Line data    Source code

       1             : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
       2             :    Copyright (c) 2015-2023 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 "core/Atoms.h"
      25             : #include "ActionWithInputGrid.h"
      26             : 
      27             : //+PLUMEDOC GRIDANALYSIS CONVERT_TO_FES
      28             : /*
      29             : Convert a histogram, \f$H(x)\f$, to a free energy surface using \f$F(x) = -k_B T \ln H(x)\f$.
      30             : 
      31             : This action allows you to take a free energy surface that was calculated using the \ref HISTOGRAM
      32             : action and to convert it to a free energy surface.  This transformation performed by doing:
      33             : 
      34             : \f[
      35             : F(x) = -k_B T \ln H(x)
      36             : \f]
      37             : 
      38             : The free energy calculated on a grid is output by this action and can be printed using \ref DUMPGRID
      39             : 
      40             : \par Examples
      41             : 
      42             : This is a typical example showing how CONVERT_TO_FES might be used when post processing a trajectory.
      43             : The input below calculates the free energy as a function of the distance between atom 1 and atom 2.
      44             : This is done by accumulating a histogram as a function of this distance using kernel density estimation
      45             : and the HISTOGRAM action.  All the data within this trajectory is used in the construction of this
      46             : HISTOGRAM.  Finally, once all the data has been read in, the histogram is converted to a free energy
      47             : using the formula above and the free energy is output to a file called fes.dat
      48             : 
      49             : \plumedfile
      50             : x: DISTANCE ATOMS=1,2
      51             : hA1: HISTOGRAM ARG=x GRID_MIN=0.0 GRID_MAX=3.0 GRID_BIN=100 BANDWIDTH=0.1
      52             : ff: CONVERT_TO_FES GRID=hA1 TEMP=300
      53             : DUMPGRID GRID=ff FILE=fes.dat
      54             : \endplumedfile
      55             : 
      56             : */
      57             : //+ENDPLUMEDOC
      58             : 
      59             : namespace PLMD {
      60             : namespace gridtools {
      61             : 
      62             : class ConvertToFES : public ActionWithInputGrid {
      63             : private:
      64             :   double simtemp;
      65             :   bool activated;
      66             :   bool mintozero;
      67             : public:
      68             :   static void registerKeywords( Keywords& keys );
      69             :   explicit ConvertToFES(const ActionOptions&ao);
      70             :   unsigned getNumberOfQuantities() const override;
      71          15 :   bool ignoreNormalization() const override { return true; }
      72          12 :   void prepare() override { activated=true; }
      73          23 :   void prepareForAveraging() override { ActionWithInputGrid::prepareForAveraging(); activated=false; }
      74             :   void compute( const unsigned& current, MultiValue& myvals ) const override;
      75             :   void finishComputations( const std::vector<double>& buffer ) override;
      76           0 :   bool isPeriodic() override { return false; }
      77        2234 :   bool onStep() const override { return activated; }
      78             :   void runFinalJobs() override;
      79             : };
      80             : 
      81       10449 : PLUMED_REGISTER_ACTION(ConvertToFES,"CONVERT_TO_FES")
      82             : 
      83          16 : void ConvertToFES::registerKeywords( Keywords& keys ) {
      84          16 :   ActionWithInputGrid::registerKeywords( keys );
      85          32 :   keys.add("optional","TEMP","the temperature at which you are operating");
      86          32 :   keys.addFlag("MINTOZERO",false,"set the minimum in the free energy to be equal to zero");
      87          48 :   keys.remove("STRIDE"); keys.remove("KERNEL"); keys.remove("BANDWIDTH");
      88          48 :   keys.remove("LOGWEIGHTS"); keys.remove("CLEAR"); keys.remove("NORMALIZATION");
      89          16 : }
      90             : 
      91          15 : ConvertToFES::ConvertToFES(const ActionOptions&ao):
      92             :   Action(ao),
      93             :   ActionWithInputGrid(ao),
      94          15 :   activated(false)
      95             : {
      96          15 :   plumed_assert( ingrid->getNumberOfComponents()==1 );
      97             : 
      98             :   // Create a grid
      99          47 :   auto grid=createGrid( "grid", "COMPONENTS=" + getLabel() + " " + ingrid->getInputString() );
     100          15 :   if( ingrid->noDerivatives() ) grid->setNoDerivatives();
     101             :   std::vector<double> fspacing;
     102          15 :   grid->setBounds( ingrid->getMin(), ingrid->getMax(), ingrid->getNbin(), fspacing);
     103          15 :   setAveragingAction( std::move(grid), true );
     104             : 
     105          30 :   simtemp=0.; parse("TEMP",simtemp); parseFlag("MINTOZERO",mintozero);
     106          15 :   if(simtemp>0) simtemp*=plumed.getAtoms().getKBoltzmann();
     107           0 :   else simtemp=plumed.getAtoms().getKbT();
     108          15 :   if( simtemp==0 ) error("TEMP not set - use keyword TEMP");
     109             : 
     110             :   // Now create task list
     111        8486 :   for(unsigned i=0; i<mygrid->getNumberOfPoints(); ++i) addTaskToList(i);
     112             :   // And activate all tasks
     113          15 :   deactivateAllTasks();
     114        8486 :   for(unsigned i=0; i<mygrid->getNumberOfPoints(); ++i) taskFlags[i]=1;
     115          15 :   lockContributors();
     116          15 : }
     117             : 
     118          92 : unsigned ConvertToFES::getNumberOfQuantities() const {
     119          92 :   if( mygrid->noDerivatives() ) return 2;
     120          64 :   return 2 + mygrid->getDimension();
     121             : }
     122             : 
     123       14199 : void ConvertToFES::compute( const unsigned& current, MultiValue& myvals ) const {
     124       14199 :   double val=getFunctionValue( current ); myvals.setValue(1, -simtemp*std::log(val) );
     125       14199 :   if( !mygrid->noDerivatives() && val>0 ) {
     126       36998 :     for(unsigned i=0; i<mygrid->getDimension(); ++i) myvals.setValue( 2+i, -(simtemp/val)*ingrid->getGridElement(current,i+1) );
     127             :   }
     128       14199 : }
     129             : 
     130          23 : void ConvertToFES::finishComputations( const std::vector<double>& buffer ) {
     131          23 :   ActionWithVessel::finishComputations( buffer );
     132          23 :   if(!mintozero) return;
     133             : 
     134           2 :   double optval = mygrid->getGridElement( 0, 0 );
     135        2602 :   for(unsigned i=0; i<mygrid->getNumberOfPoints(); ++i) {
     136        2600 :     double tval = mygrid->getGridElement( i, 0 );
     137        2600 :     if( tval<optval || std::isnan(optval) ) { optval=tval; }
     138             :   }
     139        2602 :   for(unsigned i=0; i<mygrid->getNumberOfPoints(); ++i) mygrid->addToGridElement( i, 0, -optval );
     140             : }
     141             : 
     142          15 : void ConvertToFES::runFinalJobs() {
     143          15 :   activated=true; update();
     144          15 : }
     145             : 
     146             : }
     147             : }