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Training on energy labels #128

Merged
merged 126 commits into from
May 14, 2020
Merged

Training on energy labels #128

merged 126 commits into from
May 14, 2020

Commits on Sep 29, 2019

  1. start energy gp

    @jonpvandermause
    jonpvandermause committed Sep 29, 2019
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  2. by default, add all envs of a structure to the training set

    @jonpvandermause
    jonpvandermause committed Sep 29, 2019
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Commits on Sep 30, 2019

  1. implement get_kernel_vector

    @jonpvandermause
    jonpvandermause committed Sep 30, 2019
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  2. add energy kernel

    @jonpvandermause
    jonpvandermause committed Sep 30, 2019
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  3. add get_labels method to struc

    @jonpvandermause
    jonpvandermause committed Sep 30, 2019
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  4. implement ky block

    @jonpvandermause
    jonpvandermause committed Sep 30, 2019
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  5. fix index in gp algebra

    @jonpvandermause
    jonpvandermause committed Sep 30, 2019
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  6. edit energy gp test

    @jonpvandermause
    jonpvandermause committed Sep 30, 2019
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  7. fix index error in energy_gp; default forces to none in struc

    @jonpvandermause
    jonpvandermause committed Sep 30, 2019
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  8. add fractional corrections to mc energy kernel

    @jonpvandermause
    jonpvandermause committed Sep 30, 2019
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  9. switch energy_force to force_energy to match input order

    @jonpvandermause
    jonpvandermause committed Sep 30, 2019
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  10. implement ky_mat

    @jonpvandermause
    jonpvandermause committed Sep 30, 2019
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  11. change kernel_ef to kernel_fe

    @jonpvandermause
    jonpvandermause committed Sep 30, 2019
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  12. implement noise matrix

    @jonpvandermause
    jonpvandermause committed Sep 30, 2019
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  13. add noise matrix to covariance matrix

    @jonpvandermause
    jonpvandermause committed Sep 30, 2019
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  14. check gp test

    @jonpvandermause
    jonpvandermause committed Sep 30, 2019
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  15. add ky test

    @jonpvandermause
    jonpvandermause committed Sep 30, 2019
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  16. make ky test harder

    @jonpvandermause
    jonpvandermause committed Sep 30, 2019
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  17. implement set_L_alpha

    @jonpvandermause
    jonpvandermause committed Sep 30, 2019
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  18. add sweep option to env

    @jonpvandermause
    jonpvandermause committed Sep 30, 2019
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  19. get np training labels from dict

    @jonpvandermause
    jonpvandermause committed Sep 30, 2019
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  20. add sweep as an input to env

    @jonpvandermause
    jonpvandermause committed Sep 30, 2019
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  21. add sweep option to update db

    @jonpvandermause
    jonpvandermause committed Sep 30, 2019
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  22. fix numba seg fault

    @jonpvandermause
    jonpvandermause committed Sep 30, 2019
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  23. more seg fault fixes

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    jonpvandermause committed Sep 30, 2019
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  24. account for case where energy is 0

    @jonpvandermause
    jonpvandermause committed Sep 30, 2019
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  25. remove debug print statements

    @jonpvandermause
    jonpvandermause committed Sep 30, 2019
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Commits on Oct 1, 2019

  1. fix bugs in gp algebra

    @jonpvandermause
    jonpvandermause committed Oct 1, 2019
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Commits on Oct 7, 2019

  1. make energy noise a separate hyperparameter

    @jonpvandermause
    jonpvandermause committed Oct 7, 2019
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  2. update energy test

    @jonpvandermause
    jonpvandermause committed Oct 7, 2019
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  3. add force energy kernel to mgp

    @jonpvandermause
    jonpvandermause committed Oct 7, 2019
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  4. remove training data from mgp

    @jonpvandermause
    jonpvandermause committed Oct 7, 2019
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  5. remove training data again

    @jonpvandermause
    jonpvandermause committed Oct 7, 2019
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  6. correct typo

