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修复了部分的protocol因为XDL更新导致的问题 (#61)
* 修复了部分的protocol因为XDL更新导致的问题 但是pumptransfer，add，dissolve，separate还没修，后续还需要写virtual固体加料器 * 补充了四个action * 添加了固体加样器，丰富了json，修改了add protocol * bump version to 0.9.9 * fix bugs from new actions * protocol完整修复版本& bump version to 0.9.10 * 修补了一些单位处理，bump version to 0.9.11 * 优化了全protocol的运行时间，除了pumptransfer相关的还没 * 补充了剩下的几个protocol --------- Co-authored-by: Junhan Chang <changjh@dp.tech> Co-authored-by: Xuwznln <18435084+Xuwznln@users.noreply.github.com>
This commit is contained in:
Kongchang Feng
GitHub
@@ -43,6 +43,15 @@
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Hydrogenate <Hydrogenate temp="45 °C" time="?" vessel="main_reactor"/>
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4. 参数对齐
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class PumpTransferProtocol(BaseModel):
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from_vessel: str
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to_vessel: str
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@@ -51,9 +60,9 @@ class PumpTransferProtocol(BaseModel):
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time: float = 0
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viscous: bool = False
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rinsing_solvent: str = "air" <Transfer from_vessel="main_reactor" to_vessel="rotavap"/>
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rinsing_volume: float = 5000
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rinsing_repeats: int = 2
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solid: bool = False
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rinsing_volume: float = 5000 <Transfer event="A" from_vessel="reactor" rate_spec="dropwise" to_vessel="main_reactor"/>
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rinsing_repeats: int = 2 <Transfer from_vessel="separator" through="cartridge" to_vessel="rotavap"/>
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solid: bool = False 测完了三个都能跑✅
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flowrate: float = 500
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transfer_flowrate: float = 2500
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@@ -66,25 +75,25 @@ class SeparateProtocol(BaseModel):
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waste_phase_to_vessel: str
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solvent: str
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solvent_volume: float <Separate product_phase="bottom" purpose="wash" solvent="water" vessel="separator" volume="?"/>
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through: str
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repeats: int
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stir_time: float
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through: str <Separate product_phase="top" purpose="separate" vessel="separator"/>
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repeats: int <Separate product_phase="bottom" purpose="extract" repeats="3" solvent="CH2Cl2" vessel="separator" volume="?"/>
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stir_time: float <Separate product_phase="top" product_vessel="flask" purpose="separate" vessel="separator" waste_vessel="separator"/>
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stir_speed: float
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settling_time: float
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settling_time: float 测完了能跑✅
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class EvaporateProtocol(BaseModel):
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vessel: str
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pressure: float
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temp: float <Evaporate solvent="ethanol" vessel="rotavap"/>
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time: float
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time: float 测完了能跑✅
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stir_speed: float
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class EvacuateAndRefillProtocol(BaseModel):
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vessel: str
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gas: str <EvacuateAndRefill gas="nitrogen" vessel="main_reactor"/>
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repeats: int
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repeats: int 测完了能跑✅
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class AddProtocol(BaseModel):
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vessel: str
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@@ -95,21 +104,27 @@ class AddProtocol(BaseModel):
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time: float
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stir: bool
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stir_speed: float <Add reagent="ethanol" vessel="main_reactor" volume="2.7 mL"/>
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<Add event="A" mass="19.3 g" mol="0.28 mol" rate_spec="portionwise" reagent="sodium nitrite" time="1 h" vessel="main_reactor"/>
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<Add mass="4.5 g" mol="16.2 mmol" reagent="(S)-2-phthalimido-6-hydroxyhexanoic acid" vessel="main_reactor"/>
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<Add purpose="dilute" reagent="hydrochloric acid" vessel="main_reactor" volume="?"/>
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<Add equiv="1.1" event="B" mol="25.2 mmol" rate_spec="dropwise" reagent="1-fluoro-2-nitrobenzene" time="20 min"
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vessel="main_reactor" volume="2.67 mL"/>
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<Add ratio="?" reagent="tetrahydrofuran|tert-butanol" vessel="main_reactor" volume="?"/>
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viscous: bool
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purpose: str
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purpose: str 测完了能跑✅
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class CentrifugeProtocol(BaseModel):
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vessel: str
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speed: float
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time: float 自创的
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time: float 没毛病
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temp: float
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class FilterProtocol(BaseModel):
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vessel: str
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filtrate_vessel: str
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stir: bool <Filter vessel="filter"/>
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stir_speed: float
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temp: float
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stir_speed: float <Filter filtrate_vessel="rotavap" vessel="filter"/>
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temp: float 测完了能跑✅
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continue_heatchill: bool
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volume: float
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@@ -118,7 +133,10 @@ class HeatChillProtocol(BaseModel):
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temp: float
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time: float <HeatChill pressure="1 mbar" temp_spec="room temperature" time="?" vessel="main_reactor"/>
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<HeatChill temp_spec="room temperature" time_spec="overnight" vessel="main_reactor"/>
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stir: bool
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<HeatChill temp="256 °C" time="?" vessel="main_reactor"/>
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<HeatChill reflux_solvent="methanol" temp_spec="reflux" time="2 h" vessel="main_reactor"/>
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<HeatChillToTemp temp_spec="room temperature" vessel="main_reactor"/>
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stir: bool 测完了能跑✅
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stir_speed: float
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purpose: str
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@@ -133,7 +151,9 @@ class HeatChillStopProtocol(BaseModel):
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class StirProtocol(BaseModel):
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stir_time: float
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stir_speed: float <Stir time="0.5 h" vessel="main_reactor"/>
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settling_time: float
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<Stir event="A" time="30 min" vessel="main_reactor"/>
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<Stir time_spec="several minutes" vessel="filter"/>
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settling_time: float 测完了能跑✅
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class StartStirProtocol(BaseModel):
