Line data    Source code

       1             : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
       2             :    Copyright (c) 2011-2023 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/ActionToPutData.h"
      23             : #include "core/DomainDecomposition.h"
      24             : #include "core/PlumedMain.h"
      25             : #include "core/ActionSet.h"
      26             : #include "core/ActionRegister.h"
      27             : 
      28             : namespace PLMD {
      29             : namespace colvar {
      30             : 
      31             : //+PLUMEDOC COLVAR ENERGY
      32             : /*
      33             : Calculate the total potential energy of the simulation box.
      34             : 
      35             : The potential energy can be biased e.g. with umbrella sampling \cite bart-karp98jpcb or with well-tempered metadynamics \cite Bonomi:2009p17935.
      36             : 
      37             : Notice that this CV could be unavailable with some MD code. When
      38             : it is available, and when also replica exchange is available,
      39             : metadynamics applied to ENERGY can be used to decrease the
      40             : number of required replicas.
      41             : 
      42             : \warning Some MD engines communicate to PLUMED the energy without the long tail corrections,
      43             : leading to a small mismatch. If this is the case, use the energy from the MD engine for
      44             : reweighting. See \issue{567}.
      45             : 
      46             : \bug Acceptance for replica exchange when \ref ENERGY is biased
      47             : is computed correctly only if all the replicas have the same
      48             : potential energy function. This is for instance not true when
      49             : using GROMACS with lambda replica exchange or with plumed-hrex branch.
      50             : 
      51             : \par Examples
      52             : 
      53             : The following input instructs plumed to print the energy of the system
      54             : \plumedfile
      55             : ene: ENERGY
      56             : PRINT ARG=ene
      57             : \endplumedfile
      58             : 
      59             : */
      60             : //+ENDPLUMEDOC
      61             : 
      62             : 
      63             : class Energy : public ActionToPutData {
      64             : private:
      65             : /// This is used to sum the data
      66             :   DomainDecomposition* interface;
      67             : /// This is the list of forces that must be scaled
      68             :   std::vector<ActionToPutData*> forces_to_scale;
      69             : public:
      70             :   explicit Energy(const ActionOptions&);
      71             : // active methods:
      72             :   static void registerKeywords( Keywords& keys );
      73             :   void wait() override;
      74             :   void apply() override;
      75             : };
      76             : 
      77             : 
      78             : PLUMED_REGISTER_ACTION(Energy,"ENERGY")
      79             : 
      80          40 : Energy::Energy(const ActionOptions&ao):
      81             :   Action(ao),
      82             :   ActionToPutData(ao),
      83          40 :   interface(NULL) {
      84          40 :   plumed.setEnergyValue( getLabel() );
      85             :   std::vector<unsigned> shape;
      86          40 :   addValue( shape );
      87          40 :   setNotPeriodic();
      88          80 :   setUnit( "energy", "default" );
      89          40 :   ActionToPutData* px=plumed.getActionSet().selectWithLabel< ActionToPutData*>("posx");
      90          40 :   plumed_assert(px);
      91          40 :   forces_to_scale.push_back(px);
      92          40 :   addDependency( px );
      93          40 :   ActionToPutData* py=plumed.getActionSet().selectWithLabel< ActionToPutData*>("posy");
      94          40 :   plumed_assert(py);
      95          40 :   forces_to_scale.push_back(py);
      96          40 :   addDependency( py );
      97          40 :   ActionToPutData* pz=plumed.getActionSet().selectWithLabel< ActionToPutData*>("posz");
      98          40 :   plumed_assert(pz);
      99          40 :   forces_to_scale.push_back(pz);
     100          40 :   addDependency( pz );
     101          40 :   ActionToPutData* bx=plumed.getActionSet().selectWithLabel< ActionToPutData*>("Box");
     102          40 :   plumed_assert(bx);
     103          40 :   forces_to_scale.push_back(bx);
     104          40 :   addDependency( bx );
     105          40 :   log<<"  Bibliography ";
     106          80 :   log<<plumed.cite("Bartels and Karplus, J. Phys. Chem. B 102, 865 (1998)");
     107          80 :   log<<plumed.cite("Bonomi and Parrinello, J. Comp. Chem. 30, 1615 (2009)");
     108          40 :   log<<"\n";
     109          40 : }
     110             : 
     111          44 : void Energy::registerKeywords( Keywords& keys ) {
     112          44 :   Action::registerKeywords( keys );
     113          44 : }
     114             : 
     115        3989 : void Energy::wait() {
     116        3989 :   if( !interface ) {
     117          40 :     std::vector<DomainDecomposition*> allput=plumed.getActionSet().select<DomainDecomposition*>();
     118          40 :     if( allput.size()>1 ) {
     119           0 :       warning("found more than one interface so don't know how to sum energy");
     120             :     }
     121          40 :     interface = allput[0];
     122             :   }
     123        3989 :   ActionToPutData::wait();
     124        3989 :   if( interface ) {
     125        3989 :     interface->sumOverDomains( copyOutput(0) );
     126             :   }
     127        3989 : }
     128             : 
     129        3989 : void Energy::apply() {
     130        3989 :   if( getPntrToValue()->forcesWereAdded() ) {
     131         250 :     for(unsigned i=0; i<forces_to_scale.size(); ++i) {
     132         200 :       forces_to_scale[i]->rescaleForces( 1.- getPntrToValue()->getForce(0));
     133             :     }
     134             :   }
     135        3989 : }
     136             : 
     137             : }
     138             : }
     139             : 
     140             : 
     141             :