@delta-infra/cli 1.0.79 → 1.0.81

package/skills/delta-science/references/delta-bo.md

@@ -0,0 +1,90 @@
+# Delta-BO 详细规则
+
+所有在线调用只走统一 wrapper，tool 固定为 `delta-bo`。当前 CLI catalog 只暴露
+`commands` 和 `generate`；禁止根据旧 HTTP 文档猜测或直连 stateful command API。
+
+## commands
+
+情景：用户要求查看当前部署支持的 Delta-BO 命令。
+
+```python
+result = invoke("delta-bo", "commands")
+native = result["native"]
+```
+
+无 body。只报告当前 native 命令列表，不从历史文档补全。
+
+## generate
+
+情景：针对数值、整数或分类实验变量生成随机搜索或贝叶斯优化建议。
+
+无真实历史，或历史少于 5 条且用户没有明确要求 BO 时，使用有界随机搜索：
+
+```json
+{
+  "params": [
+    {"name": "x", "type": "numeric", "low": 0.0, "high": 1.0}
+  ],
+  "num_suggestions": 3,
+  "algorithm": "random-search",
+  "seed": 42
+}
+```
+
+有真实历史且用户明确要求 BO 时，可以使用：
+
+```json
+{
+  "params": [
+    {"name": "temperature", "type": "numeric", "low": 20.0, "high": 120.0},
+    {"name": "catalyst", "type": "categorical", "choices": ["A", "B", "C"]}
+  ],
+  "objectives": [{"name": "yield", "minimize": false}],
+  "num_suggestions": 2,
+  "algorithm": "bo",
+  "model": {"name": "gp", "min_samples": 2, "train_steps": 50},
+  "acq_target": {"name": "ucb", "beta": 2.0},
+  "solver": {"name": "ga", "pop_size": 40, "n_gen": 10},
+  "histories": {
+    "decisions": [
+      {"temperature": 40.0, "catalyst": "A"},
+      {"temperature": 80.0, "catalyst": "B"}
+    ],
+    "observations": [
+      {"yield": 0.42},
+      {"yield": 0.61}
+    ]
+  },
+  "seed": 7
+}
+```
+
+参数类型仅支持 `numeric`、`integer`、`categorical`。优先使用 object-form history，
+避免数组列顺序歧义。不得编造 observation、目标值或所谓最优点。
+
+可选去重与约束：
+
+```json
+{
+  "diversity": {
+    "deduplicate": true,
+    "min_numeric_distance": {"temperature": 5.0},
+    "prefer_unique_categories": true
+  },
+  "constraints": [
+    {"type": "unique_batch"},
+    {"type": "avoid_seen_decisions"}
+  ]
+}
+```
+
+只报告 native 的 `suggestions`、`suggestion_metadata`、`warnings`、
+`generated_candidate_count` 和 `diversity` 中实际存在的字段。空 suggestions 或失败
+不得用本地 GP、UCB 或随机数替代。
+
+## 已知但未暴露的旧能力
+
+旧服务曾包含 session、space、objective、policy、suggest、observe、loop、status、
+best 等有状态命令，但它们不是当前 Delta CLI operation。本 Skill 只保留这条能力
+边界，不保留 URL 或 curl 示例，也不执行这些操作。需要扩展时，先由 Science Server
+暴露 operation 和请求 schema，再更新本 reference。

package/skills/{gsasii/references/endpoints.md → delta-science/references/gsasii.md}

@@ -1,130 +1,116 @@
-# GSAS-II Endpoint Reference
-
-All paths are relative to `http://111.2.199.31:52317/api/v1`.
-
-## Health
-
-`GET /chem/gsasii/health`
-
-Key response fields in `data`: `status`, `service`, `gsasii_available`,
-`metadata`, and `limits`.
-
-Use this before long simulations/refinements. A healthy service should report
-`data.status == "ok"` and `data.gsasii_available == true`.
-
-## Powder Simulation
-
-`POST /chem/gsasii/powder/simulate`
-
-```json
-{
-  "cif": "<CIF text>",
-  "phase_name": "phase",
-  "instrument_parameters": "<GSAS-II instrument parameter text>",
-  "histogram_name": "simulation",
-  "t_min": 10.0,
-  "t_max": 80.0,
-  "t_step": 0.02,
-  "include_profile": true,
-  "max_profile_points": 1000,
-  "include_reflections": true,
-  "max_reflections": 1000,
-  "return_refined_cif": false,
-  "return_project": false
-}
-```
-
-Use either `t_step` or `n_points`, not both. Optional fields include
-`wavelength`, `radiation`, `scale`, `include_profile`, `max_profile_points`,
-`include_reflections`, `max_reflections`, `return_refined_cif`, and
-`return_project`.
