From d03b4c3b6fb0692e19cde64ebdcc0725d57e0aa9 Mon Sep 17 00:00:00 2001 From: ZihanYAN Date: Tue, 7 Jul 2026 22:32:10 +0800 Subject: [PATCH 1/9] update skills --- AGENTS.md | 5 +- README.md | 10 +- Scripts/README.md | 2 +- Scripts/utils/completion.sh | 2 +- Scripts/utils/skill_info.sh | 58 ++++++++ docs/README_zh-CN.md | 10 +- docs/htmls/404.html | 70 ++++----- docs/htmls/en/active_learning_workflow.html | 2 +- docs/htmls/en/analyzer_scripts.html | 2 +- docs/htmls/en/calculator_scripts.html | 2 +- docs/htmls/en/command_reference.html | 2 +- docs/htmls/en/contributing_to_gpumdkit.html | 2 +- docs/htmls/en/custom_commands.html | 2 +- docs/htmls/en/format_conversion.html | 2 +- docs/htmls/en/index.html | 4 +- docs/htmls/en/plot_scripts.html | 2 +- docs/htmls/en/polar_material_analysis.html | 2 +- docs/htmls/en/quick_start.html | 2 +- docs/htmls/en/structure_sampling.html | 2 +- docs/htmls/en/workflow_scripts.html | 2 +- docs/htmls/index.html | 2 +- docs/htmls/search/search_index.json | 2 +- docs/htmls/sitemap.xml | 108 +++++++------- docs/htmls/sitemap.xml.gz | Bin 614 -> 591 bytes docs/htmls/zh/index.html | 4 +- ...\345\267\245\344\275\234\346\265\201.html" | 2 +- ...\346\236\220\345\267\245\345\205\267.html" | 2 +- ...\344\273\244\345\217\202\350\200\203.html" | 2 +- ...\346\265\201\350\204\232\346\234\254.html" | 2 +- ...\351\200\237\345\205\245\351\227\250.html" | 2 +- ...\346\226\231\345\210\206\346\236\220.html" | 2 +- ...\345\274\217\350\275\254\346\215\242.html" | 2 +- ...\346\236\204\351\207\207\346\240\267.html" | 2 +- ...\345\233\276\350\204\232\346\234\254.html" | 2 +- ...\344\271\211\345\221\275\344\273\244.html" | 2 +- ...\345\231\250\350\204\232\346\234\254.html" | 2 +- ...\347\214\256\346\214\207\345\215\227.html" | 2 +- docs/index.html | 6 +- docs/index_zh.html | 6 +- docs/mkdocs.yml | 2 +- docs/sitemap.xml | 20 +-- docs/tutorials/en/index.md | 2 +- docs/tutorials/zh/index.md | 2 +- docs/updates.info | 2 +- gpumdkit.sh | 4 + skills/README.md | 134 ++++++++---------- skills/gpumdkit-analyzers/SKILL.md | 12 +- skills/gpumdkit-calculators/SKILL.md | 9 +- skills/gpumdkit-contributing/SKILL.md | 9 +- skills/gpumdkit-format-conversion/SKILL.md | 30 +++- skills/gpumdkit-main/SKILL.md | 19 ++- skills/gpumdkit-sampling/SKILL.md | 40 +++--- skills/gpumdkit-visualization/SKILL.md | 13 +- skills/gpumdkit-workflows/SKILL.md | 11 +- 54 files changed, 381 insertions(+), 265 deletions(-) create mode 100644 Scripts/utils/skill_info.sh diff --git a/AGENTS.md b/AGENTS.md index a04d147..b7d33c2 100644 --- a/AGENTS.md +++ b/AGENTS.md @@ -10,13 +10,14 @@ gpumdkit.sh -h # Show all CLI flags gpumdkit.sh -plt train # Plot NEP training gpumdkit.sh -calc msd dump.xyz Li 10 # Calculate MSD gpumdkit.sh -dp2xyz database train.xyz # DeepMD npy → extxyz +gpumdkit.sh -skill # Show agent skill paths and install hints ``` -**Documentation**: https://zhyan0603.github.io/GPUMDkit/ +**Documentation**: https://gpumdkit.cn/ ## Agent Skills -When the user asks about GPUMDkit features, use the skills in `.opencode/skills/`: +When the user asks about GPUMDkit features, use the GPUMDkit skills. The canonical skill source is `${GPUMDkit_path}/skills`; agent tools may use global or project-local symlinks to those skills. Run `gpumdkit.sh -skill` to print the local skill path, available skills, supported install targets, and install hints. | Skill | Use When | |-------|----------| diff --git a/README.md b/README.md index a61e5c8..789d160 100644 --- a/README.md +++ b/README.md @@ -6,10 +6,10 @@  ·  简体中文  ·  - Website  ·  - Documentation + Website  ·  + Documentation  ·  - Gallery + Gallery  

