deepmd-kit chore: provide multiple typemap zbl torch

This PR resolves #3433

Mar 08 '24 07:03 anyangml

Codecov Report

All modified and coverable lines are covered by tests :white_check_mark:

Project coverage is 82.15%. Comparing base (ee47e75) to head (71b0fe4).

:exclamation: Current head 71b0fe4 differs from pull request most recent head e407d39. Consider uploading reports for the commit e407d39 to get more accurate results

Additional details and impacted files

@@           Coverage Diff           @@
##            devel    #3435   +/-   ##
=======================================
  Coverage   82.15%   82.15%           
=======================================
  Files         511      511           
  Lines       47364    47364           
  Branches     2952     2952           
=======================================
  Hits        38910    38910           
  Misses       7561     7561           
  Partials      893      893

:umbrella: View full report in Codecov by Sentry.
:loudspeaker: Have feedback on the report? Share it here.

Mar 08 '24 07:03 codecov[bot]

@wanghan-iapcm feels like we can leave this unchanged based on our discussion.

during training, user knows what type_map to use, thus, three models should share the same type_map.
during fine tuning, the new type_map should also be the same for three models, and the old type_map stored in sub-models will be remapped to the new type_map.

we can probably close this PR and the Issue.

Mar 12 '24 10:03 anyangml

Walkthrough

The recent update to DeePMD-kit broadens its interoperability by incorporating support for PyTorch and DP models alongside the existing TensorFlow backend. This enhancement facilitates more versatile handling of pairwise potentials in interpolation or combination scenarios, thereby expanding the toolkit's applicability in molecular dynamics simulations.

Changes

File Path	Changes
`.../pairtab.md`	Added icons and text to indicate support for PyTorch and DP models in sections discussing interpolation and combination with pairwise potentials. Updated supported backends to include TensorFlow, PyTorch, and DP. Adjusted existing sections to specify TensorFlow support explicitly.

Recent Review Details

Configuration used: CodeRabbit UI Review profile: CHILL

Commits

Files that changed from the base of the PR and between ee47e75748e70ac979ed54379b316e2465bcaf78 and e407d39263a8f6b6599b60bac2bf27a3d04423fd.

Files selected for processing (1)

doc/model/pairtab.md (3 hunks)

Additional Context Used

LanguageTool (104)

doc/model/pairtab.md (104)

Near line 1: Don’t put a space after the opening parenthesis. Context: ... combination with a pairwise potential {{ tensorflow_icon }} {{ pytorch_icon }} {{...

Near line 1: Don’t put a space before the closing parenthesis. Context: ... a pairwise potential {{ tensorflow_icon }} {{ pytorch_icon }} {{ dpmodel_icon }} ...

Near line 1: Don’t put a space after the opening parenthesis. Context: ...irwise potential {{ tensorflow_icon }} {{ pytorch_icon }} {{ dpmodel_icon }} :::{...

Near line 1: Don’t put a space before the closing parenthesis. Context: ...al {{ tensorflow_icon }} {{ pytorch_icon }} {{ dpmodel_icon }} :::{note} **Suppor...

Near line 1: Don’t put a space after the opening parenthesis. Context: ... tensorflow_icon }} {{ pytorch_icon }} {{ dpmodel_icon }} :::{note} **Supported b...

Near line 1: Don’t put a space before the closing parenthesis. Context: ...on }} {{ pytorch_icon }} {{ dpmodel_icon }} :::{note} Supported backends: Ten...

Near line 4: Don’t put a space after the opening parenthesis. Context: ...te} Supported backends: TensorFlow {{ tensorflow_icon }}, PyTorch {{ pytorch_i...

Near line 4: Don’t put a space before the closing parenthesis. Context: ...ackends**: TensorFlow {{ tensorflow_icon }}, PyTorch {{ pytorch_icon }}, DP {{ dpm...

Near line 4: Don’t put a space after the opening parenthesis. Context: ...sorFlow {{ tensorflow_icon }}, PyTorch {{ pytorch_icon }}, DP {{ dpmodel_icon }} :...

Near line 4: Don’t put a space before the closing parenthesis. Context: ...sorflow_icon }}, PyTorch {{ pytorch_icon }}, DP {{ dpmodel_icon }} ::: ## Theory ...

