From adee24338a4c9fa735ec8787f0eb85fee971386d Mon Sep 17 00:00:00 2001 From: Geoff Hutchison Date: Tue, 19 Nov 2024 16:46:38 -0500 Subject: [PATCH] Remove UFF files - shouldn't have been committed yet Signed-off-by: Geoff Hutchison --- avogadro/calc/uff.cpp | 56 ---------- avogadro/calc/uff.h | 56 ---------- avogadro/calc/uffdata.h | 241 ---------------------------------------- 3 files changed, 353 deletions(-) delete mode 100644 avogadro/calc/uff.cpp delete mode 100644 avogadro/calc/uff.h delete mode 100644 avogadro/calc/uffdata.h diff --git a/avogadro/calc/uff.cpp b/avogadro/calc/uff.cpp deleted file mode 100644 index f993e7cbd9..0000000000 --- a/avogadro/calc/uff.cpp +++ /dev/null @@ -1,56 +0,0 @@ -/****************************************************************************** - This source file is part of the Avogadro project. - This source code is released under the 3-Clause BSD License, (see "LICENSE"). -******************************************************************************/ - -#include "uff.h" - -#include -#include - -namespace Avogadro::Calc { - -UFF::UFF() : d(nullptr) -{ - // defined for 1-102 - for (unsigned int i = 0; i <= 102; ++i) { - m_elements.set(i); - } -} - -UFF::~UFF() {} - -void UFF::setMolecule(Core::Molecule* mol) -{ - m_molecule = mol; - - if (mol == nullptr) { - return; // nothing to do - } - - int numAtoms = mol->atomCount(); -} - -Real UFF::value(const Eigen::VectorXd& x) -{ - if (!m_molecule) - return 0.0; - - Real energy = 0.0; - - return energy; -} - -void UFF::gradient(const Eigen::VectorXd& x, Eigen::VectorXd& grad) -{ - if (!m_molecule) - return; - - // clear the gradients - grad.setZero(); - - // handle any constraints - cleanGradients(grad); -} - -} // namespace Avogadro::Calc diff --git a/avogadro/calc/uff.h b/avogadro/calc/uff.h deleted file mode 100644 index 61d7acc3ce..0000000000 --- a/avogadro/calc/uff.h +++ /dev/null @@ -1,56 +0,0 @@ -/****************************************************************************** - This source file is part of the Avogadro project. - This source code is released under the 3-Clause BSD License, (see "LICENSE"). -******************************************************************************/ - -#ifndef AVOGADRO_CALC_UFF_H -#define AVOGADRO_CALC_UFF_H - -#include "avogadrocalcexport.h" - -#include - -namespace Avogadro { -namespace Core { -class Molecule; -} - -namespace Calc { - -class UFFPrivate; - -class AVOGADROCALC_EXPORT UFF : public EnergyCalculator -{ -public: - UFF(); - ~UFF(); - - std::string identifier() const override { return "UFF"; } - - std::string name() const override { return "UFF"; } - - std::string description() const override { return "Universal Force Field"; } - - Core::Molecule::ElementMask elements() const override { return (m_elements); } - - Real value(const Eigen::VectorXd& x) override; - void gradient(const Eigen::VectorXd& x, Eigen::VectorXd& grad) override; - - /** - * Called when the current molecule changes. - */ - void setMolecule(Core::Molecule* mol) override; - -protected: - Core::Molecule* m_molecule; - - Core::Molecule::ElementMask m_elements; - - // track the particular calculations for a molecule - UFFPrivate* d; -}; - -} // namespace Calc -} // namespace Avogadro - -#endif // AVOGADRO_CALC_LENNARDJONES_H diff --git a/avogadro/calc/uffdata.h b/avogadro/calc/uffdata.h deleted file mode 100644 index 96e898699c..0000000000 --- a/avogadro/calc/uffdata.h +++ /dev/null @@ -1,241 +0,0 @@ -/****************************************************************************** - This source file is part of the Avogadro project. - This source code is released under the 3-Clause BSD License, (see "LICENSE"). -******************************************************************************/ - -// Formatted as a C / C++ header for Avogadro -// from RDKit Params.cpp -// https://github.com/rdkit/rdkit/blob/master/Code/ForceField/UFF/Params.cpp - -#ifndef AVOGADRO_CALC_UFF_DATA -#define AVOGADRO_CALC_UFF_DATA - -#include - -struct parameter -{ - int element; - std::string label; - float r1; - float theta0; - float x1; - float D1; - float zeta; - float Z1; - float Vi; - float Uj; - float Xi; - float Hard; - float Radius; -}; - -parameter uffparams[] = { - { 0, "Du", 0.01, 180, 0.4, 5000, 12, 10, 0, 0, 9.66, 14.92, 0.7 }, - { 1, "H_", 0.354, 180, 2.886, 0.044, 12, 0.712, 0, 0, 4.528, 6.9452, 0.371 }, - { 1, "H_b", 0.46, 83.5, 2.886, 0.044, 12, 0.712, 0, 0, 4.528, 6.9452, 0.371 }, - { 2, "He4+4", 0.849, 90, 2.362, 0.056, 15.24, 0.098, 0, 0, 9.66, 14.92, 1.3 }, - { 3, "Li", 1.336, 180, 2.451, 0.025, 12, 1.026, 0, 2, 3.006, 2.386, 1.557 }, - { 4, "Be3+2", 1.074, 109.47, 2.745, 0.085, 12, 1.565, 0, 2, 4.877, 4.443, - 1.24 }, - { 5, "B_3", 0.838, 109.47, 4.083, 0.18, 12.052, 1.755, 0, 2, 5.11, 4.75, - 0.822 }, - { 5, "B_2", 0.828, 120, 4.083, 0.18, 12.052, 1.755, 0, 2, 5.11, 4.75, 0.822 }, - { 6, "C_3", 0.757, 109.47, 3.851, 0.105, 12.73, 1.912, 2.119, 2, 5.343, 5.063, - 0.759 }, - { 6, "C_R", 0.729, 120, 3.851, 0.105, 12.73, 