@@ -265,13 +265,13 @@ You can also save images as PNG if your device doesn't support visualization: gpumdkit.sh -plt thermo save ``` -Refer to our [documentation](https://zhyan0603.github.io/GPUMDkit/) for more detailed examples and command options. +Refer to our [documentation](https://gpumdkit.cn/) for more detailed examples and command options. #### Custom Commands `GPUMDkit` now supports custom commands via `~/.gpumdkit.in`. -You can add your own shortcuts (e.g., `gpumdkit.sh -yourcommand`) by defining functions in this file. This allows you to extend `GPUMDkit` with personal scripts. See [custom command documentation](https://zhyan0603.github.io/GPUMDkit/) for details. +You can add your own shortcuts (e.g., `gpumdkit.sh -yourcommand`) by defining functions in this file. This allows you to extend `GPUMDkit` with personal scripts. See [custom command documentation](https://gpumdkit.cn/) for details. #### Tab Completion Support diff --git a/Scripts/README.md b/Scripts/README.md index 51497ab..424a652 100644 --- a/Scripts/README.md +++ b/Scripts/README.md @@ -194,7 +194,7 @@ Check individual subdirectory READMEs for specific requirements. ## Support -- **Documentation**: [https://zhyan0603.github.io/GPUMDkit/home.html](https://zhyan0603.github.io/GPUMDkit/home.html) +- **Documentation**: [https://gpumdkit.cn/home.html](https://gpumdkit.cn/home.html) - **Issues**: [GitHub Issues](https://github.com/zhyan0603/GPUMDkit/issues) - **Contact**: Zihan YAN (yanzihan@westlake.edu.cn) diff --git a/Scripts/utils/completion.sh b/Scripts/utils/completion.sh index 63bf70d..5c06a6e 100644 --- a/Scripts/utils/completion.sh +++ b/Scripts/utils/completion.sh @@ -13,7 +13,7 @@ _gpumdkit_completions() { prev="${COMP_WORDS[COMP_CWORD-1]}" # Previous word # List of primary options (extracted from gpumdkit.sh) - local opts="-h -help -update -U -clean -time -plt -calc -cbc -range -out2xyz -out2exyz -cp2k2xyz -pos2exyz -cif2pos -cif2exyz -exyz2pos -xdat2exyz -pos2lmp -lmp2exyz -traj2exyz -dp2xyz -addgroup -addlabel -addweight -min_dist -min_dist_pbc -filter_dist -filter_dist_pbc -filter_box -filter_value -filter_range -get_frame -clean_xyz -analyze_comp -chem_species -replicate -pda -pynep -frame_range -nep_modifier" + local opts="-h -help -skill -update -U -clean -time -plt -calc -cbc -range -out2xyz -out2exyz -cp2k2xyz -pos2exyz -cif2pos -cif2exyz -exyz2pos -xdat2exyz -pos2lmp -lmp2exyz -traj2exyz -dp2xyz -addgroup -addlabel -addweight -min_dist -min_dist_pbc -filter_dist -filter_dist_pbc -filter_box -filter_value -filter_range -get_frame -clean_xyz -analyze_comp -chem_species -replicate -pda -pynep -frame_range -nep_modifier" # Calculator subcommands local calc_subcmds="ionic-cond nep des doas neb minimize msd nlist disp avg-struct oct-tilt pol-abo3" diff --git a/Scripts/utils/skill_info.sh b/Scripts/utils/skill_info.sh new file mode 100644 index 0000000..c6605b6 --- /dev/null +++ b/Scripts/utils/skill_info.sh @@ -0,0 +1,58 @@ +#!