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/Matrix.h"
      25             : 
      26             : //+PLUMEDOC MATRIX DISTANCE_MATRIX
      27             : /*
      28             : Calculate a matrix of distances between atoms.
      29             : 
      30             : To calculate the matrix of distances between every distinct pair of atoms in a single group you can use the following command:
      31             : 
      32             : ```plumed
      33             : d1: DISTANCE_MATRIX GROUP=1-7
      34             : ```
      35             : 
      36             : If you would like to calculate the matrix of distances between the atoms in two different groups of atoms you can use the following command:
      37             : 
      38             : ```plumed
      39             : d2: DISTANCE_MATRIX GROUPA=1-7 GROUPB=8-20
      40             : ```
      41             : 
      42             : Once you have calculated your distance matrix in this way you can do many of the operations that were discussed for [CONTACT_MATRIX](CONTACT_MATRIX.md) with the output.
      43             : For example, you can use the COMPONENTS flag to calcuate the $x$, $y$ and $z$ components of the vectors connecting the atoms in your two groups by using
      44             : an input like that shown below:
      45             : 
      46             : ```plumed
      47             : d1: DISTANCE_MATRIX GROUP=1-7 COMPONENTS
      48             : ```
      49             : 
      50             : ## Optimisation details
      51             : 
      52             : If for some reaon, you only want to calculate the distances if they are less than a certain CUTOFF you can add the cutoff keyword as follows:
      53             : 
      54             : ```plumed
      55             : d3: DISTANCE_MATRIX GROUP=1-7 CUTOFF=1.0
      56             : ```
      57             : 
      58             : This command will only store those distances that are less than 1 nm.  Notice, however, that the cutoff implemented here is __not__ a continuous function.
      59             : You should thus be careful when commands such as this one above to ensure that any quantities that are forced have continuous derivatives.  If you use
      60             : the CUTOFF keyword, however, many of the features that are used to optimise [CONTACT_MATRIX](CONTACT_MATRIX.md) are used for this action.
      61             : 
      62             : */
      63             : //+ENDPLUMEDOC
      64             : 
      65             : 
      66             : namespace PLMD {
      67             : namespace adjmat {
      68             : 
      69             : class DistanceMatrix : public AdjacencyMatrixBase {
      70             : private:
      71             :   double cutoff;
      72             : public:
      73             : /// Create manual
      74             :   static void registerKeywords( Keywords& keys );
      75             : /// Constructor
      76             :   explicit DistanceMatrix(const ActionOptions&);
      77             : /// This does nothing
      78             :   double calculateWeight( const Vector& pos1, const Vector& pos2, const unsigned& natoms, MultiValue& myvals ) const ;
      79             : };
      80             : 
      81             : PLUMED_REGISTER_ACTION(DistanceMatrix,"DISTANCE_MATRIX")
      82             : 
      83         178 : void DistanceMatrix::registerKeywords( Keywords& keys ) {
      84         178 :   AdjacencyMatrixBase::registerKeywords( keys );
      85         178 :   keys.add("compulsory","CUTOFF","-1","ignore distances that have a value larger than this cutoff");
      86         178 : }
      87             : 
      88          92 : DistanceMatrix::DistanceMatrix( const ActionOptions& ao ):
      89             :   Action(ao),
      90          92 :   AdjacencyMatrixBase(ao) {
      91             :   // And set the link cell cutoff
      92          92 :   log.printf("  weight is distance between atoms \n");
      93          92 :   parse("CUTOFF",cutoff);
      94          92 :   if( cutoff<0 ) {
      95           5 :     setLinkCellCutoff( true, std::numeric_limits<double>::max() );
      96             :   } else {
      97          87 :     log.printf("  ignoring distances that are larger than %f \n", cutoff);
      98          87 :     setLinkCellCutoff( true, cutoff );
      99             :   }
     100          92 : }
     101             : 
     102     5857010 : double DistanceMatrix::calculateWeight( const Vector& pos1, const Vector& pos2, const unsigned& natoms, MultiValue& myvals ) const {
     103     5857010 :   Vector distance = pos2;
     104     5857010 :   double mod = distance.modulo();
     105     5857010 :   if( cutoff<0 || mod<cutoff ) {
     106     5157580 :     double invd = 1.0/mod;
     107     5157580 :     addAtomDerivatives( 0, (-invd)*distance, myvals );
     108     5157580 :     addAtomDerivatives( 1, (+invd)*distance, myvals );
     109     5157580 :     addBoxDerivatives( (-invd)*Tensor(distance,distance), myvals );
     110             :   }
     111     5857010 :   return mod;
     112             : }
     113             : 
     114             : }
     115             : }
     116             :