fix python 2 and python 3 compatible issues

ipudu · Jul 10, 2018 · 02dcec8 · 02dcec8
1 parent 00bcc56
commit 02dcec8
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Showing 4 changed files with 8 additions and 6 deletions.
diff --git a/order/order.py b/order/order.py
@@ -54,20 +54,20 @@ def command_line_runner():
             util.output_task('tto', args['frequency'], args['bins'], args['center'])
             tasker = tto.Translational(reader, args['center'], args['bins'])
             tasker.translational_param(args['frequency'])
-            tasker.out_put('TTO', 'Sk')
+            tasker.out_put('tto', 'Sk')
 
         if 'avc' in args['task']:
             util.output_task('avc', args['frequency'], args['bins'], args['center'])
             tasker = avc.VoronoiCell(reader, args['center'], args['bins'])
             tasker.asphericity(args['frequency'])
-            tasker.out_put('AVC', 'Eta')
+            tasker.out_put('avc', 'Eta')
 
         if 'msd' in args['task']:
             util.output_task('msd', args['frequency'], args['bins'], args['center'])
             tasker = msd.meanSquareD(reader, args['center'], args['bins'])
             #TODO:
             tasker.mean_square_displacement(1000, args['frequency'])
-            tasker.out_put('MSD')
+            tasker.out_put('msd')
 
         if 'interface' in args['task']:
             tasker = interface.WillardChandler(reader, 'interface.in')

diff --git a/order/oto.py b/order/oto.py
@@ -85,7 +85,7 @@ def orientational_param(self, freq = 1):
             bar.next()
         bar.finish()
 
-    def out_put(self, taskname='OTO', param_name='Q'):
+    def out_put(self, taskname='oto', param_name='Q'):
         """output raw data and distribution"""
         raw_data = self.fprefix + '_' + taskname + '_raw.dat'
         with open(raw_data, 'w') as f:

diff --git a/order/plot.py b/order/plot.py
@@ -38,6 +38,7 @@ def plot_distribution(self):
         plt.rcParams['figure.titlesize'] = 12
 
         #clean last plot
+        plt.figure()
         plt.clf()
 
         if self.taskname == 'oto':
@@ -61,7 +62,7 @@ def plot_distribution(self):
 
         plt.plot(x,y,linewidth=2.0)
 
-        figure = self.fprefix + '_' + self.taskname.upper() + '.pdf'
+        figure = self.fprefix + '_' + self.taskname + '.pdf'
         plt.savefig(figure, bbox_inches="tight")
 
     def plot_ionic(self):

diff --git a/order/tto.py b/order/tto.py
@@ -18,6 +18,7 @@
 import six
 from six.moves import range
 
+
 import numpy as np
 from progress.bar import ChargingBar
 from . import oto
@@ -39,7 +40,7 @@ def translational_param(self, freq = 1):
             for j in range(self.traj.n_atoms):
                 if self.traj.atom_names[i][j] == self.center:
                     s = 0.0
-                    norms = np.array(map(np.linalg.norm, foo[j]))
+                    norms = np.array([np.linalg.norm(x) for x in foo[j]])
                     sqrt_norms = (norms - norms.mean()) ** 2
                     sum_norms = sqrt_norms.sum() / ( 4 * norms.mean() ** 2)
                     s = 1 - 1 / 3 * sum_norms