clean example files

GrupEstructuraElectronicaSimetria · Apr 15, 2022 · f5914c8 · f5914c8
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Showing 18 changed files with 18 additions and 23 deletions.
diff --git a/examples/CpTiCl3.fchk → examples/data/CpTiCl3.fchk b/examples/CpTiCl3.fchk → examples/data/CpTiCl3.fchk
diff --git a/examples/connect.con → examples/data/connect.con b/examples/connect.con → examples/data/connect.con
diff --git a/examples/coord.cor → examples/data/coord.cor b/examples/coord.cor → examples/data/coord.cor
diff --git a/examples/coord.xyz → examples/data/coord.xyz b/examples/coord.xyz → examples/data/coord.xyz
diff --git a/examples/coord_2.xyz → examples/data/coord_2.xyz b/examples/coord_2.xyz → examples/data/coord_2.xyz
diff --git a/examples/ethane.xyz → examples/data/ethane.xyz b/examples/ethane.xyz → examples/data/ethane.xyz
diff --git a/examples/h.fchk → examples/data/h.fchk b/examples/h.fchk → examples/data/h.fchk
diff --git a/examples/h2.fchk → examples/data/h2.fchk b/examples/h2.fchk → examples/data/h2.fchk
diff --git a/examples/methane.pdb → examples/data/methane.pdb b/examples/methane.pdb → examples/data/methane.pdb
diff --git a/examples/pirrol.fchk → examples/data/pirrol.fchk b/examples/pirrol.fchk → examples/data/pirrol.fchk
diff --git a/examples/sf6.fchk → examples/data/sf6.fchk b/examples/sf6.fchk → examples/data/sf6.fchk
diff --git a/examples/sf6_freq.out → examples/data/sf6_freq.out b/examples/sf6_freq.out → examples/data/sf6_freq.out
diff --git a/examples/python_api.py → examples/general_api_example.py b/examples/python_api.py → examples/general_api_example.py
@@ -23,16 +23,16 @@ def print_csm(data):
     print('CSM ' + '  '.join(['{:7.3f}'.format(s) for s in data['csm']]))
 
 
-#geometries = file_io.get_geometry_from_file_xyz('../old_examples/coord.xyz')
-geometries = file_io.get_molecule_from_file_fchk('../old_examples/sf6.fchk', read_multiple=False)
+#geometries = file_io.get_geometry_from_file_xyz('data/coord.xyz')
+geometries = file_io.get_molecule_from_file_fchk('data/sf6.fchk', read_multiple=False)
 mol = Cosymlib(geometries,mode=2)
 
 print(mol.print_edensity_measure('c4'))
 
 
 # Get structures from files
-geometries_list = file_io.get_geometry_from_file_xyz('../old_examples/coord.xyz', read_multiple=True)
-fragments_list = file_io.get_geometry_from_file_cor('../old_examples/coord.cor', read_multiple=True)
+geometries_list = file_io.get_geometry_from_file_xyz('data/coord.xyz', read_multiple=True)
+fragments_list = file_io.get_geometry_from_file_cor('data/coord.cor', read_multiple=True)
 
 # Call shape as method of Geometry class
 print_shape_data(geometries_list)
@@ -54,7 +54,7 @@ def print_csm(data):
 print('\nSYMMETRY'
       '\n--------')
 
-geometries_list = file_io.get_geometry_from_file_pdb('../old_examples/methane.pdb', read_multiple=True)
+geometries_list = file_io.get_geometry_from_file_pdb('data/methane.pdb', read_multiple=True)
 print('measure C3: {} '.format(geometries_list[0].get_symmetry_measure('c3')))
 
 # Check multiple calls of symgroup one calculatioin
@@ -73,48 +73,43 @@ def print_csm(data):
 print('\nWFNSYM\n--------')
 
