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_PointWiseMapping_h
23 : #define __PLUMED_reference_PointWiseMapping_h
24 :
25 : #include "MultiReferenceBase.h"
26 :
27 : namespace PLMD {
28 :
29 16 : class PointWiseMapping : public MultiReferenceBase {
30 : private:
31 : /// This is a path
32 : bool ispath;
33 : /// The matrix of interframe distances
34 : Matrix<double> dmat;
35 : /// The names of the projection coordinates
36 : std::vector<std::string> property;
37 : /// These are where the reference configurations should be projected
38 : std::vector< std::vector<double> > low_dim;
39 : public:
40 : PointWiseMapping( const std::string& type, const bool& checksoff );
41 : /// Set the names of the low dimensional properties
42 : void setPropertyNames( const std::vector<std::string>& prop, const bool isp );
43 : /// Check if setup was completed
44 : bool mappingNeedsSetup() const;
45 : /// Delete the low dimensional projections
46 : void clearRestOfData();
47 : /// Read in the data from a file
48 : void readRestOfFrame();
49 : /// Resize everything else from a file
50 : void resizeRestOfFrame();
51 : /// Make a second copy of the frame list
52 : void duplicateFrameList();
53 : /// Get the number of points we are mapping into the lower dimensional space
54 : unsigned getNumberOfMappedPoints() const ;
55 : /// Get the number of properties
56 : unsigned getNumberOfProperties() const ;
57 : /// Get the name of the ith property
58 : std::string getPropertyName( const unsigned& i ) const ;
59 : /// Get the index of the property with name
60 : unsigned getPropertyIndex( const std::string& name ) const ;
61 : /// Get the value of the ith property for th jth frame
62 : double getPropertyValue( const unsigned& iframe, const unsigned& jprop ) const ;
63 : /// Get the derivatives wrt to the position of an atom
64 : // Vector getAtomDerivatives( const unsigned& iframe, const unsigned& jatom );
65 : /// Get the derivatives wrt to the box
66 : // bool getVirial( const unsigned& iframe, Tensor& vir );
67 : /// Ge the derivatives wrt to one of the arguments
68 : // double getArgumentDerivative( const unsigned& iframe, const unsigned& jarg );
69 : /// Copy derivative information from frame number from to frame number to
70 : void copyFrameDerivatives( const unsigned& from, const unsigned& to );
71 : /// Get a pointer to the matrix of pairwise distances
72 : Matrix<double>& modifyDmat();
73 : /// Print out the low dimensional mapping
74 : void print( const std::string& method, const double & time, OFile& afile,
75 : const std::string& fmt, const double& lunits );
76 : /// Get the low dimensional embedding coordinate
77 : double getProjectionCoordinate( const unsigned& iframe, const unsigned& jcoord ) const ;
78 : /// Set the value of the projection coordinate
79 : void setProjectionCoordinate( const unsigned& iframe, const unsigned& jcoord, const double& coord );
80 : };
81 :
82 : inline
83 7 : bool PointWiseMapping::mappingNeedsSetup() const {
84 7 : bool didsetup=(frames.size()==2*low_dim.size());
85 7 : return !didsetup;
86 : }
87 :
88 : inline
89 : void PointWiseMapping::copyFrameDerivatives( const unsigned& from, const unsigned& to ) {
90 : plumed_dbg_assert( to>=frames.size()/2 && from<frames.size()/2 );
91 : frames[to]->copyDerivatives( frames[from] );
92 : }
93 :
94 : inline
95 301 : unsigned PointWiseMapping::getNumberOfMappedPoints() const {
96 301 : return low_dim.size();
97 : }
98 :
99 : inline
100 613 : unsigned PointWiseMapping::getNumberOfProperties() const {
101 613 : return property.size();
102 : }
103 :
104 : inline
105 6 : std::string PointWiseMapping::getPropertyName( const unsigned& i ) const {
106 : plumed_dbg_assert( i<property.size() );
107 6 : return property[i];
108 : }
109 :
110 : inline
111 27071 : double PointWiseMapping::getPropertyValue( const unsigned& iframe, const unsigned& jprop ) const {
112 : plumed_dbg_assert( iframe<low_dim.size() && jprop<property.size() );
113 27071 : return low_dim[iframe][jprop];
114 : }
115 :
116 : // inline
117 : // Vector PointWiseMapping::getAtomDerivatives( const unsigned& iframe, const unsigned& jatom ){
118 : // return frames[iframe]->getAtomDerivative(jatom);
119 : // }
120 : //
121 : // inline
122 : // bool PointWiseMapping::getVirial( const unsigned& iframe, Tensor& vir ){
123 : // return frames[iframe]->getVirial( vir );
124 : // }
125 :
126 : // inline
127 : // double PointWiseMapping::getArgumentDerivative( const unsigned& iframe, const unsigned& jarg ){
128 : // return frames[iframe]->getArgumentDerivative(jarg);
129 : // }
130 :
131 : inline
132 4 : Matrix<double>& PointWiseMapping::modifyDmat() {
133 4 : if( dmat.nrows()!=frames.size() || dmat.ncols()!=frames.size() ) dmat.resize( frames.size(), frames.size() );
134 4 : return dmat;
135 : }
136 :
137 : inline
138 400 : double PointWiseMapping::getProjectionCoordinate( const unsigned& iframe, const unsigned& jcoord ) const {
139 : plumed_dbg_assert( iframe<frames.size() && jcoord<property.size() );
140 400 : return low_dim[iframe][jcoord];
141 : }
142 :
143 : inline
144 400 : void PointWiseMapping::setProjectionCoordinate( const unsigned& iframe, const unsigned& jcoord, const double& coord ) {
145 : plumed_dbg_assert( iframe<frames.size() && jcoord<property.size() );
146 400 : low_dim[iframe][jcoord]=coord;
147 400 : }
148 :
149 : }
150 : #endif
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