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Merge development into master #199

Merged
merged 797 commits into from
Jul 16, 2020
Merged

Merge development into master #199

merged 797 commits into from
Jul 16, 2020
This pull request is big! We’re only showing the most recent 250 commits.

Commits on Jun 11, 2020

  1. fixed permutation err & negative lower bound

    @YuuuXie
    YuuuXie committed Jun 11, 2020
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  2. Merge branch 'user_interface_refactory' of github.com:mir-group/flare… 

    … into user_interface_refactory
    @YuuuXie
    YuuuXie committed Jun 11, 2020
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  3. fix conflicting atomic species list and solve chdir problem

    @nw13slx
    nw13slx committed Jun 11, 2020
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  4. fix wrong bracket

    @nw13slx
    nw13slx committed Jun 11, 2020
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  5. Merge branch 'user_interface_refactory' of github.com:mir-group/flare… 

    … into user_interface_refactory
    @YuuuXie
    YuuuXie committed Jun 11, 2020
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  6. gp algebra commits

    @jonpvandermause
    jonpvandermause committed Jun 11, 2020
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Commits on Jun 12, 2020

  1. simplify test_lmp

    @nw13slx
    nw13slx committed Jun 12, 2020
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  2. add coded_species & species_labels

    @YuuuXie
    YuuuXie committed Jun 12, 2020
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  3. Add back a bit flexibility to take different kernels and different sp… 

    …ecies
    @nw13slx
    nw13slx committed Jun 12, 2020
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  4. add test_mgp_simple

    @YuuuXie
    YuuuXie committed Jun 12, 2020
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  5. Merge branch 'user_interface_refactory' of github.com:mir-group/flare… 

    … into user_interface_refactory
    @YuuuXie
    YuuuXie committed Jun 12, 2020
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  6. implement efs_kern_vec

    @jonpvandermause
    jonpvandermause committed Jun 12, 2020
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  7. unit test efs kern vec

    @jonpvandermause
    jonpvandermause committed Jun 12, 2020
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  8. add grid_kernel tests

    @nw13slx
    nw13slx committed Jun 12, 2020
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  9. implement 3-body efs self

    @jonpvandermause
    jonpvandermause committed Jun 12, 2020
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  10. merge with master

    @nw13slx
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  11. temporarily disable cp2k

    @jonpvandermause
    jonpvandermause authored Jun 12, 2020
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  12. reinstate cp2k

    @jonpvandermause
    jonpvandermause authored Jun 12, 2020
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  13. Update requirements.txt

    @jonpvandermause
    jonpvandermause authored Jun 12, 2020
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  14. test 3-body efs self

    @jonpvandermause
    jonpvandermause committed Jun 12, 2020
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  15. update pytest

    @jonpvandermause
    jonpvandermause authored Jun 12, 2020
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  16. Merge branch 'jon/feature/kernel-edits' of https://github.com/mir-gro… 

    …up/flare into jon/feature/kernel-edits
    @jonpvandermause
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  17. add 2-body efs self kernel

    @jonpvandermause
    jonpvandermause committed Jun 12, 2020
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  18. add self kernels to mc simple

    @jonpvandermause
    jonpvandermause committed Jun 12, 2020
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  19. mc simple clean up

    @jonpvandermause
    jonpvandermause committed Jun 12, 2020
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  20. update str to kern dictionaries

    @jonpvandermause
    jonpvandermause committed Jun 12, 2020
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  21. include efs self kernel in str to kern

    @jonpvandermause
    jonpvandermause committed Jun 12, 2020
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  22. fix gp dim err

    @YuuuXie
    YuuuXie committed Jun 12, 2020
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  23. rename the label to prevent deleting itself

    @YuuuXie
    YuuuXie committed Jun 12, 2020
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  24. implement efs prediction

    @jonpvandermause
    jonpvandermause committed Jun 12, 2020
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  25. fix construct_grid (meshgrid) issue & rm perm_list in grid_kernel

