[WIP] Cell-related gradient modifications #12
Closed
Conversation
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
So-Takamoto
added
bug
So-Takamoto
commented
Sep 16, 2021
| @@ -6,7 +6,7 @@ | |||
| setup_requires: List[str] = [] | |||
| install_requires: List[str] = [ | |||
| "ase>=3.18, <4.0.0", # Note that we require ase==3.21.1 for pytest. | |||
| "pymatgen", | |||
| "pymatgen>=2020.1.10", | |||
There was a problem hiding this comment.
Function get_neighbor_list() used in this library is recently introduced.
So-Takamoto
commented
Sep 16, 2021
| @@ -20,6 +20,9 @@ def _create_atoms() -> List[Atoms]: | |||
| atoms = molecule("CH3CH2OCH3") | |||
|
|
|||
| slab = fcc111("Au", size=(2, 1, 3), vacuum=80.0) | |||
| slab.set_cell( | |||
There was a problem hiding this comment.
Modified cell shape to find potential bugs related to the skewed cell.
So-Takamoto
commented
Sep 16, 2021
| @@ -58,6 +61,8 @@ def _assert_energy_force_stress_equal(calc1, calc2, atoms: Atoms): | |||
| atoms.calc = calc1 | |||
| f1 = atoms.get_forces() | |||
| e1 = atoms.get_potential_energy() | |||
| if np.all(atoms.pbc == np.array([True, True, True])): | |||
| s1 = atoms.get_stress() | |||
There was a problem hiding this comment.
Modify reported test bug in #7
So-Takamoto
commented
Sep 16, 2021
| shift = S | ||
| else: | ||
| # shift = S | ||
| shift = torch.mm(S, cell.detach()) |
There was a problem hiding this comment.
shift contains different data from the previous one.
Current shift equals to previous_shift * cell
This is because shift is used for requires_grad_(True) directly instead of cell.
So-Takamoto
changed the title
|
It seems I pushed slightly different commit. I will create PR again. Sorry for that. |
shinh
pushed a commit
to shinh/torch-dftd
that referenced
this pull request
Jun 15, 2023
fix cases where --pad_num_foobar are not specified
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
I found that the current implementation has several performance issues regarding gradient wrt. cell.
This PR modifies that. Since the changes are relatively much, I will put some comments.
Change summary:
shiftfor gradient instead ofcell.shiftis now length scale instead cell unit.Also, this PR contains bugfix related to sked cell.