update radius_bond

[rowlesmr]

See #18

lookup is now element_symbol - this needs to be changed in core to be made effective.

See:
Chemistry
. 2009;15(1):186-97. doi: 10.1002/chem.200800987.
Molecular single-bond covalent radii for elements 1-118 Pekka Pyykkö 1, Michiko Atsumi
Affiliations Expand
PMID: 19058281 DOI: 10.1002/chem.200800987

If this is too radical, i could always just remove all the ions, as their radii are the same as the element. Also change lookup to be by element.

I can't find any references to cite for the current values.

[rowlesmr]

Found a plausible source
#18 (comment)

[rowlesmr]

enum vs Pauling

Missing the Noble gases and Po and above.

Element	templenum	Pauling
[ H ]	0.37	0.37
[ He ]	0.40	
[ Li ]	1.23	1.225
[ Be ]	0.89	0.889
[ B ]	0.80	0.80
[ C ]	0.77	0.772
[ N ]	0.74	0.74
[ O ]	0.74	0.74
[ F ]	0.72	0.72
[ Ne ]	0.72	
[ Na ]	1.57	1.572
[ Mg ]	1.36	1.364
[ Al ]	1.25	1.248
[ Si ]	1.17	1.173
[ P ]	1.10	1.10
[ S ]	1.04	1.04
[ Cl ]	0.99	0.99
[ Ar ]	1.00	
[ K ]	2.03	2.025
[ Ca ]	1.74	1.736
[ Sc ]	1.44	1.439
[ Ti ]	1.35	1.324
[ V ]	1.22	1.224
[ Cr ]	1.17	1.176
[ Mn ]	1.17	1.171
[ Fe ]	1.17	1.17
[ Co ]	1.16	1.162
[ Ni ]	1.15	1.154
[ Cu ]	1.17	1.173
[ Zn ]	1.25	1.249
[ Ga ]	1.25	1.246
[ Ge ]	1.22	1.223
[ As ]	1.21	1.210
[ Se ]	1.17	1.17
[ Br ]	1.14	1.14
[ Kr ]	1.14	
[ Rb ]	2.16	2.16
[ Sr ]	1.91	1.94
[ Y ]	1.62	1.616
[ Zr ]	1.45	1.454
[ Nb ]	1.34	1.342
[ Mo ]	1.29	1.296
[ Tc ]	1.27	1.271
[ Ru ]	1.24	1.246
[ Rh ]	1.25	1.252
[ Pd ]	1.28	1.283
[ Ag ]	1.34	1.339
[ Cd ]	1.41	1.413
[ In ]	1.50	1.497
[ Sn ]	1.41	1.399
[ Sb ]	1.41	1.41
[ Te ]	1.37	1.37
[ I ]	1.33	1.33
[ Xe ]	1.33	
[ Cs ]	2.35	2.35
[ Ba ]	1.98	1.981
[ La ]	1.69	1.690
[ Ce ]	1.65	1.646
[ Pr ]	1.65	1.643
[ Nd ]	1.64	1.637
[ Pm ]	1.63	1.633
[ Sm ]	1.66	1.623
[ Eu ]	1.85	1.850
[ Gd ]	1.61	1.623
[ Tb ]	1.59	1.613
[ Dy ]	1.59	1.600
[ Ho ]	1.58	1.581
[ Er ]	1.57	1.581
[ Tm ]	1.56	1.578
[ Yb ]	1.70	1.699
[ Lu ]	1.56	1.557
[ Hf ]	1.44	1.442
[ Ta ]	1.34	1.343
[ W ]	1.30	1.304
[ Re ]	1.28	1.283
[ Os ]	1.26	1.260
[ Ir ]	1.26	1.265
[ Pt ]	1.29	1.295
[ Au ]	1.34	1.336
[ Hg ]	1.44	1.44
[ Tl ]	1.55	1.549
[ Pb ]	1.54	1.538
[ Bi ]	1.52	1.510
[ Po ]	1.53	
[ At ]	1.53	
[ Rn ]	1.53	
[ Fr ]	1.53	
[ Ra ]	1.53	
[ Ac ]	1.53	
[ Th ]	1.65	1.652
[ Pa ]	1.53	
[ U ]	1.42	1.420
[ Np ]	1.42	
[ Pu ]	1.42	
[ Am ]	1.42	
[ Cm ]	1.42	
[ Bk ]	1.42	
[ Cf ]	1.42	

[vaitkus]

Atom bonding radius is a tricky thing in general. There are multiple bonding radii sets and new ones get published from time to time (see Figure 1 from https://arxiv.org/abs/2601.02017). An atomic radius should probably not be considered an intrinsic property of an atom as is it really depends on the chemical surroundings. Furthermore, the different sets have their perks and drawbacks, e.g. some distinguish between low spin and high spin states for some elements while others routinely underestimate the radii for metal atoms.

Despite that, I guess it is probably OK to use a single set as the source for default values and the one published by Pyykkö & Atsumi seems to be the most complete one.

[rowlesmr]

I agree with you. It was more finding out the source, and providing an updated version of that same type of data. Also labelling what it actually is.

[jamesrhester]

Despite that, I guess it is probably OK to use a single set as the source for default values and the one published by Pyykkö & Atsumi seems to be the most complete one.

Yes, these are just reasonable default values which a data file can override if it wishes, just like the scattering factors.