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troubleshooting.rst

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Troubleshooting

Conda Solve Fails

If conda cannot solve the environment after attempting to install the dependencies create a new virtual environment with:

$ conda create -n autode_env
$ conda activate autode_env

then install. The autodE environment will need to be activated each time a new shell is opened, with: conda activate autode_env.

MethodUnavailable

If high and/or low level electronic structure methods cannot be found in your PATH environment variable it is possible to set the paths manually in ade.Config for e.g. XTB:

>>> from autode import methods, Config
>>> methods.get_lmethod()
autode.exceptions.MethodUnavailable
>>> Config.XTB.path = '/path/to/xtb/bin/xtb'
>>> methods.get_lmethod()
XTB(available = True)

alternatively, add to the PATH environment variable e.g. in bash:

$ export PATH=/path/to/xtb/bin/:$PATH

to set this permanently, add the above line to ~/.bash_profile or ~/.bashrc on Linux.

A Transition State Cannot be Located

Automatically finding transition states (TS) with autodE can sometimes fail due to either a misidentification of the TS as incorrect or an insufficiently good TS guess geometry being found. If a TS hasn't been found first check the reaction_name_path.png visualisation of the initial path and proceed depending on whether a peak is or is not present.

Without a path peak

Oh no! without an initial peak a TS won't be able to be found. Perhaps the reaction is electronically barrierless at this level of theory. If there are anions consider adding diffuse functions, if they are not already present e.g.:

>>> from autode import Config
>>> Config.ORCA.keywords.set_opt_basis_set('ma-def2-SVP')

With a path peak

If there is a peak then either (1) the TS guess geometry is not close enough to the TS for successful optimisation. To reduce the step size:

>>> from autode import Config
>>> Config.min_step_size = 0.02

Otherwise (2), it may be that the TS optimiser cannot locate the saddle point because of Hessian drift. Consider reducing the number of intermediate steps between Hessian updates (i.e. Config.ORCA.keywords.opt_ts for ORCA).

If you've found an interesting case where a TS cannot be found please do get in touch, we're always on the lookout for examples to improve the method!