docs: add typical reproduction program entry

README.md

@@ -81,7 +81,8 @@ The dataset is too small for industrial or universal molecular generalization. D
 | [`manuscripts/`](manuscripts/README.md) | Evidence matrix and bilingual publication positioning; no pre-submission manuscript drafts are included |
 | [`ai4s-agent/`](ai4s-agent/README.md) | Agent architecture, capabilities, evaluation, governance, and limitations |
 | [`software/`](software/README.md) | Public LFMO/conditional-SCF implementation and 69 focused tests |
-| [`reproducibility/`](reproducibility/README.md) | Runtime instructions and WSL 2 platform boundaries |
+| [Typical reproduction programs](reproducibility/TYPICAL_PROGRAMS.md) | Select evidence checks, conditional-SCF tests, or downloadable QM reruns by cost, with step-by-step computation notes |
+| [`reproducibility/`](reproducibility/README.md) | Full runtime instructions, environments, and WSL 2 platform boundaries |
 | [`figures/`](figures/README.md) | Project-authored overview figure |
 | [`science-v0.2/`](science-v0.2/README.md) | Self-contained `v0.2.0` configurations, selected machine results, decisions, reports, rebuild scripts, tests, and hashes |
 | [`science-v0.3/`](science-v0.3/README.md) | Published seven-work-package `v0.3.0` scientific-closure package; preserves `v0.1.x`, `v0.2.0`, and P01-P14 unchanged |

README_zh-CN.md

@@ -81,7 +81,8 @@ AI4OrgChem是一个面向有机结构基础理论独立计算重构与证据评
 | [`manuscripts/`](manuscripts/README.md) | 证据矩阵和双语发布定位 |
 | [`ai4s-agent/`](ai4s-agent/README.md) | Agent架构、能力、评估、证据治理和限制 |
 | [`software/`](software/README.md) | LFMO/条件SCF公开核心实现和69项测试 |
-| [`reproducibility/`](reproducibility/README.md) | 复现说明和WSL 2平台边界 |
+| [典型程序复算入口](reproducibility/TYPICAL_PROGRAMS_zh-CN.md) | 按计算难度选择证据核验、条件SCF测试和可下载QM复算，并查看逐步计算说明 |
+| [`reproducibility/`](reproducibility/README.md) | 完整复现说明、运行环境和WSL 2平台边界 |
 | [`figures/`](figures/README.md) | 项目自行生成的总览图 |
 | [`science-v0.2/`](science-v0.2/README.md) | 自包含`v0.2.0`配置、精选机器结果、判定、报告、重建脚本、测试与哈希 |
 | [`science-v0.3/`](science-v0.3/README.md) | 已发布的七工作包`v0.3.0`科学闭合包；保持`v0.1.x`、`v0.2.0`及P01-P14不变 |

