merge devel into master #2725
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merge devel into master #2725
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…2565) Our PyPi source distribution package is over 30MB which is too large! See https://pypi.org/project/deepmd-kit/2.2.2/#files By default, when using `setuptools-scm`, all files will be added to the package. This PR excludes directories that are not used for building and installing, including: - source/tests - source/api_c/tests - source/api_cc/tests - source/lib/tests - source/lmp/tests - doc - examples - data - .github After removing these files from the source distribution, the package is only 708 KB. --------- 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>
This PR uses small models to test dplr. --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
…ng#2571) In TF 2.11, TensorFlow adds a new directory, "tensorflow/tsl" where the headers should be copied. 1. add docs to install TF 2.12; 2. build_tf.py: bump to TF 2.12, and copy `tensorflow/tsl`; 3. output the detailed errors when checking ABIs. Sometimes the reason is missing header files instead of ABI. --------- 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>
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>
Signed-off-by: Jinzhe Zeng <jinzhe.zeng@rutgers.edu>
Bumps [pypa/cibuildwheel](https://github.com/pypa/cibuildwheel) from 2.12.3 to 2.13.0. <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>v2.13.0</h2> <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> </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> <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> </blockquote> </details> <details> <summary>Commits</summary> <ul> <li><a href="https://github.com/pypa/cibuildwheel/commit/51f5c7fe68ff24694d5a6ac0eb3ad476ddd062a8"><code>51f5c7f</code></a> Bump version: v2.13.0</li> <li><a href="https://github.com/pypa/cibuildwheel/commit/8499628a5b38525c047996750633a7f7536ada17"><code>8499628</code></a> feat: add Python 3.12 beta 1 (<a href="https://redirect.github.com/pypa/cibuildwheel/issues/1507">#1507</a>)</li> <li><a href="https://github.com/pypa/cibuildwheel/commit/b2bc6fdda6ac2f3e9da11e69d45aba17c7ebcbbd"><code>b2bc6fd</code></a> Merge pull request <a href="https://redirect.github.com/pypa/cibuildwheel/issues/1499">#1499</a> from pypa/docker-flags</li> <li><a href="https://github.com/pypa/cibuildwheel/commit/754a47388d5e2dcddc8f98e7c36dc605818caa9e"><code>754a473</code></a> Merge pull request <a href="https://redirect.github.com/pypa/cibuildwheel/issues/1503">#1503</a> from pypa/pre-commit-ci-update-config</li> <li><a href="https://github.com/pypa/cibuildwheel/commit/f25c8a64f6ee92473583130e5ec30ea583b90e7b"><code>f25c8a6</code></a> Merge pull request <a href="https://redirect.github.com/pypa/cibuildwheel/issues/1506">#1506</a> from artfwo/patch-1</li> <li><a href="https://github.com/pypa/cibuildwheel/commit/9b904777d4c3dd275fa23ca567c4e1ec4fa2b951"><code>9b90477</code></a> Apply suggestions from code review</li> <li><a href="https://github.com/pypa/cibuildwheel/commit/e14b8e8e2f129cdacbd49564032a2d0579d30269"><code>e14b8e8</code></a> Add aalink to examples</li> <li><a href="https://github.com/pypa/cibuildwheel/commit/da9be0a27b525a61e5b418a86e5526a93e349220"><code>da9be0a</code></a> [pre-commit.ci] pre-commit autoupdate</li> <li><a href="https://github.com/pypa/cibuildwheel/commit/301dca264f3e41b1f0d07e13019fccfaaaae6273"><code>301dca2</code></a> chore: use PyPI Trusted Publisher for releases (<a href="https://redirect.github.com/pypa/cibuildwheel/issues/1500">#1500</a>)</li> <li><a href="https://github.com/pypa/cibuildwheel/commit/c74083cfdaa286dc3a30b46c098010a60dc6429e"><code>c74083c</code></a> [Bot] Update dependencies (<a href="https://redirect.github.com/pypa/cibuildwheel/issues/1485">#1485</a>)</li> <li>Additional commits viewable in <a href="https://github.com/pypa/cibuildwheel/compare/v2.12.3...v2.13.0">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. You can achieve the same result by closing it manually - `@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>
