ppafm.defaults#
ppafm.defaults.valelec_dict#
ppafm.defaults.d3#
Contains various constants and parameters for use in Grimme-D3 calculations. The values are extracted from the original Fortran implementation and tables which can be found at https://www.chemie.uni-bonn.de/grimme/de/software/dft-d3. Some of the values have been rescaled to be in units of eV and Å.
References
- ppafm.defaults.d3.DF_DEFAULT_PARAMS = {'B1B95': {'a1': 0.2092, 'a2': 5.5545, 's6': 1.0, 's8': 1.4507}, 'B2GPPLYP': {'a1': 0.0, 'a2': 6.3332, 's6': 0.56, 's8': 0.2597}, 'B2PLYP': {'a1': 0.3065, 'a2': 5.057, 's6': 0.64, 's8': 0.9147}, 'B3LYP': {'a1': 0.3981, 'a2': 4.4211, 's6': 1.0, 's8': 1.9889}, 'B3PW91': {'a1': 0.4312, 'a2': 4.4693, 's6': 1.0, 's8': 2.8524}, 'B97D': {'a1': 0.5545, 'a2': 3.2297, 's6': 1.0, 's8': 2.2609}, 'BHLYP': {'a1': 0.2793, 'a2': 4.9615, 's6': 1.0, 's8': 1.0354}, 'BLYP': {'a1': 0.4298, 'a2': 4.2359, 's6': 1.0, 's8': 2.6996}, 'BMK': {'a1': 0.194, 'a2': 5.9197, 's6': 1.0, 's8': 2.086}, 'BOP': {'a1': 0.487, 'a2': 0.5043, 's6': 1.0, 's8': 3.295}, 'BP86': {'a1': 0.3946, 'a2': 4.8516, 's6': 1.0, 's8': 3.2822}, 'BPBE': {'a1': 0.4567, 'a2': 4.3908, 's6': 1.0, 's8': 4.0728}, 'CAMB3LYP': {'a1': 0.3708, 'a2': 5.4743, 's6': 1.0, 's8': 2.0674}, 'DSDBLYP': {'a1': 0.0, 'a2': 6.0519, 's6': 0.5, 's8': 0.213}, 'HCTH120': {'a1': 0.3563, 'a2': 4.3359, 's6': 1.0, 's8': 1.0821}, 'LCwPBE': {'a1': 0.3919, 'a2': 5.0897, 's6': 1.0, 's8': 1.8541}, 'MPW1B95': {'a1': 0.1955, 'a2': 6.4177, 's6': 1.0, 's8': 1.0508}, 'MPWB1K': {'a1': 0.1474, 'a2': 6.6223, 's6': 1.0, 's8': 0.9499}, 'OLYP': {'a1': 0.5299, 'a2': 2.8065, 's6': 1.0, 's8': 2.6205}, 'OPBE': {'a1': 0.5512, 'a2': 2.9444, 's6': 1.0, 's8': 3.3816}, 'PBE': {'a1': 0.4289, 'a2': 4.4407, 's6': 1.0, 's8': 0.7875}, 'PBE0': {'a1': 0.4145, 'a2': 4.8593, 's6': 1.0, 's8': 1.2177}, 'PBE38': {'a1': 0.3995, 'a2': 5.1405, 's6': 1.0, 's8': 1.4623}, 'PBEsol': {'a1': 0.4466, 'a2': 6.1742, 's6': 1.0, 's8': 2.9491}, 'PTPSS': {'a1': 0.0, 'a2': 6.5745, 's6': 0.75, 's8': 0.2804}, 'PW6B95': {'a1': 0.2076, 'a2': 6.375, 's6': 1.0, 's8': 0.7257}, 'PWB6K': {'a1': 0.1805, 'a2': 7.7627, 's6': 1.0, 's8': 0.9383}, 'PWPB95': {'a1': 0.0, 'a2': 7.3141, 's6': 0.82, 's8': 0.2904}, 'SSB': {'a1': -0.0952, 'a2': 5.217, 's6': 1.0, 's8': 0.1744}, 'TPSS': {'a1': 0.4535, 'a2': 4.4752, 's6': 1.0, 's8': 1.9435}, 'TPSS0': {'a1': 0.3768, 