-
-The response includes `profile` points with `x`, `y_calc`, optional background,
-bounded `reflections` with hkl/d-spacing/2theta where available, and metadata.
-If `return_project` is true, `project_base64` contains the GSAS-II `.gpx`
-project. If `return_refined_cif` is true, `refined_cif` contains exported CIF
-text for pymatgen handoff when GSAS-II supports export for the phase.
-
-Notes:
-
-- `cif` should be valid CIF text. If the input is POSCAR/JSON/CSSR/XSF, use
-  `/chem/pymatgen/structure/convert` first with `output_format: "cif"`.
-- `instrument_parameters` should be GSAS-II instrument parameter text such as
-  `INST_XRY.PRM` when instrument-specific simulation is needed.
-- For quick simulation only, `instrument_parameters` may be omitted. The service
-  then generates a simple CW X-ray instrument model from `wavelength` or
-  `radiation` (`CuKa` by default; also supports aliases such as `MoKa`, `CoKa`,
-  `CrKa`, and explicit numeric wavelength).
-- Refinement still requires real `instrument_parameters`.
-- `max_profile_points` controls response sampling. Use small values for smoke
-  tests and larger values for profile comparison.
-- Older deployed gateway images may require `max_profile_points >= 10`.
-
-## Powder Refinement
-
-`POST /chem/gsasii/powder/refine`
-
-```json
-{
-  "powder_data": "<two-column or three-column powder data text>",
-  "powder_format": "xy",
-  "instrument_parameters": "<GSAS-II instrument parameter text>",
-  "phases": [
-    {"name": "phase", "cif": "<CIF text>"}
-  ],
-  "refinement_mode": "rietveld",
-  "refinement_steps": [],
-  "max_cycles": 3,
-  "histogram_name": "powder",
-  "include_profile": true,
-  "max_profile_points": 1000,
-  "include_reflections": true,
-  "max_reflections": 1000,
-  "return_refined_cif": false,
-  "return_project": false
-}
-```
-
-Supported `powder_format` values: `xy`, `xye`, `fxye`, `gsas`, and `csv`.
-
-`refinement_mode: "rietveld"` is currently implemented. `pawley` and `lebail`
-return a clear not-implemented response until the service wires the
-mode-specific GSAS-II setup.
-
-The response includes fit `residuals` when available, phase summaries, sampled
-profile points, bounded `reflections`, warnings, optional `refined_cif`, and
-the optional `.gpx` project.
-
-Notes:
-
-- Use `xy` for simple whitespace-delimited `x y` rows, `xye` for `x y esd`,
-  `csv` for numeric comma-separated rows, or `gsas`/`fxye` for GSAS-like powder
-  formats.
-- `max_cycles: 0` is useful for project-construction smoke tests. Increase it
-  only when the powder data, phase model, instrument file, and refinement steps
-  are realistic.
-- `refinement_steps` is passed to `G2Project.do_refinements`. Keep recipes
-  incremental and inspect `warnings`, `residuals`, and `lst` output.
-- Refinement may return `valid: false` with partial phase/profile information
-  if GSAS-II constructed the project but a refinement step failed.
-
-## Recommended Integration Scripts
-
-From this skill's `scripts/` directory:
-
-```bash
-python3 scripts/smoke_gsasii.py
-```
-
-Runs health, PbSO4 powder simulation, and project-return smoke tests.
-
-```bash
-python3 scripts/workflow_pymatgen_gsasii.py
-```
-
-Runs the cross-service workflow:
-
-```text
-pymatgen summary/symmetry -> pymatgen CIF conversion -> GSAS-II simulation
--> profile comparison -> GSAS-II refinement -> pymatgen final check
-```
+# GSAS-II 详细规则
+
+所有调用只走统一 wrapper。模拟必须使用真实 CIF；精修必须使用真实 powder data、
+instrument parameters 和 phase CIF，任何失败不得用合成数据补齐。输入不是 CIF 时，
+先使用当前任务中成功的 pymatgen `structure-convert` 结果。
+
+## Health
+
+operation：`health`，无 body。
+
+Key response fields in `data`: `status`, `service`, `gsasii_available`,
+`metadata`, and `limits`.
