Merge devel into master#2559
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amcadmus merged 76 commits intodeepmodeling:masterfrom May 24, 2023
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Bumps [docker/login-action](https://github.com/docker/login-action) from 1.10.0 to 2.1.0. <details> <summary>Release notes</summary> <p><em>Sourced from <a href="https://github.com/docker/login-action/releases">docker/login-action's releases</a>.</em></p> <blockquote> <h2>v2.1.0</h2> <h2>What's Changed</h2> <ul> <li>Ensure AWS temp credentials are redacted in workflow logs by <a href="https://github.com/crazy-max"><code>@crazy-max</code></a> (<a href="https://redirect.github.com/docker/login-action/issues/275">#275</a>)</li> <li>Bump <code>@actions/core</code> from 1.6.0 to 1.10.0 (<a href="https://redirect.github.com/docker/login-action/issues/252">#252</a> <a href="https://redirect.github.com/docker/login-action/issues/292">#292</a>)</li> <li>Bump <code>@aws-sdk/client-ecr</code> from 3.53.0 to 3.186.0 (<a href="https://redirect.github.com/docker/login-action/issues/298">#298</a>)</li> <li>Bump <code>@aws-sdk/client-ecr-public</code> from 3.53.0 to 3.186.0 (<a href="https://redirect.github.com/docker/login-action/issues/299">#299</a>)</li> </ul> <p><strong>Full Changelog</strong>: <a href="https://github.com/docker/login-action/compare/v2.0.0...v2.1.0">https://github.com/docker/login-action/compare/v2.0.0...v2.1.0</a></p> <h2>v2.0.0</h2> <ul> <li>Node 16 as default runtime by <a href="https://github.com/crazy-max"><code>@crazy-max</code></a> (<a href="https://redirect.github.com/docker/login-action/issues/161">#161</a>) <ul> <li>This requires a minimum <a href="https://github.com/actions/runner/releases/tag/v2.285.0">Actions Runner</a> version of v2.285.0, which is by default available in GHES 3.4 or later.</li> </ul> </li> <li>chore: update dev dependencies and workflow by <a href="https://github.com/crazy-max"><code>@crazy-max</code></a> (<a href="https://redirect.github.com/docker/login-action/issues/170">#170</a>)</li> <li>Bump <code>@actions/exec</code> from 1.1.0 to 1.1.1 (<a href="https://redirect.github.com/docker/login-action/issues/167">#167</a>)</li> <li>Bump <code>@actions/io</code> from 1.1.1 to 1.1.2 (<a href="https://redirect.github.com/docker/login-action/issues/168">#168</a>)</li> <li>Bump minimist from 1.2.5 to 1.2.6 (<a href="https://redirect.github.com/docker/login-action/issues/176">#176</a>)</li> <li>Bump https-proxy-agent from 5.0.0 to 5.0.1 (<a href="https://redirect.github.com/docker/login-action/issues/182">#182</a>)</li> </ul> <p><strong>Full Changelog</strong>: <a href="https://github.com/docker/login-action/compare/v1.14.1...v2.0.0">https://github.com/docker/login-action/compare/v1.14.1...v2.0.0</a></p> <h2>v1.14.1</h2> <ul> <li>Revert to Node 12 as default runtime to fix issue for GHE users (<a href="https://redirect.github.com/docker/login-action/issues/160">#160</a>)</li> </ul> <h2>v1.14.0</h2> <ul> <li>Update to node 16 (<a href="https://redirect.github.com/docker/login-action/issues/158">#158</a>)</li> <li>Bump <code>@aws-sdk/client-ecr</code> from 3.45.0 to 3.53.0 (<a href="https://redirect.github.com/docker/login-action/issues/157">#157</a>)</li> <li>Bump <code>@aws-sdk/client-ecr-public</code> from 3.45.0 to 3.53.0 (<a href="https://redirect.github.com/docker/login-action/issues/156">#156</a>)</li> </ul> <h2>v1.13.0</h2> <ul> <li>Handle proxy settings for aws-sdk (<a href="https://redirect.github.com/docker/login-action/issues/152">#152</a>)</li> <li>Workload identity based authentication docs for GCR and GAR (<a href="https://redirect.github.com/docker/login-action/issues/112">#112</a>)</li> <li>Test login against ACR (<a href="https://redirect.github.com/docker/login-action/issues/49">#49</a>)</li> <li>Bump <code>@aws-sdk/client-ecr</code> from 3.44.0 to 3.45.0 (<a href="https://redirect.github.com/docker/login-action/issues/132">#132</a>)</li> <li>Bump <code>@aws-sdk/client-ecr-public</code> from 3.43.0 to 3.45.0 (<a href="https://redirect.github.com/docker/login-action/issues/131">#131</a>)</li> </ul> <h2>v1.12.0</h2> <ul> <li>ECR: only set credentials if username and password are specified (<a href="https://redirect.github.com/docker/login-action/issues/128">#128</a>)</li> <li>Refactor to use aws-sdk v3 (<a href="https://redirect.github.com/docker/login-action/issues/128">#128</a>)</li> </ul> <h2>v1.11.0</h2> <ul> <li>ECR: switch implementation to use the AWS SDK (<a href="https://redirect.github.com/docker/login-action/issues/126">#126</a>)</li> <li><code>ecr</code> input to specify whether the given registry is ECR (<a href="https://redirect.github.com/docker/login-action/issues/123">#123</a>)</li> <li>Test against Windows runner (<a href="https://redirect.github.com/docker/login-action/issues/126">#126</a>)</li> <li>Update instructions for Google registry (<a href="https://redirect.github.com/docker/login-action/issues/127">#127</a>)</li> <li>Update dev workflow (<a href="https://redirect.github.com/docker/login-action/issues/111">#111</a>)</li> <li>Small changes for GHCR doc (<a href="https://redirect.github.com/docker/login-action/issues/86">#86</a>)</li> <li>Update dev dependencies (<a href="https://redirect.github.com/docker/login-action/issues/85">#85</a>)</li> <li>Bump ansi-regex from 5.0.0 to 5.0.1 (<a href="https://redirect.github.com/docker/login-action/issues/101">#101</a>)</li> <li>Bump tmpl from 1.0.4 to 1.0.5 (<a href="https://redirect.github.com/docker/login-action/issues/100">#100</a>)</li> <li>Bump <code>@actions/core</code> from 1.4.0 to 1.6.0 (<a href="https://redirect.github.com/docker/login-action/issues/94">#94</a> <a href="https://redirect.github.com/docker/login-action/issues/103">#103</a>)</li> </ul> <!-- raw HTML omitted --> </blockquote> <p>... (truncated)</p> </details> <details> <summary>Commits</summary> <ul> <li><a href="https://github.com/docker/login-action/commit/f4ef78c080cd8ba55a85445d5b36e214a81df20a"><code>f4ef78c</code></a> Merge pull request <a href="https://redirect.github.com/docker/login-action/issues/299">#299</a> from docker/dependabot/npm_and_yarn/aws-sdk/client-ec...</li> <li><a href="https://github.com/docker/login-action/commit/9ad4ce3929bc07d004540e2ebe754234848335e2"><code>9ad4ce3</code></a> Update generated content</li> <li><a href="https://github.com/docker/login-action/commit/884eadd4f88fc6034a7a1ba10fbd2fd69404b94b"><code>884eadd</code></a> Bump <code>@aws-sdk/client-ecr-public</code> from 3.53.0 to 3.186.0</li> <li><a href="https://github.com/docker/login-action/commit/a266232f5c33001624fdfca7a1d9e5c5612a20ac"><code>a266232</code></a> Merge pull request <a href="https://redirect.github.com/docker/login-action/issues/298">#298</a> from docker/dependabot/npm_and_yarn/aws-sdk/client-ec...