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d1292d8 | 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 | """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
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