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UFF_constants.py
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UFF_constants.py
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# I am aware I have not followed the Python syntax guidlines for this data entry, but it
# really makes things easier to have justified columns -Ryther
# UFF and UFF4MOF parameters are taken directly from gulp-5.1 (uff4mof.lib)
UFF_atom_parameters = {
# type r0 theta_0 x_i D_i zeta Z_i Vi/Uj Xi
"H_": (0.354, 180.0 , 2.886, 0.044, 12.0 , 0.7120, 0.000, 4.528),
"H_b": (0.460, 83.5 , 2.886, 0.044, 12.0 , 0.7125, 0.000, 4.528),
"He4+4": (0.849, 90.0 , 2.362, 0.056, 15.24 , 0.0972, 0.000, 9.660),
"Li": (1.336, 180.0 , 2.451, 0.025, 12.0 , 1.0255, 0.000, 3.006),
"Be3+2": (1.074, 109.4712, 2.745, 0.085, 12.0 , 1.5650, 0.000, 4.877),
"B_3": (0.838, 109.4712, 4.083, 0.180, 12.052, 1.7550, 0.000, 4.068),
"B_2": (0.828, 120.0 , 4.083, 0.180, 12.052, 1.7550, 2.000, 4.068),
"C_3": (0.757, 109.4712, 3.851, 0.105, 12.73 , 1.9120, 2.119, 5.343),
"C_R": (0.729, 120.0 , 3.851, 0.105, 12.73 , 1.9120, 2.000, 5.343),
"C_2": (0.732, 120.0 , 3.851, 0.105, 12.73 , 1.9120, 2.000, 5.343),
"C_1": (0.706, 180.0 , 3.851, 0.105, 12.73 , 1.9120, 0.000, 5.343),
"N_3": (0.700, 106.7 , 3.660, 0.069, 13.407, 2.5438, 0.450, 6.899),
"N_R": (0.699, 120.0 , 3.660, 0.069, 13.407, 2.5438, 2.000, 6.899),
"N_2": (0.685, 111.3 , 3.660, 0.069, 13.407, 2.5438, 2.000, 6.899),
"N_1": (0.656, 180.0 , 3.660, 0.069, 13.407, 2.5438, 2.000, 6.899),
"O_3": (0.658, 104.51 , 3.500, 0.060, 14.085, 2.2998, 0.018, 8.741),
"O_3_z": (0.528, 145.5 , 3.500, 0.060, 14.085, 2.2998, 0.018, 8.741),
"O_R": (0.680, 110.3 , 3.500, 0.060, 14.085, 2.2998, 2.000, 8.741),
"O_2": (0.634, 120.0 , 3.500, 0.060, 14.085, 2.2998, 2.000, 8.741),
"O_1": (0.639, 180.0 , 3.500, 0.060, 14.085, 2.2998, 0.000, 8.741),
"F_": (0.668, 180.0 , 3.364, 0.050, 14.762, 1.7350, 0.000, 0.874),
"Ne4+4": (0.920, 90.0 , 3.243, 0.042, 15.440, 0.1944, 0.000, 1.040),
"Na": (1.539, 180.0 , 2.983, 0.030, 12.0, 1.0809, 0.000, 2.843),
"Mg3+2": (1.421, 109.4712, 3.021, 0.111, 12.0, 1.7866, 0.000, 3.951),
"Al6+3": (1.220, 90.0 , 4.499, 0.505, 11.278, 1.7924, 0.000, 3.041),
"Al3": (1.244, 109.4712, 4.499, 0.505, 11.278, 1.7924, 0.000, 3.041),
"Si3": (1.117, 109.4712, 4.295, 0.402, 12.175, 2.3232, 1.225, 4.168),
"P_3+3": (1.101, 93.8 , 4.147, 0.305, 13.072, 2.8627, 2.400, 5.463),
"P_3+5": (1.056, 109.4712, 4.147, 0.305, 13.072, 2.8627, 2.400, 5.463),
"P_3+q": (1.056, 109.4712, 4.147, 0.305, 13.072, 2.8627, 2.400, 5.463),
