Merge branch 'development_efrem'

GrupEstructuraElectronicaSimetria · Jan 29, 2020 · ce066ac · ce066ac
2 parents 8d0fa63 + 51304b3
commit ce066ac
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Showing 10 changed files with 66 additions and 57 deletions.
diff --git a/cosymlib/__init__.py b/cosymlib/__init__.py
@@ -1,4 +1,4 @@
-__version__ = '0.7.1'
+__version__ = '0.7.2'
 
 from cosymlib.cosym_api import Cosymlib
 from cosymlib.utils import get_shape_map
diff --git a/cosymlib/file_io/__init__.py b/cosymlib/file_io/__init__.py
@@ -43,7 +43,9 @@ def get_molecule_from_file_xyz(file_name):
     molecules = []
     with open(file_name, mode='r') as lines:
         lines.readline()
-        name = lines.readline().split()[0]
+        name = lines.readline()
+        if name.strip():
+            name = name.split()[0]
         for line in lines:
             if '$' in line or '#' in line:
                 pass

diff --git a/cosymlib/molecule/geometry/__init__.py b/cosymlib/molecule/geometry/__init__.py
@@ -14,7 +14,7 @@ def __init__(self,
         self._positions = []
         self._atom_groups = list(symbols)
 
-        if name is not None:
+        if name.strip():
             self._name = name
         else:
             self._name = ' ' * 5

diff --git a/scripts/cosym b/scripts/cosym
@@ -17,13 +17,13 @@ parser.add_argument(type=str, dest="yaml_input", nargs='?', default=None,
 parser.add_argument('-o', '--output_name', dest='output_name', default=None, help='save in file name')
 parser.add_argument('-info', action='store_true', default=False, help='return information about the input geometries')
 
-parser.add_argument('-central_atom', action='store', dest='central_atom',
+parser.add_argument('-c', '--central_atom', action='store', dest='central_atom',
                     type=int, default=0, help='position of the central atom if exist')
 parser.add_argument('-custom_ref', action='store', dest='custom_ref', default=None,
                     help='take a given structure from the file and use it as reference')
-parser.add_argument('-fix_permutation', dest='fix_permutation', action='store_true', default=False,
+parser.add_argument('-fix_perm', '--fix_permutation', dest='fix_permutation', action='store_true', default=False,
                     help='use the given permutation to perform a calculation')
-parser.add_argument('-ignore_atom_labels', dest='ignore_atom_labels', action='store_true', default=False,
+parser.add_argument('-no_labels', '--ignore_atom_labels', dest='ignore_atom_labels', action='store_true', default=False,
                     help='ignore atom labels from given structures')
 # parser.add_argument('-connectivity', dest='connectivity', action='store', default=None,
 #                     help='Connect a set of atoms by...')
@@ -36,21 +36,21 @@ parser.add_argument('-center', dest='center', action='store', default=None, narg
 
 # Shape input flags
 group_shape = parser.add_argument_group('Shape')
-group_shape.add_argument('-shp_measure',
+group_shape.add_argument('-shp_m', '--shp_measure',
                          dest='shp_measure',
                          action='store',
                          default=None,
                          help='Shape measure of input structure with reference polyhedra')
-group_shape.add_argument('-shp_labels', action='store_true',
+group_shape.add_argument('-shp_l', '--shp_labels', action='store_true',
                          dest='shp_labels',
                          default=False,
                          help='show the reference labels for a given structure')
-group_shape.add_argument('-shp_structure',
+group_shape.add_argument('-shp_s', '--shp_structure',
                          dest='shp_structure',
                          action='store_true',
                          default=False,
                          help='return the closes input structure to the reference shape')
-group_shape.add_argument('-shp_references',
+group_shape.add_argument('-shp_r', '--shp_references',
                          dest='shp_references',
                          action='store_true',
                          default=False,
@@ -67,39 +67,44 @@ group_pointgroup.add_argument('-pointgroup',
 
