electronic structure class now can set restricted occupancies via a n…

…ew method

added a few api examples for shape and symmetry
updated unittest files in order to erase old methods

cosymlib/__init__.py

@@ -309,6 +309,7 @@ def print_electronic_density_measure(self, group, axis=None, axis2=None, center=
             txt2 += 'axis  : ' + '  '.join(['{:12.8f}'.format(s) for s in axes_information['axis']])
             txt2 += '\n'
             txt2 += 'axis2 : ' + '  '.join(['{:12.8f}'.format(s) for s in axes_information['axis2']])
+            txt2 += '\n'
 
         txt += '\n' + txt2
 

cosymlib/molecule/electronic_structure/__init__.py

@@ -25,10 +25,12 @@ def __init__(self,
             for i in range(self._multiplicity-1):
                 self._beta_occupancy.append(0)
 
-    def set_alpha_occupancy(self, occupancy, restricted=False):
+    def set_occupancy(self, occupancy):
+        self.set_alpha_occupancy(occupancy)
+        self.set_beta_occupancy(occupancy)
+
+    def set_alpha_occupancy(self, occupancy):
         self._alpha_occupancy = occupancy
-        if restricted:
-            self.set_beta_occupancy(occupancy)
 
     def set_beta_occupancy(self, occupancy):
         self._beta_occupancy = occupancy

