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Make new release 1.4.0 #225

Merged
merged 174 commits into from
Nov 9, 2023
Merged

Make new release 1.4.0 #225

merged 174 commits into from
Nov 9, 2023

Commits on Jun 29, 2023

  1. Add square root eigensolver

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    timcallow committed Jun 29, 2023
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  2. Introduce solver classes, and sqrt solver

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    timcallow committed Jun 29, 2023
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  3. Add parallel solver for sqrt numerov

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    timcallow committed Jun 29, 2023
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  4. Include convsersion from P to X in update_orbs

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    timcallow committed Jun 29, 2023
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  5. update almost all integrals for sqrt solver; E_kin_dens remains

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    timcallow committed Jun 29, 2023
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Commits on Jun 30, 2023

  1. Modify E kin dens calc for sqrt grid

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    timcallow committed Jun 30, 2023
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  2. Fix method B for kinetic energy

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    timcallow committed Jun 30, 2023
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  3. Generalize EnergyAlt class for different grid types

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    timcallow committed Jun 30, 2023
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  4. Add bands support for sqrt grid

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    timcallow committed Jun 30, 2023
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  5. Fix missing return statement in calc_eigs_min

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    timcallow committed Jun 30, 2023
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Commits on Jul 3, 2023

  1. Modify finite_diff for grid options

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    timcallow committed Jul 3, 2023
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  2. Modify virial for different grid types

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    timcallow committed Jul 3, 2023
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  3. Modify stress tensor for different grid types

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    timcallow committed Jul 3, 2023
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Commits on Jul 4, 2023

  1. make sure eigfuncs_init are not initalized to zero exactly

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  2. Merge remote-tracking branch 'refs/remotes/Tim_fork/sqrt_grid' into s… 

    …qrt_grid
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  3. Add an eigfuncs backup for when l is so big everything explodes

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    timcallow committed Jul 4, 2023
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Commits on Jul 7, 2023

  1. fix localization for different grid_types

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  2. Add square root pressure test

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    timcallow committed Jul 7, 2023
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  3. Changing cache key to try and reset

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Commits on Jul 10, 2023

  1. Move to a single Solver class in numerov.py (less repeated code)

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  2. Fix numpy docstring errors

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    timcallow committed Jul 10, 2023
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  3. fix flake8 issues

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    timcallow committed Jul 10, 2023
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  4. Give an explicit token to codecov

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  5. Merge pull request #179 from timcallow/sqrt_grid 

    Implement a square root grid
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  6. Add method B for virial pressure in kinetic energy calc

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Commits on Jul 11, 2023

  1. Fix formatting issues

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    timcallow committed Jul 11, 2023
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Commits on Jul 12, 2023

  1. Merge pull request #180 from timcallow/virial_method_B 

    Add method B for virial pressure in kinetic energy calc
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  2. Fix docs error

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  3. Fix some docstrings to reflect dual choice of grids

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    timcallow committed Jul 12, 2023
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  4. Merge pull request #184 from timcallow/fix_docs 

    Fix docs error
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    timcallow authored Jul 12, 2023
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Commits on Jul 13, 2023

  1. Update pressure tests to reflect new way virial method is called

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Commits on Jul 14, 2023

  1. Fix error in defn of K[:, n]

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    timcallow committed Jul 14, 2023
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  2. fix flake8 error

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    timcallow committed Jul 14, 2023
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  3. Merge pull request #187 from timcallow/fix_numerov_sqrt_err 

    Update pressure tests and fix sqrt grid error in Numerov
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    timcallow authored Jul 14, 2023
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  4. Add more detailed installation notes

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    timcallow authored Jul 14, 2023
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  5. Remove uneccesary second windows statement

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    timcallow authored Jul 14, 2023
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  6. Add code quality badge

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Commits on Jul 17, 2023

  1. Merge pull request #188 from timcallow/update_README 

    Update README
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    timcallow authored Jul 17, 2023
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Commits on Jul 19, 2023

  1. Add support for fp32 precision (wip)

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    timcallow committed Jul 19, 2023
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Commits on Jul 20, 2023

  1. try a different implementation for fp options

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    timcallow committed Jul 20, 2023
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  2. Fix up remaining changes from arrays to np

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Commits on Jul 21, 2023

  1. Merge pull request #189 from timcallow/fp_options 

    Give users an option for float 32 as default
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    timcallow authored Jul 21, 2023
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  2. Remove some badges from README

