Line data    Source code

       1             : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
       2             :    Copyright (c) 2016-2018 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_adjmat_AlignedMatrixBase_h
      23             : #define __PLUMED_adjmat_AlignedMatrixBase_h
      24             : 
      25             : #include "tools/SwitchingFunction.h"
      26             : #include "AdjacencyMatrixBase.h"
      27             : 
      28             : 
      29             : namespace PLMD {
      30             : namespace adjmat {
      31             : 
      32           1 : class AlignedMatrixBase : public AdjacencyMatrixBase {
      33             : private:
      34             :   unsigned ncol_t;
      35             : /// switching function
      36             :   Matrix<SwitchingFunction> switchingFunction;
      37             : public:
      38             : /// Create manual
      39             :   static void registerKeywords( Keywords& keys );
      40             : /// Constructor
      41             :   explicit AlignedMatrixBase(const ActionOptions&);
      42             : ///
      43             :   void setupConnector( const unsigned& id, const unsigned& i, const unsigned& j, const std::vector<std::string>& desc );
      44             :   virtual void readOrientationConnector( const unsigned& i, const unsigned& j, const std::vector<std::string>& desc ) = 0;
      45             : /// This actually calculates the value of the contact function
      46             :   double calculateWeight( const unsigned& taskCode, const double& weight, multicolvar::AtomValuePack& myatoms ) const ;
      47             :   double compute( const unsigned& tindex, multicolvar::AtomValuePack& myatoms ) const ;
      48             : /// This transforms the dot product
      49             :   virtual double computeVectorFunction( const unsigned& iv, const unsigned& jv,
      50             :                                         const Vector& conn, const std::vector<double>& vec1, const std::vector<double>& vec2,
      51             :                                         Vector& dconn, std::vector<double>& dvec1, std::vector<double>& dvec2 ) const = 0;
      52             : };
      53             : 
      54             : 
      55             : }
      56             : }
      57             : #endif