Merge devel into master#2772
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wanghan-iapcm merged 16 commits intodeepmodeling:masterfrom Aug 31, 2023
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## Beep boop. Your images are optimized! Your image file size has been reduced by **29%** 🎉 <details> <summary> Details </summary> | File | Before | After | Percent reduction | |:--|:--|:--|:--| | /doc/nvnmd/bohrium_status.png | 148.36kb | 93.34kb | 37.09% | | /doc/nvnmd/bohrium_download.png | 148.15kb | 93.26kb | 37.05% | | /doc/nvnmd/bohrium_project.png | 114.73kb | 80.55kb | 29.79% | | /doc/nvnmd/bohrium_group.png | 32.06kb | 23.28kb | 27.39% | | /doc/nvnmd/bohrium_top-up.png | 146.08kb | 108.21kb | 25.92% | | /doc/nvnmd/bohrium_job.png | 61.90kb | 49.25kb | 20.43% | | /doc/nvnmd/bohrium_submit.png | 49.68kb | 45.04kb | 9.33% | | /doc/_static/logo-dark.svg | 4.41kb | 4.40kb | 0.13% | | /doc/_static/logo.svg | 4.41kb | 4.41kb | 0.13% | | | | | | | **Total :** | **709.79kb** | **501.75kb** | **29.31%** | </details> --- [📝 docs](https://imgbot.net/docs) | [:octocat: repo](https://github.com/imgbot/ImgBot) | [🙋🏾 issues](https://github.com/imgbot/ImgBot/issues) | [🏪 marketplace](https://github.com/marketplace/imgbot) <i>~Imgbot - Part of [Optimole](https://optimole.com/) family</i> --------- Signed-off-by: ImgBotApp <ImgBotHelp@gmail.com> Co-authored-by: ImgBotApp <ImgBotHelp@gmail.com> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Currently `pair_coeff` support customizing mapping rule by the following way ``` pair_coeff * * H O H ``` But there are cases that need to mapping specific atom type to ghost type, or type that doesn't existed in deepmd. This PR addresses the issue by treating `NULL` as ghost type, so that users can specify atoms type to be ghost type by the following way ``` pair coeff * * H O NULL ```
Bumps [pypa/cibuildwheel](https://github.com/pypa/cibuildwheel) from 2.14 to 2.15. <details> <summary>Release notes</summary> <p><em>Sourced from <a href="https://github.com/pypa/cibuildwheel/releases">pypa/cibuildwheel's releases</a>.</em></p> <blockquote> <h2>v2.15.0</h2> <ul> <li>🌟 CPython 3.12 wheels are now built by default - without the CIBW_PRERELEASE_PYTHONS flag. It's time to build and upload these wheels to PyPI! This release includes CPython 3.12.0rc1, which is guaranteed to be ABI compatible with the final release. (<a href="https://redirect.github.com/pypa/cibuildwheel/issues/1565">#1565</a>)</li> <li>✨ Adds musllinux_1_2 support - this allows packagers to build for musl-based Linux distributions on a more recent Alpine image, and a newer musl libc. (<a href="https://redirect.github.com/pypa/cibuildwheel/issues/1561">#1561</a>)</li> </ul> <h2>v2.14.1</h2> <ul> <li>🛠 Updates the prerelease CPython 3.12 version to 3.12.0b4 (<a href="https://redirect.github.com/pypa/cibuildwheel/issues/1550">#1550</a>)</li> </ul> </blockquote> </details> <details> <summary>Changelog</summary> <p><em>Sourced from <a href="https://github.com/pypa/cibuildwheel/blob/main/docs/changelog.md">pypa/cibuildwheel's changelog</a>.