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    timcallow authored Jul 21, 2023
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  3. Remove DOI, re-introduce Python 3.8

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  4. Merge pull request #190 from timcallow/remove_badges 

    Remove some badges from README
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Commits on Jul 26, 2023

  1. Fix errors that caused float64 to always be used

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    timcallow committed Jul 26, 2023
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  2. keep xgrid as float64 for extra stability

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    timcallow committed Jul 26, 2023
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Commits on Jul 27, 2023

  1. Merge pull request #191 from timcallow/fp_fix 

    Fix errors that caused float64 to always be used
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  2. Add name=main and parallel for all tests

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    timcallow committed Jul 27, 2023
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  3. reset functionals test

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  4. Merge pull request #192 from timcallow/test_improvements 

    Small improvements to tests
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    timcallow authored Jul 27, 2023
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Commits on Aug 4, 2023

  1. Convert serial numerov solve to use diags matrices

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  2. Clean up KS_matsolve_serial

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  3. Clean up KS_matsolve_serial and enable parallel

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  4. Merge remote-tracking branch 'Timfork/use_diags' into use_diags

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  5. Adapt tests for new diags method

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    timcallow committed Aug 4, 2023
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  6. fix style errors

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  7. remove unnecessary generation of big matrices

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    timcallow committed Aug 4, 2023
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  8. fix flake8 errors

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Commits on Aug 7, 2023

  1. Try to speed up hartree with numba

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  2. Try to calculate hartree pot only once

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  3. attempt to speed up hartree pot calc (WIP)

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Commits on Aug 8, 2023

  1. fix small omission in hartree pot calc

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  2. fix error in hartree pot

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    timcallow committed Aug 8, 2023
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  3. fix tests

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  4. Merge pull request #196 from timcallow/fix_hartree_error 

    Fix an error in the Hartree potential
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  5. Merge remote-tracking branch 'origin/develop' into use_diags

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Commits on Aug 11, 2023

  1. introduce grid_type param for mathtools.grad_func

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  2. allow gga to work with sqrt grid

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  3. Merge pull request #197 from timcallow/gga_sqrt 

    Implement sqrt grid for GGAs
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  4. Convert serial numerov solve to use diags matrices

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  5. Clean up KS_matsolve_serial and enable parallel

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  6. Adapt tests for new diags method

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  7. fix style errors

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  8. remove unnecessary generation of big matrices

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  9. fix flake8 errors

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  10. Merge remote-tracking branch 'refs/remotes/Timfork/use_diags' into us… 

    …e_diags
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  11. ease tolerance for spin test

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  12. remove unused time import

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  13. Merge pull request #194 from timcallow/use_diags 

    Explicitly use diagonal matrices in numerov solver
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  14. Try to speed up hartree with numba

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  15. Try to calculate hartree pot only once

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  16. attempt to speed up hartree pot calc (WIP)

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  17. fix small omission in hartree pot calc

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  18. Merge remote-tracking branch 'Timfork/hartree_pot' into hartree_pot

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  19. Remove unnecessary potential argument in Energy class

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  20. fix flake8 error

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Commits on Aug 12, 2023

  1. Merge pull request #198 from timcallow/hartree_pot 

    Speed up calculation of Hartree potential
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Commits on Aug 20, 2023

  1. Explicitly invert B to avoid errors

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  2. Add warning if B is ill-conditioned

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  3. Merge pull request #199 from timcallow/fix_guess_eigvals 

    Fix issue with eigenvalue guess
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Commits on Sep 22, 2023

  1. Remove config.fp option for float precision

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Commits on Sep 25, 2023

  1. fix flake8 errors

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  2. Merge pull request #200 from timcallow/remove_float_option 

    Remove config.fp option for float precision
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Commits on Sep 29, 2023

  1. Use a better set of defaults

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Commits on Oct 4, 2023

  1. fix issues with tests

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  2. Merge pull request #201 from timcallow/better_defaults 

    Use a better set of defaults
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Commits on Oct 8, 2023

  1. Remove libxc from dependencies

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  2. Update tests for manual libxc build

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    timcallow committed Oct 8, 2023
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  3. change from ssh to https

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    timcallow committed Oct 8, 2023
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  4. Remove shell command

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  5. Clone from https (missing in second place)

