feat(build): Add Git archives version files #3670
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…ng#3219) Co-authored-by: Han Wang <wang_han@iapcm.ac.cn>
Fix deepmodeling#3214. Signed-off-by: Jinzhe Zeng <jinzhe.zeng@rutgers.edu>
Fix deepmodeling#3045. All memory leaks have been fixed! --------- 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 is to provide backend independent implementation of PairTabModel in `numpy`. Also the cross framework `serialization` and `deserialization` are added. --------- Co-authored-by: Anyang Peng <aisi_ap@Anyangs-Laptop.local> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
add shape hit to doc string. Co-authored-by: Han Wang <wang_han@iapcm.ac.cn>
…ling#3226) To be consistent with TF, as discussed in deepmodeling#3213 (comment). Old PT models are expected to be incompatible. Signed-off-by: Jinzhe Zeng <jinzhe.zeng@rutgers.edu>
We can change the format of the global logger in the future if the additional information is helpful (e.g., time, path, etc). --------- Signed-off-by: Jinzhe Zeng <jinzhe.zeng@rutgers.edu>
Signed-off-by: Jinzhe Zeng <jinzhe.zeng@rutgers.edu>
Avoid installing tensorflow as build requires when `DP_ENABLE_TENSORFLOW` is `0`. Signed-off-by: Jinzhe Zeng <jinzhe.zeng@rutgers.edu>
- mv all dpmodel related UTs to a separate directory - split the large test_model_format_utils.py as tests for different modules. --------- Co-authored-by: Han Wang <wang_han@iapcm.ac.cn>
…modeling#3235) Co-authored-by: Han Wang <wang_han@iapcm.ac.cn>
Bumps [codecov/codecov-action](https://github.com/codecov/codecov-action) from 3 to 4. <details> <summary>Release notes</summary> <p><em>Sourced from <a href="https://github.com/codecov/codecov-action/releases">codecov/codecov-action's releases</a>.</em></p> <blockquote> <h2>v4.0.0</h2> <p>v4 of the Codecov Action uses the <a href="https://docs.codecov.com/docs/the-codecov-cli">CLI</a> as the underlying upload. The CLI has helped to power new features including local upload, the global upload token, and new upcoming features.</p> <h2>Breaking Changes</h2> <ul> <li>The Codecov Action runs as a <code>node20</code> action due to <code>node16</code> deprecation. See <a href="https://github.blog/changelog/2023-09-22-github-actions-transitioning-from-node-16-to-node-20/">this post from GitHub</a> on how to migrate.</li> <li>Tokenless uploading is unsupported. However, PRs made from forks to the upstream public repos will support tokenless (e.g. contributors to OS projects do not need the upstream repo's Codecov token). This <a href="https://docs.codecov.com/docs/adding-the-codecov-token#github-actions">doc</a> shows instructions on how to add the Codecov token.</li> <li>OS platforms have been added, though some may not be automatically detected. To see a list of platforms, see our <a href="https://cli.codecov.io">CLI download page</a></li> <li>Various arguments to the Action have been changed. Please be aware that the arguments match with the CLI's needs</li> </ul> <p><code>v3</code> versions and below will not have access to CLI features (e.g. global upload token, ATS).</p> <h2>What's Changed</h2> <ul> <li>build(deps): bump openpgp from 5.8.0 to 5.9.0 by <a href="https://github.com/dependabot"><code>@dependabot</code></a> in <a href="https://redirect.github.com/codecov/codecov-action/pull/985">codecov/codecov-action#985</a></li> <li>build(deps): bump actions/checkout from 3.0.0 to 3.5.3 by <a href="https://github.com/dependabot"><code>@dependabot</code></a> in <a href="https://redirect.github.com/codecov/codecov-action/pull/1000">codecov/codecov-action#1000</a></li> <li>build(deps): bump ossf/scorecard-action from 2.1.3 to 2.2.0 by <a href="https://github.com/dependabot"><code>@dependabot</code></a> in <a href="https://redirect.github.com/codecov/codecov-action/pull/1006">codecov/codecov-action#1006</a></li> <li>build(deps): bump tough-cookie from 4.0.0 to 4.1.3 by <a