Update blop and prepare agent

scripts/_data_export.py

@@ -200,6 +200,9 @@ def read_qepro_by_stream(uid, stream_name='primary', data_agent='tiled', beamlin
 
 
 
+## TODO: add reading scattering data
+# def read_scatter_by_stream(uid, stream_name='scattering', data_agent='tiled', beamline_acronym='xpd-ldrd20-31'):
+#     return scatter_dic, metadata_dic
 
 ## Get uids from data folders through daily experiments for export database for ML
 ## Read uid from **fluorescence** folder

scripts/_pdf_calculator.py

@@ -0,0 +1,141 @@
+import pymatgen as pm
+from diffpy.pdffit2 import PdfFit
+from diffpy.Structure import loadStructure
+from pymatgen.io.cif import CifWriter
+from pymatgen.io.cif import CifParser
+import os
+
+
+
+def _no_oxidation_cif(cif_file):
+    parser = CifParser(cif_file)
+    structure = parser.get_structures()[0] 
+    structure.remove_oxidation_states()
+    print(structure, '\n\n')
+    cif_pym = os.path.dirname(cif_file) + '/' + os.path.basename(cif_file)[:-4] + '_pym.cif'
+    w = CifWriter(structure,symprec=0.1)
+    w.write_file(cif_pym)
+
+    return cif_pym
+
+
+
+def _pdffit2_CsPbX3(gr_data, cif_list, qmax=18, qdamp=0.031, qbroad=0.032, fix_APD=True):
+
+    # Initialize the CifParser with the path to your .cif file
+    # Parse the .cif file
+    pym_cif = []
+    for cif in cif_list:
+        cif_new = _no_oxidation_cif(cif)
+        pym_cif.append(cif_new)
+
+    # Create new PDF calculator object.
+    pf = PdfFit()
+
+    # Load experimental x-ray PDF data
+    # qmax = 20.0  # Q-cutoff used in PDF calculation in 1/A
+    # qdamp = 0.03 # instrument Q-resolution factor, responsible for PDF decay
+    pf.read_data(gr_data, 'X', qmax, qdamp)
+
+    # Load and add structure ------------------------------------------------------------------
+    for pym in pym_cif:
+        stru = loadStructure(pym)
+        stru.Uisoequiv = 0.04
+        stru.title = os.path.basename(pym)[:-4]
+        #Add loaded .cif 
+        pf.add_structure(stru)
+
+    # set contrains for lattice parameter, ADP
+    _set_CsPbBr3_constrain(pf, phase_idx=1, fix_APD=fix_APD)
+
+    # set constrain for data scale
+    pf.constrain(pf.dscale, '@902')
+    pf.setpar(902, 0.65)
+
+    # Set value for Qdamp, Qbraod
+    pf.setvar(pf.qdamp, qdamp)
+    pf.setvar(pf.qbroad, qbroad)
+
+    # Refine 
+    pf.pdfrange(1, 2.5, 60)
+    pf.refine()
+
+
+    phase_fraction = pf.phase_fractions()['mass']
+
+    particel_size = []
+    for i in range(pf.num_phases()):
+        pf.setphase(i+1)
+        particel_size.append(pf.getvar(pf.spdiameter))
+
+    return phase_fraction, particel_size
+
+
+
+'''
+lat_dic = {'a':11, 'b':12, 'c':13}
+'''
+def _set_CsPbBr3_constrain(PDF_calculator_object, phase_idx=1, fix_APD=True):
+    pf = PDF_calculator_object
+    pf.setphase(phase_idx)
+
+    # Refine lattice parameters a, b, c.
+    pf.constrain(pf.lat(1), "@11")
+    pf.constrain(pf.lat(2), "@12")
+    pf.constrain(pf.lat(3), "@13")
+    # set initial value of parameter @1, @2, @3
+    pf.setpar(11, pf.lat(1))
+    pf.setpar(12, pf.lat(2))
+    pf.setpar(13, pf.lat(3))
+
+    # Refine phase scale factor.  Right side can have formulas.
+    pf.constrain('pscale', '@111')
+    pf.setpar(111, 0.5)
+    # pf.setpar(20, pf.getvar(pf.pscale) / 2.0)
+
+    # Refine sharpening factor for correlated motion of close atoms.
+    pf.constrain(pf.delta2, '@122')
+    pf.setpar(122, 6.87)
+
+    # Refine diameter for the spherical particle
+    pf.constrain(pf.spdiameter, '@133')
+    pf.setpar(133, 46)
+
+    # Set temperature factors isotropic to each atom
+    # idx starts from 1 not 0
+    # 1-4: Cs
+    for idx in range(1, 5):
+        pf.constrain(pf.u11(idx), '@101')
+        pf.constrain(pf.u22(idx), '@101')
+        pf.constrain(pf.u33(idx), '@101')
+    pf.setpar(101, 0.029385)
+
+    # 5-8: Pb
+    for idx in range(5, 9):
+        pf.constrain(pf.u11(idx), '@102')
+        pf.constrain(pf.u22(idx), '@102')
+        pf.constrain(pf.u33(idx), '@102')
+    pf.setpar(102, 0.027296)
+
+    # 9-16: Br
+    for idx in range(9, 17):
+        pf.constrain(pf.u11(idx), '@103')
+        pf.constrain(pf.u22(idx), '@103')
+        pf.constrain(pf.u33(idx), '@103')
+    pf.setpar(103, 0.041577)
+
+    # 16-20: Br
+    for idx in range(17, 21):
+        pf.constrain(pf.u11(idx), '@104')
+        pf.constrain(pf.u22(idx), '@104')
+        pf.constrain(pf.u33(idx), '@104')
+    pf.setpar(104, 0.028164)
+
+
+    if fix_APD:
+        for par in [101, 102, 103, 104]:
+            pf.fixpar(par)
+
+
+
+