1.912, 0, 2, 5.343, 5.063, - 0.759 }, - { 6, "C_2", 0.732, 120, 3.851, 0.105, 12.73, 1.912, 0, 2, 5.343, 5.063, - 0.759 }, - { 6, "C_1", 0.706, 180, 3.851, 0.105, 12.73, 1.912, 0, 2, 5.343, 5.063, - 0.759 }, - { 7, "N_3", 0.7, 106.7, 3.66, 0.069, 13.407, 2.544, 0.45, 2, 6.899, 5.88, - 0.715 }, - { 7, "N_R", 0.699, 120, 3.66, 0.069, 13.407, 2.544, 0, 2, 6.899, 5.88, - 0.715 }, - { 7, "N_2", 0.685, 111.2, 3.66, 0.069, 13.407, 2.544, 0, 2, 6.899, 5.88, - 0.715 }, - { 7, "N_1", 0.656, 180, 3.66, 0.069, 13.407, 2.544, 0, 2, 6.899, 5.88, - 0.715 }, - { 8, "O_3", 0.658, 104.51, 3.5, 0.06, 14.085, 2.3, 0.018, 2, 8.741, 6.682, - 0.669 }, - { 8, "O_3_z", 0.528, 146, 3.5, 0.06, 14.085, 2.3, 0.018, 2, 8.741, 6.682, - 0.669 }, - { 8, "O_R", 0.68, 110, 3.5, 0.06, 14.085, 2.3, 0, 2, 8.741, 6.682, 0.669 }, - { 8, "O_2", 0.634, 120, 3.5, 0.06, 14.085, 2.3, 0, 2, 8.741, 6.682, 0.669 }, - { 8, "O_1", 0.639, 180, 3.5, 0.06, 14.085, 2.3, 0, 2, 8.741, 6.682, 0.669 }, - { 9, "F_", 0.668, 180, 3.364, 0.05, 14.762, 1.735, 0, 2, 10.874, 7.474, - 0.706 }, - { 10, "Ne4+4", 0.92, 90, 3.243, 0.042, 15.44, 0.194, 0, 2, 11.04, 10.55, - 1.768 }, - { 11, "Na", 1.539, 180, 2.983, 0.03, 12, 1.081, 0, 1.25, 2.843, 2.296, - 2.085 }, - { 12, "Mg3+2", 1.421, 109.47, 3.021, 0.111, 12, 1.787, 0, 1.25, 3.951, 3.693, - 1.5 }, - { 13, "Al3", 1.244, 109.47, 4.499, 0.505, 11.278, 1.792, 0, 1.25, 4.06, 3.59, - 1.201 }, - { 14, "Si3", 1.117, 109.47, 4.295, 0.402, 12.175, 2.323, 1.225, 1.25, 4.168, - 3.487, 1.176 }, - { 15, "P_3+3", 1.101, 93.8, 4.147, 0.305, 13.072, 2.863, 2.4, 1.25, 5.463, 4, - 1.102 }, - { 15, "P_3+5", 1.056, 109.47, 4.147, 0.305, 13.072, 2.863, 2.4, 1.25, 5.463, - 4, 1.102 }, - { 15, "P_3+q", 1.056, 109.47, 4.147, 0.305, 13.072, 2.863, 2.4, 1.25, 5.463, - 4, 1.102 }, - { 16, "S_3+2", 1.064, 92.1, 4.035, 0.274, 13.969, 2.703, 0.484, 1.25, 6.928, - 4.486, 1.047 }, - { 16, "S_3+4", 1.049, 103.2, 4.035, 0.274, 13.969, 2.703, 0.484, 1.25, 6.928, - 4.486, 1.047 }, - { 16, "S_3+6", 1.027, 109.47, 4.035, 0.274, 13.969, 2.703, 0.484, 1.25, 6.928, - 4.486, 1.047 }, - { 16, "S_R", 1.077, 92.2, 4.035, 0.274, 13.969, 2.703, 0, 1.25, 6.928, 4.486, - 1.047 }, - { 16, "S_2", 0.854, 120, 4.035, 0.274, 13.969, 2.703, 0, 1.25, 6.928, 4.486, - 1.047 }, - { 17, "Cl", 1.044, 180, 3.947, 0.227, 14.866, 2.348, 0, 1.25, 8.564, 4.946, - 0.994 }, - { 18, "Ar4+4", 1.032, 90, 3.868, 0.185, 15.763, 0.3, 0, 1.25, 9.465, 6.355, - 2.108 }, - { 19, "K_", 1.953, 180, 3.812, 0.035, 12, 1.165, 0, 0.7, 2.421, 1.92, 2.586 }, - { 