<!--pre-commit.ci start--> updates: - [github.com/charliermarsh/ruff-pre-commit: v0.0.269 → v0.0.270](astral-sh/ruff-pre-commit@v0.0.269...v0.0.270) <!--pre-commit.ci end--> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
…2549) Signed-off-by: Jinzhe Zeng <jinzhe.zeng@rutgers.edu>
The corresponding functions (min_pre_force and min_post_force) in fix dplr are added so that the positions and forces of Wannier centroids can be correctly assigned during minimization. --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
so old rpath will not be removed Signed-off-by: Jinzhe Zeng <jinzhe.zeng@rutgers.edu>
Signed-off-by: Jinzhe Zeng <jinzhe.zeng@rutgers.edu>
The binary_search method in C++ is only valid for sorted vectors. The following case in "type_associate" of "fix dplr" will raise error: 4 5 3 6. 4 and 3 are real atom types and stored in sel_type. The vector sel_type is sorted. 5 and 6 are associated with 4 and 3, respectively. The resulting sel_type vector is 3 4, and the resulting dpl_type vector is 6 5. If a pair 4 5 is searched, then this line https://github.com/deepmodeling/deepmd-kit/blob/e7d68c165c20aea04af686f8a81b179154b1d679/source/lmp/fix_dplr.cpp#L195-L196 will do binary search for 4 in 3 4, which results in True; and will search for 5 in 6 5, which results in False. Therefore, I am copying dpl_type vector to the dpl_type_sorted vector and sort it. The binary search should be used on the sorted vector. ## The above solution is abandoned. In stead, do not use binary_search in the type check of get_valid_pairs. The current method is: first find the type of the real atom, and check if the type of its bonded atom is consistent with that defined by type_associate. --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
…eepmodeling#2588) Signed-off-by: Ye Ding <dingye@westlake.edu.cn> 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>
There are some cases that users may only need to compute the external electric field force on the Wannier centroids and not need the electrostatic forces between atoms and WCs. This PR makes pppm_dplr optional and supports the users to only calculate field forces in fix dplr. --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
The current model compression feature will miss data modifier if it is used to compress a dplr model. This PR builds the modifier in the compressing process if there is a modifier in the uncompressed model.
Fix deepmodeling#2590 --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
It seems to me that the previous implementation does not really work in the CI... This PR will prevent any new large files (>1MB). --------- Signed-off-by: Jinzhe Zeng <jinzhe.zeng@rutgers.edu>
`new[]` should be used with `delete[]`. --------- Signed-off-by: Jinzhe Zeng <jinzhe.zeng@rutgers.edu>
The previous `prod_force` did not support multiple frames in parallel, which was slow when the batch size was large. This PR adds support so that prod_force can be parallelized in the dimension of the samples. When the batch size is about 70, the `prod_force` op is 10x faster than before on GPU cards. --------- Signed-off-by: Jinzhe Zeng <jinzhe.zeng@rutgers.edu>
…#2611) Fix a bug introduced in deepmodeling#2549. Add tests for it. --------- Signed-off-by: Jinzhe Zeng <jinzhe.zeng@rutgers.edu>
Apply flake8-comprehensions to make codes simpler. --------- 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>