    @YuuuXie
    YuuuXie committed Jun 12, 2020
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  26. TODO: change lmp mgpf to bond length; test energy block; solve lower … 

    …bound issue
    @YuuuXie
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  27. Merge branch 'user_interface_refactory' of github.com:mir-group/flare… 

    … into user_interface_refactory
    @YuuuXie
    YuuuXie committed Jun 12, 2020
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  28. fix import

    @YuuuXie
    YuuuXie committed Jun 12, 2020
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  29. unit test predict efs method

    @jonpvandermause
    jonpvandermause committed Jun 12, 2020
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  30. add a docstring for predict efs

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

  1. fix mgp args

    @YuuuXie
    YuuuXie committed Jun 13, 2020
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  2. add energy

    @YuuuXie
    YuuuXie committed Jun 13, 2020
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  3. rm redundant predict

    @YuuuXie
    YuuuXie committed Jun 13, 2020
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  4. rm get_triplets_en

    @YuuuXie
    YuuuXie committed Jun 13, 2020
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  5. add force lmp in mgp

    @YuuuXie
    YuuuXie committed Jun 13, 2020
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  6. rm ase_parser & change arg

    @YuuuXie
    YuuuXie committed Jun 13, 2020
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  7. rm useless test file & update docs

    @YuuuXie
    YuuuXie committed Jun 13, 2020
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  8. Merge branch 'user_interface_refactory' of https://github.com/mir-gro… 

    …up/flare into user_interface_refactory
    @YuuuXie
    YuuuXie committed Jun 13, 2020
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  9. add back as_dict, from_dict etc.

    @YuuuXie
    YuuuXie committed Jun 13, 2020
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  10. TODO: add back. skip 3b force lammps unit test

    @YuuuXie
    YuuuXie committed Jun 13, 2020
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Commits on Jun 14, 2020

  1. fix import err

    @YuuuXie
    YuuuXie committed Jun 14, 2020
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  2. fix import err

    @YuuuXie
    YuuuXie committed Jun 14, 2020
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  3. add predict on atom efs

    @jonpvandermause
    jonpvandermause committed Jun 14, 2020
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  4. implement predict on structure efs

    @jonpvandermause
    jonpvandermause committed Jun 14, 2020
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Commits on Jun 15, 2020

  1. implement predict on structure efs par

    @jonpvandermause
    jonpvandermause committed Jun 15, 2020
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  2. test predict clean up

    @jonpvandermause
    jonpvandermause committed Jun 15, 2020
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  3. add predict efs test

    @jonpvandermause
    jonpvandermause committed Jun 15, 2020
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  4. add tutorial

    @YuuuXie
    YuuuXie committed Jun 15, 2020
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  5. correct parameter helper print statement

    @jonpvandermause
    jonpvandermause committed Jun 15, 2020
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  6. Update requirements.txt

    @jonpvandermause
    jonpvandermause authored Jun 15, 2020
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  7. fix species bug

    @nw13slx
    nw13slx committed Jun 15, 2020
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  8. Merge branch 'user_interface_refactory' of github.com:mir-group/flare… 

    … into user_interface_refactory

Conflicts:
	tests/test_gp_from_aimd.py
	tests/test_grid_kernel.py
    @nw13slx
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  9. correct parameter helper print statement

    @jonpvandermause
    jonpvandermause committed Jun 15, 2020
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  10. Merge branch 'user_interface_refactory' of https://github.com/mir-gro… 

    …up/flare into user_interface_refactory
    @jonpvandermause
    jonpvandermause committed Jun 15, 2020
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  11. update tutorials

    @nw13slx
    nw13slx committed Jun 15, 2020
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  12. Merge branch 'user_interface_refactory' of github.com:mir-group/flare… 

    … into user_interface_refactory
    @nw13slx
    nw13slx committed Jun 15, 2020
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  13. update docstring

    @nw13slx
    nw13slx committed Jun 15, 2020
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  14. sort utils doc

