Line data    Source code

       1             : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
       2             :    Copyright (c) 2011-2023 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             : #include "core/ActionShortcut.h"
      23             : #include "core/ActionRegister.h"
      24             : 
      25             : //+PLUMEDOC MCOLVAR VORONOI
      26             : /*
      27             : Do a voronoi analysis
      28             : 
      29             : This shortcut allows you to perform a [Voronoi analysis](https://en.wikipedia.org/wiki/Voronoi_diagram).
      30             : The input to this action is a rectangular matrix that describes the distances between two sets of points.
      31             : The points for which this action is receiving distances between could be atom positions or they could represent the
      32             : dissimilarities between various trajectory frames that have been stored using [COLLECT_FRAMES](COLLECT_FRAMES.md).
      33             : In the example below the matrix of input distances are distances between the positions of atoms:
      34             : 
      35             : ```plumed
      36             : d: DISTANCE_MATRIX GROUPA=1-10 GROUPB=11-100
      37             : v: VORONOI ARG=d
      38             : ones: ONES SIZE=90
      39             : c: MATRIX_VECTOR_PRODUCT ARG=v,ones
      40             : PRINT ARG=c FILE=colvar
      41             : ```
      42             : 
      43             : The VORONOI action outputs a rectangular matrix, $V$, with the same shape as the input matrix, $D$. $V_{ij}$
      44             : is 1 if $D_{ij}$ is the shortest distance in row $i$.
      45             : 
      46             : 
      47             : */
      48             : //+ENDPLUMEDOC
      49             : 
      50             : namespace PLMD {
      51             : namespace matrixtools {
      52             : 
      53             : class Voronoi : public ActionShortcut {
      54             : public:
      55             :   static void registerKeywords( Keywords& keys );
      56             :   explicit Voronoi(const ActionOptions&);
      57             : };
      58             : 
      59             : PLUMED_REGISTER_ACTION(Voronoi,"VORONOI")
      60             : 
      61          11 : void Voronoi::registerKeywords( Keywords& keys ) {
      62          11 :   ActionShortcut::registerKeywords(keys);
      63          22 :   keys.addInputKeyword("compulsory","ARG","matrix","the distance/adjacency matrix that should be used to perform the voronoi analysis");
      64          22 :   keys.setValueDescription("matrix","a matrix in which element ij is equal to one if the ij component of the input matrix is lower than all the ik elements of the matrix where k is not j and zero otherwise");
      65          11 :   keys.needsAction("NEIGHBORS");
      66          11 : }
      67             : 
      68           6 : Voronoi::Voronoi(const ActionOptions& ao):
      69             :   Action(ao),
      70           6 :   ActionShortcut(ao) {
      71          12 :   readInputLine( getShortcutLabel() + ": NEIGHBORS NLOWEST=1 " + convertInputLineToString() );
      72           6 : }
      73             : 
      74             : }
      75             : }