Bumps [docker/build-push-action](https://github.com/docker/build-push-action) from 4.0.0 to 4.1.0. <details> <summary>Release notes</summary> <p><em>Sourced from <a href="https://github.com/docker/build-push-action/releases">docker/build-push-action's releases</a>.</em></p> <blockquote> <h2>v4.1.0</h2> <blockquote> <p><strong>Note</strong></p> <p>Buildx v0.10 enables support for a minimal <a href="https://slsa.dev/provenance/">SLSA Provenance</a> attestation, which requires support for <a href="https://github.com/opencontainers/image-spec">OCI-compliant</a> multi-platform images. This may introduce issues with registry and runtime support (e.g. <a href="https://redirect.github.com/docker/buildx/issues/1533">Google Cloud Run and AWS Lambda</a>). You can optionally disable the default provenance attestation functionality using <code>provenance: false</code>.</p> </blockquote> <ul> <li>Switch to actions-toolkit implementation by <a href="https://github.com/crazy-max"><code>@crazy-max</code></a> in <a href="https://redirect.github.com/docker/build-push-action/pull/811">docker/build-push-action#811</a> <a href="https://redirect.github.com/docker/build-push-action/pull/838">docker/build-push-action#838</a> <a href="https://redirect.github.com/docker/build-push-action/pull/855">docker/build-push-action#855</a> <a href="https://redirect.github.com/docker/build-push-action/pull/860">docker/build-push-action#860</a> <a href="https://redirect.github.com/docker/build-push-action/pull/875">docker/build-push-action#875</a></li> <li>e2e: quay.io by <a href="https://github.com/crazy-max"><code>@crazy-max</code></a> in <a href="https://redirect.github.com/docker/build-push-action/pull/799">docker/build-push-action#799</a> <a href="https://redirect.github.com/docker/build-push-action/pull/805">docker/build-push-action#805</a></li> <li>e2e: local harbor and nexus by <a href="https://github.com/crazy-max"><code>@crazy-max</code></a> in <a href="https://redirect.github.com/docker/build-push-action/pull/800">docker/build-push-action#800</a></li> <li>e2e: add artifactory container registry to test against by <a href="https://github.com/jedevc"><code>@jedevc</code></a> in <a href="https://redirect.github.com/docker/build-push-action/pull/804">docker/build-push-action#804</a></li> <li>e2e: add distribution tests by <a href="https://github.com/jedevc"><code>@jedevc</code></a> in <a href="https://redirect.github.com/docker/build-push-action/pull/814">docker/build-push-action#814</a> <a href="https://redirect.github.com/docker/build-push-action/pull/815">docker/build-push-action#815</a></li> </ul> <p><strong>Full Changelog</strong>: <a href="https://github.com/docker/build-push-action/compare/v4.0.0...v4.1.0">https://github.com/docker/build-push-action/compare/v4.0.0...v4.1.0</a></p> </blockquote> </details> <details> <summary>Commits</summary> <ul> <li><a href="https://github.com/docker/build-push-action/commit/44ea916f6c540f9302d50c2b1e5a8dc071f15cdf"><code>44ea916</code></a> Merge pull request <a href="https://redirect.github.com/docker/build-push-action/issues/875">#875</a> from docker/dependabot/npm_and_yarn/docker/actions-to...</li> <li><a href="https://github.com/docker/build-push-action/commit/0167eef179833f48bfa0001f330d5f2d578ca25c"><code>0167eef</code></a> update generated content</li> <li><a href="https://github.com/docker/build-push-action/commit/91bf8bfc4d4cac86eb889d345ad6aaf731ac9aff"><code>91bf8bf</code></a> chore(deps): Bump <code>@docker/actions-toolkit</code> from 0.2.0 to 0.3.0</li> <li><a href="https://github.com/docker/build-push-action/commit/a799b4decf46d51b39dd396f4df5a4343afd30c4"><code>a799b4d</code></a> Merge pull request <a href="https://redirect.github.com/docker/build-push-action/issues/860">#860</a> from docker/dependabot/npm_and_yarn/docker/actions-to...