force_field.h

/*
 * This file is a part of
 *
 * ============================================
 * ###   Pteros molecular modeling library  ###
 * ============================================
 *
 * https://github.com/yesint/pteros
 *
 * (C) 2009-2021, Semen Yesylevskyy
 *
 * All works, which use Pteros, should cite the following papers:
 *
 *  1.  Semen O. Yesylevskyy, "Pteros 2.0: Evolution of the fast parallel
 *      molecular analysis library for C++ and python",
 *      Journal of Computational Chemistry, 2015, 36(19), 1480–1488.
 *      doi: 10.1002/jcc.23943.
 *
 *  2.  Semen O. Yesylevskyy, "Pteros: Fast and easy to use open-source C++
 *      library for molecular analysis",
 *      Journal of Computational Chemistry, 2012, 33(19), 1632–1636.
 *      doi: 10.1002/jcc.22989.
 *
 * This is free software distributed under Artistic License:
 * http://www.opensource.org/licenses/artistic-license-2.0.php
 *
*/
 
 
#pragma once
 
#include <vector>
#include <unordered_set>
#include <unordered_map>
#include <Eigen/Core>
 
namespace pteros {
 
class ForceField {
public:
    int natoms;
    std::vector<std::unordered_set<int> > exclusions;
 
    Eigen::MatrixXf LJ_C6, LJ_C12;
 
    std::vector<Eigen::Vector2f> LJ14_interactions;
 
    std::unordered_map<int,int> LJ14_pairs;
 
    float fudgeQQ;
 
    float rcoulomb, epsilon_r, epsilon_rf, rcoulomb_switch, rvdw_switch, rvdw;
    std::string coulomb_type, coulomb_modifier, vdw_type, vdw_modifier;
 
    std::vector<Eigen::Vector2i> bonds;
 
    // Molecules
    std::vector<Eigen::Vector2i> molecules;
 
    bool ready;
 
    float (*coulomb_kernel_ptr)(float,float,float,const ForceField&);
 
    float (*LJ_kernel_ptr)(float,float,float,const ForceField&);
 
    // Aux constants to be precomputed by set_kernels()
    float coulomb_prefactor, k_rf, c_rf;
    // potential shift constants
    Eigen::Vector3f shift_1, shift_6, shift_12;
 
    ForceField();
 
    ForceField(const ForceField& other);
 
    ForceField& operator=(ForceField other);
 
    // Clear ff
    void clear();
 
    // Setup coulomb and VDW kernel pointers
    void setup_kernels();
 
    // Computes energy of atom pair at given distance
    // Returns {Coulomb_en,LJ_en}
    Eigen::Vector2f pair_energy(int at1, int at2, float r, float q1, float q2, int type1, int type2);
 
    float get_cutoff();
};
 
}