"""Template-backed sedimentation reference for the Eppendorf 5910 Ri runtime (CHEM-010). Library: ``assets/reactions/eppendorf_5910ri_sedimentation_library/templates.json`` * 32 liquid media: density and dynamic viscosity vs temperature at 0.101325 MPa (NIST WebBook SRD 69 fluid data, liquid rows only; values come from NIST reference correlations); * 61 particles / cells / organelles / macromolecules: published (buoyant or material) densities (PubChem, BioNumbers, NIST SRM certificates, CC BY papers). The centrifuge itself reports no material readout. The template is used by an agent-visible ANALYSIS capability, ``sedimentation.estimate``: for the configured method (speed, temperature) and caller-given particle diameter, radius and path length, it evaluates Stokes settling of a rigid sphere in the medium, v = (rho_p - rho_f) d^2 omega^2 r / (18 mu), s = v / (omega^2 r), RCF = omega^2 r / g0, with rho_f(T), mu(T) linearly interpolated inside the medium's NIST liquid range (no extrapolation). """ from __future__ import annotations import json from typing import Any from scripts.basic40_templates import _analytical_common as common from scripts.template_library import get_template, index_by_id LIB_REL = "assets/reactions/eppendorf_5910ri_sedimentation_library/templates.json" G0 = 9.80665 SVEDBERG_S = 1e-13 DIAMETER_RANGE_M = (1e-9, 1e-3) RADIUS_RANGE_M = (0.01, 0.5) PATH_RANGE_M = (1e-4, 0.2) LIMITATIONS = [ "Stokes law for a single rigid sphere at low Reynolds number in an unbounded Newtonian liquid: no hindered settling, particle-particle interaction, wall effects, diffusion, shape factor, compressibility or density gradient.", "Medium properties are NIST SRD 69 reference-correlation values for the PURE fluid at 0.101325 MPa, liquid range only (no extrapolation outside it); buffers, sucrose/Percoll/CsCl gradients and suspensions are not covered.", "Biological densities are mostly BUOYANT densities measured in a specific gradient medium; inorganic/metal values are bulk material densities, not effective nanoparticle densities.", "Uses the configured method speed and temperature (setpoints), not the run's acceleration/braking or actual temperature history; the radius and path length are caller inputs because rotor geometry is unknown.", "The estimate is an analysis, not an instrument readout; no in-run separation state is simulated.", ] SYNTHETIC_PARTS = ["caller-declared radius, path length and particle diameter"] def _records() -> dict[str, dict[str, Any]]: return index_by_id(LIB_REL) def template_read(substance_id: Any) -> dict[str, Any] | None: record = get_template(LIB_REL, substance_id) if isinstance(substance_id, str) else None if record is None: return None base = {"substance_id": record["substance_id"], "template_kind": record["template_kind"], "name": record["name"], "cas": record.get("cas"), "source": record["source"], "conditions_json": json.dumps(record.get("conditions"), ensure_ascii=False)} if record["template_kind"] == "medium": base["medium"] = {"temperature_K": record["temperature_K"], "density_kg_m3": record["density_kg_m3"], "viscosity_Pa_s": record["viscosity_Pa_s"], "temperature_range_K": record["temperature_range_K"], "pressure_Pa": record["pressure_Pa"]} base["particle"] = None else: base["particle"] = {"density_kg_m3": record["density_kg_m3"], "density_range_kg_m3": record["density_range_kg_m3"], "category": record["category"]} base["medium"] = None return {**base, **common.provenance([LIB_REL], record["evidence"], [], LIMITATIONS)} def medium_properties(medium: dict[str, Any], temperature_K: float) -> tuple[float, float] | None: temps = medium["temperature_K"] density = common.interp(temperature_K, temps, medium["density_kg_m3"]) viscosity = common.interp(temperature_K, temps, medium["viscosity_Pa_s"]) return None if density is None or viscosity is None else (density, viscosity) def estimate(arguments: dict[str, Any], state: dict[str, Any]) -> dict[str, Any] | str: """Result dict, or an error code string (INVALID_ARGUMENT / PRECONDITION_FAILED).""" records = _records() particle, medium = records.get(arguments["particle_id"]), records.get(arguments["medium_id"]) if particle is None or medium is None or particle["template_kind"] != "particle" or medium["template_kind"] != "medium": return "INVALID_ARGUMENT" if not state.get("method.configured"): return "PRECONDITION_FAILED" omega, temperature = state["method.speed_rad_s"], state["method.temperature_k"] props = medium_properties(medium, temperature) if props is None: return "PRECONDITION_FAILED" rho_f, mu = props d, r, path = arguments["particle_diameter_m"], arguments["radius_m"], arguments["path_length_m"] if particle["density_kg_m3"] is not None: densities = {"central": particle["density_kg_m3"]} else: low, high = particle["density_range_kg_m3"] densities = {key: value for key, value in (("low", low), ("high", high)) if value is not None} cases = {} for key, rho_p in densities.items(): delta = rho_p - rho_f velocity = delta * d ** 2 * omega ** 2 * r / (18.0 * mu) cases[key] = {"particle_density_kg_m3": rho_p, "density_difference_kg_m3": delta, "velocity_m_s": velocity, "sedimentation_coefficient_s": velocity / (omega ** 2 * r), "time_to_traverse_path_s": None if velocity == 0 else path / abs(velocity), "direction": "sediments" if delta > 0 else ("floats" if delta < 0 else "neutral"), "reynolds_number": rho_f * abs(velocity) * d / mu} return {"particle_id": particle["substance_id"], "medium_id": medium["substance_id"], "speed_rad_s": omega, "temperature_K": temperature, "radius_m": r, "particle_diameter_m": d, "path_length_m": path, "relative_centrifugal_force": omega ** 2 * r / G0, "medium_density_kg_m3": rho_f, "medium_viscosity_Pa_s": mu, "cases": cases, "model": "stokes_rigid_sphere", **common.provenance([LIB_REL], f"medium: {medium['evidence']} (NIST SRD 69 correlations); particle: {particle['evidence']}; settling: derived (Stokes law)", SYNTHETIC_PARTS, LIMITATIONS)} def estimate_schema() -> dict[str, Any]: n, obj, nullable = common.number, common.obj, common.nullable case = obj({"particle_density_kg_m3": n("kg/m^3", 0), "density_difference_kg_m3": n("kg/m^3"), "velocity_m_s": n("m/s"), "sedimentation_coefficient_s": n("s"), "time_to_traverse_path_s": nullable(n("s", 0)), "direction": {"type": "string", "enum": ["sediments", "floats", "neutral"]}, "reynolds_number": n("1", 0)}) return obj({"particle_id": common.TEXT, "medium_id": common.TEXT, "speed_rad_s": n("rad/s", 0), "temperature_K": n("K", 0), "radius_m": n("m", 0), "particle_diameter_m": n("m", 0), "path_length_m": n("m", 0), "relative_centrifugal_force": n("1", 0), "medium_density_kg_m3": n("kg/m^3", 0), "medium_viscosity_Pa_s": n("Pa*s", 0), "cases": {"type": "object", "additionalProperties": case, "minProperties": 1, "maxProperties": 2}, "model": {"type": "string", "const": "stokes_rigid_sphere"}, **common.provenance_schema()}) def template_read_schema() -> dict[str, Any]: n, obj, nullable = common.number, common.obj, common.nullable series = lambda unit: {"type": "array", "items": n(unit, 0), "minItems": 1} medium = obj({"temperature_K": series("K"), "density_kg_m3": series("kg/m^3"), "viscosity_Pa_s": series("Pa*s"), "temperature_range_K": {"type": "array", "items": n("K", 0), "minItems": 2, "maxItems": 2}, "pressure_Pa": n("Pa", 0)}) particle = obj({"density_kg_m3": nullable(n("kg/m^3", 0)), "density_range_kg_m3": nullable({"type": "array", "items": nullable(n("kg/m^3", 0)), "minItems": 2, "maxItems": 2}), "category": common.TEXT}) return obj({"substance_id": common.TEXT, "template_kind": {"type": "string", "enum": ["medium", "particle"]}, "name": common.TEXT, "cas": nullable(common.TEXT), "source": common.TEXT, "conditions_json": common.TEXT, "medium": nullable(medium), "particle": nullable(particle), **common.provenance_schema()}) def extend_metadata(metadata: dict[str, Any]) -> dict[str, Any]: n, obj = common.number, common.obj shared = {"state_ids": [], "preconditions": [], "scene_required": False, "availability": "implemented", "errors": ["UNKNOWN_INSTANCE", "UNKNOWN_CAPABILITY", "INVALID_ARGUMENT", "PRECONDITION_FAILED", "REQUEST_CONFLICT"], "rejection_side_effects": "none", "scene_failure_side_effects": "none", "asynchronous": False, "partial_failure_zh": "只读查询/计算，无状态、场景或运行副作用。", "state_effect_timing": {}} metadata["capabilities"]["template.read"] = { "function_zh": "读取公开沉降参考：介质密度/黏度-温度（NIST）或颗粒/细胞密度（文献），与当前转子内样品无关", "kind": "query", "input_schema": obj({"substance_id": {"type": "string", "description": "medium_* or particle_* library id"}}), "output_schema": template_read_schema(), "example_arguments": [{"substance_id": "medium_water"}], "component_ids": ["display"], "invocation": "Eppendorf5910Ri.invoke(capability_id='template.read', arguments={'substance_id': ...}, request_id=...)", **shared} metadata["capabilities"]["sedimentation.estimate"] = { "function_zh": "按当前方法转速/温度与公开介质、颗粒数据做 Stokes 沉降估算（分析，不是仪器读数）", "kind": "analysis", "input_schema": obj({"particle_id": {"type": "string"}, "medium_id": {"type": "string"}, "particle_diameter_m": n("m", *DIAMETER_RANGE_M), "radius_m": n("m", *RADIUS_RANGE_M), "path_length_m": n("m", *PATH_RANGE_M)}), "output_schema": estimate_schema(), "example_arguments": [{"particle_id": "particle_escherichia_coli_cell", "medium_id": "medium_water", "particle_diameter_m": 1e-6, "radius_m": 0.15, "path_length_m": 0.03}], "component_ids": ["display"], "invocation": "Eppendorf5910Ri.invoke(capability_id='sedimentation.estimate', arguments={...}, request_id=...)", **shared} metadata["capabilities"]["sedimentation.estimate"]["preconditions"] = [ "Method configured (uses method.speed_rad_s and method.temperature_k).", "Method temperature inside the medium's NIST liquid temperature range (no extrapolation)."] metadata["parameters"]["template_library"] = {"value": LIB_REL, "unit": "1", "evidence": "measured_literature", "conditions": "NIST SRD 69 liquid density/viscosity (32 fluids) + published particle/cell densities (61)"} metadata["limitations"] = metadata["limitations"] + [ "sedimentation.estimate is a Stokes-law analysis from public density/viscosity data for the configured method; centrifuge.predict_sedimentation (in-run separation model) remains unsupported."] return metadata