Near line 4: Don’t put a space after the opening parenthesis. Context: ...con }}, PyTorch {{ pytorch_icon }}, DP {{ dpmodel_icon }} ::: ## Theory In appli...

Near line 4: Don’t put a space before the closing parenthesis. Context: ...h {{ pytorch_icon }}, DP {{ dpmodel_icon }} ::: ## Theory In applications like t...

Near line 9: Possible spelling mistake found. Context: ...ke the radiation damage simulation, the interatomic distance may become too close, so that ...

Near line 10: Possible spelling mistake found. Context: ...ced by an empirical potential, like the Ziegler-Biersack-Littmark (ZBL) screened nuclear repulsion potent...

Near line 11: Possible spelling mistake found. Context: ...n the radiation damage simulations. The DeePMD-kit package supports the interpolation betw...

Near line 16: This sentence does not start with an uppercase letter. Context: ...w_i (E_i^0 + E_i^{\mathrm{pair}}), ``` where the $w_i$ is the interpolation weight a...

Near line 17: Possible spelling mistake found. Context: ... + E_i^{\mathrm{pair}}), ``` where the $w_i$ is the interpolation weight and the ...

Near line 17: Possible spelling mistake found. Context: ...E_i^{\mathrm{pair}}), ``` where the $w_i$ is the interpolation weight and the $E_...

Near line 17: Possible spelling mistake found. Context: ..._i$ is the interpolation weight and the $E_i^{\mathrm{pair}} $ is the atomic cont...

Near line 17: Possible spelling mistake found. Context: ...the interpolation weight and the $E_i^{\mathrm{pair}} $ is the atomic contribution du...

Near line 17: Possible typo: you repeated a whitespace Context: ...tion weight and the $E_i^{\mathrm{pair}} $ is the atomic contribution due to the ...

Near line 17: Possible spelling mistake found. Context: ...tribution due to the pairwise potential $u^{\mathrm{pair}}(r)$, i.e. ```math E_...

Near line 17: Possible spelling mistake found. Context: ...tion due to the pairwise potential $u^{\mathrm{pair}}(r)$, i.e. ```math E_i^{\mathr...

Near line 23: Possible spelling mistake found. Context: ...(r_{ij}). The interpolation weight $w_i$ is defined by math w_i = ...

Near line 23: Possible spelling mistake found. Context: ...{ij}). The interpolation weight $w_i$ is defined by math w_i = \b...

Near line 33: This sentence does not start with an uppercase letter. Context: ...\sigma_i \geq r_b, \end{cases} ``` where $u_i = (\sigma_i - r_a ) / (r_b - r_a)$...

Near line 34: Possible spelling mistake found. Context: ..._i \geq r_b, \end{cases} ``` where $u_i = (\sigma_i - r_a ) / (r_b - r_a)$. $...

Near line 34: Don’t put a space before the closing parenthesis. Context: ...cases} ``` where $u_i = (\sigma_i - r_a ) / (r_b - r_a)$. $E_i^0$ is the atom ene...

Near line 34: Possible spelling mistake found. Context: ...u_i = (\sigma_i - r_a ) / (r_b - r_a)$. $E_i^0$ is the atom energy bias. In the ra...

Near line 35: The currency mark is usually put at the beginning of the number. Context: ... (\sigma_i - r_a ) / (r_b - r_a)$. $E_i^0$ is the atom energy bias. In the range $...

Near line 36: Possible spelling mistake found. Context: ...ise potential smoothly switched on from $r_b$ to $r_a$. The $\sigma_i$ is the soft...

Near line 36: Possible spelling mistake found. Context: ... potential smoothly switched on from $r_b$ to $r_a$. The $\sigma_i$ is the softmin...

Near line 36: Possible spelling mistake found. Context: ...tial smoothly switched on from $r_b$ to $r_a$. The $\sigma_i$ is the softmin of th...

Near line 36: Possible spelling mistake found. Context: ...l smoothly switched on from $r_b$ to $r_a$. The $\sigma_i$ is the softmin of the d...

