{ "kind": "review_queue", "date": "2026-10-19", "summary": { "scope": "selection", "units_all_active": 50, "units": 49, "families": 49, "legacy_units": 0, "L1": { "pending": 49, "approved": 0, "revise": 0, "stale": 0 }, "L2": { "pending": 49, "approved": 0, "revise": 0, "stale": 0 }, "instances": 160, "forms": { "family": 160, "family-version": 0, "legacy": 0 }, "stages": { "not-verified": 0, "L0": 160, "L1+L2": 0, "L3": 0, "formal": 0 }, "next_l3_batch": "l3-batch-001", "l3_sample": 160, "l3_strata": 96, "l3_steady_state_sample": 136, "model_calls": 0, "reviews_recorded": { "L1": 0, "L2": 0, "L3": 0 } }, "questions": { "version": "1.0.0", "purpose": "L3 stratified spot check: the fixed four questions a lightweight model reviewer (and the human for flagged or calibration items) answers for one instance. Changing this file changes its hash and makes earlier L3 results stale.", "questions": [ { "id": "q1_answerable", "label": "能否仅凭题干和附件作答", "prompt": "Using only the student packet (question text, attached inputs and the four options), can a competent solver determine exactly one correct option without information that is absent from the packet? Flag if a needed parameter, definition, convention or condition is missing, or if more than one option could be defended." }, { "id": "q2_scientific_meaning", "label": "科学意义", "prompt": "Does the question test a scientifically meaningful structure–property or geometry concept at the stated scale, rather than bookkeeping or string matching? Is the physics or chemistry in the question and in the correct option right? Flag errors or trivialities." }, { "id": "q3_source_correspondence", "label": "来源对应", "prompt": "Do the inputs, numbers, conditions and units in the packet correspond to the cited source as described in the reviewer packet (including any stated reduction or paper-parameter model)? Flag any mismatch or any source claim that the reviewer packet does not support." }, { "id": "q4_overclaiming", "label": "结论是否过度", "prompt": "Does the question, the answer or its explanation claim more than the evidence supports (for example, presenting a model as a measurement, using a formula outside its stated validity, or treating a correlation as a mechanism)? Flag overclaiming." } ], "output_schema": { "instance": "instance id exactly as given", "answers": "object with the four question ids as keys; each value is {\"verdict\": \"pass\" | \"flag\", \"reason\": \"one or two sentences\"}" }, "instructions": "You are reviewing one benchmark question for quality; you are not answering it for credit. Read the student packet and the reviewer packet. Answer each of the four questions independently with pass or flag and a short reason. Return only one JSON object matching the output schema, with no other text." }, "questions_sha256": "06b007286af409fc7e071171e6706671e87bbc97b6129b0882f9a8e29d559c24", "units": [ { "unit": "assembly_extent", "kind": "family", "ability": "perception", "registry_id": "assembly_size", "generator": "task_families/assembly.py", "checker": "checkers/migrated.py", "checker_function": "assembly_extent", "bindings": { "L1": { "registry_row": "a4e31c877bb0f0feb54a9322111f109d3d74a62438fcfb4758df924c84207be5", "task_families/assembly.py": "5cbb7b6b4a45f6797fe9d4f6cdd31e4b7df60da7812d4ce5a0aba6ce248c77e6" }, "L2": { "checkers/migrated.py": "f1cf6f20bca7ad81fd3b5ee5c6749084a090a32dd40b0a394768995a6e3a42eb", "checkers/common.py": "fbc9f4eb287114ac4720d27edc1ea40e25f80da0e1cff6bdee06fbdca2b73aed" } }, "L1": "pending", "L2": "pending", "instances": 6, "L1_record": null, "L2_record": null, "card": { "template": { "name": "大型组装体尺寸（最大间距 / 回转半径）", "concept": "整个颗粒尺度的几何量：分子伴侣、核小体、病毒衣壳、DNA 折纸螺旋束的最大间距与等权回转半径（10–1000 nm）。", "inputs": "每残基一点的 XYZ，或按组分标记的链质心表（可只选某一组分，如 VP5 外壳）。", "physical_conditions": "约简表示；几何量在所给点集上定义。", "reasoning_scale": "所选点集的最大间距（整个颗粒）", "scale_limits": "约简表示上的几何量，不是溶液中的流体力学尺寸。暂无数据源的格：chemistry 100-1000（规划器不据此给出路线）。", "source_basis": "RCSB PDB 大型组装体（1AON、1KX5、1A34、6CGR、6NCL、7ARQ），经沉积的对称操作展开并约简为每残基/每核苷酸一点或每链质心", "answer_method": "numpy 分块搜索最大点对 + Decimal 复核；回转半径用质心公式并以 Decimal 复核。", "distractor_mechanisms": [ "bounding_box_diagonal", "centroid_diameter", "largest_axis_span", "sphere_radius_from_rg", "single_axis_rms", "wrong_selection", "sphere_diameter_from_rg", "rg_from_dmax_solid_sphere" ], "four_choice_validation": "与正确值 > 0.3 nm；升序排列，秩按批次轮换（加入偏小的错误机制，避免正确项总是最小）。 v0.3.0：加入两个方向的实心球换算；空心外壳上其他尺寸估计常与 Dmax 重合而被拒（探针 runs/enum-v23）。枚举的回转半径题设 strict_rank。", "principle": "Dmax = max‖ri−rj‖；Rg = √(Σ‖ri−c‖²/N)。", "validation": "两种实现一致；独立检查器用成对恒等式复核。", "limits": "邻近亚基间距（约 5 nm）属于 1–10 nm 格，不在本题型中使用。", "template_review": "本轮新建（A4），待人工审核。" }, "samples": [ { "instance": "FA-ASM-EXT-1SVA", "question": "The table lists the Cα centroid of every VP1 chain of the simian virus 40 capsid (PDB 1SVA), expanded to the whole particle with the 60 operators of its biological assembly; columns are component (VP1), copy, x, y, z (angstrom). Select all points labelled VP1. What is the largest distance between any two of the selected points, in nanometres?", "options": [ { "label": "A", "value": "21.32", "unit": "nm" }, { "label": "B", "value": "42.92", "unit": "nm" }, { "label": "C", "value": "55.04", "unit": "nm" }, { "label": "D", "value": "73.53", "unit": "nm" } ], "inputs": [ "1SVA-chain-centroids.txt" ], "correct_label": "B", "audit": [ { "label": "A", "rule": "mean_radius", "reason": "用中心距的算术平均。" }, { "label": "B", "rule": "correct", "reason": "按定义在所选点上计算（numpy 分块搜索 + Decimal 复核）。" }, { "label": "C", "rule": "sphere_diameter_from_rg", "reason": "按实心球关系由回转半径推直径 D = 2√(5/3)·Rg（空心外壳会高估）。" }, { "label": "D", "rule": "bounding_box_diagonal", "reason": "用坐标轴对齐包围盒对角线代替实际最大间距。" } ] }, { "instance": "FA-ASM-EXT-2FT1", "question": "The table lists the Cα centroid of every gp5 chain of the mature bacteriophage HK97 head (Head II, PDB 2FT1), expanded to the whole particle with the 60 operators of its biological assembly; columns are component (gp5), copy, x, y, z (angstrom). Select all points labelled gp5. What is the largest distance between any two of the selected points, in nanometres?", "options": [ { "label": "A", "value": "16.21", "unit": "nm" }, { "label": "B", "value": "23.19", "unit": "nm" }, { "label": "C", "value": "59.88", "unit": "nm" }, { "label": "D", "value": "98.36", "unit": "nm" } ], "inputs": [ "2FT1-chain-centroids.txt" ], "correct_label": "C", "audit": [ { "label": "A", "rule": "single_axis_rms", "reason": "只算了一个坐标轴方向的均方根离散度，而不是三维距离。" }, { "label": "B", "rule": "rg_from_dmax_solid_sphere", "reason": "按实心球关系由最大尺寸估算回转半径 Rg = √(3/5)·Dmax/2（空心外壳会低估）。" }, { "label": "C", "rule": "correct", "reason": "按定义在所选点上计算（numpy 分块搜索 + Decimal 复核）。" }, { "label": "D", "rule": "bounding_box_diagonal", "reason": "用坐标轴对齐包围盒对角线代替实际最大间距。" } ] } ] } }, { "unit": "assembly_rg", "kind": "family", "ability": "perception", "registry_id": "assembly_size", "generator": "task_families/assembly.py", "checker": "checkers/migrated.py", "checker_function": "assembly_rg", "bindings": { "L1": { "registry_row": "a4e31c877bb0f0feb54a9322111f109d3d74a62438fcfb4758df924c84207be5", "task_families/assembly.py": "5cbb7b6b4a45f6797fe9d4f6cdd31e4b7df60da7812d4ce5a0aba6ce248c77e6" }, "L2": { "checkers/migrated.py": "f1cf6f20bca7ad81fd3b5ee5c6749084a090a32dd40b0a394768995a6e3a42eb", "checkers/common.py": "fbc9f4eb287114ac4720d27edc1ea40e25f80da0e1cff6bdee06fbdca2b73aed" } }, "L1": "pending", "L2": "pending", "instances": 5, "L1_record": null, "L2_record": null, "card": { "template": { "name": "大型组装体尺寸（最大间距 / 回转半径）", "concept": "整个颗粒尺度的几何量：分子伴侣、核小体、病毒衣壳、DNA 折纸螺旋束的最大间距与等权回转半径（10–1000 nm）。", "inputs": "每残基一点的 XYZ，或按组分标记的链质心表（可只选某一组分，如 VP5 外壳）。", "physical_conditions": "约简表示；几何量在所给点集上定义。", "reasoning_scale": "所选点集的最大间距（整个颗粒）", "scale_limits": "约简表示上的几何量，不是溶液中的流体力学尺寸。暂无数据源的格：chemistry 100-1000（规划器不据此给出路线）。", "source_basis": "RCSB PDB 大型组装体（1AON、1KX5、1A34、6CGR、6NCL、7ARQ），经沉积的对称操作展开并约简为每残基/每核苷酸一点或每链质心", "answer_method": "numpy 分块搜索最大点对 + Decimal 复核；回转半径用质心公式并以 Decimal 复核。", "distractor_mechanisms": [ "bounding_box_diagonal", "centroid_diameter", "largest_axis_span", "sphere_radius_from_rg", "single_axis_rms", "wrong_selection", "sphere_diameter_from_rg", "rg_from_dmax_solid_sphere" ], "four_choice_validation": "与正确值 > 0.3 nm；升序排列，秩按批次轮换（加入偏小的错误机制，避免正确项总是最小）。 v0.3.0：加入两个方向的实心球换算；空心外壳上其他尺寸估计常与 Dmax 重合而被拒（探针 runs/enum-v23）。枚举的回转半径题设 strict_rank。", "principle": "Dmax = max‖ri−rj‖；Rg = √(Σ‖ri−c‖²/N)。", "validation": "两种实现一致；独立检查器用成对恒等式复核。", "limits": "邻近亚基间距（约 5 nm）属于 1–10 nm 格，不在本题型中使用。", "template_review": "本轮新建（A4），待人工审核。" }, "samples": [ { "instance": "FA-ASM-RG-1KX5", "question": "The XYZ file lists one point per residue (protein Cα as C, DNA phosphorus as P) of the nucleosome core particle NCP147, PDB 1KX5 (angstrom). Select all supplied points. What is the equal-weight radius of gyration of the selected points (every point weighted equally), in nanometres?", "options": [ { "label": "A", "value": "2.61", "unit": "nm" }, { "label": "B", "value": "3.57", "unit": "nm" }, { "label": "C", "value": "3.90", "unit": "nm" }, { "label": "D", "value": "20.44", "unit": "nm" } ], "inputs": [ "1KX5-residue-points.xyz" ], "correct_label": "C", "audit": [ { "label": "A", "rule": "single_axis_rms", "reason": "只算了一个坐标轴方向的均方根离散度，而不是三维距离。" }, { "label": "B", "rule": "mean_radius", "reason": "用中心距的算术平均。" }, { "label": "C", "rule": "correct", "reason": "按定义在所选点上计算（numpy 分块搜索 + Decimal 复核）。" }, { "label": "D", "rule": "bounding_box_diagonal", "reason": "用坐标轴对齐包围盒对角线代替实际最大间距。" } ] }, { "instance": "FA-ASM-RG-2BUK", "question": "The XYZ file lists the capsid-protein Cα atoms of the complete satellite tobacco necrosis virus capsid: the deposited chain of PDB 2BUK expanded with the 60 operators of its biological assembly (angstrom). Select all supplied points. What is the equal-weight radius of gyration of the selected points (every point weighted equally), in nanometres?", "options": [ { "label": "A", "value": "4.53", "unit": "nm" }, { "label": "B", "value": "7.53", "unit": "nm" }, { "label": "C", "value": "7.85", "unit": "nm" }, { "label": "D", "value": "33.13", "unit": "nm" } ], "inputs": [ "2BUK-capsid-CA.xyz" ], "correct_label": "C", "audit": [ { "label": "A", "rule": "single_axis_rms", "reason": "只算了一个坐标轴方向的均方根离散度，而不是三维距离。" }, { "label": "B", "rule": "rg_from_dmax_solid_sphere", "reason": "按实心球关系由最大尺寸估算回转半径 Rg = √(3/5)·Dmax/2（空心外壳会低估）。" }, { "label": "C", "rule": "correct", "reason": "按定义在所选点上计算（numpy 分块搜索 + Decimal 复核）。" }, { "label": "D", "rule": "bounding_box_diagonal", "reason": "用坐标轴对齐包围盒对角线代替实际最大间距。" } ] } ] } }, { "unit": "backbone_torsion", "kind": "family", "ability": "perception", "registry_id": "backbone_torsion", "generator": "task_families/local_geometry.py", "checker": "checkers/families.py", "checker_function": "backbone_torsion", "bindings": { "L1": { "registry_row": "09d756ae0abb6a83595dcb8446ef793340b12db85652c1c14182f34b2b4e36d4", "task_families/local_geometry.py": "5f7867f2d96cbff718aa367ea23637bb59e567ddd8363e00e346bf046c4917f2" }, "L2": { "checkers/families.py": "1b44f1eab578c983fa0c433d5ba82b86888a12e5a6033b928d69ee0ced4ef88c", "checkers/common.py": "fbc9f4eb287114ac4720d27edc1ea40e25f80da0e1cff6bdee06fbdca2b73aed" } }, "L1": "pending", "L2": "pending", "instances": 2, "L1_record": null, "L2_record": null, "card": { "template": { "name": "蛋白主链二面角 φ/ψ", "concept": "Ramachandran 主链扭转角；符号区分手性（左/右手构象），需要按 IUPAC 约定定向计算。", "inputs": "PDB 连续三残基 ATOM 片段（坐标不改）、残基编号与扭转角定义。", "physical_conditions": "晶体结构单一模型，无替代构象。", "reasoning_scale": "二面角首末原子间距（约 0.3 nm）", "scale_limits": "接近 ±180° 的值因舍入歧义被拒绝。", "source_basis": "RCSB PDB 晶体结构（1CRN、1UBQ、6LYZ）", "answer_method": "法向量 atan2 与投影 atan2 两种实现；检查链连续（C–N ≤ 1.5 Å）与替代构象。", "distractor_mechanisms": [ "opposite_sign", "other_backbone_torsion", "neighbor_residue_same_torsion", "peptide_omega", "unsigned_plane_angle", "backbone_bond_angle" ], "four_choice_validation": "按 360° 周期计算间隔；与正确值 > 5°；升序排列。 v0.2.0：角度是周期量，选项按圆周递增排列，起点由批次目标位置决定（题干说明）；固定从 −180° 排序时，大多数主链二面角为负，正确项集中在 A/B（枚举探针 runs/enum-v12）。“法向量夹角丢失符号”迷惑程度调为 2。", "principle": "IUPAC 二面角：沿中心键从第二原子看向第三原子，前键顺时针转到后键为正。", "validation": "两种实现一致；周期间隔检查；四项逐一核验。", "limits": "反号干扰项形成 ± 配对线索（本批 3/3），需人工判断是否保留。", "template_review": "本轮新建，待人工审核。" }, "samples": [ { "instance": "FA-TOR-1UBQ-V26", "question": "The excerpt contains residues 25–27 of chain A from PDB entry 1UBQ (ubiquitin, X-ray), ATOM records copied unchanged (coordinates in angstrom). Compute the backbone torsion ψ of Val26, defined by atoms N(26)–CA(26)–C(26)–N(27), using the IUPAC sign convention (range −180° to +180°). The options are listed in increasing angle around the circle, starting from an arbitrary point.", "options": [ { "label": "A", "value": "-58.4", "unit": "degree" }, { "label": "B", "value": "-46.4", "unit": "degree" }, { "label": "C", "value": "46.4", "unit": "degree" }, { "label": "D", "value": "133.6", "unit": "degree" } ], "inputs": [ "1UBQ-A26-excerpt.pdb" ], "correct_label": "B", "audit": [ { "label": "A", "rule": "other_backbone_torsion", "reason": "算成同一残基的 φ 而非 ψ。" }, { "label": "B", "rule": "correct", "reason": "IUPAC 符号约定的二面角；法向量与投影两种实现一致。" }, { "label": "C", "rule": "opposite_sign", "reason": "符号约定取反：相当于把镜像手性当成原构象。" }, { "label": "D", "rule": "unsigned_plane_angle", "reason": "用两平面法向量夹角且方向取反，丢失符号（180°−|θ|）。" } ] }, { "instance": "FA-TOR-6LYZ-T43", "question": "The excerpt contains residues 42–44 of chain A from PDB entry 6LYZ (hen egg-white lysozyme, X-ray), ATOM records copied unchanged (coordinates in angstrom). Compute the backbone torsion φ of Thr43, defined by atoms C(42)–N(43)–CA(43)–C(43), using the IUPAC sign convention (range −180° to +180°). The options are listed in increasing angle around the circle, starting from an arbitrary point.", "options": [ { "label": "A", "value": "154.7", "unit": "degree" }, { "label": "B", "value": "-156.6", "unit": "degree" }, { "label": "C", "value": "-143.6", "unit": "degree" }, { "label": "D", "value": "36.4", "unit": "degree" } ], "inputs": [ "6LYZ-A43-excerpt.pdb" ], "correct_label": "C", "audit": [ { "label": "A", "rule": "other_backbone_torsion", "reason": "算成同一残基的 ψ 而非 φ。" }, { "label": "B", "rule": "neighbor_residue_same_torsion", "reason": "算成相邻残基 44 的 φ。" }, { "label": "C", "rule": "correct", "reason": "IUPAC 符号约定的二面角；法向量与投影两种实现一致。" }, { "label": "D", "rule": "unsigned_plane_angle", "reason": "用两平面法向量夹角且方向取反，丢失符号（180°−|θ|）。" } ] } ] } }, { "unit": "binding_design_choice", "kind": "family", "ability": "design", "registry_id": "binding_design_choice", "generator": "task_families/hostguest.py", "checker": "checkers/hostguest.py", "checker_function": "binding_design_choice", "bindings": { "L1": { "registry_row": "4724f3745c0952bf8a5c9f2cc1fe095eb08a10992a7c22a5b19b7f89e722f7fb", "task_families/hostguest.py": "5bab67681ba00790a7253e631a4d5fff91cf9ef722bfe368b989c8b5448e50f1" }, "L2": { "checkers/hostguest.py": "d6c8fb867e6d313c84cce0e6e3fa51e3497a11e4a0e9f826095a804dd5a46654", "checkers/common.py": "fbc9f4eb287114ac4720d27edc1ea40e25f80da0e1cff6bdee06fbdca2b73aed" } }, "L1": "pending", "L2": "pending", "instances": 2, "L1_record": null, "L2_record": null, "card": { "template": { "name": "客体设计选择（实测证据）", "concept": "从参考客体出发，在四个候选替换中选出唯一一个使实测结合增强至少给定幅度的；四个候选均有实测值，且都离阈值 ≥ 0.3 kcal/mol。", "inputs": "WP6 主体与四个候选客体 XYZ。", "physical_conditions": "与主客体结合证据题相同：ITC，1× PBS，pH 7.40，298.15 K，1:1。", "reasoning_scale": "主客体复合物", "scale_limits": "结合强弱取决于电荷、尺寸匹配、溶剂化等，不能单凭几何算出；几何附件只用于识别候选客体。", "source_basis": "SAMPL9 WP6（MIT）", "answer_method": "实测 ΔG 与阈值比较。", "distractor_mechanisms": [ "improves_but_below_target", "weakens_binding", "dication_not_sufficient" ], "four_choice_validation": "恰好一个候选达到目标；阈值附近无候选。", "principle": "有实验证据的设计题（A3）：S0 → S1，候选全部有测量值。", "validation": "独立检查器重算每个候选的改善幅度与阈值关系。", "limits": "实验误差约 0.02–0.06 kcal/mol，阈值附近不放候选；只用 WP6（条件有文档）；“设计”指在实测候选中选择，不预测新分子。", "template_review": "本轮新建（A2/A3），待人工审核。" }, "samples": [ { "instance": "FA-HG-DES1", "question": "The files give the SAMPL9 WP6 host (a carboxylated pillar[6]arene; host file shown with 12 carboxylates) and four candidate guests as 3D structures (XYZ, angstrom). Binding to WP6 was measured by isothermal titration calorimetry in 1× PBS at pH 7.40 and 298.15 K; all complexes are 1:1. You start from guest G7 (cyclohexylammonium), whose measured binding free energy to WP6 under these conditions is -6.97 kcal/mol, and want a replacement guest that binds WP6 at least 2.0 kcal/mol more strongly (measured ΔG ≤ -8.97 kcal/mol). Exactly one of the four candidates achieves this in the measured data. Which one?", "options": [ { "label": "A", "value": "G1: cyclododecylammonium (WP6-G1.xyz)" }, { "label": "B", "value": "G2: 4-(1,1-dimethylpiperidin-1-ium-4-yl)-1,1-dimethyl-piperidin-1-ium (WP6-G2.xyz)" }, { "label": "C", "value": "G6: cyclooctylammonium (WP6-G6.xyz)" }, { "label": "D", "value": "G3: norbornan-2-ylammonium (WP6-G3.xyz)" } ], "inputs": [ "WP6.xyz", "WP6-G2.xyz", "WP6-G6.xyz", "WP6-G3.xyz", "WP6-G1.xyz" ], "correct_label": "B", "audit": [ { "label": "A", "rule": "weakens_binding", "reason": "实测 ΔG = -6.43，反而减弱 0.54 kcal/mol。" }, { "label": "B", "rule": "correct", "reason": "实测 ΔG = -10.44，改善 3.47 kcal/mol，达到目标。" }, { "label": "C", "rule": "improves_but_below_target", "reason": "实测 ΔG = -7.99，只改善 1.02 kcal/mol，未达 2.0。" }, { "label": "D", "rule": "improves_but_below_target", "reason": "实测 ΔG = -7.91，只改善 0.94 kcal/mol，未达 2.0。" } ] }, { "instance": "FA-HG-DES2", "question": "The files give the SAMPL9 WP6 host (a carboxylated pillar[6]arene; host file shown with 12 carboxylates) and four candidate guests as 3D structures (XYZ, angstrom). Binding to WP6 was measured by isothermal titration calorimetry in 1× PBS at pH 7.40 and 298.15 K; all complexes are 1:1. You start from guest G13 (1-methyl-4-(1-methylpyridin-1-ium-4-yl)pyridin-1-ium), whose measured binding free energy to WP6 under these conditions is -8.47 kcal/mol, and want a replacement guest that binds WP6 at least 1.8 kcal/mol more strongly (measured ΔG ≤ -10.27 kcal/mol). Exactly one of the four candidates achieves this in the measured data. Which one?", "options": [ { "label": "A", "value": "G6: cyclooctylammonium (WP6-G6.xyz)" }, { "label": "B", "value": "G10: trimethyl-[[4-[(trimethylammonio)methyl]phenyl]methyl]ammonium (WP6-G10.xyz)" }, { "label": "C", "value": "G12: trimethyl-[6-(trimethylammonio)-2-adamantyl]ammonium (WP6-G12.xyz)" }, { "label": "D", "value": "G5: [3,5-dimethyl-7-(trimethylammonio)-1-adamantyl]-trimethyl-ammonium (WP6-G5.xyz)" } ], "inputs": [ "WP6.xyz", "WP6-G12.xyz", "WP6-G10.xyz", "WP6-G5.xyz", "WP6-G6.xyz" ], "correct_label": "C", "audit": [ { "label": "A", "rule": "weakens_binding", "reason": "实测 ΔG = -7.99，反而减弱 0.48 kcal/mol。" }, { "label": "B", "rule": "dication_not_sufficient", "reason": "双阳离子（仅凭电荷会以为结合更强），实测 ΔG = -9.83，变化 +1.36 kcal/mol，未达 1.8。" }, { "label": "C", "rule": "correct", "reason": "实测 ΔG = -10.84，改善 2.37 kcal/mol，达到目标。" }, { "label": "D", "rule": "dication_not_sufficient", "reason": "双阳离子（仅凭电荷会以为结合更强），实测 ΔG = -5.40，变化 -3.07 kcal/mol，未达 1.8。" } ] } ] } }, { "unit": "binding_evidence_choice", "kind": "family", "ability": "inference", "registry_id": "binding_evidence_choice", "generator": "task_families/hostguest.py", "checker": "checkers/hostguest.py", "checker_function": "binding_evidence_choice", "bindings": { "L1": { "registry_row": "22ac3d460b3899c5eb58ff269af9766e3ee32d5d9a8abf680f42feda995556a0", "task_families/hostguest.py": "5bab67681ba00790a7253e631a4d5fff91cf9ef722bfe368b989c8b5448e50f1" }, "L2": { "checkers/hostguest.py": "d6c8fb867e6d313c84cce0e6e3fa51e3497a11e4a0e9f826095a804dd5a46654", "checkers/common.py": "fbc9f4eb287114ac4720d27edc1ea40e25f80da0e1cff6bdee06fbdca2b73aed" } }, "L1": "pending", "L2": "pending", "instances": 1, "L1_record": null, "L2_record": null, "card": { "template": { "name": "主客体结合强弱（实测证据）", "concept": "给 WP6 主体与四个客体的 3D 结构，推断哪一个结合最强；答案依据 SAMPL9 实测 ITC ΔG（证据只在审核侧），最强者须领先 ≥ 0.8 kcal/mol。", "inputs": "WP6 主体与四个客体 XYZ（SAMPL9 结构）。", "physical_conditions": "ITC，1× PBS，pH 7.40，298.15 K，1:1。", "reasoning_scale": "主客体复合物（主体最大原子间距）", "scale_limits": "结合强弱取决于电荷、尺寸匹配、溶剂化等，不能单凭几何算出。", "source_basis": "SAMPL9 WP6 主客体挑战（MIT）：实测结合自由能与客体结构", "answer_method": "按实测 ΔG 排序；领先幅度检查。", "distractor_mechanisms": [ "next_strongest", "dication_but_weaker", "weaker_binder" ], "four_choice_validation": "四个候选均有实测值；最强者领先 ≥ 0.8 kcal/mol。", "principle": "证据型推断（A2）：答案来自实验，不来自计算。", "validation": "独立检查器读取转录表（哈希核对），核对客体文件与名称一一对应、题干写明条件，并重新排序。", "limits": "实验误差约 0.02–0.06 kcal/mol；只用 WP6（条件有文档）。", "template_review": "本轮新建（A2/A3），待人工审核。" }, "samples": [ { "instance": "FA-HG-EV1", "question": "The files give the SAMPL9 WP6 host (a carboxylated pillar[6]arene; host file shown with 12 carboxylates) and four candidate guests as 3D structures (XYZ, angstrom). Binding to WP6 was measured by isothermal titration calorimetry in 1× PBS at pH 7.40 and 298.15 K; all complexes are 1:1. Which guest binds WP6 most strongly, i.e. has the most negative measured binding free energy?", "options": [ { "label": "A", "value": "G7: cyclohexylammonium (WP6-G7.xyz)" }, { "label": "B", "value": "G1: cyclododecylammonium (WP6-G1.xyz)" }, { "label": "C", "value": "G12: trimethyl-[6-(trimethylammonio)-2-adamantyl]ammonium (WP6-G12.xyz)" }, { "label": "D", "value": "G6: cyclooctylammonium (WP6-G6.xyz)" } ], "inputs": [ "WP6.xyz", "WP6-G12.xyz", "WP6-G6.xyz", "WP6-G7.xyz", "WP6-G1.xyz" ], "correct_label": "C", "audit": [ { "label": "A", "rule": "weaker_binder", "reason": "实测 ΔG = -6.97 kcal/mol，比最强弱 3.87。" }, { "label": "B", "rule": "weaker_binder", "reason": "实测 ΔG = -6.43 kcal/mol，比最强弱 4.41。" }, { "label": "C", "rule": "correct", "reason": "实测 ΔG = -10.84 ± 0.03 kcal/mol，最负；领先 2.85。" }, { "label": "D", "rule": "next_strongest", "reason": "实测 ΔG = -7.99 kcal/mol，次强，比最强弱 2.85。" } ] }, { "instance": "FA-HG-EV2", "question": "The files give the SAMPL9 WP6 host (a carboxylated pillar[6]arene; host file shown with 12 carboxylates) and four candidate guests as 3D structures (XYZ, angstrom). Binding to WP6 was measured by isothermal titration calorimetry in 1× PBS at pH 7.40 and 298.15 K; all complexes are 1:1. Which guest binds WP6 most strongly, i.e. has the most negative measured binding free energy?", "options": [ { "label": "A", "value": "G4: trimethylsilylmethylammonium (WP6-G4.xyz)" }, { "label": "B", "value": "G5: [3,5-dimethyl-7-(trimethylammonio)-1-adamantyl]-trimethyl-ammonium (WP6-G5.xyz)" }, { "label": "C", "value": "G9: (3-hydroxy-1-adamantyl)ammonium (WP6-G9.xyz)" }, { "label": "D", "value": "G10: trimethyl-[[4-[(trimethylammonio)methyl]phenyl]methyl]ammonium (WP6-G10.xyz)" } ], "inputs": [ "WP6.xyz", "WP6-G10.xyz", "WP6-G4.xyz", "WP6-G9.xyz", "WP6-G5.xyz" ], "correct_label": "D", "audit": [ { "label": "A", "rule": "next_strongest", "reason": "实测 ΔG = -7.77 kcal/mol，次强，比最强弱 2.06。" }, { "label": "B", "rule": "dication_but_weaker", "reason": "虽为双阳离子，实测 ΔG = -5.40 kcal/mol，比最强弱 4.43（仅凭电荷判断会误选）。" }, { "label": "C", "rule": "weaker_binder", "reason": "实测 ΔG = -6.23 kcal/mol，比最强弱 3.60。" }, { "label": "D", "rule": "correct", "reason": "实测 ΔG = -9.83 ± 0.04 kcal/mol，最负；领先 2.06。" } ] } ] } }, { "unit": "capsid_architecture", "kind": "family", "ability": "inference", "registry_id": "capsid_architecture", "generator": "task_families/assembly.py", "checker": "checkers/migrated.py", "checker_function": "capsid_architecture", "bindings": { "L1": { "registry_row": "9dffa0f771eabb6fd3ed55d7320337d63a62ec0a6949d920752398a3b3d1c3a1", "task_families/assembly.py": "5cbb7b6b4a45f6797fe9d4f6cdd31e4b7df60da7812d4ce5a0aba6ce248c77e6" }, "L2": { "checkers/migrated.py": "f1cf6f20bca7ad81fd3b5ee5c6749084a090a32dd40b0a394768995a6e3a42eb", "checkers/common.py": "fbc9f4eb287114ac4720d27edc1ea40e25f80da0e1cff6bdee06fbdca2b73aed" } }, "L1": "pending", "L2": "pending", "instances": 5, "L1_record": null, "L2_record": null, "card": { "template": { "name": "病毒衣壳结构（Caspar–Klug）", "concept": "由外壳蛋白拷贝数 N 推断二十面体衣壳的三角剖分数 T=N/60、壳粒总数 10T+2 与六邻体数 10(T−1)；需要从整个衣壳计数并运用结构理论。 大型 dsDNA 病毒（PBCV-1）的主衣壳蛋白形成三聚体假六聚壳粒、五邻体由另一蛋白构成：N = 30(T−1)。", "inputs": "按组分标记的链质心表（沉积的 60 个二十面体操作展开）。", "physical_conditions": "约简表示；几何量在所给点集上定义。", "reasoning_scale": "整个外壳（所选组分点集的最大间距）", "scale_limits": "假设完整二十面体外壳，不区分门户顶点等局部不对称。", "source_basis": "RCSB PDB 大型组装体（1AON、1KX5、1A34、6CGR、6NCL、7ARQ），经沉积的对称操作展开并约简为每残基/每核苷酸一点或每链质心", "answer_method": "计数所选组分的拷贝数，按 Caspar–Klug 关系计算。", "distractor_mechanisms": [ "neighbouring_allowed_T", "all_hexamers", "all_pentamers", "hexons_only", "pentons_only", "hexon_subunits", "monomer_60T_rule", "trimers_as_60T", "forgot_pentons", "hexamer_rule" ], "four_choice_validation": "整数选项互不相同；独立检查器重新计数。", "principle": "N = 60T；壳粒 = 12 + 10(T−1)。", "validation": "独立检查器重新计数并套用同一关系。", "limits": "只适用于完整二十面体外壳。", "template_review": "本轮新建（A4），待人工审核。" }, "samples": [ { "instance": "FA-ASM-CAPS-1CWP", "question": "The table lists the Cα centroid of every capsid-protein chain of the cowpea chlorotic mottle virus capsid (PDB 1CWP), expanded to the whole particle with the 60 operators of its biological assembly; columns are component (CP), copy, x, y, z (angstrom). Each row is one copy of a protein, labelled by component. What is the total number of capsomers (pentamers plus hexamers) in the shell formed by CP?", "options": [ { "label": "A", "value": "20", "unit": "" }, { "label": "B", "value": "30", "unit": "" }, { "label": "C", "value": "32", "unit": "" }, { "label": "D", "value": "36", "unit": "" } ], "inputs": [ "1CWP-chain-centroids.txt" ], "correct_label": "C", "audit": [ { "label": "A", "rule": "hexons_only", "reason": "只数了六邻体，漏掉 12 个五邻体。" }, { "label": "B", "rule": "all_hexamers", "reason": "把所有亚基都当作六聚体。" }, { "label": "C", "rule": "correct", "reason": "N = 180 个 CP，T = N/60 = 3；五邻体 12 个，六邻体 10(T−1)。" }, { "label": "D", "rule": "all_pentamers", "reason": "把所有亚基都当作五聚体。" } ] }, { "instance": "FA-ASM-CAPS-6CGR", "question": "The table lists the Cα centroid of every protein chain of the herpes simplex virus 1 capsid with tegument complexes (PDB 6CGR), expanded to the whole particle with the 60 deposited icosahedral operators; columns are component (VP5, VP26, VP19C, VP23, pUL17, pUL25, pUL36), copy, x, y, z (angstrom). Each row is one copy of a protein, labelled by component. What is the total number of capsomers (pentamers plus hexamers) in the shell formed by VP5?", "options": [ { "label": "A", "value": "150", "unit": "" }, { "label": "B", "value": "160", "unit": "" }, { "label": "C", "value": "162", "unit": "" }, { "label": "D", "value": "192", "unit": "" } ], "inputs": [ "6CGR-chain-centroids.txt" ], "correct_label": "C", "audit": [ { "label": "A", "rule": "hexons_only", "reason": "只数了六邻体，漏掉 12 个五邻体。" }, { "label": "B", "rule": "all_hexamers", "reason": "把所有亚基都当作六聚体。" }, { "label": "C", "rule": "correct", "reason": "N = 960 个 VP5，T = N/60 = 16；五邻体 12 个，六邻体 10(T−1)。" }, { "label": "D", "rule": "all_pentamers", "reason": "把所有亚基都当作五聚体。" } ] } ] } }, { "unit": "cholesteric_design", "kind": "family", "ability": "design", "registry_id": "cholesteric_design", "generator": "task_families/cholesteric.py", "checker": "checkers/mesoscale.py", "checker_function": "cholesteric_design", "bindings": { "L1": { "registry_row": "b11976c6ac025c6229d5eac3631b920c6bf6727c223781dbaafe5db30dfd490d", "task_families/cholesteric.py": "a4072a8c071da8195827357707ad2b722ab99215104cbc90af1eac3456313dbe" }, "L2": { "checkers/mesoscale.py": "55a3a182757904d2fc9680a142005bb6015d5926687a73e3ac51f71da824342f", "checkers/common.py": "fbc9f4eb287114ac4720d27edc1ea40e25f80da0e1cff6bdee06fbdca2b73aed" } }, "L1": "pending", "L2": "pending", "instances": 3, "L1_record": null, "L2_record": null, "card": { "template": { "name": "胆甾液晶结构色设计", "concept": "在四份膜中选择：反射最接近目标色、左手且最接近目标、或在反射上限内掺杂量最少。", "inputs": "胆甾液晶指向矢场（每行 \"site x y z nx ny nz\"，每 5 nm 一点，1.5 μm，任意取向）；设计题给四份。", "physical_conditions": "理想均匀扭曲的螺旋（平面 Grandjean 织构）；λc = ⟨n⟩p，Δλ = Δn·p，p = 1/(HTP·c)；题干写明 Model conditions。", "reasoning_scale": "螺距 p（274–423 nm）", "scale_limits": "按论文参数构建的模型；模型反射与实测相差约 1–2%。", "source_basis": "Shaban et al., Materials 17, 5080 (2024)（E44 + R5011/S5011，HTP 107.5 μm⁻¹）；Dinc et al., Org. Chem. Front. (2024)（反应型异山梨醇掺杂剂涂层）", "answer_method": "逐份拟合螺距与手性，按目标规则选择。", "distractor_mechanisms": [ "extraordinary_index", "half_pitch", "right_handed_closer", "right_handed", "reflects_too_red", "meets_but_more_dopant", "farther_from_target" ], "four_choice_validation": "恰好一个候选满足目标；每个错误选项注明误选原因。", "principle": "设计 = 推断的逆问题（选掺杂浓度或膜）。", "validation": "独立检查器（checkers/mesoscale.py:cholesteric_design）逐个文件把指向矢投影到垂直于螺旋轴的平面、解卷绕后线性拟合出螺距与手性，再按题干目标规则重新选择。", "limits": "非实测浓度的候选为按论文 HTP 计算的模型。", "template_review": "本轮新建（补 100–1000 空格），待人工审核。" }, "samples": [ { "instance": "FA-CH-DES-550", "question": "The four files list the director fields of four model cholesteric liquid-crystal films (files named by composition; columns site x y z in nm and the unit director nx ny nz, n equivalent to −n). Model conditions: the only measured inputs are those reported by Shaban et al. (Materials 2024) for the nematic host E44 doped with the chiral dopant R5011 or S5011: the helical twisting power (107.5 μm⁻¹), the dopant concentration and the host refractive indices (ne = 1.7904, no = 1.5484 at 589 nm, 20 °C); the director twists uniformly about a straight helix axis (ideal planar Grandjean texture) with no defects, surface-anchoring distortion or temperature gradient, which is the idealization behind the paper's relations p = 1/(HTP·c) and λc = p·(ne + no)/2. Each file samples the director every 5 nm over 1.5 μm along an arbitrarily oriented axis. For the E44 films use the average refractive index (ne + no)/2 of E44. You must choose one film such that its normal-incidence reflection band is centred as close as possible to 550 nm. Which film should you choose?", "options": [ { "label": "A", "value": "E44-R5011-2.20wt (clc-E44-R5011-2.20wt.txt)" }, { "label": "B", "value": "E44-R5011-2.90wt (clc-E44-R5011-2.90wt.txt)" }, { "label": "C", "value": "E44-R5011-2.62wt (clc-E44-R5011-2.62wt.txt)" }, { "label": "D", "value": "E44-R5011-3.40wt (clc-E44-R5011-3.40wt.txt)" } ], "inputs": [ "clc-E44-R5011-2.20wt.txt", "clc-E44-R5011-2.62wt.txt", "clc-E44-R5011-2.90wt.txt", "clc-E44-R5011-3.40wt.txt" ], "correct_label": "B", "audit": [ { "label": "A", "rule": "half_pitch", "reason": "用 p/2 计算时它的反射（352.9 nm）最接近目标。" }, { "label": "B", "rule": "correct", "reason": "反射中心 535.5 nm，最接近目标。" }, { "label": "C", "rule": "farther_from_target", "reason": "反射 592.7 nm。" }, { "label": "D", "rule": "farther_from_target", "reason": "反射 456.7 nm。" } ] }, { "instance": "FA-CH-DES-BELOW620", "question": "The four files list the director fields of four model cholesteric liquid-crystal films (files named by composition; columns site x y z in nm and the unit director nx ny nz, n equivalent to −n). Model conditions: the only measured inputs are those reported by Shaban et al. (Materials 2024) for the nematic host E44 doped with the chiral dopant R5011 or S5011: the helical twisting power (107.5 μm⁻¹), the dopant concentration and the host refractive indices (ne = 1.7904, no = 1.5484 at 589 nm, 20 °C); the director twists uniformly about a straight helix axis (ideal planar Grandjean texture) with no defects, surface-anchoring distortion or temperature gradient, which is the idealization behind the paper's relations p = 1/(HTP·c) and λc = p·(ne + no)/2. Each file samples the director every 5 nm over 1.5 μm along an arbitrarily oriented axis. For the E44 films use the average refractive index (ne + no)/2 of E44. You must choose one film such that as little dopant as possible is used while the normal-incidence reflection band is centred at or below 620 nm. Which film should you choose?", "options": [ { "label": "A", "value": "E44-R5011-3.00wt (clc-E44-R5011-3.00wt.txt)" }, { "label": "B", "value": "E44-R5011-2.20wt (clc-E44-R5011-2.20wt.txt)" }, { "label": "C", "value": "E44-R5011-2.40wt (clc-E44-R5011-2.40wt.txt)" }, { "label": "D", "value": "E44-R5011-2.62wt (clc-E44-R5011-2.62wt.txt)" } ], "inputs": [ "clc-E44-R5011-2.20wt.txt", "clc-E44-R5011-2.40wt.txt", "clc-E44-R5011-2.62wt.txt", "clc-E44-R5011-3.00wt.txt" ], "correct_label": "D", "audit": [ { "label": "A", "rule": "meets_but_more_dopant", "reason": "反射 517.6 nm 满足，但掺杂剂更多。" }, { "label": "B", "rule": "reflects_too_red", "reason": "反射 705.9 nm，超过 620 nm；只看螺距 p（422.8 nm）会误判为满足。" }, { "label": "C", "rule": "reflects_too_red", "reason": "反射 647.1 nm，超过 620 nm；只看螺距 p（387.6 nm）会误判为满足。" }, { "label": "D", "rule": "correct", "reason": "满足上限的候选中掺杂剂最少（反射 592.7 nm）。" } ] } ] } }, { "unit": "cholesteric_geometry", "kind": "family", "ability": "perception", "registry_id": "cholesteric_geometry", "generator": "task_families/cholesteric.py", "checker": "checkers/mesoscale.py", "checker_function": "cholesteric_quantity", "bindings": { "L1": { "registry_row": "c0583543736c7f4a9fbb7b29fdb8d99df863b938d33b30861134008e391d76c8", "task_families/cholesteric.py": "a4072a8c071da8195827357707ad2b722ab99215104cbc90af1eac3456313dbe" }, "L2": { "checkers/mesoscale.py": "55a3a182757904d2fc9680a142005bb6015d5926687a73e3ac51f71da824342f", "checkers/common.py": "fbc9f4eb287114ac4720d27edc1ea40e25f80da0e1cff6bdee06fbdca2b73aed" } }, "L1": "pending", "L2": "pending", "instances": 3, "L1_record": null, "L2_record": null, "card": { "template": { "name": "胆甾液晶螺旋几何（螺距 / 手性）", "concept": "从指向矢场识别胆甾螺旋的螺距（转 360° 的距离）与手性（右手定则）。", "inputs": "胆甾液晶指向矢场（每行 \"site x y z nx ny nz\"，每 5 nm 一点，1.5 μm，任意取向）；设计题给四份。", "physical_conditions": "理想均匀扭曲的螺旋（平面 Grandjean 织构）；λc = ⟨n⟩p，Δλ = Δn·p，p = 1/(HTP·c)；题干写明 Model conditions。", "reasoning_scale": "螺距 p（274–423 nm）", "scale_limits": "按论文参数构建的模型；模型反射与实测相差约 1–2%。", "source_basis": "Shaban et al., Materials 17, 5080 (2024)（E44 + R5011/S5011，HTP 107.5 μm⁻¹）；Dinc et al., Org. Chem. Front. (2024)（反应型异山梨醇掺杂剂涂层）", "answer_method": "每步转角求螺距；(n_i × n_i+1)·前进方向 的符号定手性。", "distractor_mechanisms": [ "half_pitch", "double_pitch", "quarter_pitch", "reflection_wavelength", "opposite_handedness", "both_wrong" ], "four_choice_validation": "数值与正确值 > 10 nm；手性题四项为手性 × {p, p/2}。", "principle": "胆甾相：指向矢绕螺旋轴均匀扭转，n 与 −n 等价。", "validation": "独立检查器投影解卷绕后线性拟合。", "limits": "理想均匀扭曲：不含缺陷线、表面锚定与螺距梯度；手性按题干给出的右手定则判断。", "template_review": "本轮新建（补 100–1000 空格），待人工审核。" }, "samples": [ { "instance": "FA-CH-HAND-S5011", "question": "The file lists the director (unit vector of average molecular orientation, n equivalent to −n) at sites along the helix axis of a model cholesteric liquid-crystal film; columns are site x y z (nm) nx ny nz. Model conditions: the only measured inputs are those reported by Shaban et al. (Materials 2024) for the nematic host E44 doped with the chiral dopant R5011 or S5011: the helical twisting power (107.5 μm⁻¹), the dopant concentration and the host refractive indices (ne = 1.7904, no = 1.5484 at 589 nm, 20 °C); the director twists uniformly about a straight helix axis (ideal planar Grandjean texture) with no defects, surface-anchoring distortion or temperature gradient, which is the idealization behind the paper's relations p = 1/(HTP·c) and λc = p·(ne + no)/2. Each file samples the director every 5 nm over 1.5 μm along an arbitrarily oriented axis. A helix is right-handed if, with the right thumb pointing along the direction of travel along the helix axis, the director turns in the sense of the curled fingers; otherwise it is left-handed. What are the handedness and the helical pitch p (the distance over which the director rotates by 360°) of this helix?", "options": [ { "label": "A", "value": "right-handed, pitch 362.0 nm" }, { "label": "B", "value": "left-handed, pitch 181.0 nm" }, { "label": "C", "value": "left-handed, pitch 362.0 nm" }, { "label": "D", "value": "right-handed, pitch 181.0 nm" } ], "inputs": [ "clc-E44-S5011-2.57wt.txt" ], "correct_label": "C", "audit": [ { "label": "A", "rule": "opposite_handedness", "reason": "螺距对，但手性判反（转向与右手定则比较时看错方向）。" }, { "label": "B", "rule": "half_pitch", "reason": "手性对，但报告了 p/2（指向矢转 180° 的距离）。" }, { "label": "C", "rule": "correct", "reason": "每步转角给出 p = 361.958 nm；(n_i × n_i+1)·前进方向 的符号给出左手。" }, { "label": "D", "rule": "both_wrong", "reason": "手性判反且报告了 p/2。" } ] }, { "instance": "FA-CH-PITCH-LRCD", "question": "The file lists the director (unit vector of average molecular orientation, n equivalent to −n) at sites along the helix axis of a model cholesteric liquid-crystal film; columns are site x y z (nm) nx ny nz. Model conditions: the only measured input is the reflection wavelength reported by Dinc et al. (Org. Chem. Front. 2024) for this cholesteric polymer coating, converted to a pitch with the paper's average refractive index of 1.6; the director twists uniformly about a straight helix axis with no defects, which is the idealization behind the paper's relation λ = n·p. Each file samples the director every 5 nm over 1.5 μm along an arbitrarily oriented axis. What is the helical pitch p (the distance along the helix axis over which the director rotates by 360°), in nm?", "options": [ { "label": "A", "value": "209.37", "unit": "nm" }, { "label": "B", "value": "418.75", "unit": "nm" }, { "label": "C", "value": "670.00", "unit": "nm" }, { "label": "D", "value": "837.50", "unit": "nm" } ], "inputs": [ "clc-LRCD-coating.txt" ], "correct_label": "B", "audit": [ { "label": "A", "rule": "half_pitch", "reason": "报告了 p/2（n 与 −n 等价时的光学周期），而螺距是指向矢转 360° 的距离。" }, { "label": "B", "rule": "correct", "reason": "由指向矢每步转角得螺距 p = 418.750 nm；λc = ⟨n⟩p，Δλ = Δn·p，HTP = 1/(p c)。" }, { "label": "C", "rule": "reflection_wavelength", "reason": "报告了反射波长 n·p 而非螺距。" }, { "label": "D", "rule": "double_pitch", "reason": "报告了两个螺距。" } ] } ] } }, { "unit": "cholesteric_optics", "kind": "family", "ability": "inference", "registry_id": "cholesteric_optics", "generator": "task_families/cholesteric.py", "checker": "checkers/mesoscale.py", "checker_function": "cholesteric_quantity", "bindings": { "L1": { "registry_row": "55218cc2ac2ac021a7bd35a790055e91ca5eebb5a2f191cfe8ca0ba1ddf668e5", "task_families/cholesteric.py": "a4072a8c071da8195827357707ad2b722ab99215104cbc90af1eac3456313dbe" }, "L2": { "checkers/mesoscale.py": "55a3a182757904d2fc9680a142005bb6015d5926687a73e3ac51f71da824342f", "checkers/common.py": "fbc9f4eb287114ac4720d27edc1ea40e25f80da0e1cff6bdee06fbdca2b73aed" } }, "L1": "pending", "L2": "pending", "instances": 2, "L1_record": null, "L2_record": null, "card": { "template": { "name": "胆甾液晶选择反射与扭曲力（推断）", "concept": "由螺距与题给折射率推断反射中心波长和带宽，或由螺距与浓度推断手性掺杂剂的螺旋扭曲力 HTP。", "inputs": "胆甾液晶指向矢场（每行 \"site x y z nx ny nz\"，每 5 nm 一点，1.5 μm，任意取向）；设计题给四份。", "physical_conditions": "理想均匀扭曲的螺旋（平面 Grandjean 织构）；λc = ⟨n⟩p，Δλ = Δn·p，p = 1/(HTP·c)；题干写明 Model conditions。", "reasoning_scale": "螺距 p（274–423 nm）", "scale_limits": "按论文参数构建的模型；模型反射与实测相差约 1–2%。", "source_basis": "Shaban et al., Materials 17, 5080 (2024)（E44 + R5011/S5011，HTP 107.5 μm⁻¹）；Dinc et al., Org. Chem. Front. (2024)（反应型异山梨醇掺杂剂涂层）", "answer_method": "λc = ⟨n⟩p；Δλ = Δn·p；HTP = 1/(p c)。", "distractor_mechanisms": [ "extraordinary_index", "ordinary_index", "half_pitch", "no_index", "double_pitch", "central_wavelength", "relative_birefringence", "half_birefringence", "percent_not_fraction", "reflection_for_pitch", "nm_um_slip" ], "four_choice_validation": "与正确值 > 5–8 nm 或 5 μm⁻¹；升序排列，秩按批次轮换。", "principle": "布拉格选择反射：λc = ⟨n⟩p，带宽 Δn·p；HTP 由掺杂剂分子手性决定。", "validation": "独立检查器由拟合螺距与题干参数计算。", "limits": "模型值与实测相差约 1–2%（审核侧列出实测值）。", "template_review": "本轮新建（补 100–1000 空格），待人工审核。" }, "samples": [ { "instance": "FA-CH-BAND-R5011", "question": "The file lists the director (unit vector of average molecular orientation, n equivalent to −n) at sites along the helix axis of a model cholesteric liquid-crystal film; columns are site x y z (nm) nx ny nz. Model conditions: the only measured inputs are those reported by Shaban et al. (Materials 2024) for the nematic host E44 doped with the chiral dopant R5011 or S5011: the helical twisting power (107.5 μm⁻¹), the dopant concentration and the host refractive indices (ne = 1.7904, no = 1.5484 at 589 nm, 20 °C); the director twists uniformly about a straight helix axis (ideal planar Grandjean texture) with no defects, surface-anchoring distortion or temperature gradient, which is the idealization behind the paper's relations p = 1/(HTP·c) and λc = p·(ne + no)/2. Each file samples the director every 5 nm over 1.5 μm along an arbitrarily oriented axis. At normal incidence, what is the width Δλ of the selective (Bragg) reflection band, in nm? Use the average refractive index (ne + no)/2 of the host and its birefringence ne − no.", "options": [ { "label": "A", "value": "43.0", "unit": "nm" }, { "label": "B", "value": "51.5", "unit": "nm" }, { "label": "C", "value": "85.9", "unit": "nm" }, { "label": "D", "value": "592.7", "unit": "nm" } ], "inputs": [ "clc-E44-R5011-2.62wt.txt" ], "correct_label": "C", "audit": [ { "label": "A", "rule": "half_pitch", "reason": "用 p/2 计算带宽。" }, { "label": "B", "rule": "relative_birefringence", "reason": "用 Δn/⟨n⟩ 代替 Δn。" }, { "label": "C", "rule": "correct", "reason": "由指向矢每步转角得螺距 p = 355.051 nm；λc = ⟨n⟩p，Δλ = Δn·p，HTP = 1/(p c)。" }, { "label": "D", "rule": "central_wavelength", "reason": "报告了反射中心波长。" } ] }, { "instance": "FA-CH-LAMBDA-RRCD", "question": "The file lists the director (unit vector of average molecular orientation, n equivalent to −n) at sites along the helix axis of a model cholesteric liquid-crystal film; columns are site x y z (nm) nx ny nz. Model conditions: the only measured input is the reflection wavelength reported by Dinc et al. (Org. Chem. Front. 2024) for this cholesteric polymer coating, converted to a pitch with the paper's average refractive index of 1.6; the director twists uniformly about a straight helix axis with no defects, which is the idealization behind the paper's relation λ = n·p. Each file samples the director every 5 nm over 1.5 μm along an arbitrarily oriented axis. At normal incidence, what is the central wavelength λc of the selective (Bragg) reflection band, in nm? Use the average refractive index 1.6.", "options": [ { "label": "A", "value": "376.9", "unit": "nm" }, { "label": "B", "value": "565.3", "unit": "nm" }, { "label": "C", "value": "603.0", "unit": "nm" }, { "label": "D", "value": "659.5", "unit": "nm" } ], "inputs": [ "clc-RRCD-coating.txt" ], "correct_label": "C", "audit": [ { "label": "A", "rule": "no_index", "reason": "忽略折射率，直接取螺距。" }, { "label": "B", "rule": "ordinary_index", "reason": "用 no 代替平均折射率。" }, { "label": "C", "rule": "correct", "reason": "由指向矢每步转角得螺距 p = 376.875 nm；λc = ⟨n⟩p，Δλ = Δn·p，HTP = 1/(p c)。" }, { "label": "D", "rule": "extraordinary_index", "reason": "用 ne 代替平均折射率。" } ] } ] } }, { "unit": "conformer_target_selection", "kind": "family", "ability": "design", "registry_id": "conformer_target_selection", "generator": "task_families/conformer_design.py", "checker": "checkers/families.py", "checker_function": "conformer_selection", "bindings": { "L1": { "registry_row": "7f32047e836e58fa4b90791fe659e41b593be983caad03c10821041c324a875a", "task_families/conformer_design.py": "c1df20bcb3ca7c59938dcfc28012c37beca3d235e0181495fb2b6d9e9d54a211" }, "L2": { "checkers/families.py": "1b44f1eab578c983fa0c433d5ba82b86888a12e5a6033b928d69ee0ced4ef88c", "checkers/common.py": "fbc9f4eb287114ac4720d27edc1ea40e25f80da0e1cff6bdee06fbdca2b73aed" } }, "L1": "pending", "L2": "pending", "instances": 2, "L1_record": null, "L2_record": null, "card": { "template": { "name": "构象设计选择", "concept": "给定起始构象 S0、允许修改（仅单键旋转：原子、键连与立体中心构型不变）和目标性质（最低能量或最大偶极），从四个真实候选构象中选出唯一满足目标者。", "inputs": "S0 与四个候选的 XYZ（Å）；性质证据只在审核侧。", "physical_conditions": "性质为 QM7-X PBE0+MBD 单点值（DFTB3+MBD 优化几何）。", "reasoning_scale": "整分子构象（0.4–0.8 nm）", "scale_limits": "计算证据，不是实验构象分布或自由能；不是开放式生成。", "source_basis": "QM7-X（CC BY 4.0）", "answer_method": "逐项检查约束（原子、键连图、立体中心带符号体积、与 S0 不同、偶极矢量一致）；去除同一/镜像构象；最优项领先第二名 ≥ 阈值（能量 0.0434 eV，偶极 0.10 e·Å）。", "distractor_mechanisms": [ "real_candidate_worse_by_computed_property", "compactness_heuristic (选 Rg 最小/最大；选择时优先让正确项不是极值)", "minimal_change_heuristic (选与 S0 最接近者；记录诊断)" ], "four_choice_validation": "四个候选均满足约束；唯一最优；数据集 ID 不出现在学生包；凑不齐则记录失败。", "principle": "候选选择 + 计算性质证据。", "validation": "约束与唯一性；性质值来自数据集，未独立重算 DFT。", "limits": "未独立复算 PBE0+MBD；目标只对所述理论水平成立。", "template_review": "本轮新建，待人工审核。用户 2026-09-28 确认：以计算性质为证据的构象选择算设计题。" }, "samples": [ { "instance": "FA-CONF-7032-max_dipole", "question": "S0 is a conformer of a neutral C4H10N2S molecule. You may change it only by rotating about single bonds: the same atoms in the same order, the same bonds and the same configuration at every stereocentre. Goal: obtain the largest total dipole-moment magnitude (PBE0+MBD, at the supplied geometries). All four candidates A–D satisfy the allowed modification. Which candidate best meets the goal?", "options": [ { "label": "A", "value": "candidate_A.xyz" }, { "label": "B", "value": "candidate_B.xyz" }, { "label": "C", "value": "candidate_C.xyz" }, { "label": "D", "value": "candidate_D.xyz" } ], "inputs": [ "S0.xyz", "candidate_A.xyz", "candidate_B.xyz", "candidate_C.xyz", "candidate_D.xyz" ], "correct_label": "C", "audit": [ { "label": "A", "rule": "Geom-m7032-i1-c2-opt", "reason": "满足约束，但目标值比正确项差 0.1786 e·Å（计算证据，非实验）。" }, { "label": "B", "rule": "Geom-m7032-i1-c9-opt", "reason": "满足约束，但目标值比正确项差 0.1864 e·Å（计算证据，非实验）。" }, { "label": "C", "rule": "Geom-m7032-i1-c6-opt", "reason": "满足约束且目标值唯一最优（领先第二名 0.1786 e·Å）。" }, { "label": "D", "rule": "Geom-m7032-i1-c3-opt", "reason": "满足约束，但目标值比正确项差 0.1825 e·Å（计算证据，非实验）。" } ] }, { "instance": "FA-CONF-7095-min_energy", "question": "S0 is a conformer of a neutral C4H8N2S molecule. You may change it only by rotating about single bonds: the same atoms in the same order, the same bonds and the same configuration at every stereocentre. Goal: obtain the lowest total PBE0+MBD energy (single-point energies at the supplied geometries). All four candidates A–D satisfy the allowed modification. Which candidate best meets the goal?", "options": [ { "label": "A", "value": "candidate_A.xyz" }, { "label": "B", "value": "candidate_B.xyz" }, { "label": "C", "value": "candidate_C.xyz" }, { "label": "D", "value": "candidate_D.xyz" } ], "inputs": [ "S0.xyz", "candidate_A.xyz", "candidate_B.xyz", "candidate_C.xyz", "candidate_D.xyz" ], "correct_label": "B", "audit": [ { "label": "A", "rule": "Geom-m7095-i1-c7-opt", "reason": "满足约束，但目标值比正确项差 0.1853 eV（计算证据，非实验）。" }, { "label": "B", "rule": "Geom-m7095-i1-c3-opt", "reason": "满足约束且目标值唯一最优（领先第二名 0.1853 eV）。" }, { "label": "C", "rule": "Geom-m7095-i1-c8-opt", "reason": "满足约束，但目标值比正确项差 0.2457 eV（计算证据，非实验）。" }, { "label": "D", "rule": "Geom-m7095-i1-c6-opt", "reason": "满足约束，但目标值比正确项差 0.2088 eV（计算证据，非实验）。" } ] } ] } }, { "unit": "coordination_shell", "kind": "family", "ability": "perception", "registry_id": "coordination_shell", "generator": "task_families/crystal.py", "checker": "checkers/migrated.py", "checker_function": "coordination_shell", "bindings": { "L1": { "registry_row": "9f37f97ee78fb355bb08f1f8deb3489576816770b6805832e1a43381ffe6a770", "task_families/crystal.py": "7c8a49460aadc9cb692081d49c585fe0180b6adca63ab5ccb5db414df9771502" }, "L2": { "checkers/migrated.py": "f1cf6f20bca7ad81fd3b5ee5c6749084a090a32dd40b0a394768995a6e3a42eb", "checkers/common.py": "fbc9f4eb287114ac4720d27edc1ea40e25f80da0e1cff6bdee06fbdca2b73aed" } }, "L1": "pending", "L2": "pending", "instances": 7, "L1_record": null, "L2_record": null, "card": { "template": { "name": "配位壳层", "concept": "无限周期晶体中，指定中心周围某一物种的最近壳层（个数与距离）；包括网络节点层面的壳层（SALEM-2 的 Zn–Zn 四连接、MOF-5 μ4-O 节点的六连接）。", "inputs": "常规晶胞全部原子分数坐标表 + 晶胞参数（立方只给 a，其他晶系给 a、b、c、α、β、γ）；中心原子的分数坐标与伙伴物种描述。", "physical_conditions": "周期边界；完全占位。", "reasoning_scale": "第一壳层半径", "scale_limits": "只读完全占位的 CIF；非立方晶胞按 CIF 全部对称操作展开（task_families/cell.py）。", "source_basis": "COD", "answer_method": "立方：27 个相邻晶胞映像的近邻搜索，按 0.001 Å 归组壳层。其他晶系：125 个映像，问最短距离及该距离上的原子数（低对称把配位多面体拆成几种距离，“整个多面体”是登记的错误机制）。", "distractor_mechanisms": [ "no_periodic_images", "second_shell", "same_species_shell", "mixed_shells", "merged_first_two_shells", "whole_coordination_polyhedron" ], "four_choice_validation": "选项为“N at D Å”，恰好一项同时匹配个数与距离。", "principle": "含周期映像的最近邻搜索。", "validation": "独立 Decimal 公式复核。", "limits": "MNP004/005 待小修。", "template_review": "本轮迁移新建，待人工审核。" }, "samples": [ { "instance": "FA-COORD-ALNI", "question": "The table lists every atom of one conventional cubic cell of aluminium nickel (AlNi, ordered B2 alloy, COD 9008802). Treat the crystal as infinite and periodic. Around the Ni atom at fractional (0.5000, 0.5000, 0.5000), how many Al atoms form the nearest shell, and at what distance? Distances are rounded to 0.001 Å.", "options": [ { "label": "A", "value": "8 at 2.495 Å" }, { "label": "B", "value": "1 at 2.495 Å" }, { "label": "C", "value": "12 at 4.778 Å" }, { "label": "D", "value": "6 at 2.881 Å" } ], "inputs": [ "FA-COORD-ALNI-cell.txt" ], "correct_label": "A", "audit": [ { "label": "A", "rule": "correct", "reason": "含周期映像的最近壳层：8 个，距离 2.4950 Å。" }, { "label": "B", "rule": "no_periodic_images", "reason": "只数表中这一个晶胞内的原子，漏掉周期映像。" }, { "label": "C", "rule": "second_shell", "reason": "报告了第二壳层（更远的一组）而非最近壳层。" }, { "label": "D", "rule": "same_species_shell", "reason": "数成与中心同种元素的最近壳层。" } ] }, { "instance": "FA-COORD-K2CUF4", "question": "The table lists every atom of one conventional cell (cell parameters in the first line of the table) of potassium copper fluoride (K2CuF4, COD 1527502). Treat the crystal as infinite and periodic. Around the Cu atom at fractional (0.0000, 0.0000, 0.0000), how many F atoms lie at the shortest Cu–F distance (atoms within 0.001 Å of it count as the same distance), and what is that distance? Distances are rounded to 0.001 Å.", "options": [ { "label": "A", "value": "4 at 2.074 Å" }, { "label": "B", "value": "1 at 1.939 Å" }, { "label": "C", "value": "2 at 1.939 Å" }, { "label": "D", "value": "6 at 1.939 Å" } ], "inputs": [ "FA-COORD-K2CUF4-cell.txt" ], "correct_label": "C", "audit": [ { "label": "A", "rule": "second_shell", "reason": "报告了第二壳层（更远的一组）而非最近壳层。" }, { "label": "B", "rule": "no_periodic_images", "reason": "只数表中这一个晶胞内的原子，漏掉周期映像。" }, { "label": "C", "rule": "correct", "reason": "含周期映像的最近壳层：2 个，距离 1.9388 Å。" }, { "label": "D", "rule": "whole_coordination_polyhedron", "reason": "把整个配位多面体（6 个，含 1.939–2.074 Å 的较长键）都算作最短距离的一组。" } ] } ] } }, { "unit": "debye_intensity", "kind": "family", "ability": "inference", "registry_id": "whole_particle_scattering", "generator": "task_families/assembly.py", "checker": "checkers/migrated.py", "checker_function": "debye_intensity", "bindings": { "L1": { "registry_row": "daa3c3ac3dec267869e4c95f7ed1bfdc8fc6b4fc96edeea11c0fa94046b61ffc", "task_families/assembly.py": "5cbb7b6b4a45f6797fe9d4f6cdd31e4b7df60da7812d4ce5a0aba6ce248c77e6" }, "L2": { "checkers/migrated.py": "f1cf6f20bca7ad81fd3b5ee5c6749084a090a32dd40b0a394768995a6e3a42eb", "checkers/common.py": "fbc9f4eb287114ac4720d27edc1ea40e25f80da0e1cff6bdee06fbdca2b73aed" } }, "L1": "pending", "L2": "pending", "instances": 4, "L1_record": null, "L2_record": null, "card": { "template": { "name": "整颗粒散射强度（Debye，超出 Guinier 范围）", "concept": "由整个颗粒的点集精确计算取向平均的归一化散射强度 I(q)/I(0)，q·Rg > 1.3 时 Guinier 近似与形状模型均失效，必须用全部点对。", "inputs": "按组分标记的点表（DNA 折纸每核苷酸 C1′；HSV-1 衣壳每链质心），可只选某一组分。", "physical_conditions": "等权点散射体，无形状因子与溶剂；q = 4π sinθ/λ（题干写明）。", "reasoning_scale": "所选点集的最大间距（探测长度 2π/q 同量级）", "scale_limits": "约简表示；非实测 SAXS。暂无数据源的格：chemistry 100-1000（规划器不据此给出路线）。", "source_basis": "RCSB PDB 大型组装体（1AON、1KX5、1A34、6CGR、6NCL、7ARQ），经沉积的对称操作展开并约简为每残基/每核苷酸一点或每链质心", "answer_method": "Debye 公式 [N + 2Σ_{i 0.02；升序排列，秩按批次轮换。 v0.3.0：加入两种给出更小强度的 Guinier 误用；之前探针中正确项在 30/36 道是最小值（runs/enum-v26）。q 必须恰为题干显示的三位小数，否则拒绝。", "principle": "I(q) = Σ_ij sin(q r_ij)/(q r_ij)（Debye 1915），取向平均的精确结果。", "validation": "独立检查器不用 Debye 公式，而是对方向直接做高阶 Gauss–Legendre × 均匀 φ 求积平均 |Σ exp(iq·r)|²。", "limits": "等权点散射体只刻画形状；真实 SAXS 还需形状因子、溶剂对比与涨落。", "template_review": "本轮新建（A4），待人工审核。" }, "samples": [ { "instance": "FA-DEB-1CWP", "question": "The table lists the Cα centroid of every capsid-protein chain of the cowpea chlorotic mottle virus capsid (PDB 1CWP), expanded to the whole particle with the 60 operators of its biological assembly; columns are component (CP), copy, x, y, z (angstrom). Select all points labelled CP. Treat each selected point as an identical point scatterer (no form factor, no solvent). What is the orientation-averaged normalized scattering intensity I(q)/I(0) of the selected points at q = 0.160 nm⁻¹ (q = 4π sinθ/λ)? Compute it exactly from all point pairs; q·Rg is above the Guinier range here.", "options": [ { "label": "A", "value": "0.027", "unit": "" }, { "label": "B", "value": "0.248", "unit": "" }, { "label": "C", "value": "0.300", "unit": "" }, { "label": "D", "value": "0.669", "unit": "" } ], "inputs": [ "1CWP-chain-centroids.txt" ], "correct_label": "B", "audit": [ { "label": "A", "rule": "guinier_missing_one_third", "reason": "用 Guinier 近似且指数中漏掉 1/3（e^{−q²Rg²}）。" }, { "label": "B", "rule": "correct", "reason": "Debye 公式对全部点对取向平均：I/I0 = [N + 2Σ sin(qr)/(qr)]/N²，N = 180；qRg = 1.90。" }, { "label": "C", "rule": "guinier_outside_range", "reason": "在 qRg = 1.90 > 1.3 处仍用 Guinier 近似。" }, { "label": "D", "rule": "guinier_single_axis_spread", "reason": "用 Guinier 近似，且把单一坐标轴的均方根离散度当作 Rg。" } ] }, { "instance": "FA-DEB-6CGR", "question": "The table lists the Cα centroid of every protein chain of the herpes simplex virus 1 capsid with tegument complexes (PDB 6CGR), expanded to the whole particle with the 60 deposited icosahedral operators; columns are component (VP5, VP26, VP19C, VP23, pUL17, pUL25, pUL36), copy, x, y, z (angstrom). Select all points labelled VP5. Treat each selected point as an identical point scatterer (no form factor, no solvent). What is the orientation-averaged normalized scattering intensity I(q)/I(0) of the selected points at q = 0.035 nm⁻¹ (q = 4π sinθ/λ)? Compute it exactly from all point pairs; q·Rg is above the Guinier range here.", "options": [ { "label": "A", "value": "0.029", "unit": "" }, { "label": "B", "value": "0.066", "unit": "" }, { "label": "C", "value": "0.257", "unit": "" }, { "label": "D", "value": "0.308", "unit": "" } ], "inputs": [ "6CGR-chain-centroids.txt" ], "correct_label": "C", "audit": [ { "label": "A", "rule": "guinier_missing_one_third", "reason": "用 Guinier 近似且指数中漏掉 1/3（e^{−q²Rg²}）。" }, { "label": "B", "rule": "intensity_squared", "reason": "把算出的强度当成振幅又平方了一次（与“振幅当强度”方向相反的混淆）。" }, { "label": "C", "rule": "correct", "reason": "Debye 公式对全部点对取向平均：I/I0 = [N + 2Σ sin(qr)/(qr)]/N²，N = 960；qRg = 1.88。" }, { "label": "D", "rule": "guinier_outside_range", "reason": "在 qRg = 1.88 > 1.3 处仍用 Guinier 近似。" } ] } ] } }, { "unit": "design_choice", "kind": "family", "ability": "design", "registry_id": "design_choice", "generator": "task_families/paper_design.py", "checker": "checkers/paper_design.py", "checker_function": "design_choice", "bindings": { "L1": { "registry_row": "465159cd696cb6f9d057ddcea21d217eb1f17c4c77735b7f466dbaf28267e184", "task_families/paper_design.py": "bf19bf52f24397e4f34292a69a594455fec75575916c0ee9febfd5e89bbe5248" }, "L2": { "checkers/paper_design.py": "5931be583eb5bcc1707b4e277198e3ddb015b06f61f48d2e17e2be96d5aefa04", "checkers/common.py": "fbc9f4eb287114ac4720d27edc1ea40e25f80da0e1cff6bdee06fbdca2b73aed" } }, "L1": "pending", "L2": "pending", "instances": 3, "L1_record": null, "L2_record": null, "card": { "template": { "name": "有证据的结构优化选择（论文案例）", "concept": "从论文中记录在案的结构优化构题：作者为某个目标刻意改了一处结构特征（芳香墙加长、门户取代基加大、孔口收窄），并对每个变体都测了性质。题干给出目标（实测性质的阈值）与四个只用结构描述呈现的候选；实测表留在审核侧，所以这是设计选择，不是查表。", "inputs": "candidates.txt（四个候选的结构描述，逐项转述并带原文位置）；实测性质表与原文位置只在审核侧。", "physical_conditions": "按论文的实测条件写入题干（缓冲液与温度、溶剂与温度、暴露压力与温度）。", "reasoning_scale": "决定性质的那一处几何（芳香墙长轴 0.70–0.92 nm；C–H···X⁻ 接触 0.31 nm；孔口 0.32–0.80 nm）", "scale_limits": "尺度取决定目标性质的那一处几何，不取整个候选分子或整块晶体。", "source_basis": "2026-10-19 下载的三篇 CC BY 全文（本地 inputs/papers/，不入库）：Vincent 2025（分子夹芳香墙 H1→H2，Table 1 的 14 种染料 × 2 主体）、Rando 2025（竹环脲门户取代基 BnBU/BU1/BU2，Table 1 与 Table S3 的 10 种阴离子）、Chetry 2026（MOF 孔口与 D₂/H₂ 分离，Table 1 与 TDS 结果）。设计卡 docs/assets/families/design/*.json 逐项记录原文位置。", "answer_method": "逐个候选、逐条约束比对实测值；恰好一个候选满足全部约束，且必须是原文选定的那一个。", "distractor_mechanisms": [ "measured_inferior_analogue（同篇论文测过但不达标的同类结构）", "violates_constraint（主性质达标却破坏另一条约束，如最窄孔把容量压到 0.2 mmol g⁻¹）", "host_walls_not_extended / guest_not_extended / neither_extended（只改一侧的 π 延长）", "extended_walls_weaken_this_guest（实测反例：延长墙反而变弱）", "strongest_binder_cue（绝对结合最强但选择性方向错）", "distorted_cavity（取代基一样大，位置不同导致空腔扭曲）", "solvent_change_insufficient（换溶剂不改变几何）", "narrowest_pore_cue / pore_too_wide / interpenetrated_network（孔口几何的三种误判）" ], "four_choice_validation": "四个候选必须对每条受约束的性质都有实测值且带原文位置（“未测过”不会被当成“不行”）；每个候选与每个阈值之间必须有 margin（默认 1.2 倍）的距离；恰好一个候选满足全部约束。", "principle": "设计 = 给定目标选结构；正确答案由论文的实测值确定，干扰项是同一篇论文做过、测过但不达标的结构。", "validation": "独立检查器（checkers/paper_design.py:design_choice）读取哈希核对的设计卡，核对 candidates.txt 与卡片逐行一致，从题干文本中重新解析每个阈值（卡片只提供比较方向），用 Decimal 重新判定，并要求唯一满足者即原文选定者。单侧界（原文只给 “> 16”）只允许判定其能判定的一侧，另一侧直接报错。", "limits": "程序保证：四个候选都有实测值、恰好一个满足全部约束、该候选即原文选定者、题干印出的阈值就是代码执行的阈值。程序不能保证：所给结构描述是否足以推出答案而非靠记忆（著名材料有被认出的风险），以及结构描述是否忠于原文；两者须 L1 对照原文位置核对，难度由 L4 判定。Chetry 2026 严格说是“在已有材料中筛选”而非“为目标改造结构”，是否计入路线① 待导师审定。", "template_review": "2026-10-19 由 planned 转 pilot（导师设计题路线①），待 L1/L2 人工审核；L1 须逐项对照原文位置。" }, "samples": [ { "instance": "FA-DES-CHE-FLOW", "question": "Dihydrogen isotopologues can be separated in a nanoporous framework by kinetic quantum sieving: the thermal de Broglie wavelength of H2 is longer than that of D2, so in a pore whose aperture is comparable to that wavelength H2 meets the higher diffusion barrier and the heavier D2 diffuses faster; the effect grows as the temperature falls. All four candidates below are rigid frameworks, so framework flexibility plays no part, and the paper treats them as lacking accessible open metal sites, although its Zeo++ analysis does report an open metal site density for one of them (noted in candidates.txt). Each framework was exposed to a 1:1 D2:H2 mixture at 100 mbar and 30 K for 10 min, and the selectivity S(D2/H2) and the D2 uptake were then read off the thermal desorption spectrum. You need the sorbent for a throughput stage instead: it has to move as much D2 per gram per cycle as possible, and only needs to beat cryogenic distillation, whose selectivity is 1.4, with some room to spare. The attached candidates.txt describes four candidate structures, all of them prepared and measured in Chetry et al., ACS Appl. Mater. Interfaces (2026). The candidate must satisfy: (capacity) the measured D2 uptake at an exposure temperature of 30 K is at least 5 mmol g^-1; (selectivity) the measured D2/H2 selectivity under the same conditions is at least 2. Exactly one of the four does so in the measured data, which is not shown to you. Which candidate framework should you choose?", "options": [ { "label": "A", "value": "Ag-Bpz: Ag-Bpz, a silver bipyrazolate framework" }, { "label": "B", "value": "Cu-4Py-Me: Cu-4Py-Me, the copper triazolyl-isophthalate [Cu(Me-4py-trz-ia)]" }, { "label": "C", "value": "Cu-tetrazolate: Cu-tetrazolate, a copper tetrazolate framework" }, { "label": "D", "value": "UTSA-16(Co): UTSA-16(Co), a cobalt citrate framework" } ], "inputs": [ "candidates.txt" ], "correct_label": "B", "audit": [ { "label": "A", "rule": "interpenetrated_network", "reason": "不满足约束 capacity：孔容中有 8 Å 的一档，但高度互穿的骨架使实测 D₂ 吸附量只有 3.8 mmol g⁻¹，仍不够；“有宽孔”不等于“有可用孔容”。" }, { "label": "B", "rule": "correct", "reason": "实测值满足全部目标约束，且是原文选定的结构（Conclusions：“Cu-4Py-Me (5.5 A, S_D2/H2 = 8) represents a practical compromise, delivering … uptake with moderate selectivity”；Results 给出 S = 8 与 D₂ 吸附量）。" }, { "label": "C", "rule": "narrowest_pore_cue", "reason": "不满足约束 capacity：孔口最窄、选择性最高，但实测 D₂ 吸附量只有 0.2 mmol g⁻¹，离 5 差一个半数量级。" }, { "label": "D", "rule": "measured_inferior_analogue", "reason": "不满足约束 capacity：孔口 3.4–4.4 Å 时实测吸附量 2.7 mmol g⁻¹，选择性虽高但容量不够。" } ] }, { "instance": "FA-DES-CHE-SIEVE", "question": "Dihydrogen isotopologues can be separated in a nanoporous framework by kinetic quantum sieving: the thermal de Broglie wavelength of H2 is longer than that of D2, so in a pore whose aperture is comparable to that wavelength H2 meets the higher diffusion barrier and the heavier D2 diffuses faster; the effect grows as the temperature falls. All four candidates below are rigid frameworks, so framework flexibility plays no part, and the paper treats them as lacking accessible open metal sites, although its Zeo++ analysis does report an open metal site density for one of them (noted in candidates.txt). Each framework was exposed to a 1:1 D2:H2 mixture at 100 mbar and 30 K for 10 min, and the selectivity S(D2/H2) and the D2 uptake were then read off the thermal desorption spectrum. You need the sorbent for an enrichment stage: it has to reach a useful separation factor and still take up enough D2 per gram for a cycle to be worth running. The attached candidates.txt describes four candidate structures, all of them prepared and measured in Chetry et al., ACS Appl. Mater. Interfaces (2026). The candidate must satisfy: (selectivity) the measured D2/H2 selectivity at an exposure temperature of 30 K is at least 12; (capacity) the measured D2 uptake under the same conditions is at least 2 mmol g^-1. Exactly one of the four does so in the measured data, which is not shown to you. Which candidate framework should you choose?", "options": [ { "label": "A", "value": "UTSA-16(Co): UTSA-16(Co), a cobalt citrate framework" }, { "label": "B", "value": "Cu-tetrazolate: Cu-tetrazolate, a copper tetrazolate framework" }, { "label": "C", "value": "Ag-Bpz: Ag-Bpz, a silver bipyrazolate framework" }, { "label": "D", "value": "Cu-4Py-Me: Cu-4Py-Me, the copper triazolyl-isophthalate [Cu(Me-4py-trz-ia)]" } ], "inputs": [ "candidates.txt" ], "correct_label": "A", "audit": [ { "label": "A", "rule": "correct", "reason": "实测值满足全部目标约束，且是原文选定的结构（Conclusions：“Cu-tetrazolate (3.2-3.6 A, S > 16 at 30 K) and UTSA-16(Co) (3.4-4.4 A, S = 15) demonstrate high selectivity, although with inherently limited uptake”，并把 Cu-4Py-Me 列为“practical compromise”；Results 给出四者的 S 与 D₂ 吸附量）。" }, { "label": "B", "rule": "narrowest_pore_cue", "reason": "不满足约束 capacity：孔口最窄、选择性确实最高（原文 > 16），但实测 D₂ 吸附量只有 0.2 mmol g⁻¹，容量差一个数量级。