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deepmodeling / deepmd-kit

A deep learning package for many-body potential energy representation and molecular dynamics
https://docs.deepmodeling.com/projects/deepmd/
GNU Lesser General Public License v3.0
1.41k stars 487 forks source link

docs: improve multi-backend documentation #3875

Closed njzjz closed 3 weeks ago

njzjz commented 3 weeks ago

Summary by CodeRabbit

coderabbitai[bot] commented 3 weeks ago
Walkthrough ## Walkthrough The changes primarily update documentation to enhance clarity and improve compatibility across TensorFlow and PyTorch implementations in the DeePMD-kit project. Key modifications include revising "graph files" to "model files," introducing new command-line flags (`--tf` for TensorFlow and `--pt` for PyTorch), and adjusting command syntax in various training and testing documentation sections. Additionally, some descriptions are refined to avoid referencing specific code sources. ## Changes | File Path | Change Summary | |----------------------------------------------------|------------------------------------------------------------------------------------------------------------------------------------------------------------------------------| | `doc/freeze/freeze.md` | Updated terminology to replace `protobuf(.pb)` with `model file`, removed reference to "Morgan," and adjusted freezing process description. | | `doc/model/sel.md` | Added `--tf` and `--pt` flags to `dp neighbor-stat` command for framework-specific neighbor statistics calculations. | | `doc/test/model-deviation.md`, `doc/third-party/gromacs.md` | Changed `graph files` to `model files` in descriptions and command outputs. | | `doc/third-party/lammps-command.md` | Updated `pair_style deepmd` command by adding `graph_1.pth` and modifying `out_freq` value to `100`. | | `doc/train/training-advanced.md` | Added a TensorFlow icon to the `sel` adjustment section of a frozen model. | | `doc/train/training.md` | Introduced command-line options `--tf` for TensorFlow and `--pt` for PyTorch in DeePMD-kit training commands. | | `doc/troubleshooting/howtoset_num_nodes.md` | Reformatted content to include separate configurations for TensorFlow and PyTorch parallelism settings. | | `doc/model/train-fitting-dos.md` | Updated supported backends information, added PyTorch training and testing commands, and adjusted freezing and testing commands for both TensorFlow and PyTorch backends. | ## Sequence Diagram(s) (Sequence diagrams are not provided because the changes primarily involve documentation updates and enhancements, rather than new features or control flow modifications.)
Recent review details **Configuration used: CodeRabbit UI** **Review profile: CHILL**
Commits Files that changed from the base of the PR and between e935163563f53670e7641caebfc752373ee29756 and 6ca1ce295d1c2c21f55a3cb4c26d3691667d6a20.
Files selected for processing (1) * doc/model/train-fitting-dos.md (3 hunks)
Additional context used
Learnings (1)
doc/model/train-fitting-dos.md (1)
``` User: njzjz PR: deepmodeling/deepmd-kit#3875 File: doc/model/train-fitting-dos.md:107-107 Timestamp: 2024-06-13T16:32:13.786Z Learning: For code blocks in `doc/model/train-fitting-dos.md` that display commands, use 'txt' as the language specification as per user njzjz's preference. ```
LanguageTool
doc/model/train-fitting-dos.md
[uncategorized] ~6-~6: Possible missing comma found. (AI_HYDRA_LEO_MISSING_COMMA) Context: ...rch_icon }}, DP {{ dpmodel_icon }} ::: Here we present an API to DeepDOS model, whi... --- [uncategorized] ~17-~17: Possible missing preposition found. (AI_HYDRA_LEO_MISSING_IN) Context: ...g and validation data are also provided our examples. But note that **the data prov... --- [uncategorized] ~40-~40: Possible missing article found. (AI_HYDRA_LEO_MISSING_THE) Context: ...te that the length of `dos` provided in training set should be the same. - The rest argu... --- [uncategorized] ~70-~70: Possible missing comma found. (AI_HYDRA_LEO_MISSING_COMMA) Context: ...er` mode. - `pref_dos` and `pref_ados`, respectively specify the weight of global and atomic... --- [grammar] ~71-~71: The pronoun ‘We’ must be used with a non-third-person form of a verb. (NON3PRS_VERB) Context: ...uded in the training process. - We also provides a combination training of vector and it...