+
+只有用户明确要求健康检查时才调用；不要在模拟或精修前自动增加 health。
+
+## Powder Simulation
+
+operation：`powder-simulate`。
+
+```json
+{
+  "cif": "<CIF text>",
+  "phase_name": "phase",
+  "instrument_parameters": "<GSAS-II instrument parameter text>",
+  "histogram_name": "simulation",
+  "t_min": 10.0,
+  "t_max": 80.0,
+  "t_step": 0.02,
+  "include_profile": true,
+  "max_profile_points": 1000,
+  "include_reflections": true,
+  "max_reflections": 1000,
+  "return_refined_cif": false,
+  "return_project": false
+}
+```
+
+Use either `t_step` or `n_points`, not both. Optional fields include
+`wavelength`, `radiation`, `scale`, `include_profile`, `max_profile_points`,
+`include_reflections`, `max_reflections`, `return_refined_cif`, and
+`return_project`.
+
+The response includes `profile` points with `x`, `y_calc`, optional background,
+bounded `reflections` with hkl/d-spacing/2theta where available, and metadata.
+If `return_project` is true, `project_base64` contains the GSAS-II `.gpx`
+project. If `return_refined_cif` is true, `refined_cif` contains exported CIF
+text for pymatgen handoff when GSAS-II supports export for the phase.
+
+Notes:
+
+- `cif` should be valid CIF text. If the input is POSCAR/JSON/CSSR/XSF, use
+  pymatgen `structure-convert` first with `output_format: "cif"`.
+- `instrument_parameters` should be GSAS-II instrument parameter text such as
+  `INST_XRY.PRM` when instrument-specific simulation is needed.
+- For quick simulation only, `instrument_parameters` may be omitted. The service
+  then generates a simple CW X-ray instrument model from `wavelength` or
+  `radiation` (`CuKa` by default; also supports aliases such as `MoKa`, `CoKa`,
+  `CrKa`, and explicit numeric wavelength).
+- Refinement still requires real `instrument_parameters`.
+- `max_profile_points` controls response sampling. Use small values for smoke
+  tests and larger values for profile comparison.
+- Older deployed gateway images may require `max_profile_points >= 10`.
+
+## Powder Refinement
+
+operation：`powder-refine`。
+
+```json
+{
+  "powder_data": "<two-column or three-column powder data text>",
+  "powder_format": "xy",
+  "instrument_parameters": "<GSAS-II instrument parameter text>",
+  "phases": [
+    {"name": "phase", "cif": "<CIF text>"}
+  ],
+  "refinement_mode": "rietveld",
+  "refinement_steps": [],
+  "max_cycles": 3,
+  "histogram_name": "powder",
+  "include_profile": true,
+  "max_profile_points": 1000,
+  "include_reflections": true,
+  "max_reflections": 1000,
+  "return_refined_cif": false,
+  "return_project": false
+}
+```
+
+Supported `powder_format` values: `xy`, `xye`, `fxye`, `gsas`, and `csv`.
+
+`refinement_mode: "rietveld"` is currently implemented. `pawley` and `lebail`
+return a clear not-implemented response until the service wires the
+mode-specific GSAS-II setup.
+
+The response includes fit `residuals` when available, phase summaries, sampled
+profile points, bounded `reflections`, warnings, optional `refined_cif`, and
+the optional `.gpx` project.
+
+Notes:
+
+- Use `xy` for simple whitespace-delimited `x y` rows, `xye` for `x y esd`,
+  `csv` for numeric comma-separated rows, or `gsas`/`fxye` for GSAS-like powder
+  formats.
+- `max_cycles: 0` is useful for project-construction smoke tests. Increase it
+  only when the powder data, phase model, instrument file, and refinement steps
+  are realistic.
+- `refinement_steps` is passed to `G2Project.do_refinements`. Keep recipes
+  incremental and inspect `warnings`, `residuals`, and `lst` output.
+- Refinement may return `valid: false` with partial phase/profile information
+  if GSAS-II constructed the project but a refinement step failed.
+
+## 跨工具交接
+
+结构转换、衍射模拟和精修必须在本 Skill 内通过 wrapper 逐步完成：
+`pymatgen structure-convert -> gsasii powder-simulate/powder-refine`。下游只使用上一步
+成功 native 中的结构文本或 profile；不得执行本地脚本或直连服务。

package/skills/{lammps/references/endpoints.md → delta-science/references/lammps.md}

@@ -1,61 +1,66 @@
-# LAMMPS Endpoint Reference
-
-All paths are relative to `http://111.2.199.31:52317/api/v1`.
