Line data    Source code

       1             : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
       2             :    Copyright (c) 2012-2018 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 "PathMSDBase.h"
      23             : #include "core/PlumedMain.h"
      24             : 
      25             : using namespace std;
      26             : 
      27             : namespace PLMD {
      28             : namespace colvar {
      29             : 
      30             : //+PLUMEDOC COLVAR PATHMSD
      31             : /*
      32             : This Colvar calculates path collective variables.
      33             : 
      34             : This is the Path Collective Variables implementation
      35             : ( see \cite brand07 ).
      36             : This variable computes the progress along a given set of frames that is provided
      37             : in input ("sss" component) and the distance from them ("zzz" component).
      38             : (see below).
      39             : 
      40             : \warning
      41             : The molecule used for \ref PATHMSD calculation should be whole (both atoms used in alignment and in displacement calculation).
      42             : In case it is broken by the host MD code, please use \ref WHOLEMOLECULES to reconstruct it before \ref PATHMSD calculation.
      43             : 
      44             : \par Examples
      45             : 
      46             : Here below is a case where you have defined three frames and you want to
      47             : calculate the progress along the path and the distance from it in p1
      48             : 
      49             : \verbatim
      50             : p1: PATHMSD REFERENCE=file.pdb  LAMBDA=500.0 NEIGH_STRIDE=4 NEIGH_SIZE=8
      51             : PRINT ARG=p1.sss,p1.zzz STRIDE=1 FILE=colvar FMT=%8.4f
      52             : \endverbatim
      53             : 
      54             : note that NEIGH_STRIDE=4 NEIGH_SIZE=8 control the neighborlist parameter (optional but
      55             : recommended for performance) and states that the neighbor list will be calculated every 4
      56             : timesteps and consider only the closest 8 member to the actual md snapshots.
      57             : 
      58             : In the REFERENCE PDB file the frames must be separated either using END or ENDMDL.
      59             : 
      60             : \note
      61             : The implementation of this collective variable and of \ref PROPERTYMAP
      62             : is shared, as well as most input options.
      63             : 
      64             : 
      65             : */
      66             : //+ENDPLUMEDOC
      67             : 
      68          26 : class PathMSD : public PathMSDBase {
      69             : public:
      70             :   explicit PathMSD(const ActionOptions&);
      71             :   static void registerKeywords(Keywords& keys);
      72             : };
      73             : 
      74        2536 : PLUMED_REGISTER_ACTION(PathMSD,"PATHMSD")
      75             : 
      76          14 : void PathMSD::registerKeywords(Keywords& keys) {
      77          14 :   PathMSDBase::registerKeywords(keys);
      78          14 :   componentsAreNotOptional(keys);
      79          14 :   keys.addOutputComponent("sss","default","the position on the path");
      80          14 :   keys.addOutputComponent("zzz","default","the distance from the path");
      81          14 : }
      82             : 
      83          13 : PathMSD::PathMSD(const ActionOptions&ao):
      84          13 :   Action(ao),PathMSDBase(ao)
      85             : {
      86          13 :   checkRead();
      87             : 
      88          13 :   log<<"  Bibliography "
      89          39 :      <<plumed.cite("Branduardi, Gervasio, Parrinello J. Chem. Phys. 126, 054103 (2007)")
      90          13 :      <<"\n";
      91             :   // no need to read anything
      92          13 :   addComponentWithDerivatives("sss"); componentIsNotPeriodic("sss");
      93          13 :   addComponentWithDerivatives("zzz"); componentIsNotPeriodic("zzz");
      94          13 :   requestAtoms(pdbv[0].getAtomNumbers());
      95             : 
      96          13 :   double i=1.;
      97         583 :   for(unsigned it=0 ; it<nframes ; ++it) {
      98         570 :     vector<double> v; v.push_back(i);
      99         570 :     indexvec.push_back(v); i+=1.;
     100         570 :   }
     101          13 : }
     102             : 
     103             : }
     104             : 
     105        2523 : }