Markdownlint
doc/model/train-fitting-dos.md
28-28: Column: 1 (MD010, no-hard-tabs) Hard tabs --- 29-29: Column: 1 (MD010, no-hard-tabs) Hard tabs --- 30-30: Column: 1 (MD010, no-hard-tabs) Hard tabs --- 31-31: Column: 1 (MD010, no-hard-tabs) Hard tabs --- 32-32: Column: 1 (MD010, no-hard-tabs) Hard tabs --- 33-33: Column: 1 (MD010, no-hard-tabs) Hard tabs --- 34-34: Column: 1 (MD010, no-hard-tabs) Hard tabs --- 35-35: Column: 1 (MD010, no-hard-tabs) Hard tabs --- 36-36: Column: 1 (MD010, no-hard-tabs) Hard tabs --- 56-56: Column: 1 (MD010, no-hard-tabs) Hard tabs --- 57-57: Column: 1 (MD010, no-hard-tabs) Hard tabs --- 58-58: Column: 1 (MD010, no-hard-tabs) Hard tabs --- 59-59: Column: 1 (MD010, no-hard-tabs) Hard tabs --- 60-60: Column: 1 (MD010, no-hard-tabs) Hard tabs --- 61-61: Column: 1 (MD010, no-hard-tabs) Hard tabs --- 62-62: Column: 1 (MD010, no-hard-tabs) Hard tabs --- 63-63: Column: 1 (MD010, no-hard-tabs) Hard tabs --- 64-64: Column: 1 (MD010, no-hard-tabs) Hard tabs --- 65-65: Column: 1 (MD010, no-hard-tabs) Hard tabs --- 66-66: Column: 1 (MD010, no-hard-tabs) Hard tabs --- 107-107: null (MD040, fenced-code-language) Fenced code blocks should have a language specified --- 164-164: null (MD040, fenced-code-language) Fenced code blocks should have a language specified --- 172-172: null (MD040, fenced-code-language) Fenced code blocks should have a language specified
Additional comments not posted (1)
doc/model/train-fitting-dos.md (1)
`4-4`: Ensure consistency in icon usage for DPModel across the documentation.
Verification successful --- The search results indicate that the usage of the `{{ dpmodel_icon }}` appears consistent across the documentation files. The icon is used in various markdown files in a uniform manner. - `doc/backend.md` - `doc/model/dpa2.md` - `doc/model/train-se-atten.md` - `doc/model/train-se-e2-r.md` - `doc/model/train-se-e3.md` - `doc/model/train-hybrid.md` - `doc/model/train-fitting-dos.md` - `doc/model/train-energy-spin.md` - `doc/model/pairtab.md` - `doc/model/train-energy.md` - `doc/model/train-fitting-tensor.md` - `doc/model/dprc.md` - `doc/model/train-se-e2-a.md` No inconsistencies were found in the usage of the DPModel icon.
Scripts executed The following scripts were executed for the analysis: --- Script: ```shell #!/bin/bash # Description: Verify consistency in DPModel icon usage across documentation. # Test: Search for inconsistent DPModel icon usage. Expect: Consistent syntax. rg --type markdown '{{ dpmodel_icon }}' ``` Length of output: 135 --- --- Script: ```shell #!/bin/bash # Description: Verify consistency in DPModel icon usage across documentation. # Test: Search for inconsistent DPModel icon usage. Expect: Consistent syntax. rg --type markdown '\{\{ dpmodel_icon \}\}' ``` Length of output: 3021
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codecov[bot] commented 3 weeks ago

Codecov Report

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

Project coverage is 82.70%. Comparing base (5342a05) to head (6ca1ce2). Report is 1 commits behind head on devel.

Additional details and impacted files ```diff @@ Coverage Diff @@ ## devel #3875 +/- ## ======================================= Coverage 82.70% 82.70% ======================================= Files 517 517 Lines 50141 50141 Branches 2984 2985 +1 ======================================= Hits 41469 41469 Misses 7762 7762 Partials 910 910 ```

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