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WIP: Adaptive continuation improvements #162

Merged
merged 55 commits into from
Sep 25, 2023
Merged

WIP: Adaptive continuation improvements #162

merged 55 commits into from
Sep 25, 2023

Commits on Feb 24, 2021

  1. WIP on adaptive stepsize algorithm for arc-length continuation

    @jameskermode
    jameskermode committed Feb 24, 2021
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Commits on Jul 7, 2022

  1. WIP testing adaptive kick start

    @jameskermode
    jameskermode committed Jul 7, 2022
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  2. fix to region II definition as union of spheres centred on all region… 

    … I atoms
    @jameskermode
    jameskermode committed Jul 7, 2022
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Commits on Mar 22, 2023

  1. Merge branch 'master' of github.com:lakshenoy/matscipy into adaptivecont

    @lakshenoy
    lakshenoy committed Mar 22, 2023
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Commits on Mar 29, 2023

  1. FIRE to PreconLBFGS

    @lakshenoy
    lakshenoy committed Mar 29, 2023
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  2. ode12r for flex1&2

    @lakshenoy
    lakshenoy committed Mar 29, 2023
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  3. relaxation of flex2

    @lakshenoy
    lakshenoy committed Mar 29, 2023
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  4. updated params file

    @lakshenoy
    lakshenoy committed Mar 29, 2023
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Commits on Apr 11, 2023

  1. ode12r for arc_cont (precon still needs debugging)

    @lakshenoy
    lakshenoy committed Apr 11, 2023
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  2. surface energy function

    @lakshenoy
    lakshenoy committed Apr 11, 2023
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Commits on Apr 14, 2023

  1. animation features (zoom & remove bonds)

    @lakshenoy
    lakshenoy committed Apr 14, 2023
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  2. option to skip CLE in arcont

    @lakshenoy
    lakshenoy committed Apr 14, 2023
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Commits on Jun 2, 2023

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

    @Fraser-Birks
    Fraser-Birks committed Jun 2, 2023
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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
    Fraser-Birks committed Jun 2, 2023
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  3. WIP: Added functions to set sublattices and apply shift

    @Fraser-Birks
    Fraser-Birks committed Jun 2, 2023
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  4. WIP: Removed options for 3rd and 4th derivatives in shift corrector

    @Fraser-Birks
    Fraser-Birks committed Jun 2, 2023
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  5. WIP: Added functions for surface relaxation and counting

    @Fraser-Birks
    Fraser-Birks committed Jun 2, 2023
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  6. WIP: Updated set_atoms to work with an extended region I

    @Fraser-Birks
    Fraser-Birks committed Jun 2, 2023
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  7. Added option to output all contributions to f-alpha per atom

    @Fraser-Birks
    Fraser-Birks committed Jun 2, 2023
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  8. WIP: Added functions for plotting and saving as well as relevant library 

    imports
    @Fraser-Birks
    Fraser-Birks committed Jun 2, 2023
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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
    Fraser-Birks committed Jun 2, 2023
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Commits on Jun 5, 2023

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

    @Fraser-Birks
    Fraser-Birks committed Jun 5, 2023
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Commits on Jun 7, 2023

  1. Added regression model for fitting cauchy-born shifts

    @Fraser-Birks
    Fraser-Birks committed Jun 7, 2023
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  2. Added more options for interfacing with cauchy-born object

    @Fraser-Birks
    Fraser-Birks committed Jun 7, 2023
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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
    Fraser-Birks committed Jul 5, 2023
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  2. WIP: Added better documentation to cauchy-born shift predictor

    @Fraser-Birks
    Fraser-Birks committed Jul 5, 2023
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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
    Fraser-Birks committed Jul 5, 2023
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  4. Merge branch 'master' into adaptivecont-fork

    @Fraser-Birks
    Fraser-Birks committed Jul 5, 2023
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Commits on Jul 6, 2023

  1. Merge pull request #163 from Fraser-Birks/adaptivecont-fork 

    WIP: Bring adaptive-cont up-to-date with master and add Cauchy-Born shift and Surface Reconstruction code
    @jameskermode
    jameskermode authored Jul 6, 2023
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  2. add missing import

