@delta-infra/cli 1.1.17 → 1.1.18

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

@@ -1,68 +1,69 @@
-# pymatgen 详细规则
-
-所有调用直接使用 `delta-cli science invoke`。无机化学式、组成和式量优先使用 pymatgen，不用 PubChem
-或本地元素表替代。结构 operation 必须发送完整结构文本，不能发送本地文件路径；
-支持 `cif`、`poscar`、`json`、`cssr`、`xsf`，不接收 LAMMPS data/dump。
-
-## Health
-
-operation：`health`，无 body。
-
-## Composition Parse
-
-operation：`composition-parse`。
-
-```json
-{"formula": "LiFePO4", "format": "formula"}
-```
-
-Key response fields in `data`: `valid`, `formula`, `reduced_formula`,
-`alphabetic_formula`, `anonymous_formula`, `chemical_system`,
-`number_of_atoms`, `weight`, `element_amounts`, `atomic_fractions`,
-`weight_fractions`, `error`.
-
-## Structure Parse / Summary
-
-operation：`structure-parse` 或 `structure-summary`。
-
-```json
-{"input": "<CIF text>", "format": "cif", "primitive": false}
-```
-
-Input formats: `cif`, `poscar`, `json`, `cssr`, `xsf`.
-
-Summary fields include `formula`, `reduced_formula`, `chemical_system`,
-`nsites`, `nelements`, `density`, `volume`, `lattice`, `element_amounts`, and
-`species`.
-
-## Structure Convert
-
-operation：`structure-convert`。
-
-```json
-{
-  "input": "<CIF text>",
-  "input_format": "cif",
-  "output_format": "poscar",
-  "primitive": false
-}
-```
-
-Output formats: `cif`, `poscar`, `json`, `cssr`, `xsf`.
-
-## Symmetry
-
-operation：`structure-symmetry`。
-
-```json
-{
-  "input": "<CIF text>",
-  "format": "cif",
-  "primitive": false,
-  "symprec": 0.01,
-  "angle_tolerance": 5.0
-}
-```
-
-Returns `space_group_symbol`, `space_group_number`, `crystal_system`,
-`point_group_symbol`, `hall`, and `nsites`.
+# pymatgen reference
+
+Make all calls with `delta-cli science invoke`. Prefer pymatgen for inorganic formulae,
+composition and formula weight; do not use PubChem or a local element table as a substitute.
+Structure operations require the complete structure text, not a local file path. Supported formats
+are `cif`, `poscar`, `json`, `cssr` and `xsf`; LAMMPS data and dump files are not accepted.
+
+## Health
+
+Operation: `health`; no request body.
+
+## Composition Parse
+
+Operation: `composition-parse`.
+
+```json
+{"formula": "LiFePO4", "format": "formula"}
+```
+
+Key response fields in `data`: `valid`, `formula`, `reduced_formula`,
+`alphabetic_formula`, `anonymous_formula`, `chemical_system`,
+`number_of_atoms`, `weight`, `element_amounts`, `atomic_fractions`,
+`weight_fractions`, `error`.
+
+## Structure Parse / Summary
+
+Operation: `structure-parse` or `structure-summary`.
+
+```json
+{"input": "<CIF text>", "format": "cif", "primitive": false}
+```
+
+Input formats: `cif`, `poscar`, `json`, `cssr`, `xsf`.
+
+Summary fields include `formula`, `reduced_formula`, `chemical_system`,
+`nsites`, `nelements`, `density`, `volume`, `lattice`, `element_amounts`, and
+`species`.
+
+## Structure Convert
+
+Operation: `structure-convert`.
+
+```json
+{
+  "input": "<CIF text>",
+  "input_format": "cif",
+  "output_format": "poscar",
+  "primitive": false
+}
+```
+
+Output formats: `cif`, `poscar`, `json`, `cssr`, `xsf`.
+
+## Symmetry
+
+Operation: `structure-symmetry`.
+
+```json
+{
+  "input": "<CIF text>",
+  "format": "cif",
+  "primitive": false,
+  "symprec": 0.01,
+  "angle_tolerance": 5.0
+}
+```
+
+Returns `space_group_symbol`, `space_group_number`, `crystal_system`,
+`point_group_symbol`, `hall`, and `nsites`.