 
-molecule = file_io.get_molecule_from_file_fchk('h2.fchk', read_multiple=False)
-
+molecule = file_io.get_molecule_from_file_fchk('data/sf6.fchk', read_multiple=False)
 print(molecule.electronic_structure.coefficients_a)
-
 print(molecule.electronic_structure.basis)
+
 sym_l=[]
 coord_a=molecule.geometry._positions
 for at in range(len(molecule.electronic_structure.basis['atoms'])):
     sym_l.append(molecule.electronic_structure.basis['atoms'][at]['symbol'])
 print(sym_l)
 print(coord_a)
-measure_dict = molecule.get_wf_symmetry('C2v',
+measure_dict = molecule.get_wf_symmetry('Oh',
                                         axis=[0.000000, 0.000000, 1.000000],  # valor defecte
                                         # vector_axis2=[-2.027247,  0.000133, -0.898469],
                                         center=[0.002440, -0.000122,  0.017307])
 print_csm(measure_dict)
-
-
-
-
 print('\nCOSYMLIB\n--------')
 
-geometries_list = file_io.get_geometry_from_file_xyz('../old_examples/coord.xyz', read_multiple=True)
+geometries_list = file_io.get_geometry_from_file_xyz('data/coord.xyz', read_multiple=True)
 molecules_set = Cosymlib(geometries_list)
 
 molecules_set.print_shape_measure(['SP-4'], central_atom=1)
 molecules_set.print_minimum_distortion_path_shape('SP-4', 'SS-4', central_atom=1, max_dev=103, max_gco=200)
 
-geometries_list = file_io.get_geometry_from_file_xyz('../old_examples/coord_2.xyz', read_multiple=True)
+geometries_list = file_io.get_geometry_from_file_xyz('data/coord_2.xyz', read_multiple=True)
 molecules_set = Cosymlib(geometries_list)
 
-print('\n\n***********{}************'.format('print_electronic_symmetry_measure()'))
-
-molecules_list = file_io.read_generic_structure_file('../old_examples/pirrol.fchk', read_multiple=True)
-molecules_set = Cosymlib(molecules_list)
 print('\n\n***********{}************'.format('print_info()'))
 molecules_set.print_info()
 print('\n\n***********{}************'.format('print_wnfsym_irreducible_repr()'))
 molecules_set.print_esym_irreducible_repr('C2v', axis=[0, 0, 1], center=[0.0, 0.0, 0.0])
 print('\n\n***********{}************'.format('print_wnfsym_sym_ovelap()'))
 molecules_set.print_esym_sym_overlaps('C2v', axis=[0, 0, 1], center=[0.0, 0.0, 0.0])
 print('\n\n***********{}************'.format('print_wnfsym_sym_matrices()'))
-molecules_set.print_esym_matrices('C2v', axis=[0, 0, 1], center=[0.0, 0.0, 0.0])
 
-molecules_set.print_edensity_measure('C2v', axis=[0, 0, 1], center=[1.0, 0.0, 0.0])
+molecules_list = file_io.read_generic_structure_file('data/pirrol.fchk', read_multiple=True)
+molecules_set = Cosymlib(molecules_list)
+molecules_set.print_esym_matrices('C5', axis=[1, 0, 0], center=[0.0, 0.0, 0.0])
+
+print('\n\n***********{}************'.format('print_electronic_symmetry_measure()'))
+molecules_set.print_edensity_measure('C5', axis=[1, 0, 0], center=[0.0, 0.0, 0.0])
diff --git a/examples/cosym.yaml → examples/input_files/cosym.yaml b/examples/cosym.yaml → examples/input_files/cosym.yaml
diff --git a/examples/example_shape_file → examples/input_files/example_shape_file b/examples/example_shape_file → examples/input_files/example_shape_file
diff --git a/examples/shape.yaml → examples/input_files/shape.yaml b/examples/shape.yaml → examples/input_files/shape.yaml
diff --git a/examples/symgroup.yaml → examples/input_files/symgroup.yaml b/examples/symgroup.yaml → examples/input_files/symgroup.yaml
diff --git a/examples/normal_modes_api.py b/examples/normal_modes_api.py
@@ -44,8 +44,8 @@ def get_nm_vibration_path(geometry, normal_mode, points=10, backward=False, k=1.
     return structures_path
 
 
-molecule = read_generic_structure_file('../old_examples/sf6.fchk')
-freq, nm_martices = read_normal_modes_gaussian('../old_examples/sf6_freq.out')
+molecule = read_generic_structure_file('data/sf6.fchk')
+freq, nm_martices = read_normal_modes_gaussian('data/sf6_freq.out')
 k_points = 1.5
 points = 10
 n_freq = 1