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, H(x), to a free energy surface using F(x) = -k_B T ln H(x).
      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 {
      72          15 :     return true;
      73             :   }
      74          12 :   void prepare() override {
      75          12 :     activated=true;
      76          12 :   }
      77          23 :   void prepareForAveraging() override {
      78          23 :     ActionWithInputGrid::prepareForAveraging();
      79          23 :     activated=false;
      80          23 :   }
      81             :   void compute( const unsigned& current, MultiValue& myvals ) const override;
      82             :   void finishComputations( const std::vector<double>& buffer ) override;
      83           0 :   bool isPeriodic() override {
      84           0 :     return false;
      85             :   }
      86        2234 :   bool onStep() const override {
      87        2234 :     return activated;
      88             :   }
      89             :   void runFinalJobs() override;
      90             : };
      91             : 
      92       13815 : PLUMED_REGISTER_ACTION(ConvertToFES,"CONVERT_TO_FES")
      93             : 
      94          19 : void ConvertToFES::registerKeywords( Keywords& keys ) {
      95          19 :   ActionWithInputGrid::registerKeywords( keys );
      96          38 :   keys.add("optional","TEMP","the temperature at which you are operating");
      97          38 :   keys.addFlag("MINTOZERO",false,"set the minimum in the free energy to be equal to zero");
      98          19 :   keys.remove("STRIDE");
      99          19 :   keys.remove("KERNEL");
     100          19 :   keys.remove("BANDWIDTH");
     101          19 :   keys.remove("LOGWEIGHTS");
     102          19 :   keys.remove("CLEAR");
     103          19 :   keys.remove("NORMALIZATION");
     104          19 : }
     105             : 
     106          15 : ConvertToFES::ConvertToFES(const ActionOptions&ao):
     107             :   Action(ao),
     108             :   ActionWithInputGrid(ao),
     109          15 :   activated(false) {
     110          15 :   plumed_assert( ingrid->getNumberOfComponents()==1 );
     111             : 
     112             :   // Create a grid
     113          30 :   auto grid=createGrid( "grid", "COMPONENTS=" + getLabel() + " " + ingrid->getInputString() );
     114          15 :   if( ingrid->noDerivatives() ) {
     115           7 :     grid->setNoDerivatives();
     116             :   }
     117             :   std::vector<double> fspacing;
     118          15 :   grid->setBounds( ingrid->getMin(), ingrid->getMax(), ingrid->getNbin(), fspacing);
     119          15 :   setAveragingAction( std::move(grid), true );
     120             : 
     121          15 :   simtemp=0.;
     122          15 :   parse("TEMP",simtemp);
     123          15 :   parseFlag("MINTOZERO",mintozero);
     124          15 :   if(simtemp>0) {
     125          15 :     simtemp*=plumed.getAtoms().getKBoltzmann();
     126             :   } else {
     127           0 :     simtemp=plumed.getAtoms().getKbT();
     128             :   }
     129          15 :   if( simtemp==0 ) {
     130           0 :     error("TEMP not set - use keyword TEMP");
     131             :   }
     132             : 
     133             :   // Now create task list
     134        8486 :   for(unsigned i=0; i<mygrid->getNumberOfPoints(); ++i) {
     135        8471 :     addTaskToList(i);
     136             :   }
     137             :   // And activate all tasks
     138          15 :   deactivateAllTasks();
     139        8486 :   for(unsigned i=0; i<mygrid->getNumberOfPoints(); ++i) {
     140        8471 :     taskFlags[i]=1;
     141             :   }
     142          15 :   lockContributors();
     143          15 : }
     144             : 
     145          92 : unsigned ConvertToFES::getNumberOfQuantities() const {
     146          92 :   if( mygrid->noDerivatives() ) {
     147             :     return 2;
     148             :   }
     149          64 :   return 2 + mygrid->getDimension();
     150             : }
     151             : 
     152       14199 : void ConvertToFES::compute( const unsigned& current, MultiValue& myvals ) const {
     153       14199 :   double val=getFunctionValue( current );
     154       14199 :   myvals.setValue(1, -simtemp*std::log(val) );
     155       14199 :   if( !mygrid->noDerivatives() && val>0 ) {
     156       36998 :     for(unsigned i=0; i<mygrid->getDimension(); ++i) {
     157       27228 :       myvals.setValue( 2+i, -(simtemp/val)*ingrid->getGridElement(current,i+1) );
     158             :     }
     159             :   }
     160       14199 : }
     161             : 
     162          23 : void ConvertToFES::finishComputations( const std::vector<double>& buffer ) {
     163          23 :   ActionWithVessel::finishComputations( buffer );
     164          23 :   if(!mintozero) {
     165             :     return;
     166             :   }
     167             : 
     168           2 :   double optval = mygrid->getGridElement( 0, 0 );
     169        2602 :   for(unsigned i=0; i<mygrid->getNumberOfPoints(); ++i) {
     170        2600 :     double tval = mygrid->getGridElement( i, 0 );
     171        2600 :     if( tval<optval || std::isnan(optval) ) {
     172             :       optval=tval;
     173             :     }
     174             :   }
     175        2602 :   for(unsigned i=0; i<mygrid->getNumberOfPoints(); ++i) {
     176        2600 :     mygrid->addToGridElement( i, 0, -optval );
     177             :   }
     178             : }
     179             : 
     180          15 : void ConvertToFES::runFinalJobs() {
     181          15 :   activated=true;
     182          15 :   update();
     183          15 : }
     184             : 
     185             : }
     186             : }