working

automated-iv-curves/SIM928_commands.py

@@ -15,10 +15,10 @@ def V_source_state(on_off = 'off'):
 # Set voltage of SIM928
 def set_voltage(V_value=1e-3):  
     if abs(V_value) < 1e-3:
-        print ('Voltage too low (<|3 mV|), it is set to 0 mV')
+        print ('\nVoltage too low (<|3 mV|), it is set to 0 mV')
         V_value = 0
     elif abs(V_value) > 39:
-        print ('Voltage setting too high (>39V), it is set to 39V')
+        print ('\nVoltage setting too high (>39V), it is set to 39V')
         V_value = 40e-3
     V_value = round(V_value,3) # rounding to mV, otherwise the source does not set the voltage because it lacks the precision
     command = 'VOLT ' + str(V_value) # set voltage

automated-iv-curves/config.toml

@@ -1,16 +1,16 @@
 # Experiment parameters
 [experiment]
-V_start = -1.0
-step_size = 0.5
-V_end = 1.0
-time_average = 3 # time over which to collect voltage average (time per measurement)
-sample_name = "test"
-contact_1 = "test1"
-contact_2 = "test1"
-light = "MIR"
+V_start = -0.1
+step_size = 0.01
+V_end = 0.1
+time_average = 2 # time over which to collect voltage average (time per measurement)
+sample_name = "barrucada?"
+contact_pos = "B"
+contact_neg = "C"
+light = "dark"
 temp = 300
 amplifier = "SR570"
-gain = 1e7 # amplifier gain 
+gain = 1e4 # amplifier gain 
 
 
 # Instrument addresses: typically do NOT need to be changed
@@ -21,7 +21,7 @@ SIM928_port = 1
 
 # V_start, step size, V_end, time average, sample name, contact 1, contact 2, light, temperature, amplifier, amplifier gain
 # V_scan(-1.0, 0.05, 1.0, .1, "test", "test1", "test1", "MIR", 300, "SR570", 10**(7)) #amplifier sensitivity = 1/gain
-#V_scan(-1.0, 0.1, 1.0, 1.0, "SHADWELL", "posContactC", "negContactF", "MIR", 18, "SR570", 10**(8)) #amplifier sensitivity = 1/gain
+# V_scan(-1.0, 0.1, 1.0, 1.0, "SHADWELL", "posContactC", "negContactF", "MIR", 18, "SR570", 10**(8)) #amplifier sensitivity = 1/gain
 #V_scan(0.0, 0.1, 1.0, 1.0, "Sun", "posContactB", "negContactH", "MIR", 18, "SR570", 10**(9)) #amplifier sensitivity = 1/gain
 #V_scan(0.0, 0.2, -2.0, 1.0, "Sun", "posContactB", "negContactH", "MIR", 18, "SR570", 10**(9)) #amplifier sensitivity = 1/gain
 #V_scan(0.0, 0.2, 2.0, 1.0, "Sun", "posContactB", "negContactH", "MIR", 18, "SR570", 10**(9)) #amplifier sensitivity = 1/gain

automated-iv-curves/iv_functions.py

@@ -90,7 +90,7 @@ def measure_V(time_average=10, time_interval=0.2):
 # Function to do I-V measurements
 # Currently doesn't read the voltage that was set, due to issues with querying through mainframe
 # Errors caluclated incorrectly
-def V_scan(V_start=1e-3, step_size=1e-3, V_end=2e-3, time_average=10, sample_name='no_name', contact_1 = '', contact_2 = '', light = 'Dark', temp=777, amplifier='SR570', gain=10**3, number_of_loops=0):
+def V_scan(V_start=1e-3, step_size=1e-3, V_end=2e-3, time_average=10, sample_name='no_name', contact_pos = '', contact_neg = '', light = 'Dark', temp=777, amplifier='SR570', gain=10**3, number_of_loops=0):
     Keithley.clear() # clear the buffer
     gain = int(gain) # make sure the gain is an Int
 
@@ -106,85 +106,123 @@ def V_scan(V_start=1e-3, step_size=1e-3, V_end=2e-3, time_average=10, sample_nam
     SIM900_comm.send_command(SIM900, SIM928_port, SIM928_comm.V_source_state("off")) #set source off
     