manifests/FILE_INVENTORY.md

@@ -2,7 +2,7 @@
 
 本清单记录GitHub洁净仓库中的实质内容文件。生成型SHA清单和本文件自身不反向列入表格。
 
-- 实质内容文件：562
+- 实质内容文件：564
 - 状态：版本化发布快照；内容变更后必须重新生成并验证
 
 | 文件 | 角色 | 字节 | SHA-256 |
@@ -164,16 +164,18 @@
 | `project/RESEARCH_ITEMS_zh-CN.md` | project-narrative | 1939 | `508c64832f3b075a9d073e33badd35be764012eebb94624fc7966fa2b03b143f` |
 | `project/RESEARCH_VALUE_zh-CN.md` | project-narrative | 1319 | `7308230ee6f5dd7009de88e0483b3ff298baa2a438d8f99fc010103e24b80c5b` |
 | `project/V0.3.0_POST_RELEASE_ERRATUM_2026-09-08.md` | project-narrative | 7037 | `2ea92085a7bab6b235f75ca06bb27b97162d00656395f879309da42a48df3c9d` |
-| `README.md` | repository-root | 23487 | `357775c4f596c2b62e819d2d6ff615e9d97550e21c3d91f2e0adcbf55cda89e5` |
-| `README_zh-CN.md` | repository-root | 9897 | `7e51c54b7b3fdd8b9fd406da18423abd00bdea31d5fbf1775874a91bcce86cc8` |
+| `README.md` | repository-root | 23700 | `4fc35159d35c2fa78636e8c37c3b3a913ab8e0b111c7f268ebc71dcc0f46f090` |
+| `README_zh-CN.md` | repository-root | 10096 | `410b441037c67283cafa4b170a774ff0437ce620d3143087a6710727d17689bb` |
 | `RELEASE_NOTES_v0.3.1.md` | repository-root | 4739 | `1ff7d081ebf80aff8fd08b670b0117b2f5416268ee08e972572a2942635b56b0` |
 | `reproducibility/conda-linux-64.explicit.txt` | reproducibility | 18332 | `543abce03ee369526d83016126d7a0b7a82de48e0ef3356d3877289af90f5637` |
 | `reproducibility/environment.yml` | reproducibility | 214 | `13ae5c398dd95bf2d841fe89c4180cdd98d6d8360618de98ac3f68df27be50a6` |
 | `reproducibility/PLATFORM_MATRIX_EN.md` | reproducibility | 1963 | `1ea2cc5909ef145c93c5dcdc9c3bfaefb1726bc4c51ea47f57134fefcb5141cd` |
 | `reproducibility/PLATFORM_MATRIX_zh-CN.md` | reproducibility | 1773 | `60cd3af1c440d40f30ef58b54b35bec5c7ae764faec54ef9dbc70bb32863fa88` |
-| `reproducibility/README.md` | reproducibility | 1054 | `176c783f5614c0f0bf2d61f42a02fc1dce2f782980120ab9cd0320ca81b03274` |
+| `reproducibility/README.md` | reproducibility | 1259 | `89117413d55dfeeb8887e444c8bd85715d701a94e4a416cc5c9b579bee73da39` |
 | `reproducibility/RUNBOOK_EN.md` | reproducibility | 2854 | `2c7831ca9ee5f18ca597c66897f2f5d5e79cf766157442ee7d8e19706b5c9335` |
 | `reproducibility/RUNBOOK_zh-CN.md` | reproducibility | 3133 | `eeb5267031e04c8bc3f3585a2934000773c0ea966395c146c0c8a5a2fe7a43e8` |
+| `reproducibility/TYPICAL_PROGRAMS.md` | reproducibility | 8079 | `112593abdaa36bdf8cb598f210f894f3d4533ec1cb64c540b8ea251740f495dd` |
+| `reproducibility/TYPICAL_PROGRAMS_zh-CN.md` | reproducibility | 9696 | `630556aecb43051c26ee03b08a1ca51e9f566b9c528062add50b9b02ab8ed13f` |
 | `reproducibility/wsl/activate-ai4orgchem-public.sh` | reproducibility | 1475 | `5361fab00ebc6c614dfc191fffb4fb5c1eb0690ab862ad27000359347709cb2e` |
 | `reproducibility/wsl/ai4orgchem-verify` | reproducibility | 929 | `7eec73ec0269e9549a238707c6edf792a3bbae8161b72d714ba84abe3c43dc92` |
 | `reproducibility/wsl/README.md` | reproducibility | 1742 | `afb4d76e6f525e4b55036a446867d6ecc47b1657d7f17f6303062f4031ad832c` |

