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 bypip
), but depending on yourpython
environment and previously-installed packages, it could possibly still arise. It occurs due to a recent change in thenumpy
C API in version1.20.0
, see here for details. It should be fixed by reinstallingnumpy
andpymatgen
(so that they play nice together), so that it is rebuilt with the newnumpy
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.