</li> <li><a href="https://github.com/docker/build-push-action/commit/87480bdf698dadcc82974864fc727c54d9aa3311"><code>87480bd</code></a> update generated content</li> <li><a href="https://github.com/docker/build-push-action/commit/f9efed53cc1b0364ba947400ac02042bbbaac7fc"><code>f9efed5</code></a> Merge pull request <a href="https://redirect.github.com/docker/build-push-action/issues/871">#871</a> from dvdksn/fix/secret-example-link</li> <li><a href="https://github.com/docker/build-push-action/commit/3580b78e04abcedb47a5f22d37372e27f44aea10"><code>3580b78</code></a> fix: broken link to secret example docs</li> <li><a href="https://github.com/docker/build-push-action/commit/91df6b874e498451163feb47610c87c4a218c1ee"><code>91df6b8</code></a> Merge pull request <a href="https://redirect.github.com/docker/build-push-action/issues/859">#859</a> from docker/dependabot/github_actions/docker/bake-act...</li> <li><a href="https://github.com/docker/build-push-action/commit/ea92b18afbe5bd9e5e2d5a967eca8e52c0aa9493"><code>ea92b18</code></a> chore(deps): Bump <code>@docker/actions-toolkit</code> from 0.1.0 to 0.2.0</li> <li><a href="https://github.com/docker/build-push-action/commit/6f91eb31f77739227d3f4853c0ca3263870a31d7"><code>6f91eb3</code></a> chore(deps): Bump docker/bake-action from 2 to 3</li> <li>Additional commits viewable in <a href="https://github.com/docker/build-push-action/compare/3b5e8027fcad23fda98b2e3ac259d8d67585f671...44ea916f6c540f9302d50c2b1e5a8dc071f15cdf">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. You can achieve the same result by closing it manually - `@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>
Bumps [docker/login-action](https://github.com/docker/login-action) from 2.1.0 to 2.2.0. <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>v2.2.0</h2> <h2>What's Changed</h2> <ul> <li>Switch to actions-toolkit implementation by <a href="https://github.com/crazy-max"><code>@crazy-max</code></a> in <a href="https://redirect.github.com/docker/login-action/pull/409">docker/login-action#409</a> <a href="https://redirect.github.com/docker/login-action/pull/470">docker/login-action#470</a> <a href="https://redirect.github.com/docker/login-action/pull/476">docker/login-action#476</a></li> <li>Bump <code>@aws-sdk/client-ecr</code> and <code>@aws-sdk/client-ecr-public</code> to 3.347.1 in <a href="https://redirect.github.com/docker/login-action/pull/524">docker/login-action#524</a> <a href="https://redirect.github.com/docker/login-action/pull/364">docker/login-action#364</a> <a href="https://redirect.github.com/docker/login-action/pull/363">docker/login-action#363</a></li> <li>Bump minimatch from 3.0.4 to 3.1.2 in <a href="https://redirect.github.com/docker/login-action/pull/354">docker/login-action#354</a></li> <li>Bump json5 from 2.2.0 to 2.2.3 in <a href="https://redirect.github.com/docker/login-action/pull/378">docker/login-action#378</a></li> <li>Bump http-proxy-agent from 5.0.0 to 7.0.0 in <a href="https://redirect.github.com/docker/login-action/pull/509">docker/login-action#509</a></li> <li>Bump https-proxy-agent from 5.0.1 to 7.0.0 in <a href="https://redirect.github.com/docker/login-action/pull/508">docker/login-action#508</a></li> </ul> <p><strong>Full Changelog</strong>: <a href="https://github.com/docker/login-action/compare/v2.1.0...v2.2.0">https://github.com/docker/login-action/compare/v2.1.0...v2.2.0</a></p> </blockquote> </details> <details> <summary>Commits</summary> <ul> <li><a href="https://github.com/docker/login-action/commit/465a07811f14bebb1938fbed4728c6a1ff8901fc"><code>465a078</code></a> Merge pull request <a href="https://redirect.github.com/docker/login-action/issues/524">#524</a> from crazy-max/bump-aws</li> <li><a href="https://github.com/docker/login-action/commit/360b4b5fefbd590a50c2ff0c234dbd9fa6b08759"><code>360b4b5</code></a> Merge pull request <a href="https://redirect.github.com/docker/login-action/issues/512">#512</a> from