Line data    Source code

       1             : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
       2             :    Copyright (c) 2012-2023 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 "PathMSDBase.h"
      23             : #include "core/PlumedMain.h"
      24             : 
      25             : namespace PLMD {
      26             : namespace colvar {
      27             : 
      28             : //+PLUMEDOC COLVAR PATHMSD
      29             : /*
      30             : This Colvar calculates path collective variables.
      31             : 
      32             : Path collective variables were introduced in the paper cited in the bibliography.
      33             : This CV defines a a curvilinear path using a set of reference configurations. Variables
      34             : that measure the instantaneous position, sss, of the system on this path and the distance from
      35             : this path, zzz, are then computed.  The following input illustrates the syntax that is used
      36             : with this variable
      37             : 
      38             : ```plumed
      39             : #SETTINGS INPUTFILES=regtest/basic/rt39/all.pdb
      40             : p1: PATHMSD REFERENCE=regtest/basic/rt39/all.pdb LAMBDA=500.0 NEIGH_STRIDE=4 NEIGH_SIZE=8
      41             : PRINT ARG=p1.sss,p1.zzz STRIDE=1 FILE=colvar
      42             : ```
      43             : 
      44             : The `NEIGH_STRIDE=4` and `NEIGH_SIZE=8` keywords here control the neighbor list parameter (optional but
      45             : recommended for performance) and states that the neighbor list will be calculated every 4
      46             : steps and consider only the closest 8 member to the actual md snapshots.
      47             : 
      48             : When running with periodic boundary conditions, the atoms should be
      49             : in the proper periodic image. This is done automatically since PLUMED 2.5,
      50             : by considering the ordered list of atoms and rebuilding molecules with a procedure
      51             : that is equivalent to that done in [WHOLEMOLECULES](WHOLEMOLECULES.md). Notice that
      52             : rebuilding is local to this action. This is different from [WHOLEMOLECULES](WHOLEMOLECULES.md)
      53             : which actually modifies the coordinates stored in PLUMED.
      54             : 
      55             : In case you want to recover the old behavior you should use the NOPBC flag.
      56             : In that case you need to take care that atoms are in the correct
      57             : periodic image.
      58             : 
      59             : The implementation of this collective variable and of [PROPERTYMAP](PROPERTYMAP.md)
      60             : is shared, as well as most input options.
      61             : 
      62             : 
      63             : */
      64             : //+ENDPLUMEDOC
      65             : 
      66             : class PathMSD : public PathMSDBase {
      67             : public:
      68             :   explicit PathMSD(const ActionOptions&);
      69             :   static void registerKeywords(Keywords& keys);
      70             : };
      71             : 
      72             : PLUMED_REGISTER_ACTION(PathMSD,"PATHMSD")
      73             : 
      74          16 : void PathMSD::registerKeywords(Keywords& keys) {
      75          16 :   PathMSDBase::registerKeywords(keys);
      76          32 :   keys.addOutputComponent("sss","default","scalar","the position on the path");
      77          32 :   keys.addOutputComponent("zzz","default","scalar","the distance from the path");
      78          16 :   keys.addDOI("10.1063/1.2432340");
      79          16 : }
      80             : 
      81          14 : PathMSD::PathMSD(const ActionOptions&ao):
      82          14 :   Action(ao),PathMSDBase(ao) {
      83          14 :   checkRead();
      84             : 
      85          14 :   log<<"  Bibliography "
      86          28 :      <<plumed.cite("Branduardi, Gervasio, Parrinello J. Chem. Phys. 126, 054103 (2007)")
      87          28 :      <<"\n";
      88             :   // no need to read anything
      89          28 :   addComponentWithDerivatives("sss");
      90          28 :   componentIsNotPeriodic("sss");
      91          28 :   addComponentWithDerivatives("zzz");
      92          14 :   componentIsNotPeriodic("zzz");
      93          14 :   requestAtoms(pdbv[0].getAtomNumbers());
      94             : 
      95          14 :   double i=1.;
      96         634 :   for(unsigned it=0 ; it<nframes ; ++it) {
      97             :     std::vector<double> v;
      98             :     v.push_back(i);
      99         620 :     indexvec.push_back(v);
     100         620 :     i+=1.;
     101             :   }
     102          14 : }
     103             : 
     104             : }
     105             : 
     106             : }