Molecule.hpp

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// This file is part of GQCG-GQCP.
//
// Copyright (C) 2017-2020  the GQCG developers
//
// GQCG-GQCP is free software: you can redistribute it and/or modify
// it under the terms of the GNU Lesser General Public License as published by
// the Free Software Foundation, either version 3 of the License, or
// (at your option) any later version.
//
// GQCG-GQCP is distributed in the hope that it will be useful,
// but WITHOUT ANY WARRANTY; without even the implied warranty of
// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
// GNU Lesser General Public License for more details.
//
// You should have received a copy of the GNU Lesser General Public License
// along with GQCG-GQCP.  If not, see <http://www.gnu.org/licenses/>.
 
#pragma once
 
 
#include "Molecule/NuclearFramework.hpp"
 
#include <boost/format.hpp>
 
#include <cstdlib>
 
 
namespace GQCP {
 
 
class Molecule {
private:
    size_t N;                            // the number of electrons
    NuclearFramework nuclear_framework;  // the underlying nuclear framework
 
 
public:
    // CONSTRUCTORS
 
    Molecule(const NuclearFramework& nuclear_framework, const int charge = 0);
 
    Molecule(const std::vector<Nucleus>& nuclei, const int charge = 0);
 
 
    // NAMED CONSTRUCTORS
 
    static Molecule HChain(const size_t n, const double spacing, const int charge = 0, const CartesianDirection axis = CartesianDirection::z);
 
    static Molecule H2Chain(const size_t n, const double a, const double b, const int charge = 0, const CartesianDirection axis = CartesianDirection::z);
 
    static Molecule HRingFromDistance(const size_t n, const double distance, const int charge = 0);
 
    static Molecule HRingFromRadius(const size_t n, const double radius, const int charge = 0);
 
    static Molecule ReadXYZ(const std::string& xyz_filename, const int charge = 0);
 
 
    // OPERATORS
 
    friend std::ostream& operator<<(std::ostream& os, const Molecule& molecule);
 
 
    // PUBLIC METHODS
 
    double calculateInternuclearDistanceBetween(const size_t index1, const size_t index2) const { return this->nuclearFramework().calculateInternuclearDistanceBetween(index1, index2); }
 
    int charge() const;
 
    std::string description() const {
 
        std::string molecule_string = (boost::format("Number of electrons: %s \n") % this->numberOfElectrons()).str();
        molecule_string += this->nuclearFramework().description();
 
        return molecule_string;
    }
 
    const NuclearFramework& nuclearFramework() const { return this->nuclear_framework; }
 
    size_t numberOfAtoms() const { return this->nuclear_framework.numberOfNuclei(); }
 
    size_t numberOfElectronPairs() const { return this->numberOfElectrons() / 2; /* this floors to zero */ }
 
    size_t numberOfElectrons() const { return this->N; }
 
    size_t totalNucleicCharge() const { return this->nuclear_framework.totalNucleicCharge(); }
};
 
 
}  // namespace GQCP