/bin/bash + +# ============================================================ +# GPUMDkit agent skill information helper +# Repository: https://github.com/zhyan0603/GPUMDkit +# Author: Zihan YAN (yanzihan@westlake.edu.cn) +# ============================================================ + +function skill_info_table(){ + echo " +-------------------------------------------------------------------------------------------------------+" + echo " | GPUMDkit Agent Skills |" + echo " +-------------------------------------------------------------------------------------------------------+" + echo " Skill source path:" + echo " ${GPUMDkit_path}/skills" + echo "" + echo " Available skills:" + echo " gpumdkit-main General usage, navigation, and entry point" + echo " gpumdkit-format-conversion Structure file format conversion" + echo " gpumdkit-calculators Material property calculations" + echo " gpumdkit-analyzers Structure analysis and validation" + echo " gpumdkit-visualization Plotting and visualization" + echo " gpumdkit-workflows Batch processing and automation" + echo " gpumdkit-sampling Structure sampling and selection" + echo " gpumdkit-contributing Code conventions and adding new features" + echo "" + echo " Recommended agent behavior:" + echo " Ask the user whether to install skills globally or only for the current project." + echo " Global install is usually better when GPUMDkit is used across multiple projects." + echo " Project install is better when the user wants repository-local configuration." + echo "" + echo " Global install targets:" + echo " OpenCode: ~/.config/opencode/skills" + echo " Claude compat: ~/.claude/skills" + echo " Agents compat: ~/.agents/skills" + echo "" + echo " Project install targets:" + echo " OpenCode: .opencode/skills" + echo " Claude compat: .claude/skills" + echo " Agents compat: .agents/skills" + echo "" + echo " Example: install globally for OpenCode:" + echo " target_dir=\"\${HOME}/.config/opencode/skills\"" + echo " mkdir -p \"\${target_dir}\"" + echo " for skill_dir in \${GPUMDkit_path}/skills/gpumdkit-*; do" + echo " ln -s \"\${skill_dir}\" \"\${target_dir}/\$(basename \"\${skill_dir}\")\"" + echo " done" + echo "" + echo " Example: install for the current project only:" + echo " target_dir=\".opencode/skills\"" + echo " mkdir -p \"\${target_dir}\"" + echo " for skill_dir in \${GPUMDkit_path}/skills/gpumdkit-*; do" + echo " ln -s \"\${skill_dir}\" \"\${target_dir}/\$(basename \"\${skill_dir}\")\"" + echo " done" + echo "" + echo " Replace target_dir with another install target listed above if needed." + echo " Read ${GPUMDkit_path}/skills/README.md for details." + echo " +-------------------------------------------------------------------------------------------------------+" +} diff --git a/docs/README_zh-CN.md b/docs/README_zh-CN.md index 447d5fe..f8bf1bb 100644 --- a/docs/README_zh-CN.md +++ b/docs/README_zh-CN.md @@ -6,10 +6,10 @@  ·  简体中文  ·  - Website  ·  - Documentation + Website  ·  + Documentation  ·  - Gallery + Gallery  

@@ -264,13 +264,13 @@ gpumdkit.sh -plt thermo gpumdkit.sh -plt thermo save ``` -更多详细示例和命令选项请参考我们的[文档](https://zhyan0603.github.io/GPUMDkit/)。 +更多详细示例和命令选项请参考我们的[文档](https://gpumdkit.cn/)。 #### 自定义命令 `GPUMDkit` 支持通过 `~/.gpumdkit.in` 文件自定义命令。 -你可以在该文件中定义函数来添加自己的快捷命令（例如 `gpumdkit.sh -yourcommand`），从而扩展 `GPUMDkit` 的功能。详细用法请参见[自定义命令文档](https://zhyan0603.github.io/GPUMDkit/)。 +你可以在该文件中定义函数来添加自己的快捷命令（例如 `gpumdkit.sh -yourcommand`），从而扩展 `GPUMDkit` 的功能。详细用法请参见[自定义命令文档](https://gpumdkit.cn/)。 #### Tab 补全支持 diff --git a/docs/htmls/404.html b/docs/htmls/404.html index f5696e3..8cb6289 100644 --- a/docs/htmls/404.html +++ b/docs/htmls/404.html @@ -18,7 +18,7 @@ - + @@ -27,10 +27,10 @@ - + - + @@ -114,7 +114,7 @@ - + @@ -148,7 +148,7 @@