ReferenceCCMAAlgorithm.h

/* Portions copyright (c) 2006-2015 Stanford University and Simbios.
 * Contributors: Pande Group
 *
 * Permission is hereby granted, free of charge, to any person obtaining
 * a copy of this software and associated documentation files (the
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 * distribute, sublicense, and/or sell copies of the Software, and to
 * permit persons to whom the Software is furnished to do so, subject
 * to the following conditions:
 *
 * The above copyright notice and this permission notice shall be included
 * in all copies or substantial portions of the Software.
 *
 * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS
 * OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
 * MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT.
 * IN NO EVENT SHALL THE AUTHORS, CONTRIBUTORS OR COPYRIGHT HOLDERS BE
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 */

#ifndef __ReferenceCCMAAlgorithm_H__
#define __ReferenceCCMAAlgorithm_H__

#include "ReferenceConstraintAlgorithm.h"
#include <utility>
#include <vector>
#include <set>

namespace OpenMM {

class OPENMM_EXPORT ReferenceCCMAAlgorithm : public ReferenceConstraintAlgorithm {

protected:

    int _maximumNumberOfIterations;
    double _elementCutoff;

    int _numberOfConstraints;
    std::vector<std::pair<int, int> > _atomIndices;
    std::vector<double> _distance;

    std::vector<OpenMM::Vec3> r_ij;
    std::vector<double> d_ij2, _distanceTolerance, reducedMasses;
    bool _hasInitializedMasses;
    std::vector<std::vector<std::pair<int, double> > > _matrix;

private:

    void applyConstraints(std::vector<OpenMM::Vec3>& atomCoordinates,
                       std::vector<OpenMM::Vec3>& atomCoordinatesP, std::vector<double>& inverseMasses, bool constrainingVelocities, double tolerance);
          
public:
    class AngleInfo;

    /**
     * Create a ReferenceCCMAAlgorithm object.
     * 
     * @param numberOfAtoms            the number of atoms in the system
     * @param numberOfConstraints      the number of constraints
     * @param atomIndices              atom indices for contraints
     * @param distance                 distances for constraints
     * @param masses                   atom masses
     * @param angles                   angle force field terms
     * @param elementCutoff            the cutoff for which elements of the inverse matrix to keep
     */
    ReferenceCCMAAlgorithm(int numberOfAtoms, int numberOfConstraints, const std::vector<std::pair<int, int> >& atomIndices, const std::vector<double>& distance, std::vector<double>& masses, std::vector<AngleInfo>& angles, double elementCutoff);

    /**
     * Get the number of constraints.
     */
    int getNumberOfConstraints() const;

    /**
     * Get the maximum number of iterations to perform.
     */
    int getMaximumNumberOfIterations() const;

    /**
     * Set the maximum number of iterations to perform.
     */
    void setMaximumNumberOfIterations(int maximumNumberOfIterations);

    /**
     * Apply the constraint algorithm.
     * 
     * @param atomCoordinates  the original atom coordinates
     * @param atomCoordinatesP the new atom coordinates
     * @param inverseMasses    1/mass
     * @param tolerance        the constraint tolerance
     */
    void apply(std::vector<OpenMM::Vec3>& atomCoordinates,
                       std::vector<OpenMM::Vec3>& atomCoordinatesP, std::vector<double>& inverseMasses, double tolerance);

    /**
     * Apply the constraint algorithm to velocities.
     * 
     * @param atomCoordinates  the atom coordinates
     * @param atomCoordinatesP the velocities to modify
     * @param inverseMasses    1/mass
     * @param tolerance        the constraint tolerance
     */
    void applyToVelocities(std::vector<OpenMM::Vec3>& atomCoordinates,
                     std::vector<OpenMM::Vec3>& velocities, std::vector<double>& inverseMasses, double tolerance);

    /**
     * Get the inverse constraint matrix.  Each element represents one column, and contains a list
     * of all non-zero elements in the form (index, value).
     */
    const std::vector<std::vector<std::pair<int, double> > >& getMatrix() const;

};

class ReferenceCCMAAlgorithm::AngleInfo
{
public:
    int atom1, atom2, atom3;
    double angle;
    AngleInfo(int atom1, int atom2, int atom3, double angle) :
        atom1(atom1), atom2(atom2), atom3(atom3), angle(angle)
    {
    }
};

} // namespace OpenMM

#endif // __ReferenceCCMAAlgorithm_H__