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vessel: str
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@@ -149,11 +169,11 @@ class TransferProtocol(BaseModel):
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volume: float
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amount: str = ""
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time: float = 0
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viscous: bool = False <Transfer from_vessel="main_reactor" to_vessel="rotavap"/>
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viscous: bool = False
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rinsing_solvent: str = ""
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rinsing_volume: float = 0.0
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rinsing_repeats: int = 0
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solid: bool = False
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solid: bool = False 这个protocol早该删掉了
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class CleanVesselProtocol(BaseModel):
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vessel: str
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@@ -165,11 +185,11 @@ class CleanVesselProtocol(BaseModel):
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class DissolveProtocol(BaseModel):
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vessel: str
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solvent: str
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volume: float <Dissolve mass="2.9 g" mol="0.12 mol" reagent="magnesium" vessel="main_reactor"/>
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amount: str = ""
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temp: float = 25.0
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time: float = 0.0
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stir_speed: float = 0.0
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volume: float <Dissolve mass="2.9 g" mol="0.12 mol" reagent="magnesium" vessel="main_reactor"/>
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amount: str = "" <Dissolve mass="12.9 g" reagent="4-tert-butylbenzyl bromide" vessel="main_reactor"/>
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temp: float = 25.0 <Dissolve solvent="diisopropyl ether" vessel="rotavap" volume="?"/>
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time: float = 0.0 <Dissolve event="A" mass="?" reagent="pyridinone" vessel="main_reactor"/>
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stir_speed: float = 0.0 测完了能跑✅
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class FilterThroughProtocol(BaseModel):
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from_vessel: str
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@@ -183,16 +203,19 @@ class FilterThroughProtocol(BaseModel):
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class RunColumnProtocol(BaseModel):
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from_vessel: str
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to_vessel: str <RunColumn Rf="?" column="column" from_vessel="rotavap" pct1="40 %" pct2="50 %" solvent1="ethyl acetate" solvent2="hexane" to_vessel="rotavap"/>
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column: str
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column: str 测完了能跑✅
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class WashSolidProtocol(BaseModel):
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vessel: str
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solvent: str
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volume: float
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filtrate_vessel: str = ""
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filtrate_vessel: str = "" <WashSolid repeats="4" solvent="water" vessel="main_reactor" volume="400 mL"/>
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temp: float = 25.0 <WashSolid filtrate_vessel="rotavap" solvent="formic acid" vessel="main_reactor" volume="?"/>
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stir: bool = False
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stir_speed: float = 0.0
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stir: bool = False <WashSolid solvent="acetone" vessel="rotavap" volume="5 mL"/>
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<WashSolid solvent="ethyl alcohol" vessel="main_reactor" volume_spec="small volume"/>
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<WashSolid filtrate_vessel="rotavap" mass="10 g" solvent="toluene" vessel="separator"/>
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<WashSolid repeats_spec="several" solvent="water" vessel="main_reactor" volume="?"/>
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stir_speed: float = 0.0 测完了能跑✅
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time: float = 0.0
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repeats: int = 1
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@@ -219,4 +242,17 @@ class RecrystallizeProtocol(BaseModel):
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class HydrogenateProtocol(BaseModel):
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temp: str = Field(..., description="反应温度（如 '45 °C'）")
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time: str = Field(..., description="反应时间（如 '2 h'）") <新写的，没问题>
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vessel: str = Field(..., description="反应容器")
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vessel: str = Field(..., description="反应容器")
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还差
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<dissolve>
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<separate>
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<CleanVessel vessel="centrifuge"/>
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单位修复：
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evaporate
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heatchill
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recrysitallize
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stir
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wash solid
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@@ -32,7 +32,11 @@
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"separator_1",
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"collection_bottle_1",
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"collection_bottle_2",
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"collection_bottle_3"
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"collection_bottle_3",
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"solid_dispenser_1",
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"solid_reagent_bottle_1",
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"solid_reagent_bottle_2",
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"solid_reagent_bottle_3"
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],
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"parent": null,
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"type": "device",
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@@ -672,6 +676,98 @@
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"data": {
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"current_volume": 0.0
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}
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},
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{
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"id": "solid_dispenser_1",
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"name": "固体粉末加样器",
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"children": [],
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"parent": "OrganicSynthesisStation",
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"type": "device",
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"class": "virtual_solid_dispenser",
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"position": {
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"x": 600,
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"y": 300,
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"z": 0
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},
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"config": {
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"max_capacity": 100.0,
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"precision": 0.001
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},
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"data": {
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"status": "Ready",
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"current_reagent": "",
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"dispensed_amount": 0.0,
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"total_operations": 0
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}
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},
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{
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"id": "solid_reagent_bottle_1",
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"name": "固体试剂瓶1-氯化钠",
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"children": [],
