Regarding Overlapping atoms #12
Description
As shown in the screen shot. The reading CIF cannot run well with structure that contains overlapping atoms (K and Ba here).
Attached is the output and traceback
`Importing atoms
9 atoms added
.cif import complete.
No mag_ion ion listed, assuming Yb is the central ion.
Central ion: Yb3+ at [0.0, 0.0, 0.0]
AAAH! There is a super-close atom. Removing it...
Nearest ligand: Ba3+
Identified 2 Ba3+ ligands.
Found 2 fold axis about [1. 0. 0.]
No mirror planes; using [1. 0. 0.] as Z axis.
�[44m Axes for point charge model (in ABC space):
X axis = [-0.5 -1. 0. ]
Y axis = [ 0. 0. -1.]
Z axis = [1. 0. 0.] �[0m
�[43m WARNING: there is no mirror symmetry along the Y axis, so
�[0m �[43m we must inlcude the -m terms, and the eigenkets will be complex.�[0m
Creating a point charge model...
B_2 -2 = -0.0
B_2 -1 = -0.0
B_2 0 = 1.10592292
B_2 1 = -0.0
B_2 2 = 3.31776875
B_4 -4 = 0.0
B_4 -3 = 0.0
B_4 -2 = 0.0
B_4 -1 = 0.0
B_4 0 = 0.00114618
B_4 1 = 0.0
B_4 2 = 0.00764123
B_4 3 = 0.0
B_4 4 = 0.01337215
B_6 -6 = -0.0
B_6 -5 = -0.0
B_6 -4 = -0.0
B_6 -3 = -0.0
B_6 -2 = -0.0
B_6 -1 = -0.0
B_6 0 = 3.77e-06
B_6 1 = -0.0
B_6 2 = 3.957e-05
B_6 3 = -0.0
B_6 4 = 4.748e-05
B_6 5 = -0.0
B_6 6 = 8.705e-05
Central ion: Yb3+ at [0.0, 0.0, 0.0]
AAAH! There is a super-close atom. Removing it...
Nearest ligand: Ba3+
Identified 2 Ba3+ ligands.
Found 2 fold axis about [1. 0. 0.]
No mirror planes; using [1. 0. 0.] as Z axis.
�[44m Axes for point charge model (in ABC space):
X axis = [-0.5 -1. 0. ]
Y axis = [ 0. 0. -1.]
Z axis = [1. 0. 0.] �[0m
�[43m WARNING: there is no mirror symmetry along the Y axis, so
�[0m �[43m we must inlcude the -m terms, and the eigenkets will be complex.�[0m
Creating a point charge model...
B_2 -2 = -0.0
B_2 -1 = -0.0
B_2 0 = 1.10592292
B_2 1 = -0.0
B_2 2 = 3.31776875
B_4 -4 = 0.0
B_4 -3 = 0.0
B_4 -2 = 0.0
B_4 -1 = 0.0
B_4 0 = 0.00114618
B_4 1 = 0.0
B_4 2 = 0.00764123
B_4 3 = 0.0
B_4 4 = 0.01337215
B_6 -6 = -0.0
B_6 -5 = -0.0
B_6 -4 = -0.0
B_6 -3 = -0.0
B_6 -2 = -0.0
B_6 -1 = -0.0
B_6 0 = 3.77e-06
B_6 1 = -0.0
B_6 2 = 3.957e-05
B_6 3 = -0.0
B_6 4 = 4.748e-05
B_6 5 = -0.0
B_6 6 = 8.705e-05
Central ion: Yb3+ at [0.0, 0.0, 0.0]
Nearest ligand: Ba3+
Identified 2 Ba3+ ligands.
Found 2 fold axis about [1. 0. 0.]
No mirror planes; using [1. 0. 0.] as Z axis.
�[44m Axes for point charge model (in ABC space):
X axis = [-0.5 -1. 0. ]
Y axis = [ 0. 0. -1.]
Z axis = [1. 0. 0.] �[0m
�[43m WARNING: there is no mirror symmetry along the Y axis, so
�[0m �[43m we must inlcude the -m terms, and the eigenkets will be complex.�[0m
Creating a point charge model...
B_2 -2 = -0.0
B_2 -1 = -0.0
B_2 0 = 1.10592292
B_2 1 = -0.0
B_2 2 = 3.31776875
B_4 -4 = 0.0
B_4 -3 = 0.0
B_4 -2 = 0.0
B_4 -1 = 0.0
B_4 0 = 0.00114618
B_4 1 = 0.0
B_4 2 = 0.00764123
B_4 3 = 0.0
B_4 4 = 0.01337215
B_6 -6 = -0.0
B_6 -5 = -0.0
B_6 -4 = -0.0
B_6 -3 = -0.0
B_6 -2 = -0.0
B_6 -1 = -0.0
B_6 0 = 3.77e-06
B_6 1 = -0.0
B_6 2 = 3.957e-05
B_6 3 = -0.0
B_6 4 = 4.748e-05
B_6 5 = -0.0
B_6 6 = 8.705e-05
WARNING: more than one ligand position given...
outputting [[Ligands1, CFLevels1], [Ligands2, CFLevels2], [Ligands3, CFLevels3]]
�[0;31m---------------------------------------------------------------------------�[0m
�[0;31mValueError�[0m Traceback (most recent call last)
Cell �[0;32mIn[26], line 3�[0m
�[1;32m 1�[0m �[38;5;66;03m########### Import CIF file�[39;00m
�[0;32m----> 3�[0m YTOLig, Yb �[38;5;241m=�[39m cef�[38;5;241m.�[39mimportCIF(�[38;5;124m'�[39m�[38;5;124minput1.cif�[39m�[38;5;124m'�[39m)
�[1;32m 5�[0m �[38;5;66;03m# YTOLig, Yb = cef.importCIF('input2.cif', mag_ion='Co1',ionS=3/2,ionL=3, LS_Coupling=-22.34)�[39;00m
�[0;31mValueError�[0m: too many values to unpack (expected 2)`
`---------------------------------------------------------------------------
ValueError Traceback (most recent call last)
Cell In[26], line 3
1 ########### Import CIF file
----> 3 YTOLig, Yb = cef.importCIF('input1.cif')
5 # YTOLig, Yb = cef.importCIF('input2.cif', mag_ion='Co1',ionS=3/2,ionL=3, LS_Coupling=-22.34)
ValueError: too many values to unpack (expected 2)`