Near line 36: Possible spelling mistake found. Context: ...hed on from $r_b$ to $r_a$. The $\sigma_i$ is the softmin of the distance between ...

Near line 36: Possible spelling mistake found. Context: ...m $r_b$ to $r_a$. The $\sigma_i$ is the softmin of the distance between atom $i$ and it...

Near line 36: Possible spelling mistake found. Context: ...he softmin of the distance between atom $i$ and its neighbors, ```math \sigma_i ...

Near line 45: Possible spelling mistake found. Context: ...alpha_s}}, ``` where the scale $\alpha_s$ is a tunable scale of the interatomic d...

Near line 45: Possible spelling mistake found. Context: ...le $\alpha_s$ is a tunable scale of the interatomic distance $r_{ij}$. The pairwise potenti...

Near line 45: Possible spelling mistake found. Context: ...nable scale of the interatomic distance $r_{ij}$. The pairwise potential $u^{\text...

Near line 46: Possible spelling mistake found. Context: ...stance $r_{ij}$. The pairwise potential $u^{\textrm{pair}}(r)$ is defined by a use...

Near line 46: Possible spelling mistake found. Context: ...e $r_{ij}$. The pairwise potential $u^{\textrm{pair}}(r)$ is defined by a user-defined...

Near line 46: Possible spelling mistake found. Context: ...efined table that provides the value of $u^{\textrm{pair}}$ on an evenly discretiz...

Near line 46: Possible spelling mistake found. Context: ...d table that provides the value of $u^{\textrm{pair}}$ on an evenly discretized grid f...

Near line 48: Possible spelling mistake found. Context: ....[^1] [^1]: This section is built upon Jinzhe Zeng, Duo Zhang, Denghui Lu, Pinghui Mo...

Near line 48: Possible spelling mistake found. Context: ...[^1]: This section is built upon Jinzhe Zeng, Duo Zhang, Denghui Lu, Pinghui Mo, Zey...

Near line 48: Possible spelling mistake found. Context: ...n is built upon Jinzhe Zeng, Duo Zhang, Denghui Lu, Pinghui Mo, Zeyu Li, Yixiao Chen, M...

Near line 48: Possible spelling mistake found. Context: ...pon Jinzhe Zeng, Duo Zhang, Denghui Lu, Pinghui Mo, Zeyu Li, Yixiao Chen, Marián Rynik,...

Near line 48: Possible spelling mistake found. Context: ...eng, Duo Zhang, Denghui Lu, Pinghui Mo, Zeyu Li, Yixiao Chen, Marián Rynik, Li'ang H...

Near line 48: Possible spelling mistake found. Context: ...Zhang, Denghui Lu, Pinghui Mo, Zeyu Li, Yixiao Chen, Marián Rynik, Li'ang Huang, Ziyao...

Near line 48: Possible spelling mistake found. Context: ...i Lu, Pinghui Mo, Zeyu Li, Yixiao Chen, Marián Rynik, Li'ang Huang, Ziyao Li, Shaochen...

Near line 48: Possible spelling mistake found. Context: ...inghui Mo, Zeyu Li, Yixiao Chen, Marián Rynik, Li'ang Huang, Ziyao Li, Shaochen Shi, ...

Near line 48: Possible spelling mistake found. Context: ...ixiao Chen, Marián Rynik, Li'ang Huang, Ziyao Li, Shaochen Shi, Yingze Wang, Haotian ...

Near line 48: Possible spelling mistake found. Context: ..., Marián Rynik, Li'ang Huang, Ziyao Li, Shaochen Shi, Yingze Wang, Haotian Ye, Ping Tuo,...

Near line 48: Possible spelling mistake found. Context: ..., Li'ang Huang, Ziyao Li, Shaochen Shi, Yingze Wang, Haotian Ye, Ping Tuo, Jiabin Yang...

Near line 48: Possible spelling mistake found. Context: ...g, Ziyao Li, Shaochen Shi, Yingze Wang, Haotian Ye, Ping Tuo, Jiabin Yang, Ye Ding, Yif...

Near line 48: Possible spelling mistake found. Context: ...chen Shi, Yingze Wang, Haotian Ye, Ping Tuo, Jiabin Yang, Ye Ding, Yifan Li, Davide...