"S_3+2": (1.064, 92.1 , 4.035, 0.274, 13.969, 2.7032, 0.484, 6.928),
"S_3+4": (1.049, 103.2 , 4.035, 0.274, 13.969, 2.7032, 0.484, 6.928),
"S_3+6": (1.027, 109.4712, 4.035, 0.274, 13.969, 2.7032, 0.484, 6.928),
"S_R": (1.077, 92.2 , 4.035, 0.274, 13.969, 2.7032, 1.250, 6.928),
"S_2": (0.854, 120.0 , 4.035, 0.274, 13.969, 2.7032, 1.250, 6.928),
"S_3": (1.064, 92.1 , 4.035, 0.274, 13.969, 2.7032, 0.484, 6.928),
"Cl": (1.044, 180.0 , 3.947, 0.227, 14.866, 2.3484, 0.000, 8.564),
"Ar4+4": (1.032, 90.0 , 3.868, 0.185, 15.763, 0.2994, 0.000, 9.465),
"K": (1.953, 180.0 , 3.812, 0.035, 12.0 , 1.1645, 0.000, 2.421),
"Ca6+2": (1.761, 90.0 , 3.399, 0.238, 12.0 , 2.1414, 0.000, 3.231),
"Sc3+3": (1.513, 109.4712, 3.295, 0.019, 12.0 , 2.5924, 0.000, 3.395),
"Ti3+4": (1.412, 109.4712, 3.175, 0.017, 12.0 , 2.6595, 0.000, 3.470),
"Ti6+4": (1.412, 90.0 , 3.175, 0.017, 12.0 , 2.6595, 0.000, 3.470),
"V_3+5": (1.402, 109.4712, 3.144, 0.016, 12.0 , 2.6789, 0.000, 3.650),
"Cr6+3": (1.345, 90.0 , 3.023, 0.015, 12.0 , 2.4631, 0.000, 3.415),
"Mn6+2": (1.382, 90.0 , 2.961, 0.013, 12.0 , 2.4301, 0.000, 3.325),
"Fe3+2": (1.270, 109.4712, 2.912, 0.013, 12.0 , 2.4301, 0.000, 3.760),
"Fe6+2": (1.335, 90.0 , 2.912, 0.013, 12.0 , 2.4301, 0.000, 3.760),
"Co6+2": (1.241, 90.0 , 2.872, 0.014, 12.0 , 2.4301, 0.000, 4.105),
"Ni4+2": (1.164, 90.0 , 2.834, 0.015, 12.0 , 2.4301, 0.000, 4.465),
"Cu3+1": (1.302, 109.4712, 3.495, 0.005, 12.0 , 1.7565, 0.000, 3.729),
"Cu4+1": (1.302, 90.0 , 3.495, 0.005, 12.0 , 1.7565, 0.000, 3.729), # justed changed to angle to 90.0 for paddlewheels
"Zn3+2": (1.193, 109.4712, 2.763, 0.124, 12.0 , 1.3084, 0.000, 5.106),
"Ga3+3": (1.260, 109.4712, 4.383, 0.415, 11.0 , 1.8206, 0.000, 2.999),
"Ge3": (1.197, 109.4712, 4.280, 0.379, 12.0 , 2.7888, 0.701, 4.051),
"As3+3": (1.211, 92.1 , 4.230, 0.309, 13.0 , 2.8640, 1.500, 5.188),
"Se3+2": (1.190, 90.6 , 4.205, 0.291, 14.0 , 2.7645, 0.335, 6.428),
"Br": (1.192, 180.0 , 4.189, 0.251, 15.0 , 2.5186, 0.000, 7.790),
"Kr4+4": (1.147, 90.0 , 4.141, 0.220, 16.0 , 0.4520, 0.000, 8.505),
"Rb": (2.260, 180.0 , 4.114, 0.040, 12.0 , 1.5922, 0.000, 2.331),
"Sr6+2": (2.052, 90.0 , 3.641, 0.235, 12.0 , 2.4486, 0.000, 3.024),
"Y_3+3": (1.698, 109.4712, 3.345, 0.072, 12.0 , 3.2573, 0.000, 3.830),
"Zr3+4": (1.564, 109.4712, 3.124, 0.069, 12.0 , 3.6675, 0.000, 3.400),
"Nb3+5": (1.473, 109.4712, 3.165, 0.059, 12.0 , 3.6179, 0.000, 3.550),
"Mo6+6": (1.467, 90.0000, 3.052, 0.056, 12.0 , 3.4021, 0.000, 3.465),
"Mo3+6": (1.484, 109.4712, 3.052, 0.056, 12.0 , 3.4021, 0.000, 3.465),