    @nw13slx
    nw13slx committed Jun 15, 2020
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  15. shift module description up

    @nw13slx
    nw13slx committed Jun 15, 2020
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  16. add docs

    @YuuuXie
    YuuuXie committed Jun 15, 2020
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  17. change init

    @nw13slx
    nw13slx committed Jun 15, 2020
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  18. change args to kwargs in singlexbody

    @YuuuXie
    YuuuXie committed Jun 15, 2020
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  19. debug for json print

    @nw13slx
    nw13slx committed Jun 15, 2020
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  20. use get_kernel_term func in from_dict

    @YuuuXie
    YuuuXie committed Jun 15, 2020
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  21. Merge branch 'user_interface_refactory' of github.com:mir-group/flare… 

    … into user_interface_refactory

Conflicts:
	flare/mgp/map2b.py
	flare/mgp/map3b.py
	flare/mgp/mapxb.py
    @nw13slx
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  22. change grid sava path to mgp_grids folder

    @YuuuXie
    YuuuXie committed Jun 15, 2020
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  23. fix lower bound bug and init args in unit tests

    @nw13slx
    nw13slx committed Jun 15, 2020
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  24. fix output level

    @nw13slx
    nw13slx committed Jun 15, 2020
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  25. change kernel_info & wrap gengrid in Gengrid

    @YuuuXie
    YuuuXie committed Jun 15, 2020
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  26. revise docstring

    @nw13slx
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Commits on Jun 16, 2020

  1. change kernel_info & wrap up mapped kernel

    @YuuuXie
    YuuuXie committed Jun 16, 2020
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  2. Merge branch 'user_interface_refactory' of https://github.com/mir-gro… 

    …up/flare into user_interface_refactory
    @YuuuXie
    YuuuXie committed Jun 16, 2020
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  3. try to fix unit test

    @YuuuXie
    YuuuXie committed Jun 16, 2020
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  4. fix unit test

    @YuuuXie
    YuuuXie committed Jun 16, 2020
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  5. add prefix in test_lmp_predict

    @YuuuXie
    YuuuXie committed Jun 16, 2020
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  6. Update docstring

    @nw13slx
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  7. Merge branch 'user_interface_refactory' of github.com:mir-group/flare… 

    … into user_interface_refactory
    @nw13slx
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  8. add cell to struc (from_ase_atoms) & fix load_grid bug in mgp & repla… 

    …ce spc_set with 'sort'
    @YuuuXie
    YuuuXie committed Jun 16, 2020
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  9. fix otf logic

    @jonpvandermause
    jonpvandermause committed Jun 16, 2020
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  10. remove second md step from otf loop

    @jonpvandermause
    jonpvandermause committed Jun 16, 2020
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  11. quick fix for changing structure positions

    @jonpvandermause
    jonpvandermause committed Jun 16, 2020
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  12. have md.step return a copy of atom positions

    @jonpvandermause
    jonpvandermause committed Jun 16, 2020
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Commits on Jun 17, 2020

  1. fix one mistake in docs

    @YuuuXie
    YuuuXie committed Jun 17, 2020
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  2. change default value

    @YuuuXie
    YuuuXie committed Jun 17, 2020
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  3. Merge branch 'user_interface_refactory' of https://github.com/mir-gro… 

    …up/flare into user_interface_refactory
    @YuuuXie
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  4. sort test_gp_algebra

    @nw13slx
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  5. Merge branch 'user_interface_refactory' of github.com:mir-group/flare… 

    … into user_interface_refactory
    @nw13slx
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  6. fix bug in test_force that skipped all tests

    @nw13slx
    nw13slx committed Jun 17, 2020
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  7. Merge branch 'user_interface_refactory' into jon/feature/kernel-edits… 

    …-merge
    @jonpvandermause
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  8. correct import error

    @jonpvandermause
    jonpvandermause committed Jun 17, 2020
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  9. correct import error in test_stress_kernels

