Line data    Source code

       1             : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
       2             :    Copyright (c) 2017-2020 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 EXTRACV
      34             : /*
      35             : Allow PLUMED to use collective variables computed in the MD engine.
      36             : 
      37             : This feature requires the MD engine to use special instructions to pass to PLUMED the value of
      38             : some pre-computed collective variable. Check the documentation of the MD code to find out which
      39             : collective variables can be computed and passed to PLUMED. These variables can then be accessed by
      40             : name using the EXTRACV action.
      41             : 
      42             : \par Examples
      43             : 
      44             : This example takes the lambda variable pre-computed in GROMACS and apply to it a restraint to keep
      45             : it close to the value 3.
      46             : \plumedfile
      47             : l: EXTRACV NAME=lambda
      48             : RESTRAINT ARG=l KAPPA=10 AT=3
      49             : \endplumedfile
      50             : 
      51             : 
      52             : */
      53             : //+ENDPLUMEDOC
      54             : 
      55             : 
      56           6 : class ExtraCV : public Colvar {
      57             :   std::string name;
      58             : public:
      59             :   explicit ExtraCV(const ActionOptions&);
      60             : // active methods:
      61             :   void prepare();
      62             :   virtual void calculate();
      63             :   unsigned getNumberOfDerivatives();
      64             :   static void registerKeywords( Keywords& keys );
      65             : };
      66             : 
      67             : 
      68             : using namespace std;
      69             : 
      70             : 
      71        7360 : PLUMED_REGISTER_ACTION(ExtraCV,"EXTRACV")
      72             : 
      73           2 : ExtraCV::ExtraCV(const ActionOptions&ao):
      74           2 :   PLUMED_COLVAR_INIT(ao)
      75             : {
      76           2 :   addValueWithDerivatives(); setNotPeriodic();
      77           2 :   getPntrToValue()->resizeDerivatives(1);
      78           4 :   parse("NAME",name);
      79           2 :   log<<"  name: "<<name<<"\n";
      80           2 :   isExtraCV=true;
      81             :   setExtraCV(name);
      82           2 : }
      83             : 
      84           3 : void ExtraCV::registerKeywords( Keywords& keys ) {
      85           3 :   Action::registerKeywords( keys );
      86           3 :   ActionAtomistic::registerKeywords( keys );
      87           3 :   ActionWithValue::registerKeywords( keys );
      88           6 :   keys.remove("NUMERICAL_DERIVATIVES");
      89          12 :   keys.add("compulsory","NAME","name of the CV as computed by the MD engine");
      90           3 : }
      91             : 
      92           4 : unsigned ExtraCV::getNumberOfDerivatives() {
      93           4 :   return 1;
      94             : }
      95             : 
      96          40 : void ExtraCV::prepare() {
      97             : /// \todo: notify Atoms that this is requested
      98          40 : }
      99             : 
     100             : // calculator
     101          40 : void ExtraCV::calculate() {
     102          80 :   double value=plumed.getAtoms().getExtraCV(name);
     103          40 :   setValue( value );
     104          40 :   getPntrToComponent(0)->addDerivative(0,1.0);
     105          40 : }
     106             : 
     107             : }
     108        5517 : }
     109             : 
     110             : 
     111             :