"Tc6+5": (1.322, 90.0000, 2.998, 0.048, 12.0 , 3.4021, 0.000, 3.290),
"Ru6+2": (1.478, 90.0000, 2.963, 0.056, 12.0 , 3.4021, 0.000, 3.575),
"Rh6+3": (1.332, 90.0000, 2.929, 0.053, 12.0 , 3.5081, 0.000, 3.975),
"Pd4+2": (1.338, 90.0000, 2.899, 0.048, 12.0 , 3.2077, 0.000, 4.320),
"Ag1+1": (1.386, 180.0000, 3.148, 0.036, 12.0 , 1.9557, 0.200, 4.436),
"Cd3+2": (1.403, 109.4712, 2.848, 0.228, 12.0 , 1.6525, 0.000, 5.034),
"In3+3": (1.459, 109.4712, 4.463, 0.599, 11.0 , 2.0704, 0.000, 2.997),
"Sn3": (1.398, 109.4712, 4.392, 0.567, 12.0 , 2.9608, 0.199, 3.987),
"Sb3+3": (1.407, 91.6000, 4.420, 0.449, 13.0 , 2.7042, 1.100, 4.899),
"Te3+2": (1.386, 90.2500, 4.470, 0.398, 14.0 , 2.8821, 0.300, 5.816),
"I_": (1.382, 180.0000, 4.500, 0.339, 15.0 , 2.6537, 0.000, 6.822),
"Xe4+4": (1.267, 90.0000, 4.404, 0.332, 12.0 , 0.5560, 0.000, 7.595),
"Cs": (2.570, 180.0000, 4.517, 0.045, 12.0 , 1.5728, 0.000, 2.183),
"Ba6+2": (2.277, 90.0000, 3.703, 0.364, 12.0 , 2.7266, 0.000, 2.814),
"La3+3": (1.943, 109.4712, 3.522, 0.017, 12.0 , 3.3049, 0.000, 2.8355),
"Ce6+3": (1.841, 90.0000, 3.556, 0.013, 12.0 , 3.3049, 0.000, 2.774),
"Pr6+3": (1.823, 90.0000, 3.606, 0.010, 12.0 , 3.3049, 0.000, 2.858),
"Nd6+3": (1.816, 90.0000, 3.575, 0.010, 12.0 , 3.3049, 0.000, 2.8685),
"Pm6+3": (1.801, 90.0000, 3.547, 0.009, 12.0 , 3.3049, 0.000, 2.881),
"Sm6+3": (1.780, 90.0000, 3.520, 0.008, 12.0 , 3.3049, 0.000, 2.9115),
"Eu6+3": (1.771, 90.0000, 3.493, 0.008, 12.0 , 3.3049, 0.000, 2.8785),
"Gd6+3": (1.735, 90.0000, 3.368, 0.009, 12.0 , 3.3049, 0.000, 3.1665),
"Tb6+3": (1.732, 90.0000, 3.451, 0.007, 12.0 , 3.3049, 0.000, 3.018),
"Dy6+3": (1.710, 90.0000, 3.428, 0.007, 12.0 , 3.3049, 0.000, 3.0555),
"Ho6+3": (1.696, 90.0000, 3.409, 0.007, 12.0 , 3.4157, 0.000, 3.127),
"Er6+3": (1.673, 90.0000, 3.391, 0.007, 12.0 , 3.3049, 0.000, 3.1865),
"Tm6+3": (1.660, 90.0000, 3.374, 0.006, 12.0 , 3.3049, 0.000, 3.2514),
"Yb6+3": (1.637, 90.0000, 3.355, 0.228, 12.0 , 2.6177, 0.000, 3.2889),
"Lu6+3": (1.671, 90.0000, 3.640, 0.041, 12.0 , 3.2709, 0.000, 2.9629),
"Hf3+4": (1.611, 109.4712, 3.141, 0.072, 12.0 , 3.9212, 0.000, 3.7000),
"Ta3+5": (1.511, 109.4712, 3.170, 0.081, 12.0 , 4.0748, 0.000, 5.1000),
"W_6+6": (1.392, 90.0000, 3.069, 0.067, 12.0 , 3.6937, 0.000, 4.6300),
"W_3+4": (1.526, 109.4712, 3.069, 0.067, 12.0 , 3.6937, 0.000, 4.6300),
"W_3+6": (1.380, 109.4712, 3.069, 0.067, 12.0 , 3.6937, 0.000, 4.6300),
"Re6+5": (1.372, 90.0000, 2.954, 0.066, 12.0 , 3.6937, 0.000, 3.9600),
"Re3+7": (1.314, 109.4712, 2.954, 0.066, 12.0 , 3.6937, 0.000, 3.9600),