    @jonpvandermause
    jonpvandermause committed Jun 17, 2020
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  10. correct test_predict gp instantiation

    @jonpvandermause
    jonpvandermause committed Jun 17, 2020
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  11. fix stk error in mgp utils

    @jonpvandermause
    jonpvandermause committed Jun 17, 2020
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  12. fix sephyps tests

    @jonpvandermause
    jonpvandermause committed Jun 17, 2020
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  13. fix mask to args order

    @jonpvandermause
    jonpvandermause committed Jun 17, 2020
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  14. fix test_kernel

    @jonpvandermause
    jonpvandermause committed Jun 17, 2020
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  15. fix test grid kernel

    @jonpvandermause
    jonpvandermause committed Jun 17, 2020
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  16. fix test gp algebra

    @jonpvandermause
    jonpvandermause committed Jun 17, 2020
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  17. give str to mapped kernel the right number of return argumeents

    @jonpvandermause
    jonpvandermause committed Jun 17, 2020
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Commits on Jun 18, 2020

  1. Fix minor typo in docstring

    @stevetorr
    stevetorr authored Jun 18, 2020
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  2. rm comment lines

    @YuuuXie
    YuuuXie authored Jun 18, 2020
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  3. rm comment lines

    @YuuuXie
    YuuuXie authored Jun 18, 2020
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  4. Merge pull request #184 from mir-group/user_interface_refactory 

    Better user interface and consistency check through out env/gp/kernel modules
    @YuuuXie
    YuuuXie authored Jun 18, 2020
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  5. merge dev branch

    @YuuuXie
    YuuuXie committed Jun 18, 2020
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  6. add efs prediction to otf

    @jonpvandermause
    jonpvandermause committed Jun 18, 2020
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  7. add stress to output

    @jonpvandermause
    jonpvandermause committed Jun 18, 2020
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Commits on Jun 19, 2020

  1. Merge branch 'development' of github.com:mir-group/flare into develop… 

    …ment

Conflicts:
	requirements.txt
    @nw13slx
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  2. sort coded species

    @nw13slx
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  3. some pep8 clean up

    @jonpvandermause
    jonpvandermause committed Jun 19, 2020
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  4. Steven/feature/gp write choice (#188) 

    * Write method flexibly saves training data; strengthened unit test

* Write model auto detects format

* Slight change to test logic

* Fixed bug in compute_matrices

* Upgrade unit tests

* Fix from_dict method bug

* Improved write file docstring

* Remove force now runs faster if empty list is input
    @stevetorr
    stevetorr authored Jun 19, 2020
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  5. add 'del' to grid_kern

    @YuuuXie
    YuuuXie committed Jun 19, 2020
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  6. Merge branch 'development' of https://github.com/mir-group/flare into… 

    … development
    @YuuuXie
    YuuuXie committed Jun 19, 2020
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  7. add n_chunk for grids

    @YuuuXie
    YuuuXie committed Jun 19, 2020
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  8. Add backwards compatibility for pickled envs

    @stevetorr
    stevetorr committed Jun 19, 2020
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  9. simplify compute properties

    @jonpvandermause
    jonpvandermause committed Jun 19, 2020
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  10. add grid_chunk for mgp

    @YuuuXie
    YuuuXie committed Jun 19, 2020
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  11. rm print flag

    @YuuuXie
    YuuuXie committed Jun 19, 2020
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  12. Merge branch 'development' of github.com:mir-group/flare into develop… 

    …ment
    @nw13slx
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  13. correct stress output

    @jonpvandermause
    jonpvandermause committed Jun 19, 2020
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  14. address struc is none case

    @jonpvandermause
    jonpvandermause committed Jun 19, 2020
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  15. rm useless func

    @YuuuXie
    YuuuXie committed Jun 19, 2020
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  16. merge latest dev

    @YuuuXie
    YuuuXie committed Jun 19, 2020
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  17. update atoms forces when calling dft