</li> <li><a href="https://github.com/docker/login-action/commit/f97efcfbf9cb420547dae40adf642fc2366c979a"><code>f97efcf</code></a> Update generated content</li> <li><a href="https://github.com/docker/login-action/commit/5ae789beac0ced16338cc5996b168a5785de8ae9"><code>5ae789b</code></a> Bump <code>@aws-sdk/client-ecr</code> from 3.53.0 to 3.186.0</li> <li><a href="https://github.com/docker/login-action/commit/71c23b5b3471683fb0acf7a6c821f834735aec44"><code>71c23b5</code></a> Merge pull request <a href="https://redirect.github.com/docker/login-action/issues/292">#292</a> from docker/dependabot/npm_and_yarn/actions/core-1.10.0</li> <li><a href="https://github.com/docker/login-action/commit/6401d70aab8811e905cbf52b0eae2c58bc274b5b"><code>6401d70</code></a> Update generated content</li> <li><a href="https://github.com/docker/login-action/commit/67e8909cc694e896d07b96876522f898972abbfd"><code>67e8909</code></a> Bump <code>@actions/core</code> from 1.9.1 to 1.10.0</li> <li><a href="https://github.com/docker/login-action/commit/21f251affc0769ccac8a1cf17e937592fb492337"><code>21f251a</code></a> Merge pull request <a href="https://redirect.github.com/docker/login-action/issues/275">#275</a> from crazy-max/redact-aws-creds</li> <li>Additional commits viewable in <a href="https://github.com/docker/login-action/compare/f054a8b539a109f9f41c372932f1ae047eff08c9...f4ef78c080cd8ba55a85445d5b36e214a81df20a">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. You can also trigger a rebase manually by commenting `@dependabot rebase`. [//]: # (dependabot-automerge-start) [//]: # (dependabot-automerge-end) --- <details> <summary>Dependabot commands and options</summary> <br /> You can trigger Dependabot actions by commenting on this PR: - `@dependabot rebase` will rebase this PR - `@dependabot recreate` will recreate this PR, overwriting any edits that have been made to it - `@dependabot merge` will merge this PR after your CI passes on it - `@dependabot squash and merge` will squash and merge this PR after your CI passes on it - `@dependabot cancel merge` will cancel a previously requested merge and block automerging - `@dependabot reopen` will reopen this PR if it is closed - `@dependabot close` will close this PR and stop Dependabot recreating it. 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It looks that by default, CMake will remove the execute permission. Signed-off-by: Jinzhe Zeng <jinzhe.zeng@rutgers.edu>
Signed-off-by: Jinzhe Zeng <jinzhe.zeng@rutgers.edu>
Signed-off-by: Jinzhe Zeng <jinzhe.zeng@rutgers.edu>
<!--pre-commit.ci start--> updates: - [github.com/psf/black: 22.12.0 → 23.1.0](psf/black@22.12.0...23.1.0) - [github.com/charliermarsh/ruff-pre-commit: v0.0.243 → v0.0.257](astral-sh/ruff-pre-commit@v0.0.243...v0.0.257) <!--pre-commit.ci end--> --------- 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>
Signed-off-by: Jinzhe Zeng <jinzhe.zeng@rutgers.edu>
Fix deepmodeling#2409. By default, `source` searches the file from `PATH` (see the help from `source --help`). This might conflict with other packages. To prevent this behavior, one has to source the relative path instead. Signed-off-by: Jinzhe Zeng <jinzhe.zeng@rutgers.edu>
Resolve deepmodeling#2331. Update `setup.py` for TF 2.12. Migrate all workflows to TF 2.12 with `USE_TF_PYTHON_LIBS`. Update documentation to recommend `USE_TF_PYTHON_LIBS`. --------- 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>
When mixed systems training (deepmodeling#2372) is enabled, the mixed_type attribute will affect the data stat. --------- Signed-off-by: Jinzhe Zeng <jinzhe.zeng@rutgers.edu>
