Minor refactoring

tools/analyze_phonons.py

@@ -297,7 +297,7 @@ def print_cumulative_thermal_conductivity(analyze_obj, cumulative_mode, file_res
                       + str(beg_s) + " " + str(end_s) \
                       + " " + isotope + " " + file_isotope \
                       + " " + str(max_len) + " " \
-                      + str(d_len) + " " + options.temp + " "\
+                      + str(d_len) + " " + options.temp + " " \
                       + str(options.nsample) + " " \
                       + options.gridtype
 

tools/interface/LAMMPS.py

@@ -191,7 +191,8 @@ def _print_displacements_and_forces(self, lammps_files, file_offset):
                                                                                 f[i, 1],
                                                                                 f[i, 2]))
         else:
-            raise RuntimeError("Could not find ITEM: TIMESTEP keyword in the dump file %s" % lammps_files[0])
+            raise RuntimeError("Could not find ITEM: "
+                               "TIMESTEP keyword in the dump file %s" % lammps_files[0])
 
     @staticmethod
     def _compute_lattice_vector_from_boxparams(box_params):
@@ -292,7 +293,8 @@ def _print_displacements(self, lammps_files, file_offset):
                                                            disp[i, 2]))
 
         else:
-            raise RuntimeError("Could not find ITEM: TIMESTEP keyword in the dump file %s" % lammps_files[0])
+            raise RuntimeError("Could not find ITEM: "
+                               "TIMESTEP keyword in the dump file %s" % lammps_files[0])
 
     def _print_atomicforces(self, lammps_files, file_offset):
 
@@ -344,7 +346,7 @@ def _set_unit_conversion_factor(self, str_unit):
 
     def _set_output_flags(self, output_flags):
         self._print_disp, self._print_force, \
-        self._print_energy, self._print_born = output_flags
+            self._print_energy, self._print_born = output_flags
 
     def _set_number_of_zerofill(self, npattern):
 

tools/interface/OpenMX.py

@@ -110,13 +110,13 @@ def load_initial_structure(self, file_original):
                 lavec.append([float(t) for t in line.strip().split()])
 
             if ipos_lavec > ipos_coord:
-                common_settings.extend(lines[:ipos_coord-1])
-                common_settings.extend(lines[fpos_coord+1:ipos_lavec-1])
-                common_settings.extend(lines[fpos_lavec+1:])
+                common_settings.extend(lines[:ipos_coord - 1])
+                common_settings.extend(lines[fpos_coord + 1:ipos_lavec - 1])
+                common_settings.extend(lines[fpos_lavec + 1:])
             else:
-                common_settings.extend(lines[:ipos_lavec-1])
-                common_settings.extend(lines[fpos_lavec+1:ipos_coord-1])
-                common_settings.extend(lines[fpos_coord+1:])
+                common_settings.extend(lines[:ipos_lavec - 1])
+                common_settings.extend(lines[fpos_lavec + 1:ipos_coord - 1])
+                common_settings.extend(lines[fpos_coord + 1:])
 
         x_frac0 = np.array(x_frac0)
         lavec = np.array(lavec).transpose()
@@ -366,7 +366,7 @@ def _set_unit_conversion_factor(self, str_unit):
 
     def _set_output_flags(self, output_flags):
         self._print_disp, self._print_force, \
-        self._print_energy, self._print_born = output_flags
+            self._print_energy, self._print_born = output_flags
 
     @property
     def nat(self):

tools/interface/QE.py

@@ -10,11 +10,13 @@
 # or http://opensource.org/licenses/mit-license.php for information.
 #
 from __future__ import print_function
-import numpy as np
-import math
+
 import copy
+import math
 import sys
 
+import numpy as np
+
 
 class QEParser(object):
 
@@ -765,7 +767,7 @@ def _set_unit_conversion_factor(self, str_unit):
 
     def _set_output_flags(self, output_flags):
         self._print_disp, self._print_force, \
-        self._print_energy, self._print_born = output_flags
+            self._print_energy, self._print_born = output_flags
 
     @property
     def nat(self):
@@ -918,7 +920,7 @@ def _get_coordinates_pwout(self, pwout_file):
             line = f.readline()
 
         if not found_tag:
-            #print("%s tag not found in %s" % (search_flag, pwout_file), file=sys.stderr)
+            # print("%s tag not found in %s" % (search_flag, pwout_file), file=sys.stderr)
             return None
 
         x = self._celldm[0] * np.dot(x, self._inverse_lattice_vector.transpose()) \
@@ -1030,7 +1032,7 @@ def _get_borninfo_phout(phout_file):
 
         found_tag1 = False
         found_tag2 = False
-        
+
         while line:
             if search_tag1 in line:
                 found_tag1 = True
@@ -1055,5 +1057,3 @@ def _get_borninfo_phout(phout_file):
         dielec = np.reshape(np.array(dielec[9:]), (3, 3))
         borncharge = np.reshape(np.array(borncharge), (nat2, 3, 3))
         return dielec, borncharge[:nat2 // 2, :, :]
-
-

tools/interface/xTAPP.py

@@ -238,11 +238,12 @@ def _set_unit_conversion_factor(self, str_unit):
         else:
             raise RuntimeError("This cannot happen.")
 
-        self._force_conversion_factor = self._energy_conversion_factor / self._disp_conversion_factor
+        self._force_conversion_factor = (self._energy_conversion_factor
+                                         / self._disp_conversion_factor)
 
     def _set_output_flags(self, output_flags):
         self._print_disp, self._print_force, \
-        self._print_energy, self._print_born = output_flags
+            self._print_energy, self._print_born = output_flags
 
     @property
     def nat(self):

tools/plotband.py

@@ -230,7 +230,7 @@ def preprocess_data(files, unitname, normalize_xaxis, emin=None, emax=None):
         = gridspec_setup(data_merged, xtickslabels, xticksvars)
 
     return naxes, xticks_grids, xticklabels_grids, \
-           xmin, xmax, ymin, ymax, data_merged_grids
+        xmin, xmax, ymin, ymax, data_merged_grids
 
 
 def run_plot(files, nax, xticks_ax, xticklabels_ax, xmin_ax, xmax_ax, ymin, ymax,
@@ -318,7 +318,7 @@ def run_plot(files, nax, xticks_ax, xticklabels_ax, xmin_ax, xmax_ax, ymin, ymax
         print("Number of files = %d" % nfiles)
 
     nax, xticks_ax, xticklabels_ax, xmin_ax, xmax_ax, ymin, ymax, \
-    data_merged_ax = preprocess_data(
+        data_merged_ax = preprocess_data(
         files, options.unitname, options.normalize_xaxis, options.emin, options.emax)
 
     run_plot(files, nax, xticks_ax, xticklabels_ax,