Add new periodic module and tests

atomdb/__init__.py

@@ -24,6 +24,8 @@
 
 from atomdb.promolecule import *
 
+from atomdb.periodic import *
+
 
 __version__ = version
 r"""AtomDB version string."""

atomdb/data/data_info.csv

@@ -0,0 +1,18 @@
+#Property key,Property name,Source key,units,Property description,Reference,doi,Notes
+cov_radius,Covalent radius,cordero,angstrom,Covalent radius (derived from crystallographic data),"B. Cordero, V. Gomez, A. E. Platero-Prats, M. Reves, J. Echeverria,E. Cremades,\nF. Barragan, and S. Alvarez, Dalton Trans. pp. 2832--2838 (2008)",http://dx.doi.org/10.1039/b801115j,"For carbon the number is a weighted average over the data for different hybridizations.\nFor Mn, Fe, and Co, the number is a weighted average over the data for different spins\n(high spin and low spin)"
+cov_radius,Covalent radius,bragg,angstrom,"Bragg radius (covalent, metallic and ionic bonds, derived from crystallographic data)","W. L. Bragg, Phil. Mag. 40, 169 (1920)",http://dx.doi.org/10.1080/14786440808636111,
+cov_radius,Covalent radius,slater,angstrom,"Slater radius (covalent, metallic and ionic bonds, derived from crystallographic data)","J. C. Slater, J. Chem. Phys. 41, 3199 (1964)",http://dx.doi.org/10.1063/1.1725697,
+vdw_radius,van der Waals radius,bondi,angstrom,van der Waals radius according to Bondi,"A. Bondi, J. Phys. Chem. 68, 441 (1964)",http://dx.doi.org/10.1021/j100785a001,
+vdw_radius,van der Waals radius,truhlar,angstrom,van der Waals radii by Truhlar (corrections and additions to Bondi),M. Mantina  A. C. Chamberlin  R. Valero  C. J. Cramer  D. G. Truhlar  J. Phys. Chem. A 113  5806 (2009),http://dx.doi.org/10.1021/jp8111556,
+vdw_radius,van der Waals radius,rt,angstrom,van der Waals radius according to Rowland and Taylor,"R. S. Rowland and R. Taylor, J. Phys. Chem. 100, 7384 (1996)",http://dx.doi.org/10.1021/jp953141+,
+vdw_radius,van der Waals radius,batsanov,angstrom,van der Waals radii by Batsanov,S. S. Batsanov Inorganic Materials 37 871 (2001),http://dx.doi.org/10.1023/a%3a1011625728803,
+vdw_radius,van der Waals radius,dreiding,2angstrom,van der Waals radii from the DREIDING FF,"Stephen L. Mayo, Barry D. Olafson, and William A. Goddard III J. Phys. Chem. 94 8897 (1990)",http://dx.doi.org/10.1021/j100389a010,"R_0 parameter, unit 2angstrom is used so that numbers are divided by 2 upon reading"
+vdw_radius,van der Waals radius,uff,2angstrom,van der Waals radii from UFF ,"A. K. Rappi, C. J. Casewit, K. S. Colwell, W. A. Goddard III, and W. M. Skid J. Am. Chem. Soc. 114 10024 (1992)",http://dx.doi.org/10.1021/ja00051a040,"x_I parameter, unit 2angstrom is used so that numbers are divided by 2 upon reading"
+vdw_radius,van der Waals radius,mm3,angstrom,van der Waals radii from MM3,"N. L. Allinger, X. Zhou, and J. Bergsma, Journal of Molecular Structure: THEOCHEM 312, 69 (1994)",http://dx.doi.org/10.1016/s0166-1280(09)80008-0,
+at_radius,atomic radius,wc,angstrom,Waber-Cromer atomic radius,"J. T. Waber and D. T. Cromer, J. Chem. Phys. 42, 4116 (1965)",http://dx.doi.org/10.1063/1.1695904,"For each element, the largest radius of the outer orbitals is taken."
+at_radius,atomic radius,cr,angstrom,Clementi-Raimondi atomic radius,"E. Clementi, D. L. Raimondi, W. P. Reinhardt, J. Chem. Phys. 47, 1300 (1967)",http://dx.doi.org/10.1063/1.1712084,
+eneg,Electronegativity,pauling,,Pauling electronegativity,"A. L. Allred, J. Inorg. Nuc. Chem. 17, 215 (1961)",http://dx.doi.org/10.1016/0022-1902(61)80142-5,
+pold,Isolated atom dipole polarizability,crc,angstrom**3,Isolated atom dipole polarizability,"CRC Handbook of Chemistry and Physics (CRC, Boca Raton, FL, 2003).",,"If multiple values were present in the CRC book, the value used in Erin's postg code is taken"
+pold,Isolated atom dipole polarizability,chu,au,Isolated atom dipole polarizability,"X. Chu & A. Dalgarno, J. Chem. Phys., 121(9), 4083–4088 (2004)",http://dx.doi.org/10.1063/1.1779576,"Theoretical value for hydrogen from this paper:\nA.D. Buckingham, K.L. Clarke, Chem. Phys. Lett. 57(3), 321--325 (1978)\nhttp://dx.doi.org/10.1016/0009-2614(78)85517-1"
+c6,Isolated atom C6 dispersion coefficients,chu,au,Isolated atom C6 dispersion coefficients,"X. Chu & A. Dalgarno, J. Chem. Phys., 121(9), 4083–4088 (2004)",http://dx.doi.org/10.1063/1.1779576,"Theoretical value for hydrogen from this paper:\nK. T. Tang, J. M. Norbeck and P. R. Certain, J. Chem. Phys. 64, 3063 (1976)\nhttp://dx.doi.org/10.1063/1.432569"
+mass,Atomic mass,stb,amu,IUPAC atomic mass (or weight for the chemists),"Thomas Prohaska et. al. Pure Appl. Chem. 2022, 94",https://doi.org/10.1515/pac-2019-0603,