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  6. Add missing cd command

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Commits on Oct 9, 2023

  1. Increase time limit (for libxc install)

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    timcallow committed Oct 9, 2023
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  2. install libxc in pipenv

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    timcallow committed Oct 9, 2023
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  3. Try to use consistent pipenv environment

    @timcallow
    timcallow committed Oct 9, 2023
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  4. Add updated libxc installation instructions

    @timcallow
    timcallow committed Oct 9, 2023
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  5. Add libxc installation script

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    timcallow committed Oct 9, 2023
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  6. fix atoMEC path and use Python 3.12

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    timcallow committed Oct 9, 2023
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  7. Change Python version to 3.10 and change libxc install to pip

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    timcallow committed Oct 9, 2023
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  8. try to debug tests

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    timcallow committed Oct 9, 2023
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  9. make install script better

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    timcallow committed Oct 9, 2023
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  10. Edit Python version info in README

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    timcallow authored Oct 9, 2023
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  11. Merge pull request #203 from timcallow/libxc_change_install 

    Change the way `libxc` is installed
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    timcallow authored Oct 9, 2023
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Commits on Oct 10, 2023

  1. Rename tests so pytest picks up on them

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    timcallow committed Oct 10, 2023
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  2. Merge pull request #204 from timcallow/rename_tests 

    Rename tests so pytest picks up on them
    @timcallow
    timcallow authored Oct 10, 2023
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  3. Change Python 3.8 to 3.10

    @timcallow
    timcallow authored Oct 10, 2023
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  4. Make mixfrac explicit in tests

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    timcallow committed Oct 10, 2023
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  5. Merge pull request #206 from timcallow/fix_tests 

    Make mixfrac explicit in tests
    @timcallow
    timcallow authored Oct 10, 2023
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  6. Allow convergence after 2 scf cycles

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    timcallow committed Oct 10, 2023
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  7. Merge pull request #207 from timcallow/convergence_change 

    Allow convergence after 2 scf cycles
    @timcallow
    timcallow authored Oct 10, 2023
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  8. Add suppress warnings variable to config

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    timcallow committed Oct 10, 2023
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Commits on Oct 11, 2023

  1. Fix typo

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    timcallow committed Oct 11, 2023
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  2. Catch more exceptions

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    timcallow committed Oct 11, 2023
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  3. Add checker for s0

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    timcallow committed Oct 11, 2023
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  4. Add ngrid_coarse checks

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    timcallow committed Oct 11, 2023
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  5. Merge pull request #208 from timcallow/warnings_improve 

    Add suppress warnings variable to config
    @timcallow
    timcallow authored Oct 11, 2023
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  6. Fix stated temperature range of atoMEC

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    timcallow committed Oct 11, 2023
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  7. Merge pull request #209 from timcallow/warnings_improve 

    Fix stated temperature range of atoMEC
    @timcallow
    timcallow authored Oct 11, 2023
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  8. Update doc requirements package version numbers

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    timcallow committed Oct 11, 2023
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  9. Merge pull request #210 from timcallow/docs_packages_update 

    Update doc requirements package version numbers
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    timcallow authored Oct 11, 2023
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Commits on Nov 1, 2023

  1. Add libxc as tar.gz link in requirements

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    timcallow committed Nov 1, 2023
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  2. Remove unnecessary install_libxc.sh script

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    timcallow committed Nov 1, 2023
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Commits on Nov 6, 2023

  1. Add pylibxc dependency and upgrade Python to 3.12

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    timcallow committed Nov 6, 2023
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  2. Update to simpler pylibxc install

    @timcallow
    timcallow authored Nov 6, 2023
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  3. Change Python version to 3.12

    @timcallow
    timcallow authored Nov 6, 2023
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  4. Update gh-pages to use Python 3.12

    @timcallow
    timcallow authored Nov 6, 2023
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  5. Update installation for Python 3.12 and new libxc route

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    timcallow authored Nov 6, 2023
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  6. Merge pull request #212 from timcallow/libxc_reqs_update 

    Simplify libxc installation
    @timcallow
    timcallow authored Nov 6, 2023
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Commits on Nov 7, 2023

  1. Update atoMEC logo to use url for PyPI

    @timcallow
    timcallow authored Nov 7, 2023
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  2. Merge pull request #213 from timcallow/pypi_logo_fix 