'a2': 4.5865, 's6': 1.0, 's8': 1.2576}, 'TPSSh': {'a1': 0.4529, 'a2': 4.655, 's6': 1.0, 's8': 2.2382}, 'mPWLYP': {'a1': 0.4831, 'a2': 4.5323, 's6': 1.0, 's8': 2.0077}, 'oTPSS': {'a1': 0.4634, 'a2': 4.3153, 's6': 1.0, 's8': 2.7495}, 'rPW86PBE': {'a1': 0.4613, 'a2': 4.5062, 's6': 1.0, 's8': 1.3845}, 'revPBE': {'a1': 0.5238, 'a2': 3.5016, 's6': 1.0, 's8': 2.355}, 'revPBE0': {'a1': 0.4679, 'a2': 3.7619, 's6': 1.0, 's8': 1.7588}, 'revPBE38': {'a1': 0.4309, 'a2': 3.9446, 's6': 1.0, 's8': 1.476}, 'revSSB': {'a1': 0.472, 'a2': 4.0986, 's6': 1.0, 's8': 0.4389}}#
Default Grimme-D3 scaling parameters for a variety of density functionals using Becke-Johnson damping. Values taken from https://www.chemie.uni-bonn.de/grimme/de/software/dft-d3/bj_damping.
- ppafm.defaults.d3.K1 = 16#
Factor in exponent of coordination number calculation for Grimme-D3.
- ppafm.defaults.d3.K2 = 1.3333333333333333#
Scale factor for covalent radii in coordination number calculation for Grimme-D3.
- ppafm.defaults.d3.K3 = 4#
Factor in exponent of Gaussian weight function in reference coordination number calculation for Grimme-D3.
- ppafm.defaults.d3.R4R2 = array([1.06224333, 0.82888801, 2.65640046, 2.03933801, 1.92856832, 1.64305726, 1.43499761, 1.3724829 , 1.2638088 , 1.17224667, 3.48508457, 2.89087376, 2.9909978 , 2.58389243, 2.2740204 , 2.13845222, 1.97347304, 1.82395359, 4.22157869, 3.74458467, 3.49703613, 3.3274206 , 3.2159618 , 2.93504487, 3.07182697, 2.95500811, 2.86483063, 2.7966869 , 2.76544211, 2.69783613, 3.23935665, 2.93208485, 2.68132441, 2.57712005, 2.42939779, 2.28168674, 5.05608556, 4.59006237, 4.21865469, 3.93411462, 3.48575306, 3.27844446, 3.18309242, 3.07781854, 2.99361064, 2.92444844, 2.88011738, 2.95431897, 3.71525741, 3.42280034, 3.16495132, 3.07815323, 2.92805295, 2.78070457, 5.83261529, 5.3747446 , 4.94869507, 4.79924613, 4.74799572, 4.71016829, 4.68842987, 4.66595035, 4.65314893, 4.18033923, 4.65987342, 4.45799636, 4.52070409, 4.48521804, 4.47202839, 4.48392668, 4.1462391 , 4.34297241, 4.07762296, 3.87757775, 3.72481161, 3.54008293, 3.2039037 , 3.11554153, 3.0198106 , 3.06102925, 4.12642191, 3.84417539, 3.58862575, 3.53428553, 3.38157106, 3.22548305, 6.23982524, 5.87914635, 5.03447448, 4.58900926, 4.64162882, 4.57951396, 4.51876857, 4.68334909])#
sqrt(0.5*sqrt(Z)<r4>/<r2>(Z)) values for Grimme-D3. Units are Ångströms.
