Troubleshooting

doped/pymatgen Errors

For most error cases, doped has been designed to try and give informative error messages about why the functions are failing. In the majority of cases, if you encounter an error using doped which does not have a clear error message about the origin of the problem, it is likely to be an issue with your version of pymatgen (and/or doped), and may be fixed by doing:

pip install pymatgen --upgrade
pip install doped --upgrade

If this does not solve your issue, please contact the developers through the GitHub Issues page, or by email.

numpy Errors

• A previous known issue with numpy/pymatgen is that it could give an error similar to this:

  ValueError: numpy.ndarray size changed, may indicate binary incompatibility. Expected 88 from C header, got 80 from PyObject
  

  This should be avoided with current versions of doped, due to the package installation requirements (handled automatically by pip), but depending on your python environment and previously-installed packages, it could possibly still arise. It occurs due to a recent change in the numpy C API in version 1.20.0, see here for details. It should be fixed by reinstalling numpy and pymatgen (so that they play nice together), so that it is rebuilt with the new numpy C API:

  pip install --force --no-cache-dir numpy==1.23
  pip uninstall pymatgen
  pip install pymatgen
  

ShakeNBreak

For issues relating to the ShakeNBreak part of the defect calculation workflow, please refer to the ShakeNBreak documentation.

Note

If you run into any issues using doped, please contact the developers through the GitHub Issues page, or by email.