     # open a file to write data to 
-    # file_path = Path(__file__).parent / "data" 
-    # time_start = datetime.datetime.now().strftime("%d%m%Y_%H%M%S")
-    # filename_root = "iv_%s_%s_%s_%s_%s_scan_at_%sK_%s" % \
-    # (time_start, sample_name, contact_1, contact_2, light, temp, amplifier)
-    # filename = filename_root + "_averaging%ss.txt" % (time_average)
-    # plotname = filename_root + "_averaging%ss.png" % (time_average)
-    # filename2 = filename_root + "_raw.txt"
-    # full_name = os.path.join(file_path, filename)
-    # full_plotname = os.path.join(file_path, plotname)
+    file_path = Path(__file__).parent / "data" 
+    filename_root = "iv_%s_%s_pos%s_neg%s_%s_scan_at_%sK_%s" % \
+    (data_id, sample_name, contact_pos, contact_neg, light, temp, amplifier)
+    filename = filename_root + "_averaging%ss.txt" % (time_average)
+    plotname = filename_root + "_averaging%ss.png" % (time_average)
+    filename2 = filename_root + "_raw.txt"
+    full_name = os.path.join(file_path, filename)
+    full_plotname = os.path.join(file_path, plotname)
     # full_name2 = os.path.join(file_path, filename2)
-    #data_file=open(str(full_name),'w')
-    # with open(str(full_name),'w') as data_file, open(str(full_name2),'w') as raw_V_file:
-        # data_file.write("Time\tVoltage_source[V]\tVoltage_meas[V]\tVoltage_meas_err[V]\tGain[V/A]\n")
+    data_file=open(str(full_name),'w')
+
+    # save metadata before loop
+    file_path = Path(__file__).parent / "data"
+    file_path.mkdir(exist_ok=True)
+    h5_path = file_path / f"{filename[0:-4]}.h5"
+    with h5py.File(h5_path, "w") as f:
+        f.attrs["V_start"] = V_start
+        f.attrs["step_size"] = step_size
+        f.attrs["V_end"] = V_end
+        f.attrs["time_average"] = time_average
+        f.attrs["sample_name"] = sample_name
+        f.attrs["contact_pos"] = contact_pos
+        f.attrs["contact_neg"] = contact_neg
+        f.attrs["light"] = light
+        f.attrs["temp"] = temp
+        f.attrs["amplifier"] = amplifier
+        f.attrs["gain"] = gain
+
+
+    with open(str(full_name),'w') as data_file: #, open(str(full_name2),'w') as raw_V_file:
+        data_file.write("Time\tVoltage_source[V]\tVoltage_avg[V]\tVoltage_meas_err[V]\tGain[V/A]\tVoltage_meas\n")
         # raw_V_file.write("Voltage_source[V]\tVoltage_meas[V]\n")
-        # just for ploting here
-    V_plot_list = []
-    V_err_plot_list = []
-    V_scan_plot_list = []
-    # A loop over all currents 
-    
-    i=0
-    # set_voltage(V_scan_list[0])
-    # time.sleep(5) #wait 3 sec to avoid large noise on first measurement
 
-    for V_scan_item in V_scan_list:
+        V_avg_list = []
+        V_err_list = []
+        V_source_list = []
+        V_raw_lists = []
+        time_list = []
         
-        time_start_iteration= datetime.datetime.now()
-        i = i+1
-        set_voltage(V_scan_item)
-        time.sleep(2) #wait 5 sec	for signal to settle
+        i=0
+        for V_scan_item in V_scan_list:
+            Keithley.clear() 
+            time_start_iteration= datetime.datetime.now()
+            
+            set_voltage(V_scan_item)
+            time.sleep(2) #wait 5 sec	for signal to settle
 
-        # measure+read+write the data          
-        V_source = V_scan_item
-#           V_source = read_source_V()
-        [V_list, V_avg, V_err] = measure_V(time_average=time_average, time_interval=0.2)
-        time_now = datetime.datetime.now()
+            # measure+read+write the data          
+            V_source = V_scan_item
+            # V_source = read_source_V()
+            
+            [V_list, V_avg, V_err] = measure_V(time_average=time_average, time_interval=0.2)
+            time_now = datetime.datetime.now()
+            
 
-        # data_string = "%s\t %s\t %.5e\t %.5e\t %s\n"\
-                                                # %(time_now, V_source, V_avg, V_err, gain)
-        # data_file.write(str(data_string)) 
-        # raw_V_file.write("%s\t %s\n" %(V_source, V_list))
+            data_string = "%s\t %s\t %.5e\t %.5e\t %s\t %s\n"\
+                                                    %(time_now, V_source, V_avg, V_err, gain, V_list)
+            data_file.write(str(data_string)) 
+            # raw_V_file.write("%s\t %s\n" %(V_source, V_list))
 