 # Symgroup input flags
 group_symgroup = parser.add_argument_group('Symgroup')
-group_symgroup.add_argument('-sym_measure',
+group_symgroup.add_argument('-sym_m','--sym_measure',
                             dest='sym_measure',
                             action='store',
                             default=None,
                             help='Symgroup measure of input structure with reference group')
-group_symgroup.add_argument('-sym_structure',
+group_symgroup.add_argument('-sym_s','--sym_structure',
                             dest='sym_structure',
                             action='store_true',
                             default=False,
                             help='return the closes input structure to the reference symmetry')
-group_symgroup.add_argument('-sym_labels',
+group_symgroup.add_argument('-sym_l', '--sym_labels',
                             dest='sym_labels',
                             action='store_true',
                             default=False,
                             help='return the possible symmetry labels that can be used in symgroup')
-group_symgroup.add_argument('-sym_quirality',
-                            dest='sym_quirality',
+group_symgroup.add_argument('-sym_chirality',
+                            dest='sym_chirality',
                             action='store_true',
                             default=False,
-                            help='search for a possible quirality in molecule')
-
-# Wfnsym input flags
-group_wfnsym = parser.add_argument_group('Wfnsym')
-group_wfnsym.add_argument('-sym_wf',
-                          dest='sym_wf',
-                          action='store',
-                          default=False,
-                          help='Wfnsym measure of input structure with reference group')
-# group_wfnsym.add_argument('-psym_wf',
-#                           dest='psym_wf',
-#                           action='store',
-#                           default=False,
-#                           help='Pseudo-symmetry measure of input structure with reference group')
+                            help='search for a possible chirality in molecule')
+
+# Qsym input flags
+group_qsym = parser.add_argument_group('Qsym')
+group_qsym.add_argument('-qsym_wfn',
+                        dest='qsym_wfn',
+                        action='store',
+                        default=False,
+                        help='Wfnsym measure of input structure with reference group')
+group_qsym.add_argument('-qsym_dens',
+                        dest='qsym_dens',
+                        action='store',
+                        default=False,
+                        help='Density measure of input structure with reference group')
+group_qsym.add_argument('-qsym_mos',
+                        dest='qsym_wfn',
+                        action='store',
+                        default=False,
+                        help='Range of orbitals to analyze density or wavefunction symmetry')
 
 # Utils
 parser.add_argument('-mo_diagram', dest="mo_diagram", action='store_true', default=False,
@@ -199,22 +204,22 @@ elif args.sym_measure:
                                   output_name=args.output_name)
 
 # Wfnsym commands
-if args.sym_wf:
+if args.qsym_wfn:
     if args.axis1 is not None:
         args.axis1 = np.array(args.axis1).astype(float)
     if args.axis2 is not None:
         args.axis2 = np.array(args.axis2).astype(float)
     if args.center is not None:
         args.center = np.array(args.center).astype(float)
-    symobj.write_wnfsym_measure_2file(args.sym_wf,
+    symobj.write_wnfsym_measure_2file(args.qsym_wfn,
                                       vector_axis1=args.axis1,
                                       vector_axis2=args.axis2,
                                       center=args.center,
                                       output_name=args.output_name)
 
     #Utils
     if args.mo_diagram:
-        symobj.write_mo_diagram(args.wf_group,
+        symobj.write_mo_diagram(args.qsym_wfn,
                                 vector_axis1=args.axis1,
                                 vector_axis2=args.axis2,
                                 center=args.center)

diff --git a/scripts/cosym.yaml b/scripts/cosym.yaml
@@ -9,9 +9,9 @@ pointgroup: True
 sym_measure: "C3v"
 sym_structure: False
 sym_labels: False
-sym_quirality: False
+sym_chirality: False
 # Wfnsym command line
-sym_wf: "Td"
+qsym_wfn: "Td"
 # Optional command line
 central_atom: 1
 custom_ref: "external_file.ref"

diff --git a/scripts/example_shape_file b/scripts/example_shape_file
@@ -1,3 +1,4 @@
-shape_measure: T-4
-shape_structure: False
-central_atom: 1
+shp_measure: T-4
+shp_structure: False
+central_atom: 1
+output_name: test
diff --git a/scripts/shape b/scripts/shape
@@ -13,35 +13,36 @@ parser.add_argument(type=str, dest='input_file', help='input file name(+extensio
 parser.add_argument(type=str, dest="yaml_input", nargs='?', default=None,
                     help='Perform the calculations with the command file')
 parser.add_argument('-o', '--output_name', dest='output_name', default=None, help='save in file name')
-parser.add_argument('-info', action='store_true', default=False, help='return information about the input geometries')
+parser.add_argument('-info', action='store_true', default=False,
+                    help='return information about the input geometries')
 
-parser.add_argument('-central_atom', action='store', dest='central_atom',
+parser.add_argument('-c', '--central_atom', action='store', dest='central_atom',
                     type=int, default=0, help='position of the central atom if exist')
 parser.add_argument('-custom_ref', action='store', dest='custom_ref', default=None,
                     help='take a given structure from the file and use it as reference')
-parser.add_argument('-fix_permutation', dest='fix_permutation', action='store_true', default=False,
+parser.add_argument('-fix_perm', '--fix_permutation', dest='fix_permutation', action='store_true', default=False,
                     help='use the given permutation to perform a calculation')
 # parser.add_argument('-connectivity', dest='connectivity', action='store', default=None,
 #                     help='Connect a set of atoms by...')
 