"Os6+6": (1.372, 90.0000, 3.120, 0.037, 12.0 , 3.6937, 0.000, 5.1400),
"Ir6+3": (1.371, 90.0000, 2.840, 0.073, 12.0 , 3.7307, 0.000, 5.0000),
"Pt4+2": (1.364, 90.0000, 2.754, 0.080, 12.0 , 3.3817, 0.000, 4.7900),
"Au4+3": (1.262, 90.0000, 3.293, 0.039, 12.0 , 2.6255, 0.000, 4.8940),
"Hg1+2": (1.340, 180.0000, 2.705, 0.385, 12.0 , 1.7497, 0.000, 6.2700),
"Tl3+3": (1.518, 120.0000, 4.347, 0.680, 11.0 , 2.0685, 0.000, 3.2000),
"Pb3": (1.459, 109.4712, 4.297, 0.663, 12.0 , 2.8461, 0.100, 3.9000),
"Bi3+3": (1.512, 90.0000, 4.370, 0.518, 13.0 , 2.4700, 1.000, 4.6900),
"Po3+2": (1.500, 90.0000, 4.709, 0.325, 14.0 , 2.3329, 0.300, 4.2100),
"At": (1.545, 180.0000, 4.750, 0.284, 15.0 , 2.2357, 0.000, 4.7500),
"Rn4+4": (1.420, 90.0000, 4.765, 0.248, 16.0 , 0.5832, 0.000, 5.3700),
"Fr": (2.880, 180.0000, 4.900, 0.050, 12.0 , 1.8469, 0.000, 2.0000),
"Ra6+2": (2.512, 90.0000, 3.677, 0.404, 12.0 , 2.9161, 0.000, 2.8430),
"Ac6+3": (1.983, 90.0000, 3.478, 0.033, 12.0 , 3.8882, 0.000, 2.8350),
"Th6+4": (1.721, 90.0000, 3.396, 0.026, 12.0 , 4.2021, 0.000, 3.1750),
"Pa6+4": (1.711, 90.0000, 3.424, 0.022, 12.0 , 3.8882, 0.000, 2.9850),
"U_6+4": (1.684, 90.0000, 3.395, 0.022, 12.0 , 3.8882, 0.000, 3.3410),
"Np6+4": (1.666, 90.0000, 3.424, 0.019, 12.0 , 3.8882, 0.000, 3.5490),
"Pu6+4": (1.657, 90.0000, 3.424, 0.016, 12.0 , 3.8882, 0.000, 3.2430),
"Am6+4": (1.660, 90.0000, 3.381, 0.014, 12.0 , 3.8882, 0.000, 2.9895),
"Cm6+3": (1.801, 90.0000, 3.326, 0.013, 12.0 , 3.8882, 0.000, 2.8315),
"Bk6+3": (1.761, 90.0000, 3.339, 0.013, 12.0 , 3.8882, 0.000, 3.1935),
"Cf6+3": (1.750, 90.0000, 3.313, 0.013, 12.0 , 3.8882, 0.000, 3.1970),
"Es6+3": (1.724, 90.0000, 3.299, 0.012, 12.0 , 3.8882, 0.000, 3.3330),
"Fm6+3": (1.712, 90.0000, 3.286, 0.012, 12.0 , 3.8882, 0.000, 3.4000),
"Md6+3": (1.689, 90.0000, 3.274, 0.011, 12.0 , 3.8882, 0.000, 3.4700),
"No6+3": (1.679, 90.0000, 3.248, 0.011, 12.0 , 3.8882, 0.000, 3.4750),
"Lr6+3": (1.698, 90.0000, 3.236, 0.011, 12.0 , 3.8882, 0.000, 3.5000),
### Special O-types for using alternate bond orders
"O_2_M": (0.634, 120.0 , 3.500, 0.060, 14.085, 2.2998, 2.000, 8.741), # carboxyllic oxygen bonded to metal
"O_3_M": (0.658, 104.51 , 3.500, 0.060, 14.085, 2.2998, 0.018, 8.741) # this should be used for O in coordinated solvent
}
# without MIL-53 type nodes
UFF_bond_orders_0 = {
("Cu4+1", "Cu4+1") : 0.25,
("Cu4+1", "O_2_M") : 0.50,
("Zn3+2", "O_2_M") : 0.50,
("Zr3+4", "O_2_M") : 0.50,
("Cr6f3", "O_2_M") : 0.50,
("Zr3+4", "O_3_M") : 0.50,
("Zn3+2", "O_3_M") : 0.50,
("Cr6f3", "O_3_M") : 0.50,
'S': 1.00,
'A': 1.50,
'D': 2.00,
'T': 3.00
}