“孔越窄越好”在容量上立刻失效。" }, { "label": "C", "rule": "interpenetrated_network", "reason": "不满足约束 selectivity：孔口（3.5 Å）与最窄的一档相当，却只测到 5.5 的选择性：主要孔容来自 3.5 与 8 Å 两档且骨架高度互穿，原文把它较低的选择性与吸附量归于这种互穿结构。“孔口窄”不足以保证筛分。" }, { "label": "D", "rule": "pore_too_wide", "reason": "不满足约束 selectivity：孔口 5.5 Å 远宽于量子筛分所需，实测选择性只有 8，未达 12；它的吸附量最高（9.7 mmol g⁻¹）却不解决选择性。" } ] } ] } }, { "unit": "diffraction_design", "kind": "family", "ability": "design", "registry_id": "diffraction_design", "generator": "task_families/diffraction_design.py", "checker": "checkers/design_extra.py", "checker_function": "diffraction_design", "bindings": { "L1": { "registry_row": "9dc887771310868f148005cb1f05e8c260e8205dcbd7d618d456f2db2f1f2978", "task_families/diffraction_design.py": "5230a90d08751a30196d7e8bd3df172295adb49f4cfa415e9e66356b387834c5" }, "L2": { "checkers/design_extra.py": "0d42baeb6018399150e5e6f85a3b805b533388ba28d7198deb1cd22f4ba2a02d", "checkers/common.py": "fbc9f4eb287114ac4720d27edc1ea40e25f80da0e1cff6bdee06fbdca2b73aed" } }, "L1": "pending", "L2": "pending", "instances": 4, "L1_record": null, "L2_record": null, "card": { "template": { "name": "衍射设计：选晶体、选谱线或定波长", "concept": "first_diffraction_peak 的逆问题：在四种晶体中选首个非零反射最接近目标 2θ 者；为一种晶体在四条 X 射线谱线中选最接近目标角者；或求使首个非零反射落在目标角的波长。", "inputs": "COD 晶体（NaCl、MgO、CsCl、金刚石、MOF-5、SALEM-2）的整胞分数坐标表；谱线波长在题干给出。", "physical_conditions": "运动学结构因子、原子序数权重；一级 Bragg 衍射。", "reasoning_scale": "首个非零反射的晶面间距 d", "scale_limits": "不含原子散射因子角度依赖与吸收。", "source_basis": "COD 晶体结构（公有领域）", "answer_method": "从全部原子坐标求第一个 |F| ≠ 0 的反射，再按目标规则选择或反解。", "distractor_mechanisms": [ "lowest_index_ignoring_extinction", "theta_not_two_theta", "assumed_simple_cubic", "d_equals_a", "two_theta_as_theta", "missing_factor_two", "second_allowed", "farther_from_target" ], "four_choice_validation": "选择题：胜者领先 ≥ 1.5 倍且 ≥ 0.5°；数值题：与正确值 > 0.05 Å。", "principle": "设计 = 推断的逆问题（测量条件或材料选择）。", "validation": "独立检查器自行枚举 hkl 并求结构因子，从题干与选项读权重、波长和目标。", "limits": "选谱线、定波长属于测量条件设计，是否计为设计题需 L1 审定；选晶体属于材料选择。", "template_review": "本轮新建（设计补缺），待人工审核。" }, "samples": [ { "instance": "FA-XD-ANODE-MOF5", "question": "The table lists every atom of one conventional cubic cell of MOF-5 (Zn4O(BDC)3, COD 1516287). Use the kinematic structure factor with atomic numbers as angle-independent weights and first-order Bragg diffraction; the relevant peak is the lowest-angle reflection with non-zero intensity. Weights: C = 6, H = 1, O = 8, Zn = 30. You must choose the X-ray source line that places this lowest-angle reflection with non-zero intensity closest to 2θ = 7.00° (for example, to keep it clear of the beam stop while resolving it well). Which line should you choose?", "options": [ { "label": "A", "value": "Cr Kα1 (λ = 2.28970 Å)" }, { "label": "B", "value": "Co Kα1 (λ = 1.78897 Å)" }, { "label": "C", "value": "Cu Kα1 (λ = 1.54056 Å)" }, { "label": "D", "value": "Mo Kα1 (λ = 0.70930 Å)" } ], "inputs": [ "FA-XD-ANODE-MOF5-cell.txt" ], "correct_label": "B", "audit": [ { "label": "A", "rule": "lowest_index_ignoring_extinction", "reason": "取最低指数反射、未检查消光时它最接近目标（5.08°）。" }, { "label": "B", "rule": "correct", "reason": "首个非零反射 (1 1 1)，d = 14.9099 Å，2θ = 6.88°。" }, { "label": "C", "rule": "farther_from_target", "reason": "首个非零反射在 2θ = 5.92°，离目标更远。" }, { "label": "D", "rule": "farther_from_target", "reason": "首个非零反射在 2θ = 2.73°，离目标更远。" } ] }, { "instance": "FA-XD-ANODE-SALEM2", "question": "The table lists every atom of one conventional cubic cell of Zn(imidazolate)2 with ZIF-8 sodalite topology (SALEM-2, COD 4118891; major-occupancy linker sites). Use the kinematic structure factor with atomic numbers as angle-independent weights and first-order Bragg diffraction; the relevant peak is the lowest-angle reflection with non-zero intensity. Weights: C = 6, H = 1, N = 7, Zn = 30. You must choose the X-ray source line that places this lowest-angle reflection with non-zero intensity closest to 2θ = 11.00° (for example, to keep it clear of the beam stop while resolving it well). Which line should you choose?", "options": [ { "label": "A", "value": "Co Kα1 (λ = 1.78897 Å)" }, { "label": "B", "value": "Cu Kα1 (λ = 1.54056 Å)" }, { "label": "C", "value": "Cr Kα1 (λ = 2.28970 Å)" }, { "label": "D", "value": "Mo Kα1 (λ = 0.70930 Å)" } ], "inputs": [ "FA-XD-ANODE-SALEM2-cell.txt" ], "correct_label": "C", "audit": [ { "label": "A", "rule": "farther_from_target", "reason": "首个非零反射在 2θ = 8.62°，离目标更远。" }, { "label": "B", "rule": "farther_from_target", "reason": "首个非零反射在 2θ = 7.42°，离目标更远。" }, { "label": "C", "rule": "correct", "reason": "首个非零反射 (1 1 0)，d = 11.9008 Å，2θ = 11.04°。" }, { "label": "D", "rule": "farther_from_target", "reason": "首个非零反射在 2θ = 3.42°，离目标更远。" } ] } ] } }, { "unit": "disulfide_design", "kind": "family", "ability": "design", "registry_id": "disulfide_design", "generator": "task_families/protein_design.py", "checker": "checkers/design_extra.py", "checker_function": "disulfide_design", "bindings": { "L1": { "registry_row": "8514ef5c18c3de43a3697a41cf6b5a8c3c6c4c6648eaef87bba65976635ee812", "task_families/protein_design.py": "2786e0ba067eb1fd9ff993de8182a44a9abab151b8adaed66905c485b25b83d2" }, "L2": { "checkers/design_extra.py": "0d42baeb6018399150e5e6f85a3b805b533388ba28d7198deb1cd22f4ba2a02d", "checkers/common.py": "fbc9f4eb287114ac4720d27edc1ea40e25f80da0e1cff6bdee06fbdca2b73aed" } }, "L1": "pending", "L2": "pending", "instances": 3, "L1_record": null, "L2_record": null, "card": { "template": { "name": "二硫键工程位点选择", "concept": "蛋白工程：在真实蛋白的四个残基对中，选唯一满足题给 Cα–Cα 与 Cβ–Cβ 距离窗口、可突变为半胱氨酸形成二硫键的一对；其余每对至少偏离一个窗口 0.2 Å。", "inputs": "PDB ATOM 片段（涉及的残基，逐行照抄）。", "physical_conditions": "题给几何筛选窗口（含端点）。", "reasoning_scale": "候选残基对中最大的 Cα–Cα 距离（< 1 nm）", "scale_limits": "只按几何窗口筛选。", "source_basis": "RCSB PDB 1UBQ、6LYZ（仓库已有）", "answer_method": "Cα–Cα、Cβ–Cβ 距离与窗口比较；恰好一对满足。", "distractor_mechanisms": [ "calpha_only", "cbeta_only", "both_out" ], "four_choice_validation": "恰好一对满足；其余偏离窗口 ≥ 0.2 Å。", "principle": "二硫键工程的几何预筛（Cα、Cβ 距离）。", "validation": "独立检查器用 Decimal 距离与题干窗口重算。", "limits": "不评估二面角、应变能与稳定性。", "template_review": "本轮新建（设计补缺），待人工审核。" }, "samples": [ { "instance": "EN-1A6M-DS-2-6", "question": "The excerpt contains the ATOM records of the 7 residues involved, from chain A of PDB entry 1A6M (sperm whale oxy-myoglobin, X-ray 1.0 Å), copied unchanged (angstrom). To engineer a new disulfide bond, both residues of one pair will be mutated to cysteine. Use these screening windows: Cα–Cα distance between 4.4 and 6.8 Å and Cβ–Cβ distance between 3.45 and 4.50 Å (both inclusive). Exactly one of the four candidate pairs meets both windows. Which pair should you mutate?", "options": [ { "label": "A", "value": "Ile99–Leu104" }, { "label": "B", "value": "Ala53–Ala57" }, { "label": "C", "value": "Leu2–Glu6" }, { "label": "D", "value": "Ile101–Leu104" } ], "inputs": [ "1A6M-6-design-excerpt.pdb" ], "correct_label": "C", "audit": [ { "label": "A", "rule": "both_out", "reason": "Cα–Cα 7.77 Å、Cβ–Cβ 6.89 Å 均不在窗口内。" }, { "label": "B", "rule": "calpha_only", "reason": "Cα–Cα 6.18 Å 在窗口内，但 Cβ–Cβ 6.23 Å 不在 3.45–4.50 Å（只看 Cα 会误选）。" }, { "label": "C", "rule": "correct", "reason": "Cα–Cα 5.77 Å，Cβ–Cβ 4.09 Å，两项均在窗口内。" }, { "label": "D", "rule": "calpha_only", "reason": "Cα–Cα 5.05 Å 在窗口内，但 Cβ–Cβ 5.35 Å 不在 3.45–4.50 Å（只看 Cα 会误选）。" } ] }, { "instance": "FA-DS-1UBQ-A", "question": "The excerpt contains the ATOM records of the 7 residues involved, from chain A of PDB entry 1UBQ (ubiquitin, X-ray), copied unchanged (angstrom). To engineer a new disulfide bond, both residues of one pair will be mutated to cysteine. Use these screening windows: Cα–Cα distance between 4.4 and 6.8 Å and Cβ–Cβ distance between 3.45 and 4.50 Å (both inclusive). Exactly one of the four candidate pairs meets both windows. Which pair should you mutate?", "options": [ { "label": "A", "value": "Met1–Glu16" }, { "label": "B", "value": "Gln2–Thr14" }, { "label": "C", "value": "Met1–Leu15" }, { "label": "D", "value": "Phe4–Thr66" } ], "inputs": [ "1UBQ-A-design-excerpt.pdb" ], "correct_label": "D", "audit": [ { "label": "A", "rule": "calpha_only", "reason": "Cα–Cα 5.51 Å 在窗口内，但 Cβ–Cβ 7.16 Å 不在 3.45–4.50 Å（只看 Cα 会误选）。" }, { "label": "B", "rule": "calpha_only", "reason": "Cα–Cα 6.62 Å 在窗口内，但 Cβ–Cβ 5.83 Å 不在 3.45–4.50 Å（只看 Cα 会误选）。" }, { "label": "C", "rule": "both_out", "reason": "Cα–Cα 8.21 Å、Cβ–Cβ 9.17 Å 均不在窗口内。" }, { "label": "D", "rule": "correct", "reason": "Cα–Cα 4.52 Å，Cβ–Cβ 4.27 Å，两项均在窗口内。" } ] } ] } }, { "unit": "evidence_elimination", "kind": "family", "ability": "inference", "registry_id": "evidence_elimination", "generator": "task_families/evidence.py", "checker": "checkers/evidence.py", "checker_function": "evidence_elimination", "bindings": { "L1": { "registry_row": "5572d3ebf3b6312cc7b8f54d34c27634464c9bce131da8051912b1c6af944813", "task_families/evidence.py": "212ee0b90156c8149ae25f0014c175a2d9be5f293a49d162bd7c7750a1731f27" }, "L2": { "checkers/evidence.py": "577fb0a912b4b122cdbbc22390bf575ff1d036f522ababed9a3a40b22e128ee9", "checkers/common.py": "fbc9f4eb287114ac4720d27edc1ea40e25f80da0e1cff6bdee06fbdca2b73aed" } }, "L1": "pending", "L2": "pending", "instances": 8, "L1_record": null, "L2_record": null, "card": { "template": { "name": "论文证据 → 排除 → 结论", "concept": "给出论文中的若干观测，四个候选解释中只有一个与全部观测一致；其余三个是论文讨论并排除的解释（或超出证据的说法）。", "inputs": "evidence.txt（论文事实逐条转述，E1–En）；氢键题另附论文 SI 构象 XYZ。", "physical_conditions": "按论文的实验或计算条件写入证据条目。", "reasoning_scale": "证据所描述结构的特征尺度（0.26 nm–0.45 μm）", "scale_limits": "尺度取证据所描述结构的特征长度（莫尔晶胞、涡旋间距、螺距、O···O 距离）。", "source_basis": "第 1 步下载的论文全文（本地 inputs/papers/，不入库）与 Altun 2021 SI；证据卡 docs/assets/families/evidence/*.json 逐条记录原文位置。", "answer_method": "证据卡为每个解释写明对相关观测的预期；代码逐条比对观测，恰好一个解释无矛盾且为原文结论，其余每个至少与一条给学生的事实矛盾。", "distractor_mechanisms": [ "rejected_alternative（原文排除的解释）", "overreach（超出证据的结论）", "surface_cue（只看表面线索，如有键径即判氢键）" ], "four_choice_validation": "每个预期都对应某条观测；恰好一个解释存活且为原文结论；独立检查器重新比对。", "principle": "结论要经得起每一条证据；其他解释必须被具体证据排除。", "validation": "独立检查器（checkers/evidence.py:evidence_elimination）读取哈希核对的证据卡，核对事实与选项，重新比对预期与观测，要求唯一存活者为原文结论。", "limits": "排除逻辑由程序执行；各解释的“预期”由人从原文整理，其科学正确性须 L1 对照原文核对。", "template_review": "2026-10-16 新建（导师第六次会议“证据 → 结论”），待 L1/L2 人工审核；L1 须逐条对照原文位置。" }, "samples": [ { "instance": "FA-EVE-ALT-STABILITY", "question": "Eleven computed isomers and conformers of acetoacetamide and its enol tautomer (labelled ONE to ELEVEN) differ in their intramolecular hydrogen bonds. The attached evidence.txt gives the evidence (facts E1–E2 from Altun, Bleda & Trindle, Molecules 26, 2623 (2021); numbers as reported in the paper). Which statement about hydrogen bonding and the relative stability of these species is consistent with both facts?", "options": [ { "label": "A", "value": "Species without any hydrogen bond are always the least stable ones." }, { "label": "B", "value": "Relative stability is a property of the whole molecule and is not explained by the strength of the local hydrogen bond alone." }, { "label": "C", "value": "The stronger the local hydrogen bond, the lower the energy, so the energy order follows the hydrogen-bond ranking." }, { "label": "D", "value": "CH···O and CH···N contacts contribute nothing, so species having only them are as unstable as species with no hydrogen bond." } ], "inputs": [ "evidence.txt" ], "correct_label": "B", "audit": [ { "label": "A", "rule": "no_hbond_least_stable", "reason": "与 E1 矛盾：有 CH···OH 接触的 NINE（+91）比完全没有氢键的 THREE（+62）还高。（Table 1）" }, { "label": "B", "rule": "correct", "reason": "与全部事实一致，即原文结论（Results after Table 1: stability not simply explained by local H bonding）。" }, { "label": "C", "rule": "stronger_bond_lower_energy", "reason": "与 E2 矛盾：ELEVEN 的氢键排第二强，能量却是 +48，高于只有 CH···N 的 SEVEN（+38）。（Table 1 vs Figure 9）" }, { "label": "D", "rule": "ch_contacts_irrelevant", "reason": "与 E1 矛盾：SEVEN（+38）、SIX（+43）明显低于无氢键的 THREE（+62），与含 XH···Y 的 FIVE（+38）相当。（Table 1）" } ] }, { "instance": "FA-EVE-COT-BEND", "question": "Cryo-Lorentz TEM images of flux vortices in a 300 nm thick MgB2 lamella (pre-tilted by 45°) at 5 K, for fields between 50.8 and 188.7 G. The attached evidence.txt gives the evidence (facts E1–E4 from Cottet et al., arXiv:1401.4062; numbers as reported in the paper). Which explanation of the dark bands is consistent with all of these observations?", "options": [ { "label": "A", "value": "Ferromagnetic domains of a magnetic impurity phase in the crystal." }, { "label": "B", "value": "Vortex-free Meissner domains of an intermediate (type-1.5) superconducting state." }, { "label": "C", "value": "Bend contours: diffraction contrast where local bending of the thin crystal meets the Bragg condition; they hide vortices but do not change the vortex lattice." }, { "label": "D", "value": "Lines of strong pinning centres that hold the vortices in place." } ], "inputs": [ "evidence.txt" ], "correct_label": "C", "audit": [ { "label": "A", "rule": "magnetic_domains", "reason": "与 E2 矛盾：磁畴是样品的固有磁结构，不会因轻微倾转改变位置。（Results (bend-contour test)）" }, { "label": "B", "rule": "meissner_domains", "reason": "与 E2、E3 矛盾：磁性的无涡旋畴不会随样品轻微倾转而移动，也不会被涡旋穿越。（Introduction and Results: no stripes or gossamer patterns; conventional type-II behaviour）" }, { "label": "C", "rule": "correct", "reason": "与全部事实一致，即原文结论（Results: bend contours due to diffraction contrast; crossing curves confirm they do not affect the lattice）。" }, { "label": "D", "rule": "pinning_lines", "reason": "与 E2、E3 矛盾：钉扎线是固定缺陷，不随倾转移动，且会阻止涡旋在区域间移动。（Results: no vortex pinning except at the edge）" } ] } ] } }, { "unit": "evidence_quantity", "kind": "family", "ability": "inference", "registry_id": "evidence_quantity", "generator": "task_families/evidence.py", "checker": "checkers/evidence.py", "checker_function": "evidence_quantity", "bindings": { "L1": { "registry_row": "24357721608e582ef78e22b358bd57e6bbe6109a76da8654cf7269f7c058ac9c", "task_families/evidence.py": "212ee0b90156c8149ae25f0014c175a2d9be5f293a49d162bd7c7750a1731f27" }, "L2": { "checkers/evidence.py": "577fb0a912b4b122cdbbc22390bf575ff1d036f522ababed9a3a40b22e128ee9", "checkers/common.py": "fbc9f4eb287114ac4720d27edc1ea40e25f80da0e1cff6bdee06fbdca2b73aed" } }, "L1": "pending", "L2": "pending", "instances": 8, "L1_record": null, "L2_record": null, "card": { "template": { "name": "论文证据 → 计算 → 结论", "concept": "给出论文中的若干事实（数值与观测），先算一个几何量（载流子间距、环路面积、轨道临界场、等面积转角、涡旋数、反射带宽、HTP 比值、给体–受体距离差），再判断论文的关键结论。", "inputs": "evidence.txt（论文事实逐条转述，E1–En）；氢键题另附论文 SI 构象 XYZ。", "physical_conditions": "按论文的实验或计算条件写入证据条目。", "reasoning_scale": "由证据算出的几何量（0.26 nm–0.86 μm）", "scale_limits": "尺度取所算几何量（间距、厚度、莫尔周期、螺距、给体–受体距离等）。", "source_basis": "第 1 步下载的论文全文（本地 inputs/papers/，不入库）与 Altun 2021 SI；证据卡 docs/assets/families/evidence/*.json 逐条记录原文位置。", "answer_method": "数值由代码从证据卡计算；四个选项 = 数值（正确 / 登记的错误做法）× 结论（原文结论 / 原文排除的解释），恰好一个两者都对。", "distractor_mechanisms": [ "rejected_conclusion（原文排除的解释）", "wrong_constant（如 h/e 代替 h/2e）", "wrong_input_fact（如用总密度代替有效密度）", "wrong_formula（如垂直场公式、只取单一方向）", "confused_quantity（如 H···A 代替 D···A、中心代替带宽）" ], "four_choice_validation": "两个数值相差 ≥ 规定间隔且显示不同；四个组合齐全；独立检查器以 Decimal 复算并逐项解析选项。", "principle": "把论文结论放回它依赖的几何量上：先算对量，再选对解释。", "validation": "独立检查器（checkers/evidence.py:evidence_quantity）读取哈希核对的证据卡，核对 evidence.txt 与卡片逐条一致、数字逐个印在条目中，用不同算法复算两个数值，并要求选项正好是四个组合、只有一个正确。", "limits": "程序保证数值与组合结构；证据转录、结论措辞是否忠于原文须人工对照原文位置（L1）。选项是两个二元判断的组合（格式检查记为低严重度）。", "template_review": "2026-10-16 新建（导师第六次会议“证据 → 结论”），待 L1/L2 人工审核；L1 须逐条对照原文位置。" }, "samples": [ { "instance": "FA-EVQ-CAO-PAULI", "question": "The superconducting state of an atomically thin MA-TBG device (Tc about 0.5 K) was suppressed with magnetic fields perpendicular and parallel to the layers. The attached evidence.txt gives the evidence (facts E1–E4 from Cao et al., Nature 556, 43 (2018); numbers as reported in the paper). Estimate the in-plane critical field that orbital (Ginzburg-Landau thin-film) pair breaking would give for this thickness and coherence length, and compare it with the measurement. Choose the option in which both the value and the conclusion are correct.", "options": [ { "label": "A", "value": "Orbital in-plane critical field ≈ 0.12 T. The measured 1.1 T is set by orbital pair breaking: the in-plane field destroys superconductivity through screening currents in the bilayer." }, { "label": "B", "value": "Orbital in-plane critical field ≈ 36.54 T. The orbital limit is far above the measured 1.1 T, which lies close to the Pauli limit: in-plane superconductivity is destroyed by Zeeman (paramagnetic) pair breaking, not by orbital currents." }, { "label": "C", "value": "Orbital in-plane critical field ≈ 36.54 T. The measured 1.1 T is set by orbital pair breaking: the in-plane field destroys superconductivity through screening currents in the bilayer." }, { "label": "D", "value": "Orbital in-plane critical field ≈ 0.12 T. The orbital limit is far above the measured 1.1 T, which lies close to the Pauli limit: in-plane superconductivity is destroyed by Zeeman (paramagnetic) pair breaking, not by orbital currents." } ], "inputs": [ "evidence.txt" ], "correct_label": "B", "audit": [ { "label": "A", "rule": "perpendicular_formula+orbital_limited", "reason": "数值来自错误做法（套用垂直场的 GL 公式 Φ0/(2πξ²)，忽略了平行场下轨道效应受膜厚 d 限制。），结论也是原文排除的解释。" }, { "label": "B", "rule": "correct", "reason": "数值按原文数据计算正确，结论即原文结论（Magnetic field response (p. 5): d ≈ 0.6 nm would imply ~36 T; dependence interpreted as paramagnetic pair breaking）。" }, { "label": "C", "rule": "orbital_limited", "reason": "数值正确，但结论是原文排除的解释：原文指出原子级厚度使轨道极限约 36 T，远高于实测，因而排除轨道机制。（Magnetic field response (p. 5)）" }, { "label": "D", "rule": "perpendicular_formula", "reason": "结论措辞取自原文，但数值来自错误做法：套用垂直场的 GL 公式 Φ0/(2πξ²)，忽略了平行场下轨道效应受膜厚 d 限制。" } ] }, { "instance": "FA-EVQ-CAO-SQUID", "question": "In an MA-TBG device (twist angle 1.16°), transport near the boundary between the superconducting dome and the half-filling insulator shows oscillations in a perpendicular magnetic field B. The attached evidence.txt gives the evidence (facts E1–E3 from Cao et al., Nature 556, 43 (2018); numbers as reported in the paper). Treat the oscillation as flux quantization through a superconducting loop and find the effective loop area. Choose the option in which both the value and the conclusion are correct.", "options": [ { "label": "A", "value": "Effective loop area ≈ 0.092 µm². The loop is roughly a tenth of the device area, so the oscillation comes from SQUID-like superconducting loops around insulating islands: the superconducting state is spatially inhomogeneous on this scale." }, { "label": "B", "value": "Effective loop area ≈ 0.092 µm². The loop is essentially the whole device, so the oscillation shows a single uniform superconducting ring spanning the Hall bar." }, { "label": "C", "value": "Effective loop area ≈ 0.184 µm². The loop is essentially the whole device, so the oscillation shows a single uniform superconducting ring spanning the Hall bar." }, { "label": "D", "value": "Effective loop area ≈ 0.184 µm². The loop is roughly a tenth of the device area, so the oscillation comes from SQUID-like superconducting loops around insulating islands: the superconducting state is spatially inhomogeneous on this scale." } ], "inputs": [ "evidence.txt" ], "correct_label": "A", "audit": [ { "label": "A", "rule": "correct", "reason": "数值按原文数据计算正确，结论即原文结论（Methods, Phase-coherent transport (p. 15): S ≈ 0.09 µm² vs ~1 µm² device; Josephson junction arrays around insulating islands）。" }, { "label": "B", "rule": "uniform_whole_device", "reason": "数值正确，但结论是原文排除的解释：算出的面积远小于器件面积，原文据此推断存在绝缘“岛”与不均匀性，不是整个器件一个均匀环。（Methods (p. 15): the area is compared with ~1 µm² and attributed to inhomogeneity）" }, { "label": "C", "rule": "normal_flux_quantum+uniform_whole_device", "reason": "数值来自错误做法（用正常态磁通量子 h/e（量子霍尔用）而不是超导磁通量子 h/2e，面积大了一倍。），结论也是原文排除的解释。" }, { "label": "D", "rule": "normal_flux_quantum", "reason": "结论措辞取自原文，但数值来自错误做法：用正常态磁通量子 h/e（量子霍尔用）而不是超导磁通量子 h/2e，面积大了一倍。" } ] } ] } }, { "unit": "extent_choice_v2", "kind": "family", "ability": "perception", "registry_id": "global_extent", "generator": "task_families/extent_choice.py", "checker": "checkers/families.py", "checker_function": "extent", "bindings": { "L1": { "registry_row": "1b682f60d135757ee9f8b56a3b34c672a379549d1831839b05deb2f93088754d", "task_families/extent_choice.py": "e1ddb871279c3ae81c1e5e74590674b8f3fd71efdcd2c1c281a722ea123f4bf4" }, "L2": { "checkers/families.py": "1b44f1eab578c983fa0c433d5ba82b86888a12e5a6033b928d69ee0ced4ef88c", "checkers/common.py": "fbc9f4eb287114ac4720d27edc1ea40e25f80da0e1cff6bdee06fbdca2b73aed" } }, "L1": "pending", "L2": "pending", "instances": 14, "L1_record": null, "L2_record": null, "card": { "template": { "name": "全局最大间距", "concept": "有限点集的整体尺度：所有点对中的最大欧氏距离。", "inputs": "一个已确认 Å 单位的 XYZ，明确点集与结构选择范围。", "physical_conditions": "无；纯几何。", "reasoning_scale": "同输入尺度", "scale_limits": "只适用于有限点集；周期晶胞内的值依赖表示方式。", "source_basis": "真实结构文件（QM7-X/OE62、COD、PDB）", "answer_method": "逐对距离取最大；Decimal 独立循环复核。", "distractor_mechanisms": [ "heavy_atoms_only", "bounding_box_diagonal", "centroid_diameter", "two_largest_radii", "with_vdw_radii", "largest_axis_span", "radius_as_extent" ], "four_choice_validation": "extent_choice_v2：正确值秩按批次平衡，数值按升序排列；与正确值间隔 > 0.05 Å。 v0.3.0：radius_as_extent 迷惑程度调为 2（混淆两种尺寸量），否则答案永远不能在 D（探针 runs/enum-v20）。", "principle": "Dmax = max(i 0.3°；升序排列，秩按批次轮换。 枚举探针发现正确项多为 C（错误机制几乎都给出更小的角），v0.3.0 加入三种给出更大角的错误（布拉格式漏 2、把最强反射当第一个峰、立方公式把根号写成指数和），并把 d = a 的迷惑程度调为 2；立方晶胞即使经通用读取器也走立方路径。", "principle": "布拉格定律 λ = 2d sinθ，加运动学结构因子判定哪些低指数反射不消光。", "validation": "独立检查器（checkers/migrated.py:first_diffraction_peak）对 h、k、l ≤ 5 的全部反射用自己的结构因子求和，取 |F| ≠ 0 的最小 2θ，并核对来源文件哈希。", "limits": "运动学近似、零角度原子序数权重，不含原子散射因子的角度依赖、热振动与反常散射；只问一级衍射；不支持部分占位。", "template_review": "本轮迁移新建，待人工审核。" }, "samples": [ { "instance": "FA-PEAK-B5H9", "question": "The table lists every atom of one conventional cell (cell parameters in the first line of the table) of pentaborane (B5H9, COD 1521678). Use the kinematic structure factor with atomic numbers as angle-independent weights (B = 5, H = 1). For radiation of wavelength 1.54060 Å and first-order Bragg diffraction, at what angle 2θ does the lowest-angle reflection with non-zero intensity appear?", "options": [ { "label": "A", "value": "4.33", "unit": "degree" }, { "label": "B", "value": "8.66", "unit": "degree" }, { "label": "C", "value": "17.37", "unit": "degree" }, { "label": "D", "value": "21.61", "unit": "degree" } ], "inputs": [ "FA-PEAK-B5H9-cell.txt" ], "correct_label": "B", "audit": [ { "label": "A", "rule": "theta_not_two_theta", "reason": "报告了 θ 而非 2θ。" }, { "label": "B", "rule": "correct", "reason": "第一个 |F|≠0 的反射 (0 1 0)，d = 10.20100 Å，2θ = 2 arcsin(λ/2d)。" }, { "label": "C", "rule": "bragg_missing_factor_two", "reason": "布拉格公式漏掉 2（用 λ = d sinθ，与把二级衍射当一级相同）。" }, { "label": "D", "rule": "strongest_not_first", "reason": "把最强的反射 (1 -1 -2) 当作第一个峰（混淆了强度与出现角度）。" } ] }, { "instance": "FA-PEAK-K2CUF4", "question": "The table lists every atom of one conventional cell (cell parameters in the first line of the table) of potassium copper fluoride (K2CuF4, COD 1527502). Use the kinematic structure factor with atomic numbers as angle-independent weights (Cu = 29, F = 9, K = 19). For radiation of wavelength 1.54060 Å and first-order Bragg diffraction, at what angle 2θ does the lowest-angle reflection with non-zero intensity appear?", "options": [ { "label": "A", "value": "6.94", "unit": "degree" }, { "label": "B", "value": "13.90", "unit": "degree" }, { "label": "C", "value": "28.01", "unit": "degree" }, { "label": "D", "value": "43.62", "unit": "degree" } ], "inputs": [ "FA-PEAK-K2CUF4-cell.txt" ], "correct_label": "B", "audit": [ { "label": "A", "rule": "lowest_index_ignoring_extinction", "reason": "取最低角反射 (0 0 1)，未检查它是否消光。" }, { "label": "B", "rule": "correct", "reason": "第一个 |F|≠0 的反射 (0 0 2)，d = 6.36500 Å，2θ = 2 arcsin(λ/2d)。" }, { "label": "C", "rule": "bragg_missing_factor_two", "reason": "布拉格公式漏掉 2（用 λ = d sinθ，与把二级衍射当一级相同）。" }, { "label": "D", "rule": "cubic_d_formula", "reason": "对非立方晶胞套用立方公式 d = a/√(h²+k²+l²)（忽略 b、c 与晶胞角）。" } ] } ] } }, { "unit": "force_path_derivative", "kind": "family", "ability": "inference", "registry_id": "force_path_derivative", "generator": "task_families/force_path.py", "checker": "checkers/families.py", "checker_function": "force_path", "bindings": { "L1": { "registry_row": "b6735e8a6f52d9f49e99fc71d96dc8d96a9c4cfd64682aeb6e3f31e76c44d141", "task_families/force_path.py": "9ec4307787cd1993d35463f958a81162c70cbe580a2f21278691496866f025af" }, "L2": { "checkers/families.py": "1b44f1eab578c983fa0c433d5ba82b86888a12e5a6033b928d69ee0ced4ef88c", "checkers/common.py": "fbc9f4eb287114ac4720d27edc1ea40e25f80da0e1cff6bdee06fbdca2b73aed" } }, "L1": "pending", "L2": "pending", "instances": 1, "L1_record": null, "L2_record": null, "card": { "template": { "name": "受力沿路径的一阶能量变化", "concept": "由 F = −∂E/∂r 与两结构间位移推断沿指定路径在 B 处的能量方向导数：几何（位移方向）+ 物理条件（受力）→ 性质。", "inputs": "A、B 两个 XYZ（同原子序、同坐标系）+ B 处全原子受力表。", "physical_conditions": "PBE0+MBD 总力；直线路径；方向在题干中给定（A→B 或 B→A）。", "reasoning_scale": "全部原子参与（分子尺度 0.4–0.8 nm）", "scale_limits": "局部方向导数，不是 E(B)−E(A)，不证明极小点。", "source_basis": "QM7-X（CC BY 4.0）", "answer_method": "Decimal 与浮点投影求和一致。", "distractor_mechanisms": [ "sign_convention", "heavy_atoms_only", "trapezoid_energy_estimate", "abs_projection_sum", "magnitude_product" ], "four_choice_validation": "与正确值 > 0.05 eV；升序排列，秩按批次平衡；路径方向在实例间变化以削弱“选正数”捷径。", "principle": "dE/dλ = −Σ F_i(B)·(dr_i/dλ)。", "validation": "两种求和一致；四项逐一核验。", "limits": "仍依赖题干给出物理关系；推断深度有限。", "template_review": "本轮新建，待人工审核。" }, "samples": [ { "instance": "FA-FP-QM7X-7040-D2", "question": "Structures A and B of the same molecule share atom order and one Cartesian frame (angstrom). The table gives the total PBE0+MBD force on every atom at B (eV/angstrom), with F_i = −∂E/∂r_i. Along the straight path r_i(λ) = r_i(B) + λ[r_i(A) − r_i(B)], which starts at B and moves toward A, what is dE/dλ at λ = 0 (that is, at B), in eV? Do not realign, mass-weight or normalize the displacement.", "options": [ { "label": "A", "value": "-5.0423", "unit": "eV" }, { "label": "B", "value": "-0.6163", "unit": "eV" }, { "label": "C", "value": "5.4891", "unit": "eV" }, { "label": "D", "value": "9.5279", "unit": "eV" } ], "inputs": [ "A.xyz", "B.xyz", "forces_B.txt" ], "correct_label": "A", "audit": [ { "label": "A", "rule": "correct", "reason": "B 处沿给定路径方向的导数 = −Σ F_i(B)·(路径方向位移)；十进制与浮点实现一致。" }, { "label": "B", "rule": "heavy_atoms_only", "reason": "只累加重原子，忽略氢原子的受力与位移。" }, { "label": "C", "rule": "abs_projection_sum", "reason": "逐原子取投影绝对值后相加，丢失相互抵消。" }, { "label": "D", "rule": "magnitude_product", "reason": "只乘力与位移的模长，忽略夹角。" } ] }, { "instance": "FA-FP-QM7X-7001", "question": "Structures A and B of the same molecule share atom order and one Cartesian frame (angstrom). The table gives the total PBE0+MBD force on every atom at B (eV/angstrom), with F_i = −∂E/∂r_i. Along the straight path r_i(λ) = r_i(A) + λ[r_i(B) − r_i(A)], what is dE/dλ at λ = 1 (that is, at B), in eV? Do not realign, mass-weight or normalize the displacement.", "options": [ { "label": "A", "value": "-1.8479", "unit": "eV" }, { "label": "B", "value": "0.7856", "unit": "eV" }, { "label": "C", "value": "0.9240", "unit": "eV" }, { "label": "D", "value": "1.8479", "unit": "eV" } ], "inputs": [ "A.xyz", "B.xyz", "forces_B.txt" ], "correct_label": "D", "audit": [ { "label": "A", "rule": "sign_convention", "reason": "把力当作能量梯度（漏掉 F = −∂E/∂r 的负号），或忽略题目给定的路径方向。" }, { "label": "B", "rule": "heavy_atoms_only", "reason": "只累加重原子，忽略氢原子的受力与位移。" }, { "label": "C", "rule": "trapezoid_energy_estimate", "reason": "按 A 处受力为零的梯形估计给出能量差，而题目问的是 B 处的导数。" }, { "label": "D", "rule": "correct", "reason": "B 处沿给定路径方向的导数 = −Σ F_i(B)·(路径方向位移)；十进制与浮点实现一致。" } ] } ] } }, { "unit": "fret_design", "kind": "family", "ability": "design", "registry_id": "fret_design", "generator": "task_families/protein_design.py", "checker": "checkers/design_extra.py", "checker_function": "fret_design", "bindings": { "L1": { "registry_row": "bfc6a89e6cf3159ded832a0f27a4090ce8f66bccb7666e289b71939244e6a996", "task_families/protein_design.py": "2786e0ba067eb1fd9ff993de8182a44a9abab151b8adaed66905c485b25b83d2" }, "L2": { "checkers/design_extra.py": "0d42baeb6018399150e5e6f85a3b805b533388ba28d7198deb1cd22f4ba2a02d", "checkers/common.py": "fbc9f4eb287114ac4720d27edc1ea40e25f80da0e1cff6bdee06fbdca2b73aed" } }, "L1": "pending", "L2": "pending", "instances": 3, "L1_record": null, "L2_record": null, "card": { "template": { "name": "FRET 标记位点设计", "concept": "在真实蛋白或 tRNA 的四个候选标记对中，选点偶极 FRET 效率（题给 R0）最接近目标的一对；推断的逆问题。", "inputs": "PDB ATOM 片段（涉及的残基或核苷酸，逐行照抄）。", "physical_conditions": "点偶极 Förster 定律；R0 为题设参数。", "reasoning_scale": "候选标记对中最大的点间距离（1–10 nm）", "scale_limits": "不含染料连接臂与构象涨落。", "source_basis": "RCSB PDB 1EHZ、1UBQ、6LYZ（仓库已有）", "answer_method": "E = 1/(1+(r/R0)^6)，选最接近目标者；领先幅度检查。", "distractor_mechanisms": [ "complement", "inverse_square", "farther_from_target" ], "four_choice_validation": "胜者领先 ≥ 1.5 倍且 ≥ 0.05。", "principle": "设计 = 推断的逆问题（选择标记位点）。", "validation": "独立检查器用 Decimal 距离与题干 R0、目标重算。", "limits": "R0 为模型参数，未对应具体染料。", "template_review": "本轮新建（设计补缺），待人工审核。" }, "samples": [ { "instance": "EN-12E8-FD-25-1-11", "question": "The excerpt contains the ATOM records of the 8 residues involved, from chain H of PDB entry 12E8 (2E8 Fab fragment, heavy chain, X-ray), copied unchanged (angstrom). You will attach a donor and an acceptor dye to one of the four candidate pairs; treat each dye as a point at the CA atom of its residue, with Förster radius R0 = 2.5 nm and the standard point-dipole Förster law. You want a steady-state FRET efficiency as close as possible to 0.25. Which pair should you label?", "options": [ { "label": "A", "value": "Tyr145–Val183" }, { "label": "B", "value": "Leu4–Arg100" }, { "label": "C", "value": "Glu1–Val11" }, { "label": "D", "value": "Leu170–Ser179" } ], "inputs": [ "12E8-11-design-excerpt.pdb" ], "correct_label": "C", "audit": [ { "label": "A", "rule": "farther_from_target", "reason": "r = 2.77 nm，E = 0.349，离目标更远。" }, { "label": "B", "rule": "farther_from_target", "reason": "r = 1.19 nm，E = 0.989，离目标更远。" }, { "label": "C", "rule": "correct", "reason": "r = 3.04 nm，E = 0.235，最接近目标。" }, { "label": "D", "rule": "complement", "reason": "把效率算成 1 − E时它最接近目标（0.065）。" } ] }, { "instance": "EN-1FHA-FD-25-5-42", "question": "The excerpt contains the ATOM records of the 8 residues involved, from chain A of PDB entry 1FHA (human H-chain ferritin, X-ray), copied unchanged (angstrom). You will attach a donor and an acceptor dye to one of the four candidate pairs; treat each dye as a point at the CA atom of its residue, with Förster radius R0 = 4.0 nm and the standard point-dipole Förster law. You want a steady-state FRET efficiency as close as possible to 0.25. Which pair should you label?", "options": [ { "label": "A", "value": "Asp44–Glu67" }, { "label": "B", "value": "Thr5–Asp42" }, { "label": "C", "value": "Asn50–Asp123" }, { "label": "D", "value": "Leu120–Leu138" } ], "inputs": [ "1FHA-42-design-excerpt.pdb" ], "correct_label": "B", "audit": [ { "label": "A", "rule": "complement", "reason": "把效率算成 1 − E时它最接近目标（0.250）。" }, { "label": "B", "rule": "correct", "reason": "r = 4.84 nm，E = 0.241，最接近目标。" }, { "label": "C", "rule": "farther_from_target", "reason": "r = 4.35 nm，E = 0.376，离目标更远。" }, { "label": "D", "rule": "farther_from_target", "reason": "r = 1.48 nm，E = 0.997，离目标更远。" } ] } ] } }, { "unit": "fret_efficiency", "kind": "family", "ability": "inference", "registry_id": "scattering_model_inference", "generator": "task_families/scattering.py", "checker": "checkers/migrated.py", "checker_function": "fret_efficiency", "bindings": { "L1": { "registry_row": "5c6c1ff9d1de2befa305e12501661b48983e7ea8bc35702c229f86780a3001b2", "task_families/scattering.py": "546ac707ebadea8dd322cba363f52b8160da770f71fe48ae0afb6d835ee489c6" }, "L2": { "checkers/migrated.py": "f1cf6f20bca7ad81fd3b5ee5c6749084a090a32dd40b0a394768995a6e3a42eb", "checkers/common.py": "fbc9f4eb287114ac4720d27edc1ea40e25f80da0e1cff6bdee06fbdca2b73aed" } }, "L1": "pending", "L2": "pending", "instances": 1, "L1_record": null, "L2_record": null, "card": { "template": { "name": "散射/FRET 模型推断", "concept": "由结构几何与给定模型参数推断可观测量：FRET 效率（点探针、给定 R0）与 Guinier 近似下的归一化小角散射强度（等权点散射体、给定 q）。题干给出模型输入但不给公式。", "inputs": "PDB 链 ATOM 片段（FRET）或整分子重原子 XYZ（Guinier）。", "physical_conditions": "Förster 点偶极模型（R0 含取向与光谱因子）；Guinier 近似仅在 qRg ≤ 1.3 出题。", "reasoning_scale": "全局尺度", "scale_limits": "模型假设需人工审核。暂无数据源的格：chemistry 1-10（规划器不据此给出路线）。", "source_basis": "PDB（含 7ARQ DNA 折纸约简点表）+ 教科书/论文模型", "answer_method": "FRET：直线距离 + E=1/(1+(r/R0)^6)；Guinier：等权 Rg + exp(−q²Rg²/3)。", "distractor_mechanisms": [ "path_length_distance", "complement", "closest_atom_pair", "r_equals_R0_default", "wrong_acceptor_atom", "missing_one_third", "half_dmax_as_rg", "amplitude_not_intensity", "unit_mixups" ], "four_choice_validation": "与正确值 > 0.02–0.03；升序排列，秩按批次轮换。FRET 可由题设 R0 列表中选取使目标秩可达的值（某些秩只在 E < 0.5 或 E > 0.5 时可达；枚举探针发现只用固定 R0 时正确项总是最大）。 Guinier：q 必须恰为题干显示的两位小数（之前更精细的 q 会使题干与答案不一致）；枚举实例设 strict_rank。", "principle": "Guinier：qRg ≲ 1.3；FRET：E = 1/(1+(r/R0)^6)。", "validation": "独立检查器（checkers/migrated.py）：FRET 从题干点名的原子取坐标、从题干读 R0，按直线距离重算效率；Guinier 用成对距离恒等式求等权 Rg（出题端用质心公式），核对 qRg ≤ 1.3，并核对点集与已发布资产或源 PDB 一致。", "limits": "FRET 为点偶极模型，R0 为题设值，不含染料连接臂与取向分布；Guinier 只在小 q 区间成立，等权点散射体不等于电子密度。", "template_review": "本轮迁移新建，待人工审核。" }, "samples": [ { "instance": "FA-FRET-6LYZ", "question": "The excerpt contains the ATOM records of chain A of PDB entry 6LYZ (hen egg-white lysozyme; probes at the two chain termini), copied unchanged. Model a FRET donor as a point at atom CA of Lys1 and an acceptor as a point at atom CA of Leu129. Assume a Förster radius R0 = 2.20 nm (orientation and spectral factors already included). What transfer efficiency does the Förster model predict?", "options": [ { "label": "A", "value": "0.000", "unit": "" }, { "label": "B", "value": "0.500", "unit": "" }, { "label": "C", "value": "0.575", "unit": "" }, { "label": "D", "value": "0.930", "unit": "" } ], "inputs": [ "6LYZ-chainA.pdb" ], "correct_label": "C", "audit": [ { "label": "A", "rule": "path_length_distance", "reason": "用沿链骨架标记原子（CA）的路径长度代替空间直线距离。" }, { "label": "B", "rule": "r_equals_R0_default", "reason": "未计算距离，默认 r≈R0，直接取 E=0.5。" }, { "label": "C", "rule": "correct", "reason": "r = 2.0917 nm（直线距离），E = 1/(1+(r/R0)^6)。" }, { "label": "D", "rule": "closest_atom_pair", "reason": "用两残基间最近的重原子对距离（1.430 nm）代替指定标记原子的间距。" } ] }, { "instance": "EN-12E8-FRET-1-8", "question": "The excerpt contains the ATOM records of chain H of PDB entry 12E8 (2E8 Fab fragment, heavy chain, X-ray), copied unchanged. Model a FRET donor as a point at atom CA of Glu1 and an acceptor as a point at atom CA of Gly8. Assume a Förster radius R0 = 2.50 nm (orientation and spectral factors already included). What transfer efficiency does the Förster model predict?", "options": [ { "label": "A", "value": "0.244", "unit": "" }, { "label": "B", "value": "0.404", "unit": "" }, { "label": "C", "value": "0.756", "unit": "" }, { "label": "D", "value": "0.877", "unit": "" } ], "inputs": [ "12E8-chainH.pdb" ], "correct_label": "C", "audit": [ { "label": "A", "rule": "complement", "reason": "报告了 1−E（供体保留的比例）。" }, { "label": "B", "rule": "path_length_distance", "reason": "用沿链骨架标记原子（CA）的路径长度代替空间直线距离。" }, { "label": "C", "rule": "correct", "reason": "r = 2.0713 nm（直线距离），E = 1/(1+(r/R0)^6)。" }, { "label": "D", "rule": "closest_atom_pair", "reason": "用两残基间最近的重原子对距离（1.803 nm）代替指定标记原子的间距。" } ] } ] } }, { "unit": "guinier_intensity", "kind": "family", "ability": "inference", "registry_id": "scattering_model_inference", "generator": "task_families/scattering.py", "checker": "checkers/migrated.py", "checker_function": "guinier_intensity", "bindings": { "L1": { "registry_row": "5c6c1ff9d1de2befa305e12501661b48983e7ea8bc35702c229f86780a3001b2", "task_families/scattering.py": "546ac707ebadea8dd322cba363f52b8160da770f71fe48ae0afb6d835ee489c6" }, "L2": { "checkers/migrated.py": "f1cf6f20bca7ad81fd3b5ee5c6749084a090a32dd40b0a394768995a6e3a42eb", "checkers/common.py": "fbc9f4eb287114ac4720d27edc1ea40e25f80da0e1cff6bdee06fbdca2b73aed" } }, "L1": "pending", "L2": "pending", "instances": 3, "L1_record": null, "L2_record": null, "card": { "template": { "name": "散射/FRET 模型推断", "concept": "由结构几何与给定模型参数推断可观测量：FRET 效率（点探针、给定 R0）与 Guinier 近似下的归一化小角散射强度（等权点散射体、给定 q）。题干给出模型输入但不给公式。", "inputs": "PDB 链 ATOM 片段（FRET）或整分子重原子 XYZ（Guinier）。", "physical_conditions": "Förster 点偶极模型（R0 含取向与光谱因子）；Guinier 近似仅在 qRg ≤ 1.3 出题。", "reasoning_scale": "全局尺度", "scale_limits": "模型假设需人工审核。暂无数据源的格：chemistry 1-10（规划器不据此给出路线）。", "source_basis": "PDB（含 7ARQ DNA 折纸约简点表）+ 教科书/论文模型", "answer_method": "FRET：直线距离 + E=1/(1+(r/R0)^6)；Guinier：等权 Rg + exp(−q²Rg²/3)。", "distractor_mechanisms": [ "path_length_distance", "complement", "closest_atom_pair", "r_equals_R0_default", "wrong_acceptor_atom", "missing_one_third", "half_dmax_as_rg", "amplitude_not_intensity", "unit_mixups" ], "four_choice_validation": "与正确值 > 0.02–0.03；升序排列，秩按批次轮换。FRET 可由题设 R0 列表中选取使目标秩可达的值（某些秩只在 E < 0.5 或 E > 0.5 时可达；枚举探针发现只用固定 R0 时正确项总是最大）。 Guinier：q 必须恰为题干显示的两位小数（之前更精细的 q 会使题干与答案不一致）；枚举实例设 strict_rank。", "principle": "Guinier：qRg ≲ 1.3；FRET：E = 1/(1+(r/R0)^6)。", "validation": "独立检查器（checkers/migrated.py）：FRET 从题干点名的原子取坐标、从题干读 R0，按直线距离重算效率；Guinier 用成对距离恒等式求等权 Rg（出题端用质心公式），核对 qRg ≤ 1.3，并核对点集与已发布资产或源 PDB 一致。", "limits": "FRET 为点偶极模型，R0 为题设值，不含染料连接臂与取向分布；Guinier 只在小 q 区间成立，等权点散射体不等于电子密度。", "template_review": "本轮迁移新建，待人工审核。" }, "samples": [ { "instance": "FA-ASM-GUIN-1A34", "question": "The XYZ file lists the capsid-protein Cα atoms (60 copies) of the satellite tobacco mosaic virus capsid (PDB 1A34). Treat each supplied point as an identical point scatterer. In the Guinier approximation (which applies at this q), what is the normalized small-angle scattering intensity I(q)/I(0) at q = 0.14 nm⁻¹?", "options": [ { "label": "A", "value": "0.348", "unit": "" }, { "label": "B", "value": "0.703", "unit": "" }, { "label": "C", "value": "0.839", "unit": "" }, { "label": "D", "value": "0.889", "unit": "" } ], "inputs": [ "1A34-capsid-CA.xyz" ], "correct_label": "B", "audit": [ { "label": "A", "rule": "missing_one_third", "reason": "指数中漏掉 1/3。" }, { "label": "B", "rule": "correct", "reason": "等权 Rg = 7.3397 nm，qRg = 1.028 ≤ 1.3，I/I0 = exp(−q²Rg²/3)。" }, { "label": "C", "rule": "amplitude_not_intensity", "reason": "报告了散射振幅比（强度的平方根）而非强度比。" }, { "label": "D", "rule": "single_axis_spread_as_rg", "reason": "把单一坐标轴方向的均方根离散度当作回转半径（偏小），强度因而偏大。" } ] }, { "instance": "FA-ASM-GUIN-7ARQ", "question": "The table lists the C1' atom of every nucleotide of a DNA-origami 16-helix bundle (PDB 7ARQ). Treat each supplied point as an identical point scatterer. In the Guinier approximation (which applies at this q), what is the normalized small-angle scattering intensity I(q)/I(0) at q = 0.12 nm⁻¹?", "options": [ { "label": "A", "value": "0.252", "unit": "" }, { "label": "B", "value": "0.281", "unit": "" }, { "label": "C", "value": "0.655", "unit": "" }, { "label": "D", "value": "0.812", "unit": "" } ], "inputs": [ "7ARQ-nucleotide-points.txt" ], "correct_label": "C", "audit": [ { "label": "A", "rule": "half_dmax_as_rg", "reason": "把最大尺寸的一半当作回转半径。" }, { "label": "B", "rule": "missing_one_third", "reason": "指数中漏掉 1/3。" }, { "label": "C", "rule": "correct", "reason": "等权 Rg = 9.3858 nm，qRg = 1.126 ≤ 1.3，I/I0 = exp(−q²Rg²/3)。" }, { "label": "D", "rule": "single_axis_spread_as_rg", "reason": "把单一坐标轴方向的均方根离散度当作回转半径（偏小），强度因而偏大。" } ] } ] } }, { "unit": "hbond_geometry", "kind": "family", "ability": "perception", "registry_id": "hbond_geometry", "generator": "task_families/hbond.py", "checker": "checkers/hbonds.py", "checker_function": "hbond_geometry", "bindings": { "L1": { "registry_row": "da0d527f33a59bab08fdc18af55daa7d1be4e1c33584a3a5b2f1d71a0fabe539", "task_families/hbond.py": "1d4f4c97414f1ea9f179951b827fa412051fa5d429a918e00286dc1a59549c09" }, "L2": { "checkers/hbonds.py": "31403a45307cefac4c850430d1e6db93eaadf15c898a0d15822e7941a386ed0f", "checkers/common.py": "fbc9f4eb287114ac4720d27edc1ea40e25f80da0e1cff6bdee06fbdca2b73aed" } }, "L1": "pending", "L2": "pending", "instances": 1, "L1_record": null, "L2_record": null, "card": { "template": { "name": "氢键几何量", "concept": "分子内氢键 D–H···A 的几何量：给体–受体距离、氢–受体距离或 D–H···A 角；原子按化学角色命名（如羟基氧、羰基氧、酰胺氮）。", "inputs": "XYZ（论文 SI 的计算构象，按行号计数）。", "physical_conditions": "单一计算构象，坐标原样；不含振动平均与溶剂。", "reasoning_scale": "给体–受体或氢–受体距离（0.15–0.5 nm）", "scale_limits": "分子内单个接触的局部几何。", "source_basis": "Altun, Bleda & Trindle, Molecules 26, 2623 (2021)（CC BY 4.0）SI 第 3–6 页坐标（仓库内已有资产）", "answer_method": "指定原子的欧氏距离或以 H 为顶点的向量夹角；共价半径规则确认 D–H 成键、H–A 不成键。", "distractor_mechanisms": [ "h_acceptor_instead", "donor_acceptor_instead", "path_through_h", "linear_assumption", "covalent_d_h", "other_acceptor", "angle_at_donor", "angle_at_acceptor", "supplement", "acceptor_side" ], "four_choice_validation": "距离与正确值相差 > 0.03 Å、角度 > 3°；升序排列，秩按批次轮换。", "principle": "氢键几何由给体、氢、受体三个原子的相对位置决定；常见混淆是把 D···A 与 H···A 互换、把角度顶点放错。", "validation": "独立检查器（checkers/hbonds.py:hbond_geometry）从题干读出三个原子行号与所问量，用 Decimal 距离和余弦定理重算，并用自己的共价半径确认成键关系。", "limits": "只测几何量，不据此判定氢键强弱、能量或光谱位移。", "template_review": "2026-10-13 新建，待 L1/L2 人工审核。" }, "samples": [ { "instance": "FA-HBG-FIVE-HN", "question": "The supplied XYZ is conformer FIVE of 3-hydroxy-2-butenamide, a computed structure from Altun, Bleda & Trindle (2021) (14 atoms, angstrom). In this conformer, O5, the hydroxyl oxygen (OH), is covalently bonded to H4, and N11, the amide NH2 nitrogen, is the candidate hydrogen-bond acceptor (rows 5, 4 and 11, counted from 1 after the two XYZ header lines). What is the hydrogen–acceptor distance H4···N11?", "options": [ { "label": "A", "value": "1.757", "unit": "angstrom" }, { "label": "B", "value": "1.926", "unit": "angstrom" }, { "label": "C", "value": "2.734", "unit": "angstrom" }, { "label": "D", "value": "3.582", "unit": "angstrom" } ], "inputs": [ "HBI002-S0008.xyz" ], "correct_label": "B", "audit": [ { "label": "A", "rule": "linear_assumption", "reason": "假设氢键是直线：用 D···A 减去 D–H 键长。" }, { "label": "B", "rule": "correct", "reason": "按指定原子直接计算；成键关系由共价半径规则确认。" }, { "label": "C", "rule": "donor_acceptor_instead", "reason": "量成给体与受体重原子之间的距离，而不是 H···A。" }, { "label": "D", "rule": "other_acceptor:O10", "reason": "量到了另一个杂原子 O10（不是题目指定的受体）。" } ] }, { "instance": "FA-HBG-FOUR-ANG", "question": "The supplied XYZ is conformer FOUR of 3-hydroxy-2-butenamide, a computed structure from Altun, Bleda & Trindle (2021) (14 atoms, angstrom). In this conformer, N3, the amide NH2 nitrogen, is covalently bonded to H5, and O13, the hydroxyl oxygen (OH), is the candidate hydrogen-bond acceptor (rows 3, 5 and 13, counted from 1 after the two XYZ header lines). What is the N3–H5···O13 angle at the hydrogen H5?", "options": [ { "label": "A", "value": "16.6", "unit": "degree" }, { "label": "B", "value": "34.9", "unit": "degree" }, { "label": "C", "value": "128.6", "unit": "degree" }, { "label": "D", "value": "149.8", "unit": "degree" } ], "inputs": [ "HBI002-S0007.xyz" ], "correct_label": "C", "audit": [ { "label": "A", "rule": "angle_at_acceptor", "reason": "把顶点放在受体 O13 上。" }, { "label": "B", "rule": "angle_at_donor", "reason": "把顶点放在给体 N3 上（H–D···A 角），而不是氢上。" }, { "label": "C", "rule": "correct", "reason": "按指定原子直接计算；成键关系由共价半径规则确认。" }, { "label": "D", "rule": "acceptor_side:H14", "reason": "量成受体一侧的 H···O13–H14 角。" } ] } ] } }, { "unit": "isotopologue_design", "kind": "family", "ability": "design", "registry_id": "isotopologue_design", "generator": "task_families/rotational.py", "checker": "checkers/rotational.py", "checker_function": "isotopologue_design", "bindings": { "L1": { "registry_row": "d85d3a24919c162078bc8ffc09a6fa6acb5cf5a266457c793378a7784f05c24b", "task_families/rotational.py": "ef8570ff19cf492f975faac17305b9c59625de37a61ce1230769f63ba46616a5" }, "L2": { "checkers/rotational.py": "2ba544a31a644ef654de95c16143919963ca2afab72b5864101a1f54916f47d2", "checkers/common.py": "fbc9f4eb287114ac4720d27edc1ea40e25f80da0e1cff6bdee06fbdca2b73aed" } }, "L1": "pending", "L2": "pending", "instances": 3, "L1_record": null, "L2_record": null, "card": { "template": { "name": "单氘代位点设计", "concept": "为替代法（Kraitchman）结构测定选择单氘代位点：四个候选 H 中，换成 D 后使指定转动跃迁位移最大者。设计 = 转动谱线推断的逆问题；位移取决于到主轴的距离，而不只是到质心的距离。 题干写明每个候选 H 所连原子及其官能团角色（如“H10 连在甲基碳 C1 上”）。", "inputs": "XYZ（QM7-X 优化几何或 SAMPL9 客体结构，按行号计数）。", "physical_conditions": "刚性转子、给定平衡几何；题干写明最丰同位素质量、h 与原子质量单位；不含振动平均、离心畸变与超精细结构。", "reasoning_scale": "整分子转动惯量（分子最大原子间距 0.5–1.2 nm）", "scale_limits": "推理需要整个分子的质量分布；大于 60 个原子的主体分子不出题（超出常见转动光谱范围）。", "source_basis": "QM7-X（CC BY 4.0）、SAMPL9 客体（仓库内已有资产，不新下载）", "answer_method": "对每个候选 H 换成 D 质量，重新计算质心、惯量张量与跃迁频率，取绝对位移最大者；要求领先第二名 ≥ 15% 且 ≥ 0.5 MHz。", "distractor_mechanisms": [ "farthest_from_centre_of_mass", "best_for_other_line", "best_for_single_constant", "smaller_shift" ], "four_choice_validation": "恰好一个候选位移最大且领先足够；正确项按批次目标位置放置。枚举器优先提出“离质心更远的 H 是干扰项”的集合，并按约 1:3 加入捷径能答对的集合；runs/enum-v32 中捷径命中 52/524，改进后的候选中为 90/610（约 15%，低于随机）。", "principle": "同位素取代改变质量分布与质心，ΔI 取决于取代原子到各主轴的距离；谱线位移为两个转动常数变化之和。", "validation": "独立检查器（checkers/rotational.py:isotopologue_design）从题干读取质量（含 D）、h 与 u，核对候选均为 H、选项与候选列表一致，逐个替换质量后用 Decimal 张量与三次方程闭式解重算位移，要求唯一最大且领先足够，并核对答案键。 检查器还逐条核对题干中“Hn is bonded to Xm”的连接说法（自己的共价半径规则，取最近原子）。", "limits": "几何不随同位素改变（忽略零点振动差异）；不评估合成可行性、谱线强度与对称等价位点的统计权重。", "template_review": "2026-10-06 新建，待 L1/L2 人工审核。" }, "samples": [ { "instance": "FA-ISO-7095-111", "question": "The supplied XYZ is the DFTB3+MBD-optimized geometry of QM7-X molecule 7095 (C4H8N2S, 15 atoms, angstrom); rows are counted from 1 after the two header lines. Model conditions: a rigid rotor at exactly the supplied geometry (no vibrational averaging, no centrifugal distortion); masses of the most abundant isotopes: C 12.000000 u, H 1.007825 u, N 14.003074 u, S 31.972071 u; rotational constants A ≥ B ≥ C are h/(8π²I) with I_a ≤ I_b ≤ I_c the principal moments of inertia about the centre of mass; h = 6.62607015×10⁻³⁴ J s, 1 u = 1.66053906660×10⁻²⁷ kg. You will record the rotational spectrum of one singly deuterated isotopologue: exactly one of the hydrogen atoms H10, H12, H14, H15 (rows counted from 1 after the two XYZ header lines) is replaced by deuterium, D 2.014102 u, at the same position. Candidates: H10 is bonded to C1, the methyl carbon (CH3); H12 is bonded to N5, the thioamide N–H nitrogen; H14 is bonded to C7, the alkene carbon (C=C); H15 is bonded to C7, the alkene carbon (C=C). You want the largest change in the frequency of the J_KaKc = 1_11 ← 0_00 transition relative to the parent molecule (largest absolute shift). Exactly one candidate gives the largest shift. Which hydrogen should be substituted?", "options": [ { "label": "A", "value": "H15 (row 15)" }, { "label": "B", "value": "H12 (row 12)" }, { "label": "C", "value": "H10 (row 10)" }, { "label": "D", "value": "H14 (row 14)" } ], "inputs": [ "QM7X-7095.xyz" ], "correct_label": "C", "audit": [ { "label": "A", "rule": "farthest_from_centre_of_mass", "reason": "离质心最远（4.02 Å），但谱线位移取决于到相应主轴的距离，不是到质心的距离。" }, { "label": "B", "rule": "smaller_shift", "reason": "谱线位移 -37.62 MHz，小于正确项。" }, { "label": "C", "rule": "correct", "reason": "取代后 1_11 ← 0_00 位移 -101.96 MHz，最大（第二名 -60.92 MHz）。" }, { "label": "D", "rule": "smaller_shift", "reason": "谱线位移 -60.92 MHz，小于正确项。" } ] }, { "instance": "FA-ISO-G13-111", "question": "The supplied XYZ is guest G13 (1-methyl-4-(1-methylpyridin-1-ium-4-yl)pyridin-1-ium) of the SAMPL9 WP6 host–guest challenge, one 3D structure (28 atoms, angstrom); rows are counted from 1 after the two header lines. Model conditions: a rigid rotor at exactly the supplied geometry (no vibrational averaging, no centrifugal distortion); masses of the most abundant isotopes: C 12.000000 u, H 1.007825 u, N 14.003074 u; rotational constants A ≥ B ≥ C are h/(8π²I) with I_a ≤ I_b ≤ I_c the principal moments of inertia about the centre of mass; h = 6.62607015×10⁻³⁴ J s, 1 u = 1.66053906660×10⁻²⁷ kg. You will record the rotational spectrum of one singly deuterated isotopologue: exactly one of the hydrogen atoms H18, H23, H25, H27 (rows counted from 1 after the two XYZ header lines) is replaced by deuterium, D 2.014102 u, at the same position. Candidates: H18 is bonded to C4, the aromatic carbon in the 6-membered ring; H23 is bonded to C11, the methyl carbon (CH3); H25 is bonded to C11, the methyl carbon (CH3); H27 is bonded to C12, the methyl carbon (CH3). You want the largest change in the frequency of the J_KaKc = 1_11 ← 0_00 transition relative to the parent molecule (largest absolute shift). Exactly one candidate gives the largest shift. Which hydrogen should be substituted?", "options": [ { "label": "A", "value": "H18 (row 18)" }, { "label": "B", "value": "H25 (row 25)" }, { "label": "C", "value": "H27 (row 27)" }, { "label": "D", "value": "H23 (row 23)" } ], "inputs": [ "WP6-G13.xyz" ], "correct_label": "A", "audit": [ { "label": "A", "rule": "correct", "reason": "取代后 1_11 ← 0_00 位移 -73.09 MHz，最大（第二名 -21.04 MHz）。" }, { "label": "B", "rule": "best_for_single_constant:C", "reason": "只看转动常数 C 的变化时它最大（-4.52 MHz），忽略了谱线是两个常数之和。" }, { "label": "C", "rule": "farthest_from_centre_of_mass", "reason": "离质心最远（5.39 Å），但谱线位移取决于到相应主轴的距离，不是到质心的距离。" }, { "label": "D", "rule": "smaller_shift", "reason": "谱线位移 -20.95 MHz，小于正确项。" } ] } ] } }, { "unit": "kinematic_extinction", "kind": "family", "ability": "inference", "registry_id": "kinematic_extinction", "generator": "task_families/extinction.py", "checker": "checkers/families.py", "checker_function": "extinction", "bindings": { "L1": { "registry_row": "055b19b46354eee2381ecb2f40bae5bac9e4599d0b73aaeadf0a3fa49cea989b", "task_families/extinction.py": "f9721343ded2f4de07dfaf787d4b59f4322cbaf782248414430677ddfad71e1f" }, "L2": { "checkers/families.py": "1b44f1eab578c983fa0c433d5ba82b86888a12e5a6033b928d69ee0ced4ef88c", "checkers/common.py": "fbc9f4eb287114ac4720d27edc1ea40e25f80da0e1cff6bdee06fbdca2b73aed" } }, "L1": "pending", "L2": "pending", "instances": 1, "L1_record": null, "L2_record": null, "card": { "template": { "name": "晶体衍射消光判别", "concept": "由晶胞内全部原子坐标与运动学结构因子推断哪一个反射强度为零；优先选择由基元/滑移而非仅中心化导致的消光。", "inputs": "常规晶胞全部原子分数坐标表 + 晶胞参数 + 原子序数权重。", "physical_conditions": "运动学近似；零角度原子序数权重；忽略热振动。", "reasoning_scale": "晶胞边长（相位求和跨越整个晶胞）", "scale_limits": "弱反射（|F|/F000 < 0.05）不作选项；非立方时 (h k l) 取 0–4，并排除彼此对称等价（同 d、同 |F|）的干扰项，避免一次排除两项。", "source_basis": "COD（NaCl、金刚石、SALEM-2、MOF-5；金红石、板钛矿、ZnO、α-石英）", "answer_method": "对学生看到的同一坐标表求 F(hkl)；|F|/F000 ≤ 1e-6 判为消光。非立方晶胞以“换轴误用消光条件”（指数换轴后的反射才消光）代替中心化规则作为错误机制。", "distractor_mechanisms": [ "wrong_rule:I", "wrong_rule:F", "wrong_rule:F+d", "identical_atom_assumption", "weak_not_absent", "axis_confusion" ], "four_choice_validation": "恰好一项消光、三项 ≥ 0.05 F000；另记录 P/I/F/F+d 规则能否单独答对。", "principle": "F(hkl) = Σ Z_j exp[2πi(hx+ky+lz)]。", "validation": "独立检查器（checkers/families.py:extinction）对学生看到的同一坐标表分别累加 cos 与 sin 项求 F(hkl)，逐项判定消光或非零（≥ 0.05 F000）。", "limits": "NaCl、SALEM-2、MOF-5 的正确项仅需中心化规则即可答对（已在 rule_shortcuts 中披露）。", "template_review": "本轮新建，待人工审核。" }, "samples": [ { "instance": "FA-EXT-SALEM2", "question": "The table lists every atom of one conventional cubic cell of Zn(imidazolate)2 with ZIF-8 sodalite topology (SALEM-2, COD 4118891; major-occupancy linker sites) as fractional coordinates. Use the kinematic structure factor F(hkl) = Σ_j Z_j exp[2πi(h x_j + k y_j + l z_j)] with atomic numbers as angle-independent weights (C = 6, H = 1, N = 7, Zn = 30). Exactly one of the four reflections below has |F| = 0. Which one?", "options": [ { "label": "A", "value": "(1 1 1)" }, { "label": "B", "value": "(2 2 0)" }, { "label": "C", "value": "(2 0 0)" }, { "label": "D", "value": "(1 1 0)" } ], "inputs": [ "FA-EXT-SALEM2-cell.txt" ], "correct_label": "A", "audit": [ { "label": "A", "rule": "correct", "reason": "由表中全部原子坐标求和，|F|/F000 ≤ 1e-6。" }, { "label": "B", "rule": "weak_not_absent", "reason": "强度较弱（|F|/F000=0.146），但不为零，弱不等于消光。" }, { "label": "C", "rule": "wrong_rule:F+d", "reason": "按“面心 F 加金刚石滑移：另有全偶且 h+k+l=4n+2 消光”会判为消光，但本结构实际坐标给出非零 |F|。" }, { "label": "D", "rule": "wrong_rule:F+d", "reason": "按“面心 F 加金刚石滑移：另有全偶且 h+k+l=4n+2 消光”会判为消光，但本结构实际坐标给出非零 |F|。" } ] }, { "instance": "FA-EXT-BROOKITE", "question": "The table lists every atom of one conventional cell (cell parameters in the first line of the table) of brookite (TiO2, COD 9004137) as fractional coordinates. Use the kinematic structure factor F(hkl) = Σ_j Z_j exp[2πi(h x_j + k y_j + l z_j)] with atomic numbers as angle-independent weights (O = 8, Ti = 22). Exactly one of the four reflections below has |F| = 0. Which one?", "options": [ { "label": "A", "value": "(2 1 1)" }, { "label": "B", "value": "(1 1 1)" }, { "label": "C", "value": "(1 0 2)" }, { "label": "D", "value": "(0 1 3)" } ], "inputs": [ "FA-EXT-BROOKITE-cell.txt" ], "correct_label": "D", "audit": [ { "label": "A", "rule": "allowed_generic", "reason": "普通允许反射，非零。" }, { "label": "B", "rule": "weak_not_absent", "reason": "强度较弱（|F|/F000=0.245），但不为零，弱不等于消光。" }, { "label": "C", "rule": "axis_confusion", "reason": "指数换轴后的 (0 1 2) 是消光的；把那条消光条件套到了另一根晶轴上，但本反射 |F| 不为零。" }, { "label": "D", "rule": "correct", "reason": "由表中全部原子坐标求和，|F|/F000 ≤ 1e-6。" } ] } ] } }, { "unit": "moire_design", "kind": "family", "ability": "design", "registry_id": "moire_design", "generator": "task_families/moire.py", "checker": "checkers/moire.py", "checker_function": "moire_design", "bindings": { "L1": { "registry_row": "376b8a1e3fec67a922b5be6abb29bc4e1cb51c73ffcffd6590e853464792385a", "task_families/moire.py": "16a16b7b7816642de68f12c460964e86d96ba2ccb8b8b0e8f9d03ff2c8a0377c" }, "L2": { "checkers/moire.py": "ceee9cd8039687cea219647978e575bb01c97d8c964b596fafb8df7b5d750a50", "checkers/common.py": "fbc9f4eb287114ac4720d27edc1ea40e25f80da0e1cff6bdee06fbdca2b73aed" } }, "L1": "pending", "L2": "pending", "instances": 3, "L1_record": null, "L2_record": null, "card": { "template": { "name": "转角石墨烯样品选择设计", "concept": "在论文实际样品中选一个，使半满或完全填满密度、或莫尔周期最接近目标；四个候选各有 AA 图。", "inputs": "转角双层石墨烯模型：AA 堆垛区中心图（nm，每行 \"AA x y\"，相当于 STM 形貌亮点，确定性旋转）或 AA 位点附近两层全部碳原子（Å）；设计题给四个候选图。", "physical_conditions": "刚性转角（无晶格弛豫、无异质应变）；石墨烯晶格常数 0.246 nm；自旋×谷四重简并（n_s = 4/A）。", "reasoning_scale": "莫尔周期 λ（12–18 nm）", "scale_limits": "按论文转角构建的模型；实测样品常有少量异质应变，使莫尔周期偏离理想值（Kerelsky et al. 讨论）。", "source_basis": "Cao et al., arXiv:1803.02342（Nature 2018）器件 M1/M2/D1 转角与 n_s = 4/A 定义；Kerelsky et al., arXiv:1812.08776（Nature 2019）STM 区域 1.10°、0.79°", "answer_method": "逐个候选由 AA 图计算周期与面积，按目标规则取唯一最优；要求领先幅度足够。", "distractor_mechanisms": [ "full_filling", "no_degeneracy", "spin_only", "square_cell", "aa_to_ab_distance", "second_neighbour", "farther_from_target" ], "four_choice_validation": "恰好一个候选满足目标；每个错误选项注明在哪种错误下会被选中。", "principle": "设计 = 推断的逆问题：按目标密度或周期选择转角。", "validation": "独立检查器逐文件重算并按题干目标重选。", "limits": "候选样品的周期与载流子密度由刚性转角模型从论文转角算出，不是逐样品实测值；不含弛豫与应变。", "template_review": "本轮新建（A4），待人工审核。" }, "samples": [ { "instance": "FA-MO-DES-FULL", "question": "The four files list the centres of the AA-stacked regions (nm) of model twisted bilayer graphene samples (files named by sample; each built from that sample's published twist angle; rigid twist without relaxation or strain). Model conditions: the only measured input is the twist angle reported by Cao et al. (Nature 2018; device twist angles from transport) or Kerelsky et al. (Nature 2019; STM); both layers are ideal, unstrained graphene sheets (lattice constant 0.246 nm) rigidly rotated against each other, with no lattice relaxation, heterostrain or substrate effects, which is the idealization behind the moiré formulas used in the paper; real samples show slight heterostrain. You must choose one sample such that the superlattice density n_s (complete filling of one set of spin- and valley-degenerate moiré bands) is closest to 2.8 × 10¹² cm⁻². Which sample should you choose?", "options": [ { "label": "A", "value": "M1 (TBG-M1-AA-map.txt)" }, { "label": "B", "value": "K110 (TBG-K110-AA-map.txt)" }, { "label": "C", "value": "K079 (TBG-K079-AA-map.txt)" }, { "label": "D", "value": "D1 (TBG-D1-AA-map.txt)" } ], "inputs": [ "TBG-K079-AA-map.txt", "TBG-D1-AA-map.txt", "TBG-K110-AA-map.txt", "TBG-M1-AA-map.txt" ], "correct_label": "B", "audit": [ { "label": "A", "rule": "no_degeneracy", "reason": "漏掉自旋×谷简并时它最接近目标（0.782）。" }, { "label": "B", "rule": "correct", "reason": "正确计算为 2.813，最接近目标。" }, { "label": "C", "rule": "farther_from_target", "reason": "正确计算为 1.451，离目标更远。" }, { "label": "D", "rule": "farther_from_target", "reason": "正确计算为 2.712，离目标更远。" } ] }, { "instance": "FA-MO-DES-HALF", "question": "The four files list the centres of the AA-stacked regions (nm) of model twisted bilayer graphene samples (files named by sample; each built from that sample's published twist angle; rigid twist without relaxation or strain). Model conditions: the only measured input is the twist angle reported by Cao et al. (Nature 2018; device twist angles from transport) or Kerelsky et al. (Nature 2019; STM); both layers are ideal, unstrained graphene sheets (lattice constant 0.246 nm) rigidly rotated against each other, with no lattice relaxation, heterostrain or substrate effects, which is the idealization behind the moiré formulas used in the paper; real samples show slight heterostrain. You must choose one sample such that half filling of one set of spin- and valley-degenerate moiré bands occurs at a carrier density closest to 1.3 × 10¹² cm⁻². Which sample should you choose?", "options": [ { "label": "A", "value": "D1 (TBG-D1-AA-map.txt)" }, { "label": "B", "value": "K110 (TBG-K110-AA-map.txt)" }, { "label": "C", "value": "M1 (TBG-M1-AA-map.txt)" }, { "label": "D", "value": "M2 (TBG-M2-AA-map.txt)" } ], "inputs": [ "TBG-M2-AA-map.txt", "TBG-D1-AA-map.txt", "TBG-K110-AA-map.txt", "TBG-M1-AA-map.txt" ], "correct_label": "D", "audit": [ { "label": "A", "rule": "farther_from_target", "reason": "正确计算为 1.356，离目标更远。" }, { "label": "B", "rule": "farther_from_target", "reason": "正确计算为 1.407，离目标更远。" }, { "label": "C", "rule": "no_degeneracy", "reason": "漏掉自旋×谷简并时它最接近目标（0.782）。" }, { "label": "D", "rule": "correct", "reason": "正确计算为 1.282，最接近目标。" } ] } ] } }, { "unit": "moire_geometry", "kind": "family", "ability": "perception", "registry_id": "moire_geometry", "generator": "task_families/moire.py", "checker": "checkers/moire.py", "checker_function": "moire_quantity", "bindings": { "L1": { "registry_row": "47e7195d3cb97de72f478620b07f349f9a2871c88ada9559f946c358e199dc45", "task_families/moire.py": "16a16b7b7816642de68f12c460964e86d96ba2ccb8b8b0e8f9d03ff2c8a0377c" }, "L2": { "checkers/moire.py": "ceee9cd8039687cea219647978e575bb01c97d8c964b596fafb8df7b5d750a50", "checkers/common.py": "fbc9f4eb287114ac4720d27edc1ea40e25f80da0e1cff6bdee06fbdca2b73aed" } }, "L1": "pending", "L2": "pending", "instances": 3, "L1_record": null, "L2_record": null, "card": { "template": { "name": "转角石墨烯莫尔晶格几何（周期 / 晶胞面积）", "concept": "从 AA 堆垛区中心图识别莫尔晶格：莫尔周期与莫尔晶胞面积（10–100 nm 尺度）。", "inputs": "转角双层石墨烯模型：AA 堆垛区中心图（nm，每行 \"AA x y\"，相当于 STM 形貌亮点，确定性旋转）或 AA 位点附近两层全部碳原子（Å）；设计题给四个候选图。", "physical_conditions": "刚性转角（无晶格弛豫、无异质应变）；石墨烯晶格常数 0.246 nm；自旋×谷四重简并（n_s = 4/A）。", "reasoning_scale": "莫尔周期 λ（12–18 nm）", "scale_limits": "按论文转角构建的模型；实测样品常有少量异质应变，使莫尔周期偏离理想值（Kerelsky et al. 