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

Merged
merged 80 commits into from
Jul 6, 2023
Merged

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

merged 80 commits into from
Jul 6, 2023

Commits on Feb 10, 2023

  1. DOC: removing . and .. from sys.path for sphinx 

    The meson build broke the generation of documentation becase _version.py is a
generated file and is necessary to generate documentation.
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  2. DOC: sane default options for autodoc

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  3. DOC: restructured documentation into User Guides / API Reference

    @prs513rosewood
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  4. removed contact_mechanics submodule

    @prs513rosewood
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Commits on Mar 13, 2023

  1. DOC: added dislocation module to api documentation

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  2. DOC: added top level draft for dislocation

    @pgrigorev
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  3. DOC: added plasticity to table of contents

    @pgrigorev
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Commits on Apr 5, 2023

  1. ENH: added function to create sub-samples from gives list of atoms-ob… 

    …jects
    @simonwengert
    simonwengert committed Apr 5, 2023
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  2. ENH: added implementation of committee approach 

    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.
    @simonwengert
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  3. ENH: added __init__.py and updated meson.build for committee approach… 

    … implementation
    @simonwengert
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  4. TST: added tests for committee approach

    @simonwengert
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  5. BUG: attempt to fix failing test-suite by adding missing dependency '… 

    …quippy'
    @simonwengert
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  6. Merge pull request libAtoms#142 from libAtoms/23-delete-contact-mecha… 

    …nics

removed contact_mechanics submodule
    @pastewka
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Commits on Apr 11, 2023

  1. Removed quippy-dependency (see discussion PR#145) by switching from G… 

    …AP-based to LennardJones-based results + minor adjustments
    @simonwengert
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Commits on Apr 12, 2023

  1. TST: providing required data in more compact form

    @simonwengert
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  2. Merge pull request libAtoms#145 from simonwengert/23_committee_calcul… 

    …ator

ENH: added implementation for committe (of models) approach as a Calculator, including TST
    @jameskermode
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  3. BUG: fixed erroneous conditional

    @simonwengert
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  4. Merge pull request libAtoms#147 from simonwengert/23_committee_calcul… 

    …ator_minor_bugfix

BUG: fixed erroneous conditional
    @jameskermode
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Commits on Apr 17, 2023

  1. TST: switched to noninteractive matplotlib backend

    @pgrigorev
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  2. TST: fixed eam4 path

    @pgrigorev
    pgrigorev committed Apr 17, 2023
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  3. ENH: added FCC Shockley partial dislocation

    @pgrigorev
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  4. TST: added test for FCCShockleyPartial

    @pgrigorev
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Commits on Apr 18, 2023

  1. TST: added Sockley partial glide configs test

    @pgrigorev
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  2. TST: refactored confusing test names

    @pgrigorev
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  3. ENH: added FCC Screw110 dislocation

    @pgrigorev
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  4. TST: added test for FCC Screw 110

    @pgrigorev
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  5. TST: added FCC Screw110 glide configs test

    @pgrigorev
    pgrigorev committed Apr 18, 2023
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  6. fixed typos and flakes

    @pgrigorev
    pgrigorev committed Apr 18, 2023
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Commits on Apr 21, 2023

  1. ENH: added FCC Edge Shockley partial dislocation

    @pgrigorev
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  2. TST: added test for FCCEdgeShockleyPartial

    @pgrigorev
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Commits on Apr 24, 2023

  1. BUILD: Added pure: false

    @pastewka
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  2. BUILD: Updates meson and meson-python requirements

    @pastewka
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  3. CI: Install meson through pip

    @pastewka
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  4. ENH: added FCC Edge 110 dislocation

    @pgrigorev
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  5. TST: added test for FCCEdge110 dislocation

    @pgrigorev
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  6. TST: added FCCEdge110 glide configs test

    @pgrigorev
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  7. ENH: added displacements for dissociated dislo

    @pgrigorev
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  8. TST: enabled tests_u for dissociated dislocations

    @pgrigorev
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  9. Merge pull request libAtoms#149 from libAtoms/23_meson_pure_builds 

    BUILD: Disable pure builds
    @pastewka
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  10. CI: Use pip to install meson and ninja, also when publishing

    @pastewka
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  11. Merge pull request libAtoms#150 from libAtoms/23_install_meson 

    CI: Use pip to install meson and ninja, also when publishing
    @pastewka
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Commits on Apr 27, 2023

  1. TST: added test with non default symbol 

    This was broken for the dissociated dislocations: the symbol was not
assigned correctly.
    @pgrigorev
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  2. BUG: fixed symbol assignment 

