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Junhan Chang
230
unilabos/compile/separate_protocol.py
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230
unilabos/compile/separate_protocol.py
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import numpy as np
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import networkx as nx
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def generate_separate_protocol(
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G: nx.DiGraph,
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purpose: str, # 'wash' or 'extract'. 'wash' means that product phase will not be the added solvent phase, 'extract' means product phase will be the added solvent phase. If no solvent is added just use 'extract'.
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product_phase: str, # 'top' or 'bottom'. Phase that product will be in.
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from_vessel: str, #Contents of from_vessel are transferred to separation_vessel and separation is performed.
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separation_vessel: str, # Vessel in which separation of phases will be carried out.
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to_vessel: str, # Vessel to send product phase to.
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waste_phase_to_vessel: str, # Optional. Vessel to send waste phase to.
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solvent: str, # Optional. Solvent to add to separation vessel after contents of from_vessel has been transferred to create two phases.
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solvent_volume: float = 50000, # Optional. Volume of solvent to add.
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through: str = "", # Optional. Solid chemical to send product phase through on way to to_vessel, e.g. 'celite'.
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repeats: int = 1, # Optional. Number of separations to perform.
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stir_time: float = 30, # Optional. Time stir for after adding solvent, before separation of phases.
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stir_speed: float = 300, # Optional. Speed to stir at after adding solvent, before separation of phases.
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settling_time: float = 300 # Optional. Time
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) -> list[dict]:
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"""
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Generate a protocol to clean a vessel with a solvent.
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:param G: Directed graph. Nodes are containers and pumps, edges are fluidic connections.
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:param vessel: Vessel to clean.
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:param solvent: Solvent to clean vessel with.
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:param volume: Volume of solvent to clean vessel with.
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:param temp: Temperature to heat vessel to while cleaning.
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:param repeats: Number of cleaning cycles to perform.
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:return: List of actions to clean vessel.
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"""
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# 生成泵操作的动作序列
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pump_action_sequence = []
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reactor_volume = 500000.0
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waste_vessel = waste_phase_to_vessel
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# TODO：通过物料管理系统找到溶剂的容器
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if "," in solvent:
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solvents = solvent.split(",")
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assert len(solvents) == repeats, "Number of solvents must match number of repeats."
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else:
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solvents = [solvent] * repeats
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# TODO: 通过设备连接图找到分离容器的控制器、底部出口
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separator_controller = f"{separation_vessel}_controller"
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separation_vessel_bottom = f"flask_{separation_vessel}"
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transfer_flowrate = flowrate = 2500.0
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if from_vessel != separation_vessel:
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pump_action_sequence.append(
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{
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"device_id": "",
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"action_name": "PumpTransferProtocol",
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"action_kwargs": {
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"from_vessel": from_vessel,
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"to_vessel": separation_vessel,
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"volume": reactor_volume,
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"time": reactor_volume / flowrate,
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# "transfer_flowrate": transfer_flowrate,
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}
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}
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)
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# for i in range(2):
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# pump_action_sequence.append(
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# {
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# "device_id": "",
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# "action_name": "CleanProtocol",
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# "action_kwargs": {
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# "vessel": from_vessel,
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# "solvent": "H2O", # Solvent to clean vessel with.
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# "volume": solvent_volume, # Optional. Volume of solvent to clean vessel with.
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# "temp": 25.0, # Optional. Temperature to heat vessel to while cleaning.
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# "repeats": 1
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# }
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# }
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# )
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# pump_action_sequence.append(
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# {
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# "device_id": "",
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# "action_name": "CleanProtocol",
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# "action_kwargs": {
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# "vessel": from_vessel,
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# "solvent": "CH2Cl2", # Solvent to clean vessel with.
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# "volume": solvent_volume, # Optional. Volume of solvent to clean vessel with.
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# "temp": 25.0, # Optional. Temperature to heat vessel to while cleaning.
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# "repeats": 1
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# }
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# }
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# )
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# 生成泵操作的动作序列
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for i in range(repeats):
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# 找到当次萃取所用溶剂
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solvent_thistime = solvents[i]
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solvent_vessel = f"flask_{solvent_thistime}"
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pump_action_sequence.append(
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{
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"device_id": "",
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"action_name": "PumpTransferProtocol",
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"action_kwargs": {
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"from_vessel": solvent_vessel,
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"to_vessel": separation_vessel,
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"volume": solvent_volume,
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"time": solvent_volume / flowrate,
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# "transfer_flowrate": transfer_flowrate,
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}
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}
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)
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pump_action_sequence.extend([
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# 搅拌、静置
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{
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"device_id": separator_controller,
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"action_name": "stir",
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"action_kwargs": {
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"stir_time": stir_time,
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"stir_speed": stir_speed,
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"settling_time": settling_time
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}
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},
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# 分液（判断电导突跃）
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{
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"device_id": separator_controller,
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"action_name": "valve_open",
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"action_kwargs": {
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"command": "delta > 0.05"
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}
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}
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])
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if product_phase == "bottom":
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# 产物转移到目标瓶
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pump_action_sequence.append(
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{
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"device_id": "",
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"action_name": "PumpTransferProtocol",
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"action_kwargs": {
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"from_vessel": separation_vessel_bottom,
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"to_vessel": to_vessel,
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"volume": 250000.0,
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"time": 250000.0 / flowrate,
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# "transfer_flowrate": transfer_flowrate,
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}
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}
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)
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# 放出上面那一相，60秒后关阀门
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pump_action_sequence.append(
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{
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"device_id": separator_controller,
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"action_name": "valve_open",
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"action_kwargs": {
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"command": "time > 60"
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}
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}
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)
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# 弃去上面那一相进废液
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pump_action_sequence.append(
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{
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"device_id": "",
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"action_name": "PumpTransferProtocol",
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"action_kwargs": {
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"from_vessel": separation_vessel_bottom,
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"to_vessel": waste_vessel,
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"volume": 250000.0,
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"time": 250000.0 / flowrate,
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# "transfer_flowrate": transfer_flowrate,
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}
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}
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)
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elif product_phase == "top":
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# 弃去下面那一相进废液
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pump_action_sequence.append(
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{
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"device_id": "",
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"action_name": "PumpTransferProtocol",
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"action_kwargs": {
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"from_vessel": separation_vessel_bottom,
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"to_vessel": waste_vessel,
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"volume": 250000.0,
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"time": 250000.0 / flowrate,
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# "transfer_flowrate": transfer_flowrate,
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}
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}
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)
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# 放出上面那一相
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pump_action_sequence.append(
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{
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"device_id": separator_controller,
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"action_name": "valve_open",
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"action_kwargs": {
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"command": "time > 60"
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}
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}
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)
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# 产物转移到目标瓶
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pump_action_sequence.append(
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{
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"device_id": "",
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"action_name": "PumpTransferProtocol",
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"action_kwargs": {
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"from_vessel": separation_vessel_bottom,
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"to_vessel": to_vessel,
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"volume": 250000.0,
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"time": 250000.0 / flowrate,
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# "transfer_flowrate": transfer_flowrate,
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}
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}
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)
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elif product_phase == "organic":
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pass
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# 如果不是最后一次，从中转瓶转移回分液漏斗
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if i < repeats - 1:
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pump_action_sequence.append(
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{
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"device_id": "",
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"action_name": "PumpTransferProtocol",
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"action_kwargs": {
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"from_vessel": to_vessel,
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"to_vessel": separation_vessel,
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"volume": 250000.0,
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"time": 250000.0 / flowrate,
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# "transfer_flowrate": transfer_flowrate,
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}
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}
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)
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return pump_action_sequence
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