href="https://github.com/dependabot"><code>@dependabot</code></a> in <a href="https://redirect.github.com/codecov/codecov-action/pull/1013">codecov/codecov-action#1013</a></li> <li>build(deps-dev): bump word-wrap from 1.2.3 to 1.2.4 by <a href="https://github.com/dependabot"><code>@dependabot</code></a> in <a href="https://redirect.github.com/codecov/codecov-action/pull/1024">codecov/codecov-action#1024</a></li> <li>build(deps): bump node-fetch from 3.3.1 to 3.3.2 by <a href="https://github.com/dependabot"><code>@dependabot</code></a> in <a href="https://redirect.github.com/codecov/codecov-action/pull/1031">codecov/codecov-action#1031</a></li> <li>build(deps-dev): bump <code>@types/node</code> from 20.1.4 to 20.4.5 by <a href="https://github.com/dependabot"><code>@dependabot</code></a> in <a href="https://redirect.github.com/codecov/codecov-action/pull/1032">codecov/codecov-action#1032</a></li> <li>build(deps): bump github/codeql-action from 1.0.26 to 2.21.2 by <a href="https://github.com/dependabot"><code>@dependabot</code></a> in <a href="https://redirect.github.com/codecov/codecov-action/pull/1033">codecov/codecov-action#1033</a></li> <li>build commit,report and upload args based on codecovcli by <a href="https://github.com/dana-yaish"><code>@dana-yaish</code></a> in <a href="https://redirect.github.com/codecov/codecov-action/pull/943">codecov/codecov-action#943</a></li> <li>build(deps-dev): bump <code>@types/node</code> from 20.4.5 to 20.5.3 by <a href="https://github.com/dependabot"><code>@dependabot</code></a> in <a href="https://redirect.github.com/codecov/codecov-action/pull/1055">codecov/codecov-action#1055</a></li> <li>build(deps): bump github/codeql-action from 2.21.2 to 2.21.4 by <a href="https://github.com/dependabot"><code>@dependabot</code></a> in <a href="https://redirect.github.com/codecov/codecov-action/pull/1051">codecov/codecov-action#1051</a></li> <li>build(deps-dev): bump <code>@types/node</code> from 20.5.3 to 20.5.4 by <a href="https://github.com/dependabot"><code>@dependabot</code></a> in <a href="https://redirect.github.com/codecov/codecov-action/pull/1058">codecov/codecov-action#1058</a></li> <li>chore(deps): update outdated deps by <a href="https://github.com/thomasrockhu-codecov"><code>@thomasrockhu-codecov</code></a> in <a href="https://redirect.github.com/codecov/codecov-action/pull/1059">codecov/codecov-action#1059</a></li> <li>build(deps-dev): bump <code>@types/node</code> from 20.5.4 to 20.5.6 by <a href="https://github.com/dependabot"><code>@dependabot</code></a> in <a href="https://redirect.github.com/codecov/codecov-action/pull/1060">codecov/codecov-action#1060</a></li> <li>build(deps-dev): bump <code>@typescript-eslint/parser</code> from 6.4.1 to 6.5.0 by <a href="https://github.com/dependabot"><code>@dependabot</code></a> in <a href="https://redirect.github.com/codecov/codecov-action/pull/1065">codecov/codecov-action#1065</a></li> <li>build(deps-dev): bump <code>@typescript-eslint/eslint-plugin</code> from 6.4.1 to 6.5.0 by <a href="https://github.com/dependabot"><code>@dependabot</code></a> in <a href="https://redirect.github.com/codecov/codecov-action/pull/1064">codecov/codecov-action#1064</a></li> <li>build(deps): bump actions/checkout from 3.5.3 to 3.6.0 by <a href="https://github.com/dependabot"><code>@dependabot</code></a> in <a href="https://redirect.github.com/codecov/codecov-action/pull/1063">codecov/codecov-action#1063</a></li> <li>build(deps-dev): bump eslint from 8.47.0 to 8.48.0 by <a href="https://github.com/dependabot"><code>@dependabot</code></a> in <a href="https://redirect.github.com/codecov/codecov-action/pull/1061">codecov/codecov-action#1061</a></li> <li>build(deps-dev): bump <code>@types/node</code> from 20.5.6 to 20.5.7 by <a href="https://github.com/dependabot"><code>@dependabot</code></a> in <a href="https://redirect.github.com/codecov/codecov-action/pull/1062">codecov/codecov-action#1062</a></li> <li>build(deps): bump openpgp from 5.9.0 to 