</em></p> <blockquote> <hr /> <h2>title: Changelog</h2> <h1>Changelog</h1> <h3>v2.15.0</h3> <p><em>8 August 2023</em></p> <ul> <li>🌟 CPython 3.12 wheels are now built by default - without the CIBW_PRERELEASE_PYTHONS flag. It's time to build and upload these wheels to PyPI! This release includes CPython 3.12.0rc1, which is guaranteed to be ABI compatible with the final release. (<a href="https://redirect.github.com/pypa/cibuildwheel/issues/1565">#1565</a>)</li> <li>✨ Adds musllinux_1_2 support - this allows packagers to build for musl-based Linux distributions on a more recent Alpine image, and a newer musl libc. (<a href="https://redirect.github.com/pypa/cibuildwheel/issues/1561">#1561</a>)</li> </ul> <h3>v2.14.1</h3> <p><em>15 July 2023</em></p> <ul> <li>🛠 Updates the prerelease CPython 3.12 version to 3.12.0b4 (<a href="https://redirect.github.com/pypa/cibuildwheel/issues/1550">#1550</a>)</li> </ul> <h3>v2.14.0</h3> <p><em>10 July 2023</em></p> <ul> <li>✨ Adds support for building PyPy 3.10 wheels. (<a href="https://redirect.github.com/pypa/cibuildwheel/issues/1525">#1525</a>)</li> <li>🛠 Updates the prerelease CPython 3.12 version to 3.12.0b3.</li> <li>✨ Allow the use of the <code>{wheel}</code> placeholder in CIBW_TEST_COMMAND (<a href="https://redirect.github.com/pypa/cibuildwheel/issues/1533">#1533</a>)</li> <li>📚 Docs & examples updates (<a href="https://redirect.github.com/pypa/cibuildwheel/issues/1532">#1532</a>, <a href="https://redirect.github.com/pypa/cibuildwheel/issues/1416">#1416</a>)</li> <li>⚠️ Removed support for running cibuildwheel in Python 3.7. Python 3.7 is EOL. However, cibuildwheel continues to build Python 3.7 wheels for the moment. (<a href="https://redirect.github.com/pypa/cibuildwheel/issues/1175">#1175</a>)</li> </ul> <h3>v2.13.1</h3> <p><em>10 June 2023</em></p> <ul> <li>🛠 Updates the prerelease CPython 3.12 version to 3.12.0b2. (<a href="https://redirect.github.com/pypa/cibuildwheel/issues/1516">#1516</a>)</li> <li>🛠 Adds a moving <code>v<major>.<minor></code> tag for use in GitHub Actions workflow files. If you use this, you'll get the latest patch release within a minor version. Additionally, Dependabot won't send you PRs for patch releases. (<a href="https://redirect.github.com/pypa/cibuildwheel/issues/1517">#1517</a>)</li> </ul> <h3>v2.13.0</h3> <p><em>28 May 2023</em></p> <ul> <li> <p>✨ Adds CPython 3.12 support, under the prerelease flag <a href="https://cibuildwheel.readthedocs.io/en/stable/options/#prerelease-pythons">CIBW_PRERELEASE_PYTHONS</a>. This version of cibuildwheel uses 3.12.0b1.</p> <p>While CPython is in beta, the ABI can change, so your wheels might not be compatible with the final release. For this reason, we don't recommend distributing wheels until RC1, at which point 3.12 will be available in cibuildwheel without the flag. (<a href="https://redirect.github.com/pypa/cibuildwheel/issues/1507">#1507</a>)</p> </li> <li> <p>✨ Adds the ability to pass arguments to the container engine when the container is created, using the <a href="https://cibuildwheel.readthedocs.io/en/stable/options/#container-engine">CIBW_CONTAINER_ENGINE</a> option. (<a href="https://redirect.github.com/pypa/cibuildwheel/issues/1499">#1499</a>)</p> </li> </ul> <h3>v2.12.3</h3> <p><em>19 April 2023</em></p> <!