fixed shape classic errors

updated version
GrupEstructuraElectronicaSimetria · Oct 25, 2020 · c6403e6 · c6403e6
1 parent 734cba9
commit c6403e6
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Showing 3 changed files with 16 additions and 9 deletions.
diff --git a/cosymlib/__init__.py b/cosymlib/__init__.py
@@ -1,4 +1,4 @@
-__version__ = '0.8.7'
+__version__ = '0.8.8'
 
 from cosymlib.molecule import Molecule, Geometry
 from cosymlib import file_io
@@ -582,12 +582,12 @@ def get_path_parameters(self, shape_label1, shape_label2, central_atom=0):
 
     def print_minimum_distortion_path_shape(self, shape_label1, shape_label2, central_atom=0,
                                             min_dev=0, max_dev=15, min_gco=0, max_gco=101,
-                                            num_points=20, output_name=None):
+                                            num_points=20, output=None):
 
-        if output_name is not None:
-            output = open(output_name + '_pth.csv', 'w')
-            output2 = open(output_name + '_pth.xyz', 'w')
-            output3 = open(output_name, 'w')
+        if output is not None:
+            output = open(output + '_pth.csv', 'w')
+            output2 = open(output + '_pth.xyz', 'w')
+            output3 = open(output, 'w')
         else:
             output = sys.stdout
             output2 = sys.stdout
@@ -643,7 +643,7 @@ def print_minimum_distortion_path_shape(self, shape_label1, shape_label2, centra
                                             positions=structure, name='map_structure{}'.format(ids)))
         output2.write(file_io.get_file_xyz_txt(test_structures))
 
-        if output_name is None:
+        if output is None:
             import matplotlib.pyplot as plt
             plt.plot(path[0], path[1], 'k', linewidth=2.0)
             plt.scatter(np.array(csm[label1_name])[filter_mask],

diff --git a/scripts/shape_classic b/scripts/shape_classic
@@ -59,18 +59,25 @@ if args.input_file is not None:
                 reference_polyhedron.append(tools.get_shape_label(int(number), options['%n_atoms']))
 
     if options['%fullout']:
+        output_name = open(output_name + '.tab', 'w')
+        symobj.print_shape_measure(reference_polyhedron,
+                                   central_atom=central_atom,
+                                   output=output_name)
         symobj.print_shape_structure(reference_polyhedron,
                                      central_atom=central_atom,
                                      output=output_name)
+
     elif options['%path']:
+        output_name = open(output_name + '.tab', 'w')
         if len(reference_polyhedron) > 2:
             print('Error. No more than two labels can be specified for a path calculation')
             exit()
         symobj.print_minimum_distortion_path_shape(reference_polyhedron[0],
                                                    reference_polyhedron[1],
                                                    central_atom=central_atom,
-                                                   output_name=output_name)
+                                                   output=output_name)
     else:
+        output_name = open(output_name + '.tab', 'w')
         symobj.print_shape_measure(reference_polyhedron,
                                    central_atom=central_atom,
                                    output=output_name)

diff --git a/scripts/shape_map b/scripts/shape_map
@@ -121,6 +121,6 @@ if args.map:
                                                       min_gco=args.min_gco,
                                                       max_gco=args.max_gco,
                                                       num_points=args.n_points,
-                                                      output_name=args.output_name)
+                                                      output=args.output_name)
 
 print_footer(common_output)