Line data Source code
1 : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
2 : Copyright (c) 2013-2018 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 : #ifndef __PLUMED_reference_ReferenceArguments_h
23 : #define __PLUMED_reference_ReferenceArguments_h
24 :
25 : #include "ReferenceConfiguration.h"
26 : #include "tools/Matrix.h"
27 :
28 : namespace PLMD {
29 :
30 : /// \ingroup TOOLBOX
31 : /// In many applications (e.g. paths, fields, property maps) it is necessary to calculate
32 : /// the distance between two configurations. These distances can be calculated in a variety of
33 : /// different ways. For instance, one can assert that the distance between the two configuration
34 : /// is the distance one would have to move all the atoms to transform configuration 1 into configuration
35 : /// 2. Alternatively, one could calculate the values of a large set of collective coordinates in the two
36 : /// configurations and then calculate the Euclidean distances between these two points in the resulting
37 : /// high-dimensional vector space. Lastly, one can combine these two forms of distance calculation to calculate
38 : /// a hybrid distance. Plumed allows one to use all these forms of distance calculations and also to implement
39 : /// new forms of distance. You should inherit from this class if your distance involves reference colvar values.
40 : /// This class and \ref PLMD::ReferenceAtoms mirror the functionalities in \ref PLMD::ActionWithArguments and
41 : /// \ref PLMD::ActionAtomistic respectively but for distances.
42 :
43 859 : class ReferenceArguments :
44 : virtual public ReferenceConfiguration
45 : {
46 : private:
47 : /// The weights for normed euclidean distance
48 : std::vector<double> weights;
49 : /// The N X N matrix we are using to calculate our Malanobius distance
50 : Matrix<double> metric;
51 : std::vector<double> trig_metric;
52 : /// The values of the colvars in the reference configuration
53 : std::vector<double> reference_args;
54 : /// The names of the arguments
55 : std::vector<std::string> arg_names;
56 : /// The indices for setting derivatives
57 : std::vector<unsigned> arg_der_index;
58 : protected:
59 : /// Are we reading weights from input
60 : bool hasweights;
61 : /// Are we calculating a Malanobius distance
62 : bool hasmetric;
63 : /// Read in the atoms from the pdb file
64 : void readArgumentsFromPDB( const PDB& pdb );
65 : /// Set the values of the colvars based on their current instantanous values (used in Analysis)
66 : void setReferenceArguments();
67 : public:
68 : explicit ReferenceArguments( const ReferenceConfigurationOptions& ro );
69 : /// Get the number of reference arguments
70 : unsigned getNumberOfReferenceArguments() const ;
71 : /// Get the arguments required
72 : void getArgumentRequests( std::vector<std::string>&, bool disable_checks=false );
73 : /// Set the names of the arguments
74 : void setArgumentNames( const std::vector<std::string>& arg_vals );
75 : /// Set the positions of the refernce arguments
76 : void setReferenceArguments( const std::vector<double>& arg_vals, const std::vector<double>& sigma );
77 : /// Get the value of the ith reference argument
78 : double getReferenceArgument( const unsigned& i ) const ;
79 : /// Print the arguments out
80 : void printArguments( OFile& ofile, const std::string& fmt ) const ;
81 : /// Return all the reference arguments
82 : const std::vector<double>& getReferenceArguments();
83 : const std::vector<double>& getReferenceMetric();
84 : /// Return names
85 : const std::vector<std::string>& getArgumentNames();
86 : /// Calculate the euclidean/malanobius distance the atoms have moved from the reference
87 : /// configuration in CV space
88 : virtual double calculateArgumentDistance( const std::vector<Value*> & vals, const std::vector<double>& arg, ReferenceValuePack& myder, const bool& squared ) const ;
89 : };
90 :
91 : inline
92 0 : double ReferenceArguments::getReferenceArgument( const unsigned& i ) const {
93 : plumed_dbg_assert( i<reference_args.size() );
94 0 : return reference_args[i];
95 : }
96 :
97 : inline
98 34269 : const std::vector<double>& ReferenceArguments::getReferenceArguments() {
99 34269 : return reference_args;
100 : }
101 :
102 : inline
103 200 : const std::vector<std::string>& ReferenceArguments::getArgumentNames() {
104 200 : return arg_names;
105 : }
106 :
107 : inline
108 8 : unsigned ReferenceArguments::getNumberOfReferenceArguments() const {
109 8 : return reference_args.size();
110 : }
111 :
112 : }
113 : #endif
114 :
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