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_reference_ReferenceAtoms_h
      23             : #define __PLUMED_reference_ReferenceAtoms_h
      24             : 
      25             : #include "ReferenceConfiguration.h"
      26             : 
      27             : namespace PLMD {
      28             : 
      29             : class Pbc;
      30             : 
      31             : /// \ingroup TOOLBOX
      32             : /// In many applications (e.g. paths, fields, property maps) it is necessary to calculate
      33             : /// the distance between two configurations.  These distances can be calculated in a variety of
      34             : /// different ways.  For instance, one can assert that the distance between the two configuration
      35             : /// is the distance one would have to move all the atoms to transform configuration 1 into configuration
      36             : /// 2. Alternatively, one could calculate the values of a large set of collective coordinates in the two
      37             : /// configurations and then calculate the Euclidean distances between these two points in the resulting
      38             : /// high-dimensional vector space.  Lastly, one can combine these two forms of distance calculation to calculate
      39             : /// a hybrid distance.  Plumed allows one to use all these forms of distance calculations and also to implement
      40             : /// new forms of distance.  You should inherit from this class if your distance involves reference atomic positions.
      41             : /// This class and \ref PLMD::ReferenceArguments mirror the functionalities in and \ref PLMD::ActionAtomistic
      42             : /// and \ref PLMD::ActionWithArguments respectively but for distances.
      43             : 
      44             : class ReferenceAtoms :
      45             :   virtual public ReferenceConfiguration {
      46             :   friend class Direction;
      47             :   friend class SingleDomainRMSD;
      48             :   friend class MultiDomainRMSD;
      49             :   friend class ReferenceConfiguration;
      50             : private:
      51             : /// This flag tells us if the user has disabled checking of the input in order to
      52             : /// do fancy paths with weird inputs
      53             :   bool checks_were_disabled;
      54             : /// The atoms to be used to align the instantaneous atomic positions
      55             : /// to the reference configuration
      56             :   std::vector<double> align;
      57             : /// The atoms to be used to calculate the distance the atoms have moved
      58             : /// from the reference configuration
      59             :   std::vector<double> displace;
      60             : /// The positions of the atoms in the reference configuration
      61             :   std::vector<Vector> reference_atoms;
      62             : /// The indices of the atoms in the pdb file
      63             :   std::vector<AtomNumber> indices;
      64             : /// The indeces for setting derivatives
      65             :   std::vector<unsigned> atom_der_index;
      66             : protected:
      67             : /// Read in the atoms from the pdb file
      68             :   void readAtomsFromPDB( const PDB&, const bool allowblocks=false );
      69             : /// Add atom indices to list
      70             :   void setAtomIndices( const std::vector<AtomNumber>& atomnumbers );
      71             : /// Read a list of atoms from the pdb input file
      72             :   bool parseAtomList( const std::string&, std::vector<unsigned>& );
      73             : /// Get the position of the ith atom
      74             :   Vector getReferencePosition( const unsigned& iatom ) const ;
      75             : /// Add derivatives to iatom th atom in list
      76             : //  void addAtomicDerivatives( const unsigned& , const Vector& );
      77             : /// Get the atomic derivatives on the ith atom in the list
      78             : //  Vector retrieveAtomicDerivatives( const unsigned& ) const ;
      79             : /// Add derivatives to the viral
      80             : //  void addBoxDerivatives( const Tensor& );
      81             : /// This does the checks that are always required
      82             :   void singleDomainRequests( std::vector<AtomNumber>&, bool disable_checks );
      83             : public:
      84             :   explicit ReferenceAtoms( const ReferenceConfigurationOptions& ro );
      85             : /// This returns the number of reference atom positions
      86             :   unsigned getNumberOfReferencePositions() const override;
      87             : /// Get the reference positions
      88             :   const std::vector<Vector> & getReferencePositions() const override;
      89             : /// This allows us to use a single pos array with RMSD objects using different atom indexes
      90             :   unsigned getAtomIndex( const unsigned& ) const ;
      91             : /// Get the atoms required (additional checks are required when we have multiple domains)
      92             :   void getAtomRequests( std::vector<AtomNumber>&, bool disable_checks=false ) override;
      93             : /// Set the positions of the reference atoms
      94             :   virtual void setReferenceAtoms( const std::vector<Vector>& conf, const std::vector<double>& align_in, const std::vector<double>& displace_in )=0;
      95             : /// Return all atom indexes
      96             :   const std::vector<AtomNumber>& getAbsoluteIndexes() override;
      97             : /// This returns how many atoms there should be
      98             :   unsigned getNumberOfAtoms() const ;
      99             : /// Displace the positions of the reference atoms a bit
     100             :   void displaceReferenceAtoms( const double& weight, const std::vector<Vector>& dir );
     101             : /// Extract a displacement from a position in space
     102           0 :   virtual void extractAtomicDisplacement( const std::vector<Vector>& pos, std::vector<Vector>& direction ) const {
     103           0 :     plumed_error();
     104             :   }
     105             : /// Project the displacement on a vector
     106           0 :   virtual double projectAtomicDisplacementOnVector( const bool& normalized, const std::vector<Vector>& eigv, ReferenceValuePack& mypack ) const {
     107           0 :     plumed_error();
     108             :   }
     109             : /// Get the vector of alignment weights
     110             :   const std::vector<double> & getAlign() const ;
     111             : /// Get the vector of displacement weights
     112             :   const std::vector<double> & getDisplace() const ;
     113             : };
     114             : 
     115             : inline
     116             : const std::vector<double> & ReferenceAtoms::getAlign() const {
     117      271380 :   return align;
     118             : }
     119             : 
     120             : inline
     121             : const std::vector<double> & ReferenceAtoms::getDisplace() const {
     122      271381 :   return displace;
     123             : }
     124             : 
     125             : inline
     126      150285 : unsigned ReferenceAtoms::getNumberOfReferencePositions() const {
     127             :   plumed_dbg_assert( atom_der_index.size()==reference_atoms.size() );
     128      150285 :   return reference_atoms.size();
     129             : }
     130             : 
     131             : inline
     132             : unsigned ReferenceAtoms::getNumberOfAtoms() const {
     133      314703 :   return atom_der_index.size(); // reference_atoms.size();
     134             : }
     135             : 
     136             : inline
     137             : unsigned ReferenceAtoms::getAtomIndex( const unsigned& iatom ) const {
     138             :   plumed_dbg_assert( iatom<atom_der_index.size() );
     139             :   plumed_dbg_assert( atom_der_index[iatom]<reference_atoms.size() );
     140    17303434 :   return atom_der_index[iatom];
     141             : }
     142             : 
     143             : inline
     144             : Vector ReferenceAtoms::getReferencePosition( const unsigned& iatom ) const {
     145             :   plumed_dbg_assert( iatom<reference_atoms.size() );
     146       71395 :   return reference_atoms[iatom];
     147             : }
     148             : 
     149             : inline
     150     2690664 : const std::vector<Vector> & ReferenceAtoms::getReferencePositions() const {
     151     2690664 :   return reference_atoms;
     152             : }
     153             : 
     154             : inline
     155           4 : const std::vector<AtomNumber>& ReferenceAtoms::getAbsoluteIndexes() {
     156           4 :   return indices;
     157             : }
     158             : 
     159             : 
     160             : }
     161             : #endif
     162             :