initial commit

R_files/R_starter.py

@@ -0,0 +1,20 @@
+from MySQLdb import *
+from ftplib import FTP
+
+
+id_r = 2
+number_of_cores = 8
+#simion_dir = '"C:\\Program Files (x86)\\SIMION 8.0\\mystuff\\'
+simion_dir = '"C:\\Program Files\\SIMION-8.1\\mystuff\\'
+
+while True:
+	ftp = FTP('130.92.145.79')
+	ftp.login('R','optimizer')
+	break
+
+print 'connected to FTP server'
+ftp.retrbinary('RETR calculate_R_2.py', open('calculate_R_2.py','wb').write)
+ftp.retrbinary('RETR calculate_R_functions.py', open('calculate_R_functions.py', 'wb').write)
+ftp.retrbinary('RETR calculate_target_function.py', open('calculate_target_function.py', 'wb').write)
+
+execfile('calculate_R_2.py')

R_files/calculate_R_2.py

@@ -0,0 +1,75 @@
+import os, sys
+import time
+from ftplib import FTP
+from calculate_R_functions import *
+from calculate_target_function import calculate_target_function
+
+
+os.system('del batchfile_log.log')
+os.system('del geometry_particle_history.log')
+os.system('del tf_control_file.txt')
+os.system('del tf_control.txt')
+
+loop_counter = 0
+while True:
+	##############################################################################
+	#                           GET ALL INFOS FROM DATABASE                      #
+	##############################################################################
+
+	os.system('del optimizer_*_data.txt')
+	refiner_list, gemfile_exists,gemfile_name,iob_filename = get_simion_files_2()
+
+	# reserve jobs
+	X, volt_iteration = get_algo_param_3(id_r,number_of_cores)
+
+	if volt_iteration == 1 or loop_counter == 0:
+		print 'First voltage iteration!'
+		if gemfile_exists:
+			print 'found gemfile: %s' % gemfile_name
+			pa_name = gemfile_name.split('.')[0] + '.pa#'
+			os.system('simion gem2pa %s %s'%(gemfile_name, pa_name))
+			print 'converted gemfile to pa...'
+			print 'simion gem2pa %s %s'%(gemfile_name, pa_name)
+
+		for filename in refiner_list:
+			print 'simion --nogui --noprompt refine ' + simion_dir + filename[:-1] + '#"'
+			#os.system('simion --nogui --noprompt refine ' + simion_dir + filename[:-1] + '#"')
+		loop_counter += 1
+	##############################################################################
+	#                        FASTADJUST AN FLY IONS                              #
+	##############################################################################
+
+
+	print 'FAST ADJUSTING ADJUSTABLE VOLTAGES AND FLY EM'
+	#fastadjust_adj_voltages_and_fly_ions_2(X,iob_filename)
+	for i in range(len(X)):
+		fastadjust_adj_voltages_and_fly_ions_2(X[i],iob_filename,i)
+		os.system('START /B simion --default-num-particles=60001 --nogui --noprompt lua start_simion_session_' + str(i) + '.lua >>nul')
+	time.sleep(0.2)
+
+	print 'waiting for simulations to end...'
+	while True:
+		sum_flags = 0
+		for i in range(len(X)):
+			try:
+				f = open('finished_' + str(i) + '.txt')
+				sum_flags += int(f.readline()[0])
+			except:
+				pass
+				#print 'could not load : ' + 'finished_' + str(i) + '.txt'
+		if sum_flags == len(X):
+			break
+		time.sleep(0.2)
+
+	for i in range(len(X)):
+		os.system('echo 0 >finished_' + str(i) + '.txt ')
+	###############################################################################
+
+
+	target_function = calculate_target_function(len(X))
+	print target_function
+	print len(target_function)
+
+
+	write_zielf(id_r,target_function)
+