jhihruei/change/update-gitlab-readme</li> <li><a href="https://github.com/docker/login-action/commit/c156700b2346aa481b427d93907904c3d5f50f72"><code>c156700</code></a> update generated content</li> <li><a href="https://github.com/docker/login-action/commit/f605cf145efa455c90bb0b4759f5907b4279df40"><code>f605cf1</code></a> bump <code>@aws-sdk/client-ecr</code> and <code>@aws-sdk/client-ecr-public</code> to 3.347.1</li> <li><a href="https://github.com/docker/login-action/commit/2a93a3eddbf1aaf1b8fe1a407e435b503a11dc38"><code>2a93a3e</code></a> Merge pull request <a href="https://redirect.github.com/docker/login-action/issues/508">#508</a> from docker/dependabot/npm_and_yarn/https-proxy-agent...</li> <li><a href="https://github.com/docker/login-action/commit/422e90f61016a07919f20356abe3fe54a85301ff"><code>422e90f</code></a> update generated content</li> <li><a href="https://github.com/docker/login-action/commit/bc8c4d08b4525c19acb3460724815e0a379fa547"><code>bc8c4d0</code></a> build(deps): bump https-proxy-agent from 5.0.1 to 7.0.0</li> <li><a href="https://github.com/docker/login-action/commit/052c2c42688f7d00919d3d8d4f322da9896749d5"><code>052c2c4</code></a> Merge pull request <a href="https://redirect.github.com/docker/login-action/issues/509">#509</a> from docker/dependabot/npm_and_yarn/http-proxy-agent-...</li> <li><a href="https://github.com/docker/login-action/commit/beabccd65a41391d5831120e16e9ab294d01c78d"><code>beabccd</code></a> update generated content</li> <li><a href="https://github.com/docker/login-action/commit/b56ed1c88dfcaa0b6e59227cd67efd6b0ff7604c"><code>b56ed1c</code></a> build(deps): bump http-proxy-agent from 5.0.0 to 7.0.0</li> <li>Additional commits viewable in <a href="https://github.com/docker/login-action/compare/f4ef78c080cd8ba55a85445d5b36e214a81df20a...465a07811f14bebb1938fbed4728c6a1ff8901fc">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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Bumps [pypa/cibuildwheel](https://github.com/pypa/cibuildwheel) from 2.13.0 to 2.13.1. <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>v2.13.1</h2> <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> </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> <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> </blockquote> </details> <details> <summary>Commits</summary> <ul> <li><a href="https://github.com/pypa/cibuildwheel/commit/0ecddd92b62987d7a2ae8911f4bb8ec9e2e4496a"><code>0ecddd9</code></a> Bump version: v2.13.1</li> <li><a href="https://github.com/pypa/cibuildwheel/commit/f35d309173dfc5359b18ca3d2c9c422e4cf83abb"><code>f35d309</code></a> Merge pull request <a href="https://redirect.github.com/pypa/cibuildwheel/issues/1517">#1517</a> from pypa/major-dot-minor-tag</li> <li><a href="https://github.com/pypa/cibuildwheel/commit/3160e8dbca733f3125ba9fcf5cf6b0007cdaca73"><code>3160e8d</code></a> Merge pull request <a href="https://redirect.github.com/pypa/cibuildwheel/issues/1516">#1516</a> from pypa/update-dependencies-pr</li> <li><a href="https://github.com/pypa/cibuildwheel/commit/012ae48172b00cfbfad05e1a3fa6d0af04bc0d7b"><code>012ae48</code></a> Add workflow that updates a vX.Y tag on release</li> <li><a href="https://github.com/pypa/cibuildwheel/commit/1c3b8e112e9ceccee1712627b5377213672ae155"><code>1c3b8e1</code></a> Update dependencies</li> <li><a href="https://github.com/pypa/cibuildwheel/commit/ca7b0f75c61a9efc6dd42d7c0600f347df8ca5e0"><code>ca7b0f7</code></a> Merge pull request <a href="https://redirect.github.com/pypa/cibuildwheel/issues/1514">#1514</a> from pypa/fix-travis-windows</li> <li><a href="https://github.com/pypa/cibuildwheel/commit/8d126bc281ea9d9e62e37ec7f604fcd2157044a0"><code>8d126bc</code></a> Try removing the offending line</li> <li><a href="https://github.com/pypa/cibuildwheel/commit/2ca5ff2dcdd0bfc0d558906b2ae20e74b9c5cb51"><code>2ca5ff2</code></a> Merge