Feature: add nearest neighbours analysis #53
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Two exit codes are added, for which a possible handler can be implemented in the future.
We implement the logic to skip a certain number of relax iterations. For these iterations the check on convergence is also skipped. Some fixes are also added.
Two exit codes are added, for which a possible handler can be implemented in the future.
The `hp.x` and `pw.x` code can distinguish hubbard values for atoms with the same names, thus relabeling is not performed for the intersite case. Alghough, this is not the case when utilizing only onsite U.
We implement the logic to skip a certain number of relax iterations. For these iterations the check on convergence is also skipped. Some fixes are also added.
Modify the `SelfConsistentHubbardWorkChain` to clean the work directories at each iteration instead of cleaning everything at the end, eventually saving lots of storage space, which may be crucial for large scale calculations or for users with few space.
Some structures may have onsite atoms of the same specie but with different nearest neighbours (e.g. Fe3O4). The hp.x code can handle this only specifying a maximum radius, within which one can find the nearest neighbours. As such radius may change during relaxation of the atomic structure, an analysis is introduced to define at each iteration such maximum radius.
Fixes #55 Exit status 0 was given when at the last iteration no self-consistency (of Hubbard parameters) was reached. This is misleading, and a new exit code is added to highlitght better this condition.
Adapt the `convergence_not_reached` handler so that it only adjusts `alpha_mix`. `niter_max` is moved to the protocol.
The current raw output parser would miss some corner cases, when lots of q-points are generated and the number has no more any space left from the parenthesis. The solution is to use a more general regex search. As a sanity check, also the perturbed atom number sites regex search is changed correspondingly.
Fixes #66 The relabel function might not work if the spin configuration changes and the kinds cannot be determined uniquely by the parsed configuration from the hp.x post-processing. For this reason, we catch the error and exit smoothly with a new exit code if this would happen.
The convergence check on parameters had a bug in the logic. That logic would work for 1 Hubbard atom only, and that's the reason why this passed unseen in the tests. The fix is rather simple, and the new tests are tested again a case which made the old tests to make.
The convergence check on parameters had a bug in the logic. That logic would work for 1 Hubbard atom only, and that's the reason why this passed unseen in the tests. The fix is rather simple, and the new tests are tested again a case which made the old tests to make.
The self-consistent workflow now checks the maximum number of neighbours and defines the hp inputs so to print all the possible intersites couples. The parser is then instructed to only keep the interactions that were defined in the initial HubbardStructureData. This is useful in case the actual first neighbours are different then the activated intersite interactions, thus a screening of the HUBBARD.dat file cannot be avoided. This methodology allows for having a more consistent definition and parsing of the nearest neighbours using Voronoi tessellation.
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Complex structures may present multiple coordination environments. The
hp.xis unable to distinguish multiple neighbours at the post-processing steps with the usual approach. One can still input tohp.xa maximum radius for which to print the nearest neighbours. Such analysis is performed using pymatgen capabilities, and it is now performed by default.This should wait https://github.com/bastonero/aiida-quantumespresso/tree/feat/voronoi to be merged.