manifests/sha256-manifest.json

@@ -870,8 +870,8 @@
     {
       "path": "manifests/FILE_INVENTORY.md",
       "artifact_role": "repository-root",
-      "bytes": 89442,
-      "sha256": "c88bf28a90ea9669fbfcfb85eba24c4256f31141ce06b09548dd701df87f1f29"
+      "bytes": 89721,
+      "sha256": "969ef3e554c3388a71138d1c775a8ee6335fcdf08db7c13e08f8ecc3759240bf"
     },
     {
       "path": "manuscripts/P01-P14_evidence_matrix_zh-CN.md",
@@ -954,14 +954,14 @@
     {
       "path": "README.md",
       "artifact_role": "repository-root",
-      "bytes": 23487,
-      "sha256": "357775c4f596c2b62e819d2d6ff615e9d97550e21c3d91f2e0adcbf55cda89e5"
+      "bytes": 23700,
+      "sha256": "4fc35159d35c2fa78636e8c37c3b3a913ab8e0b111c7f268ebc71dcc0f46f090"
     },
     {
       "path": "README_zh-CN.md",
       "artifact_role": "repository-root",
-      "bytes": 9897,
-      "sha256": "7e51c54b7b3fdd8b9fd406da18423abd00bdea31d5fbf1775874a91bcce86cc8"
+      "bytes": 10096,
+      "sha256": "410b441037c67283cafa4b170a774ff0437ce620d3143087a6710727d17689bb"
     },
     {
       "path": "RELEASE_NOTES_v0.3.1.md",
@@ -996,8 +996,8 @@
     {
       "path": "reproducibility/README.md",
       "artifact_role": "reproducibility",
-      "bytes": 1054,
-      "sha256": "176c783f5614c0f0bf2d61f42a02fc1dce2f782980120ab9cd0320ca81b03274"
+      "bytes": 1259,
+      "sha256": "89117413d55dfeeb8887e444c8bd85715d701a94e4a416cc5c9b579bee73da39"
     },
     {
       "path": "reproducibility/RUNBOOK_EN.md",
@@ -1011,6 +1011,18 @@
       "bytes": 3133,
       "sha256": "eeb5267031e04c8bc3f3585a2934000773c0ea966395c146c0c8a5a2fe7a43e8"
     },
+    {
+      "path": "reproducibility/TYPICAL_PROGRAMS.md",
+      "artifact_role": "reproducibility",
+      "bytes": 8079,
+      "sha256": "112593abdaa36bdf8cb598f210f894f3d4533ec1cb64c540b8ea251740f495dd"
+    },
+    {
+      "path": "reproducibility/TYPICAL_PROGRAMS_zh-CN.md",
+      "artifact_role": "reproducibility",
+      "bytes": 9696,
+      "sha256": "630556aecb43051c26ee03b08a1ca51e9f566b9c528062add50b9b02ab8ed13f"
+    },
     {
       "path": "reproducibility/wsl/activate-ai4orgchem-public.sh",
       "artifact_role": "reproducibility",

reproducibility/README.md

@@ -2,6 +2,7 @@
 
 本目录提供平台中立的CPU环境和明确运行手册：
 
+- [`TYPICAL_PROGRAMS_zh-CN.md`](TYPICAL_PROGRAMS_zh-CN.md) / [`TYPICAL_PROGRAMS.md`](TYPICAL_PROGRAMS.md)：按成本选择典型程序，并逐步解释输入、计算、输出、门禁和科学边界；
 - `environment.yml`：Python、NumPy、SciPy、PyYAML、pytest及PySCF的最小环境；
 - `conda-linux-64.explicit.txt`：2026-08-12权威WSL科研环境的Conda层显式包URL与哈希快照；本地路径已脱敏，且不冒充后续GPU环境或pip层的完整锁；
 - `RUNBOOK_EN.md` / `RUNBOOK_zh-CN.md`：冻结证据验证、公开软件测试和适用边界；