…i-task mode (deepmodeling#2348) It is a breaking change to the user interface in multi-task mode. Please review carefully. Replace "learning_rate" with "learning_rate_dict" in multi-task mode to support different learning rate settings for each fitting net, which is familiar to "loss_dict". The format of `lcurve.out` will be like the following: ``` # step sys1_rmse_val sys1_rmse_trn sys1_rmse_e_val sys1_rmse_e_trn sys1_rmse_f_val sys1_rmse_f_trn sys1_lr sys2_rmse_val sys2_rmse_trn sys2_rmse_e_val sys2_rmse_e_trn sys2_rmse_f_val sys2_rmse_f_trn sys2_lr ... ``` The learning rate of each system will be printed separately. --------- Signed-off-by: HuangJiameng <105633685+HuangJiameng@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/charliermarsh/ruff-pre-commit: v0.0.257 → v0.0.259](astral-sh/ruff-pre-commit@v0.0.257...v0.0.259) - [github.com/pre-commit/mirrors-clang-format: v15.0.7 → v16.0.0](pre-commit/mirrors-clang-format@v15.0.7...v16.0.0) - [github.com/scop/pre-commit-shfmt: v3.6.0-1 → v3.6.0-2](scop/pre-commit-shfmt@v3.6.0-1...v3.6.0-2) <!--pre-commit.ci end--> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Co-authored-by: LiuGroupHNU <liujie123@HNU> Co-authored-by: MoPinghui <mopinghui1020@gmail.com> Co-authored-by: Han Wang <92130845+wanghan-iapcm@users.noreply.github.com> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Signed-off-by: Eisuke Kawashima <e-kwsm@users.noreply.github.com>
by pinning exhale to a specific version. (The current documentation is broken as it installs an old version) --------- 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: AnuragKr <anuragkrsingh02@outlook.com> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Signed-off-by: Chun Cai <amoycaic@gmail.com>
<!--pre-commit.ci start--> updates: - [github.com/psf/black: 23.1.0 → 23.3.0](psf/black@23.1.0...23.3.0) - [github.com/charliermarsh/ruff-pre-commit: v0.0.259 → v0.0.260](astral-sh/ruff-pre-commit@v0.0.259...v0.0.260) <!--pre-commit.ci end--> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
<!--pre-commit.ci start--> updates: - [github.com/charliermarsh/ruff-pre-commit: v0.0.260 → v0.0.261](astral-sh/ruff-pre-commit@v0.0.260...v0.0.261) <!--pre-commit.ci end--> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
…2449) here i present the implementation of DeepDOS model [Phys. Rev. B 105, 174109 (2022)] in dpkit-devel branch generally, i add a new `fitting_type = 'dos'` to allow the DP to fit a vector. this vector can be global (`dos.raw/npy`) or atomic (`atom_dos.raw/npy`), whose length is `numb_dos`. specifically, 1. `fit/dos.py`, `loss/dos.py`, `model/dos.py` and `infer/deep_dos.py` is created to allow fitting and inference 2. relevant `*/__init__.py`, `train/trainer.py`, `utils/argcheck.py` is updated 3. in `entrypoint/freeze.py`, `entrypoint/test.py` , relevant functions are added to freeze and test the DeepDOS model 4. a simple user guide is added in the `doc/model/train-fitting-dos.md` 5. an example is provide in the `examples/dos/`, the input script is provided in the `examples/dos/train/input.json`, data sets are provided in the `examples/dos/data/` --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Closes deepmodeling#2425. It takes work to explain everything in the comment. So, instead, I add a link to the documentation. --------- Signed-off-by: Jinzhe Zeng <jinzhe.zeng@rutgers.edu> Co-authored-by: Han Wang <92130845+wanghan-iapcm@users.noreply.github.com>
DPLR is broken due to the change of coeff(int narg, char **arg) function. The current coeff function requires that the number of types in LAMMPS no more than that in model. In dplr, however, there might be more types in LAMMPS than in the model. This check should be bypassed. --------- Signed-off-by: Jinzhe Zeng <jinzhe.zeng@rutgers.edu> Co-authored-by: Jinzhe Zeng <jinzhe.zeng@rutgers.edu> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
xref: deepmodeling#2348 --------- Signed-off-by: Jinzhe Zeng <jinzhe.zeng@rutgers.edu>
... as TF directories may be changed due to PEP-517.