    @jonpvandermause
    jonpvandermause committed Oct 7, 2019
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Commits on Oct 16, 2019

  1. allow variance to be computed for global energies

    @jonpvandermause
    jonpvandermause committed Oct 16, 2019
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Commits on Dec 13, 2019

  1. fix merge conflicits

    @jonpvandermause
    jonpvandermause committed Dec 13, 2019
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  2. start fixing tests

    @jonpvandermause
    jonpvandermause committed Dec 13, 2019
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  3. try flare io fix

    @jonpvandermause
    jonpvandermause committed Dec 13, 2019
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  4. fix otf_parser

    @jonpvandermause
    jonpvandermause committed Dec 13, 2019
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  5. pep8 fix

    @jonpvandermause
    jonpvandermause committed Dec 13, 2019
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Commits on Dec 14, 2019

  1. more test fixes

    @jonpvandermause
    jonpvandermause committed Dec 14, 2019
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  2. fix mc_simple tets

    @jonpvandermause
    jonpvandermause committed Dec 14, 2019
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  3. fix struc constructor

    @jonpvandermause
    jonpvandermause committed Dec 14, 2019
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Commits on Dec 15, 2019

  1. correct fractional factors in mc energy kernels

    @jonpvandermause
    jonpvandermause committed Dec 15, 2019
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  2. correct fractional factors in single element energy kernels

    @jonpvandermause
    jonpvandermause committed Dec 15, 2019
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  3. switch force/energy to energy/force in energy_gp.py

    @jonpvandermause
    jonpvandermause committed Dec 15, 2019
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  4. remove gp assertion

    @jonpvandermause
    jonpvandermause committed Dec 15, 2019
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  5. make par_en compatible with gp_energy

    @jonpvandermause
    jonpvandermause committed Dec 15, 2019
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  6. improve predict; remove training_data condition from mgp

    @jonpvandermause
    jonpvandermause committed Dec 15, 2019
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  7. fix mgp error

    @jonpvandermause
    jonpvandermause committed Dec 15, 2019
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Commits on Dec 16, 2019

  1. add training label condition to mgp

    @jonpvandermause
    jonpvandermause committed Dec 16, 2019
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Commits on Dec 17, 2019

  1. set struc forces and stds in predict; begin cleaning up output file

    @jonpvandermause
    jonpvandermause committed Dec 17, 2019
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  2. reinstate call to write_xyz

    @jonpvandermause
    jonpvandermause committed Dec 17, 2019
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  3. reinstate header definition

    @jonpvandermause
    jonpvandermause committed Dec 17, 2019
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  4. reinstate arbitrary print statements

    @jonpvandermause
    jonpvandermause committed Dec 17, 2019
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  5. make logger compatible with new ase release

    @jonpvandermause
    jonpvandermause committed Dec 17, 2019
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Commits on May 7, 2020

  1. merge development branch

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  2. merge tip of development

    @jonpvandermause
    jonpvandermause committed May 7, 2020
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  3. Update .travis.yml

    @jonpvandermause
    jonpvandermause authored May 7, 2020
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  4. Update .travis.yml

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    jonpvandermause authored May 7, 2020
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  5. fix energy gp import

    @jonpvandermause
    jonpvandermause committed May 7, 2020
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  6. Merge branch 'feature/jon/gp-energy' of https://github.com/mir-group/… 

    …flare into feature/jon/gp-energy
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  7. address test_gp errors

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    jonpvandermause committed May 7, 2020
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Commits on May 8, 2020

  1. address test_kernel errors

    @jonpvandermause
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  2. fix test_struc errors

    @jonpvandermause
    jonpvandermause committed May 8, 2020
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  3. remove test files

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    jonpvandermause committed May 8, 2020
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  4. address test_predict errors

    @jonpvandermause
    jonpvandermause committed May 8, 2020
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  5. try addressing cp2k error

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    jonpvandermause committed May 8, 2020
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  6. reinstate cp2k executable

