OptimalAlignment.h

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/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
   Copyright (c) 2013 The plumed team
   (see the PEOPLE file at the root of the distribution for a list of names)

   See http://www.plumed-code.org for more information.

   This file is part of plumed, version 2.0.

   plumed 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.

   plumed 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 plumed.  If not, see <http://www.gnu.org/licenses/>.
+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */
#ifndef __PLUMED_tools_OptimalAlignment_h
#define __PLUMED_tools_OptimalAlignment_h

#include "Vector.h"
#include "Tensor.h"
#include <vector>

namespace PLMD{

class Log;
class Kearsley;

/// A class that is intended to include or combine various optimal alignment algorithms

class   OptimalAlignment 
{
private:
        /// a pointer to the object that performs the optimal alignment via quaternions
        Kearsley *mykearsley;
        /// displacement vector : a double that says if the coordinate should be used in calculating the RMSD/MSD
        std::vector<double> displace;
        /// alignment vector: a double that says if the atom has to be used in reset COM and makeing the alignment
        std::vector<double> align;
        /// position of one frame (generally the MD)
        std::vector<Vector> p0;
        /// position of the reference frames
        std::vector<Vector> p1;
        /// derivatives of the error  respect to the p0 (MD running frame)
        std::vector<Vector> derrdp0;
        /// derivatives of the error respect to the p1 (static frame, do not remove: useful for SM)
        std::vector<Vector> derrdp1;
        /// the pointer to the logfile
        Log* log;
        /// a bool that decides to make the fast version (alignment vec= displacement vec) or the slower case
        bool fast;

public:
        /// the contructor
        OptimalAlignment( const  std::vector<double>  & align,  const std::vector<double>   & displace, const std::vector<Vector> & p0, const std::vector<Vector> & p1 , Log* &log );
        /// the destructor: delete kearsley
        ~OptimalAlignment();
        /// assignment of the running frame p0
        void assignP0(  const std::vector<Vector> & p0 );
        /// assignment to the reference frame p1
        void assignP1(  const std::vector<Vector> & p1 );
        // this updates align runtime
        void assignAlign(  const std::vector<double> & align );
        // this updates displace runtime
        void assignDisplace(  const std::vector<double> & displace );
        /// this does the real calculation
        double calculate( bool rmsd, std::vector<Vector> & derivatives);
        /// this should perform the weighted alignment
        double weightedAlignment( bool rmsd);
        // a finite difference test
        double weightedFindiffTest( bool rmsd);
};

}

#endif