fix bugs

order/msd.py

@@ -25,13 +25,12 @@
 class meanSquareD(oto.Orientational):
     """mean square displacement"""
     def __init__(self, filename, center, bins=100):
-        super(Translational, self).__init__(filename, center, bins)
+        super(meanSquareD, self).__init__(filename, center, bins)
 
     def mean_square_displacement(self, max_t = 1000, freq = 1):
         """compute mean square displacement"""
         #progress bar
-        frames = int(self.traj.n_frames / freq)
-        bar = ChargingBar('Processing', max=frames, 
+        bar = ChargingBar('Processing', max=max_t, 
         suffix='%(percent).1f%% - %(eta)ds')
 
         for t in range(max_t):
@@ -40,8 +39,8 @@ def mean_square_displacement(self, max_t = 1000, freq = 1):
             for i in range(0, self.traj.n_frames, freq):
                 if i + t < self.traj.n_frames:
                     for j in range(self.traj.n_atoms):
-                        mid += np.square(np.substract(self.traj.coords[i][j],
-                                                      self.traj.coords[i+t][j]))
+                        mid += np.square(np.subtract(self.traj.coords[i][j],
+                                                     self.traj.coords[i+t][j]))
                         ct = np.sum(mid)
             ct = ct * 1.0 / (self.traj.n_atoms * (self.traj.n_frames - t))
             self.raw.append(ct)
@@ -51,10 +50,10 @@ def mean_square_displacement(self, max_t = 1000, freq = 1):
 
     def out_put(self, taskname='MSD'):
         """output raw data of msd"""
-        raw_data = self.fprefix + '_' + taskname + '_raw.dat'
+        raw_data = self.fprefix + '_' + taskname + '.dat'
         with open(raw_data, 'w') as f:
             f.write('#' + taskname + ' generated by Order: A Python Tool\n')
             f.write('#raw data\n')
 
             for k,i in enumerate(self.raw):
-                f.write('{}\t{}\n'.format(k, i))
+                f.write('{}\t{}\n'.format(k, i))