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 "vesselbase/ActionWithAveraging.h"
      23             : #include "core/ActionRegister.h"
      24             : #include "AverageVessel.h"
      25             : 
      26             : //+PLUMEDOC GRIDCALC AVERAGE
      27             : /*
      28             : Calculate the ensemble average of a collective variable
      29             : 
      30             : The ensemble average for a non-periodic, collective variable, \f$s\f$ is given by the following expression:
      31             : 
      32             : \f[
      33             : \langle s \rangle = \frac{ \sum_{t'=0}^t w(t') s(t') }{ \sum_{t'=0}^t w(t') }
      34             : \f]
      35             : 
      36             : Here the sum runs over a the trajectory and \f$s(t')\f$ is used to denote the value of the collective variable
      37             : at time \f$t'\f$.  The final quantity evaluated is a weighted
      38             : average as the weights, \f$w(t')\f$, allow us to negate the effect any bias might have on the region of phase space
      39             : sampled by the system.  This is discussed in the section of the manual on \ref Analysis.
      40             : 
      41             : When the variable is periodic (e.g. \ref TORSION) and has a value, \f$s\f$, in \f$a \le s \le b\f$ the ensemble average is evaluated using:
      42             : 
      43             : \f[
      44             : \langle s \rangle = a + \frac{b - a}{2\pi} \arctan \left[ \frac{ \sum_{t'=0}^t w(t') \sin\left( \frac{2\pi [s(t')-a]}{b - a} \right) }{ \sum_{t'=0}^t w(t') \cos\left( \frac{2\pi [s(t')-a]}{b - a} \right) } \right]
      45             : \f]
      46             : 
      47             : \par Examples
      48             : 
      49             : The following example calculates the ensemble average for the distance between atoms 1 and 2
      50             : and output this to a file called COLVAR.  In this example it is assumed that no bias is acting
      51             : on the system and that the weights, \f$w(t')\f$ in the formulas above can thus all be set equal
      52             : to one.
      53             : 
      54             : \plumedfile
      55             : d1: DISTANCE ATOMS=1,2
      56             : d1a: AVERAGE ARG=d1
      57             : PRINT ARG=d1a FILE=colvar STRIDE=100
      58             : \endplumedfile
      59             : 
      60             : The following example calculates the ensemble average for the torsional angle involving atoms 1, 2, 3 and 4.
      61             : At variance with the previous example this quantity is periodic so the second formula in the above introduction
      62             : is used to calculate the average.  Furthermore, by using the CLEAR keyword we have specified that block averages
      63             : are to be calculated.  Consequently, after 100 steps all the information acquired thus far in the simulation is
      64             : forgotten and the process of averaging is begun again.  The quantities output in the colvar file are thus the
      65             : block averages taken over the first 100 frames of the trajectory, the block average over the second 100 frames
      66             : of trajectory and so on.
      67             : 
      68             : \plumedfile
      69             : t1: TORSION ATOMS=1,2,3,4
      70             : t1a: AVERAGE ARG=t1 CLEAR=100
      71             : PRINT ARG=t1a FILE=colvar STRIDE=100
      72             : \endplumedfile
      73             : 
      74             : This third example incorporates a bias.  Notice that the effect the bias has on the ensemble average is removed by taking
      75             : advantage of the \ref REWEIGHT_BIAS method.  The final ensemble averages output to the file are thus block ensemble averages for the
      76             : unbiased canonical ensemble at a temperature of 300 K.
      77             : 
      78             : \plumedfile
      79             : t1: TORSION ATOMS=1,2,3,4
      80             : RESTRAINT ARG=t1 AT=pi KAPPA=100.
      81             : ww: REWEIGHT_BIAS TEMP=300
      82             : t1a: AVERAGE ARG=t1 LOGWEIGHTS=ww CLEAR=100
      83             : PRINT ARG=t1a FILE=colvar STRIDE=100
      84             : \endplumedfile
      85             : 
      86             : */
      87             : //+ENDPLUMEDOC
      88             : 
      89             : namespace PLMD {
      90             : namespace analysis {
      91             : 
      92             : class Average : public vesselbase::ActionWithAveraging {
      93             : private:
      94             :   AverageVessel* myaverage;
      95             : public:
      96             :   static void registerKeywords( Keywords& keys );
      97             :   explicit Average( const ActionOptions& );
      98        1025 :   void calculate() override {}
      99        1025 :   void apply() override {}
     100             :   void performOperations( const bool& from_update ) override;
     101             :   void finishAveraging() override;
     102           0 :   bool isPeriodic() override { return false; }
     103           0 :   void performTask( const unsigned&, const unsigned&, MultiValue& ) const override { plumed_error(); }
     104             :   void accumulateAverage( MultiValue& myvals ) const override;
     105             : };
     106             : 
     107       10425 : PLUMED_REGISTER_ACTION(Average,"AVERAGE")
     108             : 
     109           4 : void Average::registerKeywords( Keywords& keys ) {
     110           4 :   vesselbase::ActionWithAveraging::registerKeywords( keys ); keys.use("ARG");
     111           8 :   keys.remove("SERIAL"); keys.remove("LOWMEM");
     112           4 : }
     113             : 
     114           3 : Average::Average( const ActionOptions& ao ):
     115             :   Action(ao),
     116           3 :   ActionWithAveraging(ao)
     117             : {
     118           3 :   addValue(); // Create a value so that we can output the average
     119           3 :   if( getNumberOfArguments()!=1 ) error("only one quantity can be averaged at a time");
     120             :   std::string instring;
     121           3 :   if( getPntrToArgument(0)->isPeriodic() ) {
     122           1 :     std::string min, max; getPntrToArgument(0)->getDomain(min,max);
     123           2 :     instring = "PERIODIC=" + min + "," + max; setPeriodic( min, max );
     124             :   } else {
     125           2 :     setNotPeriodic();
     126             :   }
     127             :   // Create a vessel to hold the average
     128           6 :   vesselbase::VesselOptions da("myaverage","",-1,instring,this);
     129           3 :   Keywords keys; AverageVessel::registerKeywords( keys );
     130           3 :   vesselbase::VesselOptions dar( da, keys );
     131           3 :   auto average=Tools::make_unique<AverageVessel>(dar);
     132           3 :   myaverage = average.get();
     133           3 :   setAveragingAction( std::move(average), false );
     134           6 : }
     135             : 
     136        1022 : void Average::performOperations( const bool& from_update ) {
     137        1022 :   myaverage->accumulate( cweight, getArgument(0) );
     138        1022 : }
     139             : 
     140           0 : void Average::accumulateAverage( MultiValue& myvals ) const {
     141             :   plumed_dbg_assert( myvals.getNumberOfValues()==3 );
     142           0 :   myaverage->accumulate( myvals.get(0), myvals.get(1) );
     143           0 : }
     144             : 
     145        1022 : void Average::finishAveraging() {
     146        1022 :   setValue( myaverage->getAverage() );
     147        1022 : }
     148             : 
     149             : }
     150             : }