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             : This is the Path Collective Variables implementation
      33             : ( see \cite brand07 ).
      34             : This variable computes the progress along a given set of frames that is provided
      35             : in input ("sss" component) and the distance from them ("zzz" component).
      36             : (see below).
      37             : 
      38             : When running with periodic boundary conditions, the atoms should be
      39             : in the proper periodic image. This is done automatically since PLUMED 2.5,
      40             : by considering the ordered list of atoms and rebuilding molecules with a procedure
      41             : that is equivalent to that done in \ref WHOLEMOLECULES . Notice that
      42             : rebuilding is local to this action. This is different from \ref WHOLEMOLECULES
      43             : which actually modifies the coordinates stored in PLUMED.
      44             : 
      45             : In case you want to recover the old behavior you should use the NOPBC flag.
      46             : In that case you need to take care that atoms are in the correct
      47             : periodic image.
      48             : 
      49             : \par Examples
      50             : 
      51             : Here below is a case where you have defined three frames and you want to
      52             : calculate the progress along the path and the distance from it in p1
      53             : 
      54             : \plumedfile
      55             : p1: PATHMSD REFERENCE=file.pdb  LAMBDA=500.0 NEIGH_STRIDE=4 NEIGH_SIZE=8
      56             : PRINT ARG=p1.sss,p1.zzz STRIDE=1 FILE=colvar FMT=%8.4f
      57             : \endplumedfile
      58             : 
      59             : note that NEIGH_STRIDE=4 NEIGH_SIZE=8 control the neighbor list parameter (optional but
      60             : recommended for performance) and states that the neighbor list will be calculated every 4
      61             : steps and consider only the closest 8 member to the actual md snapshots.
      62             : 
      63             : This input must be accompanied by a REFERENCE PDB file in which the positions of each of the frames are specified
      64             : separated using either END or ENDMDL as shown below:
      65             : 
      66             : \auxfile{file.pdb}
      67             : ATOM      1  CL  ALA     1      -3.171   0.295   2.045  1.00  1.00
      68             : ATOM      5  CLP ALA     1      -1.819  -0.143   1.679  1.00  1.00
      69             : ATOM      6  OL  ALA     1      -1.177  -0.889   2.401  1.00  1.00
      70             : ATOM      7  NL  ALA     1      -1.313   0.341   0.529  1.00  1.00
      71             : END
      72             : ATOM      1  CL  ALA     1      -3.175   0.365   2.024  1.00  1.00
      73             : ATOM      5  CLP ALA     1      -1.814  -0.106   1.685  1.00  1.00
      74             : ATOM      6  OL  ALA     1      -1.201  -0.849   2.425  1.00  1.00
      75             : ATOM      7  NL  ALA     1      -1.296   0.337   0.534  1.00  1.00
      76             : END
      77             : ATOM      1  CL  ALA     1      -2.990   0.383   2.277  1.00  1.00
      78             : ATOM      5  CLP ALA     1      -1.664  -0.085   1.831  1.00  1.00
      79             : ATOM      6  OL  ALA     1      -0.987  -0.835   2.533  1.00  1.00
      80             : ATOM      7  NL  ALA     1      -1.227   0.364   0.646  1.00  1.00
      81             : END
      82             : \endauxfile
      83             : 
      84             : \note
      85             : The implementation of this collective variable and of \ref PROPERTYMAP
      86             : is shared, as well as most input options.
      87             : 
      88             : 
      89             : */
      90             : //+ENDPLUMEDOC
      91             : 
      92             : class PathMSD : public PathMSDBase {
      93             : public:
      94             :   explicit PathMSD(const ActionOptions&);
      95             :   static void registerKeywords(Keywords& keys);
      96             : };
      97             : 
      98       10447 : PLUMED_REGISTER_ACTION(PathMSD,"PATHMSD")
      99             : 
     100          15 : void PathMSD::registerKeywords(Keywords& keys) {
     101          15 :   PathMSDBase::registerKeywords(keys);
     102          15 :   componentsAreNotOptional(keys);
     103          30 :   keys.addOutputComponent("sss","default","the position on the path");
     104          30 :   keys.addOutputComponent("zzz","default","the distance from the path");
     105          15 : }
     106             : 
     107          14 : PathMSD::PathMSD(const ActionOptions&ao):
     108          14 :   Action(ao),PathMSDBase(ao)
     109             : {
     110          14 :   checkRead();
     111             : 
     112          14 :   log<<"  Bibliography "
     113          28 :      <<plumed.cite("Branduardi, Gervasio, Parrinello J. Chem. Phys. 126, 054103 (2007)")
     114          28 :      <<"\n";
     115             :   // no need to read anything
     116          28 :   addComponentWithDerivatives("sss"); componentIsNotPeriodic("sss");
     117          28 :   addComponentWithDerivatives("zzz"); componentIsNotPeriodic("zzz");
     118          14 :   requestAtoms(pdbv[0].getAtomNumbers());
     119             : 
     120          14 :   double i=1.;
     121         634 :   for(unsigned it=0 ; it<nframes ; ++it) {
     122         620 :     std::vector<double> v; v.push_back(i);
     123         620 :     indexvec.push_back(v); i+=1.;
     124             :   }
     125          14 : }
     126             : 
     127             : }
     128             : 
     129             : }