Molecule.h

/*-------------------------------------------------------------------
Copyright 2011 Ravishankar Sundararaman, Kendra Letchworth Weaver

This file is part of JDFTx.

JDFTx is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.

JDFTx 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 General Public License for more details.

You should have received a copy of the GNU General Public License
along with JDFTx.  If not, see <http://www.gnu.org/licenses/>.
-------------------------------------------------------------------*/

#ifndef JDFTX_FLUID_MOLECULE_H
#define JDFTX_FLUID_MOLECULE_H

#include <electronic/RadialFunction.h>
#include <core/vector3.h>
#include <core/string.h>
#include <core/ScalarField.h>
#include <vector>
#include <map>

struct Molecule
{       
        string name; 
        
        struct Site
        {       string name; 
                double Rhs; 
                int atomicNumber; 
                double Znuc, sigmaNuc; 
                double Zelec, aElec; 
                double Zsite; 
                double deltaS; 
                double sigmaElec, rcElec; 
                string elecFilename, elecFilenameG; 
                double alpha, aPol; 

                std::vector< vector3<> > positions; 

                Site(string name, int atomicNumber=0);
                ~Site();
                void setup(const GridInfo& gInfo); 
                explicit operator bool() const { return initialized; } 
                
                RadialFunctionG w0, w1, w2, w3, w1v, w2m; 
                RadialFunctionG elecKernel, chargeKernel, polKernel; 
        private:
                bool initialized;
                void free();
        };
        std::vector< std::shared_ptr<Site> > sites;
        RadialFunctionG mfKernel; 

        Molecule(string name=string());
        ~Molecule();
        void setup(const GridInfo& gInfo, double Rmf);
        explicit operator bool() const { return initialized; } 
        
        bool isMonoatomic() const; 
        double getCharge() const; 
        double checkCharge(); 
        vector3<> getDipole() const; 
        double getVhs() const; 
        double getAlphaTot() const; 
        
        std::map<double,int> getBonds() const; 
        
        void setModelMonoatomic(string name, double Q, double Rhs); 
private:
        bool initialized;
};

#endif // JDFTX_FLUID_MOLECULE_H