Line data    Source code

       1             : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
       2             :    Copyright (c) 2011-2020 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 potential energy of the simulation box.
      36             : 
      37             : The potential energy can be biased e.g. 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 This \ref ENERGY does not include long tail corrections.
      45             : Thus when using e.g. LAMMPS `"pair_modify tail yes"` or GROMACS `"DispCorr Ener"` (or `"DispCorr EnerPres"`),
      46             : the potential energy from \ref ENERGY will be slightly different form the one of the MD code.
      47             : You should still be able to use \ref ENERGY and then reweight your simulation with the correct MD energy value.
      48             : 
      49             : \bug Acceptance for replica exchange when \ref ENERGY is biased
      50             : is computed correctly only if all the replicas have the same
      51             : potential energy function. This is for instance not true when
      52             : using GROMACS with lambda replica exchange or with plumed-hrex branch.
      53             : 
      54             : \par Examples
      55             : 
      56             : The following input instructs plumed to print the energy of the system
      57             : \plumedfile
      58             : ene: ENERGY
      59             : PRINT ARG=ene
      60             : \endplumedfile
      61             : 
      62             : */
      63             : //+ENDPLUMEDOC
      64             : 
      65             : 
      66          78 : class Energy : public Colvar {
      67             : 
      68             : public:
      69             :   explicit Energy(const ActionOptions&);
      70             : // active methods:
      71             :   void prepare();
      72             :   virtual void calculate();
      73             :   unsigned getNumberOfDerivatives();
      74             :   static void registerKeywords( Keywords& keys );
      75             : };
      76             : 
      77             : 
      78             : using namespace std;
      79             : 
      80             : 
      81        7434 : PLUMED_REGISTER_ACTION(Energy,"ENERGY")
      82             : 
      83          39 : Energy::Energy(const ActionOptions&ao):
      84          39 :   PLUMED_COLVAR_INIT(ao)
      85             : {
      86             : //  if(checkNumericalDerivatives())
      87             : //    error("Cannot use NUMERICAL_DERIVATIVES with ENERGY");
      88          39 :   isEnergy=true;
      89          39 :   addValueWithDerivatives(); setNotPeriodic();
      90          39 :   getPntrToValue()->resizeDerivatives(1);
      91          39 :   log<<"  Bibliography ";
      92         117 :   log<<plumed.cite("Bartels and Karplus, J. Phys. Chem. B 102, 865 (1998)");
      93         117 :   log<<plumed.cite("Bonomi and Parrinello, J. Comp. Chem. 30, 1615 (2009)");
      94          39 :   log<<"\n";
      95          39 : }
      96             : 
      97          40 : void Energy::registerKeywords( Keywords& keys ) {
      98          40 :   Action::registerKeywords( keys );
      99          40 :   ActionAtomistic::registerKeywords( keys );
     100          40 :   ActionWithValue::registerKeywords( keys );
     101          80 :   keys.remove("NUMERICAL_DERIVATIVES");
     102          40 : }
     103             : 
     104           2 : unsigned Energy::getNumberOfDerivatives() {
     105           2 :   return 1;
     106             : }
     107             : 
     108        3888 : void Energy::prepare() {
     109        3888 :   plumed.getAtoms().setCollectEnergy(true);
     110        3888 : }
     111             : 
     112             : // calculator
     113        3888 : void Energy::calculate() {
     114        7776 :   setValue( getEnergy() );
     115        3888 :   getPntrToComponent(0)->addDerivative(0,1.0);
     116        3888 : }
     117             : 
     118             : }
     119        5517 : }
     120             : 
     121             : 
     122             :