20, "Ca6+2", 1.761, 90, 3.399, 0.238, 12, 2.141, 0, 0.7, 3.231, 2.88, 2 }, - { 21, "Sc3+3", 1.513, 109.47, 3.295, 0.019, 12, 2.592, 0, 0.7, 3.395, 3.08, - 1.75 }, - { 22, "Ti3+4", 1.412, 109.47, 3.175, 0.017, 12, 2.659, 0, 0.7, 3.47, 3.38, - 1.607 }, - { 22, "Ti6+4", 1.412, 90, 3.175, 0.017, 12, 2.659, 0, 0.7, 3.47, 3.38, - 1.607 }, - { 23, "V_3+5", 1.402, 109.47, 3.144, 0.016, 12, 2.679, 0, 0.7, 3.65, 3.41, - 1.47 }, - { 24, "Cr6+3", 1.345, 90, 3.023, 0.015, 12, 2.463, 0, 0.7, 3.415, 3.865, - 1.402 }, - { 25, "Mn6+2", 1.382, 90, 2.961, 0.013, 12, 2.43, 0, 0.7, 3.325, 4.105, - 1.533 }, - { 26, "Fe3+2", 1.27, 109.47, 2.912, 0.013, 12, 2.43, 0, 0.7, 3.76, 4.14, - 1.393 }, - { 26, "Fe6+2", 1.335, 90, 2.912, 0.013, 12, 2.43, 0, 0.7, 3.76, 4.14, 1.393 }, - { 27, "Co6+3", 1.241, 90, 2.872, 0.014, 12, 2.43, 0, 0.7, 4.105, 4.175, - 1.406 }, - { 28, "Ni4+2", 1.164, 90, 2.834, 0.015, 12, 2.43, 0, 0.7, 4.465, 4.205, - 1.398 }, - { 29, "Cu3+1", 1.302, 109.47, 3.495, 0.005, 12, 1.756, 0, 0.7, 4.2, 4.22, - 1.434 }, - { 30, "Zn3+2", 1.193, 109.47, 2.763, 0.124, 12, 1.308, 0, 0.7, 5.106, 4.285, - 1.4 }, - { 31, "Ga3+3", 1.26, 109.47, 4.383, 0.415, 11, 1.821, 0, 0.7, 3.641, 3.16, - 1.211 }, - { 32, "Ge3", 1.197, 109.47, 4.28, 0.379, 12, 2.789, 0.701, 0.7, 4.051, 3.438, - 1.189 }, - { 33, "As3+3", 1.211, 92.1, 4.23, 0.309, 13, 2.864, 1.5, 0.7, 5.188, 3.809, - 1.204 }, - { 34, "Se3+2", 1.19, 90.6, 4.205, 0.291, 14, 2.764, 0.335, 0.7, 6.428, 4.131, - 1.224 }, - { 35, "Br", 1.192, 180, 4.189, 0.251, 15, 2.519, 0, 0.7, 7.79, 4.425, 1.141 }, - { 36, "Kr4+4", 1.147, 90, 4.141, 0.22, 16, 0.452, 0, 0.7, 8.505, 5.715, - 2.27 }, - { 37, "Rb", 2.26, 180, 4.114, 0.04, 12, 1.592, 0, 0.2, 2.331, 1.846, 2.77 }, - { 38, "Sr6+2", 2.052, 90, 3.641, 0.235, 12, 2.449, 0, 0.2, 3.024, 2.44, - 2.415 }, - { 39, "Y_3+3", 1.698, 109.47, 3.345, 0.072, 12, 3.257, 0, 0.2, 3.83, 2.81, - 1.998 }, - { 40, "Zr3+4", 1.564, 109.47, 3.124, 0.069, 12, 3.667, 0, 0.2, 3.4, 3.55, - 1.758 }, - { 41, "Nb3+5", 1.473, 109.47, 3.165, 0.059, 12, 3.618, 0, 0.2, 3.55, 3.38, - 1.603 }, - { 42, "Mo6+6", 1.467, 90, 3.052, 0.056, 12, 3.4, 0, 0.2, 3.465, 3.755, 1.53 }, - { 42, "Mo3+6", 1.484, 109.47, 3.052, 0.056, 12, 3.4, 0, 0.2, 3.465, 3.755, - 1.53 }, - { 43, "Tc6+5", 1.322, 90, 2.998, 0.048, 12, 3.4, 0, 0.2, 3.29, 3.99, 1.5 }, - { 44, "Ru6+2", 1.478, 90, 2.963, 0.056, 12, 3.4, 0, 0.2, 3.575, 4.015, 1.5 }, - { 45, "Rh6+3", 1.332, 90, 2.929, 0.053, 12, 3.5, 0, 0.2, 3.975, 4.005, - 1.509 }, - { 46, "Pd4+2", 1.338, 90, 2.899, 