    For the disslciated dislocations I switched to copying the properties from one of the provided partials
rather than hardcoding it again. Also added the internal testing of the
parameters of the two partials and resulting burgers vector.
    @pgrigorev
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  3. BUG: alat divided by 2 for non bcc

    @pgrigorev
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  4. TST: change the tolerance for elastic constants

    @pgrigorev
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Commits on Apr 28, 2023

  1. added docstring and updated copyright dates

    @pgrigorev
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  2. Merge remote-tracking branch 'upstream/master' into FCC

    @pgrigorev
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  3. changed \ to brackets for line continuation

    @pgrigorev
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Commits on May 2, 2023

  1. Merge pull request libAtoms#151 from pgrigorev/FCC 

    added FCC dislocations to dislocation module
    @jameskermode
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Commits on May 21, 2023

  1. Make sure that l is rotated into the x direction. 

    The current code does the opposite: align x with l.
Suppose l=[1,0,1], then x will now be [1,0,-1] rather
than the expected [1,0,1].
In lower symmetries (starting with monoclinic) these two
directions are not equivalent.

The correctness of this patch is contingent on ELATE doing
the correct thing, because it was validated against ELATE.
    @kbal
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  2. Missing change

    @kbal
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  3. Add unit test for rotation in monoclinic case

    @kbal
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Commits on May 22, 2023

  1. Update build-wheels.yml

    @jameskermode
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  2. Merge pull request libAtoms#153 from kbal/master 

    Make sure that l is rotated into the x direction.
    @jameskermode
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  3. Merge pull request libAtoms#154 from libAtoms/macos-12 

    Update build-wheels.yml
    @jameskermode
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Commits on Jun 2, 2023

  1. WIP: Added object to predict Cauchy-Born shifts in multi-lattices

    @Fraser-Birks
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  2. WIP: Added surface masking 

    Included options to extend region I or remove the surface from region
II/III
    @Fraser-Birks
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  3. WIP: Added functions to set sublattices and apply shift

    @Fraser-Birks
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  4. WIP: Removed options for 3rd and 4th derivatives in shift corrector

    @Fraser-Birks
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  5. WIP: Added functions for surface relaxation and counting

    @Fraser-Birks
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  6. WIP: Updated set_atoms to work with an extended region I

    @Fraser-Birks
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  7. Added option to output all contributions to f-alpha per atom

    @Fraser-Birks
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  8. WIP: Added functions for plotting and saving as well as relevant library 

    imports
    @Fraser-Birks
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  9. WIP: Integrated Cauchy-Born object into fracture simulation 

    Also added option to mask atoms that one does want to apply a large
strain to
    @Fraser-Birks
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Commits on Jun 5, 2023

  1. Fixed surface masking to not mask any region I.

    @Fraser-Birks
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Commits on Jun 7, 2023

  1. Avoid rotating x into itself. 

    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.
    @kbal
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  2. Merge pull request libAtoms#155 from kbal/master 

    Make sure only normalized vectors are compared.
    @jameskermode
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  3. Added regression model for fitting cauchy-born shifts

    @Fraser-Birks
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  4. Added more options for interfacing with cauchy-born object

    @Fraser-Birks
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Commits on Jun 14, 2023

  1. scipy.optimizer.NoConvergence no longer exists

    @prs513rosewood
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Commits on Jun 16, 2023

  1. fix: "\s" is now an invalid escape sequence

    @prs513rosewood
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  2. Merge pull request libAtoms#157 from libAtoms/fix/invalid_escape_sequ… 

    …ence

fix: "\s" is now an invalid escape sequence
    @jameskermode
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Commits on Jun 20, 2023

  1. always return array of length maxlength, independent of the structure… 

    … the ring statistics were computed on
    richardjana committed Jun 20, 2023
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  2. Merge pull request libAtoms#158 from richardjana/master 

    always return array of length maxlength
    @pastewka
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Commits on Jun 29, 2023

  1. Merge pull request libAtoms#141 from libAtoms/23-documentation 

    Collected documentation edits & fixes
    @pastewka
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  2. Merge pull request libAtoms#156 from libAtoms/fix/noconvergence_impor… 

    …t_error

scipy.optimize.NoConvergence no longer exists
    @pastewka
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Commits on Jul 5, 2023

  1. WIP: Surface reconstruction mapper and predictor 

    Added a surface reconstruction tool that can map and apply surface
reconstructions in simple and multilattices
    @Fraser-Birks
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  2. WIP: Added better documentation to cauchy-born shift predictor

    @Fraser-Birks
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  3. WIP: Added additional helper functions to crack.py 

    Function include plotting strain error and correcting for f_alpha
errors
    @Fraser-Birks
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  4. Merge branch 'master' into adaptivecont-fork

    @Fraser-Birks
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