讨论）。", "source_basis": "Cao et al., arXiv:1803.02342（Nature 2018）器件 M1/M2/D1 转角与 n_s = 4/A 定义；Kerelsky et al., arXiv:1812.08776（Nature 2019）STM 区域 1.10°、0.79°", "answer_method": "中心位点周围 6 个等距近邻，核对与论文转角给出的周期一致。", "distractor_mechanisms": [ "aa_to_ab_distance", "row_spacing", "second_neighbour", "half_period", "double_period", "square_cell", "triangle_only", "hexagon_twice", "ab_spacing_cell" ], "four_choice_validation": "与正确值 > 0.3 nm 或 3 nm²；升序排列，秩按批次轮换。", "principle": "刚性转角：λ = a/(2 sin(θ/2))；三角晶格晶胞面积 (√3/2)λ²。", "validation": "独立检查器由最近邻矢量选初基基矢，验证所有位点为整数组合，面积取叉积。", "limits": "理想刚性转角：不含晶格弛豫（AB/BA 畴重构）、异质应变与转角不均匀；小转角下实测周期可能偏离模型。", "template_review": "本轮新建（A4），待人工审核。" }, "samples": [ { "instance": "FA-MO-AREA-M2", "question": "The file lists the centres of the AA-stacked regions (the bright spots of an STM topograph) of a model twisted bilayer graphene sample, coordinates in nm (rigid twist without lattice relaxation or strain; built from a published twist angle). Model conditions: the only measured input is the twist angle reported by Cao et al. (Nature 2018; device twist angles from transport); both layers are ideal, unstrained graphene sheets (lattice constant 0.246 nm) rigidly rotated against each other, with no lattice relaxation, heterostrain or substrate effects, which is the idealization behind the moiré formulas used in the paper; real samples show slight heterostrain. What is the area of one moiré unit cell, in nm²?", "options": [ { "label": "A", "value": "52.0", "unit": "nm^2" }, { "label": "B", "value": "156.1", "unit": "nm^2" }, { "label": "C", "value": "180.2", "unit": "nm^2" }, { "label": "D", "value": "312.1", "unit": "nm^2" } ], "inputs": [ "TBG-M2-AA-map.txt" ], "correct_label": "B", "audit": [ { "label": "A", "rule": "ab_spacing_cell", "reason": "用 AA–AB 距离当作晶格常数。" }, { "label": "B", "rule": "correct", "reason": "θ = 1.05°，λ = a/(2 sin(θ/2)) = 13.4238 nm，A = (√3/2)λ²，n_s = 4/A。" }, { "label": "C", "rule": "square_cell", "reason": "按正方形晶胞 λ² 计算。" }, { "label": "D", "rule": "hexagon_twice", "reason": "面积多乘了 2。" } ] }, { "instance": "FA-MO-PERIOD-D1", "question": "The file lists the centres of the AA-stacked regions (the bright spots of an STM topograph) of a model twisted bilayer graphene sample, coordinates in nm (rigid twist without lattice relaxation or strain; built from a published twist angle). Model conditions: the only measured input is the twist angle reported by Cao et al. (Nature 2018; device twist angles from transport); both layers are ideal, unstrained graphene sheets (lattice constant 0.246 nm) rigidly rotated against each other, with no lattice relaxation, heterostrain or substrate effects, which is the idealization behind the moiré formulas used in the paper; real samples show slight heterostrain. What is the moiré period (the moiré lattice constant), in nm?", "options": [ { "label": "A", "value": "7.53", "unit": "nm" }, { "label": "B", "value": "11.30", "unit": "nm" }, { "label": "C", "value": "13.05", "unit": "nm" }, { "label": "D", "value": "22.60", "unit": "nm" } ], "inputs": [ "TBG-D1-AA-map.txt" ], "correct_label": "C", "audit": [ { "label": "A", "rule": "aa_to_ab_distance", "reason": "报告了 AA 到 AB 区中心的距离 λ/√3。" }, { "label": "B", "rule": "row_spacing", "reason": "报告了相邻 AA 行的间距 (√3/2)λ。" }, { "label": "C", "rule": "correct", "reason": "θ = 1.08°，λ = a/(2 sin(θ/2)) = 13.0509 nm，A = (√3/2)λ²，n_s = 4/A。" }, { "label": "D", "rule": "second_neighbour", "reason": "报告了次近邻 AA 距离 √3λ。" } ] } ] } }, { "unit": "moire_inference", "kind": "family", "ability": "inference", "registry_id": "moire_inference", "generator": "task_families/moire.py", "checker": "checkers/moire.py", "checker_function": "moire_quantity", "bindings": { "L1": { "registry_row": "a7970eb95097f6d375859f5764b7128b24a31cd28724fe8c69fed8bc1259f437", "task_families/moire.py": "16a16b7b7816642de68f12c460964e86d96ba2ccb8b8b0e8f9d03ff2c8a0377c" }, "L2": { "checkers/moire.py": "ceee9cd8039687cea219647978e575bb01c97d8c964b596fafb8df7b5d750a50", "checkers/common.py": "fbc9f4eb287114ac4720d27edc1ea40e25f80da0e1cff6bdee06fbdca2b73aed" } }, "L1": "pending", "L2": "pending", "instances": 1, "L1_record": null, "L2_record": null, "card": { "template": { "name": "转角石墨烯莫尔推断（周期、载流子密度、转角）", "concept": "由原子坐标推断两层转角并求莫尔周期；由莫尔晶胞推断完全填满与半满一组自旋×谷简并能带的载流子密度；由莫尔周期反推转角。", "inputs": "转角双层石墨烯模型：AA 堆垛区中心图（nm，每行 \"AA x y\"，相当于 STM 形貌亮点，确定性旋转）或 AA 位点附近两层全部碳原子（Å）；设计题给四个候选图。", "physical_conditions": "刚性转角（无晶格弛豫、无异质应变）；石墨烯晶格常数 0.246 nm；自旋×谷四重简并（n_s = 4/A）。", "reasoning_scale": "莫尔周期 λ（12–18 nm）", "scale_limits": "按论文转角构建的模型；实测样品常有少量异质应变，使莫尔周期偏离理想值（Kerelsky et al. 讨论）。", "source_basis": "Cao et al., arXiv:1803.02342（Nature 2018）器件 M1/M2/D1 转角与 n_s = 4/A 定义；Kerelsky et al., arXiv:1812.08776（Nature 2019）STM 区域 1.10°、0.79°", "answer_method": "λ = a/(2 sin(θ/2))；n_s = 4/A（A = (√3/2)λ²），半满 n_s/2；θ = 2 arcsin(a/2λ)。", "distractor_mechanisms": [ "sin_full_angle", "bond_length_as_lattice_constant", "angle_of_one_layer", "second_neighbour", "layer_spacing_as_lattice_constant", "no_degeneracy", "spin_only", "square_cell", "eight_per_cell", "ab_distance_as_period", "full_filling", "half_angle", "radians_as_degrees" ], "four_choice_validation": "与正确值 > 0.3 nm、0.05×10¹² cm⁻² 或 0.05°；升序排列，秩按批次轮换。", "principle": "莫尔几何与能带填充：每个莫尔晶胞 4 个态（自旋×谷）填满一组能带。", "validation": "原子块：独立检查器用每层晶格矢量的六重相位平均求取向，再求转角与晶格常数；AA 图：叉积面积。", "limits": "刚性转角模型；n_s 定义沿用 Cao et al.。", "template_review": "本轮新建（A4），待人工审核。" }, "samples": [ { "instance": "FA-MO-NHALF-K079", "question": "The file lists the centres of the AA-stacked regions (the bright spots of an STM topograph) of a model twisted bilayer graphene sample, coordinates in nm (rigid twist without lattice relaxation or strain; built from a published twist angle). Model conditions: the only measured input is the twist angle reported by Kerelsky et al. (Nature 2019; STM); both layers are ideal, unstrained graphene sheets (lattice constant 0.246 nm) rigidly rotated against each other, with no lattice relaxation, heterostrain or substrate effects, which is the idealization behind the moiré formulas used in the paper; real samples show slight heterostrain. What carrier density corresponds to half filling of one set of spin- and valley-degenerate moiré bands (where correlated insulators appear), in units of 10¹² cm⁻²?", "options": [ { "label": "A", "value": "0.363", "unit": "10^12 cm^-2" }, { "label": "B", "value": "0.628", "unit": "10^12 cm^-2" }, { "label": "C", "value": "0.725", "unit": "10^12 cm^-2" }, { "label": "D", "value": "1.451", "unit": "10^12 cm^-2" } ], "inputs": [ "TBG-K079-AA-map.txt" ], "correct_label": "C", "audit": [ { "label": "A", "rule": "no_degeneracy", "reason": "每个晶胞只算 1 个电子，漏掉自旋×谷四重简并。" }, { "label": "B", "rule": "square_cell", "reason": "晶胞面积按 λ² 计算。" }, { "label": "C", "rule": "correct", "reason": "θ = 0.79°，λ = a/(2 sin(θ/2)) = 17.8416 nm，A = (√3/2)λ²，n_s = 4/A。" }, { "label": "D", "rule": "full_filling", "reason": "报告了完全填满（n_s）而非半满。" } ] }, { "instance": "FA-MO-ATOMS-K110", "question": "The XYZ file lists all carbon atoms of both layers of a model twisted bilayer graphene near an AA-stacked site (angstrom; rigid twist, layer spacing 3.35 Å; built from a published twist angle). Model conditions: the only measured input is the twist angle reported by Kerelsky et al. (Nature 2019; STM); both layers are ideal, unstrained graphene sheets (lattice constant 0.246 nm) rigidly rotated against each other, with no lattice relaxation, heterostrain or substrate effects, which is the idealization behind the moiré formulas used in the paper; real samples show slight heterostrain. Assuming the two layers are unstrained and rigidly twisted, what is the moiré period (the moiré lattice constant) of this bilayer, in nm?", "options": [ { "label": "A", "value": "12.81", "unit": "nm" }, { "label": "B", "value": "17.45", "unit": "nm" }, { "label": "C", "value": "22.19", "unit": "nm" }, { "label": "D", "value": "25.63", "unit": "nm" } ], "inputs": [ "TBG-K110-atoms.xyz" ], "correct_label": "A", "audit": [ { "label": "A", "rule": "correct", "reason": "θ = 1.10°，λ = a/(2 sin(θ/2)) = 12.8136 nm，A = (√3/2)λ²，n_s = 4/A。" }, { "label": "B", "rule": "layer_spacing_as_lattice_constant", "reason": "把层间距 0.335 nm 当作晶格常数。" }, { "label": "C", "rule": "second_neighbour", "reason": "报告了次近邻 AA 距离 √3λ。" }, { "label": "D", "rule": "angle_of_one_layer", "reason": "用单层相对参考方向的转角 θ/2 代替两层之间的转角。" } ] } ] } }, { "unit": "named_bond_angle", "kind": "family", "ability": "perception", "registry_id": "named_bond_angle", "generator": "task_families/local_geometry.py", "checker": "checkers/families.py", "checker_function": "named_bond_angle", "bindings": { "L1": { "registry_row": "523a4573451e57b69dc1409e93a57c6c638fb633592f08809383e1610cd901e8", "task_families/local_geometry.py": "5f7867f2d96cbff718aa367ea23637bb59e567ddd8363e00e346bf046c4917f2" }, "L2": { "checkers/families.py": "1b44f1eab578c983fa0c433d5ba82b86888a12e5a6033b928d69ee0ced4ef88c", "checkers/common.py": "fbc9f4eb287114ac4720d27edc1ea40e25f80da0e1cff6bdee06fbdca2b73aed" } }, "L1": "pending", "L2": "pending", "instances": 1, "L1_record": null, "L2_record": null, "card": { "template": { "name": "命名化学键角", "concept": "指定化学连接（如糖苷桥氧 C–O–C、芳环内角、甲醚键角）在给定构象中的键角；原子身份由连接关系确认，不是任意行号。", "inputs": "完整 XYZ（Å）、三个命名原子及行号、连接描述。", "physical_conditions": "单一给定构象，不优化。", "reasoning_scale": "三原子两两最大间距（约 0.24 nm）", "scale_limits": "局部几何；结论只对该构象成立。", "source_basis": "SAMPL9 宿主结构（PDB CONECT 确认连接）", "answer_method": "acos 向量夹角；atan2 实现复核；共价半径规则确认顶点与两端成键。", "distractor_mechanisms": [ "idealized_value", "other_neighbor", "angle_at_adjacent_atom", "supplement", "triangle_angle_at_first_atom" ], "four_choice_validation": "与正确值 > 1.5°，干扰项之间 > 0.5°；升序排列，秩按批次平衡；易排除项每个计 4 个秩差惩罚。 2026-10-06：枚举实例的题干改用化学命名（task_families/chem_names.py）——按价态与登记的总电荷求键级（单 / 双 / 芳香 / 离域），按键级、邻接与氢数给出原子的官能团角色（如“硫脲碳 (C=S)”“磺酰氧 (S=O)”“铵氮 (NH3+)”），认不出的原子不出题；36 个分子的全部重原子都能命名。", "principle": "θ = arccos(u·v/|u||v|)，u、v 为顶点指向两端原子的键矢量。", "validation": "两种实现一致；四个选项逐一核验。", "limits": "键角接近理想值时难以构造足够分散的高迷惑干扰项（DMBCD 实例仍含一个易排除项）。", "template_review": "本轮新建，待人工审核。" }, "samples": [ { "instance": "FA-ANG-7040-OSO", "question": "The supplied XYZ is the DFTB3+MBD-optimized geometry of QM7-X molecule 7040 (16 atoms, angstrom). Atoms O4–S3–O5 form the O=S=O unit of the sulfonyl group on S3 (O4 = row 4, S3 = row 3, O5 = row 5; rows counted from 1 after the two XYZ header lines). What is the O4–S3–O5 bond angle at S3 in this supplied conformer?", "options": [ { "label": "A", "value": "109.47", "unit": "degree" }, { "label": "B", "value": "110.43", "unit": "degree" }, { "label": "C", "value": "111.01", "unit": "degree" }, { "label": "D", "value": "121.96", "unit": "degree" } ], "inputs": [ "QNP005-7040-opt.xyz" ], "correct_label": "D", "audit": [ { "label": "A", "rule": "idealized_value", "reason": "直接套用理想杂化角 109.47（sp3 tetrahedral），没有测量这一构象。" }, { "label": "B", "rule": "other_neighbor:C(row 2)-S3-O5", "reason": "顶点正确，但一端选成与 S3 相连的 C(row 2)。" }, { "label": "C", "rule": "other_neighbor:O4-S3-C(row 2)", "reason": "顶点正确，但另一端选成与 S3 相连的 C(row 2)。" }, { "label": "D", "rule": "correct", "reason": "按向量夹角公式在指定顶点计算；另以 atan2 实现复核。" } ] }, { "instance": "FA-ANG-BCD", "question": "The supplied XYZ is one beta-cyclodextrin host conformer (147 atoms, angstrom). Atoms C4–O3–C37 form the bridging ether linkage between two glucose units, O3 bonded to C4 and C37 as in the source PDB CONECT record (C4 = row 4, O3 = row 45, C37 = row 37; rows counted from 1 after the two XYZ header lines). What is the C4–O3–C37 bond angle at O3 in this supplied conformer?", "options": [ { "label": "A", "value": "105.31", "unit": "degree" }, { "label": "B", "value": "109.47", "unit": "degree" }, { "label": "C", "value": "111.70", "unit": "degree" }, { "label": "D", "value": "116.03", "unit": "degree" } ], "inputs": [ "BCD.xyz" ], "correct_label": "D", "audit": [ { "label": "A", "rule": "angle_at_adjacent_atom:O3-C4-C(row 3)", "reason": "测成相邻原子 C4 处的键角，而非题目指定的顶点 O3。" }, { "label": "B", "rule": "idealized_value", "reason": "直接套用理想杂化角 109.47（sp3 tetrahedral），没有测量这一构象。" }, { "label": "C", "rule": "angle_at_adjacent_atom:O3-C37-O(row 76)", "reason": "测成相邻原子 C37 处的键角，而非题目指定的顶点 O3。" }, { "label": "D", "rule": "correct", "reason": "按向量夹角公式在指定顶点计算；另以 atan2 实现复核。" } ] } ] } }, { "unit": "named_bond_distance", "kind": "family", "ability": "perception", "registry_id": "named_bond_distance", "generator": "task_families/local_geometry.py", "checker": "checkers/migrated.py", "checker_function": "named_bond_distance", "bindings": { "L1": { "registry_row": "a0a30c558f4bc4dd752ab8816af160e02d4d3c81719cc1088a9624d70c1b9cc2", "task_families/local_geometry.py": "5f7867f2d96cbff718aa367ea23637bb59e567ddd8363e00e346bf046c4917f2" }, "L2": { "checkers/migrated.py": "f1cf6f20bca7ad81fd3b5ee5c6749084a090a32dd40b0a394768995a6e3a42eb", "checkers/common.py": "fbc9f4eb287114ac4720d27edc1ea40e25f80da0e1cff6bdee06fbdca2b73aed" } }, "L1": "pending", "L2": "pending", "instances": 6, "L1_record": null, "L2_record": null, "card": { "template": { "name": "命名局部距离", "concept": "指定化学实体之间的键长：磺酰 S=O、芳环 C–Cl、末端 N–N、C–NH2、二硫键 SG–SG；原子由行号或 PDB 原子名加化学描述指定，并由成键规则确认。", "inputs": "XYZ（按行号命名）或 PDB 片段（含 SSBOND 记录与两个残基的 ATOM 行）。", "physical_conditions": "单一构象：QM7-X 的 DFTB3+MBD 优化几何，或晶体结构中的主构象；不考虑热振动与零点运动。", "reasoning_scale": "两原子距离（0.1–0.5 nm）", "scale_limits": "单一距离不能独立判定成键状态。", "source_basis": "PDB、SAMPL9、QM7-X", "answer_method": "欧氏距离（浮点与 Decimal 两种实现）；共价半径规则确认成键。", "distractor_mechanisms": [ "other_bond_same_atom", "typical_value", "covalent_radii_sum", "nearest_nonbonded_same_element", "bohr_units", "one_bond_too_far" ], "four_choice_validation": "与正确值 > 0.02 Å，干扰项之间 > 0.01 Å；升序排列，秩按批次轮换。 2026-10-04 枚举探针：新增“多数了一根键”（1–3 距离）；枚举实例设 strict_rank，目标答案位置不可达时拒绝出题而不是退到最近位置。 2026-10-06：枚举实例的题干改用化学命名（task_families/chem_names.py）——按价态与登记的总电荷求键级（单 / 双 / 芳香 / 离域），按键级、邻接与氢数给出原子的官能团角色（如“硫脲碳 (C=S)”“磺酰氧 (S=O)”“铵氮 (NH3+)”），认不出的原子不出题；36 个分子的全部重原子都能命名。", "principle": "两原子笛卡尔坐标的欧氏距离；用共价半径规则确认所问两原子确实成键。", "validation": "独立检查器（checkers/migrated.py:named_bond_distance）按题干点名的原子（PDB 原子名或 XYZ 行号）从附件取坐标，用 Decimal 重算距离，并用自己的共价半径规则确认成键；PDB 片段须与源文件逐字一致，二硫键题核对 SSBOND 记录，XYZ 核对元素与源文件哈希。", "limits": "QNP002–006 需说明元素对选择的化学意义（待小修）。", "template_review": "本轮迁移新建，待人工审核。" }, "samples": [ { "instance": "FA-DIST-1CRN-SS16", "question": "The excerpt gives the SSBOND record and the ATOM records of Cys16 and Cys26 of crambin (PDB 1CRN, chain A), copied unchanged (angstrom). In this supplied structure, atoms SG(Cys16) and SG(Cys26) form the disulfide bridge listed in the SSBOND record. What is this bond length?", "options": [ { "label": "A", "value": "1.813", "unit": "angstrom" }, { "label": "B", "value": "2.051", "unit": "angstrom" }, { "label": "C", "value": "3.013", "unit": "angstrom" }, { "label": "D", "value": "3.033", "unit": "angstrom" } ], "inputs": [ "1CRN-excerpt.pdb" ], "correct_label": "B", "audit": [ { "label": "A", "rule": "other_bond:SG(Cys16)-CB(Cys16)", "reason": "量成 SG(Cys16) 的另一根键（到 CB(Cys16)）。" }, { "label": "B", "rule": "correct", "reason": "两指定原子的欧氏距离；另以 Decimal 实现复核。" }, { "label": "C", "rule": "one_bond_too_far:SG(Cys26)-CB(Cys16)", "reason": "多数了一根键：量成 SG(Cys26) 到 SG(Cys16) 之外的 CB(Cys16) 的距离。" }, { "label": "D", "rule": "one_bond_too_far:SG(Cys16)-CB(Cys26)", "reason": "多数了一根键：量成 SG(Cys16) 到 SG(Cys26) 之外的 CB(Cys26) 的距离。" } ] }, { "instance": "FA-DIST-6LYZ-SS30", "question": "The excerpt gives the SSBOND record and the ATOM records of Cys30 and Cys115 of hen egg-white lysozyme (PDB 6LYZ, chain A), copied unchanged (angstrom). In this supplied structure, atoms SG(Cys30) and SG(Cys115) form the disulfide bridge listed in the SSBOND record. What is this bond length?", "options": [ { "label": "A", "value": "1.821", "unit": "angstrom" }, { "label": "B", "value": "2.042", "unit": "angstrom" }, { "label": "C", "value": "2.100", "unit": "angstrom" }, { "label": "D", "value": "3.112", "unit": "angstrom" } ], "inputs": [ "6LYZ-excerpt.pdb" ], "correct_label": "B", "audit": [ { "label": "A", "rule": "other_bond:SG(Cys115)-CB(Cys115)", "reason": "量成 SG(Cys115) 的另一根键（到 CB(Cys115)）。" }, { "label": "B", "rule": "correct", "reason": "两指定原子的欧氏距离；另以 Decimal 实现复核。" }, { "label": "C", "rule": "covalent_radii_sum", "reason": "用共价半径之和估计，没有测量这一结构。" }, { "label": "D", "rule": "one_bond_too_far:SG(Cys30)-CB(Cys115)", "reason": "多数了一根键：量成 SG(Cys30) 到 SG(Cys115) 之外的 CB(Cys115) 的距离。" } ] } ] } }, { "unit": "opal_bragg", "kind": "family", "ability": "inference", "registry_id": "opal_bragg", "generator": "task_families/photonic.py", "checker": "checkers/superlattice.py", "checker_function": "opal_quantity", "bindings": { "L1": { "registry_row": "ea940b6de5bae7708e45f58827b0da223da93741328ee8ecdc2177dc31548cdc", "task_families/photonic.py": "3afa16d6c06b6f3367a963632644cd375dbc0caab3e8bcca42a2b6ede7d9585c" }, "L2": { "checkers/superlattice.py": "c03a5a7bd5ced3e525f1c4d5b2c9a27971d3bc5af7a4c95115a13984f6e24fee", "checkers/common.py": "fbc9f4eb287114ac4720d27edc1ea40e25f80da0e1cff6bdee06fbdca2b73aed" } }, "L1": "pending", "L2": "pending", "instances": 3, "L1_record": null, "L2_record": null, "card": { "template": { "name": "胶体光子晶体 Bragg 反射与结构色", "concept": "由球心坐标与题给折射率推断结构色：一级 Bragg–Snell 反射波长（正入射或斜入射），或达到目标波长所需的入射角。", "inputs": "胶体晶体（蛋白石）晶粒模型的球心坐标（nm，每行 \"sphere x y z\"，177 个，经确定性旋转）；设计题给四个候选文件。", "physical_conditions": "接触球理想 FCC；密排面平行于膜面；有效折射率 n_eff² = Σ f_i n_i²（或题给 n_eff）；Bragg–Snell 一级反射。", "reasoning_scale": "晶格周期：常规晶胞边长 a（约 295–522 nm）", "scale_limits": "按论文球径构建的模型；不含尺寸分布、堆垛缺陷与多面衍射；审核侧附实测峰值供比较。", "source_basis": "Gazmeh et al., Sci. Rep. 15, 38349 (2025) 表 3（聚苯乙烯球径与实测反射峰）；Fookes et al., Sensors 23, 1433 (2023) 参数表（二氧化硅 266 nm、n_eff 1.35、30°）", "answer_method": "λ = 2 d111 √(n_eff² − sin²θ)；n_eff² = f n_s² + (1−f) n_m²，f = π/(3√2)。", "distractor_mechanisms": [ "diameter_as_spacing", "cell_edge_as_spacing", "no_factor_two", "d200_planes", "linear_index_average", "no_index", "sphere_index", "voids_as_air", "no_refraction", "ignore_angle", "angle_from_surface", "refraction_angle_inside", "sin_not_squared" ], "four_choice_validation": "波长与正确值 > 5 nm，角度 > 1°；升序排列，秩按批次轮换。", "principle": "Bragg 定律加表面折射（Bragg–Snell）；有效介质近似。", "validation": "独立检查器由倒格子求 d111，由初基胞体积求球体积分数，再按题干的有效介质规则计算。", "limits": "有效介质与理想晶格假设；模型值与实测峰相差约 1%（审核侧列出）。", "template_review": "本轮新建（A4），待人工审核。" }, "samples": [ { "instance": "FA-OP-ANGLE-SIO2", "question": "The file lists the sphere centres (nm) of a model silica opal crystallite built from a published sphere diameter; neighbouring spheres touch. Model conditions: the only measured input is the sphere diameter reported by Fookes et al. (Sensors 2023; SEM); the spheres are identical (no size dispersion), touch their neighbours and sit on an ideal close-packed lattice without stacking faults, vacancies or cracks, which is the idealization behind the paper's Bragg-law estimate of the reflection peak. Each crystallite is a finite cut of 177 spheres in an arbitrary orientation. Model the film as this lattice with its close-packed planes parallel to the film surface, and use an effective refractive index of 1.35 for the film. At what angle of incidence from the film normal, in degrees (light incident from air), does the first-order Bragg reflection from the close-packed planes occur at a vacuum wavelength of 500 nm?", "options": [ { "label": "A", "value": "29.8", "unit": "degree" }, { "label": "B", "value": "31.5", "unit": "degree" }, { "label": "C", "value": "44.9", "unit": "degree" }, { "label": "D", "value": "75.7", "unit": "degree" } ], "inputs": [ "opal-SiO2-266.xyz" ], "correct_label": "C", "audit": [ { "label": "A", "rule": "sin_not_squared", "reason": "解出 sinθ 时未开方。" }, { "label": "B", "rule": "no_refraction", "reason": "用 λ = 2 d n cosθ 反解，忽略折射。" }, { "label": "C", "rule": "correct", "reason": "sin²θ = n_eff² − (λ/2d111)²，d111 = 217.1881 nm，n_eff = 1.350。" }, { "label": "D", "rule": "diameter_as_spacing", "reason": "把球径当作密排面间距。" } ] }, { "instance": "FA-OP-PEAK-S7-WATER", "question": "The file lists the sphere centres (nm) of a model polystyrene opal crystallite built from a published sphere diameter; neighbouring spheres touch. Model conditions: the only measured input is the sphere diameter reported by Gazmeh et al. (Sci. Rep. 2025, Table 3; field-emission SEM); the spheres are identical (no size dispersion), touch their neighbours and sit on an ideal close-packed lattice without stacking faults, vacancies or cracks, which is the idealization behind the paper's Bragg-law estimate of the reflection peak. Each crystallite is a finite cut of 177 spheres in an arbitrary orientation. Model the film as this lattice with its close-packed planes parallel to the film surface. The spheres have refractive index 1.59 and the voids are filled with a medium of refractive index 1.33; take the effective index from the volume-weighted average of the squared refractive indices (n_eff² = Σ f_i n_i²), using the sphere volume fraction of this packing. Light is incident along the film normal. What is the vacuum wavelength, in nm, of the first-order Bragg reflection from the close-packed planes?", "options": [ { "label": "A", "value": "560.4", "unit": "nm" }, { "label": "B", "value": "583.6", "unit": "nm" }, { "label": "C", "value": "686.3", "unit": "nm" }, { "label": "D", "value": "970.6", "unit": "nm" } ], "inputs": [ "opal-PS-S7.xyz" ], "correct_label": "A", "audit": [ { "label": "A", "rule": "correct", "reason": "λ = 2 d111 √(n_eff² − sin²θ)，d111 = 183.5158 nm，n_eff = 1.52679。" }, { "label": "B", "rule": "sphere_index", "reason": "用球的折射率代替有效折射率。" }, { "label": "C", "rule": "diameter_as_spacing", "reason": "把球径当作密排面间距。" }, { "label": "D", "rule": "cell_edge_as_spacing", "reason": "把常规晶胞边长当作面间距。" } ] } ] } }, { "unit": "opal_design", "kind": "family", "ability": "design", "registry_id": "opal_design", "generator": "task_families/photonic.py", "checker": "checkers/superlattice.py", "checker_function": "opal_design", "bindings": { "L1": { "registry_row": "ab42f18734c176ee9b383c7eed0bce524647e38098344d4feb10e266cd7236d5", "task_families/photonic.py": "3afa16d6c06b6f3367a963632644cd375dbc0caab3e8bcca42a2b6ede7d9585c" }, "L2": { "checkers/superlattice.py": "c03a5a7bd5ced3e525f1c4d5b2c9a27971d3bc5af7a4c95115a13984f6e24fee", "checkers/common.py": "fbc9f4eb287114ac4720d27edc1ea40e25f80da0e1cff6bdee06fbdca2b73aed" } }, "L1": "pending", "L2": "pending", "instances": 3, "L1_record": null, "L2_record": null, "card": { "template": { "name": "结构色设计：选择球径样品", "concept": "在论文实际合成的四个聚苯乙烯样品中选一个，使膜的正入射反射最接近目标波长，或在波长上限内球径最大；四个候选各有模型晶粒。", "inputs": "胶体晶体（蛋白石）晶粒模型的球心坐标（nm，每行 \"sphere x y z\"，177 个，经确定性旋转）；设计题给四个候选文件。", "physical_conditions": "接触球理想 FCC；密排面平行于膜面；有效折射率 n_eff² = Σ f_i n_i²（或题给 n_eff）；Bragg–Snell 一级反射。", "reasoning_scale": "晶格周期：常规晶胞边长 a（约 295–522 nm）", "scale_limits": "按论文球径构建的模型；不含尺寸分布、堆垛缺陷与多面衍射；审核侧附实测峰值供比较。", "source_basis": "Gazmeh et al., Sci. Rep. 15, 38349 (2025) 表 3（聚苯乙烯球径与实测反射峰）；Fookes et al., Sensors 23, 1433 (2023) 参数表（二氧化硅 266 nm、n_eff 1.35、30°）", "answer_method": "逐个候选由坐标计算反射波长，按目标规则取唯一最优；要求领先幅度足够。", "distractor_mechanisms": [ "diameter_as_spacing", "no_index", "linear_index_average", "sphere_index", "passes_if_no_index", "satisfies_but_smaller", "farther_from_target" ], "four_choice_validation": "恰好一个候选满足目标；每个错误选项注明在哪种错误下会被选中。", "principle": "设计 = 推断的逆问题；论文将这些样品用作“反射标尺”。", "validation": "独立检查器逐文件分析晶格并按题干目标重选。", "limits": "候选性质来自模型；实测峰值列于审核侧。", "template_review": "本轮新建（A4），待人工审核。" }, "samples": [ { "instance": "FA-OP-DES-540", "question": "The four files list the sphere centres (nm) of model opal crystallites made from four different polystyrene sphere batches (files named by sample; each built from that sample's published sphere diameter; neighbouring spheres touch). Model conditions: the only measured input is the sphere diameter reported by Gazmeh et al. (Sci. Rep. 2025, Table 3; field-emission SEM); the spheres are identical (no size dispersion), touch their neighbours and sit on an ideal close-packed lattice without stacking faults, vacancies or cracks, which is the idealization behind the paper's Bragg-law estimate of the reflection peak. Each crystallite is a finite cut of 177 spheres in an arbitrary orientation. Model the film as this lattice with its close-packed planes parallel to the film surface. The spheres have refractive index 1.59 and the voids are filled with a medium of refractive index 1.00; take the effective index from the volume-weighted average of the squared refractive indices (n_eff² = Σ f_i n_i²), using the sphere volume fraction of this packing. You must choose one sample for a new film such that its first-order normal-incidence Bragg reflection from the close-packed planes is closest to 540 nm. Which sample should you choose?", "options": [ { "label": "A", "value": "S8 (opal-PS-S8.xyz)" }, { "label": "B", "value": "S5 (opal-PS-S5.xyz)" }, { "label": "C", "value": "S6 (opal-PS-S6.xyz)" }, { "label": "D", "value": "S7 (opal-PS-S7.xyz)" } ], "inputs": [ "opal-PS-S5.xyz", "opal-PS-S6.xyz", "opal-PS-S7.xyz", "opal-PS-S8.xyz" ], "correct_label": "D", "audit": [ { "label": "A", "rule": "diameter_as_spacing", "reason": "把球径当作密排面间距时它的反射（609.8 nm）最接近目标。" }, { "label": "B", "rule": "no_index", "reason": "忽略折射率时它的反射（422.3 nm）最接近目标。" }, { "label": "C", "rule": "farther_from_target", "reason": "正确模型下反射在 593.9 nm，离目标更远。" }, { "label": "D", "rule": "correct", "reason": "正确模型下反射在 535.9 nm，最接近目标。" } ] }, { "instance": "FA-OP-DES-820", "question": "The four files list the sphere centres (nm) of model opal crystallites made from four different polystyrene sphere batches (files named by sample; each built from that sample's published sphere diameter; neighbouring spheres touch). Model conditions: the only measured input is the sphere diameter reported by Gazmeh et al. (Sci. Rep. 2025, Table 3; field-emission SEM); the spheres are identical (no size dispersion), touch their neighbours and sit on an ideal close-packed lattice without stacking faults, vacancies or cracks, which is the idealization behind the paper's Bragg-law estimate of the reflection peak. Each crystallite is a finite cut of 177 spheres in an arbitrary orientation. Model the film as this lattice with its close-packed planes parallel to the film surface. The spheres have refractive index 1.59 and the voids are filled with a medium of refractive index 1.00; take the effective index from the volume-weighted average of the squared refractive indices (n_eff² = Σ f_i n_i²), using the sphere volume fraction of this packing. You must choose one sample for a new film such that its first-order normal-incidence Bragg reflection from the close-packed planes is closest to 820 nm. Which sample should you choose?", "options": [ { "label": "A", "value": "S3 (opal-PS-S3.xyz)" }, { "label": "B", "value": "S4 (opal-PS-S4.xyz)" }, { "label": "C", "value": "S2 (opal-PS-S2.xyz)" }, { "label": "D", "value": "S5 (opal-PS-S5.xyz)" } ], "inputs": [ "opal-PS-S2.xyz", "opal-PS-S3.xyz", "opal-PS-S4.xyz", "opal-PS-S5.xyz" ], "correct_label": "A", "audit": [ { "label": "A", "rule": "correct", "reason": "正确模型下反射在 815.0 nm，最接近目标。" }, { "label": "B", "rule": "sphere_index", "reason": "用球的折射率代替有效折射率时它的反射（849.0 nm）最接近目标。" }, { "label": "C", "rule": "no_index", "reason": "忽略折射率时它的反射（603.2 nm）最接近目标。" }, { "label": "D", "rule": "diameter_as_spacing", "reason": "把球径当作密排面间距时它的反射（755.2 nm）最接近目标。" } ] } ] } }, { "unit": "opal_geometry", "kind": "family", "ability": "perception", "registry_id": "opal_geometry", "generator": "task_families/photonic.py", "checker": "checkers/superlattice.py", "checker_function": "opal_quantity", "bindings": { "L1": { "registry_row": "f01beb20a4e98f0a57f44558b86be69fefae16161a8bb5052a092e0de31a3e54", "task_families/photonic.py": "3afa16d6c06b6f3367a963632644cd375dbc0caab3e8bcca42a2b6ede7d9585c" }, "L2": { "checkers/superlattice.py": "c03a5a7bd5ced3e525f1c4d5b2c9a27971d3bc5af7a4c95115a13984f6e24fee", "checkers/common.py": "fbc9f4eb287114ac4720d27edc1ea40e25f80da0e1cff6bdee06fbdca2b73aed" } }, "L1": "pending", "L2": "pending", "instances": 3, "L1_record": null, "L2_record": null, "card": { "template": { "name": "胶体光子晶体几何（球径 / 密排面间距 / 晶胞）", "concept": "从旋转后的球心坐标识别接触球 FCC：球径（最近邻距离）、最密排面间距、常规晶胞边长，均在 100–1000 nm。", "inputs": "胶体晶体（蛋白石）晶粒模型的球心坐标（nm，每行 \"sphere x y z\"，177 个，经确定性旋转）；设计题给四个候选文件。", "physical_conditions": "接触球理想 FCC；密排面平行于膜面；有效折射率 n_eff² = Σ f_i n_i²（或题给 n_eff）；Bragg–Snell 