Line data    Source code

       1             : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
       2             :    Copyright (c) 2013-2023 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 "PathBase.h"
      23             : #include "core/ActionRegister.h"
      24             : 
      25             : //+PLUMEDOC COLVAR GPROPERTYMAP
      26             : /*
      27             : Property maps but with a more flexible framework for the distance metric being used.
      28             : 
      29             : This colvar calculates a property map using the formalism developed by Spiwok \cite Spiwok:2011ce.
      30             : In essence if you have the value of some property, \f$X_i\f$, that it takes at a set of high-dimensional
      31             : positions then you calculate the value of the property at some arbitrary point in the high-dimensional space
      32             : using:
      33             : 
      34             : \f[
      35             : X=\frac{\sum_i X_i*\exp(-\lambda D_i(x))}{\sum_i  \exp(-\lambda D_i(x))}
      36             : \f]
      37             : 
      38             : Within PLUMED there are multiple ways to define the distance from a high-dimensional configuration, \f$D_i\f$.  You could calculate
      39             : the RMSD distance or you could calculate the amount by which a set of collective variables change.  As such this implementation
      40             : of the property map allows one to use all the different distance metric that are discussed in \ref dists. This is as opposed to
      41             : the alternative implementation \ref PROPERTYMAP which is a bit faster but which only allows one to use the RMSD distance.
      42             : 
      43             : \par Examples
      44             : 
      45             : The input shown below can be used to calculate the interpolated values of two properties called X and Y based on the values
      46             : that these properties take at a set of reference configurations and using the formula above.  For this input the distances
      47             : between the reference configurations and the instantaneous configurations are calculated using the OPTIMAL metric that is
      48             : discussed at length in the manual pages on \ref RMSD.
      49             : 
      50             : \plumedfile
      51             : p2: GPROPERTYMAP REFERENCE=allv.pdb PROPERTY=X,Y LAMBDA=69087
      52             : PRINT ARG=p2.X,p2.Y,p2.zpath STRIDE=1 FILE=colvar
      53             : \endplumedfile
      54             : 
      55             : The additional input file for this calculation, which contains the reference frames and the values of X and Y at these reference
      56             : points has the following format.
      57             : 
      58             : \auxfile{allv.pdb}
      59             : REMARK X=1 Y=2
      60             : ATOM      1  CL  ALA     1      -3.171   0.295   2.045  1.00  1.00
      61             : ATOM      5  CLP ALA     1      -1.819  -0.143   1.679  1.00  1.00
      62             : ATOM      6  OL  ALA     1      -1.177  -0.889   2.401  1.00  1.00
      63             : ATOM      7  NL  ALA     1      -1.313   0.341   0.529  1.00  1.00
      64             : ATOM      8  HL  ALA     1      -1.845   0.961  -0.011  1.00  1.00
      65             : ATOM      9  CA  ALA     1      -0.003  -0.019   0.021  1.00  1.00
      66             : ATOM     10  HA  ALA     1       0.205  -1.051   0.259  1.00  1.00
      67             : ATOM     11  CB  ALA     1       0.009   0.135  -1.509  1.00  1.00
      68             : ATOM     15  CRP ALA     1       1.121   0.799   0.663  1.00  1.00
      69             : ATOM     16  OR  ALA     1       1.723   1.669   0.043  1.00  1.00
      70             : ATOM     17  NR  ALA     1       1.423   0.519   1.941  1.00  1.00
      71             : ATOM     18  HR  ALA     1       0.873  -0.161   2.413  1.00  1.00
      72             : ATOM     19  CR  ALA     1       2.477   1.187   2.675  1.00  1.00
      73             : END
      74             : FIXED
      75             : REMARK X=2 Y=3
      76             : ATOM      1  CL  ALA     1      -3.175   0.365   2.024  1.00  1.00
      77             : ATOM      5  CLP ALA     1      -1.814  -0.106   1.685  1.00  1.00
      78             : ATOM      6  OL  ALA     1      -1.201  -0.849   2.425  1.00  1.00
      79             : ATOM      7  NL  ALA     1      -1.296   0.337   0.534  1.00  1.00
      80             : ATOM      8  HL  ALA     1      -1.807   0.951  -0.044  1.00  1.00
      81             : ATOM      9  CA  ALA     1       0.009  -0.067   0.033  1.00  1.00
      82             : ATOM     10  HA  ALA     1       0.175  -1.105   0.283  1.00  1.00
      83             : ATOM     11  CB  ALA     1       0.027   0.046  -1.501  1.00  1.00
      84             : ATOM     15  CRP ALA     1       1.149   0.725   0.654  1.00  1.00
      85             : ATOM     16  OR  ALA     1       1.835   1.491  -0.011  1.00  1.00
      86             : ATOM     17  NR  ALA     1       1.380   0.537   1.968  1.00  1.00
      87             : ATOM     18  HR  ALA     1       0.764  -0.060   2.461  1.00  1.00
      88             : ATOM     19  CR  ALA     1       2.431   1.195   2.683  1.00  1.00
      89             : END
      90             : \endauxfile
      91             : 
      92             : */
      93             : //+ENDPLUMEDOC
      94             : 
      95             : namespace PLMD {
      96             : namespace mapping {
      97             : 
      98             : class PropertyMap : public PathBase {
      99             : public:
     100             :   static void registerKeywords( Keywords& keys );
     101             :   explicit PropertyMap(const ActionOptions&);
     102             : };
     103             : 
     104       10425 : PLUMED_REGISTER_ACTION(PropertyMap,"GPROPERTYMAP")
     105             : 
     106           4 : void PropertyMap::registerKeywords( Keywords& keys ) {
     107           4 :   PathBase::registerKeywords( keys );
     108           4 :   ActionWithValue::useCustomisableComponents( keys );
     109           8 :   keys.addFlag("NOMAPPING",false,"do not calculate the position on the manifold");
     110           4 : }
     111             : 
     112           3 : PropertyMap::PropertyMap(const ActionOptions& ao):
     113             :   Action(ao),
     114           3 :   PathBase(ao)
     115             : {
     116           6 :   bool nos; parseFlag("NOMAPPING",nos);
     117             : 
     118             :   std::string empty;
     119           3 :   if(!nos) {
     120           9 :     for(std::map<std::string,std::vector<double> >::iterator it=property.begin(); it!=property.end(); ++it) {
     121          18 :       empty="LABEL="+it->first; addVessel( "SPATH", empty, 0 );
     122             :     }
     123             :   }
     124           3 :   readVesselKeywords();
     125           3 :   checkRead();
     126           3 : }
     127             : 
     128             : }
     129             : }