0.048, 12, 3.21, 0, 0.2, 4.32, 4, 1.544 }, - { 47, "Ag1+1", 1.386, 180, 3.148, 0.036, 12, 1.956, 0, 0.2, 4.436, 3.134, - 1.622 }, - { 48, "Cd3+2", 1.403, 109.47, 2.848, 0.228, 12, 1.65, 0, 0.2, 5.034, 3.957, - 1.6 }, - { 49, "In3+3", 1.459, 109.47, 4.463, 0.599, 11, 2.07, 0, 0.2, 3.506, 2.896, - 1.404 }, - { 50, "Sn3", 1.398, 109.47, 4.392, 0.567, 12, 2.961, 0.199, 0.2, 3.987, 3.124, - 1.354 }, - { 50, "Sb3+3", 1.407, 91.6, 4.42, 0.449, 13, 2.704, 1.1, 0.2, 4.899, 3.342, - 1.404 }, - { 51, "Te3+2", 1.386, 90.25, 4.47, 0.398, 14, 2.882, 0.3, 0.2, 5.816, 3.526, - 1.38 }, - { 52, "I_", 1.382, 180, 4.5, 0.339, 15, 2.65, 0, 0.2, 6.822, 3.762, 1.333 }, - { 53, "Xe4+4", 1.267, 90, 4.404, 0.332, 12, 0.556, 0, 0.2, 7.595, 4.975, - 2.459 }, - { 54, "Cs", 2.57, 180, 4.517, 0.045, 12, 1.573, 0, 0.1, 2.183, 1.711, 2.984 }, - { 55, "Ba6+2", 2.277, 90, 3.703, 0.364, 12, 2.727, 0, 0.1, 2.814, 2.396, - 2.442 }, - { 56, "La3+3", 1.943, 109.47, 3.522, 0.017, 12, 3.3, 0, 0.1, 2.8355, 2.7415, - 2.071 }, - { 57, "Ce6+3", 1.841, 90, 3.556, 0.013, 12, 3.3, 0, 0.1, 2.774, 2.692, - 1.925 }, - { 58, "Pr6+3", 1.823, 90, 3.606, 0.01, 12, 3.3, 0, 0.1, 2.858, 2.564, 2.007 }, - { 59, "Nd6+3", 1.816, 90, 3.575, 0.01, 12, 3.3, 0, 0.1, 2.8685, 2.6205, - 2.007 }, - { 60, "Pm6+3", 1.801, 90, 3.547, 0.009, 12, 3.3, 0, 0.1, 2.881, 2.673, 2 }, - { 61, "Sm6+3", 1.78, 90, 3.52, 0.008, 12, 3.3, 0, 0.1, 2.9115, 2.7195, - 1.978 }, - { 62, "Eu6+3", 1.771, 90, 3.493, 0.008, 12, 3.3, 0, 0.1, 2.8785, 2.7875, - 2.227 }, - { 63, "Gd6+3", 1.735, 90, 3.368, 0.009, 12, 3.3, 0, 0.1, 3.1665, 2.9745, - 1.968 }, - { 64, "Tb6+3", 1.732, 90, 3.451, 0.007, 12, 3.3, 0, 0.1, 3.018, 2.834, - 1.954 }, - { 65, "Dy6+3", 1.71, 90, 3.428, 0.007, 12, 3.3, 0, 0.1, 3.0555, 2.8715, - 1.934 }, - { 66, "Ho6+3", 1.696, 90, 3.409, 0.007, 12, 3.416, 0, 0.1, 3.127, 2.891, - 1.925 }, - { 67, "Er6+3", 1.673, 90, 3.391, 0.007, 12, 3.3, 0, 0.1, 3.1865, 2.9145, - 1.915 }, - { 68, "Tm6+3", 1.66, 90, 3.374, 0.006, 12, 3.3, 0, 0.1, 3.2514, 2.9329, 2 }, - { 69, "Yb6+3", 1.637, 90, 3.355, 0.228, 12, 2.618, 0, 0.1, 3.2889, 2.965, - 2.158 }, - { 70, "Lu6+3", 1.671, 90, 3.64, 0.041, 12, 3.271, 0, 0.1, 2.9629, 2.4629, - 1.896 }, - { 71, "Hf3+4", 1.611, 109.47, 3.141, 0.072, 12, 3.921, 0, 0.1, 3.7, 3.4, - 1.759 }, - { 72, "Ta3+5", 1.511, 109.47, 3.17, 0.081, 12, 4.075, 0, 0.1, 5.1, 2.85, - 1.605 }, - { 73, "W_6+6", 1.392, 90, 3.069, 0.067, 12, 3.7, 0, 0.1, 4.63, 3.31, 1.538 }, - { 73, "W_3+4", 1.526, 109.47, 3.069, 0.067, 12, 3.7, 0, 0.1, 4.63, 3.31, - 