-- raw HTML omitted --> </blockquote> <p>... (truncated)</p> </details> <details> <summary>Commits</summary> <ul> <li><a href="https://github.com/pypa/cibuildwheel/commit/39a63b5912f086dd459cf6fcb13dcdd3fe3bc24d"><code>39a63b5</code></a> Bump version: v2.15.0</li> <li><a href="https://github.com/pypa/cibuildwheel/commit/47e5d3c2cdee9d5324b6abe18c380c5ee33fd8f9"><code>47e5d3c</code></a> Merge pull request <a href="https://redirect.github.com/pypa/cibuildwheel/issues/1565">#1565</a> from henryiii/henryiii/feat/312rc</li> <li><a href="https://github.com/pypa/cibuildwheel/commit/a63e11a1c40bf45810a29b0837a72312202cb00b"><code>a63e11a</code></a> feat: build using 3.12 RC by default</li> <li><a href="https://github.com/pypa/cibuildwheel/commit/df94b5db6769eb8c3abb164caa9ab84c763570da"><code>df94b5d</code></a> [Bot] Update dependencies (<a href="https://redirect.github.com/pypa/cibuildwheel/issues/1553">#1553</a>)</li> <li><a href="https://github.com/pypa/cibuildwheel/commit/36049d86a2e21d74382d84d7a423e20e49a2ca91"><code>36049d8</code></a> feature: add musllinux_1_2 support (<a href="https://redirect.github.com/pypa/cibuildwheel/issues/1561">#1561</a>)</li> <li><a href="https://github.com/pypa/cibuildwheel/commit/229f8570b497b5fa4a201f7dd28c4f52c104218e"><code>229f857</code></a> [pre-commit.ci] pre-commit autoupdate (<a href="https://redirect.github.com/pypa/cibuildwheel/issues/1562">#1562</a>)</li> <li><a href="https://github.com/pypa/cibuildwheel/commit/5b32ee7d7bcd9433f559d8b43e9f9a180288c227"><code>5b32ee7</code></a> [pre-commit.ci] pre-commit autoupdate (<a href="https://redirect.github.com/pypa/cibuildwheel/issues/1559">#1559</a>)</li> <li><a href="https://github.com/pypa/cibuildwheel/commit/3f3bd9cff62eb311ed99891cc65132731c0a1c6f"><code>3f3bd9c</code></a> Merge pull request <a href="https://redirect.github.com/pypa/cibuildwheel/issues/1554">#1554</a> from pypa/pre-commit-ci-update-config</li> <li><a href="https://github.com/pypa/cibuildwheel/commit/8df6d59adf7f9c7876ece95d0f908b53e2014ff2"><code>8df6d59</code></a> [pre-commit.ci] pre-commit autoupdate</li> <li><a href="https://github.com/pypa/cibuildwheel/commit/4135c0a01dc11910ce118f58acc7caf4ac5c524a"><code>4135c0a</code></a> [pre-commit.ci] pre-commit autoupdate (<a href="https://redirect.github.com/pypa/cibuildwheel/issues/1546">#1546</a>)</li> <li>Additional commits viewable in <a href="https://github.com/pypa/cibuildwheel/compare/v2.14...v2.15">compare view</a></li> </ul> </details> <br /> [](https://docs.github.com/en/github/managing-security-vulnerabilities/about-dependabot-security-updates#about-compatibility-scores) Dependabot will resolve any conflicts with this PR as long as you don't alter it yourself. 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You can achieve the same result by closing it manually - `@dependabot show <dependency name> ignore conditions` will show all of the ignore conditions of the specified dependency - `@dependabot ignore this major version` will close this PR and stop Dependabot creating any more for this major version (unless you reopen the PR or upgrade to it yourself) - `@dependabot ignore this minor version` will close this PR and stop Dependabot creating any more for this minor version (unless you reopen the PR or upgrade to it yourself) - `@dependabot ignore this dependency` will close this PR and stop Dependabot creating any more for this dependency (unless you reopen the PR or upgrade to it yourself) </details> Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Signed-off-by: Jinzhe Zeng <jinzhe.zeng@rutgers.edu>
<!--pre-commit.ci start--> updates: - [github.com/astral-sh/ruff-pre-commit: v0.0.282 → v0.0.284](astral-sh/ruff-pre-commit@v0.0.282...v0.0.284) - [github.com/Lucas-C/pre-commit-hooks: v1.5.3 → v1.5.4](Lucas-C/pre-commit-hooks@v1.5.3...v1.5.4) <!--pre-commit.ci end--> --------- Signed-off-by: Jinzhe Zeng <jinzhe.zeng@rutgers.edu> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Jinzhe Zeng <jinzhe.zeng@rutgers.edu>