5.10.1 by <a href="https://github.com/dependabot"><code>@dependabot</code></a> in <a href="https://redirect.github.com/codecov/codecov-action/pull/1066">codecov/codecov-action#1066</a></li> <li>build(deps-dev): bump <code>@types/node</code> from 20.5.7 to 20.5.9 by <a href="https://github.com/dependabot"><code>@dependabot</code></a> in <a href="https://redirect.github.com/codecov/codecov-action/pull/1070">codecov/codecov-action#1070</a></li> <li>build(deps): bump github/codeql-action from 2.21.4 to 2.21.5 by <a href="https://github.com/dependabot"><code>@dependabot</code></a> in <a href="https://redirect.github.com/codecov/codecov-action/pull/1069">codecov/codecov-action#1069</a></li> <li>build(deps-dev): bump <code>@typescript-eslint/eslint-plugin</code> from 6.5.0 to 6.6.0 by <a href="https://github.com/dependabot"><code>@dependabot</code></a> in <a href="https://redirect.github.com/codecov/codecov-action/pull/1072">codecov/codecov-action#1072</a></li> <li>Update README.md by <a href="https://github.com/thomasrockhu-codecov"><code>@thomasrockhu-codecov</code></a> in <a href="https://redirect.github.com/codecov/codecov-action/pull/1073">codecov/codecov-action#1073</a></li> <li>build(deps-dev): bump <code>@typescript-eslint/parser</code> from 6.5.0 to 6.6.0 by <a href="https://github.com/dependabot"><code>@dependabot</code></a> in <a href="https://redirect.github.com/codecov/codecov-action/pull/1071">codecov/codecov-action#1071</a></li> <li>build(deps-dev): bump <code>@vercel/ncc</code> from 0.36.1 to 0.38.0 by <a href="https://github.com/dependabot"><code>@dependabot</code></a> in <a href="https://redirect.github.com/codecov/codecov-action/pull/1074">codecov/codecov-action#1074</a></li> <li>build(deps): bump <code>@actions/core</code> from 1.10.0 to 1.10.1 by <a href="https://github.com/dependabot"><code>@dependabot</code></a> in <a href="https://redirect.github.com/codecov/codecov-action/pull/1081">codecov/codecov-action#1081</a></li> <li>build(deps-dev): bump <code>@typescript-eslint/eslint-plugin</code> from 6.6.0 to 6.7.0 by <a href="https://github.com/dependabot"><code>@dependabot</code></a> in <a href="https://redirect.github.com/codecov/codecov-action/pull/1080">codecov/codecov-action#1080</a></li> <li>build(deps): bump actions/checkout from 3.6.0 to 4.0.0 by <a href="https://github.com/dependabot"><code>@dependabot</code></a> in <a href="https://redirect.github.com/codecov/codecov-action/pull/1078">codecov/codecov-action#1078</a></li> <li>build(deps): bump actions/upload-artifact from 3.1.2 to 3.1.3 by <a href="https://github.com/dependabot"><code>@dependabot</code></a> in <a href="https://redirect.github.com/codecov/codecov-action/pull/1077">codecov/codecov-action#1077</a></li> <li>build(deps-dev): bump <code>@types/node</code> from 20.5.9 to 20.6.0 by <a href="https://github.com/dependabot"><code>@dependabot</code></a> in <a href="https://redirect.github.com/codecov/codecov-action/pull/1075">codecov/codecov-action#1075</a></li> <li>build(deps-dev): bump <code>@typescript-eslint/parser</code> from 6.6.0 to 6.7.0 by <a href="https://github.com/dependabot"><code>@dependabot</code></a> in <a href="https://redirect.github.com/codecov/codecov-action/pull/1079">codecov/codecov-action#1079</a></li> <li>build(deps-dev): bump eslint from 8.48.0 to 8.49.0 by <a href="https://github.com/dependabot"><code>@dependabot</code></a> in <a href="https://redirect.github.com/codecov/codecov-action/pull/1076">codecov/codecov-action#1076</a></li> <li>use cli instead of node uploader by <a href="https://github.com/dana-yaish"><code>@dana-yaish</code></a> in <a href="https://redirect.github.com/codecov/codecov-action/pull/1068">codecov/codecov-action#1068</a></li> <li>chore(release): 4.0.0-beta.1 by <a href="https://github.com/thomasrockhu-codecov"><code>@thomasrockhu-codecov</code></a> in <a href="https://redirect.github.com/codecov/codecov-action/pull/1084">codecov/codecov-action#1084</a></li> <li>not adding -n if empty to do-upload command by <a href="https://github.com/dana-yaish"><code>@dana-yaish</code></a> in <a href="https://redirect.github.com/codecov/codecov-action/pull/1085">codecov/codecov-action#1085</a></li> <li>4.0.0-beta.2 by <a href="https://github.com/thomasrockhu-codecov"><code>@thomasrockhu-codecov</code></a> in <a href="https://redirect.github.com/codecov/codecov-action/pull/1086">codecov/codecov-action#1086</a></li> </ul> <!