    Update atoMEC logo to use url for PyPI
    @timcallow
    timcallow authored Nov 7, 2023
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  3. Update some out-of-date info in the README

    @timcallow
    timcallow authored Nov 7, 2023
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  4. Merge pull request #214 from timcallow/Update_outdated_README 

    Update some out-of-date info in the README
    @timcallow
    timcallow authored Nov 7, 2023
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  5. Add files for development test generation

    @timcallow
    timcallow committed Nov 7, 2023
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  6. Add atoMEC 1.4.0 benchmark timings

    @timcallow
    timcallow committed Nov 7, 2023
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  7. Add README draft

    @timcallow
    timcallow committed Nov 7, 2023
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  8. Delete timings benchmark file

    @timcallow
    timcallow committed Nov 7, 2023
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  9. Make README.md simpler

    @timcallow
    timcallow authored Nov 7, 2023
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  10. Add analyze_results function

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    timcallow committed Nov 7, 2023
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  11. Merge remote-tracking branch 'refs/remotes/Tim_fork/dev_tests' into d… 

    …ev_tests
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    timcallow committed Nov 7, 2023
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Commits on Nov 8, 2023

  1. Improve formatting, add function and script to compare two csv files

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    timcallow committed Nov 8, 2023
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  2. Rename P_vir_nocorr_A to P_vir_nocorr

    @timcallow
    timcallow committed Nov 8, 2023
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  3. Merge branch 'atomec-project:develop' into dev_tests

    @timcallow
    timcallow authored Nov 8, 2023
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  4. Improve README.md

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    timcallow authored Nov 8, 2023
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  5. Merge pull request #215 from timcallow/dev_tests 

    Introduce development tests to benchmark performance
    @timcallow
    timcallow authored Nov 8, 2023
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  6. Fix out-of-date docstrings

    @timcallow
    timcallow committed Nov 8, 2023
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  7. Replace log with log/sqrt in docstrings

    @timcallow
    timcallow committed Nov 8, 2023
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  8. Fix more outdated docstrings

    @timcallow
    timcallow committed Nov 8, 2023
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  9. Merge pull request #216 from timcallow/fix_docs 

    Fixes errors in a number of docstrings due to the introduction of the sqrt grid
    @timcallow
    timcallow authored Nov 8, 2023
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  10. Add python style checkers to dev dependencies

    @timcallow
    timcallow committed Nov 8, 2023
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  11. Remove unused function

    @timcallow
    timcallow committed Nov 8, 2023
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  12. Merge pull request #218 from timcallow/delete_normalize_orbs_sgrid 

    Remove normalize_orbs_sgrid function
    @timcallow
    timcallow authored Nov 8, 2023
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  13. Enforce log grid in Kubo-Greenwood class

    @timcallow
    timcallow committed Nov 8, 2023
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  14. Enforce log grid for gramschmidt

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    timcallow committed Nov 8, 2023
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  15. Merge pull request #221 from timcallow/enforce_log_grid 

    Enforce log grid
    @timcallow
    timcallow authored Nov 8, 2023
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  16. Merge pull request #217 from timcallow/stylechecks_in_pipfile 

    Add python style checkers to dev dependencies
    @timcallow
    timcallow authored Nov 8, 2023
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  17. Ensure grid_type parameter is checked and used

    @timcallow
    timcallow committed Nov 8, 2023
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  18. Update as sqrt is now the genuine default grid (overridden previously)

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    timcallow committed Nov 8, 2023
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Commits on Nov 9, 2023

  1. Add grid_type exceptions test

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    timcallow committed Nov 9, 2023
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  2. Merge pull request #222 from timcallow/calcenergy_grid_type 

    Make default "grid_type" consistent and add checker
    @timcallow
    timcallow authored Nov 9, 2023
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  3. Remove pylibxc url from requirements as unsupported by PyPI

    @timcallow
    timcallow committed Nov 9, 2023
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  4. Merge pull request #223 from timcallow/remove_libxc_from_reqs 

    Remove pylibxc url from requirements as unsupported by PyPI
    @timcallow
    timcallow authored Nov 9, 2023
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  5. Update to Python 3.12 in pypi build

    @timcallow
    timcallow authored Nov 9, 2023
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  6. Merge pull request #224 from timcallow/python312_pypi 

    Update to Python 3.12 in PyPI build
    @timcallow
    timcallow authored Nov 9, 2023
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