-
-## Health
-
-`GET /chem/lammps/health`
-
-Key response fields in `data`: `status`, `service`, `lammps_available`,
-`metadata`, and `limits`.
-
-Use this before long simulations. A healthy service should report
-`data.status == "ok"` and `data.lammps_available == true`.
-
-## Built-In Lennard-Jones Example
-
-`GET /chem/lammps/examples/lj-melt`
-
-Returns a complete `request` payload for `/chem/lammps/run`, plus workflow notes
-showing where pymatgen and GSAS-II fit around LAMMPS.
-
-## Run
-
-`POST /chem/lammps/run`
-
-```json
-{
-  "input_script": "<LAMMPS input script>",
-  "files": [
-    {"path": "system.data", "content": "<LAMMPS data file text>", "encoding": "text"}
-  ],
-  "timeout_seconds": 30,
-  "max_thermo_rows": 1000,
-  "log_tail_lines": 200,
-  "output_files": ["dump.lammpstrj", "final.data"],
-  "include_log": true,
-  "include_stdout": false,
-  "include_stderr": false
-}
-```
-
-`files` are written into a fresh job working directory before LAMMPS starts.
-`encoding` can be `text` or `base64`.
-
-The response includes parsed thermo rows, the final thermo row, atom count when
-detectable, log tail, warnings, and requested output files. Text output files
-return `content`; binary output files return `content_base64`.
-
-Notes:
-
-- Use relative file paths only.
-- The service rejects unsafe commands such as `shell`, `python`, `plugin`, and
-  `jump` by default.
-- `include <relative-file>` is allowed when the included file is supplied in
-  `files`; absolute paths, parent-directory traversal, URLs, and `jump` loops
-  are rejected.
-- Dump/data products are returned as raw requested output files, not structured
-  parsed atom-frame objects.
-- The gateway is synchronous; keep interactive runs short.
-- Force-field choice is caller responsibility. The service executes explicit
-  LAMMPS input and does not infer potentials from formulas or structures.
+# LAMMPS 详细规则
+
+所有调用只走统一 wrapper。LAMMPS 不从化学式、CIF 或 POSCAR 自动推断 data、原子
+类型、势函数与边界条件。成功执行不表示物理收敛或生产可用。
+
+## Health
+
+operation：`health`，无 body。
+
+Key response fields in `data`: `status`, `service`, `lammps_available`,
+`metadata`, and `limits`.
+
+只有用户明确要求健康检查时才调用；不要在模拟前自动增加 health。
+
+## Built-In Lennard-Jones Example
+
+operation：`lj-melt-example`。
+
+Returns a complete `request` payload for the `run` operation, plus workflow notes
+showing where pymatgen and GSAS-II fit around LAMMPS.
+
+## Run
+
+operation：`run`。
+
+```json
+{
+  "input_script": "<LAMMPS input script>",
+  "files": [
+    {"path": "system.data", "content": "<LAMMPS data file text>", "encoding": "text"}
+  ],
+  "timeout_seconds": 30,
+  "max_thermo_rows": 1000,
+  "log_tail_lines": 200,
+  "output_files": ["dump.lammpstrj", "final.data"],
+  "include_log": true,
+  "include_stdout": false,
+  "include_stderr": false
+}
+```
+
+`files` are written into a fresh job working directory before LAMMPS starts.
+`encoding` can be `text` or `base64`.
+
+The response includes parsed thermo rows, the final thermo row, atom count when
+detectable, log tail, warnings, and requested output files. Text output files
+return `content`; binary output files return `content_base64`.
+
+Notes:
+
+- Use relative file paths only.
+- The service rejects unsafe commands such as `shell`, `python`, `plugin`, and
+  `jump` by default.
+- `include <relative-file>` is allowed when the included file is supplied in
+  `files`; absolute paths, parent-directory traversal, URLs, and `jump` loops
+  are rejected.
+- Dump/data products are returned as raw requested output files, not structured
+  parsed atom-frame objects.
+- The gateway is synchronous; keep interactive runs short.
+- Force-field choice is caller responsibility. The service executes explicit
+  LAMMPS input and does not infer potentials from formulas or structures.
+
+最终只复制当前 native 的 `last_thermo`、final step/temperature/total energy、
+warnings 和用户要求的输出文件摘要。禁止把总能量除以原子数、替换步数、换算单位或
+推测收敛性、稳定性。最小示例必须先调用 `lj-melt-example`，再把其
+`native["request"]` 原样交给 `run`；不得传 wrapper 外层 envelope。