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             : As is explained in the papers in the bibliography the potential energy can be biased with umbrella sampling.
      36             : To print the potential energy from PLUMED you can use an input similar to the one below:
      37             : 
      38             : ```plumed
      39             : ene: ENERGY
      40             : PRINT ARG=ene FILE=colvar
      41             : ```
      42             : 
      43             : Notice that this CV is not available with all the MD codes. When
      44             : it is available, and when replica exchange is also available,
      45             : metadynamics applied to ENERGY can be used to decrease the
      46             : number of required replicas.
      47             : 
      48             : > [!CAUTION]
      49             : > The ENERGY output by PLUMED does not include long tail corrections.
      50             : > Thus when using e.g. LAMMPS `"pair_modify tail yes"` or GROMACS `"DispCorr Ener"` (or `"DispCorr EnerPres"`),
      51             : > the potential energy from ENERGY will be slightly different from the one that is output by the MD code.
      52             : > You should still be able to bias the ENERGY and then reweight your simulation with the correct MD energy values.
      53             : 
      54             : > [!CAUTION]
      55             : > Acceptance for replica exchange when ENERGY is biased
      56             : > is computed correctly only if all the replicas have the same
      57             : > potential energy function. This is for instance not true when
      58             : > using GROMACS with lambda replica exchange or with plumed-hrex branch.
      59             : 
      60             : */
      61             : //+ENDPLUMEDOC
      62             : 
      63             : 
      64             : class Energy : public ActionToPutData {
      65             : private:
      66             : /// This is used to sum the data
      67             :   DomainDecomposition* interface;
      68             : /// This is the list of forces that must be scaled
      69             :   std::vector<ActionToPutData*> forces_to_scale;
      70             : public:
      71             :   explicit Energy(const ActionOptions&);
      72             : // active methods:
      73             :   static void registerKeywords( Keywords& keys );
      74             :   void wait() override;
      75             :   void apply() override;
      76             : };
      77             : 
      78             : 
      79             : PLUMED_REGISTER_ACTION(Energy,"ENERGY")
      80             : 
      81          40 : Energy::Energy(const ActionOptions&ao):
      82             :   Action(ao),
      83             :   ActionToPutData(ao),
      84          40 :   interface(NULL) {
      85          40 :   plumed.setEnergyValue( getLabel() );
      86             :   std::vector<unsigned> shape;
      87          40 :   addValue( shape );
      88          40 :   setNotPeriodic();
      89          80 :   setUnit( "energy", "default" );
      90          40 :   ActionToPutData* px=plumed.getActionSet().selectWithLabel< ActionToPutData*>("posx");
      91          40 :   plumed_assert(px);
      92          40 :   forces_to_scale.push_back(px);
      93          40 :   addDependency( px );
      94          40 :   ActionToPutData* py=plumed.getActionSet().selectWithLabel< ActionToPutData*>("posy");
      95          40 :   plumed_assert(py);
      96          40 :   forces_to_scale.push_back(py);
      97          40 :   addDependency( py );
      98          40 :   ActionToPutData* pz=plumed.getActionSet().selectWithLabel< ActionToPutData*>("posz");
      99          40 :   plumed_assert(pz);
     100          40 :   forces_to_scale.push_back(pz);
     101          40 :   addDependency( pz );
     102          40 :   ActionToPutData* bx=plumed.getActionSet().selectWithLabel< ActionToPutData*>("Box");
     103          40 :   plumed_assert(bx);
     104          40 :   forces_to_scale.push_back(bx);
     105          40 :   addDependency( bx );
     106          40 :   log<<"  Bibliography ";
     107          80 :   log<<plumed.cite("Bartels and Karplus, J. Phys. Chem. B 102, 865 (1998)");
     108          80 :   log<<plumed.cite("Bonomi and Parrinello, J. Comp. Chem. 30, 1615 (2009)");
     109          40 :   log<<"\n";
     110          40 : }
     111             : 
     112          42 : void Energy::registerKeywords( Keywords& keys ) {
     113          42 :   Action::registerKeywords( keys );
     114          84 :   keys.setValueDescription("scalar","the internal energy");
     115          42 :   keys.addDOI("10.1021/jp972280j");
     116          42 :   keys.addDOI("10.1103/PhysRevLett.104.190601");
     117          42 : }
     118             : 
     119        3989 : void Energy::wait() {
     120        3989 :   if( !interface ) {
     121          40 :     std::vector<DomainDecomposition*> allput=plumed.getActionSet().select<DomainDecomposition*>();
     122          40 :     if( allput.size()>1 ) {
     123           0 :       warning("found more than one interface so don't know how to sum energy");
     124             :     }
     125          40 :     interface = allput[0];
     126             :   }
     127        3989 :   ActionToPutData::wait();
     128        3989 :   if( interface ) {
     129        3989 :     interface->sumOverDomains( copyOutput(0) );
     130             :   }
     131        3989 : }
     132             : 
     133        3989 : void Energy::apply() {
     134        3989 :   if( getPntrToValue()->forcesWereAdded() ) {
     135         250 :     for(unsigned i=0; i<forces_to_scale.size(); ++i) {
     136         200 :       forces_to_scale[i]->rescaleForces( 1.- getPntrToValue()->getForce(0));
     137             :     }
     138             :   }
     139        3989 : }
     140             : 
     141             : }
     142             : }
     143             : 
     144             : 
     145             :