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_colvar_PathMSDBase_h
      23             : #define __PLUMED_colvar_PathMSDBase_h
      24             : 
      25             : #include "Colvar.h"
      26             : #include "core/ActionRegister.h"
      27             : 
      28             : #include "tools/PDB.h"
      29             : #include "tools/RMSD.h"
      30             : 
      31             : namespace PLMD {
      32             : namespace colvar {
      33             : 
      34             : class PathMSDBase : public Colvar {
      35             : /// this class is a general container for path stuff
      36      300920 :   class ImagePath {
      37             :   public:
      38             :     // cardinal indexing: needed to map over msd
      39             :     unsigned index;
      40             :     // spiwok indexing
      41             :     std::vector<double> property;
      42             :     // distance
      43             :     double distance;
      44             :     // similarity (exp - lambda distance) or other
      45             :     double similarity;
      46             :     // derivatives of the distance
      47             :     std::vector<Vector> distder;
      48             :     // here one can add a pointer to a value (hypothetically providing a distance from a point)
      49             :   };
      50             :   struct imgOrderByDist {
      51             :     bool operator ()(ImagePath const& a, ImagePath const& b) {
      52           0 :       return (a).distance < (b).distance;
      53             :     }
      54             :   };
      55             :   struct imgOrderBySimilarity {
      56             :     bool operator ()(ImagePath const& a, ImagePath const& b) {
      57             :       return (a).similarity > (b).similarity;
      58             :     }
      59             :   };
      60             : 
      61             :   bool nopbc;
      62             : 
      63             :   double lambda;
      64             :   int neigh_size;
      65             :   int neigh_stride;
      66             :   std::vector<RMSD> msdv;
      67             :   std::string reference;
      68             :   std::vector<Vector> derivs_s;
      69             :   std::vector<Vector> derivs_z;
      70             :   std::vector <ImagePath> imgVec; // this can be used for doing neighlist
      71             : 
      72             :   //variables used for the close structure method, i is the number of reference structures
      73             :   double epsilonClose; //the maximal distance between the close and the current structure before reassignment
      74             :   int debugClose; //turns on debug mode
      75             :   int logClose; //turns on logging
      76             :   RMSD rmsdPosClose; //rmsd between the current and the close structure
      77             :   bool firstPosClose; //flag indicating the first time we need to calculate the distance between the close and the current structure
      78             :   bool computeRefClose; //flag indicating necessity to recompute accurately all distances and rotation matrices between the close structure and reference str
      79             :   std::vector<Tensor> rotationRefClose; //Tensor[i] saved rotation matrices between the close structure and reference structures
      80             :   Tensor rotationPosClose; //rotation matrix between the close and the current structure
      81             :   std::array<std::array<Tensor,3>,3> drotationPosCloseDrr01; //Tensor[3][3]; //derivation of the rotation matrix w.r.t rr01, necessary for calculation of derivations
      82             :   std::vector<unsigned> savedIndices; //saved indices of imgVec from previous steps, used for recalculating after neighbourlist update
      83             : protected:
      84             :   std::vector<PDB> pdbv;
      85             :   std::vector<std::string> labels;
      86             :   std::vector< std::vector<double> > indexvec; // use double to allow isomaps
      87             :   unsigned nframes;
      88             : public:
      89             :   explicit PathMSDBase(const ActionOptions&);
      90             :   ~PathMSDBase();
      91             : // active methods:
      92             :   void calculate() override;
      93             : //  virtual void prepare();
      94             :   static void registerKeywords(Keywords& keys);
      95             : };
      96             : 
      97             : }
      98             : }
      99             : 
     100             : #endif
     101             :