1.538 }, - { 73, "W_3+6", 1.38, 109.47, 3.069, 0.067, 12, 3.7, 0, 0.1, 4.63, 3.31, - 1.538 }, - { 74, "Re6+5", 1.372, 90, 2.954, 0.066, 12, 3.7, 0, 0.1, 3.96, 3.92, 1.6 }, - { 74, "Re3+7", 1.314, 109.47, 2.954, 0.066, 12, 3.7, 0, 0.1, 3.96, 3.92, - 1.6 }, - { 75, "Os6+6", 1.372, 90, 3.12, 0.037, 12, 3.7, 0, 0.1, 5.14, 3.63, 1.7 }, - { 76, "Ir6+3", 1.371, 90, 2.84, 0.073, 12, 3.731, 0, 0.1, 5, 4, 1.866 }, - { 77, "Pt4+2", 1.364, 90, 2.754, 0.08, 12, 3.382, 0, 0.1, 4.79, 4.43, 1.557 }, - { 78, "Au4+3", 1.262, 90, 3.293, 0.039, 12, 2.625, 0, 0.1, 4.894, 2.586, - 1.618 }, - { 79, "Hg1+2", 1.34, 180, 2.705, 0.385, 12, 1.75, 0, 0.1, 6.27, 4.16, 1.6 }, - { 80, "Tl3+3", 1.518, 120, 4.347, 0.68, 11, 2.068, 0, 0.1, 3.2, 2.9, 1.53 }, - { 81, "Pb3", 1.459, 109.47, 4.297, 0.663, 12, 2.846, 0.1, 0.1, 3.9, 3.53, - 1.444 }, - { 82, "Bi3+3", 1.512, 90, 4.37, 0.518, 13, 2.47, 1, 0.1, 4.69, 3.74, 1.514 }, - { 83, "Po3+2", 1.5, 90, 4.709, 0.325, 14, 2.33, 0.3, 0.1, 4.21, 4.21, 1.48 }, - { 84, "At", 1.545, 180, 4.75, 0.284, 15, 2.24, 0, 0.1, 4.75, 4.75, 1.47 }, - { 85, "Rn4+4", 1.42, 90, 4.765, 0.248, 16, 0.583, 0, 0.1, 5.37, 5.37, 2.2 }, - { 86, "Fr", 2.88, 180, 4.9, 0.05, 12, 1.847, 0, 0, 2, 2, 2.3 }, - { 87, "Ra6+2", 2.512, 90, 3.677, 0.404, 12, 2.92, 0, 0, 2.843, 2.434, 2.2 }, - { 88, "Ac6+3", 1.983, 90, 3.478, 0.033, 12, 3.9, 0, 0, 2.835, 2.835, 2.108 }, - { 89, "Th6+4", 1.721, 90, 3.396, 0.026, 12, 4.202, 0, 0, 3.175, 2.905, - 2.018 }, - { 90, "Pa6+4", 1.711, 90, 3.424, 0.022, 12, 3.9, 0, 0, 2.985, 2.905, 1.8 }, - { 91, "U_6+4", 1.684, 90, 3.395, 0.022, 12, 3.9, 0, 0, 3.341, 2.853, 1.713 }, - { 92, "Np6+4", 1.666, 90, 3.424, 0.019, 12, 3.9, 0, 0, 3.549, 2.717, 1.8 }, - { 93, "Pu6+4", 1.657, 90, 3.424, 0.016, 12, 3.9, 0, 0, 3.243, 2.819, 1.84 }, - { 94, "Am6+4", 1.66, 90, 3.381, 0.014, 12, 3.9, 0, 0, 2.9895, 3.0035, 1.942 }, - { 95, "Cm6+3", 1.801, 90, 3.326, 0.013, 12, 3.9, 0, 0, 2.8315, 3.1895, 1.9 }, - { 96, "Bk6+3", 1.761, 90, 3.339, 0.013, 12, 3.9, 0, 0, 3.1935, 3.0355, 1.9 }, - { 97, "Cf6+3", 1.75, 90, 3.313, 0.013, 12, 3.9, 0, 0, 3.197, 3.101, 1.9 }, - { 98, "Es6+3", 1.724, 90, 3.299, 0.012, 12, 3.9, 0, 0, 3.333, 3.089, 1.9 }, - { 99, "Fm6+3", 1.712, 90, 3.286, 0.012, 12, 3.9, 0, 0, 3.4, 3.1, 1.9 }, - { 100, "Md6+3", 1.689, 90, 3.274, 0.011, 12, 3.9, 0, 0, 3.47, 3.11, 1.9 }, - { 101, "No6+3", 1.679, 90, 3.248, 0.011, 12, 3.9, 0, 0, 3.475, 3.175, 1.9 }, - { 102, "Lw6+3", 1.698, 90, 3.236, 0.011, 12, 3.9, 0, 0, 3.5, 3.2, 1.9 } -} - -#endif // AVOGADRO_CALC_UFF_DATA_H