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

@@ -1,125 +1,134 @@
-# Quantum ESPRESSO DFT 详细规则
-
-QE 用于通过 Chemistry Gateway 执行可追踪的异步 Quantum ESPRESSO 工作流。agent 只接触
-Gateway/Science Server contract，不运行本地 `pw.x`，不调用内部 QE 容器，也不提交 shell
-命令、scheduler 脚本、`pseudo_dir`、`outdir` 或主机路径。
-
-本 reference 对应 CLI 的真实工具为 `qe`。实际 `tools.name` 与 `tool_endpoints.name`
-必须逐字取自当前 CLI catalog。下列路径是 QE 服务契约，不是可直接访问的 URL，也不是
-可以自动改写的 endpoint 别名。
-
-## 能力分组
-
-| 服务路径 | 作用 | 类型 |
-| --- | --- | --- |
-| `/chem/qe/health`、`/healthz`、`/readyz` | 运行时、scheduler、存储和 PP 就绪 | 只读 |
-| `/chem/qe/v1/qe/workflow-types` | workflow catalog 和支持状态 | 只读 |
-| `/chem/qe/v1/pp-sets`、`/pp-locks/{digest}` | 已发布 PP profile/lock | 只读 |
-| `/chem/qe/v1/pp-sets:resolve` | 按 campaign 元素全集解析 PP 候选 | 只读/校验 |
-| `/chem/qe/v1/artifacts` | 上传、查询和下载结构/fixed-coordinate artifact | 文件/二进制 |
-| `/chem/qe/v1/qe/jobs` | 提交异步计算并查询 job | 远端变更 |
-| `/chem/qe/v1/qe/jobs/{job_id}/events`、`steps`、`logs`、`artifacts` | 读取作业过程和结果 | 只读 |
-| `/chem/qe/v1/qe/jobs/{job_id}:cancel`、`:retry`、`:review` | 取消、重试和科学审核 | 远端变更 |
-
-选择新 operation 时，先使用：
-
-```text
-delta-cli science list
-delta-cli science endpoints list <exact tool name>
-```
-
-再用目录返回的精确名称调用；如果 catalog 没有 schema，不猜测 operation、路径参数、
-请求头或 body。
-
-## CLI 的文件和幂等边界
-
-结构 artifact 上传需要 `application/octet-stream` 和 query metadata，QE job 提交要求
-稳定的 `Idempotency-Key`。`science invoke` 仍只用于 JSON/query；文件通过
-`science file`，持久化 job 通过 `science task`：
-
-- `delta-cli science file invoke --tool qe --endpoint artifact-upload --file <path>` 上传
-  结构 artifact；`custom-pp-upload` 同理并在 `--data` 中提供 `custom_pp_id`；
-- `delta-cli science task submit --tool qe --operation job-submit --input JSON
-  --idempotency-key KEY` 提交 durable QE job，worker 将幂等键传给 Gateway；
-- `delta-cli science file download --tool qe --endpoint artifact-content --params JSON
-  --output <path>` 下载原始 artifact；
-- 不要把结构文本、文件路径、base64、`Idempotency-Key` 或 QE service credential 当成
-  普通业务字段发送，也不要调用公开/私有 Gateway URL 或 `qe-cloud-compute:18020`。
-
-## 新作业的正确顺序
-
-1. 读取 health；需要部署诊断时再读取 readiness，并从 workflow catalog 选择当前
-   `supported` 的 task。
-2. 计算完整 `campaign_elements` 集合，使用 `pp-sets:resolve` 得到 profile；生产作业
-   必须使用服务返回的 `pp_set_id` 与不可变 `lock_id`，不能只凭 profile 名称推断 lock。
-3. 让服务校验结构 artifact，job 只引用返回的 `sha256:<digest>` artifact ID。
-4. 用稳定幂等语义提交 `qe/jobs`；接收 `202` 只代表 accepted/queued，不代表 QE 已收敛。
-5. 轮询 job、events、steps、logs 和 artifacts；独立读取 `execution`、`solver`、
-   `scientific` 三个状态。
-6. 下载结果时校验每个 artifact 的 SHA-256，并分别报告 selected backend、资源 telemetry、
-   solver 状态、scientific review 状态和 warnings。
-
-PP 解析的最小业务数据形状如下；其中值必须来自当前服务/目录，不能填入虚构的生产 lock：
-
-```json
-{
-  "campaign_id": "si-bulk-scf-v1",
-  "campaign_elements": ["Si", "O"],
-  "workflows": ["qe.pw.scf"],
-  "explicit_mode": null
-}
-```
-
-作业的核心结构如下，`workflow_inputs` 必须遵循当前 task schema：
-
-```json
-{
-  "task": "qe.pw.scf",
-  "schema_version": "1.1",
-  "campaign_id": "si-bulk-scf-v1",
-  "campaign_elements": ["Si"],
-  "structure": {"format": "artifact", "artifact_id": "sha256:<64-hex>"},
-  "physics": {
-    "parameter_set": "<approved-parameter-set>",
-    "pp_policy": {
-      "mode": "sssp_single",
-      "pp_set_id": "<approved-pp-set>",
