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修复了部分的protocol因为XDL更新导致的问题 (#61)

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* 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
2025-07-16 11:12:02 +08:00
committed by GitHub
parent 540c5e94b7
commit acf7b6d3f7
55 changed files with 9928 additions and 3669 deletions
Download Patch File Download Diff File Expand all files Collapse all files

90
test/experiments/comprehensive_protocol/checklist.md
View File

@@ -43,6 +43,15 @@
Hydrogenate <Hydrogenate temp="45 °C" time="?" vessel="main_reactor"/>
4. 参数对齐
class PumpTransferProtocol(BaseModel):
from_vessel: str
to_vessel: str
@@ -51,9 +60,9 @@ class PumpTransferProtocol(BaseModel):
time: float = 0
viscous: bool = False
rinsing_solvent: str = "air" <Transfer from_vessel="main_reactor" to_vessel="rotavap"/>
rinsing_volume: float = 5000
rinsing_repeats: int = 2
solid: bool = False
rinsing_volume: float = 5000 <Transfer event="A" from_vessel="reactor" rate_spec="dropwise" to_vessel="main_reactor"/>
rinsing_repeats: int = 2 <Transfer from_vessel="separator" through="cartridge" to_vessel="rotavap"/>
solid: bool = False 测完了三个都能跑✅
flowrate: float = 500
transfer_flowrate: float = 2500
@@ -66,25 +75,25 @@ class SeparateProtocol(BaseModel):
waste_phase_to_vessel: str
solvent: str
solvent_volume: float <Separate product_phase="bottom" purpose="wash" solvent="water" vessel="separator" volume="?"/>
through: str
repeats: int
stir_time: float
through: str <Separate product_phase="top" purpose="separate" vessel="separator"/>
repeats: int <Separate product_phase="bottom" purpose="extract" repeats="3" solvent="CH2Cl2" vessel="separator" volume="?"/>
stir_time: float <Separate product_phase="top" product_vessel="flask" purpose="separate" vessel="separator" waste_vessel="separator"/>
stir_speed: float
settling_time: float
settling_time: float 测完了能跑✅
class EvaporateProtocol(BaseModel):
vessel: str
pressure: float
temp: float <Evaporate solvent="ethanol" vessel="rotavap"/>
time: float
time: float 测完了能跑✅
stir_speed: float
class EvacuateAndRefillProtocol(BaseModel):
vessel: str
gas: str <EvacuateAndRefill gas="nitrogen" vessel="main_reactor"/>
repeats: int
repeats: int 测完了能跑✅
class AddProtocol(BaseModel):
vessel: str
@@ -95,21 +104,27 @@ class AddProtocol(BaseModel):
time: float
stir: bool
stir_speed: float <Add reagent="ethanol" vessel="main_reactor" volume="2.7 mL"/>
<Add event="A" mass="19.3 g" mol="0.28 mol" rate_spec="portionwise" reagent="sodium nitrite" time="1 h" vessel="main_reactor"/>
<Add mass="4.5 g" mol="16.2 mmol" reagent="(S)-2-phthalimido-6-hydroxyhexanoic acid" vessel="main_reactor"/>
<Add purpose="dilute" reagent="hydrochloric acid" vessel="main_reactor" volume="?"/>
<Add equiv="1.1" event="B" mol="25.2 mmol" rate_spec="dropwise" reagent="1-fluoro-2-nitrobenzene" time="20 min"
vessel="main_reactor" volume="2.67 mL"/>
<Add ratio="?" reagent="tetrahydrofuran|tert-butanol" vessel="main_reactor" volume="?"/>
viscous: bool
purpose: str
purpose: str 测完了能跑✅
class CentrifugeProtocol(BaseModel):
vessel: str
speed: float
time: float 自创的
time: float 没毛病
temp: float
class FilterProtocol(BaseModel):
vessel: str
filtrate_vessel: str
stir: bool <Filter vessel="filter"/>
stir_speed: float
temp: float
stir_speed: float <Filter filtrate_vessel="rotavap" vessel="filter"/>
temp: float 测完了能跑✅
continue_heatchill: bool
volume: float
@@ -118,7 +133,10 @@ class HeatChillProtocol(BaseModel):
temp: float