-- raw HTML omitted --> </blockquote> <p>... (truncated)</p> </details> <details> <summary>Changelog</summary> <p><em>Sourced from <a href="https://github.com/codecov/codecov-action/blob/main/CHANGELOG.md">codecov/codecov-action's changelog</a>.</em></p> <blockquote> <h2>4.0.0-beta.2</h2> <h3>Fixes</h3> <ul> <li><a href="https://redirect.github.com/codecov/codecov-action/issues/1085">#1085</a> not adding -n if empty to do-upload command</li> </ul> <h2>4.0.0-beta.1</h2> <p><code>v4</code> represents a move from the <a href="https://github.com/codecov/uploader">universal uploader</a> to the <a href="https://github.com/codecov/codecov-cli">Codecov CLI</a>. Although this will unlock new features for our users, the CLI is not yet at feature parity with the universal uploader.</p> <h3>Breaking Changes</h3> <ul> <li>No current support for <code>aarch64</code> and <code>alpine</code> architectures.</li> <li>Tokenless uploading is unsuported</li> <li>Various arguments to the Action have been removed</li> </ul> <h2>3.1.4</h2> <h3>Fixes</h3> <ul> <li><a href="https://redirect.github.com/codecov/codecov-action/issues/967">#967</a> Fix typo in README.md</li> <li><a href="https://redirect.github.com/codecov/codecov-action/issues/971">#971</a> fix: add back in working dir</li> <li><a href="https://redirect.github.com/codecov/codecov-action/issues/969">#969</a> fix: CLI option names for uploader</li> </ul> <h3>Dependencies</h3> <ul> <li><a href="https://redirect.github.com/codecov/codecov-action/issues/970">#970</a> build(deps-dev): bump <code>@types/node</code> from 18.15.12 to 18.16.3</li> <li><a href="https://redirect.github.com/codecov/codecov-action/issues/979">#979</a> build(deps-dev): bump <code>@types/node</code> from 20.1.0 to 20.1.2</li> <li><a href="https://redirect.github.com/codecov/codecov-action/issues/981">#981</a> build(deps-dev): bump <code>@types/node</code> from 20.1.2 to 20.1.4</li> </ul> <h2>3.1.3</h2> <h3>Fixes</h3> <ul> <li><a href="https://redirect.github.com/codecov/codecov-action/issues/960">#960</a> fix: allow for aarch64 build</li> </ul> <h3>Dependencies</h3> <ul> <li><a href="https://redirect.github.com/codecov/codecov-action/issues/957">#957</a> build(deps-dev): bump jest-junit from 15.0.0 to 16.0.0</li> <li><a href="https://redirect.github.com/codecov/codecov-action/issues/958">#958</a> build(deps): bump openpgp from 5.7.0 to 5.8.0</li> <li><a href="https://redirect.github.com/codecov/codecov-action/issues/959">#959</a> build(deps-dev): bump <code>@types/node</code> from 18.15.10 to 18.15.12</li> </ul> <h2>3.1.2</h2> <h3>Fixes</h3> <ul> <li><a href="https://redirect.github.com/codecov/codecov-action/issues/718">#718</a> Update README.md</li> <li><a href="https://redirect.github.com/codecov/codecov-action/issues/851">#851</a> Remove unsupported path_to_write_report argument</li> <li><a href="https://redirect.github.com/codecov/codecov-action/issues/898">#898</a> codeql-analysis.yml</li> <li><a href="https://redirect.github.com/codecov/codecov-action/issues/901">#901</a> Update README to contain correct information - inputs and negate feature</li> <li><a href="https://redirect.github.com/codecov/codecov-action/issues/955">#955</a> fix: add in all the extra arguments for uploader</li> </ul> <h3>Dependencies</h3> <ul> <li><a href="https://redirect.github.com/codecov/codecov-action/issues/819">#819</a> build(deps): bump openpgp from 5.4.0 to 5.5.0</li> <li><a href="https://redirect.github.com/codecov/codecov-action/issues/835">#835</a> build(deps): bump