    @jameskermode
    jameskermode committed Jul 6, 2023
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Commits on Jul 7, 2023

  1. Removed dependency on sklearn by building local regression object

    @Fraser-Birks
    Fraser-Birks committed Jul 7, 2023
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Commits on Jul 12, 2023

  1. DOC: Documented cauchy-born corrector code and made compliant with PEP8

    @Fraser-Birks
    Fraser-Birks committed Jul 12, 2023
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  2. DOC: Documented Surface reconstruction code and complied with PEP8

    @Fraser-Birks
    Fraser-Birks committed Jul 12, 2023
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Commits on Jul 13, 2023

  1. rearrange functions

    @lakshenoy
    lakshenoy committed Jul 13, 2023
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  2. Merge branch 'adaptivecont' of https://github.com/libAtoms/matscipy i… 

    …nto adaptivecont
    @lakshenoy
    lakshenoy committed Jul 13, 2023
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  3. WIP: Seperated F and E evaluation into two seperate functions 

    Also added functionality to supply E functions with multiple coordinate
systems
    @Fraser-Birks
    Fraser-Birks committed Jul 13, 2023
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  4. DOC: PEP8 compliance

    @Fraser-Birks
    Fraser-Birks committed Jul 13, 2023
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  5. Merge branch 'adaptivecont' of https://github.com/libAtoms/matscipy i… 

    …nto adaptivecont
    @lakshenoy
    lakshenoy committed Jul 13, 2023
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  6. WIP: removed superfluous function

    @Fraser-Birks
    Fraser-Birks committed Jul 13, 2023
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  7. Merge branch 'adaptivecont' of github.com:libAtoms/matscipy into adap… 

    …tivecont
    @Fraser-Birks
    Fraser-Birks committed Jul 13, 2023
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  8. Merge branch 'master' into adaptivecont 

    Fixed neighbour list unit tests
    @Fraser-Birks
    Fraser-Birks committed Jul 13, 2023
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  9. BUILD: added solvers.py to meson.build

    @Fraser-Birks
    Fraser-Birks committed Jul 13, 2023
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  10. BUILD: Added cauchy_born.py and surface_reconstruction.py to build

    @Fraser-Birks
    Fraser-Birks committed Jul 13, 2023
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Commits on Jul 17, 2023

  1. BUG: Fixed bug where stretched unitcell was the transpose of what it 

    should have been
    @Fraser-Birks
    Fraser-Birks committed Jul 17, 2023
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  2. TST: Added tests for Cauchy-Born shift corrector models

    @Fraser-Birks
    Fraser-Birks committed Jul 17, 2023
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  3. TST: Loosened tolerances to allow for numerical errors in testing

    @Fraser-Birks
    Fraser-Birks committed Jul 17, 2023
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  4. DOC: Made Cauchy-Born test PEP8 compliant

    @Fraser-Birks
    Fraser-Birks committed Jul 17, 2023
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  5. TST: Added Cauchy-Born corrector tests for when F function is supplied

    @Fraser-Birks
    Fraser-Birks committed Jul 17, 2023
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  6. DOC: Made cauchy-born test PEP8 compliant

    @Fraser-Birks
    Fraser-Birks committed Jul 17, 2023
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Commits on Jul 18, 2023

  1. WIP: Generalised surface reconstruction for multiple surfaces and 

    multilattices
    @Fraser-Birks
    Fraser-Birks committed Jul 18, 2023
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  2. DOC: Made surface_reconstruction PEP8 compliant

    @Fraser-Birks
    Fraser-Birks committed Jul 18, 2023
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  3. TST: Added tests for surface reconstruction

    @Fraser-Birks
    Fraser-Birks committed Jul 18, 2023
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  4. DOC: Made surface reconstruction tests PEP8 compliant

    @Fraser-Birks
    Fraser-Birks committed Jul 18, 2023
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  5. BUG: Corrected name error

    @Fraser-Birks
    Fraser-Birks committed Jul 18, 2023
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Commits on Aug 15, 2023

  1. code feedback corrections

    @lakshenoy
    lakshenoy committed Aug 15, 2023
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