Line data    Source code

       1             : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
       2             :    Copyright (c) 2012-2019 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 "Function.h"
      23             : #include "ActionRegister.h"
      24             : #include "tools/PDB.h"
      25             : #include "reference/MetricRegister.h"
      26             : #include "reference/ArgumentOnlyDistance.h"
      27             : #include "core/Atoms.h"
      28             : #include "core/PlumedMain.h"
      29             : #include <memory>
      30             : 
      31             : using namespace std;
      32             : 
      33             : namespace PLMD {
      34             : namespace function {
      35             : 
      36             : //+PLUMEDOC DCOLVAR TARGET
      37             : /*
      38             : This function measures the Pythagorean distance from a particular structure measured in the space defined by some set of collective variables.
      39             : 
      40             : This collective variable can be used to calculate something akin to:
      41             : 
      42             : \f[
      43             : d(X,X') = \vert X - X' \vert
      44             : \f]
      45             : 
      46             : where \f$ X \f$ is the instantaneous values for a set of collective variables for the system and
      47             : \f$ X' \f$ is the values that these self-same set of collective variables take in some reference structure provided as input.
      48             : If we call our set of collective variables \f$\{s_i\}\f$ then this CV computes:
      49             : 
      50             : \f[
      51             : d = \sqrt{ \sum_{i=1}^N (s_i - s_i^{(ref)})^2 }
      52             : \f]
      53             : 
      54             : where \f$s_i^{(ref)}\f$ are the values of the CVs in the reference structure and \f$N\f$ is the number of input CVs.
      55             : 
      56             : We can also calculate normalized euclidean differences using this action and the METRIC=NORM-EUCLIDEAN flag.  In other words,
      57             : we can compute:
      58             : 
      59             : \f[
      60             : d = \sqrt{ \sum_{i=1}^N \sigma_i (s_i - s_i^{(ref)})^2 }
      61             : \f]
      62             : 
      63             : where \f$\sigma_i\f$ is a vector of weights.  Lastly, by using the METRIC=MAHALONOBIS we can compute Mahalonobis distances using:
      64             : 
      65             : \f[
      66             : d = \left( \mathbf{s} - \mathbf{s}^{(ref)} \right)^T \mathbf{\Sigma} \left( \mathbf{s} - \mathbf{s}^{(ref)} \right)
      67             : \f]
      68             : 
      69             : where \f$\mathbf{s}\f$ is a column vector containing the values of all the CVs and \f$\mathbf{s}^{(ref)}\f$ is a column vector
      70             : containing the values of the CVs in the reference configuration.  \f$\mathbf{\Sigma}\f$ is then an \f$N \times N\f$ matrix that is
      71             : specified in the input.
      72             : 
      73             : \par Examples
      74             : 
      75             : The following input calculates the distance between a reference configuration and the instantaneous position of the system in the trajectory.
      76             : The position of the reference configuration is specified by providing the values of the distance between atoms 1 and 2 and atoms 3 and 4.
      77             : 
      78             : \plumedfile
      79             : d1: DISTANCE ATOMS=1,2
      80             : d2: DISTANCE ATOMS=3,4
      81             : t1: TARGET REFERENCE=reference.pdb TYPE=EUCLIDEAN
      82             : PRINT ARG=t1 FILE=colvar
      83             : \endplumedfile
      84             : 
      85             : The contents of the file containing the reference structure (reference.pdb) is shown below.  As you can see you must provide information on the
      86             : labels of the CVs that are being used to define the position of the reference configuration in this file together with the values that these
      87             : quantities take in the reference configuration.
      88             : 
      89             : \auxfile{reference.pdb}
      90             : DESCRIPTION: a reference point.
      91             : REMARK WEIGHT=1.0
      92             : REMARK ARG=d1,d2
      93             : REMARK d1=1.0 d2=1.0
      94             : END
      95             : \endauxfile
      96             : 
      97             : */
      98             : //+ENDPLUMEDOC
      99             : 
     100           0 : class Target : public Function {
     101             : private:
     102             :   MultiValue myvals;
     103             :   ReferenceValuePack mypack;
     104             :   std::unique_ptr<PLMD::ArgumentOnlyDistance> target;
     105             : public:
     106             :   explicit Target(const ActionOptions&);
     107             :   void calculate() override;
     108             :   static void registerKeywords(Keywords& keys );
     109             : };
     110             : 
     111        7832 : PLUMED_REGISTER_ACTION(Target,"TARGET")
     112             : 
     113           1 : void Target::registerKeywords(Keywords& keys) {
     114           1 :   Function::registerKeywords(keys);
     115           5 :   keys.add("compulsory","TYPE","EUCLIDEAN","the manner in which the distance should be calculated");
     116             :   keys.add("compulsory","REFERENCE","a file in pdb format containing the reference structure. In the PDB file the atomic "
     117             :            "coordinates and box lengths should be in Angstroms unless you are working with natural units. "
     118             :            "If you are working with natural units then the coordinates should be in your natural length unit. "
     119             :            "The charges and masses of the atoms (if required) should be inserted in the beta and occupancy "
     120           4 :            "columns respectively. For more details on the PDB file format visit http://www.wwpdb.org/docs.html");
     121           1 : }
     122             : 
     123           0 : Target::Target(const ActionOptions&ao):
     124             :   Action(ao),
     125             :   Function(ao),
     126             :   myvals(1,0),
     127           0 :   mypack(0,0,myvals)
     128             : {
     129           0 :   std::string type; parse("TYPE",type);
     130           0 :   std::string reference; parse("REFERENCE",reference);
     131           0 :   checkRead(); PDB pdb;
     132           0 :   if( !pdb.read(reference,plumed.getAtoms().usingNaturalUnits(),0.1/plumed.getAtoms().getUnits().getLength()) )
     133           0 :     error("missing input file " + reference);
     134             : 
     135             :   // Use the base ActionWithArguments to expand things like a1.*
     136           0 :   expandArgKeywordInPDB( pdb );
     137             : 
     138             :   // Generate the reference structure
     139           0 :   target=metricRegister().create<ArgumentOnlyDistance>( type, pdb );
     140             : 
     141             :   // Get the argument names
     142           0 :   std::vector<std::string> args_to_retrieve;
     143           0 :   target->getArgumentRequests( args_to_retrieve, false );
     144             : 
     145             :   // Get the arguments
     146             :   std::vector<Value*> myargs;
     147           0 :   interpretArgumentList( args_to_retrieve, myargs );
     148           0 :   requestArguments( myargs );
     149             : 
     150             :   // Now create packs
     151           0 :   myvals.resize( 1, myargs.size() );
     152           0 :   mypack.resize( myargs.size(), 0 );
     153             : 
     154             :   // Create the value
     155           0 :   addValueWithDerivatives(); setNotPeriodic();
     156           0 : }
     157             : 
     158           0 : void Target::calculate() {
     159           0 :   mypack.clear(); double r=target->calculate( getArguments(), mypack, false ); setValue(r);
     160           0 :   for(unsigned i=0; i<getNumberOfArguments(); i++) setDerivative( i, mypack.getArgumentDerivative(i) );
     161           0 : }
     162             : 
     163             : }
     164        5874 : }