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WIP: Bring adaptive-cont up-to-date with master and add Cauchy-Born shift and Surface Reconstruction code #163

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merged 80 commits into from
Jul 6, 2023

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prs513rosewood and others added 30 commits February 10, 2023 18:25
The meson build broke the generation of documentation becase _version.py is a
generated file and is necessary to generate documentation.
Besides the Calculator class (CommitteeUncertainty) itself 2 more classes (Committee, CommitteeMember) are implemented that are doing the groundwork for the actual Calculator. Moreover, enabled logging for the implementation.
…nics

removed contact_mechanics submodule
…AP-based to LennardJones-based results + minor adjustments
…ator

ENH: added implementation for committe (of models) approach as a Calculator, including TST
…ator_minor_bugfix

BUG: fixed erroneous conditional
kbal and others added 29 commits May 21, 2023 21:07
Make sure that l is rotated into the x direction.
Included options to extend region I or remove the surface from region
II/III
Also added option to mask atoms that one does want to apply a large
strain to
Previous solution did not use normalized vectors, not
catching the general [a,0,0] case.
Also, numpy.allclose() does not catch the [-a,0,0] case.
Make sure only normalized vectors are compared.
…ence

fix: "\s" is now an invalid escape sequence
always return array of length maxlength
Collected documentation edits & fixes
…t_error

scipy.optimize.NoConvergence no longer exists
Added a surface reconstruction tool that can map and apply surface
reconstructions in simple and multilattices
Function include plotting strain error and correcting for f_alpha
errors
@jameskermode jameskermode merged commit 0c9d5f1 into libAtoms:adaptivecont Jul 6, 2023
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7 participants