- fix bug in checking t_efield op in the graph - delete arg atomic in `_prepare_feed_dict` (otherwise, efield cannot be imported correctly when using this method) --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Added atomic dipole to test.py The current code did not cover this case. --------- Signed-off-by: Hananeh Oliaei <94663315+hanao2@users.noreply.github.com> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
<!--pre-commit.ci start--> updates: - [github.com/astral-sh/ruff-pre-commit: v0.0.284 → v0.0.285](astral-sh/ruff-pre-commit@v0.0.284...v0.0.285) - [github.com/asottile/blacken-docs: 1.15.0 → 1.16.0](adamchainz/blacken-docs@1.15.0...1.16.0) <!--pre-commit.ci end--> --------- Signed-off-by: Jinzhe Zeng <jinzhe.zeng@rutgers.edu> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Jinzhe Zeng <jinzhe.zeng@rutgers.edu>
This PR adds a new argument `dp model-devi --real_error`. With that, the real error given in the DP-GEN paper is calculated.  One can use this feature for `dpgen simplify` if the labeled data exists. Signed-off-by: Jinzhe Zeng <jinzhe.zeng@rutgers.edu>
Previously, we need to set `numb_test` to a quite large number to test all data. In this PR, passing 0 will lead to infinity. Breaking change: the default value of `numb_test` is set to 0. --------- Signed-off-by: Jinzhe Zeng <jinzhe.zeng@rutgers.edu>
Number `_comment` keys so there will be no duplicated keys.
```py
from glob import glob
for ii in glob("**/*.json", recursive=True):
with open(ii) as f:
content = f.read()
count = 1
while True:
if r'"_comment"' not in content:
break
content = content.replace('"_comment"', '"_comment%d"' % count, 1)
count += 1
with open(ii, "w") as f:
f.write(content)
```
Signed-off-by: Jinzhe Zeng <jinzhe.zeng@rutgers.edu>
) Fix deepmodeling#2751. If `__init__.py` does not exist, `module.__file__` is `None` (it is expected to give the path to `__init__.py`). In this case, `module.__path__[0]` will give the directory path. Signed-off-by: Jinzhe Zeng <jinzhe.zeng@rutgers.edu>
<!--pre-commit.ci start--> updates: - [github.com/astral-sh/ruff-pre-commit: v0.0.285 → v0.0.286](astral-sh/ruff-pre-commit@v0.0.285...v0.0.286) <!--pre-commit.ci end--> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
This PR edits the smooth method of se_atten descriptor when using stripped type embedding: 1. Change the structure in stripped type embedding and compression ops. 2. Add smooth factor on the network output of type embedding. 3. Add a new descriptor se_atten_v2 to include these changes while keeping se_atten in old behaviors. --------- Co-authored-by: nahso <topcloud@foxmail.com> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Codecov ReportPatch coverage:
Additional details and impacted files@@ Coverage Diff @@
## master #2772 +/- ##
==========================================
+ Coverage 78.73% 78.75% +0.01%
==========================================
Files 241 242 +1
Lines 25582 25641 +59
Branches 1517 1517
==========================================
+ Hits 20142 20193 +51
- Misses 5048 5058 +10
+ Partials 392 390 -2
☔ View full report in Codecov by Sentry. |
njzjz
approved these changes
Aug 31, 2023
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