node-fetch from 3.2.4 to 3.2.10</li> <li><a href="https://redirect.github.com/codecov/codecov-action/issues/840">#840</a> build(deps): bump ossf/scorecard-action from 1.1.1 to 2.0.4</li> <li><a href="https://redirect.github.com/codecov/codecov-action/issues/841">#841</a> build(deps): bump <code>@actions/core</code> from 1.9.1 to 1.10.0</li> <li><a href="https://redirect.github.com/codecov/codecov-action/issues/843">#843</a> build(deps): bump <code>@actions/github</code> from 5.0.3 to 5.1.1</li> <li><a href="https://redirect.github.com/codecov/codecov-action/issues/869">#869</a> build(deps): bump node-fetch from 3.2.10 to 3.3.0</li> <li><a href="https://redirect.github.com/codecov/codecov-action/issues/872">#872</a> build(deps-dev): bump jest-junit from 13.2.0 to 15.0.0</li> <li><a href="https://redirect.github.com/codecov/codecov-action/issues/879">#879</a> build(deps): bump decode-uri-component from 0.2.0 to 0.2.2</li> </ul> <!-- raw HTML omitted --> </blockquote> <p>... (truncated)</p> </details> <details> <summary>Commits</summary> <ul> <li><a href="https://github.com/codecov/codecov-action/commit/e0b68c6749509c5f83f984dd99a76a1c1a231044"><code>e0b68c6</code></a> fix: show both token uses in readme (<a href="https://redirect.github.com/codecov/codecov-action/issues/1250">#1250</a>)</li> <li><a href="https://github.com/codecov/codecov-action/commit/1f9f5573d12d0967fe14551018a4b25610226551"><code>1f9f557</code></a> Add all args (<a href="https://redirect.github.com/codecov/codecov-action/issues/1245">#1245</a>)</li> <li><a href="https://github.com/codecov/codecov-action/commit/09686fcfcb6453414a5acd7f3a939670a7a77826"><code>09686fc</code></a> Update README.md (<a href="https://redirect.github.com/codecov/codecov-action/issues/1243">#1243</a>)</li> <li><a href="https://github.com/codecov/codecov-action/commit/f30e4959ba63075080d4f7f90cacc18d9f3fafd7"><code>f30e495</code></a> fix: update action.yml (<a href="https://redirect.github.com/codecov/codecov-action/issues/1240">#1240</a>)</li> <li><a href="https://github.com/codecov/codecov-action/commit/a7b945cea47ad44d8340fae2b004cb982191264f"><code>a7b945c</code></a> fix: allow for other archs (<a href="https://redirect.github.com/codecov/codecov-action/issues/1239">#1239</a>)</li> <li><a href="https://github.com/codecov/codecov-action/commit/98ab2c591b94478f4c3606d68ff73601df85ec43"><code>98ab2c5</code></a> Update package.json (<a href="https://redirect.github.com/codecov/codecov-action/issues/1238">#1238</a>)</li> <li><a href="https://github.com/codecov/codecov-action/commit/43235cc5aeeafd8aeb836fe7d647599acead161c"><code>43235cc</code></a> Update README.md (<a href="https://redirect.github.com/codecov/codecov-action/issues/1237">#1237</a>)</li> <li><a href="https://github.com/codecov/codecov-action/commit/0cf8684c821546a4e0c8c9a4cf4f21a7a0c5014b"><code>0cf8684</code></a> chore(ci): bump to node20 (<a href="https://redirect.github.com/codecov/codecov-action/issues/1236">#1236</a>)</li> <li><a href="https://github.com/codecov/codecov-action/commit/8e1e730371bf82c744e8ca9aa469e2b7011542ce"><code>8e1e730</code></a> build(deps-dev): bump <code>@typescript-eslint/eslint-plugin</code> from 6.19.1 to 6.20.0 ...</li> <li><a href="https://github.com/codecov/codecov-action/commit/61293af0e8288c75266030376a088c781ec81c18"><code>61293af</code></a> build(deps-dev): bump <code>@typescript-eslint/parser</code> from 6.19.1 to 6.20.0 (<a href="https://redirect.github.com/codecov/codecov-action/issues/1235">#1235</a>)</li> <li>Additional commits viewable in <a href="https://github.com/codecov/codecov-action/compare/v3...v4">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 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> Co-authored-by: Jinzhe Zeng <jinzhe.zeng@rutgers.edu>
