Line data    Source code

       1             : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
       2             :    Copyright (c) 2016-2023 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/ActionRegister.h"
      23             : #include "core/PlumedMain.h"
      24             : #include "ActionWithInputGrid.h"
      25             : 
      26             : //+PLUMEDOC GRIDANALYSIS INTERPOLATE_GRID
      27             : /*
      28             : Interpolate a smooth function stored on a grid onto a grid with a smaller grid spacing.
      29             : 
      30             : This action takes a function evaluated on a grid as input and can be used to interpolate the values of that
      31             : function on to a finer grained grid.  The interpolation within this algorithm is done using splines.
      32             : 
      33             : \par Examples
      34             : 
      35             : The input below can be used to post process a trajectory.  It calculates a \ref HISTOGRAM as a function the
      36             : distance between atoms 1 and 2 using kernel density estimation.  During the calculation the values of the kernels
      37             : are evaluated at 100 points on a uniform grid between 0.0 and 3.0.  Prior to outputting this function at the end of the
      38             : simulation this function is interpolated onto a finer grid of 200 points between 0.0 and 3.0.
      39             : 
      40             : \plumedfile
      41             : x: DISTANCE ATOMS=1,2
      42             : hA1: HISTOGRAM ARG=x GRID_MIN=0.0 GRID_MAX=3.0 GRID_BIN=100 BANDWIDTH=0.1
      43             : ii: INTERPOLATE_GRID GRID=hA1 GRID_BIN=200
      44             : DUMPGRID GRID=ii FILE=histo.dat
      45             : \endplumedfile
      46             : 
      47             : */
      48             : //+ENDPLUMEDOC
      49             : 
      50             : namespace PLMD {
      51             : namespace gridtools {
      52             : 
      53             : class InterpolateGrid : public ActionWithInputGrid {
      54             : public:
      55             :   static void registerKeywords( Keywords& keys );
      56             :   explicit InterpolateGrid(const ActionOptions&ao);
      57             :   unsigned getNumberOfQuantities() const override;
      58             :   void compute( const unsigned& current, MultiValue& myvals ) const override;
      59           0 :   bool isPeriodic() override {
      60           0 :     return false;
      61             :   }
      62             : };
      63             : 
      64       13789 : PLUMED_REGISTER_ACTION(InterpolateGrid,"INTERPOLATE_GRID")
      65             : 
      66           6 : void InterpolateGrid::registerKeywords( Keywords& keys ) {
      67           6 :   ActionWithInputGrid::registerKeywords( keys );
      68          12 :   keys.add("optional","GRID_BIN","the number of bins for the grid");
      69          12 :   keys.add("optional","GRID_SPACING","the approximate grid spacing (to be used as an alternative or together with GRID_BIN)");
      70           6 :   keys.remove("KERNEL");
      71           6 :   keys.remove("BANDWIDTH");
      72           6 : }
      73             : 
      74           2 : InterpolateGrid::InterpolateGrid(const ActionOptions&ao):
      75             :   Action(ao),
      76           2 :   ActionWithInputGrid(ao) {
      77           2 :   plumed_assert( ingrid->getNumberOfComponents()==1 );
      78           2 :   if( ingrid->noDerivatives() ) {
      79           0 :     error("cannot interpolate a grid that does not have derivatives");
      80             :   }
      81             :   // Create the input from the old string
      82           4 :   auto grid=createGrid( "grid", "COMPONENTS=" + getLabel() + " " + ingrid->getInputString()  );
      83             :   // notice that createGrid also sets mygrid=grid.get()
      84             : 
      85             :   std::vector<unsigned> nbin;
      86           4 :   parseVector("GRID_BIN",nbin);
      87             :   std::vector<double> gspacing;
      88           4 :   parseVector("GRID_SPACING",gspacing);
      89           2 :   if( nbin.size()!=ingrid->getDimension() && gspacing.size()!=ingrid->getDimension() ) {
      90           0 :     error("GRID_BIN or GRID_SPACING must be set");
      91             :   }
      92             : 
      93             :   // Need this for creation of tasks
      94           2 :   grid->setBounds( ingrid->getMin(), ingrid->getMax(), nbin, gspacing );
      95           2 :   setAveragingAction( std::move(grid), true );
      96             : 
      97             :   // Now create task list
      98         202 :   for(unsigned i=0; i<mygrid->getNumberOfPoints(); ++i) {
      99         200 :     addTaskToList(i);
     100             :   }
     101             :   // And activate all tasks
     102           2 :   deactivateAllTasks();
     103         202 :   for(unsigned i=0; i<mygrid->getNumberOfPoints(); ++i) {
     104         200 :     taskFlags[i]=1;
     105             :   }
     106           2 :   lockContributors();
     107           2 : }
     108             : 
     109           8 : unsigned InterpolateGrid::getNumberOfQuantities() const {
     110           8 :   return 2 + ingrid->getDimension();
     111             : }
     112             : 
     113         200 : void InterpolateGrid::compute( const unsigned& current, MultiValue& myvals ) const {
     114         200 :   std::vector<double> pos( mygrid->getDimension() );
     115         200 :   mygrid->getGridPointCoordinates( current, pos );
     116         200 :   std::vector<double> der( mygrid->getDimension() );
     117             :   double val = getFunctionValueAndDerivatives( pos, der );
     118             :   myvals.setValue( 0, 1.0 );
     119             :   myvals.setValue(1, val );
     120         400 :   for(unsigned i=0; i<mygrid->getDimension(); ++i) {
     121         200 :     myvals.setValue( 2+i, der[i] );
     122             :   }
     123         200 : }
     124             : 
     125             : }
     126             : }