examples/Symgroup/ethane.xyz

@@ -0,0 +1,130 @@
+8
+0
+6    0.000000   0.000000   0.000000
+6    0.000000   0.000000   1.549348
+1    1.024510   0.000000  -0.409437
+1   -0.509263  -0.888972  -0.409437
+1   -0.518222   0.883780  -0.409437
+1   -0.512255   0.887252   1.958785
+1   -0.515241  -0.885521   1.958785
+1    1.024487  -0.006903   1.958785
+8
+5
+6    0.000000   0.000000   0.000000
+6    0.000000   0.000000   1.549683
+1    1.024435   0.000000  -0.409551
+1   -0.512124  -0.887240  -0.409551
+1   -0.512403   0.887079  -0.409551
+1   -0.587591   0.839168   1.959233
+1   -0.433042  -0.928408   1.959233
+1    1.020555   0.089071   1.959233
+8
+10
+6    0.000000   0.000000   0.000000
+6    0.000000   0.000000   1.549468
+1    1.024512   0.000000  -0.409408
+1   -0.515081  -0.885616  -0.409408
+1   -0.506590   0.890501  -0.409408
+1   -0.658544   0.784822   1.958876
+1   -0.347334  -0.963838   1.958876
+1    1.007793   0.184333   1.958876
+8
+15
+6    0.000000   0.000000   0.000000
+6    0.000000   0.000000   1.548699
+1    1.024727   0.000000  -0.409032
+1   -0.517836  -0.884257  -0.409032
+1   -0.501359   0.893703  -0.409032
+1   -0.724592   0.724592   1.957730
+1   -0.259099  -0.991430   1.957730
+1    0.986458   0.277429   1.957730
+8
+20
+6    0.000000   0.000000   0.000000
+6    0.000000   0.000000   1.547466
+1    1.025065   0.000000  -0.408436
+1   -0.520176  -0.883275  -0.408436
+1   -0.497132   0.896447  -0.408436
+1   -0.785245   0.658899   1.955901
+1   -0.169281  -1.010991   1.955901
+1    0.957050   0.367168   1.955901
+8
+25
+6    0.000000   0.000000   0.000000
+6    0.000000   0.000000   1.545937
+1    1.025506   0.000000  -0.407643
+1   -0.522043  -0.882685  -0.407643
+1   -0.494004   0.898678  -0.407643
+1   -0.840045   0.588206   1.953580
+1   -0.078655  -1.022485   1.953580
+1    0.920125   0.452805   1.953580
+8
+30
+6    0.000000   0.000000   0.000000
+6    0.000000   0.000000   1.544261
+1    1.026016   0.000000  -0.406701
+1   -0.523300  -0.882534  -0.406701
+1   -0.492218   0.900239  -0.406701
+1   -0.888556   0.513008   1.950962
+1    0.011924  -1.025947   1.950962
+1    0.876393   0.533521   1.950962
+8
+35
+6    0.000000   0.000000   0.000000
+6    0.000000   0.000000   1.542558
+1    1.026550   0.000000  -0.405705
+1   -0.523790  -0.882864  -0.405705
+1   -0.492030   0.900950  -0.405705
+1   -0.930370   0.433839   1.948263
+1    0.101600  -1.021510   1.948263
+1    0.826689   0.608597   1.948263
+8
+40
+6    0.000000   0.000000   0.000000
+6    0.000000   0.000000   1.540938
+1    1.027066   0.000000  -0.404741
+1   -0.523565  -0.883597  -0.404741
+1   -0.493272   0.900859  -0.404741
+1   -0.965126   0.351277   1.945679
+1    0.189783  -1.009380   1.945679
+1    0.771636   0.677822   1.945679
+8
+45
+6    0.000000   0.000000   0.000000
+6    0.000000   0.000000   1.539493
+1    1.027537   0.000000  -0.403854
+1   -0.522699  -0.884657  -0.403854
+1   -0.495753   0.900035  -0.403854
+1   -0.992525   0.265946   1.943347
+1    0.275922  -0.989798   1.943347
+1    0.711807   0.741056   1.943347
+8
+50
+6    0.000000   0.000000   0.000000
+6    0.000000   0.000000   1.538318
+1    1.027936   0.000000  -0.403091
+1   -0.521157  -0.886029  -0.403091
+1   -0.499489   0.898423  -0.403091
+1   -1.012319   0.178499   1.941409
+1    0.359382  -0.963066   1.941409
+1    0.647910   0.798038   1.941409
+8
+55
+6    0.000000   0.000000   0.000000
+6    0.000000   0.000000   1.537462
+1    1.028238   0.000000  -0.402506
+1   -0.519171  -0.887544  -0.402506
+1   -0.503964   0.896266  -0.402506
+1   -1.024325   0.089617   1.939969
+1    0.439841  -0.929415   1.939969
+1    0.580161   0.848932   1.939969
+8
+60
+6    0.000000   0.000000   0.000000
+6    0.000000   0.000000   1.536946
+1    1.028425   0.000000  -0.402134
+1   -0.516804  -0.889141  -0.402134
+1   -0.509017   0.893621  -0.402134
+1   -1.028425   0.000000   1.939080
+1    0.516804  -0.889141   1.939080
+1    0.509017   0.893621   1.939080

examples/Symgroup/multiple_symmetry.py

@@ -0,0 +1,19 @@
+# This tutorial will show you how to handle a shape measure with lots of structures and later on their plot in what we
+# call shape maps.
+# Import part
+from cosymlib.file_io import get_geometry_from_file_xyz, read_generic_structure_file
+from cosymlib import Cosymlib
+
+# This example will show the user how to perform a symmetry calculation on the ethane conformation path between
+# the eclipsed and the staggered forms. The first thing to do is to read the xyz file that contains the molecules and
+# creates one or multiple Geometry objects which will storage all the structural information
+
+structures = get_geometry_from_file_xyz('../Symgroup/ethane.xyz', read_multiple=True)
+
+# Now we are going to create a Cosymlib object with all these Geometry objects to simplify the printing process
+
+structure_set = Cosymlib(structures)
+
+# Finally, it is as simple as call one of the print functions inside Cosymlib class
+
+structure_set.print_geometric_symmetry_measure('i')

