ndfes 3.5.6

Companion library to the ndfes C++ program for analyzing umbrella sampling

The configuration is performed with cmake. You will need cmake (version 3.12 or later installed). The installation of the python components is performed with pip.

To install cmake and update your version of pip, you can run:

USERBASE=$(python3 -m site --user-base)
USERSITE=$(python3 -m site --user-site)
export PATH="${USERBASE}/bin:${PATH}"
export PYTHONPATH="${USERSITE}:${PYTHONPATH}"
python3 -m pip install pip --upgrade --user
python3 -m pip install cmake --upgrade --user

You should consider adding the above export commands to your ${HOME}/.bashrc and then source ~/.bashrc.

If, for whatever reason, pip is unavailable on your system, you can install it using the directions here: https://pip.pypa.io/en/stable/installation/

To install ndfes:

cd build
bash ./run_cmake.sh
make install VERBOSE=1 -j4
cd ../local
export PATH="${PWD}/bin:${PATH}"
export PYTHONPATH="${PWD}/lib/python3.XX/site-packages:${PYTHONPATH}"

where python3.XX should be replaced by the appropriate python version.

ndfes has dependencies on blas/lapack and nlopt. The cmake configuration will check if these libraries are available. If they are not available, it will automatically download them from github and install them.

The blas/lapack libraries are installed from the openblas package.

https://github.com/OpenMathLib/OpenBLAS

The nlopt software is used to perform nonlinear optimizations.

https://github.com/stevengj/nlopt

These libraries could also be installed globally using your system’s package manager. For example, on Fedora, you could install them with:

sudo dnf install NLopt-devel openblas

See the contents of build/run_cmake.sh to see how you can adjust the compilers, compiler flags, python interpreter, and installation directory.