…ing#3237) [A segfault](https://github.com/deepmodeling/deepmd-kit/actions/runs/7782245372/job/21218255452) sometimes appears in the tests after deepmodeling#3223. The reason is that the required shape of the electric field is set to nall * 3 in the C interface, but a vector of nloc * 3 is given in the tests and lammps and used in the C++ interface. It was not caught before, as the program didn't write to these addresses (only reading it usually won't cause a segfault, unless the address is invalid). Perhaps fix deepmodeling#2895. --------- Signed-off-by: Jinzhe Zeng <jinzhe.zeng@rutgers.edu>
<!--pre-commit.ci start--> updates: - [github.com/astral-sh/ruff-pre-commit: v0.1.14 → v0.2.0](astral-sh/ruff-pre-commit@v0.1.14...v0.2.0) <!--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>
We don't need to pin them to a specific tag. This can close deepmodeling#3230. Signed-off-by: Jinzhe Zeng <jinzhe.zeng@rutgers.edu>
The `deepmd.tf.cluster.slurm` is too specialized - we are not able to support every cluster. This PR uses mpi4py as the alternatives, considering the documentation has asked users to install mpi4py. --------- Signed-off-by: Jinzhe Zeng <jinzhe.zeng@rutgers.edu>
…pmodeling#3234) Co-authored-by: Han Wang <wang_han@iapcm.ac.cn>
Signed-off-by: Jinzhe Zeng <jinzhe.zeng@rutgers.edu> Co-authored-by: Han Wang <92130845+wanghan-iapcm@users.noreply.github.com>
Co-authored-by: Han Wang <wang_han@iapcm.ac.cn>
…3240) solve some virial shape issue: should be [9] rather than [3,3] --------- Co-authored-by: Han Wang <wang_han@iapcm.ac.cn>
This PR is to implement general linear combination of several DPAtomicModels with user defined weights, as well as a special case ZBLModel with weights calculated based on this paper: `Appl. Phys. Lett. 114, 244101 (2019); doi: 10.1063/1.5098061` --------- Co-authored-by: Anyang Peng <aisi_ap@Anyangs-Laptop.local> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Han Wang <92130845+wanghan-iapcm@users.noreply.github.com> Co-authored-by: Han Wang <wang_han@iapcm.ac.cn>
Signed-off-by: Jinzhe Zeng <jinzhe.zeng@rutgers.edu>
hessian not implemented in neither tf nor pt. Co-authored-by: Han Wang <wang_han@iapcm.ac.cn>
Implement high-level `DeepEval` and low-level `DeepEvalBackend`. Ugly things: (1) `DipoleChargeModifier` is not updated in this PR. Thus, it still inherits from the old `DeepEval`. (It should not inherit from `DeepEval`!!!) (2) There are no unit tests or testing models for DeepGlobarPolar or DeepWFC. (3) The shape of the atomic tensor looks different from forces and atomic virials. TODO: - [x] Add docs --------- Signed-off-by: Jinzhe Zeng <jinzhe.zeng@rutgers.edu> Co-authored-by: Han Wang <92130845+wanghan-iapcm@users.noreply.github.com>
This PR is to fix LinearAtomicModel GPU compatibility. --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Fix deepmodeling#3118. Note: head is not supported yet in DeepEval --------- Signed-off-by: Jinzhe Zeng <jinzhe.zeng@rutgers.edu>
Signed-off-by: Jinzhe Zeng <jinzhe.zeng@rutgers.edu>
Restore deepmodeling#3233 with resolved conflicts and conversations. This PR clean up the data stat process from model init. Please note that this code PR is just an initial cleanup and refinement of the data stat, and a more detailed design of the data stat will be completed in the next PR: - independent data stat from dataloader - data stat support for hybrid descriptors --------- Signed-off-by: Duo <50307526+iProzd@users.noreply.github.com> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
…modeling#3254) To have the same behavior between TF and PT. Signed-off-by: Jinzhe Zeng <jinzhe.zeng@rutgers.edu>
Fix deepmodeling#3568. Set run path for libtorch and protobuf. Refactor the original `TensorFlow_LIBRARY_PATH` to `BACKEND_LIBRARY_PATH` (list). --------- Signed-off-by: Jinzhe Zeng <jinzhe.zeng@rutgers.edu>
- clean up the interface of `change_out_bias` - refact `compute_output_stats`, so the code is more readable. --------- Co-authored-by: Han Wang <wang_han@iapcm.ac.cn>