    @jonpvandermause
    jonpvandermause committed Jun 19, 2020
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  18. remove new pos from temperature calculation

    @jonpvandermause
    jonpvandermause committed Jun 19, 2020
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  19. have md_step update structure positions

    @jonpvandermause
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  20. update previous positions

    @jonpvandermause
    jonpvandermause committed Jun 19, 2020
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  21. report pressure

    @jonpvandermause
    jonpvandermause committed Jun 19, 2020
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  22. correct stress formatting

    @jonpvandermause
    jonpvandermause committed Jun 19, 2020
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Commits on Jun 21, 2020

  1. add mgp_test.py in the test folder

    @YuuuXie
    YuuuXie committed Jun 21, 2020
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  2. merge branch

    @YuuuXie
    YuuuXie committed Jun 21, 2020
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Commits on Jun 22, 2020

  1. add self_kernel

    @YuuuXie
    YuuuXie committed Jun 22, 2020
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Commits on Jun 23, 2020

  1. Add backwards compatibility for pickled envs (#189) 

    * Add backwards compatibility for pickled envs

* Backwards compat. for envs with no cutoff mask

* Change logic and strengthen unit tests

* Remove redundant compute matrices call
    @stevetorr
    stevetorr authored Jun 23, 2020
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  2. Merge branch 'development' of github.com:mir-group/flare into develop… 

    …ment
    @nw13slx
    nw13slx committed Jun 23, 2020
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  3. fix the verbose argument bug and optimization flag

    @nw13slx
    nw13slx committed Jun 23, 2020
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  4. clean up gp output

    @jonpvandermause
    jonpvandermause committed Jun 23, 2020
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  5. make output syntax consistent

    @jonpvandermause
    jonpvandermause committed Jun 23, 2020
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  6. correct energy stds in output

    @jonpvandermause
    jonpvandermause committed Jun 23, 2020
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  7. Merge branch 'development' of https://github.com/mir-group/flare into… 

    … development
    @stevetorr
    stevetorr committed Jun 23, 2020
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  8. write dft energy and stress to output

    @jonpvandermause
    jonpvandermause committed Jun 23, 2020
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  9. avoid redundancy in predict efs

    @jonpvandermause
    jonpvandermause committed Jun 23, 2020
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  10. add test for cut3b

    @nw13slx
    nw13slx committed Jun 23, 2020
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  11. correct stress order

    @jonpvandermause
    jonpvandermause committed Jun 23, 2020
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  12. fix gp unit test

    @jonpvandermause
    jonpvandermause committed Jun 23, 2020
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  13. fix constraint problem

    @nw13slx
    nw13slx committed Jun 23, 2020
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  14. put unit test for constraint

    @nw13slx
    nw13slx committed Jun 23, 2020
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Commits on Jun 24, 2020

  1. increase coverage

    @nw13slx
    nw13slx committed Jun 24, 2020
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  2. autopep8

    @nw13slx
    nw13slx committed Jun 24, 2020
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  3. fix cutoff_key

    @nw13slx
    nw13slx committed Jun 24, 2020
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  4. delete comments

    @jonpvandermause
    jonpvandermause committed Jun 24, 2020
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  5. correct time units in output file

    @jonpvandermause
    jonpvandermause committed Jun 24, 2020
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  6. make cell attributes properties

    @jonpvandermause
    jonpvandermause committed Jun 24, 2020
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  7. make positions a property

    @jonpvandermause
    jonpvandermause committed Jun 24, 2020
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  8. fix cp2k test

    @jonpvandermause
    jonpvandermause committed Jun 24, 2020
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  9. fix gpfa unit test

    @jonpvandermause
    jonpvandermause committed Jun 24, 2020
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  10. add mgp grids to gitignore

    @jonpvandermause
    jonpvandermause committed Jun 24, 2020
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  11. fix test qe_util

    @jonpvandermause
    jonpvandermause committed Jun 24, 2020
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  12. clean up env

    @jonpvandermause
    jonpvandermause committed Jun 24, 2020
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  13. correct env unit tests

