Installation

Prerequisites

• libffi-dev (for some reason)

• packmol (for packing water )

We recommend you use pyenv with pyenv-virtualenv, in which case you can run for instance

pyenv install 3.8.2
pyenv virtualenv 3.8.2 molecular_builder
pyenv activate molecular_builder

Warning

Make sure you have installed libffi before you install python. Otherwise, you may end up with an obscure error involving _ctypes. This is done by brew install libffi on mac or sudo apt install libffi-dev on ubuntu. You then have to reinstall python (which is simple using pyenv).

Then you install molecular_builder itself.

pip install molecular-builder

For installing packmol, something like this should work on unix systems (This is what we use when automatically generating the documentation on GitHub Actions):

wget https://github.com/m3g/packmol/archive/20.010.zip
unzip 20.010.zip
cd packmol-20.010
sed 's/\/usr\/bin\/gfortran/gfortran/g' Makefile > tmp.txt
mv tmp.txt Makefile
make
sudo cp packmol /usr/local/bin/

The regex-replacement in the makefile may not be necessary, depending on your gfortran installation.