Improvents in NEB and pseudopotentials#1213
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dbidoggia wants to merge 14 commits intoaiidateam:mainfrom
Open
Improvents in NEB and pseudopotentials#1213dbidoggia wants to merge 14 commits intoaiidateam:mainfrom
dbidoggia wants to merge 14 commits intoaiidateam:mainfrom
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Significant refactoring of the `NebParser` that moves the XML parsing for each image to a separate `parse_xml` method. The handling of exit codes is also expanded and improved. Co-authored-by: Davide Bidoggia <davide.bidoggia@units.it> Co-authored-by: ionuorah <anyianyi89@gmail.com>
In order to provide more control over the path to the user, we adapt the inputs of the `NebCalculation` to use a single `images` input with type `TrajectoryData` that contains all the structures, instead of only the `first_structure` and `last_structure`. The latter are deprecated and will be removed in the next major release. We also add the `validate_inputs` top-level validator to make sure the required inputs are provided and add a deprecation warning. Validation related to these inputs that was previously checked in the `prepare_for_submission` method is also moved to this validator so these issues are discovered before submission. Co-authored-by: Davide Bidoggia <davide.bidoggia@units.it> Co-authored-by: ionuorah <anyianyi89@gmail.com>
Add a `BaseRestartWorkChain` for the `NebCalculation` class, dealing with several common errors when running `neb.x` calculations. The following handlers are specific for `neb.x` runs: * `handle_neb_interrupted_partial_trajectory` * `handle_neb_cycle_exceeded_nstep` And are basically clean shutdowns for which we can do a full restart. The following are duplicated from the `PwBaseWorkChain`: * `handle_diagonalization_errors` * `handle_electronic_convergence_not_reached` Co-authored-by: Davide Bidoggia <davide.bidoggia@units.it> Co-authored-by: ionuorah <anyianyi89@gmail.com>
It expects that pbc are set in the `TrajectoryData` by: `trajectory.set_array('pbc', np.array([False, False, False]))`
… NEB calculations
…ined cutoff, if we manually provide the cutoffs in the overrides input
…n the calculation. In this way also pseudo families without z_valence can work in some cases
…nd improve robustness of NEB parser when calcualtion fails with image parallelization
…L parse error in `NebParser`
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in NEB:
for pseudo: