Water.h

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#include "molmodel/internal/common.h"
#include "molmodel/internal/Compound.h"
#include <iostream>
#include <fstream>
//#include <ios>




namespace SimTK 
{




class Water : public Compound { public:
        Water(DuMMForceFieldSubsystem &dumm)
        {   
 

     if (!dumm.hasAtomClass(DuMM::AtomClassIndex(400)))
     {  

        dumm.defineAtomClass_KA(
            DuMM::AtomClassIndex(400),
            "TIP3P Hydrogen"    ,
            1 , //element number
            1, //expected valence
            .0001 ,//from vdw parms
            (.0000)
            );
     }  
     if (! dumm.hasChargedAtomType(DuMM::ChargedAtomTypeIndex(8000)))
     {  
        dumm.defineChargedAtomType(
            DuMM::ChargedAtomTypeIndex(8000),
            "TIP3P Hydrogen"    ,
            DuMM::AtomClassIndex(400),
            .417                   //partial charge
            );
     }
    
     if (! Biotype::exists("TIP3P"   ,"Hydrogen" ))
         Biotype::defineBiotype(Element::Hydrogen(), 1, "TIP3P",   "Hydrogen"  ); // second arg is valence
                                                                                 // a residue name, second is an atom name
     dumm.setBiotypeChargedAtomType( DuMM::ChargedAtomTypeIndex(8000), Biotype::get("TIP3P", "Hydrogen"     ).getIndex() );
     if (!dumm.hasAtomClass(DuMM::AtomClassIndex(300)))
     {  
        dumm.defineAtomClass_KA(
            DuMM::AtomClassIndex(300),
            "TIP3P Oxygen"      ,
            16, //element number
            2, //expected valence
            1.7683,//from vdw parms
            (.1520)
            );
     }
     if (!dumm.hasChargedAtomType(DuMM::ChargedAtomTypeIndex(7000)))
     {          
        dumm.defineChargedAtomType(
            DuMM::ChargedAtomTypeIndex(7000),
            "TIP3P Oxygen"      ,//magnesium",
            DuMM::AtomClassIndex(300),
            -.834                  //partial charge
            );
     }
     if (! Biotype::exists("TIP3P"   ,"Oxygen"   ))
         Biotype::defineBiotype(Element::Oxygen(), 2, "TIP3P"   ,  "Oxygen"  ); // second arg is valence
                                                                                 // a residue name, second is an atom name
     dumm.setBiotypeChargedAtomType( DuMM::ChargedAtomTypeIndex(7000), Biotype::get("TIP3P" , "Oxygen"     ).getIndex() );
 

   
        setBaseAtom    (BivalentAtom("OW",Element::Oxygen()),Vec3(0));
        bondAtom    ( UnivalentAtom("HW0",Element::Hydrogen()),"OW/bond1",(.09572));
        bondAtom    ( UnivalentAtom("HW1",Element::Hydrogen()),"OW/bond2",(.09572));
        setDefaultBondAngle((104.52*Deg2Rad),"HW0","OW","HW1");

        setBiotypeIndex( "OW", Biotype::get("TIP3P"   ,"Oxygen").getIndex() );
        setBiotypeIndex("HW0", Biotype::get("TIP3P"   ,"Hydrogen").getIndex() );
        setBiotypeIndex("HW1", Biotype::get("TIP3P"   ,"Hydrogen").getIndex() );
        }   
};


}