-        V_plot_list.append(V_avg)
-        V_err_plot_list.append(V_err)
-        V_scan_plot_list.append(V_source)
+            V_avg_list.append(V_avg)
+            V_err_list.append(V_err)
+            V_source_list.append(V_source)
+            V_raw_lists.append(V_list)
+            time_list.append(time_now)
 
-        #make plot
-        # plt.close()
-        # plt.plot(V_scan_plot_list, V_plot_list,'+')
-        # plt.title(str(sample_name))
-        # plt.xlabel('Source Voltage / V')
-        # plt.ylabel('Measured voltage / V')
-        # plt.draw()
-        # plt.pause(0.1)
-        # plt.show(block=False) 
-        # iteration_time = datetime.datetime.now()-time_start_iteration
-        # remaining_time = iteration_time.total_seconds()*(len(V_scan_list)-i)
-        # print(time.strftime('Remaining time: %H:%M:%S',\
-        #                     time.gmtime(remaining_time)))
+            #make plot
+            plt.close()
+            plt.plot(V_source_list, V_avg_list,'+')
+            plt.title(str(sample_name))
+            plt.xlabel('Source Voltage / V')
+            plt.ylabel('Measured voltage / V')
+            plt.draw()
+            plt.pause(0.1)
+            plt.show(block=False) 
+
+            i = i+1
+            iteration_time = datetime.datetime.now()-time_start_iteration
+            remaining_time = iteration_time.total_seconds()*(len(V_scan_list)-i)
+            print(time.strftime('Remaining time: %H:%M:%S',\
+                                time.gmtime(remaining_time)))
+            
+        I_list = [V_avg_list[i]/gain for i in range(len(V_avg_list))]
+        I_err_list = [V_err_list[i]/gain for i in range(len(V_avg_list))]  
+
+        plt.close()
+        plt.figure()
+        plt.errorbar(V_source_list, I_list, yerr=I_err_list, fmt='+')
+        plt.title(str(sample_name))
+        plt.xlabel('Source Voltage / V')
+        plt.ylabel('I / A')
+        plt.tight_layout()
+        plt.grid()
+
+        plt.savefig(full_plotname)
+        plt.draw()
+        plt.pause(0.001)
+        plt.show(block=False)
+        plt.close()
         
-    I_list = [V_plot_list[i]/gain for i in range(len(V_plot_list))]
-    I_err_list = [V_err_plot_list[i]/gain for i in range(len(V_plot_list))]  
-    # plt.close()
-    # plt.figure()
-    # plt.errorbar(V_scan_plot_list, I_list, yerr=I_err_list, fmt='+')
-    # plt.title(str(sample_name))
-    # plt.xlabel('Source Voltage / V')
-    # plt.ylabel('I / A')
-    # plt.tight_layout()
-    # plt.grid()
-
-    # plt.savefig(full_plotname)
-    # plt.draw()
-    # plt.pause(0.001)
-    # plt.show(block=False)
-    # plt.close()
-    
-    # data_file.close() 
+    data_file.close() 
     # raw_V_file.close()
+
+    file_path = Path(__file__).parent / "data"
+    file_path.mkdir(exist_ok=True)
+
+    with h5py.File(file_path / f"{filename[0:-4]}.h5", "a") as f:
+        f.create_dataset("V_source", data=V_source_list)
+        f.create_dataset("V_avg", data=V_avg_list)
+        f.create_dataset("V_err", data=V_err_list)
+        f.create_dataset("V_raw", data=V_raw_lists)
+        f.create_dataset("timestamps", data=[str(t) for t in time_list])
+        f.create_dataset("I", data=I_list)
+        f.create_dataset("I_err", data=I_err_list)
+    
+
+
     set_voltage(0)
 
     SIM900_comm.send_command(SIM900, SIM928_port, SIM928_comm.V_source_state("off")) #set source off

automated-iv-curves/iv_run.py

@@ -2,8 +2,10 @@
 
 import tomllib
 from iv_functions import V_scan
+import h5py
 
 with open("automated-iv-curves/config.toml", "rb") as f:
     cfg = tomllib.load(f)
 
-V_scan(**cfg["experiment"])
+V_scan(**cfg["experiment"])
+