 
 # Shape input flags
 group_shape = parser.add_argument_group('Shape')
-group_shape.add_argument('-measure',
+group_shape.add_argument('-m', '--measure',
                          dest='measure',
                          action='store',
                          default=None,
                          help='Shape measure of input structure with reference polyhedra')
-group_shape.add_argument('-labels', action='store_true',
+group_shape.add_argument('-l', '--labels', action='store_true',
                          dest='labels',
                          default=False,
                          help='show the reference labels for a given structure')
-group_shape.add_argument('-structure',
+group_shape.add_argument('-s', '--structure',
                          dest='structure',
                          action='store_true',
                          default=False,
                          help='return the closes input structure to the reference shape')
-group_shape.add_argument('-references',
+group_shape.add_argument('-r', '--references',
                          dest='references',
                          action='store_true',
                          default=False,
@@ -113,7 +114,7 @@ elif not reference_polyhedron:
         c = int(bool(args.central_atom))
         reference_polyhedron = shape_tools.get_structure_references(n_atoms - c)
     else:
-        reference_polyhedron = [args.shape_measure]
+        reference_polyhedron = [args.measure]
 
 if args.structure:
     symobj.write_shape_structure_2file(reference_polyhedron,

diff --git a/scripts/shape_map b/scripts/shape_map
@@ -11,11 +11,11 @@ parser.add_argument(type=str, dest='input_file', help='input file name(+extensio
 parser.add_argument('-o', '--output_name', dest='output_name', default=None, help='save in file name')
 parser.add_argument(type=str, dest="yaml_input", nargs='?', default=None,
                     help='Perform the calculations with the command file')
-parser.add_argument('-central_atom', action='store', dest='central_atom',
+parser.add_argument('-c', '--central_atom', action='store', dest='central_atom',
                     type=int, default=0, help='position of the central atom if exist')
 parser.add_argument('-custom_ref', action='store', dest='custom_ref', default=None,
                     help='take a given structure from the file and use it as reference')
-parser.add_argument('-fix_permutation', dest='fix_permutation', action='store_true', default=False,
+parser.add_argument('-fix_perm', '--fix_permutation', dest='fix_permutation', action='store_true', default=False,
                     help='use the given permutation to perform a calculation')
 
 # Shape input flags

diff --git a/scripts/symgroup b/scripts/symgroup
@@ -13,11 +13,11 @@ parser.add_argument(type=str, dest="yaml_input", nargs='?', default=None,
 parser.add_argument('-o', '--output_name', dest='output_name', default=None, help='save in file name')
 parser.add_argument('-info', action='store_true', default=False, help='return information about the input geometries')
 
-parser.add_argument('-central_atom', action='store', dest='central_atom',
+parser.add_argument('-c', '--central_atom', action='store', dest='central_atom',
                     type=int, default=0, help='position of the central atom if exist')
-parser.add_argument('-fix_permutation', dest='fix_permutation', action='store_true', default=False,
+parser.add_argument('-fix_perm', '--fix_permutation', dest='fix_permutation', action='store_true', default=False,
                     help='use the given permutation to perform a calculation')
-parser.add_argument('-ignore_atom_labels', dest='ignore_atom_labels', action='store_true', default=False,
+parser.add_argument('-no_labels', '--ignore_atom_labels', dest='ignore_atom_labels', action='store_true', default=False,
                     help='ignore atom labels from given structures')
 # parser.add_argument('-connectivity', dest='connectivity', action='store', default=None,
 #                     help='Connect a set of atoms by...')
@@ -31,26 +31,26 @@ parser.add_argument('-center', dest='center', action='store', default=None, narg
 
 # Symgroup input flags
 group_symgroup = parser.add_argument_group('Symgroup')
-group_symgroup.add_argument('-measure',
+group_symgroup.add_argument('-m', '--measure',
                             dest='measure',
                             action='store',
                             default=False,
                             help='Symgroup measure of input structure with reference group')
-group_symgroup.add_argument('-structure',
+group_symgroup.add_argument('-s', '--structure',
                             dest='structure',
                             action='store_true',
                             default=False,
                             help='return the closes input structure to the reference symmetry')
-group_symgroup.add_argument('-labels',
+group_symgroup.add_argument('-l', '--labels',
                             dest='labels',
                             action='store_true',
                             default=False,
                             help='return the possible symmetry labels that can be used in symgroup')
-group_symgroup.add_argument('-quirality',
-                            dest='quirality',
+group_symgroup.add_argument('-chirality',
+                            dest='chirality',
                             action='store_true',
                             default=False,
-                            help='search for a possible quirality in molecule')
+                            help='search for a possible chirality in molecule')
 
 
 args = parser.parse_args(sys.argv[1:])

diff --git a/scripts/symgroup.yaml b/scripts/symgroup.yaml
@@ -2,7 +2,7 @@
 measure: "C3v"
 structure: False
 labels: False
-quirality: False
+chirality: False
 # Optional command line
 central_atom: 1
 custom_ref: "external_file.ref"