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…pmodeling#2461) Signed-off-by: Jinzhe Zeng <jinzhe.zeng@rutgers.edu>
Create DeePMD-kit_Quick_Start_Tutorial_EN.ipynb with Open in Bohrium logo. It has been ensured that the Bohrium Notebook can be run with just one click. --------- 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 deepmodeling#2466. `get_file_content` only throws errors for rank 0, so we should use `error->one` instead of `error->all`.
… C library (deepmodeling#2527) The libraries linking against the C library do not need to use the same `_GLIBCXX_USE_CXX11_ABI` as the TF. --------- Signed-off-by: Jinzhe Zeng <jinzhe.zeng@rutgers.edu>
<!--pre-commit.ci start--> updates: - [github.com/charliermarsh/ruff-pre-commit: v0.0.265 → v0.0.267](astral-sh/ruff-pre-commit@v0.0.265...v0.0.267) <!--pre-commit.ci end--> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Fix deepmodeling#2229. Train models and prefetch data in parallel to decouple the time when data is produced from the time when data is consumed. --------- Signed-off-by: Jinzhe Zeng <jinzhe.zeng@rutgers.edu>
…g#2470) Here for mixed systems, the system batch size is just a placeholder. Signed-off-by: Jinzhe Zeng <jinzhe.zeng@rutgers.edu>
Signed-off-by: Jinzhe Zeng <jinzhe.zeng@rutgers.edu>
…#2539) Fix deepmodeling#2516. Signed-off-by: Jinzhe Zeng <jinzhe.zeng@rutgers.edu>
This module is out-of-date, and no one maintains it. --------- 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>
…eling#2546) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Signed-off-by: Jinzhe Zeng <jinzhe.zeng@rutgers.edu>
It saves the time to build lammps --------- 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>
Fix deepmodeling#2250. --------- Signed-off-by: Jinzhe Zeng <jinzhe.zeng@rutgers.edu>
Before deepmodeling#2422, it was linked with libpython.so, so it wasn't tested as the python in the image doesn't has a library. But now it isn't linked with libpython.so anymore, so we can test it. Signed-off-by: Jinzhe Zeng <jinzhe.zeng@rutgers.edu>
Add unittest for lmp dplr --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
<!--pre-commit.ci start--> updates: - [github.com/charliermarsh/ruff-pre-commit: v0.0.267 → v0.0.269](astral-sh/ruff-pre-commit@v0.0.267...v0.0.269) - [github.com/pre-commit/mirrors-clang-format: v16.0.3 → v16.0.4](pre-commit/mirrors-clang-format@v16.0.3...v16.0.4) <!--pre-commit.ci end--> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Signed-off-by: Jinzhe Zeng <jinzhe.zeng@rutgers.edu>
Fix model-devi with mixed_type format; Add UTs; Add detection of whether models support mixed_type inference. --------- 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>
Codecov ReportPatch coverage:
Additional details and impacted files@@ Coverage Diff @@
## master #2559 +/- ##
==========================================
+ Coverage 75.20% 76.81% +1.60%
==========================================
Files 223 227 +4
Lines 22502 23805 +1303
Branches 1658 1653 -5
==========================================
+ Hits 16923 18286 +1363
+ Misses 4504 4421 -83
- Partials 1075 1098 +23
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