@delta-infra/cli 1.1.17 → 1.1.19

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

@@ -1,66 +1,68 @@
-# LAMMPS 详细规则
-
-所有调用直接使用 `delta-cli science invoke`。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.
-
-最终只复制当前业务响应的 `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
-当前业务响应的 `request` 原样交给 `run`；不得传 CLI 外层 envelope。
+# LAMMPS reference
+
+Make all calls with `delta-cli science invoke`. LAMMPS does not infer data files, atom types,
+potentials or boundary conditions from a formula, CIF or POSCAR. Successful execution does not
+establish physical convergence or production readiness.
+
+## Health
+
+Operation: `health`; no request body.
+
+Key response fields in `data`: `status`, `service`, `lammps_available`,
+`metadata`, and `limits`.
+
+Call this only when the user explicitly asks for a health check; do not add a health call automatically before simulation.
+
+## 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.
+
+In the final reply, include only `last_thermo`, the final step/temperature/total energy,
+warnings, and a summary of output files requested by the user from the current business response.
+Do not divide total energy by the atom count, substitute steps, convert units, or infer
+convergence or stability. For the minimal example, call `lj-melt-example` first, then pass its
+`request` from the current business response to `run` unchanged; do not pass the outer CLI envelope.

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

@@ -1,129 +1,132 @@
-# LDM-BO 详细规则
-
-所有调用直接使用 `delta-cli science invoke`，不是本地 PDF2Dock runner。仅用于小分子 SMILES；
-抗体、CDRH3 或 AntBO 场景必须使用 AntBO 能力边界。
-provider、模型路径、Vina/ReaSyn/GPU/LLM 配置由服务端注入，不放入请求 JSON。
-
-## Health
-
-operation：`health`，无 body。
-
-The response reports whether the adapter can see the mounted PDF2Dock
-interpreter, `bo_api.py`, Vina binary, ReaSyn repo/interpreter/checkpoints, NN
-model files, cache directory, GPU settings, and LLM configuration. Missing LLM
-settings degrade health because LDM methods need them.
-
-## One-Step Recommend
-
-operation：`recommend`。
-
-Wraps `bo_api.recommend_next_smiles`.
-
-Typical payload:
-
-```json
-{
-  "method": "bo-tanimoto",
-  "pool": ["CCO", "CCN", "CCC"],
-  "history": [
-    {"smiles": "CCO", "scores": [-7.1]},
-    {"smiles": "CCN", "scores": [-6.8]}
-  ],
-  "batch_size": 1
-}
-```
-
-Typical business response inside the documented gateway `data`:
-
-```json
-{
-  "recommendations": ["CCC"],
-  "acquisition_values": [0.12],
-  "n_objectives": 1
-}
-```
-
-LDM methods may include an `llm` diagnostics object.
-
-`acquisition_values` 只能按业务响应原值报告。除非当前业务响应明确给出字段定义，否则
-不得把它描述为预测 Vina、预测 objective、不确定性、置信度、expected improvement，
-也不得自行判断“越大/越小越好”。服务未返回推荐理由时，明确写“服务未返回推荐
-理由”，不得根据分子骨架、杂原子或模型机制补写解释。
-
-## Full Trajectory
-
-operation：`trajectory`。
-
-Wraps `bo_api.run_search_trajectory`.
-
-Small smoke payload:
-
-```json
-{
-  "method": "bo-tanimoto",
-  "seed": 42,
-  "seed-smiles": "CCO,CCN,CCC",
-  "num-evaluations": 4,
-  "batch-size": 1,
-  "objective": "vina+nn"
-}
-```
-
-Typical business response inside the documented gateway `data`:
-
-```json
-{
-  "config": {},
-  "history": [],
-  "summary": {}
-}
-```
-
-LDM methods may include `llm_trajectory`.
-
-## Error Handling
-
-The service maps `bo_api` error JSON to an upstream failure. The gateway
-returns a standard error envelope:
-
-```json
-{
-  "code": 1,
-  "message": "AutoDock Vina executable not found...",
-  "data": {
-    "endpoint": "/v1/trajectory",
-    "ldm_bo_response": {
-      "error": "...",
-      "error_type": "ValueError",
-      "traceback": "Traceback ..."
-    }
-  }
-}
-```
-
-Common causes are missing Vina, missing ReaSyn, wrong Python interpreter, CUDA
-device mismatch, missing LLM credentials for LDM methods, or an unwritable Vina