    @jonpvandermause
    jonpvandermause committed Jun 24, 2020
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  14. report cell in output file

    @jonpvandermause
    jonpvandermause committed Jun 24, 2020
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  15. correct vasp util unit test

    @jonpvandermause
    jonpvandermause committed Jun 24, 2020
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  16. Merge pull request #191 from mir-group/bugfix/lixin/parameter_helper 

    fix optimization flag in ParameterHelper class
    @nw13slx
    nw13slx authored Jun 24, 2020
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  17. change mean_only to var_map

    @YuuuXie
    YuuuXie committed Jun 24, 2020
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  18. Merge branch 'development' into jon/feature/kernel-edits-merge

    @jonpvandermause
    jonpvandermause authored Jun 24, 2020
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  19. FIx bug for MGP predictions after load 

    * Backwards compat. for envs with no cutoff mask

* Change logic and strengthen unit tests

* Remove redundant compute matrices call

* Fix bug when MGP is used to make predictions without mapping

* Move definitions to top of document, remove globality

* rm the calculation of dAd, d2Ad

Co-authored-by: Yu Shelby Xie <xieyu.fish@gmail.com>
    @stevetorr @YuuuXie
    stevetorr and YuuuXie authored Jun 24, 2020
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Commits on Jun 25, 2020

  1. change mean_only to var_map

    @YuuuXie
    YuuuXie committed Jun 25, 2020
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  2. finish debugging 2b var simple

    @YuuuXie
    YuuuXie committed Jun 25, 2020
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  3. send stds to zero when dft is called

    @jonpvandermause
    jonpvandermause committed Jun 25, 2020
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  4. Merge branch 'jon/feature/kernel-edits-merge' of https://github.com/m… 

    …ir-group/flare into jon/feature/kernel-edits-merge
    @jonpvandermause
    jonpvandermause committed Jun 25, 2020
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  5. move fi up

    @jonpvandermause
    jonpvandermause committed Jun 25, 2020
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  6. Bugfix in to_xyz

    @stevetorr
    stevetorr authored Jun 25, 2020
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Commits on Jun 26, 2020

  1. close #132

    @YuuuXie
    YuuuXie committed Jun 26, 2020
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  2. close #22

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    YuuuXie committed Jun 26, 2020
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Commits on Jun 27, 2020

  1. debugged 3b var simple

    @YuuuXie
    YuuuXie committed Jun 27, 2020
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  2. change mean_only to var_map

    @YuuuXie
    YuuuXie committed Jun 27, 2020
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  3. move E to the end

    @jonpvandermause
    jonpvandermause committed Jun 27, 2020
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  4. remove redundant fi, fijs

    @jonpvandermause
    jonpvandermause committed Jun 27, 2020
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  5. remove unnecessary dft method

    @jonpvandermause
    jonpvandermause committed Jun 27, 2020
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  6. add get_args method

    @jonpvandermause
    jonpvandermause committed Jun 27, 2020
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  7. Merge pull request #187 from mir-group/jon/feature/kernel-edits-merge 

    Stress kernels and other kernel related changes
    @jonpvandermause
    jonpvandermause authored Jun 27, 2020
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  8. finish grid_kernel & self_kern for 2b

    @YuuuXie
    YuuuXie committed Jun 27, 2020
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Commits on Jun 28, 2020

  1. fix type typo

    @YuuuXie
    YuuuXie committed Jun 28, 2020
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  2. debug 3b force map var simple

    @YuuuXie
    YuuuXie committed Jun 28, 2020
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  3. create otf_atoms

    @YuuuXie
    YuuuXie committed Jun 28, 2020
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  4. debugged self_kern gengrid

    @YuuuXie
    YuuuXie committed Jun 28, 2020
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  5. fix unit test & close #194

    @YuuuXie
    YuuuXie committed Jun 28, 2020
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Commits on Jun 29, 2020

