Line data    Source code

       1             : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
       2             :    Copyright (c) 2011-2018 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 "Colvar.h"
      23             : #include "ActionRegister.h"
      24             : #include "core/PlumedMain.h"
      25             : #include "core/Atoms.h"
      26             : 
      27             : #include <string>
      28             : #include <cmath>
      29             : 
      30             : namespace PLMD {
      31             : namespace colvar {
      32             : 
      33             : //+PLUMEDOC COLVAR ENERGY
      34             : /*
      35             : Calculate the total energy of the simulation box.
      36             : 
      37             : Total energy can be biased with umbrella sampling \cite bart-karp98jpcb or with well tempered metadynamics \cite Bonomi:2009p17935.
      38             : 
      39             : Notice that this CV could be unavailable with some MD code. When
      40             : it is available, and when also replica exchange is available,
      41             : metadynamics applied to ENERGY can be used to decrease the
      42             : number of required replicas.
      43             : 
      44             : \bug Acceptance for replica exchange when \ref ENERGY is biased
      45             : is computed correctly only of all the replicas has the same
      46             : potential energy function. This is for instance not true when
      47             : using GROMACS with lambda replica exchange of with plumed-hrex branch.
      48             : 
      49             : \par Examples
      50             : 
      51             : The following input instructs plumed to print the energy of the system
      52             : \verbatim
      53             : ENERGY LABEL=ene
      54             : PRINT ARG=ene
      55             : \endverbatim
      56             : (See also \ref PRINT).
      57             : 
      58             : */
      59             : //+ENDPLUMEDOC
      60             : 
      61             : 
      62           2 : class Energy : public Colvar {
      63             : 
      64             : public:
      65             :   explicit Energy(const ActionOptions&);
      66             : // active methods:
      67             :   void prepare();
      68             :   virtual void calculate();
      69             :   unsigned getNumberOfDerivatives();
      70             :   static void registerKeywords( Keywords& keys );
      71             : };
      72             : 
      73             : 
      74             : using namespace std;
      75             : 
      76             : 
      77        2524 : PLUMED_REGISTER_ACTION(Energy,"ENERGY")
      78             : 
      79           1 : Energy::Energy(const ActionOptions&ao):
      80           1 :   PLUMED_COLVAR_INIT(ao)
      81             : {
      82             : //  if(checkNumericalDerivatives())
      83             : //    error("Cannot use NUMERICAL_DERIVATIVES with ENERGY");
      84           1 :   isEnergy=true;
      85           1 :   addValueWithDerivatives(); setNotPeriodic();
      86           1 :   getPntrToValue()->resizeDerivatives(1);
      87           1 :   log<<"  Bibliography ";
      88           1 :   log<<plumed.cite("Bartels and Karplus, J. Phys. Chem. B 102, 865 (1998)");
      89           1 :   log<<plumed.cite("Bonomi and Parrinello, J. Comp. Chem. 30, 1615 (2009)");
      90           1 :   log<<"\n";
      91           1 : }
      92             : 
      93           2 : void Energy::registerKeywords( Keywords& keys ) {
      94           2 :   Action::registerKeywords( keys );
      95           2 :   ActionAtomistic::registerKeywords( keys );
      96           2 :   ActionWithValue::registerKeywords( keys );
      97           2 :   keys.remove("NUMERICAL_DERIVATIVES");
      98           2 : }
      99             : 
     100           2 : unsigned Energy::getNumberOfDerivatives() {
     101           2 :   return 1;
     102             : }
     103             : 
     104          50 : void Energy::prepare() {
     105          50 :   plumed.getAtoms().setCollectEnergy(true);
     106          50 : }
     107             : 
     108             : // calculator
     109          50 : void Energy::calculate() {
     110          50 :   setValue( getEnergy() );
     111          50 :   getPntrToComponent(0)->addDerivative(0,1.0);
     112          50 : }
     113             : 
     114             : }
     115        2523 : }
     116             : 
     117             : 
     118             :