add combine-qti

combine-qti/combine-qti.py

@@ -0,0 +1,104 @@
+#!/usr/bin/python2
+# combine-qti
+# Copyright (C) 2014 Evgeniy Alekseev <esalexeev@gmail.com>
+#
+# This program is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with this program. If not, see <http://www.gnu.org/licenses/>.
+
+
+import argparse, os
+
+
+def readData(file):
+    """function to read data"""
+    windows = 0
+    data = []
+    # preread
+    with open (file, "r") as input:
+        for line in input:
+            if (line.split('\t')[0] == "<windows>"):
+                windows = int(line.split('\t')[1].strip())
+    with open (file, "r") as input:
+        for window in range(windows):
+            for line in input:
+                if (line.strip() == "<table>"):
+                    data.append("<table>\n")
+                    break
+                elif (line.strip() == "<multiLayer>"):
+                    data.append("<multiLayer>\n")
+                    break
+            for line in input:
+                if (line.strip() == '</table>'):
+                    data.append("</table>\n")
+                    break
+                elif (line.strip() == '</multiLayer>'):
+                    data.append("</multiLayer>\n")
+                    break
+                data.append(line)
+    return windows, data
+
+
+def printHeader(file, windowsNum=1):
+    """function to print header"""
+    iter = 0
+    suffix = ""
+    while (os.path.exists(file + suffix)):
+        suffix = ".%i" % (iter)
+        iter = iter + 1
+    if (suffix != ""):
+        os.rename(file, file + suffix)
+    with open(file, "w") as output:
+        output.write("QtiPlot 0.9.8 project file\n")
+        output.write("<scripting-lang>\tPython\n")
+        output.write("<windows>\t%i\n" % (windowsNum))
+
+
+def printData(file, data):
+    """function to print data"""
+    with open(file, "a") as output:
+        for line in data:
+            output.write(line)
+
+
+if __name__ == "__main__":
+    parser = argparse.ArgumentParser(description = 'Combine several *.qti files into one')
+    parser.add_argument('-d', '--directory', dest = 'dir',
+        help = 'Directory with input files or use --input', action = 'store', default = False)
+    parser.add_argument('-i', '--input', dest = 'input',
+        help = 'Input files, comma separated', action = 'store', default = False)
+    parser.add_argument('-o', '--output', dest = 'output',
+        help = 'Output file', action = 'store', default = False)
+    args = parser.parse_args()
+
+    input = []
+    if (args.dir):
+        if (os.path.isdir(args.dir)):
+            input = [file for file in os.listdir(args.dir) if (os.path.splitext(file)[1] == ".qti")]
+    else:
+        if (args.input):
+            for file in args.input.split(','):
+                if (os.path.isfile(file)): input.append(file)
+    output = args.output
+    if (not input) or (not output):
+        print ("Files are not set")
+        exit()
+
+    totalWindows = 0
+    totalData = []
+    for file in input:
+        windows, data = readData(file)
+        totalWindows = totalWindows + windows
+        totalData.append(data)
+    printHeader(output, totalWindows)
+    for data in totalData:
+        printData(output, data)

get_dipole/get-dipole.py

@@ -5,8 +5,8 @@ import argparse, math
 
 def get_aver_dipole(dipole):
     """function to get average dipole moment"""
-    aver_dipole = math.sqrt((dipole[0] * dipole[0] + 
-        dipole[1] * dipole[1] + 
+    aver_dipole = math.sqrt((dipole[0] * dipole[0] +
+        dipole[1] * dipole[1] +
         dipole[2] * dipole[2]))
     aver_dipole = round(aver_dipole, 4)
     return aver_dipole
@@ -56,15 +56,15 @@ if __name__ == "__main__":
     parser.add_argument('-v', '--vector', dest = 'vector',
         help = 'Return vector', action = 'store_true', default = False)
     args = parser.parse_args()
-    
+
     if ((not args.input) or (not args.coord)):
         print "Input files are not set"
-        exit
-    
+        exit()
+
     charges = get_charges(args.input)
     coords = get_coordinates(args.coord)
     if (args.vector):
         print get_dipole(charges, coords)
     else:
         print get_aver_dipole(get_dipole(charges, coords))
-    
+