  1. merge dev

    @YuuuXie
    YuuuXie committed Jun 29, 2020
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  2. change class name

    @YuuuXie
    YuuuXie committed Jun 29, 2020
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  3. fix unit test

    @YuuuXie
    YuuuXie committed Jun 29, 2020
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  4. add user element encoder, add xyz writing options, and print mgp tota… 

    …l energy

in gp_from_aimd
    @nw13slx
    nw13slx committed Jun 29, 2020
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  5. autopep8

    @nw13slx
    nw13slx committed Jun 29, 2020
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  6. rm old gengrid_inner

    @YuuuXie
    YuuuXie committed Jun 29, 2020
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  7. fix bug for tests

    @nw13slx
    nw13slx committed Jun 29, 2020
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  8. add docstring

    @nw13slx
    nw13slx committed Jun 29, 2020
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  9. add symmetry-reduction to energy map

    @YuuuXie
    YuuuXie committed Jun 29, 2020
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  10. fix contrained optimization bugs in gpfa and otf.

    @nw13slx
    nw13slx committed Jun 29, 2020
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  11. add error info

    @nw13slx
    nw13slx committed Jun 29, 2020
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  12. fix variable name

    @nw13slx
    nw13slx committed Jun 29, 2020
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  13. fix wrong hyp_labels generated by ParameterHelper

    @nw13slx
    nw13slx committed Jun 29, 2020
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Commits on Jun 30, 2020

  1. assign wrapped positions to structure

    @YuuuXie
    YuuuXie committed Jun 30, 2020
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Commits on Jul 1, 2020

  1. change error handling

    @YuuuXie
    YuuuXie committed Jul 1, 2020
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  2. assign structure positions

    @YuuuXie
    YuuuXie committed Jul 1, 2020
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  3. ase otf uses flare atoms

    @YuuuXie
    YuuuXie committed Jul 1, 2020
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  4. fix import compatibility

    @YuuuXie
    YuuuXie committed Jul 1, 2020
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Commits on Jul 2, 2020

  1. add err handler & re-format

    @YuuuXie
    YuuuXie committed Jul 2, 2020
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  2. fix FLARE_Atoms in ASE OTF

    @YuuuXie
    YuuuXie committed Jul 2, 2020
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Commits on Jul 3, 2020

  1. rm force mapping & grid_env

    @YuuuXie
    YuuuXie committed Jul 3, 2020
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  2. rm map_force args from unit tests

    @YuuuXie
    YuuuXie committed Jul 3, 2020
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Commits on Jul 4, 2020

  1. try merging grid_kernels_2b & 3b

    @YuuuXie
    YuuuXie committed Jul 4, 2020
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  2. merge grid_kernel_2b & 3b into grid_kernels

    @YuuuXie
    YuuuXie committed Jul 4, 2020
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  3. rm mgp/utils.py

    @YuuuXie
    YuuuXie committed Jul 4, 2020
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Commits on Jul 5, 2020

  1. merging self_kern_2b and 3b

    @YuuuXie
    YuuuXie committed Jul 5, 2020
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  2. debugged map3b

    @YuuuXie
    YuuuXie committed Jul 5, 2020
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  3. allow var_map='simple' to be dumped into file

    @YuuuXie
    YuuuXie committed Jul 5, 2020
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Commits on Jul 6, 2020

  1. Add typehint

    @stevetorr
    stevetorr authored Jul 6, 2020
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  2. str typehint for logger name

    @stevetorr
    stevetorr authored Jul 6, 2020
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  3. Rename 'print_xyz' to 'print_as_xyz'

    @stevetorr
    stevetorr authored Jul 6, 2020
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  4. Update typehints in predict_on_structure mgp

    @stevetorr
    stevetorr authored Jul 6, 2020
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  5. Update struc.py

    @stevetorr
    stevetorr authored Jul 6, 2020
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  6. Refactor print_xyz

    @stevetorr
    stevetorr authored Jul 6, 2020
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  7. add 2b test