一级反射。", "reasoning_scale": "晶格周期：常规晶胞边长 a（约 295–522 nm）", "scale_limits": "按论文球径构建的模型；不含尺寸分布、堆垛缺陷与多面衍射；审核侧附实测峰值供比较。", "source_basis": "Gazmeh et al., Sci. Rep. 15, 38349 (2025) 表 3（聚苯乙烯球径与实测反射峰）；Fookes et al., Sensors 23, 1433 (2023) 参数表（二氧化硅 266 nm、n_eff 1.35、30°）", "answer_method": "中心球周围分壳，核对 12/6 与 √2 比例，并与论文球径一致。", "distractor_mechanisms": [ "cell_edge", "radius", "d111", "half_cell_edge", "d200", "in_layer_row_spacing", "nearest_neighbour", "third_shell_distance", "face_diagonal" ], "four_choice_validation": "与正确值 > 3 nm；升序排列，秩按批次轮换。", "principle": "接触球 FCC：最近邻 = 球径 D，a = √2·D，d111 = a/√3。", "validation": "独立检查器由初基基矢与倒格子求 d111 与常规边长。", "limits": "理想接触球 FCC：不含堆垛层错、球径分布、烧结或收缩；有效折射率用体积加权近似（或题给 n_eff）。", "template_review": "本轮新建（A4），待人工审核。" }, "samples": [ { "instance": "FA-OP-D111-S2", "question": "The file lists the sphere centres (nm) of a model polystyrene opal crystallite built from a published sphere diameter; neighbouring spheres touch. Model conditions: the only measured input is the sphere diameter reported by Gazmeh et al. (Sci. Rep. 2025, Table 3; field-emission SEM); the spheres are identical (no size dispersion), touch their neighbours and sit on an ideal close-packed lattice without stacking faults, vacancies or cracks, which is the idealization behind the paper's Bragg-law estimate of the reflection peak. Each crystallite is a finite cut of 177 spheres in an arbitrary orientation. What is the spacing between adjacent close-packed (most densely populated) planes of sphere centres, in nm?", "options": [ { "label": "A", "value": "301.6", "unit": "nm" }, { "label": "B", "value": "319.9", "unit": "nm" }, { "label": "C", "value": "369.4", "unit": "nm" }, { "label": "D", "value": "522.4", "unit": "nm" } ], "inputs": [ "opal-PS-S2.xyz" ], "correct_label": "A", "audit": [ { "label": "A", "rule": "correct", "reason": "由坐标：12 个最近邻在 369.3800 nm（= 球径），6 个次近邻在 a = 522.3822 nm。" }, { "label": "B", "rule": "in_layer_row_spacing", "reason": "算成密排层内相邻原子行的间距。" }, { "label": "C", "rule": "nearest_neighbour", "reason": "把最近邻间距当作面间距。" }, { "label": "D", "rule": "cell_edge", "reason": "报告了晶胞边长而非面间距。" } ] }, { "instance": "FA-OP-DIAM-S8", "question": "The file lists the sphere centres (nm) of a model polystyrene opal crystallite built from a published sphere diameter; neighbouring spheres touch. Model conditions: the only measured input is the sphere diameter reported by Gazmeh et al. (Sci. Rep. 2025, Table 3; field-emission SEM); the spheres are identical (no size dispersion), touch their neighbours and sit on an ideal close-packed lattice without stacking faults, vacancies or cracks, which is the idealization behind the paper's Bragg-law estimate of the reflection peak. Each crystallite is a finite cut of 177 spheres in an arbitrary orientation. What is the sphere diameter, in nm?", "options": [ { "label": "A", "value": "104.4", "unit": "nm" }, { "label": "B", "value": "147.7", "unit": "nm" }, { "label": "C", "value": "170.5", "unit": "nm" }, { "label": "D", "value": "208.8", "unit": "nm" } ], "inputs": [ "opal-PS-S8.xyz" ], "correct_label": "D", "audit": [ { "label": "A", "rule": "radius", "reason": "报告了半径。" }, { "label": "B", "rule": "half_cell_edge", "reason": "取晶胞边长的一半。" }, { "label": "C", "rule": "d111", "reason": "报告了密排面间距。" }, { "label": "D", "rule": "correct", "reason": "由坐标：12 个最近邻在 208.8500 nm（= 球径），6 个次近邻在 a = 295.3585 nm。" } ] } ] } }, { "unit": "qdot_design", "kind": "family", "ability": "design", "registry_id": "qdot_design", "generator": "task_families/quantum_dot.py", "checker": "checkers/quantum_dot.py", "checker_function": "qdot_design", "bindings": { "L1": { "registry_row": "62c99392e4811dfc72a9aee4d940e5e76d159856b306de55953f8dd173651429", "task_families/quantum_dot.py": "cce686e77411c9425c57ad6bb806f75765b1d1d82180914cca699e2aaae5e3db" }, "L2": { "checkers/quantum_dot.py": "d1cdad3a661f98dddac3c5d6bedfcd68e9bb6cb223a03624526e7d96cf3af63f", "checkers/common.py": "fbc9f4eb287114ac4720d27edc1ea40e25f80da0e1cff6bdee06fbdca2b73aed" } }, "L1": "pending", "L2": "pending", "instances": 2, "L1_record": null, "L2_record": null, "card": { "template": { "name": "量子点粒径选择设计", "concept": "在四个纳米晶模型中选一个，使第一激子吸收峰最接近目标，或选吸收峰不短于阈值的最小粒子（推断的逆问题）。", "inputs": "四个 CdSe 纳米晶模型 XYZ。", "physical_conditions": "题干给出 Yu 2003 的经验多项式、适用范围与 Model conditions（与 CdSe 量子点光学题相同）。", "reasoning_scale": "候选最大粒径", "scale_limits": "经验曲线只在拟合尺寸范围内可靠；模型无配体。", "source_basis": "Yu et al. (2003) 经验曲线", "answer_method": "逐个候选反解吸收峰，按目标规则选择。", "distractor_mechanisms": [ "radius_as_diameter", "two_rg", "bounding_box_diagonal", "passes_if_bounding_box_diagonal", "meets_but_larger", "farther_from_target" ], "four_choice_validation": "恰好一个候选满足目标；领先幅度或阈值距离足够。", "principle": "设计 = 推断的逆问题。", "validation": "独立检查器（checkers/quantum_dot.py:qdot_design）逐个文件用 Decimal 复核最大间距，用多项式求根（numpy.roots）反解吸收峰，再按题干目标规则重新选择。", "limits": "候选为按论文曲线构建的理想球形 CdSe 模型粒子（晶格常数 6.08 Å 为假设），不是实测样品；答案只取决于所给坐标与题干曲线。", "template_review": "本轮新建（A2/A3），待人工审核。" }, "samples": [ { "instance": "FA-QD-DES-565", "question": "The four XYZ files list every atom of four model zinc-blende CdSe nanocrystals (no ligands; angstrom). Use the empirical CdSe sizing curve of Yu et al. (Chem. Mater. 2003): D = 1.6122e-9·λ⁴ − 2.6575e-6·λ³ + 1.6242e-3·λ² − 0.4277·λ + 41.57, with D the particle diameter in nm and λ the wavelength of the first excitonic absorption peak in nm (valid for 400–700 nm), and its extinction law ε = 5857·D^2.65 M⁻¹ cm⁻¹ at that peak. Take D as the largest distance between any two atoms of the supplied nanocrystal. Model conditions: each nanocrystal is an ideal spherical cut from bulk zinc-blende CdSe (assumed lattice constant 6.08 Å) without ligands, surface relaxation or shape anisotropy; the empirical curves above were calibrated by Yu et al. on real nanocrystals whose sizes were measured by TEM, and are applied here to these ideal particles. You must choose one nanocrystal for a device such that it is the smallest particle whose first excitonic absorption peak lies at or beyond 565 nm. Which file should you choose?", "options": [ { "label": "A", "value": "CdSe-QD-D.xyz" }, { "label": "B", "value": "CdSe-QD-C.xyz" }, { "label": "C", "value": "CdSe-QD-A.xyz" }, { "label": "D", "value": "CdSe-QD-B.xyz" } ], "inputs": [ "CdSe-QD-A.xyz", "CdSe-QD-B.xyz", "CdSe-QD-C.xyz", "CdSe-QD-D.xyz" ], "correct_label": "B", "audit": [ { "label": "A", "rule": "meets_but_larger", "reason": "吸收峰 592.4 nm 满足要求，但粒子更大（D = 4.26 nm）。" }, { "label": "B", "rule": "correct", "reason": "满足要求的粒子中最小（D = 3.76 nm，吸收峰 578.1 nm）。" }, { "label": "C", "rule": "passes_if_bounding_box_diagonal", "reason": "吸收峰 536.6 nm，未达到 565 nm；若用包围盒对角线会误判为满足。" }, { "label": "D", "rule": "passes_if_bounding_box_diagonal", "reason": "吸收峰 561.1 nm，未达到 565 nm；若用包围盒对角线会误判为满足。" } ] }, { "instance": "FA-QD-DES-590", "question": "The four XYZ files list every atom of four model zinc-blende CdSe nanocrystals (no ligands; angstrom). Use the empirical CdSe sizing curve of Yu et al. (Chem. Mater. 2003): D = 1.6122e-9·λ⁴ − 2.6575e-6·λ³ + 1.6242e-3·λ² − 0.4277·λ + 41.57, with D the particle diameter in nm and λ the wavelength of the first excitonic absorption peak in nm (valid for 400–700 nm), and its extinction law ε = 5857·D^2.65 M⁻¹ cm⁻¹ at that peak. Take D as the largest distance between any two atoms of the supplied nanocrystal. Model conditions: each nanocrystal is an ideal spherical cut from bulk zinc-blende CdSe (assumed lattice constant 6.08 Å) without ligands, surface relaxation or shape anisotropy; the empirical curves above were calibrated by Yu et al. on real nanocrystals whose sizes were measured by TEM, and are applied here to these ideal particles. You must choose one nanocrystal for a device such that its first excitonic absorption peak is closest to 590 nm. Which file should you choose?", "options": [ { "label": "A", "value": "CdSe-QD-D.xyz" }, { "label": "B", "value": "CdSe-QD-C.xyz" }, { "label": "C", "value": "CdSe-QD-B.xyz" }, { "label": "D", "value": "CdSe-QD-E.xyz" } ], "inputs": [ "CdSe-QD-B.xyz", "CdSe-QD-C.xyz", "CdSe-QD-D.xyz", "CdSe-QD-E.xyz" ], "correct_label": "A", "audit": [ { "label": "A", "rule": "correct", "reason": "吸收峰 592.4 nm，最接近目标。" }, { "label": "B", "rule": "farther_from_target", "reason": "吸收峰 578.1 nm，离目标更远。" }, { "label": "C", "rule": "bounding_box_diagonal", "reason": "用包围盒对角线时它的吸收峰（618.3 nm）最接近目标。" }, { "label": "D", "rule": "radius_as_diameter", "reason": "把半径当直径时它的吸收峰（514.1 nm）最接近目标。" } ] } ] } }, { "unit": "qdot_optics", "kind": "family", "ability": "inference", "registry_id": "qdot_optics", "generator": "task_families/quantum_dot.py", "checker": "checkers/quantum_dot.py", "checker_function": "qdot_quantity", "bindings": { "L1": { "registry_row": "eea0a3f2ee513f0537ad3bd1e551313bd15b497089955526efde906729afaee9", "task_families/quantum_dot.py": "cce686e77411c9425c57ad6bb806f75765b1d1d82180914cca699e2aaae5e3db" }, "L2": { "checkers/quantum_dot.py": "d1cdad3a661f98dddac3c5d6bedfcd68e9bb6cb223a03624526e7d96cf3af63f", "checkers/common.py": "fbc9f4eb287114ac4720d27edc1ea40e25f80da0e1cff6bdee06fbdca2b73aed" } }, "L1": "pending", "L2": "pending", "instances": 3, "L1_record": null, "L2_record": null, "card": { "template": { "name": "CdSe 量子点尺寸与光学（经验曲线）", "concept": "由纳米晶模型坐标确定粒径（最大原子间距），用 Yu et al. (2003) 的经验曲线推断第一激子吸收峰、摩尔消光系数，或由吸光度求浓度。", "inputs": "闪锌矿 CdSe 纳米晶模型 XYZ（本项目构建）。", "physical_conditions": "题干给出经验多项式、适用范围与消光定律。", "reasoning_scale": "纳米晶最大原子间距", "scale_limits": "经验曲线只在拟合尺寸范围内可靠；模型无配体。", "source_basis": "Yu, Qu, Guo, Peng, Chem. Mater. 15, 2854 (2003)：CdSe 尺寸多项式与 ε = 5857 D^2.65", "answer_method": "二分法反解 D(λ)；Beer–Lambert。", "distractor_mechanisms": [ "bounding_box_diagonal", "two_rg", "radius_as_diameter", "diameter_in_angstrom", "cubic_exponent", "exponent_as_factor", "path_in_mm" ], "four_choice_validation": "与正确值 > 3 nm、0.1×10⁵ 或 0.05 µM；升序排列，秩按批次轮换。", "principle": "量子限域：粒径越小吸收越蓝移（经验标定）。", "validation": "独立检查器用 Decimal 复核最大间距，用多项式求根（numpy.roots）反解。", "limits": "论文参数模型；晶格常数 6.08 Å 为模型假设，答案只取决于所给坐标。", "template_review": "本轮新建（A2/A3），待人工审核。" }, "samples": [ { "instance": "FA-QD-CONC-B", "question": "The XYZ file lists every atom of a model zinc-blende CdSe nanocrystal (no ligands; angstrom). Use the empirical CdSe sizing curve of Yu et al. (Chem. Mater. 2003): D = 1.6122e-9·λ⁴ − 2.6575e-6·λ³ + 1.6242e-3·λ² − 0.4277·λ + 41.57, with D the particle diameter in nm and λ the wavelength of the first excitonic absorption peak in nm (valid for 400–700 nm), and its extinction law ε = 5857·D^2.65 M⁻¹ cm⁻¹ at that peak. Take D as the largest distance between any two atoms of the supplied nanocrystal. Model conditions: the nanocrystal is an ideal spherical cut from bulk zinc-blende CdSe (assumed lattice constant 6.08 Å) without ligands, surface relaxation or shape anisotropy; the empirical curves above were calibrated by Yu et al. on real nanocrystals whose sizes were measured by TEM, and are applied here to this ideal particle. A dilute solution of these nanocrystals has an absorbance of 0.25 at the first excitonic peak in a 1.0 cm cuvette. What is the nanocrystal concentration, in µM (Beer–Lambert law)?", "options": [ { "label": "A", "value": "0.464", "unit": "uM" }, { "label": "B", "value": "1.826", "unit": "uM" }, { "label": "C", "value": "3.464", "unit": "uM" }, { "label": "D", "value": "11.462", "unit": "uM" } ], "inputs": [ "CdSe-QD-B.xyz" ], "correct_label": "B", "audit": [ { "label": "A", "rule": "bounding_box_diagonal", "reason": "用包围盒对角线代替最大原子间距。" }, { "label": "B", "rule": "correct", "reason": "c = A/(ε l) = 0.25/(136902 × 1.0) = 1.8261 µM。" }, { "label": "C", "rule": "two_rg", "reason": "用 2 倍回转半径代替直径。" }, { "label": "D", "rule": "radius_as_diameter", "reason": "把半径当作直径代入。" } ] }, { "instance": "FA-QD-EPS-E", "question": "The XYZ file lists every atom of a model zinc-blende CdSe nanocrystal (no ligands; angstrom). Use the empirical CdSe sizing curve of Yu et al. (Chem. Mater. 2003): D = 1.6122e-9·λ⁴ − 2.6575e-6·λ³ + 1.6242e-3·λ² − 0.4277·λ + 41.57, with D the particle diameter in nm and λ the wavelength of the first excitonic absorption peak in nm (valid for 400–700 nm), and its extinction law ε = 5857·D^2.65 M⁻¹ cm⁻¹ at that peak. Take D as the largest distance between any two atoms of the supplied nanocrystal. Model conditions: the nanocrystal is an ideal spherical cut from bulk zinc-blende CdSe (assumed lattice constant 6.08 Å) without ligands, surface relaxation or shape anisotropy; the empirical curves above were calibrated by Yu et al. on real nanocrystals whose sizes were measured by TEM, and are applied here to this ideal particle. What is its molar extinction coefficient at the first excitonic peak, in units of 10⁵ M⁻¹ cm⁻¹?", "options": [ { "label": "A", "value": "2.092", "unit": "1e5 M^-1 cm^-1" }, { "label": "B", "value": "4.132", "unit": "1e5 M^-1 cm^-1" }, { "label": "C", "value": "7.250", "unit": "1e5 M^-1 cm^-1" }, { "label": "D", "value": "17.251", "unit": "1e5 M^-1 cm^-1" } ], "inputs": [ "CdSe-QD-E.xyz" ], "correct_label": "B", "audit": [ { "label": "A", "rule": "two_rg", "reason": "用 2 倍回转半径代替直径。" }, { "label": "B", "rule": "correct", "reason": "ε = 5857 × 4.9837^2.65 = 413219 M⁻¹ cm⁻¹。" }, { "label": "C", "rule": "cubic_exponent", "reason": "指数误用 3（体积标度）。" }, { "label": "D", "rule": "bounding_box_diagonal", "reason": "用包围盒对角线代替最大原子间距。" } ] } ] } }, { "unit": "rotational_line", "kind": "family", "ability": "inference", "registry_id": "rotational_line", "generator": "task_families/rotational.py", "checker": "checkers/rotational.py", "checker_function": "rotational_line", "bindings": { "L1": { "registry_row": "93b11060270ab4962032fcc78d6a6ae4f61b0c5fe0e1fa07a58071e9fd567ef8", "task_families/rotational.py": "ef8570ff19cf492f975faac17305b9c59625de37a61ce1230769f63ba46616a5" }, "L2": { "checkers/rotational.py": "2ba544a31a644ef654de95c16143919963ca2afab72b5864101a1f54916f47d2", "checkers/common.py": "fbc9f4eb287114ac4720d27edc1ea40e25f80da0e1cff6bdee06fbdca2b73aed" } }, "L1": "pending", "L2": "pending", "instances": 2, "L1_record": null, "L2_record": null, "card": { "template": { "name": "转动跃迁频率", "concept": "由分子几何预测转动光谱：质心 → 惯量张量 → 主转动惯量 → 转动常数 A ≥ B ≥ C → J = 1 能级 → 1_01、1_11 或 1_10 ← 0_00 跃迁频率。几何决定可观测谱线（量子力学刚性转子）。", "inputs": "XYZ（QM7-X 优化几何或 SAMPL9 客体结构，按行号计数）。", "physical_conditions": "刚性转子、给定平衡几何；题干写明最丰同位素质量、h 与原子质量单位；不含振动平均、离心畸变与超精细结构。", "reasoning_scale": "整分子转动惯量（分子最大原子间距 0.5–1.2 nm）", "scale_limits": "推理需要整个分子的质量分布；大于 60 个原子的主体分子不出题（超出常见转动光谱范围）。", "source_basis": "QM7-X（CC BY 4.0）、SAMPL9 客体（仓库内已有资产，不新下载）", "answer_method": "质量加权、平移到质心的惯量张量，循环 Jacobi 对角化；跃迁频率按非对称陀螺 J = 1 能级（B+C、A+C、A+B）；以张量迹不变量自检。", "distractor_mechanisms": [ "other_J1_level", "linear_rotor_2B", "unrotated_tensor_diagonal", "origin_not_centre_of_mass", "heavy_atoms_only", "four_pi_squared", "polar_moment_as_I", "average_atomic_weights", "equal_masses", "single_constant", "hbar_instead_of_h" ], "four_choice_validation": "与正确值相差 > 2%（且 ≥ 20 个末位），干扰项之间 > 1%；升序排列，秩按批次轮换；枚举实例设 strict_rank。2026-10-06 探针 runs/enum-v32：99 个候选接受 81，独立检查全部一致；1_10 线答案几乎不在 A、1_01 线几乎不在 D（其余能级在物理上位于一侧），三条线合起来位置均衡。", "principle": "刚性转子：X = h/(8π²I_x)；非对称陀螺 J = 1 的三个能级分别为 B+C（1_01）、A+C（1_11）、A+B（1_10）。", "validation": "独立检查器（checkers/rotational.py:rotational_line）从题干读取同位素质量、h 与 u，核对附件与源文件逐字一致，用 Decimal 累加质心与惯量张量，以三次特征方程的三角闭式解求主惯量，按自己的 J = 1 能级表重算频率，并核对四个选项与答案键。", "limits": "平衡几何不是振动平均结构（r_e ≠ r_0），与实测谱线可差约 1%；SAMPL9 客体为铵正离子；不评估跃迁的偶极强度。", "template_review": "2026-10-06 新建，待 L1/L2 人工审核。" }, "samples": [ { "instance": "FA-ROT-7029-111", "question": "The supplied XYZ is the DFTB3+MBD-optimized geometry of QM7-X molecule 7029 (C4H8N2S, 15 atoms, angstrom); rows are counted from 1 after the two header lines. Model conditions: a rigid rotor at exactly the supplied geometry (no vibrational averaging, no centrifugal distortion); masses of the most abundant isotopes: C 12.000000 u, H 1.007825 u, N 14.003074 u, S 31.972071 u; rotational constants A ≥ B ≥ C are h/(8π²I) with I_a ≤ I_b ≤ I_c the principal moments of inertia about the centre of mass; h = 6.62607015×10⁻³⁴ J s, 1 u = 1.66053906660×10⁻²⁷ kg. Predict the frequency of the J_KaKc = 1_11 ← 0_00 rotational transition of this molecule, in MHz.", "options": [ { "label": "A", "value": "2195.9", "unit": "MHz" }, { "label": "B", "value": "2477.0", "unit": "MHz" }, { "label": "C", "value": "4840.8", "unit": "MHz" }, { "label": "D", "value": "5068.4", "unit": "MHz" } ], "inputs": [ "QM7X-7029.xyz" ], "correct_label": "D", "audit": [ { "label": "A", "rule": "other_J1_level:101", "reason": "能级标号对错：算成 1_01 ← 0_00 跃迁（B + C）。" }, { "label": "B", "rule": "linear_rotor_2B", "reason": "套用线型分子公式 ν(J=1←0) = 2B，忽略了非对称陀螺 J = 1 能级按 K 分裂。" }, { "label": "C", "rule": "unrotated_tensor_diagonal", "reason": "直接用输入坐标系中惯量张量的对角元当主转动惯量，没有对角化。" }, { "label": "D", "rule": "correct", "reason": "质心 → 惯量张量 → Jacobi 对角化 → A、B、C → 1_11 ← 0_00 = A + C。" } ] }, { "instance": "FA-ROT-G2-110", "question": "The supplied XYZ is guest G2 (4-(1,1-dimethylpiperidin-1-ium-4-yl)-1,1-dimethyl-piperidin-1-ium) of the SAMPL9 WP6 host–guest challenge, one 3D structure (46 atoms, angstrom); rows are counted from 1 after the two header lines. Model conditions: a rigid rotor at exactly the supplied geometry (no vibrational averaging, no centrifugal distortion); masses of the most abundant isotopes: C 12.000000 u, H 1.007825 u, N 14.003074 u; rotational constants A ≥ B ≥ C are h/(8π²I) with I_a ≤ I_b ≤ I_c the principal moments of inertia about the centre of mass; h = 6.62607015×10⁻³⁴ J s, 1 u = 1.66053906660×10⁻²⁷ kg. Predict the frequency of the J_KaKc = 1_10 ← 0_00 rotational transition of this molecule, in MHz.", "options": [ { "label": "A", "value": "679.2", "unit": "MHz" }, { "label": "B", "value": "1724.3", "unit": "MHz" }, { "label": "C", "value": "2455.1", "unit": "MHz" }, { "label": "D", "value": "3448.5", "unit": "MHz" } ], "inputs": [ "WP6-G2.xyz" ], "correct_label": "B", "audit": [ { "label": "A", "rule": "unrotated_tensor_diagonal", "reason": "直接用输入坐标系中惯量张量的对角元当主转动惯量，没有对角化。" }, { "label": "B", "rule": "correct", "reason": "质心 → 惯量张量 → Jacobi 对角化 → A、B、C → 1_10 ← 0_00 = A + B。" }, { "label": "C", "rule": "heavy_atoms_only", "reason": "只计重原子、忽略氢原子的贡献。" }, { "label": "D", "rule": "four_pi_squared", "reason": "转动常数写成 h/(4π²I)，结果大了一倍。" } ] } ] } }, { "unit": "scattering_q_design", "kind": "family", "ability": "design", "registry_id": "scattering_q_design", "generator": "task_families/assembly.py", "checker": "checkers/migrated.py", "checker_function": "scattering_q_design", "bindings": { "L1": { "registry_row": "b6cf80ee1c743e0e7f97a12419f33675d12a2aa3958dd7de32f61683320983d5", "task_families/assembly.py": "5cbb7b6b4a45f6797fe9d4f6cdd31e4b7df60da7812d4ce5a0aba6ce248c77e6" }, "L2": { "checkers/migrated.py": "f1cf6f20bca7ad81fd3b5ee5c6749084a090a32dd40b0a394768995a6e3a42eb", "checkers/common.py": "fbc9f4eb287114ac4720d27edc1ea40e25f80da0e1cff6bdee06fbdca2b73aed" } }, "L1": "pending", "L2": "pending", "instances": 8, "L1_record": null, "L2_record": null, "card": { "template": { "name": "测量条件设计：使散射强度降到目标的 q", "concept": "推断的逆问题：给定目标 I(q)/I(0)，选择测量 q，使整个颗粒的取向平均强度首次降到该值；需要精确 Debye 计算，形状模型与 Guinier 反解都会偏。", "inputs": "按组分标记的点表（DNA 折纸每核苷酸 C1′；HSV-1 衣壳每链质心），可只选某一组分。", "physical_conditions": "等权点散射体，无形状因子与溶剂；q = 4π sinθ/λ（题干写明）。", "reasoning_scale": "所选点集的最大间距（探测长度 2π/q 同量级）", "scale_limits": "约简表示；非实测 SAXS。暂无数据源的格：chemistry 100-1000（规划器不据此给出路线）。", "source_basis": "RCSB PDB 大型组装体（1AON、1KX5、1A34、6CGR、6NCL、7ARQ），经沉积的对称操作展开并约简为每残基/每核苷酸一点或每链质心", "answer_method": "从 q = 0 以 0.02/Rg 步进找首个穿越点，再二分 60 次；两种 Debye 实现在解处一致。", "distractor_mechanisms": [ "guinier_root", "uniform_sphere_root", "single_orientation_root", "target_as_amplitude", "reported_as_s", "dmax_sphere_root", "reported_per_angstrom", "sphere_radius_equals_rg_root", "guinier_single_axis_root", "guinier_missing_one_third_root", "guinier_half_dmax_root" ], "four_choice_validation": "与正确值相差 > 5%·q*；升序排列，秩按批次轮换。 v0.3.0：同上两种 Guinier 误用（解出更小的 q）；之前探针答案多在 B。", "principle": "设计 = 推断的逆问题：选测量条件使可观测量达到目标。", "validation": "独立检查器用求积取向平均，自行以 0.013/Rg 步进并用 Illinois 试位法求根。", "limits": "这是测量条件设计（选 q），不是改变结构的分子设计；是否计为“设计题”需教授审定。", "template_review": "本轮新建（A4），待人工审核。" }, "samples": [ { "instance": "FA-QDES-1AON", "question": "The XYZ file lists one point per residue (protein Cα written as C) of the GroEL–GroES–(ADP)7 chaperonin complex, all 21 chains of PDB 1AON (angstrom). Select all supplied points. Treat each selected point as an identical point scatterer (no form factor, no solvent). A small-angle scattering measurement is to be set at the q where the orientation-averaged normalized intensity I(q)/I(0) of the selected points first falls to 0.50. Starting from q = 0, at which q (in nm⁻¹, q = 4π sinθ/λ) does I(q)/I(0) first reach 0.50? Compute the intensity exactly from all point pairs.", "options": [ { "label": "A", "value": "0.207", "unit": "nm^-1" }, { "label": "B", "value": "0.265", "unit": "nm^-1" }, { "label": "C", "value": "0.288", "unit": "nm^-1" }, { "label": "D", "value": "0.296", "unit": "nm^-1" } ], "inputs": [ "1AON-residue-points.xyz" ], "correct_label": "A", "audit": [ { "label": "A", "rule": "correct", "reason": "Debye 公式（全部点对、取向平均）从 q = 0 起步进并二分，得首次降到 0.50 的 q。" }, { "label": "B", "rule": "sphere_radius_equals_rg_root", "reason": "把回转半径直接当作均匀球的半径求交点（球偏小，q 偏大）。" }, { "label": "C", "rule": "target_as_amplitude", "reason": "把目标值当作振幅比（强度的平方根）求交点。" }, { "label": "D", "rule": "guinier_single_axis_root", "reason": "用 Guinier 反解，且把单一坐标轴的均方根离散度当作 Rg。" } ] }, { "instance": "FA-QDES-1KX5", "question": "The XYZ file lists one point per residue (protein Cα as C, DNA phosphorus as P) of the nucleosome core particle NCP147, PDB 1KX5 (angstrom). Select all supplied points. Treat each selected point as an identical point scatterer (no form factor, no solvent). A small-angle scattering measurement is to be set at the q where the orientation-averaged normalized intensity I(q)/I(0) of the selected points first falls to 0.50. Starting from q = 0, at which q (in nm⁻¹, q = 4π sinθ/λ) does I(q)/I(0) first reach 0.50? Compute the intensity exactly from all point pairs.", "options": [ { "label": "A", "value": "0.213", "unit": "nm^-1" }, { "label": "B", "value": "0.376", "unit": "nm^-1" }, { "label": "C", "value": "0.542", "unit": "nm^-1" }, { "label": "D", "value": "0.553", "unit": "nm^-1" } ], "inputs": [ "1KX5-residue-points.xyz" ], "correct_label": "B", "audit": [ { "label": "A", "rule": "guinier_missing_one_third_root", "reason": "用 Guinier 近似求 q，且指数中漏掉 1/3。" }, { "label": "B", "rule": "correct", "reason": "Debye 公式（全部点对、取向平均）从 q = 0 起步进并二分，得首次降到 0.50 的 q。" }, { "label": "C", "rule": "target_as_amplitude", "reason": "把目标值当作振幅比（强度的平方根）求交点。" }, { "label": "D", "rule": "guinier_single_axis_root", "reason": "用 Guinier 反解，且把单一坐标轴的均方根离散度当作 Rg。" } ] } ] } }, { "unit": "secondary_structure", "kind": "family", "ability": "inference", "registry_id": "secondary_structure", "generator": "task_families/local_geometry.py", "checker": "checkers/migrated.py", "checker_function": "secondary_structure", "bindings": { "L1": { "registry_row": "05d367ad84727c361f99c3d9984b26328d5d029d88ae39cb63071c0ee0ffceee", "task_families/local_geometry.py": "5f7867f2d96cbff718aa367ea23637bb59e567ddd8363e00e346bf046c4917f2" }, "L2": { "checkers/migrated.py": "f1cf6f20bca7ad81fd3b5ee5c6749084a090a32dd40b0a394768995a6e3a42eb", "checkers/common.py": "fbc9f4eb287114ac4720d27edc1ea40e25f80da0e1cff6bdee06fbdca2b73aed" } }, "L1": "pending", "L2": "pending", "instances": 2, "L1_record": null, "L2_record": null, "card": { "template": { "name": "由 φ/ψ 推断二级结构（HELIX/SHEET 为证据）", "concept": "由三残基 ATOM 片段计算中心残基的 φ/ψ，按题给参考构象（右手 α、β 链、PPII、左手 α）取最近者；条目自身的 HELIX/SHEET 记录作为审核证据，二者不一致即拒绝出题。", "inputs": "PDB 三残基 ATOM 片段（逐行照抄）。", "physical_conditions": "IUPAC 符号约定；(φ, ψ) 平面距离，360° 周期。", "reasoning_scale": "定义 φ、ψ 的五个主链原子（约 0.3–0.4 nm）", "scale_limits": "单残基局部构象；不判断整段二级结构。", "source_basis": "RCSB PDB 1UBQ、6LYZ、1CRN（仓库已有）", "answer_method": "两种二面角实现一致；最近参考构象领先 ≥ 30%；与 HELIX/SHEET 记录一致。", "distractor_mechanisms": [ "second_nearest_reference", "mirror_image", "other_reference" ], "four_choice_validation": "四个选项恰为四个参考构象；唯一最近者。", "principle": "Ramachandran 区域；作者指认的 HELIX/SHEET 为证据。", "validation": "独立检查器用 acos+三重积求二面角，并从源文件读取 HELIX/SHEET 记录核对。", "limits": "参考中心为教科书典型值；HELIX/SHEET 是作者指认。", "template_review": "本轮新建（A2/A3），待人工审核。" }, "samples": [ { "instance": "EN-12E8-SS-3", "question": "The excerpt contains residues 2–4 of chain H from PDB entry 12E8 (2E8 Fab fragment, heavy chain, X-ray), ATOM records copied unchanged (coordinates in angstrom). Compute the backbone dihedrals φ and ψ of Gln3 (IUPAC sign convention) and assign the residue to the nearest of these reference backbone conformations, measuring distance in the (φ, ψ) plane with 360° periodicity: right-handed α-helix (φ −57°, ψ −47°), β-strand (φ −120°, ψ +130°), polyproline II (φ −75°, ψ +145°), left-handed α-helix (φ +57°, ψ +47°). Which conformation does Gln3 adopt?", "options": [ { "label": "A", "value": "right-handed α-helix" }, { "label": "B", "value": "left-handed α-helix" }, { "label": "C", "value": "β-strand" }, { "label": "D", "value": "polyproline II" } ], "inputs": [ "12E8-H3-excerpt.pdb" ], "correct_label": "C", "audit": [ { "label": "A", "rule": "other_reference", "reason": "距离 193°，明显更远。" }, { "label": "B", "rule": "other_reference", "reason": "距离 182°，明显更远。" }, { "label": "C", "rule": "correct", "reason": "φ = -148.4°，ψ = 142.6°，最近参考构象（31°）；与条目 SHEET 记录一致。" }, { "label": "D", "rule": "second_nearest_reference", "reason": "次近的参考构象（距离 73°，正确者 31°）；两者易混。" } ] }, { "instance": "FA-SS-1UBQ-43", "question": "The excerpt contains residues 42–44 of chain A from PDB entry 1UBQ (ubiquitin, X-ray), ATOM records copied unchanged (coordinates in angstrom). Compute the backbone dihedrals φ and ψ of Leu43 (IUPAC sign convention) and assign the residue to the nearest of these reference backbone conformations, measuring distance in the (φ, ψ) plane with 360° periodicity: right-handed α-helix (φ −57°, ψ −47°), β-strand (φ −120°, ψ +130°), polyproline II (φ −75°, ψ +145°), left-handed α-helix (φ +57°, ψ +47°). Which conformation does Leu43 adopt?", "options": [ { "label": "A", "value": "right-handed α-helix" }, { "label": "B", "value": "left-handed α-helix" }, { "label": "C", "value": "β-strand" }, { "label": "D", "value": "polyproline II" } ], "inputs": [ "1UBQ-A43-excerpt.pdb" ], "correct_label": "C", "audit": [ { "label": "A", "rule": "other_reference", "reason": "距离 183°，明显更远。" }, { "label": "B", "rule": "other_reference", "reason": "距离 181°，明显更远。" }, { "label": "C", "rule": "correct", "reason": "φ = -103.6°，ψ = 130.2°，最近参考构象（16°）；与条目 SHEET 记录一致。" }, { "label": "D", "rule": "second_nearest_reference", "reason": "次近的参考构象（距离 32°，正确者 16°）；两者易混。" } ] } ] } }, { "unit": "stereo_design_selection", "kind": "family", "ability": "design", "registry_id": "stereo_design_selection", "generator": "task_families/stereo.py", "checker": "checkers/stereo.py", "checker_function": "stereo_design_selection", "bindings": { "L1": { "registry_row": "0f2de24667ddcb91f9927776a89a21e8e4b0efe706d479a085ebc7977545f112", "task_families/stereo.py": "6b3b6af008d12b295cd89020110e1259d4941ec02424273e8f5f758e8401c370" }, "L2": { "checkers/stereo.py": "70f02daf0cae0c92a6c79fc118cc08334330e93287e688931a653bd927489625", "checkers/common.py": "fbc9f4eb287114ac4720d27edc1ea40e25f80da0e1cff6bdee06fbdca2b73aed" } }, "L1": "pending", "L2": "pending", "instances": 1, "L1_record": null, "L2_record": null, "card": { "template": { "name": "立体构型设计选择", "concept": "给定 S0 与目标（能量降低 ≥1 kcal/mol），只允许改变构型（立体中心手性或双键顺反），从四个候选中选唯一满足者；陷阱：镜像（构型变但能量不变）、只改构象（能量更低但不允许）、构造异构体（键连不同）。", "inputs": "S0 与四个候选 XYZ（均刚性旋转；构造异构体原子顺序不同）；性质证据在审核侧。", "physical_conditions": "同 stereo_property_inference。", "reasoning_scale": "立体中心与整分子", "scale_limits": "候选须满足约束且互不等价（排除镜像/构象重复）。", "source_basis": "QM7-X 立体异构体与构象（CC BY 4.0），15 个分子的全部优化构象", "answer_method": "逐项判定与 S0 的关系（是否只改构型）+ 能量证据（数据集值；镜像按反演对称等于 S0）。", "distractor_mechanisms": [ "mirror_image_no_energy_change", "conformation_only_change", "constitution_changed" ], "four_choice_validation": "恰好一项同时满足约束与目标；独立检查器复核每一项。", "principle": "设计 = 推断的逆问题。", "validation": "独立检查器重算关系与能量差。", "limits": "计算证据只对所述理论水平成立。", "template_review": "本轮新建，待人工审核。" }, "samples": [ { "instance": "FA-SDES-7110", "question": "S0 is one conformer of a C3H7N1O2S1 molecule. You may change it only by changing the configuration of its stereo elements (the handedness of stereocentres or the cis/trans arrangement at double bonds): same atoms, same bonds; a change of conformation alone does not count. Goal: a structure whose PBE0+MBD energy (single point at the supplied geometry) is at least 0.0434 eV (1 kcal/mol) lower than that of S0. Candidates A–D have been rigidly rotated and their atom order may differ from S0. Which candidate satisfies both the allowed modification and the goal?", "options": [ { "label": "A", "value": "candidate_A.xyz" }, { "label": "B", "value": "candidate_B.xyz" }, { "label": "C", "value": "candidate_C.xyz" }, { "label": "D", "value": "candidate_D.xyz" } ], "inputs": [ "S0.xyz", "candidate_A.xyz", "candidate_B.xyz", "candidate_C.xyz", "candidate_D.xyz" ], "correct_label": "A", "audit": [ { "label": "A", "rule": "Geom-m7110-i1-c1-opt", "reason": "只改变构型（非对映体），能量低 0.1763 eV，满足目标。" }, { "label": "B", "rule": "Geom-m7038-i1-c1-opt", "reason": "分子式相同但键连不同（构造异构体），违反“键连不变”。" }, { "label": "C", "rule": "Geom-m7110-i2-c1-opt", "reason": "能量更低（-0.0962 eV）但只是同一构型的另一构象，不属于允许的修改。" }, { "label": "D", "rule": "mirror of Geom-m7110-i2-c2-opt", "reason": "镜像（对映体）：构型改变但能量按反演对称与 S0 完全相同，未达到降低目标。" } ] }, { "instance": "FA-SDES-7029", "question": "S0 is one conformer of a C4H8N2S1 molecule. You may change it only by changing the configuration of its stereo elements (the handedness of stereocentres or the cis/trans arrangement at double bonds): same atoms, same bonds; a change of conformation alone does not count. Goal: a structure whose PBE0+MBD energy (single