- ppafm.defaults.d3.REF_CN = array([[ 0.9118, 0. , -1. , -1. , -1. ], [ 0. , -1. , -1. , -1. , -1. ], [ 0. , 0.9865, -1. , -1. , -1. ], [ 0. , 0.9808, 1.9697, -1. , -1. ], [ 0. , 0.9706, 1.9441, 2.9128, 4.5856], [ 0. , 0.9868, 1.9985, 2.9987, 3.9844], [ 0. , 0.9944, 2.0143, 2.9903, -1. ], [ 0. , 0.9925, 1.9887, -1. , -1. ], [ 0. , 0.9982, -1. , -1. , -1. ], [ 0. , -1. , -1. , -1. , -1. ], [ 0. , 0.9684, -1. , -1. , -1. ], [ 0. , 0.9628, 1.9496, -1. , -1. ], [ 0. , 0.9648, 1.9311, 2.9146, -1. ], [ 0. , 0.9507, 1.9435, 2.9407, 3.8677], [ 0. , 0.9947, 2.0102, 2.9859, -1. ], [ 0. , 0.9948, 1.9903, -1. , -1. ], [ 0. , 0.9972, -1. , -1. , -1. ], [ 0. , -1. , -1. , -1. , -1. ], [ 0. , 0.9767, -1. , -1. , -1. ], [ 0. , 0.9831, 1.9349, -1. , -1. ], [ 0. , 1.8627, 2.8999, -1. , -1. ], [ 0. , 1.8299, 3.8675, -1. , -1. ], [ 0. , 1.9138, 2.911 , -1. , -1. ], [ 0. , 1.8269, 10.6191, -1. , -1. ], [ 0. , 1.6406, 9.8849, -1. , -1. ], [ 0. , 1.6483, 9.1376, -1. , -1. ], [ 0. , 1.7149, 2.9263, 7.7785, -1. ], [ 0. , 1.7937, 6.5458, 6.2918, -1. ], [ 0. , 0.9576, -1. , -1. , -1. ], [ 0. , 1.9419, -1. , -1. , -1. ], [ 0. , 0.9601, 1.9315, 2.9233, -1. ], [ 0. , 0.9434, 1.9447, 2.9186, 3.8972], [ 0. , 0.9889, 1.9793, 2.9709, -1. ], [ 0. , 0.9901, 1.9812, -1. , -1. ], [ 0. , 0.9974, -1. , -1. , -1. ], [ 0. , -1. , -1. , -1. , -1. ], [ 0. , 0.9738, -1. , -1. , -1. ], [ 0. , 0.9801, 1.9143, -1. , -1. ], [ 0. , 1.9153, 2.8903, -1. , -1. ], [ 0. , 1.9355, 3.9106, -1. , -1. ], [ 0. , 1.9545, 2.9225, -1. , -1. ], [ 0. , 1.942 , 11.0556, -1. , -1. ], [ 0. , 1.6682, 9.5402, -1. , -1. ], [ 0. , 1.8584, 8.8895, -1. , -1. ], [ 0. , 1.9003, 2.9696, -1. , -1. ], [ 0. , 1.863 , 5.7095, -1. , -1. ], [ 0. , 0.9679, -1. , -1. , -1. ], [ 0. , 1.9539, -1. , -1. , -1. ], [ 0. , 0.9633, 1.9378, 2.9353, -1. ], [ 0. , 0.9514, 1.9505, 2.9259, 3.9123], [ 0. , 0.9749, 1.9523, 2.9315, -1. ], [ 0. , 0.9811, 1.9639, -1. , -1. ], [ 0. , 0.9968, -1. , -1. , -1. ], [ 0. , -1. , -1. , -1. , -1. ], [ 0. , 0.9909, -1. , -1. , -1. ], [ 0. , 0.9797, 1.8467, -1. , -1. ], [ 0. , 1.9373, 2.9175, -1. , -1. ], [ 2.7991, -1. , -1. , -1. , -1. ], [ 0. , 2.9425, -1. , -1. , -1. ], [ 0. , 2.9455, -1. , -1. , -1. ], [ 0. , 2.9413, -1. , -1. , -1. ], [ 0. , 2.93 , -1. , -1. , -1. ], [ 0. , 1.8286, -1. , -1. , -1. ], [ 0. , 2.8732, -1. , -1. , -1. ], [ 0. , 2.9086, -1. , -1. , -1. ], [ 0. , 2.8965, -1. , -1. , -1. ], [ 0. , 2.9242, -1. , -1. , -1. ], [ 0. , 2.9282, -1. , -1. , -1. ], [ 0. , 2.9246, -1. , -1. , -1. ], [ 0. , 