    @YuuuXie
    YuuuXie committed Jul 6, 2020
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  8. change to print_as_xyz

    @nw13slx
    nw13slx committed Jul 6, 2020
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  9. fix import error and typos

    @nw13slx
    nw13slx committed Jul 6, 2020
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  10. merge write_xyz and structure.to_xyz functions

    @nw13slx
    nw13slx committed Jul 6, 2020
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Commits on Jul 7, 2020

  1. add writing var map coef

    @YuuuXie
    YuuuXie committed Jul 7, 2020
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  2. solve conflict

    @YuuuXie
    YuuuXie committed Jul 7, 2020
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  3. try fixing unit test

    @YuuuXie
    YuuuXie committed Jul 7, 2020
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  4. change atom number in unit test

    @YuuuXie
    YuuuXie committed Jul 7, 2020
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  5. Merge pull request #195 from mir-group/feature/lixin/gpfa_improvement 

    Feature/lixin/gpfa improvement
    @nw13slx
    nw13slx authored Jul 7, 2020
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Commits on Jul 11, 2020

  1. add lammps var

    @YuuuXie
    YuuuXie committed Jul 11, 2020
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  2. rm comment lines

    @YuuuXie
    YuuuXie committed Jul 11, 2020
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  3. fix otf struc & separate ase exception block

    @YuuuXie
    YuuuXie committed Jul 11, 2020
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Commits on Jul 12, 2020

  1. fix bugs in ase

    @YuuuXie
    YuuuXie committed Jul 12, 2020
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  2. change var_map

    @YuuuXie
    YuuuXie committed Jul 12, 2020
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  3. Merge branch 'feature/yu/var_upper_bound' of github.com:mir-group/fla… 

    …re into feature/yu/var_upper_bound
    @YuuuXie
    YuuuXie committed Jul 12, 2020
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Commits on Jul 13, 2020

  1. Clarify how to adjust GP hyp masks and cutoffs (#200) 

    * Update parameter_helper.py

* Update docstrings and augment update kernel method

* Update gp.py

* Update kernel only updates cutoffs if needed

* Adjust docstring

* Update parameter_helper.py

* Update gp.py

* Fix comparison statement

* Update gp.py

* update arguments and unit test

* update cutoffs arg

* update hyps assigning

* Update docstrings

Co-authored-by: nw13slx <nw13mifaso@gmail.com>
    @stevetorr @nw13slx
    stevetorr and nw13slx authored Jul 13, 2020
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Commits on Jul 14, 2020

  1. Augment docstring

    @stevetorr
    stevetorr authored Jul 14, 2020
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  2. Touch up assertion error

    @stevetorr
    stevetorr committed Jul 14, 2020
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  3. Remove rogue print statement

    @stevetorr
    stevetorr committed Jul 14, 2020
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  4. Steven/bugfix/cherrypicked bugfix (#203) 

    * Update del method

* Fix bug where GP crashes if kernel disagrees with cutoffs

* Unit tests catch mb case

* Pep8 clean up
    @stevetorr
    stevetorr authored Jul 14, 2020
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Commits on Jul 15, 2020

  1. add todo

    @YuuuXie
    YuuuXie authored Jul 15, 2020
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  2. change test_mgp threshold

    @YuuuXie
    YuuuXie authored Jul 15, 2020
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  3. Quality of life method: Structure valid method (#204) 

    * Update del method

* Fix bug where GP crashes if kernel disagrees with cutoffs

* Unit tests catch mb case

* Quality of life method is_valid

* Fix merge issue
    @stevetorr
    stevetorr authored Jul 15, 2020
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  4. mc made default in str_to_kernel_set

    @stevetorr
    stevetorr authored Jul 15, 2020
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Commits on Jul 16, 2020

  1. Merge pull request #198 from mir-group/feature/yu/var_upper_bound 

    MGP - var upper bound & ASE Atoms
    @YuuuXie
    YuuuXie authored Jul 16, 2020
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