PathMSD.cpp

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/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
   Copyright (c) 2013 The plumed team
   (see the PEOPLE file at the root of the distribution for a list of names)

   See http://www.plumed-code.org for more information.

   This file is part of plumed, version 2.0.

   plumed is free software: you can redistribute it and/or modify
   it under the terms of the GNU Lesser General Public License as published by
   the Free Software Foundation, either version 3 of the License, or
   (at your option) any later version.

   plumed is distributed in the hope that it will be useful,
   but WITHOUT ANY WARRANTY; without even the implied warranty of
   MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
   GNU Lesser General Public License for more details.

   You should have received a copy of the GNU Lesser General Public License
   along with plumed.  If not, see <http://www.gnu.org/licenses/>.
+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */
#include "PathMSDBase.h"
#include "core/PlumedMain.h"

using namespace std;

namespace PLMD{
namespace colvar{

//+PLUMEDOC COLVAR PATHMSD
/*
This Colvar calculates path collective variables. 

This is the Path Collective Variables implementation 
( see \cite brand07 ).
This variable computes the progress along a given set of frames that is provided  
in input ("sss" component) and the distance from them ("zzz" component). 
(see below).

\par Examples

Here below is a case where you have defined three frames and you want to  
calculate the progress along the path and the distance from it in p1

\verbatim
p1: PATHMSD REFERENCE=file.pdb  LAMBDA=500.0 NEIGH_STRIDE=4 NEIGH_SIZE=8 
PRINT ARG=p1.sss,p1.zzz STRIDE=1 FILE=colvar FMT=%8.4f
\endverbatim

note that NEIGH_STRIDE=4 NEIGH_SIZE=8 control the neighborlist parameter (optional but
recommended for performance) and states that the neighbor list will be calculated every 4
timesteps and consider only the closest 8 member to the actual md snapshots.

\note
The implementation of this collective variable and of \ref PROPERTYMAP
is shared, as well as most input options.


*/
//+ENDPLUMEDOC
   
class PathMSD : public PathMSDBase {
public:
  PathMSD(const ActionOptions&);
  static void registerKeywords(Keywords& keys);
};

PLUMED_REGISTER_ACTION(PathMSD,"PATHMSD")

void PathMSD::registerKeywords(Keywords& keys){
  PathMSDBase::registerKeywords(keys);
  componentsAreNotOptional(keys);
  keys.addOutputComponent("sss","default","the position on the path");
  keys.addOutputComponent("zzz","default","the distance from the path");
}

PathMSD::PathMSD(const ActionOptions&ao):
Action(ao),PathMSDBase(ao)
{
  checkRead();

  log<<"  Bibliography "
     <<plumed.cite("Branduardi, Gervasio, Parrinello J. Chem. Phys. 126, 054103 (2007)")
     <<"\n";
  // no need to read anything
  addComponentWithDerivatives("sss"); componentIsNotPeriodic("sss");
  addComponentWithDerivatives("zzz"); componentIsNotPeriodic("zzz");
  requestAtoms(pdbv[0].getAtomNumbers());  

  double i=1.;
  for(unsigned it=0 ;it<nframes ;++it){
                vector<double> v; v.push_back(i);
                indexvec.push_back(v);i+=1.; 
  }
}

}

}