examples/shape/crn6.xyz

@@ -0,0 +1,117 @@
+7
+crhs_00
+24    0.000000   0.000000   0.000000
+7    1.416275  -1.908957   0.000000
+7   -1.416275  -1.908746   0.000000
+7    1.416275   0.922765   1.598276
+7   -1.416275   0.922655   1.598086
+7    1.416275   1.052185  -1.822437
+7   -1.416275   1.052120  -1.822326
+7
+crhs_05
+24    0.000000   0.000000   0.000000
+7    1.413259  -1.840215   0.000000
+7   -1.413259  -1.887380   0.165125
+7    1.413259   0.947617   1.641320
+7   -1.413259   1.055566   1.507504
+7    1.413259   1.053774  -1.825190
+7   -1.413259   0.890797  -1.910320
+7
+crhs_10
+24    0.000000   0.000000   0.000000
+7    1.404683  -2.100818   0.000000
+7   -1.404683  -2.069937   0.364986
+7    1.404683   0.901229   1.560975
+7   -1.404683   1.218657   1.452339
+7    1.404683   0.948314  -1.642528
+7   -1.404683   0.616763  -1.694542
+7
+crhs_15
+24    0.000000   0.000000   0.000000
+7    1.391634  -1.889149   0.000000
+7   -1.391634  -1.711895   0.458701
+7    1.391634   1.040952   1.802982
+7   -1.391634   1.472290   1.472289
+7    1.391634   0.885430  -1.533610
+7   -1.391634   0.488445  -1.822903
+7
+crhs_20
+24    0.000000   0.000000   0.000000
+7    1.374597  -2.028172   0.000000
+7   -1.374597  -1.773858   0.645632
+7    1.374597   0.944141   1.635301
+7   -1.374597   1.554311   1.304221
+7    1.374597   0.882434  -1.528421
+7   -1.374597   0.306475  -1.738105
+7
+crhs_25
+24    0.000000   0.000000   0.000000
+7    1.354331  -1.735507   0.000000
+7   -1.354331  -1.705775   0.795416
+7    1.354331   0.939653   1.627528
+7   -1.354331   1.421520   0.995359
+7    1.354331   1.011192  -1.751436
+7   -1.354331   0.176046  -2.012213
+7
+crhs_30
+24    0.000000   0.000000   0.000000
+7    1.328088  -1.814846   0.000000
+7   -1.328088  -1.763298   1.018041
+7    1.328087   0.885359   1.533487
+7   -1.328088   1.532114   0.884566
+7    1.328088   1.018976  -1.764918
+7   -1.328088   0.000000  -1.818042
+7
+crhs_35
+24    0.000000   0.000000   0.000000
+7    1.297653  -1.796152   0.000000
+7   -1.297652  -1.674547   1.172531
+7    1.297652   0.893537   1.547652
+7   -1.297652   1.621065   0.755915
+7    1.297653   1.022138  -1.770395
+7   -1.297653  -0.156406  -1.787726
+7
+crhs_40
+24    0.000000   0.000000   0.000000
+7    1.261198  -1.814356   0.000000
+7   -1.261198  -1.390983   1.167174
+7    1.261197   1.028859   1.782037
+7   -1.261198   1.673314   0.609037
+7    1.261198   0.891580  -1.544261
+7   -1.261198  -0.357202  -2.025792
+7
+crhs_45
+24    0.000000   0.000000   0.000000
+7    1.218056  -1.847766   0.000000
+7   -1.218056  -1.303856   1.303856
+7    1.218056   1.035335   1.793252
+7   -1.218056   1.722614   0.461573
+7    1.218056   0.889508  -1.540673
+7   -1.218056  -0.536264  -2.001363
+7
+crhs_50
+24    0.000000   0.000000   0.000000
+7    1.166902  -1.785799   0.000000
+7   -1.166902  -1.345356   1.603333
+7    1.166902   0.941238   1.630271
+7   -1.166902   1.847867   0.325829
+7    1.166902   1.046435  -1.812478
+7   -1.166902  -0.611319  -1.679583
+7
+crhs_55
+24    0.000000   0.000000   0.000000
+7    1.159771  -1.752041   0.000000
+7   -1.159771  -1.002962   1.432379
+7    1.159771   0.876012   1.517297
+7   -1.159771   1.743547   0.152540
+7    1.159771   0.874444  -1.514581
+7   -1.159771  -0.740312  -1.587604
+7
+crhs_60
+24    0.000000   0.000000   0.000000
+7    1.113410  -1.771131   0.000000
+7   -1.113410  -0.879658   1.523612
+7    1.113410   0.881670   1.527096
+7   -1.113410   1.763543   0.000000
+7    1.113410   0.879718  -1.523717
+7   -1.113410  -0.885590  -1.533886