-cache directory.
-
-## Provider Settings
-
-Do not send provider settings in request JSON. The adapter reads these from
-deployment config and passes them as Python kwargs to `bo_api`:
-
-```text
-vina_bin
-vina_cache_dir
-vina_max_workers
-gp_device
-reasyn_repo
-reasyn_python_bin
-reasyn_model_path
-reasyn_devices
-nn_model_path
-nn_metadata_path
-llm_model
-llm_base_url
-llm_api_key
-```
-
-The CLI forwards the user payload; `bo_api` owns business defaults and schema behavior.
+# LDM-BO reference
+
+Make all calls with `delta-cli science invoke`; do not use the local PDF2Dock runner. This tool is
+for small-molecule SMILES only. Use the AntBO capability boundary for antibody, CDRH3 or AntBO
+tasks. The server injects the provider, model paths and Vina/ReaSyn/GPU/LLM settings; do not put
+them in the request JSON.
+
+## Health
+
+Operation: `health`; no request body.
+
+The response reports whether the adapter can see the mounted PDF2Dock
+interpreter, `bo_api.py`, Vina binary, ReaSyn repo/interpreter/checkpoints, NN
+model files, cache directory, GPU settings, and LLM configuration. Missing LLM
+settings degrade health because LDM methods need them.
+
+## One-Step Recommend
+
+Operation: `recommend`.
+
+Wraps `bo_api.recommend_next_smiles`.
+
+Typical payload:
+
+```json
+{
+  "method": "bo-tanimoto",
+  "pool": ["CCO", "CCN", "CCC"],
+  "history": [
+    {"smiles": "CCO", "scores": [-7.1]},
+    {"smiles": "CCN", "scores": [-6.8]}
+  ],
+  "batch_size": 1
+}
+```
+
+Typical business response inside the documented gateway `data`:
+
+```json
+{
+  "recommendations": ["CCC"],
+  "acquisition_values": [0.12],
+  "n_objectives": 1
+}
+```
+
+LDM methods may include an `llm` diagnostics object.
+
+Report `acquisition_values` exactly as returned in the business response. Unless the current
+business response explicitly defines the field, do not describe it as predicted Vina, a predicted
+objective, uncertainty, confidence or expected improvement, and do not infer whether higher or
+lower is better. If the service provides no recommendation rationale, state “The service returned
+no recommendation rationale”; do not add an explanation based on molecular scaffolds, heteroatoms
+or model mechanisms.
+
+## Full Trajectory
+
+Operation: `trajectory`.
+
+Wraps `bo_api.run_search_trajectory`.
+
+Small smoke payload:
+
+```json
+{
+  "method": "bo-tanimoto",
+  "seed": 42,
+  "seed-smiles": "CCO,CCN,CCC",
+  "num-evaluations": 4,
+  "batch-size": 1,
+  "objective": "vina+nn"
+}
+```
+
+Typical business response inside the documented gateway `data`:
+
+```json
+{
+  "config": {},
+  "history": [],
+  "summary": {}
+}
+```
+
+LDM methods may include `llm_trajectory`.
+
+## Error Handling
+
+The service maps `bo_api` error JSON to an upstream failure. The gateway
+returns a standard error envelope:
+
+```json
+{
+  "code": 1,
+  "message": "AutoDock Vina executable not found...",
+  "data": {
+    "endpoint": "/v1/trajectory",
+    "ldm_bo_response": {
+      "error": "...",
+      "error_type": "ValueError",
+      "traceback": "Traceback ..."
+    }
+  }
+}
+```
+
+Common causes are missing Vina, missing ReaSyn, wrong Python interpreter, CUDA
+device mismatch, missing LLM credentials for LDM methods, or an unwritable Vina
+cache directory.
+
+## Provider Settings
+
+Do not send provider settings in request JSON. The adapter reads these from
+deployment config and passes them as Python kwargs to `bo_api`:
+
+```text
+vina_bin
+vina_cache_dir
+vina_max_workers
+gp_device
+reasyn_repo
+reasyn_python_bin
+reasyn_model_path
+reasyn_devices
+nn_model_path
+nn_metadata_path
+llm_model
+llm_base_url
+llm_api_key
+```
+
+The CLI forwards the user payload; `bo_api` owns business defaults and schema behavior.