pull request <a href="https://redirect.github.com/pypa/cibuildwheel/issues/1508">#1508</a> from pypa/update-dependencies-pr</li> <li><a href="https://github.com/pypa/cibuildwheel/commit/7d45cf3dace7240123635298d7429bb99fad6b92"><code>7d45cf3</code></a> Merge pull request <a href="https://redirect.github.com/pypa/cibuildwheel/issues/1511">#1511</a> from ianthomas23/doc_fix_config_settings</li> <li><a href="https://github.com/pypa/cibuildwheel/commit/f6edc817df1b26def09c0278a72f2d097df6da23"><code>f6edc81</code></a> Merge pull request <a href="https://redirect.github.com/pypa/cibuildwheel/issues/1512">#1512</a> from pypa/pre-commit-ci-update-config</li> <li>Additional commits viewable in <a href="https://github.com/pypa/cibuildwheel/compare/v2.13.0...v2.13.1">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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Bumps [docker/metadata-action](https://github.com/docker/metadata-action) from 4.4.0 to 4.5.0. <details> <summary>Release notes</summary> <p><em>Sourced from <a href="https://github.com/docker/metadata-action/releases">docker/metadata-action's releases</a>.</em></p> <blockquote> <h2>v4.5.0</h2> <h2>What's Changed</h2> <ul> <li>Bump <code>@docker/actions-toolkit</code> from 0.1.0 to 0.3.0 in <a href="https://redirect.github.com/docker/metadata-action/pull/296">docker/metadata-action#296</a></li> <li>Bump csv-parse from 5.3.8 to 5.4.0 in <a href="https://redirect.github.com/docker/metadata-action/pull/294">docker/metadata-action#294</a></li> </ul> <p><strong>Full Changelog</strong>: <a href="https://github.com/docker/metadata-action/compare/v4.4.0...v4.5.0">https://github.com/docker/metadata-action/compare/v4.4.0...v4.5.0</a></p> </blockquote> </details> <details> <summary>Commits</summary> <ul> <li><a href="https://github.com/docker/metadata-action/commit/2c0bd771b40637d97bf205cbccdd294a32112176"><code>2c0bd77</code></a> Merge pull request <a href="https://redirect.github.com/docker/metadata-action/issues/296">#296</a> from docker/dependabot/npm_and_yarn/docker/actions-to...</li> <li><a href="https://github.com/docker/metadata-action/commit/b10b364e15baa3ded91bdbe07911c148aa3134c3"><code>b10b364</code></a> update generated content</li> <li><a href="https://github.com/docker/metadata-action/commit/40a1c6ff523982e692c3ca25150565193d52bc09"><code>40a1c6f</code></a> Bump <code>@docker/actions-toolkit</code> from 0.1.0 to 0.3.0</li> <li><a href="https://github.com/docker/metadata-action/commit/be8ea87c5aac32acaf2a7c98fd1c0a6483323873"><code>be8ea87</code></a> Merge pull request <a href="https://redirect.github.com/docker/metadata-action/issues/294">#294</a> from docker/dependabot/npm_and_yarn/csv-parse-5.4.0</li> <li><a href="https://github.com/docker/metadata-action/commit/dbbf01822bb698575d92e1ee5b9229d58745b0c6"><code>dbbf018</code></a> Merge pull request <a href="https://redirect.github.com/docker/metadata-action/issues/287">#287</a> from docker/dependabot/github_actions/docker/bake-act...</li> <li><a href="https://github.com/docker/metadata-action/commit/72b4ec2b6096d1aa5720167c6af2f33d01dd350e"><code>72b4ec2</code></a> Bump csv-parse from 5.3.8 to 5.4.0</li> <li><a href="https://github.com/docker/metadata-action/commit/00e2c9d34e27bf51149644254039df8da6b7f99d"><code>00e2c9d</code></a> Bump docker/bake-action from 2 to 3</li> <li>See full diff in <a href="https://github.com/docker/metadata-action/compare/c4ee3adeed93b1fa6a762f209fb01608c1a22f1e...2c0bd771b40637d97bf205cbccdd294a32112176">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. You can achieve the same result by closing it manually - `@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>
