Line data    Source code

       1             : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
       2             :    Copyright (c) 2016-2019 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 "core/Atoms.h"
      25             : #include "ActionWithInputGrid.h"
      26             : 
      27             : //+PLUMEDOC GRIDANALYSIS INTERPOLATE_GRID
      28             : /*
      29             : Interpolate a smooth function stored on a grid onto a grid with a smaller grid spacing.
      30             : 
      31             : This action takes a function evaluated on a grid as input and can be used to interpolate the values of that
      32             : function on to a finer grained grid.  The interpolation within this algorithm is done using splines.
      33             : 
      34             : \par Examples
      35             : 
      36             : The input below can be used to postprocess a trajectory.  It calculates a \ref HISTOGRAM as a function the
      37             : distance between atoms 1 and 2 using kernel density estimation.  During the calculation the values of the kernels
      38             : 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
      39             : simulation this function is interpolated onto a finer grid of 200 points between 0.0 and 3.0.
      40             : 
      41             : \plumedfile
      42             : x: DISTANCE ATOMS=1,2
      43             : hA1: HISTOGRAM ARG=x GRID_MIN=0.0 GRID_MAX=3.0 GRID_BIN=100 BANDWIDTH=0.1
      44             : ii: INTERPOLATE_GRID GRID=hA1 GRID_BIN=200
      45             : DUMPGRID GRID=ii FILE=histo.dat
      46             : \endplumedfile
      47             : 
      48             : */
      49             : //+ENDPLUMEDOC
      50             : 
      51             : namespace PLMD {
      52             : namespace gridtools {
      53             : 
      54           4 : class InterpolateGrid : public ActionWithInputGrid {
      55             : public:
      56             :   static void registerKeywords( Keywords& keys );
      57             :   explicit InterpolateGrid(const ActionOptions&ao);
      58             :   unsigned getNumberOfQuantities() const ;
      59             :   void compute( const unsigned& current, MultiValue& myvals ) const ;
      60           0 :   bool isPeriodic() { return false; }
      61             : };
      62             : 
      63        6454 : PLUMED_REGISTER_ACTION(InterpolateGrid,"INTERPOLATE_GRID")
      64             : 
      65           3 : void InterpolateGrid::registerKeywords( Keywords& keys ) {
      66           3 :   ActionWithInputGrid::registerKeywords( keys );
      67          12 :   keys.add("optional","GRID_BIN","the number of bins for the grid");
      68          12 :   keys.add("optional","GRID_SPACING","the approximate grid spacing (to be used as an alternative or together with GRID_BIN)");
      69           9 :   keys.remove("KERNEL"); keys.remove("BANDWIDTH");
      70           3 : }
      71             : 
      72           2 : InterpolateGrid::InterpolateGrid(const ActionOptions&ao):
      73             :   Action(ao),
      74           2 :   ActionWithInputGrid(ao)
      75             : {
      76           2 :   plumed_assert( ingrid->getNumberOfComponents()==1 );
      77           4 :   if( ingrid->noDerivatives() ) error("cannot interpolate a grid that does not have derivatives");
      78             :   // Create the input from the old string
      79          14 :   createGrid( "grid", "COMPONENTS=" + getLabel() + " " + ingrid->getInputString()  );
      80             : 
      81           4 :   std::vector<unsigned> nbin; parseVector("GRID_BIN",nbin);
      82           4 :   std::vector<double> gspacing; parseVector("GRID_SPACING",gspacing);
      83           4 :   if( nbin.size()!=ingrid->getDimension() && gspacing.size()!=ingrid->getDimension() ) {
      84           0 :     error("GRID_BIN or GRID_SPACING must be set");
      85             :   }
      86             : 
      87             :   // Need this for creation of tasks
      88           2 :   mygrid->setBounds( ingrid->getMin(), ingrid->getMax(), nbin, gspacing );
      89           2 :   setAveragingAction( mygrid, true );
      90             : 
      91             :   // Now create task list
      92         204 :   for(unsigned i=0; i<mygrid->getNumberOfPoints(); ++i) addTaskToList(i);
      93             :   // And activate all tasks
      94           2 :   deactivateAllTasks();
      95         604 :   for(unsigned i=0; i<mygrid->getNumberOfPoints(); ++i) taskFlags[i]=1;
      96           2 :   lockContributors();
      97           2 : }
      98             : 
      99           8 : unsigned InterpolateGrid::getNumberOfQuantities() const {
     100          16 :   return 2 + ingrid->getDimension();
     101             : }
     102             : 
     103         200 : void InterpolateGrid::compute( const unsigned& current, MultiValue& myvals ) const {
     104         400 :   std::vector<double> pos( mygrid->getDimension() ); mygrid->getGridPointCoordinates( current, pos );
     105         400 :   std::vector<double> der( mygrid->getDimension() ); double val = getFunctionValueAndDerivatives( pos, der );
     106             :   myvals.setValue( 0, 1.0 ); myvals.setValue(1, val );
     107        1200 :   for(unsigned i=0; i<mygrid->getDimension(); ++i) myvals.setValue( 2+i, der[i] );
     108         200 : }
     109             : 
     110             : }
     111        4839 : }