reproducibility/TYPICAL_PROGRAMS.md

@@ -0,0 +1,111 @@
+# Typical Reproduction and Evidence-Verification Programs
+
+[中文](TYPICAL_PROGRAMS_zh-CN.md)
+
+This page gives chemistry, quantum-chemistry, and computational-chemistry readers controlled entry points into the AI4OrgChem workflow: **scientific question → frozen protocol → electronic-structure calculation → numerical gates → machine result → scoped conclusion**.
+
+> “Verification” here is not certification of the monograph. `PASS` means only that a specified computation or consistency check satisfied its registered inputs, methods, and tolerances.
+
+## Choose a level
+
+| Level | Entry point | QM executed | Typical resources | Status |
+|---|---|---:|---|---|
+| L0 | Frozen P01–P14 evidence verification | No | Standard Python; seconds | **Runnable** |
+| L1 | P09 conditional-SCF core tests | Small tests | CPU; usually minutes | **Runnable** |
+| L2 | P14 fixed-geometry technical smoke | Yes, STO-3G | WSL2; 8 threads | **Runnable** |
+| L3 | P14 fixed-geometry scientific-level reproduction | Yes, B3LYPG/6-31G(d) | WSL2; 8 threads; adequate memory | **Runnable** |
+| L4 | P14 five-parameter production optimization | Yes; expensive | WSL2; 8 threads; at least 13 GiB available memory | **Runnable; advanced** |
+
+P09 cyclobutadiene smoke, the P10 benzene BLA scan, and the complete P09 aromatic-energy reproduction are the next public packaging targets. They are not shown with pretend commands before isolated output handling, dependency completion, and clean-clone execution pass.
+
+## Common setup
+
+The canonical scientific platform is **WSL 2 / Ubuntu 24.04**. From the repository root:
+
+```bash
+micromamba create -f reproducibility/environment.yml  # only if absent
+source reproducibility/wsl/activate-ai4orgchem-public.sh
+cd software
+python -m pip install -e ".[science,test]"
+cd ..
+```
+
+See the [English runbook](RUNBOOK_EN.md) and [platform matrix](PLATFORM_MATRIX_EN.md). Reproduction outputs belong under the Git-ignored `runs/reproduction/`; they must never overwrite frozen files under `evidence/`.
+
+## L0 — frozen P01–P14 evidence verification
+
+Purpose: verify that all fourteen published machine records can be read and that proposition IDs, verdicts, citations, key boundary states, and aggregate counts are internally consistent. No QM is rerun.
+
+Process: enumerate P01–P14 → validate JSON/JSONL structure → compare frozen verdicts with the master statistics → check key P11/P12/P14 states → emit counts and status.
+
+```bash
+python software/scripts/validate_public_evidence.py
+python software/scripts/validate_evidence_navigation.py
+```
+
+Expected output includes `status: PASS`, `propositions_checked: 14`, and `propositions_navigated: 14`. This verifies the published evidence package, not the physical correctness of the underlying calculations or peer-review status.
+
+## L1 — P09 conditional-SCF core tests
+
+Purpose: test the source-aligned infrastructure used by P09/P14: AO sigma/pi identity, fragment boundaries, Fock/overlap masking, exchange-integral classes, conditional SCF, and independent energy assembly.
+
+Process: construct test matrices or PySCF AO objects → classify sigma/pi AOs → attach pi-fragment labels → zero registered cross-fragment Fock/overlap blocks → apply the frozen 15 exchange-integral classes → iterate conditional SCF → assemble one-electron, Coulomb, exchange, and nuclear terms → test electron count, energy closure, generalized commutator, and density idempotency.
+
+```bash
+cd software
+python -m pytest -p no:cacheprovider \
+  tests/test_p09_conditional_scf.py \
+  tests/test_p09_energy_assembly.py \
+  tests/test_p09_eri_mask.py
+cd ..
+```
+
+All tests must pass. These are mathematical-contract tests, not a complete molecular reproduction of benzene ESE or cyclobutadiene ADE.
+
+## L2 — P14 fixed-geometry technical smoke
+
+Purpose: use the small STO-3G basis to establish that C12H6 geometry reconstruction, AO classification, conditional SCF, and the energy ledger execute on the user's machine.
