Instructions for compilation:
mkdir build
cd external
tar -xzf nauty27r1.tar.gz
cd nauty27r1
./configure
make
cd ../../build
cmake ..
make
Instructions for running:
cd build
mkdir run
cd run
mkdir dump
../diffusion ../../data/PotentialA.fs run.out
Frame for each time step dump/ will contain a corresponding .xyz file of all atomic coordinates (and vacancy centres).
The file run.out highlights just vacancies and H atoms with headings:
time, activation energy, vacancy coordinates [x, y, z]..., hydrogen coordinates [x, y, z]...