point at the supplied geometry) is at least 0.0434 eV (1 kcal/mol) lower than that of S0. Candidates A–D have been rigidly rotated and their atom order may differ from S0. Which candidate satisfies both the allowed modification and the goal?", "options": [ { "label": "A", "value": "candidate_A.xyz" }, { "label": "B", "value": "candidate_B.xyz" }, { "label": "C", "value": "candidate_C.xyz" }, { "label": "D", "value": "candidate_D.xyz" } ], "inputs": [ "S0.xyz", "candidate_A.xyz", "candidate_B.xyz", "candidate_C.xyz", "candidate_D.xyz" ], "correct_label": "C", "audit": [ { "label": "A", "rule": "Geom-m7030-i1-c3-opt", "reason": "分子式相同但键连不同（构造异构体），违反“键连不变”。" }, { "label": "B", "rule": "mirror of Geom-m7029-i1-c2-opt", "reason": "S0 无手性中心，镜像仍是同一化合物（仅构象镜像），未改变构型且能量相同。" }, { "label": "C", "rule": "Geom-m7029-i2-c2-opt", "reason": "只改变构型（非对映体），能量低 0.0590 eV，满足目标。" }, { "label": "D", "rule": "Geom-m7029-i1-c4-opt", "reason": "能量更低（-0.0544 eV）但只是同一构型的另一构象，不属于允许的修改。" } ] } ] } }, { "unit": "stereo_property_inference", "kind": "family", "ability": "inference", "registry_id": "stereo_property_inference", "generator": "task_families/stereo.py", "checker": "checkers/stereo.py", "checker_function": "stereo_property_inference", "bindings": { "L1": { "registry_row": "cafb6141512f88a3ffbde0a3e196ac83a66e9824e32a552bba79c1fcb17da485", "task_families/stereo.py": "6b3b6af008d12b295cd89020110e1259d4941ec02424273e8f5f758e8401c370" }, "L2": { "checkers/stereo.py": "70f02daf0cae0c92a6c79fc118cc08334330e93287e688931a653bd927489625", "checkers/common.py": "fbc9f4eb287114ac4720d27edc1ea40e25f80da0e1cff6bdee06fbdca2b73aed" } }, "L1": "pending", "L2": "pending", "instances": 1, "L1_record": null, "L2_record": null, "card": { "template": { "name": "立体异构体性质推断", "concept": "同一分子的两个或多个立体异构体，由三维构型推断哪一个的指定性质（偶极、能量或文献报道的活性）更高或落在哪个区间。", "inputs": "S0.xyz 与 X.xyz：同一分子两个非对映体各自的数据集最低能构象；X 刚性旋转。", "physical_conditions": "性质为数据集计算值或论文实测值，题干写明来源类型与条件。", "reasoning_scale": "立体中心周围与整分子取向", "scale_limits": "构型差异须由几何决定；性质差须超过阈值。", "source_basis": "QM7-X 立体异构体与构象（CC BY 4.0），15 个分子的全部优化构象", "answer_method": "由数据集 PBE0+MBD 能量与偶极得到 ΔE、Δμ 的符号；两者均须超过阈值（1 kcal/mol、0.10 e·Å）。", "distractor_mechanisms": [ "energy_direction_reversed", "dipole_direction_reversed", "both_reversed" ], "four_choice_validation": "四个陈述覆盖符号组合，恰好一个成立；位置按批次轮换。", "principle": "立体构型 → 性质。", "validation": "独立检查器按距离矩阵与手性匹配数据集结构后重算。", "limits": "手性药物的活性需论文证据。", "template_review": "本轮新建，待人工审核。" }, "samples": [ { "instance": "FA-SPROP-7089", "question": "S0 and X are two stereoisomers of the same neutral C4H6N2S1 molecule; atom order is shared and X has been rigidly rotated and translated. Each structure is the lowest-energy QM7-X conformer of its configuration. Compare X with S0 by PBE0+MBD total energy and dipole-moment magnitude at the supplied geometries; each difference is at least 0.0434 eV (1 kcal/mol) in energy and 0.10 e·Å in dipole. Which statement is correct?", "options": [ { "label": "A", "value": "X is higher in energy than S0 and has a smaller dipole moment" }, { "label": "B", "value": "X is lower in energy than S0 and has a larger dipole moment" }, { "label": "C", "value": "X is higher in energy than S0 and has a larger dipole moment" }, { "label": "D", "value": "X is lower in energy than S0 and has a smaller dipole moment" } ], "inputs": [ "S0.xyz", "X.xyz" ], "correct_label": "D", "audit": [ { "label": "A", "rule": null, "reason": "与数据集计算值不符：能量方向相反。" }, { "label": "B", "rule": null, "reason": "与数据集计算值不符：偶极方向相反。" }, { "label": "C", "rule": null, "reason": "与数据集计算值不符：能量方向、偶极方向相反。" }, { "label": "D", "rule": null, "reason": "ΔE = -0.1533 eV，Δμ = -0.3029 e·Å（X − S0，数据集计算值）。" } ] }, { "instance": "FA-SPROP-7082", "question": "S0 and X are two stereoisomers of the same neutral C4H6N2S1 molecule; atom order is shared and X has been rigidly rotated and translated. Each structure is the lowest-energy QM7-X conformer of its configuration. Compare X with S0 by PBE0+MBD total energy and dipole-moment magnitude at the supplied geometries; each difference is at least 0.0434 eV (1 kcal/mol) in energy and 0.10 e·Å in dipole. Which statement is correct?", "options": [ { "label": "A", "value": "X is higher in energy than S0 and has a smaller dipole moment" }, { "label": "B", "value": "X is lower in energy than S0 and has a larger dipole moment" }, { "label": "C", "value": "X is higher in energy than S0 and has a larger dipole moment" }, { "label": "D", "value": "X is lower in energy than S0 and has a smaller dipole moment" } ], "inputs": [ "S0.xyz", "X.xyz" ], "correct_label": "C", "audit": [ { "label": "A", "rule": null, "reason": "与数据集计算值不符：偶极方向相反。" }, { "label": "B", "rule": null, "reason": "与数据集计算值不符：能量方向相反。" }, { "label": "C", "rule": null, "reason": "ΔE = +0.1100 eV，Δμ = +0.2468 e·Å（X − S0，数据集计算值）。" }, { "label": "D", "rule": null, "reason": "与数据集计算值不符：能量方向、偶极方向相反。" } ] } ] } }, { "unit": "stereo_relationship", "kind": "family", "ability": "perception", "registry_id": "stereo_relationship", "generator": "task_families/stereo.py", "checker": "checkers/stereo.py", "checker_function": "stereo_relationship", "bindings": { "L1": { "registry_row": "0bec8505ed45aa61a551cfb7289f77ad5ed9aebaa01346850763f59e55892549", "task_families/stereo.py": "6b3b6af008d12b295cd89020110e1259d4941ec02424273e8f5f758e8401c370" }, "L2": { "checkers/stereo.py": "70f02daf0cae0c92a6c79fc118cc08334330e93287e688931a653bd927489625", "checkers/common.py": "fbc9f4eb287114ac4720d27edc1ea40e25f80da0e1cff6bdee06fbdca2b73aed" } }, "L1": "pending", "L2": "pending", "instances": 1, "L1_record": null, "L2_record": null, "card": { "template": { "name": "立体关系判别", "concept": "判断结构 X 相对 S0 是同一化合物（仅构象/取向不同）、对映体、非对映体还是构造异构体；需要在三维中区分旋转与镜像、构象改变与构型改变（会议 2 立体化学梯子第一级）。", "inputs": "S0.xyz 与 X.xyz（Å）；X 经刚性旋转平移，原子顺序可能不同。", "physical_conditions": "单键旋转可互变的结构视为同一化合物。", "reasoning_scale": "整分子立体构型（0.4–0.8 nm）", "scale_limits": "立体中心按第一配位层判定；与数据集标签不一致的实例拒绝。", "source_basis": "QM7-X 立体异构体与构象（CC BY 4.0），15 个分子的全部优化构象", "answer_method": "共价半径成键图 + 图不变量判定键连；四配位中心、锥形 S/P、氮杂环丙烷 N 的手性符号与双键顺反描述符判定构型关系。", "distractor_mechanisms": [ "conformation_mistaken_for_configuration", "rotation_mistaken_for_reflection", "partial_vs_full_inversion", "same_formula_assumed_same_bonding" ], "four_choice_validation": "四个固定类别恰好一个成立；批次内每类 2 例以平衡位置；独立检查器用自有实现复核。", "principle": "构型描述符在旋转与构象变化下不变、在镜像下全部翻转。", "validation": "生成端与独立检查器一致；数据集标签交叉核对。", "limits": "不给 R/S 描述符（需 CIP 优先级，RDKit 未安装）；7165 真对映体因数据集缺镜像构象被保守拒绝。", "template_review": "本轮新建，待人工审核。" }, "samples": [ { "instance": "FA-SREL-7110-DIAS", "question": "S0.xyz and X.xyz each contain one structure of formula C3H7N1O2S1 (angstrom). X has been rigidly rotated and translated, and its atom order may differ from S0. Treat structures that interconvert only by rotation about single bonds as the same compound. Which describes X relative to S0?", "options": [ { "label": "A", "value": "the same compound as S0 (only conformation and/or orientation differ)" }, { "label": "B", "value": "an enantiomer of S0 (its non-superimposable mirror image)" }, { "label": "C", "value": "a diastereomer of S0 (a stereoisomer that is not its mirror image)" }, { "label": "D", "value": "a constitutional isomer of S0 (same formula, different bonding)" } ], "inputs": [ "S0.xyz", "X.xyz" ], "correct_label": "C", "audit": [ { "label": "A", "rule": null, "reason": "存在构型差异或键连不同，不是同一化合物。" }, { "label": "B", "rule": null, "reason": "不满足“全部立体中心反转、双键不变”的镜像关系。" }, { "label": "C", "rule": null, "reason": "键连相同，构型部分改变（或双键顺反改变），但不是镜像。" }, { "label": "D", "rule": null, "reason": "键连图相同，不是构造异构体。" } ] }, { "instance": "FA-SREL-7029-SAME", "question": "S0.xyz and X.xyz each contain one structure of formula C4H8N2S1 (angstrom). X has been rigidly rotated and translated, and its atom order may differ from S0. Treat structures that interconvert only by rotation about single bonds as the same compound. Which describes X relative to S0?", "options": [ { "label": "A", "value": "the same compound as S0 (only conformation and/or orientation differ)" }, { "label": "B", "value": "an enantiomer of S0 (its non-superimposable mirror image)" }, { "label": "C", "value": "a diastereomer of S0 (a stereoisomer that is not its mirror image)" }, { "label": "D", "value": "a constitutional isomer of S0 (same formula, different bonding)" } ], "inputs": [ "S0.xyz", "X.xyz" ], "correct_label": "A", "audit": [ { "label": "A", "rule": null, "reason": "键连相同且所有立体描述符一致：仅构象/取向不同。" }, { "label": "B", "rule": null, "reason": "不满足“全部立体中心反转、双键不变”的镜像关系。" }, { "label": "C", "rule": null, "reason": "不是“键连相同而构型部分不同”的情形。" }, { "label": "D", "rule": null, "reason": "键连图相同，不是构造异构体。" } ] } ] } }, { "unit": "superlattice_design", "kind": "family", "ability": "design", "registry_id": "superlattice_design", "generator": "task_families/superlattice.py", "checker": "checkers/superlattice.py", "checker_function": "superlattice_design", "bindings": { "L1": { "registry_row": "cd057523b20a3ae564ac58349e2912ba1657952bb25d2fdf2c78d184ae666a0b", "task_families/superlattice.py": "7815e908c5d30f5f208fcae8f35b76afeb33003452a00e781b1973a0520a62e6" }, "L2": { "checkers/superlattice.py": "c03a5a7bd5ced3e525f1c4d5b2c9a27971d3bc5af7a4c95115a13984f6e24fee", "checkers/common.py": "fbc9f4eb287114ac4720d27edc1ea40e25f80da0e1cff6bdee06fbdca2b73aed" } }, "L1": "pending", "L2": "pending", "instances": 3, "L1_record": null, "L2_record": null, "card": { "template": { "name": "超晶格连接子设计选择", "concept": "在论文实际做出的四种 DNA 连接子中选择一种，使超晶格达到目标（首个 Bragg 反射、最近邻间距，或在金含量约束下间距最大）；四个候选各有模型晶粒。", "inputs": "DNA 连接金纳米粒子超晶格晶粒模型的粒子中心 XYZ（nm，约 177 个，经确定性旋转）；设计题给四个候选文件。", "physical_conditions": "理想无限 FCC 晶格（按论文 SAXS 晶胞边长）；粒子视为相同点散射体；金核直径 10.3 nm 在题干给出。", "reasoning_scale": "晶格周期（常规晶胞边长 a，约 40–77 nm）", "scale_limits": "按论文参数构建的模型，不是实测粒子坐标；不含位置无序、峰宽与形状因子。", "source_basis": "Hill et al., Nano Lett. 8, 2341 (2008) 表 1：五种 DNA 连接子的 SAXS 晶胞边长（论文参数模型）", "answer_method": "逐个候选由坐标计算性质，按目标规则取唯一最优；要求领先幅度足够。", "distractor_mechanisms": [ "q_from_nearest_neighbour", "q_200_as_first", "cell_edge_as_spacing", "plane_spacing_as_spacing", "diameter_as_radius_passes", "highest_gold_not_largest_spacing", "satisfies_but_smaller_spacing", "farther_from_target" ], "four_choice_validation": "恰好一个候选满足目标；每个错误选项注明在哪种错误下会被选中。", "principle": "设计 = 推断的逆问题；论文本身即以此线性关系设计连接子长度。", "validation": "独立检查器逐文件分析晶格并按题干目标重选。", "limits": "候选性质来自按 SAXS 参数构建的模型；没有新的实验证据。", "template_review": "本轮新建（A4），待人工审核。" }, "samples": [ { "instance": "FA-SL-DES-GOLD", "question": "The four XYZ files list the gold-nanoparticle centres (nm) of model crystallites of DNA-linked gold-nanoparticle superlattices assembled with four different duplex DNA linkers; each file is named after its linker and was built from that linker's published SAXS unit-cell size. Model conditions: the only measured input is the unit-cell size that Hill et al. (Nano Lett. 2008, Table 1) obtained from SAXS; the particle centres sit on an ideal, perfectly ordered lattice with no vacancies, stacking faults, positional (thermal) disorder or particle-size dispersion, which is the idealization the paper uses to index its SAXS peaks. Each crystallite is a finite cut of about 177 particles in an arbitrary orientation. You must choose one linker for a new superlattice such that the nearest-neighbour spacing is as large as possible while at least 1.0 % of the volume is gold (solid gold cores of diameter 10.3 nm; perfect infinite lattice). Which linker should you choose?", "options": [ { "label": "A", "value": "39-linker (Au-FCC-39-linker.xyz)" }, { "label": "B", "value": "X-linker (Au-FCC-X-linker.xyz)" }, { "label": "C", "value": "13-linker (Au-FCC-13-linker.xyz)" }, { "label": "D", "value": "26-linker (Au-FCC-26-linker.xyz)" } ], "inputs": [ "Au-FCC-X-linker.xyz", "Au-FCC-13-linker.xyz", "Au-FCC-26-linker.xyz", "Au-FCC-39-linker.xyz" ], "correct_label": "D", "audit": [ { "label": "A", "rule": "diameter_as_radius_passes", "reason": "金含量 0.744% 低于要求；若把直径当半径（×8）会误判为满足。" }, { "label": "B", "rule": "highest_gold_not_largest_spacing", "reason": "金含量最高（3.630%），但间距不是满足条件中最大的。" }, { "label": "C", "rule": "satisfies_but_smaller_spacing", "reason": "满足金含量（2.367%），但间距 32.46 nm 不是最大。" }, { "label": "D", "rule": "correct", "reason": "满足金含量（1.236%）的候选中最近邻最大（40.31 nm）。" } ] }, { "instance": "FA-SL-DES-NN", "question": "The four XYZ files list the gold-nanoparticle centres (nm) of model crystallites of DNA-linked gold-nanoparticle superlattices assembled with four different duplex DNA linkers; each file is named after its linker and was built from that linker's published SAXS unit-cell size. Model conditions: the only measured input is the unit-cell size that Hill et al. (Nano Lett. 2008, Table 1) obtained from SAXS; the particle centres sit on an ideal, perfectly ordered lattice with no vacancies, stacking faults, positional (thermal) disorder or particle-size dispersion, which is the idealization the paper uses to index its SAXS peaks. Each crystallite is a finite cut of about 177 particles in an arbitrary orientation. You must choose one linker for a new superlattice such that the centre-to-centre nearest-neighbour spacing of the particles is closest to 45 nm. Which linker should you choose?", "options": [ { "label": "A", "value": "13-linker (Au-FCC-13-linker.xyz)" }, { "label": "B", "value": "52-linker (Au-FCC-52-linker.xyz)" }, { "label": "C", "value": "39-linker (Au-FCC-39-linker.xyz)" }, { "label": "D", "value": "26-linker (Au-FCC-26-linker.xyz)" } ], "inputs": [ "Au-FCC-13-linker.xyz", "Au-FCC-26-linker.xyz", "Au-FCC-39-linker.xyz", "Au-FCC-52-linker.xyz" ], "correct_label": "C", "audit": [ { "label": "A", "rule": "cell_edge_as_spacing", "reason": "把常规晶胞边长当作最近邻间距时它最接近目标。" }, { "label": "B", "rule": "plane_spacing_as_spacing", "reason": "把密排面间距当作粒子间距时它最接近目标。" }, { "label": "C", "rule": "correct", "reason": "最近邻 47.7297 nm，最接近目标。" }, { "label": "D", "rule": "farther_from_target", "reason": "按正确定义离目标更远（D = 40.3051）。" } ] } ] } }, { "unit": "superlattice_metric", "kind": "family", "ability": "perception", "registry_id": "superlattice_geometry", "generator": "task_families/superlattice.py", "checker": "checkers/superlattice.py", "checker_function": "superlattice_quantity", "bindings": { "L1": { "registry_row": "ed528804599fe13763af3d1f0c278a50e076acd8d355004a2e7b04d856434985", "task_families/superlattice.py": "7815e908c5d30f5f208fcae8f35b76afeb33003452a00e781b1973a0520a62e6" }, "L2": { "checkers/superlattice.py": "c03a5a7bd5ced3e525f1c4d5b2c9a27971d3bc5af7a4c95115a13984f6e24fee", "checkers/common.py": "fbc9f4eb287114ac4720d27edc1ea40e25f80da0e1cff6bdee06fbdca2b73aed" } }, "L1": "pending", "L2": "pending", "instances": 3, "L1_record": null, "L2_record": null, "card": { "template": { "name": "纳米粒子超晶格几何（最近邻壳层 / 晶胞 / 密排面间距）", "concept": "从旋转后的粒子中心坐标识别晶格：最近邻壳层（个数与距离）、常规立方晶胞边长、最密排面间距，均在晶格周期尺度（10–100 nm）。", "inputs": "DNA 连接金纳米粒子超晶格晶粒模型的粒子中心 XYZ（nm，约 177 个，经确定性旋转）；设计题给四个候选文件。", "physical_conditions": "理想无限 FCC 晶格（按论文 SAXS 晶胞边长）；粒子视为相同点散射体；金核直径 10.3 nm 在题干给出。", "reasoning_scale": "晶格周期（常规晶胞边长 a，约 40–77 nm）", "scale_limits": "按论文参数构建的模型，不是实测粒子坐标；不含位置无序、峰宽与形状因子。", "source_basis": "Hill et al., Nano Lett. 8, 2341 (2008) 表 1：五种 DNA 连接子的 SAXS 晶胞边长（论文参数模型）", "answer_method": "中心粒子周围分壳（容差 1e-4 nm），核对 12/6 与 √2 比例（FCC），并与表 1 晶胞边长一致。", "distractor_mechanisms": [ "second_shell", "surface_particle", "bcc_assumption", "nearest_neighbour", "face_diagonal", "primitive_cell_root", "d200", "in_layer_row_spacing", "d220" ], "four_choice_validation": "壳层选项互不相同；数值与正确值 > 1 nm；升序排列，秩按批次轮换。", "principle": "FCC：12 个最近邻在 a/√2，6 个次近邻在 a；最密排面 {111}，d = a/√3。", "validation": "独立检查器从坐标选初基基矢（最小体积），验证所有粒子落在整数格点上，常规边长 = (4V)^(1/3)，面间距 = 2π/|G|min。", "limits": "理想无限 FCC 点阵：不含晶格缺陷、有限晶粒、粒径分布与 DNA 连接子的柔性；数值只对应论文 SAXS 晶胞边长所给的理想结构。", "template_review": "本轮新建（A4），待人工审核。" }, "samples": [ { "instance": "FA-SL-D111-39", "question": "The XYZ file lists the centres of the gold nanoparticles in a model crystallite of a DNA-linked gold-nanoparticle superlattice (coordinates in nm; built from a published SAXS unit-cell size). Model conditions: the only measured input is the unit-cell size that Hill et al. (Nano Lett. 2008, Table 1) obtained from SAXS; the particle centres sit on an ideal, perfectly ordered lattice with no vacancies, stacking faults, positional (thermal) disorder or particle-size dispersion, which is the idealization the paper uses to index its SAXS peaks. Each crystallite is a finite cut of about 177 particles in an arbitrary orientation. What is the spacing between adjacent close-packed (most densely populated) lattice planes of the particles, in nm?", "options": [ { "label": "A", "value": "38.97", "unit": "nm" }, { "label": "B", "value": "41.34", "unit": "nm" }, { "label": "C", "value": "47.73", "unit": "nm" }, { "label": "D", "value": "67.50", "unit": "nm" } ], "inputs": [ "Au-FCC-39-linker.xyz" ], "correct_label": "A", "audit": [ { "label": "A", "rule": "correct", "reason": "由坐标得 FCC：最近邻 12 个 47.7297 nm，第二壳层 6 个 a = 67.5000 nm；按定义计算。" }, { "label": "B", "rule": "in_layer_row_spacing", "reason": "算成密排层内相邻原子行的间距。" }, { "label": "C", "rule": "nearest_neighbour", "reason": "把最近邻间距当作面间距。" }, { "label": "D", "rule": "cell_edge", "reason": "报告了晶胞边长而非面间距。" } ] }, { "instance": "FA-SL-EDGE-26", "question": "The XYZ file lists the centres of the gold nanoparticles in a model crystallite of a DNA-linked gold-nanoparticle superlattice (coordinates in nm; built from a published SAXS unit-cell size). Model conditions: the only measured input is the unit-cell size that Hill et al. (Nano Lett. 2008, Table 1) obtained from SAXS; the particle centres sit on an ideal, perfectly ordered lattice with no vacancies, stacking faults, positional (thermal) disorder or particle-size dispersion, which is the idealization the paper uses to index its SAXS peaks. Each crystallite is a finite cut of about 177 particles in an arbitrary orientation. What is the edge length of the conventional cubic unit cell of this particle lattice, in nm?", "options": [ { "label": "A", "value": "32.91", "unit": "nm" }, { "label": "B", "value": "40.31", "unit": "nm" }, { "label": "C", "value": "57.00", "unit": "nm" }, { "label": "D", "value": "69.81", "unit": "nm" } ], "inputs": [ "Au-FCC-26-linker.xyz" ], "correct_label": "C", "audit": [ { "label": "A", "rule": "d111", "reason": "报告了密排面间距。" }, { "label": "B", "rule": "nearest_neighbour", "reason": "把最近邻间距当作晶胞边长。" }, { "label": "C", "rule": "correct", "reason": "由坐标得 FCC：最近邻 12 个 40.3051 nm，第二壳层 6 个 a = 57.0000 nm；按定义计算。" }, { "label": "D", "rule": "third_shell_distance", "reason": "把第三近邻距离当作晶胞边长。" } ] } ] } }, { "unit": "superlattice_saxs", "kind": "family", "ability": "inference", "registry_id": "superlattice_scattering", "generator": "task_families/superlattice.py", "checker": "checkers/superlattice.py", "checker_function": "superlattice_quantity", "bindings": { "L1": { "registry_row": "a13cb8da263aaf06948ad282164fd11dbf2647aa0c3b4b4996f3cae28be143dd", "task_families/superlattice.py": "7815e908c5d30f5f208fcae8f35b76afeb33003452a00e781b1973a0520a62e6" }, "L2": { "checkers/superlattice.py": "c03a5a7bd5ced3e525f1c4d5b2c9a27971d3bc5af7a4c95115a13984f6e24fee", "checkers/common.py": "fbc9f4eb287114ac4720d27edc1ea40e25f80da0e1cff6bdee06fbdca2b73aed" } }, "L1": "pending", "L2": "pending", "instances": 3, "L1_record": null, "L2_record": null, "card": { "template": { "name": "纳米粒子超晶格 SAXS 反射与金含量", "concept": "由粒子坐标推断可观测量：第一与第二个非零 Bragg 反射的 q（q = 4π sinθ/λ），以及给定金核直径时的金体积百分数。", "inputs": "DNA 连接金纳米粒子超晶格晶粒模型的粒子中心 XYZ（nm，约 177 个，经确定性旋转）；设计题给四个候选文件。", "physical_conditions": "理想无限 FCC 晶格（按论文 SAXS 晶胞边长）；粒子视为相同点散射体；金核直径 10.3 nm 在题干给出。", "reasoning_scale": "晶格周期（常规晶胞边长 a，约 40–77 nm）", "scale_limits": "按论文参数构建的模型，不是实测粒子坐标；不含位置无序、峰宽与形状因子。", "source_basis": "Hill et al., Nano Lett. 8, 2341 (2008) 表 1：五种 DNA 连接子的 SAXS 晶胞边长（论文参数模型）", "answer_method": "q* = 2π√3/a，q(200) = 4π/a；金含量 = 4·(4/3)πr³/a³。", "distractor_mechanisms": [ "q_100_forbidden", "q_from_nearest_neighbour", "q_200", "q_111_first_peak", "q_220", "missing_two_pi", "per_angstrom", "one_particle_per_cell", "two_particles_per_cell", "diameter_as_radius", "four_per_primitive_cell" ], "four_choice_validation": "与正确值 > 0.005 nm⁻¹ 或 0.05 个百分点；升序排列，秩按批次轮换。", "principle": "布拉维格子的 Bragg 反射在倒格矢 G 处；FCC 的最短 G 为 {111}。", "validation": "独立检查器由初基基矢求倒格子，枚举 |G| 并按容差归并；金含量用初基胞体积（每胞 1 个粒子）。", "limits": "点散射体、无限完美晶格；实测 SAXS 峰宽与形状因子不在题内。", "template_review": "本轮新建（A4），待人工审核。" }, "samples": [ { "instance": "FA-SL-GOLD-52", "question": "The XYZ file lists the centres of the gold nanoparticles in a model crystallite of a DNA-linked gold-nanoparticle superlattice (coordinates in nm; built from a published SAXS unit-cell size). Model conditions: the only measured input is the unit-cell size that Hill et al. (Nano Lett. 2008, Table 1) obtained from SAXS; the particle centres sit on an ideal, perfectly ordered lattice with no vacancies, stacking faults, positional (thermal) disorder or particle-size dispersion, which is the idealization the paper uses to index its SAXS peaks. Each crystallite is a finite cut of about 177 particles in an arbitrary orientation. Each particle is a solid gold sphere with a core diameter of 10.3 nm and the DNA shell contains no gold. Treating the lattice as perfect and infinite, what percentage of the total volume is gold?", "options": [ { "label": "A", "value": "0.509", "unit": "%" }, { "label": "B", "value": "1.440", "unit": "%" }, { "label": "C", "value": "2.037", "unit": "%" }, { "label": "D", "value": "4.074", "unit": "%" } ], "inputs": [ "Au-FCC-52-linker.xyz" ], "correct_label": "A", "audit": [ { "label": "A", "rule": "correct", "reason": "由坐标得 FCC：最近邻 12 个 54.1644 nm，第二壳层 6 个 a = 76.6000 nm；按定义计算。" }, { "label": "B", "rule": "nearest_neighbour_as_cell_edge", "reason": "用最近邻间距当作常规晶胞边长（仍按每胞 4 个粒子）。" }, { "label": "C", "rule": "four_per_primitive_cell", "reason": "用初基胞体积 a³/4，却仍按 4 个粒子计。" }, { "label": "D", "rule": "diameter_as_radius", "reason": "把直径当半径代入球体积。" } ] }, { "instance": "FA-SL-Q200-13", "question": "The XYZ file lists the centres of the gold nanoparticles in a model crystallite of a DNA-linked gold-nanoparticle superlattice (coordinates in nm; built from a published SAXS unit-cell size). Model conditions: the only measured input is the unit-cell size that Hill et al. (Nano Lett. 2008, Table 1) obtained from SAXS; the particle centres sit on an ideal, perfectly ordered lattice with no vacancies, stacking faults, positional (thermal) disorder or particle-size dispersion, which is the idealization the paper uses to index its SAXS peaks. Each crystallite is a finite cut of about 177 particles in an arbitrary orientation. Treat the particles as identical point scatterers on a perfect, infinite lattice with this geometry. At what q (in nm⁻¹, q = 4π sinθ/λ) does the second distinct Bragg reflection with nonzero intensity appear?", "options": [ { "label": "A", "value": "0.0436", "unit": "nm^-1" }, { "label": "B", "value": "0.1369", "unit": "nm^-1" }, { "label": "C", "value": "0.2371", "unit": "nm^-1" }, { "label": "D", "value": "0.2738", "unit": "nm^-1" } ], "inputs": [ "Au-FCC-13-linker.xyz" ], "correct_label": "D", "audit": [ { "label": "A", "rule": "missing_two_pi", "reason": "漏掉 2π。" }, { "label": "B", "rule": "q_100_forbidden", "reason": "把消光的 (100) 当作反射。" }, { "label": "C", "rule": "q_111_first_peak", "reason": "报告了第一个反射 (111)。" }, { "label": "D", "rule": "correct", "reason": "由坐标得 FCC：最近邻 12 个 32.4562 nm，第二壳层 6 个 a = 45.9000 nm；按定义计算。" } ] } ] } }, { "unit": "superlattice_shell", "kind": "family", "ability": "perception", "registry_id": "superlattice_geometry", "generator": "task_families/superlattice.py", "checker": "checkers/superlattice.py", "checker_function": "superlattice_shell", "bindings": { "L1": { "registry_row": "ed528804599fe13763af3d1f0c278a50e076acd8d355004a2e7b04d856434985", "task_families/superlattice.py": "7815e908c5d30f5f208fcae8f35b76afeb33003452a00e781b1973a0520a62e6" }, "L2": { "checkers/superlattice.py": "c03a5a7bd5ced3e525f1c4d5b2c9a27971d3bc5af7a4c95115a13984f6e24fee", "checkers/common.py": "fbc9f4eb287114ac4720d27edc1ea40e25f80da0e1cff6bdee06fbdca2b73aed" } }, "L1": "pending", "L2": "pending", "instances": 1, "L1_record": null, "L2_record": null, "card": { "template": { "name": "纳米粒子超晶格几何（最近邻壳层 / 晶胞 / 密排面间距）", "concept": "从旋转后的粒子中心坐标识别晶格：最近邻壳层（个数与距离）、常规立方晶胞边长、最密排面间距，均在晶格周期尺度（10–100 nm）。", "inputs": "DNA 连接金纳米粒子超晶格晶粒模型的粒子中心 XYZ（nm，约 177 个，经确定性旋转）；设计题给四个候选文件。", "physical_conditions": "理想无限 FCC 晶格（按论文 SAXS 晶胞边长）；粒子视为相同点散射体；金核直径 10.3 nm 在题干给出。", "reasoning_scale": "晶格周期（常规晶胞边长 a，约 40–77 nm）", "scale_limits": "按论文参数构建的模型，不是实测粒子坐标；不含位置无序、峰宽与形状因子。", "source_basis": "Hill et al., Nano Lett. 8, 2341 (2008) 表 1：五种 DNA 连接子的 SAXS 晶胞边长（论文参数模型）", "answer_method": "中心粒子周围分壳（容差 1e-4 nm），核对 12/6 与 √2 比例（FCC），并与表 1 晶胞边长一致。", "distractor_mechanisms": [ "second_shell", "surface_particle", "bcc_assumption", "nearest_neighbour", "face_diagonal", "primitive_cell_root", "d200", "in_layer_row_spacing", "d220" ], "four_choice_validation": "壳层选项互不相同；数值与正确值 > 1 nm；升序排列，秩按批次轮换。", "principle": "FCC：12 个最近邻在 a/√2，6 个次近邻在 a；最密排面 {111}，d = a/√3。", "validation": "独立检查器从坐标选初基基矢（最小体积），验证所有粒子落在整数格点上，常规边长 = (4V)^(1/3)，面间距 = 2π/|G|min。", "limits": "理想无限 FCC 点阵：不含晶格缺陷、有限晶粒、粒径分布与 DNA 连接子的柔性；数值只对应论文 SAXS 晶胞边长所给的理想结构。", "template_review": "本轮新建（A4），待人工审核。" }, "samples": [ { "instance": "FA-SL-SHELL-X", "question": "The XYZ file lists the centres of the gold nanoparticles in a model crystallite of a DNA-linked gold-nanoparticle superlattice (coordinates in nm; built from a published SAXS unit-cell size). Model conditions: the only measured input is the unit-cell size that Hill et al. (Nano Lett. 2008, Table 1) obtained from SAXS; the particle centres sit on an ideal, perfectly ordered lattice with no vacancies, stacking faults, positional (thermal) disorder or particle-size dispersion, which is the idealization the paper uses to index its SAXS peaks. Each crystallite is a finite cut of about 177 particles in an arbitrary orientation. For the particle nearest the centroid of all particles, how many particles form its nearest-neighbour shell, and at what centre-to-centre distance? Distances are rounded to 0.01 nm.", "options": [ { "label": "A", "value": "6 at 39.80 nm" }, { "label": "B", "value": "8 at 28.14 nm" }, { "label": "C", "value": "5 at 28.14 nm" }, { "label": "D", "value": "12 at 28.14 nm" } ], "inputs": [ "Au-FCC-X-linker.xyz" ], "correct_label": "D", "audit": [ { "label": "A", "rule": "second_shell", "reason": "报告了第二壳层（常规晶胞边长处的 6 个）。" }, { "label": "B", "rule": "bcc_assumption", "reason": "误认作体心立方，按 8 个最近邻计。" }, { "label": "C", "rule": "surface_particle", "reason": "数的是晶粒表面粒子的最近邻（表面缺配位）。" }, { "label": "D", "rule": "correct", "reason": "中心粒子的最近壳层：12 个，28.142850 nm（= a/√2）。" } ] } ] } }, { "unit": "vortex_design", "kind": "family", "ability": "design", "registry_id": "vortex_design", "generator": "task_families/vortex.py", "checker": "checkers/mesoscale.py", "checker_function": "vortex_design", "bindings": { "L1": { "registry_row": "5d6d04e7e623cd521fb7475a109dba5cedbb11d5b15ea0aa980bf9b090576d2e", "task_families/vortex.py": "205f5e61f90c2a6c94bcebe79138d724d0e1596242dfb6ad2a3eacb123971ed5" }, "L2": { "checkers/mesoscale.py": "55a3a182757904d2fc9680a142005bb6015d5926687a73e3ac51f71da824342f", "checkers/common.py": "fbc9f4eb287114ac4720d27edc1ea40e25f80da0e1cff6bdee06fbdca2b73aed" } }, "L1": "pending", "L2": "pending", "instances": 3, "L1_record": null, "L2_record": null, "card": { "template": { "name": "涡旋晶格磁场选择设计", "concept": "在论文实际施加的四个磁场中选一个，使涡旋间距或中子散射峰最接近目标，或在密度要求下磁场最低。", "inputs": "涡旋中心位置图（nm，每行 \"V x y\"，约 97 个，确定性旋转）；设计题给四张不同磁场的图。", "physical_conditions": "理想三角涡旋晶格，每个涡旋一个磁通量子 h/2e；题干写明 Model conditions。", "reasoning_scale": "涡旋晶格间距 a（356–855 nm）", "scale_limits": "按论文实测磁场或实测晶格常数构建的模型；不含钉扎无序；论文指出 188.7 G 时单个涡旋已难分辨。", "source_basis": "Cottet et al., arXiv:1401.4062（MgB2，低温洛伦兹透射电镜，四个实测磁场）；Schaefermeier et al., arXiv:2602.13060（BSCCO，NV 扫描磁强计，a ≈ 0.855 μm）", "answer_method": "逐张图计算晶胞，按目标规则选择；领先幅度检查。", "distractor_mechanisms": [ "row_spacing", "second_neighbour", "two_pi_over_a", "second_order_peak", "passes_if_square_cell", "meets_but_higher_field", "too_sparse", "farther_from_target" ], "four_choice_validation": "恰好一个候选满足目标；每个错误选项注明误选原因。", "principle": "设计 = 推断的逆问题（选磁场）。", "validation": "独立检查器（checkers/mesoscale.py:vortex_design）逐个文件由涡旋中心求初基晶胞，算出间距、密度或散射峰，再按题干目标规则重新选择。", "limits": "候选为论文实测磁场的理想模型。", "template_review": "本轮新建（补 100–1000 空格），待人工审核。" }, "samples": [ { "instance": "FA-VX-DES-DENSITY", "question": "The four files list the vortex centres (nm) in model images of the Abrikosov vortex lattice of an MgB2 crystal at four applied fields (files named by field). Model conditions: the only measured input is the applied magnetic field of each image reported by Cottet et al. (arXiv:1401.4062; MgB2, cryo-Lorentz TEM at 5 K); the vortices form an ideal triangular lattice with exactly one superconducting flux quantum per vortex, no pinning disorder, lattice defects or thermal motion, and a uniform field, which is the idealization the paper compares its images with; the map is a finite patch of about 97 vortices in an arbitrary orientation. You must choose one applied field such that the field is as low as possible while the areal vortex density is at least 4 vortices per square micrometre. Which field should you choose?", "options": [ { "label": "A", "value": "117.3 G (11.73 mT) (vortex-MgB2-1173G.txt)" }, { "label": "B", "value": "188.7 G (18.87 mT) (vortex-MgB2-1887G.txt)" }, { "label": "C", "value": "50.8 G (5.08 mT) (vortex-MgB2-508G.txt)" }, { "label": "D", "value": "56.1 G (5.61 mT) (vortex-MgB2-561G.txt)" } ], "inputs": [ "vortex-MgB2-508G.txt", "vortex-MgB2-561G.txt", "vortex-MgB2-1173G.txt", "vortex-MgB2-1887G.txt" ], "correct_label": "A", "audit": [ { "label": "A", "rule": "correct", "reason": "满足密度要求的候选中磁场最低（密度 5.67 /μm²）。" }, { "label": "B", "rule": "meets_but_higher_field", "reason": "密度 9.13 /μm² 