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

test/experiments/comprehensive_protocol/checklist.md

@@ -51,9 +51,9 @@ 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                 添加了缺失的参数，但是体积为0以及打印日志的问题修不好
     flowrate: float = 500
     transfer_flowrate: float = 2500
 
@@ -66,9 +66,9 @@ 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
 
@@ -77,14 +77,14 @@ class EvaporateProtocol(BaseModel):
     vessel: str
     pressure: float
     temp: float                         <Evaporate solvent="ethanol" vessel="rotavap"/>
-    time: float
+    time: float                         加完了
     stir_speed: float
 
 
 class EvacuateAndRefillProtocol(BaseModel):
     vessel: str
     gas: str                            <EvacuateAndRefill gas="nitrogen" vessel="main_reactor"/>
-    repeats: int
+    repeats: int                        处理完了
 
 class AddProtocol(BaseModel):
     vessel: str
@@ -95,21 +95,27 @@ 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
 
 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                         处理了
     continue_heatchill: bool
     volume: float
 
@@ -118,6 +124,9 @@ 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"/>
+                                        <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
     stir_speed: float
     purpose: str
@@ -133,7 +142,9 @@ 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            处理完了
 
 class StartStirProtocol(BaseModel):
     vessel: str
@@ -149,11 +160,11 @@ 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
@@ -166,8 +177,8 @@ 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
+    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
     stir_speed: float = 0.0
 
@@ -191,8 +202,8 @@ class WashSolidProtocol(BaseModel):
     volume: float
     filtrate_vessel: str = ""
     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"/>
+    stir_speed: float = 0.0     处理完了
     time: float = 0.0
     repeats: int = 1