GEMS (General Engine for Molecular Simulations) is a flexible molecular simulation framework focused on configurable interaction models, dynamic atom/group handling, and extensible simulation workflows. The project emphasizes modular architecture, programmable input-driven simulations, and a hybrid memory model that combines dynamic editable structures with compact representations optimized for compute-intensive algorithms.

Documentation¶

The full documentation is available at:

https://alexispaz.github.io/GEMS/

To preview locally use mkdocs serve

Build and install¶

First downlaod GEMS from repo:

git clone https://github.com/alexispaz/gems.git
cd gems

Then, use either meson (recommended) or autotools systems to build an install. Optionally, these can be also handle with spack.

Using spack¶

You can add the package from the local repo:

cd spack/
spack repo add .

Then install and activate the package in your preferred spack way.

spack install gems
spack load gems

Using meson¶

Configure, build an install

meson setup build
meson install -C build

Then, run meson dist to create a distribution. Installation prefix, debug flags and other variables can be modified during configuration. For instance:

meson setup build --prefix=$PWD/usr --reconfigure && meson install -C build/

All together with debug flags would be something like:

meson setup build --prefix=$(realpath ./usr) --buildtype=debug \
-Df_args='-fcheck=all -ffpe-trap=invalid,zero,overflow -fbacktrace -g3 -ggdb3 -Wextra' \
&& meson install -C build/

Using autotools¶

Configure, build an install

autoreconf -fi; # Only if no configure script is given
./configure
make
make install

Run make dist to create a distribution. Further compiling options are handle following autotools way. For instance:

export PATH=/share/apps/gcc/6.2.0/bin/:$PATH
export LD_LIBRARY_PATH=/share/apps/gcc/6.2.0/lib64:$LD_LIBRARY_PATH
export FC=gfortran
export FCFLAGS=-fno-use-linker-plugin
./configure --disable-openmp FCFLAGS='-Ofast'

See ./configure --help for more information.

Warning: If you switch between Autotools and Meson, remember that Autotools places compiled .mod files inside the src/ directory, while Meson expects the source tree to be clean. Leftover .mod files in src/ can cause incorrect dependency resolution and misleading compilation errors.

Dependencies¶

Mandatory dependencies are:

Fortran Preprocesor Templates for Dynamic Data Structures (FPT-DDS) url: (https://github.com/alexispaz/FortranTemplates)
Fortran 90 function parser v1.1 url: (https://github.com/alexispaz/fparser)

Meson build system will automatically download and install these dependencies if are no already present in the environment.

About¶

GEMS code is hosted in github.

Copyright notices and license information for the different files used in the GEMS project can be found in the ABOUT file that follows a similar format to the Debian's COPYRIGHT file format.

Files in lib/ are third party software distributed with none or quite small changes. Licenses and copyright notices can be found in there as presented by their authors.

License¶

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

GEMS 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 General Public License for more details.

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