满足，但磁场更高。" }, { "label": "C", "rule": "too_sparse", "reason": "密度 2.46 /μm²，未达到 4。" }, { "label": "D", "rule": "too_sparse", "reason": "密度 2.71 /μm²，未达到 4。" } ] }, { "instance": "FA-VX-DES-SANS", "question": "The four files list the vortex centres (nm) in model images of the Abrikosov vortex lattice of an MgB2 crystal at four applied fields (files named by field). Model conditions: the only measured input is the applied magnetic field of each image reported by Cottet et al. (arXiv:1401.4062; MgB2, cryo-Lorentz TEM at 5 K); the vortices form an ideal triangular lattice with exactly one superconducting flux quantum per vortex, no pinning disorder, lattice defects or thermal motion, and a uniform field, which is the idealization the paper compares its images with; the map is a finite patch of about 97 vortices in an arbitrary orientation. You must choose one applied field such that the first-order small-angle-neutron-scattering Bragg peak of the vortex lattice (q = 4π sinθ/λ) is closest to 20 μm⁻¹. Which field should you choose?", "options": [ { "label": "A", "value": "50.8 G (5.08 mT) (vortex-MgB2-508G.txt)" }, { "label": "B", "value": "117.3 G (11.73 mT) (vortex-MgB2-1173G.txt)" }, { "label": "C", "value": "56.1 G (5.61 mT) (vortex-MgB2-561G.txt)" }, { "label": "D", "value": "188.7 G (18.87 mT) (vortex-MgB2-1887G.txt)" } ], "inputs": [ "vortex-MgB2-508G.txt", "vortex-MgB2-561G.txt", "vortex-MgB2-1173G.txt", "vortex-MgB2-1887G.txt" ], "correct_label": "D", "audit": [ { "label": "A", "rule": "farther_from_target", "reason": "正确计算为 10.58，离目标更远。" }, { "label": "B", "rule": "farther_from_target", "reason": "正确计算为 16.08，离目标更远。" }, { "label": "C", "rule": "second_order_peak", "reason": "用第二个峰时它最接近目标（19.26）。" }, { "label": "D", "rule": "correct", "reason": "正确计算为 20.40，最接近目标。" } ] } ] } }, { "unit": "vortex_geometry", "kind": "family", "ability": "perception", "registry_id": "vortex_geometry", "generator": "task_families/vortex.py", "checker": "checkers/mesoscale.py", "checker_function": "vortex_quantity", "bindings": { "L1": { "registry_row": "f46a19e8fb78eba9474eaa9da0dcd92a04ea2f2aaca446a95cb6a949c6740624", "task_families/vortex.py": "205f5e61f90c2a6c94bcebe79138d724d0e1596242dfb6ad2a3eacb123971ed5" }, "L2": { "checkers/mesoscale.py": "55a3a182757904d2fc9680a142005bb6015d5926687a73e3ac51f71da824342f", "checkers/common.py": "fbc9f4eb287114ac4720d27edc1ea40e25f80da0e1cff6bdee06fbdca2b73aed" } }, "L1": "pending", "L2": "pending", "instances": 3, "L1_record": null, "L2_record": null, "card": { "template": { "name": "超导涡旋晶格几何（间距 / 密度）", "concept": "从涡旋中心图识别 Abrikosov 涡旋晶格：晶格间距与涡旋面密度。", "inputs": "涡旋中心位置图（nm，每行 \"V x y\"，约 97 个，确定性旋转）；设计题给四张不同磁场的图。", "physical_conditions": "理想三角涡旋晶格，每个涡旋一个磁通量子 h/2e；题干写明 Model conditions。", "reasoning_scale": "涡旋晶格间距 a（356–855 nm）", "scale_limits": "按论文实测磁场或实测晶格常数构建的模型；不含钉扎无序；论文指出 188.7 G 时单个涡旋已难分辨。", "source_basis": "Cottet et al., arXiv:1401.4062（MgB2，低温洛伦兹透射电镜，四个实测磁场）；Schaefermeier et al., arXiv:2602.13060（BSCCO，NV 扫描磁强计，a ≈ 0.855 μm）", "answer_method": "中心涡旋 6 个等距近邻；与论文参数一致。", "distractor_mechanisms": [ "row_spacing", "second_neighbour", "double_spacing", "square_cell", "half_density", "circle_cell" ], "four_choice_validation": "与正确值 > 10 nm 或 0.15 /μm²；升序排列，秩按批次轮换。", "principle": "三角涡旋晶格：a = (2Φ0/(√3B))^1/2，n = B/Φ0。", "validation": "独立检查器由初基晶胞面积计算。", "limits": "理想三角涡旋晶格：不含钉扎无序、晶界与有限尺寸效应；间距只对应论文实测磁场下的理想模型。", "template_review": "本轮新建（补 100–1000 空格），待人工审核。" }, "samples": [ { "instance": "FA-VX-DENSITY-1173", "question": "The file lists the vortex centres (nm) seen in a model image of the Abrikosov vortex lattice of a type-II superconductor in a perpendicular magnetic field. Model conditions: the only measured input is the applied magnetic field (117.3 G = 11.73 mT) reported by Cottet et al. (arXiv:1401.4062; MgB2, cryo-Lorentz TEM at 5 K); the vortices form an ideal triangular lattice with exactly one superconducting flux quantum per vortex, no pinning disorder, lattice defects or thermal motion, and a uniform field, which is the idealization the paper compares its images with; the map is a finite patch of about 97 vortices in an arbitrary orientation. How many vortices are there per square micrometre (areal vortex density)?", "options": [ { "label": "A", "value": "2.836", "unit": "um^-2" }, { "label": "B", "value": "4.913", "unit": "um^-2" }, { "label": "C", "value": "5.673", "unit": "um^-2" }, { "label": "D", "value": "6.255", "unit": "um^-2" } ], "inputs": [ "vortex-MgB2-1173G.txt" ], "correct_label": "C", "audit": [ { "label": "A", "rule": "half_density", "reason": "晶胞面积多乘了 2。" }, { "label": "B", "rule": "square_cell", "reason": "每个涡旋按 a² 的正方形面积计。" }, { "label": "C", "rule": "correct", "reason": "三角涡旋晶格：a = 451.173 nm，B = 2Φ0/(√3 a²) = 11.7300 mT，n = B/Φ0。" }, { "label": "D", "rule": "circle_cell", "reason": "每个涡旋按直径为 a 的圆面积计。" } ] }, { "instance": "FA-VX-SPACING-561", "question": "The file lists the vortex centres (nm) seen in a model image of the Abrikosov vortex lattice of a type-II superconductor in a perpendicular magnetic field. Model conditions: the only measured input is the applied magnetic field (56.1 G = 5.61 mT) reported by Cottet et al. (arXiv:1401.4062; MgB2, cryo-Lorentz TEM at 5 K); the vortices form an ideal triangular lattice with exactly one superconducting flux quantum per vortex, no pinning disorder, lattice defects or thermal motion, and a uniform field, which is the idealization the paper compares its images with; the map is a finite patch of about 97 vortices in an arbitrary orientation. What is the vortex lattice spacing (centre-to-centre distance between neighbouring vortices), in nm?", "options": [ { "label": "A", "value": "565.0", "unit": "nm" }, { "label": "B", "value": "607.1", "unit": "nm" }, { "label": "C", "value": "652.4", "unit": "nm" }, { "label": "D", "value": "1130.0", "unit": "nm" } ], "inputs": [ "vortex-MgB2-561G.txt" ], "correct_label": "C", "audit": [ { "label": "A", "rule": "row_spacing", "reason": "报告了相邻涡旋行的间距（√3/2）a。" }, { "label": "B", "rule": "square_lattice_guess", "reason": "按正方格子由密度反推间距。" }, { "label": "C", "rule": "correct", "reason": "三角涡旋晶格：a = 652.396 nm，B = 2Φ0/(√3 a²) = 5.6100 mT，n = B/Φ0。" }, { "label": "D", "rule": "second_neighbour", "reason": "报告了次近邻距离 √3 a。" } ] } ] } }, { "unit": "vortex_inference", "kind": "family", "ability": "inference", "registry_id": "vortex_inference", "generator": "task_families/vortex.py", "checker": "checkers/mesoscale.py", "checker_function": "vortex_quantity", "bindings": { "L1": { "registry_row": "668af507fbf1b4f9b94c80e5f48026a05ed2e0e7e3c381e12b125abfd7dbb48b", "task_families/vortex.py": "205f5e61f90c2a6c94bcebe79138d724d0e1596242dfb6ad2a3eacb123971ed5" }, "L2": { "checkers/mesoscale.py": "55a3a182757904d2fc9680a142005bb6015d5926687a73e3ac51f71da824342f", "checkers/common.py": "fbc9f4eb287114ac4720d27edc1ea40e25f80da0e1cff6bdee06fbdca2b73aed" } }, "L1": "pending", "L2": "pending", "instances": 1, "L1_record": null, "L2_record": null, "card": { "template": { "name": "超导涡旋晶格推断（磁场 / 磁通量子 / 中子散射峰）", "concept": "由涡旋图推断磁感应强度（每个涡旋一个 h/2e）、每个涡旋携带的磁通，以及小角中子散射首个 Bragg 峰。", "inputs": "涡旋中心位置图（nm，每行 \"V x y\"，约 97 个，确定性旋转）；设计题给四张不同磁场的图。", "physical_conditions": "理想三角涡旋晶格，每个涡旋一个磁通量子 h/2e；题干写明 Model conditions。", "reasoning_scale": "涡旋晶格间距 a（356–855 nm）", "scale_limits": "按论文实测磁场或实测晶格常数构建的模型；不含钉扎无序；论文指出 188.7 G 时单个涡旋已难分辨。", "source_basis": "Cottet et al., arXiv:1401.4062（MgB2，低温洛伦兹透射电镜，四个实测磁场）；Schaefermeier et al., arXiv:2602.13060（BSCCO，NV 扫描磁强计，a ≈ 0.855 μm）", "answer_method": "B = Φ0/A_cell；Φ = B·A_cell；q10 = 4π/(√3 a)。", "distractor_mechanisms": [ "square_lattice", "flux_h_over_e", "flux_h_over_4e", "gauss_mT_slip", "second_neighbour_as_spacing", "h_over_e", "square_cell", "triangle_cell", "hbar_over_2e", "two_pi_over_a", "missing_two_pi", "second_order_peak", "square_lattice_q" ], "four_choice_validation": "与正确值 > 0.15 mT、0.15×10⁻¹⁵ Wb 或 0.5 μm⁻¹；升序排列，秩按批次轮换。", "principle": "磁通量子化：每个涡旋携带 Φ0 = h/2e。", "validation": "独立检查器由晶胞面积与题干 Φ0 或 B 计算。", "limits": "理想三角涡旋晶格：不含钉扎无序、晶界与有限尺寸效应；磁场、磁通与散射峰按每个涡旋一个磁通量子的理想关系计算。", "template_review": "本轮新建（补 100–1000 空格），待人工审核。" }, "samples": [ { "instance": "FA-VX-FIELD-BSCCO", "question": "The file lists the vortex centres (nm) seen in a model image of the Abrikosov vortex lattice of a type-II superconductor in a perpendicular magnetic field. Model conditions: the only measured input is the measured vortex lattice constant (0.855 μm) reported by Schaefermeier et al. (arXiv:2602.13060; BSCCO-2212, scanning NV magnetometry at 71 K); the vortices form an ideal triangular lattice with exactly one superconducting flux quantum per vortex, no pinning disorder, lattice defects or thermal motion, and a uniform field, which is the idealization the paper compares its images with; the map is a finite patch of about 97 vortices in an arbitrary orientation. Each vortex carries one superconducting flux quantum Φ0 = h/(2e) = 2.0678 × 10⁻¹⁵ Wb. What is the magnetic induction B inside the superconductor that produces this lattice, in mT?", "options": [ { "label": "A", "value": "1.633", "unit": "mT" }, { "label": "B", "value": "2.829", "unit": "mT" }, { "label": "C", "value": "3.266", "unit": "mT" }, { "label": "D", "value": "6.533", "unit": "mT" } ], "inputs": [ "vortex-BSCCO-855nm.txt" ], "correct_label": "C", "audit": [ { "label": "A", "rule": "flux_h_over_4e", "reason": "磁通量子多除了 2。" }, { "label": "B", "rule": "square_lattice", "reason": "按正方格子 B = Φ0/a²。" }, { "label": "C", "rule": "correct", "reason": "三角涡旋晶格：a = 855.000 nm，B = 2Φ0/(√3 a²) = 3.2663 mT，n = B/Φ0。" }, { "label": "D", "rule": "flux_h_over_e", "reason": "用 h/e（单电子磁通量子）代替 h/2e。" } ] }, { "instance": "FA-VX-FIELD-508", "question": "The file lists the vortex centres (nm) seen in a model image of the Abrikosov vortex lattice of a type-II superconductor in a perpendicular magnetic field. Model conditions: the only measured input is the applied magnetic field (50.8 G = 5.08 mT) reported by Cottet et al. (arXiv:1401.4062; MgB2, cryo-Lorentz TEM at 5 K); the vortices form an ideal triangular lattice with exactly one superconducting flux quantum per vortex, no pinning disorder, lattice defects or thermal motion, and a uniform field, which is the idealization the paper compares its images with; the map is a finite patch of about 97 vortices in an arbitrary orientation. Each vortex carries one superconducting flux quantum Φ0 = h/(2e) = 2.0678 × 10⁻¹⁵ Wb. What is the magnetic induction B inside the superconductor that produces this lattice, in mT?", "options": [ { "label": "A", "value": "1.693", "unit": "mT" }, { "label": "B", "value": "2.540", "unit": "mT" }, { "label": "C", "value": "4.399", "unit": "mT" }, { "label": "D", "value": "5.080", "unit": "mT" } ], "inputs": [ "vortex-MgB2-508G.txt" ], "correct_label": "D", "audit": [ { "label": "A", "rule": "second_neighbour_as_spacing", "reason": "把次近邻距离 √3a 当作晶格间距。" }, { "label": "B", "rule": "flux_h_over_4e", "reason": "磁通量子多除了 2。" }, { "label": "C", "rule": "square_lattice", "reason": "按正方格子 B = Φ0/a²。" }, { "label": "D", "rule": "correct", "reason": "三角涡旋晶格：a = 685.584 nm，B = 2Φ0/(√3 a²) = 5.0800 mT，n = B/Φ0。" } ] } ] } } ], "l3_plan": [ { "stratum": "assembly_extent | pdb-bio-nm | biology 10-100", "unit": "assembly_extent", "source": "pdb-bio-nm", "cell": "biology 10-100", "size": 2, "sample": 2, "rule": "first batch: all", "ids": [ "BNP034", "BNP036" ] }, { "stratum": "assembly_extent | pdb-bio-nm | biology 100-1000", "unit": "assembly_extent", "source": "pdb-bio-nm", "cell": "biology 100-1000", "size": 2, "sample": 2, "rule": "first batch: all", "ids": [ "BNP023", "BNP025" ] }, { "stratum": "assembly_extent | pdb-dna-origami | chemistry 10-100", "unit": "assembly_extent", "source": "pdb-dna-origami", "cell": "chemistry 10-100", "size": 2, "sample": 2, "rule": "first batch: all", "ids": [ "CNP020", "CNP022" ] }, { "stratum": "assembly_rg | pdb-bio-nm | biology 10-100", "unit": "assembly_rg", "source": "pdb-bio-nm", "cell": "biology 10-100", "size": 2, "sample": 2, "rule": "first batch: all", "ids": [ "BNP020", "BNP031" ] }, { "stratum": "assembly_rg | pdb-bio-nm | biology 100-1000", "unit": "assembly_rg", "source": "pdb-bio-nm", "cell": "biology 100-1000", "size": 1, "sample": 1, "rule": "first batch: all", "ids": [ "BNP024" ] }, { "stratum": "assembly_rg | pdb-dna-origami | chemistry 10-100", "unit": "assembly_rg", "source": "pdb-dna-origami", "cell": "chemistry 10-100", "size": 2, "sample": 2, "rule": "first batch: all", "ids": [ "CNP021", "CNP023" ] }, { "stratum": "backbone_torsion | pdb-bio-nm | biology 0.1-1", "unit": "backbone_torsion", "source": "pdb-bio-nm", "cell": "biology 0.1-1", "size": 2, "sample": 2, "rule": "first batch: all", "ids": [ "BNP014", "BNP015" ] }, { "stratum": "binding_design_choice | sampl9 | chemistry 1-10", "unit": "binding_design_choice", "source": "sampl9", "cell": "chemistry 1-10", "size": 2, "sample": 2, "rule": "first batch: all", "ids": [ "CND007", "CND008" ] }, { "stratum": "binding_evidence_choice | sampl9 | chemistry 1-10", "unit": "binding_evidence_choice", "source": "sampl9", "cell": "chemistry 1-10", "size": 1, "sample": 1, "rule": "first batch: all", "ids": [ "CNI014" ] }, { "stratum": "capsid_architecture | pdb-bio-nm | biology 10-100", "unit": "capsid_architecture", "source": "pdb-bio-nm", "cell": "biology 10-100", "size": 1, "sample": 1, "rule": "first batch: all", "ids": [ "BNI037" ] }, { "stratum": "capsid_architecture | pdb-bio-nm | biology 100-1000", "unit": "capsid_architecture", "source": "pdb-bio-nm", "cell": "biology 100-1000", "size": 4, "sample": 4, "rule": "first batch: all", "ids": [ "BNI019", "BNI020", "BNI021", "BNI023" ] }, { "stratum": "cholesteric_design | paper-shaban-cholesteric | chemistry 100-1000", "unit": "cholesteric_design", "source": "paper-shaban-cholesteric", "cell": "chemistry 100-1000", "size": 3, "sample": 3, "rule": "first batch: all", "ids": [ "CND009", "CND010", "CND011" ] }, { "stratum": "cholesteric_geometry | paper-dinc-isosorbide | chemistry 100-1000", "unit": "cholesteric_geometry", "source": "paper-dinc-isosorbide", "cell": "chemistry 100-1000", "size": 1, "sample": 1, "rule": "first batch: all", "ids": [ "CNP026" ] }, { "stratum": "cholesteric_geometry | paper-shaban-cholesteric | chemistry 100-1000", "unit": "cholesteric_geometry", "source": "paper-shaban-cholesteric", "cell": "chemistry 100-1000", "size": 2, "sample": 2, "rule": "first batch: all", "ids": [ "CNP024", "CNP025" ] }, { "stratum": "cholesteric_optics | paper-dinc-isosorbide | chemistry 100-1000", "unit": "cholesteric_optics", "source": "paper-dinc-isosorbide", "cell": "chemistry 100-1000", "size": 1, "sample": 1, "rule": "first batch: all", "ids": [ "CNI020" ] }, { "stratum": "cholesteric_optics | paper-shaban-cholesteric | chemistry 100-1000", "unit": "cholesteric_optics", "source": "paper-shaban-cholesteric", "cell": "chemistry 100-1000", "size": 1, "sample": 1, "rule": "first batch: all", "ids": [ "CNI018" ] }, { "stratum": "conformer_target_selection | qm7x | quantum 0.1-1", "unit": "conformer_target_selection", "source": "qm7x", "cell": "quantum 0.1-1", "size": 2, "sample": 2, "rule": "first batch: all", "ids": [ "QND003", "QND004" ] }, { "stratum": "coordination_shell | cod-materials-cell | chemistry 0.1-1", "unit": "coordination_shell", "source": "cod-materials-cell", "cell": "chemistry 0.1-1", "size": 1, "sample": 1, "rule": "first batch: all", "ids": [ "CNP039" ] }, { "stratum": "coordination_shell | cod-materials-cell | materials 0.1-1", "unit": "coordination_shell", "source": "cod-materials-cell", "cell": "materials 0.1-1", "size": 4, "sample": 4, "rule": "first batch: all", "ids": [ "MNP011", "MNP024", "MNP034", "MNP037" ] }, { "stratum": "coordination_shell | cod-mof | materials 1-10", "unit": "coordination_shell", "source": "cod-mof", "cell": "materials 1-10", "size": 2, "sample": 2, "rule": "first batch: all", "ids": [ "MNP013", "MNP014" ] }, { "stratum": "debye_intensity | pdb-bio-nm | biology 10-100", "unit": "debye_intensity", "source": "pdb-bio-nm", "cell": "biology 10-100", "size": 1, "sample": 1, "rule": "first batch: all", "ids": [ "BNI033" ] }, { "stratum": "debye_intensity | pdb-bio-nm | biology 100-1000", "unit": "debye_intensity", "source": "pdb-bio-nm", "cell": "biology 100-1000", "size": 1, "sample": 1, "rule": "first batch: all", "ids": [ "BNI022" ] }, { "stratum": "debye_intensity | pdb-dna-origami | chemistry 10-100", "unit": "debye_intensity", "source": "pdb-dna-origami", "cell": "chemistry 10-100", "size": 2, "sample": 2, "rule": "first batch: all", "ids": [ "CNI012", "CNI013" ] }, { "stratum": "design_choice | paper-chetry-mof-isotopologue | materials 0.1-1", "unit": "design_choice", "source": "paper-chetry-mof-isotopologue", "cell": "materials 0.1-1", "size": 2, "sample": 2, "rule": "first batch: all", "ids": [ "MND013", "MND014" ] }, { "stratum": "design_choice | paper-rando-bambusuril | chemistry 0.1-1", "unit": "design_choice", "source": "paper-rando-bambusuril", "cell": "chemistry 0.1-1", "size": 1, "sample": 1, "rule": "first batch: all", "ids": [ "CND017" ] }, { "stratum": "diffraction_design | cod-materials-cell | materials 0.1-1", "unit": "diffraction_design", "source": "cod-materials-cell", "cell": "materials 0.1-1", "size": 1, "sample": 1, "rule": "first batch: all", "ids": [ "MND007" ] }, { "stratum": "diffraction_design | cod-materials-cell | materials 1-10", "unit": "diffraction_design", "source": "cod-materials-cell", "cell": "materials 1-10", "size": 3, "sample": 3, "rule": "first batch: all", "ids": [ "MND010", "MND011", "MND012" ] }, { "stratum": "disulfide_design | pdb-bio-nm | biology 0.1-1", "unit": "disulfide_design", "source": "pdb-bio-nm", "cell": "biology 0.1-1", "size": 3, "sample": 3, "rule": "first batch: all", "ids": [ "BND003", "BND004", "BND016" ] }, { "stratum": "evidence_elimination | hbond2021 | chemistry 0.1-1", "unit": "evidence_elimination", "source": "hbond2021", "cell": "chemistry 0.1-1", "size": 1, "sample": 1, "rule": "first batch: all", "ids": [ "CNI031" ] }, { "stratum": "evidence_elimination | paper-cottet-mgb2-vortex | quantum 100-1000", "unit": "evidence_elimination", "source": "paper-cottet-mgb2-vortex", "cell": "quantum 100-1000", "size": 1, "sample": 1, "rule": "first batch: all", "ids": [ "QNI033" ] }, { "stratum": "evidence_elimination | paper-cuello-kcsa-gating | biology 0.1-1", "unit": "evidence_elimination", "source": "paper-cuello-kcsa-gating", "cell": "biology 0.1-1", "size": 1, "sample": 1, "rule": "first batch: all", "ids": [ "BNI047" ] }, { "stratum": "evidence_elimination | paper-filip-perovskite-steric | materials 0.1-1", "unit": "evidence_elimination", "source": "paper-filip-perovskite-steric", "cell": "materials 0.1-1", "size": 1, "sample": 1, "rule": "first batch: all", "ids": [ "MNI038" ] }, { "stratum": "evidence_elimination | paper-kerelsky-tbg-stm | quantum 10-100", "unit": "evidence_elimination", "source": "paper-kerelsky-tbg-stm", "cell": "quantum 10-100", "size": 1, "sample": 1, "rule": "first batch: all", "ids": [ "QNI032" ] }, { "stratum": "evidence_elimination | paper-muhlbauer-mnsi-skyrmion | quantum 10-100", "unit": "evidence_elimination", "source": "paper-muhlbauer-mnsi-skyrmion", "cell": "quantum 10-100", "size": 1, "sample": 1, "rule": "first batch: all", "ids": [ "QNI038" ] }, { "stratum": "evidence_elimination | paper-rasmussen-b2ar-gs | biology 1-10", "unit": "evidence_elimination", "source": "paper-rasmussen-b2ar-gs", "cell": "biology 1-10", "size": 1, "sample": 1, "rule": "first batch: all", "ids": [ "BNI048" ] }, { "stratum": "evidence_elimination | paper-shaban-cholesteric | chemistry 100-1000", "unit": "evidence_elimination", "source": "paper-shaban-cholesteric", "cell": "chemistry 100-1000", "size": 1, "sample": 1, "rule": "first batch: all", "ids": [ "CNI029" ] }, { "stratum": "evidence_quantity | paper-cao-magic-angle | quantum 0.1-1", "unit": "evidence_quantity", "source": "paper-cao-magic-angle", "cell": "quantum 0.1-1", "size": 1, "sample": 1, "rule": "first batch: all", "ids": [ "QNI029" ] }, { "stratum": "evidence_quantity | paper-cao-magic-angle | quantum 100-1000", "unit": "evidence_quantity", "source": "paper-cao-magic-angle", "cell": "quantum 100-1000", "size": 1, "sample": 1, "rule": "first batch: all", "ids": [ "QNI028" ] }, { "stratum": "evidence_quantity | paper-dinc-isosorbide | chemistry 100-1000", "unit": "evidence_quantity", "source": "paper-dinc-isosorbide", "cell": "chemistry 100-1000", "size": 1, "sample": 1, "rule": "first batch: all", "ids": [ "CNI026" ] }, { "stratum": "evidence_quantity | paper-filip-perovskite-steric | materials 0.1-1", "unit": "evidence_quantity", "source": "paper-filip-perovskite-steric", "cell": "materials 0.1-1", "size": 1, "sample": 1, "rule": "first batch: all", "ids": [ "MNI037" ] }, { "stratum": "evidence_quantity | paper-jiang-anthrax-pa-pore | biology 1-10", "unit": "evidence_quantity", "source": "paper-jiang-anthrax-pa-pore", "cell": "biology 1-10", "size": 1, "sample": 1, "rule": "first batch: all", "ids": [ "BNI046" ] }, { "stratum": "evidence_quantity | paper-kerelsky-tbg-stm | quantum 10-100", "unit": "evidence_quantity", "source": "paper-kerelsky-tbg-stm", "cell": "quantum 10-100", "size": 1, "sample": 1, "rule": "first batch: all", "ids": [ "QNI030" ] }, { "stratum": "evidence_quantity | paper-schaefermeier-bscco-vortex | quantum 100-1000", "unit": "evidence_quantity", "source": "paper-schaefermeier-bscco-vortex", "cell": "quantum 100-1000", "size": 1, "sample": 1, "rule": "first batch: all", "ids": [ "QNI031" ] }, { "stratum": "evidence_quantity | paper-silica-opal | materials 100-1000", "unit": "evidence_quantity", "source": "paper-silica-opal", "cell": "materials 100-1000", "size": 1, "sample": 1, "rule": "first batch: all", "ids": [ "MNI036" ] }, { "stratum": "extent_choice_v2 | cod-mof | materials 1-10", "unit": "extent_choice_v2", "source": "cod-mof", "cell": "materials 1-10", "size": 2, "sample": 2, "rule": "first batch: all", "ids": [ "MNP028", "MNP030" ] }, { "stratum": "extent_choice_v2 | oe62 | quantum 1-10", "unit": "extent_choice_v2", "source": "oe62", "cell": "quantum 1-10", "size": 5, "sample": 5, "rule": "first batch: all", "ids": [ "QNP023", "QNP024", "QNP025", "QNP026", "QNP027" ] }, { "stratum": "extent_choice_v2 | pdb-1aa5-vancomycin | chemistry 1-10", "unit": "extent_choice_v2", "source": "pdb-1aa5-vancomycin", "cell": "chemistry 1-10", "size": 4, "sample": 4, "rule": "first batch: all", "ids": [ "CNP034", "CNP035", "CNP036", "CNP037" ] }, { "stratum": "extent_choice_v2 | pdb-bio-nm | biology 1-10", "unit": "extent_choice_v2", "source": "pdb-bio-nm", "cell": "biology 1-10", "size": 3, "sample": 3, "rule": "first batch: all", "ids": [ "BNP040", "BNP041", "BNP042" ] }, { "stratum": "first_diffraction_peak | cod-materials-cell | chemistry 0.1-1", "unit": "first_diffraction_peak", "source": "cod-materials-cell", "cell": "chemistry 0.1-1", "size": 1, "sample": 1, "rule": "first batch: all", "ids": [ "CNI033" ] }, { "stratum": "first_diffraction_peak | cod-materials-cell | chemistry 1-10", "unit": "first_diffraction_peak", "source": "cod-materials-cell", "cell": "chemistry 1-10", "size": 1, "sample": 1, "rule": "first batch: all", "ids": [ "CNI032" ] }, { "stratum": "first_diffraction_peak | cod-materials-cell | materials 0.1-1", 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{ "form": "family", "instance": "FA-MO-PERIOD-D1" }, "QNI012": { "form": "family", "instance": "FA-MO-NHALF-K079" }, "QND005": { "form": "family", "instance": "FA-MO-DES-HALF" }, "QND006": { "form": "family", "instance": "FA-MO-DES-PERIOD" }, "QND007": { "form": "family", "instance": "FA-MO-DES-FULL" }, "BNP025": { "form": "family", "instance": "FA-ASM-EXT-6NCL" }, "BNI023": { "form": "family", "instance": "FA-ASM-T-6NCL" }, "BND002": { "form": "family", "instance": "FA-QDES-6NCL" }, "BNI024": { "form": "family", "instance": "FA-SS-1UBQ-43" }, "CNI014": { "form": "family", "instance": "FA-HG-EV1" }, "CND007": { "form": "family", "instance": "FA-HG-DES1" }, "CND008": { "form": "family", "instance": "FA-HG-DES2" }, "QNI014": { "form": "family", "instance": "FA-QD-PEAK-C" }, "QNI015": { "form": "family", "instance": "FA-QD-EPS-E" }, "QNI016": { "form": "family", "instance": "FA-QD-CONC-B" }, "QND008": { "form": "family", "instance": "FA-QD-DES-590" }, "QND009": { "form": "family", "instance": "FA-QD-DES-565" }, "MND007": { "form": "family", "instance": "FA-XD-CRYSTAL-CU" }, "MND010": { "form": "family", "instance": "FA-XD-ANODE-MOF5" }, "MND011": { "form": "family", "instance": "FA-XD-ANODE-SALEM2" }, "MND012": { "form": "family", "instance": "FA-XD-WAVE-MOF5" }, "BND003": { "form": "family", "instance": "FA-DS-1UBQ-A" }, "BND004": { "form": "family", "instance": "FA-DS-1UBQ-B" }, "BND007": { "form": "family", "instance": "FA-FD-1UBQ" }, "BND009": { "form": "family", "instance": "FA-QDES-1AON" }, "BND010": { "form": "family", "instance": "FA-QDES-1KX5" }, "QNP020": { "form": "family", "instance": "FA-VX-SPACING-561" }, "QNP021": { "form": "family", "instance": "FA-VX-DENSITY-1173" }, "QNP022": { "form": "family", "instance": "FA-VX-SPACING-BSCCO" }, "QNI017": { "form": "family", "instance": "FA-VX-FIELD-BSCCO" }, "QND010": { "form": "family", "instance": "FA-VX-DES-SPACING" }, "QND011": { "form": "family", "instance": "FA-VX-DES-SANS" }, "QND012": { "form": "family", "instance": "FA-VX-DES-DENSITY" }, "CNP024": { "form": "family", "instance": "FA-CH-PITCH-R5011" }, "CNP025": { "form": "family", "instance": "FA-CH-HAND-S5011" }, "CNP026": { "form": "family", "instance": "FA-CH-PITCH-LRCD" }, "CNI018": { "form": "family", "instance": "FA-CH-BAND-R5011" }, "CNI020": { "form": "family", "instance": "FA-CH-LAMBDA-RRCD" }, "CND009": { "form": "family", "instance": "FA-CH-DES-550" }, "CND010": { "form": "family", "instance": "FA-CH-DES-LEFT600" }, "CND011": { "form": "family", "instance": "FA-CH-DES-BELOW620" }, "MNP024": { "form": "family", "instance": "FA-COORD-QUARTZ" }, "BNP031": { "form": "family", "instance": "FA-ASM-RG-2BUK" }, "BNP034": { "form": "family", "instance": "FA-ASM-EXT-1SVA" }, "BNP036": { "form": "family", "instance": "FA-ASM-EXT-2FT1" }, "BNI033": { "form": "family", "instance": "FA-DEB-1CWP" }, "BND015": { "form": "family", "instance": "FA-QDES-2FT1" }, "BNI037": { "form": "family", "instance": "FA-ASM-CAPS-1CWP" }, "QNI021": { "form": "family", "instance": "FA-ROT-7029-111" }, "CNI022": { "form": "family", "instance": "FA-ROT-G2-110" }, "QND013": { "form": "family", "instance": "FA-ISO-7095-111" }, "CND012": { "form": "family", "instance": "FA-ISO-G9-110" }, "CND013": { "form": "family", "instance": "FA-ISO-G13-111" }, "BNP038": { "form": "family", "instance": "FA-DIST-6LYZ-SS30" }, "BNP039": { "form": "family", "instance": "FA-DIST-1CRN-SS16" }, "CNP027": { "form": "family", "instance": "FA-DIST-WP6-C20O22" }, "BNP040": { "form": "family", "instance": "FC-BNP002-1UBQ" }, "BNP041": { "form": "family", "instance": "FC-BNP002-1CRN" }, "BNP042": { "form": "family", "instance": "FC-BNP001-1CRN" }, "CNP029": { "form": "family", "instance": "FA-HBG-FIVE-HN" }, "QNI023": { "form": "family", "instance": "FA-FP-QM7X-7040-D2" }, "QNP023": { "form": "family", "instance": "FC-QNP007" }, "QNP024": { "form": "family", "instance": "FC-QNP008" }, "QNP025": { "form": "family", "instance": "FC-QNP009" }, "QNP026": { "form": "family", "instance": "FC-QNP010" }, "QNP027": { "form": "family", "instance": "FC-QNP011" }, "MNP028": { "form": "family", "instance": "FC-MNP006" }, "MNP030": { "form": "family", "instance": "FC-MNP010" }, "CNP034": { "form": "family", "instance": "FC-CNP007" }, "CNP035": { "form": "family", "instance": "FC-CNP008" }, "CNP036": { "form": "family", "instance": "FC-CNP009" }, "CNP037": { "form": "family", "instance": "FC-CNP011" }, "QNI028": { "form": "family", "instance": "FA-EVQ-CAO-SQUID" }, "QNI029": { "form": "family", "instance": "FA-EVQ-CAO-PAULI" }, "QNI030": { "form": "family", "instance": "FA-EVQ-KER-STRAIN" }, "QNI031": { "form": "family", "instance": "FA-EVQ-SCH-FLUX" }, "QNI032": { "form": "family", "instance": "FA-EVE-KER-NEMATIC" }, "QNI033": { "form": "family", "instance": "FA-EVE-COT-BEND" }, "CNI026": { "form": "family", "instance": "FA-EVQ-DIN-HTP" }, "CNI029": { "form": "family", "instance": "FA-EVE-SHA-IONS" }, "CNI031": { "form": "family", "instance": "FA-EVE-ALT-STABILITY" }, "MNI036": { "form": "family", "instance": "FA-EVQ-FOO-LAYERS" }, "QNI038": { "form": "family", "instance": "FA-EVE-MUH-SKYRMION" }, "MNI037": { "form": "family", "instance": "FA-EVQ-FIL-RBCS" }, "MNI038": { "form": "family", "instance": "FA-EVE-FIL-ANGLE" }, "BNI046": { "form": "family", "instance": "FA-EVQ-JIA-CLAMP" }, "BNI047": { "form": "family", "instance": "FA-EVE-KCS-COLLAPSE" }, "BNI048": { "form": "family", "instance": "FA-EVE-RAS-DOMAIN" }, "MNP034": { "form": "family", "instance": "FA-COORD-ALNI" }, "CNI032": { "form": "family", "instance": "FA-PEAK-B5H9" }, "CNP039": { "form": "family", "instance": "FA-COORD-K2CUF4" }, "CNI033": { "form": "family", "instance": "FA-PEAK-K2CUF4" }, "MNI043": { "form": "family", "instance": "FA-PEAK-PARA-I" }, "MNP037": { "form": "family", "instance": "FA-COORD-PENTACENE" }, "MNI045": { "form": "family", "instance": "FA-PEAK-PENTACENE" }, "BND016": { "form": "family", "instance": "EN-1A6M-DS-2-6" }, "BND019": { "form": "family", "instance": "EN-1FHA-FD-25-5-42" }, "BNI053": { "form": "family", "instance": "EN-12E8-SS-3" }, "BND021": { "form": "family", "instance": "EN-12E8-FD-25-1-11" }, "CND017": { "form": "family", "instance": "FA-DES-RAN-BROMIDE" }, "MND013": { "form": "family", "instance": "FA-DES-CHE-SIEVE" }, "MND014": { "form": "family", "instance": "FA-DES-CHE-FLOW" } }, "note": "Tooling only: no L1/L2/L3 review has been run yet. Records are written by tools/review.py with a named human reviewer. Scope: the 160 selection (proposal pending the professor); reserve questions are reviewed later." }