Line data    Source code

       1             : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
       2             :    Copyright (c) 2012-2023 The plumed team
       3             :    (see the PEOPLE file at the root of the distribution for a list of names)
       4             : 
       5             :    See http://www.plumed.org for more information.
       6             : 
       7             :    This file is part of plumed, version 2.
       8             : 
       9             :    plumed is free software: you can redistribute it and/or modify
      10             :    it under the terms of the GNU Lesser General Public License as published by
      11             :    the Free Software Foundation, either version 3 of the License, or
      12             :    (at your option) any later version.
      13             : 
      14             :    plumed is distributed in the hope that it will be useful,
      15             :    but WITHOUT ANY WARRANTY; without even the implied warranty of
      16             :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
      17             :    GNU Lesser General Public License for more details.
      18             : 
      19             :    You should have received a copy of the GNU Lesser General Public License
      20             :    along with plumed.  If not, see <http://www.gnu.org/licenses/>.
      21             : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */
      22             : #ifndef __PLUMED_tools_KernelFunctions_h
      23             : #define __PLUMED_tools_KernelFunctions_h
      24             : 
      25             : #include "Matrix.h"
      26             : #include "core/Value.h"
      27             : #include <vector>
      28             : #include <memory>
      29             : 
      30             : namespace PLMD {
      31             : 
      32        6143 : class KernelFunctions {
      33             : private:
      34             : /// Is the metric matrix diagonal
      35             :   enum class matrixType {diagonal,multi,vonmises} dtype;
      36             : /// What type of kernel are we using
      37             :   enum class kernelType {gaussian,truncatedgaussian,stretchedgaussian,uniform,triangular} ktype;
      38             : /// The center of the kernel function
      39             :   std::vector<double> center;
      40             : /// The width of the kernel
      41             :   std::vector<double> width;
      42             : /// The height of the kernel
      43             :   double height;
      44             : 
      45             :   double stretchA=1.0;
      46             :   double stretchB=0.0;
      47             : 
      48             : /// Used to set all the data in the kernel during construction - avoids double coding as this has two constructors
      49             :   void setData( const std::vector<double>& at,
      50             :                 const std::vector<double>& sig,
      51             :                 const std::string& type,
      52             :                 const std::string& mtype,
      53             :                 const double& w );
      54             : /// Convert the width into matrix form
      55             :   Matrix<double> getMatrix() const;
      56             : public:
      57             :   explicit KernelFunctions( const std::string& input );
      58             :   KernelFunctions( const std::vector<double>& at,
      59             :                    const std::vector<double>& sig,
      60             :                    const std::string& type,
      61             :                    const std::string& mtype,
      62             :                    const double& w );
      63             :   explicit KernelFunctions( const KernelFunctions* in );
      64             : /// Normalise the function and scale the height accordingly
      65             :   void normalize( const std::vector<Value*>& myvals );
      66             : /// Get the dimensionality of the kernel
      67             :   unsigned ndim() const;
      68             : /// Get the cutoff for a kernel
      69             :   double getCutoff(double width) const ;
      70             : /// Get the position of the center
      71             :   std::vector<double> getCenter() const;
      72             : /// Get the support
      73             :   std::vector<unsigned> getSupport( const std::vector<double>& dx ) const;
      74             : /// get it in continuous form
      75             :   std::vector<double> getContinuousSupport( ) const;
      76             : /// Evaluate the kernel function with constant intervals
      77             :   double evaluate( const std::vector<Value*>& pos,
      78             :                    std::vector<double>& derivatives,
      79             :                    bool usederiv=true,
      80             :                    bool doInt=false,
      81             :                    double lowI_=-1,
      82             :                    double uppI_=-1 ) const;
      83             : /// If this is a Gaussian kernel with a diagonal metric, get the parameters to evaluate it
      84             : /// as a product over the dimensions: with t_i=(x_i-c_i)/w_i and r2=sum_i t_i^2, the kernel is
      85             : /// height*(a*prod_i exp(-t_i^2/2)+b) for r2<r2cut and zero otherwise. Returns false otherwise.
      86             :   bool getSeparableGaussian(double & h, double & a, double & b, double & r2cut, std::vector<double> & w) const;
      87             : /// Read a kernel function from a file
      88             :   static std::unique_ptr<KernelFunctions> read( IFile* ifile,
      89             :       const bool& cholesky,
      90             :       const std::vector<std::string>& valnames );
      91             : };
      92             : 
      93             : inline
      94      974872 : Matrix<double> KernelFunctions::getMatrix() const {
      95             :   unsigned k=0, ncv=ndim();
      96      974872 :   Matrix<double> mymatrix(ncv,ncv);
      97     2924616 :   for(unsigned i=0; i<ncv; i++) {
      98     4874360 :     for(unsigned j=i; j<ncv; j++) {
      99     2924616 :       mymatrix(i,j)=mymatrix(j,i)=width[k]; // recompose the full inverse matrix
     100     2924616 :       k++;
     101             :     }
     102             :   }
     103      974872 :   return mymatrix;
     104             : }
     105             : 
     106             : inline
     107             : unsigned KernelFunctions::ndim() const {
     108     3891993 :   return center.size();
     109             : }
     110             : 
     111             : inline
     112             : std::vector<double> KernelFunctions::getCenter() const {
     113        6155 :   return center;
     114             : }
     115             : 
     116             : }
     117             : #endif