Energy.cpp

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/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
   Copyright (c) 2013 The plumed team
   (see the PEOPLE file at the root of the distribution for a list of names)

   See http://www.plumed-code.org for more information.

   This file is part of plumed, version 2.0.

   plumed is free software: you can redistribute it and/or modify
   it under the terms of the GNU Lesser General Public License as published by
   the Free Software Foundation, either version 3 of the License, or
   (at your option) any later version.

   plumed is distributed in the hope that it will be useful,
   but WITHOUT ANY WARRANTY; without even the implied warranty of
   MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
   GNU Lesser General Public License for more details.

   You should have received a copy of the GNU Lesser General Public License
   along with plumed.  If not, see <http://www.gnu.org/licenses/>.
+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */
#include "Colvar.h"
#include "ActionRegister.h"
#include "core/PlumedMain.h"
#include "core/Atoms.h"

#include <string>
#include <cmath>

namespace PLMD{
namespace colvar{

//+PLUMEDOC COLVAR ENERGY
/*
Calculate the total energy of the simulation box.

Total energy can be biased with umbrella sampling \cite bart-karp98jpcb or with well tempered metadynamics \cite Bonomi:2009p17935.

Notice that this CV could be unavailable with some MD code. When
it is available, and when also replica exchange is available,
metadynamics applied to ENERGY can be used to decrease the
number of required replicas.

\bug Acceptance for replica exchange when \ref ENERGY is biased
is computed correctly only of all the replicas has the same 
potential energy function. This is for instance not true when
using GROMACS with lambda replica exchange of with plumed-hrex branch.

\par Examples
The following input instructs plumed to print the energy of the system
\verbatim
ENERGY LABEL=ene
PRINT ARG=ene
\endverbatim
(See also \ref PRINT).

*/
//+ENDPLUMEDOC


class Energy : public Colvar {

public:
  Energy(const ActionOptions&);
// active methods:
  void prepare();
  virtual void calculate();
  static void registerKeywords( Keywords& keys );
};


using namespace std;


PLUMED_REGISTER_ACTION(Energy,"ENERGY")

Energy::Energy(const ActionOptions&ao):
PLUMED_COLVAR_INIT(ao)
{
//  if(checkNumericalDerivatives())
//    error("Cannot use NUMERICAL_DERIVATIVES with ENERGY");
  isEnergy=true;
  addValueWithDerivatives(); setNotPeriodic();
  getPntrToValue()->resizeDerivatives(1);
  log<<"  Bibliography ";
  log<<plumed.cite("Bartels and Karplus, J. Phys. Chem. B 102, 865 (1998)");
  log<<plumed.cite("Bonomi and Parrinello, J. Comp. Chem. 30, 1615 (2009)");
  log<<"\n";
}

void Energy::registerKeywords( Keywords& keys ){
  Action::registerKeywords( keys );
  ActionAtomistic::registerKeywords( keys );
  ActionWithValue::registerKeywords( keys );
  keys.remove("NUMERICAL_DERIVATIVES"); 
}

void Energy::prepare(){
  plumed.getAtoms().setCollectEnergy(true);
}

// calculator
void Energy::calculate(){
  setValue( getEnergy() );
  getPntrToComponent(0)->addDerivative(0,1.0);
}

}
}