-      "lock_id": "sha256:<64-hex>"
-    },
-    "kpoints": [4, 4, 4]
-  },
-  "resources": {
-    "profile": "standard",
-    "nodes": 1,
-    "mpi_ranks_per_node": 1,
-    "omp_threads_per_rank": 1,
-    "walltime_seconds": 3600,
-    "gpu_policy": "cpu"
-  },
-  "client_request_id": "si-scf-v1",
-  "workflow_inputs": {}
-}
-```
-
-## CPU/GPU 与状态解释
-
-CPU 是默认策略，尤其适用于小/中型交互任务、PP/结构/审计/归档任务和成本敏感场景。
-只有用户明确要求或项目已有 GPU 预算，并且 live catalog 返回
-`gpu_support_status: "verified"` 时，才使用 `gpu`；强制 GPU 不得静默回退 CPU。只有
-结果明确返回 `selected_backend: "gpu"` 才能声称实际使用 GPU；`auto` 不是 GPU 使用证明。
-
-三个状态通道不可合并：
-
-- `execution`：prepared/submitted/queued/running/scheduler completion/cancelled/failed；
-- `solver`：not started/running/converged/not converged/failed/unknown；
-- `scientific`：unreviewed、scientifically accepted、accepted with limitations、needs
-  recalculation、not assessable、failed 或 archived。
-
-scheduler 完成不等于 solver 收敛，solver 收敛也不等于 scientific acceptance。按稳定
-错误码而不是 message 分支，重点包括 `PP_SET_INCOMPLETE`、`PP_POLICY_INCOMPATIBLE`、
-`PP_CAPABILITY_UNKNOWN`、`ARTIFACT_MISSING`、`SOLVER_NOT_CONVERGED`、
-`SCIENTIFIC_GATE_FAILED`、`RESTART_INCOMPATIBLE`、`IDEMPOTENCY_CONFLICT`、
-`EXECUTION_BACKEND_NOT_READY`、`GPU_UNSUPPORTED` 和 `GPU_UNAVAILABLE`。
-
-提交、取消、重试或审核属于远端变更，必须有用户明确授权；结果未知时禁止重试。不要把
-GPU smoke test、scheduler 日志或可解析的 QE 输出描述成科学结论或客户级性能保证。
+# Quantum ESPRESSO DFT reference
+
+Use QE to run traceable, asynchronous Quantum ESPRESSO workflows through Chemistry Gateway.
+The agent interacts only with the Gateway/Science Server contract: it does not run local `pw.x`,
+call internal QE containers, or submit shell commands, scheduler scripts, `pseudo_dir`, `outdir`
+or host paths.
+
+The actual CLI tool for this reference is `qe`. Copy `tools.name` and `tool_endpoints.name`
+exactly from the current CLI catalogue. The paths below describe the QE service contract; they
+are not URLs to access directly or endpoint aliases that may be rewritten automatically.
+
+## Capability groups
+
+| Service path | Purpose | Type |
+| --- | --- | --- |
+| `/chem/qe/health`, `/healthz`, `/readyz` | Runtime, scheduler, storage and PP readiness | Read-only |
+| `/chem/qe/v1/qe/workflow-types` | Workflow catalogue and support status | Read-only |
+| `/chem/qe/v1/pp-sets`, `/pp-locks/{digest}` | Published PP profiles/locks | Read-only |
+| `/chem/qe/v1/pp-sets:resolve` | Resolve PP candidates for the complete set of campaign elements | Read-only/validation |
+| `/chem/qe/v1/artifacts` | Upload, query and download structure/fixed-coordinate artifacts | File/binary |
+| `/chem/qe/v1/qe/jobs` | Submit asynchronous calculations and query jobs | Remote mutation |
+| `/chem/qe/v1/qe/jobs/{job_id}/events`, `steps`, `logs`, `artifacts` | Read job progress and results | Read-only |
+| `/chem/qe/v1/qe/jobs/{job_id}:cancel`, `:retry`, `:review` | Cancel, retry and scientifically review a job | Remote mutation |
+
+When selecting a new operation, first run:
+
+```text
+delta-cli science list
+delta-cli science endpoints list <exact tool name>
+```
+
+Then call it using the exact names returned by the catalogue. If the catalogue has no schema, do
+not guess the operation, path parameters, headers or body.