To solve this issue: deepmodeling#3641 --------- Signed-off-by: Jinzhe Zeng <jinzhe.zeng@rutgers.edu> Co-authored-by: robinzyb <yzhuang@cseasrv4.epfl.ch> 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>
Replace quick_start.ipynb with a new version. Aligned English tutorial with Chinese version(https://nb.bohrium.dp.tech/detail/3313403083) in structure and content. --------- Signed-off-by: Xu zhangmancang <myron_cang@icloud.com> Co-authored-by: Mancn <mancn@MancndeMacBook-Pro.local> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
This PR: - breaking change: the base atomic model is now a module. - reason: the out stat is a data attribute of the base atomic model. - implement the `compute_or_load_output_stat` for the base atomic model. the method computes both bias and std. - the derived atomic models call the `compute_or_load_output_stat` method for computing output stat. - atomic model provides the `apply_out_stat`, the derived class may override the method to define how the statistics is applied to an atomic model's output. @anyangml may need. - `out_stat` support statistics of output tensor of any shape. @iProzd please check if i took it correctly in [ce7ec1f](deepmodeling@ce7ec1f) To be done: - atomic statistics of the bias and std. @anyangml - erialization and deserialization. --------- Signed-off-by: Han Wang <92130845+wanghan-iapcm@users.noreply.github.com> Co-authored-by: Han Wang <wang_han@iapcm.ac.cn> Co-authored-by: Duo <50307526+iProzd@users.noreply.github.com> 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>
Refactor stat related methods in LinearAtomicModel. This should resolve deepmodeling#3585 deepmodeling#3586 deepmodeling#3528 --------- Signed-off-by: Anyang Peng <137014849+anyangml@users.noreply.github.com> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
…eepmodeling#3652) By default, `pytorch.distributed` is not enabled on macOS by default (see [`pytorch.distributed.is_available()`](https://pytorch.org/docs/stable/distributed.html#torch.distributed.is_available)). In this case, * Testing `pytorch.distributed.is_initialized()` will fail. To fix this issue, `pytorch.distributed.is_available()` needs to be tested first. * Distributed dataloader is not available. This pull request allows passing the unittests while `distributed` is disabled. `USE_DISTRIBUTED=1` to manually enable distributed training / dataloading on macOS. Set it to `0` to disable it on other platforms. Maybe this behavior needs to be documented somewhere? --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
…keLists.txt (deepmodeling#3653) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
I construct a test case in which all old implementations fail. --------- Signed-off-by: Jinzhe Zeng <jinzhe.zeng@rutgers.edu>
…g#3650) Co-authored-by: Han Wang <wang_han@iapcm.ac.cn>
) Fix the following error in docker_package_c.sh ``` -- Found Git: /usr/bin/git (found version "2.25.1") fatal: detected dubious ownership in repository at '/root/deepmd-kit' To add an exception for this directory, call: git config --global --add safe.directory /root/deepmd-kit ``` In addition, fetching git tags in actions/checkout. --------- Signed-off-by: Jinzhe Zeng <jinzhe.zeng@rutgers.edu>
<!--pre-commit.ci start--> updates: - [github.com/pre-commit/pre-commit-hooks: v4.5.0 → v4.6.0](pre-commit/pre-commit-hooks@v4.5.0...v4.6.0) - [github.com/pre-commit/mirrors-clang-format: v18.1.2 → v18.1.3](pre-commit/mirrors-clang-format@v18.1.2...v18.1.3) <!--pre-commit.ci end--> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
…tput stat (deepmodeling#3649) - implement serialize and deserialize for atomic model's compute output stat - intensive change to the linear atomic models' serialization. @anyangml please help checking the changes. --------- Co-authored-by: Han Wang <wang_han@iapcm.ac.cn>
`var_name` is no longer required as user input for `polar` and `dipole`. --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
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