Line data    Source code

       1             : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
       2             :    Copyright (c) 2013-2023 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_mapping_Mapping_h
      23             : #define __PLUMED_mapping_Mapping_h
      24             : 
      25             : #include "core/ActionAtomistic.h"
      26             : #include "core/ActionWithValue.h"
      27             : #include "core/ActionWithArguments.h"
      28             : #include "vesselbase/ActionWithVessel.h"
      29             : #include "reference/ReferenceConfiguration.h"
      30             : #include <vector>
      31             : #include <map>
      32             : #include <memory>
      33             : 
      34             : namespace PLMD {
      35             : 
      36             : class PDB;
      37             : 
      38             : namespace mapping {
      39             : 
      40             : class Mapping :
      41             :   public ActionAtomistic,
      42             :   public ActionWithArguments,
      43             :   public ActionWithValue,
      44             :   public vesselbase::ActionWithVessel
      45             : {
      46             :   friend class PropertyMap;
      47             :   friend class TrigonometricPathVessel;
      48             :   friend class AdaptivePath;
      49             : private:
      50             : //  The derivative wrt to the distance from the frame
      51             :   std::vector<double> dfframes;
      52             : /// This holds all the reference information
      53             :   std::vector<std::unique_ptr<ReferenceConfiguration> > myframes;
      54             : /// The forces on each of the derivatives (used in apply)
      55             :   std::vector<double> forcesToApply;
      56             : /// The weights of the various configurations
      57             :   std::vector<double> weights;
      58             : /// The list of properties in the property map
      59             :   std::map<std::string,std::vector<double> > property;
      60             : protected:
      61             : /// The (transformed) distance from each frame
      62             :   std::vector<double> fframes;
      63             : /// Get the number of frames in the path
      64             :   unsigned getNumberOfReferencePoints() const;
      65             : /// Finish the setup of the referenceValuePack by transferring atoms and args
      66             :   void finishPackSetup( const unsigned& ifunc, ReferenceValuePack& mypack ) const ;
      67             : /// Calculate the value of the distance from the ith frame
      68             :   double calculateDistanceFunction( const unsigned& ifunc, ReferenceValuePack& myder, const bool& squared ) const ;
      69             : /// Get the value of the weight
      70             :   double getWeight( const unsigned& weight ) const ;
      71             : /// Return the vector of refernece configurations
      72             :   std::vector<std::unique_ptr<ReferenceConfiguration>>& getAllReferenceConfigurations();
      73             : /// Return a pointer to one of the reference configurations
      74             :   ReferenceConfiguration* getReferenceConfiguration( const unsigned& ifunc );
      75             : public:
      76             :   static void registerKeywords( Keywords& keys );
      77             :   explicit Mapping(const ActionOptions&);
      78             : /// Overload the virtual functions that appear in both ActionAtomistic and ActionWithArguments
      79             :   void turnOnDerivatives() override;
      80             :   void calculateNumericalDerivatives( ActionWithValue* a=NULL ) override;
      81             :   void lockRequests() override;
      82             :   void unlockRequests() override;
      83             : /// Distance from a point is never periodic
      84           0 :   bool isPeriodic() override { return false; }
      85             : /// Get the number of derivatives for this action
      86             :   unsigned getNumberOfDerivatives() override;  // N.B. This is replacing the virtual function in ActionWithValue
      87             : /// Get the value of lambda for paths and property maps
      88             :   virtual double getLambda();
      89             : /// This does the transformation of the distance by whatever function is required
      90             :   virtual double transformHD( const double& dist, double& df ) const=0;
      91             : /// Get the number of properties we are projecting onto
      92             :   unsigned getNumberOfProperties() const ;
      93             : /// Get the name of the ith argument
      94             :   std::string getArgumentName( unsigned& iarg );
      95             : /// Get the value of the ith property for the current frame
      96             :   double getPropertyValue( const unsigned& current, const std::string& name ) const ;
      97             : /// Apply the forces
      98             :   void apply() override;
      99             : };
     100             : 
     101             : inline
     102             : unsigned Mapping::getNumberOfReferencePoints() const {
     103         469 :   return myframes.size();
     104             : }
     105             : 
     106             : inline
     107       20192 : unsigned Mapping::getNumberOfDerivatives() {
     108             :   unsigned nat=getNumberOfAtoms();
     109       20192 :   if(nat>0) return 3*nat + 9 + getNumberOfArguments();
     110        2612 :   return getNumberOfArguments();
     111             : }
     112             : 
     113             : inline
     114        5015 : void Mapping::lockRequests() {
     115             :   ActionWithArguments::lockRequests();
     116             :   ActionAtomistic::lockRequests();
     117        5015 : }
     118             : 
     119             : inline
     120        5015 : void Mapping::unlockRequests() {
     121             :   ActionWithArguments::unlockRequests();
     122             :   ActionAtomistic::unlockRequests();
     123        5015 : }
     124             : 
     125             : inline
     126       30972 : double Mapping::getPropertyValue( const unsigned& cur, const std::string& name ) const {
     127       30972 :   return property.find(name)->second[cur];
     128             : }
     129             : 
     130             : inline
     131             : double Mapping::getWeight( const unsigned& current ) const {
     132             :   return weights[current];
     133             : }
     134             : 
     135             : inline
     136             : std::vector<std::unique_ptr<ReferenceConfiguration>>& Mapping::getAllReferenceConfigurations() {
     137           2 :   return myframes;
     138             : }
     139             : 
     140             : inline
     141             : unsigned Mapping::getNumberOfProperties() const {
     142           3 :   return property.size();
     143             : }
     144             : 
     145             : }
     146             : }
     147             : #endif