+
+Process: reconstruct planar D3h G/PLG source-proxy geometries from five published descriptors → ordinary closed-shell RKS at G → ordinary RKS anchor at PLG → sigma/pi classification and fragment mapping → conditional PLG SCF → technical endpoint → gates for 78 electrons, SCF convergence, reconstructed geometry, energy closure, commutator, and idempotency.
+
+```bash
+python software/scripts/run_p14_benzotricyclobutadiene_smoke.py
+```
+
+Outputs are written under `runs/reproduction/p14/`. `smoke_gate_verdict` should be `PASS`, but the STO-3G value is implementation evidence only and is ineligible for the P14 scientific verdict.
+
+## L3 — P14 fixed-geometry scientific-level reproduction
+
+Purpose: recompute the P14 fixed-geometry endpoint at B3LYPG/6-31G(d) on the public G/PLG source-proxy geometries and compare it with the frozen `67.086899 kcal/mol` value.
+
+Process: hash public inputs → verify five-parameter reconstruction, atom order, planarity, and 78 electrons → ordinary G state → ordinary PLG density anchor → source-aligned conditional PLG state → direct-versus-memory-controlled energy equivalence → endpoint assembly → method, basis, SCF, electron-count, closure, commutator, idempotency, and memory gates.
+
+```bash
+python software/scripts/run_p14_benzotricyclobutadiene_source_level_fixed_geometry.py
+```
+
+See the [P14 input identity statement](../evidence/P01-P14/P14/inputs/README.md). These are reconstructed source-proxy coordinates because the historical Cartesian coordinates were not published.
+
+## L4 — P14 five-parameter production optimization
+
+Purpose: optimize the five planar D3h parameters independently for ordinary G and conditional PLG, then test both the structural response `dDelta-r(GP)` and the optimized endpoint.
+
+Process: require at least 13 GiB available memory → generate frozen starts → optimize ordinary G at B3LYPG/6-31G(d) → qualify termination, gradient, and active bounds → optimize conditional PLG → repeat SCF, 78-electron, gradient, boundary, and conditional-state checks → calculate structure response and endpoint → issue `production_gate_verdict: PASS` only when every eligibility gate passes.
+
+```bash
+python software/scripts/run_p14_benzotricyclobutadiene_production_optimization.py
+```
+
+Frozen references are `dDelta-r(GP) = 0.172204 Å` and `67.679719 kcal/mol`. Numeric proximity alone is insufficient: method, basis, convergence, gradient, bounds, electron count, and energy closure must all qualify. The calculation covers only the registered planar D3h five-parameter subspace.
+
+## Activation gates for the next entries
+
+- **P09 cyclobutadiene smoke:** fixed planar rectangle → ordinary G-like RKS → sigma/pi classification → two-fragment DSI SCF → 15 exchange classes → independent ledger → numerical gates. It is not the final VDE/ADE.
+- **P10 benzene BLA scan:** same-protocol P09 G/GL endpoints → `delta Ee`/`delta EN` decomposition → fixed mean C–C and C–H distances → ordinary RKS at `delta=0, 0.01, 0.02, 0.04, 0.06 Å` → independent nuclear Coulomb sum → curvature and plus/minus symmetry checks. It supports only the tested pathway.
+- **Complete P09 reproduction:** cyclobutadiene G/DSI and conditional GL paths → VDE/ADE; benzene G/three-fragment DSI → restricted GL/GE1 optimizations → `ESE=delta EA-3 delta EA1` → blind comparison with frozen anchors.
+
+Before activation, each entry must be included with its complete script and configuration, write only to `runs/reproduction/`, include geomeTRIC where required, contain no private paths or credentials, document resources, pass unit tests, pass a WSL2 clean-clone run, and reproduce the frozen evidence within registered tolerances.
+
+## Reporting an independent reproduction
+
+Include the repository tag or commit, OS, Python/PySCF versions, thread count, memory, exact command, SHA-256 of output JSON, `PASS/FAIL` status, and residual from the frozen result. Failed reproductions are scientifically useful and should not be discarded or replaced by success-only screenshots.