Add an experimental model called pairwise DPRc, which is fragment-based and integrated with QM/MM. Compression inference and training are supported. Unit tests and documentation have been added. Some features or bugfix to implement this PR have been merged in deepmodeling#2549, deepmodeling#2600, deepmodeling#2601, deepmodeling#2604, deepmodeling#2631, deepmodeling#2635, deepmodeling#2665, deepmodeling#2666, deepmodeling#2667, and deepmodeling#2679. This PR makes some changes to `model.build_descrpt` additionally: - fix errors when the suffix is not empty - fix errors when `fparam` or `aparam` are given - support model-customized `input_map` --------- 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>
…eepmodeling#2688) This is a breaking change. `rcond=1e-3` is found inaccurate. Using NumPy's default value is more accurate and not too slow. --------- 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>
See deepmodeling#2662. Forces and virials will be changed accordingly. One can turn off the new behavior by setting `srtab_add_bias` to False. --------- Signed-off-by: Jinzhe Zeng <jinzhe.zeng@rutgers.edu>
1. Add the nvnmd-v1 with `se_atten` descriptor and 31-type chemical species. nvnmd-v0 is the old version with `se_a` descriptor and 4-type chemical species. 2. Fix the error for map_flt_nvnmd.cpp for nvnmd-v1. An unexpected value of floor(-0.0)=-1 occurred at the index of the mapping table. 3. Improve the documentation about runing nvnmd in bohrium. --------- 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>
<!--pre-commit.ci start--> updates: - [github.com/astral-sh/ruff-pre-commit: v0.0.278 → v0.0.280](astral-sh/ruff-pre-commit@v0.0.278...v0.0.280) <!--pre-commit.ci end--> --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Support the loss for generalized forces. Tests and examples have been
added.
Generalized forces are given by
```math
Q_j = \sum_{i=1}^n \mathbf F_i \cdot \frac {\partial \mathbf r_i} {\partial q_j},\quad j=1,\ldots, m.
```
The loss for generalized forces is given by
```math
L_Q = \frac{1}{m} \sum_{j=1}^m (Q_j - Q_j^*)^2.
```
In the example, the generalized coordinates $q$ are the restraint
coordinates in the enhanced sampling.
This PR also improves documentation for other arguments in the loss.
---------
Signed-off-by: Jinzhe Zeng <jinzhe.zeng@rutgers.edu>
Fix deepmodeling#2627. Move the CLI method to a separate module to avoid the slow import of TensorFlow. The help message will be printed more quickly. --------- Signed-off-by: Jinzhe Zeng <jinzhe.zeng@rutgers.edu>
Although we have set it in `source/lib/src/cuda/CMakeLists.txt`, the main `CMakeLists.txt` needs it. Signed-off-by: Jinzhe Zeng <jinzhe.zeng@rutgers.edu>
Add `fitting_args_plugin` and `loss_args_plugin` into `deepmd.utils.argcheck`. With these decorators, new parameters for fitting and loss can be defined in the external package. --------- 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> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Fix deepmodeling#2712. Signed-off-by: Jinzhe Zeng <jinzhe.zeng@rutgers.edu>
Fix deepmodeling#2656. --------- 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>
Before, `model.ckpt.*` is symilnks to an abosulote path. If users wants to move the whole directory, the relative path will be more user-friendly. --------- Signed-off-by: Jinzhe Zeng <jinzhe.zeng@rutgers.edu>
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>
Codecov ReportPatch coverage:
Additional details and impacted files@@ Coverage Diff @@
## master #2725 +/- ##
==========================================
+ Coverage 76.81% 78.73% +1.91%
==========================================
Files 227 241 +14
Lines 23805 25582 +1777
Branches 1653 1517 -136
==========================================
+ Hits 18286 20141 +1855
- Misses 4421 5049 +628
+ Partials 1098 392 -706
☔ View full report in Codecov by Sentry. |
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