examples/shape/easy_measure.py

@@ -0,0 +1,31 @@
+# This tutorial will show you how to handle a simple shape measure using a python script. It will not cover the
+# reading and wrinting file which is explined in detail in the ----
+# Import part:
+from cosymlib import Geometry
+
+# In this case we got a fac-[FeCl3Br3]3- slightly distorted from his octahedral shape and we want to know how distorted
+# it is with continious shape measure. As we are analyzing shapes and not symmetry, we can avoid chemical part
+# (elements and electronic structure).
+
+structure = [[-0.000250,  -0.000142,  -0.002855],
+             [ 2.028556,   0.001959,   1.468881],
+             [-1.015070,  -1.758645,   1.467680],
+             [-1.016235,   1.757020,   1.467903],
+             [-2.158748,   0.000226,  -1.487093],
+             [ 1.079740,   1.869427,  -1.486814],
+             [ 1.082006,  -1.869845,  -1.484507]]
+symbols = ['Fe', 'Cl', 'Cl', 'Cl', 'Br', 'Br', 'Br']
+
+# The first thing we should do is to create a Geometry or Molecule object. As stated before, as we do not need the
+# chemical part, the geometry should be our choice, as it only focus on the structural part.
+# The Geometry class, only needs the position of the atoms in order to be created.
+
+fecl3br3 = Geometry(structure, symbols=symbols)
+
+# Now, different approaches can be performed, but as this tutorial try to be as simple as possible, the most striaght
+# approach is to just call for the shape measure within the Geometry class. Shape only requires an ideal or a user's
+# reference structure for the comparison with the case structure. However, as this molecule has a central atom (Fe3+),
+# it is a must to include this information in the function call.
+
+measure = fecl3br3.get_shape_measure('OC-6', central_atom=1)
+print('Oh measure: {:.2f}'.format(measure))

examples/shape/shape_maps.py

@@ -0,0 +1,29 @@
+# This tutorial will show you how to handle a shape measure with lots of structures and later on their plot in what we
+# call shape maps.
+# Import part
+from cosymlib.file_io import get_geometry_from_file_xyz, read_generic_structure_file
+from cosymlib import Cosymlib
+
+# In this case we got a scan of the dihedral angle of CrN6 molecule. The Oh and D3h shapes are going to be measure
+# to analyse the path of the molecule along both shapes. In this case the structures will be read from an xyz file
+# containing all the geometries along the path. This can be done in two ways, using the get_geometry_from_file_xyz
+# function, which is specific for the xyz files or a more generic one, the read_generic_structure_file, that allows
+# the user to read any kind of file supported by this program. In both cases we must change read_multiple to True,
+# if not the function will only read the first structure in file
+
+# structures = read_generic_structure_file('crn6.xyz', read_multiple=True)
+structures = get_geometry_from_file_xyz('crn6.xyz', read_multiple=True)
+
+# Creating shape maps is something that can be tedious to both new and veteran users. To avoid such task one can use the
+# Cosymlib class, a class that allows the user to print all possible information that the program contains in a fancy
+# format and also permits to plot shape maps more user friendly.
+
+structure_set = Cosymlib(structures)
+
+# Once a Cosymlib object is easy to print all the information in one map using the following function.
+
+structure_set.print_minimum_distortion_path_shape('OC-6',
+                                                  'TPR-6',
+                                                  central_atom=1,
+                                                  max_dev=30,
+                                                  max_gco=105)