    @jonpvandermause
    jonpvandermause authored May 8, 2020
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  7. add global training structures to gp algebra

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  8. Merge branch 'feature/jon/gp-energy' of https://github.com/mir-group/… 

    …flare into feature/jon/gp-energy
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  9. get rid of unused/untested methods

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  10. remove unused import from energy gp

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  11. add training structures and energy label attributes to the gp

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  12. update update_db to include energy labels

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  13. minor gp_algebra edits

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  14. address bare exception in gp algebra

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  15. add energy noise attribute to gp

    @jonpvandermause
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  16. change get_ky_mat to get_force_block

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  17. clean up gp algebra tests

    @jonpvandermause
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  18. add headings to gp_algebra; clean up gp

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  19. change ky_pack to force_block_pack

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  20. add parallel matrix helper function

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  21. sketch out energy block methods

    @jonpvandermause
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  22. implement energy_block_pack and force_energy_block_pack methods

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  23. implement energy_block method

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  24. give partition methods descriptive names

    @jonpvandermause
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  25. add force/energy partition method; fix mgp import

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  26. implement force/energy block

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  27. implement full covariance matrix

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Commits on May 9, 2020

  1. start energy block tesrt

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  2. add test of energy block; add appropriate fractional factors to sephy… 

    …ps energy kernel
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  3. more missing fractional factors in energy kernels

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  4. start force/energy block test; fix unit tests

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  5. finish force/energy block test

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  6. correct Ky_mat method; begin test

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  7. complete ky_mat test; get rid of redundant tests

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  8. add parallel vector construction method

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  9. fix input order

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    jonpvandermause committed May 9, 2020
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  10. fix hanging unit test

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    jonpvandermause committed May 9, 2020
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  11. unit test en_kern_vec

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  12. rename vector unit

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  13. implement force_energy vector

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    jonpvandermause committed May 9, 2020
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  14. make kernel vector names more logical

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  15. test all 4 vector methods

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Commits on May 10, 2020

  1. implement kernel vector

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  2. try correcting unit tests

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  3. try fixing tests again

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  4. unit test en_kern_vec

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Commits on May 11, 2020

  1. implement and unit test energy and force block updates

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  2. update partition_update

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  3. update force energy block

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    jonpvandermause committed May 11, 2020
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Commits on May 12, 2020

  1. implement update_ky; remove redundant tests

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    jonpvandermause committed May 12, 2020
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  2. fix update_L_alpha

    @jonpvandermause
    jonpvandermause committed May 12, 2020
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  3. minor mgp_en changes

    @jonpvandermause
    jonpvandermause committed May 12, 2020
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  4. lint mgp_en

    @jonpvandermause
    jonpvandermause committed May 12, 2020
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Commits on May 13, 2020

  1. add energy label to fake gp

    @jonpvandermause
    jonpvandermause committed May 13, 2020
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  2. add energies to test gps; update gp.py to account for energies

    @jonpvandermause
    jonpvandermause committed May 13, 2020
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  3. make mgp_en compatible with energy labels

    @jonpvandermause
    jonpvandermause committed May 13, 2020
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  4. use force labels only in mgp_ff unit test

    @jonpvandermause
    jonpvandermause committed May 13, 2020
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  5. remove old files

    @jonpvandermause
    jonpvandermause committed May 13, 2020
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  6. Merge branch 'development' into feature/jon/gp-energy

    @jonpvandermause
    jonpvandermause committed May 13, 2020
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  7. relax map test

    @jonpvandermause
    jonpvandermause committed May 13, 2020
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  8. fix failing unit test

    @jonpvandermause
    jonpvandermause committed May 13, 2020
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Commits on May 14, 2020

  1. add optional sweep argument to update_db

    @jonpvandermause
    jonpvandermause committed May 14, 2020
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  2. update structure and energy list in gp instantiation

    @jonpvandermause
    jonpvandermause committed May 14, 2020
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