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"parent": "OrganicSynthesisStation",
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"type": "container",
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"class": "container",
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"position": {
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"x": 550,
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"y": 250,
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"z": 0
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},
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"config": {
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"volume": 500.0,
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"reagent": "sodium_chloride",
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"physical_state": "solid"
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},
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"data": {
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"current_mass": 500.0,
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"reagent_name": "sodium_chloride",
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"physical_state": "solid"
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}
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},
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{
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"id": "solid_reagent_bottle_2",
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"name": "固体试剂瓶2-碳酸钠",
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"children": [],
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"parent": "OrganicSynthesisStation",
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"type": "container",
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"class": "container",
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"position": {
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"x": 600,
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"y": 250,
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"z": 0
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},
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"config": {
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"volume": 500.0,
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"reagent": "sodium_carbonate",
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"physical_state": "solid"
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},
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"data": {
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"current_mass": 500.0,
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"reagent_name": "sodium_carbonate",
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"physical_state": "solid"
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}
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},
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{
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"id": "solid_reagent_bottle_3",
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"name": "固体试剂瓶3-氯化镁",
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"children": [],
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"parent": "OrganicSynthesisStation",
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"type": "container",
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"class": "container",
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"position": {
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"x": 650,
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"y": 250,
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"z": 0
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},
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"config": {
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"volume": 500.0,
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"reagent": "magnesium_chloride",
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"physical_state": "solid"
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},
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"data": {
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"current_mass": 500.0,
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"reagent_name": "magnesium_chloride",
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"physical_state": "solid"
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}
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}
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],
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"links": [
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@@ -802,7 +898,7 @@
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"type": "fluid",
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"port": {
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"multiway_valve_2": "3",
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"solenoid_valve_2": "in"
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"solenoid_valve_2": "out"
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}
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},
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{
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@@ -812,7 +908,7 @@
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"type": "fluid",
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"port": {
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"gas_source_1": "gassource",
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"solenoid_valve_2": "out"
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"solenoid_valve_2": "in"
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}
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},
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{
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@@ -964,6 +1060,46 @@
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"solenoid_valve_3": "out",
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"main_reactor": "top"
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}
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},
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{
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"id": "link_solid_dispenser_to_reactor",
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"source": "solid_dispenser_1",
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"target": "main_reactor",
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"type": "resource",
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"port": {
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"solid_dispenser_1": "SolidOut",
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"main_reactor": "top"
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}
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},
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{
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"id": "link_solid_bottle1_to_dispenser",
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"source": "solid_reagent_bottle_1",
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"target": "solid_dispenser_1",
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"type": "resource",
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"port": {
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"solid_reagent_bottle_1": "top",
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"solid_dispenser_1": "SolidIn"
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}
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},
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{
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"id": "link_solid_bottle2_to_dispenser",
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"source": "solid_reagent_bottle_2",
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"target": "solid_dispenser_1",
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"type": "resource",
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"port": {
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"solid_reagent_bottle_2": "top",
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"solid_dispenser_1": "SolidIn"
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}
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},
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{
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"id": "link_solid_bottle3_to_dispenser",
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"source": "solid_reagent_bottle_3",
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"target": "solid_dispenser_1",
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"type": "resource",
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"port": {
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"solid_reagent_bottle_3": "top",
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"solid_dispenser_1": "SolidIn"
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}
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}
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]
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}
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