2.8482, -1. , -1. , -1. ], [ 0. , 2.9219, -1. , -1. , -1. ], [ 0. , 1.9254, 3.884 , -1. , -1. ], [ 0. , 1.9459, 2.8988, -1. , -1. ], [ 0. , 1.9292, 10.9153, -1. , -1. ], [ 0. , 1.8104, 9.8054, -1. , -1. ], [ 0. , 1.8858, 9.1527, -1. , -1. ], [ 0. , 1.8648, 2.9424, -1. , -1. ], [ 0. , 1.9188, 6.6669, -1. , -1. ], [ 0. , 0.9846, -1. , -1. , -1. ], [ 0. , 1.9896, -1. , -1. , -1. ], [ 0. , 0.9267, 1.9302, 2.942 , -1. ], [ 0. , 0.9383, 1.9356, 2.9081, 3.9098], [ 0. , 0.982 , 1.9655, 2.95 , -1. ], [ 0. , 0.9815, 1.9639, -1. , -1. ], [ 0. , 0.9954, -1. , -1. , -1. ], [ 0. , -1. , -1. , -1. , -1. ], [ 0. , 0.9705, -1. , -1. , -1. ], [ 0. , 0.9662, 1.8075, -1. , -1. ], [ 0. , 2.907 , -1. , -1. , -1. ], [ 0. , 2.8844, -1. , -1. , -1. ], [ 0. , 2.8738, -1. , -1. , -1. ], [ 0. , 2.8878, -1. , -1. , -1. ], [ 0. , 2.9095, -1. , -1. , -1. ], [ 0. , 1.9209, -1. , -1. , -1. ]])#
Reference coordination numbers for Grimme-D3. Values from: https://doi.org/10.1063/1.3382344
- ppafm.defaults.d3.R_COV = array([0.32, 0.46, 1.2 , 0.94, 0.77, 0.75, 0.71, 0.63, 0.64, 0.67, 1.4 , 1.25, 1.13, 1.04, 1.1 , 1.02, 0.99, 0.96, 1.76, 1.54, 1.33, 1.22, 1.21, 1.1 , 1.07, 1.04, 1. , 0.99, 1.01, 1.09, 1.12, 1.09, 1.15, 1.1 , 1.14, 1.17, 1.89, 1.67, 1.47, 1.39, 1.32, 1.24, 1.15, 1.13, 1.13, 1.08, 1.15, 1.23, 1.28, 1.26, 1.26, 1.23, 1.32, 1.31, 2.09, 1.76, 1.62, 1.47, 1.58, 1.57, 1.56, 1.55, 1.51, 1.52, 1.51, 1.5 , 1.49, 1.49, 1.48, 1.53, 1.46, 1.37, 1.31, 1.23, 1.18, 1.16, 1.11, 1.12, 1.13, 1.32, 1.3 , 1.3 , 1.36, 1.31, 1.38, 1.42, 2.01, 1.81, 1.67, 1.58, 1.52, 1.53, 1.54, 1.55])#
Covalent radii in Ångströms according to Pyykkö and Atsumi. Values for metals reduced by 10% for use in Grimme-D3. Units are Ångströms.
- ppafm.defaults.d3.load_R0()[source]#
Load cut-off radii values for Grimme-D3. Values from: https://doi.org/10.1063/1.3382344
Pairs of chemical elements have their own cut-off radii, corresponding to the two indices of the returned array. Units are Ångströms.
- Returns:
ref_R0 – numpy.ndarray of shape (94, 94). Cut-off radii.
- ppafm.defaults.d3.load_ref_c6()[source]#
Load the reference C6 coefficient values for Grimme-D3. Values from: https://doi.org/10.1063/1.3382344
The returned array has shape (94, 94, 5, 5). The first two indices correspond to pairs of chemical elements, and the (5, 5) array of values contains the C6 coeffiecients for the corresponding of reference coordination numbers stored in
REF_CN. Units are eV*Å^6.- Returns:
ref_c6 – numpy.ndarray of shape (94, 94, 5, 5). C6 coefficients.