scripts/_synthesis_queue_RM.py

@@ -51,6 +51,11 @@ def synthesis_queue(
 		set_target_list = set_target_list.tolist()
 
 
+	# 0. stop infuese for all pumps
+	flowplan = BPlan('stop_group', pump_list + [wash_tube[1]])
+	RM.item_add(flowplan, pos=pos)
+
+
 	for i in range(len(rate_list)):
 		# for i in range(2): 
 		## 1. Set i infuese rates
@@ -76,7 +81,12 @@ def synthesis_queue(
 
 
 		## 2. Start infuese
-		flowplan = BPlan('start_group_infuse', pump_list, rate_list[i])
+		if precursor_list[-1] == 'Toluene':
+			flowplan = BPlan('start_group_infuse', pump_list[:-1], rate_list[i][:-1])
+
+		else:
+			flowplan = BPlan('start_group_infuse', pump_list, rate_list[i])
+
 		RM.item_add(flowplan, pos=pos)
 
 
@@ -110,6 +120,14 @@ def synthesis_queue(
 			restplan = BPlan('wait_equilibrium2', mixer_pump_list, ratio=rest_time)
 			RM.item_add(restplan, pos=pos)
 
+
+		## 3.1 Wait for 30 secpnds for post dilute
+		if precursor_list[-1] == 'Toluene':
+			flowplan = BPlan('start_group_infuse', [pump_list[-1]], [rate_list[i][-1]])
+			RM.item_add(flowplan, pos=pos)
+
+			restplan = BPlan('sleep_sec_q', 60)
+			RM.item_add(restplan, pos=pos)
 
 
 		## 4-1. Take a fluorescence peak to check reaction
@@ -155,7 +173,7 @@ def synthesis_queue(
 		######  Kafka analyze data here. #######
 
 		## 7. Wash the loop and mixer
-		wash_tube_queue(pump_list, wash_tube, rate_unit, 
+		wash_tube_queue2(pump_list, wash_tube, rate_unit, 
 						pos=[pos,pos,pos,pos,pos], 
 						zmq_control_addr=zmq_control_addr,
 						zmq_info_addr=zmq_info_addr)
@@ -209,6 +227,42 @@ def wash_tube_queue(pump_list, wash_tube, rate_unit,
 
 
 
+def wash_tube_queue2(pump_list, wash_tube, rate_unit, 
+					pos=[0,1,2,3,4], 
+					zmq_control_addr='tcp://localhost:60615', 
+					zmq_info_addr='tcp://localhost:60625'):
+
+	RM = REManagerAPI(zmq_control_addr=zmq_control_addr, zmq_info_addr=zmq_info_addr)
+
+	### Stop all infusing pumps
+	flowplan = BPlan('stop_group', pump_list)
+	RM.item_add(flowplan, pos=pos[0])
+
+
+	### Set up washing tube/loop
+	flowplan = BPlan('set_group_infuse2', [wash_tube[0], wash_tube[3]], [wash_tube[1], wash_tube[4]], 
+					rate_list=[wash_tube[2], wash_tube[5]], 
+					target_vol_list=['30 ml', '15 ml'], 
+					set_target_list=[False, False], 
+					rate_unit=rate_unit)
+	RM.item_add(flowplan, pos=pos[1])	
+
+
+	### Start washing tube/loop
+	flowplan = BPlan('start_group_infuse', [wash_tube[1], wash_tube[4]], [wash_tube[2], wash_tube[5]])
+	RM.item_add(flowplan, pos=pos[2])	
+
+
+	### Wash loop/tube for xxx seconds
+	restplan = BPlan('sleep_sec_q', wash_tube[6])
+	RM.item_add(restplan, pos=pos[3])	
+
+
+
+	### Stop washing
+	flowplan = BPlan('stop_group', [wash_tube[1], wash_tube[4]])
+	RM.item_add(flowplan, pos=pos[4])
+