Common Errors

No module named ‘ccdc’

This error is analogous to ccdc module does not exist - compack method can not be used.

This is a Python ImportError which typically appears when the user tries to perform clustering in the cspy-db command using COMPACK. While CSPy does have the capabilities to use the CSD Python API, this requires a Python environment which integrates the dependencies for CSPy and the CSD Python API. Please see CSD Python API for more information.

Error parsing dmacrys_summary could not convert string to float: ‘********’

This error occurs because atoms get too close together and are able to overcome the buckingham repulsive wall. The buckingham potential becomes attractive as the interatomic distance becomes very small which results in atoms becoming strongly bound together. This is unphysical and DMACRYS no longer returns an energy from the geometry optimisation.

In a cspy-csp simulation, the optimisation is recorded as a failure and the siumulation moves on to the next job.

Note

In a future release, we plan to tidy up error handling

Command XXXXX timed out after XXXX.XXXX seconds

This error usually occurs when DMACRYS or PMIN fail to optimise a crystal structure within the specified timeout parameter. This can be adjusted in the TOML configuration file as described in Advanced Configuration.

I am providing an axis file to Neighcrys, but it can’t find it

Your axis file’s name may be too long – Neighcrys cannot read filenames beyond a certain length. Try shortening the filename.

A hydrogen cannot be connected to more than one atom. Exiting.

Contrary to the error message, this often happens when a hydrogen has //no// bonds, i.e. at least one of your X-H distances in your cutoff file is too short. Visualise your structure and measure any unusual X-H distances, ensuring your cutoff file has values large enough to accommodate them.

If the structure seems fine the MAXSCH value might be too small. Setting the MAXSCH value to 7 or greater seems to often fix this error.

Too many potentials in input file Error

This happens when the potential file you are supplying to NEIGHCRYS has too many entries for types of interactions (the current limit is 200). One way around this is to simply remove interactions not present in your system. A check has been added to the energy_minimise function in crystal.py. This will obtain the neighcrys labels from the fort.21, read the potential file and write only the terms needed for that particular system to a new file “r.pots”. This should remove the issue, unless the system involves more that 200 unique interactions in which case the neighcrys source code will need to be modified.

NEIGHCRYS (or DMACRYS) fails with halogen atoms in one of the molecules of a multi component system

NEIGHCRYS (or DMACRYS) requires molecules with halogen atoms to be last in the res file. If halogen atoms are present before any non-halogenated molecules neighcrys/dmacrys will exhibit non-standard behaviour and will most likely fail.