Near line 48: Possible spelling mistake found. Context: ...Shi, Yingze Wang, Haotian Ye, Ping Tuo, Jiabin Yang, Ye Ding, Yifan Li, Davide Tisi, Q...

Near line 48: Possible spelling mistake found. Context: ...ian Ye, Ping Tuo, Jiabin Yang, Ye Ding, Yifan Li, Davide Tisi, Qiyu Zeng, Han Bao, Yu...

Near line 48: Possible spelling mistake found. Context: ... Jiabin Yang, Ye Ding, Yifan Li, Davide Tisi, Qiyu Zeng, Han Bao, Yu Xia, Jiameng Hu...

Near line 48: Possible spelling mistake found. Context: ...n Yang, Ye Ding, Yifan Li, Davide Tisi, Qiyu Zeng, Han Bao, Yu Xia, Jiameng Huang, K...

Near line 48: Possible spelling mistake found. Context: ...g, Ye Ding, Yifan Li, Davide Tisi, Qiyu Zeng, Han Bao, Yu Xia, Jiameng Huang, Koki M...

Near line 48: Possible spelling mistake found. Context: ...an Li, Davide Tisi, Qiyu Zeng, Han Bao, Yu Xia, Jiameng Huang, Koki Muraoka, Yibo ...

Near line 48: Possible spelling mistake found. Context: ...avide Tisi, Qiyu Zeng, Han Bao, Yu Xia, Jiameng Huang, Koki Muraoka, Yibo Wang, Junhan ...

Near line 48: Possible spelling mistake found. Context: ...u Zeng, Han Bao, Yu Xia, Jiameng Huang, Koki Muraoka, Yibo Wang, Junhan Chang, Fengb...

Near line 48: Possible spelling mistake found. Context: ...g, Han Bao, Yu Xia, Jiameng Huang, Koki Muraoka, Yibo Wang, Junhan Chang, Fengbo Yuan, ...

Near line 48: Possible spelling mistake found. Context: ...o, Yu Xia, Jiameng Huang, Koki Muraoka, Yibo Wang, Junhan Chang, Fengbo Yuan, Sigbjø...

Near line 48: Possible spelling mistake found. Context: ...Jiameng Huang, Koki Muraoka, Yibo Wang, Junhan Chang, Fengbo Yuan, Sigbjørn Løland Bor...

Near line 48: Possible spelling mistake found. Context: ... Koki Muraoka, Yibo Wang, Junhan Chang, Fengbo Yuan, Sigbjørn Løland Bore, Chun Cai, Y...

Near line 48: Possible spelling mistake found. Context: ..., Yibo Wang, Junhan Chang, Fengbo Yuan, Sigbjørn Løland Bore, Chun Cai, Yinnian Lin, Bo ...

Near line 48: Possible spelling mistake found. Context: ...ng, Junhan Chang, Fengbo Yuan, Sigbjørn Løland Bore, Chun Cai, Yinnian Lin, Bo Wang, J...

Near line 48: Possible spelling mistake found. Context: ...ang, Fengbo Yuan, Sigbjørn Løland Bore, Chun Cai, Yinnian Lin, Bo Wang, Jiayan Xu, J...

Near line 48: Possible spelling mistake found. Context: ...Fengbo Yuan, Sigbjørn Løland Bore, Chun Cai, Yinnian Lin, Bo Wang, Jiayan Xu, Jia-X...

Near line 48: Possible spelling mistake found. Context: ...o Yuan, Sigbjørn Løland Bore, Chun Cai, Yinnian Lin, Bo Wang, Jiayan Xu, Jia-Xin Zhu, C...

Near line 48: Possible spelling mistake found. Context: ...d Bore, Chun Cai, Yinnian Lin, Bo Wang, Jiayan Xu, Jia-Xin Zhu, Chenxing Luo, Yuzhi Zh...

Near line 48: Possible spelling mistake found. Context: ... Chun Cai, Yinnian Lin, Bo Wang, Jiayan Xu, Jia-Xin Zhu, Chenxing Luo, Yuzhi Zhang...

Near line 48: Possible spelling mistake found. Context: ...n Cai, Yinnian Lin, Bo Wang, Jiayan Xu, Jia-Xin Zhu, Chenxing Luo, Yuzhi Zhang, Rhys E....

Near line 48: Possible spelling mistake found. Context: ...n Lin, Bo Wang, Jiayan Xu, Jia-Xin Zhu, Chenxing Luo, Yuzhi Zhang, Rhys E. A. Goodall, W...

Near line 48: Possible spelling mistake found. Context: ... Wang, Jiayan Xu, Jia-Xin Zhu, Chenxing Luo, Yuzhi Zhang, Rhys E. A. Goodall, Wensh...

Near line 48: Possible spelling mistake found. Context: ..., Jiayan Xu, Jia-Xin Zhu, Chenxing Luo, Yuzhi Zhang, Rhys E. A. Goodall, Wenshuo Lian...

Near line 48: Possible spelling mistake found. Context: ...g Luo, Yuzhi Zhang, Rhys E. A. Goodall, Wenshuo Liang, Anurag Kumar Singh, Sikai Yao, J...

Near line 48: Possible spelling mistake found. Context: ...ang, Rhys E. A. Goodall, Wenshuo Liang, Anurag Kumar Singh, Sikai Yao, Jingchao Zhang,...

Near line 48: Possible spelling mistake found. Context: ...all, Wenshuo Liang, Anurag Kumar Singh, Sikai Yao, Jingchao Zhang, Renata Wentzcovitc...

Near line 48: Possible spelling mistake found. Context: ...enshuo Liang, Anurag Kumar Singh, Sikai Yao, Jingchao Zhang, Renata Wentzcovitch, J...

Near line 48: Possible spelling mistake found. Context: ...o Liang, Anurag Kumar Singh, Sikai Yao, Jingchao Zhang, Renata Wentzcovitch, Jiequn Han,...

Near line 48: Possible spelling mistake found. Context: ...ingh, Sikai Yao, Jingchao Zhang, Renata Wentzcovitch, Jiequn Han, Jie Liu, Weile Jia, Darrin...

Near line 48: Possible spelling mistake found. Context: ...o, Jingchao Zhang, Renata Wentzcovitch, Jiequn Han, Jie Liu, Weile Jia, Darrin M. York...

Near line 48: Possible spelling mistake found. Context: ...Zhang, Renata Wentzcovitch, Jiequn Han, Jie Liu, Weile Jia, Darrin M. York, Weinan ...

Near line 48: Possible spelling mistake found. Context: ...nata Wentzcovitch, Jiequn Han, Jie Liu, Weile Jia, Darrin M. York, Weinan E, Roberto ...

Near line 48: Possible spelling mistake found. Context: ...entzcovitch, Jiequn Han, Jie Liu, Weile Jia, Darrin M. York, Weinan E, Roberto Car,...

Near line 48: Possible spelling mistake found. Context: ...an, Jie Liu, Weile Jia, Darrin M. York, Weinan E, Roberto Car, Linfeng Zhang, Han Wang...

Near line 48: Possible spelling mistake found. Context: ... Darrin M. York, Weinan E, Roberto Car, Linfeng Zhang, Han Wang, [J. Chem. Phys. 159, 0...

Near line 49: Possible spelling mistake found. Context: ...creativecommons.org/licenses/by/4.0/). DeePMD-kit also supports combination with a pairwi...

Near line 50: Don’t put a space after the opening parenthesis. Context: ... combination with a pairwise potential {{ tensorflow_icon }}: ```math E_i = E_i...

Near line 50: Don’t put a space before the closing parenthesis. Context: ... a pairwise potential {{ tensorflow_icon }}: ```math E_i = E_i^{\mathrm{DP}} + ...

Near line 58: Possible spelling mistake found. Context: ...uld be a text file that can be read by {py:meth}numpy.loadtxt. The first column ...

Near line 58: Possible spelling mistake found. Context: ... text file that can be read by {py:meth}numpy.loadtxt. The first column is the dista...

Near line 59: You might be missing the article “the” here. Context: ...s the distance between two atoms, where upper range should be larger than the cutoff ...

Near line 66: Possible spelling mistake found. Context: ...ng the available interaction data. This extrapolative procedure guarantees a smooth transitio...

