Line data    Source code

       1             : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
       2             :    Copyright (c) 2015-2017 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             : #include "AdjacencyMatrixBase.h"
      23             : #include "core/ActionRegister.h"
      24             : #include "tools/SwitchingFunction.h"
      25             : #include "tools/Matrix.h"
      26             : 
      27             : //+PLUMEDOC MATRIX DISTANCE_MATRIX
      28             : /*
      29             : Calculate a matrix of distances
      30             : 
      31             : \par Examples
      32             : 
      33             : */
      34             : //+ENDPLUMEDOC
      35             : 
      36             : 
      37             : namespace PLMD {
      38             : namespace adjmat {
      39             : 
      40             : class DistanceMatrix : public AdjacencyMatrixBase {
      41             : private:
      42             :   double cutoff;
      43             : public:
      44             : /// Create manual
      45             :   static void registerKeywords( Keywords& keys );
      46             : /// Constructor
      47             :   explicit DistanceMatrix(const ActionOptions&);
      48             : /// This does nothing
      49             :   double calculateWeight( const Vector& pos1, const Vector& pos2, const unsigned& natoms, MultiValue& myvals ) const ;
      50             : };
      51             : 
      52             : PLUMED_REGISTER_ACTION(DistanceMatrix,"DISTANCE_MATRIX")
      53             : 
      54         178 : void DistanceMatrix::registerKeywords( Keywords& keys ) {
      55         178 :   AdjacencyMatrixBase::registerKeywords( keys );
      56         356 :   keys.add("compulsory","CUTOFF","-1","ignore distances that have a value larger than this cutoff");
      57         178 : }
      58             : 
      59          92 : DistanceMatrix::DistanceMatrix( const ActionOptions& ao ):
      60             :   Action(ao),
      61          92 :   AdjacencyMatrixBase(ao)
      62             : {
      63             :   // And set the link cell cutoff
      64          92 :   log.printf("  weight is distance between atoms \n");
      65          92 :   parse("CUTOFF",cutoff);
      66          92 :   if( cutoff<0 ) {
      67           5 :     setLinkCellCutoff( true, std::numeric_limits<double>::max() );
      68             :   } else {
      69          87 :     log.printf("  ignoring distances that are larger than %f \n", cutoff);
      70          87 :     setLinkCellCutoff( true, cutoff );
      71             :   }
      72          92 : }
      73             : 
      74     5857010 : double DistanceMatrix::calculateWeight( const Vector& pos1, const Vector& pos2, const unsigned& natoms, MultiValue& myvals ) const {
      75     5857010 :   Vector distance = pos2; double mod = distance.modulo();
      76     5857010 :   if( cutoff<0 || mod<cutoff ) {
      77     5157580 :     double invd = 1.0/mod;
      78     5157580 :     addAtomDerivatives( 0, (-invd)*distance, myvals );
      79     5157580 :     addAtomDerivatives( 1, (+invd)*distance, myvals );
      80     5157580 :     addBoxDerivatives( (-invd)*Tensor(distance,distance), myvals );
      81             :   }
      82     5857010 :   return mod;
      83             : }
      84             : 
      85             : }
      86             : }
      87             :