+
+## CLI file and idempotency boundaries
+
+Structure artifact uploads require `application/octet-stream` and query metadata; QE job
+submission requires a stable `Idempotency-Key`. `science invoke` remains for JSON/query only;
+send files through `science file` and persistent jobs through `science task`:
+
+- `delta-cli science file invoke --tool qe --endpoint artifact-upload --file <path>` uploads
+  a structure artifact; for `custom-pp-upload`, also provide `custom_pp_id` in `--data`;
+- `delta-cli science task submit --tool qe --operation job-submit --input JSON
+  --idempotency-key KEY` submits a durable QE job; the worker passes the idempotency key to Gateway;
+- `delta-cli science file download --tool qe --endpoint artifact-content --params JSON
+  --output <path>` downloads a raw artifact;
+- Do not send structure text, file paths, base64, `Idempotency-Key` or QE service credentials as
+  ordinary business fields, and do not call public or private Gateway URLs or `qe-cloud-compute:18020`.
+
+## Correct sequence for a new job
+
+1. Read health. Read readiness only when diagnosing the deployment, and choose a currently
+   `supported` task from the workflow catalogue.
+2. Determine the complete `campaign_elements` set and use `pp-sets:resolve` to obtain a profile.
+   Production jobs must use the returned `pp_set_id` and immutable `lock_id`; do not infer the
+   lock from the profile name alone.
+3. Ask the service to validate the structure artifact. The job must reference only the returned
+   `sha256:<digest>` artifact ID.
+4. Submit to `qe/jobs` with stable idempotency semantics. A `202` response means accepted/queued,
+   not that QE has converged.
+5. Poll the job, events, steps, logs and artifacts; read the `execution`, `solver` and
+   `scientific` states independently.
+6. Verify each artifact's SHA-256 when downloading results. Report the selected backend, resource
+   telemetry, solver state, scientific review state and warnings separately.
+
+The minimum business-data shape for PP resolution is shown below. Values must come from the
+current service/catalogue; do not insert a fabricated production lock:
+
+```json
+{
+  "campaign_id": "si-bulk-scf-v1",
+  "campaign_elements": ["Si", "O"],
+  "workflows": ["qe.pw.scf"],
+  "explicit_mode": null
+}
+```
+
+The core job structure is shown below. `workflow_inputs` must follow the current task schema:
+
+```json
+{
+  "task": "qe.pw.scf",
+  "schema_version": "1.1",
+  "campaign_id": "si-bulk-scf-v1",
+  "campaign_elements": ["Si"],
+  "structure": {"format": "artifact", "artifact_id": "sha256:<64-hex>"},
+  "physics": {
+    "parameter_set": "<approved-parameter-set>",
+    "pp_policy": {
+      "mode": "sssp_single",
+      "pp_set_id": "<approved-pp-set>",
+      "lock_id": "sha256:<64-hex>"
+    },
+    "kpoints": [4, 4, 4]
+  },
+  "resources": {
+    "profile": "standard",
+    "nodes": 1,
+    "mpi_ranks_per_node": 1,
+    "omp_threads_per_rank": 1,
+    "walltime_seconds": 3600,
+    "gpu_policy": "cpu"
+  },
+  "client_request_id": "si-scf-v1",
+  "workflow_inputs": {}
+}
+```
+
+## CPU/GPU and state interpretation
+
+CPU is the default, particularly for small or medium interactive jobs, PP/structure/audit/archive
+jobs, and cost-sensitive work. Use `gpu` only when the user explicitly requests it or the project
+already has a GPU budget, and the live catalogue returns `gpu_support_status: "verified"`. Do not
+silently fall back to CPU when GPU is required. Claim that GPU was used only when the result
+explicitly returns `selected_backend: "gpu"`; `auto` does not prove GPU use.
+
+Keep the three state channels separate:
+
+- `execution`: prepared/submitted/queued/running/scheduler completion/cancelled/failed;
+- `solver`: not started/running/converged/not converged/failed/unknown;
+- `scientific`: unreviewed, scientifically accepted, accepted with limitations, needs
+  recalculation, not assessable, failed or archived.
+
+scheduler completion does not mean solver convergence, and solver convergence does not mean
+scientific acceptance. Branch on stable error codes rather than messages. Key codes include
+`PP_SET_INCOMPLETE`, `PP_POLICY_INCOMPATIBLE`,
+`PP_CAPABILITY_UNKNOWN`, `ARTIFACT_MISSING`, `SOLVER_NOT_CONVERGED`,
+`SCIENTIFIC_GATE_FAILED`, `RESTART_INCOMPATIBLE`, `IDEMPOTENCY_CONFLICT`,
+`EXECUTION_BACKEND_NOT_READY`, `GPU_UNSUPPORTED` and `GPU_UNAVAILABLE`.
+
+Submission, cancellation, retry and review are remote mutations and require the user's explicit
+authorisation. Do not retry when the outcome is unknown. Do not describe a GPU smoke test,
+scheduler log or parseable QE output as a scientific conclusion or a customer-level performance
+guarantee.