Near line 81: Possible spelling mistake found. Context: ...low uses a normal DP model" } ``` {ref}sw_rmin <model/sw_rmin> and {ref}`sw_rmax...

Near line 81: Possible spelling mistake found. Context: ...{ref}sw_rmin <model/sw_rmin> and {ref}sw_rmax <model/sw_rmax> must be smaller t...

Near line 83: Don’t put a space after the opening parenthesis. Context: ... Combination with a pairwise potential {{ tensorflow_icon }} To combine with a pa...

Near line 83: Don’t put a space before the closing parenthesis. Context: ... a pairwise potential {{ tensorflow_icon }} To combine with a pairwise potential,...

Near line 105: Possible spelling mistake found. Context: ... "sel": 534 } ] } ``` The {ref}rcut <model[pairtab]/rcut> can be larger th...

Additional comments not posted (4)

doc/model/pairtab.md (4)

1-4: Changes accurately reflect the expanded backend support. Good use of visual icons to denote supported models.

50-50: Inclusion of the TensorFlow icon here maintains visual consistency across the document.

83-83: The JSON configuration example is clear and enhances the documentation by providing practical usage guidance.

Line range hint 9-48: The mathematical expressions and their descriptions are well-detailed and informative, adding educational value to the documentation.

Thank you for using CodeRabbit. We offer it for free to the OSS community and would appreciate your support in helping us grow. If you find it useful, would you consider giving us a shout-out on your favorite social media?

Share

Tips

Chat

There are 3 ways to chat with CodeRabbit:

Review comments: Directly reply to a review comment made by CodeRabbit. Example:
- I pushed a fix in commit <commit_id>.
- Generate unit testing code for this file.
- Open a follow-up GitHub issue for this discussion.
Files and specific lines of code (under the "Files changed" tab): Tag @coderabbitai in a new review comment at the desired location with your query. Examples:
- @coderabbitai generate unit testing code for this file.
- @coderabbitai modularize this function.
PR comments: Tag @coderabbitai in a new PR comment to ask questions about the PR branch. For the best results, please provide a very specific query, as very limited context is provided in this mode. Examples:
- @coderabbitai generate interesting stats about this repository and render them as a table.
- @coderabbitai show all the console.log statements in this repository.
- @coderabbitai read src/utils.ts and generate unit testing code.
- @coderabbitai read the files in the src/scheduler package and generate a class diagram using mermaid and a README in the markdown format.

Note: Be mindful of the bot's finite context window. It's strongly recommended to break down tasks such as reading entire modules into smaller chunks. For a focused discussion, use review comments to chat about specific files and their changes, instead of using the PR comments.

CodeRabbit Commands (invoked as PR comments)

@coderabbitai pause to pause the reviews on a PR.
@coderabbitai resume to resume the paused reviews.
@coderabbitai review to trigger a review. This is useful when automatic reviews are disabled for the repository.
@coderabbitai resolve resolve all the CodeRabbit review comments.
@coderabbitai help to get help.

Additionally, you can add @coderabbitai ignore anywhere in the PR description to prevent this PR from being reviewed.

CodeRabbit Configration File (`.coderabbit.yaml`)

You can programmatically configure CodeRabbit by adding a .coderabbit.yaml file to the root of your repository.
Please see the configuration documentation for more information.
If your editor has YAML language server enabled, you can add the path at the top of this file to enable auto-completion and validation: # yaml-language-server: $schema=https://coderabbit.ai/integrations/schema.v2.json

Documentation and Community

Visit our Documentation for detailed information on how to use CodeRabbit.
Join our Discord Community to get help, request features, and share feedback.
Follow us on X/Twitter for updates and announcements.

Apr 30 '24 10:04 coderabbitai[bot]

deepmd-kit deepmd-kit copied to clipboard

chore: provide multiple typemap zbl torch

Codecov Report

Walkthrough

Changes

Chat

CodeRabbit Commands (invoked as PR comments)

CodeRabbit Configration File (.coderabbit.yaml)

Documentation and Community

deepmd-kit
deepmd-kit copied to clipboard

CodeRabbit Configration File (`.coderabbit.yaml`)