time: float <HeatChill pressure="1 mbar" temp_spec="room temperature" time="?" vessel="main_reactor"/>
<HeatChill temp_spec="room temperature" time_spec="overnight" vessel="main_reactor"/>
stir: bool
<HeatChill temp="256 °C" time="?" vessel="main_reactor"/>
<HeatChill reflux_solvent="methanol" temp_spec="reflux" time="2 h" vessel="main_reactor"/>
<HeatChillToTemp temp_spec="room temperature" vessel="main_reactor"/>
stir: bool 测完了能跑✅
stir_speed: float
purpose: str
@@ -133,7 +151,9 @@ class HeatChillStopProtocol(BaseModel):
class StirProtocol(BaseModel):
stir_time: float
stir_speed: float <Stir time="0.5 h" vessel="main_reactor"/>
settling_time: float
<Stir event="A" time="30 min" vessel="main_reactor"/>
<Stir time_spec="several minutes" vessel="filter"/>
settling_time: float 测完了能跑✅
class StartStirProtocol(BaseModel):
vessel: str
@@ -149,11 +169,11 @@ class TransferProtocol(BaseModel):
volume: float
amount: str = ""
time: float = 0
viscous: bool = False <Transfer from_vessel="main_reactor" to_vessel="rotavap"/>
viscous: bool = False
rinsing_solvent: str = ""
rinsing_volume: float = 0.0
rinsing_repeats: int = 0
solid: bool = False
solid: bool = False 这个protocol早该删掉了
class CleanVesselProtocol(BaseModel):
vessel: str
@@ -165,11 +185,11 @@ class CleanVesselProtocol(BaseModel):
class DissolveProtocol(BaseModel):
vessel: str
solvent: str
volume: float <Dissolve mass="2.9 g" mol="0.12 mol" reagent="magnesium" vessel="main_reactor"/>
amount: str = ""
temp: float = 25.0
time: float = 0.0
stir_speed: float = 0.0
volume: float <Dissolve mass="2.9 g" mol="0.12 mol" reagent="magnesium" vessel="main_reactor"/>
amount: str = "" <Dissolve mass="12.9 g" reagent="4-tert-butylbenzyl bromide" vessel="main_reactor"/>
temp: float = 25.0 <Dissolve solvent="diisopropyl ether" vessel="rotavap" volume="?"/>
time: float = 0.0 <Dissolve event="A" mass="?" reagent="pyridinone" vessel="main_reactor"/>
stir_speed: float = 0.0 测完了能跑✅
class FilterThroughProtocol(BaseModel):
from_vessel: str
@@ -183,16 +203,19 @@ class FilterThroughProtocol(BaseModel):
class RunColumnProtocol(BaseModel):
from_vessel: str
to_vessel: str <RunColumn Rf="?" column="column" from_vessel="rotavap" pct1="40 %" pct2="50 %" solvent1="ethyl acetate" solvent2="hexane" to_vessel="rotavap"/>
column: str
column: str 测完了能跑✅
class WashSolidProtocol(BaseModel):
vessel: str
solvent: str
volume: float
filtrate_vessel: str = ""
filtrate_vessel: str = "" <WashSolid repeats="4" solvent="water" vessel="main_reactor" volume="400 mL"/>
temp: float = 25.0 <WashSolid filtrate_vessel="rotavap" solvent="formic acid" vessel="main_reactor" volume="?"/>
stir: bool = False
stir_speed: float = 0.0
stir: bool = False <WashSolid solvent="acetone" vessel="rotavap" volume="5 mL"/>
<WashSolid solvent="ethyl alcohol" vessel="main_reactor" volume_spec="small volume"/>
<WashSolid filtrate_vessel="rotavap" mass="10 g" solvent="toluene" vessel="separator"/>
<WashSolid repeats_spec="several" solvent="water" vessel="main_reactor" volume="?"/>
stir_speed: float = 0.0 测完了能跑✅
time: float = 0.0
repeats: int = 1
@@ -219,4 +242,17 @@ class RecrystallizeProtocol(BaseModel):
class HydrogenateProtocol(BaseModel):
temp: str = Field(..., description="反应温度（如 '45 °C'）")
time: str = Field(..., description="反应时间（如 '2 h'）") <新写的，没问题>
vessel: str = Field(..., description="反应容器")
vessel: str = Field(..., description="反应容器")
还差
<dissolve>
<separate>
<CleanVessel vessel="centrifuge"/>
单位修复：
evaporate
heatchill
recrysitallize
stir
wash solid

