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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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jameskermode
merged 80 commits into
libAtoms:adaptivecont
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Fraser-Birks:adaptivecont-fork
Jul 6, 2023
Merged
WIP: Bring adaptive-cont up-to-date with master and add Cauchy-Born shift and Surface Reconstruction code #163
jameskermode
merged 80 commits into
libAtoms:adaptivecont
from
Fraser-Birks:adaptivecont-fork
Jul 6, 2023
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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
Make sure that l is rotated into the x direction.
Update build-wheels.yml
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
… the ring statistics were computed on
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
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