142
test/experiments/comprehensive_protocol/comprehensive_station.json
View File

@@ -32,7 +32,11 @@
"separator_1",
"collection_bottle_1",
"collection_bottle_2",
"collection_bottle_3"
"collection_bottle_3",
"solid_dispenser_1",
"solid_reagent_bottle_1",
"solid_reagent_bottle_2",
"solid_reagent_bottle_3"
],
"parent": null,
"type": "device",
@@ -672,6 +676,98 @@
"data": {
"current_volume": 0.0
}
},
{
"id": "solid_dispenser_1",
"name": "固体粉末加样器",
"children": [],
"parent": "OrganicSynthesisStation",
"type": "device",
"class": "virtual_solid_dispenser",
"position": {
"x": 600,
"y": 300,
"z": 0
},
"config": {
"max_capacity": 100.0,
"precision": 0.001
},
"data": {
"status": "Ready",
"current_reagent": "",
"dispensed_amount": 0.0,
"total_operations": 0
}
},
{
"id": "solid_reagent_bottle_1",
"name": "固体试剂瓶1-氯化钠",
"children": [],
"parent": "OrganicSynthesisStation",
"type": "container",
"class": "container",
"position": {
"x": 550,
"y": 250,
"z": 0
},
"config": {
"volume": 500.0,
"reagent": "sodium_chloride",
"physical_state": "solid"
},
"data": {
"current_mass": 500.0,
"reagent_name": "sodium_chloride",
"physical_state": "solid"
}
},
{
"id": "solid_reagent_bottle_2",
"name": "固体试剂瓶2-碳酸钠",
"children": [],
"parent": "OrganicSynthesisStation",
"type": "container",
"class": "container",
"position": {
"x": 600,
"y": 250,
"z": 0
},
"config": {
"volume": 500.0,
"reagent": "sodium_carbonate",
"physical_state": "solid"
},
"data": {
"current_mass": 500.0,
"reagent_name": "sodium_carbonate",
"physical_state": "solid"
}
},
{
"id": "solid_reagent_bottle_3",
"name": "固体试剂瓶3-氯化镁",
"children": [],
"parent": "OrganicSynthesisStation",
"type": "container",
"class": "container",
"position": {
"x": 650,
"y": 250,
"z": 0
},
"config": {
"volume": 500.0,
"reagent": "magnesium_chloride",
"physical_state": "solid"
},
"data": {
"current_mass": 500.0,
"reagent_name": "magnesium_chloride",
"physical_state": "solid"
}
}
],
"links": [
@@ -802,7 +898,7 @@
"type": "fluid",
"port": {
"multiway_valve_2": "3",
"solenoid_valve_2": "in"
"solenoid_valve_2": "out"
}
},
{
@@ -812,7 +908,7 @@
"type": "fluid",
"port": {
"gas_source_1": "gassource",
"solenoid_valve_2": "out"
"solenoid_valve_2": "in"
}
},
{
@@ -964,6 +1060,46 @@
"solenoid_valve_3": "out",
"main_reactor": "top"
}
},
{
"id": "link_solid_dispenser_to_reactor",
"source": "solid_dispenser_1",
"target": "main_reactor",
"type": "resource",
"port": {
"solid_dispenser_1": "SolidOut",
"main_reactor": "top"
}
},
{
"id": "link_solid_bottle1_to_dispenser",
"source": "solid_reagent_bottle_1",
"target": "solid_dispenser_1",
"type": "resource",
"port": {
"solid_reagent_bottle_1": "top",
"solid_dispenser_1": "SolidIn"
}
},
{
"id": "link_solid_bottle2_to_dispenser",
"source": "solid_reagent_bottle_2",
"target": "solid_dispenser_1",
"type": "resource",
"port": {
"solid_reagent_bottle_2": "top",
"solid_dispenser_1": "SolidIn"
}
},
{
"id": "link_solid_bottle3_to_dispenser",
"source": "solid_reagent_bottle_3",
"target": "solid_dispenser_1",
"type": "resource",
"port": {
"solid_reagent_bottle_3": "top",
"solid_dispenser_1": "SolidIn"
}
}
]
}